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Merge branch 'devel' of https://github.com/Quantum-Dynamics-Hub/libra-code into devel
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‎backup/libint2_wrappers.cpp

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‎backup/libint2_wrappers.h

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/*********************************************************************************
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* Copyright (C) 2021 Mohammad Shakiba and Alexey V. Akimov
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*
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* This file is distributed under the terms of the GNU General Public License
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* as published by the Free Software Foundation, either version 3 of
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* the License, or (at your option) any later version.
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* See the file LICENSE in the root directory of this distribution
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* or <http://www.gnu.org/licenses/>.
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*
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*********************************************************************************/
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/**
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\file libint2_wrappers.h
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\brief The file describes the classes and functions that interface libint2 functions and types with those of Libra and expose them to Python
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*/
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#ifndef LIBINT2_WRAPPERS_H
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#define LIBINT2_WRAPPERS_H
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#include "../math_linalg/liblinalg.h"
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#include "../math_specialfunctions/libspecialfunctions.h"
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// standard C++ headers
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#include <cmath>
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#include <iostream>
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#include <fstream>
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#include <sstream>
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#include <iomanip>
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#include <vector>
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#include <chrono>
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#include <thread>
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// Eigen matrix algebra library
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#include <Eigen/Dense>
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#include <Eigen/Eigenvalues>
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/*
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// Pybind11 for interface with Python
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#include <pybind11.h>
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#include <pybind11/eigen.h>
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#include <numpy.h>
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#include <stl.h>
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#include <complex.h>
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#include <functional.h>
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#include <chrono.h>
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*/
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// Libint Gaussian integrals library
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#include <libint2.hpp>
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#if !LIBINT2_CONSTEXPR_STATICS
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# include <libint2/statics_definition.h>
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#endif
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// OpenMP library
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#if defined(_OPENMP)
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#include <omp.h>
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#endif
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/// liblibra namespace
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namespace liblibra{
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using namespace liblinalg;
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using namespace libspecialfunctions;
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namespace liblibint2_wrappers{
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// fires off \c nthreads instances of lambda in parallel
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template <typename Lambda>
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void parallel_do(Lambda& lambda, int nthreads) {
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#ifdef _OPENMP
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#pragma omp parallel
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{
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auto thread_id = omp_get_thread_num();
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lambda(thread_id);
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}
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#else // use C++11 threads
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std::vector<std::thread> threads;
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for (int thread_id = 0; thread_id != libint2::nthreads; ++thread_id) {
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if (thread_id != nthreads - 1)
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threads.push_back(std::thread(lambda, thread_id));
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else
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lambda(thread_id);
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} // threads_id
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for (int thread_id = 0; thread_id < nthreads - 1; ++thread_id)
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threads[thread_id].join();
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#endif
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}
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std::vector<libint2::Shell> initialize_shell(int l_val, bool is_spherical,
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const std::vector<double>& exponents, const std::vector<double>& coeff, VECTOR& coords);
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void add_to_shell(std::vector<libint2::Shell>& shells,
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int l_val, bool is_spherical , const std::vector<double>& exponents, const std::vector<double>& coeff, VECTOR& coords);
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void print_shells(std::vector<libint2::Shell>& shells);
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size_t nbasis(const std::vector<libint2::Shell>& shells);
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size_t max_nprim(const std::vector<libint2::Shell>& shells);
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int max_l(const std::vector<libint2::Shell>& shells);
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std::vector<size_t> map_shell_to_basis_function(const std::vector<libint2::Shell>& shells);
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using real_t = libint2::scalar_type;
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typedef Eigen::Matrix<real_t, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor> Matrix;
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MATRIX compute_1body_ints(const std::vector<libint2::Shell>& shells_1, const std::vector<libint2::Shell>& shells_2,libint2::Operator obtype);
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MATRIX compute_1body_ints_parallel(const std::vector<libint2::Shell>& shells_1, const std::vector<libint2::Shell>& shells_2,libint2::Operator obtype);
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MATRIX compute_overlaps(const std::vector<libint2::Shell>& shells_1, const std::vector<libint2::Shell>& shells_2, int number_of_threads);
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MATRIX compute_overlaps_serial(const std::vector<libint2::Shell>& shells_1, const std::vector<libint2::Shell>& shells_2);
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typedef std::vector< libint2::Shell > libint2_ShellList; ///< Data type that holds a vector of libint2::Shell objects
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}// namespace liblibint2_wrappers
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}// namespace liblibra
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#endif // LIBINT2_WRAPPERS_H

