1 |
commit: bbe17657b55b52de681189473db11225a8f82f2f |
2 |
Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> |
3 |
AuthorDate: Thu Jul 28 13:08:27 2011 +0000 |
4 |
Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> |
5 |
CommitDate: Thu Jul 28 13:08:27 2011 +0000 |
6 |
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bbe17657 |
7 |
|
8 |
[sci-chemistry/ambertools] Moved to tree =D |
9 |
|
10 |
--- |
11 |
sci-chemistry/ambertools/ChangeLog | 29 -- |
12 |
sci-chemistry/ambertools/ambertools-1.4.ebuild | 133 ------- |
13 |
sci-chemistry/ambertools/ambertools-1.5-r1.ebuild | 140 ------- |
14 |
sci-chemistry/ambertools/ambertools-1.5.ebuild | 140 ------- |
15 |
.../ambertools/files/ambertools-1.4-gentoo.patch | 289 --------------- |
16 |
.../ambertools/files/ambertools-1.5-gentoo.patch | 386 -------------------- |
17 |
sci-chemistry/ambertools/metadata.xml | 10 - |
18 |
7 files changed, 0 insertions(+), 1127 deletions(-) |
19 |
|
20 |
diff --git a/sci-chemistry/ambertools/ChangeLog b/sci-chemistry/ambertools/ChangeLog |
21 |
deleted file mode 100644 |
22 |
index d51fa1a..0000000 |
23 |
--- a/sci-chemistry/ambertools/ChangeLog |
24 |
+++ /dev/null |
25 |
@@ -1,29 +0,0 @@ |
26 |
-# ChangeLog for sci-chemistry/ambertools |
27 |
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 |
28 |
-# $Header: $ |
29 |
- |
30 |
- 24 Jun 2011; Justin Lecher <jlec@g.o> ambertools-1.4.ebuild, |
31 |
- -files/ambertools-1.4-bugfix_1-18.patch, ambertools-1.5.ebuild, |
32 |
- -files/ambertools-1.5-bugfix_1-3.patch: |
33 |
- Cleaned ebuild |
34 |
- |
35 |
- 23 Jun 2011; Justin Lecher <jlec@g.o> ambertools-1.4.ebuild, |
36 |
- ambertools-1.5.ebuild: |
37 |
- Streamlined fortran-2 eclass usage |
38 |
- |
39 |
- 21 Jun 2011; Justin Lecher <jlec@g.o> ambertools-1.4.ebuild, |
40 |
- ambertools-1.5.ebuild: |
41 |
- Added fortran-2.eclass support |
42 |
- |
43 |
-*ambertools-1.5 (04 Jun 2011) |
44 |
- |
45 |
- 04 Jun 2011; Reinis Danne <rei4dan@×××××.com> +ambertools-1.5.ebuild, |
46 |
- +files/ambertools-1.5-bugfix_1-3.patch, +files/ambertools-1.5-gentoo.patch: |
47 |
- Version bump. |
48 |
- |
49 |
- 15 Mar 2011; Justin Lecher <jlec@g.o> ambertools-1.4.ebuild: |
50 |
- Remove fortran.eclass |
51 |
- |
52 |
- 14 Mar 2011; Justin Lecher <jlec@g.o> ambertools-1.4.ebuild: |
53 |
- Remove fortran.eclass removal |
54 |
- |
55 |
|
56 |
diff --git a/sci-chemistry/ambertools/ambertools-1.4.ebuild b/sci-chemistry/ambertools/ambertools-1.4.ebuild |
57 |
deleted file mode 100644 |
58 |
index 5e75cdb..0000000 |
59 |
--- a/sci-chemistry/ambertools/ambertools-1.4.ebuild |
60 |
+++ /dev/null |
61 |
@@ -1,133 +0,0 @@ |
62 |
-# Copyright 1999-2011 Gentoo Foundation |
63 |
-# Distributed under the terms of the GNU General Public License v2 |
64 |
-# $Header: $ |
65 |
- |
66 |
-EAPI=4 |
67 |
- |
68 |
-inherit eutils fortran-2 toolchain-funcs |
69 |
- |
70 |
-DESCRIPTION="A suite for carrying out complete molecular mechanics investigations" |
71 |
-HOMEPAGE="http://ambermd.org/#AmberTools" |
72 |
-SRC_URI=" |
73 |
- AmberTools-${PV}.tar.bz2 |
74 |
- mirror://gentoo/${P}-bugfix_1-18.patch.xz" |
75 |
- |
76 |
-LICENSE="GPL-2" |
77 |
-SLOT="0" |
78 |
-KEYWORDS="~amd64 ~x86" |
79 |
-IUSE="mpi openmp X" |
80 |
- |
81 |
-RESTRICT="fetch" |
82 |
- |
83 |
-RDEPEND=" |
84 |
- virtual/cblas |
85 |
- virtual/lapack |
86 |
- sci-libs/arpack |
87 |
- sci-libs/cifparse-obj |
88 |
- sci-chemistry/mopac7 |
89 |
- sci-libs/netcdf |
90 |
- sci-chemistry/reduce |
91 |
- virtual/fortran" |
92 |
-DEPEND="${RDEPEND} |
93 |
- dev-util/byacc |
94 |
- dev-libs/libf2c |
95 |
- sys-devel/ucpp" |
96 |
-S="${WORKDIR}/amber11" |
97 |
- |
98 |
-pkg_nofetch() { |
99 |
- einfo "Go to ${HOMEPAGE} and get ${A}" |
100 |
- einfo "Place it in ${DISTDIR}" |
101 |
-} |
102 |
- |
103 |
-pkg_setup() { |
104 |
- fortran-2_pkg_setup |
105 |
- if use openmp; then |
106 |
- tc-has-openmp || \ |
107 |
- die "Please select an openmp capable compiler like gcc[openmp]" |
108 |
- fi |
109 |
- AMBERHOME="${S}" |
110 |
-} |
111 |
- |
112 |
-src_prepare() { |
113 |
- epatch \ |
114 |
- "${WORKDIR}/${P}-bugfix_1-18.patch" \ |
115 |
- "${FILESDIR}/${P}-gentoo.patch" |
116 |
- cd AmberTools/src |
117 |
- rm -r arpack blas lapack fftw-2.1.5 c9x-complex cifparse netcdf pnetcdf reduce ucpp-1.3 || die |
118 |
-} |
119 |
- |
120 |
-src_configure() { |
121 |
- cd AmberTools/src |
122 |
- sed -e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \ |
123 |
- -e "s:\\\\\$(LIBDIR)/lapack.a:$(pkg-config lapack --libs) -lclapack:g" \ |
124 |
- -e "s:\\\\\$(LIBDIR)/blas.a:$(pkg-config blas cblas --libs):g" \ |
125 |
- -e "s:\\\\\$(LIBDIR)/libdrfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \ |
126 |
- -e "s:\\\\\$(LIBDIR)/libdfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \ |
127 |
- -e "s:CFLAGS=:CFLAGS=${CFLAGS} -DBINTRAJ :g" \ |
128 |
- -e "s:FFLAGS=:FFLAGS=${FFLAGS} :g" \ |
129 |
- -e "s:LDFLAGS=$ldflags:LDFLAGS=${LDFLAGS}:g" \ |
130 |
- -e "s:fc=g77:fc=$(tc-getFC):g" \ |
131 |
- -e "s:NETCDFLIB=\$netcdflib:NETCDFLIB=$(pkg-config netcdf --libs):g" \ |
132 |
- -e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \ |
133 |
- -e "s:-O3::g" \ |
134 |
- -i configure || die |
135 |
- sed -e "s:arsecond_:arscnd_:g" \ |
136 |
- -i sff/time.c \ |
137 |
- -i sff/sff.h \ |
138 |
- -i sff/sff.c || die |
139 |
- sed -e "s:\$(NAB):\$(NAB) -lrfftw:g" \ |
140 |
- -i nss/Makefile || die |
141 |
- |
142 |
- local myconf |
143 |
- |
144 |
- use X || myconf="${myconf} -noX11" |
145 |
- |
146 |
- for x in mpi openmp; do |
147 |
- use ${x} && myconf="${myconf} -${x}" |
148 |
- done |
149 |
- |
150 |
- ./configure \ |
151 |
- ${myconf} \ |
152 |
- -nobintraj \ |
153 |
- gnu |
154 |
-# $(expr match "$(tc-getCC)" '.*\([a-z]cc\)') |
155 |
-} |
156 |
- |
157 |
-src_compile() { |
158 |
- cd AmberTools/src |
159 |
- emake || die |
160 |
-} |
161 |
- |
162 |
