hi ross and wei,
i just updated the tests for PIMD/NMPIMD/CMD and NEB. Everything is in
test/PIMD.
so, i think that the following tests can be removed:
pimd_water/P=8/pimd
pimd_water/P=16/pimd
pimd_water/P=32/pimd
neb_gb
pimd_helium/P=4/pimd
pimd_spcfw
tests for pimd_gb and qmm2+pimd are still missing. for these i need your
help because i do not how to generate the proper prmtop files to run
with the new implementation of PIMD within sander.MPI.
thanks,
francesco
Ross Walker wrote:
> Hi Francesco and other PIMD people...
>
>
>> Some of the updated PIMD test cases are in the directory
>> test/PIMD and
>> these are included in the Makefile. I'm going to put also there the
>> tests for PIMD/QMMM and PIMD/GB.
>>
>
> Okay - so let me confirm the situation here...
>
> 1) All active Amber 10 PIMD test cases are now in the directory
> $AMBERHOME/test/PIMD
>
> 2) All active Amber 10 evb test cases are in the directory
> $AMBERHOME/test/evb
>
> Is this correct?
>
> If so then I assume all of the following test cases are defunct and can be
> removed from the CVS tree:
>
> test/evb_bond_umb
> test/evb_bond_umb_nmpimd_nhc
> test/evb_cnst
> test/evb_exp
> test/evb_gauss
> test/evb_morsify
> test/evb_nrg_map
> test/evb_nrg_umb
>
> These all look to be empty directories so should probably just be backed up
> and removed from the master CVS tree by Dave C.
>
> test/full_pimd (and all sub directories)
> test/part_pimd (and all sub directories)
> test/pimd_gb
> test/pimd_helium
> test/pimd_ntp
> test/pimd_spcfw
> test/pimd_water
> test/pimd_water_nhc
>
> These still contain a large number of active CVS files and were the original
> source of my confusion. I suggest all the files get removed from CVS. Dave C
> can then backup the attic files and delete the directories from the master
> cvs tree.
>
> test/neb_gb
> test/qmmm2/neb_gb
> test/qmmm2/neb_pureQM_PM3
> test/qmmm2/pimd_gb
> test/qmmm2/pimd_pme
>
> These all still have active CVS files in but are not run from the Makefile
> anymore. This of course means that the code would appear to have been
> updated but we now have no active PIMD QMMM test cases. In addition we
> actually have NO active NEB test cases either QMMM or classical.
>
> So I assume the above should also be deleted and then Francesco you will
> create verified (and I do mean verified, not just copies of the output
> files, but calculations where you explicitly verify the results) copies of
> QMMM PIMD test cases in the test/PIMD directory?
>
> Meanwhile since we have no active NEB test cases and I am in the process of
> trying to explicitly verify the NEB results - by checking that it gets the
> correct pathway for alanine dipeptide - I will create a directory called:
>
> test/NEB/
>
> and in here I will put a series of classical and QMMM NEB test cases and
> these can become the master NEB test cases.
>
> Are we all in agreement here?
>
> If so then I will start going through and cleaning up the above named
> directories using "cvs remove"
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
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>
>
>
>
Received on Wed May 09 2007 - 06:07:35 PDT
