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A couple additions to the extended Hueckel integration (#2955)
* 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
GitHub
24
External/YAeHMOP/EHTTools.cpp
vendored
24
External/YAeHMOP/EHTTools.cpp
vendored
@@ -1,5 +1,5 @@
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//
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// Copyright (C) 2018 Greg Landrum
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// Copyright (C) 2018-2020 Greg Landrum
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//
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#include "EHTTools.h"
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#include <GraphMol/RDKitBase.h>
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@@ -21,7 +21,8 @@ const std::string _EHTChargeMatrix = "_EHTChargeMatrix";
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// thread at a time. This mutex enforces that.
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std::mutex yaehmop_mutex;
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bool runMol(const ROMol &mol, EHTResults &results, int confId) {
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bool runMol(const ROMol &mol, EHTResults &results, int confId,
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bool preserveHamiltonianAndOverlapMatrices) {
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std::lock_guard<std::mutex> lock(yaehmop_mutex);
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// -----------------------------
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@@ -126,6 +127,25 @@ bool runMol(const ROMol &mol, EHTResults &results, int confId) {
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memcpy(static_cast<void *>(results.reducedOverlapPopulationMatrix.get()),
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static_cast<void *>(properties.ROP_mat), sz * sizeof(double));
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results.orbitalEnergies = std::make_unique<double[]>(num_orbs);
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std::memcpy(static_cast<void *>(results.orbitalEnergies.get()),
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static_cast<void *>(eigenset.val), num_orbs * sizeof(double));
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if (preserveHamiltonianAndOverlapMatrices) {
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// these need to be recalculated, because they were overwritten during the
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// calculation
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R_space_overlap_matrix(unit_cell, details, Overlap_R, num_orbs,
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tot_overlaps, orbital_lookup_table, 0);
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full_R_space_Hamiltonian(unit_cell, details, Overlap_R, Hamil_R, num_orbs,
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orbital_lookup_table, 1);
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sz = num_orbs * num_orbs * sizeof(double);
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results.hamiltonianMatrix = std::make_unique<double[]>(sz);
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std::memcpy(static_cast<void *>(results.hamiltonianMatrix.get()),
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static_cast<void *>(Hamil_R.mat), sz);
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results.overlapMatrix = std::make_unique<double[]>(sz);
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std::memcpy(static_cast<void *>(results.overlapMatrix.get()),
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static_cast<void *>(Overlap_R.mat), sz);
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}
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cleanup_memory();
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fclose(nullfile);
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9
External/YAeHMOP/EHTTools.h
vendored
9
External/YAeHMOP/EHTTools.h
vendored
@@ -1,5 +1,5 @@
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//
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// Copyright (C) 2018 by Greg Landrum
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// Copyright (C) 2018-2020 by Greg Landrum
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//
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#ifndef EHTTOOLS_H_20181226
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#define EHTTOOLS_H_20181226
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@@ -24,11 +24,14 @@ struct RDKIT_EHTLIB_EXPORT EHTResults {
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unsigned int numAtoms;
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unsigned int numOrbitals;
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unsigned int numElectrons;
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std::unique_ptr<double[]> overlapMatrix;
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std::unique_ptr<double[]> hamiltonianMatrix;
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std::unique_ptr<double[]> overlapPopulationMatrix;
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std::unique_ptr<double[]> reducedOverlapPopulationMatrix;
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std::unique_ptr<double[]> chargeMatrix;
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std::unique_ptr<double[]> reducedChargeMatrix;
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std::unique_ptr<double[]> atomicCharges;
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std::unique_ptr<double[]> orbitalEnergies;
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double fermiEnergy;
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double totalEnergy;
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EHTResults() = default;
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@@ -38,7 +41,9 @@ struct RDKIT_EHTLIB_EXPORT EHTResults {
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//! Runs an extended Hueckel calculation for a molecule
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//! The results are returned in the EHTResults structure
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RDKIT_EHTLIB_EXPORT bool runMol(const ROMol &mol, EHTResults &results, int confId = -1);
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RDKIT_EHTLIB_EXPORT bool runMol(
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const ROMol &mol, EHTResults &results, int confId = -1,
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bool preserveHamiltonianAndOverlapMatrices = false);
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} // namespace EHTTools
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} // namespace RDKit
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56
External/YAeHMOP/Wrap/rdEHTTools.cpp
vendored
56
External/YAeHMOP/Wrap/rdEHTTools.cpp
vendored
@@ -46,9 +46,10 @@ boost::python::object transfer_to_python(T *t) {
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return python::object(handle);
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}
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PyObject *getMatrixProp(const double *mat, unsigned int dim1, unsigned int dim2) {
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PyObject *getMatrixProp(const double *mat, unsigned int dim1,
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unsigned int dim2) {
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if (!mat) {
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throw_value_error("matrix has not be initialized");
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throw_value_error("matrix has not been initialized");
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}
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npy_intp dims[2];
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dims[0] = dim1;
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@@ -63,7 +64,7 @@ PyObject *getMatrixProp(const double *mat, unsigned int dim1, unsigned int dim2)
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}
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PyObject *getSymmMatrixProp(const double *mat, unsigned int sz) {
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if (!mat) {
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throw_value_error("matrix has not be initialized");
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throw_value_error("matrix has not been initialized");
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}
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npy_intp dims[1];
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dims[0] = sz * (sz + 1) / 2;
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@@ -77,7 +78,7 @@ PyObject *getSymmMatrixProp(const double *mat, unsigned int sz) {
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}
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PyObject *getVectorProp(const double *mat, unsigned int sz) {
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if (!mat) {
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throw_value_error("vector has not be initialized");
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throw_value_error("vector has not been initialized");
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}
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npy_intp dims[1];
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dims[0] = sz;
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@@ -90,7 +91,8 @@ PyObject *getVectorProp(const double *mat, unsigned int sz) {
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return PyArray_Return(res);
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}
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PyObject *getChargeMatrix(EHTTools::EHTResults &self) {
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return getMatrixProp(self.reducedChargeMatrix.get(), self.numAtoms, self.numOrbitals);
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return getMatrixProp(self.reducedChargeMatrix.get(), self.numAtoms,
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self.numOrbitals);
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}
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PyObject *getOPMatrix(EHTTools::EHTResults &self) {
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@@ -101,11 +103,35 @@ PyObject *getOPMatrix(EHTTools::EHTResults &self) {
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PyObject *getCharges(EHTTools::EHTResults &self) {
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return getVectorProp(self.atomicCharges.get(), self.numAtoms);
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}
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python::tuple runCalc(const RDKit::ROMol &mol, int confId) {
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PyObject *getOrbitalEnergies(EHTTools::EHTResults &self) {
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return getVectorProp(self.orbitalEnergies.get(), self.numOrbitals);
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}
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python::tuple runCalc(const RDKit::ROMol &mol, int confId, bool keepMatrices) {
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auto eRes = new RDKit::EHTTools::EHTResults();
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bool ok = RDKit::EHTTools::runMol(mol, *eRes, confId);
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bool ok = RDKit::EHTTools::runMol(mol, *eRes, confId, keepMatrices);
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return python::make_tuple(ok, transfer_to_python(eRes));
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}
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PyObject *getHamiltonian(EHTTools::EHTResults &self) {
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if (!self.hamiltonianMatrix) {
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throw_value_error(
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"Hamiltonian not available, set keepOverlapAndHamiltonianMatrices=True "
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"to preserve it.");
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}
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return getMatrixProp(self.hamiltonianMatrix.get(), self.numOrbitals,
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self.numOrbitals);
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}
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PyObject *getOverlapMatrix(EHTTools::EHTResults &self) {
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if (!self.overlapMatrix) {
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throw_value_error(
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"Overlap matrix not available, set "
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"keepOverlapAndHamiltonianMatrices=True "
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"to preserve it.");
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}
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return getMatrixProp(self.overlapMatrix.get(), self.numOrbitals,
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self.numOrbitals);
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}
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} // end of anonymous namespace
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@@ -116,7 +142,8 @@ struct EHT_wrapper {
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python::class_<RDKit::EHTTools::EHTResults, boost::noncopyable>(
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"EHTResults", docString.c_str(), python::no_init)
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.def_readonly("numOrbitals", &RDKit::EHTTools::EHTResults::numOrbitals)
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.def_readonly("numElectrons", &RDKit::EHTTools::EHTResults::numElectrons)
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.def_readonly("numElectrons",
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&RDKit::EHTTools::EHTResults::numElectrons)
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.def_readonly("fermiEnergy", &RDKit::EHTTools::EHTResults::fermiEnergy)
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.def_readonly("totalEnergy", &RDKit::EHTTools::EHTResults::totalEnergy)
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.def("GetReducedChargeMatrix", getChargeMatrix,
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@@ -124,7 +151,13 @@ struct EHT_wrapper {
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.def("GetReducedOverlapPopulationMatrix", getOPMatrix,
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"returns the reduced overlap population matrix")
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.def("GetAtomicCharges", getCharges,
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"returns the calculated atomic charges");
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"returns the calculated atomic charges")
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.def("GetHamiltonian", getHamiltonian,
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"returns the symmetric Hamiltonian matrix")
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.def("GetOverlapMatrix", getOverlapMatrix,
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"returns the symmetric overlap matrix")
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.def("GetOrbitalEnergies", getOrbitalEnergies,
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"returns the energies of the molecular orbitals as a vector");
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docString =
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R"DOC(Runs an extended Hueckel calculation for a molecule.
