Introduction
Introduction Statistics Contact Development Disclaimer Help
tShearmodel=2 refinements - sphere - GPU-based 3D discrete element method algor…
git clone git://src.adamsgaard.dk/sphere
Log
Files
Refs
LICENSE
---
commit 77d03f69783d2598c0920041d85d8d722c2c1868
parent 5e1012c4c642e3a1e740547d141434bfebe3146d
Author: Anders Damsgaard <[email protected]>
Date: Mon, 15 Oct 2012 14:29:37 +0200
Shearmodel=2 refinements
Diffstat:
M python/sphere.py | 101 ++++++++++++++++++++++-------…
M src/constants.cuh | 2 +-
M src/contactsearch.cuh | 6 +++---
M src/datatypes.h | 11 ++++++++---
M src/device.cu | 48 +++++++++++++++++++++++++++++…
M src/integration.cuh | 7 +++++--
M src/main.cpp | 9 ++++++---
7 files changed, 142 insertions(+), 42 deletions(-)
---
diff --git a/python/sphere.py b/python/sphere.py
t@@ -43,7 +43,7 @@ class Spherebin:
self.fixvel = numpy.zeros(self.np, dtype=numpy.float64)
self.xsum = numpy.zeros(self.np, dtype=numpy.float64)
self.radius = numpy.ones(self.np, dtype=numpy.float64)
- self.rho = numpy.ones(self.np, dtype=numpy.float64)
+ self.rho = numpy.ones(self.np, dtype=numpy.float64) * 2600.0
self.k_n = numpy.ones(self.np, dtype=numpy.float64) * 1.16e9
self.k_t = numpy.ones(self.np, dtype=numpy.float64) * 1.16e9
self.k_r = numpy.zeros(self.np, dtype=numpy.float64)
t@@ -62,18 +62,19 @@ class Spherebin:
self.bonds = numpy.ones(self.np*4, dtype=numpy.uint32).reshape(self.np,4…
# Constant, single-value physical parameters
- self.globalparams = numpy.zeros(1, dtype=numpy.int32)
- self.g = numpy.array([0.0, 0.0, -9.80], dtype=numpy.float64)
+ self.globalparams = numpy.ones(1, dtype=numpy.int32)
+ self.g = numpy.array([0.0, 0.0, 0.0], dtype=numpy.float64)
self.kappa = numpy.zeros(1, dtype=numpy.float64)
self.db = numpy.zeros(1, dtype=numpy.float64)
self.V_b = numpy.zeros(1, dtype=numpy.float64)
- self.shearmodel = numpy.ones(1, dtype=numpy.uint32)
+ self.shearmodel = numpy.ones(1, dtype=numpy.uint32) * 2
# Wall data
self.nw = numpy.ones(1, dtype=numpy.uint32) * nw
self.wmode = numpy.zeros(self.nw, dtype=numpy.int32)
self.w_n = numpy.zeros(self.nw*self.nd, dtype=numpy.float64).reshape(s…
- self.w_x = numpy.zeros(self.nw, dtype=numpy.float64)
+ self.w_n[nw-1,nd-1] = -1.0
+ self.w_x = numpy.ones(self.nw, dtype=numpy.float64)
self.w_m = numpy.zeros(self.nw, dtype=numpy.float64)
self.w_vel = numpy.zeros(self.nw, dtype=numpy.float64)
self.w_force = numpy.zeros(self.nw, dtype=numpy.float64)
t@@ -81,9 +82,9 @@ class Spherebin:
# x- and y-boundary behavior
self.periodic = numpy.zeros(1, dtype=numpy.uint32)
- self.gamma_wn = numpy.ones(1, dtype=numpy.float64) * 1e3
- self.gamma_ws = numpy.ones(1, dtype=numpy.float64) * 1e3
- self.gamma_wr = numpy.ones(1, dtype=numpy.float64) * 1e3
+ self.gamma_wn = numpy.ones(1, dtype=numpy.float64) * 1.0e3
+ self.gamma_ws = numpy.ones(1, dtype=numpy.float64) * 1.0e3
+ self.gamma_wr = numpy.ones(1, dtype=numpy.float64) * 1.0e3
# Read binary data
t@@ -390,7 +391,7 @@ class Spherebin:
self.shearmodel[0] = shearmodel
# Initialize upper wall
- self.wmode[0] = 0 # 0: devs, 1: vel
+ self.wmode[0] = 0 # 0: fixed, 1: devs, 2: vel
self.w_n[0,2] = -1.0
self.w_x[0] = self.L[2]
self.w_m[0] = self.rho[0] * self.np * math.pi * r_max**3
t@@ -400,23 +401,34 @@ class Spherebin:
#self.nw[0] = numpy.ones(1, dtype=numpy.uint32) * 1
self.nw = numpy.ones(1, dtype=numpy.uint32) * 1
- # Fit cell number according to world dimensions
- def fitNum(self):
- """ Create cells. cellsize is increased from 2*r_max until it fits
- the horizontal grid.
