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  • COPYING

    rc538d1 r3d078d  
     1<<<<<<< HEAD
    12                    GNU GENERAL PUBLIC LICENSE
    23                       Version 3, 29 June 2007
    … …  
    1819GNU General Public License for most of our software; it applies also to
    1920any other work released this way by its authors.  You can apply it to
     21=======
     22                    GNU GENERAL PUBLIC LICENSE
     23                       Version 2, June 1991
     24
     25 Copyright (C) 1989, 1991 Free Software Foundation, Inc.
     26     51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
     27 Everyone is permitted to copy and distribute verbatim copies
     28 of this license document, but changing it is not allowed.
     29
     30                            Preamble
     31
     32  The licenses for most software are designed to take away your
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     38using it.  (Some other Free Software Foundation software is covered by
     39the GNU Library General Public License instead.)  You can apply it to
     40>>>>>>> FETCH_HEAD
    2041your programs, too.
    2142
    … …  
    2344price.  Our General Public Licenses are designed to make sure that you
    2445have the freedom to distribute copies of free software (and charge for
     46<<<<<<< HEAD
    2547them if you wish), that you receive source code or can get it if you
    2648want it, that you can change the software or use pieces of it in new
    … …  
    622644
    623645            How to Apply These Terms to Your New Programs
     646=======
     647this service if you wish), that you receive source code or can get it
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     679  The precise terms and conditions for copying, distribution and
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     681
     682
     683                    GNU GENERAL PUBLIC LICENSE
     684   TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
     685
     686  0. This License applies to any program or other work which contains
     687a notice placed by the copyright holder saying it may be distributed
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     739These requirements apply to the modified work as a whole.  If
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     856  8. If the distribution and/or use of the Program is restricted in
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     885                            NO WARRANTY
     886
     887  11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
     888FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.  EXCEPT WHEN
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     906
     907                     END OF TERMS AND CONDITIONS
     908
     909
     910            How to Apply These Terms to Your New Programs
     911>>>>>>> FETCH_HEAD
    624912
    625913  If you develop a new program, and you want it to be of the greatest
    … …  
    629917  To do so, attach the following notices to the program.  It is safest
    630918to attach them to the start of each source file to most effectively
     919<<<<<<< HEAD
    631920state the exclusion of warranty; and each file should have at least
     921=======
     922convey the exclusion of warranty; and each file should have at least
     923>>>>>>> FETCH_HEAD
    632924the "copyright" line and a pointer to where the full notice is found.
    633925
    … …  
    635927    Copyright (C) <year>  <name of author>
    636928
     929<<<<<<< HEAD
    637930    This program is free software: you can redistribute it and/or modify
    638931    it under the terms of the GNU General Public License as published by
    639932    the Free Software Foundation, either version 3 of the License, or
     933=======
     934    This program is free software; you can redistribute it and/or modify
     935    it under the terms of the GNU General Public License as published by
     936    the Free Software Foundation; either version 2 of the License, or
     937>>>>>>> FETCH_HEAD
    640938    (at your option) any later version.
    641939
    … …  
    646944
    647945    You should have received a copy of the GNU General Public License
     946<<<<<<< HEAD
    648947    along with this program.  If not, see <http://www.gnu.org/licenses/>.
    649948
    … …  
    655954    <program>  Copyright (C) <year>  <name of author>
    656955    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
     956=======
     957    along with this program; if not, write to the Free Software
     958    Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
     959
     960
     961Also add information on how to contact you by electronic and paper mail.
     962
     963If the program is interactive, make it output a short notice like this
     964when it starts in an interactive mode:
     965
     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
    657969    This is free software, and you are welcome to redistribute it
    658970    under certain conditions; type `show c' for details.
    659971
    660972The hypothetical commands `show w' and `show c' should show the appropriate
     973<<<<<<< HEAD
    661974parts of the General Public License.  Of course, your program's commands
    662975might be different; for a GUI interface, you would use an "about box".
    … …  
    673986Public License instead of this License.  But first, please read
    674987<http://www.gnu.org/philosophy/why-not-lgpl.html>.
     988=======
     989parts of the General Public License.  Of course, the commands you use may
     990be called something other than `show w' and `show c'; they could even be
     991mouse-clicks or menu items--whatever suits your program.
     992
     993You should also get your employer (if you work as a programmer) or your
     994school, if any, to sign a "copyright disclaimer" for the program, if
     995necessary.  Here is a sample; alter the names:
     996
     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
     1002
     1003This General Public License does not permit incorporating your program into
     1004proprietary programs.  If your program is a subroutine library, you may
     1005consider it more useful to permit linking proprietary applications with the
     1006library.  If this is what you want to do, use the GNU Library General
     1007Public License instead of this License.
     1008>>>>>>> FETCH_HEAD

  • ChangeLog

    rc538d1 r3d078d  
     118.04.2008
     2        + essential switch in structure of ESPACK. Instead of having everything
     3        relative to pcp, we now have three tantamount packages: pcp, utilities and
     4        molecuilder

  • README

    rc538d1 r3d078d  
     1<<<<<<< HEAD
    12# Project: Molecuilder
    23#
    … …  
    67
    78... 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
     16
     17        Electronic Structure PACKage
     18
     19Is a collection of mathematical-physical programs to calculate via various ab-initio methods
     20such as density functional theory or Hartree-Fock electronic(-magnetic) properties including
     21the molecular (Car&Parrinello) dynamics of a many electron system. Especially, the linear
     22response of the system to a external magnetic field in a perturbation approach in terms of
     23susceptibility and chemical shielding is implemented via the Density Functional Perturbation
     24Theory. 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
     26at the University of Bonn[1].
     27
     28
     29>>>>>>> FETCH_HEAD
    830
    931INSTALLATION NOTES
    1032==================
    1133
     34<<<<<<< HEAD
    1235The following packages are needed
    1336* GCC or alike
    1437* GSL (GNU Scientific Library, available at http://www.gnu.org/software/gsl)
    1538* Boost 1.4 or newer
     39=======
     40In 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.
     41
     42LINKS
     43=====
     44[1] http://www.ins.uni-bonn.de/
     45>>>>>>> FETCH_HEAD

  • src/Actions/AtomAction/ChangeElementAction.cpp

    rc538d1 r3d078d  
    3838  std::vector<element *> elements;
    3939
    40   dialog->queryAtom(NAME, &first, MapOfActions::getInstance().getDescription(NAME));
    41   dialog->queryElement("element", &elements, MapOfActions::getInstance().getDescription("element"));
     40  dialog->queryElement(NAME, &elements, MapOfActions::getInstance().getDescription(NAME));
     41  dialog->queryAtom("atom-by-id", &first, MapOfActions::getInstance().getDescription("atom-by-id"));
    4242
    4343  if(dialog->display()) {

  • src/Actions/MapOfActions.cpp

    rc538d1 r3d078d  
    272272  TypeMap["center-in-box"] = Box;
    273273  TypeMap["change-box"] = Box;
    274   TypeMap["change-element"] = Atom;
     274  TypeMap["change-element"] = Element;
    275275  TypeMap["change-molname"] = String;
    276276  TypeMap["convex-envelope"] = Molecule;
    … …  
    323323  TypeMap["MaxDistance"] = Double;
    324324  TypeMap["molecule-by-id"] = Molecule;
    325   TypeMap["molecule-by-name"] = Molecule;
     325  TypeMap["molecule-by-name"] = String;
    326326  TypeMap["nonconvex-file"] = String;
    327327  TypeMap["order"] = Integer;

  • src/Actions/ParserAction/LoadXyzAction.cpp

    rc538d1 r3d078d  
    7878        if (UniqueList.size() != ListAfter.size()) { // only create if new atoms have been parsed
    7979          MoleculeListClass *molecules = World::getInstance().getMolecules();
    80           molecule *mol= NULL;
    81           if (molecules->ListOfMolecules.empty()) {
    82             mol = World::getInstance().createMolecule();
    83             molecules->insert(mol);
    84           } else {
    85             mol = *(molecules->ListOfMolecules.begin());
    86           }
     80          molecule *mol = World::getInstance().createMolecule();
     81          molecules->insert(mol);
    8782          for (vector<atom *>::iterator runner = ListAfter.begin(); runner != ListAfter.end(); ++runner) {
    8883            Inserter = UniqueList.insert(*runner);

  • src/Actions/WorldAction/ChangeBoxAction.cpp

    rc538d1 r3d078d  
    4141  if(dialog->display()) {
    4242    DoLog(0) && (Log() << Verbose(0) << "Setting box domain to " << cell_size.getM() << endl);
     43    World::getInstance().setDomain(cell_size.getM());
    4344    delete dialog;
    4445    return Action::success;

  • src/Actions/WorldAction/InputAction.cpp

    rc538d1 r3d078d  
    3838  MoleculeListClass *molecules = World::getInstance().getMolecules();
    3939  molecule *mol = NULL;
    40   string filename;
     40  std::string filename;
    4141  std::ifstream test;
    4242
    … …  
    4545  if(dialog->display()) {
    4646    DoLog(0) && (Log() << Verbose(0) << "Config file given." << endl);
    47     std::string FilenamePrefix = filename.substr(0,filename.find('.'));
    48     FormatParserStorage::getInstance().SetOutputPrefixForAll(FilenamePrefix);
    49     DoLog(1) && (Log() << Verbose(1) << "Setting config file name prefix to " << FilenamePrefix << "." << endl);
    50     test.open(filename.c_str());
    51     if (test == NULL) {
    52       DoLog(1) && (Log() << Verbose(1) << "Specified config file " << filename << " not found." << endl);
     47    if (filename.find('.') != string::npos) {
     48      std::string FilenamePrefix = filename.substr(0,filename.find_last_of('.'));
     49      std::string FilenameSuffix = filename.substr(filename.find_last_of('.')+1, filename.length());
     50      DoLog(1) && (Log() << Verbose(1) << "Setting config file name prefix to " << FilenamePrefix << "." << endl);
     51      test.open(filename.c_str());
     52      if (test == NULL) {
     53        DoLog(1) && (Log() << Verbose(1) << "Specified config file " << filename << " not found." << endl);
     54      } else {
     55        DoLog(1) && (Log() << Verbose(1) << "Specified config file found, parsing ... ");
     56        FormatParserStorage::getInstance().get((std::istream &)test, FilenameSuffix);
     57        test.close();
     58      }
     59      FormatParserStorage::getInstance().SetOutputPrefixForAll(FilenamePrefix);
     60      // set mol to first active molecule
     61      if (molecules->ListOfMolecules.size() != 0) {
     62        for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
     63          if ((*ListRunner)->ActiveFlag) {
     64            mol = *ListRunner;
     65            break;
     66          }
     67      }
     68      if (mol == NULL) {
     69        mol = World::getInstance().createMolecule();
     70        mol->ActiveFlag = true;
     71        molecules->insert(mol);
     72      }
     73      mol->SetNameFromFilename(filename.substr(0,filename.find('.')).c_str());
    5374    } else {
    54       DoLog(1) && (Log() << Verbose(1) << "Specified config file found, parsing ... ");
    55       FormatParserStorage::getInstance().getPcp().load(&test);
    56       test.close();
     75      DoeLog(1) && (eLog() << Verbose(1) << "Input file does not have a suffix, cannot recognize format." << endl);
    5776    }
    58     // set mol to first active molecule
    59     if (molecules->ListOfMolecules.size() != 0) {
    60       for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
    61         if ((*ListRunner)->ActiveFlag) {
    62           mol = *ListRunner;
    63           break;
    64         }
    65     }
    66     if (mol == NULL) {
    67       mol = World::getInstance().createMolecule();
    68       mol->ActiveFlag = true;
    69       molecules->insert(mol);
    70     }
    71     mol->SetNameFromFilename(filename.c_str());
    7277    delete dialog;
    7378    return Action::success;

