psi4.core.Molecule¶

class psi4.core.Molecule¶

Bases: object

Class to store the elements, coordinates, fragmentation pattern, basis sets, charge, multiplicity, etc. of a molecule.

Attributes Summary

units Units (Angstrom or Bohr) used to define the geometry

Methods Summary

`BFS`()	Perform a breadth-first search (BFS) on the real atoms in molecule, returning an array of atom indices of fragments.
`Z`((self: psi4.core.Molecule, arg0: int) -> float)	Nuclear charge of atom arg1 (0-indexed)
`activate_all_fragments`(...)	Sets all fragments in the molecule to be active
`add_atom`((self: psi4.core.Molecule, ...)	Adds to Molecule arg0 an atom with atomic number arg1, Cartesian coordinates in Bohr (arg2, arg3, arg4), atomic symbol arg5, mass arg6, charge arg7 (optional), and lineno arg8 (optional)
`atom_at_position`((self: psi4.core.Molecule, ...)	Tests to see if an atom is at the position arg2 with a given tolerance arg3
`center_of_mass`(...)	Computes center of mass of molecule (does not translate molecule)
`charge`((self: psi4.core.Molecule, ...)	Gets charge of atom arg1 (0-indexed)
`clone`(...)	Returns a new Molecule identical to arg0
`create_molecule_from_string`(...)	Returns a new Molecule with member data from the geometry string arg0 in Psi4 format
`create_psi4_string_from_molecule`(...)	Gets a string reexpressing in input format the current states of the molecule
`deactivate_all_fragments`(...)	Sets all fragments in the molecule to be inactive
`distance_matrix`(...)	Returns Matrix of interatom distances
`extract_subsets`(args, *kwargs)	Overloaded function.
`fZ`((self: psi4.core.Molecule, ...)	Nuclear charge of atom arg1 (0-indexed including dummies)
`fcharge`((self: psi4.core.Molecule, ...)	Gets charge of atom arg1 (0-indexed including dummies)
`find_point_group`((self: psi4.core.Molecule, ...)	Finds computational molecular point group, user can override this with the symmetry keyword
`fix_com`((self: psi4.core.Molecule, ...)	Whether to fix the Cartesian position, or to translate to the C.O.M.
`fix_orientation`((self: psi4.core.Molecule, ...)	Fix the orientation at its current frame
`flabel`((self: psi4.core.Molecule, ...)	Gets the original label of the atom arg1 as given in the input file (C2, H4) (0-indexed including dummies)
`fmass`((self: psi4.core.Molecule, ...)	Gets mass of atom arg1 (0-indexed including dummies)
`form_symmetry_information`(...)	Uses the point group object obtain by calling point_group()
`fsymbol`((self: psi4.core.Molecule, ...)	Gets the cleaned up label of atom arg1 (C2 => C, H4 = H) (0-indexed including dummies)
`fx`((self: psi4.core.Molecule, ...)	x position of atom arg1 (0-indexed including dummies in Bohr)
`fy`((self: psi4.core.Molecule, ...)	y position of atom arg1 (0-indexed including dummies in Bohr)
`fz`((self: psi4.core.Molecule, ...)	z position of atom arg1 (0-indexed including dummies in Bohr)
`geometry`(...)	Gets the geometry as a (Natom X 3) matrix of coordinates (in Bohr)
`get_full_point_group`(...)	Gets point group name such as C3v or S8
`get_variable`((self: psi4.core.Molecule, ...)	Checks if variable arg2 is in the list, sets it to val and returns true if it is, and returns false if not
`irrep_labels`(...)
`is_variable`((self: psi4.core.Molecule, ...)	Checks if variable arg2 is in the list, returns true if it is, and returns false if not
`label`((self: psi4.core.Molecule, ...)	Gets the original label of the atom arg1 as given in the input file (C2, H4) (0-indexed)
`mass`((self: psi4.core.Molecule, ...)	Gets mass of atom arg1 (0-indexed)
`molecular_charge`(...)	Gets the charge on full molecule
`move_to_com`((self: psi4.core.Molecule) -> None)	Moves molecule to center of mass
`multiplicity`((self: psi4.core.Molecule) -> int)	Gets the multiplicity (defined as $2M_s + 1$) of full molecule
`nactive_fragments`(...)	Gets the number of active (non-ghosted) fragments in the molecule
`nallatom`((self: psi4.core.Molecule) -> int)	Number of real and dummy atoms
`name`((self: psi4.core.Molecule) -> str)	Gets molecule name
`natom`((self: psi4.core.Molecule) -> int)	Number of real atoms
`nfragments`((self: psi4.core.Molecule) -> int)	Gets the number of fragments in the molecule