- Call after setting self.L, self.num and self.radius
+
+ # Generate grid based on particle positions
+ def initGrid(self):
+ """ Initialize grid suitable for the particle positions set previously.
+ The margin parameter adjusts the distance (in no. of max. radii)
+ from the particle boundaries.
"""
+
+
+ # Cell configuration
cellsize_min = 2.1 * numpy.amax(self.radius)
self.num[0] = numpy.ceil((self.L[0]-self.origo[0])/cellsize_min)
self.num[1] = numpy.ceil((self.L[1]-self.origo[1])/cellsize_min)
self.num[2] = numpy.ceil((self.L[2]-self.origo[2])/cellsize_min)
+ if (self.num[0] < 4 or self.num[1] < 4 or self.num[2] < 4):
+ print("Error: The grid must be at least 3 cells in each direction")
+ print(" Grid: x={}, y={}, z={}".format(self.num[0], self.num[1], self.nu…
+
+ # Put upper wall at top boundary
+ self.w_x[0] = self.L[0]
+
# Generate grid based on particle positions
- def initGrid(self, g = numpy.array([0.0, 0.0, -9.80665]),
- margin = numpy.array([2.0, 2.0, 2.0]),
- periodic = 1,
- shearmodel = 2):
+ def initGridAndWorldsize(self, g = numpy.array([0.0, 0.0, -9.80665]),
+ margin = numpy.array([2.0, 2.0, 2.0]),
+ periodic = 1,
+ shearmodel = 2):
""" Initialize grid suitable for the particle positions set previously.
The margin parameter adjusts the distance (in no. of max. radii)
from the particle boundaries.
t@@ -438,8 +450,13 @@ class Spherebin:
numpy.amax(self.x[:,2] + self.radius[:])]) \
+ margin*r_max
- # Fit cell size to world dimensions
- fitNum()
+ cellsize_min = 2.1 * r_max
+ self.num[0] = numpy.ceil((self.L[0]-self.origo[0])/cellsize_min)
+ self.num[1] = numpy.ceil((self.L[1]-self.origo[1])/cellsize_min)
+ self.num[2] = numpy.ceil((self.L[2]-self.origo[2])/cellsize_min)
+
+ if (self.num[0] < 4 or self.num[1] < 4 or self.num[2]):
+ print("Error: The grid must be at least 3 cells in each direction")
self.shearmodel[0] = shearmodel
t@@ -603,7 +620,7 @@ class Spherebin:
self.angpos = numpy.zeros(self.np*self.nd, dtype=numpy.float64).reshape(s…
# Initialize upper wall
- self.wmode[0] = 0
+ self.wmode[0] = 1 # devs
self.w_n[0,2] = -1.0
self.w_x[0] = self.L[2]
self.w_m[0] = self.rho[0] * self.np * math.pi * (cellsize/2.0)**3
t@@ -633,7 +650,7 @@ class Spherebin:
self.angpos = numpy.zeros(self.np*self.nd, dtype=numpy.float64).reshape(s…
# Initialize upper wall
- self.wmode[0] = 1
+ self.wmode[0] = 2 # strain rate controlled
self.w_n[0,2] = -1.0
self.w_x[0] = self.L[2]
self.w_m[0] = self.rho[0] * self.np * math.pi * (cellsize/2.0)**3
t@@ -929,31 +946,57 @@ class Spherebin:
def render(binary,
- out = '~/img_out/rt-out',
+ out = '../img_out/out',
graphicsformat = 'jpg',
resolution = numpy.array([800, 800]),
workhorse = 'GPU',
method = 'pressure',
max_val = 4e3,
- rt_bin = '../raytracer/rt'):
+ rt_bin = '../raytracer/rt',
+ verbose=True):
""" Render target binary using the sphere raytracer.
