Changes in / [1cf5df:1ca488]


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11 edited

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  • Makefile.am

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

  • doc/Doxyfile

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

  • src/Makefile.am

    r1cf5df r1ca488  
    55ANALYSISHEADER = analysis_bonds.hpp analysis_correlation.hpp
    66
    7 SOURCE = ${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
    8 HEADER = ${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
     7ACTIONSSOURCE = Actions/Action.cpp Actions/MethodAction.cpp Actions/ActionSequence.cpp Actions/MakroAction.cpp Actions/ErrorAction.cpp Actions/ActionRegistry.cpp
     8ACTIONSHEADER = Actions/Action.hpp Actions/MethodAction.hpp Actions/ActionSequence.hpp Actions/MakroAction.hpp Actions/ErrorAction.hpp Actions/ActionRegistry.hpp
     9
     10VIEWSOURCE = Views/View.cpp Views/StringView.cpp Views/MethodStringView.cpp Views/StreamStringView.cpp
     11VIEWHEADER = Views/View.hpp Views/StringView.hpp Views/MethodStringView.hpp Views/StreamStringView.hpp
     12
     13MENUSOURCE = Menu/Menu.cpp Menu/TextMenu.cpp Menu/MenuItem.cpp Menu/SubMenuItem.cpp Menu/ActionMenuItem.cpp Menu/SeperatorItem.cpp Menu/DisplayMenuItem.cpp
     14MENUHEADER = Menu/Menu.hpp Menu/TextMenu.hpp Menu/MenuItem.hpp Menu/SubMenuItem.hpp Menu/ActionMenuItem.hpp Menu/SeperatorItem.hpp Menu/DisplayMenuItem.hpp
     15
     16UISOURCE = ${ACTIONSSOURCE} ${VIEWSOURCE} ${MENUSOURCE} UIElements/UIFactory.cpp UIElements/TextUIFactory.cpp UIElements/MainWindow.cpp UIElements/TextWindow.cpp UIElements/Dialog.cpp UIElements/TextDialog.cpp
     17UIHEADER = ${ACTIONSHEADER} ${VIEWHEADER} ${MENUHEADER} UIElements/UIFactory.hpp UIElements/TextUIFactory.hpp UIElements/MainWindow.hpp UIElements/TextWindow.hpp UIElements/Dialog.hpp UIElements/TextDialog.hpp
     18
     19SOURCE = ${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
     20HEADER = ${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
    921
    1022BOOST_LIB = $(BOOST_LDFLAGS) $(BOOST_MPL_LIB)

  • src/builder.cpp

    r1cf5df r1ca488  
    4848
    4949
     50#include <boost/bind.hpp>
     51
    5052using namespace std;
    5153
    … …  
    6567#include "molecule.hpp"
    6668#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"
    6775#include "version.h"
    6876
    6977/********************************************* Subsubmenu routine ************************************/
    70 
     78#if 0
    7179/** Submenu for adding atoms to the molecule.
    7280 * \param *periode periodentafel
    … …  
    11531161};
    11541162
    1155 
    11561163/********************************************** Test routine **************************************/
    11571164
    … …  
    12371244};
    12381245
    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  */
    1245 static 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 };
     1246#endif
    13621247
    13631248/** Parses the command line options.
    … …  
    13711256 * \return exit code (0 - successful, all else - something's wrong)
    13721257 */
    1373 static int ParseCommandLineOptions(int argc, char **argv, MoleculeListClass *&molecules, periodentafel *&periode, config& configuration, char *&ConfigFileName)
     1258static int ParseCommandLineOptions(int argc, char **argv, MoleculeListClass *&molecules, periodentafel *&periode,\
     1259                                   config& configuration, char *&ConfigFileName)
    13741260{
    13751261  Vector x,y,z,n;  // coordinates for absolute point in cell volume
    … …  
    21962082    } while (argptr < argc);
    21972083    if (SaveFlag)
    2198       SaveConfig(ConfigFileName, &configuration, periode, molecules);
     2084      configuration.SaveAll(ConfigFileName, periode, molecules);
    21992085  } else {  // no arguments, hence scan the elements db
    22002086    if (periode->LoadPeriodentafel(configuration.databasepath))
    … …  
    22072093};
    22082094
     2095/***************************************** Functions used to build all menus **********************/
     2096
     2097void 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
    22092119/********************************************** Main routine **************************************/
    22102120
    22112121int main(int argc, char **argv)
    22122122{
    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       }
     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;
    22592151    }
    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;
     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            }
    22962160        }
    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);
     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);
    23432188  delete(configuration);
     2189
     2190
    23442191
    23452192  Log() << Verbose(0) <<  "Maximum of allocated memory: "
    … …  
    23502197  logger::purgeInstance();
    23512198  errorLogger::purgeInstance();
    2352 
     2199  UIFactory::purgeInstance();
     2200  ActionRegistry::purgeRegistry();
    23532201  return (0);
    23542202}

