Some minor tweaks

.gitignore

@@ -46,6 +46,7 @@ nosetests.xml
 coverage.xml
 *.cover
 .hypothesis/
+sim_*
 
 # Translations
 *.mo

ensemble_md/replica_exchange_EE.py

@@ -600,7 +600,7 @@ def get_ref_dist(self, pullx_file=None):
         Gets the reference distance(s) to use starting from the second iteration if distance restraint(s) are used.
         Specifically, a reference distance determined here is the initial COM distance between the pull groups
         in the input GRO file. This function initializes the attribute :code:`ref_dist`.
-        
+
         Parameter
         ---------
         pullx_file : str
@@ -920,7 +920,7 @@ def get_swapping_pattern(self, dhdl_files, states):
 
                 swap = ReplicaExchangeEE.propose_swap(swappables)
                 print(f'\nProposed swap: {swap}')
-                if swap == []:  # the same as len(swappables) == 0, self.proposal must not be exhaustive if this line is reached.
+                if swap == []:  # the same as len(swappables) == 0, self.proposal must not be exhaustive if this line is reached.  # noqa: E501
                     self.n_empty_swappable += 1
                     print('No swap is proposed because there is no swappable pair at all.')
                     break  # no need to re-identify swappable pairs and draw new samples
@@ -1332,7 +1332,7 @@ def _run_grompp(self, n, swap_pattern):
                 else:
                     gro = f"{self.gro}"
             else:
-                gro = f"{self.working_dir}/sim_{swap_pattern[i]}/iteration_{n-1}/confout.gro"  # This effectively swap out GRO files
+                gro = f"{self.working_dir}/sim_{swap_pattern[i]}/iteration_{n-1}/confout.gro"  # This effectively swap out GRO files  # noqa: E501
 
             if isinstance(self.top, list):
                 top = f"{self.top[i]}"

ensemble_md/tests/test_mpi_func.py

@@ -23,6 +23,7 @@
 comm = MPI.COMM_WORLD
 rank = comm.Get_rank()
 
+
 @pytest.fixture
 def params_dict():
     """
@@ -59,6 +60,40 @@ def get_REXEE_instance(input_dict, yml_file='params.yaml'):
     return REXEE
 
 
+def get_gmx_cmd_from_output(output):
+    """
+    Given a GROMACS output file like a LOG file or `mdout.mdp`, extract the GROMACS command that was run.
+
+    Parameters
+    ----------
+    output : str
+        The path to the GROMACS output file.
+
+    Returns
+    -------
+    cmd : str
+        The GROMACS command that was run.
+    flags : dict
+        The flags and values that were used in the GROMACS command.
+    """
+    f = open(output, 'r')
+    lines = f.readlines()
+    f.close()
+    n = -1
+    for l in lines:  # noqa: E741
+        n += 1
+        if l.startswith('Command line'):
+            cmd = lines[n+1].strip()
+
+    flags = {}
+    cmd_split = cmd.split(' ')
+    for i in range(len(cmd_split)):
+        if cmd_split[i].startswith('-'):
+            flags[cmd_split[i]] = cmd_split[i+1]
+
+    return cmd, flags
+
+
 @pytest.mark.mpi
 def test_run_grompp(params_dict):
     params_dict['grompp_args'] = {'-maxwarn': '1'}
@@ -80,4 +115,17 @@ def test_run_grompp(params_dict):
         for i in range(params_dict['n_sim']):
             assert os.path.isfile(f'{REXEE.working_dir}/sim_{i}/iteration_0/sys_EE.tpr') is True
             assert os.path.isfile(f'{REXEE.working_dir}/sim_{i}/iteration_0/mdout.mdp') is True
+
+            # Here we check if the command executed was what we expected
+            mdp = f'{REXEE.working_dir}/sim_{i}/iteration_0/mdout.mdp'
+            gro = params_dict['gro']
+            top = params_dict['top']
+            tpr = f'{REXEE.working_dir}/sim_{i}/iteration_0/sys_EE.tpr'
+            mdout = f'{REXEE.working_dir}/sim_{i}/iteration_0/mdout.mdp'
+            cmd = f'{REXEE.check_gmx_executable} -f {mdp} -c {gro} -p {top} -o {tpr} -po {mdout} -maxwarn 1'
+            assert get_gmx_cmd_from_output(mdout)[0] == cmd
+
             shutil.rmtree(f'{REXEE.working_dir}/sim_{i}')
+
+    # Case 2: Other iterations, i.e., n != 0
+    # More to come ...

ensemble_md/tests/test_replica_exchange_EE.py

@@ -460,7 +460,7 @@ def test_update_MDP(self, params_dict):
         REXEE.equil = [-1, 1, 0, -1]  # i.e., the 3rd replica will use fixed weights in the next iteration
         MDP_1 = REXEE.update_MDP(
             new_template, 2, iter_idx, states, wl_delta, weights)  # third replica
-        
+
         REXEE.get_ref_dist('ensemble_md/tests/data/pullx.xvg')  # so that we can test the pull code
         MDP_2 = REXEE.update_MDP(
             new_template, 3, iter_idx, states, wl_delta, weights, counts)  # fourth replica
@@ -663,7 +663,6 @@ def test_get_swapping_pattern(self, params_dict):
         assert pattern_4_3 == [0, 2, 1, 3]
         assert swap_list_4_3 == [(1, 2)]
 
-
     def test_calc_prob_acc(self, capfd, params_dict):
         # k = 1.380649e-23; NA = 6.0221408e23; T = 298; kT = k * NA * T / 1000 = 2.4777098766670016
         REXEE = get_REXEE_instance(params_dict)