Ignore:
Timestamp:
Feb 9, 2009, 5:24:10 PM (17 years ago)
Author:
Frederik Heber <heber@…>
Children:
451d7a
Parents:
4aef8a
git-author:
Frederik Heber <heber@…> (02/09/09 15:55:37)
git-committer:
Frederik Heber <heber@…> (02/09/09 17:24:10)
Message:

Merge branch 'ConcaveHull' of ../espack2 into ConcaveHull

Conflicts:

molecuilder/src/boundary.cpp
molecuilder/src/boundary.hpp
molecuilder/src/builder.cpp
molecuilder/src/linkedcell.cpp
molecuilder/src/linkedcell.hpp
molecuilder/src/vector.cpp
molecuilder/src/vector.hpp
util/src/NanoCreator.c

Basically, this resulted from a lot of conversions two from spaces to one tab, which is my standard indentation. The mess was caused by eclipse auto-indenting. And in espack2:ConcaveHull was the new stuff, so all from ConcaveHull was replaced in case of doubt.
Additionally, vector had ofstream << operator instead ostream << ...

File:
1 edited

Legend:

Unmodified
Added
Removed

  • molecuilder/src/joiner.cpp

    • Property mode changed from 100644 to 100755
    r4aef8a re08f45  
    22 *
    33 * Takes evaluated fragments (energy and forces) and by reading the factors files determines total energy
    4  * and each force for the whole molecule. 
    5  *   
     4 * and each force for the whole molecule.
     5 *
    66 */
    77
    88//============================ INCLUDES ===========================
    99
    10 #include "datacreator.hpp" 
    11 #include "helpers.hpp" 
    12 #include "parser.hpp" 
    13 #include "periodentafel.hpp" 
     10#include "datacreator.hpp"
     11#include "helpers.hpp"
     12#include "parser.hpp"
     13#include "periodentafel.hpp"
    1414
    1515//============================== MAIN =============================
    … …  
    1717int main(int argc, char **argv)
    1818{
    19   periodentafel *periode = NULL; // and a period table of all elements
    20   EnergyMatrix Energy;
    21   EnergyMatrix Hcorrection;
    22   ForceMatrix Force;
    23   EnergyMatrix EnergyFragments;
    24   EnergyMatrix HcorrectionFragments;
    25   ForceMatrix ForceFragments;
    26   ForceMatrix Shielding;
    27   ForceMatrix ShieldingPAS;
    28   ForceMatrix ShieldingFragments;
    29   ForceMatrix ShieldingPASFragments;
    30   KeySetsContainer KeySet; 
    31   stringstream prefix;
    32   char *dir = NULL;
    33   bool Hcorrected = true;
     19        periodentafel *periode = NULL; // and a period table of all elements
     20        EnergyMatrix Energy;
     21        EnergyMatrix Hcorrection;
     22        ForceMatrix Force;
     23        EnergyMatrix EnergyFragments;
     24        EnergyMatrix HcorrectionFragments;
     25        ForceMatrix ForceFragments;
     26        ForceMatrix Shielding;
     27        ForceMatrix ShieldingPAS;
     28        ForceMatrix ShieldingFragments;
     29        ForceMatrix ShieldingPASFragments;
     30        KeySetsContainer KeySet;
     31        stringstream prefix;
     32        char *dir = NULL;
     33        bool Hcorrected = true;
    3434
    35   cout << "Joiner" << endl;
    36   cout << "======" << endl;
    37  
    38   // Get the command line options
    39   if (argc < 3) {
    40     cout << "Usage: " << argv[0] << " <inputdir> <prefix> [elementsdb]" << endl;
    41     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;
    42     cout << "<prefix>\tprefix of energy and forces file." << endl;
    43     cout << "[elementsdb]\tpath to elements database, needed for shieldings." << endl;
    44     return 1;
    45   } else {
    46     dir = (char *) Malloc(sizeof(char)*(strlen(argv[2])+2), "main: *dir");
    47     strcpy(dir, "/");
    48     strcat(dir, argv[2]);
    49   }
    50   if (argc > 3) {
    51     periode = new periodentafel;
    52     periode->LoadPeriodentafel(argv[3]);
    53   }
    54  
    55   // Test the given directory
    56   if (!TestParams(argc, argv))
    57     return 1;
    58  
    59   // +++++++++++++++++ PARSING +++++++++++++++++++++++++++++++
    60  
    61   // ------------- Parse through all Fragment subdirs --------
    62   if (!Energy.ParseFragmentMatrix(argv[1], dir, EnergySuffix, 0,0)) return 1;
