Docs work

docs/notebooks/Spatial_dependance.ipynb

@@ -0,0 +1,65 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "6e4c0d1a",
+   "metadata": {},
+   "source": [
+    "# Spatial dependance"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "1e1703f0",
+   "metadata": {},
+   "source": [
+    "In folie, there is several possibilities for the spatial dependances of the drift and diffusion. This section"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6bca058b",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "7f59717c",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "markdown",
+   "id": "838af326",
+   "metadata": {},
+   "source": [
+    "## Multi dimensionnal system"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "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": "3.10.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

docs/notebooks/estimation.ipynb

@@ -239,13 +239,58 @@
     "\n",
     "Likelihood estimator are parallelized using n_jobs=<wanted number of cores> with computation of likelihood being parallelized over trajectories."
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "c3b93410",
+   "metadata": {},
+   "source": [
+    "## Units"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "d026be73",
+   "metadata": {},
+   "source": [
+    "folie work in units of CV and units of time. Those units are defined on the loading as the units of the inputs array."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "214fa4ac",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "data = fl.Trajectories(dt=1.0e-3)  # This define the units of time\n",
+    "n=1 # Let's use the first molecule.\n",
+    "trj = np.loadtxt(f\"DATA\")\n",
+    "data.append(trj.reshape(-1,1))  # This define the units of the CV"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "a0d4a9db",
+   "metadata": {},
+   "source": [
+    "This means we have for the units of the various quantity, if L is the units of the CV and T the units of time\n",
+    "\n",
+    "| Quantity    |  Unit           |\n",
+    "|-------------|-----------------|\n",
+    "|     Drift   |  $L. T^{-1}$    |\n",
+    "|-------------|-----------------|\n",
+    "|  Diffusion  | $L^2 .T^{-1}    |\n",
+    "|-------------|-----------------|\n",
+    "| Free energy | Units of $K_bT$ |"
+   ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3.8",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
-   "name": "python3.8"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -257,7 +302,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.18"
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,