Import MPQC 2.3.1 as biology/mpqc

MPQC is the Massively Parallel Quantum Chemistry Program.
It computes properties of atoms and molecules from first
principles using the time independent Schroedinger equation.
It runs on a wide range of architectures ranging from single
many-core computers to massively parallel computers. Its design
is object oriented, using the C++ programming language.

Capabilities

  * Closed shell, unrestricted and general restricted open shell
    Hartree-Fock energies and gradients
  * Closed shell, unrestricted and general restricted open shell
    density functional theory energies and gradients
  * Second order open shell perturbation theory (OPT2[2]) and
    Z-averaged perturbation theory (ZAPT2) energies.
  * Second order closed shell Moller-Plesset perturbation
    theory energies and gradients.
  * Second order Moller-Plesset perturbation theory
    including an R12/F12 correlation factor. Energies of closed-
    and open-shell systems are supported.
  * Explicitly-correlated R12/F12 coupled-cluster methods via
    interface to Psi3 code and via native (experimental)
    implementation.
  * Explicitly-correlated multireference methods (MRCI, CASPT2)
    via interfaces to GAMESS and MOLCAS codes.
  * Robust internal coordinate geometry optimizer that efficiently
    optimizes molecules with many degrees of freedom. Nearly
    arbitrary internal coordinate constraints can be handled.

8 files changed, 308 insertions, 0 deletions

diff --git a/biology/mpqc/DESCR b/biology/mpqc/DESCR
new file mode 100644
index 00000000000..d1dd84519d8
--- /dev/null
+++ b/biology/mpqc/DESCR
@@ -0,0 +1,28 @@
+MPQC is the Massively Parallel Quantum Chemistry Program.
+It computes properties of atoms and molecules from first
+principles using the time independent Schroedinger equation.
+It runs on a wide range of architectures ranging from single
+many-core computers to massively parallel computers. Its design
+is object oriented, using the C++ programming language.
+
+Capabilities
+
+  * Closed shell, unrestricted and general restricted open shell
+    Hartree-Fock energies and gradients
+  * Closed shell, unrestricted and general restricted open shell
+    density functional theory energies and gradients
+  * Second order open shell perturbation theory (OPT2[2]) and
+    Z-averaged perturbation theory (ZAPT2) energies.
+  * Second order closed shell Moller-Plesset perturbation
+    theory energies and gradients.
+  * Second order Moller-Plesset perturbation theory
+    including an R12/F12 correlation factor. Energies of closed-
+    and open-shell systems are supported.
+  * Explicitly-correlated R12/F12 coupled-cluster methods via
+    interface to Psi3 code and via native (experimental)
+    implementation.
+  * Explicitly-correlated multireference methods (MRCI, CASPT2)
+    via interfaces to GAMESS and MOLCAS codes.
+  * Robust internal coordinate geometry optimizer that efficiently
+    optimizes molecules with many degrees of freedom. Nearly
+    arbitrary internal coordinate constraints can be handled.
diff --git a/biology/mpqc/Makefile b/biology/mpqc/Makefile
new file mode 100644
index 00000000000..063367a4f84
--- /dev/null
+++ b/biology/mpqc/Makefile
@@ -0,0 +1,40 @@
+# $NetBSD: Makefile,v 1.1.1.1 2013/03/16 12:43:26 asau Exp $
+
+DISTNAME=	mpqc-2.3.1
+CATEGORIES=	biology
+MASTER_SITES=	$(MASTER_SITE_SOURCEFORGE:=mpqc/)
+EXTRACT_SUFX=	.tar.bz2
+
+MAINTAINER=	asau@inbox.ru
+HOMEPAGE=	http://www.mpqc.org/
+COMMENT=	The Massively Parallel Quantum Chemistry Program
+
+USE_LANGUAGES=	c c++ fortran77
+GNU_CONFIGURE=	yes
+CONFIGURE_ARGS+=	--with-libdirs="$(COMPILER_RPATH_FLAG)$(PREFIX)/lib"	# fixme
+#CONFIGURE_ARGS=	-without-f77	# this doesn't work out of the box
+CONFIGURE_ENV=	ac_cv_prog_WISH=$(REPLACE.wish.new)
+USE_TOOLS+=	perl:run
+USE_LIBTOOL=	yes
+
+USE_TOOLS+=	gmake
+BUILD_TARGET=	default
+
+# This is strange, yet...
