| 1 | /** \file joiner.cpp
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| 2 | *
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| 3 | * Takes evaluated fragments (energy and forces) and by reading the factors files determines total energy
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| 4 | * and each force for the whole molecule.
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| 5 | *
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| 6 | */
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| 7 |
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| 8 | //============================ INCLUDES ===========================
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| 9 |
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| 10 | #include <cstring>
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| 11 |
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| 12 | #include "datacreator.hpp"
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| 13 | #include "helpers.hpp"
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| 14 | #include "memoryallocator.hpp"
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| 15 | #include "parser.hpp"
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| 16 | #include "periodentafel.hpp"
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| 17 |
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| 18 | //============================== MAIN =============================
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| 19 |
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| 20 | int main(int argc, char **argv)
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| 21 | {
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| 22 | periodentafel *periode = NULL; // and a period table of all elements
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| 23 | EnergyMatrix Energy;
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| 24 | EnergyMatrix EnergyFragments;
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| 25 |
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| 26 | EnergyMatrix Hcorrection;
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| 27 | EnergyMatrix HcorrectionFragments;
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| 28 |
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| 29 | ForceMatrix Force;
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| 30 | ForceMatrix ForceFragments;
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| 31 |
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| 32 | HessianMatrix Hessian;
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| 33 | HessianMatrix HessianFragments;
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| 34 |
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| 35 | ForceMatrix Shielding;
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| 36 | ForceMatrix ShieldingPAS;
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| 37 | ForceMatrix ShieldingFragments;
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| 38 | ForceMatrix ShieldingPASFragments;
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| 39 | ForceMatrix Chi;
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| 40 | ForceMatrix ChiPAS;
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| 41 | ForceMatrix ChiFragments;
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| 42 | ForceMatrix ChiPASFragments;
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| 43 | KeySetsContainer KeySet;
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| 44 | stringstream prefix;
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| 45 | char *dir = NULL;
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| 46 | bool NoHCorrection = false;
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| 47 | bool NoHessian = false;
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| 48 |
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| 49 | DoLog(0) && (Log() << Verbose(0) << "Joiner" << endl);
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| 50 | DoLog(0) && (Log() << Verbose(0) << "======" << endl);
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| 51 |
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| 52 | // Get the command line options
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| 53 | if (argc < 3) {
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| 54 | DoLog(0) && (Log() << Verbose(0) << "Usage: " << argv[0] << " <inputdir> <prefix> [elementsdb]" << endl);
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| 55 | DoLog(0) && (Log() << Verbose(0) << "<inputdir>\ttherein the output of a molecuilder fragmentation is expected, each fragment with a subdir containing an energy.all and a forces.all file." << endl);
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| 56 | DoLog(0) && (Log() << Verbose(0) << "<prefix>\tprefix of energy and forces file." << endl);
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| 57 | DoLog(0) && (Log() << Verbose(0) << "[elementsdb]\tpath to elements database, needed for shieldings." << endl);
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| 58 | return 1;
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| 59 | } else {
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| 60 | dir = Malloc<char>(strlen(argv[2]) + 2, "main: *dir");
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| 61 | strcpy(dir, "/");
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| 62 | strcat(dir, argv[2]);
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| 63 | }
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| 64 | if (argc > 3) {
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| 65 | periode = new periodentafel;
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| 66 | periode->LoadPeriodentafel(argv[3]);
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| 67 | }
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| 68 |
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| 69 | // Test the given directory
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| 70 | if (!TestParams(argc, argv))
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| 71 | return 1;
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| 72 |
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| 73 | // +++++++++++++++++ PARSING +++++++++++++++++++++++++++++++
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| 74 |
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| 75 | // ------------- Parse through all Fragment subdirs --------
