import itertools
from typing import Any, Dict, List, Union
import numpy as np
from ..exceptions import ValidationError
from ..util import unique_everseen
def _apply_default(llist, default):
return [default if (c is None) else c for c in llist]
def _high_spin_sum(mult_list):
mm = 1
for m in mult_list:
mm += m - 1
return mm
def _mult_ok(m):
return isinstance(m, (int, np.integer)) and m >= 1
def _sufficient_electrons_for_mult(z, c, m):
"""Require sufficient electrons in total: total mult ({}) - 1 > raw electrons ({}) - total chg ({})"""
return m - 1 <= z - c
def _parity_ok(z, c, m):
"""Check total electrons (neutral protons `z` and charge `c`) is (un)paired-compatible with multiplicity `m`"""
return (m % 2) != ((z - c) % 2)
# def _alpha_beta_allocator(z, c, m):
# nbeta = (z - c - m + 1) // 2
# nalpha = nbeta + m - 1
# return nalpha, nbeta
[docs]def validate_and_fill_chgmult(
zeff: np.ndarray,
fragment_separators: np.ndarray,
molecular_charge: Union[float, None],
fragment_charges: Union[List[float], None],
molecular_multiplicity: Union[int, None],
fragment_multiplicities: Union[List[int], None],
zero_ghost_fragments: bool = False,
verbose: int = 1,
) -> Dict[str, Any]:
r"""Forms molecular and fragment charge and multiplicity specification
by completing and reconciling information from argument, supplemented
by physical constraints and sensible defaults.
Parameters
----------
zeff
(nat,) electron counts (float) for neutral atoms, generally Z nuclear charge.
0 indicates ghosts such that a full fragment of 0s will be constained
to `0 1` charge & multiplicity.
fragment_separators
(nfr - 1, ) indices splitting `zeff` into nfr fragments.
molecular_charge
Total charge for molecular system.
fragment_charges
(nfr,) known fragment charges with `None` as placeholder for
unknown. Expected pre-defaulted so even if nothing known, if
`fragment_separators` breaks `zeff` into `nfr=2` fragments, input
value should be ``fragment_charges=[None, None]``.
molecular_multiplicity
Total multiplicity for molecular system.
fragment_multiplicities
(nfr,) known fragment charges with `None` as placeholder for
unknown. Expected pre-defaulted so even if nothing known, if
`fragment_separators` breaks `zeff` into `nfr=2` fragments, input
value should be ``fragment_multiplicities=[None, None]``.
zero_ghost_fragments
Fragments composed entirely of ghost atoms (Zeff=0) are required to have
chgmult `0 1`. When `False`, violations of this will cause a
ValidationError. When `True`, treat ghost fragments indicated by `zeff` to
contain superior information over chgmult arguments that might still
correspond to full-real molecule. Clears information from
`molecular_charge` and `molecular_multiplicity` and sets ghost fragments
to `0 1`, leaving other positions free to readjust. Unused (prefer to set
up such manipulations outside function call) but works.
verbose
Amount of printing.
Returns
-------
molecular_charge : float
Total charge for molecular system.
fragment_charges : list of float
(nfr,) Charge on each fragment.
molecular_multiplicity : int
Total multiplicity for molecular system.
fragment_multiplicities : list of int
(nfr,) Multiplicity for each fragment.
Raises
------
qcelemental.ValidationError
When no solution to input arguments subject to the constraints below can be found.
Notes
-----
Returns combination of total & fragment charge & multiplicity among
values of S1-7 that fulfill rules R1-9. A few derived implications in I1-3.