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@@ -133,13 +166,16 @@ The molecule should have at least one conformation
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ARGUMENTS:
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- mol: molecule to use
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- confId: (optional) conformation to use
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- keepOverlapAndHamiltonianMatrices: (optional) triggers storing the overlap
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and hamiltonian matrices in the EHTResults object
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RETURNS: a 2-tuple:
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- a boolean indicating whether or not the calculation succeeded
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- an EHTResults object with the results
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)DOC";
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python::def("RunMol", runCalc,
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(python::arg("mol"), python::arg("confId") = -1),
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(python::arg("mol"), python::arg("confId") = -1,
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python::arg("keepOverlapAndHamiltonianMatrices") = false),
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docString.c_str());
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}
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};
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121
External/YAeHMOP/Wrap/testEHTTools.py
vendored
121
External/YAeHMOP/Wrap/testEHTTools.py
vendored
@@ -15,58 +15,83 @@ from rdkit.Chem import rdEHTTools
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class TestCase(unittest.TestCase):
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def setUp(self):
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pass
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def setUp(self):
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pass
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def test1(self):
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mol = Chem.MolFromMolFile(os.path.join(
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RDConfig.RDBaseDir, "External", "YAeHMOP", "test_data", "benzene.mol"), removeHs=False)
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self.assertEqual(mol.GetNumAtoms(), 12)
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ok, res = rdEHTTools.RunMol(mol)
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self.assertTrue(ok)
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chgs = res.GetAtomicCharges()
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self.assertAlmostEqual(chgs[1], -0.026, places=3)
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self.assertAlmostEqual(chgs[7], 0.026, places=3)
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def test1(self):
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mol = Chem.MolFromMolFile(
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os.path.join(RDConfig.RDBaseDir, "External", "YAeHMOP", "test_data", "benzene.mol"),
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removeHs=False)
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self.assertEqual(mol.GetNumAtoms(), 12)
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ok, res = rdEHTTools.RunMol(mol)
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self.assertTrue(ok)
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chgs = res.GetAtomicCharges()
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self.assertAlmostEqual(chgs[1], -0.026, places=3)
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self.assertAlmostEqual(chgs[7], 0.026, places=3)
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def test2(self):
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mol = Chem.MolFromMolFile(os.path.join(
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RDConfig.RDBaseDir, "External", "YAeHMOP", "test_data", "benzene.mol"), removeHs=False)
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self.assertEqual(mol.GetNumAtoms(), 12)
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ok, res = rdEHTTools.RunMol(mol)
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self.assertTrue(ok)
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self.assertEqual(res.numOrbitals,30)
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self.assertEqual(res.numElectrons,30)
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cm = res.GetReducedChargeMatrix()
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self.assertEqual(cm.shape, (12, res.numOrbitals))
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for i in range(6):
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self.assertAlmostEqual(cm[i][0], 0.161, places=3)
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self.assertAlmostEqual(cm[i+6][0], 0.005, places=3)
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self.assertAlmostEqual(cm[i][6], 0.1066, places=3)
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self.assertAlmostEqual(cm[i+6][6], 0.060, places=3)
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self.assertAlmostEqual(cm[i][9], 0.167, places=3)
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self.assertAlmostEqual(cm[i+6][9], 0.000, places=3)
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def test2(self):
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mol = Chem.MolFromMolFile(
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os.path.join(RDConfig.RDBaseDir, "External", "YAeHMOP", "test_data", "benzene.mol"),
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removeHs=False)
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self.assertEqual(mol.GetNumAtoms(), 12)
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ok, res = rdEHTTools.RunMol(mol)
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self.assertTrue(ok)
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self.assertEqual(res.numOrbitals, 30)
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self.assertEqual(res.numElectrons, 30)
