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#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Abinit Post Process Application
author: Martin Alexandre
last edited: May 2013
"""
import sys,os,commands
import string, math, shutil
from scipy.io import netcdf
import numpy as np
class writeHIST:
def __init__(self,pfile,pname,pni,pnf):
self.namefile = pname
self.file = pfile
self.ni = pni
self.nf = pnf
self.write()
def write(self):
# Copy _OUT.nc file
name_out_nc = str(self.file.getNameFile(fullpath=True)).replace('_HIST','_OUT.nc')
self.new_out_nc = str(self.namefile).replace('_HIST','_OUT.nc')
shutil.copyfile(name_out_nc,self.new_out_nc)
# Creation of new HIST file
f = netcdf.netcdf_file(self.namefile, 'w')
# dimensions:
f.createDimension('natom',self.file.getNatom())
f.createDimension('xyz',3)
f.createDimension('time',self.file.getNbStep())
f.createDimension('six', 6)
# variables:
xcart = f.createVariable('xcart','d',('time','natom','xyz'))
xcart[:,:,:] = self.file.xcart[self.ni-1:self.nf,0]
xcart.units = "bohr"
xcart.mnemonics = "vectors (X) of atom positions in CARTesian coordinates" ;
xred = f.createVariable('xred','d',('time','natom','xyz'))
xred[:,:,:] = self.file.xred[self.ni-1:self.nf,0]
xred.units = "dimensionless" ;
xred.mnemonics = "vectors (X) of atom positions in REDuced coordinates" ;
fcart = f.createVariable('fcart','d',('time','natom','xyz'))
fcart[:,:,:] = self.file.fcart[self.ni-1:self.nf,0]
fcart.units = "Ha/bohr" ;
fcart.mnemonics = "atom Forces in CARTesian coordinates" ;
fred = f.createVariable('fred','d',('time','natom','xyz'))
fred[:,:,:] = self.file.fred[self.ni-1:self.nf,0]
fred.units = "dimensionless" ;
fred.mnemonics = "atom Forces in REDuced coordinates" ;
vel = f.createVariable('vel','d',('time','natom','xyz'))
vel[:,:,:] = self.file.vel[self.ni-1:self.nf,0]
vel.units = "bohr*Ha/hbar" ;
vel.mnemonics = "VELocity" ;
acell = f.createVariable('acell','d',('time','xyz'))
acell[:,:] = self.file.acell[self.ni-1:self.nf,0]
acell.units = "bohr" ;
acell.mnemonics = "CELL lattice vector scaling" ;
rprimd = f.createVariable('rprimd','d',('time','xyz','xyz'))
rprimd[:,:,:] = self.file.rprimd[self.ni-1:self.nf,0]
rprimd.units = "bohr" ;
rprimd.mnemonics = "Real space PRIMitive translations, Dimensional" ;
etotal = f.createVariable('etotal','d',('time',))
etotal[:] = self.file.E_pot[self.ni-1:self.nf]
etotal.units = "Ha" ;
etotal.mnemonics = "TOTAL Energy" ;
ekin = f.createVariable('ekin','d',('time',))
ekin[:] = self.file.E_kin_ion[self.ni-1:self.nf]
ekin.units = "Ha" ;
ekin.mnemonics = "Energy KINetic ionic" ;
mdtime = f.createVariable('mdtime','d',('time',))
mdtime[:] = self.file.mdtime[self.ni-1:self.nf]
mdtime.units = "hbar/Ha" ;
mdtime.mnemonics = "Molecular Dynamics TIME" ;
strten = f.createVariable('strten','d',('time','six'))
strten[:,:] = self.file.stress[self.ni-1:self.nf,0]
strten.units = "Ha/bohr^3" ;
strten.mnemonics = "STRess tensor" ;
f.close()
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