Changeset d1df9b


Ignore:
Timestamp:
Jul 10, 2009, 9:01:40 PM (16 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:
205ccd
Parents:
6cb412
git-author:
Frederik Heber <heber@…> (07/10/09 20:21:12)
git-committer:
Frederik Heber <heber@…> (07/10/09 21:01:40)
Message:

new class ConfigFileBuffer and new overloaded function ParseForParaneter() based on this buffer

  • the problem is that we need to use molecuilder for the periodic translating of atoms in a xzy file. However, molecuilder resorts them per element. This destroty the id mapping needed for the DBOND file. The storing was corrected, but also the loading relies on this order.
  • To solve this, we have to pull off quite something: Parse file into buffer, resort the Ion_Type ones (via a map only), load atoms and then put them into the molecule in the original order!
  • Hence, in config::Load we also have a LinearList (map<int, atom*>) in order to add the atoms after the scanning in their original order into the molecule.
  • class ConfigFileBuffer parses a config file line-wise into a buffer and allows for resorting (via a map) of lines containing key_word Ion_Type.
  • BUGFIX: molecule::Output...() were writing the wrong elements, as they were numbered during the output and not before in ascending order! (I.e. if the first atom is Si, but there is also H present, then this Si would become Ion_Type1_1 instead of Ion_Type2_1, because the elements are still sorted by their Z value, hence Ion_Type1 is H!)

This is basically tested and seems to work properly

Location:
src
Files:
3 edited

Legend:

Unmodified
Added
Removed

  • src/config.cpp

    r6cb412 rd1df9b  
    66
    77#include "molecules.hpp"
     8
     9/******************************** Functions for class ConfigFileBuffer **********************/
     10
     11/** Structure containing compare function for Ion_Type sorting.
     12 */
     13struct IonTypeCompare {
     14  bool operator()(const char* s1, const char *s2) const {
     15    char number1[8];
     16    char number2[8];
     17    char *dummy1, *dummy2;
     18    //cout << s1 << "  " << s2 << endl;
     19    dummy1 = strchr(s1, '_')+sizeof(char)*5;  // go just after "Ion_Type"
     20    dummy2 = strchr(dummy1, '_');
     21    strncpy(number1, dummy1, dummy2-dummy1); // copy the number
     22    number1[dummy2-dummy1]='\0';
     23    dummy1 = strchr(s2, '_')+sizeof(char)*5;  // go just after "Ion_Type"
     24    dummy2 = strchr(dummy1, '_');
     25    strncpy(number2, dummy1, dummy2-dummy1); // copy the number
     26    number2[dummy2-dummy1]='\0';
     27    if (atoi(number1) != atoi(number2))
     28      return (atoi(number1) < atoi(number2));
     29    else {
     30      dummy1 = strchr(s1, '_')+sizeof(char);
     31      dummy1 = strchr(dummy1, '_')+sizeof(char);
     32      dummy2 = strchr(dummy1, ' ') < strchr(dummy1, '\t') ? strchr(dummy1, ' ') : strchr(dummy1, '\t');
     33      strncpy(number1, dummy1, dummy2-dummy1); // copy the number
     34      number1[dummy2-dummy1]='\0';
     35      dummy1 = strchr(s2, '_')+sizeof(char);
     36      dummy1 = strchr(dummy1, '_')+sizeof(char);
     37      dummy2 = strchr(dummy1, ' ') < strchr(dummy1, '\t') ? strchr(dummy1, ' ') : strchr(dummy1, '\t');
     38      strncpy(number2, dummy1, dummy2-dummy1); // copy the number
     39      number2[dummy2-dummy1]='\0';
     40      return (atoi(number1) < atoi(number2));
     41    }
     42  }
     43};
     44
     45/** Constructor for ConfigFileBuffer class.
     46 */
     47ConfigFileBuffer::ConfigFileBuffer()
     48{
     49  NoLines = 0;
     50  CurrentLine = 0;
     51  buffer = NULL;
     52  LineMapping = NULL;
     53}
     54
     55/** Constructor for ConfigFileBuffer class with filename to be parsed.
     56 * \param *filename file name
     57 */
     58ConfigFileBuffer::ConfigFileBuffer(char *filename)
     59{
     60  NoLines = 0;
     61  CurrentLine = 0;
     62  buffer = NULL;
     63  LineMapping = NULL;
     64  ifstream *file = NULL;
     65  char line[MAXSTRINGSIZE];
     66
     67  // prescan number of lines
     68  file= new ifstream(filename);
     69  if (file == NULL) {
     70    cerr << "ERROR: config file " << filename << " missing!" << endl;
     71    return;
     72  }
     73  NoLines = 0; // we're overcounting by one
     74  long file_position = file->tellg(); // mark current position
     75  do {
     76    file->getline(line, 256);
     77    NoLines++;
     78  } while (!file->eof());
     79  file->clear();
     80  file->seekg(file_position, ios::beg);
     81  cout << Verbose(1) << NoLines-1 << " lines were recognized." << endl;
     82
     83  // allocate buffer's 1st dimension
     84  if (buffer != NULL) {
     85    cerr << "ERROR: FileBuffer->buffer is not NULL!" << endl;
     86    return;
     87  } else
     88    buffer = (char **) Malloc(sizeof(char *)*NoLines, "ConfigFileBuffer::ConfigFileBuffer: **buffer");
     89
     90  // scan each line and put into buffer
     91  int lines=0;
     92  int i;
     93  do {
     94    buffer[lines] = (char *) Malloc(sizeof(char)*MAXSTRINGSIZE, "ConfigFileBuffer::ConfigFileBuffer: *buffer[]");
     95    file->getline(buffer[lines], MAXSTRINGSIZE-1);
     96    i = strlen(buffer[lines]);
     97    buffer[lines][i] = '\n';
     98    buffer[lines][i+1] = '\0';
     99    lines++;
     100  } while((!file->eof()) && (lines < NoLines));
     101  cout << Verbose(1) << lines-1 << " lines were read into the buffer." << endl;
     102
     103  // close and exit
     104  file->close();
     105  file->clear();
     106  delete(file);
     107}
     108
     109/** Destructor for ConfigFileBuffer class.
     110 */
     111ConfigFileBuffer::~ConfigFileBuffer()
     112{
     113  for(int i=0;i<NoLines;++i)
     114    Free((void **)&buffer[i], "ConfigFileBuffer::~ConfigFileBuffer: *buffer[]");
     115  Free((void **)&buffer, "ConfigFileBuffer::~ConfigFileBuffer: **buffer");
     116  Free((void **)&LineMapping, "ConfigFileBuffer::~ConfigFileBuffer: *LineMapping");
     117}
     118
     119
     120/** Create trivial mapping.
     121 */
     122void ConfigFileBuffer::InitMapping()
     123{
     124  LineMapping = (int *) Malloc(sizeof(int)*NoLines, "ConfigFileBuffer::InitMapping: *LineMapping");
     125  for (int i=0;i<NoLines;i++)
     126    LineMapping[i] = i;
     127}
     128
     129/** Creates a mapping for the \a *FileBuffer's lines containing the Ion_Type keyword such that they are sorted.