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cm = res.GetReducedChargeMatrix()
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self.assertEqual(cm.shape, (12, res.numOrbitals))
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for i in range(6):
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self.assertAlmostEqual(cm[i][0], 0.161, places=3)
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self.assertAlmostEqual(cm[i + 6][0], 0.005, places=3)
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self.assertAlmostEqual(cm[i][6], 0.1066, places=3)
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self.assertAlmostEqual(cm[i + 6][6], 0.060, places=3)
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self.assertAlmostEqual(cm[i][9], 0.167, places=3)
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self.assertAlmostEqual(cm[i + 6][9], 0.000, places=3)
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def test3(self):
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mol = Chem.MolFromMolFile(os.path.join(
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RDConfig.RDBaseDir, "External", "YAeHMOP", "test_data", "benzene.mol"), removeHs=False)
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self.assertEqual(mol.GetNumAtoms(), 12)
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ok, res = rdEHTTools.RunMol(mol)
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self.assertTrue(ok)
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opm = res.GetReducedOverlapPopulationMatrix()
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self.assertEqual(opm.shape, (int(12 * 13 / 2),))
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self.assertAlmostEqual(opm[0], 2.7035, 3)
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self.assertAlmostEqual(opm[2], 2.7035, 3)
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self.assertAlmostEqual(opm[3], -0.0785, 3)
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def test3(self):
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mol = Chem.MolFromMolFile(
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os.path.join(RDConfig.RDBaseDir, "External", "YAeHMOP", "test_data", "benzene.mol"),
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removeHs=False)
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self.assertEqual(mol.GetNumAtoms(), 12)
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ok, res = rdEHTTools.RunMol(mol)
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self.assertTrue(ok)
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opm = res.GetReducedOverlapPopulationMatrix()
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self.assertEqual(opm.shape, (int(12 * 13 / 2), ))
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self.assertAlmostEqual(opm[0], 2.7035, 3)
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self.assertAlmostEqual(opm[2], 2.7035, 3)
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self.assertAlmostEqual(opm[3], -0.0785, 3)
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def test1(self):
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mol = Chem.MolFromMolFile(os.path.join(
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RDConfig.RDBaseDir, "External", "YAeHMOP", "test_data", "benzene.mol"), removeHs=False)
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self.assertEqual(mol.GetNumAtoms(), 12)
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ok, res = rdEHTTools.RunMol(mol)
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self.assertTrue(ok)
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self.assertAlmostEqual(res.fermiEnergy, -12.804, places=3)
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self.assertAlmostEqual(res.totalEnergy, -535.026, places=3)
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def test4(self):
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mol = Chem.MolFromMolFile(
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os.path.join(RDConfig.RDBaseDir, "External", "YAeHMOP", "test_data", "benzene.mol"),
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removeHs=False)
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self.assertEqual(mol.GetNumAtoms(), 12)
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ok, res = rdEHTTools.RunMol(mol)
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self.assertTrue(ok)
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self.assertAlmostEqual(res.fermiEnergy, -12.804, places=3)
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self.assertAlmostEqual(res.totalEnergy, -535.026, places=3)
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def test5(self):
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mol = Chem.MolFromMolFile(
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os.path.join(RDConfig.RDBaseDir, "External", "YAeHMOP", "test_data", "benzene.mol"),
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removeHs=False)
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self.assertEqual(mol.GetNumAtoms(), 12)
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ok, res = rdEHTTools.RunMol(mol, keepOverlapAndHamiltonianMatrices=True)
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self.assertTrue(ok)
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orbEs = res.GetOrbitalEnergies()
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self.assertAlmostEqual(orbEs[0], -29.6302, places=3)
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self.assertAlmostEqual(orbEs[14], -12.804, places=3)
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self.assertAlmostEqual(orbEs[29], 67.0404, places=3)
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hamil = res.GetHamiltonian()
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self.assertAlmostEqual(hamil[0, 0], -21.4000, places=3)
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self.assertAlmostEqual(hamil[0, 4], -15.3224, places=3)
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self.assertAlmostEqual(hamil[4, 0], 0.0000, places=3)
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overlap = res.GetOverlapMatrix()
