import numpy as np
from esipy.tools import format_partition
[docs]def info_rest(aom, molinfo, nfrags=0):
"""
Print the information of the molecule and the calculation.
:param aom: The Atomic Overlap Matrices (AOMs) in the MO basis.
:type aom: list of matrices
:param molinfo: Information about the molecule and the calculation.
:type: molinfo: dict
"""
partition = format_partition(molinfo["partition"])
print(" -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ ")
print(" | Number of Atoms: {}".format(len(aom)-nfrags))
print(" | Occ. Mol. Orbitals: {}".format(np.shape(aom[0])[0]))
print(" | Wavefunction type: Restricted")
print(" | Atomic partition: {}".format(partition.upper() if partition else "Not specified"))
print(" ------------------------------------------- ")
print(" ------------------------------------------- ")
print(" | Method: ", molinfo["calctype"])
if "dft" in molinfo["method"] and molinfo["xc"] is not None:
print(" | Functional: ", molinfo["xc"])
if isinstance(molinfo["basisset"], dict) or isinstance(molinfo["basisset"], list):
print(" | Basis set: GEN")
elif isinstance(molinfo["basisset"], str):
print(" | Basis set: ", molinfo["basisset"].upper())
if isinstance(molinfo["energy"], str):
print(" | Total energy: {}".format(molinfo["energy"]))
else:
print(" | Total energy: {:<13f}".format(molinfo["energy"]))
print(" ------------------------------------------- ")
trace = np.sum([np.trace(matrix) for matrix in aom[:len(aom)-nfrags]])
print(" | Tr(Enter): {:.13f}".format(trace))
print(" ------------------------------------------- ")
[docs]def deloc_rest(aom, molinfo, fragmap={}):
"""
Population analysis, localization and delocalization indices for restricted, single-determinant calculations.
:param aom: The Atomic Overlap Matrices (AOMs) in the MO basis.
:type aom: list of matrices
:param molinfo: Information about the molecule and the calculation.
:type molinfo: dict
"""
# Checking where to read the atomic symbols from
presymbols = molinfo["symbols"]
symbols = presymbols + ["FF"] * (len(aom) - len(presymbols))
print(" ------------------------------------- ")
print(" | Atom N(Sij) loc. dloc. ")
print(" ------------------------------------- ")
# Getting the LIs and DIs
dis, lis, Ns = [], [], []
for i in range(len(aom)):
li = 2 * np.einsum('ij,ji->', aom[i], aom[i])
N = 2 * np.trace(aom[i])
lis.append(li)
Ns.append(N)
print(" | {:>2}{:>2d} {:>8.4f} {:>8.4f} {:>8.4f} ".format(
symbols[i], i + 1, N, li, N - li))
for j in range(i + 1, len(aom)):
di = 4 * np.einsum('ij,ji->', aom[i], aom[j])
if j < len(presymbols):
dis.append(di)
Ntot = np.sum(Ns[:len(presymbols)])
listot = np.sum(lis[:len(presymbols)])
distot = Ntot - listot
print(" ------------------------------------- ")
print(" | TOT: {:>8.4f} {:>8.4f} {:>8.4f}".format(
Ntot, listot, distot))
print(" ------------------------------------- ")
print(" ------------------------ ")
print(" | Pair DI ")
print(" ------------------------ ")
for i in range(len(aom)):
for j in range(i, len(aom)):
if i == j:
print(" | {:>2}{:>2}-{:>2}{:>2} {:>8.4f}".format(
symbols[i], str(i + 1).center(2), symbols[j],
str(j + 1).center(2), lis[i]))
else:
dif = 4 * np.einsum('ij,ji->', aom[i], aom[j])
print(" | {:>2}{:>2}-{:>2}{:>2} {:>8.4f}".format(
symbols[i], str(i + 1).center(2), symbols[j],
str(j + 1).center(2), dif))
print(" ------------------------ ")
print(" | TOT: {:>8.4f} ".format(Ntot))
print(" | LOC: {:>8.4f} ".format(listot))
print(" | DELOC: {:>8.4f} ".format(distot))
print(" ------------------------ ")
[docs]def arom_rest(rings, molinfo, indicators, mci=False, av1245=False, flurefs=None, homarefs=None, homerrefs=None,
ncores=1, fragmap=None):
"""
Output for the aromaticity indices for restricted, single-determinant calculations.
:param rings: List of the atoms in the rings.
:type rings: list of lists
:param molinfo: Information about the molecule and the calculation.
