Repex submission new #222
Repex submission new #222
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…s with proper conformations
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Will check it out later! |
Codecov Report
@@ Coverage Diff @@
## release3 #222 +/- ##
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- Coverage 54.63% 54.54% -0.10%
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Files 92 92
Lines 13884 13902 +18
============================================
- Hits 7586 7583 -3
- Misses 6298 6319 +21
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pygromos/files/blocks/imd_blocks.py
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| setattr(self, "NRET", int(content[3].split()[0])) | ||
| T_values = list(map(float, content[5].split())) | ||
| if(len(T_values)== self.NRET): | ||
| setattr(self, "RET", T_values) | ||
| else: | ||
| raise IOError("REPLICA: NRET was not equal to the number of Temperatures (RET) in IMD!") | ||
| setattr(self, "LRESCALE", int(content[7].split()[0])) | ||
| print (content[7]) |
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yes forgot to remove this one
… depending on multi node / single node setup
…osTools into repex_submission_new
| @@ -21,7 +21,7 @@ def do(in_simSystem: Gromos_System, | |||
| simulation_run_num: int, | |||
| equilibration_run_num: int = 0, | |||
| work_dir: str = None, | |||
| initialize_first_run= False, reinitialize_every_run= False, | |||
| initialize_first_run= True, reinitialize_every_run= False, | |||
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I'm against this change. I believe PyGromos should by default not change anything.
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@pultar Very good to hear that your simulations are unaffected and still run well with these changes. Concerning the But I don't have particularly strong feelings about it either. I just know that one (and maybe more) of the downstream functions such as those in As long as all functions with they argument have the same default then I am happy. |
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note: I only fixed some merge conflicts in this previous merge. I still have a few more things to do on this branch so it should not be merged just yet. |
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I am closing the pull request as I re-implemented these changes (with slight improvements in a different branch, see #288) |
Description
This pull request includes the addition of code to submit replica exchange (Temperature, Hamiltonian, and RE-EDS) simulations using the exact same convention as for normal simulations.
In short the call to the code in
schedule_MD_job.pywritten by the simulation scheduler will automtaically adjust everything it needs to dispatch the calculation to eithermd,md_mpiorrepex_mpi.The waiting for output files was adjusted to wait for all N (number of replicas) output cnfs. Similarly the path provided is slightly adjusted to match the convention of gromos for replica exchange depending on the presence / absence of the CONT keyword.
The code was also tested with regular MD simulations, and there was no problem in submitting / zipping files for those.
@MTLehner @pultar As you might be the most frequent users of pyGromos at the moment you might want to checkout my branch and see if the submission for your systems still works fine!
Todos
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