User Interface
Note
There are two ways to specify vectors, either as “raw” vectors or by using atom pairs.
Raw vectors are always written as x,y,z, without spaces and are automatically
normalized. Atom pairs are written as id1-id2 wherein one-based indexing
is used. In other words, the first atom has an id of 1, not 0.
Warning
Note that some of the output files have generic names
(e.g. planedata-real.bin). If files with the same name already exist
in the current working directory, these files will be overwritten. To avoid
this, you either need to rename these files or execute EDP in
separate directories.
Mandatory arguments
-i, --input <filename>
File containing electron density. The filename should start with CHGCAR or
PARCHG for automatic recognition.
Example: -i CHGCAR_calculation
-o, --output <filename>
A valid path where to write the image file to.
Example: -o projection.png
-v, --vector1 <vector designation or two atom indices>
The vector \(\vec{v}\) spanning the horizontal direction of the projection. The user should either specify a triplet of numbers representing the vector or a pair of atom indices (counting from 1). Vectors are automatically normalized.
Example: -v 0,0,1 or -v 1-2
-w, --vector2 <vector designation or two atom indices>
The vector \(\vec{w}\) spanning the vertical direction of the projection. The user should either specify a triplet of numbers representing the vector or a pair of atom indices (counting from 1). Vectors are automatically normalized.
Example: -w 0,0,1 or -w 1-2
-p, --starting_point <vector designation or single atom index>
The point \(\vec{p}\) in the unit cell through which the projection plane should pass. The user should either specify a triplet of numbers (that lies in the unit cell) or a single atom index (counting from one). The units for the vector are in ångström.
Example: -p 5,5,5 or -p 1
-s, --scaling <unsigned integer>
The number of pixels per ångström used to build the plane.
Example: -s 100
Optional arguments
-b, --bounds <double,double>
Bounds for displaying the electron density. Note that the electron density is plotted on a logarithmic scale (with a base of 10) and the lower and upper bounds as supplied correspond to the exponent.
Example: -b <-3,2>
-g, --gramschmidt
Orthogonalize the vector pair \(\vec{v}\) and \(\vec{w}\) via the Gram-Schmidt process.
Example: -g
-l, --legend
Whether to display a legend.
Example: -l
-n, --negative
Whether to allow for negative values. By convention, the electron density should not be negative and any negative densities are set to zero. However if one is projecting electron density differences, negative electron densities are of course possible and will be plotted accordingly.
Example: -n
-c, --color-scheme-id <unsigned int>
Which color scheme to use. See the overview of possible color schemes.
Example: -c 1
Note
For the color schemes, zero-based indexing is used. In other words, the first color scheme is color scheme #0.
-c, --color-scheme-id <unsigned int>
Which color scheme to use. See the overview of possible color schemes.
Example: -c 1
Additional features
Some additional command line arguments are available to execute specific jobs on the electron density. These correspond to niche features.
-z, --zaverage
Calculate the total electron density per plane for the set of planes whose normal vector lie in the \(z\)-direction. The output is written in a two-column text file z_extraction.txt.
Example: -z
-e, --extraction <vector or pair of two atom indices>
Calculate the electron density through a line defined by a normal vector \(\vec{e}\) going through point \(\vec{p}\). The output is written to line_extraction.txt.
Example: -e 1-2 or -e 1,1,1
-r, --radius <atom id,radius>
Calculate the average electron density (or electrostatic potential) at a radius \(r \in 0,R\) from an atom with 0.01 Å increments. The sampling points are based on the coordinates of the 23rd order Lebedev quadrature. The result is written to spherical_average.txt.
Example: -r 1,1.5