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  • AUTHORS

    r14c57a r51c3e4  
    1 Frederik Heber  (heber@ins.uni-bonn.de)
     1Tillmann Crueger        (crueger@ins.uni-bonn.de)
     2Daniel Dueck            (dueck@ins.uni-bonn.de)
     3Frederik Heber          (heber@ins.uni-bonn.de)
     4Saskia Metzler          (metzler@ins.uni-bonn.de)
     5Christian Neuen         (neuen@ins.uni-bonn.de)

  • COPYING

    r14c57a r51c3e4  
    1 <<<<<<< HEAD
    2                     GNU GENERAL PUBLIC LICENSE
    3                        Version 3, 29 June 2007
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    5  Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
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    221                    GNU GENERAL PUBLIC LICENSE
    232                       Version 2, June 1991
    … …  
    3817using it.  (Some other Free Software Foundation software is covered by
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    40 >>>>>>> FETCH_HEAD
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    537 covered work, and grant a patent license to some of the parties
    538 receiving the covered work authorizing them to use, propagate, modify
    539 or convey a specific copy of the covered work, then the patent license
    540 you grant is automatically extended to all recipients of the covered
    541 work and works based on it.
    542 
    543   A patent license is "discriminatory" if it does not include within
    544 the scope of its coverage, prohibits the exercise of, or is
    545 conditioned on the non-exercise of one or more of the rights that are
    546 specifically granted under this License.  You may not convey a covered
    547 work if you are a party to an arrangement with a third party that is
    548 in the business of distributing software, under which you make payment
    549 to the third party based on the extent of your activity of conveying
    550 the work, and under which the third party grants, to any of the
    551 parties who would receive the covered work from you, a discriminatory
    552 patent license (a) in connection with copies of the covered work
    553 conveyed by you (or copies made from those copies), or (b) primarily
    554 for and in connection with specific products or compilations that
    555 contain the covered work, unless you entered into that arrangement,
    556 or that patent license was granted, prior to 28 March 2007.
    557 
    558   Nothing in this License shall be construed as excluding or limiting
    559 any implied license or other defenses to infringement that may
    560 otherwise be available to you under applicable patent law.
    561 
    562   12. No Surrender of Others' Freedom.
    563 
    564   If conditions are imposed on you (whether by court order, agreement or
    565 otherwise) that contradict the conditions of this License, they do not
    566 excuse you from the conditions of this License.  If you cannot convey a
    567 covered work so as to satisfy simultaneously your obligations under this
    568 License and any other pertinent obligations, then as a consequence you may
    569 not convey it at all.  For example, if you agree to terms that obligate you
    570 to collect a royalty for further conveying from those to whom you convey
    571 the Program, the only way you could satisfy both those terms and this
    572 License would be to refrain entirely from conveying the Program.
    573 
    574   13. Use with the GNU Affero General Public License.
    575 
    576   Notwithstanding any other provision of this License, you have
    577 permission to link or combine any covered work with a work licensed
    578 under version 3 of the GNU Affero General Public License into a single
    579 combined work, and to convey the resulting work.  The terms of this
    580 License will continue to apply to the part which is the covered work,
    581 but the special requirements of the GNU Affero General Public License,
    582 section 13, concerning interaction through a network will apply to the
    583 combination as such.
    584 
    585   14. Revised Versions of this License.
    586 
    587   The Free Software Foundation may publish revised and/or new versions of
    588 the GNU General Public License from time to time.  Such new versions will
    589 be similar in spirit to the present version, but may differ in detail to
    590 address new problems or concerns.
    591 
    592   Each version is given a distinguishing version number.  If the
    593 Program specifies that a certain numbered version of the GNU General
    594 Public License "or any later version" applies to it, you have the
    595 option of following the terms and conditions either of that numbered
    596 version or of any later version published by the Free Software
    597 Foundation.  If the Program does not specify a version number of the
    598 GNU General Public License, you may choose any version ever published
    599 by the Free Software Foundation.
    600 
    601   If the Program specifies that a proxy can decide which future
    602 versions of the GNU General Public License can be used, that proxy's
    603 public statement of acceptance of a version permanently authorizes you
    604 to choose that version for the Program.
    605 
    606   Later license versions may give you additional or different
    607 permissions.  However, no additional obligations are imposed on any
    608 author or copyright holder as a result of your choosing to follow a
    609 later version.
    610 
    611   15. Disclaimer of Warranty.
    612 
    613   THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
    614 APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
    615 HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
    616 OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
    617 THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
    618 PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
    619 IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
    620 ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
    621 
    622   16. Limitation of Liability.
    623 
    624   IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
    625 WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
    626 THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
    627 GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
    628 USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
    629 DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
    630 PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
    631 EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
    632 SUCH DAMAGES.
    633 
    634   17. Interpretation of Sections 15 and 16.
    635 
    636   If the disclaimer of warranty and limitation of liability provided
    637 above cannot be given local legal effect according to their terms,
    638 reviewing courts shall apply local law that most closely approximates
    639 an absolute waiver of all civil liability in connection with the
    640 Program, unless a warranty or assumption of liability accompanies a
    641 copy of the Program in return for a fee.
    642 
    643                      END OF TERMS AND CONDITIONS
    644 
    645             How to Apply These Terms to Your New Programs
    646 =======
    64724this service if you wish), that you receive source code or can get it
    64825if you want it, that you can change the software or use pieces of it
    … …  
    909286
    910287            How to Apply These Terms to Your New Programs
    911 >>>>>>> FETCH_HEAD
    912288
    913289  If you develop a new program, and you want it to be of the greatest
    … …  
    917293  To do so, attach the following notices to the program.  It is safest
    918294to attach them to the start of each source file to most effectively
    919 <<<<<<< HEAD
    920 state the exclusion of warranty; and each file should have at least
    921 =======
    922295convey the exclusion of warranty; and each file should have at least
    923 >>>>>>> FETCH_HEAD
    924296the "copyright" line and a pointer to where the full notice is found.
    925297
    926     <one line to give the program's name and a brief idea of what it does.>
    927     Copyright (C) <year>  <name of author>
    928 
    929 <<<<<<< HEAD
    930     This program is free software: you can redistribute it and/or modify
    931     it under the terms of the GNU General Public License as published by
    932     the Free Software Foundation, either version 3 of the License, or
    933 =======
     298    MoleCuilder - to create and alter molecular systems
     299    Copyright (C) 2010  Frederik Heber
     300
    934301    This program is free software; you can redistribute it and/or modify
    935302    it under the terms of the GNU General Public License as published by
    936303    the Free Software Foundation; either version 2 of the License, or
    937 >>>>>>> FETCH_HEAD
    938304    (at your option) any later version.
    939305
    … …  
    944310
    945311    You should have received a copy of the GNU General Public License
    946 <<<<<<< HEAD
    947     along with this program.  If not, see <http://www.gnu.org/licenses/>.
    948 
    949 Also add information on how to contact you by electronic and paper mail.
    950 
    951   If the program does terminal interaction, make it output a short
    952 notice like this when it starts in an interactive mode:
    953 
    954     <program>  Copyright (C) <year>  <name of author>
    955     This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
    956 =======
    957312    along with this program; if not, write to the Free Software
    958313    Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
    … …  
    964319when it starts in an interactive mode:
    965320
    966     Gnomovision version 69, Copyright (C) year  name of author
    967     Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
    968 >>>>>>> FETCH_HEAD
     321    MoleCuilder version ??, Copyright (C) 2010  Frederik Heber
     322    MoleCuilder comes with ABSOLUTELY NO WARRANTY; for details type
     323    `molecuilder --help-warranty'.
    969324    This is free software, and you are welcome to redistribute it
    970     under certain conditions; type `show c' for details.
     325    under certain conditions; type `molecuilder --help-redistribute'
     326    for details.
    971327
    972328The hypothetical commands `show w' and `show c' should show the appropriate
    973 <<<<<<< HEAD
    974 parts of the General Public License.  Of course, your program's commands
    975 might be different; for a GUI interface, you would use an "about box".
    976 
    977   You should also get your employer (if you work as a programmer) or school,
    978 if any, to sign a "copyright disclaimer" for the program, if necessary.
    979 For more information on this, and how to apply and follow the GNU GPL, see
    980 <http://www.gnu.org/licenses/>.
    981 
    982   The GNU General Public License does not permit incorporating your program
    983 into proprietary programs.  If your program is a subroutine library, you
    984 may consider it more useful to permit linking proprietary applications with
    985 the library.  If this is what you want to do, use the GNU Lesser General
    986 Public License instead of this License.  But first, please read
    987 <http://www.gnu.org/philosophy/why-not-lgpl.html>.
    988 =======
    989329parts of the General Public License.  Of course, the commands you use may
    990330be called something other than `show w' and `show c'; they could even be
    … …  
    995335necessary.  Here is a sample; alter the names:
    996336
    997   Yoyodyne, Inc., hereby disclaims all copyright interest in the program
    998   `Gnomovision' (which makes passes at compilers) written by James Hacker.
    999 
    1000   <signature of Ty Coon>, 1 April 1989
    1001   Ty Coon, President of Vice
     337  University of Bonn, hereby disclaims all copyright interest in the program
     338  `MoleCuilder' (which creates molecular systems) written by Frederik Heber.
     339
     340  Frederik Heber, 17 Aug 2010
    1002341
    1003342This General Public License does not permit incorporating your program into
    … …  
    1006345library.  If this is what you want to do, use the GNU Library General
    1007346Public License instead of this License.
    1008 >>>>>>> FETCH_HEAD

  • README

    r14c57a r51c3e4  
    1 <<<<<<< HEAD
    2 # Project: Molecuilder
     1# Project: MoleCuilder
    32#
    43# heber@ins.uni-bonn.de
    54
    6         Molecuilder
     5        MoleCuilder
    76
    8 ... is a tool that started as a mean to edit pcp configuration files (adding/remvoing groups of atoms, measuring bond lengths and so forth) and has grown into the many-body fragmentation test base of a new method coined BOSSANOVA (Bond Order diSSection in an ANOVA (ANalysis Of VAriance) -like fashion). It spills out configuration files for each fragment and includes joining and analyzing programs, to put together the partial energies and forces of each fragment to the total energy and forces. It allows for a complete Born-Oppenheimer molecular dynamics run.
    9 =======
    10 # Project: ParallelCarParrinello
    11 # Jan Hamaekers
    12 # Frederik Heber
    13 # 2005
    14 #
    15 # File: README
     7... is a tool that started as a mean to edit pcp configuration files (adding/
     8removing groups of atoms, measuring bond lengths and so forth), grew forth into
     9a many-body fragmentation test base of a new method coined BOSSANOVA (Bond
     10Order diSSection in an ANOVA (ANalysis Of VAriance) - like fashion). It spilled
     11out configuration files for each fragment and included joining and analyzing
     12programs, to put together the partial energies and forces of each fragment to
     13the total energy and forces. Since then it has evolved into a complete toolbox
     14for creating molecular systems and worlds.
    1615
    17         Electronic Structure PACKage
    18 
    19 Is a collection of mathematical-physical programs to calculate via various ab-initio methods
    20 such as density functional theory or Hartree-Fock electronic(-magnetic) properties including
    21 the molecular (Car&Parrinello) dynamics of a many electron system. Especially, the linear
    22 response of the system to a external magnetic field in a perturbation approach in terms of
    23 susceptibility and chemical shielding is implemented via the Density Functional Perturbation
    24 Theory. It was developed mainly by Jan Hamaekers (pcp) with additional code by Frederik Heber
    25 (dfpt part in pcp) and also Ralf Wildenhuis (Gauss) at the Institute for Numerical Simulation
    26 at the University of Bonn[1].
    27 
    28 
    29 >>>>>>> FETCH_HEAD
    3016
    3117INSTALLATION NOTES
    3218==================
    3319
    34 <<<<<<< HEAD
    3520The following packages are needed
    3621* GCC or alike
    3722* GSL (GNU Scientific Library, available at http://www.gnu.org/software/gsl)
    3823* Boost 1.4 or newer
    39 =======
    40 In general gcc or alike is needed to compile the sources, for more specific demands see the README files in the sub directory of each package part.
    4124
    4225LINKS
    4326=====
    4427[1] http://www.ins.uni-bonn.de/
    45 >>>>>>> FETCH_HEAD

  • configure.ac

    r14c57a r51c3e4  
    33
    44AC_PREREQ(2.59)
    5 AC_INIT(Molecuilder, 1.0, heber@ins.uni-bonn.de, molecuilder)
     5AC_INIT(MoleCuilder, 1.0.0, heber@ins.uni-bonn.de, molecuilder)
    66AC_CONFIG_AUX_DIR(config)
    77AC_CONFIG_SRCDIR([src/builder.cpp])
    … …  
    99AC_CONFIG_MACRO_DIR([m4])
    1010
    11 AM_INIT_AUTOMAKE(dist-bzip2 parallel-tests)
     11AM_INIT_AUTOMAKE([dist-bzip2 1.11 parallel-tests color-tests])
    1212
    1313# Checks for programs.
    … …  
    1515AC_PROG_CXX
    1616AC_PROG_CC
    17 # obselete by LT_INIT
    18 #AC_PROG_RANLIB
    1917AC_PROG_INSTALL
    2018AC_CHECK_PROG([LATEX],[latex],[latex],[:])
    … …  
    8280fi
    8381
    84 # add replacement/saturation hydrogen or not
     82# use CppUnit TestRunner or not
    8583AC_ARG_ENABLE([ecut],AS_HELP_STRING([--enable-ecut],[Use ECut TestRunnerClient (default is no)]),
    8684              [enable_ecut=$enableval], [enable_ecut=no])
    … …  
    8886  AC_DEFINE(HAVE_ECUT,1, ["Use ECut TestRunnerClient instead of our own."])
    8987  AC_SUBST(HAVE_ECUT)
     88fi
     89
     90# with valgrinding testsuite or not
     91AC_ARG_WITH([valgrind],AS_HELP_STRING([--with-valgrind],[Use Valgrind on the testsuite (default is no)]),
     92              [with_valgrind=$withval], [with_valgrind=no])
     93if test x"$with_valgrind" = xyes; then
     94  AC_CHECK_HEADER([valgrind/valgrind.h],
     95    [
     96      # check header
     97      AC_DEFINE(HAVE_VALGRIND_TESTSUITE,1, ["Use Valgrind to check the testsuite."])
     98      # check path
     99      AC_PATH_PROG(VALGRIND, [valgrind], [/bin/false])
     100      # set variables
     101      AC_SUBST(HAVE_VALGRIND_TESTSUITE)
     102      AC_SUBST(VALGRIND)
     103    ],
     104    [
     105      AC_MSG_ERROR(["Valgrind support requested but headers not available."])
     106    ]
     107  )
    90108fi
    91109

  • src/Actions/Action.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * Action.cpp

  • src/Actions/ActionHistory.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * ActionHistory.cpp
    … …  
    133140
    134141bool ActionHistory::RedoAction::isActive(){
    135   std::cout << "Redo" << std::endl;
    136142  return hist->hasRedo();
    137143}
    … …  
    143149
    144150Action::state_ptr ActionHistory::RedoAction::performCall(){
     151  std::cout << "Redo" << std::endl;
    145152  hist->redoLast();
    146153  return Action::success;

  • src/Actions/ActionRegistry.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * Registry<Action>.cpp

  • src/Actions/ActionSequence.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * ActionSequenze.cpp

  • src/Actions/AnalysisAction/MolecularVolumeAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * MolecularVolumeAction.cpp

  • src/Actions/AnalysisAction/PairCorrelationAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * PairCorrelationAction.cpp

  • src/Actions/AnalysisAction/PointCorrelationAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * PointCorrelationAction.cpp
    … …  
    2633#include "World.hpp"
    2734
     35#include <cmath>
    2836#include <iostream>
    2937#include <string>

  • src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * PrincipalAxisSystemAction.cpp
    … …  
    6976      Vector x = (*iter)->getPosition();
    7077      x -= *CenterOfGravity;
    71       const double mass = (*iter)->getType()->mass;
     78      const double mass = (*iter)->getType()->getMass();
    7279      InertiaTensor.at(0,0) += mass*(x[1]*x[1] + x[2]*x[2]);
    7380      InertiaTensor.at(0,1) += mass*(-x[0]*x[1]);

  • src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * SurfaceCorrelationAction.cpp

  • src/Actions/AtomAction/AddAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * AddAction.cpp

  • src/Actions/AtomAction/ChangeElementAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * ChangeElementAction.cpp

  • src/Actions/AtomAction/RemoveAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * RemoveAction.cpp

  • src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * RotateAroundOriginByAngleAction.cpp
    … …  
    2229
    2330
     31#include <cmath>
    2432#include <iostream>
    2533#include <fstream>

  • src/Actions/AtomAction/TranslateAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * TranslateAction.cpp

  • src/Actions/CmdAction/BondLengthTableAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * BondLengthTableAction.cpp

  • src/Actions/CmdAction/ElementDbAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * ElementDbAction.cpp

  • src/Actions/CmdAction/FastParsingAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * FastParsingAction.cpp

  • src/Actions/CmdAction/HelpAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * HelpAction.cpp

  • src/Actions/CmdAction/VerboseAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * VerboseAction.cpp

  • src/Actions/CmdAction/VersionAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * VersionAction.cpp
    … …  
    4249  ASSERT(dialog,"No Dialog given when filling action dialog");
    4350
    44   dialog->queryEmpty(NAME, ESPACKVersion);
     51  dialog->queryEmpty(NAME, MOLECUILDERVERSION);
    4552
    4653  return dialog;

  • src/Actions/ErrorAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * ErrorAction.cpp

  • src/Actions/FragmentationAction/DepthFirstSearchAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * DepthFirstSearchAction.cpp

  • src/Actions/FragmentationAction/FragmentationAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * FragmentationAction.cpp

  • src/Actions/FragmentationAction/SubgraphDissectionAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * SubgraphDissectionAction.cpp

  • src/Actions/MakroAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * MakroAction.cpp

  • src/Actions/ManipulateAtomsProcess.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * ManipulateAtomsProcess.cpp

  • src/Actions/MapOfActions.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * MapOfActions.cpp
    … …  
    801808  if (typeid(const element ) == *TypeMap[name]) {
    802809    std::ostringstream stream;
    803     stream << _T->Z;
     810    stream << _T->getAtomicNumber();
    804811    CurrentValue[name] = stream.str();
    805812  } else
    … …  
    862869    std::ostringstream stream;
    863870    for (std::vector<const element *>::iterator iter = _T.begin(); iter != _T.end(); ++iter) {
    864       stream << (*iter)->Z << " ";
     871      stream << (*iter)->getAtomicNumber() << " ";
    865872    }
    866873    CurrentValue[name] = stream.str();

  • src/Actions/MethodAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * MethodAction.cpp

  • src/Actions/MoleculeAction/BondFileAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * BondFileAction.cpp

  • src/Actions/MoleculeAction/ChangeNameAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * ChangeNameAction.cpp

  • src/Actions/MoleculeAction/FillWithMoleculeAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * FillWithMoleculeAction.cpp

  • src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * LinearInterpolationofTrajectoriesAction.cpp

  • src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * RotateAroundSelfByAngleAction.cpp

  • src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * RotateToPrincipalAxisSystemAction.cpp
    … …  
    9097      Vector x = (*iter)->getPosition();
    9198      x -= *CenterOfGravity;
    92       const double mass = (*iter)->getType()->mass;
     99      const double mass = (*iter)->getType()->getMass();
    93100      InertiaTensor.at(0,0) += mass*(x[1]*x[1] + x[2]*x[2]);
    94101      InertiaTensor.at(0,1) += mass*(-x[0]*x[1]);
    … …  
    141148      Vector x = (*iter)->getPosition();
    142149      x -= *CenterOfGravity;
    143       const double mass = (*iter)->getType()->mass;
     150      const double mass = (*iter)->getType()->getMass();
    144151      InertiaTensor.at(0,0) += mass*(x[1]*x[1] + x[2]*x[2]);
    145152      InertiaTensor.at(0,1) += mass*(-x[0]*x[1]);

  • src/Actions/MoleculeAction/SaveAdjacencyAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * SaveAdjacencyAction.cpp

  • src/Actions/MoleculeAction/SaveBondsAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * SaveBondsAction.cpp

  • src/Actions/MoleculeAction/SaveTemperatureAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * SaveTemperatureAction.cpp

  • src/Actions/MoleculeAction/SuspendInWaterAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * SuspendInWaterAction.cpp

  • src/Actions/MoleculeAction/VerletIntegrationAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * VerletIntegrationAction.cpp

  • src/Actions/ParserAction/LoadXyzAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * LoadXyzAction.cpp

  • src/Actions/ParserAction/SaveXyzAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * SaveXyzAction.cpp

  • src/Actions/Process.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * Process.cpp

  • src/Actions/SelectionAction/AllAtomsAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * AllAtomsAction.cpp

  • src/Actions/SelectionAction/AllAtomsInsideCuboidAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * AllAtomsInsideCuboidAction.cpp

  • src/Actions/SelectionAction/AllAtomsInsideSphereAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * AllAtomsInsideSphereAction.cpp

  • src/Actions/SelectionAction/AllAtomsOfMoleculeAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * AllAtomsOfMoleculeAction.cpp

  • src/Actions/SelectionAction/AllMoleculesAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * AllMoleculesAction.cpp

  • src/Actions/SelectionAction/AtomByElementAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * AtomByElementAction.cpp

  • src/Actions/SelectionAction/AtomByIdAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * AtomByIdAction.cpp

  • src/Actions/SelectionAction/ClearAllAtomsAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * ClearAllAtomsAction.cpp

  • src/Actions/SelectionAction/ClearAllMoleculesAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * ClearAllMoleculesAction.cpp

  • src/Actions/SelectionAction/MoleculeByFormulaAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * MoleculeByFormulaAction.cpp

  • src/Actions/SelectionAction/MoleculeByIdAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * MoleculeByIdAction.cpp

  • src/Actions/SelectionAction/MoleculeOfAtomAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * MoleculeOfAtomAction.cpp

  • src/Actions/SelectionAction/NotAllAtomsAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * NotAllAtomsAction.cpp

  • src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * NotAllAtomsInsideCuboidAction.cpp

  • src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * NotAllAtomsInsideSphereAction.cpp

  • src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * NotAllAtomsOfMoleculeAction.cpp

