[cig-commits] [commit] devel, master: replaced in_data_files with DATA in all files and scripts (1916df6)
cig_noreply at geodynamics.org
cig_noreply at geodynamics.org
Wed Jun 18 16:50:07 PDT 2014
Repository : https://github.com/geodynamics/specfem3d
On branches: devel,master
Link : https://github.com/geodynamics/specfem3d/compare/6026e367984905ab133865f62fa6293b343759b9...47f703851338234f96397e7da9fbff63d8178b8a
>---------------------------------------------------------------
commit 1916df6d61e7af3c2880833ebdb5a7ae5f9653d3
Author: Dimitri Komatitsch <komatitsch at lma.cnrs-mrs.fr>
Date: Mon Oct 22 16:06:16 2012 +0000
replaced in_data_files with DATA in all files and scripts
>---------------------------------------------------------------
1916df6d61e7af3c2880833ebdb5a7ae5f9653d3
.../ACOUSTIC/run_inhomogeneous.bash | 12 ++++++------
.../ELASTIC/run_inhomogeneous.bash | 12 ++++++------
Mount_StHelens/README | 2 +-
Mount_StHelens/process.sh | 6 +++---
.../HOWTO_run_this_example.txt | 2 +-
.../HOWTO_run_this_example.txt | 2 +-
homogeneous_halfspace_HEX8/README | 6 +++---
homogeneous_halfspace_HEX8/README_kernel | 6 +++---
homogeneous_halfspace_HEX8/process.sh | 6 +++---
homogeneous_poroelastic/README | 2 +-
layered_halfspace/README | 6 +++---
layered_halfspace/process.sh | 6 +++---
meshfem3D_examples/many_interfaces/README | 4 ++--
.../many_interfaces/go_process_pbs.bash | 22 +++++++++++-----------
meshfem3D_examples/many_interfaces/process.sh | 20 ++++++++++----------
meshfem3D_examples/simple_model/README | 4 ++--
meshfem3D_examples/simple_model/process.sh | 6 +++---
meshfem3D_examples/socal1D/README | 10 +++++-----
meshfem3D_examples/socal1D/process.sh | 12 ++++++------
noise_tomography/NOISE_TOMOGRAPHY.m | 6 +++---
noise_tomography/README | 2 +-
noise_tomography/pre-processing.sh | 20 ++++++++++----------
tomographic_model/README | 10 +++++-----
tomographic_model/process.sh | 8 ++++----
waterlayered_halfspace/README | 6 +++---
waterlayered_halfspace/process.sh | 6 +++---
26 files changed, 102 insertions(+), 102 deletions(-)
diff --git a/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/run_inhomogeneous.bash b/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/run_inhomogeneous.bash
index e1869db..4f65cdd 100755
--- a/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/run_inhomogeneous.bash
+++ b/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/run_inhomogeneous.bash
@@ -3,9 +3,9 @@ echo
echo `date`
echo
-NSTEP=`grep NSTEP ./in_data_files/Par_file | cut -d = -f 2 | sed 's/ //g'`
-DT=`grep DT ./in_data_files/Par_file | cut -d = -f 2 | sed 's/ //g'`
-NPROC=`grep NPROC ./in_data_files/Par_file | cut -d = -f 2 `
+NSTEP=`grep NSTEP ./DATA/Par_file | cut -d = -f 2 | sed 's/ //g'`
+DT=`grep DT ./DATA/Par_file | cut -d = -f 2 | sed 's/ //g'`
+NPROC=`grep NPROC ./DATA/Par_file | cut -d = -f 2 `
#daniel:
echo "Par_file parameters:"
@@ -27,7 +27,7 @@ echo
#echo "NPROC=$NPROC"
bin="$PWD/bin"
-in_data_files="$bin/../in_data_files"
+DATA="$bin/../DATA"
in_out_files="$bin/../in_out_files"
models="$bin/../models"
SESAME="$bin/../../../../"
