debian/0000775000000000000000000000000012255326577007206 5ustar debian/README.Debian0000664000000000000000000000116712255325043011237 0ustar openmx for Debian ----------------- How to use it - unpack the upstream sources, go to the directory work and start the calculation: wget http://www.openmx-square.org/openmx3.2.tar.gz tar xzf openmx3.2.tar.gz cd openmx3.2/work openmx Methane.dat When you learn openmx, you don't have to use the upstream sources, just your own input files. The advantage of the above procedure is that it just works and gets you up and running. For other examples/documentation/tutorial, see the upstream homepage (follow the "Manual" link): http://www.openmx-square.org/ -- Ondrej Certik Sat, 09 Jun 2007 12:41:34 +0000 debian/source/0000775000000000000000000000000012255325043010471 5ustar debian/source/format0000664000000000000000000000001412255325043011677 0ustar 3.0 (quilt) debian/openmx.10000664000000000000000000000150312255325043010560 0ustar .TH "OPENMX" "1" "2007-06-09" "" "" .SH NAME openmx \- package for nano-scale material simulations .SH SYNOPSIS .B openmx .BI [ file ] .SH DESCRIPTION .B openmx is a program that calculates electronic structure using DFT. .SH OPTIONS The program doesn't accept any other options, everything is given in the file specified at the command line. .SH AUTHORS This manual page was written by \fBOndrej Certik\fR <\&ondrej@certik.cz\&> for the Debian system (but may be used by others). .PP Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 or (at your option) any later version as published by the Free Software Foundation. .PP On Debian systems, the complete text of the GNU General Public License can be found in \fI\%/usr/share/common-licenses/GPL\fR. debian/copyright0000664000000000000000000000376412255325043011136 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: OpenMX Upstream-Contact: Taisuke Ozaki Present (15/May/2013) official address . Japan Advanced Institute of Science and Technology (JAIST) Asahidai 1-1, Nomi, Ishikawa 923-1292, Japan . e-mail: Source: http://www.openmx-square.org/download.html Files: * Copyright: 2002-2013, Taisuke Ozaki Partial Copyright 2002-2013 goes to Hiori Kino, Myung Joon Han, Jaejun Yu, Fumiyuki Ishii, Hongming Weng, Kiyoyuki Terakura, T.Ohwaki and M.Otani License: GPL-2+ Files: DFT_DATA13/* Copyright: Taisuke Ozaki License: GPL-2+ Comment: See also http://www.jaist.ac.jp/~t-ozaki/vps_pao2013/. Files: debian/* Copyright: 2007, Ondrej Certik 2007-2011, Debian Science Team 2013, Daniel Leidert Comment: This package was debianized by Ondrej Certik on Sat, 09 Jun 2007 12:41:34 +0000. The current Debian maintainer is Debian Scientific Comp. Team . License: GPL-2+ License: GPL-2+ 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 of the License, or (at your option) any later version. . This program 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 program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. Comment: On Debian Systems the complete text of the GNU General Public License version 2 can be found in the file `/usr/share/common-licenses/GPL-2'. debian/changelog0000664000000000000000000000563012255326525011055 0ustar openmx (3.7.6-1) unstable; urgency=medium * Team upload using dgit. * Build