Mon Oct 22 09:06:16 PDT 2012

Author: dkomati1
Date: 2012-10-22 09:06:16 -0700 (Mon, 22 Oct 2012)
New Revision: 20872

Modified:
   seismo/3D/SPECFEM3D/trunk/Makefile.in
   seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/run_inhomogeneous.bash
   seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/run_inhomogeneous.bash
   seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/README
   seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/process.sh
   seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/HOWTO_run_this_example.txt
   seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8/HOWTO_run_this_example.txt
   seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8/README
   seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8/README_kernel
   seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8/process.sh
   seismo/3D/SPECFEM3D/trunk/examples/homogeneous_poroelastic/README
   seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/README
   seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/process.sh
   seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/many_interfaces/README
   seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/many_interfaces/go_process_pbs.bash
   seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/many_interfaces/process.sh
   seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/simple_model/README
   seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/simple_model/process.sh
   seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/README
   seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/process.sh
   seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/NOISE_TOMOGRAPHY.m
   seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/README
   seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/pre-processing.sh
   seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/README
   seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/process.sh
   seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/README
   seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/process.sh
   seismo/3D/SPECFEM3D/trunk/src/generate_databases/model_tomography.f90
   seismo/3D/SPECFEM3D/trunk/src/shared/constants.h.in
   seismo/3D/SPECFEM3D/trunk/src/shared/read_value_parameters.f90
   seismo/3D/SPECFEM3D/trunk/utils/Cluster/go_generate_databases
   seismo/3D/SPECFEM3D/trunk/utils/Cluster/go_solver
   seismo/3D/SPECFEM3D/trunk/utils/Cluster/lsf/go_generate_databases_lsf.bash
   seismo/3D/SPECFEM3D/trunk/utils/Cluster/lsf/go_mesher_solver_lsf_basin.forward
   seismo/3D/SPECFEM3D/trunk/utils/Cluster/lsf/go_mesher_solver_lsf_basin.kernel
   seismo/3D/SPECFEM3D/trunk/utils/Cluster/lsf/go_solver_lsf.bash
   seismo/3D/SPECFEM3D/trunk/utils/Cluster/lsf/run_lsf.bash
   seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_decomposer_pbs.bash
   seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_generate_databases_pbs.bash
   seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_mesher_pbs.bash
   seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_solver_pbs.bash
   seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/valgrind_go_solver_pbs.bash
   seismo/3D/SPECFEM3D/trunk/utils/Cluster/run3d.csh
   seismo/3D/SPECFEM3D/trunk/utils/Cluster/sge/go_generate_databases_sge.bash
   seismo/3D/SPECFEM3D/trunk/utils/Cluster/sge/go_solver_sge.bash
   seismo/3D/SPECFEM3D/trunk/utils/Visualization/GMT/movie2gif.gmt.pl
   seismo/3D/SPECFEM3D/trunk/utils/Visualization/GMT/plot_shakemap.gmt.pl
   seismo/3D/SPECFEM3D/trunk/utils/change_simulation_type.pl
   seismo/3D/SPECFEM3D/trunk/utils/cmt_frechet/cmt_frechet.csh
   seismo/3D/SPECFEM3D/trunk/utils/cmt_frechet/cmt_frechet1.csh
   seismo/3D/SPECFEM3D/trunk/utils/cmt_frechet/go_solver_cmt
   seismo/3D/SPECFEM3D/trunk/utils/unused_routines/create_header_file.f90
Log:
replaced in_data_files with DATA in all files and scripts


Modified: seismo/3D/SPECFEM3D/trunk/Makefile.in
===================================================================

--- seismo/3D/SPECFEM3D/trunk/Makefile.in	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/Makefile.in	2012-10-22 16:06:16 UTC (rev 20872)
@@ -84,7 +84,7 @@
 required: bin lib obj
 
 backup:
-	cp -rp src in_data_files Makefile go_generate_databases* go_mesher* go_solver* mymachines bak
+	cp -rp src DATA Makefile go_generate_databases* go_mesher* go_solver* mymachines bak
 
 bak: backup
 

Modified: seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/run_inhomogeneous.bash
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/run_inhomogeneous.bash	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/run_inhomogeneous.bash	2012-10-22 16:06:16 UTC (rev 20872)
@@ -3,9 +3,9 @@
 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 "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/../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 @@
 $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
 
