Hi All,
I will work on the pimd_gb and pimd_qmmm test case and put it into
test/PIMD directory.
Sincerely,
Wei
Francesco Paesani wrote:
> 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 |
>>
>> Note: Electronic Mail is not secure, has no guarantee of delivery,
>> may not
>> be read every day, and should not be used for urgent or sensitive
>> issues.
>>
>>
>>
>
>
>
>
Received on Sun May 13 2007 - 06:07:10 PDT
