Finished updating utils

ensemble_md/utils/gmx_parser.py

@@ -24,7 +24,7 @@
 def parse_log(log_file):
     """
     This function parses a log file generated by expanded ensemble and provides
-    important information, especially for running new iterations in EEXE.
+    important information, especially for running new iterations in REXEE.
     Typically, there are three types of log files from an expanded ensemble simulation:
 
     - **Case 1**: The weights are still updating in the simulation and have never been equilibrated.
@@ -58,7 +58,7 @@ def parse_log(log_file):
           incrementor up to equilibration will be returned.
         - In Case 3, the returned list will only have one list inside, which is the list of the final weights.
 
-        That is, for all cases, :code:`weights[-1]` will be the final weights, which are useful in EEXE.
+        That is, for all cases, :code:`weights[-1]` will be the final weights, which are useful in REXEE.
     counts : list
         The final histogram counts.
     wl_delta : float
@@ -390,7 +390,7 @@ def compare_MDPs(mdp_list, print_diff=False):
     Given a list of MDP files, identify the parameters for which not all MDP
     files have the same values. Note that this function is not aware of the default
     values of GROMACS parameters. (Currently, this function is not used in the
-    workflow adopted in :code:`run_EEXE.py` but it might be useful in some places,
+    workflow adopted in :code:`run_REXEE.py` but it might be useful in some places,
     so we decided to keep it.)
 
     Parameters

ensemble_md/utils/utils.py

@@ -289,9 +289,9 @@ def get_time_metrics(log):
     return t_metrics
 
 
-def analyze_EEXE_time(log_files=None):
+def analyze_REXEE_time(log_files=None):
     """
-    Perform simple data analysis on the wall times and performances of all iterations of an EEXE simulation.
+    Perform simple data analysis on the wall times and performances of all iterations of an REXEE simulation.
 
     Parameters
     ----------
@@ -301,7 +301,7 @@ def analyze_EEXE_time(log_files=None):
     Returns
     -------
     t_wall_tot : float
-        The total wall time GROMACS spent to finish all iterations for the EEXE simulation.
+        The total wall time GROMACS spent to finish all iterations for the REXEE simulation.
     t_sync : float
         The total time spent in synchronizing all replicas, which is the sum of the differences
         between the longest and the shortest time elapsed to finish a iteration.