+INSTALL_MAKE_FLAGS=	installroot=$(DESTDIR)
+
+REPLACE_PERL=	src/bin/mpqc/ccarun.in src/bin/mpqc/mpqcrun.in
+REPLACE_WISH=	src/bin/molrender/tkmolrender.in
+
+# optional:
+# MPI, niama-config, libr12, libderiv
+.include "../../devel/libexecinfo/buildlink3.mk" # optional
+.include "../../mk/dlopen.buildlink3.mk" # optional?
+.include "../../math/libint/buildlink3.mk" # optional
+
+.include "../../x11/tk/interpreter.mk"
+
+.include "../../math/blas/buildlink3.mk"
+.include "../../math/lapack/buildlink3.mk"
+.include "../../mk/pthread.buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/biology/mpqc/PLIST b/biology/mpqc/PLIST
new file mode 100644
index 00000000000..25f9ff5584c
--- /dev/null
+++ b/biology/mpqc/PLIST
@@ -0,0 +1,81 @@
+@comment $NetBSD: PLIST,v 1.1.1.1 2013/03/16 12:43:26 asau Exp $
+bin/ccarun
+bin/chkmpqcout
+bin/molrender
+bin/mpqc
+bin/mpqcrun
+bin/scls
+bin/scpr
+bin/tkmolrender
+share/mpqc/${PKGVERSION}/atominfo.kv
+share/mpqc/${PKGVERSION}/basis/3-21PPg.kv
+share/mpqc/${PKGVERSION}/basis/3-21PPgS.kv
+share/mpqc/${PKGVERSION}/basis/3-21g.kv
+share/mpqc/${PKGVERSION}/basis/3-21gS.kv
+share/mpqc/${PKGVERSION}/basis/4-31g.kv
+share/mpqc/${PKGVERSION}/basis/6-311PPgL2d_2pR.kv
+share/mpqc/${PKGVERSION}/basis/6-311PPgL3df_3pdR.kv
+share/mpqc/${PKGVERSION}/basis/6-311PPgSS.kv
+share/mpqc/${PKGVERSION}/basis/6-311g.kv
+share/mpqc/${PKGVERSION}/basis/6-311gL2df_2pdR.kv
+share/mpqc/${PKGVERSION}/basis/6-311gS.kv
+share/mpqc/${PKGVERSION}/basis/6-311gSS.kv
+share/mpqc/${PKGVERSION}/basis/6-31PPg.kv
+share/mpqc/${PKGVERSION}/basis/6-31PPgS.kv
+share/mpqc/${PKGVERSION}/basis/6-31PPgSS.kv
+share/mpqc/${PKGVERSION}/basis/6-31PgS.kv
+share/mpqc/${PKGVERSION}/basis/6-31g.kv
+share/mpqc/${PKGVERSION}/basis/6-31gS.kv
+share/mpqc/${PKGVERSION}/basis/6-31gSS.kv
+share/mpqc/${PKGVERSION}/basis/aug-cc-pcv5z.kv
+share/mpqc/${PKGVERSION}/basis/aug-cc-pcvdz.kv
+share/mpqc/${PKGVERSION}/basis/aug-cc-pcvqz.kv
+share/mpqc/${PKGVERSION}/basis/aug-cc-pcvtz.kv
+share/mpqc/${PKGVERSION}/basis/aug-cc-pv5z.kv
+share/mpqc/${PKGVERSION}/basis/aug-cc-pv6z.kv
+share/mpqc/${PKGVERSION}/basis/aug-cc-pvdz.kv
+share/mpqc/${PKGVERSION}/basis/aug-cc-pvqz.kv
+share/mpqc/${PKGVERSION}/basis/aug-cc-pvtz.kv
+share/mpqc/${PKGVERSION}/basis/cc-pcv5z.kv
+share/mpqc/${PKGVERSION}/basis/cc-pcvdz.kv
+share/mpqc/${PKGVERSION}/basis/cc-pcvqz.kv
+share/mpqc/${PKGVERSION}/basis/cc-pcvtz.kv
+share/mpqc/${PKGVERSION}/basis/cc-pv5z.kv
+share/mpqc/${PKGVERSION}/basis/cc-pv6z.kv
+share/mpqc/${PKGVERSION}/basis/cc-pvdz.kv
+share/mpqc/${PKGVERSION}/basis/cc-pvqz.kv
+share/mpqc/${PKGVERSION}/basis/cc-pvtz.kv
+share/mpqc/${PKGVERSION}/basis/dz_LdunningR.kv
+share/mpqc/${PKGVERSION}/basis/dzp_LdunningR.kv