‎backup/liblibint2_wrappers.cpp

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/*********************************************************************************
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* Copyright (C) 2021 Mohammad Shakiba and Alexey V. Akimov
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*
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* This file is distributed under the terms of the GNU General Public License
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* as published by the Free Software Foundation, either version 3 of
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* the License, or (at your option) any later version.
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* See the file LICENSE in the root directory of this distribution
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* or <http://www.gnu.org/licenses/>.
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*
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*********************************************************************************/
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/**
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\file liblibint2_wrappers.cpp
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\brief The file implements Python export function
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*/
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#define BOOST_PYTHON_MAX_ARITY 30
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#include <boost/python.hpp>
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#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
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#include "libint2_wrappers.h"
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/// liblibra namespace
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namespace liblibra{
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using namespace boost::python;
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using namespace liblinalg;
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using namespace libspecialfunctions;
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/// libqobjects namespace
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namespace liblibint2_wrappers{
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void export_libint2_wrappers_objects(){
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/**
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\brief Exporter of liblibint2_wrappers classes and functions
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*/
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/*
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double (*expt_electron_repulsion_integral_AO_v2)
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( AO& AOa, AO& AOb, AO& AOc, AO& AOd, int is_normalize ) = &electron_repulsion_integral;
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boost::python::list (*expt_electron_repulsion_integral_AO_v3)
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( AO& AOa, AO& AOb, AO& AOc, AO& AOd, int is_normalize, int is_derivs) = &electron_repulsion_integral;
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// ============ Now export functions =============
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// Overlaps
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def("gaussian_overlap", expt_gaussian_overlap_G_v1);
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void (PrimitiveG::*expt_set_position_PrimitiveG_v1)(VECTOR) = &PrimitiveG::set_position;
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void (AO::*expt_set_position_AO_v1)(VECTOR) = &AO::set_position;
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*/
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size_t (*expt_nbasis_v1)(const std::vector<libint2::Shell>& shells) = &nbasis;
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def("nbasis", expt_nbasis_v1);
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std::vector<libint2::Shell> (*expt_initialize_shell_v1)(
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int l_val, bool is_spherical , const std::vector<double>& exponents,
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const std::vector<double>& coeff, VECTOR& coords) = &initialize_shell;
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def("initialize_shell", expt_initialize_shell_v1);
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void (*expt_add_to_shell_v1)(std::vector<libint2::Shell>& shells,
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int l_val, bool is_spherical , const std::vector<double>& exponents,
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const std::vector<double>& coeff, VECTOR& coords) = &add_to_shell;
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def("add_to_shell", expt_add_to_shell_v1);
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void (*expt_print_shells_v1)(std::vector<libint2::Shell>& shells) = &print_shells;
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def("print_shell", expt_print_shells_v1);
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class_<libint2::Shell>("libint2_Shell",init<>())
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.def(init<const libint2::Shell&>())
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.def("__copy__", &generic__copy__<libint2::Shell>)
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.def("__deepcopy__", &generic__deepcopy__<libint2::Shell>)
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.def_readwrite("alpha",&libint2::Shell::alpha)
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.def_readwrite("contr",&libint2::Shell::contr)
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//.def("init",&PrimitiveG::init)
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;
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class_< libint2_ShellList >("libint2_ShellList")
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.def(vector_indexing_suite< libint2_ShellList >())
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;
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class_<Matrix>("Matrix",init<>())
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.def("__copy__", &generic__copy__<Matrix>)
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.def("__deepcopy__", &generic__deepcopy__<Matrix>)
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;
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MATRIX (*expt_compute_overlaps_v1)
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(const std::vector<libint2::Shell>& shells_1,
