Molecular and nonadiabatic dynamics¶
Source: gateway project 17, engine 1.3.1, commit 05361a3cc99fbad3da557084e41e21e690e5a27e. This parser reference is pinned to source version 1.3.1; it does not expand the capabilities of an installed 1.3.0 engine.
Use md(...) for nuclear propagation and namd(...) for electronic surface hopping. namd(...) md(...) is the permitted composition. temperature maps to init_temp and thermostat_temperature; friction maps to thermostat_friction. Duplicate nuclear controls across namd/md/qmmm calls are rejected. Select a complete NAMD scheme; custom subcontrols require scheme=custom.
Separate nuclear propagation and surface hopping¶
mrsf(nstate=3)/bhhlyp/6-31g* namd(S1,scheme=Overlap)
md(nstep=10,dt=0.5,temperature=300,friction=1)
geom="""
C 0.357265 0.223227 -0.756478
C 0.096381 0.077437 0.592011
H -0.777577 0.294630 -0.911117
H 0.439342 -0.722961 -1.305394
H 0.454605 0.792671 1.330762
H -0.570016 -0.665004 1.050215
"""
| Canonical control | Meaning and constraint |
|---|---|
md(nstep=10,dt=0.5) |
Positive integer nuclear steps and positive timestep in femtoseconds; duration is nstep*dt. |
md(temperature=300) |
Kelvin; maps to both initialization and thermostat temperatures. It does not by itself select an ensemble. |
md(friction=1) |
Maps to thermostat_friction; use the ensemble/backend convention in the detailed dynamics reference. |
namd(S1,scheme=Overlap) |
Physical active state and a complete coupling scheme. Omitted active state defaults to S1. |
md(restart=True,restart_file="run.chk") |
Continuation request; a compatible checkpoint is required, not merely an existing filename. |
md(...) alone is ground-state propagation. namd(...) md(...) is the
permitted combined calculation; common nuclear options must not be repeated
across calls. Custom electronic subcontrols require scheme=custom.
NAMD supplies omitted SCF/response/Z-vector thresholds of 1e-8; an explicit
value remains explicit. Continuity, state tracking, energy conservation and
restart equivalence need runtime tests, beyond a source-only parse.
Exact-source keyword appendix¶
Scientific references¶
Nonadiabatic dynamics; Dynamics libraries.
Source chain: canonical lowering → schema conversion → calculation validation → consumer entry point. Consumer links locate the relevant subsystem; they do not prove every listed key is read or executed.
md¶
Detailed meaning, units and restrictions. These pages retain stable URLs and explain canonical controls; raw names identify schema storage, not sectioned input.
| Raw section.key | Canonical spelling / ownership | Converter | Raw schema default |
|---|---|---|---|
md.common_controls |
route / global / primary driver; see concepts |
bool |
False |
md.common_control_keys |
route / global / primary driver; see concepts |
str |
empty |
md.nstep |
route / global / primary driver; see concepts |
int |
100 |
md.dt |
route / global / primary driver; see concepts |
float |
0.5 |
md.active |
route / global / primary driver; see concepts |
int |
1 |
md.substep |
route / global / primary driver; see concepts |
int |
50000 |
md.decoherence |
route / global / primary driver; see concepts |
string |
edc |
md.edc_c |
route / global / primary driver; see concepts |
float |
0.1 |
md.thrshe |
route / global / primary driver; see concepts |
float |
0.367493 |
md.tdc |
route / global / primary driver; see concepts |
string |
npi |
md.rescale |
route / global / primary driver; see concepts |
string |
auto |
md.trivial |
route / global / primary driver; see concepts |
bool |
False |
md.trivial_thresh |
route / global / primary driver; see concepts |
float |
0.5 |
md.init_temp |
route / global / primary driver; see concepts |
float |
300.0 |
md.velocity |
route / global / primary driver; see concepts |
str |
maxwell |
md.seed |
route / global / primary driver; see concepts |
int |
0 |
md.rng_stream |
route / global / primary driver; see concepts |
int |
1 |
md.first_hop_step |
route / global / primary driver; see concepts |
int |
1 |
md.nacme_check |
route / global / primary driver; see concepts |
str |
off |
md.ba_gap_max |
route / global / primary driver; see concepts |
float |
0.0734986443513 |
md.nacme_policy |
route / global / primary driver; see concepts |
str |
off |
md.nacme_policy_invariant_tol |
route / global / primary driver; see concepts |
float |
1.0e-10 |
md.nacme_policy_abs_tol |
route / global / primary driver; see concepts |
float |
1.0e-4 |
md.nacme_policy_rel_tol |
route / global / primary driver; see concepts |
