def psi4_esp(method, basis, molecule):
""" Computes QM electrostatic potential
Parameters
----------
method : str
QM method
basis : str
basis set
molecule : psi4.Molecule instance
Returns
-------
np.array
QM electrostatic potential.
Note
-----
Psi4 read grid information from grid.dat file
"""
import psi4
mol = psi4.geometry(molecule.create_psi4_string_from_molecule())
psi4.set_options({'basis': basis})
e, wfn = psi4.prop(method, properties=['GRID_ESP'], return_wfn=True)
psi4.core.clean()
return np.loadtxt('grid_esp.dat')
def compute_energy_and_charges(self, charge_method='MULLIKEN_CHARGES'):
"""
Calls Psi4 to obtain the self.energy, self.wavefunction,
and self.charges on each atom. This method for correlated methods.
Note
----
Think about passing in wavefunction instead of calling for energy and wavefunction
"""
self.set_up_psi4()
self.energy, self.wavefunction = psi4.prop(self.method,
properties=[charge_method],
return_wfn=True)
self.charges = np.asarray(self.wavefunction.atomic_point_charges())
def get_elpot(xs,ys,zs,Dnew=None,wfn=None,update=False):
if (update):
Dreal = Dnew.real
wfn.oeprop.set_Da_ao(psi4.core.Matrix.from_array(Dreal))
wfn.oeprop.compute()
Vvals = wfn.oeprop.Vvals()
else:
with open('grid.dat', 'w') as fout:
for i in range(xs.np.shape[0]):
fout.write("{: 21.18e} {: 21.18e} {: 21.18e}\n".format(xs.np[i], ys.np[i], zs.np[i]))
fout.close()
ene,wfn = psi4.prop('blyp', properties=['GRID_ESP'], return_wfn=True)
#ene,wfn = psi4.energy('blyp',return_wfn=True)
Vvals = wfn.oeprop.Vvals()
return Vvals, wfn
def CALC_ESP_PSI4(dir, params):
os.chdir(dir)
psi4.core.be_quiet()
properties_origin = ["COM"]
#psi4.core.set_output_file(dir, False)
ang_au = CONSTANTS.angstrom_to_au
xS = 0.0 * ang_au
yS = 0.0 * ang_au
zS = 0.0 * ang_au
xH1 = 0.0 * ang_au
yH1 = 0.1 * ang_au
zH1 = 1.2 * ang_au
xH2 = 0.1 * ang_au
yH2 = 1.4 * ang_au
zH2 = -0.1 * ang_au
mol = psi4.geometry("""
1 2
noreorient
units au
S {0} {1} {2}
H1 {3} {4} {5}
H2 {6} {7} {8}
""".format(xS, yS, zS, xH1, yH1, zH1, xH2, yH2, zH2))
psi4.set_options({
'basis': params['scf_basis'],
'e_convergence': params['scf_enr_conv'],
'reference': params['scf_method']
})
E, wfn = psi4.prop('scf', properties=["GRID_ESP"], return_wfn=True)
Vvals = wfn.oeprop.Vvals()
os.chdir("../")
return Vvals
def CALC_ESP_PSI4_ROT(dir, params, mol_xyz):
os.chdir(dir)
psi4.core.be_quiet()
properties_origin = [
"COM"
] #[“NUCLEAR_CHARGE”] or ["COM"] #here might be the shift!