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self.assertAlmostEqual(overlap[0, 0], 1.0000, places=3)
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self.assertAlmostEqual(overlap[0, 4], 0.4091, places=3)
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self.assertAlmostEqual(overlap[4, 0], 0.0000, places=3)
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if __name__ == '__main__':
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unittest.main()
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unittest.main()
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39
External/YAeHMOP/test1.cpp
vendored
39
External/YAeHMOP/test1.cpp
vendored
@@ -37,7 +37,9 @@ TEST_CASE("benzene", "[basics]") {
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REQUIRE(mol);
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REQUIRE(mol->getNumAtoms() == 12);
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EHTTools::EHTResults res;
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REQUIRE(EHTTools::runMol(*mol, res));
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int confId = -1;
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bool preserveMatrices = true;
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REQUIRE(EHTTools::runMol(*mol, res, confId, preserveMatrices));
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CHECK(res.numElectrons == 30);
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CHECK(res.numOrbitals == 30);
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CHECK(res.numAtoms == 12);
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@@ -48,17 +50,40 @@ TEST_CASE("benzene", "[basics]") {
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CHECK(res.atomicCharges[i] == Approx(0.026).margin(0.001));
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}
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for (unsigned int i = 0; i < 6; ++i) {
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CHECK(res.reducedChargeMatrix[i*res.numOrbitals] == Approx(0.1615).margin(0.001));
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CHECK(res.reducedChargeMatrix[i*res.numOrbitals+6] == Approx(0.1066).margin(0.001));
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CHECK(res.reducedChargeMatrix[i*res.numOrbitals+9] == Approx(0.1667).margin(0.001));
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CHECK(res.reducedChargeMatrix[i * res.numOrbitals] ==
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Approx(0.1615).margin(0.001));
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CHECK(res.reducedChargeMatrix[i * res.numOrbitals + 6] ==
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Approx(0.1066).margin(0.001));
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CHECK(res.reducedChargeMatrix[i * res.numOrbitals + 9] ==
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Approx(0.1667).margin(0.001));
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}
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for (unsigned int i = 6; i < 12; ++i) {
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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.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
|
||||
|
||||
32
External/YAeHMOP/test_data/benzene.b
vendored
Normal file
32
External/YAeHMOP/test_data/benzene.b
vendored
Normal file
@@ -0,0 +1,32 @@
|
||||
Benzene
|
||||
|
||||
|
||||
Molecular
|
||||
|
||||
|
||||
Geometry
|
||||
12
|
||||
C 1.236700 -0.644200 -0.035000
|
||||
C 1.175700 0.749200 -0.043100
|
||||
C -0.060900 1.393500 -0.008200
|
||||
C -1.236600 0.644200 0.035000
|
||||
C -1.175700 -0.749200 0.043200
|
||||
C 0.060900 -1.393500 0.008200
|
||||
H 2.200100 -1.146100 -0.062200
|
||||
H 2.091700 1.333000 -0.076800
|
||||
H -0.108400 2.479100 -0.014500
|
||||
H -2.200100 1.146100 0.062300
|
||||
H -2.091700 -1.333000 0.076800
|
||||
H 0.108400 -2.479100 0.014500
|
||||
|
||||
|
||||
|
||||
charge
|
||||
0
|
||||
|
||||
Print
|
||||
net charges
|
||||
overlap
|
||||
hamiltonian
|
||||
end_print
|
||||
|
||||
707
External/YAeHMOP/test_data/benzene.b.out
vendored
Normal file
707
External/YAeHMOP/test_data/benzene.b.out
vendored
Normal file
@@ -0,0 +1,707 @@
|
||||
#BIND_OUTPUT version: 3.0
|
||||
|
||||
#JOB_TITLE: Benzene
|
||||
|
||||
; ********* Atoms within the unit cell: *********
|
||||
# NUMBER OF ATOMS:
|
||||
12
|
||||
# ATOMIC POSITIONS
|
||||
1 C 1.236700 -0.644200 -0.035000
|
||||
2 C 1.175700 0.749200 -0.043100
|
||||
3 C -0.060900 1.393500 -0.008200
|
||||
4 C -1.236600 0.644200 0.035000
|
||||
5 C -1.175700 -0.749200 0.043200
|
||||
6 C 0.060900 -1.393500 0.008200
|
||||
7 H 2.200100 -1.146100 -0.062200
|
||||
8 H 2.091700 1.333000 -0.076800
|
||||
9 H -0.108400 2.479100 -0.014500
|
||||
10 H -2.200100 1.146100 0.062300
|
||||
11 H -2.091700 -1.333000 0.076800
|
||||
12 H 0.108400 -2.479100 0.014500
|
||||
|
||||
|
||||
# ******** Extended Hueckel Parameters ********
|
||||
; FORMAT quantum number orbital: Hii, <c1>, exponent1, <c2>, <exponent2>
|
||||
|
||||
ATOM: C Atomic number: 6 # Valence Electrons: 4
|
||||
2S: -21.4000 1.6250
|
||||
2P: -11.4000 1.6250
|
||||
ATOM: H Atomic number: 1 # Valence Electrons: 1
|
||||
1S: -13.6000 1.3000
|
||||
|
||||
; Number of orbitals
|
||||
#Num_Orbitals: 30
|
||||
; --- Overlap Matrix S(R) ---
|
||||
C( 1) 2s C( 1) 2px C( 1) 2py
|
||||
C( 1) 2s 1.0000 0.0000 0.0000
|
||||
C( 1) 2px 0.0000 1.0000 0.0000
|
||||
C( 1) 2py 0.0000 0.0000 1.0000
|
||||
C( 1) 2pz 0.0000 0.0000 0.0000
|
||||
C( 2) 2s 0.0000 0.0000 0.0000
|
||||
C( 2) 2px 0.0000 0.0000 0.0000
|
||||
C( 2) 2py 0.0000 0.0000 0.0000
|
||||
C( 2) 2pz 0.0000 0.0000 0.0000
|
||||
C( 3) 2s 0.0000 0.0000 0.0000
|
||||
C( 3) 2px 0.0000 0.0000 0.0000
|
||||
C( 3) 2py 0.0000 0.0000 0.0000
|
||||
C( 3) 2pz 0.0000 0.0000 0.0000
|
||||
C( 4) 2s 0.0000 0.0000 0.0000
|
||||
C( 4) 2px 0.0000 0.0000 0.0000
|
||||
C( 4) 2py 0.0000 0.0000 0.0000
|
||||
C( 4) 2pz 0.0000 0.0000 0.0000
|
||||
C( 5) 2s 0.0000 0.0000 0.0000
|
||||
C( 5) 2px 0.0000 0.0000 0.0000
|
||||
C( 5) 2py 0.0000 0.0000 0.0000
|
||||
C( 5) 2pz 0.0000 0.0000 0.0000
|
||||
C( 6) 2s 0.0000 0.0000 0.0000