`nuclear_dipole`(args, *kwargs)	Overloaded function.
`nuclear_repulsion_energy`(...)	Computes nuclear repulsion energy
`point_group`(...)	Returns the current point group object
`print_bond_angles`(...)	Print the bond angle geometrical parameters
`print_cluster`((self: psi4.core.Molecule) -> None)	Prints the molecule in Cartesians in input units adding fragment separators
`print_distances`(...)	Print the interatomic distance geometrical parameters
`print_in_input_format`(...)	Prints the molecule as Cartesian or ZMatrix entries, just as inputted.
`print_out`((self: psi4.core.Molecule) -> None)	Prints the molecule in Cartesians in input units
`print_out_in_angstrom`(...)	Prints the molecule in Cartesians in Angstroms
`print_out_in_bohr`(...)	Prints the molecule in Cartesians in Bohr
`print_out_of_planes`(...)	Print the out-of-plane angle geometrical parameters
`reinterpret_coordentry`(...)	Do reinterpret coordinate entries during update_geometry().
`reset_point_group`((self: psi4.core.Molecule, ...)	Overrides symmetry from outside the molecule string
`rotational_constants`(...)	Prints the rotational constants of the molecule
`run_dftd3`([func, dashlvl, dashparam, ...])	Function to call Grimme’s dftd3 program (http://toc.uni-muenster.de/DFTD3/) to compute the -D correction of level dashlvl using parameters for the functional func.
`run_gcp`([func, dertype, verbose])	Function to call Grimme’s dftd3 program (http://toc.uni-muenster.de/DFTD3/) to compute the -D correction of level dashlvl using parameters for the functional func.
`save_string_xyz`(...)	Saves the string of an XYZ file to arg2
`save_string_xyz_file`(...)	Saves an XYZ file to arg2
`save_xyz_file`((self: psi4.core.Molecule, ...)	Saves an XYZ file to arg2
`schoenflies_symbol`(...)	Returns the Schoenflies symbol
`set_active_fragment`(...)	Sets the specified fragment arg2 to be Real
`set_active_fragments`(...)	Sets the specified list arg2 of fragments to be Real
`set_basis_all_atoms`(...)	Sets basis set arg2 to all atoms
`set_basis_by_label`(...)	Sets basis set arg3 to all atoms with label (e.g., H4) arg2
`set_basis_by_symbol`(...)	Sets basis set arg3 to all atoms with symbol (e.g., H) arg2
`set_geometry`((self: psi4.core.Molecule, ...)	Sets the geometry, given a (Natom X 3) matrix arg2 of coordinates (in Bohr)
`set_ghost_fragment`(...)	Sets the specified fragment arg2 to be Ghost
`set_ghost_fragments`(...)	Sets the specified list arg2 of fragments to be Ghost
`set_mass`((self: psi4.core.Molecule, ...)	Gets mass of atom arg1
`set_molecular_charge`(...)	Sets the molecular charge
`set_multiplicity`((self: psi4.core.Molecule, ...)	Sets the multiplicity (defined as 2Ms + 1)
`set_name`((self: psi4.core.Molecule, ...)	Sets molecule name
`set_point_group`((self: psi4.core.Molecule, ...)	Sets the molecular point group to the point group object arg2
`set_variable`((self: psi4.core.Molecule, ...)	Assigns the value arg3 to the variable arg2 in the list of geometry variables, then calls update_geometry()
`symbol`((self: psi4.core.Molecule, ...)	Gets the cleaned up label of atom arg1 (C2 => C, H4 = H) (0-indexed)
`symmetrize`((self: psi4.core.Molecule, ...)	Finds the highest point Abelian point group within the specified tolerance, and forces the geometry to have that symmetry.
`translate`((self: psi4.core.Molecule, ...)	Translates molecule by arg1
`update_geometry`(...)	Reevaluates the geometry with current variable values, orientation directives, etc.
`x`((self: psi4.core.Molecule, arg0: int) -> float)	x position of atom arg1 (0-indexed in Bohr)
`y`((self: psi4.core.Molecule, arg0: int) -> float)	y position of atom arg1 (0-indexed in Bohr)
`z`((self: psi4.core.Molecule, arg0: int) -> float)	z position of atom arg1 (0-indexed in Bohr)

Attributes Documentation

units¶: Units (Angstrom or Bohr) used to define the geometry

Methods Documentation

BFS()¶: Perform a breadth-first search (BFS) on the real atoms in molecule, returning an array of atom indices of fragments. Relies upon van der Waals radii and so faulty for close (esp. hydrogen-bonded) fragments. Original code from Michael S. Marshall.

Z(self: psi4.core.Molecule, arg0: int) → float¶: Nuclear charge of atom arg1 (0-indexed)

activate_all_fragments(self: psi4.core.Molecule) → None¶: Sets all fragments in the molecule to be active

add_atom(self: psi4.core.Molecule, arg0: int, arg1: float, arg2: float, arg3: float, arg4: str, arg5: float, arg6: float, arg7: int) → None¶: Adds to Molecule arg0 an atom with atomic number arg1, Cartesian coordinates in Bohr (arg2, arg3, arg4), atomic symbol arg5, mass arg6, charge arg7 (optional), and lineno arg8 (optional)

atom_at_position(self: psi4.core.Molecule, arg0: float, arg1: float) → int¶: Tests to see if an atom is at the position arg2 with a given tolerance arg3

center_of_mass(self: psi4.core.Molecule) → psi4.core.Vector3¶: Computes center of mass of molecule (does not translate molecule)

charge(self: psi4.core.Molecule, arg0: int) → float¶: Gets charge of atom arg1 (0-indexed)

clone(self: psi4.core.Molecule) → psi4.core.Molecule¶: Returns a new Molecule identical to arg0

create_molecule_from_string(arg0: str) → psi4.core.Molecule¶: Returns a new Molecule with member data from the geometry string arg0 in Psi4 format

create_psi4_string_from_molecule(self: psi4.core.Molecule) → str¶: Gets a string reexpressing in input format the current states of the molecule

deactivate_all_fragments(self: psi4.core.Molecule) → None¶: Sets all fragments in the molecule to be inactive

distance_matrix(self: psi4.core.Molecule) → psi4.core.Matrix¶: Returns Matrix of interatom distances

extract_subsets(*args, **kwargs)¶

Overloaded function.

extract_subsets(self: psi4.core.Molecule, arg0: list, arg1: list) -> psi4.core.Molecule

Returns copy of arg1 with arg2 fragments Real and arg3 fragments Ghost

extract_subsets(self: psi4.core.Molecule, arg0: list, arg1: int) -> psi4.core.Molecule

Returns copy of arg1 with arg2 fragments Real and arg3 fragment Ghost

extract_subsets(self: psi4.core.Molecule, arg0: int, arg1: list) -> psi4.core.Molecule

Returns copy of arg1 with arg2 fragment Real and arg3 fragments Ghost

extract_subsets(self: psi4.core.Molecule, arg0: int, arg1: int) -> psi4.core.Molecule

Returns copy of arg1 with arg2 fragment Real and arg3 fragment Ghost

extract_subsets(self: psi4.core.Molecule, arg0: list) -> psi4.core.Molecule

Returns copy of arg1 with arg2 fragments Real

extract_subsets(self: psi4.core.Molecule, arg0: int) -> psi4.core.Molecule

Returns copy of arg1 with arg2 fragment Real

fZ(self: psi4.core.Molecule, arg0: int) → float¶: Nuclear charge of atom arg1 (0-indexed including dummies)

fcharge(self: psi4.core.Molecule, arg0: int) → float¶: Gets charge of atom arg1 (0-indexed including dummies)

find_point_group(self: psi4.core.Molecule, arg0: float) → psi4.core.PointGroup¶: Finds computational molecular point group, user can override this with the symmetry keyword

fix_com(self: psi4.core.Molecule, arg0: bool) → None¶: Whether to fix the Cartesian position, or to translate to the C.O.M.

fix_orientation(self: psi4.core.Molecule, arg0: bool) → None¶: Fix the orientation at its current frame

flabel(self: psi4.core.Molecule, arg0: int) → str¶: Gets the original label of the atom arg1 as given in the input file (C2, H4) (0-indexed including dummies)

fmass(self: psi4.core.Molecule, arg0: int) → float¶: Gets mass of atom arg1 (0-indexed including dummies)

form_symmetry_information(self: psi4.core.Molecule, arg0: float) → None¶: Uses the point group object obtain by calling point_group()

fsymbol(self: psi4.core.Molecule, arg0: int) → str¶: Gets the cleaned up label of atom arg1 (C2 => C, H4 = H) (0-indexed including dummies)

