run_paper.sh

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#!/bin/bash
 
# Get file name
if [ -z ${1+x} ]; then
  MESHFILE=1dTest.cub
else
  MESHFILE=$1
fi
 
# Get config file name
if [ -z ${2+x} ]; then
  CONFIGFILE=paper.cfg
else
  CONFIGFILE=$2
fi
 
# Get numbet of processors
if [ -z ${3+x} ]; then
  NBPROCS=4
else
  NBPROCS=$3
fi
 
# Get step size
if [ -z ${4+x} ]; then
  DT=0.0001
else
  DT=$4
fi
 
# Get final time
if [ -z ${5+x} ]; then
  FT=1.0
else
  FT=$5
fi
 
# Get final time
if [ -z ${6+x} ]; then
  ORDER=0
else
  ORDER=$6
fi
 
#spack load moab
 
set -x
 
# Partition mesh
../../tools/mofem_part -my_file $MESHFILE -meshsets_config $CONFIGFILE -my_nparts $NBPROCS
 
# Run code
rm -f out_*.h5m 
#make -j 4 unsaturated_transport 
 
#mpirun --allow-run-as-root -np $NBPROCS \
mpirun -np $NBPROCS ./unsaturated_transport \
-my_file out.h5m  -configure $CONFIGFILE  \
-ts_monitor \
-ts_type beuler \
-ts_dt $DT \
-ts_max_time $FT \
-ts_monitor \
-ts_adapt_always_accept true \
-ts_adapt_monitor \
-ts_adapt_type none \
-ts_adapt_dt_max 1e-1 \
-ts_adapt_dt_min 1e-3 \
-ts_rtol 0.01 \
-ts_atol 0.01 \
-ts_adapt_basic_safety 0.8 \
-ts_error_if_step_fails false \
-ts_theta_adapt false \
-ts_alpha_adapt false \
-ts_max_reject -1 \
-ts_max_snes_failures -1 \
-ksp_type gmres \
-pc_type lu \
-pc_factor_mat_solver_type mumps \
-snes_type newtonls \
-snes_linesearch_type l2 \
-snes_linesearch_minlambda 1e-3 \
-snes_linesearch_damping 1. \
-snes_linesearch_max_it 1 \
-snes_atol 1e-8 \
-snes_rtol 1e-8 \
-snes_divergence_tolerance 1e24 \
-snes_stol 0 \
-snes_max_it 32 \
-snes_converged_reason \
-my_order $ORDER \
-how_often_output 1 \
-my_max_post_proc_ref_level 0 \
-help 2>&1 | tee log && \
rm -f out_*.vtk && \
../nonlinear_elasticity/do_vtk.sh out_*h5m
 
# Will exit with status of last command.
 
exit $?