def __init__(self,
job_name,
molecule,
job_type,
basis_set,
method,
scf_print=3,
scf_final_print=3,
scf_convergence=8,
scf_save_matrices=1):
"""QChemSCFJob constructor.
Args:
job_name (str): name of the job
molecue (Molecule object): molecule job should be done on (geometry etc.)
basis_set (str): name of the basis to be used
method (str): evaluation mathod (e.g. B3LYP)
scf_convergence (int): convergence criterium (diff of energies must be
lower 10^scf_convergence)
scf_print (int): print level for every scf step
scf_final_print (int): print level for final scf step
"""
self._job_name = job_name
self._molecule = molecule
self._job_type = job_type
self._rem_array = qc.rem_array()
self._rem_array.method(method)
self._rem_array.basis(basis_set)
self._rem_array.scf_convergence(str(scf_convergence))
self._rem_array.scf_print(str(scf_print))
self._rem_array.scf_final_print(str(scf_final_print))
self._rem_array.scf_save_matrices(str(scf_save_matrices))
# pyQChem script for a AIMD follow-up with reduced basis set size
#
# AWH/RM 2015
import pyQChem as qc
# First, read all N geometries from aimd outputfile
a = qc.read('aimd_small.out')
aa = a.list_of_jobs[1]
# Second, create the template
myrem = qc.rem_array()
myrem.jobtype('sp')
myrem.exchange('hf')
myrem.basis('sto-3g')
myrem.scf_algorithm('rca_diis')
#myrem.max_rca_cycles('10')
#myrem.thresh_rca_switch('7')
myrem.scf_guess('sad')
myrem.scf_convergence('9')
myrem.thresh('14')
myrem.incfock('0')
myrem.incdft('0')
#myrem.max_scf_cycles('500')
#myrem.symmetry('false')
#myrem.sym_ignore('true')
myrem.mem_total('16000')
myrem.mem_static('4000')
# Add rem_array
myfile = qc.inputfile()
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)
#
# This makes a simple list of jobs from xyz files and runs Q-Chem on all the jobs
#
# MBG (2/2014)
#
import pyQChem as qc
import os
#make a generic rem array
rem=qc.rem_array()
rem.basis("sto-3g")
rem.exchange("hf")
#make a list of jobs
job_list=[]
#for all xyzs in a database, create and append the job to the list
for i in os.popen("ls ../../databases/a24/*.xyz").read().splitlines():
#make the jobs
job=qc.inputfile()
#give job a name
job.runinfo.name=i.split('/')[-1].replace(".xyz","")
#read the xyz
xyz=qc.read(i)
#append the molecule and rem array
job.add(qc.mol_array(xyz))
job.add(rem)
O 2.271787 -1.668771 -2.587410
H 1.328156 -1.800266 -2.490761
H 2.384794 -1.339543 -3.467573
O -0.518887 -1.685783 -2.053795
H -0.969013 -2.442055 -1.705471
H -0.524180 -1.044938 -1.342263
"""
xf=open("4water.xyz",'w')
xf.write(xyz)
xf.close()
import pyQChem as pq
#make the rem array
rem1=pq.rem_array()
rem1.basis("6-31++G**")
rem1.exchange("hf")
rem1.thresh("14")
rem1.scf_convergence("10")
from copy import deepcopy
rem2=deepcopy(rem1)
rem2.scf_guess("fragmo")
#make a rem_frgm array
rem_frgm=pq.rem_frgm_array()
rem_frgm.thresh("7")
rem_frgm.scf_convergence("3")
#make objects for holding the molecular geometries
xyz=pq.read("4water.xyz")