source: src/builder.cpp@ ae21cbd

/*
 * Project: MoleCuilder
 * Description: creates and alters molecular systems
 * Copyright (C)  2010 University of Bonn. All rights reserved.
 * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
 */

 /** \file builder.cpp
 *
 *  date: Jan 1, 2007
 *  author: heber
 *
 */

/*! \page Copyright notice
 *
 *  MoleCuilder - to create and alter molecular systems
 *  Copyright (C) 2010  University Bonn. All rights reserved.
 *
 */

/*! \mainpage MoleCuilder - a molecular set builder
 *
 * This introductory shall briefly make acquainted with the program, helping in installing and a first run.
 *
 * \section about About the Program
 *
 *  MoleCuilder is a program, written entirely in C++, that enables the construction of a coordinate set for the
 *  atoms making up an molecule. It allows for both building of simple molecules by adding atom-wise giving bond
 *  angles and distances or absolute coordinates, but also using them as templates. Regions can be specified and
 *  ordered to be filled with a molecule in a certain manner. Greater conglomerations of molecules can be tesselated
 *  and recognized as a region themselves to be subsequently surrounded by other (surface solvated) molecules.
 *  In the end, MoleCuilder allows the construction of arbitrary nano structures, whether they be crystalline or
 *  amorphic in nature.
 *
 *
 * \section install Installation
 *
 *  Installation should without problems succeed as follows:
 *  -# ./configure (or: mkdir build;mkdir run;cd build; ../configure --bindir=../run)
 *  -# make
 *  -# make install
 *
 *  Further useful commands are
 *  -# make clean uninstall: deletes .o-files and removes executable from the given binary directory\n
 *  -# make doxygen-doc: Creates these html pages out of the documented source
 *  -# make check: Runs an extensive set of unit tests and a testsuite which also gives a good overview on the set of
 *                 functions.
 *
 * \section run Running
 *
 *  The program can be executed by running: ./molecuilder
 *
 *  MoleCuilder has three interfaces at your disposal:
 *  -# Textmenu: A simple interactive console-based menu, where awaits your choices and inputs in order to set atoms
 *               as you like
 *  -# CommandLineUI: Every command can also be chained up as a sequence of actions on the command line to be executed
 *               with any user interaction.
 *  -# GraphicalUI: A graphical user interface that also display the molecular structure being built and lots of other
 *               informations to ease the construction of bigger geometries.
 *
 *  The supported output formats right now are:
 *  -# mpqc: Configuration files of the Massively Parallel Quantum Chemistry package (Sandia labs)
 *  -# pcp: Configuration files of the Parallel Car-Parrinello program (Institute for Numerical Simulation)
 *  -# tremolo: Configuration files of TREMOLO (Institute for Numerical Simulation)
 *  -# xyz: the most basic format for the 3d arrangement of atoms consisting of a list of element and 3 coordinates.
 *
 */

// include config.h
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include "Helpers/MemDebug.hpp"

#include "bondgraph.hpp"
#include "config.hpp"
#include "Helpers/Log.hpp"
#include "molecule.hpp"
#include "periodentafel.hpp"
#include "tesselationhelpers.hpp"
#include "UIElements/UIFactory.hpp"
#include "UIElements/TextUI/TextUIFactory.hpp"
#include "UIElements/CommandLineUI/CommandLineUIFactory.hpp"
#include "UIElements/CommandLineUI/CommandLineParser.hpp"
#ifdef USE_GUI_QT
#include "UIElements/Qt4/QtUIFactory.hpp"
#endif
#include "UIElements/MainWindow.hpp"
#include "UIElements/Dialog.hpp"
//#include "Menu/ActionMenuItem.hpp"
#include "Helpers/Verbose.hpp"
#include "World.hpp"

#include "Actions/ActionRegistry.hpp"
#include "Actions/ActionHistory.hpp"

#include "Parser/ChangeTracker.hpp"
#include "Parser/FormatParserStorage.hpp"

#include "UIElements/UIFactory.hpp"
#include "UIElements/TextUI/TextUIFactory.hpp"
#include "UIElements/CommandLineUI/CommandLineUIFactory.hpp"
#include "UIElements/MainWindow.hpp"
#include "UIElements/Dialog.hpp"

#include "version.h"


/********************************************** Main routine **************************************/

/** In this function all dynamicly allocated member variables to static/global
 * variables are added to the ignore list of Memory/MemDebug.
 *
 * Use this to prevent their listing in the Memory::getState() at the end of the
 * program. Check with valgrind that truely no memory leak occurs!
 */
void AddStaticEntitiestoIgnoreList()
{
  // zeroVec and unitVec are global variables (on the stack) but vectorContent
  // within is situated on the heap and has to be ignored
  Memory::ignore(zeroVec.get());
  Memory::ignore(unitVec[0].get());
  Memory::ignore(unitVec[1].get());
  Memory::ignore(unitVec[2].get());
}