ang_au = CONSTANTS.angstrom_to_au
if params['molec_name'] == "d2s":
mol = psi4.geometry("""
1 2
noreorient
units au
nocom
S {0} {1} {2}
H {3} {4} {5}
H {6} {7} {8}
""".format(
mol_xyz[0, 0],
mol_xyz[1, 0],
mol_xyz[2, 0],
mol_xyz[0, 1],
mol_xyz[1, 1],
mol_xyz[2, 1],
mol_xyz[0, 2],
mol_xyz[1, 2],
mol_xyz[2, 2],
))
if params['molec_name'] == "cmethane":
mol = psi4.geometry("""
1 2
units au
C
H 1 CH1
H 1 CH2 2 HCH
H 1 CH3 2 HCH 3 120.0
H 1 CH4 2 HCH 3 240.0
CH1 = {0}
CH2 = {1}
CH3 = {2}
CH4 = {3}
HCH = 109.471209
""".format(params['mol_geometry']['r1'], params['mol_geometry']['r2'],
params['mol_geometry']['r3'], params['mol_geometry']['r4']))
elif params['molec_name'] == "n2":
mol = psi4.geometry("""
1 2
noreorient
units au
nocom
N {0} {1} {2}
N {3} {4} {5}
""".format(mol_xyz[0, 0], mol_xyz[1, 0], mol_xyz[2, 0], mol_xyz[0, 1],
mol_xyz[1, 1], mol_xyz[2, 1]))
elif params['molec_name'] == "co":
mol = psi4.geometry("""
1 2
noreorient
units au
nocom
C {0} {1} {2}
O {3} {4} {5}
""".format(mol_xyz[0, 0], mol_xyz[1, 0], mol_xyz[2, 0], mol_xyz[0, 1],
mol_xyz[1, 1], mol_xyz[2, 1]))
elif params['molec_name'] == "ocs":
mol = psi4.geometry("""
1 2
noreorient
units au
O {0} {1} {2}
C {3} {4} {5}
S {6} {7} {8}
""".format(
mol_xyz[0, 0],
mol_xyz[1, 0],
mol_xyz[2, 0],
mol_xyz[0, 1],
mol_xyz[1, 1],
mol_xyz[2, 1],
mol_xyz[0, 2],
mol_xyz[1, 2],
mol_xyz[2, 2],
))
elif params['molec_name'] == "h2o":
mol = psi4.geometry("""
1 2
noreorient
units au
O {0} {1} {2}
H {3} {4} {5}
H {6} {7} {8}
""".format(
0.0,
0.0,
0.0,
0.0,
1.0,
1.0,
0.0,
-2.0,
2.0,
))
elif params['molec_name'] == "h":
mol = psi4.geometry("""
1 1
noreorient
units au
nocom
H {0} {1} {2}
""".format(0.0, 0.0, 1.0))
elif params['molec_name'] == "c":
mol = psi4.geometry("""
1 2
noreorient
units au
C {0} {1} {2}
""".format(0.0, 0.0, 0.0))
psi4.set_options({
'basis': params['scf_basis'],
'e_convergence': params['scf_enr_conv'],
'reference': params['scf_method']
})
E, wfn = psi4.prop('scf', properties=["GRID_ESP"], return_wfn=True)
Vvals = wfn.oeprop.Vvals()
os.chdir("../")
return Vvals
#h2o = psi4.geometry("""
#1 2
#noreorient
#O 0.0 0.0 0.000000000000
#H 0.757 0.586 0.000000000000
#H -0.757 0.586 0.000000000000
#""")
#D2S geometry (NIST)
# r(S-D) = 1.336 ang
#angle = 92.06
"""
def resp(molecules, options_list=None, intermol_constraints=None):
"""RESP code driver.
Parameters
----------
molecules : list
list of psi4.Molecule instances
options_list : list, optional
list of dictionaries of user's defined options
intermol_constraints : dict, optional
dictionary of options for multi-molecules fitting
Returns
-------
charges : list
list of charges
Note
----
output files : mol_results.dat: fitting results
mol_grid.dat: grid points in molecule.units
mol_grid_esp.dat: QM esp valuese in a.u.