:type molinfo: dict
:param indicators: Class containing the indicators for each ring.
:type indicators: class
:param mci: Boolean to compute the MCI.
:type mci: bool, optional
:param av1245: Boolean to compute the AV1245.
:type av1245: bool, optional
:param flurefs: Dictionary with custom references for the FLU.
:type flurefs: dict, optional
:param homarefs: Dictionary with custom references for the HOMA.
:type homarefs: dict, optional
:param homerrefs: Dictionary with custom references for the HOMER.
:type homerrefs: dict, optional
:param ncores: Number of cores to use for the MCI calculation. By default, 1.
:type ncores: int, optional
"""
print(" ----------------------------------------------------------------------")
print(" | Aromaticity indices - PDI [CEJ 9, 400 (2003)] ")
print(" | HOMA [Tetrahedron 52, 10255 (1996)]")
print(" | FLU [JCP 122, 014109 (2005)] ")
print(" | Iring [PCCP 2, 3381 (2000)] ")
if mci is True:
print(" | MCI [JPOC 18, 706 (2005)] ")
if av1245 is True:
print(" | AV1245 [PCCP 18, 11839 (2016)] ")
print(" | AVmin [JPCC 121, 27118 (2017)] ")
print(" | [PCCP 20, 2787 (2018)] ")
print(" | For a recent review see: [CSR 44, 6434 (2015)] ")
print(" ----------------------------------------------------------------------")
# Checking where to read the atomic symbols from
if not molinfo:
raise NameError(" 'molinfo' not found. Check input")
# Checking if the list rings is contains more than one ring to analyze
symbols = molinfo["symbols"] + ["FF"] * (len(fragmap))
partition = molinfo["partition"]
if not isinstance(rings[0], list):
rings = [rings]
# Looping through each of the rings
for ring_index, ring in enumerate(rings.copy()):
frag = False
if any(tuple(r) in fragmap for r in ring if isinstance(r, (set, list))):
frag = True
connectivity = None if frag else [symbols[int(i) - 1] for i in ring]
print(" ----------------------------------------------------------------------")
print(" |")
print(" | Ring {} ({}): {}".format(ring_index + 1, len(ring), " ".join(str(num) for num in ring)))
print(" |")
print(" ----------------------------------------------------------------------")
goodring = ring
ring = list(np.arange(1, len(ring) + 1))
if homarefs is not None:
print(" | Using HOMA references provided by the user")
else:
print(" | Using default HOMA references")
if frag:
print(" | Could not compute geometric indicators between fragments")
homa = None
else:
homa = indicators[ring_index].homa
if homa is None:
print(" | Connectivity could not match parameters")
else:
print(" | EN {} = {:>.6f}".format(ring_index + 1, indicators[ring_index].en))
print(" | GEO {} = {:>.6f}".format(ring_index + 1, indicators[ring_index].geo))
print(" | HOMA {} = {:>.6f}".format(ring_index + 1, indicators[ring_index].homa))
print(" ----------------------------------------------------------------------")
if homerrefs:
print(" | ")
print(" | Found custom HOMER references 'alpha' and 'r_opt'. Computing")
print(" | HOMER {} = {:>.6f}".format(ring_index + 1, indicators[ring_index].homer))
print(" ----------------------------------------------------------------------")
if molinfo["geom"] is not None:
bla = indicators[ring_index].bla
if bla is not None:
bla_c = indicators[ring_index].bla_c
print(" | BLA {} = {:>.6f}".format(ring_index + 1, bla))
print(" | BLAc {} = {:>.6f}".format(ring_index + 1, bla_c))
if not frag:
flu = indicators[ring_index].flu
if flu is None:
print(" | Could not compute FLU")
else:
if flurefs is not None:
print(" | Using FLU references provided by the user")
else:
print(" | Using the default FLU references")
print(" ----------------------------------------------------------------------")
print(" | Atoms : {}".format(" ".join(str(atom) for atom in connectivity)))
print(" |")
print(" | FLU {} = {:>.6f}".format(ring_index + 1, flu))
print(" ----------------------------------------------------------------------")
print(" | BOA {} = {:>.6f}".format(ring_index + 1, indicators[ring_index].boa))
print(" | BOA_cc {} = {:>.6f}".format(ring_index + 1, indicators[ring_index].boa_c))
print(" ----------------------------------------------------------------------")
