1 | /*
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2 | * Project: MoleCuilder
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3 | * Description: creates and alters molecular systems
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4 | * Copyright (C) 2010 University of Bonn. All rights reserved.
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5 | * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
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6 | */
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7 |
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8 | /** \file builder.cpp
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9 | *
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10 | * date: Jan 1, 2007
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11 | * author: heber
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12 | *
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13 | */
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14 |
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15 | /*! \page Copyright notice
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16 | *
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17 | * MoleCuilder - to create and alter molecular systems
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18 | * Copyright (C) 2010 University Bonn. All rights reserved.
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19 | *
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20 | */
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21 |
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22 | /*! \mainpage MoleCuilder - a molecular set builder
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23 | *
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24 | * This introductory shall briefly make acquainted with the program, helping in installing and a first run.
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25 | *
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26 | * \section about About the Program
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27 | *
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28 | * MoleCuilder is a program, written entirely in C++, that enables the construction of a coordinate set for the
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29 | * atoms making up an molecule. It allows for both building of simple molecules by adding atom-wise giving bond
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30 | * angles and distances or absolute coordinates, but also using them as templates. Regions can be specified and
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31 | * ordered to be filled with a molecule in a certain manner. Greater conglomerations of molecules can be tesselated
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32 | * and recognized as a region themselves to be subsequently surrounded by other (surface solvated) molecules.
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33 | * In the end, MoleCuilder allows the construction of arbitrary nano structures, whether they be crystalline or
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34 | * amorphic in nature.
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35 | *
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36 | *
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37 | * \section install Installation
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38 | *
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39 | * Installation should without problems succeed as follows:
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40 | * -# ./configure (or: mkdir build;mkdir run;cd build; ../configure --bindir=../run)
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41 | * -# make
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42 | * -# make install
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43 | *
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44 | * Further useful commands are
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45 | * -# make clean uninstall: deletes .o-files and removes executable from the given binary directory\n
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46 | * -# make doxygen-doc: Creates these html pages out of the documented source
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47 | * -# make check: Runs an extensive set of unit tests and a testsuite which also gives a good overview on the set of
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48 | * functions.
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49 | *
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50 | * \section run Running
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51 | *
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52 | * The program can be executed by running: ./molecuilder
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53 | *
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54 | * MoleCuilder has three interfaces at your disposal:
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55 | * -# Textmenu: A simple interactive console-based menu, where awaits your choices and inputs in order to set atoms
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56 | * as you like
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57 | * -# CommandLineUI: Every command can also be chained up as a sequence of actions on the command line to be executed
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58 | * with any user interaction.
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59 | * -# GraphicalUI: A graphical user interface that also display the molecular structure being built and lots of other
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60 | * informations to ease the construction of bigger geometries.
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61 | *
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62 | * The supported output formats right now are:
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63 | * -# mpqc: Configuration files of the Massively Parallel Quantum Chemistry package (Sandia labs)
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64 | * -# pcp: Configuration files of the Parallel Car-Parrinello program (Institute for Numerical Simulation)
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65 | * -# tremolo: Configuration files of TREMOLO (Institute for Numerical Simulation)
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66 | * -# xyz: the most basic format for the 3d arrangement of atoms consisting of a list of element and 3 coordinates.
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67 | *
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68 | */
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69 |
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70 | // include config.h
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71 | #ifdef HAVE_CONFIG_H
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72 | #include <config.h>
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73 | #endif
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74 |
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75 | #include "Helpers/MemDebug.hpp"
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76 |
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77 | #include "bondgraph.hpp"
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78 | #include "config.hpp"
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79 | #include "Helpers/Log.hpp"
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80 | #include "molecule.hpp"
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81 | #include "periodentafel.hpp"
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82 | #include "tesselationhelpers.hpp"
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83 | #include "UIElements/UIFactory.hpp"
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84 | #include "UIElements/TextUI/TextUIFactory.hpp"
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85 | #include "UIElements/CommandLineUI/CommandLineUIFactory.hpp"
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86 | #include "UIElements/CommandLineUI/CommandLineParser.hpp"
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87 | #ifdef USE_GUI_QT
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88 | #include "UIElements/Qt4/QtUIFactory.hpp"
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89 | #endif
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90 | #include "UIElements/MainWindow.hpp"
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91 | #include "UIElements/Dialog.hpp"
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92 | #include "Menu/ActionMenuItem.hpp"
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93 | #include "Helpers/Verbose.hpp"
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94 | #include "World.hpp"
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95 |
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96 | #include "Actions/ActionRegistry.hpp"
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97 | #include "Actions/ActionHistory.hpp"
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98 |
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99 | #include "Parser/ChangeTracker.hpp"
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100 | #include "Parser/FormatParserStorage.hpp"
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101 |
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102 | #include "UIElements/UIFactory.hpp"
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103 | #include "UIElements/TextUI/TextUIFactory.hpp"
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104 | #include "UIElements/CommandLineUI/CommandLineUIFactory.hpp"
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105 | #include "UIElements/MainWindow.hpp"
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106 | #include "UIElements/Dialog.hpp"
