Frequently Asked Questions ¶

Author:

Rohit Goswami

Frequently Asked Questions ¶

Installation ¶

How do I install rgpycrumbs?¶

pip install rgpycrumbs
pip install jax  # or: export RGPYCRUMBS_AUTO_DEPS=1  # With JAX

How do I enable auto-install?¶

export RGPYCRUMBS_AUTO_DEPS=1

Usage ¶

How do I use the batch command?¶

rgpycrumbs chemgp batch -c config.toml -j 4

How do I match atoms to target coordinates?¶

rgpycrumbs chemgp match-atoms -s pos.con -t targets.txt

Errors ¶

“ModuleNotFoundError: No module named ‘jax’”¶

Install surfaces extra:

pip install jax  # or: export RGPYCRUMBS_AUTO_DEPS=1

Or enable auto-install:

RGPYCRUMBS_AUTO_DEPS=1 rgpycrumbs chemgp ...

Performance ¶

How can I speed up batch plotting?¶

Use parallel processing:

rgpycrumbs chemgp batch -c config.toml -j 8

See Also ¶

How do I set landscape surface options without more CLI flags?¶

Use a plot TOML with --config:

[shared]
auto_thin = true
max_surface_points = 64

[min]
job_dir = ["min_job"]
plot_type = "landscape"
surface_type = "grad_imq"

rgpycrumbs eon plt-min --config plot.toml

auto_thin defaults to false (opt-in). See eOn plot TOML config.