* Constraints
* R1 require all chg & mult exist
* R2 require total charge to be the sum of frag chg
* R3 require mult is positive int
* R4 require sufficient tot electrons for mult: mult - 1 <= neut_el - chg
* R5 require total parity consistent among tot electrons and mult: (mult % 2) != ((neut_el - chg) % 2)
* R6 require chg match input argument values
* R7 require mult match input argument values
* R8 require that tot = sum(frag) mult follow high spin addition unless tot & frag mult fully specified
* R9 require that ghost fragments (zeff all 0) be neutral singlet
* Allowed values
* S1 suggest input argument values for tot chg, frag chg, tot mult or frag mult
* S2 suggest sum frag chg for tot chg, allowing for indiv frag chg defaulting to 0
* S3 suggest distributing unallocated chg onto frag chg
* S4 suggest 0 default for frag chg
* S5 suggest range of high-spin sum frag mult for tot mult, allowing for indiv frag mult defaulting to 1 or 2
* S6 suggest range of unallocated mult = tot - high_spin_sum(frag - 1), allowing for all indiv but self defaulting to 1 or 2.
* S7 suggest 1 or 2 default for frag mult
* Implications
* I1 won't form an ion just to be closed shell (would require choosing +1 vs. -1)
* I2 unallocated chg or mult lands on the first unspecified fragment able to bear it (enforced by returning first match encountered; subsequent matches distribute charge to later frags)
* I3 missing chg or mult from tot - frags will always be allocated as a block, not distributed
Examples
--------
>>> validate_and_fill_chgmult(*sys('He'), 0, [0], 1, [1])
0, [0], 1, [1]
>>> validate_and_fill_chgmult(*sys('He'), None, [None], None, [None])
0, [0], 1, [1]
>>> validate_and_fill_chgmult(*sys('He/He'), None, [None, None], None, [None, None])
0, [0, 0], 1, [1, 1])
>>> validate_and_fill_chgmult(*sys('He/He'), 2, [None, None], None, [None, None])
2, [2, 0], 1, [1, 1])
>>> validate_and_fill_chgmult(*sys('He/He'), None, [2, None], None, [None, None])
2, [2, 0], 1, [1, 1])
>>> validate_and_fill_chgmult(*sys('He/He'), 0, [2, None], None, [None, None])
0, [2, -2], 1, [1, 1])
>>> validate_and_fill_chgmult(*sys('Ne/He/He'), -2, [None, 2, None], None, [None, None, None])
-2, [-4, 2, 0], 1, [1, 1, 1]
>>> validate_and_fill_chgmult(*sys('Ne/He/He'), 2, [None, -2, None], None, [None, None, None])
2, [4, -2, 0], 1, [1, 1, 1]
# 9 - residual +4 distributes to first fragment able to wholly accept it (He+4 is no-go)
>>> validate_and_fill_chgmult(*sys('He/He/Ne'), 2, [None, -2, None], None, [None, None, None])
2, [0, -2, 4], 1, [1, 1, 1]
# 10 - residual +4 unsuited for only open fragment, He, so irreconcilable
>>> validate_and_fill_chgmult(*sys('He/He/Ne'), 2, [None, -2, 0], None, [None, None, None])
ValidationError
# 11 - non-positive multiplicity
>>> validate_and_fill_chgmult(*sys('He/He/Ne'), 2, [2, -2, None], None, [None, None, None])
2, [2, -2, 2], 1, [1, 1, 1])
>>> validate_and_fill_chgmult(*sys('He/He'), None, [-2, 2], None, [None, None])
0, [-2, 2], 1, [1, 1]
>>> validate_and_fill_chgmult(*sys('He/He'), None, [None, -2], None, [None, None])
-2, [0, -2], 1, [1, 1]
>>> validate_and_fill_chgmult(*sys('Ne/Ne'), 0, [None, 4], None, [None, None])
0, [-4, 4], 1, [1, 1]
>>> validate_and_fill_chgmult(*sys('He/He/He'), 4, [2, None, None], None, [None, None, None])
4, [2, 2, 0], 1, [1, 1, 1]
>>> validate_and_fill_chgmult(*sys('He/He'), 0, [-2, 2], None, [None, None])
0, [-2, 2], 1, [1, 1]
>>> validate_and_fill_chgmult(*sys('He/He'), 0, [-2, -2], None, [None, None])
ValidationError
>>> validate_and_fill_chgmult(*sys('He'), None, [None], 0, [None])
ValidationError
>>> validate_and_fill_chgmult(*sys('He'), None, [None], None, [1])
0, [0], 1, [1]
# 20 - doublet non consistent with closed-shell, neutral default charge
>>> validate_and_fill_chgmult(*sys('He'), None, [None], None, [2])
ValidationError
>>> validate_and_fill_chgmult(*sys('He'), None, [None], None, [3])
0, [0], 3, [3]
# 22 - insufficient electrons for pentuplet
>>> validate_and_fill_chgmult(*sys('He'), None, [None], None, [5])
ValidationError
>>> validate_and_fill_chgmult(*sys('He'), None, [-1], None, [2])
-1, [-1], 2, [2]
# 24 - doublet not consistent with even charge
>>> validate_and_fill_chgmult(*sys('He'), None, [-2], None, [2])
ValidationError
>>> validate_and_fill_chgmult(*sys('He/He'), None, [None, None], None, [1, 1])
0, [0, 0], 1, [1, 1]
>>> validate_and_fill_chgmult(*sys('He/He'), None, [None, None], None, [3, 1])
0, [0, 0], 3, [3, 1]
>>> validate_and_fill_chgmult(*sys('He/He'), None, [None, None], None, [1, 3])
0, [0, 0], 3, [1, 3]
>>> validate_and_fill_chgmult(*sys('He/He'), None, [None, None], None, [3, 3])
0, [0, 0], 5, [3, 3]
>>> validate_and_fill_chgmult(*sys('He/He'), None, [None, None], 3, [3, 3])
0, [0, 0], 3, [3, 3]
# 30 - bad parity btwn mult and total # electrons
>>> validate_and_fill_chgmult(*sys('He/He'), None, [None, None], 2, [3, 3])
ValidationError
>>> validate_and_fill_chgmult(*sys('H'), None, [None], None, [None])
0, [0], 2, [2]
>>> validate_and_fill_chgmult(*sys('H'), 1, [None], None, [None])
1, [1], 1, [1]
>>> validate_and_fill_chgmult(*sys('H'), None, [-1], None, [None])
-1, [-1], 1, [1]
>>> validate_and_fill_chgmult(*sys('funnyH'), None, [None], None, [None])
0, [0], 1, [1]
# 35 - insufficient electrons
>>> validate_and_fill_chgmult(*sys('funnierH'), None, [None], None, [None])
ValidationError
>>> validate_and_fill_chgmult(*sys('H/H'), None, [None, None], None, [None, None])
0, [0, 0], 3, [2, 2]
>>> validate_and_fill_chgmult(*sys('H/He'), None, [None, None], None, [None, None])
0, [0, 0], 2, [2, 1]
>>> validate_and_fill_chgmult(*sys('H/He'), None, [1, 1], None, [None, None])
2, [1, 1], 2, [1, 2]
>>> validate_and_fill_chgmult(*sys('H/He'), -2, [-1, None], None, [None, None])
-2, [-1, -1], 2, [1, 2]
>>> validate_and_fill_chgmult(*sys('H/He/Na/Ne'), None, [1, None, 1, None], None, [None, None, None, None])
2, [1, 0, 1, 0], 1, [1, 1, 1, 1]
>>> validate_and_fill_chgmult(*sys('H/He/Na/Ne'), None, [-1, None, 1, None], None, [None, None, None, None])
0, [-1, 0, 1, 0], 1, [1, 1, 1, 1]
>>> validate_and_fill_chgmult(*sys('H/He/Na/Ne'), 2, [None, None, 1, None], None, [None, None, None, None])
2, [1, 0, 1, 0], 1, [1, 1, 1, 1]
>>> validate_and_fill_chgmult(*sys('H/He/Na/Ne'), 3, [None, None, 1, None], None, [None, None, None, None])
3, [0, 2, 1, 0], 2, [2, 1, 1, 1]
>>> validate_and_fill_chgmult(*sys('H/He'), None, [1, None], None, [2, None])
ValidationError
