Changeset dbe929


Ignore:
Timestamp:
Apr 25, 2008, 1:54:51 PM (17 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:
cf959d
Parents:
7151c4
Message:

Huge rewrite of initial command line parsing

config file argument is now the last one. Additionally, multiple command line options may be given consecutively (i.e. -t 1 1 1 -c 5 5 5), which is done via a while loop. Also, empty config files (if given filename is not present or with unknown syntax) are checked and status stored in enumerate ConfigStatus. This is used later as certain command line options only are possible if there has been read a valid configuration.

File:
1 edited

Legend:

Unmodified
Added
Removed

  • src/builder.cpp

    r7151c4 rdbe929  
    683683};
    684684
     685/** Tries given filename or standard on saving the config file.
     686 * \param *ConfigFileName name of file
     687 * \param *configuration pointer to configuration structure with all the values
     688 * \param *periode pointer to periodentafel structure with all the elements
     689 * \param *mol pointer to molecule structure with all the atoms and coordinates
     690 */
     691void SaveConfig(char *ConfigFileName, config *configuration, periodentafel *periode, molecule *mol)
     692{
     693  char filename[255];
     694  ofstream output;
     695
     696  // get correct valence orbitals
     697  mol->CalculateOrbitals(*configuration);
     698  configuration->InitMaxMinStopStep = configuration->MaxMinStopStep = configuration->MaxPsiDouble;
     699  if (ConfigFileName != NULL)
     700    output.open(ConfigFileName, ios::trunc);
     701  if (output == NULL)
     702    output.open("main_pcp_linux", ios::trunc);
     703  if (configuration->Save(&output, periode, mol))
     704    cout << Verbose(0) << "Saving of config file successful." << endl;
     705  else
     706    cout << Verbose(0) << "Saving of config file failed." << endl;
     707  output.close();
     708  output.clear();
     709  // and save to xyz file
     710  if (ConfigFileName != NULL) {
     711    strcpy(filename, ConfigFileName);
     712    strcat(filename, ".xyz");
     713    output.open(filename, ios::trunc);
     714  }
     715  if (output == NULL) {
     716    strcpy(filename,"main_pcp_linux");
     717    strcat(filename, ".xyz");
     718    output.open(filename, ios::trunc);
     719  }
     720  if (mol->OutputXYZ(&output))
     721    cout << Verbose(0) << "Saving of XYZ file successful." << endl;
     722  else
     723    cout << Verbose(0) << "Saving of XYZ file failed." << endl;
     724  output.close();
     725  output.clear();
     726};
     727
    685728/********************************************** Main routine **************************************/
    686  
     729
    687730int main(int argc, char **argv)
    688731{
    689732  periodentafel *periode = new periodentafel; // and a period table of all elements
    690733  molecule *mol = new molecule(periode);    // first we need an empty molecule
     734  config configuration;
    691735  double tmp1;
    692736  double bond, min_bond;
    … …  
    697741        double *factor; // unit factor if desired
    698742  bool valid; // flag if input was valid or not
    699   config configuration;
    700743  ifstream test;
    701744  ofstream output;
    702745  string line;
    703746  char filename[255];
     747  char *ConfigFileName = NULL;
    704748  int flag = 1;
    705749  int Z;
    … …  
    708752  enum BondOrderScheme Scheme = NoScheme;
    709753  enum CutCyclicBond CutCyclic;
     754  enum ConfigStatus config_present = absent;
    710755  MoleculeLeafClass *Subgraphs = NULL;
    711756  clock_t start,end;
    … …  
    713758  vector **Vectors;
    714759
    715   // Greetings
    716   cout << Verbose(0) << "Molecuilder v1" << endl << endl;
    717   cout << Verbose(0) << "Build your own molecule position set." << endl;
    718 
    719760  // load element list
    720761  periode->LoadPeriodentafel();
    … …  
    722763 
    723764  // parse config file if given
    724   if (argc >= 2) { // config file specified as option
    725         cout << Verbose(0) << "Config file given." << endl;
    726     test.open(argv[1], ios::in);
    727     if (test == NULL) {
    728       cout << Verbose(1) << "Specified config file not found." << endl;
    729       //return (1);
    730     } else {
    731       cout << Verbose(1) << "Specified config file found, parsing ...";
    732       switch (configuration.TestSyntax(&test, periode, mol)) {
    733         case 1:
    734           cout << "new syntax." << endl;
    735           configuration.Load(&test, periode, mol);
    736           break;
    737         case 0:
    738           cout << "old syntax." << endl;
    739           configuration.LoadOld(&test, periode, mol);