without sse on !amd64 platforms (closes: #724260) -- Dimitri John Ledkov Sat, 21 Dec 2013 15:00:54 +0000 openmx (3.7.6-0.1) unstable; urgency=low * Non-maintainer upload * New upstream release (closes: #716563). * debian/compat: Raised to compat level 8. * debian/control: Added openmx-data. (Build-Depends): Dropped xsltproc and docbook-xsl. Added mpi-default-dev and raised dh version to 8. (Standards-Version): Bumped to 3.9.4. (Vcs-Browser, Vcs-Svn): Fixed vcs-field-not-canonical. * debian/copyright: Updated. * debian/dirs : Dropped. * debian/get-orig-source.sh: Added uscan-compliant script to create the .orig tarball from the upstream source and patches. * debian/openmx.1: Added. * debian/openmx.install, debian/openmx-data.install: Added. * debian/openmx.manpages: Added. * debian/openmx.xml: Dropped in favor of debian/openmx.1. * debian/patches/data_path.patch: Added. - Set the path to the DFT tables. * debian/patches/fix_typos.patch: Added: - Fix all lintian reported typos. * debian/patches/makefile.patch: Updated. - Fix compiler and linker programs and flags. - Don't strip the program to be policy compliant. * debian/patches/series: Adjusted. * debian/rules: Rewritten for dh. Dropped orig-tarball target in favor of debian/get-orig-source.sh. * debian/watch: Updated. Added debian/get-orig-source.sh script call. -- Daniel Leidert Thu, 05 Sep 2013 17:00:46 +0200 openmx (3.5-1) unstable; urgency=low * Team upload * New upstream release * Ondrej Certik removed from uploaders (Closes: #550414) * XS-DM-Upload-Allowed: yes removed * Standards-Version bumped to 3.9.2 * Migrated to Debian Science * Switch to dpkg-source 3.0 (quilt) format -- Sylvestre Ledru Wed, 03 Aug 2011 01:22:39 +0200 openmx (3.2.4.dfsg-3) unstable; urgency=low * Add XS-DM-Upload-Allowed: yes * Use gfortran based Lapack (Closes: #466061) * /usr/sbin empty directory removed * Homepage moved to the homepage field * Standards-Version bumped to 3.7.3 * Use quilt for patches * Vcs-Svn and Vcs-Browser fields added -- Ondrej Certik Sat, 16 Feb 2008 12:30:31 +0100 openmx (3.2.4.dfsg-2) unstable; urgency=low [Ondrej Certik] * Depends on libfftw3-dev instead of fftw3-dev (Closes: #445786) * Ondrej Certik added to Uploaders. -- Christophe Prud'homme Mon, 08 Oct 2007 13:14:43 +0200 openmx (3.2.4.dfsg-1) unstable; urgency=low * New upstream release: applied patch #4 * Upload openmx to main (Closes: #428265) -- Christophe Prud'homme Sun, 22 Jul 2007 22:44:18 +0200 openmx (3.2-0oc1) unstable; urgency=low * Initial unofficial release (Closes: #428265) -- Ondrej Certik Sat, 09 Jun 2007 12:41:34 +0000 debian/openmx-data.install0000664000000000000000000000003412255325043012773 0ustar DFT_DATA* usr/share/openmx/ debian/openmx.manpages0000664000000000000000000000002012255325043012204 0ustar debian/openmx.1 debian/control0000664000000000000000000000414412255326577010614 0ustar Source: openmx Section: science Priority: extra Maintainer: Debian Science Team Uploaders: Christophe Prud'homme Build-Depends: debhelper (>= 8), gfortran, libblas-dev, libfftw3-dev (>= 3.1.2-3~), liblapack-dev, mpi-default-dev Standards-Version: 3.9.4 Homepage: http://www.openmx-square.org/ Vcs-Svn: svn://anonscm.debian.org/debian-science/packages/openmx/trunk Vcs-Browser: http://anonscm.debian.org/viewvc/debian-science/packages/openmx/trunk/ Package: openmx Architecture: any Depends: ${misc:Depends}, ${shlibs:Depends} Recommends: openmx-data Description: package for nano-scale material simulations OpenMX (Open source package for Material eXplorer) is a program package for nano-scale material simulations based on density functional theories (DFT), norm-conserving pseudopotentials and pseudo-atomic localized basis functions. Since the code is designed for the realization of large-scale ab initio calculations on parallel computers, it is anticipated that OpenMX can be a useful and powerful tool for nano-scale material sciences in a wide variety of systems such as biomaterials, carbon nanotubes, magnetic materials, and nanoscale conductors. Package: openmx-data Architecture: all Depends: ${misc:Depends} Description: package for nano-scale material simulations (data) OpenMX (Open source package for Material eXplorer) is a program package for nano-scale material simulations based on density functional theories (DFT), norm-conserving pseudopotentials and pseudo-atomic localized basis functions. Since the code is designed for the realization of large-scale ab initio calculations on parallel computers, it is anticipated that OpenMX can be a useful and powerful tool for nano-scale material sciences in a wide variety of systems such as biomaterials, carbon nanotubes, magnetic materials, and nanoscale conductors. . This package contains the 2013 database of fully relativistic pseudopotentials (VPS) and pseudo-atomic orbitals (PAO), generated by ADPACK. debian/rules0000775000000000000000000000034212255326111010245 0ustar #!/usr/bin/make -f # -*- makefile -*- # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 %: dh $@ --sourcedirectory=source/ override_dh_clean: dh_clean source/elpa1.mod find source -name "*openmx.oo" -delete debian/watch0000664000000000000000000000020712255325043010221 0ustar version=3 http://www.openmx-square.org/download.html ./bugfixed/.*?/patch([\d.]+)\.tar\.gz \ debian /bin/sh debian/get-orig-source.sh debian/get-orig-source.sh0000775000000000000000000000225412255325043012546 0ustar #!/bin/sh set -ex UPSTREAM_VERSION=$2 UPSTREAM_VERSION_RELEASE=`echo ${UPSTREAM_VERSION} | cut -d. -f 1,2` ORIG_TARBALL=$3 WORKING_DIR=`dirname ${ORIG_TARBALL}` REAL_TARBALL=`readlink -f ${ORIG_TARBALL}` REAL_TARBALL_RELEASE="${WORKING_DIR}/openmx${UPSTREAM_VERSION_RELEASE}.tar.gz" ORIG_TARBALL_DIR=`echo ${ORIG_TARBALL} | sed -e "s/_\(${UPSTREAM_VERSION}\)/-\1/g" -e "s/\.tar\.gz//g"` ORIG_TARBALL_DIR_STRIP=`basename ${ORIG_TARBALL_DIR}` [ -f ${REAL_TARBALL_RELEASE} ] || ( wget -P ${WORKING_DIR} http://www.openmx-square.org/openmx${UPSTREAM_VERSION_RELEASE}.tar.gz || exit 1 ) [ -d ${ORIG_TARBALL_DIR} ] && rm -rf ${ORIG_TARBALL_DIR} mkdir -p ${ORIG_TARBALL_DIR} # extract the source tar --directory=${ORIG_TARBALL_DIR} --strip 1 -zxvf ${REAL_TARBALL_RELEASE} || exit 1 # apply the patch as requested in README.txt tar --directory=${ORIG_TARBALL_DIR}/source -zxvf ${REAL_TARBALL} || exit 1 # remove the PDF without source - should we add +dfsg then? rm -f ${ORIG_TARBALL_DIR}/*.pdf rm -f ${ORIG_TARBALL} ${REAL_TARBALL} ${REAL_TARBALL_RELEASE} # create the archive GZIP=-9 tar --remove-files --directory ${WORKING_DIR} -czf ${ORIG_TARBALL} ${ORIG_TARBALL_DIR_STRIP} || exit 1 exit 0 debian/openmx.install0000664000000000000000000000001712255325043012065 0ustar usr/bin/openmx debian/patches/0000775000000000000000000000000012255331276010625 5ustar debian/patches/data_path.patch0000664000000000000000000000117612255325043013573 0ustar Author: Daniel Leidert Description: Set the data path accordingly to the Debian installation. Forwarded: not-needed --- a/source/Input_std.c +++ b/source/Input_std.c @@ -91,7 +91,7 @@ input_string("System.CurrrentDirectory",filepath,"./"); input_string("System.Name",filename,"default"); - input_string("DATA.PATH",DFT_DATA_PATH,"../DFT_DATA13"); + input_string("DATA.PATH",DFT_DATA_PATH,"/usr/share/openmx/DFT_DATA13"); input_int("level.of.stdout", &level_stdout,1); input_int("level.of.fileout",&level_fileout,1); input_logical("memory.usage.fileout",&memoryusage_fileout,0); /* default=off */ debian/patches/makefile.patch0000664000000000000000000000272612255326413013427 0ustar Author: Debian Science Team Reviewed-By: Daniel Leidert Description: Adjust the makefile for the Debian build. - Enable hardening. - Fix linkage step. - Don't strip binary to be policy compliant. Forwarded: not-needed --- a/source/makefile +++ b/source/makefile @@ -93,10 +93,17 @@ # LIB= -L/opt/acml5.3.0/ifort64_mp/lib -lacml_mp -liomp5 -Wl,-rpath=/opt/acml5.3.0/ifort64_mp/lib -Wl,-rpath=/opt/acml5.3.0/ifort64_mp/lib -L/opt/fftw-3.3.3/lib -lfftw3 -pgf90libs # +include /usr/share/dpkg/default.mk +ifeq ($(DEB_HOST_MULTIARCH),amd64) +DEB_SSE = +else +DEB_SSE = -Dnosse +endif -CC = mpicc -openmp -O3 -I/usr/local/include -FC = mpif90 -openmp -O3 -I/usr/local/include -LIB = -L/usr/local/lib -lfftw3 -llapack -lblas -lg2c -static + +CC = mpicc `dpkg-buildflags --get CPPFLAGS` `dpkg-buildflags --get CFLAGS` $(DEB_SSE) -fopenmp +FC = mpif90 `dpkg-buildflags --get CPPFLAGS` `dpkg-buildflags --get FFLAGS` -fopenmp +LIB = -lfftw3 -llapack -lblas `dpkg-buildflags --get LDFLAGS` @@ -202,7 +209,7 @@ All: $(PROG) openmx: $(OBJS) - $(CC) $(OBJS) $(STACK) $(LIB) -lm -o openmx + $(FC) $(OBJS) $(STACK) $(LIB) -lm -o openmx openmx.o: openmx.c openmx_common.h tran_variables.h tran_prototypes.h $(CC) -c openmx.c @@ -575,8 +582,8 @@ # install: $(PROG) - strip $(PROG) - cp $(PROG) $(DESTDIR)/$(PROG) + mkdir -p $(DESTDIR)/usr/bin/ + cp $(PROG) $(DESTDIR)/usr/bin/$(PROG) # # debian/patches/fix_typos.patch0000664000000000000000000001701312255325043013667 0ustar Author: Daniel Leidert Description: Fix at least the typos reported by lintian. Forwarded: no --- a/source/Generate_Wannier.c +++ b/source/Generate_Wannier.c @@ -1425,7 +1425,7 @@ printf("Using Hybrid Steepest Decent (SD) and Conjugate Gradient (CG) methods for Minimization.\n"); } if(Wannier_Min_Scheme==1 || Wannier_Min_Scheme==2){ - printf("In CG: intial search step length for Secant method %10.5f.\n",fabs(Wannier_Min_Secant_StepLength)); + printf("In CG: initial search step length for Secant method %10.5f.\n",fabs(Wannier_Min_Secant_StepLength)); printf("In CG: Number of steps for Secant method %i.\n",Wannier_Min_Secant_Steps); } printf("Criteria for minimization %e\n",Wannier_Min_Conv_Criterion); @@ -2631,7 +2631,7 @@ } else{ - printf(" ... ... Writting Mmn_zero(k,b) matrix into file.