Hi, I've uploaded openmx 3.7.6-0.1 to the DELAYED/15 queue. It would close the currently open issue and update openmx to the latest version. I made some changes to the packaging files. The debdiff is attached. Feel free to comment on it. If you are ok with it, it will hit the NEW queue in 15 days (it introduces openmx-data, which ships the DFT tables).
Note, that I'm not planning to take over maintenance nor to add myself as uploader. Regards, Daniel
diff -Nru openmx-3.5/debian/changelog openmx-3.7.6/debian/changelog --- openmx-3.5/debian/changelog 2011-08-03 01:30:21.000000000 +0200 +++ openmx-3.7.6/debian/changelog 2013-09-05 15:05:49.000000000 +0200 @@ -1,3 +1,35 @@ +openmx (3.7.6-0.1) UNRELEASED; urgency=low + + * Non-maintainer upload + * New upstream release. + * 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 <dleid...@debian.org> Thu, 05 Sep 2013 12:42:35 +0200 + openmx (3.5-1) unstable; urgency=low * Team upload diff -Nru openmx-3.5/debian/compat openmx-3.7.6/debian/compat --- openmx-3.5/debian/compat 2011-08-03 01:19:15.000000000 +0200 +++ openmx-3.7.6/debian/compat 2013-09-05 13:47:15.000000000 +0200 @@ -1 +1 @@ -5 +8 diff -Nru openmx-3.5/debian/control openmx-3.7.6/debian/control --- openmx-3.5/debian/control 2011-08-03 01:22:46.000000000 +0200 +++ openmx-3.7.6/debian/control 2013-09-05 16:11:38.000000000 +0200 @@ -3,17 +3,22 @@ Priority: extra Maintainer: Debian Science Team <debian-science-maintain...@lists.alioth.debian.org> Uploaders: Christophe Prud'homme <prudh...@debian.org> -Build-Depends: debhelper (>= 5), libfftw3-dev (>= 3.1.2-3), xsltproc, - docbook-xsl, liblapack-dev, gfortran -Standards-Version: 3.9.2 +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://svn.debian.org/debian-science/packages/openmx/trunk -Vcs-Browser: http://svn.debian.org/wsvn/debian-science/packages/openmx/trunk/ +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: ${shlibs:Depends}, ${misc:Depends} -Description: Package for nano-scale material simulations +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 @@ -22,3 +27,19 @@ 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. diff -Nru openmx-3.5/debian/copyright openmx-3.7.6/debian/copyright --- openmx-3.5/debian/copyright 2011-08-03 01:19:15.000000000 +0200 +++ openmx-3.7.6/debian/copyright 2013-09-05 15:29:53.000000000 +0200 @@ -1,57 +1,49 @@ -This package was debianized by Ondrej Certik <ond...@certik.cz> on -Sat, 09 Jun 2007 12:41:34 +0000. - -The current Debian maintainer is Debian Scientific Computing Team - -It was downloaded from http://www.openmx-square.org/. The upstream tarball was -unpacked, the patch (also from upstream) applied and the file openmx3.2.pdf -removed, because its source is not included. You can use: - -debian/rules orig-tarball - -to perform all of the operations above to generate the dfsg.orig.tar.gz. - -Upstream Author: - - Taisuke Ozaki - - Present (Jan/01/2006) official address - - RICS, National Institute of Advanced Industrial Science - and Technology (AIST), central 2, 1-1-1 Umezono, Tsukuba, - Ibaraki 305-8568, Japan - - e-mail: t-oz...@aist.go.jp - -Copyright: - - Copyright (C) 2002-2007 Taisuke Ozaki - - The file source/Inputtools.c is Copyright (C), 2002, Hiori Kino. - - The file source/jx.c is Copyright (C), 2003, Myung Joon Han, Jaejun Yu, and - Taisuke Ozaki. - - The file source/polB.c is Copyright (C), 2006-2007, Fumiyuki Ishii and - Taisuke Ozaki. - -License: - - Copyright (C) 2002-2007 Taisuke Ozaki - - 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. - -The Debian packaging is (C) 2007, Ondrej Certik <ond...