新建
CALYPSO_SaaS VASP 界面结构预测 快速上手
rainvibe
A.Tの
liangws
推荐镜像 :CALYPSO:7.3.5.1
推荐机型 :c2_m4_cpu
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目录
CALYPSO_SaaS VASP 界面结构预测 快速上手
作者: 王振雨 wzy@calypso.cn，罗啸山 luoxs@calypso.cn
创建日期: 2023-10-18
最后一次修改: 罗啸山
最后一次修改时间: 2023-10
描述: 选择
calypso-bohrium:7.3.5.1镜像运行。如您遇到任何问题，请联系 bohrium@dp.tech 。
共享协议: 本作品采用知识共享署名-非商业性使用-相同方式共享 4.0 国际许可协议进行许可。
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目标
上手使用CALYPSO_SaaS做结构预测
阅读该教程【最多】约需 15 分钟，让我们开始吧！
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背景
基于群体智能的CALYPSO材料结构预测方法和软件（详见 http://www.calypso.cn ），是我国自主创新发展的方法和软件，仅依据材料的化学组分即可开展材料微观原子结构的预测，已经广泛应用于晶体、表面（含二维单/多层材料）、界面、团簇和过渡态的创新性设计，并能开展功能导向（如能隙、硬度和电子密度等）的逆向材料设计。
本教程将Ti-O界面结构预测为例，使用VASP进行结构的能量评估，介绍CALYPSO_SaaS界面结构预测的基本用法。
请与bohrium工作人员联系获取vasp的镜像进行本教程的学习。
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环境准备
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!pip install -q ase click dpdata dpdispatcher kaleido matplotlib numpy oss2 pandas \
plotly pymatgen scipy Ipython
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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!pip install -q spglib==2.0.2
# The currently latest verion of spglib==2.1.0 will print some unnecessary warning
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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可选项:
可以使用以下命令安装 scienceplots 和 latex 安装包来使图片更美观
sudo apt install texlive-latex-extra
sudo apt install texlive-fonts-recommended dvipng cm-super
pip install scienceplots
注意：Latex的安装会花费一些时间！
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我们已经为大家准备好了快速上手的案例，大家可以直接使用wget命令来下载。
注意：该临时文件将在本案例末执行删除操作。
为了方便后续的可视化，我们首先需要将例子移动到/data目录下
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cd /personal
/data
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! test ! -e CALYPSO-SaaS-example && wget https://bohrium-api.dp.tech/ds-dl/CALYPSO-SaaS-example-x7dx-v4.zip -O CALYPSO-SaaS-example.zip || echo "文件夹已存在"
--2023-10-20 13:14:07-- https://bohrium-api.dp.tech/ds-dl/CALYPSO-SaaS-example-x7dx-v4.zip Resolving ga.dp.tech (ga.dp.tech)... 10.255.254.37, 10.255.254.7, 10.255.254.18 Connecting to ga.dp.tech (ga.dp.tech)|10.255.254.37|:8118... connected. Proxy request sent, awaiting response... 307 Temporary Redirect Location: https://dataset-bohr-storage.dp.tech/lbg%2Fdataset%2Fzip%2Fdataset_tiefblue_bohr_11265_CALYPSO-SaaS-example-x7dx_v101089.zip?Expires=1697814847&OSSAccessKeyId=LTAI5tGCcUT7wz9m1fq8cuLa&Signature=vfneSVYoJgWINBz45qmmpzTrw58%3D [following] --2023-10-20 13:14:07-- https://dataset-bohr-storage.dp.tech/lbg%2Fdataset%2Fzip%2Fdataset_tiefblue_bohr_11265_CALYPSO-SaaS-example-x7dx_v101089.zip?Expires=1697814847&OSSAccessKeyId=LTAI5tGCcUT7wz9m1fq8cuLa&Signature=vfneSVYoJgWINBz45qmmpzTrw58%3D Connecting to ga.dp.tech (ga.dp.tech)|10.255.254.37|:8118... connected. Proxy request sent, awaiting response... 200 OK Length: 26594450 (25M) [application/zip] Saving to: ‘CALYPSO-SaaS-example.zip’ CALYPSO-SaaS-exampl 100%[===================>] 25.36M 39.9MB/s in 0.6s 2023-10-20 13:14:08 (39.9 MB/s) - ‘CALYPSO-SaaS-example.zip’ saved [26594450/26594450]
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!unzip CALYPSO-SaaS-example.zip
Archive: CALYPSO-SaaS-example.zip inflating: CALYPSO-SaaS-example/MgAl_example/reference/frozen_model.pb inflating: CALYPSO-SaaS-example/MgAl_example/reference/input.dat inflating: CALYPSO-SaaS-example/MgAl_example/reference/machine.json inflating: CALYPSO-SaaS-example/MgAl_example/reference/resources.json inflating: CALYPSO-SaaS-example/MgAl_example/reference/results/Analysis_Output.dat inflating: CALYPSO-SaaS-example/MgAl_example/reference/results/CALYPSO.log inflating: CALYPSO-SaaS-example/MgAl_example/reference/results/pso_ini_1 inflating: CALYPSO-SaaS-example/MgAl_example/reference/results/pso_ini_10 inflating: CALYPSO-SaaS-example/MgAl_example/reference/results/pso_ini_11 inflating: CALYPSO-SaaS-example/MgAl_example/reference/results/pso_ini_12 inflating: CALYPSO-SaaS-example/MgAl_example/reference/results/pso_ini_13 inflating: CALYPSO-SaaS-example/MgAl_example/reference/results/pso_ini_14 inflating: CALYPSO-SaaS-example/MgAl_example/reference/results/pso_ini_15 inflating: 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CALYPSO-SaaS-example/interface_vasp_example/resources.json inflating: CALYPSO-SaaS-example/interface_vasp_example/run.sh inflating: CALYPSO-SaaS-example/interface_vasp_example/submit.sh inflating: CALYPSO-SaaS-example/qe_example/B-PBE.upf inflating: CALYPSO-SaaS-example/qe_example/N-PBE.upf inflating: CALYPSO-SaaS-example/qe_example/del.sh inflating: CALYPSO-SaaS-example/qe_example/input.dat inflating: CALYPSO-SaaS-example/qe_example/machine.json inflating: CALYPSO-SaaS-example/qe_example/pw_input_1 inflating: CALYPSO-SaaS-example/qe_example/pw_input_2 inflating: CALYPSO-SaaS-example/qe_example/pw_input_3 inflating: CALYPSO-SaaS-example/qe_example/resources.json inflating: CALYPSO-SaaS-example/qe_example/run.sh inflating: CALYPSO-SaaS-example/vasp_HCNO_example/INCAR_1 inflating: CALYPSO-SaaS-example/vasp_HCNO_example/INCAR_2 inflating: CALYPSO-SaaS-example/vasp_HCNO_example/INCAR_3 inflating: CALYPSO-SaaS-example/vasp_HCNO_example/INCAR_4 inflating: CALYPSO-SaaS-example/vasp_HCNO_example/POTCAR inflating: CALYPSO-SaaS-example/vasp_HCNO_example/back.sh inflating: CALYPSO-SaaS-example/vasp_HCNO_example/del.sh inflating: CALYPSO-SaaS-example/vasp_HCNO_example/input.dat inflating: CALYPSO-SaaS-example/vasp_HCNO_example/machine.json inflating: CALYPSO-SaaS-example/vasp_HCNO_example/resources.json inflating: CALYPSO-SaaS-example/vasp_HCNO_example/run.sh inflating: CALYPSO-SaaS-example/vasp_example/INCAR_1 inflating: CALYPSO-SaaS-example/vasp_example/INCAR_2 inflating: CALYPSO-SaaS-example/vasp_example/INCAR_3 inflating: CALYPSO-SaaS-example/vasp_example/POTCAR inflating: CALYPSO-SaaS-example/vasp_example/back.sh inflating: CALYPSO-SaaS-example/vasp_example/del.sh inflating: CALYPSO-SaaS-example/vasp_example/input.dat inflating: CALYPSO-SaaS-example/vasp_example/machine.json inflating: CALYPSO-SaaS-example/vasp_example/resources.json inflating: CALYPSO-SaaS-example/vasp_example/run.sh
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cd /personal/CALYPSO-SaaS-example
/data/CALYPSO-SaaS-example
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该目录下包含
input.dat.example，进行晶体预测、变组分结构预测（VSC）、二维结构预测等的input.dat例子vasp_example，使用VASP作为第一性原理计算软件进行CALYPSO结构预测的例子abacus_example，使用ABACUS作为第一性原理计算软件进行CALYPSO结构预测的例子qe_example，使用QE作为第一性原理计算软件进行CALYPSO结构预测的例子dp_example，使用DP作为能量计算软件进行结构预测的例子interface_vasp_example，使用VASP作为第一性原理计算软件进行CALYPSO界面结构预测的例子
下文将以interface_vasp_example为例进行说明。
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cd /personal/CALYPSO-SaaS-example/interface_vasp_example
/data/CALYPSO-SaaS-example/interface_vasp_example
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[5]
ls
INCAR-1 POTCAR-Ti del.sh reference.results/ submit.sh
INCAR-2 SUBSTRATE input.dat resources.json
POTCAR-O SUBSTRATE2 machine.json run.sh
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该目录中包含
- CALYPSO及VASP的输入文件：
input.dat，CALYPSO的控制文件，(详细的参数说明请参考文档说明)INCAR-1，INCAR-2, 各结构逐次进行VASP优化的控制文件 #注意，和晶体不同，这里的INCAR使用的是短横线而不是下划线POTCAR-O，POTCAR-Ti, VASP赝势SUBSTRATE,SUBSTRATE1, 衬底文件，cif格式submit.sh, 文件中应写出运行第一性原理软件的命令，如mpirun -n 16 vasp_std > fp.log 2>&1reference.results，准备好的results文件夹可直接分析
- 计算资源配置文件：
machine.json，dpdispatcher的参数文件，包含bohrium的账号信息及相关镜像的选择等resources.json，dpdispatcher的参数文件，控制每个机器运行任务的个数
- 辅助控制文件：
run.sh，CALYPSO-SaaS的任务提交脚本del.sh，CALYPSO-Saas的目录清理脚本，用于在同一目录重新计算时对无用的文件进行批量删除back.sh，CALYPSO-Saas的续算辅助脚本，用于进行续算处理时文件批处理
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CALYPSO-SaaS的任务提交和回收全部由dpdispatcher完成，因此需要对dpdispatcher的配置文件 machine.json 进行修改，将其中的email，passwd，project-id以及镜像image_name进行相应修改(如果您希望使用vasp进行能量计算，请与bohrium工作人员联系获取vasp的镜像)
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cat machine.json
{
"batch_type": "Lebesgue",
"context_type": "LebesgueContext",
"local_root": "./",
"remote_profile": {
"email": "wzy@calypso.cn",
"password": "xxxx",
"program_id": 18995,
"_keep_backup": true,
"input_data": {
"job_name": "calypso saas surface 4",
"image_name": "xxxx",
"job_type": "indicate",
"log_file": "log",
"grouped": true,
"disk_size": 200,
"max_run_time": 4,
"machine_type": "c16_m32_cpu",
"platform": "ali",
"on_demand": 0,
"out_files": ["OUTCAR", "CONTCAR", "OSZICAR", "fp.log", "log", "err"]
}
}
}
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注意！我们需要将账号和密码更换成我们自己的Bohurium账号密码
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%%writefile machine.json
{
"batch_type": "Lebesgue",
"context_type": "LebesgueContext",
"local_root": "./",
"remote_profile": {
"email": "wzy@calypso.cn",
"password": "your_passwd",
"program_id": 10000,
"_keep_backup": true,
"input_data": {
"job_name": "calypso-saas-interface",
"image_name": " *** vasp image *** ",
"job_type": "indicate",
"log_file": "log",
"grouped": true,
"disk_size": 200,
"max_run_time": 40,
"machine_type": "c16_m32_cpu",
"platform": "ali",
"on_demand": 0,
"out_files": ["OUTCAR", "CONTCAR", "OSZICAR", "fp.log", "log", "err"]
}
}
}
Overwriting machine.json
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cat input.dat
LSurface = T #surface flag ICode = 1 #1-vasp Rand_Scheme = 3 System_type = INTERFACE Kgrid = 0.5 PopSize = 5 MaxStep = 5 Pre_surf_relax=F SPACESAVING = T InterfaceAuto = T InterfaceTranslation = b Forbi_thickness = 0.2 Interface_thickness = 3.5 @SURFACE_ATOMS #|atomic symbol|count| Ti 1 O 4 @END @COORDINATE_NUMBER Ti Ti 0 2 2.5 2.5 O O 0 4 1.8 2.3 Ti O 6 0 1.8 2.5 O Ti 3 0 1.8 2.5 @END #used to build the surface from bulk info #reconstruction symmetry Substrate = SUBSTRATE Substrate2 = SUBSTRATE2 #Twin_Interface = 1 #Twin_Surface = 1 Split=T
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cat resources.json #这个文件是激活运行环境，不需要修改
{
"group_size": 1,
"local_root":"./",
"source_list": ["/opt/intel/oneapi/setvars.sh"]
}
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修改完成后，run.sh 为准备好的任务提交脚本，运行该脚本即可提交任务
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注意！目前界面结构预测只能使用VASP作为能量计算软件
