Merge pull request #67 from maximillian-dolan/master

examples/ideal_gas_law/first_principles.ipynb

@@ -1,5 +1,15 @@
 {
  "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "import matplotlib.pyplot as plt"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -15,9 +25,39 @@
     "where, $V$ is the volume of the system and $\\Lambda$ is the de Broglie thermal wavelength, \n",
     "\n",
     "$$\n",
-    "\\Lambda = \\bigg(\\frac{\\beta h^2}{2\\pi m}\\bigg)^{1/2}.\n",
-    "$$\n",
+    "\\Lambda = \\bigg(\\frac{\\beta h^2}{2\\pi m}\\bigg)^{1/2} = \\bigg(\\frac{h^2}{2 k_B T \\pi m}\\bigg)^{1/2}\n",
+    "$$"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "The De Broglie wavelength for an electron can be calculated using electron mass:\n",
+    "\n",
+    "$$m_e = 9.11*10^{-31}$$ \n",
+    "\n",
+    "Write a function that calculates the De Broglie wavelength for an electron at room temp (293k)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "m_e = 9.11e-31\n",
+    "h = 6.626e-34\n",
+    "k_b = 1.38e-23\n",
     "\n",
+    "def db_wavelength(T)\n",
+    "    return ◽◽◽"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
     "The most useful way to work with the partition function is in its logarithmic form, \n",
     "\n",
     "$$\n",
@@ -49,12 +89,44 @@
     "$$"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "In the cell below, write a function that calculates the pressure using the ideal gas law"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
    "outputs": [],
-   "source": []
+   "source": [
+    "def ideal_pressure(◽◽◽,◽◽◽,◽◽◽)\n",
+    "    return ◽◽◽"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "See how this changes for a range of temperatures"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "T = ◽◽◽\n",
+    "p = ideal_pressure(◽◽◽,◽◽◽,◽◽◽)\n",
+    "\n",
+    "plt.plot(T, p)\n",
+    "plt.xlabel('Temperature')\n",
+    "plt.ylabel('Ideal Pressure')\n",
+    "plt.show()"
+   ]
   }
  ],
  "metadata": {

pylj/forcefields.py

@@ -1,5 +1,4 @@
 import numpy as np
-from numba import njit
 
 
 class lennard_jones(object):

pylj/md.py

@@ -1,7 +1,6 @@
 import numpy as np
 from pylj import pairwise as heavy
 from pylj import forcefields as ff
-from numba import njit
 
 
 def initialise(

pylj/pairwise.py

@@ -1,6 +1,5 @@
 from __future__ import division
 import numpy as np
-from numba import njit, jit
 from pylj import pairwise as heavy
 
 #Jit tag here had to be removed
@@ -56,7 +55,7 @@ def compute_force(particles, box_length, cut_off, constants, forcefield, mass):
     particles = update_accelerations(particles, forces, mass_kg, dx, dy, distances)
     return particles, distances, forces, energies
 
-@njit
+#Jit tag here had to be removed
 def separation(dx, dy):
     """Calculate the distance in 2D space.
     Parameters
@@ -290,7 +289,7 @@ def heat_bath(particles, temperature_sample, bath_temp):
     return particles
 
 
-@njit
+#Jit tag here had to be removed
 def dist(xposition, yposition, box_length):
     """Returns the distance array for the set of particles.
     Parameters
@@ -330,7 +329,7 @@ def dist(xposition, yposition, box_length):
     return drr, dxr, dyr
 
 
-@njit
+#Jit tag here had to be removed
 def pbc_correction(position, cell):
     """Correct for the periodic boundary condition.
     Parameters

pylj/util.py

@@ -2,7 +2,6 @@
 import numpy as np
 import webbrowser
 from pylj import md, mc
-from numba import njit
 
 
 class System:

requirements.txt

@@ -2,7 +2,6 @@ jupyter
 cython
 numpy>=1.16
 matplotlib
-numba
 coverage
 coveralls
 ipympl

setup.py

@@ -25,8 +25,8 @@
         'author_email': '[email protected]',
         'packages': packages,
         'include_package_data': True,
-        'setup_requires': ['jupyter', 'numpy', 'matplotlib', 'cython', 'numba'],
-        'install_requires': ['jupyter', 'numpy', 'matplotlib', 'cython', 'numba'],
+        'setup_requires': ['jupyter', 'numpy', 'matplotlib', 'cython'],
+        'install_requires': ['jupyter', 'numpy', 'matplotlib', 'cython'],
         'version': VERSION,
         'license': 'MIT',
         'long_description': long_description,