    740           break;
    741         default:
    742           cout << "unknown syntax or empty configuration file." << endl;
    743           //return(1);
     765  if (argc >= 1) { // config file specified as option
     766        if (argv[argc-1][0] != '-') {
     767      cout << Verbose(0) << "Config file given." << endl;
     768      test.open(argv[argc-1], ios::in);
     769      if (test == NULL) {
     770        //return (1);
     771        output.open(argv[argc-1], ios::out);
     772        if (output == NULL) {
     773          cout << Verbose(1) << "Specified config file " << argv[argc-1] << " not found." << endl;
     774          config_present = absent;
     775        } else {
     776          cout << "Empty configuration file." << endl;
     777          ConfigFileName = argv[argc-1];
     778          config_present = empty;
     779          output.close();
     780        }
     781      } else {
     782        ConfigFileName = argv[argc-1];
     783        cout << Verbose(1) << "Specified config file found, parsing ...";
     784        switch (configuration.TestSyntax(&test, periode, mol)) {
     785          case 1:
     786            cout << "new syntax." << endl;
     787            configuration.Load(&test, periode, mol);
     788            config_present = present;
     789            break;
     790          case 0:
     791            cout << "old syntax." << endl;
     792            configuration.LoadOld(&test, periode, mol);
     793            config_present = present;
     794            break;
     795          default:
     796            cout << "Unknown syntax or empty, yet present file." << endl;
     797            config_present = empty;
     798       }
     799        test.close();
    744800      }
    745       test.close();
    746     }
    747   }
    748   // command line stuff
    749   if (argc > 2) {
    750     cout << Verbose(0) << "Recognized command line argument: " << argv[2][1] << ".\n";
    751     switch(argv[2][1]) {
    752       case 't':
    753         cout << Verbose(1) << "Translating all ions to new origin." << endl;
    754         for (int i=0;i<3;i++)
    755           x.x[i] = atof(argv[3+i]);
    756         mol->Translate((const vector *)&x);
    757         break;
    758       case 'a':
    759         cout << Verbose(1) << "Adding new atom." << endl;
    760         first = new atom;
    761         for (int i=0;i<3;i++)
    762           first->x.x[i] = atof(argv[4+i]);
    763         finder = periode->start;
    764         while (finder != periode->end) {
    765           finder = finder->next;
    766           if (strncmp(finder->symbol,argv[3],3) == 0) {
    767             first->type = finder;
     801        } else
     802          config_present = absent;
     803        int argptr = 1;
     804        do {
     805          if (argv[argptr][0] == '-') {
     806        cout << Verbose(0) << "Recognized command line argument: " << argv[argptr][1] << ".\n";
     807        argptr++;
     808        switch(argv[argptr-1][1]) {
     809          case 'h':
     810          case 'H':
     811          case '?':
     812            cout << "MoleCuilder suite" << endl << "==================" << endl << endl;
     813            cout << "Usage: " << argv[0] << "[-{acsthH?vfrp}] [further arguments] [config file]" << endl;
     814            cout << "or simply " << argv[0] << " without arguments for interactive session." << endl;
     815            cout << "\t-a Z x1 x2 x3\tAdd new atom of element Z at coordinates (x1,x2,x3)." << endl;
     816            cout << "\t-c x1 x2 x3\tCenter atoms in domain with a minimum distance to boundary of (x1,x2,x3)." << endl;
     817            cout << "\t-h/-H/-?\tGive this help screen." << endl;
     818            cout << "\t-p <file>\tParse given xyz file and create raw config file from it." << endl;
     819            cout << "\t-r\t\tConvert file from an old pcp syntax." << endl;
     820            cout << "\t-t x1 x2 x3\tTranslate all atoms by this vector (x1,x2,x3)." << endl;
     821            cout << "\t-s x1 x2 x3\tScale all atom coordinates by this vector (x1,x2,x3)." << endl;
     822            cout << "\t-v/-V\t\tGives version information." << endl;
     823            return 0;
    768824            break;
     825          case 'v':
     826          case 'V':
     827            cout << argv[0] << " " << VERSIONSTRING << endl;
     828            cout << "Build your own molecule position set." << endl;
     829            return 0;
     830            break;
     831          default:   
     832            break;
     833        }
     834        if ((config_present == present) || (config_present == empty)) {
     835          switch(argv[argptr-1][1]) {
     836            case 'p':
