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Code Issues Releases Activity

Update to 4.7

Browse Source 
PR:		ports/128476
Submitted by:	fulvio ciriaco <oivulf@gmail.com>
This commit is contained in:
Wesley Shields 2008-11-04 21:55:39 +00:00
parent 586d140851
commit 05d80caef1
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=222400
8 changed files with 309 additions and 140 deletions
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20
biology/molden/Makefile
View File

@ -6,30 +6,24 @@
#
PORTNAME= molden
PORTVERSION= 4.5
PORTREVISION= 2
PORTVERSION= 4.7
CATEGORIES= biology
MASTER_SITES= ftp://ftp.cmbi.kun.nl/pub/molgraph/molden/
DISTNAME= ${PORTNAME}${PORTVERSION}
EXTRACT_SUFX= .tar.Z
DIST_SUBDIR= ${PKGNAME}
EXTRACT_ONLY= ${PORTNAME}${PORTVERSION}.tar.Z
MAINTAINER= ports@FreeBSD.org
MAINTAINER= oivulf@gmail.com
COMMENT= Display molecular orbitals and electron densities in 2D and 3D
USE_XORG= x11 xmu
USE_GL= glut
USE_FORTRAN= yes
RESTRICTED= free for academic, non profit usage; do not re-distribute source and executable.
MAKEFILE= ${WRKSRC}/makefile
.include <bsd.port.pre.mk>
USE_FORTRAN= yes
post-patch:
${REINPLACE_CMD} -e 's,malloc.h,stdlib.h,' ${WRKSRC}/xwin.c
@${REINPLACE_CMD} -e 's,malloc.h,stdlib.h,' ${WRKSRC}/xwin.c
post-configure:
@${ECHO_MSG} "********************"
@ -40,7 +34,9 @@ post-configure:
do-install:
${INSTALL_PROGRAM} ${WRKSRC}/molden ${PREFIX}/bin
${INSTALL_PROGRAM} ${WRKSRC}/moldenogl ${PREFIX}/bin
${INSTALL_PROGRAM} ${WRKSRC}/ambfor/ambfor ${PREFIX}/bin
${INSTALL_PROGRAM} ${WRKSRC}/gmolden ${PREFIX}/bin
${INSTALL_PROGRAM} ${WRKSRC}/surf/surf ${PREFIX}/bin
.if !defined(NOPORTDOCS)
${MKDIR} ${PREFIX}/share/doc/molden
${MKDIR} ${PREFIX}/share/molden/test
@ -50,4 +46,4 @@ do-install:
${INSTALL_DATA} ${WRKSRC}/utils/* ${PREFIX}/share/molden/utils
.endif
.include <bsd.port.post.mk>
.include <bsd.port.mk>

6
biology/molden/distinfo
View File

@ -1,3 +1,3 @@
MD5 (molden-4.5_2/molden4.5.tar.Z) = 2706a205de011f2dca042f8c7fe95834
SHA256 (molden-4.5_2/molden4.5.tar.Z) = 84b6905ec786bde9af8bfa6439b0c066b65a98028ffaf1ebc543e58b31fe2ca7
SIZE (molden-4.5_2/molden4.5.tar.Z) = 3605279
MD5 (molden-4.7/molden4.7.tar.gz) = 94baf00d545224d328767bfacb8ec194
SHA256 (molden-4.7/molden4.7.tar.gz) = a5f5eb207894c7cb2e437ad14bed6b52d3845cd78599c89be8de55692ae1cddf
SIZE (molden-4.7/molden4.7.tar.gz) = 2813532

17
biology/molden/files/patch-ambfor-makefile Normal file
View File

@ -0,0 +1,17 @@
--- ambfor/makefile.orig 2008-10-30 10:06:37.000000000 +0100
+++ ambfor/makefile 2008-10-30 10:07:19.000000000 +0100
@@ -14,11 +14,11 @@
#
#CC = cc
-CFLAGS = -c
-FC = g77
+CFLAGS += -DFREEBSD=1
+#FC = g77
FFLAGS = -c -O3 -ffast-math
LIBS = -lm
-LDR = g77
+LDR = $(FC)
OBJS = ambfor.o angle.o bond.o charge.o conn.o enegrd.o getinp.o \
param.o tors.o vdwlj.o math.o optimise.o wrtout.o

34
biology/molden/files/patch-aa → biology/molden/files/patch-makefile
View File

@ -1,6 +1,6 @@
--- makefile.orig Thu Sep 7 19:55:00 2006
+++ makefile Tue Apr 24 16:40:19 2007
@@ -12,9 +12,27 @@
--- makefile.orig 2008-08-25 19:55:57.000000000 +0200
+++ makefile 2008-11-01 21:48:37.000000000 +0100
@@ -12,9 +12,23 @@
#
# Disregard compiler warnings on rdmolf.f
#
@ -15,10 +15,6 @@
+#CC = gcc
+CFLAGS += -c -DDOBACK -DHASTIMER -I${LOCALBASE}/include
+#FC = f77
+.if ${MACHINE_ARCH} == i386
+FFLAGS += -malign-double
+CFLAGS += -malign-double
+.endif
+.if ${OSVERSION} < 400005
+FFLAGS += -Nn802 -Nx400
+.else
@ -30,9 +26,9 @@
# Silicon Graphics
#CFLAGS = -c -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0
@@ -46,11 +64,11 @@
# when using gfortran, replace g77 with gfortran and comment out the line
# 'external iargc' in molden.f
@@ -52,11 +66,11 @@
# with GCC4.0 or higher replace the line with:
# 'external gfortran_iargc'
#
-CFLAGS = -c -I/usr/X11R6/include -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0
-FC = g77
@ -47,8 +43,8 @@
# 64 bit machines:
#LIBS = -L/usr/X11R6/lib64 -lX11 -lm
#
@@ -178,7 +196,7 @@
# and the full opengl version of molden 'gmolden'
@@ -191,7 +205,7 @@
# and the full opengl version of molden 'gmolden', (does not need glut)
# (make gmolden)
#
-LIBSOGL = -lglut -lGLU -lGL -lXmu -lX11 -lm
@ -56,12 +52,12 @@
#
# on linux :
#
@@ -201,7 +219,7 @@
#
#LIBSG = -L/usr/X11R6/lib -Wl,-framework -Wl,GLUT -Wl,-framework -Wl,OpenGL -Wl,-framework -Wl,Cocoa -lGLU -lGL -lXmu -lX11 -lm
@@ -227,7 +241,7 @@
$(MAKE) -C ambfor
-
+all: molden moldenogl
surf/surf: surf/*.h surf/*.c
- $(MAKE) -C surf depend
+# $(MAKE) -C surf depend
$(MAKE) -C surf
molden: $(OBJS) mpdum.o xwin.o
$(LDR) -o molden $(OBJS) $(SOBJ) mpdum.o xwin.o $(LIBS)
# noxwin will not work as long as the old ocglbck calls arent in dummys

10
biology/molden/files/patch-molden.f
View File

@ -1,10 +0,0 @@
--- molden.f~ Mon Jul 10 20:46:06 2006
+++ molden.f Tue Jan 9 10:43:24 2007
@@ -255,7 +255,6 @@
common /vrmlhl/ spcdfil
common /pmflvl/ ipmfm,ipmfh,pmflev(mxpmfl),levcol(mxpmfl)
common /comsrf/ vo(3), rt(3),v1t(3),v2t(3),v3t(3)
- external iargc
dimension fcnt(mxcntr)
character title*80, keywrd*160, keyhlp*80, keyori*160
character tmpstr*80,movfil*80,vrmlfil*80,povfil*80,oglfil*80