@@ -102,7 +102,7 @@ $MPIFC $bin/../adj_seismogram.f90 -o ./xadj > $bin/../compile.log
$MPIFC $bin/../postprocessing.f90 -o ./xpostprocessing > $bin/../compile.log
########################### dat ########################################
-FILE="$in_data_files/Par_file"
+FILE="$DATA/Par_file"
sed -e "s#^SIMULATION_TYPE.*#SIMULATION_TYPE = 1 #g" < $FILE > ./tmp; mv ./tmp $FILE
sed -e "s#^SAVE_FORWARD.*#SAVE_FORWARD = .true. #g" < $FILE > ./tmp; mv ./tmp $FILE
sed -e "s#^NSTEP.*#NSTEP = $NSTEP #g" < $FILE > ./tmp; mv ./tmp $FILE
@@ -145,7 +145,7 @@ cp $in_out_files/DATABASES_MPI/*vs.bin $models/initial_model/
$MPIRUN ./xadj $NSTEP $DT
########################### adj ########################################
-FILE="$in_data_files/Par_file"
+FILE="$DATA/Par_file"
sed -e "s#^SIMULATION_TYPE.*#SIMULATION_TYPE = 3 #g" < $FILE > ./tmp; mv ./tmp $FILE
sed -e "s#^SAVE_FORWARD.*#SAVE_FORWARD = .false. #g" < $FILE > ./tmp; mv ./tmp $FILE
diff --git a/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/run_inhomogeneous.bash b/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/run_inhomogeneous.bash
index ebfc838..3811f36 100755
--- a/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/run_inhomogeneous.bash
+++ b/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/run_inhomogeneous.bash
@@ -3,9 +3,9 @@ echo
echo `date`
echo
-NSTEP=`grep NSTEP ./in_data_files/Par_file | cut -d = -f 2 | sed 's/ //g'`
-DT=`grep DT ./in_data_files/Par_file | cut -d = -f 2 | sed 's/ //g'`
-NPROC=`grep NPROC ./in_data_files/Par_file | cut -d = -f 2 `
+NSTEP=`grep NSTEP ./DATA/Par_file | cut -d = -f 2 | sed 's/ //g'`
+DT=`grep DT ./DATA/Par_file | cut -d = -f 2 | sed 's/ //g'`
+NPROC=`grep NPROC ./DATA/Par_file | cut -d = -f 2 `
#daniel:
echo "Par_file parameters:"
@@ -27,7 +27,7 @@ echo
#echo "NPROC=$NPROC"
bin="$PWD/bin"
-in_data_files="$bin/../in_data_files"
+DATA="$bin/../DATA"
in_out_files="$bin/../in_out_files"
models="$bin/../models"
SESAME="$bin/../../../../"
@@ -102,7 +102,7 @@ $MPIFC $bin/../adj_seismogram.f90 -o ./xadj > $bin/../compile.log
$MPIFC $bin/../postprocessing.f90 -o ./xpostprocessing > $bin/../compile.log
########################### dat ########################################
-FILE="$in_data_files/Par_file"
+FILE="$DATA/Par_file"
sed -e "s#^SIMULATION_TYPE.*#SIMULATION_TYPE = 1 #g" < $FILE > ./tmp; mv ./tmp $FILE
sed -e "s#^SAVE_FORWARD.*#SAVE_FORWARD = .true. #g" < $FILE > ./tmp; mv ./tmp $FILE
sed -e "s#^NSTEP.*#NSTEP = $NSTEP #g" < $FILE > ./tmp; mv ./tmp $FILE
@@ -145,7 +145,7 @@ cp $in_out_files/DATABASES_MPI/*vs.bin $models/initial_model/
$MPIRUN ./xadj $NSTEP $DT
########################### adj ########################################
-FILE="$in_data_files/Par_file"
+FILE="$DATA/Par_file"
sed -e "s#^SIMULATION_TYPE.*#SIMULATION_TYPE = 3 #g" < $FILE > ./tmp; mv ./tmp $FILE
sed -e "s#^SAVE_FORWARD.*#SAVE_FORWARD = .false. #g" < $FILE > ./tmp; mv ./tmp $FILE
diff --git a/Mount_StHelens/README b/Mount_StHelens/README
index 0470e23..4bba15f 100644
--- a/Mount_StHelens/README
+++ b/Mount_StHelens/README
@@ -96,6 +96,6 @@ step-by-step tutorial:
this script handles the following steps:
- decomposes mesh files (example creates 4 partitions from mesh files given in MESH/)
- runs the database generation
- - runs a single forward simulation (using the default setup files in in_data_files/)
+ - runs a single forward simulation (using the default setup files in DATA/)
diff --git a/Mount_StHelens/process.sh b/Mount_StHelens/process.sh
index 7e11fe3..097e37a 100755
--- a/Mount_StHelens/process.sh
+++ b/Mount_StHelens/process.sh
@@ -53,9 +53,9 @@ echo
./bin/xdecompose_mesh_SCOTCH $NPROC MESH/ in_out_files/DATABASES_MPI/
# 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/
+cp DATA/Par_file in_out_files/OUTPUT_FILES/
+cp DATA/CMTSOLUTION in_out_files/OUTPUT_FILES/
+cp DATA/STATIONS in_out_files/OUTPUT_FILES/
# runs database generation
echo
diff --git a/homogeneous_halfspace_HEX27/HOWTO_run_this_example.txt b/homogeneous_halfspace_HEX27/HOWTO_run_this_example.txt
index 6466d1a..3504ac6 100644
--- a/homogeneous_halfspace_HEX27/HOWTO_run_this_example.txt
+++ b/homogeneous_halfspace_HEX27/HOWTO_run_this_example.txt
@@ -2,7 +2,7 @@
To run this example on two processor cores for instance, type this (replace "2" with another value in the three lines below if you want to use more processor cores):
-./bin/xdecompose_mesh_SCOTCH 2 in_data_files/MESH in_out_files/DATABASES_MPI
+./bin/xdecompose_mesh_SCOTCH 2 DATA/MESH in_out_files/DATABASES_MPI
mpirun -np 2 ./bin/xgenerate_databases
diff --git a/homogeneous_halfspace_HEX8/HOWTO_run_this_example.txt b/homogeneous_halfspace_HEX8/HOWTO_run_this_example.txt
index 6466d1a..3504ac6 100644
--- a/homogeneous_halfspace_HEX8/HOWTO_run_this_example.txt
+++ b/homogeneous_halfspace_HEX8/HOWTO_run_this_example.txt
@@ -2,7 +2,7 @@
To run this example on two processor cores for instance, type this (replace "2" with another value in the three lines below if you want to use more processor cores):
-./bin/xdecompose_mesh_SCOTCH 2 in_data_files/MESH in_out_files/DATABASES_MPI
+./bin/xdecompose_mesh_SCOTCH 2 DATA/MESH in_out_files/DATABASES_MPI
mpirun -np 2 ./bin/xgenerate_databases
diff --git a/homogeneous_halfspace_HEX8/README b/homogeneous_halfspace_HEX8/README
index 817be5f..89f6210 100644
--- a/homogeneous_halfspace_HEX8/README
+++ b/homogeneous_halfspace_HEX8/README
@@ -40,10 +40,10 @@ step-by-step tutorial:
note: you may need to adjust the commands (e.g., -q or -l)
-2. copy three input files from examples directory into SPECFEM3D/in_data_files/
+2. copy three input files from examples directory into SPECFEM3D/DATA/
- > cd examples/homogeneous_halfspace/in_data_files/
- > cp CMTSOLUTION Par_file STATIONS ../../../in_data_files/
+ > cd examples/homogeneous_halfspace/DATA/
+ > cp CMTSOLUTION Par_file STATIONS ../../../DATA/
3. create mesh:
diff --git a/homogeneous_halfspace_HEX8/README_kernel b/homogeneous_halfspace_HEX8/README_kernel
index ecd3c1e..57f942e 100644
--- a/homogeneous_halfspace_HEX8/README_kernel
+++ b/homogeneous_halfspace_HEX8/README_kernel
@@ -23,7 +23,7 @@ step-by-step kernel tutorial:
> cd /SPECFEM3D
> ./utils/change_simulation_type.pl -F
- or change manually in /SPECFEM3D/in_data_files/Par_file:
+ or change manually in /SPECFEM3D/DATA/Par_file:
...