+share/mpqc/${PKGVERSION}/basis/dzp_P_diffuse_LdunningR.kv
+share/mpqc/${PKGVERSION}/basis/midi_LhuzinagaR.kv
+share/mpqc/${PKGVERSION}/basis/mini_LhuzinagaR.kv
+share/mpqc/${PKGVERSION}/basis/mini_LscaledR.kv
+share/mpqc/${PKGVERSION}/basis/nasa_ames_ano.kv
+share/mpqc/${PKGVERSION}/basis/pc-0-aug.kv
+share/mpqc/${PKGVERSION}/basis/pc-0.kv
+share/mpqc/${PKGVERSION}/basis/pc-1-aug.kv
+share/mpqc/${PKGVERSION}/basis/pc-1.kv
+share/mpqc/${PKGVERSION}/basis/pc-2-aug.kv
+share/mpqc/${PKGVERSION}/basis/pc-2.kv
+share/mpqc/${PKGVERSION}/basis/pc-3-aug.kv
+share/mpqc/${PKGVERSION}/basis/pc-3.kv
+share/mpqc/${PKGVERSION}/basis/pc-4-aug.kv
+share/mpqc/${PKGVERSION}/basis/pc-4.kv
+share/mpqc/${PKGVERSION}/basis/sto-2g.kv
+share/mpqc/${PKGVERSION}/basis/sto-3g.kv
+share/mpqc/${PKGVERSION}/basis/sto-3gS.kv
+share/mpqc/${PKGVERSION}/basis/sto-6g.kv
+share/mpqc/${PKGVERSION}/basis/tz_LdunningR.kv
+share/mpqc/${PKGVERSION}/ccarunproc
+share/mpqc/${PKGVERSION}/elisp/SC.el
+share/mpqc/${PKGVERSION}/elisp/compile.el
+share/mpqc/${PKGVERSION}/elisp/keyval.el
+share/mpqc/${PKGVERSION}/elisp/mpqc.el
+share/mpqc/${PKGVERSION}/magic
+share/mpqc/${PKGVERSION}/mpqcrunproc
+share/mpqc/${PKGVERSION}/perl/AtomicBases.pm
+share/mpqc/${PKGVERSION}/perl/AtomicBasis.pm
+share/mpqc/${PKGVERSION}/perl/Molecule.pm
+share/mpqc/${PKGVERSION}/perl/QCParse.pm
+share/mpqc/${PKGVERSION}/perl/QCResult.pm
diff --git a/biology/mpqc/distinfo b/biology/mpqc/distinfo
new file mode 100644
index 00000000000..28d5da37398
--- /dev/null
+++ b/biology/mpqc/distinfo
@@ -0,0 +1,9 @@
+$NetBSD: distinfo,v 1.1.1.1 2013/03/16 12:43:26 asau Exp $
+
+SHA1 (mpqc-2.3.1.tar.bz2) = f89fcbe6e07e90abe02fc21dbce045a2a749f65d
+RMD160 (mpqc-2.3.1.tar.bz2) = 0e3b395e9ed663b9c3de120fb4f5a00bc40c7e0f
+Size (mpqc-2.3.1.tar.bz2) = 2521392 bytes
+SHA1 (patch-configure) = ee1259c038c7a3eeadea1e71c803e6fa2e7972cc
+SHA1 (patch-configure.in) = 6c72b054c278b3ea10bbe30ba16c480afe08dc3c
+SHA1 (patch-src_bin_mpqc_ccarunproc) = 3ba0297fcda9b0a105bd1f04dea6345569a47ffe
+SHA1 (patch-src_bin_mpqc_mpqcrunproc) = f005f8eef684f2b12e27211865f726faabd59ee9
diff --git a/biology/mpqc/patches/patch-configure b/biology/mpqc/patches/patch-configure
new file mode 100644
index 00000000000..c03496ce8a3
--- /dev/null
+++ b/biology/mpqc/patches/patch-configure
@@ -0,0 +1,67 @@
+$NetBSD: patch-configure,v 1.1.1.1 2013/03/16 12:43:26 asau Exp $
+
+--- configure.orig	2006-03-22 19:13:52.000000000 +0000
++++ configure
+@@ -2290,7 +2290,7 @@ if test "${with_cca_chem_config+set}" = 
+ 
+ else
+ 
+-  if test "$components" == "yes"; then
++  if test "$components" = "yes"; then
+     # Extract the first word of "cca-chem-config", so it can be a program name with args.
