Changes in / [04b6f9:244a84]


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11 edited

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  • Makefile.am

    r04b6f9 r244a84  
    33
    44EXTRA_DIST = autogen.sh
    5 
    6 .PHONY: doc
    7 doc:
    8         cd doc && make doxygen-docs

  • doc/Doxyfile

    r04b6f9 r244a84  
    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

    r04b6f9 r244a84  
    88ANALYSISHEADER = analysis_bonds.hpp analysis_correlation.hpp
    99
    10 ACTIONSSOURCE = Actions/Action.cpp Actions/MethodAction.cpp Actions/ActionSequence.cpp Actions/MakroAction.cpp Actions/ErrorAction.cpp Actions/ActionRegistry.cpp
    11 ACTIONSHEADER = Actions/Action.hpp Actions/MethodAction.hpp Actions/ActionSequence.hpp Actions/MakroAction.hpp Actions/ErrorAction.hpp Actions/ActionRegistry.hpp
    12 
    13 VIEWSOURCE = Views/View.cpp Views/StringView.cpp Views/MethodStringView.cpp Views/StreamStringView.cpp
    14 VIEWHEADER = Views/View.hpp Views/StringView.hpp Views/MethodStringView.hpp Views/StreamStringView.hpp
    15 
    16 MENUSOURCE = Menu/Menu.cpp Menu/TextMenu.cpp Menu/MenuItem.cpp Menu/SubMenuItem.cpp Menu/ActionMenuItem.cpp Menu/SeperatorItem.cpp Menu/DisplayMenuItem.cpp
    17 MENUHEADER = Menu/Menu.hpp Menu/TextMenu.hpp Menu/MenuItem.hpp Menu/SubMenuItem.hpp Menu/ActionMenuItem.hpp Menu/SeperatorItem.hpp Menu/DisplayMenuItem.hpp
    18 
    19 UISOURCE = ${ACTIONSSOURCE} ${VIEWSOURCE} ${MENUSOURCE} UIElements/UIFactory.cpp UIElements/TextUIFactory.cpp UIElements/MainWindow.cpp UIElements/TextWindow.cpp UIElements/Dialog.cpp UIElements/TextDialog.cpp
    20 UIHEADER = ${ACTIONSHEADER} ${VIEWHEADER} ${MENUHEADER} UIElements/UIFactory.hpp UIElements/TextUIFactory.hpp UIElements/MainWindow.hpp UIElements/TextWindow.hpp UIElements/Dialog.hpp UIElements/TextDialog.hpp
    21 
    22 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
    23 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
     10SOURCE = ${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
     11HEADER = ${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
    2412
    2513BOOST_LIB = $(BOOST_LDFLAGS) $(BOOST_MPL_LIB)

  • src/builder.cpp

    r04b6f9 r244a84  
    4848
    4949
    50 #include <boost/bind.hpp>
    51 
    5250using namespace std;
    5351
    … …  
    6967#include "molecule.hpp"
    7068#include "periodentafel.hpp"
    71 #include "UIElements/UIFactory.hpp"
    72 #include "UIElements/MainWindow.hpp"
    73 #include "UIElements/Dialog.hpp"
    74 #include "Menu/ActionMenuItem.hpp"
    75 #include "Actions/ActionRegistry.hpp"
    76 #include "Actions/MethodAction.hpp"
    7769#include "version.h"
    7870
    7971/********************************************* Subsubmenu routine ************************************/
    80 #if 0
     72
    8173/** Submenu for adding atoms to the molecule.
    8274 * \param *periode periodentafel
    … …  
    11631155};
    11641156
     1157
    11651158/********************************************** Test routine **************************************/
    11661159
    … …  
    12461239};
    12471240
    1248 #endif
     1241/** Tries given filename or standard on saving the config file.
     1242 * \param *ConfigFileName name of file
     1243 * \param *configuration pointer to configuration structure with all the values
     1244 * \param *periode pointer to periodentafel structure with all the elements
     1245 * \param *molecules list of molecules structure with all the atoms and coordinates
     1246 */
     1247static void SaveConfig(char *ConfigFileName, config *configuration, periodentafel *periode, MoleculeListClass *molecules)
     1248{
     1249  char filename[MAXSTRINGSIZE];
     1250  ofstream output;
     1251  molecule *mol = new molecule(periode);
     1252  mol->SetNameFromFilename(ConfigFileName);
     1253
     1254  if (!strcmp(configuration->configpath, configuration->GetDefaultPath())) {
     1255    eLog() << Verbose(2) << "config is found under different path then stated in config file::defaultpath!" << endl;
     1256  }
     1257
     1258
     1259  // first save as PDB data
     1260  if (ConfigFileName != NULL)
     1261    strcpy(filename, ConfigFileName);
     1262  if (output == NULL)
     1263    strcpy(filename,"main_pcp_linux");
     1264  Log() << Verbose(0) << "Saving as pdb input ";
     1265  if (configuration->SavePDB(filename, molecules))
     1266    Log() << Verbose(0) << "done." << endl;
     1267  else
     1268    Log() << Verbose(0) << "failed." << endl;
     1269
     1270  // then save as tremolo data file
     1271  if (ConfigFileName != NULL)
     1272    strcpy(filename, ConfigFileName);
     1273  if (output == NULL)
     1274    strcpy(filename,"main_pcp_linux");
     1275  Log() << Verbose(0) << "Saving as tremolo data input ";
     1276  if (configuration->SaveTREMOLO(filename, molecules))
     1277    Log() << Verbose(0) << "done." << endl;
     1278  else
     1279    Log() << Verbose(0) << "failed." << endl;
     1280
     1281  // translate each to its center and merge all molecules in MoleculeListClass into this molecule
     1282  int N = molecules->ListOfMolecules.size();
     1283  int *src = new int[N];
     1284  N=0;
     1285  for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++) {
     1286    src[N++] = (*ListRunner)->IndexNr;
     1287    (*ListRunner)->Translate(&(*ListRunner)->Center);
     1288  }
     1289  molecules->SimpleMultiAdd(mol, src, N);
     1290  delete[](src);
     1291
     1292  // ... and translate back
     1293  for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++) {
     1294    (*ListRunner)->Center.Scale(-1.);
     1295    (*ListRunner)->Translate(&(*ListRunner)->Center);
     1296    (*ListRunner)->Center.Scale(-1.);
     1297  }
     1298
     1299  Log() << Verbose(0) << "Storing configuration ... " << endl;
     1300  // get correct valence orbitals
     1301  mol->CalculateOrbitals(*configuration);
     1302  configuration->InitMaxMinStopStep = configuration->MaxMinStopStep = configuration->MaxPsiDouble;
     1303  if (ConfigFileName != NULL) { // test the file name
     1304    strcpy(filename, ConfigFileName);
     1305    output.open(filename, ios::trunc);
     1306  } else if (strlen(configuration->configname) != 0) {
     1307    strcpy(filename, configuration->configname);
     1308    output.open(configuration->configname, ios::trunc);
     1309    } else {
     1310      strcpy(filename, DEFAULTCONFIG);
     1311      output.open(DEFAULTCONFIG, ios::trunc);
     1312    }
     1313  output.close();
     1314  output.clear();
     1315  Log() << Verbose(0) << "Saving of config file ";
     1316  if (configuration->Save(filename, periode, mol))
     1317    Log() << Verbose(0) << "successful." << endl;
     1318  else
