Changes in src/builder.cpp [3930eb:481601]

File:

• src/builder.cpp (modified) (7 diffs)

src/builder.cpp

@@ -49 +49 @@
 
 using namespace std;
+
+#include <cstring>
 
 #include "analysis_correlation.hpp"
@@ -1415 +1417 @@
             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/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\tFilling Box with water molecules." << 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-g <file>\tParses a bond length table from the given file." << endl;
             Log() << Verbose(0) << "\t-h/-H/-?\tGive this help screen." << endl;
@@ -1549 +1551 @@
      if (configuration.BG == NULL) {
        configuration.BG = new BondGraph(configuration.GetIsAngstroem());
-       if ((BondGraphFileName.empty()) && (configuration.BG->LoadBondLengthTable(BondGraphFileName))) {
+       if ((!BondGraphFileName.empty()) && (configuration.BG->LoadBondLengthTable(BondGraphFileName))) {
          Log() << Verbose(0) << "Bond length table loaded successfully." << endl;
        } else {
@@ -1658 +1660 @@
               Log() << Verbose(1) << "Dissecting molecular system into a set of disconnected subgraphs ... " << endl;
               // @TODO rather do the dissection afterwards
-              molecules->DissectMoleculeIntoConnectedSubgraphs(mol,&configuration);
+              molecules->DissectMoleculeIntoConnectedSubgraphs(periode, &configuration);
               mol = NULL;
               if (molecules->ListOfMolecules.size() != 0) {
@@ -1706 +1708 @@
                 int ranges[NDIM] = {1,1,1};
                 CorrelationToSurfaceMap *surfacemap = PeriodicCorrelationToSurface( molecules, elemental, TesselStruct, LCList, ranges );
+                OutputCorrelationToSurface(&output, surfacemap);
                 BinPairMap *binmap = BinData( surfacemap, 0.5, 0., 0. );
                 OutputCorrelation ( &binoutput, binmap );
@@ -1736 +1739 @@
               if (argptr+6 >=argc) {
                 ExitFlag = 255;
-                eLog() << Verbose(0) << "Not enough or invalid arguments given for filling box with water: -F <dist_x> <dist_y> <dist_z> <epsilon> <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> <boundary> <randatom> <randmol> <DoRotate>" << endl;
                 performCriticalExit();
               } else {
@@ -1742 +1745 @@
                 Log() << Verbose(1) << "Filling Box with water molecules." << endl;
                 // construct water molecule
-                molecule *filler = new molecule(periode);;
+                molecule *filler = new molecule(periode);
                 molecule *Filling = NULL;
                 atom *second = NULL, *third = NULL;
+//                first = new atom();
+//                first->type = periode->FindElement(5);
+//                first->x.Zero();
+//                filler->AddAtom(first);
                 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];