     837              cout << Verbose(1) << "Parsing xyz file for new atoms." << endl;
     838              if (!mol->AddXYZFile(argv[argptr++]))
     839                cout << Verbose(2) << "File not found." << endl;
     840              else
     841                cout << Verbose(2) << "File found and parsed." << endl;
     842              break;
     843            default:
     844              break;
    769845          }
    770846        }
    771         mol->AddAtom(first);  // add to molecule
    772         break;
    773       case 's':
    774         j = -1;
    775         cout << Verbose(1) << "Scaling all ion positions by factor." << endl;
    776         factor = (double *) Malloc(sizeof(double)*NDIM, "main: *factor");
    777         factor[0] = atof(argv[3]);
    778         factor[1] = (argc >=4) ? atof(argv[4]) : atof(argv[3]);
    779         factor[2] = (argc >=5) ? atof(argv[5]) : atof(argv[3]);
    780         mol->Scale(&factor);
    781         for (int i=0;i<3;i++) {
    782           j += i+1;
    783           x.x[i] = atof(argv[3+i]);
    784           mol->cell_size[j]*=factor[i];
     847        if (config_present != empty) {
     848          if (config_present == present) {
     849            switch(argv[argptr-1][1]) {
     850              case 't':
     851                cout << Verbose(1) << "Translating all ions to new origin." << endl;
     852                for (int i=0;i<3;i++)
     853                  x.x[i] = atof(argv[argptr+i]);
     854                mol->Translate((const vector *)&x);
     855                argptr+=3;
     856                break;
     857              case 'a':
     858                cout << Verbose(1) << "Adding new atom." << endl;
     859                first = new atom;
     860                for (int i=0;i<3;i++)
     861                  first->x.x[i] = atof(argv[argptr+1+i]);
     862                finder = periode->start;
     863                while (finder != periode->end) {
     864                  finder = finder->next;
     865                  if (strncmp(finder->symbol,argv[argptr+1],3) == 0) {
     866                    first->type = finder;
     867                    break;
     868                  }
     869                }
     870                mol->AddAtom(first);  // add to molecule
     871                argptr+=4;
     872                break;
     873              case 's':
     874                j = -1;
     875                cout << Verbose(1) << "Scaling all ion positions by factor." << endl;
     876                factor = (double *) Malloc(sizeof(double)*NDIM, "main: *factor");
     877                factor[0] = atof(argv[argptr]);
     878                if (argc > argptr+1)
     879                  argptr++;
     880                factor[1] = atof(argv[argptr]);
     881                if (argc > argptr+1)
     882                  argptr++;
     883                factor[2] = atof(argv[argptr]);
     884                mol->Scale(&factor);
     885                for (int i=0;i<3;i++) {
     886                  j += i+1;
     887                  x.x[i] = atof(argv[3+i]);
     888                  mol->cell_size[j]*=factor[i];
     889                }
     890                Free((void **)&factor, "main: *factor");
     891                argptr+=1;
     892                break;
     893              case 'c':
     894                j = -1;
     895                cout << Verbose(1) << "Centering atoms in config file within given additional boundary." << endl;
     896                // make every coordinate positive
     897                mol->CenterEdge((ofstream *)&cout, &x);
     898                // update Box of atoms by boundary
     899                mol->SetBoxDimension(&x);
     900                // translate each coordinate by boundary
     901                j=-1;
     902                for (int i=0;i<3;i++) {
     903                  j += i+1;
     904                  x.x[i] = atof(argv[argptr++]);
     905                  mol->cell_size[j] += x.x[i]*2.;
     906                }
     907                mol->Translate((const vector *)&x);
     908                break;
     909              case 'r':
     910                cout << Verbose(1) << "Converting config file from supposed old to new syntax." << endl;
     911                break;
     912              case 'f':
     913                int i,j;
     914                flag = 0;
     915                if (argc > argptr+3) {
     916                  cout << Verbose(0) << "Creating connection matrix..." << endl;
     917                  start = clock();
     918                  mol->CreateAdjacencyList((ofstream *)&cout, atof(argv[argptr++]));
     919                  cout << Verbose(0) << "Fragmenting molecule with current connection matrix ..." << endl;
