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A couple additions to the extended Hueckel integration (#2955)

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* add reference input/output files for yaehmop

* orbital energies, overlap matrix, and hamiltonian on the C++ side

* add the python wrappers for the new functions
This commit is contained in:
Greg Landrum
2020-02-24 10:32:02 +01:00
committed by GitHub
parent 96353c3a8b
commit fcdf086ee5
7 changed files with 919 additions and 69 deletions
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24
External/YAeHMOP/EHTTools.cpp vendored
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@@ -1,5 +1,5 @@
//
// Copyright (C) 2018 Greg Landrum
// Copyright (C) 2018-2020 Greg Landrum
//
#include "EHTTools.h"
#include <GraphMol/RDKitBase.h>
@@ -21,7 +21,8 @@ const std::string _EHTChargeMatrix = "_EHTChargeMatrix";
// thread at a time. This mutex enforces that.
std::mutex yaehmop_mutex;
bool runMol(const ROMol &mol, EHTResults &results, int confId) {
bool runMol(const ROMol &mol, EHTResults &results, int confId,
bool preserveHamiltonianAndOverlapMatrices) {
std::lock_guard<std::mutex> lock(yaehmop_mutex);
// -----------------------------
@@ -126,6 +127,25 @@ bool runMol(const ROMol &mol, EHTResults &results, int confId) {
memcpy(static_cast<void *>(results.reducedOverlapPopulationMatrix.get()),
static_cast<void *>(properties.ROP_mat), sz * sizeof(double));
results.orbitalEnergies = std::make_unique<double[]>(num_orbs);
std::memcpy(static_cast<void *>(results.orbitalEnergies.get()),
static_cast<void *>(eigenset.val), num_orbs * sizeof(double));
if (preserveHamiltonianAndOverlapMatrices) {
// these need to be recalculated, because they were overwritten during the
// calculation
R_space_overlap_matrix(unit_cell, details, Overlap_R, num_orbs,
tot_overlaps, orbital_lookup_table, 0);
full_R_space_Hamiltonian(unit_cell, details, Overlap_R, Hamil_R, num_orbs,
orbital_lookup_table, 1);
sz = num_orbs * num_orbs * sizeof(double);
results.hamiltonianMatrix = std::make_unique<double[]>(sz);
std::memcpy(static_cast<void *>(results.hamiltonianMatrix.get()),
static_cast<void *>(Hamil_R.mat), sz);
results.overlapMatrix = std::make_unique<double[]>(sz);
std::memcpy(static_cast<void *>(results.overlapMatrix.get()),
static_cast<void *>(Overlap_R.mat), sz);
}
cleanup_memory();
fclose(nullfile);