update to 2.2.3

5 files changed, 3053 insertions, 1734 deletions

diff --git a/science/mpqc/Makefile b/science/mpqc/Makefile
index 09c705c9eeb3..9f80d49beba8 100644
--- a/science/mpqc/Makefile
+++ b/science/mpqc/Makefile
@@ -6,13 +6,13 @@
 #
 
 PORTNAME=	mpqc
-PORTVERSION=	2.2.2
+PORTVERSION=	2.2.3
 CATEGORIES=	science parallel
 MASTER_SITES=	${MASTER_SITE_SOURCEFORGE}
 MASTER_SITE_SUBDIR=	mpqc
-DISTFILES=	mpqc-${PORTVERSION}.tar.gz mpqc-val-2.2.0.tar.gz
+DISTFILES=	mpqc-${PORTVERSION}.tar.bz2 mpqc-val-${PORTVERSION}.tar.bz2
 .if !defined(NOPORTDOCS)
-DISTFILES+=	mpqc-man-${PORTVERSION}.tar.gz mpqc-html-${PORTVERSION}.tar.gz
+DISTFILES+=	mpqc-man-${PORTVERSION}.tar.bz2 mpqc-html-${PORTVERSION}.tar.bz2
 .endif
 
 MAINTAINER=	maho@FreeBSD.org
@@ -21,10 +21,8 @@ COMMENT=	The massively parallel quantum computing library and program
 .if defined(WITH_ICC)
 BUILD_DEPENDS+=  ${LOCALBASE}/intel_cc_80/bin/icc:${PORTSDIR}/lang/icc
 .endif
-
 LIB_DEPENDS=	atlas:${PORTSDIR}/math/atlas
 
-USE_BISON=	yes
 GNU_CONFIGURE=	yes
 USE_AUTOCONF_VER=259
 
@@ -63,15 +61,11 @@ MPQC_COMMAND=	${PREFIX}/bin/mpqc
 .if defined(WITH_OPTIMIZED_FLAGS)
 CFLAGS+=	-O2 -ffast-math
 CXXFLAGS+=	-O2 -ffast-math
-.if (${MACHINE_ARCH} == "i386")
-CFLAGS+=	-mfancy-math-387
-CXXFLAGS+=	-mfancy-math-387
-.endif # i386
 .endif
 