@certik.cz> and -is licensed under the GPL, see `/usr/share/common-licenses/GPL'. +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: <t-oz...@jaist.ac.jp> +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 <ond...@certik.cz> + 2007-2011, Debian Science Team <debian-science-maintainers@l.a.d.o> + 2013, Daniel Leidert <dleid...@debian.org> +Comment: This package was debianized by Ondrej Certik <ond...@certik.cz> on + Sat, 09 Jun 2007 12:41:34 +0000. The current Debian maintainer is Debian + Scientific Comp. Team <debian-science-maintain...@lists.alioth.debian.org>. +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'. diff -Nru openmx-3.5/debian/dirs openmx-3.7.6/debian/dirs --- openmx-3.5/debian/dirs 2011-08-03 01:19:15.000000000 +0200 +++ openmx-3.7.6/debian/dirs 1970-01-01 01:00:00.000000000 +0100 @@ -1,2 +0,0 @@ -usr/bin -usr/sbin diff -Nru openmx-3.5/debian/get-orig-source.sh openmx-3.7.6/debian/get-orig-source.sh --- openmx-3.5/debian/get-orig-source.sh 1970-01-01 01:00:00.000000000 +0100 +++ openmx-3.7.6/debian/get-orig-source.sh 2013-09-05 15:11:59.000000000 +0200 @@ -0,0 +1,31 @@ +#!/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 diff -Nru openmx-3.5/debian/openmx.1 openmx-3.7.6/debian/openmx.1 --- openmx-3.5/debian/openmx.1 1970-01-01 01:00:00.000000000 +0100 +++ openmx-3.7.6/debian/openmx.1 2013-09-05 13:47:15.000000000 +0200 @@ -0,0 +1,26 @@ +.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 <\&ond...@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. diff -Nru openmx-3.5/debian/openmx-data.install openmx-3.7.6/debian/openmx-data.install --- openmx-3.5/debian/openmx-data.install 1970-01-01 01:00:00.000000000 +0100 +++ openmx-3.7.6/debian/openmx-data.install 2013-09-05 15:30:54.000000000 +0200 @@ -0,0 +1 @@ +DFT_DATA* usr/share/openmx/ diff -Nru openmx-3.5/debian/openmx.install openmx-3.7.6/debian/openmx.install --- openmx-3.5/debian/openmx.install 1970-01-01 01:00:00.000000000 +0100 +++ openmx-3.7.6/debian/openmx.install 2013-09-05 15:53:57.000000000 +0200 @@ -0,0 +1 @@ +usr/bin/openmx diff -Nru openmx-3.5/debian/openmx.manpages openmx-3.7.6/debian/openmx.manpages --- openmx-3.5/debian/openmx.manpages 1970-01-01 01:00:00.000000000 +0100 +++ openmx-3.7.6/debian/openmx.manpages 2013-09-05 13:47:15.000000000 +0200 @@ -0,0 +1 @@ +debian/openmx.1 diff -Nru openmx-3.5/debian/openmx.xml openmx-3.7.6/debian/openmx.xml --- openmx-3.5/debian/openmx.xml 2011-08-03 01:19:15.000000000 +0200 +++ openmx-3.7.6/debian/openmx.xml 1970-01-01 01:00:00.000000000 +0100 @@ -1,103 +0,0 @@ -<?xml version='1.0' encoding='ISO-8859-1'?> -<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.2//EN" -"http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd"; [ - -<!-- - -Process this file with an XSLT processor: `xsltproc \ --''-nonet /usr/share/sgml/docbook/stylesheet/xsl/nwalsh/\ -manpages/docbook.xsl manpage.dbk'. A manual page -<package>.<section> will be generated. You may view the -manual page with: nroff -man <package>.<section> | less'. A -typical entry in a Makefile or Makefile.am is: - -DB2MAN=/usr/share/sgml/docbook/stylesheet/xsl/nwalsh/\ -manpages/docbook.xsl -XP=xsltproc -''-nonet - -manpage.1: manpage.dbk - $(XP) $(DB2MAN) $< - -The xsltproc binary is found in the xsltproc package. The -XSL files are in docbook-xsl. Please remember that if you -create the nroff version in one of the debian/rules file -targets (such as build), you will need to include xsltproc -and docbook-xsl in your Build-Depends control field. - ---> - - <!