float |
1.0 |
md.nacme_policy_consecutive |
route / global / primary driver; see concepts |
int |
3 |
md.nve_policy |
route / global / primary driver; see concepts |
str |
warn |
md.nve_policy_abs_tol |
route / global / primary driver; see concepts |
float |
5.0e-3 |
md.nve_policy_step_tol |
route / global / primary driver; see concepts |
float |
1.0e-3 |
md.nve_policy_transition_tol |
route / global / primary driver; see concepts |
float |
1.0e-6 |
md.nve_policy_consecutive |
route / global / primary driver; see concepts |
int |
3 |
md.continuity |
route / global / primary driver; see concepts |
str |
on |
md.mo_reuse |
route / global / primary driver; see concepts |
bool |
true |
md.scf_guess_retry |
route / global / primary driver; see concepts |
bool |
true |
md.scf_fail |
route / global / primary driver; see concepts |
str |
escalate |
md.ref_follow |
route / global / primary driver; see concepts |
str |
soscf |
md.ref_switch_rescale |
route / global / primary driver; see concepts |
bool |
true |
md.somo_tol |
route / global / primary driver; see concepts |
float |
0.5 |
md.state_check |
route / global / primary driver; see concepts |
bool |
true |
md.state_tol |
route / global / primary driver; see concepts |
float |
0.7 |
md.frustrated |
route / global / primary driver; see concepts |
str |
reflect |
md.disc_rescale |
route / global / primary driver; see concepts |
bool |
true |
md.disc_tol |
route / global / primary driver; see concepts |
float |
0.002 |
md.disc_substeps |
route / global / primary driver; see concepts |
int |
10 |
md.trajectory_interval |
route / global / primary driver; see concepts |
int |
1 |
md.restart_interval |
route / global / primary driver; see concepts |
int |
10 |
md.trajectory_file |
route / global / primary driver; see concepts |
str |
empty |
md.energy_file |
route / global / primary driver; see concepts |
str |
empty |
md.restart_file |
route / global / primary driver; see concepts |
str |
empty |
md.continuation_checkpoint |
route / global / primary driver; see concepts |
str |
empty |
md.continuation_trajectory |
route / global / primary driver; see concepts |
str |
empty |
md.restart |
route / global / primary driver; see concepts |
bool |
False |
md.snapshot |
route / global / primary driver; see concepts |
str |
empty |
md.snapshot_interval |
route / global / primary driver; see concepts |
int |
0 |
md.ensemble |
route / global / primary driver; see concepts |
string |
nve |
md.thermostat |
route / global / primary driver; see concepts |
string |
off |
md.thermostat_temperature |
route / global / primary driver; see concepts |
float |
300.0 |
md.thermostat_friction |
route / global / primary driver; see concepts |
float |
1.0 |
md.soc |
route / global / primary driver; see concepts |
bool |
False |
md.soc_basis |
route / global / primary driver; see concepts |
string |
adiabatic |
md.soc_du_dt_corr |
route / global / primary driver; see concepts |
bool |
False |
md.soc_tdc_grad_corr |
route / global / primary driver; see concepts |
bool |
False |
md.grad_wthr |
route / global / primary driver; see concepts |
float |
0.001 |
md.init_state |
route / global / primary driver; see concepts |
string |
empty |
md.econs |
route / global / primary driver; see concepts |
bool |
False |
md.dt_adaptive |
route / global / primary driver; see concepts |
bool |
False |
md.dt_min |
route / global / primary driver; see concepts |
float |
0.05 |
md.dx_max |
route / global / primary driver; see concepts |
float |
0.02 |
| ## odp |
Detailed meaning, units and restrictions. These pages retain stable URLs and explain canonical controls; raw names identify schema storage, not sectioned input.
| Raw section.key | Canonical spelling / ownership | Converter | Raw schema default |
|---|---|---|---|
odp.enabled |
route / global / primary driver; see concepts |
bool |
False |
odp.cv |
route / global / primary driver; see concepts |
str |
empty |
odp.scale |
route / global / primary driver; see concepts |
farray |
empty |
odp.reference_r |
route / global / primary driver; see concepts |
farray |
empty |
odp.reference_p |
route / global / primary driver; see concepts |
farray |
empty |
odp.center |
route / global / primary driver; see concepts |
float |
0.0 |
odp.k_parallel |
route / global / primary driver; see concepts |
float |
0.0 |
odp.k_perpendicular |
route / global / primary driver; see concepts |
float |
0.0 |
odp.window |
route / global / primary driver; see concepts |
int |
0 |