-src_install() { |
163 |
- for x in bin/* |
164 |
- do dobin ${x} || die |
165 |
- done |
166 |
- rm "${ED}/usr/bin/yacc" |
167 |
- dobin AmberTools/src/antechamber/mopac.sh |
168 |
- sed -e "s:\$AMBERHOME/bin/mopac:mopac7:g" \ |
169 |
- -i "${ED}/usr/bin/mopac.sh" || die |
170 |
- # Make symlinks untill binpath for amber will be fixed |
171 |
- dodir /usr/share/${PN}/bin |
172 |
- cd "${ED}/usr/bin" |
173 |
- for x in * |
174 |
- do dosym /usr/bin/${x} /usr/share/${PN}/bin/${x} |
175 |
- done |
176 |
- cd "${S}" |
177 |
-# sed -e "s:\$AMBERHOME/dat:\$AMBERHOME/share/ambertools/dat:g" \ |
178 |
-# -i "${ED}/usr/bin/xleap" \ |
179 |
-# -i "${ED}/usr/bin/tleap" || die |
180 |
- dodoc doc/AmberTools.pdf doc/leap_pg.pdf |
181 |
- dolib.a lib/* |
182 |
- insinto /usr/include/${PN} |
183 |
- doins include/* |
184 |
- insinto /usr/share/${PN} |
185 |
- doins -r dat |
186 |
- cd AmberTools |
187 |
- doins -r benchmarks |
188 |
- doins -r examples |
189 |
- doins -r test |
190 |
- cat >> "${T}"/99ambertools <<- EOF |
191 |
- AMBERHOME="${EPREFIX}/usr/share/ambertools" |
192 |
- EOF |
193 |
- doenvd "${T}"/99ambertools |
194 |
-} |
195 |
|
196 |
diff --git a/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild b/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild |
197 |
deleted file mode 100644 |
198 |
index da44cf5..0000000 |
199 |
--- a/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild |
200 |
+++ /dev/null |
201 |
@@ -1,140 +0,0 @@ |
202 |
-# Copyright 1999-2011 Gentoo Foundation |
203 |
-# Distributed under the terms of the GNU General Public License v2 |
204 |
-# $Header: $ |
205 |
- |
206 |
-EAPI=4 |
207 |
- |
208 |
-inherit eutils fortran-2 toolchain-funcs |
209 |
- |
210 |
-DESCRIPTION="A suite for carrying out complete molecular mechanics investigations" |
211 |
-HOMEPAGE="http://ambermd.org/#AmberTools" |
212 |
-SRC_URI=" |
213 |
- AmberTools-${PV}.tar.bz2 |
214 |
- mirror://gentoo/${P}-bugfix_1-10.patch.xz" |
215 |
- |
216 |
-LICENSE="GPL-2" |
217 |
-SLOT="0" |
218 |
-KEYWORDS="~amd64 ~x86" |
219 |
-IUSE="mpi openmp X" |
220 |
- |
221 |
-RESTRICT="fetch" |
222 |
- |
223 |
-RDEPEND=" |
224 |
- virtual/cblas |
225 |
- virtual/lapack |
226 |
- sci-libs/clapack |
227 |
- sci-libs/arpack |
228 |
- sci-libs/cifparse-obj |
229 |
- sci-chemistry/mopac7 |
230 |
- sci-libs/netcdf |
231 |
- sci-libs/fftw:2.1 |
232 |
- sci-chemistry/reduce |
233 |
- virtual/fortran" |
234 |
-DEPEND="${RDEPEND} |
235 |
- dev-util/byacc |
236 |
- dev-libs/libf2c |
237 |
- sys-devel/ucpp" |
238 |
-S="${WORKDIR}/amber11" |
239 |
- |
240 |
-pkg_nofetch() { |
241 |
- einfo "Go to ${HOMEPAGE} and get ${A}" |
242 |
- einfo "Place it in ${DISTDIR}" |
243 |
-} |
244 |
- |
245 |
-pkg_setup() { |
246 |
- fortran-2_pkg_setup |
247 |
- if use openmp; then |
248 |
- tc-has-openmp || \ |
249 |
- die "Please select an openmp capable compiler like gcc[openmp]" |
250 |
- fi |
251 |
- AMBERHOME="${S}" |
252 |
-} |
253 |
- |
254 |
-src_prepare() { |
255 |
- epatch \ |
256 |
- "${WORKDIR}/${P}-bugfix_1-10.patch" \ |
257 |
- "${FILESDIR}/${P}-gentoo.patch" |
258 |
- cd AmberTools/src |
259 |
- rm -r arpack blas lapack fftw-2.1.5 c9x-complex cifparse netcdf pnetcdf reduce ucpp-1.3 || die |
260 |
-} |
261 |
- |
262 |
-src_configure() { |
263 |
- cd AmberTools/src |
264 |
- sed -e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \ |
265 |
- -e "s:\\\\\$(LIBDIR)/lapack.a:$(pkg-config lapack --libs) -lclapack:g" \ |
266 |
- -e "s:\\\\\$(LIBDIR)/blas.a:$(pkg-config blas cblas --libs):g" \ |
267 |
- -e "s:\\\\\$(LIBDIR)/libdrfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \ |
268 |
- -e "s:\\\\\$(LIBDIR)/libdfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \ |
269 |
- -e "s:CFLAGS=:CFLAGS=${CFLAGS} -DBINTRAJ :g" \ |
270 |
- -e "s:FFLAGS=:FFLAGS=${FFLAGS} :g" \ |
271 |
- -e "s:LDFLAGS=$ldflags:LDFLAGS=${LDFLAGS}:g" \ |
272 |
- -e "s:fc=g77:fc=$(tc-getFC):g" \ |
273 |
- -e "s:\$netcdflib:$(pkg-config netcdf --libs):g" \ |
274 |
- -e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \ |
275 |
- -e "s:-O3::g" \ |
276 |
- -i configure || die |
277 |
- sed -e "s:arsecond_:arscnd_:g" \ |
278 |
- -i sff/time.c \ |
279 |
- -i sff/sff.h \ |
280 |
- -i sff/sff.c || die |
281 |
- sed -e "s:\$(NAB):\$(NAB) -lrfftw:g" \ |
282 |
- -i nss/Makefile || die |
283 |
- |
284 |
- local myconf |
285 |
- |
286 |
- use X || myconf="${myconf} -noX11" |
287 |
- |
288 |
- for x in mpi openmp; do |
289 |
- use ${x} && myconf="${myconf} -${x}" |
290 |
- done |
291 |
- |
292 |
- ./configure \ |
293 |
- ${myconf} \ |
294 |
- -nobintraj \ |
295 |
- -nomdgx \ |
296 |
- -nopython \ |
297 |
- -nomtkpp \ |
298 |
- gnu |
299 |
-# $(expr match "$(tc-getCC)" '.*\([a-z]cc\)') |
300 |
-} |
301 |
- |
302 |
-src_compile() { |
303 |
- cd AmberTools/src |
304 |
- emake || die |
305 |
-} |
306 |
- |
307 |
-src_install() { |
308 |
- rm -r bin/chemistry bin/MMPBSA_mods |
309 |
- rm bin/ante-MMPBSA.py bin/extractFrcmod.py |
310 |
- for x in bin/* |
311 |
- do dobin ${x} || die |
312 |
- done |
313 |
- rm "${ED}/usr/bin/yacc" |
314 |
- dobin AmberTools/src/antechamber/mopac.sh |
315 |
- sed -e "s:\$AMBERHOME/bin/mopac:mopac7:g" \ |
316 |
- -i "${ED}/usr/bin/mopac.sh" || die |
317 |
- # Make symlinks untill binpath for amber will be fixed |
318 |
- dodir /usr/share/${PN}/bin |
319 |
- cd "${ED}/usr/bin" |
320 |
- for x in * |
321 |
- do dosym /usr/bin/${x} /usr/share/${PN}/bin/${x} |
322 |
- done |
323 |
- cd "${S}" |
324 |
-# sed -e "s:\$AMBERHOME/dat:\$AMBERHOME/share/ambertools/dat:g" \ |
325 |
-# -i "${ED}/usr/bin/xleap" \ |
326 |
-# -i "${ED}/usr/bin/tleap" || die |
327 |
- dodoc doc/AmberTools.pdf doc/leap_pg.pdf |
328 |
- dolib.a lib/* |
329 |
- insinto /usr/include/${PN} |
330 |
- doins include/* |
331 |
- insinto /usr/share/${PN} |
332 |
- doins -r dat |
333 |
- cd AmberTools |
334 |
- doins -r benchmarks |
335 |
