Changes in / [1ca488:1cf5df]


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52 deleted
11 edited

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  • Makefile.am

    r1ca488 r1cf5df  
    33
    44EXTRA_DIST = autogen.sh
    5 
    6 .PHONY: doc
    7 doc:
    8         cd doc && make doxygen-docs

  • doc/Doxyfile

    r1ca488 r1cf5df  
    125125# configuration options related to source browsing
    126126#---------------------------------------------------------------------------
    127 SOURCE_BROWSER         = YES
     127SOURCE_BROWSER         = NO
    128128INLINE_SOURCES         = NO
    129129STRIP_CODE_COMMENTS    = YES

  • src/Makefile.am

    r1ca488 r1cf5df  
    55ANALYSISHEADER = analysis_bonds.hpp analysis_correlation.hpp
    66
    7 ACTIONSSOURCE = Actions/Action.cpp Actions/MethodAction.cpp Actions/ActionSequence.cpp Actions/MakroAction.cpp Actions/ErrorAction.cpp Actions/ActionRegistry.cpp
    8 ACTIONSHEADER = Actions/Action.hpp Actions/MethodAction.hpp Actions/ActionSequence.hpp Actions/MakroAction.hpp Actions/ErrorAction.hpp Actions/ActionRegistry.hpp
    9 
    10 VIEWSOURCE = Views/View.cpp Views/StringView.cpp Views/MethodStringView.cpp Views/StreamStringView.cpp
    11 VIEWHEADER = Views/View.hpp Views/StringView.hpp Views/MethodStringView.hpp Views/StreamStringView.hpp
    12 
    13 MENUSOURCE = Menu/Menu.cpp Menu/TextMenu.cpp Menu/MenuItem.cpp Menu/SubMenuItem.cpp Menu/ActionMenuItem.cpp Menu/SeperatorItem.cpp Menu/DisplayMenuItem.cpp
    14 MENUHEADER = Menu/Menu.hpp Menu/TextMenu.hpp Menu/MenuItem.hpp Menu/SubMenuItem.hpp Menu/ActionMenuItem.hpp Menu/SeperatorItem.hpp Menu/DisplayMenuItem.hpp
    15 
    16 UISOURCE = ${ACTIONSSOURCE} ${VIEWSOURCE} ${MENUSOURCE} UIElements/UIFactory.cpp UIElements/TextUIFactory.cpp UIElements/MainWindow.cpp UIElements/TextWindow.cpp UIElements/Dialog.cpp UIElements/TextDialog.cpp
    17 UIHEADER = ${ACTIONSHEADER} ${VIEWHEADER} ${MENUHEADER} UIElements/UIFactory.hpp UIElements/TextUIFactory.hpp UIElements/MainWindow.hpp UIElements/TextWindow.hpp UIElements/Dialog.hpp UIElements/TextDialog.hpp
    18 
    19 SOURCE = ${ANALYSISSOURCE} ${ATOMSOURCE} ${UISOURCE} bond.cpp bondgraph.cpp boundary.cpp config.cpp element.cpp ellipsoid.cpp errorlogger.cpp graph.cpp helpers.cpp info.cpp leastsquaremin.cpp linkedcell.cpp log.cpp logger.cpp memoryusageobserver.cpp moleculelist.cpp molecule.cpp molecule_dynamics.cpp molecule_fragmentation.cpp molecule_geometry.cpp molecule_graph.cpp molecule_pointcloud.cpp parser.cpp periodentafel.cpp tesselation.cpp tesselationhelpers.cpp vector.cpp verbose.cpp menu.cpp
    20 HEADER = ${ANALYSISHEADER} ${ATOMHEADER} ${UIHEADER} bond.hpp bondgraph.hpp boundary.hpp config.hpp defs.hpp element.hpp ellipsoid.hpp errorlogger.hpp graph.hpp helpers.hpp info.hpp leastsquaremin.hpp linkedcell.hpp lists.hpp log.hpp logger.hpp memoryallocator.hpp memoryusageobserver.hpp molecule.hpp molecule_template.hpp parser.hpp periodentafel.hpp stackclass.hpp tesselation.hpp tesselationhelpers.hpp vector.hpp verbose.hpp menu.hpp
     7SOURCE = ${ANALYSISSOURCE} ${ATOMSOURCE} bond.cpp bondgraph.cpp boundary.cpp config.cpp element.cpp ellipsoid.cpp errorlogger.cpp graph.cpp helpers.cpp info.cpp leastsquaremin.cpp linkedcell.cpp log.cpp logger.cpp memoryusageobserver.cpp moleculelist.cpp molecule.cpp molecule_dynamics.cpp molecule_fragmentation.cpp molecule_geometry.cpp molecule_graph.cpp molecule_pointcloud.cpp parser.cpp periodentafel.cpp tesselation.cpp tesselationhelpers.cpp vector.cpp verbose.cpp
     8HEADER = ${ANALYSISHEADER} ${ATOMHEADER} bond.hpp bondgraph.hpp boundary.hpp config.hpp defs.hpp element.hpp ellipsoid.hpp errorlogger.hpp graph.hpp helpers.hpp info.hpp leastsquaremin.hpp linkedcell.hpp lists.hpp log.hpp logger.hpp memoryallocator.hpp memoryusageobserver.hpp molecule.hpp molecule_template.hpp parser.hpp periodentafel.hpp stackclass.hpp tesselation.hpp tesselationhelpers.hpp vector.hpp verbose.hpp
    219
    2210BOOST_LIB = $(BOOST_LDFLAGS) $(BOOST_MPL_LIB)

