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	tdevs should still be set, add function to set pressure at top wall - sphere - …
	git clone git://src.adamsgaard.dk/sphere
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	---
	commit bebe373425e17094afa919530ad3c562435e06e0
	parent 0f3a2baafbb052d268a67b86531d6ae1d25d447d
	Author: Anders Damsgaard <[email protected]>
	Date: Fri, 19 Sep 2014 11:16:39 +0200

	devs should still be set, add function to set pressure at top wall

	Diffstat:
	M python/shear-starter.py \| 6 +++---
	M python/shear2.py \| 2 +-
	M src/device.cu \| 19 +++++++++++++++++++
	M src/integration.cuh \| 6 ++++--
	M src/navierstokes.cuh \| 47 ++++++++++++++++++++++++++++-…

	5 files changed, 70 insertions(+), 10 deletions(-)
	---
	diff --git a/python/shear-starter.py b/python/shear-starter.py
	t@@ -44,7 +44,7 @@ sim.shear(1.0/20.0)
	if fluid:
	sim.num[2] *= 2
	sim.L[2] *= 2.0
	- sim.initFluid(mu = 1.787e-6, p = 1.0e5, hydrostatic = True)
	+ sim.initFluid(mu = 1.787e-6, p = 600.0e3, hydrostatic = True)
	#sim.initFluid(mu = 17.87e-4, p = 1.0e5, hydrostatic = True)
	sim.setFluidBottomNoFlow()
	sim.setFluidTopFixedPressure()
	t@@ -53,8 +53,8 @@ sim.setMaxIterations(2e5)
	sim.initTemporal(total = 20.0, file_dt = 0.01, epsilon=0.07)
	sim.c_phi[0] = c_phi
	sim.c_grad_p[0] = c_grad_p
	-#sim.w_devs[0] = sigma0
	-sim.w_devs[0] = 0.0
	+sim.w_devs[0] = sigma0
	+#sim.w_devs[0] = 0.0
	sim.w_m[0] = numpy.abs(sigma0sim.L[0]sim.L[1]/sim.g[2])
	sim.mu_s[0] = 0.5
	sim.mu_d[0] = 0.5
	diff --git a/python/shear2.py b/python/shear2.py
	t@@ -11,7 +11,7 @@ sim.shear(1.0/20.0)
	if fluid:
	sim.num[2] *= 2
	sim.L[2] *= 2.0
	- sim.initFluid(mu=1.797e-6, p=600.0e3, hydrostatic=True)
	+ sim.initFluid(mu=1.787e-6, p=600.0e3, hydrostatic=True)
	sim.setFluidBottomNoFlow()
	sim.setFluidTopFixedPressure()
	sim.setDEMstepsPerCFDstep(100)
	diff --git a/src/device.cu b/src/device.cu
	t@@ -840,6 +840,11 @@ __host__ void DEM::startTime()
	double t_start = time.current;
	double t_ratio; // ration between time flow in model vs. reality

	+ // Index of dynamic top wall (if it exists)
	+ unsigned int wall0_iz;
	+ // weight of fluid between two cells in z direction
	+ const Float dp_dz = fabs(params.rho_fparams.g[2]grid.L[2]/grid.num[2]);
	+
	// Write a log file of the number of iterations it took before
	// convergence in the fluid solver
	std::ofstream convlog;
	t@@ -1157,6 +1162,7 @@ __host__ void DEM::startTime()
	if ((iter % ns.ndem) == 0) {
	// Initial guess for the top epsilon values. These may be
	// changed in setUpperPressureNS
	+ // TODO: Check if this should only be set when top bc=Dirichlet
	Float pressure = ns.p[idx(0,0,ns.nz-1)];
	Float pressure_new = pressure; // Dirichlet
	Float epsilon_value = pressure_new - ns.beta*pressure;
	t@@ -1167,6 +1173,19 @@ __host__ void DEM::startTime()
	cudaThreadSynchronize();
	checkForCudaErrorsIter("Post setNSepsilonTop", iter);

