Added sources for SGT test case.

bench/seismic/wp/sgt/sources/README.md

+# Sources
+This directory contains the source input for the SGT runs.
+
+Used commands:
+```
+python3 ./generate.py -t ricker -s -1 -e 1 -d 1E-4 -c 1.92 -m 1 -p ricker.pdf -o ricker.ascii
+python3 ./generate.py -t gaussian -s -0.65 -e 0.65 -d 1E-4 -c 60 -m 1 -p gaussian.pdf -o gaussian.ascii
+./generate_forward.sh
+./generate_point_forces.sh
+```
+
+* Contact: Alex Breuer

bench/seismic/wp/sgt/sources/gaussian_point_force_ascii/time_series.ascii

+../gaussian.ascii
\ No newline at end of file

bench/seismic/wp/sgt/sources/generate.py

+#!/usr/bin/python3
+##
+# @file This file is part of EDGE.
+#
+# @author Alexander Breuer (anbreuer AT ucsd.edu)
+#
+# @section LICENSE
+# Copyright (c) 2018, Regents of the University of California
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+#
+# 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+#
+# 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+#
+# 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# @section DESCRIPTION
+# Generates the source time histories.
+##
+import logging
+import argparse
+import math
+
+def ricker( i_t1,
+            i_t2,
+            i_dt,
+            i_f=1.0,
+            i_M0=1.0):
+  """Generates slip rate samples as given by the Ricker wavelet.
+     Source: Geophysical Journal International 166.2 (2006): 855-877.
+             An arbitrary high-order discontinuous Galerkin method for
+             elastic waves on unstructured meshes I. The two-dimensional isotropic case with external source terms
+             Eq. (64)
+     Moment rate time history:  a*(0.5+b(t-T)^2)*exp(b*(t-T)^2) )
+
+  Arguments:
+    i_t1 {float} -- start time of the sampling.
+    i_t2 {float} -- end time of the sampling.
+    i_dt {float} -- time step of the sampling.
+    i_f {float} -- central frequency of the wavelet.
+    i_M0 {float} -- scaling used for the moment-rate time history.
+  
+  Returns:
+    [array of float] -- sampled slip rates.
+  """
+
+  # set parameters as used in the equation above
+  l_a = i_M0
+  l_b = -(math.pi * i_f)**2
+
+  # slip rate samples
+  l_sr = []
+
+  # local time
+  l_t = i_t1
+
+  while( l_t < i_t2 ):
+    l_sr.append( l_a * ( 0.5 + l_b * l_t**2 ) * math.exp( l_b * l_t**2 ) )
+    l_t = l_t + i_dt
+
+  return l_sr
+
+def gaussian( i_t1,
+              i_t2,
+              i_dt,
+              i_a,
+              i_M0 ):
+  """Generates slip rate samples, given by a Gaussian.
+     Moment rate time history:  M0*exp(-a*t^2) )
+
+  Arguments:
+    i_t1 {float} -- start time of the sampling.
+    i_t2 {float} -- end time of the sampling.
+    i_dt {float} -- time step of the sampling.
+    i_a {float} -- decay.
+    i_M0 {float} -- scaling used for the moment-rate time history.
+  
+  Returns:
+    [array of float] -- sampled slip rates.
+  """
+  # slip rate samples
+  l_sr = []
+
+  # local time
+  l_t = i_t1
+
+  while( l_t < i_t2 ):
+    l_sr.append( i_M0 * math.exp( -i_a*l_t**2 ) )
+    l_t = l_t + i_dt
+
+  return l_sr
+
+# set up logger
+logging.basicConfig( level=logging.INFO,
+                     format='%(asctime)s - %(name)s - %(levelname)s - %(message)s' )
+
+# command line arguments
+l_parser = argparse.ArgumentParser( description='Generates a sampled source time function.' )
+
+
+l_parser.add_argument( '-s',
+                       dest     = 't1',
+                       required = True,
+                       type     = float,
+                       help     = 'start time' )
+
+l_parser.add_argument( '-e',
+                       dest     = 't2',
+                       required = True,
+                       type     = float,
+                       help     = 'end time' )
+
+
+l_parser.add_argument( '-d',
+                       dest     = 'dt',
+                       required = True,
+                       type     = float,
+                       help     = 'time step of the sampling' )
+
+l_parser.add_argument( '-t',
+                       dest     = 'type',
+                       type     = str,
+                       help     = 'type of the source: either "ricker" or "gaussian"' )
+
+
+l_parser.add_argument( '-c',
+                       dest     = 'c',
+                       required = True,
+                       type     = float,
+                       help     = 'central frequency (ricker) or decay rate (gaussian)' )
+
+l_parser.add_argument( '-m',
+                       dest     = 'm',
+                       required = True,
+                       type     = float,
+                       help     = 'scaling (magnitude)' )
+
+l_parser.add_argument( '-p',
+                       dest     = 'p',
+                       required = False,
+                       default  = "",
+                       type     = str,
+                       help     = 'path to output file for plot (optional)' )
+
+l_parser.add_argument( '-o',
+                       dest     = 'o',
+                       required = True,
+                       type     = str,
+                       help     = 'path to ASCII output file' )
+
+
+l_args = vars(l_parser.parse_args())
+
+logging.info( 'generating sampled ricker wavelet' )
+
+# derive sampling
+if( l_args['type'] == 'ricker' ):
+  l_samples = ricker( l_args['t1'],
+                      l_args['t2'],
+                      l_args['dt'],
+                      l_args['c'],
+                      l_args['m'] )
+
+elif(  l_args['type'] == 'gaussian' ):
+  l_samples = gaussian( l_args['t1'],
+                        l_args['t2'],
+                        l_args['dt'],
+                        l_args['c'],
+                        l_args['m'] )
+
+else: assert( False )
+
+print( len(l_samples) )
+
+if l_args['p'] != '':
+  logging.info( 'plotting waveform and spectrum' )
+  import matplotlib.pyplot
+  from matplotlib.backends.backend_pdf import PdfPages
+  import numpy
+
+  l_pdf = PdfPages( l_args['p'] )
+  matplotlib.pyplot.plot( numpy.linspace(l_args['t1'], l_args['t2'], num=len(l_samples)), l_samples )
+  l_pdf.savefig()
+
+  matplotlib.pyplot.figure()
+  matplotlib.pyplot.xlim( (0, 10) )
+  matplotlib.pyplot.magnitude_spectrum( l_samples, Fs=1/l_args['dt'] )
+  l_pdf.savefig()
+
+  l_pdf.close()
+
+
+with open(l_args['o'], 'w') as l_file:
+    for l_sa in l_samples:
+        l_file.write("%s\n" % l_sa)

