Changeset 6a465e


Ignore:
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.
Files:
4 edited

Legend:

Unmodified
Added
Removed

  • src/ConfigFileBuffer.cpp

    r03c77c r6a465e  
    2020#include "CodePatterns/MemDebug.hpp"
    2121
     22#include <iostream>
     23#include <boost/tokenizer.hpp>
     24#include <string>
     25
    2226#include "ConfigFileBuffer.hpp"
    2327#include "Helpers/helpers.hpp"
    … …  
    3135 */
    3236struct IonTypeCompare {
    33   bool operator()(const char* s1, const char *s2) const {
    34     char number1[8];
    35     char number2[8];
    36     const char *dummy1, *dummy2;
    37     //Log() << Verbose(0) << s1 << "  " << s2 << endl;
    38     dummy1 = strchr(s1, '_')+sizeof(char)*5;  // go just after "Ion_Type"
    39     dummy2 = strchr(dummy1, '_');
    40     strncpy(number1, dummy1, dummy2-dummy1); // copy the number
    41     number1[dummy2-dummy1]='\0';
    42     dummy1 = strchr(s2, '_')+sizeof(char)*5;  // go just after "Ion_Type"
    43     dummy2 = strchr(dummy1, '_');
    44     strncpy(number2, dummy1, dummy2-dummy1); // copy the number
    45     number2[dummy2-dummy1]='\0';
    46     if (atoi(number1) != atoi(number2))
    47       return (atoi(number1) < atoi(number2));
     37  bool operator()(std::string s1, std::string s2) const {
     38    ConvertTo<int> toInt;
     39    boost::char_separator<char> sep("_");
     40    tokenizer tokens1(s1,sep);
     41    tokenizer tokens2(s2,sep);
     42    tokenizer::iterator tok_iter1 = tokens1.begin();
     43    tokenizer::iterator tok_iter2 = tokens2.begin();
     44    ++tok_iter1;
     45    ++tok_iter2;
     46
     47    std::string element1(*tok_iter1++);
     48    std::string element2(*tok_iter2++);
     49    int elementno1 = toInt(element1.substr(4,string::npos));
     50    int elementno2 = toInt(element2.substr(4,string::npos));
     51    if (elementno1 != elementno2)
     52      return elementno1 < elementno2;
    4853    else {
    49       dummy1 = strchr(s1, '_')+sizeof(char);
    50       dummy1 = strchr(dummy1, '_')+sizeof(char);
    51       dummy2 = strchr(dummy1, ' ') < strchr(dummy1, '\t') ? strchr(dummy1, ' ') : strchr(dummy1, '\t');
    52       strncpy(number1, dummy1, dummy2-dummy1); // copy the number
    53       number1[dummy2-dummy1]='\0';
    54       dummy1 = strchr(s2, '_')+sizeof(char);
    55       dummy1 = strchr(dummy1, '_')+sizeof(char);
    56       dummy2 = strchr(dummy1, ' ') < strchr(dummy1, '\t') ? strchr(dummy1, ' ') : strchr(dummy1, '\t');
    57       strncpy(number2, dummy1, dummy2-dummy1); // copy the number
    58       number2[dummy2-dummy1]='\0';
    59       return (atoi(number1) < atoi(number2));
     54      std::string atom1(*tok_iter1);
     55      std::string atom2(*tok_iter2);
     56      int atomno1 = toInt(atom1);
     57      int atomno2 = toInt(atom2);
     58      return atomno1 < atomno2;
    6059    }
    61   }
     60
     61//    char number1[8];
     62//    char number2[8];
     63//    const char *dummy1 = s1.c_str();
     64//    const char *dummy2 = s2.c_str();
     65//    //Log() << Verbose(0) << s1 << "  " << s2 << endl;
     66//    dummy1 = strchr(s1, '_')+sizeof(char)*5;  // go just after "Ion_Type"
     67//    dummy2 = strchr(dummy1, '_');
     68//    strncpy(number1, dummy1, dummy2-dummy1); // copy the number
     69//    number1[dummy2-dummy1]='\0';
     70//    dummy1 = strchr(s2, '_')+sizeof(char)*5;  // go just after "Ion_Type"
     71//    dummy2 = strchr(dummy1, '_');
     72//    strncpy(number2, dummy1, dummy2-dummy1); // copy the number
     73//    number2[dummy2-dummy1]='\0';
     74//    if (atoi(number1) != atoi(number2))
     75//      return (atoi(number1) < atoi(number2));
     76//    else {
     77//      dummy1 = strchr(s1, '_')+sizeof(char);
     78//      dummy1 = strchr(dummy1, '_')+sizeof(char);
     79//      dummy2 = strchr(dummy1, ' ') < strchr(dummy1, '\t') ? strchr(dummy1, ' ') : strchr(dummy1, '\t');
     80//      strncpy(number1, dummy1, dummy2-dummy1); // copy the number
     81//      number1[dummy2-dummy1]='\0';
     82//      dummy1 = strchr(s2, '_')+sizeof(char);
     83//      dummy1 = strchr(dummy1, '_')+sizeof(char);
     84//      dummy2 = strchr(dummy1, ' ') < strchr(dummy1, '\t') ? strchr(dummy1, ' ') : strchr(dummy1, '\t');
     85//      strncpy(number2, dummy1, dummy2-dummy1); // copy the number
     86//      number2[dummy2-dummy1]='\0';
     87//      return (atoi(number1) < atoi(number2));
     88//    }
     89  }
     90
     91  typedef boost::tokenizer<boost::char_separator<char> > tokenizer;
    6292};
     93
    6394
    6495/** Constructor for ConfigFileBuffer class.
    … …  
    182213void ConfigFileBuffer::MapIonTypesInBuffer(const int NoAtoms)
    183214{
    184   map<const char *, int, IonTypeCompare> IonTypeLineMap;
     215  std::multimap<std::string, int, IonTypeCompare> IonTypeLineMap;
    185216  if (!MappingAllocated) {
    186217    InitMapping();
    187218  }
    188219
     220  typedef boost::tokenizer<boost::char_separator<char> >
     221      tokenizer;
     222  boost::char_separator<char> sep("\t ");
     223
    189224  // put all into hashed map
    190   for (int i=0; i<NoAtoms; ++i) {
    191     IonTypeLineMap.insert(pair<const char *, int> (buffer[CurrentLine+i], CurrentLine+i));
    192   }
    193 
    194   // fill map
     225  for (int i=CurrentLine; i<NoLines; ++i) {
     226    std::string line(buffer[i]);
     227    tokenizer tokens(line, sep);
     228    if (tokens.begin() != tokens.end()) {
     229      const std::string token = *tokens.begin();
     230      if (token.find("Ion_Type") != string::npos) {
     231        IonTypeLineMap.insert(pair<std::string, int> (token, i));
     232      }
     233    }
     234  }
     235
     236  // fill map (aka IonType1_1, IonType1_1, IonType1_1, IonType1_2, IonType1_2, IonType1_2, ...
     237  // ..., IonType2_1, IonType2_1, IonType2_1, ...)
    195238  int nr=0;
    196   for (map<const char *, int, IonTypeCompare>::iterator runner = IonTypeLineMap.begin(); runner != IonTypeLineMap.end(); ++runner) {
     239  for (map<std::string, int, IonTypeCompare>::iterator runner = IonTypeLineMap.begin(); runner != IonTypeLineMap.end(); ++runner) {
    197240    if (CurrentLine+nr < NoLines)
    198241      LineMapping[CurrentLine+(nr++)] = runner->second;
    199242    else {
    200       DoeLog(0) && (eLog()<< Verbose(0) << "config::MapIonTypesInBuffer - NoAtoms is wrong: We are past the end of the file!" << endl);
     243      DoeLog(0) && (eLog()<< Verbose(0) << "config::MapIonTypesInBuffer - NoLines is wrong: We are past the end of the file!" << endl);
    201244      performCriticalExit();
    202245    }

  • src/Parser/unittests/ParserPcpUnitTest.cpp

    r03c77c r6a465e  
    111111Ion_Type2\t1\t8\t1.0\t3\t3\t15.999\tOxygen\tO\n\
    112112#Ion_TypeNr._Nr.R[0]\tR[1]\tR[2]\tMoveType (0 MoveIon, 1 FixedIon)\n\
    113 Ion_Type2_1\t0.000000000\t0.000000000\t0.000000000\t0 # molecule nr 0\n\
     113Ion_Type2_1\t1.000000000\t0.000000000\t0.000000000\t0 # molecule nr 0\n\
    114114Ion_Type1_1\t0.758602\t0.000000000\t0.504284\t0 # molecule nr 1\n\
    115115Ion_Type1_2\t0.758602\t0.000000000\t-0.504284\t0 # molecule nr 2\n";

  • src/config.cpp

    r03c77c r6a465e  
    2121#include <stdio.h>
    2222#include <cstring>
     23#include <iostream>
     24#include <boost/tokenizer.hpp>
     25#include <string>
    2326
    2427//#include "Actions/FragmentationAction/SubgraphDissectionAction.hpp"
    … …  
    457460  int MaxTypes = 0;
    458461  const element *elementhash[MAX_ELEMENTS];
    459   char name[MAX_ELEMENTS];
    460   char keyword[MAX_ELEMENTS];
     462  char name[MAXSTRINGSIZE];
     463  char keyword[MAXSTRINGSIZE];
    461464  int Z = -1;
    462465  int No[MAX_ELEMENTS];
    463   int verbose = 0;
    464   Vector tempVector;
    465   int _fixedion;
     466  int verbose = DoLog(4);
    466467  double value[3];
    467468
    … …  
    487488      NoAtoms += No[i];
    488489    }
    489     int repetition = 0; // which repeated keyword shall be read
     490    int repetition = -1; // which repeated keyword shall be read
    490491
    491492    // sort the lines via the LineMapping
    … …  
    499500    //Log() << Verbose(0) << FileBuffer->buffer[ FileBuffer->LineMapping[FileBuffer->CurrentLine]];
    500501    FileBuffer->MapIonTypesInBuffer(NoAtoms);
    501     //for (int i=0; i<(NoAtoms < 100 ? NoAtoms : 100 < 100 ? NoAtoms : 100);++i) {
    502     //  Log() << Verbose(0) << FileBuffer->buffer[ FileBuffer->LineMapping[FileBuffer->CurrentLine+i]];
    503     //}
     502    for (int i=FileBuffer->CurrentLine; i<FileBuffer->NoLines;++i) {
     503      Log() << Verbose(0) << FileBuffer->buffer[ FileBuffer->LineMapping[i] ];
     504    }
    504505
    505506    map<int, atom *> AtomList[MaxTypes];
    506507    map<int, atom *> LinearList;
    507508    atom *neues = NULL;
    508     Vector position;
    509     if (!FastParsing) {
    510       // parse in trajectories