"""
if intermol_constraints is None:
intermol_constraints = {}
if options_list is None:
options_list = []
# Check options
# Large case keys: resp options
# Small case key: internal data
intermol_constraints = {
k.upper(): v
for k, v in intermol_constraints.items()
}
if 'CHARGE' not in intermol_constraints:
intermol_constraints['CHARGE'] = []
if 'EQUAL' not in intermol_constraints:
intermol_constraints['EQUAL'] = []
# Check options for first molecule
options = {k.upper(): v for k, v in sorted(options_list[0].items())}
# VDW surface options
if 'ESP' not in options:
options['ESP'] = []
if 'GRID' not in options:
options['GRID'] = []
if 'N_VDW_LAYERS' not in options:
options['N_VDW_LAYERS'] = 4
if 'VDW_SCALE_FACTOR' not in options:
options['VDW_SCALE_FACTOR'] = 1.4
if 'VDW_INCREMENT' not in options:
options['VDW_INCREMENT'] = 0.2
if 'VDW_POINT_DENSITY' not in options:
options['VDW_POINT_DENSITY'] = 1.0
# Hyperbolic restraint options
if 'WEIGHT' not in options:
options['WEIGHT'] = 1
if 'RESTRAINT' not in options:
options['RESTRAINT'] = True
if options['RESTRAINT']:
if 'RESP_A' not in options:
options['RESP_A'] = 0.0005
if 'RESP_B' not in options:
options['RESP_B'] = 0.1
if 'IHFREE' not in options:
options['IHFREE'] = True
if 'TOLER' not in options:
options['TOLER'] = 1e-5
if 'MAX_IT' not in options:
options['MAX_IT'] = 25
# QM options
if 'METHOD_ESP' not in options:
options['METHOD_ESP'] = 'scf'
if 'BASIS_ESP' not in options:
options['BASIS_ESP'] = '6-31g*'
options_list[0] = options
final_options_list = []
n_atoms = []
symbols_list = []
for imol in range(len(molecules)):
options = {k.upper(): v for k, v in options_list[imol].items()}
# VDW surface options
if 'RADIUS' not in options:
options['RADIUS'] = {}
radii = {}
for i in options['RADIUS']:
radii[i.upper()] = options['RADIUS'][i]
options['RADIUS'] = radii
# Constraint options
if 'CONSTRAINT_CHARGE' not in options:
options['CONSTRAINT_CHARGE'] = []
if 'CONSTRAINT_GROUP' not in options:
options['CONSTRAINT_GROUP'] = []
if 'CONSTRAINT_EQUAL' not in options:
options['CONSTRAINT_EQUAL'] = []
if imol > 0:
for i in final_options_list[0]:
if i not in options and i.isupper():
options[i] = final_options_list[0][i]
options['mol_charge'] = molecules[imol].molecular_charge()
n_atoms.append(molecules[imol].natom())
coordinates = molecules[imol].geometry()
coordinates = coordinates.np.astype('float') * bohr_to_angstrom
options['coordinates'] = coordinates
symbols = []
for i in range(n_atoms[-1]):
symbols.append(molecules[imol].symbol(i))
options['symbols'] = symbols
symbols_list.append(symbols)
if options['GRID']:
# Read grid points
points = np.loadtxt(options['GRID'])
np.savetxt('grid.dat', points, fmt='%15.10f')
if 'Bohr' in str(molecules[imol].units):
points *= bohr_to_angstrom
else:
# Get the points at which we're going to calculate the ESP surface
points = []
surface = vdw_surface_helper.vdw_surface_helper()
for i in range(options['N_VDW_LAYERS']):
scale_factor = options[
'VDW_SCALE_FACTOR'] + i * options['VDW_INCREMENT']
surface.vdw_surface(coordinates, symbols, scale_factor,
options['VDW_POINT_DENSITY'],
options['RADIUS'])
points.append(surface.shell)
radii = surface.radii
points = np.concatenate(points)
if 'Bohr' in str(molecules[imol].units):