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107 |
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108 | #include "version.h"
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109 |
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110 |
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111 | /********************************************** Main routine **************************************/
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112 |
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113 | void cleanUp(){
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114 | FormatParserStorage::purgeInstance();
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115 | ChangeTracker::purgeInstance();
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116 | World::purgeInstance();
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117 | logger::purgeInstance();
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118 | errorLogger::purgeInstance();
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119 | UIFactory::purgeInstance();
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120 | ValueStorage::purgeInstance();
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121 | CommandLineParser::purgeInstance();
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122 | ActionRegistry::purgeInstance();
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123 | ActionHistory::purgeInstance();
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124 | #ifdef LOG_OBSERVER
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125 | cout << observerLog().getLog();
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126 | #endif
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127 | Memory::getState();
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128 | }
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129 |
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130 | void dumpMemory(){
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131 | ofstream ost("molecuilder.memdump");
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132 | Memory::dumpMemory(ost);
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133 | }
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134 |
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135 | int main(int argc, char **argv)
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136 | {
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137 | // while we are non interactive, we want to abort from asserts
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138 | ASSERT_DO(Assert::Abort);
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139 | ASSERT_HOOK(dumpMemory);
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140 | string line;
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141 | char **Arguments = NULL;
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142 | int ArgcSize = 0;
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143 | int ExitFlag = 0;
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144 | bool ArgumentsCopied = false;
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145 | std::string BondGraphFileName("\n");
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146 |
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147 | // print version check and copyright notice
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148 | cout << MOLECUILDERVERSION << endl;
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149 | cout << "MoleCuilder comes with ABSOLUTELY NO WARRANTY; for details type" << endl;
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150 | cout << "`molecuilder --warranty'." << endl;
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151 | cout << "`MoleCuilder - to create and alter molecular systems." << endl;
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152 | cout << "Copyright (C) 2010 University Bonn. All rights reserved." << endl;
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153 |
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154 | setVerbosity(0);
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155 | // need to init the history before any action is created
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156 | ActionHistory::init();
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157 |
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158 | // from this moment on, we need to be sure to deeinitialize in the correct order
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159 | // this is handled by the cleanup function
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160 | atexit(cleanUp);
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161 |
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162 | // Parse command line options and if present create respective UI
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163 | {
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164 | // construct bond graph
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165 | if (World::getInstance().getConfig()->BG == NULL) {
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166 | World::getInstance().getConfig()->BG = new BondGraph(World::getInstance().getConfig()->GetIsAngstroem());
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167 | if (World::getInstance().getConfig()->BG->LoadBondLengthTable(BondGraphFileName)) {
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168 | DoLog(0) && (Log() << Verbose(0) << "Bond length table loaded successfully." << endl);
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169 | } else {
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170 | DoeLog(1) && (eLog()<< Verbose(1) << "Bond length table loading failed." << endl);
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171 | }
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172 | }
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173 | // handle remaining arguments by CommandLineParser
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174 | if (argc>1) {
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175 | CommandLineParser::getInstance().InitializeCommandArguments();
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176 | CommandLineParser::getInstance().Run(argc,argv);
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177 | DoLog(0) && (Log() << Verbose(0) << "Setting UI to CommandLine." << endl);
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178 | UIFactory::registerFactory(new CommandLineUIFactory::description());
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179 | UIFactory::makeUserInterface("CommandLine");
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180 | } else {
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181 | // In the interactive mode, we can leave the user the choice in case of error
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182 | ASSERT_DO(Assert::Ask);
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183 | #ifdef USE_GUI_QT
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184 | DoLog(0) && (Log() << Verbose(0) << "Setting UI to Qt4." << endl);
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185 | UIFactory::registerFactory(new QtUIFactory::description());
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186 | UIFactory::makeUserInterface("Qt4");
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187 | #else
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188 | DoLog(0) && (Log() << Verbose(0) << "Setting UI to Text." << endl);
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189 | cout << MOLECUILDERVERSION << endl;
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190 | UIFactory::registerFactory(new TextUIFactory::description());
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191 | UIFactory::makeUserInterface("Text");
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192 | #endif
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193 | }
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194 | }
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195 |
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196 | {
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197 | MainWindow *mainWindow = UIFactory::getInstance().makeMainWindow();
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198 | mainWindow->display();
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199 | delete mainWindow;
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200 | }
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201 |
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202 | FormatParserStorage::getInstance().SaveAll();
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203 | ChangeTracker::getInstance().saveStatus();
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204 |
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205 | // free the new argv
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206 | if (ArgumentsCopied) {
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207 | for (int i=0; i<ArgcSize;i++)
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208 | delete[](Arguments[i]);
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209 | delete[](Arguments);
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210 | }
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211 | //delete[](ConfigFileName);
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212 |
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213 | ExitFlag = World::getInstance().getExitFlag();
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214 | return (ExitFlag == 1 ? 0 : ExitFlag);
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215 | }
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216 |
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217 | /********************************************** E N D **************************************************/
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