Update BAOAB/g-BAOAB docstrings, default collision_rate
@@ -1685,7 +1685,7 @@ class BAOABIntegrator(LangevinSplittingIntegrator):
"""Create a velocity Verlet with velocity randomization (VVVR) integrator."""
def __init__(self,
temperature=298.0 * simtk.unit.kelvin,
- collision_rate=91.0 / simtk.unit.picoseconds,
+ collision_rate=1.0 / simtk.unit.picoseconds,
timestep=1.0 * simtk.unit.femtoseconds,
constraint_tolerance=1e-8,
measure_shadow_work=False,
@@ -1704,16 +1704,13 @@ class BAOABIntegrator(LangevinSplittingIntegrator):
timestep : numpy.unit.Quantity compatible with femtoseconds, default: 1.0*simtk.unit.femtoseconds
Integration timestep
- constraint_tolerance : float
+ constraint_tolerance : float, default: 1.0e-8
Tolerance for constraint solver
- override_splitting_checks : boolean
- If True, skip sanity-checks on `splitting` string.
-
- measure_shadow_work : boolean
+ measure_shadow_work : boolean, default: False
Accumulate the shadow work performed by the symplectic substeps, in the global `shadow_work`
- measure_heat : boolean
+ measure_heat : boolean, default: True
Accumulate the heat exchanged with the bath in each step, in the global `heat`
References
@@ -1744,7 +1741,7 @@ class GeodesicBAOABIntegrator(LangevinSplittingIntegrator):
def __init__(self, K_r=2,
temperature=298.0 * simtk.unit.kelvin,
- collision_rate=91.0 / simtk.unit.picoseconds,
+ collision_rate=1.0 / simtk.unit.picoseconds,
timestep=1.0 * simtk.unit.femtoseconds,
constraint_tolerance=1e-8,
measure_shadow_work=False,
@@ -1754,7 +1751,7 @@ class GeodesicBAOABIntegrator(LangevinSplittingIntegrator):
Parameters
----------
- K_r : integer
+ K_r : integer, default: 2
Number of geodesic drift steps.
temperature : numpy.unit.Quantity compatible with kelvin, default: 298.0*simtk.unit.kelvin
@@ -1766,16 +1763,13 @@ class GeodesicBAOABIntegrator(LangevinSplittingIntegrator):
timestep : numpy.unit.Quantity compatible with femtoseconds, default: 1.0*simtk.unit.femtoseconds
Integration timestep
- constraint_tolerance : float
+ constraint_tolerance : float, default: 1.0e-8
Tolerance for constraint solver
- override_splitting_checks : boolean
- If True, skip sanity-checks on `splitting` string.
-
- measure_shadow_work : boolean
+ measure_shadow_work : boolean, default: False
Accumulate the shadow work performed by the symplectic substeps, in the global `shadow_work`
- measure_heat : boolean
+ measure_heat : boolean, default: True
Accumulate the heat exchanged with the bath in each step, in the global `heat`
References
