add gaussian98, an ab-initio molecular orbital calculation program.

PR:             23577
Submitted by:   NAKATA, Maho <chat95@mbox.kyoto-inet.or.jp>

biology/Makefile

@@ -8,6 +8,7 @@
     SUBDIR += deft
     SUBDIR += emboss
     SUBDIR += fastdnaml
+    SUBDIR += gaussian98
     SUBDIR += gperiodic
     SUBDIR += hmmer
     SUBDIR += kinemage

biology/gaussian98/Makefile

@@ -0,0 +1,73 @@
+# New ports collection makefile for:	gaussian98
+# Date created:		Feb 10 2001
+# Whom:			NAKATA, Maho <chat95@mbox.kyoto-inet.or.jp>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	gaussian98
+PORTVERSION=	1.0.7
+CATEGORIES=	biology
+MASTER_SITES=	file:${CD_MOUNTPT}/TAR/
+DISTNAME=	WKSSRC
+EXTRACT_SUFX=	.TAR
+
+MAINTAINER=	chat95@mbox.kyoto-inet.or.jp
+
+LIB_DEPENDS=	blas:${PORTSDIR}/math/blas
+
+USE_GMAKE=	yes
+INSTALLS_SHLIB=	yes
+WRKSRC=		${WRKDIR}/g98
+
+NO_CDROM=	"You must purchase a licensed copy from Gaussian inc."
+NO_PACKAGE=	"You must purchase a licensed copy from Gaussian inc."
+RESTRICTED=	"You must purchase a licensed copy from Gaussian inc."
+
+.include <bsd.port.pre.mk>
+
+.if ${OSVERSION} < 400013
+USE_NEWGCC=	yes
+F77?=		g77
+.else
+F77?=		f77
+.endif
+
+post-extract:
+	${RM} ${DISTDIR}/${DISTFILES}
+
+post-patch:
+	@${SED} -e s+@PREFIX@+${PREFIX}+ ${FILESDIR}/gaussian98  > ${WRKSRC}/gaussian98
+	@${ECHO} "You can override and FFLAGS on the command line."
+	@${ECHO} "Following is an recommended one."
+	@${ECHO} "make FFLAGS=\"-malign-double -fexpensive-optimizations -O4 -ffast-math -funroll-loops\""
+
+MAKE_ENV=	"GMAKE=${GMAKE} F77=${F77} PREFIX=${PREFIX}"
+
+do-build:
+	(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} csh ./bsd/bldg98)
+
+do-install:
+	@${MKDIR} ${PREFIX}/bin/g98/bsd \
+	 	  ${PREFIX}/share/gaussian98/explore/examples \
+	 	  ${PREFIX}/share/gaussian98/explore/exercise \
+		  ${PREFIX}/share/gaussian98/explore/quick
+	@(cd ${WRKSRC}/bsd; \
+	  ${INSTALL_SCRIPT} gau-unlimit set-mflags g98.login \
+		${PREFIX}/bin/g98/bsd; \
+	  cd ${WRKSRC}; \
+	  ${INSTALL_PROGRAM} gauopt ghelp newzmat testrt cubegen cubman \
+		c8698 ham506 cktoig rwfdump chkmove freqchk freqmem formchk \
+		demofc chkchk pluck unfchk g98 *.exe gau-machine \
+		${PREFIX}/bin/g98; \
+	  ${INSTALL_SCRIPT} gaussian98 ${PREFIX}/bin; \
+	  ${INSTALL_DATA} ${WRKSRC}/libgauutil.so.1 ${PREFIX}/lib; \
+	  cd ${PREFIX}/lib; ${LN} -sf libgauutil.so.1 libgauutil.so; \
+	  cd ${WRKSRC}/explore/examples; \
+	  ${INSTALL_DATA} * ${PREFIX}/share/gaussian98/explore/examples; \
+	  cd ${WRKSRC}/explore/exercise; \
+	  ${INSTALL_DATA} *  ${PREFIX}/share/gaussian98/explore/exercise; \
+	  cd ${WRKSRC}/explore/quick; \
+	  ${INSTALL_DATA} * ${PREFIX}/share/gaussian98/explore/quick)
+
+.include <bsd.port.post.mk>

biology/gaussian98/distinfo

@@ -0,0 +1 @@
+MD5 (WKSSRC.TAR) = a02fb7694140912c2e45905c3bbc26fa

biology/gaussian98/files/gaussian98

@@ -0,0 +1,15 @@
+#!/bin/csh -f
+#   usage:  gaussian98 InputFile 
+# 
+setenv g98root @PREFIX@/bin/
+setenv GAUSS_SCRDIR $cwd
+source @PREFIX@/bin/g98/bsd/g98.login
+setenv GAUSS_EXEDIR @PREFIX@/bin/g98
+if ($#argv == 0 ) then
+	echo "Usage: gaussian98 <input file>"
+	echo "   or  gaussian98 <input file> <output file>"
+else if ($#argv == 1 ) then
+	cat $1 | @PREFIX@/bin/g98/g98 
+else
+	cat $1 | @PREFIX@/bin/g98/g98 >& $2
+endif 

biology/gaussian98/files/patch-aa

@@ -0,0 +1,11 @@
+--- bsd/bldg98.orig	Thu Jun 10 01:50:31 1999
++++ bsd/bldg98	Sun Dec 10 20:01:51 2000
+@@ -13,7 +13,7 @@
+ #
+ uname -a
+ set makeflag = ""
+-set makename = "make"
++set makename = "${GMAKE}"
+ setenv TMPDIR .
+ setenv LC_COLLATE C
+ setenv LANG C

