Merge pull request #833 from danielpeter/devel

revisits geocentric vs geographic positioning; updates SIEM meshing; updates source positioning and reference solutions; increases version to 8.1.1

CITATION.cff

@@ -1,17 +1,16 @@
 cff-version: 1.2.0
 
 message: "If this software turns out to be helpful for your research, please cite both the article from preferred-citation and the software itself. More detailed citation suggestions can be found in the user manual."
-title: 'SPECFEM/specfem3d_globe: SPECFEM3D_GLOBE v8.1.0'
-version: v8.1.0
-date-released: 2023-12-20
-repository-code: https://github.com/SPECFEM/specfem3d_globe/tree/v8.1.0
+title: 'SPECFEM/specfem3d_globe: SPECFEM3D_GLOBE v8.1.1'
+version: v8.1.1
+date-released: '2024-03-18'
+repository-code: https://github.com/SPECFEM/specfem3d_globe/tree/v8.1.1
 url: "https://github.com/SPECFEM/specfem3d_globe"
 type: software
 identifiers:
   - type: doi
   - value: 10.5281/zenodo.10411115
-license:
-  - gpl-3.0-or-later
+license: "GPL-3.0"
 
 authors:
 - family-names: Komatitsch

DATA/topo_bathy/convert_etopo_files_from_specfem_ASCII_to_binary_topo_format_ascii2bin.py

@@ -41,7 +41,7 @@ def convert_etopo_ascii2bin(filename_in,filename_out):
         text = inf.readlines(1024*1024)  # 1M at a time
         if not len(text):
             break
-        ioin = BytesIO(''.join(text))
+        ioin = BytesIO(b"".join(text))
         data = np.genfromtxt(ioin)
         if not len(data):
             break

DATA/topo_bathy/run_create_topo_bathy_file.py

@@ -151,6 +151,9 @@
 # plots PNM image
 plot_image = True
 
+## smoothing (turned on by default)
+use_smoothing = True
+
 ####################################################################
 
 # global parameters
@@ -967,6 +970,12 @@ def create_topo_bathy(topo):
         print("Unrecognized option %s" % topo)
         sys.exit(1)
 
+    # for raw, unmodified output sets filter size to zero
+    if not use_smoothing:
+        SIZE_FILTER_ONE_SIDE = 0
+        print("  not using smoothing")
+        print("")
+
     # 1-degree in km
     if 'mars' in topo:
         radius = 3390.0
@@ -1004,6 +1013,15 @@ def create_topo_bathy(topo):
         #filename_grid = 'etopo1_ice_c_resampled_at_2minutes.grd'
         #filename_out = 'topo_bathy_etopo1_ice_c_resampled_at_2minutes_original_unmodified_unsmoothed.dat'
 
+    # raw topo output filenames
+    if not use_smoothing:
+        # special case for etopo1 & etopo2 handling
+        if topo == 'etopo1':
+            filename_out_smoothed = 'topo_bathy_etopo1_unmodified_unsmoothed.dat'
+        elif topo == 'etopo2':
+            filename_out_smoothed = 'topo_bathy_etopo2_unmodified_unsmoothed.dat'
+        # for all other topo, it will use a default 'topo_bathy_***_smoothed_window_0.dat' output name
+
     # data file download
     download_data_file(topo,filename_web)
 
@@ -1038,13 +1056,32 @@ def create_topo_bathy(topo):
     print("all done")
 
 
+def usage():
+    print("usage: ./run_create_topo_bathy_file.py topo [== etopo1,etopo2,etopo4,etopo5,etopo15,mars,moon] [--raw]")
+    sys.exit(1)
+
+
 if __name__ == '__main__':
+
     # gets arguments
-    if '--help' in sys.argv or '-h' in sys.argv or len(sys.argv) != 2:
-        print("usage: ./run_create_topo_bathy_file.py topo [== etopo1,etopo2,etopo4,etopo5,etopo15,mars,moon]")
-        sys.exit(1)
-    else:
-        topo = sys.argv[1]
+    if len(sys.argv) <= 1:
+        usage()
+
+    topo = sys.argv[1]
+
+    # reads arguments
+    i = 0
+    for arg in sys.argv:
+        i += 1
+        #print("arg: ",i,arg)
+        # get arguments
+        if "--help" in arg or '-h' in arg:
+            usage()
+        elif "--raw" in arg:
+            use_smoothing = False
+        elif i > 2:
+            print("argument not recognized: ",arg)
+            sys.exit(1)
 
     create_topo_bathy(topo)
 

