Index: ThirdParty/mpqc_open/src/bin/Makefile
===================================================================
--- ThirdParty/mpqc_open/src/bin/Makefile	(revision 22d43161cc7d52aaecc31906f73b0aa9a0329126)
+++ 	(revision )
@@ -1,10 +1,0 @@
-TOPDIR=../..
-ifndef SRCDIR
-  SRCDIR=$(shell pwd)
-endif
-
-include $(SRCDIR)/$(TOPDIR)/lib/GlobalMakefile
-
-SUBDIRS = mpqc scpr scls molrender
-
-include $(SRCDIR)/$(TOPDIR)/lib/GlobalSubDirs
Index: ThirdParty/mpqc_open/src/bin/molrender/LIBS.h
===================================================================
--- ThirdParty/mpqc_open/src/bin/molrender/LIBS.h	(revision 22d43161cc7d52aaecc31906f73b0aa9a0329126)
+++ 	(revision )
@@ -1,8 +1,0 @@
-#include <util/options/LIBS.h>
-#include <util/misc/LIBS.h>
-#include <util/keyval/LIBS.h>
-#include <math/isosurf/LIBS.h>
-#include <chemistry/molecule/LIBS.h>
-#ifdef HAVE_CHEMISTRY_CCA
-  #include <util/misc/LIBS.h>
-#endif
Index: ThirdParty/mpqc_open/src/bin/molrender/Makefile
===================================================================
--- ThirdParty/mpqc_open/src/bin/molrender/Makefile	(revision 22d43161cc7d52aaecc31906f73b0aa9a0329126)
+++ 	(revision )
@@ -1,53 +1,0 @@
-TOPDIR=../../..
-ifndef SRCDIR
-  SRCDIR=$(shell pwd)
-endif
-
-include $(SRCDIR)/$(TOPDIR)/lib/GlobalMakefile
-include $(TOPDIR)/lib/Makedirlist
-INCLUDE += -I. -I$(SRCDIR)
-CXXINCLUDE += -I. -I$(SRCDIR)
-
-TARGET_TO_MAKE = molrender
-
-CXXSRC = main.cc
-CSRC =
-INC =
-
-DEPENDINCLUDE = $(INC)
-
-BINOBJ = $(CXXSRC:%.cc=%.o) $(CSRC:%.c=%.o)
-
-DISTFILES = $(CXXSRC) $(CSRC) $(INC) Makefile LIBS.h molrender.in
-
-default:: molrender
-
-ifeq ($(HAVE_SC_SRC_LIB_CHEMISTRY_CCA),yes)
-  DEFINES += -DHAVE_CHEMISTRY_CCA
-endif
-
-LIBS := $(shell $(LISTLIBS) $(INCLUDE) $(DEFINES) $(SRCDIR)/LIBS.h)
-
-include $(SRCDIR)/$(TOPDIR)/lib/GlobalRules
-
-molrender: $(BINOBJ) $(LIBS)
-	$(LTLINK) $(LD) $(LDFLAGS) -o $@ $^ $(SYSLIBS) $(LTLINKBINOPTS)
-
-install:: molrender
-	$(INSTALL) $(INSTALLDIROPT) $(installroot)$(bindir)
-	$(LTINST) $(INSTALL) $(INSTALLBINOPT) $< $(installroot)$(bindir)
-	cd $(TOPDIR); CONFIG_FILES=src/bin/molrender/tkmolrender CONFIG_HEADERS= ./config.status
-	$(INSTALL) $(INSTALLBINOPT) tkmolrender $(installroot)$(bindir)
-	/bin/rm -f tkmolrender
-
-clean::
-	/bin/rm -f molrender
-
-distclean::
-	/bin/rm -f molrender
-
-$(BINOBJ:.o=.d): $(DEPENDINCLUDE)
-ifneq ($(DODEPEND),no)
-include $(BINOBJ:.o=.d)
-endif
-
Index: ThirdParty/mpqc_open/src/bin/molrender/main.cc
===================================================================
--- ThirdParty/mpqc_open/src/bin/molrender/main.cc	(revision 22d43161cc7d52aaecc31906f73b0aa9a0329126)
+++ 	(revision )
@@ -1,152 +1,0 @@
-
-#include <stdio.h>
-#include <util/keyval/keyval.h>
-#include <util/render/render.h>
-#include <util/render/oogl.h>
-#include <util/render/object.h>
-#include <math/isosurf/surf.h>
-#include <chemistry/molecule/molecule.h>
-#include <chemistry/molecule/molrender.h>
-#include <chemistry/molecule/molshape.h>
-
-#include <util/state/linkage.h>
-
-using namespace sc;
-
-int
-main(int argc, char** argv)
-{
-  int i;
-  const char* model = "stick";
-  const char* keyword = "molecule";
-  const char* inputfile = "molrender.in";
-  int level = 3;
-  enum InputType { PDB, KEYVAL } input = KEYVAL;
-  const char* render = 0;
-  int quiet = 0;
-
-  for (i=1; i<argc; i++) {
-      if (!strcmp(argv[i], "-model")) {
-          i++;
-          model = argv[i];
-        }
-      else if (!strcmp(argv[i], "-quiet")) {
-          quiet = 1;
-        }
-      else if (!strcmp(argv[i], "-render")) {
-          i++;
-          render = argv[i];
-        }
-      else if (!strcmp(argv[i], "-keyword")) {
-          i++;
-          keyword = argv[i];
-        }
-      else if (!strcmp(argv[i], "-pdb")) {
-          i++;
-          input = PDB;
-          inputfile = argv[i];
-        }
-      else if (!strcmp(argv[i], "-keyval")) {
-          i++;
-          input = KEYVAL;
-          inputfile = argv[i];
-        }
-      else if (!strcmp(argv[i], "-level")) {
-          i++;
-          level = atoi(argv[i]);
-        }
-      else {
-          fprintf(stderr,"%s: unknown option: \"%s\"\n", argv[0], argv[i]);
-          abort();
-        }
-    }
-
-  // Find the molecule.
-  Ref<Molecule> mol;
-  if (input == PDB) {
-      Ref<AssignedKeyVal> keyval = new AssignedKeyVal();
-      keyval->assign("pdb_file", inputfile);
-      mol = new Molecule(keyval.pointer());
-    }
-  else {
-      Ref<KeyVal> keyval = new ParsedKeyVal(inputfile);
-      mol = new Molecule(new PrefixKeyVal(keyval, keyword));
-    }
-
-  // Set up the rendered molecule object.
-  Ref<AssignedKeyVal> tmpkv = new AssignedKeyVal();
-  Ref<AssignedKeyVal> keyval = new AssignedKeyVal();
-
-  keyval->assign("molecule", mol.pointer());
-  keyval->assign("model", model);
-
-  Ref<DescribedClass> atominfo = new AtomInfo(tmpkv.pointer());
-  keyval->assign("atominfo", atominfo);
-  tmpkv->clear();
-
-  Ref<RenderedObject> molobject;
-  if (!strcmp(model,"stick")) {
-      molobject = new RenderedStickMolecule(keyval.pointer());
-    }
-  else if (!strcmp(model,"ball")) {
-      molobject = new RenderedBallMolecule(keyval.pointer());
-    }
-  else if (!strcmp(model,"connolly")) {
-      tmpkv->assign("molecule", mol.pointer());
-      tmpkv->assign("atominfo", atominfo);
-      Ref<DescribedClass> volume = new ConnollyShape(tmpkv.pointer());
-      tmpkv->clear();
-      tmpkv->assignboolean("verbose", !quiet);
-      Ref<DescribedClass> trisurf = new TriangulatedSurface(tmpkv.pointer());
-      tmpkv->clear();
-      tmpkv->assign("surface", trisurf);
-      tmpkv->assign("volume", volume);
-      tmpkv->assign("resolution", 1.0);
-      tmpkv->assignboolean("remove_short_edges", 0);
-      tmpkv->assignboolean("remove_slender_edges", 0);
-      Ref<DescribedClass> surface
-          = new TriangulatedImplicitSurface(tmpkv.pointer());
-      tmpkv->clear();
-      keyval->assign("surface", surface);
-      molobject = new RenderedMolecularSurface(keyval.pointer());
-    }
-  else {
-      fprintf(stderr,"%s: unknown model \"%s\"\n", argv[0], model);
-      abort();
-    }
-
-  Ref<RenderedObjectSet> object;
-
-  if (render) {
-      object = new RenderedObjectSet;
-      object->add(molobject);
-      Ref<Appearance> appearance = new Appearance;
-      appearance->level().set(level);
-      object->appearance(appearance);
-      if (object.null()) {
-          fprintf(stderr,"%s: got a null object to render\n",argv[0]);
-          abort();
-        }
-
-      // Set up the renderer.
-      Ref<Render> renderer;
-      if (!strcmp("oogl", render)) {
-          renderer = new OOGLRender;
-        }
-      else {
-          fprintf(stderr,"%s: unknown renderer: \"%s\"\n", argv[0], render);
-        }
-
-      // Render the object.
-      renderer->render(object.pointer());
-    }
-
-  if (!quiet) {
-      ConnollyShape::print_counts();
-      CS2Sphere::print_counts();
-    }
-
-  fflush(stdout);
-  fflush(stderr);
-  return 0;
-}
Index: ThirdParty/mpqc_open/src/bin/molrender/molrender.dox
===================================================================
--- ThirdParty/mpqc_open/src/bin/molrender/molrender.dox	(revision 22d43161cc7d52aaecc31906f73b0aa9a0329126)
+++ 	(revision )
@@ -1,47 +1,0 @@
-
-/** \page molrender
-
-The molrender program reads a molecule from an input file and can render it
-in a variety of ways.  The output is an OOGL file that the <a
-href="http://www.geom.umn.edu/software/download/geomview.html">Geomview</a>
-program can read and display.
