#
#@BEGIN LICENSE
#
# PSI4: an ab initio quantum chemistry software package
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along
# with this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
#@END LICENSE
#
from __future__ import absolute_import
from __future__ import print_function
import os
import re
import copy
import math
try:
from collections import OrderedDict
except ImportError:
from .oldpymodules import OrderedDict
from .periodictable import *
from .physconst import *
from .vecutil import *
from .exceptions import *
#from libmintscoordentry import *
from .libmintscoordentry import NumberValue, VariableValue, CartesianEntry, ZMatrixEntry
from .libmintspointgrp import SymmOps, similar, SymmetryOperation, PointGroup
#from libmintspointgrp import PointGroups
#print PointGroups
LINEAR_A_TOL = 1.0E-2 # When sin(a) is below this, we consider the angle to be linear
DEFAULT_SYM_TOL = 1.0E-8
FULL_PG_TOL = 1.0e-8
ZERO = 1.0E-14
NOISY_ZERO = 1.0E-8
[docs]class LibmintsMolecule(object):
"""Class to store the elements, coordinates, fragmentation pattern,
charge, multiplicity of a molecule. Largely replicates psi4's libmints
Molecule class, developed by Justin M. Turney and Andy M. Simmonett
with incremental improvements by other psi4 developers. Major
differences from the C++ class are: no basisset handling, no symmetry,
no pubchem, no efp, no discarding dummies. This class translated so
that databases can function independently of psi4.
>>> H2OH2O = qcdb.Molecule(\"\"\"
0 1
O1 -1.551007 -0.114520 0.000000
H1 -1.934259 0.762503 0.000000
H2 -0.599677 0.040712 0.000000
--
0 1
X 0.000000 0.000000 0.000000
O2 1.350625 0.111469 0.000000
H3 1.680398 -0.373741 -0.758561
H4 1.680398 -0.373741 0.758561
no_com
no_reorient
units angstrom
\"\"\")
>>> H2O = qcdb.Molecule.init_with_xyz('h2o.xyz')
"""
FullPointGroupList = ["ATOM", "C_inf_v", "D_inf_h", "C1", "Cs", "Ci", \
"Cn", "Cnv", "Cnh", "Sn", "Dn", "Dnd", "Dnh", "Td", "Oh", "Ih"]
def __init__(self, psi4molstr=None):
"""Initialize Molecule object from string in psi4 format"""
# <<< Basic Molecule Information >>>
# Molecule (or fragment) name
self.PYname = 'default'
# The molecular charge
self.PYmolecular_charge = 0
# Whether the charge was given by the user
self.PYcharge_specified = False
# The multiplicity (defined as 2Ms + 1)
self.PYmultiplicity = 1
# Whether the multiplicity was specified by the user
self.PYmultiplicity_specified = False
# The units used to define the geometry
self.PYunits = 'Angstrom'
# The conversion factor to take input units to Bohr
self.input_units_to_au = 1.0 / psi_bohr2angstroms
# Whether this molecule has at least one zmatrix entry
self.zmat = False # TODO None?
# <<< Coordinates >>>
# Atom info vector (no knowledge of dummy atoms)
self.atoms = []
# Atom info vector (includes dummy atoms)
self.full_atoms = []
# A list of all variables known, whether they have been set or not.
self.all_variables = []
# A listing of the variables used to define the geometries
self.geometry_variables = {}
# <<< Fragmentation >>>
# The list of atom ranges defining each fragment from parent molecule
self.fragments = []
# A list describing how to handle each fragment
self.fragment_types = []
# The charge of each fragment
self.fragment_charges = []
# The multiplicity of each fragment
self.fragment_multiplicities = []
# <<< Frame >>>
# Move to center of mass or not?
self.PYmove_to_com = True
# Reorient or not? UNUSED
self.PYfix_orientation = False
# Reinterpret the coord entries or not (Default is true, except for findif)
self.PYreinterpret_coordentries = True
# Nilpotence boolean (flagged upon first determination of symmetry frame,
# reset each time a substantiative change is made)
self.lock_frame = False
# <<< Symmetry >>>
# Point group to use with this molecule
self.pg = None
# Full point group
self.full_pg = 'C1'
# n of the highest rotational axis Cn
self.PYfull_pg_n = 1
# Symmetry string from geometry specification
self.PYsymmetry_from_input = None
# Number of unique atoms
self.PYnunique = 0
# Number of equivalent atoms per unique atom (length nunique)
self.nequiv = 0
# Equivalent atom mapping array (length 1st dim nunique)
self.equiv = 0
# Atom to unique atom mapping array (length natom)
self.PYatom_to_unique = 0
if psi4molstr:
self.create_molecule_from_string(psi4molstr)
# <<< Simple Methods for Basic Molecule Information >>>
[docs] def name(self):
"""Get molecule name
>>> print H2OH2O.name()
water_dimer
"""
return self.PYname
[docs] def set_name(self, name):
"""Set molecule name
>>> H2OH2O.set_name('water_dimer')
"""
self.PYname = name
[docs] def natom(self):
"""Number of atoms
>>> print H2OH2O.natom()
6
"""
return len(self.atoms)
[docs] def nallatom(self):
"""Number of all atoms (includes dummies)
>>> print H2OH2O.nallatom()
7
"""
return len(self.full_atoms)
[docs] def molecular_charge(self):
"""Gets the molecular charge
>>> print H2OH2O.molecular_charge()
-2
"""
return self.PYmolecular_charge
[docs] def set_molecular_charge(self, charge):
"""Sets the molecular charge
>>> H2OH2O.set_molecular_charge(-2)
"""
self.PYcharge_specified = True
self.PYmolecular_charge = charge
[docs] def charge_specified(self):
"""Whether the charge was given by the user
>>> print H2OH2O.charge_specified()
True
"""
return self.PYcharge_specified
[docs] def multiplicity(self):
"""Get the multiplicity (defined as 2Ms + 1)
>>> print H2OH2O.multiplicity()
"""
return self.PYmultiplicity
[docs] def set_multiplicity(self, mult):
"""Sets the multiplicity (defined as 2Ms + 1)
>>> H2OH2O.set_multiplicity(3)
"""
self.PYmultiplicity_specified = True
self.PYmultiplicity = mult
[docs] def multiplicity_specified(self):
"""Whether the multiplicity was given by the user
>>> print H2OH2O.multiplicity_specified()
True
"""
return self.PYmultiplicity_specified
[docs] def units(self):
"""Gets the geometry units
>>> print H2OH2O.units()
Angstrom
"""
return self.PYunits
[docs] def set_units(self, units):
"""Sets the geometry units
>>> H2OH2O.set_units('Angstom')
"""
if units == 'Angstrom' or units == 'Bohr':
self.PYunits = units
else:
raise ValidationError("""Molecule::set_units: argument must be 'Angstrom' or 'Bohr'.""")
[docs] def has_zmatrix(self):
"""Gets the presence of any zmatrix entry
>>> print H2OH2O.has_zmatrix()
False
"""
return self.zmat
[docs] def set_has_zmatrix(self, tf):
"""Sets the presence of any zmatrix entry
>>> H2OH2O.set_has_zmatrix(True)
"""
self.zmat = tf
# <<< Simple Methods for Coordinates >>>
[docs] def Z(self, atom):
"""Nuclear charge of atom (0-indexed)
>>> print H2OH2O.Z(4)
1
"""
return self.atoms[atom].Z()
[docs] def x(self, atom):
"""x position of atom (0-indexed) in Bohr
>>> print H2OH2O.x(4)
3.17549201425
"""
return self.input_units_to_au * self.atoms[atom].compute()[0]
[docs] def y(self, atom):
"""y position of atom (0-indexed) in Bohr
>>> print H2OH2O.y(4)
-0.706268134631
"""
return self.input_units_to_au * self.atoms[atom].compute()[1]
[docs] def z(self, atom):
"""z position of atom (0-indexed) in Bohr
>>> print H2OH2O.z(4)
-1.43347254509
"""
return self.input_units_to_au * self.atoms[atom].compute()[2]
[docs] def xyz(self, atom, posn=None):
"""Returns a Vector3 with x, y, z position of atom (0-indexed)
in Bohr or coordinate at *posn*
>>> print H2OH2O.xyz(4)
[3.175492014248769, -0.7062681346308132, -1.4334725450878665]
"""
temp = scale(self.atoms[atom].compute(), self.input_units_to_au)
if posn is None:
return temp
else:
return temp[posn]
[docs] def mass(self, atom):
"""Returns mass of atom (0-indexed)
>>> print H2OH2O.mass(4)
1.00782503207
"""
if self.atoms[atom].mass() != 0.0:
return self.atoms[atom].mass()
if math.fabs(self.atoms[atom].Z() - int(self.atoms[atom].Z())) > 0.0:
print("""WARNING: Obtaining masses from atom with fractional charge...may be incorrect!!!\n""")
# TODO outfile
return z2mass[int(self.atoms[atom].Z())]
[docs] def symbol(self, atom):
"""Returns the cleaned up label of the atom (C2 => C, H4 = H) (0-indexed)
>>> print H2OH2O.symbol(4)
H
"""
return self.atoms[atom].symbol()
[docs] def label(self, atom):
"""Returns the original label of the atom (0-indexed) as given in the input file (C2, H4). (0-indexed)
>>> print H2OH2O.label(4)
H3
"""
return self.atoms[atom].label()
[docs] def charge(self, atom):
"""Returns charge of atom (0-indexed).
Related to SAD guess in libmints version.
>>> print H2OH2O.charge(4)
1.0
"""
return self.atoms[atom].charge()
[docs] def fZ(self, atom):
"""Nuclear charge of atom (includes dummies)
>>> print H2OH2O.fZ(4)
8
"""
return self.full_atoms[atom].Z()
[docs] def fx(self, atom):
"""x position of atom (0-indexed, includes dummies) in Bohr
>>> print H2OH2O.fx(4)
2.55231135823
"""
return self.input_units_to_au * self.full_atoms[atom].compute()[0]
[docs] def fy(self, atom):
"""y position of atom (0-indexed, includes dummies) in Bohr
>>> print H2OH2O.fy(4)
0.210645882307
"""
return self.input_units_to_au * self.full_atoms[atom].compute()[1]
[docs] def fz(self, atom):
"""z position of atom (0-indexed, includes dummies) in Bohr
>>> print H2OH2O.fz(4)
0.0
"""
return self.input_units_to_au * self.full_atoms[atom].compute()[2]
[docs] def fxyz(self, atom):
"""Returns a Vector3 with x, y, z position of atom
(0-indexed) in Bohr (includes dummies)
>>> print H2OH2O.fxyz(4)
[2.5523113582286716, 0.21064588230662976, 0.0]
"""
return scale(self.full_atoms[atom].compute(), self.input_units_to_au)
[docs] def fmass(self, atom):
"""Returns mass of atom (0-indexed, includes dummies)
>>> print H2OH2O.fmass(4)
15.9949146196
"""
return self.full_atoms[atom].mass()
[docs] def fsymbol(self, atom):
"""Returns the cleaned up label of the atom (C2 => C, H4 = H) (includes dummies) (0-indexed)
>>> print H2OH2O.fsymbol(4)
O
"""
return self.full_atoms[atom].symbol()
[docs] def flabel(self, atom):
"""Returns the original label of the atom (0-indexed) as given in
the input file (C2, H4) (includes dummies)
>>> print H2OH2O.flabel(4)
O2
"""
return self.full_atoms[atom].label()
[docs] def fcharge(self, atom):
"""Returns charge of atom (0-indexed, includes dummies).
Related to SAD guess in libmints version.
>>> print H2OH2O.fcharge(4)
8.0
"""
return self.full_atoms[atom].charge()
# <<< Simple Methods for Fragmentation >>>
[docs] def nfragments(self):
"""The number of fragments in the molecule.
>>> print H2OH2O.nfragments()
2
"""
return len(self.fragments)
[docs] def nactive_fragments(self):
"""The number of active fragments in the molecule.
>>> print H2OH2O.nactive_fragments()
2
"""
n = 0
for fr in range(self.nfragments()):
if self.fragment_types[fr] == 'Real':
n += 1
return n
[docs] def activate_all_fragments(self):
"""Sets all fragments in the molecule to be active."""
self.lock_frame = False
for fr in range(self.nfragments()):
self.fragment_types[fr] = 'Real'
[docs] def set_active_fragment(self, fr):
"""Tags fragment index *fr* as composed of real atoms."""
self.lock_frame = False
self.fragment_types[fr - 1] = 'Real'
[docs] def set_active_fragments(self, reals):
"""Tags the fragments in array *reals* as composed of real atoms."""
self.lock_frame = False
for fr in reals:
self.fragment_types[fr - 1] = 'Real'
[docs] def set_ghost_fragment(self, fr):
"""Tags fragment index *fr* as composed of ghost atoms."""
self.lock_frame = False
self.fragment_types[fr - 1] = 'Ghost'
[docs] def set_ghost_fragments(self, ghosts):
"""Tags the fragments in array *ghosts* as composed of ghost atoms."""
self.lock_frame = False
for fr in ghosts:
self.fragment_types[fr - 1] = 'Ghost'
[docs] def deactivate_all_fragments(self):
"""Sets all fragments in the molecule to be inactive."""
self.lock_frame = False
for fr in range(self.nfragments()):
self.fragment_types[fr] = 'Absent'
# <<< Methods for Construction >>>
[docs] def create_molecule_from_string(self, text):
"""Given a string *text* of psi4-style geometry specification
(including newlines to separate lines), builds a new molecule.
