Manual/Plot Scripts/MD and Structure

MD and Structure

Plots for thermodynamic output and structural analysis of MD runs, including polar-material plane profiles.

Thermodynamic Properties

thermo (plt_thermo.py)

Primary script for comprehensive thermodynamic property visualization.

Input File: thermo.out

bash
gpumdkit.sh -plt thermo
Thermo plot

thermo2 (plt_thermo2.py)

The previous default thermodynamic plot, kept as an alternative style.

Input File: thermo.out

bash
gpumdkit.sh -plt thermo2

Note: thermo3 has become the default thermo plot. gpumdkit.sh -plt thermo3 still works for now and prints a reminder, but it will be removed in a future release; use gpumdkit.sh -plt thermo instead.

Structural Analysis

rdf (plt_rdf.py)

Plots all RDF value columns in rdf.out (the radius column is used as the x-axis).

Input File: rdf.out

bash
gpumdkit.sh -plt rdf               # Plot all RDF pairs
gpumdkit.sh -plt rdf save          # Save the figure as rdf.png

The rdf plotter does not select a single column. Use rdf_pmf when a specific RDF output column is needed for PMF analysis.

RDF output:

Complete RDF

xrd (plt_xrd.py)

Plots the X-ray diffraction (XRD) output generated by calculator 413.

Input File: xrd.out by default; an alternative XRD output path can be passed as the first argument.

bash
gpumdkit.sh -plt xrd
gpumdkit.sh -plt xrd path/to/xrd.out save

With save, the figure is written to xrd.png in the current working directory.

Example:

X-ray diffraction example

xrd_comp (plt_xrd_comp.py)

Compares XRD curves from several temperature folders in the current working directory. Each folder must be named <temperature>K and contain an xrd.out file written by calculator 413. All curves are drawn in one panel, shifted along y so that the highest peak never reaches the curve above, with low temperature at the bottom. Each curve is labelled with its temperature and colored by a temperature colorbar.

Run the comparison from the directory containing the *K subdirectories. This command does not take a directory argument:

bash
cd /path/to/xrd_series
gpumdkit.sh -plt xrd_comp
gpumdkit.sh -plt xrd_comp save

With save, the figure is written to xrd_comp.png in the current working directory.

rdf_pmf (plt_rdf_pmf.py)

Plots RDF combined with potential of mean force (PMF).

Input File: rdf.out

bash
gpumdkit.sh -plt rdf_pmf
gpumdkit.sh -plt rdf_pmf 300 2 save

Both arguments are optional: the temperature in K used to convert the RDF into a PMF, and column_index, the rdf.out column to use (column 2 is the total RDF; columns 3 and above are pair RDFs).

vac (plt_vac.py)

Plots velocity autocorrelation function (VAC). Useful for analyzing phonon properties and atomic dynamics.

Input File: sdc.out written by GPUMD compute_sdc (the VAC columns are read from this file by the plotting script). This is separate from the msd.out input used by -plt sdc and -plt msd_sdc.

Output: Interactive plot or vac.png (with save option)

bash
gpumdkit.sh -plt vac

cohesive (plt_cohesive.py)

Plots cohesive energy curve from cohesive.out. Useful for analyzing lattice stability and equilibrium lattice constants.

Input File: cohesive.out (isotropic scaling factor vs cohesive energy)

Output: Interactive plot or cohesive.png (with save option)

bash
gpumdkit.sh -plt cohesive

The sampled energy curve is drawn as open circles, and a vertical dashed line marks the scaling factor at which the energy is lowest. This value, a_min, is read directly from the data, so its precision is the step of the scaling factor in compute_cohesive. The values below come from an LLZO NEP model scaled isotropically with compute_cohesive 0.9 1.1 6.

Cohesive energy curve

net_force (plt_net_force.py)

Plots distribution of net forces on structures, useful for identifying problematic configurations.

Input File: train.xyz (extxyz format)

bash
gpumdkit.sh -plt net_force train.xyz

Reference: arXiv:2510.19774

Net force distribution

Plane-Grid Plot for Polar Materials

This workflow maps displacement or polarization data onto a grid and plots selected plane profiles. For detailed usage and real-world examples, see Polar Material Analysis.

Dependency:

bash
pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git

Typical upstream steps:

bash
gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Pb Sr -E O
gpumdkit.sh -calc disp -i movie.xyz -n nl-Pb_Sr-O.dat -o displacements.dat
gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.2 -o averaged_structure.xyz

Usage:

bash
gpumdkit.sh -plt plane-grid -i averaged_structure.xyz -d displacements.dat -e Pb Sr
gpumdkit.sh -plt plane-grid -i averaged_structure.xyz -d displacements.dat -e Pb Sr --select-xy 0 1
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