def genPythonStringEn(conf):
'''Python script'''
pythonpart_list = ['python']
# validate the conf
conf = validate_conf(conf)
if len(conf) < 1:
logging.error('Failed to validate conf!')
return ''
# all conf keys
confkeys = [i.lower() for i in conf.keys()]
if 'python_script' in confkeys and 'path_name' in confkeys and 'nbeads' in confkeys and 'theory' in confkeys:
script = conf['Python_script']
script = script.replace('PATH_NAME', conf['Path_name']).replace(
'NBEADS', str(1 + conf['NBeads'])).replace('THEORY',
conf['Theory'])
pythonpart_list.append(script)
else:
print conf
# ending
pythonpart_list.append('end')
pythonpart_str = '\n'.join(pythonpart_list)
return pythonpart_str
def genCosmo(conf):
cosmopart_list = ['cosmo']
# validate the conf
conf = validate_conf(conf)
if len(conf) < 1:
logging.error('Failed to validate conf!')
return ''
# all conf keys
confkeys = [i.lower() for i in conf.keys()]
if 'scrf' in confkeys:
if 'scrf_solvent' in confkeys:
cosmopart_list.append(' solvent %s' % conf['SCRF_solvent'])
if 'scrf_model' in confkeys:
if conf['SCRF_model'] in ['SMD', 'smd']:
cosmopart_list.append(' do_cosmo_smd .true.')
if 'scrf_others_nw' in confkeys:
cosmopart_list.append(' %s' % conf['SCRF_others_nw'])
if 'scrf_parameters_nw' in confkeys:
cosmopart_list.append(' parameters %s' %
conf['SCRF_parameters_nw'])
# ending
cosmopart_list.append('end')
cosmopart_str = '\n'.join(cosmopart_list)
else:
cosmopart_str = ''
return cosmopart_str
def genRelativistic(conf):
relativisticpart_list = ['relativistic']
# validate the conf
conf = validate_conf(conf)
if len(conf) < 1:
logging.error('Failed to validate conf!')
return ''
# all conf keys
confkeys = [i.lower() for i in conf.keys()]
if 'zora' in confkeys:
relativisticpart_list.append(' zora on')
if 'zora_others' in confkeys:
relativisticpart_list.append(' %s' % conf['Zora_others'])
if 'modelpotential' in confkeys:
relativisticpart_list.append(' modelpotential %s' %
str(conf['Modelpotential']))
# ending
relativisticpart_list.append('end')
relativisticpart_str = '\n'.join(relativisticpart_list)
return relativisticpart_str
def genCoordinates(conf, path_to_xyz='path_to_input_xyz'):
'''
Generate coordinates strings for g09 input file.
1. validate the conf
2. check the input path. NOTE: input file is necessary!
3. read the coordinate file with pybel
4. get the coordinate part and return
:param conf:
:return:
'''
# validate the conf
conf = validate_conf(conf)
if len(conf) < 1:
return ''
# check input path
if path_to_xyz not in conf.keys():
logging.info('WARN: No path is found to access to the xyz file.')
return ''
# read the coordinates
mol = pybel.readfile('xyz', conf[path_to_xyz]).next()
#mol.OBMol.SetTotalCharge(conf['Charge'])
#mol.OBMol.SetTotalSpinMultiplicity(conf['Spin'])
# get the coordinate part
raw_str = mol.write('gjf')
coor_str = '\n'.join(raw_str.split('\n')[5:-2])
return coor_str
def genHeader(conf):
'''
Generate header of the NWChem input file
1. validate the conf
2. if starts from previous, set restart
3. if path_to_input_xyz is provided, then set the name of .chk file (to the same as .xyz file).
