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	tadd advection stability check - sphere - GPU-based 3D discrete element method …
	git clone git://src.adamsgaard.dk/sphere
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	---
	commit 9c151584116fc9b0a5b998903775373d1b7db9b0
	parent a911141e8df42ba8a6b2be040a989889cbd93a96
	Author: Anders Damsgaard <[email protected]>
	Date: Thu, 6 Nov 2014 12:36:06 +0100

	add advection stability check

	Diffstat:
	M python/sphere.py \| 10 ++++++----
	M src/darcy.cpp \| 40 ++++++++++++++++++++++++++++-…
	M src/sphere.h \| 1 +

	3 files changed, 44 insertions(+), 7 deletions(-)
	---
	diff --git a/python/sphere.py b/python/sphere.py
	t@@ -2785,9 +2785,10 @@ class sim:
	self.cellSize()
	#self.hydraulicPermeability()
	#alpha_max = numpy.max(self.k/(self.beta_f0.9self.mu))
	- k_max = 2.7e-8 # hardcoded
	- phi_min = 0.1 # hardcoded
	+ k_max = 2.7e-8 # hardcoded in darcy.cuh
	+ phi_min = 0.1 # hardcoded in darcy.cuh
	alpha_max = k_max/(self.beta_fphi_minself.mu)
	+ print(alpha_max)
	return safety * 1.0/(2.0alpha_max)1.0/(
	1.0/(self.dx[0]**2) + \
	1.0/(self.dx[1]**2) + \
	t@@ -2907,8 +2908,9 @@ class sim:

	# Check numerical stability of the fluid phase, by criteria derived by
	# von Neumann stability analysis of the diffusion and advection terms
	- elif self.fluid:
	- self.time_dt[0] = self.largestFluidTimeStep(safety = 0.5)
	+ if self.fluid:
	+ fluid_time_dt = self.largestFluidTimeStep(safety = 0.5)
	+ self.time_dt[0] = numpy.min([fluid_time_dt, self.time_dt[0]])

	else:
	raise Exception('Error: Could not automatically set a time step.')
	diff --git a/src/darcy.cpp b/src/darcy.cpp
	t@@ -109,6 +109,25 @@ Float DEM::smallestDarcyPorosity()
	return phi_min;
	}

	+// Component-wise max absolute velocities
	+Float3 DEM::largestDarcyVelocities()
	+{
	+ Float3 v_max_abs = MAKE_FLOAT3(0.0, 0.0, 0.0);
	+ Float3 v;
	+ for (unsigned int z=0; z<grid.num[2]; z++)
	+ for (unsigned int y=0; y<grid.num[1]; y++)
	+ for (unsigned int x=0; x<grid.num[0]; x++) {
	+ v = darcy.v[d_idx(x,y,z)];
	+ if (v.x > v_max_abs.x)
	+ v_max_abs.x = fabs(v.x);
	+ if (v.y > v_max_abs.y)
	+ v_max_abs.y = fabs(v.y);
	+ if (v.z > v_max_abs.z)
	+ v_max_abs.z = fabs(v.z);
	+ }
	+ return v_max_abs;
	+}
	+
	// Determine if the FTCS (forward time, central space) solution of the Navier
	// Stokes equations is unstable
	void DEM::checkDarcyStability()
	t@@ -121,17 +140,32 @@ void DEM::checkDarcyStability()
	const Float alpha_max = largestDarcyPermeability()
	/(darcy.beta_fsmallestDarcyPorosity()darcy.mu);

	- // Check the diffusion term using von Neumann stability analysis
	- //if (darcy.mutime.dt/(dmindmin) > 0.5) {
	+ // von Neumann stability analysis
	if (time.dt >= 1.0/(2.0alpha_max)
	1.0/(1.0/(dxdx) + 1.0/(dydy) + 1.0/(dz*dz))) {
	std::cerr
	<< "\nError: The time step is too large to ensure stability in "
	"the diffusive term of the fluid momentum equation.\n"
	- "Increase the viscosity, decrease the time step, and/or increase "
	+ "Decrease the time step, increase the fluid viscosity, increase "
	+ "the fluid compressibility and/or increase "
	"the fluid grid cell size." << std::endl;
	//exit(1);
	}
	+
	+ // Courant-Friedrichs-Lewy criteria
	+ Float3 v_max_abs = largestDarcyVelocities();
	+ if (v_max_abs.x*time.dt > dx \|\|
	+ v_max_abs.y*time.dt > dy \|\|
	+ v_max_abs.z*time.dt > dz) {
	+ std::cerr
	+ << "\nError: The time step is too large to ensure stability due to…
	+ "large fluid velocities.\n v_max_abs = "
	+ << v_max_abs.x << ", "
	+ << v_max_abs.y << ", "
	+ << v_max_abs.z <<
	+ " m/s.\nDecrease the time step "
	+ "and/or increase the fluid grid cell size." << std::endl;
	+ }
	}

	// Print array values to file stream (stdout, stderr, other file)
	diff --git a/src/sphere.h b/src/sphere.h
	t@@ -310,6 +310,7 @@ class DEM {
	void initDarcyMem();
	Float largestDarcyPermeability();
	Float smallestDarcyPorosity();
	+ Float3 largestDarcyVelocities();
	void initDarcyMemDev();
	unsigned int darcyCells();
	unsigned int darcyCellsVelocity();