Changes in src/config.cpp [49e1ae:46d958]

File:

• src/config.cpp (modified) (5 diffs)

src/config.cpp

@@ -8 +8 @@
 #include <cstring>
 
+#include "World.hpp"
 #include "atom.hpp"
 #include "bond.hpp"
@@ -732 +733 @@
             sprintf(keyword,"%s_%i",name, j+1);
             if (repetition == 0) {
-              neues = new atom();
+              neues = World::get()->createAtom();
               AtomList[i][j] = neues;
               LinearList[ FileBuffer->LineMapping[FileBuffer->CurrentLine] ] = neues;
@@ -811 +812 @@
           sprintf(keyword,"%s_%i",name, j+1);
           if (repetition == 0) {
-            neues = new atom();
+            neues = World::get()->createAtom();
             AtomList[i][j] = neues;
             LinearList[ FileBuffer->LineMapping[FileBuffer->CurrentLine] ] = neues;
@@ -1287 +1288 @@
         }
         istringstream input2(zeile);
-        atom *neues = new atom();
+        atom *neues = World::get()->createAtom();
         input2 >> neues->x.x[0]; // x
         input2 >> neues->x.x[1]; // y
@@ -1777 +1778 @@
 };
 
+
+/** Tries given filename or standard on saving the config file.
+ * \param *ConfigFileName name of file
+ * \param *periode pointer to periodentafel structure with all the elements
+ * \param *molecules list of molecules structure with all the atoms and coordinates
+ */
+void config::SaveAll(char *ConfigFileName, periodentafel *periode, MoleculeListClass *molecules)
+{
+  char filename[MAXSTRINGSIZE];
+  ofstream output;
+  molecule *mol = new molecule(periode);
+  mol->SetNameFromFilename(ConfigFileName);
+
+  if (!strcmp(configpath, GetDefaultPath())) {
+    eLog() << Verbose(2) << "config is found under different path then stated in config file::defaultpath!" << endl;
+  }
+
+
+  // first save as PDB data
+  if (ConfigFileName != NULL)
+    strcpy(filename, ConfigFileName);
+  if (output == NULL)
+    strcpy(filename,"main_pcp_linux");
+  Log() << Verbose(0) << "Saving as pdb input ";
+  if (SavePDB(filename, molecules))
+    Log() << Verbose(0) << "done." << endl;
+  else
+    Log() << Verbose(0) << "failed." << endl;
+
+  // then save as tremolo data file
+  if (ConfigFileName != NULL)
+    strcpy(filename, ConfigFileName);
+  if (output == NULL)
+    strcpy(filename,"main_pcp_linux");
+  Log() << Verbose(0) << "Saving as tremolo data input ";
+  if (SaveTREMOLO(filename, molecules))
+    Log() << Verbose(0) << "done." << endl;
+  else
+    Log() << Verbose(0) << "failed." << endl;
+
+  // translate each to its center and merge all molecules in MoleculeListClass into this molecule
+  int N = molecules->ListOfMolecules.size();
+  int *src = new int[N];
+  N=0;
+  for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++) {
+    src[N++] = (*ListRunner)->IndexNr;
+    (*ListRunner)->Translate(&(*ListRunner)->Center);
+  }
+  molecules->SimpleMultiAdd(mol, src, N);
+  delete[](src);
+
+  // ... and translate back
+  for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++) {
+    (*ListRunner)->Center.Scale(-1.);
+    (*ListRunner)->Translate(&(*ListRunner)->Center);
+    (*ListRunner)->Center.Scale(-1.);
+  }
+
+  Log() << Verbose(0) << "Storing configuration ... " << endl;
+  // get correct valence orbitals
+  mol->CalculateOrbitals(*this);
+  InitMaxMinStopStep = MaxMinStopStep = MaxPsiDouble;
+  if (ConfigFileName != NULL) { // test the file name
+    strcpy(filename, ConfigFileName);
+    output.open(filename, ios::trunc);
+  } else if (strlen(configname) != 0) {
+    strcpy(filename, configname);
+    output.open(configname, ios::trunc);
+    } else {
+      strcpy(filename, DEFAULTCONFIG);
+      output.open(DEFAULTCONFIG, ios::trunc);
+    }
+  output.close();
+  output.clear();
+  Log() << Verbose(0) << "Saving of config file ";
+  if (Save(filename, periode, mol))
+    Log() << Verbose(0) << "successful." << endl;
+  else
+    Log() << Verbose(0) << "failed." << endl;
+
+  // and save to xyz file
+  if (ConfigFileName != NULL) {
+    strcpy(filename, ConfigFileName);
+    strcat(filename, ".xyz");
+    output.open(filename, ios::trunc);
+  }
+  if (output == NULL) {
+    strcpy(filename,"main_pcp_linux");
+    strcat(filename, ".xyz");
+    output.open(filename, ios::trunc);
+  }
+  Log() << Verbose(0) << "Saving of XYZ file ";
+  if (mol->MDSteps <= 1) {
+    if (mol->OutputXYZ(&output))
+      Log() << Verbose(0) << "successful." << endl;
+    else
+      Log() << Verbose(0) << "failed." << endl;
+  } else {
+    if (mol->OutputTrajectoriesXYZ(&output))
+      Log() << Verbose(0) << "successful." << endl;
+    else
+      Log() << Verbose(0) << "failed." << endl;
+  }
+  output.close();
+  output.clear();
+
+  // and save as MPQC configuration
+  if (ConfigFileName != NULL)
+    strcpy(filename, ConfigFileName);
+  if (output == NULL)
+    strcpy(filename,"main_pcp_linux");
+  Log() << Verbose(0) << "Saving as mpqc input ";
+  if (SaveMPQC(filename, mol))
+    Log() << Verbose(0) << "done." << endl;
+  else
+    Log() << Verbose(0) << "failed." << endl;
+
+  if (!strcmp(configpath, GetDefaultPath())) {
+    eLog() << Verbose(2) << "config is found under different path then stated in config file::defaultpath!" << endl;
+  }
+
+  delete(mol);
+};
+
 /** Reads parameter from a parsed file.
  * The file is either parsed for a certain keyword or if null is given for