    511       bool status = true;
    512       while (status) {
    513         DoLog(0) && (Log() << Verbose(0) << "Currently parsing MD step " << repetition << "." << endl);
    514         for (int i=0; i < MaxTypes; i++) {
    515           sprintf(name,"Ion_Type%i",i+1);
    516           for(int j=0;j<No[i];j++) {
    517             sprintf(keyword,"%s_%i",name, j+1);
    518             if (repetition == 0) {
    519               neues = World::getInstance().createAtom();
    520               AtomList[i][j] = neues;
    521               LinearList[ FileBuffer->LineMapping[FileBuffer->CurrentLine] ] = neues;
    522               neues->setType(elementhash[i]); // find element type
    523             } else
    524               neues = AtomList[i][j];
    525             status = (status &&
    526                     ParseForParameter(verbose,FileBuffer, keyword, 0, 1, 1, double_type, &position[0], 1, (repetition == 0) ? critical : optional) &&
    527                     ParseForParameter(verbose,FileBuffer, keyword, 0, 2, 1, double_type, &position[1], 1, (repetition == 0) ? critical : optional) &&
    528                     ParseForParameter(verbose,FileBuffer, keyword, 0, 3, 1, double_type, &position[2], 1, (repetition == 0) ? critical : optional) &&
    529                     ParseForParameter(verbose,FileBuffer, keyword, 0, 4, 1, int_type, &_fixedion, 1, (repetition == 0) ? critical : optional));
    530             if (!status)
     509    Vector tempVector;
     510    int _fixedion;
     511
     512    typedef boost::tokenizer<boost::char_separator<char> >
     513        tokenizer;
     514    boost::char_separator<char> sep("\t ");
     515    ConvertTo<double> toDouble;
     516    ConvertTo<int> toInt;
     517
     518    for (int i=0; i < MaxTypes; i++) {
     519      for(int j=0;j<No[i];j++) {
     520        int step = 0;
     521        std::stringstream keyword_stream;
     522        keyword_stream << "Ion_Type" << i+1 << "_" << j+1;
     523        const std::string keyword = keyword_stream.str();
     524        DoLog(3) && (Log() << Verbose(3) << "INFO: Parsing for " << keyword << "." << std::endl);
     525        while (true) {
     526          const std::string line(FileBuffer->buffer[ FileBuffer->LineMapping[FileBuffer->CurrentLine] ]);
     527          const std::string line_without_comment = line.substr(0,line.find("#"));
     528          tokenizer tokens(line_without_comment, sep);
     529          if (tokens.begin() != tokens.end()) {
     530            tokenizer::iterator tok_iter = tokens.begin();
     531            const std::string token = *tok_iter++;
     532            if (token == keyword) {
     533              DoLog(3) && (Log() << Verbose(3) << "INFO: Found keyword " << keyword << " in line " << FileBuffer->CurrentLine << std::endl);
     534              if (step == 0) {
     535                neues = World::getInstance().createAtom();
     536                AtomList[i][j] = neues;
     537                std::cout << "filling LinearList [ (FileBuffer->LineMapping[" << FileBuffer->CurrentLine << "]) = " << FileBuffer->LineMapping[FileBuffer->CurrentLine] << " with " << neues << endl;
     538                LinearList[ FileBuffer->LineMapping[FileBuffer->CurrentLine] ] = neues;
     539                neues->setType(elementhash[i]); // find element type
     540              } else
     541                neues = AtomList[i][j];
     542
     543              // count tokens
     544              size_t tokens_size = 0;
     545              for (tokenizer::iterator tokiter = tokens.begin(); tokiter != tokens.end(); ++tokiter)
     546                ++tokens_size;
     547              DoLog(3) && (Log() << Verbose(3) << "INFO: Line contains " << tokens_size << " tokens." << std::endl);
     548              // and parse
     549              if (tokens_size >= 5) { // only AtomicPosition and FixedIon
     550                DoLog(3) && (Log() << Verbose(3) << "INFO: Parsing AtomicPosition and FixedIon" << std::endl);
     551                for (int i=0;i<NDIM;++i)
     552                  tempVector[i] = toDouble(*tok_iter++);
     553                neues->setPositionAtStep(step, tempVector);
     554                _fixedion = toInt(*tok_iter++);
     555                neues->setFixedIon(_fixedion == 1);