\n\n"); + printf(" ... ... Writing Mmn_zero(k,b) matrix into file.\n\n"); fprintf(fp,"Mmn_zero(k,b). band_num, kpt_num, bvector num, spinsize\n"); fprintf(fp,"%13d%13d%13d%13d\n",BANDNUM,kpt_num,tot_bvector,spinsize); } @@ -3001,7 +3001,7 @@ }/* spin */ /* Then we can find the initial guess for Utilde matrix which is usded for optimizing the omega_Tilde part */ Getting_Utilde(Amnk, spinsize, kpt_num, WANNUM, WANNUM, Utilde); - /* and update Mmnk matrix to that with intial guess M_opt= Utilde^dagger * M_zero * Utilde(k+b) */ + /* and update Mmnk matrix to that with initial guess M_opt= Utilde^dagger * M_zero * Utilde(k+b) */ Initial_Guess_Mmnkb(Utilde, spinsize, kpt_num, WANNUM, WANNUM, Mmnkb_zero, Mmnkb_dis, kg, frac_bv, tot_bvector, kplusb, Nk); /* Mmnkb_zero now is the disentangled WANNUMxWANNUM overlap matrix */ @@ -3010,7 +3010,7 @@ else{ /* NOT disentangle */ - /* update Mmnk matrix to that with intial guess M_opt= Utilde^dagger * M_zero * Utilde(k+b) */ + /* update Mmnk matrix to that with initial guess M_opt= Utilde^dagger * M_zero * Utilde(k+b) */ Initial_Guess_Mmnkb(Uk, spinsize, kpt_num, BANDNUM, WANNUM, Mmnkb_dis, Mmnkb_zero, kg, frac_bv, tot_bvector, kplusb, Nk); /* Mmnkb_zero now is the disentangled WANNUMxWANNUM overlap matrix */ for(k=0;k(abc[k]+smallvalue)){ break; /* no search for vector[k]-vector[(k+1k%2)%3], break to + case */ } @@ -1836,7 +1836,7 @@ rlatt[k][1]=rlatt[k][1]+rlatt[(k+1+k%2)%3][1]; rlatt[k][2]=rlatt[k][2]+rlatt[(k+1+k%2)%3][2]; absv=sqrt(rlatt[k][0]*rlatt[k][0]+rlatt[k][1]*rlatt[k][1]+rlatt[k][2]*rlatt[k][2]); - /* printf("%2d+%2d vector: new lenght is %10.5f, old one is %10.5f\n",k,(k+1)%3,absv,abc[k]);*/ + /* printf("%2d+%2d vector: new length is %10.5f, old one is %10.5f\n",k,(k+1)%3,absv,abc[k]);*/ if(absv>(abc[k]+smallvalue)){ break;/* no search for vector[k]+vector[(k+1+k%2)%3], break */ } @@ -1857,7 +1857,7 @@ rlatt[k][1]=rlatt[k][1]-rlatt[(k+2-k%2)%3][1]; rlatt[k][2]=rlatt[k][2]-rlatt[(k+2-k%2)%3][2]; absv=sqrt(rlatt[k][0]*rlatt[k][0]+rlatt[k][1]*rlatt[k][1]+rlatt[k][2]*rlatt[k][2]); - /* printf("%2d-%2d vector: new lenght is %10.5f, old one is %10.5f\n",k,(k+2)%3,absv,abc[k]);*/ + /* printf("%2d-%2d vector: new length is %10.5f, old one is %10.5f\n",k,(k+2)%3,absv,abc[k]);*/ if(absv>(abc[k]+smallvalue)){ break; /* no search for vector[k]-vector[(k+2-k%2)%3], break to + case */ } @@ -1877,7 +1877,7 @@ rlatt[k][1]=rlatt[k][1]+rlatt[(k+2-k%2)%3][1]; rlatt[k][2]=rlatt[k][2]+rlatt[(k+2-k%2)%3][2]; absv=sqrt(rlatt[k][0]*rlatt[k][0]+rlatt[k][1]*rlatt[k][1]+rlatt[k][2]*rlatt[k][2]); - /* printf("%2d+%2d vector: new lenght is %10.5f, old one is %10.5f\n",k,(k+2)%3,absv,abc[k]);*/ + /* printf("%2d+%2d vector: new length is %10.5f, old one is %10.5f\n",k,(k+2)%3,absv,abc[k]);*/ if(absv>(abc[k]+smallvalue)){ break;/* no search for vector[k]+vector[(k+2-k%2)%3], break */ } @@ -2043,7 +2043,7 @@ cell_parameters[2]=c/a; } }else{/*all angles are equal but not right angle, it would be cF, cI, or hR*/ - if(fabs(a-b)smallvalue && (a*a+b*b+2.0*a*b*cos(gamma)-(a*a+c*c+2.0*a*c*cos(beta)))>smallvalue){ --- a/source/Set_Allocate_Atom2CPU.c +++ b/source/Set_Allocate_Atom2CPU.c @@ -413,7 +413,7 @@ if (myid==Host_ID && 1<=MD_iter && 0