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From DFT to MD: A Comprehensive 「Deep Potential」 Guide to Getting Started with Materials Computation

notebook

Letian

更新于 2024-07-10

推荐镜像 :ABACUS:3.2.1-deepmd-2.2.1

推荐机型 :c2_m4_cpu

数据集

licl-data(v1)

From DFT to MD: A Comprehensive 「Deep Potential」 Guide to Getting Started with Materials Computation

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Background

In this tutorial, we will take LiCl (lithium chloride) Melt as an example to detail the training and application of the Deep Potential model. The Deep Potential model is a machine learning-based approach used to accurately describe the potential energy surfaces of atomic interactions. By training this model, we can efficiently simulate the structural, dynamical, and thermodynamic properties of materials. Specifically, the following examples are included:

Chapter 1: LAMMPS Classical Molecular Dynamics Simulation
Chapter 2: ABACUS First-Principles Calculations
Chapter 3: DeePMD-kit Deep Potential Model Training
Chapter 4: DP-GEN Building Training Data and Generating Deep Potential Models
Chapter 5: LAMMPS Deep Potential Molecular Dynamics Study

Overall, by combining classical molecular dynamics simulations (such as LAMMPS), first-principles calculations (such as ABACUS), and Deep Potential model construction (DeePMD-kit and DP-GEN), we can study the properties of LiCl melt from multiple perspectives. The combination of these methods and tools provides robust support for researching complex material systems, helping us better understand the performance of materials under various conditions.

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Before You Start

We are eager to share our knowledge with you, but for now:

You don't need to know everything (at least not yet). Your goal is to complete this tutorial from start to finish and get results. You don't need to understand everything on your first try. Write down your questions as you go. Use the rich API documentation to understand all the functions you are using.

You don't need to know how the algorithms work. It's important to understand the advantages and limitations of various computational simulations and how to configure material computation parameters. However, this learning can come later. You need to gradually build this computational simulation knowledge over a long period, and you can review the steps of material computation projects by reading many tutorials. Today, focus on getting familiar with this platform.

Understanding the following basic concepts can help you grasp this tutorial more quickly:

Molecular Dynamics (MD). If you're not yet familiar, we recommend reading:
- Quick Introduction to Molecular Dynamics
Density Functional Theory (DFT). If you're not yet familiar, we recommend reading:
- Quick Introduction to Density Functional Theory

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Chapter 1: LAMMPS Classical Molecular Dynamics Simulation

For the LiCl melt, classical molecular dynamics simulations can be performed using the LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) software. LAMMPS is a highly flexible and scalable molecular dynamics simulation software that supports various interatomic potentials and simulation conditions. In this example, we use the classical BMH potential function to simulate the structural and dynamic properties of the LiCl melt.

This chapter uses the pre-configured LAMMPS program in the DeePMD-kit (2.2.1) software package.

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Objectives of This Chapter

After studying this chapter, you will be able to:

Understand LAMMPS input and output files;
Write a LAMMPS MD simulation input file for the LiCl melt;
Calculate the microstructure and diffusion properties of the LiCl melt.

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1.1 Download Tutorial Resources

In this chapter, we will perform a LAMMPS classical molecular dynamics simulation using the LiCl melt molecule as an example. We have prepared the necessary files in LiCl_DP_Tutorial_Example/chapter1, which you can view by clicking on the dataset on the left.

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[2]

# For security reasons, we do not have write permissions to the dataset folder, so we will copy it to the `/data/` directory:

! cp -nr /bohr/ /personal/

# Here, we define some paths and switch to the working directory for easy subsequent calls:

import os

bohr_dataset_url = "/bohr/licl-dp-tutorial-unuc/v1/" # The dataset URL can be copied from the dataset on the left

work_path = os.path.join("/personal", bohr_dataset_url[1:]) # Perform a slice to remove the initial "/" from the path

os.chdir(work_path)

print(f"Current path: {os.getcwd()}")

Current path: /personal/bohr/licl-dp-tutorial-unuc/v1

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The LiCl_DP_Tutorial_Example/chapter1 folder contains the following files:

licl.in: LAMMPS input file, used to control the details of the LAMMPS MD simulation;
licl.data: Used to store the initial configuration of the MD simulation;

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1.2 LAMMPS Input File

The input file tells the LAMMPS software how to perform the calculation. Typically, the file is named “input.in,” where “input” can be any descriptive name to identify the type or parameters of the simulation.

Below is an example of a LAMMPS molecular dynamics simulation input file for LiCl melt:

# this input script is for simulating a 3d LiCl melt at 900K using LAMMPS.

# initialize simulation settings
units           metal
boundary        p p p
atom_style      charge

# define the simulation cell
read_data       licl.data
group           Li  type 1
group           Cl  type 2
set             type 1 charge 1
set             type 2 charge -1

# set force field
pair_style      born/coul/long 7
pair_coeff      1 1 0.4225000 0.3425 1.632 0.045625 0.01875
pair_coeff      1 2 0.2904688 0.3425 2.401 1.250000 1.50000
pair_coeff      2 2 0.1584375 0.3425 3.170 69.37500 139.375
kspace_style    ewald 1.0e-6 	

# nvt simulation  
velocity        all create 900 23456789
fix             1 all nvt temp 900 900 0.5
timestep        0.001

# rdf calculation 
compute         rdf all rdf 100 1 1 1 2 2 2
fix             2 all ave/time 100 1 100 c_rdf[*] file licl.rdf mode vector

# msd calculation
compute         msd1 Li msd
compute         msd2 Cl msd
fix             3 all ave/time 100 1 100 c_msd1[4] c_msd2[4] file licl.msd

# output
thermo_style    custom step temp pe ke etotal press lx ly lz vol
thermo          1000
dump            1 all custom 1000 licl.dump id type x y z 

log             ./LiCl_DP_Tutorial_Example/Chapter1/Outputs/log.lammps
run             500000

Let's take a look at the meaning of each parameter in the input file:

units metal: Sets the unit system used in the simulation. For metal, the units are: time (ps), length (Å), mass (amu), energy (eV), temperature (K), pressure (bar), velocity (Å/ps).
boundary p p p: Sets the boundary conditions for the simulation. In this tutorial, periodic boundary conditions are used in the x, y, and z directions. "p" stands for periodic, and "f" (fixed) stands for fixed boundary conditions.
atom_style charge: Sets the atom type and attributes. In this example, a charged atom model is used, hence the charge type.
read_data licl.data: Reads the data file licl.data, which contains the initial configuration used for the MD simulation in this case.
group Li type 1 and group Cl type 2: Creates two groups based on atom type, containing all atoms of type 1 (Li) and type 2 (Cl) respectively.
set type 1 charge 1 and set type 2 charge -1: Sets the charges for atom types 1 and 2. In this example, type 1 (Li) atoms are set to +1 charge, and type 2 (Cl) atoms are set to -1 charge.
pair_style born/coul/long 7: This command sets the interatomic potential function. In this example, the Born−Mayer−Huggins potential is used with a cutoff distance of 7 Å:

$U_{ij} (r) = \frac{q _{i} q _{j}}{r} + A_{ij} b exp (\frac{σ _{ij} - r}{ρ}) - \frac{C _{ij}}{r ^{6}} - \frac{D _{ij}}{r ^{8}}$

where the first term describes the electrostatic interaction between ions ( $q_{i}$ is the ion charge, $q_{L i}$ = +1, $q_{Cl}$ =-1); the second term describes the short-range repulsion due to electron cloud overlap, $A_{ij}$ is the Pauling factor ( $A_{L i L i}$ =2.00, $A_{L i Cl}$ =1.375, $A_{ClCl}$ =0.75), b is a constant ( $b = 0.338 \times 1 0^{- 19} J$ ), $σ_{ij}$ is the crystal ion radius, and ρ is the hardness parameter ( $ρ_{L i Cl}$ = 0.3425 Å); the last two terms correspond to dipole-dipole and dipole-quadrupole dispersion interactions, where $C_{ij}$ and $D_{ij}$ are dispersion parameters. $r$ is the cutoff distance in Å, beyond which the interatomic interactions are ignored.

	$A_{ij} b$ (eV)	$σ_{ij}$ (Å)	$C_{ij}$ (eV)	$D_{ij}$ (eV)
++	0.4225000	1.632	0.045625	0.01875
+-	0.2904688	2.401	1.250000	1.50000
--	0.1584375	3.170	69.37500	139.375

pair_coeff: These commands set the parameters for the interatomic potential function. Each pair_coeff command sets the parameters between specified atom types in the potential function. In this example, we set the parameters for 1 1, 1 2, and 2 2.
kspace_style ewald 1.0e-6: This command sets the Ewald method for calculating long-range Coulombic interactions. In this example, we use the Ewald method with a precision of 1.0e-6.
velocity all create 900 23456789: This command sets random velocities for all atoms in the simulation system.
fix 1 all nvt temp 900 900 0.5: This command performs an NVT (constant temperature and volume) simulation on the system. In this example, we maintain the system at a constant temperature of 900K using the Nose-Hoover thermostat. 0.5 is the temperature damping parameter.
timestep 0.001: This command sets the simulation timestep. In this example, the timestep is 0.001 picoseconds. (1 second = 10^3 milliseconds = 10^6 microseconds = 10^9 nanoseconds = 10^12 picoseconds)
compute rdf all rdf 100 1 1 1 2 2 2: This command calculates the radial distribution function (RDF) between two types of atoms in the simulation system. 100 indicates 100 bins, 1 1 denotes Li-Li RDF, 1 2 denotes Li-Cl RDF, and 2 2 denotes Cl-Cl RDF.
fix 2 all ave/time 100 1 100 c_rdf[*] file licl.rdf mode vector: This command time-averages the computed RDF data and outputs the results to a file. Fix 2 time-averages the RDF data with 100 1 100 indicating Nevery (every 100 steps compute RDF), Nrepeat (average over the last 1 computed RDF), and Nfrequency (output every 100 steps). The results are output to a file named licl.rdf in vector format.
compute msd1 Li msd and compute msd2 Cl msd: These commands compute the mean square displacement (MSD) for two types of atoms during the simulation. In this example, compute msd1 calculates the MSD for Li atoms, and compute msd2 calculates the MSD for Cl atoms.
fix 3 all ave/time 100 1 100 c_msd1[4] c_msd2[4] file licl.msd: This command time-averages the computed MSD data and outputs the results to a file. Fix 3 time-averages the MSD data, with c_msd1[4] and c_msd2[4] averaging the MSDs of the two types of atoms. The results are output to a file named licl.msd.
thermo_style custom step temp pe ke etotal press lx ly lz vol: This command sets the thermodynamic information output by LAMMPS during the simulation. In this example, thermo_style custom indicates a custom output format, with step temp pe ke etotal press lx ly lz vol indicating the information to be output, including simulation step, temperature, potential energy, kinetic energy, total energy, pressure, and the dimensions and volume of the simulation box.
thermo 1000: This command sets the frequency of thermodynamic information output. In this example, we output thermodynamic information every 1000 steps.
dump 1 all custom 1000 licl.dump id type x y z: This command outputs the atomic coordinate information during the simulation. In this example, dump 1 all indicates that all atoms in the simulation system are output, custom specifies the use of a custom output format, 1000 specifies the output frequency, licl.dump specifies the name of the output file, and id type x y z specifies the atomic information to be output, including the atom's ID, type, and coordinates in the x, y, and z directions.
run 500000: This command runs the LAMMPS simulation for a certain number of steps. In this example, the command evolves the simulation system for 500000 steps. At each timestep, LAMMPS calculates new positions, velocities, and potential energies based on the current atomic positions, velocities, and potential energies. Through this process, we can observe the time evolution behavior of the simulation system, such as temperature, pressure, and molecular trajectories. It is important to note that the run command needs to be set according to the actual situation to ensure the adequacy and accuracy of the simulation process.

You can view the LAMMPS input file you just downloaded with the following command. Compare it with the example above and see what you find.

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[2]

! cd ./LiCl_DP_Tutorial_Example/chapter1/ && cat licl.in

# this input script is for simulating a 3d LiCl melt at 900K using LAMMPS.

# initialize simulation settings
units           metal
boundary        p p p
atom_style      charge

# define the simulation cell
read_data	licl.data
group		Li  type 1
group		Cl  type 2
set 		type 1 charge 1
set 		type 2 charge -1

# set force field
pair_style      born/coul/long 7
pair_coeff	1 1 0.4225000 0.3425 1.632 0.045625 0.01875
pair_coeff	1 2 0.2904688 0.3425 2.401 1.250000 1.50000
pair_coeff	2 2 0.1584375 0.3425 3.170 69.37500 139.375
kspace_style	ewald 1.0e-6 	

# nvt  
velocity        all create 900 23456789
fix             1 all nvt temp 900 900 0.5
timestep        0.001

# rdf calculation 
compute 	 rdf all rdf 100 1 1 1 2 2 2
fix 		 2 all ave/time 100 1 100 c_rdf[*] file licl.rdf mode vector

# msd calculation
compute          msd1 Li msd
compute          msd2 Cl msd
fix              3 all ave/time 100 1 100 c_msd1[4] c_msd2[4] file licl.msd

# output
thermo_style    custom step temp pe ke etotal press lx ly lz vol
thermo          1000
dump		1 all custom 1000 licl.dump id type x y z 

run             200000

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To shorten the required runtime, we have appropriately reduced the number of steps. Do you have new ideas? Don't hesitate, quickly try out your new ideas.

If you haven't been lazy, you've carefully read the LAMMPS input file 2-3 times. By now, you should have a basic understanding of the input file.

Still have many doubts? Don't worry, it's normal. You need to gradually build your knowledge over time. The LAMMPS Commands Official Documentation provides comprehensive and detailed explanations, so don't forget to refer to it when needed.

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1.3 LAMMPS Initial Configuration File

Below is an example of an initial configuration for a LAMMPS MD simulation of LiCl melt:

# LAMMPS data file 
108 atoms
2 atom types
0.0 13.4422702789 xlo xhi
0.0 13.4422702789 ylo yhi
0.0 13.4422702789 zlo zhi

Masses

1 6.941  # Li
2 35.453  # Cl

Atoms  # charge

1 1 0.0 9.10297966 1.4528499842 12.3941898346  
2 1 0.0 11.53647995 2.3037500381 1.6365799904
3 1 0.0 1.3658800125 9.3088798523 4.9590802193
...
106 2 0.0 5.8468399048 2.629529953 3.9059700966
107 2 0.0 7.0047798157 5.3034000397 10.0816297531
108 2 0.0 4.4860801697 11.4718704224 13.3586997986

This file describes the basic information and initial state of the simulation system (LiCl).

First, the basic information of the simulation system: there are 108 atoms in the simulation system, two types of atoms (Li and Cl), and the box size of the simulation system in the x, y, and z directions is from 0.0 to 13.4422702789. The masses of the two types of atoms are 6.941 and 35.453, respectively.

The latter part contains the atomic positions and charge information: each line sequentially represents the atom's ID, type, charge, and coordinates in the x, y, and z directions. Note that the charges here are all 0.0; we can redefine the charges in the licl.in file.

Similarly, you can view the configuration data file of the LAMMPS case you just downloaded with the following command. Give it a try yourself.

cat ./LiCl_DP_Tutorial_Example/chapter1/licl.data

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1.4 Running LAMMPS Classical Molecular Dynamics Simulation

Classical Molecular Dynamics (CMD) uses Newtonian mechanics to describe the interactions between atoms or molecules.

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After understanding the licl.in and licl.data files, we can execute the following command to start the LAMMPS molecular dynamics simulation of the LiCl melt:

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# The following commands check if the required modules are present in the environment, and if not, quickly install them using pip.

! ! if ! pip show deepmd-kit > /dev/null; then pip install deepmd-kit[gpu,cu11,lmp]; fi;

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[4]

# ############### Time Warning: 3 mins 35 secs ###################

! cd ./LiCl_DP_Tutorial_Example/chapter1/ && lmp -i licl.in

Warning:
This LAMMPS executable is in a conda environment, but the environment has
not been activated. Libraries may fail to load. To activate this environment
please see https://conda.io/activation.
LAMMPS (23 Jun 2022 - Update 1)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
Loaded 1 plugins from /opt/deepmd-kit-2.2.1/lib/deepmd_lmp
Reading data file ...
  orthogonal box = (0 0 0) to (13.44227 13.44227 13.44227)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  108 atoms
  read_data CPU = 0.028 seconds
54 atoms in group Li
54 atoms in group Cl
Setting atom values ...
  54 settings made for charge
Setting atom values ...
  54 settings made for charge
Ewald initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
  G vector (1/distance) = 0.4944418
  estimated absolute RMS force accuracy = 1.4603535e-05
  estimated relative force accuracy = 1.0141594e-06
  KSpace vectors: actual max1d max3d = 1054 8 2456
                  kxmax kymax kzmax  = 8 8 8
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 9
  ghost atom cutoff = 9
  binsize = 4.5, bins = 3 3 3
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) pair born/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d
      bin: standard
  (2) compute rdf, occasional, copy from (1)
      attributes: half, newton on
      pair build: copy
      stencil: none
      bin: none
Setting up Verlet run ...
  Unit style    : metal
  Current step  : 0
  Time step     : 0.001
Per MPI rank memory allocation (min/avg/max) = 19.04 | 19.04 | 19.04 Mbytes
   Step          Temp          PotEng         KinEng         TotEng         Press            Lx             Ly             Lz           Volume    
         0   900           -440.62097      12.447752     -428.17322     -1521.1289      13.44227       13.44227       13.44227       2428.9461    
      1000   968.13503     -446.75864      13.390116     -433.36852      9597.5075      13.44227       13.44227       13.44227       2428.9461    
      2000   799.37501     -446.68596      11.056024     -435.62994      8193.9962      13.44227       13.44227       13.44227       2428.9461    
      3000   1055.152      -447.36257      14.593633     -432.76893      11403.113      13.44227       13.44227       13.44227       2428.9461    
      4000   942.59913     -447.06653      13.036933     -434.02959      8839.626       13.44227       13.44227       13.44227       2428.9461    
      5000   932.98321     -447.92318      12.903937     -435.01924      9611.9418      13.44227       13.44227       13.44227       2428.9461    
      6000   962.5954      -447.64155      13.313499     -434.32805      7867.1085      13.44227       13.44227       13.44227       2428.9461    
      7000   1029.0803     -446.70018      14.233041     -432.46714      8821.9229      13.44227       13.44227       13.44227       2428.9461    
      8000   804.74153     -446.89508      11.130248     -435.76483      9897.7414      13.44227       13.44227       13.44227       2428.9461    
      9000   968.94865     -447.30266      13.401369     -433.90129      7578.9257      13.44227       13.44227       13.44227       2428.9461    
     10000   853.03493     -449.26907      11.798186     -437.47089      4303.6631      13.44227       13.44227       13.44227       2428.9461    
     11000   949.03035     -448.79576      13.125883     -435.66988      6921.9392      13.44227       13.44227       13.44227       2428.9461    
     12000   1019.3028     -447.97287      14.097809     -433.87506      7439.8101      13.44227       13.44227       13.44227       2428.9461    
     13000   866.33976     -448.59725      11.982203     -436.61505      3645.5216      13.44227       13.44227       13.44227       2428.9461    
     14000   881.02097     -448.12247      12.185256     -435.93721      5532.0359      13.44227       13.44227       13.44227       2428.9461    
     15000   1010.6473     -448.61779      13.978097     -434.6397       2001.8255      13.44227       13.44227       13.44227       2428.9461    
     16000   859.14143     -448.23488      11.882644     -436.35223      4184.2035      13.44227       13.44227       13.44227       2428.9461    
     17000   832.33933     -450.00984      11.511948     -438.49789      4760.8295      13.44227       13.44227       13.44227       2428.9461    
     18000   758.53076     -445.65033      10.491114     -435.15922      10261.657      13.44227       13.44227       13.44227       2428.9461    
     19000   978.13123     -448.43327      13.528372     -434.9049       3920.768       13.44227       13.44227       13.44227       2428.9461    
     20000   922.91518     -450.61153      12.764688     -437.84685      6338.3806      13.44227       13.44227       13.44227       2428.9461    
     21000   792.15579     -449.75475      10.956176     -438.79858      2586.8977      13.44227       13.44227       13.44227       2428.9461    
     22000   850.74729     -446.89796      11.766546     -435.13141      10089.477      13.44227       13.44227       13.44227       2428.9461    
     23000   981.62229     -447.76538      13.576656     -434.18873      4595.2063      13.44227       13.44227       13.44227       2428.9461    
     24000   840.42983     -447.37612      11.623847     -435.75227      8734.1244      13.44227       13.44227       13.44227       2428.9461    
     25000   762.77107     -447.12438      10.549761     -436.57462      7349.5293      13.44227       13.44227       13.44227       2428.9461    
     26000   874.86752     -445.31886      12.100149     -433.21871      5652.4325      13.44227       13.44227       13.44227       2428.9461    
     27000   841.99527     -447.2667       11.645498     -435.6212       7022.4019      13.44227       13.44227       13.44227       2428.9461    
     28000   803.09407     -447.34821      11.107462     -436.24075      8183.1314      13.44227       13.44227       13.44227       2428.9461    
     29000   1015.8598     -449.13998      14.05019      -435.08979      4561.5234      13.44227       13.44227       13.44227       2428.9461    
     30000   869.36995     -447.74387      12.024113     -435.71976      8731.7835      13.44227       13.44227       13.44227       2428.9461    
     31000   865.67141     -447.69156      11.972959     -435.7186       5631.2005      13.44227       13.44227       13.44227       2428.9461    
     32000   1072.8189     -447.57728      14.837981     -432.7393       8334.566       13.44227       13.44227       13.44227       2428.9461    
     33000   778.19103     -447.0946       10.763032     -436.33157      7617.1961      13.44227       13.44227       13.44227       2428.9461    
     34000   897.67633     -447.46617      12.415614     -435.05056      8298.9541      13.44227       13.44227       13.44227       2428.9461    
     35000   907.33876     -446.45274      12.549253     -433.90349      11690.195      13.44227       13.44227       13.44227       2428.9461    
     36000   871.2225      -449.90596      12.049735     -437.85623      5878.1909      13.44227       13.44227       13.44227       2428.9461    
     37000   925.28988     -447.76226      12.797532     -434.96472      10973.765      13.44227       13.44227       13.44227       2428.9461    
     38000   965.44168     -448.47937      13.352865     -435.1265       7130.6017      13.44227       13.44227       13.44227       2428.9461    
     39000   791.02189     -448.77284      10.940494     -437.83234      5283.7909      13.44227       13.44227       13.44227       2428.9461    
     40000   836.15353     -446.80314      11.564702     -435.23844      5927.6367      13.44227       13.44227       13.44227       2428.9461    
     41000   915.52667     -446.82918      12.662499     -434.16668      6456.9301      13.44227       13.44227       13.44227       2428.9461    
     42000   813.43728     -449.08152      11.250517     -437.83101      7797.7577      13.44227       13.44227       13.44227       2428.9461    
     43000   852.21244     -447.65953      11.78681      -435.87272      4858.4925      13.44227       13.44227       13.44227       2428.9461    
     44000   952.43823     -447.37362      13.173016     -434.20061      6664.4747      13.44227       13.44227       13.44227       2428.9461    
     45000   908.93391     -449.79151      12.571315     -437.22019      6270.6965      13.44227       13.44227       13.44227       2428.9461    
     46000   748.50279     -447.51898      10.352419     -437.16656      7144.0906      13.44227       13.44227       13.44227       2428.9461    
     47000   881.68235     -446.21433      12.194404     -434.01993      10070.238      13.44227       13.44227       13.44227       2428.9461    
     48000   815.76098     -445.96865      11.282656     -434.686        7309.0874      13.44227       13.44227       13.44227       2428.9461    
     49000   789.00182     -448.35397      10.912554     -437.44141      9432.5533      13.44227       13.44227       13.44227       2428.9461    
     50000   804.70742     -446.36177      11.129776     -435.232        7342.0588      13.44227       13.44227       13.44227       2428.9461    
     51000   909.22121     -447.41009      12.575289     -434.8348       10285.45       13.44227       13.44227       13.44227       2428.9461    
     52000   761.63008     -446.96042      10.53398      -436.42644      5602.6415      13.44227       13.44227       13.44227       2428.9461    
     53000   808.76919     -449.85284      11.185954     -438.66688      6119.577       13.44227       13.44227       13.44227       2428.9461    
     54000   833.51029     -447.03276      11.528144     -435.50462      12510.642      13.44227       13.44227       13.44227       2428.9461    
     55000   944.50633     -446.31011      13.063312     -433.2468       14246.873      13.44227       13.44227       13.44227       2428.9461    
     56000   936.78474     -445.96572      12.956516     -433.00921      12465.188      13.44227       13.44227       13.44227       2428.9461    
     57000   841.71263     -447.53963      11.641589     -435.89804      10386.921      13.44227       13.44227       13.44227       2428.9461    
     58000   928.5016      -446.7878       12.841953     -433.94584      8404.4477      13.44227       13.44227       13.44227       2428.9461    
     59000   855.13954     -446.0453       11.827294     -434.21801      11876.025      13.44227       13.44227       13.44227       2428.9461    
     60000   936.57819     -448.48445      12.953659     -435.53079      13667.54       13.44227       13.44227       13.44227       2428.9461    
     61000   1035.5138     -447.46839      14.322022     -433.14637      8984.2872      13.44227       13.44227       13.44227       2428.9461    
     62000   896.91385     -448.50798      12.405068     -436.10291      12145.891      13.44227       13.44227       13.44227       2428.9461    
     63000   835.23576     -447.57915      11.552008     -436.02715      8294.6728      13.44227       13.44227       13.44227       2428.9461    
     64000   884.41734     -446.38607      12.232231     -434.15384      6173.496       13.44227       13.44227       13.44227       2428.9461    
     65000   818.15033     -448.157        11.315703     -436.84129      6905.2238      13.44227       13.44227       13.44227       2428.9461    
     66000   725.98462     -447.7929       10.040974     -437.75192      5460.9135      13.44227       13.44227       13.44227       2428.9461    
     67000   948.22967     -447.88104      13.114809     -434.76623      10022.118      13.44227       13.44227       13.44227       2428.9461    
     68000   819.77685     -447.2582       11.338199     -435.92         5861.8161      13.44227       13.44227       13.44227       2428.9461    
     69000   799.74646     -448.13799      11.061162     -437.07683      11270.452      13.44227       13.44227       13.44227       2428.9461    
     70000   940.84634     -446.90068      13.012691     -433.88799      11233.827      13.44227       13.44227       13.44227       2428.9461    
     71000   1030.332      -448.14601      14.250353     -433.89566      11380.668      13.44227       13.44227       13.44227       2428.9461    
     72000   924.79288     -449.3942       12.790658     -436.60354      3679.2325      13.44227       13.44227       13.44227       2428.9461    
     73000   855.75624     -446.06831      11.835824     -434.23249      7583.462       13.44227       13.44227       13.44227       2428.9461    
     74000   819.55186     -444.9279       11.335087     -433.59282      7307.3214      13.44227       13.44227       13.44227       2428.9461    
     75000   829.77483     -448.61772      11.476479     -437.14125      5820.9788      13.44227       13.44227       13.44227       2428.9461    
     76000   923.30868     -448.54104      12.77013      -435.77091      10937.125      13.44227       13.44227       13.44227       2428.9461    
     77000   965.26945     -447.10734      13.350483     -433.75686      6684.5996      13.44227       13.44227       13.44227       2428.9461    
     78000   886.29645     -448.7182       12.25822      -436.45998      6548.4903      13.44227       13.44227       13.44227       2428.9461    
     79000   852.03157     -448.05997      11.784308     -436.27566      6440.6704      13.44227       13.44227       13.44227       2428.9461    
     80000   885.15846     -445.99723      12.242481     -433.75475      8354.7332      13.44227       13.44227       13.44227       2428.9461    
     81000   981.8257      -448.77065      13.57947      -435.19118      9891.3852      13.44227       13.44227       13.44227       2428.9461    
     82000   792.07444     -448.20065      10.955051     -437.2456       5660.0712      13.44227       13.44227       13.44227       2428.9461    
     83000   932.15942     -447.70841      12.892544     -434.81586      7665.5227      13.44227       13.44227       13.44227       2428.9461    
     84000   923.48756     -446.51455      12.772604     -433.74194      2378.3956      13.44227       13.44227       13.44227       2428.9461    
     85000   741.22754     -447.1757       10.251796     -436.92391      2958.1244      13.44227       13.44227       13.44227       2428.9461    
     86000   1021.5647     -449.32353      14.129093     -435.19444      7298.1944      13.44227       13.44227       13.44227       2428.9461    
     87000   918.67946     -446.57546      12.706105     -433.86935      5031.0923      13.44227       13.44227       13.44227       2428.9461    
     88000   1002.299      -448.45785      13.862633     -434.59522      11126.938      13.44227       13.44227       13.44227       2428.9461    
     89000   821.8597      -447.11641      11.367006     -435.74941      6371.4778      13.44227       13.44227       13.44227       2428.9461    
     90000   994.76606     -446.98255      13.758446     -433.22411      11702.708      13.44227       13.44227       13.44227       2428.9461    
     91000   764.33716     -446.11499      10.571422     -435.54357      9183.5927      13.44227       13.44227       13.44227       2428.9461    
     92000   895.78488     -447.91216      12.389453     -435.52271      7647.0962      13.44227       13.44227       13.44227       2428.9461    
     93000   1060.9308     -446.85838      14.67356      -432.18482      3372.0891      13.44227       13.44227       13.44227       2428.9461    
     94000   857.15014     -445.69073      11.855103     -433.83563      9168.0177      13.44227       13.44227       13.44227       2428.9461    
     95000   826.68792     -447.14606      11.433785     -435.71227      3120.7142      13.44227       13.44227       13.44227       2428.9461    
     96000   907.58973     -448.32895      12.552724     -435.77623      5548.4105      13.44227       13.44227       13.44227       2428.9461    
     97000   790.39244     -446.5355       10.931788     -435.60371      8705.077       13.44227       13.44227       13.44227       2428.9461    
     98000   904.00759     -445.80326      12.50318      -433.30008      9231.0483      13.44227       13.44227       13.44227       2428.9461    
     99000   848.35203     -448.24554      11.733417     -436.51212      8870.4366      13.44227       13.44227       13.44227       2428.9461    
    100000   858.85781     -447.97588      11.878721     -436.09715      3816.5981      13.44227       13.44227       13.44227       2428.9461    
    101000   837.52185     -445.8777       11.583627     -434.29407      7015.7058      13.44227       13.44227       13.44227       2428.9461    
    102000   825.36683     -446.08522      11.415513     -434.66971      10060.208      13.44227       13.44227       13.44227       2428.9461    
    103000   861.1587      -447.80968      11.910544     -435.89913      7846.5612      13.44227       13.44227       13.44227       2428.9461    
    104000   966.62836     -446.84957      13.369278     -433.4803       6433.8448      13.44227       13.44227       13.44227       2428.9461    
    105000   947.66633     -449.38361      13.107017     -436.2766       7423.6998      13.44227       13.44227       13.44227       2428.9461    
    106000   860.22459     -448.20013      11.897625     -436.30251      6778.849       13.44227       13.44227       13.44227       2428.9461    
    107000   975.8158      -446.38747      13.496348     -432.89112      12796.098      13.44227       13.44227       13.44227       2428.9461    
    108000   819.33558     -448.13407      11.332096     -436.80197      5369.3216      13.44227       13.44227       13.44227       2428.9461    
    109000   895.67954     -447.08332      12.387996     -434.69532      6592.9186      13.44227       13.44227       13.44227       2428.9461    
    110000   956.55719     -447.06299      13.229985     -433.83301      5643.5402      13.44227       13.44227       13.44227       2428.9461    
    111000   871.19517     -448.54648      12.049357     -436.49712      8604.1522      13.44227       13.44227       13.44227       2428.9461    
    112000   840.40436     -447.07744      11.623495     -435.45395      10547.689      13.44227       13.44227       13.44227       2428.9461    
    113000   1029.3846     -447.43078      14.237249     -433.19353      8856.9606      13.44227       13.44227       13.44227       2428.9461    
    114000   988.7004      -449.66188      13.674553     -435.98733      7988.7498      13.44227       13.44227       13.44227       2428.9461    
    115000   975.6549      -448.66092      13.494122     -435.1668       6001.9213      13.44227       13.44227       13.44227       2428.9461    
    116000   1013.1805     -446.55507      14.013132     -432.54194      12339.786      13.44227       13.44227       13.44227       2428.9461    
    117000   951.80343     -449.65437      13.164237     -436.49014      6460.0683      13.44227       13.44227       13.44227       2428.9461    
    118000   866.11795     -447.42654      11.979135     -435.4474       10188.576      13.44227       13.44227       13.44227       2428.9461    
    119000   900.53134     -445.98984      12.455101     -433.53474      6230.6033      13.44227       13.44227       13.44227       2428.9461    
    120000   749.33637     -446.96925      10.363948     -436.6053       12284.467      13.44227       13.44227       13.44227       2428.9461    
    121000   830.91376     -447.46308      11.492232     -435.97085      8476.8902      13.44227       13.44227       13.44227       2428.9461    
    122000   963.08154     -446.92419      13.320222     -433.60397      12047.404      13.44227       13.44227       13.44227       2428.9461    
    123000   822.13312     -448.07144      11.370788     -436.70065      8694.1516      13.44227       13.44227       13.44227       2428.9461    
    124000   917.32545     -448.74012      12.687377     -436.05274      5075.294       13.44227       13.44227       13.44227       2428.9461    
    125000   921.10219     -446.57636      12.739613     -433.83674      10109.19       13.44227       13.44227       13.44227       2428.9461    
    126000   876.40984     -446.45556      12.12148      -434.33408      9319.9786      13.44227       13.44227       13.44227       2428.9461    
    127000   817.7293      -448.35213      11.309879     -437.04225      9416.5937      13.44227       13.44227       13.44227       2428.9461    
    128000   822.26552     -445.75579      11.372619     -434.38317      9522.1448      13.44227       13.44227       13.44227       2428.9461    
    129000   915.89964     -446.54872      12.667657     -433.88107      4919.1352      13.44227       13.44227       13.44227       2428.9461    
    130000   818.94898     -448.18933      11.326749     -436.86258      7526.0556      13.44227       13.44227       13.44227       2428.9461    
    131000   929.11986     -449.46307      12.850504     -436.61256      8950.3404      13.44227       13.44227       13.44227       2428.9461    
    132000   862.45175     -447.07155      11.928428     -435.14312      10325.189      13.44227       13.44227       13.44227       2428.9461    
    133000   1003.9721     -448.37695      13.885773     -434.49118      9293.3913      13.44227       13.44227       13.44227       2428.9461    
    135000   800.45494     -447.08512      11.070961     -436.01416      7268.921       13.44227       13.44227       13.44227       2428.9461    
    136000   991.29708     -447.45599      13.710467     -433.74552      9704.8549      13.44227       13.44227       13.44227       2428.9461    
    137000   906.86916     -448.65115      12.542758     -436.1084       2813.3224      13.44227       13.44227       13.44227       2428.9461    
    138000   736.7968      -449.78277      10.190515     -439.59226      1631.9435      13.44227       13.44227       13.44227       2428.9461    
    139000   844.24781     -450.05149      11.676653     -438.37484      7716.5954      13.44227       13.44227       13.44227       2428.9461    
    140000   807.56359     -446.48045      11.169279     -435.31117      8733.9129      13.44227       13.44227       13.44227       2428.9461    
    141000   923.35263     -446.52203      12.770738     -433.75129      6457.0609      13.44227       13.44227       13.44227       2428.9461    
    142000   793.11393     -448.1535       10.969428     -437.18407      6008.6258      13.44227       13.44227       13.44227       2428.9461    
    143000   881.25764     -447.92144      12.18853      -435.73291      4117.1976      13.44227       13.44227       13.44227       2428.9461    
    144000   967.61068     -448.95923      13.382864     -435.57637      8184.5555      13.44227       13.44227       13.44227       2428.9461    
    145000   768.46996     -449.04589      10.628582     -438.4173       3551.6168      13.44227       13.44227       13.44227       2428.9461    
    146000   847.79377     -447.25021      11.725696     -435.52451      6861.9653      13.44227       13.44227       13.44227       2428.9461    
    147000   941.86992     -447.26683      13.026848     -434.23998      11022.249      13.44227       13.44227       13.44227       2428.9461    
    148000   888.92088     -445.14616      12.294518     -432.85164      9285.372       13.44227       13.44227       13.44227       2428.9461    
    149000   868.59899     -447.77784      12.01345      -435.76439      7841.3668      13.44227       13.44227       13.44227       2428.9461    
    150000   869.94163     -447.88066      12.03202      -435.84864      6666.5273      13.44227       13.44227       13.44227       2428.9461    
    151000   1025.9435     -446.9241       14.189655     -432.73444      11561.02       13.44227       13.44227       13.44227       2428.9461    
    152000   820.44005     -446.85938      11.347371     -435.51201      5526.6729      13.44227       13.44227       13.44227       2428.9461    
    153000   838.9451      -447.83716      11.603312     -436.23385      8319.0259      13.44227       13.44227       13.44227       2428.9461    
    154000   803.85304     -445.55584      11.117959     -434.43788      6618.0311      13.44227       13.44227       13.44227       2428.9461    
    155000   893.20948     -446.74828      12.353833     -434.39445      5277.4573      13.44227       13.44227       13.44227       2428.9461    
    156000   840.30348     -446.53082      11.622099     -434.90872      2929.223       13.44227       13.44227       13.44227       2428.9461    
    157000   837.11447     -446.61864      11.577993     -435.04065      8329.4129      13.44227       13.44227       13.44227       2428.9461    
    158000   805.23492     -446.47885      11.137072     -435.34177      10512.463      13.44227       13.44227       13.44227       2428.9461    
    159000   969.3103      -445.50776      13.406371     -432.10139      12530.411      13.44227       13.44227       13.44227       2428.9461    
    160000   918.63819     -447.56984      12.705534     -434.8643       8536.2361      13.44227       13.44227       13.44227       2428.9461    
    161000   969.33864     -448.7203       13.406763     -435.31353      8937.9252      13.44227       13.44227       13.44227       2428.9461    
    162000   903.2513      -448.1911       12.49272      -435.69838      6702.4355      13.44227       13.44227       13.44227       2428.9461    
    163000   795.79596     -449.16258      11.006523     -438.15606      4923.056       13.44227       13.44227       13.44227       2428.9461    
    164000   806.73504     -446.44735      11.15782      -435.28953      9302.5683      13.44227       13.44227       13.44227       2428.9461    
    165000   950.94286     -446.89904      13.152334     -433.74671      9966.2733      13.44227       13.44227       13.44227       2428.9461    
    166000   982.43252     -445.50258      13.587863     -431.91472      10636.754      13.44227       13.44227       13.44227       2428.9461    
    167000   894.11295     -448.1689       12.366329     -435.80257      8273.6357      13.44227       13.44227       13.44227       2428.9461    
    168000   940.05823     -447.84592      13.001791     -434.84412      7811.2249      13.44227       13.44227       13.44227       2428.9461    
    169000   954.60066     -446.44533      13.202925     -433.2424       8525.8779      13.44227       13.44227       13.44227       2428.9461    
    170000   891.02694     -447.11949      12.323647     -434.79584      6315.9767      13.44227       13.44227       13.44227       2428.9461    
    171000   820.64023     -446.65828      11.35014      -435.30814      6700.267       13.44227       13.44227       13.44227       2428.9461    
    172000   927.36112     -447.73684      12.826179     -434.91066      3356.1483      13.44227       13.44227       13.44227       2428.9461    
    173000   847.52843     -447.56611      11.722026     -435.84408      7921.7197      13.44227       13.44227       13.44227       2428.9461    
    174000   805.34588     -448.50089      11.138606     -437.36228      7259.0081      13.44227       13.44227       13.44227       2428.9461    
    175000   917.57253     -447.48652      12.690795     -434.79572      3965.3925      13.44227       13.44227       13.44227       2428.9461    
    176000   862.45248     -447.17391      11.928438     -435.24547      7410.1343      13.44227       13.44227       13.44227       2428.9461    
    177000   888.26593     -449.31061      12.28546      -437.02515      5133.7781      13.44227       13.44227       13.44227       2428.9461    
    178000   928.01925     -447.60273      12.835282     -434.76745      13497.351      13.44227       13.44227       13.44227       2428.9461    
    179000   928.5132      -446.12937      12.842113     -433.28725      7682.4814      13.44227       13.44227       13.44227       2428.9461    
    180000   780.09732     -447.65732      10.789398     -436.86793      4828.3269      13.44227       13.44227       13.44227       2428.9461    
    181000   954.91969     -447.30681      13.207337     -434.09948      7164.5291      13.44227       13.44227       13.44227       2428.9461    
    182000   967.69326     -446.67474      13.384006     -433.29073      53.98061       13.44227       13.44227       13.44227       2428.9461    
    183000   907.37937     -448.33498      12.549815     -435.78517      10026.747      13.44227       13.44227       13.44227       2428.9461    
    184000   961.35453     -449.32723      13.296336     -436.0309       6793.7497      13.44227       13.44227       13.44227       2428.9461    
    185000   898.7912      -444.98736      12.431033     -432.55633      11057.089      13.44227       13.44227       13.44227       2428.9461    
    186000   872.1631      -445.83323      12.062744     -433.77049      3163.7455      13.44227       13.44227       13.44227       2428.9461    
    187000   953.9991      -447.79383      13.194605     -434.59923      7799.4581      13.44227       13.44227       13.44227       2428.9461    
    188000   853.70051     -446.79945      11.807391     -434.99205      7155.6164      13.44227       13.44227       13.44227       2428.9461    
    189000   904.16233     -447.27755      12.505321     -434.77223      6458.5134      13.44227       13.44227       13.44227       2428.9461    
    190000   955.38615     -445.88396      13.213789     -432.67017      13407.872      13.44227       13.44227       13.44227       2428.9461    
    191000   868.84979     -446.47419      12.016919     -434.45727      5605.3551      13.44227       13.44227       13.44227       2428.9461    
    192000   946.62224     -449.23223      13.092577     -436.13965      7425.6747      13.44227       13.44227       13.44227       2428.9461    
    193000   991.6896      -446.31754      13.715896     -432.60165      12463.628      13.44227       13.44227       13.44227       2428.9461    
    194000   971.45787     -446.87584      13.436074     -433.43977      9789.9933      13.44227       13.44227       13.44227       2428.9461    
    195000   853.58226     -447.38632      11.805756     -435.58057      3902.412       13.44227       13.44227       13.44227       2428.9461    
    196000   742.65661     -448.30093      10.271561     -438.02936      4160.0535      13.44227       13.44227       13.44227       2428.9461    
    197000   961.42026     -448.80947      13.297245     -435.51223      6976.6933      13.44227       13.44227       13.44227       2428.9461    
    198000   953.8282      -447.17925      13.192241     -433.98701      9963.9553      13.44227       13.44227       13.44227       2428.9461    
    199000   867.81204     -448.32292      12.002566     -436.32036      7735.4293      13.44227       13.44227       13.44227       2428.9461    
    200000   767.00712     -447.3289       10.608349     -436.72055      8036.8208      13.44227       13.44227       13.44227       2428.9461    
Loop time of 231.381 on 1 procs for 200000 steps with 108 atoms

Performance: 74.682 ns/day, 0.321 hours/ns, 864.374 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 35.975     | 35.975     | 35.975     |   0.0 | 15.55
Kspace  | 190.34     | 190.34     | 190.34     |   0.0 | 82.26
Neigh   | 1.7711     | 1.7711     | 1.7711     |   0.0 |  0.77
Comm    | 1.3309     | 1.3309     | 1.3309     |   0.0 |  0.58
Output  | 0.04576    | 0.04576    | 0.04576    |   0.0 |  0.02
Modify  | 1.5983     | 1.5983     | 1.5983     |   0.0 |  0.69
Other   |            | 0.3212     |            |       |  0.14

Nlocal:            108 ave         108 max         108 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           1249 ave        1249 max        1249 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:           7292 ave        7292 max        7292 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 7292
Ave neighs/atom = 67.518519
Neighbor list builds = 5707
Dangerous builds = 0
Total wall time: 0:03:52

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1.5 LAMMPS Molecular Dynamics Simulation Results and Analysis

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After the simulation is completed, we can see the following files generated in the current folder:

log.lammps: The log file, which records various output information during the simulation process, including the initial system state, physical quantities such as energy, temperature, and pressure during the MD process, and the results of various calculations.
licl.dump: The trajectory file, which records the positions, velocities, and other information of all atoms in the simulation system at each timestep.
licl.rdf: The radial distribution function (RDF) file, which records the RDF output at every Nfrequency steps.
licl.msd: The mean square displacement (MSD) file, which records the change of the ions' mean square displacement over time in the simulation system.

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For the licl.dump file, we can use software like OVITO to visualize the complete trajectory. Here, we will use ASE to view only the last frame of the image. To learn how to use ASE, you can read “Quick Start with ASE”.

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# The following commands check if the required modules are present in the environment, and if not, quickly install them using pip.

! if ! /opt/mamba/bin/pip show ase > /dev/null; then /opt/mamba/bin/pip install --upgrade ase; fi;

WARNING: Package(s) not found: ase
Looking in indexes: https://pypi.tuna.tsinghua.edu.cn/simple
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WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv

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from ase.io import lammpsrun

from ase.visualize import view

from ase import Atoms

# Import the trajectory file

traj = lammpsrun.read_lammps_dump('./LiCl_DP_Tutorial_Example/chapter1/licl.dump')

# Define the list of element names

elements = ['Li', 'Cl']

# Assign element names to the atoms in the trajectory

# Set atom names based on atom types

for atom in traj:

atom_type = atom.number - 1 # Atom types start from 1, while list indices start from 0

atom.symbol = elements[atom_type]

print(traj)

view(traj, viewer='x3d')

Atoms(symbols='Cl54Li54', pbc=True, cell=[13.4422702789, 13.4422702789, 13.4422702789])

ASE atomic visualization

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What is a Radial Distribution Function (RDF)? Why is it important to calculate the RDF in Molecular Dynamics?

