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.

4 files changed, 150 insertions, 0 deletions

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' \