Changeset 6a465e for src/ConfigFileBuffer.cpp

Timestamp:

Feb 24, 2011, 7:47:41 PM (14 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:

fcac72

Parents:

03c77c

git-author:

Frederik Heber <heber@…> (02/24/11 11:20:52)

git-committer:

Frederik Heber <heber@…> (02/24/11 19:47:41)

Message:

Rewrote LoadMolecule() for PcpParser.

• LoadMolecule() rewritten as only because of getter/setter introduction the PcpParser did not work properly anymore. Used boost::tokenizer for parsing all Ion_Type stuff.
• TESTFIX: Molecules/SaveTemperature - has been buggy since a long time! LoadMolecule() did the messed up sequence of Ion_Type right only for the first step not for all subsequent steps. Hence, we lacked the velocities of all non-hydrogen atoms and obtained a different (wrong) temperature.
• TESTFIX: ParserPcpUnitTest made first atom at (1,0,0) instead of (0,0,0) as this rather shows up parsing errors than zero vector which is default value.

File:

• src/ConfigFileBuffer.cpp (modified) (3 diffs)

src/ConfigFileBuffer.cpp

@@ -20 +20 @@
 #include "CodePatterns/MemDebug.hpp"
 
+#include <iostream>
+#include <boost/tokenizer.hpp>
+#include <string>
+
 #include "ConfigFileBuffer.hpp"
 #include "Helpers/helpers.hpp"
@@ -31 +35 @@
  */
 struct IonTypeCompare {
-  bool operator()(const char* s1, const char *s2) const {
-    char number1[8];
-    char number2[8];
-    const char *dummy1, *dummy2;
-    //Log() << Verbose(0) << s1 << "  " << s2 << endl;
-    dummy1 = strchr(s1, '_')+sizeof(char)*5;  // go just after "Ion_Type"
-    dummy2 = strchr(dummy1, '_');
-    strncpy(number1, dummy1, dummy2-dummy1); // copy the number
-    number1[dummy2-dummy1]='\0';
-    dummy1 = strchr(s2, '_')+sizeof(char)*5;  // go just after "Ion_Type"
-    dummy2 = strchr(dummy1, '_');
-    strncpy(number2, dummy1, dummy2-dummy1); // copy the number
-    number2[dummy2-dummy1]='\0';
-    if (atoi(number1) != atoi(number2))
-      return (atoi(number1) < atoi(number2));
+  bool operator()(std::string s1, std::string s2) const {
+    ConvertTo<int> toInt;
+    boost::char_separator<char> sep("_");
+    tokenizer tokens1(s1,sep);
+    tokenizer tokens2(s2,sep);
+    tokenizer::iterator tok_iter1 = tokens1.begin();
+    tokenizer::iterator tok_iter2 = tokens2.begin();
+    ++tok_iter1;
+    ++tok_iter2;
+
+    std::string element1(*tok_iter1++);
+    std::string element2(*tok_iter2++);
+    int elementno1 = toInt(element1.substr(4,string::npos));
+    int elementno2 = toInt(element2.substr(4,string::npos));
+    if (elementno1 != elementno2)
+      return elementno1 < elementno2;
     else {
-      dummy1 = strchr(s1, '_')+sizeof(char);
-      dummy1 = strchr(dummy1, '_')+sizeof(char);
-      dummy2 = strchr(dummy1, ' ') < strchr(dummy1, '\t') ? strchr(dummy1, ' ') : strchr(dummy1, '\t');
-      strncpy(number1, dummy1, dummy2-dummy1); // copy the number
-      number1[dummy2-dummy1]='\0';
-      dummy1 = strchr(s2, '_')+sizeof(char);
-      dummy1 = strchr(dummy1, '_')+sizeof(char);
-      dummy2 = strchr(dummy1, ' ') < strchr(dummy1, '\t') ? strchr(dummy1, ' ') : strchr(dummy1, '\t');
-      strncpy(number2, dummy1, dummy2-dummy1); // copy the number
-      number2[dummy2-dummy1]='\0';
-      return (atoi(number1) < atoi(number2));
+      std::string atom1(*tok_iter1);
+      std::string atom2(*tok_iter2);
+      int atomno1 = toInt(atom1);
+      int atomno2 = toInt(atom2);
+      return atomno1 < atomno2;
     }
-  }
+
+//    char number1[8];
+//    char number2[8];
+//    const char *dummy1 = s1.c_str();
+//    const char *dummy2 = s2.c_str();
+//    //Log() << Verbose(0) << s1 << "  " << s2 << endl;
+//    dummy1 = strchr(s1, '_')+sizeof(char)*5;  // go just after "Ion_Type"
+//    dummy2 = strchr(dummy1, '_');
+//    strncpy(number1, dummy1, dummy2-dummy1); // copy the number
+//    number1[dummy2-dummy1]='\0';
+//    dummy1 = strchr(s2, '_')+sizeof(char)*5;  // go just after "Ion_Type"
+//    dummy2 = strchr(dummy1, '_');
+//    strncpy(number2, dummy1, dummy2-dummy1); // copy the number
+//    number2[dummy2-dummy1]='\0';
+//    if (atoi(number1) != atoi(number2))
+//      return (atoi(number1) < atoi(number2));
+//    else {
+//      dummy1 = strchr(s1, '_')+sizeof(char);
+//      dummy1 = strchr(dummy1, '_')+sizeof(char);
+//      dummy2 = strchr(dummy1, ' ') < strchr(dummy1, '\t') ? strchr(dummy1, ' ') : strchr(dummy1, '\t');
+//      strncpy(number1, dummy1, dummy2-dummy1); // copy the number
+//      number1[dummy2-dummy1]='\0';
+//      dummy1 = strchr(s2, '_')+sizeof(char);
+//      dummy1 = strchr(dummy1, '_')+sizeof(char);
+//      dummy2 = strchr(dummy1, ' ') < strchr(dummy1, '\t') ? strchr(dummy1, ' ') : strchr(dummy1, '\t');
+//      strncpy(number2, dummy1, dummy2-dummy1); // copy the number
+//      number2[dummy2-dummy1]='\0';
+//      return (atoi(number1) < atoi(number2));
+//    }
+  }
+
+  typedef boost::tokenizer<boost::char_separator<char> > tokenizer;
 };
+
 