     556              }
     557              if (tokens_size >= 8) { // AtomicVelocity
     558                DoLog(3) && (Log() << Verbose(3) << "INFO: Parsing AtomicVelocity" << std::endl);
     559                for (int i=0;i<NDIM;++i)
     560                  tempVector[i] = toDouble(*tok_iter++);
     561                neues->setAtomicVelocityAtStep(step, tempVector);
     562              }
     563              if (tokens_size >= 11) {  // AtomicForce
     564                DoLog(3) && (Log() << Verbose(3) << "INFO: Parsing AtomicForce" << std::endl);
     565                for (int i=0;i<NDIM;++i)
     566                  tempVector[i] = toDouble(*tok_iter++);
     567                neues->setAtomicForceAtStep(step, tempVector);
     568              }
     569              std::stringstream output;
     570              output << "Parsed position of step " << (step+1) << ": ";
     571              output << neues->getPositionAtStep(step);          // next step
     572              output << "\t";
     573              output << (neues->getFixedIon() ? "true" : "false");
     574              output << "\t";
     575              output << neues->getAtomicVelocityAtStep(step);          // next step
     576              output << "\t";
     577              output << neues->getAtomicForceAtStep(step);          // next step
     578              DoLog(2) && (Log() << Verbose(2) << output.str() << endl);
     579
     580              step++;
     581            } else {
     582              if ((repetition > step) || (repetition == -1))
     583                repetition = step;
    531584              break;
    532 
    533             // check size of vectors
    534             if (neues->getTrajectorySize() <= (unsigned int)(repetition)) {
    535               //Log() << Verbose(0) << "Increasing size for trajectory array of " << keyword << " to " << (repetition+10) << "." << endl;
    536               neues->ResizeTrajectory(repetition+1);
    537               neues->ResizeTrajectory(repetition+1);
    538               neues->ResizeTrajectory(repetition+1);
    539585            }
    540             neues->setFixedIon(_fixedion);
    541             neues->setPositionAtStep(repetition,position);
    542 
    543             // parse velocities if present
    544             tempVector.Zero();
    545             if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 5, 1, double_type, &tempVector[0], 1,optional))
    546               tempVector[0] = 0.;
    547             if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 6, 1, double_type, &tempVector[1], 1,optional))
    548               tempVector[1] = 0.;
    549             if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 7, 1, double_type, &tempVector[2], 1,optional))
    550               tempVector[2] = 0.;
    551             neues->setAtomicVelocityAtStep(repetition, tempVector);
    552 
    553             // parse forces if present
    554             tempVector.Zero();
    555             if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 8, 1, double_type, &tempVector[0], 1,optional))
    556               tempVector[0] = 0.;
    557             if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 9, 1, double_type, &tempVector[1], 1,optional))
    558               tempVector[1] = 0.;
    559             if(!ParseForParameter(verbose,FileBuffer, keyword, 1, 10, 1, double_type, &tempVector[2], 1,optional))
    560               tempVector[2] = 0.;
    561             neues->setAtomicForceAtStep(repetition, tempVector);
    562 
    563   //            Log() << Verbose(0) << "Parsed position of step " << (repetition) << ": (";
    564   //            Log() << Verbose(0) << neues->getPosition(repetition) << " ";          // next step
    565   //            Log() << Verbose(0) << neues->getAtomicVelocity(repetition) << " ";          // next step
    566   //            Log() << Verbose(0) << neues->getAtomicForce(repetition) << " ";          // next step
    567   //            Log() << Verbose(0) << ")" << endl;
    568586          }
    569         }
    570         repetition++;
    571       }
    572       repetition--;
    573       DoLog(0) && (Log() << Verbose(0) << "Found " << repetition << " trajectory steps." << endl);
    574       if (repetition <= 1)  // if onyl one step, desactivate use of trajectories
