# Generic rules
*.c filter=uncrustify
*.cpp filter=uncrustify
+*.cu filter=uncrustify
*.h filter=uncrustify
+*.cuh filter=uncrustify
CMakeLists.txt filter=copyright
*.cmake filter=copyright
*.cmakein filter=copyright
*.l filter=copyright
*.y filter=copyright
*.pre filter=copyright
+*.tex filter=copyright
+*.bm filter=copyright
# Exceptions: extra files to include
admin/uncrustify.sh filter=copyright
admin/git-pre-commit filter=copyright
cmake/Platform/BluegeneQ*.cmake !filter
cmake/*.c !filter
cmake/*.c.cmakein !filter
-doxygen/*.cmakein !filter
+doxygen/Doxyfile-*.cmakein !filter
doxygen/*.cpp !filter
manual/UseLATEX.cmake !filter
scripts/GMXRC.* !filter
scripts/make_gromos_rtp.py !filter
src/contrib/* !filter
-src/gromacs/gmxlib/gpu_utils/memtestG80_core.h !filter
+src/gromacs/gmxlib/gpu_utils/memtestG80_core.* !filter
src/gromacs/gmxlib/nonbonded/preprocessor/gmxpreprocess.py !filter
**/thread_mpi/** filter=uncrustify_only
src/gromacs/legacyheaders/thread_mpi.h filter=uncrustify_only
output.append(' */')
return output
-class CommentHandlerSh(object):
+class CommentHandlerSimple(object):
- """Handler for extracting and creating sh-style comments."""
+ """Handler for extracting and creating sh-style comments.
+
+ Also other comments of the same type, but with a different comment
+ character are supported."""
+
+ def __init__(self, comment_char):
+ self._comment_char = comment_char
def extract_first_comment_block(self, content_lines):
- if not content_lines or not content_lines[0].startswith('#'):
+ if not content_lines or not content_lines[0].startswith(self._comment_char):
return ([], 0)
comment_block = []
line_index = 0
while line_index < len(content_lines):
line = content_lines[line_index]
- if not line.startswith('#'):
+ if not line.startswith(self._comment_char):
break
- comment_block.append(line.lstrip('# ').rstrip())
+ comment_block.append(line.lstrip(self._comment_char + ' ').rstrip())
line_index += 1
- if line == '# the research papers on the package. Check out http://www.gromacs.org.':
+ if line == self._comment_char + ' the research papers on the package. Check out http://www.gromacs.org.':
break
while line_index < len(content_lines):
line = content_lines[line_index].rstrip()
- if len(line) > 0 and line != '#':
+ if len(line) > 0 and line != self._comment_char:
break
line_index += 1
return (comment_block, line_index)
def create_comment_block(self, lines):
output = []
- output.extend([('# ' + x).rstrip() for x in lines])
+ output.extend([(self._comment_char + ' ' + x).rstrip() for x in lines])
output.append('')
return output
-comment_handlers = {'c': CommentHandlerC(), 'sh': CommentHandlerSh()}
+comment_handlers = {
+ 'c': CommentHandlerC(),
+ 'tex': CommentHandlerSimple('%'),
+ 'sh': CommentHandlerSimple('#')
+ }
def select_comment_handler(override, filename):
"""Select comment handler for a file based on file name and input options."""
dummy, ext2 = os.path.splitext(root)
if ext2:
ext = ext2
- if ext in ('.c', '.cpp', '.h', '.y', '.l', '.pre'):
+ if ext in ('.c', '.cu', '.cpp', '.h', '.cuh', '.y', '.l', '.pre', '.bm'):
filetype = 'c'
+ elif ext in ('.tex',):
+ filetype = 'tex'
elif basename in ('CMakeLists.txt', 'GMXRC', 'git-pre-commit') or \
ext in ('.cmake', '.cmakein', '.py', '.sh', '.bash', '.csh', '.zsh'):
filetype = 'sh'
+%
+% This file is part of the GROMACS molecular simulation package.
+%
+% Copyright (c) 2013, by the GROMACS development team, led by
+% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+% and including many others, as listed in the AUTHORS file in the
+% top-level source directory and at http://www.gromacs.org.
