[fbf005] | 1 | //
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| 2 | // mpqc_extract.cc
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| 3 | //
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| 4 | // Copyright (C) 1996 Limit Point Systems, Inc.
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| 5 | //
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| 6 | // Author: Edward Seidl <seidl@janed.com>
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| 7 | // Maintainer: LPS
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| 8 | //
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| 9 | // This file is part of MPQC.
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| 10 | //
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| 11 | // MPQC is free software; you can redistribute it and/or modify
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| 12 | // it under the terms of the GNU General Public License as published by
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| 13 | // the Free Software Foundation; either version 2, or (at your option)
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| 14 | // any later version.
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| 15 | //
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| 16 | // MPQC is distributed in the hope that it will be useful,
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| 17 | // but WITHOUT ANY WARRANTY; without even the implied warranty of
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| 18 | // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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| 19 | // GNU General Public License for more details.
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| 20 | //
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| 21 | // You should have received a copy of the GNU General Public License
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| 22 | // along with the MPQC; see the file COPYING. If not, write to
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| 23 | // the Free Software Foundation, 675 Mass Ave, Cambridge, MA 02139, USA.
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| 24 | //
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| 25 | // The U.S. Government is granted a limited license as per AL 91-7.
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| 26 | //
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| 27 | // \note This was extracted from \file mpqc.cc for refactoring into a library.
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| 28 |
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| 29 | #ifdef HAVE_CONFIG_H
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| 30 | #include <scconfig.h>
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| 31 | #endif
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| 32 |
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| 33 | #ifdef HAVE_JOBMARKET
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| 34 | // include headers that implement a archive in simple text format
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| 35 | // otherwise BOOST_CLASS_EXPORT_IMPLEMENT has no effect
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| 36 | #include <boost/archive/text_oarchive.hpp>
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| 37 | #include <boost/archive/text_iarchive.hpp>
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| 38 |
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| 39 | #include "JobMarket/Results/FragmentResult.hpp"
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| 40 | #include "JobMarket/poolworker_main.hpp"
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| 41 |
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| 42 | #include "chemistry/qc/scf/scfops.h"
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| 43 |
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| 44 | #ifdef HAVE_MPQCDATA
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| 45 | #include "Jobs/MPQCJob.hpp"
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| 46 | #include "Fragmentation/Summation/Containers/MPQCData.hpp"
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| 47 |
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| 48 | #include <chemistry/qc/basis/obint.h>
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| 49 | #include <chemistry/qc/basis/symmint.h>
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| 50 | #endif
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| 51 |
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| 52 | #include <algorithm>
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| 53 | #include <stdlib.h>
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| 54 | #endif
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| 55 |
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| 56 | #include <chemistry/qc/scf/linkage.h>
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| 57 | #include <chemistry/qc/dft/linkage.h>
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| 58 | #include <chemistry/qc/mbpt/linkage.h>
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| 59 | #ifdef HAVE_SC_SRC_LIB_CHEMISTRY_QC_MBPTR12
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| 60 | # include <chemistry/qc/mbptr12/linkage.h>
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| 61 | #endif
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| 62 | #ifdef HAVE_SC_SRC_LIB_CHEMISTRY_QC_CINTS
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| 63 | # include <chemistry/qc/cints/linkage.h>
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| 64 | #endif
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| 65 | //#include <chemistry/qc/psi/linkage.h>
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| 66 | #include <util/state/linkage.h>
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| 67 | #ifdef HAVE_SC_SRC_LIB_CHEMISTRY_QC_CC
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| 68 | # include <chemistry/qc/cc/linkage.h>
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| 69 | #endif
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| 70 | #ifdef HAVE_SC_SRC_LIB_CHEMISTRY_QC_PSI
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| 71 | # include <chemistry/qc/psi/linkage.h>
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| 72 | #endif
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| 73 | #ifdef HAVE_SC_SRC_LIB_CHEMISTRY_QC_INTCCA
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| 74 | # include <chemistry/qc/intcca/linkage.h>
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| 75 | #endif
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| 76 |
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| 77 | #include "mpqc_extract.h"
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| 78 |
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| 79 | using namespace std;
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| 80 | using namespace sc;
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| 81 |
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| 82 | static int getCoreElectrons(const int z)
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| 83 | {
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| 84 | int n=0;
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| 85 | if (z > 2) n += 2;
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| 86 | if (z > 10) n += 8;
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| 87 | if (z > 18) n += 8;
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| 88 | if (z > 30) n += 10;
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| 89 | if (z > 36) n += 8;
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| 90 | if (z > 48) n += 10;
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| 91 | if (z > 54) n += 8;
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| 92 | return n;
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| 93 | }
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| 94 |
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| 95 | /** Finds the region index to a given timer region name.