Called from constructor.
"""
comment = re.compile(r'^\s*#')
blank = re.compile(r'^\s*$')
bohr = re.compile(r'^\s*units?[\s=]+(bohr|au|a.u.)\s*$', re.IGNORECASE)
ang = re.compile(r'^\s*units?[\s=]+(ang|angstrom)\s*$', re.IGNORECASE)
orient = re.compile(r'^\s*(no_reorient|noreorient)\s*$', re.IGNORECASE)
com = re.compile(r'^\s*(no_com|nocom)\s*$', re.IGNORECASE)
symmetry = re.compile(r'^\s*symmetry[\s=]+(\w+)\s*$', re.IGNORECASE)
ATOM = '((([A-Z]{1,3})_\w+)|(([A-Z]{1,3})\d*))' # match 'C', 'al', 'p88', 'p_pass' not 'Ofail', 'h99_text' # good, but unused
atom = re.compile(r'^(?:(?P<gh1>@)|(?P<gh2>Gh\())?(?P<label>(?P<symbol>[A-Z]{1,3})(?:(_\w+)|(\d+))?)(?(gh2)\))(?:@(?P<mass>\d+\.\d+))?$', re.IGNORECASE)
cgmp = re.compile(r'^\s*(-?\d+)\s+(\d+)\s*$')
frag = re.compile(r'^\s*--\s*$')
variable = re.compile(r'^\s*(\w+)\s*=\s*(-?\d+\.\d+|-?\d+\.|-?\.\d+|-?\d+|tda)\s*$', re.IGNORECASE)
ghost = re.compile(r'@(.*)|Gh\((.*)\)', re.IGNORECASE)
lines = re.split('\n', text)
glines = []
ifrag = 0
for line in lines:
# handle comments
if comment.match(line) or blank.match(line):
pass
# handle units
elif ang.match(line):
self.set_units('Angstrom')
self.input_units_to_au = 1.0 / psi_bohr2angstroms
elif bohr.match(line):
self.set_units('Bohr')
self.input_units_to_au = 1.0
# handle no_reorient
elif orient.match(line):
self.fix_orientation(True)
# handle no_com
elif com.match(line):
self.PYmove_to_com = False
# handle symmetry
elif symmetry.match(line):
self.PYsymmetry_from_input = symmetry.match(line).group(1).lower()
# handle variables
elif variable.match(line):
vname = variable.match(line).group(1).upper()
vval = float(variable.match(line).group(2))
tda = 360.0 * math.atan(math.sqrt(2)) / math.pi
self.geometry_variables['%s' % vname] = tda if vname == 'TDA' else vval
# handle charge and multiplicity
elif cgmp.match(line):
tempCharge = int(cgmp.match(line).group(1))
tempMultiplicity = int(cgmp.match(line).group(2))
if ifrag == 0:
self.PYcharge_specified = True
self.PYmultiplicity_specified = True
self.PYmolecular_charge = tempCharge
self.PYmultiplicity = tempMultiplicity
self.fragment_charges.append(tempCharge)
self.fragment_multiplicities.append(tempMultiplicity)
# handle fragment markers and default fragment cgmp
elif frag.match(line):
try:
self.fragment_charges[ifrag]
except:
self.fragment_charges.append(0)
self.fragment_multiplicities.append(1)
ifrag += 1
glines.append(line)
elif atom.match(line.split()[0].strip()):
glines.append(line)
else:
raise ValidationError('Molecule::create_molecule_from_string: Unidentifiable line in geometry specification: %s' % (line))
# catch last default fragment cgmp
try:
self.fragment_charges[ifrag]
except:
self.fragment_charges.append(0)
self.fragment_multiplicities.append(1)
# Now go through the rest of the lines looking for fragment markers
ifrag = 0
iatom = 0
tempfrag = []
atomSym = ""
atomLabel = ""
zmatrix = False
for line in glines:
# handle fragment markers
if frag.match(line):
ifrag += 1
self.fragments.append([tempfrag[0], tempfrag[-1]])
self.fragment_types.append('Real')
tempfrag = []
# handle atom markers
else:
entries = re.split(r'\s+|\s*,\s*', line.strip())
atomm = atom.match(line.split()[0].strip().upper())
atomLabel = atomm.group('label')
atomSym = atomm.group('symbol')
# We don't know whether the @C or Gh(C) notation matched. Do a quick check.
ghostAtom = False if (atomm.group('gh1') is None and atomm.group('gh2') is None) else True
# Check that the atom symbol is valid
if not atomSym in el2z:
raise ValidationError('Molecule::create_molecule_from_string: Illegal atom symbol in geometry specification: %s' % (atomSym))
zVal = el2z[atomSym]
atomMass = el2mass[atomSym] if atomm.group('mass') is None else float(atomm.group('mass'))
charge = float(zVal)
if ghostAtom:
zVal = 0
charge = 0.0
# handle cartesians
if len(entries) == 4:
tempfrag.append(iatom)
xval = self.get_coord_value(entries[1])
yval = self.get_coord_value(entries[2])
zval = self.get_coord_value(entries[3])
self.full_atoms.append(CartesianEntry(iatom, zVal, charge, \
atomMass, atomSym, atomLabel, \
xval, yval, zval))
# handle first line of Zmat
elif len(entries) == 1:
zmatrix = True
tempfrag.append(iatom)
self.full_atoms.append(ZMatrixEntry(iatom, zVal, charge, \
atomMass, atomSym, atomLabel))
# handle second line of Zmat
elif len(entries) == 3:
zmatrix = True
tempfrag.append(iatom)
rTo = self.get_anchor_atom(entries[1], line)
if rTo >= iatom:
raise ValidationError("Molecule::create_molecule_from_string: Error on geometry input line %s. Atom %s has not been defined yet.\n" % (line, entries[1]))
rval = self.get_coord_value(entries[2])
if self.full_atoms[rTo].symbol() == 'X':
rval.set_fixed(True)
self.full_atoms.append(ZMatrixEntry(iatom, zVal, charge, \
atomMass, atomSym, atomLabel, \
self.full_atoms[rTo], rval))
# handle third line of Zmat
elif len(entries) == 5:
zmatrix = True
tempfrag.append(iatom)
rTo = self.get_anchor_atom(entries[1], line)
if rTo >= iatom:
raise ValidationError("Molecule::create_molecule_from_string: Error on geometry input line %s. Atom %s has not been defined yet.\n" % (line, entries[1]))
aTo = self.get_anchor_atom(entries[3], line)
if aTo >= iatom:
raise ValidationError("Molecule::create_molecule_from_string: Error on geometry input line %s. Atom %s has not been defined yet.\n" % (line, entries[3]))
if aTo == rTo:
raise ValidationError("Molecule::create_molecule_from_string: Atom used multiple times on line %s." % (line))
rval = self.get_coord_value(entries[2])
aval = self.get_coord_value(entries[4])
if self.full_atoms[rTo].symbol() == 'X':
rval.set_fixed(True)
if self.full_atoms[aTo].symbol() == 'X':
aval.set_fixed(True)
self.full_atoms.append(ZMatrixEntry(iatom, zVal, charge, \
atomMass, atomSym, atomLabel, \
self.full_atoms[rTo], rval, \
self.full_atoms[aTo], aval))
# handle fourth line of Zmat
elif len(entries) == 7:
zmatrix = True
tempfrag.append(iatom)
rTo = self.get_anchor_atom(entries[1], line)
if rTo >= iatom:
raise ValidationError("Molecule::create_molecule_from_string: Error on geometry input line %s. Atom %s has not been defined yet.\n" % (line, entries[1]))
aTo = self.get_anchor_atom(entries[3], line)
if aTo >= iatom:
raise ValidationError("Molecule::create_molecule_from_string: Error on geometry input line %s. Atom %s has not been defined yet.\n" % (line, entries[3]))
dTo = self.get_anchor_atom(entries[5], line)
if dTo >= iatom:
raise ValidationError("Molecule::create_molecule_from_string: Error on geometry input line %s. Atom %s has not been defined yet.\n" % (line, entries[5]))
if aTo == rTo or rTo == dTo or aTo == dTo: # for you star wars fans
raise ValidationError("Molecule::create_molecule_from_string: Atom used multiple times on line %s" % (line))
rval = self.get_coord_value(entries[2])
aval = self.get_coord_value(entries[4])
dval = self.get_coord_value(entries[6])
if self.full_atoms[rTo].symbol() == 'X':
rval.set_fixed(True)
if self.full_atoms[aTo].symbol() == 'X':
aval.set_fixed(True)
if self.full_atoms[dTo].symbol() == 'X':
dval.set_fixed(True)
self.full_atoms.append(ZMatrixEntry(iatom, zVal, charge, \
atomMass, atomSym, atomLabel, \
self.full_atoms[rTo], rval, \
self.full_atoms[aTo], aval, \
self.full_atoms[dTo], dval))
else:
raise ValidationError('Molecule::create_molecule_from_string: Illegal geometry specification line : %s. \
You should provide either Z-Matrix or Cartesian input' % (line))
iatom += 1
self.fragments.append([tempfrag[0], tempfrag[-1]])
self.fragment_types.append('Real')
self.set_has_zmatrix(zmatrix)
[docs] def init_with_checkpoint(self, chkpt):
""" **NYI** Pull information from the *chkpt* object passed
(method name in libmints is init_with_chkpt)
"""
raise FeatureNotImplemented('Molecule::init_with_checkpoint') # FINAL
[docs] def init_with_io(self, psio):
""" **NYI** Pull information from a chkpt object created from psio
(method name in libmints is init_with_psio)
"""
raise FeatureNotImplemented('Molecule::init_with_io') # FINAL
@classmethod
[docs] def init_with_xyz(cls, xyzfilename):
"""Pull information from an XYZ file. No fragment or chg/mult info detected.
>>> H2O = qcdb.Molecule.init_with_xyz('h2o.xyz')
"""
instance = cls()
instance.lock_frame = False
try:
infile = open(xyzfilename, 'r')
except IOError:
raise ValidationError("""Molecule::init_with_xyz: given filename '%s' does not exist.""" % (xyzfilename))
if os.stat(xyzfilename).st_size == 0:
raise ValidationError("""Molecule::init_with_xyz: given filename '%s' is blank.""" % (xyzfilename))
text = infile.readlines()
xyz1 = re.compile(r"^\s*(\d+)\s*(bohr|au)?\s*$", re.IGNORECASE)
xyzN = re.compile(r"(?:\s*)([A-Z](?:[a-z])?)(?:\s+)(-?\d+\.\d+)(?:\s+)(-?\d+\.\d+)(?:\s+)(-?\d+\.\d+)(?:\s*)", re.IGNORECASE)
# Try to match the first line
if xyz1.match(text[0]):
fileNatom = int(xyz1.match(text[0]).group(1))
if xyz1.match(text[0]).group(2) == None:
fileUnits = 'Angstrom'
else:
fileUnits = 'Bohr'
else:
raise ValidationError("Molecule::init_with_xyz: Malformed first line\n%s" % (text[0]))
# Skip the second line
# Next line begins the useful information.
for i in range(fileNatom):
try:
if xyzN.match(text[2 + i]):
fileAtom = xyzN.match(text[2 + i]).group(1).upper()
fileX = float(xyzN.match(text[2 + i]).group(2))
fileY = float(xyzN.match(text[2 + i]).group(3))
fileZ = float(xyzN.match(text[2 + i]).group(4))
# Coordinates in Molecule must be bohr.
if fileUnits == 'Angstrom':
fileX /= psi_bohr2angstroms
fileY /= psi_bohr2angstroms
fileZ /= psi_bohr2angstroms
# Check that the atom symbol is valid
if not fileAtom in el2z:
raise ValidationError('Molecule::init_with_xyz: Illegal atom symbol in geometry specification: %s' % (atomSym))
# Add it to the molecule.
instance.add_atom(el2z[fileAtom], fileX, fileY, fileZ, fileAtom, el2mass[fileAtom])
else:
raise ValidationError("Molecule::init_with_xyz: Malformed atom information line %d." % (i + 3))
except IndexError:
raise ValidationError("Molecule::init_with_xyz: Expected atom in file at line %d.\n%s" % (i + 3, text[i + 2]))
# We need to make 1 fragment with all atoms
instance.fragments.append([0, fileNatom - 1])
instance.fragment_types.append('Real')
instance.fragment_charges.append(0)
instance.fragment_multiplicities.append(1)
# Set the units to bohr since we did the conversion above, if needed.
instance.PYunits = 'Bohr'
instance.input_units_to_au = 1.0
instance.update_geometry()
return instance
[docs] def clone(self):
"""Returns new, independent Molecule object.
>>> dimer = H2OH2O.clone()
"""
return copy.deepcopy(self)
# <<< Methods for Printing >>>
[docs] def print_out(self):
"""Print the molecule.
(method name in libmints is print)
>>> H2OH2O.print_out()
Geometry (in Angstrom), charge = -2, multiplicity = 3:
Center X Y Z
------------ ----------------- ----------------- -----------------
O -1.551007000000 -0.114520000000 0.000000000000
H -1.934259000000 0.762503000000 0.000000000000
H -0.599677000000 0.040712000000 0.000000000000
O 1.350625000000 0.111469000000 0.000000000000
H 1.680398000000 -0.373741000000 -0.758561000000
H 1.680398000000 -0.373741000000 0.758561000000
"""
text = ""
if self.natom():
if self.pg:
text += """ Molecular point group: %s\n""" % (self.pg.symbol())
if self.full_pg:
text += """ Full point group: %s\n\n""" % (self.get_full_point_group())
text += """ Geometry (in %s), charge = %d, multiplicity = %d:\n\n""" % \
('Angstrom' if self.units() == 'Angstrom' else 'Bohr', self.molecular_charge(), self.multiplicity())
text += """ Center X Y Z \n"""
text += """ ------------ ----------------- ----------------- -----------------\n"""
for i in range(self.natom()):
geom = self.atoms[i].compute()
text += """ %8s%4s """ % (self.symbol(i), "" if self.Z(i) else "(Gh)")
for j in range(3):
text += """ %17.12f""" % (geom[j])
text += "\n"
# TODO if (Process::environment.options.get_int("PRINT") > 2) {
text += "\n"
for i in range(self.natom()):
text += """ %8s\n""" % (self.label(i))
for bas in self.atoms[i].basissets().keys():
text += """ %-15s %-20s %s\n""" % (bas,
self.atoms[i].basissets()[bas], self.atoms[i].shells()[bas])
text += "\n"
else:
text += " No atoms in this molecule.\n"
print(text)
# TODO outfile
[docs] def print_out_in_bohr(self):
"""Print the molecule in Bohr. Same as :py:func:`print_out` only in Bohr.
(method name in libmints is print_in_bohr)
"""
text = ""
if self.natom():
if self.pg:
text += """ Molecular point group: %s\n""" % (self.pg.symbol())
if self.full_pg:
text += """ Full point group: %s\n\n""" % (self.get_full_point_group())
text += """ Geometry (in %s), charge = %d, multiplicity = %d:\n\n""" % \
('Bohr', self.molecular_charge(), self.multiplicity())
text += """ Center X Y Z \n"""
text += """ ------------ ----------------- ----------------- -----------------\n"""
for i in range(self.natom()):
text += """ %8s%4s """ % (self.symbol(i), "" if self.Z(i) else "(Gh)")
for j in range(3):
text += """ %17.12f""" % (self.xyz(i, j))
text += "\n"
text += "\n"
else:
text += " No atoms in this molecule.\n"
print(text)
# TODO outfile
[docs] def print_out_in_angstrom(self):
"""Print the molecule in Angstroms. Same as :py:func:`print_out` only always in Angstroms.
(method name in libmints is print_in_angstrom)
"""
text = ""
if self.natom():
if self.pg:
text += """ Molecular point group: %s\n""" % (self.pg.symbol())
if self.full_pg:
text += """ Full point group: %s\n\n""" % (self.get_full_point_group())
text += """ Geometry (in %s), charge = %d, multiplicity = %d:\n\n""" % \
('Angstrom', self.molecular_charge(), self.multiplicity())
text += """ Center X Y Z \n"""
text += """ ------------ ----------------- ----------------- -----------------\n"""
for i in range(self.natom()):
text += """ %8s%4s """ % (self.symbol(i), "" if self.Z(i) else "(Gh)")
for j in range(3):
text += """ %17.12f""" % (self.xyz(i, j) * psi_bohr2angstroms)
text += "\n"
text += "\n"
else:
text += " No atoms in this molecule.\n"
print(text)
# TODO outfile
[docs] def print_full(self):
"""Print full atom list. Same as :py:func:`print_out` only displays dummy atoms.
"""
text = ""
if self.natom():
if self.pg:
text += """ Molecular point group: %s\n""" % (self.pg.symbol())
if self.full_pg:
text += """ Full point group: %s\n\n""" % (self.get_full_point_group())
text += """ Geometry (in %s), charge = %d, multiplicity = %d:\n\n""" % \
(self.units(), self.molecular_charge(), self.multiplicity())
text += """ Center X Y Z \n"""
text += """ ------------ ----------------- ----------------- -----------------\n"""
for i in range(self.nallatom()):
geom = self.full_atoms[i].compute()
text += """ %8s%4s """ % (self.fsymbol(i), "" if self.fZ(i) else "(Gh)")
for j in range(3):
text += """ %17.12f""" % (geom[j])
text += "\n"
text += "\n"
else:
text += " No atoms in this molecule.\n"
print(text)
# TODO outfile
# TODO outfile
[docs] def everything(self):
"""Quick print of class data"""
text = """ ==> qcdb Molecule %s <==\n\n""" % (self.name())
text += """ Natom %d\t\tNallatom %d\n""" % (self.natom(), self.nallatom())
text += """ charge %d\t\tspecified? %s\n""" % (self.molecular_charge(), self.charge_specified())
text += """ multiplicity %d\t\tspecified? %s\n""" % (self.multiplicity(), self.multiplicity_specified())
text += """ units %s\tconversion %f\n""" % (self.units(), self.input_units_to_au)
text += """ DOcom? %s\t\tDONTreorient? %s\n""" % (self.PYmove_to_com, self.orientation_fixed())
text += """ reinterpret? %s\t\tlock_frame? %s\n""" % (self.PYreinterpret_coordentries, self.lock_frame)
text += """ input symm %s\n""" % (self.symmetry_from_input())
text += """ Nfragments %d\t\tNactive %d\n""" % (self.nfragments(), self.nactive_fragments())
text += """ zmat? %s\n""" % (self.has_zmatrix())
print(text)
[docs] def create_psi4_string_from_molecule(self):
"""Regenerates a input file molecule specification string from the
current state of the Molecule. Contains geometry info,
fragmentation, charges and multiplicities, and any frame
restriction.
"""
text = ""
if self.nallatom():
# append units and any other non-default molecule keywords
text += " units %-s\n" % ("Angstrom" if self.units() == 'Angstrom' else "Bohr")
if not self.PYmove_to_com:
text += " no_com\n"
if self.PYfix_orientation:
text += " no_reorient\n"
# append atoms and coordentries and fragment separators with charge and multiplicity
Pfr = 0
for fr in range(self.nfragments()):
if self.fragment_types[fr] == 'Absent' and not self.has_zmatrix():
continue
text += "%s %s%d %d\n" % (
"" if Pfr == 0 else " --\n",
"#" if self.fragment_types[fr] == 'Ghost' or self.fragment_types[fr] == 'Absent' else "",
self.fragment_charges[fr], self.fragment_multiplicities[fr])
Pfr += 1
for at in range(self.fragments[fr][0], self.fragments[fr][1] + 1):
if self.fragment_types[fr] == 'Absent':
text += " %-8s" % ("X")
elif self.fZ(at) or self.fsymbol(at) == "X":
text += " %-8s" % (self.flabel(at))
else:
text += " %-8s" % ("Gh(" + self.flabel(at) + ")")
text += " %s" % (self.full_atoms[at].print_in_input_format())
text += "\n"
# append any coordinate variables
if len(self.geometry_variables):
for vb, val in self.geometry_variables.items():
text += """ %-10s=%16.10f\n""" % (vb, val)
text += "\n"
return text
# <<< Involved Methods for Coordinates >>>
[docs] def get_coord_value(self, vstr):
"""Attempts to interpret a string as a double, if not it assumes it's a variable.
"""
vstr = vstr.upper()
realNumber = re.compile(r"""[-+]?(?:(?:\d*\.\d+)|(?:\d+\.?))(?:[Ee][+-]?\d+)?""", re.VERBOSE)
# handle number values
if realNumber.match(vstr):
return NumberValue(float(vstr))
# handle variable values, whether defined or not
else:
if vstr == 'TDA':
self.geometry_variables[vstr] = 360.0 * math.atan(math.sqrt(2)) / math.pi
# handle negative variable values (ignore leading '-' and return minus the value)
if vstr[0] == '-':
self.all_variables.append(vstr[1:])
return VariableValue(vstr[1:], self.geometry_variables, True)
# handle normal variable values
else:
self.all_variables.append(vstr)
return VariableValue(vstr, self.geometry_variables)
[docs] def add_atom(self, Z, x, y, z, label="", mass=0.0, charge=0.0, lineno=-1):
"""Add an atom to the molecule
*Z* atomic number
*x* cartesian coordinate
*y* cartesian coordinate
*z* cartesian coordinate
*symb* atomic symbol to use
*mass* mass to use if non standard
*charge* charge to use if non standard
*lineno* line number when taken from a string
"""
self.lock_frame = False
if self.atom_at_position([x, y, z]) == -1:
# Dummies go to full_atoms, ghosts need to go to both.
self.full_atoms.append(CartesianEntry(self.nallatom(), Z, charge, mass, label, label, \
NumberValue(x), NumberValue(y), NumberValue(z)))
if label.upper() != 'X':
self.atoms.append(self.full_atoms[-1])
else:
raise ValidationError("Molecule::add_atom: Adding atom on top of an existing atom.")
[docs] def atom_entry(self, atom):
"""Returns the CoordEntry for an atom."""
return self.atoms[atom]
[docs] def atom_at_position(self, b, tol=0.05):
"""Tests to see of an atom is at the passed position *b* in Bohr with a tolerance *tol*.
>>> print H2OH2O.atom_at_position([1.35*(1.0/psi_bohr2angstroms), 0.10*(1.0/psi_bohr2angstroms), 0.0*(1.0/psi_bohr2angstroms)])
3
"""
if len(b) != 3:
raise ValidationError('Molecule::atom_at_position: Argument vector not of length 3\n')
for at in range(self.natom()):
a = self.xyz(at)
if distance(b, a) < tol:
return at
return -1
[docs] def is_variable(self, vstr):
"""Checks to see if the variable str is in the list, returns
true if it is, and returns false if not.
>>> H2OH2O.is_variable('R')
False
"""
#if self.all_variables
#print 'vstr', vstr, 'all_variables', self.all_variables, (vstr.upper() in self.all_variables), '\n'
return True if vstr.upper() in self.all_variables else False
[docs] def get_variable(self, vstr):
"""Checks to see if the variable str is in the list, sets it to
val and returns true if it is, and returns false if not.
"""
vstr = vstr.upper()
try:
return self.geometry_variables[vstr]
except KeyError:
raise ValidationError('Molecule::get_variable: Geometry variable %s not known.\n' % (vstr))
[docs] def set_variable(self, vstr, val):
"""Assigns the value val to the variable labelled string in the
list of geometry variables. Also calls update_geometry()
"""
self.__dict__['lock_frame'] = False
self.__dict__['geometry_variables'][vstr.upper()] = val
print("""Setting geometry variable %s to %f""" % (vstr.upper(), val))
try:
self.update_geometry()
except IncompleteAtomError:
# Update geometry might have added some atoms, delete them to be safe.
self.atoms = []
# TODO outfile
# def __setattr__(self, name, value):
# """Function to overload setting attributes to allow geometry
# variable assigment as if member data.
#
# """
# try:
# if name.upper() in self.__dict__['all_variables']:
# self.set_variable(name, value)
# else:
# self.__dict__[name] = value
# except KeyError:
# self.__dict__[name] = value
#
# def __getattr__(self, name):
# """Function to overload accessing attribute contents to allow
# retrivial geometry variable values as if member data.
#
# """
## #if not name in self.__dict__:
## if not name in self.__dict__['__dict__']:
## if object.__getattribute__(self, 'is_variable')(name):
## return object.__getattribute__(self, 'get_variable')(name)
## else:
## raise AttributeError
## else:
## #return self.__dict__[name]
## return self.__dict__['__dict__'][name]
#
## if name in self.__dict__:
## return self.__dict__[name]
## elif '__dict__' in self.__dict__ and name in self.__dict__['__dict__']:
## return self.__dict__['__dict__'][name]
## elif object.__getattribute__(self, 'is_variable')(name):
## return object.__getattribute__(self, 'get_variable')(name)
## else:
## raise AttributeError
#
# if not name in self.__dict__:
# if object.__getattribute__(self, 'is_variable')(name):
# return object.__getattribute__(self, 'get_variable')(name)
# else:
# raise AttributeError
# else:
# return self.__dict__[name]
def __setattr__(self, name, value):
"""Function to overload setting attributes to allow geometry
variable assigment as if member data.
"""
try:
if name.upper() in self.__dict__['all_variables']:
self.set_variable(name, value)
else:
self.__dict__[name] = value
except KeyError:
self.__dict__[name] = value
def __getattr__(self, name):
"""Function to overload accessing attribute contents to allow
retrivial geometry variable values as if member data.
"""
if not name in self.__dict__:
if object.__getattribute__(self, 'is_variable')(name):
return object.__getattribute__(self, 'get_variable')(name)
else:
raise AttributeError
else:
return self.__dict__[name]
[docs] def get_anchor_atom(self, vstr, line):
"""Attempts to interpret a string *vstr* as an atom specifier in
a zmatrix. Takes the current *line* for error message printing.
Returns the atom number (adjusted to zero-based counting).
"""
integerNumber = re.compile(r"(-?\d+)", re.IGNORECASE)
if integerNumber.match(vstr):
# This is just a number, return it
return int(vstr) - 1
else:
# Look to see if this string is known
for i in range(self.nallatom()):
if self.full_atoms[i].label() == vstr:
return i
raise ValidationError("Molecule::get_anchor_atom: Illegal value %s in atom specification on line %s.\n" % (vstr, line))
[docs] def geometry(self):
"""Returns the geometry in Bohr as a N X 3 array.
