NAMD Diagnostics

These options compare numerical quantities and report deviations. They are separate from the four numerical-continuity cases described in NAMD Numerical Continuity.

Coupling Comparisons

Keyword	Default	Meaning
nacme_check	off	Compare the propagation coupling with baeck_an or analytic; off performs no comparison.
ba_gap_max	0.0734986443513 Ha (2 eV)	Largest state gap included in a Baeck--An comparison.
nacme_policy	off	off, warn, or error response to the comparison criteria.
nacme_policy_invariant_tol	1.0e-10	Antisymmetry and diagonal-invariant tolerance.
nacme_policy_abs_tol	1.0e-4 au⁻¹	Absolute comparison tolerance.
nacme_policy_rel_tol	1.0	Relative comparison tolerance.
nacme_policy_consecutive	3	Consecutive reference-comparison failures required by error.

Use warn while establishing appropriate thresholds for a molecular system. error can terminate a trajectory and should be used only after that assessment.

NVE Energy Diagnostics

Keyword	Default	Meaning
nve_policy	warn	off, warn, or error response to NVE energy criteria.
nve_policy_abs_tol	5.0e-3 Ha	Total drift from the initial NVE energy.
nve_policy_step_tol	1.0e-3 Ha	Change between adjacent recorded steps.
nve_policy_transition_tol	1.0e-6 Ha	Residual across a hop or trivial crossing after its energy-conserving adjustment.
nve_policy_consecutive	3	Consecutive drift or step failures required by error.

nve_policy=warn is the default and does not terminate the trajectory. nve_policy=error terminates immediately for a failed transition-energy criterion or after the configured number of consecutive drift/step failures. This policy is independent of case-D substepping.

Additional Diagnostics

Keyword	Default	Meaning
first_hop_step	1	First interval in which a stochastic hop can be accepted.
trivial	False	Enable overlap-triggered trivial-crossing following.
trivial_thresh	0.5	State-overlap criterion for that optional treatment.

Trivial-crossing following is a separate approximation and is not enabled by the four continuity treatments.