Modernize config/configure.ac_scripts/start

Old version no longer works with new autoconfig.

Changes made as specified by the error messages.

git-svn-id: svn+ssh://vummath.ma.man.ac.uk/home/svn-oomphlib/public/trunk@478 595e1d82-adf1-4282-bac7-b6073fa2ca8e
Remove strange line from "config/configure.ac_scripts/end"

The line is "AS_DIRNAME([/* automatically generated */], $ac_prefix_conf_OUT)".

The autoconfig documentation says this should get the directory name of
        "/* automatically generated */"
which obviously is not a file...

Instead I think it attempts to get the dirname of everything in the glob
"/*", i.e. everything in your root dir. Depending on the version of
autotools this either gives an error or a (long) list of "/"s.

It can't possibly be doing anything useful because the result of the macro
isn't assigned to a variable. So I removed it.

git-svn-id: svn+ssh://vummath.ma.man.ac.uk/home/svn-oomphlib/public/trunk@479 595e1d82-adf1-4282-bac7-b6073fa2ca8e
Make fpdiff work when python3 is default

By explicitly specifying python2 in the hashbang line.

git-svn-id: svn+ssh://vummath.ma.man.ac.uk/home/svn-oomphlib/public/trunk@480 595e1d82-adf1-4282-bac7-b6073fa2ca8e
Quote the compiler names in hypre and trilinos build scripts

Otherwise compiler commands that contain spaces (e.g. "ccache mpicc") crash
the build scripts in weird ways, even if they are quoted in the configure
options file.

git-svn-id: svn+ssh://vummath.ma.man.ac.uk/home/svn-oomphlib/public/trunk@481 595e1d82-adf1-4282-bac7-b6073fa2ca8e
Remove "current" options file and "user_drivers.dir_list" from version control

* Useless but constantly cause clashes when updating svn because everyone
  uses different settings.

* Add code to autogen.sh to copy in the "defaults options if no current options
  exists.

* user_drivers.dir_list is already automatically generated in autogen.sh

* Both files are already in .gitignore, I need someone who uses svn directly to
  do the equivalent in svn.

git-svn-id: svn+ssh://vummath.ma.man.ac.uk/home/svn-oomphlib/public/trunk@482 595e1d82-adf1-4282-bac7-b6073fa2ca8e
Fix warning spam generated by src/generic/partitioning.cc

Many METIS partitioning functions were declared in one place and then
declared again when they were defined (as though they were part of a
class).

This gives warnings for redundant function declarations.

Removed the unnecessary extra declarations.

git-svn-id: svn+ssh://vummath.ma.man.ac.uk/home/svn-oomphlib/public/trunk@483 595e1d82-adf1-4282-bac7-b6073fa2ca8e
Add file open PARANOID checks in creation of triangle meshes from files

git-svn-id: svn+ssh://vummath.ma.man.ac.uk/home/svn-oomphlib/public/trunk@484 595e1d82-adf1-4282-bac7-b6073fa2ca8e
Use -isystem instead of -I for external distributions (hides warnings)

This has one side effect: the external distributions are moved to the end
of the list of libraries. I very much doubt that this could break anything
but it's something to keep in mind.

git-svn-id: svn+ssh://vummath.ma.man.ac.uk/home/svn-oomphlib/public/trunk@485 595e1d82-adf1-4282-bac7-b6073fa2ca8e
A bunch of small changes

* Initialise Nnewton_iter_taken

* Make get_some_non_boundary_node const

* Add broken virtual nvertex_node() function to FiniteElement

* Rename nprev_values_for_value_at_evaluation_time (new function added by me)
  to nprev_values_for_value_at_evaluation_time, more consistent.

* Move some variable declarations into/out of #ifdefs to get rid of warnings:
** f_ml_settings in demo_drivers/womersley/one_d_womersley/one_d_womersley.cc
** nproc in src/generic/block_preconditioner.h

git-svn-id: svn+ssh://vummath.ma.man.ac.uk/home/svn-oomphlib/public/trunk@486 595e1d82-adf1-4282-bac7-b6073fa2ca8e
Fix bug in variable_from_makefile in parallel_self_test.py

If there is no Makefile in the pwd then this function would always fail
because make fails (even though a Makefile in the pwd is not really
needed).