>>> validate_and_fill_chgmult(*sys('H/He'), None, [None, 0], None, [None, 2])
ValidationError
>>> validate_and_fill_chgmult(*sys('H/He'), None, [None, -1], None, [None, 3])
ValidationError
>>> validate_and_fill_chgmult(*sys('H/He/Na/Ne'), None, [None, 1, 0, 1], None, [None, None, None, None])
2, [0, 1, 0, 1], 5, [2, 2, 2, 2]
>>> validate_and_fill_chgmult(*sys('H/He/Na/Ne'), None, [None, 1, 0, None], None, [None, None, None, None])
1, [0, 1, 0, 0], 4, [2, 2, 2, 1]
>>> validate_and_fill_chgmult(*sys('H/He/Na/Ne'), None, [None, 1, 0, None], None, [None, None, 4, None])
1, [0, 1, 0, 0], 6, [2, 2, 4, 1]
>>> validate_and_fill_chgmult(*sys('He/He/He'), 0, [None, None, 1], None, [1, None, 2])
0, [0, -1, 1], 3, [1, 2, 2]
>>> validate_and_fill_chgmult(*sys('N/N/N'), None, [1, 1, 1], 3, [None, 3, None])
3, [1, 1, 1], 3, [1, 3, 1]
>>> validate_and_fill_chgmult(*sys('N/N/N'), None, [1, 1, 1], 3, [None, None, None])
3, [1, 1, 1], 3, [3, 1, 1]
>>> validate_and_fill_chgmult(*sys('N/N/N'), None, [None, None, None], 3, [None, None, 2])
ValidationError
>>> validate_and_fill_chgmult(*sys('N/N/N'), 1, [None, -1, None], 3, [None, None, 2])
1, [2, -1, 0], 3, [2, 1, 2]
# 55 - both (1, (1, 0.0, 0.0), 4, (1, 3, 2)) and (1, (0.0, 0.0, 1), 4, (2, 3, 1)) plausible
>>> validate_and_fill_chgmult(*sys('N/Ne/N'), 1, [None, None, None], 4, [None, 3, None])
1, [1, 0, 0], 4, [1, 3, 2]
>>> validate_and_fill_chgmult(*sys('N/Ne/N'), None, [None, None, 1], 4, [None, 3, None])
1, [0, 0, 1], 4, [2, 3, 1]
>>> validate_and_fill_chgmult(*sys('He/He'), None, [-1, 1], None, [None, None])
0, [-1, 1], 3, [2, 2]
>>> validate_and_fill_chgmult(*sys('Gh'), 1, [None], None, [None])
ValidationError
>>> validate_and_fill_chgmult(*sys('Gh'), -1, [None], None, [None])
ValidationError
>>> validate_and_fill_chgmult(*sys('Gh'), None, [None], 3, [None])
ValidationError
>>> validate_and_fill_chgmult(*sys('He/Gh'), None, [2, None], None, [None, None])
2, [2, 0], 1, [1, 1]
>>> validate_and_fill_chgmult(*sys('Gh/He'), None, [2, None], None, [None, None])
ValidationError
>>> validate_and_fill_chgmult(*sys('Gh/He/Ne'), 2, [None, -2, None], None, [None, None, None])
2, [0, -2, 4], 1, [1, 1, 1]
>>> validate_and_fill_chgmult(*sys('Gh/He/Gh'), 1, [None, None, None], None, [None, None, None])
1, [0, 1, 0], 2, [1, 2, 1]
>>> sys = {
'He': (np.array([2]), np.array([])),
'He/He': (np.array([2, 2]), np.array([1])),
'Ne/He/He': (np.array([10, 2, 2]), np.array([1, 2])),
'He/He/Ne': (np.array([2, 2, 10]), np.array([1, 2])),
'Ne/Ne': (np.array([10, 10]), np.array([1])),
'He/He/He': (np.array([2, 2, 2]), np.array([1, 2])),
'H': (np.array([1]), np.array([])),
'funnyH': (np.array([0]), np.array([])), # has no electrons
'funnierH': (np.array([-1]), np.array([])), # has positron
'H/H': (np.array([1, 1]), np.array([1])),
'H/He': (np.array([1, 2]), np.array([1])),
'H/He/Na/Ne': (np.array([1, 2, 11, 10]), np.array([1, 2, 3])),
'N/N/N': (np.array([7, 7, 7]), np.array([1, 2])),
'N/Ne/N': (np.array([7, 10, 7]), np.array([1, 2])),
'He/Gh': (np.array([2, 0]), np.array([1])),
'Gh/He': (np.array([0, 2]), np.array([1])),
'Gh': (np.array([0, 0]), np.array([])),
'Gh/He/Ne': (np.array([0, 0, 2, 10]), np.array([2, 3])),
'Gh/He/Gh': (np.array([0, 2, 0]), np.array([1, 2]))}