>>> print H2OH2O.geometry()
[[-2.930978460188563, -0.21641143673806384, 0.0], [-3.655219780069251, 1.4409218455037016, 0.0], [-1.1332252981904638, 0.0769345303220403, 0.0], [2.5523113582286716, 0.21064588230662976, 0.0], [3.175492014248769, -0.7062681346308132, -1.4334725450878665], [3.175492014248769, -0.7062681346308132, 1.4334725450878665]]
"""
geom = []
for at in range(self.natom()):
geom.append([self.x(at), self.y(at), self.z(at)])
return geom
[docs] def full_geometry(self):
"""Returns the full (dummies included) geometry in Bohr as a N X 3 array.
>>> print H2OH2O.full_geometry()
[[-2.930978460188563, -0.21641143673806384, 0.0], [-3.655219780069251, 1.4409218455037016, 0.0], [-1.1332252981904638, 0.0769345303220403, 0.0], [0.0, 0.0, 0.0], [2.5523113582286716, 0.21064588230662976, 0.0], [3.175492014248769, -0.7062681346308132, -1.4334725450878665], [3.175492014248769, -0.7062681346308132, 1.4334725450878665]]
"""
geom = []
for at in range(self.nallatom()):
geom.append([self.fx(at), self.fy(at), self.fz(at)])
return geom
[docs] def set_geometry(self, geom):
"""Sets the geometry, given a N X 3 array of coordinates *geom* in Bohr.
>>> H2OH2O.set_geometry([[1,2,3],[4,5,6],[7,8,9],[-1,-2,-3],[-4,-5,-6],[-7,-8,-9]])
"""
self.lock_frame = False
for at in range(self.natom()):
self.atoms[at].set_coordinates(geom[at][0] / self.input_units_to_au,
geom[at][1] / self.input_units_to_au,
geom[at][2] / self.input_units_to_au)
[docs] def set_full_geometry(self, geom):
"""Sets the full geometry (dummies included), given a N X 3 array of coordinates *geom* in Bohr.
>>> H2OH2O.set_full geometry([[1,2,3],[4,5,6],[7,8,9],[0,0,0],[-1,-2,-3],[-4,-5,-6],[-7,-8,-9]])
"""
self.lock_frame = False
for at in range(self.nallatom()):
self.full_atoms[at].set_coordinates(geom[at][0] / self.input_units_to_au,
geom[at][1] / self.input_units_to_au,
geom[at][2] / self.input_units_to_au)
[docs] def distance_matrix(self):
"""Computes a matrix depicting distances between atoms. Prints
formatted and returns array.
>>> H2OH2O.distance_matrix()
Interatomic Distances (Angstroms)
[1] [2] [3] [4] [5] [6]
[1] 0.00000
[2] 0.95711 0.00000
[3] 0.96391 1.51726 0.00000
[4] 2.91042 3.34878 1.95159 0.00000
[5] 3.32935 3.86422 2.43843 0.95895 0.00000
[6] 3.32935 3.86422 2.43843 0.95895 1.51712 0.00000
"""
distm = [[None] * self.natom() for _ in range(self.natom())]
text = " Interatomic Distances (Angstroms)\n\n "
for i in range(self.natom()):
text += '%11s ' % ('[' + str(i + 1) + ']')
text += "\n"
for i in range(self.natom()):
text += ' %-8s ' % ('[' + str(i + 1) + ']')
for j in range(self.natom()):
if j > i:
continue
if j == i:
text += '%10.5f ' % (0.0)
distm[i][j] = 0.0
else:
eij = sub(self.xyz(j), self.xyz(i))
dist = norm(eij) * psi_bohr2angstroms
text += '%10.5f ' % (dist)
distm[i][j] = dist
distm[j][i] = dist
text += "\n"
text += "\n\n"
print(text)
return distm
# TODO outfile
[docs] def print_distances(self):
"""Print the geometrical parameters (distances) of the molecule.
suspect libmints version actually prints Bohr.
>>> print H2OH2O.print_distances()
Interatomic Distances (Angstroms)
Distance 1 to 2 0.957
Distance 1 to 3 0.964
Distance 1 to 4 2.910
...
"""
text = " Interatomic Distances (Angstroms)\n\n"
for i in range(self.natom()):
for j in range(i + 1, self.natom()):
eij = sub(self.xyz(j), self.xyz(i))
dist = norm(eij) * psi_bohr2angstroms
text += " Distance %d to %d %-8.3lf\n" % (i + 1, j + 1, dist)
text += "\n\n"
return text
# TODO outfile
[docs] def print_bond_angles(self):
"""Print the geometrical parameters (bond_angles) of the molecule.
>>> print H2OH2O.print_bond_angles()
Bond Angles (degrees)
Angle 2-1-3: 104.337
Angle 2-1-4: 109.152
Angle 2-1-5: 117.387
...
"""
text = " Bond Angles (degrees)\n\n"
for j in range(self.natom()):
for i in range(self.natom()):
if j == i:
continue
for k in range(i + 1, self.natom()):
if j == k:
continue
eji = sub(self.xyz(i), self.xyz(j))
eji = normalize(eji)
ejk = sub(self.xyz(k), self.xyz(j))
ejk = normalize(ejk)
dotproduct = dot(eji, ejk)
phi = 180.0 * math.acos(dotproduct) / math.pi
text += " Angle %d-%d-%d: %8.3lf\n" % (i + 1, j + 1, k + 1, phi)
text += "\n\n"
return text
# TODO outfile
[docs] def print_dihedrals(self):
"""Print the geometrical parameters (dihedrals) of the molecule.
>>> print H2OH2O.print_dihedrals()
Dihedral Angles (Degrees)
Dihedral 1-2-3-4: 180.000
Dihedral 1-2-3-5: 133.511
Dihedral 1-2-3-6: 133.511
...
"""
text = " Dihedral Angles (Degrees)\n\n"
for i in range(self.natom()):
for j in range(self.natom()):
if i == j:
continue
for k in range(self.natom()):
if i == k or j == k:
continue
for l in range(self.natom()):
if i == l or j == l or k == l:
continue
eij = sub(self.xyz(j), self.xyz(i))
eij = normalize(eij)
ejk = sub(self.xyz(k), self.xyz(j))
ejk = normalize(ejk)
ekl = sub(self.xyz(l), self.xyz(k))
ekl = normalize(ekl)
# Compute angle ijk
angleijk = math.acos(dot(scale(eij, -1.0), ejk))
# Compute angle jkl
anglejkl = math.acos(dot(scale(ejk, -1.0), ekl))
# compute term1 (eij x ejk)
term1 = cross(eij, ejk)
# compute term2 (ejk x ekl)
term2 = cross(ejk, ekl)
numerator = dot(term1, term2)
denominator = math.sin(angleijk) * math.sin(anglejkl)
try:
costau = numerator / denominator
except ZeroDivisionError:
costau = 0.0
if costau > 1.00 and costau < 1.000001:
costau = 1.00
if costau < -1.00 and costau > -1.000001:
costau = -1.00
tau = 180.0 * math.acos(costau) / math.pi
text += " Dihedral %d-%d-%d-%d: %8.3lf\n" % (i + 1, j + 1, k + 1, l + 1, tau)
text += "\n\n"
return text
# TODO outfile
[docs] def print_out_of_planes(self):
"""Print the geometrical parameters (out_of_planes) of the molecule.
>>> print H2OH2O.print_out_of_planes()
Out-Of-Plane Angles (Degrees)
Out-of-plane 1-2-3-4: 0.000
Out-of-plane 1-2-3-5: -7.373
Out-of-plane 1-2-3-6: 7.373
...
"""
text = " Out-Of-Plane Angles (Degrees)\n\n"
for i in range(self.natom()):
for j in range(self.natom()):
if i == j:
continue
for k in range(self.natom()):
if i == k or j == k:
continue
for l in range(self.natom()):
if i == l or j == l or k == l:
continue
# Compute vectors we need first
elj = sub(self.xyz(j), self.xyz(l))
elj = normalize(elj)
elk = sub(self.xyz(k), self.xyz(l))
elk = normalize(elk)
eli = sub(self.xyz(i), self.xyz(l))
eli = normalize(eli)
# Denominator
denominator = math.sin(math.acos(dot(elj, elk)))
# Numerator
eljxelk = cross(elj, elk)
numerator = dot(eljxelk, eli)
# compute angle
try:
sinetheta = numerator / denominator
except ZeroDivisionError:
sinetheta = 0.0
if sinetheta > 1.00:
sinetheta = 1.000
if sinetheta < -1.00:
sinetheta = -1.000
theta = 180.0 * math.asin(sinetheta) / math.pi
text += " Out-of-plane %d-%d-%d-%d: %8.3lf\n" % (i + 1, j + 1, k + 1, l + 1, theta)
text += "\n\n"
return text
# TODO outfile
[docs] def reinterpret_coordentry(self, rc):
"""Do we reinterpret coordentries during a call to update_geometry?
(method name in libmints is set_reinterpret_coordentry)
"""
self.PYreinterpret_coordentries = rc
[docs] def reinterpret_coordentries(self):
"""Reinterpret the fragments for reals/ghosts and build the atom list.
"""
self.atoms = []
for item in self.full_atoms:
item.invalidate()
temp_charge = self.PYmolecular_charge
temp_multiplicity = self.PYmultiplicity
self.PYmolecular_charge = 0
self.PYmultiplicity = 1
for fr in range(self.nfragments()):
if self.fragment_types[fr] == 'Absent':
continue
if self.fragment_types[fr] == 'Real':
self.PYmolecular_charge += self.fragment_charges[fr]
self.PYmultiplicity += self.fragment_multiplicities[fr] - 1
for at in range(self.fragments[fr][0], self.fragments[fr][1] + 1):
self.full_atoms[at].compute()
self.full_atoms[at].set_ghosted(self.fragment_types[fr] == 'Ghost')
if self.full_atoms[at].symbol() != 'X':
self.atoms.append(self.full_atoms[at])
# TODO: This is a hack to ensure that set_multiplicity and set_molecular_charge
# work for single-fragment molecules.
if self.nfragments() < 2:
self.PYmolecular_charge = temp_charge
self.PYmultiplicity = temp_multiplicity
[docs] def update_geometry(self):
"""Updates the geometry, by (re)interpreting the string used to
create the molecule, and the current values of the variables.
The atoms list is cleared, and then rebuilt by this routine.
This function must be called after first instantiation of Molecule.
>>> H2 = qcdb.Molecule("H\\nH 1 0.74\\n")
>>> print H2.natom()
0
>>> H2.update_geometry()
>>> print H2.natom()
2
"""
if self.nfragments() == 0:
raise ValidationError("Molecule::update_geometry: There are no fragments in this molecule.")
# Idempotence condition
if self.lock_frame:
return
#print "beginning update_geometry:"
#self.print_full()
if self.PYreinterpret_coordentries:
self.reinterpret_coordentries()
#print "after reinterpret_coordentries:"
#self.print_full()
if self.PYmove_to_com:
self.move_to_com()
#print "after com:"
#self.print_full()
# If the no_reorient command was given, don't reorient
if not self.PYfix_orientation:
# Now we need to rotate the geometry to its symmetry frame
# to align the axes correctly for the point group
# symmetry_frame looks for the highest point group so that we can align
# the molecule according to its actual symmetry, rather than the symmetry
# the the user might have provided.
frame = self.symmetry_frame()
self.rotate_full(frame)
#print "after rotate:"
#self.print_full()
# Recompute point group of the molecule, so the symmetry info is updated to the new frame
self.set_point_group(self.find_point_group())
self.set_full_point_group()
# Disabling symmetrize for now if orientation is fixed, as it is not
# correct. We may want to fix this in the future, but in some cases of
# finite-differences the set geometry is not totally symmetric anyway.
# Symmetrize the molecule to remove any noise
self.symmetrize()
#print "after symmetry:"
#self.print_full()
self.lock_frame = True
# <<< Methods for Miscellaneous >>>
[docs] def clear(self):
"""Zero it out."""
self.lock_frame = False
self.atoms = []
self.full_atoms = []
[docs] def nuclear_repulsion_energy(self):
"""Computes nuclear repulsion energy.