+%
+% GROMACS is free software; you can redistribute it and/or
+% modify it under the terms of the GNU Lesser General Public License
+% as published by the Free Software Foundation; either version 2.1
+% of the License, or (at your option) any later version.
+%
+% GROMACS is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+% Lesser General Public License for more details.
+%
+% You should have received a copy of the GNU Lesser General Public
+% License along with GROMACS; if not, see
+% http://www.gnu.org/licenses, or write to the Free Software Foundation,
+% Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+%
+% If you want to redistribute modifications to GROMACS, please
+% consider that scientific software is very special. Version
+% control is crucial - bugs must be traceable. We will be happy to
+% consider code for inclusion in the official distribution, but
+% derived work must not be called official GROMACS. Details are found
+% in the README & COPYING files - if they are missing, get the
+% official version at http://www.gromacs.org.
+%
+% To help us fund GROMACS development, we humbly ask that you cite
+% the research papers on the package. Check out http://www.gromacs.org.
+
% Process from LaTeX via XML to XHTML with
% latexml --destination installguide.xml --xml installguide.tex
% latexmlpost --destination installguide.xhtml --format=xhtml installguide.xml
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2013, by the GROMACS development team, led by
-# David van der Spoel, Berk Hess, Erik Lindahl, and including many
-# others, as listed in the AUTHORS file in the top-level source
-# directory and at http://www.gromacs.org.
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
#
# GROMACS is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public License
+%
% This file is part of the GROMACS molecular simulation package.
%
% Copyright (c) 2013, by the GROMACS development team, led by
-% David van der Spoel, Berk Hess, Erik Lindahl, and including many
-% others, as listed in the AUTHORS file in the top-level source
-% directory and at http://www.gromacs.org.
+% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+% and including many others, as listed in the AUTHORS file in the
+% top-level source directory and at http://www.gromacs.org.
%
% GROMACS is free software; you can redistribute it and/or
% modify it under the terms of the GNU Lesser General Public License
%
% GROMACS is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
-% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
% Lesser General Public License for more details.
%
% You should have received a copy of the GNU Lesser General Public
% official version at http://www.gromacs.org.
%
% To help us fund GROMACS development, we humbly ask that you cite
-% the research papers on the package. Check out http://www.gromacs.org
+% the research papers on the package. Check out http://www.gromacs.org.
\newcommand{\nproc}{\mbox{$M$}}
\newcommand{\natom}{\mbox{$N$}}
+%
% This file is part of the GROMACS molecular simulation package.
%
% Copyright (c) 2013, by the GROMACS development team, led by
-% David van der Spoel, Berk Hess, Erik Lindahl, and including many
-% others, as listed in the AUTHORS file in the top-level source
-% directory and at http://www.gromacs.org.
+% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+% and including many others, as listed in the AUTHORS file in the
+% top-level source directory and at http://www.gromacs.org.
%
% GROMACS is free software; you can redistribute it and/or
% modify it under the terms of the GNU Lesser General Public License
%
% GROMACS is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
-% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
% Lesser General Public License for more details.
%
% You should have received a copy of the GNU Lesser General Public
% official version at http://www.gromacs.org.
%
% To help us fund GROMACS development, we humbly ask that you cite
-% the research papers on the package. Check out http://www.gromacs.org
+% the research papers on the package. Check out http://www.gromacs.org.
\chapter{Analysis}
\label{ch:analysis}
+%
% This file is part of the GROMACS molecular simulation package.
%
% Copyright (c) 2013, by the GROMACS development team, led by
-% David van der Spoel, Berk Hess, Erik Lindahl, and including many
-% others, as listed in the AUTHORS file in the top-level source
-% directory and at http://www.gromacs.org.
+% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+% and including many others, as listed in the AUTHORS file in the
+% top-level source directory and at http://www.gromacs.org.
%
% GROMACS is free software; you can redistribute it and/or
% modify it under the terms of the GNU Lesser General Public License
%
% GROMACS is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
-% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
% Lesser General Public License for more details.
%
% You should have received a copy of the GNU Lesser General Public
% official version at http://www.gromacs.org.