- doins -r examples |
336 |
- doins -r test |
337 |
- cat >> "${T}"/99ambertools <<- EOF |
338 |
- AMBERHOME="${EPREFIX}/usr/share/ambertools" |
339 |
- EOF |
340 |
- doenvd "${T}"/99ambertools |
341 |
-} |
342 |
|
343 |
diff --git a/sci-chemistry/ambertools/ambertools-1.5.ebuild b/sci-chemistry/ambertools/ambertools-1.5.ebuild |
344 |
deleted file mode 100644 |
345 |
index 9ac9755..0000000 |
346 |
--- a/sci-chemistry/ambertools/ambertools-1.5.ebuild |
347 |
+++ /dev/null |
348 |
@@ -1,140 +0,0 @@ |
349 |
-# Copyright 1999-2011 Gentoo Foundation |
350 |
-# Distributed under the terms of the GNU General Public License v2 |
351 |
-# $Header: $ |
352 |
- |
353 |
-EAPI=4 |
354 |
- |
355 |
-inherit eutils fortran-2 toolchain-funcs |
356 |
- |
357 |
-DESCRIPTION="A suite for carrying out complete molecular mechanics investigations" |
358 |
-HOMEPAGE="http://ambermd.org/#AmberTools" |
359 |
-SRC_URI=" |
360 |
- AmberTools-${PV}.tar.bz2 |
361 |
- mirror://gentoo/${P}-bugfix_1-3.patch.xz" |
362 |
- |
363 |
-LICENSE="GPL-2" |
364 |
-SLOT="0" |
365 |
-KEYWORDS="~amd64 ~x86" |
366 |
-IUSE="mpi openmp X" |
367 |
- |
368 |
-RESTRICT="fetch" |
369 |
- |
370 |
-RDEPEND=" |
371 |
- virtual/cblas |
372 |
- virtual/lapack |
373 |
- sci-libs/clapack |
374 |
- sci-libs/arpack |
375 |
- sci-libs/cifparse-obj |
376 |
- sci-chemistry/mopac7 |
377 |
- sci-libs/netcdf |
378 |
- sci-libs/fftw:2.1 |
379 |
- sci-chemistry/reduce |
380 |
- virtual/fortran" |
381 |
-DEPEND="${RDEPEND} |
382 |
- dev-util/byacc |
383 |
- dev-libs/libf2c |
384 |
- sys-devel/ucpp" |
385 |
-S="${WORKDIR}/amber11" |
386 |
- |
387 |
-pkg_nofetch() { |
388 |
- einfo "Go to ${HOMEPAGE} and get ${A}" |
389 |
- einfo "Place it in ${DISTDIR}" |
390 |
-} |
391 |
- |
392 |
-pkg_setup() { |
393 |
- fortran-2_pkg_setup |
394 |
- if use openmp; then |
395 |
- tc-has-openmp || \ |
396 |
- die "Please select an openmp capable compiler like gcc[openmp]" |
397 |
- fi |
398 |
- AMBERHOME="${S}" |
399 |
-} |
400 |
- |
401 |
-src_prepare() { |
402 |
- epatch \ |
403 |
- "${WORKDIR}/${P}-bugfix_1-3.patch" \ |
404 |
- "${FILESDIR}/${P}-gentoo.patch" |
405 |
- cd AmberTools/src |
406 |
- rm -r arpack blas lapack fftw-2.1.5 c9x-complex cifparse netcdf pnetcdf reduce ucpp-1.3 || die |
407 |
-} |
408 |
- |
409 |
-src_configure() { |
410 |
- cd AmberTools/src |
411 |
- sed -e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \ |
412 |
- -e "s:\\\\\$(LIBDIR)/lapack.a:$(pkg-config lapack --libs) -lclapack:g" \ |
413 |
- -e "s:\\\\\$(LIBDIR)/blas.a:$(pkg-config blas cblas --libs):g" \ |
414 |
- -e "s:\\\\\$(LIBDIR)/libdrfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \ |
415 |
- -e "s:\\\\\$(LIBDIR)/libdfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \ |
416 |
- -e "s:CFLAGS=:CFLAGS=${CFLAGS} -DBINTRAJ :g" \ |
417 |
- -e "s:FFLAGS=:FFLAGS=${FFLAGS} :g" \ |
418 |
- -e "s:LDFLAGS=$ldflags:LDFLAGS=${LDFLAGS}:g" \ |
419 |
- -e "s:fc=g77:fc=$(tc-getFC):g" \ |
420 |
- -e "s:\$netcdflib:$(pkg-config netcdf --libs):g" \ |
421 |
- -e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \ |
422 |
- -e "s:-O3::g" \ |
423 |
- -i configure || die |
424 |
- sed -e "s:arsecond_:arscnd_:g" \ |
425 |
- -i sff/time.c \ |
426 |
- -i sff/sff.h \ |
427 |
- -i sff/sff.c || die |
428 |
- sed -e "s:\$(NAB):\$(NAB) -lrfftw:g" \ |
429 |
- -i nss/Makefile || die |
430 |
- |
431 |
- local myconf |
432 |
- |
433 |
- use X || myconf="${myconf} -noX11" |
434 |
- |
435 |
- for x in mpi openmp; do |
436 |
- use ${x} && myconf="${myconf} -${x}" |
437 |
- done |
438 |
- |
439 |
- ./configure \ |
440 |
- ${myconf} \ |
441 |
- -nobintraj \ |
442 |
- -nomdgx \ |
443 |
- -nopython \ |
444 |
- -nomtkpp \ |
445 |
- gnu |
446 |
-# $(expr match "$(tc-getCC)" '.*\([a-z]cc\)') |
447 |
-} |
448 |
- |
449 |
-src_compile() { |
450 |
- cd AmberTools/src |
451 |
- emake || die |
452 |
-} |
453 |
- |
454 |
-src_install() { |
455 |
- rm -r bin/chemistry bin/MMPBSA_mods |
456 |
- rm bin/ante-MMPBSA.py bin/extractFrcmod.py |
457 |
- for x in bin/* |
458 |
- do dobin ${x} || die |
459 |
- done |
460 |
- rm "${ED}/usr/bin/yacc" |
461 |
- dobin AmberTools/src/antechamber/mopac.sh |
462 |
- sed -e "s:\$AMBERHOME/bin/mopac:mopac7:g" \ |
463 |
- -i "${ED}/usr/bin/mopac.sh" || die |
464 |
- # Make symlinks untill binpath for amber will be fixed |
465 |
- dodir /usr/share/${PN}/bin |
466 |
- cd "${ED}/usr/bin" |
467 |
- for x in * |
468 |
- do dosym /usr/bin/${x} /usr/share/${PN}/bin/${x} |
469 |
- done |
470 |
- cd "${S}" |
471 |
-# sed -e "s:\$AMBERHOME/dat:\$AMBERHOME/share/ambertools/dat:g" \ |
472 |
-# -i "${ED}/usr/bin/xleap" \ |
473 |
-# -i "${ED}/usr/bin/tleap" || die |
474 |
- dodoc doc/AmberTools.pdf doc/leap_pg.pdf |
475 |
- dolib.a lib/* |
476 |
- insinto /usr/include/${PN} |
477 |
- doins include/* |
478 |
- insinto /usr/share/${PN} |
479 |
- doins -r dat |
480 |
- cd AmberTools |
481 |
- doins -r benchmarks |
482 |
- doins -r examples |
483 |
- doins -r test |
484 |
- cat >> "${T}"/99ambertools <<- EOF |
485 |
- AMBERHOME="${EPREFIX}/usr/share/ambertools" |
486 |
- EOF |
487 |
- doenvd "${T}"/99ambertools |
488 |
-} |
489 |
|
490 |
diff --git a/sci-chemistry/ambertools/files/ambertools-1.4-gentoo.patch b/sci-chemistry/ambertools/files/ambertools-1.4-gentoo.patch |
491 |
deleted file mode 100644 |
492 |
index c067928..0000000 |
493 |
--- a/sci-chemistry/ambertools/files/ambertools-1.4-gentoo.patch |
494 |
+++ /dev/null |
495 |
@@ -1,289 +0,0 @@ |
496 |
-diff -urN amber11.orig/AmberTools/src/configure amber11/AmberTools/src/configure |
497 |
---- amber11.orig/AmberTools/src/configure 2010-04-23 18:17:17.000000000 +0400 |
498 |
-+++ amber11/AmberTools/src/configure 2011-03-07 03:39:14.000000000 +0300 |
499 |
-@@ -288,11 +288,11 @@ |
500 |
- mpi_flag= |
501 |
- lex=flex |
502 |
- flibs_mkl= |
503 |
--lapack=install |
504 |
--blas=install |
505 |
-+lapack=skip |
506 |
-+blas=skip |
