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结构预测软件使用过程中的一些细节

已有 2959 次阅读 2020-2-17 15:28 |个人分类:结构预测|系统分类:科研笔记

关注:

1) input.dat设置细节

2)   读取能量数据的一些细节



(1) input.dat


cat  input.dat

################################ The Basic Parameters of CALYPSO ################################

# A string of one or several words contain a descriptive name of the system (max. 40 characters).

SystemName =CeH1

# Number of different atomic species in the simulation.

NumberOfSpecies = 2

# Element symbols of the different chemical species.

NameOfAtoms = Ce H

# Number of atoms for each chemical species in one formula unit.

NumberOfAtoms =  1 1

# The range of formula unit per cell in your simulation.

NumberOfFormula = 1 4

# The volume per formula unit. Unit is in angstrom^3.

Volume=0.0

# Minimal distance between atoms of each chemical species. Unit is in angstrom.

@DistanceOfIon

1.8  1.6

1.6  0.7

@End

# It determines which algorithm should be adopted in the simulation.

Ialgo = 2

# Ialgo = 1 for Global PSO

# Ialgo = 2 for Local PSO (default value)

# The proportion of the structures generated by PSO.

PsoRatio = 0.6

# The popu2ation size. Normally, it has a larger number for larger systems.

PopSize = 30

# It determines which local optimization method should be interfaced in the simulation.

ICode= 1

# ICode= 1 interfaced with VASP

# ICode= 2 interfaced with SIESTA

# ICode= 3 interfaced with GULP

# The number of lbest for local PSO

NumberOfLbest=4

# The Number of local optimization for each structure.

NumberOfLocalOptim= 3

# The command to perform local optimiztion calculation (e.g., VASP, SIESTA) on your computer.

Command = sh submit.sh

# The Max step for iteration

MaxStep =50

# If True, a previous calculation will be continued.

PickUp= F

# At which step will the previous calculation be picked up.

PickStep =5

# If True, the local optimizations performed by parallel

Parallel= F

# The number node for parallel

NumberOfParallel=4


(2)  vegP

#!/bin/sh


rm -f pv_et.txt


for file in OUTCAR_*4


do

pre=$(awk '/external pressure/{ print $4+$9 }' $file |tail -n 1)

vol=$(awk '/volume of cell/{print $5}' $file |tail -n 1) 

et=$(awk '$3=="TOTEN"{print $5}' $file |tail -n 1)

#et=$(awk '/free  energy   TOTEN/{print $5}' $file |tail -n 1)

echo $pre \ \  $vol \ \  $et \ \ $file >> vv_et.txt

done

cat vv_et.txt|sort  -n -k 1 >pv_et.txt

rm vv_et.txt

a=$(awk '{print NR}' pv_et.txt)


echo $a

exit




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