Otherwise, neglect the .chk file
:param conf: configure dict for g09 job
:return: the header string
'''
# validate the conf
conf = validate_conf(conf)
if len(conf) < 1:
logging.error('Failed to validate conf!')
return ''
header_list = ['echo']
## for start new calculation
# jobname and title
Jname, title = suggest_jobname_title(conf)
if Jname == '':
logging.info(
'Failed to gen title for the job. Check "path_to_input_xyz"')
return ''
# for restart
if 'Start_from_previous' in conf.keys(
) and conf['Start_from_previous'] == True:
# start
header_list.append('restart %s' % Jname)
else:
# start
header_list.append('start %s' % Jname)
# title
header_list.append('title %s' % title)
# scratch
header_list.append('scratch_dir ./tmp')
# memory
header_list.append('memory %s %s' %
(''.join(re.findall('[0-9]+', conf['Mem'])), ''.join(
re.findall('[a-zA-Z]+', conf['Mem']))))
header_str = '\n'.join(header_list)
#print header_str
return header_str
def genSO(conf):
sopart_list = ['so']
# validate the conf
conf = validate_conf(conf)
if len(conf) < 1:
logging.error('Failed to validate conf!')
return ''
# all conf keys
confkeys = [i.lower() for i in conf.keys()]
if 'so_str' in confkeys:
sopart_list.append(conf['SO_str'])
# ending
sopart_list.append('end')
sopart_str = '\n'.join(sopart_list)
return sopart_str
def genDISP(conf):
disppart_list = ['disp']
# validate the conf
conf = validate_conf(conf)
if len(conf) < 1:
logging.error('Failed to validate conf!')
return ''
# all conf keys
confkeys = [i.lower() for i in conf.keys()]
# scf g09
try:
opt_str = conf['Others']
except:
opt_str = ''
opt_list = opt_str.lower().split(' ')
flag_empiricaldispersion = False
for s in opt_list:
if s.startswith('empiricaldispersion'):
flag_empiricaldispersion = True
disp = s.split('=')[1]
if disp in ['gd3bj', 'd3bj']:
disppart_list.append(' vdw 4')
elif disp in ['d3']:
disppart_list.append(' vdw 3')
# if no empirical dispersion option, turn off this function in NWChem
if not flag_empiricaldispersion:
disppart_list.append(' off')
if not flag_empiricaldispersion:
disppart_list = []
disppart_str = ' '.join(disppart_list)
return disppart_str
def genString(conf):
'''string method'''
stringpart_list = ['string']
# validate the conf
conf = validate_conf(conf)
if len(conf) < 1:
logging.error('Failed to validate conf!')
return ''
# all conf keys
confkeys = [i.lower() for i in conf.keys()]
if 'string_nbeads' in confkeys:
stringpart_list.append(' nbeads %s' % str(conf['String_nbeads']))
if 'string_maxiter' in confkeys:
stringpart_list.append(' maxiter %s' % str(conf['String_maxiter']))
if 'string_stepsize' in confkeys:
stringpart_list.append(' stepsize %s' %
str(conf['String_stepsize']))
if 'string_interpol' in confkeys:
stringpart_list.append(' interpol %s' %
str(conf['String_interpol']))
if 'string_freeze1' in confkeys:
stringpart_list.append(' freeze1 %s' % str(conf['String_freeze1']))
if 'string_freezen' in confkeys:
stringpart_list.append(' freezen %s' % str(conf['String_freezen']))
if 'string_tol' in confkeys:
stringpart_list.append(' %s' % str(conf['String_tol']))
if 'string_xyzpath' in confkeys:
stringpart_list.append(' xyzpath %s' % str(conf['String_xyzpath']))
if 'string_print_shift' in confkeys:
stringpart_list.append(' print_shift %s' %
str(conf['String_print_shift']))
# ending
stringpart_list.append('end')
stringpart_str = '\n'.join(stringpart_list)
return stringpart_str
def genInputFile(conf):
'''
Generate input file for NWChem.
1. validate the conf
2. check the input path. NOTE: input file is necessary!