  • src/Box.cpp

    rc538d1 r3d078d  
    4646
    4747void Box::setM(Matrix _M){
    48   ASSERT(_M.at(1,0)==_M.at(0,1),"Matrix used as cell_size was not symmetric");
    49   ASSERT(_M.at(2,0)==_M.at(0,2),"Matrix used as cell_size was not symmetric");
    50   ASSERT(_M.at(1,2)==_M.at(2,1),"Matrix used as cell_size was not symmetric");
     48  ASSERT(_M.determinant()!=0,"Matrix in Box construction was not invertible");
    5149  *M    =_M;
    5250  *Minv = M->invert();

  • src/Descriptors/AtomDescriptor.cpp

    rc538d1 r3d078d  
    8282  vector<atom*> res;
    8383  World::AtomSet atoms = getAtoms();
    84   atoms_iter_t iter;
    85   for(iter=atoms.begin_internal();iter!=atoms.end_internal();++iter) {
    86     if(predicate(*iter)){
    87       res.push_back((*iter).second);
    88     }
     84  for_each(atoms.begin_internal(),
     85           atoms.end_internal(),
     86           boost::bind(&AtomDescriptor_impl::checkAndAdd,
     87                       this,&res,_1));
     88  return res;
     89}
     90
     91void AtomDescriptor_impl::checkAndAdd(std::vector<atom*> *v,std::pair<atomId_t,atom*> p){
     92  if(predicate(p)){
     93    v->push_back(p.second);
    8994  }
    90   return res;
    9195}
    9296

  • src/Descriptors/AtomDescriptor_impl.hpp

    rc538d1 r3d078d  
    5050   */
    5151  World::AtomSet& getAtoms();
     52
     53  void checkAndAdd(std::vector<atom*>*,std::pair<atomId_t,atom*>);
    5254};
    5355

  • src/Descriptors/AtomIdDescriptor.cpp

    rc538d1 r3d078d  
    3333
    3434atom *AtomIdDescriptor_impl::find(){
    35   World::AtomSet atoms = getAtoms();
     35  World::AtomSet &atoms = getAtoms();
    3636  World::AtomSet::iterator res = atoms.find(id);
    3737  return (res!=atoms.end())?((*res).second):0;

  • src/Descriptors/MoleculeDescriptor.cpp

    rc538d1 r3d078d  
    7474
    7575molecule* MoleculeDescriptor_impl::find() {
    76   World::MoleculeSet molecules = getMolecules();
     76  World::MoleculeSet &molecules = getMolecules();
    7777  molecules_iter_t res = find_if(molecules.begin_internal(),molecules.end_internal(),boost::bind(&MoleculeDescriptor_impl::predicate,this,_1));
    7878  return (res!=molecules.end_internal())?((*res).second):0;
    … …  
    8181vector<molecule*> MoleculeDescriptor_impl::findAll() {
    8282  vector<molecule*> res;
    83   World::MoleculeSet molecules = getMolecules();
    84   molecules_iter_t iter;
    85   for(iter=molecules.begin_internal();iter!=molecules.end_internal();++iter) {
    86     if(predicate(*iter)){
    87       res.push_back((*iter).second);
    88     }
     83  World::MoleculeSet &molecules = getMolecules();
     84  for_each(molecules.begin_internal(),
     85           molecules.end_internal(),
     86           boost::bind(&MoleculeDescriptor_impl::checkAndAdd,
     87                       this,&res,_1));
     88  return res;
     89}
     90
     91void MoleculeDescriptor_impl::checkAndAdd(std::vector<molecule*> *v,std::pair<moleculeId_t,molecule*> p){
     92  if(predicate(p)){
     93    v->push_back(p.second);
    8994  }
    90   return res;
    9195}
    9296

  • src/Descriptors/MoleculeDescriptor_impl.hpp

    rc538d1 r3d078d  
    5050   */
    5151  World::MoleculeSet& getMolecules();
     52
     53  void checkAndAdd(std::vector<molecule*>*,std::pair<moleculeId_t,molecule*>);
    5254};
    5355

  • src/Descriptors/MoleculeIdDescriptor.cpp

    rc538d1 r3d078d  
    3434
    3535molecule *MoleculeIdDescriptor_impl::find(){
    36   World::MoleculeSet molecules = getMolecules();
     36  World::MoleculeSet &molecules = getMolecules();
    3737  World::MoleculeSet::iterator res = molecules.find(id);
    3838  return (res!=molecules.end())?((*res).second):0;

  • src/Makefile.am

    rc538d1 r3d078d  
    150150DESCRIPTORSOURCE = Descriptors/AtomDescriptor.cpp \
    151151  Descriptors/AtomIdDescriptor.cpp \
     152  Descriptors/AtomSelectionDescriptor.cpp \
    152153  Descriptors/AtomTypeDescriptor.cpp \
    153154  Descriptors/MoleculeDescriptor.cpp \
    154155  Descriptors/MoleculeIdDescriptor.cpp \
    155156  Descriptors/MoleculeNameDescriptor.cpp \
    156   Descriptors/MoleculePtrDescriptor.cpp
     157  Descriptors/MoleculePtrDescriptor.cpp \
     158  Descriptors/MoleculeSelectionDescriptor.cpp
    157159                                   
    158160
    159161DESCRIPTORHEADER = Descriptors/AtomDescriptor.hpp \
    160162  Descriptors/AtomIdDescriptor.hpp \
     163  Descriptors/AtomSelectionDescriptor.hpp \
    161164  Descriptors/AtomTypeDescriptor.hpp \
    162165  Descriptors/MoleculeDescriptor.hpp \
    163166  Descriptors/MoleculeIdDescriptor.hpp \
    164167  Descriptors/MoleculeNameDescriptor.hpp \
    165   Descriptors/MoleculePtrDescriptor.hpp
     168  Descriptors/MoleculePtrDescriptor.hpp \
     169  Descriptors/MoleculeSelectionDescriptor.cpp
    166170                                 
    167171QTUISOURCE = ${QTUIMOC_TARGETS} \

  • src/Parser/FormatParserStorage.cpp

    rc538d1 r3d078d  
    4242  ParserSuffix.resize(ParserTypes_end, "");
    4343
    44   ParserSuffix[mpqc] = "conf.in";
     44  ParserSuffix[mpqc] = "in";
    4545  ParserSuffix[pcp] = "conf";
    46   ParserSuffix[tremolo] = "conf.data";
    47   ParserSuffix[xyz] = "conf.xyz";
     46  ParserSuffix[tremolo] = "data";
     47  ParserSuffix[xyz] = "xyz";
    4848}
    4949
    … …  
    133133}
    134134
     135/** Parses an istream depending on its suffix
     136 * \param &input input stream
     137 * \param suffix
     138 * \return true - parsing ok, false - suffix unknown
     139 */
     140bool FormatParserStorage::get(std::istream &input, std::string suffix)
     141{
     142  if (suffix == ParserSuffix[mpqc]) {
     143    getMpqc().load(&input);
     144  } else if (suffix == ParserSuffix[pcp]) {
     145    getPcp().load(&input);
     146  } else if (suffix == ParserSuffix[tremolo]) {
     147    getTremolo().load(&input);
     148  } else if (suffix == ParserSuffix[xyz]) {
     149    getXyz().load(&input);
     150  } else {
     151    DoeLog(1) && (eLog() << Verbose(1) << "Unknown suffix to for FormatParserStorage::get()." << endl);
     152    return false;
     153  }
     154  return true;
     155}
     156
    135157/** Returns reference to the output MpqcParser, adds if not present.
    136158 * \return reference to the output MpqcParser

  • src/Parser/FormatParserStorage.hpp

    rc538d1 r3d078d  
    4141  void addXyz();
    4242
     43  bool get(std::istream &input, std::string suffix);
    4344  MpqcParser &getMpqc();
    4445  PcpParser &getPcp();

  • src/Parser/XyzParser.cpp

    rc538d1 r3d078d  
    5959  if (comment == "") {
    6060    time_t now = time((time_t *)NULL);   // Get the system time and put it into 'now' as 'calender time'
    61     comment = "\tCreated by molecuilder on ";
     61    comment = "Created by molecuilder on ";
    6262    // ctime ends in \n\0, we have to cut away the newline
    6363    std::string time(ctime(&now));
    … …  
    6868      comment += time;
    6969  }
    70   *file << World::getInstance().numAtoms() << endl << comment << endl;
     70  *file << World::getInstance().numAtoms() << endl << "\t" << comment << endl;
    7171
    7272  vector<atom*> atoms = World::getInstance().getAllAtoms();

  • src/World.cpp

    rc538d1 r3d078d  
    99
    1010#include "World.hpp"
    11 #include "Patterns/ObservedContainer_impl.hpp"
     11
     12#include <functional>
    1213
    1314#include "atom.hpp"
    … …  
    2829
    2930#include "Patterns/Singleton_impl.hpp"
     31#include "Patterns/ObservedContainer_impl.hpp"
    3032
    3133using namespace std;
    … …  
    8385
    8486void World::setDomain(const Matrix &mat){
     87  OBSERVE;
    8588  *cell_size = mat;
    8689}
    … …  
    8891void World::setDomain(double * matrix)
    8992{
     93  OBSERVE;
    9094  Matrix M = ReturnFullMatrixforSymmetric(matrix);
    9195  cell_size->setM(M);
    … …  
    98102void World::setDefaultName(std::string name)
    99103{
     104  OBSERVE;
    100105  defaultName = name;
    101106};
    … …  
    485490}
    486491
     492/************************** Selection of Atoms and molecules ******************/
     493
     494// Atoms
     495
     496void World::clearAtomSelection(){
     497  selectedAtoms.clear();
     498}
     499
     500void World::selectAtom(atom *atom){
     501  ASSERT(atom,"Invalid pointer in selection of atom");
     502  selectedAtoms[atom->getId()]=atom;
     503}
     504
     505void World::selectAtom(atomId_t id){
     506  ASSERT(atoms.count(id),"Atom Id selected that was not in the world");
     507  selectedAtoms[id]=atoms[id];
     508}
     509
     510void World::selectAllAtoms(AtomDescriptor descr){
     511  internal_AtomIterator begin = getAtomIter_internal(descr);
     512  internal_AtomIterator end = atomEnd_internal();
     513  void (World::*func)(atom*) = &World::selectAtom; // needed for type resolution of overloaded function
     514  for_each(begin,end,bind1st(mem_fun(func),this)); // func is select... see above
     515}
     516
     517void World::selectAtomsOfMolecule(molecule *_mol){
     518  ASSERT(_mol,"Invalid pointer to molecule in selection of Atoms of Molecule");
     519  // need to make it const to get the fast iterators
     520  const molecule *mol = _mol;
     521  void (World::*func)(atom*) = &World::selectAtom; // needed for type resolution of overloaded function
     522  for_each(mol->begin(),mol->end(),bind1st(mem_fun(func),this)); // func is select... see above
     523}
     524
     525void World::selectAtomsOfMolecule(moleculeId_t id){
     526  ASSERT(molecules.count(id),"No molecule with the given id upon Selection of atoms from molecule");
     527  selectAtomsOfMolecule(molecules[id]);
     528}
     529
     530void World::unselectAtom(atom *atom){
     531  ASSERT(atom,"Invalid pointer in unselection of atom");
     532  unselectAtom(atom->getId());
     533}
     534
     535void World::unselectAtom(atomId_t id){
     536  ASSERT(atoms.count(id),"Atom Id unselected that was not in the world");
     537  selectedAtoms.erase(id);
     538}
     539
     540void World::unselectAllAtoms(AtomDescriptor descr){
     541  internal_AtomIterator begin = getAtomIter_internal(descr);
     542  internal_AtomIterator end = atomEnd_internal();
     543  void (World::*func)(atom*) = &World::unselectAtom; // needed for type resolution of overloaded function
     544  for_each(begin,end,bind1st(mem_fun(func),this)); // func is unselect... see above
     545}
     546
     547void World::unselectAtomsOfMolecule(molecule *_mol){
     548  ASSERT(_mol,"Invalid pointer to molecule in selection of Atoms of Molecule");
     549  // need to make it const to get the fast iterators
     550  const molecule *mol = _mol;
     551  void (World::*func)(atom*) = &World::unselectAtom; // needed for type resolution of overloaded function
     552  for_each(mol->begin(),mol->end(),bind1st(mem_fun(func),this)); // func is unsselect... see above
     553}
     554
     555void World::unselectAtomsOfMolecule(moleculeId_t id){
     556  ASSERT(molecules.count(id),"No molecule with the given id upon Selection of atoms from molecule");
     557  unselectAtomsOfMolecule(molecules[id]);
     558}
     559
     560// Molecules
     561
     562void World::clearMoleculeSelection(){
     563  selectedMolecules.clear();
     564}
     565
     566void World::selectMolecule(molecule *mol){
     567  ASSERT(mol,"Invalid pointer to molecule in selection");
     568  selectedMolecules[mol->getId()]=mol;
     569}
     570
     571void World::selectMolecule(moleculeId_t id){
     572  ASSERT(molecules.count(id),"Molecule Id selected that was not in the world");
     573  selectedMolecules[id]=molecules[id];
     574}
     575
     576void World::selectAllMoleculess(MoleculeDescriptor descr){
     577  internal_MoleculeIterator begin = getMoleculeIter_internal(descr);
     578  internal_MoleculeIterator end = moleculeEnd_internal();
     579  void (World::*func)(molecule*) = &World::selectMolecule; // needed for type resolution of overloaded function
     580  for_each(begin,end,bind1st(mem_fun(func),this)); // func is select... see above
     581}
     582
     583void World::selectMoleculeOfAtom(atom *atom){
     584  ASSERT(atom,"Invalid atom pointer in selection of MoleculeOfAtom");
     585  molecule *mol=atom->getMolecule();
     586  // the atom might not be part of a molecule
     587  if(mol){
     588    selectMolecule(mol);
     589  }
     590}
     591
     592void World::selectMoleculeOfAtom(atomId_t id){
     593  ASSERT(atoms.count(id),"No such atom with given ID in selection of Molecules of Atom");\
     594  selectMoleculeOfAtom(atoms[id]);
     595}
     596
     597void World::unselectMolecule(molecule *mol){
     598  ASSERT(mol,"invalid pointer in unselection of molecule");
     599  unselectMolecule(mol->getId());
     600}
     601
     602void World::unselectMolecule(moleculeId_t id){
     603  ASSERT(molecules.count(id),"No such molecule with ID in unselection");
     604  selectedMolecules.erase(id);
     605}
     606
     607void World::unselectAllMoleculess(MoleculeDescriptor descr){
     608  internal_MoleculeIterator begin = getMoleculeIter_internal(descr);
     609  internal_MoleculeIterator end = moleculeEnd_internal();
     610  void (World::*func)(molecule*) = &World::unselectMolecule; // needed for type resolution of overloaded function
     611  for_each(begin,end,bind1st(mem_fun(func),this)); // func is unselect... see above
     612}
     613
     614void World::unselectMoleculeOfAtom(atom *atom){
     615  ASSERT(atom,"Invalid atom pointer in selection of MoleculeOfAtom");
     616  molecule *mol=atom->getMolecule();
     617  // the atom might not be part of a molecule
     618  if(mol){
     619    unselectMolecule(mol);
     620  }
     621}
     622
     623void World::unselectMoleculeOfAtom(atomId_t id){
     624  ASSERT(atoms.count(id),"No such atom with given ID in selection of Molecules of Atom");\
     625  unselectMoleculeOfAtom(atoms[id]);
     626}
     627
     628/******************* Iterators over Selection *****************************/
     629World::AtomSelectionIterator World::beginAtomSelection(){
     630  return selectedAtoms.begin();
     631}
     632
     633World::AtomSelectionIterator World::endAtomSelection(){
     634  return selectedAtoms.end();
     635}
     636
     637
     638World::MoleculeSelectionIterator World::beginMoleculeSelection(){
     639  return selectedMolecules.begin();
     640}
     641
     642World::MoleculeSelectionIterator World::endMoleculeSelection(){
     643  return selectedMolecules.end();
     644}
     645
    487646/******************************* Singleton Stuff **************************/
    488647
    … …  
    494653    ExitFlag(0),
    495654    atoms(this),
     655    selectedAtoms(this),
    496656    currAtomId(0),
    497657    lastAtomPoolSize(0),
    498658    numAtomDefragSkips(0),
    499659    molecules(this),
     660    selectedMolecules(this),
    500661    currMoleculeId(0),
    501662    molecules_deprecated(new MoleculeListClass(this))

