Merge branch 'develop' into hse-dev

Conflicts:
	src/ExchangeOperator.C
	src/ExchangeOperator.h
	src/KPGridConnectivity.C
	src/KPGridConnectivity.h
	src/Species.C
	src/XCPotential.h
	src/Xc.h
	src/notes
	util/cell.plt
	util/econst.plt
	util/econst_cmp.plt
	util/econste.plt
	util/econste_cmp.plt
	util/egap.sh
	util/etotal.plt
	util/etotal_cmp.plt
	util/etotal_int.plt
	util/etotal_int_cmp.plt
	util/force.plt
	util/kpgen/kpgen.C
	util/qbox_msd.py
	util/sigma.plt
	util/temp_ion.plt
	util/volume.plt

build/bgq-anl-omp.mk

+#-------------------------------------------------------------------------------
+#
+#  bgq.mk
+#
+#-------------------------------------------------------------------------------
+#
+ PLT=BGQ
+#-------------------------------------------------------------------------------
+# use the following .soft environment
+####~/.soft###
+# @default
+# +mpiwrapper-xl 
+
+ CXX=mpic++
+ LD=$(CXX)
+
+ PLTFLAGS += -DUSE_MPI -DSCALAPACK
+ PLTFLAGS +=  -D__linux__ -DPLT_BIG_ENDIAN
+ PLTFLAGS += -DUSE_XERCES 
+ PLTFLAGS += -D_LARGEFILE_SOURCE
+ PLTFLAGS += -D_FILE_OFFSET_BITS=64
+ PLTFLAGS += -DMPICH_IGNORE_CXX_SEEK
+ PLTFLAGS += -DUSE_MASSV
+
+# FFT must be FFTW2, FFTW3, ESSL or NOLIB
+ FFT=ESSL
+
+ifeq ($(FFT),FFTW2)
+ PLTFLAGS += -DUSE_FFTW2
+ PLTFLAGS += -DUSE_DFFTW
+ PLTFLAGS += -DFFTWMEASURE
+ FFTWDIR=/soft/libraries/alcf/current/xl/FFTW2
+ FFTWINCLUDEDIR=$(FFTWDIR)/include
+ FFTWLIBDIR=$(FFTWDIR)/lib
+ INCLUDE += -I$(FFTWINCLUDEDIR)
+ LIBPATH += -L$(FFTWLIBDIR)
+ LIBS += -ldfftw
+endif
+
+ifeq ($(FFT),FFTW3)
+ PLTFLAGS += -DUSE_FFTW3
+ PLTFLAGS += -DFFTWMEASURE
+ FFTWDIR=/soft/libraries/alcf/current/xl/FFTW3
+ FFTWINCLUDEDIR=$(FFTWDIR)/include
+ FFTWLIBDIR=$(FFTWDIR)/lib
+ INCLUDE += -I$(FFTWINCLUDEDIR)
+ LIBPATH += -L$(FFTWLIBDIR)
+ LIBS += -lfftw3
+endif
+
+ifeq ($(FFT),ESSL)
+ PLTFLAGS += -DUSE_ESSL_FFT
+ #PLTFLAGS += -DUSE_ESSL_2DFFT
+endif
+
+ifeq ($(FFT),NOLIB)
+ PLTFLAGS += -DFFT_NOLIB
+endif
+
+ XERCESCDIR=$(HOME)/software/xerces/xerces-c-src_2_8_0
+ XERCESCLIBDIR=$(XERCESCDIR)/lib
+
+ SCALAPACKLIBDIR=/soft/libraries/alcf/current/xl/SCALAPACK/lib
+ SCALAPACKLIB=-lscalapack
+ LAPACKLIBDIR=/soft/libraries/alcf/current/xl/LAPACK/lib
+ LAPACKLIB=-llapack
+ BLASLIBDIR=/soft/libraries/essl/current/lib64
+ BLASLIB=-lesslsmpbg
+
+ INCLUDE +=  -I$(XERCESCDIR)/include
+
+ CXXFLAGS= -g -O3 -qsmp=omp -qarch=qp -qtune=qp \
+           -D$(PLT) $(INCLUDE) $(PLTFLAGS) $(DFLAGS)
+
+ LIBPATH += -L$(XERCESCLIBDIR) -L$(SCALAPACKLIBDIR) \
+            -L$(LAPACKLIBDIR) -L$(BLASLIBDIR) \
+            -L${IBM_FCMP}/bglib64 \
+            -L${IBM_MAIN_DIR}/xlmass/bg/7.3/bglib64 \
+            -L${IBM_MAIN_DIR}/xlf/bg/14.1/bglib64 \
+            -L${IBM_MAIN_DIR}/xlsmp/bg/3.1/bglib64 \
+            -L$(IBM_MAIN_DIR)/xlf/bg/14.1/bglib64
+
+ LIBS +=  $(PLIBS) $(SCALAPACKLIB) $(LAPACKLIB) $(BLASLIB) \
+         -lmass -lmassv  -lxerces-c \
+         -lxlf90_r -lxlfmath -lxl \
+         -lxlsmp -lxlomp_ser \
+         -lpthread -lgomp
+
+ LDFLAGS = $(LIBPATH) $(LIBS)
+#-------------------------------------------------------------------------------

