tadded template for shear experiments - 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 1fcb3abb988953ceb7db153556a3e25b1b9cb080
 (DIR) parent dfece9039322d71d77530a83ae1fb60c6b364ae2
 (HTM) Author: Anders Damsgaard <anders.damsgaard@geo.au.dk>
       Date:   Fri,  4 Jul 2014 19:15:25 +0200
       
       added template for shear experiments
       
       Diffstat:
         A python/shear-1-2-3.sh               |      49 +++++++++++++++++++++++++++++++
         A python/shear-4-5-6.sh               |      49 +++++++++++++++++++++++++++++++
         A python/shear1.py                    |      45 +++++++++++++++++++++++++++++++
       
       3 files changed, 143 insertions(+), 0 deletions(-)
       ---
 (DIR) diff --git a/python/shear-1-2-3.sh b/python/shear-1-2-3.sh
       t@@ -0,0 +1,49 @@
       +#!/bin/sh
       +#PBS -N shear-1-2-3
       +#PBS -l nodes=1:ppn=3
       +#PBS -l walltime=1920:00:00
       +#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 && make test
       +cd python
       +python shear1.py &
       +python shear2.py &
       +python shear3.py &
       +wait
       +
       +#cp $WORKDIR/output/* $ORIGDIR/output/
       +
       +echo "End at `date`"
 (DIR) diff --git a/python/shear-4-5-6.sh b/python/shear-4-5-6.sh
       t@@ -0,0 +1,49 @@
       +#!/bin/sh
       +#PBS -N shear-4-5-6
       +#PBS -l nodes=1:ppn=3
       +#PBS -l walltime=1920:00:00
       +#PBS -q qfermi
       +#PBS -M adc@geo.au.dk
       +#PBS -m abe
       +
       +# Grendel CUDA
       +source /com/gcc/4.6.4/load.sh
       +CUDAPATH=/com/cuda/5.5.22
       +export PATH=$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 && make test
       +cd python
       +python shear4.py &
       +python shear5.py &
       +python shear6.py &
       +wait
       +
       +#cp $WORKDIR/output/* $ORIGDIR/output/
       +
       +echo "End at `date`"
 (DIR) diff --git a/python/shear1.py b/python/shear1.py
       t@@ -0,0 +1,45 @@
       +#!/usr/bin/env python
       +import sphere
       +import numpy
       +
       +for sigma0 in [10.0e3, 20.0e3]:
       +
       +    sim = sphere.sim()
       +    sim.sid = 'diffusivity-sigma0=' + str(sigma0)
       +    sim.readlast()
       +    sim.sid = 'shear-sigma0=' + str(sigma0)
       +
       +    # 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()
       +    shear_strain = 1.0
       +    total_time = 20.0
       +    sim.shear(shear_strain_rate = shear_strain/total_time)
       +    sim.shear(normal_stress = 10.0e3)
       +    sim.initFluid(mu = 17.87e-4, p = 1.0e5, hydrostatic = True)
       +    sim.setFluidBottomNoFlow()
       +    sim.setFluidTopFixedPressure()
       +    sim.setDEMstepsPerCFDstep(10)
       +    sim.initTemporal(total = total_time, file_dt = 0.01, epsilon=0.07)
       +    sim.run(dry=True)
       +    sim.run()
       +    #sim.writeVTKall()
       +    sim.visualize('walls')
       +    sim.visualize('shear')
       +    sim.visualize('fluid-pressure')