  • src/World.hpp

    rc538d1 r3d078d  
    6262friend class MoleculeDescriptor_impl;
    6363friend class MoleculeDescriptor;
     64// coupling with descriptors over selection
     65friend class AtomSelectionDescriptor_impl;
     66friend class MoleculeSelectionDescriptor_impl;
    6467
    6568// Actions, calculations etc associated with the World
    … …  
    222225   * All these iterators are observed to track changes.
    223226   * There is a corresponding protected section with unobserved iterators,
    224    * which ca be used internally when the extra speed is needed
     227   * which can be used internally when the extra speed is needed
    225228   */
    226229
    … …  
    239242  typedef SelectiveIterator<molecule*,MoleculeSet,MoleculeDescriptor>   MoleculeIterator;
    240243
     244  /**
     245   * returns an iterator over all Molecules matching a given descriptor.
     246   * This iterator is observed, so don't keep it around unnecessary to
     247   * avoid unintended blocking.
     248   */
    241249  MoleculeIterator getMoleculeIter(MoleculeDescriptor descr);
    242250  MoleculeIterator getMoleculeIter();
    243251
    244252  MoleculeIterator moleculeEnd();
     253
     254  /******** Selections of molecules and Atoms *************/
     255  void clearAtomSelection();
     256  void selectAtom(atom*);
     257  void selectAtom(atomId_t);
     258  void selectAllAtoms(AtomDescriptor);
     259  void selectAtomsOfMolecule(molecule*);
     260  void selectAtomsOfMolecule(moleculeId_t);
     261  void unselectAtom(atom*);
     262  void unselectAtom(atomId_t);
     263  void unselectAllAtoms(AtomDescriptor);
     264  void unselectAtomsOfMolecule(molecule*);
     265  void unselectAtomsOfMolecule(moleculeId_t);
     266
     267  void clearMoleculeSelection();
     268  void selectMolecule(molecule*);
     269  void selectMolecule(moleculeId_t);
     270  void selectAllMoleculess(MoleculeDescriptor);
     271  void selectMoleculeOfAtom(atom*);
     272  void selectMoleculeOfAtom(atomId_t);
     273  void unselectMolecule(molecule*);
     274  void unselectMolecule(moleculeId_t);
     275  void unselectAllMoleculess(MoleculeDescriptor);
     276  void unselectMoleculeOfAtom(atom*);
     277  void unselectMoleculeOfAtom(atomId_t);
     278
     279  /******************** Iterators to selections *****************/
     280  typedef AtomSet::iterator AtomSelectionIterator;
     281  AtomSelectionIterator beginAtomSelection();
     282  AtomSelectionIterator endAtomSelection();
     283
     284  typedef MoleculeSet::iterator MoleculeSelectionIterator;
     285  MoleculeSelectionIterator beginMoleculeSelection();
     286  MoleculeSelectionIterator endMoleculeSelection();
    245287
    246288protected:
    … …  
    308350  class ThermoStatContainer *Thermostats;
    309351  int ExitFlag;
    310 public:
     352private:
     353
    311354  AtomSet atoms;
    312 private:
     355  AtomSet selectedAtoms;
    313356  typedef std::set<std::pair<atomId_t, atomId_t> > atomIdPool_t;
    314 
    315357  /**
    316358   * stores the pool for all available AtomIds below currAtomId
    … …  
    324366
    325367  MoleculeSet molecules;
     368  MoleculeSet selectedMolecules;
    326369  typedef std::set<std::pair<moleculeId_t, moleculeId_t> > moleculeIdPool_t;
     370  /**
     371   * stores the pool for all available AtomIds below currAtomId
     372   *
     373   * The pool contains ranges of free ids in the form [bottom,top).
     374   */
    327375  moleculeIdPool_t moleculeIdPool;
    328376  moleculeId_t currMoleculeId;

  • src/atom.cpp

    rc538d1 r3d078d  
    330330}
    331331
     332molecule* atom::getMolecule(){
     333  return mol;
     334}
     335
    332336void atom::removeFromMolecule(){
    333337  if(mol){

  • src/atom.hpp

    rc538d1 r3d078d  
    9090
    9191   void setMolecule(molecule*);
     92   molecule* getMolecule();
    9293   void removeFromMolecule();
    9394

  • src/unittests/ParserUnitTest.cpp

    rc538d1 r3d078d  
    131131\tmolecule = $:molecule\n\
    132132)\n";
    133 static string waterXyz = "3\nH2O: water molecule\nO\t0\t0\t0\nH\t0.758602\t0\t0.504284\nH\t0.758602\t0\t-0.504284\n";
     133static string waterXyz = "3\n\tH2O: water molecule\nO\t0\t0\t0\nH\t0.758602\t0\t0.504284\nH\t0.758602\t0\t-0.504284\n";
    134134static string Tremolo_Atomdata1 = "# ATOMDATA\tId\tname\tType\tx=3\n";
    135135static string Tremolo_Atomdata2 = "#\n#ATOMDATA Id name Type x=3\n1 hydrogen H 3.0 4.5 0.1\n\n";

  • tests/Tesselations/defs.in

    rc538d1 r3d078d  
    5959        fi
    6060        #echo "Molecuilder done with exitcode $exitcode."
     61        cd ../..
    6162        #cat stderr
    6263        #cat stdout
    63         grep -E "^[0-9]* [0-9]* [0-9]*$" ../../@srcdir@/$mol/$2/${FILENAME}-$mol.dat | sort -n >reference-triangles.dat
    64         grep -E "^[0-9]* [0-9]* [0-9]*$" ${FILENAME}.dat | sort -n >new-triangles.dat
    65         diff reference-triangles.dat new-triangles.dat 2>diffstderr >diffstdout || exitcode=$?
     64        grep -E "^[0-9]* [0-9]* [0-9]*$" @srcdir@/$mol/$2/${FILENAME}-$mol.dat | sort -n >$testdir/$RADIUS/reference-triangles.dat
     65        grep -E "^[0-9]* [0-9]* [0-9]*$" $testdir/$RADIUS/${FILENAME}.dat | sort -n >$testdir/$RADIUS/new-triangles.dat
     66        diff $testdir/$RADIUS/reference-triangles.dat $testdir/$RADIUS/new-triangles.dat 2>$testdir/$RADIUS/diffstderr >$testdir/$RADIUS/diffstdout || exitcode=$?
    6667        #echo "Diff done with exitcode $exitcode."
    6768        #cat diffstderr
    6869        #cat diffstdout
    69         cd ../..
    7070        test $exitcode = $expected_exitcode || exit 1
    7171}