-- Fill in your name for FIRSTNAME and SURNAME. --> - <!ENTITY dhfirstname "<firstname>Ondrej</firstname>"> - <!ENTITY dhsurname "<surname>Certik</surname>"> - <!-- Please adjust the date whenever revising the manpage. --> - <!ENTITY dhdate "<date>June 9, 2007</date>"> - <!-- SECTION should be 1-8, maybe w/ subsection other parameters are - allowed: see man(7), man(1). --> - <!ENTITY dhsection "<manvolnum>1</manvolnum>"> - <!ENTITY dhemail "<email>ond...@certik.cz</email>"> - <!ENTITY dhusername "Ondrej Certik"> - <!ENTITY dhucpackage "<refentrytitle>OPENMX</refentrytitle>"> - <!ENTITY dhpackage "openmx"> - - <!ENTITY debian "<productname>Debian</productname>"> - <!ENTITY gnu "<acronym>GNU</acronym>"> - <!ENTITY gpl "&gnu; <acronym>GPL</acronym>"> -]> - -<refentry> - <refentryinfo> - <address> - &dhemail; - </address> - <copyright> - <year>2007</year> - <holder>&dhusername;</holder> - </copyright> - &dhdate; - </refentryinfo> - <refmeta> - &dhucpackage; - - &dhsection; - </refmeta> - <refnamediv> - <refname>&dhpackage;</refname> - - <refpurpose>Package for nano-scale material simulations</refpurpose> - </refnamediv> - <refsynopsisdiv> - <cmdsynopsis> - <command>&dhpackage;</command> - - <arg>file</arg> - </cmdsynopsis> - </refsynopsisdiv> - <refsect1> - <title>DESCRIPTION</title> - - <para>This manual page documents briefly the - <command>&dhpackage;</command> command.</para> - - <para><command>&dhpackage;</command> is a program that calculates - electronic structure using DFT.</para> - - <para>The program doesn't accept any other options, everything is given in - the file specified at the command line.</para> - - </refsect1> - <refsect1> - <title>AUTHOR</title> - - <para>This manual page was written by &dhusername; &dhemail; for - the &debian; system (but may be used by others). Permission is - granted to copy, distribute and/or modify this document under - the terms of the &gnu; General Public License, Version 2 any - later version published by the Free Software Foundation. - </para> - <para> - On Debian systems, the complete text of the GNU General Public - License can be found in /usr/share/common-licenses/GPL. - </para> - - </refsect1> -</refentry> diff -Nru openmx-3.5/debian/patches/data_path.patch openmx-3.7.6/debian/patches/data_path.patch --- openmx-3.5/debian/patches/data_path.patch 1970-01-01 01:00:00.000000000 +0100 +++ openmx-3.7.6/debian/patches/data_path.patch 2013-09-05 15:33:51.000000000 +0200 @@ -0,0 +1,15 @@ +Author: Daniel Leidert <dleid...@debian.org> +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 */ diff -Nru openmx-3.5/debian/patches/fix_typos.patch openmx-3.7.6/debian/patches/fix_typos.patch --- openmx-3.5/debian/patches/fix_typos.patch 1970-01-01 01:00:00.000000000 +0100 +++ openmx-3.7.6/debian/patches/fix_typos.patch 2013-09-05 15:18:48.000000000 +0200 @@ -0,0 +1,140 @@ +Author: Daniel Leidert <dleid...@debian.org> +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<kpt_num;k++){ +@@ -4537,7 +4537,7 @@ + printf("* Error in openning file for Amn(k).\n"); + printf("******************************************************************\n"); + }else{ +- printf(" ... ... Writting Amn(k) matrix into file.\n\n"); ++ printf(" ... ... Writing Amn(k) matrix into file.\n\n"); + fprintf(fp,"Amn. Fist line BANDNUM, KPTNUM, WANNUM, spinsize. Next is m n k and elements.Spin is the most outer loop.