     1319    Log() << Verbose(0) << "failed." << endl;
     1320
     1321  // and save to xyz file
     1322  if (ConfigFileName != NULL) {
     1323    strcpy(filename, ConfigFileName);
     1324    strcat(filename, ".xyz");
     1325    output.open(filename, ios::trunc);
     1326  }
     1327  if (output == NULL) {
     1328    strcpy(filename,"main_pcp_linux");
     1329    strcat(filename, ".xyz");
     1330    output.open(filename, ios::trunc);
     1331  }
     1332  Log() << Verbose(0) << "Saving of XYZ file ";
     1333  if (mol->MDSteps <= 1) {
     1334    if (mol->OutputXYZ(&output))
     1335      Log() << Verbose(0) << "successful." << endl;
     1336    else
     1337      Log() << Verbose(0) << "failed." << endl;
     1338  } else {
     1339    if (mol->OutputTrajectoriesXYZ(&output))
     1340      Log() << Verbose(0) << "successful." << endl;
     1341    else
     1342      Log() << Verbose(0) << "failed." << endl;
     1343  }
     1344  output.close();
     1345  output.clear();
     1346
     1347  // and save as MPQC configuration
     1348  if (ConfigFileName != NULL)
     1349    strcpy(filename, ConfigFileName);
     1350  if (output == NULL)
     1351    strcpy(filename,"main_pcp_linux");
     1352  Log() << Verbose(0) << "Saving as mpqc input ";
     1353  if (configuration->SaveMPQC(filename, mol))
     1354    Log() << Verbose(0) << "done." << endl;
     1355  else
     1356    Log() << Verbose(0) << "failed." << endl;
     1357
     1358  if (!strcmp(configuration->configpath, configuration->GetDefaultPath())) {
     1359    eLog() << Verbose(2) << "config is found under different path then stated in config file::defaultpath!" << endl;
     1360  }
     1361
     1362  delete(mol);
     1363};
    12491364
    12501365/** Parses the command line options.
    … …  
    12581373 * \return exit code (0 - successful, all else - something's wrong)
    12591374 */
    1260 static int ParseCommandLineOptions(int argc, char **argv, MoleculeListClass *&molecules, periodentafel *&periode,\
    1261                                    config& configuration, char *&ConfigFileName)
     1375static int ParseCommandLineOptions(int argc, char **argv, MoleculeListClass *&molecules, periodentafel *&periode, config& configuration, char *&ConfigFileName)
    12621376{
    12631377  Vector x,y,z,n;  // coordinates for absolute point in cell volume
    … …  
    20962210    } while (argptr < argc);
    20972211    if (SaveFlag)
    2098       configuration.SaveAll(ConfigFileName, periode, molecules);
     2212      SaveConfig(ConfigFileName, &configuration, periode, molecules);
    20992213  } else {  // no arguments, hence scan the elements db
    21002214    if (periode->LoadPeriodentafel(configuration.databasepath))
    … …  
    21072221};
    21082222
    2109 /***************************************** Functions used to build all menus **********************/
    2110 
    2111 void populateEditMoleculesMenu(Menu* editMoleculesMenu,MoleculeListClass *molecules, config *configuration, periodentafel *periode){
    2112   // build the EditMoleculesMenu
    2113   Action *createMoleculeAction = new MethodAction("createMoleculeAction",boost::bind(&MoleculeListClass::createNewMolecule,molecules,periode));
    2114   new ActionMenuItem('c',"create new molecule",editMoleculesMenu,createMoleculeAction);
    2115 
    2116   Action *loadMoleculeAction = new MethodAction("loadMoleculeAction",boost::bind(&MoleculeListClass::loadFromXYZ,molecules,periode));
    2117   new ActionMenuItem('l',"load molecule from xyz file",editMoleculesMenu,loadMoleculeAction);
    2118 
    2119   Action *changeFilenameAction = new MethodAction("changeFilenameAction",boost::bind(&MoleculeListClass::changeName,molecules));
    2120   new ActionMenuItem('n',"change molecule's name",editMoleculesMenu,changeFilenameAction);
    2121 
    2122   Action *giveFilenameAction = new MethodAction("giveFilenameAction",boost::bind(&MoleculeListClass::setMoleculeFilename,molecules));
    2123   new ActionMenuItem('N',"give molecules filename",editMoleculesMenu,giveFilenameAction);
    2124 
    2125   Action *parseAtomsAction = new MethodAction("parseAtomsAction",boost::bind(&MoleculeListClass::parseXYZIntoMolecule,molecules));
    2126   new ActionMenuItem('p',"parse atoms in xyz file into molecule",editMoleculesMenu,parseAtomsAction);
    2127 
    2128   Action *eraseMoleculeAction = new MethodAction("eraseMoleculeAction",boost::bind(&MoleculeListClass::eraseMolecule,molecules));
    2129   new ActionMenuItem('r',"remove a molecule",editMoleculesMenu,eraseMoleculeAction);
    2130 }
