王月昊-第8天-2403-计算材料学实战 | Bohrium-玻尔科研空间站

空间站广场

论文

Notebooks

比赛

课程

Apps

我的主页

我的Notebooks

我的论文库

我的足迹

我的工作空间

任务

节点

文件

数据集

镜像

项目

数据库

公开

王月昊-第8天-2403-计算材料学实战

2403-计算材料学实战

Rigel

发布于 2024-03-18

推荐镜像 :DeePMD-kit:3.0.0a0-cuda12.1

推荐机型 :c2_m4_cpu

组队共读活动打卡Day8（3月16日，周六）

▶ 今日学习内容：LAMMPS热力学性质计算（对应视频 12 部分）。

▶ 周末作业（利用周六、周日两天完成）

第7个LAMMPS程序：绘制石墨烯材料在受力时的应力应变曲线，并计算其杨氏模量。这需要使用LAMMPS模拟石墨烯在不同应力下的响应，并从模拟结果中提取应力应变数据来计算杨氏模量。在报告中详细说明模拟过程、参数选择和结果分析，并提供相应的LAMMPS脚本。

拓展：石墨烯的建模

atomsk https://www.bilibili.com/video/BV1VM4y1578J/
Material Studio https://www.bilibili.com/video/BV1Zd4y1R7ny/ https://www.bilibili.com/video/BV17A4y1o7bJ/
VESTA https://www.bilibili.com/video/BV1af4y1N7UB/ 参考资料： https://github.com/nuwan-d/graphene_tensile_test https://github.com/JeroenMulkers/lammps_graphene

代码

文本

[2]

%%writefile in.stretch

# UNITS

units real

timestep 1

variable fpress equal 0.000101325 #atm ->GPa

variavle fenergy equal 0.043 #Kcal/mole ->eV

# GRAPHENE SHEET

dimension 3

boundary p p f

atom_style charge

read_data grapheneLarge.dat

pair_style reax/c NULL checkqeq no

pair_coeff * * ffield.reax C

# TEMPERATURE SETTINGS

variable temp equal 300

variable seed equal 1717

velocity all create ${temp} ${seed} dist uniform

# EQUILIBRATION

fix fnpt all npt temp ${temp} ${temp} 10 x 0 0 500 y 0 0 500

thermo 100

run 1000

# OUTPUT

# assume that the thickness of graphene is 3.35A.

variable tmp equal lx

variable lx0 equal ${tmp}

variable tmp equal ly

variable ly0 equal ${tmp}

variable Eavg equal etotal/atoms*${fenergy} #eV/atom

variable pe equal pe/atoms*${fenergy} #eV/atom

variable ke equal ke/atoms*${fenergy} #eV/atom

variable strainx equal (lx-${lx0})/${lx0}

variable strainy equal (ly-${ly0})/${ly0}

variable stressx equal -pxx*(lz/3.35)*${fpress} #GPa

variable stressy equal -pyy*(lz/3.35)*${fpress} #GPa

thermo_style custom step time temp etotal press v_Eavg

v_pe v_ke & v_strainx v_stressx v_strainy v_stressy

# DEFORMATION

fix boxdeform all deform 1 x scale 2 remap x

fix fnpt all npt temp ${temp} ${temp} 10 y 0 0 500

dump 1 all atom 10 dmp.lammpstrj

thermo 100

run 10000

Writing in.stretch

代码

文本

[3]

!lmp -i in.stretch

LAMMPS (2 Aug 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
DeePMD-kit: Successfully load libcudart.so.11.0
2024-03-18 23:43:51.110306: E tensorflow/compiler/xla/stream_executor/cuda/cuda_dnn.cc:9342] Unable to register cuDNN factory: Attempting to register factory for plugin cuDNN when one has already been registered
2024-03-18 23:43:51.110383: E tensorflow/compiler/xla/stream_executor/cuda/cuda_fft.cc:609] Unable to register cuFFT factory: Attempting to register factory for plugin cuFFT when one has already been registered
2024-03-18 23:43:51.110492: E tensorflow/compiler/xla/stream_executor/cuda/cuda_blas.cc:1518] Unable to register cuBLAS factory: Attempting to register factory for plugin cuBLAS when one has already been registered
Loaded 1 plugins from /opt/deepmd-kit-3.0.0/lib/deepmd_lmp
ERROR: Unknown command: variavle fenergy equal 0.043 #Kcal/mole ->eV (src/input.cpp:303)
Last command: variavle fenergy equal 0.043 #Kcal/mole ->eV

代码

文本

2403-计算材料学实战

点个赞吧