-
-\if html
-<h1>Compiling molrender</h1>
-
- molrender is distributed with the SC Toolkit.  molrender will automatically
-be compiled when SC is compiled.  See \ref compile
-for more information.
-\endif
-
-<h1>Running molrender</h1>
-
-If you have wish installed, tkmolrender script can be run to bring up a
-simple GUI to let you set up the molrender options.  Otherwise, molrender
-can be run directly and takes the following command line options:
-
-<dl>
- <dt><tt>-model</tt><dd>Must be followed by one of ball, stick, or connolly
- <dt><tt>-render</tt><dd>Must be followed by the argument oogl
- <dt><tt>-pdb</tt><dd>Indicates that the input is a PDB file
- <dt><tt>-keyval</tt><dd>Indicates that the input is a KeyVal input
- <dt><tt>-keyword</tt><dd>Must be followed by keyword to read in a KeyVal input
- <dt><tt>-level</tt><dd>Must be Followed by an integer which is the sphere
-   subdivision level
-</dl>
-
-<h1>License</h1>
-
-molrender is open-source software; you can redistribute it and/or modify it
-under the terms of the GNU General Public License as published by the Free
-Software Foundation; either version 2 of the License, or (at your option)
-any later version.
-
-<h1>Warranty</h1>
-
-molrender is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
-details.
-
-*/
Index: ThirdParty/mpqc_open/src/bin/molrender/molrender.in
===================================================================
--- ThirdParty/mpqc_open/src/bin/molrender/molrender.in	(revision 22d43161cc7d52aaecc31906f73b0aa9a0329126)
+++ 	(revision )
@@ -1,24 +1,0 @@
-% Emacs should use -*- keyval -*- mode.
-
-molecule<Molecule>: (
-    symmetry=c2v
-    {atoms geometry} = {
-      H  [   1.5  0.0  -0.3 ]
-      O  [   0.0  0.0   1.0 ]
-     }
-  )
-
-xmolecule<Molecule>: (
-    {atoms geometry} = {
-      H  [   0.0  0.0   1.0 ]
-      H  [   0.0  0.0  -1.0 ]
-     }
-  )
-
-ymolecule<Molecule>: (
-    {atoms geometry} = {
-      H  [   0.0  1.0   0.0 ]
-      H  [   0.866025403  -0.5 0.0 ]
-      H  [  -0.866025403  -0.5 0.0 ]
-     }
-  )
Index: ThirdParty/mpqc_open/src/bin/molrender/tkmolrender.in
===================================================================
--- ThirdParty/mpqc_open/src/bin/molrender/tkmolrender.in	(revision 22d43161cc7d52aaecc31906f73b0aa9a0329126)
+++ 	(revision )
@@ -1,87 +1,0 @@
-#!@WISH@
-
-wm title . "MolRender"
-
-set level 3
-set model "ball"
-set inputoption "-keyval"
-set inputfile "molrender.in"
-set keyvalkey "molecule"
-
-proc make_inputoption { w } {
-  frame $w.frame -borderwidth 10
-  label $w.label -text "Input File Type"
-  pack $w.label $w.frame -side top -pady 2
-  radiobutton $w.frame.pdb -text "PDB File" -variable inputoption -value "-pdb" -relief flat
-  radiobutton $w.frame.keyval -text "KeyVal File" -variable inputoption -value "-keyval" -relief flat
-  pack $w.frame.pdb $w.frame.keyval -side top -pady 2 -expand yes -fill both
-}
-
-proc make_model { w } {
-  frame $w.frame -borderwidth 10
-  label $w.label -text "Model"
-  pack $w.label $w.frame -side top -pady 2
-  radiobutton $w.frame.ball -text "Ball" -variable model -value "ball" -relief flat
-  radiobutton $w.frame.stick -text "Stick" -variable model -value "stick" -relief flat
-  radiobutton $w.frame.connolly -text "Connolly" -variable model -value "connolly" -relief flat
-  pack $w.frame.ball $w.frame.stick $w.frame.connolly -side top -pady 2 -expand yes -fill both
-}
-
-proc make_level { w } {
-  frame $w.frame -borderwidth 10
-  label $w.label -text "Sphere Subdivision Level"
-  pack $w.label $w.frame -side top -pady 2
-  radiobutton $w.frame.a -text "1" -variable level -value 1 -relief flat
-  radiobutton $w.frame.b -text "2" -variable level -value 2 -relief flat
-  radiobutton $w.frame.c -text "3" -variable level -value 3 -relief flat
-  radiobutton $w.frame.d -text "4" -variable level -value 4 -relief flat
-  radiobutton $w.frame.e -text "5" -variable level -value 5 -relief flat
-  pack $w.frame.a $w.frame.b $w.frame.c $w.frame.d $w.frame.e -side top -pady 2 -expand yes -fill both
-}
-
-proc render {} {
-  global model inputoption inputfile level keyvalkey
-  #puts stdout "molrender -quiet -model $model -keyword $keyvalkey $inputoption $inputfile -level $level"
-  set result [exec @prefix@/bin/molrender -quiet -render oogl -model $model -keyword $keyvalkey $inputoption $inputfile -level $level]
-  #puts stdout "(geometry $model $result)"
-  flush stdout
-}
-
-proc clear {} {
-  #puts stdout "(geometry ball {})"
-  #puts stdout "(geometry stick {})"
-  #puts stdout "(geometry connolly {})"
-  #flush stdout
-}
-
-proc done {} {
-  destroy .
-}
-
-frame .inputarea
-frame .inputarea.inputoption
-frame .inputarea.model
-frame .inputarea.level
-make_inputoption .inputarea.inputoption
-make_model .inputarea.model
-make_level .inputarea.level
-
-frame .inputfile
-label .inputfile.label -text "Input File:"
-entry .inputfile.entry -relief sunken -textvariable inputfile
-pack .inputfile.label .inputfile.entry -side left -expand yes -fill both
-
-frame .keyvalkey
-label .keyvalkey.label -text "Keyword:"
-entry .keyvalkey.entry -relief sunken -textvariable keyvalkey
-pack .keyvalkey.label .keyvalkey.entry -side left -expand yes -fill both
-
-frame .buttons
-button .buttons.render -text "Render" -command render
-button .buttons.clear -text "Clear" -command clear
-button .buttons.done -text "Done" -command done
-pack .buttons.render .buttons.clear .buttons.done -side left -padx 2 -expand yes -fill both
-pack .inputarea.inputoption .inputarea.model .inputarea.level -side left -padx 2 -expand yes -fill both
-pack .inputarea .inputfile .keyvalkey .buttons -side top -pady 2
-
-clear
Index: ThirdParty/mpqc_open/src/bin/mpqc/Makefile
===================================================================
--- ThirdParty/mpqc_open/src/bin/mpqc/Makefile	(revision 22d43161cc7d52aaecc31906f73b0aa9a0329126)
+++ 	(revision )
@@ -1,213 +1,0 @@
-TOPDIR=../../..
-ifndef SRCDIR
-  BUILDING_IN_SRCDIR=yes
-  SRCDIR=$(shell pwd)
-endif
-BUILDDIR=$(shell pwd)
-
-LOCALMAKEFILE_OPTIONAL = yes
-include $(SRCDIR)/$(TOPDIR)/lib/GlobalMakefile
-
-ifeq ($(LOCALMAKEFILE_FOUND),yes)
-
-include $(TOPDIR)/lib/Makedirlist
-INCLUDE += -I. -I$(SRCDIR)
-CXXINCLUDE += -I. -I$(SRCDIR)
-
-TARGET_TO_MAKE = mpqc
-
-CXXSRC = mpqc.cc mpqcin.cc
-GENCXXSRC = parse.cc scan.cc
-CSRC =
-INC =
-GENINC = parse.h
-
-DEPENDINCLUDE = $(INC)
-
-BINOBJ = $(CXXSRC:%.cc=%.$(OBJSUF)) $(GENCXXSRC:%.cc=%.$(OBJSUF)) $(CSRC:%.c=%.$(OBJSUF))
-
-DISTFILES = $(CXXSRC) $(CSRC) $(INC) Makefile LIBS.h
-
-default:: mpqc
-
-DEFINES += \
-	-DHAVE_JOBMARKET -I$(SRCDIR)/$(TOPDIR)/../JobMarket/src -I$(TOPDIR)/../JobMarket -I$(SRCDIR)/$(TOPDIR)/../../src -I$(SRCDIR)/$(TOPDIR)/../LinearAlgebra/src $(BOOST_SYSTEM_CFLAGS)\
-	-DHAVE_MPQCDATA -I$(TOPDIR)/../../src
-
-XDEF =
-XLIBS = -L$(TOPDIR)/../JobMarket/src/JobMarket/.libs -Wl,-rpath,$(BUILDDIR)/$(TOPDIR)/../JobMarket/src/JobMarket/.libs -lJobMarketPoolWorker -lJobMarket -L$(TOPDIR)/../../src/.libs -Wl,-rpath,$(BUILDDIR)/$(TOPDIR)/../../src/.libs -lMolecuilderJobs -lMolecuilderFragmentationSummation $(BOOST_SYSTEM_LDFLAGS) -lboost_serialization
-ifeq ($(HAVE_SC_SRC_LIB_CHEMISTRY_QC_PSI),yes)
-XDEF += -DHAVE_CHEMISTRY_QC_PSI
-endif
-ifeq ($(HAVE_SC_SRC_LIB_CHEMISTRY_QC_CC),yes)
-XDEF += -DHAVE_CHEMISTRY_QC_CC
-endif
-ifeq ($(HAVE_SC_SRC_LIB_CHEMISTRY_QC_CINTS),yes)
- ifeq ($(HAVE_SC_SRC_LIB_CHEMISTRY_QC_MBPTR12),yes)
- XDEF += -DHAVE_CHEMISTRY_QC_MBPTR12
- endif
-XDEF += -DHAVE_CHEMISTRY_QC_CINTS
-endif
-
-ifeq ($(HAVE_LIBINT),yes)
-  XLIBS += -lint
-endif
-ifeq ($(HAVE_LIBR12),yes)
-  XLIBS += -lr12
-endif
-ifeq ($(HAVE_LIBDERIV),yes)
-  XLIBS += -lderiv
-endif
-ifeq ($(HAVE_SC_SRC_LIB_CHEMISTRY_CCA),yes)
-  ifeq ($(ENABLESHARED),yes)
-    LTLINKBINOPTS += -R$(CCAFE_LIB) -R$(CCA_CHEM_LIB)
-  else
-    XLIBS += -L$(CCA_CHEM_LIB) -L$(CCAFE_LIB) -L$(CCA_SPEC_BABEL_LIB) -L$(BABEL_LIB) \