    575         mol->MDSteps = 0;
    576       else
    577         mol->MDSteps = repetition;
    578     } else {
    579       // 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)
    580       repetition = 0;
    581       while ( ParseForParameter(verbose,FileBuffer, "Ion_Type1_1", 0, 1, 1, double_type, &value[0], repetition, (repetition == 0) ? critical : optional) &&
    582               ParseForParameter(verbose,FileBuffer, "Ion_Type1_1", 0, 2, 1, double_type, &value[1], repetition, (repetition == 0) ? critical : optional) &&
    583               ParseForParameter(verbose,FileBuffer, "Ion_Type1_1", 0, 3, 1, double_type, &value[2], repetition, (repetition == 0) ? critical : optional))
    584         repetition++;
    585       DoLog(0) && (Log() << Verbose(0) << "I found " << repetition << " times the keyword Ion_Type1_1." << endl);
    586       // parse in molecule coordinates
    587       for (int i=0; i < MaxTypes; i++) {
    588         sprintf(name,"Ion_Type%i",i+1);
    589         for(int j=0;j<No[i];j++) {
    590           sprintf(keyword,"%s_%i",name, j+1);
    591           if (repetition == 0) {
    592             neues = World::getInstance().createAtom();
    593             AtomList[i][j] = neues;
    594             LinearList[ FileBuffer->LineMapping[FileBuffer->CurrentLine] ] = neues;
    595             neues->setType(elementhash[i]); // find element type
    596           } else
    597             neues = AtomList[i][j];
    598           // then parse for each atom the coordinates as often as present
    599           tempVector.Zero();
    600           ParseForParameter(verbose,FileBuffer, keyword, 0, 1, 1, double_type, &tempVector[0], repetition,critical);
    601           ParseForParameter(verbose,FileBuffer, keyword, 0, 2, 1, double_type, &tempVector[1], repetition,critical);
    602           ParseForParameter(verbose,FileBuffer, keyword, 0, 3, 1, double_type, &tempVector[2], repetition,critical);
    603           neues->setPosition(tempVector);
    604           // fixed ion
    605           ParseForParameter(verbose,FileBuffer, keyword, 0, 4, 1, int_type, &_fixedion, repetition,critical);
    606           neues->setFixedIon(_fixedion);
    607           // and velocity
    608           tempVector.Zero();
    609           if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 5, 1, double_type, &tempVector[0], repetition,optional))
    610             tempVector[0] = 0.;
    611           if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 6, 1, double_type, &tempVector[1], repetition,optional))
    612             tempVector[1] = 0.;
    613           if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 7, 1, double_type, &tempVector[2], repetition,optional))
    614             tempVector[2] = 0.;
    615           neues->setAtomicVelocity(tempVector);
    616           // here we don't care if forces are present (last in trajectories is always equal to current position)
    617           neues->setType(elementhash[i]); // find element type
    618           mol->AddAtom(neues);
     587          FileBuffer->CurrentLine++;
    619588        }
    620589      }
    621590    }
     591
     592    if (repetition <= 1)  // if onyl one step, desactivate use of trajectories
     593      mol->MDSteps = 0;
     594    else {
     595      DoLog(0) && (Log() << Verbose(0) << "Found " << repetition << " trajectory step(s)." << endl);
     596      mol->MDSteps = repetition;
     597    }
     598
     599//    if (!FastParsing) {
     600//      // parse in trajectories
     601//      bool status = true;
     602//      while (status) {
     603//        DoLog(0) && (Log() << Verbose(0) << "Currently checking on MD step " << repetition+1 << "." << endl);
     604//        for (int i=0; i < MaxTypes; i++) {
     605//          sprintf(name,"Ion_Type%i",i+1);
     606//          for(int j=0;j<No[i];j++) {
     607//            sprintf(keyword,"%s_%i",name, j+1);
     608//            DoLog(3) && (Log() << Verbose(3) << "Looking for " << keyword << " of " << (repetition) << " repetition." << std::endl);
     609//            DoLog(3) && (Log() << Verbose(3) << "INFO: Parsing AtomicPosition." << std::endl);
     610//            for (int k=0;k<NDIM;++k) { // repetition=1 is correct, as we advance eventually by sequential=1!
