sh.write(tmp_row, tmp_col+7, 'SP Energy in energy')
sh.write(tmp_row, tmp_col+8, 'SP Energy (0 K) in energy corrected with freq scaling factor')
sh.write(tmp_row, tmp_col+9, 'SP Enthalpy (298.15 K) in energy corrected with freq scaling factor')
sh.write(tmp_row, tmp_col+10, 'Multiplicity')
sh.write(tmp_row, tmp_col+11, 'External Symmetry Number')
sh.write(tmp_row, tmp_col+12, 'Geometry')
sh.write(tmp_row, tmp_col+13, 'Frequencies')
tmp_row = 1
tmp_col = 0
for i in xrange(speciesNum):
sh.write(tmp_row, tmp_col, name[i])
sh.write(tmp_row, tmp_col+1, name[i])
sh.write(tmp_row, tmp_col+2, formula[i])
sh.write(tmp_row, tmp_col+3, atomsNum[i])
sh.write(tmp_row, tmp_col+4, optEnergy[i])
sh.write(tmp_row, tmp_col+5, optZPE[i])
sh.write(tmp_row, tmp_col+6, optEnthalpy[i])
sh.write(tmp_row, tmp_col+7, SPEnergy[i])
# ZPE scaling factor from Truhlar used here
sh.write(tmp_row, tmp_col+8, SPEnergy[i] + (optZPE[i]-optEnergy[i])*0.977)
sh.write(tmp_row, tmp_col+9, SPEnergy[i] + (optZPE[i]-optEnergy[i])*0.977 + optEnthalpy[i]-optZPE[i])
sh.write(tmp_row, tmp_col+10, multi[i])
sh.write(tmp_row, tmp_col+11, RSN[i])
sh.write(tmp_row, tmp_col+12, textExtractor.geometryExtractor(geom[i]).replace('\t',' '))
sh.write(tmp_row, tmp_col+13, ' '.join(freq[i]))
tmp_row += 1
wb.close()
multi = int(tmp_m.group(1))
multi_done = 1
elif optimized_done != 1:
tmp_m = pattern_optimized.match(tmp_line)
if tmp_m:
optimized_done = 1
elif standard_done != 1:
tmp_m = pattern_standard.match(tmp_line)
if tmp_m:
tmp_num = lineNum + 5
standard_done = 1
elif coordinate_done != 1:
tmp_m = pattern_endline.match(tmp_line)
if tmp_m:
if lineNum > tmp_num:
tmp_geom = textExtractor.geometryExtractor(tmp_lines[tmp_num: lineNum])
coordinate_done = 1
fw = file(os.path.join('..', '_i_radicalSPEnergy', tmp_file[0]+'.gjf'), 'w')
fw.write(
'''%mem=28GB
%nprocshared=12
%chk=''' + tmp_file[0] + '''.chk
#p B3LYP/6-31G(d) opt freq
using B3LYP/6-31G(d) to do opt and freq calc.
0 '''+str(multi) + '\n' + tmp_geom + '\n\n\n\n\n\n')
fw.close()
fr.close()
else:
print 'Error! There is no jobs about molecule ' + tmp_mole
multi = int(tmp_m.group(1))
multi_done = 1
elif optimized_done != 1:
tmp_m = pattern_optimized.match(tmp_line)
if tmp_m:
optimized_done = 1
elif standard_done != 1:
tmp_m = pattern_standard.match(tmp_line)
if tmp_m:
tmp_num = lineNum + 5
standard_done = 1
elif coordinate_done != 1:
tmp_m = pattern_endline.match(tmp_line)
if tmp_m:
if lineNum > tmp_num:
tmp_geom = textExtractor.geometryExtractor(
tmp_lines[tmp_num:lineNum])
coordinate_done = 1
fw = file(os.path.join('..', '_g_SPEnergy', tmp_file[0] + '.gjf'), 'w')
fw.write('''%mem=28GB
%nprocshared=12
%chk=''' + tmp_file[0] + '''.chk
#p B3LYP/6-31G(d) opt freq
using B3LYP/6-31G(d) to do opt and freq calc.
