tadd docstrings to all functions - Granular.jl - Julia package for granular dynamics simulation
(HTM) git clone git://src.adamsgaard.dk/Granular.jl
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---
(DIR) commit aa49a17a7ce969f67b58e7f4196f65a48a5f0e5c
(DIR) parent 5b777d9bdb78d24eab9387b0ab15e99ba074737f
(HTM) Author: Anders Damsgaard <andersd@riseup.net>
Date: Thu, 20 Apr 2017 15:51:52 -0400
add docstrings to all functions
Diffstat:
M src/SeaIce.jl | 25 +++++--------------------
D src/arrays.jl | 1 -
M src/contact_search.jl | 7 +++++++
M src/datatypes.jl | 1 -
M src/interaction.jl | 4 ++++
M src/io.jl | 5 +++++
M src/simulation.jl | 67 ++++++++++++++++++++++++++++---
M src/temporal.jl | 27 +++++++++++++++++++++++++--
M src/temporal_integration.jl | 18 +++++++++++++++++-
M test/contact-search-and-geometry.jl | 4 ++--
10 files changed, 126 insertions(+), 33 deletions(-)
---
(DIR) diff --git a/src/SeaIce.jl b/src/SeaIce.jl
t@@ -1,30 +1,15 @@
#!/usr/bin/env julia
-##############################
-# Sea-ice dynamics simulator #
-##############################
-
-#=
-Add SeaIce to your julia path, e.g. by:
- push!(LOAD_PATH, "/home/user/src/seaice/")
-
-If this statement is added to `~/.juliarc.jl`, it will become persistent between
-julia sessions. Note that the `~` symbol for the home folder does not seem to
-work (julia v. 0.4.1) in the `.juliarc.jl` file.
-
-Import package contents with:
- import SeaIce
-
-If this file is changed, reimport it with:
- reload("SeaIce")
-=#
-
+"""
+# SeaIce.jl
+Offline sea-ice dynamics simulator by [Anders Damsgaard](mailto:andersd@riseup.net),
+[www.adamsgaard.dk](https://adamsgaard.dk)
+"""
module SeaIce
include("datatypes.jl")
include("icefloe.jl")
include("simulation.jl")
-include("arrays.jl")
include("grid.jl")
include("packing.jl")
include("contact_search.jl")
(DIR) diff --git a/src/arrays.jl b/src/arrays.jl
t@@ -1 +0,0 @@
-## Global arrays for general simulation data
(DIR) diff --git a/src/contact_search.jl b/src/contact_search.jl
t@@ -1,4 +1,11 @@
## Contact mapping
+"""
+Top-level function to perform an inter-ice floe contact search, based on ice
+floe linear positions and contact radii.
+
+The simplest contact search algorithm (`method="all to all"`) is the most
+computationally expensive (O(n^2)).
+"""
function findContacts!(simulation::Simulation,
method::String = "all to all")
(DIR) diff --git a/src/datatypes.jl b/src/datatypes.jl
t@@ -3,7 +3,6 @@ const float = Float64
const vector = Array{Float64, 1}
## Particle composite types
-
type IceFloeCylindrical
# Material properties
(DIR) diff --git a/src/interaction.jl b/src/interaction.jl
t@@ -45,6 +45,10 @@ function interactIceFloes!(simulation::Simulation,
end
+"""
+Resolves linear-elastic interaction between two ice floes in the contact-normal
+direction.
+"""
function interactNormalLinearElastic(simulation::Simulation,
i::Integer, j::Integer,
overlap_vector::vector)
(DIR) diff --git a/src/io.jl b/src/io.jl
t@@ -2,6 +2,11 @@ import WriteVTK # Install with Pkg.add("WriteVTK")
## IO functions
+"""
+Write a VTK file to disk containing all ice floes in the `simulation` in an
+unstructured mesh (file type `.vtu`). These files can be read by ParaView and
+can be visualized by applying a *Glyph* filter.
+"""
function writeVTK(simulation::Simulation;
folder::String=".",
verbose::Bool=false)
(DIR) diff --git a/src/simulation.jl b/src/simulation.jl
t@@ -1,5 +1,24 @@
## General simulation functions
+"""
+ createSimulation([id::String="unnamed",
+ time_iteration::Int=0,
+ time::Float64=0.0,
+ time_total::Float64=-1.,
+ time_step::Float64=-1.,
+ file_time_step::Float64=-1.,
+ file_number::Int=0,
+ ice_floes=Array{IceFloeCylindrical, 1}[],
+ contact_pairs=Array{Int64, 1}[],
+ overlaps=Array{Array{Float64, 1}, 1}[],
+ wall_contacts=Array{Int64, 1}[]])
+
+Create a simulation object containing all relevant variables such as temporal
+parameters, and lists of ice floes and contacts.
+
+The parameter `id` is used to uniquely identify the simulation when it is
+written to disk.
+"""
function createSimulation(;id::String="unnamed",
time_iteration::Int=0,
time::Float64=0.0,
t@@ -25,12 +44,43 @@ function createSimulation(;id::String="unnamed",
wall_contacts)
end
+"""
+ run!(simulation[,
+ verbose::Bool = true,
+ status_interval = 100.,
+ show_file_output = true,
+ single_step=false,
+ temporal_integration_method="Three-term Taylor"])
+
+Run the `simulation` through time until `simulation.time` equals or exceeds
+`simulatim.time_total`. This function requires that all ice floes are added to
+the simulation and that the length of the computational time step is adjusted
+accordingly.
+
+The function will search for contacts, determine the force balance on each ice
+floe, and integrate all kinematic degrees of freedom accordingly. The temporal
+integration is explicit and of length `simulation.time_step`. This function
+will write VTK files to disk in the intervals `simulation.file_time_step` by the
+function `writeVTK`. If this value is negative, no output files will be written
+to disk.
+
+# Arguments
+* `simulation::Simulation`: the simulation to run (object is modified)
+* `verbose::Bool=true`: show verbose information during the time loop
+* `status_interval::Bool=true`: show verbose information during the time loop
+* `show_file_output::Bool=true`: report to stdout when output file is written
+* `single_step::Bool=false`: run simulation for a single time step only. If
+ this causes `simulation.time` to exceed `simulation.time_total`, the latter
+ is increased accordingly.
+* `temporal_integration_method::String="Three-term Taylor"`: type of integration
+ method to use. See `updateIceFloeKinematics` for details.
+"""
function run!(simulation::Simulation;
- verbose::Bool = true,
- status_interval = 100.,
- show_file_output = true,
- single_step=false,
- temporal_integration_method="Three-term Taylor")
+ verbose::Bool=true,
+ status_interval::Int=100.,
+ show_file_output::Bool=true,
+ single_step::Bool=false,
+ temporal_integration_method::String="Three-term Taylor")
if single_step && simulation.time >= simulation.time_total
simulation.time_total += simulation.time_step
t@@ -63,7 +113,7 @@ function run!(simulation::Simulation;
# Update time variables
simulation.time_iteration += 1
- simulation.time += simulation.time_step
+ incrementCurrentTime(simulation, simulation.time_step)
time_since_output_file = time_since_output_file + simulation.time_step
if single_step
t@@ -79,6 +129,8 @@ function run!(simulation::Simulation;
end
end
+"Add an `icefloe` to the `simulation` object. If `verbose` is true, a short
+confirmation message will be printed to stdout`."
function addIceFloe!(simulation::Simulation,
icefloe::IceFloeCylindrical,
verbose::Bool = False)
t@@ -90,6 +142,7 @@ function addIceFloe!(simulation::Simulation,
end
end
+"Remove ice floe with index `i` from the `simulation` object."
function removeIceFloe!(simulation::Simulation, i::Integer)
if i < 1
error("Index must be greater than 0 (i = $i)")
t@@ -98,6 +151,7 @@ function removeIceFloe!(simulation::Simulation, i::Integer)
delete!(simulation.ice_floes, i)
end
+"Sets the `force` and `torque` values of all ice floes to zero."
function zeroForcesAndTorques!(simulation::Simulation)
for icefloe in simulation.ice_floes
icefloe.force = zeros(2)
t@@ -105,6 +159,7 @@ function zeroForcesAndTorques!(simulation::Simulation)
end
end
+"Prints the current simulation time and total time to standard out"
function reportSimulationTimeToStdout(simulation::Simulation)
print("\r t = ", simulation.time, '/', simulation.time_total,
" s ")
(DIR) diff --git a/src/temporal.jl b/src/temporal.jl
t@@ -1,4 +1,9 @@
-## Set temporal parameters
+"""
+ setTotalTime!(simulation::Simulation, t::float)
+
+Sets the total simulation time of the `simulation` object to `t`, with parameter
+value checks.
+"""
function setTotalTime!(simulation::Simulation, t::float)
if t <= 0.0
error("Total time should be a positive value (t = $t s)")
t@@ -6,6 +11,12 @@ function setTotalTime!(simulation::Simulation, t::float)
simulation.time_total = t
end
+"""
+ setCurrentTime!(simulation::Simulation, t::float)
+
+Sets the current simulation time of the `simulation` object to `t`, with
+parameter value checks.
+"""
function setCurrentTime!(simulation::Simulation, t::float)
if t <= 0.0
error("Current time should be a positive value (t = $t s)")
t@@ -13,11 +24,17 @@ function setCurrentTime!(simulation::Simulation, t::float)
simulation.time = t
end
+"""
+ incrementCurrentTime!(simulation::Simulation, t::float)
+
+Sets the current simulation time of the `simulation` object to `t`, with
+parameter value checks.
+"""
function incrementCurrentTime!(simulation::Simulation, t::float)
if t <= 0.0
error("Current time increment should be a positive value (t = $t s)")
end
- simulation.time = simulation.time + t
+ simulation.time += t
end
function setOutputFileInterval!(simulation::Simulation, t::float)
t@@ -27,10 +44,12 @@ function setOutputFileInterval!(simulation::Simulation, t::float)
simulation.file_time_step = t
end
+"Disables the write of output files to disk during a simulation."
function disableOutputFiles!(simulation::Simulation)
simulation.file_time_step = 0.0
end
+"Checks if simulation parameters are of reasonable values."
function checkTimeParameters(simulation::Simulation)
if simulation.time_total <= 0.0 || simulation.time_total <= simulation.time
error("Total time should be positive and larger than current time.\n",
t@@ -42,6 +61,8 @@ function checkTimeParameters(simulation::Simulation)
end
end
+"Finds the smallest mass of all ice floes in a simulation. Used to determine
+the optimal time step length."
function findSmallestIceFloeMass(simulation::Simulation)
m_min = 1e20
i_min = -1
t@@ -55,6 +76,8 @@ function findSmallestIceFloeMass(simulation::Simulation)
return m_min, i_min
end
+"Finds the largest elastic stiffness of all ice floes in a simulation. Used to
+determine the optimal time step length."
function findLargestIceFloeStiffness(simulation::Simulation)
k_n_max = 0.
k_t_max = 0.
(DIR) diff --git a/src/temporal_integration.jl b/src/temporal_integration.jl
t@@ -1,6 +1,19 @@
"""
+ updateIceFloeKinematics!(simulation::Simulation[,
+ method::String = "Three-term Taylor"])
+
Update the ice floe kinematic parameters using a temporal integration scheme,
the current force and torque balance, and gravitational acceleration.
+
+# Arguments
+* `simulation::Simulation`: update the ice floe positions in this object
+ according to temporal integration of length `simulation.time_step`.
+* `method::String = "Three-term Taylor"`: the integration method to use.
+ Available methods are "Two-term Taylor" and "Three-term Taylor". The
+ three-term Taylor expansion is slightly more computationally expensive than
+ the two-term Taylor expansion, but offers an order-of-magnitude increase in
+ precision of ice floe positions. The two-term expansion can obtain similar
+ precision if the time step is 1/10 the length.
"""
function updateIceFloeKinematics!(simulation::Simulation;
method::String = "Three-term Taylor")
t@@ -18,6 +31,8 @@ function updateIceFloeKinematics!(simulation::Simulation;
end
end
+"Use a two-term Taylor expansion for integrating the kinematic degrees of
+freedom for an `icefloe`."
function updateIceFloeKinematicsTwoTermTaylor(icefloe::IceFloeCylindrical,
simulation::Simulation)
icefloe.lin_acc = icefloe.force/icefloe.mass
t@@ -41,6 +56,8 @@ function updateIceFloeKinematicsTwoTermTaylor(icefloe::IceFloeCylindrical,
icefloe.ang_vel += icefloe.ang_acc * simulation.time_step
end
+"Use a three-term Taylor expansion for integrating the kinematic degrees of
+freedom for an `icefloe`."
function updateIceFloeKinematicsThreeTermTaylor(icefloe::IceFloeCylindrical,
simulation::Simulation)
t@@ -80,4 +97,3 @@ function updateIceFloeKinematicsThreeTermTaylor(icefloe::IceFloeCylindrical,
icefloe.ang_vel += icefloe.ang_acc * simulation.time_step +
0.5 * d_ang_acc_dt * simulation.time_step^2.
end
-
(DIR) diff --git a/test/contact-search-and-geometry.jl b/test/contact-search-and-geometry.jl
t@@ -14,8 +14,8 @@ SeaIce.addIceFloeCylindrical(sim, [18., 0.], 10., 1., verbose=false)
position_ij = SeaIce.interIceFloePositionVector(sim, 1, 2)
overlap_ij = SeaIce.findOverlap(sim, 1, 2, position_ij)
-Base.Test.@test_approx_eq [18., 0.] position_ij
-Base.Test.@test_approx_eq -2. overlap_ij
+Base.Test.@test [18., 0.] \approx position_ij
+Base.Test.@test -2. \approx overlap_ij
info("Testing findContactsAllToAll(...)")