advanced.md

Advanced Parameters

Device and Parallelism

Parameter	Type	Default	Description
device	string	auto-detected	GPU device ID
device_optimized_block	int	-	GPU block size optimization

Domain Decomposition

MPI domain decomposition parameters are read from the [DOM_DEC] scope:

[DOM_DEC]
update_interval = 100
split_nx = 2
split_ny = 2
split_nz = 1

Parameter	Scope	Type	Default	Description
update_interval	DOM_DEC	int	100	Domain-decomposition refresh interval
split_nx	DOM_DEC	int	auto	Number of splits in X
split_ny	DOM_DEC	int	auto	Number of splits in Y
split_nz	DOM_DEC	int	auto	Number of splits in Z

When the split counts are omitted, SPONGE chooses them automatically from the PP MPI size and box geometry. Current MPI domain decomposition only supports orthogonal boxes.

Minimization

Minimization-specific parameters use the [minimization] scope:

mode = "minimization"

[minimization]
dynamic_dt = 1
max_move = 0.1
beta1 = 0.9
epsilon = 1e-4

Parameter	Scope	Type	Default	Description
dynamic_dt	minimization	int	1	Use the ADAM-like dynamic-step minimizer
max_move	minimization	float	0.1	Maximum coordinate displacement per step in angstrom
momentum_keep	minimization	float	0.0 when dynamic_dt = 0	Momentum retention factor in gradient-descent mode
beta1	minimization	float	0.9	First ADAM parameter used when dynamic_dt != 0
beta2	minimization	float	0.9 in the current source	Second ADAM parameter used when dynamic_dt != 0
epsilon	minimization	float	1e-4	Numerical stabilizer used when dynamic_dt != 0

When dynamic_dt != 0, SPONGE internally resets dt to 3e-4 ps. When dynamic_dt = 0, it uses a tiny fixed dt and the gradient-descent path.

Rerun Mode

rerun uses the normal top-level trajectory file keys plus several rerun-specific flat keys:

mode = "rerun"
crd = "traj.dat"
box = "traj.box"
vel = "traj.vel"
frame_limit = 1000
rerun_start = 0
rerun_strip = 0
rerun_need_box_update = 0

Parameter	Scope	Type	Default	Description
crd	top-level	string	required	Input coordinate trajectory for rerun
box	top-level	string	required	Input box trajectory for rerun
vel	top-level	string	optional	Input velocity trajectory for rerun
frame_limit	top-level	int	-	Maximum number of rerun frames
rerun_frame_limit	top-level	int	alias of frame_limit	Compatibility alias
rerun_start	top-level	int	0	Starting frame offset
rerun_strip	top-level	int	0	Number of frames skipped between processed frames
rerun_need_box_update	top-level	int	0	Whether to update the box deformation tensor during rerun

The current source uses flat rerun_* keys rather than a [rerun] TOML section.

Wall Constraints

Hard Walls

Hard-wall limits are configured through the [hard_wall] prefix:

[hard_wall]
x_low = 0.0
x_high = 40.0

Parameter	Scope	Type	Description
x_low, x_high	hard_wall	float	Hard-wall position in the X direction
y_low, y_high	hard_wall	float	Hard-wall position in the Y direction
z_low, z_high	hard_wall	float	Hard-wall position in the Z direction

Hard walls cannot be used in npt mode.

Soft Walls

Soft walls are enabled by providing a configuration file:

[soft_walls]
in_file = "soft_walls.txt"

Parameter	Scope	Type	Description
in_file	soft_walls	string	Soft-wall configuration file path

ReaxFF Reactive Force Field

Configured via [REAXFF] section:

[REAXFF]
in_file = "ffield.reax.cho"
type_in_file = "atom_types.txt"

Parameter	Type	Description
in_file	string	ReaxFF parameter file
type_in_file	string	Atom type mapping file

Generalized Born

Generalized Born parameters are configured through the [gb] scope:

[gb]
in_file = "gb.txt"
epsilon = 78.5
radii_offset = 0.09
radii_cutoff = 25.0

Parameter	Scope	Type	Default	Description
in_file	gb	string	-	Native GB parameter file
epsilon	gb	float	78.5	Relative dielectric constant
radii_offset	gb	float	0.09	Offset subtracted from self radii
radii_cutoff	gb	float	cutoff	Cutoff used when building effective Born radii

LJ Soft Core

If a native soft-core LJ parameter file is provided through LJ_soft_core_in_file, SPONGE also reads several top-level alchemical parameters:

Parameter	Scope	Type	Default	Description
lambda_lj	top-level	float	required	Soft-core LJ coupling parameter
soft_core_alpha	top-level	float	0.5	Soft-core alpha parameter
soft_core_powfer	top-level	float	1.0	Soft-core power parameter
soft_core_sigma	top-level	float	3.0	Soft-core sigma parameter
soft_core_sigma_min	top-level	float	0.0	Lower bound for the effective sigma term

These keys are top-level in the current source, not nested under [LJ_soft_core].

Custom Forces

Parameter	Scope	Type	Description
in_file	pairwise_force	string	Pairwise-force configuration file
in_file	listed_forces	string	Listed-force configuration file

Output Mapping For Periodic Molecules

Parameter	Scope	Type	Default	Description
force_whole_output	top-level	bool	false	Force whole-molecule output mapping for periodic systems
make_output_whole	top-level	string	-	Extra connectivity edges written as atom_i-atom_j pairs to help rebuild whole molecules

These keys are only meaningful when pbc = true.

Solvent LJ Shortcut

Parameter	Scope	Type	Default	Description
solvent_LJ	top-level	bool	auto	Enable the water-specific solvent LJ shortcut

On GPU builds, if solvent_LJ is omitted, SPONGE may enable it automatically for suitable water-only tail residues. Setting the key explicitly overrides that heuristic.

Plugins

Plugins are configured by the top-level key plugin, which is a whitespace- separated list of shared-library paths. This is not currently a TOML table interface.

Control Parameters

Parameter	Type	Default	Description
command_only	bool	false	Use command-line arguments only, skip mdin file
dont_check_input	bool	false	Skip unused parameter checking
end_pause	bool	false	Pause after simulation ends