  • tests/Tesselations/heptan/1.5/NonConvexEnvelope-heptan.dat

    rc538d1 r3d078d  
    11TITLE = "3D CONVEX SHELL"
    22VARIABLES = "X" "Y" "Z" "U"
    3 ZONE T="heptan", N=23, E=64, DATAPACKING=POINT, ZONETYPE=FETRIANGLE
     3ZONE T="none", N=23, E=64, DATAPACKING=POINT, ZONETYPE=FETRIANGLE
    44-7.27e-07 -1.22006 0.930455 18.7229
    55-7.27e-07 -1.22006 -0.849545 18.7229
    … …  
    77-1.2492 0.921941 -0.849545 18.7227
    881.2492 0.921941 -0.849545 18.7222
    9 1.2492 0.921941 0.930455 27.0641
    10 -2.4985 -1.22006 -0.849545 19.9769
    11 -2.4985 -1.22006 0.930455 27.4727
    12 2.4985 -1.22006 0.930455 19.9769
    13 2.4985 -1.22006 -0.849545 27.4727
     91.2492 0.921941 0.930455 18.7222
     10-2.4985 -1.22006 -0.849545 27.4727
     11-2.4985 -1.22006 0.930455 19.9769
     122.4985 -1.22006 0.930455 27.4727
     132.4985 -1.22006 -0.849545 19.9769
    1414-4.6377 -0.336759 0.0404545 21.541
    1515-3.7477 0.921941 0.930455 18.8853
    … …  
    17174.6377 -0.336759 0.0404545 10.6618
    18183.7477 0.921941 -0.849545 18.5406
    19 3.7477 0.921941 0.930455 12.1988
     193.7477 0.921941 0.930455 18.5406
    2020-7.27e-07 -0.590759 0.0404545 23.0174
    2121-1.2492 0.292641 0.0404545 23.0167
    22 1.2492 0.292641 0.0404545 20.1632
     221.2492 0.292641 0.0404545 23.0172
    2323-2.4985 -0.590759 0.0404545 18.9798
    24242.4985 -0.590759 0.0404545 18.9798
    2525-3.7477 0.292641 0.0404545 39.5267
    26 3.7477 0.292641 0.0404545 23.2512
     263.7477 0.292641 0.0404545 20.5497
    2727
    282814 15 23
    … …  
    343415 19 23
    35355 15 19
     3616 19 23
     376 16 19
    36385 6 19
    37395 6 19
    … …  
    42443 4 18
    43453 4 18
     463 18 22
     473 12 22
    44484 18 22
    45494 13 22
    46 3 18 22
    47 3 12 22
    485012 13 22
    495112 13 22
    50 6 19 23
    51 6 16 23
     5211 12 22
     5311 12 22
     548 11 22
     558 12 22
    525611 13 22
    535711 13 22
    54587 11 22
    55597 13 22
    56 11 12 22
    57 11 12 22
    58 8 11 22
    59 8 12 22
    606014 16 23
    616114 16 23
    … …  
    76769 10 21
    77779 14 21
    78 10 17 21
    79 2 10 17
     789 17 21
     791 9 17
    80801 2 17
    81811 2 17
    82 1 17 21
    83 1 9 21
    84 2 17 20
    85 2 7 20
     822 17 21
     832 10 21
     841 17 20
     851 8 20
    86867 8 20
    87877 8 20
     888 11 20
    88897 11 20
    89 8 11 20
    90 8 17 20
    91 1 8 17
     907 17 20
     912 7 17

  • tests/regression/testsuite-analysis.at

    rc538d1 r3d078d  
    3939AT_KEYWORDS([analysis])
    4040AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/4/pre/test.conf .], 0)
    41 AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -v 3 -I -C S --elements 1 --output-file output.csv --bin-output-file bin_output.csv --bin-start 0 --bin-width 1. --bin-end 20 --molecule-by-id 208], 0, [stdout], [stderr])
     41AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -v 3 -I -C S --elements 1 --output-file output.csv --bin-output-file bin_output.csv --bin-start 0 --bin-width 1. --bin-end 20 --molecule-by-id 207], 0, [stdout], [stderr])
    4242AT_CHECK([fgrep "Begin of CorrelationToSurface" stdout], 0, [ignore], [ignore])
    4343#AT_CHECK([file=output.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/4/post/$file], 0, [ignore], [ignore])