    63   Hcorrected = Hcorrection.ParseFragmentMatrix(argv[1], "", HCORRECTIONSUFFIX, 0,0);
    64   if (!Force.ParseFragmentMatrix(argv[1], dir, ForcesSuffix, 0,0)) return 1;
    65   if (periode != NULL) { // also look for PAS values
    66     if (!Shielding.ParseFragmentMatrix(argv[1], dir, ShieldingSuffix, 1, 0)) return 1;
    67     if (!ShieldingPAS.ParseFragmentMatrix(argv[1], dir, ShieldingPASSuffix, 1, 0)) return 1;
    68   }
     35        cout << "Joiner" << endl;
     36        cout << "======" << endl;
    6937
    70   // ---------- Parse the TE Factors into an array -----------------
    71   if (!Energy.ParseIndices()) return 1;
    72   if (Hcorrected) Hcorrection.ParseIndices();
    73  
    74   // ---------- Parse the Force indices into an array ---------------
    75   if (!Force.ParseIndices(argv[1])) return 1;
     38        // Get the command line options
     39        if (argc < 3) {
     40                cout << "Usage: " << argv[0] << " <inputdir> <prefix> [elementsdb]" << endl;
     41                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;
     42                cout << "<prefix>\tprefix of energy and forces file." << endl;
     43                cout << "[elementsdb]\tpath to elements database, needed for shieldings." << endl;
     44                return 1;
     45        } else {
     46                dir = (char *) Malloc(sizeof(char)*(strlen(argv[2])+2), "main: *dir");
     47                strcpy(dir, "/");
     48                strcat(dir, argv[2]);
     49        }
     50        if (argc > 3) {
     51                periode = new periodentafel;
     52                periode->LoadPeriodentafel(argv[3]);
     53        }
    7654
    77   // ---------- Parse the shielding indices into an array ---------------
    78   if (periode != NULL) { // also look for PAS values
    79     if(!Shielding.ParseIndices(argv[1])) return 1;
    80     if(!ShieldingPAS.ParseIndices(argv[1])) return 1;
    81   }
     55        // Test the given directory
     56        if (!TestParams(argc, argv))
     57                return 1;
    8258
    83   // ---------- Parse the KeySets into an array ---------------
    84   if (!KeySet.ParseKeySets(argv[1], Force.RowCounter, Force.MatrixCounter)) return 1;
     59        // +++++++++++++++++ PARSING +++++++++++++++++++++++++++++++
    8560
    86   if (!KeySet.ParseManyBodyTerms()) return 1;
    87   if (!EnergyFragments.AllocateMatrix(Energy.Header, Energy.MatrixCounter, Energy.RowCounter, Energy.ColumnCounter)) return 1;
    88   if (Hcorrected)  HcorrectionFragments.AllocateMatrix(Hcorrection.Header, Hcorrection.MatrixCounter, Hcorrection.RowCounter, Hcorrection.ColumnCounter);
    89   if (!ForceFragments.AllocateMatrix(Force.Header, Force.MatrixCounter, Force.RowCounter, Force.ColumnCounter)) return 1;
    90   if (periode != NULL) { // also look for PAS values
    91     if (!ShieldingFragments.AllocateMatrix(Shielding.Header, Shielding.MatrixCounter, Shielding.RowCounter, Shielding.ColumnCounter)) return 1;
    92     if (!ShieldingPASFragments.AllocateMatrix(ShieldingPAS.Header, ShieldingPAS.MatrixCounter, ShieldingPAS.RowCounter, ShieldingPAS.ColumnCounter)) return 1;
    93   }
    94  
    95   // ----------- Resetting last matrices (where full QM values are stored right now)
    96   if(!Energy.SetLastMatrix(0., 0)) return 1;
    97   if(!Force.SetLastMatrix(0., 2)) return 1;
    98   if (periode != NULL) { // also look for PAS values
    99     if(!Shielding.SetLastMatrix(0., 2)) return 1;
    100     if(!ShieldingPAS.SetLastMatrix(0., 2)) return 1;
    101   }
     61        // ------------- Parse through all Fragment subdirs --------
     62        if (!Energy.ParseFragmentMatrix(argv[1], dir, EnergySuffix, 0,0)) return 1;
     63        Hcorrected = Hcorrection.ParseFragmentMatrix(argv[1], "", HCORRECTIONSUFFIX, 0,0);
     64        if (!Force.ParseFragmentMatrix(argv[1], dir, ForcesSuffix, 0,0)) return 1;
     65        if (periode != NULL) { // also look for PAS values
     66                if (!Shielding.ParseFragmentMatrix(argv[1], dir, ShieldingSuffix, 1, 0)) return 1;
