Changeset 35b698


Ignore:
Timestamp:
Jun 23, 2010, 3:52:50 PM (15 years ago)
Author:
Frederik Heber <heber@…>
Branches:
Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable
Children:
d0fbec
Parents:
dc0d21
git-author:
Frederik Heber <heber@…> (06/23/10 15:20:35)
git-committer:
Frederik Heber <heber@…> (06/23/10 15:52:50)
Message:

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

Fragmentation:

  • FIX: MoleculeFillWithMoleculeAction: filler atoms have to be removed before the system can be stored to file.
  • FIX: PcpParser::load() - has to put the molecule also into World's MoleculeListClass (otherwise the name cannot be set right after loading)
  • new Libparser.a
  • all sources from PARSER subdir are compiled into libparser such that only ParserUnitTest is recompiled.

Testfixes:

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

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

Files:
33 edited

Legend:

Unmodified
Added
Removed

  • src/Actions/FragmentationAction/FragmentationAction.cpp

    rdc0d21 r35b698  
    4242  double distance = -1.;
    4343  int order = 0;
     44  std::string path;
    4445  config *configuration = World::getInstance().getConfig();
    4546  int ExitFlag = 0;
    4647
    4748  cout << "pre-dialog"<< endl;
    48   dialog->queryMolecule(NAME, &mol, MapOfActions::getInstance().getDescription(NAME));
     49  dialog->queryString(NAME, &path, MapOfActions::getInstance().getDescription(NAME));
     50  dialog->queryMolecule("molecule-by-id", &mol, MapOfActions::getInstance().getDescription("molecule-by-id"));
    4951  dialog->queryDouble("distance", &distance, MapOfActions::getInstance().getDescription("distance"));
    5052  dialog->queryInt("order", &order, MapOfActions::getInstance().getDescription("order"));
    … …  
    5961    DoLog(0) && (Log() << Verbose(0) << "Fragmenting molecule with current connection matrix ..." << endl);
    6062    if (mol->hasBondStructure()) {
    61       ExitFlag = mol->FragmentMolecule(order, configuration);
     63      ExitFlag = mol->FragmentMolecule(order, path);
    6264    }
    6365    World::getInstance().setExitFlag(ExitFlag);

  • src/Actions/MapOfActions.cpp

    rdc0d21 r35b698  
    185185  TypeMap["fastparsing"] = Boolean;
    186186  TypeMap["fill-molecule"] = String;
    187   TypeMap["fragment-mol"] = Molecule;
     187  TypeMap["fragment-mol"] = String;
    188188  TypeMap["input"] = String;
    189189  TypeMap["linear-interpolate"] = String;

  • src/Actions/MoleculeAction/FillWithMoleculeAction.cpp

    rdc0d21 r35b698  
    102102      World::getInstance().getMolecules()->insert(Filling);
    103103    }
     104    for (molecule::iterator iter = filler->begin(); !filler->empty(); iter = filler->begin()) {
     105      atom *Walker = *iter;
     106      filler->erase(iter);
     107      World::getInstance().destroyAtom(Walker);
     108    }
    104109    World::getInstance().destroyMolecule(filler);
    105110

  • src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp

    rdc0d21 r35b698  
    6969    if (IdMapping)
    7070      DoLog(1) && (Log() << Verbose(1) << "Using Identity for the permutation map." << endl);
    71     char outputname[MAXSTRINGSIZE];
    72     strcpy(outputname, filename.c_str());
    73     // TODO: LinearInterpolationBetweenConfiguration should use stream, not the filename directly! (better for unit test)
    74     if (!mol->LinearInterpolationBetweenConfiguration(start, end, outputname, *(World::getInstance().getConfig()), IdMapping))
    75       DoLog(2) && (Log() << Verbose(2) << "Could not store " << outputname << " files." << endl);
     71    if (!mol->LinearInterpolationBetweenConfiguration(start, end, filename, *(World::getInstance().getConfig()), IdMapping))
     72      DoLog(2) && (Log() << Verbose(2) << "Could not store " << filename << " files." << endl);
    7673    else
    7774      DoLog(2) && (Log() << Verbose(2) << "Steps created and " << filename << " files stored." << endl);

  • src/Actions/MoleculeAction/SaveAdjacencyAction.cpp

    rdc0d21 r35b698  
    6565    World::getInstance().getConfig()->BG->ConstructBondGraph(mol);
    6666    // TODO: sollte stream nicht filename benutzen, besser fuer unit test
    67     char outputname[MAXSTRINGSIZE];
    68     strcpy(outputname, filename.c_str());
    69     mol->StoreAdjacencyToFile(NULL, outputname);
     67    mol->StoreAdjacencyToFile(filename);
    7068    delete dialog;
    7169    return Action::success;

  • src/Actions/MoleculeAction/SaveBondsAction.cpp

    rdc0d21 r35b698  
    6464    DoLog(0) && (Log() << Verbose(0) << "Storing bonds to path " << filename << "." << endl);
    6565    World::getInstance().getConfig()->BG->ConstructBondGraph(mol);
    66     // TODO: sollte stream, nicht filenamen direkt nutzen, beser fuer unit tests
    67     char outputname[MAXSTRINGSIZE];
    68     strcpy(outputname, filename.c_str());
    69     mol->StoreBondsToFile(NULL, outputname);
     66    // TODO: sollte stream, nicht filenamen direkt nutzen, besser fuer unit tests
     67    mol->StoreBondsToFile(filename);
    7068    delete dialog;
    7169    return Action::success;

  • src/Legacy/oldmenu.cpp

    rdc0d21 r35b698  
    609609{
    610610  int Order1;
     611  std::string path;
    611612  clock_t start, end;
    612613
    … …  
    614615  Log() << Verbose(0) << "What's the desired bond order: ";
    615616  cin >> Order1;
     617  DoLog(0) && (Log() << Verbose(0) << "What's the output path and prefix [e.g. /home/foo/BondFragment]: ");
     618  cin >> path;
    616619  if (mol->hasBondStructure()) {
    617620    start = clock();
    618     mol->FragmentMolecule(Order1, configuration);
     621    mol->FragmentMolecule(Order1, path);
    619622    end = clock();
    620623    Log() << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl;

  • src/Makefile.am

    rdc0d21 r35b698  
    245245INCLUDES = -I$(top_srcdir)/src/unittests -I$(top_srcdir)/src/Actions -I$(top_srcdir)/src/UIElements
    246246
    247 noinst_LIBRARIES = libmolecuilder.a libgslwrapper.a
     247noinst_LIBRARIES = libmolecuilder.a libgslwrapper.a libparser.a
    248248bin_PROGRAMS = molecuilder joiner analyzer
    249249molecuilderdir = ${bindir}
    250250libmolecuilder_a_SOURCES = ${SOURCE} ${HEADER}
     251libparser_a_SOURCES = ${PARSERSOURCE} ${PARSERHEADER}
    251252libgslwrapper_a_SOURCES = ${LINALGSOURCE} ${LINALGHEADER}
    252253molecuilder_DATA = elements.db valence.db orbitals.db Hbonddistance.db Hbondangle.db
    253254molecuilder_LDFLAGS = $(BOOST_LDFLAGS)
    254255molecuilder_SOURCES = builder.cpp
    255 molecuilder_LDADD =  UIElements/libMolecuilderUI.a Actions/libMolecuilderActions.a libmolecuilder.a libgslwrapper.a $(BOOST_LIB) ${BOOST_THREAD_LIB} ${BOOST_PROGRAM_OPTIONS_LIB}
     256molecuilder_LDADD =  UIElements/libMolecuilderUI.a Actions/libMolecuilderActions.a libmolecuilder.a libparser.a libgslwrapper.a $(BOOST_LIB) ${BOOST_THREAD_LIB} ${BOOST_PROGRAM_OPTIONS_LIB}
    256257joiner_SOURCES = joiner.cpp datacreator.cpp parser.cpp datacreator.hpp helpers.hpp parser.hpp periodentafel.hpp
    257258joiner_LDADD = libmolecuilder.a $(BOOST_LIB) ${BOOST_THREAD_LIB}

  • src/Parser/PcpParser.cpp

    rdc0d21 r35b698  
    3030
    3131  Paths.databasepath = NULL;
    32   Paths.configpath = NULL;
    3332  Paths.configname = NULL;
    3433  Paths.mainname = NULL;
    … …  
    307306  // 3. parse the molecule in
    308307  molecule *mol = World::getInstance().createMolecule();
     308  MoleculeListClass *molecules = World::getInstance().getMolecules();
     309  molecules->insert(mol);
    309310  LoadMolecule(mol, FileBuffer, World::getInstance().getPeriode(), FastParsing);
    310311  //mol->SetNameFromFilename(filename);
    … …  
    615616  if ((Paths.databasepath != NULL) && (b.Paths.databasepath != NULL))
    616617    ASSERT(strcmp(Paths.databasepath, b.Paths.databasepath), "PcpParser ==: databasepath not");
    617   if ((Paths.configpath != NULL) && (b.Paths.configpath != NULL))
    618     ASSERT(strcmp(Paths.configpath, b.Paths.configpath), "PcpParser ==: configpath not");
    619618  if ((Paths.configname != NULL) && (b.Paths.configname != NULL))
    620619    ASSERT(strcmp(Paths.configname, b.Paths.configname), "PcpParser ==: configname not");

  • src/Parser/PcpParser.hpp

    rdc0d21 r35b698  
    4141  struct StructPaths {
    4242    char *databasepath;
    43     char *configpath;
    4443    char *configname;
    4544    char *mainname;

  • src/World.cpp

    rdc0d21 r35b698  
    112112  molecule *mol = NULL;
    113113  mol = NewMolecule();
     114  cout << "Creating molecule with id " << currMoleculeId << "." << endl;
    114115  assert(!molecules.count(currMoleculeId));
    115116  mol->setId(currMoleculeId++);