# forward or adjoint simulation
SIMULATION_TYPE = 1
@@ -70,7 +70,7 @@ step-by-step kernel tutorial:
- setup adjoint stations file STATIONS_ADJOINT containing the receiver stations locations
which will have adjoint source files in in_out_files/SEM/:
> cd /SPECFEM3D
- > cp examples/homogeneous_halfspace/in_data_files/STATIONS_ADJOINT in_data_files/
+ > cp examples/homogeneous_halfspace/DATA/STATIONS_ADJOINT DATA/
3. run adjoint simulation with restored backward wavefields:
@@ -79,7 +79,7 @@ step-by-step kernel tutorial:
> cd /SPECFEM3D
> ./utils/change_simulation_type.pl -b
- or change manually in /SPECFEM3D/in_data_files/Par_file:
+ or change manually in /SPECFEM3D/DATA/Par_file:
# forward or adjoint simulation
SIMULATION_TYPE = 3
SAVE_FORWARD = .false.
diff --git a/homogeneous_halfspace_HEX8/process.sh b/homogeneous_halfspace_HEX8/process.sh
index 54da7bd..76001ce 100755
--- a/homogeneous_halfspace_HEX8/process.sh
+++ b/homogeneous_halfspace_HEX8/process.sh
@@ -53,9 +53,9 @@ echo
./bin/xdecompose_mesh_SCOTCH $NPROC MESH/ in_out_files/DATABASES_MPI/
# 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/
+cp DATA/Par_file in_out_files/OUTPUT_FILES/
+cp DATA/CMTSOLUTION in_out_files/OUTPUT_FILES/
+cp DATA/STATIONS in_out_files/OUTPUT_FILES/
# runs database generation
echo
diff --git a/homogeneous_poroelastic/README b/homogeneous_poroelastic/README
index fe4d096..c891f17 100644
--- a/homogeneous_poroelastic/README
+++ b/homogeneous_poroelastic/README
@@ -84,7 +84,7 @@ step-by-step tutorial:
5. run simulation:
- copy three files -- Par_file CMTSOLUTION STATIONS -- from
- SPECFEM3D/examples/homogeneous_poro/ to SPECFEM3D/in_data_files/
+ SPECFEM3D/examples/homogeneous_poro/ to SPECFEM3D/DATA/
- compile specfem3D:
> make xspecfem3D
diff --git a/layered_halfspace/README b/layered_halfspace/README
index 2548487..e6337d8 100644
--- a/layered_halfspace/README
+++ b/layered_halfspace/README
@@ -11,10 +11,10 @@ step-by-step tutorial:
0. run the example in the directory homogeneous_halfspace
-1. copy three input files from examples directory into SPECFEM3D/in_data_files/:
+1. copy three input files from examples directory into SPECFEM3D/DATA/:
- > cd examples/layered_halfspace/in_data_files/
- > cp CMTSOLUTION Par_file STATIONS ../../../in_data_files/
+ > cd examples/layered_halfspace/DATA/
+ > cp CMTSOLUTION Par_file STATIONS ../../../DATA/
2. create mesh:
diff --git a/layered_halfspace/process.sh b/layered_halfspace/process.sh
index 7b36e96..a21795a 100755
--- a/layered_halfspace/process.sh
+++ b/layered_halfspace/process.sh
@@ -51,9 +51,9 @@ echo
./bin/xdecompose_mesh_SCOTCH $NPROC MESH/ in_out_files/DATABASES_MPI/
# 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/
+cp DATA/Par_file in_out_files/OUTPUT_FILES/
+cp DATA/CMTSOLUTION in_out_files/OUTPUT_FILES/
+cp DATA/STATIONS in_out_files/OUTPUT_FILES/
# runs database generation
echo
diff --git a/meshfem3D_examples/many_interfaces/README b/meshfem3D_examples/many_interfaces/README
index d410f86..0b0d222 100644
--- a/meshfem3D_examples/many_interfaces/README
+++ b/meshfem3D_examples/many_interfaces/README
@@ -19,9 +19,9 @@ WARNING: We do not recommend running this as a test example, due to its requirem
1. Set up input files.
> cd SPECFEM3D
- > rsync -av examples/meshfem3D_examples/many_interfaces/ in_data_files/meshfem3D_files/
+ > rsync -av examples/meshfem3D_examples/many_interfaces/ DATA/meshfem3D_files/
- > cd in_data_files/meshfem3D_files/
+ > cd DATA/meshfem3D_files/
> cp Par_file CMTSOLUTION STATIONS ..