\n"); + fprintf(fp,"%13d%13d%13d%13d\n",band_num,kpt_num,wan_num,spinsize); + } +--- a/source/Generating_MP_Special_Kpt.c ++++ b/source/Generating_MP_Special_Kpt.c +@@ -406,9 +406,9 @@ + /* Number of primitive unit cell contained in the original lattice */ + int npcell; + /*cell_parameters is for unit cell's lattice parameters: +- cell_parameters[0] lenght of a vector +- cell_parameters[1] lenght of b vector +- cell_parameters[2] lenght of c vector ++ cell_parameters[0] length of a vector ++ cell_parameters[1] length of b vector ++ cell_parameters[2] length of c vector + cell_parameters[3] angle between b and c vector in radian (alpha) + cell_parameters[4] angle between a and c vector in radian (beta) + cell_parameters[5] angle between a and b vector in radian (gamma) +@@ -1816,7 +1816,7 @@ + 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+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&&fabs(b-c)<smallvalue){ /*all the vectors' lenght are equal */ ++ if(fabs(a-b)<smallvalue&&fabs(b-c)<smallvalue){ /*all the vectors' length are equal */ + if(fabs(cos(alpha)-1.0/2.0)<smallvalue){/* if all angles are 60 degree, it is Face-centred cubic (cF) */ + bravais_type = 3; + cell_parameters[0]=sqrt(2.0)*a; +@@ -2063,7 +2063,7 @@ + }else if(fabs(alpha-beta)<smallvalue){ + if(fabs(alpha-pi/2.0)<smallvalue){/* If two equal angles are right angle, it would be hP, oC or mP */ + if(fabs(a-b)<smallvalue){ +- /*If the two vectors perpendicular and their lenghts are equal, it would be hP or oC instead of mP*/ ++ /*If the two vectors perpendicular and their lengths are equal, it would be hP or oC instead of mP*/ + if(fabs(cos(gamma)+1.0/2.0)<smallvalue){ /*If gamma is 120 degree, it is hP*/ + bravais_type = 4; + cell_parameters[0]=a; +@@ -2138,7 +2138,7 @@ + Attention! Generally the lattice vectors are chosen so that alpha=beta + */ + }else{/* all of the angles are different */ +- if(fabs(a-b)<smallvalue&&fabs(b-c)<smallvalue){/*all the vectors' lenght are equal, oI*/ ++ if(fabs(a-b)<smallvalue&&fabs(b-c)<smallvalue){/*all the vectors' length are equal, oI*/ + if(fabs(c*c+a*b*cos(gamma)+a*c*cos(beta)+b*c*cos(alpha))<smallvalue + && (a*a+c*c+2.0*a*c*cos(beta)-(c*c+b*b+2.0*c*b*cos(alpha)))>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<level_stdout){ + printf("\n"); + printf("*******************************************************\n"); +- printf(" Allocation of atoms to proccesors at MD_iter=%5d \n", MD_iter ); ++ printf(" Allocation of atoms to processors at MD_iter=%5d \n", MD_iter ); + printf("*******************************************************\n\n"); + } + diff -Nru openmx-3.5/debian/patches/makefile.patch openmx-3.7.6/debian/patches/makefile.patch --- openmx-3.5/debian/patches/makefile.patch 2011-08-03 09:32:00.000000000 +0200 +++ openmx-3.7.6/debian/patches/makefile.patch 2013-09-05 15:46:12.000000000 +0200 @@ -1,23 +1,42 @@ -Index: openmx-3.5/source/makefile -=================================================================== ---- openmx-3.5.orig/source/makefile 2011-08-03 09:19:11.000000000 +0200 -+++ openmx-3.5/source/makefile 2011-08-03 09:19:43.000000000 +0200 -@@ -95,8 +95,8 @@ +Author: Debian Science Team <debian-science-maintain...@lists.alioth.debian.org> +Reviewed-By: Daniel Leidert <dleid...