|
||||
C( 6) 2px 0.0000 0.0000 0.0000
|
||||
C( 6) 2py 0.0000 0.0000 0.0000
|
||||
C( 6) 2pz 0.0000 0.0000 0.0000
|
||||
H( 7) 1s 0.0000 0.0000 0.0000
|
||||
H( 8) 1s 0.0000 0.0000 0.0000
|
||||
H( 9) 1s 0.0000 0.0000 0.0000
|
||||
H( 10) 1s 0.0000 0.0000 0.0000
|
||||
H( 11) 1s 0.0000 0.0000 0.0000
|
||||
H( 12) 1s 0.0000 0.0000 0.0000
|
||||
C( 1) 2pz C( 2) 2s C( 2) 2px
|
||||
C( 1) 2s 0.0000 0.4091 0.0181
|
||||
C( 1) 2px 0.0000 -0.0181 0.2454
|
||||
C( 1) 2py 0.0000 0.4146 0.0252
|
||||
C( 1) 2pz 1.0000 -0.0024 -0.0001
|
||||
C( 2) 2s 0.0000 1.0000 0.0000
|
||||
C( 2) 2px 0.0000 0.0000 1.0000
|
||||
C( 2) 2py 0.0000 0.0000 0.0000
|
||||
C( 2) 2pz 0.0000 0.0000 0.0000
|
||||
C( 3) 2s 0.0000 0.0000 0.0000
|
||||
C( 3) 2px 0.0000 0.0000 0.0000
|
||||
C( 3) 2py 0.0000 0.0000 0.0000
|
||||
C( 3) 2pz 0.0000 0.0000 0.0000
|
||||
C( 4) 2s 0.0000 0.0000 0.0000
|
||||
C( 4) 2px 0.0000 0.0000 0.0000
|
||||
C( 4) 2py 0.0000 0.0000 0.0000
|
||||
C( 4) 2pz 0.0000 0.0000 0.0000
|
||||
C( 5) 2s 0.0000 0.0000 0.0000
|
||||
C( 5) 2px 0.0000 0.0000 0.0000
|
||||
C( 5) 2py 0.0000 0.0000 0.0000
|
||||
C( 5) 2pz 0.0000 0.0000 0.0000
|
||||
C( 6) 2s 0.0000 0.0000 0.0000
|
||||
C( 6) 2px 0.0000 0.0000 0.0000
|
||||
C( 6) 2py 0.0000 0.0000 0.0000
|
||||
C( 6) 2pz 0.0000 0.0000 0.0000
|
||||
H( 7) 1s 0.0000 0.0000 0.0000
|
||||
H( 8) 1s 0.0000 0.0000 0.0000
|
||||
H( 9) 1s 0.0000 0.0000 0.0000
|
||||
H( 10) 1s 0.0000 0.0000 0.0000
|
||||
H( 11) 1s 0.0000 0.0000 0.0000
|
||||
H( 12) 1s 0.0000 0.0000 0.0000
|
||||
C( 2) 2py C( 2) 2pz C( 3) 2s
|
||||
C( 1) 2s -0.4146 0.0024 0.0873
|
||||
C( 1) 2px 0.0252 -0.0001 -0.0611
|
||||
C( 1) 2py -0.3295 0.0033 0.0960
|
||||
C( 1) 2pz 0.0033 0.2465 0.0013
|
||||
C( 2) 2s 0.0000 0.0000 0.4091
|
||||
C( 2) 2px 0.0000 0.0000 -0.3679
|
||||
C( 2) 2py 1.0000 0.0000 0.1917
|
||||
C( 2) 2pz 0.0000 1.0000 0.0104
|
||||
C( 3) 2s 0.0000 0.0000 1.0000
|
||||
C( 3) 2px 0.0000 0.0000 0.0000
|
||||
C( 3) 2py 0.0000 0.0000 0.0000
|
||||
C( 3) 2pz 0.0000 0.0000 0.0000
|
||||
C( 4) 2s 0.0000 0.0000 0.0000
|
||||
C( 4) 2px 0.0000 0.0000 0.0000
|
||||
C( 4) 2py 0.0000 0.0000 0.0000
|
||||
C( 4) 2pz 0.0000 0.0000 0.0000
|
||||
C( 5) 2s 0.0000 0.0000 0.0000
|
||||
C( 5) 2px 0.0000 0.0000 0.0000
|
||||
C( 5) 2py 0.0000 0.0000 0.0000
|
||||
C( 5) 2pz 0.0000 0.0000 0.0000
|
||||
C( 6) 2s 0.0000 0.0000 0.0000
|
||||
C( 6) 2px 0.0000 0.0000 0.0000
|
||||
C( 6) 2py 0.0000 0.0000 0.0000
|
||||
C( 6) 2pz 0.0000 0.0000 0.0000
|
||||
H( 7) 1s 0.0000 0.0000 0.0000
|
||||
H( 8) 1s 0.0000 0.0000 0.0000
|
||||
H( 9) 1s 0.0000 0.0000 0.0000
|
||||
H( 10) 1s 0.0000 0.0000 0.0000
|
||||
H( 11) 1s 0.0000 0.0000 0.0000
|
||||
H( 12) 1s 0.0000 0.0000 0.0000
|
||||
C( 3) 2px C( 3) 2py C( 3) 2pz
|
||||
C( 1) 2s 0.0611 -0.0960 -0.0013
|
||||
C( 1) 2px -0.0164 0.0801 0.0011
|
||||
C( 1) 2py 0.0801 -0.0912 -0.0017
|
||||
C( 1) 2pz 0.0011 -0.0017 0.0346
|
||||
C( 2) 2s 0.3679 -0.1917 -0.0104
|
||||
C( 2) 2px -0.2071 0.2363 0.0128
|
||||
C( 2) 2py 0.2363 0.1233 -0.0067
|
||||
C( 2) 2pz 0.0128 -0.0067 0.2461
|
||||
C( 3) 2s 0.0000 0.0000 0.0000
|
||||
C( 3) 2px 1.0000 0.0000 0.0000
|
||||
C( 3) 2py 0.0000 1.0000 0.0000
|
||||
C( 3) 2pz 0.0000 0.0000 1.0000
|
||||
C( 4) 2s 0.0000 0.0000 0.0000
|
||||
C( 4) 2px 0.0000 0.0000 0.0000
|
||||
C( 4) 2py 0.0000 0.0000 0.0000
|
||||
C( 4) 2pz 0.0000 0.0000 0.0000
|
||||
C( 5) 2s 0.0000 0.0000 0.0000
|
||||
C( 5) 2px 0.0000 0.0000 0.0000
|
||||
C( 5) 2py 0.0000 0.0000 0.0000
|
||||
C( 5) 2pz 0.0000 0.0000 0.0000
|
||||
C( 6) 2s 0.0000 0.0000 0.0000
|
||||
C( 6) 2px 0.0000 0.0000 0.0000
|
||||
C( 6) 2py 0.0000 0.0000 0.0000
|
||||
C( 6) 2pz 0.0000 0.0000 0.0000
|
||||
H( 7) 1s 0.0000 0.0000 0.0000
|
||||
H( 8) 1s 0.0000 0.0000 0.0000
|
||||
H( 9) 1s 0.0000 0.0000 0.0000
|
||||
H( 10) 1s 0.0000 0.0000 0.0000
|
||||
H( 11) 1s 0.0000 0.0000 0.0000
|
||||
H( 12) 1s 0.0000 0.0000 0.0000
|
||||
C( 4) 2s C( 4) 2px C( 4) 2py
|
||||
C( 1) 2s 0.0441 0.0533 -0.0278
|
||||
C( 1) 2px -0.0533 -0.0594 0.0389
|
||||
C( 1) 2py 0.0278 0.0389 -0.0049
|
||||
C( 1) 2pz 0.0015 0.0021 -0.0011
|
||||
C( 2) 2s 0.0873 0.1136 0.0049
|
||||
C( 2) 2px -0.1136 -0.1417 -0.0077
|
||||
C( 2) 2py -0.0049 -0.0077 0.0343
|
||||
C( 2) 2pz 0.0037 0.0057 0.0002
|
||||
C( 3) 2s 0.4091 0.3498 0.2229
|
||||
C( 3) 2px -0.3498 -0.1636 -0.2613
|
||||
C( 3) 2py -0.2229 -0.2613 0.0799
|
||||
C( 3) 2pz 0.0129 0.0151 0.0096
|
||||
C( 4) 2s 1.0000 0.0000 0.0000
|
||||
C( 4) 2px 0.0000 1.0000 0.0000
|
||||
C( 4) 2py 0.0000 0.0000 1.0000
|
||||
C( 4) 2pz 0.0000 0.0000 0.0000
|
||||
C( 5) 2s 0.0000 0.0000 0.0000
|
||||
C( 5) 2px 0.0000 0.0000 0.0000
|
||||
C( 5) 2py 0.0000 0.0000 0.0000
|
||||
C( 5) 2pz 0.0000 0.0000 0.0000
|
||||
C( 6) 2s 0.0000 0.0000 0.0000
|
||||
C( 6) 2px 0.0000 0.0000 0.0000
|
||||
C( 6) 2py 0.0000 0.0000 0.0000
|
||||
C( 6) 2pz 0.0000 0.0000 0.0000
|
||||
H( 7) 1s 0.0000 0.0000 0.0000
|
||||
H( 8) 1s 0.0000 0.0000 0.0000
|
||||
H( 9) 1s 0.0000 0.0000 0.0000
|
||||
H( 10) 1s 0.0000 0.0000 0.0000
|
||||
H( 11) 1s 0.0000 0.0000 0.0000
|
||||
H( 12) 1s 0.0000 0.0000 0.0000
|
||||
C( 4) 2pz C( 5) 2s C( 5) 2px
|
||||
C( 1) 2s -0.0015 0.0873 0.1136
|
||||
C( 1) 2px 0.0021 -0.1136 -0.1416
|
||||
C( 1) 2py -0.0011 -0.0049 -0.0077
|
||||
C( 1) 2pz 0.0153 0.0037 0.0057
|
||||
C( 2) 2s -0.0037 0.0441 0.0507
|
||||
C( 2) 2px 0.0057 -0.0507 -0.0522
|
||||
C( 2) 2py 0.0002 -0.0323 -0.0431
|
||||
C( 2) 2pz 0.0344 0.0019 0.0025
|
||||
C( 3) 2s -0.0129 0.0873 0.0525
|
||||
C( 3) 2px 0.0151 -0.0525 -0.0030
|
||||
C( 3) 2py 0.0096 -0.1009 -0.0723
|
||||
C( 3) 2pz 0.2459 0.0024 0.0017
|
||||
C( 4) 2s 0.0000 0.4091 -0.0181
|
||||
C( 4) 2px 0.0000 0.0181 0.2454
|
||||
C( 4) 2py 0.0000 -0.4146 0.0252
|
||||
C( 4) 2pz 1.0000 0.0024 -0.0001
|
||||
C( 5) 2s 0.0000 1.0000 0.0000
|
||||
C( 5) 2px 0.0000 0.0000 1.0000
|
||||
C( 5) 2py 0.0000 0.0000 0.0000
|
||||
C( 5) 2pz 0.0000 0.0000 0.0000
|
||||
C( 6) 2s 0.0000 0.0000 0.0000
|
||||
C( 6) 2px 0.0000 0.0000 0.0000
|
||||
C( 6) 2py 0.0000 0.0000 0.0000
|
||||
C( 6) 2pz 0.0000 0.0000 0.0000
|
||||
H( 7) 1s 0.0000 0.0000 0.0000
|
||||
H( 8) 1s 0.0000 0.0000 0.0000
|
||||
H( 9) 1s 0.0000 0.0000 0.0000
|
||||
H( 10) 1s 0.0000 0.0000 0.0000
|
||||
H( 11) 1s 0.0000 0.0000 0.0000
|
||||
