Rename the EEXE method as REXEE method

README.md

@@ -12,7 +12,7 @@ Ensemble Molecular Dynamics
 [![Downloads](https://static.pepy.tech/badge/ensemble-md)](https://pepy.tech/project/ensemble-md)
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-**ensemble_md** is a Python package that provides methods for setting up, running, and analyzing molecular dynamics ensembles in GROMACS. The current implementation is mainly for synchronous ensemble of expanded ensemble (EXEE), but we will develop methods like asynchronous EEXE, or ensemble of alchemical metadynamics in the future. For installation instructions, theory overview, tutorials, and API references, please visit the [documentation](https://ensemble-md.readthedocs.io/en/latest/?badge=latest).
+**ensemble_md** is a Python package that provides methods for setting up, running, and analyzing molecular dynamics ensembles in GROMACS. The current implementation is 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. For installation instructions, theory overview, tutorials, and API references, please visit the [documentation](https://ensemble-md.readthedocs.io/en/latest/?badge=latest).
 
 ### Copyright
 

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/examples/analyze_EEXE.ipynb → docs/examples/analyze_REXEE.ipynb

@@ -5,8 +5,14 @@
    "id": "cc81ea4a",
    "metadata": {},
    "source": [
-    "# Tutorial 2: Analyzing an ensemble of expanded ensemble"
+    "# Tutorial 2: Analyzing a REXEE simulation"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "c3014606",
+   "metadata": {},
+   "source": []
   }
  ],
  "metadata": {

docs/examples/run_EEXE.ipynb → docs/examples/run_REXEE.ipynb

@@ -5,15 +5,15 @@
    "id": "87324540",
    "metadata": {},
    "source": [
-    "# Tutorial 1: Launching an ensemble of expanded ensemble"
+    "# Tutorial 1: Launching a REXEE simulation"
    ]
   },
   {
    "cell_type": "markdown",
    "id": "b2d9b443",
    "metadata": {},
    "source": [
-    "In this tutorial, we will show how one can launch an ensemble of expanded ensemble simulations in parallel using functions in `ensemble_md`. To this end, we will at least need 4 files: one top file (`sys.top`) and one gro file (`sys.gro`) for the system of interest, one mdp file as the template for customizing mdp files for different replicas (`expanded.mdp`), and finally a yaml file speciying the EEXE-relevant parameters (`params.yaml`). \n",
+    "In this tutorial, we will show how one can launch an ensemble of expanded ensemble simulations in parallel using functions in `ensemble_md`. To this end, we will at least need 4 files: one top file (`sys.top`) and one gro file (`sys.gro`) for the system of interest, one mdp file as the template for customizing mdp files for different replicas (`expanded.mdp`), and finally a yaml file speciying the REXEE-relevant parameters (`params.yaml`). \n",
     "\n",
     "In our case, the system of interest is a linear model composed of 4 interaction sites, where the first and last atom have a charge of +0.2 and -0.2, respectively. In `expanded.mdp`, we define 9 alchemical states in total to decouple the van der Waals interactions and coulombic interactions. Our goal is to run an ensemble composed of 4 replicas of expanded ensemble, each of which sample 6 alchemical states, with the shift between adjacent replicas being 1 state. That is, we want replicas 0 to 3 to sample states 0 to 6, 1 to 7, 2 to 8, and 3 to 9, respectively. Each replica will be performed for 5 iterations, with the length of each iteration being 500 steps (i.e. 1 ps). We will use the Metropolis MC scheme to swap replicas, and use exponential averaging with histogram correction for combining weights of exchanging replicas. The histogram cutoff will be set as 1000 to avoid overcorrection and we will swap 2 pairs of replicas in each attempt when possible. All STDOUT will be redirected to `results.txt`. \n",
     "\n",
@@ -33,6 +33,12 @@
     "outfile: 'results.txt'       # The output file for logging how replicas interact with each other.\n",
     "```"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "6cedf8d9",
+   "metadata": {},
+   "source": []
   }
  ],
  "metadata": {

docs/examples/run_EEXE_modify_inputs.ipynb → docs/examples/run_REXEE_modify_inputs.ipynb

@@ -5,8 +5,14 @@
    "id": "87324540",
    "metadata": {},
    "source": [
-    "# Tutorial 3: EEXE for multiple serial mutations"
+    "# Tutorial 3: REXEE for multiple serial mutations"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "46970a2d",
+   "metadata": {},
+   "source": []
   }
  ],
  "metadata": {

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: