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Enhanced Sampling Parameters

Collective Variables (CV)

Parameter Type Description
cv_in_file string Collective variable definition file path

CV definitions are loaded from the file pointed to by cv_in_file. New CV files should use TOML; the legacy block format remains supported for compatibility. See Collective Variables Guide for the supported CV types, virtual atoms, printing, and complete examples.

Bundled sponge.input.v2 protocols store CV virtual atoms as typed HDF5 objects below /cv/virtual_atom/<name>. Each object contains type, atom_indices, enabled_default, and, for a center, weight. A regular CV can use /cv/<name>/atom_refs to mix physical atom indices and virtual-atom names without embedding a large legacy configuration string.

Metadynamics

Configured via [META] or [meta] section:

Parameter Type Description
sink string Sink metadynamics mode

Detailed SinkMeta parameter list: sinkmeta.md

SITS

SITS parameters live under the [SITS] scope:

[SITS]
mode = "iteration"
atom_numbers = "ALL"
k_numbers = 40
T_low = 300.0
T_high = 600.0
record_interval = 1
update_interval = 100

Common Parameters

Parameter Scope Type Default Description
mode SITS string required SITS run mode
atom_in_file SITS string - File-based atom partition definition for selective enhancement
atom_numbers SITS int or string required if atom_in_file is absent Number of leading atoms in the selectively enhanced set, or "ALL" / "ITS"
cross_enhance_factor SITS float 0.5 Enhancement factor for the cross term
fb_interval SITS int 1 Feedback-bias update interval

Exactly one atom-selection method is required: atom_in_file or atom_numbers.

Iteration / Production Parameters

Parameter Scope Type Default Description
k_numbers SITS int 40 Number of temperature points
T_low SITS float - Lower temperature bound for generated ladder
T_high SITS float - Upper temperature bound for generated ladder
T SITS slash-separated string - Explicit temperature ladder used instead of T_low / T_high
record_interval SITS int 1 Energy record interval
update_interval SITS int 100 Parameter update interval
pe_a SITS float 1.0 Multiplicative energy scaling factor
pe_b SITS float 0.0 Additive energy offset
fb_bias SITS float 0.0 Additional bias applied to fb
nk_rest SITS bool false in iteration, true otherwise Whether to read restart Nk values
nk_in_file SITS string required when nk_rest = true or in production mode Input file for restarting Nk
nk_fix SITS bool false in iteration, true otherwise Freeze Nk during the run
nk_rest_file SITS string auto-generated Output file for restart Nk values when nk_fix = false
nk_traj_file SITS string auto-generated Output file for Nk history when nk_fix = false

mode options:

Value Description
"observation" Observation phase
"iteration" Iteration phase
"production" Production phase
"empirical" Empirical mode
"amd" AMD mode
"gamd" GaMD mode

Empirical / AMD / GaMD Parameters

Parameter Scope Type Default Description
pe_a SITS float required in amd / gamd, 1.0 in empirical Bias strength parameter
pe_b SITS float required in amd / gamd, 0.0 in empirical Bias threshold parameter
T_low SITS float required in empirical Lower temperature bound
T_high SITS float required in empirical Upper temperature bound

Notes:

  • amd, gamd, and empirical do not use the full k_numbers / Nk update workflow.
  • The current source reads T as a slash-separated string rather than a TOML numeric array.