@@ -155,7 +155,7 @@
 #daniel
 cp -rp $in_out_files/OUTPUT_FILES $in_out_files/OUTPUT_FILES.syn.adjoint
 
-./xpostprocessing $NSTEP $DT $NPROC 
+./xpostprocessing $NSTEP $DT $NPROC
 
 if [ "$do_setup" == "" ]; then
 
@@ -171,7 +171,7 @@
 
 fi
 
-echo 
+echo
 echo "done: `date`"
 echo
 

Modified: seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/run_inhomogeneous.bash
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/run_inhomogeneous.bash	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/run_inhomogeneous.bash	2012-10-22 16:06:16 UTC (rev 20872)
@@ -3,9 +3,9 @@
 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 "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/../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 @@
 $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
 
@@ -155,7 +155,7 @@
 #daniel
 cp -rp $in_out_files/OUTPUT_FILES $in_out_files/OUTPUT_FILES.syn.adjoint
 
-./xpostprocessing $NSTEP $DT $NPROC 
+./xpostprocessing $NSTEP $DT $NPROC
 
 if [ "$do_setup" == "" ]; then
 
@@ -171,7 +171,7 @@
 
 fi
 
-echo 
+echo
 echo "done: `date`"
 echo
 

Modified: seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/README
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/README	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/README	2012-10-22 16:06:16 UTC (rev 20872)
@@ -70,8 +70,8 @@
       and should create a file: topo.stl
 
       note: CUBIT has limited features when using facets/STL file formats.
-            It is in general preferable to work with ACIS formats. 
-            
+            It is in general preferable to work with ACIS formats.
+
             However, using an ACIS topography file leads to a slower meshing process.
             This is why we prefer to use STL file formats here, but rely on
             a developer command (script was tested using CUBIT version 12.2).
@@ -92,10 +92,10 @@
 
     - run script 'process.sh' in this example directory:
       > ./process.sh
-            
-      this script handles the following steps: 
-        - decomposes mesh files (example creates 4 partitions from mesh files given in MESH/) 
+
+      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/)
 
 

Modified: seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/process.sh
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/process.sh	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/process.sh	2012-10-22 16:06:16 UTC (rev 20872)
@@ -53,9 +53,9 @@
 ./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

Modified: seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/HOWTO_run_this_example.txt
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/HOWTO_run_this_example.txt	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/HOWTO_run_this_example.txt	2012-10-22 16:06:16 UTC (rev 20872)
@@ -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
 

Modified: seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8/HOWTO_run_this_example.txt
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8/HOWTO_run_this_example.txt	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8/HOWTO_run_this_example.txt	2012-10-22 16:06:16 UTC (rev 20872)
@@ -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
 

Modified: seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8/README
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8/README	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8/README	2012-10-22 16:06:16 UTC (rev 20872)
@@ -40,10 +40,10 @@
      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:
@@ -131,7 +131,7 @@
       SPECFEM3D/examples/homogeneous_halfspace/REF_SEIS/
 
    - option 1: from SPECFEM3D/, quick viewing using xmgrace (if available):
-     
+
      > xmgrace examples/homogeneous_halfspace/REF_SEIS/*Z.semd &
      > xmgrace in_out_files/OUTPUT_FILES/*Z.semd &
 

Modified: seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8/README_kernel
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8/README_kernel	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8/README_kernel	2012-10-22 16:06:16 UTC (rev 20872)
@@ -23,7 +23,7 @@
      > 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
@@ -53,7 +53,7 @@
      > cd /SPECFEM3D
      > ./utils/adjoint_sources/traveltime/xcreate_adjsrc_traveltime 10. 25. 3 in_out_files/OUTPUT_FILES/X20.DB.BX*.semd
 
-     note: the traveltime adjoint source above uses the signal which arrives 
+     note: the traveltime adjoint source above uses the signal which arrives
            within a time window between 10 - 25 seconds and on the Z-component only.
 