%
% To help us fund GROMACS development, we humbly ask that you cite
-% the research papers on the package. Check out http://www.gromacs.org
+% the research papers on the package. Check out http://www.gromacs.org.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
+%
% This file is part of the GROMACS molecular simulation package.
%
% Copyright (c) 2013, by the GROMACS development team, led by
-% David van der Spoel, Berk Hess, Erik Lindahl, and including many
-% others, as listed in the AUTHORS file in the top-level source
-% directory and at http://www.gromacs.org.
+% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+% and including many others, as listed in the AUTHORS file in the
+% top-level source directory and at http://www.gromacs.org.
%
% GROMACS is free software; you can redistribute it and/or
% modify it under the terms of the GNU Lesser General Public License
%
% GROMACS is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
-% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
% Lesser General Public License for more details.
%
% You should have received a copy of the GNU Lesser General Public
% official version at http://www.gromacs.org.
%
% To help us fund GROMACS development, we humbly ask that you cite
-% the research papers on the package. Check out http://www.gromacs.org
+% the research papers on the package. Check out http://www.gromacs.org.
\chapter{Definitions and Units}
\label{ch:defunits}
+%
% This file is part of the GROMACS molecular simulation package.
%
% Copyright (c) 2013, by the GROMACS development team, led by
-% David van der Spoel, Berk Hess, Erik Lindahl, and including many
-% others, as listed in the AUTHORS file in the top-level source
-% directory and at http://www.gromacs.org.
+% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+% and including many others, as listed in the AUTHORS file in the
+% top-level source directory and at http://www.gromacs.org.
%
% GROMACS is free software; you can redistribute it and/or
% modify it under the terms of the GNU Lesser General Public License
%
% GROMACS is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
-% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
% Lesser General Public License for more details.
%
% You should have received a copy of the GNU Lesser General Public
% official version at http://www.gromacs.org.
%
% To help us fund GROMACS development, we humbly ask that you cite
-% the research papers on the package. Check out http://www.gromacs.org
+% the research papers on the package. Check out http://www.gromacs.org.
% TODO generate this from the code!
\begin{table}
+%
% This file is part of the GROMACS molecular simulation package.
%
% Copyright (c) 2013, by the GROMACS development team, led by
-% David van der Spoel, Berk Hess, Erik Lindahl, and including many
-% others, as listed in the AUTHORS file in the top-level source
-% directory and at http://www.gromacs.org.
+% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+% and including many others, as listed in the AUTHORS file in the
+% top-level source directory and at http://www.gromacs.org.
%
% GROMACS is free software; you can redistribute it and/or
% modify it under the terms of the GNU Lesser General Public License
%
% GROMACS is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
-% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
% Lesser General Public License for more details.
%
% You should have received a copy of the GNU Lesser General Public
% official version at http://www.gromacs.org.
%
% To help us fund GROMACS development, we humbly ask that you cite
-% the research papers on the package. Check out http://www.gromacs.org
+% the research papers on the package. Check out http://www.gromacs.org.
\chapter{Interaction function and force fields\index{force field}}
\label{ch:ff}
+%
% This file is part of the GROMACS molecular simulation package.
%
% Copyright (c) 2013, by the GROMACS development team, led by
-% David van der Spoel, Berk Hess, Erik Lindahl, and including many
-% others, as listed in the AUTHORS file in the top-level source
-% directory and at http://www.gromacs.org.
+% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+% and including many others, as listed in the AUTHORS file in the
+% top-level source directory and at http://www.gromacs.org.
%
% GROMACS is free software; you can redistribute it and/or
% modify it under the terms of the GNU Lesser General Public License
%
% GROMACS is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
-% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
% Lesser General Public License for more details.
%
% You should have received a copy of the GNU Lesser General Public
% official version at http://www.gromacs.org.
%
% To help us fund GROMACS development, we humbly ask that you cite
-% the research papers on the package. Check out http://www.gromacs.org
+% the research papers on the package. Check out http://www.gromacs.org.
\section{Parallelization}
\label{sec:par}
+%
% This file is part of the GROMACS molecular simulation package.
%
% Copyright (c) 2013, by the GROMACS development team, led by
-% David van der Spoel, Berk Hess, Erik Lindahl, and including many
-% others, as listed in the AUTHORS file in the top-level source
-% directory and at http://www.gromacs.org.
+% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+% and including many others, as listed in the AUTHORS file in the
+% top-level source directory and at http://www.gromacs.org.
%
% GROMACS is free software; you can redistribute it and/or
% modify it under the terms of the GNU Lesser General Public License
%
% GROMACS is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
-% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
% Lesser General Public License for more details.
%
% You should have received a copy of the GNU Lesser General Public
% official version at http://www.gromacs.org.
%
% To help us fund GROMACS development, we humbly ask that you cite
-% the research papers on the package. Check out http://www.gromacs.org
+% the research papers on the package. Check out http://www.gromacs.org.
\documentclass[11pt,a4paper,twoside]{gmxmanual}
\usepackage{here,picins,fancy,array,tabularx,multicol,dcolumn,makeidx,times,ifthen,enumitem,longtable,pdflscape}
+%
% This file is part of the GROMACS molecular simulation package.
%
% Copyright (c) 2013, by the GROMACS development team, led by
-% David van der Spoel, Berk Hess, Erik Lindahl, and including many
-% others, as listed in the AUTHORS file in the top-level source
-% directory and at http://www.gromacs.org.
+% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+% and including many others, as listed in the AUTHORS file in the
+% top-level source directory and at http://www.gromacs.org.
%
% GROMACS is free software; you can redistribute it and/or
% modify it under the terms of the GNU Lesser General Public License
%
% GROMACS is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
-% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
% Lesser General Public License for more details.
%
% You should have received a copy of the GNU Lesser General Public
% official version at http://www.gromacs.org.
%
% To help us fund GROMACS development, we humbly ask that you cite
-% the research papers on the package. Check out http://www.gromacs.org
+% the research papers on the package. Check out http://www.gromacs.org.
\chapter{Some implementation details}
In this chapter we will present some implementation details. This is
+%
% This file is part of the GROMACS molecular simulation package.
%
% Copyright (c) 2013, by the GROMACS development team, led by
-% David van der Spoel, Berk Hess, Erik Lindahl, and including many
-% others, as listed in the AUTHORS file in the top-level source
-% directory and at http://www.gromacs.org.
+% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+% and including many others, as listed in the AUTHORS file in the
+% top-level source directory and at http://www.gromacs.org.
%
% GROMACS is free software; you can redistribute it and/or
% modify it under the terms of the GNU Lesser General Public License
%
% GROMACS is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
-% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
% Lesser General Public License for more details.
%
% You should have received a copy of the GNU Lesser General Public
% official version at http://www.gromacs.org.
%
% To help us fund GROMACS development, we humbly ask that you cite
-% the research papers on the package. Check out http://www.gromacs.org
+% the research papers on the package. Check out http://www.gromacs.org.
\chapter{Technical Details}
\label{ch:install}
+%
% This file is part of the GROMACS molecular simulation package.
%
% Copyright (c) 2013, by the GROMACS development team, led by
-% David van der Spoel, Berk Hess, Erik Lindahl, and including many
-% others, as listed in the AUTHORS file in the top-level source
-% directory and at http://www.gromacs.org.
+% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+% and including many others, as listed in the AUTHORS file in the
+% top-level source directory and at http://www.gromacs.org.
%
% GROMACS is free software; you can redistribute it and/or
% modify it under the terms of the GNU Lesser General Public License
%
% GROMACS is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
-% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
% Lesser General Public License for more details.
%
% You should have received a copy of the GNU Lesser General Public
% official version at http://www.gromacs.org.
%
% To help us fund GROMACS development, we humbly ask that you cite
-% the research papers on the package. Check out http://www.gromacs.org
+% the research papers on the package. Check out http://www.gromacs.org.
\chapter{Introduction}
+%
% This file is part of the GROMACS molecular simulation package.
%
% Copyright (c) 2013, by the GROMACS development team, led by
-% David van der Spoel, Berk Hess, Erik Lindahl, and including many
-% others, as listed in the AUTHORS file in the top-level source
-% directory and at http://www.gromacs.org.
+% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+% and including many others, as listed in the AUTHORS file in the
+% top-level source directory and at http://www.gromacs.org.