"""
log_full = verbose >= 2
log_brief = verbose >= 2 # TODO: Move back to 1
text = []
felez = np.split(zeff, fragment_separators)
nfr = len(felez)
if log_full:
text.append("felez: {}".format(felez))
cgmp_exact_c = [] # exact_* are candidates for the final value
cgmp_exact_fc: List[List[float]] = [[] for f in range(nfr)]
cgmp_exact_m = []
cgmp_exact_fm: List[List[int]] = [[] for f in range(nfr)]
cgmp_range = [] # tests that the final value must pass to be valid
cgmp_rules = [] # key to what rules in cgmp_range are T/F
real_fragments = np.array([not all(f == 0 for f in felez[ifr]) for ifr in range(nfr)])
all_fc_known = all(f is not None for f in fragment_charges)
all_fm_known = all(f is not None for f in fragment_multiplicities)
if log_full:
text.append("all_fc_known: {}".format(all_fc_known))
text.append("all_fm_known: {}".format(all_fm_known))
if zero_ghost_fragments and not all(real_fragments):
if log_brief:
print("possibly adjusting charges")
molecular_charge = None
fragment_charges = [(fr if real_fragments[ifr] else 0.0) for ifr, fr in enumerate(fragment_charges)]
molecular_multiplicity = None
fragment_multiplicities = [(fr if real_fragments[ifr] else 1) for ifr, fr in enumerate(fragment_multiplicities)]
# <<< assert broad physical requirements
# * (R1) require all chg & mult exist
cgmp_range.append(
lambda c, fc, m, fm: c is not None
and all(f is not None for f in fc)
and m is not None
and all(f is not None for f in fm)
)
cgmp_rules.append("1")
# * (R2) require total charge to be the sum of fragment charges
cgmp_range.append(lambda c, fc, m, fm: c == sum(fc))
cgmp_rules.append("2")
# * (R3) require mult is positive int
cgmp_range.append(lambda c, fc, m, fm: _mult_ok(m) and all(_mult_ok(f) for f in fm))
cgmp_rules.append("3")
# <<< assert electron count requirements
zel = np.sum(zeff) # note: number electrons in neutral species, not number total electrons
fzel = [np.sum(f) for f in felez]
if log_full:
text.append("zel: {}".format(zel))
text.append("fzel: {}".format(fzel))
# * (R4) require sufficient electrons for mult: mult - 1 <= neutral_electrons - chg
cgmp_range.append(lambda c, fc, m, fm: _sufficient_electrons_for_mult(zel, c, m))
cgmp_rules.append("4")
for ifr in range(nfr):
cgmp_range.append(
lambda c, fc, m, fm, ifr=ifr: _sufficient_electrons_for_mult(fzel[ifr], fc[ifr], fm[ifr]) # type: ignore
)
cgmp_rules.append("4-" + str(ifr))
# * (R5) require total parity consistent among neutral_electrons, chg, and mult
cgmp_range.append(lambda c, fc, m, fm: _parity_ok(zel, c, m))
cgmp_rules.append("5")
for ifr in range(nfr):
cgmp_range.append(lambda c, fc, m, fm, ifr=ifr: _parity_ok(fzel[ifr], fc[ifr], fm[ifr])) # type: ignore
cgmp_rules.append("5-" + str(ifr))
# <<< (R6, R7, S1) assert & suggest input values
if molecular_charge is not None:
cgmp_exact_c.append(molecular_charge)
cgmp_range.append(lambda c, fc, m, fm: c == molecular_charge)
cgmp_rules.append("6")
for ifr, chg in enumerate(fragment_charges):
if chg is not None:
cgmp_exact_fc[ifr].append(chg)
cgmp_range.append(lambda c, fc, m, fm, ifr=ifr, chg=chg: fc[ifr] == chg) # type: ignore
cgmp_rules.append("6-" + str(ifr))
if molecular_multiplicity is not None:
cgmp_exact_m.append(molecular_multiplicity)
cgmp_range.append(lambda c, fc, m, fm: m == molecular_multiplicity)
cgmp_rules.append("7")
for ifr, mult in enumerate(fragment_multiplicities):
if mult is not None:
cgmp_exact_fm[ifr].append(mult)
cgmp_range.append(lambda c, fc, m, fm, ifr=ifr, mult=mult: fm[ifr] == mult) # type: ignore
cgmp_rules.append("7-" + str(ifr))
# <<< assert high-spin-rule and suggest "missing quantity" and default values
# * (S2) suggest net frag charge for total charge, allowing for indiv frag defaulting to 0
cgmp_exact_c.append(sum(filter(None, fragment_charges)))
missing_frag_chg = 0.0 if molecular_charge is None else molecular_charge
missing_frag_chg -= sum(filter(None, fragment_charges))
# * (S3) suggest distributing unallocated charge onto fragment
# * (S4) suggest 0 default charge for fragment
for ifr in range(nfr):
if fragment_charges[ifr] is None: # unneeded, but shortens the exact lists
cgmp_exact_fc[ifr].append(missing_frag_chg)
cgmp_exact_fc[ifr].append(0.0)
# * (R8) require that frag mult follow high spin addition unless fully specified
if molecular_multiplicity is None or any(f is None for f in fragment_multiplicities):
cgmp_range.append(lambda c, fc, m, fm: m == _high_spin_sum(fm))
cgmp_rules.append("8")
# * (S5) suggest range of net frag mult for total mult, allowing for indiv frag defaulting to 1 or 2.
# many in range may be unphysical, but those will be caught by physical rules.
if molecular_multiplicity is None: # unneeded, but shortens the exact lists
frag_mult_hi = _high_spin_sum(_apply_default(fragment_multiplicities, 2))
frag_mult_lo = _high_spin_sum(_apply_default(fragment_multiplicities, 1))
for m in range(frag_mult_lo, frag_mult_hi + 1):
cgmp_exact_m.append(m)
# * (S6) suggest range of missing mult = tot - high_spin_sum(frag - 1),
# allowing for all indiv but self defaulting to 1 or 2. Many in range
# may be unphysical, but those will be caught by physical rules.
# * (S7) suggest 1 or 2 default multiplicity for fragment
if molecular_multiplicity is not None and any(f is None for f in fragment_multiplicities):
frag_mult_less_one_none = fragment_multiplicities[:]
frag_mult_less_one_none.remove(None) # "missing" slot to solve for
frag_mult_hi = _high_spin_sum(_apply_default(frag_mult_less_one_none, 2))
frag_mult_lo = _high_spin_sum(_apply_default(frag_mult_less_one_none, 1))
missing_mult_hi = molecular_multiplicity - frag_mult_lo + 1
missing_mult_lo = molecular_multiplicity - frag_mult_hi + 1
else:
missing_mult_hi = 0
missing_mult_lo = 0
for ifr in range(nfr):
if fragment_multiplicities[ifr] is None: # unneeded, but shortens the exact lists
for m in reversed(range(max(missing_mult_lo, 1), missing_mult_hi + 1)):
cgmp_exact_fm[ifr].append(m)
cgmp_exact_fm[ifr].append(1)
cgmp_exact_fm[ifr].append(2)
# * (R9) require that ghost fragments be neutral singlet
for ifr in range(nfr):
if all(f == 0 for f in felez[ifr]):
cgmp_range.append(lambda c, fc, m, fm, ifr=ifr: fc[ifr] == 0 and fm[ifr] == 1) # type: ignore
cgmp_rules.append("9-" + str(ifr))
# <<< reconcile and report
def reconcile(exact_c, exact_fc, exact_m, exact_fm):
"""Returns a member from all combinations of `exact` that passes all tests in cgmp_range, else raises error."""