    - make designated directory for adjoint sources:
@@ -70,7 +70,7 @@
    - 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 @@
      > 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.

Modified: seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8/process.sh
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8/process.sh	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8/process.sh	2012-10-22 16:06:16 UTC (rev 20872)
@@ -53,9 +53,9 @@
 ./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

Modified: seismo/3D/SPECFEM3D/trunk/examples/homogeneous_poroelastic/README
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/homogeneous_poroelastic/README	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/examples/homogeneous_poroelastic/README	2012-10-22 16:06:16 UTC (rev 20872)
@@ -84,7 +84,7 @@
 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

Modified: seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/README
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/README	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/README	2012-10-22 16:06:16 UTC (rev 20872)
@@ -11,10 +11,10 @@
 
 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:

Modified: seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/process.sh
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/process.sh	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/process.sh	2012-10-22 16:06:16 UTC (rev 20872)
@@ -51,9 +51,9 @@
 ./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

Modified: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/many_interfaces/README
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/many_interfaces/README	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/many_interfaces/README	2012-10-22 16:06:16 UTC (rev 20872)
@@ -19,9 +19,9 @@
 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
 
@@ -30,7 +30,7 @@
 
    - note: go_decomposer_pbs.bash is not used with the internal mesher
 
-2. compile and run internal mesher 
+2. compile and run internal mesher
 
    > make xmeshfem3D
 
@@ -49,7 +49,7 @@
    - submit job script:
      > qsub go_generate_databases_pbs.bash
 
-     this job will take about XX minutes and will create binary mesh files, 
+     this job will take about XX minutes and 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).

Modified: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/many_interfaces/go_process_pbs.bash
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/many_interfaces/go_process_pbs.bash	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/many_interfaces/go_process_pbs.bash	2012-10-22 16:06:16 UTC (rev 20872)
@@ -42,15 +42,15 @@
 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 @@
 # 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 @@
 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

Modified: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/many_interfaces/process.sh
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/many_interfaces/process.sh	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/many_interfaces/process.sh	2012-10-22 16:06:16 UTC (rev 20872)
@@ -30,15 +30,15 @@
 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 @@
 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

Modified: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/simple_model/README
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/simple_model/README	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/simple_model/README	2012-10-22 16:06:16 UTC (rev 20872)
@@ -15,9 +15,9 @@
 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
 
@@ -26,7 +26,7 @@
 
    - note: go_decomposer_pbs.bash is not used with the internal mesher
 
-2. compile and run internal mesher 
+2. compile and run internal mesher
 
    > make xmeshfem3D
 

Modified: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/simple_model/process.sh
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/simple_model/process.sh	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/simple_model/process.sh	2012-10-22 16:06:16 UTC (rev 20872)
@@ -42,9 +42,9 @@
 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

Modified: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/README
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/README	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/README	2012-10-22 16:06:16 UTC (rev 20872)
@@ -24,9 +24,9 @@
 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
 
@@ -83,9 +83,9 @@
 
 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:
 
   - open Par_file and modify NPROC: NPROC = 1 --> NPROC = 168
@@ -107,9 +107,9 @@
 
 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:
 
   - open Par_file and modify NPROC: NPROC = 168 --> NPROC = 42
@@ -126,4 +126,4 @@
    - 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
+---------------------------------------------------------------------

Modified: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/process.sh
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/process.sh	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/process.sh	2012-10-22 16:06:16 UTC (rev 20872)
@@ -30,12 +30,12 @@
 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 ../../../
-make 
+make
 make combine_vol_data
 cd $currentdir
 
@@ -45,10 +45,10 @@
 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
@@ -88,7 +88,7 @@
 # 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/ 
+# cd ../in_out_files/DATABASES_MPI/
 # (check that mesh2vtu.pl is working)
 # ../../../../../utils/Visualization/Paraview/mesh2vtu.pl -i vs.mesh -o vs.vtu
 #