 pre-configure:
 	@${ECHO} "You can optimize by setting WITH_OPTIMIZED_FLAGS=yes."
-	@${CP} ${FILESDIR}/FlexLexer.h ${WRKDIR}
+	#${CP} ${FILESDIR}/FlexLexer.h ${WRKDIR}
 do-install:
 	@cd ${WRKSRC} ; ${GMAKE} install
 	@cd ${WRKSRC} ; ${GMAKE} install_devel
diff --git a/science/mpqc/distinfo b/science/mpqc/distinfo
index 00fd0c5c7335..08478585d911 100644
--- a/science/mpqc/distinfo
+++ b/science/mpqc/distinfo
@@ -1,8 +1,8 @@
-MD5 (mpqc-2.2.2.tar.gz) = 7f5d2e6340aa9eba76a6e37cebc5fb9d
-SIZE (mpqc-2.2.2.tar.gz) = 2061755
-MD5 (mpqc-val-2.2.0.tar.gz) = 467e197ab4fdad807c230f9da6d8f3d2
-SIZE (mpqc-val-2.2.0.tar.gz) = 1845129
-MD5 (mpqc-man-2.2.2.tar.gz) = 2602c914c9181e92c77153ce21e13116
-SIZE (mpqc-man-2.2.2.tar.gz) = 166450
-MD5 (mpqc-html-2.2.2.tar.gz) = 31acce5e574e0989f520b82cb78e188f
-SIZE (mpqc-html-2.2.2.tar.gz) = 5453684
+MD5 (mpqc-2.2.3.tar.bz2) = 893a104bc6119058a6fe102803d0bdb9
+SIZE (mpqc-2.2.3.tar.bz2) = 1615558
+MD5 (mpqc-val-2.2.3.tar.bz2) = 4096807cd04559accfd861089777f82a
+SIZE (mpqc-val-2.2.3.tar.bz2) = 929332
+MD5 (mpqc-man-2.2.3.tar.bz2) = 4048680d977d336096e57f7721f21c0e
+SIZE (mpqc-man-2.2.3.tar.bz2) = 105008
+MD5 (mpqc-html-2.2.3.tar.bz2) = 2ccc566eed507244160f765342fd4681
+SIZE (mpqc-html-2.2.3.tar.bz2) = 2756615
diff --git a/science/mpqc/files/FlexLexer.h b/science/mpqc/files/FlexLexer.h
deleted file mode 100644
index 07777079406b..000000000000
--- a/science/mpqc/files/FlexLexer.h
+++ /dev/null
@@ -1,186 +0,0 @@
-// $Header: /home/daffy/u0/vern/flex/RCS/FlexLexer.h,v 1.19 96/05/25 20:43:02 vern Exp $
-// $FreeBSD: /tmp/pcvs/ports/science/mpqc/files/Attic/FlexLexer.h,v 1.1 2004-08-16 11:04:04 maho Exp $
-
-// FlexLexer.h -- define interfaces for lexical analyzer classes generated
-//		  by flex
-
-// Copyright (c) 1993 The Regents of the University of California.
-// All rights reserved.
-//
-// This code is derived from software contributed to Berkeley by
-// Kent Williams and Tom Epperly.
-//
-// Redistribution and use in source and binary forms are permitted provided
-// that: (1) source distributions retain this entire copyright notice and
-// comment, and (2) distributions including binaries display the following
-// acknowledgement:  ``This product includes software developed by the
-// University of California, Berkeley and its contributors'' in the
-// documentation or other materials provided with the distribution and in
-// all advertising materials mentioning features or use of this software.
-// Neither the name of the University nor the names of its contributors may
-// be used to endorse or promote products derived from this software without
-// specific prior written permission.
-// THIS SOFTWARE IS PROVIDED ``AS IS'' AND WITHOUT ANY EXPRESS OR IMPLIED
-// WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
-// MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-
-// This file defines FlexLexer, an abstract class which specifies the
-// external interface provided to flex C++ lexer objects, and yyFlexLexer,
-// which defines a particular lexer class.
-//
-// If you want to create multiple lexer classes, you use the -P flag
-// to rename each yyFlexLexer to some other xxFlexLexer.  You then
-// include <FlexLexer.h> in your other sources once per lexer class:
-//
-//	#undef yyFlexLexer
-//	#define yyFlexLexer xxFlexLexer
-//	#include <FlexLexer.h>
-//
-//	#undef yyFlexLexer
-//	#define yyFlexLexer zzFlexLexer
-//	#include <FlexLexer.h>
-//	...
-
-#ifndef __FLEX_LEXER_H
-// Never included before - need to define base class.
-#define __FLEX_LEXER_H
-#include <iostream.h>
-
-extern "C++" {
-
-struct yy_buffer_state;
-typedef int yy_state_type;
-
-class FlexLexer {
-public:
-	virtual ~FlexLexer()	{ }
-
-	const char* YYText()	{ return yytext; }
-	int YYLeng()		{ return yyleng; }
-
-	virtual void