     130 * \a *map on return contains a list of NoAtom entries such that going through the list, yields indices to the
     131 * lines in \a *FileBuffer in a sorted manner of the Ion_Type?_? keywords. We assume that ConfigFileBuffer::CurrentLine
     132 * points to first Ion_Type entry.
     133 * \param *FileBuffer pointer to buffer structure
     134 * \param NoAtoms of subsequent lines to look at
     135 */
     136void ConfigFileBuffer::MapIonTypesInBuffer(int NoAtoms)
     137{
     138  map<const char *, int, IonTypeCompare> LineList;
     139  if (LineMapping == NULL) {
     140    cerr << "map pointer is NULL: " << LineMapping << endl;
     141    return;
     142  }
     143
     144  // put all into hashed map
     145  for (int i=0; i<NoAtoms; ++i) {
     146    LineList.insert(pair<const char *, int> (buffer[CurrentLine+i], CurrentLine+i));
     147  }
     148
     149  // fill map
     150  int nr=0;
     151  for (map<const char *, int, IonTypeCompare>::iterator runner = LineList.begin(); runner != LineList.end(); ++runner) {
     152    if (CurrentLine+nr < NoLines)
     153      LineMapping[CurrentLine+(nr++)] = runner->second;
     154    else
     155      cerr << "config::MapIonTypesInBuffer - NoAtoms is wrong: We are past the end of the file!" << endl;
     156  }
     157}
    8158
    9159/************************************* Functions for class config ***************************/
    … …  
    447597void config::Load(char *filename, periodentafel *periode, molecule *mol)
    448598{
    449         ifstream *file = new ifstream(filename);
    450         if (file == NULL) {
    451                 cerr << "ERROR: config file " << filename << " missing!" << endl;
    452                 return;
    453         }
    454599        RetrieveConfigPathAndName(filename);
    455         // ParseParameters
     600
     601        // ParseParameterFile
     602  struct ConfigFileBuffer *FileBuffer = new ConfigFileBuffer(filename);
     603        FileBuffer->InitMapping();
    456604
    457605        /* Oeffne Hauptparameterdatei */
    … …  
    469617        /* Namen einlesen */
    470618
    471         ParseForParameter(verbose,file, "mainname", 0, 1, 1, string_type, (config::mainname), 1, critical);
    472         ParseForParameter(verbose,file, "defaultpath", 0, 1, 1, string_type, (config::defaultpath), 1, critical);
    473         ParseForParameter(verbose,file, "pseudopotpath", 0, 1, 1, string_type, (config::pseudopotpath), 1, critical);
    474         ParseForParameter(verbose,file,"ProcPEGamma", 0, 1, 1, int_type, &(config::ProcPEGamma), 1, critical);
    475         ParseForParameter(verbose,file,"ProcPEPsi", 0, 1, 1, int_type, &(config::ProcPEPsi), 1, critical);
    476 
    477         if (!ParseForParameter(verbose,file,"Seed", 0, 1, 1, int_type, &(config::Seed), 1, optional))
     619        ParseForParameter(verbose,FileBuffer, "mainname", 0, 1, 1, string_type, (config::mainname), 1, critical);
     620        ParseForParameter(verbose,FileBuffer, "defaultpath", 0, 1, 1, string_type, (config::defaultpath), 1, critical);
     621        ParseForParameter(verbose,FileBuffer, "pseudopotpath", 0, 1, 1, string_type, (config::pseudopotpath), 1, critical);
     622        ParseForParameter(verbose,FileBuffer,"ProcPEGamma", 0, 1, 1, int_type, &(config::ProcPEGamma), 1, critical);
     623        ParseForParameter(verbose,FileBuffer,"ProcPEPsi", 0, 1, 1, int_type, &(config::ProcPEPsi), 1, critical);
     624
     625        if (!ParseForParameter(verbose,FileBuffer,"Seed", 0, 1, 1, int_type, &(config::Seed), 1, optional))
    478626                config::Seed = 1;
    479627
    480         if(!ParseForParameter(verbose,file,"DoOutOrbitals", 0, 1, 1, int_type, &(config::DoOutOrbitals), 1, optional)) {
     628        if(!ParseForParameter(verbose,FileBuffer,"DoOutOrbitals", 0, 1, 1, int_type, &(config::DoOutOrbitals), 1, optional)) {
    481629                config::DoOutOrbitals = 0;
    482630        } else {
    … …  
    484632                if (config::DoOutOrbitals > 1) config::DoOutOrbitals = 1;
    485633        }
    486         ParseForParameter(verbose,file,"DoOutVis", 0, 1, 1, int_type, &(config::DoOutVis), 1, critical);
     634        ParseForParameter(verbose,FileBuffer,"DoOutVis", 0, 1, 1, int_type, &(config::DoOutVis), 1, critical);
    487635        if (config::DoOutVis < 0) config::DoOutVis = 0;
    488636        if (config::DoOutVis > 1) config::DoOutVis = 1;
    489         if (!ParseForParameter(verbose,file,"VectorPlane", 0, 1, 1, int_type, &(config::VectorPlane), 1, optional))
     637        if (!ParseForParameter(verbose,FileBuffer,"VectorPlane", 0, 1, 1, int_type, &(config::VectorPlane), 1, optional))
    490638                config::VectorPlane = -1;
    491         if (!ParseForParameter(verbose,file,"VectorCut", 0, 1, 1, double_type, &(config::VectorCut), 1, optional))
     639        if (!ParseForParameter(verbose,FileBuffer,"VectorCut", 0, 1, 1, double_type, &(config::VectorCut), 1, optional))
    492640                config::VectorCut = 0.;
    493         ParseForParameter(verbose,file,"DoOutMes", 0, 1, 1, int_type, &(config::DoOutMes), 1, critical);
     641        ParseForParameter(verbose,FileBuffer,"DoOutMes", 0, 1, 1, int_type, &(config::DoOutMes), 1, critical);
    494642        if (config::DoOutMes < 0) config::DoOutMes = 0;
    495643        if (config::DoOutMes > 1) config::DoOutMes = 1;
    496         if (!ParseForParameter(verbose,file,"DoOutCurr", 0, 1, 1, int_type, &(config::DoOutCurrent), 1, optional))
     644        if (!ParseForParameter(verbose,FileBuffer,"DoOutCurr", 0, 1, 1, int_type, &(config::DoOutCurrent), 1, optional))
    497645                config::DoOutCurrent = 0;
    498646        if (config::DoOutCurrent < 0) config::DoOutCurrent = 0;
    499647        if (config::DoOutCurrent > 1) config::DoOutCurrent = 1;
    500         ParseForParameter(verbose,file,"AddGramSch", 0, 1, 1, int_type, &(config::UseAddGramSch), 1, critical);
     648        ParseForParameter(verbose,FileBuffer,"AddGramSch", 0, 1, 1, int_type, &(config::UseAddGramSch), 1, critical);
    501649        if (config::UseAddGramSch < 0) config::UseAddGramSch = 0;
    502650        if (config::UseAddGramSch > 2) config::UseAddGramSch = 2;
    503         if(!ParseForParameter(verbose,file,"DoWannier", 0, 1, 1, int_type, &(config::DoWannier), 1, optional)) {
     651        if(!ParseForParameter(verbose,FileBuffer,"DoWannier", 0, 1, 1, int_type, &(config::DoWannier), 1, optional)) {
    504652                config::DoWannier = 0;
    505653        } else {
    … …  
    507655                if (config::DoWannier > 1) config::DoWannier = 1;
    508656        }
    509         if(!ParseForParameter(verbose,file,"CommonWannier", 0, 1, 1, int_type, &(config::CommonWannier), 1, optional)) {
