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	tMerge branch 'varN' Sinusoidal modulation of N, choose w_devs_A=0.0 to disable…
	git clone git://src.adamsgaard.dk/sphere
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	---
	commit 158d3182d4b897921eb8909106d2ab118a8c9a0f
	parent 5dbc0a8544a6dfa40505639271fb7ca1a1834be5
	Author: Anders Damsgaard <[email protected]>
	Date: Sun, 17 Mar 2013 21:25:27 +0100

	Merge branch 'varN'
	Sinusoidal modulation of N, choose w_devs_A=0.0 to disable

	Diffstat:
	M python/sphere.py \| 19 +++++++++++++++++--
	M src/datatypes.h \| 2 ++
	M src/device.cu \| 3 ++-
	M src/file_io.cpp \| 9 ++++++++-
	M src/integration.cuh \| 11 +++++++----
	M tests/pytestutils.py \| 2 +-
	D tests/sphere.py \| 2 --

	7 files changed, 37 insertions(+), 11 deletions(-)
	---
	diff --git a/python/sphere.py b/python/sphere.py
	t@@ -98,6 +98,8 @@ class Spherebin:
	self.w_vel = numpy.zeros(self.nw, dtype=numpy.float64)
	self.w_force = numpy.zeros(self.nw, dtype=numpy.float64)
	self.w_devs = numpy.zeros(self.nw, dtype=numpy.float64)
	+ self.w_devs_A = numpy.zeros(1, dtype=numpy.float64)
	+ self.w_devs_f = numpy.zeros(1, dtype=numpy.float64)

	self.lambda_bar = numpy.ones(1, dtype=numpy.float64)
	self.nb0 = numpy.zeros(1, dtype=numpy.uint32)
	t@@ -161,6 +163,8 @@ class Spherebin:
	(self.w_vel == other.w_vel).all() and\
	(self.w_force == other.w_force).all() and\
	(self.w_devs == other.w_devs).all() and\
	+ self.w_devs_A == other.w_devs_A and\
	+ self.w_devs_f == other.w_devs_f and\
	self.gamma_wn == other.gamma_wn and\
	self.gamma_wt == other.gamma_wt and\
	self.lambda_bar == other.lambda_bar and\
	t@@ -179,7 +183,7 @@ class Spherebin:



	- def readbin(self, targetbin, verbose = True, bonds = True):
	+ def readbin(self, targetbin, verbose = True, bonds = True, devsmod = True):
	'Reads a target SPHERE binary file'

	fh = None
	t@@ -285,6 +289,9 @@ class Spherebin:
	self.w_vel[i] = numpy.fromfile(fh, dtype=numpy.float64, coun…
	self.w_force[i] = numpy.fromfile(fh, dtype=numpy.float64, coun…
	self.w_devs[i] = numpy.fromfile(fh, dtype=numpy.float64, coun…
	+ if (devsmod == True):
	+ self.w_devs_A = numpy.fromfile(fh, dtype=numpy.float64, count=…
	+ self.w_devs_f = numpy.fromfile(fh, dtype=numpy.float64, count=…

	if (bonds == True):
	# Inter-particle bonds
	t@@ -391,6 +398,8 @@ class Spherebin:
	fh.write(self.w_vel[i].astype(numpy.float64))
	fh.write(self.w_force[i].astype(numpy.float64))
	fh.write(self.w_devs[i].astype(numpy.float64))
	+ fh.write(self.w_devs_A.astype(numpy.float64))
	+ fh.write(self.w_devs_f.astype(numpy.float64))

	fh.write(self.lambda_bar.astype(numpy.float64))
	fh.write(self.nb0.astype(numpy.uint32))
	t@@ -1043,6 +1052,10 @@ class Spherebin:
	# Increment the number of bonds with one
	self.nb0 += 1

	+ def currentDevs(self):
	+ ''' Return current magnitude of the deviatoric normal stress '''
	+ return w_devs[0] + w_devs_A * numpy.sin(2.0 * numpy.pi * self.time_cur…
	+

	def energy(self, method):
	""" Calculate the sum of the energy components of all particles.
	t@@ -1180,8 +1193,10 @@ class Spherebin:
	if (cudamemcheck == True):
	cudamemchk = "cuda-memcheck "

