source: src/joiner.cpp@ 3d919e

/** \file joiner.cpp
 *
 * Takes evaluated fragments (energy and forces) and by reading the factors files determines total energy
 * and each force for the whole molecule.
 *
 */

//============================ INCLUDES ===========================

#include "datacreator.hpp"
#include "helpers.hpp"
#include "parser.hpp"
#include "periodentafel.hpp"

//============================== MAIN =============================

int main(int argc, char **argv)
{
        periodentafel *periode = NULL; // and a period table of all elements
        EnergyMatrix Energy;
        EnergyMatrix Hcorrection;
        ForceMatrix Force;
        EnergyMatrix EnergyFragments;
        EnergyMatrix HcorrectionFragments;
        ForceMatrix ForceFragments;
        ForceMatrix Shielding;
        ForceMatrix ShieldingPAS;
        ForceMatrix ShieldingFragments;
        ForceMatrix ShieldingPASFragments;
        KeySetsContainer KeySet;
        stringstream prefix;
        char *dir = NULL;
        bool Hcorrected = true;

        cout << "Joiner" << endl;
        cout << "======" << endl;

        // Get the command line options
        if (argc < 3) {
                cout << "Usage: " << argv[0] << " <inputdir> <prefix> [elementsdb]" << endl;
                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;
                cout << "<prefix>\tprefix of energy and forces file." << endl;
                cout << "[elementsdb]\tpath to elements database, needed for shieldings." << endl;
                return 1;
        } else {
                dir = (char *) Malloc(sizeof(char)*(strlen(argv[2])+2), "main: *dir");
                strcpy(dir, "/");
                strcat(dir, argv[2]);
        }
        if (argc > 3) {
                periode = new periodentafel;
                periode->LoadPeriodentafel(argv[3]);
        }

        // Test the given directory
        if (!TestParams(argc, argv))
                return 1;

        // +++++++++++++++++ PARSING +++++++++++++++++++++++++++++++

        // ------------- Parse through all Fragment subdirs --------
        if (!Energy.ParseFragmentMatrix(argv[1], dir, EnergySuffix, 0,0)) return 1;
        Hcorrected = Hcorrection.ParseFragmentMatrix(argv[1], "", HCORRECTIONSUFFIX, 0,0);
        if (!Force.ParseFragmentMatrix(argv[1], dir, ForcesSuffix, 0,0)) return 1;
        if (periode != NULL) { // also look for PAS values
                if (!Shielding.ParseFragmentMatrix(argv[1], dir, ShieldingSuffix, 1, 0)) return 1;
                if (!ShieldingPAS.ParseFragmentMatrix(argv[1], dir, ShieldingPASSuffix, 1, 0)) return 1;
        }

        // ---------- Parse the TE Factors into an array -----------------
        if (!Energy.ParseIndices()) return 1;
        if (Hcorrected) Hcorrection.ParseIndices();

        // ---------- Parse the Force indices into an array ---------------
        if (!Force.ParseIndices(argv[1])) return 1;

        // ---------- Parse the shielding indices into an array ---------------
        if (periode != NULL) { // also look for PAS values
                if(!Shielding.ParseIndices(argv[1])) return 1;
                if(!ShieldingPAS.ParseIndices(argv[1])) return 1;
        }

        // ---------- Parse the KeySets into an array ---------------
        if (!KeySet.ParseKeySets(argv[1], Force.RowCounter, Force.MatrixCounter)) return 1;

        if (!KeySet.ParseManyBodyTerms()) return 1;
        if (!EnergyFragments.AllocateMatrix(Energy.Header, Energy.MatrixCounter, Energy.RowCounter, Energy.ColumnCounter)) return 1;
        if (Hcorrected) HcorrectionFragments.AllocateMatrix(Hcorrection.Header, Hcorrection.MatrixCounter, Hcorrection.RowCounter, Hcorrection.ColumnCounter);
        if (!ForceFragments.AllocateMatrix(Force.Header, Force.MatrixCounter, Force.RowCounter, Force.ColumnCounter)) return 1;
        if (periode != NULL) { // also look for PAS values
                if (!ShieldingFragments.AllocateMatrix(Shielding.Header, Shielding.MatrixCounter, Shielding.RowCounter, Shielding.ColumnCounter)) return 1;
                if (!ShieldingPASFragments.AllocateMatrix(ShieldingPAS.Header, ShieldingPAS.MatrixCounter, ShieldingPAS.RowCounter, ShieldingPAS.ColumnCounter)) return 1;
        }

        // ----------- Resetting last matrices (where full QM values are stored right now)
        if(!Energy.SetLastMatrix(0., 0)) return 1;
        if(!Force.SetLastMatrix(0., 2)) return 1;
        if (periode != NULL) { // also look for PAS values
                if(!Shielding.SetLastMatrix(0., 2)) return 1;
                if(!ShieldingPAS.SetLastMatrix(0., 2)) return 1;
        }