The Radial Distribution Function (RDF) is a statistical measure that describes the relative positions and distance distributions between atoms or molecules in multi-atomic systems such as solids, liquids, and gases. It represents the probability density of finding an atom or molecule at a distance r from a selected atom or molecule. The RDF, g(r), can be expressed as:

$g (r) = \frac{N}{V} \times \frac{1}{ρ} \times \frac{d N}{d r}$

where N is the number of atoms or molecules within the distance r, V is the volume, ρ is the average density of the atoms or molecules, and $(\frac{d N}{d r})$ is the rate of increase of the number of atoms or molecules near distance r.

Let's take oxygen as an example. In oxygen, the molecules mainly interact through van der Waals forces. We can calculate the RDF between oxygen molecules to analyze this interaction.

Considering an oxygen molecule in the system as the center, we calculate the probability density of other oxygen molecules within distance r. The RDF, g(r), describes the probability density of finding another oxygen molecule at distance r relative to the probability density of finding it in a completely random distribution.

When calculating the RDF, g(r), between oxygen molecules, we observe that:

When r is very small, g(r) approaches 0, indicating that it is improbable to find oxygen molecules very close together due to repulsive forces.
As r increases, g(r) shows a peak corresponding to the most probable distance between oxygen molecules where van der Waals forces are strongest.
When r continues to increase, g(r) gradually approaches 1, indicating that at larger distances, the distribution of oxygen molecules tends to be random.

The reason g(r) approaches 1 as r increases is that g(r) is a relative probability density compared to a completely random distribution. At larger distances, the interactions between atoms or molecules become weaker, and their distribution becomes more random.

When we say g(r) approaches 1, we describe a phenomenon where at larger distances, the interaction between molecules becomes less significant, and their distribution approaches randomness. In this case, the probability of finding a molecule in the actual system is close to the probability of finding it in a random distribution, thus g(r) is close to 1.

It is important to note that g(r) itself is not a probability but a probability density. For the RDF, g(r), it represents the relative likelihood of finding another molecule near distance r, making it a probability density function. The value of g(r) does not directly reflect the probability of finding a molecule at distance r, but the relative probability density compared to a random distribution. Therefore, as r increases, g(r) does not grow indefinitely but stabilizes at a value of 1, indicating that the molecular distribution in the region far from the central molecule tends to be random.

From this simple example, we see how the RDF helps us understand the interactions and distributions between oxygen molecules. The same method can be applied to other gaseous systems to reveal their atomic or molecular interactions and structural properties.

In Molecular Dynamics (MD) simulations, the RDF is an important tool because it provides structural information about the system, helping us understand the interactions between atoms or molecules and the organization of the system. Calculating the RDF can help us:

Describe and quantify the distance distribution between atoms or molecules, thus analyzing molecular interactions and ordering.
Analyze phase transitions in the system, such as liquid-solid transitions and liquid-gas transitions.
Understand the local structure of the system, such as cluster formation in liquids and distribution patterns of atoms or molecules in gases.
Compare with experimental data (e.g., X-ray diffraction, neutron scattering) to verify the accuracy of simulation results.

Therefore, calculating the RDF in MD simulations is crucial for analyzing and interpreting simulation results.

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For the licl.rdf file, we can use the following Python script for further processing and plotting:

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# The following commands check if the required modules are present in the environment, and if not, quickly install them using pip.

! if ! pip show matplotlib > /dev/null; then pip install matplotlib; fi;

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import numpy as np

import matplotlib.pyplot as plt

nbins = 100 # define the number of bins in the RDF

with open("./LiCl_DP_Tutorial_Example/chapter1/licl.rdf", "r") as f: # read the licl.rdf file

lines = f.readlines()

lines = lines[3:]

data = np.zeros((nbins, 7))

count = 0

for line in lines:

nums = line.split()

if len(nums) == 8:

for i in range(1, 8):

data[int(nums[0])-1, i-1] += float(nums[i]) # accumulatie data for each bin

if len(nums) == 2:

count += 1 # count the number of accumulations for each bin

ave_rdf = data / count # calculate the averaged RDF data

np.savetxt('./LiCl_DP_Tutorial_Example/chapter1/ave_rdf.txt', ave_rdf)

labels = ['Li-Li', 'Li-Cl', 'Cl-Cl']

colors = ['orange', 'purple', 'green']

for i, label, color in zip(range(1, 7, 2), labels, colors):

plt.plot(ave_rdf[:, 0], ave_rdf[:, i], color=color, label=label)

plt.title('RDF')

plt.xlabel('r/Å')

plt.ylabel('g(r)')

plt.legend()

plt.savefig('./LiCl_DP_Tutorial_Example/chapter1/rdf.png', dpi=300)

plt.show()

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For the licl.msd file, we can use the following Python script to further process and calculate the diffusion coefficient (D) and plot the data:

How can we calculate the diffusion coefficient from the Mean Square Displacement (MSD)?

We can calculate the diffusion coefficient from the Mean Square Displacement (MSD) because there is a direct mathematical relationship between them. The diffusion coefficient is a physical quantity that measures the rate at which particles spread in a substance, and it is related to the particles' MSD.

In the diffusion process, particle motion follows the random walk or Brownian motion model. For a three-dimensional random walk, the displacement in each direction is independent, and we can express the total MSD as the average of the sum of the squares of the displacements in the three directions:

$MSD (t) = ⟨ ∣ Δ r_{i} (t) ∣^{2} ⟩ = \frac{1}{N} ⟨ i \sum ∣ r_{i} (t) - r_{i} (0) ∣^{2} ⟩$

According to the Einstein Relation and Fick's Law, we can obtain the relationship between the diffusion coefficient (D) and the MSD:

$D = \frac{1}{6} t \to \infty lim \frac{d ( MSD )}{d t}$

In this formula, (t) is time, and (D) is the diffusion coefficient. The formula indicates that the MSD increases linearly with time, and its slope is proportional to the diffusion coefficient. Therefore, we can calculate the diffusion coefficient by performing a linear fit on the MSD data, obtaining the linear relationship between MSD and time.

It is important to note that this method is based on the assumption that the particles' motion during diffusion is random and memoryless. In some cases, this assumption may not hold, such as in the motion of particles with long-range interactions or in an ordered lattice. In such cases, other methods may be needed to calculate the diffusion coefficient. However, in many practical applications, especially in the diffusion of particles in liquids and gases, using MSD to calculate the diffusion coefficient is a very effective method.

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import numpy as np

import matplotlib.pyplot as plt

# Load the MSD data

data = np.loadtxt('./LiCl_DP_Tutorial_Example/chapter1/licl.msd', skiprows=2)

# Extract time and MSD values for Li+ and Cl-

time = data[:, 0]

msd1 = data[:, 1]

msd2 = data[:, 2]

# Plot the MSD data

plt.plot(time/1000, msd1, 'b-', label='$Li^+$') # 1fs= 1/1000ps

plt.plot(time/1000, msd2, 'r-', label='$Cl^-$')

plt.xlabel('time (ps)')

plt.ylabel('$MSD (Å^2)$')

plt.title('Mean Square Displacement (MSD)')

plt.legend()

plt.savefig('./LiCl_DP_Tutorial_Example/chapter1/msd.png', dpi=300)

plt.show()

# Calculate diffusion coefficients

slope1, _ = np.polyfit(time, msd1, 1) # Linear fit for Li+ MSD data to get slope

slope2, _ = np.polyfit(time, msd2, 1) # Linear fit for Cl- MSD data to get slope

# Diffusion coefficient D = slope / 6; 1 Å^2/fs = 1e-5 m^2/s

Diff1 = slope1 / 6 * 1e-5

Diff2 = slope2 / 6 * 1e-5

print(f"Diffusion Coefficient of Li+: {Diff1} m^2/s")

print(f"Diffusion Coefficient of Cl-: {Diff2} m^2/s")

Diffusion Coefficients of Li+: 7.543639618987788e-09 m^2/s
Diffusion Coefficients of Cl-: 3.5602726197335397e-09 m^2/s

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Note: The values of the diffusion coefficients may differ from those reported in the literature. To obtain more accurate values, we can consider the following aspects:

First, perform simulations in the NPT ensemble to fix the pressure at 0 GPa and obtain the equilibrium volume. Then conduct NVT simulations at the equilibrium volume.
Use a larger simulation box.
Set a longer simulation time.

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Chapter 2: ABACUS First-Principles Calculation

For the LiCl melt, we can also use ABACUS (Atomic-orbital Based Ab-initio Computation at UStc) software to perform first-principles calculations. ABACUS is a material simulation software based on Density Functional Theory (DFT), which can accurately calculate interatomic interactions. By using ABACUS, we can study the properties of the LiCl melt from an electronic structure perspective.

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Objectives of This Chapter

After studying this chapter, you will be able to:

Understand the input and output files of ABACUS software;
Write an ABACUS SCF calculation input file for the LiCl melt and perform the calculation;
Write an ABACUS MD calculation input file for the LiCl melt and perform the calculation;

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2.1 Download Tutorial Resources

In this chapter, we will perform ABACUS first-principles calculations using the LiCl melt molecule as an example. We have prepared the necessary files in LiCl_DP_Tutorial_Example/chapter2. This tutorial is completed using ABACUS v3.1.0.

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In the LiCl_DP_Tutorial_Example/chapter2 folder, there are the following 5 types of files:

INPUT: Contains various parameters needed for the calculation process, defining and controlling the calculation task.
STRU: The structure file, which contains information about atom types, atomic positions, lattice constants, and lattice vectors.
KPT: Contains k-point information needed for Brillouin zone integration.
*.upf: Contains pseudopotential information for the atoms.
*.orb: Contains the numerical representation of atomic orbitals.

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2.2 ABACUS Self-Consistent Calculation

First, we will use ABACUS software to perform a self-consistent calculation for the LiCl melt.

Self-consistent refers to the Self-Consistent Field (SCF) calculation, which is the foundation of the Density Functional Theory (DFT) algorithm and the reason DFT is considered a first-principles method.

From a self-consistent field calculation, we can obtain the ground-state structure and ground-state energy of a system.

The ground-state structure allows us to determine structural parameters of the system, such as cell parameters, bond lengths, and bond angles, while the ground-state energy enables us to further understand atomic forces and the stress-strain properties of crystalline materials.

Therefore, self-consistent field calculations are the foundation for starting DFT calculations.

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2.2.1 ABACUS Self-Consistent Calculation Input File

You have just downloaded the ABACUS input files we prepared for this case. Let's view them using the following commands.

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INPUT File: The INPUT file contains parameters related to the SCF calculation of the LiCl melt:

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! cd ./LiCl_DP_Tutorial_Example/chapter2/abacus_scf && cat INPUT

INPUT_PARAMETERS

#Parameters (1.General)
ntype                   2
symmetry                0
vdw_method              d3_bj

#Parameters (2.Iteration)
ecutwfc                 100
scf_thr                 1e-7
scf_nmax                120

#Parameters (3.Basis)
basis_type              lcao

#Parameters (4.Smearing)
smearing_method         gauss
smearing_sigma          0.002

#Parameters (5.Mixing)
mixing_type             pulay
mixing_beta             0.4

#Parameters (6.sfc)
calculation             scf
cal_force               1
cal_stress              1

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对 INPUT 中各参数的介绍如下：

INPUT_PARAMETERS

#Parameters (1.General)
ntype                   2           # Number of atom types, set to 2
symmetry                0           # Whether to use crystal symmetry, 0 means not using
vdw_method              d3_bj       # Method for calculating van der Waals forces, here using the D3 method with Becke-Johnson damping function (d3_bj)

#Parameters (2.Iteration)
ecutwfc                 100         # Cutoff energy for plane wave basis set, set to 100 Ry
scf_thr                 1e-7        # Convergence threshold for self-consistent field, set to 1.0e-7
scf_nmax                120         # Maximum number of iterations for self-consistent field, set to 120

#Parameters (3.Basis)
basis_type              lcao        # Basis set type, here choosing Linear Combination of Atomic Orbitals (LCAO)                     

#Parameters (4.Smearing)
smearing_method         gauss       # Smearing method, here choosing Gaussian smearing (gauss)
smearing_sigma          0.002       # Smearing parameter, set to 0.002 Ry

#Parameters (5.Mixing)
mixing_type             pulay       # Method for charge density mixing, here choosing Pulay mixing
mixing_beta             0.4         # Mixing parameter, set to 0.4

#Parameters (6.sfc)
calculation             scf                
cal_force               1           # Whether to calculate atomic forces, set to 1 to calculate
cal_stress              1           # Whether to calculate stress, set to 1 to calculate

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STRU File: The STRU file contains information about the atom types, atomic positions, lattice constants, and lattice vectors of the LiCl melt. Considering the relatively high cost of DFT calculations, a smaller computational system (64 atoms) is designed here:

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! cd ./LiCl_DP_Tutorial_Example/chapter2/abacus_scf && cat STRU

ATOMIC_SPECIES
Li 6.941 Li_ONCV_PBE-1.2.upf
Cl 35.453 Cl_ONCV_PBE-1.2.upf

NUMERICAL_ORBITAL
Li_gga_8au_100Ry_4s1p.orb
Cl_gga_8au_100Ry_2s2p1d.orb

LATTICE_CONSTANT
1.8897261246257702

LATTICE_VECTORS
11.858 0.0 0.0 
0.0 11.858 0.0 
0.0 0.0 11.858 

ATOMIC_POSITIONS
Cartesian    # Cartesian(Unit is LATTICE_CONSTANT)
Li
0.0
32
3.01682  1.77597  4.37873  1  1  1
3.47660  5.23243  2.05957  1  1  1
0.90851  3.90744  4.56133  1  1  1
1.45547  -0.05347  0.89671  1  1  1
9.58599  4.38419  1.31575  1  1  1
5.33635  11.08600  4.46604  1  1  1
7.53108  3.19151  10.88540  1  1  1
6.20144  2.27490  2.29226  1  1  1
10.86000  11.28090  4.03153  1  1  1
8.72296  1.91404  5.01236  1  1  1
0.56714  5.94286  11.29220  1  1  1
4.56436  1.51683  10.93970  1  1  1
6.47417  6.48432  2.26679  1  1  1
2.67649  9.86711  5.62938  1  1  1
10.52500  6.89521  4.55821  1  1  1
7.31791  10.82390  10.75460  1  1  1
9.98168  8.34648  1.34799  1  1  1
8.55005  9.02160  5.95048  1  1  1
0.22956  2.27927  10.61770  1  1  1
5.35174  4.64974  5.89709  1  1  1
2.77623  2.83912  8.65057  1  1  1
0.72266  0.78088  7.23018  1  1  1
9.32377  4.62855  7.16868  1  1  1
7.04620  1.65735  7.19938  1  1  1
9.46563  0.30375  0.94568  1  1  1
0.33212  9.50630  8.83283  1  1  1
2.15335  5.79070  7.99947  1  1  1
3.67904  11.03680  8.96262  1  1  1
5.68956  7.47681  6.72704  1  1  1
4.38374  7.94229  10.64750  1  1  1
9.46514  7.37079  8.86447  1  1  1
9.83567  11.76610  9.57714  1  1  1
Cl
0.0
32
2.40263  3.44380  3.15593  1  1  1
4.71432  5.62464  3.99601  1  1  1
5.02722  1.62164  4.70153  1  1  1
2.01218  2.40381  6.74421  1  1  1
11.34250  5.35053  5.74131  1  1  1
5.73025  3.70554  0.70594  1  1  1
8.40485  2.87640  2.43455  1  1  1
10.28650  2.52149  11.26940  1  1  1
8.49700  7.00646  2.73858  1  1  1
11.20110  0.08803  2.05881  1  1  1
4.15535  7.02362  0.82488  1  1  1
2.06075  10.42340  7.60314  1  1  1
2.84183  11.23460  4.03930  1  1  1
5.11946  9.46550  6.20652  1  1  1
6.79921  0.74965  -0.06418  1  1  1
11.24310  6.60439  0.79167  1  1  1
10.99020  8.95220  4.58075  1  1  1
2.66309  1.24239  11.46430  1  1  1
1.50200  4.24863  10.00090  1  1  1
4.58981  1.26528  8.80842  1  1  1
4.17519  5.64115  7.14293  1  1  1
7.53446  3.25664  6.13640  1  1  1
8.18598  0.50707  8.64081  1  1  1
10.58380  1.54594  5.84851  1  1  1
0.05259  0.20666  9.59310  1  1  1
1.53699  7.84114  9.74525  1  1  1
5.13504  9.58460  9.80476  1  1  1
9.50581  10.09210  11.41870  1  1  1
8.14839  10.98370  4.15793  1  1  1
10.36210  9.23839  8.34472  1  1  1
9.08894  5.61878  9.58466  1  1  1
8.15206  7.23734  6.57717  1  1  1

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The STRU file is described as follows:

ATOMIC_SPECIES
Li 6.941 Li_ONCV_PBE-1.2.upf           # Element, atomic mass, pseudopotential file used
Cl 35.453 Cl_ONCV_PBE-1.2.upf

NUMERICAL_ORBITAL
Li_gga_8au_100Ry_4s1p.orb              # Numerical orbital file
Cl_gga_8au_100Ry_2s2p1d.orb

LATTICE_CONSTANT
1.889726                               # 1.889726 Bohr = 1.0 Angstrom

LATTICE_VECTORS
11.858 0.0 0.0                         # Lattice vectors
0.0 11.858 0.0 
0.0 0.0 11.858 

ATOMIC_POSITIONS
Cartesian                              # Represented in Cartesian coordinates, unit is the lattice constant
Li                                     # Element name
0.0                                    # Element magnetism
32                                     # Number of atoms
3.01682  1.77597  4.37873  1  1  1     # Each atom's x, y, z coordinates and constraints (1 indicates allowed to move in that direction, 0 indicates fixed)
3.47660  5.23243  2.05957  1  1  1
0.90851  3.90744  4.56133  1  1  1
... (omitted)
Cl
0.0
32
2.40263  3.44380  3.15593  1  1  1
4.71432  5.62464  3.99601  1  1  1
5.02722  1.62164  4.70153  1  1  1
... (omitted)

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KPT File: The KPT file contains the k-point settings for the SCF calculation of the LiCl melt:

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[25]

! cd ./LiCl_DP_Tutorial_Example/chapter2/abacus_scf && cat KPT

K_POINTS
0
Gamma
1 1 1 0 0 0

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*.upf and *.orb Files: For Li and Cl, we use Li_ONCV_PBE-1.2.upf and Cl_ONCV_PBE-1.2.upf, as well as Li_gga_8au_100Ry_4s1p.orb and Cl_gga_8au_100Ry_2s2p1d.orb. The upf and orb files for each atom can be downloaded from the ABACUS official website.

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2.2.2 Running ABACUS Self-Consistent Calculation

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After preparing all the input files, we can perform the SCF calculation for the LiCl melt. For example, using the command line:

In this image, since ABACUS is installed in an Intel oneAPI environment, we need to load the appropriate environment by running the command . /opt/intel/oneapi/setvars.sh before running ABACUS.
Set OMP_NUM_THREADS=1 to use a single thread for the calculation.
abacus is the command for the ABACUS executable program.

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[4]

# ############### Time Warning: 1 minute ###################

! cd ./LiCl_DP_Tutorial_Example/chapter2/abacus_scf && OMP_NUM_THREADS=1 mpirun -np 2 abacus

                                                                                     
                              ABACUS v3.2                                            

               Atomic-orbital Based Ab-initio Computation at UStc                    

                     Website: http://abacus.ustc.edu.cn/                             
               Documentation: https://abacus.deepmodeling.com/                       
                  Repository: https://github.com/abacusmodeling/abacus-develop       
                              https://github.com/deepmodeling/abacus-develop         

 Wed Jul 10 02:50:09 2024
 MAKE THE DIR         : OUT.ABACUS/

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 Warning: the number of valence electrons in pseudopotential > 1 for Li: [He] 2s1
 Pseudopotentials with additional electrons can yield (more) accurate outcomes, but may be less efficient.
 If you're confident that your chosen pseudopotential is appropriate, you can safely ignore this warning.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

 UNIFORM GRID DIM     : 144 * 144 * 144
 UNIFORM GRID DIM(BIG): 36 * 36 * 36
 DONE(0.700222   SEC) : SETUP UNITCELL
 DONE(0.710906   SEC) : INIT K-POINTS
 ---------------------------------------------------------
 Self-consistent calculations for electrons
 ---------------------------------------------------------
 SPIN    KPOINTS         PROCESSORS  NBASE       
 1       1               2           640         
 ---------------------------------------------------------
 Use Systematically Improvable Atomic bases
 ---------------------------------------------------------
 ELEMENT ORBITALS        NBASE       NATOM       XC          
 Li      4s1p-8au        7           32          
 Cl      2s2p1d-8au      13          32          
 ---------------------------------------------------------
 Initial plane wave basis and FFT box
 ---------------------------------------------------------
 -------------------------------------------
 SELF-CONSISTENT : 
 -------------------------------------------
 START CHARGE      : atomic
 DONE(9.42136    SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.944585e+04  0.000000e+00   1.040e-01  2.294e+01  
 GE2    -1.944795e+04  -2.106730e+00  4.813e-02  2.129e+01  
 GE3    -1.944810e+04  -1.467777e-01  2.243e-02  2.113e+01  
 GE4    -1.944812e+04  -2.553504e-02  2.190e-03  2.121e+01  
 GE5    -1.944812e+04  -6.356407e-04  7.985e-04  2.118e+01  
 GE6    -1.944812e+04  -3.915026e-05  1.419e-04  2.121e+01  
 GE7    -1.944812e+04  -4.710773e-06  2.405e-05  2.120e+01  
 GE8    -1.944812e+04  -8.613757e-08  8.159e-06  2.131e+01  
 GE9    -1.944812e+04  -1.561019e-08  1.821e-06  2.118e+01  
 GE10   -1.944812e+04  8.352659e-11   5.889e-07  2.128e+01  
 GE11   -1.944812e+04  -3.124513e-10  7.240e-08  2.112e+01  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 1.431e+01      6.895e-02      -1.646e+00     
 6.895e-02      6.743e+00      -3.705e+00     
 -1.646e+00     -3.705e+00     5.271e+00      
 TOTAL-PRESSURE: 8.776e+00 KBAR

  |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%-------
                       total               321.65         7         46        1e+02     %
   Driver              driver_line         321.6          1         3.2e+02   1e+02     %
   mymath              heapsort            0.20213        2         0.1       0.063     %
   PW_Basis            setup_struc_factor  2.5577         1         2.6       0.8       %
   ORB_control         read_orb_first      0.15599        1         0.16      0.048     %
   LCAO_Orbitals       Read_Orbitals       0.15592        1         0.16      0.048     %
   ORB_control         set_orb_tables      3.1279         1         3.1       0.97      %
   ORB_gen_tables      gen_tables          3.1279         1         3.1       0.97      %
   ORB_table_phi       init_Table          1.942          1         1.9       0.6       %
   ORB_table_phi       cal_ST_Phi12_R      1.9286         178       0.011     0.6       %
   ORB_table_beta      init_Table_Beta     0.81809        1         0.82      0.25      %
   ORB_table_beta      VNL_PhiBeta_R       0.81442        96        0.0085    0.25      %
   Ions                opt_ions            314.86         1         3.1e+02   98        %
   ESolver_KS_LCAO     Run                 237.72         1         2.4e+02   74        %
   ESolver_KS_LCAO     beforescf           2.6624         1         2.7       0.83      %
   ESolver_KS_LCAO     beforesolver        0.14765        1         0.15      0.046     %
   ESolver_KS_LCAO     set_matrix_grid     0.12529        1         0.13      0.039     %
   Charge              atomic_rho          0.29189        1         0.29      0.091     %
   PW_Basis            recip2real          6.1206         65        0.094     1.9       %
   PW_Basis            gathers_scatterp    2.4599         65        0.038     0.76      %
   Potential           init_pot            2.0982         1         2.1       0.65      %
   Potential           update_from_charge  22.645         12        1.9       7         %
   Potential           cal_fixed_v         0.14369        1         0.14      0.045     %
   PotLocal            cal_fixed_v         0.13781        1         0.14      0.043     %
   Potential           cal_v_eff           22.501         12        1.9       7         %
   H_Hartree_pw        v_hartree           2.9576         12        0.25      0.92      %
   PW_Basis            real2recip          8.2592         100       0.083     2.6       %
   PW_Basis            gatherp_scatters    3.2306         100       0.032     1         %
   PotXC               cal_v_eff           19.373         12        1.6       6         %
   XC_Functional       v_xc                19.313         12        1.6       6         %
   HSolverLCAO         solve               209.45         11        19        65        %
   HamiltLCAO          updateHk            102.47         11        9.3       32        %
   OperatorLCAO        init                100.69         22        4.6       31        %
   Veff                contributeHk        100.68         11        9.2       31        %
   Gint_interface      cal_gint            235.48         23        10        73        %
   Gint_interface      cal_gint_vlocal     90.849         11        8.3       28        %
   Gint_Tools          cal_psir_ylm        56.336         513216    0.00011   18        %
   Gint_k              folding_vl_k        9.8315         11        0.89      3.1       %
   Gint_k              Distri              9.7498         11        0.89      3         %
   Overlap             contributeHR        0.20028        1         0.2       0.062     %
   LCAO_gen_fixedH     calculate_S_no      0.20028        1         0.2       0.062     %
   Ekin<LCAO>          contributeHR        0.2093         1         0.21      0.065     %
   Nonlocal<LCAO>      contributeHR        0.94124        1         0.94      0.29      %
   LCAO_gen_fixedH     b_NL_mu_new         3.3137         2         1.7       1         %
   ORB_gen_tables      snap_psibeta_half   0.23571        53133     4.4e-06   0.073     %
   OperatorLCAO        folding_fixed       0.42838        11        0.039     0.13      %
   LCAO_nnr            folding_fixedH      0.40262        11        0.037     0.13      %
   HSolverLCAO         hamiltSolvePsiK     4.0264         11        0.37      1.3       %
   OperatorLCAO        get_hs_pointers     116.62         6         19        36        %
   DiagoElpa           elpa_solve          3.94           11        0.36      1.2       %
   ElecStateLCAO       psiToRho            102.95         11        9.4       32        %
   elecstate           cal_dm              0.25834        12        0.022     0.08      %
   psiMulPsiMpi        pdgemm              0.24058        12        0.02      0.075     %
   LCAO_Charge         cal_dk_k            1.575          11        0.14      0.49      %
   Gint_interface      cal_gint_rho        91.339         11        8.3       28        %
   Charge              mix_rho             2.6904         10        0.27      0.84      %
   Charge              Pulay_mixing        2.592          10        0.26      0.81      %
   Force_Stress_LCAO   getForceStress      77.141         1         77        24        %
   Forces              cal_force_loc       1.9559         1         2         0.61      %
   Forces              cal_force_ew        1.8757         1         1.9       0.58      %
   Forces              cal_force_scc       2.2231         1         2.2       0.69      %
   Stress_Func         stress_loc          0.40057        1         0.4       0.12      %
   Stress_Func         stress_har          0.14033        1         0.14      0.044     %
   Stress_Func         stress_ewa          0.8441         1         0.84      0.26      %
   Stress_Func         stress_gga          0.92777        1         0.93      0.29      %
   Force_LCAO_k        ftable_k            67.994         1         68        21        %
   Force_LCAO_k        allocate_k          4.2926         1         4.3       1.3       %
   Force_LCAO_k        cal_fvl_dphi_k      53.291         1         53        17        %
   Gint_interface      cal_gint_force      53.291         1         53        17        %
   Gint_Tools          cal_dpsir_ylm       32.294         23328     0.0014    10        %
   Gint_Tools          cal_dpsirr_ylm      3.4116         23328     0.00015   1.1       %
   Force_LCAO_k        cal_fvnl_dbeta_k_new6.0315         1         6         1.9       %
   Vdwd3               cal_force           0.38405        1         0.38      0.12      %
   Vdwd3               cal_stress          0.3735         1         0.37      0.12      %
 ----------------------------------------------------------------------------------------

 START  Time  : Wed Jul 10 02:50:09 2024
 FINISH Time  : Wed Jul 10 02:55:31 2024
 TOTAL  Time  : 322
 SEE INFORMATION IN : OUT.ABACUS/

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2.2.3 Results and Analysis

The main calculation information is stored in the file OUT.ABACUS/running_scf.log.

We can view this file using the command cat LiCl_DP_Tutorial_Example/chapter2/OUT.ABACUS/running_scf.log.

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Here, we provide an example to focus on the important content:


                                                                                     
                             WELCOME TO ABACUS v3.0                                  
                                                                                     
               'Atomic-orbital Based Ab-initio Computation at UStc'                  
                                                                                     
                     Website: http://abacus.ustc.edu.cn/                             
                                                                                     
    Version: Parallel, in development
    Processor Number is 16
    Start Time is Fri Mar 17 11:12:54 2023
                                                                                     
 ------------------------------------------------------------------------------------

...（skip）

 LCAO ALGORITHM --------------- ION=   1  ELEC=   1--------------------------------

 Density error is 0.104045211662

       Energy                       Rydberg                            eV
   E_KohnSham                 -1429.2427444                 -19445.845149
     E_Harris                -1430.40301784                 -19461.631479
      E_Fermi              +0.0524155151601               +0.713149669783

...（skip）

 LCAO ALGORITHM --------------- ION=   1  ELEC=  11--------------------------------
 Memory of pvpR : 2.89599609375 MB

 Density error is 7.23978511026e-08

       Energy                       Rydberg                            eV
   E_KohnSham                -1429.41030086                -19448.1248715
     E_Harris                -1429.41030086                -19448.1248715
       E_band                -310.415111989                -4223.41426836
   E_one_elec                -849.674984163                -11560.4212327
    E_Hartree                +459.864819535                +6256.78185542
         E_xc                -294.061400137                -4000.91060373
      E_Ewald                -744.876355072                -10134.5627344
      E_demet            -3.01381081966e-88            -4.10049998414e-87
      E_descf                            +0                            +0
      E_vdwD3                -0.66238101901                -9.01215610558
        E_exx                            +0                            +0
      E_Fermi              +0.0508640615939                 +0.6920410611

 charge density convergence is achieved
 final etot is -19448.1248715 eV

...（skip）

As we can see, after 11 iterations, the charge density converges with a density error of 7.23978511026e-08, and the final total energy is -19448.1248715 eV.

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In this exercise, we became familiar with the input files of ABACUS software, learned how to write ABACUS SCF calculation input files for the LiCl melt, performed the calculation, and checked the convergence status.

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2.3 ABACUS Quantum Molecular Dynamics Calculation

Quantum Molecular Dynamics (QMD) applies the principles of quantum mechanics to molecular dynamics, considering both the wave-like and particle-like nature of electrons.

In addition to the types of molecular dynamics mentioned in sections 1.4 and 2.3, there are other types such as:

Monte Carlo Molecular Dynamics (MCMD): Uses random simulation methods to model molecular motion and obtain the state of the molecular system through statistical simulation.
Multiscale Molecular Dynamics (MMD): Combines molecular dynamics methods at different scales to improve simulation efficiency and accuracy.
Lagrangian Molecular Dynamics (LMD): Uses the methods of Lagrangian mechanics to describe the motion of molecular systems.
Machine Learning Molecular Dynamics (MLMD): Utilizes machine learning methods to assist molecular dynamics simulations, enhancing efficiency and accuracy.

The DeePMD-kit, which we will learn in this tutorial, is an example of machine learning-based molecular dynamics.

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2.3.1 ABACUS MD Calculation Input File

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The input files required for ABACUS MD calculation are similar to those for the ABACUS SCF calculation mentioned above.

We only need to modify the INPUT file, while the other files remain unchanged. Here is an example of the modified INPUT file:

INPUT_PARAMETERS

#Parameters (1.General)
ntype           2              
symmetry        0                      
vdw_method      d3_bj          

#Parameters (2.Iteration)
ecutwfc         100            
scf_thr         1.0e-7         
scf_nmax        120            

#Parameters (3.Basis)        
basis_type      lcao           
          
#Parameters (4.Smearing)
smearing_method gauss          
smearing_sigma  0.002          

#Parameters (5.Mixing)
mixing_type     pulay          
mixing_beta     0.4            

#Parameters (6.md)
calculation     md             # calculation: the type of calculation, molecular dynamics (md) is chosen here
cal_force       1              
cal_stress      1              
md_nstep        500            # md_nstep: the total number of steps for the molecular dynamics simulation, set to 500
md_type         1              # md_type: the type of simulation, NVT ensemble is chosen here
md_dt           1              # md_dt: the time step, set to 1
md_tfirst       900            # md_tfirst: the target temperature, set to 900 K
md_restart      0              # md_restart: whether it is a continuation calculation, set to 0 means it is not a continuation
md_dumpfreq     1              # md_dumpfreq: the frequency of outputting molecular dynamics information, set to 1 means output at every step
out_stru        1              # out_stru: the option for outputting structural information, set to 1 means to output

The INPUT file defines the Molecular Dynamics (MD) simulation of the LiCl melt. Consistent with the previous LAMMPS MD simulation, the simulation is performed under the NVT ensemble with a timestep of $1 fs$ and a temperature of 900 K.

In the LiCl_DP_Tutorial_Example/chapter2/abacus_md/ folder, we have prepared the input files needed for this calculation.

Considering the relatively high cost of DFT calculations, the simulation time here is $0.5 ps$ ( $1 ps = 1000 fs = 1 0^{- 12} s$ ).

Note: When using the LCAO basis set, it is usually necessary to test the convergence of energy, force, and stress with different cutoff values for orbital radii and different k-point (k_spacing) settings. For the purpose of simplifying this tutorial, we have not performed such tests here.

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2.3.2 Running ABACUS MD Calculation

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After preparing all the input files, we can perform the MD calculation for the LiCl melt. For example, using the command line:

Note: Since we need ABACUS version 3.1, this step requires changing the image to abacus:3.1.4-toolkit-notebook.

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[ ]

# ############ Time Warning: 9 h 30 mins 58 secs ############

# The output of this command is very long. You can right-click on the output content to select

# the scroll mode for viewing or directly click the blue bar on the left to hide the output.

# ! cd ./LiCl_DP_Tutorial_Example/chapter2/abacus_md && . /opt/intel/oneapi/setvars.sh && OMP_NUM_THREADS=1 mpirun -np 32 abacus

 
:: initializing oneAPI environment ...
   dash: SH_VERSION = unknown
   args: Using "$@" for setvars.sh arguments: 
:: compiler -- latest
:: debugger -- latest
:: dev-utilities -- latest
:: mkl -- latest
:: mpi -- latest
:: tbb -- latest
:: vtune -- latest
:: oneAPI environment initialized ::
 
                                                                                     
                              ABACUS v3.1                                            

               Atomic-orbital Based Ab-initio Computation at UStc                    

                     Website: http://abacus.ustc.edu.cn/                             
               Documentation: https://abacus.deepmodeling.com/                       
                  Repository: https://github.com/abacusmodeling/abacus-develop       
                              https://github.com/deepmodeling/abacus-develop         

 Sun May 21 16:17:00 2023
 MAKE THE DIR         : OUT.ABACUS/
 MAKE THE STRU DIR    : OUT.ABACUS/STRU/

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 Warning: number valence electrons > 1 for Li: [He] 2s1
 Please make sure the pseudopotential file is what you need
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