  • src/builder.cpp

    rdc0d21 r35b698  
    8080#include "Menu/ActionMenuItem.hpp"
    8181#include "Parser/ChangeTracker.hpp"
     82#include "Parser/FormatParserStorage.hpp"
     83#include "Parser/PcpParser.hpp"
     84#include "Parser/XyzParser.hpp"
    8285#include "Actions/ActionRegistry.hpp"
    8386#include "Actions/ActionHistory.hpp"
    … …  
    654657  int Order1;
    655658  clock_t start, end;
     659  std::string path;
    656660
    657661  DoLog(0) && (Log() << Verbose(0) << "Fragmenting molecule with current connection matrix ..." << endl);
    658662  DoLog(0) && (Log() << Verbose(0) << "What's the desired bond order: ");
    659663  cin >> Order1;
     664  DoLog(0) && (Log() << Verbose(0) << "What's the output path and prefix [e.g. /home/foo/BondFragment]: ");
     665  cin >> path;
    660666  if (mol->first->next != mol->last) {  // there are bonds
    661667    start = clock();
    662     mol->FragmentMolecule(Order1, configuration);
     668    mol->FragmentMolecule(Order1, path);
    663669    end = clock();
    664670    DoLog(0) && (Log() << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl);
    … …  
    13731379  mol->SetNameFromFilename(ConfigFileName);
    13741380
    1375   if (!strcmp(configuration->configpath, configuration->GetDefaultPath())) {
    1376     DoeLog(2) && (eLog()<< Verbose(2) << "config is found under different path then stated in config file::defaultpath!" << endl);
    1377   }
    1378 
    1379 
    13801381  // first save as PDB data
    13811382  if (ConfigFileName != NULL)
    … …  
    14771478    DoLog(0) && (Log() << Verbose(0) << "failed." << endl);
    14781479
    1479   if (!strcmp(configuration->configpath, configuration->GetDefaultPath())) {
    1480     DoeLog(2) && (eLog()<< Verbose(2) << "config is found under different path then stated in config file::defaultpath!" << endl);
    1481   }
    1482 
    14831480  World::getInstance().destroyMolecule(mol);
    14841481};
    … …  
    15001497 */
    15011498static int ParseCommandLineOptions(int argc, char **argv, MoleculeListClass *&molecules, periodentafel *&periode,
    1502                                    config& configuration, char **ConfigFileName, set<int> &ArgcList)
     1499                                   config& configuration, char **ConfigFileName, std::string &BondGraphFileName, set<int> &ArgcList)
    15031500{
    15041501  Vector x,y,z,n;  // coordinates for absolute point in cell volume
    … …  
    15131510  int argptr;
    15141511  molecule *mol = NULL;
    1515   string BondGraphFileName("\n");
    15161512
    15171513  if (argc > 1) { // config file specified as option
    … …  
    16251621      // simply create a new molecule, wherein the config file is loaded and the manipulation takes place
    16261622      DoLog(0) && (Log() << Verbose(0) << "Config file given." << endl);
     1623      std::string filenameprefix(argv[1]);
     1624      strcpy(*ConfigFileName, filenameprefix.substr(0,filenameprefix.find('.')).c_str());
     1625      DoLog(1) && (Log() << Verbose(1) << "Setting config file name prefix to " << *ConfigFileName << "." << endl);
    16271626      test.open(argv[1], ios::in);
    16281627      if (test == NULL) {
    1629         //return (1);
    1630         output.open(argv[1], ios::out);
    1631         if (output == NULL) {
    1632           DoLog(1) && (Log() << Verbose(1) << "Specified config file " << argv[1] << " not found." << endl);
    1633           configPresent = absent;
    1634         } else {
    1635           DoLog(0) && (Log() << Verbose(0) << "Empty configuration file." << endl);
    1636           strcpy(*ConfigFileName, argv[1]);
    1637           configPresent = empty;
    1638           output.close();
    1639         }
     1628        DoLog(1) && (Log() << Verbose(1) << "Specified config file " << argv[1] << " not found." << endl);
     1629        configPresent = empty;
    16401630      } else {
     1631        configPresent = present;
     1632        DoLog(1) && (Log() << Verbose(1) << "Specified config file found, parsing ... ");
     1633        FormatParserStorage::getInstance().getPcp().load(&test);
    16411634        test.close();
    1642         strcpy(*ConfigFileName, argv[1]);
    1643         DoLog(1) && (Log() << Verbose(1) << "Specified config file found, parsing ... ");
    1644         switch (configuration.TestSyntax(*ConfigFileName, periode)) {
    1645           case 1:
    1646             DoLog(0) && (Log() << Verbose(0) << "new syntax." << endl);
    1647             configuration.Load(*ConfigFileName, BondGraphFileName, periode, molecules);
    1648             configPresent = present;
    1649             break;
    1650           case 0:
    1651             DoLog(0) && (Log() << Verbose(0) << "old syntax." << endl);
    1652             configuration.LoadOld(*ConfigFileName, BondGraphFileName, periode, molecules);
    1653             configPresent = present;
    1654             break;
    1655           default:
    1656             DoLog(0) && (Log() << Verbose(0) << "Unknown syntax or empty, yet present file." << endl);
    1657             configPresent = empty;
    1658        }
    16591635      }
    16601636    } else
    … …  
    16711647       mol = World::getInstance().createMolecule();
    16721648       mol->ActiveFlag = true;
    1673        if (*ConfigFileName != NULL)
    1674          mol->SetNameFromFilename(*ConfigFileName);
    16751649       molecules->insert(mol);
    16761650     }
     1651     if (*ConfigFileName != NULL)
     1652       mol->SetNameFromFilename(*ConfigFileName);
    16771653
    16781654    // 4. parse again through options, now for those depending on elements db and config presence
    … …  
    17331709              break;
    17341710            case 'I':
    1735               DoLog(1) && (Log() << Verbose(1) << "Dissecting molecular system into a set of disconnected subgraphs ... " << endl);
    17361711              ArgcList.insert(argptr-1);
    17371712              argptr+=0;
    … …  
    19771952            case 't':
    19781953              if (ExitFlag == 0) ExitFlag = 1;
    1979               if ((argptr+4 >= argc) || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) ) {
     1954              if ((argptr+6 >= argc) || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) ) {
    19801955                ExitFlag = 255;
    19811956                DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for translation: -t <x> <y> <z> --molecule-by-id <molecule_id> --periodic <0/1>" << endl);
    … …  
    20742049            case 'f':
    20752050              if (ExitFlag == 0) ExitFlag = 1;
    2076               if ((argptr+1 >= argc) || (argv[argptr][0] == '-')) {
     2051              if ((argptr+4 >= argc) || (argv[argptr][0] == '-')) {
    20772052                ExitFlag = 255;
    2078                 DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments for fragmentation: -f <max. bond distance> <bond order>" << endl);
     2053                DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments for fragmentation: -f <path/prefix> --molecule-by-id <molecule id> --distance <max_distance> --order <order>" << endl);
     2054                performCriticalExit();
     2055              } else {
     2056                ArgcList.insert(argptr-1);
     2057                ArgcList.insert(argptr);
     2058                ArgcList.insert(argptr+1);
     2059                ArgcList.insert(argptr+2);
     2060                ArgcList.insert(argptr+3);
     2061                ArgcList.insert(argptr+4);
     2062                ArgcList.insert(argptr+5);
     2063                ArgcList.insert(argptr+6);
     2064                argptr+=7;
     2065              }
     2066              break;
     2067            case 'm':
     2068              if (ExitFlag == 0) ExitFlag = 1;
     2069              j = atoi(argv[argptr++]);
     2070              if ((j<0) || (j>1)) {
     2071                DoeLog(1) && (eLog()<< Verbose(1) << "Argument of '-m' should be either 0 for no-rotate or 1 for rotate." << endl);
     2072                j = 0;
     2073              }
     2074              if (j) {
     2075                SaveFlag = true;
     2076                DoLog(0) && (Log() << Verbose(0) << "Converting to prinicipal axis system." << endl);
     2077                mol->PrincipalAxisSystem((bool)j);
     2078              } else
     2079                ArgcList.insert(argptr-1);
     2080                argptr+=0;
     2081              break;
     2082            case 'o':
     2083              if (ExitFlag == 0) ExitFlag = 1;
     2084              if ((argptr+4 >= argc) || (argv[argptr][0] == '-')){
     2085                ExitFlag = 255;
     2086                DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for convex envelope: -o <molecule_id> --output-file <output file> --output-file <binned output file>" << endl);
    20792087                performCriticalExit();
    20802088              } else {
    … …  
    20882096              }
    20892097              break;
    2090             case 'm':
    2091               if (ExitFlag == 0) ExitFlag = 1;
    2092               j = atoi(argv[argptr++]);
    2093               if ((j<0) || (j>1)) {
    2094                 DoeLog(1) && (eLog()<< Verbose(1) << "Argument of '-m' should be either 0 for no-rotate or 1 for rotate." << endl);
    2095                 j = 0;
    2096               }
    2097               if (j) {
    2098                 SaveFlag = true;
    2099                 DoLog(0) && (Log() << Verbose(0) << "Converting to prinicipal axis system." << endl);
    2100                 mol->PrincipalAxisSystem((bool)j);
    2101               } else
    2102                 ArgcList.insert(argptr-1);
    2103                 argptr+=0;
    2104               break;
    2105             case 'o':
    2106               if (ExitFlag == 0) ExitFlag = 1;
    2107               if ((argptr+4 >= argc) || (argv[argptr][0] == '-')){
    2108                 ExitFlag = 255;
    2109                 DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for convex envelope: -o <molecule_id> --output-file <output file> --output-file <binned output file>" << endl);
    2110                 performCriticalExit();
    2111               } else {
    2112                 ArgcList.insert(argptr-1);
    2113                 ArgcList.insert(argptr);
    2114                 ArgcList.insert(argptr+1);
    2115                 ArgcList.insert(argptr+2);
    2116                 ArgcList.insert(argptr+3);
    2117                 ArgcList.insert(argptr+4);
    2118                 argptr+=5;
    2119               }
    2120               break;
    21212098            case 'U':
    21222099              if (ExitFlag == 0) ExitFlag = 1;
    … …  
    21642141      } else argptr++;
    21652142    } while (argptr < argc);
    2166     if (SaveFlag)
    2167       configuration.SaveAll(*ConfigFileName, periode, molecules);
    21682143  } else {  // no arguments, hence scan the elements db
    21692144    if (periode->LoadPeriodentafel(configuration.databasepath))
    … …  
    21712146    else
    21722147      DoLog(0) && (Log() << Verbose(0) << "Element list loading failed." << endl);
    2173     configuration.RetrieveConfigPathAndName("main_pcp_linux");
    21742148  }
    21752149  return(ExitFlag);
    … …  
    21792153
    21802154void cleanUp(){
     2155  FormatParserStorage::purgeInstance();
    21812156  ChangeTracker::purgeInstance();
    21822157  World::purgeInstance();
    … …  
    22072182    bool ArgumentsCopied = false;
    22082183    char *ConfigFileName = new char[MAXSTRINGSIZE];
     2184    std::string BondGraphFileName("\n");
     2185    FormatParserStorage::getInstance().addMpqc();
     2186    FormatParserStorage::getInstance().addPcp();
     2187    FormatParserStorage::getInstance().addXyz();
    22092188
    22102189    // print version check whether arguments are present at all
    … …  
    22352214      ArgcList.insert(1); // push back config file name
    22362215      // handle arguments by ParseCommandLineOptions()
    2237       ExitFlag = ParseCommandLineOptions(argc,argv,World::getInstance().getMolecules(),World::getInstance().getPeriode(),*World::getInstance().getConfig(), &ConfigFileName, ArgcList);
     2216      ExitFlag = ParseCommandLineOptions(argc,argv,World::getInstance().getMolecules(),World::getInstance().getPeriode(),*World::getInstance().getConfig(), &ConfigFileName, BondGraphFileName, ArgcList);
    22382217      World::getInstance().setExitFlag(ExitFlag);
    22392218      // copy all remaining arguments to a new argv
    … …  
    22482227      cout << endl;
    22492228      ArgumentsCopied = true;
     2229
     2230      // construct bond graph
     2231      if (World::getInstance().getConfig()->BG == NULL) {
     2232        World::getInstance().getConfig()->BG = new BondGraph(World::getInstance().getConfig()->GetIsAngstroem());
     2233        if (World::getInstance().getConfig()->BG->LoadBondLengthTable(BondGraphFileName)) {
     2234          DoLog(0) && (Log() << Verbose(0) << "Bond length table loaded successfully." << endl);
     2235        } else {
     2236          DoeLog(1) && (eLog()<< Verbose(1) << "Bond length table loading failed." << endl);
     2237        }
     2238      }
    22502239      // handle remaining arguments by CommandLineParser
    22512240      MapOfActions::getInstance().AddOptionsToParser();
    … …  
    22692258    }
    22702259
    2271     Log() << Verbose(0) << "Saving to " << ConfigFileName << "." << endl;
    2272     World::getInstance().getConfig()->SaveAll(ConfigFileName, World::getInstance().getPeriode(), World::getInstance().getMolecules());
     2260    std::string FilenamePrefix(ConfigFileName);
     2261    FormatParserStorage::getInstance().SetOutputPrefixForAll(FilenamePrefix);
     2262    FormatParserStorage::getInstance().SaveAll();
     2263    ChangeTracker::getInstance().saveStatus();
    22732264
    22742265  // free the new argv

