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)
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)
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)
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")
O2_indices = self.O2coord()
#print("O2 indices:", O2_indices)
self.cdft_arr.add_line("1 %s %s s" %
(O2_indices[0] + 1, O2_indices[1] + 1))
# error if O2coord() returns None
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]]
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)