Fixed by setting the cwd for the make command to be that of the Makefile
from which the variable is being extracted.

git-svn-id: svn+ssh://vummath.ma.man.ac.uk/home/svn-oomphlib/public/trunk@487 595e1d82-adf1-4282-bac7-b6073fa2ca8e
Add const versions of some functions

* Problem::time_stepper_pt()
* TimeStepper::adaptive_flag()

git-svn-id: svn+ssh://vummath.ma.man.ac.uk/home/svn-oomphlib/public/trunk@488 595e1d82-adf1-4282-bac7-b6073fa2ca8e
Add an untemplated base class for UnsteadyHeatEquations

This allows us to do things like setting the source function and getting
the type of the function pointer without needing to know the dimension at
compile time (i.e. without templating the problem class by dimension).

git-svn-id: svn+ssh://vummath.ma.man.ac.uk/home/svn-oomphlib/public/trunk@489 595e1d82-adf1-4282-bac7-b6073fa2ca8e
Python 3 compatability for parallel_self_test.py

git-svn-id: svn+ssh://vummath.ma.man.ac.uk/home/svn-oomphlib/public/trunk@490 595e1d82-adf1-4282-bac7-b6073fa2ca8e
Add option to CommandLineArgs to throw error on unrecognised args

Default value is false, so nothing should change for currently existing
code.

git-svn-id: svn+ssh://vummath.ma.man.ac.uk/home/svn-oomphlib/public/trunk@491 595e1d82-adf1-4282-bac7-b6073fa2ca8e
Move minimal mpi tests out of autogen.sh and into a separate script

This allows them to be easily reused in other build scripts.

git-svn-id: svn+ssh://vummath.ma.man.ac.uk/home/svn-oomphlib/public/trunk@492 595e1d82-adf1-4282-bac7-b6073fa2ca8e
Initial commit of midpoint method

Includes a self test for unsteady heat (and so requires some slightly
different unsteady heat elements which can use an Interpolator object).

git-svn-id: svn+ssh://vummath.ma.man.ac.uk/home/svn-oomphlib/public/trunk@493 595e1d82-adf1-4282-bac7-b6073fa2ca8e
Remove calls to new from inside BlockPreconditioner::get_block(...)

* This should massively reduce the risk of memory leaks in block preconditioners

* Also removed old obsolete functions in BlockPreconditioner base

* Also added obsolete wrapper functions to allow existing block
  preconditioners to continue working unmodified.

* Removed get_block<CCDoubleMatrix>(...) because CC matrices don't have any
  way of filling in the values except in the constructor (i.e. using new).

* Moved BlockPreconditioner::get_block(...) to the header (because it's only
  a tiny dispatch function now).

git-svn-id: svn+ssh://vummath.ma.man.ac.uk/home/svn-oomphlib/public/trunk@494 595e1d82-adf1-4282-bac7-b6073fa2ca8e
Moved error test in master_block_preconditioner_pt() from ifdef MPI to PARANOID

Presumably it was just a mistake to have it in ifdef MPI in the first place

git-svn-id: svn+ssh://vummath.ma.man.ac.uk/home/svn-oomphlib/public/trunk@495 595e1d82-adf1-4282-bac7-b6073fa2ca8e
Move some processing from turn_into_subs_prec(..) to block_setup()

This allows us to construct and assign subsiduary block preconditioners at
any time (e.g. in the setup phase of the driver code) whereas before it
could only be done somewhere in the middle of setup() in the master
preconditioner.

git-svn-id: svn+ssh://vummath.ma.man.ac.uk/home/svn-oomphlib/public/trunk@496 595e1d82-adf1-4282-bac7-b6073fa2ca8e
Add function to split a string up into substrings

e.g. for use when parsing parts of a command line argument.

git-svn-id: svn+ssh://vummath.ma.man.ac.uk/home/svn-oomphlib/public/trunk@497 595e1d82-adf1-4282-bac7-b6073fa2ca8e