  • src/builder.cpp

    r1ca488 r1cf5df  
    4848
    4949
    50 #include <boost/bind.hpp>
    51 
    5250using namespace std;
    5351
    … …  
    6765#include "molecule.hpp"
    6866#include "periodentafel.hpp"
    69 #include "UIElements/UIFactory.hpp"
    70 #include "UIElements/MainWindow.hpp"
    71 #include "UIElements/Dialog.hpp"
    72 #include "Menu/ActionMenuItem.hpp"
    73 #include "Actions/ActionRegistry.hpp"
    74 #include "Actions/MethodAction.hpp"
    7567#include "version.h"
    7668
    7769/********************************************* Subsubmenu routine ************************************/
    78 #if 0
     70
    7971/** Submenu for adding atoms to the molecule.
    8072 * \param *periode periodentafel
    … …  
    11611153};
    11621154
     1155
    11631156/********************************************** Test routine **************************************/
    11641157
    … …  
    12441237};
    12451238
    1246 #endif
     1239/** Tries given filename or standard on saving the config file.
     1240 * \param *ConfigFileName name of file
     1241 * \param *configuration pointer to configuration structure with all the values
     1242 * \param *periode pointer to periodentafel structure with all the elements
     1243 * \param *molecules list of molecules structure with all the atoms and coordinates
     1244 */
     1245static void SaveConfig(char *ConfigFileName, config *configuration, periodentafel *periode, MoleculeListClass *molecules)
     1246{
     1247  char filename[MAXSTRINGSIZE];
     1248  ofstream output;
     1249  molecule *mol = new molecule(periode);
     1250  mol->SetNameFromFilename(ConfigFileName);
     1251
     1252  if (!strcmp(configuration->configpath, configuration->GetDefaultPath())) {
     1253    eLog() << Verbose(2) << "config is found under different path then stated in config file::defaultpath!" << endl;
     1254  }
     1255
     1256
     1257  // first save as PDB data
     1258  if (ConfigFileName != NULL)
     1259    strcpy(filename, ConfigFileName);
     1260  if (output == NULL)
     1261    strcpy(filename,"main_pcp_linux");
     1262  Log() << Verbose(0) << "Saving as pdb input ";
     1263  if (configuration->SavePDB(filename, molecules))
     1264    Log() << Verbose(0) << "done." << endl;
     1265  else
     1266    Log() << Verbose(0) << "failed." << endl;
     1267
     1268  // then save as tremolo data file
     1269  if (ConfigFileName != NULL)
     1270    strcpy(filename, ConfigFileName);
     1271  if (output == NULL)
     1272    strcpy(filename,"main_pcp_linux");
     1273  Log() << Verbose(0) << "Saving as tremolo data input ";
     1274  if (configuration->SaveTREMOLO(filename, molecules))
     1275    Log() << Verbose(0) << "done." << endl;
     1276  else
     1277    Log() << Verbose(0) << "failed." << endl;
     1278
     1279  // translate each to its center and merge all molecules in MoleculeListClass into this molecule
     1280  int N = molecules->ListOfMolecules.size();
     1281  int *src = new int[N];
     1282  N=0;
     1283  for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++) {
     1284    src[N++] = (*ListRunner)->IndexNr;
     1285    (*ListRunner)->Translate(&(*ListRunner)->Center);
     1286  }
     1287  molecules->SimpleMultiAdd(mol, src, N);
     1288  delete[](src);
     1289
     1290  // ... and translate back
     1291  for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++) {
     1292    (*ListRunner)->Center.Scale(-1.);
     1293    (*ListRunner)->Translate(&(*ListRunner)->Center);
     1294    (*ListRunner)->Center.Scale(-1.);
     1295  }
     1296
     1297  Log() << Verbose(0) << "Storing configuration ... " << endl;
     1298  // get correct valence orbitals
     1299  mol->CalculateOrbitals(*configuration);
     1300  configuration->InitMaxMinStopStep = configuration->MaxMinStopStep = configuration->MaxPsiDouble;
     1301  if (ConfigFileName != NULL) { // test the file name
     1302    strcpy(filename, ConfigFileName);
     1303    output.open(filename, ios::trunc);
     1304  } else if (strlen(configuration->configname) != 0) {
     1305    strcpy(filename, configuration->configname);
     1306    output.open(configuration->configname, ios::trunc);
     1307    } else {
     1308      strcpy(filename, DEFAULTCONFIG);
     1309      output.open(DEFAULTCONFIG, ios::trunc);
     1310    }
     1311  output.close();
     1312  output.clear();
     1313  Log() << Verbose(0) << "Saving of config file ";
     1314  if (configuration->Save(filename, periode, mol))
     1315    Log() << Verbose(0) << "successful." << endl;
     1316  else
     1317    Log() << Verbose(0) << "failed." << endl;
     1318
     1319  // and save to xyz file
     1320  if (ConfigFileName != NULL) {
     1321    strcpy(filename, ConfigFileName);
     1322    strcat(filename, ".xyz");
     1323    output.open(filename, ios::trunc);
     1324  }
     1325  if (output == NULL) {
     1326    strcpy(filename,"main_pcp_linux");
     1327    strcat(filename, ".xyz");
     1328    output.open(filename, ios::trunc);
     1329  }
     1330  Log() << Verbose(0) << "Saving of XYZ file ";
     1331  if (mol->MDSteps <= 1) {
     1332    if (mol->OutputXYZ(&output))
     1333      Log() << Verbose(0) << "successful." << endl;
     1334    else
     1335      Log() << Verbose(0) << "failed." << endl;
     1336  } else {
     1337    if (mol->OutputTrajectoriesXYZ(&output))
     1338      Log() << Verbose(0) << "successful." << endl;
     1339    else
     1340      Log() << Verbose(0) << "failed." << endl;
     1341  }
     1342  output.close();
     1343  output.clear();
     1344
     1345  // and save as MPQC configuration
     1346  if (ConfigFileName != NULL)
     1347    strcpy(filename, ConfigFileName);
     1348  if (output == NULL)
     1349    strcpy(filename,"main_pcp_linux");
     1350  Log() << Verbose(0) << "Saving as mpqc input ";
     1351  if (configuration->SaveMPQC(filename, mol))
     1352    Log() << Verbose(0) << "done." << endl;
     1353  else
     1354    Log() << Verbose(0) << "failed." << endl;
     1355
     1356  if (!strcmp(configuration->configpath, configuration->GetDefaultPath())) {
     1357    eLog() << Verbose(2) << "config is found under different path then stated in config file::defaultpath!" << endl;
     1358  }
     1359
     1360  delete(mol);
     1361};
    12471362
    12481363/** Parses the command line options.
    … …  
    12561371 * \return exit code (0 - successful, all else - something's wrong)
    12571372 */
    1258 static int ParseCommandLineOptions(int argc, char **argv, MoleculeListClass *&molecules, periodentafel *&periode,\
    1259                                    config& configuration, char *&ConfigFileName)
     1373static int ParseCommandLineOptions(int argc, char **argv, MoleculeListClass *&molecules, periodentafel *&periode, config& configuration, char *&ConfigFileName)
    12601374{
    12611375  Vector x,y,z,n;  // coordinates for absolute point in cell volume
    … …  
    20822196    } while (argptr < argc);
    20832197    if (SaveFlag)
    2084       configuration.SaveAll(ConfigFileName, periode, molecules);
     2198      SaveConfig(ConfigFileName, &configuration, periode, molecules);
    20852199  } else {  // no arguments, hence scan the elements db
    20862200    if (periode->LoadPeriodentafel(configuration.databasepath))
    … …  
    20932207};
    20942208
    2095 /***************************************** Functions used to build all menus **********************/
    2096 
    2097 void populateEditMoleculesMenu(Menu* editMoleculesMenu,MoleculeListClass *molecules, config *configuration, periodentafel *periode){
    2098   // build the EditMoleculesMenu
    2099   Action *createMoleculeAction = new MethodAction("createMoleculeAction",boost::bind(&MoleculeListClass::createNewMolecule,molecules,periode));
    2100   new ActionMenuItem('c',"create new molecule",editMoleculesMenu,createMoleculeAction);
    2101 
    2102   Action *loadMoleculeAction = new MethodAction("loadMoleculeAction",boost::bind(&MoleculeListClass::loadFromXYZ,molecules,periode));
    2103   new ActionMenuItem('l',"load molecule from xyz file",editMoleculesMenu,loadMoleculeAction);
    2104 
    2105   Action *changeFilenameAction = new MethodAction("changeFilenameAction",boost::bind(&MoleculeListClass::changeName,molecules));
    2106   new ActionMenuItem('n',"change molecule's name",editMoleculesMenu,changeFilenameAction);
    2107 
    2108   Action *giveFilenameAction = new MethodAction("giveFilenameAction",boost::bind(&MoleculeListClass::setMoleculeFilename,molecules));
    2109   new ActionMenuItem('N',"give molecules filename",editMoleculesMenu,giveFilenameAction);
    2110 
    2111   Action *parseAtomsAction = new MethodAction("parseAtomsAction",boost::bind(&MoleculeListClass::parseXYZIntoMolecule,molecules));
    2112   new ActionMenuItem('p',"parse atoms in xyz file into molecule",editMoleculesMenu,parseAtomsAction);
    2113 
    2114   Action *eraseMoleculeAction = new MethodAction("eraseMoleculeAction",boost::bind(&MoleculeListClass::eraseMolecule,molecules));
    2115   new ActionMenuItem('r',"remove a molecule",editMoleculesMenu,eraseMoleculeAction);
    2116 }