    2131 
    2132 
    21332223/********************************************** Main routine **************************************/
    21342224
    21352225int main(int argc, char **argv)
    21362226{
    2137   periodentafel *periode = new periodentafel;
    2138     MoleculeListClass *molecules = new MoleculeListClass;
    2139     molecule *mol = NULL;
    2140     config *configuration = new config;
    2141     Vector x, y, z, n;
    2142     ifstream test;
    2143     ofstream output;
    2144     string line;
    2145     char *ConfigFileName = NULL;
    2146     int j;
    2147     setVerbosity(0);
    2148     /* structure of ParseCommandLineOptions will be refactored later */
    2149     j = ParseCommandLineOptions(argc, argv, molecules, periode, *configuration, ConfigFileName);
    2150     switch (j){
    2151         case 255:
    2152         case 2:
    2153         case 1:
    2154             delete (molecules);
    2155             delete (periode);
    2156             delete (configuration);
    2157             Log() << Verbose(0) << "Maximum of allocated memory: " << MemoryUsageObserver::getInstance()->getMaximumUsedMemory() << endl;
    2158             Log() << Verbose(0) << "Remaining non-freed memory: " << MemoryUsageObserver::getInstance()->getUsedMemorySize() << endl;
    2159             MemoryUsageObserver::getInstance()->purgeInstance();
    2160             logger::purgeInstance();
    2161             errorLogger::purgeInstance();
    2162             return (j == 1 ? 0 : j);
    2163         default:
    2164             break;
     2227  periodentafel *periode = new periodentafel; // and a period table of all elements
     2228  MoleculeListClass *molecules = new MoleculeListClass;  // list of all molecules
     2229  molecule *mol = NULL;
     2230  config *configuration = new config;
     2231  char choice;  // menu choice char
     2232  Vector x,y,z,n;  // coordinates for absolute point in cell volume
     2233  ifstream test;
     2234  ofstream output;
     2235  string line;
     2236  char *ConfigFileName = NULL;
     2237  int j;
     2238
     2239  cout << ESPACKVersion << endl;
     2240
     2241  setVerbosity(0);
     2242
     2243  // =========================== PARSE COMMAND LINE OPTIONS ====================================
     2244  j = ParseCommandLineOptions(argc, argv, molecules, periode, *configuration, ConfigFileName);
     2245  switch(j) {
     2246    case 255:  // something went wrong
     2247    case 2:  // just for -f option
     2248    case 1:  // just for -v and -h options
     2249      delete(molecules); // also free's all molecules contained
     2250      delete(periode);
     2251      delete(configuration);
     2252      Log() << Verbose(0) <<  "Maximum of allocated memory: "
     2253        << MemoryUsageObserver::getInstance()->getMaximumUsedMemory() << endl;
     2254      Log() << Verbose(0) <<  "Remaining non-freed memory: "
     2255        << MemoryUsageObserver::getInstance()->getUsedMemorySize() << endl;
     2256      MemoryUsageObserver::getInstance()->purgeInstance();
     2257      logger::purgeInstance();
     2258      errorLogger::purgeInstance();
     2259     return (j == 1 ? 0 : j);
     2260    default:
     2261      break;
     2262  }
     2263
     2264  // General stuff
     2265  if (molecules->ListOfMolecules.size() == 0) {
     2266    mol = new molecule(periode);
     2267    if (mol->cell_size[0] == 0.) {
     2268      Log() << Verbose(0) << "enter lower tridiagonal form of basis matrix" << endl << endl;
     2269      for (int i=0;i<6;i++) {
     2270        Log() << Verbose(1) << "Cell size" << i << ": ";
     2271        cin >> mol->cell_size[i];
     2272      }
    21652273    }
    2166     if(molecules->ListOfMolecules.size() == 0){
    2167         mol = new molecule(periode);
    2168         if(mol->cell_size[0] == 0.){
    2169             Log() << Verbose(0) << "enter lower tridiagonal form of basis matrix" << endl << endl;
    2170             for(int i = 0;i < 6;i++){
    2171                 Log() << Verbose(1) << "Cell size" << i << ": ";
    2172                 cin >> mol->cell_size[i];
    2173             }
     2274    mol->ActiveFlag = true;
     2275    molecules->insert(mol);
     2276  }
     2277
     2278  // =========================== START INTERACTIVE SESSION ====================================
     2279
     2280  // now the main construction loop
     2281  Log() << Verbose(0) << endl << "Now comes the real construction..." << endl;
     2282  do {
     2283    Log() << Verbose(0) << endl << endl;