fx(self: psi4.core.Molecule, arg0: int) → float¶: x position of atom arg1 (0-indexed including dummies in Bohr)

fy(self: psi4.core.Molecule, arg0: int) → float¶: y position of atom arg1 (0-indexed including dummies in Bohr)

fz(self: psi4.core.Molecule, arg0: int) → float¶: z position of atom arg1 (0-indexed including dummies in Bohr)

geometry(self: psi4.core.Molecule) → psi4.core.Matrix¶: Gets the geometry as a (Natom X 3) matrix of coordinates (in Bohr)

get_full_point_group(self: psi4.core.Molecule) → str¶: Gets point group name such as C3v or S8

get_variable(self: psi4.core.Molecule, arg0: str) → float¶: Checks if variable arg2 is in the list, sets it to val and returns true if it is, and returns false if not

irrep_labels(self: psi4.core.Molecule) → List[str]¶

is_variable(self: psi4.core.Molecule, arg0: str) → bool¶: Checks if variable arg2 is in the list, returns true if it is, and returns false if not

label(self: psi4.core.Molecule, arg0: int) → str¶: Gets the original label of the atom arg1 as given in the input file (C2, H4) (0-indexed)

mass(self: psi4.core.Molecule, arg0: int) → float¶: Gets mass of atom arg1 (0-indexed)

molecular_charge(self: psi4.core.Molecule) → int¶: Gets the charge on full molecule

move_to_com(self: psi4.core.Molecule) → None¶: Moves molecule to center of mass

multiplicity(self: psi4.core.Molecule) → int¶: Gets the multiplicity (defined as $2M_s + 1$) of full molecule

nactive_fragments(self: psi4.core.Molecule) → int¶: Gets the number of active (non-ghosted) fragments in the molecule

nallatom(self: psi4.core.Molecule) → int¶: Number of real and dummy atoms

name(self: psi4.core.Molecule) → str¶: Gets molecule name

natom(self: psi4.core.Molecule) → int¶: Number of real atoms

nfragments(self: psi4.core.Molecule) → int¶: Gets the number of fragments in the molecule

nuclear_dipole(*args, **kwargs)¶

Overloaded function.

nuclear_dipole(self: psi4.core.Molecule, arg0: psi4.core.Vector3) -> psi4.core.Vector3

Gets the nuclear contribution to the dipole, withe respect to a specified origin

nuclear_dipole(self: psi4.core.Molecule) -> psi4.core.Vector3

Gets the nuclear contribution to the dipole, withe respect to the origin

nuclear_repulsion_energy(self: psi4.core.Molecule) → float¶: Computes nuclear repulsion energy

point_group(self: psi4.core.Molecule) → psi4.core.PointGroup¶: Returns the current point group object

print_bond_angles(self: psi4.core.Molecule) → None¶: Print the bond angle geometrical parameters

print_cluster(self: psi4.core.Molecule) → None¶: Prints the molecule in Cartesians in input units adding fragment separators

print_distances(self: psi4.core.Molecule) → None¶: Print the interatomic distance geometrical parameters

print_in_input_format(self: psi4.core.Molecule) → None¶: Prints the molecule as Cartesian or ZMatrix entries, just as inputted.

print_out(self: psi4.core.Molecule) → None¶: Prints the molecule in Cartesians in input units

print_out_in_angstrom(self: psi4.core.Molecule) → None¶: Prints the molecule in Cartesians in Angstroms

print_out_in_bohr(self: psi4.core.Molecule) → None¶: Prints the molecule in Cartesians in Bohr

print_out_of_planes(self: psi4.core.Molecule) → None¶: Print the out-of-plane angle geometrical parameters

reinterpret_coordentry(self: psi4.core.Molecule, arg0: bool) → None¶: Do reinterpret coordinate entries during update_geometry().

reset_point_group(self: psi4.core.Molecule, arg0: str) → None¶: Overrides symmetry from outside the molecule string

rotational_constants(self: psi4.core.Molecule, arg0: float) → psi4.core.Vector¶: Prints the rotational constants of the molecule

run_dftd3(func=None, dashlvl=None, dashparam=None, dertype=None, verbose=False)¶

Function to call Grimme’s dftd3 program (http://toc.uni-muenster.de/DFTD3/) to compute the -D correction of level dashlvl using parameters for the functional func. The dictionary dashparam can be used to supply a full set of dispersion parameters in the absense of func or to supply individual overrides in the presence of func. Returns energy if dertype is 0, gradient if dertype is 1, else tuple of energy and gradient if dertype unspecified. The dftd3 executable must be independently compiled and found in PATH or PSIPATH. self may be either a qcdb.Molecule (sensibly) or a psi4.Molecule (works b/c psi4.Molecule has been extended by this method py-side and only public interface fns used) or a string that can be instantiated into a qcdb.Molecule.

