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