biology/gaussian98/files/patch-ab

@@ -0,0 +1,345 @@
+--- bsd/i386.make.orig	Sun May 16 09:08:58 1999
++++ bsd/i386.make	Thu Feb  8 12:13:25 2001
+@@ -48,12 +48,12 @@
+ #
+ # switch the following two lines if the optimized blas library is not available.  This
+ # library is highly recommended
+-# BLAS = blas.a
+-BLAS = /usr/local/lib/blas-opt.a /usr/local/lib/blas-f2c.a
++BLAS = -lblas
++# BLAS = /usr/local/lib/blas-opt.a /usr/local/lib/blas-f2c.a
+ BLASFLAG = -DCA1_DGEMM -DCA2_DGEMM -DCAB_DGEMM -DLV_DSP
+ # switch the following two lines if compilation for the pentium is desired instead
+ # of for the P6/Pentium-II
+-MACH = -tp p6 
++MACH = #-tp p6 
+ # MACH = -tp p5
+ #
+ BSDDIR = bsd
+@@ -61,6 +61,7 @@
+ BSDDIR1 = ../bsd
+ MAKELOC1 = -f $(BSDDIR1)/g98.make
+ UTILDIR = ..
++LDFLAGS = -L${PREFIX}/lib
+ HLIBDIR = $(g98root)/hermes/lib
+ HSRC = $(g98root)/hermes/gxinterface
+ HINC = $(g98root)/hermes/include
+@@ -72,7 +73,7 @@
+ #
+ GAULIBA = util.a 
+ #GAULIB = $(GAULIBA) $(BLAS)
+-GAULIB = util.so
++GAULIB = libgauutil.so.1 $(BLAS)
+ #
+ # Directory pointers only used for linking the profiling version:
+ #
+@@ -96,35 +97,36 @@
+ # control compilation.
+ #
+ RUNF2C = f2c -kr -T. -R -Nx400 -Nn1604 -NL800
+-RUNCC = cc -g
++RUNCC = $(CC) -g
+ RUNAR  = ar
+ RUNRAN = ranlib
+ RUNCPP = gau-cpp
+ RUNFSP = gau-fsplit
+-RUNMAKE = make#
+-OPTFLAGO = -malign-double -m486 -fexpensive-optimizations -O3 -ffast-math -funroll-loops
+-# Flags for portland compiler.
++RUNMAKE = ${GMAKE}
++OPTFLAGO = 
++# Flags for G77(GNU fortran compiler)
+ #
+-RUNF77 = pgf77 
++RUNF77 = ${F77}
+ F2CLIB =
+ LIBS = 
+-UNROLL = -Munroll
+-VECTOR = -Mvect=cachesize:524288
++UNROLL = #-Munroll
++VECTOR = #-Mvect=cachesize:524288
+ TWOH = 
+-PC64 = -pc 64 -Kieee
++PC64 = #-pc 64 -Kieee
+ #
+ # Standard compilation flags:
+ #
+ DIMENS = $(DIMENSX) $(TWOH)
+-FNOOPT = $(PROFFLAG) -O0 $(TIME)
+-FNOOPT64 = $(FNOOPT) $(PC64)
+-FOPT1 = $(PROFFLAG) -O1 $(MACH)
+-FOPT2 = $(PROFFLAG) -O2 $(MACH)
+-FOPT2UN = $(FOPT2) $(UNROLL)
+-FOPT2VC = $(FOPT2) $(VECTOR)
+-OPTFLAG = $(FOPT2) $(UNROLL) $(VECTOR)
+-FFLAGS = $(PROFFLAG) $(OPTFLAG)
+-CFLAGS = $(DIMENS) $(OPTFLAGO) $(PROFFLAG)
++# g77+FreeBSD box is stable enough
++FNOOPT = $(PROFFLAG) $(FFLAGS)
++FNOOPT64 = $(PROFFLAG) $(FFLAGS)
++FOPT1 = $(PROFFLAG) $(FFLAGS)
++FOPT2 = $(PROFFLAG) $(FFLAGS)
++FOPT2UN = $(PROFFLAG) $(FFLAGS)
++FOPT2VC = $(PROFFLAG) $(FFLAGS)
++#OPTFLAG = $(FOPT2) $(UNROLL) $(VECTOR)
++#FFLAGS = $(PROFFLAG) $(OPTFLAGS) 
++CFLAGS = $(DIMENS) $(PROFFLAG) #$(OPTFLAGO) 
+ EXTOBJ =
+ TESTRTO = 
+ #
+@@ -136,7 +138,11 @@
+ #
+ # Rules for Fortran and C compilation, possible including "on machine"
+ #
+-#.F.o:
++.F.o:
++%.o : %.F
++	$(RUNCPP) $(DIMENS) $*.F $*.f
++	$(RUNF77) $(FFLAGS) -c $*.f
++	rm -f $*.f $*.c
+ %.o : %.F
+ 	$(RUNCPP) $(DIMENS) $*.F $*.f
