Changeset 35b698 for src/builder.cpp

Timestamp:

Jun 23, 2010, 3:52:50 PM (15 years ago)

Author:

Frederik Heber <heber@…>

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:

d0fbec

Parents:

dc0d21

git-author:

Frederik Heber <heber@…> (06/23/10 15:20:35)

git-committer:

Frederik Heber <heber@…> (06/23/10 15:52:50)

Message:

BIG CHANGE: config::load and config::save in ParseCommandLineOptions() and main() replaced with FormatParser replacements.

Fragmentation:

• FragmentMolecule() - configuration is not needed anymore, but a path (including prefix)
• class molecule:
  • lots of changes from char * to std:string (due to above): LinearInterpolationBetweenConfiguration(), CheckOrderAtSite(), StoreBondsToFile(), StoreAdjacencyToFile(), CheckAdjacencyFileAgainstMolecule(), CheckAdjacencyFileAgainstMolecule_Init(), ParseOrderAtSiteFromFile(), StoreOrderAtSiteFile(), StoreForcesFile(), ScanAdaptiveFileIntoMap(), StoreForcesFile(), AddHydrogenCorrection(), OutputConfigForListOfFragments()
  • in all above functions, also stringstreams have been replaced by simple strings and file != NULL by file.good()
  • no more CalculateOrbitals(), shifted to class PcpParser
• FragmentationAction: argument of -f is now the prefix, molecule is obtained by molecule-by-id
• no more strcpy needed in: MoleculeLinearInterpolationofTrajectoriesAction, MoleculeSaveAdjacencyAction, MoleculeSaveBondsAction
• oldmenu::FragmentAtoms() - needs to ask for path with prefix now
• config: RetrieveConfigPathAndName() and configpath removed (replaced by above path with prefix)
• changes due to this removal: SaveConfig(), config::Load(), config::LoadOld()

• FIX: MoleculeFillWithMoleculeAction: filler atoms have to be removed before the system can be stored to file.
• FIX: PcpParser::load() - has to put the molecule also into World's MoleculeListClass (otherwise the name cannot be set right after loading)

• ParseCommandLineOptions()
  • new parameter BondGraphFileName and creation of bond graph is done in main()
  • no more config::load, just parser->load(), ConfigFileName is set extra and we always set configPresent to present.
  • FIX: filename is only set when no molecule was allocated before
  • FIX: case 't' and 'f' had wrong argc checks
• main()
  • FormatParserStorage is set with mpqc, pcp and xyz
  • BondGraph is constructed from new string BondGrapghFileName

• new Libparser.a
• all sources from PARSER subdir are compiled into libparser such that only ParserUnitTest is recompiled.

Testfixes:

• testsuite-fragmentation - changes to due to different -f calling syntax.
• most of the xyz files had to be replaced due to a single whitespace at the end of each entry: Domain/6, Simple_configuration/2, Simple_configuration/3, Simple_configuration/4, Simple_configuration/5, Simple_configuration/8
• in many cases were the number orbitals (and thus MaxMinStopStep) wrong: Filling/1, Simple_configuration/4, Simple_configuration/5

Signed-off-by: Frederik Heber <heber@…>

File:

• src/builder.cpp (modified) (19 diffs)

src/builder.cpp

@@ -80 +80 @@
 #include "Menu/ActionMenuItem.hpp"
 #include "Parser/ChangeTracker.hpp"
+#include "Parser/FormatParserStorage.hpp"
+#include "Parser/PcpParser.hpp"
+#include "Parser/XyzParser.hpp"
 #include "Actions/ActionRegistry.hpp"
 #include "Actions/ActionHistory.hpp"
@@ -654 +657 @@
   int Order1;
   clock_t start, end;
+  std::string path;
 