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| 96 | *
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| 97 | * @param nregion number of regions
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| 98 | * @param region_names array with name of each region
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| 99 | * @param name name of desired region
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| 100 | * @return index of desired region in array
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| 101 | */
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| 102 | int findTimerRegion(const int &nregion, const char **®ion_names, const char *name)
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| 103 | {
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| 104 | int region=0;
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| 105 | for (;region<nregion;++region) {
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| 106 | //std::cout << "Comparing " << region_names[region] << " and " << name << "." << std::endl;
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| 107 | if (strcmp(region_names[region], name) == 0)
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| 108 | break;
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| 109 | }
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| 110 | if (region == nregion)
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| 111 | region = 0;
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| 112 | return region;
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| 113 | }
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| 114 |
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| 115 | /** Extractor function that is called after all calculations have been made.
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| 116 | *
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| 117 | * \param data result structure to fill
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| 118 | */
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| 119 | void extractResults(
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| 120 | Ref<MolecularEnergy> &mole,
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| 121 | void *_data
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| 122 | )
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| 123 | {
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| 124 | MPQCData &data = *static_cast<MPQCData *>(_data);
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| 125 | Ref<Wavefunction> wfn;
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| 126 | wfn << mole;
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| 127 | // ExEnv::out0() << "The number of atomic orbitals: " << wfn->ao_dimension()->n() << endl;
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| 128 | // ExEnv::out0() << "The AO density matrix is ";
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| 129 | // wfn->ao_density()->print(ExEnv::out0());
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| 130 | // ExEnv::out0() << "The natural density matrix is ";
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| 131 | // wfn->natural_density()->print(ExEnv::out0());
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| 132 | // ExEnv::out0() << "The Gaussian basis is " << wfn->basis()->name() << endl;
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| 133 | // ExEnv::out0() << "The Gaussians sit at the following centers: " << endl;
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| 134 | // for (int nr = 0; nr< wfn->basis()->ncenter(); ++nr) {
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| 135 | // ExEnv::out0() << nr << " basis function has its center at ";
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| 136 | // for (int i=0; i < 3; ++i)
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| 137 | // ExEnv::out0() << wfn->basis()->r(nr,i) << "\t";
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| 138 | // ExEnv::out0() << endl;
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| 139 | // }
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| 140 | // store accuracies
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| 141 | data.accuracy = mole->value_result().actual_accuracy();
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| 142 | data.desired_accuracy = mole->value_result().desired_accuracy();
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| 143 | // print the energy
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| 144 | data.energies.total = wfn->energy();
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| 145 | data.energies.nuclear_repulsion = wfn->nuclear_repulsion_energy();
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| 146 | {
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| 147 | CLHF *clhf = dynamic_cast<CLHF*>(wfn.pointer());
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| 148 | if (clhf != NULL) {
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| 149 | double ex, ec;
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| 150 | clhf->two_body_energy(ec, ex);
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| 151 | data.energies.electron_coulomb = ec;
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| 152 | data.energies.electron_exchange = ex;
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| 153 | clhf = NULL;
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| 154 | } else {
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| 155 | ExEnv::out0() << "INFO: There is no direct CLHF information available." << endl;
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| 156 | data.energies.electron_coulomb = 0.;
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| 157 | data.energies.electron_exchange = 0.;
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| 158 | }
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| 159 | }
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| 160 | SCF *scf = NULL;
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| 161 | {
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| 162 | MBPT2 *mbpt2 = dynamic_cast<MBPT2*>(wfn.pointer());
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| 163 | if (mbpt2 != NULL) {
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| 164 | data.energies.correlation = mbpt2->corr_energy();
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| 165 | scf = mbpt2->ref().pointer();
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| 166 | CLHF *clhf = dynamic_cast<CLHF*>(scf);
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| 167 | if (clhf != NULL) {
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| 168 | double ex, ec;
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| 169 | clhf->two_body_energy(ec, ex);
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| 170 | data.energies.electron_coulomb = ec;
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| 171 | data.energies.electron_exchange = ex;
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| 172 | clhf = NULL;
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| 173 | } else {
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| 174 | ExEnv::out0() << "INFO: There is no reference CLHF information available either." << endl;
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| 175 | data.energies.electron_coulomb = 0.;
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| 176 | data.energies.electron_exchange = 0.;
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| 177 | }
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| 178 | mbpt2 = 0;
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| 179 | } else {
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| 180 | ExEnv::out0() << "INFO: There is no MBPT2 information available." << endl;
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| 181 | data.energies.correlation = 0.;
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| 182 | scf = dynamic_cast<SCF*>(wfn.pointer());
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| 183 | if (scf == NULL)
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| 184 | abort();
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| 185 | }
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| 186 | }
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| 187 | {
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| 188 | // taken from clscf.cc: CLSCF::scf_energy() (but see also Szabo/Ostlund)
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| 189 |
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| 190 | RefSymmSCMatrix t = scf->overlap();
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| 191 | RefSymmSCMatrix cl_dens_ = scf->ao_density();
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| 192 |
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| 193 | SCFEnergy *eop = new SCFEnergy;
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| 194 | eop->reference();
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| 195 | if (t.dim()->equiv(cl_dens_.dim())) {
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| 196 | Ref<SCElementOp2> op = eop;
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| 197 | t.element_op(op,cl_dens_);
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| 198 | op=0;
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| 199 | }
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| 200 | eop->dereference();
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| 201 |
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| 202 | data.energies.overlap = eop->result();
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| 203 |
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| 204 | delete eop;
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| 205 | t = 0;
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| 206 | cl_dens_ = 0;
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| 207 | }
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| 208 | {
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| 209 | // taken from Wavefunction::core_hamiltonian()
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| 210 | RefSymmSCMatrix hao(scf->basis()->basisdim(), scf->basis()->matrixkit());
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| 211 | hao.assign(0.0);
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| 212 | Ref<PetiteList> pl = scf->integral()->petite_list();
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| 213 | Ref<SCElementOp> hc =
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| 214 | new OneBodyIntOp(new SymmOneBodyIntIter(scf->integral()->kinetic(), pl));
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| 215 | hao.element_op(hc);
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| 216 | hc=0;
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| 217 |
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| 218 | RefSymmSCMatrix h(scf->so_dimension(), scf->basis_matrixkit());
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| 219 | pl->symmetrize(hao,h);
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| 220 |
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| 221 | // taken from clscf.cc: CLSCF::scf_energy() (but see also Szabo/Ostlund)
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| 222 | RefSymmSCMatrix cl_dens_ = scf->ao_density();
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| 223 |
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| 224 | SCFEnergy *eop = new SCFEnergy;
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| 225 | eop->reference();
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| 226 | if (h.dim()->equiv(cl_dens_.dim())) {
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| 227 | Ref<SCElementOp2> op = eop;
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| 228 | h.element_op(op,cl_dens_);
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| 229 | op=0;
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| 230 | }
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| 231 | eop->dereference();
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| 232 |
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| 233 | data.energies.kinetic = 2.*eop->result();
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| 234 |
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| 235 | delete eop;
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| 236 | hao = 0;
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| 237 | h = 0;
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| 238 | cl_dens_ = 0;
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| 239 | }
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| 240 | {
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| 241 | // set to potential energy between nuclei and electron charge distribution
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| 242 | RefSymmSCMatrix hao(scf->basis()->basisdim(), scf->basis()->matrixkit());
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| 243 | hao.assign(0.0);
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| 244 | Ref<PetiteList> pl = scf->integral()->petite_list();
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| 245 | Ref<SCElementOp> hc =
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| 246 | new OneBodyIntOp(new SymmOneBodyIntIter(scf->integral()->nuclear(), pl));
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| 247 | hao.element_op(hc);
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| 248 | hc=0;
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| 249 |
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| 250 | RefSymmSCMatrix h(scf->so_dimension(), scf->basis_matrixkit());
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| 251 | pl->symmetrize(hao,h);
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| 252 |
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| 253 | // taken from clscf.cc: CLSCF::scf_energy() (but see also Szabo/Ostlund)
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| 254 | RefSymmSCMatrix cl_dens_ = scf->ao_density();
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| 255 |
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| 256 | SCFEnergy *eop = new SCFEnergy;
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| 257 | eop->reference();
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| 258 | if (h.dim()->equiv(cl_dens_.dim())) {
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| 259 | Ref<SCElementOp2> op = eop;
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| 260 | h.element_op(op,cl_dens_);
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| 261 | op=0;
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| 262 | }
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| 263 | eop->dereference();
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| 264 |