    2117 
    2118 
    21192209/********************************************** Main routine **************************************/
    21202210
    21212211int main(int argc, char **argv)
    21222212{
    2123   periodentafel *periode = new periodentafel;
    2124     MoleculeListClass *molecules = new MoleculeListClass;
    2125     molecule *mol = NULL;
    2126     config *configuration = new config;
    2127     Vector x, y, z, n;
    2128     ifstream test;
    2129     ofstream output;
    2130     string line;
    2131     char *ConfigFileName = NULL;
    2132     int j;
    2133     setVerbosity(0);
    2134     /* structure of ParseCommandLineOptions will be refactored later */
    2135     j = ParseCommandLineOptions(argc, argv, molecules, periode, *configuration, ConfigFileName);
    2136     switch (j){
    2137         case 255:
    2138         case 2:
    2139         case 1:
    2140             delete (molecules);
    2141             delete (periode);
    2142             delete (configuration);
    2143             Log() << Verbose(0) << "Maximum of allocated memory: " << MemoryUsageObserver::getInstance()->getMaximumUsedMemory() << endl;
    2144             Log() << Verbose(0) << "Remaining non-freed memory: " << MemoryUsageObserver::getInstance()->getUsedMemorySize() << endl;
    2145             MemoryUsageObserver::getInstance()->purgeInstance();
    2146             logger::purgeInstance();
    2147             errorLogger::purgeInstance();
    2148             return (j == 1 ? 0 : j);
    2149         default:
    2150             break;
     2213  periodentafel *periode = new periodentafel; // and a period table of all elements
     2214  MoleculeListClass *molecules = new MoleculeListClass;  // list of all molecules
     2215  molecule *mol = NULL;
     2216  config *configuration = new config;
     2217  char choice;  // menu choice char
     2218  Vector x,y,z,n;  // coordinates for absolute point in cell volume
     2219  ifstream test;
     2220  ofstream output;
     2221  string line;
     2222  char *ConfigFileName = NULL;
     2223  int j;
     2224
     2225  cout << ESPACKVersion << endl;
     2226
     2227  setVerbosity(0);
     2228
     2229  // =========================== PARSE COMMAND LINE OPTIONS ====================================
     2230  j = ParseCommandLineOptions(argc, argv, molecules, periode, *configuration, ConfigFileName);
     2231  switch(j) {
     2232    case 255:  // something went wrong
     2233    case 2:  // just for -f option
     2234    case 1:  // just for -v and -h options
     2235      delete(molecules); // also free's all molecules contained
     2236      delete(periode);
     2237      delete(configuration);
     2238      Log() << Verbose(0) <<  "Maximum of allocated memory: "
     2239        << MemoryUsageObserver::getInstance()->getMaximumUsedMemory() << endl;
     2240      Log() << Verbose(0) <<  "Remaining non-freed memory: "
     2241        << MemoryUsageObserver::getInstance()->getUsedMemorySize() << endl;
     2242      MemoryUsageObserver::getInstance()->purgeInstance();
     2243      logger::purgeInstance();
     2244      errorLogger::purgeInstance();
     2245     return (j == 1 ? 0 : j);
     2246    default:
     2247      break;
     2248  }
     2249
     2250  // General stuff
     2251  if (molecules->ListOfMolecules.size() == 0) {
     2252    mol = new molecule(periode);
     2253    if (mol->cell_size[0] == 0.) {
     2254      Log() << Verbose(0) << "enter lower tridiagonal form of basis matrix" << endl << endl;
     2255      for (int i=0;i<6;i++) {
     2256        Log() << Verbose(1) << "Cell size" << i << ": ";
     2257        cin >> mol->cell_size[i];
     2258      }
    21512259    }
    2152     if(molecules->ListOfMolecules.size() == 0){
    2153         mol = new molecule(periode);
    2154         if(mol->cell_size[0] == 0.){
    2155             Log() << Verbose(0) << "enter lower tridiagonal form of basis matrix" << endl << endl;
    2156             for(int i = 0;i < 6;i++){
    2157                 Log() << Verbose(1) << "Cell size" << i << ": ";
    2158                 cin >> mol->cell_size[i];
    2159             }
     2260    mol->ActiveFlag = true;
     2261    molecules->insert(mol);
     2262  }
     2263
     2264  // =========================== START INTERACTIVE SESSION ====================================
     2265
     2266  // now the main construction loop
     2267  Log() << Verbose(0) << endl << "Now comes the real construction..." << endl;
     2268  do {
     2269    Log() << Verbose(0) << endl << endl;
