[cig-commits] r18163 - in seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples: . socal1D
carltape at geodynamics.org
carltape at geodynamics.org
Fri Apr 1 16:10:54 PDT 2011
Author: carltape
Date: 2011-04-01 16:10:54 -0700 (Fri, 01 Apr 2011)
New Revision: 18163
Added:
seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/
seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/CMTSOLUTION
seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/Mesh_Par_file
seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/Par_file
seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/README
seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/STATIONS
seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/interface1.dat
seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/interface2.dat
seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/interface3.dat
seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/interface4.dat
seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/interfaces.dat
seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/process.sh
seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/socal1D_koma2004.png
seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/socal1D_sesame.png
Log:
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
Added: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/CMTSOLUTION
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/CMTSOLUTION (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/CMTSOLUTION 2011-04-01 23:10:54 UTC (rev 18163)
@@ -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
Added: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/Mesh_Par_file
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/Mesh_Par_file (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/Mesh_Par_file 2011-04-01 23:10:54 UTC (rev 18163)
@@ -0,0 +1,58 @@
+
+# coordinates of mesh block in latitude/longitude and depth in km
+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.
+
+# file that contains the interfaces of the model / mesh
+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 = 24
+NEX_ETA = 24
+
+# number of MPI processors along xi and eta (can be different)
+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 = 2
+# NZ_DOUGLING_1 is the parameter to set up if there is only one doubling layer
+NZ_DOUGLING_1 = 6
+NZ_DOUGLING_2 = 9
+
+# create mesh files for visualisation or further checking
+CREATE_ABAQUS_FILES = .true.
+CREATE_DX_FILES = .true.
+
+# path to store the databases files
+LOCAL_PATH = ../in_out_files/DATABASES_MPI
+
+# number of materials
+NMATERIALS = 4
+# define the different materials in the model as :
+# #material_id #rho #vp #vs #Q #anisotropy_flag #domain_id
+# Q : quality factor
+# anisotropy_flag : 0=no anisotropy/ 1,2,.. check with implementation in aniso_model.f90
+# domain_id : 1=acoustic / 2=elastic
+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 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
+
Added: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/Par_file
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/Par_file (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/Par_file 2011-04-01 23:10:54 UTC (rev 18163)
@@ -0,0 +1,55 @@
+
+# forward or adjoint simulation
+SIMULATION_TYPE = 1 # 1 = forward, 2 = adjoint, 3 = both simultaneously
+NOISE_TOMOGRAPHY = 0 # 0 = earthquake simulation, 1/2/3 = three steps in noise simulation
+SAVE_FORWARD = .false.
+
+# UTM projection parameters
+UTM_PROJECTION_ZONE = 11
+SUPPRESS_UTM_PROJECTION = .false.
+
+# number of MPI processors
+NPROC = 1
+
+# time step parameters
+NSTEP = 840
+DT = 0.012
+
+# parameters describing the model
+OCEANS = .false.
+TOPOGRAPHY = .false.
+ATTENUATION = .false.
+USE_OLSEN_ATTENUATION = .false.
+ANISOTROPY = .false.
+
+# absorbing boundary conditions for a regional simulation
+ABSORBING_CONDITIONS = .true.
+
+# save AVS or OpenDX movies
+MOVIE_SURFACE = .false.
+MOVIE_VOLUME = .false.
+NTSTEP_BETWEEN_FRAMES = 200
+CREATE_SHAKEMAP = .false.
+SAVE_DISPLACEMENT = .false.
+USE_HIGHRES_FOR_MOVIES = .false.
+HDUR_MOVIE = 0.0
+
+# save AVS or OpenDX mesh files to check the mesh
+SAVE_MESH_FILES = .true.
+
+# path to store the local database file on each node
+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 = 100
+
+# interval in time steps for writing of seismograms
+NTSTEP_BETWEEN_OUTPUT_SEISMOS = 10000
+
+# interval in time steps for reading adjoint traces
+NTSTEP_BETWEEN_READ_ADJSRC = 0 # 0 = read the whole adjoint sources at the same time
+
+# print source time function
+PRINT_SOURCE_TIME_FUNCTION = .true.
+
+
Added: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/README
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/README (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/README 2011-04-01 23:10:54 UTC (rev 18163)
@@ -0,0 +1,74 @@
+----------------------------------------------------------------------
+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)
+
+----------------------------------------------------------------------
+
+0. Run the default homogeneous halfspace example (external mesh).
+
+1. Set up input files.
+
+ > cd SPECFEM3D
+ > rsync -av examples/meshfem3D_examples/socal1D/ in_data_files/meshfem3D_files/
+
+ > cd in_data_files/meshfem3D_files/
+ > cp Par_file CMTSOLUTION STATIONS ..