-             -lccachem_cxx_server -lccachem_cxx_client -lccafeCore -lcca -lsidl -lxml2 -lz
-  endif
-  DEFINES += -DHAVE_CHEMISTRY_CCA -DCCA_PATH=\"$(libdir)/cca\"
-  CPPFLAGS += -I../../lib/chemistry/cca
-endif
-
-LIBS := $(shell $(LISTLIBS) $(INCLUDE) $(DEFINES) $(XDEF) $(SRCDIR)/LIBS.h)
-
-#################################################################
-
-default:: $(DEPENDINCLUDE)
-
-include $(SRCDIR)/$(TOPDIR)/lib/GlobalRules
-
-mpqc: $(BINOBJ) $(LIBS)
-	echo "$(LISTLIBS) $(INCLUDE) $(DEFINES) $(XDEF) $(SRCDIR)/LIBS.h"
-	$(LTLINK) $(LD) $(LDFLAGS) -o $@ $^ $(XLIBS) $(SYSLIBS) $(LTLINKBINOPTS)
-
-$(TOPDIR)/lib/libmpqc.a: $(BINOBJ)
-	/bin/rm -f $@
-	$(AR) $(ARFLAGS) $@ $^
-	$(RANLIB) $@
-
-$(TOPDIR)/lib/libmpqc.la: $(BINOBJ)
-	$(LTLINK) $(CXX) -o $@ $^ $(LTLINKLIBOPTS)
-
-install_devel:: $(TOPDIR)/lib/libmpqc.$(LIBSUF)
-	$(INSTALL) $(INSTALLDIROPT) $(installroot)$(libdir)
-	$(LTINST) $(INSTALL) $(INSTALLLIBOPT) $< $(installroot)$(libdir)
-
-install:: mpqc
-	$(INSTALL) $(INSTALLDIROPT) $(installroot)$(bindir)
-	$(LTINST) $(INSTALL) $(INSTALLBINOPT) $< $(installroot)$(bindir)
-	$(INSTALL) $(INSTALLSCRIPTOPT) mpqcrun $(installroot)$(bindir)/mpqcrun
-	$(INSTALL) $(INSTALLSCRIPTOPT) ccarun $(installroot)$(bindir)/ccarun
-	$(INSTALL) $(INSTALLDIROPT) $(installroot)$(scdatadir)
-	$(INSTALL) $(INSTALLSCRIPTOPT) $(SRCDIR)/mpqcrunproc $(installroot)$(scdatadir)/mpqcrunproc
-	$(INSTALL) $(INSTALLSCRIPTOPT) $(SRCDIR)/ccarunproc $(installroot)$(scdatadir)/ccarunproc
-
-install::
-	/bin/rm -f $(installroot)$(bindir)/chkmpqcout
-	sed "s+exec perl+exec perl -I$(scdatadir)/perl+" \
-		< $(SRCDIR)/validate/checkout.pl \
-		> $(installroot)$(bindir)/chkmpqcout
-	chmod 555 $(installroot)$(bindir)/chkmpqcout
-
-clean::
-	/bin/rm -f mpqc
-	/bin/rm -f parse.tmp*
-
-distclean::
-	/bin/rm -f mpqc
-	/bin/rm -f parse.tmp*
-	/bin/rm -f $(GENCXXSRC) $(GENINC) parse.output
-	/bin/rm -f mpqcrun
-
-ifneq ($(BUILDING_IN_SRCDIR),yes)
-ifeq ($(wildcard parse.cc),parse.cc)
-$(error "parse.cc exists in an object directory.  This is now longer necessary or allowed.  Delete the file to continue.")
-endif
-ifeq ($(wildcard scan.cc),scan.cc)
-$(error "scan.cc exists in an object directory.  This is now longer necessary or allowed.  Delete the file to continue.")
-endif
-ifeq ($(wildcard parse.h),parse.h)
-$(error "parse.h exists in an object directory.  This is now longer necessary or allowed.  Delete the file to continue.")
-endif
-endif
-
-$(SRCDIR)/parse.cc: $(SRCDIR)/parse.yy
-	@echo WARNING: The file $@ is out of date.
-	@echo It can be built by running \"make parser DODEPEND=no\" in the source directory.
-	@echo You may also get the message on files checked out of CVS, in which case you can touch $@ to stop getting this message.
-
-$(SRCDIR)/parse.h: $(SRCDIR)/parse.yy
-	@echo WARNING: The file $@ is out of date.
-	@echo It can be built by running \"make parser DODEPEND=no\" in the source directory.
-	@echo You may also get the message on files checked out of CVS, in which case you can touch $@ to stop getting this message.
-
-$(SRCDIR)/scan.cc: $(SRCDIR)/scan.ll
-	@echo WARNING: The file $@ is out of date.
-	@echo It can be built by running \"make scanner DODEPEND=no\" in the source directory.
-	@echo You may also get the message on files checked out of CVS, in which case you can touch $@ to stop getting this message.
-
-#################################################################
-
-$(BINOBJ:.$(OBJSUF)=.d): $(DEPENDINCLUDE)
-ifneq ($(DODEPEND),no)
-include $(BINOBJ:.$(OBJSUF)=.d)
-endif
-
-endif
-
-ifndef FLEX
-FLEX=flex
-endif
-
-ifndef BISON
-BISON=bison
-endif
-
-notobjdir_default:
-	@echo "Building in an unconfigured source directory."
-	@echo "The following make targets are available:"
-	@echo "  make FLEX=<flex> scanner"
-	@echo "  make BISON=<bison> parser"
-	@echo "Be sure to replace FlexLexer.h in the include"
-	@echo "directory with the correct version."
-
-# (only works with bison and flex)
-.PHONY: parser
-parser:
-	$(BISON) -v -d -o parse.tmp.cc parse.yy
-	cat parse.tmp.cc \
-		| sed "s/^int yyparse.*;$$//" \
-		| sed "s/^YYPARSE_RETURN_TYPE yyparse.*;$$//" \
-		| sed "s/yylval/MPQCInylval/g" \
-		> parse.cc
-	if test -f parse.tmp.cc.h; then \
-	  echo "Older bison detected."; \
-	  cat parse.tmp.cc.h | sed "s/yylval/MPQCInylval/g" > parse.h; \
-	  /bin/mv parse.tmp.cc.output parse.output; \
-	else \
-	  echo "Newer bison detected."; \
-	  cat parse.tmp.hh | sed "s/yylval/MPQCInylval/g" > parse.h; \
-	  /bin/mv parse.tmp.output parse.output; \
-	fi
-	#-@rm -f parse.tmp*
-
-.PHONY: scanner
-scanner:
-	echo "#ifdef HAVE_CONFIG_H"  > scan.cc
-	echo "#include <scconfig.h>" >> scan.cc
-	echo "#endif" >> scan.cc
-	echo "#include <iostream>" >> scan.cc
-	echo "#ifdef USING_NAMESPACE_STD" >> scan.cc
-	echo "using namespace std;" >> scan.cc
-	echo "#endif" >> scan.cc
-	$(FLEX) -L -t scan.ll | grep -v "extern FILE .yyin" \
-	                | grep -v "static int yy_get_next_buffer.*;" \
-	                | grep -v "class istream;" \
-	                | sed "s/static int yy_get_next_buffer/int yy_get_next_buffer/" \
-	                | grep -v "static void yyunput.*;" \
-	                | sed "s/static void yyunput/void yyunput/" \
-	                | grep -v "static int yyinput.*;" \
-	                | grep -v "extern.*isatty" \
-	                | sed "s/static int yyinput/int yyinput/" \
-			| sed "s/yylval/MPQCInylval/g" \
-	                >> scan.cc
Index: ThirdParty/mpqc_open/src/bin/mpqc/Makefile.am
===================================================================
--- ThirdParty/mpqc_open/src/bin/mpqc/Makefile.am	(revision 5b29460dd8d43349c43ded528ff70ee67e177cc7)
+++ ThirdParty/mpqc_open/src/bin/mpqc/Makefile.am	(revision 5b29460dd8d43349c43ded528ff70ee67e177cc7)
@@ -0,0 +1,38 @@
+AM_CPPFLAGS = -I$(top_srcdir)/include -I$(top_srcdir)/src/lib
+
+bin_PROGRAMS = mpqc
+
+mpqc_SOURCES = \
+	mpqc.cc \
+	mpqcin.cc
+	parse.cc \
+	parse.h \
+	scan.cc
+mpqc_CPPFLAGS = \
+	$(AM_CPPFLAGS) \
+	-DHAVE_JOBMARKET -I$(top_srcdir)/../JobMarket/src -I$(top_builddir)/../JobMarket -I$(top_srcdir)/../../src -I$(top_srcdir)/../LinearAlgebra/src $(BOOST_SYSTEM_CFLAGS) \
+	-DHAVE_MPQCDATA -I$(top_builddir)/../../src
+mpqc_LDFLAGS = \
+	$(AM_LDFLAGS) \
+	-L$(top_builddir)/../JobMarket/src/JobMarket/.libs -Wl,-rpath,$(top_builddir)/../JobMarket/src/JobMarket/.libs \
+	-L$(top_builddir)/../../src/.libs -Wl,-rpath,$(top_builddir)/../../src/.libs \
+	$(BOOST_SYSTEM_LDFLAGS)
+mpqc_LDADD = \
+	-lJobMarketPoolWorker -lJobMarket  \
+	-lMolecuilderJobs -lMolecuilderFragmentationSummation \
+	-lboost_serialization
+if CONDLIBINT
+mpqc_LDADD += -lint
+endif
+if CONDLIBR12
+mpqc_LDADD += -lr12
+endif
+if CONDLIBDERIV
+mpqc_LDADD += -lderiv
+endif
+
+#if HAVE_SC_SRC_LIB_CHEMISTRY_CCA
+#mpqc_CPPFLAGS += -DHAVE_CHEMISTRY_CCA -DCCA_PATH=\"$(libdir)/cca\" -I../../lib/chemistry/cca
+#mpqc_LDFLAGS += -L$(CCA_CHEM_LIB) -L$(CCAFE_LIB) -L$(CCA_SPEC_BABEL_LIB) -L$(BABEL_LIB)
+#mpqc_LDADD += -lccachem_cxx_server -lccachem_cxx_client -lccafeCore -lcca -lsidl -lxml2 -lz
+#endif
Index: ThirdParty/mpqc_open/src/bin/mpqc/ccarun.in
===================================================================
--- ThirdParty/mpqc_open/src/bin/mpqc/ccarun.in	(revision 22d43161cc7d52aaecc31906f73b0aa9a0329126)
+++ 	(revision )
@@ -1,451 +1,0 @@
-#!/usr/bin/env perl
-#eval 'exec perl $0 $*'
-#    if 0;
-
-$prefix = '@prefix@';
-$exec_prefix = "@exec_prefix@";
-$bindir = "@bindir@";
-$scdatadir = "@scdatadir@";
-
-$pwd = `pwd`;
-chomp $pwd;
-$pwd =~ s/\/$//;
-
-use POSIX;
-
-# The path to the ccaffiene executable
-$ccafe = "@CCAFE_BIN@/ccafe-batch";
-
-# The threadgrp specialization
-$threadgrp = "none";
-
-# The mpi launch command
-$launch = "@CCALAUNCH@";
-
-# The number of tasks
-$ntask = 1;
-
-# A filename with a list of nodes.
