tMerge branch 'master' of github.com:anders-dc/Granular.jl - Granular.jl - Julia package for granular dynamics simulation
(HTM) git clone git://src.adamsgaard.dk/Granular.jl
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(DIR) README
(DIR) LICENSE
---
(DIR) commit be609c80406b4b964b420d58d939fb3dd6e62647
(DIR) parent 61a6dfbb5653a440e9a76183d34f059e065baf95
(HTM) Author: Anders Damsgaard <andersd@riseup.net>
Date: Tue, 16 Jan 2018 12:50:31 -0800
Merge branch 'master' of github.com:anders-dc/Granular.jl
Diffstat:
M Makefile | 12 +++++++++---
M src/datatypes.jl | 2 +-
M src/grain.jl | 172 +++++++++++++++++++++----------
M src/io.jl | 28 +++++++++++++++++++++++++---
M test/collision-2floes-normal.jl | 73 +++++++++++++++++++++++++++++++
M test/runtests.jl | 6 +++---
M test/vtk.jl | 2 +-
7 files changed, 227 insertions(+), 68 deletions(-)
---
(DIR) diff --git a/Makefile b/Makefile
t@@ -1,15 +1,21 @@
default: test
.PHONY: test
-test: test-julia-0.6 test-julia-0.7
+test: test-julia-0.6 #test-julia-0.7
.PHONY: test-julia-0.6
test-julia-0.6:
- julia --color=yes -e 'Pkg.test("Granular")'
+ @#julia --color=yes -e 'Pkg.test("Granular")'
+ julia --color=yes -e 'Pkg.test("Granular")' \
+ && notify-send Granular.jl tests completed successfully on Julia 0.6 \
+ || notify-send Granular.jl failed on Julia 0.6
.PHONY: test-julia-0.7
test-julia-0.7:
- julia-0.7 --color=yes -e 'Pkg.test("Granular")'
+ @#julia-0.7 --color=yes -e 'Pkg.test("Granular")'
+ julia-0.7 --color=yes -e 'Pkg.test("Granular")' \
+ && notify-send Granular.jl tests completed successfully on Julia 0.7 \
+ || notify-send Granular.jl failed on Julia 0.7
.PHONY: docs
docs:
(DIR) diff --git a/src/datatypes.jl b/src/datatypes.jl
t@@ -138,7 +138,7 @@ mutable struct GrainArrays
youngs_modulus::Vector{Float64}
poissons_ratio::Vector{Float64}
tensile_strength::Vector{Float64}
- #tensile_heal_rate::Vector{Float64}
+ tensile_heal_rate::Vector{Float64}
compressive_strength_prefactor::Vector{Float64}
ocean_drag_coeff_vert::Vector{Float64}
(DIR) diff --git a/src/grain.jl b/src/grain.jl
t@@ -331,63 +331,119 @@ arrays in an `GrainArrays` structure.
function convertGrainDataToArrays(simulation::Simulation)
ifarr = GrainArrays(
- Array{Float64}(length(simulation.grains)),
-
- Array{Float64}(length(simulation.grains)),
- Array{Float64}(length(simulation.grains)),
- Array{Float64}(length(simulation.grains)),
- Array{Float64}(length(simulation.grains)),
- Array{Float64}(length(simulation.grains)),
- Array{Float64}(length(simulation.grains)),
- Array{Float64}(length(simulation.grains)),
- Array{Float64}(length(simulation.grains)),
- Array{Float64}(length(simulation.grains)),
-
- zeros(Float64, 3, length(simulation.grains)),
- zeros(Float64, 3, length(simulation.grains)),
- zeros(Float64, 3, length(simulation.grains)),
- zeros(Float64, 3, length(simulation.grains)),
- zeros(Float64, 3, length(simulation.grains)),
- zeros(Float64, 3, length(simulation.grains)),
-
- zeros(Float64, 3, length(simulation.grains)),
- zeros(Float64, 3, length(simulation.grains)),
- zeros(Float64, 3, length(simulation.grains)),
- zeros(Float64, 3, length(simulation.grains)),
-
- Array{Int}(length(simulation.grains)),
- Array{Int}(length(simulation.grains)),
