[cig-commits] [commit] devel, master: cleanup in all examples directories (3bfd19c)
cig_noreply at geodynamics.org
cig_noreply at geodynamics.org
Wed Jun 18 16:50:20 PDT 2014
Repository : https://github.com/geodynamics/specfem3d
On branches: devel,master
Link : https://github.com/geodynamics/specfem3d/compare/6026e367984905ab133865f62fa6293b343759b9...47f703851338234f96397e7da9fbff63d8178b8a
>---------------------------------------------------------------
commit 3bfd19cbd8d1092c6743dce383be8fb2e33d4bdf
Author: Joseph Charles <jcharles at lma.cnrs-mrs.fr>
Date: Thu Oct 25 14:58:44 2012 +0000
cleanup in all examples directories
>---------------------------------------------------------------
3bfd19cbd8d1092c6743dce383be8fb2e33d4bdf
.../ACOUSTIC/{in_data_files => DATA}/CMTSOLUTION | 0
.../ACOUSTIC/{in_data_files => DATA}/FORCESOLUTION | 0
.../ACOUSTIC/{in_data_files => DATA}/Par_file | 0
.../ACOUSTIC/{in_data_files => DATA}/STATIONS | 0
.../ACOUSTIC/{in_data_files => DATA}/STATIONS_ADJOINT | 0
.../meshfem3D_files/Mesh_Par_file | 0
.../meshfem3D_files/interface3.dat | 0
.../meshfem3D_files/interfaces.dat | 0
.../ELASTIC/{in_data_files => DATA}/CMTSOLUTION | 0
.../ELASTIC/{in_data_files => DATA}/FORCESOLUTION | 0
.../ELASTIC/{in_data_files => DATA}/Par_file | 0
.../ELASTIC/{in_data_files => DATA}/STATIONS | 0
.../ELASTIC/{in_data_files => DATA}/STATIONS_ADJOINT | 0
.../meshfem3D_files/Mesh_Par_file | 0
.../meshfem3D_files/interface3.dat | 0
.../meshfem3D_files/interfaces.dat | 0
Mount_StHelens/{in_data_files => DATA}/CMTSOLUTION | 0
Mount_StHelens/{in_data_files => DATA}/FORCESOLUTION | 0
Mount_StHelens/{in_data_files => DATA}/Par_file | 0
Mount_StHelens/{in_data_files => DATA}/STATIONS | 0
Mount_StHelens/process.sh | 6 +++---
.../{in_data_files => DATA}/CMTSOLUTION | 0
.../{in_data_files => DATA}/FORCESOLUTION | 0
.../{in_data_files => DATA}/Par_file | 0
.../{in_data_files => DATA}/STATIONS | 0
.../{in_data_files => DATA}/STATIONS_ADJOINT | 0
.../{HOWTO_run_this_example.txt => README} | 0
.../{in_data_files => DATA}/CMTSOLUTION | 0
.../{in_data_files => DATA}/FORCESOLUTION | 0
.../{in_data_files => DATA}/Par_file | 0
.../{in_data_files => DATA}/STATIONS | 0
layered_halfspace/{in_data_files => DATA}/CMTSOLUTION | 0
layered_halfspace/{in_data_files => DATA}/FORCESOLUTION | 0
layered_halfspace/{in_data_files => DATA}/Par_file | 0
layered_halfspace/{in_data_files => DATA}/STATIONS | 0
layered_halfspace/{in_data_files => DATA}/STATIONS_X | 0
layered_halfspace/{in_data_files => DATA}/STATIONS_Y | 0
layered_halfspace/README | 4 +---
layered_halfspace/process.sh | 17 ++++++++++-------
meshfem3D_examples/many_interfaces/README | 15 +++++----------
meshfem3D_examples/simple_model/README | 17 ++++-------------
.../socal1D/{in_data_files => DATA}/CMTSOLUTION | 0
.../socal1D/{in_data_files => DATA}/FORCESOLUTION | 0
.../socal1D/{in_data_files => DATA}/Par_file | 0
.../socal1D/{in_data_files => DATA}/STATIONS | 0
.../meshfem3D_files/Mesh_Par_file | 0
.../meshfem3D_files/Mesh_Par_file_001 | 0
.../meshfem3D_files/Mesh_Par_file_042 | 0
.../meshfem3D_files/Mesh_Par_file_168 | 0
.../meshfem3D_files/interface1.dat | 0
.../meshfem3D_files/interface2.dat | 0
.../meshfem3D_files/interface3.dat | 0
.../meshfem3D_files/interface4.dat | 0
.../meshfem3D_files/interfaces.dat | 0
meshfem3D_examples/socal1D/README | 13 ++++---------
meshfem3D_examples/socal1D/process.sh | 2 +-
noise_tomography/{in_data_files => DATA}/CMTSOLUTION | 0
.../DATA}/FORCESOLUTION | 0
noise_tomography/{in_data_files => DATA}/Par_file_step1 | 0
noise_tomography/{in_data_files => DATA}/Par_file_step2 | 0
noise_tomography/{in_data_files => DATA}/Par_file_step3 | 0
noise_tomography/{in_data_files => DATA}/STATIONS | 0
.../{in_data_files => DATA}/STATIONS_ADJOINT | 0
noise_tomography/README | 4 ++--
noise_tomography/pre-processing.sh | 12 ++++--------
tomographic_model/{in_data_files => DATA}/CMTSOLUTION | 0
tomographic_model/{in_data_files => DATA}/FORCESOLUTION | 0
tomographic_model/{in_data_files => DATA}/Par_file | 0
tomographic_model/{in_data_files => DATA}/STATIONS | 0
tomographic_model/README | 8 ++------
tomographic_model/process.sh | 16 ++++++++--------
.../{in_data_files => DATA}/CMTSOLUTION | 0
.../{in_data_files => DATA}/FORCESOLUTION | 0
waterlayered_halfspace/{in_data_files => DATA}/Par_file | 0
waterlayered_halfspace/{in_data_files => DATA}/STATIONS | 0
waterlayered_halfspace/README | 9 ++-------
waterlayered_halfspace/process.sh | 16 ++++++++--------
77 files changed, 54 insertions(+), 85 deletions(-)
diff --git a/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/in_data_files/CMTSOLUTION b/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/CMTSOLUTION
similarity index 100%
rename from BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/in_data_files/CMTSOLUTION
rename to BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/CMTSOLUTION
diff --git a/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/in_data_files/FORCESOLUTION b/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/FORCESOLUTION
similarity index 100%
rename from BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/in_data_files/FORCESOLUTION
rename to BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/FORCESOLUTION
diff --git a/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/in_data_files/Par_file b/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/Par_file
similarity index 100%
rename from BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/in_data_files/Par_file
rename to BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/Par_file
diff --git a/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/in_data_files/STATIONS b/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/STATIONS
similarity index 100%
rename from BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/in_data_files/STATIONS
rename to BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/STATIONS
diff --git a/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/in_data_files/STATIONS_ADJOINT b/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/STATIONS_ADJOINT
similarity index 100%
rename from BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/in_data_files/STATIONS_ADJOINT
rename to BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/STATIONS_ADJOINT
diff --git a/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/in_data_files/meshfem3D_files/Mesh_Par_file b/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/meshfem3D_files/Mesh_Par_file
similarity index 100%
rename from BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/in_data_files/meshfem3D_files/Mesh_Par_file
rename to BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/meshfem3D_files/Mesh_Par_file
diff --git a/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/in_data_files/meshfem3D_files/interface3.dat b/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/meshfem3D_files/interface3.dat
similarity index 100%
rename from BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/in_data_files/meshfem3D_files/interface3.dat
rename to BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/meshfem3D_files/interface3.dat
diff --git a/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/in_data_files/meshfem3D_files/interfaces.dat b/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/meshfem3D_files/interfaces.dat
similarity index 100%
rename from BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/in_data_files/meshfem3D_files/interfaces.dat
rename to BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/meshfem3D_files/interfaces.dat
diff --git a/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/in_data_files/CMTSOLUTION b/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/CMTSOLUTION
similarity index 100%
rename from BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/in_data_files/CMTSOLUTION
rename to BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/CMTSOLUTION
diff --git a/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/in_data_files/FORCESOLUTION b/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/FORCESOLUTION
similarity index 100%
rename from BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/in_data_files/FORCESOLUTION
rename to BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/FORCESOLUTION
diff --git a/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/in_data_files/Par_file b/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/Par_file
similarity index 100%
rename from BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/in_data_files/Par_file
rename to BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/Par_file
diff --git a/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/in_data_files/STATIONS b/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/STATIONS
similarity index 100%
rename from BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/in_data_files/STATIONS
rename to BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/STATIONS
diff --git a/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/in_data_files/STATIONS_ADJOINT b/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/STATIONS_ADJOINT
similarity index 100%
rename from BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/in_data_files/STATIONS_ADJOINT
rename to BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/STATIONS_ADJOINT
diff --git a/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/in_data_files/meshfem3D_files/Mesh_Par_file b/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/meshfem3D_files/Mesh_Par_file
similarity index 100%
rename from BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/in_data_files/meshfem3D_files/Mesh_Par_file
rename to BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/meshfem3D_files/Mesh_Par_file
diff --git a/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/in_data_files/meshfem3D_files/interface3.dat b/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/meshfem3D_files/interface3.dat
similarity index 100%
rename from BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/in_data_files/meshfem3D_files/interface3.dat
rename to BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/meshfem3D_files/interface3.dat
diff --git a/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/in_data_files/meshfem3D_files/interfaces.dat b/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/meshfem3D_files/interfaces.dat
similarity index 100%
rename from BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/in_data_files/meshfem3D_files/interfaces.dat
rename to BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/meshfem3D_files/interfaces.dat
diff --git a/Mount_StHelens/in_data_files/CMTSOLUTION b/Mount_StHelens/DATA/CMTSOLUTION
similarity index 100%
rename from Mount_StHelens/in_data_files/CMTSOLUTION
rename to Mount_StHelens/DATA/CMTSOLUTION
diff --git a/Mount_StHelens/in_data_files/FORCESOLUTION b/Mount_StHelens/DATA/FORCESOLUTION
similarity index 100%
copy from Mount_StHelens/in_data_files/FORCESOLUTION
copy to Mount_StHelens/DATA/FORCESOLUTION
diff --git a/Mount_StHelens/in_data_files/Par_file b/Mount_StHelens/DATA/Par_file
similarity index 100%
rename from Mount_StHelens/in_data_files/Par_file
rename to Mount_StHelens/DATA/Par_file
diff --git a/Mount_StHelens/in_data_files/STATIONS b/Mount_StHelens/DATA/STATIONS
similarity index 100%
rename from Mount_StHelens/in_data_files/STATIONS
rename to Mount_StHelens/DATA/STATIONS
diff --git a/Mount_StHelens/process.sh b/Mount_StHelens/process.sh
index 83c8b5d..c4e6dc1 100755
--- a/Mount_StHelens/process.sh
+++ b/Mount_StHelens/process.sh
@@ -27,15 +27,15 @@ echo " setting up example..."