     2270    Log() << Verbose(0) << "============Molecule list=======================" << endl;
     2271    molecules->Enumerate((ofstream *)&cout);
     2272    Log() << Verbose(0) << "============Menu===============================" << endl;
     2273    Log() << Verbose(0) << "a - set molecule (in)active" << endl;
     2274    Log() << Verbose(0) << "e - edit molecules (load, parse, save)" << endl;
     2275    Log() << Verbose(0) << "g - globally manipulate atoms in molecule" << endl;
     2276    Log() << Verbose(0) << "M - Merge molecules" << endl;
     2277    Log() << Verbose(0) << "m - manipulate atoms" << endl;
     2278    Log() << Verbose(0) << "-----------------------------------------------" << endl;
     2279    Log() << Verbose(0) << "c - edit the current configuration" << endl;
     2280    Log() << Verbose(0) << "-----------------------------------------------" << endl;
     2281    Log() << Verbose(0) << "s - save current setup to config file" << endl;
     2282    Log() << Verbose(0) << "T - call the current test routine" << endl;
     2283    Log() << Verbose(0) << "q - quit" << endl;
     2284    Log() << Verbose(0) << "===============================================" << endl;
     2285    Log() << Verbose(0) << "Input: ";
     2286    cin >> choice;
     2287
     2288    switch (choice) {
     2289      case 'a':  // (in)activate molecule
     2290        {
     2291          Log() << Verbose(0) << "Enter index of molecule: ";
     2292          cin >> j;
     2293          for(MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
     2294            if ((*ListRunner)->IndexNr == j)
     2295              (*ListRunner)->ActiveFlag = !(*ListRunner)->ActiveFlag;
    21602296        }
    2161 
    2162         mol->ActiveFlag = true;
    2163         molecules->insert(mol);
    2164     }
    2165 
    2166     {
    2167       cout << ESPACKVersion << endl;
    2168 
    2169       setVerbosity(0);
    2170 
    2171       menuPopulaters populaters;
    2172       populaters.MakeEditMoleculesMenu = populateEditMoleculesMenu;
    2173 
    2174       UIFactory::makeUserInterface(UIFactory::Text);
    2175       MainWindow *mainWindow = UIFactory::get()->makeMainWindow(populaters,molecules, configuration, periode, ConfigFileName);
    2176       mainWindow->display();
    2177       delete mainWindow;
    2178     }
    2179 
    2180     if(periode->StorePeriodentafel(configuration->databasepath))
    2181         Log() << Verbose(0) << "Saving of elements.db successful." << endl;
    2182 
    2183     else
    2184         Log() << Verbose(0) << "Saving of elements.db failed." << endl;
    2185 
    2186     delete (molecules);
    2187     delete(periode);
     2297        break;
     2298
     2299      case 'c': // edit each field of the configuration
     2300       configuration->Edit();
     2301       break;
     2302
     2303      case 'e': // create molecule
     2304        EditMolecules(periode, molecules);
     2305        break;
     2306
     2307      case 'g': // manipulate molecules
     2308        ManipulateMolecules(periode, molecules, configuration);
     2309        break;
     2310
     2311      case 'M':  // merge molecules
     2312        MergeMolecules(periode, molecules);
     2313        break;
     2314
     2315      case 'm': // manipulate atoms
     2316        ManipulateAtoms(periode, molecules, configuration);
     2317        break;
     2318
     2319      case 'q': // quit
     2320        break;
     2321
     2322      case 's': // save to config file
     2323        SaveConfig(ConfigFileName, configuration, periode, molecules);
     2324        break;
     2325
     2326      case 'T':
     2327        testroutine(molecules);
     2328        break;
     2329
     2330      default:
     2331        break;
     2332    };
     2333  } while (choice != 'q');
     2334
     2335  // save element data base
     2336  if (periode->StorePeriodentafel(configuration->databasepath)) //ElementsFileName
     2337    Log() << Verbose(0) << "Saving of elements.db successful." << endl;
     2338  else
     2339    Log() << Verbose(0) << "Saving of elements.db failed." << endl;
     2340
     2341  delete(molecules); // also free's all molecules contained
     2342  delete(periode);
    21882343  delete(configuration);
    2189 
    2190 
    21912344
    21922345  Log() << Verbose(0) <<  "Maximum of allocated memory: "
    … …  
    21972350  logger::purgeInstance();
    21982351  errorLogger::purgeInstance();
    2199   UIFactory::purgeInstance();
    2200   ActionRegistry::purgeRegistry();
     2352
    22012353  return (0);
    22022354}