- Array{Int}(length(simulation.grains)),
- Array{Int}(length(simulation.grains)),
- Array{Int}(length(simulation.grains)),
-
- Array{Float64}(length(simulation.grains)),
- Array{Float64}(length(simulation.grains)),
- Array{Float64}(length(simulation.grains)),
- Array{Float64}(length(simulation.grains)),
- Array{Float64}(length(simulation.grains)),
- Array{Float64}(length(simulation.grains)),
-
- Array{Float64}(length(simulation.grains)),
- Array{Float64}(length(simulation.grains)),
- Array{Float64}(length(simulation.grains)),
- Array{Float64}(length(simulation.grains)),
-
- Array{Float64}(length(simulation.grains)),
- Array{Float64}(length(simulation.grains)),
- Array{Float64}(length(simulation.grains)),
- Array{Float64}(length(simulation.grains)),
-
- Array{Float64}(length(simulation.grains)),
- Array{Int}(length(simulation.grains)),
-
- zeros(Float64, 3, length(simulation.grains)),
- zeros(Float64, 3, length(simulation.grains)),
- zeros(Float64, 3, length(simulation.grains)),
-
- Array{Int}(length(simulation.grains)),
-
- )
+ # Material properties
+ ## density
+ Array{Float64}(length(simulation.grains)),
+
+ # Geometrical properties
+ ## thickness
+ Array{Float64}(length(simulation.grains)),
+ ## contact_radius
+ Array{Float64}(length(simulation.grains)),
+ ## areal_radius
+ Array{Float64}(length(simulation.grains)),
+ ## circumreference
+ Array{Float64}(length(simulation.grains)),
+ ## horizontal_surface_area
+ Array{Float64}(length(simulation.grains)),
+ ## side_surface_area
+ Array{Float64}(length(simulation.grains)),
+ ## volume
+ Array{Float64}(length(simulation.grains)),
+ ## mass
+ Array{Float64}(length(simulation.grains)),
+ ## moment_of_inertia
+ Array{Float64}(length(simulation.grains)),
+
+ # Linear kinematic degrees of freedom along horiz plane
+ ## lin_pos
+ zeros(Float64, 3, length(simulation.grains)),
+ ## lin_vel
+ zeros(Float64, 3, length(simulation.grains)),
+ ## lin_acc
+ zeros(Float64, 3, length(simulation.grains)),
+ ## force
+ zeros(Float64, 3, length(simulation.grains)),
+ ## external_body_force
+ zeros(Float64, 3, length(simulation.grains)),
+ ## lin_disp
+ zeros(Float64, 3, length(simulation.grains)),
+
+ # Angular kinematic degrees of freedom for vert. rot.
+ ## ang_pos
+ zeros(Float64, 3, length(simulation.grains)),
+ ## ang_vel
+ zeros(Float64, 3, length(simulation.grains)),
+ ## ang_acc
+ zeros(Float64, 3, length(simulation.grains)),
+ ## torque
+ zeros(Float64, 3, length(simulation.grains)),
+
+ # Kinematic constraint flags
+ ## fixed
+ Array{Int}(length(simulation.grains)),
+ ## allow_x_acc
+ Array{Int}(length(simulation.grains)),
+ ## allow_y_acc
+ Array{Int}(length(simulation.grains)),
+ ## rotating
+ Array{Int}(length(simulation.grains)),
+ ## enabled
+ Array{Int}(length(simulation.grains)),
+
+ # Rheological parameters
+ ## contact_stiffness_normal
+ Array{Float64}(length(simulation.grains)),
+ ## contact_stiffness_tangential
+ Array{Float64}(length(simulation.grains)),
+ ## contact_viscosity_normal
+ Array{Float64}(length(simulation.grains)),
+ ## contact_viscosity_tangential
+ Array{Float64}(length(simulation.grains)),
+ ## contact_static_friction
+ Array{Float64}(length(simulation.grains)),
+ ## contact_dynamic_friction
+ Array{Float64}(length(simulation.grains)),