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| 76 | if (!Energy.ParseFragmentMatrix(argv[1], dir, EnergySuffix, 0,0)) return 1;
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| 77 | if (!Hcorrection.ParseFragmentMatrix(argv[1], "", HCORRECTIONSUFFIX, 0,0)) {
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| 78 | NoHCorrection = true;
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| 79 | DoLog(0) && (Log() << Verbose(0) << "No HCorrection matrices found, skipping these." << endl);
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| 80 | }
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| 81 | if (!Force.ParseFragmentMatrix(argv[1], dir, ForcesSuffix, 0,0)) return 1;
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| 82 | if (!Hessian.ParseFragmentMatrix(argv[1], dir, HessianSuffix, 0,0)) {
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| 83 | NoHessian = true;
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| 84 | DoLog(0) && (Log() << Verbose(0) << "No hessian matrices found, skipping these." << endl);
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| 85 | }
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| 86 | if (periode != NULL) { // also look for PAS values
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| 87 | if (!Shielding.ParseFragmentMatrix(argv[1], dir, ShieldingSuffix, 1, 0)) return 1;
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| 88 | if (!ShieldingPAS.ParseFragmentMatrix(argv[1], dir, ShieldingPASSuffix, 1, 0)) return 1;
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| 89 | if (!Chi.ParseFragmentMatrix(argv[1], dir, ChiSuffix, 1, 0)) return 1;
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| 90 | if (!ChiPAS.ParseFragmentMatrix(argv[1], dir, ChiPASSuffix, 1, 0)) return 1;
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| 91 | }
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| 92 |
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| 93 | // ---------- Parse the TE Factors into an array -----------------
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| 94 | if (!Energy.InitialiseIndices()) return 1;
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| 95 | if (!NoHCorrection)
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| 96 | Hcorrection.InitialiseIndices();
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| 97 |
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| 98 | // ---------- Parse the Force indices into an array ---------------
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| 99 | if (!Force.ParseIndices(argv[1])) return 1;
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| 100 |
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| 101 | // ---------- Parse the Hessian (=force) indices into an array ---------------
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| 102 | if (!NoHessian)
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| 103 | if (!Hessian.InitialiseIndices((class MatrixContainer *)&Force)) return 1;
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| 104 |
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| 105 | // ---------- Parse the shielding indices into an array ---------------
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| 106 | if (periode != NULL) { // also look for PAS values
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| 107 | if(!Shielding.ParseIndices(argv[1])) return 1;
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| 108 | if(!ShieldingPAS.ParseIndices(argv[1])) return 1;
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| 109 | if(!Chi.ParseIndices(argv[1])) return 1;
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| 110 | if(!ChiPAS.ParseIndices(argv[1])) return 1;
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| 111 | }
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| 112 |
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| 113 | // ---------- Parse the KeySets into an array ---------------
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| 114 | if (!KeySet.ParseKeySets(argv[1], Force.RowCounter, Force.MatrixCounter)) return 1;
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| 115 |
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| 116 | if (!KeySet.ParseManyBodyTerms()) return 1;
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| 117 |
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| 118 | if (!EnergyFragments.AllocateMatrix(Energy.Header, Energy.MatrixCounter, Energy.RowCounter, Energy.ColumnCounter)) return 1;
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| 119 | if (!NoHCorrection)
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| 120 | HcorrectionFragments.AllocateMatrix(Hcorrection.Header, Hcorrection.MatrixCounter, Hcorrection.RowCounter, Hcorrection.ColumnCounter);
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| 121 | if (!ForceFragments.AllocateMatrix(Force.Header, Force.MatrixCounter, Force.RowCounter, Force.ColumnCounter)) return 1;
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| 122 | if (!NoHessian)
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| 123 | if (!HessianFragments.AllocateMatrix(Hessian.Header, Hessian.MatrixCounter, Hessian.RowCounter, Hessian.ColumnCounter)) return 1;
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| 124 | if (periode != NULL) { // also look for PAS values
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| 125 | if (!ShieldingFragments.AllocateMatrix(Shielding.Header, Shielding.MatrixCounter, Shielding.RowCounter, Shielding.ColumnCounter)) return 1;
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| 126 | if (!ShieldingPASFragments.AllocateMatrix(ShieldingPAS.Header, ShieldingPAS.MatrixCounter, ShieldingPAS.RowCounter, ShieldingPAS.ColumnCounter)) return 1;
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| 127 | if (!ChiFragments.AllocateMatrix(Chi.Header, Chi.MatrixCounter, Chi.RowCounter, Chi.ColumnCounter)) return 1;
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| 128 | if (!ChiPASFragments.AllocateMatrix(ChiPAS.Header, ChiPAS.MatrixCounter, ChiPAS.RowCounter, ChiPAS.ColumnCounter)) return 1;
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| 129 | }
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| 130 |
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| 131 | // ----------- Resetting last matrices (where full QM values are stored right now)
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| 132 | if(!Energy.SetLastMatrix(0., 0)) return 1;