  • src/Actions/SelectionAction/NotAllMoleculesAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * NotAllMoleculesAction.cpp

  • src/Actions/SelectionAction/NotAtomByElementAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * NotAtomByElementAction.cpp

  • src/Actions/SelectionAction/NotAtomByIdAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * NotAtomByIdAction.cpp

  • src/Actions/SelectionAction/NotMoleculeByFormulaAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * NotMoleculeByFormulaAction.cpp

  • src/Actions/SelectionAction/NotMoleculeByIdAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * NotMoleculeByIdAction.cpp

  • src/Actions/SelectionAction/NotMoleculeOfAtomAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * NotMoleculeOfAtomAction.cpp

  • src/Actions/TesselationAction/ConvexEnvelopeAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * ConvexEnvelopeAction.cpp

  • src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * NonConvexEnvelopeAction.cpp

  • src/Actions/ValueStorage.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * ValueStorage.cpp

  • src/Actions/WorldAction/AddEmptyBoundaryAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * AddEmptyBoundaryAction.cpp

  • src/Actions/WorldAction/BoundInBoxAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * BoundInBoxAction.cpp

  • src/Actions/WorldAction/CenterInBoxAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * CenterInBoxAction.cpp

  • src/Actions/WorldAction/CenterOnEdgeAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * CenterOnEdgeAction.cpp

  • src/Actions/WorldAction/ChangeBoxAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * ChangeBoxAction.cpp

  • src/Actions/WorldAction/InputAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * InputAction.cpp

  • src/Actions/WorldAction/OutputAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * OutputAction.cpp

  • src/Actions/WorldAction/RepeatBoxAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * RepeatBoxAction.cpp

  • src/Actions/WorldAction/ScaleBoxAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * ScaleBoxAction.cpp

  • src/Actions/WorldAction/SetDefaultNameAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * SetDefaultNameAction.cpp

  • src/Actions/WorldAction/SetGaussianBasisAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * SetGaussianBasisAction.cpp

  • src/Actions/WorldAction/SetOutputFormatsAction.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * SetOutputFormatsAction.cpp

  • src/AtomicInfo.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * AtomicInfo.cpp

  • src/BoundaryLineSet.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * BoundaryLineSet.cpp

  • src/BoundaryPointSet.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * BoundaryPointSet.cpp

  • src/BoundaryPolygonSet.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * BoundaryPolygonSet.cpp

  • src/BoundaryTriangleSet.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * BoundaryTriangleSet.cpp

  • src/Box.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * Box.cpp

  • src/CandidateForTesselation.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * CandidateForTesselation.cpp

  • src/CommandLineParser.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * CommandLineParser.cpp

  • src/ConfigFileBuffer.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * ConfigFileBuffer.cpp

  • src/Descriptors/AtomDescriptor.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * AtomDescriptor.cpp

  • src/Descriptors/AtomIdDescriptor.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * AtomIdDescriptor.cpp

  • src/Descriptors/AtomSelectionDescriptor.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * AtomSelectionDescriptor.cpp

  • src/Descriptors/AtomShapeDescriptor.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * AtomShapeDescriptor.cpp

  • src/Descriptors/AtomTypeDescriptor.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * AtomTypeDescriptor_impl.cpp

  • src/Descriptors/MoleculeDescriptor.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * MoleculeDescriptor.cpp

  • src/Descriptors/MoleculeFormulaDescriptor.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * MoleculeFormulaDescriptor.cpp

  • src/Descriptors/MoleculeIdDescriptor.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * MoleculeIdDescriptor.cpp

  • src/Descriptors/MoleculeNameDescriptor.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * MoleculeNameDescriptor.cpp

  • src/Descriptors/MoleculePtrDescriptor.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * MoleculePtrDescriptor.cpp

  • src/Descriptors/MoleculeSelectionDescriptor.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * MoleculeSelectionDescriptor.cpp

  • src/Exceptions/CustomException.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * CustomException.cpp

  • src/Exceptions/IllegalTypeException.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * IllegalTypeException.cpp

  • src/Exceptions/LinearDependenceException.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * LinearDependenceException.cpp

  • src/Exceptions/MathException.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * MathException.cpp

  • src/Exceptions/MissingValueException.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * MissingValueException.cpp

  • src/Exceptions/NotInvertibleException.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * NotInvertibleException.cpp

  • src/Exceptions/ParseError.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * ParseError.cpp

  • src/Exceptions/SkewException.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * SkewException.cpp

  • src/Exceptions/ZeroVectorException.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * ZeroVectorException.cpp

  • src/Formula.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * Formula.cpp

  • src/Helpers/Assert.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * Assert.cpp

  • src/Helpers/Info.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * Info.cpp

  • src/Helpers/Log.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * log.cpp

  • src/Helpers/MemDebug.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * MemDebug.cpp

  • src/Helpers/Verbose.cpp

    r14c57a r51c3e4  
     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
    18/** \file Verbose.cpp
    29 *

  • src/Helpers/errorlogger.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * errorLogger.cpp

  • src/Helpers/helpers.cpp

    r14c57a r51c3e4  
     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
    18/** \file helpers.cpp
    29 *

  • src/Helpers/logger.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * logger.cpp

  • src/LinearAlgebra/Line.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * Line.cpp

  • src/LinearAlgebra/Matrix.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * Matrix.cpp
    … …  
    274281  gsl_eigen_symmv_free(T);
    275282  gsl_matrix_memcpy(content->content, evec);
     283  gsl_matrix_free(evec);
    276284  Vector evalues(gsl_vector_get(eval,0), gsl_vector_get(eval,1), gsl_vector_get(eval,2));
     285  gsl_vector_free(eval);
    277286  return evalues;
    278287}
    … …  
    336345
    337346Vector operator*(const Matrix &mat,const Vector &vec){
    338   gsl_vector *res = gsl_vector_calloc(NDIM);
    339   gsl_blas_dgemv( CblasNoTrans, 1.0, mat.content->content, vec.content->content, 0.0, res);
    340   VectorContent *content = new VectorContent();
    341   content->content = res;
    342   return Vector(content);
     347  Vector res;
     348  gsl_blas_dgemv( CblasNoTrans, 1.0, mat.content->content, vec.content->content, 0.0, res.content->content);
     349  return res;
    343350}
    344351

  • src/LinearAlgebra/Plane.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * Plane.cpp

  • src/LinearAlgebra/Space.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * Space.cpp

  • src/LinearAlgebra/Vector.cpp

    r14c57a r51c3e4  
     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
    18/** \file vector.cpp
    29 *

  • src/LinearAlgebra/VectorInterface.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * VectorInterface.cpp

  • src/LinearAlgebra/gslmatrix.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * gslmatrix.cpp

  • src/LinearAlgebra/gslvector.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * gslvector.cpp

  • src/LinearAlgebra/linearsystemofequations.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * linearsystemofequations.cpp

  • src/LinearAlgebra/vector_ops.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * vector_ops.cpp

  • src/Makefile.am

    r14c57a r51c3e4  
    394394
    395395$(srcdir)/version.c: $(srcdir)/.git-version
    396         echo "const char *ESPACKVersion = \"$(PACKAGE_NAME) -- git version: "`cat $(srcdir)/.git-version`"\";" > $@
     396        echo "const char *MOLECUILDERVERSION = \"$(PACKAGE_NAME) version "`cat $(srcdir)/.git-version`"\";" > $@
    397397
    398398

  • src/Parser/ChangeTracker.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * ChangeTracker.cpp

  • src/Parser/FormatParser.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * FormatParser.cpp

  • src/Parser/FormatParserStorage.cpp

    r14c57a r51c3e4  
     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
    18/** \file FormatParserStorage.cpp
    29 *

  • src/Parser/MpqcParser.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * MpqcParser.cpp

  • src/Parser/PcpParser.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * PcpParser.cpp
    … …  
    478485  PlaneWaveSpecifics.MaxPsiDouble = PlaneWaveSpecifics.PsiMaxNoDown = PlaneWaveSpecifics.PsiMaxNoUp = PlaneWaveSpecifics.PsiType = 0;
    479486  for (vector<atom *>::iterator runner = allatoms.begin(); runner != allatoms.end(); ++runner) {
    480     PlaneWaveSpecifics.MaxPsiDouble += (*runner)->getType()->NoValenceOrbitals;
     487    PlaneWaveSpecifics.MaxPsiDouble += (*runner)->getType()->getNoValenceOrbitals();
    481488  }
    482489  cout << PlaneWaveSpecifics.MaxPsiDouble << endl;
    … …  
    513520  // insert all found elements into the map
    514521  for (vector<atom *>::iterator AtomRunner = allatoms.begin();AtomRunner != allatoms.end();++AtomRunner) {
    515     Inserter = PresentElements.insert(pair<int, int>((*AtomRunner)->getType()->Z, 1));
     522    Inserter = PresentElements.insert(pair<int, int>((*AtomRunner)->getType()->getAtomicNumber(), 1));
    516523    if (!Inserter.second) // increase if present
    517524      Inserter.first->second += 1;
    … …  
    528535    const element * const elemental = World::getInstance().getPeriode()->FindElement(iter->first);
    529536    ZtoIndexMap.insert( pair<int,int> (iter->first, counter) );
    530     *file << "Ion_Type" << counter++ << "\t" << iter->second << "\t" << elemental->Z << "\t1.0\t3\t3\t" << fixed << setprecision(11) << showpoint << elemental->mass << "\t" << elemental->getName() << "\t" << elemental->getSymbol() <<endl;
     537    *file << "Ion_Type" << counter++ << "\t" << iter->second << "\t" << elemental->getAtomicNumber() << "\t1.0\t3\t3\t" << fixed << setprecision(11) << showpoint << elemental->getMass() << "\t" << elemental->getName() << "\t" << elemental->getSymbol() <<endl;
    531538  }
    532539}
    … …  
    544551  int nr = 0;
    545552  for (vector<atom *>::iterator AtomRunner = allatoms.begin();AtomRunner != allatoms.end();++AtomRunner) {
    546     Inserter = ZtoCountMap.insert( pair<int, int>((*AtomRunner)->getType()->Z, 1) );
     553    Inserter = ZtoCountMap.insert( pair<int, int>((*AtomRunner)->getType()->getAtomicNumber(), 1) );
    547554    if (!Inserter.second)
    548555      Inserter.first->second += 1;
    549     const int Z = (*AtomRunner)->getType()->Z;
     556    const int Z = (*AtomRunner)->getType()->getAtomicNumber();
    550557    *file << "Ion_Type" << ZtoIndexMap[Z] << "_" << ZtoCountMap[Z] << "\t"  << fixed << setprecision(9) << showpoint;
    551558    *file << (*AtomRunner)->at(0) << "\t" << (*AtomRunner)->at(1) << "\t" << (*AtomRunner)->at(2);

  • src/Parser/TremoloParser.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * TremoloParser.cpp

  • src/Parser/XyzParser.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * XyzParser.cpp

  • src/Patterns/Observer.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * Observer.cpp

  • src/PointCloud.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * PointCloud.cpp

  • src/Shapes/BaseShapes.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * BaseShapes_impl.cpp

  • src/Shapes/Shape.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * Shape.cpp

  • src/Shapes/ShapeOps.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * ShapeOps.cpp

  • src/TesselPoint.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * TesselPoint.cpp

