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Jul 22, 2021
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fixes to make tests pass locally
- fix encoding issues in file
- allow GROMACS to choose number of threads in most of the tests to avoid problems when GROMACS was not compiled
  to change thread numbers (ERROR: Setting the total number of threads is only supported with thread-MPI
  but this version of GROMACS was not compiled with tMPI)
orbeckst committed Jul 21, 2021
commit 6d86f7b571cc57cbe1ab433e9e9e5646c833762f
3 changes: 2 additions & 1 deletion mdpow/forcefields.py
Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
# -*- coding: utf-8 -*-
# POW package __init__.py
# Copyright (c) 2012 Oliver Beckstein <[email protected]>
# Released under the GNU Public License 3 (or higher, your choice)
@@ -146,7 +147,7 @@ def get_water_model(watermodel=DEFAULT_WATER_MODEL):

#: Other solvents (not water, see :data:`GROMACS_WATER_MODELS` for those).
new_octanol = '''Zangi R (2018) Refinement of the OPLSAA force-field
for liquid alcohols.; ACS Omega 3(12):1808918099.
for liquid alcohols.; ACS Omega 3(12):18089-18099.
doi: 10.1021/acsomega.8b03132'''

OPLS_SOLVENT_MODELS = {
2 changes: 1 addition & 1 deletion mdpow/tests/test_runinput.py
Original file line number Diff line number Diff line change
@@ -79,7 +79,7 @@ class TestAlteredConfig(object):
'stepout': 12000,
'verbose': False,
'nice': 12,
'maxthreads': 3
'maxthreads': 1
}
}

4 changes: 1 addition & 3 deletions mdpow/tests/testing_resources/states/base/runinput.yml
Original file line number Diff line number Diff line change
@@ -119,8 +119,6 @@ mdrun:
# report progress verbosely (True is -v)
nice: 19
# nicel level
maxthreads: 3
maxthreads: None
# maximum number of threads (-nt), 0 or None lets mdrun
# automatically choose
# For testing on travis, needs to be either 3 or 1.
# See https://github.com/Becksteinlab/MDPOW/pull/77
5 changes: 2 additions & 3 deletions mdpow/tests/testing_resources/states/md_npt/runinput.yml
Original file line number Diff line number Diff line change
@@ -119,8 +119,7 @@ mdrun:
# report progress verbosely (True is -v)
nice: 19
# nicel level
maxthreads: 3
maxthreads: None
# maximum number of threads (-nt), 0 or None lets mdrun
# automatically choose
# For testing on travis, needs to be either 3 or 1.
# See https://github.com/Becksteinlab/MDPOW/pull/77

Original file line number Diff line number Diff line change
@@ -119,5 +119,5 @@ mdrun:
# report progress verbosely (True is -v)
nice: 12
# nicel level
maxthreads: 3
maxthreads: 1
# maximum number of threads (-nt), 0 or None lets mdrun automatically choose