   DoLog(0) && (Log() << Verbose(0) << "Fragmenting molecule with current connection matrix ..." << endl);
   DoLog(0) && (Log() << Verbose(0) << "What's the desired bond order: ");
   cin >> Order1;
+  DoLog(0) && (Log() << Verbose(0) << "What's the output path and prefix [e.g. /home/foo/BondFragment]: ");
+  cin >> path;
   if (mol->first->next != mol->last) {  // there are bonds
     start = clock();
-    mol->FragmentMolecule(Order1, configuration);
+    mol->FragmentMolecule(Order1, path);
     end = clock();
     DoLog(0) && (Log() << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl);
@@ -1373 +1379 @@
   mol->SetNameFromFilename(ConfigFileName);
 
-  if (!strcmp(configuration->configpath, configuration->GetDefaultPath())) {
-    DoeLog(2) && (eLog()<< Verbose(2) << "config is found under different path then stated in config file::defaultpath!" << endl);
-  }
-
-
   // first save as PDB data
   if (ConfigFileName != NULL)
@@ -1477 +1478 @@
     DoLog(0) && (Log() << Verbose(0) << "failed." << endl);
 
-  if (!strcmp(configuration->configpath, configuration->GetDefaultPath())) {
-    DoeLog(2) && (eLog()<< Verbose(2) << "config is found under different path then stated in config file::defaultpath!" << endl);
-  }
-
   World::getInstance().destroyMolecule(mol);
 };
@@ -1500 +1497 @@
  */
 static int ParseCommandLineOptions(int argc, char **argv, MoleculeListClass *&molecules, periodentafel *&periode,
-                                   config& configuration, char **ConfigFileName, set<int> &ArgcList)
+                                   config& configuration, char **ConfigFileName, std::string &BondGraphFileName, set<int> &ArgcList)
 {
   Vector x,y,z,n;  // coordinates for absolute point in cell volume
@@ -1513 +1510 @@
   int argptr;
   molecule *mol = NULL;
-  string BondGraphFileName("\n");
 
   if (argc > 1) { // config file specified as option
@@ -1625 +1621 @@
       // simply create a new molecule, wherein the config file is loaded and the manipulation takes place
       DoLog(0) && (Log() << Verbose(0) << "Config file given." << endl);
+      std::string filenameprefix(argv[1]);
+      strcpy(*ConfigFileName, filenameprefix.substr(0,filenameprefix.find('.')).c_str());
+      DoLog(1) && (Log() << Verbose(1) << "Setting config file name prefix to " << *ConfigFileName << "." << endl);
       test.open(argv[1], ios::in);
       if (test == NULL) {
-        //return (1);
-        output.open(argv[1], ios::out);
-        if (output == NULL) {
-          DoLog(1) && (Log() << Verbose(1) << "Specified config file " << argv[1] << " not found." << endl);
-          configPresent = absent;
-        } else {
-          DoLog(0) && (Log() << Verbose(0) << "Empty configuration file." << endl);
-          strcpy(*ConfigFileName, argv[1]);
-          configPresent = empty;
-          output.close();
-        }
+        DoLog(1) && (Log() << Verbose(1) << "Specified config file " << argv[1] << " not found." << endl);
+        configPresent = empty;
       } else {
+        configPresent = present;
+        DoLog(1) && (Log() << Verbose(1) << "Specified config file found, parsing ... ");
+        FormatParserStorage::getInstance().getPcp().load(&test);
         test.close();
-        strcpy(*ConfigFileName, argv[1]);
-        DoLog(1) && (Log() << Verbose(1) << "Specified config file found, parsing ... ");
-        switch (configuration.TestSyntax(*ConfigFileName, periode)) {
-          case 1:
-            DoLog(0) && (Log() << Verbose(0) << "new syntax." << endl);
-            configuration.Load(*ConfigFileName, BondGraphFileName, periode, molecules);
-            configPresent = present;
-            break;
-          case 0:
-            DoLog(0) && (Log() << Verbose(0) << "old syntax." << endl);
-            configuration.LoadOld(*ConfigFileName, BondGraphFileName, periode, molecules);
-            configPresent = present;
-            break;
-          default:
-            DoLog(0) && (Log() << Verbose(0) << "Unknown syntax or empty, yet present file." << endl);
-            configPresent = empty;
-       }
       }
     } else
@@ -1671 +1647 @@
        mol = World::getInstance().createMolecule();
        mol->ActiveFlag = true;
-       if (*ConfigFileName != NULL)
-         mol->SetNameFromFilename(*ConfigFileName);
        molecules->insert(mol);
      }
+     if (*ConfigFileName != NULL)
+       mol->SetNameFromFilename(*ConfigFileName);
 