  • src/ThermoStatContainer.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * ThermoStatContainer.cpp

  • src/Thermostats/Berendsen.cpp

    r14c57a r51c3e4  
    5959    if ((*iter)->FixedIon == 0) { // even FixedIon moves, only not by other's forces
    6060      U *= sqrt(1+(World::getInstance().getConfig()->Deltat/TempFrequency)*(ScaleTempFactor-1));
    61       ekin += 0.5*(*iter)->getType()->mass * U.NormSquared();
     61      ekin += 0.5*(*iter)->getType()->getMass() * U.NormSquared();
    6262    }
    6363  }

  • src/Thermostats/GaussianThermostat.cpp

    r14c57a r51c3e4  
    6666    if ((*iter)->FixedIon == 0) {// even FixedIon moves, only not by other's forces
    6767      U += World::getInstance().getConfig()->Deltat * G_over_E * U;
    68       ekin += (*iter)->getType()->mass * U.NormSquared();
     68      ekin += (*iter)->getType()->getMass() * U.NormSquared();
    6969    }
    7070  }
    … …  
    8181    if ((*iter)->FixedIon == 0){ // even FixedIon moves, only not by other's forces
    8282      G += U.ScalarProduct(F);
    83       E += U.NormSquared()*(*iter)->getType()->mass;
     83      E += U.NormSquared()*(*iter)->getType()->getMass();
    8484    }
    8585  }

  • src/Thermostats/Langevin.cpp

    r14c57a r51c3e4  
    6868  double ekin=0;
    6969  for(ForwardIterator iter=begin;iter!=end;++iter){
    70     double sigma  = sqrt(getContainer().TargetTemp/(*iter)->getType()->mass); // sigma = (k_b T)/m (Hartree/atomicmass = atomiclength/atomictime)
     70    double sigma  = sqrt(getContainer().TargetTemp/(*iter)->getType()->getMass()); // sigma = (k_b T)/m (Hartree/atomicmass = atomiclength/atomictime)
    7171    Vector &U = (*iter)->Trajectory.U.at(step);
    7272    if ((*iter)->FixedIon == 0) { // even FixedIon moves, only not by other's forces
    … …  
    8080        DoLog(2) && (Log() << Verbose(2) << U.Norm() << endl);
    8181      }
    82       ekin += 0.5*(*iter)->getType()->mass * U.NormSquared();
     82      ekin += 0.5*(*iter)->getType()->getMass() * U.NormSquared();
    8383    }
    8484  }

  • src/Thermostats/NoseHoover.cpp

    r14c57a r51c3e4  
    6363    Vector &U = (*iter)->Trajectory.U.at(step);
    6464    if ((*iter)->FixedIon == 0) { // even FixedIon moves, only not by other's forces
    65       U += World::getInstance().getConfig()->Deltat/(*iter)->getType()->mass * (alpha * (U * (*iter)->getType()->mass));
    66       ekin += (0.5*(*iter)->getType()->mass) * U.NormSquared();
     65      U += World::getInstance().getConfig()->Deltat/(*iter)->getType()->getMass() * (alpha * (U * (*iter)->getType()->getMass()));
     66      ekin += (0.5*(*iter)->getType()->getMass()) * U.NormSquared();
    6767    }
    6868  }
    … …  
    7777    Vector &U = (*iter)->Trajectory.U.at(step);
    7878    if ((*iter)->FixedIon == 0) { // even FixedIon moves, only not by other's forces
    79       delta_alpha += U.NormSquared()*(*iter)->getType()->mass;
     79      delta_alpha += U.NormSquared()*(*iter)->getType()->getMass();
    8080    }
    8181    ++count;

  • src/Thermostats/Woodcock.cpp

    r14c57a r51c3e4  
    6363      if ((*iter)->FixedIon == 0){ // even FixedIon moves, only not by other's forces
    6464        U *= ScaleTempFactor;
    65         ekin += 0.5*(*iter)->getType()->mass * U.NormSquared();
     65        ekin += 0.5*(*iter)->getType()->getMass() * U.NormSquared();
    6666      }
    6767    }

  • src/UIElements/CommandLineUI/CommandLineDialog.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * CommandLineDialog.cpp

  • src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * CommandLineStatusIndicator.cpp

  • src/UIElements/CommandLineUI/CommandLineUIFactory.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * CommandLineUIFactory.cpp

  • src/UIElements/CommandLineUI/CommandLineWindow.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * CommandLineWindow.cpp

  • src/UIElements/Dialog.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * Dialog.cpp

  • src/UIElements/MainWindow.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * Window.cpp

  • src/UIElements/Menu/ActionMenuItem.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * ActionMenuItem.cpp

  • src/UIElements/Menu/DisplayMenuItem.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * DisplayMenuItem.cpp

  • src/UIElements/Menu/Menu.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * Menu.cpp

  • src/UIElements/Menu/MenuItem.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * MenuItem.cpp

  • src/UIElements/Menu/QT4/QTMenu.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * QTMenu.cpp

  • src/UIElements/Menu/SeperatorItem.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * SeperatorItem.cpp

  • src/UIElements/Menu/SubMenuItem.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * SubMenuItem.cpp

  • src/UIElements/Menu/TextMenu.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * TextMenu.cpp

  • src/UIElements/QT4/QTDialog.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * QTDialog.cpp

  • src/UIElements/QT4/QTMainWindow.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * QTMainWindow.cpp

  • src/UIElements/QT4/QTUIFactory.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * QTUIFactory.cpp
    … …  
    3441  argv = new char*[1];
    3542  argv[0] = new char[256];
    36   strcpy(argv[0],ESPACKVersion);
     43  strcpy(argv[0],MOLECUILDERVERSION);
    3744  app = new QApplication(argc,argv);
    3845}

  • src/UIElements/TextUI/TextDialog.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * TextDialog.cpp

  • src/UIElements/TextUI/TextStatusIndicator.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * TextStatusIndicator.cpp

  • src/UIElements/TextUI/TextUIFactory.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * TextUIFactory.cpp

  • src/UIElements/TextUI/TextWindow.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * TextWindow.cpp
    … …  
    4956{
    5057  map <std::string, TextMenu *> NametoTextMenuMap;
     58  std::set <char> ShortcutList;
     59  // reserve s for save and q for quite
     60  ShortcutList.insert('s');
     61  ShortcutList.insert('q');
    5162
    5263  // populate all actions
    … …  
    6172  new SeperatorItem(main_menu);
    6273
    63   Action* undoAction = ActionRegistry::getInstance().getActionByName("Undo");
    64   new ActionMenuItem('u',"Undo last operation",main_menu,undoAction);
     74  Action* undoAction = ActionRegistry::getInstance().getActionByName("undo");
     75  new ActionMenuItem(getSuitableShortForm(ShortcutList,"Undo last operation"),"Undo last operation",main_menu,undoAction);
    6576
    66   Action* redoAction = ActionRegistry::getInstance().getActionByName("Redo");
    67   new ActionMenuItem('r',"Redo last operation",main_menu,redoAction);
     77  Action* redoAction = ActionRegistry::getInstance().getActionByName("redo");
     78  new ActionMenuItem(getSuitableShortForm(ShortcutList,"Redo last operation"),"Redo last operation",main_menu,redoAction);
    6879
    6980  new SeperatorItem(main_menu);
    7081
    71   Action *setMoleculeAction = new MethodAction("setMoleculeAction",boost::bind(&MoleculeListClass::flipChosen,World::getInstance().getMolecules()));
    72   new ActionMenuItem('a',"set molecule (in)active",main_menu,setMoleculeAction);
    73 
    74   TextMenu *Menu = NULL;
    75   std::set <char> ShortcutList;
    7682  for(map<std::string, pair<std::string,std::string> >::iterator iter = MapOfActions::getInstance().MenuDescription.begin(); iter != MapOfActions::getInstance().MenuDescription.end(); ++iter) {
    77     Menu = new TextMenu(Log() << Verbose(0), iter->second.second);
     83    TextMenu *Menu = new TextMenu(Log() << Verbose(0), iter->second.second);
    7884    NametoTextMenuMap.insert( pair <std::string, TextMenu *> (iter->first, Menu) );
    7985    new SubMenuItem(getSuitableShortForm(ShortcutList,iter->first),iter->second.first.c_str(),main_menu,Menu);
    … …  
    8288  new SeperatorItem(main_menu);
    8389
     90  // save has reserved key 's'
    8491  Action *saveConfigAction = ActionRegistry::getInstance().getActionByName("output");
    8592  new ActionMenuItem('s',"save current setup to config files",main_menu,saveConfigAction);
    … …  
    8895  new ActionMenuItem('q',"quit",main_menu,quitAction);
    8996
     97  // quit has reserved key 'q'
    9098  // go through all menus and create them
    91   for (map <std::string, TextMenu *>::iterator MenuRunner = NametoTextMenuMap.begin(); MenuRunner != NametoTextMenuMap.end(); ++MenuRunner) {
    92     cout << "Creating Menu " << MenuRunner->first << "." << endl;
     99  for (map <std::string, TextMenu *>::iterator MenuRunner = NametoTextMenuMap.begin(); MenuRunner != NametoTextMenuMap.end(); ++MenuRunner)
    93100    populateMenu(MenuRunner->second, MenuRunner->first);
    94   }
    95101
    96102  // Add status indicators etc...
    … …  
    114120{
    115121  for (std::string::const_iterator CharRunner = name.begin(); CharRunner != name.end(); ++CharRunner) {
    116     if (ShortcutList.find(*CharRunner) == ShortcutList.end())
     122    if (ShortcutList.find(*CharRunner) == ShortcutList.end()) {
     123      ShortcutList.insert(*CharRunner);
    117124      return *CharRunner;
     125    }
    118126  }
    119   DoeLog(1) && (eLog() << Verbose(1) << "Could not find a suitable shortform for TextWindow::getSuitableShortForm()." << endl);
    120   return ((char)(ShortcutList.size() % 10) + '0');
     127  // if no letter matches, take digits
     128  int i=0;
     129  for (;i<10;++i) {
     130    if (ShortcutList.find((char)i + '0') == ShortcutList.end())
     131      break;
     132  }
     133  if (i != 10) {
     134    ShortcutList.insert((char)i + '0');
     135    return ((char)i + '0');
     136  } else {
     137    DoeLog(1) && (eLog() << Verbose(1) << "Could not find a suitable shortform for " << name << "." << endl);
     138    return '#';
     139  }
    121140}
    122141
    … …  
    125144  Action *ActionItem = NULL;
    126145  set <char> ShortcutList;
     146  // reserve 'q' for quit
     147  ShortcutList.insert('q');
    127148  // through all actions for this menu
    128149  pair < multimap <std::string, std::string>::iterator, multimap <std::string, std::string>::iterator > MenuActions = MapOfActions::getInstance().MenuContainsActionMap.equal_range(MenuName);
    129150  for (multimap <std::string, std::string>::const_iterator MenuRunner = MenuActions.first; MenuRunner != MenuActions.second; ++MenuRunner) {
    130     cout << " Adding " << MenuRunner->second << " to submenu " << MenuName << endl;
    131151    ActionItem = ActionRegistry::getInstance().getActionByName(MenuRunner->second);
    132152    new ActionMenuItem(getSuitableShortForm(ShortcutList, MenuRunner->second),MapOfActions::getInstance().getDescription(MenuRunner->second).c_str(),Menu,ActionItem);

