def run_scf_qmmm_solvent(mol, fname_pqr, solvent_radii, solvent_lebedev_order):
from pyscf import scf, qmmm # , solvent
import ddcosmo_qmmm
"""
There is one key difference between pyscf.solvent.ddcosmo and ddcosmo_qmmm.
The former (pyscf) generates the grid points of both QM and MM regions,
which are used to estimate the electronic density.
'ddcosmo_qmmm' does not generate the grid points in the MM region.
"""
mm_atm_list, mm_xyz_list, mm_q_list = parmed_load_pqr(fname_pqr)
mm_mol = qmmm.create_mm_mol(mm_atm_list, mm_q_list, unit='Bohr')
qmmm_sol = ddcosmo_qmmm.DDCOSMO(mol, mm_mol)
#wat_radius = 1.4*ang2bohr
#qmmm_sol.radii_table = radii.VDW + wat_radius
qmmm_sol.radii_table = solvent_radii
qmmm_sol.lebedev_order = solvent_lebedev_order
# ddCOSMO-QMMM-SCF
mf = mol.RHF()
mf = mf.QMMM(mm_xyz_list, mm_q_list)
mf = ddcosmo_qmmm.ddcosmo_for_scf(mf, qmmm_sol) # mf.DDCOSMO(qmmm_sol)
mf.run(verbose=0)
#print('DONE RHF/MM/SOLVENT', mf.e_tot)
return mf
def _pyscf_qmmm(qm_atnm,
qm_crds,
qm_basis,
qm_chg_tot,
mm_crds,
mm_q_list,
l_esp=False,
esp_opts={}):
atm_list = []
for ia, xyz in enumerate(qm_crds):
sym = qm_atnm[ia] # .split(':')[0]
atm_list.append([sym, (xyz[0], xyz[1], xyz[2])])
#print(ia, sym, xyz)
#print('qm_chg_tot', qm_chg_tot)
qm_mol = _pyscf_mol_build(atm_list, qm_basis, qm_chg_tot)
mm_mol = qmmm.create_mm_mol(mm_crds, mm_q_list, unit='Bohr')
mf = qmmm.qmmm_for_scf(scf.RHF(qm_mol), mm_mol)
mf.run()
ener_QMMM = mf.e_tot
grds_QM = mf.Gradients().kernel()
qm_dm = mf.make_rdm1()
grds_MM = _pyscf_mm_gradients(qm_mol, qm_dm, mm_mol)
esp_chg = None
if l_esp:
esp_chg = esp_atomic_charges(qm_mol, qm_dm, esp_opts)
return ener_QMMM, grds_QM, grds_MM, esp_chg
# load all modeuls
from pyscf import __all__
mol = gto.M(atom='''
C 0.000000 0.000000 -0.542500
O 0.000000 0.000000 0.677500
H 0.000000 0.9353074360871938 -1.082500
H 0.000000 -0.9353074360871938 -1.082500
''',
verbose=4)
numpy.random.seed(1)
coords = numpy.random.random((5, 3)) * 10
charges = (numpy.arange(5) + 1.) * .1
mm_atoms = [('C', c) for c in coords]
mm_mol = qmmm.create_mm_mol(mm_atoms, charges)
# Make a giant system include both QM and MM particles
qmmm_mol = mol + mm_mol
# The solvent model is based on the giant system
sol = solvent.DDCOSMO(qmmm_mol)
# According to Lipparini's suggestion in issue #446
sol.radii_table = radii.VDW
#
# The order to apply solvent model and QM/MM charges does not affect results
#
# ddCOSMO-QMMM-SCF
#