diff options
| author | bapt <bapt@FreeBSD.org> | 2014-09-02 18:07:49 +0800 |
|---|---|---|
| committer | bapt <bapt@FreeBSD.org> | 2014-09-02 18:07:49 +0800 |
| commit | 10e03167f487d64719cc43ea4950b4d925234d80 (patch) | |
| tree | abf5fbbdc4b27a245ff76b9850f4eb6e73e4ba19 /science | |
| parent | e36550b4b5e2ea827b9bd0c16daa7304d897c23b (diff) | |
| download | freebsd-ports-gnome-10e03167f487d64719cc43ea4950b4d925234d80.tar.gz freebsd-ports-gnome-10e03167f487d64719cc43ea4950b4d925234d80.tar.zst freebsd-ports-gnome-10e03167f487d64719cc43ea4950b4d925234d80.zip | |
Remove non staged ports without pending PR from s*
Diffstat (limited to 'science')
96 files changed, 0 insertions, 7591 deletions
diff --git a/science/2dhf/Makefile b/science/2dhf/Makefile deleted file mode 100644 index a601e6c04c91..000000000000 --- a/science/2dhf/Makefile +++ /dev/null @@ -1,86 +0,0 @@ -# Created by: NAKATA, Maho <maho@FreeBSD.org> -# $FreeBSD$ - -PORTNAME= 2dhf -PORTVERSION= 2005.05 -PORTREVISION= 6 -CATEGORIES= science -MASTER_SITES= http://www.fizyka.umk.pl/~jkob/2dhf/ -DISTNAME= ${PORTNAME}-05.05 -EXTRACT_SUFX= .tgz - -MAINTAINER= ports@FreeBSD.org -COMMENT= Numerical Hartree-Fock Program for Diatomic Molecules - -BUILD_DEPENDS= bash:${PORTSDIR}/shells/bash -.if defined(WITH_INTEL) -USES+= fortran:ifort -BUILD_DEPENDS+= ${LOCALBASE}/intel_cc_80/bin/icc:${PORTSDIR}/lang/icc -.else -USES+= fortran -.endif - -.if exists(${LOCALBASE}/lib/libatlas.so) && !defined(WITH_BLAS) -WITH_ATLAS= yes -.endif -.if defined(WITH_ATLAS) -LIB_DEPENDS+= libatlas.so${PORTSDIR}/math/atlas -BLAS= -lf77blas -.else -LIB_DEPENDS+= libblas.so:${PORTSDIR}/math/blas -LIB_DEPENDS+= liblapack.so:${PORTSDIR}/math/lapack -BLAS= -lblas -.endif - -.if defined(WITH_OPTIMIZED_FLAGS) -FFLAGS+= -O3 -ffast-math -finline-functions -fomit-frame-pointer -funroll-loops -fexpensive-optimizations -malign-double -.if (${MACHINE_ARCH} == "i386") -FFLAGS+= -mfancy-math-387 -.endif # i386 -.endif - -.if defined(WITH_INTEL) -FC= ${LOCALBASE}/intel_fc_80/bin/ifort -CC= ${LOCALBASE}/intel_cc_80/bin/icc -FFLAGS= -O3 -tpp7 -xKW -Vaxlib -FFLAGS_ADD= -w -132 -CFLAGS= -O3 -tpp7 -xKW -Vaxlib -BLAS+= -lg2c -lm -.else -FFLAGS_ADD= -w -ffixed-line-length-none -.endif -WRKSRC= ${WRKDIR}/${PORTNAME} -USES+= gmake -ALL_TARGET= all - -NO_STAGE= yes -pre-everything:: - @${ECHO_CMD} "You can optimize by setting WITH_OPTIMIZED_FLAGS=yes." - -do-extract: - ${MKDIR} ${WRKSRC} - @(cd ${WRKSRC} ; ${TAR} xfz ${DISTDIR}/${DISTNAME}${EXTRACT_SUFX}) - -post-patch: - @${REINPLACE_CMD} -e 's|%%FC%%|${FC}|g ; \ - s|%%FFLAGS%%|${FFLAGS}|g ; \ - s|%%FFLAGS_ADD%%|${FFLAGS_ADD}|g ; \ - s|%%CC%%|${CC}|g ; \ - s|%%CFLAGS%%|${CFLAGS}|g ; \ - s|%%LOCALBASE%%|${LOCALBASE}|g ;\ - s|%%BLAS%%|${BLAS}|g' \ - ${WRKSRC}/Makefile - @${REINPLACE_CMD} -e 's|%%PREFIX%%|${PREFIX}|g' \ - ${WRKSRC}/bin/xhf - -do-install: - @cd ${WRKSRC} ; ${INSTALL_PROGRAM} bin/x2dhf ${PREFIX}/bin/x2dhf - @cd ${WRKSRC} ; ${INSTALL_SCRIPT} bin/xhf ${PREFIX}/bin/xhf -.if !defined(NOPORTDOCS) - @${MKDIR} ${DOCSDIR} - @cd ${WRKSRC}/doc ; ${INSTALL_DATA} 2dhf.pdf users-guide.pdf users-guide.html ${DOCSDIR} - @${MKDIR} ${EXAMPLESDIR} - @cd ${WRKSRC}/examples/ ; ${TAR} -chf - . | \ - ${TAR} -xf - -C ${EXAMPLESDIR} -.endif -.include <bsd.port.mk> diff --git a/science/2dhf/distinfo b/science/2dhf/distinfo deleted file mode 100644 index 97c03b2c3258..000000000000 --- a/science/2dhf/distinfo +++ /dev/null @@ -1,2 +0,0 @@ -SHA256 (2dhf-05.05.tgz) = ace9c6b96d7588cf72c331b0b52baaea76d125c86ea737d31d0b016e50b9354c -SIZE (2dhf-05.05.tgz) = 1033962 diff --git a/science/2dhf/files/patch-Makefile b/science/2dhf/files/patch-Makefile deleted file mode 100644 index 0841a548e559..000000000000 --- a/science/2dhf/files/patch-Makefile +++ /dev/null @@ -1,50 +0,0 @@ ---- Makefile.orig Tue May 17 02:15:36 2005 -+++ Makefile Tue Jan 9 17:36:22 2007 -@@ -45,21 +45,22 @@ - # of grid and orbital parameters according to expected range of input - # data - --#MEMALLOC = main-static.inc -+# MEMALLOC = main-static.inc - - # For a Sun workstation with f77 or a PC with g77 compiler --MEMALLOC = main-dynamic-f77.inc -+# MEMALLOC = main-dynamic-f77.inc - - # For a DEC workstation and f77 compiler - # MEMALLOC = main-dynamic-f77-dec.inc - - # For f90 compiler --# MEMALLOC = main-dynamic-f90.inc -+MEMALLOC = main-dynamic-f90.inc - - # set system type/compiler - # available keywords are: cray, dec, ibm, lahey, linux, sgi, solaris -+# and freebsd - --SYSTEM = linux -+SYSTEM = freebsd - #SYSTEM = intel - - # if BLAS library is available set the BLAS variable to yes -@@ -189,6 +190,20 @@ - CC = cc - CFLAGS = - endif -+# FreeBSD -+ifeq ($(SYSTEM),freebsd) -+ FC = %%FC%% -+ FFLAGS = %%FFLAGS%% -+# -fstrength-reduce -funroll-loops -+# FFLAGS = -O1 -malign-double -+# FFLAGS = -g -C -+ FFLAGS_ADD = %%FFLAGS_ADD%% -+ FLIB = -L%%LOCALBASE%%/lib %%BLAS%% -+ BLAS = yes -+ -+ CC = %%CC%% -+ CFLAGS = %%CFLAGS%% -+ endif - - - # nothing to be set below this line diff --git a/science/2dhf/files/patch-bin+xhf b/science/2dhf/files/patch-bin+xhf deleted file mode 100644 index 1a83897b39c4..000000000000 --- a/science/2dhf/files/patch-bin+xhf +++ /dev/null @@ -1,11 +0,0 @@ ---- bin/xhf.org Thu Jul 24 18:25:05 2003 -+++ bin/xhf Thu Jul 24 18:26:38 2003 -@@ -99,7 +99,7 @@ - endif - echo ' ' - # envoke x2dhf program -- nice +19 ./x2dhf < $1.data -+ nice +19 %%PREFIX%%/bin/x2dhf < $1.data - endif - - if ( $1 != 'remove' ) then diff --git a/science/2dhf/files/patch-main-dynamic-f90.inc b/science/2dhf/files/patch-main-dynamic-f90.inc deleted file mode 100644 index 6c7aeb414ae7..000000000000 --- a/science/2dhf/files/patch-main-dynamic-f90.inc +++ /dev/null @@ -1,9 +0,0 @@ ---- src/main-dynamic-f90.inc~ Tue May 17 02:22:50 2005 -+++ src/main-dynamic-f90.inc Tue Jan 9 17:39:08 2007 -@@ -1,5 +1,5 @@ - real*8, dimension(:),allocatable :: cw_orb -- real*8, dimension(:),allocatable : -+ real*8, dimension(:),allocatable :: cw_coul - real*8, dimension(:),allocatable :: cw_exch - real*8, dimension(:),allocatable :: cw_suppl - real*8, dimension(:),allocatable :: cw_sctch diff --git a/science/2dhf/files/patch-src+fmalloc.c b/science/2dhf/files/patch-src+fmalloc.c deleted file mode 100644 index a051ab093525..000000000000 --- a/science/2dhf/files/patch-src+fmalloc.c +++ /dev/null @@ -1,14 +0,0 @@ ---- src/fmalloc.c.orig Thu Jul 24 17:32:52 2003 -+++ src/fmalloc.c Thu Jul 24 17:33:22 2003 -@@ -15,7 +15,11 @@ - - #include <stdio.h> - #include <sys/types.h> -+#ifdef __FreeBSD__ -+#include <stdlib.h> -+#else - #include <malloc.h> -+#endif - - /* - bv: is an integer to contain the address to the reserved diff --git a/science/2dhf/files/patch-src+getusedcpu.c b/science/2dhf/files/patch-src+getusedcpu.c deleted file mode 100644 index 5d1b54b6c4ae..000000000000 --- a/science/2dhf/files/patch-src+getusedcpu.c +++ /dev/null @@ -1,37 +0,0 @@ ---- src/getusedcpu.c.orig Sat Jan 4 21:21:37 2003 -+++ src/getusedcpu.c Tue Aug 5 07:02:39 2003 -@@ -67,7 +67,6 @@ - #include <string.h> - #include <ctype.h> - -- - #include <sys/types.h> - #include <sys/times.h> - #include <sys/param.h> -@@ -76,7 +75,7 @@ - #include <sys/acct.h> - #endif - --#if defined(ymp) -+#if defined(ymp) || defined (__FreeBSD__) - #include <time.h> - #endif - -@@ -106,7 +105,7 @@ - #if defined(dec) - start = (float)(buffer.tms_utime + buffer.tms_stime) / (float)(AHZ); - start_child = (float)(buffer.tms_cutime + buffer.tms_cstime)/ (float)(AHZ); --#elif defined(ymp) -+#elif defined(ymp) || defined(__FreeBSD__) - start = (float)(buffer.tms_utime + buffer.tms_stime) / (float)(CLK_TCK); - start_child = (float)(buffer.tms_cutime + buffer.tms_cstime) / (float)(CLK_TCK); - #else -@@ -118,7 +117,7 @@ - #if defined(dec) - *Msecs = (float)(buffer.tms_utime + buffer.tms_stime) / (float)(AHZ) - start_child; - *Csecs = (float)(buffer.tms_cutime + buffer.tms_cstime)/ (float)(AHZ) - start_child; --#elif defined(ymp) -+#elif defined(ymp) || defined(__FreeBSD__) - *Msecs = (float)(buffer.tms_utime + buffer.tms_stime) / (float)(CLK_TCK) - start; - *Csecs = (float)(buffer.tms_cutime + buffer.tms_cstime) / (float)(CLK_TCK) - start_child; - #else diff --git a/science/2dhf/files/patch-src+inihf.f b/science/2dhf/files/patch-src+inihf.f deleted file mode 100644 index b8eda8a214dd..000000000000 --- a/science/2dhf/files/patch-src+inihf.f +++ /dev/null @@ -1,10 +0,0 @@ ---- src/inihf.f~ Tue May 17 02:22:50 2005 -+++ src/inihf.f Tue Jan 9 17:12:22 2007 -@@ -20,6 +20,7 @@ - implicit integer*4 (i-n) - implicit real*8 (a-h,o-z) - character*8 atom1,term1,atom2,term2 -+ integer ouf2dhf1, ouf2dhf2 - include 'commons8.inc' - dimension psi(*),pot(*),excp(*),f2(*),f4(*),wgt2(*),wk0(*) - dimension rhf1(9999),phf1(20,9999),ehf1(20),qc1(20), diff --git a/science/2dhf/files/patch-src+setconst.f b/science/2dhf/files/patch-src+setconst.f deleted file mode 100644 index efd798b3a872..000000000000 --- a/science/2dhf/files/patch-src+setconst.f +++ /dev/null @@ -1,11 +0,0 @@ ---- src/setconst.f.org Tue Jan 9 17:41:30 2007 -+++ src/setconst.f Tue Jan 9 17:41:42 2007 -@@ -31,7 +31,7 @@ - - c set default lengths of integer and real constants and variables used - -- i8tmp1=2**31 -+ i8tmp1=2**30 - i8tmp2=100000*i8tmp1 - i4tmp1=i8tmp2 - if (i4tmp1.eq.0) then diff --git a/science/2dhf/pkg-descr b/science/2dhf/pkg-descr deleted file mode 100644 index a2bcfdc89b95..000000000000 --- a/science/2dhf/pkg-descr +++ /dev/null @@ -1,9 +0,0 @@ -A Numerical Hartree-Fock Program for Diatomic Molecules - -The program finds virtually exact solution of the Hartree-Fock -and Hartree-Fock-Slater equations for diatomic molecules. The -lowest eigenstates of a given irreducible representation and -spin can be obtained. Distributed under GPL. - -WWW: http://scarecrow.1g.fi/2d/admin/getit.html - diff --git a/science/2dhf/pkg-plist b/science/2dhf/pkg-plist deleted file mode 100644 index a00732ad3b6d..000000000000 --- a/science/2dhf/pkg-plist +++ /dev/null @@ -1,92 +0,0 @@ -bin/xhf -bin/x2dhf -%%PORTDOCS%%%%DOCSDIR%%/2dhf.pdf -%%PORTDOCS%%%%DOCSDIR%%/users-guide.pdf -%%PORTDOCS%%%%DOCSDIR%%/users-guide.html -%%PORTDOCS%%@dirrm %%DOCSDIR%% -%%PORTDOCS%%%%EXAMPLESDIR%%/bf/bf_g94la.out -%%PORTDOCS%%%%EXAMPLESDIR%%/bf/bf_g94.out -%%PORTDOCS%%%%EXAMPLESDIR%%/bf/bf_g94.data -%%PORTDOCS%%%%EXAMPLESDIR%%/bf/bf_g94l.data -%%PORTDOCS%%%%EXAMPLESDIR%%/bf/bf_g94la.output -%%PORTDOCS%%%%EXAMPLESDIR%%/bf/bf_g94lb.output -%%PORTDOCS%%%%EXAMPLESDIR%%/bf/bf.inp -%%PORTDOCS%%%%EXAMPLESDIR%%/bf/bf_g94.pun -%%PORTDOCS%%%%EXAMPLESDIR%%/bf/bf_g94lb.out -%%PORTDOCS%%%%EXAMPLESDIR%%/bf/bf_g94.output -%%PORTDOCS%%%%EXAMPLESDIR%%/n2/n2.data -%%PORTDOCS%%%%EXAMPLESDIR%%/n2/n2.output -%%PORTDOCS%%%%EXAMPLESDIR%%/th89/th89_2s.data -%%PORTDOCS%%%%EXAMPLESDIR%%/th89/th89_1s.output -%%PORTDOCS%%%%EXAMPLESDIR%%/th89/th89_1s.data -%%PORTDOCS%%%%EXAMPLESDIR%%/th89/th89_2s.output -%%PORTDOCS%%%%EXAMPLESDIR%%/h2/h2.data -%%PORTDOCS%%%%EXAMPLESDIR%%/h2/h2.output -%%PORTDOCS%%%%EXAMPLESDIR%%/h2/h2a.data -%%PORTDOCS%%%%EXAMPLESDIR%%/h2/h2b.data -%%PORTDOCS%%%%EXAMPLESDIR%%/h2+/h2+.data -%%PORTDOCS%%%%EXAMPLESDIR%%/h2+/h2+.output -%%PORTDOCS%%%%EXAMPLESDIR%%/h2+/h2plus.data -%%PORTDOCS%%%%EXAMPLESDIR%%/h2+/h2plus.output -%%PORTDOCS%%%%EXAMPLESDIR%%/c/c.data -%%PORTDOCS%%%%EXAMPLESDIR%%/c/cplus.data -%%PORTDOCS%%%%EXAMPLESDIR%%/c/c.output -%%PORTDOCS%%%%EXAMPLESDIR%%/c/cplus.output -%%PORTDOCS%%%%EXAMPLESDIR%%/c/c1d2.data -%%PORTDOCS%%%%EXAMPLESDIR%%/c/c3p1.data -%%PORTDOCS%%%%EXAMPLESDIR%%/c/c1d2.output -%%PORTDOCS%%%%EXAMPLESDIR%%/c/c3p1.output -%%PORTDOCS%%%%EXAMPLESDIR%%/be/be.data -%%PORTDOCS%%%%EXAMPLESDIR%%/be/be.output -%%PORTDOCS%%%%EXAMPLESDIR%%/be/be-1.data -%%PORTDOCS%%%%EXAMPLESDIR%%/be/be-1.output -%%PORTDOCS%%%%EXAMPLESDIR%%/bef/bef.data -%%PORTDOCS%%%%EXAMPLESDIR%%/bef/bef.output -%%PORTDOCS%%%%EXAMPLESDIR%%/c2/c2.out -%%PORTDOCS%%%%EXAMPLESDIR%%/c2/c2a.data -%%PORTDOCS%%%%EXAMPLESDIR%%/c2/c2.pun -%%PORTDOCS%%%%EXAMPLESDIR%%/c2/c2b.data -%%PORTDOCS%%%%EXAMPLESDIR%%/c2/c2c.data -%%PORTDOCS%%%%EXAMPLESDIR%%/c2/c2a.output -%%PORTDOCS%%%%EXAMPLESDIR%%/bo/bo.output -%%PORTDOCS%%%%EXAMPLESDIR%%/bo/bo.data -%%PORTDOCS%%%%EXAMPLESDIR%%/bo/bo.out -%%PORTDOCS%%%%EXAMPLESDIR%%/bo/bo.pun -%%PORTDOCS%%%%EXAMPLESDIR%%/bo/bo.inp -%%PORTDOCS%%%%EXAMPLESDIR%%/f2/f2.data -%%PORTDOCS%%%%EXAMPLESDIR%%/f2/f2.out -%%PORTDOCS%%%%EXAMPLESDIR%%/f2/f2.pun -%%PORTDOCS%%%%EXAMPLESDIR%%/f2/f2.output -%%PORTDOCS%%%%EXAMPLESDIR%%/gaf/gaf.data -%%PORTDOCS%%%%EXAMPLESDIR%%/gaf/gaf.output -%%PORTDOCS%%%%EXAMPLESDIR%%/li2/li2.out -%%PORTDOCS%%%%EXAMPLESDIR%%/li2/li2.pun -%%PORTDOCS%%%%EXAMPLESDIR%%/li2/li2.data -%%PORTDOCS%%%%EXAMPLESDIR%%/li2/li2.output -%%PORTDOCS%%%%EXAMPLESDIR%%/fh/fh-223-150-0-1.output -%%PORTDOCS%%%%EXAMPLESDIR%%/fh/fh-223-150-m1-1.output -%%PORTDOCS%%%%EXAMPLESDIR%%/fh/Run_FH -%%PORTDOCS%%%%EXAMPLESDIR%%/fh/Run_elprop.pl -%%PORTDOCS%%%%EXAMPLESDIR%%/fh/fh-223-150-m2-1.output -%%PORTDOCS%%%%EXAMPLESDIR%%/fh/fh-223-150-p1-1.output -%%PORTDOCS%%%%EXAMPLESDIR%%/fh/fh-223-150-p2-1.output -%%PORTDOCS%%%%EXAMPLESDIR%%/fh/fh-m2.data -%%PORTDOCS%%%%EXAMPLESDIR%%/fh/fh-p2.data -%%PORTDOCS%%%%EXAMPLESDIR%%/fh/fh-m1.data -%%PORTDOCS%%%%EXAMPLESDIR%%/fh/fh-0.data -%%PORTDOCS%%%%EXAMPLESDIR%%/fh/fh-p1.data -%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/bf -%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/n2 -%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/th89 -%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/h2+ -%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/h2 -%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/c -%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/be -%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/bef -%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/c2 -%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/bo -%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/f2 -%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/gaf -%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/li2 -%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/fh -%%PORTDOCS%%@dirrm %%EXAMPLESDIR%% diff --git a/science/Makefile b/science/Makefile index b59a81725b9b..efa3109a5bb4 100644 --- a/science/Makefile +++ b/science/Makefile @@ -4,7 +4,6 @@ COMMENT = Scientific ports SUBDIR += 2d-rewriter - SUBDIR += 2dhf SUBDIR += InsightToolkit SUBDIR += R-cran-AMORE SUBDIR += R-cran-DCluster @@ -15,7 +14,6 @@ SUBDIR += R-cran-epicalc SUBDIR += R-cran-snow SUBDIR += R-cran-som - SUBDIR += abinit SUBDIR += afni SUBDIR += avogadro SUBDIR += bddsolve @@ -38,14 +36,11 @@ SUBDIR += dcl SUBDIR += devisor SUBDIR += dlpoly-classic - SUBDIR += dtiquery SUBDIR += ecs SUBDIR += elmer-eio - SUBDIR += elmer-hutiter SUBDIR += elmer-matc SUBDIR += elmer-meshgen2d SUBDIR += elmergrid - SUBDIR += elmerpost SUBDIR += epte SUBDIR += fastcap SUBDIR += fasthenry @@ -53,8 +48,6 @@ SUBDIR += fvcom SUBDIR += fvcom-mpi SUBDIR += fvm - SUBDIR += g3data - SUBDIR += gamess SUBDIR += gchemutils SUBDIR += getdp SUBDIR += ghemical @@ -90,12 +83,10 @@ SUBDIR += linsmith SUBDIR += massxpert SUBDIR += mbdyn - SUBDIR += mcstas SUBDIR += medit SUBDIR += meep SUBDIR += mei SUBDIR += metaf2xml - SUBDIR += minc SUBDIR += minc2 SUBDIR += mol2ps SUBDIR += mpb @@ -141,7 +132,6 @@ SUBDIR += paje SUBDIR += paraview SUBDIR += pnetcdf - SUBDIR += psi3 SUBDIR += psychopy SUBDIR += pulseview SUBDIR += py-DendroPy @@ -188,9 +178,7 @@ SUBDIR += veusz SUBDIR += vmd SUBDIR += voro++ - SUBDIR += x11iraf SUBDIR += xfce4-equake-plugin SUBDIR += xmakemol - SUBDIR += xmds .include <bsd.port.subdir.mk> diff --git a/science/abinit/Makefile b/science/abinit/Makefile deleted file mode 100644 index 7f1a021a8a16..000000000000 --- a/science/abinit/Makefile +++ /dev/null @@ -1,88 +0,0 @@ -# Created by: NAKATA Maho <maho@FreeBSD.org> -# $FreeBSD$ - -PORTNAME= abinit -PORTVERSION= 5.7.3 -PORTREVISION= 16 -CATEGORIES= science -MASTER_SITES= ftp://ftp.abinit.org/pub/abinitio/ABINIT_v${PORTVERSION}/ - -MAINTAINER= ports@FreeBSD.org -COMMENT= Abinit calculates electronic structure of systems - -BUILD_DEPENDS= python:${PORTSDIR}/lang/python \ - ${PYTHON_SITELIBDIR}/numarray/__init__.py:${PORTSDIR}/math/py-numarray -LIB_DEPENDS= libnetcdff.so:${PORTSDIR}/science/netcdf-fortran \ - libgsl.so:${PORTSDIR}/math/gsl - -USES= fortran gmake perl5 -USE_PYTHON= yes -USE_PERL5= build -USE_AUTOTOOLS= autoconf automake -CONFIGURE_ENV= WGET=${TRUE} -CONFIGURE_ARGS= --disable-wannier90 --disable-bigdft --disable-etsf-io \ - --with-plugins-tardir=/dev/null \ - --with-netcdf-includes="-I${LOCALBASE}/include" \ - --enable-bindings --enable-gsl \ - --with-netcdf-libs="-L${LOCALBASE}/lib -lnetcdff -lnetcdf" -CPPFLAGS+= -I${LOCALBASE}/include -LDFLAGS+= -L${LOCALBASE}/lib - -OPTIONS_DEFINE= DOCS EXAMPLES - -NO_STAGE= yes -.include <bsd.port.options.mk> - -.if ${PORT_OPTIONS:MDOCS} -USE_TEX= latex:build dvipsk:build -BUILD_DEPENDS+= gm4:${PORTSDIR}/devel/m4 \ - markdown:${PORTSDIR}/textproc/markdown -USE_GHOSTSCRIPT_BUILD= yes -.endif - -.if ${ARCH} == "ia64" || ${ARCH} == "powerpc" || ${ARCH} == "sparc64" -MANUAL_PACKAGE_BUILD= takes a tremendous amount of time to build on pointyhat nodes -.endif - -.if exists(${LOCALBASE}/lib/libatlas.so) && !defined(WITH_BLAS) -WITH_ATLAS= yes -.endif -.if defined(WITH_ATLAS) -LIB_DEPENDS+= libatlas.so:${PORTSDIR}/math/atlas -BLAS= -lf77blas -LAPACK= -lalapack -lcblas -.else -LIB_DEPENDS+= libblas.so:${PORTSDIR}/math/blas -LIB_DEPENDS+= liblapack.so:${PORTSDIR}/math/lapack -BLAS= -lblas -LAPACK= -llapack -.endif - -pre-configure: -.if ! ${PORT_OPTIONS:MDOCS} - ${REINPLACE_CMD} -e '/^abinit_top_subdirs =/s| doc||' ${WRKSRC}/config/specs/other.cf -.endif -.if ! ${PORT_OPTIONS:MEXAMPLES} - ${REINPLACE_CMD} -e '/^abinit_top_subdirs =/s| tests||' ${WRKSRC}/config/specs/other.cf -.endif - (cd ${WRKSRC} && ./config/scripts/makemake) - ${CHMOD} a+x ${WRKSRC}/bindings/parser/*.py - -post-build: - @(cd ${BUILD_WRKSRC} && ${SETENV} ${MAKE_ENV} ${MAKE_CMD} \ - ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} libabinit) - -post-install: - ${MKDIR} ${PREFIX}/include ${PREFIX}/lib -.for lf in libabinip.a libabinis.a - ${INSTALL_DATA} ${WRKSRC}/${lf} ${PREFIX}/lib -.endfor -.for lf in ab_dtset_c.h dtset_c.h dtset_c.static.h dtset_f90.inc dtset_py.h \ - ab_dtset_f90_get.f90 - ${INSTALL_DATA} ${WRKSRC}/bindings/parser/${lf} ${PREFIX}/include -.endfor - -regression-test: - cd ${WRKSRC}/tests ; ${MAKE_CMD} tests_min - -.include <bsd.port.mk> diff --git a/science/abinit/distinfo b/science/abinit/distinfo deleted file mode 100644 index f7a015b72b79..000000000000 --- a/science/abinit/distinfo +++ /dev/null @@ -1,2 +0,0 @@ -SHA256 (abinit-5.7.3.tar.gz) = caac56530ceaa5e16326fd4407adcd0b1aede07ded51017f3eb6a6a3696c2867 -SIZE (abinit-5.7.3.tar.gz) = 31683174 diff --git a/science/abinit/files/makefile_macros b/science/abinit/files/makefile_macros deleted file mode 100644 index 3fec072104db..000000000000 --- a/science/abinit/files/makefile_macros +++ /dev/null @@ -1,50 +0,0 @@ -# This file contains the definitions needed for every possible script -# to be used with the ABINIT makefiles. It is very much machine-dependent. -# It is read by makemake and makearch. - -# This file for cernunnos (Pentium 4, Slackware Linux) at the Institute for -# Materials Physics, University of Vienna, by Wolfgang Pichl -# with the Intel compiler, Version 7.1 -# see http://www.intel.com/software/products/compilers/flin/noncom.htm - -# In this file, the blas library is linked in the same way as the other -# libraries (lapack, ffts, numrecip). - -# Explanations about this file can be found in the help.makefile_macros file, -# in the Infos subdirectory - -#################################################################### -# Only for the sequential version - -# Machine type -MACHINE=P6 -# Fortran optimized compilation -FC=%%FC%% -FFLAGS=%%FFLAGS%% -FFLAGS_LIBS=%%FFLAGS_LIBS%% - -# C preprocessor, used to preprocess the fortran source. -CPP=%%CPP%% -CPP_FLAGS=-P -traditional -D__IFC -# The cpp directive CHGSTDIO changes the standard I/O definition -# Uncomment the next line for this to happen. -#CPP_FLAGS=-P -DCHGSTDIO - -# C optimized compilation. -CC=%%CC%% -CFLAGS=%%CFLAGS%% - -# Location of perl . Used to generate the script fldiff, in ~ABINIT/Utilities . -PERL=%%PERL%% - -# List of machine-dependent routines -MACHINE_DEP_C_SEQ_SUBS_LIST=etime.o - -# Create BLAS library from abinis source -# The following lines should be redundant, since this is the default -# however, we got troubles when they where missing -BLAS=%%BLAS%% -LAPACK=%%LAPACK%% -LIBS=$(LAPACK) $(BLAS) - -# This is a last line in makefile_macros ---------- diff --git a/science/abinit/files/patch-bindings_parser_ab_dtset_c.c b/science/abinit/files/patch-bindings_parser_ab_dtset_c.c deleted file mode 100644 index e1f4eb3da3ec..000000000000 --- a/science/abinit/files/patch-bindings_parser_ab_dtset_c.c +++ /dev/null @@ -1,11 +0,0 @@ ---- bindings/parser/ab_dtset_c.c.orig 2009-02-22 07:08:32.000000000 +0100 -+++ bindings/parser/ab_dtset_c.c 2009-03-26 22:21:33.000000000 +0100 -@@ -7,6 +7,8 @@ - /* g95 : #define FC_MOD_NAME(A) ab_dtset_MP_ ## A */ - #define FC_MOD_CALL(A,...) FC_MOD_NAME(A)(__VA_ARGS__) - -+typedef unsigned int uint; -+ - /* Fortran interface. */ - void FC_MOD_NAME(ab_dtset_new)(int *dt, const char *filename, int *len); - void FC_MOD_NAME(ab_dtset_new_from_string)(int *dt, const char *string, int *len); diff --git a/science/abinit/files/patch-bindings_parser_parser.mk b/science/abinit/files/patch-bindings_parser_parser.mk deleted file mode 100644 index 8ce3bac27ce3..000000000000 --- a/science/abinit/files/patch-bindings_parser_parser.mk +++ /dev/null @@ -1,11 +0,0 @@ ---- bindings/parser/parser.mk~ 2009-03-11 14:12:20.000000000 +0900 -+++ bindings/parser/parser.mk 2009-04-13 11:53:44.000000000 +0900 -@@ -25,7 +25,7 @@ - $(RANLIB) libbindings.a - - ab_dtset_py.o: dtset_py.h ab_dtset_c.h -- $(CC) $(CPPFLAGS) $(PYTHON_CPPFLAGS) -I. $(CFLAGS) -c $(abinit_srcdir)/bindings/parser/ab_dtset_py.c -+ $(CC) $(CPPFLAGS) $(CFLAGS_EXTRA) $(PYTHON_CPPFLAGS) -I. $(CFLAGS) -c $(abinit_srcdir)/bindings/parser/ab_dtset_py.c - - - python: ab_dtset_py.o diff --git a/science/abinit/files/patch-config+m4+init.m4 b/science/abinit/files/patch-config+m4+init.m4 deleted file mode 100644 index 0d31f2013a99..000000000000 --- a/science/abinit/files/patch-config+m4+init.m4 +++ /dev/null @@ -1,129 +0,0 @@ ---- ./config/m4/init.m4.orig 2009-03-11 06:12:22.000000000 +0100 -+++ ./config/m4/init.m4 2009-03-28 16:29:06.000000000 +0100 -@@ -231,6 +231,101 @@ - abi_cpu_bits="64" - ;; - -+ i386-*freebsd*) -+ dnl Pentium 3 ? -+ if test "${abi_cpu_model}" = ""; then -+ abi_cpu_model=`sysctl hw.model | grep 'Pentium III'` -+ if test "${abi_cpu_model}" != ""; then -+ abi_cpu_model="pentium3" -+ abi_cpu_64bits="no" -+ abi_cpu_bits="32" -+ fi -+ fi -+ dnl Pentium 4 ? -+ if test "${abi_cpu_model}" = ""; then -+ abi_cpu_model=`sysctl hw.model | grep 'Intel(R) Pentium(R) 4'` -+ if test "${abi_cpu_model}" != ""; then -+ abi_cpu_model="pentium4" -+ abi_cpu_64bits="no" -+ abi_cpu_bits="32" -+ fi -+ fi -+ dnl Pentium 4M ? -+ if test "${abi_cpu_model}" = ""; then -+ abi_cpu_model=`sysctl hw.model | grep 'Intel(R) Pentium(R) M'` -+ if test "${abi_cpu_model}" != ""; then -+ abi_cpu_model="pentium4" -+ abi_cpu_64bits="no" -+ abi_cpu_bits="32" -+ fi -+ fi -+ dnl Unknown -+ if test "${abi_cpu_model}" = ""; then -+ abi_cpu_model="unknown" -+ fi -+ dnl The processor is anyway 32-bit -+ abi_cpu_64bits="no" -+ abi_cpu_bits="32" -+ ;; -+ -+ amd64-*freebsd*) -+ dnl Opteron ? -+ if test "${abi_cpu_model}" = ""; then -+ abi_cpu_model=`sysctl hw.model | grep 'Opteron'` -+ if test "${abi_cpu_model}" != ""; then -+ abi_cpu_model="opteron" -+ abi_cpu_64bits="yes" -+ abi_cpu_bits="64" -+ fi -+ fi -+ dnl Xeon ? -+ if test "${abi_cpu_model}" = ""; then -+ abi_cpu_model=`sysctl hw.model | grep 'Intel(R) XEON(TM)'` -+ if test "${abi_cpu_model}" != ""; then -+ abi_cpu_model="xeon" -+ abi_cpu_64bits="yes" -+ abi_cpu_bits="64" -+ fi -+ fi -+ dnl Unknown -+ if test "${abi_cpu_model}" = ""; then -+ abi_cpu_model="unknown" -+ fi -+ dnl The processor is anyway 64-bit -+ abi_cpu_64bits="yes" -+ abi_cpu_bits="64" -+ ;; -+ -+ ia64-*freebsd*) -+ dnl Itanium 1 ? -+ if test "${abi_cpu_model}" = ""; then -+ abi_cpu_model=`sysctl hw.model | grep 'Itanium 1'` -+ if test "${abi_cpu_model}" = ""; then -+ abi_cpu_model="itanium1" -+ fi -+ fi -+ dnl Itanium 2 ? -+ if test "${abi_cpu_model}" = ""; then -+ abi_cpu_model=`sysctl hw.model | grep 'Itanium 2'` -+ if test "${abi_cpu_model}" != ""; then -+ abi_cpu_model="itanium2" -+ fi -+ fi -+ dnl Unknown -+ if test "${abi_cpu_model}" = ""; then -+ abi_cpu_model="unknown" -+ fi -+ dnl The processor is anyway 64-bit -+ abi_cpu_64bits="yes" -+ abi_cpu_bits="64" -+ ;; -+ -+ sparc64-*freebsd*) -+ abi_cpu_model="unknown" -+ abi_cpu_64bits="yes" -+ abi_cpu_bits="64" -+ ;; -+ - esac - - AC_SUBST(abi_cpu_vendor) -@@ -289,15 +384,15 @@ - fi - - dnl Set-up all directory names -- abinit_bindir="${abinit_prefix}/abinit/${ABINIT_VERSION_BASE}/bin" -- abinit_chkdir="${abinit_prefix}/abinit/${ABINIT_VERSION_BASE}/tests" -- abinit_datdir="${abinit_prefix}/abinit" -- abinit_docdir="${abinit_prefix}/abinit/${ABINIT_VERSION_BASE}/doc" -- abinit_incdir="${abinit_prefix}/abinit/${ABINIT_VERSION_BASE}/include" -- abinit_libdir="${abinit_prefix}/abinit/${ABINIT_VERSION_BASE}/lib" -- abinit_mandir="${abinit_prefix}/abinit/man" -- abinit_rundir="${abinit_prefix}/abinit/bin" -- abinit_wwwdir="${abinit_prefix}/abinit/${ABINIT_VERSION_BASE}/www" -+ abinit_bindir="${abinit_prefix}/bin" -+ abinit_chkdir="${abinit_prefix}/share/examples/abinit/tests" -+ abinit_datdir="${abinit_prefix}/share/abinit" -+ abinit_docdir="${abinit_prefix}/share/doc/abinit/" -+ abinit_incdir="${abinit_prefix}/include/abinit" -+ abinit_libdir="${abinit_prefix}/lib" -+ abinit_mandir="${abinit_prefix}/man" -+ abinit_rundir="${abinit_prefix}/bin" -+ abinit_wwwdir="${abinit_prefix}/www/abinit" - - dnl Substitute all variables - AC_SUBST(abinit_prefix) diff --git a/science/abinit/files/patch-config+optflags b/science/abinit/files/patch-config+optflags deleted file mode 100644 index 148b307fe95d..000000000000 --- a/science/abinit/files/patch-config+optflags +++ /dev/null @@ -1,14 +0,0 @@ ---- /dev/null Wed Jan 17 11:53:59 2007 -+++ config/optflags/gnu_fc/all/opteron Wed Jan 17 11:53:27 2007 -@@ -0,0 +1 @@ -+FCFLAGS_OPT="-O2 -fforce-addr -ffast-math -mmmx -msse -msse2" - ---- /dev/null Wed Jan 17 11:55:01 2007 -+++ config/optflags/gnu_cc/all/opteron Wed Jan 17 11:54:40 2007 -@@ -0,0 +1 @@ -+CFLAGS_OPT="-O2 -fforce-addr -ffast-math -mmmx -msse -msse2" - ---- /dev/null Wed Jan 17 11:55:01 2007 -+++ config/optflags/gnu_cxx/all/opteron Wed Jan 17 11:54:40 2007 -@@ -0,0 +1 @@ -+CFLAGS_OPT="-O2 -fforce-addr -ffast-math -mmmx -msse -msse2" diff --git a/science/abinit/files/patch-config.mk.in b/science/abinit/files/patch-config.mk.in deleted file mode 100644 index e69c33ab59cb..000000000000 --- a/science/abinit/files/patch-config.mk.in +++ /dev/null @@ -1,11 +0,0 @@ ---- config.mk.in.orig 2009-02-22 07:08:32.000000000 +0100 -+++ config.mk.in 2009-03-08 09:54:35.000000000 +0100 -@@ -41,7 +41,7 @@ - PYTHON = @PYTHON@ - LN_S = @LN_S@ - EGREP = @EGREP@ --MKDIR_P = @MKDIR_P@ -+MKDIR_P = @abinit_builddir@/@MKDIR_P@ - - # Architecture - target = @target@ diff --git a/science/abinit/files/patch-config_scripts_make-macros-autotools b/science/abinit/files/patch-config_scripts_make-macros-autotools deleted file mode 100644 index 690b7c8cb422..000000000000 --- a/science/abinit/files/patch-config_scripts_make-macros-autotools +++ /dev/null @@ -1,11 +0,0 @@ ---- ./config/scripts/make-macros-autotools.orig 2009-02-22 07:08:33.000000000 +0100 -+++ ./config/scripts/make-macros-autotools 2009-03-25 22:34:01.000000000 +0100 -@@ -413,7 +413,7 @@ - now = strftime("%Y/%m/%d %H:%M:%S +0000",gmtime()) - - # Get Autotools versions --(m4_ret,m4_version) = commands.getstatusoutput("m4 --version") -+(m4_ret,m4_version) = commands.getstatusoutput("gm4 --version") - (ac_ret,ac_version) = commands.getstatusoutput("autoconf --version") - (am_ret,am_version) = commands.getstatusoutput("automake --version") - (lt_ret,lt_version) = commands.getstatusoutput("libtool --version") diff --git a/science/abinit/files/patch-configure b/science/abinit/files/patch-configure deleted file mode 100644 index 64c8c2e1efdf..000000000000 --- a/science/abinit/files/patch-configure +++ /dev/null @@ -1,27 +0,0 @@ ---- configure.orig 2009-02-22 08:32:10.000000000 +0100 -+++ configure 2009-03-09 20:01:48.000000000 +0100 -@@ -5151,15 +5151,15 @@ - abinit_prefix="${prefix}" - fi - -- abinit_bindir="${abinit_prefix}/abinit/${ABINIT_VERSION_BASE}/bin" -- abinit_chkdir="${abinit_prefix}/abinit/${ABINIT_VERSION_BASE}/tests" -- abinit_datdir="${abinit_prefix}/abinit" -- abinit_docdir="${abinit_prefix}/abinit/${ABINIT_VERSION_BASE}/doc" -- abinit_incdir="${abinit_prefix}/abinit/${ABINIT_VERSION_BASE}/include" -- abinit_libdir="${abinit_prefix}/abinit/${ABINIT_VERSION_BASE}/lib" -- abinit_mandir="${abinit_prefix}/abinit/man" -- abinit_rundir="${abinit_prefix}/abinit/bin" -- abinit_wwwdir="${abinit_prefix}/abinit/${ABINIT_VERSION_BASE}/www" -+ abinit_bindir="${abinit_prefix}/bin" -+ abinit_chkdir="${abinit_prefix}/share/examples/abinit/tests" -+ abinit_datdir="${abinit_prefix}/share/abinit" -+ abinit_docdir="${abinit_prefix}/share/doc/abinit/" -+ abinit_incdir="${abinit_prefix}/include/abinit" -+ abinit_libdir="${abinit_prefix}/lib" -+ abinit_mandir="${abinit_prefix}/man" -+ abinit_rundir="${abinit_prefix}/bin" -+ abinit_wwwdir="${abinit_prefix}/www/abinit" - - - diff --git a/science/abinit/files/patch-prereqs+linalg+linalg.mk b/science/abinit/files/patch-prereqs+linalg+linalg.mk deleted file mode 100644 index c64ff71cbca9..000000000000 --- a/science/abinit/files/patch-prereqs+linalg+linalg.mk +++ /dev/null @@ -1,11 +0,0 @@ ---- prereqs/linalg/linalg.mk~ 2009-03-11 14:12:18.000000000 +0900 -+++ prereqs/linalg/linalg.mk 2009-04-13 11:39:18.000000000 +0900 -@@ -32,7 +32,7 @@ - touch build-stamp - - install-stamp: build -- $(MKDIR_P) tmp/lib -+ mkdir -p tmp/lib - cp blas/libblas.a lapack/liblapack.a tmp/lib - touch install-stamp - diff --git a/science/abinit/pkg-descr b/science/abinit/pkg-descr deleted file mode 100644 index 54c997fdb564..000000000000 --- a/science/abinit/pkg-descr +++ /dev/null @@ -1,7 +0,0 @@ -ABINIT is a package whose main program allows one to find -the total energy, charge density and electronic structure of -systems made of electrons and nulcei (molecules and periodic -solids) within Density Functional Theory (DFT), using pseudo- -potentials and a planewave basis. - -WWW: http://www.abinit.org/ diff --git a/science/abinit/pkg-plist b/science/abinit/pkg-plist deleted file mode 100644 index 9d0e50ca46a3..000000000000 --- a/science/abinit/pkg-plist +++ /dev/null @@ -1,2407 +0,0 @@ -bin/abinetcdf -bin/abinis -bin/aim -bin/anaddb -bin/band2eps -bin/conducti -bin/cut3d -bin/lwf -bin/macroave -bin/mrgddb -bin/mrggkk -bin/mrgscr -bin/newsp -bin/optic -include/ab_dtset_c.h -include/ab_dtset_f90_get.f90 -include/dtset_c.h -include/dtset_c.static.h -include/dtset_f90.inc -include/dtset_py.h -lib/libabibase.a -lib/libabinip.a -lib/libabinis.a -%%PORTDOCS%%%%DOCSDIR%%/README -%%PORTDOCS%%%%DOCSDIR%%/build/README -%%PORTDOCS%%%%DOCSDIR%%/build/adding-extlibs.tex -%%PORTDOCS%%%%DOCSDIR%%/build/before-starting.tex -%%PORTDOCS%%%%DOCSDIR%%/build/build-docs.mk -%%PORTDOCS%%%%DOCSDIR%%/build/build-system-guide.pdf -%%PORTDOCS%%%%DOCSDIR%%/build/build-system-guide.tex -%%PORTDOCS%%%%DOCSDIR%%/build/configure-options.tex -%%PORTDOCS%%%%DOCSDIR%%/build/contributors.tex -%%PORTDOCS%%%%DOCSDIR%%/build/conventions.tex -%%PORTDOCS%%%%DOCSDIR%%/build/extending-the-build-system.tex -%%PORTDOCS%%%%DOCSDIR%%/build/overview.tex -%%PORTDOCS%%%%DOCSDIR%%/build/preprocessing-macros.tex -%%PORTDOCS%%%%DOCSDIR%%/config/build-config.ac -%%PORTDOCS%%%%DOCSDIR%%/config/build-examples/README 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-%%PORTDOCS%%@dirrm %%DOCSDIR%%/tutorial/lesson_1 -%%PORTDOCS%%@dirrm %%DOCSDIR%%/tutorial -%%PORTDOCS%%@dirrm %%DOCSDIR%%/theory -%%PORTDOCS%%@dirrm %%DOCSDIR%%/release_notes -%%PORTDOCS%%@dirrm %%DOCSDIR%%/psp_infos -%%PORTDOCS%%@dirrm %%DOCSDIR%%/presentation -%%PORTDOCS%%@dirrm %%DOCSDIR%%/misc -%%PORTDOCS%%@dirrm %%DOCSDIR%%/manpages -%%PORTDOCS%%@dirrm %%DOCSDIR%%/maintainers -%%PORTDOCS%%@dirrm %%DOCSDIR%%/macroave -%%PORTDOCS%%@dirrm %%DOCSDIR%%/known_problems -%%PORTDOCS%%@dirrm %%DOCSDIR%%/install_notes -%%PORTDOCS%%@dirrm %%DOCSDIR%%/input_variables -%%PORTDOCS%%@dirrm %%DOCSDIR%%/help_make -%%PORTDOCS%%@dirrm %%DOCSDIR%%/gallery -%%PORTDOCS%%@dirrm %%DOCSDIR%%/features -%%PORTDOCS%%@dirrm %%DOCSDIR%%/developers/strain_nonlocal -%%PORTDOCS%%@dirrm %%DOCSDIR%%/developers -%%PORTDOCS%%@dirrm %%DOCSDIR%%/config/build-examples -%%PORTDOCS%%@dirrm %%DOCSDIR%%/config -%%PORTDOCS%%@dirrm %%DOCSDIR%%/build -%%PORTDOCS%%@dirrm %%DOCSDIR%% diff --git a/science/dtiquery/Makefile b/science/dtiquery/Makefile deleted file mode 100644 index f31bd42d4c9a..000000000000 --- a/science/dtiquery/Makefile +++ /dev/null @@ -1,61 +0,0 @@ -# Created by: Jason W. Bacon <jwbacon@tds.net> -# $FreeBSD$ - -PORTNAME= dtiquery -PORTVERSION= 1.1 -PORTREVISION= 5 -CATEGORIES= science biology -MASTER_SITES= http://graphics.stanford.edu/projects/dti/ - -MAINTAINER= ports@FreeBSD.org -COMMENT= Stanford DTI Visualization tool - -BUILD_DEPENDS= ${LOCALBASE}/include/tnt/tnt.h:${PORTSDIR}/devel/tnt \ - ${LOCALBASE}/include/tnt/jama_cholesky.h:${PORTSDIR}/math/jama \ - ${LOCALBASE}/lib/libRAPID.a:${PORTSDIR}/math/rapid -EXTRACT_DEPENDS= dos2unix:${PORTSDIR}/converters/unix2dos -LIB_DEPENDS= libwx_gtk2_core-2.8.so:${PORTSDIR}/x11-toolkits/wxgtk28 \ - libvtkCommon.so:${PORTSDIR}/math/vtk5 - -CONFLICTS= dtiquery-1.0* - -RESTRICTED= Must register to download at http://graphics.stanford.edu/projects/dti/ - -SUB_FILES= pkg-message -PKGMESSAGE= ${WRKDIR}/pkg-message - -USES= gmake - -PLIST_FILES= bin/dtiquery \ - bin/dtiprecompute_cmd \ - bin/dtiprecompute_gui - -ALL_TARGET= - -MAN1= dtiquery.1 \ - dtiprecompute_cmd.1 \ - dtiprecompute_gui.1 - -NO_STAGE= yes -.include <bsd.port.pre.mk> - -.if !exists(${DISTDIR}/${DISTNAME}.tar.gz) -IGNORE= you must manually fetch ${DISTNAME}.tar.gz from http://graphics.stanford.edu/projects/dti/, place it in ${DISTDIR}, and then run make again -.endif - -post-extract: - dos2unix ${WRKSRC}/*/Makefile ${WRKSRC}/Makefile* - ${REINPLACE_CMD} "s/zlib-1.2.2 RAPID201//g" ${WRKSRC}/Makefile - -do-install: - ${INSTALL_PROGRAM} ${WRKSRC}/DTIQuery/dtiquery ${PREFIX}/bin - ${INSTALL_PROGRAM} ${WRKSRC}/precompute/dtiprecompute_cmd ${PREFIX}/bin - ${INSTALL_PROGRAM} ${WRKSRC}/precompute/dtiprecompute_gui ${PREFIX}/bin - ${INSTALL_MAN} ${FILESDIR}/dtiquery.1 ${MAN1PREFIX}/man/man1 - ${INSTALL_MAN} ${FILESDIR}/dtiquery.1 ${MAN1PREFIX}/man/man1/dtiprecompute_cmd.1 - ${INSTALL_MAN} ${FILESDIR}/dtiquery.1 ${MAN1PREFIX}/man/man1/dtiprecompute_gui.1 - -post-install: - @${CAT} ${PKGMESSAGE} - -.include <bsd.port.post.mk> diff --git a/science/dtiquery/distinfo b/science/dtiquery/distinfo deleted file mode 100644 index 1e123f870e56..000000000000 --- a/science/dtiquery/distinfo +++ /dev/null @@ -1,2 +0,0 @@ -SHA256 (dtiquery-1.1.tar.gz) = c59f5911e633f1f364cfd03ed18c296f99963184e2c2ddea937109f45f4b456e -SIZE (dtiquery-1.1.tar.gz) = 285780 diff --git a/science/dtiquery/files/dtiquery.1 b/science/dtiquery/files/dtiquery.1 deleted file mode 100644 index 46b0516f3f0c..000000000000 --- a/science/dtiquery/files/dtiquery.1 +++ /dev/null @@ -1,35 +0,0 @@ -.TH DTIQUERY 1 -.SH NAME \" Section header -.PP - -DTIQuery - DTI Visualization Software - -.SH SYNOPSIS -.PP -.nf -.na -dtiquery -dtiprecompute_cmd [args] -dtiprecompute_gui - -.ad -.fi - -.SH "DESCRIPTION" - -DTIQuery is a software suite for analyzing DTI (Diffusion Tensor Imaging) -data obtained via MRI (Magnetic Resonence Imaging). For full documentation, -please visit - -http://graphics.stanford.edu/projects/dti/software/. - -.SH "SEE ALSO" - -afni(1), caret(1), freesurfer(1), fsl(1) - -.SH AUTHOR -.nf -.na -David Akers -Stanford University - diff --git a/science/dtiquery/files/patch-DTIQuery-Makefile b/science/dtiquery/files/patch-DTIQuery-Makefile deleted file mode 100644 index c7f205c84822..000000000000 --- a/science/dtiquery/files/patch-DTIQuery-Makefile +++ /dev/null @@ -1,13 +0,0 @@ ---- DTIQuery/Makefile.orig Thu Dec 6 13:48:54 2007 -+++ DTIQuery/Makefile Thu Dec 6 13:49:24 2007 -@@ -12,8 +12,8 @@ - - VTK_LIBS = -lvtkIO \ - -lvtkRendering -lvtkGraphics -lvtkImaging \ -- -lvtkFiltering -lvtkCommon -lvtkHybrid -lvtkpng -lvtkzlib \ -- -lvtkftgl -lvtkfreetype -lvtkjpeg -lvtkDICOMParser \ -+ -lvtkFiltering -lvtkCommon -lvtkHybrid -lpng -lz \ -+ -lvtkftgl -lvtkfreetype -ljpeg -lvtkDICOMParser \ - - # for FreeBSD, need -lpng -ljpeg -lz instead of -lvtkpng -lvtkzlib -lvtkjpeg - diff --git a/science/dtiquery/files/patch-Makefile.definitions b/science/dtiquery/files/patch-Makefile.definitions deleted file mode 100644 index 0471a7a2b2ba..000000000000 --- a/science/dtiquery/files/patch-Makefile.definitions +++ /dev/null @@ -1,34 +0,0 @@ ---- Makefile.definitions.orig Wed Dec 19 10:50:50 2007 -+++ Makefile.definitions Wed Dec 19 10:51:13 2007 -@@ -1,6 +1,6 @@ --CYGWIN = 1 -+# CYGWIN = 1 - # mac = 1 --# FreeBSD = 1 -+FreeBSD = 1 - # linux = 1 - - # Uncomment the line above corresponding to your system. Then find the -@@ -46,18 +46,19 @@ - - ifdef FreeBSD - --WX_CONFIG_BIN ?= /usr/X11R6/bin/wxgtk2-2.8-config -+WX_CONFIG_BIN ?= ${LOCALBASE}/bin/wxgtk2-2.8-config - VTK_INCLUDE_PATHS ?= -I/usr/local/include/vtk-5.4/ - VTK_LIB_PATHS ?= -L/usr/local/lib/vtk-5.4/ - WX_INCLUDE_PATHS ?= `$(WX_CONFIG_BIN) --cxxflags` - WX_LIB_PATHS ?= `$(WX_CONFIG_BIN) --libs` `$(WX_CONFIG_BIN) \ - --gl-libs` --RAPID_INCLUDE_PATH ?= -I/usr/local/include -+RAPID_INCLUDE_PATH ?= -I/usr/local/include/RAPID - RAPID_LIB_PATH ?= -L/usr/local/lib - TNT_INCLUDE_PATH ?= -I/usr/local/include/tnt/ - JAMA_INCLUDE_PATH ?= -I/usr/local/include/ - ZLIB_INCLUDE_PATH ?= -I/usr/include --SYS_INCLUDE_PATHS ?= -I/usr/include -I/usr/X11R6/include -I/usr/local/include/gtk-2.0 -I/usr/X11R6/include/gtk-2.0 -I/usr/local/include/glib-2.0 -I/usr/local/include/cairo -I/usr/local/include/pango-1.0 -I/usr/X11R6/include/pango-1.0 -I/usr/local/include/atk-1.0 -+SYS_INCLUDE_PATHS ?= -I/usr/include -I${LOCALBASE}/include -I/usr/local/include/gtk-2.0 -I${LOCALBASE}/include/gtk-2.0 -I/usr/local/include/glib-2.0 -I/usr/local/include/cairo -I/usr/local/include/pango-1.0 -I${LOCALBASE}/include/pango-1.0 -I/usr/local/include/atk-1.0 -+SYS_CXXFLAGS ?= -g - SYS_LIBS ?= -L/usr/local/lib -lXt -lGL -lpng - - else diff --git a/science/dtiquery/files/patch-precompute-Makefile b/science/dtiquery/files/patch-precompute-Makefile deleted file mode 100644 index c6ce2354c1ac..000000000000 --- a/science/dtiquery/files/patch-precompute-Makefile +++ /dev/null @@ -1,13 +0,0 @@ ---- precompute/Makefile.orig Thu Dec 6 13:51:44 2007 -+++ precompute/Makefile Thu Dec 6 13:52:16 2007 -@@ -21,8 +21,8 @@ - - VTK_LIBS = -lvtkIO \ - -lvtkRendering -lvtkGraphics -lvtkImaging \ -- -lvtkFiltering -lvtkCommon -lvtkHybrid -lvtkpng -lvtkzlib \ -- -lvtkftgl -lvtkfreetype -lvtkjpeg -lvtkDICOMParser \ -+ -lvtkFiltering -lvtkCommon -lvtkHybrid -lpng -lz \ -+ -lvtkftgl -lvtkfreetype -ljpeg -lvtkDICOMParser \ - - # for FreeBSD, need -lpng -ljpeg -lz instead of -lvtkpng -lvtkzlib -lvtkjpeg - diff --git a/science/dtiquery/files/pkg-message.in b/science/dtiquery/files/pkg-message.in deleted file mode 100644 index eb6f29e44f07..000000000000 --- a/science/dtiquery/files/pkg-message.in +++ /dev/null @@ -1,10 +0,0 @@ -============================================================================= -DTI Query users will need %%PREFIX%%/bin in their PATH. - -For questions or comments regarding this port, please contact the -port maintainer. - -For dtiquery usage, please visit the WEB site at - -http://graphics.stanford.edu/projects/dti/ -============================================================================= diff --git a/science/dtiquery/pkg-descr b/science/dtiquery/pkg-descr deleted file mode 100644 index 0791de735e9c..000000000000 --- a/science/dtiquery/pkg-descr +++ /dev/null @@ -1,3 +0,0 @@ -DTI visualization software from Stanford. - -WWW: http://graphics.stanford.edu/projects/dti/ diff --git a/science/elmer-hutiter/Makefile b/science/elmer-hutiter/Makefile deleted file mode 100644 index 8ed5c18fa629..000000000000 --- a/science/elmer-hutiter/Makefile +++ /dev/null @@ -1,54 +0,0 @@ -# Created by: Pedro Giffuni <giffunip@asme.org> -# $FreeBSD$ - -PORTNAME= hutiter -PORTVERSION= 5.4.0 -PORTREVISION= 6 -CATEGORIES= science -MASTER_SITES= http://www.nic.funet.fi/index/files/index/elmer/src/old/ \ - http://www.bezopasnik.org/unix/ports/distfiles/ -PKGNAMEPREFIX= elmer- - -MAINTAINER= ports@FreeBSD.org -COMMENT= HUTIter library for use in the ELMER FEM package - -LIB_DEPENDS= libarpack.so:${PORTSDIR}/math/arpack - -USES= fortran - -NO_STAGE= yes -.include <bsd.port.pre.mk> - -.if exists(${LOCALBASE}/lib/libatlas.so) && !defined(WITH_BLAS) -WITH_ATLAS= yes -.endif -.if defined(WITH_ATLAS) -LIB_DEPENDS+= libatlas.so:${PORTSDIR}/math/atlas -BLAS= -lf77blas -LAPACK= -lalapack -lcblas -.else -LIB_DEPENDS+= liblapack.so:${PORTSDIR}/math/lapack -LIB_DEPENDS+= libblas.so:${PORTSDIR}/math/blas -BLAS= -lblas -LAPACK= -llapack -.endif - -post-patch: - @${REINPLACE_CMD} -e 's|%%CC%%|${CC}|' -e 's|%%FC%%|${FC}|' ${WRKSRC}/configure.in - -GNU_CONFIGURE= yes -USE_AUTOTOOLS= autoconf -ALL_TARGET= - -PLIST_FILES= include/huti_defs.h include/huti_fdefs.h lib/libhuti.a - -.if ${ARCH} == "amd64" || ${ARCH} == "ia64" -CFLAGS+= -fPIC -FFLAGS+= -fPIC - -post-configure: - @${REINPLACE_CMD} -e 's+-O +-O -fPIC +g;' ${WRKSRC}/src/Makefile - -.endif - -.include <bsd.port.post.mk> diff --git a/science/elmer-hutiter/distinfo b/science/elmer-hutiter/distinfo deleted file mode 100644 index 40e4db14f8fb..000000000000 --- a/science/elmer-hutiter/distinfo +++ /dev/null @@ -1,2 +0,0 @@ -SHA256 (hutiter-5.4.0.tar.gz) = b5d7b01dc4a5b6da6147e6bf31d00048548c54609e77108cac0d359a0ee2379c -SIZE (hutiter-5.4.0.tar.gz) = 172341 diff --git a/science/elmer-hutiter/pkg-descr b/science/elmer-hutiter/pkg-descr deleted file mode 100644 index bc46c7011c51..000000000000 --- a/science/elmer-hutiter/pkg-descr +++ /dev/null @@ -1,9 +0,0 @@ -HUTIter library for use in the Elmer FEM package. - -Elmer is an open-source computational tool for multi-physics problems. - -Elmer includes physical models of fluid dynamics, structural mechanics, -electromagnetics and heat transfer. These are described by partial -differential equations which Elmer solves by the Finite Element Method (FEM). - -WWW: http://www.csc.fi/elmer/ diff --git a/science/elmerpost/Makefile b/science/elmerpost/Makefile deleted file mode 100644 index cde5d8aa4112..000000000000 --- a/science/elmerpost/Makefile +++ /dev/null @@ -1,33 +0,0 @@ -# Created by: Pedro Giffuni <giffunip@asme.org> -# $FreeBSD$ - -PORTNAME= elmerpost -PORTVERSION= 5.4.0 -PORTREVISION= 7 -CATEGORIES= science -MASTER_SITES= http://garr.dl.sourceforge.net/sourceforge/elmerfem/ - -MAINTAINER= ports@FreeBSD.org -COMMENT= Visualization of Numerical Results in the ELMER FEM package - -BUILD_DEPENDS= ${LOCALBASE}/lib/libmatc.a:${PORTSDIR}/science/elmer-matc \ - wish8.4:${PORTSDIR}/x11-toolkits/tk84 -RUN_DEPENDS= wish8.4:${PORTSDIR}/x11-toolkits/tk84 - -# Elmer avoids the new C++ headers because they cause problems -# on older systems (Irix) -CXXFLAGS+= -Wno-deprecated - -USE_GL= yes -USE_XORG= x11 xt xi -GNU_CONFIGURE= yes -USES= gmake fortran - -NO_STAGE= yes -.include <bsd.port.pre.mk> - -.if ${ARCH} == "amd64" -CFLAGS+= -fPIC -.endif - -.include <bsd.port.post.mk> diff --git a/science/elmerpost/distinfo b/science/elmerpost/distinfo deleted file mode 100644 index 50cffbc869ca..000000000000 --- a/science/elmerpost/distinfo +++ /dev/null @@ -1,2 +0,0 @@ -SHA256 (elmerpost-5.4.0.tar.gz) = 196e8d9fb5ff9e9e30785b5c762eb45f41a664c3592595b23a0c1832ed4a9445 -SIZE (elmerpost-5.4.0.tar.gz) = 1424120 diff --git a/science/elmerpost/files/patch-src-Makefile.am b/science/elmerpost/files/patch-src-Makefile.am deleted file mode 100644 index b6cab4444840..000000000000 --- a/science/elmerpost/files/patch-src-Makefile.am +++ /dev/null @@ -1,8 +0,0 @@ ---- src/Makefile.am.orig 2009-07-05 17:46:44.000000000 -0300 -+++ src/Makefile.am 2009-07-05 17:47:17.000000000 -0300 -@@ -1,4 +1,4 @@ --SUBDIRS=tk glaux camera graphics modules sico2elmer objects visuals tcl elements -+SUBDIRS=tk glaux camera graphics modules objects visuals tcl elements - - if NOTWINDOWS - diff --git a/science/elmerpost/files/patch-src-Makefile.in b/science/elmerpost/files/patch-src-Makefile.in deleted file mode 100644 index 36dda6f71331..000000000000 --- a/science/elmerpost/files/patch-src-Makefile.in +++ /dev/null @@ -1,11 +0,0 @@ ---- src/Makefile.in.orig 2009-07-05 17:46:35.000000000 -0300 -+++ src/Makefile.in 2009-07-05 17:47:03.000000000 -0300 -@@ -235,7 +235,7 @@ - target_cpu = @target_cpu@ - target_os = @target_os@ - target_vendor = @target_vendor@ --SUBDIRS = tk glaux camera graphics modules sico2elmer objects visuals tcl elements -+SUBDIRS = tk glaux camera graphics modules objects visuals tcl elements - @NOTWINDOWS_FALSE@ElmerPost_SOURCES = \ - @NOTWINDOWS_FALSE@ ElmerPost.c \ - @NOTWINDOWS_FALSE@ elmerpost.h \ diff --git a/science/elmerpost/pkg-descr b/science/elmerpost/pkg-descr deleted file mode 100644 index 6ca1de8e9715..000000000000 --- a/science/elmerpost/pkg-descr +++ /dev/null @@ -1,11 +0,0 @@ -ElmerPost - the Visualization of Numerical Results. - -The function of ElmerPost is to visualize the numerical results produced -by ElmerSolver and other finite element programs. ElmerPost operates with -the data specific to the unknown variables (temperature, velocity, -pressure, displacement etc.) defined in the mathematical model. ElmerPost -plots e.g. contours and vector fields, and can manipulate computed data -into another form using the built-in MATC-language (for instance heat -fluxes from temperature distributions). - -WWW: http://www.csc.fi/elmer/elmerpost/ diff --git a/science/elmerpost/pkg-plist b/science/elmerpost/pkg-plist deleted file mode 100644 index b3e52960f3c1..000000000000 --- a/science/elmerpost/pkg-plist +++ /dev/null @@ -1,285 +0,0 @@ -bin/ElmerPost -bin/QueryGLXExt -%%DATADIR%%/help/dspl.html -%%DATADIR%%/help/edit.html -%%DATADIR%%/help/figs/a.log -%%DATADIR%%/help/figs/background.gif -%%DATADIR%%/help/figs/benzene_cut.gif -%%DATADIR%%/help/figs/benzene_iso.gif -%%DATADIR%%/help/figs/camera.gif -%%DATADIR%%/help/figs/clip.gif -%%DATADIR%%/help/figs/colormap.gif -%%DATADIR%%/help/figs/cols.gif -%%DATADIR%%/help/figs/cont.gif -%%DATADIR%%/help/figs/crystal_flow.gif -%%DATADIR%%/help/figs/crystal_stream.gif -%%DATADIR%%/help/figs/crystal_temp.gif -%%DATADIR%%/help/figs/diff.gif 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-%%DATADIR%%/tcl/particle.tcl -%%DATADIR%%/tcl/readfile.tcl -%%DATADIR%%/tcl/saveimage.tcl -%%DATADIR%%/tcl/sphere.tcl -%%DATADIR%%/tcl/text.tcl -%%DATADIR%%/tcl/timestep.tcl -%%DATADIR%%/tcl/vectors.tcl -@dirrm %%DATADIR%%/help/figs -@dirrm %%DATADIR%%/help/html_library-0.3 -@dirrm %%DATADIR%%/help/matc/lh-figs -@dirrm %%DATADIR%%/help/matc -@dirrm %%DATADIR%%/help -@dirrm %%DATADIR%%/lib/cameras -@dirrm %%DATADIR%%/lib/colormaps -@dirrm %%DATADIR%%/lib/images -@dirrm %%DATADIR%%/lib -@dirrm %%DATADIR%%/modules -@dirrm %%DATADIR%%/tcl -@dirrm %%DATADIR%% diff --git a/science/g3data/Makefile b/science/g3data/Makefile deleted file mode 100644 index 82acf4076b87..000000000000 --- a/science/g3data/Makefile +++ /dev/null @@ -1,34 +0,0 @@ -# Created by: trasz <trasz@pin.if.uz.zgora.pl> -# $FreeBSD$ - -PORTNAME= g3data -PORTVERSION= 1.5.3 -PORTREVISION= 5 -CATEGORIES= science -MASTER_SITES= http://www.frantz.fi/software/ - -MAINTAINER= ports@FreeBSD.org -COMMENT= Utility for extracting data from graphs - -BUILD_DEPENDS= nsgmls:${PORTSDIR}/textproc/jade \ - ${LOCALBASE}/share/sgml/docbook/utils-0.6.14/helpers/docbook2man-spec.pl:${PORTSDIR}/textproc/docbook-utils \ - ${LOCALBASE}/share/sgml/docbook/4.1:${PORTSDIR}/textproc/docbook-sgml - -USES= pkgconfig -USE_GNOME= gtk20 -ALL_TARGET= -MAN1= g3data.1 -MANCOMPRESSED= yes -PLIST_FILES= bin/g3data %%EXAMPLESDIR%%/test1.png %%EXAMPLESDIR%%/test1.values \ - %%EXAMPLESDIR%%/test2.png %%EXAMPLESDIR%%/test2.values -PLIST_DIRS= %%EXAMPLESDIR%% - -NO_STAGE= yes -post-install: - @${MKDIR} ${EXAMPLESDIR} - ${INSTALL_DATA} ${WRKSRC}/test1.png ${EXAMPLESDIR} - ${INSTALL_DATA} ${WRKSRC}/test1.values ${EXAMPLESDIR} - ${INSTALL_DATA} ${WRKSRC}/test2.png ${EXAMPLESDIR} - ${INSTALL_DATA} ${WRKSRC}/test2.values ${EXAMPLESDIR} - -.include <bsd.port.mk> diff --git a/science/g3data/distinfo b/science/g3data/distinfo deleted file mode 100644 index 0f2238eda6e5..000000000000 --- a/science/g3data/distinfo +++ /dev/null @@ -1,2 +0,0 @@ -SHA256 (g3data-1.5.3.tar.gz) = afedb9e4ad8968dbf8f0ffddab149f24c41f028fe984f4d0740009e8b2de1de0 -SIZE (g3data-1.5.3.tar.gz) = 52051 diff --git a/science/g3data/files/patch-Makefile b/science/g3data/files/patch-Makefile deleted file mode 100644 index 8539039f022c..000000000000 --- a/science/g3data/files/patch-Makefile +++ /dev/null @@ -1,24 +0,0 @@ ---- Makefile.orig 2008-12-14 09:20:17.000000000 +0100 -+++ Makefile 2009-01-11 15:19:56.000000000 +0100 -@@ -1,8 +1,7 @@ --CC=gcc --CFLAGS=-Wall `pkg-config --cflags gtk+-2.0` -+CFLAGS+=-Wall `pkg-config --cflags gtk+-2.0` - LIBS=`pkg-config --libs gtk+-2.0` --bindir ?= /usr/bin --mandir ?= /usr/share/man -+bindir= ${PREFIX}/bin -+mandir= ${PREFIX}/man - - .c.o: - $(CC) -c $(CFLAGS) $(CPPFLAGS) $< -@@ -21,7 +20,8 @@ - - g3data.1.gz: g3data.sgml - rm -f *.1 -- onsgmls g3data.sgml | sgmlspl /usr/share/sgml/docbook/utils-0.6.14/helpers/docbook2man-spec.pl -+ nsgmls g3data.sgml | sgmlspl /usr/local/share/sgml/docbook/utils-0.6.14/helpers/docbook2man-spec.pl -+ mv *.1 g3data.1 - gzip g3data.1 - - clean: diff --git a/science/g3data/pkg-descr b/science/g3data/pkg-descr deleted file mode 100644 index 88ddc777c014..000000000000 --- a/science/g3data/pkg-descr +++ /dev/null @@ -1,5 +0,0 @@ -g3data is used for extracting data from graphs. In publications -graphs often are included, but the actual data is missing. g3data -makes the extracting process much easier. - -WWW: http://www.frantz.fi/software/g3data.php diff --git a/science/gamess/Makefile b/science/gamess/Makefile deleted file mode 100644 index 2645cc13ee94..000000000000 --- a/science/gamess/Makefile +++ /dev/null @@ -1,164 +0,0 @@ -# Created by: NAKATA Maho <maho@FreeBSD.org> -# $FreeBSD$ - -PORTNAME= gamess -PORTVERSION= ${SNAPDATE} -PORTREVISION= 1 -CATEGORIES= science -MASTER_SITES= #http://www.msg.ameslab.gov/GAMESS/License_Agreement.html -DISTNAME= gamess-current -DIST_SUBDIR= ${PORTNAME}/${PORTVERSION} - -MAINTAINER= ports@FreeBSD.org -COMMENT= Freely obtainable ab-initio molecular orbital calculation program - -USES= fortran gmake -WRKSRC= ${WRKDIR}/gamess -SNAPDATE= 20130501.1 - -RESTRICTED= No Redistribution - -.if !exists(${DISTDIR}/${DISTFILES}) -IGNORE=you must manually get the source distribution from master site. http://www.msg.ameslab.gov/GAMESS/download.html. Please select "Source code distribution", and check on "running on Intel compatible PC running Linux". You must have license, and freely obtainable -.endif - -MANUAL_PACKAGE_BUILD=You must manually get the source distribution from master site. http://www.msg.ameslab.gov/GAMESS/download.html. Please select "Source code distribution", and check on "running on Intel compatible PC running Linux". You must have license, and freely obtainable. - -NO_STAGE= yes -.include <bsd.port.pre.mk> - -.if exists(${LOCALBASE}/lib/libgoto2.so) -WITH_BLAS?= gotoblas -.elif exists(${LOCALBASE}/lib/libatlas.so) -WITH_BLAS?= atlas -.else -WITH_BLAS?= reference -.endif - -. if ${WITH_BLAS} == reference -LIB_DEPENDS+= libblas.so:${PORTSDIR}/math/blas -LIB_DEPENDS+= liblapack.so:${PORTSDIR}/math/lapack -BLAS= -lblas -LAPACK= -llapack -.elif ${WITH_BLAS} == gotoblas -LIB_DEPENDS+= libgoto2.so:${PORTSDIR}/math/gotoblas -BLAS= -lgoto2p -LAPACK= -lgoto2p -.elif ${WITH_BLAS} == atlas -LIB_DEPENDS+= libatlas.so:${PORTSDIR}/math/atlas -BLAS= -lptf77blas -LAPACK= -lalapack -lptcblas -.endif - -.if defined(WITH_OPTIMIZED_FLAGS) -.if ${ARCH} == "amd64" -CFLAGS+= -pipe -O3 -ffast-math -funroll-all-loops -fpeel-loops -ftracer -funswitch-loops -funit-at-a-time -FFLAGS+= -pipe -O3 -ffast-math -funroll-all-loops -fpeel-loops -ftracer -funswitch-loops -funit-at-a-time -.elif ${ARCH} == "i386" -CFLAGS+= -pipe -O3 -ffast-math -finline-functions -fomit-frame-pointer -funroll-loops -fexpensive-optimizations -malign-double -mcpu=i686 -march=i686 -mfancy-math-387 -FFLAGS+= -pipe -O3 -ffast-math -finline-functions -fomit-frame-pointer -funroll-loops -fexpensive-optimizations -malign-double -mcpu=i686 -march=i686 -mfancy-math-387 -.endif -.endif - -#WITH_IFC= yes #currently building with ifc is broken -.if defined(WITH_IFC) -FC= ${LOCALBASE}/intel_fc_80/bin/ifort -F77= ${LOCALBASE}/intel_fc_80/bin/ifort -CC= ${LOCALBASE}/intel_cc_80/bin/icc -FFLAGS= -axP -xW -ipo -O3 -Vaxlib -CFLAGS= -axP -xW -ipo -O3 -Vaxlib -LIBSVM= -lsvml -LIBG2C= -lg2c -.else -LIBG2C= -LIBSVM= -.endif - -.if defined(WITH_IFC) -FORTRAN= ifort -.else -FORTRAN= gfortran -.endif - -pre-build: - ${CP} ${FILESDIR}/install.info ${WRKSRC} - ${CP} ${FILESDIR}/Makefile.top ${WRKSRC}/Makefile - @${REINPLACE_CMD} -e 's+%%PREFIX%%+${PREFIX}+g' ${WRKSRC}/gms-files.csh -.if ${ARCH} == "amd64" - @${REINPLACE_CMD} -e 's+%%ARCH%%+freebsd64+g' ${WRKSRC}/comp - @${REINPLACE_CMD} -e 's+%%ARCH%%+freebsd64+g' ${WRKSRC}/compall - @${REINPLACE_CMD} -e 's+%%ARCH%%+freebsd64+g' ${WRKSRC}/ddi/compddi - @${REINPLACE_CMD} -e 's+%%ARCH%%+freebsd64+g' ${WRKSRC}/lked - @${REINPLACE_CMD} -e 's+%%GMS_TARGET%%+freebsd64+g' ${WRKSRC}/install.info -.elif ${ARCH} == "i386" - @${REINPLACE_CMD} -e 's+%%ARCH%%+freebsd32+g' ${WRKSRC}/comp - @${REINPLACE_CMD} -e 's+%%ARCH%%+freebsd32+g' ${WRKSRC}/compall - @${REINPLACE_CMD} -e 's+%%ARCH%%+freebsd32+g' ${WRKSRC}/ddi/compddi - @${REINPLACE_CMD} -e 's+%%ARCH%%+freebsd32+g' ${WRKSRC}/lked - @${REINPLACE_CMD} -e 's+%%GMS_TARGET%%+freebsd32+g' ${WRKSRC}/install.info -.endif - @${REINPLACE_CMD} -e 's+%%GMS_PATH%%+${WRKSRC}+g ; \ - s+%%GMS_BUILD_DIR%%+${WRKSRC}+g ; \ - s+%%GMS_FORTRAN%%+${FORTRAN}+g ; \ - s+%%FC%%+${FC}+g ; \ - s+%%GMS_GFORTRAN_VERNO%%+${GCC_DEFAULT_VERSION}+g ; \ - s+%%GMS_DDI_COMM%%+sockets+g ; \ - s+%%GMS_MATHLIB%%+none+g ; \ - s+%%GMS_MATHLIB_PATH%%+${LOCALBASE}/lib+g' ${WRKSRC}/install.info - ${REINPLACE_CMD} -e 's+%%FC%%+${FC}+g ; \ - s+%%LDFLAGS%%+${LDFLAGS}+g ; \ - s+%%LOCALBASE%%+${LOCALBASE}+g ; \ - s+%%LIBSVM%%+${LIBSVM}+g ; \ - s+%%LIBG2C%%+${LIBG2C}+g ; \ - s+%%BLAS%%+${BLAS}+g ; \ - s+%%PTHREAD_LIBS%%+${PTHREAD_LIBS}+g' \ - ${WRKSRC}/lked - ${REINPLACE_CMD} -e 's+%%FC%%+${FC}+g ; \ - s+%%FFLAGS%%+${FFLAGS}+g' \ - ${WRKSRC}/comp - ${REINPLACE_CMD} -e 's+%%CC%%+${CC}+g' \ - ${WRKSRC}/compall - ${REINPLACE_CMD} -e 's+%%PREFIX%%+${PREFIX}+g' \ - ${WRKSRC}/rungms - ${REINPLACE_CMD} -e 's+%%FC%%+${FC}+g ; \ - s+%%GMS_FORTRAN%%+${FORTRAN}+g ; \ - s+%%PTHREAD_CFLAGS%%+${PTHREAD_CFLAGS}+g ; \ - s+%%PTHREAD_LIBS%%+${PTHREAD_LIBS}+g ; \ - s+%%UNDERSCORES%%+${UNDERSCORES}+g ; \ - s+%%CC%%+${CC}+g' \ - ${WRKSRC}/ddi/compddi - - ${CP} ${FILESDIR}/Makefile.tools ${WRKSRC}/tools/Makefile - ${REINPLACE_CMD} -e 's+%%FC%%+${FC}+g ; \ - s+%%FFLAGS%%+${FFLAGS}+g' \ - ${WRKSRC}/tools/Makefile - -do-build: - (cd ${WRKSRC}; ${MAKE_CMD}) - -do-install: - ${MKDIR} ${PREFIX}/bin/gms - ${MKDIR} ${PREFIX}/share/gamess - ${MKDIR} ${PREFIX}/share/gamess/mcpdata - ${MKDIR} ${PREFIX}/share/doc/gamess - ${MKDIR} ${PREFIX}/share/examples/gamess - ${INSTALL_SCRIPT} ${WRKDIR}/gamess/rungms ${PREFIX}/bin/gamess - ${CHMOD} 555 ${PREFIX}/bin/gamess - ${INSTALL_SCRIPT} ${WRKDIR}/gamess/gms-files.csh ${PREFIX}/bin/gms - ${INSTALL_PROGRAM} ${WRKDIR}/gamess/gamess.00.x ${PREFIX}/bin/gms - ${INSTALL_PROGRAM} ${WRKDIR}/gamess/ddi/ddikick.x ${PREFIX}/bin/gms - ${INSTALL_DATA} ${WRKDIR}/gamess/*.DOC ${PREFIX}/share/doc/gamess/ - ${INSTALL_DATA} ${WRKDIR}/gamess/tests/standard/*.inp ${PREFIX}/share/examples/gamess/ - ${MKDIR} ${PREFIX}/share/gamess/auxdata - ${MKDIR} ${PREFIX}/share/gamess/auxdata/BASES - ${MKDIR} ${PREFIX}/share/gamess/auxdata/EFP - ${MKDIR} ${PREFIX}/share/gamess/auxdata/MCP - ${MKDIR} ${PREFIX}/share/gamess/auxdata/QUANPOL - ${INSTALL_DATA} ${WRKDIR}/gamess/auxdata/ericfmt.dat ${PREFIX}/share/gamess/auxdata/ - ${INSTALL_DATA} ${WRKDIR}/gamess/auxdata/BASES/* ${PREFIX}/share/gamess/auxdata/BASES - ${INSTALL_DATA} ${WRKDIR}/gamess/auxdata/EFP/* ${PREFIX}/share/gamess/auxdata/EFP - ${INSTALL_DATA} ${WRKDIR}/gamess/auxdata/MCP/* ${PREFIX}/share/gamess/auxdata/MCP - ${INSTALL_DATA} ${WRKDIR}/gamess/auxdata/QUANPOL/* ${PREFIX}/share/gamess/auxdata/QUANPOL - ${INSTALL_DATA} ${WRKDIR}/gamess/ddi/readme.ddi ${PREFIX}/share/doc/gamess/ - -.include <bsd.port.post.mk> diff --git a/science/gamess/distinfo b/science/gamess/distinfo deleted file mode 100644 index 5e8d1f486fb8..000000000000 --- a/science/gamess/distinfo +++ /dev/null @@ -1,2 +0,0 @@ -SHA256 (gamess/20130501.1/gamess-current.tar.gz) = 315e6fa8f1947d8419b6f1adccf3fc7dd47b581fce107d304b7b99ef0cb15498 -SIZE (gamess/20130501.1/gamess-current.tar.gz) = 29013211 diff --git a/science/gamess/files/Makefile.tools b/science/gamess/files/Makefile.tools deleted file mode 100644 index 6943a7b77a53..000000000000 --- a/science/gamess/files/Makefile.tools +++ /dev/null @@ -1,11 +0,0 @@ -all: actvte.f actvte.x - -actvte.x: actvte.f - %%FC%% %%FFLAGS%% -o actvte.x actvte.f - -actvte.f: actvte.code - sed 's/*UNX/ /g' < actvte.code > actvte.f - -clean: - rm actvte.x actvte.f - diff --git a/science/gamess/files/Makefile.top b/science/gamess/files/Makefile.top deleted file mode 100644 index f39cbaa33782..000000000000 --- a/science/gamess/files/Makefile.top +++ /dev/null @@ -1,11 +0,0 @@ -# Makefile for gamess -all: gamess_exe - -gamess_exe: - (cd tools ; ${MAKE} ) - (cd ddi ; ./compddi ) - ./compall - csh lked - -clean: - rm -rf object/*.o *.o *.f diff --git a/science/gamess/files/install.info b/science/gamess/files/install.info deleted file mode 100644 index 4fe3c0fc6f73..000000000000 --- a/science/gamess/files/install.info +++ /dev/null @@ -1,15 +0,0 @@ -#!/bin/csh -# $FreeBSD$ -# compilation configuration for GAMESS -setenv GMS_PATH %%GMS_PATH%% -setenv GMS_BUILD_DIR %%GMS_BUILD_DIR%% -# machine type -setenv GMS_TARGET %%GMS_TARGET%% -# FORTRAN compiler setup -setenv GMS_FORTRAN %%GMS_FORTRAN%% -setenv GMS_GFORTRAN_VERNO %%GMS_GFORTRAN_VERNO%% -# mathematical library setup -setenv GMS_MATHLIB %%GMS_MATHLIB%% -setenv GMS_MATHLIB_PATH %%GMS_MATHLIB_PATH%% -# parallel message passing model setup -setenv GMS_DDI_COMM %%GMS_DDI_COMM%% diff --git a/science/gamess/files/patch-comp b/science/gamess/files/patch-comp deleted file mode 100644 index 7d76843c8846..000000000000 --- a/science/gamess/files/patch-comp +++ /dev/null @@ -1,322 +0,0 @@ ---- comp.orig 2012-12-05 05:49:41.000000000 +0900 -+++ comp 2013-02-27 15:56:56.000000000 +0900 -@@ -97,6 +97,8 @@ - if ($TARGET == ibm-bg) set OK=true - if ($TARGET == linux32) set OK=true - if ($TARGET == linux64) set OK=true -+if ($TARGET == freebsd32) set OK=true -+if ($TARGET == freebsd64) set OK=true - if ($TARGET == mac32) set OK=true - if ($TARGET == mac64) set OK=true - if ($TARGET == necsx) set OK=true -@@ -149,6 +151,8 @@ - if ($TARGET == ibm-bg) set BLAS3=true - if (($TARGET == linux32) && ($GMS_MATHLIB != none)) set BLAS3=true - if (($TARGET == linux64) && ($GMS_MATHLIB != none)) set BLAS3=true -+if (($TARGET == freebsd32) && ($GMS_MATHLIB != none)) set BLAS3=true -+if (($TARGET == freebsd64) && ($GMS_MATHLIB != none)) set BLAS3=true - if ($TARGET == mac32) set BLAS3=true - if ($TARGET == mac64) set BLAS3=true - if ($TARGET == sgi32) set BLAS3=true -@@ -579,6 +583,26 @@ - endif - endif - # -+if ($TARGET == freebsd32) then -+ setenv MACHIN '*I32' -+ if ($MODULE == ddi) setenv MACHIN '*SOC' -+ if ($MODULE == iolib) setenv MACHIN '*UNX' -+ if ($MODULE == unport) setenv MACHIN '*L32' -+endif -+# -+if ($TARGET == freebsd64) then -+ setenv MACHIN '*I64' -+ if ($MODULE == ddi) setenv MACHIN '*SOC' -+ if ($MODULE == iolib) setenv MACHIN '*UNX' -+ if ($MODULE == unport) then -+ if ($GMS_FORTRAN == ifort) then -+ setenv MACHIN '*INT' -+ else -+ setenv MACHIN '*L64' -+ endif -+ endif -+endif -+ - if ($TARGET == mac32) then - setenv MACHIN '*I32' - if ($MODULE == ddi) setenv MACHIN '*SOC' -@@ -1640,6 +1664,137 @@ - endsw - # ... end of Linux on 32 bit processors. - endif -+if ($TARGET == freebsd32) then -+# -+# there are three supported 32 bit compilers: g77, gfortran, ifort -+# g77, -+# the gnu FORTRAN being included in older Linux distributions -+# lacks support for unit numbers over 99, or REAL*16 -+# gfortran, -+# the gnu FORTRAN being included in newer Linux distributions -+# this allows unit numbers over 99, but not REAL*16 -+# Intel's commercial ifort, -+# supports unit numbers above 99 and REAL*16 (runs all of GAMESS) -+ -+ switch ($GMS_FORTRAN) -+# -+# The meaning of g77's flags are -+# -O0, -O1, -O2, -O3 are the optimization levels, -O means -O1 -+# -Wno-globals -fno-globals together suppress argument type checking. -+# -fautomatic defeats use of static storage -+# -malign-double uses 64 bit data alignment -+# g77 does not support FORTRAN logical units above 99, or 128 bit math. -+# -+ case g77: -+ set OPT = '-O2' -+ if ($MODULE == ormas1) set OPT='-O2 -fno-move-all-movables' # RH9, g77 3.3 -+ if ($MODULE == zheev) set OPT='-O0' # defensive compiling -+ if (($MODULE == qeigen) || ($MODULE == int2c)) then -+ mv -f $MODULE_F $MODULE.junk -+ sed -e "s/Q-/D-/g" \ -+ -e "s/Q+00/D+00/g" \ -+ -e "s/REAL\*16/DOUBLE PRECISION/" $MODULE.junk > $MODULE_F -+ rm -f $MODULE.junk -+ endif -+ if (($MODULE == iolib) || ($MODULE == inputa) || \ -+ ($MODULE == gamess) || ($MODULE == mp2ims)) then -+ mv -f $MODULE_F $MODULE.junk -+ sed -e "s/MXUNIT=299/MXUNIT=99/g" $MODULE.junk > $MODULE_F -+ rm -f $MODULE.junk -+ endif -+ set echo -+ g77 -c $OPT -malign-double -fautomatic \ -+ -Wno-globals -fno-globals $MODULE_F -+ unset echo -+ breaksw -+# -+# gfortran was included with Fedora Core distributions starting around FC4. -+# This is a 32 bit version, i.e. not using -fdefault-integer-8! -+# Unlike g77, gfortran allows for unit numbers above 100. -+# Like g77, gfortran does not support quadruple precision. -+# -Ox optimization level is from the gcc back end, x can be 0,1,2,3 -+# -std=legacy suppresses warnings about use of f77 constructs. -+# -+ case gfortran: -+ set OPT='-O2' -+ if ($MODULE == zheev) set OPT='-O0' # defensive compiling -+ if ($MODULE == pcmcv2) set OPT='-O1' # EFP+CPCM, ala Francois, v4.1.2 -+ if ($GMS_GFORTRAN_VERNO == 4.6) then -+ if ($MODULE == cosmo) set OPT='-O0' # this issue seen in 4.6.x -+ if ($MODULE == tddgrd) set OPT='-O0' # this issue seen in 4.6.1 -+ endif -+ if ($GMS_GFORTRAN_VERNO == 4.7) then -+ if ($MODULE == cosmo) set OPT='-O0' -+ if ($MODULE == dcscf) set OPT='-O0' -+ if ($MODULE == rohfcc) set OPT='-O0' -+ if ($MODULE == tddgrd) set OPT='-O0' -+ endif -+# as of 4.6 tested in late 2011, gfortran can do q.p.! -+ switch ($GMS_GFORTRAN_VERNO) -+ case 4.0: -+ case 4.1: -+ case 4.2: -+ case 4.3: -+ case 4.4: -+ case 4.5: -+ set extraflags='' -+ if (($MODULE == qeigen) || ($MODULE == int2c)) then -+ mv -f $MODULE_F $MODULE.junk -+ sed -e "s/Q-/D-/g" \ -+ -e "s/Q+00/D+00/g" \ -+ -e "s/REAL\*16/DOUBLE PRECISION/" $MODULE.junk > $MODULE_F -+ rm -f $MODULE.junk -+ endif -+ breaksw -+ case 4.6: -+ case 4.7: -+ set extraflags='-fno-whole-file' -+ breaksw -+ default: -+ echo Unrecognized gfortran version -+ exit 4 -+ breaksw -+ endsw -+# -+ set echo -+ %%FC%% -c $OPT -std=legacy $MODULE_F -+ unset echo -+ breaksw -+# -+# 3. Intel Fortran Compiler for Linux -+# -+# Note that this is more agressive (-O3 compared to -O2) than the -+# 64 bit compile below. If an ifort version gives you problems, -+# drop the optimization back to -O2. -+# Dmitri likes to use "-O3 -xN -ssp -unroll8 -ip -pad -opt_report", -+# but that may cause certain ifort versions to fail on some files. -+# See http://staff.aist.go.jp/d.g.fedorov/compgms.html for aggressive -+# optimizations in 32 bit mode, as a function of the ifort version. -+# -+ case ifort: -+ set OPT = '-O3' -+ if ($MODULE == delocl) set OPT='-O0' # from Cheol -+ if ($MODULE == prpamm) set OPT='-O0' # for exam13 -+ if ($MODULE == zheev) set OPT='-O0' -+ set EXTRAOPT=" " -+ if ($GMS_IFORT_VERNO >= 8) set EXTRAOPT="$EXTRAOPT -assume byterecl" -+ if ($GMS_IFORT_VERNO >= 10) set EXTRAOPT="$EXTRAOPT -vec-report0" -+ if ($GMS_IFORT_VERNO < 12) set EXTRAOPT="$EXTRAOPT -w95 -cm" -+ if ($GMS_IFORT_VERNO >= 12) set EXTRAOPT="$EXTRAOPT -warn nousage -inline-level=0" -+ set echo -+ ifort -c -i4 $OPT -ftz -auto $EXTRAOPT $MODULE_F -+ unset echo -+ breaksw -+# -+ default: -+ echo "Please spell your Linux 32 bit FORTRAN compiler name correctly." -+ exit 4 -+ breaksw -+ endsw -+# ... end of FreeBSD on 32 bit processors. -+endif -+ -+ - # - # ------ Linux on 64 bit chips ------ - # This should work on any 64 bit Linux release, for any type of -@@ -1897,6 +2052,136 @@ - endsw - # ... end of Linux on 64 bit processors. - endif -+ -+if ($TARGET == freebsd64) then -+# -+# there are two supported 64 bit compilers: gfortran, ifort -+# -+ switch ($GMS_FORTRAN) -+ -+ case gfortran: -+# -finit-real=<zero|inf|-inf|nan> could be interesting debug opt -+# -fno-automatic forces static storage of all local variables -+# -fno-whole-file suppresses argument's data type checking -+ set OPT='-O2' -+ if (".