507 |
- f2c=skip |
508 |
--ucpp=install |
509 |
--cpp="\$(BINDIR)/ucpp -l" |
510 |
-+ucpp=skip |
511 |
-+cpp="\$(EPREFIX)/usr/bin/ucpp -l" |
512 |
- |
513 |
- #----------------------------------- |
514 |
- # skip building of sleap? |
515 |
-@@ -1241,24 +1241,24 @@ |
516 |
- #-------------------------------------------------------------------------- |
517 |
- # Configure fftw-3.2.2: |
518 |
- #-------------------------------------------------------------------------- |
519 |
-- if [ "$mdgx" = 'yes' ]; then |
520 |
-- mdgxflag="--prefix=$AMBERHOME --disable-fortran" |
521 |
-- echo |
522 |
-- echo "Configuring fftw-3.2.2; (may be time-consuming)" |
523 |
-- echo |
524 |
-- cd fftw-3.2.2 && \ |
525 |
-- env CC="$cc" CFLAGS="$cflags" ./configure $mdgxflag \ |
526 |
-- > ../fftw3_config.log 2>&1 |
527 |
-- ncerror=$? |
528 |
-- if [ $ncerror -gt 0 ]; then |
529 |
-- echo " Error: fftw configure returned $ncerror" |
530 |
-- echo " fftw configure failed! Check the fftw3_config.log file." |
531 |
-- exit 1 |
532 |
-- else |
533 |
-- echo " fftw-3.2.2 configure succeeded." |
534 |
-- fi |
535 |
-- cd .. |
536 |
-- fi |
537 |
-+ #if [ "$mdgx" = 'yes' ]; then |
538 |
-+ # mdgxflag="--prefix=$AMBERHOME --disable-fortran" |
539 |
-+ # echo |
540 |
-+ # echo "Configuring fftw-3.2.2; (may be time-consuming)" |
541 |
-+ # echo |
542 |
-+ # cd fftw-3.2.2 && \ |
543 |
-+ # env CC="$cc" CFLAGS="$cflags" ./configure $mdgxflag \ |
544 |
-+ # > ../fftw3_config.log 2>&1 |
545 |
-+ # ncerror=$? |
546 |
-+ # if [ $ncerror -gt 0 ]; then |
547 |
-+ # echo " Error: fftw configure returned $ncerror" |
548 |
-+ # echo " fftw configure failed! Check the fftw3_config.log file." |
549 |
-+ # exit 1 |
550 |
-+ # else |
551 |
-+ # echo " fftw-3.2.2 configure succeeded." |
552 |
-+ # fi |
553 |
-+ # cd .. |
554 |
-+ #fi |
555 |
- |
556 |
- #-------------------------------------------------------------------------- |
557 |
- # Set up MPI 3D-RISM in NAB and SANDER |
558 |
-@@ -1307,23 +1307,23 @@ |
559 |
- echo |
560 |
- echo "Configuring fftw-2.1.5; (may be time-consuming)" |
561 |
- echo |
562 |
-- cd fftw-2.1.5 |
563 |
-- if [ "$mpi" = 'yes' ]; then |
564 |
-- ./configure $rismflag --enable-mpi CC="$cc" CFLAGS="$cflags" F77="$fc" FFLAGS="$fflags" \ |
565 |
-- > ../fftw2_config.log 2>&1 |
566 |
-- else |
567 |
-- ./configure $rismflag CC="$cc" CFLAGS="$cflags" F77="$fc" FFLAGS="$fflags" \ |
568 |
-- > ../fftw2_config.log 2>&1 |
569 |
-- fi |
570 |
-- ncerror=$? |
571 |
-- if [ $ncerror -gt 0 ]; then |
572 |
-- echo " Error: fftw configure returned $ncerror" |
573 |
-- echo " fftw configure failed! Check the fftw2_config.log file." |
574 |
-- exit 1 |
575 |
-- else |
576 |
-- echo " fftw-2.1.5 configure succeeded." |
577 |
-- fi |
578 |
-- cd .. |
579 |
-+ # cd fftw-2.1.5 |
580 |
-+ # if [ "$mpi" = 'yes' ]; then |
581 |
-+ # ./configure $rismflag --enable-mpi CC="$cc" CFLAGS="$cflags" F77="$fc" FFLAGS="$fflags" \ |
582 |
-+ # > ../fftw2_config.log 2>&1 |
583 |
-+ # else |
584 |
-+ # ./configure $rismflag CC="$cc" CFLAGS="$cflags" F77="$fc" FFLAGS="$fflags" \ |
585 |
-+ # > ../fftw2_config.log 2>&1 |
586 |
-+ # fi |
587 |
-+ # ncerror=$? |
588 |
-+ # if [ $ncerror -gt 0 ]; then |
589 |
-+ # echo " Error: fftw configure returned $ncerror" |
590 |
-+ # echo " fftw configure failed! Check the fftw2_config.log file." |
591 |
-+ # exit 1 |
592 |
-+ # else |
593 |
-+ # echo " fftw-2.1.5 configure succeeded." |
594 |
-+ # fi |
595 |
-+ # cd .. |
596 |
- flibs_fftw2="\$(LIBDIR)/libdrfftw.a \$(LIBDIR)/libdfftw.a" |
597 |
- if [ "$mpi" = 'yes' ]; then |
598 |
- flibs_fftw2="\$(LIBDIR)/libdrfftw_mpi.a \$(LIBDIR)/libdfftw_mpi.a $flibs_fftw2" |
599 |
-diff -urN amber11.orig/AmberTools/src/Makefile amber11/AmberTools/src/Makefile |
600 |
---- amber11.orig/AmberTools/src/Makefile 2010-04-14 17:36:31.000000000 +0400 |
601 |
-+++ amber11/AmberTools/src/Makefile 2011-03-07 03:39:38.000000000 +0300 |
602 |
-@@ -8,15 +8,15 @@ |
603 |
- |
604 |
- install: serial |
605 |
- |
606 |
--serial: configured_serial $(NETCDFLIB) |
607 |
-+serial: configured_serial |
608 |
- @echo "Starting installation of ${AMBERTOOLS} serial at `date`". |
609 |
- # utility routines and libraries: |
610 |
-- (cd ucpp-1.3 && $(MAKE) $(UCPP) ) |
611 |
-+# (cd ucpp-1.3 && $(MAKE) $(UCPP) ) |
612 |
- (cd byacc && $(MAKE) install ) |
613 |
-- (cd arpack && $(MAKE) install ); |
614 |
-- (cd lapack && $(MAKE) $(LAPACK) ) |
615 |
-- (cd blas && $(MAKE) $(BLAS) ) |
616 |
-- (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) |
617 |
-+# (cd arpack && $(MAKE) install ); |
618 |
-+# (cd lapack && $(MAKE) $(LAPACK) ) |
619 |
-+# (cd blas && $(MAKE) $(BLAS) ) |
620 |
-+# (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) |
621 |
- (cd etc && $(MAKE) install ) |
622 |
- (cd chamber && $(MAKE) install ) |
623 |
- (cd pbsa && $(MAKE) install ) |
624 |
-@@ -30,14 +30,14 @@ |
625 |
- (cd ptraj && $(MAKE) install ) |
626 |
- |
627 |
- # miscellaneous: |
628 |
-- (cd reduce && $(MAKE) install ) |
629 |
-+# (cd reduce && $(MAKE) install ) |
630 |
- |
631 |
- # leap and gleap: |
632 |
- (cd leap && $(MAKE) install ) |
633 |
- (cd gleap && $(MAKE) install ) |
634 |
- |
635 |
- # nab: |
636 |
-- (cd cifparse && $(MAKE) install ) |
637 |
-+# (cd cifparse && $(MAKE) install ) |
638 |
- (cd nab && $(MAKE) install ) |
639 |
- (cd nss && $(MAKE) install ) |
640 |
- |
641 |
-@@ -50,15 +50,15 @@ |
642 |
- |
643 |
- nabonly: $(NETCDFLIB) |
644 |
- # utility routines and libraries: |
645 |
-- (cd ucpp-1.3 && $(MAKE) $(UCPP) ) |
646 |
-+# (cd ucpp-1.3 && $(MAKE) $(UCPP) ) |
647 |
- (cd byacc && $(MAKE) install ) |
648 |
-- (cd arpack && $(MAKE) install ); |
649 |
-- (cd lapack && $(MAKE) $(LAPACK) ) |
650 |
-- (cd blas && $(MAKE) $(BLAS) ) |
651 |
-- (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) |
652 |
-+# (cd arpack && $(MAKE) install ); |