echo
mkdir -p bin
-mkdir -p OUTPUT_FILES
mkdir -p OUTPUT_FILES/DATABASES_MPI
-rm -rf OUTPUT_FILES/*
+rm -f OUTPUT_FILES/*
rm -rf OUTPUT_FILES/DATABASES_MPI/*
# compiles executables in root directory
cd ../../
-make >& $currentdir/tmp.log
+make clean
+make > $currentdir/tmp.log
cd $currentdir
# links executables
diff --git a/homogeneous_halfspace_HEX27/in_data_files/CMTSOLUTION b/homogeneous_halfspace_HEX27/DATA/CMTSOLUTION
similarity index 100%
rename from homogeneous_halfspace_HEX27/in_data_files/CMTSOLUTION
rename to homogeneous_halfspace_HEX27/DATA/CMTSOLUTION
diff --git a/homogeneous_halfspace_HEX27/in_data_files/FORCESOLUTION b/homogeneous_halfspace_HEX27/DATA/FORCESOLUTION
similarity index 100%
rename from homogeneous_halfspace_HEX27/in_data_files/FORCESOLUTION
rename to homogeneous_halfspace_HEX27/DATA/FORCESOLUTION
diff --git a/homogeneous_halfspace_HEX27/in_data_files/Par_file b/homogeneous_halfspace_HEX27/DATA/Par_file
similarity index 100%
rename from homogeneous_halfspace_HEX27/in_data_files/Par_file
rename to homogeneous_halfspace_HEX27/DATA/Par_file
diff --git a/homogeneous_halfspace_HEX27/in_data_files/STATIONS b/homogeneous_halfspace_HEX27/DATA/STATIONS
similarity index 100%
rename from homogeneous_halfspace_HEX27/in_data_files/STATIONS
rename to homogeneous_halfspace_HEX27/DATA/STATIONS
diff --git a/homogeneous_halfspace_HEX27/in_data_files/STATIONS_ADJOINT b/homogeneous_halfspace_HEX27/DATA/STATIONS_ADJOINT
similarity index 100%
rename from homogeneous_halfspace_HEX27/in_data_files/STATIONS_ADJOINT
rename to homogeneous_halfspace_HEX27/DATA/STATIONS_ADJOINT
diff --git a/homogeneous_halfspace_HEX27/HOWTO_run_this_example.txt b/homogeneous_halfspace_HEX27/README
similarity index 100%
rename from homogeneous_halfspace_HEX27/HOWTO_run_this_example.txt
rename to homogeneous_halfspace_HEX27/README
diff --git a/homogeneous_poroelastic/in_data_files/CMTSOLUTION b/homogeneous_poroelastic/DATA/CMTSOLUTION
similarity index 100%
rename from homogeneous_poroelastic/in_data_files/CMTSOLUTION
rename to homogeneous_poroelastic/DATA/CMTSOLUTION
diff --git a/homogeneous_poroelastic/in_data_files/FORCESOLUTION b/homogeneous_poroelastic/DATA/FORCESOLUTION
similarity index 100%
rename from homogeneous_poroelastic/in_data_files/FORCESOLUTION
rename to homogeneous_poroelastic/DATA/FORCESOLUTION
diff --git a/homogeneous_poroelastic/in_data_files/Par_file b/homogeneous_poroelastic/DATA/Par_file
similarity index 100%
rename from homogeneous_poroelastic/in_data_files/Par_file
rename to homogeneous_poroelastic/DATA/Par_file
diff --git a/homogeneous_poroelastic/in_data_files/STATIONS b/homogeneous_poroelastic/DATA/STATIONS
similarity index 100%
rename from homogeneous_poroelastic/in_data_files/STATIONS
rename to homogeneous_poroelastic/DATA/STATIONS
diff --git a/layered_halfspace/in_data_files/CMTSOLUTION b/layered_halfspace/DATA/CMTSOLUTION
similarity index 100%
rename from layered_halfspace/in_data_files/CMTSOLUTION
rename to layered_halfspace/DATA/CMTSOLUTION
diff --git a/layered_halfspace/in_data_files/FORCESOLUTION b/layered_halfspace/DATA/FORCESOLUTION
similarity index 100%
rename from layered_halfspace/in_data_files/FORCESOLUTION
rename to layered_halfspace/DATA/FORCESOLUTION