  • src/config.cpp

    r1ca488 r1cf5df  
    17761776};
    17771777
    1778 
    1779 /** Tries given filename or standard on saving the config file.
    1780  * \param *ConfigFileName name of file
    1781  * \param *periode pointer to periodentafel structure with all the elements
    1782  * \param *molecules list of molecules structure with all the atoms and coordinates
    1783  */
    1784 void config::SaveAll(char *ConfigFileName, periodentafel *periode, MoleculeListClass *molecules)
    1785 {
    1786   char filename[MAXSTRINGSIZE];
    1787   ofstream output;
    1788   molecule *mol = new molecule(periode);
    1789   mol->SetNameFromFilename(ConfigFileName);
    1790 
    1791   if (!strcmp(configuration->configpath, configuration->GetDefaultPath())) {
    1792     eLog() << Verbose(2) << "config is found under different path then stated in config file::defaultpath!" << endl;
    1793   }
    1794 
    1795 
    1796   // first save as PDB data
    1797   if (ConfigFileName != NULL)
    1798     strcpy(filename, ConfigFileName);
    1799   if (output == NULL)
    1800     strcpy(filename,"main_pcp_linux");
    1801   Log() << Verbose(0) << "Saving as pdb input ";
    1802   if (configuration->SavePDB(filename, molecules))
    1803     Log() << Verbose(0) << "done." << endl;
    1804   else
    1805     Log() << Verbose(0) << "failed." << endl;
    1806 
    1807   // then save as tremolo data file
    1808   if (ConfigFileName != NULL)
    1809     strcpy(filename, ConfigFileName);
    1810   if (output == NULL)
    1811     strcpy(filename,"main_pcp_linux");
    1812   Log() << Verbose(0) << "Saving as tremolo data input ";
    1813   if (configuration->SaveTREMOLO(filename, molecules))
    1814     Log() << Verbose(0) << "done." << endl;
    1815   else
    1816     Log() << Verbose(0) << "failed." << endl;
    1817 
    1818   // translate each to its center and merge all molecules in MoleculeListClass into this molecule
    1819   int N = molecules->ListOfMolecules.size();
    1820   int *src = new int[N];
    1821   N=0;
    1822   for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++) {
    1823     src[N++] = (*ListRunner)->IndexNr;
    1824     (*ListRunner)->Translate(&(*ListRunner)->Center);
    1825   }
    1826   molecules->SimpleMultiAdd(mol, src, N);
    1827   delete[](src);
    1828 
    1829   // ... and translate back
    1830   for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++) {
    1831     (*ListRunner)->Center.Scale(-1.);
    1832     (*ListRunner)->Translate(&(*ListRunner)->Center);
    1833     (*ListRunner)->Center.Scale(-1.);
    1834   }
    1835 
    1836   Log() << Verbose(0) << "Storing configuration ... " << endl;
    1837   // get correct valence orbitals
    1838   mol->CalculateOrbitals(*configuration);
    1839   configuration->InitMaxMinStopStep = configuration->MaxMinStopStep = configuration->MaxPsiDouble;
    1840   if (ConfigFileName != NULL) { // test the file name
    1841     strcpy(filename, ConfigFileName);
    1842     output.open(filename, ios::trunc);
    1843   } else if (strlen(configuration->configname) != 0) {
    1844     strcpy(filename, configuration->configname);
    1845     output.open(configuration->configname, ios::trunc);
    1846     } else {
    1847       strcpy(filename, DEFAULTCONFIG);
    1848       output.open(DEFAULTCONFIG, ios::trunc);
    1849     }
    1850   output.close();
    1851   output.clear();
    1852   Log() << Verbose(0) << "Saving of config file ";
    1853   if (configuration->Save(filename, periode, mol))
    1854     Log() << Verbose(0) << "successful." << endl;
    1855   else
    1856     Log() << Verbose(0) << "failed." << endl;
    1857 
    1858   // and save to xyz file
    1859   if (ConfigFileName != NULL) {
    1860     strcpy(filename, ConfigFileName);
    1861     strcat(filename, ".xyz");
    1862     output.open(filename, ios::trunc);
    1863   }
    1864   if (output == NULL) {
    1865     strcpy(filename,"main_pcp_linux");
    1866     strcat(filename, ".xyz");
    1867     output.open(filename, ios::trunc);
    1868   }
    1869   Log() << Verbose(0) << "Saving of XYZ file ";
    1870   if (mol->MDSteps <= 1) {
    1871     if (mol->OutputXYZ(&output))
    1872       Log() << Verbose(0) << "successful." << endl;
    1873     else
    1874       Log() << Verbose(0) << "failed." << endl;
    1875   } else {
    1876     if (mol->OutputTrajectoriesXYZ(&output))
    1877       Log() << Verbose(0) << "successful." << endl;
    1878     else
    1879       Log() << Verbose(0) << "failed." << endl;
    1880   }
    1881   output.close();
    1882   output.clear();
    1883 
    1884   // and save as MPQC configuration
    1885   if (ConfigFileName != NULL)
    1886     strcpy(filename, ConfigFileName);
    1887   if (output == NULL)
    1888     strcpy(filename,"main_pcp_linux");
    1889   Log() << Verbose(0) << "Saving as mpqc input ";
    1890   if (configuration->SaveMPQC(filename, mol))
    1891     Log() << Verbose(0) << "done." << endl;
    1892   else
    1893     Log() << Verbose(0) << "failed." << endl;
    1894 
    1895   if (!strcmp(configuration->configpath, configuration->GetDefaultPath())) {
    1896     eLog() << Verbose(2) << "config is found under different path then stated in config file::defaultpath!" << endl;
    1897   }
    1898 
    1899   delete(mol);
    1900 };
    1901 
    19021778/** Reads parameter from a parsed file.
    19031779 * The file is either parsed for a certain keyword or if null is given for