bench/seismic/wp/sgt/sources/generate_forward.sh

+#!/bin/bash
+##
+# @file This file is part of EDGE.
+#
+# @author Alexander Breuer (anbreuer AT ucsd.edu)
+#
+# @section LICENSE
+# Copyright (c) 2018, Regents of the University of California
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+#
+# 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+#
+# 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+#
+# 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# @section DESCRIPTION
+# Converts the ASCII sources to HDF5.
+##
+for base in ricker_forward
+do
+  args=""
+  for type in points scalings time_parameters time_pointers time_series
+  do
+    args="${args} ${base}_ascii/${type}.ascii -c ${base}_ascii/${type}.dmp"
+  done
+  rm ${base}.h5 2> /dev/null
+  h5import ${args} -o ${base}.h5 > /dev/null
+done

bench/seismic/wp/sgt/sources/generate_point_forces.sh

+#!/bin/bash
+##
+# @file This file is part of EDGE.
+#
+# @author Alexander Breuer (anbreuer AT ucsd.edu)
+#
+# @section LICENSE
+# Copyright (c) 2018, Regents of the University of California
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+#
+# 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+#
+# 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+#
+# 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# @section DESCRIPTION
+# Generates the HDF5 source for the point forces.
+##
+rm -r point_forces
+mkdir point_forces
+cd point_forces
+
+while IFS=, read -r recv_name recv_x recv_y recv_z
+do
+  for dim in x y
+  do
+    mkdir ${recv_name}_${dim}_ascii
+    cd ${recv_name}_${dim}_ascii
+    ln -s ../../gaussian_point_force_ascii/* .
+
+    # set location
+    echo "${recv_x} ${recv_y} ${recv_z}" > points.ascii
+
+    # set scaling