monomial for Wilson clover with even/pdd checked now. It is working
correctly on PCs, compared against old code of Martin Hasenbusch.

To be done:
- add in twisted mass term
merge with etmc/master
added sample results for given parameters
extended exchange routine for including clover INDEX_INDEP_GEOM not touched, must be maintained by someone else
typos in comments fixed
cloverdet monomial docu added
first version combining clover and twisted, not tested yet
twisted clover seems to be rather close to working!

solver converges, with CSW=0 everything appears to be fine when
the CLOVERDET monomial is used. with CSW!=0 dh is slightly too
largish, but not giantic... Probably some small bug somewhere...

bug fixed
- g_mu wasn't properly set to mnl->mu in cloverdet_monomial

introduced Qsw_pm_psi with twisted mass term opposed to Qsw_sq_psi,
the latter of which has mu=0 explicitly
Remove .NOTPARALLEL specifier from Makefile.in
Add test/*.[o,d] and tests/*.[o,d] to compile clean target.
sign bug fixed, hmc still not working with twisted and clover
update_momenta.c: typo corrected

test/check_xchange.c broken, xchange_deri() needs an argument

clover.c: removed VOLUME parameter to init_sw_fields

clover_leaf.c: replaced uggly macros with proper inline functions

hybrid_update.c: renamed ini_momenta -> init_momenta

test/check_xchange.c: corrected missing argument to xchange_deri

cloverdet_monomial.c: removed non-even/odd branch

new xchange_deri version checked for 1-dim case
- comments added

- in case of CSW=0, mu>0 I get binary identical results if I replace in cloverdet_monomial
  Qsw_pm_psi       with  Qtm_pm_psi
  Qsw_plus_psi     with  Qtm_plus_psi
  Qsw_minus_psi    with  Qtm_minus_psi
  H_eo_sw_inv_psi  with  H_eo_tm_inv_psi

- for mu>0 and CSW=0 running with CLOVERDET monomial and DET monomial give binary
  identical results

- running with CSW>0 and mu!=0, but only for S_det (so, speudofermion
  part twisted only) seems to be working. -> sw_deriv, sw_all and
  sw_trace correct? or is the contribution from S_det too small?

- still running with both CSW>0 and mu!=0 doesn't work
svn remnants removed
name of monomial changed to CLOVERTRLOG consistently
Merge pull request #64 from urbach/IntegratorFlexibleGauge

1) introduction of a new type hamiltonian_field_t as container for gauge, momenta and derivative fields needed in the progress of a HMC trajectory. This is set in update_tm and then propagated to the integrator object.

The derivative and exchange routines have been rewritten to get a hamiltonian_field_t, a gauge or a derivative field as parameters, as appropriate. Still missing is the Dirac operator and the Hopping_Matrix, which continue to operate on g_gauge_field. This needs to be changed in future.

This part of the patch is in preparation for dynamical smearing.

A point for discussion is the mechanism currently implemented by global variables to trigger recomputation of for instance the plaquette value if the gauge field changed, or of the gauge_copy. Only for this reason the Dirac operator would need a whole hamiltonian_field_t, however, I think it would be cleaner to have only a dependence on the gauge field, aso in view of the inverter executable.

2) a new monomial has been introduced, called cloverdet
CLOVERDET
which implements a Wilson-clover determinant monomial with even/odd preconditioning. The twisted mass term is not yet included and needs to be done. The monomial was tested against an old code of Martin Hasenbusch.
added a proper inversion routine for the CLOVER operator plus a sample
input file for this case

again, it works for CSW=0 and mu>0 or CSW>0 and mu = 0, but it doesn't work
with both together yet. So, I suspect that sw_invert has some problem
in that situation...
Merge pull request #68 from kostrzewa/NOTPARALLEL

Remove .NOTPARALLEL specifier from Makefile.in
first version combining clover and twisted, not tested yet
twisted clover seems to be rather close to working!

solver converges, with CSW=0 everything appears to be fine when
the CLOVERDET monomial is used. with CSW!=0 dh is slightly too
largish, but not giantic... Probably some small bug somewhere...

bug fixed
- g_mu wasn't properly set to mnl->mu in cloverdet_monomial

introduced Qsw_pm_psi with twisted mass term opposed to Qsw_sq_psi,
the latter of which has mu=0 explicitly
sign bug fixed, hmc still not working with twisted and clover