     920                  cout << Verbose(0) << "What's the desired bond scheme [(B)ottomUp/(T)opDown/(A)NOVA/(C)ombined]: ";
     921                  CutCyclic = SaturateBond;
     922                  switch (argv[argptr+1][0]) {
     923                    default:
     924                        Scheme = NoScheme;
     925                      break;
     926                    case 'B':
     927                      CutCyclic = KeepBond;
     928                    case 'b':
     929                        Scheme = BottomUp;
     930                        i = atoi(argv[argptr]);
     931                        j = 0;
     932                      break;
     933                    case 'T':
     934                      CutCyclic = KeepBond;
     935                    case 't':
     936                        Scheme = TopDown;
     937                        i = 0;
     938                        j = atoi(argv[argptr]);
     939                      break;
     940                    case 'A':
     941                      CutCyclic = KeepBond;
     942                    case 'a':
     943                        Scheme = ANOVA;
     944                        i = atoi(argv[argptr]);
     945                        j = 0;
     946                      break;
     947    //                case 'C':
     948    //                  CutCyclic = KeepBond;
     949    //                case 'c':
     950    //                    if (argc > 5) {
     951    //                      i = atoi(argv[4]);
     952    //                      j = atoi(argv[6]);
     953    //                      Scheme = Combined;
     954    //                    }
     955    //                    else
     956    //                      cerr << "Missing second bond order for TopDown fragmentation in combined approach." << endl;
     957    //                  break;
     958                  };
     959                  if (mol->first->next != mol->last) {
     960                    mol->FragmentMolecule((ofstream *)&cout, i, j, Scheme, &configuration, CutCyclic);
     961                  }
     962                  end = clock();
     963                  cout << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl;
     964                  argptr+=2;
     965                }
     966                break;
     967              default:
     968                break;
     969            }
     970          } else {
     971            cout << "Cannot apply command line parameter as no valid config file was found." << endl;
     972            return 1;
     973          }
    785974        }
    786         Free((void **)&factor, "main: *factor");
    787         break;
    788       case 'c':
    789         j = -1;
    790         cout << Verbose(1) << "Centering atoms in config file within given additional boundary." << endl;
    791         // make every coordinate positive
    792         mol->CenterEdge((ofstream *)&cout, &x);
    793         // update Box of atoms by boundary
    794         mol->SetBoxDimension(&x);
    795         // translate each coordinate by boundary
    796         j=-1;
    797         for (int i=0;i<3;i++) {
    798           j += i+1;
    799           x.x[i] = atof(argv[3+i]);
    800           mol->cell_size[j] += x.x[i]*2.;
    801         }
    802         mol->Translate((const vector *)&x);
    803         break;
    804       case 'r':
    805         cout << Verbose(1) << "Converting config file from supposed old to new syntax." << endl;
    806         break;
    807       case 'p':
    808         cout << Verbose(1) << "Parsing xyz file for new atoms." << endl;
    809         if (!mol->AddXYZFile(argv[3]))
    810           cout << Verbose(2) << "File not found." << endl;
    811         else
    812           cout << Verbose(2) << "File found and parsed." << endl;
    813         break;
    814       case 'f':
    815         int i,j;
    816         flag = 0;
    817         if (argc > 4) {
    818           cout << Verbose(0) << "Creating connection matrix..." << endl;
    819           start = clock();
    820           mol->CreateAdjacencyList((ofstream *)&cout, atof(argv[3]));
    821           cout << Verbose(0) << "Fragmenting molecule with current connection matrix ..." << endl;
    822           cout << Verbose(0) << "What's the desired bond scheme [(B)ottomUp/(T)opDown/(A)NOVA/(C)ombined]: ";
    823           CutCyclic = SaturateBond;
    824           switch (argv[5][0]) {
    825             default:
    826                 Scheme = NoScheme;
    827               break;
    828             case 'B':
    829               CutCyclic = KeepBond;
    830             case 'b':
    831                 Scheme = BottomUp;
    832                 i = atoi(argv[4]);
    833                 j = 0;
    834               break;