  • tests/regression/testsuite-domain.at

    rc538d1 r3d078d  
    4545AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/pre/test.conf .], 0)
    4646AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -o xyz -d "1, 1, 1"], 0, [stdout], [stderr])
    47 AT_CHECK([file=test.conf.xyz;sort -n $file | grep -v "Created by" >$file-sorted], 0, [ignore], [ignore])
    48 AT_CHECK([file=test.conf.xyz;sort -n ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/post/$file  | grep -v "Created by" >$file-sorted2], 0, [ignore], [ignore])
    49 AT_CHECK([file=test.conf.xyz; diff $file-sorted $file-sorted2], 0, [ignore], [ignore])
     47AT_CHECK([file=test.xyz;sort -n $file | grep -v "Created by" >$file-sorted], 0, [ignore], [ignore])
     48AT_CHECK([file=test.xyz;sort -n ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/post/$file  | grep -v "Created by" >$file-sorted2], 0, [ignore], [ignore])
     49AT_CHECK([file=test.xyz; diff $file-sorted $file-sorted2], 0, [ignore], [ignore])
    5050AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/pre/test.conf test-x.conf], 0)
    5151AT_CHECK([../../molecuilder -i test-x.conf -e ${abs_top_srcdir}/src/ -o xyz -d "2, 1, 1"], 0, [stdout], [stderr])
    52 AT_CHECK([file=test-x.conf.xyz;sort -n $file | grep -v "Created by" >$file-sorted], 0, [ignore], [ignore])
    53 AT_CHECK([file=test-x.conf.xyz;sort -n ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/post/$file  | grep -v "Created by" >$file-sorted2], 0, [ignore], [ignore])
    54 AT_CHECK([file=test-x.conf.xyz; diff $file-sorted $file-sorted2], 0, [ignore], [ignore])
     52AT_CHECK([file=test-x.xyz;sort -n $file | grep -v "Created by" >$file-sorted], 0, [ignore], [ignore])
     53AT_CHECK([file=test-x.xyz;sort -n ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/post/$file  | grep -v "Created by" >$file-sorted2], 0, [ignore], [ignore])
     54AT_CHECK([file=test-x.xyz; diff $file-sorted $file-sorted2], 0, [ignore], [ignore])
    5555AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/pre/test.conf test-y.conf], 0)
    5656AT_CHECK([../../molecuilder -i test-y.conf -e ${abs_top_srcdir}/src/ -o xyz -d "1, 2, 1"], 0, [stdout], [stderr])
    57 AT_CHECK([file=test-y.conf.xyz;sort -n $file | grep -v "Created by" >$file-sorted], 0, [ignore], [ignore])
    58 AT_CHECK([file=test-y.conf.xyz;sort -n ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/post/$file  | grep -v "Created by" >$file-sorted2], 0, [ignore], [ignore])
    59 AT_CHECK([file=test-y.conf.xyz; diff $file-sorted $file-sorted2], 0, [ignore], [ignore])
     57AT_CHECK([file=test-y.xyz;sort -n $file | grep -v "Created by" >$file-sorted], 0, [ignore], [ignore])
     58AT_CHECK([file=test-y.xyz;sort -n ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/post/$file  | grep -v "Created by" >$file-sorted2], 0, [ignore], [ignore])
     59AT_CHECK([file=test-y.xyz; diff $file-sorted $file-sorted2], 0, [ignore], [ignore])
    6060AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/pre/test.conf test-z.conf], 0)
    6161AT_CHECK([../../molecuilder -i test-z.conf -e ${abs_top_srcdir}/src/ -o xyz -d "1, 1, 2"], 0, [stdout], [stderr])
    62 AT_CHECK([file=test-z.conf.xyz;sort -n $file | grep -v "Created by" >$file-sorted], 0, [ignore], [ignore])
    63 AT_CHECK([file=test-z.conf.xyz;sort -n ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/post/$file  | grep -v "Created by" >$file-sorted2], 0, [ignore], [ignore])
    64 AT_CHECK([file=test-z.conf.xyz; diff $file-sorted $file-sorted2], 0, [ignore], [ignore])
     62AT_CHECK([file=test-z.xyz;sort -n $file | grep -v "Created by" >$file-sorted], 0, [ignore], [ignore])
     63AT_CHECK([file=test-z.xyz;sort -n ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/post/$file  | grep -v "Created by" >$file-sorted2], 0, [ignore], [ignore])
     64AT_CHECK([file=test-z.xyz; diff $file-sorted $file-sorted2], 0, [ignore], [ignore])
    6565#AT_CHECK([/bin/false], 12, [ignore], [ignore])
    6666AT_CLEANUP

  • tests/regression/testsuite-simple_configuration.at

    rc538d1 r3d078d  
    1818], [ignore])
    1919AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
    20 AT_CHECK([file=test.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
    21 AT_CHECK([file=test.conf.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
     20AT_CHECK([file=test.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
     21AT_CHECK([file=test.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
    2222AT_CLEANUP
    2323
    … …  
    2727AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -o mpqc pcp xyz -a 1 --position "10., 10., 10."], 0, [ignore], [ignore])
    2828AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
    29 AT_CHECK([file=test.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
    30 AT_CHECK([file=test.conf.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
     29AT_CHECK([file=test.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
     30AT_CHECK([file=test.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
    3131AT_CHECK([../../molecuilder -i test2.conf -e ${abs_top_srcdir}/src/ -o mpqc pcp xyz -a 1 --position "0., 0., -1."], 0, [ignore], [ignore])
    3232AT_CHECK([file=test2.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
    33 AT_CHECK([file=test2.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
    34 AT_CHECK([file=test2.conf.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
     33AT_CHECK([file=test2.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
     34AT_CHECK([file=test2.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
    3535AT_CLEANUP
    3636
    … …  
    3838AT_SETUP([Simple configuration - Changing element])
    3939AT_KEYWORDS([configuration])
    40 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/4/pre/test.conf test.conf], 0)
    41 AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -E 0 --element 6], 0, [ignore], [ignore])
    42 AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/4/post/$file], 0, [ignore], [ignore])
     40AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/4/pre/test.xyz test.xyz], 0)
     41AT_CHECK([../../molecuilder -i test.xyz -e ${abs_top_srcdir}/src/ -E 6 --atom-by-id 0], 0, [ignore], [ignore])
     42AT_CHECK([file=test.xyz; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/4/post/$file], 0, [ignore], [ignore])
    4343AT_CLEANUP
    4444
    … …  
    4949AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -o mpqc pcp xyz -r 0], 0, [ignore], [ignore])
    5050AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
    51 AT_CHECK([file=test.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
    52 AT_CHECK([file=test.conf.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
     51AT_CHECK([file=test.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
     52AT_CHECK([file=test.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
    5353AT_CLEANUP
    5454
    … …  
    8080AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/8/pre/test.* .], 0)
    8181AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -o xyz -R 7. --position "7.283585982, 3.275186040, 3.535886037"], 0, [stdout], [stderr])
    82 AT_CHECK([sort -n test.conf.xyz | grep -v "Created by" >test.conf.xyz-sorted], 0, [ignore], [ignore])
    83 AT_CHECK([sort -n ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/8/post/test.conf.xyz  | grep -v "Created by" >${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/8/post/test.conf.xyz-sorted], 0, [ignore], [ignore])
    84 AT_CHECK([file=test.conf.xyz-sorted; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/8/post/$file], 0, [ignore], [ignore])
     82AT_CHECK([sort -n test.xyz | grep -v "Created by" >test.xyz-sorted], 0, [ignore], [ignore])
     83AT_CHECK([sort -n ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/8/post/test.xyz  | grep -v "Created by" >${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/8/post/test.xyz-sorted], 0, [ignore], [ignore])
     84AT_CHECK([file=test.xyz-sorted; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/8/post/$file], 0, [ignore], [ignore])
    8585AT_CLEANUP
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