dump_xyz

Write per-atom data into user-specified file(s) in extended XYZ format.

Syntax

dump_xyz <interval> <filename> [group <grouping_method> <group_id>] [precision <single|double>] {<property_1> <property_2> ...}

  • interval is the output interval (number of steps) of the data.

  • filename is the output file.

If it is ended by a star (*), the data for one frame will be output to one file, named by changing the star to the step number.

  • The group option restricts the output to the atoms in group group_id of grouping method grouping_method.

If it is omitted, data for the whole system will be output.

  • The precision option controls the number of significant digits written for every floating-point value.

single (the default) writes nine significant digits, which is enough to recover a single-precision value exactly. double writes 17 significant digits, which is enough to recover a double-precision value exactly.

  • Then one can write the properties to be output, and the allowed properties include: mass, velocity, force, potential, virial, charge, bec, group_labels, and unwrapped_position.

The group_labels property writes one integer column per grouping method, holding the label of the group each atom belongs to.

  • The wrapped positions will always be included in the output.

Examples

ensemble xxx # some ensemble

# dump positions every 1000 steps, for the whole system:
dump_xyz 1000 positions.xyz

# dump many other quantities every 100 steps, for atoms in group 0 of grouping method 1:
dump_xyz 100 properties.xyz group 1 0 mass velocity potential force virial

# dump forces with the full precision of the underlying double-precision values:
dump_xyz 100 forces.xyz precision double force

run 1000000

Caveats

  • This keyword is not propagating. That means, its effect will not be passed from one run to the next.

  • The output file has an appending behavior.

  • Different from many of the other keywords, this keyword is allowed to be invoked multiple times within one run.

  • For qNEP models, the charge values dumped out are predicted by the qNEP models. For other models, the charge values are those specified in model.xyz via charge:R:1.

  • The Born effective charge (BEC) is only meaningful for a qNEP model trained with target BEC.