"""
+ stdout = ""
+ if (verbose == False):
+ stdout = " > /dev/null"
+
# Use raytracer to render the scene into a temporary PPM file
if workhorse == 'GPU':
- subprocess.call(rt_bin + " GPU {0} {1} {2} {3}.ppm {4} {5}" \
- .format(binary, resolution[0], resolution[1], out, method, max_val), s…
+ subprocess.call(rt_bin + " GPU {0} {1} {2} {3}.ppm {4} {5}"\
+ .format(binary, resolution[0], resolution[1], out, method, max_val) + …
if workhorse == 'CPU':
- subprocess.call(rt_bin + " CPU {0} {1} {2} {3}.ppm" \
- .format(binary, resolution[0], resolution[1], out), shell=True)
+ subprocess.call(rt_bin + " CPU {0} {1} {2} {3}.ppm"\
+ .format(binary, resolution[0], resolution[1], out) + stdout, shell=Tru…
# Use ImageMagick's convert command to change the graphics format
- subprocess.call("convert {0}.ppm {0}.{1}" \
+ subprocess.call("convert {0}.ppm {0}.{1}"\
.format(out, graphicsformat), shell=True)
# Delete temporary PPM file
subprocess.call("rm {0}.ppm".format(out), shell=True)
+def renderAll(project,
+ rt_bin = "~/code/sphere/raytracer/rt",
+ out_folder = "../img_out",
+ graphics_format = "png",
+ workhorse = "GPU",
+ method = "pressure",
+ max_val = 10e3,
+ resolution = numpy.array([800, 800])):
+
+ lastfile = status(project)
+
+ for i in range(lastfile+1):
+ # Input binary filename
+ fn = "../output/{0}.output{1}.bin".format(project, i)
+
+ # Output image name (without extension)
+ out = out_folder + "/{0}.output{1}".format(project, i)
+
+ # Call raytracer, also converts to format
+ render(fn, out, graphics_format, resolution, workhorse, method, max_val, r…
+
def visualize(project, method = 'energy', savefig = False, outformat = 'png'):
""" Visualize output from the target project,
diff --git a/src/constants.cuh b/src/constants.cuh
t@@ -9,7 +9,7 @@ __constant__ Float devC_dt; // Time step leng…
__constant__ int devC_global; // Parameter properties, 1: g…
__constant__ Float devC_g[ND]; // Gravitational acceleration …
__constant__ unsigned int devC_np; // Number of particles
-__constant__ char devC_nc; // Max. number of contacts a par…
+__constant__ int devC_nc; // Max. number of contacts a part…
__constant__ unsigned int devC_shearmodel; // Shear force model: 1: viscous, f…
__constant__ Float devC_k_n; // Material normal stiffness
__constant__ Float devC_k_t; // Material tangential stiffness
diff --git a/src/contactsearch.cuh b/src/contactsearch.cuh
t@@ -437,7 +437,7 @@ __global__ void interact(unsigned int* dev_gridParticleInd…
// Loop over all possible contacts, and remove contacts
// that no longer are valid (delta_n > 0.0)
- for (int i = 0; i<(int)devC_nc; ++i) {
+ for (int i = 0; i<devC_nc; ++i) {
mempos = (unsigned int)(idx_a_orig * devC_nc + i);
__syncthreads();
idx_b_orig = dev_contacts[mempos];
t@@ -484,11 +484,11 @@ __global__ void interact(unsigned int* dev_gridParticleI…
dev_delta_t[mempos] = MAKE_FLOAT4(0.0f, 0.0f, 0.0f, 0.0f);
}
- }/* else { // if dev_contacts[mempos] == devC_np
+ } else { // if dev_contacts[mempos] == devC_np
__syncthreads();
// Zero sum of shear displacement in this position
dev_delta_t[mempos] = MAKE_FLOAT4(0.0f, 0.0f, 0.0f, 0.0f);
- } */
+ }
} // Contact loop end
diff --git a/src/datatypes.h b/src/datatypes.h
t@@ -10,10 +10,15 @@
// Enable profiling of kernel runtimes?