points /= bohr_to_angstrom
np.savetxt('grid.dat', points, fmt='%15.10f')
points *= bohr_to_angstrom
else:
np.savetxt('grid.dat', points, fmt='%15.10f')
# Calculate ESP values at the grid
if options['ESP']:
# Read electrostatic potential values
options['esp_values'] = np.loadtxt(options['ESP'])
np.savetxt('grid_esp.dat', options['esp_values'], fmt='%15.10f')
else:
import psi4
psi4.core.set_active_molecule(molecules[imol])
psi4.set_options({'basis': options['BASIS_ESP']})
psi4.set_options(options.get('PSI4_OPTIONS', {}))
psi4.prop(options['METHOD_ESP'], properties=['GRID_ESP'])
options['esp_values'] = np.loadtxt('grid_esp.dat')
psi4.core.clean()
os.system("mv grid.dat %i_%s_grid.dat" %
(imol + 1, molecules[imol].name()))
os.system("mv grid_esp.dat %i_%s_grid_esp.dat" %
(imol + 1, molecules[imol].name()))
# Build a matrix of the inverse distance from each ESP point to each nucleus
invr = np.zeros((len(points), len(coordinates)))
for i in range(invr.shape[0]):
for j in range(invr.shape[1]):
invr[i, j] = 1 / np.linalg.norm(points[i] - coordinates[j])
options['invr'] = invr * bohr_to_angstrom # convert to atomic units
options['coordinates'] /= bohr_to_angstrom # convert to angstroms
final_options_list.append(options)
# Calculate charges
qf, labelf, notes = espfit.fit(final_options_list, intermol_constraints)
index = 0
charges = []
# Extract the charges
for imol in range(len(molecules)):
q = [i[index:index + n_atoms[imol]] for i in qf]
index += n_atoms[imol]
charges.append(q)
for imol in range(len(molecules)):
options = final_options_list[imol]
# Write the results to disk
with open(
str(imol + 1) + '_' + molecules[imol].name() + "_results.out",
"w") as f:
f.write("\n Electrostatic potential parameters\n")
f.write("\n Grid information (see %i_%s_grid.dat in %s)\n" %
(imol + 1, molecules[imol].name(),
str(molecules[imol].units).split('.')[1]))
f.write(" van der Waals radii (Angstrom):\n")
for i, j in radii.items():
f.write(" %8s%8.3f\n" %
(i, j / scale_factor))
f.write(" Number of VDW layers: %d\n" %
(options["N_VDW_LAYERS"]))
f.write(" VDW scale facotr: %.3f\n" %
(options["VDW_SCALE_FACTOR"]))
f.write(" VDW increment: %.3f\n" %
(options["VDW_INCREMENT"]))
f.write(" VDW point density: %.3f\n" %
(options["VDW_POINT_DENSITY"]))
f.write(" Number of grid points: %d\n" %
len(options['esp_values']))
f.write(
"\n Quantum electrostatic potential (see %i_%s_grid_esp.dat)\n"
% (imol + 1, molecules[imol].name()))
f.write(" ESP method: %s\n" %
options['METHOD_ESP'])
f.write(" ESP basis set: %s\n" %
options['BASIS_ESP'])
f.write("\n Constraints\n")
if options['CONSTRAINT_CHARGE']:
f.write(" Charge constraints\n")
for i in options['CONSTRAINT_CHARGE']:
f.write(" Total charge of %8.5f on the set" % i[0])
for j in i[1]:
f.write("%4d" % j)
f.write("\n")
if options['CONSTRAINT_GROUP'] or options['CONSTRAINT_EQUAL']:
f.write(" Equality constraints\n")
f.write(" Equal charges on atoms\n")
for i in options['CONSTRAINT_GROUP']:
f.write(" ")
for j in i:
f.write("%4d" % j)
f.write("\n")
for i in options['CONSTRAINT_EQUAL']:
for j in range(len(i)):
f.write(" ")
f.write("%4d%4d" % (i[0][j], i[1][j]))
f.write("\n")
if intermol_constraints['CHARGE'] or intermol_constraints['EQUAL']:
f.write('\n Intermolecular constraints\n')
