tMerge branch 'master' of github.com:anders-dc/sphere - sphere - GPU-based 3D discrete element method algorithm with optional fluid coupling
(HTM) git clone git://src.adamsgaard.dk/sphere
(DIR) Log
(DIR) Files
(DIR) Refs
(DIR) LICENSE
---
(DIR) commit 7626d19392ecba63c4b2e5f4d419e8423d7a90a0
(DIR) parent f8c44ac1a8fcdc4d6d1112db0cc1467597912e69
(HTM) Author: Anders Damsgaard <anders.damsgaard@geo.au.dk>
Date: Mon, 11 Aug 2014 10:16:44 +0200
Merge branch 'master' of github.com:anders-dc/sphere
Diffstat:
A python/diffusivity-c_grad_p=0.01.sh | 49 +++++++++++++++++++++++++++++++
A python/diffusivity-c_grad_p=0.1.sh | 49 +++++++++++++++++++++++++++++++
A python/diffusivity-c_grad_p=0.5.sh | 49 +++++++++++++++++++++++++++++++
A python/diffusivity-c_phi=0.1.sh | 49 +++++++++++++++++++++++++++++++
A python/diffusivity-c_phi=0.5.sh | 49 +++++++++++++++++++++++++++++++
A python/diffusivity-starter.py | 53 ++++++++++++++++++++++++++++++
6 files changed, 298 insertions(+), 0 deletions(-)
---
(DIR) diff --git a/python/diffusivity-c_grad_p=0.01.sh b/python/diffusivity-c_grad_p=0.01.sh
t@@ -0,0 +1,49 @@
+#!/bin/sh
+#PBS -N diffusivity-c_grad_p=0.01
+#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
+cd python
+python diffusivity-starter.py 0 1.0 0.01 10.0e3 20.0e3 &
+python diffusivity-starter.py 1 1.0 0.01 40.0e3 60.0e3 &
+python diffusivity-starter.py 2 1.0 0.01 80.0e3 120.0e3 &
+wait
+
+#cp $WORKDIR/output/* $ORIGDIR/output/
+
+echo "End at `date`"
(DIR) diff --git a/python/diffusivity-c_grad_p=0.1.sh b/python/diffusivity-c_grad_p=0.1.sh
t@@ -0,0 +1,49 @@
+#!/bin/sh
+#PBS -N diffusivity-c_grad_p=0.1
+#PBS -l nodes=1:ppn=3
+#PBS -l walltime=1920:00:00
+#PBS -q qfermi
+#PBS -M adc@geo.au.dk
+#PBS -m abe
+
+# Grendel CUDA
+source /com/gcc/4.6.4/load.sh
+CUDAPATH=/com/cuda/5.5.22
+export PATH=$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
+cd python
+python diffusivity-starter.py 0 1.0 0.1 10.0e3 20.0e3 &
+python diffusivity-starter.py 1 1.0 0.1 40.0e3 60.0e3 &
+python diffusivity-starter.py 2 1.0 0.1 80.0e3 120.0e3 &
+wait
+
+#cp $WORKDIR/output/* $ORIGDIR/output/
+
+echo "End at `date`"
(DIR) diff --git a/python/diffusivity-c_grad_p=0.5.sh b/python/diffusivity-c_grad_p=0.5.sh
t@@ -0,0 +1,49 @@
+#!/bin/sh
+#PBS -N diffusivity-c_grad_p=0.5
+#PBS -l nodes=1:ppn=3
+#PBS -l walltime=1920:00:00
+#PBS -q qfermi
+#PBS -M adc@geo.au.dk
+#PBS -m abe
+
+# Grendel CUDA
+source /com/gcc/4.6.4/load.sh
+CUDAPATH=/com/cuda/5.5.22
+export PATH=$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
+cd python
+python diffusivity-starter.py 0 1.0 0.5 10.0e3 20.0e3 &
+python diffusivity-starter.py 1 1.0 0.5 40.0e3 60.0e3 &
+python diffusivity-starter.py 2 1.0 0.5 80.0e3 120.0e3 &
+wait
+
+#cp $WORKDIR/output/* $ORIGDIR/output/
+
+echo "End at `date`"
(DIR) diff --git a/python/diffusivity-c_phi=0.1.sh b/python/diffusivity-c_phi=0.1.sh
t@@ -0,0 +1,49 @@
+#!/bin/sh
+#PBS -N diffusivity-c_phi=0.1
+#PBS -l nodes=1:ppn=3
+#PBS -l walltime=1920:00:00
+#PBS -q qfermi
+#PBS -M adc@geo.au.dk
+#PBS -m abe
+
+# Grendel CUDA
+source /com/gcc/4.6.4/load.sh
+CUDAPATH=/com/cuda/5.5.22
+export PATH=$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
+cd python
+python diffusivity-starter.py 0 0.1 1.0 10.0e3 20.0e3 &
+python diffusivity-starter.py 1 0.1 1.0 40.0e3 60.0e3 &
+python diffusivity-starter.py 2 0.1 1.0 80.0e3 120.0e3 &
+wait
+
+#cp $WORKDIR/output/* $ORIGDIR/output/
+
+echo "End at `date`"
(DIR) diff --git a/python/diffusivity-c_phi=0.5.sh b/python/diffusivity-c_phi=0.5.sh
t@@ -0,0 +1,49 @@
+#!/bin/sh
+#PBS -N diffusivity-c_phi=0.5
+#PBS -l nodes=1:ppn=3
+#PBS -l walltime=1920:00:00
+#PBS -q qfermi
+#PBS -M adc@geo.au.dk
+#PBS -m abe
+
+# Grendel CUDA
+source /com/gcc/4.6.4/load.sh
+CUDAPATH=/com/cuda/5.5.22
+export PATH=$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
+cd python
+python diffusivity-starter.py 0 0.5 1.0 10.0e3 20.0e3 &
+python diffusivity-starter.py 1 0.5 1.0 40.0e3 60.0e3 &
+python diffusivity-starter.py 2 0.5 1.0 80.0e3 120.0e3 &
+wait
+
+#cp $WORKDIR/output/* $ORIGDIR/output/
+
+echo "End at `date`"
(DIR) diff --git a/python/diffusivity-starter.py b/python/diffusivity-starter.py
t@@ -0,0 +1,53 @@
+#!/usr/bin/env python
+import sphere
+import numpy
+import sys
+
+# launch with:
+# $ python diffusivity-starter <DEVICE> <C_PHI> <C_GRAD_P> <DP_1, DP_2, ...>
+
+for sigma0_str in sys.argv[4:]:
+
+ sigma0 = float(sigma0_str)
+ device = int(sys.argv[1])
+ c_phi = float(sys.argv[2])
+ c_grad_p = float(sys.argv[3])
+
+ sim = sphere.sim('diffusivity-relax')
+ sim.readlast()
+
+ sim.sid = 'permeability-dp=' + str(dp) + '-c_phi=' + str(c_phi) + \
+ '-c_grad_p=' + str(c_grad_p)
+ print(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 = 10.0e3)
+ 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)
+ sim.run(dry=True)
+ sim.run(device=0)
+ #sim.writeVTKall()
+ sim.visualize('walls')
+ sim.visualize('fluid-pressure')