     657        if(!ParseForParameter(verbose,FileBuffer,"CommonWannier", 0, 1, 1, int_type, &(config::CommonWannier), 1, optional)) {
    510658                config::CommonWannier = 0;
    511659        } else {
    … …  
    513661                if (config::CommonWannier > 4) config::CommonWannier = 4;
    514662        }
    515         if(!ParseForParameter(verbose,file,"SawtoothStart", 0, 1, 1, double_type, &(config::SawtoothStart), 1, optional)) {
     663        if(!ParseForParameter(verbose,FileBuffer,"SawtoothStart", 0, 1, 1, double_type, &(config::SawtoothStart), 1, optional)) {
    516664                config::SawtoothStart = 0.01;
    517665        } else {
    … …  
    520668        }
    521669
    522         ParseForParameter(verbose,file,"MaxOuterStep", 0, 1, 1, int_type, &(config::MaxOuterStep), 1, critical);
    523         if (!ParseForParameter(verbose,file,"Deltat", 0, 1, 1, double_type, &(config::Deltat), 1, optional))
     670        ParseForParameter(verbose,FileBuffer,"MaxOuterStep", 0, 1, 1, int_type, &(config::MaxOuterStep), 1, critical);
     671        if (!ParseForParameter(verbose,FileBuffer,"Deltat", 0, 1, 1, double_type, &(config::Deltat), 1, optional))
    524672                config::Deltat = 1;
    525         ParseForParameter(verbose,file,"OutVisStep", 0, 1, 1, int_type, &(config::OutVisStep), 1, optional);
    526         ParseForParameter(verbose,file,"OutSrcStep", 0, 1, 1, int_type, &(config::OutSrcStep), 1, optional);
    527         ParseForParameter(verbose,file,"TargetTemp", 0, 1, 1, double_type, &(config::TargetTemp), 1, optional);
    528         //ParseForParameter(verbose,file,"Thermostat", 0, 1, 1, int_type, &(config::ScaleTempStep), 1, optional);
    529         if (!ParseForParameter(verbose,file,"EpsWannier", 0, 1, 1, double_type, &(config::EpsWannier), 1, optional))
     673        ParseForParameter(verbose,FileBuffer,"OutVisStep", 0, 1, 1, int_type, &(config::OutVisStep), 1, optional);
     674        ParseForParameter(verbose,FileBuffer,"OutSrcStep", 0, 1, 1, int_type, &(config::OutSrcStep), 1, optional);
     675        ParseForParameter(verbose,FileBuffer,"TargetTemp", 0, 1, 1, double_type, &(config::TargetTemp), 1, optional);
     676        //ParseForParameter(verbose,FileBuffer,"Thermostat", 0, 1, 1, int_type, &(config::ScaleTempStep), 1, optional);
     677        if (!ParseForParameter(verbose,FileBuffer,"EpsWannier", 0, 1, 1, double_type, &(config::EpsWannier), 1, optional))
    530678                config::EpsWannier = 1e-8;
    531679
    532680        // stop conditions
    533681        //if (config::MaxOuterStep <= 0) config::MaxOuterStep = 1;
    534         ParseForParameter(verbose,file,"MaxPsiStep", 0, 1, 1, int_type, &(config::MaxPsiStep), 1, critical);
     682        ParseForParameter(verbose,FileBuffer,"MaxPsiStep", 0, 1, 1, int_type, &(config::MaxPsiStep), 1, critical);
    535683        if (config::MaxPsiStep <= 0) config::MaxPsiStep = 3;
    536684
    537         ParseForParameter(verbose,file,"MaxMinStep", 0, 1, 1, int_type, &(config::MaxMinStep), 1, critical);
    538         ParseForParameter(verbose,file,"RelEpsTotalE", 0, 1, 1, double_type, &(config::RelEpsTotalEnergy), 1, critical);
    539         ParseForParameter(verbose,file,"RelEpsKineticE", 0, 1, 1, double_type, &(config::RelEpsKineticEnergy), 1, critical);
    540         ParseForParameter(verbose,file,"MaxMinStopStep", 0, 1, 1, int_type, &(config::MaxMinStopStep), 1, critical);
    541         ParseForParameter(verbose,file,"MaxMinGapStopStep", 0, 1, 1, int_type, &(config::MaxMinGapStopStep), 1, critical);
     685        ParseForParameter(verbose,FileBuffer,"MaxMinStep", 0, 1, 1, int_type, &(config::MaxMinStep), 1, critical);
     686        ParseForParameter(verbose,FileBuffer,"RelEpsTotalE", 0, 1, 1, double_type, &(config::RelEpsTotalEnergy), 1, critical);
     687        ParseForParameter(verbose,FileBuffer,"RelEpsKineticE", 0, 1, 1, double_type, &(config::RelEpsKineticEnergy), 1, critical);
     688        ParseForParameter(verbose,FileBuffer,"MaxMinStopStep", 0, 1, 1, int_type, &(config::MaxMinStopStep), 1, critical);
     689        ParseForParameter(verbose,FileBuffer,"MaxMinGapStopStep", 0, 1, 1, int_type, &(config::MaxMinGapStopStep), 1, critical);
    542690        if (config::MaxMinStep <= 0) config::MaxMinStep = config::MaxPsiStep;
    543691        if (config::MaxMinStopStep < 1) config::MaxMinStopStep = 1;
    544692        if (config::MaxMinGapStopStep < 1) config::MaxMinGapStopStep = 1;
    545693
    546         ParseForParameter(verbose,file,"MaxInitMinStep", 0, 1, 1, int_type, &(config::MaxInitMinStep), 1, critical);
    547         ParseForParameter(verbose,file,"InitRelEpsTotalE", 0, 1, 1, double_type, &(config::InitRelEpsTotalEnergy), 1, critical);
    548         ParseForParameter(verbose,file,"InitRelEpsKineticE", 0, 1, 1, double_type, &(config::InitRelEpsKineticEnergy), 1, critical);
    549         ParseForParameter(verbose,file,"InitMaxMinStopStep", 0, 1, 1, int_type, &(config::InitMaxMinStopStep), 1, critical);
    550         ParseForParameter(verbose,file,"InitMaxMinGapStopStep", 0, 1, 1, int_type, &(config::InitMaxMinGapStopStep), 1, critical);
     694        ParseForParameter(verbose,FileBuffer,"MaxInitMinStep", 0, 1, 1, int_type, &(config::MaxInitMinStep), 1, critical);
     695        ParseForParameter(verbose,FileBuffer,"InitRelEpsTotalE", 0, 1, 1, double_type, &(config::InitRelEpsTotalEnergy), 1, critical);
     696        ParseForParameter(verbose,FileBuffer,"InitRelEpsKineticE", 0, 1, 1, double_type, &(config::InitRelEpsKineticEnergy), 1, critical);
     697        ParseForParameter(verbose,FileBuffer,"InitMaxMinStopStep", 0, 1, 1, int_type, &(config::InitMaxMinStopStep), 1, critical);
     698        ParseForParameter(verbose,FileBuffer,"InitMaxMinGapStopStep", 0, 1, 1, int_type, &(config::InitMaxMinGapStopStep), 1, critical);
    551699        if (config::MaxInitMinStep <= 0) config::MaxInitMinStep = config::MaxPsiStep;
    552700        if (config::InitMaxMinStopStep < 1) config::InitMaxMinStopStep = 1;
    … …  
    554702
    555703        // Unit cell and magnetic field
    556         ParseForParameter(verbose,file, "BoxLength", 0, 3, 3, lower_trigrid, BoxLength, 1, critical); /* Lattice->RealBasis */
     704        ParseForParameter(verbose,FileBuffer, "BoxLength", 0, 3, 3, lower_trigrid, BoxLength, 1, critical); /* Lattice->RealBasis */
    557705        mol->cell_size[0] = BoxLength[0];
    558706        mol->cell_size[1] = BoxLength[3];
    … …  
    561709        mol->cell_size[4] = BoxLength[7];
    562710        mol->cell_size[5] = BoxLength[8];
    563         if (1) fprintf(stderr,"\n");
    564 
    565         ParseForParameter(verbose,file,"DoPerturbation", 0, 1, 1, int_type, &(config::DoPerturbation), 1, optional);
    566         ParseForParameter(verbose,file,"DoOutNICS", 0, 1, 1, int_type, &(config::DoOutNICS), 1, optional);
    567         if (!ParseForParameter(verbose,file,"DoFullCurrent", 0, 1, 1, int_type, &(config::DoFullCurrent), 1, optional))
     711        //if (1) fprintf(stderr,"\n");
     712
     713        ParseForParameter(verbose,FileBuffer,"DoPerturbation", 0, 1, 1, int_type, &(config::DoPerturbation), 1, optional);
     714        ParseForParameter(verbose,FileBuffer,"DoOutNICS", 0, 1, 1, int_type, &(config::DoOutNICS), 1, optional);
     715        if (!ParseForParameter(verbose,FileBuffer,"DoFullCurrent", 0, 1, 1, int_type, &(config::DoFullCurrent), 1, optional))
    568716                config::DoFullCurrent = 0;
    569717        if (config::DoFullCurrent < 0) config::DoFullCurrent = 0;
    … …  
    576724        }
    577725
    578         ParseForParameter(verbose,file,"ECut", 0, 1, 1, double_type, &(config::ECut), 1, critical);
    579         ParseForParameter(verbose,file,"MaxLevel", 0, 1, 1, int_type, &(config::MaxLevel), 1, critical);
    580         ParseForParameter(verbose,file,"Level0Factor", 0, 1, 1, int_type, &(config::Lev0Factor), 1, critical);
     726        ParseForParameter(verbose,FileBuffer,"ECut", 0, 1, 1, double_type, &(config::ECut), 1, critical);
     727        ParseForParameter(verbose,FileBuffer,"MaxLevel", 0, 1, 1, int_type, &(config::MaxLevel), 1, critical);
     728        ParseForParameter(verbose,FileBuffer,"Level0Factor", 0, 1, 1, int_type, &(config::Lev0Factor), 1, critical);
    581729        if (config::Lev0Factor < 2) {
    582730                config::Lev0Factor = 2;
    583731        }
    584         ParseForParameter(verbose,file,"RiemannTensor", 0, 1, 1, int_type, &di, 1, critical);
     732        ParseForParameter(verbose,FileBuffer,"RiemannTensor", 0, 1, 1, int_type, &di, 1, critical);
    585733        if (di >= 0 && di < 2) {
    586734                config::RiemannTensor = di;
    … …  
    601749                                config::MaxLevel = 3;
    602750                        }
    603                         ParseForParameter(verbose,file,"RiemannLevel", 0, 1, 1, int_type, &(config::RiemannLevel), 1, critical);
     751                        ParseForParameter(verbose,FileBuffer,"RiemannLevel", 0, 1, 1, int_type, &(config::RiemannLevel), 1, critical);
    604752                        if (config::RiemannLevel < 2) {
    605753                                config::RiemannLevel = 2;
    … …  
    608756                                config::RiemannLevel = config::MaxLevel-1;
    609757                        }
    610                         ParseForParameter(verbose,file,"LevRFactor", 0, 1, 1, int_type, &(config::LevRFactor), 1, critical);
     758                        ParseForParameter(verbose,FileBuffer,"LevRFactor", 0, 1, 1, int_type, &(config::LevRFactor), 1, critical);
    611759                        if (config::LevRFactor < 2) {
    612760                                config::LevRFactor = 2;
    … …  
    616764                        break;
    617765        }
    618         ParseForParameter(verbose,file,"PsiType", 0, 1, 1, int_type, &di, 1, critical);
     766        ParseForParameter(verbose,FileBuffer,"PsiType", 0, 1, 1, int_type, &di, 1, critical);
    619767        if (di >= 0 && di < 2) {
    620768                config::PsiType = di;
    … …  
    625773        switch (config::PsiType) {
    626774        case 0: // SpinDouble
    627                 ParseForParameter(verbose,file,"MaxPsiDouble", 0, 1, 1, int_type, &(config::MaxPsiDouble), 1, critical);
    628                 ParseForParameter(verbose,file,"AddPsis", 0, 1, 1, int_type, &(config::AddPsis), 1, optional);
     775                ParseForParameter(verbose,FileBuffer,"MaxPsiDouble", 0, 1, 1, int_type, &(config::MaxPsiDouble), 1, critical);
     776                ParseForParameter(verbose,FileBuffer,"AddPsis", 0, 1, 1, int_type, &(config::AddPsis), 1, optional);
    629777                break;
    630778        case 1: // SpinUpDown
    631779                if (config::ProcPEGamma % 2) config::ProcPEGamma*=2;
    632                 ParseForParameter(verbose,file,"PsiMaxNoUp", 0, 1, 1, int_type, &(config::PsiMaxNoUp), 1, critical);
    633                 ParseForParameter(verbose,file,"PsiMaxNoDown", 0, 1, 1, int_type, &(config::PsiMaxNoDown), 1, critical);
    634                 ParseForParameter(verbose,file,"AddPsis", 0, 1, 1, int_type, &(config::AddPsis), 1, optional);
     780                ParseForParameter(verbose,FileBuffer,"PsiMaxNoUp", 0, 1, 1, int_type, &(config::PsiMaxNoUp), 1, critical);
     781                ParseForParameter(verbose,FileBuffer,"PsiMaxNoDown", 0, 1, 1, int_type, &(config::PsiMaxNoDown), 1, critical);
     782                ParseForParameter(verbose,FileBuffer,"AddPsis", 0, 1, 1, int_type, &(config::AddPsis), 1, optional);
    635783                break;
    636784        }
    … …  
    638786        // IonsInitRead
    639787
    640         ParseForParameter(verbose,file,"RCut", 0, 1, 1, double_type, &(config::RCut), 1, critical);
    641         ParseForParameter(verbose,file,"IsAngstroem", 0, 1, 1, int_type, &(config::IsAngstroem), 1, critical);
    642         ParseForParameter(verbose,file,"MaxTypes", 0, 1, 1, int_type, &(config::MaxTypes), 1, critical);
    643         if (!ParseForParameter(verbose,file,"RelativeCoord", 0, 1, 1, int_type, &(config::RelativeCoord) , 1, optional))
     788        ParseForParameter(verbose,FileBuffer,"RCut", 0, 1, 1, double_type, &(config::RCut), 1, critical);
     789        ParseForParameter(verbose,FileBuffer,"IsAngstroem", 0, 1, 1, int_type, &(config::IsAngstroem), 1, critical);
     790        ParseForParameter(verbose,FileBuffer,"MaxTypes", 0, 1, 1, int_type, &(config::MaxTypes), 1, critical);
     791        if (!ParseForParameter(verbose,FileBuffer,"RelativeCoord", 0, 1, 1, int_type, &(config::RelativeCoord) , 1, optional))
    644792                config::RelativeCoord = 0;
    645         if (!ParseForParameter(verbose,file,"StructOpt", 0, 1, 1, int_type, &(config::StructOpt), 1, optional))
     793        if (!ParseForParameter(verbose,FileBuffer,"StructOpt", 0, 1, 1, int_type, &(config::StructOpt), 1, optional))
    646794                config::StructOpt = 0;
    647795        if (MaxTypes == 0) {
    … …  
    650798                // prescan number of ions per type
    651799                cout << Verbose(0) << "Prescanning ions per type: " << endl;
     800                int NoAtoms = 0;
    652801                for (int i=0; i < config::MaxTypes; i++) {
    653802                        sprintf(name,"Ion_Type%i",i+1);
    654                         ParseForParameter(verbose,file, (const char*)name, 0, 1, 1, int_type, &No[i], 1, critical);
    655                         ParseForParameter(verbose,file, name, 0, 2, 1, int_type, &Z, 1, critical);
     803                        ParseForParameter(verbose,FileBuffer, (const char*)name, 0, 1, 1, int_type, &No[i], 1, critical);
     804                        ParseForParameter(verbose,FileBuffer, name, 0, 2, 1, int_type, &Z, 1, critical);
    656805                        elementhash[i] = periode->FindElement(Z);
    657806                        cout << Verbose(1) << i << ". Z = " << elementhash[i]->Z << " with " << No[i] << " ions." << endl;
     807                        NoAtoms += No[i];
    658808                }
    659809                int repetition = 0; // which repeated keyword shall be read
    660810
     811                // sort the lines via the LineMapping
     812    sprintf(name,"Ion_Type%i",config::MaxTypes);
     813                if (!ParseForParameter(verbose,FileBuffer, (const char*)name, 1, 1, 1, int_type, &value[0], 1, critical)) {
     814                  cerr << "There are no atoms in the config file!" << endl;
     815      return;
     816    }
     817                FileBuffer->CurrentLine++;
     818                //cout << FileBuffer->buffer[ FileBuffer->LineMapping[FileBuffer->CurrentLine]];
     819                FileBuffer->MapIonTypesInBuffer(NoAtoms);
     820                //for (int i=0; i<(NoAtoms < 100 ? NoAtoms : 100 < 100 ? NoAtoms : 100);++i) {
     821                //      cout << FileBuffer->buffer[ FileBuffer->LineMapping[FileBuffer->CurrentLine+i]];
     822                //}
     823
    661824                map<int, atom *> AtomList[config::MaxTypes];
     825                map<int, atom *> LinearList;
    662826                if (!FastParsing) {
    663827                        // parse in trajectories
    … …  
    673837                                                        neues = new atom();
    674838                                                        AtomList[i][j] = neues;
     839                                                        LinearList[FileBuffer->CurrentLine] = neues;
    675840                                                        neues->type = elementhash[i]; // find element type
    676                                                         mol->AddAtom(neues);
    677841                                                } else
    678842                                                        neues = AtomList[i][j];
    679                                                 status = (status &&
    680                                                                                 ParseForParameter(verbose,file, keyword, 0, 1, 1, double_type, &neues->x.x[0], 1, (repetition == 0) ? critical : optional) &&
    681                                                                                 ParseForParameter(verbose,file, keyword, 0, 2, 1, double_type, &neues->x.x[1], 1, (repetition == 0) ? critical : optional) &&
    682                                                                                 ParseForParameter(verbose,file, keyword, 0, 3, 1, double_type, &neues->x.x[2], 1, (repetition == 0) ? critical : optional) &&
    683                                                                                 ParseForParameter(verbose,file, keyword, 0, 4, 1, int_type, &neues->FixedIon, 1, (repetition == 0) ? critical : optional));
     843            status = (status &&
     844                                                                                ParseForParameter(verbose,FileBuffer, keyword, 0, 1, 1, double_type, &neues->x.x[0], 1, (repetition == 0) ? critical : optional) &&
     845                                                                                ParseForParameter(verbose,FileBuffer, keyword, 0, 2, 1, double_type, &neues->x.x[1], 1, (repetition == 0) ? critical : optional) &&
     846                                                                                ParseForParameter(verbose,FileBuffer, keyword, 0, 3, 1, double_type, &neues->x.x[2], 1, (repetition == 0) ? critical : optional) &&
     847                                                                                ParseForParameter(verbose,FileBuffer, keyword, 0, 4, 1, int_type, &neues->FixedIon, 1, (repetition == 0) ? critical : optional));
    684848                                                if (!status) break;
    685849
    … …  
    697861
    698862                                                // parse velocities if present
    699                                                 if(!ParseForParameter(verbose,file, keyword, 0, 5, 1, double_type, &neues->v.x[0], 1,optional))
     863                                                if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 5, 1, double_type, &neues->v.x[0], 1,optional))
    700864                                                        neues->v.x[0] = 0.;
    701                                                 if(!ParseForParameter(verbose,file, keyword, 0, 6, 1, double_type, &neues->v.x[1], 1,optional))
     865                                                if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 6, 1, double_type, &neues->v.x[1], 1,optional))
    702866                                                        neues->v.x[1] = 0.;
    703                                                 if(!ParseForParameter(verbose,file, keyword, 0, 7, 1, double_type, &neues->v.x[2], 1,optional))
     867                                                if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 7, 1, double_type, &neues->v.x[2], 1,optional))
    704868                                                        neues->v.x[2] = 0.;
    705869                                                for (int d=0;d<NDIM;d++)
    … …  
    707871
    708872                                                // parse forces if present
    709                                                 if(!ParseForParameter(verbose,file, keyword, 0, 8, 1, double_type, &value[0], 1,optional))
     873                                                if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 8, 1, double_type, &value[0], 1,optional))
    710874                                                        value[0] = 0.;
    711                                                 if(!ParseForParameter(verbose,file, keyword, 0, 9, 1, double_type, &value[1], 1,optional))
     875                                                if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 9, 1, double_type, &value[1], 1,optional))
    712876                                                        value[1] = 0.;
    713                                                 if(!ParseForParameter(verbose,file, keyword, 1, 10, 1, double_type, &value[2], 1,optional))
     877                                                if(!ParseForParameter(verbose,FileBuffer, keyword, 1, 10, 1, double_type, &value[2], 1,optional))
    714878                                                        value[2] = 0.;
    715879                                                for (int d=0;d<NDIM;d++)
    … …  
    730894                                repetition++;
    731895                        }
     896                        // put atoms into the molecule in their original order
     897                        for(map<int, atom*>::iterator runner = LinearList.begin(); runner != LinearList.end(); ++runner) {
     898                                mol->AddAtom(runner->second);
     899                        }
    732900                        repetition--;
    733901                        cout << "Found " << repetition << " trajectory steps." << endl;
    … …  
    736904                        // 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)
    737905                        repetition = 0;
    738                         while ( ParseForParameter(verbose,file, "Ion_Type1_1", 0, 1, 1, double_type, &value[0], repetition, (repetition == 0) ? critical : optional) &&
    739                                                         ParseForParameter(verbose,file, "Ion_Type1_1", 0, 2, 1, double_type, &value[1], repetition, (repetition == 0) ? critical : optional) &&
    740                                                         ParseForParameter(verbose,file, "Ion_Type1_1", 0, 3, 1, double_type, &value[2], repetition, (repetition == 0) ? critical : optional))
     906                        while ( ParseForParameter(verbose,FileBuffer, "Ion_Type1_1", 0, 1, 1, double_type, &value[0], repetition, (repetition == 0) ? critical : optional) &&
     907                                                        ParseForParameter(verbose,FileBuffer, "Ion_Type1_1", 0, 2, 1, double_type, &value[1], repetition, (repetition == 0) ? critical : optional) &&
     908                                                        ParseForParameter(verbose,FileBuffer, "Ion_Type1_1", 0, 3, 1, double_type, &value[2], repetition, (repetition == 0) ? critical : optional))
    741909                                repetition++;
    742910                        cout << "I found " << repetition << " times the keyword Ion_Type1_1." << endl;
    … …  
    748916                                        atom *neues = new atom();
    749917                                        // then parse for each atom the coordinates as often as present
    750                                         ParseForParameter(verbose,file, keyword, 0, 1, 1, double_type, &neues->x.x[0], repetition,critical);
    751                                         ParseForParameter(verbose,file, keyword, 0, 2, 1, double_type, &neues->x.x[1], repetition,critical);
    752                                         ParseForParameter(verbose,file, keyword, 0, 3, 1, double_type, &neues->x.x[2], repetition,critical);
    753                                         ParseForParameter(verbose,file, keyword, 0, 4, 1, int_type, &neues->FixedIon, repetition,critical);
    754                                         if(!ParseForParameter(verbose,file, keyword, 0, 5, 1, double_type, &neues->v.x[0], repetition,optional))
     918                                        ParseForParameter(verbose,FileBuffer, keyword, 0, 1, 1, double_type, &neues->x.x[0], repetition,critical);
     919                                        ParseForParameter(verbose,FileBuffer, keyword, 0, 2, 1, double_type, &neues->x.x[1], repetition,critical);
     920                                        ParseForParameter(verbose,FileBuffer, keyword, 0, 3, 1, double_type, &neues->x.x[2], repetition,critical);
     921                                        ParseForParameter(verbose,FileBuffer, keyword, 0, 4, 1, int_type, &neues->FixedIon, repetition,critical);
     922                                        if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 5, 1, double_type, &neues->v.x[0], repetition,optional))
    755923                                                neues->v.x[0] = 0.;
    756                                         if(!ParseForParameter(verbose,file, keyword, 0, 6, 1, double_type, &neues->v.x[1], repetition,optional))
     924                                        if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 6, 1, double_type, &neues->v.x[1], repetition,optional))
    757925                                                neues->v.x[1] = 0.;
    758                                         if(!ParseForParameter(verbose,file, keyword, 0, 7, 1, double_type, &neues->v.x[2], repetition,optional))
     926                                        if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 7, 1, double_type, &neues->v.x[2], repetition,optional))
    759927                                                neues->v.x[2] = 0.;
    760928                                        // here we don't care if forces are present (last in trajectories is always equal to current position)
    … …  
    765933                }
    766934        }
    767         file->close();
    768         delete(file);
     935        delete(FileBuffer);
    769936};
    770937
    … …  
    12031370 * \warning value is modified (both in contents and position)!
    12041371 * \param verbose 1 - print found value to stderr, 0 - don't
    1205  * \param file file to be parsed
     1372 * \param *file file to be parsed
    12061373 * \param name Name of value in file (at least 3 chars!)
    12071374 * \param sequential 1 - do not reset file pointer to begin of file, 0 - set to beginning
    … …  
    14321599        return (found); // true if found, false if not
    14331600}
     1601
     1602
     1603/** Reads parameter from a parsed file.
     1604 * The file is either parsed for a certain keyword or if null is given for
     1605 * the value in row yth and column xth. If the keyword was necessity#critical,
     1606 * then an error is thrown and the programme aborted.
     1607 * \warning value is modified (both in contents and position)!
     1608 * \param verbose 1 - print found value to stderr, 0 - don't
     1609 * \param *FileBuffer pointer to buffer structure
     1610 * \param name Name of value in file (at least 3 chars!)
     1611 * \param sequential 1 - do not reset file pointer to begin of file, 0 - set to beginning
     1612 *        (if file is sequentially parsed this can be way faster! However, beware of multiple values per line, as whole line is read -
     1613 *         best approach: 0 0 0 1 (not resetted only on last value of line) - and of yth, which is now
     1614 *         counted from this unresetted position!)
     1615 * \param xth Which among a number of parameters it is (in grid case it's row number as grid is read as a whole!)