  • src/config.cpp

    rdc0d21 r35b698  
    3131/** Constructor for config file class.
    3232 */
    33 config::config() : BG(NULL), Thermostats(0), PsiType(0), MaxPsiDouble(0), PsiMaxNoUp(0), PsiMaxNoDown(0), MaxMinStopStep(1), InitMaxMinStopStep(1), ProcPEGamma(8), ProcPEPsi(1), configpath(NULL),
     33config::config() : BG(NULL), Thermostats(0), PsiType(0), MaxPsiDouble(0), PsiMaxNoUp(0), PsiMaxNoDown(0), MaxMinStopStep(1), InitMaxMinStopStep(1), ProcPEGamma(8), ProcPEPsi(1),
    3434    configname(NULL), FastParsing(false), Deltat(0.01), basis(""), databasepath(NULL), DoConstrainedMD(0), MaxOuterStep(0), mainname(NULL), defaultpath(NULL), pseudopotpath(NULL),
    3535    DoOutVis(0), DoOutMes(1), DoOutNICS(0), DoOutOrbitals(0), DoOutCurrent(0), DoFullCurrent(0), DoPerturbation(0), DoWannier(0), CommonWannier(0), SawtoothStart(0.01),
    … …  
    4242  pseudopotpath = new char[MAXSTRINGSIZE];
    4343  databasepath = new char[MAXSTRINGSIZE];
    44   configpath = new char[MAXSTRINGSIZE];
    4544  configname = new char[MAXSTRINGSIZE];
    4645  Thermostats = new ThermoStatContainer();
    … …  
    4847  strcpy(defaultpath,"not specified");
    4948  strcpy(pseudopotpath,"not specified");
    50   configpath[0]='\0';
    5149  configname[0]='\0';
    5250  basis = "3-21G";
    … …  
    6159  delete[](pseudopotpath);
    6260  delete[](databasepath);
    63   delete[](configpath);
    6461  delete[](configname);
    6562  if (Thermostats != NULL)
    … …  
    383380};
    384381
    385 /** Retrieves the path in the given config file name.
    386  * \param filename config file string
    387  */
    388 void config::RetrieveConfigPathAndName(const string filename)
    389 {
    390   char *ptr = NULL;
    391   char *buffer = new char[MAXSTRINGSIZE];
    392   strncpy(buffer, filename.c_str(), MAXSTRINGSIZE);
    393   int last = -1;
    394   for(last=MAXSTRINGSIZE;last--;) {
    395     if (buffer[last] == '/')
    396       break;
    397   }
    398   if (last == -1) { // no path in front, set to local directory.
    399     strcpy(configpath, "./");
    400     ptr = buffer;
    401   } else {
    402     strncpy(configpath, buffer, last+1);
    403     ptr = &buffer[last+1];
    404     if (last < 254)
    405       configpath[last+1]='\0';
    406   }
    407   strcpy(configname, ptr);
    408   DoLog(0) && (Log() << Verbose(0) << "Found configpath: " << configpath << ", dir slash was found at " << last << ", config name is " << configname << "." << endl);
    409   delete[](buffer);
    410 };
    411 
    412382/** Loads a molecule from a ConfigFileBuffer.
    413383 * \param *mol molecule to load
    … …  
    603573  file->close();
    604574  delete(file);
    605   RetrieveConfigPathAndName(filename);
    606575
    607576  // ParseParameterFile
    … …  
    840809    return;
    841810  }
    842   RetrieveConfigPathAndName(filename);
    843811  // ParseParameters
    844812
    … …  
    15251493  molecule *mol = NULL;
    15261494
    1527   if (!strcmp(configpath, GetDefaultPath())) {
    1528     eLog() << Verbose(2) << "config is found under different path then stated in config file::defaultpath!" << endl;
    1529   }
    1530 
    1531 
    15321495  // first save as PDB data
    15331496  if (ConfigFileName != NULL)
    … …  
    15661529    mol->doCountAtoms();
    15671530    mol->CountElements();
    1568     mol->CalculateOrbitals(*this);
     1531    //mol->CalculateOrbitals(*this);
    15691532    delete[](src);
    15701533  } else {
    … …  
    15721535      mol = *(molecules->ListOfMolecules.begin());
    15731536      mol->doCountAtoms();
    1574       mol->CalculateOrbitals(*this);
     1537      //mol->CalculateOrbitals(*this);
    15751538    } else {
    15761539      DoeLog(1) && (eLog() << Verbose(1) << "There are no molecules to save!" << endl);
    … …  
    16341597  else
    16351598    Log() << Verbose(0) << "\t... failed." << endl;
    1636 
    1637   if (!strcmp(configpath, GetDefaultPath())) {
    1638     eLog() << Verbose(2) << "config is found under different path then stated in config file::defaultpath!" << endl;
    1639   }
    16401599
    16411600  // don't destroy molecule as it contains all our atoms

  • src/config.hpp

    rdc0d21 r35b698  
    4747    int ProcPEGamma;
    4848    int ProcPEPsi;
    49     char *configpath;
    5049    char *configname;
    5150    bool FastParsing;
    … …  
    117116  void Load(const char * const filename, const string &BondGraphFileName, const periodentafel * const periode, MoleculeListClass * const &MolList);
    118117  void LoadOld(const char * const filename, const string &BondGraphFileName, const periodentafel * const periode, MoleculeListClass * const &MolList);
    119   void RetrieveConfigPathAndName(const string filename);
    120118  bool Save(const char * const filename, const periodentafel * const periode, molecule * const mol) const;
    121119  bool SaveMPQC(const char * const filename, const molecule * const mol) const;

  • src/molecule.cpp

    rdc0d21 r35b698  
    7979void molecule::setName(const std::string _name){
    8080  OBSERVE;
     81  cout << "Set name of molecule " << getId() << " to " << _name << endl;
    8182  strncpy(name,_name.c_str(),MAXSTRINGSIZE);
    8283}
    … …  
    740741  else
    741742    length = strlen(molname) - strlen(endname);
     743  cout << "Set name of molecule " << getId() << " to " << molname << endl;
    742744  strncpy(name, molname, length);
    743745  name[length]='\0';
    … …  
    10041006  for(int i=MAX_ELEMENTS;i--;)
    10051007    ElementCount += (ElementsInMolecule[i] != 0 ? 1 : 0);
    1006 };
    1007 
    1008 
    1009 /** Counts necessary number of valence electrons and returns number and SpinType.
    1010  * \param configuration containing everything
    1011  */
    1012 void molecule::CalculateOrbitals(class config &configuration)
    1013 {
    1014   configuration.MaxPsiDouble = configuration.PsiMaxNoDown = configuration.PsiMaxNoUp = configuration.PsiType = 0;
    1015   for(int i=MAX_ELEMENTS;i--;) {
    1016     if (ElementsInMolecule[i] != 0) {
    1017       //Log() << Verbose(0) << "CalculateOrbitals: " << elemente->FindElement(i)->name << " has a valence of " << (int)elemente->FindElement(i)->Valence << " and there are " << ElementsInMolecule[i] << " of it." << endl;
    1018       configuration.MaxPsiDouble += ElementsInMolecule[i]*((int)elemente->FindElement(i)->Valence);
    1019     }
    1020   }
    1021   configuration.PsiMaxNoDown = configuration.MaxPsiDouble/2 + (configuration.MaxPsiDouble % 2);
    1022   configuration.PsiMaxNoUp = configuration.MaxPsiDouble/2;
    1023   configuration.MaxPsiDouble /= 2;
    1024   configuration.PsiType = (configuration.PsiMaxNoDown == configuration.PsiMaxNoUp) ? 0 : 1;
    1025   if ((configuration.PsiType == 1) && (configuration.ProcPEPsi < 2) && ((configuration.PsiMaxNoDown != 1) || (configuration.PsiMaxNoUp != 0))) {
    1026     configuration.ProcPEGamma /= 2;
    1027     configuration.ProcPEPsi *= 2;
    1028   } else {
    1029     configuration.ProcPEGamma *= configuration.ProcPEPsi;
    1030     configuration.ProcPEPsi = 1;
    1031   }
    1032   cout << configuration.PsiMaxNoDown << ">" << configuration.PsiMaxNoUp << endl;
    1033   if (configuration.PsiMaxNoDown > configuration.PsiMaxNoUp) {
    1034     configuration.InitMaxMinStopStep = configuration.MaxMinStopStep = configuration.PsiMaxNoDown;
    1035     cout << configuration.PsiMaxNoDown << " " << configuration.InitMaxMinStopStep << endl;
    1036   } else {
    1037     configuration.InitMaxMinStopStep = configuration.MaxMinStopStep = configuration.PsiMaxNoUp;
    1038     cout << configuration.PsiMaxNoUp << " " << configuration.InitMaxMinStopStep << endl;
    1039   }
    10401008};
    10411009

  • src/molecule.hpp

    rdc0d21 r35b698  
    261261  /// Count and change present atoms' coordination.
    262262  void CountElements();
    263   void CalculateOrbitals(class config &configuration);
    264263  bool CenterInBox();
    265264  bool BoundInBox();
    … …  
    288287  double MinimiseConstrainedPotential(atom **&permutation, int startstep, int endstep, bool IsAngstroem);
    289288  void EvaluateConstrainedForces(int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force);
    290   bool LinearInterpolationBetweenConfiguration(int startstep, int endstep, const char *prefix, config &configuration, bool MapByIdentity);
     289  bool LinearInterpolationBetweenConfiguration(int startstep, int endstep, std::string &prefix, config &configuration, bool MapByIdentity);
    291290       
    292291  bool CheckBounds(const Vector *x) const;
    … …  
    320319
    321320  /// Fragment molecule by two different approaches:
    322   int FragmentMolecule(int Order, config *configuration);
    323   bool CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, char *path = NULL);
    324   bool StoreBondsToFile(char *path, char *filename);
    325   bool StoreAdjacencyToFile(char *path, char *filename);
    326   bool CheckAdjacencyFileAgainstMolecule(char *path, atom **ListOfAtoms);
    327   bool ParseOrderAtSiteFromFile(char *path);
    328   bool StoreOrderAtSiteFile(char *path);
    329   bool StoreForcesFile(MoleculeListClass *BondFragments, char *path, int *SortIndex);
     321  int FragmentMolecule(int Order, std::string &prefix);
     322  bool CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, std::string path = "");
     323  bool StoreBondsToFile(std::string &filename, std::string path = "");
     324  bool StoreAdjacencyToFile(std::string &filename, std::string path = "");
     325  bool CheckAdjacencyFileAgainstMolecule(std::string &path, atom **ListOfAtoms);
     326  bool ParseOrderAtSiteFromFile(std::string &path);
     327  bool StoreOrderAtSiteFile(std::string &path);
     328  bool StoreForcesFile(MoleculeListClass *BondFragments, std::string &path, int *SortIndex);
    330329  bool CreateMappingLabelsToConfigSequence(int *&SortIndex);
    331330  bool CreateFatherLookupTable(atom **&LookupTable, int count = 0);
    … …  
    376375  ~MoleculeListClass();
    377376
    378   bool AddHydrogenCorrection(char *path);
    379   bool StoreForcesFile(char *path, int *SortIndex);
     377  bool AddHydrogenCorrection(std::string &path);
     378  bool StoreForcesFile(std::string &path, int *SortIndex);
    380379  void insert(molecule *mol);
    381380  void erase(molecule *mol);
    382381  molecule * ReturnIndex(int index);
    383   bool OutputConfigForListOfFragments(config *configuration, int *SortIndex);
     382  bool OutputConfigForListOfFragments(std::string &prefix, int *SortIndex);
    384383  int NumberOfActiveMolecules();
    385384  void Enumerate(ostream *out);