+ set dummy cca-chem-config; ac_word=$2
+ echo "$as_me:$LINENO: checking for $ac_word" >&5
+@@ -5207,7 +5207,7 @@ case $target_cpu in
+      ;;
+ esac
+ 
+-if test X$GXX == Xyes; then
++if test X$GXX = Xyes; then
+   echo "$as_me:$LINENO: checking for C++ cpu tuning flag" >&5
+ echo $ECHO_N "checking for C++ cpu tuning flag... $ECHO_C" >&6
+ 
+@@ -5265,7 +5265,7 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
+ echo "${ECHO_T}$cxx_tuneflag" >&6
+ fi
+ 
+-if test X$GCC == Xyes; then
++if test X$GCC = Xyes; then
+   echo "$as_me:$LINENO: checking for C cpu tuning flag" >&5
+ echo $ECHO_N "checking for C cpu tuning flag... $ECHO_C" >&6
+   CFLAGS_SAV=$CFLAGS
+@@ -28629,10 +28629,10 @@ ENABLESHARED=$enable_shared
+ 
+ 
+ 
+-if test $components == "yes"; then
++if test $components = "yes"; then
+ 
+-  if test $HAVE_MPI == "yes" &&
+-     test $HAVE_MPIPP == "no"; then
++  if test $HAVE_MPI = "yes" &&
++     test $HAVE_MPIPP = "no"; then
+     { { echo "$as_me:$LINENO: error: libmpi++ needed for mpi cca components" >&5
+ echo "$as_me: error: libmpi++ needed for mpi cca components" >&2;}
+    { (exit 1); exit 1; }; }
+@@ -28808,10 +28808,10 @@ echo "$as_me: WARNING: Ccaffeine not con
+ 
+ 
+ 
+-  if test $ENABLE_PYTHON == "yes"; then
++  if test $ENABLE_PYTHON = "yes"; then
+     # check for babel python
+     BABEL_PYTHON_ENABLE=`$BABEL_CONFIG --query-var=SUPPORT_PYTHON`
+-    if test $BABEL_PYTHON_ENABLE == "false"; then
++    if test $BABEL_PYTHON_ENABLE = "false"; then
+       { { echo "$as_me:$LINENO: error: Babel not properly configured for python" >&5
+ echo "$as_me: error: Babel not properly configured for python" >&2;}
+    { (exit 1); exit 1; }; }
+@@ -28846,7 +28846,7 @@ echo "$as_me: error: Ccaffeine not prope
+   echo -e "ccafe bin:\n  $CCAFE_BIN"
+   echo -e "ccafe python enabled:\n  $CCAFE_PYTHON_ENABLE"
+   echo -e "ccafe mpi enabled\n  $CCAFE_MPI_ENABLE"
+-  if test $CCAFE_MPI_ENABLE == "yes"; then
++  if test $CCAFE_MPI_ENABLE = "yes"; then
+     echo -e "ccafe mpi include:\n  $CCAFE_MPI_INCLUDE"
+     echo -e "ccafe mpi lib:\n  $CCAFE_MPI_LIB"
+     echo -e "ccafe mpi bin:\n  $CCAFE_MPI_BIN"
diff --git a/biology/mpqc/patches/patch-configure.in b/biology/mpqc/patches/patch-configure.in
new file mode 100644
index 00000000000..9628e922028
--- /dev/null
+++ b/biology/mpqc/patches/patch-configure.in
@@ -0,0 +1,45 @@
+$NetBSD: patch-configure.in,v 1.1.1.1 2013/03/16 12:43:26 asau Exp $
+
+--- configure.in.orig	2006-03-22 18:04:54.000000000 +0000
++++ configure.in
+@@ -488,7 +488,7 @@ AC_ARG_WITH(cca-chem-config,
+   CCA_CHEM_CONFIG=$withval
+   echo Using cca-chem-config: $withval
+ ],[