     1616 * \param yth In grid case specifying column number, otherwise the yth \a name matching line
     1617 * \param type Type of the Parameter to be read
     1618 * \param value address of the value to be read (must have been allocated)
     1619 * \param repetition determines, if the keyword appears multiply in the config file, which repetition shall be parsed, i.e. 1 if not multiply
     1620 * \param critical necessity of this keyword being specified (optional, critical)
     1621 * \return 1 - found, 0 - not found
     1622 * \note Routine is taken from the pcp project and hack-a-slack adapted to C++
     1623 */
     1624int config::ParseForParameter(int verbose, struct ConfigFileBuffer *FileBuffer, const char *name, int sequential, int const xth, int const yth, int type, void *value, int repetition, int critical) {
     1625  int i,j;  // loop variables
     1626  int length = 0, maxlength = -1;
     1627  int OldCurrentLine = FileBuffer->CurrentLine;
     1628  char *dummy1, *dummy;    // pointers in the line that is read in per step
     1629
     1630  //fprintf(stderr,"Parsing for %s\n",name);
     1631  if (repetition == 0)
     1632    //Error(SomeError, "ParseForParameter(): argument repetition must not be 0!");
     1633    return 0;
     1634
     1635  int line = 0; // marks line where parameter was found
     1636  int found = (type >= grid) ? 0 : (-yth + 1);  // marks if yth parameter name was found
     1637  while((found != repetition)) {
     1638    dummy1 = dummy = NULL;
     1639    do {
     1640      dummy1 = FileBuffer->buffer[ FileBuffer->LineMapping[FileBuffer->CurrentLine++] ];
     1641      if (FileBuffer->CurrentLine >= FileBuffer->NoLines) {
     1642        if ((critical) && (found == 0)) {
     1643          //Error(InitReading, name);
     1644          fprintf(stderr,"Error:InitReading, critical %s not found\n", name);
     1645          exit(255);
     1646        } else {
     1647          FileBuffer->CurrentLine = OldCurrentLine; // rewind to start position
     1648          return 0;
     1649        }
     1650      }
     1651      if (dummy1 == NULL) {
     1652        if (verbose) fprintf(stderr,"Error reading line %i\n",line);
     1653      } else {
     1654        //fprintf(stderr,"Now parsing the line %i: %s\n", line, dummy1);
     1655      }
     1656      line++;
     1657    } while (dummy1 != NULL && ((dummy1[0] == '#') || (dummy1[0] == '\0'))); // skip commentary and empty lines
     1658
     1659    // Seek for possible end of keyword on line if given ...
     1660    if (name != NULL) {
     1661      dummy = strchr(dummy1,'\t');  // set dummy on first tab or space which ever's nearer
     1662      if (dummy == NULL) {
     1663        dummy = strchr(dummy1, ' ');  // if not found seek for space
     1664        while ((dummy != NULL) && ((*dummy == '\t') || (*dummy == ' ')))    // skip some more tabs and spaces if necessary
     1665          dummy++;
     1666      }
     1667      if (dummy == NULL) {
     1668        dummy = strchr(dummy1, '\n'); // set on line end then (whole line = keyword)
     1669        //fprintf(stderr,"Error: Cannot find tabs or spaces on line %i in search for %s\n", line, name);
     1670        //Free((void **)&free_dummy);
     1671        //Error(FileOpenParams, NULL);
     1672      } else {
     1673        //fprintf(stderr,"found tab at %i\n",(char *)dummy-(char *)dummy1);
     1674      }
     1675    } else dummy = dummy1;
     1676    // ... and check if it is the keyword!
     1677    //fprintf(stderr,"name %p, dummy %i/%c, dummy1 %i/%c, strlen(name) %i\n", &name, dummy, *dummy, dummy1, *dummy1, strlen(name));
     1678    if ((name == NULL) || (((dummy-dummy1 >= 3) && (strncmp(dummy1, name, strlen(name)) == 0)) && ((unsigned int)(dummy-dummy1) == strlen(name)))) {
     1679      found++; // found the parameter!
     1680      //fprintf(stderr,"found %s at line %i between %i and %i\n", name, line, dummy1, dummy);
     1681
     1682      if (found == repetition) {
     1683        for (i=0;i<xth;i++) { // i = rows
     1684          if (type >= grid) {
     1685            // grid structure means that grid starts on the next line, not right after keyword
     1686            dummy1 = dummy = NULL;
     1687            do {
     1688              dummy1 = FileBuffer->buffer[ FileBuffer->LineMapping[ FileBuffer->CurrentLine++] ];
     1689              if (FileBuffer->CurrentLine >= FileBuffer->NoLines) {
     1690                if ((critical) && (found == 0)) {
     1691                  //Error(InitReading, name);
     1692                  fprintf(stderr,"Error:InitReading, critical %s not found\n", name);
     1693                  exit(255);
     1694                } else {
     1695                  FileBuffer->CurrentLine = OldCurrentLine; // rewind to start position
     1696                  return 0;
     1697                }
     1698              }
     1699              if (dummy1 == NULL) {
     1700                if (verbose) fprintf(stderr,"Error reading line %i\n", line);
     1701              } else {
     1702                //fprintf(stderr,"Reading next line %i: %s\n", line, dummy1);
     1703              }
     1704              line++;
     1705            } while (dummy1 != NULL && (dummy1[0] == '#') || (dummy1[0] == '\n'));
     1706            dummy = dummy1;
     1707          } else { // simple int, strings or doubles start in the same line
     1708            while ((*dummy == '\t') || (*dummy == ' '))  // skip interjacent tabs and spaces
     1709              dummy++;
     1710          }
     1711
     1712          for (j=((type >= grid) ? 0 : yth-1);j<yth;j++) { // j = columns
     1713            // check for lower triangular area and upper triangular area
     1714            if ( ((i > j) && (type == upper_trigrid)) || ((j > i) && (type == lower_trigrid))) {
     1715              *((double *)value) = 0.0;
     1716              fprintf(stderr,"%f\t",*((double *)value));
     1717              value = (void *)((long)value + sizeof(double));
     1718              //value += sizeof(double);
     1719            } else {
     1720              // otherwise we must skip all interjacent tabs and spaces and find next value
     1721              dummy1 = dummy;
     1722              dummy = strchr(dummy1, '\t'); // seek for tab or space
     1723              if (dummy == NULL)
     1724                dummy = strchr(dummy1, ' ');  // if not found seek for space
     1725              if (dummy == NULL) { // if still zero returned ...
     1726                dummy = strchr(dummy1, '\n'); // ... at line end then
     1727                if ((j < yth-1) && (type < 4)) {  // check if xth value or not yet
     1728                  if (critical) {
     1729                    if (verbose) fprintf(stderr,"Error: EoL at %i and still missing %i value(s) for parameter %s\n", line, yth-j, name);
     1730                    //return 0;
     1731                    exit(255);
     1732                    //Error(FileOpenParams, NULL);
     1733                  } else {
     1734                    if (!sequential) { // here we need it!
     1735                      FileBuffer->CurrentLine = OldCurrentLine; // rewind to start position
     1736                    }
     1737                    return 0;
     1738                  }
     1739                }
     1740              } else {
     1741                //fprintf(stderr,"found tab at %i\n",(char *)dummy-(char *)free_dummy);
     1742              }
     1743              if (*dummy1 == '#') {
     1744                // found comment, skipping rest of line
     1745                //if (verbose) fprintf(stderr,"Error: '#' at %i and still missing %i value(s) for parameter %s\n", line, yth-j, name);
     1746                if (!sequential) { // here we need it!
     1747                  FileBuffer->CurrentLine = OldCurrentLine; // rewind to start position
     1748                }
     1749                return 0;
     1750              }
     1751              //fprintf(stderr,"value from %i to %i\n",(char *)dummy1-(char *)free_dummy,(char *)dummy-(char *)free_dummy);
     1752              switch(type) {
     1753                case (row_int):
     1754                  *((int *)value) = atoi(dummy1);
     1755                  if ((verbose) && (i==0) && (j==0)) fprintf(stderr,"%s = ", name);
     1756                  if (verbose) fprintf(stderr,"%i\t",*((int *)value));
     1757                    value = (void *)((long)value + sizeof(int));
     1758                    //value += sizeof(int);
     1759                  break;
     1760                case(row_double):
     1761                case(grid):
     1762                case(lower_trigrid):
     1763                case(upper_trigrid):
     1764                  *((double *)value) = atof(dummy1);
     1765                  if ((verbose) && (i==0) && (j==0)) fprintf(stderr,"%s = ", name);
     1766                  if (verbose) fprintf(stderr,"%lg\t",*((double *)value));
     1767                  value = (void *)((long)value + sizeof(double));
     1768                  //value += sizeof(double);
     1769                  break;
     1770                case(double_type):
     1771                  *((double *)value) = atof(dummy1);
     1772                  if ((verbose) && (i == xth-1)) fprintf(stderr,"%s = %lg\n", name, *((double *) value));
     1773                  //value += sizeof(double);
     1774                  break;
     1775                case(int_type):
     1776                  *((int *)value) = atoi(dummy1);
     1777                  if ((verbose) && (i == xth-1)) fprintf(stderr,"%s = %i\n", name, *((int *) value));
     1778                  //value += sizeof(int);
     1779                  break;
     1780                default:
     1781                case(string_type):
     1782                  if (value != NULL) {
     1783                    //if (maxlength == -1) maxlength = strlen((char *)value); // get maximum size of string array
     1784                    maxlength = MAXSTRINGSIZE;
     1785                    length = maxlength > (dummy-dummy1) ? (dummy-dummy1) : maxlength; // cap at maximum
     1786                    strncpy((char *)value, dummy1, length); // copy as much
     1787                    ((char *)value)[length] = '\0'; // and set end marker
     1788                    if ((verbose) && (i == xth-1)) fprintf(stderr,"%s is '%s' (%i chars)\n",name,((char *) value), length);
     1789                    //value += sizeof(char);
     1790                  } else {
     1791                  }
     1792                break;
     1793              }
     1794            }
     1795            while (*dummy == '\t')
     1796              dummy++;
     1797          }
     1798        }
     1799      }
     1800    }
     1801  }
     1802  if ((type >= row_int) && (verbose)) fprintf(stderr,"\n");
     1803  if (!sequential) {
     1804    FileBuffer->CurrentLine = OldCurrentLine; // rewind to start position
     1805  }
     1806  //fprintf(stderr, "End of Parsing\n\n");
     1807
     1808  return (found); // true if found, false if not
     1809}

  • src/molecules.cpp

    r6cb412 rd1df9b  
    14711471        atom *walker = NULL;
    14721472        int ElementNo[MAX_ELEMENTS], AtomNo[MAX_ELEMENTS];
    1473         int CurrentMaxElement = 0;
    14741473        CountElements();
    14751474
    … …  
    14851484    while (walker->next != end) { // go through every atom of this element
    14861485      walker = walker->next;
    1487       if (ElementNo[walker->type->Z] == 0) // new element
    1488         ElementNo[walker->type->Z] = ++CurrentMaxElement;
     1486      ElementNo[walker->type->Z] = 1;
     1487    }
     1488    int current=1;
     1489    for (int i=0;i<MAX_ELEMENTS;++i) {
     1490      if (ElementNo[i] == 1)
     1491        ElementNo[i] = current++;
     1492    }
     1493    walker = start;
     1494    while (walker->next != end) { // go through every atom of this element
     1495      walker = walker->next;
    14891496      AtomNo[walker->type->Z]++;
    14901497      walker->Output(ElementNo[walker->type->Z], AtomNo[walker->type->Z], out); // removed due to trajectories
    … …  
    15011508        atom *walker = NULL;
    15021509  int ElementNo[MAX_ELEMENTS], AtomNo[MAX_ELEMENTS];
    1503   int CurrentMaxElement = 0;
    15041510        CountElements();
    15051511
    … …  
    15171523                    ElementNo[i] = 0;
    15181524                  }
    1519       walker = start;
     1525    walker = start;
     1526    while (walker->next != end) { // go through every atom of this element
     1527      walker = walker->next;
     1528      ElementNo[walker->type->Z] = 1;
     1529    }
     1530    int current=1;
     1531    for (int i=0;i<MAX_ELEMENTS;++i) {
     1532      if (ElementNo[i] == 1)
     1533        ElementNo[i] = current++;
     1534    }
     1535    walker = start;
    15201536      while (walker->next != end) { // go through every atom of this element
    15211537        walker = walker->next;
    1522         if (ElementNo[walker->type->Z] == 0) // new element
    1523           ElementNo[walker->type->Z] = ++CurrentMaxElement;
    15241538        AtomNo[walker->type->Z]++;
    15251539        *out << "Ion_Type" << ElementNo[walker->type->Z] << "_" << AtomNo[walker->type->Z] << "\t"      << fixed << setprecision(9) << showpoint;

  • src/molecules.hpp

    r6cb412 rd1df9b  
    392392};
    393393
     394class ConfigFileBuffer {
     395  public:
     396    char **buffer;
     397    int *LineMapping;
     398    int CurrentLine;
     399    int NoLines;
     400
     401    ConfigFileBuffer();
     402    ConfigFileBuffer(char *filename);
     403    ~ConfigFileBuffer();
     404
     405    void InitMapping();
     406    void MapIonTypesInBuffer(int NoAtoms);
     407};
     408
     409
    394410/** The config file.
    395411 * The class contains all parameters that control a dft run also functions to load and save.
    … …  
    469485
    470486        int ParseForParameter(int verbose, ifstream *file, const char *name, int sequential, int const xth, int const yth, int type, void *value, int repetition, int critical);
     487        int ParseForParameter(int verbose, struct ConfigFileBuffer *FileBuffer, const char *name, int sequential, int const xth, int const yth, int type, void *value, int repetition, int critical);
    471488
    472489        public:
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