tnew scripts to test diffusivity - sphere - GPU-based 3D discrete element metho… | |
git clone git://src.adamsgaard.dk/sphere | |
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LICENSE | |
--- | |
commit 691512da76d9cead278563ec13a6805fb263b530 | |
parent 1699089cd735a2dea713d15dd7dd4108f9631767 | |
Author: Anders Damsgaard <[email protected]> | |
Date: Thu, 14 Aug 2014 10:58:46 +0200 | |
new scripts to test diffusivity | |
Diffstat: | |
A python/diffusivity-test.py | 74 +++++++++++++++++++++++++++++… | |
A python/diffusivity-test.sh | 49 +++++++++++++++++++++++++++++… | |
2 files changed, 123 insertions(+), 0 deletions(-) | |
--- | |
diff --git a/python/diffusivity-test.py b/python/diffusivity-test.py | |
t@@ -0,0 +1,74 @@ | |
+#!/usr/bin/env python | |
+import sphere | |
+import numpy | |
+import sys | |
+ | |
+# launch with: | |
+# $ python diffusivity-test <DEVICE> <C_PHI> <C_GRAD_P> | |
+ | |
+# Unique simulation parameters | |
+device = int(sys.argv[1]) | |
+c_phi = float(sys.argv[2]) | |
+c_grad_p = float(sys.argv[3]) | |
+ | |
+# Unconsolidated input | |
+sim = sphere.sim('diffusivity-relax') | |
+sim.readlast() | |
+ | |
+# Load sequence as per Bowles 1992, p. 135, units: Pa. dp/p = 1 | |
+sigma0_list = numpy.array([5.0e3, 10.0e3, 20.0e3, 40.0e3, 80.0e3, 160.0e3]) | |
+ | |
+i = 0 | |
+for sigma0 in sigma0_list: | |
+ | |
+ # Read previous output if not first load test | |
+ if (i > 0): | |
+ sim.sid = 'cons-sigma0=' + str(sigma0_list[i-1]) + '-c_phi=' + \ | |
+ str(c_phi) + '-c_grad_p=' + str(c_grad_p) | |
+ sim.readlast() | |
+ | |
+ sim.sid = 'cons-sigma0=' + str(sigma0) + '-c_phi=' + str(c_phi) + \ | |
+ '-c_grad_p=' + str(c_grad_p) | |
+ print('\n###### ' + sim.sid + ' ######') | |
+ | |
+ # Checkerboard colors | |
+ x_min = numpy.min(sim.x[:,0]) | |
+ x_max = numpy.max(sim.x[:,0]) | |
+ y_min = numpy.min(sim.x[:,1]) | |
+ y_max = numpy.max(sim.x[:,1]) | |
+ z_min = numpy.min(sim.x[:,2]) | |
+ z_max = numpy.max(sim.x[:,2]) | |
+ color_nx = 6 | |
+ color_ny = 6 | |
+ color_nz = 6 | |
+ for i in range(sim.np): | |
+ ix = numpy.floor((sim.x[i,0] - x_min)/(x_max/color_nx)) | |
+ iy = numpy.floor((sim.x[i,1] - y_min)/(y_max/color_ny)) | |
+ iz = numpy.floor((sim.x[i,2] - z_min)/(z_max/color_nz)) | |
+ sim.color[i] = (-1)**ix + (-1)**iy + (-1)**iz | |
+ | |
+ sim.cleanup() | |
+ sim.adjustUpperWall() | |
+ sim.zeroKinematics() | |
+ | |
+ sim.consolidate(normal_stress = sigma0) | |
+ | |
+ sim.initFluid(mu = 17.87e-4, p = 1.0e5, hydrostatic = True) | |
+ sim.setFluidBottomNoFlow() | |
+ sim.setFluidTopFixedPressure() | |
+ sim.setDEMstepsPerCFDstep(10) | |
+ sim.setMaxIterations(2e5) | |
+ sim.initTemporal(total = 5.0, file_dt = 0.01, epsilon=0.07) | |
+ | |
+ # Fix lowermost particles | |
+ dz = sim.L[2]/sim.num[2] | |
+ I = numpy.nonzero(sim.x[:,2] < 1.5*dz) | |
+ sim.fixvel[I] = 1 | |
+ | |
+ sim.run(dry=True) | |
+ sim.run(device=0) | |
+ #sim.writeVTKall() | |
+ sim.visualize('walls') | |
+ sim.visualize('fluid-pressure') | |
+ | |
+ i += 1 | |
diff --git a/python/diffusivity-test.sh b/python/diffusivity-test.sh | |
t@@ -0,0 +1,49 @@ | |
+#!/bin/sh | |
+#PBS -N diffusivity-test | |
+#PBS -l nodes=1:ppn=3 | |
+#PBS -l walltime=19200:00:00 | |
+#PBS -q qfermi | |
+#PBS -M [email protected] | |
+#PBS -m abe | |
+ | |
+# Grendel CUDA | |
+source /com/gcc/4.6.4/load.sh | |
+CUDAPATH=/com/cuda/5.5.22 | |
+export PATH=$HOME/bin:$PATH | |
+export PATH=$CUDAPATH/bin:$PATH | |
+export LD_LIBRARY_PATH=$CUDAPATH/lib64:$CUDAPATH/lib:$LD_LIBRARY_PATH | |
+ | |
+# Manually installed Python modules | |
+export PYTHONPATH=$HOME/.local/lib/python:$PYTHONPATH | |
+export PYTHONPATH=$HOME/.local/lib64/python:$PYTHONPATH | |
+ | |
+# Manually installed Python | |
+#export PATH=/home/adc/.local/bin:$PATH | |
+ | |
+# Shared Python2.7 | |
+PYTHON=/com/python/2.7.6 | |
+export PYTHONPATH=$PYTHON/lib:$PYTHONPATH | |
+export PATH=$PYTHON/bin:$PATH | |
+ | |
+echo "`whoami`@`hostname`" | |
+echo "Start at `date`" | |
+ | |
+ORIGDIR=/home/adc/code/sphere | |
+#WORKDIR=/scratch/$PBS_JOBID | |
+WORKDIR=$ORIGDIR | |
+ | |
+#cp -r $ORIGDIR/* $WORKDIR | |
+ | |
+cd $WORKDIR | |
+nvidia-smi | |
+rm CMakeCache.txt | |
+cmake . && make | |
+cd python | |
+python diffusivity-test.py 0 1.0 1.00 & | |
+python diffusivity-test.py 1 1.0 0.10 & | |
+python diffusivity-test.py 2 1.0 0.01 & | |
+wait | |
+ | |
+#cp $WORKDIR/output/* $ORIGDIR/output/ | |
+ | |
+echo "End at `date`" |