$GMS_DEBUG_FLAGS" != .) set OPT="$GMS_DEBUG_FLAGS" -+ -+ if ($GMS_GFORTRAN_VERNO == 4.6) then -+ if ($MODULE == cosmo) set OPT='-O0' # this issue seen in 4.6.1 -+ if ($MODULE == tddgrd) set OPT='-O0' # exam41, seen in 4.6.1 -+ endif -+ if ($GMS_GFORTRAN_VERNO == 4.7) then -+ if ($MODULE == cosmo) set OPT='-O0' -+ if ($MODULE == dcscf) set OPT='-O0' # exam44, seen in 4.7 only -+ if ($MODULE == rohfcc) set OPT='-O0' # exam47, seen in 4.7 only -+ if ($MODULE == tddgrd) set OPT='-O0' -+ endif -+ if ($MODULE == zheev) set OPT='-O0' # defensive compiling -+ -+ set EXTRAOPT=" " -+ -+ if (($MODULE == cchem) || ($MODULE == ga)) then -+ mv $MODULE.f $MODULE.F -+ set MODULE_F=$MODULE.F -+ if ($GMS_LIBCCHEM == true) then -+ if ($MODULE == cchem) set EXTRAOPT="-DHAVE_CCHEM $extraflags" -+ if ($MODULE == ga) set EXTRAOPT="-I$GMS_PATH/libcchem/ga/include" -+ endif -+ endif -+# -+# as of 4.6 tested in late 2011, gfortran can do q.p.! -+ switch ($GMS_GFORTRAN_VERNO) -+ case 4.0: -+ case 4.1: -+ case 4.2: -+ case 4.3: -+ case 4.4: -+ case 4.5: -+ if (($MODULE == qeigen) || ($MODULE == int2c)) then -+ mv -f $MODULE_F $MODULE.junk -+ sed -e "s/Q-/D-/g" \ -+ -e "s/Q+00/D+00/g" \ -+ -e "s/REAL\*16/DOUBLE PRECISION/" $MODULE.junk > $MODULE_F -+ rm -f $MODULE.junk -+ endif -+ breaksw -+ case 4.6: -+ case 4.7: -+ set EXTRAOPT="$EXTRAOPT -fno-whole-file" -+ breaksw -+ default: -+ echo Unrecognized gfortran version -+ exit 4 -+ breaksw -+ endsw -+ -+ set echo -+ %%FC%% -c -fdefault-integer-8 $OPT -std=legacy $EXTRAOPT $MODULE_F -+ unset echo -+ breaksw -+ -+ case ifort: -+# -i4/-i8 set default integer length -+# -On can have n=1,2,3. Use of 3 caused problems with earlier -+# compilers, so it isn't being used here. Try it if you like. -+# stack storage for locals is governed by -auto versus -save. -+# -assume byterecl was introduced at ifort 8.0 (older versions will -+# print a message saying this flag is ignored). Newer versions -+# need this so that direct access file opens are measured in -+# bytes rather than the new default in v8.0, namely 4-byte units. -+# -vec-report0 suppresses loop vectorization messages (new in 10.0) -+# -w95 suppresses Hollerith initialization and other f90-like warnings -+# -cm means suppress comments about programming practices, -+# these two options spelled '-warn nousage' at version 12. -+# -WB means warn but don't fail on out-of-bounds array references -+# -ftz flushes underflow results to zero -+# -+ set OPT = '-O2' -+ if (".$GMS_DEBUG_FLAGS" != .) set OPT="$GMS_DEBUG_FLAGS" -+# alas, I'm so tired of hearing about so many versions failing to -+# diagonalize, that this time critical code is run w/o optimization. -+# Very many (all?) ifort versions have problems with eigen.src. -+ if ($MODULE == eigen) set OPT='-O0' # read note just above. -+ if ($MODULE == fmo) set OPT='-O1' # 12.0.4, exam37 -+ if ($MODULE == guess) set OPT='-O0' # 10.0, exam39 -+ if ($MODULE == locpol) set OPT='-O1' # 10.0, makefp/gmres -+ if ($MODULE == morokm) set OPT='-O0' # Jan Fredin -+ if ($MODULE == prpel) set OPT='-O1' # 10.0, exam13 -+ if (($MODULE == rohfcc) && ($GMS_IFORT_VERNO == 12)) \ -+ set OPT='-O0' # exam42+exam47 (op.sh.CC,IP-EOM) -+ if ($MODULE == tdxitr) set OPT='-O1' # 10.0, exam39 -+ if ($MODULE == vscf) set OPT='-O0' # intensities for combinations -+ if ($MODULE == zheev) set OPT='-O0' # defensive compiling -+ -+ set EXTRAOPT=" " -+ -+ if (($MODULE == cchem) || ($MODULE == ga)) then -+ mv $MODULE.f $MODULE.F -+ set MODULE_F=$MODULE.F -+ if ($GMS_LIBCCHEM == true) then -+ if ($MODULE == cchem) set EXTRAOPT="-DHAVE_CCHEM" -+ if ($MODULE == ga) set EXTRAOPT="-I$GMS_PATH/libcchem/ga/include" -+ endif -+ endif -+ -+ if ($GMS_IFORT_VERNO >= 8) set EXTRAOPT="$EXTRAOPT -assume byterecl" -+ if ($GMS_IFORT_VERNO >= 10) set EXTRAOPT="$EXTRAOPT -vec-report0" -+ if ($GMS_IFORT_VERNO < 12) set EXTRAOPT="$EXTRAOPT -w95 -cm" -+ if ($GMS_IFORT_VERNO >= 12) set EXTRAOPT="$EXTRAOPT -warn nousage -inline-level=0" -+ set echo -+ ifort -c -i8 $OPT -ftz -auto $EXTRAOPT $MODULE_F -+ unset echo -+ breaksw -+# -+ default: -+ echo "Please spell your FreeBSD 64 bit FORTRAN compiler name correctly." -+ exit 4 -+ breaksw -+ endsw -+# ... end of FreeBSD on 64 bit processors. -+endif -+ -+ - # - # Apple Macintosh system using OS X - # jargon: 10.0=cheetah, 10.1=puma, 10.2=jaguar, 10.3=panther, diff --git a/science/gamess/files/patch-compall b/science/gamess/files/patch-compall deleted file mode 100644 index 27a1c1e4ec88..000000000000 --- a/science/gamess/files/patch-compall +++ /dev/null @@ -1,38 +0,0 @@ ---- compall.orig 2012-09-07 22:32:57.000000000 +0900 -+++ compall 2013-02-27 15:59:37.000000000 +0900 -@@ -58,6 +58,8 @@ - if (($TARGET == ibm-bg) && ($GMS_BG_MODEL == P)) set CCOMP='bgxlc_r' - if ($TARGET == linux32) set CCOMP='gcc' - if ($TARGET == linux64) set CCOMP='gcc' -+if ($TARGET == freebsd32) set CCOMP='%%CC%%' -+if ($TARGET == freebsd64) set CCOMP='%%CC%%' - if ($TARGET == necsx) set CCOMP='c++' - # - unset extraflags -@@ -96,6 +98,8 @@ - if ($chip == x86_64) set extraflags='-DLINUX64 -m64' - if ($chip == ia64) set extraflags='-DLINUX64' # this always 64 bits - endif -+if ($TARGET == freebsd32) set extraflags='-DLINUX32' -+if ($TARGET == freebsd64) set extraflags='-DLINUX64 -m64' - if ($TARGET == mac32) set extraflags='-DLINUX32' - if ($TARGET == mac64) set extraflags='-DLINUX64 -m64 -I/usr/include/malloc' - if ($TARGET == necsx) set extraflags='-DNECSX -size_t64' -@@ -211,6 +215,8 @@ - if ($TARGET == ibm-bg) ./comp blas - if ($TARGET == linux32) ./comp blas - if ($TARGET == linux64) ./comp blas -+if ($TARGET == freebsd32) ./comp blas -+if ($TARGET == freebsd64) ./comp blas - if ($TARGET == mac64) ./comp blas - if ($TARGET == sun32) ./comp blas - if ($TARGET == sun64) ./comp blas -@@ -547,6 +553,8 @@ - set VB2000=false - if ($TARGET == linux64) set VB2000=true - if ($TARGET == linux32) set VB2000=true -+if ($TARGET == freebsd64) set VB2000=true -+if ($TARGET == freebsd32) set VB2000=true - if ($TARGET == mac64) set VB2000=true - if ($VB2000 == true) then - ./comp vb2000 diff --git a/science/gamess/files/patch-compddi b/science/gamess/files/patch-compddi deleted file mode 100644 index b80836382993..000000000000 --- a/science/gamess/files/patch-compddi +++ /dev/null @@ -1,82 +0,0 @@ ---- ddi/compddi.orig 2013-03-05 12:39:40.000000000 +0900 -+++ ddi/compddi 2013-03-05 12:40:52.000000000 +0900 -@@ -630,7 +630,79 @@ - set FORT_FLAGS = '-O2 -qarch=440 -qflag=W:W -qhalt=W -qnosave ' - set FORT_LIBS = '' - endif -+# --------------------------------------- # -+# FreeBSD for x86 PCs # -+# --------------------------------------- # - -+ if($TARGET == freebsd32) then -+ -+ set FORTRAN=%%GMS_FORTRAN%% # choose from g77, gfortran, ifort, pgf77, f2c -+ -+ set CC = %%CC%% -+ set CFLAGS = "-DLINUX -O3 -fstrict-aliasing -I./include" -+ -+ switch ($FORTRAN) -+ case g77: -+ case pgf77: -+ case f2c: -+ set NumUS=2 -+ breaksw -+ case gfortran: -+ set CFLAGS = "$CFLAGS -Dgetarg_=_gfortran_getarg_i4" -+ set CFLAGS = "$CFLAGS -Diargc_=_gfortran_iargc" -+ set NumUS=1 -+ breaksw -+ case ifort: -+ set NumUS=1 -+ breaksw -+ default: -+ echo Please spell your ia32 compiler correctly. -+ exit 4 -+ endsw -+ -+ set CLIBS = "%%PTHREAD_LIBS%%" -+ set F77_OPTS = "-DINT_SIZE=int -D_UNDERSCORES=$NumUS" -+ set FORT_FLAGS = '-O2' -+ set AR_FLAGS = 'cr' -+ set RANLIB_FLAGS = ' ' -+ set FORT_LIBS = ' ' -+ endif -+ -+# ------------- # -+# FreeBSD amd64 # -+# ------------- # -+ if($TARGET == freebsd64) then -+ -+ set CC = %%CC%% -+ set CFLAGS = "-DLINUX -m64 -O3 -fstrict-aliasing -I./include" -+ -+ set FORTRAN=%%GMS_FORTRAN%% -+ switch ($FORTRAN) -+ case g77: -+ case pgf77: -+ case f2c: -+ set NumUS=2 -+ breaksw -+ case gfortran: -+ set CFLAGS = "$CFLAGS -Dgetarg_=_gfortran_getarg_i4" -+ set CFLAGS = "$CFLAGS -Diargc_=_gfortran_iargc" -+ set FORT_FLAGS = "-O2 $ARCH -fdefault-integer-8 -std=legacy" -+ set NumUS=1 -+ breaksw -+ case ifort: -+ set NumUS=1 -+ breaksw -+ default: -+ echo Please spell your x86_64 compiler correctly. -+ exit 4 -+ endsw -+ -+ set CLIBS = "%%PTHREAD_LIBS%%" -+ set F77_OPTS = "-DINT_SIZE=long -D_UNDERSCORES=$NumUS" -+ set AR_FLAGS = 'cr' -+ set RANLIB_FLAGS = ' ' -+ set FORT_LIBS = ' ' -+ endif - - # ---------------------------------------- # - # Linux for 32 bit systems (Red Hat, etc.) # diff --git a/science/gamess/files/patch-gms-files.csh b/science/gamess/files/patch-gms-files.csh deleted file mode 100644 index b6bf0b877f34..000000000000 --- a/science/gamess/files/patch-gms-files.csh +++ /dev/null @@ -1,13 +0,0 @@ -$FreeBSD$ - ---- gms-files.csh 2013-03-05 18:04:02.000000000 +0900 -+++ gms-files.csh 2013-03-05 18:05:38.000000000 +0900 -@@ -28,7 +28,7 @@ - # to see all the file definitions (one is just below). - # - #---quiet---set echo --setenv AUXDATA $GMSPATH/auxdata -+setenv AUXDATA %%PREFIX%%/share/gamess/auxdata - setenv EXTBAS /dev/null - setenv NUCBAS /dev/null - setenv POSBAS /dev/null diff --git a/science/gamess/files/patch-lked b/science/gamess/files/patch-lked deleted file mode 100644 index e9075b2fc12d..000000000000 --- a/science/gamess/files/patch-lked +++ /dev/null @@ -1,288 +0,0 @@ ---- lked.orig 2012-10-27 01:12:07.000000000 +0900 -+++ lked 2013-02-27 16:06:32.000000000 +0900 -@@ -57,6 +57,8 @@ - set VB2000=false - if ($TARGET == linux64) set VB2000=true - if ($TARGET == linux32) set VB2000=true -+if ($TARGET == freebsd64) set VB2000=true -+if ($TARGET == freebsd32) set VB2000=true - if ($TARGET == mac64) set VB2000=true - set XMVB=false - # -@@ -632,6 +634,243 @@ - endif - # - endif -+ -+if ($TARGET == freebsd32) then -+ set VECTOR=' ' -+ set QUICHE='zunix.o' -+# -+# settings which depend on the compiler choice: -+# -+ switch ($GMS_FORTRAN) -+ case g77: -+ set LDR='g77' -+ set LDOPTS=' ' # add '-Wl,-M' to see load map -+ set FORTLIBS=' ' -+ breaksw -+ case gfortran: -+ set LDR=%%FC%% -+ set LDOPTS=' ' -+ set FORTLIBS=' ' -+ breaksw -+ case ifort: -+ set LDR='ifort' -+ set LDOPTS=' ' # add '-Wl,-M' to see load map -+ set FORTLIBS='-Vaxlib' -+ breaksw -+ case f2c: -+ set LDR='gcc' -+ set LDOPTS=' ' -+ set FORTLIBS='-lf2c -lm' -+ breaksw -+ default: -+ echo Please spell your freebsd32 compiler correctly. -+ exit 4 -+ endsw -+# -+# settings which depend on the math library: mkl, atlas, acml, none -+# -+ switch ($GMS_MATHLIB) -+ -+# for MKL, we lack experience. The following is the 64-bit -+# stuff, with all 64's removed. It might be right! -+# For the case of "11", this has actually been verified. -+ case mkl: -+ set mpath=$GMS_MATHLIB_PATH -+ switch ($GMS_MKL_VERNO) -+ case 8: -+ set MATHLIBS="-L$mpath -lmkl_lapack -lmkl -lguide -lpthread" -+ breaksw -+ case 9: -+ set MATHLIBS="-L$mpath -lmkl_lapack -lmkl -lguide -lpthread" -+ breaksw -+ case 10: -+ # next one forces single-threaded usage only...exactly what we want. -+ set MATHLIBS="-L$mpath -lmkl_intel -lmkl_sequential -lmkl_core" -+ breaksw -+ case 11: -+ case 12: -+ # next attempts a static link, whereas 10 above is a dynamic link. -+ # if this fails to work, try the version 10 lines shown just above. -+ set MATHLIBS="$mpath/libmkl_intel.a" -+ set MATHLIBS="$MATHLIBS $mpath/libmkl_sequential.a" -+ set MATHLIBS="$MATHLIBS $mpath/libmkl_core.a" -+ breaksw -+ default: -+ echo "unknown version number for MKL/linux32" -+ echo "please edit 'lked' to select the right 32 bit MKL libraries." -+ exit -+ breaksw -+ endsw -+ set BLAS=' ' -+ breaksw -+ -+ case atlas: -+ # If the ATLAS comes with static libraries, link to them, -+ # so that only the compile node has to have the libraries. -+ # Otherwise, attempt a link against shared object libs. -+ # See the 64 bit Atlas below for a way to fix the linker's -+ # not being able to locate -lf77blas, if that happens. -+ if (-e $GMS_MATHLIB_PATH/libf77blas.a) then -+ set MATHLIBS="$GMS_MATHLIB_PATH/libf77blas.a" -+ set MATHLIBS="$MATHLIBS $GMS_MATHLIB_PATH/libatlas.a" -+ else -+ set MATHLIBS="-L$GMS_MATHLIB_PATH -lf77blas -latlas" -+ endif -+ set BLAS=' ' -+ breaksw -+ -+ case acml: -+ # do a static link so that only compile node needs to install ACML -+ set MATHLIBS="$GMS_MATHLIB_PATH/libacml.a" -+ set BLAS=' ' -+ breaksw -+ -+ case none: -+ default: -+ echo "Warning. No math library was found, you should install one." -+ echo " MP2 calculations speed up about 2x with a math library." -+ echo "CCSD(T) calculations speed up about 5x with a math library." -+ set BLAS='%%BLAS%% %%LAPACK%%' -+ set MATHLIBS=' ' -+ breaksw -+ endsw -+# -+ set LIBRARIES="$FORTLIBS $MATHLIBS" -+endif -+# -+# ------ FreeBSD on 64 bit chips ----- -+# -+if ($TARGET == freebsd64) then -+ set VECTOR=' ' -+ set QUICHE='zunix.o' -+# -+# settings which depend on the FORTRAN: -+# -+ switch ($GMS_FORTRAN) -+ case gfortran: -+ set LDR=%%FC%% -+ set LDOPTS=' ' -+ set FORTLIBS=' ' -+ breaksw -+ case ifort: -+ set LDR='ifort' -+ set LDOPTS='-i8' # -Wl,-M generates a load map -+# this auxiliary library seems to have disappeared in ifort 10 -+ set FORTLIBS=' ' -+ if($GMS_IFORT_VERNO < 10) set FORTLIBS='-Vaxlib' -+ breaksw -+ default: -+ echo "don't know how to use a freebsd64 compiler named $GMS_FORTRAN" -+ exit 4 -+ breaksw -+ endsw -+# -+# settings which depend on the math library: mkl, atlas, acml, none -+# -+ switch ($GMS_MATHLIB) -+ -+ case mkl: -+ set mpath=$GMS_MATHLIB_PATH -+ set mklver=$GMS_MKL_VERNO -+ if ($CCHEM == true) set mklver=${mklver}-so -+ switch ($mklver) -+ case 8: -+ set MATHLIBS="-L$mpath -lmkl_lapack64 -lmkl -lguide -lpthread" -+ breaksw -+ case 9: -+ set MATHLIBS="-L$mpath -lmkl_lapack -lmkl -lguide -lpthread" -+ breaksw -+ breaksw -+ case 10: -+ case 11: -+ case 12: -+ # next are a static link, in single-threaded mode (serial BLAS). -+ # The choices preclude any need to -+ # a) install .so shared object libraries on every node, -+ # b) define LD_LIBRARY_PATH to find the .so libraries, or -+ # c) define MKL_NUM_THREADS=1 -+ # If desired, there is a single-threaded shared object link below. -+ # Note, there's now a gfortran-specific compiler interface library. -+ set iflib=intel -+ if ($GMS_FORTRAN == gfortran) set iflib=gf -+ set MATHLIBS=" $mpath/libmkl_${iflib}_ilp64.a" -+ set MATHLIBS="$MATHLIBS $mpath/libmkl_sequential.a" -+ set MATHLIBS="$MATHLIBS $mpath/libmkl_core.a" -+ breaksw -+ case 10-so: -+ case 11-so: -+ case 12-so: -+ # next one chooses dynamic linking (so= shared object libs) -+ # Just hand edit GMS_MKL_VERNO in your 'install.info' to use this. -+ # run-time libs (and LD_LIBRARY_PATH) needed on every compute node! -+ # note that it does force single-threaded usage. -+ # LIBCCHEM fails to link properly against static libraries. -+ # LIBCCHEM prefers to use threading -+ set iflib=intel -+ if ($GMS_FORTRAN == gfortran) set iflib=gf -+ if ($CCHEM == false) then -+ set MATHLIBS="-L$mpath -lmkl_${iflib}_ilp64 -lmkl_sequential -lmkl_core" -+ else -+ set MATHLIBS="-L$mpath -lmkl_${iflib}_ilp64 -lmkl_${iflib}_thread -lmkl_core -liomp5" -+ endif -+ breaksw -+ default: -+ echo "unknown version number for MKL/linux64" -+ echo "please edit 'lked' to select the right 64 bit MKL libraries." -+ exit -+ breaksw -+ endsw -+ set BLAS=' ' -+ breaksw -+ -+ case atlas: -+ # If the ATLAS comes with static libraries, link to them, -+ # so that only the compile node has to have the libraries. -+ # Otherwise, attempt a link against shared object libs. -+ # -+ # Some versions of Atlas come without proper setup to use them. -+ # For example, you may need to give some specific version such -+ # as 3.0 some generic names, by doing the right soft links: -+ # chdir /usr/lib64/atlas (just 'lib' for linux32) -+ # ln -s libatlas.so.3.0 libatlas.so -+ # ln -s libblas.so.3.0 libblas.so -+ # ln -s libcblas.so.3.0 libcblas.so -+ # ln -s libf77blas.so.3.0 libf77blas.so -+ # ln -s liblapack_atlas.so.3.0 liblapack.so -+ # ln -s liblapack.so.3.0 liblapack.so -+ # It is strange the RPM's don't do these soft links for us. -+ if (-e $GMS_MATHLIB_PATH/libf77blas.a) then -+ set MATHLIBS="$GMS_MATHLIB_PATH/libf77blas.a" -+ set MATHLIBS="$MATHLIBS $GMS_MATHLIB_PATH/libatlas.a" -+ else -+ set MATHLIBS="-L$GMS_MATHLIB_PATH -lf77blas -latlas" -+ endif -+ set BLAS=' ' -+ breaksw -+ -+ case acml: -+ # do a static link so that only compile node needs to install ACML -+ set MATHLIBS="$GMS_MATHLIB_PATH/libacml.a" -+ # if you want to try a dynamic link, use this: -+ #---set MATHLIBS="-L$GMS_MATHLIB_PATH -lacml -lacml_mv" -+ set BLAS=' ' -+ breaksw -+ -+ case none: -+ default: -+ echo "Warning. No math library was found, you should install one." -+ echo " MP2 calculations speed up about 2x with a math library." -+ echo "CCSD(T) calculations speed up about 5x with a math library." -+ set BLAS='%%BLAS%% %%LAPACK%%' -+ set MATHLIBS=' ' -+ breaksw -+ endsw -+# -+ set LIBRARIES="$FORTLIBS $MATHLIBS" -+endif -+# -+endif -+ - # - # MacIntosh - # -@@ -675,6 +914,23 @@ - set VECTOR=' ' - set QUICHE='zunix.o' - endif -+#FreeBSD settings -+if ($TARGET == freebsd32) then -+ set LDR=%%FC%% -+ set LDOPTS='%%LDFLAGS%%' -+ set LIBRARIES='' -+ set BLAS="-L%%LOCALBASE%%/lib %%BLAS%% %%LIBSVM%% %%LIBG2C%%" -+ set VECTOR=' ' -+ set QUICHE='zunix.o' -+endif -+if ($TARGET == freebsd64) then -+ set LDR=%%FC%% -+ set LDOPTS='%%LDFLAGS%%' -+ set LIBRARIES='' -+ set BLAS="-L%%LOCALBASE%%/lib %%BLAS%%" -+ set VECTOR=' ' -+ set QUICHE='zunix.o' -+endif - # - if ($TARGET == necsx) then - set LDR='f90' -@@ -1199,6 +1199,8 @@ - case ibm64: - case linux32: - case linux64: -+ case freebsd32: -+ case freebsd64: - case mac32: - case mac64: - case sgi32: diff --git a/science/gamess/files/patch-rungms b/science/gamess/files/patch-rungms deleted file mode 100644 index 910b99fa94fa..000000000000 --- a/science/gamess/files/patch-rungms +++ /dev/null @@ -1,21 +0,0 @@ ---- rungms 2013-03-05 17:53:14.000000000 +0900 -+++ rungms 2013-03-05 17:53:45.000000000 +0900 -@@ -1,4 +1,4 @@ --#!