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const std::vector<libint2::Shell>& shells_2, int number_of_threads) = &compute_overlaps;
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def("compute_overlaps", expt_compute_overlaps_v1);
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MATRIX (*expt_compute_overlaps_serial_v1)
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(const std::vector<libint2::Shell>& shells_1, const std::vector<libint2::Shell>& shells_2) = &compute_overlaps_serial;
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def("compute_overlaps_serial", expt_compute_overlaps_serial_v1);
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/**
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class_<libint2::Operator>("libint2_Operator",init<>())
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.def(init<const libint2::Operator&>())
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.def("__copy__", &generic__copy__<libint2::Operator>)
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.def("__deepcopy__", &generic__deepcopy__<libint2::Operator>)
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//.def_readwrite("x_exp",&PrimitiveG::x_exp)
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.def("nbasis",&libint2::Operator::nbasis)
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;
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*/
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/*
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py::class_<libint2::Operator>(m, "Operator");
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m.def("nbasis", &nbasis, "A function for number of basis sets", py::return_value_policy::reference_internal);
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m.def("compute_1body_ints_parallel", &compute_1body_ints_parallel, "A function for computing AO overlaps parallel", py::return_value_policy::reference_internal);
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m.def("compute_1body_ints", &compute_1body_ints, "A function for computing integrals serial", py::return_value_policy::reference_internal);
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m.def("initialize_shell", &initialize_shell, "A function for creating shells", py::return_value_policy::reference_internal);
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m.def("initialize_atom", &initialize_atom, "A function for initializing Atom", py::return_value_policy::reference_internal);
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m.def("add_to_shell", &add_to_shell, "A function to add the exponents, contraction coefficients, and Atom structure to a predefined shell", py::return_value_policy::reference_internal);
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m.def("print_shell", &print_shell, "A function for printing a shell", py::return_value_policy::reference_internal);
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m.def("compute_overlaps", &compute_overlaps, "A function that computes overlaps between pairs of shells", py::return_value_policy::reference_internal);
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*/
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}
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#ifdef CYGWIN
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BOOST_PYTHON_MODULE(cyglibint2_wrappers){
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#else
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BOOST_PYTHON_MODULE(liblibint2_wrappers){
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#endif
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// Register converters:
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// See here: https://misspent.wordpress.com/2009/09/27/how-to-write-boost-python-converters/
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//to_python_converter<std::vector<DATA>, VecToList<DATA> >();
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export_libint2_wrappers_objects();
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}
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}// namespace libqobject
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}// namespace liblibra
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‎backup/liblibint2_wrappers.h

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/*********************************************************************************
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* Copyright (C) 2021 Mohammad Shakiba and Alexey V. Akimov
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*
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* This file is distributed under the terms of the GNU General Public License
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* as published by the Free Software Foundation, either version 3 of
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* the License, or (at your option) any later version.
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* See the file LICENSE in the root directory of this distribution
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* or <http://www.gnu.org/licenses/>.
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*
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*********************************************************************************/
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/**
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\file liblibint2_wrappers.h
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\brief The file describes Python export function
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*/
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#ifndef LIB_LIBINT2_WRAPPERS_H
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#define LIB_LIBINT2_WRAPPERS_H
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#include "libint2_wrappers.h"
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/// liblibra namespace
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namespace liblibra{
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/// liblibint2_wrappers namespace
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namespace liblibint2_wrappers{
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void export_libint2_wrappers_objects();
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}// namespace libqobjects
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}// namespace liblibra
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#endif// LIB_LIBINT2_WRAPPERS_H

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