### Install Pymatgen from source using pip

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/index.md

Install the developmental version of pymatgen by cloning the GitHub repository and installing from the root.

```shell
uv pip install .
```

--------------------------------

### Example POTCAR Configuration Process

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/installation.md

This example demonstrates the complete process of configuring POTCAR paths for both PBE and LDA functionals and adding the Pymatgen PSP directory to the configuration.

```bash
pmg config -p /path/to/pseudos/potcar_PBE.54 /path/to/pseudos/pmg_potcars
pmg config -p /path/to/pseudos/potcar_LDA.54 /path/to/pseudos/pmg_potcars
pmg config --add PMG_VASP_PSP_DIR /path/to/pseudos/pmg_potcars
```

--------------------------------

### Install Pymatgen Core Package

Source: https://github.com/materialsproject/pymatgen/blob/main/README.md

Installs only the core pymatgen objects and file I/O functionality, providing a minimal installation.

```sh
pip install pymatgen-core
```

--------------------------------

### Install Pre-commit Hooks

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/contributing.md

Install the pre-commit hook for linters to ensure code quality before committing changes.

```sh
uv run pre-commit install  # Install pre-commit hook for linters.
```

--------------------------------

### Text Transition Setup

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/assets/team-map.html

Sets up a transition for the text content of an element.

```javascript
ji.text=function(t){return Vi(this,"text",t,Hi)}
```

--------------------------------

### Setup Painter in Mapbox GL JS

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/assets/team-map.html

Initializes the map's painter, which is responsible for rendering. It attempts to get a WebGL rendering context and creates a painter instance.

```javascript
i.prototype._setupPainter=function(){var r=t.extend({},e.webGLContextAttributes,{failIfMajorPerformanceCaveat:this._failIfMajorPerformanceCaveat,preserveDrawingBuffer:this._preserveDrawingBuffer,antialias:this._antialias||!1}),n=this._canvas.getContext("webgl",r)||this._canvas.getContext("experimental-webgl",r);n?(this.painter=new _n(n,this.transform),t.webpSupported.testSupport(n)):this.fire(new t.ErrorEvent(new Error("Failed ")))}
```

--------------------------------

### Install Full Pymatgen Package

Source: https://github.com/materialsproject/pymatgen/blob/main/README.md

Installs the complete pymatgen package, including analyses, applications, and external integrations, along with core data objects and file I/O.

```sh
pip install pymatgen
```

--------------------------------

### Start a polygon

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/assets/team-map.html

Sets the point and line handlers for the start of a polygon. This prepares the projection for polygon rendering.

```javascript
function Gt(){Bt.point=Wt}
```

--------------------------------

### Install Pymatgen using pip

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/index.md

Use this command to install the latest stable release of pymatgen from PyPI.

```shell
uv pip install pymatgen
```

--------------------------------

### Install Optional Libraries using pmg

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/installation.md

Installs optional libraries like enumlib and bader using the pmg command-line tool. These are only for OSX and Linux.

```shell
pmg config --install enumlib
pmg config --install bader
```

--------------------------------

### Install and Run Pymatgen Pre-commit Hooks

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/contributing.md

Install pre-commit hooks to automatically check code style and quality before commits. Optionally, run pre-commit manually on specific files or the entire codebase.

```sh
uv run pre-commit install  # ensure linters are run prior to all future commits

# (Optional) Run pre-commit manually
uv run pre-commit run --files path/to/changed/files  # ensure certain file don't offend linters
# or
uv run pre-commit run --all-files  # ensure your entire codebase passes linters
```

--------------------------------

### Style Tween Setup

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/assets/team-map.html

Sets up a tween for style transitions, allowing custom interpolation.

```javascript
ji.styleTween=function(t,e,r){function n(n,i){var a=e.call(this,n,i,o(this).getComputedStyle(this,null).getPropertyValue(t));return a&&function(e){this.style.setProperty(t,a(e),r)}}return arguments.length<3&&(r=""),this.tween("style."+t,n)}
```

--------------------------------

### Voronoi Edge Start and End Points

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/assets/team-map.html

Helper methods for a Voronoi edge to get its start and end sites based on the current site context.

```javascript
$e.prototype={start:function(){return this.edge.l===this.site?this.edge.a:this.edge.b},end:function(){return this.edge.l===this.site?this.edge.b:this.edge.a}}
```

--------------------------------

### Start and End Angle Accessors

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/assets/team-map.html

Functions to get and set the start and end angles for arc-based path generation. These define the portion of the circle or ellipse used.

```javascript
function ei(t){return t.startAngle}
function ri(t){return t.endAngle}
```

--------------------------------

### Style Transition Setup

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/assets/team-map.html

Sets up a transition for CSS properties. Handles property removal if the value is null.

```javascript
ji.style=function(t,e,r){var n=arguments.length;if(n<3){if("string"!=typeof t){for(r in n<2&&(e=""),t)this.style(r,t\[r\],e);return this}r=""}function i(){this.style.removeProperty(t)}function a(e){return null==e?i:(e+="",function(){var n,i=o(this).getComputedStyle(this,null).getPropertyValue(t);return i!==e&&(n=yr(i,e),function(e){this.style.setProperty(t,n(e),r)})})}return Vi(this,"style."+t,e,a)}
```

--------------------------------

### Synchronize Dependencies with uv

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/contributing.md

Set up your development environment by synchronizing dependencies using uv. You can install optional dependencies or all of them.

```sh
uv sync
# uv sync --extra optional  # Install a specific optional dependency
# uv sync --all-extras      # Install all optional dependencies
```

--------------------------------

### Deprecated Method Aliases

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/assets/team-map.html

Provides aliases for previously used method names, throwing an error to guide users to the current, renamed methods. For example, `radians2degrees` is now `radiansToDegrees`.

```javascript
r.radians2degrees=function(){throw new Error("method has been renamed to \`radiansToDegrees`")},r.degrees2radians=function(){throw new Error("method has been renamed to \`degreesToRadians`")},r.distanceToDegrees=function(){throw new Error("method has been renamed to \`lengthToDegrees`")},r.distanceToRadians=function(){throw new Error("method has been renamed to \`lengthToRadians`")},r.radiansToDistance=function(){throw new Error("method has been renamed to \`radiansToLength`")},r.bearingToAngle=function(){throw new Error("method has been renamed to \`bearingToAzimuth`")},r.convertDistance=function(){throw new Error("method has been renamed to \`convertLength`")}
```

--------------------------------

### Element and Composition Basics

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/index.md

Demonstrates creating Element and Composition objects and accessing their properties like atomic mass, melting point, and weight. Composition objects allow for easy querying of atomic fractions.

```python
from pymatgen.core import Composition, Element, Lattice, Molecule, Structure

# Integrated symmetry analysis tools from spglib
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer


si = Element("Si")
si.atomic_mass  # 28.0855
print(si.melting_point)
# 1687.0 K

comp = Composition("Fe2O3")
comp.weight  # 159.6882
# Note that Composition conveniently allows strings to be treated just like an Element object.
comp["Fe"]  # 2.0
comp.get_atomic_fraction("Fe")  # 0.4
```

--------------------------------

### Rendering Engine Setup

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/assets/team-map.html

Sets up various buffers and index buffers required for rendering tiles, debug information, raster bounds, and viewports. Also initializes an empty texture and stencil clear mode.

```javascript
_n.prototype.setup=function(){var e=this.context,r=new t.StructArrayLayout2i4;r.emplaceBack(0,0),r.emplaceBack(t.EXTENT,0),r.emplaceBack(0,t.EXTENT),r.emplaceBack(t.EXTENT,t.EXTENT),this.tileExtentBuffer=e.createVertexBuffer(r,Ge.members),this.tileExtentSegments=t.SegmentVector.simpleSegment(0,0,4,2);var n=new t.StructArrayLayout2i4;n.emplaceBack(0,0),n.emplaceBack(t.EXTENT,0),n.emplaceBack(0,t.EXTENT),n.emplaceBack(t.EXTENT,t.EXTENT),this.debugBuffer=e.createVertexBuffer(n,Ge.members),this.debugSegments=t.SegmentVector.simpleSegment(0,0,4,5);var i=new t.StructArrayLayout4i8;i.emplaceBack(0,0,0,0),i.emplaceBack(t.EXTENT,0,t.EXTENT,0),i.emplaceBack(0,t.EXTENT,0,t.EXTENT),i.emplaceBack(t.EXTENT,t.EXTENT,t.EXTENT,t.EXTENT),this.rasterBoundsBuffer=e.createVertexBuffer(i,P.members),this.rasterBoundsSegments=t.SegmentVector.simpleSegment(0,0,4,2);var a=new t.StructArrayLayout2i4;a.emplaceBack(0,0),a.emplaceBack(1,0),a.emplaceBack(0,1),a.emplaceBack(1,1),this.viewportBuffer=e.createVertexBuffer(a,Ge.members),this.viewportSegments=t.SegmentVector.simpleSegment(0,0,4,2);var o=new t.StructArrayLayout1ui2;o.emplaceBack(0),o.emplaceBack(1),o.emplaceBack(3),o.emplaceBack(2),o.emplaceBack(0),this.tileBorderIndexBuffer=e.createIndexBuffer(o);var s=new t.StructArrayLayout3ui6;s.emplaceBack(0,1,2),s.emplaceBack(2,1,3),this.quadTriangleIndexBuffer=e.createIndexBuffer(s),this.emptyTexture=new t.Texture(e,{width:1,height:1,data:new Uint8Array([0,0,0,0])},e.gl.RGBA);var l=this.context.gl;this.stencilClearMode=new Mt({func:l.ALWAYS,mask:0},0,255,l.ZERO,l.ZERO,l.ZERO)},

```

--------------------------------

### Buffer Creation and Initialization

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/assets/team-map.html

Demonstrates how to allocate and initialize Buffer objects. Supports filling with a specific value or creating an unsafe buffer.

```javascript
a.alloc=function(t,e,r){return function(t,e,r){return s(t),t<=0?i(t):void 0!==e?"string"==typeof r?i(t).fill(e,r):i(t).fill(e):i(t)}(t,e,r)},
```

```javascript
a.allocUnsafe=function(t){return l(t)},
```

```javascript
a.allocUnsafeSlow=function(t){return l(t)},
```

--------------------------------

### Initialize Clustering Utility

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/assets/team-map.html

Sets up the clustering utility with provided options and initializes an array to hold Quadtrees for different zoom levels.

```javascript
var U=function(t){this.options=X(Object.create(j),t),this.trees=new Array(this.options.maxZoom+1)}
```