     2284    Log() << Verbose(0) << "============Molecule list=======================" << endl;
     2285    molecules->Enumerate((ofstream *)&cout);
     2286    Log() << Verbose(0) << "============Menu===============================" << endl;
     2287    Log() << Verbose(0) << "a - set molecule (in)active" << endl;
     2288    Log() << Verbose(0) << "e - edit molecules (load, parse, save)" << endl;
     2289    Log() << Verbose(0) << "g - globally manipulate atoms in molecule" << endl;
     2290    Log() << Verbose(0) << "M - Merge molecules" << endl;
     2291    Log() << Verbose(0) << "m - manipulate atoms" << endl;
     2292    Log() << Verbose(0) << "-----------------------------------------------" << endl;
     2293    Log() << Verbose(0) << "c - edit the current configuration" << endl;
     2294    Log() << Verbose(0) << "-----------------------------------------------" << endl;
     2295    Log() << Verbose(0) << "s - save current setup to config file" << endl;
     2296    Log() << Verbose(0) << "T - call the current test routine" << endl;
     2297    Log() << Verbose(0) << "q - quit" << endl;
     2298    Log() << Verbose(0) << "===============================================" << endl;
     2299    Log() << Verbose(0) << "Input: ";
     2300    cin >> choice;
     2301
     2302    switch (choice) {
     2303      case 'a':  // (in)activate molecule
     2304        {
     2305          Log() << Verbose(0) << "Enter index of molecule: ";
     2306          cin >> j;
     2307          for(MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
     2308            if ((*ListRunner)->IndexNr == j)
     2309              (*ListRunner)->ActiveFlag = !(*ListRunner)->ActiveFlag;
    21742310        }
    2175 
    2176         mol->ActiveFlag = true;
    2177         molecules->insert(mol);
    2178     }
    2179 
    2180     {
    2181       cout << ESPACKVersion << endl;
    2182 
    2183       setVerbosity(0);
    2184 
    2185       menuPopulaters populaters;
    2186       populaters.MakeEditMoleculesMenu = populateEditMoleculesMenu;
    2187 
    2188       UIFactory::makeUserInterface(UIFactory::Text);
    2189       MainWindow *mainWindow = UIFactory::get()->makeMainWindow(populaters,molecules, configuration, periode, ConfigFileName);
    2190       mainWindow->display();
    2191       delete mainWindow;
    2192     }
    2193 
    2194     if(periode->StorePeriodentafel(configuration->databasepath))
    2195         Log() << Verbose(0) << "Saving of elements.db successful." << endl;
    2196 
    2197     else
    2198         Log() << Verbose(0) << "Saving of elements.db failed." << endl;
    2199 
    2200     delete (molecules);
    2201     delete(periode);
     2311        break;
     2312
     2313      case 'c': // edit each field of the configuration
     2314       configuration->Edit();
     2315       break;
     2316
     2317      case 'e': // create molecule
     2318        EditMolecules(periode, molecules);
     2319        break;
     2320
     2321      case 'g': // manipulate molecules
     2322        ManipulateMolecules(periode, molecules, configuration);
     2323        break;
     2324
     2325      case 'M':  // merge molecules
     2326        MergeMolecules(periode, molecules);
     2327        break;
     2328
     2329      case 'm': // manipulate atoms
     2330        ManipulateAtoms(periode, molecules, configuration);
     2331        break;
     2332
     2333      case 'q': // quit
     2334        break;
     2335
     2336      case 's': // save to config file
     2337        SaveConfig(ConfigFileName, configuration, periode, molecules);
     2338        break;
     2339
     2340      case 'T':
     2341        testroutine(molecules);
     2342        break;
     2343
     2344      default:
     2345        break;
     2346    };
     2347  } while (choice != 'q');
     2348
     2349  // save element data base
     2350  if (periode->StorePeriodentafel(configuration->databasepath)) //ElementsFileName
     2351    Log() << Verbose(0) << "Saving of elements.db successful." << endl;
     2352  else
     2353    Log() << Verbose(0) << "Saving of elements.db failed." << endl;
     2354
     2355  delete(molecules); // also free's all molecules contained
     2356  delete(periode);
    22022357  delete(configuration);
    2203 
    2204 
    22052358
    22062359  Log() << Verbose(0) <<  "Maximum of allocated memory: "
    … …  
    22112364  logger::purgeInstance();
    22122365  errorLogger::purgeInstance();
    2213   UIFactory::purgeInstance();
    2214   ActionRegistry::purgeRegistry();
     2366
    22152367  return (0);
    22162368}

