/usr/include/libint2/basis.h is in libint2-dev 2.3.0~beta3-2.
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* This file is a part of Libint.
* Copyright (C) 2004-2014 Edward F. Valeev
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Library General Public License, version 2,
* as published by the Free Software Foundation.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU Library General Public License
* along with this program. If not, see http://www.gnu.org/licenses/.
*
*/
#ifndef _libint2_src_lib_libint_basis_h_
#define _libint2_src_lib_libint_basis_h_
#include <libint2/util/cxxstd.h>
#if LIBINT2_CPLUSPLUS_STD < 2011
# error "libint2/basis.h requires C++11 support"
#endif
#include <iostream>
#include <fstream>
#include <locale>
#include <vector>
#include <stdexcept>
#include <sys/types.h>
#include <sys/stat.h>
#include <unistd.h>
#include <libint2.h>
#include <libint2/shell.h>
#include <libint2/atom.h>
namespace libint2 {
/// BasisSet is a slightly decorated \c std::vector of \c libint2::Shell objects.
class BasisSet : public std::vector<libint2::Shell> {
public:
BasisSet() : name_(""), nbf_(-1), max_nprim_(0), max_l_(-1) {}
BasisSet(const BasisSet&) = default;
BasisSet(BasisSet&& other) :
std::vector<libint2::Shell>(std::move(other)),
name_(std::move(other.name_)),
nbf_(other.nbf_),
max_nprim_(other.max_nprim_),
max_l_(other.max_l_),
shell2bf_(std::move(other.shell2bf_))
{
}
~BasisSet() = default;
BasisSet& operator=(const BasisSet&) = default;
/// Construct from basis set name and vector of atoms
/**
* @param name basis set name
* @param atoms \c std::vector of Atom objects
* \note All atoms receive the same basis set
* \note \c name will be "canonicalized" using BasisSet::canonicalize(name) to
* produce the file name where the basis will be sought. This file needs to contain
* the basis set definition in Gaussian94 format (see \c lib/basis directory for examples).
* The file will be searched in the following directories (in decreasing order of preference)
* <ol>
* <li> specified by LIBINT_DATA_PATH environmental variable, if defined </li>
* <li> specified by DATADIR macro variable, if defined </li>
* <li> specified by SRCDATADIR macro variable, if defined </li>
* <li> hardwired to directory \c /usr/share/libint/2.3.0/basis </li>
* </ol>
*/
BasisSet(std::string name,
const std::vector<Atom>& atoms) : name_(std::move(name)) {
// read in the library file contents
std::string basis_lib_path = data_path();
auto canonical_name = canonicalize_name(name_);
// some basis sets use cartesian d shells by convention, the convention is taken from Gaussian09
auto force_cartesian_d = gaussian_cartesian_d_convention(canonical_name);
// parse the name into components
std::vector<std::string> basis_component_names = decompose_name_into_components(canonical_name);
// ref_shells[component_idx][Z] => vector of Shells
std::vector<std::vector<std::vector<libint2::Shell>>> component_basis_sets;
component_basis_sets.reserve(basis_component_names.size());
// read in ALL basis set components
for(const auto& basis_component_name: basis_component_names) {
auto file_dot_g94 = basis_lib_path + "/" + basis_component_name + ".g94";
// use same cartesian_d convention for all components!
component_basis_sets.emplace_back(read_g94_basis_library(file_dot_g94, force_cartesian_d));
}
// for each atom find the corresponding basis components
for(auto a=0; a<atoms.size(); ++a) {
auto Z = atoms[a].atomic_number;
// add each component in order
for(auto comp_idx=0; comp_idx!=component_basis_sets.size(); ++comp_idx) {
const auto& component_basis_set = component_basis_sets[comp_idx];
if (component_basis_set[Z].empty())
throw std::string("did not find the basis for this Z in ") +
basis_lib_path + "/" + basis_component_names[comp_idx] + ".g94";
for(auto s: component_basis_set[Z]) {
this->push_back(std::move(s));
this->back().move({{atoms[a].x, atoms[a].y, atoms[a].z}});
} // shell loop
} // basis component loop
} // atom loop
init();
}
/// forces solid harmonics/Cartesian Gaussians
/// @param solid if true, force all shells with L>1 to be solid harmonics, otherwise force all shells to Cartesian
void set_pure(bool solid) {
for(auto& s: *this) {
s.contr[0].pure = solid;
}
init();
}
/// @return the number of basis functions in the basis; -1 if uninitialized
long nbf() const {
return nbf_;
}
/// @return the maximum number of primitives in a contracted Shell, i.e. maximum contraction length; 0 if uninitialized
size_t max_nprim() const {
return max_nprim_;
}
/// @return the maximum angular momentum of a contraction; -1 if uninitialized
long max_l() const {
return max_l_;
}
/// @return the map from shell index to index of the first basis function from this shell
/// \note basis functions are ordered as shells, i.e. shell2bf[i] >= shell2bf[j] iff i >= j
const std::vector<size_t>& shell2bf() const {
return shell2bf_;
}
/// Computes the map from shells to the corresponding atoms in \c atoms. If no atom matches the origin of a shell, it is mapped to -1.
/// @note coordinates must match \em exactly , i.e. shell2atom[k] == l iff atoms[l].x == *this[k].O[0] && atoms[l].y == *this[k].O[1] && atoms[l].z == *this[k].O[2]
/// @return the map from shell index to the atom in the list \c atoms that coincides with its origin;
std::vector<long> shell2atom(const std::vector<Atom>& atoms) const {
std::vector<long> result;
result.reserve(size());
for(const auto& s: *this) {
auto a = std::find_if(atoms.begin(), atoms.end(), [&s](const Atom& a){ return s.O[0] == a.x && s.O[1] == a.y && s.O[2] == a.z; } );
result.push_back( a != atoms.end() ? a - atoms.begin() : -1);
}
return result;
}
private:
std::string name_;
long nbf_;
size_t max_nprim_;
int max_l_;
std::vector<size_t> shell2bf_;
void init() {
nbf_ = nbf(*this);
max_nprim_ = max_nprim(*this);
max_l_ = max_l(*this);
shell2bf_ = compute_shell2bf(*this);
}
struct canonicalizer {
char operator()(char c) {
char cc = ::tolower(c);
switch (cc) {
case '/': cc = 'I'; break;
}
return cc;
}
};
static std::string canonicalize_name(const std::string& name) {
auto result = name;
std::transform(name.begin(), name.end(),
result.begin(), BasisSet::canonicalizer());
return result;
}
// see http://www.gaussian.com/g_tech/g_ur/m_basis_sets.htm
bool gaussian_cartesian_d_convention(const std::string& canonical_name) {
// 3-21??g??, 4-31g??
if (canonical_name.find("3-21") == 0 ||
canonical_name.find("4-31g") == 0)
return true;
// 6-31??g?? but not 6-311 OR 6-31g()
if (canonical_name.find("6-31") == 0 && canonical_name[4] != '1') {
// to exclude 6-31??g() find the g, then check the next character
auto g_pos = canonical_name.find('g');
if (g_pos == std::string::npos) // wtf, I don't even know what this is, assume spherical d is OK
return false;
if (g_pos+1 == canonical_name.size()) // 6-31??g uses cartesian d
return true;
if (canonical_name[g_pos+1] == '*') // 6-31??g*? uses cartesian d
return true;
}
return false;
}
/// decompose basis set name into components
std::vector<std::string> decompose_name_into_components(std::string name) {
std::vector<std::string> component_names;
// aug-cc-pvxz* = cc-pvxz* + augmentation-... , except aug-cc-pvxz-cabs
if ( (name.find("aug-cc-pv") == 0) && (name.find("cabs")==std::string::npos) ) {
std::string base_name = name.substr(4);
component_names.push_back(base_name);
component_names.push_back(std::string("augmentation-") + base_name);
}
else
component_names.push_back(name);
return component_names;
}
/** determines the path to the data directory, as follows:
* <ol>
* <li> specified by LIBINT_DATA_PATH environmental variable, if defined </li>
* <li> specified by DATADIR macro variable, if defined </li>
* <li> specified by SRCDATADIR macro variable, if defined </li>
* <li> hardwired to directory \c /usr/share/libint/2.3.0/basis </li>
* </ol>
* @throw std::runtime_error if the path is not valid, or cannot be determined
* @return valid path to the data directory
*/
static std::string data_path() {
std::string path;
const char* data_path_env = getenv("LIBINT_DATA_PATH");
if (data_path_env) {
path = data_path_env;
}
else {
#if defined(DATADIR)
path = std::string{DATADIR};
#elif defined(SRCDATADIR)
path = std::string{SRCDATADIR};
#else
path = std::string("/usr/share/libint/2.3.0") + std::string("/basis");
#endif
}
// validate path
bool error = true;
if (not path.empty()) {
struct stat sb;
error = (::stat(path.c_str(), &sb) == -1);
error = error && not S_ISDIR(sb.st_mode);
}
if (error) {
std::ostringstream oss; oss << "BasisSet::data_path(): path \"" << path << "\" is not valid";
throw std::runtime_error(oss.str());
}
return path;
}
/// converts fortran scientific-notation floats that use d/D instead of e/E in \c str
/// @param[in,out] str string in which chars 'd' and 'D' are replaced with 'e' and 'E',
/// respectively
static void fortran_dfloats_to_efloats(std::string& str) {
for(auto& ch: str) {
if (ch == 'd') ch = 'e';
if (ch == 'D') ch = 'E';
}
}
public:
/** reads in all basis sets from a Gaussian94-formatted basis set file (see https://bse.pnl.gov/bse/portal)
* @param[in] file_dot_g94 file name
* @param[in] force_cartesian_d force use of Cartesian d shells, if true
