diff options
author | Johannes M Dieterich <jmd@FreeBSD.org> | 2022-01-05 16:59:11 -0600 |
---|---|---|
committer | Johannes M Dieterich <jmd@FreeBSD.org> | 2022-01-05 17:01:00 -0600 |
commit | 1571a428a0e2ca81bbd5609eee2e41d8eed5b5c0 (patch) | |
tree | 141679fbf49c9183f32fe4dfd723cf3934cc33d7 /biology/molden | |
parent | textproc/py-xmlschema: Update to 1.9.2 (diff) |
biology/molden: update to 6.7
PR: 238858
Reported by: yuri@
Diffstat (limited to 'biology/molden')
-rw-r--r-- | biology/molden/Makefile | 47 | ||||
-rw-r--r-- | biology/molden/distinfo | 6 | ||||
-rw-r--r-- | biology/molden/files/patch-ambfor-makefile | 28 | ||||
-rw-r--r-- | biology/molden/files/patch-surf-Makefile | 789 | ||||
-rw-r--r-- | biology/molden/files/patch-xwin.c | 32 | ||||
-rw-r--r-- | biology/molden/pkg-descr | 36 |
6 files changed, 48 insertions, 890 deletions
diff --git a/biology/molden/Makefile b/biology/molden/Makefile index 101b12f668b9..cc945bed3a96 100644 --- a/biology/molden/Makefile +++ b/biology/molden/Makefile @@ -1,52 +1,52 @@ # Created by: Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp> PORTNAME= molden -DISTVERSION= 5.8.2 -PORTREVISION= 4 +DISTVERSION= 6.7 PORTEPOCH= 1 CATEGORIES= biology MASTER_SITES= ftp://ftp.cmbi.umcn.nl/pub/molgraph/molden/ -DISTNAME= ${PORTNAME}${PORTVERSION} +DISTNAME= ${PORTNAME}${DISTVERSION} MAINTAINER= jmd@FreeBSD.org COMMENT= Display molecular orbitals and electron densities in 2D and 3D LICENSE= Molden -LICENSE_NAME= Molden +LICENSE_NAME= Molden License LICENSE_FILE= ${WRKSRC}/CopyRight -# free for academic, non profit usage; do not re-distribute source and executable. -LICENSE_PERMS= auto-accept +LICENSE_PERMS= auto-accept dist-mirror pkg-mirror # free for academic, non profit use -WRKSRC= ${WRKDIR}/${PORTNAME}${PORTVERSION:R} +BUILD_DEPENDS= makedepend:devel/makedepend USES= fortran gl gmake xorg -USE_XORG= x11 +USE_XORG= x11 xmu USE_GL= gl glu + MAKEFILE= makefile -MAKE_JOBS_UNSAFE=yes CFLAGS+= -D${OPSYS:tu} -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 \ -I${LOCALBASE}/include -Wno-return-type PORTDOCS= * PORTDATA= * -PLIST_FILES= bin/ambfor bin/gmolden bin/molden bin/surf + +PLIST_FILES= bin/ambfor \ + bin/ambmd \ + bin/gmolden \ + bin/molden \ + bin/surf PORTSCOUT= limit:^5\.0\. OPTIONS_DEFINE= DATA DOCS OPTIONS_DEFAULT= DATA -post-patch: - @${REINPLACE_CMD} -e \ - 's|^CC |#CC | ; \ - s|^FC |#FC | ; \ - s|/usr/X11R6|${LOCALBASE}| ; \ - s|$$(LIBS)|$$(LIBS) $$(LDFLAGS)| ; \ - s|-lXmu|| ; \ - /depend/s|^|#|' ${WRKSRC}/makefile +post-extract: + # remove object modules + @${FIND} ${WRKSRC} -name "*.o" | ${XARGS} ${RM} + # remove pre-built executables + @${RM} ${WRKSRC}/bin/* -post-configure: +xpost-configure: @${ECHO_MSG} "********************" @${ECHO_MSG} "** If you want to use a larger MOLDEN," @${ECHO_MSG} "** edit change_parameter.sh and run it," @@ -54,11 +54,8 @@ post-configure: @${ECHO_MSG} "********************" do-install: -.for i in molden gmolden - (cd ${WRKSRC} && ${INSTALL_PROGRAM} ${i} ${STAGEDIR}${PREFIX}/bin) -.endfor -.for i in ambfor surf - (cd ${WRKSRC}/${i} && ${INSTALL_PROGRAM} ${i} ${STAGEDIR}/${PREFIX}/bin) +.for e in molden gmolden ambfor ambmd surf + ${INSTALL_PROGRAM} ${WRKSRC}/bin/${e} ${STAGEDIR}${PREFIX}/bin .endfor do-install-DATA-on: @@ -69,7 +66,7 @@ do-install-DATA-on: do-install-DOCS-on: ${MKDIR} ${STAGEDIR}${DOCSDIR} - (cd ${WRKSRC}/doc && ${COPYTREE_SHARE} . ${STAGEDIR}${DOCSDIR}) + cd ${WRKSRC}/doc && ${COPYTREE_SHARE} . ${STAGEDIR}${DOCSDIR} .include <bsd.port.pre.mk> diff --git a/biology/molden/distinfo b/biology/molden/distinfo index f5bedab276c4..b3c287258481 100644 --- a/biology/molden/distinfo +++ b/biology/molden/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1541594934 -SHA256 (molden5.8.2.tar.gz) = 65a24db9e80b4fb6038cc1e57c7d6e2457414812c9389bc651af7cb33f01dbe9 -SIZE (molden5.8.2.tar.gz) = 5770998 +TIMESTAMP = 1639879141 +SHA256 (molden6.7.tar.gz) = ebd73e8d95271eb82a1464a7eab28a042662483bbff6e6dcc7db0d1c9b2e4432 +SIZE (molden6.7.tar.gz) = 11600372 diff --git a/biology/molden/files/patch-ambfor-makefile b/biology/molden/files/patch-ambfor-makefile deleted file mode 100644 index 5b71286b335f..000000000000 --- a/biology/molden/files/patch-ambfor-makefile +++ /dev/null @@ -1,28 +0,0 @@ ---- ambfor/makefile.orig 2015-05-02 19:49:10 UTC -+++ ambfor/makefile -@@ -12,12 +12,12 @@ - # - # - --CFLAGS = -c -g ${EXT} -+CFLAGS += -c - #FC = g77 --FC = gfortran --FFLAGS = -c -g -ffast-math -funroll-loops -O3 -+#FC = gfortran -+#FFLAGS = -c -g -ffast-math -funroll-loops -O3 - LIBS = -lm --LDR = ${FC} -g -+LDR = ${FC} - EXT := - - ifeq ($(uname), Darwin) -@@ -56,7 +56,7 @@ ambmd: md.o verlet.o qvdw.o allocmd.o $( - $(LDR) -o ambmd md.o verlet.o qvdw.o allocmd.o $(OBJS) $(LIBS) - - ambfor.o: ambfor.f -- ${FC} -c -g -ffast-math -funroll-loops -o ambfor.o ambfor.f -+ ${FC} -c ${FFLAGS} -o ambfor.o ambfor.f - - allocmd.o: alloc.c - $(CC) $(CFLAGS) -DMD -c alloc.c -o allocmd.o diff --git a/biology/molden/files/patch-surf-Makefile b/biology/molden/files/patch-surf-Makefile deleted file mode 100644 index 94b6eea01746..000000000000 --- a/biology/molden/files/patch-surf-Makefile +++ /dev/null @@ -1,789 +0,0 @@ ---- surf/Makefile.orig 2015-05-02 19:48:48 UTC -+++ surf/Makefile -@@ -1,12 +1,8 @@ - # Compilation flags --#CC = cc --CC = cc - INCLUDE = -I. - #LINCLUDE = -lcurses -ltermcap -lm - LINCLUDE = -lm --OPT_CFLAGS = -O2 $(FLAGS) $(INCLUDE) - #CFLAGS = -g $(FLAGS) $(INCLUDE) --CFLAGS = -O2 $(FLAGS) $(INCLUDE) ${EXT} - - ifeq ($(uname), Darwin) - # -@@ -73,670 +69,117 @@ depend: $(DEPEND) - # DO NOT DELETE - - surf.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h --surf.o: /usr/include/sys/_symbol_aliasing.h --surf.o: /usr/include/sys/_posix_availability.h /usr/include/Availability.h --surf.o: /usr/include/AvailabilityInternal.h /usr/include/_types.h --surf.o: /usr/include/sys/_types.h /usr/include/machine/_types.h --surf.o: /usr/include/i386/_types.h /usr/include/sys/_pthread/_pthread_types.h --surf.o: /usr/include/sys/_types/_va_list.h /usr/include/sys/_types/_size_t.h --surf.o: /usr/include/sys/_types/_null.h /usr/include/sys/stdio.h --surf.o: /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h --surf.o: /usr/include/secure/_stdio.h /usr/include/secure/_common.h --surf.o: /usr/include/math.h /usr/include/stdlib.h /usr/include/sys/wait.h --surf.o: /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h --surf.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h --surf.o: /usr/include/machine/signal.h /usr/include/i386/signal.h --surf.o: /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h --surf.o: /usr/include/mach/i386/_structs.h --surf.o: /usr/include/sys/_pthread/_pthread_attr_t.h --surf.o: /usr/include/sys/_types/_sigaltstack.h --surf.o: /usr/include/sys/_types/_ucontext.h --surf.o: /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h --surf.o: /usr/include/sys/resource.h /usr/include/stdint.h --surf.o: /usr/include/sys/_types/_int8_t.h /usr/include/sys/_types/_int16_t.h --surf.o: /usr/include/sys/_types/_int32_t.h /usr/include/sys/_types/_int64_t.h --surf.o: /usr/include/_types/_uint8_t.h /usr/include/_types/_uint16_t.h --surf.o: /usr/include/_types/_uint32_t.h /usr/include/_types/_uint64_t.h --surf.o: /usr/include/sys/_types/_intptr_t.h --surf.o: /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h --surf.o: /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h --surf.o: /usr/include/machine/endian.h /usr/include/i386/endian.h --surf.o: /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h --surf.o: /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h --surf.o: /usr/include/sys/_types/_ct_rune_t.h --surf.o: /usr/include/sys/_types/_rune_t.h /usr/include/sys/_types/_wchar_t.h --surf.o: /usr/include/machine/types.h /usr/include/i386/types.h --surf.o: /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h --surf.o: /usr/include/string.h /usr/include/sys/_types/_rsize_t.h --surf.o: /usr/include/sys/_types/_errno_t.h /usr/include/strings.h --surf.o: /usr/include/secure/_string.h /usr/include/sys/time.h --surf.o: /usr/include/sys/_types/_fd_def.h /usr/include/sys/_types/_timespec.h --surf.o: /usr/include/sys/_types/_time_t.h --surf.o: /usr/include/sys/_types/_suseconds_t.h --surf.o: /usr/include/sys/_types/_fd_setsize.h --surf.o: /usr/include/sys/_types/_fd_set.h /usr/include/sys/_types/_fd_clr.h --surf.o: /usr/include/sys/_types/_fd_isset.h --surf.o: /usr/include/sys/_types/_fd_zero.h /usr/include/sys/_types/_fd_copy.h --surf.o: /usr/include/time.h /usr/include/sys/_types/_clock_t.h --surf.o: /usr/include/sys/_select.h linalg.h -+surf.o: /usr/include/sys/_null.h /usr/include/sys/_types.h -+surf.o: /usr/include/machine/_types.h /usr/include/math.h -+surf.o: /usr/include/machine/_limits.h /usr/include/stdlib.h -+surf.o: /usr/include/string.h /usr/include/strings.h /usr/include/sys/time.h -+surf.o: /usr/include/sys/_timeval.h /usr/include/sys/types.h -+surf.o: /usr/include/machine/endian.h /usr/include/sys/_pthreadtypes.h -+surf.o: /usr/include/sys/select.h /usr/include/sys/_sigset.h -+surf.o: /usr/include/sys/timespec.h /usr/include/time.h linalg.h - io.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h --io.o: /usr/include/sys/_symbol_aliasing.h --io.o: /usr/include/sys/_posix_availability.h /usr/include/Availability.h --io.o: /usr/include/AvailabilityInternal.h /usr/include/_types.h --io.o: /usr/include/sys/_types.h /usr/include/machine/_types.h --io.o: /usr/include/i386/_types.h /usr/include/sys/_pthread/_pthread_types.h --io.o: /usr/include/sys/_types/_va_list.h /usr/include/sys/_types/_size_t.h --io.o: /usr/include/sys/_types/_null.h /usr/include/sys/stdio.h --io.o: /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h --io.o: /usr/include/secure/_stdio.h /usr/include/secure/_common.h --io.o: /usr/include/math.h /usr/include/stdlib.h /usr/include/sys/wait.h --io.o: /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h --io.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h --io.o: /usr/include/machine/signal.h /usr/include/i386/signal.h --io.o: /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h --io.o: /usr/include/mach/i386/_structs.h --io.o: /usr/include/sys/_pthread/_pthread_attr_t.h --io.o: /usr/include/sys/_types/_sigaltstack.h --io.o: /usr/include/sys/_types/_ucontext.h /usr/include/sys/_types/_sigset_t.h --io.o: /usr/include/sys/_types/_uid_t.h /usr/include/sys/resource.h --io.o: /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h --io.o: /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h --io.o: /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h --io.o: /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h --io.o: /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h --io.o: /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h --io.o: /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h --io.o: /usr/include/machine/endian.h /usr/include/i386/endian.h --io.o: /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h --io.o: /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h --io.o: /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h --io.o: /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h --io.o: /usr/include/i386/types.h /usr/include/sys/_types/_dev_t.h --io.o: /usr/include/sys/_types/_mode_t.h /usr/include/string.h --io.o: /usr/include/sys/_types/_rsize_t.h /usr/include/sys/_types/_errno_t.h --io.o: /usr/include/strings.h /usr/include/secure/_string.h --io.o: /usr/include/sys/time.h /usr/include/sys/_types/_fd_def.h --io.o: /usr/include/sys/_types/_timespec.h /usr/include/sys/_types/_time_t.h --io.o: /usr/include/sys/_types/_suseconds_t.h --io.o: /usr/include/sys/_types/_fd_setsize.h /usr/include/sys/_types/_fd_set.h --io.o: /usr/include/sys/_types/_fd_clr.h /usr/include/sys/_types/_fd_isset.h --io.o: /usr/include/sys/_types/_fd_zero.h /usr/include/sys/_types/_fd_copy.h --io.o: /usr/include/time.h /usr/include/sys/_types/_clock_t.h --io.o: /usr/include/sys/_select.h linalg.h -+io.o: /usr/include/sys/_null.h /usr/include/sys/_types.h -+io.o: /usr/include/machine/_types.h /usr/include/math.h -+io.o: /usr/include/machine/_limits.h /usr/include/stdlib.h -+io.o: /usr/include/string.h /usr/include/strings.h /usr/include/sys/time.h -+io.o: /usr/include/sys/_timeval.h /usr/include/sys/types.h -+io.o: /usr/include/machine/endian.h /usr/include/sys/_pthreadtypes.h -+io.o: /usr/include/sys/select.h /usr/include/sys/_sigset.h -+io.o: /usr/include/sys/timespec.h /usr/include/time.h linalg.h - compute.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h --compute.o: /usr/include/sys/_symbol_aliasing.h --compute.o: /usr/include/sys/_posix_availability.h /usr/include/Availability.h --compute.o: /usr/include/AvailabilityInternal.h /usr/include/_types.h --compute.o: /usr/include/sys/_types.h /usr/include/machine/_types.h --compute.o: /usr/include/i386/_types.h --compute.o: /usr/include/sys/_pthread/_pthread_types.h --compute.o: /usr/include/sys/_types/_va_list.h --compute.o: /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h --compute.o: /usr/include/sys/stdio.h /usr/include/sys/_types/_off_t.h --compute.o: /usr/include/sys/_types/_ssize_t.h /usr/include/secure/_stdio.h --compute.o: /usr/include/secure/_common.h /usr/include/math.h --compute.o: /usr/include/stdlib.h /usr/include/sys/wait.h --compute.o: /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h --compute.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h --compute.o: /usr/include/machine/signal.h /usr/include/i386/signal.h --compute.o: /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h --compute.o: /usr/include/mach/i386/_structs.h --compute.o: /usr/include/sys/_pthread/_pthread_attr_t.h --compute.o: /usr/include/sys/_types/_sigaltstack.h --compute.o: /usr/include/sys/_types/_ucontext.h --compute.o: /usr/include/sys/_types/_sigset_t.h --compute.o: /usr/include/sys/_types/_uid_t.h /usr/include/sys/resource.h --compute.o: /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h --compute.o: /usr/include/sys/_types/_int16_t.h --compute.o: /usr/include/sys/_types/_int32_t.h --compute.o: /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h --compute.o: /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h --compute.o: /usr/include/_types/_uint64_t.h --compute.o: /usr/include/sys/_types/_intptr_t.h --compute.o: /usr/include/sys/_types/_uintptr_t.h --compute.o: /usr/include/_types/_intmax_t.h /usr/include/_types/_uintmax_t.h --compute.o: /usr/include/sys/_types/_timeval.h /usr/include/machine/endian.h --compute.o: /usr/include/i386/endian.h /usr/include/sys/_endian.h --compute.o: /usr/include/libkern/_OSByteOrder.h --compute.o: /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h --compute.o: /usr/include/sys/_types/_ct_rune_t.h --compute.o: /usr/include/sys/_types/_rune_t.h --compute.o: /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h --compute.o: /usr/include/i386/types.h /usr/include/sys/_types/_dev_t.h --compute.o: /usr/include/sys/_types/_mode_t.h /usr/include/string.h --compute.o: /usr/include/sys/_types/_rsize_t.h --compute.o: /usr/include/sys/_types/_errno_t.h /usr/include/strings.h --compute.o: /usr/include/secure/_string.h /usr/include/sys/time.h --compute.o: /usr/include/sys/_types/_fd_def.h --compute.o: /usr/include/sys/_types/_timespec.h --compute.o: /usr/include/sys/_types/_time_t.h --compute.o: /usr/include/sys/_types/_suseconds_t.h --compute.o: /usr/include/sys/_types/_fd_setsize.h --compute.o: /usr/include/sys/_types/_fd_set.h --compute.o: /usr/include/sys/_types/_fd_clr.h --compute.o: /usr/include/sys/_types/_fd_isset.h --compute.o: /usr/include/sys/_types/_fd_zero.h --compute.o: /usr/include/sys/_types/_fd_copy.h /usr/include/time.h --compute.o: /usr/include/sys/_types/_clock_t.h /usr/include/sys/_select.h --compute.o: linalg.h chull.h dual.h -+compute.o: /usr/include/sys/_null.h /usr/include/sys/_types.h -+compute.o: /usr/include/machine/_types.h /usr/include/math.h -+compute.o: /usr/include/machine/_limits.h /usr/include/stdlib.h -+compute.o: /usr/include/string.h /usr/include/strings.h -+compute.o: /usr/include/sys/time.h /usr/include/sys/_timeval.h -+compute.o: /usr/include/sys/types.h /usr/include/machine/endian.h -+compute.o: /usr/include/sys/_pthreadtypes.h /usr/include/sys/select.h -+compute.o: /usr/include/sys/_sigset.h /usr/include/sys/timespec.h -+compute.o: /usr/include/time.h linalg.h chull.h dual.h - 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tessel_concave.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h --tessel_concave.o: /usr/include/sys/_symbol_aliasing.h --tessel_concave.o: /usr/include/sys/_posix_availability.h --tessel_concave.o: /usr/include/Availability.h --tessel_concave.o: /usr/include/AvailabilityInternal.h /usr/include/_types.h --tessel_concave.o: /usr/include/sys/_types.h /usr/include/machine/_types.h --tessel_concave.o: /usr/include/i386/_types.h --tessel_concave.o: /usr/include/sys/_pthread/_pthread_types.h --tessel_concave.o: /usr/include/sys/_types/_va_list.h --tessel_concave.o: /usr/include/sys/_types/_size_t.h --tessel_concave.o: /usr/include/sys/_types/_null.h /usr/include/sys/stdio.h --tessel_concave.o: /usr/include/sys/_types/_off_t.h --tessel_concave.o: /usr/include/sys/_types/_ssize_t.h --tessel_concave.o: /usr/include/secure/_stdio.h /usr/include/secure/_common.h --tessel_concave.o: /usr/include/math.h /usr/include/stdlib.h --tessel_concave.o: /usr/include/sys/wait.h /usr/include/sys/_types/_pid_t.h --tessel_concave.o: /usr/include/sys/_types/_id_t.h /usr/include/sys/signal.h --tessel_concave.o: /usr/include/sys/appleapiopts.h --tessel_concave.o: /usr/include/machine/signal.h /usr/include/i386/signal.h --tessel_concave.o: /usr/include/machine/_mcontext.h --tessel_concave.o: /usr/include/i386/_mcontext.h --tessel_concave.o: /usr/include/mach/i386/_structs.h --tessel_concave.o: /usr/include/sys/_pthread/_pthread_attr_t.h --tessel_concave.o: /usr/include/sys/_types/_sigaltstack.h --tessel_concave.o: /usr/include/sys/_types/_ucontext.h --tessel_concave.o: /usr/include/sys/_types/_sigset_t.h --tessel_concave.o: /usr/include/sys/_types/_uid_t.h --tessel_concave.o: /usr/include/sys/resource.h /usr/include/stdint.h --tessel_concave.o: /usr/include/sys/_types/_int8_t.h --tessel_concave.o: /usr/include/sys/_types/_int16_t.h --tessel_concave.o: /usr/include/sys/_types/_int32_t.h --tessel_concave.o: /usr/include/sys/_types/_int64_t.h --tessel_concave.o: /usr/include/_types/_uint8_t.h --tessel_concave.o: /usr/include/_types/_uint16_t.h --tessel_concave.o: /usr/include/_types/_uint32_t.h --tessel_concave.o: /usr/include/_types/_uint64_t.h --tessel_concave.o: /usr/include/sys/_types/_intptr_t.h --tessel_concave.o: /usr/include/sys/_types/_uintptr_t.h --tessel_concave.o: /usr/include/_types/_intmax_t.h --tessel_concave.o: /usr/include/_types/_uintmax_t.h --tessel_concave.o: /usr/include/sys/_types/_timeval.h --tessel_concave.o: /usr/include/machine/endian.h /usr/include/i386/endian.h --tessel_concave.o: /usr/include/sys/_endian.h --tessel_concave.o: /usr/include/libkern/_OSByteOrder.h --tessel_concave.o: /usr/include/libkern/i386/_OSByteOrder.h --tessel_concave.o: /usr/include/alloca.h /usr/include/sys/_types/_ct_rune_t.h --tessel_concave.o: /usr/include/sys/_types/_rune_t.h --tessel_concave.o: /usr/include/sys/_types/_wchar_t.h --tessel_concave.o: /usr/include/machine/types.h /usr/include/i386/types.h --tessel_concave.o: /usr/include/sys/_types/_dev_t.h --tessel_concave.o: /usr/include/sys/_types/_mode_t.h /usr/include/string.h --tessel_concave.o: /usr/include/sys/_types/_rsize_t.h --tessel_concave.o: /usr/include/sys/_types/_errno_t.h /usr/include/strings.h --tessel_concave.o: /usr/include/secure/_string.h /usr/include/sys/time.h --tessel_concave.o: /usr/include/sys/_types/_fd_def.h --tessel_concave.o: /usr/include/sys/_types/_timespec.h --tessel_concave.o: /usr/include/sys/_types/_time_t.h --tessel_concave.o: /usr/include/sys/_types/_suseconds_t.h --tessel_concave.o: /usr/include/sys/_types/_fd_setsize.h --tessel_concave.o: /usr/include/sys/_types/_fd_set.h --tessel_concave.o: /usr/include/sys/_types/_fd_clr.h --tessel_concave.o: /usr/include/sys/_types/_fd_isset.h --tessel_concave.o: /usr/include/sys/_types/_fd_zero.h --tessel_concave.o: /usr/include/sys/_types/_fd_copy.h /usr/include/time.h --tessel_concave.o: /usr/include/sys/_types/_clock_t.h --tessel_concave.o: /usr/include/sys/_select.h linalg.h -+tessel_concave.o: /usr/include/sys/_null.h /usr/include/sys/_types.h -+tessel_concave.o: /usr/include/machine/_types.h /usr/include/math.h -+tessel_concave.o: /usr/include/machine/_limits.h /usr/include/stdlib.h -+tessel_concave.o: /usr/include/string.h /usr/include/strings.h -+tessel_concave.o: /usr/include/sys/time.h /usr/include/sys/_timeval.h -+tessel_concave.o: /usr/include/sys/types.h /usr/include/machine/endian.h -+tessel_concave.o: /usr/include/sys/_pthreadtypes.h /usr/include/sys/select.h -+tessel_concave.o: /usr/include/sys/_sigset.h /usr/include/sys/timespec.h -+tessel_concave.o: /usr/include/time.h linalg.h - tessel_torus.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h --tessel_torus.o: /usr/include/sys/_symbol_aliasing.h --tessel_torus.o: /usr/include/sys/_posix_availability.h --tessel_torus.o: /usr/include/Availability.h --tessel_torus.o: /usr/include/AvailabilityInternal.h /usr/include/_types.h --tessel_torus.o: /usr/include/sys/_types.h /usr/include/machine/_types.h --tessel_torus.o: /usr/include/i386/_types.h --tessel_torus.o: /usr/include/sys/_pthread/_pthread_types.h --tessel_torus.o: /usr/include/sys/_types/_va_list.h --tessel_torus.o: /usr/include/sys/_types/_size_t.h --tessel_torus.o: /usr/include/sys/_types/_null.h /usr/include/sys/stdio.h --tessel_torus.o: /usr/include/sys/_types/_off_t.h --tessel_torus.o: /usr/include/sys/_types/_ssize_t.h --tessel_torus.o: /usr/include/secure/_stdio.h /usr/include/secure/_common.h --tessel_torus.o: /usr/include/math.h /usr/include/stdlib.h --tessel_torus.o: /usr/include/sys/wait.h /usr/include/sys/_types/_pid_t.h --tessel_torus.o: /usr/include/sys/_types/_id_t.h /usr/include/sys/signal.h --tessel_torus.o: /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h --tessel_torus.o: /usr/include/i386/signal.h /usr/include/machine/_mcontext.h --tessel_torus.o: /usr/include/i386/_mcontext.h --tessel_torus.o: /usr/include/mach/i386/_structs.h --tessel_torus.o: /usr/include/sys/_pthread/_pthread_attr_t.h --tessel_torus.o: /usr/include/sys/_types/_sigaltstack.h --tessel_torus.o: /usr/include/sys/_types/_ucontext.h --tessel_torus.o: /usr/include/sys/_types/_sigset_t.h --tessel_torus.o: /usr/include/sys/_types/_uid_t.h /usr/include/sys/resource.h --tessel_torus.o: /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h --tessel_torus.o: /usr/include/sys/_types/_int16_t.h --tessel_torus.o: /usr/include/sys/_types/_int32_t.h --tessel_torus.o: /usr/include/sys/_types/_int64_t.h --tessel_torus.o: /usr/include/_types/_uint8_t.h --tessel_torus.o: /usr/include/_types/_uint16_t.h --tessel_torus.o: /usr/include/_types/_uint32_t.h --tessel_torus.o: /usr/include/_types/_uint64_t.h --tessel_torus.o: /usr/include/sys/_types/_intptr_t.h --tessel_torus.o: /usr/include/sys/_types/_uintptr_t.h --tessel_torus.o: /usr/include/_types/_intmax_t.h --tessel_torus.o: /usr/include/_types/_uintmax_t.h --tessel_torus.o: /usr/include/sys/_types/_timeval.h --tessel_torus.o: /usr/include/machine/endian.h /usr/include/i386/endian.h --tessel_torus.o: /usr/include/sys/_endian.h --tessel_torus.o: /usr/include/libkern/_OSByteOrder.h --tessel_torus.o: /usr/include/libkern/i386/_OSByteOrder.h --tessel_torus.o: /usr/include/alloca.h /usr/include/sys/_types/_ct_rune_t.h --tessel_torus.o: /usr/include/sys/_types/_rune_t.h --tessel_torus.o: /usr/include/sys/_types/_wchar_t.h --tessel_torus.o: /usr/include/machine/types.h /usr/include/i386/types.h --tessel_torus.o: /usr/include/sys/_types/_dev_t.h --tessel_torus.o: /usr/include/sys/_types/_mode_t.h /usr/include/string.h --tessel_torus.o: /usr/include/sys/_types/_rsize_t.h --tessel_torus.o: /usr/include/sys/_types/_errno_t.h /usr/include/strings.h --tessel_torus.o: /usr/include/secure/_string.h /usr/include/sys/time.h --tessel_torus.o: /usr/include/sys/_types/_fd_def.h --tessel_torus.o: /usr/include/sys/_types/_timespec.h --tessel_torus.o: /usr/include/sys/_types/_time_t.h --tessel_torus.o: /usr/include/sys/_types/_suseconds_t.h --tessel_torus.o: /usr/include/sys/_types/_fd_setsize.h --tessel_torus.o: /usr/include/sys/_types/_fd_set.h --tessel_torus.o: /usr/include/sys/_types/_fd_clr.h --tessel_torus.o: /usr/include/sys/_types/_fd_isset.h --tessel_torus.o: /usr/include/sys/_types/_fd_zero.h --tessel_torus.o: /usr/include/sys/_types/_fd_copy.h /usr/include/time.h --tessel_torus.o: /usr/include/sys/_types/_clock_t.h /usr/include/sys/_select.h --tessel_torus.o: linalg.h -- --# DEPENDENCIES MUST END AT END OF FILE --# IF YOU PUT STUFF HERE IT WILL GO AWAY --# see make depend above -- -+tessel_torus.o: /usr/include/sys/_null.h /usr/include/sys/_types.h -+tessel_torus.o: /usr/include/machine/_types.h /usr/include/math.h -+tessel_torus.o: /usr/include/machine/_limits.h /usr/include/stdlib.h -+tessel_torus.o: /usr/include/string.h /usr/include/strings.h -+tessel_torus.o: /usr/include/sys/time.h /usr/include/sys/_timeval.h -+tessel_torus.o: /usr/include/sys/types.h /usr/include/machine/endian.h -+tessel_torus.o: /usr/include/sys/_pthreadtypes.h /usr/include/sys/select.h -+tessel_torus.o: /usr/include/sys/_sigset.h /usr/include/sys/timespec.h -+tessel_torus.o: /usr/include/time.h linalg.h diff --git a/biology/molden/files/patch-xwin.c b/biology/molden/files/patch-xwin.c deleted file mode 100644 index 