--------------------------------

### Start Request Performance Measurement

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/assets/team-map.html

Starts performance measurement for a request by marking the start time. This is used to track the duration of various operations.

```javascript
var gu=self.performance,mu=function(t){this._marks={start:[t.url,"start"].join("#"),end:[t.url,"end"].join("#"),measure:t.url.toString()},gu.mark(this._marks.start)};mu.prototype.finish=function(){gu.mark(this._marks.end);var t=gu.getEntriesByName(this._marks.measure);return 0===t.length&&(gu.measure(this._marks.measure,this._marks.start,this._marks.end),t=gu.getEntriesByName(this._marks.measure),gu.clearMarks(this._marks.start),gu.clearMarks(this._marks.end),gu.clearMeasures(this._marks.measure)),t}
```

--------------------------------

### Install Pymatgen with Pip after Conda Dependencies

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/installation.md

Use this method if the direct Conda installation fails. It installs critical dependencies via Conda first, then uses Pip for pymatgen.

```shell
conda install --yes numpy scipy matplotlib
pip install pymatgen
```

--------------------------------

### Use Program

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/assets/team-map.html

Selects a rendering program (shader) for use. Initializes a cache if it doesn't exist. This is a fundamental step before issuing rendering commands.

```javascript
t,e;this.cache=this.cache||{};var 
```

--------------------------------

### Geo Projection: Polygon Start

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/assets/team-map.html

Initializes polygon projection. Use when starting to draw a polygon.

```javascript
V.polygonStart=function(){j.reset(),V.lineStart=H,V.lineEnd=q}
```

--------------------------------

### Initialize Buffers and Textures

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/assets/team-map.html

Sets up WebGL buffers and textures required for rendering. This includes creating dynamic buffers for attributes and a texture for the color palette.

```javascript
var a = n(["precision highp float;\n#define GLSLIFY 1\n\nvarying vec4 fragColor;\n\nvoid main() {\n gl_FragColor = fragColor;\n}\n"]),
 o = t("./constants").maxDimensionCount,
 s = t("../../lib"),
 l = new Uint8Array(4),
 c = new Uint8Array(4),
 u = {shape:[256,1],format:"rgba",type:"uint8",mag:"nearest",min:"nearest"};

function f(t,e,r,n,i){var a=t._gl;a.enable(a.SCISSOR_TEST),a.scissor(e,r,n,i),t.clear({color:[0,0,0,0],depth:1})}
function h(t,e,r,n,i,a){var o=a.key;r.drawCompleted||(!function s(l){var c=Math.min(n,i-l*n);0===l&&(window.cancelAnimationFrame(r.currentRafs[o]),delete r.currentRafs[o],f(t,a.scissorX,a.scissorY,a.scissorWidth,a.viewBoxSize[1])),r.clearOnly||(a.count=2*c,a.offset=2*l*n,e(a),l*n+c<i&&(r.currentRafs[o]=window.requestAnimationFrame((function(){s(l+1)}))),r.drawCompleted=!1)}(0),r.drawCompleted=!0)}
function p(t,e){for(var r=new Array(256),n=0;n<256;n++)r[n]=t(n/255).concat(e);return r}
function d(t,e){return(t>>>8*e)%256/255}
function g(t,e,r){for(var n=new Array(8*e),i=0,a=0;a<e;a++)for(var o=0;o<2;o++)for(var s=0;s<4;s++){var l=4*t+s,c=r[64*a+l];63===l&&0===o&&(c*=-1),n[i++]=c}return n}
function m(t){var e="0"+t;return e.substr(e.length-2)}
function v(t){return t<o?"p"+m(t+1)+"_"+m(t+4):"colors"}
function y(t,e,r,n,i,a,o,l,c,u,f,h,p,d){for(var g=[[[],[]],m=0;m<64;m++)g[0][m]=m===i?1:0,g[1][m]=m===a?1:0;o*=d,l*=d,c*=d,u*=d;var v=t.lines.canvasOverdrag*d,y=t.domain,x=t.canvasWidth*d,b=t.canvasHeight*d,_=t.pad.l*d,w=t.pad.b*d,T=t.layoutHeight*d,k=t.layoutWidth*d,A=t.deselectedLines.color;return s.extendFlat({key:f,resolution:[x,b],viewBoxPos:[o+v,l],viewBoxSize:[c,u],i0:i,i1:a,dim0A:g[0].slice(0,16),dim0B:g[0].slice(16,32),dim0C:g[0].slice(32,48),dim0D:g[0].slice(48,64),dim1A:g[1].slice(0,16),dim1B:g[1].slice(16,32),dim1C:g[1].slice(32,48),dim1D:g[1].slice(48,64),drwLayer:h,contextColor:[A[0]/255,A[1]/255,A[2]/255,A[3]<1?A[3]:Math.max(1/255,Math.pow(1/t.lines.color.length,1/3))],scissorX:(n===e?0:o+v)+(_-v)+k*y.x[0],scissorWidth:(n===r?x-o+v:c+.5)+(n===e?o+v:0),scissorY:l+w+T*y.y[0],scissorHeight:u,viewportX:_-v+k*y.x[0],viewportY:w+T*y.y[0],viewportWidth:x,viewportHeight:b},p)}
function x(t){var e=Math.max(0,Math.floor(2047*t[0]),0),r=Math.min(2047,Math.ceil(2047*t[1]),2047);return[Math.min(e,r),Math.max(e,r)]}

e.exports=function(t,e){var r,n,l,m,b,_=e.context,w=e.pick,T=e.regl,k=T._gl,A=k.getParameter(k.ALIASED_LINE_WIDTH_RANGE),M=Math.max(A[0],Math.min(A[1],e.viewModel.plotGlPixelRatio)),S={currentRafs:{},drawCompleted:!0,clearOnly:!1},E=function(t){for(var e={},r=0;r<=o;r+=4)e[v(r)]=t.buffer({usage:"dynamic",type:"float",data:new Uint8Array(0)});return e}(T),L=T.texture(u),C=[];

```

--------------------------------

### Run Runnable Python Scripts for VASP Calculations

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/CHANGES.md

This example demonstrates how to use the VaspInput class to create runnable Python scripts for VASP calculations, including k-point convergence tests. It utilizes MPRester to fetch structures and MPRelaxSet for input set generation, directly running VASP using a specified command.

```python
from pymatgen import MPRester
from pymatgen.io.vasp.sets import MPRelaxSet


VASP_CMD = ["mpirun", "-machinefile", "$PBS_NODEFILE", "-np", "16", "vasp"]


def main():
    mpr = MPRester()
    structure = mpr.get_structures("Li2O")[0]
    for k_dens in [100, 200, 400, 800]:
        vis = MPRelaxSet(structure,
            user_kpoints_settings={"reciprocal_density": k_dens})
        vi = vis.get_vasp_input()
        kpoints = vi["KPOINTS"].kpts[0][0]
        d = f"Li2O_kpoints_{kpoints}"

        # Directly run vasp.
        vi.run_vasp(d, vasp_cmd=VASP_CMD)
        # Use the final structure as the new initial structure to speed up calculations.
        structure = Vasprun(f"{d}/vasprun.xml").final_structure


if __name__ == "__main__":
    main()
```

--------------------------------

### Geo Projection: Line Start

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/assets/team-map.html

Initializes line projection. Use when starting to draw a line segment.

```javascript
V.lineStart=E
```

--------------------------------

### Manually Create a Silicon Structure

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/usage.md

Demonstrates the manual creation of a basic silicon crystal structure with specified lattice parameters and atomic coordinates. Also shows creating a methane molecule.

```python
from pymatgen.core import Lattice, Structure, Molecule

coords = [[0, 0, 0], [0.75,0.5,0.75]]
lattice = Lattice.from_parameters(a=3.84, b=3.84, c=3.84, alpha=120,
                                  beta=90, gamma=60)
struct = Structure(lattice, ["Si", "Si"], coords)

coords = [[0.000000, 0.000000, 0.000000],
          [0.000000, 0.000000, 1.089000],
          [1.026719, 0.000000, -0.363000],
          [-0.513360, -0.889165, -0.363000],
          [-0.513360, 0.889165, -0.363000]]
methane = Molecule(["C", "H", "H", "H", "H"], coords)
```

--------------------------------

### BasicAbinitInput Methods

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/pymatgen.md

Outlines the methods for the BasicAbinitInput class, a concrete implementation for creating basic ABINIT input files.

```APIDOC
## BasicAbinitInput Methods

### Description
Represents a basic ABINIT input structure, allowing for the addition of ABIOBJECTS and conversion to/from dictionaries.

### Methods
- `add_abiobjects()`: Adds ABIOBJECTS to the input.
- `as_dict()`: Converts the input object to a dictionary.
- `from_dict()`: Creates an input object from a dictionary.
```

--------------------------------

### Install GCC using Conda

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/index.md

Install the GCC compiler using conda, which may be required for pymatgen compilation.

```shell
conda install gcc
```

--------------------------------

### Mesh Creation Utility

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/assets/team-map.html

Core utility for creating 3D meshes. Handles shader compilation, buffer creation, and VAO setup. Requires various gl- utilities.

```javascript
var n=t("gl-shader"),i=t("gl-buffer"),a=t("gl-vao"),o=t("gl-texture2d"),s=t("gl-mat4/multiply"),l=t("gl-mat4/invert"),c=t("ndarray"),u=t("colormap"),f=\[1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1\];function h(t,e,r,n,i,a,o,s,l,c,u){this.gl=t,this.pixelRatio=1,this.cells=\[\] ,this.positions=\[\] ,this.intensity=\[\] ,this.texture=e,this.dirty=!0,this.triShader=r,this.pickShader=n,this.trianglePositions=i,this.triangleVectors=a,this.triangleColors=s,this.triangleUVs=l,this.triangleIds=o,this.triangleVAO=c,this.triangleCount=0,this.pickId=1,this.bounds=\[\[1/0,1/0,1/0\],\[-1/0,-1/0,-1/0\]\] ,this.clipBounds=\[\[-1/0,-1/0,-1/0\],\[1/0,1/0,1/0\]\] ,this.lightPosition=\[1e5,1e5,0\] ,this.ambientLight=.8,this.diffuseLight=.8,this.specularLight=2,this.roughness=.5,this.fresnel=1.5,this.opacity=1,this.traceType=u,this.tubeScale=1,this.coneScale=2,this.vectorScale=1,this.coneOffset=.25,this._model=f,this._view=f,this._projection=f,this._resolution=\[1,1\]}var p=h.prototype;function d(t,e){var r=n(t,e.meshShader.vertex,e.meshShader.fragment,null,e.meshShader.attributes);return r.attributes.position.location=0,r.attributes.color.location=2,r.attributes.uv.location=3,r.attributes.vector.location=4,r}function g(t,e){var r=n(t,e.pickShader.vertex,e.pickShader.fragment,null,e.pickShader.attributes);return r.attributes.position.location=0,r.attributes.id.location=1,r.attributes.vector.location=4,r}p.isOpaque=function(){return this.opacity>=1},p.isTransparent=function(){return this.opacity<1},p.pickSlots=1,p.setPickBase=function(t){this.pickId=t},p.update=function(t){t=t||{};var e=this.gl;this.dirty=!0,"lightPosition"in t&&(this.lightPosition=t.lightPosition),"opacity"in t&&(this.opacity=t.opacity),"ambient"in t&&(this.ambientLight=t.ambient),"diffuse"in t&&(this.diffuseLight=t.diffuse),"specular"in t&&(this.specularLight=t.specular),"roughness"in t&&(this.roughness=t.roughness),"fresnel"in t&&(this.fresnel=t.fresnel),void 0!==t.tubeScale&&(this.tubeScale=t.tubeScale),void 0!==t.vectorScale&&(this.vectorScale=t.vectorScale),void 0!==t.coneScale&&(this.coneScale=t.coneScale),void 0!==t.coneOffset&&(this.coneOffset=t.coneOffset),t.colormap&&(this.texture.shape=\[256,256\] ,this.texture.minFilter=e.LINEAR_MIPMAP_LINEAR,this.texture.magFilter=e.LINEAR,this.texture.setPixels(function(t){for(var e=u({colormap:t,nshades:256,format:"rgba"}),r=new Uint8Array(1024),n=0;n<256;++n){for(var i=e[n],a=0;a<3;++a)r[4*n+a]=i[a];r[4*n+3]=255*i[3]}return c(r,[256,256,4],[4,0,1])}(t.colormap)),this.texture.generateMipmap());var r=t.cells,n=t.positions,i=t.vectors;if(n&&r&&i){var a=\[\] ,o=\[\] ,s=\[\] ,l=\[\] ,f=\[\];this.cells=r,this.positions=n,this.vectors=i;var h=t.meshColor||\[1,1,1,1\] ,p=t.vertexIntensity,d=1/0,g=-1/0;if(p)if(t.vertexIntensityBounds)d=+t.vertexIntensityBounds[0],g=+t.vertexIntensityBounds[1];else for(var m=0;m<p.length;++m){var v=p[m];d=Math.min(d,v),g=Math.max(g,v)}else for(m=0;m<n.length;++m){v=n[m][2];d=Math.min(d,v),g=Math.max(g,v)}this.intensity=p||function(t){for(var e=t.length,r=new Array(e),n=0;n<e;++n)r[n]=t[n][2];return r}(n),this.bounds=\[\[1/0,1/0,1/0\],\[-1/0,-1/0,-1/0\]\];for(m=0;m<n.length;++m)for(var y=n[m],x=0;x<3;++x)!isNaN(y[x])&&isFinite(y[x])&&(this.bounds[0][x]=Math.min(this.bounds[0][x],y[x]),this.bounds[1][x]=Math.max(this.bounds[1][x],y[x]));var b=0;t:for(m=0;m<r.length;++m){var _=r[m];switch(_.length){case 3:for(x=0;x<3;++x){y=n[T=_[x]] ;for(var w=0;w<3;++w)if(isNaN(y[w])||!isFinite(y[w]))continue t}for(x=0;x<3;++x){var T;y=n[T=_[2-x]];a.push(y[0],y[1],y[2],y[3]);var k=i[T];o.push(k[0],k[1],k[2],k[3]||0);var A,M=h;3===M.length?s.push(M[0],M[1],M[2],1):s.push(M[0],M[1],M[2],M[3]),A=p?(p[T]-d)/(g-d),0]:(y[2]-d)/(g-d),0],l.push(A[0],A[1]),f.push(m)}}this.triangleCount=b,this.trianglePositions.update(a),this.triangleVectors.update(o),this.triangleColors.update(s),this.triangleUVs.update(l),this.triangleIds.update(new Uint32Array(f))}},p.drawTransparent=p.draw=function(t){t=t||{};for(var e=this.gl,r=t.model||f,n=t.view||f,i=t.projection||f,a=\[\[-1e6,-1e6,-1e6\],\[1e6,1e6,1e6\]\] ,o=0;o<3;++o)a[0][o]=Math.max(a[0][o],this.clipBounds[0][o]),a[1][o]=Math.min(a[1][o],this.clipBounds[1][o])}
```

--------------------------------

### Install Pymatgen using Conda-forge

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/installation.md

Installs pymatgen from the conda-forge channel on Anaconda Cloud. This is the primary recommended method.

```shell
conda install --channel conda-forge pymatgen
```

--------------------------------

### Geo Projection: Path Handler - Line Start

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/assets/team-map.html

Initializes line path handling. Use when starting to process a line.

```javascript
St.lineStart=Ct
```

--------------------------------

### Initialize WebGL Shaders and Textures

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/assets/team-map.html

Sets up essential WebGL components including shaders and textures. This is typically called during the initialization of a visualization context.

```javascript
e.exports=function(t,e){1===arguments.length&&(t=(e=t).gl);var r=t.getExtension("OES_standard_derivatives")||t.getExtension("MOZ_OES_standard_derivatives")||t.getExtension("WEBKIT_OES_standard_derivatives");if(!r)throw new Error("derivatives not supported");var n=M(t),s=S(t),l=E(t),c=L(t),f=C(t),h=P(t),p=o(t,u(new Uint8Array([255,255,255,255]),[1,1,4]));p.generateMipmap(),p.minFilter=t.LINEAR_MIPMAP_LINEAR,p.magFilter=t.LINEAR;
```

--------------------------------

### Shared Cluster Installation with Conda

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/index.md

Steps for installing pymatgen on shared computing clusters using Miniconda for a local, self-contained environment.

```shell
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh -b

# Reload bash profile.
source $HOME/.bashrc
source $HOME/.bash_profile

# Install numpy and other pydata stack packages via conda.
conda install --yes numpy scipy pandas
conda install --yes --channel conda-forge pymatgen
```

--------------------------------

### LineBucket Upload and Initialization

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/assets/team-map.html

Initializes and uploads line geometry data to the GPU. Ensures program configurations are also uploaded.

```javascript
qs.prototype.uploadPending=function(){return!this.uploaded||this.programConfigurations.needsUpload},qs.prototype.upload=function(t){this.uploaded||(this.layoutVertexBuffer=t.createVertexBuffer(this.layoutVertexArray,js),this.indexBuffer=t.createIndexBuffer(this.indexArray)),this.programConfigurations.upload(t),this.uploaded=!0}
```

--------------------------------

### Install Pymatgen in developmental mode using pip

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/index.md

Install the developmental version of pymatgen in editable mode, allowing for direct code changes to take effect.

```shell
uv pip install -e .
```

--------------------------------

### Shader Compilation and Program Setup

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/assets/team-map.html

Handles shader compilation, program linking, and setting up WebGL state for rendering. It manages context dependencies and program variables.

```javascript
function(a,o){function r(t){return t.contextDep&&i||t.propDep}var n=t.proc("batch",2);t.batchId="0",B(t,n);var i=!1,a=!0;Object.keys(e.context).forEach((function(t){i=i||e.context[t].propDep}));if(!i){M(t,n,e.context),a=!1}var o=!1;if(s=e.framebuffer)?(s.propDep?i=o=!0:s.contextDep&&i&&(o=!0),o||S(t,n,s)):S(t,n,null);e.state.viewport&&e.state.viewport.propDep&&(i=!0),E(t,n,e),L(t,n,e.state,(function(t){return!r(t)})),e.profile&&r(e.profile)||N(t,n,e,!1,"a1");e.contextDep=i,e.needsContext=a,e.needsFramebuffer=o;(a=e.shader.progVar).contextDep&&i||a.propDep)X(t,n,e,null);else if(a=a.append(t,n),n(t.shared.gl,".useProgram(",a,".program);"),e.shader.program)X(t,n,e,e.shader.program);else{n(t.shared.vao,".setVAO(null);");var s=t.global.def("{}"),l=(o=n.def(a,".id"),n.def(s,"[",o,"]"));n(t.cond(l).then(l,".call(this,a0,a1);",
).else(l,"=",s,"[",o,"]=",t.link((function(r){return G(X,t,e,r,2)})),"(",a,");",l,".call(this,a0,a1);"))}0<Object.keys(e.state).length&&n(t.shared.current,".dirty=true;"),t.shared.vao&&n(t.shared.vao,".setVAO(null);")}(a,o),j(a.compile(),{destroy:function(){o.shader.program.destroy()}})}}
```

--------------------------------

### Install Miniconda for Mac or Linux

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/installation.md

Download and run the Miniconda installer script for your operating system. You may need to restart your terminal for changes to take effect.

```bash
# If Mac
bash Miniconda3-latest-MacOSX-x86_64.sh

# If Linux
bash Miniconda3-latest-Linux-x86_64.sh
```

--------------------------------

### Initialize Bucket Parts

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/assets/team-map.html

Initializes a new instance of Oe, setting up properties related to symbol sorting and tracking the current placement progress.

```javascript
var Ie=0,Oe=function(t){this._sortAcrossTiles="viewport-y"!==t.layout.get("symbol-z-order")&&void 0!==t.layout.get("symbol-sort-key").constantOr(1),this._currentTileIndex=0,this._currentPartIndex=0,this._seenCrossTileIDs={},this._bucketParts=[]}
```

--------------------------------

### Initialize WebGL Buffers and Shaders

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/assets/team-map.html

Initializes WebGL buffers and shaders for rendering. Requires a WebGL context and shader definitions.

```javascript
e.exports=function(t){var e=t.gl,r=n(e, [0,0,0,1,1,0,1,1]),s=i(e,a.boxVert,a.lineFrag);return new o(t,r,s)};var n=t("gl-buffer"),i=t("gl-shader"),a=t("./shaders");function o(t,e,r){this.plot=t,this.vbo=e,this.shader=r}var s,l,c=o.prototype;c.bind=function(){var t=this.shader;this.vbo.bind(),this.shader.bind(),t.attributes.coord.pointer(),t.uniforms.screenBox=this.plot.screenBox},c.drawBox=(s=[0,0],l=[0,0],function(t,e,r,n,i){var a=this.plot,o=this.shader,c=a.gl;s[0]=t,s[1]=e,l[0]=r,l[1]=n,o.uniforms.lo=s,o.uniforms.hi=l,o.uniforms.color=i,c.drawArrays(c.TRIANGLE_STRIP,0,4)}),c.dispose=function(){this.vbo.dispose(),this.shader.dispose()}},{"./shaders":116,"gl-buffer":78,"gl-shader":132}
```

--------------------------------

### Handle Slider Interaction Start

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/assets/team-map.html

Initiates the slider interaction sequence when a user clicks or drags the grip. Records the starting mouse position and emits a 'plotly_sliderstart' event.

```javascript
function A(t,e,r){var i=r.node(),o=n.select(e);function s(){return r.data()[0]}function l(){var t=s();e.emit("plotly_sliderstart",{slider:t});var l=r.select("."+f.gripRectClass);n.event.stopPropagation(),n.event.preventDefault();var c=L(t,n.mouse(i)[0]);function u(){var t=s(),a=L(t,n.mouse(i)[0]);T(e,r,t,a,!1)}function h(){var
```

--------------------------------

### WebGL Context Initialization and Extension Handling

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/assets/team-map.html

Initializes a WebGL rendering context and checks for required extensions. Handles extension availability and provides error feedback if essential extensions are missing.

```javascript
var y=function(t,e){function r(e){var r;e=e.toLowerCase();try{r=n[e]=t.getExtension(e)}catch(t){}return!!r}for(var n={},i=0;i<e.extensions.length;++i){var a=e.extensions[i];if(!r(a))return e.onDestroy(),e.onDone('"'+a+'" extension is not supported by the current WebGL context, try upgrading your system or a different browser'),null}return e.optionalExtensions.forEach(r),{extensions:n,restore:function(){Object.keys(n).forEach((function(t){if(n[t]&&!r(t))throw Error("(regl): error restoring extension "+t)}))}}}(m,t);if(!y)return null;
```

--------------------------------

### Get Popup Element

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/assets/team-map.html

Returns the DOM element that represents the popup.

```javascript
return this._container
```

--------------------------------

### Touch Start Event Handler

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/assets/team-map.html

Handles the touchstart event for multi-touch zoom and pan. It identifies touch points, calculates scale and translation, and updates the zoom state.

```javascript
function I(){
  var e,r=this,n=_.of(r,arguments),i={},a=0,o=".zoom-"+t.event.changedTouches[0].identifier,l="touchmove"+o,c="touchend"+o,u=[],f=t.select(r),p=bt(r);
  function d(){
    var n=t.touches(r);
    return e=h.k,
    n.forEach((function(t){t.identifier in i&&(i[t.identifier]=T(t))})),
    n
  }
  function g(){
    var e=t.event.target;
    t.select(e).on(l,m).on(c,y),
    u.push(e);
    for(var n=t.event.changedTouches,o=0,f=n.length;o<f;++o)i[n[o].identifier]=null;
    var p=d(),g=Date.now();
    if(1===p.length){
      if(g-s<500){var v=p[0];M(r,v,i[v.identifier],Math.floor(Math.log(h.k)/Math.LN2)+1),F()}
      s=g
    }else if(p.length>1){
      v=p[0];var x=p[1],b=v[0]-x[0],_=v[1]-x[1];a=b*b+_*
      o=[(o[0]+c[0])/2,(o[1]+c[1])/2],
      l=[(l[0]+u[0])/2,(l[1]+u[1])/2],
      k(g*e)
    }
    s=null,A(o,l),L(n)
  }
  function m(){
    var o,l,c,u,f=t.touches(r);
    Di.call(r);
    for(var h=0,p=f.length;h<p;++h,u=null)if(c=f[h],u=i[c.identifier]){
      if(l)break;
      o=c,l=u
    }
    if(u){
      var d=(d=c[0]-o[0])*d+(d=c[1]-o[1])*d,
      g=a&&Math.sqrt(d/a);
      o=[(o[0]+c[0])/2,(o[1]+c[1])/2],
      l=[(l[0]+u[0])/2,(l[1]+u[1])/2],
      k(g*e)
    }
    s=null,A(o,l),L(n)
  }
  function y(){
    if(t.event.touches.length){
      for(var e=t.event.changedTouches,r=0,a=e.length;r<a;++r)delete i[e[r].identifier];
      for(var s in i)return void d()
    }
    t.selectAll(u).on(o,null),f.on(v,P).on(b,I),p(),C(n)
  }
  g(),E(n),f.on(v,null).on(b,g)
}
```

--------------------------------

### Get Canonical ID

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/assets/team-map.html

Returns the canonical ID of the feature, if set.

```javascript
ye.prototype.canonicalID=function(){return this.canonical};
```

--------------------------------

### Initialize Camera Viewport

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/assets/team-map.html

Sets up the initial state for a camera viewport, including defining limits for zoom and pitch, and setting default values for various camera properties.

```javascript
this.tileSize=512,this.maxValidLatitude=85.051129,this._renderWorldCopies=void 0===a||a,this._minZoom=e||0,this._maxZoom=r||22,this._minPitch=null==n?0:n,this._maxPitch=null==i?60:i,this.setMaxBounds(),this.width=0,this.height=0,this._center=new t.LngLat(0,0),this.zoom=0,this.angle=0,this._fov=.6435011087932844,this._pitch=0,this._unmodified=!0,this._edgeInsets=new kn,this._posMatrixCache={},this._alignedPosMatrixCache={}}
```

--------------------------------

### Get Min/Max Range

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/assets/team-map.html

Calculates the minimum and maximum values in an array.

```javascript
function yn(e){return[t.min(e),t.max(e)]}
```

--------------------------------

### Initialize and Render 3D Scene

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/assets/team-map.html

Sets up the rendering context, camera, and objects for a 3D scene. Handles mouse interactions and redraws the scene on demand.

```javascript
T=r.drawingBufferWidth,k=r.drawingBufferHeight;F[0]=T,F[1]=k,j[0]=0|Math.max(T/N.pixelRatio,1),j[1]=0|Math.max(k/N.pixelRatio,1),function(t,e){var r=t.bounds,n=t.cameraParams,i=n.projection,a=n.model,o=t.gl.drawingBufferWidth,s=t.gl.drawingBufferHeight,l=t.zNear,c=t.zFar,u=t.fovy,p=o/s;e?(h(i,-p,p,-1,1,l,c),n._ortho=!0):(f(i,u,p,l,c),n._ortho=!1);for(var d=0;d<16;++d)a[d]=0;a[15]=1;var g=0;for(d=0;d<3;++d)g=Math.max(g,r[1][d]-r[0][d]);for(d=0;d<3;++d)t.autoScale?a[5*d]=t.aspect[d]/(r[1][d]-r[0][d]):a[5*d]=1/g,t.autoCenter&&(a[12+d]=.5*-a[5*d]*(r[0][d]+r[1][d]))}(N,w);for(o=0;o<e;++o){(C=E[o]).axesBounds=d,N.clipToBounds&&(C.clipBounds=d)}x.object&&(N.snapToData?S.position=x.dataCoordinate:S.position=x.dataPosition,S.bounds=d),O&&(O=!1,function(){if(!H()){r.colorMask(!0,!0,!0,!0),r.depthMask(!0),r.disable(r.BLEND),r.enable(r.DEPTH_TEST),r.depthFunc(r.LEQUAL);for(var t=E.length,e=P.length,n=0;n<e;++n){var i=P[n];i.shape=j,i.begin();for(var a=0;a<t;++a)if(L[a]===n){var o=E[a];o.drawPick&&(o.pixelRatio=1,o.drawPick(R))}i.end()}}}()),N.axesPixels=a(N.axes,R,T,k),N.onrender&&N.onrender(),r.bindFramebuffer(r.FRAMEBUFFER,null),r.viewport(0,0,T,k),N.clearRGBA(),r.depthMask(!0),r.colorMask(!0,!0,!0,!0),r.enable(r.DEPTH_TEST),r.depthFunc(r.LEQUAL),r.disable(r.BLEND),r.disable(r.CULL_FACE);var M=!1;A.enable&&(M=M||A.isTransparent(),A.draw(R)),S.axes=A,x.object&&S.draw(R),r.disable(r.CULL_FACE);for(o=0;o<e;++o){(C=E[o]).axes=A,C.pixelRatio=N.pixelRatio,C.isOpaque&&C.isOpaque()&&C.draw(R),C.isTransparent&&C.isTransparent()&&(M=!0)}if(M){b.shape=F,b.bind(),r.clear(r.DEPTH_BUFFER_BIT),r.colorMask(!1,!1,!1,!1),r.depthMask(!0),r.depthFunc(r.LESS),A.enable&&A.isTransparent()&&A.drawTransparent(R);for(o=0;o<e;++o){(C=E[o]).isOpaque&&C.isOpaque()&&C.draw(R)}r.enable(r.BLEND),r.blendEquation(r.FUNC_ADD),r.blendFunc(r.ONE,r.ONE_MINUS_SRC_ALPHA),r.colorMask(!0,!0,!0,!0),r.depthMask(!1),r.clearColor(0,0,0,0),r.clear(r.COLOR_BUFFER_BIT),A.isTransparent()&&A.drawTransparent(R);for(o=0;o<e;++o){var C;(C=E[o]).isTransparent&&C.isTransparent()&&C.drawTransparent(R)}r.bindFramebuffer(r.FRAMEBUFFER,null),r.blendFunc(r.ONE,r.ONE_MINUS_SRC_ALPHA),r.disable(r.DEPTH_TEST),_.bind(),b.color[0].bind(0),_.uniforms.accumBuffer=0,c(r),r.disable(r.BLEND)}I=!1;for(o=0;o<e;++o)E[o].dirty=!1}}}return N.enableMouseListeners(),function t(){if(N._stopped||N.contextLost)return;Y(),requestAnimationFrame(t)}(),N.redraw=function(){N._stopped||(I=!0,Y())},N},createCamera:n
```

--------------------------------

### Map Framework Initialization

Source: https://github.com/materialsproject/pymatgen/blob/main/docs/assets/team-map.html

Creates and appends a map container div to the main container. Initializes map axes and sets up a mock axis for framework conversion.

```javascript
r.createFramework=function(t){var e=this,r=e.div=document.createElement("div");r.id=e.uid,r.style.position="absolute",e.container.appendChild(r),e.xaxis={"_id":"x",c2p:function(t){return e.project(t).x}},e.yaxis={"_id":"y",c2p:function(t){return e.project(t).y}},e.updateFramework(t),e.mockAxis={"type":"linear","showexponent":"all","exponentformat":"B"},s.setConvert(e.mockAxis,t)}
```