if intermol_constraints['CHARGE']:
f.write(' Charge constraints\n')
for i in intermol_constraints['CHARGE']:
f.write(
' Total charge of %8.5f on the set:' %
i[0])
for j in i[1]:
f.write('\n molecule %4d, atoms' %
j[0])
for k in j[1]:
f.write('%4d' % k)
f.write('\n')
if intermol_constraints['EQUAL']:
f.write(' Equality constraints\n')
f.write(' Equal charges on\n')
for i in intermol_constraints['EQUAL']:
f.write(' ')
f.write('molecule %4d, atoms' % i[0][0])
for j in i[0][1]:
f.write('%4d' % j)
f.write('\n molecule %4d, atoms' %
i[1][0])
for j in i[1][1]:
f.write('%4d' % j)
f.write('\n\n')
f.write("\n Restraint\n")
if options['RESTRAINT']:
f.write(" Hyperbolic restraint to a charge of zero\n")
if options['IHFREE']:
f.write(" Hydrogen atoms are not restrained\n")
f.write(" resp_a: %.4f\n" %
(options["RESP_A"]))
f.write(" resp_b: %.4f\n" %
(options["RESP_B"]))
f.write("\n Fit\n")
for i in notes:
if i:
f.write(i + '\n')
f.write("\n Electrostatic Potential Charges\n")
f.write(" Center Symbol")
for i in labelf:
f.write("%10s" % i)
f.write("\n")
for i in range(n_atoms[imol]):
f.write(" %5d %s " % (i + 1, symbols_list[imol][i]))
for j in charges[imol]:
f.write("%10.5f" % j[i])
f.write("\n")
f.write(" Total Charge: ")
for i in charges[imol]:
f.write("%10.5f" % np.sum(i))
f.write('\n')
return charges
def resp(wfn, options={}):
mol = wfn.molecule()
n_atoms = mol.natom()
# Check options
check_options = {}
for i in options.keys():
check_options[i.upper()] = options[i]
options = check_options
if not ('N_VDW_LAYERS' in options.keys()):
options['N_VDW_LAYERS'] = 4
if not ('VDW_SCALE_FACTOR' in options.keys()):
options['VDW_SCALE_FACTOR'] = 1.4
if not ('VDW_INCREMENT' in options.keys()):
options['VDW_INCREMENT'] = 0.2
if not ('VDW_POINT_DENSITY' in options.keys()):
options['VDW_POINT_DENSITY'] = 1.0
if not ('RESP_A' in options.keys()):
options['RESP_A'] = 0.0005
if not ('RESP_B' in options.keys()):
options['RESP_B'] = 0.1
if not ('METHOD' in options.keys()):
options['METHOD'] = 'scf'
if not ('CHARGE_GROUPS' in options.keys()):
options['CHARGE_GROUPS'] = range(n_atoms)
if not ('TWO_STAGE_FIT' in options.keys()):
options['TWO_STAGE_FIT'] = False
if options['TWO_STAGE_FIT']:
if not ('RESP_A2' in options.keys()):
options['RESP_A2'] = 0.001
if not ('FIT2' in options.keys()):
options['FIT2'] = range(n_atoms)
if not ('CHARGE_GROUPS2' in options.keys()):
options['CHARGE_GROUPS2'] = range(n_atoms)
options['mol_charge'] = mol.molecular_charge()
# Get the coordinates of the nuclei in Angstroms
symbols = []
coordinates = np.asarray(mol.geometry())
# the vdwsurface code expects coordinates in angstroms
coordinates *= bohr_to_angstrom
for i in range(n_atoms):
symbols.append(mol.symbol(i))
# Get the points at which we're going to calculate the ESP surface
points = []
for i in range(options['N_VDW_LAYERS']):
scale_factor = options[
'VDW_SCALE_FACTOR'] + i * options['VDW_INCREMENT']
this_shell = vdw_surface(coordinates, symbols, scale_factor,
options['VDW_POINT_DENSITY'])
points.append(this_shell)
points = np.concatenate(points)
if 'Bohr' in str(mol.units):
points /= bohr_to_angstrom
np.savetxt('grid.dat', points, fmt='%.9f', delimiter='\t')
points *= bohr_to_angstrom
else:
np.savetxt('grid.dat', points, fmt='%.9f', delimiter='\t')