> cd SPECFEM3D
diff --git a/meshfem3D_examples/many_interfaces/go_process_pbs.bash b/meshfem3D_examples/many_interfaces/go_process_pbs.bash
index f6be768..a83e7ff 100755
--- a/meshfem3D_examples/many_interfaces/go_process_pbs.bash
+++ b/meshfem3D_examples/many_interfaces/go_process_pbs.bash
@@ -42,15 +42,15 @@ 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/
+mkdir -p DATA
+mkdir -p DATA/meshfem3D_files/
-cp Mesh_Par_file in_data_files/meshfem3D_files/
-cp example_*.dat in_data_files/meshfem3D_files/
+cp Mesh_Par_file DATA/meshfem3D_files/
+cp example_*.dat DATA/meshfem3D_files/
-cp Par_file in_data_files/
-cp CMTSOLUTION in_data_files/
-cp STATIONS in_data_files/
+cp Par_file DATA/
+cp CMTSOLUTION DATA/
+cp STATIONS DATA/
# compilation of executables must have been done prior on front node
# links executables
@@ -63,7 +63,7 @@ cd ../
# script to run the mesher and the solver
# read Par_file to get information about the run
# compute total number of nodes needed
-NPROC=`grep NPROC in_data_files/Par_file | cut -d = -f 2 `
+NPROC=`grep NPROC DATA/Par_file | cut -d = -f 2 `
# total number of nodes is the product of the values read
numnodes=$NPROC
@@ -78,9 +78,9 @@ 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/
+cp DATA/Par_file in_out_files/OUTPUT_FILES/
+cp DATA/CMTSOLUTION in_out_files/OUTPUT_FILES/
+cp DATA/STATIONS in_out_files/OUTPUT_FILES/
# runs database generation
echo
diff --git a/meshfem3D_examples/many_interfaces/process.sh b/meshfem3D_examples/many_interfaces/process.sh
index 0586c4d..d1c6349 100755
--- a/meshfem3D_examples/many_interfaces/process.sh
+++ b/meshfem3D_examples/many_interfaces/process.sh
@@ -30,15 +30,15 @@ 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/
+mkdir -p DATA
+mkdir -p DATA/meshfem3D_files/
-cp Mesh_Par_file in_data_files/meshfem3D_files/
-cp example_*.dat in_data_files/meshfem3D_files/
+cp Mesh_Par_file DATA/meshfem3D_files/
+cp example_*.dat DATA/meshfem3D_files/
-cp Par_file in_data_files/
-cp CMTSOLUTION in_data_files/
-cp STATIONS in_data_files/
+cp Par_file DATA/
+cp CMTSOLUTION DATA/
+cp STATIONS DATA/
# compiles executables in root directory
@@ -63,9 +63,9 @@ 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/
+cp DATA/Par_file in_out_files/OUTPUT_FILES/
+cp DATA/CMTSOLUTION in_out_files/OUTPUT_FILES/
+cp DATA/STATIONS in_out_files/OUTPUT_FILES/
# runs database generation
echo
diff --git a/meshfem3D_examples/simple_model/README b/meshfem3D_examples/simple_model/README
index 9ce22ad..7d0590c 100644
--- a/meshfem3D_examples/simple_model/README
+++ b/meshfem3D_examples/simple_model/README
@@ -15,9 +15,9 @@ 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/simple_model/ DATA/meshfem3D_files/
- > cd in_data_files/meshfem3D_files/
+ > cd DATA/meshfem3D_files/
> cp Par_file CMTSOLUTION STATIONS ..
> cd SPECFEM3D
diff --git a/meshfem3D_examples/simple_model/process.sh b/meshfem3D_examples/simple_model/process.sh
index abc1a52..95df350 100755
--- a/meshfem3D_examples/simple_model/process.sh
+++ b/meshfem3D_examples/simple_model/process.sh
@@ -42,9 +42,9 @@ cp ../../../bin/* bin/
if [ ! -e bin/xspecfem3D ]; then echo "compilation failed, please check..."; exit 1; fi
# 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/
+cp DATA/Par_file in_out_files/OUTPUT_FILES/
+cp DATA/CMTSOLUTION in_out_files/OUTPUT_FILES/
+cp DATA/STATIONS in_out_files/OUTPUT_FILES/
# creates and decomposes mesh
echo
diff --git a/meshfem3D_examples/socal1D/README b/meshfem3D_examples/socal1D/README
index d023047..b9fa51a 100644
--- a/meshfem3D_examples/socal1D/README
+++ b/meshfem3D_examples/socal1D/README
@@ -24,9 +24,9 @@ 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/ in_data_files/meshfem3D_files/
+ > rsync -av examples/meshfem3D_examples/socal1D/ DATA/meshfem3D_files/
- > cd in_data_files/meshfem3D_files/
+ > cd DATA/meshfem3D_files/
> cp Par_file CMTSOLUTION STATIONS ..
> cd SPECFEM3D
@@ -83,7 +83,7 @@ To use the same 1D model but covering a larger region using 168 cores, follow th
1. modify Mesh_Par_file:
- > cd in_data_files/meshfem3D_files
+ > cd DATA/meshfem3D_files
> cp Mesh_Par_file_168 Mesh_Par_file
2. modify Par_file:
@@ -107,7 +107,7 @@ To run the same simulation but using 42 cores, follow these steps.
1. modify Mesh_Par_file:
- > cd in_data_files/meshfem3D_files
+ > cd DATA/meshfem3D_files
> cp Mesh_Par_file_042 Mesh_Par_file
2. modify Par_file:
@@ -126,4 +126,4 @@ To run the same simulation but using 42 cores, follow these steps.
- simulation should take about 5 minutes.
- seismograms will not exactly match those in REF_SEIS, since the simulation volume is different.
-----------------------------------------------------------------------
\ No newline at end of file
+---------------------------------------------------------------------
diff --git a/meshfem3D_examples/socal1D/process.sh b/meshfem3D_examples/socal1D/process.sh
index 2b69495..c97cbb0 100755
--- a/meshfem3D_examples/socal1D/process.sh
+++ b/meshfem3D_examples/socal1D/process.sh
@@ -30,8 +30,8 @@ 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/
+mkdir -p DATA
+mkdir -p DATA/meshfem3D_files/
# compiles executables in root directory
cd ../../../
@@ -45,10 +45,10 @@ cp ../../../bin/* bin/
if [ ! -e bin/xspecfem3D ]; then echo "compilation failed, please check..."; exit 1; fi
# stores setup
-cp in_data_files/meshfem3D_files/Mesh_Par_file in_out_files/OUTPUT_FILES/
-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/
+cp DATA/meshfem3D_files/Mesh_Par_file in_out_files/OUTPUT_FILES/
+cp DATA/Par_file in_out_files/OUTPUT_FILES/
+cp DATA/CMTSOLUTION in_out_files/OUTPUT_FILES/
+cp DATA/STATIONS in_out_files/OUTPUT_FILES/
# decomposes mesh
echo
diff --git a/noise_tomography/NOISE_TOMOGRAPHY.m b/noise_tomography/NOISE_TOMOGRAPHY.m
index d8e2fc9..322cf8a 100644
--- a/noise_tomography/NOISE_TOMOGRAPHY.m
+++ b/noise_tomography/NOISE_TOMOGRAPHY.m
@@ -25,11 +25,11 @@ function [] = NOISE_TOMOGRAPHY(NSTEP,dt,Tmin,Tmax,NOISE_MODEL)
% ATTENTION:
% ***NEVER*** try to calculate "NSTEP" and "dt" by yourself!
% They can be found when you compile the SPECFEM3D package,
-% with the correct in_data_files/Par_file
-% If in_data_files/Par_file is not specified for noise tomography simulations,
+% with the correct DATA/Par_file
+% If DATA/Par_file is not specified for noise tomography simulations,
% you won't get correct values either!
