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authorJustin Lecher (jlec) <jlec@j-schmitz.net>2009-11-13 11:09:59 +0100
committerJustin Lecher (jlec) <jlec@j-schmitz.net>2009-11-13 12:19:07 +0100
commit5ba58293d135dc945b85485d6939b484538d8fc8 (patch)
treeae3761cb9ffabe201d7cc1db21e0ada27010d52f
parentremoved ntl, in main tree (diff)
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sci-chemistry/smmp ifrst checkin
(Portage version: 2.2_rc49/git/Linux i686) (Signed Manifest commit)
-rw-r--r--sci-chemistry/smmp/ChangeLog10
-rw-r--r--sci-chemistry/smmp/Manifest15
-rw-r--r--sci-chemistry/smmp/files/3.0.5-flags.patch81
-rw-r--r--sci-chemistry/smmp/metadata.xml8
-rw-r--r--sci-chemistry/smmp/smmp-3.0.5.ebuild57
5 files changed, 171 insertions, 0 deletions
diff --git a/sci-chemistry/smmp/ChangeLog b/sci-chemistry/smmp/ChangeLog
new file mode 100644
index 000000000..6d26191dc
--- /dev/null
+++ b/sci-chemistry/smmp/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-chemistry/smmp
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*smmp-3.0.5 (13 Nov 2009)
+
+ 13 Nov 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+ +files/3.0.5-flags.patch, +smmp-3.0.5.ebuild, +metadata.xml:
+ Initial ebuild, written by me
+
diff --git a/sci-chemistry/smmp/Manifest b/sci-chemistry/smmp/Manifest
new file mode 100644
index 000000000..ac755e53b
--- /dev/null
+++ b/sci-chemistry/smmp/Manifest
@@ -0,0 +1,15 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
+AUX 3.0.5-flags.patch 2801 RMD160 ace7706b1f1e47def71176994bdf96ad24d2ddfb SHA1 ec19536f048b7ba3635c14a9f60ddbe4ccc730a4 SHA256 c05d6fa67dcfb3e5cced5efaff07e4a7422903df6ae1ce15576cefafe985c0ef
+DIST SMMP-3.0.5.tar.bz2 233378 RMD160 a951eb826c3af743aae4156fb21bffe028d68846 SHA1 fda498e9aac93efcf57787da4aa190ec3f70f1c7 SHA256 70d6b719d2c2ef1d34fd9897ad1c89a37c4d7531d80c904eee39dc8855aca31c
+EBUILD smmp-3.0.5.ebuild 940 RMD160 adb9bd06999974a3a8455c2073c38943c2732a50 SHA1 682df3c78f3f28ac08a13efb8d30b7e533dae722 SHA256 c15472df6de248aaaec9aa2ca02b8d5758ced836a63bf1d8bbd52127212486b5
+MISC ChangeLog 299 RMD160 82f448f3ecda1dbeb58d3374956880704566f395 SHA1 486c7d8ffad439e711c3159a5a0dd635c4c0cf27 SHA256 db4d048669de7da1dc7d3a4967541b23dd898353224ea1f1250319b8cf9fd87e
+MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.11 (GNU/Linux)
+
+iEYEARECAAYFAkr9MHcACgkQgAnW8HDreRZGTQCfYVzEReqvoEPgwPb4Xr3aocqC
+iMAAmQEGC+zLNdreuo+znKtW7UHTF7vr
+=RWhH
+-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/smmp/files/3.0.5-flags.patch b/sci-chemistry/smmp/files/3.0.5-flags.patch
new file mode 100644
index 000000000..6e37fdba8
--- /dev/null
+++ b/sci-chemistry/smmp/files/3.0.5-flags.patch
@@ -0,0 +1,81 @@
+diff --git a/Makefile b/Makefile
+index adf6cda..5104567 100644
+--- a/Makefile
++++ b/Makefile
+@@ -3,15 +3,15 @@
+ #.SILENT:
+
+ %_p.o : %_p.f
+- $(MPIF90) $(F_FLAGS) $<
++ $(FC) $(CFLAGS) -c $<
+
+ .SUFFIXES: .o .f
+ .f.o:
+- $(F90) $(F_FLAGS) $<
++ $(FC) $(CFLAGS) -c $<
+
+ .SUFFIXES: .o .f90
+ .f90.o:
+- $(F90) $(F_FLAGS) $<
++ $(FC) $(CFLAGS) -c $<
+
+ # ==================================== Variables for compiling and linking
+ # L_FLAGS=-g
+@@ -87,11 +87,11 @@ anneal canon outpdb minim regul contacts interhbond hbond
+ # ============================================== Linking
+
+ $(PROG): $(OBJ) $(SOBJ) main.o
+- $(F90) -o $(PROG) $(L_FLAGS) main.o $(OBJ) $(SOBJ)
++ $(FC) $(LDFLAGS) $(CFLAGS) -o $(PROG) main.o $(OBJ) $(SOBJ)
+
+ # Build parallel version of SMMP.
+ parallel: $(OBJ) $(POBJ) main_p.o
+- $(MPIF90) -o $(PROG) $(L_FLAGS) main_p.o $(OBJ) $(POBJ)
++ $(FC) $(LDFLAGS) $(CFLAGS) -o $(PROG) main_p.o $(OBJ) $(POBJ)
+
+ # Cross compile for BlueGene/P
+ bgl: BGL_L_FLAGS = -L$(BGLSYS)/lib -lmpich.rts -lfmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts -qextname=flush
+diff --git a/EXAMPLES/Makefile b/EXAMPLES/Makefile
+index e30d086..1ccf590 100644
+--- a/EXAMPLES/Makefile
++++ b/EXAMPLES/Makefile
+@@ -2,15 +2,15 @@
+
+ #.SILENT:
+ %_p.o : %_p.f
+- $(MPIF90) $(F_FLAGS) $<
++ $(FC) $(CFLAGS) -c $<
+
+ .SUFFIXES: .o .f
+ .f.o:
+- $(F90) $(F_FLAGS) $<
++ $(FC) $(CFLAGS) -c $<
+
+ .SUFFIXES: .o .f90
+ .f90.o:
+- $(F90) $(F_FLAGS) $<
++ $(FC) $(CFLAGS) -c $<
+
+ # ==================================== Variables for compiling and linking
+ # L_FLAGS=-O0 -g
+@@ -59,16 +59,16 @@ MCOBJ = ../canon.o ../metropolis.o ../rgyr.o
+ all: minimization annealing multicanonical regularization parallel_tempering_s # rootmeansquaredev
+
+ minimization: $(BASEOBJ) $(ENOBJ) minimization.o
+- $(F90) -o minimization $(L_FLAGS) $(BASEOBJ) $(ENOBJ) minimization.o
++ $(F90) $(LDFLAGS) -o minimization $(BASEOBJ) $(ENOBJ) minimization.o
+
+ annealing: $(BASEOBJ) $(MCOBJS) $(ENOBJ) annealing.o
+- $(F90) -o annealing $(L_FLAGS) $(BASEOBJ) $(MCOBJ) $(ENOBJ) ../anneal.o ../zimmer.o annealing.o
++ $(F90) $(LDFLAGS) -o annealing $(BASEOBJ) $(MCOBJ) $(ENOBJ) ../anneal.o ../zimmer.o annealing.o
+
+ multicanonical: $(BASEOBJ) $(MCOBJS) $(ENOBJ) multicanonical.o ../mulcan_par_mod.o
+- $(F90) -o multicanonical $(L_FLAGS) $(BASEOBJ) $(MCOBJ) $(ENOBJ) multicanonical.o ../mulcan_par_mod.o
++ $(F90) $(LDFLAGS) -o multicanonical $(BASEOBJ) $(MCOBJ) $(ENOBJ) multicanonical.o ../mulcan_par_mod.o
+
+ regularization: $(BASEOBJ) $(ENOBJ) regularization.o
+- $(F90) -o regularization $(L_FLAGS) $(BASEOBJ) $(ENOBJ) regularization.o
++ $(F90) $(LDFLAGS) -o regularization $(BASEOBJ) $(ENOBJ) regularization.o
+
+ # rootmeansquaredev: $(BASEOBJ) $(ENOBJ) rootmeansquaredev.o
+ # $(F90) -o rootmeansquaredev $(L_FLAGS) $(BASEOBJ) $(ENOBJ) rootmeansquaredev.o
diff --git a/sci-chemistry/smmp/metadata.xml b/sci-chemistry/smmp/metadata.xml
new file mode 100644
index 000000000..efb490d78
--- /dev/null
+++ b/sci-chemistry/smmp/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<maintainer>
+ <email>sci@gentoo.org</email>
+</maintainer>
+</pkgmetadata>
diff --git a/sci-chemistry/smmp/smmp-3.0.5.ebuild b/sci-chemistry/smmp/smmp-3.0.5.ebuild
new file mode 100644
index 000000000..e2c200d63
--- /dev/null
+++ b/sci-chemistry/smmp/smmp-3.0.5.ebuild
@@ -0,0 +1,57 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="2"
+
+inherit eutils toolchain-funcs
+
+MY_PN="SMMP"
+MY_P="${MY_PN}-${PV}"
+
+DESCRIPTION="Simple Molecular Mechanics for Proteins"
+HOMEPAGE="http://smmp.berlios.de/"
+SRC_URI="mirror://berlios/${PN}/${MY_P}.tar.bz2"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+LICENSE="GPL-2"
+IUSE="doc mpi test"
+
+RDEPEND="mpi? ( virtual/mpi )"
+DEPEND="${RDEPEND}
+ doc? ( app-doc/doxygen )"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+ epatch "${FILESDIR}"/${PV}-flags.patch
+}
+
+src_compile() {
+ if use mpi; then
+ FC="mpif90"
+ target="parallel"
+ else
+ FC=$(tc-getFC)
+ target="${PN}"
+ fi
+
+ emake FC=${FC} ${target} || die
+
+ if use test; then
+ emake FC=${FC} examples || die
+ fi
+}
+
+src_test() {
+ cd EXAMPLES
+ bash smmp.cmd || die
+}
+
+src_install() {
+ dobin ${PN} || die
+ insinto $(python_get_sitedir)/${PN}
+ doins *.py || die
+ dodoc README || die
+}