  • src/UIElements/UIFactory.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * UIFactory.cpp

  • src/UIElements/Views/MethodStringView.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * MethodStringView.cpp

  • src/UIElements/Views/QT4/GLMoleculeView.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * GLMoleculeView.cpp

  • src/UIElements/Views/QT4/QTMoleculeView.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * QTMoleculeView.cpp

  • src/UIElements/Views/QT4/QTStatusBar.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * QTStatusBar.cpp

  • src/UIElements/Views/QT4/QTWorldView.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * QTWorldView.cpp

  • src/UIElements/Views/StreamStringView.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * StreamStringView.cpp

  • src/UIElements/Views/StringView.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * StringView.cpp

  • src/UIElements/Views/View.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * View.cpp

  • src/World.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * World.cpp
    … …  
    731738    selectedMolecules(this),
    732739    currMoleculeId(0),
     740    lastMoleculePoolSize(0),
     741    numMoleculeDefragSkips(0),
    733742    molecules_deprecated(new MoleculeListClass(this))
    734743{

  • src/analysis_bonds.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * analysis_bonds.cpp
    … …  
    143150        molecule::iterator Runner = (*MolRunner)->begin();
    144151        for(;Runner!=(*MolRunner)->end();++Runner){
    145           if (((*Walker)->getType()->Z  == 8) && ((*Runner)->getType()->Z  == 8)) {
     152          if (((*Walker)->getType()->getAtomicNumber()  == 8) && ((*Runner)->getType()->getAtomicNumber()  == 8)) {
    146153            // check distance
    147154            const double distance = (*Runner)->DistanceSquared(*(*Walker));
    … …  
    157164                atom * const OtherAtom = (*BondRunner)->GetOtherAtom(*Runner);
    158165                // if hydrogen, check angle to be greater(!) than 30 degrees
    159                 if (OtherAtom->getType()->Z == 1) {
     166                if (OtherAtom->getType()->getAtomicNumber() == 1) {
    160167                  const double angle = CalculateAngle(OtherAtom->getPosition(), (*Runner)->getPosition(), (*Walker)->getPosition());
    161168                  OtherHydrogenFlag = OtherHydrogenFlag && (angle > M_PI*(30./180.) + MYEPSILON);
    … …  
    182189                for (BondList::const_iterator BondRunner = (*Walker)->ListOfBonds.begin(); BondRunner != (*Walker)->ListOfBonds.end(); BondRunner++) {
    183190                  atom * const OtherAtom = (*BondRunner)->GetOtherAtom(*Walker);
    184                   if (OtherAtom->getType()->Z == 1) {
     191                  if (OtherAtom->getType()->getAtomicNumber() == 1) {
    185192                    // check angle
    186193                    if (CheckHydrogenBridgeBondAngle(*Walker, OtherAtom, *Runner)) {

  • src/analysis_correlation.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * analysis.cpp

  • src/analysis_correlation.hpp

    r14c57a r51c3e4  
    1818#endif
    1919
     20#include <cmath>
    2021#include <fstream>
    2122

  • src/analyzer.cpp

    r14c57a r51c3e4  
     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
    18/** \file analyzer.cpp
    29 *

  • src/atom.cpp

    r14c57a r51c3e4  
     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
    18/** \file atom.cpp
    29 *
    … …  
    173180bool atom::OutputArrayIndexed(ostream * const out,const enumeration<const element*> &elementLookup, int *AtomNo, const char *comment) const
    174181{
    175   AtomNo[getType()->Z]++;  // increment number
     182  AtomNo[getType()->getAtomicNumber()]++;  // increment number
    176183  if (out != NULL) {
    177184    const element *elemental = getType();
    178185    cout << "Looking for atom with element " << *elemental << endl;
    179186    ASSERT(elementLookup.there.find(elemental)!=elementLookup.there.end(),"Type of this atom was not in the formula upon enumeration");
    180     *out << "Ion_Type" << elementLookup.there.find(elemental)->second << "_" << AtomNo[elemental->Z] << "\t"  << fixed << setprecision(9) << showpoint;
     187    *out << "Ion_Type" << elementLookup.there.find(elemental)->second << "_" << AtomNo[elemental->getAtomicNumber()] << "\t"  << fixed << setprecision(9) << showpoint;
    181188    *out << at(0) << "\t" << at(1) << "\t" << at(2);
    182189    *out << "\t" << FixedIon;
    … …  
    214221bool atom::OutputTrajectory(ofstream * const out, const int *ElementNo, int *AtomNo, const int step) const
    215222{
    216   AtomNo[getType()->Z]++;
    217   if (out != NULL) {
    218     *out << "Ion_Type" << ElementNo[getType()->Z] << "_" << AtomNo[getType()->Z] << "\t"  << fixed << setprecision(9) << showpoint;
     223  AtomNo[getType()->getAtomicNumber()]++;
     224  if (out != NULL) {
     225    *out << "Ion_Type" << ElementNo[getType()->getAtomicNumber()] << "_" << AtomNo[getType()->getAtomicNumber()] << "\t"  << fixed << setprecision(9) << showpoint;
    219226    *out << Trajectory.R.at(step)[0] << "\t" << Trajectory.R.at(step)[1] << "\t" << Trajectory.R.at(step)[2];
    220227    *out << "\t" << FixedIon;

  • src/atom_atominfo.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * atom_atominfo.cpp

  • src/atom_bondedparticle.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * atom_bondedparticle.cpp
    … …  
    157164  NoBonds = CountBonds();
    158165  //Log() << Verbose(3) << "Walker " << *this << ": " << (int)this->type->NoValenceOrbitals << " > " << NoBonds << "?" << endl;
    159   if ((int)(getType()->NoValenceOrbitals) > NoBonds) { // we have a mismatch, check all bonding partners for mismatch
     166  if ((int)(getType()->getNoValenceOrbitals()) > NoBonds) { // we have a mismatch, check all bonding partners for mismatch
    160167    for (BondList::const_iterator Runner = ListOfBonds.begin(); Runner != ListOfBonds.end(); (++Runner)) {
    161168      OtherWalker = (*Runner)->GetOtherAtom(this);
    162169      OtherNoBonds = OtherWalker->CountBonds();
    163170      //Log() << Verbose(3) << "OtherWalker " << *OtherWalker << ": " << (int)OtherWalker->type->NoValenceOrbitals << " > " << OtherNoBonds << "?" << endl;
    164       if ((int)(OtherWalker->getType()->NoValenceOrbitals) > OtherNoBonds) { // check if possible candidate
     171      if ((int)(OtherWalker->getType()->getNoValenceOrbitals()) > OtherNoBonds) { // check if possible candidate
    165172        if ((CandidateBond == NULL) || (ListOfBonds.size() > OtherWalker->ListOfBonds.size())) { // pick the one with fewer number of bonds first
    166173          CandidateBond = (*Runner);

  • src/atom_bondedparticleinfo.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * atom_bondedparticleinfo.cpp

  • src/atom_graphnode.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * atom_graphnode.cpp

  • src/atom_graphnodeinfo.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * atom_graphnodeinfo.cpp

  • src/atom_particleinfo.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * atom_particleinfo.cpp

  • src/atom_trajectoryparticle.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * atom_trajectoryparticle.cpp
    … …  
    3845 *  returns the kinetic energy of this atom at a given time step
    3946 */
     47
    4048double TrajectoryParticle::getKineticEnergy(unsigned int step) const{
    41   return getType()->mass * Trajectory.U.at(step).NormSquared();
     49  return getType()->getMass() * Trajectory.U.at(step).NormSquared();
    4250}
    4351
    … …  
    6674  for(int d=0;d<NDIM;d++) {
    6775    Trajectory.U.at(Step)[d] -= CoGVelocity->at(d);
    68     *ActualTemp += 0.5 * getType()->mass * Trajectory.U.at(Step)[d] * Trajectory.U.at(Step)[d];
     76    *ActualTemp += 0.5 * getType()->getMass() * Trajectory.U.at(Step)[d] * Trajectory.U.at(Step)[d];
    6977  }
    7078};
    … …  
    114122    Trajectory.R.at(NextStep)[d] = Trajectory.R.at(NextStep-1)[d];
    115123    Trajectory.R.at(NextStep)[d] += configuration->Deltat*(Trajectory.U.at(NextStep-1)[d]);     // s(t) = s(0) + v * deltat + 1/2 a * deltat^2
    116     Trajectory.R.at(NextStep)[d] += 0.5*configuration->Deltat*configuration->Deltat*(Trajectory.F.at(NextStep)[d]/getType()->mass);     // F = m * a and s =
     124    Trajectory.R.at(NextStep)[d] += 0.5*configuration->Deltat*configuration->Deltat*(Trajectory.F.at(NextStep)[d]/getType()->getMass());     // F = m * a and s =
    117125  }
    118126  // Update U
    119127  for (int d=0; d<NDIM; d++) {
    120128    Trajectory.U.at(NextStep)[d] = Trajectory.U.at(NextStep-1)[d];
    121     Trajectory.U.at(NextStep)[d] += configuration->Deltat * (Trajectory.F.at(NextStep)[d]+Trajectory.F.at(NextStep-1)[d]/getType()->mass); // v = F/m * t
     129    Trajectory.U.at(NextStep)[d] += configuration->Deltat * (Trajectory.F.at(NextStep)[d]+Trajectory.F.at(NextStep-1)[d]/getType()->getMass()); // v = F/m * t
    122130  }
    123131  // Update R (and F)
    … …  
    138146void TrajectoryParticle::SumUpKineticEnergy( int Step, double *TotalMass, Vector *TotalVelocity ) const
    139147{
    140   *TotalMass += getType()->mass;  // sum up total mass
     148  *TotalMass += getType()->getMass();  // sum up total mass
    141149  for(int d=0;d<NDIM;d++) {
    142     TotalVelocity->at(d) += Trajectory.U.at(Step)[d]*getType()->mass;
     150    TotalVelocity->at(d) += Trajectory.U.at(Step)[d]*getType()->getMass();
    143151  }
    144152};

  • src/atom_trajectoryparticle.hpp

    r14c57a r51c3e4  
    2020#include <fstream>
    2121
    22 #include <gsl/gsl_inline.h>
    2322#include <gsl/gsl_randist.h>
    2423

  • src/atom_trajectoryparticleinfo.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * atom_trajectoryparticleinfo.cpp

  • src/bond.cpp

    r14c57a r51c3e4  
     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
    18/** \file bond.cpp
    29 *
    … …  
    5663{
    5764  if ((left != NULL) && (right != NULL)) {
    58     if ((left->getType() != NULL) && (left->getType()->Z == 1))
     65    if ((left->getType() != NULL) && (left->getType()->getAtomicNumber() == 1))
    5966      HydrogenBond++;
    60     if ((right->getType() != NULL) && (right->getType()->Z == 1))
     67    if ((right->getType() != NULL) && (right->getType()->getAtomicNumber() == 1))
    6168      HydrogenBond++;
    6269  }

  • src/bondgraph.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * bondgraph.cpp
    … …  
    137144
    138145  for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
    139     if ((*iter)->getType()->CovalentRadius > max_distance)
    140       max_distance = (*iter)->getType()->CovalentRadius;
     146    if ((*iter)->getType()->getCovalentRadius() > max_distance)
     147      max_distance = (*iter)->getType()->getCovalentRadius();
    141148  }
    142149  max_distance *= 2.;
    … …  
    154161void BondGraph::CovalentMinMaxDistance(BondedParticle * const Walker, BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem)
    155162{
    156   MinDistance = OtherWalker->getType()->CovalentRadius + Walker->getType()->CovalentRadius;
     163  MinDistance = OtherWalker->getType()->getCovalentRadius() + Walker->getType()->getCovalentRadius();
    157164  MinDistance *= (IsAngstroem) ? 1. : 1. / AtomicLengthToAngstroem;
    158165  MaxDistance = MinDistance + BondThreshold;
    … …  
    175182    CovalentMinMaxDistance(Walker, OtherWalker, MinDistance, MaxDistance, IsAngstroem);
    176183  } else {
    177     MinDistance = GetBondLength(Walker->getType()->Z-1, OtherWalker->getType()->Z-1);
     184    MinDistance = GetBondLength(Walker->getType()->getAtomicNumber()-1, OtherWalker->getType()->getAtomicNumber()-1);
    178185    MinDistance *= (IsAngstroem) ? 1. : 1. / AtomicLengthToAngstroem;
    179186    MaxDistance = MinDistance + BondThreshold;

  • src/boundary.cpp

    r14c57a r51c3e4  
     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
    18/** \file boundary.cpp
    29 *
    … …  
    710717  // sum up the atomic masses
    711718  for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
    712       totalmass += (*iter)->getType()->mass;
     719      totalmass += (*iter)->getType()->getMass();
    713720  }
    714721  DoLog(0) && (Log() << Verbose(0) << "RESULT: The summed mass is " << setprecision(10) << totalmass << " atomicmassunit." << endl);

  • src/builder.cpp

    r14c57a r51c3e4  
    1 /** \file builder.cpp
     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
    29 *
    310 *  date: Jan 1, 2007
    411 *  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.
    519 *
    620 */
    … …  
    132146  std::string BondGraphFileName("\n");
    133147
    134   // print version check whether arguments are present at all
    135   cout << ESPACKVersion << endl;
     148  // print version check and copyright notice
     149  cout << MOLECUILDERVERSION << endl;
     150  cout << "MoleCuilder comes with ABSOLUTELY NO WARRANTY; for details type" << endl;
     151  cout << "`molecuilder --help-warranty'." << endl;
     152  cout << "`MoleCuilder - to create and alter molecular systems." << endl;
     153  cout << "Copyright (C) 2010  University Bonn. All rights reserved." << endl;
    136154
    137155  setVerbosity(0);
    … …  
    171189      #else
    172190        DoLog(0) && (Log() << Verbose(0) << "Setting UI to Text." << endl);
    173         cout << ESPACKVersion << endl;
     191        cout << MOLECUILDERVERSION << endl;
    174192        UIFactory::registerFactory(new TextUIFactory::description());
    175193        UIFactory::makeUserInterface("Text");

  • src/config.cpp

    r14c57a r51c3e4  
     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
    18/** \file config.cpp
    29 *
    … …  
    477484      ParseForParameter(verbose,FileBuffer, name, 0, 2, 1, int_type, &Z, 1, critical);
    478485      elementhash[i] = periode->FindElement(Z);
    479       DoLog(1) && (Log() << Verbose(1) << i << ". Z = " << elementhash[i]->Z << " with " << No[i] << " ions." << endl);
     486      DoLog(1) && (Log() << Verbose(1) << i << ". Z = " << elementhash[i]->getAtomicNumber() << " with " << No[i] << " ions." << endl);
    480487      NoAtoms += No[i];
    481488    }
    … …  
    859866    AtomNo = 0;
    860867    for (molecule::const_iterator iter = (*MolRunner)->begin(); iter != (*MolRunner)->end(); ++iter) {
    861       sprintf(name, "%2s%2d",(*iter)->getType()->getSymbol().c_str(), elementNo[(*iter)->getType()->Z]);
    862       elementNo[(*iter)->getType()->Z] = (elementNo[(*iter)->getType()->Z]+1) % 100;   // confine to two digits
     868      sprintf(name, "%2s%2d",(*iter)->getType()->getSymbol().c_str(), elementNo[(*iter)->getType()->getAtomicNumber()]);
     869      elementNo[(*iter)->getType()->getAtomicNumber()] = (elementNo[(*iter)->getType()->getAtomicNumber()]+1) % 100;   // confine to two digits
    863870      fprintf(f,
    864871             "ATOM %6u %-4s %4s%c%4u    %8.3f%8.3f%8.3f%6.2f%6.2f      %4s%2s%2s\n",
    … …  
    871878             (*iter)->at(1),                 /* position Y in Angstroem */
    872879             (*iter)->at(2),                 /* position Z in Angstroem */
    873              (double)(*iter)->getType()->Valence,         /* occupancy */
    874              (double)(*iter)->getType()->NoValenceOrbitals,          /* temperature factor */
     880             (double)(*iter)->getType()->getValence(),         /* occupancy */
     881             (double)(*iter)->getType()->getNoValenceOrbitals(),          /* temperature factor */
    875882             "0",            /* segment identifier */
    876883             (*iter)->getType()->getSymbol().c_str(),    /* element symbol */
    … …  
    912919  AtomNo = 0;
    913920  for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
    914     sprintf(name, "%2s%2d",(*iter)->getType()->getSymbol().c_str(), elementNo[(*iter)->getType()->Z]);
    915     elementNo[(*iter)->getType()->Z] = (elementNo[(*iter)->getType()->Z]+1) % 100;   // confine to two digits
     921    sprintf(name, "%2s%2d",(*iter)->getType()->getSymbol().c_str(), elementNo[(*iter)->getType()->getAtomicNumber()]);
     922    elementNo[(*iter)->getType()->getAtomicNumber()] = (elementNo[(*iter)->getType()->getAtomicNumber()]+1) % 100;   // confine to two digits
    916923    fprintf(f,
    917924           "ATOM %6u %-4s %4s%c%4u    %8.3f%8.3f%8.3f%6.2f%6.2f      %4s%2s%2s\n",
    … …  
    924931           (*iter)->at(1),                 /* position Y in Angstroem */
    925932           (*iter)->at(2),                 /* position Z in Angstroem */
    926            (double)(*iter)->getType()->Valence,         /* occupancy */
    927            (double)(*iter)->getType()->NoValenceOrbitals,          /* temperature factor */
     933           (double)(*iter)->getType()->getValence(),         /* occupancy */
     934           (double)(*iter)->getType()->getNoValenceOrbitals(),          /* temperature factor */
    928935           "0",            /* segment identifier */
    929936           (*iter)->getType()->getSymbol().c_str(),    /* element symbol */
    … …  
    971978    *output << 0 << "\t";
    972979    *output << (*iter)->at(0) << "\t" << (*iter)->at(1) << "\t" << (*iter)->at(2) << "\t";
    973     *output << static_cast<double>((*iter)->getType()->Valence) << "\t";
     980    *output << static_cast<double>((*iter)->getType()->getValence()) << "\t";
    974981    *output << (*iter)->getType()->getSymbol() << "\t";
    975982    for (BondList::iterator runner = (*iter)->ListOfBonds.begin(); runner != (*iter)->ListOfBonds.end(); runner++)
    … …  
    10431050        *output << MolCounter+1 << "\t";
    10441051        *output << (*iter)->at(0) << "\t" << (*iter)->at(1) << "\t" << (*iter)->at(2) << "\t";
    1045         *output << (double)(*iter)->getType()->Valence << "\t";
     1052        *output << (double)(*iter)->getType()->getValence() << "\t";
    10461053        *output << (*iter)->getType()->getSymbol() << "\t";
    10471054        for (BondList::iterator runner = (*iter)->ListOfBonds.begin(); runner != (*iter)->ListOfBonds.end(); runner++)

  • src/datacreator.cpp

    r14c57a r51c3e4  
     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
    18/** \file datacreator.cpp
    29 *

  • src/defs.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * defs.cpp

  • src/element.cpp

    r14c57a r51c3e4  
     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
    18/** \file element.cpp
    29 *
    … …  
    1522#include <fstream>
    1623
     24#include "Helpers/Assert.hpp"
    1725#include "element.hpp"
    1826
    … …  
    100108}
    101109
     110double element::getMass() const
     111{
     112  return mass;
     113}
     114
     115double element::getCovalentRadius() const
     116{
     117  return CovalentRadius;
     118}
     119
     120double element::getVanDerWaalsRadius() const
     121{
     122  return VanDerWaalsRadius;
     123}
     124
     125int element::getAtomicNumber() const
     126{
     127  return Z;
     128}
     129
     130double element::getValence() const
     131{
     132  return Valence;
     133}
     134
     135int element::getNoValenceOrbitals() const
     136{
     137  return NoValenceOrbitals;
     138}
     139
     140double element::getHBondDistance(const int i) const
     141{
     142  ASSERT((i>=0) && (i<3), "Access to element::HBondDistance out of bounds.");
     143  return HBondDistance[i];
     144}
     145
     146double element::getHBondAngle(const int i) const
     147{
     148  ASSERT((i>=0) && (i<3), "Access to element::HBondAngle out of bounds.");
     149  return HBondAngle[i];
     150}
     151
    102152string &element::getSymbol(){
    103153  return symbol;
    … …  
    106156const string &element::getSymbol() const{
    107157  return symbol;
     158}
     159
     160void element::setSymbol(const std::string &temp)
     161{
     162  symbol = temp;
    108163}
    109164
    … …  
    116171}
    117172
     173void element::setName(const std::string &temp)
     174{
     175  name = temp;
     176}
     177
    118178std::ostream &operator<<(std::ostream &ost,const element &elem){
    119179  ost << elem.getName() << "(" << elem.getNumber() << ")";

  • src/element.hpp

    r14c57a r51c3e4  
    2222#include "types.hpp"
    2323
     24class periodentafel;
     25
    2426/********************************************** declarations *******************************/
    2527
    … …  
    2830 */
    2931class element {
     32  friend class periodentafel;
    3033  public:
     34    element();
     35    element(const element&);
     36    ~element();
     37
     38    element &operator=(const element&);
     39
     40    // accessor functions
     41    atomicNumber_t getNumber() const;
     42    double getMass() const;
     43    double getCovalentRadius() const;
     44    double getVanDerWaalsRadius() const;
     45    int getAtomicNumber() const;
     46    double getValence() const;
     47    int getNoValenceOrbitals() const;
     48    double getHBondDistance(const int i) const;
     49    double getHBondAngle(const int i) const;
     50
     51    std::string &getSymbol();
     52    const std::string &getSymbol() const;
     53    void setSymbol(const std::string &temp);
     54
     55    std::string &getName();
     56    const std::string &getName() const;
     57    void setName(const std::string &temp);
     58
     59    //> print element entries to screen
     60    bool Output(std::ostream * const out) const;
     61    bool Checkout(std::ostream * const out, const int No, const int NoOfAtoms) const;
     62
     63  private:
    3164    double mass;    //!< mass in g/mol
    3265    double CovalentRadius;  //!< covalent radius
    … …  
    4174    double HBondAngle[NDIM];     //!< typical angle for one, two, three bonded hydrogen (in degrees)
    4275
    43     element();
    44     element(const element&);
    45     ~element();
    46 
    47     element &operator=(const element&);
    48 
    49     // accessor functions
    50     atomicNumber_t getNumber() const;
    51     std::string &getSymbol();
    52     const std::string &getSymbol() const;
    53     std::string &getName();
    54     const std::string &getName() const;
    55 
    56     //> print element entries to screen
    57     bool Output(std::ostream * const out) const;
    58     bool Checkout(std::ostream * const out, const int No, const int NoOfAtoms) const;
    59 
    60   private:
    61     std::string name;  //!< atom name, i.e. "Hydrogren"
     76    std::string name;  //!< atom name, i.e. "Hydrogen"
    6277    std::string symbol; //!< short form of the atom, i.e. "H"
    6378};