>>> print H2OH2O.nuclear_repulsion_energy()
36.6628478528
"""
e = 0.0
for at1 in range(self.natom()):
for at2 in range(self.natom()):
if at2 < at1:
Zi = self.Z(at1)
Zj = self.Z(at2)
dist = distance(self.xyz(at1), self.xyz(at2))
e += Zi * Zj / dist
return e
[docs] def nuclear_repulsion_energy_deriv1(self):
"""Computes nuclear repulsion energy derivatives
>>> print H2OH2O.nuclear_repulsion_energy_deriv1()
[[3.9020946901323774, 2.76201566471991, 0.0], [1.3172905807089021, -2.3486366050337293, 0.0], [-1.8107598525022435, -0.32511212499256564, 0.0], [-1.217656141385739, -2.6120090867576717, 0.0], [-1.0954846384766488, 1.2618710760320282, 2.1130743287465603], [-1.0954846384766488, 1.2618710760320282, -2.1130743287465603]]
"""
de = []
for i in range(self.natom()):
entry = [0.0, 0.0, 0.0]
for j in range(self.natom()):
if i != j:
temp = distance(self.xyz(i), self.xyz(j)) ** 3.0
Zi = self.Z(i)
Zj = self.Z(j)
entry[0] -= (self.x(i) - self.x(j)) * Zi * Zj / temp
entry[1] -= (self.y(i) - self.y(j)) * Zi * Zj / temp
entry[2] -= (self.z(i) - self.z(j)) * Zi * Zj / temp
de.append(entry)
return de
[docs] def nuclear_repulsion_energy_deriv2(self):
""" **NYI** Computes nuclear repulsion energy second derivatives"""
raise FeatureNotImplemented('Molecule::nuclear_repulsion_energy_deriv2') # FINAL
[docs] def set_basis_all_atoms(self, name, role="BASIS"):
"""Assigns basis *name* to all atoms."""
uc = name.upper()
if uc in ['SPECIAL', 'GENERAL', 'CUSTOM']:
# These aren't really basis set specifications, just return.
return
for atom in self.full_atoms:
atom.set_basisset(name, role)
[docs] def set_basis_by_symbol(self, symbol, name, role="BASIS"):
"""Assigns basis *name* to all *symbol* atoms."""
for atom in self.full_atoms:
if symbol.upper() == atom.symbol():
atom.set_basisset(name, role)
[docs] def clear_basis_all_atoms(self):
"""Remove all basis information from atoms."""
for atom in self.full_atoms:
atom.PYbasissets = OrderedDict()
[docs] def set_basis_by_number(self, number, name, role="BASIS"):
"""Assigns basis *name* to atom number *number* (0-indexed, excludes dummies)."""
# change from libmints to 0-indexing and to real/ghost numbering, dummies not included (libmints >= error)
if number >= self.natom():
raise ValidationError("Molecule::set_basis_by_number: Basis specified for atom %d, but there are only %d atoms in this molecule." % \
(number, self.natom()))
self.atoms[number].set_basisset(name, role)
[docs] def set_basis_by_label(self, label, name, role="BASIS"):
"""Assigns basis *name* to all atoms with *label*."""
for atom in self.full_atoms:
if label.upper() == atom.label():
atom.set_basisset(name, role)
[docs] def set_shell_by_number(self, number, bshash, role="BASIS"):
"""Assigns BasisSet *bshash* to atom number *number* (0-indexed, excludes dummies)."""
self.lock_frame = False
if number >= self.natom():
raise ValidationError("Molecule::set_shell_by_number: Basis specified for atom %d, but there are only %d atoms in this molecule." % \
(number, self.natom()))
self.atoms[number].set_shell(bshash, role)
[docs] def nfrozen_core(self, depth=False):
"""Number of frozen core for molecule given freezing state.
>>> print H2OH2O.nfrozen_core()
2
"""
if depth == False or depth.upper() == 'FALSE':
return 0
elif depth == True or depth.upper() == 'TRUE':
# Freeze the number of core electrons corresponding to the
# nearest previous noble gas atom. This means that the 4p block
# will still have 3d electrons active. Alkali earth atoms will
# have one valence electron in this scheme.
nfzc = 0
for A in range(self.natom()):
if self.Z(A) > 2:
nfzc += 1
if self.Z(A) > 10:
nfzc += 4
if self.Z(A) > 18:
nfzc += 4
if self.Z(A) > 36:
nfzc += 9
if self.Z(A) > 54:
nfzc += 9
if self.Z(A) > 86:
nfzc += 16
if self.Z(A) > 108:
raise ValidationError("Molecule::nfrozen_core: Invalid atomic number")
return nfzc
else:
raise ValidationError("Molecule::nfrozen_core: Frozen core '%s' is not supported, options are {true, false}." % (depth))
# <<< Involved Methods for Frame >>>
[docs] def translate(self, r):
"""Translates molecule by r.
>>> H2OH2O.translate([1.0, 1.0, 0.0])
"""
temp = [None, None, None]
for at in range(self.nallatom()):
temp = scale(self.full_atoms[at].compute(), self.input_units_to_au)
temp = add(temp, r)
temp = scale(temp, 1.0 / self.input_units_to_au)
self.full_atoms[at].set_coordinates(temp[0], temp[1], temp[2])
[docs] def center_of_mass(self):
"""Computes center of mass of molecule (does not translate molecule).
>>> H2OH2O.center_of_mass()
[-0.12442647346606871, 0.00038657002584110707, 0.0]
"""
ret = [0.0, 0.0, 0.0]
total_m = 0.0
for at in range(self.natom()):
m = self.mass(at)
ret = add(ret, scale(self.xyz(at), m))
total_m += m
ret = scale(ret, 1.0 / total_m)
return ret
[docs] def move_to_com(self):
"""Moves molecule to center of mass
"""
com = scale(self.center_of_mass(), -1.0)
self.translate(com)
[docs] def set_com_fixed(self, _fix=True):
""" **NYI** Fix the center of mass at its current frame.
Not used in libmints so not implemented.
"""
raise FeatureNotImplemented('Molecule::set_com_fixed') # FINAL
[docs] def inertia_tensor(self):
"""Compute inertia tensor.
>>> print H2OH2O.inertia_tensor()
[[8.704574864178731, -8.828375721817082, 0.0], [-8.828375721817082, 280.82861714077666, 0.0], [0.0, 0.0, 281.249500988553]]
"""
tensor = [[0, 0, 0], [0, 0, 0], [0, 0, 0]]
for i in range(self.natom()):
# I(alpha, alpha)
tensor[0][0] += self.mass(i) * (self.y(i) * self.y(i) + self.z(i) * self.z(i))
tensor[1][1] += self.mass(i) * (self.x(i) * self.x(i) + self.z(i) * self.z(i))
tensor[2][2] += self.mass(i) * (self.x(i) * self.x(i) + self.y(i) * self.y(i))
# I(alpha, beta)
tensor[0][1] -= self.mass(i) * self.x(i) * self.y(i)
tensor[0][2] -= self.mass(i) * self.x(i) * self.z(i)
tensor[1][2] -= self.mass(i) * self.y(i) * self.z(i)
# mirror
tensor[1][0] = tensor[0][1]
tensor[2][0] = tensor[0][2]
tensor[2][1] = tensor[1][2]
# Check the elements for zero and make them a hard zero.
for i in range(3):
for j in range(3):
if math.fabs(tensor[i][j]) < ZERO:
tensor[i][j] = 0.0
return tensor
[docs] def rotational_constants(self, tol=FULL_PG_TOL):
"""Compute the rotational constants and return them in wavenumbers"""
evals, evecs = diagonalize3x3symmat(self.inertia_tensor())
evals = sorted(evals)
isLinear = True if evals[0] < ZERO else False
isOne = True if evals[1] < ZERO else False
isAtom = True if evals[2] < ZERO else False
im_amuA = psi_bohr2angstroms * psi_bohr2angstroms
im_ghz = psi_h * psi_na * 1E14 / (8.0 * math.pi * math.pi * psi_bohr2angstroms * psi_bohr2angstroms)
im_mhz = im_ghz * 1000
im_cm = im_ghz * 1E7 / psi_c
text = " Moments of Inertia and Rotational Constants\n\n"
text += ' %-12s %3s %16.8f %3s %16.8f %3s %16.8f\n' % \
('[amu B^2]', 'I_A', evals[0], 'I_B', evals[1], 'I_C', evals[2])
text += ' %-12s %3s %16.8f %3s %16.8f %3s %16.8f\n' % \
('[amu A^2]', 'I_A', evals[0] * im_amuA, 'I_B', evals[1] * im_amuA, 'I_C', evals[2] * im_amuA)
text += ' %-12s %3s %16s %3s %16s %3s %16s\n' % ('[GHz]', \
'A', '%16.8f' % (im_ghz / evals[0]) if not isLinear else '*****', \
'B', '%16.8f' % (im_ghz / evals[1]) if not isOne else '*****', \
'C', '%16.8f' % (im_ghz / evals[2]) if not isAtom else '*****')
text += ' %-12s %3s %16s %3s %16s %3s %16s\n' % ('[MHz]', \
'A', '%16.8f' % (im_mhz / evals[0]) if not isLinear else '*****', \
'B', '%16.8f' % (im_mhz / evals[1]) if not isOne else '*****', \
'C', '%16.8f' % (im_mhz / evals[2]) if not isAtom else '*****')
text += ' %-12s %3s %16s %3s %16s %3s %16s\n' % ('[cm^-1]', \
'A', '%16.8f' % (im_cm / evals[0]) if not isLinear else '*****', \
'B', '%16.8f' % (im_cm / evals[1]) if not isOne else '*****', \
'C', '%16.8f' % (im_cm / evals[2]) if not isAtom else '*****')
print(text)
# TODO outfile
rot_const = []
rot_const.append(im_cm / evals[0] if not isLinear else None)
rot_const.append(im_cm / evals[1] if not isOne else None)
rot_const.append(im_cm / evals[2] if not isAtom else None)
return rot_const
[docs] def rotor_type(self, tol=FULL_PG_TOL):
"""Returns the rotor type.
>>> H2OH2O.rotor_type()
RT_ASYMMETRIC_TOP
"""
rot_const = self.rotational_constants()
for i in range(3):
if rot_const[i] == None:
rot_const[i] = 0.0
# Determine degeneracy of rotational constants.
degen = 0
for i in range(2):
for j in range(i + 1, 3):
if degen >= 2:
continue
rabs = math.fabs(rot_const[i] - rot_const[j])
tmp = rot_const[i] if rot_const[i] > rot_const[j] else rot_const[j]
if rabs > ZERO:
rel = rabs / tmp
else:
rel = 0.0
if rel < tol:
degen += 1
#print "\tDegeneracy is %d\n" % (degen)
# Determine rotor type
if self.natom() == 1:
rotor_type = 'RT_ATOM'
elif rot_const[0] == 0.0:
rotor_type = 'RT_LINEAR' # 0 < IB == IC inf > B == C
elif degen == 2:
rotor_type = 'RT_SPHERICAL_TOP' # IA == IB == IC A == B == C
elif degen == 1:
rotor_type = 'RT_SYMMETRIC_TOP' # IA < IB == IC A > B == C --or--
# IA == IB < IC A == B > C
else:
rotor_type = 'RT_ASYMMETRIC_TOP' # IA < IB < IC A > B > C
return rotor_type
[docs] def rotate(self, R):
"""Rotates the molecule using rotation matrix *R*.
>>> H2OH2O.rotate([[0,-1,0],[-1,0,0],[0,0,1]])
"""
new_geom = zero(3, self.natom())
geom = self.geometry()
new_geom = mult(geom, R)
self.set_geometry(new_geom)
[docs] def rotate_full(self, R):
"""Rotates the full molecule using rotation matrix *R*.
>>> H2OH2O.rotate_full([[0,-1,0],[-1,0,0],[0,0,1]])
"""
new_geom = zero(3, self.nallatom())
geom = self.full_geometry()
new_geom = mult(geom, R)
self.set_full_geometry(new_geom)
[docs] def orientation_fixed(self):
"""Get whether or not orientation is fixed.
>>> H2OH2O.orientation_fixed()
True
"""
return self.PYfix_orientation
[docs] def fix_orientation(self, _fix=True):
"""Fix the orientation at its current frame
(method name in libmints is set_orientation_fixed)
"""
if _fix:
self.PYfix_orientation = True # tells update_geometry() not to change orientation
# Compute original cartesian coordinates - code coped from update_geometry()
self.atoms = []
for item in self.full_atoms:
item.invalidate()
for fr in range(self.nfragments()):
for at in range(self.fragments[fr][0], self.fragments[fr][1] + 1):
self.full_atoms[at].compute()
self.full_atoms[at].set_ghosted(self.fragment_types[fr] == 'Ghost')
if self.full_atoms[at].symbol() != 'X':
self.atoms.append(self.full_atoms[at])
else: # release orientation to be free
self.PYfix_orientation = False
# <<< Methods for Saving >>>
[docs] def save_string_xyz(self, save_ghosts=True):
"""Save a string for a XYZ-style file.
>>> H2OH2O.save_string_xyz()
6
_
O -1.551007000000 -0.114520000000 0.000000000000
H -1.934259000000 0.762503000000 0.000000000000
H -0.599677000000 0.040712000000 0.000000000000
O 1.350625000000 0.111469000000 0.000000000000
H 1.680398000000 -0.373741000000 -0.758561000000
H 1.680398000000 -0.373741000000 0.758561000000
"""
factor = 1.0 if self.PYunits == 'Angstrom' else psi_bohr2angstroms
N = self.natom()
if not save_ghosts:
N = 0
for i in range(self.natom()):
if self.Z(i):
N += 1
text = "%d\n\n" % (N)
for i in range(self.natom()):
[x, y, z] = self.atoms[i].compute()
if save_ghosts or self.Z(i):
text += '%2s %17.12f %17.12f %17.12f\n' % ((self.symbol(i) if self.Z(i) else "Gh"), \
x * factor, y * factor, z * factor)
return text
[docs] def save_xyz(self, filename, save_ghosts=True):
"""Save an XYZ file.