 UNIFORM GRID DIM     : 144 * 144 * 144
 UNIFORM GRID DIM(BIG): 48 * 48 * 48
 DONE(0.274503   SEC) : SETUP UNITCELL
 DONE(0.311294   SEC) : INIT K-POINTS
 ---------------------------------------------------------
 Molecular Dynamics simulations
 ---------------------------------------------------------
 ENSEMBLE                 : NVT
 Time interval(fs)        : 1
 ---------------------------------------------------------
 SPIN    KPOINTS         PROCESSORS  NBASE       
 1       1               32          640         
 ---------------------------------------------------------
 Use Systematically Improvable Atomic bases
 ---------------------------------------------------------
 ELEMENT ORBITALS        NBASE       NATOM       XC          
 Li      4s1p-8au        7           32          
 Cl      2s2p1d-8au      13          32          
 ---------------------------------------------------------
 Initial plane wave basis and FFT box
 ---------------------------------------------------------
--------------------------------- INITVEL DONE ------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 0
 -------------------------------------------
 START CHARGE      : atomic
 DONE(5.22409    SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.944585e+04  0.000000e+00   1.040e-01  2.936e+00  
 GE2    -1.944795e+04  -2.106730e+00  4.813e-02  2.802e+00  
 GE3    -1.944810e+04  -1.467778e-01  2.243e-02  2.767e+00  
 GE4    -1.944812e+04  -2.553504e-02  2.190e-03  2.674e+00  
 GE5    -1.944812e+04  -6.356405e-04  7.985e-04  2.663e+00  
 GE6    -1.944812e+04  -3.915076e-05  1.419e-04  2.667e+00  
 GE7    -1.944812e+04  -4.710544e-06  2.405e-05  2.760e+00  
 GE8    -1.944812e+04  -8.613139e-08  8.159e-06  2.564e+00  
 GE9    -1.944812e+04  -1.534414e-08  1.821e-06  2.662e+00  
 GE10   -1.944812e+04  -3.217321e-10  5.889e-07  2.671e+00  
 GE11   -1.944812e+04  -8.971375e-11  7.240e-08  2.646e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 1.431e+01      6.895e-02      -1.646e+00     
 6.895e-02      6.743e+00      -3.705e+00     
 -1.646e+00     -3.705e+00     5.271e+00      
 TOTAL-PRESSURE: 8.776e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.144e+02          -7.147e+02          2.693e-01           9.000e+02           1.347e+01           
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 1
 -------------------------------------------
 DONE(4.392e+01  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.944810e+04  0.000000e+00   1.950e-03  2.775e+00  
 GE2    -1.944810e+04  -2.394310e-03  1.049e-03  2.654e+00  
 GE3    -1.944810e+04  -1.650769e-04  1.406e-04  2.562e+00  
 GE4    -1.944810e+04  -6.853193e-06  4.312e-05  2.556e+00  
 GE5    -1.944810e+04  -3.459177e-07  1.551e-05  2.749e+00  
 GE6    -1.944810e+04  -3.788704e-08  2.513e-06  2.756e+00  
 GE7    -1.944810e+04  -2.298528e-09  7.767e-07  2.588e+00  
 GE8    -1.944810e+04  -9.899448e-11  1.436e-07  2.830e+00  
 GE9    -1.944810e+04  -3.093578e-11  4.251e-08  2.646e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 1.370e+01      4.028e-01      -1.439e+00     
 4.028e-01      6.940e+00      -4.174e+00     
 -1.439e+00     -4.174e+00     5.615e+00      
 TOTAL-PRESSURE: 8.750e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.144e+02          -7.147e+02          2.685e-01           8.971e+02           1.343e+01           
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 2
 -------------------------------------------
 DONE(7.707e+01  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.944815e+04  0.000000e+00   1.949e-03  2.779e+00  
 GE2    -1.944815e+04  -2.395884e-03  1.050e-03  2.667e+00  
 GE3    -1.944815e+04  -1.639592e-04  1.408e-04  2.564e+00  
 GE4    -1.944815e+04  -6.894248e-06  4.275e-05  3.052e+00  
 GE5    -1.944815e+04  -3.300600e-07  1.551e-05  2.691e+00  
 GE6    -1.944815e+04  -3.672077e-08  2.547e-06  2.665e+00  
 GE7    -1.944815e+04  7.517393e-10   7.821e-07  2.567e+00  
 GE8    -1.944815e+04  -1.206495e-10  1.464e-07  2.549e+00  
 GE9    -1.944815e+04  -6.187155e-12  4.274e-08  2.736e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 1.282e+01      7.260e-01      -1.140e+00     
 7.260e-01      6.946e+00      -4.601e+00     
 -1.140e+00     -4.601e+00     5.802e+00      
 TOTAL-PRESSURE: 8.523e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.144e+02          -7.147e+02          2.703e-01           9.033e+02           1.323e+01           
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 3
 -------------------------------------------
 DONE(1.102e+02  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.944827e+04  0.000000e+00   1.970e-03  3.191e+00  
 GE2    -1.944827e+04  -2.418738e-03  1.060e-03  2.843e+00  
 GE3    -1.944827e+04  -1.681375e-04  1.442e-04  2.664e+00  
 GE4    -1.944827e+04  -7.310124e-06  4.274e-05  2.718e+00  
 GE5    -1.944827e+04  -3.347622e-07  1.571e-05  2.585e+00  
 GE6    -1.944827e+04  -3.635882e-08  2.627e-06  2.904e+00  
 GE7    -1.944827e+04  7.393650e-10   7.969e-07  2.808e+00  
 GE8    -1.944827e+04  -1.237431e-10  1.492e-07  2.655e+00  
 GE9    -1.944827e+04  -3.093578e-12  4.328e-08  2.624e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 1.173e+01      1.030e+00      -7.603e-01     
 1.030e+00      6.748e+00      -4.969e+00     
 -7.603e-01     -4.969e+00     5.829e+00      
 TOTAL-PRESSURE: 8.104e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.144e+02          -7.147e+02          2.747e-01           9.181e+02           1.289e+01           
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 4
 -------------------------------------------
 DONE(1.445e+02  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.944845e+04  0.000000e+00   2.009e-03  2.897e+00  
 GE2    -1.944846e+04  -2.462904e-03  1.077e-03  2.568e+00  
 GE3    -1.944846e+04  -1.772813e-04  1.506e-04  2.760e+00  
 GE4    -1.944846e+04  -8.043961e-06  4.312e-05  2.669e+00  
 GE5    -1.944846e+04  -3.507993e-07  1.607e-05  2.755e+00  
 GE6    -1.944846e+04  -3.917088e-08  2.740e-06  2.563e+00  
 GE7    -1.944846e+04  -9.002311e-10  8.192e-07  2.659e+00  
 GE8    -1.944846e+04  -1.082752e-10  1.517e-07  2.658e+00  
 GE9    -1.944846e+04  -2.784220e-11  4.412e-08  2.532e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 1.049e+01      1.308e+00      -3.162e-01     
 1.308e+00      6.347e+00      -5.267e+00     
 -3.162e-01     -5.267e+00     5.703e+00      
 TOTAL-PRESSURE: 7.513e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.144e+02          -7.147e+02          2.815e-01           9.406e+02           1.242e+01           
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 5
 -------------------------------------------
 DONE(1.778e+02  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.944869e+04  0.000000e+00   2.058e-03  2.982e+00  
 GE2    -1.944869e+04  -2.544136e-03  1.100e-03  2.602e+00  
 GE3    -1.944869e+04  -1.903247e-04  1.590e-04  2.563e+00  
 GE4    -1.944869e+04  -8.997967e-06  4.388e-05  2.553e+00  
 GE5    -1.944869e+04  -3.817846e-07  1.654e-05  2.558e+00  
 GE6    -1.944869e+04  -4.287698e-08  2.873e-06  2.665e+00  
 GE7    -1.944869e+04  -1.011600e-09  8.460e-07  2.763e+00  
 GE8    -1.944869e+04  -1.330238e-10  1.540e-07  2.757e+00  
 GE9    -1.944869e+04  -6.187155e-12  4.522e-08  2.849e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 9.128e+00      1.555e+00      1.724e-01      
 1.555e+00      5.759e+00      -5.490e+00     
 1.724e-01      -5.490e+00     5.437e+00      
 TOTAL-PRESSURE: 6.775e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.144e+02          -7.147e+02          2.900e-01           9.691e+02           1.183e+01           
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 6
 -------------------------------------------
 DONE(2.110e+02  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.944896e+04  0.000000e+00   2.114e-03  2.903e+00  
 GE2    -1.944896e+04  -2.644982e-03  1.126e-03  2.579e+00  
 GE3    -1.944896e+04  -2.058803e-04  1.685e-04  2.667e+00  
 GE4    -1.944896e+04  -1.004807e-05  4.500e-05  2.894e+00  
 GE5    -1.944896e+04  -4.152262e-07  1.704e-05  2.875e+00  
 GE6    -1.944896e+04  -4.498990e-08  3.014e-06  2.663e+00  
 GE7    -1.944896e+04  -1.039442e-09  8.751e-07  2.676e+00  
 GE8    -1.944896e+04  -1.361174e-10  1.566e-07  2.888e+00  
 GE9    -1.944896e+04  -1.856147e-11  4.657e-08  2.643e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 7.702e+00      1.771e+00      6.832e-01      
 1.771e+00      5.016e+00      -5.640e+00     
 6.832e-01      -5.640e+00     5.053e+00      
 TOTAL-PRESSURE: 5.924e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.144e+02          -7.147e+02          2.998e-01           1.002e+03           1.115e+01           
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 7
 -------------------------------------------
 DONE(2.450e+02  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.944924e+04  0.000000e+00   2.174e-03  3.030e+00  
 GE2    -1.944925e+04  -2.751073e-03  1.153e-03  2.724e+00  
 GE3    -1.944925e+04  -2.223695e-04  1.784e-04  2.614e+00  
 GE4    -1.944925e+04  -1.105829e-05  4.636e-05  2.838e+00  
 GE5    -1.944925e+04  -4.534195e-07  1.754e-05  2.691e+00  
 GE6    -1.944925e+04  -5.115230e-08  3.153e-06  2.671e+00  
 GE7    -1.944925e+04  -1.058004e-09  9.042e-07  2.837e+00  
 GE8    -1.944925e+04  -1.453981e-10  1.597e-07  2.840e+00  
 GE9    -1.944925e+04  -2.165504e-11  4.808e-08  2.982e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 6.265e+00      1.958e+00      1.194e+00      
 1.958e+00      4.162e+00      -5.726e+00     
 1.194e+00      -5.726e+00     4.576e+00      
 TOTAL-PRESSURE: 5.001e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.144e+02          -7.147e+02          3.102e-01           1.037e+03           1.041e+01           
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 8
 -------------------------------------------
 DONE(2.791e+02  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.944953e+04  0.000000e+00   2.232e-03  3.084e+00  
 GE2    -1.944953e+04  -2.848622e-03  1.179e-03  2.765e+00  
 GE3    -1.944953e+04  -2.383912e-04  1.878e-04  2.560e+00  
 GE4    -1.944953e+04  -1.198808e-05  4.781e-05  2.676e+00  
 GE5    -1.944953e+04  -4.913591e-07  1.801e-05  2.747e+00  
 GE6    -1.944953e+04  -5.432632e-08  3.282e-06  2.659e+00  
 GE7    -1.944953e+04  -1.302396e-09  9.321e-07  2.647e+00  
 GE8    -1.944953e+04  -2.103633e-10  1.632e-07  2.678e+00  
 GE9    -1.944953e+04  -2.474862e-11  4.964e-08  2.573e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 4.863e+00      2.120e+00      1.684e+00      
 2.120e+00      3.244e+00      -5.761e+00     
 1.684e+00      -5.761e+00     4.033e+00      
 TOTAL-PRESSURE: 4.047e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.144e+02          -7.148e+02          3.206e-01           1.071e+03           9.635e+00           
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 9
 -------------------------------------------
 DONE(3.125e+02  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.944980e+04  0.000000e+00   2.283e-03  2.883e+00  
 GE2    -1.944980e+04  -2.949410e-03  1.202e-03  2.666e+00  
 GE3    -1.944980e+04  -2.526952e-04  1.960e-04  2.682e+00  
 GE4    -1.944980e+04  -1.276600e-05  4.922e-05  2.642e+00  
 GE5    -1.944980e+04  -5.398571e-07  1.841e-05  2.892e+00  
 GE6    -1.944980e+04  -5.609275e-08  3.396e-06  2.662e+00  
 GE7    -1.944980e+04  -1.036348e-09  9.574e-07  2.762e+00  
 GE8    -1.944980e+04  -2.382055e-10  1.667e-07  2.759e+00  
 GE9    -1.944980e+04  1.237431e-11   5.113e-08  2.536e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 3.530e+00      2.265e+00      2.136e+00      
 2.265e+00      2.312e+00      -5.759e+00     
 2.136e+00      -5.759e+00     3.449e+00      
 TOTAL-PRESSURE: 3.097e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.144e+02          -7.148e+02          3.302e-01           1.103e+03           8.853e+00           
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 10
 -------------------------------------------
 DONE(3.463e+02  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945004e+04  0.000000e+00   2.326e-03  2.771e+00  
 GE2    -1.945004e+04  -3.033916e-03  1.222e-03  2.573e+00  
 GE3    -1.945005e+04  -2.642710e-04  2.027e-04  2.560e+00  
 GE4    -1.945005e+04  -1.336743e-05  5.051e-05  2.560e+00  
 GE5    -1.945005e+04  -5.785330e-07  1.873e-05  2.657e+00  
 GE6    -1.945005e+04  -5.996591e-08  3.490e-06  2.729e+00  
 GE7    -1.945005e+04  -9.992256e-10  9.794e-07  2.576e+00  
 GE8    -1.945005e+04  -2.382055e-10  1.702e-07  2.561e+00  
 GE9    -1.945005e+04  -4.021651e-11  5.247e-08  2.575e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 2.293e+00      2.398e+00      2.535e+00      
 2.398e+00      1.409e+00      -5.736e+00     
 2.535e+00      -5.736e+00     2.848e+00      
 TOTAL-PRESSURE: 2.183e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.144e+02          -7.148e+02          3.387e-01           1.132e+03           8.088e+00           
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 11
 -------------------------------------------
 DONE(3.788e+02  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945024e+04  0.000000e+00   2.358e-03  2.979e+00  
 GE2    -1.945025e+04  -3.094563e-03  1.237e-03  2.871e+00  
 GE3    -1.945025e+04  -2.725062e-04  2.076e-04  2.786e+00  
 GE4    -1.945025e+04  -1.376412e-05  5.159e-05  2.570e+00  
 GE5    -1.945025e+04  -6.142422e-07  1.897e-05  2.582e+00  
 GE6    -1.945025e+04  -5.773544e-08  3.562e-06  2.774e+00  
 GE7    -1.945025e+04  -9.621026e-10  9.977e-07  2.759e+00  
 GE8    -1.945025e+04  -2.815156e-10  1.736e-07  2.669e+00  
 GE9    -1.945025e+04  -1.856147e-11  5.363e-08  2.542e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 1.175e+00      2.530e+00      2.872e+00      
 2.530e+00      5.756e-01      -5.707e+00     
 2.872e+00      -5.707e+00     2.247e+00      
 TOTAL-PRESSURE: 1.333e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.144e+02          -7.148e+02          3.456e-01           1.155e+03           7.357e+00           
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 12
 -------------------------------------------
 DONE(4.122e+02  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945040e+04  0.000000e+00   2.378e-03  2.869e+00  
 GE2    -1.945040e+04  -3.162837e-03  1.247e-03  2.576e+00  
 GE3    -1.945040e+04  -2.769466e-04  2.106e-04  2.682e+00  
 GE4    -1.945040e+04  -1.394947e-05  5.241e-05  2.788e+00  
 GE5    -1.945040e+04  -6.401571e-07  1.911e-05  2.665e+00  
 GE6    -1.945040e+04  -6.184371e-08  3.609e-06  2.799e+00  
 GE7    -1.945040e+04  -9.497283e-10  1.012e-06  2.663e+00  
 GE8    -1.945040e+04  -2.567669e-10  1.765e-07  2.651e+00  
 GE9    -1.945040e+04  -5.259082e-11  5.453e-08  2.750e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 1.937e-01      2.667e+00      3.140e+00      
 2.667e+00      -1.601e-01     -5.682e+00     
 3.140e+00      -5.682e+00     1.663e+00      
 TOTAL-PRESSURE: 5.655e-01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.144e+02          -7.148e+02          3.507e-01           1.172e+03           6.679e+00           
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 13
 -------------------------------------------
 DONE(4.455e+02  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945050e+04  0.000000e+00   2.385e-03  2.866e+00  
 GE2    -1.945050e+04  -3.207836e-03  1.252e-03  2.668e+00  
 GE3    -1.945050e+04  -2.777287e-04  2.117e-04  2.575e+00  
 GE4    -1.945050e+04  -1.392725e-05  5.294e-05  2.663e+00  
 GE5    -1.945050e+04  -6.576637e-07  1.915e-05  2.562e+00  
 GE6    -1.945050e+04  -6.260473e-08  3.630e-06  2.584e+00  
 GE7    -1.945050e+04  -9.806641e-10  1.022e-06  2.604e+00  
 GE8    -1.945050e+04  -3.279192e-10  1.789e-07  2.688e+00  
 GE9    -1.945050e+04  -1.856147e-11  5.517e-08  2.643e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -6.389e-01     2.813e+00      3.336e+00      
 2.813e+00      -7.810e-01     -5.668e+00     
 3.336e+00      -5.668e+00     1.103e+00      
 TOTAL-PRESSURE: -1.056e-01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.144e+02          -7.148e+02          3.538e-01           1.182e+03           6.062e+00           
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 14
 -------------------------------------------
 DONE(4.783e+02  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945056e+04  0.000000e+00   2.382e-03  2.912e+00  
 GE2    -1.945056e+04  -3.203606e-03  1.252e-03  2.694e+00  
 GE3    -1.945056e+04  -2.750142e-04  2.111e-04  2.682e+00  
 GE4    -1.945056e+04  -1.374313e-05  5.316e-05  2.560e+00  
 GE5    -1.945056e+04  -6.605964e-07  1.909e-05  2.793e+00  
 GE6    -1.945056e+04  -6.427217e-08  3.625e-06  2.564e+00  
 GE7    -1.945056e+04  -2.338745e-09  1.028e-06  2.964e+00  
 GE8    -1.945056e+04  -3.124513e-10  1.807e-07  2.747e+00  
 GE9    -1.945056e+04  -9.280733e-12  5.553e-08  2.756e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.319e+00     2.972e+00      3.461e+00      
 2.972e+00      -1.282e+00     -5.667e+00     
 3.461e+00      -5.667e+00     5.737e-01      
 TOTAL-PRESSURE: -6.759e-01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.144e+02          -7.148e+02          3.549e-01           1.186e+03           5.511e+00           
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 15
 -------------------------------------------
 DONE(5.124e+02  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945057e+04  0.000000e+00   2.368e-03  2.865e+00  
 GE2    -1.945057e+04  -3.185011e-03  1.247e-03  2.794e+00  
 GE3    -1.945057e+04  -2.690460e-04  2.089e-04  2.680e+00  
 GE4    -1.945057e+04  -1.339163e-05  5.308e-05  2.857e+00  
 GE5    -1.945057e+04  -6.533698e-07  1.894e-05  2.655e+00  
 GE6    -1.945057e+04  -6.221803e-08  3.596e-06  2.760e+00  
 GE7    -1.945057e+04  -2.116007e-09  1.031e-06  2.637e+00  
 GE8    -1.945057e+04  -3.464807e-10  1.820e-07  2.556e+00  
 GE9    -1.945057e+04  -2.784220e-11  5.564e-08  2.648e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.852e+00     3.145e+00      3.518e+00      
 3.145e+00      -1.667e+00     -5.679e+00     
 3.518e+00      -5.679e+00     7.424e-02      
 TOTAL-PRESSURE: -1.148e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.144e+02          -7.148e+02          3.543e-01           1.184e+03           5.028e+00           
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 16
 -------------------------------------------
 DONE(5.459e+02  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945054e+04  0.000000e+00   2.345e-03  3.075e+00  
 GE2    -1.945054e+04  -3.166572e-03  1.239e-03  2.569e+00  
 GE3    -1.945054e+04  -2.604727e-04  2.053e-04  2.568e+00  
 GE4    -1.945054e+04  -1.293899e-05  5.270e-05  2.565e+00  
 GE5    -1.945054e+04  -6.324541e-07  1.870e-05  2.563e+00  
 GE6    -1.945054e+04  -6.252739e-08  3.545e-06  2.773e+00  
 GE7    -1.945054e+04  -2.329464e-09  1.029e-06  2.575e+00  
 GE8    -1.945054e+04  -3.341064e-10  1.825e-07  2.571e+00  
 GE9    -1.945054e+04  -2.474862e-11  5.546e-08  2.935e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -2.247e+00     3.329e+00      3.514e+00      
 3.329e+00      -1.953e+00     -5.699e+00     
 3.514e+00      -5.699e+00     -3.987e-01     
 TOTAL-PRESSURE: -1.533e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.144e+02          -7.148e+02          3.521e-01           1.177e+03           4.605e+00           
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 17
 -------------------------------------------
 DONE(5.791e+02  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945048e+04  0.000000e+00   2.315e-03  2.898e+00  
 GE2    -1.945048e+04  -3.112721e-03  1.227e-03  2.869e+00  
 GE3    -1.945048e+04  -2.502851e-04  2.006e-04  2.674e+00  
 GE4    -1.945048e+04  -1.240596e-05  5.207e-05  2.552e+00  
 GE5    -1.945048e+04  -6.138060e-07  1.840e-05  2.753e+00  
 GE6    -1.945048e+04  -5.790249e-08  3.475e-06  2.658e+00  
 GE7    -1.945048e+04  -7.115228e-10  1.024e-06  2.530e+00  
 GE8    -1.945048e+04  -2.784220e-10  1.824e-07  2.756e+00  
 GE9    -1.945048e+04  -7.733944e-11  5.506e-08  3.265e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -2.518e+00     3.518e+00      3.457e+00      
 3.518e+00      -2.161e+00     -5.720e+00     
 3.457e+00      -5.720e+00     -8.508e-01     
 TOTAL-PRESSURE: -1.843e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.144e+02          -7.148e+02          3.486e-01           1.165e+03           4.234e+00           
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 18
 -------------------------------------------
 DONE(6.131e+02  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945040e+04  0.000000e+00   2.280e-03  2.876e+00  
 GE2    -1.945040e+04  -3.047571e-03  1.213e-03  2.567e+00  
 GE3    -1.945040e+04  -2.389958e-04  1.949e-04  2.763e+00  
 GE4    -1.945040e+04  -1.185042e-05  5.124e-05  2.682e+00  
 GE5    -1.945040e+04  -5.789259e-07  1.804e-05  2.576e+00  
 GE6    -1.945040e+04  -5.907186e-08  3.390e-06  2.581e+00  
 GE7    -1.945040e+04  -2.100539e-09  1.015e-06  2.691e+00  
 GE8    -1.945040e+04  -3.217321e-10  1.812e-07  2.694e+00  
 GE9    -1.945040e+04  -2.784220e-11  5.446e-08  2.671e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -2.681e+00     3.704e+00      3.358e+00      
 3.704e+00      -2.321e+00     -5.733e+00     
 3.358e+00      -5.733e+00     -1.290e+00     
 TOTAL-PRESSURE: -2.098e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.144e+02          -7.148e+02          3.443e-01           1.151e+03           3.904e+00           
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 19
 -------------------------------------------
 DONE(6.466e+02  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945031e+04  0.000000e+00   2.244e-03  3.014e+00  
 GE2    -1.945031e+04  -2.992306e-03  1.198e-03  2.587e+00  
 GE3    -1.945031e+04  -2.271575e-04  1.886e-04  2.612e+00  
 GE4    -1.945031e+04  -1.132285e-05  5.029e-05  2.785e+00  
 GE5    -1.945031e+04  -5.389631e-07  1.765e-05  2.569e+00  
 GE6    -1.945031e+04  -5.494812e-08  3.292e-06  2.798e+00  
 GE7    -1.945031e+04  -7.053357e-10  1.003e-06  2.552e+00  
 GE8    -1.945031e+04  -2.877027e-10  1.790e-07  2.730e+00  
 GE9    -1.945031e+04  -6.805871e-11  5.368e-08  2.726e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -2.752e+00     3.875e+00      3.232e+00      
 3.875e+00      -2.462e+00     -5.725e+00     
 3.232e+00      -5.725e+00     -1.727e+00     
 TOTAL-PRESSURE: -2.314e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.144e+02          -7.148e+02          3.395e-01           1.134e+03           3.604e+00           
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 20
 -------------------------------------------
 DONE(6.801e+02  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945021e+04  0.000000e+00   2.209e-03  2.945e+00  
 GE2    -1.945022e+04  -2.914355e-03  1.183e-03  2.759e+00  
 GE3    -1.945022e+04  -2.156079e-04  1.823e-04  2.859e+00  
 GE4    -1.945022e+04  -1.082106e-05  4.930e-05  2.569e+00  
 GE5    -1.945022e+04  -5.060784e-07  1.724e-05  2.580e+00  
 GE6    -1.945022e+04  -5.236808e-08  3.188e-06  2.781e+00  
 GE7    -1.945022e+04  -7.269907e-10  9.887e-07  2.572e+00  
 GE8    -1.945022e+04  -2.629541e-10  1.762e-07  2.574e+00  
 GE9    -1.945022e+04  -3.402935e-11  5.281e-08  2.749e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -2.749e+00     4.021e+00      3.091e+00      
 4.021e+00      -2.614e+00     -5.687e+00     
 3.091e+00      -5.687e+00     -2.167e+00     
 TOTAL-PRESSURE: -2.510e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.144e+02          -7.148e+02          3.345e-01           1.118e+03           3.322e+00           
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 21
 -------------------------------------------
 DONE(7.138e+02  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945013e+04  0.000000e+00   2.176e-03  2.873e+00  
 GE2    -1.945013e+04  -2.833309e-03  1.168e-03  2.773e+00  
 GE3    -1.945013e+04  -2.052380e-04  1.764e-04  2.680e+00  
 GE4    -1.945013e+04  -1.041275e-05  4.837e-05  2.661e+00  
 GE5    -1.945013e+04  -4.642037e-07  1.684e-05  2.652e+00  
 GE6    -1.945013e+04  -5.127295e-08  3.081e-06  2.560e+00  
 GE7    -1.945013e+04  -6.341834e-10  9.731e-07  2.738e+00  
 GE8    -1.945013e+04  -3.062642e-10  1.727e-07  2.675e+00  
 GE9    -1.945013e+04  3.093578e-12   5.186e-08  2.527e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -2.686e+00     4.129e+00      2.951e+00      
 4.129e+00      -2.802e+00     -5.608e+00     
 2.951e+00      -5.608e+00     -2.620e+00     
 TOTAL-PRESSURE: -2.703e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.144e+02          -7.148e+02          3.298e-01           1.102e+03           3.046e+00           
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 22
 -------------------------------------------
 DONE(7.471e+02  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945006e+04  0.000000e+00   2.148e-03  2.881e+00  
 GE2    -1.945006e+04  -2.767474e-03  1.156e-03  2.684e+00  
 GE3    -1.945006e+04  -1.968148e-04  1.714e-04  2.568e+00  
 GE4    -1.945006e+04  -1.008307e-05  4.754e-05  2.669e+00  
 GE5    -1.945006e+04  -4.370080e-07  1.648e-05  3.069e+00  
 GE6    -1.945006e+04  -4.847017e-08  2.970e-06  2.858e+00  
 GE7    -1.945006e+04  8.507338e-10   9.568e-07  3.179e+00  
 GE8    -1.945006e+04  -2.846091e-10  1.684e-07  2.787e+00  
 GE9    -1.945006e+04  -4.331009e-11  5.085e-08  2.542e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -2.578e+00     4.188e+00      2.826e+00      
 4.188e+00      -3.048e+00     -5.480e+00     
 2.826e+00      -5.480e+00     -3.091e+00     
 TOTAL-PRESSURE: -2.906e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          3.255e-01           1.088e+03           2.769e+00           
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 23
 -------------------------------------------
 DONE(7.812e+02  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945001e+04  0.000000e+00   2.126e-03  2.908e+00  
 GE2    -1.945001e+04  -2.710485e-03  1.146e-03  2.571e+00  
 GE3    -1.945001e+04  -1.904627e-04  1.675e-04  2.666e+00  
 GE4    -1.945001e+04  -9.866251e-06  4.685e-05  2.583e+00  
 GE5    -1.945001e+04  -4.161604e-07  1.614e-05  2.584e+00  
 GE6    -1.945001e+04  -4.449493e-08  2.862e-06  2.689e+00  
 GE7    -1.945001e+04  -2.171691e-09  9.410e-07  2.784e+00  
 GE8    -1.945001e+04  -2.753284e-10  1.638e-07  2.581e+00  
 GE9    -1.945001e+04  -3.712293e-11  4.981e-08  2.850e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -2.436e+00     4.192e+00      2.727e+00      
 4.192e+00      -3.368e+00     -5.298e+00     
 2.727e+00      -5.298e+00     -3.581e+00     
 TOTAL-PRESSURE: -3.129e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          3.220e-01           1.076e+03           2.484e+00           
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 24
 -------------------------------------------
 DONE(8.144e+02  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.944998e+04  0.000000e+00   2.110e-03  2.768e+00  
 GE2    -1.944999e+04  -2.657417e-03  1.138e-03  2.692e+00  
 GE3    -1.944999e+04  -1.863924e-04  1.650e-04  2.877e+00  
 GE4    -1.944999e+04  -9.753209e-06  4.632e-05  2.648e+00  
 GE5    -1.944999e+04  -3.972339e-07  1.586e-05  2.560e+00  
 GE6    -1.944999e+04  -4.110746e-08  2.764e-06  2.663e+00  
 GE7    -1.944999e+04  -6.249027e-10  9.265e-07  2.861e+00  
 GE8    -1.944999e+04  -2.938899e-10  1.591e-07  2.607e+00  
 GE9    -1.944999e+04  -1.546789e-11  4.874e-08  2.748e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -2.269e+00     4.136e+00      2.664e+00      
 4.136e+00      -3.768e+00     -5.059e+00     
 2.664e+00      -5.059e+00     -4.092e+00     
 TOTAL-PRESSURE: -3.376e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          3.191e-01           1.066e+03           2.187e+00           
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 25
 -------------------------------------------
 DONE(8.480e+02  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.944998e+04  0.000000e+00   2.101e-03  2.879e+00  
 GE2    -1.944998e+04  -2.619929e-03  1.133e-03  2.756e+00  
 GE3    -1.944998e+04  -1.846545e-04  1.636e-04  2.676e+00  
 GE4    -1.944998e+04  -9.725122e-06  4.596e-05  2.549e+00  
 GE5    -1.944998e+04  -3.822270e-07  1.565e-05  2.690e+00  
 GE6    -1.944998e+04  -4.174474e-08  2.684e-06  2.857e+00  
 GE7    -1.944998e+04  7.857687e-10   9.138e-07  2.758e+00  
 GE8    -1.944998e+04  -2.753284e-10  1.542e-07  2.666e+00  
 GE9    -1.944998e+04  -3.402935e-11  4.762e-08  2.662e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -2.083e+00     4.022e+00      2.642e+00      
 4.022e+00      -4.250e+00     -4.767e+00     
 2.642e+00      -4.767e+00     -4.620e+00     
 TOTAL-PRESSURE: -3.651e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          3.171e-01           1.060e+03           1.877e+00           
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 26
 -------------------------------------------
 DONE(8.816e+02  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945000e+04  0.000000e+00   2.099e-03  2.765e+00  
 GE2    -1.945000e+04  -2.595889e-03  1.132e-03  2.566e+00  
 GE3    -1.945000e+04  -1.850262e-04  1.632e-04  2.681e+00  
 GE4    -1.945000e+04  -9.747674e-06  4.581e-05  2.683e+00  
 GE5    -1.945000e+04  -3.817970e-07  1.552e-05  2.882e+00  
 GE6    -1.945000e+04  -3.988859e-08  2.631e-06  2.586e+00  
 GE7    -1.945000e+04  -6.310898e-10  9.037e-07  2.800e+00  
 GE8    -1.945000e+04  -3.093578e-10  1.494e-07  2.789e+00  
 GE9    -1.945000e+04  9.280733e-12   4.649e-08  2.561e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.883e+00     3.852e+00      2.663e+00      
 3.852e+00      -4.808e+00     -4.427e+00     
 2.663e+00      -4.427e+00     -5.162e+00     
 TOTAL-PRESSURE: -3.951e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          3.158e-01           1.055e+03           1.554e+00           
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 27
 -------------------------------------------
 DONE(9.150e+02  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945003e+04  0.000000e+00   2.100e-03  2.964e+00  
 GE2    -1.945004e+04  -2.590409e-03  1.132e-03  2.774e+00  
 GE3    -1.945004e+04  -1.868595e-04  1.635e-04  2.575e+00  
 GE4    -1.945004e+04  -9.792658e-06  4.582e-05  2.763e+00  
 GE5    -1.945004e+04  -3.834706e-07  1.548e-05  2.657e+00  
 GE6    -1.945004e+04  -3.777568e-08  2.611e-06  2.658e+00  
 GE7    -1.945004e+04  -6.465577e-10  8.976e-07  2.681e+00  
 GE8    -1.945004e+04  -3.279192e-10  1.456e-07  2.549e+00  
 GE9    -1.945004e+04  -1.237431e-11  4.557e-08  2.538e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.672e+00     3.638e+00      2.723e+00      
 3.638e+00      -5.425e+00     -4.049e+00     
 2.723e+00      -4.049e+00     -5.710e+00     
 TOTAL-PRESSURE: -4.269e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          3.150e-01           1.053e+03           1.222e+00           
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 28
 -------------------------------------------
 DONE(9.480e+02  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945008e+04  0.000000e+00   2.101e-03  2.770e+00  
 GE2    -1.945008e+04  -2.601781e-03  1.132e-03  2.664e+00  
 GE3    -1.945008e+04  -1.894875e-04  1.640e-04  2.700e+00  
 GE4    -1.945008e+04  -9.818666e-06  4.595e-05  2.752e+00  
 GE5    -1.945008e+04  -3.863755e-07  1.551e-05  2.693e+00  
 GE6    -1.945008e+04  -3.782827e-08  2.622e-06  2.546e+00  
 GE7    -1.945008e+04  -6.898678e-10  8.958e-07  2.546e+00  
 GE8    -1.945008e+04  -2.722348e-10  1.438e-07  2.773e+00  
 GE9    -1.945008e+04  -6.187155e-12  4.517e-08  2.550e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.451e+00     3.390e+00      2.817e+00      
 3.390e+00      -6.085e+00     -3.644e+00     
 2.817e+00      -3.644e+00     -6.257e+00     
 TOTAL-PRESSURE: -4.598e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          3.146e-01           1.051e+03           8.869e-01           
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 29
 -------------------------------------------
 DONE(9.807e+02  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945013e+04  0.000000e+00   2.100e-03  2.972e+00  
 GE2    -1.945014e+04  -2.607016e-03  1.131e-03  2.690e+00  
 GE3    -1.945014e+04  -1.922340e-04  1.645e-04  2.550e+00  
 GE4    -1.945014e+04  -9.807940e-06  4.616e-05  2.665e+00  
 GE5    -1.945014e+04  -3.862734e-07  1.560e-05  2.869e+00  
 GE6    -1.945014e+04  -3.875943e-08  2.657e-06  2.653e+00  
 GE7    -1.945014e+04  -2.211908e-09  8.974e-07  2.539e+00  
 GE8    -1.945014e+04  -2.938899e-10  1.440e-07  2.755e+00  
 GE9    -1.945014e+04  -2.165504e-11  4.538e-08  2.884e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.223e+00     3.121e+00      2.935e+00      
 3.121e+00      -6.767e+00     -3.226e+00     
 2.935e+00      -3.226e+00     -6.796e+00     
 TOTAL-PRESSURE: -4.929e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          3.144e-01           1.051e+03           5.519e-01           
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 30
 -------------------------------------------
 DONE(1.014e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945019e+04  0.000000e+00   2.096e-03  2.861e+00  
 GE2    -1.945019e+04  -2.610190e-03  1.130e-03  2.545e+00  
 GE3    -1.945019e+04  -1.946072e-04  1.648e-04  2.798e+00  
 GE4    -1.945019e+04  -9.726233e-06  4.643e-05  2.645e+00  
 GE5    -1.945019e+04  -3.994922e-07  1.572e-05  2.647e+00  
 GE6    -1.945019e+04  -3.819640e-08  2.706e-06  2.549e+00  
 GE7    -1.945019e+04  -7.238971e-10  9.014e-07  2.558e+00  
 GE8    -1.945019e+04  -2.969834e-10  1.457e-07  2.756e+00  
 GE9    -1.945019e+04  -2.165504e-11  4.594e-08  2.757e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -9.892e-01     2.843e+00      3.065e+00      
 2.843e+00      -7.456e+00     -2.807e+00     
 3.065e+00      -2.807e+00     -7.318e+00     
 TOTAL-PRESSURE: -5.254e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          3.141e-01           1.050e+03           2.218e-01           
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 31
 -------------------------------------------
 DONE(1.047e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945024e+04  0.000000e+00   2.088e-03  2.961e+00  
 GE2    -1.945024e+04  -2.626805e-03  1.127e-03  2.540e+00  
 GE3    -1.945024e+04  -1.963077e-04  1.647e-04  2.604e+00  
 GE4    -1.945024e+04  -9.576157e-06  4.673e-05  2.760e+00  
 GE5    -1.945024e+04  -4.034953e-07  1.585e-05  2.715e+00  
 GE6    -1.945024e+04  -4.050421e-08  2.760e-06  2.678e+00  
 GE7    -1.945024e+04  -7.950494e-10  9.063e-07  2.641e+00  
 GE8    -1.945024e+04  -2.629541e-10  1.478e-07  2.643e+00  
 GE9    -1.945024e+04  -4.331009e-11  4.655e-08  2.635e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -7.558e-01     2.570e+00      3.196e+00      
 2.570e+00      -8.132e+00     -2.397e+00     
 3.196e+00      -2.397e+00     -7.816e+00     
 TOTAL-PRESSURE: -5.568e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          3.137e-01           1.048e+03           -9.920e-02          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 32
 -------------------------------------------
 DONE(1.080e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945028e+04  0.000000e+00   2.078e-03  3.181e+00  
 GE2    -1.945029e+04  -2.640383e-03  1.122e-03  2.652e+00  
 GE3    -1.945029e+04  -1.971267e-04  1.641e-04  2.660e+00  
 GE4    -1.945029e+04  -9.341685e-06  4.703e-05  2.856e+00  
 GE5    -1.945029e+04  -4.153313e-07  1.598e-05  2.548e+00  
 GE6    -1.945029e+04  -3.806338e-08  2.812e-06  2.622e+00  
 GE7    -1.945029e+04  -8.352659e-10  9.115e-07  2.644e+00  
 GE8    -1.945029e+04  -2.412990e-10  1.498e-07  2.744e+00  
 GE9    -1.945029e+04  -4.021651e-11  4.711e-08  2.534e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -5.307e-01     2.309e+00      3.317e+00      
 2.309e+00      -8.783e+00     -2.006e+00     
 3.317e+00      -2.006e+00     -8.285e+00     
 TOTAL-PRESSURE: -5.866e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          3.130e-01           1.046e+03           -4.093e-01          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 33
 -------------------------------------------
 DONE(1.114e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945032e+04  0.000000e+00   2.066e-03  2.860e+00  
 GE2    -1.945032e+04  -2.646226e-03  1.117e-03  2.552e+00  
 GE3    -1.945033e+04  -1.971103e-04  1.631e-04  2.711e+00  
 GE4    -1.945033e+04  -9.038583e-06  4.734e-05  2.748e+00  
 GE5    -1.945033e+04  -4.117335e-07  1.610e-05  2.545e+00  
 GE6    -1.945033e+04  -4.232942e-08  2.853e-06  2.845e+00  
 GE7    -1.945033e+04  -8.816696e-10  9.161e-07  2.646e+00  
 GE8    -1.945033e+04  -2.815156e-10  1.512e-07  2.856e+00  
 GE9    -1.945033e+04  -2.784220e-11  4.755e-08  2.545e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -3.243e-01     2.069e+00      3.415e+00      
 2.069e+00      -9.401e+00     -1.644e+00     
 3.415e+00      -1.644e+00     -8.720e+00     
 TOTAL-PRESSURE: -6.148e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          3.120e-01           1.043e+03           -7.090e-01          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 34
 -------------------------------------------
 DONE(1.147e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945035e+04  0.000000e+00   2.050e-03  2.922e+00  
 GE2    -1.945036e+04  -2.643438e-03  1.110e-03  2.573e+00  
 GE3    -1.945036e+04  -1.962214e-04  1.617e-04  2.650e+00  
 GE4    -1.945036e+04  -8.695564e-06  4.762e-05  2.661e+00  
 GE5    -1.945036e+04  -4.070251e-07  1.620e-05  2.558e+00  
 GE6    -1.945036e+04  -4.671611e-08  2.882e-06  2.756e+00  
 GE7    -1.945036e+04  -9.095118e-10  9.198e-07  2.846e+00  
 GE8    -1.945036e+04  -2.815156e-10  1.521e-07  2.553e+00  
 GE9    -1.945036e+04  -2.474862e-11  4.791e-08  2.529e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.486e-01     1.853e+00      3.479e+00      
 1.853e+00      -9.982e+00     -1.314e+00     
 3.479e+00      -1.314e+00     -9.117e+00     
 TOTAL-PRESSURE: -6.416e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          3.107e-01           1.038e+03           -9.989e-01          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 35
 -------------------------------------------
 DONE(1.180e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945038e+04  0.000000e+00   2.034e-03  2.880e+00  
 GE2    -1.945038e+04  -2.635525e-03  1.103e-03  2.920e+00  
 GE3    -1.945038e+04  -1.946600e-04  1.599e-04  2.574e+00  
 GE4    -1.945038e+04  -8.331057e-06  4.788e-05  2.552e+00  
 GE5    -1.945038e+04  -4.058959e-07  1.628e-05  2.627e+00  
 GE6    -1.945038e+04  -4.464342e-08  2.898e-06  2.870e+00  
 GE7    -1.945038e+04  -9.095118e-10  9.228e-07  2.566e+00  
 GE8    -1.945038e+04  -2.536734e-10  1.525e-07  2.778e+00  
 GE9    -1.945038e+04  -4.640366e-11  4.818e-08  2.533e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.603e-02     1.661e+00      3.503e+00      
 1.661e+00      -1.052e+01     -1.022e+00     
 3.503e+00      -1.022e+00     -9.473e+00     
 TOTAL-PRESSURE: -6.671e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          3.092e-01           1.033e+03           -1.281e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 36
 -------------------------------------------
 DONE(1.214e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945040e+04  0.000000e+00   2.017e-03  3.264e+00  
 GE2    -1.945041e+04  -2.622631e-03  1.095e-03  2.675e+00  
 GE3    -1.945041e+04  -1.926136e-04  1.581e-04  2.656e+00  
 GE4    -1.945041e+04  -7.970661e-06  4.810e-05  2.642e+00  
 GE5    -1.945041e+04  -4.049276e-07  1.635e-05  2.769e+00  
 GE6    -1.945041e+04  -4.447327e-08  2.903e-06  2.756e+00  
 GE7    -1.945041e+04  -9.342604e-10  9.249e-07  2.661e+00  
 GE8    -1.945041e+04  -2.598605e-10  1.527e-07  2.656e+00  
 GE9    -1.945041e+04  -2.165504e-11  4.838e-08  2.538e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 5.885e-02      1.493e+00      3.477e+00      
 1.493e+00      -1.103e+01     -7.696e-01     
 3.477e+00      -7.696e-01     -9.787e+00     
 TOTAL-PRESSURE: -6.918e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          3.075e-01           1.028e+03           -1.558e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 37
 -------------------------------------------
 DONE(1.247e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945042e+04  0.000000e+00   2.001e-03  2.862e+00  
 GE2    -1.945043e+04  -2.602614e-03  1.088e-03  2.565e+00  
 GE3    -1.945043e+04  -1.904359e-04  1.563e-04  2.744e+00  
 GE4    -1.945043e+04  -7.636261e-06  4.829e-05  2.643e+00  
 GE5    -1.945043e+04  -3.991581e-07  1.640e-05  2.556e+00  
 GE6    -1.945043e+04  -4.464032e-08  2.898e-06  2.686e+00  
 GE7    -1.945043e+04  -9.435412e-10  9.265e-07  2.569e+00  
 GE8    -1.945043e+04  -2.443926e-10  1.527e-07  2.656e+00  
 GE9    -1.945043e+04  -3.093578e-12  4.851e-08  2.544e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 6.247e-02      1.345e+00      3.398e+00      
 1.345e+00      -1.149e+01     -5.582e-01     
 3.398e+00      -5.582e-01     -1.006e+01     
 TOTAL-PRESSURE: -7.163e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          3.057e-01           1.022e+03           -1.834e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 38
 -------------------------------------------
 DONE(1.280e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945045e+04  0.000000e+00   1.986e-03  2.776e+00  
 GE2    -1.945045e+04  -2.572913e-03  1.082e-03  2.845e+00  
 GE3    -1.945045e+04  -1.884949e-04  1.548e-04  2.756e+00  
 GE4    -1.945045e+04  -7.356336e-06  4.846e-05  2.555e+00  
 GE5    -1.945045e+04  -3.908457e-07  1.642e-05  2.652e+00  
 GE6    -1.945045e+04  -4.384837e-08  2.884e-06  2.666e+00  
 GE7    -1.945045e+04  -1.194121e-09  9.277e-07  2.646e+00  
 GE8    -1.945045e+04  -2.443926e-10  1.528e-07  2.558e+00  
 GE9    -1.945045e+04  -2.784220e-11  4.855e-08  2.635e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.693e-02     1.213e+00      3.263e+00      
 1.213e+00      -1.193e+01     -3.874e-01     
 3.263e+00      -3.874e-01     -1.028e+01     
 TOTAL-PRESSURE: -7.410e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          3.039e-01           1.016e+03           -2.112e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 39
 -------------------------------------------
 DONE(1.313e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945047e+04  0.000000e+00   1.975e-03  2.853e+00  
 GE2    -1.945048e+04  -2.540491e-03  1.078e-03  2.541e+00  
 GE3    -1.945048e+04  -1.868474e-04  1.536e-04  2.758e+00  
 GE4    -1.945048e+04  -7.158155e-06  4.863e-05  2.539e+00  
 GE5    -1.945048e+04  -3.877830e-07  1.643e-05  2.740e+00  
 GE6    -1.945048e+04  -4.546631e-08  2.866e-06  2.638e+00  
 GE7    -1.945048e+04  -9.590090e-10  9.289e-07  2.664e+00  
 GE8    -1.945048e+04  -2.289247e-10  1.529e-07  2.550e+00  
 GE9    -1.945048e+04  0.000000e+00   4.854e-08  2.798e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.861e-01     1.090e+00      3.071e+00      
 1.090e+00      -1.234e+01     -2.560e-01     
 3.071e+00      -2.560e-01     -1.046e+01     
 TOTAL-PRESSURE: -7.663e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          3.022e-01           1.010e+03           -2.395e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 40
 -------------------------------------------
 DONE(1.345e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945050e+04  0.000000e+00   1.967e-03  2.854e+00  
 GE2    -1.945050e+04  -2.503239e-03  1.074e-03  2.605e+00  
 GE3    -1.945051e+04  -1.856419e-04  1.528e-04  2.599e+00  
 GE4    -1.945051e+04  -7.020735e-06  4.882e-05  2.733e+00  
 GE5    -1.945051e+04  -3.819083e-07  1.641e-05  2.540e+00  
 GE6    -1.945051e+04  -4.830312e-08  2.843e-06  2.663e+00  
 GE7    -1.945051e+04  -9.249797e-10  9.302e-07  2.658e+00  
 GE8    -1.945051e+04  -2.382055e-10  1.530e-07  2.743e+00  
 GE9    -1.945051e+04  -6.187155e-12  4.848e-08  2.624e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -4.471e-01     9.694e-01      2.827e+00      
 9.694e-01      -1.273e+01     -1.616e-01     
 2.827e+00      -1.616e-01     -1.059e+01     
 TOTAL-PRESSURE: -7.924e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          3.006e-01           1.004e+03           -2.684e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 41
 -------------------------------------------
 DONE(1.378e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945054e+04  0.000000e+00   1.963e-03  2.950e+00  
 GE2    -1.945054e+04  -2.476801e-03  1.072e-03  2.882e+00  
 GE3    -1.945054e+04  -1.850849e-04  1.525e-04  2.552e+00  
 GE4    -1.945054e+04  -6.976611e-06  4.904e-05  2.531e+00  
 GE5    -1.945054e+04  -3.689153e-07  1.638e-05  2.543e+00  
 GE6    -1.945054e+04  -4.587466e-08  2.817e-06  2.634e+00  
 GE7    -1.945054e+04  -9.404476e-10  9.325e-07  2.635e+00  
 GE8    -1.945054e+04  -2.258312e-10  1.533e-07  2.546e+00  
 GE9    -1.945054e+04  -1.546789e-11  4.838e-08  2.531e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -8.012e-01     8.450e-01      2.535e+00      
 8.450e-01      -1.311e+01     -1.007e-01     
 2.535e+00      -1.007e-01     -1.068e+01     
 TOTAL-PRESSURE: -8.196e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          2.992e-01           9.996e+02           -2.981e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 42
 -------------------------------------------
 DONE(1.411e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945058e+04  0.000000e+00   1.966e-03  2.980e+00  
 GE2    -1.945058e+04  -2.444909e-03  1.073e-03  2.556e+00  
 GE3    -1.945058e+04  -1.850764e-04  1.527e-04  2.743e+00  
 GE4    -1.945058e+04  -7.000454e-06  4.926e-05  2.566e+00  
 GE5    -1.945058e+04  -3.670839e-07  1.634e-05  2.554e+00  
 GE6    -1.945058e+04  -4.514148e-08  2.793e-06  2.543e+00  
 GE7    -1.945058e+04  -9.373540e-10  9.362e-07  2.547e+00  
 GE8    -1.945058e+04  -2.072697e-10  1.538e-07  2.786e+00  
 GE9    -1.945058e+04  -6.187155e-12  4.828e-08  2.667e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.243e+00     7.105e-01      2.205e+00      
 7.105e-01      -1.346e+01     -6.855e-02     
 2.205e+00      -6.855e-02     -1.073e+01     
 TOTAL-PRESSURE: -8.479e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          2.979e-01           9.953e+02           -3.287e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 43
 -------------------------------------------
 DONE(1.444e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945062e+04  0.000000e+00   1.971e-03  2.854e+00  
 GE2    -1.945062e+04  -2.426640e-03  1.076e-03  2.536e+00  
 GE3    -1.945062e+04  -1.855734e-04  1.533e-04  2.553e+00  
 GE4    -1.945062e+04  -7.088593e-06  4.949e-05  2.636e+00  
 GE5    -1.945062e+04  -3.615433e-07  1.630e-05  2.623e+00  
 GE6    -1.945062e+04  -4.712756e-08  2.771e-06  2.624e+00  
 GE7    -1.945062e+04  -9.404476e-10  9.406e-07  2.636e+00  
 GE8    -1.945062e+04  -2.041761e-10  1.544e-07  2.636e+00  
 GE9    -1.945062e+04  -6.187155e-12  4.817e-08  2.655e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.763e+00     5.614e-01      1.846e+00      
 5.614e-01      -1.381e+01     -6.049e-02     
 1.846e+00      -6.049e-02     -1.074e+01     
 TOTAL-PRESSURE: -8.770e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          2.967e-01           9.913e+02           -3.598e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 44
 -------------------------------------------
 DONE(1.476e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945067e+04  0.000000e+00   1.976e-03  3.068e+00  
 GE2    -1.945067e+04  -2.409948e-03  1.078e-03  2.773e+00  
 GE3    -1.945067e+04  -1.864239e-04  1.541e-04  2.640e+00  
 GE4    -1.945067e+04  -7.202065e-06  4.971e-05  2.642e+00  
 GE5    -1.945067e+04  -3.705982e-07  1.628e-05  2.658e+00  
 GE6    -1.945067e+04  -4.673158e-08  2.753e-06  2.532e+00  
 GE7    -1.945067e+04  -2.645009e-09  9.456e-07  2.620e+00  
 GE8    -1.945067e+04  -2.072697e-10  1.550e-07  2.717e+00  
 GE9    -1.945067e+04  0.000000e+00   4.805e-08  2.512e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -2.344e+00     3.939e-01      1.470e+00      
 3.939e-01      -1.414e+01     -7.154e-02     
 1.470e+00      -7.154e-02     -1.071e+01     
 TOTAL-PRESSURE: -9.064e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          2.955e-01           9.876e+02           -3.913e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 45
 -------------------------------------------
 DONE(1.510e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945071e+04  0.000000e+00   1.981e-03  2.851e+00  
 GE2    -1.945072e+04  -2.398847e-03  1.080e-03  2.539e+00  
 GE3    -1.945072e+04  -1.873897e-04  1.549e-04  3.031e+00  
 GE4    -1.945072e+04  -7.337913e-06  4.991e-05  2.727e+00  
 GE5    -1.945072e+04  -3.646276e-07  1.626e-05  2.524e+00  
 GE6    -1.945072e+04  -4.553127e-08  2.736e-06  2.633e+00  
 GE7    -1.945072e+04  -8.445467e-10  9.505e-07  2.534e+00  
 GE8    -1.945072e+04  -2.412990e-10  1.556e-07  2.628e+00  
 GE9    -1.945072e+04  4.331009e-11   4.794e-08  2.510e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -2.971e+00     2.062e-01      1.088e+00      
 2.062e-01      -1.445e+01     -9.658e-02     
 1.088e+00      -9.658e-02     -1.066e+01     
 TOTAL-PRESSURE: -9.360e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          2.944e-01           9.838e+02           -4.227e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 46
 -------------------------------------------
 DONE(1.542e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945076e+04  0.000000e+00   1.984e-03  3.041e+00  