H( 12) 1s 0.0000 0.0000 0.0000
|
||||
C( 5) 2py C( 5) 2pz C( 6) 2s
|
||||
C( 1) 2s 0.0049 -0.0037 0.4091
|
||||
C( 1) 2px -0.0077 0.0057 -0.3498
|
||||
C( 1) 2py 0.0343 0.0002 -0.2229
|
||||
C( 1) 2pz 0.0002 0.0344 0.0129
|
||||
C( 2) 2s 0.0323 -0.0019 0.0873
|
||||
C( 2) 2px -0.0431 0.0025 -0.0525
|
||||
C( 2) 2py -0.0120 0.0016 -0.1009
|
||||
C( 2) 2pz 0.0016 0.0153 0.0024
|
||||
C( 3) 2s 0.1009 -0.0024 0.0441
|
||||
C( 3) 2px -0.0723 0.0017 0.0026
|
||||
C( 3) 2py -0.1045 0.0033 -0.0600
|
||||
C( 3) 2pz 0.0033 0.0345 0.0004
|
||||
C( 4) 2s 0.4146 -0.0024 0.0873
|
||||
C( 4) 2px 0.0252 -0.0001 0.0611
|
||||
C( 4) 2py -0.3295 0.0034 -0.0960
|
||||
C( 4) 2pz 0.0034 0.2465 -0.0013
|
||||
C( 5) 2s 0.0000 0.0000 0.4091
|
||||
C( 5) 2px 0.0000 0.0000 0.3679
|
||||
C( 5) 2py 1.0000 0.0000 -0.1917
|
||||
C( 5) 2pz 0.0000 1.0000 -0.0104
|
||||
C( 6) 2s 0.0000 0.0000 1.0000
|
||||
C( 6) 2px 0.0000 0.0000 0.0000
|
||||
C( 6) 2py 0.0000 0.0000 0.0000
|
||||
C( 6) 2pz 0.0000 0.0000 0.0000
|
||||
H( 7) 1s 0.0000 0.0000 0.0000
|
||||
H( 8) 1s 0.0000 0.0000 0.0000
|
||||
H( 9) 1s 0.0000 0.0000 0.0000
|
||||
H( 10) 1s 0.0000 0.0000 0.0000
|
||||
H( 11) 1s 0.0000 0.0000 0.0000
|
||||
H( 12) 1s 0.0000 0.0000 0.0000
|
||||
C( 6) 2px C( 6) 2py C( 6) 2pz
|
||||
C( 1) 2s 0.3498 0.2229 -0.0129
|
||||
C( 1) 2px -0.1636 -0.2613 0.0151
|
||||
C( 1) 2py -0.2613 0.0799 0.0096
|
||||
C( 1) 2pz 0.0151 0.0096 0.2459
|
||||
C( 2) 2s 0.0525 0.1009 -0.0024
|
||||
C( 2) 2px -0.0030 -0.0723 0.0017
|
||||
C( 2) 2py -0.0723 -0.1045 0.0033
|
||||
C( 2) 2pz 0.0017 0.0033 0.0345
|
||||
C( 3) 2s -0.0026 0.0600 -0.0004
|
||||
C( 3) 2px 0.0152 0.0041 0.0000
|
||||
C( 3) 2py 0.0041 -0.0795 0.0006
|
||||
C( 3) 2pz 0.0000 0.0006 0.0154
|
||||
C( 4) 2s -0.0611 0.0960 0.0013
|
||||
C( 4) 2px -0.0164 0.0801 0.0011
|
||||
C( 4) 2py 0.0801 -0.0912 -0.0017
|
||||
C( 4) 2pz 0.0011 -0.0017 0.0346
|
||||
C( 5) 2s -0.3679 0.1917 0.0104
|
||||
C( 5) 2px -0.2071 0.2363 0.0128
|
||||
C( 5) 2py 0.2363 0.1233 -0.0067
|
||||
C( 5) 2pz 0.0128 -0.0067 0.2461
|
||||
C( 6) 2s 0.0000 0.0000 0.0000
|
||||
C( 6) 2px 1.0000 0.0000 0.0000
|
||||
C( 6) 2py 0.0000 1.0000 0.0000
|
||||
C( 6) 2pz 0.0000 0.0000 1.0000
|
||||
H( 7) 1s 0.0000 0.0000 0.0000
|
||||
H( 8) 1s 0.0000 0.0000 0.0000
|
||||
H( 9) 1s 0.0000 0.0000 0.0000
|
||||
H( 10) 1s 0.0000 0.0000 0.0000
|
||||
H( 11) 1s 0.0000 0.0000 0.0000
|
||||
H( 12) 1s 0.0000 0.0000 0.0000
|
||||
H( 7) 1s H( 8) 1s H( 9) 1s
|
||||
C( 1) 2s 0.4943 0.1039 0.0100
|
||||
C( 1) 2px 0.4367 0.0527 -0.0055
|
||||
C( 1) 2py -0.2275 0.1218 0.0128
|
||||
C( 1) 2pz -0.0123 -0.0026 0.0000
|
||||
C( 2) 2s 0.1039 0.4942 0.1039
|
||||
C( 2) 2px 0.0631 0.4152 -0.0791
|
||||
C( 2) 2py -0.1168 0.2646 0.1065
|
||||
C( 2) 2pz -0.0012 -0.0153 0.0018
|
||||
C( 3) 2s 0.0100 0.1039 0.4942
|
||||
C( 3) 2px 0.0093 0.1326 -0.0215
|
||||
C( 3) 2py -0.0104 -0.0037 0.4921
|
||||
C( 3) 2pz -0.0002 -0.0042 -0.0029
|
||||
C( 4) 2s 0.0038 0.0100 0.1039
|
||||
C( 4) 2px 0.0048 0.0137 0.0695
|
||||
C( 4) 2py -0.0025 0.0028 0.1130
|
||||
C( 4) 2pz -0.0001 -0.0005 -0.0030
|
||||
C( 5) 2s 0.0100 0.0038 0.0100
|
||||
C( 5) 2px 0.0139 0.0045 0.0044
|
||||
C( 5) 2py -0.0016 0.0029 0.0133
|
||||
C( 5) 2pz -0.0004 -0.0002 -0.0002
|
||||
C( 6) 2s 0.1039 0.0100 0.0038
|
||||
C( 6) 2px 0.1318 0.0083 -0.0002
|
||||
C( 6) 2py 0.0152 0.0112 0.0054
|
||||
C( 6) 2pz -0.0043 -0.0003 0.0000
|
||||
H( 7) 1s 1.0000 0.0439 0.0013
|
||||
H( 8) 1s 0.0000 1.0000 0.0439
|
||||
H( 9) 1s 0.0000 0.0000 1.0000
|
||||
H( 10) 1s 0.0000 0.0000 0.0000
|
||||
H( 11) 1s 0.0000 0.0000 0.0000
|
||||
H( 12) 1s 0.0000 0.0000 0.0000
|
||||
H( 10) 1s H( 11) 1s H( 12) 1s
|
||||
C( 1) 2s 0.0038 0.0100 0.1039
|
||||
C( 1) 2px -0.0048 -0.0137 -0.0695
|
||||
C( 1) 2py 0.0025 -0.0028 -0.1130
|
||||
C( 1) 2pz 0.0001 0.0005 0.0030
|
||||
C( 2) 2s 0.0100 0.0038 0.0100
|
||||
C( 2) 2px -0.0139 -0.0045 -0.0044
|
||||
C( 2) 2py 0.0016 -0.0029 -0.0133
|
||||
C( 2) 2pz 0.0004 0.0002 0.0002
|
||||
C( 3) 2s 0.1039 0.0100 0.0038
|
||||
C( 3) 2px -0.1318 -0.0083 0.0002
|
||||
C( 3) 2py -0.0152 -0.0112 -0.0054
|
||||
C( 3) 2pz 0.0043 0.0003 0.0000
|
||||
C( 4) 2s 0.4942 0.1039 0.0100
|
||||
C( 4) 2px -0.4367 -0.0527 0.0055
|
||||
C( 4) 2py 0.2275 -0.1218 -0.0128
|
||||
C( 4) 2pz 0.0124 0.0026 0.0000
|
||||
C( 5) 2s 0.1039 0.4942 0.1039
|
||||
C( 5) 2px -0.0631 -0.4152 0.0791
|
||||
C( 5) 2py 0.1168 -0.2646 -0.1065
|
||||
C( 5) 2pz 0.0012 0.0152 -0.0018
|
||||
C( 6) 2s 0.0100 0.1039 0.4942
|
||||
C( 6) 2px -0.0093 -0.1326 0.0215
|
||||
C( 6) 2py 0.0104 0.0037 -0.4921
|
||||
C( 6) 2pz 0.0002 0.0042 0.0029
|
||||
H( 7) 1s 0.0003 0.0013 0.0439
|
||||
H( 8) 1s 0.0013 0.0003 0.0013
|
||||
H( 9) 1s 0.0439 0.0013 0.0003
|
||||
H( 10) 1s 1.0000 0.0439 0.0013
|
||||
H( 11) 1s 0.0000 1.0000 0.0439
|
||||
H( 12) 1s 0.0000 0.0000 1.0000
|
||||
|
||||
|
||||
; --- Hamiltonian H(R) ---
|
||||
C( 1) 2s C( 1) 2px C( 1) 2py
|
||||
C( 1) 2s -21.4000 0.0000 0.0000
|
||||
C( 1) 2px 0.0000 -11.4000 0.0000
|
||||
C( 1) 2py 0.0000 0.0000 -11.4000
|
||||
C( 1) 2pz 0.0000 0.0000 0.0000
|
||||
C( 2) 2s 0.0000 0.0000 0.0000
|
||||
C( 2) 2px 0.0000 0.0000 0.0000
|
||||
C( 2) 2py 0.0000 0.0000 0.0000
|
||||
C( 2) 2pz 0.0000 0.0000 0.0000
|
||||
C( 3) 2s 0.0000 0.0000 0.0000
|
||||
C( 3) 2px 0.0000 0.0000 0.0000
|
||||
C( 3) 2py 0.0000 0.0000 0.0000
|
||||
C( 3) 2pz 0.0000 0.0000 0.0000
|
||||
C( 4) 2s 0.0000 0.0000 0.0000
|
||||
C( 4) 2px 0.0000 0.0000 0.0000
|
||||
C( 4) 2py 0.0000 0.0000 0.0000
|
||||
C( 4) 2pz 0.0000 0.0000 0.0000
|
||||
C( 5) 2s 0.0000 0.0000 0.0000
|
||||
C( 5) 2px 0.0000 0.0000 0.0000
|
||||
C( 5) 2py 0.0000 0.0000 0.0000
|
||||
C( 5) 2pz 0.0000 0.0000 0.0000
|
||||
C( 6) 2s 0.0000 0.0000 0.0000
|
||||
C( 6) 2px 0.0000 0.0000 0.0000
|
||||
C( 6) 2py 0.0000 0.0000 0.0000
|
||||
C( 6) 2pz 0.0000 0.0000 0.0000
|
||||
H( 7) 1s 0.0000 0.0000 0.0000
|
||||
H( 8) 1s 0.0000 0.0000 0.0000
|
||||
H( 9) 1s 0.0000 0.0000 0.0000
|
||||
H( 10) 1s 0.0000 0.0000 0.0000
|
||||
H( 11) 1s 0.0000 0.0000 0.0000
|
||||
H( 12) 1s 0.0000 0.0000 0.0000
|
||||
C( 1) 2pz C( 2) 2s C( 2) 2px
|
||||
C( 1) 2s 0.0000 -15.3224 -0.5466
|
||||
C( 1) 2px 0.0000 0.5466 -4.8954
|
||||
C( 1) 2py 0.0000 -12.4867 -0.5031
|
||||
C( 1) 2pz -11.4000 0.0726 0.0029
