Diffusion model

examples/component_collection.ipynb

@@ -0,0 +1,83 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "64deaa41",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "\n",
+    "from easydynamics.sample_model import Gaussian\n",
+    "from easydynamics.sample_model import Lorentzian\n",
+    "from easydynamics.sample_model import DampedHarmonicOscillator\n",
+    "from easydynamics.sample_model import Polynomial\n",
+    "\n",
+    "from easydynamics.sample_model import ComponentCollection\n",
+    "\n",
+    "\n",
+    "import matplotlib.pyplot as plt\n",
+    "\n",
+    "\n",
+    "%matplotlib widget"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "784d9e82",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "component_collection=ComponentCollection()\n",
+    "\n",
+    "# Creating components\n",
+    "gaussian=Gaussian(display_name='Gaussian',width=0.5,area=1)\n",
+    "dho = DampedHarmonicOscillator(display_name='DHO',center=1.0,width=0.3,area=2.0)\n",
+    "lorentzian = Lorentzian(display_name='Lorentzian',center=-1.0,width=0.2,area=1.0)\n",
+    "polynomial = Polynomial(display_name='Polynomial',coefficients=[0.1, 0, 0.5])  # y=0.1+0.5*x^2\n",
+    "\n",
+    "# Adding components to the component collection\n",
+    "component_collection.add_component(gaussian)\n",
+    "component_collection.add_component(dho)\n",
+    "component_collection.add_component(lorentzian)\n",
+    "component_collection.add_component(polynomial)\n",
+    "\n",
+    "x=np.linspace(-2, 2, 100)\n",
+    "\n",
+    "plt.figure()\n",
+    "y=component_collection.evaluate(x)\n",
+    "plt.plot(x, y, label='Component collection')\n",
+    "\n",
+    "for component in component_collection.components:\n",
+    "    y = component.evaluate(x)\n",
+    "    plt.plot(x, y, label=component.display_name)\n",
+    "\n",
+    "plt.legend()\n",
+    "plt.show()"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "easydynamics_newbase",
+   "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": "3.12.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

examples/component_example.ipynb → examples/components.ipynb

@@ -19,7 +19,7 @@
     "import matplotlib.pyplot as plt\n",
     "\n",
     "\n",
-    "%matplotlib widget"
+    "%matplotlib widget\n"
    ]
   },
   {
@@ -30,10 +30,10 @@
    "outputs": [],
    "source": [
     "# Creating a component\n",
-    "gaussian=Gaussian(name='Gaussian',width=0.5,area=1)\n",
-    "dho = DampedHarmonicOscillator(name='DHO',center=1.0,width=0.3,area=2.0)\n",
-    "lorentzian = Lorentzian(name='Lorentzian',center=-1.0,width=0.2,area=1.0)\n",
-    "polynomial = Polynomial(name='Polynomial',coefficients=[0.1, 0, 0.5])  # y=0.1+0.5*x^2\n",
+    "gaussian=Gaussian(display_name='Gaussian',width=0.5,area=1)\n",
+    "dho = DampedHarmonicOscillator(display_name='DHO',center=1.0,width=0.3,area=2.0)\n",
+    "lorentzian = Lorentzian(display_name='Lorentzian',center=-1.0,width=0.2,area=1.0)\n",
+    "polynomial = Polynomial(display_name='Polynomial',coefficients=[0.1, 0, 0.5])  # y=0.1+0.5*x^2\n",
     "\n",
     "x=np.linspace(-2, 2, 100)\n",
     "\n",
@@ -72,7 +72,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "delta = DeltaFunction(name='Delta', center=0.0, area=1.0)\n",
+    "delta = DeltaFunction(display_name='Delta', center=0.0, area=1.0)\n",
     "x1=np.linspace(-2, 2, 100)\n",
     "y=delta.evaluate(x1)\n",
     "x2=np.linspace(-2,2,51)\n",
@@ -100,7 +100,7 @@
     "x1=sc.linspace(dim='x', start=-2.0, stop=2.0, num=100, unit='meV')\n",
     "x2=sc.linspace(dim='x', start=-2.0*1e3, stop=2.0*1e3, num=101, unit='microeV')\n",
     "\n",
-    "polynomial = Polynomial(name='Polynomial',coefficients=[0.1, 0, 0.5])  # y=0.1+0.5*x^2\n",
+    "polynomial = Polynomial(display_name='Polynomial',coefficients=[0.1, 0, 0.5])  # y=0.1+0.5*x^2\n",
     "y1=polynomial.evaluate(x1)\n",
     "y2=polynomial.evaluate(x2)\n",
     "\n",
@@ -114,7 +114,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "newdynamics",
+   "display_name": "easydynamics_newbase",
    "language": "python",
    "name": "python3"
   },
@@ -128,7 +128,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.13"
+   "version": "3.12.12"
   }
  },
  "nbformat": 4,

examples/diffusion_model.ipynb

@@ -0,0 +1,77 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "64deaa41",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "\n",
+    "from easydynamics.sample_model import BrownianTranslationalDiffusion\n",
+    "\n",
+    "import matplotlib.pyplot as plt\n",
+    "\n",
+    "%matplotlib widget"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "784d9e82",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Create Brownian Translational Diffusion model and plot the model for different Q values.\n",
+    "# Q is in Angstrom^-1 and energy in meV.\n",
+    "\n",
+    "Q=np.linspace(0.5,2,7)\n",
+    "energy=np.linspace(-2, 2, 501)\n",
+    "scale=1.0\n",
+    "diffusion_coefficient = 2.4e-9  # m^2/s\n",
+    "diffusion_unit= \"m**2/s\"\n",
+    "\n",
+    "diffusion_model=BrownianTranslationalDiffusion(display_name=\"DiffusionModel\", scale=scale, diffusion_coefficient= diffusion_coefficient, diffusion_unit=diffusion_unit)\n",
+    "\n",
+    "component_collections=diffusion_model.create_component_collections(Q)\n",
+    "\n",
+    "\n",
+    "cmap = plt.cm.jet\n",
+    "nQ = len(component_collections)\n",
+    "plt.figure()\n",
+    "for Q_index in range(len(component_collections)):\n",
+    "    color = cmap(Q_index / (nQ - 1))\n",
+    "    y=component_collections[Q_index].evaluate(energy)\n",
+    "    plt.plot(energy, y, label=f'Q={Q[Q_index]} Å^-1',color=color)\n",
+    "    \n",
+    "plt.legend()\n",
+    "plt.show()\n",
+    "plt.xlabel('Energy (meV)')\n",
+    "plt.ylabel('Intensity (arb. units)')\n",
+    "plt.title('Brownian Translational Diffusion Model')    "
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "easydynamics_newbase",
+   "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": "3.12.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

src/easydynamics/sample_model/__init__.py

@@ -1,3 +1,4 @@
+from .component_collection import ComponentCollection
 from .components import (
     DampedHarmonicOscillator,
     DeltaFunction,
@@ -6,13 +7,16 @@
     Polynomial,
     Voigt,
 )
+from .diffusion_model import BrownianTranslationalDiffusion, DiffusionModel
 
 __all__ = [
-    "SampleModel",
+    "ComponentCollection",
     "Gaussian",
     "Lorentzian",
     "Voigt",
     "DeltaFunction",
     "DampedHarmonicOscillator",
     "Polynomial",
+    "DiffusionModel",
+    "BrownianTranslationalDiffusion",
 ]