debian/0000775000000000000000000000000012253504461007172 5ustar debian/rules0000775000000000000000000000151512243212306010245 0ustar #!/usr/bin/make -f export OMPI_MCA_plm_rsh_agent=/bin/false #workaround to start MPI-applications in chroot export NUMJOBS = $(patsubst parallel=%,%,$(filter parallel=%,$(DEB_BUILD_OPTIONS))) disable_auto_test_archs_mpi = hurd-i386 mips mipsel s390 s390x %: dh $@ --parallel override_dh_auto_clean: cd src; make clean-all dh_clean override_dh_auto_build: cd src; $(MAKE) -j$(NUMJOBS) yes-all; $(MAKE) -j$(NUMJOBS) no-lib; $(MAKE) -j$(NUMJOBS) openmpi mv src/lmp_openmpi src/lammps chmod 644 examples/USER/sph/shock_tube/shock2d.lmp override_dh_auto_test: mkdir test; cp examples/crack/* test/ cd test; ./../src/lammps < in.crack rm -rf test ifeq (,$(filter $(DEB_HOST_ARCH),$(disable_auto_test_archs_mpi))) mkdir test; cp examples/crack/* test/ cd test; mpirun -np 2 ./../src/lammps < in.crack rm -rf test endif debian/lammps-doc.examples0000664000000000000000000000001312243212306012751 0ustar examples/* debian/changelog0000664000000000000000000000475312253504456011061 0ustar lammps (0~20131119.git7162cf0-1build1) trusty; urgency=medium * No-change rebuild for libopenmpi1.3 -> libopenmpi1.6 transition. -- Logan Rosen Mon, 16 Dec 2013 00:01:18 -0500 lammps (0~20131119.git7162cf0-1) unstable; urgency=low * [e65b919] Imported Upstream version 0~20131119.git7162cf0 * [f7bddd4] Fix some problems, introduced by upstream recently. * [3616dfc] Use wrap-and-sort script. * [7e92030] Ignore quilt dir -- Anton Gladky Wed, 20 Nov 2013 22:41:36 +0100 lammps (0~20130503.gitd2adfba-1) unstable; urgency=low * [4a7ac95] Imported Upstream version 0~20130503.gitd2adfba * [2f578c3] Minor description update. * [fdb3192] Use parallel build. * [afade40] Add doc-base file. -- Anton Gladky Tue, 07 May 2013 21:27:12 +0200 lammps (0~20130201.gitdf9c707-1) experimental; urgency=low * [acf02f1] Imported Upstream version 0~20130201.gitdf9c707 * [9477729] Add -fopenmp option to compilation flags. * [a422953] Use Standards-Version: 3.9.4. No changes. * [3b9caec] Remove obsolete DM-Upload-Allowed flag. * [84d264e] Remove parallel option due to high RAM-consumption. -- Anton Gladky Sun, 03 Feb 2013 21:40:03 +0100 lammps (0~20121116.git9eeec79-1~exp1) experimental; urgency=low * [8b791e7] Update git_orig-script. Use more effective xz-compression. * [c4ee715] Imported Upstream version 0~20121116.git9eeec79 * [e9300f9] Update patch. -- Anton Gladky Mon, 19 Nov 2012 18:55:39 +0100 lammps (0~20120615.gite442279-1) unstable; urgency=low * [de9ec1f] Imported Upstream version 0~20120615.gite442279 * [864de63] Remove patch, applied by upstream. -- Anton Gladky Mon, 18 Jun 2012 20:34:59 +0200 lammps (0~20120426.git67de404-1) unstable; urgency=low * [cf6ee1b] Disable mpirun-test on some platforms, where it crashes. * [b4a9875] Imported Upstream version 0~20120426.git67de404 * [8abc62b] Enable additional modules before compiling. (Closes: #670547) -- Anton Gladky Fri, 27 Apr 2012 00:04:27 +0200 lammps (0~20120305.git5d7feb1-1) unstable; urgency=low * [23cace5] Imported Upstream version 0~20120305.git5d7feb1 * [c2d8e83] Enable auto-test. -- Anton Gladky Tue, 06 Mar 2012 20:03:14 +0100 lammps (0~20120228.git268a14f-1) unstable; urgency=low * Initial Release. (Closes: #610622). -- Anton Gladky Sat, 25 Feb 2012 22:49:48 +0100 debian/compat0000664000000000000000000000000212243212306010361 0ustar 9 debian/lammps.manpages0000664000000000000000000000002012243212306012161 0ustar debian/lammps.1 debian/lammps.10000664000000000000000000000241612243212306010541 0ustar .TH LAMMPS "2012-02-23" .SH NAME .B LAMMPS \- Molecular Dynamics Simulator. .SH SYNOPSIS .B lammps < in.file or mpirun \-np 2 .B lammps < in.file .SH DESCRIPTION .B LAMMPS LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. See http://lammps.sandia.gov/ for documentation. .SH COPYRIGHT © 2003--2012 Sandia Corporation This package 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 