/
qcIn.py
executable file
·317 lines (253 loc) · 11 KB
/
qcIn.py
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#!/usr/bin/env python
import pyQChem as qc
import sys
import os
import copy
charge_tran = {'a2':'-2','a1':'-1','a0':'0','c1':'1','c2':'2','c3':'3','c4':'4'}
revd=dict([reversed(i) for i in charge_tran.items()])
charge_tran.update(revd)
class QcIn(object):
def __init__(self, infile,charge=0,mult=1,jobtype='opt',basis='6-31+g*',method='tpssh', \
geom_read=False, nametrunc=True, bond_cons = None, infodump=False):
self.jobdict = {'sp':self.jobSp, 'opt':self.jobOpt, 'fq':self.jobFreq, 'sopt':self.jobSopt, \
'cube':self.jobCube, 'constr':self.jobConstrainedOpt, 'fixbonds':self.jobFixedBondOpt, \
'cdft':self.jobCdft, \
}
# self.bond_cons = [[2,5,con_N_x],[3,4,con_N_x],[2,3,con_N_y],[4,5,con_N_y]]
self.bond_cons = bond_cons
self.info_dump = infodump
# self.free_atom = ['Fe','O']
self.free_atom = ['O']
self.job_arr_list = []
self.charge = charge
self.mult = mult
self.jobtype = jobtype
self.pcm_arr = None; self.sol_arr = None; self.plot_arr = None
#if nametrunc == True: self.name = (infile.split('.')[0]).split('_')[0]
#else: self.name = infile.split('.')[0]
splinfile = infile.split('/')
if len(splinfile) == 1:
self.path = ''
else:
self.path = '/'.join(splinfile[:-1])+'/'
if nametrunc == True: self.name = (splinfile[-1].split('.')[0]).split('_')[0]
else: self.name = (splinfile[-1].split('.'))[0]
print(splinfile)
print(splinfile[-1])
print(self.name)
print(self.charge)
print(self.mult)
self.out = qc.read(infile)
self.rem = qc.rem_array()
self.rem.basis(basis)
self.rem.method(method)
self.rem.thresh("14")
self.rem.add('mem_total','4096')
self.rem.add('mem_static','256')
self.rem.add('max_scf_cycles','500')
# self.rem.add('scf_convergence','7')
# self.rem.add('scf_algorithm','diis_gdm')
##For these metal-centered systems
self.rem.add('unrestricted','true')
# if self.mult == '1': ## I didn't find that this worked at all for any of the metal-macrocycle systems
# self.rem.add("scf_guess_mix", "1")
# self.rem.add("scf_guess", "gwh")
if geom_read:
self.mol = qc.mol_array()
self.mol.geometry("read")
self.rem.add('scf_guess', 'read')
else:
if infile.split('.')[-1] == 'out':
# self.mol=qc.mol_array(self.out.opt.geometries[-1])
self.mol = qc.mol_array(self.out.general.final_geometry)
# self.mol = qc.mol_array(self.out.general.initial_geometry)
else:
xyz = qc.cartesian(atom_list=self.out.list_of_atoms)
self.mol = qc.mol_array(xyz)
self.mol.charge(charge)
self.mol.multiplicity(mult)
def addSolvent(self):
self.rem.solvent_method('PCM')
self.pcm_arr = qc._unsupported_array("pcm")
self.pcm_arr.add_line("theory cpcm")
self.pcm_arr.add_line("method swig")
self.pcm_arr.add_line("solver inversion")
self.pcm_arr.add_line("heavypoints 194")
self.pcm_arr.add_line("hpoints 194")
self.pcm_arr.add_line("radii bondi")
self.pcm_arr.add_line("vdwscale 1.2")
self.sol_arr = qc._unsupported_array("solvent")
self.sol_arr.add_line("dielectric 78.39")
self.vdw_arr = qc._unsupported_array("van_der_waals")
self.vdw_arr.add_line("1")
"""Source: http://periodictable.com/Properties/A/VanDerWaalsRadius.v.html"""
#self.vdw_arr.add_line("24 1.97")
#self.vdw_arr.add_line("25 1.96")
#self.vdw_arr.add_line("26 1.96")
#self.vdw_arr.add_line("27 1.95")
#self.vdw_arr.add_line("28 1.63")
#self.vdw_arr.add_line("29 1.40")
#self.vdw_arr.add_line("30 1.39")
"""Source: https://physlab.lums.edu.pk/images/f/f6/Franck_ref2.pdf0""Source: http://periodictable.com/Properties/A/VanDerWaalsRadius.v.html"""
self.vdw_arr.add_line("24 1.97")
self.vdw_arr.add_line("25 1.96")
self.vdw_arr.add_line("26 1.96")
self.vdw_arr.add_line("27 1.95")
self.vdw_arr.add_line("28 1.94")
self.vdw_arr.add_line("29 2.00")
self.vdw_arr.add_line("30 2.02")
self.job_arr_list.append(self.pcm_arr)
self.job_arr_list.append(self.sol_arr)
self.job_arr_list.append(self.vdw_arr)
#CDFT calculation
def jobCdft(self):
self.rem.add('CDFT', 'True')
self.rem.add('SCF_PRINT', 'True')
self.cdft_arr = qc._unsupported_array("cdft")
self.cdft_arr.add_line("1")
self.cdft_arr.add_line("1 1 2 s")
self.job_arr_list.append(self.cdft_arr)
atoms = copy.copy(self.out.list_of_atoms)
first_two = [atoms[0][0], atoms[1][0]]
last_two = [atoms[-2][0], atoms[-1][0]]
if first_two != ['O','O'] and last_two == ['O','O']:
atoms.insert(0, atoms.pop()); atoms.insert(0, atoms.pop())
xyz = qc.cartesian(atom_list=atoms)
self.mol = qc.mol_array(xyz)
self.mol.charge(self.charge)
self.mol.multiplicity(self.mult)
#Fix all but selected atom numbers
def jobConstrainedOpt(self):
self.rem.jobtype("opt")
self.con_arr = qc._unsupported_array("opt")
self.con_arr.add_line("FIXED")
for i,atom in enumerate(self.out.list_of_atoms):
if atom[0] in self.free_atom:
continue
else:
self.con_arr.add_line(str(i+1) + " XYZ")
self.con_arr.add_line("ENDFIXED")
self.job_arr_list.append(self.con_arr)
#Fix bond lengths
def jobFixedBondOpt(self):
self.rem.jobtype("opt")
self.con_arr = qc._unsupported_array("opt")
self.con_arr.add_line("CONSTRAINT")
for constr in self.bond_cons: #need to implement this to read these from file if we used this for other systems
self.con_arr.add_line("stre %i %i %f" % (constr[0], constr[1], constr[2]))
self.con_arr.add_line("ENDCONSTRAINT")
self.job_arr_list.append(self.con_arr)
def jobCube(self):
self.jobSp()
self.rem.add("make_cube_files", "true")
self.plot_arr = qc._unsupported_array("plots")
self.plot_arr.add_line("Grid information comment")
self.plot_arr.add_line("200 -10.0 10.0")
self.plot_arr.add_line("200 -10.0 10.0")
self.plot_arr.add_line("200 -10.0 10.0")
self.plot_arr.add_line("1 0 0 0")
self.plot_arr.add_line("1")
self.job_arr_list.append(self.plot_arr)
#Single point job
def jobSp(self):
self.rem.jobtype("sp")
self.rem.add("print_orbitals","true")
self.rem.add("chelpg", "true")
#self.rem.add("lowdin_population", "true")
if self.info_dump == True:
self.rem.add("gui=2", "")
self.rem.add("molden_format", "true")
self.addSolvent()
#Geometry Optimization Job
def jobOpt(self):
self.rem.jobtype("opt")
# self.rem.add("geom_opt_tol_gradient", "5")
# self.rem.add("geom_opt_tol_displacement", "10")
# self.rem.add("geom_opt_tol_energy", "5")
def jobSopt(self):