diff --git a/layered_halfspace/in_data_files/Par_file b/layered_halfspace/DATA/Par_file
similarity index 100%
rename from layered_halfspace/in_data_files/Par_file
rename to layered_halfspace/DATA/Par_file
diff --git a/layered_halfspace/in_data_files/STATIONS b/layered_halfspace/DATA/STATIONS
similarity index 100%
rename from layered_halfspace/in_data_files/STATIONS
rename to layered_halfspace/DATA/STATIONS
diff --git a/layered_halfspace/in_data_files/STATIONS_X b/layered_halfspace/DATA/STATIONS_X
similarity index 100%
rename from layered_halfspace/in_data_files/STATIONS_X
rename to layered_halfspace/DATA/STATIONS_X
diff --git a/layered_halfspace/in_data_files/STATIONS_Y b/layered_halfspace/DATA/STATIONS_Y
similarity index 100%
rename from layered_halfspace/in_data_files/STATIONS_Y
rename to layered_halfspace/DATA/STATIONS_Y
diff --git a/layered_halfspace/README b/layered_halfspace/README
index 0d430c6..1595ca4 100644
--- a/layered_halfspace/README
+++ b/layered_halfspace/README
@@ -107,10 +107,8 @@ step-by-step tutorial:
5. run simulation:
- - compile specfem3D:
+ - compile and run specfem3D:
> make xspecfem3D
-
- - submit job script:
> qsub go_solver_pbs.bash
note: simulation will take about 25 minutes and generate
diff --git a/layered_halfspace/process.sh b/layered_halfspace/process.sh
index dde6c77..8e9f566 100755
--- a/layered_halfspace/process.sh
+++ b/layered_halfspace/process.sh
@@ -28,12 +28,15 @@ echo " setting up example..."
echo
mkdir -p bin
-mkdir -p OUTPUT_FILES
mkdir -p OUTPUT_FILES/DATABASES_MPI
-rm -rf OUTPUT_FILES/*
+rm -f OUTPUT_FILES/*
rm -rf OUTPUT_FILES/DATABASES_MPI/*
+# compiles executables in root directory
+cd ../../
+make clean
+make > $currentdir/tmp.log
cd $currentdir
# links executables
@@ -44,17 +47,17 @@ cp ../../../bin/xgenerate_databases ./
cp ../../../bin/xspecfem3D ./
cd ../
+# stores setup
+cp DATA/Par_file OUTPUT_FILES/
+cp DATA/CMTSOLUTION OUTPUT_FILES/
+cp DATA/STATIONS OUTPUT_FILES/
+
# decomposes mesh
echo
echo " decomposing mesh..."
echo
./bin/xdecompose_mesh_SCOTCH $NPROC MESH/ OUTPUT_FILES/DATABASES_MPI/
-# stores setup
-cp DATA/Par_file OUTPUT_FILES/
-cp DATA/CMTSOLUTION OUTPUT_FILES/
-cp DATA/STATIONS OUTPUT_FILES/
-
# runs database generation
echo
echo " running database generation..."
diff --git a/meshfem3D_examples/many_interfaces/README b/meshfem3D_examples/many_interfaces/README
index 72dfc63..b9989b8 100644
--- a/meshfem3D_examples/many_interfaces/README
+++ b/meshfem3D_examples/many_interfaces/README
@@ -29,7 +29,6 @@ WARNING: We do not recommend running this as a test example, due to its requirem
2. compile and run internal mesher
> make xmeshfem3D
-
> qsub go_mesher_pbs.bash
- this should generate "proc000***_Database" files in OUTPUT_FILES/DATABASES_MPI/.
@@ -39,23 +38,19 @@ WARNING: We do not recommend running this as a test example, due to its requirem
3. generate databases:
- - compile generate_databases in directory SPECFEM3D/:
+ - compile and run generate_databases in directory SPECFEM3D/:
> make xgenerate_databases
-
- - submit job script:
> qsub go_generate_databases_pbs.bash
- this job will take about XX minutes and will create binary mesh files,
- e.g. "proc000***_external_mesh.bin", in directory OUTPUT_FILES/DATABASES_MPI/.
