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  • AUTHORS

    rb21cb9 rba9f5b  
    1 Jan Hamaekers (hamaekers@ins.uni-bonn.de)
    2 Frederik Heber (heber@ins.uni-bonn.de)
    3 Ralf Wildenhuis (wildenhuis@ins.uni-bonn.de)
     1Frederik Heber  (heber@ins.uni-bonn.de)

  • COPYING

    rb21cb9 rba9f5b  
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     2                    GNU GENERAL PUBLIC LICENSE
     3                       Version 3, 29 June 2007
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     527patent license for this particular work, or (3) arrange, in a manner
     528consistent with the requirements of this License, to extend the patent
     529license to downstream recipients.  "Knowingly relying" means you have
     530actual knowledge that, but for the patent license, your conveying the
     531covered work in a country, or your recipient's use of the covered work
     532in a country, would infringe one or more identifiable patents in that
     533country that you have reason to believe are valid.
     534
     535  If, pursuant to or in connection with a single transaction or
     536arrangement, you convey, or propagate by procuring conveyance of, a
     537covered work, and grant a patent license to some of the parties
     538receiving the covered work authorizing them to use, propagate, modify
     539or convey a specific copy of the covered work, then the patent license
     540you grant is automatically extended to all recipients of the covered
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     542
     543  A patent license is "discriminatory" if it does not include within
     544the scope of its coverage, prohibits the exercise of, or is
     545conditioned on the non-exercise of one or more of the rights that are
     546specifically granted under this License.  You may not convey a covered
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     551parties who would receive the covered work from you, a discriminatory
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     554for and in connection with specific products or compilations that
     555contain the covered work, unless you entered into that arrangement,
     556or that patent license was granted, prior to 28 March 2007.
     557
     558  Nothing in this License shall be construed as excluding or limiting
     559any implied license or other defenses to infringement that may
     560otherwise 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
     565otherwise) that contradict the conditions of this License, they do not
     566excuse you from the conditions of this License.  If you cannot convey a
     567covered work so as to satisfy simultaneously your obligations under this
     568License and any other pertinent obligations, then as a consequence you may
     569not convey it at all.  For example, if you agree to terms that obligate you
     570to collect a royalty for further conveying from those to whom you convey
     571the Program, the only way you could satisfy both those terms and this
     572License 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
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     578under version 3 of the GNU Affero General Public License into a single
     579combined work, and to convey the resulting work.  The terms of this
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     581but the special requirements of the GNU Affero General Public License,
     582section 13, concerning interaction through a network will apply to the
     583combination as such.
     584
     585  14. Revised Versions of this License.
     586
     587  The Free Software Foundation may publish revised and/or new versions of
     588the GNU General Public License from time to time.  Such new versions will
     589be similar in spirit to the present version, but may differ in detail to
     590address new problems or concerns.
     591
     592  Each version is given a distinguishing version number.  If the
     593Program specifies that a certain numbered version of the GNU General
     594Public License "or any later version" applies to it, you have the
     595option of following the terms and conditions either of that numbered
     596version or of any later version published by the Free Software
     597Foundation.  If the Program does not specify a version number of the
     598GNU General Public License, you may choose any version ever published
     599by the Free Software Foundation.
     600
     601  If the Program specifies that a proxy can decide which future
     602versions of the GNU General Public License can be used, that proxy's
     603public statement of acceptance of a version permanently authorizes you
     604to choose that version for the Program.
     605
     606  Later license versions may give you additional or different
     607permissions.  However, no additional obligations are imposed on any
     608author or copyright holder as a result of your choosing to follow a
     609later version.
     610
     611  15. Disclaimer of Warranty.
     612
     613  THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
     614APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
     615HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
     616OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
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     619IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
     620ALL 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
     625WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
     626THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
     627GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
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     629DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
     630PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
     631EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
     632SUCH DAMAGES.
     633
     634  17. Interpretation of Sections 15 and 16.
     635
     636  If the disclaimer of warranty and limitation of liability provided
     637above cannot be given local legal effect according to their terms,
     638reviewing courts shall apply local law that most closely approximates
     639an absolute waiver of all civil liability in connection with the
     640Program, unless a warranty or assumption of liability accompanies a
     641copy 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=======
    24647this service if you wish), that you receive source code or can get it
    25648if you want it, that you can change the software or use pieces of it
    … …  
    286909
    287910            How to Apply These Terms to Your New Programs
     911>>>>>>> FETCH_HEAD
    288912
    289913  If you develop a new program, and you want it to be of the greatest
    … …  
    293917  To do so, attach the following notices to the program.  It is safest
    294918to attach them to the start of each source file to most effectively
     919<<<<<<< HEAD
     920state the exclusion of warranty; and each file should have at least
     921=======
    295922convey the exclusion of warranty; and each file should have at least
     923>>>>>>> FETCH_HEAD
    296924the "copyright" line and a pointer to where the full notice is found.
    297925
    … …  
    299927    Copyright (C) <year>  <name of author>
    300928
     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=======
    301934    This program is free software; you can redistribute it and/or modify
    302935    it under the terms of the GNU General Public License as published by
    303936    the Free Software Foundation; either version 2 of the License, or
     937>>>>>>> FETCH_HEAD
    304938    (at your option) any later version.
    305939
    … …  
    310944
    311945    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
     949Also 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
     952notice 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=======
    312957    along with this program; if not, write to the Free Software
    313958    Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
    … …  
    321966    Gnomovision version 69, Copyright (C) year  name of author
    322967    Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
     968>>>>>>> FETCH_HEAD
    323969    This is free software, and you are welcome to redistribute it
    324970    under certain conditions; type `show c' for details.
    325971
    326972The hypothetical commands `show w' and `show c' should show the appropriate
     973<<<<<<< HEAD
     974parts of the General Public License.  Of course, your program's commands
     975might 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,
     978if any, to sign a "copyright disclaimer" for the program, if necessary.
     979For 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
     983into proprietary programs.  If your program is a subroutine library, you
     984may consider it more useful to permit linking proprietary applications with
     985the library.  If this is what you want to do, use the GNU Lesser General
     986Public License instead of this License.  But first, please read
     987<http://www.gnu.org/philosophy/why-not-lgpl.html>.
     988=======
    327989parts of the General Public License.  Of course, the commands you use may
    328990be called something other than `show w' and `show c'; they could even be
    … …  
    3441006library.  If this is what you want to do, use the GNU Library General
    3451007Public License instead of this License.
     1008>>>>>>> FETCH_HEAD