>>> H2OH2O.save_xyz('h2o.xyz')
"""
outfile = open(filename, 'w')
outfile.write(self.save_string_xyz(save_ghosts))
outfile.close()
[docs] def save_to_checkpoint(self, chkpt, prefix=""):
""" **NYI** Save information to checkpoint file
(method name in libmints is save_to_chkpt)
"""
raise FeatureNotImplemented('Molecule::save_to_checkpoint') # FINAL
# <<< Methods for Symmetry >>>
[docs] def has_symmetry_element(self, op, tol=DEFAULT_SYM_TOL):
""" **NYI** Whether molecule satisfies the vector symmetry
operation *op*. Not used by libmints.
"""
raise FeatureNotImplemented('Molecule::has_symmetry_element') # FINAL
for i in range(self.natom()):
result = naivemult(self.xyz(i), op)
atom = self.atom_at_position(result, tol)
if atom != -1:
if not self.atoms[atom].is_equivalent_to(self.atoms[i]):
return False
else:
return False
return True
[docs] def point_group(self):
"""Returns the point group (object) if set"""
if self.pg is None:
raise ValidationError("Molecule::point_group: Molecular point group has not been set.")
return self.pg
[docs] def set_point_group(self, pg):
"""Set the point group to object *pg* """
self.pg = pg
# Call this here, the programmer will forget to call it, as I have many times.
self.form_symmetry_information()
[docs] def set_full_point_group(self, tol=FULL_PG_TOL):
"""Determine and set FULL point group. self.PYfull_pg_n is highest
order n in Cn. 0 for atoms or infinity.
"""
verbose = 1 # TODO
# Get cartesian geometry and put COM at origin
geom = self.geometry()
com = self.center_of_mass()
for at in range(self.natom()):
geom[at][0] += -com[0]
geom[at][1] += -com[1]
geom[at][2] += -com[2]
# Get rotor type
rotor = self.rotor_type(tol)
if verbose > 2:
print(""" Rotor type : %s""" % (rotor))
# Get the D2h point group from Jet and Ed's code: c1 ci c2 cs d2 c2v c2h d2h
# and ignore the user-specified subgroup in this case.
pg = self.find_highest_point_group(tol)
d2h_subgroup = pg.symbol()
if verbose > 2:
print(""" D2h_subgroup : %s""" % (self.point_group().symbol()))
# Check inversion
v3_zero = [0.0, 0.0, 0.0]
op_i = self.has_inversion(v3_zero, tol)
if verbose > 2:
print(""" Inversion symmetry : %s""" % ('yes' if op_i else 'no'))
x_axis = [1, 0, 0]
y_axis = [0, 1, 0]
z_axis = [0, 0, 1]
rot_axis = [0.0, 0.0, 0.0]
if rotor == 'RT_ATOM': # atoms
self.full_pg = 'ATOM'
self.PYfull_pg_n = 0
elif rotor == 'RT_LINEAR': # linear molecules
self.full_pg = 'D_inf_h' if op_i else 'C_inf_v'
self.PYfull_pg_n = 0
elif rotor == 'RT_SPHERICAL_TOP': # spherical tops
if not op_i: # The only spherical top without inversion is Td.
self.full_pg = 'Td'
self.PYfull_pg_n = 3
else: # Oh or Ih ?
# Oh has a S4 and should be oriented properly already.
test_mat = matrix_3d_rotation(geom, z_axis, math.pi / 2.0, True)
op_symm = equal_but_for_row_order(geom, test_mat, tol)
if verbose > 2:
print(""" S4z : %s""" % ('yes' if op_symm else 'no'))
if op_symm:
self.full_pg = 'Oh'
self.PYfull_pg_n = 4
else:
self.full_pg = 'Ih'
self.PYfull_pg_n = 5
elif rotor == 'RT_ASYMMETRIC_TOP': # asymmetric tops cannot exceed D2h, right?
if d2h_subgroup == 'c1':
self.full_pg = 'C1'
self.PYfull_pg_n = 1
elif d2h_subgroup == 'ci':
self.full_pg = 'Ci'
self.PYfull_pg_n = 1
elif d2h_subgroup == 'c2':
self.full_pg = 'Cn'
self.PYfull_pg_n = 2
elif d2h_subgroup == 'cs':
self.full_pg = 'Cs'
self.PYfull_pg_n = 1
elif d2h_subgroup == 'd2':
self.full_pg = 'Dn'
self.PYfull_pg_n = 2
elif d2h_subgroup == 'c2v':
self.full_pg = 'Cnv'
self.PYfull_pg_n = 2
elif d2h_subgroup == 'c2h':
self.full_pg = 'Cnh'
self.PYfull_pg_n = 2
elif d2h_subgroup == 'd2h':
self.full_pg = 'Dnh'
self.PYfull_pg_n = 2
else:
print(""" Warning: Cannot determine point group.""")
elif rotor in ['RT_SYMMETRIC_TOP', 'RT_PROLATE_SYMMETRIC_TOP', 'RT_OBLATE_SYMMETRIC_TOP']:
# Find principal axis that is unique and make it z-axis.
It = self.inertia_tensor()
I_evals, I_evecs = diagonalize3x3symmat(It)
ev_list = list(zip(I_evals, transpose(I_evecs))) # eigenvectors are cols of I_evecs
ev_list.sort(key=lambda tup: tup[0], reverse=False)
I_evals, I_evecs = zip(*ev_list) # sorted eigenvectors are now rows of I_evecs
if verbose > 2:
print(""" I_evals: %15.10lf %15.10lf %15.10lf""" % (I_evals[0], I_evals[1], I_evals[2]))
unique_axis = 1
if abs(I_evals[0] - I_evals[1]) < tol:
unique_axis = 2
elif abs(I_evals[1] - I_evals[2]) < tol:
unique_axis = 0
# Compute angle between unique axis and the z-axis
old_axis = I_evecs[unique_axis]
ddot = dot(z_axis, old_axis)
if abs(ddot - 1) < 1.0e-10:
phi = 0.0
elif abs(ddot + 1) < 1.0e-10:
phi = math.pi
else:
phi = math.acos(ddot)
# Rotate geometry to put unique axis on the z-axis, if it isn't already.
if abs(phi) > 1.0e-14:
rot_axis = cross(z_axis, old_axis) # right order?
test_mat = matrix_3d_rotation(geom, rot_axis, phi, False)
if verbose > 2:
print(""" Rotating by %lf to get principal axis on z-axis ...""" % (phi))
geom = [row[:] for row in test_mat]
if verbose > 2:
print(""" Geometry to analyze - principal axis on z-axis:""")
for at in range(self.natom()):
print("""%20.15lf %20.15lf %20.15lf""" % (geom[at][0], geom[at][1], geom[at][2]))
print('\n')
# Determine order Cn and Sn of principal axis.
Cn_z = matrix_3d_rotation_Cn(geom, z_axis, False, tol)
if verbose > 2:
print(""" Highest rotation axis (Cn_z) : %d""" % (Cn_z))
Sn_z = matrix_3d_rotation_Cn(geom, z_axis, True, tol)
if verbose > 2:
print(""" Rotation axis (Sn_z) : %d""" % (Sn_z))
# Check for sigma_h (xy plane).
op_sigma_h = False
for at in range(self.natom()):
if abs(geom[at][2]) < tol:
continue # atom is in xy plane
else:
test_atom = [geom[at][0], geom[at][1], -1 * geom[at][2]]
if not atom_present_in_geom(geom, test_atom, tol):
break
else:
op_sigma_h = True
if verbose > 2:
print(""" sigma_h : %s""" % ('yes' if op_sigma_h else 'no'))
# Rotate one off-axis atom to the yz plane and check for sigma_v's.
for at in range(self.natom()):
dist_from_z = math.sqrt(geom[at][0] * geom[at][0] + geom[at][1] * geom[at][1])
if abs(dist_from_z) > tol:
pivot_atom_i = at
break
if pivot_atom_i == self.natom(): # needs to be in else clause?
raise ValidationError("Molecule::set_full_point_group: Not a linear molecule but could not find off-axis atom.")
# Rotate around z-axis to put pivot atom in the yz plane
xy_point = normalize([geom[pivot_atom_i][0], geom[pivot_atom_i][1], 0])
ddot = dot(y_axis, xy_point)
if abs(ddot - 1) < 1.0e-10:
phi = 0.0
elif abs(ddot + 1) < 1.0e-10:
phi = math.pi
else:
phi = math.acos(ddot)
is_D = False
if abs(phi) > 1.0e-14:
test_mat = matrix_3d_rotation(geom, z_axis, phi, False)
if verbose > 2:
print(""" Rotating by %8.3e to get atom %d in yz-plane ...""" % (phi, pivot_atom_i + 1))
geom = [row[:] for row in test_mat]
# Check for sigma_v (yz plane).
op_sigma_v = False
for at in range(self.natom()):
if abs(geom[at][0]) < tol:
continue # atom is in yz plane
else:
test_atom = [-1 * geom[at][0], geom[at][1], geom[at][2]]
if not atom_present_in_geom(geom, test_atom, tol):
break
else:
#if at == self.natom():
op_sigma_v = True
if verbose > 2:
print(""" sigma_v : %s""" % ('yes' if op_sigma_v else 'no'))
print(""" geom to analyze - one atom in yz plane:""")
for at in range(self.natom()):
print("""%20.15lf %20.15lf %20.15lf""" % (geom[at][0], geom[at][1], geom[at][2]))
print('\n')
# Check for perpendicular C2's.
# Loop through pairs of atoms to find c2 axis candidates.
for i in range(self.natom()):
A = [geom[i][0], geom[i][1], geom[i][2]]
AdotA = dot(A, A)
for j in range(at):
if self.Z(at) != self.Z(j):
continue # ensure same atomic number
B = [geom[j][0], geom[j][1], geom[j][2]] # ensure same distance from com
if abs(AdotA - dot(B, B)) > 1.0e-6:
continue # loose check
# Use sum of atom vectors as axis if not 0.
axis = add(A, B)
if norm(axis) < 1.0e-12:
continue
axis = normalize(axis)
# Check if axis is perpendicular to z-axis.
if abs(dot(axis, z_axis)) > 1.0e-6:
continue
# Do the thorough check for C2.
if matrix_3d_rotation_Cn(geom, axis, False, tol, 2) == 2:
is_D = True
if verbose > 2:
print(""" perp. C2's : %s""" % ('yes' if is_D else 'no'))
# Now assign point groups! Sn first.
if Sn_z == 2 * Cn_z and not is_D:
self.full_pg = 'Sn'
self.PYfull_pg_n = Sn_z
return
if is_D: # has perpendicular C2's
if op_sigma_h and op_sigma_v: # Dnh : Cn, nC2, sigma_h, nSigma_v
self.full_pg = 'Dnh'
self.PYfull_pg_n = Cn_z
elif Sn_z == 2 * Cn_z: # Dnd : Cn, nC2, S2n axis coincident with Cn
self.full_pg = 'Dnd'
self.PYfull_pg_n = Cn_z
else: # Dn : Cn, nC2
self.full_pg = 'Dn'
self.PYfull_pg_n = Cn_z
else: # lacks perpendicular C2's
if op_sigma_h and Sn_z == Cn_z: # Cnh : Cn, sigma_h, Sn coincident with Cn
self.full_pg = 'Cnh'
self.PYfull_pg_n = Cn_z
elif op_sigma_v: # Cnv : Cn, nCv
self.full_pg = 'Cnv'
self.PYfull_pg_n = Cn_z
else: # Cn : Cn
self.full_pg = 'Cn'
self.PYfull_pg_n = Cn_z
return
[docs] def has_inversion(self, origin, tol=DEFAULT_SYM_TOL):
"""Does the molecule have an inversion center at origin
"""
for i in range(self.natom()):
inverted = sub(origin, sub(self.xyz(i), origin))
atom = self.atom_at_position(inverted, tol)
if atom < 0 or not self.atoms[atom].is_equivalent_to(self.atoms[i]):
return False
return True
[docs] def is_plane(self, origin, uperp, tol=DEFAULT_SYM_TOL):
"""Is a plane?
"""
for i in range(self.natom()):
A = sub(self.xyz(i), origin)
Apar = scale(uperp, dot(uperp, A))
Aperp = sub(A, Apar)
A = add(sub(Aperp, Apar), origin)
atom = self.atom_at_position(A, tol)
if atom < 0 or not self.atoms[atom].is_equivalent_to(self.atoms[i]):
return False
return True
[docs] def is_axis(self, origin, axis, order, tol=DEFAULT_SYM_TOL):
"""Is *axis* an axis of order *order* with respect to *origin*?
"""
for i in range(self.natom()):
A = sub(self.xyz(i), origin)
for j in range(1, order):
R = A
R = rotate(R, j * 2.0 * math.pi / order, axis)
R = add(R, origin)
atom = self.atom_at_position(R, tol)
if atom < 0 or not self.atoms[atom].is_equivalent_to(self.atoms[i]):
return False
return True
[docs] def is_linear_planar(self, tol=DEFAULT_SYM_TOL):
"""Is the molecule linear, or planar?