/bin/csh -+#!/bin/csh -f - # - # last update = 26 October 2012 - # -@@ -60,9 +60,9 @@ - # See also a very old LoadLeveler "ll-gms" for some IBM systems. - # - set TARGET=sockets --set SCR=/scr/$USER --set USERSCR=~$USER/scr --set GMSPATH=/u1/mike/gamess -+set SCR=. -+set USERSCR=. -+set GMSPATH=%%PREFIX%%/bin/gms/ - # - set JOB=$1 # name of the input file xxx.inp, give only the xxx part - set VERNO=$2 # revision number of the executable created by 'lked' step diff --git a/science/gamess/files/patch-zunix.c b/science/gamess/files/patch-zunix.c deleted file mode 100644 index 2e1cd4cff1b0..000000000000 --- a/science/gamess/files/patch-zunix.c +++ /dev/null @@ -1,10 +0,0 @@ ---- source/zunix.c~ 2008-10-31 23:05:41.000000000 +0900 -+++ source/zunix.c 2009-06-08 15:37:42.000000000 +0900 -@@ -440,7 +440,6 @@ - #ifdef LINUX64 - - #include <stdlib.h> --#include <malloc.h> - - #define FORTINT long - diff --git a/science/gamess/pkg-descr b/science/gamess/pkg-descr deleted file mode 100644 index 9b2696c53bea..000000000000 --- a/science/gamess/pkg-descr +++ /dev/null @@ -1,16 +0,0 @@ -GAMESS is freely available ab-initio molecular orbital -calculation program calculates energy, molecular structure, -vibrational frequencies from the basic principle of quantum mechanics. - -A site license for GAMESS is available at no cost to both academic -and industrial users. Please refer -http://www.msg.ameslab.gov/gamess/download.html -for details. - -We also included simple launcher called `gamess' -for your convenience. You don't set any environment variable -to run gamess. Just type -% gamess <somefile.inp> -is enough. - -WWW: http://www.msg.ameslab.gov/gamess/gamess.html diff --git a/science/gamess/pkg-message b/science/gamess/pkg-message deleted file mode 100644 index e445f5a70499..000000000000 --- a/science/gamess/pkg-message +++ /dev/null @@ -1,13 +0,0 @@ -WARNING!!WARNING!!WARNING!!WARNING!! - -If you got the following error -'Error ENOMEM: Not enough memory to allocate ** bytes of shared memory.', -then add ipc memory by: -sudo sysctl -w kern.ipc.shmmax=3064372224 -sudo sysctl -w kern.ipc.shmall=748137 -or if you want to enable at boot time -add following lines to -kern.ipc.shmmax=3064372224 -kern.ipc.shmall=748137 -/boot/loader.conf -. diff --git a/science/gamess/pkg-plist b/science/gamess/pkg-plist deleted file mode 100644 index 01bd8768f86b..000000000000 --- a/science/gamess/pkg-plist +++ /dev/null @@ -1,154 +0,0 @@ -bin/gamess -bin/gms/ddikick.x -bin/gms/gamess.00.x -bin/gms/gms-files.csh -share/doc/gamess/INPUT.DOC -share/doc/gamess/INTRO.DOC -share/doc/gamess/IRON.DOC -share/doc/gamess/PROG.DOC -share/doc/gamess/REFS.DOC -share/doc/gamess/TESTS.DOC -share/doc/gamess/readme.ddi -share/gamess/auxdata/ericfmt.dat -share/gamess/auxdata/BASES/SPK-TZP -share/gamess/auxdata/BASES/SPKRDZC -share/gamess/auxdata/BASES/SPK-DZC -share/gamess/auxdata/BASES/SPKRQZCD -share/gamess/auxdata/BASES/SPK-QZP -share/gamess/auxdata/BASES/SPKRTZP -share/gamess/auxdata/BASES/SPKRAQZP -share/gamess/auxdata/BASES/SPK-ADZP -share/gamess/auxdata/BASES/SPKRTZC -share/gamess/auxdata/BASES/SPK-ATZP -share/gamess/auxdata/BASES/SPKRDZP -share/gamess/auxdata/BASES/SPK-AQZP -share/gamess/auxdata/BASES/SPKRQZP -share/gamess/auxdata/BASES/SPKRQZC -share/gamess/auxdata/BASES/SPKRATZP -share/gamess/auxdata/BASES/SPK-QZC -share/gamess/auxdata/BASES/SPKRADZP -share/gamess/auxdata/BASES/SPKRDZCD -share/gamess/auxdata/BASES/SPKRTZCD -share/gamess/auxdata/BASES/SPK-DZP -share/gamess/auxdata/BASES/SPK-QZCD -share/gamess/auxdata/BASES/SPK-TZC -share/gamess/auxdata/BASES/SPK-DZCD -share/gamess/auxdata/BASES/SPK-TZCD -share/gamess/auxdata/EFP/ADENI2.efp -share/gamess/auxdata/EFP/THYMI2.efp -share/gamess/auxdata/EFP/PYRAZI.efp -share/gamess/auxdata/EFP/ADENIN.efp -share/gamess/auxdata/EFP/PENTAN.efp -share/gamess/auxdata/EFP/INDOLE.efp -share/gamess/auxdata/EFP/PHENOL.efp -share/gamess/auxdata/EFP/ACNH2B.efp -share/gamess/auxdata/EFP/FORMID.efp -share/gamess/auxdata/EFP/CYCPEN.efp -share/gamess/auxdata/EFP/HCN.efp -share/gamess/auxdata/EFP/URACIL.efp -share/gamess/auxdata/EFP/BENZEN.efp -share/gamess/auxdata/EFP/MENH2.efp -share/gamess/auxdata/EFP/FORMIC.efp -share/gamess/auxdata/EFP/PEPTID.efp -share/gamess/auxdata/EFP/ACOHG.efp -share/gamess/auxdata/EFP/METHAN.efp -share/gamess/auxdata/EFP/MEOH.efp -share/gamess/auxdata/EFP/THYMIN.efp -share/gamess/auxdata/EFP/NEOPEN.efp -share/gamess/auxdata/EFP/AMINOP.efp -share/gamess/auxdata/EFP/PYRIDI.efp -share/gamess/auxdata/EFP/AMONIA.efp -share/gamess/auxdata/EFP/WATER.efp -share/gamess/auxdata/EFP/PYRIDO.efp -share/gamess/auxdata/EFP/ACNH2G.efp -share/gamess/auxdata/EFP/ETHENE.efp -share/gamess/auxdata/EFP/URACG.efp -share/gamess/auxdata/EFP/ETHYNE.efp -share/gamess/auxdata/EFP/ACOHB.efp -share/gamess/auxdata/MCP/MCP-ATZP -share/gamess/auxdata/MCP/MCPCDZP -share/gamess/auxdata/MCP/ZFK5-DK3 -share/gamess/auxdata/MCP/MCPCTZP -share/gamess/auxdata/MCP/MCPACQZP -share/gamess/auxdata/MCP/ZFK4-DK3 -share/gamess/auxdata/MCP/IMCP-SR2 -share/gamess/auxdata/MCP/MCP-DZP -share/gamess/auxdata/MCP/MCP-QZP -share/gamess/auxdata/MCP/MCP-TZP -share/gamess/auxdata/MCP/ZFK3-DK3 -share/gamess/auxdata/MCP/MCPACTZP -share/gamess/auxdata/MCP/IMCP-NR1 -share/gamess/auxdata/MCP/ZFK5LDK3 -share/gamess/auxdata/MCP/MCPCQZP -share/gamess/auxdata/MCP/ZFK3LDK3 -share/gamess/auxdata/MCP/MCPACDZP -share/gamess/auxdata/MCP/ZFK4LDK3 -share/gamess/auxdata/MCP/IMCP-SR1 -share/gamess/auxdata/MCP/MCP-AQZP -share/gamess/auxdata/MCP/IMCP-NR2 -share/gamess/auxdata/QUANPOL/RXNFLD3840.DAT -share/gamess/auxdata/QUANPOL/CHARMM22.CMAP -share/gamess/auxdata/QUANPOL/RXNFLD0060.DAT -share/gamess/auxdata/QUANPOL/RXNFLD0240.DAT -share/gamess/auxdata/QUANPOL/LOUT314159.TOP -share/gamess/auxdata/QUANPOL/CHARMM22.LIB -share/gamess/auxdata/QUANPOL/RXNFLD0960.DAT -share/gamess/auxdata/QUANPOL/WATER4096.DAT -share/gamess/auxdata/QUANPOL/LOUT314159.PAR -share/examples/gamess/exam01.inp -share/examples/gamess/exam02.inp -share/examples/gamess/exam03.inp -share/examples/gamess/exam04.inp -share/examples/gamess/exam05.inp -share/examples/gamess/exam06.inp -share/examples/gamess/exam07.inp -share/examples/gamess/exam08.inp -share/examples/gamess/exam09.inp -share/examples/gamess/exam10.inp -share/examples/gamess/exam11.inp -share/examples/gamess/exam12.inp -share/examples/gamess/exam13.inp -share/examples/gamess/exam14.inp -share/examples/gamess/exam15.inp -share/examples/gamess/exam16.inp -share/examples/gamess/exam17.inp -share/examples/gamess/exam18.inp -share/examples/gamess/exam19.inp -share/examples/gamess/exam20.inp -share/examples/gamess/exam21.inp -share/examples/gamess/exam22.inp -share/examples/gamess/exam23.inp -share/examples/gamess/exam24.inp -share/examples/gamess/exam25.inp -share/examples/gamess/exam26.inp -share/examples/gamess/exam27.inp -share/examples/gamess/exam28.inp -share/examples/gamess/exam29.inp -share/examples/gamess/exam30.inp -share/examples/gamess/exam31.inp -share/examples/gamess/exam32.inp -share/examples/gamess/exam33.inp -share/examples/gamess/exam34.inp -share/examples/gamess/exam35.inp -share/examples/gamess/exam36.inp -share/examples/gamess/exam37.inp -share/examples/gamess/exam38.inp -share/examples/gamess/exam39.inp -share/examples/gamess/exam40.inp -share/examples/gamess/exam41.inp -share/examples/gamess/exam42.inp -share/examples/gamess/exam43.inp -share/examples/gamess/exam44.inp -share/examples/gamess/exam45.inp -share/examples/gamess/exam46.inp -share/examples/gamess/exam47.inp -@dirrm bin/gms -@dirrm share/doc/gamess -@dirrm share/gamess/mcpdata -@dirrm share/examples/gamess -@dirrm share/gamess/auxdata/QUANPOL -@dirrm share/gamess/auxdata/MCP -@dirrm share/gamess/auxdata/EFP -@dirrm share/gamess/auxdata/BASES -@dirrm share/gamess/auxdata -@dirrm share/gamess diff --git a/science/mcstas/Makefile b/science/mcstas/Makefile deleted file mode 100644 index 14cc9e9a21e1..000000000000 --- a/science/mcstas/Makefile +++ /dev/null @@ -1,44 +0,0 @@ -# Created by: Joerg Pulz <Joerg.Pulz@frm2.tum.de> -# $FreeBSD$ - -PORTNAME= mcstas -PORTVERSION= 1.12c -PORTREVISION= 3 -CATEGORIES= science -MASTER_SITES= http://www.mcstas.org/download/ \ - http://www.c-s.li/ports/ -DISTNAME= ${PORTNAME}-${PORTVERSION}-src - -MAINTAINER= ports@FreeBSD.org -COMMENT= Neutron ray-trace simulation package - -LICENSE= GPLv2 - -BUILD_DEPENDS= pgxwin_server:${PORTSDIR}/graphics/pgplot -RUN_DEPENDS= PDL>=0:${PORTSDIR}/math/PDL \ - p5-Tk>=0:${PORTSDIR}/x11-toolkits/p5-Tk - -STRIP= -USES= perl5 gmake -GNU_CONFIGURE= yes -NO_MTREE= yes -WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION} - -PERL_ARCHNAME!= perl -V:archname 2>/dev/null || echo - -PLIST_SUB+= PERL_PORT=perl5 PERL_ARCHNAME=${PERL_ARCHNAME:S/archname='//:S/';//} - -MAN1= mcconvert.1 \ - mcdisplay.1 \ - mcdoc.1 \ - mcformat.1 \ - mcgui.1 \ - mcplot.1 \ - mcrun.1 \ - mcstas.1 \ - -NO_STAGE= yes -post-configure: - @cd ${WRKSRC}; make pgplot - -.include <bsd.port.mk> diff --git a/science/mcstas/distinfo b/science/mcstas/distinfo deleted file mode 100644 index 76dcce58517a..000000000000 --- a/science/mcstas/distinfo +++ /dev/null @@ -1,2 +0,0 @@ -SHA256 (mcstas-1.12c-src.tar.gz) = 03c516bda33f140e4e92ba542235277165d6a79d29a63c1d4cd2366f0e5f6821 -SIZE (mcstas-1.12c-src.tar.gz) = 29424258 diff --git a/science/mcstas/files/patch-Makefile.in b/science/mcstas/files/patch-Makefile.in deleted file mode 100644 index fed2d44007ab..000000000000 --- a/science/mcstas/files/patch-Makefile.in +++ /dev/null @@ -1,13 +0,0 @@ ---- Makefile.in.orig Thu Jun 9 09:13:42 2005 -+++ Makefile.in Tue Feb 28 13:27:55 2006 -@@ -98,10 +98,6 @@ - for pgm in $(PERLBIN); do \ - $(INSTALL_PROGRAM) $$pgm.fixpl $(bindir)/$$pgm; \ - done -- if [ -d $(mc_libdir) ]; then \ -- echo "Moving your old library dir $(mc_libdir) to $(mc_libdir).`date +%Y%m%d_%H.%M`"; \ -- mv -f $(mc_libdir) $(mc_libdir).`date +%Y%m%d_%H.%M`;\ -- fi; - $(srcdir)/mkinstalldirs $(mc_libdir) - for file in `cd lib; ls`; do \ - if [ -d lib/$$file ]; then \ diff --git a/science/mcstas/pkg-descr b/science/mcstas/pkg-descr deleted file mode 100644 index 795c24d792ef..000000000000 --- a/science/mcstas/pkg-descr +++ /dev/null @@ -1,21 +0,0 @@ -McStas - Monte Carlo simulation of neutron instruments - -McStas is an ongoing project to create a general tool for simulating neutron -scattering instruments. The project is conducted at Risoe National Laboratory -in cooperation with the ILL. The Risoe efforts have been funded through -multiple EU programs. - -McStas is based on a compiler that reads a high-level specification language -defining the instrument to be simulated and produces C code that performs the -Monte Carlo Simulation. The system is very fast in use, both when setting up -the instrument definition and when doing calculations. -Typical figures are 20000-50000 neutron histories per second on a fast PC. - -McStas supports triple-axis, time-of-flight instruments, and polarised -neutrons. It comes with a comprehensive manual and a library of well-tested -components that include most standard elements of neutron scattering -instruments, including steady-state and pulsed sources, -monochromators/analysers, guides, collimators, vanadium and powder samples, -velocity selectors and choppers, and a variety of detectors. - -WWW: http://www.mcstas.org/ diff --git a/science/mcstas/pkg-plist b/science/mcstas/pkg-plist deleted file mode 100644 index 5a07a72a7dea..000000000000 --- a/science/mcstas/pkg-plist +++ /dev/null @@ -1,865 +0,0 @@ -bin/gscan -bin/mcconvert -bin/mcdaemon -bin/mcdisplay -bin/mcdoc -bin/mcformat -bin/mcformatgui -bin/mcgui -bin/mcplot -bin/mcresplot -bin/mcrun -bin/mcstas -bin/mcstas2vitess -lib/mcstas/LGPL -lib/mcstas/LICENSE.LIB -lib/mcstas/README -lib/mcstas/contrib/Al_window.comp -lib/mcstas/contrib/Al_window.html -lib/mcstas/contrib/Collimator_ROC.comp -lib/mcstas/contrib/Collimator_ROC.html -lib/mcstas/contrib/Exact_radial_coll.comp 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lib/mcstas/tools/perl/modules/lib/%%PERL_PORT%% -@dirrm lib/mcstas/tools/perl/modules/lib -@dirrm lib/mcstas/tools/scilab/plotlib/man -@dirrm lib/mcstas/tools/scilab/plotlib/macros -@dirrm lib/mcstas/tools/scilab/plotlib -@dirrm lib/mcstas/tools/scilab -@dirrm lib/mcstas/tools/perl/modules/auto/Proc/Simple -@dirrm lib/mcstas/tools/perl/modules/auto/Proc -@dirrm lib/mcstas/tools/perl/modules/auto -@dirrm lib/mcstas/tools/perl/modules/%%PERL_ARCHNAME%%/auto/Tk/CodeText -@dirrm lib/mcstas/tools/perl/modules/%%PERL_ARCHNAME%%/auto/Tk -@dirrm lib/mcstas/tools/perl/modules/%%PERL_ARCHNAME%%/auto/Proc/Simple -@dirrm lib/mcstas/tools/perl/modules/%%PERL_ARCHNAME%%/auto/Proc -@dirrm lib/mcstas/tools/perl/modules/%%PERL_ARCHNAME%%/auto/Math/Amoeba -@dirrm lib/mcstas/tools/perl/modules/%%PERL_ARCHNAME%%/auto/Math -@dirrm lib/mcstas/tools/perl/modules/%%PERL_ARCHNAME%%/auto -@dirrm lib/mcstas/tools/perl/modules/%%PERL_ARCHNAME%% -@dirrm lib/mcstas/tools/perl/modules/Tk/CodeText -@dirrm lib/mcstas/tools/perl/modules/Tk -@dirrm lib/mcstas/tools/perl/modules/Proc -@dirrm lib/mcstas/tools/perl/modules/Math -@dirrm lib/mcstas/tools/perl/modules -@dirrm lib/mcstas/tools/perl -@dirrm lib/mcstas/tools/matlab -@dirrm lib/mcstas/tools -@dirrm lib/mcstas/sources -@dirrm lib/mcstas/share -@dirrm lib/mcstas/samples -@dirrm lib/mcstas/optics -@dirrm lib/mcstas/obsolete -@dirrm lib/mcstas/monitors -@dirrm lib/mcstas/misc -@dirrm lib/mcstas/examples -@dirrm lib/mcstas/editors -@dirrm lib/mcstas/doc/tutorial/pics -@dirrm lib/mcstas/doc/tutorial/html -@dirrm lib/mcstas/doc/tutorial -@dirrm lib/mcstas/doc -@dirrm lib/mcstas/data -@dirrm lib/mcstas/contrib/doc -@dirrm lib/mcstas/contrib/ISIS_tables -@dirrm lib/mcstas/contrib/Gas_tables -@dirrm lib/mcstas/contrib -@dirrm lib/mcstas diff --git a/science/minc/Makefile b/science/minc/Makefile deleted file mode 100644 index a3a7a77d9fe3..000000000000 --- a/science/minc/Makefile +++ /dev/null @@ -1,79 +0,0 @@ -# Created by: jbacon -# $FreeBSD$ - -############################################################################ -# http://www.bic.mni.mcgill.ca/software/minc/ -# is the ultimate source for MINC, and will always contain the latest -# source release. If this port is not up to date enough for you, -# you can download the latest sources and build manually. On FreeBSD, -# you must configure with the environment variable LDFLAGS set to -# ${LOCALBASE}/lib so that the configure script will find libnetcdf. -# Of course, the netcdf port must be installed first. - -PORTNAME= minc -PORTVERSION= 1.5.1 -PORTREVISION= 1 -CATEGORIES= science biology -MASTER_SITES= http://www.nitrc.org/frs/downloadlink.php/400/ - -MAINTAINER= jwbacon@tds.net -COMMENT= Medical Imaging NetCDF - -BROKEN= Fails to build - -LIB_DEPENDS= libnetcdf.so:${PORTSDIR}/science/netcdf - -USE_AUTOTOOLS= libtool -USE_LDCONFIG= yes -GNU_CONFIGURE= yes -CPPFLAGS+= -I${LOCALBASE}/include -LDFLAGS+= -L${LOCALBASE}/lib -CONFIGURE_ARGS= --enable-static=yes --enable-shared=yes - -CONFLICTS= minc-2* zh-tk-[0-9]* - -WRKSRC= ${WRKDIR}/${PORTNAME}-1.5 - -MAN1= dcm2mnc.1 \ - ecattominc.1 \ - invert_raw_image.1 \ - minc_modify_header.1 \ - mincaverage.1 \ - minccalc.1 \ - mincconcat.1 \ - minccopy.1 \ - mincdiff.1 \ - mincedit.1 \ - mincexpand.1 \ - mincextract.1 \ - mincheader.1 \ - minchistory.1 \ - mincinfo.1 \ - minclookup.1 \ - mincmakescalar.1 \ - mincmakevector.1 \ - mincmath.1 \ - mincpik.1 \ - mincresample.1 \ - mincreshape.1 \ - mincstats.1 \ - minctoecat.1 \ - minctoraw.1 \ - mincview.1 \ - mincwindow.1 \ - mnc2nii.1 \ - nii2mnc.1 \ - rawtominc.1 \ - transformtags.1 \ - upet2mnc.1 \ - voxeltoworld.1 \ - xfmconcat.1 \ - xfminvert.1 - -MAN3= ParseArgv.3 - -NO_STAGE= yes -post-install: - @${CAT} ${PKGMESSAGE} - -.include <bsd.port.mk> diff --git a/science/minc/distinfo b/science/minc/distinfo deleted file mode 100644 index 8eca6102f52f..000000000000 --- a/science/minc/distinfo +++ /dev/null @@ -1,2 +0,0 @@ -SHA256 (minc-1.5.1.tar.gz) = 