	+ // find cell containing top wall
	+ if (walls.nw > 0 && walls.wmode[0] == 1) {
	+ wall0_iz = walls.nx->w/(grid.L[2]/grid.num[2]);
	+ setNSepsilonAtTopWall<<<dimGridFluid, dimBlockFluid>>>(
	+ dev_ns_epsilon,
	+ dev_ns_epsilon_new,
	+ wall0_iz,
	+ epsilon_value,
	+ dp_dz);
	+ cudaThreadSynchronize();
	+ checkForCudaErrorsIter("Post setNSepsilonAtTopWall", iter);
	+ }
	+
	// Modulate the pressures at the upper boundary cells
	if ((ns.p_mod_A > 1.0e-5 \|\| ns.p_mod_A < -1.0e-5) &&
	ns.p_mod_f > 1.0e-7) {
	diff --git a/src/integration.cuh b/src/integration.cuh
	t@@ -334,10 +334,12 @@ __global__ void integrateWalls(

	const Float dt = devC_dt;

	- // Normal load = Deviatoric stress times wall surface area,
	- // directed downwards.
	+ // Apply sinusoidal variation if specified
	const Float sigma_0 = w_mvfd.w
	+ devC_params.devs_Asin(2.0PIdevC_params.devs_f t_current…
	+
	+ // Normal load = Normal stress times wall surface area,
	+ // directed downwards.
	const Float N = -sigma_0devC_grid.L[0]devC_grid.L[1];

	// Calculate resulting acceleration of wall
	diff --git a/src/navierstokes.cuh b/src/navierstokes.cuh
	t@@ -417,11 +417,9 @@ __global__ void setNSepsilonBottom(
	}
	}

	-// Set the constant values of epsilon at the lower boundary. Since the
	+// Set the constant values of epsilon at the upper boundary. Since the
	// Dirichlet boundary values aren't transfered during array swapping, the valu…
	-// also need to be written to the new array of epsilons. A value of 0 equals
	-// the Dirichlet boundary condition: the new value should be identical to the
	-// old value, i.e. the temporal gradient is 0
	+// also need to be written to the new array of epsilons.
	__global__ void setNSepsilonTop(
	Float* __restrict__ dev_ns_epsilon,
	Float* __restrict__ dev_ns_epsilon_new,
	t@@ -442,6 +440,47 @@ __global__ void setNSepsilonTop(
	dev_ns_epsilon_new[cellidx] = value;
	}
	}
	+
	+// Set the constant values of epsilon and grad_z(epsilon) at the upper wall, if
	+// it is dynamic (Dirichlet+Neumann). Since the Dirichlet boundary values aren…
	+// transfered during array swapping, the values also need to be written to the
	+// new array of epsilons.
	+__global__ void setNSepsilonAtTopWall(
	+ Float* __restrict__ dev_ns_epsilon,
	+ Float* __restrict__ dev_ns_epsilon_new,
	+ const unsigned int iz,
	+ const Float value,
	+ const Float dp_dz)
	+{
	+ // 3D thread index
	+ const unsigned int x = blockDim.x * blockIdx.x + threadIdx.x;
	+ const unsigned int y = blockDim.y * blockIdx.y + threadIdx.y;
	+ const unsigned int z = blockDim.z * blockIdx.z + threadIdx.z;
	+
	+ const unsigned int cellidx = idx(x,y,z);
	+
	+ // cells containing the wall
	+ if (x < devC_grid.num[0] && y < devC_grid.num[1] && z == iz) {
	+ __syncthreads();
	+ dev_ns_epsilon[cellidx] = value;
	+ dev_ns_epsilon_new[cellidx] = value;
	+ }
	+
	+ // cells above the wall
	+ if (x < devC_grid.num[0] && y < devC_grid.num[1] && z == iz+1) {
	+
	+ // Pressure value in order to obtain hydrostatic pressure distribution
	+ // for Neumann BC. The pressure should equal the value at the top wall
	+ // minus the contribution due to the fluid weight.
	+ // p_iz+1 = p_iz - rho_fgdz
	+ const Float p = value - dp_dz;
	+
	+ __syncthreads();
	+ dev_ns_epsilon[cellidx] = p;
	+ dev_ns_epsilon_new[cellidx] = p;
	+ }
	+}
	+
	__device__ void copyNSvalsDev(
	const unsigned int read,
	const unsigned int write,