+ 	$(RUNF77) $(FFLAGS) -c $*.f
+@@ -241,7 +247,7 @@
+ 	- (cd extras ; make -f extras.make delexe)
+ 
+ clean: delexe
+-	rm -f util.so cubegen *.a *.o *.lo local/*.a local/*.o local/rpac/*.a \
++	rm -f libgauutil.so.1 cubegen *.a *.o *.lo local/*.a local/*.o local/rpac/*.a \
+ 	  local/rpac/*.o bsd/g98.make local/rpac/rpac.make
+ 	- (cd extras ; make -f extras.make clean)
+ #
+@@ -257,18 +263,31 @@
+ #
+ # The generic command line for making a link from its library:
+ #
+-#.F.exe: 
++.F.exe: 
++	$(RUNFSP) -e m$* $(BSDDIR)/main.F
++	$(RUNMAKE) $(MAKELOC) OPTFLAG='$(OPTFLAG)' $(EXTRAS) $*.a m$*.o
++	$(RUNF77) $(FFLAGS) $(LDFLAGS) -o $*.exe m$*.o $(EXTOBJ) $*.a $(EXTRAS) $(GAULIB) $(LIBS)
++	rm -f m$*.*
+ %.exe : %.F
+ 	$(RUNFSP) -e m$* $(BSDDIR)/main.F
+ 	$(RUNMAKE) $(MAKELOC) OPTFLAG='$(OPTFLAG)' $(EXTRAS) $*.a m$*.o
+-	$(RUNF77) $(FFLAGS) -o $*.exe m$*.o $(EXTOBJ) $*.a $(EXTRAS) $(GAULIB) $(LIBS)
++	$(RUNF77) $(FFLAGS) $(LDFLAGS) -o $*.exe m$*.o $(EXTOBJ) $*.a $(EXTRAS) $(GAULIB) $(LIBS)
+ 	rm -f m$*.*
+ 
+ #
+ #
+ # The generic command for making a link library from source:
+ #
+-#.F.a:
++.F.a:
++	rm -f -r temp-$*
++	mkdir temp-$*
++	(cd temp-$* ; $(RUNFSP) ../$*.F ; \
++	  $(BSDDIR1)/updatelink1 $(BSDDIR1)/g98.make OPTFLAG='$(OPTFLAG)' DO-LIB [a-l]*.F ; \
++	  ($(RUNAR) rlv ../$*.a [a-l]*.o; exit 0); \
++	  $(BSDDIR1)/updatelink1 $(BSDDIR1)/g98.make OPTFLAG='$(OPTFLAG)' DO-LIB [m-z]*.F ; \
++	  ($(RUNAR) rlv ../$*.a [m-z]*.o; exit 0))
++	rm -f -r temp-$*
++	$(RUNRAN) $*.a
+ %.a : %.F
+ 	rm -f -r temp-$*
+ 	mkdir temp-$*
+@@ -335,78 +354,78 @@
+ g98: $(GAULIB) $(EXTRAS)
+ 	$(RUNFSP) -e ml0 $(BSDDIR)/main.F
+ 	$(RUNMAKE) $(MAKELOC) OPTFLAG='$(OPTFLAG)' $(EXTRAS) ml0.o
+-	$(RUNF77) $(FFLAGS) -o g98 ml0.o $(EXTOBJ) $(EXTRAS) $(GAULIB) $(LIBS)
++	$(RUNF77) $(FFLAGS) $(LDFLAGS) -o g98 ml0.o $(EXTOBJ) $(EXTRAS) $(GAULIB) $(LIBS)
+ 	rm -f ml0.*
+ 
+ l302.exe l307.exe l314.exe l701.exe l703.exe l1101.exe l1110.exe: $(EXTRAS)
+ 	ar x $(GAULIBA) bdrys.o
+ 	$(RUNFSP) -e m$* $(BSDDIR)/main.F
+ 	$(RUNMAKE) $(MAKELOC) OPTFLAG='$(OPTFLAG)' $(EXTRAS) $*.a m$*.o 
+-	$(RUNF77) $(FFLAGS) -o $*.exe m$*.o $(EXTOBJ) $*.a bdrys.o $(EXTRAS) $(GAULIB) $(LIBS)
++	$(RUNF77) $(FFLAGS) $(LDFLAGS) -o $*.exe m$*.o $(EXTOBJ) $*.a bdrys.o $(EXTRAS) $(GAULIB) $(LIBS)
+ 	rm -f m$*.* bdrys.o 
+ 
+ l402.exe: $(EXTRAS) l402.a  
+ 	$(RUNFSP) -e m$* $(BSDDIR)/main.F
+ 	$(RUNMAKE) $(MAKELOC) OPTFLAG='$(OPTFLAG)' $(EXTRAS) $*.a m$*.o 
+ 	ar x l402.a bd0402.o
+-	$(RUNF77) $(FFLAGS) -o $*.exe m$*.o $(EXTOBJ) $*.a bd0402.o $(EXTRAS) $(GAULIB) $(LIBS)
++	$(RUNF77) $(FFLAGS) $(LDFLAGS) -o $*.exe m$*.o $(EXTOBJ) $*.a $(EXTRAS) $(GAULIB) $(LIBS)
+ 	rm -f m$*.* bd0402.o 
+ 
+ l609.exe: $(EXTRAS) l609.a  
+ 	$(RUNFSP) -e m$* $(BSDDIR)/main.F
+ 	$(RUNMAKE) $(MAKELOC) OPTFLAG='$(OPTFLAG)' $(EXTRAS) $*.a m$*.o 
+ 	ar x l609.a bd0609.o
+-	$(RUNF77) $(FFLAGS) -o $*.exe m$*.o $(EXTOBJ) $*.a bd0609.o $(EXTRAS) $(GAULIB) $(LIBS)
++	$(RUNF77) $(FFLAGS) $(LDFLAGS) -o $*.exe m$*.o $(EXTOBJ) $*.a $(EXTRAS) $(GAULIB) $(LIBS)
+ 	rm -f m$*.* bd0609.o 
+ 
+ l705.exe: $(EXTRAS) l306.a l705.a
+ 	$(RUNFSP) -e ml705 $(BSDDIR)/main.F
+ 	$(RUNMAKE) $(MAKELOC) OPTFLAG='$(OPTFLAG)' $(EXTRAS) ml705.o
+-	$(RUNF77) $(FFLAGS) -o l705.exe ml705.o $(EXTOBJ) l705.a l306.a $(EXTRAS) $(GAULIB) $(LIBS)
++	$(RUNF77) $(FFLAGS) $(LDFLAGS) -o l705.exe ml705.o $(EXTOBJ) l705.a l306.a $(EXTRAS) $(GAULIB) $(LIBS)
+ 	rm -f ml705.*
+ 
+ l709.exe: $(EXTRAS) l309.a l709.a
+ 	$(RUNFSP) -e ml709 $(BSDDIR)/main.F
+ 	$(RUNMAKE) $(MAKELOC) OPTFLAG='$(OPTFLAG)' $(EXTRAS) ml709.o
+-	$(RUNF77) $(FFLAGS) -o l709.exe ml709.o $(EXTOBJ) l709.a l309.a $(EXTRAS) $(GAULIB) $(LIBS)
++	$(RUNF77) $(FFLAGS) $(LDFLAGS) -o l709.exe ml709.o $(EXTOBJ) l709.a l309.a $(EXTRAS) $(GAULIB) $(LIBS)
+ 	rm -f ml709.*
+ 
+ l806.exe: $(EXTRAS) l806.a  
+ 	$(RUNFSP) -e m$* $(BSDDIR)/main.F
+ 	$(RUNMAKE) $(MAKELOC) OPTFLAG='$(OPTFLAG)' $(EXTRAS) $*.a m$*.o 
+ 	ar x l806.a bd0806.o
+-	$(RUNF77) $(FFLAGS) -o $*.exe m$*.o $(EXTOBJ) $*.a bd0806.o $(EXTRAS) $(GAULIB) $(LIBS)
++	$(RUNF77) $(FFLAGS) $(LDFLAGS) -o $*.exe m$*.o $(EXTOBJ) $*.a bd0806.o $(EXTRAS) $(GAULIB) $(LIBS)
+ 	rm -f m$*.* bd0806.o 
+ 
+ l1003.exe: $(EXTRAS) l510.a l1003.a
+ 	$(RUNFSP) -e ml1003 $(BSDDIR)/main.F
+ 	$(RUNMAKE) $(MAKELOC) OPTFLAG='$(OPTFLAG)' $(EXTRAS) ml1003.o
+-	$(RUNF77) $(FFLAGS) -o l1003.exe ml1003.o $(EXTOBJ) l1003.a l510.a $(EXTRAS) $(GAULIB) $(LIBS)
++	$(RUNF77) $(FFLAGS) $(LDFLAGS) -o l1003.exe ml1003.o $(EXTOBJ) l1003.a l510.a $(EXTRAS) $(GAULIB) $(LIBS)
+ 	rm -f ml1003.*
+ 
+ l1004.exe: $(EXTRAS) l1112.a l1004.a
+ 	$(RUNFSP) -e ml1004 $(BSDDIR)/main.F
+ 	$(RUNMAKE) $(MAKELOC) OPTFLAG='$(OPTFLAG)' $(EXTRAS) ml1004.o
+-	$(RUNF77) $(FFLAGS) -o l1004.exe ml1004.o $(EXTOBJ) l1004.a l1112.a $(EXTRAS) $(GAULIB) $(LIBS)
++	$(RUNF77) $(FFLAGS) $(LDFLAGS) -o l1004.exe ml1004.o $(EXTOBJ) l1004.a l1112.a $(EXTRAS) $(GAULIB) $(LIBS)
+ 	rm -f ml1004.*
+ 
+ l1014.exe: $(EXTRAS) l1112.a l1014.a l914.a
+ 	$(RUNFSP) -e ml1014 $(BSDDIR)/main.F
+ 	$(RUNMAKE) $(MAKELOC) OPTFLAG='$(OPTFLAG)' $(EXTRAS) ml1014.o
+-	$(RUNF77) $(FFLAGS) -o l1014.exe ml1014.o $(EXTOBJ) l1014.a l1112.a l914.a $(EXTRAS) $(GAULIB) $(LIBS)
++	$(RUNF77) $(FFLAGS) $(LDFLAGS) -o l1014.exe ml1014.o $(EXTOBJ) l1014.a l1112.a l914.a $(EXTRAS) $(GAULIB) $(LIBS)
+ 	rm -f ml1014.*
+ 
+ l9999.exe: $(EXTRAS) l9999.a dummy.o dummy-narch.o
+ 	$(RUNFSP) -e ml9999 $(BSDDIR)/main.F
+ 	$(RUNMAKE) $(MAKELOC) OPTFLAG='$(OPTFLAG)' $(EXTRAS) ml9999.o
+-	$(RUNF77) $(FFLAGS) -o l9999.exe ml9999.o $(EXTOBJ) $(EXTRAS) l9999.a \
++	$(RUNF77) $(FFLAGS) $(LDFLAGS) -o l9999.exe ml9999.o $(EXTOBJ) $(EXTRAS) l9999.a \
+ 	   dummy.o $(GAULIB) dummy-narch.o $(LIBS)
+ 	rm -f ml9999.*
+ 
+ l9999-hermes: $(EXTRAS) l9999.a archlib.a mdarch.a $(HLIBS) gxxlnk.o
+ 	$(RUNFSP) -e ml9999 $(BSDDIR)/main.F
+ 	$(RUNMAKE) $(MAKELOC) OPTFLAG='$(OPTFLAG)' $(EXTRAS) ml9999.o
+-	$(RUNF77) $(FFLAGS) -o l9999.exe ml9999.o $(EXTOBJ) $(EXTRAS) \
++	$(RUNF77) $(FFLAGS) $(LDFLAGS) -o l9999.exe ml9999.o $(EXTOBJ) $(EXTRAS) \
+ 	  gxxlnk.o l9999.a archlib.a mdarch.a $(GAULIB) dummy-narch.o \
+ 	  $(HLIBS) $(LIBS)
+ 	rm -f ml9999.*
+@@ -430,13 +449,13 @@
+ 
+ c8698: $(EXTRAS) c8698.o
+ 	$(RUNMAKE) $(MAKELOC) OPTFLAG='$(OPTFLAG)' $(EXTRAS) c8698.o
+-	$(RUNF77) $(FFLAGS) -o c8698 c8698.o $(EXTOBJ) $(EXTRAS) $(GAULIB) $(LIBS)
++	$(RUNF77) $(FFLAGS) $(LDFLAGS) -o c8698 c8698.o $(EXTOBJ) $(EXTRAS) $(GAULIB) $(LIBS)
+ 
+ chkchk: $(EXTRAS) chkchk.o
+-	$(RUNF77) $(FFLAGS) -o chkchk chkchk.o $(EXTOBJ) $(EXTRAS) $(GAULIB) $(LIBS)
++	$(RUNF77) $(FFLAGS) $(LDFLAGS) -o chkchk chkchk.o $(EXTOBJ) $(EXTRAS) $(GAULIB) $(LIBS)
+ 
+ cktoig: $(EXTRAS) cktoig.o
+-	$(RUNF77) $(FFLAGS) -o cktoig cktoig.o $(EXTOBJ) $(EXTRAS) $(GAULIB) $(LIBS)
++	$(RUNF77) $(FFLAGS) $(LDFLAGS) -o cktoig cktoig.o $(EXTOBJ) $(EXTRAS) $(GAULIB) $(LIBS)
+ 
+ crendx: crendx.o crendxmfl.o $(GAULIB) $(EXTRAS) archlib.a mdarch.a
+ 	$(RUNF77) $(FFLAGS) -o crendx crendx.o crendxmfl.o $(EXTOBJ) $(EXTRAS) \
+@@ -445,62 +464,62 @@
+ chkmove: chkmove.o
+ 	$(RUNFSP) -e mchkmov $(BSDDIR)/main.F
+ 	$(RUNMAKE) $(MAKELOC) OPTFLAG='$(OPTFLAG)' mchkmov.o
+-	$(RUNF77) $(FFLAGS) -o chkmove mchkmov.o chkmove.o \
++	$(RUNF77) $(FFLAGS) $(LDFLAGS) -o chkmove mchkmov.o chkmove.o \
+ 	  $(EXTOBJ) $(EXTRAS) $(GAULIB) $(LIBS)
+ 	rm mchkmov.*
+ 
+ cubman: cubman.o
+-	$(RUNF77) $(FFLAGS) -o cubman cubman.o $(EXTOBJ) $(EXTRAS) $(GAULIB) $(LIBS)
++	$(RUNF77) $(FFLAGS) $(LDFLAGS) -o cubman cubman.o $(EXTOBJ) $(EXTRAS) $(GAULIB) $(LIBS)
+ 
+ cubegen: cubegen.o
+-	$(RUNF77) $(FFLAGS) -o cubegen cubegen.o $(EXTOBJ) $(EXTRAS) $(GAULIB) $(LIBS)
++	$(RUNF77) $(FFLAGS) $(LDFLAGS) -o cubegen cubegen.o $(EXTOBJ) $(EXTRAS) $(GAULIB) $(LIBS)
+ 
+ freqchk: freqchk.o l716.a newzmat.a
+-	$(RUNF77) $(FFLAGS) -o freqchk freqchk.o l716.a newzmat.a $(EXTOBJ) $(EXTRAS) $(GAULIB) $(LIBS)
++	$(RUNF77) $(FFLAGS) $(LDFLAGS) -o freqchk freqchk.o l716.a newzmat.a $(EXTOBJ) $(EXTRAS) $(GAULIB) $(LIBS)
+ 
+ freqmem: freqmem.o
+-	$(RUNF77) $(FFLAGS) -o freqmem freqmem.o $(EXTOBJ) $(EXTRAS) $(GAULIB) $(LIBS)
++	$(RUNF77) $(FFLAGS) $(LDFLAGS) -o freqmem freqmem.o $(EXTOBJ) $(EXTRAS) $(GAULIB) $(LIBS)
+ 
+ formchk: formchk.o
+-	$(RUNF77) $(FFLAGS) -o formchk formchk.o $(EXTOBJ) $(EXTRAS) $(GAULIB) $(LIBS)
++	$(RUNF77) $(FFLAGS) $(LDFLAGS) -o formchk formchk.o $(EXTOBJ) $(EXTRAS) $(GAULIB) $(LIBS)
+ 
+ demofc: demofc.o
+-	$(RUNF77) $(FFLAGS) -o demofc demofc.o $(EXTOBJ) $(EXTRAS) $(GAULIB) $(LIBS)
++	$(RUNF77) $(FFLAGS) $(LDFLAGS) -o demofc demofc.o $(EXTOBJ) $(EXTRAS) $(GAULIB) $(LIBS)
+ 
+ gauopt: $(EXTRAS) gauopt.o
+ 	$(RUNMAKE) $(MAKELOC) OPTFLAG='$(OPTFLAG)' $(EXTRAS) gauopt.o
+-	$(RUNF77) $(FFLAGS) -o gauopt gauopt.o $(EXTOBJ) $(EXTRAS) $(GAULIB) $(LIBS)
++	$(RUNF77) $(FFLAGS) $(LDFLAGS) -o gauopt gauopt.o $(EXTOBJ) $(EXTRAS) $(GAULIB) $(LIBS)
+ 
+ ghelp: $(EXTRAS) ghelp.o
+ 	$(RUNFSP) -e mghelp $(BSDDIR)/main.F
+ 	$(RUNMAKE) $(MAKELOC) OPTFLAG='$(OPTFLAG)' $(EXTRAS) ghelp.o mghelp.o
+-	$(RUNF77) $(FFLAGS) -o ghelp mghelp.o ghelp.o l9999.a $(EXTOBJ) $(EXTRAS) $(GAULIB) $(LIBS)
++	$(RUNF77) $(FFLAGS) $(LDFLAGS) -o ghelp mghelp.o ghelp.o l9999.a $(EXTOBJ) $(EXTRAS) $(GAULIB) $(LIBS)
+ 	rm -f mghelp.*
+ 
+ ham506: ham506.o
+-	$(RUNF77) $(FFLAGS) -o ham506 ham506.o $(EXTOBJ) $(EXTRAS) $(GAULIB) $(LIBS)
++	$(RUNF77) $(FFLAGS) $(LDFLAGS) -o ham506 ham506.o $(EXTOBJ) $(EXTRAS) $(GAULIB) $(LIBS)
+ 
+ newzmat: $(EXTRAS) newzmat.a newzmat-bsd.o l101.a l716.a
+ 	$(RUNMAKE) $(MAKELOC) OPTFLAG='$(OPTFLAG)' $(EXTRAS) newzmat.a newzmat-bsd.o
+-	$(RUNF77) $(FFLAGS) -o newzmat newzmat-bsd.o newzmat.a $(EXTOBJ) \
++	$(RUNF77) $(FFLAGS) $(LDFLAGS) -o newzmat newzmat-bsd.o newzmat.a $(EXTOBJ) \
+ 	    l101.a l401.a l716.a $(EXTRAS) $(GAULIB) $(LIBS)
+ 
+ pluck: pluck.o
+-	$(RUNF77) $(FFLAGS) -o pluck pluck.o $(EXTOBJ) $(EXTRAS) $(GAULIB) $(LIBS)
++	$(RUNF77) $(FFLAGS) $(LDFLAGS) -o pluck pluck.o $(EXTOBJ) $(EXTRAS) $(GAULIB) $(LIBS)
+ 
+ unfchk: unfchk.o
+-	$(RUNF77) $(FFLAGS) -o unfchk unfchk.o $(EXTOBJ) $(EXTRAS) $(GAULIB) $(LIBS)
++	$(RUNF77) $(FFLAGS) $(LDFLAGS) -o unfchk unfchk.o $(EXTOBJ) $(EXTRAS) $(GAULIB) $(LIBS)
+ 
+ reform: reform.o $(GAULIB) $(EXTRAS) archlib.a mdarch.a
+ 	$(RUNF77) $(FFLAGS) -o reform reform.o $(EXTOBJ) $(EXTRAS) archlib.a \
+ 	   mdarch.a $(GAULIB) $(LIBS)
+ 
+ rwfdump: rwfdump.o
+-	$(RUNF77) $(FFLAGS) -o rwfdump rwfdump.o $(EXTOBJ) $(EXTRAS) $(GAULIB) $(LIBS)
++	$(RUNF77) $(FFLAGS) $(LDFLAGS) -o rwfdump rwfdump.o $(EXTOBJ) $(EXTRAS) $(GAULIB) $(LIBS)
+ 
+ testrt: $(EXTRAS) testrt.o l1.a $(TESTRTO)
+ 	$(RUNMAKE) $(MAKELOC) OPTFLAG='$(OPTFLAG)' $(EXTRAS) testrt.o $(TESTRTO)
+-	$(RUNF77) $(FFLAGS) -o testrt testrt.o $(TESTRTO) $(EXTOBJ) l1.a l9999.a $(EXTRAS) $(GAULIB) $(LIBS)
++	$(RUNF77) $(FFLAGS) $(LDFLAGS) -o testrt testrt.o $(TESTRTO) $(EXTOBJ) l1.a l9999.a $(EXTRAS) $(GAULIB) $(LIBS)
+ 
+ gau-cpp: $(BSDDIR)/cpp.c $(BSDDIR)/cpp.h
+ 	$(RUNCC) -o gau-cpp -DHOST=SYS_UNIX -Dstrchr=index -Dstrrchr=rindex \
+@@ -784,9 +803,9 @@
+ 	rm -f $(@:o=f) $(@:o=c)
+ 
+ MARCHOBJ = dummy.o
+-util.so: $(GAULIBA) dummy.o $(BLAS)
+-	ld -shared -o util.so dummy.o --whole-archive util.a \
+-	  --no-whole-archive $(BLAS)
++libgauutil.so.1: $(GAULIBA) dummy.o $(BLAS)
++	ld  -shared -o libgauutil.so.1 \
++	    dummy.o  --whole-archive util.a  
+ 
+ #
+ # Here are rules specific to the Gaussian/Linda parallel version:

biology/gaussian98/files/patch-ac

@@ -0,0 +1,36 @@
+--- bsd/mdutil.c.orig	Fri Jun 11 01:44:58 1999
++++ bsd/mdutil.c	Sun Dec 10 20:01:51 2000
+@@ -1362,6 +1362,11 @@
+ #ifndef i386
+   char *sbrk();
+ #endif
++
++#ifdef __FreeBSD__
++  char *sbrk();
++#endif
++
+   lenbuf = (char *) sbrk(0) - end;
+ #endif
+   ifd = (int) *fd;
+@@ -2610,6 +2615,8 @@
+ #endif
+ 
+ #ifdef i386
++f77_int wait_() { return(wait()); }
++f77_int fork_() { return(fork()); }
+ f77_int loc_ (r) f77_wp *r; {return (f77_int) r; }
+ 
+ f77_int time_ () { return((f77_int) time((time_t *) NULL)); }
+@@ -2637,7 +2644,12 @@
+   offset_type n;
+ #ifdef DO_SHM
+   int shmflags = 0;
++#ifndef __FreeBSD__
+   void *brkadr, *sbrk();
++#else
++  void *brkadr;
++  char *sbrk();
++#endif
+   key_t shmkey;
+ #ifndef IBM_RS6K
+ #ifndef sgi

biology/gaussian98/files/patch-ad

@@ -0,0 +1,28 @@
+--- bsd/setup-make.orig	Tue Jun  1 10:13:16 1999
++++ bsd/setup-make	Sun Dec 10 20:01:51 2000
+@@ -31,17 +31,18 @@
+   set mstr = "make"
+   set pstr = "-p"
+ else if ("$mach" == "i386") then
+-  if (-e $PGI/linux86/bin/pgf77) then
+-    set fcflag = "FC='pgf77'"
+-    set fcflagp = ""
+-    set blas = "BLAS='' UTIL_NAME='{util,archlib,mdarch,lapack}.a'"
+-    set fc2flag = "FC2='/usr/local/lib/blas-{opt,f2c}.a'"
+-  else
++# comment out for non-pgf but g77 compiler environment
++#  if (-e $PGI/linux86/bin/pgf77) then
++#    set fcflag = "FC='pgf77'"
++#    set fcflagp = ""
++#    set blas = "BLAS='' UTIL_NAME='{util,archlib,mdarch,lapack}.a'"
++#    set fc2flag = "FC2='/usr/local/lib/blas-{opt,f2c}.a'"
++#  else
+     set fcflag = "FC='cc -g'"
+     set fc2flag = "FC2='-lf2c -lm'"
+     set blas = "UTIL_NAME='{util,archlib,mdarch,util,lapack,blas}.a'"
+     set fc2flag = "FC2=''"
+-    endif
++#   endif
+   set blasp = "$blas"
+   set mstr = "make"
+   set pstr = "-p"

biology/gaussian98/pkg-comment

@@ -0,0 +1 @@
+An ab-initio molecular orbital calculation program

biology/gaussian98/pkg-descr

@@ -0,0 +1,11 @@
+Gaussian is ab-initio molecular orbital calculation program
+calculates energy, molecular structure, vibrational frequencies
+from the basic principle of quantum mechanics.
+
+We also included simple launcher called `gaussian98'
+for your convenience. You don't need to set any environment variable
+to run gaussian.
+
+WWW: http://www.gaussian.com
+- NAKATA, Maho
+  E-mail: chat95@mbox.kyoto-inet.or.jp

