Addresses issues #167 and #171

[pultar]

Description

Gromos_System objects can now also hold a QMMM object (QM/MM specification file). When this Gromos_System is used in the new submission system, the correct flags are passed to GROMOS.

Documentation is provided in form of a Jupyter notebook.

Smaller bugs and features have been addressed:

(1)

system.imd = imd_path  # imd_path is type string (updates the imd file according to the system's parameters)
system.imd = imd_file # imd_file is type Imd (no updates take place, unexpected behavior)

(2)

PyGromosTools reformatted QMMM specification files in a way they were unreadable for GROMOS and caused a segmentation fault. The bug could be resolved by replacing tabs with spaces. Reason being: GROMOS ignores the first 24 characters in QMMM specification files but PyGromosTools only provided five tabs.

(3) GromosXX and GromosPP in Gromos_System can be changed with setters. That enables users to run some simulations (e.g. energy minimization, equilibration) with one version of GROMOS and change to another built later (e.g. for QM/MM functionality).

(4) Two issues (#179 and #180) regarding OMP jobs have been resolved.

Summary

• [x] Support of QMMM specification files in Gromos_System
• [x] QM/MM calculations fully supported from PyGromosTools
• [x] Documentation in Jupyter notebook (#166)
• [x] Small new features: GromosXX and GromosPP in Gromos_System can be changed with setters
• [x] Small bugfixes (improvement of #167 and formatting changes in QMMM specification file)
• [x] Problem for default settings with OMP solved: #179
• [x] Problem with invalid bash scripts for OMP jobs is solved: #180
• [x] Last position of a given configuration can be retrieved easily: #181

Status

• [ ] Ready to go

[codecov[bot]]

Codecov Report

Merging #177 (d9fb3e1) into release3 (ed2dcf0) will decrease coverage by 0.11%. The diff coverage is 46.47%.

:exclamation: Current head d9fb3e1 differs from pull request most recent head 9a6e188. Consider uploading reports for the commit 9a6e188 to get more accurate results

@@             Coverage Diff              @@
##           release3     #177      +/-   ##
============================================
- Coverage     50.32%   50.21%   -0.12%     
============================================
  Files            90       90              
  Lines         11715    11800      +85     
============================================
+ Hits           5896     5925      +29     
- Misses         5819     5875      +56     

Flag	Coverage Δ
unittests	50.21% <46.47%> (-0.12%)	:arrow_down:

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
pygromos/gromos/gromosXX.py	19.56% <0.00%> (-0.29%)	:arrow_down:
...orkers/simulation_workers/simulation_run_worker.py	11.88% <5.00%> (-0.08%)	:arrow_down:
.../simulations/hpc_queuing/submission_systems/lsf.py	45.49% <30.00%> (-0.36%)	:arrow_down:
pygromos/files/gromos_system/gromos_system.py	64.65% <32.00%> (-2.78%)	:arrow_down:
pygromos/files/coord/cnf.py	40.76% <50.00%> (+0.03%)	:arrow_up:
.../job_scheduling/schedulers/simulation_scheduler.py	72.83% <50.00%> (-0.58%)	:arrow_down:
...g/job_scheduling/schedulers/scheduler_functions.py	67.46% <67.85%> (+0.03%)	:arrow_up:
...imulations/hpc_queuing/submission_systems/local.py	60.00% <75.00%> (+0.54%)	:arrow_up:
...c_queuing/submission_systems/_submission_system.py	76.40% <87.50%> (+1.09%)	:arrow_up:
pygromos/files/blocks/imd_blocks.py	76.13% <100.00%> (ø)
... and 8 more

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Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update 5127c40...9a6e188. Read the comment docs.

[lgtm-com[bot]]

This pull request introduces 1 alert when merging 6387e2cb16c85c7e787fd080438736d942368dc1 into 3d91010a84e8f31ef31860036d261a4be43b6882 - view on LGTM.com

new alerts:

• 1 for Unused local variable

[lgtm-com[bot]]

This pull request introduces 1 alert when merging 7fb0dd2e7e858b6dccaeffc2cf9d51f5bca880cf into 3d91010a84e8f31ef31860036d261a4be43b6882 - view on LGTM.com

new alerts:

• 1 for Unused local variable