653 |
-+# (cd lapack && $(MAKE) $(LAPACK) ) |
654 |
-+# (cd blas && $(MAKE) $(BLAS) ) |
655 |
-+# (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) |
656 |
- |
657 |
- # nab: |
658 |
-- (cd cifparse && $(MAKE) install ) |
659 |
-+# (cd cifparse && $(MAKE) install ) |
660 |
- (cd nab && $(MAKE) install ) |
661 |
- (cd nss && $(MAKE) install ) |
662 |
- |
663 |
-diff -urN amber11.orig/AmberTools/src/pbsa/Makefile amber11/AmberTools/src/pbsa/Makefile |
664 |
---- amber11.orig/AmberTools/src/pbsa/Makefile 2010-04-14 17:26:17.000000000 +0400 |
665 |
-+++ amber11/AmberTools/src/pbsa/Makefile 2011-03-07 03:39:15.000000000 +0300 |
666 |
-@@ -47,10 +47,10 @@ |
667 |
- $(LIBDIR)/libpbsa.a $(LIBDIR)/libFpbsa.a |
668 |
- |
669 |
- #--------------------------------------------------------------------------- |
670 |
--pbsa$(SFX): $(OBJ) syslib netlib c9x-complex |
671 |
-+pbsa$(SFX): $(OBJ) syslib |
672 |
- $(FC) -o pbsa$(SFX) $(OBJ) ../lib/nxtsec.o $(FLIBSF) $(LDFLAGS) |
673 |
- |
674 |
--simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib netlib c9x-complex |
675 |
-+simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib |
676 |
- $(FC) -o simplepbsa$(SFX) simplepbsa.o gopt.o libpbsa.a \ |
677 |
- $(LIBDIR)/libsff.a ../lib/nxtsec.o $(FLIBSF) $(LDFLAGS) |
678 |
- /bin/mv simplepbsa$(SFX) $(BINDIR) |
679 |
-@@ -76,15 +76,15 @@ |
680 |
- sfflib: |
681 |
- cd ../sff && $(MAKE) install |
682 |
- |
683 |
--netlib: |
684 |
-- cd ../lapack && $(MAKE) $(LAPACK) |
685 |
-- cd ../blas && $(MAKE) $(BLAS) |
686 |
-- cd ../arpack && $(MAKE) install |
687 |
-- |
688 |
--c9x-complex: |
689 |
-- @if test $(C9XCOMPLEX) != "skip"; then \ |
690 |
-- cd ../c9x-complex && $(MAKE) libmc.a; \ |
691 |
-- fi |
692 |
-+#netlib: |
693 |
-+# cd ../lapack && $(MAKE) $(LAPACK) |
694 |
-+# cd ../blas && $(MAKE) $(BLAS) |
695 |
-+# cd ../arpack && $(MAKE) install |
696 |
-+ |
697 |
-+#c9x-complex: |
698 |
-+# @if test $(C9XCOMPLEX) != "skip"; then \ |
699 |
-+# cd ../c9x-complex && $(MAKE) libmc.a; \ |
700 |
-+# fi |
701 |
- |
702 |
- %.LIBPBSA.o: %.f |
703 |
- $(FPP) -DLIBPBSA $< > _$< |
704 |
-diff -urN amber11.orig/AmberTools/src/ptraj/Makefile amber11/AmberTools/src/ptraj/Makefile |
705 |
---- amber11.orig/AmberTools/src/ptraj/Makefile 2010-03-31 07:05:16.000000000 +0400 |
706 |
-+++ amber11/AmberTools/src/ptraj/Makefile 2011-03-07 03:39:16.000000000 +0300 |
707 |
-@@ -60,20 +60,20 @@ |
708 |
- rdparm$(SFX): libs $(NETCDFLIB) $(OBJECTS) |
709 |
- $(CC) $(LDFLAGS) -o rdparm$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM) |
710 |
- |
711 |
--ptraj$(SFX): libs netlib $(NETCDFLIB) $(OBJECTS) |
712 |
-+ptraj$(SFX): libs $(NETCDFLIB) $(OBJECTS) |
713 |
- $(CC) $(LDFLAGS) -o ptraj$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM) |
714 |
- |
715 |
--ptraj.MPI$(SFX): libs netlib $(PNETCDFLIB) $(OBJECTS) |
716 |
-+ptraj.MPI$(SFX): libs $(PNETCDFLIB) $(OBJECTS) |
717 |
- $(CC) $(LDFLAGS) -o ptraj.MPI$(SFX) $(OBJECTS) $(LIBS) $(PNETCDFLIB) $(LM) |
718 |
- # |
719 |
- |
720 |
- libs: |
721 |
- cd pdb && $(MAKE) |
722 |
-- cd ../arpack && $(MAKE) |
723 |
-+# cd ../arpack && $(MAKE) |
724 |
- |
725 |
--netlib: |
726 |
-- cd ../lapack; $(MAKE) $(LAPACK) |
727 |
-- cd ../blas; $(MAKE) $(BLAS) |
728 |
-+#netlib: |
729 |
-+# cd ../lapack; $(MAKE) $(LAPACK) |
730 |
-+# cd ../blas; $(MAKE) $(BLAS) |
731 |
- |
732 |
- clean: |
733 |
- cd pdb; $(MAKE) clean |
734 |
-diff -urN amber11.orig/AmberTools/src/ptraj/netcdf_ptraj.h amber11/AmberTools/src/ptraj/netcdf_ptraj.h |
735 |
---- amber11.orig/AmberTools/src/ptraj/netcdf_ptraj.h 2010-03-31 07:05:16.000000000 +0400 |
736 |
-+++ amber11/AmberTools/src/ptraj/netcdf_ptraj.h 2011-03-07 03:39:17.000000000 +0300 |
737 |
-@@ -4,7 +4,7 @@ |
738 |
- # include "../pnetcdf/include/pnetcdf.h" |
739 |
- # define nc_strerror ncmpi_strerror |
740 |
- # else |
741 |
--# include "../netcdf/include/netcdf.h" |
742 |
-+# include <netcdf.h> |
743 |
- # endif |
744 |
- #endif |
745 |
- |
746 |
-diff -urN amber11.orig/AmberTools/src/ptraj/ptraj.h amber11/AmberTools/src/ptraj/ptraj.h |
747 |
---- amber11.orig/AmberTools/src/ptraj/ptraj.h 2010-03-31 07:05:16.000000000 +0400 |
748 |
-+++ amber11/AmberTools/src/ptraj/ptraj.h 2011-03-07 03:39:17.000000000 +0300 |
749 |
-@@ -94,7 +94,7 @@ |
750 |
- #define nc_strerror ncmpi_strerror |
751 |
- #include "../pnetcdf/include/pnetcdf.h" |
752 |
- #else |
753 |
--#include "../netcdf/include/netcdf.h" |
754 |
-+#include <netcdf.h> |
755 |
- #endif |
756 |
- #endif |
757 |
- |
758 |
-diff -urN amber11.orig/AmberTools/src/sqm/Makefile amber11/AmberTools/src/sqm/Makefile |
759 |
---- amber11.orig/AmberTools/src/sqm/Makefile 2010-04-14 16:13:28.000000000 +0400 |
760 |
-+++ amber11/AmberTools/src/sqm/Makefile 2011-03-07 03:39:17.000000000 +0300 |
761 |
-@@ -77,7 +77,7 @@ |
762 |
- install: sqm$(SFX) |
763 |
- mv sqm$(SFX) $(BINDIR) |
764 |
- |
765 |
--sqm$(SFX): $(SQMOBJ) $(QMOBJ) netlib sys |
766 |
-+sqm$(SFX): $(SQMOBJ) $(QMOBJ) sys |
767 |
- $(FC) -o sqm$(SFX) $(SQMOBJ) $(QMOBJ) $(FLIBSF) ../lib/sys.a $(LDFLAGS) |
768 |
- |
769 |
- #-----------LIBS |
770 |
-@@ -93,10 +93,10 @@ |
771 |
- sys: |
772 |
- cd ../lib; $(MAKE) sys.a |
773 |
- |
774 |
--netlib: |
775 |
-- cd ../lapack; $(MAKE) $(LAPACK) |
776 |
-- cd ../blas; $(MAKE) $(BLAS) |
777 |
-- cd ../arpack && $(MAKE) install |
778 |
-+#netlib: |
779 |
-+# cd ../lapack; $(MAKE) $(LAPACK) |
780 |
-+# cd ../blas; $(MAKE) $(BLAS) |
781 |
-+# cd ../arpack && $(MAKE) install |
782 |
- |
783 |
- clean: |
784 |
- /bin/rm -f *.o _*.f *.mod *.d sqm$(SFX) |
785 |
|
786 |
diff --git a/sci-chemistry/ambertools/files/ambertools-1.5-gentoo.patch b/sci-chemistry/ambertools/files/ambertools-1.5-gentoo.patch |
787 |
deleted file mode 100644 |
788 |
index 0e41d26..0000000 |
789 |
--- a/sci-chemistry/ambertools/files/ambertools-1.5-gentoo.patch |
790 |
+++ /dev/null |
791 |
@@ -1,386 +0,0 @@ |
