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Update atomic_density.ipynb #19

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32 changes: 19 additions & 13 deletions examples/atomic_density.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"## 1. Specify a radial grid."
"## Specify Numerical Grid"
]
},
{
Expand All @@ -62,16 +62,15 @@
"import numpy as np\n",
"from bfit.grid import ClenshawRadialGrid\n",
"\n",
"atomic_numb = 4\n",
"grid = ClenshawRadialGrid(atomic_numb, num_core_pts=400, num_diffuse_pts=500, \n",
" extra_pts=[25, 50, 75])"
"atnum = 4\n",
"grid = ClenshawRadialGrid(atnum, num_core_pts=400, num_diffuse_pts=500, extra_pts=[25, 50, 75])"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## 2. Get Slater density."
"## Compute Slater Density"
]
},
{
Expand Down Expand Up @@ -113,13 +112,13 @@
"source": [
"from bfit.density import AtomicDensity\n",
"\n",
"# Grab information about potassium.\n",
"# Load Slater wave-function of Beryllium\n",
"be = AtomicDensity(\"be\")\n",
"\n",
"# Get the total electronic density.\n",
"# Compute total electronic density of Beryllium\n",
"density = be.atomic_density(grid.points, \"total\")\n",
"\n",
"print(\"The integral of potassium is: \", grid.integrate(density))\n",
"print(\"The integral of Beryllium density gives \", grid.integrate(density))\n",
"\n",
"# Plot only the first 500 points.\n",
"import matplotlib.pyplot as plt\n",
Expand All @@ -142,7 +141,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"## 3. Specify the Gaussian model."
"## Specify Gaussian Basis"
]
},
{
Expand All @@ -162,16 +161,16 @@
},
"outputs": [],
"source": [
"from fitting.model import AtomicGaussianDensity\n",
"from bfit.model import AtomicGaussianDensity\n",
"\n",
"model = AtomicGaussianDensity(grid.points, num_s=5, num_p=3, normalize=True)\n"
"model = AtomicGaussianDensity(grid.points, num_s=5, num_p=3, normalize=True)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## 4. Specify the Kullback-Leibler Self-Consistent Field Method."
"## Specify Deviation Measure"
]
},
{
Expand All @@ -191,7 +190,7 @@
},
"outputs": [],
"source": [
"from fitting.fit import KLDivergenceSCF\n",
"from bfit.fit import KLDivergenceSCF\n",
"\n",
"fit = KLDivergenceSCF(grid, density, model)"
]
Expand Down Expand Up @@ -244,6 +243,13 @@
"plt.show()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Fit Electron Density"
]
},
{
"cell_type": "markdown",
"metadata": {},
Expand Down