{
"cells": [
{
"cell_type": "markdown",
"id": "3836140c",
"metadata": {},
"source": [
"# Setup magnetic entites and pairs"
]
},
{
"cell_type": "markdown",
"id": "ef0e83cc",
"metadata": {},
"source": [
"There are many different systems, where the magnetic entities can be very different. Sometimes it is just one atom from the cell, sometimes it is one element and sometimes it is a cluster of atoms, a quasi-molecule. grogupy can handle all these different systems and provide a hopefully intuitive way to autoamtically generate the pairs."
]
},
{
"cell_type": "code",
"execution_count": 10,
"id": "5e8fae98",
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
" \n",
" \n",
" "
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"import grogupy\n",
"import grogupy.viz\n",
"\n",
"################################################################################\n",
"# this is just for the html export of interactive figures, but it is not part of\n",
"# grogupy\n",
"import plotly\n",
"\n",
"plotly.offline.init_notebook_mode()\n",
"################################################################################"
]
},
{
"cell_type": "markdown",
"id": "a7d0fd79",
"metadata": {},
"source": [
"## Simple systems, with one magnetic element"
]
},
{
"cell_type": "markdown",
"id": "a8061235",
"metadata": {},
"source": [
"Let's start by setting up a ``Builder`` instance from the **CrI3** benchmark as shown in the Calculate Magnetic Parameters tutorial."
]
},
{
"cell_type": "code",
"execution_count": 11,
"id": "fe5b21cd",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"Setting up Hamiltonian: 100%|██████████| 147/147 [00:00<00:00, 1170.90it/s]\n"
]
},
{
"data": {
"text/plain": [
""
]
},
"execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"CrI3_path = \"./../../../benchmarks/CrI3/CrI3.fdf\"\n",
"\n",
"CrI3 = grogupy.Builder()\n",
"CrI3.add_kspace(grogupy.Kspace(kset=[21, 21, 1]))\n",
"CrI3.add_contour(grogupy.Contour(eset=100, eigfile=CrI3_path))\n",
"CrI3.add_hamiltonian(grogupy.Hamiltonian(CrI3_path))\n",
"CrI3"
]
},
{
"cell_type": "markdown",
"id": "a8c6548f",
"metadata": {},
"source": [
"In case of a simple system like this, where only the **Cr** atoms are magnetic we can set up the magnetic entities and pairs automatically, by defining a range for the pairs and the subset of atoms we want to use. "
]
},
{
"cell_type": "code",
"execution_count": 12,
"id": "85131dd8",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"Add magnetic entities: 100%|██████████| 2/2 [00:00<00:00, 32.97it/s]\n",
"Add pairs: 100%|██████████| 114/114 [00:00<00:00, 13500.98it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"[\n",
"]\n",
"[\n",
" ]\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
}
],
"source": [
"CrI3.setup_from_range(R=20, subset=\"Cr\")\n",
"print(CrI3.magnetic_entities)\n",
"print(CrI3.pairs[:2])"
]
},
{
"cell_type": "markdown",
"id": "e712ddfa",
"metadata": {},
"source": [
"We have to take into account, that some orbitals are more localized, than others and the approximation of the Heisenberg model works better, if we only take into account these localized orbitals. we can define them by indexing directly from the atom, but this needs an in depth knowledge about the basis of the Hamiltonian. Instead we could simply choose the shell of orbitals, in this case the d orbitals."
]
},
{
"cell_type": "code",
"execution_count": 13,
"id": "27edc36c",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"Add magnetic entities: 100%|██████████| 2/2 [00:00<00:00, 69.87it/s]\n",
"Add pairs: 100%|██████████| 114/114 [00:00<00:00, 5591.03it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"[\n",
"]\n",
"[\n",
" ]\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
}
],
"source": [
"CrI3.setup_from_range(R=20, subset=\"Cr\", l=2)\n",
"print(CrI3.magnetic_entities)\n",
"print(CrI3.pairs[:2])"
]
},
{
"cell_type": "markdown",
"id": "4fdedada",
"metadata": {},
"source": [
"The ``setup_from_range`` method takes keyword arguments, when it defines the magnetic entities. For more information on what is possible take a look at the ``MagneticEntity`` class in the API reference. Let's take a look at the final system."
]
},
{
"cell_type": "code",
"execution_count": 14,
"id": "72b7e647",
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.plotly.v1+json": {
"config": {
"plotlyServerURL": "https://plot.ly"
},
"data": [
{
"marker": {
"color": "#1F77B4",
"opacity": 0.5,
"size": 10
},
"mode": "markers",
"name": "Center:0Cr(l:2)",
"type": "scatter3d",
"x": [
-0.0000521955
],
"y": [
0.00003006233980938
],
"z": [
15
]
},
{
"marker": {
"color": "#1F77B4",
"opacity": 0.5,
"size": 5
},
"mode": "markers",
"name": "Pairs on: 0Cr(l:2)",
"type": "scatter3d",
"x": [
-14.000052195499997,
-17.500052195499997,
-3.5000521955,
-7.0000521954999995,
-10.500052195499999,
-14.000052195499999,
-17.500052195499997,
3.499947804499999,
-0.0000521955,
-3.5000521954999995,
-7.0000521954999995,
-10.500052195499999,
-14.000052195499999,
6.999947804499999,
3.4999478044999996,
-3.5000521954999995,
-7.0000521954999995,
13.999947804499998,
10.499947804499998,
6.999947804499999,
3.4999478044999996,
-0.0000521955,
-3.500052195499999,
17.499947804499996,
13.999947804499998,
10.499947804499998,
6.999947804499999,
3.4999478045,
17.499947804499996,
13.999947804499996,
-6.999947443999998,
-10.499947443999996,
-13.999947443999996,
-17.499947443999996,
0.000052555999999981395,
-3.499947443999999,
-6.999947443999998,
-10.499947443999998,
-13.999947443999996,
7.000052555999999,
3.500052556,
0.000052556000000425485,
-3.499947443999999,
-6.999947443999998,
-10.499947443999998,
10.500052556,
7.000052556,
3.500052556,
0.000052556000000425485,
-3.499947443999999,
14.000052555999998,
10.500052556,
7.000052556,
3.500052556,
17.500052556,
14.000052555999998,
10.500052556
],
"y": [
-12.12432557766019,
-6.06214775766019,