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| 265 | data.energies.hcore = 2.*eop->result();
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| 266 |
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| 267 | delete eop;
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| 268 | hao = 0;
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| 269 | h = 0;
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| 270 | cl_dens_ = 0;
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| 271 | }
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| 272 | ExEnv::out0() << "total is " << data.energies.total << endl;
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| 273 | ExEnv::out0() << "nuclear_repulsion is " << data.energies.nuclear_repulsion << endl;
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| 274 | ExEnv::out0() << "electron_coulomb is " << data.energies.electron_coulomb << endl;
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| 275 | ExEnv::out0() << "electron_exchange is " << data.energies.electron_exchange << endl;
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| 276 | ExEnv::out0() << "correlation is " << data.energies.correlation << endl;
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| 277 | ExEnv::out0() << "overlap is " << data.energies.overlap << endl;
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| 278 | ExEnv::out0() << "kinetic is " << data.energies.kinetic << endl;
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| 279 | ExEnv::out0() << "hcore is " << data.energies.hcore << endl;
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| 280 | ExEnv::out0() << "sum is " <<
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| 281 | data.energies.nuclear_repulsion
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| 282 | + data.energies.electron_coulomb
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| 283 | + data.energies.electron_exchange
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| 284 | + data.energies.correlation
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| 285 | + data.energies.kinetic
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| 286 | + data.energies.hcore
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| 287 | << endl;
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| 288 |
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| 289 | ExEnv::out0() << endl << indent
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| 290 | << scprintf("Value of the MolecularEnergy: %15.10f",
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| 291 | mole->energy())
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| 292 | << endl;
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| 293 | // print the gradient
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| 294 | RefSCVector grad;
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| 295 | if (mole->gradient_result().computed()) {
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| 296 | grad = mole->gradient_result().result_noupdate();
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| 297 | }
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| 298 | // gradient calculation needs to be activated in the configuration
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| 299 | // some methods such as open shell MBPT2 do not allow for gradient calc.
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| 300 | // else {
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| 301 | // grad = mole->gradient();
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| 302 | // }
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| 303 | if (grad.nonnull()) {
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| 304 | data.forces.resize(grad.dim()/3);
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| 305 | for (int j=0;j<grad.dim()/3; ++j) {
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| 306 | data.forces[j].resize(3, 0.);
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| 307 | }
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| 308 | ExEnv::out0() << "Gradient of the MolecularEnergy:" << std::endl;
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| 309 | for (int j=0;j<grad.dim()/3; ++j) {
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| 310 | ExEnv::out0() << "\t";
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| 311 | for (int i=0; i< 3; ++i) {
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| 312 | data.forces[j][i] = grad[3*j+i];
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| 313 | ExEnv::out0() << grad[3*j+i] << "\t";
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| 314 | }
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| 315 | ExEnv::out0() << endl;
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| 316 | }
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| 317 | } else {
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| 318 | ExEnv::out0() << "INFO: There is no gradient information available." << endl;
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| 319 | }
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| 320 | grad = NULL;
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| 321 |
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| 322 | {
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| 323 | // eigenvalues (this only works if we have a OneBodyWavefunction, i.e. SCF procedure)
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| 324 | // eigenvalues seem to be invalid for unrestricted SCF calculation
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| 325 | // (see UnrestrictedSCF::eigenvalues() implementation)
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| 326 | UnrestrictedSCF *uscf = dynamic_cast<UnrestrictedSCF*>(wfn.pointer());
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| 327 | if ((scf != NULL) && (uscf == NULL)) {
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| 328 | // const double scfernergy = scf->energy();
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| 329 | RefDiagSCMatrix evals = scf->eigenvalues();
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| 330 |
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| 331 | ExEnv::out0() << "Eigenvalues:" << endl;
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| 332 | for(int i=0;i<wfn->oso_dimension(); ++i) {
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| 333 | data.energies.eigenvalues.push_back(evals(i));
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| 334 | ExEnv::out0() << i << "th eigenvalue is " << evals(i) << endl;
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| 335 | }
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| 336 | } else {
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| 337 | ExEnv::out0() << "INFO: There is no eigenvalue information available." << endl;
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| 338 | }
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| 339 | }
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| 340 | // we do sample the density only on request
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| 341 | {
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| 342 | // fill positions and charges (NO LONGER converting from bohr radii to angstroem)
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| 343 | const double AtomicLengthToAngstroem = 1.;//0.52917721;
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| 344 | data.positions.reserve(wfn->molecule()->natom());