  • src/config.cpp

    r04b6f9 r244a84  
    17771777};
    17781778
    1779 
    1780 /** Tries given filename or standard on saving the config file.
    1781  * \param *ConfigFileName name of file
    1782  * \param *periode pointer to periodentafel structure with all the elements
    1783  * \param *molecules list of molecules structure with all the atoms and coordinates
    1784  */
    1785 void config::SaveAll(char *ConfigFileName, periodentafel *periode, MoleculeListClass *molecules)
    1786 {
    1787   char filename[MAXSTRINGSIZE];
    1788   ofstream output;
    1789   molecule *mol = new molecule(periode);
    1790   mol->SetNameFromFilename(ConfigFileName);
    1791 
    1792   if (!strcmp(configpath, GetDefaultPath())) {
    1793     eLog() << Verbose(2) << "config is found under different path then stated in config file::defaultpath!" << endl;
    1794   }
    1795 
    1796 
    1797   // first save as PDB data
    1798   if (ConfigFileName != NULL)
    1799     strcpy(filename, ConfigFileName);
    1800   if (output == NULL)
    1801     strcpy(filename,"main_pcp_linux");
    1802   Log() << Verbose(0) << "Saving as pdb input ";
    1803   if (SavePDB(filename, molecules))
    1804     Log() << Verbose(0) << "done." << endl;
    1805   else
    1806     Log() << Verbose(0) << "failed." << endl;
    1807 
    1808   // then save as tremolo data file
    1809   if (ConfigFileName != NULL)
    1810     strcpy(filename, ConfigFileName);
    1811   if (output == NULL)
    1812     strcpy(filename,"main_pcp_linux");
    1813   Log() << Verbose(0) << "Saving as tremolo data input ";
    1814   if (SaveTREMOLO(filename, molecules))
    1815     Log() << Verbose(0) << "done." << endl;
    1816   else
    1817     Log() << Verbose(0) << "failed." << endl;
    1818 
    1819   // translate each to its center and merge all molecules in MoleculeListClass into this molecule
    1820   int N = molecules->ListOfMolecules.size();
    1821   int *src = new int[N];
    1822   N=0;
    1823   for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++) {
    1824     src[N++] = (*ListRunner)->IndexNr;
    1825     (*ListRunner)->Translate(&(*ListRunner)->Center);
    1826   }
    1827   molecules->SimpleMultiAdd(mol, src, N);
    1828   delete[](src);
    1829 
    1830   // ... and translate back
    1831   for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++) {
    1832     (*ListRunner)->Center.Scale(-1.);
    1833     (*ListRunner)->Translate(&(*ListRunner)->Center);
    1834     (*ListRunner)->Center.Scale(-1.);
    1835   }
    1836 
    1837   Log() << Verbose(0) << "Storing configuration ... " << endl;
    1838   // get correct valence orbitals
    1839   mol->CalculateOrbitals(*this);
    1840   InitMaxMinStopStep = MaxMinStopStep = MaxPsiDouble;
    1841   if (ConfigFileName != NULL) { // test the file name
    1842     strcpy(filename, ConfigFileName);
    1843     output.open(filename, ios::trunc);
    1844   } else if (strlen(configname) != 0) {
    1845     strcpy(filename, configname);
    1846     output.open(configname, ios::trunc);
    1847     } else {
    1848       strcpy(filename, DEFAULTCONFIG);
    1849       output.open(DEFAULTCONFIG, ios::trunc);
    1850     }
    1851   output.close();
    1852   output.clear();
    1853   Log() << Verbose(0) << "Saving of config file ";
    1854   if (Save(filename, periode, mol))
    1855     Log() << Verbose(0) << "successful." << endl;
    1856   else
    1857     Log() << Verbose(0) << "failed." << endl;
    1858 
    1859   // and save to xyz file
    1860   if (ConfigFileName != NULL) {
    1861     strcpy(filename, ConfigFileName);
    1862     strcat(filename, ".xyz");
    1863     output.open(filename, ios::trunc);
    1864   }
    1865   if (output == NULL) {
    1866     strcpy(filename,"main_pcp_linux");
    1867     strcat(filename, ".xyz");
    1868     output.open(filename, ios::trunc);
    1869   }
    1870   Log() << Verbose(0) << "Saving of XYZ file ";
    1871   if (mol->MDSteps <= 1) {
    1872     if (mol->OutputXYZ(&output))
    1873       Log() << Verbose(0) << "successful." << endl;
    1874     else
    1875       Log() << Verbose(0) << "failed." << endl;
    1876   } else {
    1877     if (mol->OutputTrajectoriesXYZ(&output))
    1878       Log() << Verbose(0) << "successful." << endl;
    1879     else
    1880       Log() << Verbose(0) << "failed." << endl;
    1881   }
    1882   output.close();
    1883   output.clear();
    1884 
    1885   // and save as MPQC configuration
    1886   if (ConfigFileName != NULL)
    1887     strcpy(filename, ConfigFileName);
    1888   if (output == NULL)
    1889     strcpy(filename,"main_pcp_linux");
    1890   Log() << Verbose(0) << "Saving as mpqc input ";
    1891   if (SaveMPQC(filename, mol))
    1892     Log() << Verbose(0) << "done." << endl;
    1893   else
    1894     Log() << Verbose(0) << "failed." << endl;
    1895 
    1896   if (!strcmp(configpath, GetDefaultPath())) {
    1897     eLog() << Verbose(2) << "config is found under different path then stated in config file::defaultpath!" << endl;
    1898   }
    1899 
    1900   delete(mol);
    1901 };
    1902 
    19031779/** Reads parameter from a parsed file.
    19041780 * The file is either parsed for a certain keyword or if null is given for