-// 0: No
+// 0: No (default)
// 1: Yes
#define PROFILING 0
+// Output information about contacts to stdout?
+// 0: No (default)
+// 1: Yes
+#define CONTACTINFO 0
+
//////////////////////
// TYPE DEFINITIONS //
t@@ -60,8 +65,8 @@ const unsigned int ND = 3;
const Float VERS = 0.25;
// Max. number of contacts per particle
-//const char NC = 16;
-const char NC = 32;
+//const int NC = 16;
+const int NC = 32;
///////////////////////////
diff --git a/src/device.cu b/src/device.cu
t@@ -95,7 +95,7 @@ __host__ void transferToConstantMemory(Particles* p,
cout << "\n Transfering data to constant device memory: ";
cudaMemcpyToSymbol("devC_np", &p->np, sizeof(p->np));
- cudaMemcpyToSymbol("devC_nc", &NC, sizeof(char));
+ cudaMemcpyToSymbol("devC_nc", &NC, sizeof(int));
cudaMemcpyToSymbol("devC_origo", grid->origo, sizeof(Float)*ND);
cudaMemcpyToSymbol("devC_L", grid->L, sizeof(Float)*ND);
cudaMemcpyToSymbol("devC_num", grid->num, sizeof(unsigned int)*ND);
t@@ -217,11 +217,14 @@ __host__ void gpuMain(Float4* host_x,
// Particle contact bookkeeping
unsigned int* dev_contacts;
+ unsigned int* host_contacts = new unsigned int[p->np*NC];
// Particle pair distance correction across periodic boundaries
Float4* dev_distmod;
+ Float4* host_distmod = new Float4[p->np*NC];
// x,y,z contains the interparticle vector, corrected if contact
// is across a periodic boundary.
Float4* dev_delta_t; // Accumulated shear distance of contact
+ Float4* host_delta_t = new Float4[p->np*NC];
// Particle memory size
unsigned int memSizeF = sizeof(Float) * p->np;
t@@ -616,6 +619,14 @@ __host__ void gpuMain(Float4* host_x,
cudaMemcpy(host_w_mvfd, dev_w_mvfd,
sizeof(Float)*params->nw*4, cudaMemcpyDeviceToHost);
+
+ // Contact information
+ if (CONTACTINFO == 1) {
+ cudaMemcpy(host_contacts, dev_contacts, sizeof(unsigned int)*p->np*NC,…
+ cudaMemcpy(host_delta_t, dev_delta_t, memSizeF4*NC, cudaMemcpyDeviceTo…
+ cudaMemcpy(host_distmod, dev_distmod, memSizeF4*NC, cudaMemcpyDeviceTo…
+ }
+
// Pause the CPU thread until all CUDA calls previously issued are compl…
cudaThreadSynchronize();
t@@ -633,6 +644,36 @@ __host__ void gpuMain(Float4* host_x,
exit(EXIT_FAILURE);
}
+ if (CONTACTINFO == 1) {
+ // Write contact information to stdout
+ cout << "\n\n---------------------------\n"
+ << "t = " << time->current << " s.\n"
+ << "---------------------------\n";
+
+ for (int n = 0; n < p->np; ++n) {
+ cout << "\n## Particle " << n << " ##\n";
+
+ cout << "- contacts:\n";
+ for (int nc = 0; nc < NC; ++nc)
+ cout << "[" << nc << "]=" << host_contacts[nc+NC*n] << '\n';
+
+ cout << "\n- delta_t:\n";
+ for (int nc = 0; nc < NC; ++nc)
+ cout << host_delta_t[nc+NC*n].x << '\t'
+ << host_delta_t[nc+NC*n].y << '\t'
+ << host_delta_t[nc+NC*n].z << '\t'
+ << host_delta_t[nc+NC*n].w << '\n';
+
+ cout << "\n- distmod:\n";
+ for (int nc = 0; nc < NC; ++nc)
+ cout << host_distmod[nc+NC*n].x << '\t'
+ << host_distmod[nc+NC*n].y << '\t'
+ << host_distmod[nc+NC*n].z << '\t'
+ << host_distmod[nc+NC*n].w << '\n';
+ }
+ cout << '\n';
+ }
+
// Update status.dat at the interval of filetime
sprintf(file,"%s/output/%s.status.dat", cwd, inputbin);
fp = fopen(file, "w");
t@@ -726,5 +767,10 @@ __host__ void gpuMain(Float4* host_x,
cudaFree(dev_w_force);
cudaFree(dev_w_force_partial);
+ // Contact info arrays
+ delete [] host_contacts;
+ delete [] host_distmod;
+ delete [] host_delta_t;
+
printf("Done\n");
} /* EOF */
diff --git a/src/integration.cuh b/src/integration.cuh
t@@ -181,9 +181,12 @@ __global__ void integrateWalls(Float4* dev_w_nx,
// write-after-read, or write-after-write hazards.