3ca7045c6eaa32daea184af3f78e30969bb0a0dddce2a1b292ba1624d23a61c9 -SIZE (minc-1.5.1.tar.gz) = 1356462 diff --git a/science/minc/files/patch-conversion__minctoecat__machine_indep.c b/science/minc/files/patch-conversion__minctoecat__machine_indep.c deleted file mode 100644 index b1e87762e631..000000000000 --- a/science/minc/files/patch-conversion__minctoecat__machine_indep.c +++ /dev/null @@ -1,11 +0,0 @@ ---- conversion/minctoecat/machine_indep.c.orig 2012-07-20 17:16:13.000000000 +0200 -+++ conversion/minctoecat/machine_indep.c 2012-07-20 17:17:48.000000000 +0200 -@@ -84,7 +84,7 @@ - bufr[1] = ret >>16; - } - #else /* BIG ENDIAN : sun hp sgi*/ --ftovaxf(orig,number) -+void ftovaxf(orig,number) - unsigned short number[2]; - float orig; - { diff --git a/science/minc/pkg-descr b/science/minc/pkg-descr deleted file mode 100644 index 7d6f542bcb1c..000000000000 --- a/science/minc/pkg-descr +++ /dev/null @@ -1,10 +0,0 @@ -MINC (Medical Imaging NetCDF) is a medical imaging data format and an -associated set of tools and libraries. MINC was created in 1993 by Peter -Neelin at the McConnell Brain Imaging Centre of the Montreal Neurological -Institute. Many others have contributed to the design and implementation -MINC over the years. - -WWW: http://www.bic.mni.mcgill.ca/ServicesSoftware/MINC - -Port maintainer: Jason W. Bacon - jwbacon@tds.net diff --git a/science/minc/pkg-message b/science/minc/pkg-message deleted file mode 100644 index cc3dd854da2b..000000000000 --- a/science/minc/pkg-message +++ /dev/null @@ -1,8 +0,0 @@ -============================================================================= -For questions or comments regarding this port, please contact the -port maintainer: jwbacon@tds.net - -For MINC usage, please visit the MINC WEB site at - -http://www.bic.mni.mcgill.ca/ServicesSoftware/MINC -============================================================================= diff --git a/science/minc/pkg-plist b/science/minc/pkg-plist deleted file mode 100644 index 293bf89a7dff..000000000000 --- a/science/minc/pkg-plist +++ /dev/null @@ -1,68 +0,0 @@ -bin/dcm2mnc -bin/ecattominc -bin/invert_raw_image -bin/minc_modify_header -bin/mincaverage -bin/minccalc -bin/mincconcat -bin/minccopy -bin/mincdiff -bin/mincedit -bin/mincexpand -bin/mincextract -bin/mincheader -bin/minchistory -bin/mincinfo -bin/minclookup -bin/mincmakescalar -bin/mincmakevector -bin/mincmath -bin/mincpik -bin/mincresample -bin/mincreshape -bin/mincstats -bin/minctoecat -bin/minctoraw -bin/mincview -bin/mincwindow -bin/mnc2nii -bin/nii2mnc -bin/rawtominc -bin/transformtags -bin/upet2mnc -bin/voxeltoworld -bin/worldtovoxel -bin/xfmconcat -bin/xfminvert -include/ParseArgv.h -include/minc.h -include/minc_simple.h -include/nd_loop.h -include/time_stamp.h -include/volume_io.h -include/volume_io/alloc.h -include/volume_io/arrays.h -include/volume_io/basic.h -include/volume_io/def_math.h -include/volume_io/files.h -include/volume_io/geom_structs.h -include/volume_io/geometry.h -include/volume_io/internal_volume_io.h -include/volume_io/multidim.h -include/volume_io/progress.h -include/volume_io/string_funcs.h -include/volume_io/system_dependent.h -include/volume_io/transforms.h -include/volume_io/vol_io_prototypes.h -include/volume_io/volume.h -include/volume_io/volume_cache.h -include/voxel_loop.h -lib/libminc.a -lib/libminc.la -lib/libminc.so -lib/libminc.so.1 -lib/libvolume_io.a -lib/libvolume_io.la -lib/libvolume_io.so -lib/libvolume_io.so.0 -@dirrm include/volume_io diff --git a/science/psi3/Makefile b/science/psi3/Makefile deleted file mode 100644 index c2940f857478..000000000000 --- a/science/psi3/Makefile +++ /dev/null @@ -1,110 +0,0 @@ -# Created by: NAKATA Maho <maho@FreeBSD.org> -# $FreeBSD$ - -PORTNAME= psi3 -PORTVERSION= 3.4.0 -PORTREVISION= 4 -CATEGORIES= science -MASTER_SITES= SF/psicode/psi/${PORTVERSION} \ - http://www.psicode.org/doc/:doc \ - ${MASTER_SITE_LOCAL:S|%SUBDIR%|maho/psi3|}:doc - -DISTNAME= psi-${PORTVERSION} -.if !defined(NOPORTDOCS) -DISTFILES+= ${DISTNAME}${EXTRACT_SUFX} installation.pdf:doc userman.pdf:doc progman.pdf:doc -.endif -DIST_SUBDIR= psi3 -EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} - -MAINTAINER= ports@FreeBSD.org -COMMENT= Electronic structure programs for high-accuracy computations - -BROKEN= Fails to build - -.if exists(${LOCALBASE}/lib/libgoto2.so) -WITH_BLAS?= gotoblas -.elif exists(${LOCALBASE}/lib/libatlas.so) -WITH_BLAS?= atlas -.else -WITH_BLAS?= reference -.endif - -. if ${WITH_BLAS} == reference -LIB_DEPENDS+= libblas.so:${PORTSDIR}/math/blas -LIB_DEPENDS+= liblapack.so:${PORTSDIR}/math/lapack -BLAS= -lblas -LAPACK= -llapack -.elif ${WITH_BLAS} == gotoblas -LIB_DEPENDS+= libgoto2.so:${PORTSDIR}/math/gotoblas -LIB_DEPENDS+= liblapack.so:${PORTSDIR}/math/lapack -BLAS= -lgoto2p -LAPACK= -lgoto2p -.elif ${WITH_BLAS} == atlas -LIB_DEPENDS+= libatlas.so:${PORTSDIR}/math/atlas -BLAS= -lptf77blas -LAPACK= -lalapack -lptcblas -.endif - -GNU_CONFIGURE= yes -USES= fortran gmake tar:bzip2 -CONFIGURE_ARGS= --with-cc=${CC} \ - --with-cxx=${CXX} \ - --with-fc=${FC} \ - --with-opt="${CFLAGS}" \ - --with-lapack="${LAPACK}" \ - --with-blas="${BLAS}" \ - --datadir=${PREFIX}/share/psi3 \ - --docdir=${WRKSRC}/tmpdoc/ \ - --with-libdirs="-L${LOCALBASE}/lib" \ - --with-libs="-lcompat" -CFLAGS+= -Wno-error=return-type - -NO_STAGE= yes -.include <bsd.port.pre.mk> - -.if defined(WITH_OPTIMIZED_FLAGS) -FFLAGS+= -O3 -ffast-math -finline-functions -fomit-frame-pointer -funroll-loops -fexpensive-optimizations -malign-double -CFLAGS+= -O3 -ffast-math -finline-functions -fomit-frame-pointer -funroll-loops -fexpensive-optimizations -malign-double -CXXFLAGS+= -O3 -ffast-math -finline-functions -fomit-frame-pointer -funroll-loops -fexpensive-optimizations -malign-double -Wno-multichar -.if (${ARCH} == "i386") -FFLAGS+= -mfancy-math-387 -CFLAGS+= -mfancy-math-387 -CXXFLAGS+= -mfancy-math-387 -.endif # i386 -.endif - -WRKSRC= ${WRKDIR}/${PORTNAME} -MAN1= ccenergy.1 cceom.1 cints.1 clag.1 cscf.1 dboc.1 detcas.1 \ - detcasman.1 detci.1 geom.1 input.1 intder.1 mocube.1 mp2.1 mp2r12.1 \ - nonbonded.1 oeprop.1 optking.1 psi3.1 psiclean.1 stable.1 tocprint.1 \ - transqt.1 - -pre-configure: - @${ECHO} "You can optimize by setting WITH_OPTIMIZED_FLAGS=yes." - @${REINPLACE_CMD} -e 's|%%PTHREAD_CFLAGS%%|${PTREAD_CFLAGS}|g ; \ - s|%%PTHREAD_LIBS%%|${PTHREAD_LIBS}|g' ${WRKSRC}/src/bin/cints/Makefile.in - @${REINPLACE_CMD} -e 's|%%PTHREAD_CFLAGS%%|${PTREAD_CFLAGS}|g ; \ - s|%%PTHREAD_LIBS%%|${PTHREAD_LIBS}|g' ${WRKSRC}/src/bin/detci/Makefile.in - -MAKE_ENV+= SCRATCH=${WRKSRC}/tmp - -do-build: - @(cd ${WRKSRC} ; ${SETENV} ${MAKE_ENV} ${MAKE_CMD}) - -do-install: - @(cd ${WRKSRC} ; ${SETENV} ${MAKE_ENV} ${MAKE_CMD} install) - @${TAR} cf - -C ${WRKSRC}/tmpdoc/man . | ${TAR} xf - -C ${PREFIX}/man -.if !defined(NOPORTDOCS) - @${MKDIR} ${PREFIX}/share/doc/psi3 - @${TAR} cf - -C ${WRKSRC}/tmpdoc/html . | ${TAR} xf - -C ${PREFIX}/share/doc/psi3 - @${TAR} cf - -C ${WRKSRC}/tmpdoc/txt . | ${TAR} xf - -C ${PREFIX}/share/doc/psi3 - @${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/installation.pdf ${DOCSDIR} - @${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/userman.pdf ${DOCSDIR} - @${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/progman.pdf ${DOCSDIR} -.endif -.if !defined(NOPORTEXAMPLES) - @${MKDIR} ${PREFIX}/share/examples/psi3 - @${TAR} cf - -C ${WRKSRC}/tests . | ${TAR} xf - -C ${PREFIX}/share/examples/psi3 -.endif - -.include <bsd.port.post.mk> diff --git a/science/psi3/distinfo b/science/psi3/distinfo deleted file mode 100644 index 1d7a92df9401..000000000000 --- a/science/psi3/distinfo +++ /dev/null @@ -1,8 +0,0 @@ -SHA256 (psi3/psi-3.4.0.tar.bz2) = 8776cc5ed8358ff2eba74ae02b5d3d6a80d61cd7c68d4cf76febfea3992d52b5 -SIZE (psi3/psi-3.4.0.tar.bz2) = 5806391 -SHA256 (psi3/installation.pdf) = 7f0a58f074d35d0f8e6c2a1d6e18232b9fafb28a161a2af82e6d0e56e90d4488 -SIZE (psi3/installation.pdf) = 76622 -SHA256 (psi3/userman.pdf) = 6b2fb4c42b248eda4f6f421f1369dfe2e0fd7f69744c710f7d39e1099fcdb4d6 -SIZE (psi3/userman.pdf) = 331573 -SHA256 (psi3/progman.pdf) = ea406c1df4902e6a42cc26ede515ebde4f96eb5b81fc6de82382f3a00b361358 -SIZE (psi3/progman.pdf) = 1693839 diff --git a/science/psi3/files/patch-cstdio b/science/psi3/files/patch-cstdio deleted file mode 100644 index 39cfff087c56..000000000000 --- a/science/psi3/files/patch-cstdio +++ /dev/null @@ -1,72 +0,0 @@ ---- src/lib/libpsio/psio.hpp~ 2008-11-25 02:50:44.000000000 +0900 -+++ src/lib/libpsio/psio.hpp 2009-08-03 19:03:57.000000000 +0900 -@@ -3,7 +3,7 @@ - - #include <string> - #include <map> -- -+#include <cstdio> - #include <libpsio/config.h> - - namespace psi { ---- src/lib/libutil/libutil.h~ 2008-12-09 05:23:16.000000000 +0900 -+++ src/lib/libutil/libutil.h 2009-08-03 19:07:37.000000000 +0900 -@@ -4,6 +4,7 @@ - #include <vector> - #include <iostream> - #include <sstream> -+#include <cstdio> - #include <sys/time.h> - - extern FILE *outfile; ---- src/bin/mcscf/block_matrix.h~ 2008-12-09 05:23:16.000000000 +0900 -+++ src/bin/mcscf/block_matrix.h 2009-08-03 19:37:15.000000000 +0900 -@@ -4,7 +4,7 @@ - #include "block_vector.h" - #include "matrix_base.h" - #include <string> -- -+#include <cstdio> - extern FILE* outfile; - - namespace psi{ namespace mcscf{ ---- src/bin/mcscf/sblock_vector.cc~ 2008-12-09 05:23:16.000000000 +0900 -+++ src/bin/mcscf/sblock_vector.cc 2009-08-03 20:00:47.000000000 +0900 -@@ -2,6 +2,7 @@ - #include <psifiles.h> - - #include "sblock_vector.h" -+#include <cstdio> - - extern FILE* outfile; - ---- src/bin/mcscf/block_vector.cc~ 2008-12-09 05:23:16.000000000 +0900 -+++ src/bin/mcscf/block_vector.cc 2009-08-03 20:27:14.000000000 +0900 -@@ -1,6 +1,7 @@ - #include "block_vector.h" - #include "vector_base.h" - #include "memory_manager.h" -+#include <cstdio> - - extern FILE* outfile; - ---- src/bin/mcscf/memory_manager.h~ 2008-12-09 05:23:16.000000000 +0900 -+++ src/bin/mcscf/memory_manager.h 2009-08-03 21:09:02.000000000 +0900 -@@ -3,6 +3,7 @@ - - #include <map> - #include <vector> -+#include <cstdio> - #include <string> - - namespace psi{ namespace mcscf{ ---- src/bin/psimrcc/memory_manager.h~ 2008-08-14 07:25:41.000000000 +0900 -+++ src/bin/psimrcc/memory_manager.h 2009-08-03 21:10:00.000000000 +0900 -@@ -10,6 +10,7 @@ - #include <map> - #include <vector> - #include <string> -+#include <cstdio> - - namespace psi{ namespace psimrcc{ - diff --git a/science/psi3/files/patch-src+bin+cints+Makefile.in b/science/psi3/files/patch-src+bin+cints+Makefile.in deleted file mode 100644 index 9b7661db1670..000000000000 --- a/science/psi3/files/patch-src+bin+cints+Makefile.in +++ /dev/null @@ -1,21 +0,0 @@ ---- src/bin/cints/Makefile.in~ 2008-12-19 06:51:42.000000000 +0900 -+++ src/bin/cints/Makefile.in 2009-04-13 16:42:30.000000000 +0900 -@@ -92,15 +92,15 @@ - - include ../MakeVars - --CFLAGS = $(CDBG) $(COPT) $(CDEF) $(COTH) $(CINC) -+CFLAGS = $(CDBG) $(COPT) $(CDEF) $(COTH) $(CINC) %%PTHREAD_CFLAGS%% - CINC += -I$(srcdir) $(DIRS:%=-I$(srcdir)/%) - CDEF += $(OPTIONS) - --CXXFLAGS = $(CXXDBG) $(CXXOPT) $(CXXDEF) $(CXXOTH) $(CXXINC) -+CXXFLAGS = $(CXXDBG) $(CXXOPT) $(CXXDEF) $(CXXOTH) $(CXXINC) %%PTHREAD_CFLAGS%% - CXXINC += -I$(srcdir) $(DIRS:%=-I$(srcdir)/%) - CXXDEF += $(OPTIONS) - --LDLIBS += $(BLAS) -lpthread -+LDLIBS += $(BLAS) -lpthread %%PTHREAD_LIBS%% - PSILIBS = -lPSI_qt -lPSI_chkpt $(INTLIBS) -lPSI_iwl \ - -lPSI_psio -lPSI_ciomr -lPSI_ipv1 - ifeq ($(findstring CC,$(SUBDIRS)),CC) diff --git a/science/psi3/files/patch-src+util+tocprint+Makefile.in b/science/psi3/files/patch-src+util+tocprint+Makefile.in deleted file mode 100644 index 06984a615909..000000000000 --- a/science/psi3/files/patch-src+util+tocprint+Makefile.in +++ /dev/null @@ -1,11 +0,0 @@ ---- src/util/tocprint/Makefile.in.org Fri Mar 19 17:32:31 2004 -+++ src/util/tocprint/Makefile.in Fri Mar 19 17:33:46 2004 -@@ -18,4 +18,4 @@ - - install_man:: tocprint.1 - $(MKDIRS) $(mandir)/man1 -- $(INSTALL_PROGRAM) $(srcdir)/tocprint.1 $(mandir)/man1 -+ $(INSTALL_INCLUDE) $^ $(mandir)/man1 - - - diff --git a/science/psi3/files/patch-src-bin-clag-clag.cc b/science/psi3/files/patch-src-bin-clag-clag.cc deleted file mode 100644 index 936ec5520098..000000000000 --- a/science/psi3/files/patch-src-bin-clag-clag.cc +++ /dev/null @@ -1,10 +0,0 @@ ---- src/bin/clag/clag.cc.orig -+++ src/bin/clag/clag.cc -@@ -46,6 +46,7 @@ - /***************************************************************************/ - using namespace psi::clag; - -+int - main(int argc, char **argv) - { - diff --git a/science/psi3/files/patch-src-bin-geom-geom.cc b/science/psi3/files/patch-src-bin-geom-geom.cc deleted file mode 100644 index 12a3a4afde46..000000000000 --- a/science/psi3/files/patch-src-bin-geom-geom.cc +++ /dev/null @@ -1,10 +0,0 @@ ---- src/bin/geom/geom.cc.orig -+++ src/bin/geom/geom.cc -@@ -115,6 +115,7 @@ - void fill_sym_matrix(double **A, int size); - }} // namespace psi::geom - -+int - main(int argc, char* argv[]) - { - using namespace psi::geom; diff --git a/science/psi3/files/patch-src-bin-nonbonded-nonbonded.cc b/science/psi3/files/patch-src-bin-nonbonded-nonbonded.cc deleted file mode 100644 index c959af29e2f5..000000000000 --- a/science/psi3/files/patch-src-bin-nonbonded-nonbonded.cc +++ /dev/null @@ -1,10 +0,0 @@ ---- src/bin/nonbonded/nonbonded.cc.orig -+++ src/bin/nonbonded/nonbonded.cc -@@ -32,7 +32,6 @@ - #include <physconst.h> - #include <psifiles.h> - #include <masses.h> --#include <string> - - #include "globals.h" - #include "nonbonded.h" diff --git a/science/psi3/files/patch-src-bin-transqt2-transqt.cc b/science/psi3/files/patch-src-bin-transqt2-transqt.cc deleted file mode 100644 index 1dd018025cf9..000000000000 --- a/science/psi3/files/patch-src-bin-transqt2-transqt.cc +++ /dev/null @@ -1,10 +0,0 @@ ---- src/bin/transqt2/transqt.cc.orig -+++ src/bin/transqt2/transqt.cc -@@ -65,6 +65,7 @@ - - using namespace psi::transqt2; - -+int - main(int argc, char *argv[]) - { - int nso, nmo, ntri_so, ntri_mo, nirreps; diff --git a/science/psi3/files/patch-src-lib-libbasis-combinate.cc b/science/psi3/files/patch-src-lib-libbasis-combinate.cc deleted file mode 100644 index 3bae2543e928..000000000000 --- a/science/psi3/files/patch-src-lib-libbasis-combinate.cc +++ /dev/null @@ -1,12 +0,0 @@ ---- src/lib/libbasis/combinate.cc.orig -+++ src/lib/libbasis/combinate.cc -@@ -3,9 +3,7 @@ - \brief Enter brief description of file here - */ - --extern "C" { - #include <libciomr/libciomr.h> --} - - #include <stdexcept> - #include "combinate.h" diff --git a/science/psi3/files/patch-src-lib-libipv1-ip_read.cc b/science/psi3/files/patch-src-lib-libipv1-ip_read.cc deleted file mode 100644 index 34d6e0b5e0bf..000000000000 --- a/science/psi3/files/patch-src-lib-libipv1-ip_read.cc +++ /dev/null @@ -1,20 +0,0 @@ ---- src/lib/libipv1/ip_read.cc.orig -+++ src/lib/libipv1/ip_read.cc -@@ -12,7 +12,9 @@ - #include "ip_types.h" - #define _IP_ALLOCATE_GLOBAL_ - #include "ip_global.h" -+extern "C" { - #include "y.tab.h" -+} - - #include "ip_read.gbl" - #include "ip_read.lcl" -@@ -27,7 +29,6 @@ - - /* The input for yacc. */ - extern FILE *yyin; --extern void yyparse(void); - - /* Set up static variables. */ - /*static ip_keyword_tree_t *sub_tree = NULL;*/ diff --git a/science/psi3/files/patch-src-lib-libpsio-psio.hpp b/science/psi3/files/patch-src-lib-libpsio-psio.hpp deleted file mode 100644 index 789d4bd464fb..000000000000 --- a/science/psi3/files/patch-src-lib-libpsio-psio.hpp +++ /dev/null @@ -1,17 +0,0 @@ ---- src/lib/libpsio/psio.hpp.orig -+++ src/lib/libpsio/psio.hpp -@@ -157,10 +157,11 @@ - - }; - --extern "C" { -- extern int psiopp_ipv1_config(PSIO *psio_obj); --} - extern PSIO* _default_psio_lib_; - } - -+extern "C" { -+ int psiopp_ipv1_config(psi::PSIO *psio_obj); -+} -+ - #endif /* header guard */ diff --git a/science/psi3/pkg-descr b/science/psi3/pkg-descr deleted file mode 100644 index da9cce6ea8d2..000000000000 --- a/science/psi3/pkg-descr +++ /dev/null @@ -1,21 +0,0 @@ -The PSI3 suite of quantum chemical programs is designed for efficient, -high-accuracy calculations of properties of small to medium-sized molecules. -The package's current capabilities include a variety of Hartree-Fock, -coupled cluster, complete-active-space self-consistent-field, and -multi-reference configuration interaction models. Molecular point-group -symmetry is utilized throughout to maximize efficiency. - - * Arbitrarily high angular momentum levels in integrals - and derivative integrals. (Up to k-type functions have been tested.) - * Coupled cluster methods including CCSD and CCSD(T) with - RHF, ROHF, UHF, and Brueckner orbitals. - * Determinant-based