import numpy as np
from esipy.tools import format_partition
[docs]def info_rest(aom, molinfo):
"""
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)))
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"])
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])
print(" | Tr(Enter): {:.13f}".format(trace))
print(" ------------------------------------------- ")
[docs]def deloc_rest(aom, molinfo):
"""
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
symbols = molinfo["symbols"]
print(" ------------------------------------- ")
print(" | Atom N(Sij) loc. dloc. ")
print(" ------------------------------------- ")
# Getting the LIs and DIs
dis, lis, N = [], [], []
for i in range(len(aom)):
li = 2 * np.trace(np.dot(aom[i], aom[i]))
lis.append(li)
N.append(2 * np.trace(aom[i]))
print(" | {:>2}{:>2d} {:>8.4f} {:>8.4f} {:>8.4f} ".format(
symbols[i], i + 1, N[i], lis[i], N[i] - lis[i]))
for j in range(i + 1, len(aom)):
di = 4 * np.trace(np.dot(aom[i], aom[j]))
dis.append(di)
print(" ------------------------------------- ")
print(" | TOT: {:>8.4f} {:>8.4f} {:>8.4f}".format(
sum(N), sum(N) - sum(dis), sum(dis)))
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:
print(" | {:>2}{:>2}-{:>2}{:>2} {:>8.4f}".format(
symbols[i], str(i + 1).center(2), symbols[j],
str(j + 1).center(2), 4 * np.trace(np.dot(aom[i], aom[j]))))
print(" ------------------------ ")
print(" | TOT: {:>8.4f} ".format(np.sum(dis) + np.sum(lis)))
print(" | LOC: {:>8.4f} ".format(np.sum(lis)))
print(" | DELOC: {:>8.4f} ".format(np.sum(dis)))
print(" ------------------------ ")
[docs]def arom_rest(rings, molinfo, indicators, mci=False, av1245=False, flurefs=None, homarefs=None, homerrefs=None,
ncores=1):
"""
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 molinfo:
symbols = molinfo["symbols"]
partition = molinfo["partition"]
else:
raise NameError(" 'molinfo' not found. Check input")
# Checking if the list rings is contains more than one ring to analyze
if not isinstance(rings[0], list):
rings = [rings]
# Looping through each of the rings
for ring_index, ring in enumerate(rings):
print(" ----------------------------------------------------------------------")
print(" |")
print(" | Ring {} ({}): {}".format(ring_index + 1, len(ring), " ".join(str(num) for num in ring)))
print(" |")
print(" ----------------------------------------------------------------------")
connectivity = [symbols[int(i) - 1] for i in ring]
if homarefs is not None:
print(" | Using HOMA references provided by the user")
else:
print(" | Using default HOMA references")
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))
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(" ----------------------------------------------------------------------")
print(" | BLA {} = {:>.6f}".format(ring_index + 1, indicators[ring_index].bla))
print(" | BLAc {} = {:>.6f}".format(ring_index + 1, indicators[ring_index].bla_c))
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 = [(ring[i % len(ring)], ring[(i + 1) % len(ring)], ring[(i + 3) % len(ring)],
ring[(i + 4) % len(ring)])
for i in range(len(ring))]
for j in range(len(ring)):
print(" | {} {} - {} {} - {} {} - {} {} | {:>6.4f}".format(
str(ring[j]).rjust(2), symbols[av1245_pairs[j][0] - 1].ljust(2),
str(ring[(j + 1) % len(ring)]).rjust(2), symbols[av1245_pairs[j][1] - 1].ljust(2),
str(ring[(j + 3) % len(ring)]).rjust(2), symbols[av1245_pairs[j][2] - 1].ljust(2),
str(ring[(j + 4) % len(ring)]).rjust(2), symbols[av1245_pairs[j][3] - 1].ljust(2),
av1245_list[(ring[j] - 1) % len(ring)]))
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(" ---------------------------------------------------------------------- ")