Float4 w_nx = dev_w_nx[idx];
Float4 w_mvfd = dev_w_mvfd[idx];
- int wmode = devC_wmode[idx]; // Wall BC, 0: devs, 1: vel
+ int wmode = devC_wmode[idx]; // Wall BC, 0: fixed, 1: devs, 2: vel
Float acc;
+ if (wmode == 0) // Wall fixed: do nothing
+ return;
+
// Find the final sum of forces on wall
w_mvfd.z = 0.0f;
for (int i=0; i<blocksPerGrid; ++i) {
t@@ -201,7 +204,7 @@ __global__ void integrateWalls(Float4* dev_w_nx,
acc = (w_mvfd.z + N)/w_mvfd.x;
// If Wall BC is controlled by velocity, it should not change
- if (wmode == 1) {
+ if (wmode == 2) {
acc = 0.0f;
}
diff --git a/src/main.cpp b/src/main.cpp
t@@ -180,7 +180,7 @@ int main(int argc, char *argv[])
p.es = new Float[p.np]; // Total shear energy dissipation
p.ev = new Float[p.np]; // Total viscous energy dissipation
p.p = new Float[p.np]; // Pressure excerted onto particle
- params.wmode = new int[MAXWALLS]; // Wall BC's, 0: devs, 1: vel
+ params.wmode = new int[MAXWALLS]; // Wall BC's, 0: fixed, 1: devs, 2: vel
// Allocate Float4 host arrays
Float4 *host_x = new Float4[p.np]; // Center coordinates for each part…
t@@ -300,6 +300,7 @@ int main(int argc, char *argv[])
if (fread(&params.g[i], sizeof(params.g[i]), 1, fp) != 1)
exit(1);
}
+
if (fread(&params.kappa, sizeof(params.kappa), 1, fp) != 1)
exit(1);
if (fread(&params.db, sizeof(params.db), 1, fp) != 1)
t@@ -328,7 +329,7 @@ int main(int argc, char *argv[])
// Read wall data
for (j=0; j<params.nw; ++j) {
- // Wall condition mode: 0: devs, 1: vel
+ // Wall condition mode: 0: fixed, 1: devs, 2: vel
if (fread(&params.wmode[j], sizeof(params.wmode[j]), 1, fp) != 1)
exit(1);
t@@ -409,8 +410,10 @@ int main(int argc, char *argv[])
cout << " - Top BC: ";
if (params.wmode[0] == 0)
- cout << "Deviatoric stress\n";
+ cout << "Fixed\n";
else if (params.wmode[0] == 1)
+ cout << "Deviatoric stress\n";
+ else if (params.wmode[0] == 2)
cout << "Velocity\n";
else {
cerr << "Top boundary condition not recognized!\n";
You are viewing proxied material from mx1.adamsgaard.dk. The copyright of proxied material belongs to its original authors. Any comments or complaints in relation to proxied material should be directed to the original authors of the content concerned. Please see the disclaimer for more details.