792 |
-diff -urN amber11.orig/AmberTools/src/configure amber11/AmberTools/src/configure |
793 |
---- amber11.orig/AmberTools/src/configure 2011-04-14 15:30:55.000000000 +0300 |
794 |
-+++ amber11/AmberTools/src/configure 2011-06-04 12:26:45.000000000 +0300 |
795 |
-@@ -293,7 +293,8 @@ |
796 |
- echo "Your AMBERHOME environment variable is not set! It should be set to" |
797 |
- echo "$ambhome NOT doing so may cause errors when you compile. Continue" |
798 |
- echo "anyway? (yes or no)" |
799 |
-- read answer |
800 |
-+ #read answer |
801 |
-+ answer='yes' |
802 |
- if [ "$answer" = 'yes' -o "$answer" = 'Yes' -o "$answer" = 'YES' -o "$answer" = 'y' -o "$answer" = 'Y' ]; then |
803 |
- echo "" |
804 |
- echo "Continuing anyway... Setting AMBERHOME to $ambhome temporarily" |
805 |
-@@ -356,11 +357,11 @@ |
806 |
- mpi_flag= |
807 |
- lex=flex |
808 |
- flibs_mkl= |
809 |
--lapack=install |
810 |
--blas=install |
811 |
-+lapack=skip |
812 |
-+blas=skip |
813 |
- f2c=skip |
814 |
--ucpp=install |
815 |
--cpp="\$(BINDIR)/ucpp -l" |
816 |
-+ucpp=skip |
817 |
-+cpp="\$(EPREFIX)/usr/bin/ucpp -l" |
818 |
- |
819 |
- #----------------------------------- |
820 |
- # skip building of sleap? |
821 |
-@@ -1655,24 +1656,24 @@ |
822 |
- #-------------------------------------------------------------------------- |
823 |
- # Configure fftw-3.2.2: |
824 |
- #-------------------------------------------------------------------------- |
825 |
-- if [ "$mdgx" = 'yes' ]; then |
826 |
-- mdgxflag="--prefix=$AMBERHOME --disable-fortran" |
827 |
-- echo |
828 |
-- echo "Configuring fftw-3.2.2 (may be time-consuming)..." |
829 |
-- echo |
830 |
-- cd fftw-3.2.2 && \ |
831 |
-- env CC="$cc" CFLAGS="$cflags $cnooptflags" \ |
832 |
-- ./configure $mdgxflag > ../fftw3_config.log 2>&1 |
833 |
-- ncerror=$? |
834 |
-- if [ $ncerror -gt 0 ]; then |
835 |
-- echo " Error: FFTW configure returned $ncerror" |
836 |
-- echo " FFTW configure failed! Check the fftw3_config.log file." |
837 |
-- exit 1 |
838 |
-- else |
839 |
-- echo " fftw-3.2.2 configure succeeded." |
840 |
-- fi |
841 |
-- cd .. |
842 |
-- fi |
843 |
-+ #if [ "$mdgx" = 'yes' ]; then |
844 |
-+ # mdgxflag="--prefix=$AMBERHOME --disable-fortran" |
845 |
-+ # echo |
846 |
-+ # echo "Configuring fftw-3.2.2 (may be time-consuming)..." |
847 |
-+ # echo |
848 |
-+ # cd fftw-3.2.2 && \ |
849 |
-+ # env CC="$cc" CFLAGS="$cflags $cnooptflags" \ |
850 |
-+ # ./configure $mdgxflag > ../fftw3_config.log 2>&1 |
851 |
-+ # ncerror=$? |
852 |
-+ # if [ $ncerror -gt 0 ]; then |
853 |
-+ # echo " Error: FFTW configure returned $ncerror" |
854 |
-+ # echo " FFTW configure failed! Check the fftw3_config.log file." |
855 |
-+ # exit 1 |
856 |
-+ # else |
857 |
-+ # echo " fftw-3.2.2 configure succeeded." |
858 |
-+ # fi |
859 |
-+ # cd .. |
860 |
-+ #fi |
861 |
- |
862 |
- #-------------------------------------------------------------------------- |
863 |
- # Configure python |
864 |
-@@ -1792,27 +1793,27 @@ |
865 |
- echo |
866 |
- echo "Configuring fftw-2.1.5 (may be time-consuming)..." |
867 |
- echo |
868 |
-- cd fftw-2.1.5 |
869 |
-- if [ "$mpi" = 'yes' ]; then |
870 |
-- ./configure $rismflag --enable-mpi \ |
871 |
-- CC="$cc" CFLAGS="$cflags $coptflags" \ |
872 |
-- F77="$fc" FFLAGS="$fflags $foptflags" \ |
873 |
-- FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1 |
874 |
-- else |
875 |
-- ./configure $rismflag \ |
876 |
-- CC="$cc" CFLAGS="$cflags $coptflags" \ |
877 |
-- F77="$fc" FFLAGS="$fflags $foptflags" \ |
878 |
-- FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1 |
879 |
-- fi |
880 |
-- ncerror=$? |
881 |
-- if [ $ncerror -gt 0 ]; then |
882 |
-- echo " Error: fftw configure returned $ncerror" |
883 |
-- echo " fftw configure failed! Check the fftw2_config.log file." |
884 |
-- exit 1 |
885 |
-- else |
886 |
-- echo " fftw-2.1.5 configure succeeded." |
887 |
-- fi |
888 |
-- cd .. |
889 |
-+ # cd fftw-2.1.5 |
890 |
-+ # if [ "$mpi" = 'yes' ]; then |
891 |
-+ # ./configure $rismflag --enable-mpi \ |
892 |
-+ # CC="$cc" CFLAGS="$cflags $coptflags" \ |
893 |
-+ # F77="$fc" FFLAGS="$fflags $foptflags" \ |
894 |
-+ # FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1 |
895 |
-+ # else |
896 |
-+ # ./configure $rismflag \ |
897 |
-+ # CC="$cc" CFLAGS="$cflags $coptflags" \ |
898 |
-+ # F77="$fc" FFLAGS="$fflags $foptflags" \ |
899 |
-+ # FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1 |
900 |
-+ # fi |
901 |
-+ # ncerror=$? |
902 |
-+ # if [ $ncerror -gt 0 ]; then |
903 |
-+ # echo " Error: fftw configure returned $ncerror" |
904 |
-+ # echo " fftw configure failed! Check the fftw2_config.log file." |
905 |
-+ # exit 1 |
906 |
-+ # else |
907 |
-+ # echo " fftw-2.1.5 configure succeeded." |
908 |
-+ # fi |
909 |
-+ # cd .. |
910 |
- flibs_fftw2="-ldrfftw -ldfftw" |
911 |
- if [ "$mpi" = 'yes' ]; then |
912 |
- flibs_fftw2="-ldrfftw_mpi -ldfftw_mpi $flibs_fftw2" |
913 |
-diff -urN amber11.orig/AmberTools/src/cpptraj/src/Makefile_at amber11/AmberTools/src/cpptraj/src/Makefile_at |
914 |
---- amber11.orig/AmberTools/src/cpptraj/src/Makefile_at 2011-04-14 15:30:16.000000000 +0300 |
915 |
-+++ amber11/AmberTools/src/cpptraj/src/Makefile_at 2011-05-20 00:45:48.000000000 +0300 |
916 |
-@@ -65,8 +65,8 @@ |
917 |
- -/bin/rm FindDepend.o |
918 |
- -/bin/rm findDepend |
919 |
- |
920 |
--cpptraj$(SFX): $(NETCDFLIB) $(OBJECTS) |
921 |
-- $(CXX) $(LDFLAGS) -o cpptraj$(SFX) $(OBJECTS) $(NETCDFLIB) $(ZLIB) $(BZLIB) |
922 |
-+cpptraj$(SFX): $(OBJECTS) |
923 |
-+ $(CXX) $(LDFLAGS) -o cpptraj$(SFX) $(OBJECTS) $(NETCDFLIB) $(ZLIB) $(BZLIB) -lgomp |
924 |
- |
925 |
- $(NETCDFLIB): ../../netcdf_config.log |
926 |
- cd ../../netcdf/src && $(MAKE) install |
927 |
-diff -urN amber11.orig/AmberTools/src/Makefile amber11/AmberTools/src/Makefile |
928 |
---- amber11.orig/AmberTools/src/Makefile 2011-04-14 15:30:12.000000000 +0300 |
