Changeset fcac72

Timestamp:

Feb 24, 2011, 7:48:13 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:

9dba5f

Parents:

6a465e

git-author:

Frederik Heber <heber@…> (02/24/11 12:48:45)

git-committer:

Frederik Heber <heber@…> (02/24/11 19:48:13)

Message:

Added multiple time steps to PcpParser::OutputAtoms().

• removed Fastparsing part in comments in LoadMolecule().

Files:

• src/Parser/PcpParser.cpp (modified) (1 diff)
• src/config.cpp (modified) (6 diffs)
• tests/regression/Parser/Pcp/post/testmulti.conf (added)
• tests/regression/Parser/Pcp/pre/testmulti.conf (added)
• tests/regression/Parser/Pcp/testsuite-parser-pcp.at (modified) (1 diff)

src/Parser/PcpParser.cpp

@@ -548 +548 @@
   *file << "#Ion_TypeNr._Nr.R[0]    R[1]    R[2]    MoveType (0 MoveIon, 1 FixedIon)" << endl;
   map<int, int> ZtoCountMap;
+  map<atom *, int> AtomtoCountMap;
   pair <   map<int, int>::iterator, bool > Inserter;
-  int nr = 0;
-  for (vector<atom *>::const_iterator AtomRunner = allatoms.begin();AtomRunner != allatoms.end();++AtomRunner) {
-    Inserter = ZtoCountMap.insert( pair<int, int>((*AtomRunner)->getType()->getAtomicNumber(), 1) );
-    if (!Inserter.second)
-      Inserter.first->second += 1;
-    const int Z = (*AtomRunner)->getType()->getAtomicNumber();
-    *file << "Ion_Type" << ZtoIndexMap[Z] << "_" << ZtoCountMap[Z] << "\t"  << fixed << setprecision(9) << showpoint;
-    *file << (*AtomRunner)->at(0) << "\t" << (*AtomRunner)->at(1) << "\t" << (*AtomRunner)->at(2);
-    *file << "\t" << (int)((*AtomRunner)->getFixedIon());
-    if ((*AtomRunner)->getAtomicVelocity().Norm() > MYEPSILON)
-      *file << "\t" << scientific << setprecision(6) << (*AtomRunner)->getAtomicVelocity()[0] << "\t" << (*AtomRunner)->getAtomicVelocity()[1] << "\t" << (*AtomRunner)->getAtomicVelocity()[2] << "\t";
-    *file << " # molecule nr " << nr++ << endl;
-  }
+  bool ContinueStatus = true;
+  bool AddNewLine = false;
+  size_t step = 0;
+  do {
+    int nr = 0;
+    ContinueStatus = false;
+    for (vector<atom *>::const_iterator AtomRunner = allatoms.begin();AtomRunner != allatoms.end();++AtomRunner) {
+      if ((*AtomRunner)->getTrajectorySize() > step) {
+        if (step == 0) {  // fill list only on first step
+          Inserter = ZtoCountMap.insert( pair<int, int>((*AtomRunner)->getType()->getAtomicNumber(), 1) );
+          if (!Inserter.second)
+            Inserter.first->second += 1;
+          AtomtoCountMap.insert( make_pair((*AtomRunner), Inserter.first->second) );
+        }
+        if (AddNewLine) {
+          AddNewLine = false;
+          *file << endl;
+        }
+        const int Z = (*AtomRunner)->getType()->getAtomicNumber();
+        *file << "Ion_Type" << ZtoIndexMap[Z] << "_" << AtomtoCountMap[(*AtomRunner)] << "\t"  << fixed << setprecision(9) << showpoint;
+        *file << (*AtomRunner)->atStep(0, step)
+            << "\t" << (*AtomRunner)->atStep(1,step)
+            << "\t" << (*AtomRunner)->atStep(2,step);
+        *file << "\t" << (int)((*AtomRunner)->getFixedIon());
+        if ((*AtomRunner)->getAtomicVelocityAtStep(step).Norm() > MYEPSILON)
+          *file << "\t" << scientific << setprecision(6)
+              << (*AtomRunner)->getAtomicVelocityAtStep(step)[0] << "\t"
+              << (*AtomRunner)->getAtomicVelocityAtStep(step)[1] << "\t"
+              << (*AtomRunner)->getAtomicVelocityAtStep(step)[2] << "\t";
+        *file << " # molecule nr " << nr++ << endl;
+        ContinueStatus = true;  // as long as a single atom still has trajectory points, continue
+      }
+    }
+    ++step;
+    if (ContinueStatus)
+      AddNewLine = true;
+  } while (ContinueStatus);
 }
 