of the License, or (at your option) any later version. This package 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 General Public License for more details. On Debian systems, the complete text of the GNU General Public License can be found in `/usr/share/common-licenses/GPL-2'. debian/copyright0000664000000000000000000003330712243226106011127 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: http://lammps.sandia.gov/ Files: * Copyright: Sandia Corporation (2003) U.S. Government Steve Plimpton Ahmed Ismail Aidan Thompson Alexander Stukowski Ase Henry Axel Kohlmeyer Carolyn Phillips Christina Payne Chuanfu Luo Craig Maloney Eduardo Bringa Eric Simon Greg Wagner G. Ziegenhain Jeff Greathouse Kurt Smith Mark Stevens Mathias Puetz Mike Brown Mike Parks Naveen Michaud-Agrawal Paul Crozier Pieter in 't Veld Pim Schravendijk Randy Schunk Ravi Agrawal Wan Liang Ilya Valuev Keir Novik License: GPL-2 This package 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 of the License, or (at your option) any later version. . This package 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 General Public License for more details. . You should have received a copy of the GNU General Public License along with this package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA . On Debian systems, the complete text of the GNU General Public License can be found in `/usr/share/common-licenses/GPL-2'. Files: lib/poems/* Copyright: KURT S ANDERSON (2004) RUDRANARAYAN M MUKHERJEE (2004) JAMES H CRITCHLEY (2004) JOHN L ZIEGLER (2004) SCOTT LIPTON (2004) GEOFFREY BASORE (2004) JOHN EVANS (2004) License: POEMS-License Authors as indicated in Author List and Rensselaer Polytechnic Institute . Parallelizable Open source Efficient Multibody Software (POEMS) is written and maintained by the authors as indicated in Author's List as a part of Scientific Computation Research Center (SCOREC) at Rensselaer Polytechnic Intitute, Troy, NY, USA. . This License Agreement applies to any software library or other program which contains a notice placed by the copyright holder saying it may be distributed under the terms of this Rensselaer Public License (also called "this License"). Each licensee is addressed as "you". . A "library" means a collection of software functions and/or data prepared so as to be conveniently linked with application programs (which use some of those functions and data) to form executables. The "Library", below, refers to any such software library or work which has been distributed under these terms. A "work based on the Library" means either the Library/code or any derivative work under copyright law. . "Source code" for a work means the preferred form of the work for making modifications to it including any associated interface definition files, and scripts used to control compilation and installation of the library. . This library is free software; Redistribution and use in source code and binary forms, with or without modification, are permitted provided that the following conditions are met: . 1. Redistributions of source code must retain the above copyright notice, this list of conditions, the authors list, the grants list, and the following disclaimer without any modifications and in its current form. . 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions, the authors list, the grants list, and the following disclaimer in the documentation and/or other materials provided with the distribution. . 3. You must cause the files modified to carry prominent notices stating that you changed the files and dates of the change. . 4. At your discretion, you may submit the differences between the program and your work based on the program for inclusion in the source code repository maintained by Rensselaer Polytechnic Institute. The mechanics of the submission are explained in the file named CONTRIBUTE distributed with the Library. Should you decide to submit the changes, you agree to provide Rensselaer Polytechnic Institute with a joint copyright assignment of the changes, and you agree to sign such a copyright assignment form at the request of Rensselaer Polytechnic Institute. Changes will then made as appropriate to the authors list at the Resselaer repository. . 5. The authors as listed in "Authors_List" reserve the right to distribute the software or any modified work in any other license form if they so choose to without infringing on any previous or concurrent license agreement. . 6. The name of the authors or their employer(s), Rensselaer Polytechnic Institute, the Computational Dynamics Laboratory, the Scientific Computation Research Center (SCoReC), nor the names of any of the software distributors may not be used to endorse or promote products derived from this software without specific prior written permission. . THIS SOFTWARE IS PROVIDED BY THE AUTHORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR THE SCIENTIFIC COMPUTATION RESEARCH CENTER BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Files: src/USER-REAXC/* Copyright: Purdue University (2010) Hasan Metin Aktulga Joseph Fogarty Sagar Pandit Ananth Y Grama License: GPL-2+ This package 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 of the License, or (at your option) any later version. . On Debian systems, the complete text of the GNU General Public License can be found in `/usr/share/common-licenses/GPL-2'. Files: lib/gpu/geryon/* Copyright: Sandia Corporation (2010) U.S. Government License: Simplified BSD Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: . 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. . 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. . THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. . The views and conclusions contained in the software and documentation are those of the authors and should not be interpreted as representing official policies, either expressed or implied, of Sandia Corporation. . http://users.nccs.gov/~wb8/geryon/license.htm Files: python/examples/pizza/* tools/python/pizza/* Copyright: Sandia Corporation (2005) U.S. Government License: GPL On Debian systems, the complete text of the GNU General Public License can be found in `/usr/share/common-licenses/GPL'. Files: src/WINDOWS/extra/inttypes.h src/WINDOWS/extra/stdint.h Copyright: Alexander Chemeris (2006-2008) License: BSD (2 clause) Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: . 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. . 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. . 3. The name of the author may be used to endorse or promote products derived from this software without specific prior written permission. . THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Files: src/USER-MISC/pair_meam_spline.cpp src/USER-MISC/pair_meam_spline.h Copyright: Sandia Corporation (2003) Lawrence Livermore National Security, LLC (2011) License: GPL On Debian systems, the complete text of the GNU General Public License can be found in `/usr/share/common-licenses/GPL'. Files: src/WINDOWS/extra/fftw2/fftw.h Copyright: Massachusetts Institute of Technology (1997-1999, 2003) License: GPL-2+ On Debian systems, the complete text of the GNU General Public License can be found in `/usr/share/common-licenses/GPL-2'. Files: src/WINDOWS/extra/dirent.h Copyright: Toni Ronkko (2006) License: MIT/X11 (BSD like) Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the ``Software''), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: . The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. . THE SOFTWARE IS PROVIDED ``AS IS'', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL TONI RONKKO BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. Files: lib/gpu/cudpp_mini/* Copyright: University of California (2007-2010) NVIDIA Corporation License: Simplified BSD Copyright (c) 2007-2010 The Regents of the University of California, Davis campus ("The Regents") and NVIDIA Corporation ("NVIDIA"). All rights reserved. . Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: . * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the The Regents, nor NVIDIA, nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. . THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Files: src/WINDOWS/extra/erf_namd.c Copyright: Sun Microsystems, Inc (1993) License: Simplified BSD Developed at SunPro, a Sun Microsystems, Inc. business. Permission to use, copy, modify, and distribute this software is freely granted, provided that this notice is preserved. debian/source/0000775000000000000000000000000012243212306010463 5ustar debian/source/format0000664000000000000000000000001412243212306011671 0ustar 3.0 (quilt) debian/lammps.install0000664000000000000000000000002312243226106012042 0ustar src/lammps usr/bin debian/lammps-doc.docs0000664000000000000000000000000512243212306012064 0ustar doc/ debian/control0000664000000000000000000000411312243226106010570 0ustar Source: lammps Section: science Priority: extra Build-Depends: debhelper (>= 9), libfftw3-dev, libjpeg-dev, mpi-default-bin, mpi-default-dev Maintainer: Debian Science Maintainers Uploaders: Anton Gladky Homepage: http://lammps.sandia.gov/ Standards-Version: 3.9.4 Vcs-Git: git://git.debian.org/git/debian-science/packages/lammps.git Vcs-Browser: http://git.debian.org/?p=debian-science/packages/lammps.git Package: lammps Architecture: any Depends: ${misc:Depends}, ${shlibs:Depends} Recommends: lammps-doc, mpi-default-bin Description: Molecular Dynamics Simulator LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. . LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. . LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality. Package: lammps-doc Architecture: all Depends: ${misc:Depends} Section: doc Description: Molecular Dynamics Simulator. Documentation and examples LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. . LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. . LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality. . The package contains documentation and examples. debian/scripts/0000775000000000000000000000000012243212306010652 5ustar debian/scripts/get_orig_src.sh0000775000000000000000000000171612243212306013664 0ustar #!/bin/bash # The script creates a tar.xz tarball from git-repository of LAMMPS-project # ./get_orig_src.sh commitID - creates a tarball of specified commit # ./get_orig_src.sh - creates a tarball of the latest version # Packages, that needs to be installed to use the script: # atool, git-core git clone http://git.icms.temple.edu/lammps-ro.git git_temp_packaging cd git_temp_packaging if [ $1 ] then echo 'Checking out the revision ' $1 git checkout -b newvers $1 else echo 'Using the latest revision' fi GIT_REV=$(git log -n 1 --pretty="format:%h") GIT_DAT=$(git log -n 1 --pretty="format:%ai") GIT_DAT=${GIT_DAT:0:10} GIT_DAT=$(echo $GIT_DAT | sed 's/-//g') VER_DEB=0~$GIT_DAT.git$GIT_REV FOLDER_NAME=lammps-0~$GIT_DAT.git$GIT_REV TARBALL_NAME=lammps_0~$GIT_DAT.git$GIT_REV.orig.tar.xz echo $VER_DEB echo $FOLDER_NAME echo $TARBALL_NAME cd .. mv git_temp_packaging $FOLDER_NAME rm -rf $FOLDER_NAME/.git tar Jcvf $TARBALL_NAME $FOLDER_NAME debian/scripts/get_orig.py0000775000000000000000000000254712243212306013036 0ustar #!/usr/bin/python # -*- coding: utf-8 -*- # The script creates a tar.xz tarball from git-repository of LAMMPS-project # ./get_orig commitID - creates a tarball of specified commit # ./get_orig - creates a tarball of the latest version # Packages, that needs to be installed to use the script: # atool, python-git, git-core import os, sys, git print "Cloning the git-repo." os.system('git clone http://git.icms.temple.edu/lammps-ro.git git_temp_packaging') repo = git.Repo("./git_temp_packaging/") rev = '' head = '' if (len(sys.argv) > 1): rev = str(sys.argv[1]) print 'Trying to clone the specified revision %s.' % (rev) os.system('cd ./git_temp_packaging/; git checkout -b temp %s' % (rev)) head = repo.commits('temp')[0] else: print "Cloned the latest revision." head = repo.commits()[0] rev = str(head)[:7] dateP = head.authored_date versionN = "0~%04d%02d%02d.git%s" % (dateP.tm_year, dateP.tm_mon, dateP.tm_mday, rev) folderName = 'lammps-%s' % (versionN) print 'Packaged commit is %s' % (rev) print 'Version number %s' % (versionN) #renaming the folder os.system('mv git_temp_packaging %s' % (folderName)) #removing git-dir os.system('rm -rf %s/.git' % (folderName)) #packing print "Creating a tarball." os.system('apack lammps_%s.orig.tar.xz %s' % (versionN, folderName)) print 'Removing temporary cloned git-repo.' os.system('rm -rf folderName') debian/lammps-doc.doc-base0000664000000000000000000000056012243212306012617 0ustar Document: lammps Title: LAMMPS Documentation Author: Sandia National Laboratories Abstract: LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator Section: Science/Mathematics Format: pdf Files: /usr/share/doc/lammps-doc/doc/Manual.pdf.gz Format: HTML Index: /usr/share/doc/lammps-doc/doc/Manual.html Files: /usr/share/doc/lammps-doc/doc/*.html debian/patches/0000775000000000000000000000000012243226042010614 5ustar debian/patches/fix_FTBFS_timer.patch0000664000000000000000000000142312243226036014552 0ustar Description: fix FTBFS due to timers. Author: Anton Gladky Last-Update: 2013-10-27 --- a/src/USER-OMP/pair_adp_omp.cpp +++ b/src/USER-OMP/pair_adp_omp.cpp @@ -200,7 +200,6 @@ if (NEWTON_PAIR) { // reduce per thread density - thr->timer(Timer::PAIR); data_reduce_thr(&(rho[0]), nall, comm->nthreads, 1, tid); data_reduce_thr(&(mu[0][0]), nall, comm->nthreads, 3, tid); data_reduce_thr(&(lambda[0][0]), nall, comm->nthreads, 6, tid); @@ -218,7 +217,6 @@ } else { // reduce per thread density - thr->timer(Timer::PAIR); data_reduce_thr(&(rho[0]), nlocal, comm->nthreads, 1, tid); data_reduce_thr(&(mu[0][0]), nlocal, comm->nthreads, 3, tid); data_reduce_thr(&(lambda[0][0]), nlocal, comm->nthreads, 6, tid); debian/patches/fix_format_not_a_string.patch0000664000000000000000000000064412243226027016550 0ustar Description: fix FTBFS due "format not a string" error Author: Anton Gladky Last-Update: 2013-11-22 --- a/src/citeme.cpp +++ b/src/citeme.cpp @@ -47,8 +47,8 @@ delete cs; - if (screen) fprintf(screen,cite_nagline); - if (logfile) fprintf(logfile,cite_nagline); + if (screen) fprintf(screen,"%s",cite_nagline); + if (logfile) fprintf(logfile,"%s",cite_nagline); if (fp) fclose(fp); } debian/patches/series0000664000000000000000000000011612243225657012042 0ustar set_configure_flags.patch fix_FTBFS_timer.patch fix_format_not_a_string.patch debian/patches/set_configure_flags.patch0000664000000000000000000000250512243226042015647 0ustar Description: use CXX and LD-flags, proposed by build environment instead of hardcoded. Fix linkage problem with fftw3. Author: Anton Gladky Last-Update: 2013-02-03 --- a/src/MAKE/Makefile.openmpi +++ b/src/MAKE/Makefile.openmpi @@ -7,14 +7,13 @@ # specify flags and libraries needed for your compiler CC = mpic++ -CCFLAGS = -O2 \ - -funroll-loops -fstrict-aliasing -Wall -W -Wno-uninitialized +CCFLAGS = -Wall $(shell dpkg-buildflags --get CXXFLAGS) -fopenmp SHFLAGS = -fPIC DEPFLAGS = -M LINK = mpic++ -LINKFLAGS = -O -LIB = -lstdc++ +LINKFLAGS = -O $(shell dpkg-buildflags --get LDFLAGS) +LIB = -lstdc++ -fopenmp SIZE = size ARCHIVE = ar @@ -29,7 +28,7 @@ # LAMMPS ifdef settings, OPTIONAL # see possible settings in doc/Section_start.html#2_2 (step 4) -LMP_INC = -DLAMMPS_GZIP +LMP_INC = -DLAMMPS_GZIP -DLAMMPS_JPEG # MPI library, REQUIRED # see discussion in doc/Section_start.html#2_2 (step 5) @@ -51,7 +50,7 @@ FFT_INC = -DFFT_FFTW3 FFT_PATH = -FFT_LIB = -lfftw +FFT_LIB = -lfftw3 # JPEG and/or PNG library, OPTIONAL # see discussion in doc/Section_start.html#2_2 (step 7) @@ -62,7 +61,7 @@ JPG_INC = JPG_PATH = -JPG_LIB = +JPG_LIB = -ljpeg # --------------------------------------------------------------------- # build rules and dependencies