+ this will create binary mesh files, e.g. "proc000***_external_mesh.bin"
+ in directory OUTPUT_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 simple_model.png).
4. run simulation:
- - compile specfem3D:
+ - compile and run specfem3D:
> make xspecfem3D
-
- - submit job script:
> qsub go_solver_pbs.bash
- the job should take about 70 minutes
diff --git a/meshfem3D_examples/simple_model/README b/meshfem3D_examples/simple_model/README
index 2154acf..6d42fbf 100644
--- a/meshfem3D_examples/simple_model/README
+++ b/meshfem3D_examples/simple_model/README
@@ -15,11 +15,7 @@ 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/ DATA/meshfem3D_files/
-
- > cd DATA/meshfem3D_files/
- > cp Par_file CMTSOLUTION STATIONS ..
- > cd SPECFEM3D
+ > rsync -av examples/meshfem3D_examples/simple_model/DATA DATA
- 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
@@ -29,7 +25,6 @@ Option 2: follow instructions below for submitting separate jobs with qsub (or b
2. compile and run internal mesher
> make xmeshfem3D
-
> qsub go_mesher_pbs.bash
This should generate these files in OUTPUT_FILES/DATABASES_MPI/:
@@ -52,23 +47,19 @@ Option 2: follow instructions below for submitting separate jobs with qsub (or b
3. generate databases:
- - compile generate_databases in directory SPECFEM3D/:
+ - compile and run 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 OUTPUT_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 simple_model.png).
4. run simulation:
- - compile specfem3D:
+ - compile and run specfem3D:
> make xspecfem3D
-
- - submit job script:
> qsub go_solver_pbs.bash
- the job should take about 10 minutes
diff --git a/meshfem3D_examples/socal1D/in_data_files/CMTSOLUTION b/meshfem3D_examples/socal1D/DATA/CMTSOLUTION
similarity index 100%
rename from meshfem3D_examples/socal1D/in_data_files/CMTSOLUTION
rename to meshfem3D_examples/socal1D/DATA/CMTSOLUTION
diff --git a/meshfem3D_examples/socal1D/in_data_files/FORCESOLUTION b/meshfem3D_examples/socal1D/DATA/FORCESOLUTION
similarity index 100%
rename from meshfem3D_examples/socal1D/in_data_files/FORCESOLUTION
rename to meshfem3D_examples/socal1D/DATA/FORCESOLUTION
diff --git a/meshfem3D_examples/socal1D/in_data_files/Par_file b/meshfem3D_examples/socal1D/DATA/Par_file
similarity index 100%
rename from meshfem3D_examples/socal1D/in_data_files/Par_file
rename to meshfem3D_examples/socal1D/DATA/Par_file
diff --git a/meshfem3D_examples/socal1D/in_data_files/STATIONS b/meshfem3D_examples/socal1D/DATA/STATIONS
similarity index 100%
rename from meshfem3D_examples/socal1D/in_data_files/STATIONS
rename to meshfem3D_examples/socal1D/DATA/STATIONS
diff --git a/meshfem3D_examples/socal1D/in_data_files/meshfem3D_files/Mesh_Par_file b/meshfem3D_examples/socal1D/DATA/meshfem3D_files/Mesh_Par_file
similarity index 100%
rename from meshfem3D_examples/socal1D/in_data_files/meshfem3D_files/Mesh_Par_file
rename to meshfem3D_examples/socal1D/DATA/meshfem3D_files/Mesh_Par_file
diff --git a/meshfem3D_examples/socal1D/in_data_files/meshfem3D_files/Mesh_Par_file_001 b/meshfem3D_examples/socal1D/DATA/meshfem3D_files/Mesh_Par_file_001
similarity index 100%
rename from meshfem3D_examples/socal1D/in_data_files/meshfem3D_files/Mesh_Par_file_001
rename to meshfem3D_examples/socal1D/DATA/meshfem3D_files/Mesh_Par_file_001
diff --git a/meshfem3D_examples/socal1D/in_data_files/meshfem3D_files/Mesh_Par_file_042 b/meshfem3D_examples/socal1D/DATA/meshfem3D_files/Mesh_Par_file_042
similarity index 100%
rename from meshfem3D_examples/socal1D/in_data_files/meshfem3D_files/Mesh_Par_file_042
rename to meshfem3D_examples/socal1D/DATA/meshfem3D_files/Mesh_Par_file_042
diff --git a/meshfem3D_examples/socal1D/in_data_files/meshfem3D_files/Mesh_Par_file_168 b/meshfem3D_examples/socal1D/DATA/meshfem3D_files/Mesh_Par_file_168
similarity index 100%
rename from meshfem3D_examples/socal1D/in_data_files/meshfem3D_files/Mesh_Par_file_168
rename to meshfem3D_examples/socal1D/DATA/meshfem3D_files/Mesh_Par_file_168
diff --git a/meshfem3D_examples/socal1D/in_data_files/meshfem3D_files/interface1.dat b/meshfem3D_examples/socal1D/DATA/meshfem3D_files/interface1.dat
similarity index 100%
rename from meshfem3D_examples/socal1D/in_data_files/meshfem3D_files/interface1.dat
rename to meshfem3D_examples/socal1D/DATA/meshfem3D_files/interface1.dat
diff --git a/meshfem3D_examples/socal1D/in_data_files/meshfem3D_files/interface2.dat b/meshfem3D_examples/socal1D/DATA/meshfem3D_files/interface2.dat
similarity index 100%
rename from meshfem3D_examples/socal1D/in_data_files/meshfem3D_files/interface2.dat