  • src/elements_db.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * elements_db.cpp

  • src/ellipsoid.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * ellipsoid.cpp

  • src/graph.cpp

    r14c57a r51c3e4  
     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
    18/** \file graph.cpp
    29 *

  • src/joiner.cpp

    r14c57a r51c3e4  
     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
    18/** \file joiner.cpp
    29 *

  • src/leastsquaremin.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * leastsquaremin.cpp

  • src/linkedcell.cpp

    r14c57a r51c3e4  
     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
    18/** \file linkedcell.cpp
    29 *

  • src/molecule.cpp

    r14c57a r51c3e4  
     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
    18/** \file molecules.cpp
    29 *
    … …  
    227234    pointer->sort = &pointer->nr;
    228235    if (pointer->getType() != NULL) {
    229       if (pointer->getType()->Z != 1)
     236      if (pointer->getType()->getAtomicNumber() != 1)
    230237        NoNonHydrogen++;
    231238      if(pointer->getName() == "Unknown"){
    … …  
    255262    walker->nr = last_atom++;  // increase number within molecule
    256263    insert(walker);
    257     if ((pointer->getType() != NULL) && (pointer->getType()->Z != 1))
     264    if ((pointer->getType() != NULL) && (pointer->getType()->getAtomicNumber() != 1))
    258265      NoNonHydrogen++;
    259266    retval=walker;
    … …  
    341348  // get typical bond length and store as scale factor for later
    342349  ASSERT(TopOrigin->getType() != NULL, "AddHydrogenReplacementAtom: element of TopOrigin is not given.");
    343   BondRescale = TopOrigin->getType()->HBondDistance[TopBond->BondDegree-1];
     350  BondRescale = TopOrigin->getType()->getHBondDistance(TopBond->BondDegree-1);
    344351  if (BondRescale == -1) {
    345352    DoeLog(1) && (eLog()<< Verbose(1) << "There is no typical hydrogen bond distance in replacing bond (" << TopOrigin->getName() << "<->" << TopReplacement->getName() << ") of degree " << TopBond->BondDegree << "!" << endl);
    … …  
    358365      FirstOtherAtom->AtomicVelocity = TopReplacement->AtomicVelocity; // copy velocity
    359366      FirstOtherAtom->FixedIon = TopReplacement->FixedIon;
    360       if (TopReplacement->getType()->Z == 1) { // neither rescale nor replace if it's already hydrogen
     367      if (TopReplacement->getType()->getAtomicNumber() == 1) { // neither rescale nor replace if it's already hydrogen
    361368        FirstOtherAtom->father = TopReplacement;
    362369        BondRescale = bondlength;
    … …  
    427434      FirstOtherAtom->father = NULL;  // we are just an added hydrogen with no father
    428435      SecondOtherAtom->father = NULL;  //  we are just an added hydrogen with no father
    429       bondangle = TopOrigin->getType()->HBondAngle[1];
     436      bondangle = TopOrigin->getType()->getHBondAngle(1);
    430437      if (bondangle == -1) {
    431438        DoeLog(1) && (eLog()<< Verbose(1) << "There is no typical hydrogen bond angle in replacing bond (" << TopOrigin->getName() << "<->" << TopReplacement->getName() << ") of degree " << TopBond->BondDegree << "!" << endl);
    … …  
    503510
    504511      // create correct coordination for the three atoms
    505       alpha = (TopOrigin->getType()->HBondAngle[2])/180.*M_PI/2.;  // retrieve triple bond angle from database
     512      alpha = (TopOrigin->getType()->getHBondAngle(2))/180.*M_PI/2.;  // retrieve triple bond angle from database
    506513      l = BondRescale;        // desired bond length
    507514      b = 2.*l*sin(alpha);    // base length of isosceles triangle
    … …  
    711718  atom1->RegisterBond(Binder);
    712719  atom2->RegisterBond(Binder);
    713   if ((atom1->getType() != NULL) && (atom1->getType()->Z != 1) && (atom2->getType() != NULL) && (atom2->getType()->Z != 1))
     720  if ((atom1->getType() != NULL) && (atom1->getType()->getAtomicNumber() != 1) && (atom2->getType() != NULL) && (atom2->getType()->getAtomicNumber() != 1))
    714721    NoNonBonds++;
    715722
    … …  
    905912        ElementNo[i] = 0;
    906913      }
    907       SetIndexedArrayForEachAtomTo ( ElementNo, &element::Z, &AbsoluteValue, 1);
     914      for(molecule::iterator iter = begin(); iter != end(); ++iter) {
     915        ElementNo[(*iter)->getType()->getAtomicNumber()] = 1;
     916      }
    908917      int current=1;
    909918      for (int i=0;i<MAX_ELEMENTS;++i) {
    … …  
    979988  for (molecule::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
    980989    (*iter)->nr = i;   // update number in molecule (for easier referencing in FragmentMolecule lateron)
    981     if ((*iter)->getType()->Z != 1) // count non-hydrogen atoms whilst at it
     990    if ((*iter)->getType()->getAtomicNumber() != 1) // count non-hydrogen atoms whilst at it
    982991      NoNonHydrogen++;
    983992    stringstream sstr;

  • src/molecule.hpp

    r14c57a r51c3e4  
    371371  // Methods moved here from the menus
    372372  // TODO: more refactoring needed on these methods
    373   void flipChosen();
    374373  void createNewMolecule(periodentafel *periode);
    375374  void loadFromXYZ(periodentafel *periode);

  • src/molecule_dynamics.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * molecule_dynamics.cpp

  • src/molecule_fragmentation.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * molecule_fragmentation.cpp
    … …  
    456463      for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
    457464    #ifdef ADDHYDROGEN
    458         if ((*iter)->getType()->Z != 1) // skip hydrogen
     465        if ((*iter)->getType()->getAtomicNumber() != 1) // skip hydrogen
    459466    #endif
    460467        {
    … …  
    476483    for(molecule::const_iterator iter = begin(); iter != end(); ++iter) {
    477484  #ifdef ADDHYDROGEN
    478       if ((*iter)->getType()->Z != 1) // skip hydrogen
     485      if ((*iter)->getType()->getAtomicNumber() != 1) // skip hydrogen
    479486  #endif
    480487      {
    … …  
    885892  for (KeySet::iterator runner = Leaf->begin(); runner != Leaf->end(); runner++) {
    886893    Runner = FindAtom((*runner));
    887     if (Runner->getType()->Z != 1) { // skip all those added hydrogens when re-filling snake stack
     894    if (Runner->getType()->getAtomicNumber() != 1) { // skip all those added hydrogens when re-filling snake stack
    888895      if (ShortestPathList[(*runner)] > SP) {  // remove the oldest one with longest shortest path
    889896        SP = ShortestPathList[(*runner)];
    … …  
    974981    ++iter;
    975982#ifdef ADDHYDROGEN
    976     while ((iter != Leaf->end()) && ((*iter)->getType()->Z == 1)){ // skip added hydrogen
     983    while ((iter != Leaf->end()) && ((*iter)->getType()->getAtomicNumber() == 1)){ // skip added hydrogen
    977984      iter++;
    978985    }
    … …  
    13521359        if ((RestrictedKeySet.find(OtherWalker->nr) != RestrictedKeySet.end())
    13531360  #ifdef ADDHYDROGEN
    1354          && (OtherWalker->getType()->Z != 1)
     1361         && (OtherWalker->getType()->getAtomicNumber() != 1)
    13551362  #endif
    13561363                                                              ) {  // skip hydrogens and restrict to fragment

  • src/molecule_geometry.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * molecule_geometry.cpp
    … …  
    179186  if (iter != end()) {   //list not empty?
    180187    for (; iter != end(); ++iter) {  // continue with second if present
    181       Num += (*iter)->getType()->mass;
    182       tmp = (*iter)->getType()->mass * (*iter)->getPosition();
     188      Num += (*iter)->getType()->getMass();
     189      tmp = (*iter)->getType()->getMass() * (*iter)->getPosition();
    183190      (*a) += tmp;
    184191    }
    … …  
    292299    for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
    293300#ifdef ADDHYDROGEN
    294       if ((*iter)->getType()->Z != 1) {
     301      if ((*iter)->getType()->getAtomicNumber() != 1) {
    295302#endif
    296303        Testvector = inversematrix * (*iter)->getPosition();
    … …  
    317324        // now also change all hydrogens
    318325        for (BondList::const_iterator Runner = (*iter)->ListOfBonds.begin(); Runner != (*iter)->ListOfBonds.end(); (++Runner)) {
    319           if ((*Runner)->GetOtherAtom((*iter))->getType()->Z == 1) {
     326          if ((*Runner)->GetOtherAtom((*iter))->getType()->getAtomicNumber() == 1) {
    320327            Testvector = inversematrix * (*Runner)->GetOtherAtom((*iter))->getPosition();
    321328            Testvector += Translationvector;

  • src/molecule_graph.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * molecule_graph.cpp
    … …  
    738745        OtherAtom = (*Runner)->GetOtherAtom(Walker);
    739746#ifdef ADDHYDROGEN
    740         if (OtherAtom->getType()->Z != 1) {
     747        if (OtherAtom->getType()->getAtomicNumber() != 1) {
    741748#endif
    742749        DoLog(2) && (Log() << Verbose(2) << "Current OtherAtom is: " << OtherAtom->getName() << " for bond " << *(*Runner) << "." << endl);

  • src/molecule_pointcloud.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * molecule_pointcloud.cpp