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import os
get_ipython().system = os.system
!nohup run_calypso --dft vasp > out 2>&1 &
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我们在镜像中提供了命令查看任务showjob，可直接在命令行运行即可
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!showjob
name PID work_path run_calypso 320 /data/CALYPSO-SaaS-example/interface_vasp_example
0
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或者可以实时的查看任务的日志文件
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! tail -n 5 out
2023-10-20 13:16:26,340 - INFO : job: ee99a0c1a9a4ca8bf57b7d5c3743ccb6b0c99479 submit; job_id is 9250869:job_group_id:11269980 2023-10-20 13:16:26,742 - INFO : job: e6a43fbc8a7d21a3d06cb9893bea973738395519 submit; job_id is 9250870:job_group_id:11269980 2023-10-20 13:16:27,153 - INFO : job: b8882ebbf372416920655b58963ee502511f575e submit; job_id is 9250871:job_group_id:11269980 2023-10-20 13:16:27,551 - INFO : job: 479584826eed93380bfbfdfdf91358ecd2c69fc8 submit; job_id is 9250872:job_group_id:11269980 2023-10-20 13:16:27,942 - INFO : job: 1ae80c62e98bfbf138609ebcb725f61bd599d681 submit; job_id is 9250873:job_group_id:11269980
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cd /personal/CALYPSO-SaaS-example/interface_vasp_example/reference.results
/data/CALYPSO-SaaS-example/interface_vasp_example/reference.results
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ls
Analysis_Output.dat CALYPSO.log CALYPSO_input.dat Generation_1/ Generation_2/ Generation_3/ Generation_4/ Generation_5/ dir_origin/
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- struct.dat为保存的所有结构信息
- CALYPSO.log Local_Structure_List.dat为CALYPSO运行的日志文件与临时文件
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!cak.py --vasp -a
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cat ./Analysis_Output.dat #里面存放了寻找到的能量最低的结构的相关信息
No. Enthalpy 1 ( 24) 1571.76319 2 ( 16) 1572.97899 3 ( 3) 1580.17792 4 ( 2) 1584.15801 5 ( 10) 1614.55104 6 ( 14) 1615.13867 7 ( 4) 1616.06449 8 ( 18) 1625.41710 9 ( 6) 1633.32619 10 ( 5) 1660.30055 11 ( 1) 1681.60477 12 ( 12) 1682.32393 13 ( 25) 1693.08232 14 ( 15) 1699.88187 15 ( 17) 2402.01592 16 ( 13) 3212.78679 17 ( 19) 3288.32451 18 ( 20) 3330.59264 19 ( 21) 3352.85415 20 ( 8) 3399.38980 21 ( 22) 3407.50324 22 ( 9) 3415.54238 23 ( 7) 3450.84713 24 ( 23) 3594.70423 25 ( 11) NULL
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cd /personal/CALYPSO-SaaS-example/interface_vasp_example/reference.results/dir_origin
/data/CALYPSO-SaaS-example/interface_vasp_example/reference.results/dir_origin
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ls /personal/CALYPSO-SaaS-example/interface_vasp_example/reference.results/dir_origin
OCell_1.vasp OCell_10.vasp OCell_11.vasp OCell_12.vasp OCell_13.vasp OCell_14.vasp OCell_15.vasp OCell_16.vasp OCell_17.vasp OCell_18.vasp OCell_19.vasp OCell_2.vasp OCell_20.vasp OCell_21.vasp OCell_22.vasp OCell_23.vasp OCell_24.vasp OCell_25.vasp OCell_3.vasp OCell_4.vasp OCell_5.vasp OCell_6.vasp OCell_7.vasp OCell_8.vasp OCell_9.vasp
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#可以通过ase初步观察一下，也可以拖出来用可视化软件如VESTA等查看
from ase.io import read
from ase.visualize import view
atoms = read("/personal/CALYPSO-SaaS-example/interface_vasp_example/reference.results/dir_origin/OCell_1.vasp") #读入结构信息，转为atoms object
view(atoms, viewer='x3d')
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