@debian.org> +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 +@@ -94,9 +94,9 @@ # --CC = gcc -O3 -Dnompi -Dnoomp -I/usr/local/include -I/home/ozaki/include --LIB = -L/usr/local/lib -lfftw3 -llapack -lblas -lg2c -static -+CC = gcc -O3 -Dnompi -Dnoomp -+LIB = -lfftw3 -llapack -lblas +-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` -fopenmp ++FC = mpif90 `dpkg-buildflags --get CPPFLAGS` `dpkg-buildflags --get FFLAGS` -fopenmp ++LIB = -lfftw3 -llapack -lblas `dpkg-buildflags --get LDFLAGS` -@@ -554,7 +554,7 @@ +@@ -202,7 +202,7 @@ + All: $(PROG) - install: $(PROG) - strip $(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 +575,8 @@ + # + + install: $(PROG) +- strip $(PROG) - cp $(PROG) $(DESTDIR)/$(PROG) ++ mkdir -p $(DESTDIR)/usr/bin/ + cp $(PROG) $(DESTDIR)/usr/bin/$(PROG) # diff -Nru openmx-3.5/debian/patches/series openmx-3.7.6/debian/patches/series --- openmx-3.5/debian/patches/series 2011-08-03 09:23:17.000000000 +0200 +++ openmx-3.7.6/debian/patches/series 2013-09-05 15:34:40.000000000 +0200 @@ -1 +1,3 @@ +data_path.patch makefile.patch +fix_typos.patch diff -Nru openmx-3.5/debian/rules openmx-3.7.6/debian/rules --- openmx-3.5/debian/rules 2011-08-03 01:25:14.000000000 +0200 +++ openmx-3.7.6/debian/rules 2013-09-05 15:39:20.000000000 +0200 @@ -1,89 +1,12 @@ #!/usr/bin/make -f # -*- makefile -*- -# Sample debian/rules that uses debhelper. -# This file was originally written by Joey Hess and Craig Small. -# As a special exception, when this file is copied by dh-make into a -# dh-make output file, you may use that output file without restriction. -# This special exception was added by Craig Small in version 0.37 of dh-make. # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 +%: + dh $@ --sourcedirectory=source/ -configure: configure-stamp -configure-stamp: - dh_testdir - touch configure-stamp - -DB2MAN=/usr/share/sgml/docbook/stylesheet/xsl/nwalsh/manpages/docbook.xsl -XP=xsltproc -''-nonet - -build: build-stamp - -build-stamp: configure-stamp - dh_testdir - - cd source;$(MAKE) - $(XP) $(DB2MAN) debian/openmx.xml - - touch $@ - -clean: - dh_testdir - dh_testroot - rm -f build-stamp configure-stamp - - cd source;$(MAKE) clean - rm -rf .pc/ - - dh_clean - -install: build - dh_testdir - dh_testroot - dh_clean -k - dh_installdirs - - # Add here commands to install the package into debian/openmx. - cd source;$(MAKE) DESTDIR=$(CURDIR)/debian/openmx install - rm -r $(CURDIR)/debian/openmx/usr/sbin - - -# Build architecture-independent files here. -binary-indep: build install -# We have nothing to do by default. - -# Build architecture-dependent files here. -binary-arch: build install - dh_testdir - dh_testroot - dh_installchangelogs - dh_installdocs - dh_installexamples - dh_installman openmx.1 - dh_link - dh_strip - dh_compress - dh_fixperms - dh_installdeb - dh_shlibdeps - dh_gencontrol - dh_md5sums - dh_builddeb - -binary: binary-indep binary-arch -.PHONY: build clean binary-indep binary-arch binary install configure - -orig-tarball: - mkdir tmp; \ - cd tmp; \ - wget http://www.openmx-square.org/openmx3.2.tar.gz; \ - wget http://www.openmx-square.org/bugfixed/07July02/patch3.2.4.tar.gz; \ - tar xzf openmx3.2.tar.gz; \ - cd openmx3.2/source/; \ - tar xzf ../../patch3.2.4.tar.gz; \ - cd .. ; \ - rm openmx3.2.pdf; \ - cd .. ; \ - tar czf ../openmx_3.2.4.dfsg.orig.tar.gz openmx3.2; \ - cd ..; rm -rf tmp +override_dh_clean: + dh_clean source/elpa1.mod + find source -name "*openmx.oo" -delete diff -Nru openmx-3.5/debian/watch openmx-3.7.6/debian/watch --- openmx-3.5/debian/watch 2011-08-03 01:19:15.000000000 +0200 +++ openmx-3.7.6/debian/watch 2013-09-05 13:47:15.000000000 +0200 @@ -1,2 +1,3 @@ version=3 -http://www.openmx-square.org/download.html ./openmx([\d\.]+)\.tar\.gz +http://www.openmx-square.org/download.html ./bugfixed/.*?/patch([\d.]+)\.tar\.gz \ + debian /bin/sh debian/get-orig-source.sh
