Finished updating the documentation

docs/analysis.rst

@@ -1,7 +1,7 @@
 1. An overview
 ==============
-Automated data analysis of an EEXE simulation is allowed by the CLI :code:`analyze_EEXE`, which
-share the same input YAML file as the CLI :code:`run_EEXE`. Relevant parameters specified in the YAML
+Automated data analysis of an REXEE simulation is allowed by the CLI :code:`analyze_REXEE`, which
+share the same input YAML file as the CLI :code:`run_REXEE`. Relevant parameters specified in the YAML
 file for data analysis can be found in this section: :ref:`doc_analysis_params`.
 
 - Analysis based on transitions between replicas

docs/getting_started.rst

@@ -2,8 +2,8 @@
 ===============
 :code:`ensemble_md` is a Python package that provides methods for setting up, 
 running, and analyzing GROMACS simulation ensembles. The current implementation is
-mainly for synchronous ensemble of expanded ensemble (EEXE), but we will develop
-methods like asynchronous EEXE, or ensemble of alchemical metadynamics in the future.
+mainly for synchronous replica exchange (REX) of expanded ensemble (EE), abbreviated as
+REXEE. In the future, we will develop methods like asynchronous REXEE, or multi-topology REXEE.
 In the current implementation, the module :code:`subprocess`
 is used to launch GROMACS commands, but we will switch to `SCALE-MS`_ for this purpose
 in the future when possible.

docs/index.rst

@@ -24,17 +24,17 @@ the future.
 .. toctree::
    simulations
    :maxdepth: 2
-   :caption: Launching EEXE simulations:
+   :caption: Launching REXEE simulations:
 
 .. toctree::
    analysis
    :maxdepth: 2
    :caption: Data analysis:
 
 .. toctree::
-   examples/run_EEXE
-   examples/analyze_EEXE
-   examples/run_EEXE_modify_inputs
+   examples/run_REXEE
+   examples/analyze_REXEE
+   examples/run_REXEE_modify_inputs
    :maxdepth: 2
    :caption: Tutorials:
 

docs/theory.rst

@@ -2,13 +2,12 @@
 
 1. Basic idea
 =============
-Ensemble of expanded ensemble (EEXE) integrates the core principles of replica exchange 
-molecular dynamics (REMD) and expanded ensemble (EXE).  Specifically, an ensemble of 
-expanded ensembles includes multiple non-interacting, parallel expanded ensemble simulations 
+Replica exchange of expanded ensemble (REXEE) integrates the core principles of replica exchange 
+molecular dynamics (REMD) and expanded ensemble (EXE).  Specifically, a REXEE simulation includes multiple non-interacting, parallel expanded ensemble simulations 
 that collectively sample a number of alchemical states spanning between the coupled state 
 (:math:`\lambda=0`) and the uncoupled state (:math:`\lambda=1`). Each expanded ensemble 
 samples a subset of these states such that the range of its allowed alchemical states 
-overlaps with that of the adjacent replicas. In EEXE, the exchange of coordinates/alchemical 
+overlaps with that of the adjacent replicas. In REXEE, the exchange of coordinates/alchemical 
 states occurs at a specified frequency, which is beneficial for allowing better mixing 
 in the alchemical space given sufficiently long simulation time, properly specified parameters 
 and highly parallelizable computing architectures. 
@@ -401,10 +400,10 @@ sampling different alchemical ranges would have different references. Therefore,
 
 2.4. How is swapping performed?
 -------------------------------
-As implied in :ref:`doc_basic_idea`, in an EEXE simulation, we could either choose to swap configurations
+As implied in :ref:`doc_basic_idea`, in an REXEE simulation, we could either choose to swap configurations
 (via swapping GRO files) or replicas (via swapping MDP files). In this package, we chose the former when
-implementing the EEXE algorithm. Specifically, in the CLI :code:`run_EEXE`, the function :obj:`.get_swapping_pattern`
-is called once for each iteration and returns a list :code:`swap_pattern` that informs :code:`run_EEXE` how
+implementing the REXEE algorithm. Specifically, in the CLI :code:`run_REXEE`, the function :obj:`.get_swapping_pattern`
+is called once for each iteration and returns a list :code:`swap_pattern` that informs :code:`run_REXEE` how
 the GRO files should be swapped. (To better understand the list :code:`swap_pattern`, see the docstring of
 the function :obj:`.get_swapping_pattern`.) Internally, the function :obj:`.get_swapping_pattern` not only swaps
 the list :code:`swap_pattern` when an attempted move is accepted, but also swaps elements in lists that contains
@@ -419,7 +418,7 @@ in the list of states. Check the source code of :obj :`.get_swapping_pattern` if
 3.1. Basic idea
 ---------------
 To leverage the stastics of the states collected from multiple replicas, we recommend 
-combining the alchemical weights of these states across replicas during an weight-updating EEXE simulation.
+combining the alchemical weights of these states across replicas during an weight-updating REXEE simulation.
 Ideally, the modified weights should facilitate the convergence of the alchemical weights in expanded ensemble, 
 which in the limit of inifinite simulation time correspond to dimensionless free energies of the alchemical states. 
 The modified weights also directly influence the the accpetance ratio, hence the convergence of the simulation
@@ -539,5 +538,5 @@ To deal with this, the user can choose to specify :code:`N_cutoff` in the input
 correction will performed only when :math:`\text{argmin}(N_k, N_{k-1})` is larger than the cutoff. Also, this histogram correction 
 should always be carried out before weight combination. This method is implemented in :obj:`.histogram_correction`.
 
-4. Parameter space of EEXE
+4. Parameter space of REXEE
 ===========================

ensemble_md/cli/analyze_REXEE.py

@@ -35,7 +35,7 @@
 
 def initialize(args):
     parser = argparse.ArgumentParser(
-        description='This code analyzes an ensemble of expanded ensemble. Note that the template MDP\
+        description='This code analyzes a REXEE simulation. Note that the template MDP\
                 file specified in the YAML file needs to be available in the working directory.')
     parser.add_argument('-y',
                         '--yaml',

ensemble_md/cli/run_REXEE.py

@@ -24,7 +24,7 @@
 
 def initialize(args):
     parser = argparse.ArgumentParser(
-        description='This code runs an ensemble of expanded ensemble given necessary inputs.')
+        description='This code runs a REXEE simulation given necessary inputs.')
     parser.add_argument('-y',
                         '--yaml',
                         type=str,
@@ -99,7 +99,7 @@ def main():
                 MDP = REXEE.initialize_MDP(i)
                 MDP.write(f"sim_{i}/iteration_0/expanded.mdp", skipempty=True)
 
-        # 2-2. Run the first ensemble of simulations
+        # 2-2. Run the first set of simulations
         REXEE.run_REXEE(0)
 
     else:
@@ -280,7 +280,7 @@ def main():
                     print(f'\nAn error occurred on rank 0:\n{traceback.format_exc()}')
                     MPI.COMM_WORLD.Abort(1)
 
-        # 4-2. Run another ensemble of simulations
+        # 4-2. Run another set of simulations
         REXEE.run_REXEE(i, swap_pattern)
 
         # 4-3. Save data