|
||||
C( 2) 2s 0.0000 -21.4000 0.0000
|
||||
C( 2) 2px 0.0000 0.0000 -11.4000
|
||||
C( 2) 2py 0.0000 0.0000 0.0000
|
||||
C( 2) 2pz 0.0000 0.0000 0.0000
|
||||
C( 3) 2s 0.0000 0.0000 0.0000
|
||||
C( 3) 2px 0.0000 0.0000 0.0000
|
||||
C( 3) 2py 0.0000 0.0000 0.0000
|
||||
C( 3) 2pz 0.0000 0.0000 0.0000
|
||||
C( 4) 2s 0.0000 0.0000 0.0000
|
||||
C( 4) 2px 0.0000 0.0000 0.0000
|
||||
C( 4) 2py 0.0000 0.0000 0.0000
|
||||
C( 4) 2pz 0.0000 0.0000 0.0000
|
||||
C( 5) 2s 0.0000 0.0000 0.0000
|
||||
C( 5) 2px 0.0000 0.0000 0.0000
|
||||
C( 5) 2py 0.0000 0.0000 0.0000
|
||||
C( 5) 2pz 0.0000 0.0000 0.0000
|
||||
C( 6) 2s 0.0000 0.0000 0.0000
|
||||
C( 6) 2px 0.0000 0.0000 0.0000
|
||||
C( 6) 2py 0.0000 0.0000 0.0000
|
||||
C( 6) 2pz 0.0000 0.0000 0.0000
|
||||
H( 7) 1s 0.0000 0.0000 0.0000
|
||||
H( 8) 1s 0.0000 0.0000 0.0000
|
||||
H( 9) 1s 0.0000 0.0000 0.0000
|
||||
H( 10) 1s 0.0000 0.0000 0.0000
|
||||
H( 11) 1s 0.0000 0.0000 0.0000
|
||||
H( 12) 1s 0.0000 0.0000 0.0000
|
||||
C( 2) 2py C( 2) 2pz C( 3) 2s
|
||||
C( 1) 2s 12.4867 -0.0726 -3.2707
|
||||
C( 1) 2px -0.5031 0.0029 1.8404
|
||||
C( 1) 2py 6.5739 -0.0668 -2.8901
|
||||
C( 1) 2pz -0.0668 -4.9171 -0.0380
|
||||
C( 2) 2s 0.0000 0.0000 -15.3212
|
||||
C( 2) 2px 0.0000 0.0000 11.0805
|
||||
C( 2) 2py -11.4000 0.0000 -5.7732
|
||||
C( 2) 2pz 0.0000 -11.4000 -0.3127
|
||||
C( 3) 2s 0.0000 0.0000 -21.4000
|
||||
C( 3) 2px 0.0000 0.0000 0.0000
|
||||
C( 3) 2py 0.0000 0.0000 0.0000
|
||||
C( 3) 2pz 0.0000 0.0000 0.0000
|
||||
C( 4) 2s 0.0000 0.0000 0.0000
|
||||
C( 4) 2px 0.0000 0.0000 0.0000
|
||||
C( 4) 2py 0.0000 0.0000 0.0000
|
||||
C( 4) 2pz 0.0000 0.0000 0.0000
|
||||
C( 5) 2s 0.0000 0.0000 0.0000
|
||||
C( 5) 2px 0.0000 0.0000 0.0000
|
||||
C( 5) 2py 0.0000 0.0000 0.0000
|
||||
C( 5) 2pz 0.0000 0.0000 0.0000
|
||||
C( 6) 2s 0.0000 0.0000 0.0000
|
||||
C( 6) 2px 0.0000 0.0000 0.0000
|
||||
C( 6) 2py 0.0000 0.0000 0.0000
|
||||
C( 6) 2pz 0.0000 0.0000 0.0000
|
||||
H( 7) 1s 0.0000 0.0000 0.0000
|
||||
H( 8) 1s 0.0000 0.0000 0.0000
|
||||
H( 9) 1s 0.0000 0.0000 0.0000
|
||||
H( 10) 1s 0.0000 0.0000 0.0000
|
||||
H( 11) 1s 0.0000 0.0000 0.0000
|
||||
H( 12) 1s 0.0000 0.0000 0.0000
|
||||
C( 3) 2px C( 3) 2py C( 3) 2pz
|
||||
C( 1) 2s -1.8404 2.8901 0.0380
|
||||
C( 1) 2px 0.3272 -1.5975 -0.0210
|
||||
C( 1) 2py -1.5975 1.8185 0.0330
|
||||
C( 1) 2pz -0.0210 0.0330 -0.6897
|
||||
C( 2) 2s -11.0805 5.7732 0.3127
|
||||
C( 2) 2px 4.1325 -4.7150 -0.2554
|
||||
C( 2) 2py -4.7150 -2.4603 0.1331
|
||||
C( 2) 2pz -0.2554 0.1331 -4.9097
|
||||
C( 3) 2s 0.0000 0.0000 0.0000
|
||||
C( 3) 2px -11.4000 0.0000 0.0000
|
||||
C( 3) 2py 0.0000 -11.4000 0.0000
|
||||
C( 3) 2pz 0.0000 0.0000 -11.4000
|
||||
C( 4) 2s 0.0000 0.0000 0.0000
|
||||
C( 4) 2px 0.0000 0.0000 0.0000
|
||||
C( 4) 2py 0.0000 0.0000 0.0000
|
||||
C( 4) 2pz 0.0000 0.0000 0.0000
|
||||
C( 5) 2s 0.0000 0.0000 0.0000
|
||||
C( 5) 2px 0.0000 0.0000 0.0000
|
||||
C( 5) 2py 0.0000 0.0000 0.0000
|
||||
C( 5) 2pz 0.0000 0.0000 0.0000
|
||||
C( 6) 2s 0.0000 0.0000 0.0000
|
||||
C( 6) 2px 0.0000 0.0000 0.0000
|
||||
C( 6) 2py 0.0000 0.0000 0.0000
|
||||
C( 6) 2pz 0.0000 0.0000 0.0000
|
||||
H( 7) 1s 0.0000 0.0000 0.0000
|
||||
H( 8) 1s 0.0000 0.0000 0.0000
|
||||
H( 9) 1s 0.0000 0.0000 0.0000
|
||||
H( 10) 1s 0.0000 0.0000 0.0000
|
||||
H( 11) 1s 0.0000 0.0000 0.0000
|
||||
H( 12) 1s 0.0000 0.0000 0.0000
|
||||
C( 4) 2s C( 4) 2px C( 4) 2py
|
||||
C( 1) 2s -1.6524 -1.6049 0.8360
|
||||
C( 1) 2px 1.6049 1.1843 -0.7769
|
||||
C( 1) 2py -0.8360 -0.7769 0.0976
|
||||
C( 1) 2pz -0.0454 -0.0422 0.0220
|
||||
C( 2) 2s -3.2711 -3.4220 -0.1489
|
||||
C( 2) 2px 3.4220 2.8262 0.1531
|
||||
C( 2) 2py 0.1489 0.1531 -0.6836
|
||||
C( 2) 2pz -0.1108 -0.1138 -0.0050
|
||||
C( 3) 2s -15.3208 -10.5344 -6.7138
|
||||
C( 3) 2px 10.5344 3.2629 5.2131
|
||||
C( 3) 2py 6.7138 5.2131 -1.5943
|
||||
C( 3) 2pz -0.3871 -0.3006 -0.1916
|
||||
C( 4) 2s -21.4000 0.0000 0.0000
|
||||
C( 4) 2px 0.0000 -11.4000 0.0000
|
||||
C( 4) 2py 0.0000 0.0000 -11.4000
|
||||
C( 4) 2pz 0.0000 0.0000 0.0000
|
||||
C( 5) 2s 0.0000 0.0000 0.0000
|
||||
C( 5) 2px 0.0000 0.0000 0.0000
|
||||
C( 5) 2py 0.0000 0.0000 0.0000
|
||||
C( 5) 2pz 0.0000 0.0000 0.0000
|
||||
C( 6) 2s 0.0000 0.0000 0.0000
|
||||
C( 6) 2px 0.0000 0.0000 0.0000
|
||||
C( 6) 2py 0.0000 0.0000 0.0000
|
||||
C( 6) 2pz 0.0000 0.0000 0.0000
|
||||
H( 7) 1s 0.0000 0.0000 0.0000
|
||||
H( 8) 1s 0.0000 0.0000 0.0000
|
||||
H( 9) 1s 0.0000 0.0000 0.0000
|
||||
H( 10) 1s 0.0000 0.0000 0.0000
|
||||
H( 11) 1s 0.0000 0.0000 0.0000
|
||||
H( 12) 1s 0.0000 0.0000 0.0000
|
||||
C( 4) 2pz C( 5) 2s C( 5) 2px
|
||||
C( 1) 2s 0.0454 -3.2705 -3.4214
|
||||
C( 1) 2px -0.0422 3.4214 2.8258
|
||||
C( 1) 2py 0.0220 0.1489 0.1530
|
||||
C( 1) 2pz -0.3059 -0.1109 -0.1140
|
||||
C( 2) 2s 0.1108 -1.6526 -1.5260
|
||||
C( 2) 2px -0.1138 1.5260 1.0411
|
||||
C( 2) 2py -0.0050 0.9725 0.8591
|
||||
C( 2) 2pz -0.6865 -0.0560 -0.0495
|
||||
C( 3) 2s 0.3871 -3.2708 -1.5812
|
||||
C( 3) 2px -0.3006 1.5812 0.0607
|
||||
C( 3) 2py -0.1916 3.0392 1.4432
|
||||
C( 3) 2pz -4.9057 -0.0729 -0.0346
|
||||
C( 4) 2s 0.0000 -15.3224 0.5457
|
||||
C( 4) 2px 0.0000 -0.5457 -4.8955
|
||||
C( 4) 2py 0.0000 12.4867 -0.5022
|
||||
C( 4) 2pz -11.4000 -0.0735 0.0030
|
||||
C( 5) 2s 0.0000 -21.4000 0.0000
|
||||
C( 5) 2px 0.0000 0.0000 -11.4000
|
||||
C( 5) 2py 0.0000 0.0000 0.0000
|
||||
C( 5) 2pz 0.0000 0.0000 0.0000
|
||||
C( 6) 2s 0.0000 0.0000 0.0000
|
||||
C( 6) 2px 0.0000 0.0000 0.0000
|
||||
C( 6) 2py 0.0000 0.0000 0.0000
|
||||
C( 6) 2pz 0.0000 0.0000 0.0000
|
||||
H( 7) 1s 0.0000 0.0000 0.0000
|
||||
H( 8) 1s 0.0000 0.0000 0.0000
|
||||
H( 9) 1s 0.0000 0.0000 0.0000
|
||||
H( 10) 1s 0.0000 0.0000 0.0000
|
||||
H( 11) 1s 0.0000 0.0000 0.0000
|
||||
H( 12) 1s 0.0000 0.0000 0.0000
|
||||
C( 5) 2py C( 5) 2pz C( 6) 2s
|
||||
C( 1) 2s -0.1489 0.1109 -15.3192
|
||||
C( 1) 2px 0.1530 -0.1140 10.5340
|
||||
C( 1) 2py -0.6834 -0.0050 6.7130
|
||||
C( 1) 2pz -0.0050 -0.6864 -0.3870
|
||||
C( 2) 2s -0.9725 0.0560 -3.2708
|
||||
C( 2) 2px 0.8591 -0.0495 1.5812
|
||||
C( 2) 2py 0.2403 -0.0315 3.0392
|
||||
C( 2) 2pz -0.0315 -0.3053 -0.0728
|
||||
C( 3) 2s -3.0392 0.0729 -1.6522
|
||||
C( 3) 2px 1.4432 -0.0346 -0.0790
|
||||
C( 3) 2py 2.0838 -0.0665 1.8082
|
||||
C( 3) 2pz -0.0665 -0.6886 -0.0106
|
||||
C( 4) 2s -12.4867 0.0735 -3.2710
|
||||
C( 4) 2px -0.5022 0.0030 -1.8405
|
||||
C( 4) 2py 6.5739 -0.0676 2.8904
|
||||
C( 4) 2pz -0.0676 -4.9171 0.0380
|
||||
C( 5) 2s 0.0000 0.0000 -15.3212
|
||||
C( 5) 2px 0.0000 0.0000 -11.0805
|
||||
C( 5) 2py -11.4000 0.0000 5.7732
|
||||
C( 5) 2pz 0.0000 -11.4000 0.3136
|
||||
C( 6) 2s 0.0000 0.0000 -21.4000
|
||||
C( 6) 2px 0.0000 0.0000 0.0000
|
||||
C( 6) 2py 0.0000 0.0000 0.0000
|
||||
C( 6) 2pz 0.0000 0.0000 0.0000
|
||||
H( 7) 1s 0.0000 0.0000 0.0000
|
||||
H( 8) 1s 0.0000 0.0000 0.0000
|
||||
H( 9) 1s 0.0000 0.0000 0.0000
|
||||
H( 10) 1s 0.0000 0.0000 0.0000
|
||||
H( 11) 1s 0.0000 0.0000 0.0000
|
||||
H( 12) 1s 0.0000 0.0000 0.0000
|
||||
C( 6) 2px C( 6) 2py C( 6) 2pz
|
||||
C( 1) 2s -10.5340 -6.7130 0.3870
|
||||
C( 1) 2px 3.2636 5.2126 -0.3005
|
||||
C( 1) 2py 5.2126 -1.5942 -0.1915
|
||||
C( 1) 2pz -0.3005 -0.1915 -4.9050
|
||||
C( 2) 2s -1.5812 -3.0392 0.0728
|
||||
C( 2) 2px 0.0607 1.4433 -0.0346
|
||||
C( 2) 2py 1.4433 2.0839 -0.0664
|
||||
C( 2) 2pz -0.0346 -0.0664 -0.6886
|
||||
C( 3) 2s 0.0790 -1.8082 0.0106
|
||||
C( 3) 2px -0.3034 -0.0827 0.0005
|
||||
C( 3) 2py -0.0827 1.5864 -0.0111
|
||||
C( 3) 2pz 0.0005 -0.0111 -0.3070
|
||||
C( 4) 2s 1.8405 -2.8904 -0.0380
|
||||
C( 4) 2px 0.3271 -1.5976 -0.0210
|
||||
C( 4) 2py -1.5976 1.8188 0.0330
|
||||
C( 4) 2pz -0.0210 0.0330 -0.6898
|
||||
C( 5) 2s 11.0805 -5.7732 -0.3136
|
||||
C( 5) 2px 4.1325 -4.7150 -0.2561
|
||||
C( 5) 2py -4.7150 -2.4603 0.1334
|
||||
C( 5) 2pz -0.2561 0.1334 -4.9097
|
||||
C( 6) 2s 0.0000 0.0000 0.0000
|
||||
C( 6) 2px -11.4000 0.0000 0.0000
|
||||
C( 6) 2py 0.0000 -11.4000 0.0000
|
||||
C( 6) 2pz 0.0000 0.0000 -11.4000
|
||||
H( 7) 1s 0.0000 0.0000 0.0000
|
||||
H( 8) 1s 0.0000 0.0000 0.0000
|
||||
H( 9) 1s 0.0000 0.0000 0.0000
|
||||
H( 10) 1s 0.0000 0.0000 0.0000
|
||||
H( 11) 1s 0.0000 0.0000 0.0000
|
||||
H( 12) 1s 0.0000 0.0000 0.0000
|
||||
H( 7) 1s H( 8) 1s H( 9) 1s
|
||||
C( 1) 2s -15.5501 -3.2693 -0.3144
|
||||
C( 1) 2px -9.5955 -1.1571 0.1214
|
||||
C( 1) 2py 4.9990 -2.6759 -0.2819
|
||||
C( 1) 2pz 0.2709 0.0566 -0.0019
|
||||
C( 2) 2s -3.2695 -15.5482 -3.2691
|
||||
C( 2) 2px -1.3865 -9.1218 1.7377
|
||||
C( 2) 2py 2.5652 -5.8137 -2.3410
|
||||
C( 2) 2pz 0.0259 0.3356 -0.0387
|
||||
C( 3) 2s -0.3144 -3.2694 -15.5497
|
||||
C( 3) 2px -0.2041 -2.9133 0.4731
|
||||
C( 3) 2py 0.2293 0.0819 -10.8123
|
||||
C( 3) 2pz 0.0049 0.0928 0.0627
|
||||
C( 4) 2s -0.1186 -0.3144 -3.2692
|
||||
C( 4) 2px -0.1045 -0.3005 -1.5268
|
||||
C( 4) 2py 0.0544 -0.0622 -2.4832
|
||||
C( 4) 2pz 0.0030 0.0101 0.0670
|
||||
C( 5) 2s -0.3144 -0.1186 -0.3144
|
||||
C( 5) 2px -0.3047 -0.0994 -0.0964
|
||||
C( 5) 2py 0.0358 -0.0633 -0.2914
|
||||
C( 5) 2pz 0.0095 0.0036 0.0052
|
||||
C( 6) 2s -3.2690 -0.3144 -0.1186
|
||||
C( 6) 2px -2.8948 -0.1833 0.0051
|
||||
C( 6) 2py -0.3348 -0.2461 -0.1177
|
||||
C( 6) 2pz 0.0953 0.0077 0.0007
|
||||
H( 7) 1s -13.6000 -1.0442 -0.0301
|
||||
H( 8) 1s 0.0000 -13.6000 -1.0442
|
||||
H( 9) 1s 0.0000 0.0000 -13.6000
|
||||
H( 10) 1s 0.0000 0.0000 0.0000
|
||||
H( 11) 1s 0.0000 0.0000 0.0000
|
||||
H( 12) 1s 0.0000 0.0000 0.0000
|
||||
H( 10) 1s H( 11) 1s H( 12) 1s
|
||||
C( 1) 2s -0.1186 -0.3144 -3.2690
|
||||
C( 1) 2px 0.1045 0.3004 1.5268
|
||||
C( 1) 2py -0.0544 0.0622 2.4829
|
||||
C( 1) 2pz -0.0030 -0.0101 -0.0670
|
||||
C( 2) 2s -0.3144 -0.1186 -0.3144
|
||||
C( 2) 2px 0.3047 0.0994 0.0964
|
||||
C( 2) 2py -0.0358 0.0633 0.2914
|
||||
C( 2) 2pz -0.0095 -0.0036 -0.0052
|
||||
C( 3) 2s -3.2690 -0.3144 -0.1186
|
||||
C( 3) 2px 2.8947 0.1833 -0.0051
|
||||
C( 3) 2py 0.3348 0.2461 0.1177
|
||||
C( 3) 2pz -0.0954 -0.0077 -0.0007
|
||||
C( 4) 2s -15.5484 -3.2691 -0.3144
|
||||
C( 4) 2px 9.5951 1.1572 -0.1214
|
||||
C( 4) 2py -4.9982 2.6756 0.2820
|
||||
C( 4) 2pz -0.2719 -0.0566 0.0019
|
||||
C( 5) 2s -3.2695 -15.5482 -3.2691
|
||||
C( 5) 2px 1.3865 9.1219 -1.7377
|
||||
C( 5) 2py -2.5652 5.8137 2.3410
|
||||
C( 5) 2pz -0.0259 -0.3346 0.0388
|
||||
C( 6) 2s -0.3144 -3.2694 -15.5497
|
||||
C( 6) 2px 0.2041 2.9133 -0.4731
|
||||
C( 6) 2py -0.2292 -0.0819 10.8123
|
||||
C( 6) 2pz -0.0049 -0.0928 -0.0627
|
||||
H( 7) 1s -0.0076 -0.0301 -1.0442
|
||||
H( 8) 1s -0.0301 -0.0076 -0.0301
|
||||
H( 9) 1s -1.0442 -0.0301 -0.0076
|
||||
H( 10) 1s -13.6000 -1.0442 -0.0301
|
||||
H( 11) 1s 0.0000 -13.6000 -1.0442
|
||||
H( 12) 1s 0.0000 0.0000 -13.6000
|
||||
|
||||
|
||||
|
||||
# ******* Energies (in eV) and Occupation Numbers *******
|
||||
1:---> -29.6302 [2.000 Electrons]
|
||||
2:---> -25.9874 [2.000 Electrons]
|
||||
3:---> -25.9871 [2.000 Electrons]
|
||||
4:---> -20.3719 [2.000 Electrons]
|
||||
5:---> -20.3713 [2.000 Electrons]
|
||||
6:---> -17.4138 [2.000 Electrons]
|
||||
7:---> -16.6094 [2.000 Electrons]
|
||||
8:---> -14.9472 [2.000 Electrons]
|
||||
9:---> -14.9471 [2.000 Electrons]
|
||||
10:---> -14.5301 [2.000 Electrons]
|
||||
11:---> -14.2938 [2.000 Electrons]
|
||||
12:---> -13.4081 [2.000 Electrons]
|
||||
13:---> -13.4076 [2.000 Electrons]
|
||||
14:---> -12.8042 [2.000 Electrons]
|
||||
15:---> -12.8038 [2.000 Electrons]
|
||||
16:---> -8.30729 [0.000 Electrons]
|
||||
17:---> -8.30635 [0.000 Electrons]
|
||||
18:---> -4.7058 [0.000 Electrons]
|
||||
19:---> 3.67608 [0.000 Electrons]
|
||||
20:---> 3.68046 [0.000 Electrons]
|
||||
21:---> 10.4728 [0.000 Electrons]
|
||||
22:---> 10.4983 [0.000 Electrons]
|
||||
23:---> 10.4994 [0.000 Electrons]
|
||||
24:---> 14.0807 [0.000 Electrons]
|
||||
25:---> 15.3177 [0.000 Electrons]
|
||||
26:---> 32.5886 [0.000 Electrons]
|
||||
27:---> 32.5998 [0.000 Electrons]
|
||||
28:---> 47.5602 [0.000 Electrons]
|
||||
29:---> 47.5706 [0.000 Electrons]
|
||||
30:---> 67.0404 [0.000 Electrons]
|
||||
Total_Energy: -535.026
|
||||
|
||||
; Net Atomic Charges for 30.000 electrons:
|
||||
1 C: -0.026034
|
||||
2 C: -0.025962
|
||||
3 C: -0.026026
|
||||
4 C: -0.025974
|
||||
5 C: -0.025981
|
||||
6 C: -0.026033
|
||||
7 H: 0.026026
|
||||
8 H: 0.025975
|
||||
9 H: 0.026021
|
||||
10 H: 0.025984
|
||||
11 H: 0.025984
|
||||
12 H: 0.026020
|
||||
; Total Charge is: 0.000000
|
||||
Reference in New Issue
Block a user