# Calculate ESP values at the grid
e, wfn = psi4.prop(options['METHOD'],
properties=['GRID_ESP', 'MULLIKEN_CHARGES'],
molecule=wfn.molecule(),
return_wfn=True)
options['esp_values'] = wfn.oeprop.Vvals()
options['charges'] = np.asarray(wfn.atomic_point_charges())
# Build a matrix of the inverse distance from each ESP point to each nucleus
options['invr'] = 1.0 / scipy.spatial.distance_matrix(points, coordinates)
options['invr'] *= bohr_to_angstrom
# Run the optimization using SciPy
charges = scipy.optimize.minimize(
resp_objective,
options['charges'],
args=(options),
jac=True,
method='SLSQP',
tol=1e-8,
options={'ftol': 1e-8},
constraints={
'type': 'eq',
'fun': resp_constraint,
'args': [options['mol_charge'], options['CHARGE_GROUPS'], False]
})
charges = charges.x
if options['TWO_STAGE_FIT']:
a = options['RESP_A']
options['RESP_A'] = options['RESP_A2']
options['charges'] = charges
charges2 = scipy.optimize.minimize(resp_objective,
charges[options['FIT2']],
args=(options, True),
jac=True,
method='SLSQP',
tol=1e-8,
options={'ftol': 1e-8},
constraints={
'type':
'eq',
'fun':
resp_constraint,
'args': [
options['mol_charge'],
options['CHARGE_GROUPS2'],
True, options['charges'],
options['FIT2']
]
})
charges[options['FIT2']] = charges2.x
options['RESP_A'] = a
np.savetxt('charges', charges)
# Print the parameters to disk
psi4.core.print_out(
"\n ---------------------------------------------------\n")
psi4.core.print_out(" RESTRAINED ELECTROSTATIC POTENTIAL PARAMETERS\n")
psi4.core.print_out(
" ---------------------------------------------------\n")
psi4.core.print_out(" N_VDW_LAYERS: %d\n" %
(options["N_VDW_LAYERS"]))
psi4.core.print_out(" VDW_SCALE_FACTOR: %.3f\n" %
(options["VDW_SCALE_FACTOR"]))
psi4.core.print_out(" VDW_INCREMENT: %.3f\n" %
(options["VDW_INCREMENT"]))
psi4.core.print_out(" VDW_POINT_DENSITY: %.3f\n" %
(options["VDW_POINT_DENSITY"]))
psi4.core.print_out(" RESP_A: %.4f\n" % (options["RESP_A"]))
psi4.core.print_out(" RESP_B: %.4f\n" % (options["RESP_B"]))
psi4.core.print_out(" CHARGE_GROUPS: [")
for i in options['CHARGE_GROUPS'][:-1]:
psi4.core.print_out('%d, ' % i)
psi4.core.print_out('%d]\n' % options['CHARGE_GROUPS'][-1])
psi4.core.print_out(" TWO_STAGE_FIT: %s\n" %
(options["TWO_STAGE_FIT"]))
if options["TWO_STAGE_FIT"]:
psi4.core.print_out(" RESP_A2: %.4f\n" %
(options["RESP_A2"]))
psi4.core.print_out(" FIT2: [")
for i in options["FIT2"][:-1]:
psi4.core.print_out('%d, ' % i)
psi4.core.print_out('%d]\n' % options["FIT2"][-1])
psi4.core.print_out(" CHARGE_GROUPS2: [")
for i in options['CHARGE_GROUPS2'][:-1]:
psi4.core.print_out('%d, ' % i)
psi4.core.print_out('%d]\n' % options['CHARGE_GROUPS2'][-1])
psi4.core.print_out(" METHOD: %s\n" % (options["METHOD"]))
psi4.core.print_out(
" ---------------------------------------------------\n")
# Print the results to disk
psi4.core.print_out("\n ----------------------------------------------\n")
psi4.core.print_out(" RESTRAINED ELECTROSTATIC POTENTIAL CHARGES\n")
psi4.core.print_out(" Center Symbol RESP Charge (a.u.)\n")
psi4.core.print_out(" ----------------------------------------------\n")
for i in range(len(charges)):
psi4.core.print_out(" %5d %s %8.5f\n" %
(i, symbols[i], charges[i]))
def resp(molecules, options=None):
"""RESP code driver.