  • src/molecule_dynamics.cpp

    rdc0d21 r35b698  
    473473 * \param startstep stating initial configuration in molecule::Trajectories
    474474 * \param endstep stating final configuration in molecule::Trajectories
     475 * \param &prefix path and prefix
    475476 * \param &config configuration structure
    476477 * \param MapByIdentity if true we just use the identity to map atoms in start config to end config, if not we find mapping by \sa MinimiseConstrainedPotential()
    477478 * \return true - success in writing step files, false - error writing files or only one step in molecule::Trajectories
    478479 */
    479 bool molecule::LinearInterpolationBetweenConfiguration(int startstep, int endstep, const char *prefix, config &configuration, bool MapByIdentity)
     480bool molecule::LinearInterpolationBetweenConfiguration(int startstep, int endstep, std::string &prefix, config &configuration, bool MapByIdentity)
    480481{
    481482  molecule *mol = NULL;
    … …  
    525526  for (int i=getAtomCount(); i--; )
    526527    SortIndex[i] = i;
    527   status = MoleculePerStep->OutputConfigForListOfFragments(&configuration, SortIndex);
     528
     529  status = MoleculePerStep->OutputConfigForListOfFragments(prefix, SortIndex);
    528530  delete[](SortIndex);
    529531

  • src/molecule_fragmentation.cpp

    rdc0d21 r35b698  
    8282 * -# Scans TEFactors file and sets the TEFactor of each key set in the temporary graph accordingly
    8383 * Finally, the temporary graph is inserted into the given \a FragmentList for return.
    84  * \param *out output stream for debugging
    85  * \param *path path to file
     84 * \param &path path to file
    8685 * \param *FragmentList empty, filled on return
    8786 * \return true - parsing successfully, false - failure on parsing (FragmentList will be NULL)
    8887 */
    89 bool ParseKeySetFile(char *path, Graph *&FragmentList)
     88bool ParseKeySetFile(std::string &path, Graph *&FragmentList)
    9089{
    9190  bool status = true;
    … …  
    9493  GraphTestPair testGraphInsert;
    9594  int NumberOfFragments = 0;
    96   char filename[MAXSTRINGSIZE];
     95  string filename;
    9796
    9897  if (FragmentList == NULL) { // check list pointer
    … …  
    102101  // 1st pass: open file and read
    103102  DoLog(1) && (Log() << Verbose(1) << "Parsing the KeySet file ... " << endl);
    104   sprintf(filename, "%s/%s%s", path, FRAGMENTPREFIX, KEYSETFILE);
    105   InputFile.open(filename);
    106   if (InputFile != NULL) {
     103  filename = path + KEYSETFILE;
     104  InputFile.open(filename.c_str());
     105  if (InputFile.good()) {
    107106    // each line represents a new fragment
    108107    char buffer[MAXSTRINGSIZE];
    … …  
    181180
    182181/** Stores key sets to file.
    183  * \param *out output stream for debugging
    184182 * \param KeySetList Graph with Keysets
    185  * \param *path path to file
     183 * \param &path path to file
    186184 * \return true - file written successfully, false - writing failed
    187185 */
    188 bool StoreKeySetFile(Graph &KeySetList, char *path)
    189 {
    190   ofstream output;
     186bool StoreKeySetFile(Graph &KeySetList, std::string &path)
     187{
    191188  bool status =  true;
    192   string line;
     189  string line = path + KEYSETFILE;
     190  ofstream output(line.c_str());
    193191
    194192  // open KeySet file
    195   line = path;
    196   line.append("/");
    197   line += FRAGMENTPREFIX;
    198   line += KEYSETFILE;
    199   output.open(line.c_str(), ios::out);
    200193  DoLog(1) && (Log() << Verbose(1) << "Saving key sets of the total graph ... ");
    201   if(output != NULL) {
     194  if(output.good()) {
    202195    for(Graph::iterator runner = KeySetList.begin(); runner != KeySetList.end(); runner++) {
    203196      for (KeySet::iterator sprinter = (*runner).first.begin();sprinter != (*runner).first.end(); sprinter++) {
    … …  
    302295
    303296/** Scans the adaptive order file and insert (index, value) into map.
    304  * \param *out output stream for debugging
    305  * \param *path path to ENERGYPERFRAGMENT file (may be NULL if Order is non-negative)
     297 * \param &path path to ENERGYPERFRAGMENT file (may be NULL if Order is non-negative)
    306298 * \param &IndexedKeySetList list to find key set for a given index \a No
    307299 * \return adaptive criteria list from file
    308300 */
    309 map<int, pair<double,int> > * ScanAdaptiveFileIntoMap(char *path, map<int,KeySet> &IndexKeySetList)
     301map<int, pair<double,int> > * ScanAdaptiveFileIntoMap(std::string &path, map<int,KeySet> &IndexKeySetList)
    310302{
    311303  map<int, pair<double,int> > *AdaptiveCriteriaList = new map<int, pair<double,int> >;
    … …  
    313305  double Value = 0.;
    314306  char buffer[MAXSTRINGSIZE];
    315   sprintf(buffer, "%s/%s%s.dat", path, FRAGMENTPREFIX, ENERGYPERFRAGMENT);
    316   ifstream InputFile(buffer, ios::in);
     307  string filename = path + ENERGYPERFRAGMENT;
     308  ifstream InputFile(filename.c_str());
     309
     310  if (InputFile.fail()) {
     311    DoeLog(1) && (eLog() << Verbose(1) << "Cannot find file " << filename << "." << endl);
     312    return AdaptiveCriteriaList;
     313  }
    317314
    318315  if (CountLinesinFile(InputFile) > 0) {
    … …  
    419416
    420417/** Checks whether the OrderAtSite is still below \a Order at some site.
    421  * \param *out output stream for debugging
    422418 * \param *AtomMask defines true/false per global Atom::nr to mask in/out each nuclear site, used to activate given number of site to increment order adaptively
    423419 * \param *GlobalKeySetList list of keysets with global ids (valid in "this" molecule) needed for adaptive increase
    424420 * \param Order desired Order if positive, desired exponent in threshold criteria if negative (0 is single-step)
    425421 * \param *MinimumRingSize array of max. possible order to avoid loops
    426  * \param *path path to ENERGYPERFRAGMENT file (may be NULL if Order is non-negative)
     422 * \param path path to ENERGYPERFRAGMENT file (may be NULL if Order is non-negative)
    427423 * \return true - needs further fragmentation, false - does not need fragmentation
    428424 */
    429 bool molecule::CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, char *path)
     425bool molecule::CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, std::string path)
    430426{
    431427  bool status = false;
    … …  
    585581 * of vertex indices: Global always means the index in "this" molecule, whereas local refers to the molecule or
    586582 * subgraph in the MoleculeListClass.
    587  * \param *out output stream for debugging
    588583 * \param Order up to how many neighbouring bonds a fragment contains in BondOrderScheme::BottumUp scheme
    589  * \param *configuration configuration for writing config files for each fragment
     584 * \param &prefix path and prefix of the bond order configs to be written
    590585 * \return 1 - continue, 2 - stop (no fragmentation occured)
    591586 */
    592 int molecule::FragmentMolecule(int Order, config *configuration)
     587int molecule::FragmentMolecule(int Order, std::string &prefix)
    593588{
    594589  MoleculeListClass *BondFragments = NULL;
    … …  
    624619
    625620  // === compare it with adjacency file ===
    626   FragmentationToDo = FragmentationToDo && CheckAdjacencyFileAgainstMolecule(configuration->configpath, ListOfAtoms);
     621  FragmentationToDo = FragmentationToDo && CheckAdjacencyFileAgainstMolecule(prefix, ListOfAtoms);
    627622  delete[](ListOfAtoms);
    628623
    … …  
    658653
    659654  // ===== 3. if structure still valid, parse key set file and others =====
    660   FragmentationToDo = FragmentationToDo && ParseKeySetFile(configuration->configpath, ParsedFragmentList);
     655  FragmentationToDo = FragmentationToDo && ParseKeySetFile(prefix, ParsedFragmentList);
    661656
    662657  // ===== 4. check globally whether there's something to do actually (first adaptivity check)
    663   FragmentationToDo = FragmentationToDo && ParseOrderAtSiteFromFile(configuration->configpath);
     658  FragmentationToDo = FragmentationToDo && ParseOrderAtSiteFromFile(prefix);
    664659
    665660  // =================================== Begin of FRAGMENTATION ===============================
    … …  
    672667  AtomMask[getAtomCount()] = false;
    673668  FragmentationToDo = false;  // if CheckOrderAtSite just ones recommends fragmentation, we will save fragments afterwards
    674   while ((CheckOrder = CheckOrderAtSite(AtomMask, ParsedFragmentList, Order, MinimumRingSize, configuration->configpath))) {
     669  while ((CheckOrder = CheckOrderAtSite(AtomMask, ParsedFragmentList, Order, MinimumRingSize, prefix))) {
    675670    FragmentationToDo = FragmentationToDo || CheckOrder;
    676671    AtomMask[getAtomCount()] = true;   // last plus one entry is used as marker that we have been through this loop once already in CheckOrderAtSite()
    … …  
    727722    KeySet test = (*runner).first;
    728723    DoLog(0) && (Log() << Verbose(0) << "Fragment No." << (*runner).second.first << " with TEFactor " << (*runner).second.second << "." << endl);
    729     BondFragments->insert(StoreFragmentFromKeySet(test, configuration));
     724    BondFragments->insert(StoreFragmentFromKeySet(test, World::getInstance().getConfig()));
    730725    k++;
    731726  }
    … …  
    739734
    740735    DoLog(1) && (Log() << Verbose(1) << "Writing " << BondFragments->ListOfMolecules.size() << " possible bond fragmentation configs" << endl);
    741     if (BondFragments->OutputConfigForListOfFragments(configuration, SortIndex))
     736    if (BondFragments->OutputConfigForListOfFragments(prefix, SortIndex))
    742737      DoLog(1) && (Log() << Verbose(1) << "All configs written." << endl);
    743738    else
    … …  
    745740
    746741    // store force index reference file
    747     BondFragments->StoreForcesFile(configuration->configpath, SortIndex);
     742    BondFragments->StoreForcesFile(prefix, SortIndex);
    748743
    749744    // store keysets file
    750     StoreKeySetFile(TotalGraph, configuration->configpath);
     745    StoreKeySetFile(TotalGraph, prefix);
    751746
    752747    {
    753748      // store Adjacency file
    754       char filename[MAXSTRINGSIZE];
    755       strcpy(filename, FRAGMENTPREFIX);
    756       strcat(filename, ADJACENCYFILE);
    757       StoreAdjacencyToFile(configuration->configpath, filename);
     749      std::string filename = prefix + ADJACENCYFILE;
     750      StoreAdjacencyToFile(filename);
    758751    }
    759752
    760753    // store Hydrogen saturation correction file
    761     BondFragments->AddHydrogenCorrection(configuration->configpath);
     754    BondFragments->AddHydrogenCorrection(prefix);
    762755
    763756    // store adaptive orders into file
    764     StoreOrderAtSiteFile(configuration->configpath);
     757    StoreOrderAtSiteFile(prefix);
    765758
    766759    // restore orbital and Stop values
    767     CalculateOrbitals(*configuration);
     760    //CalculateOrbitals(*configuration);
    768761
    769762    // free memory for bond part
    … …  
    782775/** Stores pairs (Atom::nr, Atom::AdaptiveOrder) into file.
    783776 * Atoms not present in the file get "-1".
    784  * \param *out output stream for debugging
    785  * \param *path path to file ORDERATSITEFILE
     777 * \param &path path to file ORDERATSITEFILE
    786778 * \return true - file writable, false - not writable
    787779 */
    788 bool molecule::StoreOrderAtSiteFile(char *path)
    789 {
    790   stringstream line;
     780bool molecule::StoreOrderAtSiteFile(std::string &path)
     781{
     782  string line;
    791783  ofstream file;
    792784
    793   line << path << "/" << FRAGMENTPREFIX << ORDERATSITEFILE;
    794   file.open(line.str().c_str());
     785  line = path + ORDERATSITEFILE;
     786  file.open(line.c_str());
    795787  DoLog(1) && (Log() << Verbose(1) << "Writing OrderAtSite " << ORDERATSITEFILE << " ... " << endl);
    796   if (file != NULL) {
     788  if (file.good()) {
    797789    ActOnAllAtoms( &atom::OutputOrder, &file );
    798790    file.close();
    … …  
    800792    return true;
    801793  } else {
    802     DoLog(1) && (Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl);
     794    DoLog(1) && (Log() << Verbose(1) << "failed to open file " << line << "." << endl);
    803795    return false;
    804796  }
    … …  
    807799/** Parses pairs(Atom::nr, Atom::AdaptiveOrder) from file and stores in molecule's Atom's.
    808800 * Atoms not present in the file get "0".
    809  * \param *out output stream for debugging
    810  * \param *path path to file ORDERATSITEFILEe
     801 * \param &path path to file ORDERATSITEFILEe
    811802 * \return true - file found and scanned, false - file not found
    812803 * \sa ParseKeySetFile() and CheckAdjacencyFileAgainstMolecule() as this is meant to be used in conjunction with the two
    813804 */
    814 bool molecule::ParseOrderAtSiteFromFile(char *path)
     805bool molecule::ParseOrderAtSiteFromFile(std::string &path)
    815806{
    816807  unsigned char *OrderArray = new unsigned char[getAtomCount()];
    … …  
    818809  bool status;
    819810  int AtomNr, value;
    820   stringstream line;
     811  string line;
    821812  ifstream file;
    822813
    … …  
    827818
    828819  DoLog(1) && (Log() << Verbose(1) << "Begin of ParseOrderAtSiteFromFile" << endl);
    829   line << path << "/" << FRAGMENTPREFIX << ORDERATSITEFILE;
    830   file.open(line.str().c_str());
    831   if (file != NULL) {
     820  line = path + ORDERATSITEFILE;
     821  file.open(line.c_str());
     822  if (file.good()) {
    832823    while (!file.eof()) { // parse from file
    833824      AtomNr = -1;
    … …  
    850841    status = true;
    851842  } else {
    852     DoLog(1) && (Log() << Verbose(1) << "\t ... failed to open file " << line.str() << "." << endl);
     843    DoLog(1) && (Log() << Verbose(1) << "\t ... failed to open file " << line << "." << endl);
    853844    status = false;
    854845  }

