source: src/builder.cpp@ b60804

Action_Thermostats Add_AtomRandomPerturbation Add_FitFragmentPartialChargesAction Add_RotateAroundBondAction Add_SelectAtomByNameAction Added_ParseSaveFragmentResults AddingActions_SaveParseParticleParameters Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_ParticleName_to_Atom Adding_StructOpt_integration_tests AtomFragments Automaking_mpqc_open AutomationFragmentation_failures Candidate_v1.5.4 Candidate_v1.6.0 Candidate_v1.6.1 Candidate_v1.7.0 ChangeBugEmailaddress ChangingTestPorts ChemicalSpaceEvaluator CombiningParticlePotentialParsing Combining_Subpackages Debian_Package_split Debian_package_split_molecuildergui_only Disabling_MemDebug Docu_Python_wait EmpiricalPotential_contain_HomologyGraph EmpiricalPotential_contain_HomologyGraph_documentation Enable_parallel_make_install Enhance_userguide Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph FitPartialCharges_GlobalError Fix_BoundInBox_CenterInBox_MoleculeActions Fix_ChargeSampling_PBC Fix_ChronosMutex Fix_FitPartialCharges Fix_FitPotential_needs_atomicnumbers Fix_ForceAnnealing Fix_IndependentFragmentGrids Fix_ParseParticles Fix_ParseParticles_split_forward_backward_Actions Fix_PopActions Fix_QtFragmentList_sorted_selection Fix_Restrictedkeyset_FragmentMolecule Fix_StatusMsg Fix_StepWorldTime_single_argument Fix_Verbose_Codepatterns Fix_fitting_potentials Fixes ForceAnnealing_goodresults ForceAnnealing_oldresults ForceAnnealing_tocheck ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion FragmentAction_writes_AtomFragments FragmentMolecule_checks_bonddegrees GeometryObjects Gui_Fixes Gui_displays_atomic_force_velocity ImplicitCharges IndependentFragmentGrids IndependentFragmentGrids_IndividualZeroInstances IndependentFragmentGrids_IntegrationTest IndependentFragmentGrids_Sole_NN_Calculation JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool JobMarket_unresolvable_hostname_fix MoreRobust_FragmentAutomation ODR_violation_mpqc_open PartialCharges_OrthogonalSummation PdbParser_setsAtomName PythonUI_with_named_parameters QtGui_reactivate_TimeChanged_changes Recreated_GuiChecks Rewrite_FitPartialCharges RotateToPrincipalAxisSystem_UndoRedo SaturateAtoms_findBestMatching SaturateAtoms_singleDegree StoppableMakroAction Subpackage_CodePatterns Subpackage_JobMarket Subpackage_LinearAlgebra Subpackage_levmar Subpackage_mpqc_open Subpackage_vmg Switchable_LogView ThirdParty_MPQC_rebuilt_buildsystem TrajectoryDependenant_MaxOrder TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps TremoloParser_setsAtomName Ubuntu_1604_changes stable
Last change on this file since b60804 was f4d063, checked in by Frederik Heber <heber@…>, 15 years ago

MEMFIX: MemDebug ignores all unknown sources. Removed all dependencies around main(), moved to builder_init.?pp.

  • this has been an attempt to fix the warning of a memory leak that actually results into the libboost_filesystem.so over which we have no control. As of now, i I do not quite look through the whole affair. That is, I have a now idea why Till's new memory allocator is used during the initialization of some external library already, but apparently it must have to do with lookup tables present in the exectuable already. Hence, we can not do much about.
  • Nonetheless, we split up main() into some initializating functions which have been outsourced to builder_init.cpp.
  • The only fix then is that we ignore all values of unknown source in MemDebug.
  • Note: We only do accouting of stuff allocated on the heap (e.g. int *test = new int;) and not on stack (int test;)! However, stack space is limited anyway.
  • Property mode set to 100755
File size: 3.4 KB
Line 
1/*
2 * Project: MoleCuilder
3 * Description: creates and alters molecular systems
4 * Copyright (C) 2010 University of Bonn. All rights reserved.
5 * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
6 */
7
8 /** \file builder.cpp
9 *
10 * date: Jan 1, 2007
11 * author: heber
12 *
13 */
14
15/*! \page Copyright notice
16 *
17 * MoleCuilder - to create and alter molecular systems
18 * Copyright (C) 2010 University Bonn. All rights reserved.
19 *
20 */
21
22/*! \mainpage MoleCuilder - a molecular set builder
23 *
24 * This introductory shall briefly make acquainted with the program, helping in installing and a first run.
25 *
26 * \section about About the Program
27 *
28 * MoleCuilder is a program, written entirely in C++, that enables the construction of a coordinate set for the
29 * atoms making up an molecule. It allows for both building of simple molecules by adding atom-wise giving bond
30 * angles and distances or absolute coordinates, but also using them as templates. Regions can be specified and
31 * ordered to be filled with a molecule in a certain manner. Greater conglomerations of molecules can be tesselated
32 * and recognized as a region themselves to be subsequently surrounded by other (surface solvated) molecules.
33 * In the end, MoleCuilder allows the construction of arbitrary nano structures, whether they be crystalline or
34 * amorphic in nature.
35 *
36 *
37 * \section install Installation
38 *
39 * Installation should without problems succeed as follows:
40 * -# ./configure (or: mkdir build;mkdir run;cd build; ../configure --bindir=../run)
41 * -# make
42 * -# make install
43 *
44 * Further useful commands are
45 * -# make clean uninstall: deletes .o-files and removes executable from the given binary directory\n
46 * -# make doxygen-doc: Creates these html pages out of the documented source
47 * -# make check: Runs an extensive set of unit tests and a testsuite which also gives a good overview on the set of
48 * functions.
49 *
50 * \section run Running
51 *
52 * The program can be executed by running: ./molecuilder
53 *
54 * MoleCuilder has three interfaces at your disposal:
55 * -# Textmenu: A simple interactive console-based menu, where awaits your choices and inputs in order to set atoms
56 * as you like
57 * -# CommandLineUI: Every command can also be chained up as a sequence of actions on the command line to be executed
58 * with any user interaction.
59 * -# GraphicalUI: A graphical user interface that also display the molecular structure being built and lots of other
60 * informations to ease the construction of bigger geometries.
61 *
62 * The supported output formats right now are:
63 * -# mpqc: Configuration files of the Massively Parallel Quantum Chemistry package (Sandia labs)
64 * -# pcp: Configuration files of the Parallel Car-Parrinello program (Institute for Numerical Simulation)
65 * -# tremolo: Configuration files of TREMOLO (Institute for Numerical Simulation)
66 * -# xyz: the most basic format for the 3d arrangement of atoms consisting of a list of element and 3 coordinates.
67 *
68 */
69
70// include config.h
71#ifdef HAVE_CONFIG_H
72#include <config.h>
73#endif
74
75#include "builder_init.hpp"
76
77/********************************************** Main routine **************************************/
78
79int main(int argc, char **argv)
80{
81 initGeneral();
82
83 initUI(argc,argv);
84
85 doUI();
86
87 return saveAll();
88}
89
90/********************************************** E N D **************************************************/
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