+
+ ## youngs_modulus
+ Array{Float64}(length(simulation.grains)),
+ ## poissons_ratio
+ Array{Float64}(length(simulation.grains)),
+ ## tensile_strength
+ Array{Float64}(length(simulation.grains)),
+ ## tensile_heal_rate
+ Array{Float64}(length(simulation.grains)),
+ ## compressive_strength_prefactor
+ Array{Float64}(length(simulation.grains)),
+
+ # Ocean/atmosphere interaction parameters
+ ## ocean_drag_coeff_vert
+ Array{Float64}(length(simulation.grains)),
+ ## ocean_drag_coeff_horiz
+ Array{Float64}(length(simulation.grains)),
+ ## atmosphere_drag_coeff_vert
+ Array{Float64}(length(simulation.grains)),
+ ## atmosphere_drag_coeff_horiz
+ Array{Float64}(length(simulation.grains)),
+
+ # Interaction
+ ## pressure
+ Array{Float64}(length(simulation.grains)),
+ ## n_contacts
+ Array{Int}(length(simulation.grains)),
+
+ ## granular_stress
+ zeros(Float64, 3, length(simulation.grains)),
+ ## ocean_stress
+ zeros(Float64, 3, length(simulation.grains)),
+ ## atmosphere_stress
+ zeros(Float64, 3, length(simulation.grains)),
+
+ # Visualization parameters
+ ## color
+ Array{Int}(length(simulation.grains)),
+
+ )
# fill arrays
for i=1:length(simulation.grains)
t@@ -439,6 +495,7 @@ function convertGrainDataToArrays(simulation::Simulation)
ifarr.youngs_modulus[i] = simulation.grains[i].youngs_modulus
ifarr.poissons_ratio[i] = simulation.grains[i].poissons_ratio
ifarr.tensile_strength[i] = simulation.grains[i].tensile_strength
+ ifarr.tensile_heal_rate[i] = simulation.grains[i].tensile_heal_rate
ifarr.compressive_strength_prefactor[i] =
simulation.grains[i].compressive_strength_prefactor
t@@ -510,6 +567,7 @@ function deleteGrainArrays!(ifarr::GrainArrays)
ifarr.youngs_modulus = f1
ifarr.poissons_ratio = f1
ifarr.tensile_strength = f1
+ ifarr.tensile_heal_rate = f1
ifarr.compressive_strength_prefactor = f1
ifarr.ocean_drag_coeff_vert = f1
(DIR) diff --git a/src/io.jl b/src/io.jl
t@@ -376,6 +376,10 @@ function writeGrainVTK(simulation::Simulation,
WriteVTK.vtk_point_data(vtkfile, ifarr.torque, "Sum of torques [N*m]")
WriteVTK.vtk_point_data(vtkfile, ifarr.fixed, "Fixed in space [-]")
+ WriteVTK.vtk_point_data(vtkfile, ifarr.allow_x_acc,
+ "Fixed but allow (x) acceleration [-]")
+ WriteVTK.vtk_point_data(vtkfile, ifarr.allow_y_acc,
+ "Fixed but allow (y) acceleration [-]")
WriteVTK.vtk_point_data(vtkfile, ifarr.rotating, "Free to rotate [-]")
WriteVTK.vtk_point_data(vtkfile, ifarr.enabled, "Enabled [-]")
t@@ -398,6 +402,8 @@ function writeGrainVTK(simulation::Simulation,
"Poisson's ratio [-]")
WriteVTK.vtk_point_data(vtkfile, ifarr.tensile_strength,
"Tensile strength [Pa]")
+ WriteVTK.vtk_point_data(vtkfile, ifarr.tensile_heal_rate,
+ "Tensile healing rate [1/s]")
WriteVTK.vtk_point_data(vtkfile, ifarr.compressive_strength_prefactor,
"Compressive strength prefactor [m^0.5 Pa]")
t@@ -412,7 +418,6 @@ function writeGrainVTK(simulation::Simulation,
WriteVTK.vtk_point_data(vtkfile, ifarr.pressure,
"Contact pressure [Pa]")
-
WriteVTK.vtk_point_data(vtkfile, ifarr.n_contacts,
"Number of contacts [-]")
t@@ -447,8 +452,8 @@ Saves grain interactions to `.vtp` files for visualization with VTK, for
example in Paraview. Convert Cell Data to Point Data and use with Tube filter.
