svn commit: r505255 - in head/science: . molden molden/files
Yuri Victorovich
yuri at FreeBSD.org
Fri Jun 28 03:51:28 UTC 2019
Author: yuri
Date: Fri Jun 28 03:51:26 2019
New Revision: 505255
URL: https://svnweb.freebsd.org/changeset/ports/505255
Log:
New port: science/molden: Program for molecular and electronic structure visualization
Added:
head/science/molden/
head/science/molden/Makefile (contents, props changed)
head/science/molden/distinfo (contents, props changed)
head/science/molden/files/
head/science/molden/files/patch-makefile (contents, props changed)
head/science/molden/files/patch-surf_Makefile (contents, props changed)
head/science/molden/files/patch-surf_utils.c (contents, props changed)
head/science/molden/pkg-descr (contents, props changed)
Modified:
head/science/Makefile
Modified: head/science/Makefile
==============================================================================
--- head/science/Makefile Fri Jun 28 02:46:07 2019 (r505254)
+++ head/science/Makefile Fri Jun 28 03:51:26 2019 (r505255)
@@ -154,6 +154,7 @@
SUBDIR += mmdb2
SUBDIR += mmtf-cpp
SUBDIR += mol2ps
+ SUBDIR += molden
SUBDIR += molgif
SUBDIR += molscript
SUBDIR += molsketch
Added: head/science/molden/Makefile
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/science/molden/Makefile Fri Jun 28 03:51:26 2019 (r505255)
@@ -0,0 +1,49 @@
+# $FreeBSD$
+
+PORTNAME= molden
+DISTVERSION= 6.1
+CATEGORIES= science
+MASTER_SITES= ftp://ftp.cmbi.umcn.nl/pub/molgraph/molden/
+DISTNAME= ${PORTNAME}${DISTVERSION}
+
+MAINTAINER= yuri at FreeBSD.org
+COMMENT= Program for molecular and electronic structure visualization
+
+LICENSE= Molden
+LICENSE_NAME= Molden License
+LICENSE_FILE= ${WRKSRC}/CopyRight
+LICENSE_PERMS= auto-accept dist-mirror pkg-mirror
+
+BUILD_DEPENDS= makedepend:devel/makedepend
+
+USES= fortran gl gmake localbase
+USE_GL= gl glu
+USE_XORG= x11 xmu
+
+MAKEFILE= makefile
+MAKE_ARGS= CFLAGS="${CFLAGS}" FFLAGS="${FFLAGS}"
+
+CFLAGS+= -DFREEBSD -DHASTIMER
+FFLAGS+= -DFREEBSD
+
+EXES= molden gmolden ambfor/ambfor ambfor/ambmd surf/surf
+PLIST_FILES= ${EXES:C/.*\///:S/^/bin\//}
+
+OPTIONS_DEFINE= DOCS
+
+PORTDOCS= *
+
+RESTRICTED= No commercial use
+
+do-install:
+.for e in ${EXES}
+ ${INSTALL_PROGRAM} ${WRKSRC}/${e} ${STAGEDIR}${PREFIX}/bin
+.endfor
+
+do-install-DOCS-on:
+ ${MKDIR} ${STAGEDIR}${DOCSDIR}
+.for d in figures.ps.Z manual.ps.Z manual.txt.Z
+ ${INSTALL_DATA} ${WRKSRC}/doc/${d} ${STAGEDIR}${DOCSDIR}
+.endfor
+
+.include <bsd.port.mk>
Added: head/science/molden/distinfo
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/science/molden/distinfo Fri Jun 28 03:51:26 2019 (r505255)
@@ -0,0 +1,3 @@
+TIMESTAMP = 1561690466
+SHA256 (molden6.1.tar.gz) = ba228b863e8f405a9f6c9f6c502e50462a570daeff74661fb317338fcc6d7fb0
+SIZE (molden6.1.tar.gz) = 6263424
Added: head/science/molden/files/patch-makefile
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/science/molden/files/patch-makefile Fri Jun 28 03:51:26 2019 (r505255)
@@ -0,0 +1,18 @@
+--- makefile.orig 2019-06-28 03:02:40 UTC
++++ makefile
+@@ -96,13 +96,13 @@ ifneq ($(comgcc), $(empty))
+ EXTRAZ = -Wno-implicit-function-declaration
+ EXT = ${EXTRAZ}
+ endif
+-FFLAGS = -g ${AFLAG}
++FFLAGS += -g ${AFLAG}
+ LIBS = -L/usr/X11R6/lib -lX11 -lm
+ ifeq ($(AFLAG),"-m64")
+ LIBS = -L/usr/X11R6/lib64 -lX11 -lm
+ endif
+ LDR = ${FC} -g ${AFLAG}
+-CFLAGS = ${AFLAG} ${EXTRAZ} -c -g -I/usr/X11R6/include -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0
++CFLAGS += ${AFLAG} ${EXTRAZ} -c -g -I/usr/X11R6/include -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0
+ ifeq ($(os), Debian)
+ CFLAGS = ${AFLAG} ${EXTRAZ} -c -I/usr/include/X11 -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0
+ LIBS = -L/usr/lib/X11 -lX11 -lm
Added: head/science/molden/files/patch-surf_Makefile
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/science/molden/files/patch-surf_Makefile Fri Jun 28 03:51:26 2019 (r505255)
@@ -0,0 +1,888 @@
+--- surf/Makefile.orig 2015-05-02 19:48:48 UTC
++++ surf/Makefile
+@@ -53,12 +53,12 @@ DEPEND = $(SRCS)
+ depend: $(DEPEND)
+ @ echo making dependencies...
