NAMD Advanced Controls¶
.oqp control reference
Use canonical routes and controls in input files. Raw names
identify implementation storage. A control without an accepted canonical
spelling is not available in .oqp files.
This page collects controls that are not needed in a standard NAMD input.
Start with the four named scheme values in
the main md manual. Add an option from this page only when the
chosen physical treatment, diagnostic comparison, or restart procedure
requires it.
Initial Electronic-State Index¶
Use a state label such as namd(S1,...) in normal concise input. The
lower-level active keyword selects the initial 1-based response-state index
and defaults to 1. A state label is clearer and takes precedence when both
forms are present.
Custom Surface-Hopping Scheme¶
Use scheme=custom only when none of the four named schemes represents the
intended calculation. All four low-level choices are then required:
| Keyword | Meaning | Allowed values |
|---|---|---|
tdc |
time-derivative coupling used to propagate electronic amplitudes | fd, npi, analytic, baeck_an |
rescale |
direction used to adjust nuclear velocity after an allowed hop | auto, isotropic, analytic_nac, hop_analytic_nac |
thrshe |
maximum energy gap for a hop attempt, in Hartree | positive number |
frustrated |
treatment of a directional hop with insufficient kinetic energy | none, reflect |
The four named schemes expand as follows:
scheme |
tdc |
rescale |
thrshe |
frustrated |
|---|---|---|---|---|
BaeckAn |
baeck_an |
isotropic |
0.015936 |
none |
Overlap |
npi |
isotropic |
0.015936 |
none |
TDC_NAC |
npi |
hop_analytic_nac |
0.367493 |
reflect |
NAC |
analytic |
analytic_nac |
0.367493 |
reflect |
Do not combine a named scheme with any of the four low-level keywords. A custom scheme must state all four explicitly:
namd(S1,scheme=custom,tdc=npi,rescale=isotropic,
thrshe=0.367493,frustrated=reflect)
md(nstep=400,dt=0.5,velocity="molecule.vel")
QM/MM NAMD supports TDC_NAC and NAC for a QM region without link atoms,
using the documented frozen-embedding-field QM-region NAC approximation.
SOC-NAMD remains experimental and is provided for method development and
numerical verification. It requires a defined overlap/isotropic custom scheme,
for example:
namd(scheme=custom,tdc=npi,rescale=isotropic,
thrshe=0.367493,frustrated=reflect,
soc=true,soc_basis=mch,init_state=S1)
md(nstep=400,dt=0.5)
Diagnostic and Numerical Controls¶
| Purpose | Keywords and defaults |
|---|---|
| Decoherence parameter | decoherence=edc, edc_c=0.1 Ha |
| Baeck--An or analytic-NACME comparison | nacme_check=off, ba_gap_max=0.0734986443513 Ha, nacme_policy=off |
| NACME comparison criteria | nacme_policy_invariant_tol=1.0e-10, nacme_policy_abs_tol=1.0e-4 au⁻¹, nacme_policy_rel_tol=1.0, nacme_policy_consecutive=3 |
| NVE energy criteria | nve_policy_abs_tol=5.0e-3 Ha, nve_policy_step_tol=1.0e-3 Ha, nve_policy_transition_tol=1.0e-6 Ha, nve_policy_consecutive=3 |
| Delayed hopping or trivial-crossing following | first_hop_step=1, trivial=False, trivial_thresh=0.5 |
| Electronic propagation resolution | substep=50000 |
Use nacme_policy=warn or nve_policy=warn to print the corresponding
diagnostic result without terminating the trajectory. Use error only after
the relevant numerical thresholds have been established for the molecular
system and timestep.
Electronic-Structure Continuity¶
Use the default continuity=on for the complete analytic-NAC cases A--D
treatment. The physical origins, termination behavior, thresholds, and every
manual control are documented on
NAMD Numerical Continuity. Do not copy an isolated
continuity option from an old input; select continuity=manual and report the
complete changed set.
Output, Restart, and Continuation¶
| Purpose | Keywords and defaults |
|---|---|
| Packed trajectory output | trajectory_interval=1; trajectory_file derived from the project name |
| Atomic checkpoint | restart_interval=10; restart_file derived from the project name |
| Restart the same calculation | restart=False; normally run the generated .namd.restart.oqp file |
| Continue into new output files | continuation_checkpoint, continuation_trajectory empty by default |
Local continuation with a changed timestep is restricted to fixed-step,
same-spin NAC dynamics. The new timestep cannot exceed the timestep stored in
the source checkpoint.
NVT and SOC-Specific Controls¶
| Purpose | Keywords and defaults |
|---|---|
| Langevin NVT | md(ensemble=nvt,temperature=300.0,friction=1.0) |
| SOC initial MCH character | init_state empty by default |
| SOC force diagnostics | soc_du_dt_corr=False, soc_tdc_grad_corr=False, grad_wthr=0.001 |
| Adaptive SOC timestep | dt_adaptive=False, dt_min=0.05 fs, dx_max=0.02 bohr |
With the default velocity=maxwell, OpenQP samples initial velocities at
temperature=300.0 K even for NVE dynamics. temperature does not alter a
velocity read from a file or set to zero; with ensemble=nvt, the same
value is the NVT target. The underlying configuration storage names are
init_temp, thermostat_temperature, and thermostat_friction.
Detailed Definitions¶
The complete definitions are separated by purpose: coupling schemes, numerical continuity, diagnostics, initial conditions and restart, and ensembles and SOC-NAMD. This page is the short index for deciding whether an advanced control is needed.
Internal Concise-Input Markers¶
common_controls and common_control_keys are generated internally when
OpenQP lowers a concise md(...) call to the sectioned runtime configuration.
They preserve which common nuclear controls were written by the user and are
not user-facing scientific options. Do not place either keyword in a
hand-written input.