Changes in molecuilder/src/builder.cpp [1aa2a5:ef87ee]

File:

• molecuilder/src/builder.cpp (modified) (10 diffs)

molecuilder/src/builder.cpp

@@ -49 +49 @@
 
 using namespace std;
-
-#include <cstring>
 
 #include "analysis_correlation.hpp"
@@ -1412 +1410 @@
             Log() << Verbose(0) << "\t-B xx xy xz yy yz zz\tBound atoms by domain with given symmetric matrix of (xx,xy,xz,yy,yz,zz)." << endl;
             Log() << Verbose(0) << "\t-c x1 x2 x3\tCenter atoms in domain with a minimum distance to boundary of (x1,x2,x3)." << endl;
-            Log() << Verbose(0) << "\t-C <Z> <output> <bin output>\tPair Correlation analysis." << endl;
+            Log() << Verbose(0) << "\t-C\tPair Correlation analysis." << endl;
             Log() << Verbose(0) << "\t-d x1 x2 x3\tDuplicate cell along each axis by given factor." << endl;
             Log() << Verbose(0) << "\t-D <bond distance>\tDepth-First-Search Analysis of the molecule, giving cycles and tree/back edges." << endl;
             Log() << Verbose(0) << "\t-e <file>\tSets the databases path to be parsed (default: ./)." << endl;
             Log() << Verbose(0) << "\t-E <id> <Z>\tChange atom <id>'s element to <Z>, <id> begins at 0." << endl;
-            Log() << Verbose(0) << "\t-f <dist> <order>\tFragments the molecule in BOSSANOVA manner (with/out rings compressed) and stores config files in same dir as config (return code 0 - fragmented, 2 - no fragmentation necessary)." << endl;
-            Log() << Verbose(0) << "\t-F <dist_x> <dist_y> <dist_z> <epsilon> <randatom> <randmol> <DoRotate>\tFilling Box with water molecules." << endl;
+            Log() << Verbose(0) << "\t-f/F <dist> <order>\tFragments the molecule in BOSSANOVA manner (with/out rings compressed) and stores config files in same dir as config (return code 0 - fragmented, 2 - no fragmentation necessary)." << endl;
             Log() << Verbose(0) << "\t-g <file>\tParses a bond length table from the given file." << endl;
             Log() << Verbose(0) << "\t-h/-H/-?\tGive this help screen." << endl;
-            Log() << Verbose(0) << "\t-I\t Dissect current system of molecules into a set of disconnected (subgraphs of) molecules." << endl;
             Log() << Verbose(0) << "\t-L <step0> <step1> <prefix>\tStore a linear interpolation between two configurations <step0> and <step1> into single config files with prefix <prefix> and as Trajectories into the current config file." << endl;
             Log() << Verbose(0) << "\t-m <0/1>\tCalculate (0)/ Align in(1) PAS with greatest EV along z axis." << endl;
@@ -1579 +1575 @@
                 else {
                   Log() << Verbose(2) << "File found and parsed." << endl;
+                  // @TODO rather do the dissection afterwards
+//                  mol->SetNameFromFilename(argv[argptr]);
+//                  molecules->ListOfMolecules.remove(mol);
+//                  molecules->DissectMoleculeIntoConnectedSubgraphs(mol,&configuration);
+//                  delete(mol);
+//                  if (molecules->ListOfMolecules.size() != 0) {
+//                    for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
+//                      if ((*ListRunner)->ActiveFlag) {
+//                        mol = *ListRunner;
+//                        break;
+//                      }
+//                  }
                   configPresent = present;
                 }
@@ -1657 +1665 @@
               //argptr+=1;
               break;
-            case 'I':
-              Log() << Verbose(1) << "Dissecting molecular system into a set of disconnected subgraphs ... " << endl;
-              // @TODO rather do the dissection afterwards
-              molecules->DissectMoleculeIntoConnectedSubgraphs(mol,&configuration);
-              mol = NULL;
-              if (molecules->ListOfMolecules.size() != 0) {
-                for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
-                  if ((*ListRunner)->ActiveFlag) {
-                    mol = *ListRunner;
-                    break;
-                  }
-              }
-              if (mol == NULL) {
-                mol = *(molecules->ListOfMolecules.begin());
-                mol->ActiveFlag = true;
-              }
-              break;
             case 'C':
               if (ExitFlag == 0) ExitFlag = 1;
@@ -1681 +1672 @@
                 performCriticalExit();
               } else {
+                SaveFlag = false;
                 ofstream output(argv[argptr+1]);
                 ofstream binoutput(argv[argptr+2]);
@@ -1700 +1692 @@
                 counter = 0;
                 for (MoleculeList::iterator BigFinder = molecules->ListOfMolecules.begin(); BigFinder != molecules->ListOfMolecules.end(); BigFinder++) {
-                  Actives[counter++] = (*BigFinder)->ActiveFlag;
+                  Actives[counter] = (*BigFinder)->ActiveFlag;
                   (*BigFinder)->ActiveFlag = (*BigFinder == Boundary) ? false : true;
                 }
@@ -1713 +1705 @@
                 binoutput.close();
                 for (MoleculeList::iterator BigFinder = molecules->ListOfMolecules.begin(); BigFinder != molecules->ListOfMolecules.end(); BigFinder++)
-                  (*BigFinder)->ActiveFlag = Actives[counter++];
+                  (*BigFinder)->ActiveFlag = Actives[counter];
                 Free(&Actives);
                 delete(LCList);
@@ -1736 +1728 @@
             case 'F':
               if (ExitFlag == 0) ExitFlag = 1;
-              if (argptr+6 >=argc) {
+              if (argptr+5 >=argc) {
                 ExitFlag = 255;
-                eLog() << Verbose(0) << "Not enough or invalid arguments given for filling box with water: -F <dist_x> <dist_y> <dist_z> <boundary> <randatom> <randmol> <DoRotate>" << endl;
+                eLog() << Verbose(0) << "Not enough or invalid arguments given for filling box with water: -F <dist_x> <dist_y> <dist_z> <randatom> <randmol> <DoRotate>" << endl;
                 performCriticalExit();
               } else {
@@ -1746 +1738 @@
                 molecule *filler = new molecule(periode);;
                 molecule *Filling = NULL;
-//                atom *second = NULL, *third = NULL;
+                atom *second = NULL, *third = NULL;
                 first = new atom();
-                first->type = periode->FindElement(5);
-                first->x.Zero();
+                first->type = periode->FindElement(1);
+                first->x.Init(0.441, -0.143, 0.);
                 filler->AddAtom(first);
-//                first = new atom();
-//                first->type = periode->FindElement(1);
-//                first->x.Init(0.441, -0.143, 0.);
-//                filler->AddAtom(first);
-//                second = new atom();
-//                second->type = periode->FindElement(1);
-//                second->x.Init(-0.464, 1.137, 0.0);
-//                filler->AddAtom(second);
-//                third = new atom();
-//                third->type = periode->FindElement(8);
-//                third->x.Init(-0.464, 0.177, 0.);
-//                filler->AddAtom(third);
-//                filler->AddBond(first, third, 1);
-//                filler->AddBond(second, third, 1);
+                second = new atom();
+                second->type = periode->FindElement(1);
+                second->x.Init(-0.464, 1.137, 0.0);
+                filler->AddAtom(second);
+                third = new atom();
+                third->type = periode->FindElement(8);
+                third->x.Init(-0.464, 0.177, 0.);
+                filler->AddAtom(third);
+                filler->AddBond(first, third, 1);
+                filler->AddBond(second, third, 1);
                 // call routine
                 double distance[NDIM];
                 for (int i=0;i<NDIM;i++)
                   distance[i] = atof(argv[argptr+i]);
-                Filling = FillBoxWithMolecule(molecules, filler, configuration, distance, atof(argv[argptr+3]), atof(argv[argptr+4]), atof(argv[argptr+5]), atoi(argv[argptr+6]));
+                Filling = FillBoxWithMolecule(molecules, filler, configuration, distance, atof(argv[argptr+3]), atof(argv[argptr+4]), atoi(argv[argptr+5]));
                 if (Filling != NULL) {
-                  Filling->ActiveFlag = false;
                   molecules->insert(Filling);
                 }
@@ -2120 +2107 @@
                 if (volume != -1)
                   ExitFlag = 255;
-                  eLog() << Verbose(0) << "Not enough or invalid arguments given for suspension: -u <density>" << endl;
+                  eLog() << Verbose(0) << "Not enough arguments given for suspension: -u <density>" << endl;
                   performCriticalExit();
               } else {