create 3D plot of the one-electron density of the entire molecule or a designated molecular orbital
DensityPlot3D(molecule, data, options)
list of lists; each list has 4 elements, the string of an atom's symbol and atom's x, y, and z coordinates
table returned by one of the electronic structure methods including 'HartreeFock', 'DensityFunctional', 'ActiveSpaceCI', 'ActiveSpaceSCF', 'CoupledCluster', 'FullCI', 'MP2', 'Variational2RDM', 'Parametric2RDM', and 'ContractedSchrodinger'
(optional) equation(s) of the form options = value where options is one of orbitalindex, densitycutoff, phase, vanderwaalsradii, gridspacing, maximumpoints, bonds, colors (or an option of the molecule such as basis or charge)
The DensityPlot3D procedure generates a 3D plot of a molecule's electron density.
The procedure can generate the electron density of the entire molecule or a designated molecular orbital.
Two arguments, molecule and data, are required where molecule defines the atom or molecule while data is the Maple table returned by one of the electronic structure methods including 'HartreeFock', 'DensityFunctional', 'ActiveSpaceCI', 'ActiveSpaceSCF', 'CoupledCluster', 'FullCI', 'MP2', 'Parametric2RDM', 'ContractedSchrodinger', and 'Variational2RDM'.
The orbitalindex integer (optional) -- denotes the molecular orbital to plot; default is 0 which plots the molecule's density.
The densitycutoff float (optional) -- sets the cutoff for the electron density contour. Typically, less than 0.01; default is 0.005.
The phase boolean (optional) -- displays the phase of the molecular orbital when set to true; default is true.
The vanderwaalsradii float (optional) -- is the weight (>1) for Van der Waals radii for defining the density grid; default is 1.8.
The gridspacing float (optional) -- is the spacing between grid points; default is 0.1.
The maximumpoints integer (optional) -- is the maximum total number of grid points in the density plot; default is 100000.
The bonds set of sets (optional) is a set of sets where each set contains two integers denoting the atoms to be connected by a chemical bond. The integers correspond to the positions of the atoms in molecule. If the optional keyword bonds is not set, the bonds to be shown are determined automatically.
The colors list of strings (optional) is a list of two strings containing the colors of the positive and negative lobes of the molecular orbitals. Any color strings from Maple's ColorTools package is supported. If the optional keyword colors is not set, the plot uses the default colors, "green" and "purple".
The options also include the options available for PlotMolecule.
The keyword viewpoint generates a molecular fly-through animation. It can be set to one of the following strings "flythrough", "flythrough2", "flythrough3", "flythrough4", "circleleft", and "circleright". It can also be set to a custom fly-through animation as described on the help page for viewpoint.
Density plot of the hydrogen fluoride HF molecule
molecule ≔ H,0,0,0,F,0,0,0.95;
output_hf ≔ HartreeFockmolecule, basis=dz;
DensityPlot3Dmolecule,output_hf, basis=dz, orbitalindex=3, densitycutoff=0.0005;
or using the colors option to change the colors
DensityPlot3Dmolecule,output_hf, basis=dz, orbitalindex=3, densitycutoff=0.0005,colors=Nautical Red,Nautical Light Blue;
Consider the 1,3-dichlorobenzene molecule
Generate a fly-through animation of the molecule and its density
data ≔ Variational2RDMmol;
DensityPlot3Dmol, data,viewpoint=flythrough3,maximumpoints=400000, gridspacing=0.001;
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