mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
fcdf086ee5
* 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
102 lines
3.4 KiB
C++
102 lines
3.4 KiB
C++
//
|
|
// Copyright (C) 2018 Greg Landrum
|
|
//
|
|
#define CATCH_CONFIG_MAIN // This tells Catch to provide a main() - only do
|
|
// this in one cpp file per test
|
|
#include "catch.hpp"
|
|
|
|
#include <GraphMol/RDKitBase.h>
|
|
#include "EHTTools.h"
|
|
|
|
#include <GraphMol/FileParsers/FileParsers.h>
|
|
|
|
using namespace RDKit;
|
|
|
|
#if 1
|
|
TEST_CASE("methanol", "[basics]") {
|
|
std::string pathName = getenv("RDBASE");
|
|
pathName += "/External/YAeHMOP/test_data/";
|
|
bool sanitize = true;
|
|
bool removeHs = false;
|
|
std::unique_ptr<RWMol> mol(
|
|
MolFileToMol(pathName + "methanol.mol", sanitize, removeHs));
|
|
REQUIRE(mol);
|
|
REQUIRE(mol->getNumAtoms() == 6);
|
|
EHTTools::EHTResults res;
|
|
REQUIRE(EHTTools::runMol(*mol, res));
|
|
}
|
|
#endif
|
|
#if 1
|
|
TEST_CASE("benzene", "[basics]") {
|
|
std::string pathName = getenv("RDBASE");
|
|
pathName += "/External/YAeHMOP/test_data/";
|
|
bool sanitize = true;
|
|
bool removeHs = false;
|
|
std::unique_ptr<RWMol> mol(
|
|
MolFileToMol(pathName + "benzene.mol", sanitize, removeHs));
|
|
REQUIRE(mol);
|
|
REQUIRE(mol->getNumAtoms() == 12);
|
|
EHTTools::EHTResults res;
|
|
int confId = -1;
|
|
bool preserveMatrices = true;
|
|
REQUIRE(EHTTools::runMol(*mol, res, confId, preserveMatrices));
|
|
CHECK(res.numElectrons == 30);
|
|
CHECK(res.numOrbitals == 30);
|
|
CHECK(res.numAtoms == 12);
|
|
for (unsigned int i = 0; i < 6; ++i) {
|
|
CHECK(res.atomicCharges[i] == Approx(-0.026).margin(0.001));
|
|
}
|
|
for (unsigned int i = 6; i < 12; ++i) {
|
|
CHECK(res.atomicCharges[i] == Approx(0.026).margin(0.001));
|
|
}
|
|
for (unsigned int i = 0; i < 6; ++i) {
|
|
CHECK(res.reducedChargeMatrix[i * res.numOrbitals] ==
|
|
Approx(0.1615).margin(0.001));
|
|
CHECK(res.reducedChargeMatrix[i * res.numOrbitals + 6] ==
|
|
Approx(0.1066).margin(0.001));
|
|
CHECK(res.reducedChargeMatrix[i * res.numOrbitals + 9] ==
|
|
Approx(0.1667).margin(0.001));
|
|
}
|
|
for (unsigned int i = 6; i < 12; ++i) {
|
|
CHECK(res.reducedChargeMatrix[i * res.numOrbitals] ==
|
|
Approx(0.0052).margin(0.001));
|
|
CHECK(res.reducedChargeMatrix[i * res.numOrbitals + 6] ==
|
|
Approx(0.0600).margin(0.001));
|
|
CHECK(res.reducedChargeMatrix[i * res.numOrbitals + 9] ==
|
|
Approx(0.0000).margin(0.001));
|
|
}
|
|
CHECK(res.orbitalEnergies[0] == Approx(-29.6302).margin(0.001));
|
|
CHECK(res.orbitalEnergies[14] == Approx(-12.804).margin(0.001));
|
|
CHECK(res.orbitalEnergies[29] == Approx(67.0404).margin(0.001));
|
|
|
|
CHECK(res.totalEnergy == Approx(-535.026).margin(0.001));
|
|
CHECK(res.fermiEnergy == Approx(-12.804).margin(0.001));
|
|
|
|
CHECK(res.hamiltonianMatrix[0 * res.numOrbitals + 0] ==
|
|
Approx(-21.4000).margin(0.001));
|
|
CHECK(res.hamiltonianMatrix[0 * res.numOrbitals + 4] ==
|
|
Approx(-15.3224).margin(0.001));
|
|
CHECK(res.hamiltonianMatrix[4 * res.numOrbitals + 0] ==
|
|
Approx(0.0000).margin(0.001));
|
|
CHECK(res.overlapMatrix[0 * res.numOrbitals + 0] ==
|
|
Approx(1.0000).margin(0.001));
|
|
CHECK(res.overlapMatrix[0 * res.numOrbitals + 4] ==
|
|
Approx(0.4091).margin(0.001));
|
|
CHECK(res.overlapMatrix[4 * res.numOrbitals + 0] ==
|
|
Approx(0.0000).margin(0.001));
|
|
}
|
|
#endif
|
|
#if 1
|
|
TEST_CASE("phenol", "[basics]") {
|
|
std::string pathName = getenv("RDBASE");
|
|
pathName += "/External/YAeHMOP/test_data/";
|
|
bool sanitize = true;
|
|
bool removeHs = false;
|
|
std::unique_ptr<RWMol> mol(
|
|
MolFileToMol(pathName + "phenol.mol", sanitize, removeHs));
|
|
REQUIRE(mol);
|
|
REQUIRE(mol->getNumAtoms() == 13);
|
|
EHTTools::EHTResults res;
|
|
REQUIRE(EHTTools::runMol(*mol, res));
|
|
}
|
|
#endif |