>>> print H2OH2O.is_linear_planar()
(False, False)
"""
linear = None
planar = None
if self.natom() < 3:
linear = True
planar = True
return linear, planar
# find three atoms not on the same line
A = self.xyz(0)
B = self.xyz(1)
BA = sub(B, A)
BA = normalize(BA)
CA = [None, None, None]
min_BAdotCA = 1.0
for i in range(2, self.natom()):
tmp = sub(self.xyz(i), A)
tmp = normalize(tmp)
if math.fabs(dot(BA, tmp)) < min_BAdotCA:
CA = copy.deepcopy(tmp)
min_BAdotCA = math.fabs(dot(BA, tmp))
if min_BAdotCA >= 1.0 - tol:
linear = True
planar = True
return linear, planar
linear = False
if self.natom() < 4:
planar = True
return linear, planar
# check for nontrivial planar molecules
BAxCA = normalize(cross(BA, CA))
for i in range(2, self.natom()):
tmp = sub(self.xyz(i), A)
if math.fabs(dot(tmp, BAxCA)) > tol:
planar = False
return linear, planar
planar = True
return linear, planar
@staticmethod
[docs] def like_world_axis(axis, worldxaxis, worldyaxis, worldzaxis):
"""Returns which worldaxis *axis* most overlaps with.
Inverts axis when indicated.
"""
like = None
xlikeness = math.fabs(dot(axis, worldxaxis))
ylikeness = math.fabs(dot(axis, worldyaxis))
zlikeness = math.fabs(dot(axis, worldzaxis))
if (xlikeness - ylikeness) > 1.0E-12 and (xlikeness - zlikeness) > 1.0E-12:
like = 'XAxis'
if dot(axis, worldxaxis) < 0:
axis = scale(axis, -1.0)
elif (ylikeness - zlikeness) > 1.0E-12:
like = 'YAxis'
if dot(axis, worldyaxis) < 0:
axis = scale(axis, -1.0)
else:
like = 'ZAxis'
if dot(axis, worldzaxis) < 0:
axis = scale(axis, -1.0)
return like, axis
[docs] def find_point_group(self, tol=DEFAULT_SYM_TOL):
"""Find computational molecular point group, user can override
this with the "symmetry" keyword. Result is highest D2h subgroup
attendant on molecule and allowed by the user.
"""
pg = self.find_highest_point_group(tol) # D2h subgroup
user = self.symmetry_from_input()
if user is not None:
# Need to handle the cases that the user only provides C2, C2v, C2h, Cs.
# These point groups need directionality.
# Did the user provide directionality? If they did, the last letter would be x, y, or z
# Directionality given, assume the user is smart enough to know what they're doing.
user_specified_direction = True if user[-1] in ['X', 'x', 'Y', 'y', 'Z', 'z'] else False
if self.symmetry_from_input() != pg.symbol():
user = PointGroup(self.symmetry_from_input())
if user_specified_direction:
# Assume the user knows what they're doing.
# Make sure user is subgroup of pg
if (pg.bits() & user.bits()) != user.bits():
raise ValidationError("Molecule::find_point_group: User specified point group (%s) is not a subgroup of the highest detected point group (%s)" % (PointGroup.bits_to_full_name(user.bits()), PointGroup.bits_to_full_name(pg.bits())))
else:
similars, count = similar(user.bits())
found = False
for typ in range(count):
# If what the user specified and the similar type
# matches the full point group we've got a match
if (similars[typ] & pg.bits()) == similars[typ]:
found = True
break
if found:
# Construct a point group object using the found similar
user = PointGroup(similars[typ])
else:
raise ValidationError("Molecule::find_point_group: User specified point group (%s) is not a subgroup of the highest detected point group (%s). If this is because the symmetry increased, try to start the calculation again from the last geometry, after checking any symmetry-dependent input, such as DOCC." % (PointGroup.bits_to_full_name(user.bits()), PointGroup.bits_to_full_name(pg.bits())))
# If we make it here, what the user specified is good.
pg = user
return pg
[docs] def reset_point_group(self, pgname):
"""Override symmetry from outside the molecule string"""
self.PYsymmetry_from_input = pgname.lower()
self.set_point_group(self.find_point_group())
[docs] def find_highest_point_group(self, tol=DEFAULT_SYM_TOL):
"""Find the highest D2h point group from Jet and Ed's code: c1
ci c2 cs d2 c2v c2h d2h. Ignore the user-specified subgroup in
this case.
"""
pg_bits = 0
# The order of the next 2 arrays MUST match!
symm_bit = [
SymmOps['C2_z'],
SymmOps['C2_y'],
SymmOps['C2_x'],
SymmOps['i'],
SymmOps['Sigma_xy'],
SymmOps['Sigma_xz'],
SymmOps['Sigma_yz']]
symm_func = [
SymmetryOperation.c2_z,
SymmetryOperation.c2_y,
SymmetryOperation.c2_x,
SymmetryOperation.i,
SymmetryOperation.sigma_xy,
SymmetryOperation.sigma_xz,
SymmetryOperation.sigma_yz]
symop = SymmetryOperation()
matching_atom = -1
# Only needs to detect the 8 symmetry operations
for g in range(7):
# Call the function pointer
symm_func[g](symop)
found = True
for at in range(self.natom()):
op = [symop[0][0], symop[1][1], symop[2][2]]
pos = naivemult(self.xyz(at), op)
matching_atom = self.atom_at_position(pos, tol)
if matching_atom >= 0:
if not self.atoms[at].is_equivalent_to(self.atoms[matching_atom]):
found = False
break
else:
found = False
break
if found:
pg_bits |= symm_bit[g]
return PointGroup(pg_bits)
[docs] def symmetry_frame(self, tol=DEFAULT_SYM_TOL):
"""Determine symmetry reference frame. If noreorient is not set,
this is the rotation matrix applied to the geometry in update_geometry.
>>> print H2OH2O.symmetry_frame()
[[1.0, -0.0, 0.0], [0.0, 1.0, 0.0], [0.0, -0.0, 1.0]]
"""
com = self.center_of_mass()
worldxaxis = [1.0, 0.0, 0.0]
worldyaxis = [0.0, 1.0, 0.0]
worldzaxis = [0.0, 0.0, 1.0]
sigma = [0.0, 0.0, 0.0]
sigmav = [0.0, 0.0, 0.0]
c2axis = [0.0, 0.0, 0.0]
c2axisperp = [0.0, 0.0, 0.0]
linear, planar = self.is_linear_planar(tol)
have_inversion = self.has_inversion(com, tol)
# check for C2 axis
have_c2axis = False
if self.natom() < 2:
have_c2axis = True
c2axis = [0.0, 0.0, 1.0]
elif linear:
have_c2axis = True
c2axis = sub(self.xyz(1), self.xyz(0))
c2axis = normalize(c2axis)
elif planar and have_inversion:
# there is a c2 axis that won't be found using the usual
# algorithm. find two noncolinear atom-atom vectors (we know
# that linear == 0)
BA = sub(self.xyz(1), self.xyz(0))
BA = normalize(BA)
for i in range(2, self.natom()):
CA = sub(self.xyz(i), self.xyz(0))
CA = normalize(CA)
BAxCA = cross(BA, CA)
if norm(BAxCA) > tol:
have_c2axis = True
BAxCA = normalize(BAxCA)
c2axis = copy.deepcopy(BAxCA)
break
else:
# loop through pairs of atoms to find c2 axis candidates
for i in range(self.natom()):
A = sub(self.xyz(i), com)
AdotA = dot(A, A)
for j in range(i + 1):
# the atoms must be identical
if not self.atoms[i].is_equivalent_to(self.atoms[j]):
continue
B = sub(self.xyz(j), com)
# the atoms must be the same distance from the com
if math.fabs(AdotA - dot(B, B)) > tol:
continue
axis = add(A, B)
# atoms colinear with the com don't work
if norm(axis) < tol:
continue
axis = normalize(axis)
if self.is_axis(com, axis, 2, tol):
have_c2axis = True
c2axis = copy.deepcopy(axis)
break
else:
continue
break
# symmframe found c2axis
c2like = 'ZAxis'
if have_c2axis:
# try to make the sign of the axis correspond to one of the world axes
c2like, c2axis = self.like_world_axis(c2axis, worldxaxis, worldyaxis, worldzaxis)
# check for c2 axis perp to first c2 axis
have_c2axisperp = False
if have_c2axis:
if self.natom() < 2:
have_c2axisperp = True
c2axisperp = [1.0, 0.0, 0.0]
elif linear:
if have_inversion:
have_c2axisperp = True
c2axisperp = perp_unit(c2axis, [0.0, 0.0, 1.0])
else:
# loop through paris of atoms to find c2 axis candidates
for i in range(self.natom()):
A = sub(self.xyz(i), com)
AdotA = dot(A, A)
for j in range(i):
# the atoms must be identical
if not self.atoms[i].is_equivalent_to(self.atoms[j]):
continue
B = sub(self.xyz(j), com)
# the atoms must be the same distance from the com
if math.fabs(AdotA - dot(B, B)) > tol:
continue
axis = add(A, B)
# atoms colinear with the com don't work
if norm(axis) < tol:
continue
axis = normalize(axis)
# if axis is not perp continue
if math.fabs(dot(axis, c2axis)) > tol:
continue
if self.is_axis(com, axis, 2, tol):
have_c2axisperp = True
c2axisperp = copy.deepcopy(axis)
break
else:
continue
break
# symmframe found c2axisperp
if have_c2axisperp:
# try to make the sign of the axis correspond to one of the world axes
c2perplike, c2axisperp = self.like_world_axis(c2axisperp, worldxaxis, worldyaxis, worldzaxis)
# try to make c2axis the z axis
if c2perplike == 'ZAxis':
tmpv = copy.deepcopy(c2axisperp)
c2axisperp = copy.deepcopy(c2axis)
c2axis = copy.deepcopy(tmpv)
c2perplike = c2like
c2like = 'ZAxis'
if c2like != 'ZAxis':
if c2like == 'XAxis':
c2axis = cross(c2axis, c2axisperp)
else:
c2axis = cross(c2axisperp, c2axis)
c2like, c2axis = self.like_world_axis(c2axis, worldxaxis, worldyaxis, worldzaxis)
# try to make c2axisperplike the x axis
if c2perplike == 'YAxis':
c2axisperp = cross(c2axisperp, c2axis)
c2perplike, c2axisperp = self.like_world_axis(c2axisperp, worldxaxis, worldyaxis, worldzaxis)
# Check for vertical plane
have_sigmav = False
if have_c2axis:
if self.natom() < 2:
have_sigmav = True
sigmav = copy.deepcopy(c2axisperp)
elif linear:
have_sigmav = True
if have_c2axisperp:
sigmav = copy.deepcopy(c2axisperp)
else:
sigmav = perp_unit(c2axis, [0.0, 0.0, 1.0])
else:
# loop through pairs of atoms to find sigma v plane candidates
for i in range(self.natom()):
A = sub(self.xyz(i), com)
AdotA = dot(A, A)
# the second atom can equal i because i might be in the plane
for j in range(i + 1):
# the atoms must be identical
if not self.atoms[i].is_equivalent_to(self.atoms[j]):
continue
B = sub(self.xyz(j), com)
# the atoms must be the same distance from the com
if math.fabs(AdotA - dot(B, B)) > tol:
continue
inplane = add(B, A)
norm_inplane = norm(inplane)
if norm_inplane < tol:
continue
inplane = scale(inplane, 1.0 / norm_inplane)
perp = cross(c2axis, inplane)
norm_perp = norm(perp)
if norm_perp < tol:
continue
perp = scale(perp, 1.0 / norm_perp)
if self.is_plane(com, perp, tol):
have_sigmav = True
sigmav = copy.deepcopy(perp)
break
else:
continue
break
# symmframe found sigmav
if have_sigmav:
# try to make the sign of the oop vec correspond to one of the world axes
sigmavlike, sigmav = self.like_world_axis(sigmav, worldxaxis, worldyaxis, worldzaxis)
# Choose sigmav to be the world x axis, if possible
if c2like == 'ZAxis' and sigmavlike == 'YAxis':
sigmav = cross(sigmav, c2axis)
elif c2like == 'YAxis' and sigmavlike == 'ZAxis':
sigmav = cross(c2axis, sigmav)
# under certain conditions i need to know if there is any sigma plane
have_sigma = False
if not have_inversion and not have_c2axis:
if planar:
# find two noncolinear atom-atom vectors
# we know that linear==0 since !have_c2axis
BA = sub(self.xyz(1), self.xyz(0))
BA = normalize(BA)
for i in range(2, self.natom()):
CA = sub(self.xyz(i), self.xyz(0))
CA = normalize(CA)
BAxCA = cross(BA, CA)
if norm(BAxCA) > tol:
have_sigma = True
BAxCA = normalize(BAxCA)
sigma = copy.deepcopy(BAxCA)
break
else:
# loop through pairs of atoms to contruct trial planes
for i in range(self.natom()):
A = sub(self.xyz(i), com)
AdotA = dot(A, A)
for j in range(i):
# the atoms must be identical
if not self.atoms[i].is_equivalent_to(self.atoms[j]):
continue
B = sub(self.xyz(j), com)
BdotB = dot(B, B)
# the atoms must be the same distance from the com
if math.fabs(AdotA - BdotB) > tol:
continue
perp = sub(B, A)
norm_perp = norm(perp)
if norm_perp < tol:
continue
perp = scale(perp, 1.0 / norm_perp)
if self.is_plane(com, perp, tol):
have_sigma = True
sigma = copy.deepcopy(perp)
break
else:
continue
break
# foundsigma
if have_sigma:
# try to make the sign of the oop vec correspond to one of the world axes
xlikeness = math.fabs(dot(sigma, worldxaxis))
ylikeness = math.fabs(dot(sigma, worldyaxis))
zlikeness = math.fabs(dot(sigma, worldzaxis))
if xlikeness > ylikeness and xlikeness > zlikeness:
if dot(sigma, worldxaxis) < 0:
sigma = scale(sigma, -1.0)
elif ylikeness > zlikeness:
if dot(sigma, worldyaxis) < 0:
sigma = scale(sigma, -1.0)
else:
if dot(sigma, worldzaxis) < 0:
sigma = scale(sigma, -1.0)
# Find the three axes for the symmetry frame
xaxis = copy.deepcopy(worldxaxis)
zaxis = copy.deepcopy(worldzaxis)
if have_c2axis:
zaxis = copy.deepcopy(c2axis)
if have_sigmav:
xaxis = copy.deepcopy(sigmav)
elif have_c2axisperp:
xaxis = copy.deepcopy(c2axisperp)
else:
# any axis orthogonal to the zaxis will do
xaxis = perp_unit(zaxis, zaxis)
elif have_sigma:
zaxis = copy.deepcopy(sigma)
xaxis = perp_unit(zaxis, zaxis)
# Clean up our z axis
if math.fabs(zaxis[0]) < NOISY_ZERO:
zaxis[0] = 0.0
if math.fabs(zaxis[1]) < NOISY_ZERO:
zaxis[1] = 0.0
if math.fabs(zaxis[2]) < NOISY_ZERO:
zaxis[2] = 0.0
# Clean up our x axis
if math.fabs(xaxis[0]) < NOISY_ZERO:
xaxis[0] = 0.0
if math.fabs(xaxis[1]) < NOISY_ZERO:
xaxis[1] = 0.0
if math.fabs(xaxis[2]) < NOISY_ZERO:
xaxis[2] = 0.0
# the y is then -x cross z
yaxis = scale(cross(xaxis, zaxis), -1.0)
#print "xaxis %20.14lf %20.14lf %20.14lf" % (xaxis[0], xaxis[1], xaxis[2])
#print "yaxis %20.14lf %20.14lf %20.14lf" % (yaxis[0], yaxis[1], yaxis[2])
#print "zaxis %20.14lf %20.14lf %20.14lf" % (zaxis[0], zaxis[1], zaxis[2])
frame = zero(3, 3)
for i in range(3):
frame[i][0] = xaxis[i]
frame[i][1] = yaxis[i]
frame[i][2] = zaxis[i]
return frame
#print 'nunique', self.PYnunique
#print 'nequiv', self.nequiv
#print 'atom_to_unique', self.PYatom_to_unique
#print 'equiv', self.equiv
[docs] def sym_label(self):
"""Returns the symmetry label"""
if self.pg is None:
self.set_point_group(self.find_point_group())
return self.pg.symbol()
[docs] def irrep_labels(self):
"""Returns the irrep labels"""
if self.pg is None:
self.set_point_group(self.find_point_group())
return [self.pg.char_table().gamma(i).symbol_ns() for i in range(self.pg.char_table().nirrep())]
[docs] def symmetrize(self):
"""Force the molecule to have the symmetry specified in pg.