3. generate header routine charge spin coordinates sequencially
4. check if starts from previous or not
5. check if Pseudo potential is used
:param conf:
:return: NWChem input string, suggest_inp_name, conf
'''
# validate the conf
conf = validate_conf(conf)
if len(conf) < 1:
return ''
# check input path
if 'path_to_input_xyz' not in conf.keys():
print 'WARN: No path is found to access to the xyz file.'
return ''
# get the strings for each part
geometry_str = genGeometry(conf)
charge, spin = getChargeSpin(conf)
inp_list = [
'Arrows::', 'xyzinput:', 'label: aquamer :label', geometry_str,
':xyzinput', '',
'molecule: label=aquamer charge{%s} mult{%s} theory{dft} xc{%s} basis{%s} solvation_type{COSMO-SMD} :molecule'
% (charge, spin, conf['functional'].lower(),
convBasis_G09toNW(conf['basis_set'])), '::Arrows', ''
]
# combine
inp_str = '\n'.join(inp_list)
return inp_str
def genFreq(conf):
freqpart_list = ['freq']
# validate the conf
conf = validate_conf(conf)
if len(conf) < 1:
logging.error('Failed to validate conf!')
return ''
# all conf keys
confkeys = [i.lower() for i in conf.keys()]
if 'nwreusehess' in confkeys:
freqpart_list.append(' reuse')
if 'nwfreqanimate' in confkeys:
freqpart_list.append(' animate')
# ending
freqpart_list.append('end')
freqpart_str = '\n'.join(freqpart_list)
return freqpart_str
def genNEB(conf):
nebpart_list = ['neb']
# validate the conf
conf = validate_conf(conf)
if len(conf) < 1:
logging.error('Failed to validate conf!')
return ''
# all conf keys
confkeys = [i.lower() for i in conf.keys()]
if 'neb_nbeads' in confkeys:
nebpart_list.append(' nbeads %s' % str(conf['NEB_nbeads']))
if 'neb_kbeads' in confkeys:
nebpart_list.append(' kbeads %s' % str(conf['NEB_kbeads']))
if 'neb_maxiter' in confkeys:
nebpart_list.append(' maxiter %s' % str(conf['NEB_maxiter']))
if 'neb_stepsize' in confkeys:
nebpart_list.append(' stepsize %s' % str(conf['NEB_stepsize']))
if 'neb_convergence' in confkeys and conf['NEB_convergence'] not in [
'default', 'Default'
]:
nebpart_list.append(' %s' % str(conf['NEB_convergence']))
if 'neb_xyzpath' in confkeys:
nebpart_list.append(' xyz_path ./%s' %
str(os.path.basename(conf['NEB_xyzpath'])))
if 'neb_print_shift' in confkeys:
nebpart_list.append(' print_shift %s' %
str(conf['NEB_print_shift']))
# ending
nebpart_list.append('end')
nebpart_str = '\n'.join(nebpart_list)
return nebpart_str
def getChargeSpin(conf):
'''
Generate charge and spin strings for nwchem input file.
1. validate the conf
2. if no charge settings, set to '0'
3. if spin is setted by user, use it directly, otherwise, calculated it according number of electrons
4. check the input path. NOTE: input file is necessary!
5. read the coordinate file with pybel
6. calculate the total number of electrons (sum of atomic numbers + charge)
7. calculate the spin, number of single electrons + 1
NOTE:
The procedure for calculate spin is simple.
Specify the conf['Spin'] value if intend to have higher multiplicity.
:param conf:
:return:
'''
# validate the conf
conf = validate_conf(conf)
if len(conf) < 1:
return ''
# check charge
if 'Charge' not in conf.keys():
logging.info('WARN: No Charge is found, set default value 0')
conf['Charge'] = '0'
# check spin
if 'Spin' in conf.keys():
logging.info('WARN: Using specified SPIN, %s' % conf['Spin'])
else:
logging.info(
'WARN: No specified SPIN is found, trying to calculate it.')
# check input path
if 'path_to_input_xyz' not in conf.keys():
logging.error(
'ERROR: No path is found to access to the xyz file, which is required to calculate the spin.'