482160e326b6..000000000000 --- a/biology/molden/files/patch-xwin.c +++ /dev/null @@ -1,32 +0,0 @@ ---- xwin.c.orig 2018-11-07 12:54:20 UTC -+++ xwin.c -@@ -4218,8 +4218,12 @@ void makeRasterFont(Display *dpy); - #include <math.h> - - #include <fcntl.h> --#if defined(__APPLE__) || defined(__FreeBSD__) -+#if defined(__APPLE__) - #include <copyfile.h> -+#elif defined(__FreeBSD__) -+#include <sys/types.h> -+#include <sys/socket.h> -+#include <sys/uio.h> - #else - #include <sys/sendfile.h> - #endif -@@ -4238,9 +4242,14 @@ int OSCopyFile(const char* source, const - } - - //Here we use kernel-space copying for performance reasons --#if defined(__APPLE__) || defined(__FreeBSD__) -+#if defined(__APPLE__) - //fcopyfile works on FreeBSD and OS X 10.5+ - int result = fcopyfile(input, output, 0, COPYFILE_ALL); -+#elif defined(__FreeBSD__) -+ off_t bytesCopied = 0; -+ struct stat fileinfo = {0}; -+ fstat(input, &fileinfo); -+ int result = sendfile(output, input, 0/*ofset*/, fileinfo.st_size, 0/*hdtr*/, &bytesCopied, 0/*flags*/); - #else - //sendfile will work with non-socket output (i.e. regular file) on Linux 2.6.33+ - off_t bytesCopied = 0; diff --git a/biology/molden/pkg-descr b/biology/molden/pkg-descr index f27324fc3da3..45612201a3c7 100644 --- a/biology/molden/pkg-descr +++ b/biology/molden/pkg-descr @@ -1,14 +1,24 @@ -Visualizing the results of molecular orbital calculations - 1) MO program: gaussian, gamess, mopac, etc. - 2) display molecule in 3D: geo-opt, single-point, nomal mode (animation) - 3) density: contour plot or 3D view for electron density and MO coefficient -Everything what you want about MO calculation can be seen. +Molden is a package for displaying Molecular Density from the Ab Initio packages +GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac, +it also supports a number of other programs via the Molden Format. Molden reads +all the required information from the GAMESS / GAUSSIAN outputfile. Molden is +capable of displaying Molecular Orbitals, the electron density and the Molecular +minus Atomic density. Either the spherically averaged atomic density or the +oriented ground state atomic density can be subtracted for a number of standard +basis sets. Molden supports contour plots, 3-d grid plots with hidden lines and +a combination of both. It can write a variety of graphics instructions; +postscript, XWindows, VRML, povray, OpenGL, tekronix4014, hpgl, hp2392 and +Figure. Both Xwindows and OpenGL versions of Molden are also capable of +importing and displaying of chemx, PDB, and a variety of mopac/ampac files and +lots of other formats. Molden also can animate reaction paths and molecular +vibrations. It can calculate and display the true or Multipole Derived +Electrostatic Potential and atomic charges can be fitted to the Electrostatic +Potential calculated on a Connolly surface. Molden also features an stand alone +forcefield program ambfor, which can optimise geometries with the combined Amber +(protein) and GAFF (small molecules) force fields. Atom typing can be done +automatically and interactively from within Molden, as well as firing +optimisation jobs. Molden has a powerful Z-matrix editor which give full control +over the geometry and allows you to build molecules from scratch, including +polypeptides. -By the distribution policy of the author; - * Only the latest version is supplied. - * Users must get the `distfiles' from the original site. - * Do not re-distribute the source and the executable. - * Using a not-so-latest version is prohibited, because - the author may only respond about the latest version. - -WWW: http://www.cmbi.ru.nl/molden/ +WWW: http://cheminf.cmbi.ru.nl/molden/ |