-$nodefile = "";
-
-# A command line argument with a list of nodes.
-$nodes = "";
-
-# A format string to convert a node number to a node name
-$nodename = "%d";
-
-# The number of nodes each job will use.
-$nnodeperjob = "nnode";
-
-# The number of threads each process will use.
-$nthreadperproc = 1;
-
-# The number of processes to run on each node.
-$nprocpernode = 1;
-
-# The directory where the input file is to be found.
-$inputprefix = "";
-
-# The directory where the output file is to be placed.
-$outputprefix = "";
-
-# If true, then print out help info and exit
-$help = 0;
-
-# If true, then don't actually run anything
-$debug = 0;
-
-# If true, then print out extra info.
-$verbose = 0;
-
-# If true, then overwrite output files that seem up-to-date
-$rerun = 0;
-
-# If true, then do not overwrite any output file.
-$onlynew = 0;
-
-######################################################################
-
-use Getopt::Long;
-
-if (!GetOptions("launch=s" => \$launch,
-                "threadgrp=s" => \$threadgrp,
-                "nnodeperjob=i" => \$nnodeperjob,
-                "nthreadperproc=i" => \$nthreadperproc,
-                "nprocpernode=i" => \$nprocpernode,
-                "outputprefix=s" => \$outputprefix,
-                "inputprefix=s" => \$inputprefix,
-                "nodefile=s" => \$nodefile,
-                "nodes=s" => \$nodes,
-                "nodename=s" => \$nodename,
-                "help!" => \$help,
-                "rerun!" => \$rerun,
-                "onlynew!" => \$onlynew,
-                "debug!" => \$debug,
-                "verbose!" => \$verbose,
-      )) {
-    $help=1;
-}
-
-if ("$launch" eq "@" . "CCALAUNCH@") {
-    $launch = "mpirun [-hf %NODEFILE%] -n %NPROC% %CCARUNPROC% %CCAFE% --ccafe-rc %INPUT% --ccafe-remap-stdio --ccafe-outputdir %OUTPUT%"; 
-}
-
-$outputprefix =~ s/\/$//;
-$inputprefix =~ s/\/$//;
-
-######################################################################
-
-if ($help) {
-    print  "Usage: $ARGV[0] [options] [rcfile1.in] [rcfile2.in] ...\n";
-    print  "Options:\n";
-    print  "  --nnodeperjob n    run with n nodes per job (value: $nnodeperjob)\n";
-    print  "  --nprocpernode n   run with n procs per node (value: $nprocpernode)\n";
-    print  "  --nthreadperproc n use n threads per process (value: $nthreadperproc)\n";
-    print  "  --threadgrp grp    use the given threading layer (value: $threadgrp)\n";
-    print  "                     none: uses MPQC's default\n";
-    print  "                     proc: does a single threaded run\n";
-    print  "                     posix: use POSIX threads\n";
-    printf "  --launch cmd       use the given cmd to launch jobs--see below (value: %s)\n",
-          (($launch eq "")?"<not set>":$launch);
-    printf "  --nodefile file    a file listing nodes to use (value: %s)\n",
-          (($nodefile eq "")?"<not set>":$nodefile);
-    printf "  --nodes nodes      a command line list of machines to use (value: %s)\n",
-          (($nodes eq "")?"<not set>":$nodes);
-    printf "                     groups can be given as 8-10,12,15-17 for example\n";
-    printf "  --nodename fmt     converts node num to name (value: %s)\n", $nodename;
-    print  "  --rerun            overwrite output file, even if up-to-date\n";
-    print  "  --onlynew          do not overwrite output file, even if not up-to-date\n";
-    print  "  --inputprefix dir  path to prefix input files with\n";
-    print  "  --outputprefix dir path to prefix output files with\n";
-    print  "  --debug            don't actually run mpqc\n";
-    print  "  --help             print this help\n";
-    print  "\n";
-    print  "The launch command can contain special strings that will be substituted.\n";
-    print  "These are:\n";
-    print  "  %NPROC%    The number of processes to start.\n";
-    print  "  %NODEFILE% The name of a file containing the node names.\n";
-    print  "  %NODELIST% A comma separated list of node names.\n";
-    print  "  For these last two, if they are contained within square brackets\n";
-    print  "  and a substitution is not available, then everything within the\n";
-    print  "  the brackets is removed.\n";
-    print  "Examples of the launch argument:\n";
-    print  "  mpirun [-hf %NODEFILE%] -n %NPROC% %CCAFE% --ccafe-rc %INPUT% --ccafe-remap-stdio --ccafe-outp
-utdir %OUTPUT%\n";
-    print  "  mpirun [-H %NODELIST%] -n %NPROC% %CCAFE% --ccafe-rc %INPUT% --ccafe-remap-stdio --ccafe-outp
-utdir %OUTPUT%\n";
-    exit 0;
-}
-
-######################################################################
-
-@nodelist = ();
-if ($nodes ne "") {
-    $nodes =~ s/-/../g;
-    foreach my $i (eval $nodes) {
-        $nodelist[$#nodelist + 1] = sprintf "$nodename", $i;
-    }
-}
-elsif ("$nodefile" eq "" && exists($ENV{"PBS_NODEFILE"})) {
-    $nodefile=$ENV{"PBS_NODEFILE"};
-}
-if ("$nodefile" ne "" && -f "$nodefile") {
-    my %nodesfound = {};
-    open(NODEFILE,"<$nodefile");
-    while(<NODEFILE>) {
-        if (/(\S+)/) {
-            my $nodename = $1;
-            if (!exists($nodesfound{$nodename})) {
-                $nodelist[$#nodelist + 1] = $nodename;
-                $nodesfound{$nodename} = 1;
-            }
-        }
-    }
-    close(NODEFILE);
-}
-
-if ($#nodelist == -1) {
-    $nnode = 1;
-}
-else {
-    $nnode = $#nodelist + 1;
-}
-
-if ($nnodeperjob eq "nnode") {
-    $nnodeperjob = $nnode;
-}
-
-$nprocperjob = $nnodeperjob * $nprocpernode;
-
-$nnodeperjob = POSIX::ceil($nprocperjob / $nprocpernode);
-
-@jobnodes = ();
-%jobnnodes = {};
-%nodelist = {};
-%nodefile = {};
-$maxjobs = 0;
-while (($maxjobs + 1) * $nnodeperjob <= $nnode) {
-    $jobnnodes[$maxjobs++] = $nnodeperjob;
-}
-
-if ($maxjobs == 0) {
-    die "requested $nnodeperjob nodes but have $nnode nodes";
-}
-
-$nodesbegin = 0;
-foreach my $i (0..$maxjobs-1) {
-    my $nodesend = $nodesbegin + $jobnnodes[$i];
-    my @slice = (@nodelist)[$nodesbegin..($nodesend-1)];
-    $jobnodes{$i} = \@slice;
-    $nodesbegin = $nodesend;
-    foreach my $j (@slice) {
-        if ($nodelist{$i} eq "") { $nodelist{$i} = $j; }
-        else { $nodelist{$i} = sprintf "%s,%s", $nodelist{$i}, $j; }
-    }
-    $nodefile{$i} = ".tmp.nodefile.$$.$i";
-    open(NODEFILE,">" . $nodefile{$i});
-    foreach my $j (@slice) {
-        printf NODEFILE "%s\n", $j;
-    }
-    close(NODEFILE);
-}
-
-######################################################################
-
-if ($threadgrp eq "none" && $nthreadperproc > 1) {
-    $threadgrp = "posix";
-}
-
-if ($threadgrp eq "proc") {
-  $ENV{"THREADGRP"} = "<ProcThreadGrp>:()";
-}
-elsif ($threadgrp eq "posix") {
-  $ENV{"THREADGRP"} = "<PthreadThreadGrp>:(num_threads=$nthreadperproc)";
-}
-
-######################################################################
-
-$usingthreads = 0;
-if ($maxjobs > 1) {
-    require threads;
-    require threads::shared;
-    $usingthreads = 1;
-}
-
-######################################################################
-
-# autoflush output
-$| = 1;
-
-@allfiles = reverse(get_file_list());
-
-my @seqfiles : shared = ();
-my @files : shared = ();
-foreach my $file (@allfiles) {
-    $files[$#files+1] = $file;
-}
-
-printf "Running a maximum of %d jobs at a time.\n", $maxjobs;
-printf "Running %d processes per job.\n", $nprocperjob;
-printf "Running %d threads per process.\n", $nthreadperproc;
-foreach my $i (0..$maxjobs-1) {
-    print "Nodes in slot $i:";
-    foreach my $j (@{$jobnodes{$i}}) {
-        printf " \"%s\"", $j;
-    }
-    print "\n";
-}
-printenvvar("MESSAGEGRP");
-printenvvar("THREADGRP");
-printenvvar("MEMORYGRP");
-printenvvar("SCLIBDIR");
-printenvvar("INTEGRAL");
-
-$thecount = 0;
-$n = 0;
-
-if ($usingthreads) {
-    @threads = ();
-
-    foreach my $jobnum (0..$maxjobs-1) {
-        my $thr = threads->new(\&jobrunner, $jobnum);
-        $threads[$#threads+1] = $thr;
-    }
-
-    foreach my $thr (@threads) {
-        $thr->join();
-    }
-
-    @threads = ();
-}
-else {
-    foreach my $jobnum (0..$maxjobs-1) {
-        jobrunner($jobnum);
-    }
-}
-
-foreach $i (values(%nodefile)) {
-    unlink "$i";
-}
-
-sub get_next_file {
-    my $jobnum = shift;
-    lock(@seqfiles) if ($usingthreads);
-    if ($#seqfiles >= 0 && $jobnum == 0) {
-        return pop(@seqfiles);
-    }
-    lock(@files) if ($usingthreads);
-    if ($#files >= 0) {
-        return pop(@files);
-    }
-    return "";
-}
-
-sub jobrunner {
-    my $jobslot = shift;
-
-    my $file;
-
-    while ( ($file = get_next_file($jobslot)) ne "") {
-        $file =~ s/\.in//;
-        $tmp_out = "$pwd/$outputprefix/$file.tmp";
-	$ENV{"CCACHEM_RESULTS_DIR"} = "$tmp_out";
-        my $in = "$inputprefix/$file.in";
-        my $cmd = "$launch";
-        $cmd =~ s/%CCAFE%/$ccafe/;
-        $cmd =~ s/%NPROC%/$nprocperjob/;
-        $cmd =~ s/%INPUT%/$in/;
-
-	my $ccarunproc = "$scdatadir/ccarunproc $ccafe";
-        if (exists($ENV{THREADGRP})) {
-           $ccarunproc = "$ccarunproc " . &isoencode("$ENV{THREADGRP}");
-        }
-        else {
-           $ccarunproc = "$ccarunproc none";
-        }
-        # no mem/message groups for now
-        $ccarunproc = "$ccarunproc none none";
-        #results dir
-        $ccarunproc = "$ccarunproc " . &isoencode("$ENV{CCACHEM_RESULTS_DIR}");
-
-        $cmd =~ s|%CCARUNPROC%|$ccarunproc|;
-
-        $cmd = substitute_optional_parameter($cmd, "%OUTPUT%", "$tmp_out");
-        $cmd = substitute_optional_parameter($cmd, "%NODELIST%", $nodelist{$jobslot});
-        $cmd = substitute_optional_parameter($cmd, "%NODEFILE%", $nodefile{$jobslot});
-
-        mkdir $tmp_out;
-        printf "starting in slot %d: %s\n", $jobslot, "$cmd";
-        $cmd = "true" if ($debug);
-        $pid = fork();
-        if ($pid == 0) {
-            exec("$cmd");
-            die "exec returned";
-        }
-        waitpid($pid,'');
-        
-        rename "$tmp_out/pOut0", "$pwd/$outputprefix/$file.out";       
-        unlink "$tmp_out/pErr0";
-        rename "$tmp_out/results.txt", "$pwd/$outputprefix/$file.results";
-        rmdir "$tmp_out";
-    }
-}
-
-sub get_file_list {
-    my @dirfiles;
-    my @argfiles;
-
-    if ($readdir ne "") {
-        opendir(DIR,"$readdir");
-        @tdirfiles = sort(readdir(DIR));
-        foreach my $j (@tdirfiles) {
-            if ($j =~ /\.in$/) {
-                $dirfiles[$#dirfiles+1] = $j;
-            }
-        }
-        closedir(DIR);
-    }
-
-    @argfiles = sort(@ARGV);
-
-    my @allfiles = (@dirfiles, @argfiles);
-
-    my @files;
-
-    foreach my $infile (@allfiles) {
-        my $out = outfile("$infile");
-        $out = "$outputprefix$out";
-        $in = "$inputprefix$infile";
-        if (!$rerun
-            && (-f "$out")
-            && ($onlynew
-                || (-M "$out" < -M "$in" && (! -f "$ccafe" || -M "$out" < -M "$mpqc")))) {
-            if ($verbose) {
-                print "$in: skipping: $out up-to-date\n";
-            }
-        }
-        else {
-            if ($verbose) {
-                print "$in: will be run\n";
-            }
-            $files[$#files+1] = "$infile";
-        }
-    }
-
-    return @files;
-}
-
-sub outfile {
-    my $in = shift;
-
-    my $outbase = "$in";
-    $outbase =~ s/\.[^.]*$//;
-    $outbase = sprintf "%s.out", "$outbase";
-    my $out;
-
-    if ($uniqout) {
-        $out = "$outbase";
-        my $outversion = 1;
-        while (-f "$out") {
-            $outversion++;
-            $out = sprintf "%s.%02d", "$outbase", $outversion;
-        }
-    }
-
-    return "$out";
-}
-
-sub printenvvar {
-    my $envvar = shift;
-    if (exists($ENV{$envvar})) {
-        printf "Using %s = \"%s\"\n", $envvar, $ENV{$envvar};
-    }
-}
-
-sub substitute_optional_parameter {
-    my $str = shift;
-    my $name = shift;
-    my $value = shift;
-    if ($value ne "") {
-        $str =~ s/\[([^[]*$name[^[]*)\]/$1/;
-        $str =~ s/$name/$value/;
-    }
-    else {
-        $str =~ s/\[([^[]*$name[^[]*)\]//;
-    }
-    return $str;
-}
-
-sub isoencode {
-    my $str = shift;
-    $str =~ s/ /%20/g;
-    $str =~ s/\</%3c/g;
-    $str =~ s/\>/%3e/g;
-    $str =~ s/\[/%5b/g;
-    $str =~ s/\]/%5d/g;
-    $str =~ s/\$/%24/g;
-    $str =~ s/:/%38/g;
-    $str =~ s/\(/%28/g;
-    $str =~ s/\)/%29/g;
-    return $str;
-}
Index: ThirdParty/mpqc_open/src/bin/mpqc/ccarunproc
===================================================================
--- ThirdParty/mpqc_open/src/bin/mpqc/ccarunproc	(revision 22d43161cc7d52aaecc31906f73b0aa9a0329126)
+++ 	(revision )
@@ -1,48 +1,0 @@
-#!/bin/bash
-
-# This script starts up a single MPI process.
-# It is used in parallel environments where it
-# is difficult to set up environment variables
-# or command line arguments that contain special
-# shell characters.
