第一版
下载
运行环境为Python2.7.x。
安装
- 修改
.bashrc，
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# python 2
export PATH="/THFS/home/longr/soft/anaconda2/bin:$PATH"
export PYTHONPATH=/THFS/home/longr/soft/anaconda2/lib/python2.7/site-packages
#phonopy
#export PATH=/THFS/home/longr/soft/phonopy-1.12.8.4/scripts:$PATH
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- 运行，
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python setup.py install --user #not root
python setup.py install #root
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Force Calculators方法
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phonopy -d --dim="2 2 2"
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运行build.py。
-
提交job.sh。
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phonopy -f {001..072}/vasprun.xml
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生成FORCE_SETS。
- 修改
mesh.conf，
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ATOM_NAME = C N H Pb I
DIM = 2 2 2
MP = 1 1 1
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运行，
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phonopy -p mesh.conf #生成total_dos.dat，遇到matplotlib报错正常，依旧生成dat文件。
python phonon_dos_plot.py #plot
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- 修改
band.conf，
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ATOM_NAME = C N H Pb I
DIM = 2 2 2
BAND = 0.5 0.5 0.5 0.0 0.0 0.0 0.5 0.5 0.0 0.0 0.5 0.0
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运行，
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phonopy -p band.conf #获得band.yaml
phonopy-bandplot --gnuplot band.yaml > band.dat #将band.yaml转为origin dat数据
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Total Time: 38.45 h
DFPT Force Constants方法
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phonopy -d --dim="2 2 2" -c POSCAR-unitcell
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将SPOSCAR为POSCAR，提交job.sh。
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phonopy --fc vasprun.xml
phonopy --dim="2 2 2" -c POSCAR-unitcell -p mesh.conf
phonopy --dim="2 2 2" -c POSCAR-unitcell -p band.conf
phonopy-bandplot --gnuplot band.yaml > band.dat
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Total Time: 41.59 h
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QXcbConnection: Could not connect to display
Aborted (core dumped)
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上述错误信息请直接忽略。
文档
第二版
离线安装
- 修改集群
/root/.condarc，离线环境使用proxy，
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channels:
- defaults
show_channel_urls: true
default_channels:
- https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
- https://mirrors.bfsu.edu.cn/anaconda/pkgs/r
- https://mirrors.bfsu.edu.cn/anaconda/pkgs/msys2
custom_channels:
conda-forge: https://mirrors.bfsu.edu.cn/anaconda/cloud
msys2: https://mirrors.bfsu.edu.cn/anaconda/cloud
bioconda: https://mirrors.bfsu.edu.cn/anaconda/cloud
menpo: https://mirrors.bfsu.edu.cn/anaconda/cloud
pytorch: https://mirrors.bfsu.edu.cn/anaconda/cloud
pytorch-lts: https://mirrors.bfsu.edu.cn/anaconda/cloud
simpleitk: https://mirrors.bfsu.edu.cn/anaconda/cloud
deepmodeling: https://mirrors.bfsu.edu.cn/anaconda/cloud/
proxy_servers:
http: http://10.81.5.36:7890
https: http://10.81.5.36:7890
ssl_verify: False
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https: http://10.81.5.36:7890
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清理缓存，
- 运行
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pip install phonopy==2.9.0 --proxy=10.82.0.107:7890
conda install -c conda-forge phonopy
conda install -c conda-forge phono3py
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pip phonopy与conda phonopy都安装。
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[root@master ~]# conda install -c conda-forge phono3py
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
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多等几分钟即可。
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[root@master ~]# conda install -c conda-forge phono3py
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: -
The environment is inconsistent, please check the package plan carefully
The following packages are causing the inconsistency:
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- 下载Phonopy-Spectroscopy（可计算IR和Raman光谱），解压缩，并修改
.bashrc，
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# Phonopy-Spectroscopy
export PYTHONPATH=${PYTHONPATH}:/opt/ohpc/pub/apps/Phonopy-Spectroscopy-master/lib
export PATH=${PATH}:/opt/ohpc/pub/apps/Phonopy-Spectroscopy-master/scripts
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提升权限，
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# Phonopy-Spectroscopy
cd /opt/ohpc/pub/apps/Phonopy-Spectroscopy-master
chmod +x scripts/*
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检查，
参考