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| 345 | data.atomicnumbers.reserve(wfn->molecule()->natom());
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| 346 | data.charges.reserve(wfn->molecule()->natom());
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| 347 | for (int iatom=0;iatom < wfn->molecule()->natom(); ++iatom) {
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| 348 | data.atomicnumbers.push_back(wfn->molecule()->Z(iatom));
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| 349 | double charge = wfn->molecule()->Z(iatom);
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| 350 | if (data.DoValenceOnly == MPQCData::DoSampleValenceOnly)
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| 351 | charge -= getCoreElectrons((int)charge);
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| 352 | data.charges.push_back(charge);
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| 353 | std::vector<double> pos(3, 0.);
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| 354 | for (int j=0;j<3;++j)
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| 355 | pos[j] = wfn->molecule()->r(iatom, j)*AtomicLengthToAngstroem;
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| 356 | data.positions.push_back(pos);
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| 357 | }
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| 358 | ExEnv::out0() << "We have "
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| 359 | << data.positions.size() << " positions and "
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| 360 | << data.charges.size() << " charges." << endl;
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| 361 | }
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| 362 | if (data.DoLongrange) {
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| 363 | if (data.sampled_grid.level != 0)
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| 364 | {
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| 365 | // we now need to sample the density on the grid
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| 366 | // 1. get max and min over all basis function positions
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| 367 | assert( scf->basis()->ncenter() > 0 );
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| 368 | SCVector3 bmin( scf->basis()->r(0,0), scf->basis()->r(0,1), scf->basis()->r(0,2) );
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| 369 | SCVector3 bmax( scf->basis()->r(0,0), scf->basis()->r(0,1), scf->basis()->r(0,2) );
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| 370 | for (int nr = 1; nr< scf->basis()->ncenter(); ++nr) {
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| 371 | for (int i=0; i < 3; ++i) {
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| 372 | if (scf->basis()->r(nr,i) < bmin(i))
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| 373 | bmin(i) = scf->basis()->r(nr,i);
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| 374 | if (scf->basis()->r(nr,i) > bmax(i))
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| 375 | bmax(i) = scf->basis()->r(nr,i);
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| 376 | }
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| 377 | }
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| 378 | ExEnv::out0() << "Basis min is at " << bmin << " and max is at " << bmax << endl;
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| 379 |
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| 380 | // 2. choose an appropriately large grid
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| 381 | // we have to pay attention to capture the right amount of the exponential decay
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| 382 | // and also to have a power of two size of the grid at best
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| 383 | SCVector3 boundaryV(5.); // boundary extent around compact domain containing basis functions
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| 384 | bmin -= boundaryV;
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| 385 | bmax += boundaryV;
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| 386 | for (size_t i=0;i<3;++i) {
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| 387 | if (bmin(i) < data.sampled_grid.begin[i])
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| 388 | bmin(i) = data.sampled_grid.begin[i];
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| 389 | if (bmax(i) > data.sampled_grid.end[i])
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| 390 | bmax(i) = data.sampled_grid.end[i];
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| 391 | }
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| 392 | // set the non-zero window of the sampled_grid
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| 393 | data.sampled_grid.setWindow(bmin.data(), bmax.data());
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| 394 |
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| 395 | // for the moment we always generate a grid of full size
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| 396 | // (NO LONGER converting grid dimensions from angstroem to bohr radii)
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| 397 | const double AtomicLengthToAngstroem = 1.;//0.52917721;
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| 398 | SCVector3 min;
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| 399 | SCVector3 max;
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| 400 | SCVector3 delta;
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| 401 | size_t samplepoints[3];
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| 402 | // due to periodic boundary conditions, we don't need gridpoints-1 here
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| 403 | // TODO: in case of open boundary conditions, we need data on the right
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| 404 | // hand side boundary as well
|
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| 405 | // const int gridpoints = data.sampled_grid.getGridPointsPerAxis();
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| 406 | for (size_t i=0;i<3;++i) {
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| 407 | min(i) = data.sampled_grid.begin_window[i]/AtomicLengthToAngstroem;
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| 408 | max(i) = data.sampled_grid.end_window[i]/AtomicLengthToAngstroem;
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| 409 | delta(i) = data.sampled_grid.getDeltaPerAxis(i)/AtomicLengthToAngstroem;
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| 410 | samplepoints[i] = data.sampled_grid.getWindowGridPointsPerAxis(i);
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| 411 | }
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| 412 | ExEnv::out0() << "Grid starts at " << min
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| 413 | << " and ends at " << max
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| 414 | << " with a delta of " << delta
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| 415 | << " to get "
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| 416 | << samplepoints[0] << ","
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| 417 | << samplepoints[1] << ","
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| 418 | << samplepoints[2] << " samplepoints."