Parameters
----------
molecules : list
list of psi4.Molecule instances
options_list : dict, optional
a dictionary of user's defined options
Returns
-------
charges : list
list of charges
Note
----
output files : mol_results.dat: fitting results
mol_grid.dat: grid points in molecule.units
mol_grid_esp.dat: QM esp valuese in a.u.
"""
if options is None:
options = {}
# Check options
# RESP options have large case keys
options = {k.upper(): v for k, v in sorted(options.items())}
# VDW surface options
if 'ESP' not in options:
options['ESP'] = []
if 'GRID' not in options:
options['GRID'] = []
if 'VDW_SCALE_FACTORS' not in options:
options['VDW_SCALE_FACTORS'] = [1.4, 1.6, 1.8, 2.0]
if 'VDW_POINT_DENSITY' not in options:
options['VDW_POINT_DENSITY'] = 1.0
# Hyperbolic restraint options
if 'WEIGHT' not in options:
options['WEIGHT'] = [1] * len(molecules)
if 'RESTRAINT' not in options:
options['RESTRAINT'] = True
if options['RESTRAINT']:
if 'RESP_A' not in options:
options['RESP_A'] = 0.0005
if 'RESP_B' not in options:
options['RESP_B'] = 0.1
if 'IHFREE' not in options:
options['IHFREE'] = True
if 'TOLER' not in options:
options['TOLER'] = 1e-5
if 'MAX_IT' not in options:
options['MAX_IT'] = 25
# QM options
if 'METHOD_ESP' not in options:
options['METHOD_ESP'] = 'scf'
if 'BASIS_ESP' not in options:
options['BASIS_ESP'] = '6-31g*'
# VDW surface options
if 'VDW_RADII' not in options:
options['VDW_RADII'] = {}
radii = {}
for i in options['VDW_RADII']:
radii[i.upper()] = options['VDW_RADII'][i]
options['VDW_RADII'] = radii
# Constraint options
if 'CONSTRAINT_CHARGE' not in options:
options['CONSTRAINT_CHARGE'] = []
if 'CONSTRAINT_GROUP' not in options:
options['CONSTRAINT_GROUP'] = []
data = {}
# Same data for all conformer
data['natoms'] = molecules[0].natom()
data['symbols'] = []
for i in range(data['natoms']):
data['symbols'].append(molecules[0].symbol(i))
data['mol_charge'] = molecules[0].molecular_charge()
# Data for each conformer
data['coordinates'] = []
data['esp_values'] = []
data['invr'] = []
for imol in range(len(molecules)):
coordinates = molecules[imol].geometry()
coordinates = coordinates.np.astype('float') * bohr_to_angstrom
data['coordinates'].append(coordinates)
if options['GRID']:
# Read grid points
points = np.loadtxt(options['GRID'][imol])
np.savetxt('grid.dat', points, fmt='%15.10f')
if 'Bohr' in str(molecules[imol].units()):
points *= bohr_to_angstrom
else:
# Get the points at which we're going to calculate the ESP
points = []
for scale_factor in options['VDW_SCALE_FACTORS']:
shell, radii = vdw_surface.vdw_surface(
coordinates, data['symbols'], scale_factor,
options['VDW_POINT_DENSITY'], options['VDW_RADII'])
points.append(shell)
points = np.concatenate(points)
if 'Bohr' in str(molecules[imol].units()):
points /= bohr_to_angstrom
np.savetxt('grid.dat', points, fmt='%15.10f')
points *= bohr_to_angstrom
else:
np.savetxt('grid.dat', points, fmt='%15.10f')
# Calculate ESP values at the grid
if options['ESP']:
# Read electrostatic potential values
data['esp_values'].append(np.loadtxt(options['ESP'][imol]))
