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Devv2 #4

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6b7f67a
Updated notebooks
Apr 13, 2026
87a2b06
I tried to add a native support for CompFunction and i think it worked
May 13, 2026
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56 changes: 56 additions & 0 deletions docs/notebooks/BoundingBox.ipynb
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@@ -0,0 +1,56 @@
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"id": "7408efd9",
"metadata": {},
"outputs": [],
"source": [
"import vampyr as vp\n",
"import numpy as np\n",
"epsilon = 1.0e-3\n",
"\n",
"D = 1\n",
"k = 5\n",
"N = -2\n",
"world = vp.BoundingBox(dim=1, scale=N)\n",
"mra = vp.MultiResolutionAnalysis(box=world, order=k)\n",
"\n",
"r0 = [0.8]\n",
"beta = 10.0\n",
"alpha = (beta / np.pi) ** (D / 2.0)\n",
"ffunc = vp.GaussFunc(alpha=alpha, beta=beta, position=r0)\n"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "0442bf58",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "vampyr (3.13.11)",
"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": "3.13.11"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
45 changes: 20 additions & 25 deletions docs/notebooks/PCMSolvent.ipynb
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Expand Up @@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"execution_count": 23,
"id": "ea98d79d",
"metadata": {
"tags": [
Expand Down Expand Up @@ -47,13 +47,13 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 24,
"id": "687f3715",
"metadata": {},
"outputs": [],
"source": [
"# Import necessary packages\n",
"from vampyr import vampyr3d as vp\n",
"import vampyr as vp\n",
"import numpy as np\n",
"from scipy.special import erf"
]
Expand Down Expand Up @@ -109,7 +109,7 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 25,
"id": "a74a3d77",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -176,7 +176,7 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 26,
"id": "7036a9eb",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -253,7 +253,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 27,
"id": "77a9524b",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -307,7 +307,7 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 28,
"id": "5996cb89",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -336,7 +336,7 @@
"source": [
"k = 5\n",
"L = [-10, 10]\n",
"MRA = vp.MultiResolutionAnalysis(order=k, box=L)\n",
"MRA = vp.MultiResolutionAnalysis(dim=3, order=k, box=L)\n",
"print(MRA)"
]
},
Expand All @@ -350,7 +350,7 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 29,
"id": "898a27c8",
"metadata": {},
"outputs": [],
Expand All @@ -371,7 +371,7 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 30,
"id": "980ddc95",
"metadata": {},
"outputs": [],
Expand All @@ -392,7 +392,7 @@
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": 31,
"id": "84cee3c8",
"metadata": {},
"outputs": [],
Expand All @@ -415,7 +415,7 @@
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": 32,
"id": "c04749f8",
"metadata": {},
"outputs": [],
Expand All @@ -434,7 +434,7 @@
},
{
"cell_type": "code",
"execution_count": 11,
"execution_count": 33,
"id": "624ae35d",
"metadata": {},
"outputs": [],
Expand All @@ -453,7 +453,7 @@
},
{
"cell_type": "code",
"execution_count": 12,
"execution_count": 34,
"id": "71337e6c",
"metadata": {},
"outputs": [
Expand All @@ -470,7 +470,7 @@
"4 6.0252390e+00 1.8435902e-03 -2.6266231e-01 6.5638875e-05\n",
"5 6.0254219e+00 1.8305719e-04 -2.6266876e-01 -6.4520209e-06\n",
"6 6.0254060e+00 1.5950934e-05 -2.6266820e-01 5.5755347e-07\n",
"7 6.0254072e+00 1.2399247e-06 -2.6266825e-01 -4.3037920e-08\n"
"7 6.0254072e+00 1.2399247e-06 -2.6266825e-01 -4.3037921e-08\n"
]
}
],
Expand Down Expand Up @@ -518,17 +518,17 @@
},
{
"cell_type": "code",
"execution_count": 13,
"execution_count": 35,
"id": "50f238b2",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"-0.2626682475802428"
"-0.2626682475802452"
]
},
"execution_count": 13,
"execution_count": 35,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -540,7 +540,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3.11.4 ('MRPyCM-env')",
"display_name": "devv2_env (3.12.3)",
"language": "python",
"name": "python3"
},
Expand All @@ -554,12 +554,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.4"
},
"vscode": {
"interpreter": {
"hash": "487dd71aba060d73bfc278ebf788be90cc4e85b80399312c78d8b97665a3c999"
}
"version": "3.12.3"
}
},
"nbformat": 4,
Expand Down
62 changes: 36 additions & 26 deletions docs/notebooks/beryllium_atom.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 1,
"metadata": {
"tags": [
"hide-cell"
Expand Down Expand Up @@ -87,21 +87,36 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"from vampyr import vampyr3d as vp\n",
"import vampyr as vp\n",
"import numpy as np\n",
"import numpy.linalg as LA\n",
"import matplotlib.pyplot as plt"
]
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 3,
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"<>:36: SyntaxWarning: invalid escape sequence '\\s'\n",
"<>:86: SyntaxWarning: invalid escape sequence '\\s'\n",
"<>:36: SyntaxWarning: invalid escape sequence '\\s'\n",
"<>:86: SyntaxWarning: invalid escape sequence '\\s'\n",
"/tmp/ipykernel_1553354/3248586940.py:36: SyntaxWarning: invalid escape sequence '\\s'\n",
" K(phi) = \\sum_i P[phi * psi_i] * psi_i\n",
"/tmp/ipykernel_1553354/3248586940.py:86: SyntaxWarning: invalid escape sequence '\\s'\n",
" J(phi) = \\sum_i P[psi_i * psi_i] * phi\n"
]
}
],
"source": [
"class HelmholtzOperator():\n",
" \"\"\"\n",
Expand Down Expand Up @@ -283,7 +298,7 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -437,7 +452,7 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -452,7 +467,7 @@
"# Define MRA basis and computational domain\n",
"k = 5 # Polynomial order of MRA basis\n",
"world = [-20, 20] # Computational domain [-L,L]^3 (a.u.)\n",
"MRA = vp.MultiResolutionAnalysis(order=k, box=world)\n",
"MRA = vp.MultiResolutionAnalysis(dim=3, order=k, box=world)\n",
"\n",
"# Setup guess for the orbitals and the Fock matrix\n",
"Phi_n = starting_guess(mra=MRA, atom=mol[0], n_orbs=2, prec=precision)\n",
Expand All @@ -464,22 +479,22 @@
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": 6,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"0 | E_tot: -12.158806160497663 | dPhi: 0.9554261103233852\n",
"1 | E_tot: -13.910545962062471 | dPhi: 0.6030032083595198\n",
"2 | E_tot: -14.425154911621195 | dPhi: 0.11248971009686566\n",
"3 | E_tot: -14.550559502300937 | dPhi: 0.056367744794410625\n",
"4 | E_tot: -14.573091352701868 | dPhi: 0.024464066721782796\n",
"5 | E_tot: -14.576656010668405 | dPhi: 0.009607118621517596\n",
"6 | E_tot: -14.577184437878596 | dPhi: 0.0036909439005734903\n",
"7 | E_tot: -14.577255599761454 | dPhi: 0.0017015854922230098\n",
"8 | E_tot: -14.577262672068981 | dPhi: 0.0009093846224262461\n"
"0 | E_tot: -12.158806160497662 | dPhi: 0.9554261103233839\n",
"1 | E_tot: -13.910545962062479 | dPhi: 0.6030032083595226\n",
"2 | E_tot: -14.425154911621192 | dPhi: 0.11248971009686642\n",
"3 | E_tot: -14.550559502300938 | dPhi: 0.05636774479441057\n",
"4 | E_tot: -14.573091352701868 | dPhi: 0.02446406672178261\n",
"5 | E_tot: -14.576656010668403 | dPhi: 0.009607118621517379\n",
"6 | E_tot: -14.577184437878591 | dPhi: 0.003690943900573473\n",
"7 | E_tot: -14.57725559976145 | dPhi: 0.0017015854922230302\n",
"8 | E_tot: -14.577262672068983 | dPhi: 0.0009093846224265751\n"
]
}
],
Expand All @@ -498,7 +513,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3.9.6 64-bit",
"display_name": "vampyr (3.13.11)",
"language": "python",
"name": "python3"
},
Expand All @@ -512,14 +527,9 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.6"
"version": "3.13.11"
},
"orig_nbformat": 4,
"vscode": {
"interpreter": {
"hash": "31f2aee4e71d21fbe5cf8b01ff0e069b9275f58929596ceb00d14d90e3e16cd6"
}
}
"orig_nbformat": 4
},
"nbformat": 4,
"nbformat_minor": 2
Expand Down
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