Tempering update

docs/_docs/moves.md

@@ -321,6 +321,7 @@ The default value of `repeat` is the number of atoms in the `molecule` minus two
 `volume_scale=isotropic` | How to apply exchanged volumes: `z`, `xy`, `isotropic`, `isochoric`
 `nstep=1`                | Number of sweeps between samples.
 `partner_policy=oddeven` | Policy used to create partner pairs (currently only `oddeven`)
+`file`                   | Exchange statistics from the tempering moves (`.dat|.dat.gz`)
 
 We consider an extended ensemble, consisting of _n_
 sub-systems or replicas, each in a distinct thermodynamic state (different
@@ -352,8 +353,15 @@ Support for fluctuating number of particles, i.e.
 grand canonical moves is currently untested and should be
 considered experimental.
 
-#Exchange statistics
-In the output file, the acceptance and attempts of an exchange direction can be found under exchange in temper;moves. Next, the first tap under  exchangempi gives which mpi box the outfile represents (ex. 0, 1,...). Under this number the tab exchanges all executed temper movements are listed. For each movement two placeholders  are given, which represents the mpi's the tempering algorithm tries to switch. If the tempering move was not accepted, both the placeholders will be -1. When the tempering move is accepted do the placeholders contain the numbers of the interchanged mpi's. In faunus/examples/temper there is a notebook "temper\_exchange\_statistics.ipynb" illustrating how this aquired data can be used to study how the mpi's are exchanged.  
+
+# Exchange statistics
+
+If `file` is provided, an exchange file for each MPI rank is created.
+For respective step accepted and rejected attempts of exchange direction are recorded. 
+If the tempering move was rejected, the number -1 is recorded.
+When the tempering move is accepted, the number of the interchanged mpi is recorded. 
+For example, in the exchange file for MPI rank 2 an accepted temper move with rank 3 will record a 3, meaning the mpi's `2 <-> 3` etc. 
+In `examples/temper/` contains a notebook illustrating how this can be used to study how exchange statistics.  
 
 
 ## Volume Move

examples/temper/temper_exchange_statictics.ipynb

@@ -0,0 +1,89 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "d5e44a45",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%matplotlib inline\n",
+    "import matplotlib as mpl\n",
+    "import matplotlib.pyplot as plt\n",
+    "import pandas as pd\n",
+    "import numpy as np\n",
+    "import os.path, os, sys, glob, json, copy\n",
+    "from jinja2 import Template\n",
+    "from itertools import product\n",
+    "import ruamel_yaml as yaml\n",
+    "from io import StringIO \n",
+    "import json\n",
+    "\n",
+    "workdir = 'workdir_example_name' #Change to name of directory where files are located\n",
+    "\n",
+    "counter = 0 \n",
+    "mpi_where = 0 #Which mpi to start in"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "c30e78d2",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "\n",
+    "counter = 1 \n",
+    "mpi_where = 9 #which mpi to start in\n",
+    "steps = 10 #number of tempering events\n",
+    "\n",
+    "plt.plot(0, mpi_where, 'k*', markersize=7) #starting point\n",
+    "plt.title(f'Movement of original mpi {mpi_where}')\n",
+    "\n",
+    "\n",
+    "mpiX = np.loadtxt(f'{workdir}/mpi{mpi_where}.exchange.dat', delimiter=' ', skiprows=1) # mpi exchange file to start with\n",
+    "\n",
+    "while counter <= len(mpiX):# go throuhg all exchanges, once the counter is larger than the length of the exchange file, there where no more exchanges\n",
+    "    if counter != mpiX[counter-1][0]: # check if the counter is the same as the step number\n",
+    "        plt.plot(counter, mpi_where, 'r*') # if not, there was no exchange and mpi_where stays the same\n",
+    "        counter += 1\n",
+    "        continue\n",
+    "                       \n",
+    "    if mpiX[counter-1][1] == -1: # if -1 the exchanges was not accepted add to counter, mpi_where stays the same\n",
+    "        plt.plot(counter, mpi_where, 'r*')\n",
+    "        counter += 1\n",
+    "        continue\n",
+    "    else: # check between which ranks were swapped \n",
+    "        if mpi_where < mpiX[counter-1][1]: # if mpi_where is smaller than the rank the exchange was made with mpi number mpi_where + 1\n",
+    "            mpi_where += 1 \n",
+    "        if mpi_where > mpiX[counter-1][1]: # if mpi_where is larger than the rank the exchange was made with mpi number mpi_where - 1\n",
+    "            mpi_where -= 1 \n",
+    "\n",
+    "        plt.plot(counter, mpi_where, 'bo')\n",
+    "        mpiX = np.loadtxt(f'{workdir}/mpi{mpi_where}.exchange.dat', delimiter=' ', skiprows=1) # load exchange file for currect mpi \n",
+    "        counter += 1\n"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.16"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}