% It is highly recommended that you compile the package with the correct
-% in_data_files/Par_file you will be using
+% DATA/Par_file you will be using
%
%
% Output from the example above:
diff --git a/noise_tomography/README b/noise_tomography/README
index 9a2974b..58f06a8 100644
--- a/noise_tomography/README
+++ b/noise_tomography/README
@@ -21,7 +21,7 @@ Noise Cross-Correlation Sensitivity Kernels (Tromp et al., 2010, GJI)
**************
This file --- ./README
- Four folders contain default input files for the example --- ./bin ./DATABASES_MPI ./in_data_files ./NOISE_TOMOGRAPHY
+ Four folders contain default input files for the example --- ./bin ./DATABASES_MPI ./DATA ./NOISE_TOMOGRAPHY
Two matlab files may help you to calculate noise spectrum --- ./NOISE_TOMOGRAPHY.m ./PetersonNoiseModel.m
Job script --- ./pre-processing.sh
One folder shows the reference kernels --- ./REF_KERNELS
diff --git a/noise_tomography/pre-processing.sh b/noise_tomography/pre-processing.sh
index ec29f7e..af5239c 100755
--- a/noise_tomography/pre-processing.sh
+++ b/noise_tomography/pre-processing.sh
@@ -29,7 +29,7 @@ cd $script_dir
# those values are default for SPECFEM3D
bin="$script_dir/bin"
in_out_files="$script_dir/in_out_files"
-in_data_files="$script_dir/in_data_files"
+DATA="$script_dir/DATA"
# specify which kernel we want to visualize
# since the Rayleigh wave is dominantly dependent on shear wave speed, we choose shear wave speed kernels
@@ -57,9 +57,9 @@ cp $script_dir/NOISE_TOMOGRAPHY/nu_master $in_out_files/NOISE_TOM
cp $script_dir/DATABASES_MPI/proc* $in_out_files/DATABASES_MPI/
# copy simulation parameter files
-#cp $script_dir/in_data_files/Par_file* $in_data_files/
-#cp $script_dir/in_data_files/CMTSOLUTION $in_data_files/
-#cp $script_dir/in_data_files/STATIONS* $in_data_files/
+#cp $script_dir/DATA/Par_file* $DATA/
+#cp $script_dir/DATA/CMTSOLUTION $DATA/
+#cp $script_dir/DATA/STATIONS* $DATA/
# copy and compile subroutine for adjoint source calculation
#cp $script_dir/bin/adj_traveltime_filter.f90 $bin/
@@ -90,12 +90,12 @@ echo
cp $in_out_files/NOISE_TOMOGRAPHY/irec_master_noise_contribution1 $in_out_files/NOISE_TOMOGRAPHY/irec_master_noise
# step 1 of noise simulation
-cp $in_data_files/Par_file_step1 $in_data_files/Par_file
+cp $DATA/Par_file_step1 $DATA/Par_file
mpirun -np 4 ./xgenerate_databases
mpirun -np 4 ./xspecfem3D
# step 2 of noise simulation
-cp $in_data_files/Par_file_step2 $in_data_files/Par_file
+cp $DATA/Par_file_step2 $DATA/Par_file
mpirun -np 4 ./xspecfem3D
mv $in_out_files/OUTPUT_FILES/X2.DB.BXZ.semd $in_out_files/SEM/
@@ -117,7 +117,7 @@ awk '{print $1,0.0}' $in_out_files/SEM/X2.DB.BXZ.adj > $in_out_files/SEM/X1.DB.B
# step 3 of noise simulation
-cp $in_data_files/Par_file_step3 $in_data_files/Par_file
+cp $DATA/Par_file_step3 $DATA/Par_file
mpirun -np 4 ./xspecfem3D
# store kernels
@@ -148,11 +148,11 @@ echo
cp $in_out_files/NOISE_TOMOGRAPHY/irec_master_noise_contribution2 $in_out_files/NOISE_TOMOGRAPHY/irec_master_noise
# step 1 of noise simulation
-cp $in_data_files/Par_file_step1 $in_data_files/Par_file
+cp $DATA/Par_file_step1 $DATA/Par_file
mpirun -np 4 ./xspecfem3D
# step 2 of noise simulation
-cp $in_data_files/Par_file_step2 $in_data_files/Par_file
+cp $DATA/Par_file_step2 $DATA/Par_file
mpirun -np 4 ./xspecfem3D