 GE2    -1.945076e+04  -2.368001e-03  1.082e-03  2.722e+00  
 GE3    -1.945076e+04  -1.883447e-04  1.557e-04  2.627e+00  
 GE4    -1.945076e+04  -7.451513e-06  5.007e-05  2.521e+00  
 GE5    -1.945076e+04  -3.710313e-07  1.626e-05  2.624e+00  
 GE6    -1.945076e+04  -4.414226e-08  2.726e-06  2.521e+00  
 GE7    -1.945076e+04  -8.631081e-10  9.555e-07  2.631e+00  
 GE8    -1.945076e+04  -1.763339e-10  1.564e-07  2.555e+00  
 GE9    -1.945076e+04  1.237431e-11   4.787e-08  2.521e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -3.629e+00     -2.473e-03     7.134e-01      
 -2.473e-03     -1.475e+01     -1.309e-01     
 7.134e-01      -1.309e-01     -1.057e+01     
 TOTAL-PRESSURE: -9.651e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          2.932e-01           9.799e+02           -4.540e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 47
 -------------------------------------------
 DONE(1.575e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945080e+04  0.000000e+00   1.985e-03  2.731e+00  
 GE2    -1.945080e+04  -2.356315e-03  1.083e-03  2.622e+00  
 GE3    -1.945080e+04  -1.891143e-04  1.562e-04  2.744e+00  
 GE4    -1.945080e+04  -7.541001e-06  5.020e-05  2.524e+00  
 GE5    -1.945080e+04  -3.673190e-07  1.626e-05  2.749e+00  
 GE6    -1.945080e+04  -4.649338e-08  2.722e-06  2.540e+00  
 GE7    -1.945080e+04  -9.930384e-10  9.602e-07  2.543e+00  
 GE8    -1.945080e+04  -1.856147e-10  1.571e-07  2.519e+00  
 GE9    -1.945080e+04  -3.093578e-11  4.784e-08  2.493e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -4.296e+00     -2.313e-01     3.570e-01      
 -2.313e-01     -1.504e+01     -1.700e-01     
 3.570e-01      -1.700e-01     -1.046e+01     
 TOTAL-PRESSURE: -9.933e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          2.919e-01           9.755e+02           -4.845e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 48
 -------------------------------------------
 DONE(1.608e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945084e+04  0.000000e+00   1.984e-03  2.733e+00  
 GE2    -1.945084e+04  -2.341584e-03  1.083e-03  2.512e+00  
 GE3    -1.945084e+04  -1.895443e-04  1.565e-04  2.930e+00  
 GE4    -1.945084e+04  -7.595212e-06  5.029e-05  2.530e+00  
 GE5    -1.945084e+04  -3.739578e-07  1.628e-05  2.751e+00  
 GE6    -1.945084e+04  -4.646553e-08  2.727e-06  2.756e+00  
 GE7    -1.945084e+04  -7.455522e-10  9.642e-07  2.542e+00  
 GE8    -1.945084e+04  -2.010825e-10  1.576e-07  2.555e+00  
 GE9    -1.945084e+04  -1.546789e-11  4.786e-08  2.709e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -4.952e+00     -4.796e-01     2.975e-02      
 -4.796e-01     -1.531e+01     -2.101e-01     
 2.975e-02      -2.101e-01     -1.034e+01     
 TOTAL-PRESSURE: -1.020e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          2.904e-01           9.705e+02           -5.138e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 49
 -------------------------------------------
 DONE(1.640e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945087e+04  0.000000e+00   1.980e-03  3.027e+00  
 GE2    -1.945087e+04  -2.329213e-03  1.082e-03  2.626e+00  
 GE3    -1.945087e+04  -1.897587e-04  1.564e-04  2.644e+00  
 GE4    -1.945087e+04  -7.583107e-06  5.035e-05  2.829e+00  
 GE5    -1.945087e+04  -3.756902e-07  1.631e-05  2.716e+00  
 GE6    -1.945087e+04  -4.471148e-08  2.739e-06  2.613e+00  
 GE7    -1.945087e+04  1.918018e-10   9.672e-07  2.825e+00  
 GE8    -1.945087e+04  -1.856147e-10  1.579e-07  2.524e+00  
 GE9    -1.945087e+04  3.093578e-12   4.794e-08  2.511e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -5.583e+00     -7.458e-01     -2.589e-01     
 -7.458e-01     -1.556e+01     -2.480e-01     
 -2.589e-01     -2.480e-01     -1.021e+01     
 TOTAL-PRESSURE: -1.045e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          2.887e-01           9.646e+02           -5.417e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 50
 -------------------------------------------
 DONE(1.674e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945089e+04  0.000000e+00   1.974e-03  2.940e+00  
 GE2    -1.945090e+04  -2.303122e-03  1.080e-03  2.529e+00  
 GE3    -1.945090e+04  -1.896402e-04  1.559e-04  2.769e+00  
 GE4    -1.945090e+04  -7.533298e-06  5.038e-05  2.723e+00  
 GE5    -1.945090e+04  -3.764265e-07  1.634e-05  2.598e+00  
 GE6    -1.945090e+04  -4.582516e-08  2.758e-06  2.808e+00  
 GE7    -1.945090e+04  -7.053357e-10  9.692e-07  2.514e+00  
 GE8    -1.945090e+04  -2.351119e-10  1.580e-07  2.503e+00  
 GE9    -1.945090e+04  -3.712293e-11  4.805e-08  2.798e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -6.178e+00     -1.028e+00     -5.015e-01     
 -1.028e+00     -1.578e+01     -2.827e-01     
 -5.015e-01     -2.827e-01     -1.007e+01     
 TOTAL-PRESSURE: -1.068e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          2.866e-01           9.578e+02           -5.681e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 51
 -------------------------------------------
 DONE(1.707e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945091e+04  0.000000e+00   1.966e-03  2.828e+00  
 GE2    -1.945091e+04  -2.286117e-03  1.077e-03  2.629e+00  
 GE3    -1.945091e+04  -1.890387e-04  1.550e-04  2.622e+00  
 GE4    -1.945091e+04  -7.433718e-06  5.038e-05  2.710e+00  
 GE5    -1.945091e+04  -3.752324e-07  1.636e-05  2.633e+00  
 GE6    -1.945091e+04  -4.593653e-08  2.777e-06  2.536e+00  
 GE7    -1.945091e+04  -6.898678e-10  9.695e-07  2.528e+00  
 GE8    -1.945091e+04  -2.072697e-10  1.577e-07  2.713e+00  
 GE9    -1.945091e+04  -2.784220e-11  4.820e-08  2.759e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -6.721e+00     -1.323e+00     -6.927e-01     
 -1.323e+00     -1.599e+01     -3.133e-01     
 -6.927e-01     -3.133e-01     -9.937e+00     
 TOTAL-PRESSURE: -1.088e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          2.843e-01           9.500e+02           -5.926e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 52
 -------------------------------------------
 DONE(1.740e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945092e+04  0.000000e+00   1.956e-03  2.836e+00  
 GE2    -1.945092e+04  -2.275582e-03  1.073e-03  2.616e+00  
 GE3    -1.945092e+04  -1.879463e-04  1.538e-04  2.497e+00  
 GE4    -1.945092e+04  -7.296101e-06  5.033e-05  2.708e+00  
 GE5    -1.945092e+04  -3.796469e-07  1.637e-05  2.502e+00  
 GE6    -1.945092e+04  -4.605100e-08  2.799e-06  2.627e+00  
 GE7    -1.945092e+04  -6.651192e-10  9.686e-07  2.532e+00  
 GE8    -1.945092e+04  -2.505798e-10  1.573e-07  2.615e+00  
 GE9    -1.945092e+04  2.474862e-11   4.838e-08  2.602e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -7.202e+00     -1.628e+00     -8.282e-01     
 -1.628e+00     -1.617e+01     -3.399e-01     
 -8.282e-01     -3.399e-01     -9.811e+00     
 TOTAL-PRESSURE: -1.106e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          2.817e-01           9.412e+02           -6.151e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 53
 -------------------------------------------
 DONE(1.773e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945091e+04  0.000000e+00   1.944e-03  2.712e+00  
 GE2    -1.945092e+04  -2.261697e-03  1.068e-03  2.509e+00  
 GE3    -1.945092e+04  -1.864210e-04  1.523e-04  2.513e+00  
 GE4    -1.945092e+04  -7.117150e-06  5.024e-05  2.712e+00  
 GE5    -1.945092e+04  -3.738527e-07  1.636e-05  2.522e+00  
 GE6    -1.945092e+04  -4.635107e-08  2.818e-06  2.709e+00  
 GE7    -1.945092e+04  -6.867742e-10  9.663e-07  2.506e+00  
 GE8    -1.945092e+04  -1.763339e-10  1.566e-07  2.614e+00  
 GE9    -1.945092e+04  3.093578e-12   4.859e-08  2.605e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -7.618e+00     -1.942e+00     -9.064e-01     
 -1.942e+00     -1.633e+01     -3.640e-01     
 -9.064e-01     -3.640e-01     -9.697e+00     
 TOTAL-PRESSURE: -1.121e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          2.787e-01           9.313e+02           -6.356e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 54
 -------------------------------------------
 DONE(1.805e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945090e+04  0.000000e+00   1.930e-03  3.077e+00  
 GE2    -1.945091e+04  -2.250166e-03  1.061e-03  2.535e+00  
 GE3    -1.945091e+04  -1.844150e-04  1.506e-04  2.643e+00  
 GE4    -1.945091e+04  -6.915423e-06  5.009e-05  2.707e+00  
 GE5    -1.945091e+04  -3.759470e-07  1.633e-05  2.610e+00  
 GE6    -1.945091e+04  -4.739051e-08  2.832e-06  2.689e+00  
 GE7    -1.945091e+04  -6.249027e-10  9.625e-07  2.523e+00  
 GE8    -1.945091e+04  -2.165504e-10  1.557e-07  2.607e+00  
 GE9    -1.945091e+04  9.280733e-12   4.878e-08  2.483e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -7.969e+00     -2.261e+00     -9.263e-01     
 -2.261e+00     -1.646e+01     -3.878e-01     
 -9.263e-01     -3.878e-01     -9.597e+00     
 TOTAL-PRESSURE: -1.134e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          2.754e-01           9.203e+02           -6.541e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 55
 -------------------------------------------
 DONE(1.838e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945088e+04  0.000000e+00   1.915e-03  2.739e+00  
 GE2    -1.945089e+04  -2.236561e-03  1.053e-03  2.623e+00  
 GE3    -1.945089e+04  -1.818565e-04  1.488e-04  2.549e+00  
 GE4    -1.945089e+04  -6.699566e-06  4.988e-05  2.615e+00  
 GE5    -1.945089e+04  -3.804605e-07  1.626e-05  2.517e+00  
 GE6    -1.945089e+04  -4.493112e-08  2.841e-06  2.702e+00  
 GE7    -1.945089e+04  -6.249027e-10  9.574e-07  2.813e+00  
 GE8    -1.945089e+04  -2.072697e-10  1.545e-07  2.616e+00  
 GE9    -1.945089e+04  1.546789e-11   4.896e-08  2.799e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -8.252e+00     -2.584e+00     -8.889e-01     
 -2.584e+00     -1.657e+01     -4.143e-01     
 -8.889e-01     -4.143e-01     -9.512e+00     
 TOTAL-PRESSURE: -1.144e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          2.719e-01           9.085e+02           -6.704e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 56
 -------------------------------------------
 DONE(1.871e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945086e+04  0.000000e+00   1.898e-03  2.809e+00  
 GE2    -1.945086e+04  -2.228099e-03  1.045e-03  2.607e+00  
 GE3    -1.945086e+04  -1.790204e-04  1.470e-04  2.502e+00  
 GE4    -1.945086e+04  -6.488531e-06  4.963e-05  2.505e+00  
 GE5    -1.945086e+04  -3.751272e-07  1.618e-05  2.616e+00  
 GE6    -1.945086e+04  -4.666971e-08  2.843e-06  2.617e+00  
 GE7    -1.945086e+04  4.454752e-10   9.508e-07  2.606e+00  
 GE8    -1.945086e+04  -1.856147e-10  1.531e-07  2.624e+00  
 GE9    -1.945086e+04  1.079659e-09   4.913e-08  2.600e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -8.470e+00     -2.908e+00     -7.968e-01     
 -2.908e+00     -1.665e+01     -4.468e-01     
 -7.968e-01     -4.468e-01     -9.440e+00     
 TOTAL-PRESSURE: -1.152e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          2.681e-01           8.957e+02           -6.847e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 57
 -------------------------------------------
 DONE(1.903e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945082e+04  0.000000e+00   1.881e-03  2.981e+00  
 GE2    -1.945083e+04  -2.214761e-03  1.036e-03  2.715e+00  
 GE3    -1.945083e+04  -1.760117e-04  1.451e-04  2.610e+00  
 GE4    -1.945083e+04  -6.260321e-06  4.934e-05  2.627e+00  
 GE5    -1.945083e+04  -3.723956e-07  1.607e-05  2.603e+00  
 GE6    -1.945083e+04  -4.371844e-08  2.841e-06  2.606e+00  
 GE7    -1.945083e+04  -1.865427e-09  9.431e-07  2.619e+00  
 GE8    -1.945083e+04  -2.041761e-10  1.515e-07  2.511e+00  
 GE9    -1.945083e+04  -1.330238e-09  4.924e-08  2.482e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -8.630e+00     -3.231e+00     -6.542e-01     
 -3.231e+00     -1.671e+01     -4.879e-01     
 -6.542e-01     -4.879e-01     -9.382e+00     
 TOTAL-PRESSURE: -1.157e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          2.640e-01           8.823e+02           -6.971e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 58
 -------------------------------------------
 DONE(1.935e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945078e+04  0.000000e+00   1.862e-03  2.704e+00  
 GE2    -1.945078e+04  -2.204980e-03  1.026e-03  2.520e+00  
 GE3    -1.945078e+04  -1.727993e-04  1.432e-04  2.608e+00  
 GE4    -1.945078e+04  -6.055168e-06  4.899e-05  2.520e+00  
 GE5    -1.945078e+04  -3.724822e-07  1.595e-05  2.650e+00  
 GE6    -1.945078e+04  -4.373081e-08  2.835e-06  2.617e+00  
 GE7    -1.945078e+04  -1.815930e-09  9.345e-07  2.612e+00  
 GE8    -1.945078e+04  -2.041761e-10  1.497e-07  2.816e+00  
 GE9    -1.945078e+04  9.280733e-12   4.934e-08  2.592e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -8.743e+00     -3.550e+00     -4.656e-01     
 -3.550e+00     -1.675e+01     -5.406e-01     
 -4.656e-01     -5.406e-01     -9.333e+00     
 TOTAL-PRESSURE: -1.161e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          2.598e-01           8.682e+02           -7.079e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 59
 -------------------------------------------
 DONE(1.968e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945074e+04  0.000000e+00   1.842e-03  2.920e+00  
 GE2    -1.945074e+04  -2.197028e-03  1.015e-03  2.615e+00  
 GE3    -1.945074e+04  -1.691824e-04  1.413e-04  2.509e+00  
 GE4    -1.945074e+04  -5.866592e-06  4.858e-05  2.823e+00  
 GE5    -1.945074e+04  -3.639161e-07  1.580e-05  2.812e+00  
 GE6    -1.945074e+04  -4.403089e-08  2.825e-06  2.662e+00  
 GE7    -1.945074e+04  -5.723118e-10  9.250e-07  2.513e+00  
 GE8    -1.945074e+04  -2.227376e-10  1.478e-07  2.502e+00  
 GE9    -1.945074e+04  3.093578e-12   4.941e-08  2.591e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -8.819e+00     -3.864e+00     -2.373e-01     
 -3.864e+00     -1.677e+01     -6.067e-01     
 -2.373e-01     -6.067e-01     -9.292e+00     
 TOTAL-PRESSURE: -1.163e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          2.555e-01           8.537e+02           -7.173e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 60
 -------------------------------------------
 DONE(2.000e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945069e+04  0.000000e+00   1.822e-03  2.823e+00  
 GE2    -1.945069e+04  -2.195287e-03  1.004e-03  2.631e+00  
 GE3    -1.945069e+04  -1.652659e-04  1.394e-04  2.517e+00  
 GE4    -1.945069e+04  -5.690342e-06  4.813e-05  2.530e+00  
 GE5    -1.945069e+04  -3.603337e-07  1.566e-05  2.740e+00  
 GE6    -1.945069e+04  -4.434334e-08  2.814e-06  2.643e+00  
 GE7    -1.945069e+04  -5.784990e-10  9.154e-07  2.534e+00  
 GE8    -1.945069e+04  -1.979890e-10  1.459e-07  2.623e+00  
 GE9    -1.945069e+04  1.546789e-11   4.944e-08  2.484e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -8.868e+00     -4.170e+00     2.351e-02      
 -4.170e+00     -1.677e+01     -6.881e-01     
 2.351e-02      -6.881e-01     -9.255e+00     
 TOTAL-PRESSURE: -1.163e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.145e+02          -7.148e+02          2.510e-01           8.388e+02           -7.256e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 61
 -------------------------------------------
 DONE(2.033e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945063e+04  0.000000e+00   1.802e-03  2.923e+00  
 GE2    -1.945064e+04  -2.175794e-03  9.927e-04  2.499e+00  
 GE3    -1.945064e+04  -1.613435e-04  1.374e-04  2.615e+00  
 GE4    -1.945064e+04  -5.530472e-06  4.763e-05  2.710e+00  
 GE5    -1.945064e+04  -3.602502e-07  1.552e-05  2.504e+00  
 GE6    -1.945064e+04  -4.392880e-08  2.803e-06  2.505e+00  
 GE7    -1.945064e+04  -2.320183e-10  9.055e-07  2.602e+00  
 GE8    -1.945064e+04  -2.320183e-10  1.438e-07  2.806e+00  
 GE9    -1.945064e+04  -2.474862e-11  4.944e-08  2.575e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -8.902e+00     -4.464e+00     3.093e-01      
 -4.464e+00     -1.676e+01     -7.851e-01     
 3.093e-01      -7.851e-01     -9.218e+00     
 TOTAL-PRESSURE: -1.163e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.465e-01           8.238e+02           -7.330e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 62
 -------------------------------------------
 DONE(2.065e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945058e+04  0.000000e+00   1.784e-03  3.025e+00  
 GE2    -1.945058e+04  -2.162929e-03  9.821e-04  2.613e+00  
 GE3    -1.945058e+04  -1.574920e-04  1.355e-04  2.715e+00  
 GE4    -1.945058e+04  -5.380298e-06  4.707e-05  2.615e+00  
 GE5    -1.945058e+04  -3.542518e-07  1.539e-05  2.500e+00  
 GE6    -1.945058e+04  -4.183136e-08  2.791e-06  2.747e+00  
 GE7    -1.945058e+04  -5.537504e-10  8.954e-07  2.721e+00  
 GE8    -1.945058e+04  -1.577725e-10  1.418e-07  2.594e+00  
 GE9    -1.945058e+04  -2.784220e-11  4.943e-08  2.731e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -8.932e+00     -4.745e+00     6.128e-01      
 -4.745e+00     -1.674e+01     -8.976e-01     
 6.128e-01      -8.976e-01     -9.179e+00     
 TOTAL-PRESSURE: -1.162e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.421e-01           8.088e+02           -7.398e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 63
 -------------------------------------------
 DONE(2.098e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945052e+04  0.000000e+00   1.765e-03  2.900e+00  
 GE2    -1.945052e+04  -2.154359e-03  9.717e-04  2.658e+00  
 GE3    -1.945052e+04  -1.535341e-04  1.337e-04  2.614e+00  
 GE4    -1.945052e+04  -5.245421e-06  4.651e-05  2.814e+00  
 GE5    -1.945052e+04  -3.526555e-07  1.526e-05  2.713e+00  
 GE6    -1.945052e+04  -3.914922e-08  2.779e-06  2.625e+00  
 GE7    -1.945052e+04  -5.166275e-10  8.847e-07  2.502e+00  
 GE8    -1.945052e+04  -2.010825e-10  1.398e-07  2.714e+00  
 GE9    -1.945052e+04  -6.187155e-12  4.939e-08  2.495e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -8.974e+00     -5.008e+00     9.264e-01      
 -5.008e+00     -1.671e+01     -1.025e+00     
 9.264e-01      -1.025e+00     -9.138e+00     
 TOTAL-PRESSURE: -1.161e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.376e-01           7.941e+02           -7.466e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 64
 -------------------------------------------
 DONE(2.131e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945047e+04  0.000000e+00   1.747e-03  2.929e+00  
 GE2    -1.945047e+04  -2.165852e-03  9.615e-04  2.701e+00  
 GE3    -1.945047e+04  -1.496829e-04  1.320e-04  2.606e+00  
 GE4    -1.945047e+04  -5.108183e-06  4.593e-05  2.761e+00  
 GE5    -1.945047e+04  -3.467220e-07  1.515e-05  2.574e+00  
 GE6    -1.945047e+04  -4.302238e-08  2.768e-06  2.769e+00  
 GE7    -1.945047e+04  -5.011596e-10  8.740e-07  2.604e+00  
 GE8    -1.945047e+04  -1.515853e-10  1.378e-07  2.704e+00  
 GE9    -1.945047e+04  -4.021651e-11  4.935e-08  2.582e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -9.036e+00     -5.251e+00     1.242e+00      
 -5.251e+00     -1.667e+01     -1.165e+00     
 1.242e+00      -1.165e+00     -9.097e+00     
 TOTAL-PRESSURE: -1.160e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.333e-01           7.797e+02           -7.535e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 65
 -------------------------------------------
 DONE(2.164e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945042e+04  0.000000e+00   1.729e-03  2.825e+00  
 GE2    -1.945042e+04  -2.153957e-03  9.515e-04  2.698e+00  
 GE3    -1.945042e+04  -1.459209e-04  1.303e-04  2.707e+00  
 GE4    -1.945042e+04  -4.976292e-06  4.536e-05  2.616e+00  
 GE5    -1.945042e+04  -3.410051e-07  1.503e-05  2.628e+00  
 GE6    -1.945042e+04  -3.959779e-08  2.755e-06  2.619e+00  
 GE7    -1.945042e+04  1.061097e-09   8.629e-07  2.598e+00  
 GE8    -1.945042e+04  -1.670532e-10  1.359e-07  2.514e+00  
 GE9    -1.945042e+04  -1.546789e-11  4.929e-08  2.537e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -9.124e+00     -5.469e+00     1.551e+00      
 -5.469e+00     -1.663e+01     -1.315e+00     
 1.551e+00      -1.315e+00     -9.057e+00     
 TOTAL-PRESSURE: -1.160e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.292e-01           7.660e+02           -7.608e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 66
 -------------------------------------------
 DONE(2.197e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945037e+04  0.000000e+00   1.711e-03  2.718e+00  
 GE2    -1.945037e+04  -2.126893e-03  9.422e-04  2.608e+00  
 GE3    -1.945037e+04  -1.420406e-04  1.288e-04  2.810e+00  
 GE4    -1.945037e+04  -4.825059e-06  4.483e-05  2.601e+00  
 GE5    -1.945037e+04  -3.368597e-07  1.493e-05  2.499e+00  
 GE6    -1.945037e+04  -3.695588e-08  2.739e-06  2.603e+00  
 GE7    -1.945037e+04  7.517393e-10   8.515e-07  2.497e+00  
 GE8    -1.945037e+04  -1.515853e-10  1.341e-07  2.518e+00  
 GE9    -1.945037e+04  -6.187155e-12  4.923e-08  2.577e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -9.244e+00     -5.660e+00     1.846e+00      
 -5.660e+00     -1.659e+01     -1.471e+00     
 1.846e+00      -1.471e+00     -9.025e+00     
 TOTAL-PRESSURE: -1.162e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.254e-01           7.531e+02           -7.689e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 67
 -------------------------------------------
 DONE(2.229e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945033e+04  0.000000e+00   1.694e-03  2.729e+00  
 GE2    -1.945033e+04  -2.097776e-03  9.334e-04  2.797e+00  
 GE3    -1.945033e+04  -1.382157e-04  1.274e-04  2.505e+00  
 GE4    -1.945033e+04  -4.662192e-06  4.435e-05  2.497e+00  
 GE5    -1.945033e+04  -3.369679e-07  1.483e-05  2.705e+00  
 GE6    -1.945033e+04  -3.799841e-08  2.721e-06  2.489e+00  
 GE7    -1.945033e+04  -4.795045e-10  8.402e-07  2.621e+00  
 GE8    -1.945033e+04  -1.237431e-10  1.324e-07  2.602e+00  
 GE9    -1.945033e+04  -2.474862e-11  4.918e-08  2.679e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -9.402e+00     -5.820e+00     2.117e+00      
 -5.820e+00     -1.654e+01     -1.631e+00     
 2.117e+00      -1.631e+00     -9.010e+00     
 TOTAL-PRESSURE: -1.165e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.219e-01           7.414e+02           -7.782e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 68
 -------------------------------------------
 DONE(2.262e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945030e+04  0.000000e+00   1.678e-03  2.801e+00  
 GE2    -1.945030e+04  -2.065981e-03  9.255e-04  2.511e+00  
 GE3    -1.945030e+04  -1.347177e-04  1.261e-04  2.495e+00  
 GE4    -1.945030e+04  -4.503516e-06  4.393e-05  2.713e+00  
 GE5    -1.945030e+04  -3.336887e-07  1.473e-05  2.496e+00  
 GE6    -1.945030e+04  -3.618248e-08  2.699e-06  2.508e+00  
 GE7    -1.945030e+04  -4.795045e-10  8.293e-07  2.597e+00  
 GE8    -1.945030e+04  -1.144624e-10  1.308e-07  2.539e+00  
 GE9    -1.945030e+04  -3.093578e-12  4.917e-08  2.575e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -9.604e+00     -5.947e+00     2.358e+00      
 -5.947e+00     -1.649e+01     -1.789e+00     
 2.358e+00      -1.789e+00     -9.023e+00     
 TOTAL-PRESSURE: -1.170e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.188e-01           7.311e+02           -7.891e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 69
 -------------------------------------------
 DONE(2.293e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945028e+04  0.000000e+00   1.662e-03  2.907e+00  
 GE2    -1.945029e+04  -2.033862e-03  9.185e-04  2.698e+00  
 GE3    -1.945029e+04  -1.318304e-04  1.248e-04  2.501e+00  
 GE4    -1.945029e+04  -4.353251e-06  4.357e-05  2.701e+00  
 GE5    -1.945029e+04  -3.376485e-07  1.463e-05  2.594e+00  
 GE6    -1.945029e+04  -3.498218e-08  2.672e-06  2.488e+00  
 GE7    -1.945029e+04  -4.485687e-10  8.191e-07  2.801e+00  
 GE8    -1.945029e+04  -1.732403e-10  1.295e-07  2.678e+00  
 GE9    -1.945029e+04  2.474862e-11   4.918e-08  2.615e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -9.851e+00     -6.039e+00     2.561e+00      
 -6.039e+00     -1.644e+01     -1.943e+00     
 2.561e+00      -1.943e+00     -9.074e+00     
 TOTAL-PRESSURE: -1.179e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.162e-01           7.226e+02           -8.018e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 70
 -------------------------------------------
 DONE(2.326e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945028e+04  0.000000e+00   1.648e-03  2.836e+00  
 GE2    -1.945028e+04  -2.004274e-03  9.126e-04  2.496e+00  
 GE3    -1.945028e+04  -1.294220e-04  1.238e-04  2.589e+00  
 GE4    -1.945028e+04  -4.218736e-06  4.328e-05  2.689e+00  
 GE5    -1.945028e+04  -3.353469e-07  1.455e-05  2.688e+00  
 GE6    -1.945028e+04  -3.591953e-08  2.642e-06  2.526e+00  
 GE7    -1.945028e+04  -4.485687e-10  8.105e-07  2.601e+00  
 GE8    -1.945028e+04  -1.361174e-10  1.285e-07  2.702e+00  
 GE9    -1.945028e+04  1.546789e-11   4.922e-08  2.786e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.014e+01     -6.093e+00     2.720e+00      
 -6.093e+00     -1.639e+01     -2.090e+00     
 2.720e+00      -2.090e+00     -9.174e+00     
 TOTAL-PRESSURE: -1.190e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.143e-01           7.159e+02           -8.166e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 71
 -------------------------------------------
 DONE(2.359e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945029e+04  0.000000e+00   1.637e-03  2.726e+00  
 GE2    -1.945029e+04  -1.983641e-03  9.085e-04  2.912e+00  
 GE3    -1.945029e+04  -1.275566e-04  1.229e-04  2.502e+00  
 GE4    -1.945029e+04  -4.109329e-06  4.305e-05  2.516e+00  
 GE5    -1.945029e+04  -3.382332e-07  1.447e-05  2.490e+00  
 GE6    -1.945029e+04  -3.647328e-08  2.609e-06  2.596e+00  
 GE7    -1.945029e+04  -4.300073e-10  8.043e-07  2.581e+00  
 GE8    -1.945029e+04  -1.237431e-10  1.280e-07  2.696e+00  
 GE9    -1.945029e+04  2.165504e-11   4.931e-08  2.477e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.047e+01     -6.110e+00     2.832e+00      
 -6.110e+00     -1.633e+01     -2.228e+00     
 2.832e+00      -2.228e+00     -9.333e+00     
 TOTAL-PRESSURE: -1.205e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.129e-01           7.114e+02           -8.334e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 72
 -------------------------------------------
 DONE(2.391e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945032e+04  0.000000e+00   1.631e-03  2.701e+00  
 GE2    -1.945032e+04  -1.958602e-03  9.070e-04  2.583e+00  
 GE3    -1.945032e+04  -1.267011e-04  1.223e-04  2.514e+00  
 GE4    -1.945032e+04  -4.046802e-06  4.286e-05  2.696e+00  
 GE5    -1.945032e+04  -3.407668e-07  1.442e-05  2.988e+00  
 GE6    -1.945032e+04  -3.277955e-08  2.577e-06  2.881e+00  
 GE7    -1.945032e+04  -3.897908e-10  8.005e-07  2.595e+00  
 GE8    -1.945032e+04  -8.043302e-11  1.280e-07  2.690e+00  
 GE9    -1.945032e+04  0.000000e+00   4.946e-08  2.562e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.083e+01     -6.090e+00     2.894e+00      
 -6.090e+00     -1.628e+01     -2.355e+00     
 2.894e+00      -2.355e+00     -9.558e+00     
 TOTAL-PRESSURE: -1.222e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.122e-01           7.090e+02           -8.525e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 73
 -------------------------------------------
 DONE(2.424e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945036e+04  0.000000e+00   1.632e-03  2.900e+00  
 GE2    -1.945036e+04  -1.929550e-03  9.087e-04  2.493e+00  
 GE3    -1.945036e+04  -1.269079e-04  1.220e-04  2.995e+00  
 GE4    -1.945036e+04  -4.035290e-06  4.273e-05  2.510e+00  
 GE5    -1.945036e+04  -3.359316e-07  1.438e-05  2.501e+00  
 GE6    -1.945036e+04  -3.470994e-08  2.546e-06  2.499e+00  
 GE7    -1.945036e+04  2.109820e-09   7.996e-07  2.583e+00  
 GE8    -1.945036e+04  -4.640366e-11  1.286e-07  2.508e+00  
 GE9    -1.945036e+04  -3.712293e-11  4.969e-08  2.749e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.123e+01     -6.034e+00     2.907e+00      
 -6.034e+00     -1.622e+01     -2.472e+00     
 2.907e+00      -2.472e+00     -9.851e+00     
 TOTAL-PRESSURE: -1.243e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.121e-01           7.087e+02           -8.735e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 74
 -------------------------------------------
 DONE(2.457e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945042e+04  0.000000e+00   1.639e-03  2.818e+00  
 GE2    -1.945042e+04  -1.924379e-03  9.131e-04  2.717e+00  
 GE3    -1.945042e+04  -1.276183e-04  1.222e-04  3.001e+00  
 GE4    -1.945042e+04  -4.068961e-06  4.266e-05  2.532e+00  
 GE5    -1.945042e+04  -3.408287e-07  1.437e-05  2.637e+00  
 GE6    -1.945042e+04  -3.454907e-08  2.517e-06  2.487e+00  
 GE7    -1.945042e+04  7.610201e-10   8.014e-07  2.500e+00  
 GE8    -1.945042e+04  -9.590090e-11  1.297e-07  2.482e+00  
 GE9    -1.945042e+04  0.000000e+00   4.998e-08  2.602e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.164e+01     -5.944e+00     2.873e+00      
 -5.944e+00     -1.616e+01     -2.578e+00     
 2.873e+00      -2.578e+00     -1.021e+01     
 TOTAL-PRESSURE: -1.267e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.126e-01           7.102e+02           -8.963e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 75
 -------------------------------------------
 DONE(2.489e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945048e+04  0.000000e+00   1.650e-03  2.905e+00  
 GE2    -1.945049e+04  -1.912619e-03  9.193e-04  2.506e+00  
 GE3    -1.945049e+04  -1.292513e-04  1.227e-04  2.504e+00  
 GE4    -1.945049e+04  -4.157706e-06  4.267e-05  2.604e+00  
 GE5    -1.945049e+04  -3.373392e-07  1.436e-05  2.711e+00  
 GE6    -1.945049e+04  -3.223198e-08  2.491e-06  2.497e+00  
 GE7    -1.945049e+04  -3.928844e-10  8.056e-07  2.693e+00  
 GE8    -1.945049e+04  -4.640366e-11  1.313e-07  2.620e+00  
 GE9    -1.945049e+04  -3.093578e-12  5.035e-08  2.473e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.207e+01     -5.823e+00     2.799e+00      
 -5.823e+00     -1.609e+01     -2.676e+00     
 2.799e+00      -2.676e+00     -1.062e+01     
 TOTAL-PRESSURE: -1.293e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.135e-01           7.134e+02           -9.205e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 76
 -------------------------------------------
 DONE(2.522e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945056e+04  0.000000e+00   1.662e-03  2.847e+00  
 GE2    -1.945056e+04  -1.900396e-03  9.262e-04  2.510e+00  
 GE3    -1.945056e+04  -1.316004e-04  1.234e-04  2.694e+00  
 GE4    -1.945056e+04  -4.276874e-06  4.274e-05  2.686e+00  
 GE5    -1.945056e+04  -3.367514e-07  1.436e-05  2.490e+00  
 GE6    -1.945056e+04  -3.163183e-08  2.462e-06  2.586e+00  
 GE7    -1.945056e+04  -3.557614e-10  8.107e-07  2.605e+00  
 GE8    -1.945056e+04  -3.402935e-11  1.329e-07  2.506e+00  
 GE9    -1.945056e+04  -2.165504e-11  5.069e-08  2.555e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.250e+01     -5.674e+00     2.689e+00      
 -5.674e+00     -1.601e+01     -2.765e+00     
 2.689e+00      -2.765e+00     -1.108e+01     
 TOTAL-PRESSURE: -1.320e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.148e-01           7.177e+02           -9.454e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 77
 -------------------------------------------
 DONE(2.554e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945064e+04  0.000000e+00   1.673e-03  2.749e+00  
 GE2    -1.945064e+04  -1.909927e-03  9.332e-04  2.788e+00  
 GE3    -1.945064e+04  -1.340448e-04  1.242e-04  2.484e+00  
 GE4    -1.945064e+04  -4.376342e-06  4.284e-05  2.597e+00  
 GE5    -1.945064e+04  -3.379579e-07  1.435e-05  2.515e+00  
 GE6    -1.945064e+04  -3.750035e-08  2.433e-06  2.599e+00  
 GE7    -1.945064e+04  -4.083522e-10  8.167e-07  2.510e+00  
 GE8    -1.945064e+04  -2.474862e-11  1.344e-07  2.497e+00  
 GE9    -1.945064e+04  1.237431e-11   5.101e-08  2.573e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.293e+01     -5.500e+00     2.551e+00      
 -5.500e+00     -1.592e+01     -2.848e+00     
 2.551e+00      -2.848e+00     -1.158e+01     
 TOTAL-PRESSURE: -1.348e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.163e-01           7.228e+02           -9.705e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 78
 -------------------------------------------
 DONE(2.586e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945072e+04  0.000000e+00   1.684e-03  2.816e+00  
 GE2    -1.945073e+04  -1.907720e-03  9.396e-04  2.707e+00  
 GE3    -1.945073e+04  -1.364702e-04  1.250e-04  2.597e+00  
 GE4    -1.945073e+04  -4.491377e-06  4.296e-05  2.627e+00  
 GE5    -1.945073e+04  -3.404513e-07  1.433e-05  2.607e+00  
 GE6    -1.945073e+04  -3.423044e-08  2.405e-06  2.617e+00  
 GE7    -1.945073e+04  -3.681357e-10  8.231e-07  2.799e+00  
 GE8    -1.945073e+04  -1.218870e-09  1.358e-07  2.698e+00  
 GE9    -1.945073e+04  -2.784220e-11  5.128e-08  2.453e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.334e+01     -5.305e+00     2.393e+00      
 -5.305e+00     -1.583e+01     -2.924e+00     
 2.393e+00      -2.924e+00     -1.208e+01     
 TOTAL-PRESSURE: -1.375e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.179e-01           7.282e+02           -9.953e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 79
 -------------------------------------------
 DONE(2.619e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945081e+04  0.000000e+00   1.693e-03  2.806e+00  
 GE2    -1.945081e+04  -1.907710e-03  9.451e-04  2.606e+00  
 GE3    -1.945081e+04  -1.389166e-04  1.255e-04  2.489e+00  
 GE4    -1.945081e+04  -4.566817e-06  4.309e-05  2.705e+00  
 GE5    -1.945081e+04  -3.429571e-07  1.429e-05  2.492e+00  
 GE6    -1.945081e+04  -3.659702e-08  2.372e-06  2.582e+00  
 GE7    -1.945081e+04  -3.557614e-10  8.281e-07  2.700e+00  
 GE8    -1.945081e+04  -1.856147e-11  1.365e-07  2.492e+00  
 GE9    -1.945081e+04  -3.402935e-11  5.141e-08  2.704e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.374e+01     -5.091e+00     2.221e+00      
 -5.091e+00     -1.573e+01     -2.994e+00     
 2.221e+00      -2.994e+00     -1.260e+01     
 TOTAL-PRESSURE: -1.402e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.196e-01           7.337e+02           -1.019e+01          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 80
 -------------------------------------------
 DONE(2.652e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945088e+04  0.000000e+00   1.699e-03  2.703e+00  
 GE2    -1.945089e+04  -1.917483e-03  9.495e-04  2.582e+00  
 GE3    -1.945089e+04  -1.409046e-04  1.258e-04  2.584e+00  
 GE4    -1.945089e+04  -4.612719e-06  4.323e-05  2.689e+00  
 GE5    -1.945089e+04  -3.381992e-07  1.424e-05  2.669e+00  
 GE6    -1.945089e+04  -3.580507e-08  2.341e-06  2.616e+00  
 GE7    -1.945089e+04  -3.650422e-10  8.321e-07  2.491e+00  
 GE8    -1.945089e+04  -1.856147e-11  1.367e-07  2.516e+00  
 GE9    -1.945089e+04  -3.093578e-12  5.140e-08  2.459e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.411e+01     -4.863e+00     2.042e+00      
 -4.863e+00     -1.562e+01     -3.057e+00     
 2.042e+00      -3.057e+00     -1.310e+01     
 TOTAL-PRESSURE: -1.428e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.211e-01           7.388e+02           -1.042e+01          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 81
 -------------------------------------------
 DONE(2.683e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945096e+04  0.000000e+00   1.704e-03  2.798e+00  
 GE2    -1.945096e+04  -1.929565e-03  9.527e-04  2.483e+00  
 GE3    -1.945096e+04  -1.423169e-04  1.259e-04  2.701e+00  
 GE4    -1.945096e+04  -4.631414e-06  4.336e-05  2.490e+00  
 GE5    -1.945096e+04  -3.328225e-07  1.418e-05  2.493e+00  
 GE6    -1.945096e+04  -3.607730e-08  2.312e-06  2.563e+00  
 GE7    -1.945096e+04  -3.712293e-10  8.352e-07  2.834e+00  
 GE8    -1.945096e+04  9.280733e-12   1.365e-07  2.715e+00  
 GE9    -1.945096e+04  6.187155e-12   5.123e-08  2.563e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.445e+01     -4.623e+00     1.861e+00      
 -4.623e+00     -1.551e+01     -3.111e+00     
 1.861e+00      -3.111e+00     -1.357e+01     
 TOTAL-PRESSURE: -1.451e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.225e-01           7.434e+02           -1.064e+01          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 82
 -------------------------------------------
 DONE(2.716e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945102e+04  0.000000e+00   1.706e-03  3.000e+00  
 GE2    -1.945103e+04  -1.928910e-03  9.547e-04  2.480e+00  
 GE3    -1.945103e+04  -1.434670e-04  1.258e-04  2.586e+00  
 GE4    -1.945103e+04  -4.617418e-06  4.350e-05  2.828e+00  
 GE5    -1.945103e+04  -3.414969e-07  1.410e-05  2.682e+00  
 GE6    -1.945103e+04  -3.466972e-08  2.284e-06  2.484e+00  
 GE7    -1.945103e+04  -3.588550e-10  8.365e-07  2.474e+00  
 GE8    -1.945103e+04  2.165504e-11   1.358e-07  2.677e+00  
 GE9    -1.945103e+04  -1.546789e-11  5.085e-08  2.446e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.476e+01     -4.375e+00     1.682e+00      
 -4.375e+00     -1.540e+01     -3.154e+00     
 1.682e+00      -3.154e+00     -1.403e+01     
 TOTAL-PRESSURE: -1.473e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.237e-01           7.475e+02           -1.083e+01          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 83
 -------------------------------------------
 DONE(2.748e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945109e+04  0.000000e+00   1.706e-03  2.998e+00  
 GE2    -1.945109e+04  -1.936338e-03  9.558e-04  2.488e+00  
 GE3    -1.945109e+04  -1.441599e-04  1.255e-04  2.481e+00  
 GE4    -1.945109e+04  -4.590761e-06  4.365e-05  2.580e+00  
 GE5    -1.945109e+04  -3.400708e-07  1.403e-05  2.604e+00  
 GE6    -1.945109e+04  -3.660940e-08  2.264e-06  2.630e+00  
 GE7    -1.945109e+04  -3.186385e-10  8.373e-07  2.685e+00  
 GE8    -1.945109e+04  0.000000e+00   1.348e-07  2.675e+00  
 GE9    -1.945109e+04  2.165504e-11   5.029e-08  2.565e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.504e+01     -4.122e+00     1.508e+00      
 -4.122e+00     -1.529e+01     -3.183e+00     
 1.508e+00      -3.183e+00     -1.445e+01     
 TOTAL-PRESSURE: -1.493e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.248e-01           7.511e+02           -1.101e+01          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 84
 -------------------------------------------
 DONE(2.781e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945114e+04  0.000000e+00   1.705e-03  2.702e+00  
 GE2    -1.945114e+04  -1.946485e-03  9.562e-04  2.578e+00  
 GE3    -1.945114e+04  -1.444445e-04  1.252e-04  2.596e+00  
 GE4    -1.945114e+04  -4.545288e-06  4.381e-05  2.487e+00  
 GE5    -1.945114e+04  -3.447390e-07  1.398e-05  2.907e+00  
 GE6    -1.945114e+04  -3.635882e-08  2.251e-06  2.570e+00  
 GE7    -1.945114e+04  -3.433871e-10  8.375e-07  2.480e+00  
 GE8    -1.945114e+04  -9.961320e-10  1.336e-07  2.575e+00  
 GE9    -1.945114e+04  -5.320953e-10  4.960e-08  2.653e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.529e+01     -3.867e+00     1.340e+00      
 -3.867e+00     -1.519e+01     -3.196e+00     
 1.340e+00      -3.196e+00     -1.483e+01     
 TOTAL-PRESSURE: -1.510e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.257e-01           7.543e+02           -1.117e+01          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 85
 -------------------------------------------
 DONE(2.813e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945120e+04  0.000000e+00   1.704e-03  2.695e+00  
 GE2    -1.945120e+04  -1.955397e-03  9.562e-04  2.593e+00  
 GE3    -1.945120e+04  -1.446730e-04  1.250e-04  3.008e+00  
 GE4    -1.945120e+04  -4.505016e-06  4.398e-05  2.816e+00  
 GE5    -1.945120e+04  -3.436563e-07  1.393e-05  2.674e+00  
 GE6    -1.945120e+04  -3.809122e-08  2.246e-06  2.487e+00  
 GE7    -1.945120e+04  -3.402935e-10  8.377e-07  2.589e+00  
 GE8    -1.945120e+04  -6.187155e-12  1.324e-07  2.679e+00  
 GE9    -1.945120e+04  2.784220e-11   4.890e-08  2.574e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.550e+01     -3.614e+00     1.182e+00      
 -3.614e+00     -1.509e+01     -3.190e+00     
 1.182e+00      -3.190e+00     -1.518e+01     
 TOTAL-PRESSURE: -1.526e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.266e-01           7.571e+02           -1.131e+01          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 86
 -------------------------------------------
 DONE(2.846e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945125e+04  0.000000e+00   1.702e-03  2.682e+00  
 GE2    -1.945125e+04  -1.961967e-03  9.559e-04  2.681e+00  
 GE3    -1.945125e+04  -1.446889e-04  1.249e-04  2.685e+00  
 GE4    -1.945125e+04  -4.483169e-06  4.417e-05  2.691e+00  
 GE5    -1.945125e+04  -3.510870e-07  1.392e-05  2.607e+00  
 GE6    -1.945125e+04  -3.758697e-08  2.250e-06  2.479e+00  
 GE7    -1.945125e+04  -3.619486e-10  8.386e-07  2.597e+00  
 GE8    -1.945125e+04  1.546789e-11   1.313e-07  2.696e+00  
 GE9    -1.945125e+04  2.165504e-11   4.839e-08  2.754e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.568e+01     -3.367e+00     1.033e+00      
 -3.367e+00     -1.500e+01     -3.164e+00     
 1.033e+00      -3.164e+00     -1.550e+01     
 TOTAL-PRESSURE: -1.539e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.274e-01           7.598e+02           -1.143e+01          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 87
 -------------------------------------------
 DONE(2.879e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945130e+04  0.000000e+00   1.702e-03  2.835e+00  
 GE2    -1.945130e+04  -1.969872e-03  9.558e-04  2.685e+00  
 GE3    -1.945130e+04  -1.447830e-04  1.251e-04  2.480e+00  
 GE4    -1.945130e+04  -4.475664e-06  4.436e-05  2.884e+00  
 GE5    -1.945130e+04  -3.462146e-07  1.394e-05  2.487e+00  
 GE6    -1.945130e+04  -3.894814e-08  2.262e-06  2.469e+00  
 GE7    -1.945130e+04  -3.743229e-10  8.409e-07  2.775e+00  
 GE8    -1.945130e+04  5.259082e-11   1.306e-07  2.499e+00  
 GE9    -1.945130e+04  -9.280733e-12  4.825e-08  2.676e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.583e+01     -3.129e+00     8.954e-01      
 -3.129e+00     -1.492e+01     -3.117e+00     
 8.954e-01      -3.117e+00     -1.578e+01     
 TOTAL-PRESSURE: -1.551e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.282e-01           7.625e+02           -1.153e+01          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 88
 -------------------------------------------
 DONE(2.911e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945135e+04  0.000000e+00   1.702e-03  2.688e+00  
 GE2    -1.945135e+04  -1.987446e-03  9.560e-04  2.697e+00  
 GE3    -1.945135e+04  -1.450211e-04  1.256e-04  2.795e+00  
 GE4    -1.945135e+04  -4.490161e-06  4.457e-05  2.567e+00  
 GE5    -1.945135e+04  -3.438883e-07  1.399e-05  2.564e+00  
 GE6    -1.945135e+04  -3.862022e-08  2.280e-06  2.473e+00  
 GE7    -1.945135e+04  -3.526678e-10  8.442e-07  2.469e+00  
 GE8    -1.945135e+04  4.949724e-11   1.302e-07  2.571e+00  
 GE9    -1.945135e+04  -1.546789e-11  4.840e-08  2.439e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.596e+01     -2.904e+00     7.681e-01      
 -2.904e+00     -1.486e+01     -3.049e+00     
 7.681e-01      -3.049e+00     -1.603e+01     
 TOTAL-PRESSURE: -1.562e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.291e-01           7.654e+02           -1.162e+01          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 89
 -------------------------------------------
 DONE(2.943e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945140e+04  0.000000e+00   1.705e-03  2.683e+00  
 GE2    -1.945140e+04  -2.000532e-03  9.568e-04  2.690e+00  
 GE3    -1.945140e+04  -1.455843e-04  1.265e-04  2.570e+00  
 GE4    -1.945140e+04  -4.525279e-06  4.477e-05  2.701e+00  
 GE5    -1.945140e+04  -3.423910e-07  1.406e-05  2.482e+00  
 GE6    -1.945140e+04  -3.855835e-08  2.305e-06  2.695e+00  
 GE7    -1.945140e+04  -3.402935e-10  8.484e-07  2.576e+00  
 GE8    -1.945140e+04  2.165504e-11   1.301e-07  2.470e+00  
 GE9    -1.945140e+04  -6.187155e-12  4.870e-08  2.461e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.606e+01     -2.696e+00     6.506e-01      
 -2.696e+00     -1.481e+01     -2.961e+00     
 6.506e-01      -2.961e+00     -1.624e+01     
 TOTAL-PRESSURE: -1.571e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.300e-01           7.686e+02           -1.170e+01          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 90
 -------------------------------------------
 DONE(2.975e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945145e+04  0.000000e+00   1.708e-03  2.982e+00  
 GE2    -1.945146e+04  -2.027940e-03  9.578e-04  2.497e+00  
 GE3    -1.945146e+04  -1.464647e-04  1.277e-04  2.771e+00  
 GE4    -1.945146e+04  -4.591014e-06  4.498e-05  2.668e+00  
 GE5    -1.945146e+04  -3.421373e-07  1.416e-05  2.458e+00  
 GE6    -1.945146e+04  -4.184064e-08  2.332e-06  2.479e+00  
 GE7    -1.945146e+04  -3.990715e-10  8.533e-07  2.675e+00  
 GE8    -1.945146e+04  4.640366e-11   1.304e-07  2.465e+00  
 GE9    -1.945146e+04  -9.280733e-12  4.904e-08  2.759e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.614e+01     -2.508e+00     5.418e-01      
 -2.508e+00     -1.478e+01     -2.855e+00     
 5.418e-01      -2.855e+00     -1.642e+01     
 TOTAL-PRESSURE: -1.578e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.311e-01           7.721e+02           -1.175e+01          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 91
 -------------------------------------------
 DONE(3.008e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945151e+04  0.000000e+00   1.713e-03  2.798e+00  
 GE2    -1.945151e+04  -2.051682e-03  9.592e-04  2.591e+00  
 GE3    -1.945151e+04  -1.477455e-04  1.291e-04  2.578e+00  
 GE4    -1.945151e+04  -4.691191e-06  4.519e-05  2.674e+00  
 GE5    -1.945151e+04  -3.346942e-07  1.428e-05  2.470e+00  
 GE6    -1.945151e+04  -4.097134e-08  2.360e-06  2.566e+00  
 GE7    -1.945151e+04  -4.145394e-10  8.582e-07  2.971e+00  
 GE8    -1.945151e+04  4.021651e-11   1.308e-07  2.466e+00  
 GE9    -1.945151e+04  6.187155e-12   4.927e-08  2.479e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.620e+01     -2.342e+00     4.405e-01      
 -2.342e+00     -1.477e+01     -2.733e+00     
 4.405e-01      -2.733e+00     -1.656e+01     
 TOTAL-PRESSURE: -1.584e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.322e-01           7.759e+02           -1.180e+01          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 92
 -------------------------------------------
 DONE(3.040e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945156e+04  0.000000e+00   1.719e-03  2.770e+00  
 GE2    -1.945157e+04  -2.086007e-03  9.610e-04  2.680e+00  
 GE3    -1.945157e+04  -1.492653e-04  1.308e-04  2.668e+00  
 GE4    -1.945157e+04  -4.835404e-06  4.543e-05  2.777e+00  
 GE5    -1.945157e+04  -3.318388e-07  1.440e-05  2.594e+00  
 GE6    -1.945157e+04  -4.009895e-08  2.389e-06  2.486e+00  
 GE7    -1.945157e+04  -4.176330e-10  8.632e-07  2.559e+00  
 GE8    -1.945157e+04  3.402935e-11   1.314e-07  2.496e+00  
 GE9    -1.945157e+04  1.237431e-11   4.941e-08  2.460e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.624e+01     -2.201e+00     3.455e-01      
 -2.201e+00     -1.478e+01     -2.598e+00     
 3.455e-01      -2.598e+00     -1.665e+01     
 TOTAL-PRESSURE: -1.589e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.334e-01           7.800e+02           -1.182e+01          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 93
 -------------------------------------------
 DONE(3.073e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945162e+04  0.000000e+00   1.727e-03  2.691e+00  
 GE2    -1.945162e+04  -2.119875e-03  9.631e-04  2.469e+00  
 GE3    -1.945162e+04  -1.511723e-04  1.325e-04  2.479e+00  
 GE4    -1.945162e+04  -4.998996e-06  4.568e-05  2.672e+00  
 GE5    -1.945162e+04  -3.333020e-07  1.453e-05  2.700e+00  
 GE6    -1.945162e+04  -4.077026e-08  2.414e-06  2.482e+00  
 GE7    -1.945162e+04  -4.423816e-10  8.681e-07  2.465e+00  
 GE8    -1.945162e+04  6.187155e-11   1.322e-07  2.480e+00  
 GE9    -1.945162e+04  9.280733e-12   4.945e-08  2.484e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.626e+01     -2.086e+00     2.549e-01      
 -2.086e+00     -1.479e+01     -2.452e+00     
 2.549e-01      -2.452e+00     -1.670e+01     
 TOTAL-PRESSURE: -1.592e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.347e-01           7.843e+02           -1.183e+01          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 94
 -------------------------------------------
 DONE(3.104e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945168e+04  0.000000e+00   1.736e-03  2.795e+00  
 GE2    -1.945168e+04  -2.150750e-03  9.654e-04  2.495e+00  
 GE3    -1.945168e+04  -1.531626e-04  1.343e-04  2.474e+00  
 GE4    -1.945168e+04  -5.168103e-06  4.595e-05  2.486e+00  
 GE5    -1.945168e+04  -3.339177e-07  1.465e-05  2.577e+00  
 GE6    -1.945168e+04  -4.126832e-08  2.437e-06  2.681e+00  
 GE7    -1.945168e+04  -4.547559e-10  8.728e-07  2.848e+00  
 GE8    -1.945168e+04  3.093578e-11   1.331e-07  2.467e+00  
 GE9    -1.945168e+04  0.000000e+00   4.940e-08  2.575e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.627e+01     -1.998e+00     1.671e-01      
 -1.998e+00     -1.482e+01     -2.298e+00     
 1.671e-01      -2.298e+00     -1.669e+01     
 TOTAL-PRESSURE: -1.593e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.360e-01           7.887e+02           -1.181e+01          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 95