np.savetxt('grid_esp.dat', data['esp_values'][-1], fmt='%15.10f')
else:
import psi4
psi4.core.set_active_molecule(molecules[imol])
psi4.set_options({'basis': options['BASIS_ESP']})
psi4.set_options(options.get('PSI4_OPTIONS', {}))
psi4.prop(options['METHOD_ESP'], properties=['GRID_ESP'])
data['esp_values'].append(np.loadtxt('grid_esp.dat'))
psi4.core.clean()
os.system("mv grid.dat %i_%s_grid.dat" %
(imol + 1, molecules[imol].name()))
os.system("mv grid_esp.dat %i_%s_grid_esp.dat" %
(imol + 1, molecules[imol].name()))
# Build a matrix of the inverse distance from each ESP point to each nucleus
invr = np.zeros((len(points), len(coordinates)))
for i in range(invr.shape[0]):
for j in range(invr.shape[1]):
invr[i, j] = 1 / np.linalg.norm(points[i] - coordinates[j])
data['invr'].append(invr * bohr_to_angstrom) # convert to atomic units
data['coordinates'][-1] /= bohr_to_angstrom # convert to angstroms
# Calculate charges
qf, labelf, notes = espfit.fit(options, data)
# Write the results to disk
with open("results.out", "w") as f:
f.write("Electrostatic potential parameters\n")
if not options['GRID']:
f.write(" van der Waals radii (Angstrom):\n")
for i, j in radii.items():
f.write(" %8s%8.3f\n" %
(i, j / scale_factor))
f.write(" VDW scale factors: ")
for i in options["VDW_SCALE_FACTORS"]:
f.write('%6.2f' % i)
f.write('\n')
f.write(" VDW point density: %.3f\n" %
(options["VDW_POINT_DENSITY"]))
if not options['ESP']:
f.write(" ESP method: %s\n" %
options['METHOD_ESP'])
f.write(" ESP basis set: %s\n" %
options['BASIS_ESP'])
for imol in range(len(molecules)):
f.write(
"\nGrid information (see %i_%s_grid.dat in %s)\n" %
(imol + 1, molecules[imol].name(), molecules[imol].units()))
f.write(" Number of grid points: %d\n" %
len(data['esp_values'][imol]))
f.write(
"\nQuantum electrostatic potential (see %i_%s_grid_esp.dat)\n"
% (imol + 1, molecules[imol].name()))
f.write("\nConstraints\n")
if options['CONSTRAINT_CHARGE']:
f.write(" Charge constraints\n")
for i in options['CONSTRAINT_CHARGE']:
f.write(" Total charge of %12.8f on the set" % i[0])
for j in i[1]:
f.write("%4d" % j)
f.write("\n")
if options['CONSTRAINT_GROUP']:
f.write(" Equality constraints\n")
f.write(" Equal charges on atoms\n")
for i in options['CONSTRAINT_GROUP']:
f.write(" ")
for j in i:
f.write("%4d" % j)
f.write("\n")
f.write("\nRestraint\n")
if options['RESTRAINT']:
f.write(" Hyperbolic restraint to a charge of zero\n")
if options['IHFREE']:
f.write(" Hydrogen atoms are not restrained\n")
f.write(" resp_a: %.4f\n" %
(options["RESP_A"]))
f.write(" resp_b: %.4f\n" %
(options["RESP_B"]))
f.write("\nFit\n")
f.write(notes)
f.write("\nElectrostatic Potential Charges\n")
f.write(" Center Symbol")
for i in labelf:
f.write("%10s" % i)
f.write("\n")
for i in range(data['natoms']):
f.write(" %5d %s " % (i + 1, data['symbols'][i]))
for j in qf:
f.write("%12.8f" % j[i])
f.write("\n")
f.write("Total Charge: ")
for i in qf:
f.write("%12.8f" % np.sum(i))
f.write('\n')
return qf