  • src/molecule_graph.cpp

    rdc0d21 r35b698  
    1212#include "bondgraph.hpp"
    1313#include "config.hpp"
     14#include "defs.hpp"
    1415#include "element.hpp"
    1516#include "helpers.hpp"
    … …  
    10241025/** Storing the bond structure of a molecule to file.
    10251026 * Simply stores Atom::nr and then the Atom::nr of all bond partners per line.
    1026  * \param *path path to file
    1027  * \param *filename name of file
     1027 * \param &filename name of file
     1028 * \param path path to file, defaults to empty
    10281029 * \return true - file written successfully, false - writing failed
    10291030 */
    1030 bool molecule::StoreAdjacencyToFile(char *path, char *filename)
     1031bool molecule::StoreAdjacencyToFile(std::string &filename, std::string path)
    10311032{
    10321033  ofstream AdjacencyFile;
    1033   stringstream line;
     1034  string line;
    10341035  bool status = true;
    10351036
    1036   if (path != NULL)
    1037     line << path << "/" << filename;
     1037  if (path != "")
     1038    line = path + "/" + filename;
    10381039  else
    1039     line << filename;
    1040   AdjacencyFile.open(line.str().c_str(), ios::out);
     1040    line = filename;
     1041  AdjacencyFile.open(line.c_str(), ios::out);
    10411042  DoLog(1) && (Log() << Verbose(1) << "Saving adjacency list ... " << endl);
    1042   if (AdjacencyFile != NULL) {
     1043  if (AdjacencyFile.good()) {
    10431044    AdjacencyFile << "m\tn" << endl;
    10441045    ActOnAllAtoms(&atom::OutputAdjacency, &AdjacencyFile);
    … …  
    10461047    DoLog(1) && (Log() << Verbose(1) << "\t... done." << endl);
    10471048  } else {
    1048     DoLog(1) && (Log() << Verbose(1) << "\t... failed to open file " << line.str() << "." << endl);
     1049    DoLog(1) && (Log() << Verbose(1) << "\t... failed to open file " << line << "." << endl);
    10491050    status = false;
    10501051  }
    … …  
    10561057/** Storing the bond structure of a molecule to file.
    10571058 * Simply stores Atom::nr and then the Atom::nr of all bond partners, one per line.
    1058  * \param *path path to file
    1059  * \param *filename name of file
     1059 * \param &filename name of file
     1060 * \param path path to file, defaults to empty
    10601061 * \return true - file written successfully, false - writing failed
    10611062 */
    1062 bool molecule::StoreBondsToFile(char *path, char *filename)
     1063bool molecule::StoreBondsToFile(std::string &filename, std::string path)
    10631064{
    10641065  ofstream BondFile;
    1065   stringstream line;
     1066  string line;
    10661067  bool status = true;
    10671068
    1068   if (path != NULL)
    1069     line << path << "/" << filename;
     1069  if (path != "")
     1070    line = path + "/" + filename;
    10701071  else
    1071     line << filename;
    1072   BondFile.open(line.str().c_str(), ios::out);
     1072    line = filename;
     1073  BondFile.open(line.c_str(), ios::out);
    10731074  DoLog(1) && (Log() << Verbose(1) << "Saving adjacency list ... " << endl);
    1074   if (BondFile != NULL) {
     1075  if (BondFile.good()) {
    10751076    BondFile << "m\tn" << endl;
    10761077    ActOnAllAtoms(&atom::OutputBonds, &BondFile);
    … …  
    10781079    DoLog(1) && (Log() << Verbose(1) << "\t... done." << endl);
    10791080  } else {
    1080     DoLog(1) && (Log() << Verbose(1) << "\t... failed to open file " << line.str() << "." << endl);
     1081    DoLog(1) && (Log() << Verbose(1) << "\t... failed to open file " << line << "." << endl);
    10811082    status = false;
    10821083  }
    … …  
    10861087;
    10871088
    1088 bool CheckAdjacencyFileAgainstMolecule_Init(char *path, ifstream &File, int *&CurrentBonds)
    1089 {
    1090   stringstream filename;
    1091   filename << path << "/" << FRAGMENTPREFIX << ADJACENCYFILE;
    1092   File.open(filename.str().c_str(), ios::out);
     1089bool CheckAdjacencyFileAgainstMolecule_Init(std::string &path, ifstream &File, int *&CurrentBonds)
     1090{
     1091  string filename;
     1092  filename = path + ADJACENCYFILE;
     1093  File.open(filename.c_str(), ios::out);
    10931094  DoLog(1) && (Log() << Verbose(1) << "Looking at bond structure stored in adjacency file and comparing to present one ... " << endl);
    1094   if (File == NULL)
     1095  if (File.fail())
    10951096    return false;
    10961097
    … …  
    11461147 * \return true - structure is equal, false - not equivalence
    11471148 */
    1148 bool molecule::CheckAdjacencyFileAgainstMolecule(char *path, atom **ListOfAtoms)
     1149bool molecule::CheckAdjacencyFileAgainstMolecule(std::string &path, atom **ListOfAtoms)
    11491150{
    11501151  ifstream File;