src/config.cpp

@@ -461 +461 @@
   const element *elementhash[MAX_ELEMENTS];
   char name[MAXSTRINGSIZE];
-  char keyword[MAXSTRINGSIZE];
   int Z = -1;
   int No[MAX_ELEMENTS];
@@ -497 +496 @@
       return;
     }
-    FileBuffer->CurrentLine++;
-    //Log() << Verbose(0) << FileBuffer->buffer[ FileBuffer->LineMapping[FileBuffer->CurrentLine]];
+
+    FileBuffer->CurrentLine++;  // skip to next line
     FileBuffer->MapIonTypesInBuffer(NoAtoms);
     for (int i=FileBuffer->CurrentLine; i<FileBuffer->NoLines;++i) {
-      Log() << Verbose(0) << FileBuffer->buffer[ FileBuffer->LineMapping[i] ];
+      DoLog(4) && (Log() << Verbose(4) << FileBuffer->buffer[ FileBuffer->LineMapping[i] ]);
     }
 
@@ -535 +534 @@
                 neues = World::getInstance().createAtom();
                 AtomList[i][j] = neues;
-                std::cout << "filling LinearList [ (FileBuffer->LineMapping[" << FileBuffer->CurrentLine << "]) = " << FileBuffer->LineMapping[FileBuffer->CurrentLine] << " with " << neues << endl;
+                DoLog(4) && (Log() << Verbose(4) << "Filling LinearList [ (FileBuffer->LineMapping[" << FileBuffer->CurrentLine << "]) = " << FileBuffer->LineMapping[FileBuffer->CurrentLine] << " with " << neues << endl);
                 LinearList[ FileBuffer->LineMapping[FileBuffer->CurrentLine] ] = neues;
                 neues->setType(elementhash[i]); // find element type
@@ -547 +546 @@
               DoLog(3) && (Log() << Verbose(3) << "INFO: Line contains " << tokens_size << " tokens." << std::endl);
               // and parse
+              tempVector.Zero();
               if (tokens_size >= 5) { // only AtomicPosition and FixedIon
                 DoLog(3) && (Log() << Verbose(3) << "INFO: Parsing AtomicPosition and FixedIon" << std::endl);
@@ -555 +555 @@
                 neues->setFixedIon(_fixedion == 1);
               }
+              tempVector.Zero();
               if (tokens_size >= 8) { // AtomicVelocity
                 DoLog(3) && (Log() << Verbose(3) << "INFO: Parsing AtomicVelocity" << std::endl);
                 for (int i=0;i<NDIM;++i)
                   tempVector[i] = toDouble(*tok_iter++);
-                neues->setAtomicVelocityAtStep(step, tempVector);
               }
+              neues->setAtomicVelocityAtStep(step, tempVector);
+              tempVector.Zero();
               if (tokens_size >= 11) {  // AtomicForce
                 DoLog(3) && (Log() << Verbose(3) << "INFO: Parsing AtomicForce" << std::endl);
                 for (int i=0;i<NDIM;++i)
                   tempVector[i] = toDouble(*tok_iter++);
-                neues->setAtomicForceAtStep(step, tempVector);
               }
+              neues->setAtomicForceAtStep(step, tempVector);
               std::stringstream output;
               output << "Parsed position of step " << (step+1) << ": ";
@@ -597 +599 @@
     }
 