/** Cleans all singleton instances in an orderly fashion.
 * C++ does not guarantee any specific sequence of removal of single instances
 * which have static/global variables. Some singletons depend on others hence we
 * acertain a specific ordering here, which is is used via the atexit() hook.
 */
void cleanUp(){
  FormatParserStorage::purgeInstance();
  ChangeTracker::purgeInstance();
  World::purgeInstance();
  UIFactory::purgeInstance();
  ValueStorage::purgeInstance();
  CommandLineParser::purgeInstance();
  ActionRegistry::purgeInstance();
  OptionRegistry::purgeInstance();
  ActionHistory::purgeInstance();
  // we have to remove these two static as otherwise their boost::shared_ptrs are still present
  Action::removeStaticStateEntities();
  // put some static variables' dynamic contents on the Memory::ignore map to avoid their
  // admonishing lateron
  AddStaticEntitiestoIgnoreList();
  logger::purgeInstance();
  errorLogger::purgeInstance();
#ifdef LOG_OBSERVER
  cout << observerLog().getLog();
#endif
  Memory::getState();
}

void dumpMemory(){
  ofstream ost("molecuilder.memdump");
  Memory::dumpMemory(ost);
}

int main(int argc, char **argv)
{
  // while we are non interactive, we want to abort from asserts
  ASSERT_DO(Assert::Abort);
  ASSERT_HOOK(dumpMemory);
  string line;
  char **Arguments = NULL;
  int ArgcSize = 0;
  int ExitFlag = 0;
  bool ArgumentsCopied = false;
  std::string BondGraphFileName("\n");

  // print version check and copyright notice
  cout << MOLECUILDERVERSION << endl;
  cout << "MoleCuilder comes with ABSOLUTELY NO WARRANTY; for details type" << endl;
  cout << "`molecuilder --warranty'." << endl;
  cout << "`MoleCuilder - to create and alter molecular systems." << endl;
  cout << "Copyright (C) 2010  University Bonn. All rights reserved." << endl;

  setVerbosity(0);
  // need to init the history before any action is created
  ActionHistory::init();

  // from this moment on, we need to be sure to deeinitialize in the correct order
  // this is handled by the cleanup function
  atexit(cleanUp);

  // Parse command line options and if present create respective UI
  {
    // construct bond graph
    if (World::getInstance().getConfig()->BG == NULL) {
      World::getInstance().getConfig()->BG = new BondGraph(World::getInstance().getConfig()->GetIsAngstroem());
      if (World::getInstance().getConfig()->BG->LoadBondLengthTable(BondGraphFileName)) {
        DoLog(0) && (Log() << Verbose(0) << "Bond length table loaded successfully." << endl);
      } else {
        DoeLog(1) && (eLog()<< Verbose(1) << "Bond length table loading failed." << endl);
      }
    }
    // handle remaining arguments by CommandLineParser
    if (argc>1) {
      CommandLineParser::getInstance().InitializeCommandArguments();
      CommandLineParser::getInstance().Run(argc,argv);
      DoLog(0) && (Log() << Verbose(0) << "Setting UI to CommandLine." << endl);
      UIFactory::registerFactory(new CommandLineUIFactory::description());
      UIFactory::makeUserInterface("CommandLine");
    } else {
      // In the interactive mode, we can leave the user the choice in case of error
      ASSERT_DO(Assert::Ask);
      #ifdef USE_GUI_QT
        DoLog(0) && (Log() << Verbose(0) << "Setting UI to Qt4." << endl);
        UIFactory::registerFactory(new QtUIFactory::description());
        UIFactory::makeUserInterface("Qt4");
      #else
        DoLog(0) && (Log() << Verbose(0) << "Setting UI to Text." << endl);
        cout << MOLECUILDERVERSION << endl;
        UIFactory::registerFactory(new TextUIFactory::description());
        UIFactory::makeUserInterface("Text");
      #endif
    }
  }

  {
    MainWindow *mainWindow = UIFactory::getInstance().makeMainWindow();
    mainWindow->display();
    delete mainWindow;
  }

  FormatParserStorage::getInstance().SaveAll();
  ChangeTracker::getInstance().saveStatus();

  // free the new argv
  if (ArgumentsCopied) {
    for (int i=0; i<ArgcSize;i++)
      delete[](Arguments[i]);
    delete[](Arguments);
  }
  //delete[](ConfigFileName);

  ExitFlag = World::getInstance().getExitFlag();
  return (ExitFlag == 1 ? 0 : ExitFlag);
}

/********************************************** E N D **************************************************/