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	timplement shear stress BC - sphere - GPU-based 3D discrete element method algo…
	git clone git://src.adamsgaard.dk/sphere
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	---
	commit d299ad9ed8edbb6652677fe9568ce4f9a78b6299
	parent cbd624d82308f27331fa8781ba282eff5661645f
	Author: Anders Damsgaard <[email protected]>
	Date: Wed, 14 Jan 2015 13:54:53 +0100

	implement shear stress BC

	Diffstat:
	M src/device.cu \| 38 +++++++++++++++++++++++++++++…
	M src/file_io.cpp \| 4 ++--
	M src/integration.cuh \| 24 +++++++++++++++---------

	3 files changed, 54 insertions(+), 12 deletions(-)
	---
	diff --git a/src/device.cu b/src/device.cu
	t@@ -2159,6 +2159,36 @@ __host__ void DEM::startTime()
	//break; // end after first iteration

	if (np > 0) {
	+
	+ // Find shear stresses on upper fixed particles if a shear stress …
	+ // is specified (wmode[0] == 3)
	+ if (walls.nw > 0 && walls.wmode[0] == 3) {
	+
	+ if (PROFILING == 1)
	+ startTimer(&kernel_tic);
	+ findShearStressOnFixedMovingParticles<<<dimGrid, dimBlock>>>
	+ (dev_x,
	+ dev_vel,
	+ dev_force,
	+ dev_walls_tau_eff_x_pp);
	+ cudaThreadSynchronize();
	+ if (PROFILING == 1)
	+ stopTimer(&kernel_tic, &kernel_toc, &kernel_elapsed,
	+ &t_summation);
	+ checkForCudaErrorsIter(
	+ "Post findShearStressOnFixedMovingParticles", iter);
	+
	+ if (PROFILING == 1)
	+ startTimer(&kernel_tic);
	+ summation<<<dimGrid, dimBlock>>>(dev_walls_tau_eff_x_pp,
	+ dev_walls_tau_eff_x_partial);
	+ cudaThreadSynchronize();
	+ if (PROFILING == 1)
	+ stopTimer(&kernel_tic, &kernel_toc, &kernel_elapsed,
	+ &t_summation);
	+ checkForCudaErrorsIter("Post shear stress summation", iter);
	+ }
	+
	// Update particle kinematics
	if (PROFILING == 1)
	startTimer(&kernel_tic);
	t@@ -2177,7 +2207,13 @@ __host__ void DEM::startTime()
	dev_angvel0,
	dev_xyzsum,
	dev_gridParticleIndex,
	- iter);
	+ iter,
	+ dev_walls_wmode,
	+ dev_walls_mvfd,
	+ dev_walls_tau_eff_x_partial,
	+ dev_walls_tau_x,
	+ walls.tau_x[0],
	+ blocksPerGrid);
	cudaThreadSynchronize();
	checkForCudaErrorsIter("Post integrate", iter);
	if (PROFILING == 1)
	diff --git a/src/file_io.cpp b/src/file_io.cpp
	t@@ -220,7 +220,7 @@ void DEM::readbin(const char *target)
	}
	ifs.read(as_bytes(params.sigma0_A), sizeof(params.sigma0_A));
	ifs.read(as_bytes(params.sigma0_f), sizeof(params.sigma0_f));
	- ifs.read(as_bytes(walls.tau_x), sizeof(walls.tau_x));
	+ ifs.read(as_bytes(walls.tau_x[0]), sizeof(walls.tau_x[0]));

	// Read bond parameters
	ifs.read(as_bytes(params.lambda_bar), sizeof(params.lambda_bar));
	t@@ -522,7 +522,7 @@ void DEM::writebin(const char *target)
	}
	ofs.write(as_bytes(params.sigma0_A), sizeof(params.sigma0_A));
	ofs.write(as_bytes(params.sigma0_f), sizeof(params.sigma0_f));
	- ofs.write(as_bytes(walls.tau_x), sizeof(walls.tau_x));
	+ ofs.write(as_bytes(walls.tau_x[0]), sizeof(walls.tau_x[0]));

	// Write bond parameters
	ofs.write(as_bytes(params.lambda_bar), sizeof(params.lambda_bar));
	diff --git a/src/integration.cuh b/src/integration.cuh
	t@@ -29,8 +29,10 @@ __global__ void integrate(
	const unsigned int* __restrict__ dev_gridParticleIndex,
	const unsigned int iter,
	const int* __restrict__ dev_walls_wmode,
	+ const Float4* __restrict__ dev_walls_mvfd,
	const Float* __restrict__ dev_walls_tau_eff_x_partial,
	const Float* __restrict__ dev_walls_tau_x,
	+ const Float tau_x,
	const unsigned int blocksPerGrid)
	{
	unsigned int idx = threadIdx.x + blockIdx.x * blockDim.x; // Thread id
	t@@ -50,12 +52,16 @@ __global__ void integrate(
	Float4 xyzsum = dev_xyzsum[orig_idx];

	// Read the mode of the top wall
	- const int wall0mode = dev_walls_wmode[0];
	- const Float wall0mass = dev_walls_mvfd[0].x;
	+ int wall0mode;
	+ Float wall0mass;
	+ if (devC_nw > 0) {
	+ wall0mode = dev_walls_wmode[0];
	+ wall0mass = dev_walls_mvfd[0].x;
	+ }

	// Find the final sum of shear stresses on the top particles
	Float tau_eff_x = 0.0;
	- if (wall0mode == 3)
	+ if (devC_nw > 0 && wall0mode == 3)
	for (int i=0; i<blocksPerGrid; ++i)
	tau_eff_x += dev_walls_tau_eff_x_partial[i];

	t@@ -108,9 +114,9 @@ __global__ void integrate(
	// Fixed shear stress BC
	if (wall0mode == 3 && vel.w > 0.0001 && x.z > devC_grid.L[2]*0.5) {

	- // the force should be positive when abs(tau) > abs(tau_eff_x)
	+ // the force should be positive when abs(tau_x) > abs(tau_eff_x)
	const Float f_tau_x =
	- (tau + tau_eff_x)devC_grid.L[0]devC_grid.L[1];
	+ (tau_x + tau_eff_x)devC_grid.L[0]devC_grid.L[1];

	acc.x = f_tau_x/wall0mass; // acceleration = force/mass
	acc.y = 0.0;
	t@@ -449,15 +455,15 @@ __global__ void findShearStressOnFixedMovingParticles(
	// Copy data to temporary arrays to avoid any potential
	// read-after-write, write-after-read, or write-after-write hazards.
	__syncthreads();
	- const Float4 x = dev_x[idx];
	- const Float4 force = dev_force[orig_idx];
	+ const Float4 x = dev_x[idx];
	+ const Float force_x = dev_force[idx].x;

	- Float4 f_x = 0.0;
	+ Float f_x = 0.0;

	// Only select fixed velocity (fixvel > 0.0, fixvel = vel.w) particles
	// at the top boundary (z > L[0]/2)
	if (vel.w > 0.0 && x.z > devC_grid.L[2]*0.5)
	- f_x = force.x;
	+ f_x = force_x;

	__syncthreads();
	// Convert force to shear stress and save