+ @ echo ' ' > makedep
+- @ makedepend $(INCLUDE) -f makedep $(DEPEND)
++ @ $(CC) $(INCLUDE) -M $(SRCS) > makedep
+ @ echo '/^# DO NOT DELETE THIS LINE/+2,$$d' >eddep
+ @ echo '$$r makedep' >>eddep
+ @ echo 'w' >>eddep
+ @ cp Makefile Makefile.bak
+- @ ex - Makefile < eddep
++ #@ ex - Makefile < eddep
+ @ rm eddep makedep
+ @ echo ' ' >> Makefile
+ @ echo '# DEPENDENCIES MUST END AT END OF FILE' >> Makefile
+@@ -69,672 +69,204 @@ depend: $(DEPEND)
+
+ # DO NOT DELETE THIS LINE -- make depend depends on it.
+
+-
+-# 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
+-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
+-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
+-dual.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
+-dual.o: /usr/include/sys/_symbol_aliasing.h
+-dual.o: /usr/include/sys/_posix_availability.h /usr/include/Availability.h
+-dual.o: /usr/include/AvailabilityInternal.h /usr/include/_types.h
+-dual.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
+-dual.o: /usr/include/i386/_types.h /usr/include/sys/_pthread/_pthread_types.h
+-dual.o: /usr/include/sys/_types/_va_list.h /usr/include/sys/_types/_size_t.h
+-dual.o: /usr/include/sys/_types/_null.h /usr/include/sys/stdio.h
+-dual.o: /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h
+-dual.o: /usr/include/secure/_stdio.h /usr/include/secure/_common.h
+-dual.o: /usr/include/math.h /usr/include/stdlib.h /usr/include/sys/wait.h
+-dual.o: /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h
+-dual.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
+-dual.o: /usr/include/machine/signal.h /usr/include/i386/signal.h
+-dual.o: /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h
+-dual.o: /usr/include/mach/i386/_structs.h
+-dual.o: /usr/include/sys/_pthread/_pthread_attr_t.h
+-dual.o: /usr/include/sys/_types/_sigaltstack.h
+-dual.o: /usr/include/sys/_types/_ucontext.h
+-dual.o: /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h
+-dual.o: /usr/include/sys/resource.h /usr/include/stdint.h
+-dual.o: /usr/include/sys/_types/_int8_t.h /usr/include/sys/_types/_int16_t.h
+-dual.o: /usr/include/sys/_types/_int32_t.h /usr/include/sys/_types/_int64_t.h
+-dual.o: /usr/include/_types/_uint8_t.h /usr/include/_types/_uint16_t.h
+-dual.o: /usr/include/_types/_uint32_t.h /usr/include/_types/_uint64_t.h
+-dual.o: /usr/include/sys/_types/_intptr_t.h
+-dual.o: /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h
+-dual.o: /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h
+-dual.o: /usr/include/machine/endian.h /usr/include/i386/endian.h
+-dual.o: /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h
+-dual.o: /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h
+-dual.o: /usr/include/sys/_types/_ct_rune_t.h
+-dual.o: /usr/include/sys/_types/_rune_t.h /usr/include/sys/_types/_wchar_t.h
+-dual.o: /usr/include/machine/types.h /usr/include/i386/types.h
+-dual.o: /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h
+-dual.o: /usr/include/string.h /usr/include/sys/_types/_rsize_t.h
+-dual.o: /usr/include/sys/_types/_errno_t.h /usr/include/strings.h
+-dual.o: /usr/include/secure/_string.h /usr/include/sys/time.h
+-dual.o: /usr/include/sys/_types/_fd_def.h /usr/include/sys/_types/_timespec.h
+-dual.o: /usr/include/sys/_types/_time_t.h
+-dual.o: /usr/include/sys/_types/_suseconds_t.h
+-dual.o: /usr/include/sys/_types/_fd_setsize.h
+-dual.o: /usr/include/sys/_types/_fd_set.h /usr/include/sys/_types/_fd_clr.h
+-dual.o: /usr/include/sys/_types/_fd_isset.h
+-dual.o: /usr/include/sys/_types/_fd_zero.h /usr/include/sys/_types/_fd_copy.h
+-dual.o: /usr/include/time.h /usr/include/sys/_types/_clock_t.h
+-dual.o: /usr/include/sys/_select.h linalg.h dual.h chull.h
+-utils.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
+-utils.o: /usr/include/sys/_symbol_aliasing.h
+-utils.o: /usr/include/sys/_posix_availability.h /usr/include/Availability.h
+-utils.o: /usr/include/AvailabilityInternal.h /usr/include/_types.h
+-utils.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
+-utils.o: /usr/include/i386/_types.h
+-utils.o: /usr/include/sys/_pthread/_pthread_types.h
+-utils.o: /usr/include/sys/_types/_va_list.h /usr/include/sys/_types/_size_t.h
+-utils.o: /usr/include/sys/_types/_null.h /usr/include/sys/stdio.h
+-utils.o: /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h
+-utils.o: /usr/include/secure/_stdio.h /usr/include/secure/_common.h
+-utils.o: /usr/include/math.h /usr/include/stdlib.h /usr/include/sys/wait.h
+-utils.o: /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h
+-utils.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
+-utils.o: /usr/include/machine/signal.h /usr/include/i386/signal.h
+-utils.o: /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h
+-utils.o: /usr/include/mach/i386/_structs.h
+-utils.o: /usr/include/sys/_pthread/_pthread_attr_t.h
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+-tessel_torus.o: /usr/include/sys/_types/_mode_t.h /usr/include/string.h
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+-tessel_torus.o: /usr/include/sys/_types/_clock_t.h /usr/include/sys/_select.h
+-tessel_torus.o: linalg.h
++surf.o: surf.c surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h \
++ /usr/include/sys/_null.h /usr/include/sys/_types.h \
++ /usr/include/machine/_types.h /usr/include/x86/_types.h \
++ /usr/include/machine/_limits.h /usr/include/x86/_limits.h \
++ /usr/include/math.h /usr/include/stdlib.h /usr/include/string.h \
++ /usr/include/strings.h /usr/include/xlocale/_strings.h \
++ /usr/include/xlocale/_string.h /usr/include/sys/time.h \
++ /usr/include/sys/_timeval.h /usr/include/sys/types.h \
++ /usr/include/machine/endian.h /usr/include/x86/endian.h \
++ /usr/include/sys/_pthreadtypes.h /usr/include/sys/_stdint.h \
++ /usr/include/sys/select.h /usr/include/sys/_sigset.h \
++ /usr/include/sys/timespec.h /usr/include/sys/_timespec.h \
++ /usr/include/time.h /usr/include/xlocale/_time.h linalg.h
++io.o: io.c surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h \
++ /usr/include/sys/_null.h /usr/include/sys/_types.h \
++ /usr/include/machine/_types.h /usr/include/x86/_types.h \
++ /usr/include/machine/_limits.h /usr/include/x86/_limits.h \
++ /usr/include/math.h /usr/include/stdlib.h /usr/include/string.h \
++ /usr/include/strings.h /usr/include/xlocale/_strings.h \
++ /usr/include/xlocale/_string.h /usr/include/sys/time.h \
++ /usr/include/sys/_timeval.h /usr/include/sys/types.h \
++ /usr/include/machine/endian.h /usr/include/x86/endian.h \
++ /usr/include/sys/_pthreadtypes.h /usr/include/sys/_stdint.h \
++ /usr/include/sys/select.h /usr/include/sys/_sigset.h \
++ /usr/include/sys/timespec.h /usr/include/sys/_timespec.h \
++ /usr/include/time.h /usr/include/xlocale/_time.h linalg.h
++compute.o: compute.c surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h \
++ /usr/include/sys/_null.h /usr/include/sys/_types.h \
++ /usr/include/machine/_types.h /usr/include/x86/_types.h \
++ /usr/include/machine/_limits.h /usr/include/x86/_limits.h \
++ /usr/include/math.h /usr/include/stdlib.h /usr/include/string.h \
++ /usr/include/strings.h /usr/include/xlocale/_strings.h \
++ /usr/include/xlocale/_string.h /usr/include/sys/time.h \
++ /usr/include/sys/_timeval.h /usr/include/sys/types.h \
++ /usr/include/machine/endian.h /usr/include/x86/endian.h \
++ /usr/include/sys/_pthreadtypes.h /usr/include/sys/_stdint.h \
++ /usr/include/sys/select.h /usr/include/sys/_sigset.h \
++ /usr/include/sys/timespec.h /usr/include/sys/_timespec.h \
++ /usr/include/time.h /usr/include/xlocale/_time.h linalg.h chull.h \
++ dual.h
++dual.o: dual.c surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h \
++ /usr/include/sys/_null.h /usr/include/sys/_types.h \
++ /usr/include/machine/_types.h /usr/include/x86/_types.h \
++ /usr/include/machine/_limits.h /usr/include/x86/_limits.h \
++ /usr/include/math.h /usr/include/stdlib.h /usr/include/string.h \
++ /usr/include/strings.h /usr/include/xlocale/_strings.h \
++ /usr/include/xlocale/_string.h /usr/include/sys/time.h \
++ /usr/include/sys/_timeval.h /usr/include/sys/types.h \
++ /usr/include/machine/endian.h /usr/include/x86/endian.h \
++ /usr/include/sys/_pthreadtypes.h /usr/include/sys/_stdint.h \
++ /usr/include/sys/select.h /usr/include/sys/_sigset.h \
++ /usr/include/sys/timespec.h /usr/include/sys/_timespec.h \
++ /usr/include/time.h /usr/include/xlocale/_time.h linalg.h dual.h \
++ chull.h
++utils.o: utils.c surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h \
++ /usr/include/sys/_null.h /usr/include/sys/_types.h \
++ /usr/include/machine/_types.h /usr/include/x86/_types.h \
++ /usr/include/machine/_limits.h /usr/include/x86/_limits.h \
++ /usr/include/math.h /usr/include/stdlib.h /usr/include/string.h \
++ /usr/include/strings.h /usr/include/xlocale/_strings.h \
++ /usr/include/xlocale/_string.h /usr/include/sys/time.h \
++ /usr/include/sys/_timeval.h /usr/include/sys/types.h \
++ /usr/include/machine/endian.h /usr/include/x86/endian.h \
++ /usr/include/sys/_pthreadtypes.h /usr/include/sys/_stdint.h \
++ /usr/include/sys/select.h /usr/include/sys/_sigset.h \
++ /usr/include/sys/timespec.h /usr/include/sys/_timespec.h \
++ /usr/include/time.h /usr/include/xlocale/_time.h linalg.h
++lp.o: lp.c surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h \
++ /usr/include/sys/_null.h /usr/include/sys/_types.h \
++ /usr/include/machine/_types.h /usr/include/x86/_types.h \
++ /usr/include/machine/_limits.h /usr/include/x86/_limits.h \
++ /usr/include/math.h /usr/include/stdlib.h /usr/include/string.h \
++ /usr/include/strings.h /usr/include/xlocale/_strings.h \
++ /usr/include/xlocale/_string.h /usr/include/sys/time.h \
++ /usr/include/sys/_timeval.h /usr/include/sys/types.h \
++ /usr/include/machine/endian.h /usr/include/x86/endian.h \
++ /usr/include/sys/_pthreadtypes.h /usr/include/sys/_stdint.h \
++ /usr/include/sys/select.h /usr/include/sys/_sigset.h \
++ /usr/include/sys/timespec.h /usr/include/sys/_timespec.h \
++ /usr/include/time.h /usr/include/xlocale/_time.h linalg.h
++chull.o: chull.c surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h \