  • src/config.hpp

    r1ca488 r1cf5df  
    146146  bool SaveTREMOLO(const char * const filename, const MoleculeListClass * const MolList) const;
    147147
    148   void SaveAll(char *ConfigFileName, periodentafel *periode, MoleculeListClass *molecules);
    149 
    150148  void Edit();
    151149  bool GetIsAngstroem() const;

  • src/defs.hpp

    r1ca488 r1cf5df  
    7777#define UPDATECOUNT 10  //!< update ten sites per BOSSANOVA interval
    7878
    79 #define STD_MENU_LENGTH 60
    80 #define STD_MENU_TITLE_SPACER '='
    81 #define STD_SEPERATOR_SPACER '-'
    82 
    8379#endif /*DEFS_HPP_*/

  • src/molecule.cpp

    r1ca488 r1cf5df  
    10811081  }
    10821082};
    1083 
    1084 void molecule::flipActiveFlag(){
    1085   ActiveFlag = !ActiveFlag;
    1086 }

  • src/molecule.hpp

    r1ca488 r1cf5df  
    297297  bool OutputTemperatureFromTrajectories(ofstream * const output, int startstep, int endstep);
    298298
    299   // Manipulation routines
    300   void flipActiveFlag();
    301 
    302299  private:
    303300  int last_atom;      //!< number given to last atom
    … …  
    328325  int CountAllAtoms() const;
    329326
    330   // Methods moved here from the menus
    331   // TODO: more refactoring needed on these methods
    332   void flipChosen();
    333   void createNewMolecule(periodentafel *periode);
    334   void loadFromXYZ(periodentafel *periode);
    335   void changeName();
    336   void setMoleculeFilename();
    337   void parseXYZIntoMolecule();
    338   void eraseMolecule();
    339 
    340 
    341327  // merging of molecules
    342328  bool SimpleMerge(molecule *mol, molecule *srcmol);