929 |
-+++ amber11/AmberTools/src/Makefile 2011-05-19 23:36:36.000000000 +0300 |
930 |
-@@ -8,15 +8,15 @@ |
931 |
- |
932 |
- install: $(INSTALLTYPE) |
933 |
- |
934 |
--serial: configured_serial $(NETCDFLIB) $(PYINSTALL) $(MTKPP) |
935 |
-+serial: configured_serial |
936 |
- @echo "Starting installation of ${AMBERTOOLS} serial at `date`". |
937 |
- # utility routines and libraries: |
938 |
-- (cd ucpp-1.3 && $(MAKE) $(UCPP) ) |
939 |
-+# (cd ucpp-1.3 && $(MAKE) $(UCPP) ) |
940 |
- (cd byacc && $(MAKE) install ) |
941 |
-- (cd arpack && $(MAKE) install ); |
942 |
-- (cd lapack && $(MAKE) $(LAPACK) ) |
943 |
-- (cd blas && $(MAKE) $(BLAS) ) |
944 |
-- (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) |
945 |
-+# (cd arpack && $(MAKE) install ); |
946 |
-+# (cd lapack && $(MAKE) $(LAPACK) ) |
947 |
-+# (cd blas && $(MAKE) $(BLAS) ) |
948 |
-+# (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) |
949 |
- (cd etc && $(MAKE) install ) |
950 |
- (cd chamber && $(MAKE) install ) |
951 |
- (cd pbsa && $(MAKE) install ) |
952 |
-@@ -32,7 +32,7 @@ |
953 |
- (cd cpptraj && $(MAKE) $(CPPTRAJ)) |
954 |
- |
955 |
- # miscellaneous: |
956 |
-- (cd reduce && $(MAKE) install ) |
957 |
-+# (cd reduce && $(MAKE) install ) |
958 |
- |
959 |
- # leap and gleap: |
960 |
- (cd leap && $(MAKE) install ) |
961 |
-@@ -42,7 +42,7 @@ |
962 |
- (cd rism && $(MAKE) install ) |
963 |
- |
964 |
- # nab: |
965 |
-- (cd cifparse && $(MAKE) install ) |
966 |
-+# (cd cifparse && $(MAKE) install ) |
967 |
- (cd sff && $(MAKE) install ) |
968 |
- (cd pbsa && $(MAKE) libinstall ) |
969 |
- (cd nab && $(MAKE) install ) |
970 |
-@@ -63,19 +63,19 @@ |
971 |
- @echo "Installation of ${AMBERTOOLS} serial is complete at `date`." |
972 |
- @echo "" |
973 |
- |
974 |
--nabonly: $(NETCDFLIB) |
975 |
-+nabonly: |
976 |
- # utility routines and libraries: |
977 |
-- (cd ucpp-1.3 && $(MAKE) $(UCPP) ) |
978 |
-+# (cd ucpp-1.3 && $(MAKE) $(UCPP) ) |
979 |
- (cd byacc && $(MAKE) install ) |
980 |
-- (cd arpack && $(MAKE) install ); |
981 |
-- (cd lapack && $(MAKE) $(LAPACK) ) |
982 |
-- (cd blas && $(MAKE) $(BLAS) ) |
983 |
-- (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) |
984 |
-+# (cd arpack && $(MAKE) install ); |
985 |
-+# (cd lapack && $(MAKE) $(LAPACK) ) |
986 |
-+# (cd blas && $(MAKE) $(BLAS) ) |
987 |
-+# (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) |
988 |
- (cd pbsa && $(MAKE) libinstall ) |
989 |
- (cd rism && $(MAKE) install ) |
990 |
- |
991 |
- # nab: |
992 |
-- (cd cifparse && $(MAKE) install ) |
993 |
-+# (cd cifparse && $(MAKE) install ) |
994 |
- (cd sff && $(MAKE) install ) |
995 |
- (cd nab && $(MAKE) install ) |
996 |
- (cd nss && $(MAKE) install ) |
997 |
-diff -urN amber11.orig/AmberTools/src/mdgx/Makefile amber11/AmberTools/src/mdgx/Makefile |
998 |
---- amber11.orig/AmberTools/src/mdgx/Makefile 2011-04-14 15:30:17.000000000 +0300 |
999 |
-+++ amber11/AmberTools/src/mdgx/Makefile 2011-05-20 12:44:38.000000000 +0300 |
1000 |
-@@ -109,7 +109,7 @@ |
1001 |
- |
1002 |
- FFTW_LIBS = $(LIBDIR)/libfftw3.a |
1003 |
- |
1004 |
--mdgx$(SFX) : $(MDGX_OBJS) $(FFTW_LIBS) $(NETCDFLIB) |
1005 |
-+mdgx$(SFX) : $(MDGX_OBJS) |
1006 |
- $(CC) $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) \ |
1007 |
- -o $@ $(MDGX_OBJS) $(FFTW_LIBS) $(NETCDFLIB) $(LM) |
1008 |
- |
1009 |
-diff -urN amber11.orig/AmberTools/src/pbsa/Makefile amber11/AmberTools/src/pbsa/Makefile |
1010 |
---- amber11.orig/AmberTools/src/pbsa/Makefile 2011-04-14 15:30:19.000000000 +0300 |
1011 |
-+++ amber11/AmberTools/src/pbsa/Makefile 2011-05-19 22:27:40.000000000 +0300 |
1012 |
-@@ -148,7 +148,7 @@ |
1013 |
- ) |
1014 |
- |
1015 |
- #--------------------------------------------------------------------------- |
1016 |
--pbsa$(SFX): $(OBJ) syslib netlib c9x-complex configured_serial |
1017 |
-+pbsa$(SFX): $(OBJ) syslib configured_serial |
1018 |
- $(FC) $(FFLAGS) $(AMBERFFLAGS) -o pbsa$(SFX) $(OBJ) \ |
1019 |
- ../lib/nxtsec.o ../lib/random.o \ |
1020 |
- $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS) |
1021 |
-@@ -158,7 +158,7 @@ |
1022 |
- ../lib/nxtsec.o ../lib/random.o \ |
1023 |
- $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS) |
1024 |
- |
1025 |
--simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib netlib c9x-complex |
1026 |
-+simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib |
1027 |
- $(FC) $(FFLAGS) $(AMBERFFLAGS) -o simplepbsa$(SFX) simplepbsa.o gopt.o \ |
1028 |
- libpbsa.a $(LIBDIR)/libsff.a ../lib/nxtsec.o $(FLIBSF) \ |
1029 |
- $(LDFLAGS) $(AMBERLDFLAGS) |
1030 |
-@@ -194,15 +194,15 @@ |
1031 |
- sfflib: |
1032 |
- cd ../sff && $(MAKE) install |
1033 |
- |
1034 |
--netlib: |
1035 |
-- cd ../lapack && $(MAKE) $(LAPACK) |
1036 |
-- cd ../blas && $(MAKE) $(BLAS) |
1037 |
-- cd ../arpack && $(MAKE) install |
1038 |
-- |
1039 |
--c9x-complex: |
1040 |
-- @if test $(C9XCOMPLEX) != "skip"; then \ |
1041 |
-- cd ../c9x-complex && $(MAKE) libmc.a; \ |
1042 |
-- fi |
1043 |
-+#netlib: |
1044 |
-+# cd ../lapack && $(MAKE) $(LAPACK) |
1045 |
-+# cd ../blas && $(MAKE) $(BLAS) |
1046 |
-+# cd ../arpack && $(MAKE) install |
1047 |
-+ |
1048 |
-+#c9x-complex: |
1049 |
-+# @if test $(C9XCOMPLEX) != "skip"; then \ |
1050 |
-+# cd ../c9x-complex && $(MAKE) libmc.a; \ |
1051 |
-+# fi |
1052 |
- |
1053 |
- %.LIBPBSA.o: %.f |
1054 |
- $(FPP) $(FPPFLAGS) $(AMBERFPPFLAGS) -DLIBPBSA $< > _$< |
1055 |
-diff -urN amber11.orig/AmberTools/src/ptraj/Makefile amber11/AmberTools/src/ptraj/Makefile |
1056 |
---- amber11.orig/AmberTools/src/ptraj/Makefile 2011-04-14 15:30:19.000000000 +0300 |
1057 |
-+++ amber11/AmberTools/src/ptraj/Makefile 2011-05-19 23:38:36.000000000 +0300 |
1058 |
-@@ -57,25 +57,25 @@ |
1059 |
- pubfft.o: pubfft.f |
1060 |
- $(FC) -c $(FREEFORMAT_FLAG) $(FOPTFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $< |
1061 |
- |
1062 |