     // 4. parse again through options, now for those depending on elements db and config presence
@@ -1733 +1709 @@
               break;
             case 'I':
-              DoLog(1) && (Log() << Verbose(1) << "Dissecting molecular system into a set of disconnected subgraphs ... " << endl);
               ArgcList.insert(argptr-1);
               argptr+=0;
@@ -1977 +1952 @@
             case 't':
               if (ExitFlag == 0) ExitFlag = 1;
-              if ((argptr+4 >= argc) || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) ) {
+              if ((argptr+6 >= argc) || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) ) {
                 ExitFlag = 255;
                 DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for translation: -t <x> <y> <z> --molecule-by-id <molecule_id> --periodic <0/1>" << endl);
@@ -2074 +2049 @@
             case 'f':
               if (ExitFlag == 0) ExitFlag = 1;
-              if ((argptr+1 >= argc) || (argv[argptr][0] == '-')) {
+              if ((argptr+4 >= argc) || (argv[argptr][0] == '-')) {
                 ExitFlag = 255;
-                DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments for fragmentation: -f <max. bond distance> <bond order>" << endl);
+                DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments for fragmentation: -f <path/prefix> --molecule-by-id <molecule id> --distance <max_distance> --order <order>" << endl);
+                performCriticalExit();
+              } else {
+                ArgcList.insert(argptr-1);
+                ArgcList.insert(argptr);
+                ArgcList.insert(argptr+1);
+                ArgcList.insert(argptr+2);
+                ArgcList.insert(argptr+3);
+                ArgcList.insert(argptr+4);
+                ArgcList.insert(argptr+5);
+                ArgcList.insert(argptr+6);
+                argptr+=7;
+              }
+              break;
+            case 'm':
+              if (ExitFlag == 0) ExitFlag = 1;
+              j = atoi(argv[argptr++]);
+              if ((j<0) || (j>1)) {
+                DoeLog(1) && (eLog()<< Verbose(1) << "Argument of '-m' should be either 0 for no-rotate or 1 for rotate." << endl);
+                j = 0;
+              }
+              if (j) {
+                SaveFlag = true;
+                DoLog(0) && (Log() << Verbose(0) << "Converting to prinicipal axis system." << endl);
+                mol->PrincipalAxisSystem((bool)j);
+              } else
+                ArgcList.insert(argptr-1);
+                argptr+=0;
+              break;
+            case 'o':
+              if (ExitFlag == 0) ExitFlag = 1;
+              if ((argptr+4 >= argc) || (argv[argptr][0] == '-')){
+                ExitFlag = 255;
+                DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for convex envelope: -o <molecule_id> --output-file <output file> --output-file <binned output file>" << endl);
                 performCriticalExit();
               } else {
@@ -2088 +2096 @@
               }
               break;
-            case 'm':
-              if (ExitFlag == 0) ExitFlag = 1;
-              j = atoi(argv[argptr++]);
-              if ((j<0) || (j>1)) {
-                DoeLog(1) && (eLog()<< Verbose(1) << "Argument of '-m' should be either 0 for no-rotate or 1 for rotate." << endl);
-                j = 0;
-              }
-              if (j) {
-                SaveFlag = true;
-                DoLog(0) && (Log() << Verbose(0) << "Converting to prinicipal axis system." << endl);
-                mol->PrincipalAxisSystem((bool)j);
-              } else
-                ArgcList.insert(argptr-1);
-                argptr+=0;
-              break;
-            case 'o':
-              if (ExitFlag == 0) ExitFlag = 1;
-              if ((argptr+4 >= argc) || (argv[argptr][0] == '-')){
-                ExitFlag = 255;
-                DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for convex envelope: -o <molecule_id> --output-file <output file> --output-file <binned output file>" << endl);
-                performCriticalExit();
-              } else {
-                ArgcList.insert(argptr-1);
-                ArgcList.insert(argptr);
-                ArgcList.insert(argptr+1);
-                ArgcList.insert(argptr+2);
-                ArgcList.insert(argptr+3);
-                ArgcList.insert(argptr+4);
-                argptr+=5;
-              }
-              break;
             case 'U':
               if (ExitFlag == 0) ExitFlag = 1;
@@ -2164 +2141 @@
       } else argptr++;
     } while (argptr < argc);
-    if (SaveFlag)
-      configuration.SaveAll(*ConfigFileName, periode, molecules);
   } else {  // no arguments, hence scan the elements db
     if (periode->LoadPeriodentafel(configuration.databasepath))
@@ -2171 +2146 @@
     else
       DoLog(0) && (Log() << Verbose(0) << "Element list loading failed." << endl);
-    configuration.RetrieveConfigPathAndName("main_pcp_linux");
   }
   return(ExitFlag);
@@ -2179 +2153 @@
 