EXAMPLES/README → EXAMPLES/README.md

@@ -1,6 +1,5 @@
-----------------------------------------------------------
 README
-----------------------------------------------------------
+======
 
 
 This folder contains several examples of how to run forward and adjoint simulations.
@@ -11,23 +10,23 @@ The following examples are provided:
 
 - basic usage:
 
-  * regional_Greece_small/
+  * `regional_Greece_small/`
 
   contains an example for a small regional simulation and an event located in southern Greece;
   the example can be run as a small test on a single desktop machine
-  (4 CPUs, forward simulation lasts ~5min, kernel simulation lasts ~10min) 
+  (4 CPUs, forward simulation lasts ~5min, kernel simulation lasts ~10min)
 
-  * regional_MiddleEast/
+  * `regional_MiddleEast/`
 
   contains an example for a regional simulation for the Middle East region
   (64 CPUs, forward simulation lasts ~7min, kernel simulation lasts ~15min)
 
-  * global_s362ani_shakemovie/
+  * `global_s362ani_shakemovie/`
 
   contains an example for a global shakemovie simulation using S362ANI as 3-D background model
   (384 CPUs, forward simulation lasts ~1h 55min)
 
-  * global_PREM_kernels/
+  * `global_PREM_kernels/`
 
   contains examples for amplitude and traveltime kernels using PREM as background model;
   both examples focus on how adjoint sources for filtered measurements would be constructed and used.
@@ -36,15 +35,15 @@ The following examples are provided:
 
 - PREM benchmark solutions:
 
-  * benchmarks/ 
+  * `benchmarks/`
 
-  contains PREM benchmarks for comparing SEM outputs with normal-mode solutions 
-  (various resolutions: Vanuatu 384 CPUs/ Bolivia 1536 CPUs) 
+  contains PREM benchmarks for comparing SEM outputs with normal-mode solutions
+  (various resolutions: Vanuatu 384 CPUs/ Bolivia 1536 CPUs)
 
 
 - seismic interferometry:
 
-  * noise_examples/
+  * `noise_examples/`
 
   contains examples of how to compute noise sensitivity kernels for global and regional simulations
   (various resolutions: global 600 CPUs/ regional 400 CPUs)

EXAMPLES/benchmarks/attenuation_benchmark_GJI_2002_versus_normal_modes/convolve_jeroen.f90

@@ -12,9 +12,9 @@ program convolve_jeroen
 
   implicit none
 
-  double precision, parameter :: DECAY_RATE=2.628d0
+  double precision, parameter :: DECAY_RATE = 2.628d0
 
-  double precision, parameter :: PI=3.141592653589793d0
+  double precision, parameter :: PI = 3.141592653589793d0
 
 ! number of samples in the ASCII seismogram files (i.e. it is the value of NSTEP in the SPECFEM3D code)
   integer, parameter :: nlines = 15500
@@ -42,14 +42,14 @@ program convolve_jeroen
   allocate(time(nlines),sem(nlines),sem_fil(nlines))
 
 ! read the seismogram from the standard input
-  do i=1,nlines
+  do i = 1,nlines
     read(*,*) time(i),sem(i)
   enddo
 
-  alpha=DECAY_RATE/hdur
-  dt=dble(time(2))-dble(time(1))
+  alpha = DECAY_RATE/hdur
+  dt = dble(time(2))-dble(time(1))
   N_j=int(hdur/dt)
-  do i=1,nlines
+  do i = 1,nlines
     sem_fil(i)=0.0d0
     do j=-N_j,N_j
       tau_j=dble(j)*dt
@@ -78,7 +78,7 @@ program convolve_jeroen
       else
 
