def getforce(self, filename, numele, outname, potential, symb, starttime,
intcycle):
if intcycle:
resultname = filename + str(intcycle)
else:
resultname = filename
if not os.path.isfile("%s//gradient" % resultname):
writefile.werror(outname, 'forces', starttime)
exit('no force in outfile')
resultfile = open("%s//gradient" % resultname).readlines()
numf = resultfile[numele + 2:numele + 2 + numele]
sfar = []
for i in range(numele):
nuf = numf[i].replace("D", "e")
eachforce = nuf.split()
sfar.append(eachforce)
far = np.array(sfar, dtype=float)
far = far * -1
return far
def getenergy(self, filename, outname, potential, starttime, intcycle):
'''
get the energy
'''
if intcycle:
resultname = filename + str(intcycle)
else:
resultname = filename
resultfile = open("%s.out" % resultname).readlines()
try:
ev = resultfile[-3].split()[0]
outenergy = float(ev)
potential.append(outenergy)
outfile = open(outname, 'a+')
outfile.write('the total potential is %f a.u. \n' % outenergy)
outfile.close()
except:
writefile.werror(outname, 'energy', starttime)
exit('no energy in outfile')
return potential
def getforce(self, filename, numele, outname, potential, symb, starttime,
intcycle):
'''
get the force and position from the soft output file
only use to calculate the Hartree-Fork theory
'''
if intcycle:
resultname = filename + str(intcycle)
else:
resultname = filename
resultfile = open("%s.out" % resultname).readlines()
signf = 0
for i, line in enumerate(resultfile):
if 'GRADIENT FOR ' in line:
signf = i
if 'GRADIENT FOR ' in resultfile[signf]:
numf = resultfile[signf + 4:signf + 4 + numele]
else:
writefile.werror(outname, 'forces', starttime)
exit('no force in outfile')
sfar = []
for i in range(numele):
eachforce = numf[i].split()
sfar.append(eachforce[1:])
far = np.array(sfar, dtype=float)
far = far * -1.0
return far
def reinpotfile(self, filename, newpos, symb, intcycle, numele, getname):
'''
use the new position to create a new in file
'''
oldcycle = intcycle - 1
if oldcycle:
oldname = filename + str(oldcycle)
else:
oldname = filename
oldfile = open("%s.in" % oldname).readlines()
newfile = open("%s%d.in" % (filename, intcycle), 'w')
for i, line in enumerate(oldfile):
if 'geometry' in line:
geoline = i + 3
if 'geometry' not in oldfile[geoline - 3]:
writefile.werror(out0, 'geometry', starttime)
for i in range(geoline):
newfile.write(oldfile[i])
for i in range(geoline, geoline + numele):
newfile.write(symb[i - geoline])
newfile.write(' ')
for ii in range(3):
newfile.write(' ')
newfile.write(str(newpos[i - geoline][ii]))
newfile.write('\n')
for i in range(geoline + numele, len(oldfile)):
newfile.write(oldfile[i])
newfile.close()
return
def getenergy(self, filename, outname, potential, starttime, intcycle):
if intcycle:
resultname = filename + str(intcycle)
else:
resultname = filename
if not os.path.isfile("%s//energy" % resultname):
writefile.werror(outname, 'energy', starttime)
exit('no energy in outfile')
resultfile = open("%s//energy" % resultname).readlines()
ev = resultfile[1].split()[1]
outenergy = float(ev)
potential.append(outenergy)
outfile = open(outname, 'a+')
outfile.write('the total potential is %f a.u. \n' % outenergy)
outfile.close()
return potential
def getenergy(self, filename, outname, potential, starttime, intcycle):
'''
get the energy
'''
if intcycle:
resultname = filename + str(intcycle)
else:
resultname = filename
resultfile = open("%s.log" % resultname).readlines()
signe = []
for i, line in enumerate(resultfile):
if 'SCF Done' in line:
signe.append(i)
if '\\MP2=' in line:
signe.append(i)
if '\\CISD=' in line:
signe.append(i)
if 'ITN=' in line:
signe.append(i)
ii = signe[-1]
if 'SCF Done' in resultfile[ii]:
energyrow = resultfile[ii].split()
outenergy = float(energyrow[4])
potential.append(outenergy)
outfile = open(outname, 'a+')
outfile.write('the total potential is %f a.u. \n' % outenergy)
outfile.close()
elif '\\MP2=' in resultfile[ii]:
energyrow = resultfile[ii].split('\\')
for linemp in energyrow:
if 'MP2' in linemp:
outenergy = linemp.split('=')
outenergy = float(outenergy[1])
potential.append(outenergy)
outfile = open(outname, 'a+')
outfile.write('the total potential is %f a.u. \n' % outenergy)
outfile.close()
elif '\\CISD=' in resultfile[ii]:
energyrow = resultfile[ii].split('\\')
for linemp in energyrow:
if 'CISD' in linemp:
outenergy = linemp.split('=')
outenergy = float(outenergy[1])
potential.append(outenergy)
outfile = open(outname, 'a+')
outfile.write('the total potential is %f a.u. \n' % outenergy)
outfile.close()
elif 'ITN' in resultfile[ii]:
energyrow = resultfile[ii].split()
outenergy = float(energyrow[5])
potential.append(outenergy)
outfile = open(outname, 'a+')
outfile.write('the total potential is %f a.u. \n' % outenergy)
outfile.close()
else:
writefile.werror(outname, 'energy', starttime)
exit('no energy in outfile')
return potential