  • src/config.hpp

    r04b6f9 r244a84  
    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

    r04b6f9 r244a84  
    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

    r04b6f9 r244a84  
    10831083  }
    10841084};
    1085 
    1086 void molecule::flipActiveFlag(){
    1087   ActiveFlag = !ActiveFlag;
    1088 }

  • src/molecule.hpp

    r04b6f9 r244a84  
    298298  bool OutputTemperatureFromTrajectories(ofstream * const output, int startstep, int endstep);
    299299
    300   // Manipulation routines
    301   void flipActiveFlag();
    302 
    303300  private:
    304301  int last_atom;      //!< number given to last atom
    … …  
    329326  int CountAllAtoms() const;
    330327
    331   // Methods moved here from the menus
    332   // TODO: more refactoring needed on these methods
    333   void flipChosen();
    334   void createNewMolecule(periodentafel *periode);
    335   void loadFromXYZ(periodentafel *periode);
    336   void changeName();
    337   void setMoleculeFilename();
    338   void parseXYZIntoMolecule();
    339   void eraseMolecule();
    340 
    341 
    342328  // merging of molecules
    343329  bool SimpleMerge(molecule *mol, molecule *srcmol);

  • src/moleculelist.cpp

    r04b6f9 r244a84  
    144144
    145145  // header
    146   (*out) << "Index\tName\t\tAtoms\tFormula\tCenter\tSize" << endl;
    147   (*out) << "-----------------------------------------------" << endl;
     146  Log() << Verbose(0) << "Index\tName\t\tAtoms\tFormula\tCenter\tSize" << endl;
     147  Log() << Verbose(0) << "-----------------------------------------------" << endl;
    148148  if (ListOfMolecules.size() == 0)
    149     (*out) << "\tNone" << endl;
     149    Log() << Verbose(0) << "\tNone" << endl;
    150150  else {
    151151    Origin.Zero();
    … …  
    164164      }
    165165      // output Index, Name, number of atoms, chemical formula
    166       (*out) << ((*ListRunner)->ActiveFlag ? "*" : " ") << (*ListRunner)->IndexNr << "\t" << (*ListRunner)->name << "\t\t" << (*ListRunner)->AtomCount << "\t";
     166      Log() << Verbose(0) << ((*ListRunner)->ActiveFlag ? "*" : " ") << (*ListRunner)->IndexNr << "\t" << (*ListRunner)->name << "\t\t" << (*ListRunner)->AtomCount << "\t";
    167167      Elemental = (*ListRunner)->elemente->end;
    168168      while(Elemental->previous != (*ListRunner)->elemente->start) {
    169169        Elemental = Elemental->previous;
    170170        if (Counts[Elemental->Z] != 0)
    171           (*out) << Elemental->symbol << Counts[Elemental->Z];
     171          Log() << Verbose(0) << Elemental->symbol << Counts[Elemental->Z];
    172172      }
    173173      // Center and size
    174       (*out) << "\t" << (*ListRunner)->Center << "\t" << sqrt(size) << endl;
     174      Log() << Verbose(0) << "\t" << (*ListRunner)->Center << "\t" << sqrt(size) << endl;
    175175    }
    176176  }
    … …  
    875875}
    876876
    877 /***********
    878  * Methods Moved here from the menus
    879  */
    880 
    881 void MoleculeListClass::flipChosen() {
    882   int j;
    883   Log() << Verbose(0) << "Enter index of molecule: ";
    884   cin >> j;
    885   for(MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++)
    886     if ((*ListRunner)->IndexNr == j)
    887       (*ListRunner)->ActiveFlag = !(*ListRunner)->ActiveFlag;
    888 }
    889 
    890 void MoleculeListClass::createNewMolecule(periodentafel *periode) {
    891   molecule *mol = NULL;
    892   mol = new molecule(periode);
    893   insert(mol);
    894 };
    895 
    896 void MoleculeListClass::loadFromXYZ(periodentafel *periode){
    897   molecule *mol = NULL;
    898   Vector center;
    899   char filename[MAXSTRINGSIZE];