* @param[in] locale_name specifies the locale to use
* @throw std::runtime_error if the path is not valid, or cannot be determined
* @return vector of basis sets for each element
* @warning the included library basis sets should be parsed using POSIX locale
*/
static std::vector<std::vector<libint2::Shell>> read_g94_basis_library(std::string file_dot_g94,
bool force_cartesian_d = false,
std::string locale_name = std::string("POSIX")) {
std::locale locale(locale_name.c_str()); // TODO omit c_str() with up-to-date stdlib
std::cout << "Will read basis set from " << file_dot_g94 << std::endl;
std::ifstream is(file_dot_g94);
is.imbue(locale);
if (not is.good()) {
std::ostringstream oss;
oss << "BasisSet::read_g94_basis_library(): could not open \"" << file_dot_g94 << "\"" << std::endl;
throw std::runtime_error(oss.str());
}
std::vector<std::vector<libint2::Shell>> ref_shells(118); // 118 = number of chemical elements
std::string line, rest;
// skip till first basis
while(std::getline(is, line) && line != "****") {
}
#define LIBINT2_LINE_TO_STRINGSTREAM(line) \
std::istringstream iss(line); \
iss.imbue(locale);
size_t Z;
auto nextbasis = true, nextshell = false;
// read lines till end
while(std::getline(is, line)) {
// skipping empties and starting with '!' (the comment delimiter)
if (line.empty() || line[0] == '!') continue;
if (line == "****") {
nextbasis = true;
nextshell = false;
continue;
}
if (nextbasis) {
nextbasis = false;
LIBINT2_LINE_TO_STRINGSTREAM(line);
std::string elemsymbol;
iss >> elemsymbol >> rest;
bool found = false;
using libint2::chemistry::element_info;
for(const auto& e: element_info) {
if (strcaseequal(e.symbol, elemsymbol)) {
Z = e.Z;
found = true;
break;
}
}
if (not found) {
std::ostringstream oss;
oss << "in file " << file_dot_g94
<< " found G94 basis set for element symbol \""
<< elemsymbol << "\", not found in Periodic Table.";
throw std::runtime_error(oss.str());
}
nextshell = true;
continue;
}
if (nextshell) {
LIBINT2_LINE_TO_STRINGSTREAM(line);
std::string amlabel;
unsigned nprim;
iss >> amlabel >> nprim >> rest;
if (amlabel != "SP" && amlabel != "sp") {
assert(amlabel.size() == 1);
auto l = Shell::am_symbol_to_l(amlabel[0]);
std::vector<double> exps;
std::vector<double> coeffs;
for(auto p = 0; p!=nprim; ++p) {
while(std::getline(is, line) && (line.empty() || line[0] == '!')) {}
fortran_dfloats_to_efloats(line);
LIBINT2_LINE_TO_STRINGSTREAM(line);
double e, c;
iss >> e >> c;
exps.emplace_back(e);
coeffs.emplace_back(c);
}
auto pure = force_cartesian_d ? (l>2) : (l>1);
ref_shells[Z].push_back(
libint2::Shell{
exps,
{
{l, pure, coeffs}
},
{{0.0, 0.0, 0.0}}
}
);
}
else { // split the SP shells
std::vector<double> exps;
std::vector<double> coeffs_s, coeffs_p;
for(auto p = 0; p!=nprim; ++p) {
while(std::getline(is, line) && (line.empty() || line[0] == '!')) {}
fortran_dfloats_to_efloats(line);
LIBINT2_LINE_TO_STRINGSTREAM(line);
double e, c1, c2;
iss >> e >> c1 >> c2;
exps.emplace_back(e);
coeffs_s.emplace_back(c1);
coeffs_p.emplace_back(c2);
}
ref_shells[Z].push_back(
libint2::Shell{exps,
{
{0, false, coeffs_s}
},
{{0.0, 0.0, 0.0}}
}
);
ref_shells[Z].push_back(
libint2::Shell{ exps,
{
{1, false, coeffs_p}
},
{{0.0, 0.0, 0.0}}
}
);
}
}
}
#undef LIBINT2_LINE_TO_STRINGSTREAM
return ref_shells;
}
static size_t nbf(const std::vector<libint2::Shell>& shells) {
size_t n = 0;
for (const auto& shell: shells)
n += shell.size();
return n;
}
static size_t max_nprim(const std::vector<libint2::Shell>& shells) {
size_t n = 0;
for (auto shell: shells)
n = std::max(shell.nprim(), n);
return n;
}
static int max_l(const std::vector<libint2::Shell>& shells) {
int l = 0;
for (auto shell: shells)
for (auto c: shell.contr)
l = std::max(c.l, l);
return l;
}
static std::vector<size_t> compute_shell2bf(const std::vector<libint2::Shell>& shells) {
std::vector<size_t> result;
result.reserve(shells.size());
size_t n = 0;
for (auto shell: shells) {
result.push_back(n);
n += shell.size();
}
return result;
}
}; // BasisSet
} // namespace libint2
#endif /* _libint2_src_lib_libint_basis_h_ */
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