     67                if (!ShieldingPAS.ParseFragmentMatrix(argv[1], dir, ShieldingPASSuffix, 1, 0)) return 1;
     68        }
    10269
    103   // +++++++++++++++++ SUMMING +++++++++++++++++++++++++++++++
     70        // ---------- Parse the TE Factors into an array -----------------
     71        if (!Energy.ParseIndices()) return 1;
     72        if (Hcorrected) Hcorrection.ParseIndices();
    10473
    105   // --------- sum up and write for each order----------------
    106   for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
    107     // --------- sum up energy --------------------
    108     cout << "Summing energy of order " << BondOrder+1 << " ..." << endl;
    109     if (!EnergyFragments.SumSubManyBodyTerms(Energy, KeySet, BondOrder)) return 1;
    110     if (Hcorrected) {
    111       HcorrectionFragments.SumSubManyBodyTerms(Hcorrection, KeySet, BondOrder);
    112       if (!Energy.SumSubEnergy(EnergyFragments, &HcorrectionFragments, KeySet, BondOrder, 1.)) return 1;
    113       if (Hcorrected) Hcorrection.SumSubEnergy(HcorrectionFragments, NULL, KeySet, BondOrder, 1.);
    114     } else
    115       if (!Energy.SumSubEnergy(EnergyFragments, NULL, KeySet, BondOrder, 1.)) return 1;
    116     // --------- sum up Forces --------------------
    117     cout << "Summing forces of order " << BondOrder+1 << " ..." << endl;
    118     if (!ForceFragments.SumSubManyBodyTerms(Force, KeySet, BondOrder)) return 1;
    119     if (!Force.SumSubForces(ForceFragments, KeySet, BondOrder, 1.)) return 1;
    120     if (periode != NULL) { // also look for PAS values
    121       cout << "Summing shieldings of order " << BondOrder+1 << " ..." << endl;
    122       if (!ShieldingFragments.SumSubManyBodyTerms(Shielding, KeySet, BondOrder)) return 1;
    123       if (!Shielding.SumSubForces(ShieldingFragments, KeySet, BondOrder, 1.)) return 1;
    124       if (!ShieldingPASFragments.SumSubManyBodyTerms(ShieldingPAS, KeySet, BondOrder)) return 1;
    125       if (!ShieldingPAS.SumSubForces(ShieldingPASFragments, KeySet, BondOrder, 1.)) return 1;
    126     }
     74        // ---------- Parse the Force indices into an array ---------------
     75        if (!Force.ParseIndices(argv[1])) return 1;
    12776
    128     // --------- write the energy and forces file --------------------
    129     prefix.str(" ");
    130     prefix << dir << OrderSuffix << (BondOrder+1);
    131     cout << "Writing files " << argv[1] << prefix.str() << ". ..." << endl;
    132     // energy
    133     if (!Energy.WriteLastMatrix(argv[1], (prefix.str()).c_str(), EnergySuffix)) return 1;
    134     // forces
    135     if (!Force.WriteLastMatrix(argv[1], (prefix.str()).c_str(), ForcesSuffix)) return 1;
    136     // shieldings
    137     if (periode != NULL) { // also look for PAS values
    138       if (!Shielding.WriteLastMatrix(argv[1], (prefix.str()).c_str(), ShieldingSuffix)) return 1;
    139       if (!ShieldingPAS.WriteLastMatrix(argv[1], (prefix.str()).c_str(), ShieldingPASSuffix)) return 1;
    140     }
    141   }
    142   // fragments
    143   prefix.str(" ");
    144   prefix << dir << EnergyFragmentSuffix;
    145   if (!EnergyFragments.WriteTotalFragments(argv[1], (prefix.str()).c_str())) return 1;
    146   if (Hcorrected) {
    147     prefix.str(" ");
    148     prefix << dir << HcorrectionFragmentSuffix;
    149     if (!HcorrectionFragments.WriteTotalFragments(argv[1], (prefix.str()).c_str())) return 1;
    150   }
    151   prefix.str(" ");
    152   prefix << dir << ForceFragmentSuffix;
    153   if (!ForceFragments.WriteTotalFragments(argv[1], (prefix.str()).c_str())) return 1;
    154   if (!CreateDataFragment(EnergyFragments, KeySet, argv[1], FRAGMENTPREFIX ENERGYPERFRAGMENT, "fragment energy versus the Fragment No", "today", CreateEnergy)) return 1;
    155   if (periode != NULL) { // also look for PAS values
    156     prefix.str(" ");
    157     prefix << dir << ShieldingFragmentSuffix;
    158     if (!ShieldingFragments.WriteTotalFragments(argv[1], (prefix.str()).c_str())) return 1;
    159     prefix.str(" ");