 -------------------------------------------
 DONE(3.137e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945173e+04  0.000000e+00   1.746e-03  2.674e+00  
 GE2    -1.945174e+04  -2.181159e-03  9.680e-04  2.596e+00  
 GE3    -1.945174e+04  -1.552938e-04  1.359e-04  2.763e+00  
 GE4    -1.945174e+04  -5.331700e-06  4.623e-05  2.467e+00  
 GE5    -1.945174e+04  -3.375093e-07  1.477e-05  2.467e+00  
 GE6    -1.945174e+04  -4.302857e-08  2.456e-06  2.576e+00  
 GE7    -1.945174e+04  -4.856917e-10  8.770e-07  2.595e+00  
 GE8    -1.945174e+04  1.237431e-11   1.340e-07  2.472e+00  
 GE9    -1.945174e+04  1.252899e-09   4.928e-08  2.449e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.626e+01     -1.935e+00     8.048e-02      
 -1.935e+00     -1.485e+01     -2.140e+00     
 8.048e-02      -2.140e+00     -1.664e+01     
 TOTAL-PRESSURE: -1.591e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.373e-01           7.930e+02           -1.178e+01          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 96
 -------------------------------------------
 DONE(3.169e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945179e+04  0.000000e+00   1.755e-03  2.685e+00  
 GE2    -1.945179e+04  -2.211864e-03  9.708e-04  2.478e+00  
 GE3    -1.945179e+04  -1.572272e-04  1.374e-04  2.458e+00  
 GE4    -1.945179e+04  -5.494089e-06  4.650e-05  2.466e+00  
 GE5    -1.945179e+04  -3.398388e-07  1.488e-05  2.840e+00  
 GE6    -1.945179e+04  -4.464651e-08  2.473e-06  2.682e+00  
 GE7    -1.945179e+04  -4.578495e-10  8.810e-07  2.679e+00  
 GE8    -1.945179e+04  7.424586e-11   1.350e-07  2.752e+00  
 GE9    -1.945179e+04  -3.402935e-11  4.912e-08  2.546e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.623e+01     -1.897e+00     -6.424e-03     
 -1.897e+00     -1.488e+01     -1.981e+00     
 -6.424e-03     -1.981e+00     -1.652e+01     
 TOTAL-PRESSURE: -1.588e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.385e-01           7.970e+02           -1.172e+01          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 97
 -------------------------------------------
 DONE(3.201e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945183e+04  0.000000e+00   1.763e-03  2.671e+00  
 GE2    -1.945184e+04  -2.246841e-03  9.733e-04  2.575e+00  
 GE3    -1.945184e+04  -1.591642e-04  1.387e-04  2.551e+00  
 GE4    -1.945184e+04  -5.630757e-06  4.674e-05  2.746e+00  
 GE5    -1.945184e+04  -3.426354e-07  1.498e-05  2.557e+00  
 GE6    -1.945184e+04  -4.393499e-08  2.487e-06  2.443e+00  
 GE7    -1.945184e+04  -4.609431e-10  8.847e-07  2.551e+00  
 GE8    -1.945184e+04  5.568440e-11   1.361e-07  2.462e+00  
 GE9    -1.945184e+04  -2.474862e-11  4.895e-08  2.748e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.618e+01     -1.882e+00     -9.531e-02     
 -1.882e+00     -1.490e+01     -1.823e+00     
 -9.531e-02     -1.823e+00     -1.634e+01     
 TOTAL-PRESSURE: -1.581e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.396e-01           8.006e+02           -1.163e+01          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 98
 -------------------------------------------
 DONE(3.233e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945188e+04  0.000000e+00   1.771e-03  2.705e+00  
 GE2    -1.945188e+04  -2.281197e-03  9.753e-04  2.759e+00  
 GE3    -1.945188e+04  -1.608975e-04  1.396e-04  2.579e+00  
 GE4    -1.945188e+04  -5.732696e-06  4.697e-05  2.609e+00  
 GE5    -1.945188e+04  -3.429695e-07  1.506e-05  2.474e+00  
 GE6    -1.945188e+04  -4.426909e-08  2.496e-06  2.893e+00  
 GE7    -1.945188e+04  -3.402935e-10  8.876e-07  2.567e+00  
 GE8    -1.945188e+04  8.043302e-11   1.369e-07  2.566e+00  
 GE9    -1.945188e+04  -1.546789e-11  4.874e-08  2.532e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.611e+01     -1.885e+00     -1.874e-01     
 -1.885e+00     -1.491e+01     -1.670e+00     
 -1.874e-01     -1.670e+00     -1.610e+01     
 TOTAL-PRESSURE: -1.571e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.405e-01           8.036e+02           -1.151e+01          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 99
 -------------------------------------------
 DONE(3.266e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945191e+04  0.000000e+00   1.776e-03  2.793e+00  
 GE2    -1.945191e+04  -2.310627e-03  9.766e-04  2.663e+00  
 GE3    -1.945191e+04  -1.622265e-04  1.403e-04  2.664e+00  
 GE4    -1.945191e+04  -5.795041e-06  4.719e-05  2.468e+00  
 GE5    -1.945191e+04  -3.464250e-07  1.512e-05  2.555e+00  
 GE6    -1.945191e+04  -4.310900e-08  2.501e-06  2.688e+00  
 GE7    -1.945191e+04  -4.702238e-10  8.893e-07  2.577e+00  
 GE8    -1.945191e+04  5.259082e-11   1.375e-07  2.882e+00  
 GE9    -1.945191e+04  3.093578e-12   4.849e-08  2.480e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.601e+01     -1.905e+00     -2.839e-01     
 -1.905e+00     -1.491e+01     -1.524e+00     
 -2.839e-01     -1.524e+00     -1.579e+01     
 TOTAL-PRESSURE: -1.557e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.411e-01           8.058e+02           -1.137e+01          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 100
 -------------------------------------------
 DONE(3.298e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945194e+04  0.000000e+00   1.780e-03  2.697e+00  
 GE2    -1.945194e+04  -2.343607e-03  9.770e-04  2.573e+00  
 GE3    -1.945194e+04  -1.630427e-04  1.406e-04  2.464e+00  
 GE4    -1.945194e+04  -5.787691e-06  4.736e-05  2.676e+00  
 GE5    -1.945194e+04  -3.498434e-07  1.516e-05  2.818e+00  
 GE6    -1.945194e+04  -4.334102e-08  2.504e-06  2.760e+00  
 GE7    -1.945194e+04  2.657383e-09   8.901e-07  2.681e+00  
 GE8    -1.945194e+04  3.712293e-11   1.377e-07  2.566e+00  
 GE9    -1.945194e+04  6.187155e-12   4.822e-08  2.449e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.589e+01     -1.938e+00     -3.855e-01     
 -1.938e+00     -1.488e+01     -1.391e+00     
 -3.855e-01     -1.391e+00     -1.543e+01     
 TOTAL-PRESSURE: -1.540e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.416e-01           8.072e+02           -1.119e+01          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 101
 -------------------------------------------
 DONE(3.331e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945196e+04  0.000000e+00   1.781e-03  2.670e+00  
 GE2    -1.945196e+04  -2.371872e-03  9.764e-04  2.565e+00  
 GE3    -1.945196e+04  -1.634061e-04  1.406e-04  2.466e+00  
 GE4    -1.945196e+04  -5.748903e-06  4.749e-05  2.775e+00  
 GE5    -1.945196e+04  -3.534412e-07  1.519e-05  2.574e+00  
 GE6    -1.945196e+04  -4.423816e-08  2.504e-06  2.672e+00  
 GE7    -1.945196e+04  2.258312e-10   8.896e-07  2.497e+00  
 GE8    -1.945196e+04  5.568440e-11   1.377e-07  2.684e+00  
 GE9    -1.945196e+04  1.546789e-11   4.793e-08  2.482e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.575e+01     -1.980e+00     -4.922e-01     
 -1.980e+00     -1.484e+01     -1.272e+00     
 -4.922e-01     -1.272e+00     -1.500e+01     
 TOTAL-PRESSURE: -1.520e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.417e-01           8.076e+02           -1.098e+01          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 102
 -------------------------------------------
 DONE(3.363e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945197e+04  0.000000e+00   1.781e-03  2.778e+00  
 GE2    -1.945197e+04  -2.388681e-03  9.749e-04  2.556e+00  
 GE3    -1.945197e+04  -1.632198e-04  1.403e-04  2.566e+00  
 GE4    -1.945197e+04  -5.672251e-06  4.760e-05  2.588e+00  
 GE5    -1.945197e+04  -3.586230e-07  1.520e-05  2.489e+00  
 GE6    -1.945197e+04  -4.197985e-08  2.502e-06  2.604e+00  
 GE7    -1.945197e+04  -4.331009e-10  8.880e-07  2.581e+00  
 GE8    -1.945197e+04  4.021651e-11   1.372e-07  2.670e+00  
 GE9    -1.945197e+04  3.093578e-12   4.758e-08  2.727e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.558e+01     -2.028e+00     -6.037e-01     
 -2.028e+00     -1.477e+01     -1.172e+00     
 -6.037e-01     -1.172e+00     -1.452e+01     
 TOTAL-PRESSURE: -1.496e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.415e-01           8.071e+02           -1.074e+01          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 103
 -------------------------------------------
 DONE(3.396e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945197e+04  0.000000e+00   1.778e-03  2.957e+00  
 GE2    -1.945197e+04  -2.403662e-03  9.722e-04  2.587e+00  
 GE3    -1.945197e+04  -1.627626e-04  1.396e-04  2.465e+00  
 GE4    -1.945197e+04  -5.559774e-06  4.766e-05  2.694e+00  
 GE5    -1.945197e+04  -3.642100e-07  1.519e-05  2.761e+00  
 GE6    -1.945197e+04  -4.349879e-08  2.496e-06  2.573e+00  
 GE7    -1.945197e+04  1.447794e-09   8.854e-07  2.571e+00  
 GE8    -1.945197e+04  3.712293e-11   1.364e-07  2.573e+00  
 GE9    -1.945197e+04  6.187155e-12   4.719e-08  2.568e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.538e+01     -2.077e+00     -7.192e-01     
 -2.077e+00     -1.467e+01     -1.093e+00     
 -7.192e-01     -1.093e+00     -1.400e+01     
 TOTAL-PRESSURE: -1.468e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.411e-01           8.057e+02           -1.048e+01          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 104
 -------------------------------------------
 DONE(3.428e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945197e+04  0.000000e+00   1.774e-03  2.769e+00  
 GE2    -1.945197e+04  -2.423174e-03  9.688e-04  2.801e+00  
 GE3    -1.945197e+04  -1.619964e-04  1.387e-04  2.788e+00  
 GE4    -1.945197e+04  -5.396718e-06  4.769e-05  2.448e+00  
 GE5    -1.945197e+04  -3.648411e-07  1.517e-05  2.629e+00  
 GE6    -1.945197e+04  -4.574473e-08  2.488e-06  2.563e+00  
 GE7    -1.945197e+04  -4.207265e-10  8.815e-07  2.577e+00  
 GE8    -1.945197e+04  6.187155e-11   1.354e-07  2.447e+00  
 GE9    -1.945197e+04  -6.187155e-12  4.678e-08  2.445e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.515e+01     -2.125e+00     -8.370e-01     
 -2.125e+00     -1.455e+01     -1.038e+00     
 -8.370e-01     -1.038e+00     -1.343e+01     
 TOTAL-PRESSURE: -1.438e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.405e-01           8.035e+02           -1.018e+01          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 105
 -------------------------------------------
 DONE(3.460e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945195e+04  0.000000e+00   1.768e-03  2.797e+00  
 GE2    -1.945196e+04  -2.438118e-03  9.648e-04  2.568e+00  
 GE3    -1.945196e+04  -1.608148e-04  1.376e-04  2.729e+00  
 GE4    -1.945196e+04  -5.214395e-06  4.767e-05  2.563e+00  
 GE5    -1.945196e+04  -3.760398e-07  1.514e-05  2.479e+00  
 GE6    -1.945196e+04  -4.537660e-08  2.479e-06  2.552e+00  
 GE7    -1.945196e+04  -4.547559e-10  8.766e-07  2.445e+00  
 GE8    -1.945196e+04  4.640366e-11   1.341e-07  2.490e+00  
 GE9    -1.945196e+04  2.474862e-11   4.634e-08  2.471e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.490e+01     -2.169e+00     -9.551e-01     
 -2.169e+00     -1.441e+01     -1.010e+00     
 -9.551e-01     -1.010e+00     -1.282e+01     
 TOTAL-PRESSURE: -1.404e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.396e-01           8.006e+02           -9.866e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 106
 -------------------------------------------
 DONE(3.492e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945194e+04  0.000000e+00   1.762e-03  3.070e+00  
 GE2    -1.945194e+04  -2.442892e-03  9.607e-04  2.446e+00  
 GE3    -1.945194e+04  -1.595310e-04  1.363e-04  2.853e+00  
 GE4    -1.945194e+04  -5.010893e-06  4.762e-05  2.555e+00  
 GE5    -1.945194e+04  -3.773020e-07  1.510e-05  2.558e+00  
 GE6    -1.945194e+04  -4.439284e-08  2.466e-06  2.541e+00  
 GE7    -1.945194e+04  -4.083522e-10  8.706e-07  2.653e+00  
 GE8    -1.945194e+04  3.093578e-11   1.326e-07  2.637e+00  
 GE9    -1.945194e+04  -1.856147e-11  4.586e-08  2.433e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.462e+01     -2.205e+00     -1.071e+00     
 -2.205e+00     -1.425e+01     -1.010e+00     
 -1.071e+00     -1.010e+00     -1.220e+01     
 TOTAL-PRESSURE: -1.369e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.386e-01           7.971e+02           -9.528e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 107
 -------------------------------------------
 DONE(3.524e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945191e+04  0.000000e+00   1.755e-03  2.848e+00  
 GE2    -1.945192e+04  -2.439479e-03  9.563e-04  2.541e+00  
 GE3    -1.945192e+04  -1.580986e-04  1.348e-04  2.459e+00  
 GE4    -1.945192e+04  -4.787364e-06  4.753e-05  2.455e+00  
 GE5    -1.945192e+04  -3.816330e-07  1.505e-05  2.543e+00  
 GE6    -1.945192e+04  -4.407111e-08  2.452e-06  2.445e+00  
 GE7    -1.945192e+04  -4.300073e-10  8.640e-07  2.660e+00  
 GE8    -1.945192e+04  1.856147e-11   1.310e-07  2.540e+00  
 GE9    -1.945192e+04  -3.093578e-12  4.537e-08  2.422e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.431e+01     -2.230e+00     -1.182e+00     
 -2.230e+00     -1.407e+01     -1.037e+00     
 -1.182e+00     -1.037e+00     -1.155e+01     
 TOTAL-PRESSURE: -1.331e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.374e-01           7.933e+02           -9.175e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 108
 -------------------------------------------
 DONE(3.556e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945189e+04  0.000000e+00   1.748e-03  2.768e+00  
 GE2    -1.945189e+04  -2.436072e-03  9.520e-04  2.577e+00  
 GE3    -1.945189e+04  -1.567369e-04  1.334e-04  2.623e+00  
 GE4    -1.945189e+04  -4.574185e-06  4.741e-05  2.526e+00  
 GE5    -1.945189e+04  -3.840305e-07  1.498e-05  2.544e+00  
 GE6    -1.945189e+04  -4.252432e-08  2.436e-06  2.655e+00  
 GE7    -1.945189e+04  -3.743229e-10  8.571e-07  2.669e+00  
 GE8    -1.945189e+04  1.856147e-11   1.296e-07  2.579e+00  
 GE9    -1.945189e+04  3.093578e-11   4.488e-08  2.451e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.399e+01     -2.244e+00     -1.286e+00     
 -2.244e+00     -1.388e+01     -1.092e+00     
 -1.286e+00     -1.092e+00     -1.091e+01     
 TOTAL-PRESSURE: -1.293e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.362e-01           7.893e+02           -8.809e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 109
 -------------------------------------------
 DONE(3.589e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945187e+04  0.000000e+00   1.743e-03  2.689e+00  
 GE2    -1.945187e+04  -2.431674e-03  9.488e-04  2.710e+00  
 GE3    -1.945187e+04  -1.553880e-04  1.320e-04  2.608e+00  
 GE4    -1.945187e+04  -4.380976e-06  4.725e-05  2.469e+00  
 GE5    -1.945187e+04  -3.884172e-07  1.492e-05  2.620e+00  
 GE6    -1.945187e+04  -4.462486e-08  2.419e-06  2.426e+00  
 GE7    -1.945187e+04  1.160092e-09   8.499e-07  2.537e+00  
 GE8    -1.945187e+04  5.259082e-11   1.283e-07  2.729e+00  
 GE9    -1.945187e+04  -1.546789e-11  4.440e-08  2.404e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.365e+01     -2.244e+00     -1.380e+00     
 -2.244e+00     -1.368e+01     -1.173e+00     
 -1.380e+00     -1.173e+00     -1.027e+01     
 TOTAL-PRESSURE: -1.253e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.350e-01           7.852e+02           -8.435e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 110
 -------------------------------------------
 DONE(3.621e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945184e+04  0.000000e+00   1.738e-03  2.688e+00  
 GE2    -1.945184e+04  -2.423288e-03  9.461e-04  2.634e+00  
 GE3    -1.945184e+04  -1.541224e-04  1.308e-04  2.658e+00  
 GE4    -1.945184e+04  -4.194121e-06  4.707e-05  2.424e+00  
 GE5    -1.945184e+04  -3.862579e-07  1.484e-05  2.465e+00  
 GE6    -1.945184e+04  -4.191488e-08  2.401e-06  2.432e+00  
 GE7    -1.945184e+04  -3.866972e-10  8.427e-07  2.653e+00  
 GE8    -1.945184e+04  0.000000e+00   1.271e-07  2.546e+00  
 GE9    -1.945184e+04  1.856147e-11   4.392e-08  2.467e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.329e+01     -2.230e+00     -1.464e+00     
 -2.230e+00     -1.348e+01     -1.277e+00     
 -1.464e+00     -1.277e+00     -9.639e+00     
 TOTAL-PRESSURE: -1.213e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.338e-01           7.812e+02           -8.059e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 111
 -------------------------------------------
 DONE(3.652e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945181e+04  0.000000e+00   1.734e-03  3.076e+00  
 GE2    -1.945182e+04  -2.417216e-03  9.440e-04  2.438e+00  
 GE3    -1.945182e+04  -1.530547e-04  1.296e-04  2.537e+00  
 GE4    -1.945182e+04  -4.042616e-06  4.688e-05  2.527e+00  
 GE5    -1.945182e+04  -3.892556e-07  1.477e-05  2.555e+00  
 GE6    -1.945182e+04  -4.176639e-08  2.383e-06  2.538e+00  
 GE7    -1.945182e+04  -3.928844e-10  8.359e-07  2.437e+00  
 GE8    -1.945182e+04  3.093578e-11   1.263e-07  2.447e+00  
 GE9    -1.945182e+04  3.093578e-11   4.347e-08  2.517e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.291e+01     -2.201e+00     -1.535e+00     
 -2.201e+00     -1.327e+01     -1.401e+00     
 -1.535e+00     -1.401e+00     -9.035e+00     
 TOTAL-PRESSURE: -1.174e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.327e-01           7.774e+02           -7.682e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 112
 -------------------------------------------
 DONE(3.684e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945179e+04  0.000000e+00   1.730e-03  2.680e+00  
 GE2    -1.945179e+04  -2.404232e-03  9.427e-04  2.455e+00  
 GE3    -1.945179e+04  -1.520902e-04  1.287e-04  2.670e+00  
 GE4    -1.945179e+04  -3.926180e-06  4.668e-05  2.636e+00  
 GE5    -1.945179e+04  -3.904342e-07  1.469e-05  2.525e+00  
 GE6    -1.945179e+04  -4.146631e-08  2.362e-06  2.647e+00  
 GE7    -1.945179e+04  1.079659e-09   8.295e-07  2.518e+00  
 GE8    -1.945179e+04  3.093578e-11   1.256e-07  2.434e+00  
 GE9    -1.945179e+04  -6.187155e-12  4.306e-08  2.515e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.252e+01     -2.158e+00     -1.592e+00     
 -2.158e+00     -1.306e+01     -1.540e+00     
 -1.592e+00     -1.540e+00     -8.459e+00     
 TOTAL-PRESSURE: -1.135e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.316e-01           7.740e+02           -7.310e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 113
 -------------------------------------------
 DONE(3.716e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945177e+04  0.000000e+00   1.728e-03  2.655e+00  
 GE2    -1.945177e+04  -2.398244e-03  9.421e-04  2.550e+00  
 GE3    -1.945177e+04  -1.513821e-04  1.278e-04  2.549e+00  
 GE4    -1.945177e+04  -3.841122e-06  4.648e-05  2.552e+00  
 GE5    -1.945177e+04  -3.969926e-07  1.461e-05  2.529e+00  
 GE6    -1.945177e+04  -3.739826e-08  2.342e-06  2.533e+00  
 GE7    -1.945177e+04  -3.557614e-10  8.238e-07  2.453e+00  
 GE8    -1.945177e+04  -1.856147e-11  1.254e-07  2.436e+00  
 GE9    -1.945177e+04  1.237431e-11   4.270e-08  2.511e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.213e+01     -2.100e+00     -1.636e+00     
 -2.100e+00     -1.286e+01     -1.691e+00     
 -1.636e+00     -1.691e+00     -7.918e+00     
 TOTAL-PRESSURE: -1.097e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.308e-01           7.711e+02           -6.944e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 114
 -------------------------------------------
 DONE(3.747e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945175e+04  0.000000e+00   1.726e-03  2.756e+00  
 GE2    -1.945176e+04  -2.386506e-03  9.416e-04  2.535e+00  
 GE3    -1.945176e+04  -1.508584e-04  1.271e-04  2.637e+00  
 GE4    -1.945176e+04  -3.790892e-06  4.629e-05  2.533e+00  
 GE5    -1.945176e+04  -3.986755e-07  1.455e-05  2.748e+00  
 GE6    -1.945176e+04  -3.831705e-08  2.322e-06  2.440e+00  
 GE7    -1.945176e+04  -7.362715e-10  8.184e-07  2.539e+00  
 GE8    -1.945176e+04  4.021651e-11   1.254e-07  2.426e+00  
 GE9    -1.945176e+04  6.187155e-12   4.242e-08  2.627e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.172e+01     -2.029e+00     -1.666e+00     
 -2.029e+00     -1.265e+01     -1.848e+00     
 -1.666e+00     -1.848e+00     -7.416e+00     
 TOTAL-PRESSURE: -1.060e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.300e-01           7.686e+02           -6.588e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 115
 -------------------------------------------
 DONE(3.779e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945174e+04  0.000000e+00   1.722e-03  2.977e+00  
 GE2    -1.945174e+04  -2.371117e-03  9.409e-04  2.570e+00  
 GE3    -1.945174e+04  -1.503990e-04  1.265e-04  2.538e+00  
 GE4    -1.945174e+04  -3.776670e-06  4.611e-05  2.429e+00  
 GE5    -1.945174e+04  -3.979578e-07  1.449e-05  2.450e+00  
 GE6    -1.945174e+04  -3.905951e-08  2.302e-06  2.629e+00  
 GE7    -1.945174e+04  -3.124513e-10  8.133e-07  2.741e+00  
 GE8    -1.945174e+04  -4.083522e-10  1.257e-07  2.452e+00  
 GE9    -1.945174e+04  -6.187155e-12  4.223e-08  2.633e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.132e+01     -1.947e+00     -1.683e+00     
 -1.947e+00     -1.245e+01     -2.007e+00     
 -1.683e+00     -2.007e+00     -6.955e+00     
 TOTAL-PRESSURE: -1.024e+01 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.295e-01           7.667e+02           -6.243e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 116
 -------------------------------------------
 DONE(3.811e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945173e+04  0.000000e+00   1.718e-03  2.942e+00  
 GE2    -1.945173e+04  -2.362179e-03  9.404e-04  2.427e+00  
 GE3    -1.945173e+04  -1.498953e-04  1.261e-04  2.431e+00  
 GE4    -1.945173e+04  -3.790242e-06  4.592e-05  2.425e+00  
 GE5    -1.945173e+04  -3.973515e-07  1.444e-05  2.522e+00  
 GE6    -1.945173e+04  -3.843770e-08  2.283e-06  2.528e+00  
 GE7    -1.945173e+04  -3.372000e-10  8.087e-07  2.545e+00  
 GE8    -1.945173e+04  0.000000e+00   1.263e-07  2.526e+00  
 GE9    -1.945173e+04  -2.165504e-11  4.212e-08  2.731e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.092e+01     -1.856e+00     -1.687e+00     
 -1.856e+00     -1.226e+01     -2.161e+00     
 -1.687e+00     -2.161e+00     -6.536e+00     
 TOTAL-PRESSURE: -9.905e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.291e-01           7.654e+02           -5.912e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 117
 -------------------------------------------
 DONE(3.842e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945172e+04  0.000000e+00   1.714e-03  2.635e+00  
 GE2    -1.945172e+04  -2.346484e-03  9.399e-04  2.523e+00  
 GE3    -1.945172e+04  -1.495351e-04  1.257e-04  2.728e+00  
 GE4    -1.945172e+04  -3.828262e-06  4.573e-05  2.533e+00  
 GE5    -1.945172e+04  -3.903291e-07  1.439e-05  2.635e+00  
 GE6    -1.945172e+04  -3.944621e-08  2.268e-06  2.422e+00  
 GE7    -1.945172e+04  1.225057e-09   8.047e-07  2.433e+00  
 GE8    -1.945172e+04  1.856147e-11   1.270e-07  2.419e+00  
 GE9    -1.945172e+04  -2.784220e-11  4.213e-08  2.515e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.054e+01     -1.757e+00     -1.678e+00     
 -1.757e+00     -1.206e+01     -2.307e+00     
 -1.678e+00     -2.307e+00     -6.161e+00     
 TOTAL-PRESSURE: -9.588e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.289e-01           7.648e+02           -5.598e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 118
 -------------------------------------------
 DONE(3.874e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945172e+04  0.000000e+00   1.710e-03  2.751e+00  
 GE2    -1.945172e+04  -2.347711e-03  9.395e-04  2.896e+00  
 GE3    -1.945172e+04  -1.494796e-04  1.255e-04  2.452e+00  
 GE4    -1.945172e+04  -3.890208e-06  4.554e-05  2.514e+00  
 GE5    -1.945172e+04  -3.852432e-07  1.437e-05  2.610e+00  
 GE6    -1.945172e+04  -3.739826e-08  2.257e-06  2.505e+00  
 GE7    -1.945172e+04  -3.279192e-10  8.020e-07  2.518e+00  
 GE8    -1.945172e+04  1.856147e-11   1.280e-07  2.501e+00  
 GE9    -1.945172e+04  9.280733e-12   4.225e-08  2.590e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -1.017e+01     -1.654e+00     -1.658e+00     
 -1.654e+00     -1.188e+01     -2.439e+00     
 -1.658e+00     -2.439e+00     -5.827e+00     
 TOTAL-PRESSURE: -9.292e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.289e-01           7.648e+02           -5.303e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 119
 -------------------------------------------
 DONE(3.906e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945172e+04  0.000000e+00   1.707e-03  2.726e+00  
 GE2    -1.945172e+04  -2.345555e-03  9.396e-04  2.524e+00  
 GE3    -1.945172e+04  -1.495334e-04  1.254e-04  2.399e+00  
 GE4    -1.945172e+04  -3.976420e-06  4.535e-05  2.509e+00  
 GE5    -1.945172e+04  -3.915572e-07  1.436e-05  2.695e+00  
 GE6    -1.945172e+04  -3.365503e-08  2.252e-06  2.509e+00  
 GE7    -1.945172e+04  -3.402935e-10  8.003e-07  2.522e+00  
 GE8    -1.945172e+04  -1.237431e-11  1.291e-07  2.804e+00  
 GE9    -1.945172e+04  -1.856147e-11  4.246e-08  2.390e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -9.834e+00     -1.548e+00     -1.628e+00     
 -1.548e+00     -1.169e+01     -2.556e+00     
 -1.628e+00     -2.556e+00     -5.534e+00     
 TOTAL-PRESSURE: -9.021e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.291e-01           7.655e+02           -5.027e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 120
 -------------------------------------------
 DONE(3.938e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945173e+04  0.000000e+00   1.707e-03  3.036e+00  
 GE2    -1.945173e+04  -2.340206e-03  9.404e-04  2.701e+00  
 GE3    -1.945173e+04  -1.497363e-04  1.254e-04  2.603e+00  
 GE4    -1.945173e+04  -4.082229e-06  4.518e-05  2.511e+00  
 GE5    -1.945173e+04  -3.829292e-07  1.438e-05  2.615e+00  
 GE6    -1.945173e+04  -3.506570e-08  2.253e-06  2.599e+00  
 GE7    -1.945173e+04  -3.217321e-10  7.991e-07  2.417e+00  
 GE8    -1.945173e+04  -2.474862e-11  1.303e-07  2.622e+00  
 GE9    -1.945173e+04  6.187155e-12   4.270e-08  2.413e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -9.527e+00     -1.441e+00     -1.590e+00     
 -1.441e+00     -1.151e+01     -2.654e+00     
 -1.590e+00     -2.654e+00     -5.280e+00     
 TOTAL-PRESSURE: -8.773e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.295e-01           7.668e+02           -4.773e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 121
 -------------------------------------------
 DONE(3.970e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945174e+04  0.000000e+00   1.709e-03  2.844e+00  
 GE2    -1.945174e+04  -2.328789e-03  9.419e-04  2.720e+00  
 GE3    -1.945174e+04  -1.499805e-04  1.257e-04  2.600e+00  
 GE4    -1.945174e+04  -4.203395e-06  4.502e-05  2.725e+00  
 GE5    -1.945174e+04  -3.794706e-07  1.441e-05  2.410e+00  
 GE6    -1.945174e+04  -3.762100e-08  2.260e-06  2.410e+00  
 GE7    -1.945174e+04  -2.815156e-10  7.986e-07  2.600e+00  
 GE8    -1.945174e+04  -3.712293e-11  1.316e-07  2.528e+00  
 GE9    -1.945174e+04  -1.856147e-11  4.296e-08  2.590e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -9.257e+00     -1.333e+00     -1.545e+00     
 -1.333e+00     -1.133e+01     -2.736e+00     
 -1.545e+00     -2.736e+00     -5.060e+00     
 TOTAL-PRESSURE: -8.549e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.300e-01           7.687e+02           -4.539e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 122
 -------------------------------------------
 DONE(4.001e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945175e+04  0.000000e+00   1.712e-03  2.734e+00  
 GE2    -1.945175e+04  -2.312328e-03  9.441e-04  2.600e+00  
 GE3    -1.945175e+04  -1.502913e-04  1.261e-04  2.510e+00  
 GE4    -1.945175e+04  -4.323411e-06  4.489e-05  2.617e+00  
 GE5    -1.945175e+04  -3.827189e-07  1.447e-05  2.711e+00  
 GE6    -1.945175e+04  -3.628766e-08  2.273e-06  2.521e+00  
 GE7    -1.945175e+04  -3.310128e-10  7.987e-07  2.611e+00  
 GE8    -1.945175e+04  -5.568440e-11  1.329e-07  2.477e+00  
 GE9    -1.945175e+04  -9.280733e-12  4.322e-08  2.685e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -9.028e+00     -1.223e+00     -1.497e+00     
 -1.223e+00     -1.115e+01     -2.802e+00     
 -1.497e+00     -2.802e+00     -4.874e+00     
 TOTAL-PRESSURE: -8.350e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.308e-01           7.712e+02           -4.327e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 123
 -------------------------------------------
 DONE(4.033e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945177e+04  0.000000e+00   1.718e-03  2.722e+00  
 GE2    -1.945177e+04  -2.304091e-03  9.470e-04  2.411e+00  
 GE3    -1.945177e+04  -1.506827e-04  1.266e-04  2.597e+00  
 GE4    -1.945177e+04  -4.432843e-06  4.475e-05  2.405e+00  
 GE5    -1.945177e+04  -3.854072e-07  1.452e-05  2.390e+00  
 GE6    -1.945177e+04  -3.888008e-08  2.289e-06  2.612e+00  
 GE7    -1.945177e+04  -3.310128e-10  7.992e-07  2.450e+00  
 GE8    -1.945177e+04  -4.640366e-11  1.342e-07  2.716e+00  
 GE9    -1.945177e+04  -4.021651e-11  4.346e-08  2.583e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -8.841e+00     -1.111e+00     -1.450e+00     
 -1.111e+00     -1.097e+01     -2.857e+00     
 -1.450e+00     -2.857e+00     -4.719e+00     
 TOTAL-PRESSURE: -8.176e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.317e-01           7.741e+02           -4.138e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 124
 -------------------------------------------
 DONE(4.064e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945178e+04  0.000000e+00   1.723e-03  2.822e+00  
 GE2    -1.945179e+04  -2.296743e-03  9.501e-04  2.598e+00  
 GE3    -1.945179e+04  -1.512767e-04  1.271e-04  2.388e+00  
 GE4    -1.945179e+04  -4.546495e-06  4.462e-05  2.495e+00  
 GE5    -1.945179e+04  -3.819981e-07  1.458e-05  2.393e+00  
 GE6    -1.945179e+04  -3.364266e-08  2.305e-06  2.403e+00  
 GE7    -1.945179e+04  -3.372000e-10  7.996e-07  2.531e+00  
 GE8    -1.945179e+04  -4.949724e-11  1.354e-07  2.529e+00  
 GE9    -1.945179e+04  1.237431e-11   4.364e-08  2.406e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -8.694e+00     -9.949e-01     -1.407e+00     
 -9.949e-01     -1.078e+01     -2.908e+00     
 -1.407e+00     -2.908e+00     -4.596e+00     
 TOTAL-PRESSURE: -8.024e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.326e-01           7.774e+02           -3.969e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 125
 -------------------------------------------
 DONE(4.096e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945180e+04  0.000000e+00   1.728e-03  2.795e+00  
 GE2    -1.945181e+04  -2.276798e-03  9.531e-04  2.504e+00  
 GE3    -1.945181e+04  -1.518864e-04  1.275e-04  2.494e+00  
 GE4    -1.945181e+04  -4.639305e-06  4.447e-05  2.501e+00  
 GE5    -1.945181e+04  -3.760986e-07  1.463e-05  2.587e+00  
 GE6    -1.945181e+04  -3.823971e-08  2.321e-06  2.639e+00  
 GE7    -1.945181e+04  -1.806649e-09  8.007e-07  2.622e+00  
 GE8    -1.945181e+04  -9.899448e-11  1.364e-07  2.499e+00  
 GE9    -1.945181e+04  0.000000e+00   4.377e-08  2.501e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -8.583e+00     -8.721e-01     -1.369e+00     
 -8.721e-01     -1.060e+01     -2.961e+00     
 -1.369e+00     -2.961e+00     -4.504e+00     
 TOTAL-PRESSURE: -7.894e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.337e-01           7.810e+02           -3.820e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 126
 -------------------------------------------
 DONE(4.128e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945182e+04  0.000000e+00   1.732e-03  2.720e+00  
 GE2    -1.945183e+04  -2.263628e-03  9.559e-04  2.715e+00  
 GE3    -1.945183e+04  -1.522849e-04  1.278e-04  2.536e+00  
 GE4    -1.945183e+04  -4.726779e-06  4.432e-05  2.611e+00  
 GE5    -1.945183e+04  -3.697630e-07  1.466e-05  2.408e+00  
 GE6    -1.945183e+04  -3.565657e-08  2.335e-06  2.628e+00  
 GE7    -1.945183e+04  -3.681357e-10  8.019e-07  2.609e+00  
 GE8    -1.945183e+04  -1.608660e-09  1.373e-07  2.508e+00  
 GE9    -1.945183e+04  9.280733e-12   4.385e-08  2.496e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -8.501e+00     -7.411e-01     -1.340e+00     
 -7.411e-01     -1.041e+01     -3.026e+00     
 -1.340e+00     -3.026e+00     -4.444e+00     
 TOTAL-PRESSURE: -7.786e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.349e-01           7.848e+02           -3.692e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 127
 -------------------------------------------
 DONE(4.160e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945184e+04  0.000000e+00   1.735e-03  2.829e+00  
 GE2    -1.945185e+04  -2.254206e-03  9.585e-04  2.494e+00  
 GE3    -1.945185e+04  -1.526142e-04  1.280e-04  2.700e+00  
 GE4    -1.945185e+04  -4.804147e-06  4.415e-05  2.611e+00  
 GE5    -1.945185e+04  -3.691009e-07  1.469e-05  2.901e+00  
 GE6    -1.945185e+04  -3.354057e-08  2.347e-06  2.708e+00  
 GE7    -1.945185e+04  -3.866972e-10  8.029e-07  2.411e+00  
 GE8    -1.945185e+04  -7.115228e-11  1.379e-07  2.400e+00  
 GE9    -1.945185e+04  -3.093578e-11  4.384e-08  2.394e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -8.444e+00     -6.003e-01     -1.320e+00     
 -6.003e-01     -1.023e+01     -3.110e+00     
 -1.320e+00     -3.110e+00     -4.420e+00     
 TOTAL-PRESSURE: -7.699e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.361e-01           7.888e+02           -3.584e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 128
 -------------------------------------------
 DONE(4.192e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945186e+04  0.000000e+00   1.738e-03  2.761e+00  
 GE2    -1.945187e+04  -2.255006e-03  9.609e-04  2.515e+00  
 GE3    -1.945187e+04  -1.530584e-04  1.282e-04  2.630e+00  
 GE4    -1.945187e+04  -4.872805e-06  4.398e-05  2.555e+00  
 GE5    -1.945187e+04  -3.626539e-07  1.470e-05  2.525e+00  
 GE6    -1.945187e+04  -3.517398e-08  2.357e-06  2.511e+00  
 GE7    -1.945187e+04  -3.650422e-10  8.041e-07  2.730e+00  
 GE8    -1.945187e+04  -1.113688e-10  1.385e-07  2.808e+00  
 GE9    -1.945187e+04  1.546789e-11   4.379e-08  2.610e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -8.403e+00     -4.494e-01     -1.311e+00     
 -4.494e-01     -1.006e+01     -3.222e+00     
 -1.311e+00     -3.222e+00     -4.433e+00     
 TOTAL-PRESSURE: -7.632e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.373e-01           7.929e+02           -3.496e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 129
 -------------------------------------------
 DONE(4.225e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945188e+04  0.000000e+00   1.740e-03  2.622e+00  
 GE2    -1.945188e+04  -2.256413e-03  9.633e-04  2.409e+00  
 GE3    -1.945188e+04  -1.535121e-04  1.285e-04  2.398e+00  
 GE4    -1.945188e+04  -4.934037e-06  4.381e-05  2.510e+00  
 GE5    -1.945188e+04  -3.627343e-07  1.470e-05  2.391e+00  
 GE6    -1.945188e+04  -3.495433e-08  2.367e-06  2.516e+00  
 GE7    -1.945188e+04  -4.052587e-10  8.055e-07  2.630e+00  
 GE8    -1.945188e+04  -9.590090e-11  1.390e-07  2.518e+00  
 GE9    -1.945188e+04  0.000000e+00   4.368e-08  2.479e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -8.372e+00     -2.896e-01     -1.310e+00     
 -2.896e-01     -9.899e+00     -3.366e+00     
 -1.310e+00     -3.366e+00     -4.486e+00     
 TOTAL-PRESSURE: -7.586e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.385e-01           7.970e+02           -3.428e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 130
 -------------------------------------------
 DONE(4.256e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945190e+04  0.000000e+00   1.745e-03  2.614e+00  
 GE2    -1.945190e+04  -2.252741e-03  9.661e-04  2.466e+00  
 GE3    -1.945190e+04  -1.537122e-04  1.289e-04  2.440e+00  
 GE4    -1.945190e+04  -5.004286e-06  4.363e-05  2.399e+00  
 GE5    -1.945190e+04  -3.606709e-07  1.469e-05  2.598e+00  
 GE6    -1.945190e+04  -3.529463e-08  2.377e-06  2.572e+00  
 GE7    -1.945190e+04  -4.361944e-10  8.071e-07  2.611e+00  
 GE8    -1.945190e+04  -9.899448e-11  1.394e-07  2.401e+00  
 GE9    -1.945190e+04  -1.237431e-11  4.353e-08  2.583e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -8.345e+00     -1.233e-01     -1.317e+00     
 -1.233e-01     -9.756e+00     -3.548e+00     
 -1.317e+00     -3.548e+00     -4.578e+00     
 TOTAL-PRESSURE: -7.560e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.398e-01           8.012e+02           -3.380e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 131
 -------------------------------------------
 DONE(4.288e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945192e+04  0.000000e+00   1.754e-03  2.910e+00  
 GE2    -1.945192e+04  -2.252746e-03  9.694e-04  2.402e+00  
 GE3    -1.945192e+04  -1.538343e-04  1.295e-04  2.454e+00  
 GE4    -1.945192e+04  -5.090247e-06  4.347e-05  2.497e+00  
 GE5    -1.945192e+04  -3.592974e-07  1.467e-05  2.495e+00  
 GE6    -1.945192e+04  -3.570298e-08  2.387e-06  2.396e+00  
 GE7    -1.945192e+04  -4.733174e-10  8.089e-07  2.509e+00  
 GE8    -1.945192e+04  -1.175559e-10  1.396e-07  2.400e+00  
 GE9    -1.945192e+04  2.165504e-11   4.335e-08  2.388e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -8.317e+00     4.567e-02      -1.328e+00     
 4.567e-02      -9.634e+00     -3.767e+00     
 -1.328e+00     -3.767e+00     -4.711e+00     
 TOTAL-PRESSURE: -7.554e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.410e-01           8.054e+02           -3.352e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 132
 -------------------------------------------
 DONE(4.319e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945193e+04  0.000000e+00   1.764e-03  2.780e+00  
 GE2    -1.945194e+04  -2.264822e-03  9.730e-04  2.657e+00  
 GE3    -1.945194e+04  -1.539630e-04  1.303e-04  2.514e+00  
 GE4    -1.945194e+04  -5.158494e-06  4.332e-05  2.825e+00  
 GE5    -1.945194e+04  -3.578001e-07  1.464e-05  2.402e+00  
 GE6    -1.945194e+04  -3.457073e-08  2.397e-06  2.531e+00  
 GE7    -1.945194e+04  -4.609431e-10  8.108e-07  2.502e+00  
 GE8    -1.945194e+04  -1.392110e-10  1.397e-07  2.509e+00  
 GE9    -1.945194e+04  1.856147e-11   4.314e-08  2.393e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -8.285e+00     2.118e-01      -1.340e+00     
 2.118e-01      -9.535e+00     -4.019e+00     
 -1.340e+00     -4.019e+00     -4.882e+00     
 TOTAL-PRESSURE: -7.567e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.423e-01           8.096e+02           -3.344e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 133
 -------------------------------------------
 DONE(4.350e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945195e+04  0.000000e+00   1.774e-03  2.614e+00  
 GE2    -1.945195e+04  -2.265327e-03  9.763e-04  2.507e+00  
 GE3    -1.945195e+04  -1.541460e-04  1.310e-04  2.430e+00  
 GE4    -1.945195e+04  -5.217306e-06  4.320e-05  2.598e+00  
 GE5    -1.945195e+04  -3.477429e-07  1.459e-05  2.503e+00  
 GE6    -1.945195e+04  -3.377877e-08  2.407e-06  2.617e+00  
 GE7    -1.945195e+04  -2.057229e-09  8.128e-07  2.599e+00  
 GE8    -1.945195e+04  -1.237431e-10  1.398e-07  2.808e+00  
 GE9    -1.945195e+04  -3.093578e-12  4.295e-08  2.496e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -8.250e+00     3.680e-01      -1.349e+00     
 3.680e-01      -9.464e+00     -4.298e+00     
 -1.349e+00     -4.298e+00     -5.087e+00     
 TOTAL-PRESSURE: -7.600e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.435e-01           8.137e+02           -3.356e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 134
 -------------------------------------------
 DONE(4.383e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945196e+04  0.000000e+00   1.781e-03  2.641e+00  
 GE2    -1.945197e+04  -2.269829e-03  9.786e-04  2.504e+00  
 GE3    -1.945197e+04  -1.539232e-04  1.316e-04  2.428e+00  
 GE4    -1.945197e+04  -5.298800e-06  4.311e-05  2.495e+00  
 GE5    -1.945197e+04  -3.375031e-07  1.453e-05  2.500e+00  
 GE6    -1.945197e+04  -3.247638e-08  2.412e-06  2.501e+00  
 GE7    -1.945197e+04  -5.166275e-10  8.139e-07  2.400e+00  
 GE8    -1.945197e+04  -6.187155e-11  1.397e-07  2.587e+00  
 GE9    -1.945197e+04  -1.546789e-11  4.279e-08  2.479e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -8.211e+00     5.068e-01      -1.348e+00     
 5.068e-01      -9.425e+00     -4.595e+00     
 -1.348e+00     -4.595e+00     -5.322e+00     
 TOTAL-PRESSURE: -7.653e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.447e-01           8.177e+02           -3.387e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 135
 -------------------------------------------
 DONE(4.414e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945198e+04  0.000000e+00   1.784e-03  2.813e+00  
 GE2    -1.945198e+04  -2.276426e-03  9.795e-04  2.459e+00  
 GE3    -1.945198e+04  -1.533366e-04  1.318e-04  2.410e+00  
 GE4    -1.945198e+04  -5.347595e-06  4.303e-05  2.509e+00  
 GE5    -1.945198e+04  -3.401853e-07  1.444e-05  2.610e+00  
 GE6    -1.945198e+04  -3.012216e-08  2.410e-06  2.414e+00  
 GE7    -1.945198e+04  -5.166275e-10  8.141e-07  2.398e+00  
 GE8    -1.945198e+04  -9.899448e-11  1.395e-07  2.419e+00  
 GE9    -1.945198e+04  -2.784220e-11  4.268e-08  2.492e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -8.175e+00     6.204e-01      -1.334e+00     
 6.204e-01      -9.420e+00     -4.897e+00     
 -1.334e+00     -4.897e+00     -5.583e+00     
 TOTAL-PRESSURE: -7.726e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.459e-01           8.218e+02           -3.439e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 136
 -------------------------------------------
 DONE(4.445e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945199e+04  0.000000e+00   1.784e-03  2.699e+00  
 GE2    -1.945199e+04  -2.287144e-03  9.791e-04  2.588e+00  
 GE3    -1.945199e+04  -1.527164e-04  1.318e-04  2.397e+00  
 GE4    -1.945199e+04  -5.389476e-06  4.299e-05  2.427e+00  
 GE5    -1.945199e+04  -3.315975e-07  1.433e-05  2.385e+00  
 GE6    -1.945199e+04  -3.585147e-08  2.401e-06  2.735e+00  
 GE7    -1.945199e+04  8.074237e-10   8.133e-07  2.422e+00  
 GE8    -1.945199e+04  -1.051816e-10  1.391e-07  2.512e+00  
 GE9    -1.945199e+04  -1.856147e-11  4.264e-08  2.402e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -8.144e+00     7.022e-01      -1.302e+00     
 7.022e-01      -9.451e+00     -5.195e+00     
 -1.302e+00     -5.195e+00     -5.866e+00     
 TOTAL-PRESSURE: -7.820e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.472e-01           8.260e+02           -3.511e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 137
 -------------------------------------------
 DONE(4.476e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945200e+04  0.000000e+00   1.780e-03  2.625e+00  
 GE2    -1.945201e+04  -2.294613e-03  9.774e-04  2.423e+00  
 GE3    -1.945201e+04  -1.521656e-04  1.318e-04  2.483e+00  
 GE4    -1.945201e+04  -5.435230e-06  4.302e-05  2.608e+00  
 GE5    -1.945201e+04  -3.226385e-07  1.422e-05  2.582e+00  
 GE6    -1.945201e+04  -3.193191e-08  2.386e-06  2.406e+00  
 GE7    -1.945201e+04  -4.856917e-10  8.114e-07  2.591e+00  
 GE8    -1.945201e+04  -7.733944e-11  1.386e-07  2.399e+00  
 GE9    -1.945201e+04  -1.237431e-11  4.262e-08  2.478e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -8.124e+00     7.473e-01      -1.246e+00     
 7.473e-01      -9.522e+00     -5.475e+00     
 -1.246e+00     -5.475e+00     -6.167e+00     
 TOTAL-PRESSURE: -7.938e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.486e-01           8.306e+02           -3.605e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 138
 -------------------------------------------
 DONE(4.508e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945202e+04  0.000000e+00   1.776e-03  2.934e+00  
 GE2    -1.945203e+04  -2.294677e-03  9.752e-04  2.420e+00  
 GE3    -1.945203e+04  -1.517031e-04  1.318e-04  2.688e+00  
 GE4    -1.945203e+04  -5.459580e-06  4.311e-05  2.418e+00  
 GE5    -1.945203e+04  -3.209525e-07  1.409e-05  2.511e+00  
 GE6    -1.945203e+04  -3.136578e-08  2.363e-06  2.530e+00  
 GE7    -1.945203e+04  -5.135339e-10  8.079e-07  2.546e+00  
 GE8    -1.945203e+04  2.617167e-09   1.379e-07  2.547e+00  
 GE9    -1.945203e+04  3.093578e-12   4.265e-08  2.430e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -8.122e+00     7.529e-01      -1.164e+00     
 7.529e-01      -9.634e+00     -5.728e+00     
 -1.164e+00     -5.728e+00     -6.485e+00     
 TOTAL-PRESSURE: -8.080e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.501e-01           8.357e+02           -3.721e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 139
 -------------------------------------------
 DONE(4.540e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945205e+04  0.000000e+00   1.774e-03  2.737e+00  
 GE2    -1.945205e+04  -2.293588e-03  9.733e-04  2.449e+00  
 GE3    -1.945205e+04  -1.514685e-04  1.321e-04  2.510e+00  
 GE4    -1.945205e+04  -5.495113e-06  4.329e-05  2.703e+00  
 GE5    -1.945205e+04  -3.204142e-07  1.398e-05  2.505e+00  
 GE6    -1.945205e+04  -3.285070e-08  2.339e-06  2.592e+00  
 GE7    -1.945205e+04  -4.918788e-10  8.031e-07  2.408e+00  
 GE8    -1.945205e+04  -1.330238e-10  1.369e-07  2.532e+00  
 GE9    -1.945205e+04  2.784220e-11   4.264e-08  2.633e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -8.143e+00     7.190e-01      -1.052e+00     
 7.190e-01      -9.787e+00     -5.947e+00     
 -1.052e+00     -5.947e+00     -6.819e+00     
 TOTAL-PRESSURE: -8.250e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.148e+02          2.518e-01           8.415e+02           -3.860e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 140
 -------------------------------------------
 DONE(4.572e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945208e+04  0.000000e+00   1.777e-03  2.724e+00  
 GE2    -1.945208e+04  -2.302788e-03  9.730e-04  2.398e+00  
 GE3    -1.945208e+04  -1.517882e-04  1.328e-04  2.502e+00  
 GE4    -1.945208e+04  -5.541519e-06  4.352e-05  2.513e+00  
 GE5    -1.945208e+04  -3.259239e-07  1.390e-05  2.404e+00  
 GE6    -1.945208e+04  -3.294660e-08  2.322e-06  2.506e+00  
 GE7    -1.945208e+04  -3.341064e-10  7.981e-07  2.510e+00  
 GE8    -1.945208e+04  -7.115228e-11  1.359e-07  2.412e+00  
 GE9    -1.945208e+04  -9.280733e-12  4.266e-08  2.379e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -8.190e+00     6.489e-01      -9.111e-01     
 6.489e-01      -9.980e+00     -6.125e+00     
 -9.111e-01     -6.125e+00     -7.168e+00     
 TOTAL-PRESSURE: -8.446e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.149e+02          2.538e-01           8.481e+02           -4.022e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 141
 -------------------------------------------
 DONE(4.603e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945211e+04  0.000000e+00   1.783e-03  2.900e+00  
 GE2    -1.945212e+04  -2.306102e-03  9.746e-04  2.411e+00  
 GE3    -1.945212e+04  -1.525096e-04  1.337e-04  2.885e+00  
 GE4    -1.945212e+04  -5.598240e-06  4.383e-05  2.520e+00  
 GE5    -1.945212e+04  -3.341682e-07  1.387e-05  2.501e+00  
 GE6    -1.945212e+04  -3.225055e-08  2.317e-06  2.705e+00  
 GE7    -1.945212e+04  -4.764109e-10  7.948e-07  2.509e+00  
 GE8    -1.945212e+04  -1.113688e-10  1.349e-07  2.558e+00  
 GE9    -1.945212e+04  6.187155e-12   4.266e-08  2.491e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -8.266e+00     5.482e-01      -7.417e-01     
 5.482e-01      -1.021e+01     -6.262e+00     
 -7.417e-01     -6.262e+00     -7.535e+00     
 TOTAL-PRESSURE: -8.670e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.149e+02          2.561e-01           8.557e+02           -4.206e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 142
 -------------------------------------------
 DONE(4.635e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945216e+04  0.000000e+00   1.789e-03  2.603e+00  
 GE2    -1.945216e+04  -2.320619e-03  9.773e-04  2.420e+00  
 GE3    -1.945216e+04  -1.536648e-04  1.349e-04  2.692e+00  
 GE4    -1.945216e+04  -5.677154e-06  4.420e-05  2.693e+00  
 GE5    -1.945216e+04  -3.336578e-07  1.391e-05  2.403e+00  
 GE6    -1.945216e+04  -3.069448e-08  2.330e-06  2.526e+00  
 GE7    -1.945216e+04  -1.695281e-09  7.940e-07  2.692e+00  
 GE8    -1.945216e+04  -1.268367e-10  1.340e-07  2.504e+00  
 GE9    -1.945216e+04  1.237431e-11   4.270e-08  2.373e+00  
 ><><><><><><><><><><><><><><><><><><><><><><
 TOTAL-STRESS (KBAR):
 ><><><><><><><><><><><><><><><><><><><><><><
 -8.373e+00     4.247e-01      -5.470e-01     
 4.247e-01      -1.046e+01     -6.357e+00     
 -5.470e-01     -6.357e+00     -7.918e+00     
 TOTAL-PRESSURE: -8.919e+00 KBAR
 ------------------------------------------------------------------------------------------------
 Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
 -7.146e+02          -7.149e+02          2.586e-01           8.643e+02           -4.410e+00          
 ------------------------------------------------------------------------------------------------
 -------------------------------------------
 STEP OF MOLECULAR DYNAMICS : 143
 -------------------------------------------
 DONE(4.666e+03  SEC) : INIT SCF
 ITER   ETOT(eV)       EDIFF(eV)      DRHO       TIME(s)    
 GE1    -1.945221e+04  0.000000e+00   1.797e-03  2.848e+00  
 GE2    -1.945221e+04  -2.339829e-03  9.807e-04  2.617e+00  
 GE3    -1.945221e+04  -1.555546e-04  1.364e-04  2.396e+00  
 GE4    -1.945221e+04  -5.777550e-06  4.462e-05  2.504e+00  
 GE5    -1.945221e+04  -3.501682e-07  1.401e-05  2.599e+00  
 GE6    -1.945221e+04  -3.210515e-08  2.363e-06  2.597e+00  
 GE7    -1.945221e+04  -1.522040e-09  7.963e-07  2.900e+00

