Merging trunk changes into the branch

docs/install_examples/cygwin_gcc344_dbg_f2c_numeric.sh

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+#!/bin/sh
+# ------------------------------------------------------------------------------
+#
+#     Example Cantera pre-preconfig configuration script
+#        10/20/09
+#
+#  Platform:            cygwin
+#  Compiler:            gcc v. 3.4.4
+#  Optimization:        Debug version
+#  python:              v. 2.5.2 (full installation)
+#  matlab:              no
+#  f2c:                 yes
+#  num python           numeric
+#
+#
+# ---------------------------------------------------------------------------
+# The only place where the User must custimize this installation
+# is located at the top here:
+#
+#   Specify the installation directory here:
+#
+Cantera_Install_Dir='/cygdrive/c/cygwin_env/arch/cygwin/cantera-1.8_develop'
+#
+#   Specify the Sundials installation directory here (leave it as a null script
+#   if you don't want to link sundials in
+#
+# Sundials_Home=''
+Sundials_Home='/cygdrive/c/cygwin_env/arch/cygwin/sundials-2.3.0_dbg'
+#
+#   Specify the Sundials version number (either 2.2, 2.3, or 2.4)
+Sundials_Version='2.3'
+# Sundials_Version=2.4'
+# -----------------------------------------------------------------------------
+#
+#  User may optionally customize below this line (but doesn't have to) -- 
+#
+CANTERA_CONFIG_PREFIX=$Cantera_Install_Dir
+export CANTERA_CONFIG_PREFIX
+
+SET_PYTHON_SITE_PACKAGE_TOPDIR=y
+export SET_PYTHON_SITE_PACKAGE_TOPDIR
+
+PYTHON_SITE_PACKAGE_TOPDIR=$CANTERA_CONFIG_PREFIX
+export PYTHON_SITE_PACKAGE_TOPDIR
+
+PYTHON_CMD=/usr/bin/python
+export PYTHON_CMD
+
+#
+# The full python package works within cygwin. Minimal is needed at the least
+#
+PYTHON_PACKAGE='full'
+#PYTHON_PACKAGE='minimal'
+export PYTHON_PACKAGE
+
+WITH_IDEAL_SOLUTIONS="y"
+export WITH_IDEAL_SOLUTIONS
+
+WITH_ELECTROLYTES="y"
+export WITH_ELECTROLYTES
+
+WITH_VCSNONIDEAL="y"
+export WITH_VCSNONIDEAL
+
+#
+#  Matlab on the pc is supported through the windows vc++ 8.0 compilation
+#  environment
+#
+BUILD_MATLAB_TOOLBOX="n"
+export BUILD_MATLAB_TOOLBOX
+
+NUMARRAY_HOME=''
+export NUMARRAY_HOME
+#
+# Turns on extra debugging
+#
+DEBUG_MODE='y'
+export DEBUG_MODE
+#
+#  Numeric must have already been installed in the
+#              /usr/lib/python2.5/site-packages
+#  directory before the Cantera installation. If not, you can always
+#  do a minimal python installation and forego forming Cantera's python interface.
+#
+USE_NUMERIC="y"
+export USE_NUMERIC
+#
+#  We use F2C with the cygwin installation. However, the g77 interface should 
+#  work too.
+#
+BUILD_WITH_F2C="y"
+export BUILD_WITH_F2C
+
+BITCOMPILE="32"
+export BITCOMPILE
+#
+#  We use the default gcc compilers that come with cygwin. Currently, this
+#  is gcc v. 3.4.4.
+#
+CXX='g++'
+export CXX
+#
+CC='gcc'
+export CC
+#
+F77='g77'
+export F77
+#
+# Debug options
+#
+# -DDEBUG_HKM
+# -DDEBUG_BASISOPTIMIZE
+# -DDEBUG_CHEMEQUIL
+#
+CXXFLAGS="-g -Wall "
+export CXXFLAGS
+
+CFLAGS=$CXXFLAGS
+export CFLAGS
+
+FFLAGS="-g "
+export FFLAGS
+
+LDFLAGS='-g'
+export LDFLAGS
+
+LCXX_END_LIBS="-lm -lstdc++"
+export LCXX_END_LIBS
+
+# The gcc compiler in cygwin will put a .exe extension on anyway. So,
+# we might as well define this field as .exe. cygwin will automagically
+# equate executable files with no extension as having an .exe extension.
+# This is very mysterious. However, the mystery goes away if you define
+# these files to have a .exe suffix from the getgo.
+EXE_EXT=".exe"
+export EXE_EXT
+
+EXTRA_LINK=""
+export EXTRA_LINK
+
+MAKE=make
+export MAKE
+#
+# Specify the SUNDIALS option
+#
+if test -n "$Sundials_Home"
+then
+  USE_SUNDIALS='y'
+  SUNDIALS_VERSION=$Sundials_Version
+else
+  USE_SUNDIALS='n'
+fi
+export USE_SUNDIALS
+export SUNDIALS_VERSION
+#
+# Specify where to find the sundials installation directories
+#
+SUNDIALS_HOME=$Sundials_Home
+export SUNDIALS_HOME
+#
+#  Ok, fire off the main preconfig script
+#
+./preconfig
+

docs/install_examples/cygwin_gcc344_dbg_f2c_numpy.sh

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+#!/bin/sh
+# ------------------------------------------------------------------------------
+#
+#     Example Cantera pre-preconfig configuration script
+#       10/20/09
+#
+#  Platform:            cygwin
+#  Compiler:            gcc v. 3.4.4
+#  Optimization:        Debug version
+#  python:              v. 2.5.2 (full installation)
+#  matlab:              no
+#  f2c:                 yes
+#  num python:          numpy, which is distributed with cygwin
+#
+#
+# ---------------------------------------------------------------------------
+# The only place where the User must custimize this installation
+# is located at the top here:
+#
+#   Specify the installation directory here:
+#
+Cantera_Install_Dir='/cygdrive/c/cygwin_env/arch/cygwin/cantera-1.8_develop'
+#
+#   Specify the Sundials installation directory here (leave it as a null script
+#   if you don't want to link sundials in
+#
+# Sundials_Home=''
+Sundials_Home='/cygdrive/c/cygwin_env/arch/cygwin/sundials-2.3.0_dbg'
+#
+#   Specify the Sundials version number (either 2.2, 2.3, or 2.4)
+Sundials_Version='2.3'
+# Sundials_Version=2.4'
+# -----------------------------------------------------------------------------
+#
+CANTERA_CONFIG_PREFIX=$Cantera_Install_Dir
+export CANTERA_CONFIG_PREFIX
+
+SET_PYTHON_SITE_PACKAGE_TOPDIR=y
+export SET_PYTHON_SITE_PACKAGE_TOPDIR
+
+PYTHON_SITE_PACKAGE_TOPDIR=$CANTERA_CONFIG_PREFIX
+export PYTHON_SITE_PACKAGE_TOPDIR
+
+PYTHON_CMD=/usr/bin/python
+export PYTHON_CMD
+
+#
+# The full python package works within cygwin. Minimal is needed at the least
+#
+PYTHON_PACKAGE='full'
+#PYTHON_PACKAGE='minimal'
+export PYTHON_PACKAGE
+
+WITH_IDEAL_SOLUTIONS="y"
+export WITH_IDEAL_SOLUTIONS
+
+WITH_ELECTROLYTES="y"
+export WITH_ELECTROLYTES
+
+WITH_VCSNONIDEAL="y"
+export WITH_VCSNONIDEAL
+
+#
+#  Matlab on the pc is supported through the windows vc++ 8.0 compilation
+#  environment. Therefore, we turn it off here.
