Changeset 235bed

Timestamp:

Jan 5, 2010, 9:23:25 AM (15 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, 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:

820a42

Parents:

6b932c7

Message:

Moved saveConfig method from oldmenu to a method inside config class

Location:

src

Files:

• builder.cpp (modified) (3 diffs)
• config.cpp (modified) (1 diff)
• config.hpp (modified) (1 diff)
• menu.cpp (modified) (2 diffs)
• menu.hpp (modified) (1 diff)

src/builder.cpp

@@ -78 +78 @@
  */
 static int ParseCommandLineOptions(int argc, char **argv, MoleculeListClass *&molecules, periodentafel *&periode,\
-                                   config& configuration, char *&ConfigFileName, oldmenu *main_menu)
+                                   config& configuration, char *&ConfigFileName)
 {
   Vector x,y,z,n;  // coordinates for absolute point in cell volume
@@ -879 +879 @@
     } while (argptr < argc);
     if (SaveFlag)
-      main_menu->SaveConfig(ConfigFileName, &configuration, periode, molecules);
+      configuration.SaveAll(ConfigFileName, periode, molecules);
   } else {  // no arguments, hence scan the elements db
     if (periode->LoadPeriodentafel(configuration.databasepath))
@@ -907 +907 @@
     main_menu = new oldmenu;
     setVerbosity(0);
-    /* main menu is needed to call actions inside the menu */
     /* structure of ParseCommandLineOptions will be refactored later */
-    j = ParseCommandLineOptions(argc, argv, molecules, periode, *configuration, ConfigFileName,main_menu);
+    j = ParseCommandLineOptions(argc, argv, molecules, periode, *configuration, ConfigFileName);
     switch (j){
         case 255:

src/config.cpp

@@ -1771 +1771 @@
 };
 
+
+/** 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);
+
+  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);
+  else
+    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);
+  else
+    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);
+  }
+  else {
+    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);
+  else
+    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

src/config.hpp

@@ -146 +146 @@
   bool SaveTREMOLO(const char * const filename, const MoleculeListClass * const MolList) const;
 
+  void SaveAll(char *ConfigFileName, periodentafel *periode, MoleculeListClass *molecules);
+
   void Edit();
   bool GetIsAngstroem() const;

src/menu.cpp

@@ -1142 +1142 @@
   new SeperatorItem(main_menu);
 
-  Action *saveConfigAction = new MethodAction(boost::bind(&oldmenu::SaveConfig,this,ConfigFileName, configuration, periode, molecules));
+  Action *saveConfigAction = new MethodAction(boost::bind(&config::SaveAll,configuration, ConfigFileName, periode, molecules));
   new ActionMenuItem('s',"save current setup to config file",main_menu,saveConfigAction);
 
@@ -1204 +1204 @@
   delete returnAction;
 };
-
-/** Tries given filename or standard on saving the config file.
- * \param *ConfigFileName name of file
- * \param *configuration pointer to configuration structure with all the values
- * \param *periode pointer to periodentafel structure with all the elements
- * \param *molecules list of molecules structure with all the atoms and coordinates
- */
-void oldmenu::SaveConfig(char *ConfigFileName, config *configuration, periodentafel *periode, MoleculeListClass *molecules)
-{
-  char filename[MAXSTRINGSIZE];
-  ofstream output;
-  molecule *mol = new molecule(periode);
-
-  if (!strcmp(configuration->configpath, configuration->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);
-  else
-    strcpy(filename,"main_pcp_linux");
-  Log() << Verbose(0) << "Saving as pdb input ";
-  if (configuration->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);
-  else
-    strcpy(filename,"main_pcp_linux");
-  Log() << Verbose(0) << "Saving as tremolo data input ";
-  if (configuration->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(*configuration);
-  configuration->InitMaxMinStopStep = configuration->MaxMinStopStep = configuration->MaxPsiDouble;
-  if (ConfigFileName != NULL) { // test the file name
-    strcpy(filename, ConfigFileName);
-    output.open(filename, ios::trunc);
-  } else if (strlen(configuration->configname) != 0) {
-    strcpy(filename, configuration->configname);
-    output.open(configuration->configname, ios::trunc);
-    } else {
-      strcpy(filename, DEFAULTCONFIG);
-      output.open(DEFAULTCONFIG, ios::trunc);
-    }
-  output.close();
-  output.clear();
-  Log() << Verbose(0) << "Saving of config file ";
-  if (configuration->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);
-  }
-  else {
-    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);
-  else
-    strcpy(filename,"main_pcp_linux");
-  Log() << Verbose(0) << "Saving as mpqc input ";
-  if (configuration->SaveMPQC(filename, mol))
-    Log() << Verbose(0) << "done." << endl;
-  else
-    Log() << Verbose(0) << "failed." << endl;
-
-  if (!strcmp(configuration->configpath, configuration->GetDefaultPath())) {
-    eLog() << Verbose(2) << "config is found under different path then stated in config file::defaultpath!" << endl;
-  }
-
-  delete(mol);
-};

src/menu.hpp

@@ -24 +24 @@
   void notImplementedYet();
   void perform(MoleculeListClass *, config *, periodentafel *, char *);
-  void SaveConfig(char *, config *, periodentafel *, MoleculeListClass *);
 
 protected: