texport functions from module namespace, improve docstrings - Granular.jl - Julia package for granular dynamics simulation
(HTM) git clone git://src.adamsgaard.dk/Granular.jl
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---
(DIR) commit 1d1b5457fd62a9751f2983af9432ade2cfe9b8f5
(DIR) parent 600cc4b3910ffc0a17661f3061ea3c659c9696aa
(HTM) Author: Anders Damsgaard <andersd@riseup.net>
Date: Thu, 27 Apr 2017 15:28:06 -0400
export functions from module namespace, improve docstrings
Diffstat:
M src/contact_search.jl | 7 +++++++
M src/grid.jl | 7 +++++++
M src/icefloe.jl | 35 +++++++++++++++++++++++++++++--
M src/interaction.jl | 3 +++
M src/io.jl | 1 +
M src/simulation.jl | 6 ++++++
M src/temporal.jl | 23 +++++++++++++++++++----
M src/temporal_integration.jl | 15 +++++++++++----
8 files changed, 87 insertions(+), 10 deletions(-)
---
(DIR) diff --git a/src/contact_search.jl b/src/contact_search.jl
t@@ -1,4 +1,5 @@
## Contact mapping
+export findContacts
"""
Top-level function to perform an inter-ice floe contact search, based on ice
floe linear positions and contact radii.
t@@ -16,6 +17,7 @@ function findContacts!(simulation::Simulation,
end
end
+export interIceFloePositionVector
function interIceFloePositionVector(simulation::Simulation,
i::Integer, j::Integer)
return simulation.ice_floes[j].lin_pos - simulation.ice_floes[i].lin_pos
t@@ -31,6 +33,11 @@ function findOverlap(simulation::Simulation, i::Integer, j::Integer,
simulation.ice_floes[j].contact_radius)
end
+export findContactsAllToAll
+"""
+Perform an O(n^2) all-to-all contact search between all ice floes in the
+`simulation` object.
+"""
function findContactsAllToAll!(simulation::Simulation)
for i = 1:length(simulation.ice_floes)
(DIR) diff --git a/src/grid.jl b/src/grid.jl
t@@ -28,6 +28,7 @@ function bilinearInterpolation(field::Array{Float64, 4},
field[i-1, j-1, k, it]*(1. - x_tilde))*(1. - y_tilde)
end
+export sortIceFloesInOceanGrid
"""
Find ice-floe positions in ocean grid, based on their center positions.
"""
t@@ -49,6 +50,7 @@ function sortIceFloesInOceanGrid!(simulation::Simulation, verbose=true)
end
end
+export findCellContainingPoint
"""
Returns the `i`, `j` index of the ocean grid cell containing the `point`.
"""
t@@ -71,6 +73,7 @@ function findCellContainingPoint(ocean::Ocean, point::Array{float, 1})
end
+export isPointInCell
"""
Check if a 2d point is contained inside a cell from the ocean grid.
The function uses either an area-based approach (`method = "Area"`), or a
t@@ -106,6 +109,7 @@ function isPointInCell(ocean::Ocean, i::Int, j::Int, point::Array{float, 1};
end
end
+export getCellCornerCoordinates
"""
Returns ocean-grid corner coordinates in the following order (south-west corner,
south-east corner, north-east corner, north-west corner).
t@@ -118,6 +122,7 @@ function getCellCornerCoordinates(ocean::Ocean, i::Int, j::Int)
return sw, se, ne, nw
end
+export areaOfTriangle
"Returns the area of an triangle with corner coordinates `a`, `b`, and `c`."
function areaOfTriangle(a::Array{float, 1},
b::Array{float, 1},
t@@ -129,6 +134,7 @@ function areaOfTriangle(a::Array{float, 1},
)
end
+export areaOfQuadrilateral
"""
Returns the area of a quadrilateral with corner coordinates `a`, `b`, `c`, and
`d`. Corners `a` and `c` should be opposite of each other, the same must be
t@@ -142,6 +148,7 @@ function areaOfQuadrilateral(a::Array{float, 1},
return areaOfTriangle(a, b, c) + areaOfTriangle(c, d, a)
end
+export conformalQuadrilateralCoordinates
"""
Returns the non-dimensional coordinates `[x_tilde, y_tilde]` of a point `p`
within a quadrilateral with corner coordinates `A`, `B`, `C`, and `D`.