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As we can see, even though the number of steps in the ABACUS quantum molecular dynamics calculation is only $500/200000 = 1/400$ of that in the LAMMPS classical molecular dynamics calculation,

the time required for ABACUS quantum molecular dynamics is $9 h 30 mins 58 secs \div 3 min 35 secs = 159.33$ times that of LAMMPS classical molecular dynamics!

The cost ratio is as high as approximately 63732 times!

First-principles calculations are very expensive!

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2.3.3 Results and Analysis

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As mentioned above, the main calculation information is stored in the file OUT.ABACUS/running_scf.log. In addition, the MD simulation trajectory is stored in the file OUT.ABACUS/MD_dump.

The content of the MD_dump file is as follows:

MDSTEP:  0
LATTICE_CONSTANT: 1.889726124626
LATTICE_VECTORS
  11.858000000000  0.000000000000  0.000000000000
  0.000000000000  11.858000000000  0.000000000000
  0.000000000000  0.000000000000  11.858000000000
VIRIAL (KBAR)
  14.314395848598  0.068950391132  -1.646206932245
  0.068950391132  6.742623812696  -3.705349135941
  -1.646206932245  -3.705349135941  5.270646592369
INDEX    LABEL    POSITIONS    FORCE (eV/Angstrom)
  0  Li  3.016819999993  1.775969999997  4.378729999996  -0.812213164484  -0.585472450641  0.311819994732
  1  Li  3.476600000010  5.232430000004  2.059570000010  0.352252495274  -0.175519926585  0.080617217948
  2  Li  0.908510000006  3.907440000006  4.561330000000  -0.649106916034  0.039426589767  0.878683371838
  ...
  61  Cl  10.362100000004  9.238389999995  8.344720000004  -2.421125883128  0.103626611523  -1.137264969726
  62  Cl  9.088940000007  5.618780000000  9.584660000001  -0.546302523476  -2.531252034211  0.628161793135
  63  Cl  8.152059999999  7.237340000007  6.577169999999  -0.867749328458  -2.567100713260  0.810628619279

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This file records information from the molecular dynamics simulation, including:

Number of MD steps (MDSTEP)
Lattice constants (LATTICE_CONSTANT) and lattice vectors (LATTICE_VECTORS)
Stress tensor (VIRIAL), in units of KBAR
Index, label, coordinate positions (POSITIONS), and forces (FORCE) on each atom, with force units in eV/Å.

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Here is a Python script that can extract atomic coordinates, calculate the RDF, and save the RDF data to files named gr_Li-Cl, gr_Li-Li, and gr_Cl-Cl.

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[6]

import numpy as np

import matplotlib.pyplot as plt

def get_atom_positions(file_path, nLi, nCl):

Li, Cl = [], []

with open(file_path, 'r') as file:

for line in file:

if 'Li' in line:

Li.append([float(line.split()[2]), float(line.split()[3]), float(line.split()[4])])

if 'Cl' in line:

Cl.append([float(line.split()[2]), float(line.split()[3]), float(line.split()[4])])

return np.array(Li).reshape(-1, nLi, 3), np.array(Cl).reshape(-1, nCl, 3)

def get_gr(x, y, L):

batchsize, n, dim = x.shape[0], x.shape[1], x.shape[2]

i,j = np.triu_indices(n, k=1)

rij = (np.reshape(x, (-1, n, 1, dim)) - np.reshape(y, (-1, 1, n, dim)))[:,i,j]

rij = rij - L*np.rint(rij/L)

dist = np.linalg.norm(rij, axis=-1) # (batchsize, n*(n-1)/2)

hist, bin_edges = np.histogram(dist.reshape(-1,), range=[0, L/2], bins=200)

dr = bin_edges[1] - bin_edges[0]

hist = hist*2/(n * batchsize)

rmesh = np.arange(hist.shape[0])*dr

h_id = 4/3*np.pi*n/(L**3)* ((rmesh+dr)**3 - rmesh**3 )

return rmesh, hist/h_id

L = 11.858

nLi, nCl = 32, 32

Li, Cl = get_atom_positions('./LiCl_DP_Tutorial_Example/chapter2/abacus_md/OUT.ABACUS/MD_dump', nLi, nCl)

atom_pairs = {'Li-Cl': (Li, Cl),'Li-Li': (Li, Li),'Cl-Cl': (Cl, Cl)}

plt.figure(figsize=(10, 6))

colors = ['purple', 'orange', 'green']

for (label, (x, y)), color in zip(atom_pairs.items(), colors):

rmesh, gr = get_gr(x, y, L)

plt.plot(rmesh, gr, label=label, color=color)

np.savetxt(f'./LiCl_DP_Tutorial_Example/chapter2/abacus_md/OUT.ABACUS/gr_{label}', np.column_stack((rmesh, gr)))

plt.legend()

plt.title('abacus_md_rdf')

plt.savefig('./LiCl_DP_Tutorial_Example/chapter2/abacus_md/abacus_md_rdf.png', dpi=300)

plt.show()

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The RDF from the ABACUS MD calculation is shown in the figure. We can observe whether there are differences between the RDFs obtained from ABACUS and LAMMPS MD simulations of the LiCl melt at 900K. Note that due to the small simulation system and short simulation time, the RDF curve from the ABACUS MD calculation is not smooth. A larger simulation system or longer simulation time would help improve this.

In this exercise, we learned how to write ABACUS MD calculation input files for the LiCl melt, perform the calculation, and process MD trajectories.

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Chapter 3: DeePMD-kit Deep Potential (DP) Model Training

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For the LiCl melt, we can use the DeePMD-kit software package to train a Deep Potential (DP) model. DeePMD-kit is a deep learning-based molecular dynamics simulation tool that can train high-precision DP models based on first-principles data. In this example, we can use the first-principles data from ABACUS and DeePMD-kit to train a DP model for the LiCl melt.

The detailed principle of DeePMD-kit is to establish a deep learning model to learn the data obtained from high-cost first-principles calculations. The resulting Deep Potential model is then applied to subsequent molecular dynamics simulations to control the interatomic potentials. This is the origin of the term "Deep Potential Molecular Dynamics."

The DeePMD-kit deep potential molecular dynamics method significantly reduces the computational cost required for quantum molecular dynamics, scaling the molecular dynamics simulation from thousands of atoms to the level of billions of atoms, while retaining the accuracy significantly superior to classical molecular dynamics simulations. This method was awarded the ACM Gordon Bell Prize in 2020, the highest award in the field of high-performance computing.

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Objectives of This Chapter

After completing this chapter, you will be able to:

Master writing DeePMD-kit input files
Prepare data, perform training/freezing/compression/testing, and conduct molecular dynamics tasks

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Download Tutorial Resources

In this chapter, we will train a Deep Potential model using the LiCl melt molecule as an example. We have prepared the necessary files in ./LiCl_DP_Tutorial_Example/chapter3.

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Under the ./LiCl_DP_Tutorial_Example/chapter3 folder, there are three subfolders: 00.data, 01.train, and 02.lmp.

The 00.data folder is used to store training and testing data.
The 01.train folder contains example scripts for training the model using DeePMD-kit.
The 02.lmp folder contains example scripts for molecular dynamics simulations using LAMMPS.

This tutorial is completed using the DeePMD-kit (2.2.1) program.

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3.1 Prepare Training Data

In section 2.3, we have already performed the ABACUS MD calculation. You can use the following Python script, which calls the tools from dpdata, to convert the data generated by ABACUS MD (data format abacus/md) into the data format required for DeePMD-kit training (NumPy arrays).

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[7]

import dpdata

import numpy as np

# Load data in abacus/md format

data = dpdata.LabeledSystem('./LiCl_DP_Tutorial_Example/chapter2/abacus_md', fmt = 'abacus/md')

# Randomly select 100 indices for the validation set; use the remaining indices for the training set

index_validation = np.random.choice(len(data), size=100, replace=False)

index_training = list(set(range(len(data))) - set(index_validation))

# Create subsets: training set and validation set

data_training = data.sub_system(index_training)

data_validation = data.sub_system(index_validation)

# Export training set and validation set (deepmd/npy format)

data_training.to_deepmd_npy('./LiCl_DP_Tutorial_Example/chapter3/00.data/training_data')

data_validation.to_deepmd_npy('./LiCl_DP_Tutorial_Example/chapter3/00.data/validation_data')

print('# The dataset contains %d frames' % len(data))

print('# The training set contains %d frames' % len(data_training))

print('# The validation set contains %d frames' % len(data_validation))

# The dataset contains 501 frames
# The training set contains 401 frames
# The validation set contains 100 frames

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We can see that the abacus_md folder contains 501 frames of data. We randomly selected 100 frames as validation data, leaving the remaining 401 frames for training data. Before starting the training, we can check the contents of the training_data or validation_data folders.

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! cd ./LiCl_DP_Tutorial_Example/chapter3/00.data/ && ls training_data

box.raw    energy.raw  set.000	 type_map.raw
coord.raw  force.raw   type.raw  virial.raw

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These files serve the following purposes:

set.000: This directory contains compressed data in NumPy compressed array format. All training data should be first converted to this format before use in DeePMD-kit. The data format is detailed in the DeePMD-kit manual, available at DeePMD-kit Data Introduction.
type.raw: This file contains the types of atoms represented as integers.
type_map.raw: This file contains the names corresponding to each atom type.

Let's take a closer look at these files:

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[27]

! cd ./LiCl_DP_Tutorial_Example/chapter3/00.data/ && cat training_data/type.raw

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It indicates that in this example, there are 108 atoms in total, with 54 atoms represented by type "0" and another 54 atoms represented by type "1". Sometimes, it's necessary to map these integer types back to atom names. This mapping can be provided by the type_map.raw file.

Since all frames in the system have the same atomic types and numbering, we only need to specify the type information for the entire system once.

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[28]

! cd ./LiCl_DP_Tutorial_Example/chapter3/00.data/ && cat training_data/type_map.raw

Li
Cl

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The atom Li is assigned type 0, and the atom Cl is assigned type 1.

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3.2 Preparation of Input Scripts

After preparing the training data, the next step is to proceed with the training. Let's navigate to the training directory to examine the scripts required for execution.

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! cd ./LiCl_DP_Tutorial_Example/chapter3/01.train/ && cat input.json

{
    "_comment": " model parameters",
    "model": {
	"type_map":	["Li", "Cl"],
	"descriptor" :{
	    "type":		"se_e2_a",
	    "sel":		[128, 128],
	    "rcut_smth":	0.50,
	    "rcut":		7.00,
	    "neuron":		[20, 40, 80],
	    "resnet_dt":	false,
	    "axis_neuron":	4,
	    "seed":		1,
	    "_comment":		" that's all"
	},
	"fitting_net" : {
	    "neuron":		[200, 200, 200],
	    "resnet_dt":	true,
	    "seed":		1,
	    "_comment":		" that's all"
	},
	"_comment":	" that's all"
    },

    "learning_rate" :{
	"type":		"exp",
	"decay_steps":	5000,
	"start_lr":	0.001,	
	"stop_lr":	3.51e-8,
	"_comment":	"that's all"
    },

    "loss" :{
	"type":		"ener",
	"start_pref_e":	0.02,
	"limit_pref_e":	1,
	"start_pref_f":	1000,
	"limit_pref_f":	1,
	"start_pref_v":	0,
	"limit_pref_v":	0,
	"_comment":	" that's all"
    },

    "training" : {
	"training_data": {
	    "systems":     ["../00.data/training_data"],
	    "batch_size":  "auto",
	    "_comment":	   "that's all"
	},
	"validation_data":{
	    "systems":	   ["../00.data/validation_data"],
	    "batch_size":  "auto",
	    "numb_btch":   1,
	    "_comment":	   "that's all"
	},
	"numb_steps":	400000,
	"seed":		10,
	"disp_file":	"lcurve.out",
	"disp_freq":	1000,
	"save_freq":	10000,
	"_comment":	"that's all"
    },    

    "_comment":		"that's all"
}

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input.json contains various parameters necessary for the DP model training process, defining and controlling the training tasks. These parameters are detailed in the DeePMD-kit manual, so only a brief introduction is provided here.

In the model module, parameters for embedding and fitting networks are specified.

    "model":{
    "type_map":    ["Li", "Cl"],                         # Element names
    "descriptor":{
        "type":            "se_e2_a",                    # Descriptor type
        "rcut":            7.00,                         # Cutoff radius
        "rcut_smth":       0.50,                         # Smooth cutoff radius
        "sel":             [128, 128],                   # Number of selected neighbors for an atom
        "neuron":          [20, 40, 80],                 # Embedding network size
        "resnet_dt":       false,
        "axis_neuron":     12,                           # Embedding subnetwork horizontal size
        "seed":            1,
        "_comment":        "that's all"
    },
    "fitting_net":{
        "neuron":          [200, 200, 200],              # Fitting network size
        "resnet_dt":       true,
        "seed":            1,
        "_comment":        "that's all"
    },
    "_comment":    "that's all"'
},

Descriptor se_e2_a is used for training the DP model. The sizes of the embedding and fitting neural networks are set to [20, 40, 80] and [200, 200, 200], respectively. Components in $\tilde{R}^{i}$ smoothly decay from 0.5 to 7 Å.

Below parameters specify learning rate and loss function:

    "learning_rate" :{
        "type":                "exp",
        "decay_steps":         5000,                      # Learning rate decay interval
        "start_lr":            0.001,                     # Initial learning rate  
        "stop_lr":             3.51e-8,                   # Final learning rate 
        "_comment":            "that's all"
    },
    "loss" :{
        "type":                "ener",
        "start_pref_e":        0.02,                      # Initial energy weight
        "limit_pref_e":        1,                         # Final energy weight
        "start_pref_f":        1000,                      # Initial force weight
        "limit_pref_f":        1,                         # Final force weight
        "start_pref_v":        0,                         # Virial
        "limit_pref_v":        0,
        "_comment":            "that's all"
    },

In the loss function, pref_e increases gradually from 0.02 to 1 eV^-2, while pref_f decreases from 1000 to 1 Å² eV^-2. This means that initially, the force term dominates, while the energy term and virial term become important towards the end. This strategy is highly effective and reduces the total training time. pref_v is set to 0 eV^-2, indicating no virial data is included during training. The initial learning rate, final learning rate, and decay steps are set to 0.001, 3.51e-8, and 5000 respectively. The model is trained for 10⁶ steps.

training parameters:

    "training": {
        "training_data": {
            "systems": ["../00.data/training_data"],              # Path to the training data
            "batch_size": "auto",                                 # Automatically determined, natoms*batch_size should be ≥32
            "_comment": "that's all"
        },
        "validation_data": {
            "systems": ["../00.data/validation_data/"],
            "batch_size": "auto",
            "numb_btch": 1,                                       # Number of batches for testing
            "_comment": "that's all"
        },
        "numb_steps": 400000,                                     # Number of training steps
        "seed": 10,
        "disp_file": "lcurve.out",                                # Learning curve is written to this file
        "disp_freq": 1000,                                        # Frequency of writing the learning curve
        "save_freq": 10000,                                       # Frequency of saving model-related files
    }

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3.3 Model Training

After preparing the training script, we can start training with DeePMD-kit by simply running:

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[ ]

# ############## Time Warning: 7 hours ##################

#! cd ./LiCl_DP_Tutorial_Example/chapter3/01.train/ && dp train input.json

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DEEPMD INFO      ----------------------------------------------------------------------------------------------------
DEEPMD INFO      ---Summary of DataSystem: training     -------------------------------------------------------------
DEEPMD INFO      found 1 system(s):
DEEPMD INFO                              system        natoms        bch_sz        n_bch          prob        pbc
DEEPMD INFO           ../00.data/training_data/            64             1          401         1.000          T
DEEPMD INFO      -----------------------------------------------------------------------------------------------------
DEEPMD INFO      ---Summary of DataSystem: validation   --------------------------------------------------------------
DEEPMD INFO      found 1 system(s):
DEEPMD INFO                               system       natoms        bch_sz        n_bch          prob        pbc
DEEPMD INFO          ../00.data/validation_data/           64             1          100         1.000          T

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DEEPMD INFO      start training at lr 1.00e-03 (== 1.00e-03), decay_step 5000, decay_rate 0.950006, final lr will be 3.51e-08

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If everything goes smoothly, you will see information printed on the screen every 1000 steps, for example

DEEPMD INFO    batch    1000 training time 69.23 s, testing time 0.06 s
DEEPMD INFO    batch    2000 training time 68.00 s, testing time 0.06 s
DEEPMD INFO    batch    3000 training time 67.80 s, testing time 0.06 s
DEEPMD INFO    batch    4000 training time 69.92 s, testing time 0.07 s
DEEPMD INFO    batch    5000 training time 67.98 s, testing time 0.06 s

At the end of step 10000, the model is saved in the TensorFlow checkpoint file model.ckpt. Additionally, training and validation errors are displayed in the file lcurve.out

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! head -n 3 ./LiCl_DP_Tutorial_Example/chapter3/01.train/lcurve.out && tail -n 2 ./LiCl_DP_Tutorial_Example/chapter3/01.train/lcurve.out

'''

# step rmse_val rmse_trn rmse_e_val rmse_e_trn rmse_f_val rmse_f_trn lr

0 1.41e+01 1.27e+01 3.50e-01 3.35e-01 4.45e-01 4.02e-01 1.0e-03

...

399000 1.57e-02 1.55e-02 8.17e-05 4.88e-04 1.53e-02 1.47e-02 4.0e-08

400000 1.55e-02 1.54e-02 2.68e-04 4.64e-04 1.51e-02 1.47e-02 3.5e-08

'''

#  step      rmse_val    rmse_trn    rmse_e_val  rmse_e_trn    rmse_f_val  rmse_f_trn         lr
      0      1.59e+01    1.52e+01      3.66e-01    3.41e-01      5.01e-01    4.80e-01    1.0e-03
   1000      1.60e+00    1.51e+00      5.06e-02    4.82e-02      5.07e-02    4.78e-02    1.0e-03
 399000      1.44e-02    1.61e-02      1.82e-04    4.83e-05      1.41e-02    1.58e-02    4.0e-08
 400000      1.61e-02    1.44e-02      5.06e-04    5.25e-04      1.53e-02    1.36e-02    3.5e-08

'\n#  step      rmse_val    rmse_trn    rmse_e_val  rmse_e_trn    rmse_f_val  rmse_f_trn         lr\n      0      1.41e+01    1.27e+01      3.50e-01    3.35e-01      4.45e-01    4.02e-01    1.0e-03\n...\n 399000      1.57e-02    1.55e-02      8.17e-05    4.88e-04      1.53e-02    1.47e-02    4.0e-08\n 400000      1.55e-02    1.54e-02      2.68e-04    4.64e-04      1.51e-02    1.47e-02    3.5e-08\n'

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Columns 4, 5, 6, and 7 respectively represent the training and testing errors for energy and forces. After 400,000 training steps, the energy testing error is less than 1 meV, and the force testing error is less than 20 meV/Å. This data can be visualized using a simple Python script with the file.

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[9]

import numpy as np

import matplotlib.pyplot as plt

data = np.genfromtxt("./LiCl_DP_Tutorial_Example/chapter3/01.train/lcurve.out", names=True)

for name in data.dtype.names[1:-1]:

plt.plot(data['step'], data[name], label=name)

plt.legend()

plt.xlabel('Step')

plt.ylabel('Loss')

plt.yscale('log')

plt.show()

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When the training process stops abnormally, we can restart training from the provided checkpoint by simply running

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[10]

! cd ./LiCl_DP_Tutorial_Example/chapter3/01.train/ && dp train --restart model.ckpt input.json

WARNING:tensorflow:From /opt/deepmd-kit-2.2.1/lib/python3.10/site-packages/tensorflow/python/compat/v2_compat.py:107: disable_resource_variables (from tensorflow.python.ops.variable_scope) is deprecated and will be removed in a future version.
Instructions for updating:
non-resource variables are not supported in the long term
WARNING:root:To get the best performance, it is recommended to adjust the number of threads by setting the environment variables OMP_NUM_THREADS, TF_INTRA_OP_PARALLELISM_THREADS, and TF_INTER_OP_PARALLELISM_THREADS. See https://deepmd.rtfd.io/parallelism/ for more information.
WARNING:root:Environment variable KMP_BLOCKTIME is empty. Use the default value 0
WARNING:root:Environment variable KMP_AFFINITY is empty. Use the default value granularity=fine,verbose,compact,1,0
/opt/deepmd-kit-2.2.1/lib/python3.10/importlib/__init__.py:169: UserWarning: The NumPy module was reloaded (imported a second time). This can in some cases result in small but subtle issues and is discouraged.
  _bootstrap._exec(spec, module)
DEEPMD INFO    Calculate neighbor statistics... (add --skip-neighbor-stat to skip this step)
2024-07-10 03:01:32.993225: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcuda.so.1'; dlerror: libcuda.so.1: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /opt/intel/oneapi/tbb/2021.5.1/env/../lib/intel64/gcc4.8:/opt/intel/oneapi/mpi/2021.5.1//libfabric/lib:/opt/intel/oneapi/mpi/2021.5.1//lib/release:/opt/intel/oneapi/mpi/2021.5.1//lib:/opt/intel/oneapi/mkl/2022.0.2/lib/intel64:/opt/intel/oneapi/debugger/2021.5.0/gdb/intel64/lib:/opt/intel/oneapi/debugger/2021.5.0/libipt/intel64/lib:/opt/intel/oneapi/debugger/2021.5.0/dep/lib:/opt/intel/oneapi/compiler/2022.0.2/linux/lib:/opt/intel/oneapi/compiler/2022.0.2/linux/lib/x64:/opt/intel/oneapi/compiler/2022.0.2/linux/lib/oclfpga/host/linux64/lib:/opt/intel/oneapi/compiler/2022.0.2/linux/compiler/lib/intel64_lin:/opt/intel/oneapi/tbb/latest/env/../lib/intel64/gcc4.8:/opt/intel/oneapi/mpi/latest//libfabric/lib:/opt/intel/oneapi/mpi/latest//lib/release:/opt/intel/oneapi/mpi/latest//lib:/opt/intel/oneapi/mkl/latest/lib/intel64:/opt/intel/oneapi/debugger/10.1.2/gdb/intel64/lib:/opt/intel/oneapi/debugger/10.1.2/libipt/intel64/lib:/opt/intel/oneapi/debugger/10.1.2/dep/lib:/opt/intel/oneapi/compiler/latest/linux/lib:/opt/intel/oneapi/compiler/latest/linux/lib/x64:/opt/intel/oneapi/compiler/latest/linux/lib/emu:/opt/intel/oneapi/compiler/latest/linux/compiler/lib/intel64_lin
2024-07-10 03:01:32.993272: W tensorflow/stream_executor/cuda/cuda_driver.cc:269] failed call to cuInit: UNKNOWN ERROR (303)
OMP: Info #155: KMP_AFFINITY: Initial OS proc set respected: 0,1
OMP: Info #216: KMP_AFFINITY: decoding x2APIC ids.
OMP: Info #157: KMP_AFFINITY: 2 available OS procs
OMP: Info #158: KMP_AFFINITY: Uniform topology
OMP: Info #287: KMP_AFFINITY: topology layer "LL cache" is equivalent to "socket".
OMP: Info #287: KMP_AFFINITY: topology layer "L3 cache" is equivalent to "socket".
OMP: Info #287: KMP_AFFINITY: topology layer "L2 cache" is equivalent to "socket".
OMP: Info #287: KMP_AFFINITY: topology layer "L1 cache" is equivalent to "socket".
OMP: Info #192: KMP_AFFINITY: 1 socket x 1 core/socket x 2 threads/core (1 total cores)
OMP: Info #218: KMP_AFFINITY: OS proc to physical thread map:
OMP: Info #172: KMP_AFFINITY: OS proc 0 maps to socket 0 core 0 thread 0 
OMP: Info #172: KMP_AFFINITY: OS proc 1 maps to socket 0 core 0 thread 1 
OMP: Info #254: KMP_AFFINITY: pid 648 tid 658 thread 1 bound to OS proc set 1
OMP: Info #254: KMP_AFFINITY: pid 648 tid 660 thread 2 bound to OS proc set 0
OMP: Info #254: KMP_AFFINITY: pid 648 tid 657 thread 3 bound to OS proc set 1
OMP: Info #254: KMP_AFFINITY: pid 648 tid 661 thread 4 bound to OS proc set 0
DEEPMD INFO    training data with min nbor dist: 1.8824245191000222
DEEPMD INFO    training data with max nbor size: [33 34]
DEEPMD INFO     _____               _____   __  __  _____           _     _  _   
DEEPMD INFO    |  __ \             |  __ \ |  \/  ||  __ \         | |   (_)| |  
DEEPMD INFO    | |  | |  ___   ___ | |__) || \  / || |  | | ______ | | __ _ | |_ 
DEEPMD INFO    | |  | | / _ \ / _ \|  ___/ | |\/| || |  | ||______|| |/ /| || __|
DEEPMD INFO    | |__| ||  __/|  __/| |     | |  | || |__| |        |   < | || |_ 
DEEPMD INFO    |_____/  \___| \___||_|     |_|  |_||_____/         |_|\_\|_| \__|
DEEPMD INFO    Please read and cite:
DEEPMD INFO    Wang, Zhang, Han and E, Comput.Phys.Comm. 228, 178-184 (2018)
DEEPMD INFO    installed to:         /home/conda/feedstock_root/build_artifacts/deepmd-kit_1678943793317/work/_skbuild/linux-x86_64-3.10/cmake-install
DEEPMD INFO    source :              v2.2.1
DEEPMD INFO    source brach:         HEAD
DEEPMD INFO    source commit:        3ac8c4c7
DEEPMD INFO    source commit at:     2023-03-16 12:33:24 +0800
DEEPMD INFO    build float prec:     double
DEEPMD INFO    build variant:        cuda
DEEPMD INFO    build with tf inc:    /opt/deepmd-kit-2.2.1/lib/python3.10/site-packages/tensorflow/include;/opt/deepmd-kit-2.2.1/lib/python3.10/site-packages/tensorflow/../../../../include
DEEPMD INFO    build with tf lib:    
DEEPMD INFO    ---Summary of the training---------------------------------------
DEEPMD INFO    running on:           bohrium-16664-1159988
DEEPMD INFO    computing device:     cpu:0
DEEPMD INFO    CUDA_VISIBLE_DEVICES: unset
DEEPMD INFO    Count of visible GPU: 0
DEEPMD INFO    num_intra_threads:    0
DEEPMD INFO    num_inter_threads:    0
DEEPMD INFO    -----------------------------------------------------------------
DEEPMD INFO    ---Summary of DataSystem: training     -----------------------------------------------
DEEPMD INFO    found 1 system(s):
DEEPMD INFO                                        system  natoms  bch_sz   n_bch   prob  pbc
DEEPMD INFO                      ../00.data/training_data      64       1     401  1.000    T
DEEPMD INFO    --------------------------------------------------------------------------------------
DEEPMD INFO    ---Summary of DataSystem: validation   -----------------------------------------------
DEEPMD INFO    found 1 system(s):
DEEPMD INFO                                        system  natoms  bch_sz   n_bch   prob  pbc
DEEPMD INFO                    ../00.data/validation_data      64       1     100  1.000    T
DEEPMD INFO    --------------------------------------------------------------------------------------
DEEPMD INFO    training without frame parameter
Traceback (most recent call last):
  File "/opt/deepmd-kit-2.2.1/bin/dp", line 10, in <module>
    sys.exit(main())
  File "/opt/deepmd-kit-2.2.1/lib/python3.10/site-packages/deepmd/entrypoints/main.py", line 631, in main
    train_dp(**dict_args)
  File "/opt/deepmd-kit-2.2.1/lib/python3.10/site-packages/deepmd/entrypoints/train.py", line 164, in train
    _do_work(jdata, run_opt, is_compress)
  File "/opt/deepmd-kit-2.2.1/lib/python3.10/site-packages/deepmd/entrypoints/train.py", line 273, in _do_work
    model.build(train_data, stop_batch, origin_type_map=origin_type_map)
  File "/opt/deepmd-kit-2.2.1/lib/python3.10/site-packages/deepmd/train/trainer.py", line 509, in build
    self._init_from_ckpt(self.run_opt.restart)
  File "/opt/deepmd-kit-2.2.1/lib/python3.10/site-packages/deepmd/train/trainer.py", line 1178, in _init_from_ckpt
    tf.train.import_meta_graph(f"{ckpt_meta}.meta", clear_devices=True)
  File "/opt/deepmd-kit-2.2.1/lib/python3.10/site-packages/tensorflow/python/training/saver.py", line 1582, in import_meta_graph
    return _import_meta_graph_with_return_elements(meta_graph_or_file,
  File "/opt/deepmd-kit-2.2.1/lib/python3.10/site-packages/tensorflow/python/training/saver.py", line 1598, in _import_meta_graph_with_return_elements
    meta_graph_def = meta_graph.read_meta_graph_file(meta_graph_or_file)
  File "/opt/deepmd-kit-2.2.1/lib/python3.10/site-packages/tensorflow/python/framework/meta_graph.py", line 634, in read_meta_graph_file
    raise IOError(f"File does not exist. Received: {filename}.")
OSError: File does not exist. Received: /personal/bohr/licl-dp-tutorial-unuc/v1/LiCl_DP_Tutorial_Example/chapter3/01.train/model.ckpt.meta.

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Please note that input.json needs to remain consistent with the previous one.

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3.4 Freezing and Compressing the Model

At the end of training, the model parameters saved in the TensorFlow checkpoint file typically need to be frozen into a model file with the extension .pb. Simply execute:

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[11]

# This step requires you to complete the previous training steps and generate the necessary intermediate files before proceeding.

! cd ./LiCl_DP_Tutorial_Example/chapter3/01.train/ && dp freeze -o licl.pb

WARNING:tensorflow:From /opt/deepmd-kit-2.2.1/lib/python3.10/site-packages/tensorflow/python/compat/v2_compat.py:107: disable_resource_variables (from tensorflow.python.ops.variable_scope) is deprecated and will be removed in a future version.
Instructions for updating:
non-resource variables are not supported in the long term
WARNING:root:To get the best performance, it is recommended to adjust the number of threads by setting the environment variables OMP_NUM_THREADS, TF_INTRA_OP_PARALLELISM_THREADS, and TF_INTER_OP_PARALLELISM_THREADS. See https://deepmd.rtfd.io/parallelism/ for more information.
WARNING:root:Environment variable KMP_BLOCKTIME is empty. Use the default value 0
WARNING:root:Environment variable KMP_AFFINITY is empty. Use the default value granularity=fine,verbose,compact,1,0
/opt/deepmd-kit-2.2.1/lib/python3.10/importlib/__init__.py:169: UserWarning: The NumPy module was reloaded (imported a second time). This can in some cases result in small but subtle issues and is discouraged.
  _bootstrap._exec(spec, module)
Traceback (most recent call last):
  File "/opt/deepmd-kit-2.2.1/bin/dp", line 10, in <module>
    sys.exit(main())
  File "/opt/deepmd-kit-2.2.1/lib/python3.10/site-packages/deepmd/entrypoints/main.py", line 633, in main
    freeze(**dict_args)
  File "/opt/deepmd-kit-2.2.1/lib/python3.10/site-packages/deepmd/entrypoints/freeze.py", line 501, in freeze
    saver = tf.train.import_meta_graph(
  File "/opt/deepmd-kit-2.2.1/lib/python3.10/site-packages/tensorflow/python/training/saver.py", line 1582, in import_meta_graph
    return _import_meta_graph_with_return_elements(meta_graph_or_file,
  File "/opt/deepmd-kit-2.2.1/lib/python3.10/site-packages/tensorflow/python/training/saver.py", line 1598, in _import_meta_graph_with_return_elements
    meta_graph_def = meta_graph.read_meta_graph_file(meta_graph_or_file)
  File "/opt/deepmd-kit-2.2.1/lib/python3.10/site-packages/tensorflow/python/framework/meta_graph.py", line 634, in read_meta_graph_file
    raise IOError(f"File does not exist. Received: {filename}.")
OSError: File does not exist. Received: ./model.ckpt-400000.meta.

