geomopt — Geometry optimization

The geomopt module implements geometry optimization via interfaces to geomeTRIC and PyBerny. The following example shows how to optimize the structure of the N₂ molecule with PyBerny:

from pyscf import gto, scf
from pyscf.geomopt.berny_solver import optimize
mol = gto.M(atom='N 0 0 0; N 0 0 1.2', basis='ccpvdz')
mf = scf.RHF(mol)
mol_eq = optimize(mf)
print(mol_eq.tostring())

Examples

• examples/geomopt/01-geomeTRIC.py

• examples/geomopt/01-pyberny.py

• examples/geomopt/02-as_pyscf_method.py

• examples/geomopt/10-with_qmmm.py

• examples/geomopt/11-with_ghost_atom.py

• examples/geomopt/12-excited_states.py

• examples/geomopt/12-mcscf_excited_states.py

• examples/geomopt/13-ccsd_t.py

• examples/geomopt/14-with_solvent.py

• examples/geomopt/15-tddft_with_solvent.py

• examples/geomopt/20-callback.py

Program reference

Helper functions for geometry optimizer

pyscf.geomopt.addons.as_pyscf_method(mol, scan_function)

Creat an wrapper for the given scan_function, to make it work as a pyscf gradients scanner. The wrapper can be passed to optimize().

Args:

scan_function : [mol] => (e_tot, grad)

Examples:: >>> mol = gto.M(atom=’H; H 1 1.2’, basis=’ccpvdz’) >>> scan_fn = scf.RHF(mol).nuc_grad_method().as_scanner() >>> m = as_pyscf_method(mol, scan_fn) >>> pyscf.geomopt.berny_solver.kernel(m)

pyscf.geomopt.addons.dump_mol_geometry(mol, new_coords, log=None)

Dump the molecular geometry (new_coords) and the displacement wrt old geometry.

Args:

new_coords (ndarray) : Cartesian coordinates in Angstrom

pyscf.geomopt.addons.symmetrize(mol, coords)

Symmetrize the structure of a molecule.