tnew scripts to test diffusivity - sphere - GPU-based 3D discrete element method algorithm with optional fluid coupling
 (HTM) git clone git://src.adamsgaard.dk/sphere
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       ---
 (DIR) commit 691512da76d9cead278563ec13a6805fb263b530
 (DIR) parent 1699089cd735a2dea713d15dd7dd4108f9631767
 (HTM) Author: Anders Damsgaard <anders.damsgaard@geo.au.dk>
       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(-)
       ---
 (DIR) 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
 (DIR) 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 adc@geo.au.dk
       +#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`"