%
% GROMACS is free software; you can redistribute it and/or
% modify it under the terms of the GNU Lesser General Public License
%
% GROMACS is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
-% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
% Lesser General Public License for more details.
%
% You should have received a copy of the GNU Lesser General Public
% official version at http://www.gromacs.org.
%
% To help us fund GROMACS development, we humbly ask that you cite
-% the research papers on the package. Check out http://www.gromacs.org
+% the research papers on the package. Check out http://www.gromacs.org.
\setlength {\parindent}{0.0cm}
\setlength {\parskip}{1ex}
+%
% This file is part of the GROMACS molecular simulation package.
%
% Copyright (c) 2013, by the GROMACS development team, led by
-% David van der Spoel, Berk Hess, Erik Lindahl, and including many
-% others, as listed in the AUTHORS file in the top-level source
-% directory and at http://www.gromacs.org.
+% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+% and including many others, as listed in the AUTHORS file in the
+% top-level source directory and at http://www.gromacs.org.
%
% GROMACS is free software; you can redistribute it and/or
% modify it under the terms of the GNU Lesser General Public License
%
% GROMACS is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
-% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
% Lesser General Public License for more details.
%
% You should have received a copy of the GNU Lesser General Public
% official version at http://www.gromacs.org.
%
% To help us fund GROMACS development, we humbly ask that you cite
-% the research papers on the package. Check out http://www.gromacs.org
+% the research papers on the package. Check out http://www.gromacs.org.
\chapter{Run parameters and Programs}
\label{ch:programs}
+%
% This file is part of the GROMACS molecular simulation package.
%
% Copyright (c) 2013, by the GROMACS development team, led by
-% David van der Spoel, Berk Hess, Erik Lindahl, and including many
-% others, as listed in the AUTHORS file in the top-level source
-% directory and at http://www.gromacs.org.
+% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+% and including many others, as listed in the AUTHORS file in the
+% top-level source directory and at http://www.gromacs.org.
%
% GROMACS is free software; you can redistribute it and/or
% modify it under the terms of the GNU Lesser General Public License
%
% GROMACS is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
-% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
% Lesser General Public License for more details.
%
% You should have received a copy of the GNU Lesser General Public
% official version at http://www.gromacs.org.
%
% To help us fund GROMACS development, we humbly ask that you cite
-% the research papers on the package. Check out http://www.gromacs.org
+% the research papers on the package. Check out http://www.gromacs.org.
\chapter{Special Topics}
\label{ch:special}
+%
% This file is part of the GROMACS molecular simulation package.
%
% Copyright (c) 2013, by the GROMACS development team, led by
-% David van der Spoel, Berk Hess, Erik Lindahl, and including many
-% others, as listed in the AUTHORS file in the top-level source
-% directory and at http://www.gromacs.org.
+% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+% and including many others, as listed in the AUTHORS file in the
+% top-level source directory and at http://www.gromacs.org.
%
% GROMACS is free software; you can redistribute it and/or
% modify it under the terms of the GNU Lesser General Public License
%
% GROMACS is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
-% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
% Lesser General Public License for more details.
%
% You should have received a copy of the GNU Lesser General Public
% official version at http://www.gromacs.org.
%
% To help us fund GROMACS development, we humbly ask that you cite
-% the research papers on the package. Check out http://www.gromacs.org
+% the research papers on the package. Check out http://www.gromacs.org.
\chapter{Topologies}
\label{ch:top}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
- * Copyright (c) 2012, by the GROMACS development team, led by
- * David van der Spoel, Berk Hess, Erik Lindahl, and including many
- * others, as listed in the AUTHORS file in the top-level source
- * directory and at http://www.gromacs.org.
+ * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
*
* GROMACS is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
+ * Copyright (c) 2012, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
*
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2012, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
- * If you want to redistribute modifications, please consider that
- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to consider code for
- * inclusion in the official distribution, but derived work must not
- * be called official GROMACS. Details are found in the README & COPYING
- * files - if they are missing, get the official version at www.gromacs.org.