self.jobOpt()
self.addSolvent()
#Frequency Job
def jobFreq(self):
self.rem.jobtype("freq")
self.rem.add("cpscf_nseg", "4")
#standardized Q-Chem job naming scheme
def genName(self):
chmult = charge_tran[self.charge]+'m'+self.mult
#self.name = self.path + self.name
#print(self.name)
name = self.path+'_'.join([self.name, self.jobtype, chmult])+'.in'
return name
@staticmethod
def ReadChMult(chmult):
ch, mult = chmult[:2], chmult[2:]
ch = charge_tran[ch]
mult = mult[1]
return ch, mult
def assembleJob(self):
job = qc.inputfile()
self.jobdict[self.jobtype]()
job.add(self.rem)
job.add(self.mol)
for job_arr in self.job_arr_list:
job.add(job_arr)
return job
def writeQcIn(self,qc_infile=None):
job = self.assembleJob()
print("QC infile: ", qc_infile)
if qc_infile == None:
qc_infile = self.genName()
job.write(qc_infile)
def WriteJob(infile, args, indir='.'):
if args.ParseName == True:
aNmN = infile.split('.')[0].split('_')[-1]
read_c, read_m = QcIn.ReadChMult(aNmN)
else:
read_c, read_m = args.c, args.m
if indir == '.':
readfile = infile
# qcw = QcIn(infile,read_c,read_m,args.j,basis=args.basis,method=args.method, \
# nametrunc=args.name)
else:
readfile = indir+'/'+infile
# qcw = QcIn(indir+'/'+infile,read_c,read_m,args.j,basis=args.basis,method=args.method, \
# nametrunc=args.name)
qcw = QcIn(readfile,read_c,read_m,args.j,basis=args.basis,method=args.method, \
nametrunc=args.name, infodump=args.infodump)
qcw.writeQcIn()
if __name__ == "__main__":
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('-f', help='Q-Chem Output File or Parent Directory', type=str)
parser.add_argument('-j', help='Job Type', type=str,default='sp')
parser.add_argument('-c', help='Charge', type=str,default='0')
parser.add_argument('-m', help='Multiplicity', type=str,default='1')
parser.add_argument('-basis', help='Basis Set', type=str,default='6-31+g*')
parser.add_argument('-method', help='EST Method', type=str,default='tpssh')
parser.add_argument('-name', help='Truncate name at first _', type=int,default=1)
parser.add_argument('-ParseName', help='Parse name for charge, spin mult', type=int,default=0)
parser.add_argument('-infodump', help='add Molden format, save checkpoint', type=int, default=0)
args = parser.parse_args()
f = args.f
if os.path.isfile(f):
WriteJob(f, args)
# if args.ParseName == True:
# aNmN = f.split('.')[0].split('_')[-1]
# read_c, read_m = QcIn.ReadChMult(aNmN)
# qcw = QcIn(f,args.c,args.m,args.j,basis=args.basis,method=args.method,nametrunc=args.name)
# qcw.writeQcIn()
elif os.path.isdir(f):
print("Directory found")
for qcoutfile in os.listdir(f):
if qcoutfile.split('.')[-1] in ('xyz', 'out'):
print(qcoutfile)
WriteJob(qcoutfile, args, f)
# if args.ParseName == True:
# aNmN = qcoutfile.split('.')[0].split('_')[-1]
# read_c, read_m = QcIn.ReadChMult(aNmN)
# qcw = QcIn(f+'/'+qcoutfile,read_c,read_m,args.j,basis=args.basis,method=args.method, \
# nametrunc=args.name)
# else:
# qcw = QcIn(f+'/'+qcoutfile,args.c,args.m,args.j,basis=args.basis,method=args.method, \
# nametrunc=args.name)
# qcw.writeQcIn()