+ > cd SPECFEM3D
+
+ - adapt the submission scripts for the appropriate queues and number of cores:
+ go_mesher_pbs.bash, go_generate_databases_pbs.bash, go_solver_pbs.bash
+
+ - note: go_decomposer_pbs.bash is not used with the internal mesher
+
+2. compile and run internal mesher
+
+ > make xmeshfem3D
+
+ > qsub go_mesher_pbs.bash
+
+ This should generate these files in in_out_files/DATABASES_MPI/:
+
+ proc000000_Database
+ proc000000_.dx
+ proc000000_.INP
+
+ - save output file
+ > cp in_out_files/OUTPUT_FILES/output_mesher.txt in_out_files/OUTPUT_FILES/output_meshfem3D.txt
+
+3. generate databases:
+
+ - compile generate_databases in directory SPECFEM3D/:
+ > make xgenerate_databases
+
+ - submit job script:
+ > qsub go_generate_databases_pbs.bash
+
+ 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 socal1D_sesame.png).
+
+4. run simulation:
+
+ - compile specfem3D:
+ > make xspecfem3D
+
+ - submit job script:
+ > qsub go_solver_pbs.bash
+
+ - the job should take about 5 minutes
+ - when the job is complete, you should have 3 sets (semd,semv,sema)
+ 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 WTT*.semd &
+
+----------------------------------------------------------------------
Added: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/STATIONS
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/STATIONS (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/STATIONS 2011-04-01 23:10:54 UTC (rev 18163)
@@ -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
Added: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/interface1.dat
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/interface1.dat (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/interface1.dat 2011-04-01 23:10:54 UTC (rev 18163)
@@ -0,0 +1,4 @@
+-32000
+-32000
+-32000
+-32000
Added: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/interface2.dat
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/interface2.dat (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/interface2.dat 2011-04-01 23:10:54 UTC (rev 18163)
@@ -0,0 +1,4 @@
+-16000
+-16000
+-16000
+-16000
Added: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/interface3.dat
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/interface3.dat (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/interface3.dat 2011-04-01 23:10:54 UTC (rev 18163)
@@ -0,0 +1,4 @@
+-5500
+-5500
+-5500
+-5500
Added: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/interface4.dat
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/interface4.dat (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/interface4.dat 2011-04-01 23:10:54 UTC (rev 18163)
@@ -0,0 +1,4 @@
+0
+0
+0
+0
Added: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/interfaces.dat
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/interfaces.dat (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/interfaces.dat 2011-04-01 23:10:54 UTC (rev 18163)
@@ -0,0 +1,30 @@
+# number of interfaces
+ 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 (moho)
+ .false. 2 2 -121.d0 32.d0 6.0d0 6.0d0
+ interface1.dat
+# 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)
+ 3
+# layer number 2
+ 3
+# layer number 4
+ 3
+# layer number 5 (top layer)
+ 3
\ No newline at end of file
Added: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/process.sh
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/process.sh (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/process.sh 2011-04-01 23:10:54 UTC (rev 18163)
@@ -0,0 +1,104 @@
+#!/bin/bash
+#
+# script runs mesher,database generation and solver
+# using this example setup
+#
+
+###################################################
+
+# number of processes
+NPROC=1
+
+##################################################
+
+echo "running example: `date`"
+currentdir=`pwd`
+
+echo
+echo "(will take about 5 minutes)"
+echo
+
+# sets up directory structure in current example directoy
+echo
+echo " setting up example..."
+echo
+
+mkdir -p bin
+mkdir -p in_out_files/OUTPUT_FILES
+mkdir -p in_out_files/DATABASES_MPI
+
+rm -rf in_out_files/OUTPUT_FILES/*
+rm -rf in_out_files/DATABASES_MPI/*
+
+mkdir -p in_data_files
+mkdir -p in_data_files/meshfem3D_files/
+
+cp Mesh_Par_file in_data_files/meshfem3D_files/
+cp interface*.dat in_data_files/meshfem3D_files/
+
+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
+cd bin/
+ln -s ../../../../bin/xmeshfem3D
+ln -s ../../../../bin/xgenerate_databases
+ln -s ../../../../bin/xspecfem3D
+ln -s ../../../../bin/xcombine_vol_data
+cd ../
+
+# decomposes mesh
+echo
+echo " meshing..."
+echo
+cd bin/
+mpirun -np $NPROC ./xmeshfem3D
+cd ../
+mv in_out_files/OUTPUT_FILES/output_mesher.txt in_out_files/OUTPUT_FILES/output_meshfem3D.txt
+
+# stores setup
+cp in_data_files/Par_file in_out_files/OUTPUT_FILES/
+cp in_data_files/CMTSOLUTION in_out_files/OUTPUT_FILES/
+cp in_data_files/STATIONS in_out_files/OUTPUT_FILES/
+
+# runs database generation
+echo
+echo " running database generation..."
+echo
+cd bin/
+mpirun -np $NPROC ./xgenerate_databases
+cd ../
+
+# exit here if you want to do mesher only
+#exit
+
+# runs simulation
+echo
+echo " running solver..."
+echo
+cd bin/
+mpirun -np $NPROC ./xspecfem3D
+cd ../
+
+echo
+echo "see results in directory: in_out_files/OUTPUT_FILES/"
+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
+#
+
+
Property changes on: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/process.sh
___________________________________________________________________
Name: svn:executable
+ *
Added: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/socal1D_koma2004.png
===================================================================
(Binary files differ)
Property changes on: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/socal1D_koma2004.png
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/socal1D_sesame.png
===================================================================
(Binary files differ)
Property changes on: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/socal1D_sesame.png
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
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