rename to meshfem3D_examples/socal1D/DATA/meshfem3D_files/interface2.dat
diff --git a/meshfem3D_examples/socal1D/in_data_files/meshfem3D_files/interface3.dat b/meshfem3D_examples/socal1D/DATA/meshfem3D_files/interface3.dat
similarity index 100%
rename from meshfem3D_examples/socal1D/in_data_files/meshfem3D_files/interface3.dat
rename to meshfem3D_examples/socal1D/DATA/meshfem3D_files/interface3.dat
diff --git a/meshfem3D_examples/socal1D/in_data_files/meshfem3D_files/interface4.dat b/meshfem3D_examples/socal1D/DATA/meshfem3D_files/interface4.dat
similarity index 100%
rename from meshfem3D_examples/socal1D/in_data_files/meshfem3D_files/interface4.dat
rename to meshfem3D_examples/socal1D/DATA/meshfem3D_files/interface4.dat
diff --git a/meshfem3D_examples/socal1D/in_data_files/meshfem3D_files/interfaces.dat b/meshfem3D_examples/socal1D/DATA/meshfem3D_files/interfaces.dat
similarity index 100%
rename from meshfem3D_examples/socal1D/in_data_files/meshfem3D_files/interfaces.dat
rename to meshfem3D_examples/socal1D/DATA/meshfem3D_files/interfaces.dat
diff --git a/meshfem3D_examples/socal1D/README b/meshfem3D_examples/socal1D/README
index 2b07eee..6eaaaf9 100644
--- a/meshfem3D_examples/socal1D/README
+++ b/meshfem3D_examples/socal1D/README
@@ -24,24 +24,19 @@ 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/socal1D/ DATA/meshfem3D_files/
-
- > cd DATA/meshfem3D_files/
- > cp Par_file CMTSOLUTION STATIONS ..
- > cd SPECFEM3D
+ > rsync -av examples/meshfem3D_examples/socal1D/DATA/ DATA
- adapt the submission scripts for the appropriate queues (-q) and number of cores (-l):
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. generate internal mesh:
+2. compile and run internal mesher
- - compile and run meshfem3D:
> make xmeshfem3D
> qsub go_mesher_pbs.bash
- this should generate these files in OUTPUT_FILES/DATABASES_MPI/:
+ - this should generate these files in OUTPUT_FILES/DATABASES_MPI/:
proc000000_Database
proc000000_.dx
@@ -52,7 +47,7 @@ Option 2: follow instructions below for submitting separate jobs with qsub (or b
3. generate databases:
- - compile and run generate_databases:
+ - compile and run generate_databases in directory SPECFEM3D/:
> make xgenerate_databases
> qsub go_generate_databases_pbs.bash
diff --git a/meshfem3D_examples/socal1D/process.sh b/meshfem3D_examples/socal1D/process.sh
index 51abe0d..73a1ba5 100755
--- a/meshfem3D_examples/socal1D/process.sh
+++ b/meshfem3D_examples/socal1D/process.sh
@@ -32,7 +32,7 @@ rm -rf OUTPUT_FILES/DATABASES_MPI/*
# compiles executables in root directory
cd ../../../
make clean
-make
+make > $currentdir/tmp.log
#make combine_vol_data
cd $currentdir
diff --git a/noise_tomography/in_data_files/CMTSOLUTION b/noise_tomography/DATA/CMTSOLUTION
similarity index 100%
rename from noise_tomography/in_data_files/CMTSOLUTION
rename to noise_tomography/DATA/CMTSOLUTION
diff --git a/Mount_StHelens/in_data_files/FORCESOLUTION b/noise_tomography/DATA/FORCESOLUTION
similarity index 100%
rename from Mount_StHelens/in_data_files/FORCESOLUTION
rename to noise_tomography/DATA/FORCESOLUTION
diff --git a/noise_tomography/in_data_files/Par_file_step1 b/noise_tomography/DATA/Par_file_step1
similarity index 100%
rename from noise_tomography/in_data_files/Par_file_step1
rename to noise_tomography/DATA/Par_file_step1
diff --git a/noise_tomography/in_data_files/Par_file_step2 b/noise_tomography/DATA/Par_file_step2
similarity index 100%
rename from noise_tomography/in_data_files/Par_file_step2
rename to noise_tomography/DATA/Par_file_step2
diff --git a/noise_tomography/in_data_files/Par_file_step3 b/noise_tomography/DATA/Par_file_step3
similarity index 100%
rename from noise_tomography/in_data_files/Par_file_step3
rename to noise_tomography/DATA/Par_file_step3
diff --git a/noise_tomography/in_data_files/STATIONS b/noise_tomography/DATA/STATIONS
similarity index 100%
rename from noise_tomography/in_data_files/STATIONS
rename to noise_tomography/DATA/STATIONS
diff --git a/noise_tomography/in_data_files/STATIONS_ADJOINT b/noise_tomography/DATA/STATIONS_ADJOINT
similarity index 100%
rename from noise_tomography/in_data_files/STATIONS_ADJOINT
rename to noise_tomography/DATA/STATIONS_ADJOINT
diff --git a/noise_tomography/README b/noise_tomography/README
index 3332dad..daccd2a 100644
--- a/noise_tomography/README
+++ b/noise_tomography/README
@@ -56,9 +56,9 @@ Noise Cross-Correlation Sensitivity Kernels (Tromp et al., 2010, GJI)
Refer to '../examples/homogeneous_halfspace', if you don't know how to get them from CUBIT and SCOTCH.
3.2 - Source and Receivers
- Since NO earthquakes are allowed for noise simulations, we have a ZERO moment tensor in "./in_data_file/CMTSOLUTION"
+ Since NO earthquakes are allowed for noise simulations, we have a ZERO moment tensor in "./DATA/CMTSOLUTION"
As for receivers, instead of having a lot of stations in '../examples/homogeneous_halfspace',
- we have only two receivers in "./in_data_file/STATIONS" and "./in_data_file/STATIONS_ADJOINT"
+ we have only two receivers in "./DATA/STATIONS" and "./DATA/STATIONS_ADJOINT"
3.3 - Noise statistics
"./NOISE_TOMOGRAPHY" contains:
diff --git a/noise_tomography/pre-processing.sh b/noise_tomography/pre-processing.sh
index 3c490cd..84627c5 100755
--- a/noise_tomography/pre-processing.sh
+++ b/noise_tomography/pre-processing.sh
@@ -15,14 +15,11 @@ echo
echo "(will take about 3 h 30 min)"
echo
-
-# return to the main SPECFEM3D directory
+# compile the package in root directory
cd ../../
-
-# compile the package
-make > tmp.log
-make combine_vol_data >> tmp.log
-
+make clean
+make > $script_dir/tmp.log
+make combine_vol_data >> $script_dir/tmp.log
cd $script_dir
# specify directories for executables, input files and output files
@@ -190,4 +187,3 @@ mesh2vtu.pl -i $OUTPUT_FILES/$kernel.mesh -o $OUTPUT_FILES/NOISE_TOMOGRAPHY/2nd_
echo
echo `date`
echo "done"
-
diff --git a/tomographic_model/in_data_files/CMTSOLUTION b/tomographic_model/DATA/CMTSOLUTION
similarity index 100%
rename from tomographic_model/in_data_files/CMTSOLUTION
rename to tomographic_model/DATA/CMTSOLUTION
diff --git a/tomographic_model/in_data_files/FORCESOLUTION b/tomographic_model/DATA/FORCESOLUTION
similarity index 100%
rename from tomographic_model/in_data_files/FORCESOLUTION
rename to tomographic_model/DATA/FORCESOLUTION
diff --git a/tomographic_model/in_data_files/Par_file b/tomographic_model/DATA/Par_file
similarity index 100%
rename from tomographic_model/in_data_files/Par_file
rename to tomographic_model/DATA/Par_file
diff --git a/tomographic_model/in_data_files/STATIONS b/tomographic_model/DATA/STATIONS
similarity index 100%
rename from tomographic_model/in_data_files/STATIONS
rename to tomographic_model/DATA/STATIONS
diff --git a/tomographic_model/README b/tomographic_model/README
index 57f1b45..1aee3e9 100644
--- a/tomographic_model/README
+++ b/tomographic_model/README
@@ -57,19 +57,15 @@ step-by-step tutorial:
5. generate databases:
- - compile generate_databases from SPECFEM3D/ :
+ - compile and run generate_databases in directory SPECFEM3D/:
> make xgenerate_databases
-
- - submit job script
> qsub go_generate_databases_pbs.bash
6. run simulation:
- - compile specfem3D:
+ - compile and run specfem3D:
> make xspecfem3D
-
- - submit job script:
> qsub go_solver_pbs.bash
the simulation will take about 10 minutes
diff --git a/tomographic_model/process.sh b/tomographic_model/process.sh
index 4496b74..231b563 100755
--- a/tomographic_model/process.sh
+++ b/tomographic_model/process.sh
@@ -27,10 +27,9 @@ echo " setting up example..."
