Changeset b8d1aeb for src/config.cpp

Timestamp:

Feb 2, 2010, 11:38:06 AM (16 years ago)

Author:

Tillmann Crueger <crueger@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, Candidate_v1.7.0, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

7ba324

Parents:

9fe36b (diff), 2ededc2 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'MenuRefactoring' into QT4Refactoring

Conflicts:

molecuilder/src/Makefile.am
molecuilder/src/builder.cpp
molecuilder/src/unittests/Makefile.am

File:

• src/config.cpp (modified) (11 diffs)

src/config.cpp

@@ -6 +6 @@
 
 #include <stdio.h>
+#include <cstring>
 
 #include "atom.hpp"
@@ -27 +28 @@
     char number1[8];
     char number2[8];
-    char *dummy1, *dummy2;
+    const char *dummy1, *dummy2;
     //Log() << Verbose(0) << s1 << "  " << s2 << endl;
     dummy1 = strchr(s1, '_')+sizeof(char)*5;  // go just after "Ion_Type"
@@ -140 +141 @@
 void ConfigFileBuffer::MapIonTypesInBuffer(const int NoAtoms)
 {
-  map<const char *, int, IonTypeCompare> LineList;
+  map<const char *, int, IonTypeCompare> IonTypeLineMap;
   if (LineMapping == NULL) {
     eLog() << Verbose(0) << "map pointer is NULL: " << LineMapping << endl;
@@ -149 +150 @@
   // put all into hashed map
   for (int i=0; i<NoAtoms; ++i) {
-    LineList.insert(pair<const char *, int> (buffer[CurrentLine+i], CurrentLine+i));
+    IonTypeLineMap.insert(pair<const char *, int> (buffer[CurrentLine+i], CurrentLine+i));
   }
 
   // fill map
   int nr=0;
-  for (map<const char *, int, IonTypeCompare>::iterator runner = LineList.begin(); runner != LineList.end(); ++runner) {
+  for (map<const char *, int, IonTypeCompare>::iterator runner = IonTypeLineMap.begin(); runner != IonTypeLineMap.end(); ++runner) {
     if (CurrentLine+nr < NoLines)
       LineMapping[CurrentLine+(nr++)] = runner->second;
@@ -1056 +1057 @@
 
   // 2. parse the bond graph file if given
-  BG = new BondGraph(IsAngstroem);
-  if (BG->LoadBondLengthTable(BondGraphFileName)) {
-    Log() << Verbose(0) << "Bond length table loaded successfully." << endl;
-  } else {
-    eLog() << Verbose(1) << "Bond length table loading failed." << endl;
+  if (BG == NULL) {
+    BG = new BondGraph(IsAngstroem);
+    if (BG->LoadBondLengthTable(BondGraphFileName)) {
+      Log() << Verbose(0) << "Bond length table loaded successfully." << endl;
+    } else {
+      eLog() << Verbose(1) << "Bond length table loading failed." << endl;
+    }
   }
 
   // 3. parse the molecule in
   LoadMolecule(mol, FileBuffer, periode, FastParsing);
+  mol->SetNameFromFilename(filename);
   mol->ActiveFlag = true;
+  MolList->insert(mol);
 
   // 4. dissect the molecule into connected subgraphs
-  MolList->DissectMoleculeIntoConnectedSubgraphs(mol,this);
-
-  delete(mol);
+  // don't do this here ...
+  //MolList->DissectMoleculeIntoConnectedSubgraphs(mol,this);
+  //delete(mol);
+
   delete(FileBuffer);
 };
@@ -1782 +1788 @@
   ofstream output;
   molecule *mol = new molecule(periode);
+  mol->SetNameFromFilename(ConfigFileName);
 
   if (!strcmp(configpath, GetDefaultPath())) {
@@ -1791 +1798 @@
   if (ConfigFileName != NULL)
     strcpy(filename, ConfigFileName);
-  else
+  if (output == NULL)
     strcpy(filename,"main_pcp_linux");
   Log() << Verbose(0) << "Saving as pdb input ";
@@ -1802 +1809 @@
   if (ConfigFileName != NULL)
     strcpy(filename, ConfigFileName);
-  else
+  if (output == NULL)
     strcpy(filename,"main_pcp_linux");
   Log() << Verbose(0) << "Saving as tremolo data input ";
@@ -1856 +1863 @@
     output.open(filename, ios::trunc);
   }
-  else {
+  if (output == NULL) {
     strcpy(filename,"main_pcp_linux");
     strcat(filename, ".xyz");
@@ -1879 +1886 @@
   if (ConfigFileName != NULL)
     strcpy(filename, ConfigFileName);
-  else
+  if (output == NULL)
     strcpy(filename,"main_pcp_linux");
   Log() << Verbose(0) << "Saving as mpqc input ";
@@ -2241 +2248 @@
               }
               line++;
-            } while (dummy1 != NULL && (dummy1[0] == '#') || (dummy1[0] == '\n'));
+            } while ((dummy1 != NULL) && ((dummy1[0] == '#') || (dummy1[0] == '\n')));
             dummy = dummy1;
           } else { // simple int, strings or doubles start in the same line