  • ChangeLog

    • Property mode changed from 100644 to 100755

  • Makefile.am

    rb21cb9 rba9f5b  
    1 #ACLOCAL_AMFLAGS = -I m4
    2 SUBDIRS = pcp util molecuilder
    3 #<F2>util/molecuilder
    4 DIST_SUBDIRS = ${SUBDIRS}
    5 #defaults/pseudopot
     1ACLOCAL_AMFLAGS = -I m4
     2SUBDIRS = src src/unittests doc tests
    63
    7 #include aminclude.am
     4EXTRA_DIST = autogen.sh
    85
    9 pcpdir = ${bindir}
    10 
    11 EXTRA_DIST = util/suffix autogen.sh configs.tar.gz pseudopots.tar.gz util/visual.cfg util/visual.net
    12 
    13 configs.tar.gz:
    14         $(TAR) -zcvf $(srcdir)/configs.tar.gz `find  $(srcdir) -name 'main_pcp_linux'`
    15 
    16 
    17 pseudopots.tar.gz:
    18         $(TAR) -zcvf $(srcdir)/pseudopots.tar.gz `find  $(srcdir) -name 'pseudo.??'`
     6.PHONY: doc
     7doc:
     8        cd doc && make doxygen-docs

  • README

    rb21cb9 rba9f5b  
     1<<<<<<< HEAD
     2# Project: Molecuilder
     3#
     4# heber@ins.uni-bonn.de
     5
     6        Molecuilder
     7
     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=======
    110# Project: ParallelCarParrinello
    211# Jan Hamaekers
    … …  
    1827
    1928
     29>>>>>>> FETCH_HEAD
    2030
    2131INSTALLATION NOTES
    2232==================
    2333
     34<<<<<<< HEAD
     35The following packages are needed
     36* GCC or alike
     37* GSL (GNU Scientific Library, available at http://www.gnu.org/software/gsl)
     38* Boost 1.4 or newer
     39=======
    2440In 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.
    2541
    … …  
    2743=====
    2844[1] http://www.ins.uni-bonn.de/
     45>>>>>>> FETCH_HEAD

