More changes to notebooks

Author: DrPaulSharp

RATapi/examples/absorption/absorption.ipynb

@@ -1,27 +1,13 @@
 {
  "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Convert between RasCAL1 and RAT"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "RasCAL1 (R1) project structs can be converted to RAT `Project` classes, and vice versa.\n",
-    "This is done via the functions `r1_to_project_class` and `project_class_to_r1`."
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "### RasCAL1 to RAT\n",
+    "### RasCAL-1 to RAT\n",
+    "\n",
+    "RasCAL-1 (R1) project structs can be converted to RAT Project classes, and vice versa. This is done via the functions r1_to_project_class and project_class_to_r1.\n",
+    "\n",
     "Converting from R1 to a `Project` is very simple. We use the example R1 project in the file `R1monolayerVolumeModel.mat`, which is a project for analysing a monolayer of DSPC with various deuterations (tail-deuterated, head-deuterated, fully deuterated, hydrogenated)"
    ]
   },
@@ -48,7 +34,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Note that there are various features of RAT which do not feature in R1, such as `prior_type`, `mu` and `sigma` for parameters. These are given sensible default values (again e.g. for parameters, `prior_type = uniform`, `mu = 0.0`, `sigma=inf`), but you may change these if you would like to use these new features:"
+    "Note that there are various features of RAT which do not feature in RasCAL-1, such as `prior_type`, `mu` and `sigma` for parameters. These are given sensible default values (again e.g. for parameters, `prior_type = uniform`, `mu = 0.0`, `sigma=inf`), but you may change these if you would like to use these new features:"
    ]
   },
   {
@@ -102,7 +88,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### RAT to RasCAL1\n",
+    "### RAT to RasCAL-1\n",
     "\n",
     "To demonstrate the other way around, we will use the DSPC lipid bilayer model project from another tutorial."
    ]

RATapi/examples/convert_rascal_project/convert_rascal.ipynb

@@ -59,10 +59,12 @@
     "    Parameter(name=\"L1 SLD\", min=3.0e-6, value=4.1e-6, max=5.0e-6, fit=False),\n",
     "    Parameter(name=\"L1 Roughness\", min=2.0, value=5.0, max=20.0, fit=True),\n",
     "    Parameter(name=\"L1 Hydration\", min=10.0, value=20.0, max=30.0, fit=True),\n",
+    "    #\n",
     "    Parameter(name=\"L2 Thickness\", min=5.0, value=60.0, max=100.0, fit=True),\n",
     "    Parameter(name=\"L2 SLD\", min=2.1e-6, value=3.0e-6, max=5.0e-6, fit=False),\n",
     "    Parameter(name=\"L2 Roughness\", min=2.0, value=5.0, max=20.0, fit=True),\n",
     "    Parameter(name=\"L2 Hydration\", min=10.0, value=20.0, max=30.0, fit=True),\n",
+    "    #\n",
     "    Parameter(name=\"L3 Thickness\", min=5.0, value=200.0, max=300.0, fit=True),\n",
     "    Parameter(name=\"L3 SLD\", min=3.0e-6, value=7.0e-6, max=8.0e-6, fit=False),\n",
     "    Parameter(name=\"L3 Roughness\", min=2.0, value=5.0, max=20.0, fit=True),\n",

RATapi/examples/domains/.ipynb_checkpoints/domains_standard_layers-checkpoint.ipynb

@@ -90,7 +90,7 @@
    "id": "b1fe7c6e-2200-4c83-9485-ec3590e950d5",
    "metadata": {},
    "source": [
-    "Need to add the relevant Bulk SLD's. Change the bulk in from air to silicon, and add two additional water contrasts:"
+    "Need to add the relevant Bulk SLDs. Change the bulk in from air to silicon, and add two additional water contrasts:"
    ]
   },
   {
@@ -262,20 +262,9 @@
       "\n",
       "\n",
       "Running Differential Evolution\n",
-      "\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": []
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "\n",
       "Final chi squared is 8.39155\n",
-      "Elapsed time is 103.555 seconds\n",
+      "Elapsed time is 119.992 seconds\n",
       "\n",
       "Finished RAT ───────────────────────────────────────────────────────────────────────────────────────────────────────────\n",
       "\n"