Build #66

[frankmenglin]

For some reasons test on this pull request
http://not0rious.stanford.edu:8080/job/forcebalance-pull-request/66/
has been run for more than 1 day, I'm not sure if it's still running properly.
#68 is an update on Energy Estimator(Centroid estimator instead of Primitive Estimator, and )

[frankmenglin]

and the energy estimator is used to calculate KE and PE for both equilibrium and production run.

[leeping]

Yeah there's a problem with Jenkins. I don't know whether something has changed in the code, or something has gone wrong with how Jenkins interacts with GitHub. Can you run the tests locally (python test in your source folder) and see if they all successfully complete?

[frankmenglin]

I've install it locally and run and it works(finish w/o error but not long enough to compare the numerical result). There are a few tests fail but those are related to Gromacs.

Error message
/home/frank000/opt/gromacs/bin/gmxdump -s gmx.tpr -sys gave a return code of -4 (it may have crashed)

[leeping]

Can you paste the entire error message?

• Lee-Ping

[leeping]

By the way, the Jenkins tests are now working. Your PR passes all of the tests. We can either continue your implementation in the same PR or start a different one, but there's no real difference (in fact, let's just keep working in the same PR).

[frankmenglin]

OK cool. The test pass but for some reasons the (RPMD)simulation blows(finish with inf value in lots of properties). Trying to fix that now.

[leeping]

Okay. You may run npt.py directly to test things more easily, if you aren't already doing that. Just make sure you're in one of the temp-directories (and the forcebalance.p file exists). Then run python npt.py openmm 298.15 1.0 (for room temperature and atmospheric pressure for example).

[frankmenglin]

Will that be an RPMD simulation? The simulation currently only blows when using RPMD.

[leeping]

Yes, it will be a RPMD simulation. Remember the simulation settings are all stored inside forcebalance.p .