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It will output a model file named licl.pb in the current directory. Compressing the DP model typically enhances computational speed by an order of magnitude and requires less memory. licl.pb can be compressed as follows:

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[12]

! cd ./LiCl_DP_Tutorial_Example/chapter3/01.train/ && dp compress -i licl.pb -o licl-compress.pb

WARNING:tensorflow:From /opt/deepmd-kit-2.2.1/lib/python3.10/site-packages/tensorflow/python/compat/v2_compat.py:107: disable_resource_variables (from tensorflow.python.ops.variable_scope) is deprecated and will be removed in a future version.
Instructions for updating:
non-resource variables are not supported in the long term
WARNING:root:To get the best performance, it is recommended to adjust the number of threads by setting the environment variables OMP_NUM_THREADS, TF_INTRA_OP_PARALLELISM_THREADS, and TF_INTER_OP_PARALLELISM_THREADS. See https://deepmd.rtfd.io/parallelism/ for more information.
WARNING:root:Environment variable KMP_BLOCKTIME is empty. Use the default value 0
WARNING:root:Environment variable KMP_AFFINITY is empty. Use the default value granularity=fine,verbose,compact,1,0
/opt/deepmd-kit-2.2.1/lib/python3.10/importlib/__init__.py:169: UserWarning: The NumPy module was reloaded (imported a second time). This can in some cases result in small but subtle issues and is discouraged.
  _bootstrap._exec(spec, module)
2024-07-10 03:04:47.667937: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcuda.so.1'; dlerror: libcuda.so.1: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /opt/intel/oneapi/tbb/2021.5.1/env/../lib/intel64/gcc4.8:/opt/intel/oneapi/mpi/2021.5.1//libfabric/lib:/opt/intel/oneapi/mpi/2021.5.1//lib/release:/opt/intel/oneapi/mpi/2021.5.1//lib:/opt/intel/oneapi/mkl/2022.0.2/lib/intel64:/opt/intel/oneapi/debugger/2021.5.0/gdb/intel64/lib:/opt/intel/oneapi/debugger/2021.5.0/libipt/intel64/lib:/opt/intel/oneapi/debugger/2021.5.0/dep/lib:/opt/intel/oneapi/compiler/2022.0.2/linux/lib:/opt/intel/oneapi/compiler/2022.0.2/linux/lib/x64:/opt/intel/oneapi/compiler/2022.0.2/linux/lib/oclfpga/host/linux64/lib:/opt/intel/oneapi/compiler/2022.0.2/linux/compiler/lib/intel64_lin:/opt/intel/oneapi/tbb/latest/env/../lib/intel64/gcc4.8:/opt/intel/oneapi/mpi/latest//libfabric/lib:/opt/intel/oneapi/mpi/latest//lib/release:/opt/intel/oneapi/mpi/latest//lib:/opt/intel/oneapi/mkl/latest/lib/intel64:/opt/intel/oneapi/debugger/10.1.2/gdb/intel64/lib:/opt/intel/oneapi/debugger/10.1.2/libipt/intel64/lib:/opt/intel/oneapi/debugger/10.1.2/dep/lib:/opt/intel/oneapi/compiler/latest/linux/lib:/opt/intel/oneapi/compiler/latest/linux/lib/x64:/opt/intel/oneapi/compiler/latest/linux/lib/emu:/opt/intel/oneapi/compiler/latest/linux/compiler/lib/intel64_lin
2024-07-10 03:04:47.668016: W tensorflow/stream_executor/cuda/cuda_driver.cc:269] failed call to cuInit: UNKNOWN ERROR (303)
DEEPMD INFO    


DEEPMD INFO    stage 1: compress the model
DEEPMD INFO     _____               _____   __  __  _____           _     _  _   
DEEPMD INFO    |  __ \             |  __ \ |  \/  ||  __ \         | |   (_)| |  
DEEPMD INFO    | |  | |  ___   ___ | |__) || \  / || |  | | ______ | | __ _ | |_ 
DEEPMD INFO    | |  | | / _ \ / _ \|  ___/ | |\/| || |  | ||______|| |/ /| || __|
DEEPMD INFO    | |__| ||  __/|  __/| |     | |  | || |__| |        |   < | || |_ 
DEEPMD INFO    |_____/  \___| \___||_|     |_|  |_||_____/         |_|\_\|_| \__|
DEEPMD INFO    Please read and cite:
DEEPMD INFO    Wang, Zhang, Han and E, Comput.Phys.Comm. 228, 178-184 (2018)
DEEPMD INFO    installed to:         /home/conda/feedstock_root/build_artifacts/deepmd-kit_1678943793317/work/_skbuild/linux-x86_64-3.10/cmake-install
DEEPMD INFO    source :              v2.2.1
DEEPMD INFO    source brach:         HEAD
DEEPMD INFO    source commit:        3ac8c4c7
DEEPMD INFO    source commit at:     2023-03-16 12:33:24 +0800
DEEPMD INFO    build float prec:     double
DEEPMD INFO    build variant:        cuda
DEEPMD INFO    build with tf inc:    /opt/deepmd-kit-2.2.1/lib/python3.10/site-packages/tensorflow/include;/opt/deepmd-kit-2.2.1/lib/python3.10/site-packages/tensorflow/../../../../include
DEEPMD INFO    build with tf lib:    
DEEPMD INFO    ---Summary of the training---------------------------------------
DEEPMD INFO    running on:           bohrium-16664-1159988
DEEPMD INFO    computing device:     cpu:0
DEEPMD INFO    CUDA_VISIBLE_DEVICES: unset
DEEPMD INFO    Count of visible GPU: 0
DEEPMD INFO    num_intra_threads:    0
DEEPMD INFO    num_inter_threads:    0
DEEPMD INFO    -----------------------------------------------------------------
DEEPMD INFO    training without frame parameter
DEEPMD INFO    training data with lower boundary: [-0.24472768 -0.24716247]
DEEPMD INFO    training data with upper boundary: [10.1033889  10.30164264]
OMP: Info #155: KMP_AFFINITY: Initial OS proc set respected: 0,1
OMP: Info #216: KMP_AFFINITY: decoding x2APIC ids.
OMP: Info #157: KMP_AFFINITY: 2 available OS procs
OMP: Info #158: KMP_AFFINITY: Uniform topology
OMP: Info #287: KMP_AFFINITY: topology layer "LL cache" is equivalent to "socket".
OMP: Info #287: KMP_AFFINITY: topology layer "L3 cache" is equivalent to "socket".
OMP: Info #287: KMP_AFFINITY: topology layer "L2 cache" is equivalent to "socket".
OMP: Info #287: KMP_AFFINITY: topology layer "L1 cache" is equivalent to "socket".
OMP: Info #192: KMP_AFFINITY: 1 socket x 1 core/socket x 2 threads/core (1 total cores)
OMP: Info #218: KMP_AFFINITY: OS proc to physical thread map:
OMP: Info #172: KMP_AFFINITY: OS proc 0 maps to socket 0 core 0 thread 0 
OMP: Info #172: KMP_AFFINITY: OS proc 1 maps to socket 0 core 0 thread 1 
OMP: Info #254: KMP_AFFINITY: pid 665 tid 665 thread 0 bound to OS proc set 0
DEEPMD INFO    built lr
DEEPMD INFO    built network
DEEPMD INFO    built training
WARNING:root:To get the best performance, it is recommended to adjust the number of threads by setting the environment variables OMP_NUM_THREADS, TF_INTRA_OP_PARALLELISM_THREADS, and TF_INTER_OP_PARALLELISM_THREADS. See https://deepmd.rtfd.io/parallelism/ for more information.
DEEPMD INFO    initialize model from scratch
DEEPMD INFO    finished compressing
DEEPMD INFO    


DEEPMD INFO    stage 2: freeze the model
DEEPMD INFO    The following nodes will be frozen: ['model_type', 'descrpt_attr/rcut', 'descrpt_attr/ntypes', 'model_attr/tmap', 'model_attr/model_type', 'model_attr/model_version', 'train_attr/min_nbor_dist', 'train_attr/training_script', 'o_energy', 'o_force', 'o_virial', 'o_atom_energy', 'o_atom_virial', 'fitting_attr/dfparam', 'fitting_attr/daparam']
WARNING:tensorflow:From /opt/deepmd-kit-2.2.1/lib/python3.10/site-packages/deepmd/entrypoints/freeze.py:354: convert_variables_to_constants (from tensorflow.python.framework.graph_util_impl) is deprecated and will be removed in a future version.
Instructions for updating:
Use `tf.compat.v1.graph_util.convert_variables_to_constants`
WARNING:tensorflow:From /opt/deepmd-kit-2.2.1/lib/python3.10/site-packages/deepmd/entrypoints/freeze.py:354: convert_variables_to_constants (from tensorflow.python.framework.graph_util_impl) is deprecated and will be removed in a future version.
Instructions for updating:
Use `tf.compat.v1.graph_util.convert_variables_to_constants`
WARNING:tensorflow:From /opt/deepmd-kit-2.2.1/lib/python3.10/site-packages/tensorflow/python/framework/convert_to_constants.py:925: extract_sub_graph (from tensorflow.python.framework.graph_util_impl) is deprecated and will be removed in a future version.
Instructions for updating:
Use `tf.compat.v1.graph_util.extract_sub_graph`
WARNING:tensorflow:From /opt/deepmd-kit-2.2.1/lib/python3.10/site-packages/tensorflow/python/framework/convert_to_constants.py:925: extract_sub_graph (from tensorflow.python.framework.graph_util_impl) is deprecated and will be removed in a future version.
Instructions for updating:
Use `tf.compat.v1.graph_util.extract_sub_graph`
DEEPMD INFO    847 ops in the final graph.

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It will output a model file named licl-compress.pb

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3.5 Model Testing

We can check the quality of the trained model by running the following command

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[13]

! cd ./LiCl_DP_Tutorial_Example/chapter3/01.train/ && dp test -m licl-compress.pb -s ../00.data/validation_data -n 100 -d results

WARNING:tensorflow:From /opt/deepmd-kit-2.2.1/lib/python3.10/site-packages/tensorflow/python/compat/v2_compat.py:107: disable_resource_variables (from tensorflow.python.ops.variable_scope) is deprecated and will be removed in a future version.
Instructions for updating:
non-resource variables are not supported in the long term
WARNING:root:To get the best performance, it is recommended to adjust the number of threads by setting the environment variables OMP_NUM_THREADS, TF_INTRA_OP_PARALLELISM_THREADS, and TF_INTER_OP_PARALLELISM_THREADS. See https://deepmd.rtfd.io/parallelism/ for more information.
WARNING:root:Environment variable KMP_BLOCKTIME is empty. Use the default value 0
WARNING:root:Environment variable KMP_AFFINITY is empty. Use the default value granularity=fine,verbose,compact,1,0
/opt/deepmd-kit-2.2.1/lib/python3.10/importlib/__init__.py:169: UserWarning: The NumPy module was reloaded (imported a second time). This can in some cases result in small but subtle issues and is discouraged.
  _bootstrap._exec(spec, module)
2024-07-10 03:07:20.858856: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcuda.so.1'; dlerror: libcuda.so.1: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /opt/intel/oneapi/tbb/2021.5.1/env/../lib/intel64/gcc4.8:/opt/intel/oneapi/mpi/2021.5.1//libfabric/lib:/opt/intel/oneapi/mpi/2021.5.1//lib/release:/opt/intel/oneapi/mpi/2021.5.1//lib:/opt/intel/oneapi/mkl/2022.0.2/lib/intel64:/opt/intel/oneapi/debugger/2021.5.0/gdb/intel64/lib:/opt/intel/oneapi/debugger/2021.5.0/libipt/intel64/lib:/opt/intel/oneapi/debugger/2021.5.0/dep/lib:/opt/intel/oneapi/compiler/2022.0.2/linux/lib:/opt/intel/oneapi/compiler/2022.0.2/linux/lib/x64:/opt/intel/oneapi/compiler/2022.0.2/linux/lib/oclfpga/host/linux64/lib:/opt/intel/oneapi/compiler/2022.0.2/linux/compiler/lib/intel64_lin:/opt/intel/oneapi/tbb/latest/env/../lib/intel64/gcc4.8:/opt/intel/oneapi/mpi/latest//libfabric/lib:/opt/intel/oneapi/mpi/latest//lib/release:/opt/intel/oneapi/mpi/latest//lib:/opt/intel/oneapi/mkl/latest/lib/intel64:/opt/intel/oneapi/debugger/10.1.2/gdb/intel64/lib:/opt/intel/oneapi/debugger/10.1.2/libipt/intel64/lib:/opt/intel/oneapi/debugger/10.1.2/dep/lib:/opt/intel/oneapi/compiler/latest/linux/lib:/opt/intel/oneapi/compiler/latest/linux/lib/x64:/opt/intel/oneapi/compiler/latest/linux/lib/emu:/opt/intel/oneapi/compiler/latest/linux/compiler/lib/intel64_lin
2024-07-10 03:07:20.858922: W tensorflow/stream_executor/cuda/cuda_driver.cc:269] failed call to cuInit: UNKNOWN ERROR (303)
WARNING:tensorflow:From /opt/deepmd-kit-2.2.1/lib/python3.10/site-packages/deepmd/utils/batch_size.py:61: is_gpu_available (from tensorflow.python.framework.test_util) is deprecated and will be removed in a future version.
Instructions for updating:
Use `tf.config.list_physical_devices('GPU')` instead.
WARNING:tensorflow:From /opt/deepmd-kit-2.2.1/lib/python3.10/site-packages/deepmd/utils/batch_size.py:61: is_gpu_available (from tensorflow.python.framework.test_util) is deprecated and will be removed in a future version.
Instructions for updating:
Use `tf.config.list_physical_devices('GPU')` instead.
DEEPMD WARNING You can use the environment variable DP_INFER_BATCH_SIZE tocontrol the inference batch size (nframes * natoms). The default value is 1024.
DEEPMD INFO    # ---------------output of dp test--------------- 
DEEPMD INFO    # testing system : ../00.data/validation_data
OMP: Info #155: KMP_AFFINITY: Initial OS proc set respected: 0,1
OMP: Info #216: KMP_AFFINITY: decoding x2APIC ids.
OMP: Info #157: KMP_AFFINITY: 2 available OS procs
OMP: Info #158: KMP_AFFINITY: Uniform topology
OMP: Info #287: KMP_AFFINITY: topology layer "LL cache" is equivalent to "socket".
OMP: Info #287: KMP_AFFINITY: topology layer "L3 cache" is equivalent to "socket".
OMP: Info #287: KMP_AFFINITY: topology layer "L2 cache" is equivalent to "socket".
OMP: Info #287: KMP_AFFINITY: topology layer "L1 cache" is equivalent to "socket".
OMP: Info #192: KMP_AFFINITY: 1 socket x 1 core/socket x 2 threads/core (1 total cores)
OMP: Info #218: KMP_AFFINITY: OS proc to physical thread map:
OMP: Info #172: KMP_AFFINITY: OS proc 0 maps to socket 0 core 0 thread 0 
OMP: Info #172: KMP_AFFINITY: OS proc 1 maps to socket 0 core 0 thread 1 
OMP: Info #254: KMP_AFFINITY: pid 902 tid 907 thread 1 bound to OS proc set 1
OMP: Info #254: KMP_AFFINITY: pid 902 tid 909 thread 2 bound to OS proc set 0
OMP: Info #254: KMP_AFFINITY: pid 902 tid 906 thread 3 bound to OS proc set 1
OMP: Info #254: KMP_AFFINITY: pid 902 tid 910 thread 4 bound to OS proc set 0
DEEPMD INFO    # number of test data : 100 
DEEPMD INFO    Energy MAE         : 1.472397e-02 eV
DEEPMD INFO    Energy RMSE        : 1.823565e-02 eV
DEEPMD INFO    Energy MAE/Natoms  : 2.300620e-04 eV
DEEPMD INFO    Energy RMSE/Natoms : 2.849320e-04 eV
DEEPMD INFO    Force  MAE         : 1.161022e-02 eV/A
DEEPMD INFO    Force  RMSE        : 1.451888e-02 eV/A
DEEPMD INFO    Virial MAE         : 1.847978e+00 eV
DEEPMD INFO    Virial RMSE        : 3.063811e+00 eV
DEEPMD INFO    Virial MAE/Natoms  : 2.887466e-02 eV
DEEPMD INFO    Virial RMSE/Natoms : 4.787205e-02 eV
DEEPMD INFO    # -----------------------------------------------

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On the screen, you can see the prediction error information for the validation data.

It will output files named results.e.out and results.f.out in the current directory. Similarly, you can visualize this file using a simple Python script:

代码

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[14]

import numpy as np

import matplotlib.pyplot as plt

# 定义绘制散点图和对角线的函数

def plot(ax, data, key, xlabel, ylabel, min_val, max_val):

data_key = f'data_{key}'

pred_key = f'pred_{key}'

ax.scatter(data[data_key], data[pred_key], label=key, s=6)

ax.legend()

ax.set_xlabel(xlabel)

ax.set_ylabel(ylabel)

ax.set_xlim(min_val, max_val)

ax.set_ylim(min_val, max_val)

ax.plot([min_val, max_val], [min_val, max_val], 'r', lw=1)

# 读取数据，并对e数据进行原子化处理

natom = 64

data_e = np.genfromtxt("./LiCl_DP_Tutorial_Example/chapter3/01.train/results.e.out", names=["data_e", "pred_e"])

data_f = np.genfromtxt("./LiCl_DP_Tutorial_Example/chapter3/01.train/results.f.out", names=["data_fx", "data_fy", "data_fz", "pred_fx", "pred_fy", "pred_fz"])

for col in ['data_e', 'pred_e']:

data_e[col] /= natom

# 计算e和f的最小值和最大值

data_e_stacked = np.column_stack((data_e['data_e'], data_e['pred_e']))

data_f_stacked = np.column_stack((data_f['data_fx'], data_f['data_fy'], data_f['data_fz'], data_f['pred_fx'], data_f['pred_fy'], data_f['pred_fz']))

min_val_e, max_val_e = np.min(data_e_stacked), np.max(data_e_stacked)

min_val_f, max_val_f = np.min(data_f_stacked), np.max(data_f_stacked)

# 绘制散点图并保存结果

fig, axs = plt.subplots(1, 2, figsize=(12, 5))

plot(axs[0], data_e, 'e', 'DFT energy (eV/atom)', 'DP energy (eV/atom)', min_val_e, max_val_e)

for force_direction in ['fx', 'fy', 'fz']:

plot(axs[1], data_f, force_direction, 'DFT force (eV/Å)', 'DP force (eV/Å)', min_val_f, max_val_f)

plt.show()

代码

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3.6 Running Deep Potential Molecular Dynamics with LAMMPS

代码

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First, we will copy the DP model from the 01.train directory to the 02.lmp directory.

代码

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[15]

! cd ./LiCl_DP_Tutorial_Example/chapter3/02.lmp/ && cp ../01.train/licl-compress.pb ./

代码

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[16]

! cd ./LiCl_DP_Tutorial_Example/chapter3/02.lmp/ && ls

64_dpmd_rdf.png  licl-compress.pb  licl.dump  licl.rdf
ave_rdf.txt	 licl.data	   licl.in    log.lammps

代码

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The file licl.data provides the initial configuration for LiCl molten salt MD simulation, while licl.in is the LAMMPS input script. You can inspect licl.in and find that it is a fairly standard LAMMPS input file for MD simulation, with slight differences in atomic types and potential parameters settings compared to licl.in in Chapter 1:

atom_style  atomic

and

pair_style  licl-compress.pb
pair_coeff  * *

Here, the pair_style command invokes the licl-compress.pb pair style, using the DP model file licl-compress.pb, indicating that the atomic interactions will be computed by the DP model named licl-compress.pb. You can execute it in the usual manner:

代码

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[17]

# ###### Time Warning: 19 minutes 16 seconds #####################

! cd ./LiCl_DP_Tutorial_Example/chapter3/02.lmp/ && lmp -i licl.in

Warning:
This LAMMPS executable is in a conda environment, but the environment has
not been activated. Libraries may fail to load. To activate this environment
please see https://conda.io/activation.
LAMMPS (23 Jun 2022 - Update 1)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
Loaded 1 plugins from /opt/deepmd-kit-2.2.1/lib/deepmd_lmp
Reading data file ...
  orthogonal box = (0 0 0) to (11.858 11.858 11.858)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  64 atoms
  read_data CPU = 0.020 seconds
DeePMD-kit WARNING: Environmental variable TF_INTRA_OP_PARALLELISM_THREADS is not set. Tune TF_INTRA_OP_PARALLELISM_THREADS for the best performance. See https://deepmd.rtfd.io/parallelism/ for more information.
DeePMD-kit WARNING: Environmental variable TF_INTER_OP_PARALLELISM_THREADS is not set. Tune TF_INTER_OP_PARALLELISM_THREADS for the best performance. See https://deepmd.rtfd.io/parallelism/ for more information.
DeePMD-kit WARNING: Environmental variable OMP_NUM_THREADS is not set. Tune OMP_NUM_THREADS for the best performance. See https://deepmd.rtfd.io/parallelism/ for more information.
Summary of lammps deepmd module ...
  >>> Info of deepmd-kit:
  installed to:       /opt/deepmd-kit-2.2.1
  source:             v2.2.1
  source branch:       HEAD
  source commit:      3ac8c4c7
  source commit at:   2023-03-16 12:33:24 +0800
  surpport model ver.:1.1 
  build variant:      cuda
  build with tf inc:  /opt/deepmd-kit-2.2.1/include;/opt/deepmd-kit-2.2.1/include
  build with tf lib:  /opt/deepmd-kit-2.2.1/lib/libtensorflow_cc.so
  set tf intra_op_parallelism_threads: 0
  set tf inter_op_parallelism_threads: 0
  >>> Info of lammps module:
  use deepmd-kit at:  /opt/deepmd-kit-2.2.1DeePMD-kit WARNING: Environmental variable TF_INTRA_OP_PARALLELISM_THREADS is not set. Tune TF_INTRA_OP_PARALLELISM_THREADS for the best performance. See https://deepmd.rtfd.io/parallelism/ for more information.
DeePMD-kit WARNING: Environmental variable TF_INTER_OP_PARALLELISM_THREADS is not set. Tune TF_INTER_OP_PARALLELISM_THREADS for the best performance. See https://deepmd.rtfd.io/parallelism/ for more information.
DeePMD-kit WARNING: Environmental variable OMP_NUM_THREADS is not set. Tune OMP_NUM_THREADS for the best performance. See https://deepmd.rtfd.io/parallelism/ for more information.
DeePMD-kit: Successfully load libcudart.so
2024-07-10 03:11:04.107250: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  SSE4.1 SSE4.2 AVX AVX2 AVX512F FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
2024-07-10 03:11:04.111795: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcuda.so.1'; dlerror: libcuda.so.1: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /opt/intel/oneapi/tbb/2021.5.1/env/../lib/intel64/gcc4.8:/opt/intel/oneapi/mpi/2021.5.1//libfabric/lib:/opt/intel/oneapi/mpi/2021.5.1//lib/release:/opt/intel/oneapi/mpi/2021.5.1//lib:/opt/intel/oneapi/mkl/2022.0.2/lib/intel64:/opt/intel/oneapi/debugger/2021.5.0/gdb/intel64/lib:/opt/intel/oneapi/debugger/2021.5.0/libipt/intel64/lib:/opt/intel/oneapi/debugger/2021.5.0/dep/lib:/opt/intel/oneapi/compiler/2022.0.2/linux/lib:/opt/intel/oneapi/compiler/2022.0.2/linux/lib/x64:/opt/intel/oneapi/compiler/2022.0.2/linux/lib/oclfpga/host/linux64/lib:/opt/intel/oneapi/compiler/2022.0.2/linux/compiler/lib/intel64_lin:/opt/intel/oneapi/tbb/latest/env/../lib/intel64/gcc4.8:/opt/intel/oneapi/mpi/latest//libfabric/lib:/opt/intel/oneapi/mpi/latest//lib/release:/opt/intel/oneapi/mpi/latest//lib:/opt/intel/oneapi/mkl/latest/lib/intel64:/opt/intel/oneapi/debugger/10.1.2/gdb/intel64/lib:/opt/intel/oneapi/debugger/10.1.2/libipt/intel64/lib:/opt/intel/oneapi/debugger/10.1.2/dep/lib:/opt/intel/oneapi/compiler/latest/linux/lib:/opt/intel/oneapi/compiler/latest/linux/lib/x64:/opt/intel/oneapi/compiler/latest/linux/lib/emu:/opt/intel/oneapi/compiler/latest/linux/compiler/lib/intel64_lin
2024-07-10 03:11:04.111847: W tensorflow/stream_executor/cuda/cuda_driver.cc:269] failed call to cuInit: UNKNOWN ERROR (303)
2024-07-10 03:11:04.111873: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:156] kernel driver does not appear to be running on this host (bohrium-16664-1159988): /proc/driver/nvidia/version does not exist
2024-07-10 03:11:04.113327: I tensorflow/core/common_runtime/process_util.cc:146] Creating new thread pool with default inter op setting: 2. Tune using inter_op_parallelism_threads for best performance.
2024-07-10 03:11:04.197233: I tensorflow/compiler/mlir/mlir_graph_optimization_pass.cc:354] MLIR V1 optimization pass is not enabled
  >>> Info of model(s):
  using   1 model(s): licl-compress.pb 
  rcut in model:      7
  ntypes in model:    2

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:
- USER-DEEPMD package:
The log file lists these citations in BibTeX format.

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 9
  ghost atom cutoff = 9
  binsize = 4.5, bins = 3 3 3
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) pair deepmd, perpetual
      attributes: full, newton on
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
  (2) compute rdf, occasional, half/full from (1)
      attributes: half, newton on
      pair build: halffull/newton
      stencil: none
      bin: none
Setting up Verlet run ...
  Unit style    : metal
  Current step  : 0
  Time step     : 0.001
Per MPI rank memory allocation (min/avg/max) = 4.977 | 4.977 | 4.977 Mbytes
   Step          Temp          PotEng         KinEng         TotEng         Press            Lx             Ly             Lz           Volume    
         0   900           -19445.201      7.3290502     -19437.872      36588.638      11.858         11.858         11.858         1667.379     
       100   1239.5096     -19448.148      10.093809     -19438.054      7389.6631      11.858         11.858         11.858         1667.379     
       200   1388.4727     -19449.85       11.306874     -19438.543     -1175.0665      11.858         11.858         11.858         1667.379     
       300   1267.658      -19449.685      10.323033     -19439.362     -7593.0439      11.858         11.858         11.858         1667.379     
       400   1072.3278     -19448.761      8.7323827     -19440.028     -7637.8198      11.858         11.858         11.858         1667.379     
       500   1094.3278     -19449.474      8.9115375     -19440.563      4726.4417      11.858         11.858         11.858         1667.379     
       600   1091.9255     -19449.857      8.891974      -19440.965     -1639.5567      11.858         11.858         11.858         1667.379     
       700   978.45083     -19449.26       7.9679058     -19441.292     -6562.0427      11.858         11.858         11.858         1667.379     
       800   938.34051     -19449.267      7.6412719     -19441.626     -6032.7519      11.858         11.858         11.858         1667.379     
       900   900.18891     -19449.251      7.3305886     -19441.921     -1348.8699      11.858         11.858         11.858         1667.379     
      1000   970.49173     -19450.159      7.9030918     -19442.256     -668.55083      11.858         11.858         11.858         1667.379     
      1100   983.43404     -19450.608      8.0084861     -19442.6       -7984.5791      11.858         11.858         11.858         1667.379     
      1200   900.66127     -19450.292      7.3344352     -19442.958     -8906.7617      11.858         11.858         11.858         1667.379     
      1300   835.29156     -19450.09       6.8021042     -19443.288     -10500.828      11.858         11.858         11.858         1667.379     
      1400   841.41153     -19450.403      6.8519415     -19443.551      456.59552      11.858         11.858         11.858         1667.379     
      1500   986.60961     -19451.818      8.034346      -19443.784     -10780.037      11.858         11.858         11.858         1667.379     
      1600   816.36169     -19450.65       6.6479509     -19444.002     -9841.5386      11.858         11.858         11.858         1667.379     
      1700   820.90107     -19450.862      6.6849168     -19444.177     -3949.8897      11.858         11.858         11.858         1667.379     
      1800   760.01078     -19450.492      6.1890636     -19444.303      1945.8401      11.858         11.858         11.858         1667.379     
      1900   882.7417      -19451.541      7.1885092     -19444.353     -5293.7636      11.858         11.858         11.858         1667.379     
      2000   737.65659     -19450.371      6.0070247     -19444.364     -9450.7702      11.858         11.858         11.858         1667.379     
      2100   882.05965     -19451.508      7.182955      -19444.325      396.60561      11.858         11.858         11.858         1667.379     
      2200   871.18362     -19451.348      7.0943872     -19444.253     -3338.5898      11.858         11.858         11.858         1667.379     
      2300   865.78292     -19451.216      7.0504072     -19444.166     -7554.1853      11.858         11.858         11.858         1667.379     
      2400   801.34553     -19450.584      6.5256685     -19444.059     -5283.7631      11.858         11.858         11.858         1667.379     
      2500   820.80847     -19450.567      6.6841628     -19443.882     -4840.4647      11.858         11.858         11.858         1667.379     
      2600   884.65087     -19450.82       7.2040563     -19443.616     -3597.7613      11.858         11.858         11.858         1667.379     
      2700   931.48309     -19450.925      7.5854293     -19443.339     -10656.046      11.858         11.858         11.858         1667.379     
      2800   980.0337      -19451.009      7.9807958     -19443.028     -5559.4892      11.858         11.858         11.858         1667.379     
      2900   925.82281     -19450.327      7.5393354     -19442.788     -3044.4207      11.858         11.858         11.858         1667.379     
      3000   958.20434     -19450.379      7.8030308     -19442.576     -3534.319       11.858         11.858         11.858         1667.379     
      3100   885.92683     -19449.577      7.2144469     -19442.363     -212.83756      11.858         11.858         11.858         1667.379     
      3200   920.74873     -19449.697      7.4980152     -19442.199     -7681.316       11.858         11.858         11.858         1667.379     
      3300   977.98169     -19450.006      7.9640855     -19442.042     -7198.5226      11.858         11.858         11.858         1667.379     
      3400   1054.3709     -19450.515      8.5861527     -19441.929     -6022.7063      11.858         11.858         11.858         1667.379     
      3500   964.30139     -19449.713      7.8526815     -19441.86       1401.5708      11.858         11.858         11.858         1667.379     
      3600   1165.7123     -19451.31       9.4928486     -19441.818     -753.13809      11.858         11.858         11.858         1667.379     
      3700   926.47227     -19449.435      7.5446242     -19441.89      -1048.1011      11.858         11.858         11.858         1667.379     
      3800   1008.2885     -19450.343      8.2108859     -19442.132     -7800.0004      11.858         11.858         11.858         1667.379     
      3900   871.37135     -19449.664      7.095916      -19442.568     -3755.2675      11.858         11.858         11.858         1667.379     
      4000   1005.0823     -19451.354      8.1847765     -19443.17      -5656.4755      11.858         11.858         11.858         1667.379     
      4100   849.62925     -19450.649      6.9188616     -19443.73      -5239.5105      11.858         11.858         11.858         1667.379     
      4200   801.89385     -19450.66       6.5301336     -19444.13      -5234.341       11.858         11.858         11.858         1667.379     
      4300   883.90854     -19451.617      7.1980112     -19444.419      2994.9141      11.858         11.858         11.858         1667.379     
      4400   802.8445      -19451.138      6.5378752     -19444.6       -3870.7097      11.858         11.858         11.858         1667.379     
      4500   768.29633     -19450.972      6.256536      -19444.715     -4446.9026      11.858         11.858         11.858         1667.379     
      4600   781.50618     -19451.143      6.364109      -19444.779     -8048.6244      11.858         11.858         11.858         1667.379     
      4700   959.66851     -19452.592      7.8149541     -19444.777     -6215.3084      11.858         11.858         11.858         1667.379     
      4800   838.23065     -19451.573      6.8260383     -19444.747     -2781.335       11.858         11.858         11.858         1667.379     
      4900   775.8097      -19451.003      6.3177203     -19444.685     -1734.4792      11.858         11.858         11.858         1667.379     
      5000   876.92682     -19451.722      7.1411563     -19444.581      165.4065       11.858         11.858         11.858         1667.379     
      5100   907.32634     -19451.822      7.3887115     -19444.433     -2678.2293      11.858         11.858         11.858         1667.379     
      5200   901.78337     -19451.567      7.3435729     -19444.223     -5548.0703      11.858         11.858         11.858         1667.379     
      5300   1001.7427     -19452.158      8.1575807     -19444.001     -8312.1587      11.858         11.858         11.858         1667.379     
      5400   1061.5537     -19452.417      8.6446447     -19443.772     -3882.3033      11.858         11.858         11.858         1667.379     
      5500   980.33792     -19451.558      7.9832731     -19443.575     -6080.0686      11.858         11.858         11.858         1667.379     
      5600   984.77745     -19451.429      8.019426      -19443.409     -4697.2902      11.858         11.858         11.858         1667.379     
      5700   871.7185      -19450.368      7.098743      -19443.27      -7665.9346      11.858         11.858         11.858         1667.379     
      5800   966.00081     -19450.956      7.8665205     -19443.089     -3766.6574      11.858         11.858         11.858         1667.379     
      5900   933.80693     -19450.488      7.6043532     -19442.884     -1407.0886      11.858         11.858         11.858         1667.379     
      6000   847.00552     -19449.567      6.8974956     -19442.67      -7817.712       11.858         11.858         11.858         1667.379     
      6100   892.15468     -19449.648      7.2651627     -19442.382     -7506.6098      11.858         11.858         11.858         1667.379     
      6200   1077.2616     -19450.831      8.7725604     -19442.058     -6312.2392      11.858         11.858         11.858         1667.379     
      6300   1179.695      -19451.327      9.6067154     -19441.72      -2762.2864      11.858         11.858         11.858         1667.379     
      6400   1046.8684     -19449.96       8.5250571     -19441.435      1455.9489      11.858         11.858         11.858         1667.379     
      6500   1075.4062     -19449.918      8.7574511     -19441.161     -576.47835      11.858         11.858         11.858         1667.379     
      6600   1091.8995     -19449.852      8.8917624     -19440.96       2689.4395      11.858         11.858         11.858         1667.379     
      6700   1232.6158     -19450.892      10.03767      -19440.854      1566.4043      11.858         11.858         11.858         1667.379     
      6800   1095.0453     -19449.849      8.91738       -19440.932     -2917.5259      11.858         11.858         11.858         1667.379     
      6900   1009.6373     -19449.388      8.2218696     -19441.166      6069.5849      11.858         11.858         11.858         1667.379     
      7000   1092.2163     -19450.495      8.8943421     -19441.6        2566.2643      11.858         11.858         11.858         1667.379     
      7100   970.46111     -19450.115      7.9028424     -19442.213     -5767.9383      11.858         11.858         11.858         1667.379     
      7200   1005.6022     -19451.057      8.1890102     -19442.868      810.97943      11.858         11.858         11.858         1667.379     
      7300   954.99041     -19451.204      7.7768585     -19443.427     -6672.0336      11.858         11.858         11.858         1667.379     
      7400   856.16408     -19450.719      6.9720773     -19443.746     -4413.0927      11.858         11.858         11.858         1667.379     
      7500   868.70131     -19450.994      7.0741728     -19443.919     -4944.6173      11.858         11.858         11.858         1667.379     
      7600   935.58442     -19451.68       7.618828      -19444.061     -11057.741      11.858         11.858         11.858         1667.379     
      7700   903.97401     -19451.536      7.3614121     -19444.174     -2039.7116      11.858         11.858         11.858         1667.379     
      7800   869.55213     -19451.334      7.0811014     -19444.252     -1133.7715      11.858         11.858         11.858         1667.379     
      7900   945.00262     -19451.999      7.6955241     -19444.303     -78.130308      11.858         11.858         11.858         1667.379     
      8000   907.79099     -19451.743      7.3924953     -19444.351     -4234.4188      11.858         11.858         11.858         1667.379     
      8100   860.19995     -19451.38       7.0049429     -19444.376     -861.50397      11.858         11.858         11.858         1667.379     
      8200   842.76442     -19451.251      6.8629586     -19444.388     -6525.0298      11.858         11.858         11.858         1667.379     
      8300   852.84077     -19451.32       6.9450143     -19444.375     -2955.9908      11.858         11.858         11.858         1667.379     
      8400   868.26305     -19451.422      7.0706039     -19444.352      5417.0974      11.858         11.858         11.858         1667.379     
      8500   899.19081     -19451.671      7.3224607     -19444.348     -274.70671      11.858         11.858         11.858         1667.379     
      8600   895.79521     -19451.677      7.2948089     -19444.382      1665.2578      11.858         11.858         11.858         1667.379     
      8700   992.20886     -19452.496      8.0799429     -19444.416      1270.3339      11.858         11.858         11.858         1667.379     
      8800   921.31806     -19451.98       7.5026515     -19444.477     -2968.8086      11.858         11.858         11.858         1667.379     
      8900   762.6794      -19450.744      6.2107952     -19444.533      1642.7641      11.858         11.858         11.858         1667.379     
      9000   822.7083      -19451.257      6.6996339     -19444.558     -8685.9783      11.858         11.858         11.858         1667.379     
      9100   872.89789     -19451.672      7.1083472     -19444.564     -813.3125       11.858         11.858         11.858         1667.379     
      9200   904.52922     -19451.941      7.3659335     -19444.575      1520.4786      11.858         11.858         11.858         1667.379     
      9300   936.94122     -19452.217      7.629877      -19444.588     -5771.194       11.858         11.858         11.858         1667.379     
      9400   843.49045     -19451.457      6.868871      -19444.588      3036.8212      11.858         11.858         11.858         1667.379     
      9500   821.34841     -19451.215      6.6885597     -19444.527     -7464.5921      11.858         11.858         11.858         1667.379     
      9600   958.3948      -19452.214      7.8045818     -19444.41      -3067.1472      11.858         11.858         11.858         1667.379     
      9700   821.31266     -19450.946      6.6882686     -19444.258     -519.75183      11.858         11.858         11.858         1667.379     
      9800   904.86511     -19451.402      7.3686687     -19444.033      104.44263      11.858         11.858         11.858         1667.379     
      9900   1027.937      -19452.114      8.3708908     -19443.743     -1637.1414      11.858         11.858         11.858         1667.379     
     10000   1015.2749     -19451.673      8.2677788     -19443.405     -946.42914      11.858         11.858         11.858         1667.379     
     10100   930.45187     -19450.703      7.5770316     -19443.126     -2132.9258      11.858         11.858         11.858         1667.379     
     10200   974.84537     -19450.821      7.9385452     -19442.883     -8185.7659      11.858         11.858         11.858         1667.379     
     10300   941.90903     -19450.36       7.6703317     -19442.69      -1190.0634      11.858         11.858         11.858         1667.379     
     10400   889.07736     -19449.761      7.2401029     -19442.521     -4593.7157      11.858         11.858         11.858         1667.379     
     10500   1125.7626     -19451.489      9.1675229     -19442.321     -3800.7046      11.858         11.858         11.858         1667.379     
     10600   988.83705     -19450.241      8.0524848     -19442.188     -173.63884      11.858         11.858         11.858         1667.379     
     10700   939.91691     -19449.768      7.6541091     -19442.114     -1321.8809      11.858         11.858         11.858         1667.379     
     10800   1032.6052     -19450.491      8.4089057     -19442.082     -908.09522      11.858         11.858         11.858         1667.379     
     10900   1000.3665     -19450.283      8.1463734     -19442.136     -196.22543      11.858         11.858         11.858         1667.379     
     11000   1099.4244     -19451.288      8.9530407     -19442.335     -1033.1407      11.858         11.858         11.858         1667.379     
     11100   860.89707     -19449.698      7.0106199     -19442.687     -1282.3909      11.858         11.858         11.858         1667.379     
     11200   920.91989     -19450.628      7.499409      -19443.129     -1021.304       11.858         11.858         11.858         1667.379     
     11300   944.61994     -19451.383      7.6924077     -19443.691     -4818.4872      11.858         11.858         11.858         1667.379     
     11400   860.91678     -19451.208      7.0107804     -19444.197     -858.28843      11.858         11.858         11.858         1667.379     
     11500   895.15049     -19451.842      7.2895588     -19444.553     -2358.8996      11.858         11.858         11.858         1667.379     
     11600   979.88449     -19452.767      7.9795807     -19444.787     -6365.3316      11.858         11.858         11.858         1667.379     
     11700   850.23805     -19451.855      6.9238193     -19444.931     -7478.0874      11.858         11.858         11.858         1667.379     
     11800   818.09662     -19451.661      6.6620791     -19444.999     -7415.6814      11.858         11.858         11.858         1667.379     
     11900   857.36666     -19451.984      6.9818704     -19445.002     -4572.9732      11.858         11.858         11.858         1667.379     
     12000   807.69216     -19451.552      6.5773515     -19444.975     -2795.4317      11.858         11.858         11.858         1667.379     
     12100   741.62733     -19450.952      6.03936       -19444.912     -1394.4209      11.858         11.858         11.858         1667.379     
     12200   908.34512     -19452.181      7.3970078     -19444.784     -1930.7645      11.858         11.858         11.858         1667.379     
     12300   897.33569     -19451.936      7.3073537     -19444.629     -6187.4877      11.858         11.858         11.858         1667.379     
     12400   901.64597     -19451.792      7.342454      -19444.45      -1147.7175      11.858         11.858         11.858         1667.379     
     12500   766.58734     -19450.511      6.242619      -19444.269     -675.64962      11.858         11.858         11.858         1667.379     
     12600   850.71791     -19450.974      6.927727      -19444.046     -2771.755       11.858         11.858         11.858         1667.379     
     12700   974.121       -19451.722      7.9326464     -19443.79      -2042.1607      11.858         11.858         11.858         1667.379     
     12800   895.49624     -19450.817      7.2923743     -19443.524      2100.2115      11.858         11.858         11.858         1667.379     
     12900   908.4402      -19450.643      7.3977821     -19443.245     -3928.2175      11.858         11.858         11.858         1667.379     
     13000   927.28224     -19450.529      7.5512201     -19442.978      1155.3615      11.858         11.858         11.858         1667.379     
     13100   1032.6551     -19451.174      8.4093123     -19442.764      2575.5447      11.858         11.858         11.858         1667.379     
     13200   987.56702     -19450.628      8.0421425     -19442.586      2724.7539      11.858         11.858         11.858         1667.379     
     13300   1070.5873     -19451.17       8.7182093     -19442.452     -2068.3525      11.858         11.858         11.858         1667.379     
     13400   885.04843     -19449.607      7.2072938     -19442.4       -3305.7266      11.858         11.858         11.858         1667.379     
     13500   1049.6079     -19450.933      8.5473653     -19442.386     -4538.0827      11.858         11.858         11.858         1667.379     
     13600   941.60384     -19450.131      7.6678465     -19442.463     -6382.9625      11.858         11.858         11.858         1667.379     
     13700   937.72532     -19450.21       7.6362622     -19442.574      6324.1167      11.858         11.858         11.858         1667.379     
     13800   970.60817     -19450.626      7.90404       -19442.721     -3839.3083      11.858         11.858         11.858         1667.379     
     13900   858.1171      -19449.856      6.9879815     -19442.868     -5054.3814      11.858         11.858         11.858         1667.379     
     14000   953.25604     -19450.754      7.7627349     -19442.991     -5555.6524      11.858         11.858         11.858         1667.379     
     14100   983.98372     -19451.115      8.0129623     -19443.102     -9725.8115      11.858         11.858         11.858         1667.379     
     14200   974.65722     -19451.158      7.937013      -19443.221     -10878.788      11.858         11.858         11.858         1667.379     
     14300   972.21465     -19451.265      7.9171223     -19443.348     -1764.8943      11.858         11.858         11.858         1667.379     
     14400   971.07842     -19451.396      7.9078695     -19443.488      1375.8279      11.858         11.858         11.858         1667.379     
     14500   874.30554     -19450.74       7.1198102     -19443.621     -3994.272       11.858         11.858         11.858         1667.379     
     14600   1052.3152     -19452.277      8.5694122     -19443.708     -4514.7934      11.858         11.858         11.858         1667.379     
     14700   919.16403     -19451.274      7.4851104     -19443.789     -3568.6534      11.858         11.858         11.858         1667.379     
     14800   933.35051     -19451.458      7.6006364     -19443.858     -1644.3771      11.858         11.858         11.858         1667.379     
     14900   991.59305     -19451.989      8.074928      -19443.914     -4230.5541      11.858         11.858         11.858         1667.379     
     15000   998.28419     -19452.138      8.1294166     -19444.009     -2440.2205      11.858         11.858         11.858         1667.379     
     15100   934.86544     -19451.737      7.6129731     -19444.124     -301.81912      11.858         11.858         11.858         1667.379     
     15200   762.9606      -19450.447      6.2130851     -19444.234     -2985.4104      11.858         11.858         11.858         1667.379     
     15300   893.08738     -19451.62       7.2727581     -19444.347      1423.8829      11.858         11.858         11.858         1667.379     
     15400   825.93838     -19451.177      6.7259376     -19444.451     -2285.6376      11.858         11.858         11.858         1667.379     
     15500   765.07878     -19450.761      6.2303342     -19444.53      -6814.2127      11.858         11.858         11.858         1667.379     
     15600   875.69264     -19451.707      7.1311059     -19444.576     -4271.5604      11.858         11.858         11.858         1667.379     
     15700   888.00431     -19451.862      7.2313646     -19444.63      -4044.4893      11.858         11.858         11.858         1667.379     
     15800   700.45992     -19450.39       5.7041177     -19444.686     -3521.1877      11.858         11.858         11.858         1667.379     
     15900   863.17395     -19451.696      7.0291614     -19444.667     -4560.7245      11.858         11.858         11.858         1667.379     
     16000   883.24571     -19451.752      7.1926135     -19444.559     -5998.1815      11.858         11.858         11.858         1667.379     
     16100   886.11941     -19451.585      7.2160152     -19444.369     -2220.1583      11.858         11.858         11.858         1667.379     
     16200   889.68582     -19451.327      7.2450578     -19444.082      1222.6832      11.858         11.858         11.858         1667.379     
     16300   943.42027     -19451.397      7.6826384     -19443.714      712.39402      11.858         11.858         11.858         1667.379     
     16400   1047.896      -19451.839      8.5334245     -19443.305     -503.43105      11.858         11.858         11.858         1667.379     
     16500   896.21637     -19450.309      7.2982386     -19443.01       516.68013      11.858         11.858         11.858         1667.379     
     16600   1068.5938     -19451.442      8.7019749     -19442.74       6760.6771      11.858         11.858         11.858         1667.379     
     16700   867.1609      -19449.645      7.0616286     -19442.583     -2655.5148      11.858         11.858         11.858         1667.379     
     16800   1063.2177     -19451.149      8.6581951     -19442.491      817.26711      11.858         11.858         11.858         1667.379     
     16900   1047.3566     -19451.023      8.5290321     -19442.494      2370.7724      11.858         11.858         11.858         1667.379     
     17000   871.52982     -19449.658      7.0972065     -19442.561     -2727.7829      11.858         11.858         11.858         1667.379     
     17100   994.05433     -19450.807      8.0949712     -19442.712     -1500.9596      11.858         11.858         11.858         1667.379     
     17200   862.72451     -19449.934      7.0255014     -19442.908     -4028.8069      11.858         11.858         11.858         1667.379     
     17300   1009.363      -19451.345      8.2196356     -19443.125     -2633.4978      11.858         11.858         11.858         1667.379     
     17400   997.12301     -19451.521      8.1199607     -19443.401     -2327.5488      11.858         11.858         11.858         1667.379     
     17500   770.71526     -19450.005      6.2762342     -19443.729      76.243512      11.858         11.858         11.858         1667.379     
     17600   952.93586     -19451.799      7.7601275     -19444.039     -2040.4263      11.858         11.858         11.858         1667.379     
     17700   837.99034     -19451.173      6.8240814     -19444.349     -7151.994       11.858         11.858         11.858         1667.379     
     17800   844.37393     -19451.499      6.8760655     -19444.622     -408.45156      11.858         11.858         11.858         1667.379     
     17900   828.27132     -19451.576      6.7449357     -19444.831     -815.39355      11.858         11.858         11.858         1667.379     
^C

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Please wait a moment. After the MD simulation completes, it will generate log.lammps and licl.dump files. These files store thermodynamic information and the trajectory of molecules, respectively. We can use the Python script provided in Chapter 1 to compute the RDF.