"""
function writeGrainInteractionVTK(simulation::Simulation,
- filename::String;
- verbose::Bool=false)
+ filename::String;
+ verbose::Bool=false)
i1 = Int64[]
i2 = Int64[]
t@@ -460,6 +465,7 @@ function writeGrainInteractionVTK(simulation::Simulation,
tensile_stress = Float64[]
shear_displacement = Vector{Float64}[]
contact_age = Float64[]
+
for i=1:length(simulation.grains)
for ic=1:simulation.Nc_max
if simulation.grains[i].contacts[ic] > 0
t@@ -476,6 +482,19 @@ function writeGrainInteractionVTK(simulation::Simulation,
r_i = simulation.grains[i].contact_radius
r_j = simulation.grains[j].contact_radius
+
+ # skip visualization of contacts across periodic BCs
+ if dist > 5.0*(r_i + r_j) &&
+ (simulation.ocean.bc_west == 2 ||
+ simulation.ocean.bc_east == 2 ||
+ simulation.ocean.bc_north == 2 ||
+ simulation.ocean.bc_south == 2 ||
+ simulation.atmosphere.bc_west == 2 ||
+ simulation.atmosphere.bc_east == 2 ||
+ simulation.atmosphere.bc_north == 2 ||
+ simulation.atmosphere.bc_south == 2)
+ continue
+ end
δ_n = dist - (r_i + r_j)
R_ij = harmonicMean(r_i, r_j)
t@@ -809,6 +828,8 @@ imagegrains.PointArrayStatus = [
'Angular acceleration [rad s^-2]',
'Sum of torques [N*m]',
'Fixed in space [-]',
+'Fixed but allow (x) acceleration [-]',
+'Fixed but allow (y) acceleration [-]',
'Free to rotate [-]',
'Enabled [-]',
'Contact stiffness (normal) [N m^-1]',
t@@ -820,6 +841,7 @@ imagegrains.PointArrayStatus = [
"Young's modulus [Pa]",
"Poisson's ratio [-]",
'Tensile strength [Pa]'
+'Tensile heal rate [1/s]'
'Compressive strength prefactor [m^0.5 Pa]',
'Ocean drag coefficient (vertical) [-]',
'Ocean drag coefficient (horizontal) [-]',
(DIR) diff --git a/test/collision-2floes-normal.jl b/test/collision-2floes-normal.jl
t@@ -273,3 +273,76 @@ E_kin_rot_final = Granular.totalGrainKineticRotationalEnergy(sim)
@test E_kin_rot_init ≈ E_kin_rot_final
@test sim.grains[2].lin_pos[1] > grain2_pos_init[1]
+r = 10.
+for angle in linspace(0, 2π, 4)
+ info("## Contact angle: $angle")
+
+ info("Testing behavior with two fixed grains and allow_*_acc")
+ sim = Granular.createSimulation(id="test")
+ Granular.addGrainCylindrical!(sim, [0., 0.], r, 1., verbose=verbose)
+ Granular.addGrainCylindrical!(sim, [2.0*r*cos(angle), 2.0*r*sin(angle)],
+ r, 1., verbose=verbose)
+ sim.grains[1].fixed = true
+ sim.grains[2].fixed = true
+
+ E_kin_lin_init = Granular.totalGrainKineticTranslationalEnergy(sim)
+ E_kin_rot_init = Granular.totalGrainKineticRotationalEnergy(sim)
+ grain1_pos_init = sim.grains[1].lin_pos
+ grain2_pos_init = sim.grains[2].lin_pos
+
+ Granular.setTotalTime!(sim, 10.0)
+ Granular.setTimeStep!(sim, epsilon=0.07)
+ sim_init = deepcopy(sim)
+
+ info("Both fixed, no allow_*_acc, no cohesion (TY2)")
+ sim = deepcopy(sim_init)
+ #sim.grains[2].allow_y_acc = true # should not influence result
+ tol = 0.02
+ Granular.run!(sim, temporal_integration_method="Two-term Taylor", verbose=verbose)
+ E_kin_lin_final = Granular.totalGrainKineticTranslationalEnergy(sim)
+ E_kin_rot_final = Granular.totalGrainKineticRotationalEnergy(sim)