+#
+BUILD_MATLAB_TOOLBOX="n"
+export BUILD_MATLAB_TOOLBOX
+
+NUMARRAY_HOME=''
+export NUMARRAY_HOME
+#
+# Turns on extra debugging
+#
+DEBUG_MODE='y'
+export DEBUG_MODE
+#
+#  Numpy must have already been installed in the
+#              /usr/lib/python2.5/site-packages
+#  directory before the Cantera installation. If not, you can always
+#  do a minimal python installation and forego forming Cantera's python interface.
+#
+USE_NUMPY="y"
+export USE_NUMPY
+#
+#      Specify where to find the include files within the numpy distribution
+#
+NUMPY_INC_DIR="/usr/lib/python2.5/site-packages/numpy/core/include"
+export NUMPY_INC_DIR
+#
+#  We use F2C with the cygwin installation. However, the g77 interface should 
+#  work too.
+#
+BUILD_WITH_F2C="y"
+export BUILD_WITH_F2C
+
+BITCOMPILE="32"
+export BITCOMPILE
+#
+#  We use the default gcc compilers that come with cygwin. Currently, this
+#  is gcc v. 3.4.4.
+#
+CXX='g++'
+export CXX
+#
+CC='gcc'
+export CC
+#
+F77='g77'
+export F77
+#
+# Debug options
+#
+# -DDEBUG_HKM
+# -DDEBUG_BASISOPTIMIZE
+# -DDEBUG_CHEMEQUIL
+#
+CXXFLAGS="-g -Wall "
+export CXXFLAGS
+
+CFLAGS=$CXXFLAGS
+export CFLAGS
+
+FFLAGS="-g "
+export FFLAGS
+
+LDFLAGS='-g'
+export LDFLAGS
+
+LCXX_END_LIBS="-lm -lstdc++"
+export LCXX_END_LIBS
+
+# The gcc compiler in cygwin will put a .exe extension on anyway. So,
+# we might as well define this field as .exe. cygwin will automagically
+# equate executable files with no extension as having an .exe extension.
+# This is very mysterious. However, the mystery goes away if you define
+# these files to have a .exe suffix from the getgo.
+EXE_EXT=".exe"
+export EXE_EXT
+
+EXTRA_LINK=""
+export EXTRA_LINK
+
+MAKE=make
+export MAKE
+#
+# Specify the SUNDIALS option
+#
+if test -n "$Sundials_Home"
+then
+  USE_SUNDIALS='y'
+  SUNDIALS_VERSION=$Sundials_Version
+else
+  USE_SUNDIALS='n'
+fi
+export USE_SUNDIALS
+export SUNDIALS_VERSION
+#
+# Specify where to find the sundials installation directories
+#
+SUNDIALS_HOME=$Sundials_Home
+export SUNDIALS_HOME
+#
+#  Ok, fire off the main preconfig script
+#
+./preconfig
+

docs/install_examples/sol10_64bit_CC57_dbg_py24_numarray

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+#!/bin/sh
+#
+#  Sierra 64 bit setup:
+#  -xO4 -xtarget=native64 -xarch=native64 -xcode=pic32 -DSUN10 -library=stlport4 
+# 
+#  Sierra warnings setup:
+#  +w2 -errtags -erroff=doubunder,reftotemp,ppextraw,inllargeint,inllargeuse,wnoelseretvalue,truncwarn,diffenumtype,notused,wvarhid enmem,badcastw,hidef -errwarn=%all,no%wunreachable,no%partinit 
+#
+#  Notes:
+#    When you add flsgs with % in them python won't build, because there is an
+#    error in the python distutils routines. I am currently manually
+#    fixing these.