--rdparm$(SFX): libs $(NETCDFLIB) $(OBJECTS) |
1063 |
-+rdparm$(SFX): libs $(OBJECTS) |
1064 |
- $(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \ |
1065 |
- -o rdparm$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM) |
1066 |
- |
1067 |
--ptraj$(SFX): libs netlib $(NETCDFLIB) $(OBJECTS) |
1068 |
-+ptraj$(SFX): libs $(OBJECTS) |
1069 |
- $(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \ |
1070 |
- -o ptraj$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM) |
1071 |
- |
1072 |
--ptraj.MPI$(SFX): libs netlib $(PNETCDFLIB) $(OBJECTS) |
1073 |
-+ptraj.MPI$(SFX): libs $(PNETCDFLIB) $(OBJECTS) |
1074 |
- $(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \ |
1075 |
- -o ptraj.MPI$(SFX) $(OBJECTS) $(LIBS) $(PNETCDFLIB) $(LM) |
1076 |
- |
1077 |
- libs: |
1078 |
- cd pdb && $(MAKE) |
1079 |
-- cd ../arpack && $(MAKE) |
1080 |
-+# cd ../arpack && $(MAKE) |
1081 |
- |
1082 |
--netlib: |
1083 |
-- cd ../lapack && $(MAKE) $(LAPACK) |
1084 |
-- cd ../blas && $(MAKE) $(BLAS) |
1085 |
-+#netlib: |
1086 |
-+# cd ../lapack && $(MAKE) $(LAPACK) |
1087 |
-+# cd ../blas && $(MAKE) $(BLAS) |
1088 |
- |
1089 |
- clean: |
1090 |
- cd pdb && $(MAKE) clean |
1091 |
-diff -urN amber11.orig/AmberTools/src/ptraj/netcdf_ptraj.h amber11/AmberTools/src/ptraj/netcdf_ptraj.h |
1092 |
---- amber11.orig/AmberTools/src/ptraj/netcdf_ptraj.h 2011-04-14 15:30:19.000000000 +0300 |
1093 |
-+++ amber11/AmberTools/src/ptraj/netcdf_ptraj.h 2011-05-19 22:30:43.000000000 +0300 |
1094 |
-@@ -4,7 +4,7 @@ |
1095 |
- # include "../../include/pnetcdf.h" |
1096 |
- # define nc_strerror ncmpi_strerror |
1097 |
- # else |
1098 |
--# include "../../include/netcdf.h" |
1099 |
-+# include <netcdf.h> |
1100 |
- # endif |
1101 |
- #endif |
1102 |
- |
1103 |
-diff -urN amber11.orig/AmberTools/src/ptraj/ptraj.h amber11/AmberTools/src/ptraj/ptraj.h |
1104 |
---- amber11.orig/AmberTools/src/ptraj/ptraj.h 2011-04-14 15:30:19.000000000 +0300 |
1105 |
-+++ amber11/AmberTools/src/ptraj/ptraj.h 2011-06-04 13:25:01.000000000 +0300 |
1106 |
-@@ -94,7 +94,7 @@ |
1107 |
- #define nc_strerror ncmpi_strerror |
1108 |
- #include "../../include/pnetcdf.h" |
1109 |
- #else |
1110 |
--#include "../../include/netcdf.h" |
1111 |
-+#include <netcdf.h> |
1112 |
- #endif |
1113 |
- #endif |
1114 |
- |
1115 |
-diff -urN amber11.orig/AmberTools/src/rism/Makefile amber11/AmberTools/src/rism/Makefile |
1116 |
---- amber11.orig/AmberTools/src/rism/Makefile 2011-04-14 15:30:19.000000000 +0300 |
1117 |
-+++ amber11/AmberTools/src/rism/Makefile 2011-05-20 01:07:26.000000000 +0300 |
1118 |
-@@ -49,7 +49,7 @@ |
1119 |
- mdiis_orig_c.o mdiis_blas_c.o mdiis_blas2_c.o mdiis_c.o \ |
1120 |
- fce_c.o erfcfun.o safemem.o blend.o timer_c.o |
1121 |
- |
1122 |
--librism: $(LIBOBJ) $(FLIBS_FFTW2) |
1123 |
-+librism: $(LIBOBJ) |
1124 |
- $(AR) $(LIBDIR)/$@.a $(LIBOBJ) |
1125 |
- $(RANLIB) $(LIBDIR)/$@.a |
1126 |
- |
1127 |
-diff -urN amber11.orig/AmberTools/src/sff/AmberNetcdf.c amber11/AmberTools/src/sff/AmberNetcdf.c |
1128 |
---- amber11.orig/AmberTools/src/sff/AmberNetcdf.c 2011-04-14 15:30:19.000000000 +0300 |
1129 |
-+++ amber11/AmberTools/src/sff/AmberNetcdf.c 2011-05-20 10:49:06.000000000 +0300 |
1130 |
-@@ -27,7 +27,7 @@ |
1131 |
- #endif |
1132 |
- |
1133 |
- #ifdef BINTRAJ |
1134 |
--#include "../../include/netcdf.h" |
1135 |
-+#include <netcdf.h> |
1136 |
- |
1137 |
- #define NCFRAME "frame" |
1138 |
- #define NCSPATIAL "spatial" |
1139 |
-diff -urN amber11.orig/AmberTools/src/sff/Makefile amber11/AmberTools/src/sff/Makefile |
1140 |
---- amber11.orig/AmberTools/src/sff/Makefile 2011-04-14 15:30:19.000000000 +0300 |
1141 |
-+++ amber11/AmberTools/src/sff/Makefile 2011-05-20 09:53:27.000000000 +0300 |
1142 |
-@@ -1,7 +1,7 @@ |
1143 |
- include ../config.h |
1144 |
- |
1145 |
- .c.o: |
1146 |
-- $(CC) -c -Dflex $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(RISMSFF) -o $@ $< |
1147 |
-+ $(CC) -c -Dflex $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(RISMSFF) $(NETCDFLIB) -o $@ $< |
1148 |
- |
1149 |
- OBJS = binpos.o conjgrad.o lmodC.o memutil.o nblist.o newton.o nmode.o \ |
1150 |
- prm.o rand2.o sasad.o sff.o time.o xminC.o AmberNetcdf.o \ |
1151 |
-diff -urN amber11.orig/AmberTools/src/sqm/Makefile amber11/AmberTools/src/sqm/Makefile |
1152 |
---- amber11.orig/AmberTools/src/sqm/Makefile 2011-04-14 15:30:20.000000000 +0300 |
1153 |
-+++ amber11/AmberTools/src/sqm/Makefile 2011-05-19 22:31:49.000000000 +0300 |
1154 |
-@@ -77,7 +77,7 @@ |
1155 |
- install: sqm$(SFX) |
1156 |
- mv sqm$(SFX) $(BINDIR) |
1157 |
- |
1158 |
--sqm$(SFX): $(SQMOBJ) $(QMOBJ) netlib sys |
1159 |
-+sqm$(SFX): $(SQMOBJ) $(QMOBJ) sys |
1160 |
- $(FC) $(FFLAGS) $(AMBERFFLAGS) -o sqm$(SFX) $(SQMOBJ) $(QMOBJ) \ |
1161 |
- $(FLIBSF) ../lib/sys.a $(LDFLAGS) $(AMBERLDFLAGS) |
1162 |
- |
1163 |
-@@ -94,10 +94,10 @@ |
1164 |
- sys: |
1165 |
- cd ../lib; $(MAKE) sys.a |
1166 |
- |
1167 |
--netlib: |
1168 |
-- cd ../lapack; $(MAKE) $(LAPACK) |
1169 |
-- cd ../blas; $(MAKE) $(BLAS) |
1170 |
-- cd ../arpack && $(MAKE) install |
1171 |
-+#netlib: |
1172 |
-+# cd ../lapack; $(MAKE) $(LAPACK) |
1173 |
-+# cd ../blas; $(MAKE) $(BLAS) |
1174 |
-+# cd ../arpack && $(MAKE) install |
1175 |
- |
1176 |
- clean: |
1177 |
- /bin/rm -f *.o _*.f *.mod *.d sqm$(SFX) |
1178 |
|
1179 |
diff --git a/sci-chemistry/ambertools/metadata.xml b/sci-chemistry/ambertools/metadata.xml |
1180 |
deleted file mode 100644 |
1181 |
index 20e218e..0000000 |
1182 |
--- a/sci-chemistry/ambertools/metadata.xml |
1183 |
+++ /dev/null |
1184 |
@@ -1,10 +0,0 @@ |
1185 |
-<?xml version="1.0" encoding="UTF-8"?> |
1186 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
1187 |
-<pkgmetadata> |
1188 |
- <herd>sci-chemistry</herd> |
1189 |
- <maintainer> |
1190 |
- <email>alexxy@g.o</email> |
1191 |
- <name>Alexey Shvetsov</name> |
1192 |
- </maintainer> |
1193 |
-</pkgmetadata> |
1194 |
- |