Fix typo.

[alexxy/gromacs.git] / python_packaging / src / gmxapi / simulation / mdrun.py

diff --git a/python_packaging/src/gmxapi/simulation/mdrun.py b/python_packaging/src/gmxapi/simulation/mdrun.py
index 066d40c4c09744f90b244b2226576446d700335c..dae0c1effe3073ffb2a40dbaf6b611cd54d6d8e6 100644 (file)
--- a/python_packaging/src/gmxapi/simulation/mdrun.py
+++ b/python_packaging/src/gmxapi/simulation/mdrun.py
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2019, by the GROMACS development team, led by
+# Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.
@@ -216,7 +216,7 @@ class LegacyImplementationSubscription(object):
                             # It is unspecified by the API, but at least through gmxapi 0.1,
                             # all simulations are initialized with a checkpoint file named state.cpt
                             # (see src/api/cpp/context.cpp)
-                            checkpoint_file = os.path.join(self.workdir, 'state.cpp')
+                            checkpoint_file = os.path.join(self.workdir, 'state.cpt')
                             expected_working_files.append(checkpoint_file)
 
                             for file in expected_working_files:
@@ -261,8 +261,11 @@ class LegacyImplementationSubscription(object):
                                                                       ensemble_rank,
                                                                       self.workdir
                                                                       ))
-                    # TODO: We have not exposed the ability to pass any run time parameters to mdrun.
-                    work = workflow.from_tpr(tpr_filenames)
+                    # TODO: (#3718) Normalize the way we pass run time parameters to mdrun.
+                    kwargs = getattr(resource_manager, 'mdrun_kwargs', {})
+                    for key, value in kwargs.items():
+                        logger.debug('Adding mdrun run time argument: {}'.format(key + '=' + str(value)))
+                    work = workflow.from_tpr(tpr_filenames, **kwargs)
                     self.workspec = work.workspec
                     context = LegacyContext(work=self.workspec, workdir_list=workdir_list, communicator=ensemble_comm)
                     self.simulation_module_context = context