  • src/moleculelist.cpp

    r14c57a r51c3e4  
     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
    18/** \file MoleculeListClass.cpp
    29 *
    … …  
    340347    for (molecule::const_iterator iter = (*ListRunner)->begin(); iter != (*ListRunner)->end(); ++iter) {
    341348      //Log() << Verbose(1) << "(*iter): " << *(*iter) << " with first bond " << *((*iter)->ListOfBonds.begin()) << "." << endl;
    342       if (((*iter)->getType()->Z == 1) && (((*iter)->father == NULL)
    343           || ((*iter)->father->getType()->Z != 1))) { // if it's a hydrogen
     349      if (((*iter)->getType()->getAtomicNumber() == 1) && (((*iter)->father == NULL)
     350          || ((*iter)->father->getType()->getAtomicNumber() != 1))) { // if it's a hydrogen
    344351        for (molecule::const_iterator runner = (*ListRunner)->begin(); runner != (*ListRunner)->end(); ++runner) {
    345352          //Log() << Verbose(2) << "Runner: " << *(*runner) << " with first bond " << *((*iter)->ListOfBonds.begin()) << "." << endl;
    346353          // 3. take every other hydrogen that is the not the first and not bound to same bonding partner
    347354          Binder = *((*runner)->ListOfBonds.begin());
    348           if (((*runner)->getType()->Z == 1) && ((*runner)->nr > (*iter)->nr) && (Binder->GetOtherAtom((*runner)) != Binder->GetOtherAtom((*iter)))) { // (hydrogens have only one bonding partner!)
     355          if (((*runner)->getType()->getAtomicNumber() == 1) && ((*runner)->nr > (*iter)->nr) && (Binder->GetOtherAtom((*runner)) != Binder->GetOtherAtom((*iter)))) { // (hydrogens have only one bonding partner!)
    349356            // 4. evaluate the morse potential for each matrix component and add up
    350357            distance = (*runner)->distance(*(*iter));
    … …  
    602609 */
    603610
    604 void MoleculeListClass::flipChosen() {
    605   int j;
    606   Log() << Verbose(0) << "Enter index of molecule: ";
    607   cin >> j;
    608   for(MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++)
    609     if ((*ListRunner)->IndexNr == j)
    610       (*ListRunner)->ActiveFlag = !(*ListRunner)->ActiveFlag;
    611 }
    612 
    613611void MoleculeListClass::createNewMolecule(periodentafel *periode) {
    614612  OBSERVE;
    … …  
    829827        if (AtomMask[Father->nr]) // apply mask
    830828#ifdef ADDHYDROGEN
    831           if ((*iter)->getType()->Z != 1) // skip hydrogen
     829          if ((*iter)->getType()->getAtomicNumber() != 1) // skip hydrogen
    832830#endif
    833831          RootStack[FragmentCounter].push_front((*iter)->nr);

  • src/parser.cpp

    r14c57a r51c3e4  
     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
    18/** \file parsing.cpp
    29 *

  • src/periodentafel.cpp

    r14c57a r51c3e4  
     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
    18/** \file periodentafel.cpp
    29 *
    … …  
    303310    while (!input.eof()) {
    304311      element *neues = new element;
    305       input >> neues->getName();;
    306       //(*input) >> ws;
    307       input >> neues->getSymbol();
     312      input >> neues->name;
     313      //(*input) >> ws;
     314      input >> neues->symbol;
    308315      //(*input) >> ws;
    309316      input >> neues->period;
    … …  
    355362        // pointer to old element might still be in use, so we have to replace into the old element
    356363        *(elements[iter->first])=*iter->second;
     364        delete(iter->second);
    357365      }
    358366      else {

  • src/tesselation.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * tesselation.cpp

  • src/tesselationhelpers.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * TesselationHelpers.cpp

  • src/triangleintersectionlist.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * triangleintersectionlist.cpp

  • src/unittests/ActOnAllUnitTest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * ActOnAllUnitTest.cpp

  • src/unittests/ActionSequenceTest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * ActionSequenzTest.cpp

  • src/unittests/AnalysisCorrelationToPointUnitTest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * AnalysisCorrelationToPointUnitTest.cpp

  • src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * AnalysisCorrelationToSurfaceUnitTest.cpp

  • src/unittests/AnalysisPairCorrelationUnitTest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * AnalysisPairCorrelationUnitTest.cpp

  • src/unittests/AtomDescriptorTest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * DescriptorUnittest.cpp

  • src/unittests/BaseShapesUnittest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * BaseShapesUnittest.cpp

  • src/unittests/BoxUnittest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * BoxUnittest.cpp

  • src/unittests/CacheableTest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * CacheableTest.cpp

  • src/unittests/CountBondsUnitTest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * CountBondsUnitTest.cpp

  • src/unittests/FormulaUnittest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * FormulaUnittest.cpp

  • src/unittests/LineUnittest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * LineUnittest.cpp

  • src/unittests/LinkedCellUnitTest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * LinkedCellUnitTest.cpp

  • src/unittests/MapofActionsTest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * analysisbondsunittest.cpp

  • src/unittests/MatrixUnittest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * MatrixUnittest.cpp

  • src/unittests/MoleculeDescriptorTest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * MoleculeDescriptorTest.cpp

  • src/unittests/ObserverTest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * ObserverTest.cpp

  • src/unittests/ParserUnitTest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * ParserUnitTest.cpp

  • src/unittests/PlaneUnittest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * PlaneUnittest.cpp

  • src/unittests/ShapeUnittest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * ShapeUnittest.cpp

  • src/unittests/SingletonTest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * SingletonTest.cpp

  • src/unittests/TestRunnerMain.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * TestRunnerMain.cpp

  • src/unittests/UnitTestMain.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * UnitTestMain.cpp

  • src/unittests/analysisbondsunittest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * analysisbondsunittest.cpp

  • src/unittests/atomsCalculationTest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * atomsCalculationTest.cpp

  • src/unittests/bondgraphunittest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * bondgraphunittest.cpp

  • src/unittests/gslmatrixsymmetricunittest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * gslmatrixunittest.cpp

  • src/unittests/gslmatrixunittest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * gslmatrixunittest.cpp

  • src/unittests/gslvectorunittest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * gslvectorunittest.cpp

  • src/unittests/infounittest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * InfoUnitTest.cpp

  • src/unittests/linearsystemofequationsunittest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * linearsystemofequationsunittest.cpp

  • src/unittests/listofbondsunittest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * listofbondsunittest.cpp

  • src/unittests/logunittest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * logunittest.cpp

  • src/unittests/manipulateAtomsTest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * manipulateAtomsTest.cpp

  • src/unittests/memoryallocatorunittest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * memoryallocatorunittest.cpp

  • src/unittests/memoryusageobserverunittest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * memoryusageobserverunittest.cpp

  • src/unittests/periodentafelTest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * periodentafelTest.cpp

  • src/unittests/stackclassunittest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * stackclassunittest.cpp

  • src/unittests/tesselation_boundarytriangleunittest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * tesselation_boundarytriangleunittest.cpp

  • src/unittests/tesselation_insideoutsideunittest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * tesselation_insideoutsideunittest.cpp

  • src/unittests/tesselationunittest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * tesselationunittest.cpp

  • src/unittests/vectorunittest.cpp

    r14c57a r51c3e4  
     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
    18/*
    29 * unittest.cpp

  • src/version.h

    r14c57a r51c3e4  
    22#define VERSION_H_
    33
    4 extern const char *ESPACKVersion;
     4extern const char *MOLECUILDERVERSION;
    55
    66#endif /* VERSION_H_ */

  • test_all.sh

    r14c57a r51c3e4  
    11#!/bin/bash
    22
    3 optimizations=("-O0"\
     3optimizations=("-g3"\
     4               "-O0"\
    45               "-O1"\
    56               "-O2"\
    … …  
    4950}
    5051
     52function logdate()
     53{
     54  echo -e "Launched on `date`.\n\n" >> $logfile 2>&1;
     55}
     56
     57
    5158while getopts “ho:f:j:scO:t:p:” OPTION
    5259do
    … …  
    105112function configure(){
    106113  echo "Configuring";
    107   CXXFLAGS="$2" $1/configure --prefix=$PWD >> $logfile 2>&1;
     114  $1/configure $3 --prefix=$PWD CXXFLAGS="-Wall $2" >> $logfile 2>&1;
    108115}
    109116
    … …  
    134141    then
    135142      echo -n "    $test: " >> $outfile;
    136       valgrind -v --error-exitcode=255 $test >> $logfile 2>&1;
     143      valgrind -v --leak-check=full --leak-resolution=high --show-reachable=yes --error-exitcode=255 $test >> $logfile 2>&1;
    137144      if [ $? ]
    138145      then
    … …  
    149156function test(){
    150157
    151   echo "Testing with \"$2\"";
     158  echo "Testing with \"$2 $3\"";
    152159  echo "" >> $logfile;
    153160  echo "" >> $logfile;
    154161  echo "" >> $logfile;
    155   echo "Testing with \"$2\"" >> $logfile;
    156 
    157   echo -n "  Configuring: " >> $outfile;
    158   if configure "$1" "$2"
     162  echo "Testing with \"$2 $3\"" >> $logfile;
     163
     164  if [ x"$2" == x"-g3" ]
     165  then
     166    valgrind="--with-valgrind"
     167  else
     168    valgrind="--without-valgrind"
     169  fi
     170  echo -n "  Configuring $valgrind: " >> $outfile;
     171  if configure "$1" "$2 $3" "$valgrind"
    159172  then
    160173    echo "OK" >> $outfile;
    … …  
    201214
    202215function run(){
    203   echo "Testing with \"$1\":" >> $outfile;
     216  echo "Testing with \"$1 $2\":" >> $outfile;
    204217  testdir=`mktemp -d --tmpdir=$tmpdir $tmppattern.XXXXXXXXXX`;
    205218  basedir=$PWD;
    206219  cd $testdir;
    207   test "$basedir" "$1";
     220  test "$basedir" "$1" "$2";
    208221  cd $basedir;
    209222  rm -rf $testdir;
    … …  
    220233  for option in "${options[@]}"
    221234  do
    222     run "$optimization $option";
     235    run "$optimization" "$option";
    223236  done
    224237done

  • tests/regression/Makefile.am

    r14c57a r51c3e4  
    11AUTOM4TE = autom4te
    2 EXTRA_DIST = testsuite.at $(TESTSUITE) atlocal.in regression
     2EXTRA_DIST = \
     3        testsuite*.at \
     4        $(TESTSUITE) \
     5        atlocal.in \
     6        molecuider.in \
     7        Analysis \
     8        Domain \
     9        Filling \
     10        Fragmentation \
     11        Graph \
     12        Molecules \
     13        Simple_configuration \
     14        Tesselation
    315TESTSUITE = $(srcdir)/testsuite
    416

  • tests/regression/atlocal.in

    r14c57a r51c3e4  
    11prefix='@prefix@'
    22exec_prefix='@prefix@'
    3 topdir='@topdir@'
     3topdir='@abs_top_builddir@'
    44bindir='@bindir@'
     5valgrind='@VALGRIND@'

  • tests/regression/molecuilder.in

    r14c57a r51c3e4  
    33# wrapper for testing molecuilder
    44
    5 . ../../atconfig
     5. ../../atlocal
    66
    7 "${abs_top_builddir}/src/molecuilder" \
    8         ${1+"$@"}
     7if test ! -z ${valgrind}
     8then
     9G_SLICE=always-malloc G_DEBUG=gc-friendly \
     10libtool --mode=execute \
     11${valgrind} -v \
     12--log-file=valgrind.log \
     13--xml=yes \
     14--xml-file=valgrind.err \
     15--time-stamp=yes \
     16--error-exitcode=255 \
     17--leak-check=full \
     18--leak-resolution=high \
     19--num-callers=20 \
     20--track-origins=yes \
     21--show-reachable=yes \
     22"${topdir}/src/molecuilder" \
     23${1+"$@"}
     24else
     25"${topdir}/src/molecuilder" \
     26${1+"$@"}
     27fi
     28
    929status=$?
    1030

  • tests/regression/testsuite.at

    r14c57a r51c3e4  
    77AT_TESTED(diff fgrep grep)
    88
     9# Use colored output with new-enough Autotest.
     10m4_ifdef([AT_COLOR_TESTS], [AT_COLOR_TESTS])
    911
    1012m4_include(testsuite-standard_options.at)
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