参考：http://blog.sina.com.cn/s/blog_4aba6f3d0100wjoe.html

先python2.7的安装

./configure --prefix=/home/ljzhou86/app/python2.7

make

make install

vi ~/.bashrc

   export PATH=$PATH:/home/ljzhou86/app/python2.7:/home/ljzhou86/app/python2.7/bin

phonopy计算所需要的模板的安装：

cd /home/ljzhou86/software/phonopy-1.6.4-pre/numpy-1.6.1

python  setup.py install --home=/home/ljzhou86/app/python2.7

cd ..

cd /home/ljzhou86/software/phonopy-1.6.4-pre/matplotlib-0.99.1.1

python  setup.py install --home=/home/ljzhou86/app/python2.7

cd ..

再进入PyYAML-3.01 ; lxml-2.2.4的目录，同样运行：

python  setup.py install --home=/home/ljzhou86/app/python2.7

cd ..

Phonopy的安装：

cd /home/ljzhou86/software/phonopy-1.6.4-pre/phonopy-1.7.4

python  setup.py install --home=/home/ljzhou86/app/phonopy-1.7

vi ~/.bashrc

export PYTHONPATH=/home/ljzhou86/app/python2.7/lib/python:/home/ljzhou86/app/phonopy-1.7/lib/python

自由能计算

band.conf

ATOM_NAME = Th As Rb O  

#Mass = 63.546 63.546 63.546 63.546 63.546 63.546 63.546 63.546 63.546 63.546 63.546 63.546 63.546 63.546 63.546 63.546 63.546 63.546  79.904 79.904 79.904 79.904 79.904 79.904 79.904 79.904 79.9

04 79.904 79.904 79.904 79.904 79.904 79.904 79.904 79.904 79.904

DIM=1 1 1

#BAND=0.0 0.5 0.0  0.0 0.0 0.0  0.5 0.0 0.0 0.5 0.5 0.0  0.0 0.0 0.0

MP= 7 3 5

#BAND_POINTS = 101

#BAND_LABELS = X \Gamma Y M \Gamma

BAND_CONNECTION = .TRUE.

#FC_SYMMETRY = 100

phonopy -f vasprun.xml-*

phonopy -t band.conf --tmax=1200 --tstep=5 >CsP.therm

吉布斯自由能计算脚本：

#!/bin/bash

#PBS -j oe

#PBS -l feature=mpp1

#PBS -l nodes=4:ppn=24

#PBS -l walltime=12:00:00

#PBS -q  mpp1q  # mpp1q, smp1q, dataq, post1q, mpp1testq, smp1testq

#PBS -A  hbp00027

module load vasp/5.3.3

module load phonopy/1.8.4.2-rc3

cd $PBS_O_WORKDIR

mkdir 01free

for i in -0.1 -0.08 -0.06 -0.04 -0.02 0.02 0.04 0.06  0.08 0.1

#for i in 0.1 0.20 0.3 0.4 0.6 0.7 0.8 0.9

do

#echo $i | defvector.x

#cp fort.3 POSCAR.$i

cp POSCAR.$i POSCAR

mkdir m$i

cp INCAR POSCAR.$i therm.conf POTCAR KPOINTS m$i

cd m$i

cp POSCAR.$i POSCAR

phonopy -d --dim="2 2 1"

for a in 01 02 03 04 05 06

do

cp POSCAR-0$a POSCAR

aprun -n 96 vasp_cd  >>out.vasp

cp vasprun.xml vasprun.xml-$a

done

phonopy -f vasprun.xml-*

cp POSCAR.$i POSCAR

phonopy -t therm.conf --tmax=1000 --tstep=5

cp thermal_properties.yaml thermal_properties-$i.yaml

cp thermal_properties-$i.yaml ../01free

cp out.vasp out.vasp-$a

cp OUTCAR OUTCAR-$a

cd ..

aprun -n 96 vasp_cd  >>out.vasp

cp OUTCAR OUTCAR.$i

vol=`grep vol OUTCAR |tail -1|awk '{print $5}'`

echo "ENCUT = $i eV" ; time vasp

E=`grep "TOTEN" OUTCAR | tail -1 | awk '{printf "%12.6f \n", $5 }'`

echo $vol $E >>e-v.dat

done