func - functional alias or None dashlvl - functional type d2gr/d3zero/d3bj/d3mzero/d3mbj dashparam - dictionary dertype = derivative level

run_gcp(func=None, dertype=None, verbose=False)¶: Function to call Grimme’s dftd3 program (http://toc.uni-muenster.de/DFTD3/) to compute the -D correction of level dashlvl using parameters for the functional func. The dictionary dashparam can be used to supply a full set of dispersion parameters in the absense of func or to supply individual overrides in the presence of func. Returns energy if dertype is 0, gradient if dertype is 1, else tuple of energy and gradient if dertype unspecified. The dftd3 executable must be independently compiled and found in PATH or PSIPATH. self may be either a qcdb.Molecule (sensibly) or a psi4.Molecule (works b/c psi4.Molecule has been extended by this method py-side and only public interface fns used) or a string that can be instantiated into a qcdb.Molecule.

save_string_xyz(self: psi4.core.Molecule) → str¶: Saves the string of an XYZ file to arg2

save_string_xyz_file(self: psi4.core.Molecule) → str¶: Saves an XYZ file to arg2

save_xyz_file(self: psi4.core.Molecule, arg0: str, arg1: bool) → None¶: Saves an XYZ file to arg2

schoenflies_symbol(self: psi4.core.Molecule) → str¶: Returns the Schoenflies symbol

set_active_fragment(self: psi4.core.Molecule, arg0: int) → None¶: Sets the specified fragment arg2 to be Real

set_active_fragments(self: psi4.core.Molecule, arg0: list) → None¶: Sets the specified list arg2 of fragments to be Real

set_basis_all_atoms(self: psi4.core.Molecule, arg0: str, arg1: str) → None¶: Sets basis set arg2 to all atoms

set_basis_by_label(self: psi4.core.Molecule, arg0: str, arg1: str, arg2: str) → None¶: Sets basis set arg3 to all atoms with label (e.g., H4) arg2

set_basis_by_symbol(self: psi4.core.Molecule, arg0: str, arg1: str, arg2: str) → None¶: Sets basis set arg3 to all atoms with symbol (e.g., H) arg2

set_geometry(self: psi4.core.Molecule, arg0: psi4.core.Matrix) → None¶: Sets the geometry, given a (Natom X 3) matrix arg2 of coordinates (in Bohr)

set_ghost_fragment(self: psi4.core.Molecule, arg0: int) → None¶: Sets the specified fragment arg2 to be Ghost

set_ghost_fragments(self: psi4.core.Molecule, arg0: list) → None¶: Sets the specified list arg2 of fragments to be Ghost

set_mass(self: psi4.core.Molecule, arg0: int, arg1: float) → None¶: Gets mass of atom arg1

set_molecular_charge(self: psi4.core.Molecule, arg0: int) → None¶: Sets the molecular charge

set_multiplicity(self: psi4.core.Molecule, arg0: int) → None¶: Sets the multiplicity (defined as 2Ms + 1)

set_name(self: psi4.core.Molecule, arg0: str) → None¶: Sets molecule name

set_point_group(self: psi4.core.Molecule, arg0: psi4.core.PointGroup) → None¶: Sets the molecular point group to the point group object arg2

set_variable(self: psi4.core.Molecule, arg0: str, arg1: float) → None¶: Assigns the value arg3 to the variable arg2 in the list of geometry variables, then calls update_geometry()

symbol(self: psi4.core.Molecule, arg0: int) → str¶: Gets the cleaned up label of atom arg1 (C2 => C, H4 = H) (0-indexed)

symmetrize(self: psi4.core.Molecule, arg0: float) → None¶: Finds the highest point Abelian point group within the specified tolerance, and forces the geometry to have that symmetry.

translate(self: psi4.core.Molecule, arg0: psi4.core.Vector3) → None¶: Translates molecule by arg1

update_geometry(self: psi4.core.Molecule) → None¶: Reevaluates the geometry with current variable values, orientation directives, etc. Must be called after initial Molecule definition by string.

x(self: psi4.core.Molecule, arg0: int) → float¶: x position of atom arg1 (0-indexed in Bohr)

y(self: psi4.core.Molecule, arg0: int) → float¶: y position of atom arg1 (0-indexed in Bohr)

z(self: psi4.core.Molecule, arg0: int) → float¶: z position of atom arg1 (0-indexed in Bohr)

BFS(): Perform a breadth-first search (BFS) on the real atoms in molecule, returning an array of atom indices of fragments. Relies upon van der Waals radii and so faulty for close (esp. hydrogen-bonded) fragments. Original code from Michael S. Marshall.