 /** Constructor for ConfigFileBuffer class.
@@ -182 +213 @@
 void ConfigFileBuffer::MapIonTypesInBuffer(const int NoAtoms)
 {
-  map<const char *, int, IonTypeCompare> IonTypeLineMap;
+  std::multimap<std::string, int, IonTypeCompare> IonTypeLineMap;
   if (!MappingAllocated) {
     InitMapping();
   }
 
+  typedef boost::tokenizer<boost::char_separator<char> >
+      tokenizer;
+  boost::char_separator<char> sep("\t ");
+
   // put all into hashed map
-  for (int i=0; i<NoAtoms; ++i) {
-    IonTypeLineMap.insert(pair<const char *, int> (buffer[CurrentLine+i], CurrentLine+i));
-  }
-
-  // fill map
+  for (int i=CurrentLine; i<NoLines; ++i) {
+    std::string line(buffer[i]);
+    tokenizer tokens(line, sep);
+    if (tokens.begin() != tokens.end()) {
+      const std::string token = *tokens.begin();
+      if (token.find("Ion_Type") != string::npos) {
+        IonTypeLineMap.insert(pair<std::string, int> (token, i));
+      }
+    }
+  }
+
+  // fill map (aka IonType1_1, IonType1_1, IonType1_1, IonType1_2, IonType1_2, IonType1_2, ...
+  // ..., IonType2_1, IonType2_1, IonType2_1, ...)
   int nr=0;
-  for (map<const char *, int, IonTypeCompare>::iterator runner = IonTypeLineMap.begin(); runner != IonTypeLineMap.end(); ++runner) {
+  for (map<std::string, int, IonTypeCompare>::iterator runner = IonTypeLineMap.begin(); runner != IonTypeLineMap.end(); ++runner) {
     if (CurrentLine+nr < NoLines)
       LineMapping[CurrentLine+(nr++)] = runner->second;
     else {
-      DoeLog(0) && (eLog()<< Verbose(0) << "config::MapIonTypesInBuffer - NoAtoms is wrong: We are past the end of the file!" << endl);
+      DoeLog(0) && (eLog()<< Verbose(0) << "config::MapIonTypesInBuffer - NoLines is wrong: We are past the end of the file!" << endl);
       performCriticalExit();
     }