-		yy_switch_to_buffer( struct yy_buffer_state* new_buffer ) = 0;
-	virtual struct yy_buffer_state*
-		yy_create_buffer( istream* s, int size ) = 0;
-	virtual void yy_delete_buffer( struct yy_buffer_state* b ) = 0;
-	virtual void yyrestart( istream* s ) = 0;
-
-	virtual int yylex() = 0;
-
-	// Call yylex with new input/output sources.
-	int yylex( istream* new_in, ostream* new_out = 0 )
-		{
-		switch_streams( new_in, new_out );
-		return yylex();
-		}
-
-	// Switch to new input/output streams.  A nil stream pointer
-	// indicates "keep the current one".
-	virtual void switch_streams( istream* new_in = 0,
-					ostream* new_out = 0 ) = 0;
-
-	int lineno() const		{ return yylineno; }
-
-	int debug() const		{ return yy_flex_debug; }
-	void set_debug( int flag )	{ yy_flex_debug = flag; }
-
-protected:
-	char* yytext;
-	int yyleng;
-	int yylineno;		// only maintained if you use %option yylineno
-	int yy_flex_debug;	// only has effect with -d or "%option debug"
-};
-
-}
-#endif
-
-#if defined(yyFlexLexer) || ! defined(yyFlexLexerOnce)
-// Either this is the first time through (yyFlexLexerOnce not defined),
-// or this is a repeated include to define a different flavor of
-// yyFlexLexer, as discussed in the flex man page.
-#define yyFlexLexerOnce
-
-class yyFlexLexer : public FlexLexer {
-public:
-	// arg_yyin and arg_yyout default to the cin and cout, but we
-	// only make that assignment when initializing in yylex().
-	yyFlexLexer( istream* arg_yyin = 0, ostream* arg_yyout = 0 );
-
-	virtual ~yyFlexLexer();
-
-	void yy_switch_to_buffer( struct yy_buffer_state* new_buffer );
-	struct yy_buffer_state* yy_create_buffer( istream* s, int size );
-	void yy_delete_buffer( struct yy_buffer_state* b );
-	void yyrestart( istream* s );
-
-	virtual int yylex();
-	virtual void switch_streams( istream* new_in, ostream* new_out );
-
-protected:
-	virtual int LexerInput( char* buf, int max_size );
-	virtual void LexerOutput( const char* buf, int size );
-	virtual void LexerError( const char* msg );
-
-	void yyunput( int c, char* buf_ptr );
-	int yyinput();
-
-	void yy_load_buffer_state();
-	void yy_init_buffer( struct yy_buffer_state* b, istream* s );
-	void yy_flush_buffer( struct yy_buffer_state* b );
-
-	int yy_start_stack_ptr;
-	int yy_start_stack_depth;
-	int* yy_start_stack;
-
-	void yy_push_state( int new_state );
-	void yy_pop_state();
-	int yy_top_state();
-
-	yy_state_type yy_get_previous_state();
-	yy_state_type yy_try_NUL_trans( yy_state_type current_state );
-	int yy_get_next_buffer();
-
-	istream* yyin;	// input source for default LexerInput
-	ostream* yyout;	// output sink for default LexerOutput
-
-	struct yy_buffer_state* yy_current_buffer;
-
-	// yy_hold_char holds the character lost when yytext is formed.
-	char yy_hold_char;
-
-	// Number of characters read into yy_ch_buf.
-	int yy_n_chars;
-
-	// Points to current character in buffer.
-	char* yy_c_buf_p;
-
-	int yy_init;		// whether we need to initialize
-	int yy_start;		// start state number
-
-	// Flag which is used to allow yywrap()'s to do buffer switches
-	// instead of setting up a fresh yyin.  A bit of a hack ...
-	int yy_did_buffer_switch_on_eof;
-
-	// The following are not always needed, but may be depending
-	// on use of certain flex features (like REJECT or yymore()).
-
-	yy_state_type yy_last_accepting_state;
-	char* yy_last_accepting_cpos;
-
-	yy_state_type* yy_state_buf;
-	yy_state_type* yy_state_ptr;
-
-	char* yy_full_match;
-	int* yy_full_state;
-	int yy_full_lp;
-
-	int yy_lp;
-	int yy_looking_for_trail_begin;
-
-	int yy_more_flag;
-	int yy_more_len;
-	int yy_more_offset;
-	int yy_prev_more_offset;
-};
-
-#endif
diff --git a/science/mpqc/files/manpages b/science/mpqc/files/manpages
index ecd8adbad5e5..5b97cf5eda53 100644
--- a/science/mpqc/files/manpages
+++ b/science/mpqc/files/manpages
@@ -1,24 +1,4 @@