++ /usr/include/sys/_null.h /usr/include/sys/_types.h \
++ /usr/include/machine/_types.h /usr/include/x86/_types.h \
++ /usr/include/machine/_limits.h /usr/include/x86/_limits.h \
++ /usr/include/math.h /usr/include/stdlib.h /usr/include/string.h \
++ /usr/include/strings.h /usr/include/xlocale/_strings.h \
++ /usr/include/xlocale/_string.h /usr/include/sys/time.h \
++ /usr/include/sys/_timeval.h /usr/include/sys/types.h \
++ /usr/include/machine/endian.h /usr/include/x86/endian.h \
++ /usr/include/sys/_pthreadtypes.h /usr/include/sys/_stdint.h \
++ /usr/include/sys/select.h /usr/include/sys/_sigset.h \
++ /usr/include/sys/timespec.h /usr/include/sys/_timespec.h \
++ /usr/include/time.h /usr/include/xlocale/_time.h linalg.h chull.h
++tessel_cases.o: tessel_cases.c surf.h /usr/include/stdio.h \
++ /usr/include/sys/cdefs.h /usr/include/sys/_null.h \
++ /usr/include/sys/_types.h /usr/include/machine/_types.h \
++ /usr/include/x86/_types.h /usr/include/machine/_limits.h \
++ /usr/include/x86/_limits.h /usr/include/math.h /usr/include/stdlib.h \
++ /usr/include/string.h /usr/include/strings.h \
++ /usr/include/xlocale/_strings.h /usr/include/xlocale/_string.h \
++ /usr/include/sys/time.h /usr/include/sys/_timeval.h \
++ /usr/include/sys/types.h /usr/include/machine/endian.h \
++ /usr/include/x86/endian.h /usr/include/sys/_pthreadtypes.h \
++ /usr/include/sys/_stdint.h /usr/include/sys/select.h \
++ /usr/include/sys/_sigset.h /usr/include/sys/timespec.h \
++ /usr/include/sys/_timespec.h /usr/include/time.h \
++ /usr/include/xlocale/_time.h linalg.h dual.h
++tessel_patches.o: tessel_patches.c surf.h /usr/include/stdio.h \
++ /usr/include/sys/cdefs.h /usr/include/sys/_null.h \
++ /usr/include/sys/_types.h /usr/include/machine/_types.h \
++ /usr/include/x86/_types.h /usr/include/machine/_limits.h \
++ /usr/include/x86/_limits.h /usr/include/math.h /usr/include/stdlib.h \
++ /usr/include/string.h /usr/include/strings.h \
++ /usr/include/xlocale/_strings.h /usr/include/xlocale/_string.h \
++ /usr/include/sys/time.h /usr/include/sys/_timeval.h \
++ /usr/include/sys/types.h /usr/include/machine/endian.h \
++ /usr/include/x86/endian.h /usr/include/sys/_pthreadtypes.h \
++ /usr/include/sys/_stdint.h /usr/include/sys/select.h \
++ /usr/include/sys/_sigset.h /usr/include/sys/timespec.h \
++ /usr/include/sys/_timespec.h /usr/include/time.h \
++ /usr/include/xlocale/_time.h linalg.h
++tessel_convex.o: tessel_convex.c surf.h /usr/include/stdio.h \
++ /usr/include/sys/cdefs.h /usr/include/sys/_null.h \
++ /usr/include/sys/_types.h /usr/include/machine/_types.h \
++ /usr/include/x86/_types.h /usr/include/machine/_limits.h \
++ /usr/include/x86/_limits.h /usr/include/math.h /usr/include/stdlib.h \
++ /usr/include/string.h /usr/include/strings.h \
++ /usr/include/xlocale/_strings.h /usr/include/xlocale/_string.h \
++ /usr/include/sys/time.h /usr/include/sys/_timeval.h \
++ /usr/include/sys/types.h /usr/include/machine/endian.h \
++ /usr/include/x86/endian.h /usr/include/sys/_pthreadtypes.h \
++ /usr/include/sys/_stdint.h /usr/include/sys/select.h \
++ /usr/include/sys/_sigset.h /usr/include/sys/timespec.h \
++ /usr/include/sys/_timespec.h /usr/include/time.h \
++ /usr/include/xlocale/_time.h linalg.h
++tessel_concave.o: tessel_concave.c surf.h /usr/include/stdio.h \
++ /usr/include/sys/cdefs.h /usr/include/sys/_null.h \
++ /usr/include/sys/_types.h /usr/include/machine/_types.h \