)
return ''
# read the coordinates
mol = pybel.readfile('xyz', conf['path_to_input_xyz']).next()
# calculate the total number of electrons
total_atomicnum = sum([i.atomicnum for i in mol.atoms])
electron_num = total_atomicnum + int(conf['Charge'])
# set spin, odd electron --> 2, even --> 1
conf['Spin'] = str(electron_num % 2 + 1)
logging.info(
'WARN: No specified SPIN is found, assign %s automatically' %
conf['Spin'])
charge_str = conf['Charge']
spin_str = conf['Spin']
return charge_str, spin_str
def genDFT(conf):
dftpart_list = ['dft']
dftpart_list.append(' decomp')
# validate the conf
conf = validate_conf(conf)
if len(conf) < 1:
logging.error('Failed to validate conf!')
return ''
# all conf keys
confkeys = [i.lower() for i in conf.keys()]
# scf g09
try:
scf_str = conf['SCF']
except:
scf_str = ''
scf_list = scf_str.lower().replace('(',
'').replace(')',
'').replace(' ',
'').split(',')
for s in scf_list:
if s.startswith('maxcyc'):
dftpart_list.append(' iterations %s' % s.split('=')[1])
elif s.startswith('tight'):
dftpart_list.append(' convergence density 1e-8')
dftpart_list.append(' convergence energy 1e-6')
dftpart_list.append(' tolerances tight')
# grid
if 'integral' in confkeys:
grid_str = conf['Integral'].lower()
if grid_str in ['ultrafine']:
dftpart_list.append(' grid xfine')
elif grid_str in ['', 'fine']:
dftpart_list.append(' grid fine')
# XC
xc_str = conf['functional'].lower()
if xc_str in ['b3lyp', 'pbe0']:
dftpart_list.append(' xc %s' % xc_str)
elif xc_str in ['m06l', 'm06-l']:
dftpart_list.append(' xc m06-l')
elif xc_str in ['m062x', 'm06-2x']:
dftpart_list.append(' xc m06-2x')
elif xc_str in ['m052x', 'm05-2x']:
dftpart_list.append(' xc m05-2x')
elif xc_str in ['b3pw91']:
dftpart_list.append(
' xc hfexch 0.20 slater 0.80 becke88 nonlocal 0.72 perdew91 0.81 pw91lda 1.00'
)
elif xc_str in ['blyp']:
dftpart_list.append(' xc becke88 lyp')
else:
logging.error(
'ERROR: Cannot find a equivalent XC in NWChem. Please define yourself'
)
return ''
# disp
disp_str = genDISP(conf)
if len(disp_str) > 0:
dftpart_list.append(' %s' % disp_str)
# mult
charge, mult = getChargeSpin(conf)
dftpart_list.append(' mult %s' % mult)
# additional keyword for DFT
if 'dft_others_nw' in confkeys:
dftpart_list.append(' %s' % conf['DFT_others_nw'])
# ending
dftpart_list.append('end')
dftpart_str = '\n'.join(dftpart_list)
return dftpart_str
def genBasis(conf):
basispart_list = ['basis']
ecppart_list = ['ecp']
# validate the conf
conf = validate_conf(conf)
if len(conf) < 1:
logging.error('Failed to validate conf!')
return ''
# all conf keys
confkeys = [i.lower() for i in conf.keys()]
# check input path
if 'path_to_input_xyz' not in conf.keys():
logging.info('WARN: No path is found to access to the xyz file.')
