[cig-commits] [commit] devel,master: added the four-layer socal1D model as an internal mesher example; mesh is comparable to the DT=0.011 s mesh from the old SPECFEM3D_BASIN (99e98ab)
cig_noreply at geodynamics.org
cig_noreply at geodynamics.org
Wed Jun 18 16:48:37 PDT 2014
Repository : https://github.com/geodynamics/specfem3d
On branches: devel,master
Link : https://github.com/geodynamics/specfem3d/compare/6026e367984905ab133865f62fa6293b343759b9...47f703851338234f96397e7da9fbff63d8178b8a
>---------------------------------------------------------------
commit 99e98ab769ff33175d361e4b3c9df6e9e08ff29b
Author: Carl Tape <carltape at gi.alaska.edu>
Date: Fri Apr 1 23:10:54 2011 +0000
added the four-layer socal1D model as an internal mesher example; mesh is comparable to the DT=0.011 s mesh from the old SPECFEM3D_BASIN
>---------------------------------------------------------------
99e98ab769ff33175d361e4b3c9df6e9e08ff29b
meshfem3D_examples/socal1D/CMTSOLUTION | 13 +++++++
.../{simple_model => socal1D}/Mesh_Par_file | 40 ++++++++++-----------
.../{simple_model => socal1D}/Par_file | 12 +++----
.../{simple_model => socal1D}/README | 27 +++++---------
meshfem3D_examples/socal1D/STATIONS | 30 ++++++++++++++++
meshfem3D_examples/socal1D/interface1.dat | 4 +++
meshfem3D_examples/socal1D/interface2.dat | 4 +++
meshfem3D_examples/socal1D/interface3.dat | 4 +++
.../socal1D/interface4.dat | 3 +-
.../{simple_model => socal1D}/interfaces.dat | 27 +++++++++-----
.../{simple_model => socal1D}/process.sh | 18 ++++++++--
meshfem3D_examples/socal1D/socal1D_koma2004.png | Bin 0 -> 58074 bytes
meshfem3D_examples/socal1D/socal1D_sesame.png | Bin 0 -> 44070 bytes
13 files changed, 124 insertions(+), 58 deletions(-)
diff --git a/meshfem3D_examples/socal1D/CMTSOLUTION b/meshfem3D_examples/socal1D/CMTSOLUTION
new file mode 100644
index 0000000..10609f9
--- /dev/null
+++ b/meshfem3D_examples/socal1D/CMTSOLUTION
@@ -0,0 +1,13 @@
+PDE 2001 9 9 23 59 17.78 34.0745 -118.3792 6.4 4.2 4.2 HOLLYWOOD POLET SEM
+event name: 9703873
+time shift: 0.0000
+half duration: 0.3114
+latitude: 34.0745
+longitude: -118.3792
+depth: 5.4000
+Mrr: -0.002000e+23
+Mtt: -0.064000e+23
+Mpp: 0.066000e+23
+Mrt: -0.090000e+23
+Mrp: -0.002000e+23
+Mtp: 0.188000e+23
diff --git a/meshfem3D_examples/simple_model/Mesh_Par_file b/meshfem3D_examples/socal1D/Mesh_Par_file
similarity index 63%
copy from meshfem3D_examples/simple_model/Mesh_Par_file
copy to meshfem3D_examples/socal1D/Mesh_Par_file
index 32a4e33..acb120f 100644
--- a/meshfem3D_examples/simple_model/Mesh_Par_file
+++ b/meshfem3D_examples/socal1D/Mesh_Par_file
@@ -1,10 +1,10 @@
# coordinates of mesh block in latitude/longitude and depth in km
-LATITUDE_MIN = 33.1d0
-LATITUDE_MAX = 34.1d0
-LONGITUDE_MIN = -118.9d0
-LONGITUDE_MAX = -117.9d0
-DEPTH_BLOCK_KM = 30.d0
+LATITUDE_MIN = 33.790d0
+LATITUDE_MAX = 34.157d0
+LONGITUDE_MIN = -118.728d0
+LONGITUDE_MAX = -118.237d0
+DEPTH_BLOCK_KM = 60.d0
UTM_PROJECTION_ZONE = 11
SUPPRESS_UTM_PROJECTION = .false.
@@ -14,20 +14,20 @@ INTERFACES_FILE = interfaces.dat
# number of elements at the surface along edges of the mesh at the surface
# (must be 8 * multiple of NPROC below if mesh is not regular and contains mesh doublings)
# (must be multiple of NPROC below if mesh is regular)
-NEX_XI = 64
-NEX_ETA = 64
+NEX_XI = 24
+NEX_ETA = 24
# number of MPI processors along xi and eta (can be different)
-NPROC_XI = 2
-NPROC_ETA = 2
+NPROC_XI = 1
+NPROC_ETA = 1
# Regular/irregular mesh
USE_REGULAR_MESH = .false.
# Only for irregular meshes, number of doubling layers (1 or 2) and their position
-NDOUBLINGS = 1
+NDOUBLINGS = 2
# NZ_DOUGLING_1 is the parameter to set up if there is only one doubling layer
-NZ_DOUGLING_1 = 11
-NZ_DOUGLING_2 = 0
+NZ_DOUGLING_1 = 6
+NZ_DOUGLING_2 = 9
# create mesh files for visualisation or further checking
CREATE_ABAQUS_FILES = .true.
@@ -43,16 +43,16 @@ NMATERIALS = 4
# Q : quality factor
# anisotropy_flag : 0=no anisotropy/ 1,2,.. check with implementation in aniso_model.f90
# domain_id : 1=acoustic / 2=elastic
-1 1200 1500 750 40.0 0 2
-2 1100 1600 0 50.0 0 1
-3 1000 1500 700 0 0 2
-4 1300 1400 700 50.0 0 2
+1 3000 7800 4500 0.0 0 2
+2 2800 6700 3870 0.0 0 2
+3 2670 6300 3640 0.0 0 2
+4 2400 5500 3180 0.0 0 2
# number of regions
NREGIONS = 4
# define the different regions of the model as :
#NEX_XI_BEGIN #NEX_XI_END #NEX_ETA_BEGIN #NEX_ETA_END #NZ_BEGIN #NZ_END #material_id
-1 64 1 64 1 4 1
-1 64 1 64 5 5 2
-1 64 1 64 6 15 3
-14 25 7 19 7 10 4
+1 24 1 24 1 3 1
+1 24 1 24 4 6 2
+1 24 1 24 7 9 3
+1 24 1 24 10 12 4
diff --git a/meshfem3D_examples/simple_model/Par_file b/meshfem3D_examples/socal1D/Par_file
similarity index 87%
copy from meshfem3D_examples/simple_model/Par_file
copy to meshfem3D_examples/socal1D/Par_file
index c97b11c..1b89c1f 100644
--- a/meshfem3D_examples/simple_model/Par_file
+++ b/meshfem3D_examples/socal1D/Par_file
@@ -9,11 +9,11 @@ UTM_PROJECTION_ZONE = 11
SUPPRESS_UTM_PROJECTION = .false.
# number of MPI processors
-NPROC = 4
+NPROC = 1
# time step parameters
-NSTEP = 2000
-DT = 0.03
+NSTEP = 840
+DT = 0.012
# parameters describing the model
OCEANS = .false.
@@ -26,7 +26,7 @@ ANISOTROPY = .false.
ABSORBING_CONDITIONS = .true.
# save AVS or OpenDX movies
-MOVIE_SURFACE = .true.
+MOVIE_SURFACE = .false.
MOVIE_VOLUME = .false.
NTSTEP_BETWEEN_FRAMES = 200
CREATE_SHAKEMAP = .false.
@@ -41,7 +41,7 @@ SAVE_MESH_FILES = .true.
LOCAL_PATH = ../in_out_files/DATABASES_MPI
# interval at which we output time step info and max of norm of displacement
-NTSTEP_BETWEEN_OUTPUT_INFO = 500
+NTSTEP_BETWEEN_OUTPUT_INFO = 100
# interval in time steps for writing of seismograms
NTSTEP_BETWEEN_OUTPUT_SEISMOS = 10000
@@ -50,6 +50,6 @@ NTSTEP_BETWEEN_OUTPUT_SEISMOS = 10000
NTSTEP_BETWEEN_READ_ADJSRC = 0 # 0 = read the whole adjoint sources at the same time
# print source time function
-PRINT_SOURCE_TIME_FUNCTION = .false.
+PRINT_SOURCE_TIME_FUNCTION = .true.
diff --git a/meshfem3D_examples/simple_model/README b/meshfem3D_examples/socal1D/README
similarity index 72%
copy from meshfem3D_examples/simple_model/README
copy to meshfem3D_examples/socal1D/README
index 9ce22ad..3431145 100644
--- a/meshfem3D_examples/simple_model/README
+++ b/meshfem3D_examples/socal1D/README
@@ -1,9 +1,10 @@
----------------------------------------------------------------------
README
-(/SPECFEM3D/examples/meshfem3D_examples/simple_model/README)
+(/SPECFEM3D/examples/meshfem3D_examples/socal1D/README)
----------------------------------------------------------------------
This is a very simple example to explain the use of the internal mesher meshfem3D.
+The example uses the standard 1D model used in southern California (SoCal-1D).
Option 1: run process.sh from local directory (must have access to mpi)
Option 2: follow instructions below for submitting separate jobs with qsub (or bsub)
@@ -15,7 +16,7 @@ Option 2: follow instructions below for submitting separate jobs with qsub (or b
1. Set up input files.
> cd SPECFEM3D
- > rsync -av examples/meshfem3D_examples/simple_model/ in_data_files/meshfem3D_files/
+ > rsync -av examples/meshfem3D_examples/socal1D/ in_data_files/meshfem3D_files/
> cd in_data_files/meshfem3D_files/
> cp Par_file CMTSOLUTION STATIONS ..
@@ -37,15 +38,6 @@ Option 2: follow instructions below for submitting separate jobs with qsub (or b
proc000000_Database
proc000000_.dx
proc000000_.INP
- proc000001_Database
- proc000001_.dx
- proc000001_.INP
- proc000002_Database
- proc000002_.dx
- proc000002_.INP
- proc000003_Database
- proc000003_.dx
- proc000003_.INP
- save output file
> cp in_out_files/OUTPUT_FILES/output_mesher.txt in_out_files/OUTPUT_FILES/output_meshfem3D.txt
@@ -61,7 +53,7 @@ Option 2: follow instructions below for submitting separate jobs with qsub (or b
this will create binary mesh files, e.g. "proc000***_external_mesh.bin"
in directory in_out_files/DATABASES_MPI/.
- Optional: If you have paraview, load the .vtk files (see simple_model.png).
+ Optional: If you have paraview, load the .vtk files (see socal1D_sesame.png).
4. run simulation:
@@ -71,15 +63,12 @@ Option 2: follow instructions below for submitting separate jobs with qsub (or b
- submit job script:
> qsub go_solver_pbs.bash
- - the job should take about 10 minutes
+ - the job should take about 5 minutes
- when the job is complete, you should have 3 sets (semd,semv,sema)
- of 27 (ls -1 *semd | wc) seismogram files in the directory in_out_files/OUTPUT_FILES,
- as well as 5 timestamp****** files
+ of 84 (ls -1 *semd | wc) seismogram files in the directory in_out_files/OUTPUT_FILES,
+ as well as 9 timestamp****** files
- view seismograms, for example, using xmgrace:
- - xmgrace K400.CE.BXZ.semd K851.CE.BXZ.semd K853.CE.BXZ.semd &
-
- - compare with reference seismograms in
- examples/meshfem3D_examples/simple_model/REF_SEIS/
+ - xmgrace WTT*.semd &