 ! convolve with a Gaussian
-        source=alpha*dexp(-alpha*alpha*tau_j*tau_j)/dsqrt(PI)
+        source = alpha*dexp(-alpha*alpha*tau_j*tau_j)/dsqrt(PI)
 
       endif
 
@@ -90,7 +90,7 @@ program convolve_jeroen
 ! compute number of samples to remove from end of seismograms
   number_remove = int(hdur / dt) + 1
 ! write the convolved seismogram to the standard output
-  do i=1,nlines - number_remove
+  do i = 1,nlines - number_remove
     write(*,*) time(i),sngl(sem_fil(i))
   enddo
 

EXAMPLES/global_PREM_kernels/amplitude/xcombine_vol_data.sh

@@ -1,7 +1,6 @@
 #!/bin/bash
 #
 #
-# note: script requires executable 'mesh2vtu'
 ##############################################
 # USER PARAMETERS
 
@@ -40,18 +39,17 @@ else
 fi
 
 # for visualization
-cp -v ~/SPECFEM3D_GLOBE/utils/Visualization/VTK_ParaView/AVS_continent_boundaries.inp .
-cp -v ~/SPECFEM3D_GLOBE/utils/Visualization/VTK_ParaView/paraviewpython-example.py .
+ln -s ../../../utils/Visualization/VTK_ParaView/AVS_continent_boundaries.inp
+ln -s ../../../utils/Visualization/VTK_ParaView/paraviewpython-example.py
 
 # only for crust_mantle region
 echo
 echo "alpha kernel"
 echo
-./bin/xcombine_vol_data $slice alpha_kernel $dir $dir OUTPUT_FILES/ $res 1
-echo ""
-mesh2vtu OUTPUT_FILES/reg_1_alpha_kernel.mesh OUTPUT_FILES/reg_1_alpha_kernel.vtu
-echo ""
-rm -f OUTPUT_FILES/reg_*alpha*.mesh
+./bin/xcombine_vol_data_vtu $slice alpha_kernel $dir $dir OUTPUT_FILES/ $res 1
+
+# checks exit code
+if [[ $? -ne 0 ]]; then exit 1; fi
 
 # colorbar
 # see RGBPoints section
@@ -60,32 +58,39 @@ echo
 sed "s:1e-09:$maxcolor:g" state_alpha_kernel.pvsm > tmp_alpha.pvsm
 
 ./paraviewpython-example.py tmp_alpha.pvsm
+# checks exit code
+if [[ $? -ne 0 ]]; then exit 1; fi
+
 mv -v image.jpg image_alpha_kernel.jpg
 
 echo
 echo "beta kernel"
 echo
-./bin/xcombine_vol_data $slice beta_kernel $dir $dir OUTPUT_FILES/ $res 1
-echo ""
-mesh2vtu OUTPUT_FILES/reg_1_beta_kernel.mesh OUTPUT_FILES/reg_1_beta_kernel.vtu
-echo ""
-rm -f OUTPUT_FILES/reg_*beta*.mesh
+./bin/xcombine_vol_data_vtu $slice beta_kernel $dir $dir OUTPUT_FILES/ $res 1
+
+# checks exit code
+if [[ $? -ne 0 ]]; then exit 1; fi
 
 sed "s:alpha:beta:g" tmp_alpha.pvsm > tmp_beta.pvsm
 ./paraviewpython-example.py tmp_beta.pvsm
+# checks exit code
+if [[ $? -ne 0 ]]; then exit 1; fi
+
 mv -v image.jpg image_beta_kernel.jpg
 
 echo
 echo "rho kernel"
 echo
-./bin/xcombine_vol_data $slice rho_kernel $dir $dir OUTPUT_FILES/ $res 1
-echo ""
-mesh2vtu OUTPUT_FILES/reg_1_rho_kernel.mesh OUTPUT_FILES/reg_1_rho_kernel.vtu
-echo ""
-rm -f OUTPUT_FILES/reg_*rho*.mesh
+./bin/xcombine_vol_data_vtu $slice rho_kernel $dir $dir OUTPUT_FILES/ $res 1
+
+# checks exit code
+if [[ $? -ne 0 ]]; then exit 1; fi
 
 sed "s:alpha:rho:g" tmp_alpha.pvsm > tmp_rho.pvsm
 ./paraviewpython-example.py tmp_rho.pvsm
+# checks exit code
+if [[ $? -ne 0 ]]; then exit 1; fi
+
 mv -v image.jpg image_rho_kernel.jpg
 
 echo

EXAMPLES/global_PREM_kernels/traveltime/xcombine_vol_data.sh

@@ -1,7 +1,6 @@
 #!/bin/bash
 #
 #
-# note: script requires executable 'mesh2vtu'
 ##############################################
 # USER PARAMETERS
 
@@ -40,18 +39,17 @@ else
 fi
 
 # for visualization
-cp -v ~/SPECFEM3D_GLOBE/utils/Visualization/VTK_ParaView/AVS_continent_boundaries.inp .
-cp -v ~/SPECFEM3D_GLOBE/utils/Visualization/VTK_ParaView/paraviewpython-example.py .
+ln -s ../../../utils/Visualization/VTK_ParaView/AVS_continent_boundaries.inp
+ln -s ../../../utils/Visualization/VTK_ParaView/paraviewpython-example.py
 
 # only for crust_mantle region
 echo
 echo "alpha kernel"
 echo
-./bin/xcombine_vol_data $slice alpha_kernel $dir $dir OUTPUT_FILES/ $res 1
-echo ""
-mesh2vtu OUTPUT_FILES/reg_1_alpha_kernel.mesh OUTPUT_FILES/reg_1_alpha_kernel.vtu
-echo ""
-rm -f OUTPUT_FILES/reg_*alpha*.mesh
+./bin/xcombine_vol_data_vtu $slice alpha_kernel $dir $dir OUTPUT_FILES/ $res 1
+
+# checks exit code
+if [[ $? -ne 0 ]]; then exit 1; fi
 
 # colorbar
 # see RGBPoints section
@@ -60,32 +58,40 @@ echo
 sed "s:1e-09:$maxcolor:g" state_alpha_kernel.pvsm > tmp_alpha.pvsm
 
 ./paraviewpython-example.py tmp_alpha.pvsm
+# checks exit code
+if [[ $? -ne 0 ]]; then exit 1; fi
+
 mv -v image.jpg image_alpha_kernel.jpg
 
 echo
 echo "beta kernel"
 echo
-./bin/xcombine_vol_data $slice beta_kernel $dir $dir OUTPUT_FILES/ $res 1
-echo ""
-mesh2vtu OUTPUT_FILES/reg_1_beta_kernel.mesh OUTPUT_FILES/reg_1_beta_kernel.vtu
-echo ""
-rm -f OUTPUT_FILES/reg_*beta*.mesh
+./bin/xcombine_vol_data_vtu $slice beta_kernel $dir $dir OUTPUT_FILES/ $res 1
+
+# checks exit code
+if [[ $? -ne 0 ]]; then exit 1; fi
 
 sed "s:alpha:beta:g" tmp_alpha.pvsm > tmp_beta.pvsm
 ./paraviewpython-example.py tmp_beta.pvsm
+# checks exit code
+if [[ $? -ne 0 ]]; then exit 1; fi
+
 mv -v image.jpg image_beta_kernel.jpg
 
 echo
 echo "rho kernel"
 echo
-./bin/xcombine_vol_data $slice rho_kernel $dir $dir OUTPUT_FILES/ $res 1
-echo ""
-mesh2vtu OUTPUT_FILES/reg_1_rho_kernel.mesh OUTPUT_FILES/reg_1_rho_kernel.vtu
-echo ""
-rm -f OUTPUT_FILES/reg_*rho*.mesh
+./bin/xcombine_vol_data_vtu $slice rho_kernel $dir $dir OUTPUT_FILES/ $res 1
+
+# checks exit code
+if [[ $? -ne 0 ]]; then exit 1; fi
+
 
 sed "s:alpha:rho:g" tmp_alpha.pvsm > tmp_rho.pvsm
 ./paraviewpython-example.py tmp_rho.pvsm
+# checks exit code
+if [[ $? -ne 0 ]]; then exit 1; fi
+
 mv -v image.jpg image_rho_kernel.jpg
 
 echo