  • src/moleculelist.cpp

    rdc0d21 r35b698  
    380380 * bonded to the same atom, then we add for this pair a correction term constructed from a Morse
    381381 * potential function fit to QM calculations with respecting to the interatomic hydrogen distance.
    382  * \param *out output stream for debugging
    383  * \param *path path to file
    384  */
    385 bool MoleculeListClass::AddHydrogenCorrection(char *path)
     382 * \param &path path to file
     383 */
     384bool MoleculeListClass::AddHydrogenCorrection(std::string &path)
    386385{
    387386  bond *Binder = NULL;
    … …  
    401400  // 0a. find dimension of matrices with constants
    402401  line = path;
    403   line.append("/");
    404   line += FRAGMENTPREFIX;
    405402  line += "1";
    406403  line += FITCONSTANTSUFFIX;
    407404  input.open(line.c_str());
    408   if (input == NULL) {
     405  if (input.fail()) {
    409406    DoLog(1) && (Log() << Verbose(1) << endl << "Unable to open " << line << ", is the directory correct?" << endl);
    410407    return false;
    … …  
    570567
    571568/** Store force indices, i.e. the connection between the nuclear index in the total molecule config and the respective atom in fragment config.
    572  * \param *out output stream for debugging
    573  * \param *path path to file
     569 * \param &path path to file
    574570 * \param *SortIndex Index to map from the BFS labeling to the sequence how of Ion_Type in the config
    575571 * \return true - file written successfully, false - writing failed
    576572 */
    577 bool MoleculeListClass::StoreForcesFile(char *path,
    578     int *SortIndex)
     573bool MoleculeListClass::StoreForcesFile(std::string &path, int *SortIndex)
    579574{
    580575  bool status = true;
    581   ofstream ForcesFile;
    582   stringstream line;
     576  string filename(path);
     577  filename += FORCESFILE;
     578  ofstream ForcesFile(filename.c_str());
    583579  periodentafel *periode=World::getInstance().getPeriode();
    584580
    585581  // open file for the force factors
    586582  DoLog(1) && (Log() << Verbose(1) << "Saving  force factors ... ");
    587   line << path << "/" << FRAGMENTPREFIX << FORCESFILE;
    588   ForcesFile.open(line.str().c_str(), ios::out);
    589   if (ForcesFile != NULL) {
     583  if (!ForcesFile.fail()) {
    590584    //Log() << Verbose(1) << "Final AtomicForcesList: ";
    591585    //output << prefix << "Forces" << endl;
    … …  
    612606  } else {
    613607    status = false;
    614     DoLog(1) && (Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl);
     608    DoLog(1) && (Log() << Verbose(1) << "failed to open file " << filename << "." << endl);
    615609  }
    616610  ForcesFile.close();
    … …  
    621615/** Writes a config file for each molecule in the given \a **FragmentList.
    622616 * \param *out output stream for debugging
    623  * \param *configuration standard configuration to attach atoms in fragment molecule to.
     617 * \param &prefix path and prefix to the fragment config files
    624618 * \param *SortIndex Index to map from the BFS labeling to the sequence how of Ion_Type in the config
    625619 * \return true - success (each file was written), false - something went wrong.
    626620 */
    627 bool MoleculeListClass::OutputConfigForListOfFragments(config *configuration, int *SortIndex)
     621bool MoleculeListClass::OutputConfigForListOfFragments(std::string &prefix, int *SortIndex)
    628622{
    629623  ofstream outputFragment;
    630   char FragmentName[MAXSTRINGSIZE];
     624  std::string FragmentName;
    631625  char PathBackup[MAXSTRINGSIZE];
    632626  bool result = true;
    … …  
    646640  for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
    647641    // save default path as it is changed for each fragment
    648     path = configuration->GetDefaultPath();
     642    path = World::getInstance().getConfig()->GetDefaultPath();
    649643    if (path != NULL)
    650644      strcpy(PathBackup, path);
    … …  
    659653    // output xyz file
    660654    FragmentNumber = FixedDigitNumber(ListOfMolecules.size(), FragmentCounter++);
    661     sprintf(FragmentName, "%s/%s%s.conf.xyz", configuration->configpath, FRAGMENTPREFIX, FragmentNumber);
    662     outputFragment.open(FragmentName, ios::out);
     655    FragmentName = prefix + FragmentNumber + ".conf.xyz";
     656    outputFragment.open(FragmentName.c_str(), ios::out);
    663657    DoLog(2) && (Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as XYZ ...");
    664658    if ((intermediateResult = (*ListRunner)->OutputXYZ(&outputFragment)))
    … …  
    683677    for (int k = 0; k < NDIM; k++) {
    684678      j += k + 1;
    685       BoxDimension[k] = 2.5 * (configuration->GetIsAngstroem() ? 1. : 1. / AtomicLengthToAngstroem);
     679      BoxDimension[k] = 2.5 * (World::getInstance().getConfig()->GetIsAngstroem() ? 1. : 1. / AtomicLengthToAngstroem);
    686680      cell_size[j] = BoxDimension[k] * 2.;
    687681    }
    … …  
    690684    // also calculate necessary orbitals
    691685    (*ListRunner)->CountElements(); // this is a bugfix, atoms should shoulds actually be added correctly to this fragment
    692     (*ListRunner)->CalculateOrbitals(*configuration);
     686    //(*ListRunner)->CalculateOrbitals(*World::getInstance().getConfig);
    693687
    694688    // change path in config
    695     //strcpy(PathBackup, configuration->configpath);
    696     sprintf(FragmentName, "%s/%s%s/", PathBackup, FRAGMENTPREFIX, FragmentNumber);
    697     configuration->SetDefaultPath(FragmentName);
     689    FragmentName = PathBackup;
     690    FragmentName += "/";
     691    FragmentName += FRAGMENTPREFIX;
     692    FragmentName += FragmentNumber;
     693    FragmentName += "/";
     694    World::getInstance().getConfig()->SetDefaultPath(FragmentName.c_str());
    698695
    699696    // and save as config
    700     sprintf(FragmentName, "%s/%s%s.conf", configuration->configpath, FRAGMENTPREFIX, FragmentNumber);
     697    FragmentName = prefix + FragmentNumber + ".conf";
    701698    DoLog(2) && (Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as config ...");
    702     if ((intermediateResult = configuration->Save(FragmentName, (*ListRunner)->elemente, (*ListRunner))))
     699    if ((intermediateResult = World::getInstance().getConfig()->Save(FragmentName.c_str(), (*ListRunner)->elemente, (*ListRunner))))
    703700      DoLog(0) && (Log() << Verbose(0) << " done." << endl);
    704701    else
    … …  
    707704
    708705    // restore old config
    709     configuration->SetDefaultPath(PathBackup);
     706    World::getInstance().getConfig()->SetDefaultPath(PathBackup);
    710707
    711708    // and save as mpqc input file
    712     sprintf(FragmentName, "%s/%s%s.conf", configuration->configpath, FRAGMENTPREFIX, FragmentNumber);
     709    FragmentName = prefix + FragmentNumber + ".conf";
    713710    DoLog(2) && (Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as mpqc input ...");
    714     if ((intermediateResult = configuration->SaveMPQC(FragmentName, (*ListRunner))))
     711    if ((intermediateResult = World::getInstance().getConfig()->SaveMPQC(FragmentName.c_str(), (*ListRunner))))
    715712      DoLog(2) && (Log() << Verbose(2) << " done." << endl);
    716713    else
    … …  
    768765
    769766  // 1. dissect the molecule into connected subgraphs
    770   if (!configuration->BG->ConstructBondGraph(mol)) {
    771     World::getInstance().destroyMolecule(mol);
    772     DoeLog(1) && (eLog()<< Verbose(1) << "There are no bonds." << endl);
     767  if (configuration->BG != NULL) {
     768    if (!configuration->BG->ConstructBondGraph(mol)) {
     769      World::getInstance().destroyMolecule(mol);
     770      DoeLog(1) && (eLog()<< Verbose(1) << "There are no bonds." << endl);
     771      return;
     772    }
     773  } else {
     774    DoeLog(1) && (eLog()<< Verbose(1) << "There is no BondGraph class present to create bonds." << endl);
    773775    return;
    774776  }

  • src/unittests/Makefile.am

    rdc0d21 r35b698  
    5252GSLLIBS = ../libgslwrapper.a $(BOOST_LIB) ${BOOST_THREAD_LIB}
    5353ALLLIBS = ../libmolecuilder.a ${GSLLIBS}
     54PARSERLIBS = ../libparser.a ${ALLLIBS}
    5455
    5556TESTSOURCES = \
    … …  
    201202
    202203ParserUnitTest_SOURCES = UnitTestMain.cpp ParserUnitTest.cpp ParserUnitTest.hpp
    203 ParserUnitTest_LDADD = ${ALLLIBS}
     204ParserUnitTest_LDADD = ${PARSERLIBS}
    204205
    205206periodentafelTest_SOURCES = UnitTestMain.cpp periodentafelTest.cpp periodentafelTest.hpp

  • tests/regression/Domain/6/post/test-x.conf.xyz

    rdc0d21 r35b698  
    1122
    22        Created by molecuilder on Mon May 31 19:07:16 2010
    3 H       9.78209 2.64589 2.64589 
    4 C       27.2836 3.27519 3.53589 
    5 C       28.5328 4.15859 3.53589 
    6 C       29.7821 3.27519 3.53589 
    7 H       27.2836 2.64589 4.42589 
    8 H       9.78209 2.64589 4.42589 
    9 H       10.672  3.90454 3.53589 
    10 H       8.53279 4.78789 2.64589 
    11 H       27.2836 2.64589 2.64589 
    12 H       26.3936 3.90454 3.53589 
    13 H       28.5328 4.78789 4.42589 
    14 H       28.5328 4.78789 2.64589 
    15 H       30.672  3.90454 3.53589 
    16 H       29.7821 2.64589 4.42589 
    17 H       29.7821 2.64589 2.64589 
    18 H       8.53279 4.78789 4.42589 
    19 H       6.39363 3.90454 3.53589 
    20 H       7.28359 2.64589 2.64589 
    21 H       7.28359 2.64589 4.42589 
    22 C       9.78209 3.27519 3.53589 
    23 C       8.53279 4.15859 3.53589 
    24 C       7.28359 3.27519 3.53589 
     3H       9.78209 2.64589 2.64589
     4C       27.2836 3.27519 3.53589
     5C       28.5328 4.15859 3.53589
     6C       29.7821 3.27519 3.53589
     7H       27.2836 2.64589 4.42589
     8H       9.78209 2.64589 4.42589
     9H       10.672  3.90454 3.53589
     10H       8.53279 4.78789 2.64589
     11H       27.2836 2.64589 2.64589
     12H       26.3936 3.90454 3.53589
     13H       28.5328 4.78789 4.42589
     14H       28.5328 4.78789 2.64589
     15H       30.672  3.90454 3.53589
     16H       29.7821 2.64589 4.42589
     17H       29.7821 2.64589 2.64589
     18H       8.53279 4.78789 4.42589
     19H       6.39363 3.90454 3.53589
     20H       7.28359 2.64589 2.64589
     21H       7.28359 2.64589 4.42589
     22C       9.78209 3.27519 3.53589
     23C       8.53279 4.15859 3.53589
     24C       7.28359 3.27519 3.53589

  • tests/regression/Domain/6/post/test-y.conf.xyz

    rdc0d21 r35b698  
    1122
    22        Created by molecuilder on Mon May 31 19:07:16 2010
    3 H       9.78209 2.64589 2.64589 
    4 C       7.28359 23.2752 3.53589 
    5 C       8.53279 24.1586 3.53589 
    6 C       9.78209 23.2752 3.53589 
    7 H       7.28359 22.6459 4.42589 
    8 H       9.78209 2.64589 4.42589 
    9 H       10.672  3.90454 3.53589 
    10 H       8.53279 4.78789 2.64589 
    11 H       7.28359 22.6459 2.64589 
    12 H       6.39363 23.9045 3.53589 
    13 H       8.53279 24.7879 4.42589 
    14 H       8.53279 24.7879 2.64589 
    15 H       10.672  23.9045 3.53589 
    16 H       9.78209 22.6459 4.42589 
    17 H       9.78209 22.6459 2.64589 
    18 H       8.53279 4.78789 4.42589 
    19 H       6.39363 3.90454 3.53589 
    20 H       7.28359 2.64589 2.64589 
    21 H       7.28359 2.64589 4.42589 
    22 C       9.78209 3.27519 3.53589 
    23 C       8.53279 4.15859 3.53589 
    24 C       7.28359 3.27519 3.53589 
     3H       9.78209 2.64589 2.64589
     4C       7.28359 23.2752 3.53589
     5C       8.53279 24.1586 3.53589
     6C       9.78209 23.2752 3.53589
     7H       7.28359 22.6459 4.42589
     8H       9.78209 2.64589 4.42589
     9H       10.672  3.90454 3.53589
     10H       8.53279 4.78789 2.64589
     11H       7.28359 22.6459 2.64589
     12H       6.39363 23.9045 3.53589
     13H       8.53279 24.7879 4.42589
     14H       8.53279 24.7879 2.64589
     15H       10.672  23.9045 3.53589
     16H       9.78209 22.6459 4.42589
     17H       9.78209 22.6459 2.64589
     18H       8.53279 4.78789 4.42589
     19H       6.39363 3.90454 3.53589
     20H       7.28359 2.64589 2.64589
     21H       7.28359 2.64589 4.42589
     22C       9.78209 3.27519 3.53589
     23C       8.53279 4.15859 3.53589
     24C       7.28359 3.27519 3.53589