  • src/config.cpp

    r1cf5df r1ca488  
    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 */
     1784void 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
    17781902/** Reads parameter from a parsed file.
    17791903 * The file is either parsed for a certain keyword or if null is given for

  • src/config.hpp

    r1cf5df r1ca488  
    146146  bool SaveTREMOLO(const char * const filename, const MoleculeListClass * const MolList) const;
    147147
     148  void SaveAll(char *ConfigFileName, periodentafel *periode, MoleculeListClass *molecules);
     149
    148150  void Edit();
    149151  bool GetIsAngstroem() const;

  • src/defs.hpp

    r1cf5df r1ca488  
    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
    7983#endif /*DEFS_HPP_*/

  • src/molecule.cpp

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

  • src/molecule.hpp

    r1cf5df r1ca488  
    297297  bool OutputTemperatureFromTrajectories(ofstream * const output, int startstep, int endstep);
    298298
     299  // Manipulation routines
     300  void flipActiveFlag();
     301
    299302  private:
    300303  int last_atom;      //!< number given to last atom
    … …  
    325328  int CountAllAtoms() const;
    326329
     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
    327341  // merging of molecules
    328342  bool SimpleMerge(molecule *mol, molecule *srcmol);

  • src/moleculelist.cpp

    r1cf5df r1ca488  
    142142
    143143  // header
    144   Log() << Verbose(0) << "Index\tName\t\tAtoms\tFormula\tCenter\tSize" << endl;
    145   Log() << Verbose(0) << "-----------------------------------------------" << endl;
     144  (*out) << "Index\tName\t\tAtoms\tFormula\tCenter\tSize" << endl;
     145  (*out) << "-----------------------------------------------" << endl;
    146146  if (ListOfMolecules.size() == 0)
    147     Log() << Verbose(0) << "\tNone" << endl;
     147    (*out) << "\tNone" << endl;
    148148  else {
    149149    Origin.Zero();
    … …  
    162162      }
    163163      // output Index, Name, number of atoms, chemical formula
    164       Log() << Verbose(0) << ((*ListRunner)->ActiveFlag ? "*" : " ") << (*ListRunner)->IndexNr << "\t" << (*ListRunner)->name << "\t\t" << (*ListRunner)->AtomCount << "\t";
     164      (*out) << ((*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           Log() << Verbose(0) << Elemental->symbol << Counts[Elemental->Z];
     169          (*out) << Elemental->symbol << Counts[Elemental->Z];
    170170      }
    171171      // Center and size
    172       Log() << Verbose(0) << "\t" << (*ListRunner)->Center << "\t" << sqrt(size) << endl;
     172      (*out) << "\t" << (*ListRunner)->Center << "\t" << sqrt(size) << endl;
    173173    }
    174174  }
    … …  
    844844}
    845845
     846/***********
     847 * Methods Moved here from the menus
     848 */
     849
     850void 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
     859void MoleculeListClass::createNewMolecule(periodentafel *periode) {
     860  molecule *mol = NULL;
     861  mol = new molecule(periode);
     862  insert(mol);
     863};
     864
     865void 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
     887void 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
     901void 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
     915void 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
     933void 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
    846947
    847948/******************************************* Class MoleculeLeafClass ************************************************/

  • src/unittests/Makefile.am

    r1cf5df r1ca488  
    44AM_CXXFLAGS = $(CPPUNIT_CFLAGS)
    55
    6 TESTS = ActOnAllUnitTest AnalysisBondsUnitTests AnalysisCorrelationToPointUnitTest AnalysisCorrelationToSurfaceUnitTest AnalysisPairCorrelationUnitTest BondGraphUnitTest InfoUnitTest ListOfBondsUnitTest LogUnitTest MemoryUsageObserverUnitTest MemoryAllocatorUnitTest StackClassUnitTest VectorUnitTest
     6MENUTESTS = ActionSequenceTest
     7
     8TESTS = ActOnAllUnitTest AnalysisBondsUnitTests AnalysisCorrelationToPointUnitTest AnalysisCorrelationToSurfaceUnitTest AnalysisPairCorrelationUnitTest BondGraphUnitTest InfoUnitTest ListOfBondsUnitTest LogUnitTest MemoryUsageObserverUnitTest MemoryAllocatorUnitTest StackClassUnitTest VectorUnitTest ${MENUTESTS}
     9
    710check_PROGRAMS = $(TESTS)
    811noinst_PROGRAMS = $(TESTS)
    … …  
    4750VectorUnitTest_LDADD = ../libmolecuilder.a
    4851
     52ActionSequenceTest_SOURCES = ActionSequenceTest.cpp ActionSequenceTest.hpp
     53ActionSequenceTest_LDADD = ../libmolecuilder.a
    4954
    5055#AUTOMAKE_OPTIONS = parallel-tests
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