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
*
- * To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
- * For more info, check our website at http://www.gromacs.org
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
*
- * And Hey:
- * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
#include <stdlib.h>
-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
+ * Copyright (c) 2012, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
*
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2012, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
- * If you want to redistribute modifications, please consider that
- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to consider code for
- * inclusion in the official distribution, but derived work must not
- * be called official GROMACS. Details are found in the README & COPYING
- * files - if they are missing, get the official version at www.gromacs.org.
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
*
- * To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
- * For more info, check our website at http://www.gromacs.org
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
*
- * And Hey:
- * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
#ifndef CUDAUTILS_CUH
-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
+ * Copyright (c) 2012, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
*
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2012, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
- * If you want to redistribute modifications, please consider that
- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to consider code for
- * inclusion in the official distribution, but derived work must not
- * be called official GROMACS. Details are found in the README & COPYING
- * files - if they are missing, get the official version at www.gromacs.org.
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
*
- * To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
- * For more info, check our website at http://www.gromacs.org
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
*
- * And Hey:
- * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
#include <stdlib.h>
-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
+ * Copyright (c) 2012, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
*
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2012, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
- * If you want to redistribute modifications, please consider that
- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to consider code for
- * inclusion in the official distribution, but derived work must not
- * be called official GROMACS. Details are found in the README & COPYING
- * files - if they are missing, get the official version at www.gromacs.org.
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
*
- * To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
- * For more info, check our website at http://www.gromacs.org
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
*
- * And Hey:
- * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
#ifndef VECTYPE_OPS_CUH
-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
- *
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2010,2012 The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
- *
- * If you want to redistribute modifications, please consider that
- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to consider code for
- * inclusion in the official distribution, but derived work must not
- * be called official GROMACS. Details are found in the README & COPYING
- * files - if they are missing, get the official version at www.gromacs.org.
- *
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
* To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
- *
- * For more info, check our website at http://www.gromacs.org
- *
- * And Hey:
- * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
#include <stdio.h>
-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
+ * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
*
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2012, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
- * If you want to redistribute modifications, please consider that
- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to consider code for
- * inclusion in the official distribution, but derived work must not
- * be called official GROMACS. Details are found in the README & COPYING
- * files - if they are missing, get the official version at www.gromacs.org.
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
*
- * To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
- * For more info, check our website at http://www.gromacs.org
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
*
- * And Hey:
- * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
#include <stdlib.h>
-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
+ * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
*
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2012, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
- * If you want to redistribute modifications, please consider that
- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to consider code for
- * inclusion in the official distribution, but derived work must not
- * be called official GROMACS. Details are found in the README & COPYING
- * files - if they are missing, get the official version at www.gromacs.org.
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
*
- * To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
- * For more info, check our website at http://www.gromacs.org
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
*
- * And Hey:
- * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
- *
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2012, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
+ * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
*
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
- * If you want to redistribute modifications, please consider that
- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to consider code for
- * inclusion in the official distribution, but derived work must not
- * be called official GROMACS. Details are found in the README & COPYING
- * files - if they are missing, get the official version at www.gromacs.org.
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
*
- * To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
- * For more info, check our website at http://www.gromacs.org
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
*
- * And Hey:
- * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
#include "maths.h"
-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
+ * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
*
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2012, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
- * If you want to redistribute modifications, please consider that
- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to consider code for
- * inclusion in the official distribution, but derived work must not
- * be called official GROMACS. Details are found in the README & COPYING
- * files - if they are missing, get the official version at www.gromacs.org.
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
*
- * To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
- * For more info, check our website at http://www.gromacs.org
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
*
- * And Hey:
- * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
/* Note that floating-point constants in CUDA code should be suffixed
-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
+ * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
*
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2012, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
- * If you want to redistribute modifications, please consider that
- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to consider code for
- * inclusion in the official distribution, but derived work must not
- * be called official GROMACS. Details are found in the README & COPYING
- * files - if they are missing, get the official version at www.gromacs.org.
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
*
- * To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
- * For more info, check our website at http://www.gromacs.org
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
*
- * And Hey:
- * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
/*! \file
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 1991-2001
- * BIOSON Research Institute, Dept. of Biophysical Chemistry
- * University of Groningen, The Netherlands
- * Copyright (c) 2012, by the GROMACS development team, led by
- * David van der Spoel, Berk Hess, Erik Lindahl, and including many
- * others, as listed in the AUTHORS file in the top-level source
- * directory and at http://www.gromacs.org.