 MAN3= \
-class.3 \
-compile.3 \
-develop.3 \
-download.3 \
-group.3 \
-keyval.3 \
-molrender.3 \
-mpqc.3 \
-mpqccomp.3 \
-mpqcinp.3 \
-mpqclic.3 \
-mpqcoo.3 \
-mpqcover.3 \
-mpqcpsi.3 \
-mpqcrun.3 \
-mpqcsimp.3 \
-mpqcval.3 \
-mpqcwar.3 \
-overview.3 \
-ref.3 \
 sc_ARMCIMemoryGrp.3 \
 sc_AccResult.3 \
 sc_AccResultInfo.3 \
@@ -36,6 +16,7 @@ sc_Becke88XFunctional.3 \
 sc_BeckeIntegrationWeight.3 \
 sc_BendSimpleCo.3 \
 sc_CLHF.3 \
+sc_CLKS.3 \
 sc_CLSCF.3 \
 sc_CartMolecularCoor.3 \
 sc_CartesianIter.3 \
@@ -74,6 +55,7 @@ sc_GaussianBasisSet.3 \
 sc_GaussianBasisSet_ValueData.3 \
 sc_GaussianShell.3 \
 sc_HSOSHF.3 \
+sc_HSOSKS.3 \
 sc_HSOSSCF.3 \
 sc_HessianUpdate.3 \
 sc_ISphericalTransform.3 \
@@ -264,6 +246,8 @@ sc_TwoBodyDerivIntV3.3 \
 sc_TwoBodyInt.3 \
 sc_TwoBodyIntCints.3 \
 sc_TwoBodyIntV3.3 \
+sc_UHF.3 \
+sc_UKS.3 \
 sc_UnionShape.3 \
 sc_Units.3 \
 sc_UnrestrictedSCF.3 \
@@ -285,10 +269,3 @@ sc_canonical_abcd.3 \
 sc_intMessageGrp.3 \
 sc_mPW91XFunctional.3 \
 sc_scprintf.3 \
-scls.3 \
-scmat.3 \
-scpr.3 \
-srctree.3 \
-state.3 \
-symmetry.3
-
diff --git a/science/mpqc/pkg-plist b/science/mpqc/pkg-plist
index 6ac2de23384b..52761ac72224 100644
--- a/science/mpqc/pkg-plist
+++ b/science/mpqc/pkg-plist
@@ -52,9 +52,11 @@ include/util/misc/compute.h
 include/util/misc/exenv.h
 include/util/misc/formio.h
 include/util/misc/ieee.h
+include/util/misc/math.h
 include/util/misc/newstring.h
 include/util/misc/regtime.h
 include/util/misc/scint.h
+include/util/misc/string.h
 include/util/misc/timer.h
 include/util/misc/units.h
 include/util/keyval/LIBS.h
@@ -393,1586 +395,3112 @@ share/mpqc/%%VERSION%%/perl/QCParse.pm
 share/mpqc/%%VERSION%%/perl/QCResult.pm
 share/mpqc/%%VERSION%%/atominfo.kv
 share/mpqc/%%VERSION%%/magic
-%%PORTDOCS%%%%DOCSDIR%%/12_2distsh_8h-source.html
-%%PORTDOCS%%%%DOCSDIR%%/GetLongOpt_8h-source.html
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-%%PORTDOCS%%%%DOCSDIR%%/accum_8h-source.html
-%%PORTDOCS%%%%DOCSDIR%%/algebra3_8h-source.html
-%%PORTDOCS%%%%DOCSDIR%%/animate_8h-source.html
-%%PORTDOCS%%%%DOCSDIR%%/annotated.html
-%%PORTDOCS%%%%DOCSDIR%%/appearance_8h-source.html
-%%PORTDOCS%%%%DOCSDIR%%/ar2tem_8h-source.html
-%%PORTDOCS%%%%DOCSDIR%%/artem_8h-source.html
-%%PORTDOCS%%%%DOCSDIR%%/atominfo_8h-source.html
-%%PORTDOCS%%%%DOCSDIR%%/autovec_8h-source.html
-%%PORTDOCS%%%%DOCSDIR%%/avlmap_8h-source.html
-%%PORTDOCS%%%%DOCSDIR%%/avlset_8h-source.html
-%%PORTDOCS%%%%DOCSDIR%%/basis_2obint_8h-source.html
-%%PORTDOCS%%%%DOCSDIR%%/basis_2tbint_8h-source.html
-%%PORTDOCS%%%%DOCSDIR%%/basis_8h-source.html
-%%PORTDOCS%%%%DOCSDIR%%/bem_8h-source.html
-%%PORTDOCS%%%%DOCSDIR%%/bin_2molrender_2LIBS_8h-source.html
-%%PORTDOCS%%%%DOCSDIR%%/bin_2mpqc_2LIBS_8h-source.html
-%%PORTDOCS%%%%DOCSDIR%%/bin_2orbixme_2LIBS_8h-source.html
-%%PORTDOCS%%%%DOCSDIR%%/bin_2scls_2LIBS_8h-source.html
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-%%PORTDOCS%%%%DOCSDIR%%/chemistry_2molecule_2linkage_8h-source.html
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 share/mpqc/ref/basis1_beh2scf321gd2h.in
 share/mpqc/ref/basis1_beh2scf321gd2h.out
@@ -4218,6 +5746,9 @@ share/mpqc/ref/input_ksh2o.qci
 share/mpqc/ref/input_ksh2oco.in
 share/mpqc/ref/input_ksh2oco.out
 share/mpqc/ref/input_ksh2oco.qci
+share/mpqc/ref/input_mp2h2o.in
+share/mpqc/ref/input_mp2h2o.out
+share/mpqc/ref/input_mp2h2o.qci
 share/mpqc/ref/input_mp2r12ah2o.in
 share/mpqc/ref/input_mp2r12ah2o.out
 share/mpqc/ref/input_mp2r12ah2o.qci
@@ -4236,6 +5767,9 @@ share/mpqc/ref/input_uhfch2opt.qci
 share/mpqc/ref/input_uksch2.in
 share/mpqc/ref/input_uksch2.out
 share/mpqc/ref/input_uksch2.qci
+share/mpqc/ref/input_zapt2ch2.in
+share/mpqc/ref/input_zapt2ch2.out
+share/mpqc/ref/input_zapt2ch2.qci
 share/mpqc/ref/mbpt_mp2mem.in
 share/mpqc/ref/mbpt_mp2mem.out
 share/mpqc/ref/mbpt_mp2mem.qci