  • tests/regression/Domain/6/post/test-z.conf.xyz

    rdc0d21 r35b698  
    1122
    22        Created by molecuilder on Mon May 31 19:07:16 2010
    3 H       9.78209 2.64589 2.64589 
    4 C       7.28359 3.27519 23.5359 
    5 C       8.53279 4.15859 23.5359 
    6 C       9.78209 3.27519 23.5359 
    7 H       7.28359 2.64589 24.4259 
    8 H       9.78209 2.64589 4.42589 
    9 H       10.672  3.90454 3.53589 
    10 H       8.53279 4.78789 2.64589 
    11 H       7.28359 2.64589 22.6459 
    12 H       6.39363 3.90454 23.5359 
    13 H       8.53279 4.78789 24.4259 
    14 H       8.53279 4.78789 22.6459 
    15 H       10.672  3.90454 23.5359 
    16 H       9.78209 2.64589 24.4259 
    17 H       9.78209 2.64589 22.6459 
    18 H       8.53279 4.78789 4.42589 
    19 H       6.39363 3.90454 3.53589 
    20 H       7.28359 2.64589 2.64589 
    21 H       7.28359 2.64589 4.42589 
    22 C       9.78209 3.27519 3.53589 
    23 C       8.53279 4.15859 3.53589 
    24 C       7.28359 3.27519 3.53589 
     3H       9.78209 2.64589 2.64589
     4C       7.28359 3.27519 23.5359
     5C       8.53279 4.15859 23.5359
     6C       9.78209 3.27519 23.5359
     7H       7.28359 2.64589 24.4259
     8H       9.78209 2.64589 4.42589
     9H       10.672  3.90454 3.53589
     10H       8.53279 4.78789 2.64589
     11H       7.28359 2.64589 22.6459
     12H       6.39363 3.90454 23.5359
     13H       8.53279 4.78789 24.4259
     14H       8.53279 4.78789 22.6459
     15H       10.672  3.90454 23.5359
     16H       9.78209 2.64589 24.4259
     17H       9.78209 2.64589 22.6459
     18H       8.53279 4.78789 4.42589
     19H       6.39363 3.90454 3.53589
     20H       7.28359 2.64589 2.64589
     21H       7.28359 2.64589 4.42589
     22C       9.78209 3.27519 3.53589
     23C       8.53279 4.15859 3.53589
     24C       7.28359 3.27519 3.53589

  • tests/regression/Domain/6/post/test.conf.xyz

    rdc0d21 r35b698  
    1111
    22        Created by molecuilder on Mon May 31 19:21:12 2010
    3 H       9.78209 2.64589 2.64589 
    4 H       9.78209 2.64589 4.42589 
    5 H       10.672  3.90454 3.53589 
    6 H       8.53279 4.78789 2.64589 
    7 H       8.53279 4.78789 4.42589 
    8 H       6.39363 3.90454 3.53589 
    9 H       7.28359 2.64589 2.64589 
    10 H       7.28359 2.64589 4.42589 
    11 C       9.78209 3.27519 3.53589 
    12 C       8.53279 4.15859 3.53589 
    13 C       7.28359 3.27519 3.53589 
     3H       9.78209 2.64589 2.64589
     4H       9.78209 2.64589 4.42589
     5H       10.672  3.90454 3.53589
     6H       8.53279 4.78789 2.64589
     7H       8.53279 4.78789 4.42589
     8H       6.39363 3.90454 3.53589
     9H       7.28359 2.64589 2.64589
     10H       7.28359 2.64589 4.42589
     11C       9.78209 3.27519 3.53589
     12C       8.53279 4.15859 3.53589
     13C       7.28359 3.27519 3.53589

  • tests/regression/Filling/1/post/test.conf

    rdc0d21 r35b698  
    3535RelEpsTotalE    1e-07   # relative change in total energy
    3636RelEpsKineticE  1e-05   # relative change in kinetic energy
    37 MaxMinStopStep  1350    # check every ..th steps
     37MaxMinStopStep  680     # check every ..th steps
    3838MaxMinGapStopStep       1       # check every ..th steps
    3939
    … …  
    4242InitRelEpsTotalE        1e-05   # relative change in total energy
    4343InitRelEpsKineticE      0.0001  # relative change in kinetic energy
    44 InitMaxMinStopStep      1350    # check every ..th steps
     44InitMaxMinStopStep      680     # check every ..th steps
    4545InitMaxMinGapStopStep   1       # check every ..th steps
    4646
    … …  
    5555RiemannTensor   0       # (Use metric)
    5656PsiType         0       # 0 - doubly occupied, 1 - SpinUp,SpinDown
    57 MaxPsiDouble    1350    # here: specifying both maximum number of SpinUp- and -Down-states
    58 PsiMaxNoUp      1350    # here: specifying maximum number of SpinUp-states
    59 PsiMaxNoDown    1350    # here: specifying maximum number of SpinDown-states
     57MaxPsiDouble    680     # here: specifying both maximum number of SpinUp- and -Down-states
     58PsiMaxNoUp      680     # here: specifying maximum number of SpinUp-states
     59PsiMaxNoDown    680     # here: specifying maximum number of SpinDown-states
    6060AddPsis         0       # Additional unoccupied Psis for bandgap determination
    6161

  • tests/regression/Simple_configuration/2/post/test.conf.xyz

    rdc0d21 r35b698  
    111
    22        Created by molecuilder on Tue Oct  6 18:34:23 2009
    3 H       10      10      10     
     3H       10      10      10

  • tests/regression/Simple_configuration/3/post/test.conf.xyz

    rdc0d21 r35b698  
    111
    22        Created by molecuilder on Tue Oct  6 18:34:23 2009
    3 H       10      10      10     
     3H       10      10      10

  • tests/regression/Simple_configuration/4/post/test.conf

    rdc0d21 r35b698  
    3535RelEpsTotalE    1e-07   # relative change in total energy
    3636RelEpsKineticE  1e-05   # relative change in kinetic energy
    37 MaxMinStopStep  1       # check every ..th steps
     37MaxMinStopStep  2       # check every ..th steps
    3838MaxMinGapStopStep       1       # check every ..th steps
    3939
    … …  
    4242InitRelEpsTotalE        1e-05   # relative change in total energy
    4343InitRelEpsKineticE      0.0001  # relative change in kinetic energy
    44 InitMaxMinStopStep      1       # check every ..th steps
     44InitMaxMinStopStep      2       # check every ..th steps
    4545InitMaxMinGapStopStep   1       # check every ..th steps
    4646
    … …  
    5454Level0Factor    2       # factor by which node number increases from S to 0 level
    5555RiemannTensor   0       # (Use metric)
    56 PsiType         1       # 0 - doubly occupied, 1 - SpinUp,SpinDown
    57 MaxPsiDouble    0       # here: specifying both maximum number of SpinUp- and -Down-states
    58 PsiMaxNoUp      0       # here: specifying maximum number of SpinUp-states
    59 PsiMaxNoDown    1       # here: specifying maximum number of SpinDown-states
     56PsiType         0       # 0 - doubly occupied, 1 - SpinUp,SpinDown
     57MaxPsiDouble    2       # here: specifying both maximum number of SpinUp- and -Down-states
     58PsiMaxNoUp      2       # here: specifying maximum number of SpinUp-states
     59PsiMaxNoDown    2       # here: specifying maximum number of SpinDown-states
    6060AddPsis         0       # Additional unoccupied Psis for bandgap determination
    6161

  • tests/regression/Simple_configuration/4/post/test.conf.xyz

    rdc0d21 r35b698  
    111
    22        Created by molecuilder on Tue Oct  6 18:31:23 2009
    3 C       10      10      10     
     3C       10      10      10

  • tests/regression/Simple_configuration/5/post/test.conf

    rdc0d21 r35b698  
    3535RelEpsTotalE    1e-07   # relative change in total energy
    3636RelEpsKineticE  1e-05   # relative change in kinetic energy
    37 MaxMinStopStep  1       # check every ..th steps
     37MaxMinStopStep  0       # check every ..th steps
    3838MaxMinGapStopStep       1       # check every ..th steps
    3939
    … …  
    4242InitRelEpsTotalE        1e-05   # relative change in total energy
    4343InitRelEpsKineticE      0.0001  # relative change in kinetic energy
    44 InitMaxMinStopStep      1       # check every ..th steps
     44InitMaxMinStopStep      0       # check every ..th steps
    4545InitMaxMinGapStopStep   1       # check every ..th steps
    4646
    … …  
    5454Level0Factor    2       # factor by which node number increases from S to 0 level
    5555RiemannTensor   0       # (Use metric)
    56 PsiType         1       # 0 - doubly occupied, 1 - SpinUp,SpinDown
     56PsiType         0       # 0 - doubly occupied, 1 - SpinUp,SpinDown
    5757MaxPsiDouble    0       # here: specifying both maximum number of SpinUp- and -Down-states
    5858PsiMaxNoUp      0       # here: specifying maximum number of SpinUp-states
    59 PsiMaxNoDown    1       # here: specifying maximum number of SpinDown-states
     59PsiMaxNoDown    0       # here: specifying maximum number of SpinDown-states
    6060AddPsis         0       # Additional unoccupied Psis for bandgap determination
    6161

