Changeset 375dcf for molecuilder/src/joiner.cpp

Timestamp:

Jun 27, 2008, 9:14:58 PM (17 years ago)

Author:

Frederik Heber <heber@…>

Children:

74baec

Parents:

d7b1bf

git-author:

Frederik Heber <heber@…> (06/27/08 21:12:52)

git-committer:

Frederik Heber <heber@…> (06/27/08 21:14:58)

Message:

introduced shieldings to analyzer and joiner

both now handle pcp.sigma_all...csv files just as pcp.forces.all. Therefore the data format in pcp/perturbed.c was adapted a bit, as we need a header.
periodentafel.hpp got periodentafel and element class from molecules.hpp

File:

• molecuilder/src/joiner.cpp (modified) (8 diffs)

molecuilder/src/joiner.cpp

@@ -11 +11 @@
 #include "helpers.hpp" 
 #include "parser.hpp" 
+#include "periodentafel.hpp" 
 
 //============================== MAIN =============================
@@ -16 +17 @@
 int main(int argc, char **argv)
 {
+  periodentafel *periode = NULL; // and a period table of all elements
   EnergyMatrix Energy;
   ForceMatrix Force;
   EnergyMatrix EnergyFragments;
   ForceMatrix ForceFragments;
+  ForceMatrix Shielding;
+  ForceMatrix ShieldingPAS;
+  ForceMatrix ShieldingFragments;
+  ForceMatrix ShieldingPASFragments;
   KeySetsContainer KeySet;  
   stringstream prefix;
@@ -28 +34 @@
   // Get the command line options
   if (argc < 3) {
-    cout << "Usage: " << argv[0] << " <inputdir> <prefix>" << endl;
+    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;
+  }
+  if (argc > 3) {
+    periode = new periodentafel;
+    periode->LoadPeriodentafel(argv[3]);
   }
   
@@ -42 +53 @@
   // ------------- Parse through all Fragment subdirs --------
   if (!Energy.ParseMatrix(argv[1], argv[2], EnergySuffix, 0,0)) return 1;
-  //if (!ParseSubEnergies(argv[1], argv[2], EnergySuffix, data.EnergyHeader, data.Energies, data.EnergyIndices, data.LevelCounter, data.ColumnCounter, data.FragmentCounter)) return 1;
   if (!Force.ParseMatrix(argv[1], argv[2], ForcesSuffix, 0,0)) return 1;
-  //if (!ParseSubForces(argv[1], argv[2], ForcesSuffix, data.ForcesHeader, data.Forces, data.AtomCounter, data.Column2Counter, data.FragmentCounter)) return 1;
+  if (periode != NULL) { // also look for PAS values
+    if (!Shielding.ParseMatrix(argv[1], argv[2], ShieldingSuffix, 1, 0)) return 1;
+    if (!ShieldingPAS.ParseMatrix(argv[1], argv[2], ShieldingPASSuffix, 1, 0)) return 1;
+  }
 
   // ---------- Parse the TE Factors into an array -----------------
@@ -51 +64 @@
   // ---------- Parse the Force indices into an array ---------------
   if (!Force.ParseIndices(argv[1])) return 1;
-  //if (!ParseForceIndices(argv[1], data.ForcesIndices, data.AtomCounter, data.FragmentCounter)) 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 (!ParseKeySets(argv[1], data.KeySets, data.AtomCounter, data.FragmentCounter)) return 1;
 
   if (!KeySet.ParseManyBodyTerms()) return 1;
-  //if (!ParseManyBodyTerms(data.Order, data.OrderSet, data.FragmentsPerOrder, data.KeySets, data.AtomCounter, data.FragmentCounter)) return 1;
   if (!EnergyFragments.AllocateMatrix(Energy.Header, Energy.MatrixCounter, Energy.RowCounter, Energy.ColumnCounter)) return 1;
-  //if (!ParseSubEnergies(argv[1], argv[2], EnergyFragmentSuffix, data.EnergyHeader, data.EnergyFragments, data.EnergyFragmentIndices, data.LevelFragmentCounter, data.ColumnFragmentCounter, data.FragmentCounter)) return 1;
   if (!ForceFragments.AllocateMatrix(Force.Header, Force.MatrixCounter, Force.RowCounter, Force.ColumnCounter)) return 1;
-  //if (!ParseSubForces(argv[1], argv[2], ForceFragmentSuffix, data.ForcesHeader, data.ForceFragments, data.AtomCounter, data.Column2Counter, data.FragmentCounter)) 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., 0)) return 1;
+    if(!ShieldingPAS.SetLastMatrix(0., 2)) return 1;
+  }
+
   // +++++++++++++++++ SUMMING +++++++++++++++++++++++++++++++
 
@@ -80 +102 @@
     if (!ForceFragments.SumSubManyBodyTerms(Force, KeySet, BondOrder)) return 1;
     if (!Force.SumSubForces(ForceFragments, KeySet, BondOrder)) 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)) return 1;
+      if (!ShieldingPASFragments.SumSubManyBodyTerms(ShieldingPAS, KeySet, BondOrder)) return 1;
+      if (!ShieldingPAS.SumSubForces(ShieldingPASFragments, KeySet, BondOrder)) return 1;
+    }
 
     // --------- write the energy and forces file --------------------
@@ -89 +118 @@
     // 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
@@ -98 +132 @@
   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 << argv[2] << ShieldingFragmentSuffix;
+    if (!ShieldingFragments.WriteTotalFragments(argv[1], (prefix.str()).c_str())) return 1;
+    prefix.str(" ");
+    prefix << argv[2] << 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], argv[2], EnergyFragmentSuffix)) return 1;
   if (!Force.WriteLastMatrix(argv[1], argv[2], ForceFragmentSuffix)) return 1;
+  if (periode != NULL) { // also look for PAS values
+    if (!Shielding.WriteLastMatrix(argv[1], argv[2], ShieldingFragmentSuffix)) return 1;
+    if (!ShieldingPAS.WriteLastMatrix(argv[1], argv[2], ShieldingPASFragmentSuffix)) return 1;
+  }
 
   // exit  
+  delete(periode);
   cout << "done." << endl;
   return 0;