  • configure.ac

    rb21cb9 rba9f5b  
    33
    44AC_PREREQ(2.59)
    5 AC_INIT([ElectronicStructurePACKage], 1.1, heber@ins.uni-bonn.de, ESPACK)
    6 AC_CONFIG_AUX_DIR([config])
    7 AC_CONFIG_SRCDIR([pcp/src/pcp.c])
     5AC_INIT(Molecuilder, 1.0, heber@ins.uni-bonn.de, molecuilder)
     6AC_CONFIG_AUX_DIR(config)
     7AC_CONFIG_SRCDIR([src/builder.cpp])
    88AC_CONFIG_HEADER([config.h])
    99
    1010AM_INIT_AUTOMAKE(dist-bzip2)
    1111
    12 AC_CANONICAL_HOST
     12# Checks for programs.
     13AM_PATH_CPPUNIT(1.9.6)
     14AC_PROG_CXX
     15AC_PROG_CC
     16AC_PROG_RANLIB
     17AC_PROG_INSTALL
     18AC_CHECK_PROG([LATEX],[latex],[latex],[:])
     19AC_CHECK_PROG([BIBTEX],[bibtex],[bibtex],[:])
     20AC_CHECK_PROG([DVIPS],[dvips],[dvips],[:])
     21AC_CHECK_PROG([PDFLATEX],[pdflatex],[pdflatex],[:])
     22AC_CHECK_PROG([XMLTO],[xmlto],[xmlto],[:])
     23AM_MISSING_PROG([DOXYGEN], [doxygen])
    1324
    14 AC_CONFIG_FILES([Makefile])
    15 AC_CONFIG_SUBDIRS([pcp util molecuilder])
     25# Checks for libraries.
     26AC_CHECK_LIB(m, sqrt, ,AC_MSG_ERROR([compatible libc math library not found]))
     27
     28# Boost libraries
     29AX_BOOST_BASE([1.40])
     30AX_BOOST_PROGRAM_OPTIONS
     31#AX_BOOST_FOREACH
     32#AX_BOOST_FILESYSTEM
     33AX_BOOST_THREAD
     34#AX_BOOST_SERIALIZATION
     35
     36#QT4 libraries
     37gw_CHECK_QT4
     38AX_CHECK_GLU
     39AC_MSG_NOTICE(["GLU_CFLAGS: $GLU_CFLAGS, GLU_CXXFLAGS: $GLU_CXXFLAGS, GLU_LDFLAGS: $GLU_LDFLAGS, GLU_LIBS: $GLU_LIBS"])
     40
     41
     42# Checks for header files.
     43AC_HEADER_STDC
     44AC_CHECK_HEADERS([sys/time.h])
     45AC_HEADER_STDBOOL
     46
     47AC_FUNC_MALLOC
     48AC_FUNC_REALLOC
     49AC_CHECK_FUNCS([floor pow sqrt strchr])
     50
     51# Checks for typedefs, structures, and compiler characteristics.
     52AC_C_CONST
     53AC_C_INLINE
     54AC_C_RESTRICT
     55AC_TYPE_SIZE_T
     56
     57# Checks for library functions.
     58# check for GNU Scientific Library
     59AC_CHECK_HEADERS([gsl/gsl_blas.h])
     60AC_SEARCH_LIBS(dnrm2, goto blas cblas gslblas gslcblas)
     61AC_CHECK_LIB(gsl, main, [],
     62        [AC_SEARCH_LIBS(cblas_dnrm2, blas cblas gslblas gslcblas)])
     63AC_CHECK_LIB(gsl, gsl_blas_dnrm2, , [AC_MSG_ERROR(["No working BLAS found for GSL, stopping."])])
     64
     65# add replacement/saturation hydrogen or not
     66AC_ARG_ENABLE([hydrogen],AS_HELP_STRING([--enable-hydrogen],[Adding saturation hydrogen (default is yes)]),
     67              [enable_hydrogen=$enableval], [enable_hydrogen=yes])
     68if test x"$enable_hydrogen" = xyes; then
     69  AC_DEFINE(ADDHYDROGEN,1, ["Adding saturation hydrogen"])
     70  AC_SUBST(ADDHYDROGEN)
     71fi
     72
     73# add replacement/saturation hydrogen or not
     74AC_ARG_ENABLE([ecut],AS_HELP_STRING([--enable-ecut],[Use ECut TestRunnerClient (default is no)]),
     75              [enable_ecut=$enableval], [enable_ecut=no])
     76if test x"$enable_ecut" = xyes; then
     77  AC_DEFINE(HAVE_ECUT,1, ["Use ECut TestRunnerClient instead of our own."])
     78  AC_SUBST(HAVE_ECUT)
     79fi
     80
     81# Check for "extern inline", using a modified version
     82# of the test for AC_C_INLINE from acspecific.mt
     83AC_CACHE_CHECK([for extern inline], ac_cv_c_extern_inline,
     84[ac_cv_c_extern_inline=no
     85AC_TRY_COMPILE([extern $ac_cv_c_inline double foo(double x);
     86extern $ac_cv_c_inline double foo(double x) { return x+1.0; };
     87double foo (double x) { return x + 1.0; };],
     88[  foo(1.0)  ],
     89[ac_cv_c_extern_inline="yes"])
     90])
     91
     92if test "$ac_cv_c_inline" != no ; then
     93  AC_DEFINE(HAVE_INLINE,1, ["May use inline routines"])
     94  AC_SUBST(HAVE_INLINE)
     95fi
     96
     97#AC_MSG_NOTICE(["CFLAGS: $CFLAGS, CXXFLAGS: $CXXFLAGS, LDFLAGS: $LDFLAGS, CC: $CC, CXX:, $CXX, MPICC: $MPICC, MPILIBS: $MPILIBS, LIBS: $LIBS"])
     98
     99# test suite
     100AC_CONFIG_TESTDIR(tests/regression)
     101AC_CONFIG_FILES([
     102        tests/Makefile
     103        tests/regression/atlocal
     104        tests/regression/Makefile])
     105AC_CONFIG_FILES([tests/regression/molecuilder], [chmod +x tests/regression/molecuilder])
     106AC_CONFIG_FILES([
     107        tests/Tesselations/Makefile
     108        tests/Tesselations/defs])
     109AC_CONFIG_FILES([
     110        doc/molecuilder.xml])
     111AC_CONFIG_FILES([
     112        Makefile
     113        doc/Makefile
     114        src/Makefile
     115        src/Actions/Makefile
     116        src/UIElements/Makefile
     117        src/unittests/Makefile])
    16118AC_OUTPUT
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