echo
mkdir -p bin
-mkdir -p OUTPUT_FILES
mkdir -p OUTPUT_FILES/DATABASES_MPI
-rm -rf OUTPUT_FILES/*
+rm -f OUTPUT_FILES/*
rm -rf OUTPUT_FILES/DATABASES_MPI/*
# sets up tomography model file
@@ -40,7 +39,8 @@ echo
# compiles executables in root directory
cd ../../
-make > tmp.log
+make clean
+make > $currentdir/tmp.log
cd $currentdir
# links executables
@@ -51,17 +51,17 @@ cp ../../../bin/xgenerate_databases ./
cp ../../../bin/xspecfem3D ./
cd ../
+# stores setup
+cp DATA/Par_file OUTPUT_FILES/
+cp DATA/CMTSOLUTION OUTPUT_FILES/
+cp DATA/STATIONS OUTPUT_FILES/
+
# decomposes mesh
echo
echo " decomposing mesh..."
echo
./bin/xdecompose_mesh_SCOTCH $NPROC MESH/ OUTPUT_FILES/DATABASES_MPI/
-# stores setup
-cp DATA/Par_file OUTPUT_FILES/
-cp DATA/CMTSOLUTION OUTPUT_FILES/
-cp DATA/STATIONS OUTPUT_FILES/
-
# runs database generation
echo
echo " running database generation..."
diff --git a/waterlayered_halfspace/in_data_files/CMTSOLUTION b/waterlayered_halfspace/DATA/CMTSOLUTION
similarity index 100%
rename from waterlayered_halfspace/in_data_files/CMTSOLUTION
rename to waterlayered_halfspace/DATA/CMTSOLUTION
diff --git a/waterlayered_halfspace/in_data_files/FORCESOLUTION b/waterlayered_halfspace/DATA/FORCESOLUTION
similarity index 100%
rename from waterlayered_halfspace/in_data_files/FORCESOLUTION
rename to waterlayered_halfspace/DATA/FORCESOLUTION
diff --git a/waterlayered_halfspace/in_data_files/Par_file b/waterlayered_halfspace/DATA/Par_file
similarity index 100%
rename from waterlayered_halfspace/in_data_files/Par_file
rename to waterlayered_halfspace/DATA/Par_file
diff --git a/waterlayered_halfspace/in_data_files/STATIONS b/waterlayered_halfspace/DATA/STATIONS
similarity index 100%
rename from waterlayered_halfspace/in_data_files/STATIONS
rename to waterlayered_halfspace/DATA/STATIONS
diff --git a/waterlayered_halfspace/README b/waterlayered_halfspace/README
index 6cf03f8..636dd97 100644
--- a/waterlayered_halfspace/README
+++ b/waterlayered_halfspace/README
@@ -6,7 +6,6 @@ This example creates a layered model as in example layered_halfspace/
with a water layer on top and an elastic layer below, using CUBIT.
It then runs a forward simulation which couples acoustic & elastic waves.
-
step-by-step tutorial:
0. run the example in the directory homogeneous_halfspace
@@ -44,10 +43,8 @@ step-by-step tutorial:
4. generate databases:
- - compile generate_databases:
+ - compile and run 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"
@@ -58,10 +55,8 @@ step-by-step tutorial:
5. run simulation:
- - compile specfem3D:
+ - compile and run specfem3D:
> make xspecfem3D
-
- - submit job script:
> qsub go_solver_pbs.bash
note: simulation will take about 1 h 45 minutes and generate
diff --git a/waterlayered_halfspace/process.sh b/waterlayered_halfspace/process.sh
index 1bbf261..a590a2a 100755
--- a/waterlayered_halfspace/process.sh
+++ b/waterlayered_halfspace/process.sh
@@ -27,15 +27,15 @@ echo " setting up example..."
echo
mkdir -p bin
-mkdir -p OUTPUT_FILES
mkdir -p OUTPUT_FILES/DATABASES_MPI
-rm -rf OUTPUT_FILES/*
+rm -f OUTPUT_FILES/*
rm -rf OUTPUT_FILES/DATABASES_MPI/*
# compiles executables in root directory
cd ../../
-make > tmp.log
+make clean
+make > $currentdir/tmp.log
cd $currentdir
# links executables
@@ -46,17 +46,17 @@ cp ../../../bin/xgenerate_databases ./
cp ../../../bin/xspecfem3D ./
cd ../
+# stores setup
+cp DATA/Par_file OUTPUT_FILES/
+cp DATA/CMTSOLUTION OUTPUT_FILES/
+cp DATA/STATIONS OUTPUT_FILES/
+
# decomposes mesh
echo
echo " decomposing mesh..."
echo
./bin/xdecompose_mesh_SCOTCH $NPROC MESH/ OUTPUT_FILES/DATABASES_MPI/
-# stores setup
-cp DATA/Par_file OUTPUT_FILES/
-cp DATA/CMTSOLUTION OUTPUT_FILES/
-cp DATA/STATIONS OUTPUT_FILES/
-
# runs database generation
echo
echo " running database generation..."
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