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| 133 | if(!Force.SetLastMatrix(0., 2)) return 1;
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| 134 | if (!NoHessian)
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| 135 | if (!Hessian.SetLastMatrix(0., 0)) return 1;
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| 136 | if (periode != NULL) { // also look for PAS values
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| 137 | if(!Shielding.SetLastMatrix(0., 2)) return 1;
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| 138 | if(!ShieldingPAS.SetLastMatrix(0., 2)) return 1;
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| 139 | if(!Chi.SetLastMatrix(0., 2)) return 1;
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| 140 | if(!ChiPAS.SetLastMatrix(0., 2)) return 1;
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| 141 | }
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| 142 |
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| 143 | // +++++++++++++++++ SUMMING +++++++++++++++++++++++++++++++
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| 144 |
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| 145 | // --------- sum up and write for each order----------------
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| 146 | for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
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| 147 | // --------- sum up energy --------------------
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| 148 | DoLog(0) && (Log() << Verbose(0) << "Summing energy of order " << BondOrder+1 << " ..." << endl);
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| 149 | if (!EnergyFragments.SumSubManyBodyTerms(Energy, KeySet, BondOrder)) return 1;
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| 150 | if (!NoHCorrection) {
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| 151 | HcorrectionFragments.SumSubManyBodyTerms(Hcorrection, KeySet, BondOrder);
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| 152 | if (!Energy.SumSubEnergy(EnergyFragments, &HcorrectionFragments, KeySet, BondOrder, 1.)) return 1;
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| 153 | Hcorrection.SumSubEnergy(HcorrectionFragments, NULL, KeySet, BondOrder, 1.);
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| 154 | } else
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| 155 | if (!Energy.SumSubEnergy(EnergyFragments, NULL, KeySet, BondOrder, 1.)) return 1;
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| 156 | // --------- sum up Forces --------------------
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| 157 | DoLog(0) && (Log() << Verbose(0) << "Summing forces of order " << BondOrder+1 << " ..." << endl);
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| 158 | if (!ForceFragments.SumSubManyBodyTerms(Force, KeySet, BondOrder)) return 1;
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| 159 | if (!Force.SumSubForces(ForceFragments, KeySet, BondOrder, 1.)) return 1;
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| 160 | // --------- sum up Hessian --------------------
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| 161 | if (!NoHessian) {
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| 162 | DoLog(0) && (Log() << Verbose(0) << "Summing Hessian of order " << BondOrder+1 << " ..." << endl);
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| 163 | if (!HessianFragments.SumSubManyBodyTerms(Hessian, KeySet, BondOrder)) return 1;
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| 164 | if (!Hessian.SumSubHessians(HessianFragments, KeySet, BondOrder, 1.)) return 1;
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| 165 | }
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| 166 | if (periode != NULL) { // also look for PAS values
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| 167 | DoLog(0) && (Log() << Verbose(0) << "Summing shieldings and susceptibilities of order " << BondOrder+1 << " ..." << endl);
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| 168 | if (!ShieldingFragments.SumSubManyBodyTerms(Shielding, KeySet, BondOrder)) return 1;
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| 169 | if (!Shielding.SumSubForces(ShieldingFragments, KeySet, BondOrder, 1.)) return 1;
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| 170 | if (!ShieldingPASFragments.SumSubManyBodyTerms(ShieldingPAS, KeySet, BondOrder)) return 1;
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| 171 | if (!ShieldingPAS.SumSubForces(ShieldingPASFragments, KeySet, BondOrder, 1.)) return 1;
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| 172 | if (!ChiFragments.SumSubManyBodyTerms(Chi, KeySet, BondOrder)) return 1;
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| 173 | if (!Chi.SumSubForces(ChiFragments, KeySet, BondOrder, 1.)) return 1;
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| 174 | if (!ChiPASFragments.SumSubManyBodyTerms(ChiPAS, KeySet, BondOrder)) return 1;
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| 175 | if (!ChiPAS.SumSubForces(ChiPASFragments, KeySet, BondOrder, 1.)) return 1;
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| 176 | }
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| 177 |
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| 178 | // --------- write the energy and forces file --------------------
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| 179 | prefix.str(" ");
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| 180 | prefix << dir << OrderSuffix << (BondOrder+1);
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| 181 | DoLog(0) && (Log() << Verbose(0) << "Writing files " << argv[1] << prefix.str() << ". ..." << endl);
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| 182 | // energy
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| 183 | if (!Energy.WriteLastMatrix(argv[1], (prefix.str()).c_str(), EnergySuffix)) return 1;
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| 184 | // forces
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| 185 | if (!Force.WriteLastMatrix(argv[1], (prefix.str()).c_str(), ForcesSuffix)) return 1;
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| 186 | // hessian
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| 187 | if (!NoHessian)
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| 188 | if (!Hessian.WriteLastMatrix(argv[1], (prefix.str()).c_str(), HessianSuffix)) return 1;
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| 189 | // shieldings
