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More docs fixes
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@juntyr
juntyr committed Feb 29, 2024
1 parent 3a3db15 commit 582b39c
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8 changes: 4 additions & 4 deletions docs/replay.ron
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Expand Up @@ -3,13 +3,13 @@
/* selection of event log segments which will be analysed in the replay */
segments: [
/* a PathBuf which can contain Unix glob patterns
* e.g. use "event_log / ** / *" (without spaces)
* where the event log was stored to the "event_log" directory */
* e.g. use "event_log / ** / *" (without spaces)
* where the event log was stored to the "event_log" directory */
(GlobPathBuf),
],
/* in-memory buffering capacity of each log segment
* a higher capacity will batch up disk read calls but use more RAM */
/* optional, default = 100000 */
* a higher capacity will batch up disk read calls but use more RAM
* optional, default = 100000 */
capacity: (0 < usize),
),

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92 changes: 46 additions & 46 deletions docs/simulate.ron
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Original file line number Diff line number Diff line change
Expand Up @@ -2,14 +2,14 @@
/* per-individual per-generation probability that an individual speciates
* i.e. is the creator of a new unique species */
speciation: (0.0 < f64 <= 1.0),
/* selection of the sample of individuals that are simulatd */
/* optional, default = Sample(percentage: 1.0, origin: Habitat, mode: Genesis) */
/* selection of the sample of individuals that are simulatd
* optional, default = Sample(percentage: 1.0, origin: Habitat, mode: Genesis) */
sample: Sample(
/* percentage of individuals from the sample that are simulated */
/* optional, default = 1.0 */
/* percentage of individuals from the sample that are simulated
* optional, default = 1.0 */
percentage: (0.0 <= f64 <= 1.0),
/* selection of the base sample of individuals */
/* optional, default = Habitat */
/* selection of the base sample of individuals
* optional, default = Habitat */
origin: (
/* all individuals living inside the habitat are sampled
* only compatible with mode = Genesis */
Expand All @@ -36,8 +36,8 @@
file: (PathBuf)
)
),
/* selection of the simulation initialisation mode */
/* optional, default = Genesis */
/* selection of the simulation initialisation mode
* optional, default = Genesis */
mode: (
/* the simulation starts from the beginning with all individuals
* only compatible with origin = Habitat */
Expand All @@ -59,8 +59,8 @@
* requires an immediate pause at the same time as the original pause */
| FixUp(
/* selection of how to handle individuals at a valid location that is
* already occupied by too many other individuals, i.e. the deme is full
* optional, default = Abort */
* already occupied by too many other individuals, i.e. the deme is full
* optional, default = Abort */
out_of_deme: (
/* Abort the simulation during configuration before it runs */
| Abort
Expand All @@ -69,7 +69,7 @@
| Dispersal
),
/* selection of how to handle individuals at an inhabitable location
* optional, default = Abort */
* optional, default = Abort */
out_of_habitat: (
/* Abort the simulation during configuration before it runs */
| Abort
Expand Down Expand Up @@ -100,8 +100,8 @@
)
),
),
/* selection of whether the simulation should pause before completing */
/* optional, default = None */
/* selection of whether the simulation should pause before completing
* optional, default = None */
pause: (
/* the simulation will run until completion */
| None
Expand All @@ -125,13 +125,13 @@
* only compatible with sample.origin = List */
| Bincode(
/* file path to where the new binary file listing the remaining
* individuals will be written */
* individuals will be written */
file: (PathBuf),
)
),
/* selection of the pause mode, which affects how the simulation is
* resumed afterwards */
/* optional, default = Resume */
* resumed afterwards
* optional, default = Resume */
mode: (
/* the simulation can be resumed with continuity after the pause
* no changes in configuration should be made */
Expand All @@ -148,27 +148,27 @@
),
/* selection of the initialisation of the random number generator */
rng: (
/* seeds from OS-provided randomness */
/* forbidden for partitioned simulations */
/* infallible for monolithic simulations (unless the OS malfunctions) */
/* seeds from OS-provided randomness
* forbidden for partitioned simulations
* infallible for monolithic simulations (unless the OS malfunctions) */
| Entropy
/* seeds based on the given 64bit seed */
/* infallible */
/* seeds based on the given 64bit seed
* infallible */
| Seed(u64)
/* seeds based on the given base32-string, which goes through a
* sponge function to fit the RNG's seed size */
/* fails if the base32-string is actually an RNG state
