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	tadd rs2 experiment generation script - sphere - GPU-based 3D discrete element …
	git clone git://src.adamsgaard.dk/sphere
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	---
	commit bf598ca922f970507d22b8e7af93fc08c32b5299
	parent f716750528e004ea166228f06b59f02b7c5e8e59
	Author: Anders Damsgaard Christensen <[email protected]>
	Date: Fri, 17 Jun 2016 09:51:12 -0700

	add rs2 experiment generation script

	Diffstat:
	A python/generate-rate-state-scripts… \| 172 +++++++++++++++++++++++++++…

	1 file changed, 172 insertions(+), 0 deletions(-)
	---
	diff --git a/python/generate-rate-state-scripts-comet-rs2.py b/python/generate-…
	t@@ -0,0 +1,172 @@
	+#!/usr/bin/env python
	+
	+# rs2: identical to rs1 but step postponed 5s
	+# wall viscosity
	+
	+# Account and cluster information
	+# https://portal.xsede.org/sdsc-comet
	+# https://www.sdsc.edu/support/user_guides/comet.html
	+account = 'csd492' # from `show_accounts`
	+jobname_prefix = 'rs2-'
	+walltime = '2-0' # hours:minutes:seconds or days-hours
	+partition = 'gpu-shared'
	+no_gpus = 1
	+no_nodes = 1
	+ntasks_per_node = 1
	+folder = '~/code/sphere/python'
	+
	+
	+# Simulation parameter values
	+effective_stresses = [10e3, 20e3, 100e3, 200e3, 1000e3, 2000e3]
	+velfacs = [0.1, 1.0, 10.0]
	+mu_s_vals = [0.5]
	+mu_d_vals = [0.5]
	+
	+
	+# Script generating functions
	+
	+def generate_slurm_script(jobname):
	+
	+ script = '''#!/bin/bash
	+#SBATCH -A {account}
	+#SBATCH --job-name="{jobname}"
	+#SBATCH --output="{jobname}.%j.%N.out"
	+#SBATCH --time={walltime}
	+#SBATCH --partition={partition}
	+#SBATCH --gres=gpu:{no_gpus}
	+#SBATCH --nodes={no_nodes}
	+#SBATCH --ntasks-per-node={ntasks_per_node}
	+#SBATCH --export=ALL
	+
	+echo Job start `whoami`@`hostname`, `date`
	+module load cmake
	+module load cuda/7.0
	+module load python
	+module load scipy
	+
	+cd {folder}
	+python ./{jobname}.py
	+
	+echo Job end `whoami`@`hostname`, `date`
	+'''.format(account=account,
	+ jobname=jobname,
	+ walltime=walltime,
	+ partition=partition,
	+ no_gpus=no_gpus,
	+ no_nodes=no_nodes,
	+ ntasks_per_node=ntasks_per_node,
	+ folder=folder)
	+ with open(jobname + '.sh', 'w') as file:
	+ file.write(script)
	+
	+
	+def generate_slurm_continue_script(jobname):
	+
	+ script = '''#!/bin/bash
	+#SBATCH -A {account}
	+#SBATCH --job-name="{jobname}"
	+#SBATCH --output="{jobname}.%j.%N.out"
	+#SBATCH --time={walltime}
	+#SBATCH --partition={partition}
	+#SBATCH --gres=gpu:{no_gpus}
	+#SBATCH --nodes={no_nodes}
	+#SBATCH --ntasks-per-node={ntasks_per_node}
	+#SBATCH --export=ALL
	+
	+echo Job start `whoami`@`hostname`, `date`
	+module load cmake
	+module load cuda/7.0
	+module load python
	+module load scipy
	+
	+cd {folder}
	+python ./continue_sim.py {jobname} 0
	+
	+echo Job end `whoami`@`hostname`, `date`
	+'''.format(account=account,
	+ jobname=jobname,
	+ walltime=walltime,
	+ partition=partition,
	+ no_gpus=no_gpus,
	+ no_nodes=no_nodes,
	+ ntasks_per_node=ntasks_per_node,
	+ folder=folder)
	+ with open(jobname + '-cont.sh', 'w') as file:
	+ file.write(script)
	+
	+
	+# Generate scripts for sphere
	+def generate_simulation_script(jobname, effective_stress, velfac, mu_s, mu_d):
	+
	+ script = '''#!/usr/bin/env python
	+import sphere
	+import numpy
	+
	+# load consolidated granular assemblage
	+sim = sphere.sim(fluid=False)
	+cons_jobname = 'cons-1e4-' + '{{}}Pa'.format({effective_stress})
	+sim = sphere.sim(cons_jobname, fluid=False)
	+sim.readlast()
	+sim.id('{jobname}')
	+
	+sim.checkerboardColors(nx=6, ny=6, nz=6)
	+sim.cleanup()
	+sim.adjustUpperWall()
	+sim.zeroKinematics()
	+
	+sim.shear(1.0/20.0 * {velfac})
	+
	+sim.setStiffnessNormal(1.16e7)
	+sim.setStiffnessTangential(1.16e7)
	+sim.setStaticFriction({mu_s})
	+sim.setDynamicFriction({mu_d})
	+sim.setDampingNormal(0.0)
	+sim.setDampingTangential(0.0)
	+
	+sim.w_sigma0[0] = {effective_stress}
	+sim.w_m[0] = sim.totalMass()
	+sim.gamma_wn[0] = 0.0
	+
	+sim.initTemporal(total = 20.0, file_dt = 0.01, epsilon=0.07)
	+
	+I = numpy.nonzero(sim.fixvel > 0)
	+sim.fixvel[I] = 8.0 # step-wise velocity change when fixvel in ]5.0; 10.0[
	+
	+sim.run(dry=True)
	+sim.run(device=0)
	+sim.writeVTKall()
	+sim.visualize('shear')
	+'''.format(jobname=jobname,
	+ effective_stress=effective_stress,
	+ velfac=velfac,
	+ mu_s=mu_s,
	+ mu_d=mu_d)
	+
	+ with open(jobname + '.py', 'w') as file:
	+ file.write(script)
	+
	+
	+# Generate scripts
	+for effective_stress in effective_stresses:
	+ for velfac in velfacs:
	+ for mu_s in mu_s_vals:
	+ for mu_d in mu_s_vals:
	+
	+ jobname = jobname_prefix + '{}Pa-v={}-mu_s={}-mu_d={}'.format(
	+ effective_stress,
	+ velfac,
	+ mu_s,
	+ mu_d)
	+
	+ print(jobname)
	+
	+ # Generate scripts for slurm, submit with `sbatch <script>`
	+ generate_slurm_script(jobname)
	+
	+ generate_slurm_continue_script(jobname)
	+
	+ generate_simulation_script(jobname,
	+ effective_stress,
	+ velfac,
	+ mu_s,
	+ mu_d)