This is to handle noise coming in from optking.
"""
#raise FeatureNotImplemented('Molecule::symmetrize') # FINAL SYMM
temp = zero(self.natom(), 3)
ct = self.point_group().char_table()
# Obtain atom mapping of atom * symm op to atom
atom_map = compute_atom_map(self)
# Symmetrize the molecule to remove any noise
for at in range(self.natom()):
for g in range(ct.order()):
Gatom = atom_map[at][g]
so = ct.symm_operation(g)
# Full so must be used if molecule is not in standard orientation
temp[at][0] += so[0][0] * self.x(Gatom) / ct.order()
temp[at][0] += so[0][1] * self.y(Gatom) / ct.order()
temp[at][0] += so[0][2] * self.z(Gatom) / ct.order()
temp[at][1] += so[1][0] * self.x(Gatom) / ct.order()
temp[at][1] += so[1][1] * self.y(Gatom) / ct.order()
temp[at][1] += so[1][2] * self.z(Gatom) / ct.order()
temp[at][2] += so[2][0] * self.x(Gatom) / ct.order()
temp[at][2] += so[2][1] * self.y(Gatom) / ct.order()
temp[at][2] += so[2][2] * self.z(Gatom) / ct.order()
# Set the geometry to ensure z-matrix variables get updated
self.set_geometry(temp)
[docs] def schoenflies_symbol(self):
"""Returns the Schoenflies symbol"""
return self.point_group().symbol()
[docs] def valid_atom_map(self, tol=0.01):
"""Check if current geometry fits current point group
"""
np = [0.0, 0.0, 0.0]
ct = self.point_group().char_table()
# loop over all centers
for at in range(self.natom()):
ac = self.xyz(at)
# For each operation in the pointgroup, transform the coordinates of
# center "at" and see which atom it maps into
for g in range(ct.order()):
so = ct.symm_operation(g)
for ii in range(3):
np[ii] = 0
for jj in range(3):
np[ii] += so[ii][jj] * ac[jj]
if self.atom_at_position(np, tol) < 0:
return False
return True
[docs] def full_point_group_with_n(self):
"""Return point group name such as Cnv or Sn."""
return self.full_pg
[docs] def full_pg_n(self):
"""Return n in Cnv, etc.; If there is no n (e.g. Td)
it's the highest-order rotation axis.
"""
return self.PYfull_pg_n
[docs] def get_full_point_group(self):
"""Return point group name such as C3v or S8.
(method name in libmints is full_point_group)
"""
pg_with_n = self.full_pg
if pg_with_n in ['D_inf_h', 'C_inf_v', 'C1', 'Cs', 'Ci', 'Td', 'Oh', 'Ih']:
return pg_with_n # These don't need changes - have no 'n'.
else:
return pg_with_n.replace('n', str(self.PYfull_pg_n), 1)
# <<< Methods for Uniqueness >>> (assume molecular point group has been determined)
[docs] def nunique(self):
"""Return the number of unique atoms."""
return self.PYnunique
[docs] def unique(self, iuniq):
"""Returns the overall number of the iuniq'th unique atom."""
return self.equiv[iuniq][0]
[docs] def nequivalent(self, iuniq):
"""Returns the number of atoms equivalent to iuniq."""
return self.nequiv[iuniq]
[docs] def equivalent(self, iuniq, j):
"""Returns the j'th atom equivalent to iuniq."""
return self.equiv[iuniq][j]
[docs] def atom_to_unique(self, iatom):
"""Converts an atom number to the number of its generating unique atom.
The return value is in [0, nunique).
"""
return self.PYatom_to_unique[iatom]
[docs] def atom_to_unique_offset(self, iatom):
"""Converts an atom number to the offset of this atom
in the list of generated atoms. The unique atom itself is allowed offset 0.
"""
iuniq = self.PYatom_to_unique[iatom]
nequiv = self.nequiv[iuniq]
for i in range(nequiv):
if self.equiv[iuniq][i] == iatom:
return i
raise ValidationError("Molecule::atom_to_unique_offset: I should've found the atom requested...but didn't.")
return -1
[docs] def max_nequivalent(self):
"""Returns the maximum number of equivalent atoms."""
mmax = 0
for i in range(self.nunique()):
if mmax < self.nequivalent(i):
mmax = self.nequivalent(i)
return mmax
[docs]def atom_present_in_geom(geom, b, tol=DEFAULT_SYM_TOL):
"""Function used by set_full_point_group() to scan a given geometry
and determine if an atom is present at a given location.
"""
for i in range(len(geom)):
a = [geom[i][0], geom[i][1], geom[i][2]]
if distance(b, a) < tol:
return True
return False
[docs]def matrix_3d_rotation_Cn(coord, axis, reflect, tol=DEFAULT_SYM_TOL, max_Cn_to_check=-1):
"""Find maximum n in Cn around given axis, i.e., the highest-order rotation axis.
@param coord Matrix : points to rotate - column dim is 3
@param axis Vector3 : axis around which to rotate, does not need to be normalized
@param bool reflect : if true, really look for Sn not Cn
@returns n
"""
# Check all atoms. In future, make more intelligent.
max_possible = len(coord) if max_Cn_to_check == -1 else max_Cn_to_check
Cn = 1 # C1 is there for sure
for n in range(2, max_possible + 1):
rotated_mat = matrix_3d_rotation(coord, axis, 2 * math.pi / n, reflect)
if equal_but_for_row_order(coord, rotated_mat, tol):
Cn = n
return Cn
[docs]def matrix_3d_rotation(mat, axis, phi, Sn):
"""For a matrix of 3D vectors (ncol==3), rotate a set of points around an
arbitrary axis. Vectors are the rows of the matrix.
@param axis Vector3 : axis around which to rotate (need not be normalized)
@param phi double : magnitude of rotation in rad
@param Sn bool : if true, then also reflect in plane through origin and perpendicular to rotation
@returns SharedMatrix with rotated points (rows)
"""
if len(mat[0]) != 3 or len(axis) != 3:
raise ValidationError("matrix_3d_rotation: Can only rotate matrix with 3d vectors")
# Normalize rotation vector
[wx, wy, wz] = normalize(axis)
cp = 1.0 - math.cos(phi)
R = zero(3, 3)
R[0][0] = wx * wx * cp + math.cos(phi)
R[0][1] = wx * wy * cp + math.sin(phi) * wz * -1
R[0][2] = wx * wz * cp + math.sin(phi) * wy
R[1][0] = wx * wy * cp + math.sin(phi) * wz
R[1][1] = wy * wy * cp + math.cos(phi)
R[1][2] = wy * wz * cp + math.sin(phi) * wx * -1
R[2][0] = wx * wz * cp + math.sin(phi) * wy * -1
R[2][1] = wy * wz * cp + math.sin(phi) * wx
R[2][2] = wz * wz * cp + math.cos(phi)
# R * coord^t = R_coord^t or coord * R^t = R_coord
#Matrix rotated_coord(nrow(),3);
#rotated_coord.gemm(false, true, 1.0, *this, R, 0.0);
rotated_coord = mult(mat, transpose(R))
# print 'after C'
# show(rotated_coord)
if Sn: # delta_ij - 2 a_i a_j / ||a||^2
R = identity(3)
#R = zero(3, 3)
R[0][0] -= 2 * wx * wx
R[1][1] -= 2 * wy * wy
R[2][2] -= 2 * wz * wz
#R[0][0] = 1 - 2 * wx * wx
#R[1][1] = 1 - 2 * wy * wy
#R[2][2] = 1 - 2 * wz * wz
R[1][0] = 2 * wx * wy
R[2][0] = 2 * wx * wz
R[2][1] = 2 * wy * wz
R[0][1] = 2 * wx * wy
R[0][2] = 2 * wx * wz
R[1][2] = 2 * wy * wz
rotated_coord = mult(rotated_coord, transpose(R))
#tmp = mult(rotated_coord, transpose(R))
#Matrix tmp(nrow(),3);
#tmp.gemm(false, true, 1.0, rotated_coord, R, 0.0);
#rotated_coord.copy(tmp);
#rotated_coord = [row[:] for row in tmp]
#SharedMatrix to_return = rotated_coord.clone();
#return to_return
return rotated_coord
[docs]def equal_but_for_row_order(mat, rhs, tol=DEFAULT_SYM_TOL):
"""Checks matrix equality, but allows rows to be in a different order.
@param rhs Matrix to compare to.
@returns true if equal, otherwise false.
"""
for m in range(len(mat)):
for m_rhs in range(len(mat)):
for n in range(len(mat[m])):
if abs(mat[m][n] - rhs[m_rhs][n]) > tol:
break # from n
else:
# whole row matched, goto next m row
break # from m_rhs
else:
# no matching row was found
return False
else:
return True
[docs]def compute_atom_map(mol):
"""Computes atom mappings during symmetry operations. Useful in
generating SO information and Cartesian displacement SALCs.
param mol Molecule to form mapping matrix from.
returns Integer matrix of dimension natoms X nirreps.
"""
# create the character table for the point group
ct = mol.point_group().char_table()
natom = mol.natom()
ng = ct.order()
atom_map = [0] * natom
for i in range(natom):
atom_map[i] = [0] * ng
np = [0.0, 0.0, 0.0]
so = SymmetryOperation()
# loop over all centers
for i in range(natom):
ac = mol.xyz(i)
# then for each symop in the pointgroup, transform the coordinates of
# center "i" and see which atom it maps into
for g in range(ng):
so = ct.symm_operation(g)
for ii in range(3):
np[ii] = 0
for jj in range(3):
np[ii] += so[ii][jj] * ac[jj]
atom_map[i][g] = mol.atom_at_position(np, 0.05)
if atom_map[i][g] < 0:
print(""" Molecule:\n""")
mol.print_out()
print(""" attempted to find atom at\n""")
print(""" %lf %lf %lf\n""" % (np[0], np[1], np[2]))
raise ValidationError("ERROR: Symmetry operation %d did not map atom %d to another atom:\n" % (g, i + 1))
return atom_map
# TODO outfile
# ignored =, +, 0, += assignment operators
# no pubchem
# TODO rename save_string_for_psi4
# TODO add no_com no_reorint in save string for psi4