        // +++++++++++++++++ SUMMING +++++++++++++++++++++++++++++++

        // --------- sum up and write for each order----------------
        for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
                // --------- sum up energy --------------------
                cout << "Summing energy of order " << BondOrder+1 << " ..." << endl;
                if (!EnergyFragments.SumSubManyBodyTerms(Energy, KeySet, BondOrder)) return 1;
                if (Hcorrected) {
                        HcorrectionFragments.SumSubManyBodyTerms(Hcorrection, KeySet, BondOrder);
                        if (!Energy.SumSubEnergy(EnergyFragments, &HcorrectionFragments, KeySet, BondOrder, 1.)) return 1;
                        if (Hcorrected) Hcorrection.SumSubEnergy(HcorrectionFragments, NULL, KeySet, BondOrder, 1.);
                } else
                        if (!Energy.SumSubEnergy(EnergyFragments, NULL, KeySet, BondOrder, 1.)) return 1;
                // --------- sum up Forces --------------------
                cout << "Summing forces of order " << BondOrder+1 << " ..." << endl;
                if (!ForceFragments.SumSubManyBodyTerms(Force, KeySet, BondOrder)) return 1;
                if (!Force.SumSubForces(ForceFragments, KeySet, BondOrder, 1.)) return 1;
                if (periode != NULL) { // also look for PAS values
                        cout << "Summing shieldings of order " << BondOrder+1 << " ..." << endl;
                        if (!ShieldingFragments.SumSubManyBodyTerms(Shielding, KeySet, BondOrder)) return 1;
                        if (!Shielding.SumSubForces(ShieldingFragments, KeySet, BondOrder, 1.)) return 1;
                        if (!ShieldingPASFragments.SumSubManyBodyTerms(ShieldingPAS, KeySet, BondOrder)) return 1;
                        if (!ShieldingPAS.SumSubForces(ShieldingPASFragments, KeySet, BondOrder, 1.)) return 1;
                }

                // --------- write the energy and forces file --------------------
                prefix.str(" ");
                prefix << dir << OrderSuffix << (BondOrder+1);
                cout << "Writing files " << argv[1] << prefix.str() << ". ..." << endl;
                // energy
                if (!Energy.WriteLastMatrix(argv[1], (prefix.str()).c_str(), EnergySuffix)) return 1;
                // forces
                if (!Force.WriteLastMatrix(argv[1], (prefix.str()).c_str(), ForcesSuffix)) return 1;
                // shieldings
                if (periode != NULL) { // also look for PAS values
                        if (!Shielding.WriteLastMatrix(argv[1], (prefix.str()).c_str(), ShieldingSuffix)) return 1;
                        if (!ShieldingPAS.WriteLastMatrix(argv[1], (prefix.str()).c_str(), ShieldingPASSuffix)) return 1;
                }
        }
        // fragments
        prefix.str(" ");
        prefix << dir << EnergyFragmentSuffix;
        if (!EnergyFragments.WriteTotalFragments(argv[1], (prefix.str()).c_str())) return 1;
        if (Hcorrected) {
                prefix.str(" ");
                prefix << dir << HcorrectionFragmentSuffix;
                if (!HcorrectionFragments.WriteTotalFragments(argv[1], (prefix.str()).c_str())) return 1;
        }
        prefix.str(" ");
        prefix << dir << ForceFragmentSuffix;
        if (!ForceFragments.WriteTotalFragments(argv[1], (prefix.str()).c_str())) return 1;
        if (!CreateDataFragment(EnergyFragments, KeySet, argv[1], FRAGMENTPREFIX ENERGYPERFRAGMENT, "fragment energy versus the Fragment No", "today", CreateEnergy)) return 1;
        if (periode != NULL) { // also look for PAS values
                prefix.str(" ");
                prefix << dir << ShieldingFragmentSuffix;
                if (!ShieldingFragments.WriteTotalFragments(argv[1], (prefix.str()).c_str())) return 1;
                prefix.str(" ");
                prefix << dir << ShieldingPASFragmentSuffix;
                if (!ShieldingPASFragments.WriteTotalFragments(argv[1], (prefix.str()).c_str())) return 1;
        }

        // write last matrices as fragments into central dir (not subdir as above), for analyzer to know index bounds
        if (!Energy.WriteLastMatrix(argv[1], dir, EnergyFragmentSuffix)) return 1;
        if (Hcorrected) Hcorrection.WriteLastMatrix(argv[1], dir, HcorrectionFragmentSuffix);
        if (!Force.WriteLastMatrix(argv[1], dir, ForceFragmentSuffix)) return 1;
        if (periode != NULL) { // also look for PAS values
                if (!Shielding.WriteLastMatrix(argv[1], dir, ShieldingFragmentSuffix)) return 1;
                if (!ShieldingPAS.WriteLastMatrix(argv[1], dir, ShieldingPASFragmentSuffix)) return 1;
        }

        // exit
        delete(periode);
        Free((void **)&dir, "main: *dir");
        cout << "done." << endl;
        return 0;
};

//============================ END ===========================