0 ''' + str(multi) + '\n' + tmp_geom + '\n\n\n\n\n\n')
fw.close()
fr.close()
else:
print 'Error! There is no jobs about molecule ' + tmp_mole
os.chdir('../')
def generateJobFromLog(self, fileName, path='', nosym=False, jobName=''):
#variables
multi = 1
#flags
multi_done = -1
freqCom_done = -1
standard_done = -1
coordinate_done = -1
# temporary variables
tmp_m = []
tmp_num = 0
if jobName == '':
tmp_dir = fileName[0:-4] + '_2_cbs'
else:
tmp_dir = jobName
if path == '':
tmp_dir_path = tmp_dir
fr = file(fileName, 'r')
else:
tmp_dir_path = os.path.join(path, tmp_dir)
fr = file(os.path.join(path, fileName), 'r')
tmp_lines = fr.readlines()
for (lineNum, tmp_line) in enumerate(tmp_lines):
if multi_done != 1:
tmp_m = pattern_logMulti.match(tmp_line)
if tmp_m:
multi = int(tmp_m.group(1))
multi_done = 1
elif freqCom_done != 1:
if lineNum < len(tmp_lines) - 1:
tmp2_line = tmp_lines[lineNum].strip() + tmp_lines[lineNum+1].strip()
tmp_m = pattern_logFreqCom.match(tmp2_line)
if tmp_m:
freqCom_done = 1
elif standard_done != 1:
if nosym == False:
tmp_m = pattern_logStandard.match(tmp_line)
else:
tmp_m = pattern_logInput.match(tmp_line)
if tmp_m:
tmp_num = lineNum + 5
standard_done = 1
elif coordinate_done != 1:
tmp_m = pattern_logEndline.match(tmp_line)
if tmp_m:
if lineNum > tmp_num:
tmp_geom = textExtractor.geometryExtractor(tmp_lines[tmp_num: lineNum])
coordinate_done = 1
if os.path.exists(tmp_dir):
shutil.rmtree(tmp_dir)
os.mkdir(tmp_dir)
fw = file(os.path.join(tmp_dir_path, tmp_dir+'.gjf'), 'w')
if self.name == 'Tianhe' or self.name == 'Tianhe2':
fw.write(
'''%mem=16GB
%nprocshared=12
''')
else:
fw.write(
'''%mem=28GB
%nprocshared=12
''')
if self._TS == False:
fw.write('#p cbs-qb3')
else:
fw.write('#p cbs-qb3 opt=(TS, calcfc) freq')
if self._dispersionD3 == False:
fw.write('\n')
else:
print 'Warning! It should be verified whether D3 could be used in CBS-QB3 calculation!'
fw.write(' EmpiricalDispersion=GD3\n')
fw.write('''
using ub3lyp/6-31G(d) to scan
0 ''')
fw.write(''.join([str(multi), '\n', tmp_geom]) + '\n\n\n\n\n')
fw.close()
os.system("..\\dos2unix-6.0.6-win64\\bin\\dos2unix.exe " + fw.name + ' > log_dos2unix.txt 2>&1')
fw = file(os.path.join(tmp_dir_path, tmp_dir+'.job'), 'w')
if self.name == 'cce':
if self._g09D01 == False:
fw.write(
# cce cluster
'''#!/bin/csh
#
#$ -cwd
#$ -j y
#$ -S /bin/csh
#
setenv GAUSS_SCRDIR /state/partition1
setenv g09root /share/apps
source $g09root/g09/bsd/g09.login
cd ''' + self.jobLocation + '/' + tmp_dir + '''
$g09root/g09/g09 ''' + tmp_dir + '''.gjf
$g09root/g09/formchk ''' + tmp_dir + '''.chk
''')
else:
fw.write(
# cce cluster
'''#!/bin/csh
#
#$ -cwd
#$ -j y
#$ -S /bin/csh
#
setenv GAUSS_SCRDIR /state/partition1
setenv g09root /home/hetanjin/apps/g09D01
source $g09root/g09/bsd/g09.login
cd ''' + self.jobLocation + '/' + tmp_dir + '''
$g09root/g09/g09 ''' + tmp_dir + '''.gjf
$g09root/g09/formchk ''' + tmp_dir + '''.chk
''')
elif self.name == 'Tsinghua100':
fw.write(
# Tsinghua100 cluster
'''#BSUB -J ''' + tmp_dir + '''
#BSUB -q hpc_linux
#BSUB -R "select[mem>30000]"
#BSUB -n 12
#BSUB -R "span[hosts=1]"
#BSUB -o ''' + self.jobLocation + '/' + tmp_dir + '''/output.%J
#BSUB -e ''' + self.jobLocation + '/' + tmp_dir + '''/error.%J
export g09root=/home/hexin/gaussian
export GAUSS_SCRDIR=/scratch
source $g09root/g09/bsd/g09.profile
''')
if self._scratchStrategy == True:
fw.write(
'''rm /scratch/*
cd ''' + self.jobLocation + '/' + tmp_dir + '''
$g09root/g09/g09 ''' + tmp_dir + '''.gjf ''' + tmp_dir + '''.log
$g09root/g09/formchk /scratch/''' + tmp_dir + '''.chk