CI including CASSCF, RAS-CI, and Full CI. - * Multithreaded integral-direct SCF, MP2, and MP2-R12. - * Excited state methods: CIS, CIS(D), RPA, and EOM-CCSD. - * Analytic energy gradients for CCSD with RHF, ROHF, and UHF orbitals. - * Coupled cluster linear response methods for static and - dynamic polarizabilities and optical rotation. - * Diagonal Born-Oppenheimer correction (DBOC) for - RHF, ROHF, UHF, and CI wave functions. - -WWW: http://www.psicode.org/ diff --git a/science/psi3/pkg-message b/science/psi3/pkg-message deleted file mode 100644 index 6964ca9df8fe..000000000000 --- a/science/psi3/pkg-message +++ /dev/null @@ -1,6 +0,0 @@ -The following citation should be used in any publication -utilizing the PSI3 program package: - -"T. Daniel Crawford, C. David Sherrill, Edward F. Valeev, Justin T. Fermann, -Rollin A. King, Matthew L. Leininger, Shawn T. Brown, Curtis L. Janssen, -Edward T. Seidl, Joseph P. Kenny, and Wesley D. Allen, PSI 3.2, 2003." diff --git a/science/psi3/pkg-plist b/science/psi3/pkg-plist deleted file mode 100644 index 7b921cb0fb07..000000000000 --- a/science/psi3/pkg-plist +++ /dev/null @@ -1,939 +0,0 @@ -bin/ccdensity -bin/ccenergy -bin/cceom -bin/cchbar -bin/cclambda -bin/ccresponse -bin/ccsort -bin/cctriples -bin/cints -bin/cis -bin/clag -bin/cphf -bin/cscf -bin/dboc -bin/detcas -bin/detcasman -bin/detci -bin/extrema -bin/geom -bin/input -bin/intder -bin/localize -bin/mcscf -bin/mocube -bin/mp2 -bin/mp2r12 -bin/nonbonded -bin/oeprop -bin/optking -bin/psi2molden -bin/psi3 -bin/psiclean -bin/psimrcc -bin/response -bin/stable -bin/tocprint -bin/transqt -bin/transqt2 -include/ccfiles.h -include/chkpt_params.h -include/libbasis/basisset.h -include/libbasis/combinate.h -include/libbasis/gnorm.h -include/libbasis/osrecur.h -include/libbasis/overlap.h -include/libbasis/rotation.h -include/libbasis/shell.h -include/libchkpt/chkpt.h -include/libchkpt/chkpt.hpp -include/libchkpt/config.h -include/libciomr/libciomr.h -include/libderiv/libderiv.h -include/libdpd/dpd.h -include/libint/hrr_header.h -include/libint/libint.h -include/libint/vrr_header.h -include/libipv1/ip_alloc.gbl -include/libipv1/ip_cwk.gbl -include/libipv1/ip_data.gbl -include/libipv1/ip_error.gbl -include/libipv1/ip_error.h -include/libipv1/ip_global.h -include/libipv1/ip_karray.gbl -include/libipv1/ip_lib.h -include/libipv1/ip_print.gbl -include/libipv1/ip_read.gbl -include/libipv1/ip_types.h -include/libipv1/scan.gbl -include/libipv1/tmpl.h -include/libipv1/y.tab.gbl -include/libiwl/config.h -include/libiwl/iwl.h -include/libiwl/iwl.hpp -include/libmints/basisset.h -include/libmints/dipole.h -include/libmints/eri.h -include/libmints/factory.h -include/libmints/gshell.h -include/libmints/integral.h -include/libmints/kinetic.h -include/libmints/matrix.h -include/libmints/matrix_i.cc -include/libmints/molecule.h -include/libmints/onebody.h -include/libmints/osrecur.h -include/libmints/overlap.h -include/libmints/potential.h -include/libmints/quadrupole.h -include/libmints/ref.h -include/libmints/sobasis.h -include/libmints/symmetry.h -include/libmints/twobody.h -include/libmints/vector.h -include/libmints/vector3.h -include/libmints/vector3_i.cc -include/libmints/wavefunction.h -include/libmoinfo/libmoinfo.h -include/libmoinfo/moinfo.h -include/libmoinfo/moinfo_base.h -include/libmoinfo/moinfo_scf.h -include/liboptions/liboptions.h -include/libpsio/config.h -include/libpsio/psio.h -include/libpsio/psio.hpp -include/libqt/qt.h -include/libr12/libr12.h -include/libutil/libutil.h -include/masses.h -include/physconst.h -include/psiconfig.h -include/psifiles.h -include/psitypes.h -include/rgb.h -include/symmetry.h -include/vdw_radii.h -lib/libPSI_basis.a -lib/libPSI_chkpt.a -lib/libPSI_ciomr.a -lib/libPSI_deriv.a -lib/libPSI_dpd.a -lib/libPSI_int.a -lib/libPSI_ipv1.a -lib/libPSI_iwl.a -lib/libPSI_mints.a -lib/libPSI_moinfo.a -lib/libPSI_options.a -lib/libPSI_psio.a -lib/libPSI_qt.a -lib/libPSI_r12.a -lib/libPSI_util.a -%%PORTDOCS%%%%DOCSDIR%%/installation.pdf -%%PORTDOCS%%%%DOCSDIR%%/libiwl.txt -%%PORTDOCS%%%%DOCSDIR%%/progman.pdf -%%PORTDOCS%%%%DOCSDIR%%/userman.pdf -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Basis_Tests/Benchmarks -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Basis_Tests/input.dat -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Basis_Tests/psi_test.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Basis_Tests/standard.input -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/INDEX -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MakeRules -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MakeRules.in -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MakeVars -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MakeVars.in -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Makefile -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Makefile.in -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/README-NEW-TESTS -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/casscf-fzc-sp/Makefile -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/casscf-fzc-sp/Makefile.in -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/casscf-fzc-sp/input.dat 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include/libmints -@dirrm include/libiwl -@dirrm include/libipv1 -@dirrm include/libint -@dirrm include/libdpd -@dirrm include/libderiv -@dirrm include/libciomr -@dirrm include/libchkpt -@dirrm include/libbasis diff --git a/science/x11iraf/Makefile b/science/x11iraf/Makefile deleted file mode 100644 index 80ac60c89762..000000000000 --- a/science/x11iraf/Makefile +++ /dev/null @@ -1,43 +0,0 @@ -# Created by: David Syphers <dsyphers@u.washington.edu> -# $FreeBSD$ - -PORTNAME= x11iraf -PORTVERSION= 1.3.1 -PORTREVISION= 3 -CATEGORIES= science astro -MASTER_SITES= ftp://iraf.noao.edu/iraf/x11iraf/ -DISTNAME= x11iraf-v${PORTVERSION}-bin.freebsd - -MAINTAINER= ports@FreeBSD.org -COMMENT= Provides graphical tools to work with IRAF - -CONFLICTS= xterm-[0-9]* - -LIB_DEPENDS= libc.so.4:${PORTSDIR}/misc/compat4x - -NO_BUILD= yes - -# this may work on other archs, but I'm making no bets -ONLY_FOR_ARCHS= i386 - -BINS= ism_wcspix.e obmsh resize vximtool xgterm ximtool xtapemon - -MAN1= obmsh.1 \ - resize.1 \ - vximtool.1 \ - xgterm.1 \ - ximtool.1 \ - xtapemon.1 - -NO_STAGE= yes -do-install: - @${ECHO_MSG} "===> Installing binaries" - @${INSTALL_PROGRAM} ${BINS:S|^|${WRKDIR}/bin.freebsd/|} ${PREFIX}/bin/ - @${INSTALL_SCRIPT} ${WRKDIR}/bin.freebsd/ximtool-alt ${PREFIX}/bin/ - @${ECHO_MSG} "===> Installing manpages" - @${INSTALL_MAN} ${WRKDIR}/man/* ${PREFIX}/man/man1/ - @${ECHO_MSG} "===> Installing CDL library" - @${INSTALL_DATA} ${WRKDIR}/include/* ${PREFIX}/include/ - @${INSTALL_DATA} ${WRKDIR}/lib.freebsd/libcdl.a ${PREFIX}/lib/ - -.include <bsd.port.mk> diff --git a/science/x11iraf/distinfo b/science/x11iraf/distinfo deleted file mode 100644 index d3f2c085c90b..000000000000 --- a/science/x11iraf/distinfo +++ /dev/null @@ -1,2 +0,0 @@ -SHA256 (x11iraf-v1.3.1-bin.freebsd.tar.gz) = 04b1a5e1f337459f5389fb901566314eacf2ae3a6ba79bd7623314c5d5a4747d -SIZE (x11iraf-v1.3.1-bin.freebsd.tar.gz) = 2238249 diff --git a/science/x11iraf/pkg-descr b/science/x11iraf/pkg-descr deleted file mode 100644 index 83a76e5ecd9d..000000000000 --- a/science/x11iraf/pkg-descr +++ /dev/null @@ -1,9 +0,0 @@ -x11iraf provides graphical tools to work with IRAF, notably xgterm and XImtool. - -Note: IRAF = Image Reduction and Analysis Facility, a general purpose software -system for the reduction and analysis of astronomical data. - -WWW: http://iraf.noao.edu - --David Syphers -dsyphers@u.washington.edu diff --git a/science/x11iraf/pkg-plist b/science/x11iraf/pkg-plist deleted file mode 100644 index 10b2575660af..000000000000 --- a/science/x11iraf/pkg-plist +++ /dev/null @@ -1,12 +0,0 @@ -bin/ism_wcspix.e -bin/obmsh -bin/resize -bin/vximtool -bin/xgterm -bin/ximtool -bin/ximtool-alt -bin/xtapemon -include/cdl.h -include/cdlftn.inc -include/cdlspp.h -lib/libcdl.a diff --git a/science/xmds/Makefile b/science/xmds/Makefile deleted file mode 100644 index 704c873618cd..000000000000 --- a/science/xmds/Makefile +++ /dev/null @@ -1,31 +0,0 @@ -# Created by: EelVex -# $FreeBSD$ - -PORTNAME= xmds -PORTVERSION= 1.6 -CATEGORIES= science -MASTER_SITES= SF/${PORTNAME}/${PORTNAME}/${PORTNAME}-${PORTVERSION}.5 -DISTNAME= xmds-1.6.5 - -MAINTAINER= ports@FreeBSD.org -COMMENT= XMDS is a code generator that integrates equations; - -MAN1= loadxsil.1 xmds.1 xsil2graphics.1 - -OPTIONS_DEFINE= FFTW3 -FFTW3_DESC= Use fftw3 instead of fftw2 - -GNU_CONFIGURE= yes - -NO_STAGE= yes -.include <bsd.port.options.mk> - -.if ${PORT_OPTIONS:MFFTW3} -BUILD_DEPENDS= ${LOCALBASE}/include/fftw3.h:${PORTSDIR}/math/fftw3 -CONFIGURE_ARGS= --enable-fftw3 --with-fftw3-path=${LOCALBASE} -.else -BUILD_DEPENDS= ${LOCALBASE}/include/fftw.h:${PORTSDIR}/math/fftw -CONFIGURE_ARGS= --with-fftw-path=${LOCALBASE} -.endif - -.include <bsd.port.mk> diff --git a/science/xmds/distinfo b/science/xmds/distinfo deleted file mode 100644 index 36925c989d41..000000000000 --- a/science/xmds/distinfo +++ /dev/null @@ -1,2 +0,0 @@ -SHA256 (xmds-1.6.5.tar.gz) = f7128c7c847bafd3a5ed582415cbddd1f31234278d62231faaeb9bec04d6b5ff -SIZE (xmds-1.6.5.tar.gz) = 528593 diff --git a/science/xmds/files/patch-Makefile.in b/science/xmds/files/patch-Makefile.in deleted file mode 100644 index 04e7248ff066..000000000000 --- a/science/xmds/files/patch-Makefile.in +++ /dev/null @@ -1,82 +0,0 @@ ---- Makefile.in.orig 2008-02-25 21:32:56.000000000 -0600 -+++ Makefile.in 2010-09-22 14:22:17.000000000 -0500 -@@ -150,4 +150,5 @@ - EXTRA_DIST = $(example_files) $(m4files) $(manfiles) MANIFEST README.Windows source/loadxsil.m --dist_doc_data = AUTHORS NEWS COPYING README README.Windows source/loadxsil.m --doc_examplesdir = ${docdir}/examples -+xmdsdocdir = ${datadir}/doc/xmds-${VERSION} -+dist_xmdsdoc_DATA = AUTHORS NEWS COPYING README README.Windows source/loadxsil.m -+doc_examplesdir = ${xmdsdocdir}/examples - dist_doc_examples_DATA = $(example_files) -@@ -162,3 +163,3 @@ - MANS = $(man1_MANS) --DATA = $(dist_doc_examples_DATA) -+DATA = $(dist_doc_examples_DATA) $(dist_xmdsdoc_DATA) - -@@ -169,5 +170,5 @@ - uninstall-recursive check-recursive installcheck-recursive --DIST_COMMON = README $(dist_doc_examples_DATA) AUTHORS COPYING \ -- ChangeLog INSTALL Makefile.am Makefile.in NEWS TODO \ -- acinclude.m4 aclocal.m4 config.guess config.sub configure \ -+DIST_COMMON = README $(dist_doc_examples_DATA) $(dist_xmdsdoc_DATA) \ -+ AUTHORS COPYING ChangeLog INSTALL Makefile.am Makefile.in NEWS \ -+ TODO acinclude.m4 aclocal.m4 config.guess config.sub configure \ - configure.in depcomp install-sh ltmain.sh missing mkinstalldirs -@@ -255,2 +256,20 @@ - done -+dist_xmdsdocDATA_INSTALL = $(INSTALL_DATA) -+install-dist_xmdsdocDATA: $(dist_xmdsdoc_DATA) -+ @$(NORMAL_INSTALL) -+ $(mkinstalldirs) $(DESTDIR)$(xmdsdocdir) -+ @list='$(dist_xmdsdoc_DATA)'; for p in $$list; do \ -+ if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \ -+ f="`echo $$p | sed -e 's|^.*/||'`"; \ -+ echo " $(dist_xmdsdocDATA_INSTALL) $$d$$p $(DESTDIR)$(xmdsdocdir)/$$f"; \ -+ $(dist_xmdsdocDATA_INSTALL) $$d$$p $(DESTDIR)$(xmdsdocdir)/$$f; \ -+ done -+ -+uninstall-dist_xmdsdocDATA: -+ @$(NORMAL_UNINSTALL) -+ @list='$(dist_xmdsdoc_DATA)'; for p in $$list; do \ -+ f="`echo $$p | sed -e 's|^.*/||'`"; \ -+ echo " rm -f $(DESTDIR)$(xmdsdocdir)/$$f"; \ -+ rm -f $(DESTDIR)$(xmdsdocdir)/$$f; \ -+ done - -@@ -458,3 +477,3 @@ - installdirs-am: -- $(mkinstalldirs) $(DESTDIR)$(man1dir) $(DESTDIR)$(doc_examplesdir) -+ $(mkinstalldirs) $(DESTDIR)$(man1dir) $(DESTDIR)$(doc_examplesdir) $(DESTDIR)$(xmdsdocdir) - -@@ -500,3 +519,4 @@ - --install-data-am: install-dist_doc_examplesDATA install-man -+install-data-am: install-dist_doc_examplesDATA install-dist_xmdsdocDATA \ -+ install-man - -@@ -519,4 +539,4 @@ - --uninstall-am: uninstall-dist_doc_examplesDATA uninstall-info-am \ -- uninstall-man -+uninstall-am: uninstall-dist_doc_examplesDATA uninstall-dist_xmdsdocDATA \ -+ uninstall-info-am uninstall-man - -@@ -532,10 +552,12 @@ - install-data-recursive install-dist_doc_examplesDATA \ -- install-exec install-exec-am install-exec-recursive \ -- install-info install-info-am install-info-recursive install-man \ -- install-man1 install-recursive install-strip installcheck \ -- installcheck-am installdirs installdirs-am \ -- installdirs-recursive maintainer-clean maintainer-clean-generic \ -+ install-dist_xmdsdocDATA install-exec install-exec-am \ -+ install-exec-recursive install-info install-info-am \ -+ install-info-recursive install-man install-man1 \ -+ install-recursive install-strip installcheck installcheck-am \ -+ installdirs installdirs-am installdirs-recursive \ -+ maintainer-clean maintainer-clean-generic \ - maintainer-clean-recursive mostlyclean mostlyclean-generic \ - mostlyclean-recursive tags tags-recursive uninstall \ -- uninstall-am uninstall-dist_doc_examplesDATA uninstall-info-am \ -+ uninstall-am uninstall-dist_doc_examplesDATA \ -+ uninstall-dist_xmdsdocDATA uninstall-info-am \ - uninstall-info-recursive uninstall-man uninstall-man1 \ diff --git a/science/xmds/pkg-descr b/science/xmds/pkg-descr deleted file mode 100644 index 91549853a953..000000000000 --- a/science/xmds/pkg-descr +++ /dev/null @@ -1,25 +0,0 @@ -eXtensible multi-dimensional Simulator - * An open-source XML based simulation package - * From Ordinary Differential Equations (ODEs) up to stochastic Partial - Differential Equations (PDEs) - * Many applications: - o physics - o mathematics - o engineering - o finance - o economics - o chemistry - o theoretical biology - * Generates fast, C++ compiled code - * Documentation and source are free! - * Runs on Linux, Unix, MacOS X and Cygwin (Windows) -XMDS is a code generator that integrates equations. You write them down in -human readable form in an XML file, and it goes away and writes and compiles a -C++ program that integrates those equations as fast as it can possibly be done -in your architecture. - -Author: Paul Cochrane (principal developer) cochrane@physics.uq.edu.au - Joseph Hope (second author) Joseph.Hope@anu.edu.au - Peter Drummond (xmds project leader) drummond@physics.uq.edu.au - -WWW: http://www.xmds.org/ diff --git a/science/xmds/pkg-plist b/science/xmds/pkg-plist deleted file mode 100644 index f2c5c0c2b526..000000000000 --- a/science/xmds/pkg-plist +++ /dev/null @@ -1,52 +0,0 @@ -bin/xmds -bin/xsil2graphics -include/getopt_xmds.h -include/xmds_complex.h -include/xmds_config.h -lib/libxmds.a -share/doc/xmds-1.6.5/AUTHORS -share/doc/xmds-1.6.5/COPYING -share/doc/xmds-1.6.5/NEWS -share/doc/xmds-1.6.5/README -share/doc/xmds-1.6.5/README.Windows -share/doc/xmds-1.6.5/examples/HighdimPlotExample.nb -share/doc/xmds-1.6.5/examples/atomlaser.xmds -share/doc/xmds-1.6.5/examples/branch.xmds -share/doc/xmds-1.6.5/examples/brusselator.xmds -share/doc/xmds-1.6.5/examples/catcycle.xmds -share/doc/xmds-1.6.5/examples/chain.xmds -share/doc/xmds-1.6.5/examples/chemkin.xmds -share/doc/xmds-1.6.5/examples/diffusion.xmds -share/doc/xmds-1.6.5/examples/duffing.xmds -share/doc/xmds-1.6.5/examples/fibre.xmds -share/doc/xmds-1.6.5/examples/fisher_reaction_diffusion.xmds -share/doc/xmds-1.6.5/examples/fullpos3D.xmds -share/doc/xmds-1.6.5/examples/gaugeatomlaser.xmds -share/doc/xmds-1.6.5/examples/groundstate.xmds -share/doc/xmds-1.6.5/examples/highdim.xmds -share/doc/xmds-1.6.5/examples/highdim_vector_version.xmds -share/doc/xmds-1.6.5/examples/hires.xmds -share/doc/xmds-1.6.5/examples/krebs.xmds -share/doc/xmds-1.6.5/examples/kubo.xmds -share/doc/xmds-1.6.5/examples/lane_emden.xmds -share/doc/xmds-1.6.5/examples/lorenz.xmds -share/doc/xmds-1.6.5/examples/lorenzInput.dat -share/doc/xmds-1.6.5/examples/lotka_volterra.xmds -share/doc/xmds-1.6.5/examples/nan.xmds -share/doc/xmds-1.6.5/examples/ndparamp.xmds -share/doc/xmds-1.6.5/examples/nlse.xmds -share/doc/xmds-1.6.5/examples/oregonator.xmds -share/doc/xmds-1.6.5/examples/paraxial_wave.xmds -share/doc/xmds-1.6.5/examples/pendulum.xmds -share/doc/xmds-1.6.5/examples/ring_modulator.xmds -share/doc/xmds-1.6.5/examples/sech_soliton.xmds -share/doc/xmds-1.6.5/examples/sech_soliton_tdepk.xmds -share/doc/xmds-1.6.5/examples/sine.xmds -share/doc/xmds-1.6.5/examples/soliton.xmds -share/doc/xmds-1.6.5/examples/thermkin.xmds -share/doc/xmds-1.6.5/examples/tla.xmds -share/doc/xmds-1.6.5/examples/van_der_pol.xmds -share/doc/xmds-1.6.5/examples/vibstring.xmds -share/doc/xmds-1.6.5/loadxsil.m -@dirrm share/doc/xmds-1.6.5/examples -@dirrm share/doc/xmds-1.6.5 |