# remove duplicates
uniq_c = unique_everseen(exact_c)
uniq_fc = [unique_everseen(f) for f in exact_fc]
uniq_m = unique_everseen(exact_m)
uniq_fm = [unique_everseen(f) for f in exact_fm]
text.append("c: {}".format(list(exact_c)))
for f in exact_fc:
text.append("fc: {}".format(list(f)))
text.append("m: {}".format(list(exact_m)))
for f in exact_fm:
text.append("fm: {}".format(list(f)))
header = True
for candidate in itertools.product(*[uniq_c, itertools.product(*uniq_fc), uniq_m, itertools.product(*uniq_fm)]):
cc, cfc, cm, cfm = candidate
if header:
if log_full:
text.append(
"""Assess candidate {}: {}""".format(
candidate, " ".join(("{:3}".format(r) for r in cgmp_rules))
)
)
header = False
assessment = [fn(cc, cfc, cm, cfm) for fn in cgmp_range]
sass = ["{:3}".format("T" if b else "") for b in assessment]
if log_full:
text.append("""Assess candidate {:}: {} --> {}""".format(candidate, " ".join(sass), all(assessment)))
if all(assessment):
return candidate
err = """Inconsistent or unspecified chg/mult: sys chg: {}, frag chg: {}, sys mult: {}, frag mult: {}""".format(
molecular_charge, fragment_charges, molecular_multiplicity, fragment_multiplicities
)
if verbose > -1:
print("\n\n" + "\n".join(text))
raise ValidationError(err)
def stringify(start, final):
fcgmp = "{:^4}"
return fcgmp.format(final) if final == start else fcgmp.format("(" + str(int(final)) + ")")
# TODO could winnow down the exact_* lists a bit by ruling out
# independent values. do this if many-frag molecular systems take too
# long in the itertools.product
c_final, fc_final, m_final, fm_final = reconcile(cgmp_exact_c, cgmp_exact_fc, cgmp_exact_m, cgmp_exact_fm)
c_text = stringify(molecular_charge, c_final)
fc_text = ", ".join((stringify(fs, ff) for fs, ff in zip(fragment_charges, fc_final)))
m_text = stringify(molecular_multiplicity, m_final)
fm_text = ", ".join((stringify(fs, ff) for fs, ff in zip(fragment_multiplicities, fm_final)))
brief = []
if log_brief:
brief.append(" {:26} {}".format(" charge = " + c_text, "fragments = " + fc_text))
brief.append(" {:26} {}".format("multiplicity = " + m_text, "fragments = " + fm_text))
been_defaulted = []
if c_text.count("(") + fc_text.count("(") > 1:
been_defaulted.append("charge")
if "(" in m_text or "(" in fm_text:
been_defaulted.append("multiplicity")
if been_defaulted and log_brief:
brief.append(
" Note: Default values have been applied for {}. Specify intentions in molecule input block".format(
" and ".join(been_defaulted)
)
)
if (m_final != _high_spin_sum(fm_final)) and log_brief:
brief.append(
" Warning: Total multiplicity is not high-spin sum of fragments; may be clobbered by psi4.core.Molecule.update_geometry()."
)
if log_full:
print("\n".join(text))
if log_brief:
# TODO add back when printing worked out
# print('\n'.join(brief))
pass
return {
"molecular_charge": float(c_final),
"fragment_charges": [float(f) for f in fc_final],
"molecular_multiplicity": m_final,
"fragment_multiplicities": list(fm_final),
}