def __init__(self,
infile,
charge,
mult,
joblist,
method='tpssh',
nametrunc=True,
basis='6-31+g*'):
self.charge_tran = {
'a2': '-2',
'a1': '-1',
'a0': '0',
'c1': '1',
'c2': '2',
'c3': '3',
'c4': '4'
}
revd = dict([reversed(i) for i in self.charge_tran.items()])
self.charge_tran.update(revd)
splinfile = infile.split('/')
if len(splinfile) == 1:
self.path = ''
else:
self.path = '/'.join(splinfile[:-1]) + '/'
self.name = (splinfile[-1].split('.'))[0]
if nametrunc == True:
self.name = self.name.split('_')[0]
self.infile = infile
self.charge = charge
self.mult = mult
print(self.charge, self.mult)
self.joblist = joblist #joblist is a list of Q-Chem jobtypes
self.method = method
self.jobconcat = ''.join(joblist)
self.job = qc.multifile()
self.nametrunc = nametrunc
self.basis = basis
#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")
frag=pq.fragment(atom_list=xyz.list_of_atoms)
#make molecule array from cartesian object
mol1=pq.mol_array(xyz)
mol2=pq.mol_array(frag)
#make input object and write to disk
job1=pq.inputfile()
job1.add(rem1)
job1.add(mol1)
job2=pq.inputfile()
job2.add(rem2)
job2.rem.scf_guess("fragmo")
job2.add(rem_frgm)
job2.add(mol2)
job=pq.multifile()
job.add(job1)
job.add(job2)
job.write("4water.in")
#make molecule array from cartesian object
molec=qc.mol_array(xyz)
#assemble the job from the arrays
job1=qc.inputfile()
job1.add(rem)
job1.add(molec)
#write it to file
job1.write("h2.in")
#make another rem to do the second job
rem2=qc.deepcopy(rem)
rem2.jobtype("freq")
#define the molecule array as "READ" so we grab the right geometry
molec2=qc.mol_array()
molec2.geometry("read")
#assemble the second job
job2=qc.inputfile()
job2.add(rem2)
job2.add(molec2)
#make the multifile input and save it
job=qc.multifile()
job.add(job1)
job.add(job2)
job.write("h2_opt.in")