-18.18650339766019,
-12.12432557766019,
-6.06214775766019,
0.00003006233980938,
6.062207882339809,
-18.18650339766019,
-12.12432557766019,
-6.06214775766019,
0.00003006233980938,
6.062207882339809,
12.124385702339808,
-12.12432557766019,
-6.06214775766019,
6.062207882339809,
12.124385702339808,
-12.12432557766019,
-6.06214775766019,
0.00003006233980938,
6.062207882339809,
12.124385702339808,
18.18656352233981,
-6.06214775766019,
0.00003006233980938,
6.062207882339809,
12.124385702339808,
18.18656352233981,
6.062207882339809,
12.124385702339808,
-16.165837923842492,
-10.103660103842493,
-4.041482283842493,
2.0206955361575063,
-16.165837923842492,
-10.103660103842493,
-4.041482283842493,
2.0206955361575063,
8.082873356157506,
-16.165837923842492,
-10.103660103842493,
-4.041482283842493,
2.0206955361575063,
8.082873356157506,
14.145051176157505,
-10.103660103842493,
-4.041482283842493,
2.0206955361575063,
8.082873356157506,
14.145051176157505,
-4.041482283842493,
2.0206955361575063,
8.082873356157506,
14.145051176157505,
2.0206955361575063,
8.082873356157506,
14.145051176157505
],
"z": [
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998
]
},
{
"marker": {
"color": "#FF7F0E",
"opacity": 0.5,
"size": 10
},
"mode": "markers",
"name": "Center:1Cr(l:2)",
"type": "scatter3d",
"x": [
3.500052556
],
"y": [
2.0206955361575063
],
"z": [
14.999999969999998
]
},
{
"marker": {
"color": "#FF7F0E",
"opacity": 0.5,
"size": 5
},
"mode": "markers",
"name": "Pairs on: 1Cr(l:2)",
"type": "scatter3d",
"x": [
-7.0000521954999995,
-10.500052195499999,
-14.000052195499999,
-0.0000521955,
-3.5000521954999995,
-7.0000521954999995,
-10.500052195499999,
6.999947804499999,
3.4999478044999996,
-0.0000521955,
-3.5000521954999995,
-7.0000521954999995,
13.999947804499998,
10.499947804499998,
6.999947804499999,
3.4999478044999996,
-0.0000521955,
-3.500052195499999,
17.499947804499996,
13.999947804499998,
10.499947804499998,
6.999947804499999,
3.4999478045,
20.999947804499996,
17.499947804499996,
13.999947804499996,
10.499947804499998,
-10.499947443999996,
-13.999947443999996,
0.000052555999999981395,
-3.499947443999999,
-6.999947443999998,
-10.499947443999998,
-13.999947443999996,
7.000052555999999,
3.500052556,
0.000052556000000425485,
-3.499947443999999,
-6.999947443999998,
-10.499947443999998,
10.500052556,
7.000052556,
0.000052556000000425485,
-3.499947443999999,
17.500052556,
14.000052555999998,
10.500052556,
7.000052556,
3.500052556,
0.000052556000000869574,
21.000052555999996,
17.500052556,
14.000052555999998,
10.500052556,
7.000052556,
21.000052555999996,
17.500052555999996
],
"y": [
-12.12432557766019,
-6.06214775766019,
0.00003006233980938,
-12.12432557766019,
-6.06214775766019,
0.00003006233980938,
6.062207882339809,
-12.12432557766019,
-6.06214775766019,
0.00003006233980938,
6.062207882339809,
12.124385702339808,
-12.12432557766019,
-6.06214775766019,
0.00003006233980938,
6.062207882339809,
12.124385702339808,
18.18656352233981,
-6.06214775766019,
0.00003006233980938,
6.062207882339809,
12.124385702339808,
18.18656352233981,
0.00003006233980938,
6.062207882339809,
12.124385702339808,
18.18656352233981,
-10.103660103842493,
-4.041482283842493,
-16.165837923842492,
-10.103660103842493,
-4.041482283842493,
2.0206955361575063,
8.082873356157506,
-16.165837923842492,
-10.103660103842493,
-4.041482283842493,
2.0206955361575063,
8.082873356157506,
14.145051176157505,
-10.103660103842493,
-4.041482283842493,
8.082873356157506,
14.145051176157505,
-10.103660103842493,
-4.041482283842493,
2.0206955361575063,
8.082873356157506,
14.145051176157505,
20.207228996157507,
-4.041482283842493,
2.0206955361575063,
8.082873356157506,
14.145051176157505,
20.207228996157507,
8.082873356157506,
14.145051176157505
],
"z": [
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
15,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998,
14.999999969999998
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0,
6.999999999999999
],
"y": [
0,
0
],
"z": [
0,
0
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0,
-3.4999999999999996
],
"y": [
0,
6.06217782
],
"z": [
0,
0
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0,
0
],
"y": [
0,
0
],
"z": [
0,
30
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
6.999999999999999,
3.4999999999999996
],
"y": [
0,
6.06217782
],
"z": [
0,
0
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
6.999999999999999,
6.999999999999999
],
"y": [
0,
0
],
"z": [
0,
30
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-3.4999999999999996,
3.4999999999999996
],
"y": [
6.06217782,
6.06217782
],
"z": [
0,
0
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-3.4999999999999996,
-3.4999999999999996
],
"y": [
6.06217782,
6.06217782
],
"z": [
0,
30
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0,
6.999999999999999
],
"y": [
0,
0
],
"z": [
30,
30
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0,
-3.4999999999999996
],
"y": [
0,
6.06217782
],
"z": [
30,
30
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.4999999999999996,
3.4999999999999996
],
"y": [
6.06217782,
6.06217782
],
"z": [
30,
0
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.4999999999999996,
6.999999999999999
],
"y": [
6.06217782,
0
],
"z": [
30,
30
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.4999999999999996,
-3.4999999999999996
],
"y": [
6.06217782,
6.06217782
],
"z": [
30,
30
]
}
],
"layout": {
"autosize": false,
"height": 500,
"scene": {
"aspectmode": "data",
"xaxis": {
"gridwidth": 1,
"showgrid": true,
"title": {
"text": "X Axis"
}
},
"yaxis": {
"gridwidth": 1,
"showgrid": true,
"title": {
"text": "Y Axis"
}
},
"zaxis": {
"gridwidth": 1,
"showgrid": true,
"title": {
"text": "Z Axis"
}
}
},
"showlegend": true,
"template": {
"data": {
"bar": [
{
"error_x": {
"color": "#2a3f5f"
},
"error_y": {
"color": "#2a3f5f"
},
"marker": {
"line": {
"color": "#E5ECF6",
"width": 0.5
},
"pattern": {
"fillmode": "overlay",
"size": 10,
"solidity": 0.2
}
},
"type": "bar"
}
],
"barpolar": [
{
"marker": {
"line": {
"color": "#E5ECF6",
"width": 0.5
},
"pattern": {
"fillmode": "overlay",
"size": 10,
"solidity": 0.2
}
},
"type": "barpolar"
}
],
"carpet": [
{
"aaxis": {
"endlinecolor": "#2a3f5f",
"gridcolor": "white",
"linecolor": "white",
"minorgridcolor": "white",
"startlinecolor": "#2a3f5f"
},
"baxis": {
"endlinecolor": "#2a3f5f",
"gridcolor": "white",
"linecolor": "white",
"minorgridcolor": "white",
"startlinecolor": "#2a3f5f"
},
"type": "carpet"
}
],
"choropleth": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"type": "choropleth"
}
],
"contour": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"colorscale": [
[
0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1,
"#f0f921"
]
],
"type": "contour"
}
],
"contourcarpet": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"type": "contourcarpet"
}
],
"heatmap": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"colorscale": [
[
0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1,
"#f0f921"
]
],
"type": "heatmap"
}
],
"histogram": [
{
"marker": {
"pattern": {
"fillmode": "overlay",
"size": 10,
"solidity": 0.2
}
},
"type": "histogram"
}
],
"histogram2d": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"colorscale": [
[
0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1,
"#f0f921"
]
],
"type": "histogram2d"
}
],
"histogram2dcontour": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"colorscale": [
[
0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1,
"#f0f921"
]
],
"type": "histogram2dcontour"
}
],
"mesh3d": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"type": "mesh3d"
}
],
"parcoords": [
{
"line": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "parcoords"
}
],
"pie": [
{
"automargin": true,
"type": "pie"
}
],
"scatter": [
{
"fillpattern": {
"fillmode": "overlay",
"size": 10,
"solidity": 0.2
},
"type": "scatter"
}
],
"scatter3d": [
{
"line": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scatter3d"
}
],
"scattercarpet": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scattercarpet"
}
],
"scattergeo": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scattergeo"
}
],
"scattergl": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scattergl"
}
],
"scattermap": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scattermap"
}
],
"scattermapbox": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scattermapbox"
}
],
"scatterpolar": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scatterpolar"
}
],
"scatterpolargl": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scatterpolargl"
}
],
"scatterternary": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scatterternary"
}
],
"surface": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"colorscale": [
[
0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1,
"#f0f921"
]
],
"type": "surface"
}
],
"table": [
{
"cells": {
"fill": {
"color": "#EBF0F8"
},
"line": {
"color": "white"
}
},
"header": {
"fill": {
"color": "#C8D4E3"
},
"line": {
"color": "white"
}
},
"type": "table"
}
]
},
"layout": {
"annotationdefaults": {
"arrowcolor": "#2a3f5f",
"arrowhead": 0,
"arrowwidth": 1
},
"autotypenumbers": "strict",
"coloraxis": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"colorscale": {
"diverging": [
[
0,
"#8e0152"
],
[
0.1,
"#c51b7d"
],
[
0.2,
"#de77ae"
],
[
0.3,
"#f1b6da"
],
[
0.4,
"#fde0ef"
],
[
0.5,
"#f7f7f7"
],
[
0.6,
"#e6f5d0"
],
[
0.7,
"#b8e186"
],
[
0.8,
"#7fbc41"
],
[
0.9,
"#4d9221"
],
[
1,
"#276419"
]
],
"sequential": [
[
0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1,
"#f0f921"
]
],
"sequentialminus": [
[
0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1,
"#f0f921"
]
]
},
"colorway": [
"#636efa",
"#EF553B",
"#00cc96",
"#ab63fa",
"#FFA15A",
"#19d3f3",
"#FF6692",
"#B6E880",
"#FF97FF",
"#FECB52"
],
"font": {
"color": "#2a3f5f"
},
"geo": {
"bgcolor": "white",
"lakecolor": "white",
"landcolor": "#E5ECF6",
"showlakes": true,
"showland": true,
"subunitcolor": "white"
},
"hoverlabel": {
"align": "left"
},
"hovermode": "closest",
"mapbox": {
"style": "light"
},
"paper_bgcolor": "white",
"plot_bgcolor": "#E5ECF6",
"polar": {
"angularaxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
},
"bgcolor": "#E5ECF6",
"radialaxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
}
},
"scene": {
"xaxis": {
"backgroundcolor": "#E5ECF6",
"gridcolor": "white",
"gridwidth": 2,
"linecolor": "white",
"showbackground": true,
"ticks": "",
"zerolinecolor": "white"
},
"yaxis": {
"backgroundcolor": "#E5ECF6",
"gridcolor": "white",
"gridwidth": 2,
"linecolor": "white",
"showbackground": true,
"ticks": "",
"zerolinecolor": "white"
},
"zaxis": {
"backgroundcolor": "#E5ECF6",
"gridcolor": "white",
"gridwidth": 2,
"linecolor": "white",
"showbackground": true,
"ticks": "",
"zerolinecolor": "white"
}
},
"shapedefaults": {
"line": {
"color": "#2a3f5f"
}
},
"ternary": {
"aaxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
},
"baxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
},
"bgcolor": "#E5ECF6",
"caxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
}
},
"title": {
"x": 0.05
},
"xaxis": {
"automargin": true,
"gridcolor": "white",
"linecolor": "white",
"ticks": "",
"title": {
"standoff": 15
},
"zerolinecolor": "white",
"zerolinewidth": 2
},
"yaxis": {
"automargin": true,
"gridcolor": "white",
"linecolor": "white",
"ticks": "",
"title": {
"standoff": 15
},
"zerolinecolor": "white",
"zerolinewidth": 2
}
}
},
"title": {},
"width": 800
}
},
"text/html": [
""
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"CrI3.plot_pairs()"
]
},
{
"cell_type": "markdown",
"id": "beab95e8",
"metadata": {},
"source": [
"## Complicated systems, with molecule like magnetic entities"
]
},
{
"cell_type": "markdown",
"id": "9b6a48c4",
"metadata": {},
"source": [
"Triangulene are coming soon..."
]
},
{
"cell_type": "markdown",
"id": "fb079f51",
"metadata": {},
"source": [
"## Defining magnetic entities and pairs by hand"
]
},
{
"cell_type": "markdown",
"id": "34d767d4",
"metadata": {},
"source": [
"If you are only interested in some specific magnetic entities and pairs, in this case the first-, second- and third neighbour, then you can define these using dictionaries. Internally all the above methods first create these dictionaries, then use them to create the ``MagneticEntityList`` and ``PairList`` of the ``Builder`` instance."
]
},
{
"cell_type": "code",
"execution_count": 15,
"id": "0ae8ad57",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"Add magnetic entities: 100%|██████████| 2/2 [00:00<00:00, 67.47it/s]\n",
"Add pairs: 100%|██████████| 6/6 [00:00<00:00, 4298.18it/s]\n"
]
}
],
"source": [
"# clear magnetic entities and pairs\n",
"CrI3.magnetic_entities = grogupy.MagneticEntityList()\n",
"CrI3.pairs = grogupy.PairList()\n",
"\n",
"# use the same atoms as in the first example\n",
"magnetic_entities = [\n",
" dict(atom=[0], l=[2]),\n",
" dict(orb=[15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]),\n",
"]\n",
"pairs = [\n",
" dict(ai=0, aj=1, Ruc=[0, 0, 0]),\n",
" dict(ai=0, aj=0, Ruc=[1, 0, 0]),\n",
" dict(ai=0, aj=1, Ruc=[1, 0, 0]),\n",
" dict(ai=1, aj=0, Ruc=[0, 0, 0]),\n",
" dict(ai=1, aj=1, Ruc=[-1, 0, 0]),\n",
" dict(ai=1, aj=0, Ruc=[-1, 0, 0]),\n",
"]\n",
"CrI3.add_magnetic_entities(magnetic_entities)\n",
"CrI3.add_pairs(pairs)"
]
},
{
"cell_type": "code",
"execution_count": 16,
"id": "64e7ca0b",
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.plotly.v1+json": {
"config": {
"plotlyServerURL": "https://plot.ly"
},
"data": [
{
"marker": {
"color": "#1F77B4",
"opacity": 0.5,
"size": 10
},
"mode": "markers",
"name": "Center:0Cr(l:2)",
"type": "scatter3d",
"x": [
-0.0000521955
],
"y": [
0.00003006233980938
],
"z": [
15
]
},
{
"legendgroup": "pair 0Cr(l:2)-1Cr(o:0-1-2-3-4-5-6-7-8-9-10-11-12-13-14), ruc:[0, 0, 0]",
"marker": {
"color": "#1F77B4",
"opacity": 0.5,
"size": 5
},
"mode": "markers",
"name": "1Cr(o:0-1-2-3-4-5-6-7-8-9-10-11-12-13-14), ruc:[0, 0, 0]",
"type": "scatter3d",
"x": [
3.500052556
],
"y": [
2.0206955361575063
],
"z": [
14.999999969999998
]
},
{
"legendgroup": "pair 0Cr(l:2)-0Cr(l:2), ruc:[1, 0, 0]",
"marker": {
"color": "#1F77B4",
"opacity": 0.5,
"size": 5
},
"mode": "markers",
"name": "0Cr(l:2), ruc:[1, 0, 0]",
"type": "scatter3d",
"x": [
6.999947804499999
],
"y": [
0.00003006233980938
],
"z": [
15
]
},
{
"legendgroup": "pair 0Cr(l:2)-1Cr(o:0-1-2-3-4-5-6-7-8-9-10-11-12-13-14), ruc:[1, 0, 0]",
"marker": {
"color": "#1F77B4",
"opacity": 0.5,
"size": 5
},
"mode": "markers",
"name": "1Cr(o:0-1-2-3-4-5-6-7-8-9-10-11-12-13-14), ruc:[1, 0, 0]",
"type": "scatter3d",
"x": [
10.500052556
],
"y": [
2.0206955361575063
],
"z": [
14.999999969999998
]
},
{
"marker": {
"color": "#FF7F0E",
"opacity": 0.5,
"size": 10
},
"mode": "markers",
"name": "Center:1Cr(o:0-1-2-3-4-5-6-7-8-9-10-11-12-13-14)",
"type": "scatter3d",
"x": [
3.500052556
],
"y": [
2.0206955361575063
],
"z": [
14.999999969999998
]
},
{
"legendgroup": "pair 1Cr(o:0-1-2-3-4-5-6-7-8-9-10-11-12-13-14)-0Cr(l:2), ruc:[0, 0, 0]",
"marker": {
"color": "#FF7F0E",
"opacity": 0.5,
"size": 5
},
"mode": "markers",
"name": "0Cr(l:2), ruc:[0, 0, 0]",
"type": "scatter3d",
"x": [
-0.0000521955
],
"y": [
0.00003006233980938
],
"z": [
15
]
},
{
"legendgroup": "pair 1Cr(o:0-1-2-3-4-5-6-7-8-9-10-11-12-13-14)-1Cr(o:0-1-2-3-4-5-6-7-8-9-10-11-12-13-14), ruc:[-1, 0, 0",
"marker": {
"color": "#FF7F0E",
"opacity": 0.5,
"size": 5
},
"mode": "markers",
"name": "1Cr(o:0-1-2-3-4-5-6-7-8-9-10-11-12-13-14), ruc:[-1, 0, 0",
"type": "scatter3d",
"x": [
-3.499947443999999
],
"y": [
2.0206955361575063
],
"z": [
14.999999969999998
]
},
{
"legendgroup": "pair 1Cr(o:0-1-2-3-4-5-6-7-8-9-10-11-12-13-14)-0Cr(l:2), ruc:[-1, 0, 0",
"marker": {
"color": "#FF7F0E",
"opacity": 0.5,
"size": 5
},
"mode": "markers",
"name": "0Cr(l:2), ruc:[-1, 0, 0",
"type": "scatter3d",
"x": [
-7.0000521954999995
],
"y": [
0.00003006233980938
],
"z": [
15
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0,
6.999999999999999
],
"y": [
0,
0
],
"z": [
0,
0
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0,
-3.4999999999999996
],
"y": [
0,
6.06217782
],
"z": [
0,
0
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0,
0
],
"y": [
0,
0
],
"z": [
0,
30
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
6.999999999999999,
3.4999999999999996
],
"y": [
0,
6.06217782
],
"z": [
0,
0
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
6.999999999999999,
6.999999999999999
],
"y": [
0,
0
],
"z": [
0,
30
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-3.4999999999999996,
3.4999999999999996
],
"y": [
6.06217782,
6.06217782
],
"z": [
0,
0
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-3.4999999999999996,
-3.4999999999999996
],
"y": [
6.06217782,
6.06217782
],
"z": [
0,
30
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0,
6.999999999999999
],
"y": [
0,
0
],
"z": [
30,
30
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0,
-3.4999999999999996
],
"y": [
0,
6.06217782
],
"z": [
30,
30
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.4999999999999996,
3.4999999999999996
],
"y": [
6.06217782,
6.06217782
],
"z": [
30,
0
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.4999999999999996,
6.999999999999999
],
"y": [
6.06217782,
0
],
"z": [
30,
30
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.4999999999999996,
-3.4999999999999996
],
"y": [
6.06217782,
6.06217782
],
"z": [
30,
30
]
}
],
"layout": {
"autosize": false,
"height": 500,
"scene": {
"aspectmode": "data",
"xaxis": {
"gridwidth": 1,
"showgrid": true,
"title": {
"text": "X Axis"
}
},
"yaxis": {
"gridwidth": 1,
"showgrid": true,
"title": {
"text": "Y Axis"
}
},
"zaxis": {
"gridwidth": 1,
"showgrid": true,
"title": {
"text": "Z Axis"
}
}
},
"showlegend": true,
"template": {
"data": {
"bar": [
{
"error_x": {
"color": "#2a3f5f"
},
"error_y": {
"color": "#2a3f5f"
},
"marker": {
"line": {
"color": "#E5ECF6",
"width": 0.5
},
"pattern": {
"fillmode": "overlay",
"size": 10,
"solidity": 0.2
}
},
"type": "bar"
}
],
"barpolar": [
{
"marker": {
"line": {
"color": "#E5ECF6",
"width": 0.5
},
"pattern": {
"fillmode": "overlay",
"size": 10,
"solidity": 0.2
}
},
"type": "barpolar"
}
],
"carpet": [
{
"aaxis": {
"endlinecolor": "#2a3f5f",
"gridcolor": "white",
"linecolor": "white",
"minorgridcolor": "white",
"startlinecolor": "#2a3f5f"
},
"baxis": {
"endlinecolor": "#2a3f5f",
"gridcolor": "white",
"linecolor": "white",
"minorgridcolor": "white",
"startlinecolor": "#2a3f5f"
},
"type": "carpet"
}
],
"choropleth": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"type": "choropleth"
}
],
"contour": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"colorscale": [
[
0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1,
"#f0f921"
]
],
"type": "contour"
}
],
"contourcarpet": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"type": "contourcarpet"
}
],
"heatmap": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"colorscale": [
[
0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1,
"#f0f921"
]
],
"type": "heatmap"
}
],
"histogram": [
{
"marker": {
"pattern": {
"fillmode": "overlay",
"size": 10,
"solidity": 0.2
}
},
"type": "histogram"
}
],
"histogram2d": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"colorscale": [
[
0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1,
"#f0f921"
]
],
"type": "histogram2d"
}
],
"histogram2dcontour": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"colorscale": [
[
0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1,
"#f0f921"
]
],
"type": "histogram2dcontour"
}
],
"mesh3d": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"type": "mesh3d"
}
],
"parcoords": [
{
"line": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "parcoords"
}
],
"pie": [
{
"automargin": true,
"type": "pie"
}
],
"scatter": [
{
"fillpattern": {
"fillmode": "overlay",
"size": 10,
"solidity": 0.2
},
"type": "scatter"
}
],
"scatter3d": [
{
"line": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scatter3d"
}
],
"scattercarpet": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scattercarpet"
}
],
"scattergeo": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scattergeo"
}
],
"scattergl": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scattergl"
}
],
"scattermap": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scattermap"
}
],
"scattermapbox": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scattermapbox"
}
],
"scatterpolar": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scatterpolar"
}
],
"scatterpolargl": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scatterpolargl"
}
],
"scatterternary": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scatterternary"
}
],
"surface": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"colorscale": [
[
0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1,
"#f0f921"
]
],
"type": "surface"
}
],
"table": [
{
"cells": {
"fill": {
"color": "#EBF0F8"
},
"line": {
"color": "white"
}
},
"header": {
"fill": {
"color": "#C8D4E3"
},
"line": {
"color": "white"
}
},
"type": "table"
}
]
},
"layout": {
"annotationdefaults": {
"arrowcolor": "#2a3f5f",
"arrowhead": 0,
"arrowwidth": 1
},
"autotypenumbers": "strict",
"coloraxis": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"colorscale": {
"diverging": [
[
0,
"#8e0152"
],
[
0.1,
"#c51b7d"
],
[
0.2,
"#de77ae"
],
[
0.3,
"#f1b6da"
],
[
0.4,
"#fde0ef"
],
[
0.5,
"#f7f7f7"
],
[
0.6,
"#e6f5d0"
],
[
0.7,
"#b8e186"
],
[
0.8,
"#7fbc41"
],
[
0.9,
"#4d9221"
],
[
1,
"#276419"
]
],
"sequential": [
[
0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1,
"#f0f921"
]
],
"sequentialminus": [
[
0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1,
"#f0f921"
]
]
},
"colorway": [
"#636efa",
"#EF553B",
"#00cc96",
"#ab63fa",
"#FFA15A",
"#19d3f3",
"#FF6692",
"#B6E880",
"#FF97FF",
"#FECB52"
],
"font": {
"color": "#2a3f5f"
},
"geo": {
"bgcolor": "white",
"lakecolor": "white",
"landcolor": "#E5ECF6",
"showlakes": true,
"showland": true,
"subunitcolor": "white"
},
"hoverlabel": {
"align": "left"
},
"hovermode": "closest",
"mapbox": {
"style": "light"
},
"paper_bgcolor": "white",
"plot_bgcolor": "#E5ECF6",
"polar": {
"angularaxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
},
"bgcolor": "#E5ECF6",
"radialaxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
}
},
"scene": {
"xaxis": {
"backgroundcolor": "#E5ECF6",
"gridcolor": "white",
"gridwidth": 2,
"linecolor": "white",
"showbackground": true,
"ticks": "",
"zerolinecolor": "white"
},
"yaxis": {
"backgroundcolor": "#E5ECF6",
"gridcolor": "white",
"gridwidth": 2,
"linecolor": "white",
"showbackground": true,
"ticks": "",
"zerolinecolor": "white"
},
"zaxis": {
"backgroundcolor": "#E5ECF6",
"gridcolor": "white",
"gridwidth": 2,
"linecolor": "white",
"showbackground": true,
"ticks": "",
"zerolinecolor": "white"
}
},
"shapedefaults": {
"line": {
"color": "#2a3f5f"
}
},
"ternary": {
"aaxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
},
"baxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
},
"bgcolor": "#E5ECF6",
"caxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
}
},
"title": {
"x": 0.05
},
"xaxis": {
"automargin": true,
"gridcolor": "white",
"linecolor": "white",
"ticks": "",
"title": {
"standoff": 15
},
"zerolinecolor": "white",
"zerolinewidth": 2
},
"yaxis": {
"automargin": true,
"gridcolor": "white",
"linecolor": "white",
"ticks": "",
"title": {
"standoff": 15
},
"zerolinecolor": "white",
"zerolinewidth": 2
}
}
},
"title": {},
"width": 800
}
},
"text/html": [
""
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"CrI3.plot_pairs(group=False)"
]
},
{
"cell_type": "markdown",
"id": "98efb176",
"metadata": {},
"source": [
"The firs magnetic entity is the same as in the first example, but the second is defined by taking all the orbitals, not just the d orbitlas, from the second atom. As you can see the 'atom' and 'l' keys in the dictionary are list, so, for more complicated systems, you can define quasi-molecules with different shells. A not so physically meaningful example, where we combine a cromium, with a neighbouring iodine would look something like this."
]
},
{
"cell_type": "code",
"execution_count": 17,
"id": "5ee077f7",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"Add magnetic entities: 100%|██████████| 2/2 [00:00<00:00, 137.01it/s]\n",
"Add pairs: 100%|██████████| 8/8 [00:00<00:00, 24873.56it/s]\n"
]
}
],
"source": [
"# clear magnetic entities and pairs\n",
"CrI3.magnetic_entities = grogupy.MagneticEntityList()\n",
"CrI3.pairs = grogupy.PairList()\n",
"\n",
"# use the same atoms as in the first example\n",
"magnetic_entities = [\n",
" dict(atom=[0, 2], l=[[None], [2]]),\n",
" dict(atom=[1]),\n",
"]\n",
"pairs = [\n",
" dict(ai=0, aj=1, Ruc=[1, 0, 0]),\n",
" dict(ai=0, aj=1, Ruc=[1, 1, 0]),\n",
" dict(ai=0, aj=1, Ruc=[0, 1, 0]),\n",
" dict(ai=0, aj=1, Ruc=[-1, 1, 0]),\n",
" dict(ai=0, aj=1, Ruc=[-1, 0, 0]),\n",
" dict(ai=0, aj=1, Ruc=[-1, -1, 0]),\n",
" dict(ai=0, aj=1, Ruc=[0, -1, 0]),\n",
" dict(ai=0, aj=1, Ruc=[1, -1, 0]),\n",
"]\n",
"CrI3.add_magnetic_entities(magnetic_entities)\n",
"CrI3.add_pairs(pairs)"
]
},
{
"cell_type": "code",
"execution_count": 18,
"id": "07714eae",
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.plotly.v1+json": {
"config": {
"plotlyServerURL": "https://plot.ly"
},
"data": [
{
"marker": {
"color": "#1F77B4",
"opacity": 0.5,
"size": 10
},
"mode": "markers",
"name": "Center:0Cr(l:0-1-2-3-4-5-6-7-8-9-10-11-12-13-14)--2I(l:2)",
"type": "scatter3d",
"x": {
"bdata": "VzVXuY9dC7+Ut2D/LgcCQA==",
"dtype": "f8"
},
"y": {
"bdata": "tGjbQsyF/z6huSF36bbBPw==",
"dtype": "f8"
},
"z": {
"bdata": "AAAAAAAALkArtlG2q5cwQA==",
"dtype": "f8"
}
},
{
"legendgroup": "pair 0Cr(l:0-1-2-3-4-5-6-7-8-9-10-11-12-13-14)--2I(l:2)-1Cr(l:All), ruc:[1, 0, 0]",
"marker": {
"color": "#1F77B4",
"opacity": 0.5,
"size": 5
},
"mode": "markers",
"name": "1Cr(l:All), ruc:[1, 0, 0]",
"type": "scatter3d",
"x": {
"bdata": "OJp84wYAJUA=",
"dtype": "f8"
},
"y": {
"bdata": "5cHXa2IqAEA=",
"dtype": "f8"
},
"z": {
"bdata": "TE3+/v//LUA=",
"dtype": "f8"
}
},
{
"legendgroup": "pair 0Cr(l:0-1-2-3-4-5-6-7-8-9-10-11-12-13-14)--2I(l:2)-1Cr(l:All), ruc:[1, 1, 0]",
"marker": {
"color": "#1F77B4",
"opacity": 0.5,
"size": 5
},
"mode": "markers",
"name": "1Cr(l:All), ruc:[1, 1, 0]",
"type": "scatter3d",
"x": {
"bdata": "cDT5xg0AHEA=",
"dtype": "f8"
},
"y": {
"bdata": "ANBkYG4qIEA=",
"dtype": "f8"
},
"z": {
"bdata": "TE3+/v//LUA=",
"dtype": "f8"
}
},
{
"legendgroup": "pair 0Cr(l:0-1-2-3-4-5-6-7-8-9-10-11-12-13-14)--2I(l:2)-1Cr(l:All), ruc:[0, 1, 0]",
"marker": {
"color": "#1F77B4",
"opacity": 0.5,
"size": 5
},
"mode": "markers",
"name": "1Cr(l:All), ruc:[0, 1, 0]",
"type": "scatter3d",
"x": {
"bdata": "AADhaPKNCz8=",
"dtype": "f8"
},
"y": {
"bdata": "ANBkYG4qIEA=",
"dtype": "f8"
},
"z": {
"bdata": "TE3+/v//LUA=",
"dtype": "f8"
}
},
{
"legendgroup": "pair 0Cr(l:0-1-2-3-4-5-6-7-8-9-10-11-12-13-14)--2I(l:2)-1Cr(l:All), ruc:[-1, 1, 0",
"marker": {
"color": "#1F77B4",
"opacity": 0.5,
"size": 5
},
"mode": "markers",
"name": "1Cr(l:All), ruc:[-1, 1, 0",
"type": "scatter3d",
"x": {
"bdata": "jssGOfL/G8A=",
"dtype": "f8"
},
"y": {
"bdata": "ANBkYG4qIEA=",
"dtype": "f8"
},
"z": {
"bdata": "TE3+/v//LUA=",
"dtype": "f8"
}
},
{
"legendgroup": "pair 0Cr(l:0-1-2-3-4-5-6-7-8-9-10-11-12-13-14)--2I(l:2)-1Cr(l:All), ruc:[-1, 0, 0",
"marker": {
"color": "#1F77B4",
"opacity": 0.5,
"size": 5
},
"mode": "markers",
"name": "1Cr(l:All), ruc:[-1, 0, 0",
"type": "scatter3d",
"x": {
"bdata": "HpcNcuT/C8A=",
"dtype": "f8"
},
"y": {
"bdata": "5cHXa2IqAEA=",
"dtype": "f8"
},
"z": {
"bdata": "TE3+/v//LUA=",
"dtype": "f8"
}
},
{
"legendgroup": "pair 0Cr(l:0-1-2-3-4-5-6-7-8-9-10-11-12-13-14)--2I(l:2)-1Cr(l:All), ruc:[-1, -1, ",
"marker": {
"color": "#1F77B4",
"opacity": 0.5,
"size": 5
},
"mode": "markers",
"name": "1Cr(l:All), ruc:[-1, -1, ",
"type": "scatter3d",
"x": {
"bdata": "AADhaPKNCz8=",
"dtype": "f8"
},
"y": {
"bdata": "Gt7xVHoqEMA=",
"dtype": "f8"
},
"z": {
"bdata": "TE3+/v//LUA=",
"dtype": "f8"
}
},
{
"legendgroup": "pair 0Cr(l:0-1-2-3-4-5-6-7-8-9-10-11-12-13-14)--2I(l:2)-1Cr(l:All), ruc:[0, -1, 0",
"marker": {
"color": "#1F77B4",
"opacity": 0.5,
"size": 5
},
"mode": "markers",
"name": "1Cr(l:All), ruc:[0, -1, 0",
"type": "scatter3d",
"x": {
"bdata": "cDT5xg0AHEA=",
"dtype": "f8"
},
"y": {
"bdata": "Gt7xVHoqEMA=",
"dtype": "f8"
},
"z": {
"bdata": "TE3+/v//LUA=",
"dtype": "f8"
}
},
{
"legendgroup": "pair 0Cr(l:0-1-2-3-4-5-6-7-8-9-10-11-12-13-14)--2I(l:2)-1Cr(l:All), ruc:[1, -1, 0",
"marker": {
"color": "#1F77B4",
"opacity": 0.5,
"size": 5
},
"mode": "markers",
"name": "1Cr(l:All), ruc:[1, -1, 0",
"type": "scatter3d",
"x": {
"bdata": "N5p84wYALEA=",
"dtype": "f8"
},
"y": {
"bdata": "Gt7xVHoqEMA=",
"dtype": "f8"
},
"z": {
"bdata": "TE3+/v//LUA=",
"dtype": "f8"
}
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0,
6.999999999999999
],
"y": [
0,
0
],
"z": [
0,
0
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0,
-3.4999999999999996
],
"y": [
0,
6.06217782
],
"z": [
0,
0
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0,
0
],
"y": [
0,
0
],
"z": [
0,
30
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
6.999999999999999,
3.4999999999999996
],
"y": [
0,
6.06217782
],
"z": [
0,
0
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
6.999999999999999,
6.999999999999999
],
"y": [
0,
0
],
"z": [
0,
30
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-3.4999999999999996,
3.4999999999999996
],
"y": [
6.06217782,
6.06217782
],
"z": [
0,
0
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-3.4999999999999996,
-3.4999999999999996
],
"y": [
6.06217782,
6.06217782
],
"z": [
0,
30
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0,
6.999999999999999
],
"y": [
0,
0
],
"z": [
30,
30
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0,
-3.4999999999999996
],
"y": [
0,
6.06217782
],
"z": [
30,
30
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.4999999999999996,
3.4999999999999996
],
"y": [
6.06217782,
6.06217782
],
"z": [
30,
0
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.4999999999999996,
6.999999999999999
],
"y": [
6.06217782,
0
],
"z": [
30,
30
]
},
{
"line": {
"color": "black",
"width": 1
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.4999999999999996,
-3.4999999999999996
],
"y": [
6.06217782,
6.06217782
],
"z": [
30,
30
]
}
],
"layout": {
"autosize": false,
"height": 500,
"scene": {
"aspectmode": "data",
"xaxis": {
"gridwidth": 1,
"showgrid": true,
"title": {
"text": "X Axis"
}
},
"yaxis": {
"gridwidth": 1,
"showgrid": true,
"title": {
"text": "Y Axis"
}
},
"zaxis": {
"gridwidth": 1,
"showgrid": true,
"title": {
"text": "Z Axis"
}
}
},
"showlegend": true,
"template": {
"data": {
"bar": [
{
"error_x": {
"color": "#2a3f5f"
},
"error_y": {
"color": "#2a3f5f"
},
"marker": {
"line": {
"color": "#E5ECF6",
"width": 0.5
},
"pattern": {
"fillmode": "overlay",
"size": 10,
"solidity": 0.2
}
},
"type": "bar"
}
],
"barpolar": [
{
"marker": {
"line": {
"color": "#E5ECF6",
"width": 0.5
},
"pattern": {
"fillmode": "overlay",
"size": 10,
"solidity": 0.2
}
},
"type": "barpolar"
}
],
"carpet": [
{
"aaxis": {
"endlinecolor": "#2a3f5f",
"gridcolor": "white",
"linecolor": "white",
"minorgridcolor": "white",
"startlinecolor": "#2a3f5f"
},
"baxis": {
"endlinecolor": "#2a3f5f",
"gridcolor": "white",
"linecolor": "white",
"minorgridcolor": "white",
"startlinecolor": "#2a3f5f"
},
"type": "carpet"
}
],
"choropleth": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"type": "choropleth"
}
],
"contour": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"colorscale": [
[
0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1,
"#f0f921"
]
],
"type": "contour"
}
],
"contourcarpet": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"type": "contourcarpet"
}
],
"heatmap": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"colorscale": [
[
0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1,
"#f0f921"
]
],
"type": "heatmap"
}
],
"histogram": [
{
"marker": {
"pattern": {
"fillmode": "overlay",
"size": 10,
"solidity": 0.2
}
},
"type": "histogram"
}
],
"histogram2d": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"colorscale": [
[
0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1,
"#f0f921"
]
],
"type": "histogram2d"
}
],
"histogram2dcontour": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"colorscale": [
[
0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1,
"#f0f921"
]
],
"type": "histogram2dcontour"
}
],
"mesh3d": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"type": "mesh3d"
}
],
"parcoords": [
{
"line": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "parcoords"
}
],
"pie": [
{
"automargin": true,
"type": "pie"
}
],
"scatter": [
{
"fillpattern": {
"fillmode": "overlay",
"size": 10,
"solidity": 0.2
},
"type": "scatter"
}
],
"scatter3d": [
{
"line": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scatter3d"
}
],
"scattercarpet": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scattercarpet"
}
],
"scattergeo": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scattergeo"
}
],
"scattergl": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scattergl"
}
],
"scattermap": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scattermap"
}
],
"scattermapbox": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scattermapbox"
}
],
"scatterpolar": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scatterpolar"
}
],
"scatterpolargl": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scatterpolargl"
}
],
"scatterternary": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scatterternary"
}
],
"surface": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"colorscale": [
[
0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1,
"#f0f921"
]
],
"type": "surface"
}
],
"table": [
{
"cells": {
"fill": {
"color": "#EBF0F8"
},
"line": {
"color": "white"
}
},
"header": {
"fill": {
"color": "#C8D4E3"
},
"line": {
"color": "white"
}
},
"type": "table"
}
]
},
"layout": {
"annotationdefaults": {
"arrowcolor": "#2a3f5f",
"arrowhead": 0,
"arrowwidth": 1
},
"autotypenumbers": "strict",
"coloraxis": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"colorscale": {
"diverging": [
[
0,
"#8e0152"
],
[
0.1,
"#c51b7d"
],
[
0.2,
"#de77ae"
],
[
0.3,
"#f1b6da"
],
[
0.4,
"#fde0ef"
],
[
0.5,
"#f7f7f7"
],
[
0.6,
"#e6f5d0"
],
[
0.7,
"#b8e186"
],
[
0.8,
"#7fbc41"
],
[
0.9,
"#4d9221"
],
[
1,
"#276419"
]
],
"sequential": [
[
0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1,
"#f0f921"
]
],
"sequentialminus": [
[
0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1,
"#f0f921"
]
]
},
"colorway": [
"#636efa",
"#EF553B",
"#00cc96",
"#ab63fa",
"#FFA15A",
"#19d3f3",
"#FF6692",
"#B6E880",
"#FF97FF",
"#FECB52"
],
"font": {
"color": "#2a3f5f"
},
"geo": {
"bgcolor": "white",
"lakecolor": "white",
"landcolor": "#E5ECF6",
"showlakes": true,
"showland": true,
"subunitcolor": "white"
},
"hoverlabel": {
"align": "left"
},
"hovermode": "closest",
"mapbox": {
"style": "light"
},
"paper_bgcolor": "white",
"plot_bgcolor": "#E5ECF6",
"polar": {
"angularaxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
},
"bgcolor": "#E5ECF6",
"radialaxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
}
},
"scene": {
"xaxis": {
"backgroundcolor": "#E5ECF6",
"gridcolor": "white",
"gridwidth": 2,
"linecolor": "white",
"showbackground": true,
"ticks": "",
"zerolinecolor": "white"
},
"yaxis": {
"backgroundcolor": "#E5ECF6",
"gridcolor": "white",
"gridwidth": 2,
"linecolor": "white",
"showbackground": true,
"ticks": "",
"zerolinecolor": "white"
},
"zaxis": {
"backgroundcolor": "#E5ECF6",
"gridcolor": "white",
"gridwidth": 2,
"linecolor": "white",
"showbackground": true,
"ticks": "",
"zerolinecolor": "white"
}
},
"shapedefaults": {
"line": {
"color": "#2a3f5f"
}
},
"ternary": {
"aaxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
},
"baxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
},
"bgcolor": "#E5ECF6",
"caxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
}
},
"title": {
"x": 0.05
},
"xaxis": {
"automargin": true,
"gridcolor": "white",
"linecolor": "white",
"ticks": "",
"title": {
"standoff": 15
},
"zerolinecolor": "white",
"zerolinewidth": 2
},
"yaxis": {
"automargin": true,
"gridcolor": "white",
"linecolor": "white",
"ticks": "",
"title": {
"standoff": 15
},
"zerolinecolor": "white",
"zerolinewidth": 2
}
}
},
"title": {},
"width": 800
}
},
"text/html": [
""
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"CrI3.plot_pairs(group=False)"
]
},
{
"cell_type": "markdown",
"id": "1e24b02a",
"metadata": {},
"source": [
"Here we took different shells from the chromium and iodine. If you set the atoms you could also use the 'orb' key, but in this case the indexing is not done directly from the Hamiltonian, but from the atomic orbitals."
]
}
],
"metadata": {
"kernelspec": {
"display_name": ".venv (3.13.8)",
"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": "3.13.8"
}
},
"nbformat": 4,
"nbformat_minor": 5
}