    835             case 'T':
    836               CutCyclic = KeepBond;
    837             case 't':
    838                 Scheme = TopDown;
    839                 i = 0;
    840                 j = atoi(argv[4]);
    841               break;
    842             case 'A':
    843               CutCyclic = KeepBond;
    844             case 'a':
    845                 Scheme = ANOVA;
    846                 i = atoi(argv[4]);
    847                 j = 0;
    848               break;
    849             case 'C':
    850               CutCyclic = KeepBond;
    851             case 'c':
    852                 if (argc > 5) {
    853                   i = atoi(argv[4]);
    854                   j = atoi(argv[6]);
    855                   Scheme = Combined;
    856                 }
    857                 else
    858                   cerr << "Missing second bond order for TopDown fragmentation in combined approach." << endl;
    859               break;
    860           };
    861           if (mol->first->next != mol->last) {
    862             mol->FragmentMolecule((ofstream *)&cout, i, j, Scheme, &configuration, CutCyclic);
    863           }
    864           end = clock();
    865           cout << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl;
    866         }
    867         break;               
    868       default:
    869         break;
    870     }
    871     if (flag) {
    872       mol->CountElements();  // this is a bugfix, atoms should should actually be added correctly to this fragment
    873       mol->CalculateOrbitals(configuration);
    874       configuration.InitMaxMinStopStep = configuration.MaxMinStopStep = configuration.MaxPsiDouble;
    875       if (argc >= 1)
    876         output.open(argv[1], ios::trunc);
    877       if (!output)
    878         output.open("main_pcp_linux", ios::trunc);
    879       if (configuration.Save(&output, periode, mol))
    880         cout << Verbose(1) << "Saving of config file successful." << endl;
    881       else
    882         cout << Verbose(1) << "Saving of config file failed." << endl;
    883       output.close();
    884       output.clear();
    885       // and save to xyz file
    886       if (argc >= 1) {
    887         strcpy(filename, argv[1]);
    888         strcat(filename, ".xyz");
    889         output.open(filename, ios::trunc);
    890       }
    891       if (output == NULL) {
    892         strcpy(filename,"main_pcp_linux");
    893         strcat(filename, ".xyz");
    894         output.open(filename, ios::trunc);
    895       }
    896       if (mol->OutputXYZ(&output))
    897         cout << Verbose(0) << "Saving of XYZ file successful." << endl;
    898       else
    899         cout << Verbose(0) << "Saving of XYZ file failed." << endl;
    900       output.close();
    901       output.clear();
    902     }
     975          } else argptr++;
     976        } while (argptr < (argc-1));
     977    if (flag)
     978      SaveConfig(ConfigFileName, &configuration, periode, mol);
    903979    delete(mol);
    904980    delete(periode);
    … …  
    11151191     
    11161192      case 's': // save to config file
    1117         // get correct valence orbitals
    1118         mol->CalculateOrbitals(configuration);
    1119         configuration.InitMaxMinStopStep = configuration.MaxMinStopStep = configuration.MaxPsiDouble;
    1120         if (argc >= 1)
    1121           output.open(argv[1], ios::trunc);
    1122         if (output == NULL)
    1123           output.open("main_pcp_linux", ios::trunc);
    1124         if (configuration.Save(&output, periode, mol))
    1125           cout << Verbose(0) << "Saving of config file successful." << endl;
    1126         else
    1127           cout << Verbose(0) << "Saving of config file failed." << endl;
    1128         output.close();
    1129         output.clear();
    1130         // and save to xyz file
    1131         if (argc >= 1) {
    1132           strcpy(filename, argv[1]);
    1133           strcat(filename, ".xyz");
    1134           output.open(filename, ios::trunc);
    1135         }
    1136         if (output == NULL) {
    1137           strcpy(filename,"main_pcp_linux");
    1138           strcat(filename, ".xyz");
    1139           output.open(filename, ios::trunc);
    1140         }
    1141         if (mol->OutputXYZ(&output))
    1142           cout << Verbose(0) << "Saving of XYZ file successful." << endl;
    1143         else
    1144           cout << Verbose(0) << "Saving of XYZ file failed." << endl;
    1145         output.close();
    1146         output.clear();
     1193        SaveConfig(ConfigFileName, &configuration, periode, mol);
    11471194        break;
    11481195    };
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