return ''
# read the coordinates
mol = pybel.readfile('xyz', conf['path_to_input_xyz']).next()
ele_Table = pybel.ob.OBElementTable()
# get element labels
atomicNumbers = sorted(list(set([i.atomicnum for i in mol.atoms])))
all_elements = [ele_Table.GetSymbol(i) for i in atomicNumbers]
# pseudo
if 'pseudo' in confkeys:
for ele in all_elements:
if ele in conf['Pseudo_elements']:
if 'NOAuto_Basis_set' not in conf.keys():
basispart_list.append(
' %s library %s' %
(ele, convBasis_G09toNW(conf['Pseudo_potential'])))
# ecp part
ecppart_list.append(
' %s library %s' %
(ele, convBasis_G09toNW(conf['Pseudo_potential'])))
else:
if 'NOAuto_Basis_set' not in conf.keys():
basispart_list.append(
' %s library %s' %
(ele, convBasis_G09toNW(conf['basis_set'])))
else:
for ele in all_elements:
if 'NOAuto_Basis_set' not in conf.keys():
basispart_list.append(
' %s library %s' %
(ele, convBasis_G09toNW(conf['basis_set'])))
# additional keywords for basis set
if 'basis_set_others_nw' in confkeys:
basispart_list.append(' %s' % conf['basis_set_others_nw'])
# ending
basispart_list.append('end')
# ecp part ending
if len(ecppart_list) > 1:
ecppart_list.append('end')
basispart_list.append('')
basispart_list += ecppart_list
# convert to str
basispart_str = '\n'.join(basispart_list)
return basispart_str
def genGeometry(conf):
# validate the conf
conf = validate_conf(conf)
if len(conf) < 1:
logging.error('Failed to validate conf!')
return ''
# all conf keys
confkeys = [i.lower() for i in conf.keys()]
# generate NEB geometry or NOT
if 'neb' in confkeys:
if 'neb_path_to_startgoem' in confkeys:
# start geom
geo_list = ['geometry nocenter noautoz noautosym']
coor_str = genCoordinates(conf,
path_to_xyz='NEB_path_to_startgoem')
geo_list.append(coor_str)
geo_list.append('end\n')
if 'neb_path_to_midgoem' in confkeys:
# mid geom
geo_list += ['geometry midgeom nocenter noautoz noautosym']
coor_str = genCoordinates(conf, path_to_xyz='NEB_path_to_midgoem')
geo_list.append(coor_str)
geo_list.append('end\n')
if 'neb_path_to_endgoem' in confkeys:
# end geom
geo_list += ['geometry endgeom nocenter noautoz noautosym']
coor_str = genCoordinates(conf, path_to_xyz='NEB_path_to_endgoem')
geo_list.append(coor_str)
geo_list.append('end')
elif 'string' in confkeys:
if 'string_path_to_startgoem' in confkeys:
# start geom
geo_list = ['geometry nocenter noautoz noautosym']
coor_str = genCoordinates(conf,
path_to_xyz='String_path_to_startgoem')
geo_list.append(coor_str)
geo_list.append('end\n')
if 'string_path_to_midgoem' in confkeys:
# mid geom
geo_list += ['geometry midgeom nocenter noautoz noautosym']
coor_str = genCoordinates(conf,
path_to_xyz='String_path_to_midgoem')
geo_list.append(coor_str)
geo_list.append('end\n')
if 'string_path_to_endgoem' in confkeys:
# end geom
geo_list += ['geometry endgeom nocenter noautoz noautosym']
coor_str = genCoordinates(conf,
path_to_xyz='String_path_to_endgoem')
geo_list.append(coor_str)
geo_list.append('end')
elif 'geometry_load' in confkeys:
# NoSymm
if 'nosymm' in confkeys:
if conf['NoSymm'] in [True, 1]:
geo_list = ['geometry units angstroms noautoz noautosym']
else:
geo_list = ['geometry units angstroms noautoz']
# load command
load_str = ' load frame %d %s' % (conf['ith_Bead'],
conf['Geometry_load'])
geo_list.append(load_str.replace('PATH_NAME', conf['Path_name']))
# end
geo_list.append('end')
else:
# NoSymm
if 'nosymm' in confkeys:
if conf['NoSymm'] in [True, 1]:
geo_list = ['xyzdata:']
else:
geo_list = ['xyzdata:']
# coordinates
coor_str = genCoordinates(conf)
geo_list.append(coor_str)
# end
geo_list.append(':xyzdata')
geo_str = '\n'.join(geo_list)
return geo_str
def genTask(conf):
# validate the conf
conf = validate_conf(conf)
if len(conf) < 1:
logging.error('Failed to validate conf!')