 void cleanUp(){
+  FormatParserStorage::purgeInstance();
   ChangeTracker::purgeInstance();
   World::purgeInstance();
@@ -2207 +2182 @@
     bool ArgumentsCopied = false;
     char *ConfigFileName = new char[MAXSTRINGSIZE];
+    std::string BondGraphFileName("\n");
+    FormatParserStorage::getInstance().addMpqc();
+    FormatParserStorage::getInstance().addPcp();
+    FormatParserStorage::getInstance().addXyz();
 
     // print version check whether arguments are present at all
@@ -2235 +2214 @@
       ArgcList.insert(1); // push back config file name
       // handle arguments by ParseCommandLineOptions()
-      ExitFlag = ParseCommandLineOptions(argc,argv,World::getInstance().getMolecules(),World::getInstance().getPeriode(),*World::getInstance().getConfig(), &ConfigFileName, ArgcList);
+      ExitFlag = ParseCommandLineOptions(argc,argv,World::getInstance().getMolecules(),World::getInstance().getPeriode(),*World::getInstance().getConfig(), &ConfigFileName, BondGraphFileName, ArgcList);
       World::getInstance().setExitFlag(ExitFlag);
       // copy all remaining arguments to a new argv
@@ -2248 +2227 @@
       cout << endl;
       ArgumentsCopied = true;
+
+      // construct bond graph
+      if (World::getInstance().getConfig()->BG == NULL) {
+        World::getInstance().getConfig()->BG = new BondGraph(World::getInstance().getConfig()->GetIsAngstroem());
+        if (World::getInstance().getConfig()->BG->LoadBondLengthTable(BondGraphFileName)) {
+          DoLog(0) && (Log() << Verbose(0) << "Bond length table loaded successfully." << endl);
+        } else {
+          DoeLog(1) && (eLog()<< Verbose(1) << "Bond length table loading failed." << endl);
+        }
+      }
       // handle remaining arguments by CommandLineParser
       MapOfActions::getInstance().AddOptionsToParser();
@@ -2269 +2258 @@
     }
 
-    Log() << Verbose(0) << "Saving to " << ConfigFileName << "." << endl;
-    World::getInstance().getConfig()->SaveAll(ConfigFileName, World::getInstance().getPeriode(), World::getInstance().getMolecules());
+    std::string FilenamePrefix(ConfigFileName);
+    FormatParserStorage::getInstance().SetOutputPrefixForAll(FilenamePrefix);
+    FormatParserStorage::getInstance().SaveAll();
+    ChangeTracker::getInstance().saveStatus();
 
   // free the new argv