    160     prefix << dir << ShieldingPASFragmentSuffix;
    161     if (!ShieldingPASFragments.WriteTotalFragments(argv[1], (prefix.str()).c_str())) return 1;
    162   }
     77        // ---------- Parse the shielding indices into an array ---------------
     78        if (periode != NULL) { // also look for PAS values
     79                if(!Shielding.ParseIndices(argv[1])) return 1;
     80                if(!ShieldingPAS.ParseIndices(argv[1])) return 1;
     81        }
    16382
    164   // write last matrices as fragments into central dir (not subdir as above), for analyzer to know index bounds
    165   if (!Energy.WriteLastMatrix(argv[1], dir, EnergyFragmentSuffix)) return 1;
    166   if (Hcorrected) Hcorrection.WriteLastMatrix(argv[1], dir, HcorrectionFragmentSuffix);
    167   if (!Force.WriteLastMatrix(argv[1], dir, ForceFragmentSuffix)) return 1;
    168   if (periode != NULL) { // also look for PAS values
    169     if (!Shielding.WriteLastMatrix(argv[1], dir, ShieldingFragmentSuffix)) return 1;
    170     if (!ShieldingPAS.WriteLastMatrix(argv[1], dir, ShieldingPASFragmentSuffix)) return 1;
    171   }
     83        // ---------- Parse the KeySets into an array ---------------
     84        if (!KeySet.ParseKeySets(argv[1], Force.RowCounter, Force.MatrixCounter)) return 1;
    17285
    173   // exit 
    174   delete(periode);
    175   Free((void **)&dir, "main: *dir");
    176   cout << "done." << endl;
    177   return 0;
     86        if (!KeySet.ParseManyBodyTerms()) return 1;
     87        if (!EnergyFragments.AllocateMatrix(Energy.Header, Energy.MatrixCounter, Energy.RowCounter, Energy.ColumnCounter)) return 1;
     88        if (Hcorrected) HcorrectionFragments.AllocateMatrix(Hcorrection.Header, Hcorrection.MatrixCounter, Hcorrection.RowCounter, Hcorrection.ColumnCounter);
     89        if (!ForceFragments.AllocateMatrix(Force.Header, Force.MatrixCounter, Force.RowCounter, Force.ColumnCounter)) return 1;
     90        if (periode != NULL) { // also look for PAS values
     91                if (!ShieldingFragments.AllocateMatrix(Shielding.Header, Shielding.MatrixCounter, Shielding.RowCounter, Shielding.ColumnCounter)) return 1;
     92                if (!ShieldingPASFragments.AllocateMatrix(ShieldingPAS.Header, ShieldingPAS.MatrixCounter, ShieldingPAS.RowCounter, ShieldingPAS.ColumnCounter)) return 1;
     93        }
     94
     95        // ----------- Resetting last matrices (where full QM values are stored right now)
     96        if(!Energy.SetLastMatrix(0., 0)) return 1;
     97        if(!Force.SetLastMatrix(0., 2)) return 1;
     98        if (periode != NULL) { // also look for PAS values
     99                if(!Shielding.SetLastMatrix(0., 2)) return 1;
     100                if(!ShieldingPAS.SetLastMatrix(0., 2)) return 1;
     101        }
     102
     103        // +++++++++++++++++ SUMMING +++++++++++++++++++++++++++++++
     104
     105        // --------- sum up and write for each order----------------
     106        for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
     107                // --------- sum up energy --------------------
     108                cout << "Summing energy of order " << BondOrder+1 << " ..." << endl;
     109                if (!EnergyFragments.SumSubManyBodyTerms(Energy, KeySet, BondOrder)) return 1;
     110                if (Hcorrected) {
     111                        HcorrectionFragments.SumSubManyBodyTerms(Hcorrection, KeySet, BondOrder);
     112                        if (!Energy.SumSubEnergy(EnergyFragments, &HcorrectionFragments, KeySet, BondOrder, 1.)) return 1;
     113                        if (Hcorrected) Hcorrection.SumSubEnergy(HcorrectionFragments, NULL, KeySet, BondOrder, 1.);
     114                } else
     115                        if (!Energy.SumSubEnergy(EnergyFragments, NULL, KeySet, BondOrder, 1.)) return 1;
     116                // --------- sum up Forces --------------------
     117                cout << "Summing forces of order " << BondOrder+1 << " ..." << endl;
     118                if (!ForceFragments.SumSubManyBodyTerms(Force, KeySet, BondOrder)) return 1;