Z(self: psi4.core.Molecule, arg0: int) → float: Nuclear charge of atom arg1 (0-indexed)

activate_all_fragments(self: psi4.core.Molecule) → None: Sets all fragments in the molecule to be active

add_atom(self: psi4.core.Molecule, arg0: int, arg1: float, arg2: float, arg3: float, arg4: str, arg5: float, arg6: float, arg7: int) → None: Adds to Molecule arg0 an atom with atomic number arg1, Cartesian coordinates in Bohr (arg2, arg3, arg4), atomic symbol arg5, mass arg6, charge arg7 (optional), and lineno arg8 (optional)

atom_at_position(self: psi4.core.Molecule, arg0: float, arg1: float) → int: Tests to see if an atom is at the position arg2 with a given tolerance arg3

center_of_mass(self: psi4.core.Molecule) → psi4.core.Vector3: Computes center of mass of molecule (does not translate molecule)

charge(self: psi4.core.Molecule, arg0: int) → float: Gets charge of atom arg1 (0-indexed)

clone(self: psi4.core.Molecule) → psi4.core.Molecule: Returns a new Molecule identical to arg0

create_molecule_from_string(arg0: str) → psi4.core.Molecule: Returns a new Molecule with member data from the geometry string arg0 in Psi4 format

create_psi4_string_from_molecule(self: psi4.core.Molecule) → str: Gets a string reexpressing in input format the current states of the molecule

deactivate_all_fragments(self: psi4.core.Molecule) → None: Sets all fragments in the molecule to be inactive

distance_matrix(self: psi4.core.Molecule) → psi4.core.Matrix: Returns Matrix of interatom distances

extract_subsets(*args, **kwargs)

Overloaded function.

extract_subsets(self: psi4.core.Molecule, arg0: list, arg1: list) -> psi4.core.Molecule

Returns copy of arg1 with arg2 fragments Real and arg3 fragments Ghost

extract_subsets(self: psi4.core.Molecule, arg0: list, arg1: int) -> psi4.core.Molecule

Returns copy of arg1 with arg2 fragments Real and arg3 fragment Ghost

extract_subsets(self: psi4.core.Molecule, arg0: int, arg1: list) -> psi4.core.Molecule

Returns copy of arg1 with arg2 fragment Real and arg3 fragments Ghost

extract_subsets(self: psi4.core.Molecule, arg0: int, arg1: int) -> psi4.core.Molecule

Returns copy of arg1 with arg2 fragment Real and arg3 fragment Ghost

extract_subsets(self: psi4.core.Molecule, arg0: list) -> psi4.core.Molecule

Returns copy of arg1 with arg2 fragments Real

extract_subsets(self: psi4.core.Molecule, arg0: int) -> psi4.core.Molecule

Returns copy of arg1 with arg2 fragment Real

fZ(self: psi4.core.Molecule, arg0: int) → float: Nuclear charge of atom arg1 (0-indexed including dummies)

fcharge(self: psi4.core.Molecule, arg0: int) → float: Gets charge of atom arg1 (0-indexed including dummies)

find_point_group(self: psi4.core.Molecule, arg0: float) → psi4.core.PointGroup: Finds computational molecular point group, user can override this with the symmetry keyword

fix_com(self: psi4.core.Molecule, arg0: bool) → None: Whether to fix the Cartesian position, or to translate to the C.O.M.

fix_orientation(self: psi4.core.Molecule, arg0: bool) → None: Fix the orientation at its current frame

flabel(self: psi4.core.Molecule, arg0: int) → str: Gets the original label of the atom arg1 as given in the input file (C2, H4) (0-indexed including dummies)

fmass(self: psi4.core.Molecule, arg0: int) → float: Gets mass of atom arg1 (0-indexed including dummies)

form_symmetry_information(self: psi4.core.Molecule, arg0: float) → None: Uses the point group object obtain by calling point_group()

fsymbol(self: psi4.core.Molecule, arg0: int) → str: Gets the cleaned up label of atom arg1 (C2 => C, H4 = H) (0-indexed including dummies)

fx(self: psi4.core.Molecule, arg0: int) → float: x position of atom arg1 (0-indexed including dummies in Bohr)

fy(self: psi4.core.Molecule, arg0: int) → float: y position of atom arg1 (0-indexed including dummies in Bohr)

fz(self: psi4.core.Molecule, arg0: int) → float: z position of atom arg1 (0-indexed including dummies in Bohr)

geometry(self: psi4.core.Molecule) → psi4.core.Matrix: Gets the geometry as a (Natom X 3) matrix of coordinates (in Bohr)

get_full_point_group(self: psi4.core.Molecule) → str: Gets point group name such as C3v or S8

get_variable(self: psi4.core.Molecule, arg0: str) → float: Checks if variable arg2 is in the list, sets it to val and returns true if it is, and returns false if not

irrep_labels(self: psi4.core.Molecule) → List[str]

is_variable(self: psi4.core.Molecule, arg0: str) → bool: Checks if variable arg2 is in the list, returns true if it is, and returns false if not

label(self: psi4.core.Molecule, arg0: int) → str: Gets the original label of the atom arg1 as given in the input file (C2, H4) (0-indexed)

mass(self: psi4.core.Molecule, arg0: int) → float: Gets mass of atom arg1 (0-indexed)

molecular_charge(self: psi4.core.Molecule) → int: Gets the charge on full molecule

move_to_com(self: psi4.core.Molecule) → None: Moves molecule to center of mass

multiplicity(self: psi4.core.Molecule) → int: Gets the multiplicity (defined as $2M_s + 1$) of full molecule

nactive_fragments(self: psi4.core.Molecule) → int: Gets the number of active (non-ghosted) fragments in the molecule

nallatom(self: psi4.core.Molecule) → int: Number of real and dummy atoms

name(self: psi4.core.Molecule) → str: Gets molecule name

natom(self: psi4.core.Molecule) → int: Number of real atoms

nfragments(self: psi4.core.Molecule) → int: Gets the number of fragments in the molecule

nuclear_dipole(*args, **kwargs)

Overloaded function.

nuclear_dipole(self: psi4.core.Molecule, arg0: psi4.core.Vector3) -> psi4.core.Vector3

Gets the nuclear contribution to the dipole, withe respect to a specified origin

nuclear_dipole(self: psi4.core.Molecule) -> psi4.core.Vector3

Gets the nuclear contribution to the dipole, withe respect to the origin

nuclear_repulsion_energy(self: psi4.core.Molecule) → float: Computes nuclear repulsion energy

point_group(self: psi4.core.Molecule) → psi4.core.PointGroup: Returns the current point group object

print_bond_angles(self: psi4.core.Molecule) → None: Print the bond angle geometrical parameters

print_cluster(self: psi4.core.Molecule) → None: Prints the molecule in Cartesians in input units adding fragment separators

print_distances(self: psi4.core.Molecule) → None: Print the interatomic distance geometrical parameters

print_in_input_format(self: psi4.core.Molecule) → None: Prints the molecule as Cartesian or ZMatrix entries, just as inputted.

print_out(self: psi4.core.Molecule) → None: Prints the molecule in Cartesians in input units

print_out_in_angstrom(self: psi4.core.Molecule) → None: Prints the molecule in Cartesians in Angstroms

print_out_in_bohr(self: psi4.core.Molecule) → None: Prints the molecule in Cartesians in Bohr

print_out_of_planes(self: psi4.core.Molecule) → None: Print the out-of-plane angle geometrical parameters

reinterpret_coordentry(self: psi4.core.Molecule, arg0: bool) → None: Do reinterpret coordinate entries during update_geometry().

reset_point_group(self: psi4.core.Molecule, arg0: str) → None: Overrides symmetry from outside the molecule string

rotational_constants(self: psi4.core.Molecule, arg0: float) → psi4.core.Vector: Prints the rotational constants of the molecule

run_dftd3(func=None, dashlvl=None, dashparam=None, dertype=None, verbose=False)

Function to call Grimme’s dftd3 program (http://toc.uni-muenster.de/DFTD3/) to compute the -D correction of level dashlvl using parameters for the functional func. The dictionary dashparam can be used to supply a full set of dispersion parameters in the absense of func or to supply individual overrides in the presence of func. Returns energy if dertype is 0, gradient if dertype is 1, else tuple of energy and gradient if dertype unspecified. The dftd3 executable must be independently compiled and found in PATH or PSIPATH. self may be either a qcdb.Molecule (sensibly) or a psi4.Molecule (works b/c psi4.Molecule has been extended by this method py-side and only public interface fns used) or a string that can be instantiated into a qcdb.Molecule.