     611//              status = status && ParseForParameter(verbose,FileBuffer, (const char*)keyword, 0, 1+k, 1, double_type, &tempVector[k], 1, (repetition == 0) ? critical : optional);
     612//            }
     613//            if (!status)
     614//              break;
     615//
     616//            if (repetition == 0) {
     617//              neues = World::getInstance().createAtom();
     618//              AtomList[i][j] = neues;
     619//              std::cout << "filling LinearList [ (FileBuffer->LineMapping[" << FileBuffer->CurrentLine << "]) = " << FileBuffer->LineMapping[FileBuffer->CurrentLine] << " with " << neues << endl;
     620//              LinearList[ FileBuffer->LineMapping[FileBuffer->CurrentLine] ] = neues;
     621//              neues->setType(elementhash[i]); // find element type
     622//            } else
     623//              neues = AtomList[i][j];
     624//
     625//            DoLog(3) && (Log() << Verbose(3) << "INFO: Parsing FixedIon." << std::endl);
     626//            status = status && ParseForParameter(verbose,FileBuffer, (const char*)keyword, 0, 4, 1, int_type, &_fixedion, 1, (repetition == 0) ? critical : optional);
     627//            neues->setFixedIon(_fixedion == 1);
     628//
     629//            // check size of vectors
     630//            if (neues->getTrajectorySize() <= (unsigned int)(repetition)) {
     631//              neues->ResizeTrajectory(repetition+10);
     632//              //Log() << Verbose(0) << "Increasing size for trajectory array of " << keyword << " to " << (repetition+10) << "." << endl;
     633//            }
     634//
     635//            // put into trajectories list
     636//            neues->setPosition(repetition, tempVector);
     637//
     638//            // parse velocities if present
     639//            DoLog(3) && (Log() << Verbose(3) << "INFO: Parsing AtomicVelocity." << std::endl);
     640//            bool velocityStatus = true;
     641//            for (int k=0;k<NDIM;++k)
     642//              velocityStatus = velocityStatus && ParseForParameter(verbose,FileBuffer, (const char*)keyword, 0, 5+k, 1, double_type, &tempVector[k], 1,optional);
     643//            if (!velocityStatus) {
     644//              neues->setAtomicVelocity(repetition, zeroVec);
     645//            } else
     646//              neues->setAtomicVelocity(repetition, tempVector);
     647//
     648//            // parse forces if present
     649//            DoLog(3) && (Log() << Verbose(3) << "INFO: Parsing AtomicForce." << std::endl);
     650//            bool forceStatus = true;
     651//            for (int k=0;k<NDIM;++k)
     652//              forceStatus = forceStatus && ParseForParameter(verbose,FileBuffer, (const char*)keyword, (k==(NDIM-1)) ? 1 : 0, 8+k, 1, double_type, &tempVector[k], 1,optional);
     653//            if (!forceStatus) {
     654//              ++FileBuffer->CurrentLine;  // as above sequential=1 did not apply due to end of file
     655//              neues->setAtomicForce(repetition, zeroVec);
     656//            } else {
     657//              neues->setAtomicForce(repetition, tempVector);
     658//            }
     659//
     660//            std::stringstream output;
     661//            output << "Parsed position of step " << (repetition+1) << ": ";
     662//            output << neues->getPosition(repetition);          // next step
     663//            output << "\t";
     664//            output << (neues->getFixedIon() ? "true" : "false");
     665//            output << "\t";
     666//            output << neues->getAtomicVelocity(repetition);          // next step
     667//            output << "\t";
     668//            output << neues->getAtomicForce(repetition);          // next step
     669//            DoLog(2) && (Log() << Verbose(2) << output.str() << endl);
     670//          }
     671//        }
     672//        repetition++;
     673//      }
     674//      repetition--;
     675//      if (repetition <= 1)  // if onyl one step, desactivate use of trajectories
     676//        mol->MDSteps = 0;
     677//      else {
     678//        DoLog(0) && (Log() << Verbose(0) << "Found " << repetition+1 << " trajectory step(s)." << endl);
     679//        mol->MDSteps = repetition;
     680//      }
     681//    } else {
     682//      // 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)
     683//      repetition = 0;
     684//      while ( ParseForParameter(verbose,FileBuffer, "Ion_Type1_1", 0, 1, 1, double_type, &value[0], repetition, (repetition == 0) ? critical : optional) &&
     685//              ParseForParameter(verbose,FileBuffer, "Ion_Type1_1", 0, 2, 1, double_type, &value[1], repetition, (repetition == 0) ? critical : optional) &&
     686//              ParseForParameter(verbose,FileBuffer, "Ion_Type1_1", 0, 3, 1, double_type, &value[2], repetition, (repetition == 0) ? critical : optional))
     687//        repetition++;
     688//      DoLog(0) && (Log() << Verbose(0) << "I found " << repetition << " times the keyword Ion_Type1_1." << endl);
     689//      // parse in molecule coordinates