return ''
# all conf keys
confkeys = [i.lower() for i in conf.keys()]
taskpart_list = []
if 'nwcalhess' in confkeys:
if 'scrf' in confkeys:
taskpart_list.append('task dft hessian')
else:
taskpart_list.append('task scf hessian')
if 'energy' in confkeys and 'theory' in confkeys:
taskpart_list.append('task %s energy' % conf['Theory'])
if 'opt' in confkeys and 'saddle' not in confkeys:
if 'scrf' in confkeys:
taskpart_list.append('task dft optimize')
else:
taskpart_list.append('task scf optimize')
if 'saddle' in confkeys:
if 'scrf' in confkeys:
taskpart_list.append('task dft saddle')
else:
taskpart_list.append('task scf saddle')
#taskpart_list.append('task scf hessian')
if 'freq' in confkeys:
if 'scrf' in confkeys:
#taskpart_list.append('task dft hessian')
taskpart_list.append('task dft frequencies')
else:
#taskpart_list.append('task scf hessian')
taskpart_list.append('task scf frequencies')
if 'nwfindsaddle' in confkeys:
if 'scrf' in confkeys:
taskpart_list.append('task dft saddle')
else:
taskpart_list.append('task scf saddle')
if 'neb' in confkeys and 'neb_ignore' in confkeys:
if 'scrf' in confkeys:
taskpart_list.append('task dft neb ignore')
else:
taskpart_list.append('task scf neb ignore')
if 'neb' in confkeys and 'neb_ignore' not in confkeys:
if 'scrf' in confkeys:
taskpart_list.append('task dft neb')
else:
taskpart_list.append('task scf neb')
if 'string' in confkeys and 'string_ignore' in confkeys:
if 'scrf' in confkeys:
taskpart_list.append('task dft string ignore')
else:
taskpart_list.append('task scf string ignore')
if 'string' in confkeys and 'string_ignore' not in confkeys:
if 'scrf' in confkeys:
taskpart_list.append('task dft string')
else:
taskpart_list.append('task scf string')
if 'pythonstringen' in confkeys:
taskpart_list.append('task python')
# ending
taskpart_str = '\n'.join(taskpart_list)
return taskpart_str
def genDriver(conf):
driverpart_list = ['driver']
# validate the conf
conf = validate_conf(conf)
if len(conf) < 1:
logging.error('Failed to validate conf!')
return ''
## title
#Jname, title = suggest_jobname_title(conf)
#driverpart_list.append(' xyz %s' % title)
# all conf keys
confkeys = [i.lower() for i in conf.keys()]
# scf g09
try:
opt_str = conf['Opt']
except:
opt_str = ''
opt_list = opt_str.lower().replace('(',
'').replace(')',
'').replace(' ',
'').split(',')
for s in opt_list:
if s.startswith('maxcyc'):
driverpart_list.append(' maxiter %s' % s.split('=')[1])
elif s.startswith('tight'):
driverpart_list.append(
' GMAX 0.000015\n GRMS 0.00001\n XMAX 0.00006\n XRMS 0.00004'
)
elif s.startswith('nwstep'):
if 'saddle' in confkeys:
driverpart_list.append(' sadstp %s' % s.split('=')[1])
else:
driverpart_list.append(' trust %s' % s.split('=')[1])
# initial hessian
if 'guess' in confkeys:
if conf['Guess'] in ['Harris', 'harris']:
driverpart_list.append(' inhess 1')
elif conf['Guess'] in ['Read', 'read']:
driverpart_list.append(' inhess 0')
# initial hessian
if 'nwinhess' in confkeys:
driverpart_list.append(' inhess %s' % str(conf['NWInhess']))
driverpart_list.append(' maxiter 250')
# additional keyword for Opt
if 'opt_others_nw' in confkeys:
driverpart_list.append(' %s' % conf['Opt_others_nw'])
# ending
driverpart_list.append('end')
driverpart_str = '\n'.join(driverpart_list)
return driverpart_str
def genInputFile(conf):
'''
Generate input file for NWChem.
1. validate the conf
2. check the input path. NOTE: input file is necessary!
3. generate header routine charge spin coordinates sequencially
4. check if starts from previous or not
5. check if Pseudo potential is used
:param conf:
:return: NWChem input string, suggest_inp_name, conf
'''
# validate the conf
conf = validate_conf(conf)
if len(conf) < 1:
return ''
# check input path
if 'path_to_input_xyz' not in conf.keys():
print 'WARN: No path is found to access to the xyz file.'
return ''
# get the strings for each part
header_str = genHeader(conf)
charge_str = genCharge(conf)
geometry_str = genGeometry(conf)
basis_str = genBasis(conf)
dft_str = genDFT(conf)
relativistic_str = genRelativistic(conf)
so_str = genSO(conf)
driver_str = genDriver(conf)
freq_str = genFreq(conf)
neb_str = genNEB(conf)
string_str = genString(conf)
pythonstringen_str = genPythonStringEn(conf)
cosmo_str = genCosmo(conf)
task_str = genTask(conf)
mol_name = os.path.basename(conf['path_to_input_xyz'])[:-4]
# start from previous or not
if 'Start_from_previous' in conf.keys(
) and conf['Start_from_previous'] == True:
inp_list = [header_str, '']
if 'Opt' in conf.keys():
inp_list += [driver_str, '']
if 'NWFindSaddle' in conf.keys():
inp_list += [driver_str, '']
if 'Freq' in conf.keys():
inp_list += [freq_str, '']
if 'Relativistic' in conf.keys():
inp_list += [relativistic_str, '']
if 'SO' in conf.keys():
inp_list += [so_str, '']
if 'NEB' in conf.keys():
inp_list += [neb_str, '']
mol_name = conf['NEB_path_name']
if 'String' in conf.keys():
inp_list += [string_str, '']
mol_name = conf['String_path_name']
if 'Python' in conf.keys():
inp_list += [pythonstringen_str, '']
mol_name = conf['Path_name']
if 'CalStringEn' in conf.keys():
mol_name = conf['Path_name']
inp_list.append(task_str)
else:
inp_list = [header_str, '']
inp_list += [charge_str, '']
if 'NoGeometry' not in conf.keys():
inp_list += [geometry_str, '']
inp_list += [basis_str, '']
if 'SO' in conf.keys():
inp_list += [so_str, '']
inp_list += [dft_str, '']
if 'SCRF' in conf.keys():
inp_list += [cosmo_str, '']
if 'Opt' in conf.keys():
inp_list += [driver_str, '']
if 'Freq' in conf.keys():
inp_list += [freq_str, '']
if 'Relativistic' in conf.keys():
inp_list += [relativistic_str, '']
if 'NEB' in conf.keys():
inp_list += [neb_str, '']
mol_name = conf['NEB_path_name']
if 'String' in conf.keys():
inp_list += [string_str, '']
mol_name = conf['String_path_name']
if 'PythonStringEn' in conf.keys():
inp_list += [pythonstringen_str, '']
mol_name = conf['Path_name']
if 'CalStringEn' in conf.keys():
mol_name = conf['Path_name']
inp_list.append(task_str)
# combine
inp_str = '\n'.join(inp_list)
# suggest input file name, without suffix
if 'CalStringEn' in conf.keys():
suggest_inp_name = '%s_%s' % (mol_name, conf['ith_Bead'])
else:
suggest_inp_name = 'step%s_%s_%s' % (conf['Step'], conf['Substep'],
mol_name)
return inp_str, suggest_inp_name