cp /scratch/''' + tmp_dir + '''.chk ''' + tmp_dir + '''.chk
cp /scratch/''' + tmp_dir + '''.fchk ''' + tmp_dir + '''.fchk
rm /scratch/*
''')
else:
fw.write(
'''cd ''' + self.jobLocation + '/' + tmp_dir + '''
$g09root/g09/g09 ''' + tmp_dir + '''.gjf ''' + tmp_dir + '''.log
$g09root/g09/formchk ''' + tmp_dir + '''.chk
''')
elif self.name == 'Tianhe':
if self._g09D01 == False:
fw.write(
# Tianhe cluster
'''#!/bin/bash
cd ''' + self.jobLocation + '/' + tmp_dir + '''
/vol-th/home/you/g09/g09 ''' + tmp_dir + '''.gjf
''')
else:
fw.write(
# Tianhe cluster
'''#!/bin/bash
export GAUSS_SCRDIR=/vol-th/home/you/scratch
export g09root=/vol-th/home/you/softwares/gaussian/g09D01
source $g09root/g09/bsd/g09.profile
cd ''' + self.jobLocation + '/' + tmp_dir + '''
$g09root/g09/g09 ''' + tmp_dir + '''.gjf
''')
elif self.name == 'Tianhe2':
if self._g09D01 == False:
fw.write(
# Tianhe cluster
'''#!/bin/bash
cd ''' + self.jobLocation + '/' + tmp_dir + '''
/vol-th/home/you1/g09/g09 ''' + tmp_dir + '''.gjf
''')
else:
fw.write(
# Tianhe cluster
'''#!/bin/bash
export GAUSS_SCRDIR=/vol-th/home/you1/scratch
export g09root=/vol-th/home/you1/softwares/gaussian/g09D01
source $g09root/g09/bsd/g09.profile
cd ''' + self.jobLocation + '/' + tmp_dir + '''
$g09root/g09/g09 ''' + tmp_dir + '''.gjf
''')
fw.close()
os.system("..\\dos2unix-6.0.6-win64\\bin\\dos2unix.exe " + fw.name + ' > log_dos2unix.txt 2>&1')
sh.write(tmp_row, tmp_col + 10, 'Multiplicity')
sh.write(tmp_row, tmp_col + 11, 'External Symmetry Number')
sh.write(tmp_row, tmp_col + 12, 'Geometry')
sh.write(tmp_row, tmp_col + 13, 'Frequencies')
tmp_row = 1
tmp_col = 0
for i in xrange(speciesNum):
sh.write(tmp_row, tmp_col, name[i])
sh.write(tmp_row, tmp_col + 1, name[i])
sh.write(tmp_row, tmp_col + 2, formula[i])
sh.write(tmp_row, tmp_col + 3, atomsNum[i])
sh.write(tmp_row, tmp_col + 4, optEnergy[i])
sh.write(tmp_row, tmp_col + 5, optZPE[i])
sh.write(tmp_row, tmp_col + 6, optEnthalpy[i])
sh.write(tmp_row, tmp_col + 7, SPEnergy[i])
# ZPE scaling factor from Truhlar used here
sh.write(tmp_row, tmp_col + 8,
SPEnergy[i] + (optZPE[i] - optEnergy[i]) * 0.977)
sh.write(
tmp_row, tmp_col + 9, SPEnergy[i] +
(optZPE[i] - optEnergy[i]) * 0.977 + optEnthalpy[i] - optZPE[i])
sh.write(tmp_row, tmp_col + 10, multi[i])
sh.write(tmp_row, tmp_col + 11, RSN[i])
sh.write(tmp_row, tmp_col + 12,
textExtractor.geometryExtractor(geom[i]).replace('\t', ' '))
sh.write(tmp_row, tmp_col + 13, ' '.join(freq[i]))
tmp_row += 1
wb.close()
print 'Error! ' + tmp_species + ' not found in mole_dict!'
break
molecule1.getLogGeom(mole_dict[tmp_species])
molecule1.fulfillBonds()
molecule1.calcFormula()
tmp_groups = molecule1.get1stOrderGroup()
tmp_groupDict = {}
for tmp_atom in molecule1.atoms:
if tmp_atom.symbol != 'H':
tmp_groupDict[tmp_atom.label] = tmp_groups.pop(0)
if len(tmp_groups) != 0:
print 'Error! The number of groups is larger than the number of non-H atoms!'
shw.write(tmp_row, tmp_col, tmp_species)
shw.write(tmp_row, tmp_col+1, tmp_species)
shw.write(tmp_row, tmp_col+2, molecule1.formula)
shw.write(tmp_row, tmp_col+3, textExtractor.geometryExtractor(mole_dict[tmp_species]).replace('\t',' '))
for tmp_rot in HR_dict[tmp_species]:
tmp_list = sorted([tmp_groupDict[tmp_rot[0]], tmp_groupDict[tmp_rot[1]]])
tmp_rotText = tmp_list[0] + '-' + tmp_list[1]
shw.write(tmp_row, tmp_col+4, tmp_rotText)
shw.write(tmp_row, tmp_col+5, tmp_rot[0])
shw.write(tmp_row, tmp_col+6, tmp_rot[1])
for (i, tmp_T) in enumerate(temperature):
shw.write(tmp_row, tmp_col+7+i, tmp_rot[5][tmp_T])
tmp_row += 1
wbw.close()