# Checking the length of the ring. PDI only computed for len(ring)=6.
if len(ring) != 6:
print(" | PDI could not be calculated as the number of centers is not 6")
else:
pdi_list = indicators[ring_index].pdi_list
print(" | DI ({:>2} -{:>2} ) = {:.4f}".format(ring[0], ring[3], pdi_list[0]))
print(" | DI ({:>2} -{:>2} ) = {:.4f}".format(ring[1], ring[4], pdi_list[1]))
print(" | DI ({:>2} -{:>2} ) = {:.4f}".format(ring[2], ring[5], pdi_list[2]))
print(" | PDI {} = {:.4f} ".format(ring_index + 1, indicators[ring_index].pdi))
print(" ----------------------------------------------------------------------")
if av1245 == True:
if len(ring) < 6:
print(" | AV1245 could not be calculated as the number of centers is smaller than 6 ")
else:
av1245_list = indicators[ring_index].av1245_list
av1245_pairs, av1245_indices = [], []
for i in range(len(goodring)):
first = fragmap[tuple(goodring[i % len(goodring)])] if isinstance(goodring[i % len(goodring)], set) else goodring[i % len(goodring)]
second = fragmap[tuple(goodring[(i + 1) % len(goodring)])] if isinstance(
goodring[(i + 1) % len(goodring)], set) else goodring[(i + 1) % len(goodring)]
third = fragmap[tuple(goodring[(i + 3) % len(goodring)])] if isinstance(
goodring[(i + 3) % len(goodring)], set) else goodring[(i + 3) % len(goodring)]
fourth = fragmap[tuple(goodring[(i + 4) % len(goodring)])] if isinstance(
goodring[(i + 4) % len(goodring)], set) else goodring[(i + 4) % len(goodring)]
# Create the ring with corresponding symbols
symbs = [
symbols[first - 1] if isinstance(first, int) else symbols[first],
symbols[second - 1] if isinstance(second, int) else symbols[second],
symbols[third - 1] if isinstance(third, int) else symbols[third],
symbols[fourth - 1] if isinstance(fourth, int) else symbols[fourth]
]
av1245_pairs.append(symbs)
av1245_indices.append((first, second, third, fourth))
print(" | {} {} - {} {} - {} {} - {} {} | {:>6.4f}".format(
str(av1245_indices[-1][0]).rjust(2), symbs[0].ljust(2),
str(av1245_indices[-1][1]).rjust(2), symbs[1].ljust(2),
str(av1245_indices[-1][2]).rjust(2), symbs[2].ljust(2),
str(av1245_indices[-1][3]).rjust(2), symbs[3].ljust(2),
av1245_list[i % len(goodring)]))
print(" | AV1245 {} = {:.4f}".format(ring_index + 1, indicators[ring_index].av1245))
print(" | AVmin {} = {:.4f}".format(ring_index + 1, indicators[ring_index].avmin))
print(" ---------------------------------------------------------------------- ")
iring_total = indicators[ring_index].iring
print(" | Iring {} = {:>.6f}".format(ring_index + 1, iring_total))
if iring_total < 0:
print(" | Iring**(1/n) {} = {:>.6f}".format(ring_index + 1, -(np.abs(iring_total) ** (1 / len(ring)))))
else:
print(" | Iring**(1/n) {} = {:>.6f}".format(ring_index + 1, iring_total ** (1 / len(ring))))
print(" ---------------------------------------------------------------------- ")
if mci == True:
import time
# SINGLE-CORE
if ncores == 1:
if partition is None:
print(" | Partition not specified. Will assume symmetric AOMs")
start_mci = time.time()
mci_total = indicators[ring_index].mci
end_mci = time.time()
time_mci = end_mci - start_mci
print(" | The MCI calculation using 1 core took {:.4f} seconds".format(time_mci))
print(" | MCI {} = {:.6f}".format(ring_index + 1, mci_total))
# MULTI-CORE
else:
start_mci = time.time()
mci_total = indicators[ring_index].mci
end_mci = time.time()
time_mci = end_mci - start_mci
print(" | The MCI calculation using {} cores took {:.4f} seconds".format(ncores, time_mci))
print(" | MCI {} = {:.6f}".format(ring_index + 1, mci_total))
if mci_total < 0:
print(" | MCI**(1/n) {} = {:>6f}".format(ring_index + 1, -((np.abs(mci_total)) ** (1 / len(ring)))))
else:
print(" | MCI**(1/n) {} = {:>6f}".format(ring_index + 1, mci_total ** (1 / len(ring))))
print(" ---------------------------------------------------------------------- ")