-
-mpqc=$1 && shift
-messagegrp=$1 && shift
-threadgrp=$1 && shift
-memorygrp=$1 && shift
-integral=$1 && shift
-results=$1 && shift
-
-function isodecode() {
-  str=$1 && shift
-  echo $str | sed -e 's/%20/ /g' \
-                  -e 's/%3c/</g' -e 's/%3e/>/g' \
-                  -e 's/%5b/[/g' -e 's/%5d/]/g' \
-                  -e 's/%24/$/g' \
-                  -e 's/%38/:/g' \
-                  -e 's/%28/(/g' -e 's/%29/)/g' \
-                  -e 's/%25/%/g'
-}
-
-if [ "$messagegrp" != none ]; then
-  export MESSAGEGRP=`isodecode $messagegrp`
-fi
-
-if [ "$threadgrp" != none ]; then
-  export THREADGRP=`isodecode $threadgrp`
-fi
-
-if [ "$memorygrp" != none ]; then
-  export MEMORYGRP=`isodecode $memorygrp`
-fi
-
-if [ "$integral" != none ]; then
-  export INTEGRAL=`isodecode $integral`
-fi
-
-if [ "$results" != none ]; then
-  export CCACHEM_RESULTS_DIR=`isodecode $results`
-fi
-
-$mpqc $*
-
Index: ThirdParty/mpqc_open/src/bin/mpqc/scdirlist.h
===================================================================
--- ThirdParty/mpqc_open/src/bin/mpqc/scdirlist.h	(revision 5b29460dd8d43349c43ded528ff70ee67e177cc7)
+++ ThirdParty/mpqc_open/src/bin/mpqc/scdirlist.h	(revision 5b29460dd8d43349c43ded528ff70ee67e177cc7)
@@ -0,0 +1,34 @@
+#define HAVE_SC_DOC 1
+#define HAVE_SC_LIB 1
+#define HAVE_SC_LIB_ELISP 1
+#define HAVE_SC_LIB_PERL 1
+#define HAVE_SC_LIB_BASIS 1
+#define HAVE_SC_SRC_LIB_UTIL_REF 1
+#define HAVE_SC_SRC_LIB_UTIL_CONTAINER 1
+#define HAVE_SC_SRC_LIB_UTIL 1
+#define HAVE_SC_SRC_LIB_UTIL_STATE 1
+#define HAVE_SC_SRC_LIB_UTIL_OPTIONS 1
+#define HAVE_SC_SRC_LIB_UTIL_KEYVAL 1
+#define HAVE_SC_SRC_LIB_UTIL_MISC 1
+#define HAVE_SC_SRC_LIB_UTIL_GROUP 1
+#define HAVE_SC_SRC_LIB_UTIL_PSI3 1
+#define HAVE_SC_SRC_LIB_UTIL_PSI3_LIBPSIO 1
+#define HAVE_SC_SRC_LIB_UTIL_CLASS 1
+#define HAVE_SC_SRC_LIB_UTIL_RENDER 1
+#define HAVE_SC_SRC_LIB_MATH 1
+#define HAVE_SC_SRC_LIB_MATH_OPTIMIZE 1
+#define HAVE_SC_SRC_LIB_MATH_SYMMETRY 1
+#define HAVE_SC_SRC_LIB_MATH_SCMAT 1
+#define HAVE_SC_SRC_LIB_MATH_ISOSURF 1
+#define HAVE_SC_SRC_LIB_CHEMISTRY_SOLVENT 1
+#define HAVE_SC_SRC_LIB_CHEMISTRY_MOLECULE 1
+#define HAVE_SC_SRC_LIB_CHEMISTRY_QC 1
+#define HAVE_SC_SRC_LIB_CHEMISTRY_QC_WFN 1
+#define HAVE_SC_SRC_LIB_CHEMISTRY_QC_OINT3 1
+#define HAVE_SC_SRC_LIB_CHEMISTRY_QC_MBPT 1
+#define HAVE_SC_SRC_LIB_CHEMISTRY_QC_SCF 1
+#define HAVE_SC_SRC_LIB_CHEMISTRY_QC_INTV3 1
+#define HAVE_SC_SRC_LIB_CHEMISTRY_QC_DFT 1
+#define HAVE_SC_SRC_LIB_CHEMISTRY_QC_BASIS 1
+#define HAVE_SC_SRC_LIB_CHEMISTRY_QC_PSI 1
+#define HAVE_SC_SRC_BIN_MPQC_VALIDATE 1
Index: ThirdParty/mpqc_open/src/bin/scls/LIBS.h
===================================================================
--- ThirdParty/mpqc_open/src/bin/scls/LIBS.h	(revision 22d43161cc7d52aaecc31906f73b0aa9a0329126)
+++ 	(revision )
@@ -1,5 +1,0 @@
-#include <util/group/LIBS.h>
-#include <util/state/LIBS.h>
-#ifdef HAVE_CHEMISTRY_CCA
-#  include<util/misc/LIBS.h>
-#endif
Index: ThirdParty/mpqc_open/src/bin/scls/Makefile
===================================================================
--- ThirdParty/mpqc_open/src/bin/scls/Makefile	(revision 22d43161cc7d52aaecc31906f73b0aa9a0329126)
+++ 	(revision )
@@ -1,55 +1,0 @@
-TOPDIR=../../..
-ifndef SRCDIR
-  SRCDIR=$(shell pwd)
-endif
-
-include $(SRCDIR)/$(TOPDIR)/lib/GlobalMakefile
-include $(TOPDIR)/lib/Makedirlist
-INCLUDE += -I. -I$(SRCDIR)
-CXXINCLUDE += -I. -I$(SRCDIR)
-
-TARGET_TO_MAKE = scls
-
-CXXSRC = scls.cc
-CSRC =
-INC = 
-
-DEPENDINCLUDE = $(INC)
-
-BINOBJ = $(CXXSRC:%.cc=%.$(OBJSUF)) $(CSRC:%.c=%.$(OBJSUF))
-
-DISTFILES = $(CXXSRC) $(CSRC) $(INC) Makefile LIBS.h
-
-default:: scls
-
-ifeq ($(HAVE_SC_SRC_LIB_CHEMISTRY_CCA),yes)
-  XDEF += -DHAVE_CHEMISTRY_CCA
-endif
-
-LIBS := $(shell $(LISTLIBS) $(INCLUDE) $(XDEF) $(SRCDIR)/LIBS.h)
-
-#################################################################
-
-default:: $(DEPENDINCLUDE)
-
-include $(SRCDIR)/$(TOPDIR)/lib/GlobalRules
-
-scls: $(BINOBJ) $(LIBS)
-	$(LTLINK) $(LD) $(LDFLAGS) -o $@ $^ $(SYSLIBS) $(LTLINKBINOPTS)
-
-install:: scls
-	$(INSTALL) $(INSTALLDIROPT) $(installroot)$(bindir)
-	$(LTINST) $(INSTALL) $(INSTALLBINOPT) $< $(installroot)$(bindir)
-
-clean::
-	/bin/rm -f scls
-
-distclean::
-	/bin/rm -f scls
-
-#################################################################
-
-$(BINOBJ:.$(OBJSUF)=.d): $(DEPENDINCLUDE)
-ifneq ($(DODEPEND),no)
-include $(BINOBJ:.$(OBJSUF)=.d)
-endif
Index: ThirdParty/mpqc_open/src/bin/scls/scls.cc
===================================================================
--- ThirdParty/mpqc_open/src/bin/scls/scls.cc	(revision 22d43161cc7d52aaecc31906f73b0aa9a0329126)
+++ 	(revision )
@@ -1,216 +1,0 @@
-//
-// scls.cc
-//
-// Copyright (C) 1997 Limit Point Systems, Inc.
-//
-// Author: Curtis Janssen <cljanss@limitpt.com>
-// Maintainer: LPS
-//
-// This file is part of the SC Toolkit utilities.
-//
-// The SC Toolkit utilities are free software; you can redistribute them
-// and/or modify them under the terms of the GNU General Public License as
-// published by the Free Software Foundation; either version 2, or (at your
-// option) any later version.
-//
-// The SC Toolkit utilities are distributed in the hope that they will be
-// useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-// General Public License for more details.
-//
-// You should have received a copy of the GNU General Public License along
-// with the SC Toolkit utilities; see the file COPYING.  If not, write to
-// the Free Software Foundation, 675 Mass Ave, Cambridge, MA 02139, USA.
-//
-// The U.S. Government is granted a limited license as per AL 91-7.
-//
-
-#ifdef HAVE_CONFIG_H
-#include <scconfig.h>
-#endif
-
-#include <new>
-#include <unistd.h>
-
-#include <util/class/scexception.h>
-#include <util/misc/exenv.h>
-#include <util/misc/formio.h>
-#include <util/group/mstate.h>
-#include <util/group/message.h>
-#include <util/group/thread.h>
-#include <util/group/memory.h>
-
-// Force linkages:
-#include <util/state/linkage.h>
-
-#ifdef HAVE_MPI
-#define MPICH_SKIP_MPICXX
-#include <mpi.h>
-#endif
-
-using namespace std;
-using namespace sc;
-
-//////////////////////////////////////////////////////////////////////////
-
-// This forces the exception classes to be linked in.  Otherwise they won't
-// for single pass linkage of static libraries.  This is because of library
-// ordering and interdependency issues.
-static SCException ex;
-
-static void
-clean_up(void)
-{
-  MessageGrp::set_default_messagegrp(0);
-}
-
-static void
-out_of_memory()
-{
-  cerr << "ERROR: out of memory" << endl;
-  abort();
-}
-
-int
-main(int argc, char *argv[])
-{
-  atexit(clean_up);
-  std::set_new_handler(out_of_memory);
-
-  ExEnv::init(argc, argv);
-  ExEnv::set_out(&cout);
-
-#ifdef HAVE_MPI
-  // MPI is allowed wait until MPI_Init to fill in argc and argv,
-  // so we may have to call MPI_Init before we even know that we
-  // want an MPIMessageGrp.  The command name is used to let scls
-  // know that an early init is needed.
-  if (!strcmp(ExEnv::program_name(), "scls-mpi")) {
-    MPI_Init(&argc, &argv);
-  }
-#endif
-
-  int i;
-  int debug = 0;
-  int version = 0;
-  int warranty = 0;
-  int license = 0;
-  int help = 0;
-  const char *working_dir = 0;
-  char **files = 0;
-  int nfile = 0;
-  for (i=1; i<argc; i++) {
-      char *arg = argv[i];
-      if (!strcmp(arg,"-messagegrp")) i++;
-      else if (!strcmp(arg,"-memorygrp")) i++;
-      else if (!strcmp(arg,"-threadgrp")) i++;
-      else if (!strcmp(arg,"-W")) working_dir = argv[++i];
-      else if (!strcmp(arg,"-d")) debug = 1;
-      else if (!strcmp(arg,"-h")) help = 1;
-      else if (!strcmp(arg,"-v")) version = 1;
-      else if (!strcmp(arg,"-l")) SCFormIO::setverbose(cout,1);
-      else if (!strcmp(arg,"-w")) warranty = 1;
-      else if (!strcmp(arg,"-L")) license = 1;
-      else {
-          char **newfiles = new char *[nfile+1];
-          memcpy(newfiles, files, sizeof(char*)*nfile);
-          delete[] files;
-          files = newfiles;
-          files[nfile++] = arg;
-        }
-    }
-
-  if (help) {
-      ExEnv::out0()
-           << indent << "scls version " << SC_VERSION << endl
-           << SCFormIO::copyright << endl
-           << indent << "-memorygrp <$val> (which memory group to use)" << endl
-           << indent << "-threadgrp <$val> (which thread group to use)" << endl
-           << indent << "-messagegrp <$val> (which message group to use)"<<endl
-           << indent << "-W <$val> (set the working directory)" << endl
-           << indent << "-d (turn on debugging)" << endl
-           << indent << "-v (print the version)" << endl
-           << indent << "-w (print the warranty)" << endl
-           << indent << "-l (detailed list of objects)" << endl
-           << indent << "-L (print the license)" << endl
-           << indent << "-h (print this help)" << endl;
-      exit(0);
-    }
-  
-  if (version) {
-      ExEnv::out0()
-         << indent << "scls version " << SC_VERSION << endl
-         << SCFormIO::copyright;
-    exit(0);
-  }
-  
-  if (warranty) {
-      ExEnv::out0()
-         << indent << "scls version " << SC_VERSION << endl
-         << SCFormIO::copyright << endl
-         << SCFormIO::warranty;
-    exit(0);
-  }
-  
-  if (license) {
-      ExEnv::out0()
-         << indent << "scls version " << SC_VERSION << endl
-         << SCFormIO::copyright << endl
-         << SCFormIO::license;
-    exit(0);
-  }
-
-  // set the working dir
-  if (working_dir && strcmp(working_dir,"."))