+ * Copyright (c) 1991-2001, University of Groningen, The Netherlands.
+ * Copyright (c) 2002,2009,2013, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
*
* GROMACS is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-
-#ifndef _alert_bm
-#define _alert_bm
-
+#ifndef GMX_VIEW_ALERT_BM
+#define GMX_VIEW_ALERT_BM
#define alert_width 48
#define alert_height 42
0xf8, 0x00, 0x00, 0x00, 0x00, 0x1f, 0x7c, 0x00, 0x00, 0x00, 0x00, 0x3e,
0xfc, 0xff, 0xff, 0xff, 0xff, 0x3f, 0xfe, 0xff, 0xff, 0xff, 0xff, 0x7f,
0xfe, 0xff, 0xff, 0xff, 0xff, 0x7f, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff};
-#endif /* _alert_bm */
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 1991-2001
- * BIOSON Research Institute, Dept. of Biophysical Chemistry
- * University of Groningen, The Netherlands
- * Copyright (c) 2012, by the GROMACS development team, led by
- * David van der Spoel, Berk Hess, Erik Lindahl, and including many
- * others, as listed in the AUTHORS file in the top-level source
- * directory and at http://www.gromacs.org.
+ * Copyright (c) 1991-2001, University of Groningen, The Netherlands.
+ * Copyright (c) 2002,2009,2013, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
*
* GROMACS is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-
-#ifndef _ff_bm
-#define _ff_bm
+#ifndef GMX_VIEW_FF_BM
+#define GMX_VIEW_FF_BM
#define ff_width 40
#define ff_height 32
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00};
-#endif /* _ff_bm */
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 1991-2001
- * BIOSON Research Institute, Dept. of Biophysical Chemistry
- * University of Groningen, The Netherlands
- * Copyright (c) 2012, by the GROMACS development team, led by
- * David van der Spoel, Berk Hess, Erik Lindahl, and including many
- * others, as listed in the AUTHORS file in the top-level source
- * directory and at http://www.gromacs.org.
+ * Copyright (c) 1991-2001, University of Groningen, The Netherlands.
+ * Copyright (c) 2002,2009,2013, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
*
* GROMACS is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-
-
-#ifndef _gromacs_bm
-#define _gromacs_bm
-
+#ifndef GMX_VIEW_GROMACS_BM
+#define GMX_VIEW_GROMACS_BM
#define gromacs_width 48
#define gromacs_height 48
0x00, 0x0f, 0xf0, 0x01, 0xf0, 0x00, 0x00, 0x3c, 0x00, 0x00, 0x3c, 0x00,
0x00, 0xf8, 0x00, 0x00, 0x1f, 0x00, 0x00, 0xe0, 0x0f, 0xf0, 0x07, 0x00,
0x00, 0x80, 0xff, 0xff, 0x01, 0x00, 0x00, 0x00, 0xf8, 0x1f, 0x00, 0x00};
-#endif /* _gromacs_bm */
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 1991-2001
- * BIOSON Research Institute, Dept. of Biophysical Chemistry
- * University of Groningen, The Netherlands
- * Copyright (c) 2012, by the GROMACS development team, led by
- * David van der Spoel, Berk Hess, Erik Lindahl, and including many
- * others, as listed in the AUTHORS file in the top-level source
- * directory and at http://www.gromacs.org.
+ * Copyright (c) 1991-2001, University of Groningen, The Netherlands.
+ * Copyright (c) 2002,2009,2013, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
*
* GROMACS is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-
-#ifndef _info_bm
-#define _info_bm
+#ifndef GMX_VIEW_INFO_BM
+#define GMX_VIEW_INFO_BM
#define info_width 48
#define info_height 48
0x00, 0xf8, 0xff, 0xff, 0x3f, 0x00, 0x00, 0xf0, 0xff, 0xff, 0x1f, 0x00,
0x00, 0xc0, 0xff, 0xff, 0x07, 0x00, 0x00, 0x00, 0xff, 0xff, 0x01, 0x00,
0x00, 0x00, 0xf0, 0x1f, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00};
-#endif /* _info_bm */
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 1991-2001
- * BIOSON Research Institute, Dept. of Biophysical Chemistry
- * University of Groningen, The Netherlands
- * Copyright (c) 2012, by the GROMACS development team, led by
- * David van der Spoel, Berk Hess, Erik Lindahl, and including many
- * others, as listed in the AUTHORS file in the top-level source
- * directory and at http://www.gromacs.org.