# calculating adjoint source
@@ -170,7 +170,7 @@ awk '{print $1,0.0}' $in_out_files/SEM/X1.DB.BXZ.adj > $in_out_files/SEM/X2.DB.B
# step 3 of noise simulation
-cp $in_data_files/Par_file_step3 $in_data_files/Par_file
+cp $DATA/Par_file_step3 $DATA/Par_file
mpirun -np 4 ./xspecfem3D
# store kernels
diff --git a/tomographic_model/README b/tomographic_model/README
index 6d345a5..8e7aaa6 100644
--- a/tomographic_model/README
+++ b/tomographic_model/README
@@ -9,9 +9,9 @@ step-by-step tutorial:
0. run the example in the directory homogeneous_halfspace
-1. copy three input files from examples directory into SPECFEM3D/in_data_files/:
- > cd examples/tomographic_model/in_data_files/
- > cp CMTSOLUTION Par_file STATIONS ../../../in_data_files/
+1. copy three input files from examples directory into SPECFEM3D/DATA/:
+ > cd examples/tomographic_model/DATA/
+ > cp CMTSOLUTION Par_file STATIONS ../../../DATA/
2. create mesh:
@@ -35,8 +35,8 @@ step-by-step tutorial:
which creates an example model: tomography_model.xyz
( elastic model with a constant velocity gradient with depth)
- - copy (or link) this file into directory SPECFEM3D/in_data_files/
- > cp tomography_model.xyz ../../in_data_files/
+ - copy (or link) this file into directory SPECFEM3D/DATA/
+ > cp tomography_model.xyz ../../DATA/
note: this file is read in by subroutine read_model_tomography in
SPECFEM3D/src/generate_databases/model_tomography.f90,
diff --git a/tomographic_model/process.sh b/tomographic_model/process.sh
index 0fbf359..45c3ba4 100755
--- a/tomographic_model/process.sh
+++ b/tomographic_model/process.sh
@@ -35,7 +35,7 @@ rm -rf in_out_files/DATABASES_MPI/*
# sets up tomography model file
./create_tomography_model_file.sh
-mv tomography_model.xyz in_data_files/
+mv tomography_model.xyz DATA/
echo
# compiles executables in root directory
@@ -58,9 +58,9 @@ echo
./bin/xdecompose_mesh_SCOTCH $NPROC MESH/ in_out_files/DATABASES_MPI/
# 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/
+cp DATA/Par_file in_out_files/OUTPUT_FILES/
+cp DATA/CMTSOLUTION in_out_files/OUTPUT_FILES/
+cp DATA/STATIONS in_out_files/OUTPUT_FILES/
# runs database generation
echo
diff --git a/waterlayered_halfspace/README b/waterlayered_halfspace/README
index 641b6d4..26d4a40 100644
--- a/waterlayered_halfspace/README
+++ b/waterlayered_halfspace/README
@@ -11,10 +11,10 @@ step-by-step tutorial:
0. run the example in the directory homogeneous_halfspace
-1. copy three input files from examples directory into SPECFEM3D/in_data_files/
+1. copy three input files from examples directory into SPECFEM3D/DATA/
- > cd examples/waterlayered_halfspace/in_data_files/
- > cp CMTSOLUTION Par_file STATIONS ../../../in_data_files/
+ > cd examples/waterlayered_halfspace/DATA/
+ > cp CMTSOLUTION Par_file STATIONS ../../../DATA/
2. create mesh:
diff --git a/waterlayered_halfspace/process.sh b/waterlayered_halfspace/process.sh
index 1d38e3f..f538e22 100755
--- a/waterlayered_halfspace/process.sh
+++ b/waterlayered_halfspace/process.sh
@@ -53,9 +53,9 @@ echo
./bin/xdecompose_mesh_SCOTCH $NPROC MESH/ in_out_files/DATABASES_MPI/
# 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/
+cp DATA/Par_file in_out_files/OUTPUT_FILES/
+cp DATA/CMTSOLUTION in_out_files/OUTPUT_FILES/
+cp DATA/STATIONS in_out_files/OUTPUT_FILES/
# runs database generation
echo
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