-//    if (!FastParsing) {
-//      // parse in trajectories
-//      bool status = true;
-//      while (status) {
-//        DoLog(0) && (Log() << Verbose(0) << "Currently checking on MD step " << repetition+1 << "." << endl);
-//        for (int i=0; i < MaxTypes; i++) {
-//          sprintf(name,"Ion_Type%i",i+1);
-//          for(int j=0;j<No[i];j++) {
-//            sprintf(keyword,"%s_%i",name, j+1);
-//            DoLog(3) && (Log() << Verbose(3) << "Looking for " << keyword << " of " << (repetition) << " repetition." << std::endl);
-//            DoLog(3) && (Log() << Verbose(3) << "INFO: Parsing AtomicPosition." << std::endl);
-//            for (int k=0;k<NDIM;++k) { // repetition=1 is correct, as we advance eventually by sequential=1!
-//              status = status && ParseForParameter(verbose,FileBuffer, (const char*)keyword, 0, 1+k, 1, double_type, &tempVector[k], 1, (repetition == 0) ? critical : optional);
-//            }
-//            if (!status)
-//              break;
-//
-//            if (repetition == 0) {
-//              neues = World::getInstance().createAtom();
-//              AtomList[i][j] = neues;
-//              std::cout << "filling LinearList [ (FileBuffer->LineMapping[" << FileBuffer->CurrentLine << "]) = " << FileBuffer->LineMapping[FileBuffer->CurrentLine] << " with " << neues << endl;
-//              LinearList[ FileBuffer->LineMapping[FileBuffer->CurrentLine] ] = neues;
-//              neues->setType(elementhash[i]); // find element type
-//            } else
-//              neues = AtomList[i][j];
-//
-//            DoLog(3) && (Log() << Verbose(3) << "INFO: Parsing FixedIon." << std::endl);
-//            status = status && ParseForParameter(verbose,FileBuffer, (const char*)keyword, 0, 4, 1, int_type, &_fixedion, 1, (repetition == 0) ? critical : optional);
-//            neues->setFixedIon(_fixedion == 1);
-//
-//            // check size of vectors
-//            if (neues->getTrajectorySize() <= (unsigned int)(repetition)) {
-//              neues->ResizeTrajectory(repetition+10);
-//              //Log() << Verbose(0) << "Increasing size for trajectory array of " << keyword << " to " << (repetition+10) << "." << endl;
-//            }
-//
-//            // put into trajectories list
-//            neues->setPosition(repetition, tempVector);
-//
-//            // parse velocities if present
-//            DoLog(3) && (Log() << Verbose(3) << "INFO: Parsing AtomicVelocity." << std::endl);
-//            bool velocityStatus = true;
-//            for (int k=0;k<NDIM;++k)
-//              velocityStatus = velocityStatus && ParseForParameter(verbose,FileBuffer, (const char*)keyword, 0, 5+k, 1, double_type, &tempVector[k], 1,optional);
-//            if (!velocityStatus) {
-//              neues->setAtomicVelocity(repetition, zeroVec);
-//            } else
-//              neues->setAtomicVelocity(repetition, tempVector);
-//
-//            // parse forces if present
-//            DoLog(3) && (Log() << Verbose(3) << "INFO: Parsing AtomicForce." << std::endl);
-//            bool forceStatus = true;
-//            for (int k=0;k<NDIM;++k)
-//              forceStatus = forceStatus && ParseForParameter(verbose,FileBuffer, (const char*)keyword, (k==(NDIM-1)) ? 1 : 0, 8+k, 1, double_type, &tempVector[k], 1,optional);
-//            if (!forceStatus) {
-//              ++FileBuffer->CurrentLine;  // as above sequential=1 did not apply due to end of file
-//              neues->setAtomicForce(repetition, zeroVec);
-//            } else {
-//              neues->setAtomicForce(repetition, tempVector);
-//            }
-//
-//            std::stringstream output;
-//            output << "Parsed position of step " << (repetition+1) << ": ";
-//            output << neues->getPosition(repetition);          // next step
-//            output << "\t";
-//            output << (neues->getFixedIon() ? "true" : "false");
-//            output << "\t";
-//            output << neues->getAtomicVelocity(repetition);          // next step
-//            output << "\t";
-//            output << neues->getAtomicForce(repetition);          // next step