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| 419 | << endl;
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| 420 | assert( data.sampled_grid.sampled_grid.size() == samplepoints[0]*samplepoints[1]*samplepoints[2]);
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| 421 |
|
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| 422 | // 3. sample the atomic density
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| 423 | const double element_volume_conversion =
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| 424 | 1./AtomicLengthToAngstroem/AtomicLengthToAngstroem/AtomicLengthToAngstroem;
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| 425 | SCVector3 r = min;
|
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| 426 |
|
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| 427 | std::set<int> valence_indices;
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| 428 | RefDiagSCMatrix evals = scf->eigenvalues();
|
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| 429 | if (data.DoValenceOnly == MPQCData::DoSampleValenceOnly) {
|
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| 430 | // find valence orbitals
|
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| 431 | // std::cout << "All Eigenvalues:" << std::endl;
|
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| 432 | // for(int i=0;i<wfn->oso_dimension(); ++i)
|
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| 433 | // std::cout << i << "th eigenvalue is " << evals(i) << std::endl;
|
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| 434 | // int n_electrons = scf->nelectron();
|
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| 435 | int n_core_electrons = wfn->molecule()->n_core_electrons();
|
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| 436 | std::set<double> evals_sorted;
|
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| 437 | {
|
---|
| 438 | int i=0;
|
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| 439 | double first_positive_ev = std::numeric_limits<double>::max();
|
---|
| 440 | for(i=0;i<wfn->oso_dimension(); ++i) {
|
---|
| 441 | if (evals(i) < 0.)
|
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| 442 | evals_sorted.insert(evals(i));
|
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| 443 | else
|
---|
| 444 | first_positive_ev = std::min(first_positive_ev, (double)evals(i));
|
---|
| 445 | }
|
---|
| 446 | // add the first positive for the distance
|
---|
| 447 | evals_sorted.insert(first_positive_ev);
|
---|
| 448 | }
|
---|
| 449 | std::set<double> evals_distances;
|
---|
| 450 | std::set<double>::const_iterator advancer = evals_sorted.begin();
|
---|
| 451 | std::set<double>::const_iterator iter = advancer++;
|
---|
| 452 | for(;advancer != evals_sorted.end(); ++advancer,++iter)
|
---|
| 453 | evals_distances.insert((*advancer)-(*iter));
|
---|
| 454 | const double largest_distance = *(evals_distances.rbegin());
|
---|
| 455 | ExEnv::out0() << "Largest distance between EV is " << largest_distance << std::endl;
|
---|
| 456 | advancer = evals_sorted.begin();
|
---|
| 457 | iter = advancer++;
|
---|
| 458 | for(;advancer != evals_sorted.begin(); ++advancer,++iter)
|
---|
| 459 | if (fabs(fabs((*advancer)-(*iter)) - largest_distance) < 1e-10)
|
---|
| 460 | break;
|
---|
| 461 | assert( advancer != evals_sorted.begin() );
|
---|
| 462 | const double last_core_ev = (*iter);
|
---|
| 463 | ExEnv::out0() << "Last core EV might be " << last_core_ev << std::endl;
|
---|
| 464 | ExEnv::out0() << "First valence index is " << n_core_electrons/2 << std::endl;
|
---|
| 465 | for(int i=n_core_electrons/2;i<wfn->oso_dimension(); ++i)
|
---|
| 466 | if (evals(i) > last_core_ev)
|
---|
| 467 | valence_indices.insert(i);
|
---|
| 468 | // {
|
---|
| 469 | // int i=0;
|
---|
| 470 | // std::cout << "Valence eigenvalues:" << std::endl;
|
---|
| 471 | // for (std::set<int>::const_iterator iter = valence_indices.begin();
|
---|
| 472 | // iter != valence_indices.end(); ++iter)
|
---|
| 473 | // std::cout << i++ << "th eigenvalue is " << (*iter) << std::endl;
|
---|
| 474 | // }
|
---|
| 475 | } else {
|
---|
| 476 | // just insert all indices
|
---|
| 477 | for(int i=0;i<wfn->oso_dimension(); ++i)
|
---|
| 478 | valence_indices.insert(i);
|
---|
| 479 | }
|
---|
| 480 |
|
---|
| 481 | // testing alternative routine from SCF::so_density()
|
---|
| 482 | RefSCMatrix oso_vector = scf->oso_eigenvectors();
|
---|
| 483 | RefSCMatrix vector = scf->so_to_orthog_so().t() * oso_vector;
|
---|
| 484 | oso_vector = 0;
|
---|
| 485 | RefSymmSCMatrix occ(scf->oso_dimension(), scf->basis_matrixkit());
|
---|
| 486 | occ.assign(0.0);
|
---|
| 487 | for (std::set<int>::const_iterator iter = valence_indices.begin();
|
---|
| 488 | iter != valence_indices.end(); ++iter) {
|
---|
| 489 | const int i = *iter;
|
---|
| 490 | occ(i,i) = scf->occupation(i);
|
---|
| 491 | ExEnv::out0() << "# " << i << " has ev of " << evals(i) << ", occupied by " << scf->occupation(i) << std::endl;
|
---|
| 492 | }
|
---|
| 493 | RefSymmSCMatrix d2(scf->so_dimension(), scf->basis_matrixkit());
|
---|
| 494 | d2.assign(0.0);
|
---|
| 495 | d2.accumulate_transform(vector, occ);
|
---|
| 496 |
|
---|
| 497 | // taken from scf::density()
|
---|
| 498 | RefSCMatrix nos
|
---|
| 499 | = scf->integral()->petite_list()->evecs_to_AO_basis(scf->natural_orbitals());
|
---|
| 500 | RefDiagSCMatrix nd = scf->natural_density();
|
---|
| 501 | GaussianBasisSet::ValueData *valdat
|
---|
| 502 | = new GaussianBasisSet::ValueData(scf->basis(), scf->integral());
|
---|
| 503 | std::vector<double>::iterator griditer = data.sampled_grid.sampled_grid.begin();
|
---|
| 504 | const int nbasis = scf->basis()->nbasis();
|
---|
| 505 | double *bs_values = new double[nbasis];
|
---|
| 506 |
|
---|
| 507 | // TODO: need to take care when we have periodic boundary conditions.
|
---|
| 508 | for (size_t x = 0; x < samplepoints[0]; ++x, r.x() += delta(0)) {
|
---|
| 509 | std::cout << "Sampling now for x=" << r.x() << std::endl;
|
---|
| 510 | for (size_t y = 0; y < samplepoints[1]; ++y, r.y() += delta(1)) {
|
---|
| 511 | for (size_t z = 0; z < samplepoints[2]; ++z, r.z() += delta(2)) {
|
---|
| 512 | scf->basis()->values(r,valdat,bs_values);
|
---|
| 513 |
|
---|
| 514 | // loop over natural orbitals adding contributions to elec_density
|
---|
| 515 | double elec_density=0.0;
|
---|
| 516 | for (int i=0; i<nbasis; ++i) {
|
---|
| 517 | double tmp = 0.0;
|
---|
| 518 | for (int j=0; j<nbasis; ++j) {
|
---|
| 519 | tmp += d2(j,i)*bs_values[j]*bs_values[i];
|
---|
| 520 | }
|
---|
| 521 | elec_density += tmp;
|
---|
| 522 | }
|
---|
| 523 | const double dens_at_r = elec_density * element_volume_conversion;
|
---|
| 524 | // const double dens_at_r = scf->density(r) * element_volume_conversion;
|
---|
| 525 |
|
---|
| 526 | // if (fabs(dens_at_r) > 1e-4)
|
---|
| 527 | // std::cout << "Electron density at " << r << " is " << dens_at_r << std::endl;
|
---|
| 528 | if (griditer != data.sampled_grid.sampled_grid.end())
|
---|
| 529 | *griditer++ = dens_at_r;
|
---|
| 530 | else
|
---|
| 531 | std::cerr << "PAST RANGE!" << std::endl;
|
---|
| 532 | }
|
---|
| 533 | r.z() = min.z();
|
---|
| 534 | }
|
---|
| 535 | r.y() = min.y();
|
---|
| 536 | }
|
---|
| 537 | delete[] bs_values;
|
---|
| 538 | delete valdat;
|
---|
| 539 | assert( griditer == data.sampled_grid.sampled_grid.end());
|
---|
| 540 | // normalization of electron charge to equal electron number
|
---|
| 541 | {
|
---|
| 542 | double integral_value = 0.;
|
---|
| 543 | const double volume_element = pow(AtomicLengthToAngstroem,3)*delta(0)*delta(1)*delta(2);
|
---|
| 544 | for (std::vector<double>::const_iterator diter = data.sampled_grid.sampled_grid.begin();
|
---|
| 545 | diter != data.sampled_grid.sampled_grid.end(); ++diter)
|
---|
| 546 | integral_value += *diter;
|
---|
| 547 | integral_value *= volume_element;
|
---|
| 548 | int n_electrons = scf->nelectron();
|
---|
| 549 | if (data.DoValenceOnly == MPQCData::DoSampleValenceOnly)
|
---|
| 550 | n_electrons -= wfn->molecule()->n_core_electrons();
|
---|
| 551 | const double normalization =
|
---|
| 552 | ((integral_value == 0) || (n_electrons == 0)) ?
|
---|
| 553 | 1. : n_electrons/integral_value;
|
---|
| 554 | std::cout << "Created " << data.sampled_grid.sampled_grid.size() << " grid points"
|
---|
| 555 | << " with integral value of " << integral_value
|
---|
| 556 | << " against " << ((data.DoValenceOnly == MPQCData::DoSampleValenceOnly) ? "n_valence_electrons" : "n_electrons")
|
---|
| 557 | << " of " << n_electrons << "." << std::endl;
|
---|
| 558 | // with normalization we also get the charge right : -1.
|
---|
| 559 | for (std::vector<double>::iterator diter = data.sampled_grid.sampled_grid.begin();
|
---|
| 560 | diter != data.sampled_grid.sampled_grid.end(); ++diter)
|
---|
| 561 | *diter *= -1.*normalization;
|
---|
| 562 | }
|
---|
| 563 | }
|
---|
| 564 | }
|
---|
| 565 | scf = 0;
|
---|
| 566 | }
|
---|
| 567 |
|
---|
| 568 | void extractTimings(
|
---|
| 569 | Ref<RegionTimer> &tim,
|
---|
| 570 | void *_data)
|
---|
| 571 | {
|
---|
| 572 | MPQCData &data = *static_cast<MPQCData *>(_data);
|
---|
| 573 | // times obtain from key "mpqc" which should be the first
|
---|
| 574 | const int nregion = tim->nregion();
|
---|
| 575 | //std::cout << "There are " << nregion << " timed regions." << std::endl;
|
---|
| 576 | const char **region_names = new const char*[nregion];
|
---|
| 577 | tim->get_region_names(region_names);
|
---|
| 578 | // find "gather"
|
---|
| 579 | size_t gather_region = findTimerRegion(nregion, region_names, "gather");
|
---|
| 580 | size_t mpqc_region = findTimerRegion(nregion, region_names, "mpqc");
|
---|
| 581 | delete[] region_names;
|
---|
| 582 |
|
---|
| 583 | // get timings
|
---|
| 584 | double *cpu_time = new double[nregion];
|
---|
| 585 | double *wall_time = new double[nregion];
|
---|
| 586 | double *flops = new double[nregion];
|
---|
| 587 | tim->get_cpu_times(cpu_time);
|
---|
| 588 | tim->get_wall_times(wall_time);
|
---|
| 589 | tim->get_flops(flops);
|
---|
| 590 | if (cpu_time != NULL) {
|
---|
| 591 | data.times.total_cputime = cpu_time[mpqc_region];
|
---|
| 592 | data.times.gather_cputime = cpu_time[gather_region];
|
---|
| 593 | }
|
---|
| 594 | if (wall_time != NULL) {
|
---|
| 595 | data.times.total_walltime = wall_time[mpqc_region];
|
---|
| 596 | data.times.gather_walltime = wall_time[gather_region];
|
---|
| 597 | }
|
---|
| 598 | if (flops != NULL) {
|
---|
| 599 | data.times.total_flops = flops[mpqc_region];
|
---|
| 600 | data.times.gather_flops = flops[gather_region];
|
---|
| 601 | }
|
---|
| 602 | delete[] cpu_time;
|
---|
| 603 | delete[] wall_time;
|
---|
| 604 | delete[] flops;
|
---|
| 605 | }
|
---|
| 606 |
|
---|