elastic

name	elastic
description	Prepare GPUMD elastic-constant calculations using the strain-fluctuation method. Use when the user needs `compute_elastic`, the full `C_ij` tensor, or elastic moduli (bulk, shear, Young's) from an anisotropic NPT trajectory.
compatibility	Requires GPUMD and a potential that is stable under the anisotropic NPT used for strain-fluctuation sampling.
catalog-hidden	true
license	GPL-3.0-only
metadata	{"author":"Jhin","version":"0.2.0"}

GPUMD Elastic Constants

Use this subskill when the target observable is the elastic tensor C_ij. GPUMD uses the strain-fluctuation method: an anisotropic NPT trajectory is sampled at the target temperature, and compute_elastic extracts C_ij from the box-shape fluctuations without a finite-difference stress sweep.

Quick start

gpumd < run.in | tee gpumd.log
cat elastic.out

Agent responsibilities

1. Confirm the crystal symmetry (cubic, hexagonal, tetragonal, orthorhombic). The symmetry is NOT an argument to compute_elastic — GPUMD computes the full 6x6 tensor automatically. Symmetry matters for interpreting how many independent C_ij the user should report.
2. Confirm the structure is relaxed under the chosen potential. Unrelaxed inputs produce biased C_ij.
3. Use an anisotropic NPT barostat (e.g. npt_scr with separate diagonal parameters). Isotropic NPT cannot sample shear modes.
4. Run long enough for the strain-fluctuation average to converge. The strain-fluctuation method is noisier than direct stress-response.
5. Report C_ij plus derived moduli (B, G, E, ν) if requested, and state the temperature and averaging window.

Workflow

Step 1. Prepare the structure

• primitive or conventional cell — the strain-fluctuation method is sensitive to the cell choice
• use a supercell large enough to suppress shape-fluctuation noise (for cubic semiconductors, a few thousand atoms is typical)
• relax under the same potential before sampling

Step 2. Write run.in

Annotated example (see assets/examples/elastic/run.in):

potential   nep.txt
velocity    300

ensemble    npt_scr 300 300 100 0 0 0 0 0 0 100 100 100 100 100 100 2000
time_step   1
dump_thermo 100
compute_elastic 0.01
run         1100000

• ensemble npt_scr block
  • T_start T_stop tau_T p_xx p_yy p_zz p_xy p_xz p_yz C_xx C_yy C_zz C_xy C_xz C_yz tau_p
  • Using six target pressures and six compressibility-like barostat parameters is what makes the barostat anisotropic. All six diagonal compressibilities (C_xx ... C_yz) must be nonzero so that the box shape is free to fluctuate.
• compute_elastic <strain_value>
  • Takes a single parameter: the strain amplitude used in the fluctuation estimator. 0.01 is a robust starting value.
  • Output is written to elastic.out.
• run 1100000
  • Long trajectories are required. 10^6 steps is a practical minimum.

Step 3. Extract C_ij

At the end of the run, GPUMD writes the elastic constants to elastic.out. Read them directly or parse with a simple script:

cat elastic.out

The output contains the full 6x6 elastic tensor. For cubic crystals the independent constants are C_11, C_12, C_44. Derive isotropic moduli via the Voigt-Reuss-Hill average if requested by the user.

Step 4. Convergence

• tested that the box shape actually fluctuates (not pinned by a rigid barostat)
• trajectory length increased until C_ij is stable to the needed tolerance
• supercell size is not so small that shape noise dominates
• C_ij is positive-definite and satisfies Born stability for the symmetry

Common pitfalls

• using isotropic npt_scr — the method cannot sample C_44
• taking a single short trajectory as the final answer
• reporting C_ij at 300 K when the input was only relaxed at 0 K and never equilibrated under the chosen potential
• mixing temperature-dependent C_ij(T) with static DFT C_ij(0) in the same table without labeling

Read first

• references/elastic-constants.md

Read when needed:

• references/core-files-and-ensembles.md
• references/gpumd-keyword-cheatsheet.md

Bundled templates and helpers

• assets/examples/elastic/run.in
• assets/examples/elastic/model.xyz
• scripts/parse_thermo.py

Expected output

1. a GPUMD run.in configured for the correct crystal symmetry
2. an anisotropic NPT block that allows box-shape fluctuations
3. a post-processing plan for C_ij and, if requested, derived moduli
4. explicit convergence and reporting notes

References

• compute_elastic: https://gpumd.org/gpumd/input_parameters/compute_elastic.html
• GPUMD-Tutorials example 30_Elastic_constants__strain_fluctuation_method
• Parrinello and Rahman, J. Appl. Phys. 52, 7182 (1981)