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| 190 | if (periode != NULL) { // also look for PAS values
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| 191 | if (!Shielding.WriteLastMatrix(argv[1], (prefix.str()).c_str(), ShieldingSuffix)) return 1;
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| 192 | if (!ShieldingPAS.WriteLastMatrix(argv[1], (prefix.str()).c_str(), ShieldingPASSuffix)) return 1;
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| 193 | if (!Chi.WriteLastMatrix(argv[1], (prefix.str()).c_str(), ChiSuffix)) return 1;
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| 194 | if (!ChiPAS.WriteLastMatrix(argv[1], (prefix.str()).c_str(), ChiPASSuffix)) return 1;
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| 195 | }
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| 196 | }
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| 197 | // fragments
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| 198 | prefix.str(" ");
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| 199 | prefix << dir << EnergyFragmentSuffix;
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| 200 | if (!EnergyFragments.WriteTotalFragments(argv[1], (prefix.str()).c_str())) return 1;
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| 201 | if (!NoHCorrection) {
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| 202 | prefix.str(" ");
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| 203 | prefix << dir << HcorrectionFragmentSuffix;
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| 204 | if (!HcorrectionFragments.WriteTotalFragments(argv[1], (prefix.str()).c_str())) return 1;
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| 205 | }
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| 206 | prefix.str(" ");
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| 207 | prefix << dir << ForceFragmentSuffix;
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| 208 | if (!ForceFragments.WriteTotalFragments(argv[1], (prefix.str()).c_str())) return 1;
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| 209 | if (!CreateDataFragment(EnergyFragments, KeySet, argv[1], FRAGMENTPREFIX ENERGYPERFRAGMENT, "fragment energy versus the Fragment No", "today", CreateEnergy)) return 1;
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| 210 | if (!NoHessian) {
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| 211 | prefix.str(" ");
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| 212 | prefix << dir << HessianFragmentSuffix;
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| 213 | if (!HessianFragments.WriteTotalFragments(argv[1], (prefix.str()).c_str())) return 1;
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| 214 | }
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| 215 | if (periode != NULL) { // also look for PAS values
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| 216 | prefix.str(" ");
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| 217 | prefix << dir << ShieldingFragmentSuffix;
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| 218 | if (!ShieldingFragments.WriteTotalFragments(argv[1], (prefix.str()).c_str())) return 1;
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| 219 | prefix.str(" ");
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| 220 | prefix << dir << ShieldingPASFragmentSuffix;
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| 221 | if (!ShieldingPASFragments.WriteTotalFragments(argv[1], (prefix.str()).c_str())) return 1;
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| 222 | prefix.str(" ");
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| 223 | prefix << dir << ChiFragmentSuffix;
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| 224 | if (!ChiFragments.WriteTotalFragments(argv[1], (prefix.str()).c_str())) return 1;
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| 225 | prefix.str(" ");
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| 226 | prefix << dir << ChiPASFragmentSuffix;
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| 227 | if (!ChiPASFragments.WriteTotalFragments(argv[1], (prefix.str()).c_str())) return 1;
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| 228 | }
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| 229 |
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| 230 | // write last matrices as fragments into central dir (not subdir as above), for analyzer to know index bounds
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| 231 | if (!Energy.WriteLastMatrix(argv[1], dir, EnergyFragmentSuffix)) return 1;
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| 232 | if (!NoHCorrection) Hcorrection.WriteLastMatrix(argv[1], dir, HcorrectionFragmentSuffix);
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| 233 | if (!Force.WriteLastMatrix(argv[1], dir, ForceFragmentSuffix)) return 1;
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| 234 | if (!NoHessian)
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| 235 | if (!Hessian.WriteLastMatrix(argv[1], dir, HessianFragmentSuffix)) return 1;
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| 236 | if (periode != NULL) { // also look for PAS values
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| 237 | if (!Shielding.WriteLastMatrix(argv[1], dir, ShieldingFragmentSuffix)) return 1;
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| 238 | if (!ShieldingPAS.WriteLastMatrix(argv[1], dir, ShieldingPASFragmentSuffix)) return 1;
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| 239 | if (!Chi.WriteLastMatrix(argv[1], dir, ChiFragmentSuffix)) return 1;
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| 240 | if (!ChiPAS.WriteLastMatrix(argv[1], dir, ChiPASFragmentSuffix)) return 1;
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| 241 | }
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| 242 |
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| 243 | // exit
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| 244 | delete(periode);
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| 245 | Free(&dir);
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| 246 | DoLog(0) && (Log() << Verbose(0) << "done." << endl);
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| 247 | return 0;
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| 248 | };
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| 249 |
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| 250 | //============================ END ===========================
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