165
biology/molden/files/patch-surf-makefile Normal file
View File

@ -0,0 +1,165 @@
--- surf/Makefile.orig 2008-10-30 10:12:27.000000000 +0100
+++ surf/Makefile 2008-10-30 10:08:43.000000000 +0100
@@ -63,46 +63,120 @@
# DO NOT DELETE THIS LINE -- make depend depends on it.
-# DO NOT DELETE THIS LINE -- make depend depends on it.
+# DO NOT DELETE
-surf.o: surf.h /usr/include/stdio.h /usr/include/math.h /usr/include/stdlib.h
-surf.o: /usr/include/sgidefs.h /usr/include/string.h /usr/include/sys/time.h
-surf.o: linalg.h
-io.o: surf.h /usr/include/stdio.h /usr/include/math.h /usr/include/stdlib.h
-io.o: /usr/include/sgidefs.h /usr/include/string.h /usr/include/sys/time.h
-io.o: linalg.h
-compute.o: surf.h /usr/include/stdio.h /usr/include/math.h
-compute.o: /usr/include/stdlib.h /usr/include/sgidefs.h /usr/include/string.h
-compute.o: /usr/include/sys/time.h linalg.h chull.h dual.h
-dual.o: surf.h /usr/include/stdio.h /usr/include/math.h /usr/include/stdlib.h
-dual.o: /usr/include/sgidefs.h /usr/include/string.h /usr/include/sys/time.h
-dual.o: linalg.h dual.h chull.h
-utils.o: surf.h /usr/include/stdio.h /usr/include/math.h
-utils.o: /usr/include/stdlib.h /usr/include/sgidefs.h /usr/include/string.h
-utils.o: /usr/include/sys/time.h linalg.h
-lp.o: surf.h /usr/include/stdio.h /usr/include/math.h /usr/include/stdlib.h
-lp.o: /usr/include/sgidefs.h /usr/include/string.h /usr/include/sys/time.h
-lp.o: linalg.h
-chull.o: surf.h /usr/include/stdio.h /usr/include/math.h
-chull.o: /usr/include/stdlib.h /usr/include/sgidefs.h /usr/include/string.h
-chull.o: /usr/include/sys/time.h linalg.h chull.h
-tessel_cases.o: surf.h /usr/include/stdio.h /usr/include/math.h
-tessel_cases.o: /usr/include/stdlib.h /usr/include/sgidefs.h
-tessel_cases.o: /usr/include/string.h /usr/include/sys/time.h linalg.h dual.h
-tessel_patches.o: surf.h /usr/include/stdio.h /usr/include/math.h
-tessel_patches.o: /usr/include/stdlib.h /usr/include/sgidefs.h
-tessel_patches.o: /usr/include/string.h /usr/include/sys/time.h linalg.h
-tessel_convex.o: surf.h /usr/include/stdio.h /usr/include/math.h
-tessel_convex.o: /usr/include/stdlib.h /usr/include/sgidefs.h
-tessel_convex.o: /usr/include/string.h /usr/include/sys/time.h linalg.h
-tessel_concave.o: surf.h /usr/include/stdio.h /usr/include/math.h
-tessel_concave.o: /usr/include/stdlib.h /usr/include/sgidefs.h
-tessel_concave.o: /usr/include/string.h /usr/include/sys/time.h linalg.h
-tessel_torus.o: surf.h /usr/include/stdio.h /usr/include/math.h
-tessel_torus.o: /usr/include/stdlib.h /usr/include/sgidefs.h
-tessel_torus.o: /usr/include/string.h /usr/include/sys/time.h linalg.h
-
-# DEPENDENCIES MUST END AT END OF FILE
-# IF YOU PUT STUFF HERE IT WILL GO AWAY
-# see make depend above
-
+surf.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.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/_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/_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
+dual.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
+dual.o: /usr/include/sys/_null.h /usr/include/sys/_types.h
+dual.o: /usr/include/machine/_types.h /usr/include/math.h
+dual.o: /usr/include/machine/_limits.h /usr/include/stdlib.h
+dual.o: /usr/include/string.h /usr/include/strings.h /usr/include/sys/time.h
+dual.o: /usr/include/sys/_timeval.h /usr/include/sys/types.h
+dual.o: /usr/include/machine/endian.h /usr/include/sys/_pthreadtypes.h
+dual.o: /usr/include/sys/select.h /usr/include/sys/_sigset.h
+dual.o: /usr/include/sys/timespec.h /usr/include/time.h linalg.h dual.h
+dual.o: chull.h
+utils.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
+utils.o: /usr/include/sys/_null.h /usr/include/sys/_types.h
+utils.o: /usr/include/machine/_types.h /usr/include/math.h
+utils.o: /usr/include/machine/_limits.h /usr/include/stdlib.h
+utils.o: /usr/include/string.h /usr/include/strings.h /usr/include/sys/time.h
+utils.o: /usr/include/sys/_timeval.h /usr/include/sys/types.h
+utils.o: /usr/include/machine/endian.h /usr/include/sys/_pthreadtypes.h
+utils.o: /usr/include/sys/select.h /usr/include/sys/_sigset.h
+utils.o: /usr/include/sys/timespec.h /usr/include/time.h linalg.h
+lp.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
+lp.o: /usr/include/sys/_null.h /usr/include/sys/_types.h
+lp.o: /usr/include/machine/_types.h /usr/include/math.h
+lp.o: /usr/include/machine/_limits.h /usr/include/stdlib.h
+lp.o: /usr/include/string.h /usr/include/strings.h /usr/include/sys/time.h
+lp.o: /usr/include/sys/_timeval.h /usr/include/sys/types.h
+lp.o: /usr/include/machine/endian.h /usr/include/sys/_pthreadtypes.h
+lp.o: /usr/include/sys/select.h /usr/include/sys/_sigset.h
+lp.o: /usr/include/sys/timespec.h /usr/include/time.h linalg.h
+chull.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
+chull.o: /usr/include/sys/_null.h /usr/include/sys/_types.h
+chull.o: /usr/include/machine/_types.h /usr/include/math.h
+chull.o: /usr/include/machine/_limits.h /usr/include/stdlib.h
+chull.o: /usr/include/string.h /usr/include/strings.h /usr/include/sys/time.h
+chull.o: /usr/include/sys/_timeval.h /usr/include/sys/types.h
+chull.o: /usr/include/machine/endian.h /usr/include/sys/_pthreadtypes.h
+chull.o: /usr/include/sys/select.h /usr/include/sys/_sigset.h
+chull.o: /usr/include/sys/timespec.h /usr/include/time.h linalg.h chull.h
+tessel_cases.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
+tessel_cases.o: /usr/include/sys/_null.h /usr/include/sys/_types.h
+tessel_cases.o: /usr/include/machine/_types.h /usr/include/math.h
+tessel_cases.o: /usr/include/machine/_limits.h /usr/include/stdlib.h
+tessel_cases.o: /usr/include/string.h /usr/include/strings.h
+tessel_cases.o: /usr/include/sys/time.h /usr/include/sys/_timeval.h
+tessel_cases.o: /usr/include/sys/types.h /usr/include/machine/endian.h
+tessel_cases.o: /usr/include/sys/_pthreadtypes.h /usr/include/sys/select.h
+tessel_cases.o: /usr/include/sys/_sigset.h /usr/include/sys/timespec.h
+tessel_cases.o: /usr/include/time.h linalg.h dual.h
+tessel_patches.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
+tessel_patches.o: /usr/include/sys/_null.h /usr/include/sys/_types.h
+tessel_patches.o: /usr/include/machine/_types.h /usr/include/math.h
+tessel_patches.o: /usr/include/machine/_limits.h /usr/include/stdlib.h
+tessel_patches.o: /usr/include/string.h /usr/include/strings.h
+tessel_patches.o: /usr/include/sys/time.h /usr/include/sys/_timeval.h
+tessel_patches.o: /usr/include/sys/types.h /usr/include/machine/endian.h
+tessel_patches.o: /usr/include/sys/_pthreadtypes.h /usr/include/sys/select.h
+tessel_patches.o: /usr/include/sys/_sigset.h /usr/include/sys/timespec.h
+tessel_patches.o: /usr/include/time.h linalg.h
+tessel_convex.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
+tessel_convex.o: /usr/include/sys/_null.h /usr/include/sys/_types.h
+tessel_convex.o: /usr/include/machine/_types.h /usr/include/math.h
+tessel_convex.o: /usr/include/machine/_limits.h /usr/include/stdlib.h
+tessel_convex.o: /usr/include/string.h /usr/include/strings.h
+tessel_convex.o: /usr/include/sys/time.h /usr/include/sys/_timeval.h
+tessel_convex.o: /usr/include/sys/types.h /usr/include/machine/endian.h
+tessel_convex.o: /usr/include/sys/_pthreadtypes.h /usr/include/sys/select.h
+tessel_convex.o: /usr/include/sys/_sigset.h /usr/include/sys/timespec.h
+tessel_convex.o: /usr/include/time.h linalg.h
+tessel_concave.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.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/_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

82
biology/molden/files/patch-xwin.c
View File

@ -1,15 +1,15 @@
--- xwin.c~ Mon Jul 10 20:46:06 2006
+++ xwin.c Tue Jan 9 10:43:24 2007
@@ -3177,7 +3177,7 @@
static int *icopth;
static int *icoptl;
static int *icoptm;
--- xwin.c.orig 2008-11-03 09:37:45.707629185 -0500
+++ xwin.c 2008-11-03 09:37:55.118628907 -0500
@@ -3747,7 +3747,7 @@
static int ibopth = 0;
static int iboptl = 0;
static int iboptm = 0;
-static int linkat = 0;
+static int link_at = 0;
static QBOXSTRU IANZboxes[MAXAT];
static QBOXSTRU IZboxes[MAXAT][4];
@@ -11622,7 +11622,7 @@
@@ -19086,7 +19086,7 @@
if (ioniom == 1) {
int ism, isl;
@ -18,20 +18,20 @@
/* Counting the number of Link atoms between H and lower
levels*/
@@ -11635,10 +11635,10 @@
@@ -19099,10 +19099,10 @@
if (ionij != 0) continue;
nconn = atomptr->iconn[j][0];
nconn = xyzp->iconn[j*(MXCON+1)];
for (k=1;k<=nconn;k++) {
- if (ityp[atomptr->iconn[j][k]-1]/10000 > 0) linkat++;
+ if (ityp[atomptr->iconn[j][k]-1]/10000 > 0) link_at++;
- if (xyzp->ityp[xyzp->iconn[j*(MXCON+1)+k]-1]/10000 > 0) linkat++;
+ if (xyzp->ityp[xyzp->iconn[j*(MXCON+1)+k]-1]/10000 > 0) link_at++;
}
}
- linkat += 20000;
+ link_at += 20000;
*itotc = *icopth;
*imult = *ispopth;
jobcom->itotc = jobcom->icopth;
jobcom->imult = jobcom->ispopth;
if (CheckChargeMult()) {
@@ -11659,7 +11659,7 @@
@@ -19123,7 +19123,7 @@
} else if (ioniom == 2) {
@ -40,20 +40,20 @@
/* Counting the number of Link atoms between H and
lower levels*/
@@ -11669,10 +11669,10 @@
@@ -19133,10 +19133,10 @@
if(ionij != 0) continue;
nconn = atomptr->iconn[j][0];
nconn = xyzp->iconn[j*(MXCON+1)];
for (k=1;k<=nconn;k++) {
- if (ityp[atomptr->iconn[j][k]-1]/10000 > 0) linkat++;
+ if (ityp[atomptr->iconn[j][k]-1]/10000 > 0) link_at++;
- if (xyzp->ityp[xyzp->iconn[j*(MXCON+1)+k]-1]/10000 > 0) linkat++;
+ if (xyzp->ityp[xyzp->iconn[j*(MXCON+1)+k]-1]/10000 > 0) link_at++;
}
}
- linkat += 20000;
+ link_at += 20000;
*itotc = *icopth;
*imult = *ispopth;
jobcom->itotc = jobcom->icopth;
jobcom->imult = jobcom->ispopth;
if (CheckChargeMult()) {
@@ -11684,7 +11684,7 @@
@@ -19148,7 +19148,7 @@
break;
*/
}
@ -62,29 +62,29 @@
/* Counting the number of Link atoms between H+M and
lower levels*/
@@ -11694,10 +11694,10 @@
@@ -19158,10 +19158,10 @@
if (ionij == 2) continue;
nconn = atomptr->iconn[j][0];
nconn = xyzp->iconn[j*(MXCON+1)];
for (k=1;k<=nconn;k++) {
- if (ityp[atomptr->iconn[j][k]-1]/10000 == 2) linkat++;
+ if (ityp[atomptr->iconn[j][k]-1]/10000 == 2) link_at++;
- if (xyzp->ityp[xyzp->iconn[j*(MXCON+1)+k]-1]/10000 == 2) linkat++;
+ if (xyzp->ityp[xyzp->iconn[j*(MXCON+1)+k]-1]/10000 == 2) link_at++;
}
}
- linkat += 20000;
+ link_at += 20000;
*itotc = *icoptm;
*imult = *ispoptm;
jobcom->itotc = jobcom->icoptm;
jobcom->imult = jobcom->ispoptm;
if (CheckChargeMult()) {
@@ -11712,7 +11712,7 @@
icopt = *icoptl+3;
ispopt = *ispoptl-1;
@@ -19176,7 +19176,7 @@
icopt = jobcom->icoptl+3;
ispopt = jobcom->ispoptl-1;
}
- linkat = 0;
+ link_at = 0;
*itotc = icopt - 3;
*imult = ispopt + 1;
*ito = itopt[jmode] + 1;
@@ -11964,10 +11964,10 @@
jobcom->itotc = icopt - 3;
jobcom->imult = ispopt + 1;
jobcom->ito = itopt[jmode] + 1;
@@ -19428,10 +19428,10 @@
ionil = 0;
if (ioniom) {
@ -97,18 +97,18 @@
+ link_at = 0;
}
if (*zmptr.ihaszm) {
@@ -11990,10 +11990,10 @@
if (*zmptrp->ihaszm) {
@@ -19454,10 +19454,10 @@
}
}
/*
- fprintf(stderr,"ionil %d ne %d itotc %d linkat %d mult %d\n",
- ionil,ne,*itotc,linkat,*imult);
- ionil,ne,jobcom->itotc,linkat,jobcom->imult);
+ fprintf(stderr,"ionil %d ne %d itotc %d link_at %d mult %d\n",
+ ionil,ne,*itotc,link_at,*imult);
+ ionil,ne,jobcom->itotc,link_at,jobcom->imult);
*/
- ne = ne - *itotc + linkat;
+ ne = ne - *itotc + link_at;
if (ne % 2 == *imult % 2) return(1);
- ne = ne - jobcom->itotc + linkat;
+ ne = ne - jobcom->itotc + link_at;
if (ne % 2 == jobcom->imult % 2) return(1);
return(0);
}