+ @test E_kin_lin_init ≈ E_kin_lin_final atol=E_kin_lin_init*tol
+ @test E_kin_rot_init ≈ E_kin_rot_final
+ @test sim.grains[1].lin_pos ≈ grain1_pos_init
+ @test sim.grains[2].lin_pos ≈ grain2_pos_init
+
+ info("Both fixed, no allow_*_acc, no cohesion (TY3)")
+ sim = deepcopy(sim_init)
+ #sim.grains[2].allow_y_acc = true # should not influence result
+ tol = 0.02
+ Granular.run!(sim, temporal_integration_method="Three-term Taylor", verbose=verbose)
+ E_kin_lin_final = Granular.totalGrainKineticTranslationalEnergy(sim)
+ E_kin_rot_final = Granular.totalGrainKineticRotationalEnergy(sim)
+ @test E_kin_lin_init ≈ E_kin_lin_final atol=E_kin_lin_init*tol
+ @test E_kin_rot_init ≈ E_kin_rot_final
+ @test sim.grains[1].lin_pos ≈ grain1_pos_init
+ @test sim.grains[2].lin_pos ≈ grain2_pos_init
+
+ info("Both fixed, no allow_*_acc, cohesion (TY2)")
+ sim = deepcopy(sim_init)
+ #sim.grains[2].allow_y_acc = true # should not influence result
+ sim.grains[1].tensile_strength = 200e3
+ sim.grains[2].tensile_strength = 200e3
+ tol = 0.2
+ Granular.run!(sim, temporal_integration_method="Two-term Taylor", verbose=verbose)
+ E_kin_lin_final = Granular.totalGrainKineticTranslationalEnergy(sim)
+ E_kin_rot_final = Granular.totalGrainKineticRotationalEnergy(sim)
+ @test E_kin_lin_init ≈ E_kin_lin_final atol=E_kin_lin_init*tol
+ @test E_kin_rot_init ≈ E_kin_rot_final
+ @test sim.grains[1].lin_pos ≈ grain1_pos_init
+ @test sim.grains[2].lin_pos ≈ grain2_pos_init
+
+ info("Both fixed, no allow_*_acc, cohesion (TY3)")
+ sim = deepcopy(sim_init)
+ #sim.grains[2].allow_y_acc = true # should not influence result
+ sim.grains[1].tensile_strength = 200e3
+ sim.grains[2].tensile_strength = 200e3
+ tol = 0.02
+ Granular.run!(sim, temporal_integration_method="Three-term Taylor", verbose=verbose)
+ E_kin_lin_final = Granular.totalGrainKineticTranslationalEnergy(sim)
+ E_kin_rot_final = Granular.totalGrainKineticRotationalEnergy(sim)
+ @test E_kin_lin_init ≈ E_kin_lin_final atol=E_kin_lin_init*tol
+ @test E_kin_rot_init ≈ E_kin_rot_final
+ @test sim.grains[1].lin_pos ≈ grain1_pos_init
+ @test sim.grains[2].lin_pos ≈ grain2_pos_init
+end
(DIR) diff --git a/test/runtests.jl b/test/runtests.jl
t@@ -1,6 +1,9 @@
using Compat.Test
import Granular
+include("collision-2floes-normal.jl")
+include("collision-5floes-normal.jl")
+include("collision-2floes-oblique.jl")
include("grid.jl")
include("contact-search-and-geometry.jl")
include("grid-boundaries.jl")
t@@ -11,9 +14,6 @@ include("grain.jl")
include("packing.jl")
include("util.jl")
include("temporal.jl")
-include("collision-2floes-normal.jl")
-include("collision-5floes-normal.jl")
-include("collision-2floes-oblique.jl")
include("cohesion.jl")
include("netcdf.jl")
include("vtk.jl")
(DIR) diff --git a/test/vtk.jl b/test/vtk.jl
t@@ -29,7 +29,7 @@ end
grainpath = "test/test.grains.1.vtu"
grainchecksum =
-"c1e85bf2c5379050ba6dd674eecedaf6857f309015e94544d1dc27e8b46607c8 " *
+"f5a5106bffaaa2fd556ab0cac602127aecdb9cd9fc74141b75d1a7e7f39e21d6 " *
grainpath * "\n"
graininteractionpath = "test/test.grain-interaction.1.vtp"