++ /usr/include/x86/_types.h /usr/include/machine/_limits.h \
++ /usr/include/x86/_limits.h /usr/include/math.h /usr/include/stdlib.h \
++ /usr/include/string.h /usr/include/strings.h \
++ /usr/include/xlocale/_strings.h /usr/include/xlocale/_string.h \
++ /usr/include/sys/time.h /usr/include/sys/_timeval.h \
++ /usr/include/sys/types.h /usr/include/machine/endian.h \
++ /usr/include/x86/endian.h /usr/include/sys/_pthreadtypes.h \
++ /usr/include/sys/_stdint.h /usr/include/sys/select.h \
++ /usr/include/sys/_sigset.h /usr/include/sys/timespec.h \
++ /usr/include/sys/_timespec.h /usr/include/time.h \
++ /usr/include/xlocale/_time.h linalg.h
++tessel_torus.o: tessel_torus.c surf.h /usr/include/stdio.h \
++ /usr/include/sys/cdefs.h /usr/include/sys/_null.h \
++ /usr/include/sys/_types.h /usr/include/machine/_types.h \
++ /usr/include/x86/_types.h /usr/include/machine/_limits.h \
++ /usr/include/x86/_limits.h /usr/include/math.h /usr/include/stdlib.h \
++ /usr/include/string.h /usr/include/strings.h \
++ /usr/include/xlocale/_strings.h /usr/include/xlocale/_string.h \
++ /usr/include/sys/time.h /usr/include/sys/_timeval.h \
++ /usr/include/sys/types.h /usr/include/machine/endian.h \
++ /usr/include/x86/endian.h /usr/include/sys/_pthreadtypes.h \
++ /usr/include/sys/_stdint.h /usr/include/sys/select.h \
++ /usr/include/sys/_sigset.h /usr/include/sys/timespec.h \
++ /usr/include/sys/_timespec.h /usr/include/time.h \
++ /usr/include/xlocale/_time.h linalg.h
++
++# DEPENDENCIES MUST END AT END OF FILE
++# IF YOU PUT STUFF HERE IT WILL GO AWAY
++# see make depend above
++
++
++# DEPENDENCIES MUST END AT END OF FILE
++# IF YOU PUT STUFF HERE IT WILL GO AWAY
++# see make depend above
++
++
++# DEPENDENCIES MUST END AT END OF FILE
++# IF YOU PUT STUFF HERE IT WILL GO AWAY
++# see make depend above
++
++
++# DEPENDENCIES MUST END AT END OF FILE
++# IF YOU PUT STUFF HERE IT WILL GO AWAY
++# see make depend above
++
++
++# DEPENDENCIES MUST END AT END OF FILE
++# IF YOU PUT STUFF HERE IT WILL GO AWAY
++# see make depend above
++
++
++# DEPENDENCIES MUST END AT END OF FILE
++# IF YOU PUT STUFF HERE IT WILL GO AWAY
++# see make depend above
++
++
++# DEPENDENCIES MUST END AT END OF FILE
++# IF YOU PUT STUFF HERE IT WILL GO AWAY
++# see make depend above
++
+
+ # DEPENDENCIES MUST END AT END OF FILE
+ # IF YOU PUT STUFF HERE IT WILL GO AWAY
Added: head/science/molden/files/patch-surf_utils.c
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/science/molden/files/patch-surf_utils.c Fri Jun 28 03:51:26 2019 (r505255)
@@ -0,0 +1,10 @@
+--- surf/utils.c.orig 2019-06-28 03:23:08 UTC
++++ surf/utils.c
+@@ -76,6 +76,7 @@ find_ray_sphere_int computes the intersection of a ra
+ uses method given in Graphics Gems I, pp 388-389.
+ the direction vector of the ray need not be normalized.
+ ----------------------------------------------------------------------------------*/
++void
+ find_ray_sphere_int(int_point, ray_pt, ray_dir, center, radius)
+ float int_point[3], center[3];
+ float ray_pt[3], ray_dir[3];
Added: head/science/molden/pkg-descr
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/science/molden/pkg-descr Fri Jun 28 03:51:26 2019 (r505255)
@@ -0,0 +1,24 @@
+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
*** DIFF OUTPUT TRUNCATED AT 1000 LINES ***
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