     119                if (!Force.SumSubForces(ForceFragments, KeySet, BondOrder, 1.)) return 1;
     120                if (periode != NULL) { // also look for PAS values
     121                        cout << "Summing shieldings of order " << BondOrder+1 << " ..." << endl;
     122                        if (!ShieldingFragments.SumSubManyBodyTerms(Shielding, KeySet, BondOrder)) return 1;
     123                        if (!Shielding.SumSubForces(ShieldingFragments, KeySet, BondOrder, 1.)) return 1;
     124                        if (!ShieldingPASFragments.SumSubManyBodyTerms(ShieldingPAS, KeySet, BondOrder)) return 1;
     125                        if (!ShieldingPAS.SumSubForces(ShieldingPASFragments, KeySet, BondOrder, 1.)) return 1;
     126                }
     127
     128                // --------- write the energy and forces file --------------------
     129                prefix.str(" ");
     130                prefix << dir << OrderSuffix << (BondOrder+1);
     131                cout << "Writing files " << argv[1] << prefix.str() << ". ..." << endl;
     132                // energy
     133                if (!Energy.WriteLastMatrix(argv[1], (prefix.str()).c_str(), EnergySuffix)) return 1;
     134                // forces
     135                if (!Force.WriteLastMatrix(argv[1], (prefix.str()).c_str(), ForcesSuffix)) return 1;
     136                // shieldings
     137                if (periode != NULL) { // also look for PAS values
     138                        if (!Shielding.WriteLastMatrix(argv[1], (prefix.str()).c_str(), ShieldingSuffix)) return 1;
     139                        if (!ShieldingPAS.WriteLastMatrix(argv[1], (prefix.str()).c_str(), ShieldingPASSuffix)) return 1;
     140                }
     141        }
     142        // fragments
     143        prefix.str(" ");
     144        prefix << dir << EnergyFragmentSuffix;
     145        if (!EnergyFragments.WriteTotalFragments(argv[1], (prefix.str()).c_str())) return 1;
     146        if (Hcorrected) {
     147                prefix.str(" ");
     148                prefix << dir << HcorrectionFragmentSuffix;
     149                if (!HcorrectionFragments.WriteTotalFragments(argv[1], (prefix.str()).c_str())) return 1;
     150        }
     151        prefix.str(" ");
     152        prefix << dir << ForceFragmentSuffix;
     153        if (!ForceFragments.WriteTotalFragments(argv[1], (prefix.str()).c_str())) return 1;
     154        if (!CreateDataFragment(EnergyFragments, KeySet, argv[1], FRAGMENTPREFIX ENERGYPERFRAGMENT, "fragment energy versus the Fragment No", "today", CreateEnergy)) return 1;
     155        if (periode != NULL) { // also look for PAS values
     156                prefix.str(" ");
     157                prefix << dir << ShieldingFragmentSuffix;
     158                if (!ShieldingFragments.WriteTotalFragments(argv[1], (prefix.str()).c_str())) return 1;
     159                prefix.str(" ");
     160                prefix << dir << ShieldingPASFragmentSuffix;
     161                if (!ShieldingPASFragments.WriteTotalFragments(argv[1], (prefix.str()).c_str())) return 1;
     162        }
     163
     164        // write last matrices as fragments into central dir (not subdir as above), for analyzer to know index bounds
     165        if (!Energy.WriteLastMatrix(argv[1], dir, EnergyFragmentSuffix)) return 1;
     166        if (Hcorrected) Hcorrection.WriteLastMatrix(argv[1], dir, HcorrectionFragmentSuffix);
     167        if (!Force.WriteLastMatrix(argv[1], dir, ForceFragmentSuffix)) return 1;
     168        if (periode != NULL) { // also look for PAS values
     169                if (!Shielding.WriteLastMatrix(argv[1], dir, ShieldingFragmentSuffix)) return 1;
     170                if (!ShieldingPAS.WriteLastMatrix(argv[1], dir, ShieldingPASFragmentSuffix)) return 1;
     171        }
     172
     173        // exit
     174        delete(periode);
     175        Free((void **)&dir, "main: *dir");
     176        cout << "done." << endl;
     177        return 0;
    178178};
    179179
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