----------------------------------------------------------------------
diff --git a/meshfem3D_examples/socal1D/STATIONS b/meshfem3D_examples/socal1D/STATIONS
new file mode 100644
index 0000000..e330ae1
--- /dev/null
+++ b/meshfem3D_examples/socal1D/STATIONS
@@ -0,0 +1,30 @@
+24851 CE 34.070000 -118.346000 0.000000 0.000000
+24853 CE 34.077000 -118.286000 0.000000 0.000000
+K851 CE 34.070000 -118.346000 0.000000 0.000000
+K853 CE 34.077000 -118.286000 0.000000 0.000000
+BVH CI 34.076180 -118.395900 0.000000 0.000000
+CAB CI 34.155730 -118.640930 0.000000 0.000000
+DJJ CI 34.106180 -118.455050 0.000000 0.000000
+DJJB CI 34.106180 -118.455050 0.000000 0.000000
+GR2 CI 34.118300 -118.299400 0.000000 0.000000
+GRF CI 34.119200 -118.300400 0.000000 0.000000
+LAF CI 33.868890 -118.331430 0.000000 0.000000
+LAX CI 33.943820 -118.413900 0.000000 0.000000
+LCG CI 34.000330 -118.377940 0.000000 0.000000
+PDR CI 33.962730 -118.437020 0.000000 0.000000
+SMF CI 34.021590 -118.446750 0.000000 0.000000
+SMS CI 34.014380 -118.456170 0.000000 0.000000
+SPF CI 34.059330 -118.646140 0.000000 0.000000
+TCF CI 34.083770 -118.599000 0.000000 0.000000
+USC CI 34.019190 -118.286310 0.000000 0.000000
+WNS CI 34.115000 -118.380000 0.000000 0.000000
+WTT CI 33.948690 -118.255470 0.000000 0.000000
+FABS FA 34.066670 -118.571113 0.000000 0.000000
+5081 NP 34.084000 -118.600000 0.000000 0.000000
+5399 NP 33.943000 -118.411000 0.000000 0.000000
+5402 NP 34.076000 -118.395000 0.000000 0.000000
+5404 NP 34.155000 -118.641000 0.000000 0.000000
+BVH NP 34.076180 -118.395900 0.000000 0.000000
+GRF NP 34.119200 -118.300400 0.000000 0.000000
+LAX NP 33.943820 -118.413900 0.000000 0.000000
+TCF NP 34.083770 -118.599000 0.000000 0.000000
diff --git a/meshfem3D_examples/socal1D/interface1.dat b/meshfem3D_examples/socal1D/interface1.dat
new file mode 100644
index 0000000..3a799f0
--- /dev/null
+++ b/meshfem3D_examples/socal1D/interface1.dat
@@ -0,0 +1,4 @@
+-32000
+-32000
+-32000
+-32000
diff --git a/meshfem3D_examples/socal1D/interface2.dat b/meshfem3D_examples/socal1D/interface2.dat
new file mode 100644
index 0000000..86e17b7
--- /dev/null
+++ b/meshfem3D_examples/socal1D/interface2.dat
@@ -0,0 +1,4 @@
+-16000
+-16000
+-16000
+-16000
diff --git a/meshfem3D_examples/socal1D/interface3.dat b/meshfem3D_examples/socal1D/interface3.dat
new file mode 100644
index 0000000..765197f
--- /dev/null
+++ b/meshfem3D_examples/socal1D/interface3.dat
@@ -0,0 +1,4 @@
+-5500
+-5500
+-5500
+-5500
diff --git a/noise_tomography/NOISE_TOMOGRAPHY/nu_master b/meshfem3D_examples/socal1D/interface4.dat
similarity index 50%
copy from noise_tomography/NOISE_TOMOGRAPHY/nu_master
copy to meshfem3D_examples/socal1D/interface4.dat
index bb5ee5c..44e0be8 100644
--- a/noise_tomography/NOISE_TOMOGRAPHY/nu_master
+++ b/meshfem3D_examples/socal1D/interface4.dat
@@ -1,3 +1,4 @@
0
0
-1
+0
+0
diff --git a/meshfem3D_examples/simple_model/interfaces.dat b/meshfem3D_examples/socal1D/interfaces.dat
similarity index 54%
copy from meshfem3D_examples/simple_model/interfaces.dat
copy to meshfem3D_examples/socal1D/interfaces.dat
index a326e85..6395dba 100644
--- a/meshfem3D_examples/simple_model/interfaces.dat
+++ b/meshfem3D_examples/socal1D/interfaces.dat
@@ -1,21 +1,30 @@
# number of interfaces
- 2
+ 4
#
# We describe each interface below, structured as a 2D-grid, with several parameters :
# number of points along XI and ETA, minimal XI ETA coordinates
# and spacing between points which must be constant.
# Then the records contain the Z coordinates of the NXI x NETA points.
#
-# interface number 1
-# SUPPRESS_UTM_PROJECTION NXI NETA LONG_MIN LAT_MIN SPACING_XI SPACING_ETA
- .true. 161 144 316000.d0 3655000.d0 20000.d0 20000.d0
+# interface number 1 (moho)
+ .false. 2 2 -121.d0 32.d0 6.0d0 6.0d0
interface1.dat
-# interface number 2 (topography, top of the mesh)
- .false. 1401 1001 -121.d0 32.d0 0.005d0 0.005d0
+# interface number 2
+ .false. 2 2 -121.d0 32.d0 6.0d0 6.0d0
interface2.dat
+# interface number 3
+ .false. 2 2 -121.d0 32.d0 6.0d0 6.0d0
+ interface3.dat
+# interface number 4 (topography, top of the mesh)
+ .false. 2 2 -121.d0 32.d0 6.0d0 6.0d0
+ interface4.dat
#
# for each layer, we give the number of spectral elements in the vertical direction
# layer number 1 (bottom layer)
- 11
-# layer number 2 (top layer)
- 4
+ 3
+# layer number 2
+ 3
+# layer number 4
+ 3
+# layer number 5 (top layer)
+ 3
\ No newline at end of file
diff --git a/meshfem3D_examples/simple_model/process.sh b/meshfem3D_examples/socal1D/process.sh
similarity index 79%
copy from meshfem3D_examples/simple_model/process.sh
copy to meshfem3D_examples/socal1D/process.sh
index 14ffa32..f6d8eea 100755
--- a/meshfem3D_examples/simple_model/process.sh
+++ b/meshfem3D_examples/socal1D/process.sh
@@ -7,7 +7,7 @@
###################################################
# number of processes
-NPROC=4
+NPROC=1
##################################################
@@ -15,7 +15,7 @@ echo "running example: `date`"
currentdir=`pwd`
echo
-echo "(will take about 15 minutes)"
+echo "(will take about 5 minutes)"
echo
# sets up directory structure in current example directoy
@@ -40,10 +40,10 @@ cp Par_file in_data_files/
cp CMTSOLUTION in_data_files/
cp STATIONS in_data_files/
-
# compiles executables in root directory
cd ../../../
make > tmp.log
+make combine_vol_data
cd $currentdir
# links executables
@@ -51,6 +51,7 @@ cd bin/
ln -s ../../../../bin/xmeshfem3D
ln -s ../../../../bin/xgenerate_databases
ln -s ../../../../bin/xspecfem3D
+ln -s ../../../../bin/xcombine_vol_data
cd ../
# decomposes mesh
@@ -75,6 +76,9 @@ cd bin/
mpirun -np $NPROC ./xgenerate_databases
cd ../
+# exit here if you want to do mesher only
+#exit
+
# runs simulation
echo
echo " running solver..."
@@ -89,4 +93,12 @@ echo
echo "done"
echo `date`
+# To make a full mesh using combine_vol_data:
+# cd bin
+# xcombine_vol_data 0 0 vs ../in_out_files/DATABASES_MPI/ ../in_out_files/DATABASES_MPI/ 1
+# cd ../in_out_files/DATABASES_MPI/
+# (check that mesh2vtu.pl is working)
+# ../../../../../utils/Visualization/Paraview/mesh2vtu.pl -i vs.mesh -o vs.vtu
+#
+
diff --git a/meshfem3D_examples/socal1D/socal1D_koma2004.png b/meshfem3D_examples/socal1D/socal1D_koma2004.png
new file mode 100644
index 0000000..7dea4f5
Binary files /dev/null and b/meshfem3D_examples/socal1D/socal1D_koma2004.png differ
diff --git a/meshfem3D_examples/socal1D/socal1D_sesame.png b/meshfem3D_examples/socal1D/socal1D_sesame.png
new file mode 100644
index 0000000..f5bb21b
Binary files /dev/null and b/meshfem3D_examples/socal1D/socal1D_sesame.png differ
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