+#
+# Program Names:
+#
+MAKE=gmake
+export MAKE
+
+#
+# Pointers to the 64 bit python built with Sunpro compilers
+PYTHON_DIR=${HOME}/arch/sol_py64
+export PYTHON_DIR
+PYTHON_CMD=${HOME}/arch/sol_py64/bin/python
+export PYTHON_CMD
+
+#
+# Use the CC compiler for C++ code
+CXX=CC
+export CXX
+#
+# Specification of the c compiler
+#
+CC=cc
+export CC
+
+CXX_DEPENDS='CC -xM1'
+export CXX_DEPENDS
+
+USE_NUMERIC='n'
+export USE_NUMERIC
+
+#
+#  HKM 7/22/09
+#  The matlab option is currently not working. Matlab uses the gcc
+#  compiler. This setup uses the solaris compiler. I can get
+#  the matlab extensions to compile. But, when I run matlab
+#  I get an unsatisfied external
+#   When I add the commands:
+#      -l/opt/SUNWspro/lib/f9 -lCrun -lCstd -lfsu 
+#   to the matlab build, I can get rid of the runtime unsatisfied
+#   external. However, I immediate crash dump matlab. This
+#   suggests that there are duplicate Cstd routines from gcc and
+#   from the solaris compilers fighting it out.
+#      I believe the solution will involve compiling everything
+#   with gcc in order to get matlab on solaris to work. 
+#
+BUILD_MATLAB_TOOLBOX="n"
+export BUILD_MATLAB_TOOLBOX
+
+DEBUG_MODE="y"
+export DEBUG_MODE
+
+#
+# Compiler Flags
+#
+BITCOMPILE="64"
+export BITCOMPILE
+#
+#  remember the issue with % and python
+#
+EFLAGS=" +w2 -errtags -erroff=doubunder,reftotemp,ppextraw,inllargeint,inllargeuse,wnoelseretvalue,truncwarn,diffenumtype,notused,wvarhidenmem,badcastw,hidef -errwarn=%all,no%wunreachable,no%partinit" 
+#AFLAGS=" -xtarget=native64 -xarch=native64 -xcode=pic32 -library=stlport4"
+AFLAGS=" -xtarget=native64 -xarch=native64 -xcode=pic32"
+export AFLAGS
+
+F77=f77
+export F77
+
+F90=f95
+export F90
+
+FFLAGS="-g -xtarget=native64 -xarch=native64 -xcode=pic32 "
+export FFLAGS
+
+CFLAGS="-g -xtarget=native64 -xarch=native64 -xcode=pic32 -v "
+export CFLAGS
+
+CXXFLAGS="-g $AFLAGS $EFLAGS -DDEBUG_HKM" 
+export CXXFLAGS
+
+LCXX_END_LIBS="-lm "
+export LCXX_END_LIBS
+
+# other useful endlibs for solaris 64 bit are
+#  -mt -lsunmath -lfsu
+
+USE_SUNDIALS='n'
+export USE_SUNDIALS
+
+WITH_VCSNONIDEAL='y'
+export WITH_VCSNONIDEAL
+
+#
+# Location Variables - set the directory to point to 
+#                      a 64-bit specific directory.
+#
+CANTERA_INSTALL_DIR=${HOME}/arch/sol_py64/cantera-1.8
+export CANTERA_INSTALL_DIR
+
+CANTERA_CONFIG_PREFIX=${HOME}/arch/sol_py64/cantera-1.8
+export CANTERA_CONFIG_PREFIX
+
+#CANTERA_PYTHON_HOME=${CANTERA_PYTHON_HOME:="$HOME/python_modules"}
+#export CANTERA_PYTHON_HOME
+
+SET_PYTHON_SITE_PACKAGE_TOPDIR="y"
+export SET_PYTHON_SITE_PACKAGE_TOPDIR
+
+PYTHON_SITE_PACKAGE_TOPDIR=${HOME}"/arch/sol_py64/cantera-1.8"
+export PYTHON_SITE_PACKAGE_TOPDIR
+
+PYTHON_PACKAGE="full"
+#PYTHON_PACKAGE="minimal"
+#PYTHON_PACKAGE="none"
+export PYTHON_PACKAGE
+
+BUILD_WITH_F2C="n"
+export BUILD_WITH_F2C
+
+# 
+# Archive commands
+#
+ARCHIVE="CC -xar -xcode=pic32 -o "
+export ARCHIVE
+
+
+#
+# Invoke the regular configure script 
+#
+./preconfig
+