build/centos6.mk

+#-------------------------------------------------------------------------------
+#
+# Copyright (c) 2008-2015 The Regents of the University of California
+#
+# This file is part of Qbox
+#
+# Qbox is distributed 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.
+# See the file COPYING in the root directory of this distribution
+# or <http://www.gnu.org/licenses/>.
+#
+#-------------------------------------------------------------------------------
+#
+#  centos6.mk
+#
+#-------------------------------------------------------------------------------
+# Prerequisites: 
+# On a Centos-6.6 system, install the following packages:
+# yum install xerces-c xerces-c-devel
+# yum install openmpi openmpi-devel
+# yum install lapack lapack-devel
+# yum install fftw fftw-devel
+# yum install scalapack-common scalapack-openmpi \
+#             scalapack-openmpi-devel scalapack-openmpi-static
+# yum install libuuid libuuid-devel
+#
+#-------------------------------------------------------------------------------
+ PLT=Linux_x8664
+#-------------------------------------------------------------------------------
+
+ PLTOBJECTS = readTSC.o
+ SVN_VER :=$(shell svnversion -n)
+ DFLAGS += -DSVN_VERSION='"$(SVN_VER)"'
+
+ CXX=mpicxx
+ LD=$(CXX)
+
+ PLTFLAGS += -DIA32 -D_LARGEFILE_SOURCE \
+             -D_FILE_OFFSET_BITS=64 -DUSE_MPI -DSCALAPACK -DADD_ \
+             -DAPP_NO_THREADS -DXML_USE_NO_THREADS -DUSE_XERCES \
+             -DXERCESC_3 -DMPICH_IGNORE_CXX_SEEK -DUSE_UUID
+
+# FFT must be FFTW2, FFTW3, ESSL or NOLIB
+ FFT=FFTW3
+
+ifeq ($(FFT),FFTW2)
+ PLTFLAGS += -DUSE_FFTW2
+ PLTFLAGS += -DFFTWMEASURE
+ FFTWDIR=$(HOME)/software/fftw/Linux_x8664/fftw-2.1.5/fftw
+ FFTWINCLUDEDIR=$(FFTWDIR)
+ FFTWLIBDIR=$(FFTWDIR)/.libs
+ INCLUDE += -I$(FFTWINCLUDEDIR)
+ LIBPATH += -L$(FFTWLIBDIR)
+ LIBS += -lfftw
+endif
+
+ifeq ($(FFT),FFTW3)
+ PLTFLAGS += -DUSE_FFTW3
+ PLTFLAGS += -DFFTWMEASURE
+#PLTFLAGS += -DFFTW_TRANSPOSE
+ PLTFLAGS += -DFFTW3_2D
+#FFTWDIR=$(HOME)/software/fftw/fftw-3.3.4
+#FFTWINCLUDEDIR=$(FFTWDIR)/api
+#FFTWLIBDIR=$(FFTWDIR)/.libs
+#INCLUDE += -I$(FFTWINCLUDEDIR)
+#LIBPATH += -L$(FFTWLIBDIR)
+ LIBS += -lfftw3
+endif
+
+ifeq ($(FFT),ESSL)
+$(error ESSL library not available)
+endif
+
+ifeq ($(FFT),NOLIB)
+ PLTFLAGS += -DFFT_NOLIB
+endif
+
+ CXXFLAGS= -g -O3 -Wunused -D$(PLT) $(INCLUDE) $(PLTFLAGS) $(DFLAGS)
+ LIBS += -lpthread -lxerces-c -lscalapack -llapack -lblas -luuid
+ LDFLAGS = $(LIBPATH) $(LIBS)
+
+#-------------------------------------------------------------------------------

build/gcc_atlas.mk

+#-------------------------------------------------------------------------------
+#
+# Copyright (c) 2008 The Regents of the University of California
+#
+# This file is part of Qbox
+#
+# Qbox is distributed 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.
+# See the file COPYING in the root directory of this distribution
+# or <http://www.gnu.org/licenses/>.
+#
+#-------------------------------------------------------------------------------
+#
+#  gcc_atlas.mk
+#
+#-------------------------------------------------------------------------------
+ PLT=Linux_x8664
+#-------------------------------------------------------------------------------
+ SCALAPACKDIR = $(HOME)/software/scalapack/scalapack-2.0.2
+ XERCESCDIR=$(HOME)/software/xerces/xerces-c-src_2_8_0
+ ATLASDIR=/usr/lib64/atlas
+
+ PLTOBJECTS = readTSC.o
+ SVN_VER :=$(shell svnversion -n)
+ DFLAGS += -DSVN_VERSION='"$(SVN_VER)"'
+
+ CXX=mpicxx
+ LD=$(CXX)
+
+ PLTFLAGS += -DIA32 -D_LARGEFILE_SOURCE \
+             -D_FILE_OFFSET_BITS=64 -DUSE_MPI -DSCALAPACK -DADD_ \
+             -DAPP_NO_THREADS -DXML_USE_NO_THREADS -DUSE_XERCES \
+             -DMPICH_IGNORE_CXX_SEEK
+
+# FFT must be FFTW2, FFTW3, ESSL or NOLIB
+ FFT=FFTW2
+
+ifeq ($(FFT),FFTW2)
+ PLTFLAGS += -DUSE_FFTW2
+ PLTFLAGS += -DFFTWMEASURE
+ FFTWDIR=$(HOME)/software/fftw/Linux_x8664/fftw-2.1.5/fftw
+ FFTWINCLUDEDIR=$(FFTWDIR)
+ FFTWLIBDIR=$(FFTWDIR)/.libs
+ INCLUDE += -I$(FFTWINCLUDEDIR)
+ LIBPATH += -L$(FFTWLIBDIR)
+ LIBS += -lfftw
+endif
+
+ifeq ($(FFT),FFTW3)
+ PLTFLAGS += -DUSE_FFTW3
+ PLTFLAGS += -DFFTWMEASURE
+#PLTFLAGS += -DFFTW_TRANSPOSE
+ PLTFLAGS += -DFFTW3_2D
+ FFTWDIR=$(HOME)/software/fftw/fftw-3.3.4
+ FFTWINCLUDEDIR=$(FFTWDIR)/api
+ FFTWLIBDIR=$(FFTWDIR)/.libs
+ INCLUDE += -I$(FFTWINCLUDEDIR)
+ LIBPATH += -L$(FFTWLIBDIR)
+ LIBS += -lfftw3
+endif
+
+ifeq ($(FFT),ESSL)
+$(error ESSL library not available)
+endif
+
+ifeq ($(FFT),NOLIB)
+ PLTFLAGS += -DFFT_NOLIB
+endif
+
+ INCLUDE += -I$(XERCESCDIR)/include
+
+ CXXFLAGS= -g -O3 -Wunused -D$(PLT) $(INCLUDE) $(PLTFLAGS) $(DFLAGS)
+
+ LIBPATH += -L$(XERCESCDIR)/lib \
+            -L$(ATLASDIR) -L$(SCALAPACKDIR) -L/usr/lib64
+
+ LIBS += -lpthread -lxerces-c -lscalapack -llapack -lf77blas -latlas 
+
+ LDFLAGS = $(LIBPATH) $(LIBS)
+
+#-------------------------------------------------------------------------------