+-  if test "$components" == "yes"; then
++  if test "$components" = "yes"; then
+     AC_PATH_PROG(CCA_CHEM_CONFIG,cca-chem-config,"not-found")
+   fi
+ ]
+@@ -747,7 +747,7 @@ case $target_cpu in
+      ;;
+ esac
+ 
+-if test X$GXX == Xyes; then
++if test X$GXX = Xyes; then
+   AC_MSG_CHECKING([for C++ cpu tuning flag])
+   AC_LANG_SAVE
+   AC_LANG_CPLUSPLUS
+@@ -759,7 +759,7 @@ if test X$GXX == Xyes; then
+   AC_MSG_RESULT($cxx_tuneflag)
+ fi
+ 
+-if test X$GCC == Xyes; then
++if test X$GCC = Xyes; then
+   AC_MSG_CHECKING([for C cpu tuning flag])
+   CFLAGS_SAV=$CFLAGS
+   CFLAGS="-mtune=$opt_target_cpu $CFLAGS_SAV"
+@@ -1769,10 +1769,10 @@ AC_SUBST(ENABLESHARED)
+ 
+ dnl --------- CCA component configuration ---------
+ 
+-if test $components == "yes"; then
++if test $components = "yes"; then
+ 
+-  if test $HAVE_MPI == "yes" &&
+-     test $HAVE_MPIPP == "no"; then
++  if test $HAVE_MPI = "yes" &&
++     test $HAVE_MPIPP = "no"; then
+     AC_MSG_ERROR([libmpi++ needed for mpi cca components])
+   fi
+ 
diff --git a/biology/mpqc/patches/patch-src_bin_mpqc_ccarunproc b/biology/mpqc/patches/patch-src_bin_mpqc_ccarunproc
new file mode 100644
index 00000000000..6cdf89b4939
--- /dev/null
+++ b/biology/mpqc/patches/patch-src_bin_mpqc_ccarunproc
@@ -0,0 +1,19 @@
+$NetBSD: patch-src_bin_mpqc_ccarunproc,v 1.1.1.1 2013/03/16 12:43:26 asau Exp $
+
+--- src/bin/mpqc/ccarunproc.orig	2005-07-28 17:52:36.000000000 +0000
++++ src/bin/mpqc/ccarunproc
+@@ -1,4 +1,4 @@
+-#!/bin/bash
++#!/bin/sh
+ 
+ # This script starts up a single MPI process.
+ # It is used in parallel environments where it
+@@ -13,7 +13,7 @@ memorygrp=$1 && shift
+ integral=$1 && shift
+ results=$1 && shift
+ 
+-function isodecode() {
++isodecode() {
+   str=$1 && shift
+   echo $str | sed -e 's/%20/ /g' \
+                   -e 's/%3c/</g' -e 's/%3e/>/g' \
diff --git a/biology/mpqc/patches/patch-src_bin_mpqc_mpqcrunproc b/biology/mpqc/patches/patch-src_bin_mpqc_mpqcrunproc
new file mode 100644
index 00000000000..ffd93525d9e
--- /dev/null
+++ b/biology/mpqc/patches/patch-src_bin_mpqc_mpqcrunproc
@@ -0,0 +1,19 @@
+$NetBSD: patch-src_bin_mpqc_mpqcrunproc,v 1.1.1.1 2013/03/16 12:43:26 asau Exp $
+
+--- src/bin/mpqc/mpqcrunproc.orig	2005-03-17 05:56:57.000000000 +0000
++++ src/bin/mpqc/mpqcrunproc
+@@ -1,4 +1,4 @@
+-#!/bin/bash
++#!/bin/sh
+ 
+ # This script starts up a single MPI process.
+ # It is used in parallel environments where it
+@@ -12,7 +12,7 @@ threadgrp=$1 && shift
+ memorygrp=$1 && shift
+ integral=$1 && shift
+ 
+-function isodecode() {
++isodecode() {
+   str=$1 && shift
+   echo $str | sed -e 's/%20/ /g' \
+                   -e 's/%3c/</g' -e 's/%3e/>/g' \