	+ status = subprocess.call("cd ..; " + valgrindbin + cudamemchk + "./sph…

	- subprocess.call("cd ..; " + valgrindbin + cudamemchk + "./sphere " + q…
	+ if (status != 0):
	+ raise Exception("Error, the sphere run returned with status " + st…


	def torqueScript(self,
	diff --git a/src/datatypes.h b/src/datatypes.h
	t@@ -94,6 +94,8 @@ struct Params {
	unsigned int nb0; // Number of inter-particle bonds at t=0
	Float sigma_b; // Bond tensile strength
	Float tau_b; // Bond shear strength
	+ Float devs_A; // Amplitude of modulations in deviatoric normal str…
	+ Float devs_f; // Frequency of modulations in deviatoric normal str…
	};

	// Structure containing wall parameters
	diff --git a/src/device.cu b/src/device.cu
	t@@ -801,7 +801,8 @@ __host__ void DEM::startTime()
	dev_walls_wmode,
	dev_walls_force_partial,
	dev_walls_vel0,
	- blocksPerGrid);
	+ blocksPerGrid,
	+ time.current);
	}

	// Synchronization point
	diff --git a/src/file_io.cpp b/src/file_io.cpp
	t@@ -204,13 +204,18 @@ void DEM::readbin(const char *target)
	ifs.read(as_bytes(walls.mvfd[i].z), sizeof(Float));
	ifs.read(as_bytes(walls.mvfd[i].w), sizeof(Float));
	}
	+ ifs.read(as_bytes(params.devs_A), sizeof(params.devs_A));
	+ ifs.read(as_bytes(params.devs_f), sizeof(params.devs_f));
	+

	// Read bond parameters
	ifs.read(as_bytes(params.lambda_bar), sizeof(params.lambda_bar));
	ifs.read(as_bytes(params.nb0), sizeof(params.nb0));
	ifs.read(as_bytes(params.sigma_b), sizeof(params.sigma_b));
	ifs.read(as_bytes(params.tau_b), sizeof(params.tau_b));
	- k.bonds = new uint2[params.nb0];
	+ std::cout << "\nparams.nb0 = " << params.nb0 << std::endl;
	+ if (params.nb0 > 0)
	+ k.bonds = new uint2[params.nb0];
	k.bonds_delta = new Float4[np];
	k.bonds_omega = new Float4[np];
	for (i = 0; i<params.nb0; ++i) {
	t@@ -363,6 +368,8 @@ void DEM::writebin(const char *target)
	ofs.write(as_bytes(walls.mvfd[i].z), sizeof(Float));
	ofs.write(as_bytes(walls.mvfd[i].w), sizeof(Float));
	}
	+ ofs.write(as_bytes(params.devs_A), sizeof(params.devs_A));
	+ ofs.write(as_bytes(params.devs_f), sizeof(params.devs_f));

	// 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@@ -221,12 +221,14 @@ __global__ void summation(Float* in, Float *out)
	}

	// Update wall positions
	-__global__ void integrateWalls(Float4* dev_walls_nx,
	+__global__ void integrateWalls(
	+ Float4* dev_walls_nx,
	Float4* dev_walls_mvfd,
	int* dev_walls_wmode,
	Float* dev_walls_force_partial,
	Float* dev_walls_vel0,
	- unsigned int blocksPerGrid)
	+ unsigned int blocksPerGrid,
	+ Float t_current)
	{
	unsigned int idx = threadIdx.x + blockIdx.x * blockDim.x; // Thread id

	t@@ -253,10 +255,11 @@ __global__ void integrateWalls(Float4* dev_walls_nx,

	// Normal load = Deviatoric stress times wall surface area,
	// directed downwards.
	- Float N = -w_mvfd.wdevC_grid.L[0]devC_grid.L[1];
	+ Float sigma_0 = w_mvfd.w + devC_params.devs_A * sin(2.0 * 3.141596654 …
	+ Float N = -sigma_0devC_grid.L[0]devC_grid.L[1];

	// Calculate resulting acceleration of wall
	- // (Wall mass is stored in w component of position Float4)
	+ // (Wall mass is stored in x component of position Float4)
	acc = (w_mvfd.z + N)/w_mvfd.x;

	// If Wall BC is controlled by velocity, it should not change
	diff --git a/tests/pytestutils.py b/tests/pytestutils.py
	t@@ -1,6 +1,6 @@
	#!/usr/bin/env python

	-from sphere import *
	+from ../python/sphere import *
	import subprocess
	import sys

	diff --git a/tests/sphere.py b/tests/sphere.py
	t@@ -1 +0,0 @@
	-../python/sphere.py
	-\ No newline at end of file