func - functional alias or None dashlvl - functional type d2gr/d3zero/d3bj/d3mzero/d3mbj dashparam - dictionary dertype = derivative level

run_gcp(func=None, dertype=None, verbose=False): Function to call Grimme’s dftd3 program (http://toc.uni-muenster.de/DFTD3/) to compute the -D correction of level dashlvl using parameters for the functional func. The dictionary dashparam can be used to supply a full set of dispersion parameters in the absense of func or to supply individual overrides in the presence of func. Returns energy if dertype is 0, gradient if dertype is 1, else tuple of energy and gradient if dertype unspecified. The dftd3 executable must be independently compiled and found in PATH or PSIPATH. self may be either a qcdb.Molecule (sensibly) or a psi4.Molecule (works b/c psi4.Molecule has been extended by this method py-side and only public interface fns used) or a string that can be instantiated into a qcdb.Molecule.

save_string_xyz(self: psi4.core.Molecule) → str: Saves the string of an XYZ file to arg2

save_string_xyz_file(self: psi4.core.Molecule) → str: Saves an XYZ file to arg2

save_xyz_file(self: psi4.core.Molecule, arg0: str, arg1: bool) → None: Saves an XYZ file to arg2

schoenflies_symbol(self: psi4.core.Molecule) → str: Returns the Schoenflies symbol

set_active_fragment(self: psi4.core.Molecule, arg0: int) → None: Sets the specified fragment arg2 to be Real

set_active_fragments(self: psi4.core.Molecule, arg0: list) → None: Sets the specified list arg2 of fragments to be Real

set_basis_all_atoms(self: psi4.core.Molecule, arg0: str, arg1: str) → None: Sets basis set arg2 to all atoms

set_basis_by_label(self: psi4.core.Molecule, arg0: str, arg1: str, arg2: str) → None: Sets basis set arg3 to all atoms with label (e.g., H4) arg2

set_basis_by_symbol(self: psi4.core.Molecule, arg0: str, arg1: str, arg2: str) → None: Sets basis set arg3 to all atoms with symbol (e.g., H) arg2

set_geometry(self: psi4.core.Molecule, arg0: psi4.core.Matrix) → None: Sets the geometry, given a (Natom X 3) matrix arg2 of coordinates (in Bohr)

set_ghost_fragment(self: psi4.core.Molecule, arg0: int) → None: Sets the specified fragment arg2 to be Ghost

set_ghost_fragments(self: psi4.core.Molecule, arg0: list) → None: Sets the specified list arg2 of fragments to be Ghost

set_mass(self: psi4.core.Molecule, arg0: int, arg1: float) → None: Gets mass of atom arg1

set_molecular_charge(self: psi4.core.Molecule, arg0: int) → None: Sets the molecular charge

set_multiplicity(self: psi4.core.Molecule, arg0: int) → None: Sets the multiplicity (defined as 2Ms + 1)

set_name(self: psi4.core.Molecule, arg0: str) → None: Sets molecule name

set_point_group(self: psi4.core.Molecule, arg0: psi4.core.PointGroup) → None: Sets the molecular point group to the point group object arg2

set_variable(self: psi4.core.Molecule, arg0: str, arg1: float) → None: Assigns the value arg3 to the variable arg2 in the list of geometry variables, then calls update_geometry()

symbol(self: psi4.core.Molecule, arg0: int) → str: Gets the cleaned up label of atom arg1 (C2 => C, H4 = H) (0-indexed)

symmetrize(self: psi4.core.Molecule, arg0: float) → None: Finds the highest point Abelian point group within the specified tolerance, and forces the geometry to have that symmetry.

translate(self: psi4.core.Molecule, arg0: psi4.core.Vector3) → None: Translates molecule by arg1

units: Units (Angstrom or Bohr) used to define the geometry

update_geometry(self: psi4.core.Molecule) → None: Reevaluates the geometry with current variable values, orientation directives, etc. Must be called after initial Molecule definition by string.

x(self: psi4.core.Molecule, arg0: int) → float: x position of atom arg1 (0-indexed in Bohr)

y(self: psi4.core.Molecule, arg0: int) → float: y position of atom arg1 (0-indexed in Bohr)

z(self: psi4.core.Molecule, arg0: int) → float: z position of atom arg1 (0-indexed in Bohr)