     690//      for (int i=0; i < MaxTypes; i++) {
     691//        sprintf(name,"Ion_Type%i",i+1);
     692//        for(int j=0;j<No[i];j++) {
     693//          sprintf(keyword,"%s_%i",name, j+1);
     694//          if (repetition == 0) {
     695//            neues = World::getInstance().createAtom();
     696//            AtomList[i][j] = neues;
     697//            LinearList[ FileBuffer->LineMapping[FileBuffer->CurrentLine] ] = neues;
     698//            neues->setType(elementhash[i]); // find element type
     699//          } else
     700//            neues = AtomList[i][j];
     701//          // then parse for each atom the coordinates as often as present
     702//          ParseForParameter(verbose,FileBuffer, keyword, 0, 1, 1, double_type, &tempVector[0], repetition,critical);
     703//          ParseForParameter(verbose,FileBuffer, keyword, 0, 2, 1, double_type, &tempVector[1], repetition,critical);
     704//          ParseForParameter(verbose,FileBuffer, keyword, 0, 3, 1, double_type, &tempVector[2], repetition,critical);
     705//          neues->setPosition(tempVector);
     706//          bool _fixedion;
     707//          ParseForParameter(verbose,FileBuffer, keyword, 0, 4, 1, int_type, &_fixedion, repetition,critical);
     708//          neues->setFixedIon(_fixedion);
     709//          bool velocityStatus = true;
     710//          velocityStatus = velocityStatus &&
     711//              ParseForParameter(verbose,FileBuffer, keyword, 0, 5, 1, double_type, &tempVector[0], repetition,optional) &&
     712//              ParseForParameter(verbose,FileBuffer, keyword, 0, 6, 1, double_type, &tempVector[1], repetition,optional) &&
     713//              ParseForParameter(verbose,FileBuffer, keyword, 1, 7, 1, double_type, &tempVector[2], repetition,optional);
     714//          if (!velocityStatus)
     715//            neues->setAtomicVelocity(zeroVec);
     716//          else
     717//            neues->setAtomicVelocity(tempVector);
     718//
     719//          // here we don't care if forces are present (last in trajectories is always equal to current position)
     720//          neues->setType(elementhash[i]); // find element type
     721//          mol->AddAtom(neues);
     722//        }
     723//      }
     724//    }
    622725    // put atoms into the molecule in their original order
    623726    for(map<int, atom*>::iterator runner = LinearList.begin(); runner != LinearList.end(); ++runner) {
    … …  
    14581561  char *dummy1 = NULL;
    14591562  char *dummy = NULL;    // pointers in the line that is read in per step
    1460 
    1461   //fprintf(stderr,"Parsing for %s\n",name);
     1563  char *free_dummy = NULL;
     1564
     1565  if (verbose) fprintf(stderr,"Begin of Parsing for %s\n",name);
    14621566  if (repetition == 0)
    14631567    //Error(SomeError, "ParseForParameter(): argument repetition must not be 0!");
    14641568    return 0;
    14651569
    1466   int line = 0; // marks line where parameter was found
    14671570  int found = (type >= grid) ? 0 : (-yth + 1);  // marks if yth parameter name was found
    14681571  while((found != repetition)) {
    14691572    dummy1 = dummy = NULL;
    14701573    do {
    1471       dummy1 = FileBuffer->buffer[ FileBuffer->LineMapping[FileBuffer->CurrentLine++] ];
     1574      free_dummy = dummy1 = FileBuffer->buffer[ FileBuffer->LineMapping[FileBuffer->CurrentLine++] ];
    14721575      if (FileBuffer->CurrentLine >= FileBuffer->NoLines) {
    14731576        if ((critical) && (found == 0)) {
    … …  
    14761579          exit(255);
    14771580        } else {
     1581          //fprintf(stdout,"Rewinding to OldCurrentLine due to search till end of file.\n");
    14781582          FileBuffer->CurrentLine = OldCurrentLine; // rewind to start position
    14791583          return 0;
    … …  
    14811585      }
    14821586      if (dummy1 == NULL) {
    1483         if (verbose) fprintf(stderr,"Error reading line %i\n",line);
     1587        if (verbose) fprintf(stderr,"Error reading line %i\n",FileBuffer->CurrentLine);
    14841588      } else {
    1485         //fprintf(stderr,"Now parsing the line %i: %s\n", line, dummy1);
     1589        if (verbose) fprintf(stderr,"Now parsing the line %i: %s\n", FileBuffer->CurrentLine, dummy1);
    14861590      }
    1487       line++;
     1591      //FileBuffer->CurrentLine++;
    14881592    } while (dummy1 != NULL && ((dummy1[0] == '#') || (dummy1[0] == '\0'))); // skip commentary and empty lines
    14891593
    … …  
    15011605        //Error(FileOpenParams, NULL);
    15021606      } else {
    1503         //fprintf(stderr,"found tab at %i\n",(char *)dummy-(char *)dummy1);
     1607        if (verbose) fprintf(stderr,"found tab at line %i at position %li\n",FileBuffer->CurrentLine, (char *)dummy-(char *)dummy1);
    15041608      }
    15051609    } else dummy = dummy1;
    … …  
    15081612    if ((name == NULL) || (((dummy-dummy1 >= 3) && (strncmp(dummy1, name, strlen(name)) == 0)) && ((unsigned int)(dummy-dummy1) == strlen(name)))) {
    15091613      found++; // found the parameter!
    1510       //fprintf(stderr,"found %s at line %i between %i and %i\n", name, line, dummy1, dummy);
     1614      if (verbose) fprintf(stderr,"found %s at line %i between %li and %li\n", name, FileBuffer->CurrentLine, (unsigned long)dummy1, (unsigned long)dummy);
    15111615
    15121616      if (found == repetition) {
    … …  
    15231627                  exit(255);
    15241628                } else {
     1629                  //fprintf(stdout,"Rewinding to OldCurrentLine due to search till end of line.\n");
    15251630                  FileBuffer->CurrentLine = OldCurrentLine; // rewind to start position
    15261631                  return 0;
    … …  
    15281633              }
    15291634              if (dummy1 == NULL) {
    1530                 if (verbose) fprintf(stderr,"Error reading line %i\n", line);
     1635                if (verbose) fprintf(stderr,"Error reading line %i\n", FileBuffer->CurrentLine);
    15311636              } else {
    1532                 //fprintf(stderr,"Reading next line %i: %s\n", line, dummy1);
     1637                if (verbose) fprintf(stderr,"Reading next line %i: %s\n", FileBuffer->CurrentLine, dummy1);
    15331638              }
    1534               line++;
     1639              //FileBuffer->CurrentLine++;
    15351640            } while ((dummy1 != NULL) && ((dummy1[0] == '#') || (dummy1[0] == '\n')));
    15361641            dummy = dummy1;
    … …  
    15571662                if ((j < yth-1) && (type < 4)) {  // check if xth value or not yet
    15581663                  if (critical) {
    1559                     if (verbose) fprintf(stderr,"Error: EoL at %i and still missing %i value(s) for parameter %s\n", line, yth-j, name);
     1664                    if (verbose) fprintf(stderr,"Error: EoL at %i and still missing %i value(s) for parameter %s\n", FileBuffer->CurrentLine, yth-j, name);
    15601665                    //return 0;
    15611666                    exit(255);
    … …  
    15631668                  } else {
    15641669                    if (!sequential) { // here we need it!
     1670                      //fprintf(stdout,"Rewinding to OldCurrentLine due to end of line and sequential %d.\n", sequential);
    15651671                      FileBuffer->CurrentLine = OldCurrentLine; // rewind to start position
    15661672                    }
    … …  
    15691675                }
    15701676              } else {
    1571                 //fprintf(stderr,"found tab at %i\n",(char *)dummy-(char *)free_dummy);
     1677                if (verbose) fprintf(stderr,"found tab at line %i at position %li\n",FileBuffer->CurrentLine, (char *)dummy-(char *)free_dummy);
    15721678              }
    15731679              if (*dummy1 == '#') {
    … …  
    15751681                //if (verbose) fprintf(stderr,"Error: '#' at %i and still missing %i value(s) for parameter %s\n", line, yth-j, name);
    15761682                if (!sequential) { // here we need it!
     1683                  //fprintf(stdout,"Rewinding to OldCurrentLine due to comment and sequential %d.\n", sequential);
    15771684                  FileBuffer->CurrentLine = OldCurrentLine; // rewind to start position
    15781685                }
    15791686                return 0;
    15801687              }
    1581               //fprintf(stderr,"value from %i to %i\n",(char *)dummy1-(char *)free_dummy,(char *)dummy-(char *)free_dummy);
     1688              if (verbose) fprintf(stderr,"value from %li to %li\n",(char *)dummy1-(char *)free_dummy,(char *)dummy-(char *)free_dummy);
    15821689              switch(type) {
    15831690                case (row_int):
    … …  
    16321739  if ((type >= row_int) && (verbose)) fprintf(stderr,"\n");
    16331740  if (!sequential) {
     1741    //fprintf(stdout,"Rewinding to OldCurrentLine due to sequential %d.\n", sequential);
    16341742    FileBuffer->CurrentLine = OldCurrentLine; // rewind to start position
    16351743  }
    1636   //fprintf(stderr, "End of Parsing\n\n");
     1744  if (verbose) fprintf(stderr, "End of Parsing for %s\n\n",name);
    16371745
    16381746  return (found); // true if found, false if not

  • tests/regression/Molecules/SaveTemperature/post/test.ekin

    r03c77c r6a465e  
    11# Step Temperature [K] Temperature [a.u.]
    220       139247  0.44097
    3 1       25464.1 0.08064
     31       139247  0.44097
    442       0       0
     53       0       0
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