(DIR) diff --git a/src/icefloe.jl b/src/icefloe.jl
t@@ -1,5 +1,6 @@
## Manage icefloes in the model
+export addIceFloeCylindrical
"""
Adds a grain to the simulation. Example:
t@@ -111,30 +112,47 @@ function addIceFloeCylindrical(simulation::Simulation,
addIceFloe!(simulation, icefloe, verbose)
end
+export iceFloeCircumreference
+"Returns the circumreference of the ice floe"
function iceFloeCircumreference(icefloe::IceFloeCylindrical)
return pi*icefloe.areal_radius*2.
end
+export iceFloeHorizontalSurfaceArea
+"Returns the top or bottom (horizontal) surface area of the ice floe"
function iceFloeHorizontalSurfaceArea(icefloe::IceFloeCylindrical)
return pi*icefloe.areal_radius^2.
end
+export iceFloeSideSurfaceArea
+"Returns the surface area of the ice-floe sides"
function iceFloeSideSurfaceArea(icefloe::IceFloeCylindrical)
return iceFloeCircumreference(icefloe)*icefloe.thickness
end
+export iceFloeVolume
+"Returns the volume of the ice floe"
function iceFloeVolume(icefloe::IceFloeCylindrical)
return iceFloeHorizontalSurfaceArea(icefloe)*icefloe.thickness
end
+export iceFloeMass
+"Returns the mass of the ice floe"
function iceFloeMass(icefloe::IceFloeCylindrical)
return iceFloeVolume(icefloe)*icefloe.density
end
+export iceFloeMomentOfInertia
+"Returns the moment of inertia of the ice floe"
function iceFloeMomentOfInertia(icefloe::IceFloeCylindrical)
return 0.5*iceFloeMass(icefloe)*icefloe.areal_radius^2.
end
+export convertIceFloeDataToArrays
+"""
+Gathers all ice-floe parameters from the `IceFloeCylindrical` type in continuous
+arrays in an `IceFloeArrays` structure.
+"""
function convertIceFloeDataToArrays(simulation::Simulation)
ifarr = IceFloeArrays(
t@@ -220,24 +238,37 @@ function convertIceFloeDataToArrays(simulation::Simulation)
return ifarr
end
+export iceFloeKineticTranslationalEnergy
+"Returns the translational kinetic energy of the ice floe"
function iceFloeKineticTranslationalEnergy(icefloe::IceFloeCylindrical)
return 0.5*icefloe.mass*norm(icefloe.lin_vel)^2.
end
+export totalIceFloeKineticTranslationalEnergy
+"""
+Returns the sum of translational kinetic energies of all ice floes in a
+simulation
+"""
function totalIceFloeKineticTranslationalEnergy(simulation::Simulation)
- E_sum = 0
+ E_sum = 0.
for icefloe in simulation.ice_floes
E_sum += iceFloeKineticTranslationalEnergy(icefloe)
end
return E_sum
end
+export iceFloeKineticRotationalEnergy
+"Returns the rotational kinetic energy of the ice floe"
function iceFloeKineticRotationalEnergy(icefloe::IceFloeCylindrical)
return 0.5*icefloe.moment_of_inertia*norm(icefloe.ang_vel)^2.
end
+export totalIceFloeKineticRotationalEnergy
+"""
+Returns the sum of rotational kinetic energies of all ice floes in a simulation
+"""
function totalIceFloeKineticRotationalEnergy(simulation::Simulation)
- E_sum = 0
+ E_sum = 0.
for icefloe in simulation.ice_floes
E_sum += iceFloeKineticRotationalEnergy(icefloe)
end
(DIR) diff --git a/src/interaction.jl b/src/interaction.jl
t@@ -1,5 +1,6 @@
## Interaction functions
+export interact
"""
Resolve mechanical interaction between all particle pairs.
"""
t@@ -14,6 +15,7 @@ function interact!(simulation::Simulation)
end
end
+export interactIceFloes
"""
Resolve an grain-to-grain interaction using a prescibed contact law. This
function adds the compressive force of the interaction to the ice floe
t@@ -45,6 +47,7 @@ function interactIceFloes!(simulation::Simulation,
norm(force)/simulation.ice_floes[j].side_surface_area;
end
+export interactNormalLinearElastic
"""
Resolves linear-elastic interaction between two ice floes in the contact-normal
direction.
(DIR) diff --git a/src/io.jl b/src/io.jl
t@@ -3,6 +3,7 @@ import NetCDF
## IO functions
+export writeVTK
"""
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
(DIR) diff --git a/src/simulation.jl b/src/simulation.jl
t@@ -1,5 +1,6 @@
## General simulation functions
+export createSimulation
"""
createSimulation([id::String="unnamed",
time_iteration::Int=0,
t@@ -43,6 +44,7 @@ function createSimulation(;id::String="unnamed",
ocean)
end
+export run
"""
run!(simulation[,
verbose::Bool = true,
t@@ -131,6 +133,7 @@ function run!(simulation::Simulation;
end
end
+export addIceFloe
"Add an `icefloe` to the `simulation` object. If `verbose` is true, a short
confirmation message will be printed to stdout`."
function addIceFloe!(simulation::Simulation,
t@@ -144,6 +147,7 @@ function addIceFloe!(simulation::Simulation,
end
end
+export removeIceFloe
"Remove ice floe with index `i` from the `simulation` object."
function removeIceFloe!(simulation::Simulation, i::Integer)
if i < 1
t@@ -153,6 +157,7 @@ function removeIceFloe!(simulation::Simulation, i::Integer)
delete!(simulation.ice_floes, i)
end
+export zeroForcesAndTorques
"Sets the `force` and `torque` values of all ice floes to zero."
function zeroForcesAndTorques!(simulation::Simulation)
for icefloe in simulation.ice_floes
t@@ -162,6 +167,7 @@ function zeroForcesAndTorques!(simulation::Simulation)
end
end
+export reportSimulationTimeToStdout
"Prints the current simulation time and total time to standard out"
function reportSimulationTimeToStdout(simulation::Simulation)
print("\r t = ", simulation.time, '/', simulation.time_total,
(DIR) diff --git a/src/temporal.jl b/src/temporal.jl
t@@ -1,3 +1,4 @@
+export setTotalTime
"""
setTotalTime!(simulation::Simulation, t::float)
t@@ -11,6 +12,7 @@ function setTotalTime!(simulation::Simulation, t::float)
simulation.time_total = t
end
+export setCurrentTime
"""
setCurrentTime!(simulation::Simulation, t::float)
t@@ -24,6 +26,7 @@ function setCurrentTime!(simulation::Simulation, t::float)
simulation.time = t
end
+export incrementCurrentTime
"""
incrementCurrentTime!(simulation::Simulation, t::float)
t@@ -37,19 +40,28 @@ function incrementCurrentTime!(simulation::Simulation, t::float)
simulation.time += t
end
-function setOutputFileInterval!(simulation::Simulation, t::float)
- if t <= 0.0
- info("The output file interval should be a positive value (t = $t s)")
+export setOutputFileInterval
+"""
+ setOutputFileInterval!(simulation::Simulation, t::float)
+
+Sets the simulation-time interval between output files are written to disk. If
+this value is zero or negative, no output files will be written.
+"""
+function setOutputFileInterval!(simulation::Simulation, t::float; verbose=true)
+ if t <= 0.0 && verbose
+ info("No output files will be written")
end
simulation.file_time_step = t
end
+export disableOutputFiles
"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."
+export checkTimeParameters
+"Checks if simulation temporal 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@@ -61,6 +73,7 @@ function checkTimeParameters(simulation::Simulation)
end
end
+export findSmallestIceFloeMass
"Finds the smallest mass of all ice floes in a simulation. Used to determine
the optimal time step length."
function findSmallestIceFloeMass(simulation::Simulation)
t@@ -76,6 +89,7 @@ function findSmallestIceFloeMass(simulation::Simulation)
return m_min, i_min
end
+export findLargestIceFloeStiffness
"Finds the largest elastic stiffness of all ice floes in a simulation. Used to
determine the optimal time step length."
function findLargestIceFloeStiffness(simulation::Simulation)
t@@ -97,6 +111,7 @@ function findLargestIceFloeStiffness(simulation::Simulation)
return k_n_max, k_t_max, i_n_max, i_t_max
end
+export setTimeStep
"""
Find the computational time step length suitable given the grain radii, contact
stiffnesses, and grain density. Uses the scheme by Radjaii et al. 2011.
(DIR) diff --git a/src/temporal_integration.jl b/src/temporal_integration.jl
t@@ -1,3 +1,4 @@
+export updateIceFloeKinematics
"""
updateIceFloeKinematics!(simulation::Simulation[,
method::String = "Three-term Taylor"])
t@@ -31,8 +32,11 @@ function updateIceFloeKinematics!(simulation::Simulation;
end
end
-"Use a two-term Taylor expansion for integrating the kinematic degrees of
-freedom for an `icefloe`."
+export updateIceFloeKinematicsTwoTermTaylor
+"""
+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@@ -56,8 +60,11 @@ 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`."
+export updateIceFloeKinematicsThreeTermTaylor
+"""
+Use a three-term Taylor expansion for integrating the kinematic degrees of
+freedom for an `icefloe`.
+"""
function updateIceFloeKinematicsThreeTermTaylor(icefloe::IceFloeCylindrical,
simulation::Simulation)