-//            DoLog(2) && (Log() << Verbose(2) << output.str() << endl);
-//          }
-//        }
-//        repetition++;
-//      }
-//      repetition--;
-//      if (repetition <= 1)  // if onyl one step, desactivate use of trajectories
-//        mol->MDSteps = 0;
-//      else {
-//        DoLog(0) && (Log() << Verbose(0) << "Found " << repetition+1 << " trajectory step(s)." << endl);
-//        mol->MDSteps = repetition;
-//      }
-//    } else {
-//      // find the maximum number of MD steps so that we may parse last one (Ion_Type1_1 must always be present, because is the first atom)
-//      repetition = 0;
-//      while ( ParseForParameter(verbose,FileBuffer, "Ion_Type1_1", 0, 1, 1, double_type, &value[0], repetition, (repetition == 0) ? critical : optional) &&
-//              ParseForParameter(verbose,FileBuffer, "Ion_Type1_1", 0, 2, 1, double_type, &value[1], repetition, (repetition == 0) ? critical : optional) &&
-//              ParseForParameter(verbose,FileBuffer, "Ion_Type1_1", 0, 3, 1, double_type, &value[2], repetition, (repetition == 0) ? critical : optional))
-//        repetition++;
-//      DoLog(0) && (Log() << Verbose(0) << "I found " << repetition << " times the keyword Ion_Type1_1." << endl);
-//      // parse in molecule coordinates
-//      for (int i=0; i < MaxTypes; i++) {
-//        sprintf(name,"Ion_Type%i",i+1);
-//        for(int j=0;j<No[i];j++) {
-//          sprintf(keyword,"%s_%i",name, j+1);
-//          if (repetition == 0) {
-//            neues = World::getInstance().createAtom();
-//            AtomList[i][j] = neues;
-//            LinearList[ FileBuffer->LineMapping[FileBuffer->CurrentLine] ] = neues;
-//            neues->setType(elementhash[i]); // find element type
-//          } else
-//            neues = AtomList[i][j];
-//          // then parse for each atom the coordinates as often as present
-//          ParseForParameter(verbose,FileBuffer, keyword, 0, 1, 1, double_type, &tempVector[0], repetition,critical);
-//          ParseForParameter(verbose,FileBuffer, keyword, 0, 2, 1, double_type, &tempVector[1], repetition,critical);
-//          ParseForParameter(verbose,FileBuffer, keyword, 0, 3, 1, double_type, &tempVector[2], repetition,critical);
-//          neues->setPosition(tempVector);
-//          bool _fixedion;
-//          ParseForParameter(verbose,FileBuffer, keyword, 0, 4, 1, int_type, &_fixedion, repetition,critical);
-//          neues->setFixedIon(_fixedion);
-//          bool velocityStatus = true;
-//          velocityStatus = velocityStatus &&
-//              ParseForParameter(verbose,FileBuffer, keyword, 0, 5, 1, double_type, &tempVector[0], repetition,optional) &&
-//              ParseForParameter(verbose,FileBuffer, keyword, 0, 6, 1, double_type, &tempVector[1], repetition,optional) &&
-//              ParseForParameter(verbose,FileBuffer, keyword, 1, 7, 1, double_type, &tempVector[2], repetition,optional);
-//          if (!velocityStatus)
-//            neues->setAtomicVelocity(zeroVec);
-//          else
-//            neues->setAtomicVelocity(tempVector);
-//
-//          // here we don't care if forces are present (last in trajectories is always equal to current position)
-//          neues->setType(elementhash[i]); // find element type
-//          mol->AddAtom(neues);
-//        }
-//      }
-//    }
     // put atoms into the molecule in their original order
     for(map<int, atom*>::iterator runner = LinearList.begin(); runner != LinearList.end(); ++runner) {

tests/regression/Parser/Pcp/testsuite-parser-pcp.at

@@ -12 +12 @@
 AT_CHECK([diff store.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Pcp/post/test.conf], 0, [ignore], [ignore])
 AT_CLEANUP
+
+AT_SETUP([Parser - loading with multiple time steps])
+AT_KEYWORDS([parser,pcp])
+AT_CHECK([../../molecuilder -i testmulti.conf -o pcp -l ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Pcp/pre/testmulti.conf], 0, [ignore], [ignore])
+AT_CHECK([file=testmulti.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Pcp/post/$file], 0, [ignore], [ignore])
+AT_CLEANUP