biology/gaussian98/pkg-plist

@@ -0,0 +1,283 @@
+bin/gaussian98
+bin/g98/c8698
+bin/g98/chkchk
+bin/g98/chkmove
+bin/g98/cktoig
+bin/g98/cubegen
+bin/g98/cubman
+bin/g98/demofc
+bin/g98/formchk
+bin/g98/freqchk
+bin/g98/freqmem
+bin/g98/g98
+bin/g98/gau-machine
+bin/g98/gauopt
+bin/g98/ghelp
+bin/g98/ham506
+bin/g98/l1.exe
+bin/g98/l1002.exe
+bin/g98/l1003.exe
+bin/g98/l101.exe
+bin/g98/l1014.exe
+bin/g98/l102.exe
+bin/g98/l103.exe
+bin/g98/l105.exe
+bin/g98/l106.exe
+bin/g98/l107.exe
+bin/g98/l108.exe
+bin/g98/l109.exe
+bin/g98/l110.exe
+bin/g98/l1101.exe
+bin/g98/l1102.exe
+bin/g98/l111.exe
+bin/g98/l1110.exe
+bin/g98/l1111.exe
+bin/g98/l1112.exe
+bin/g98/l113.exe
+bin/g98/l114.exe
+bin/g98/l115.exe
+bin/g98/l116.exe
+bin/g98/l117.exe
+bin/g98/l118.exe
+bin/g98/l120.exe
+bin/g98/l202.exe
+bin/g98/l301.exe
+bin/g98/l302.exe
+bin/g98/l303.exe
+bin/g98/l307.exe
+bin/g98/l308.exe
+bin/g98/l310.exe
+bin/g98/l311.exe
+bin/g98/l314.exe
+bin/g98/l315.exe
+bin/g98/l316.exe
+bin/g98/l317.exe
+bin/g98/l318.exe
+bin/g98/l319.exe
+bin/g98/l320.exe
+bin/g98/l401.exe
+bin/g98/l402.exe
+bin/g98/l405.exe
+bin/g98/l502.exe
+bin/g98/l503.exe
+bin/g98/l504.exe
+bin/g98/l506.exe
+bin/g98/l508.exe
+bin/g98/l510.exe
+bin/g98/l601.exe
+bin/g98/l602.exe
+bin/g98/l604.exe
+bin/g98/l607.exe
+bin/g98/l608.exe
+bin/g98/l609.exe
+bin/g98/l610.exe
+bin/g98/l701.exe
+bin/g98/l702.exe
+bin/g98/l703.exe
+bin/g98/l716.exe
+bin/g98/l801.exe
+bin/g98/l802.exe
+bin/g98/l803.exe
+bin/g98/l804.exe
+bin/g98/l811.exe
+bin/g98/l901.exe
+bin/g98/l902.exe
+bin/g98/l903.exe
+bin/g98/l905.exe
+bin/g98/l906.exe
+bin/g98/l908.exe
+bin/g98/l909.exe
+bin/g98/l913.exe
+bin/g98/l914.exe
+bin/g98/l915.exe
+bin/g98/l916.exe
+bin/g98/l918.exe
+bin/g98/l9999.exe
+bin/g98/newzmat
+bin/g98/pluck
+bin/g98/rwfdump
+bin/g98/testrt
+bin/g98/unfchk
+bin/g98/bsd/g98.login
+bin/g98/bsd/gau-unlimit
+bin/g98/bsd/set-mflags
+lib/libgauutil.so
+lib/libgauutil.so.1
+share/gaussian98/explore/examples/e10_01a.com
+share/gaussian98/explore/examples/e10_01b.com
+share/gaussian98/explore/examples/e10_02a.com
+share/gaussian98/explore/examples/e10_02b.com
+share/gaussian98/explore/examples/e10_02c.com
+share/gaussian98/explore/examples/e2_01.com
+share/gaussian98/explore/examples/e2_02.com
+share/gaussian98/explore/examples/e3_01.com
+share/gaussian98/explore/examples/e3_02.com
+share/gaussian98/explore/examples/e3_03.com
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+share/gaussian98/explore/examples/e4_02a.com
+share/gaussian98/explore/examples/e4_02b.com
+share/gaussian98/explore/examples/e4_02c.com
+share/gaussian98/explore/examples/e4_02d.com
+share/gaussian98/explore/examples/e5_01.com
+share/gaussian98/explore/examples/e5_02.com
+share/gaussian98/explore/examples/e6_01.com
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+share/gaussian98/explore/examples/e6_03.com
+share/gaussian98/explore/examples/e6_04.com
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+share/gaussian98/explore/examples/e6_05b.com
+share/gaussian98/explore/examples/e6_05c.com
+share/gaussian98/explore/examples/e6_05d.com
+share/gaussian98/explore/examples/e6_05e.com
+share/gaussian98/explore/examples/e6_05f.com
+share/gaussian98/explore/examples/e6_05g.com
+share/gaussian98/explore/examples/e6_06.com
+share/gaussian98/explore/examples/e7_01.com
+share/gaussian98/explore/examples/e7_02.com
+share/gaussian98/explore/examples/e7_03.com
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+share/gaussian98/explore/examples/e7_05.com
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+share/gaussian98/explore/examples/e8_01a.com
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+share/gaussian98/explore/examples/e8_02.com
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+share/gaussian98/explore/examples/e8_07.com
+share/gaussian98/explore/examples/e9_01.com
+share/gaussian98/explore/examples/e9_02.com
+share/gaussian98/explore/examples/ea_01a.com
+share/gaussian98/explore/examples/ea_01b.com
+share/gaussian98/explore/examples/ea_01c.com
+share/gaussian98/explore/exercise/10_01a.com
+share/gaussian98/explore/exercise/10_01b.com
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+share/gaussian98/explore/exercise/9_04b.com
+share/gaussian98/explore/exercise/9_05.pdb
+share/gaussian98/explore/exercise/9_05a.com
+share/gaussian98/explore/exercise/9_05b.com
+share/gaussian98/explore/exercise/9_06_ci.pdb
+share/gaussian98/explore/exercise/9_06_gs.pdb
+share/gaussian98/explore/exercise/9_06a.com
+share/gaussian98/explore/exercise/9_06b.com
+share/gaussian98/explore/exercise/9_06c.com
+share/gaussian98/explore/exercise/9_06d.com
+share/gaussian98/explore/exercise/plus.gbs
+share/gaussian98/explore/quick/qs.com
+share/gaussian98/explore/quick/water.pdb
+@dirrm bin/g98/bsd
+@dirrm bin/g98
+@dirrm share/gaussian98/explore/examples
+@dirrm share/gaussian98/explore/exercise
+@dirrm share/gaussian98/explore/quick
+@dirrm share/gaussian98/explore
+@dirrm share/gaussian98

biology/gaussian98/scripts/pre-fetch

@@ -0,0 +1,17 @@
+#!/bin/sh
+
+[ -f ${CD_MOUNTPT}/TAR/WKSSRC.TAR ] && exit 0
+
+cat <<_E_O_F
+*****************************************************************
+To Install Gaussian, make sure your purchased CD-ROM is
+mounted on at ${CD_MOUNTPT} or an arbitrary mount point that can be
+specified by setting CD_MOUNTPT variable in a make command line.
+
+e.g.
+	mount /dev/cd0c /mnt/cdrom
+	make CD_MOUNTPT=/mnt/cdrom install
+*****************************************************************
+_E_O_F
+
+exit 1