Added the YAML parameter working_dir

.circleci/config.yml

@@ -53,7 +53,8 @@ jobs:
           name: Run unit tests
           command: |
             source $HOME/pkgs/bin/GMXRC
-            pip3 install pytest 
+            pip3 install pytest
+            pip3 install pytest-mpi
             pip3 install pytest-cov
             pytest -vv --disable-pytest-warnings --cov=ensemble_md --cov-report=xml --color=yes ensemble_md/tests/
             mpirun -np 4 pytest -vv --disable-pytest-warnings --cov=ensemble_md --cov-report=xml --color=yes ensemble_md/tests/test_mpi.py --with-mpi

docs/simulations.rst

@@ -222,8 +222,8 @@ include parameters for data analysis here.
       :code:`/usr/local/gromacs/bin/gmx`, the path returned by the command :code:`which gmx`) should be used.
       Note that REXEE only works with MPI-enabled GROMACS. 
 
-3.2. Input files
-----------------
+3.2. Input settings
+-------------------
 
   - :code:`gro`: (Required)
       The input system configuration in the form of GRO file(s) used to initiate the REXEE simulation. If only one GRO file is specified,
@@ -242,6 +242,8 @@ include parameters for data analysis here.
       exchanges only occur in the end states, then one could have :math:`λ` values like :code:`0.0 0.3 0.7 1.0 0.0 0.3 ...`. Notably, unlike
       the parameters :code:`gro` and :code:`top`, only one MDP file can be specified for the parameter :code:`mdp`. If you wish to use
       different parameters for different replicas, please use the parameter :code:`mdp_args`.
+  - :code:`working_dir`: (Optional, Default: :code:`os.getcwd()`)
+      The working directory where the REXEE simulation will be performed. If not specified, the current working directory will be used.
   - :code:`modify_coords`: (Optional, Default: :code:`None`)
       The name of the Python module (without including the :code:`.py` extension) for modifying the output coordinates of the swapping replicas
       before the coordinate exchange, which is generally required in REXEE simulations for multiple serial mutations.

ensemble_md/replica_exchange_EE.py

@@ -152,6 +152,7 @@ def set_params(self, analysis):
         # Step 3: Handle the optional YAML parameters
         # Key: Optional argument; Value: Default value
         optional_args = {
+            "working_dir": os.getcwd(),
             "add_swappables": None,
             "modify_coords": None,
             "nst_sim": None,
@@ -592,7 +593,7 @@ def initialize_MDP(self, idx):
 
         return MDP
 
-    def get_ref_dist(self, pullx_file = 'sim_0/iteration_0/pullx.xvg'):
+    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
@@ -605,6 +606,8 @@ def get_ref_dist(self, pullx_file = 'sim_0/iteration_0/pullx.xvg'):
             Usually, this should be the path of the pullx file of the first iteration. The default
             is :code:`sim_0/iteration_0/pullx.xvg`.
         """
+        if pullx_file is None:
+            pullx_file = f"{self.working_dir}/sim_0/iteration_0/pullx.xvg"
         if hasattr(self, 'set_ref_dist'):
             self.ref_dist = []
             for i in range(len(self.set_ref_dist)):
@@ -1320,14 +1323,14 @@ def _run_grompp(self, n, swap_pattern):
             arguments = [self.gmx_executable, 'grompp']
 
             # Input files
-            mdp = f"sim_{i}/iteration_{n}/{self.mdp.split('/')[-1]}"
+            mdp = f"{self.working_dir}/sim_{i}/iteration_{n}/{self.mdp.split('/')[-1]}"
             if n == 0:
                 if isinstance(self.gro, list):
                     gro = f"{self.gro[i]}"
                 else:
                     gro = f"{self.gro}"
             else:
-                gro = f"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
 
             if isinstance(self.top, list):
                 top = f"{self.top[i]}"
@@ -1339,8 +1342,8 @@ def _run_grompp(self, n, swap_pattern):
 
             # Add output file arguments
             arguments.extend([
-                "-o", f"sim_{i}/iteration_{n}/sys_EE.tpr",
-                "-po", f"sim_{i}/iteration_{n}/mdout.mdp"
+                "-o", f"{self.working_dir}/sim_{i}/iteration_{n}/sys_EE.tpr",
+                "-po", f"{self.working_dir}/sim_{i}/iteration_{n}/mdout.mdp"
             ])
 
             # Add additional arguments if any
@@ -1394,7 +1397,7 @@ def _run_mdrun(self, n):
         if rank == 0:
             print('Running EXE simulations ...')
         if rank < self.n_sim:
-            os.chdir(f'sim_{rank}/iteration_{n}')
+            os.chdir(f'{self.working_dir}/sim_{rank}/iteration_{n}')
             returncode, stdout, stderr = utils.run_gmx_cmd(arguments)
             if returncode != 0:
                 print(f'Error on rank {rank} (return code: {returncode}):\n{stderr}')