115
biology/molden/pkg-plist
View File

@ -1,56 +1,61 @@
bin/ambfor
bin/gmolden
bin/molden
bin/moldenogl
%%PORTDOCS%%%%DOCSDIR%%/figures.ps.Z
%%PORTDOCS%%%%DOCSDIR%%/manual.ps.Z
%%PORTDOCS%%%%DOCSDIR%%/manual.txt.Z
%%PORTDOCS%%share/molden/test/adf.molf
%%PORTDOCS%%share/molden/test/ampac.arc
%%PORTDOCS%%share/molden/test/ampac.test
%%PORTDOCS%%share/molden/test/bucky.xyz
%%PORTDOCS%%share/molden/test/chemx.test
%%PORTDOCS%%share/molden/test/complex2.out
%%PORTDOCS%%share/molden/test/cpeptide.gro
%%PORTDOCS%%share/molden/test/esp.test
%%PORTDOCS%%share/molden/test/esp.txt
%%PORTDOCS%%share/molden/test/esp.xyz
%%PORTDOCS%%share/molden/test/fragment
%%PORTDOCS%%share/molden/test/gamess_uk.freq
%%PORTDOCS%%share/molden/test/gamess_uk.input
%%PORTDOCS%%share/molden/test/gamess_uk.test1
%%PORTDOCS%%share/molden/test/gamess_uk.test2
%%PORTDOCS%%share/molden/test/gamess_us.h2o_631g_opt.out
%%PORTDOCS%%share/molden/test/gamess_us.irc
%%PORTDOCS%%share/molden/test/gamess_us_uhf_opt
%%PORTDOCS%%share/molden/test/gaussian.freq
%%PORTDOCS%%share/molden/test/gaussian.input
%%PORTDOCS%%share/molden/test/gaussian.test
%%PORTDOCS%%share/molden/test/jaguar.cube
%%PORTDOCS%%share/molden/test/molden.ogl
%%PORTDOCS%%share/molden/test/mopac.freq
%%PORTDOCS%%share/molden/test/mopac.test
%%PORTDOCS%%share/molden/test/pdb.test
%%PORTDOCS%%share/molden/test/qchem.test
%%PORTDOCS%%share/molden/test/reacpth.xyz
%%PORTDOCS%%share/molden/test/shelx.ins
%%PORTDOCS%%share/molden/test/surface.molf
%%PORTDOCS%%share/molden/test/test.fdat
%%PORTDOCS%%share/molden/test/test.mol2
%%PORTDOCS%%share/molden/test/test_homo.cube
%%PORTDOCS%%share/molden/test/tinker_charmm.xyz
%%PORTDOCS%%share/molden/test/tinker_mm3.xyz
%%PORTDOCS%%share/molden/test/uracil.fdat
%%PORTDOCS%%share/molden/test/uracil_gauss.out
%%PORTDOCS%%share/molden/test/vamp.test
%%PORTDOCS%%share/molden/utils/INFO
%%PORTDOCS%%share/molden/utils/ch_backspace
%%PORTDOCS%%share/molden/utils/ch_mxcon
%%PORTDOCS%%share/molden/utils/ch_par
%%PORTDOCS%%share/molden/utils/colors
%%PORTDOCS%%share/molden/utils/ircextract.awk
%%PORTDOCS%%share/molden/utils/molden
%%PORTDOCS%%share/molden/utils/multi_vrml.csh
%%PORTDOCS%%share/molden/utils/multi_vrml_orbitals.csh
%%PORTDOCS%%@dirrm share/molden/test
%%PORTDOCS%%@dirrm share/molden/utils
%%PORTDOCS%%@dirrm share/molden
%%PORTDOCS%%@dirrm %%DOCSDIR%%
bin/surf
share/doc/molden/figures.ps.Z
share/doc/molden/manual.ps.Z
share/doc/molden/manual.txt.Z
share/molden/test/adf.molf
share/molden/test/ambfor_amber.xyz
share/molden/test/ambfor_gaff.xyz
share/molden/test/ampac.arc
share/molden/test/ampac.test
share/molden/test/bucky.xyz
share/molden/test/chemx.test
share/molden/test/complex2.out
share/molden/test/cpeptide.gro
share/molden/test/esp.test
share/molden/test/esp.txt
share/molden/test/esp.xyz
share/molden/test/fragment
share/molden/test/gamess_uk.freq
share/molden/test/gamess_uk.input
share/molden/test/gamess_uk.test1
share/molden/test/gamess_uk.test2
share/molden/test/gamess_us.h2o_631g_opt.out
share/molden/test/gamess_us.irc
share/molden/test/gamess_us_uhf_opt
share/molden/test/gaussian.freq
share/molden/test/gaussian.input
share/molden/test/gaussian.test
share/molden/test/jaguar.cube
share/molden/test/molden.ogl
share/molden/test/mopac.freq
share/molden/test/mopac.test
share/molden/test/pdb.test
share/molden/test/pdb.test.omap
share/molden/test/qchem.test
share/molden/test/reacpth.xyz
share/molden/test/shelx.ins
share/molden/test/surface.molf
share/molden/test/test.fdat
share/molden/test/test.mol2
share/molden/test/test_homo.cube
share/molden/test/tinker_charmm.xyz
share/molden/test/tinker_mm3.xyz
share/molden/test/uracil.fdat
share/molden/test/uracil_gauss.out
share/molden/test/vamp.test
share/molden/utils/INFO
share/molden/utils/ch_backspace
share/molden/utils/ch_mxcon
share/molden/utils/ch_par
share/molden/utils/colors
share/molden/utils/ircextract.awk
share/molden/utils/molden
share/molden/utils/multi_vrml.csh
share/molden/utils/multi_vrml_orbitals.csh
@dirrm share/molden/utils
@dirrm share/molden/test
@dirrm share/molden
@dirrm share/doc/molden