-    chdir(working_dir);
-
-  // get the message group.  first try the commandline and environment
-  Ref<MessageGrp> grp = MessageGrp::initial_messagegrp(argc, argv);
-  if (grp.nonnull())
-    MessageGrp::set_default_messagegrp(grp);
-  else
-    grp = MessageGrp::get_default_messagegrp();
-
-  // get the thread group.  first try the commandline and environment
-  Ref<ThreadGrp> thread = ThreadGrp::initial_threadgrp(argc, argv);
-  if (thread.nonnull())
-    ThreadGrp::set_default_threadgrp(thread);
-  else
-    thread = ThreadGrp::get_default_threadgrp();
-
-  // set up output classes
-  SCFormIO::setindent(ExEnv::outn(), 0);
-  SCFormIO::setindent(ExEnv::errn(), 0);
-  SCFormIO::setindent(cout, 0);
-  SCFormIO::setindent(cerr, 0);
-
-  SCFormIO::set_printnode(0);
-  if (grp->n() > 1)
-    SCFormIO::init_mp(grp->me());
-
-  if (debug)
-    SCFormIO::set_debug(1);
-
-
-  for (i=0; i<nfile; i++) {
-      ExEnv::out0() << indent << files[i] << ":" << endl;
-      BcastStateInBin s(grp,files[i]);
-      ExEnv::out0() << incindent;
-      s.list_objects(ExEnv::out0());
-      if (s.has_directory() && !s.seekable()) {
-          ExEnv::out0() << "(objects cannot be listed since cannot seek file)" << endl;
-        }
-      ExEnv::out0() << decindent;
-    }
-
-  delete[] files;
-
-  return 0;
-}
-
-/////////////////////////////////////////////////////////////////////////////
-
-// Local Variables:
-// mode: c++
-// c-file-style: "CLJ"
-// End:
Index: ThirdParty/mpqc_open/src/bin/scls/scls.dox
===================================================================
--- ThirdParty/mpqc_open/src/bin/scls/scls.dox	(revision 22d43161cc7d52aaecc31906f73b0aa9a0329126)
+++ 	(revision )
@@ -1,47 +1,0 @@
-
-/** \page scls
-
-The scls program is used to list objects in checkpoint files.
-\if html
-See \ref state for more information.
-\endif
-
-\if html
-<h1>Compiling scls</h1>
- scls is distributed with the SC Toolkit.  scls will automatically
-be compiled when SC is compiled.  See \ref compile
-for more information.
-\endif
-
-<h1>Running scls</h1>
-
-scls takes the following command line options followed by a list of files.
-
-<dl>
- <dt><tt>-memorygrp</tt> <i>val</i><dd>Which memory group to use.
- <dt><tt>-threadgrp</tt> <i>val</i><dd>Which thread group to use.
- <dt><tt>-messagegrp</tt> <i>val</i><dd>Which message group to use.
- <dt><tt>-W</tt> <i>val</i><dd>Set the working directory.
- <dt><tt>-d</tt><dd>Turn on debugging.
- <dt><tt>-v</tt><dd>Print the version.
- <dt><tt>-w</tt><dd>Print the warranty.
- <dt><tt>-l</tt><dd>Detailed list of objects.
- <dt><tt>-L</tt><dd>Print the license.
- <dt><tt>-h</tt><dd>Print this help.
-</dl>
-
-<h1>License</h1>
-
-scls is open-source software; you can redistribute it and/or modify it
-under the terms of the GNU General Public License as published by the Free
-Software Foundation; either version 2 of the License, or (at your option)
-any later version.
-
-<h1>Warranty</h1>
-
-scls is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
-details.
-
-*/
Index: ThirdParty/mpqc_open/src/bin/scpr/LIBS.h
===================================================================
--- ThirdParty/mpqc_open/src/bin/scpr/LIBS.h	(revision 22d43161cc7d52aaecc31906f73b0aa9a0329126)
+++ 	(revision )
@@ -1,13 +1,0 @@
-#ifdef HAVE_CHEMISTRY_QC_CINTS
-#  include <chemistry/qc/cints/LIBS.h>
- #ifdef HAVE_CHEMISTRY_QC_MBPTR12
- #    include <chemistry/qc/mbptr12/LIBS.h>
- #endif
-#endif
-#ifdef HAVE_CHEMISTRY_CCA
-#  include <util/misc/LIBS.h>
-#endif
-#include <chemistry/qc/mbpt/LIBS.h>
-#include <chemistry/qc/dft/LIBS.h>
-#include <chemistry/qc/scf/LIBS.h>
-#include <util/options/LIBS.h>
Index: ThirdParty/mpqc_open/src/bin/scpr/Makefile
===================================================================
--- ThirdParty/mpqc_open/src/bin/scpr/Makefile	(revision 22d43161cc7d52aaecc31906f73b0aa9a0329126)
+++ 	(revision )
@@ -1,74 +1,0 @@
-TOPDIR=../../..
-ifndef SRCDIR
-  SRCDIR=$(shell pwd)
-endif
-
-include $(SRCDIR)/$(TOPDIR)/lib/GlobalMakefile
-include $(TOPDIR)/lib/Makedirlist
-INCLUDE += -I. -I$(SRCDIR)
-CXXINCLUDE += -I. -I$(SRCDIR)
-
-TARGET_TO_MAKE = scpr
-
-CXXSRC = scpr.cc
-CSRC =
-INC = 
-
-DEPENDINCLUDE = $(INC)
-
-BINOBJ = $(CXXSRC:%.cc=%.$(OBJSUF)) $(CSRC:%.c=%.$(OBJSUF))
-
-DISTFILES = $(CXXSRC) $(CSRC) $(INC) Makefile LIBS.h
-
-default:: scpr
-
-XDEF=
-XLIBS=
-ifeq ($(HAVE_SC_SRC_LIB_CHEMISTRY_QC_CINTS),yes)
- ifeq ($(HAVE_SC_SRC_LIB_CHEMISTRY_QC_MBPTR12),yes)
- XDEF += -DHAVE_CHEMISTRY_QC_MBPTR12
- endif
-XDEF += -DHAVE_CHEMISTRY_QC_CINTS
-endif
-
-ifeq ($(HAVE_LIBINT),yes)
-  XLIBS += -lint
-endif
-ifeq ($(HAVE_LIBR12),yes)
-  XLIBS += -lr12
-endif
-ifeq ($(HAVE_LIBDERIV),yes)
-  XLIBS += -lderiv
-endif
-
-ifeq ($(HAVE_SC_SRC_LIB_CHEMISTRY_CCA),yes)
-  XDEF += -DHAVE_CHEMISTRY_CCA
-endif
-
-LIBS := $(shell $(LISTLIBS) $(INCLUDE) $(XDEF) $(SRCDIR)/LIBS.h)
-
-#################################################################
-
-default:: $(DEPENDINCLUDE)
-
-include $(SRCDIR)/$(TOPDIR)/lib/GlobalRules
-
-scpr: $(BINOBJ) $(LIBS)
-	$(LTLINK) $(LD) $(LDFLAGS) -o $@ $^ $(XLIBS) $(SYSLIBS) $(LTLINKBINOPTS)
-
-install:: scpr
-	$(INSTALL) $(INSTALLDIROPT) $(installroot)$(bindir)
-	$(LTINST) $(INSTALL) $(INSTALLBINOPT) $< $(installroot)$(bindir)
-
-clean::
-	/bin/rm -f scpr
-
-distclean::
-	/bin/rm -f scpr
-
-#################################################################
-
-$(BINOBJ:.$(OBJSUF)=.d): $(DEPENDINCLUDE)
-ifneq ($(DODEPEND),no)
-include $(BINOBJ:.$(OBJSUF)=.d)
-endif
Index: ThirdParty/mpqc_open/src/bin/scpr/scpr.cc
===================================================================
--- ThirdParty/mpqc_open/src/bin/scpr/scpr.cc	(revision 22d43161cc7d52aaecc31906f73b0aa9a0329126)
+++ 	(revision )
@@ -1,248 +1,0 @@
-//
-// scpr.cc
-//
-// Copyright (C) 1997 Limit Point Systems, Inc.
-//
-// Author: Curtis Janssen <cljanss@limitpt.com>
-// Maintainer: LPS
-//
-// This file is part of the SC Toolkit utilities.
-//
-// The SC Toolkit utilities are free software; you can redistribute them
-// and/or modify them under the terms of the GNU General Public License as
-// published by the Free Software Foundation; either version 2, or (at your
-// option) any later version.
-//
-// The SC Toolkit utilities are distributed in the hope that they will be
-// useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-// General Public License for more details.
-//
-// You should have received a copy of the GNU General Public License along
-// with the SC Toolkit utilities; see the file COPYING.  If not, write to
-// the Free Software Foundation, 675 Mass Ave, Cambridge, MA 02139, USA.