  • src/moleculelist.cpp

    r1ca488 r1cf5df  
    142142
    143143  // header
    144   (*out) << "Index\tName\t\tAtoms\tFormula\tCenter\tSize" << endl;
    145   (*out) << "-----------------------------------------------" << endl;
     144  Log() << Verbose(0) << "Index\tName\t\tAtoms\tFormula\tCenter\tSize" << endl;
     145  Log() << Verbose(0) << "-----------------------------------------------" << endl;
    146146  if (ListOfMolecules.size() == 0)
    147     (*out) << "\tNone" << endl;
     147    Log() << Verbose(0) << "\tNone" << endl;
    148148  else {
    149149    Origin.Zero();
    … …  
    162162      }
    163163      // output Index, Name, number of atoms, chemical formula
    164       (*out) << ((*ListRunner)->ActiveFlag ? "*" : " ") << (*ListRunner)->IndexNr << "\t" << (*ListRunner)->name << "\t\t" << (*ListRunner)->AtomCount << "\t";
     164      Log() << Verbose(0) << ((*ListRunner)->ActiveFlag ? "*" : " ") << (*ListRunner)->IndexNr << "\t" << (*ListRunner)->name << "\t\t" << (*ListRunner)->AtomCount << "\t";
    165165      Elemental = (*ListRunner)->elemente->end;
    166166      while(Elemental->previous != (*ListRunner)->elemente->start) {
    167167        Elemental = Elemental->previous;
    168168        if (Counts[Elemental->Z] != 0)
    169           (*out) << Elemental->symbol << Counts[Elemental->Z];
     169          Log() << Verbose(0) << Elemental->symbol << Counts[Elemental->Z];
    170170      }
    171171      // Center and size
    172       (*out) << "\t" << (*ListRunner)->Center << "\t" << sqrt(size) << endl;
     172      Log() << Verbose(0) << "\t" << (*ListRunner)->Center << "\t" << sqrt(size) << endl;
    173173    }
    174174  }
    … …  
    844844}
    845845
    846 /***********
    847  * Methods Moved here from the menus
    848  */
    849 
    850 void MoleculeListClass::flipChosen() {
    851   int j;
    852   Log() << Verbose(0) << "Enter index of molecule: ";
    853   cin >> j;
    854   for(MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++)
    855     if ((*ListRunner)->IndexNr == j)
    856       (*ListRunner)->ActiveFlag = !(*ListRunner)->ActiveFlag;
    857 }
    858 
    859 void MoleculeListClass::createNewMolecule(periodentafel *periode) {
    860   molecule *mol = NULL;
    861   mol = new molecule(periode);
    862   insert(mol);
    863 };
    864 
    865 void MoleculeListClass::loadFromXYZ(periodentafel *periode){
    866   molecule *mol = NULL;
    867   Vector center;
    868   char filename[MAXSTRINGSIZE];
    869   Log() << Verbose(0) << "Format should be XYZ with: ShorthandOfElement\tX\tY\tZ" << endl;
    870   mol = new molecule(periode);
    871   do {
    872     Log() << Verbose(0) << "Enter file name: ";
    873     cin >> filename;
    874   } while (!mol->AddXYZFile(filename));
    875   mol->SetNameFromFilename(filename);
    876   // center at set box dimensions
    877   mol->CenterEdge(&center);
    878   mol->cell_size[0] = center.x[0];
    879   mol->cell_size[1] = 0;
    880   mol->cell_size[2] = center.x[1];
    881   mol->cell_size[3] = 0;
    882   mol->cell_size[4] = 0;
    883   mol->cell_size[5] = center.x[2];
    884   insert(mol);
    885 }
    886 
    887 void MoleculeListClass::changeName(){
    888   char filename[MAXSTRINGSIZE];
    889   molecule *mol = NULL;
    890   int nr;
    891   do {
    892     Log() << Verbose(0) << "Enter index of molecule: ";
    893     cin >> nr;
    894     mol = ReturnIndex(nr);
    895   } while (mol == NULL);
    896   Log() << Verbose(0) << "Enter name: ";
    897   cin >> filename;
    898   strcpy(mol->name, filename);
    899 }
    900 
    901 void MoleculeListClass::setMoleculeFilename() {
    902   char filename[MAXSTRINGSIZE];
    903   int nr;
    904   molecule *mol = NULL;
    905   do {
    906     Log() << Verbose(0) << "Enter index of molecule: ";
    907     cin >> nr;
    908     mol = ReturnIndex(nr);
    909   } while (mol == NULL);
    910   Log() << Verbose(0) << "Enter name: ";
    911   cin >> filename;
    912   mol->SetNameFromFilename(filename);
    913 }
    914 
    915 void MoleculeListClass::parseXYZIntoMolecule(){
    916   char filename[MAXSTRINGSIZE];
    917   int nr;
    918   molecule *mol = NULL;
    919   mol = NULL;
    920   do {
    921    Log() << Verbose(0) << "Enter index of molecule: ";
    922    cin >> nr;
    923    mol = ReturnIndex(nr);
    924   } while (mol == NULL);
    925   Log() << Verbose(0) << "Format should be XYZ with: ShorthandOfElement\tX\tY\tZ" << endl;
    926   do {
    927    Log() << Verbose(0) << "Enter file name: ";
    928    cin >> filename;
    929   } while (!mol->AddXYZFile(filename));
    930   mol->SetNameFromFilename(filename);
    931 };
    932 
    933 void MoleculeListClass::eraseMolecule(){
    934   int nr;
    935   molecule *mol = NULL;
    936   Log() << Verbose(0) << "Enter index of molecule: ";
    937   cin >> nr;
    938   for(MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++)
    939     if (nr == (*ListRunner)->IndexNr) {
    940       mol = *ListRunner;
    941       ListOfMolecules.erase(ListRunner);
    942       delete(mol);
    943       break;
    944     }
    945 };
    946 
    947846
    948847/******************************************* Class MoleculeLeafClass ************************************************/

  • src/unittests/Makefile.am

    r1ca488 r1cf5df  
    44AM_CXXFLAGS = $(CPPUNIT_CFLAGS)
    55
    6 MENUTESTS = ActionSequenceTest
    7 
    8 TESTS = ActOnAllUnitTest AnalysisBondsUnitTests AnalysisCorrelationToPointUnitTest AnalysisCorrelationToSurfaceUnitTest AnalysisPairCorrelationUnitTest BondGraphUnitTest InfoUnitTest ListOfBondsUnitTest LogUnitTest MemoryUsageObserverUnitTest MemoryAllocatorUnitTest StackClassUnitTest VectorUnitTest ${MENUTESTS}
    9 
     6TESTS = ActOnAllUnitTest AnalysisBondsUnitTests AnalysisCorrelationToPointUnitTest AnalysisCorrelationToSurfaceUnitTest AnalysisPairCorrelationUnitTest BondGraphUnitTest InfoUnitTest ListOfBondsUnitTest LogUnitTest MemoryUsageObserverUnitTest MemoryAllocatorUnitTest StackClassUnitTest VectorUnitTest
    107check_PROGRAMS = $(TESTS)
    118noinst_PROGRAMS = $(TESTS)
    … …  
    5047VectorUnitTest_LDADD = ../libmolecuilder.a
    5148
    52 ActionSequenceTest_SOURCES = ActionSequenceTest.cpp ActionSequenceTest.hpp
    53 ActionSequenceTest_LDADD = ../libmolecuilder.a
    5449
    5550#AUTOMAKE_OPTIONS = parallel-tests
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