    900   Log() << Verbose(0) << "Format should be XYZ with: ShorthandOfElement\tX\tY\tZ" << endl;
    901   mol = new molecule(periode);
    902   do {
    903     Log() << Verbose(0) << "Enter file name: ";
    904     cin >> filename;
    905   } while (!mol->AddXYZFile(filename));
    906   mol->SetNameFromFilename(filename);
    907   // center at set box dimensions
    908   mol->CenterEdge(&center);
    909   mol->cell_size[0] = center.x[0];
    910   mol->cell_size[1] = 0;
    911   mol->cell_size[2] = center.x[1];
    912   mol->cell_size[3] = 0;
    913   mol->cell_size[4] = 0;
    914   mol->cell_size[5] = center.x[2];
    915   insert(mol);
    916 }
    917 
    918 void MoleculeListClass::changeName(){
    919   char filename[MAXSTRINGSIZE];
    920   molecule *mol = NULL;
    921   int nr;
    922   do {
    923     Log() << Verbose(0) << "Enter index of molecule: ";
    924     cin >> nr;
    925     mol = ReturnIndex(nr);
    926   } while (mol == NULL);
    927   Log() << Verbose(0) << "Enter name: ";
    928   cin >> filename;
    929   strcpy(mol->name, filename);
    930 }
    931 
    932 void MoleculeListClass::setMoleculeFilename() {
    933   char filename[MAXSTRINGSIZE];
    934   int nr;
    935   molecule *mol = NULL;
    936   do {
    937     Log() << Verbose(0) << "Enter index of molecule: ";
    938     cin >> nr;
    939     mol = ReturnIndex(nr);
    940   } while (mol == NULL);
    941   Log() << Verbose(0) << "Enter name: ";
    942   cin >> filename;
    943   mol->SetNameFromFilename(filename);
    944 }
    945 
    946 void MoleculeListClass::parseXYZIntoMolecule(){
    947   char filename[MAXSTRINGSIZE];
    948   int nr;
    949   molecule *mol = NULL;
    950   mol = NULL;
    951   do {
    952    Log() << Verbose(0) << "Enter index of molecule: ";
    953    cin >> nr;
    954    mol = ReturnIndex(nr);
    955   } while (mol == NULL);
    956   Log() << Verbose(0) << "Format should be XYZ with: ShorthandOfElement\tX\tY\tZ" << endl;
    957   do {
    958    Log() << Verbose(0) << "Enter file name: ";
    959    cin >> filename;
    960   } while (!mol->AddXYZFile(filename));
    961   mol->SetNameFromFilename(filename);
    962 };
    963 
    964 void MoleculeListClass::eraseMolecule(){
    965   int nr;
    966   molecule *mol = NULL;
    967   Log() << Verbose(0) << "Enter index of molecule: ";
    968   cin >> nr;
    969   for(MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++)
    970     if (nr == (*ListRunner)->IndexNr) {
    971       mol = *ListRunner;
    972       ListOfMolecules.erase(ListRunner);
    973       delete(mol);
    974       break;
    975     }
    976 };
    977 
    978877
    979878/******************************************* Class MoleculeLeafClass ************************************************/

  • src/unittests/Makefile.am

    r04b6f9 r244a84  
    33AM_LDFLAGS = $(CPPUNIT_LIBS) -ldl
    44AM_CXXFLAGS = $(CPPUNIT_CFLAGS)
    5 
    6 MENUTESTS = ActionSequenceTest
    75
    86TESTS = \
    … …  
    2725  Tesselation_InOutsideUnitTest \
    2826  VectorUnitTest
    29    
    3027 
    31 check_PROGRAMS = $(TESTS) ${MENUTESTS}
    32 noinst_PROGRAMS = $(TESTS) ${MENUTESTS}
     28check_PROGRAMS = $(TESTS)
     29noinst_PROGRAMS = $(TESTS)
    3330
    3431ActOnAllUnitTest_SOURCES = ../test/ActOnAllTest.hpp ActOnAllUnitTest.cpp ActOnAllUnitTest.hpp
    … …  
    9289VectorUnitTest_LDADD = ../libmolecuilder.a ../libgslwrapper.a
    9390
    94 ActionSequenceTest_SOURCES = ActionSequenceTest.cpp ActionSequenceTest.hpp
    95 ActionSequenceTest_LDADD = ../libmolecuilder.a
    9691
    9792#AUTOMAKE_OPTIONS = parallel-tests
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