build/icc_mkl.mk

+#-------------------------------------------------------------------------------
+#
+#  icc_mkl.mk
+#
+#-------------------------------------------------------------------------------
+#
+ PLT=x86_64
+#-------------------------------------------------------------------------------
+ MPIDIR=/opt/openmpi
+ XERCESCDIR=/share/apps/xerces/xerces-c-src_2_8_0
+ PLTOBJECTS = readTSC.o
+ INCLUDE = -I$(MKLROOT)/include
+
+ CXX=icc
+ LD=mpicxx
+
+ PLTFLAGS += -DIA32 -D_LARGEFILE_SOURCE \
+             -D_FILE_OFFSET_BITS=64 -DUSE_MPI -DSCALAPACK -DADD_ \
+             -DAPP_NO_THREADS -DXML_USE_NO_THREADS -DUSE_XERCES
+
+# FFT must be FFTW2, FFTW3, ESSL or NOLIB
+  FFT=FFTW2
+
+ifeq ($(FFT),FFTW2)
+ PLTFLAGS += -DUSE_FFTW2
+ PLTFLAGS += -DFFTWMEASURE
+ FFTWDIR=/share/apps/fftw/fftw-2.1.5/fftw
+ FFTWINCLUDEDIR=$(FFTWDIR)
+ FFTWLIBDIR=$(FFTWDIR)/.libs
+ INCLUDE += -I$(FFTWINCLUDEDIR)
+ LIBPATH += -L$(FFTWLIBDIR)
+ LIBS += -lfftw
+endif
+
+ifeq ($(FFT),FFTW3)
+ PLTFLAGS += -DUSE_FFTW3
+ PLTFLAGS += -DFFTWMEASURE
+#PLTFLAGS += -DFFTW_TRANSPOSE
+ PLTFLAGS += -DFFTW3_2D
+ FFTWDIR=$(HOME)/software/fftw/fftw-3.3.4
+ FFTWINCLUDEDIR=$(FFTWDIR)/api
+ FFTWLIBDIR=$(FFTWDIR)/.libs
+ INCLUDE += -I$(FFTWINCLUDEDIR)
+ LIBPATH += -L$(FFTWLIBDIR)
+ LIBS += -lfftw3
+endif
+
+ifeq ($(FFT),ESSL)
+$(error ESSL library not available)
+endif
+
+ifeq ($(FFT),NOLIB)
+ PLTFLAGS += -DFFT_NOLIB
+endif
+
+
+ INCLUDE += -I$(MPIDIR)/include -I$(XERCESCDIR)/include 
+
+ CXXFLAGS=  -g -O3 -vec-report1 -D$(PLT) $(INCLUDE) $(PLTFLAGS) $(DFLAGS)
+
+ LIBPATH += -L$(MPIDIR)/lib64 \
+            -L$(MKLDIR)/lib/intel64  \
+            -L$(XERCESCDIR)/lib
+
+ LIBS +=  $(PLIBS) \
+          -lmkl_intel_lp64 \
+          -lmkl_lapack95_lp64 -lmkl_sequential -lmkl_core \
+          -lirc -lifcore -lsvml \
+          -luuid $(XERCESCDIR)/lib/libxerces-c.a -lpthread 
+
+# Parallel libraries
+ PLIBS = -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64
+
+ LDFLAGS = $(LIBPATH) $(LIBS)
+#-------------------------------------------------------------------------------

build/icc_mkl_omp.mk

+#-------------------------------------------------------------------------------
+#
+# icc_mkl_omp.mk 
+#
+#-------------------------------------------------------------------------------
+#
+ PLT=x86_64
+#-------------------------------------------------------------------------------
+ MPIDIR=/opt/openmpi
+ XERCESCDIR=/share/apps/xerces/xerces-c-src_2_8_0
+ PLTOBJECTS = readTSC.o
+
+ CXX=icc
+ LD=mpicxx
+
+ PLTFLAGS += -DIA32 -D_LARGEFILE_SOURCE \
+             -D_FILE_OFFSET_BITS=64 -DUSE_MPI -DSCALAPACK -DADD_ \
+             -DAPP_NO_THREADS -DXML_USE_NO_THREADS -DUSE_XERCES
+
+# FFT must be FFTW2, FFTW3, ESSL or NOLIB
+  FFT=FFTW2
+
+ifeq ($(FFT),FFTW2)
+ PLTFLAGS += -DUSE_FFTW2
+ PLTFLAGS += -DFFTWMEASURE
+ FFTWDIR=/share/apps/fftw/fftw-2.1.5/fftw
+ FFTWINCLUDEDIR=$(FFTWDIR)
+ FFTWLIBDIR=$(FFTWDIR)/.libs
+ INCLUDE += -I$(FFTWINCLUDEDIR)
+ LIBPATH += -L$(FFTWLIBDIR)
+ LIBS += -lfftw
+endif
+
+ifeq ($(FFT),FFTW3)
+ PLTFLAGS += -DUSE_FFTW3
+ PLTFLAGS += -DFFTWMEASURE
+#PLTFLAGS += -DFFTW_TRANSPOSE
+ PLTFLAGS += -DFFTW3_2D
+ FFTWDIR=$(HOME)/software/fftw/fftw-3.3.4
+ FFTWINCLUDEDIR=$(FFTWDIR)/api
+ FFTWLIBDIR=$(FFTWDIR)/.libs
+ INCLUDE += -I$(FFTWINCLUDEDIR)
+ LIBPATH += -L$(FFTWLIBDIR)
+ LIBS += -lfftw3
+endif
+
+ifeq ($(FFT),ESSL)
+$(error ESSL library not available)
+endif
+
+ifeq ($(FFT),NOLIB)
+ PLTFLAGS += -DFFT_NOLIB
+endif
+
+ INCLUDE += -I$(MPIDIR)/include -I$(XERCESCDIR)/include 
+
+ CXXFLAGS=  -g -openmp -O3 -vec-report1 -D$(PLT) \
+            $(INCLUDE) $(PLTFLAGS) $(DFLAGS)
+
+ LIBPATH += -L$(MPIDIR)/lib64 \
+           -L$(MKLDIR)/lib/intel64  \
+           -L$(XERCESCDIR)/lib
+
+ LIBS += $(PLIBS) \
+         -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread \
+         -lifcoremt -lirc -lsvml \
+         -luuid $(XERCESCDIR)/lib/libxerces-c.a -liomp5 -lpthread 
+
+# Parallel libraries
+ PLIBS = -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64
+
+ LDFLAGS = $(LIBPATH) $(LIBS)
+#-------------------------------------------------------------------------------

src/AlphaPBE0.h

+////////////////////////////////////////////////////////////////////////////////
+//
+// Copyright (c) 2014 The Regents of the University of California
+//
+// This file is part of Qbox
+//
+// Qbox is distributed 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.
+// See the file COPYING in the root directory of this distribution
+// or <http://www.gnu.org/licenses/>.
+//
+////////////////////////////////////////////////////////////////////////////////
+//
+// AlphaPBE0.h
+//
+////////////////////////////////////////////////////////////////////////////////
+
+#ifndef ALPHAPBE0_H
+#define ALPHAPBE0_H
+
+#include<iostream>
+#include<iomanip>
+#include<sstream>
+#include<stdlib.h>
+
+#include "Sample.h"
+
+class AlphaPBE0 : public Var
+{
+  Sample *s;
+
+  public:
+
+  const char *name ( void ) const { return "alpha_PBE0"; };
+
+  int set ( int argc, char **argv )
+  {
+    if ( argc != 2 )
+    {
+      if ( ui->onpe0() )
+      cout << " alpha_PBE0 takes only one value" << endl;
+      return 1;
+    }
+
+    double v = atof(argv[1]);
+    if ( v < 0.0 )
+    {
+      if ( ui->onpe0() )
+        cout << " alpha_PBE0 must be non-negative" << endl;
+      return 1;
+    }
+
+    s->ctrl.alpha_PBE0 = v;
+
+    return 0;
+  }
+
+  string print (void) const
+  {
+     ostringstream st;
+     st.setf(ios::left,ios::adjustfield);
+     st << setw(10) << name() << " = ";
+     st.setf(ios::right,ios::adjustfield);
+     st << s->ctrl.alpha_PBE0;
+     return st.str();
+  }
+
+  AlphaPBE0(Sample *sample) : s(sample)
+  {
+    s->ctrl.alpha_PBE0 = 0.25;
+  }
+};
+#endif

src/AngleCmd.h

@@ -15,7 +15,6 @@
 // AngleCmd.h:
 //
 ////////////////////////////////////////////////////////////////////////////////
-// $Id: AngleCmd.h,v 1.5 2008-09-08 15:56:17 fgygi Exp $
 
 #ifndef ANGLECMD_H
 #define ANGLECMD_H
@@ -38,24 +37,48 @@ class AngleCmd : public Cmd
   {
     return
     "\n angle\n\n"
-    " syntax: angle name1 name2 name3\n\n"
-    "   The angle command prints the angle defined by three atoms.\n\n";
+    " syntax: angle [-pbc] name1 name2 name3\n\n"
+    "   The angle command prints the angle defined by three atoms.\n"
+    "   If the -pbc option is used, the angle is computed using the\n"
+    "   nearest atoms taking into account periodic boundary conditions.\n\n";
   }
 
   int action(int argc, char **argv)
   {
-    if ( argc != 4 )
+    if ( ! ( argc == 4 || argc == 5 ) )
     {
       if ( ui->onpe0() )
       {
-        cout << " use: angle name1 name2 name3" << endl;
+        cout << " use: angle [-pbc] name1 name2 name3" << endl;
       }
       return 1;
     }
 
-    string name1(argv[1]);
-    string name2(argv[2]);
-    string name3(argv[3]);
+    string name1, name2, name3;
+    bool use_pbc = false;
+
+    if ( argc == 4 )
+    {
+      name1 = argv[1];
+      name2 = argv[2];
+      name3 = argv[3];
+    }
+    if ( argc == 5 )
+    {
+      if ( strcmp(argv[1],"-pbc") )
+      {
+        if ( ui->onpe0() )
+        {
+          cout << " use: angle [-pbc] name1 name2 name3" << endl;
+        }
+        return 1;
+      }
+      use_pbc = true;
+      name1 = argv[2];
+      name2 = argv[3];
+      name3 = argv[4];
+    }
+
     Atom* a1 = s->atoms.findAtom(name1);
     Atom* a2 = s->atoms.findAtom(name2);
     Atom* a3 = s->atoms.findAtom(name3);
@@ -83,22 +106,25 @@ class AngleCmd : public Cmd
       return 1;
     }
 
-    D3vector r12(a1->position()-a2->position());
-    D3vector r32(a3->position()-a2->position());
-    if ( norm(r12) == 0.0 || norm(r32) == 0.0 )
+    if ( ui->onpe0() )
     {
-      if ( ui->onpe0() )
+      D3vector r12(a1->position()-a2->position());
+      D3vector r32(a3->position()-a2->position());
+      if ( norm2(r12) == 0.0 || norm2(r32) == 0.0 )
       {
         cout << " AngleCmd: atoms are too close" << endl;
+        return 1;
       }
-      return 1;
-    }
 
-    const double sp = normalized(r12) * normalized(r32);
-    const double c = max(-1.0,min(1.0,sp));
-    const double a = (180.0/M_PI)*acos(c);
-    if ( ui->onpe0() )
-    {
+      if ( use_pbc )
+      {
+        const UnitCell& cell = s->wf.cell();
+        cell.fold_in_ws(r12);
+        cell.fold_in_ws(r32);
+      }
+      const double sp = normalized(r12) * normalized(r32);
+      const double c = max(-1.0,min(1.0,sp));
+      const double a = (180.0/M_PI)*acos(c);
       cout.setf(ios::fixed,ios::floatfield);
       cout << " angle " << name1 << "-" << name2  << "-" << name3
            << ": "

src/AngleConstraint.C

@@ -12,10 +12,9 @@
 //
 ////////////////////////////////////////////////////////////////////////////////
 //
-//  AngleConstraint.C
+// AngleConstraint.C
 //
 ////////////////////////////////////////////////////////////////////////////////
-// $Id: AngleConstraint.C,v 1.6 2008-09-08 15:56:17 fgygi Exp $
 
 #include "AngleConstraint.h"
 #include "AtomSet.h"
@@ -323,8 +322,8 @@ void AngleConstraint::grad_sigma(const D3vector &r1, const D3vector &r2,
 {
   D3vector r12(r1-r2);
   D3vector r32(r3-r2);
-  assert(norm(r12) > 0.0);
-  assert(norm(r32) > 0.0);
+  assert(norm2(r12) > 0.0);
+  assert(norm2(r32) > 0.0);
   D3vector e12(normalized(r12));
   D3vector e32(normalized(r32));
   const double ss = length(e12^e32);
@@ -344,7 +343,7 @@ void AngleConstraint::grad_sigma(const D3vector &r1, const D3vector &r2,
     {
       // choose direction e as e12+e32
       D3vector e(e12+e32);
-      assert(norm(e)>0.0);
+      assert(norm2(e)>0.0);
       e = normalized(e);
       const double r12_inv = 1.0/length(r12);
       const double r32_inv = 1.0/length(r32);
@@ -408,9 +407,10 @@ ostream& AngleConstraint::print( ostream &os )
   os << name2_ << " " << name3_ << "\"\n";
   os.setf(ios::fixed,ios::floatfield);
   os.setf(ios::right,ios::adjustfield);
-  os << "  value=\"" << setprecision(6) << angle_;
-  os << "\" velocity=\"" << setprecision(6) << velocity_ << "\"\n";
-  os << "  force=\"" << setprecision(6) << force_;
-  os << "\" weight=\"" << setprecision(6) << weight_ << "\"/>";
+  os << "  velocity=\"" << setprecision(6) << velocity_ << "\"";
+  os << " weight=\"" << setprecision(6) << weight_ << "\">\n";
+  os << "  <value> " << setprecision(6) << angle_ << " </value>";
+  os << " <force> " << setprecision(6) << force_ << " </force>\n";
+  os << " </constraint>";
   return os;
 }