* sponge function to fit the RNG's seed size
* fails if the base32-string is actually an RNG state
* (safeguards confusing State and Sponge, unlikely by accident) */
| Sponge(Base32)
/* tries to set the RNG's state from the given base32-string */
/* fails if the the base32-string is not a valid RNG state
/* tries to set the RNG's state from the given base32-string
* fails if the the base32-string is not a valid RNG state
* (use only for resuming a paused + unchanged simulation)
* (must come from the same RNG that the simulation was paused with) */
| State(Base32)
/* combination of the State and Sponge initialisation methods
* (a) try the State initialisation
* (b) on failure, use the Sponge initialisation */
/* fails if the base32-string could not have come from a paused RNG */
* (b) on failure, use the Sponge initialisation
* fails if the base32-string could not have come from a paused RNG */
| StateElseSponge(Base32)
),

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/* circular sample area */
| Circle(
/* centre (x, y) of the circle
* optional, default = (x: 2147483647, y: 2147483647)
* note that 2147483647 = 2^31 - 1 */
* optional, default = (x: 2147483647, y: 2147483647)
* note that 2147483647 = 2^31 - 1 */
centre: (
x: (u32),
y: (u32),
Expand Down Expand Up @@ -274,9 +274,9 @@
/* shape (u) for the Clark 2Dt dispersal kernel */
shape_u: (0.0 < f64),
/* tail (p) for the Clark 2Dt dispersal kernel
* - Clark 2Dt dispersal tends to Gaussian as p becomes large
* - Clark 2Dt dispersal tends to Cauchy as p goes to zero
* optional, default = 1.0 */
* - Clark 2Dt dispersal tends to Gaussian as p becomes large
* - Clark 2Dt dispersal tends to Cauchy as p goes to zero
* optional, default = 1.0 */
tail_p: (0.0 < f64),
)
),
Expand All @@ -299,7 +299,7 @@
persistence: (0.0 < f64 <= 1.0),
/* number of noise octaves that are accumulated for each sample
* a larger number of octaves provides finer-grained habitat boundaries
but is less efficient to simulate
* but is less efficient to simulate
* choose 1 for only one noise sample per location and maximum efficiency */
octaves: (0 < usize),
/* rectangular sample area, individuals living in here are simulated
Expand All @@ -325,8 +325,8 @@
/* monolithic; optimised for low self-dispersal (i.e. small demes); CPU-based
* requires the `gillespie-algorithms` feature */
| Gillespie(
/* selection of how the algorithm should be parallelised across partitions */
/* optional, dynamic default = Monolithic / Lockstep */
/* selection of how the algorithm should be parallelised across partitions
* optional, dynamic default = Monolithic / Lockstep */
parallelism_mode: (
/* no parallelisation, the algorithm runs on a single partition only
* invalid when the simulation is internally parallelised */
Expand Down Expand Up @@ -372,8 +372,8 @@
* self-dispersal (i.e. large demes); CPU-based
* requires the `gillespie-algorithms` feature */
| EventSkipping(
/* selection of how the algorithm should be parallelised across partitions */
/* optional, dynamic default = Monolithic / Lockstep */
/* selection of how the algorithm should be parallelised across partitions
* optional, dynamic default = Monolithic / Lockstep */
parallelism_mode: (
/* no parallelisation, the algorithm runs on a single partition only
* invalid when the simulation is internally parallelised */
Expand Down Expand Up @@ -446,7 +446,7 @@
),
/* selection of the mode in which the simulation is parallelised
* optional, dynamic default = Monolithic(event_slice: Relative(factor: 2.0))
/ Probabilistic(communication: 0.25) */
* / Probabilistic(communication: 0.25) */
parallelism_mode: (
/* no partitioning occurs
* invalid when the simulation is internally parallelised */
Expand Down Expand Up @@ -666,14 +666,14 @@
* single-threaded, multi-process
* requires the `mpi-partitioning` feature */
| MPI(
/* explicit size of the MPI universe, must match the MPI universe */
/* optional, dynamic default = MPI's world size */
/* explicit size of the MPI universe, must match the MPI universe
* optional, dynamic default = MPI's world size */
world: (1 < u32),
/* minimum time interval between migration messages */
/* optional, default = "100ms" */
/* minimum time interval between migration messages
* optional, default = "100ms" */
migration: (DurationString),
/* minimum time interval between progress messages */
/* optional, default = "100ms" */
/* minimum time interval between progress messages
* optional, default = "100ms" */
progress: (DurationString),
)
),
Expand All @@ -691,8 +691,8 @@
| EventLog(
/* file path to a directory in which a log of all events will be saved */
directory: (PathBuf),
/* event capacity of each log segment */
/* optional, default = 1000000 */
/* event capacity of each log segment
* optional, default = 1000000 */
capacity: (0 < usize),
)
),
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