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[18]

import numpy as np

import matplotlib.pyplot as plt

nbins = 100 # define the number of bins in the RDF

with open("./LiCl_DP_Tutorial_Example/chapter3/02.lmp/licl.rdf", "r") as f: # read the licl.rdf file

lines = f.readlines()

lines = lines[3:]

data = np.zeros((nbins, 7))

count = 0

for line in lines:

nums = line.split()

if len(nums) == 8:

for i in range(1, 8):

data[int(nums[0])-1, i-1] += float(nums[i]) # accumulatie data for each bin

if len(nums) == 2:

count += 1 # count the number of accumulations for each bin

ave_rdf = data / count # calculate the averaged RDF data

np.savetxt('./LiCl_DP_Tutorial_Example/chapter3/02.lmp/ave_rdf.txt', ave_rdf)

labels = ['Li-Li', 'Li-Cl', 'Cl-Cl']

colors = ['orange', 'purple', 'green']

for i, label, color in zip(range(1, 7, 2), labels, colors):

plt.plot(ave_rdf[:, 0], ave_rdf[:, i], label=label, color=color)

plt.xlabel('r/Å')

plt.ylabel('g(r)')

plt.legend()

plt.savefig('./LiCl_DP_Tutorial_Example/chapter3/02.lmp/64_dpmd_rdf.png', dpi=300)

plt.show()

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[1]

import matplotlib.pyplot as plt

import matplotlib.image as mpimg

# 读取图片

cmd_rdf = mpimg.imread('./LiCl_DP_Tutorial_Example/chapter1/rdf.png')

qmd_rdf = mpimg.imread('./LiCl_DP_Tutorial_Example/chapter2/abacus_md/abacus_md_rdf.png')

dpmd_rdf = mpimg.imread('./LiCl_DP_Tutorial_Example/chapter3/02.lmp/64_dpmd_rdf.png')

# 设置画布大小

fig, axd = plt.subplot_mosaic([['upleft', 'right'],

['lowleft', 'right']], figsize=(10,8), dpi=300)

# 添加子图1

axd['upleft'].set_title('LAMMPS CMD')

axd['upleft'].imshow(cmd_rdf)

axd['upleft'].axis('off')

# 添加子图2

axd['right'].set_title('ABACUS QMD')

axd['right'].imshow(qmd_rdf)

axd['right'].axis('off')

# 添加子图3

axd['lowleft'].set_title('DeePMD-kit DPMD')

axd['lowleft'].imshow(dpmd_rdf)

axd['lowleft'].axis('off')

# 显示图片

plt.savefig('./LiCl_DP_Tutorial_Example/chapter3/02.lmp/all_rdf.png')

plt.show()

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It can be observed that the results obtained from DeePMD-kit deep potential molecular dynamics calculations are closer to those obtained from ABACUS quantum molecular dynamics compared to results from LAMMPS classical molecular dynamics. This indicates higher accuracy.

Moreover, with the simulation steps being 200 times that of quantum molecular dynamics (1000000/500 = 200), the time taken is only 19 mins / 9 h 30 mins = 0.03. This significantly reduces computational costs while maintaining high accuracy.

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Next, we will use the DP-GEN workflow to further enhance our deep potential molecular dynamics simulations. This will allow us to investigate the structure, dynamics, and thermodynamic properties of LiCl molten salt at larger spatial and temporal scales.

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Chapter 4*: DP-GEN: Building Training Data and Generating Deep Potential Models

To construct a high-quality training dataset for the LiCl molten salt deep potential energy model, we can utilize DP-GEN (Deep Potential GENerator) software. DP-GEN is an automated tool for generating training datasets that searches material structure and phase space based on predefined parameters and conditions.

This tutorial utilizes DeePMD-kit (2.2.1), ABACUS (3.2.0), and DP-GEN (0.11.0) programs.

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Chapter Objectives:

Upon completing this chapter, you will be able to:

Master the configuration of key settings in DP-GEN input files (param.json and machine.json).
Use DP-GEN to construct training data and generate deep potential models for LiCl molten salt.
Analyze and interpret the results and output files from DP-GEN iterations to better understand the process and effectiveness of model training.

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4.1 Download Tutorial Resources

In this tutorial, we use LiCl molten salt molecules as an example to construct training data and generate deep potential models. We have prepared the necessary files in LiCl_DP_Tutorial_Example/chapter4 for this purpose.

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[3]

! if ! pip show dpgen > /dev/null; then pip install dpgen; fi;

/usr/bin/sh: 1: pip: not found
/usr/bin/sh: 1: pip: not found

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[23]

! tree LiCl_DP_Tutorial_Example/chapter4 -L 2

LiCl_DP_Tutorial_Example/chapter4
├── abacus
│   ├── Cl_ONCV_PBE-1.2.upf
│   ├── Cl_gga_8au_100Ry_2s2p1d.orb
│   ├── Li_ONCV_PBE-1.2.upf
│   └── Li_gga_8au_100Ry_4s1p.orb
├── dpgen.log
├── iter.000000
│   └── 00.train
├── machine.json
├── max-devi-f.png
├── max_devi_f.py
└── param_abacus.json

3 directories, 9 files

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*.upf and *.orb are input files for ABACUS.
param.json is the DP-GEN settings file for running the current task.
machine.json is a task scheduler specifying the computing environment and resource requirements.

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4.2 DP-GEN input

The DP-GEN running process consists of a series of consecutive iterations, carried out sequentially, such as heating the system to a specific temperature. Each iteration consists of three steps:

Exploration
Labeling
Training

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param.json

param.json

System and Data: Used to specify atomic types, initial data, etc.
Training: Mainly used to specify tasks during the training steps.
Exploration: Mainly used to specify tasks during the exploration steps.
Labeling: Mainly used to specify tasks during the labeling steps.

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[7]

! cat LiCl_DP_Tutorial_Example/chapter4/param_abacus.json

{
     "type_map": ["Li","Cl"],
     "mass_map": [6.941,35.453],
     "init_data_prefix": "../chapter3",
     "init_data_sys": ["00.data/training_data"],
     "sys_format": "abacus/stru",
     "sys_configs_prefix": "../chapter2",
     "sys_configs": [["01.md/STRU"]],
     "_comment": " that's all ",

     "numb_models": 4,
     "default_training_param": {
         "model": {
             "type_map": ["Li","Cl"],
             "descriptor": {
                 "type": "se_e2_a",
                 "sel": [128,128],                
                 "rcut_smth": 0.5,
                 "rcut": 7.0,
                 "neuron": [20,40,80],
                 "resnet_dt": false,
                 "axis_neuron": 12,
                 "seed": 1
             },
             "fitting_net": {
                 "neuron": [200,200,200],
                 "resnet_dt": true,
                 "seed": 1
             }
         },
         "learning_rate": {
             "type": "exp",
             "start_lr": 0.001,
             "decay_steps": 5000
         },
         "loss": {
             "start_pref_e": 0.02,
             "limit_pref_e": 1,
             "start_pref_f": 1000,
             "limit_pref_f": 1,
             "start_pref_v": 0,
             "limit_pref_v": 0
         },
         "training": {
             "numb_steps": 400000,
             "disp_file": "lcurve.out",
             "disp_freq": 1000,
             "numb_test": 1,
             "save_freq": 10000,
             "save_ckpt": "model.ckpt",
             "disp_training": true,
             "time_training": true,
             "profiling": false,
             "profiling_file": "timeline.json",
             "_comment": "that's all"
         }
     },

     "model_devi_dt": 0.001,
     "model_devi_skip": 0,
     "model_devi_f_trust_lo": 0.08,
     "model_devi_f_trust_hi": 0.18,
     "model_devi_merge_traj": true,
     "model_devi_clean_traj": false,
     "model_devi_jobs":  [
        {"sys_idx": [0],"temps": [900,1000,1100,1200],"press": [0,10,100,1000,10000], "trj_freq": 10, "nsteps": 100000,"ensemble": "npt", "_idx": "00"},
        {"sys_idx": [0],"temps": [900,1000,1100,1200],"press": [0,10,100,1000,10000], "trj_freq": 10, "nsteps": 100000,"ensemble": "npt", "_idx": "01"},
        {"sys_idx": [0],"temps": [900,1000,1100,1200],"press": [0,10,100,1000,10000], "trj_freq": 10, "nsteps": 100000,"ensemble": "npt", "_idx": "02"}   
     ],

    "fp_style": "abacus",
    "shuffle_poscar": false,
    "fp_task_max": 200,
    "fp_task_min": 50,
    "fp_pp_path": "./abacus",
    "fp_pp_files": ["Li_ONCV_PBE-1.2.upf","Cl_ONCV_PBE-1.2.upf"],   
    "fp_orb_files": ["Li_gga_8au_100Ry_4s1p.orb","Cl_gga_8au_100Ry_2s2p1d.orb"],  
    "k_points":[1, 1, 1, 0, 0, 0],  
    "user_fp_params":{  
    "ntype": 2, 
    "symmetry": 0,
    "vdw_method":"d3_bj",
    "ecutwfc": 100,      
    "scf_thr":1e-7,
    "scf_nmax":120, 
    "basis_type":"lcao", 
    "smearing_method": "gauss",
    "smearing_sigma": 0.002,
    "mixing_type": "pulay",
    "mixing_beta": 0.4,
    "cal_force":1,
    "cal_stress":1
    }
}

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System and Data

{
     "type_map": ["Li","Cl"],
     "mass_map": [6.941,35.453],
     "init_data_prefix": "../chapter3",
     "init_data_sys": ["00.data/training_data"],
     "sys_format": "abacus/stru",
     "sys_configs_prefix": "../chapter2",
     "sys_configs": [["01.md/STRU"]],
     "_comment": " that's all ",

keywords	type	details
"type_map"	list	Li, Cl
"mass_map"	list	list of element mass
"init_data_prefix"	str	initial data dic
"init_data_sys"	list	List of paths to initial training data files. Absolute or relative paths can be used.
"sys_format"	str	The format specifying configurations.
"sys_configs_prefix"	str	sys_configs pre-dic
"sys_configs"	list	A list of paths to configuration files, supporting wildcards here

"type_map" and "mass_map" provide the element types and atomic masses. Here, the system consists of lithium (Li) with a mass of 6.941 and chlorine (Cl) with a mass of 35.453.

"init_data_prefix" and "init_data_sys" together specify the location of the initial training data.

"sys_configs_prefix" and "sys_configs" together specify the location of configuration files for exploration.

"sys_format" specifies the format of the configurations.

In this context, the training data is located in the directory ./LiCl_DP_Tutorial_Example/chapter3/00.data/training_data.

The configuration files are located in the directory ../ex2/01.md/STRU, using the abacus/stru format from ABACUS software.

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Training

     "numb_models": 4,
     "default_training_param": {
         "model": {
             "type_map": ["Li","Cl"],
             "descriptor": {
                 "type": "se_e2_a",
                 "sel": [128,128],                
                 "rcut_smth": 0.5,
                 "rcut": 7.0,
                 "neuron": [20,40,80],
                 "resnet_dt": false,
                 "axis_neuron": 12,
                 "seed": 1
             },
             "fitting_net": {
                 "neuron": [200,200,200],
                 "resnet_dt": true,
                 "seed": 1
             }
         },
         "learning_rate": {
             "type": "exp",
             "start_lr": 0.001,
             "decay_steps": 5000
         },
         "loss": {
             "start_pref_e": 0.02,
             "limit_pref_e": 1,
             "start_pref_f": 1000,
             "limit_pref_f": 1,
             "start_pref_v": 0,
             "limit_pref_v": 0
         },
         "training": {
             "numb_steps": 400000,
             "disp_file": "lcurve.out",
             "disp_freq": 1000,
             "numb_test": 1,
             "save_freq": 10000,
             "save_ckpt": "model.ckpt",
             "disp_training": true,
             "time_training": true,
             "profiling": false,
             "profiling_file": "timeline.json",
             "_comment": "that's all"
         }
     },

keywords	type	details
"numb_models"	int	00.train training model parameters
"default_training_param"	dict	DeePMD-kit training parameters

The training-related keys specify details about the training tasks. numb_models specifies the number of models to train. default_training_param specifies the training parameters for DeePMD-kit. Here, we will train 4 DP models.

Since DP-GEN executes the training part using DeePMD-kit, the keywords used here are the same as those in DeePMD-kit. Detailed explanations of these keywords can be found in theDeePMD-kit docs。

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Exploration

     "model_devi_dt": 0.001,
     "model_devi_skip": 0,
     "model_devi_f_trust_lo": 0.08,
     "model_devi_f_trust_hi": 0.18,
     "model_devi_merge_traj": true,
     "model_devi_clean_traj": false,
     "model_devi_jobs":  [
        {"sys_idx": [0],"temps": [900,1000,1100,1200],"press": [0,10,100,1000,10000], "trj_freq": 10, "nsteps": 100000,"ensemble": "npt", "_idx": "00"},
        {"sys_idx": [0],"temps": [900,1000,1100,1200],"press": [0,10,100,1000,10000], "trj_freq": 10, "nsteps": 100000,"ensemble": "npt", "_idx": "01"},
        {"sys_idx": [0],"temps": [900,1000,1100,1200],"press": [0,10,100,1000,10000], "trj_freq": 10, "nsteps": 100000,"ensemble": "npt", "_idx": "02"}   
     ],

键词	type	details
"model_devi_dt"	float	MD timestep
"model_devi_skip"	int	Number of structures skipped for fp in each MD数
"model_devi_f_trust_lo"	float	Selected force thresholds. If a list, should be set individually for each index.sys_configs。
"model_devi_f_trust_hi"	int	Selected force upper limits. If a list, should be set individually for each index.sys_configs。
"model_devi_clean_traj"	bool or int	If model_devi_clean_traj is of boolean type, it indicates whether to clean the traj files in MD. If it is of integer type, it will retain the latest n iterations in the traj folder, and delete the rest.
"model_devi_clean_traj"	bool	Control whether to merge generated trajectory files during the model deviation (model_devi) phase
"model_devi_jobs"	list	The exploration settings in 01.model_devi. Each dictionary in the list corresponds to one iteration. The indices of model_devi_jobs align perfectly with the indices of iterations.
"sys_idx"	List of integer	Select the system as the initial structure for MD and explore it. The sequence corresponds exactly to sys_configs.
"temps"	list	temperature (K)
"press"	list	pressure (Bar)
"trj_freq"	int	Save frequency of trajectories in MD.
"nsteps"	int	Number of molecular dynamics simulation steps
"ensembles"	str	The choice of ensemble algorithm used in MD, options include "npt", "nvt", etc.

Case Study

Three iterations are set in "model_devi_jobs".

For each iteration, simulations are conducted for 100,000 steps with configurations specified by "sys_configs_prefix" and "sys_configs" under different temperatures (900, 1000, 1100, and 1200 K) and pressure conditions (0, 1e-3, 1e-2, 1e-1, and 1 GPa), using the NPT ensemble and a time step of 0.001 ps.

We choose to save MD trajectory files with a saving frequency "trj_freq" set to 10. If configurations in the trajectory have "max_devi_f" values between 0.08 and 0.18, DP-GEN considers them as candidate structures.

To save the latest n iterations of the traj folder, you can set "model_devi_clean_traj" to an integer.

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Labeling

    "fp_style": "abacus",
    "shuffle_poscar": false,
    "fp_task_max": 200,
    "fp_task_min": 50,
    "fp_pp_path": "./abacus",
    "fp_pp_files": ["Li_ONCV_PBE-1.2.upf","Cl_ONCV_PBE-1.2.upf"],
    "fp_orb_files": ["Li_gga_8au_100Ry_4s1p.orb","Cl_gga_8au_100Ry_2s2p1d.orb"],
    "k_points":[1, 1, 1, 0, 0, 0],
    "user_fp_params":{
    "ntype": 2, 
    "symmetry": 0,
    "vdw_method":"d3_bj",
    "ecutwfc": 100,
    "scf_thr":1e-7,
    "scf_nmax":120, 
    "basis_type":"lcao", 
    "smearing_method": "gauss",
    "smearing_sigma": 0.002,
    "mixing_type": "pulay",
    "mixing_beta": 0.4,
    "cal_force":1,
    "cal_stress":1

keywords	type	details
"fp_style"	String	The first-principle software. Options include ABACUS, VASP, etc.
"shuffle_poscar"	Whether to shuffle POSCAR files.Boolean
"fp_task_max"	Integer	The maximum number of structures to be calculated in 02.fp for each iteration.
"fp_task_min"	Integer	The minimum number of structures to be calculated in 02.fp for each iteration.
"fp_pp_path"	String	Path for the pseudopotential files used in 02.fp.
"fp_pp_files"	List of string	Pseudopotential files used in 02.fp. Note that the order of elements should correspond to the order in type_map.
"fp_orb_files"	List of string	Orbital files used in 02.fp. Note that the order of elements should correspond to the order in type_map.
"k_points"	List of Integer	Used to generate the ABACUS KPT file.
"user_fp_params"	dict	Used to generate the ABACUS INPUT file. If "kspacing" is specified in "user_fp_params", "k_points" is not needed.

Case Study:

Labeling-related keywords specify details of the labeling task.

Here, a minimum of 50 and a maximum of 200 structures will be labeled using the ABACUS code. In each iteration, the INPUT file is generated based on “user_fp_params”, and the KPT file is generated based on “k_points”.

Please note that the order of elements in "fp_pp_files" and "fp_orb_files" should correspond to the order in type_map.

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machine.json

Each iteration in the DP-GEN running process consists of three steps: exploration, labeling, and training. Therefore, machine.json consists of three steps: train, model_devi, and fp. Each step is a list of dictionaries. Each dictionary can be considered an independent computing environment.

In this section, we will show you how to execute the train, model_devi, and fp steps on Bohrium. For each step, three types of keywords are required:

Command: Provides the command to execute each step.
Machine: Specifies the machine environment (local workstation, local or remote cluster, or cloud server).
Resources: Specifies the group, number of nodes, CPUs, and GPUs; enables virtual environments. In this example, we execute the train step on Bohrium.

{
  "api_version": "1.0",
  "deepmd_version": "2.1.5",
  "train" :[
    {
      "command": "dp",
      "machine": {
        "batch_type": "Lebesgue",
        "context_type": "LebesgueContext",
        "local_root" : "./",
        "remote_profile":{
          "email": "xxx", 
          "password": "xxx", 
          "program_id": xxx,
            "keep_backup":true,
            "input_data":{
                "job_type": "container",
                "log_file": "00*/train.log",
                "grouped":true,
                "job_name": "dpgen_train_job",
                "disk_size": 100,
                "scass_type":"c12_m92_1 * NVIDIA V100",
                "checkpoint_files":["00*/checkpoint","00*/model.ckpt*"],
                "checkpoint_time":5,
                "platform": "ali",
                "image_name":"registry.dp.tech/dptech/deepmd-kit:2.1.5-cuda11.6",
                "on_demand":0
            }
        }
      },
      "resources": {
        "local_root":"./",
        "group_size": 1
      }
    }],
  "model_devi":
    [{
      "command": "export LAMMPS_PLUGIN_PATH=/opt/deepmd-kit-2.1.5/lib/deepmd_lmp && lmp -i input.lammps -v restart 0",
      "machine": {
        "batch_type": "Lebesgue",
        "context_type": "LebesgueContext",
        "local_root" : "./",
        "remote_profile":{
          "email": "xxx", 
          "password": "xxx", 
          "program_id": xxx,
            "keep_backup":true,
            "input_data":{
              "job_type": "container",
              "log_file": "task*/model_devi.out",
              "grouped":true,
              "job_name": "dpgen_model_devi_job",
              "disk_size": 200,
              "scass_type":"c12_m92_1 * NVIDIA V100",
              "platform": "ali",
              "image_name":"registry.dp.tech/dptech/deepmd-kit:2.1.5-cuda11.6",
              "checkpoint_files": "sync_files",
              "checkpoint_time":5,
              "on_demand":0
            }
        }
      },
      "resources": {
        "local_root":"./",
        "group_size": 1
      }
    }],
  "fp":
    [{
      "command": "OMP_NUM_THREADS=1 mpirun -np 4 abacus",
      "machine": {
        "batch_type": "Lebesgue",
        "context_type": "LebesgueContext",
        "local_root" : "./",
        "remote_profile":{
          "email": "xxx", 
          "password": "xxx", 
          "program_id": xxx,
            "keep_backup":true,
            "input_data":{
              "log_file": "task*/output",
              "grouped":true,
              "job_name": "dpgen_fp_job",
              "checkpoint_files": "sync_files",
              "checkpoint_time":5,
              "scass_type":"c8_m64_cpu",
              "platform": "ali",
              "image_name":"registry.dp.tech/dptech/abacus:3.1.0",
              "job_type": "container",
              "on_demand":0
            }
        }
      },
      "resources": {
        "group_size": 2,
        "local_root":"./",
        "source_list": []
      }
    }
  ]
}

Case Study:

In the command parameters, the programs used for the train, model_devi, and fp steps are DeePMD-kit, LAMMPS, and ABACUS, respectively. Their respective call commands are:

dp

export LAMMPS_PLUGIN_PATH=/opt/deepmd-kit-2.1.5/lib/deepmd_lmp && lmp -i input.lammps -v restart 0

OMP_NUM_THREADS=1 mpirun -np 4 abacus

In the machine parameters, "scass_type" specifies the type of machine used for training.

For the train and model_devi steps, it is recommended to use GPU machines. Here, the machine type used is “c12_m92_1 * NVIDIA V100”. For the fp step, it is recommended to use CPU machines. Here, the machine type used is “c8_m64_cpu”.

In the resources parameters, "group_size" specifies the number of tasks in a group.

For the train and model_devi steps, since the number of tasks is small (4 and 20, respectively), we can set "group_size" to 1 to execute all tasks simultaneously. For the fp step, since the number of tasks is large (200), we can set "group_size" to 2 to execute 100 tasks simultaneously.

Note: Users need to fill in their own Bohrium account email, password, and project ID (three places). Other parameters usually do not need to be modified.

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4.3 Running DP-GEN

With param.json and machine.json prepared, we can easily run DP-GEN using the following method:

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[27]

import json

import getpass

from monty.serialization import loadfn, dumpfn

file_path = './LiCl_DP_Tutorial_Example/chapter4/machine.json'

j = loadfn(file_path)

email = input('请输入你的 Bohrium 账户： ')

password = getpass.getpass('请输入你的 Bohrium 密码： ')

program_id = int(input('请输入你的 Bohrium 项目 ID【请输入整数】：'))

dpgen_steps = ['train', 'model_devi', 'fp']

for i in dpgen_steps:

j[i][0]['machine']['remote_profile']['email'] = email

j[i][0]['machine']['remote_profile']['password'] = password

j[i][0]['machine']['remote_profile']['program_id'] = program_id

with open(file_path, 'w') as f:

json.dump(j, f, indent=4)

请输入你的 Bohrium 账户：  quehaohui@dp.tech
请输入你的 Bohrium 密码：  ········
请输入你的 Bohrium 项目 ID【请输入整数】： 12788

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After modifying the configuration file, it contains your personal account information. Please keep it confidential!

Usually, this file is not shared. You can run the code in the appendix of this document to initialize the configuration file.

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[1]

# ################# Time Warning: 9 hours ##################

! cd LiCl_DP_Tutorial_Example/chapter4/ && dpgen run param_abacus.json machine.json

/usr/bin/sh: 1: cd: can't cd to LiCl_DP_Tutorial_Example/chapter4/

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Successfully Running DP-GEN

After successfully running DP-GEN, you can find a folder and two files generated under LiCl_DP_Tutorial_Example/chapter4:

iter.000000 folder: Contains the main results of the first iteration during the DP-GEN process.
dpgen.log file: Mainly records the time and iteration information.
record.dpgen file: Records the current stage of the iteration process.

If the DP-GEN process stops for some reason, DP-GEN will automatically resume the main process through the record.dpgen file. We can also manually change it according to our purposes, such as deleting the last iteration and resuming from a checkpoint.

The record.dpgen file contains two numbers on each line: the first is the iteration index, and the second is a number between 0 and 9, recording which stage of each iteration is currently running.

Index of iterations	Stage in each iteration	Process
0	0	make_train
0	1	run_train
0	2	post_train
0	3	make_model_devi
0	4	run_model_devi
0	5	post_model_devi
0	6	make_fp
0	7	run_fp
0	8	post_fp

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4.4 Results Analysis

After the first iteration is completed, the folder structure of iter.000000 is as follows, primarily consisting of three folders:

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[31]

! cd LiCl_DP_Tutorial_Example/chapter4 && tree iter.000000/ -L 1

/usr/bin/sh: 1: cd: can't cd to LiCl_DP_Tutorial_Example/chapter4

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00.train folder: Contains multiple DP models trained based on existing data (default is 4 models).
01.model_devi folder: Uses the DP models from 00.train to perform MD simulations and generate new configurations.
02.fp folder: Conducts first-principles calculations on selected configurations and converts the results into training data.

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First, check iter.000000/ 00.train。

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[ ]

! cd LiCl_DP_Tutorial_Example/chapter4 && tree iter.000000/00.train -L 1

iter.000000/00.train
├── data.init -> /data/bohrium-notebook/Proem/CH/LiCl_DP_Tutorial_Example/ex3
└── data.iters

1 directory, 1 file

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The 00x folder contains DeePMD-kit input and output files, where the model was trained.
graph.00x.pb, linked to 00x/frozen.pb, is the model generated by DeePMD-kit. The only difference between these models is the random seed used to initialize the neural network.

Let's randomly select one to examine, for example, 000.

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[ ]

! cd LiCl_DP_Tutorial_Example/chapter4 && tree iter.000000/00.train/000 -L 1

iter.000000/00.train/000  [error opening dir]

0 directories, 0 files

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input.json is the DeePMD-kit settings for the current task.
checkpoint is used to resume training.
model.ckpt* are files related to the model.
frozen_model.pb is the frozen model.
lcurve.out records the training accuracy of energy and forces.
train.log includes information on the version, data, hardware, time, etc.

Next, let's check iter.000000/01.model_devi.

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[ ]

! cd LiCl_DP_Tutorial_Example/chapter4 && tree iter.000000/01.model_devi -L 1

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The confs folder contains the initial configurations for LAMMPS MD, converted from the STRU settings you specified in param.json under "sys_configs".
The task.000.00000x folder contains LAMMPS input and output files. We can randomly select one of these, for example, task.000.000000.

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双击即可修改

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[ ]

! cd LiCl_DP_Tutorial_Example/chapter4 && tree iter.000000/01.model_devi/task.000.000001

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conf.lmp, linked to 000.0001.lmp in the confs folder, serves as the initial configuration for MD.
input.lammps is the input file for LAMMPS.
model_devi.out records the relevant labels, energy, and force model deviations during MD training. It is the criterion for selecting structures and performing first-principles calculations.
traj stores the LAMMPS MD trajectories.

By viewing the first few lines of model_devi.out, you will see:

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! cd LiCl_DP_Tutorial_Example/chapter4 && head -n 5 ./iter.000000/01.model_devi/task.000.000001/model_devi.out

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Consider that we set trj_freq to 10, so structures are saved every 10 steps.

The selection of structures depends on their max_devi_f. If it is between model_devi_f_trust_lo (0.08) and model_devi_f_trust_hi (0.18), DP-GEN considers the structure as a candidate.

For steps 0, 10, 20, and 30, the saved structures have max_devi_f values less than 0.08, so they are not considered as candidate structures.

Finally, let's check iter.000000/02.fp.

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! cd LiCl_DP_Tutorial_Example/chapter4 && tree iter.000000/02.fp

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candidate.shuffle.000.out records which structures are selected from the last step 01.model_devi. The number of candidates always far exceeds the maximum number you expect to calculate at one time. In this case, DP-GEN will randomly select up to fp_task_max structures and form folder tasks.
rest_accurate.shuffle.000.out records other structures where our model is accurate (max_devi_f less than model_devi_f_trust_lo).
rest_failed.shuffled.000.out records other structures where our model is too inaccurate, which are usually non-physical (greater than model_devi_f_trust_hi).
data.000: After the ABACUS SCF calculation, DP-GEN will collect these data and change them into the format required by DeePMD-kit. In the next iteration's "00.train", these data will be trained together with the initial data.

By running cat candidate.shuffled.000.out | grep task.000.000000, you will see the candidate configurations collected from task.000.000000:

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! cd LiCl_DP_Tutorial_Example/chapter4 && cat ./iter.000000/02.fp/candidate.shuffled.000.out | grep task.000.000000

Usage: grep [OPTION]... PATTERNS [FILE]...
Try 'grep --help' for more information.
cat: ./iter.000000/02.fp/candidate.shuffled.000.out: No such file or directory

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check dpgen.log

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! cd LiCl_DP_Tutorial_Example/chapter4 && cat dpgen.log

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It can be observed that 200,020 structures were generated in iter.000000, among which there were 21,098 candidate configurations. Out of these, 200 structures were selected for ABACUS SCF calculations, and all successfully converged.

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check LiCl_DP_Tutorial_Example/chapter4

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! cd LiCl_DP_Tutorial_Example/chapter4 && tree -L 2

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and dpgen.log

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! cd LiCl_DP_Tutorial_Example/chapter4 && cat cat dpgen.log | grep system

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It can be observed that after just three iterations, the accurate ratio is close to 100.00%. In iter.000002, 9 candidate structures were collected, which is less than the 50 specified by the fp_task_min keyword in param.json. Therefore, the model will not be updated in iter.000003/00.train.

To monitor the iteration process more intuitively, we provide a Python script named max_devi_f.py to count the distribution of max_devi_f for all configurations in each iteration.

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import os

import numpy as np

import matplotlib.pyplot as plt

for i in range(0,3): # Specify the number of iterations

max_devi_f_values = []

for j in range(20): # 20 LAMMPS tasks in iter*/01.model_devi

directory = "./LiCl_DP_Tutorial_Example/chapter4/iter.{:06d}/01.model_devi/task.000.{:06d}".format(i, j%20)

file_path = os.path.join(directory, "model_devi.out")

data = np.genfromtxt(file_path, skip_header=1, usecols=4)

max_devi_f_values.append(data)

# Convert the list to a numpy array

max_devi_f_values = np.concatenate(max_devi_f_values)

# Use numpy.histogram() to calculate the frequency of each value

hist, bin_edges = np.histogram(max_devi_f_values, range=(0, 0.2), bins=100)

# Normalize the frequency to percentage

hist = hist / len(max_devi_f_values) * 100

# Use matplotlib.pyplot.plot() to plot the frequency of each value

plt.plot(bin_edges[:-1], hist,label = 'iter{:02d}'.format(i))

plt.legend()

plt.xlabel("max_devi_f eV/Å")

plt.ylabel("Distribution %")

with open(f'./iter{i:02d}_dist-max-devi-f.txt'.format(i), 'w') as f:

f.write("{:>12} {:>12}\n".format("bin_edges", "hist"))

for x, y in zip(bin_edges[:-1], hist):

f.write('{:>12.3f} {:>12.3f}\n'.format(x, y))

plt.savefig('./LiCl_DP_Tutorial_Example/chapter4/max-devi-f.png',dpi=300)

plt.show()

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At this point, we should have learned how to use DP-GEN to generate and train deep potential models, as well as how to analyze the output results.

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Chapter 5: LAMMPS Deep Potential Molecular Dynamics Study

After training the DP model, we can apply it in the LAMMPS software to efficiently simulate the properties of LiCl melt. This allows us to study the structure, dynamics, and thermodynamic properties of LiCl melt on large scales and over long time periods, providing a deeper understanding of material behavior.

Objectives of this Chapter:

After completing this chapter, you will be able to:

Utilize iterative methods for LAMMPS simulations;
Perform NPT and NVT calculations for LiCl melt.

5.1 Download Tutorial Resources

In this tutorial, we take the LiCl melt as an example to construct training data and generate a deep potential model. The necessary files are prepared in the LiCl_DP_Tutorial_Example/chapter5 directory.

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! tree ./LiCl_DP_Tutorial_Example/chapter5 -L 2

./LiCl_DP_Tutorial_Example/chapter5
├── 00.npt
│   ├── licl.data
│   └── licl.in
└── 01.nvt
    ├── licl.in
    ├── msd_all_temperatures.png
    └── rdf_all_temperatures.png

2 directories, 5 files

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5.2 NPT-MD Simulation

We can find the final four DP models in the ex4/iter.000002/01.train/* directory. Using the dp compress command, we can compress the models and name the compressed models as licl_compress_0.pb to licl_compress_3.pb. Copy the compressed models into the 00.npt and 01.nvt directories. Next, we will perform a LAMMPS NPT-MD simulation to predict the density of the LiCl melt. The control file for the LiCl melt LAMMPS NPT-MD simulation is as follows:

variable        a loop 4 pad
variable        b equal <span class="katex"><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.6667em;vertical-align:-0.0833em;"></span><span class="mord mathnormal">a</span><span class="mspace" style="margin-right:0.2222em;"></span><span class="mbin">−</span><span class="mspace" style="margin-right:0.2222em;"></span></span><span class="base"><span class="strut" style="height:0.8889em;vertical-align:-0.1944em;"></span><span class="mord">1</span><span class="mord mathnormal" style="margin-right:0.03588em;">v</span><span class="mord mathnormal">a</span><span class="mord mathnormal" style="margin-right:0.02778em;">r</span><span class="mord mathnormal">iab</span><span class="mord mathnormal" style="margin-right:0.01968em;">l</span><span class="mord mathnormal">e</span><span class="mord mathnormal" style="margin-right:0.10764em;">f</span><span class="mord mathnormal">e</span><span class="mord mathnormal" style="margin-right:0.03588em;">q</span><span class="mord mathnormal">u</span><span class="mord mathnormal">a</span><span class="mord mathnormal" style="margin-right:0.01968em;">l</span></span></span></span>b*100
variable        t equal 900+$f

log             log$t.lammps

units           metal
boundary        p p p
atom_style      atomic

read_data       licl.data
replicate       2 2 2 
mass            1 6.94
mass            2 35.45

pair_style      deepmd ./licl_compress_0.pb ./licl_compress_1.pb ./licl_compress_2.pb ./licl_compress_3.pb  out_freq 100 out_file model_devi$t.out
pair_coeff  	* *	

velocity        all create $t 23456789

fix             1 all npt temp <span class="katex"><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.6151em;"></span><span class="mord mathnormal">t</span></span></span></span>t 0.1 iso 0 0 0.5
timestep        0.001

thermo_style    custom step temp pe ke etotal press density lx ly lz vol
thermo          100 

run             1000000
write_data      licl.data$t

clear
next            a
jump            in.licl_npt

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Compared to the licl.in file in Chapter 1, there are several points to explain:

variable a loop 4 pad: Creates a variable named a and loops 4 times in the script. The variable a will take values 1, 2, 3, and 4 during the loop.
variable b equal $a-1: Creates a variable named b whose value is equal to a minus 1. This means that in the loop, the value of b will start from 0 to 3.
variable f equal $b*100: Creates a variable named f whose value is equal to b times 100. During the loop, the values of f will be 0, 100, 200, and 300.
variable t equal 900+$f: Creates a variable named t whose value is equal to 900 plus f. During the loop, the values of t will be 900, 1000, 1100, and 1200.
replicate 2 2 2: Replicates the original system along the x, y, and z directions. This will increase the simulation system from 64 atoms to 512 atoms.
pair_style deepmd ./licl_compress_0.pb ./licl_compress_1.pb ./licl_compress_2.pb ./licl_compress_3.pb out_freq 100 out_file model_devi$t.out: Loads 4 neural network models, and outputs the model deviation to a file named model_devit.out every 100 time steps, where $t represents the temperature.
thermo_style custom step temp pe ke etotal press density lx ly lz vol: Adds density to the thermo_style for easy calculation of the simulation system's density.
write_data licl$t.data: Writes the simulation system's information into a file named licl$t.data at the end of each simulation.
jump in.licl_npt: Clears the previous settings after each simulation and jumps back to the beginning of the input file to start the next simulation.

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import numpy as np

def calculate_mean(file_name, column_name):

with open(file_name, 'r') as file:

lines = file.readlines()

step_line = next(i for i, line in enumerate(lines) if 'Step' in line)

loop_line = next(i for i, line in enumerate(lines) if 'Loop' in line)

column_index = lines[step_line].split().index(column_name)

data = [float(line.split()[column_index]) for line in lines[step_line+1:loop_line]]

mean = sum(data[2001:]) / len(data[2001:]) #skip the first 200000 md steps

return mean

temps=[900,1000,1100,1200]

for temp in temps:

mean_density = calculate_mean(f'log{temp}.lammps', 'Density')

mean_Lx = calculate_mean(f'log{temp}.lammps', 'Lx')

print(round(mean_density,3), round(mean_Lx,15))

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The predicted densities are as follows:

Table 5.1 Calculated density and corresponding simulation box length of LiCl melt at different temperatures.

T(K)	Density(g/cm³)	Lx
900	1.602	22.405256609375005
1000	1.562	22.596664576249935
1100	1.523	22.789268989874945
1200	1.485	22.981117881750063

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5.3 NVT-MD Simulation

Adjust the box length in the licl.data file generated by the LAMMPS NPT-MD simulation according to the values of Lx in Table 5.1. Next, perform a LAMMPS NVT-MD simulation to predict the structural information and ionic diffusion coefficients of the LiCl melt. The control file for the LiCl melt LAMMPS NVT-MD simulation is as follows:

variable        a loop 4 pad
variable        b equal <span class="katex"><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.6667em;vertical-align:-0.0833em;"></span><span class="mord mathnormal">a</span><span class="mspace" style="margin-right:0.2222em;"></span><span class="mbin">−</span><span class="mspace" style="margin-right:0.2222em;"></span></span><span class="base"><span class="strut" style="height:0.8889em;vertical-align:-0.1944em;"></span><span class="mord">1</span><span class="mord mathnormal" style="margin-right:0.03588em;">v</span><span class="mord mathnormal">a</span><span class="mord mathnormal" style="margin-right:0.02778em;">r</span><span class="mord mathnormal">iab</span><span class="mord mathnormal" style="margin-right:0.01968em;">l</span><span class="mord mathnormal">e</span><span class="mord mathnormal" style="margin-right:0.10764em;">f</span><span class="mord mathnormal">e</span><span class="mord mathnormal" style="margin-right:0.03588em;">q</span><span class="mord mathnormal">u</span><span class="mord mathnormal">a</span><span class="mord mathnormal" style="margin-right:0.01968em;">l</span></span></span></span>b*100
variable        t equal 900+$f

log             log$t.lammps

units           metal
boundary        p p p
atom_style      atomic

read_data	licl$t.data
#replicate       2 2 2 
mass 		1 6.94
mass		2 35.45
group		Li  type 1
group		Cl  type 2


pair_style	deepmd ./licl_compress_0.pb ./licl_compress_1.pb ./licl_compress_2.pb ./licl_compress_3.pb  out_freq 100 out_file model_devi$t.out
pair_coeff  	* *	

velocity        all create $t 23456789

fix             1 all nvt temp $t $t 0.5
timestep        0.001

#rdf calculation 
compute 	 rdf all rdf 100 1 1 1 2 2 2
fix 		 2 all ave/time 100 1 100 c_rdf[*] file licl$t.rdf mode vector

#msd calculation
compute          msd1 Li msd
compute          msd2 Cl msd
fix              3 all ave/time 100 1 100 c_msd1[4] c_msd2[4] file licl$t.msd

thermo_style    custom step temp pe ke etotal press density lx ly lz vol
thermo          100 

dump		1 all custom 100 licl$t.dump id type x y z

run             1000000

clear
next            a
jump            licl.in

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Python script, from licl.rdf and licl.msd get RDF and diffusion coefficients

RDF

table 5.2

T(K)	Li-Li	Li-Cl	Cl-Cl
900	3.605	2.345	3.675
1000	3.605	2.345	3.675
1100	3.605	2.345	3.745
1200	3.605	2.345	3.745

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MSR and diffusion coefficients

表5.3 $L i^{+}$ and $C l^{-}$ diffusion coefficients $(m^{2} / s \times 1 0^{- 9})$ 。

T(K)	$D_{L i^{+}}$	$D_{C l^{-}}$
900	8.48	3.28
1000	10.78	4.59
1100	12.54	5.96
1200	18.07	8.75

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Conclusion

In this work, we studied the local structure and transport properties of the typical alkali metal chloride, LiCl, using newly trained Deep Potential (DP) models. We extracted datasets from ab initio molecular dynamics (AIMD) calculations and used these data to train and validate the DPs. Large-scale, long-duration molecular dynamics simulations were conducted over a wider temperature range than AIMD to confirm the reliability and generality of the DPs. We demonstrated that the generated DP models could serve as powerful tools for simulating alkali metal chlorides. The DPs provided accuracy comparable to AIMD and efficiency similar to empirical potentials. The partial radial distribution functions and angular distribution functions predicted using the DPs were very close to the results obtained from AIMD. This work provides confidence that DPs can be used to explore other systems, including chloride mixtures or entirely different salts.

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参考文献

[1] Wenshuo Liang, Guimin Lu, Jianguo Yu,Theoretical prediction on the local structure and transport properties of molten alkali chlorides by deep potentials,Journal of Materials Science & Technology 75 (2021) 78–85,点击访问

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附录：

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[17]

# 运行以下代码以初始化 machine.json 配置文件

import json

import getpass

from monty.serialization import loadfn, dumpfn

file_path = './LiCl_DP_Tutorial_Example/chapter4/machine.json'

j = loadfn(file_path)

dpgen_steps = ['train', 'model_devi', 'fp']

for i in dpgen_steps:

j[i][0]['machine']['remote_profile']['email'] = 'email'

j[i][0]['machine']['remote_profile']['password'] = 'password'

j[i][0]['machine']['remote_profile']['program_id'] = 12345

with open(file_path, 'w') as f:

json.dump(j, f, indent=4)

print('初始化配置文件完成！')

初始化配置文件完成！

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# ########### 注意，以下操作会删除本 Notebook 所有输出。

# ! if ! pip show nbstripout > /dev/null; then pip install nbstripout; fi;

# ! nbstripout LiCl_DP_Tutoria.ipynb

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[3]

# ############### Time Warning: 1 minute ###################

! cd ./LiCl_DP_Tutorial_Example/chapter2/abacus_scf && . /opt/intel/oneapi/setvars.sh && OMP_NUM_THREADS=1 mpirun -np 2 abacus

 
:: WARNING: setvars.sh has already been run. Skipping re-execution.
   To force a re-execution of setvars.sh, use the '--force' option.
   Using '--force' can result in excessive use of your environment variables.
  
usage: source setvars.sh [--force] [--config=file] [--help] [...]
  --force        Force setvars.sh to re-run, doing so may overload environment.
  --config=file  Customize env vars using a setvars.sh configuration file.
  --help         Display this help message and exit.
  ...            Additional args are passed to individual env/vars.sh scripts
                 and should follow this script's arguments.
  
  Some POSIX shells do not accept command-line options. In that case, you can pass
  command-line options via the SETVARS_ARGS environment variable. For example:
  
  $ SETVARS_ARGS="ia32 --config=config.txt" ; export SETVARS_ARGS
  $ . path/to/setvars.sh
  
  The SETVARS_ARGS environment variable is cleared on exiting setvars.sh.

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notebook

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