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//
// Copyright (C) 2018-2020 Greg Landrum
//
#include "EHTTools.h"
#include <GraphMol/RDKitBase.h>
#include <GraphMol/MolOps.h>
#include <RDGeneral/BadFileException.h>
#ifdef RDK_BUILD_THREADSAFE_SSS
#include <mutex>
#endif
#include <fstream>
#include <cstdio>
#include <filesystem>
extern "C" {
#include <yaehmop/tightbind/bind.h>
}
namespace RDKit {
namespace EHTTools {
// we should only call into the C code, which uses tons of globals, from one
// thread at a time. This mutex enforces that.
#ifdef RDK_BUILD_THREADSAFE_SSS
std::mutex yaehmop_mutex;
#endif
namespace {
std::string randomstring(unsigned int len = 8) {
const std::string alphanum{
"0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz"};
const auto strSize = alphanum.size();
std::string res;
res.reserve(len);
while (res.size() != len) {
const auto pos = rand() % strSize;
res.push_back(alphanum[pos]);
}
return res;
}
// RAII tempfile class
struct Tempfile {
std::filesystem::path fname;
FILE *fptr = nullptr;
Tempfile() {
fname = std::filesystem::temp_directory_path() / randomstring();
fptr = std::fopen(fname.string().c_str(), "w+");
if (!fptr) {
throw BadFileException("could not open temporary file");
}
}
~Tempfile() {
if (!fptr) {
return;
}
#ifdef WIN32
std::fclose(fptr);
#else
if (fcntl(fileno(fptr), F_GETFD) != -1) {
std::fclose(fptr);
}
#endif
std::filesystem::remove(fname);
}
Tempfile(const Tempfile &o) = delete;
Tempfile &operator=(const Tempfile &o) = delete;
Tempfile(Tempfile &&o) = default;
Tempfile &operator=(Tempfile &&o) = default;
};
} // namespace
bool runMol(const ROMol &mol, EHTResults &results, int confId,
bool preserveHamiltonianAndOverlapMatrices) {
#ifdef RDK_BUILD_THREADSAFE_SSS
std::lock_guard<std::mutex> lock(yaehmop_mutex);
#endif
// -----------------------------
// ----- BOILERPLATE -----------
// -----------------------------
Tempfile nullHolder;
FILE *nullfile = nullHolder.fptr;
status_file = nullfile;
output_file = nullfile;
Tempfile destHolder;
FILE *dest = destHolder.fptr;
unit_cell = (cell_type *)calloc(1, sizeof(cell_type));
details = (detail_type *)calloc(1, sizeof(detail_type));
set_details_defaults(details);
set_cell_defaults(unit_cell);
safe_strcpy(details->title, (char *)"RDKit job");
// molecular calculation
details->Execution_Mode = MOLECULAR;
details->num_KPOINTS = 1;
details->K_POINTS = (k_point_type *)calloc(1, sizeof(k_point_type));
details->K_POINTS[0].weight = 1.0;
details->avg_props = 1;
details->use_symmetry = 1;
details->find_princ_axes = 0;
details->net_chg_PRT = 1;
details->ROP_mat_PRT = 1;
details->Rchg_mat_PRT = 1;
unit_cell->using_Zmat = 0;
unit_cell->using_xtal_coords = 0;
// ---------------------------------
// ----- END BOILERPLATE -----------
// ---------------------------------
unit_cell->num_atoms = mol.getNumAtoms();
unit_cell->num_raw_atoms = unit_cell->num_atoms;
unit_cell->atoms =
(atom_type *)calloc(unit_cell->num_atoms, sizeof(atom_type));
const Conformer &conf = mol.getConformer(confId);
for (unsigned int i = 0; i < mol.getNumAtoms(); ++i) {
safe_strcpy(unit_cell->atoms[i].symb,
(char *)mol.getAtomWithIdx(i)->getSymbol().c_str());
auto p = conf.getAtomPos(i);
unit_cell->atoms[i].loc.x = p.x;
unit_cell->atoms[i].loc.y = p.y;
unit_cell->atoms[i].loc.z = p.z;
}
unit_cell->charge = MolOps::getFormalCharge(mol);
// -----------------------------
// ----- BOILERPLATE -----------
// -----------------------------
const char *parmFilePtr = nullptr;
std::string pfName = "";
if (std::getenv("BIND_PARM_FILE") == nullptr) {
auto rdbase = std::getenv("RDBASE");
if (rdbase != nullptr) {
pfName += rdbase;
pfName += "/Data/eht_parms.dat";
std::ifstream f(pfName.c_str());
if (f.good()) {
parmFilePtr = pfName.c_str();
} else {
std::cerr << "file " << pfName << " doesn't seem to exist" << std::endl;
}
}
}
fill_atomic_parms(unit_cell->atoms, unit_cell->num_atoms, nullptr,
const_cast<char *>(parmFilePtr));
unit_cell->num_raw_atoms = unit_cell->num_atoms;
charge_to_num_electrons(unit_cell);
build_orbital_lookup_table(unit_cell, &num_orbs, &orbital_lookup_table);
run_eht(dest);
// ---------------------------------
// ----- END BOILERPLATE -----------
// ---------------------------------
// pull properties
results.numAtoms = mol.getNumAtoms();
results.numOrbitals = num_orbs;
results.numElectrons = std::lround(unit_cell->num_electrons);
results.fermiEnergy = properties.Fermi_E;
results.totalEnergy = properties.total_E;
results.atomicCharges = std::make_unique<double[]>(mol.getNumAtoms());
std::memcpy(static_cast<void *>(results.atomicCharges.get()),
static_cast<void *>(properties.net_chgs),
mol.getNumAtoms() * sizeof(double));
size_t sz = mol.getNumAtoms() * num_orbs;
results.reducedChargeMatrix = std::make_unique<double[]>(sz);
memcpy(static_cast<void *>(results.reducedChargeMatrix.get()),
static_cast<void *>(properties.Rchg_mat), sz * sizeof(double));
sz = mol.getNumAtoms() * (mol.getNumAtoms() + 1) / 2;
results.reducedOverlapPopulationMatrix = std::make_unique<double[]>(sz);
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);
fclose(dest);
return true;
}
} // end of namespace EHTTools
} // end of namespace RDKit
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