-//
-// The U.S. Government is granted a limited license as per AL 91-7.
-//
-
-#ifdef HAVE_CONFIG_H
-#include <scconfig.h>
-#endif
-
-#include <unistd.h>
-#include <new>
-
-#include <util/misc/exenv.h>
-#include <util/misc/formio.h>
-#include <util/group/mstate.h>
-#include <util/group/message.h>
-#include <util/group/thread.h>
-#include <util/group/memory.h>
-
-// Force linkages:
-#include <chemistry/qc/wfn/linkage.h>
-#include <chemistry/qc/dft/linkage.h>
-#include <chemistry/qc/mbpt/linkage.h>
-#ifdef HAVE_SC_SRC_LIB_CHEMISTRY_QC_MBPTR12
-#  include <chemistry/qc/mbptr12/linkage.h>
-#endif
-#ifdef HAVE_SC_SRC_LIB_CHEMISTRY_QC_CINTS
-#  include <chemistry/qc/cints/linkage.h>
-#endif
-//#include <chemistry/qc/psi/linkage.h>
-#include <util/state/linkage.h>
-
-using namespace std;
-using namespace sc;
-
-#ifdef HAVE_MPI
-#define MPICH_SKIP_MPICXX
-#include <mpi.h>
-#endif
-
-//////////////////////////////////////////////////////////////////////////
-
-static void
-clean_up(void)
-{
-  MessageGrp::set_default_messagegrp(0);
-}
-
-static void
-out_of_memory()
-{
-  ExEnv::errn() << "ERROR: out of memory" << endl;
-  abort();
-}
-
-int
-main(int argc, char *argv[])
-{
-  atexit(clean_up);
-  std::set_new_handler(out_of_memory);
-
-  ExEnv::init(argc, argv);
-  ExEnv::set_out(&cout);
-
-#ifdef HAVE_MPI
-  // MPI is allowed wait until MPI_Init to fill in argc and argv,
-  // so we may have to call MPI_Init before we even know that we
-  // want an MPIMessageGrp.  The command name is used to let scpr
-  // know that an early init is needed.
-  if (!strcmp(ExEnv::program_name(), "scpr-mpi")) {
-    MPI_Init(&argc, &argv);
-  }
-#endif
-
-  int i;
-  int debug = 0;
-  int version = 0;
-  int warranty = 0;
-  int license = 0;
-  int help = 0;
-  const char *working_dir = 0;
-  char **files = 0;
-  char **objects = 0;
-  int nfile = 0;
-  int nobject = 0;
-  for (i=1; i<argc; i++) {
-      char *arg = argv[i];
-      if (!strcmp(arg,"-messagegrp")) i++;
-      else if (!strcmp(arg,"-memorygrp")) i++;
-      else if (!strcmp(arg,"-threadgrp")) i++;
-      else if (!strcmp(arg,"-W")) working_dir = argv[++i];
-      else if (!strcmp(arg,"-d")) debug = 1;
-      else if (!strcmp(arg,"-h")) help = 1;
-      else if (!strcmp(arg,"-l")) SCFormIO::setverbose(ExEnv::outn(),1);
-      else if (!strcmp(arg,"-v")) version = 1;
-      else if (!strcmp(arg,"-w")) warranty = 1;
-      else if (!strcmp(arg,"-L")) license = 1;
-      else if (!strcmp(arg,"-o")) {
-          if (argc > i+1) {
-              char **newobjects = new char *[nobject+1];
-              memcpy(newobjects, objects, sizeof(char*)*nobject);
-              delete[] objects;
-              objects = newobjects;
-              objects[nobject++] = argv[++i];
-            }
-          else help = 1;
-        }
-      else {
-          char **newfiles = new char *[nfile+1];
-          memcpy(newfiles, files, sizeof(char*)*nfile);
-          delete[] files;
-          files = newfiles;
-          files[nfile++] = arg;
-        }
-    }
-
-  if (help || nobject == 0 || nfile == 0) {
-      ExEnv::out0()
-           << indent << "scpr version " << SC_VERSION << endl
-           << SCFormIO::copyright << endl
-           << indent << "usage: " << argv[0] << " [options] file ..." << endl
-           << indent << "where options are chosen from:" << endl
-           << indent << "-o <$val> (print the object with the name $val)"<<endl
-           << indent << "-memorygrp <$val> (which memory group to use)" << endl
-           << indent << "-threadgrp <$val> (which thread group to use)" << endl
-           << indent << "-messagegrp <$val> (which message group to use)"<<endl
-           << indent << "-W <$val> (set the working directory)" << endl
-           << indent << "-d (turn on debugging)" << endl
-           << indent << "-l (verbose printing)" << endl
-           << indent << "-v (print the version)" << endl
-           << indent << "-w (print the warranty)" << endl
-           << indent << "-L (print the license)" << endl
-           << indent << "-h (print this help)" << endl;
-
-      ExEnv::out0() << endl
-           << indent << "object names take the form classname:ordinal_number"
-           << endl
-           << indent << "at least one file and object name must be given"
-           << endl;
-      exit(0);
-    }
-  
-  if (version) {
-      ExEnv::out0()
-         << indent << "scpr version " << SC_VERSION << endl
-         << SCFormIO::copyright;
-    exit(0);
-  }
-  
-  if (warranty) {
-      ExEnv::out0()
-         << indent << "scpr version " << SC_VERSION << endl
-         << SCFormIO::copyright << endl
-         << SCFormIO::warranty;
-    exit(0);
-  }
-  
-  if (license) {
-      ExEnv::out0()
-         << indent << "scpr version " << SC_VERSION << endl
-         << SCFormIO::copyright << endl
-         << SCFormIO::license;
-    exit(0);
-  }
-
-  // set the working dir
-  if (working_dir && strcmp(working_dir,"."))
-    chdir(working_dir);
-
-  // get the message group.  first try the commandline and environment
-  Ref<MessageGrp> grp = MessageGrp::initial_messagegrp(argc, argv);
-  if (grp.nonnull())
-    MessageGrp::set_default_messagegrp(grp);
-  else
-    grp = MessageGrp::get_default_messagegrp();
-
-  // get the thread group.  first try the commandline and environment
-  Ref<ThreadGrp> thread = ThreadGrp::initial_threadgrp(argc, argv);
-  if (thread.nonnull())
-    ThreadGrp::set_default_threadgrp(thread);
-  else
-    thread = ThreadGrp::get_default_threadgrp();
-
-  // set up output classes
-  SCFormIO::setindent(ExEnv::outn(), 0);
-  SCFormIO::setindent(ExEnv::errn(), 0);
-  SCFormIO::setindent(cout, 0);
-  SCFormIO::setindent(cerr, 0);
-
-  SCFormIO::set_printnode(0);
-  if (grp->n() > 1)
-    SCFormIO::init_mp(grp->me());
-
-  if (debug)
-    SCFormIO::set_debug(1);
-
-  for (i=0; i<nfile; i++) {
-      if (nfile > 1) {
-          ExEnv::out0() << indent << files[i] << ":" << endl;
-          ExEnv::out0() << incindent;
-        }
-      BcastStateInBin s(grp,files[i]);
-      for (int j=0; j<nobject; j++) {
-          if (nobject > 1) {
-              ExEnv::out0() << indent << objects[j] << ":" << endl;
-              ExEnv::out0() << incindent;
-            }
-          Ref<SavableState> o;
-          o << SavableState::dir_restore_state(s,objects[j]);
-          o->print(ExEnv::out0());
-          if (nobject > 1) ExEnv::out0() << decindent;
-        }
-      if (nfile > 1) ExEnv::out0() << decindent;
-    }
-
-  delete[] files;
-
-  return 0;
-}
-
-/////////////////////////////////////////////////////////////////////////////
-
-// Local Variables:
-// mode: c++
-// c-file-style: "CLJ"
-// End:
Index: ThirdParty/mpqc_open/src/bin/scpr/scpr.dox
===================================================================
--- ThirdParty/mpqc_open/src/bin/scpr/scpr.dox	(revision 22d43161cc7d52aaecc31906f73b0aa9a0329126)
+++ 	(revision )
@@ -1,50 +1,0 @@
-
-/** \page scpr
-
-The scpr program is used to print out objects in checkpoint files.
-\if html
-See \ref state for more information.
-\endif
-
-\if html
-<h1>Compiling scpr</h1>
-
- scpr is distributed with the SC Toolkit.  scpr will automatically
-be compiled when SC is compiled.  See \ref compile
-for more information.
-\endif
-
-<h1>Running scpr</h1>
-
-scpr takes the following command line options followed by a list of files.
-
-<dl>
- <dt><tt>-o</tt> <i>val</i><dd>Print the object with the name val.  Object names
-           take the form "<classname>:<ordinal_number>".  At least one file
-           and object name must be given.
- <dt><tt>-memorygrp</tt> <i>val</i><dd>Which memory group to use.
- <dt><tt>-threadgrp</tt> <i>val</i><dd>Which thread group to use.
- <dt><tt>-messagegrp</tt> <i>val</i><dd>Which message group to use.
- <dt><tt>-W</tt> <i>val</i><dd>Set the working directory.
- <dt><tt>-d</tt><dd>Turn on debugging.
- <dt><tt>-v</tt><dd>Print the version.
- <dt><tt>-w</tt><dd>Print the warranty.
- <dt><tt>-L</tt><dd>Print the license.
- <dt><tt>-h</tt><dd>Print this help.
-</dl>
-
-<h1>License</h1>
-
-scpr is open-source software; you can redistribute it and/or modify it
-under the terms of the GNU General Public License as published by the Free
-Software Foundation; either version 2 of the License, or (at your option)
-any later version.
-
-<h1>Warranty</h1>
-
-scpr is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
-details.
-
-*/