+ * Copyright (c) 1991-2001, University of Groningen, The Netherlands.
+ * Copyright (c) 2002,2009,2013, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
*
* GROMACS is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-
-#ifndef _play_bm
-#define _play_bm
+#ifndef GMX_VIEW_PLAY_BM
+#define GMX_VIEW_PLAY_BM
#define play_width 40
#define play_height 32
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00};
-#endif /* _play_bm */
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 1991-2001
- * BIOSON Research Institute, Dept. of Biophysical Chemistry
- * University of Groningen, The Netherlands
- * Copyright (c) 2012, by the GROMACS development team, led by
- * David van der Spoel, Berk Hess, Erik Lindahl, and including many
- * others, as listed in the AUTHORS file in the top-level source
- * directory and at http://www.gromacs.org.
+ * Copyright (c) 1991-2001, University of Groningen, The Netherlands.
+ * Copyright (c) 2002,2009,2013, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
*
* GROMACS is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _rewind_bm
-#define _rewind_bm
+#ifndef GMX_VIEW_REWIND_BM
+#define GMX_VIEW_REWIND_BM
#define rewind_width 40
#define rewind_height 32
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00};
-#endif /* _rewind_bm */
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 1991-2001
- * BIOSON Research Institute, Dept. of Biophysical Chemistry
- * University of Groningen, The Netherlands
- * Copyright (c) 2012, by the GROMACS development team, led by
- * David van der Spoel, Berk Hess, Erik Lindahl, and including many
- * others, as listed in the AUTHORS file in the top-level source
- * directory and at http://www.gromacs.org.
+ * Copyright (c) 1991-2001, University of Groningen, The Netherlands.
+ * Copyright (c) 2002,2009,2013, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
*
* GROMACS is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-
-#ifndef _stop_bm
-#define _stop_bm
-
+#ifndef GMX_VIEW_STOP_BM
+#define GMX_VIEW_STOP_BM
#define stop_width 48
#define stop_height 48
-#define stop_x_hot -1
-#define stop_y_hot -1
static unsigned char stop_bits[] = {
0x00, 0xf0, 0xff, 0xff, 0x0f, 0x00, 0x00, 0xf8, 0xff, 0xff, 0x1f, 0x00,
0x00, 0x1c, 0x00, 0x00, 0x38, 0x00, 0x00, 0xee, 0xff, 0xff, 0x77, 0x00,
0x00, 0xf7, 0xff, 0xff, 0xef, 0x00, 0x00, 0xee, 0xff, 0xff, 0x77, 0x00,
0x00, 0xdc, 0xff, 0xff, 0x3b, 0x00, 0x00, 0x38, 0x00, 0x00, 0x1c, 0x00,
0x00, 0xf0, 0xff, 0xff, 0x0f, 0x00, 0x00, 0xe0, 0xff, 0xff, 0x07, 0x00};
-#endif /* _stop_bm */
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 1991-2001
- * BIOSON Research Institute, Dept. of Biophysical Chemistry
- * University of Groningen, The Netherlands
- * Copyright (c) 2012, by the GROMACS development team, led by
- * David van der Spoel, Berk Hess, Erik Lindahl, and including many
- * others, as listed in the AUTHORS file in the top-level source
- * directory and at http://www.gromacs.org.
+ * Copyright (c) 1991-2001, University of Groningen, The Netherlands.
+ * Copyright (c) 2002,2009,2013, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
*
* GROMACS is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-
-#ifndef _stop_ani_bm
-#define _stop_ani_bm
-
+#ifndef GMX_VIEW_STOP_ANI_BM
+#define GMX_VIEW_STOP_ANI_BM
#define stop_ani_width 40
#define stop_ani_height 32
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00};
-#endif /* _stop_ani_bm */
+#endif
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff