trj2fig (energy profile of a trajectory)

trj2fig plots the energy along an XYZ trajectory, such as one written by opt, scan, path-opt, path-search, or irc. It reads the energy of each frame from its comment line, or recomputes it with an MLIP (machine-learning interatomic potential) when -q or -m is given. It exports PNG, JPEG, SVG, PDF, or interactive HTML figures and a CSV table. By default it plots ΔE in kcal/mol relative to the first frame.

What it is for

  • Energy profiles of paths: minimum energy path (MEP), scan, and intrinsic reaction coordinate (IRC) trajectories as ΔE plots.

  • Checking an optimization: how the energy fell over the optimization cycles.

  • Data for your own plots: per-frame energies as CSV.

Examples

1. Default PNG

Plot ΔE relative to the first frame and write energy.png.

pdb2reaction trj2fig -i traj.xyz --out-json

The console prints [trj2fig] Saved figure -> energy.png, and result.json has n_frames, the number of frames read.

2. CSV and SVG relative to frame 5, in hartree

Write a table and a figure in hartree, relative to frame index 5 (counted from 0, so the sixth frame).

pdb2reaction trj2fig -i traj.xyz -o energy.csv energy.svg -r 5 --unit hartree

3. Several formats, x-axis reversed

Put the last frame on the left; ΔE is then relative to the last frame.

pdb2reaction trj2fig -i traj.xyz --reverse-x -o energy.png energy.html energy.pdf

4. Recompute energies with an MLIP

Recompute every frame with the default MLIP, UMA, for a neutral singlet instead of reading the comments.

pdb2reaction trj2fig -i traj.xyz -q 0 -m 1 -o energy.png

How it works

  1. Reading the energies: Each frame’s comment line gives its energy. Trajectories written by pdb2reaction, such as optimization_trj.xyz (opt --dump), scan_trj.xyz, mep_trj.xyz, and finished_irc_trj.xyz, are read as they are. In other files, write E=<value> with an optional unit (Ha, Eh, hartree, eV, kcal/mol); without a unit it is hartree, except that energy= in a comment with Properties= or Lattice= (extended XYZ) is eV. With -q or -m, the MLIP backend recomputes every frame instead.

  2. Choosing the reference: -r init is the frame at the left end: the first frame, or the last with --reverse-x; an integer is a 0-based frame index; none plots absolute energies.

  3. Converting the unit: The energies are converted to kcal/mol (default) or hartree, and the reference is subtracted to give ΔE. The y-axis reads ΔE (kcal/mol), or E (…) for absolute energies.

  4. Exporting: Each output gets its format from its extension: .png, .jpg, .jpeg, .svg, .pdf, and .html are figures, and .csv is a table. PNG is written at twice the pixel width and height of the figure.

Output files

energy.png      # Figure (default when no output is given)
energy.csv      # Energy table (when a .csv output is given)
result.json     # Summary (with --out-json)
summary.json    # Same content as result.json (with --out-json)

  • CSV columns: frame, energy_hartree, and the plotted value in the --unit unit. The third column is named delta_kcal or delta_hartree with a reference, and energy_kcal or energy_hartree with -r none.

  • result.json is written in the directory of the first output. It has n_frames, min_energy_hartree, max_energy_hartree, energy_source, and output_files; the mlip_* fields are null unless the energies were recomputed. See JSON Output Reference.

Main options

Option

Type

Default

Description

-i, --input

path

(required)

XYZ trajectory

-o, --output

path

energy.png

Output files (.png, .jpg, .jpeg, .html, .svg, .pdf, .csv); repeat -o, or list more file names after it (-o energy.csv energy.svg)

--unit

kcal / hartree

kcal

Unit of the plotted and exported values

-r, --reference

text

init

Reference: init, none, or a 0-based frame index

-q, --charge

integer

None

Total charge; recomputes the energies with the MLIP when given

-m, --multiplicity

integer

None

Spin multiplicity (2S+1); recomputes the energies with the MLIP when given

--reverse-x/--no-reverse-x

flag

False

Put the last frame on the left

-b, --backend

text

uma

MLIP for recomputation (uma, orb, mace, aimnet2; see MLIP Backends)

--backend-model

text

None

Model of the selected backend (e.g. uma-s-1p2); without it, the backend’s default model

--precision

fp32 / fp64

per backend

Precision of the recomputation (UMA fp32; ORB and MACE fp64); AIMNet2 accepts only fp32

--out-json/--no-out-json

flag

False

Write result.json and summary.json

See the generated CLI reference for every option.

Notes

  • Recomputation: with only one of -q and -m, the other is taken as charge 0 or multiplicity 1.

  • Comments without a readable energy, such as one that holds only an integer or several numbers, stop the run with an error that names the frame.

  • Unsupported extensions stop the run with an error.

  • Exit codes: see Exit codes.

See also