  • tests/regression/Simple_configuration/8/post/test.conf.xyz

    rdc0d21 r35b698  
    11144
    22        Created by molecuilder on Mon May 31 18:50:20 2010
    3 H       9.78209 2.64589 2.64589 
    4 H       9.78209 2.64589 4.42589 
    5 H       10.672  3.90454 3.53589 
    6 H       8.53279 4.78789 2.64589 
    7 H       8.53279 4.78789 4.42589 
    8 H       6.39363 3.90454 3.53589 
    9 H       7.28359 2.64589 2.64589 
    10 H       7.28359 2.64589 4.42589 
    11 H       0.758602        2.85714 3.86571 
    12 H       0.758602        2.85714 2.85714 
    13 H       0.758602        2.85714 5.71429 
    14 H       0.758602        5.71429 3.86571 
    15 H       0.758602        5.71429 2.85714 
    16 H       3.61574 0       1.00857 
    17 H       3.61574 0       0       
    18 H       3.61574 0       3.86571 
    19 H       3.61574 0       2.85714 
    20 H       3.61574 0       6.72285 
    21 H       3.61574 0       5.71429 
    22 H       3.61574 2.85714 1.00857 
    23 H       3.61574 2.85714 0       
    24 H       3.61574 2.85714 3.86571 
    25 H       3.61574 2.85714 2.85714 
    26 H       3.61574 2.85714 6.72285 
    27 H       3.61574 2.85714 5.71429 
    28 H       3.61574 2.85714 8.57143 
    29 H       3.61574 5.71429 1.00857 
    30 H       3.61574 5.71429 0       
    31 H       3.61574 5.71429 3.86571 
    32 H       3.61574 5.71429 2.85714 
    33 H       3.61574 5.71429 6.72285 
    34 H       3.61574 5.71429 5.71429 
    35 H       3.61574 5.71429 8.57143 
    36 H       3.61574 8.57143 1.00857 
    37 H       3.61574 8.57143 3.86571 
    38 H       3.61574 8.57143 2.85714 
    39 H       3.61574 8.57143 5.71429 
    40 H       6.47289 0       1.00857 
    41 H       6.47289 0       0       
    42 H       6.47289 0       3.86571 
    43 H       6.47289 0       2.85714 
    44 H       6.47289 0       6.72285 
    45 H       6.47289 0       5.71429 
    46 H       6.47289 0       9.58   
    47 H       6.47289 0       8.57143 
    48 H       6.47289 2.85714 0       
    49 H       6.47289 2.85714 6.72285 
    50 H       6.47289 2.85714 9.58   
    51 H       6.47289 2.85714 8.57143 
    52 H       6.47289 5.71429 1.00857 
    53 H       6.47289 5.71429 0       
    54 H       6.47289 5.71429 6.72285 
    55 H       6.47289 5.71429 5.71429 
    56 H       6.47289 5.71429 9.58   
    57 H       6.47289 5.71429 8.57143 
    58 H       6.47289 8.57143 1.00857 
    59 H       6.47289 8.57143 0       
    60 H       6.47289 8.57143 3.86571 
    61 H       6.47289 8.57143 2.85714 
    62 H       6.47289 8.57143 6.72285 
    63 H       6.47289 8.57143 5.71429 
    64 H       9.33003 0       1.00857 
    65 H       9.33003 0       0       
    66 H       9.33003 0       3.86571 
    67 H       9.33003 0       2.85714 
    68 H       9.33003 0       6.72285 
    69 H       9.33003 0       5.71429 
    70 H       9.33003 0       8.57143 
    71 H       9.33003 2.85714 0       
    72 H       9.33003 2.85714 6.72285 
    73 H       9.33003 2.85714 9.58   
    74 H       9.33003 2.85714 8.57143 
    75 H       9.33003 5.71429 0       
    76 H       9.33003 5.71429 6.72285 
    77 H       9.33003 5.71429 9.58   
    78 H       9.33003 5.71429 8.57143 
    79 H       9.33003 8.57143 1.00857 
    80 H       9.33003 8.57143 0       
    81 H       9.33003 8.57143 3.86571 
    82 H       9.33003 8.57143 2.85714 
    83 H       9.33003 8.57143 6.72285 
    84 H       9.33003 8.57143 5.71429 
    85 H       12.1872 0       1.00857 
    86 H       12.1872 0       0       
    87 H       12.1872 0       3.86571 
    88 H       12.1872 0       2.85714 
    89 H       12.1872 0       6.72285 
    90 H       12.1872 0       5.71429 
    91 H       12.1872 2.85714 1.00857 
    92 H       12.1872 2.85714 0       
    93 H       12.1872 2.85714 6.72285 
    94 H       12.1872 2.85714 5.71429 
    95 H       12.1872 5.71429 1.00857 
    96 H       12.1872 5.71429 0       
    97 H       12.1872 5.71429 3.86571 
    98 H       12.1872 5.71429 2.85714 
    99 H       12.1872 5.71429 6.72285 
    100 H       12.1872 5.71429 5.71429 
    101 C       9.78209 3.27519 3.53589 
    102 C       8.53279 4.15859 3.53589 
    103 C       7.28359 3.27519 3.53589 
    104 O       2.85714 0       0.504284       
    105 O       2.85714 0       3.36143 
    106 O       2.85714 0       6.21857 
    107 O       2.85714 2.85714 0.504284       
    108 O       2.85714 2.85714 3.36143 
    109 O       2.85714 2.85714 6.21857 
    110 O       2.85714 5.71429 0.504284       
    111 O       2.85714 5.71429 3.36143 
    112 O       2.85714 5.71429 6.21857 
    113 O       2.85714 8.57143 3.36143 
    114 O       5.71429 0       0.504284       
    115 O       5.71429 0       3.36143 
    116 O       5.71429 0       6.21857 
    117 O       5.71429 0       9.07571 
    118 O       5.71429 2.85714 0.504284       
    119 O       5.71429 2.85714 6.21857 
    120 O       5.71429 2.85714 9.07571 
    121 O       5.71429 5.71429 0.504284       
    122 O       5.71429 5.71429 6.21857 
    123 O       5.71429 5.71429 9.07571 
    124 O       5.71429 8.57143 0.504284       
    125 O       5.71429 8.57143 3.36143 
    126 O       5.71429 8.57143 6.21857 
    127 O       8.57143 0       0.504284       
    128 O       8.57143 0       3.36143 
    129 O       8.57143 0       6.21857 
    130 O       8.57143 0       9.07571 
    131 O       8.57143 2.85714 0.504284       
    132 O       8.57143 2.85714 9.07571 
    133 O       8.57143 5.71429 0.504284       
    134 O       8.57143 5.71429 9.07571 
    135 O       8.57143 8.57143 0.504284       
    136 O       8.57143 8.57143 3.36143 
    137 O       8.57143 8.57143 6.21857 
    138 O       11.4286 0       0.504284       
    139 O       11.4286 0       3.36143 
    140 O       11.4286 0       6.21857 
    141 O       11.4286 2.85714 0.504284       
    142 O       11.4286 2.85714 6.21857 
    143 O       11.4286 2.85714 9.07571 
    144 O       11.4286 5.71429 0.504284       
    145 O       11.4286 5.71429 6.21857 
    146 O       11.4286 8.57143 3.36143 
     3H       9.78209 2.64589 2.64589
     4H       9.78209 2.64589 4.42589
     5H       10.672  3.90454 3.53589
     6H       8.53279 4.78789 2.64589
     7H       8.53279 4.78789 4.42589
     8H       6.39363 3.90454 3.53589
     9H       7.28359 2.64589 2.64589
     10H       7.28359 2.64589 4.42589
     11H       0.758602        2.85714 3.86571
     12H       0.758602        2.85714 2.85714
     13H       0.758602        2.85714 5.71429
     14H       0.758602        5.71429 3.86571
     15H       0.758602        5.71429 2.85714
     16H       3.61574 0       1.00857
     17H       3.61574 0       0
     18H       3.61574 0       3.86571
     19H       3.61574 0       2.85714
     20H       3.61574 0       6.72285
     21H       3.61574 0       5.71429
     22H       3.61574 2.85714 1.00857
     23H       3.61574 2.85714 0
     24H       3.61574 2.85714 3.86571
     25H       3.61574 2.85714 2.85714
     26H       3.61574 2.85714 6.72285
     27H       3.61574 2.85714 5.71429
     28H       3.61574 2.85714 8.57143
     29H       3.61574 5.71429 1.00857
     30H       3.61574 5.71429 0
     31H       3.61574 5.71429 3.86571
     32H       3.61574 5.71429 2.85714
     33H       3.61574 5.71429 6.72285
     34H       3.61574 5.71429 5.71429
     35H       3.61574 5.71429 8.57143
     36H       3.61574 8.57143 1.00857
     37H       3.61574 8.57143 3.86571
     38H       3.61574 8.57143 2.85714
     39H       3.61574 8.57143 5.71429
     40H       6.47289 0       1.00857
     41H       6.47289 0       0
     42H       6.47289 0       3.86571
     43H       6.47289 0       2.85714
     44H       6.47289 0       6.72285
     45H       6.47289 0       5.71429
     46H       6.47289 0       9.58
     47H       6.47289 0       8.57143
     48H       6.47289 2.85714 0
     49H       6.47289 2.85714 6.72285
     50H       6.47289 2.85714 9.58
     51H       6.47289 2.85714 8.57143
     52H       6.47289 5.71429 1.00857
     53H       6.47289 5.71429 0
     54H       6.47289 5.71429 6.72285
     55H       6.47289 5.71429 5.71429
     56H       6.47289 5.71429 9.58
     57H       6.47289 5.71429 8.57143
     58H       6.47289 8.57143 1.00857
     59H       6.47289 8.57143 0
     60H       6.47289 8.57143 3.86571
     61H       6.47289 8.57143 2.85714
     62H       6.47289 8.57143 6.72285
     63H       6.47289 8.57143 5.71429
     64H       9.33003 0       1.00857
     65H       9.33003 0       0
     66H       9.33003 0       3.86571
     67H       9.33003 0       2.85714
     68H       9.33003 0       6.72285
     69H       9.33003 0       5.71429
     70H       9.33003 0       8.57143
     71H       9.33003 2.85714 0
     72H       9.33003 2.85714 6.72285
     73H       9.33003 2.85714 9.58
     74H       9.33003 2.85714 8.57143
     75H       9.33003 5.71429 0
     76H       9.33003 5.71429 6.72285
     77H       9.33003 5.71429 9.58
     78H       9.33003 5.71429 8.57143
     79H       9.33003 8.57143 1.00857
     80H       9.33003 8.57143 0
     81H       9.33003 8.57143 3.86571
     82H       9.33003 8.57143 2.85714
     83H       9.33003 8.57143 6.72285
     84H       9.33003 8.57143 5.71429
     85H       12.1872 0       1.00857
     86H       12.1872 0       0
     87H       12.1872 0       3.86571
     88H       12.1872 0       2.85714
     89H       12.1872 0       6.72285
     90H       12.1872 0       5.71429
     91H       12.1872 2.85714 1.00857
     92H       12.1872 2.85714 0
     93H       12.1872 2.85714 6.72285
     94H       12.1872 2.85714 5.71429
     95H       12.1872 5.71429 1.00857
     96H       12.1872 5.71429 0
     97H       12.1872 5.71429 3.86571
     98H       12.1872 5.71429 2.85714
     99H       12.1872 5.71429 6.72285
     100H       12.1872 5.71429 5.71429
     101C       9.78209 3.27519 3.53589
     102C       8.53279 4.15859 3.53589
     103C       7.28359 3.27519 3.53589
     104O       2.85714 0       0.504284
     105O       2.85714 0       3.36143
     106O       2.85714 0       6.21857
     107O       2.85714 2.85714 0.504284
     108O       2.85714 2.85714 3.36143
     109O       2.85714 2.85714 6.21857
     110O       2.85714 5.71429 0.504284
     111O       2.85714 5.71429 3.36143
     112O       2.85714 5.71429 6.21857
     113O       2.85714 8.57143 3.36143
     114O       5.71429 0       0.504284
     115O       5.71429 0       3.36143
     116O       5.71429 0       6.21857
     117O       5.71429 0       9.07571
     118O       5.71429 2.85714 0.504284
     119O       5.71429 2.85714 6.21857
     120O       5.71429 2.85714 9.07571
     121O       5.71429 5.71429 0.504284
     122O       5.71429 5.71429 6.21857
     123O       5.71429 5.71429 9.07571
     124O       5.71429 8.57143 0.504284
     125O       5.71429 8.57143 3.36143
     126O       5.71429 8.57143 6.21857
     127O       8.57143 0       0.504284
     128O       8.57143 0       3.36143
     129O       8.57143 0       6.21857
     130O       8.57143 0       9.07571
     131O       8.57143 2.85714 0.504284
     132O       8.57143 2.85714 9.07571
     133O       8.57143 5.71429 0.504284
     134O       8.57143 5.71429 9.07571
     135O       8.57143 8.57143 0.504284
     136O       8.57143 8.57143 3.36143
     137O       8.57143 8.57143 6.21857
     138O       11.4286 0       0.504284
     139O       11.4286 0       3.36143
     140O       11.4286 0       6.21857
     141O       11.4286 2.85714 0.504284
     142O       11.4286 2.85714 6.21857
     143O       11.4286 2.85714 9.07571
     144O       11.4286 5.71429 0.504284
     145O       11.4286 5.71429 6.21857
     146O       11.4286 8.57143 3.36143

  • tests/regression/testsuite-fragmentation.at

    rdc0d21 r35b698  
    1212AT_SETUP([Fragmentation - Fragmentation])
    1313AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Fragmentation/2/pre/test.conf .], 0)
    14 AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 1 -f 0 --distance 1.55 --order 2], 0, [ignore], [ignore])
     14AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 1 -f ./BondFragment --molecule-by-id 0 --distance 1.55 --order 2], 0, [ignore], [ignore])
    1515AT_CHECK([ls -l BondFragment*.conf | wc -l], 0, [5
    1616], [ignore])
    … …  
    2121AT_SETUP([Fragmentation - BROKEN: Fragmentation is at MaxOrder])
    2222AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Fragmentation/3/pre/test.conf .], 0)
    23 AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 1 -f 0 --distance 1.55 --order 2], 0, [ignore], [ignore])
    24 AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 1 -f 0 --distance 1.55 --order 2], [ignore], [ignore], [ignore])
     23AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 1 -f ./BondFragment --molecule-by-id 0 --distance 1.55 --order 2], 0, [ignore], [ignore])
     24AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 1 -f ./BondFragment --molecule-by-id 0 --distance 1.55 --order 2], [ignore], [ignore], [ignore])
    2525AT_CLEANUP
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