Modified: seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/NOISE_TOMOGRAPHY.m
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/NOISE_TOMOGRAPHY.m	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/NOISE_TOMOGRAPHY.m	2012-10-22 16:06:16 UTC (rev 20872)
@@ -25,11 +25,11 @@
 % 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:

Modified: seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/README
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/README	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/README	2012-10-22 16:06:16 UTC (rev 20872)
@@ -21,7 +21,7 @@
 **************
 
    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
@@ -51,8 +51,8 @@
 
          "./DATABASES_MPI" contains the four partitions for the model which you can also create by
          copying the MESH files from example '../examples/homogeneous_halfspace' and
-         run 'xdecompose_mesh_SCOTCH' as explained in the file README in '../examples/homogeneous_halfspace'        
-         
+         run 'xdecompose_mesh_SCOTCH' as explained in the file README in '../examples/homogeneous_halfspace'
+
          Refer to '../examples/homogeneous_halfspace', if you don't know how to get them from CUBIT and SCOTCH.
 
    3.2 - Source and Receivers

Modified: seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/pre-processing.sh
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/pre-processing.sh	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/pre-processing.sh	2012-10-22 16:06:16 UTC (rev 20872)
@@ -29,7 +29,7 @@
 # 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/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 @@
 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 @@
 
 
 # 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
@@ -135,7 +135,7 @@
 # at the end of this part, we obtain the 1st contribution of the noise sensitivity kernel, stored as:
 # $in_out_files/NOISE_TOMOGRAPHY/1st_$kernel.vtu
 
-echo 
+echo
 
 #################### second contribution ###########################################################################
 # in this part, we start noise simulations for 2nd contribution of the noise sensitivity kernels
@@ -148,11 +148,11 @@
 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 @@
 
 
 # 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
@@ -188,6 +188,6 @@
 # $in_out_files/NOISE_TOMOGRAPHY/2nd_$kernel.vtu
 
 echo
-echo `date` 
+echo `date`
 echo "done"
 

Modified: seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/README
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/README	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/README	2012-10-22 16:06:16 UTC (rev 20872)
@@ -9,9 +9,9 @@
 
 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 @@
     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,

Modified: seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/process.sh
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/process.sh	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/process.sh	2012-10-22 16:06:16 UTC (rev 20872)
@@ -35,7 +35,7 @@
 
 # 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 @@
 ./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

Modified: seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/README
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/README	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/README	2012-10-22 16:06:16 UTC (rev 20872)
@@ -11,10 +11,10 @@
 
 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:

Modified: seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/process.sh
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/process.sh	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/process.sh	2012-10-22 16:06:16 UTC (rev 20872)
@@ -53,9 +53,9 @@
 ./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

Modified: seismo/3D/SPECFEM3D/trunk/src/generate_databases/model_tomography.f90
===================================================================
--- seismo/3D/SPECFEM3D/trunk/src/generate_databases/model_tomography.f90	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/src/generate_databases/model_tomography.f90	2012-10-22 16:06:16 UTC (rev 20872)
@@ -39,7 +39,7 @@
   include "constants.h"
 
   ! for external tomography:
-  ! file must be in ../in_data_files/ directory
+  ! file must be in ../DATA/ directory
   ! (regular spaced, xyz-block file in ascii)
 
   character (len=80) :: TOMO_FILENAME = 'tomography_model.xyz'

Modified: seismo/3D/SPECFEM3D/trunk/src/shared/constants.h.in
===================================================================
--- seismo/3D/SPECFEM3D/trunk/src/shared/constants.h.in	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/src/shared/constants.h.in	2012-10-22 16:06:16 UTC (rev 20872)
@@ -162,8 +162,8 @@
 !!-----------------------------------------------------------
 
 ! paths for inputs and outputs files
-  character(len=256), parameter :: IN_DATA_FILES_PATH = '../in_data_files/'
-  character(len=256), parameter :: MF_IN_DATA_FILES_PATH = '../in_data_files/meshfem3D_files/'
+  character(len=256), parameter :: IN_DATA_FILES_PATH = '../DATA/'
+  character(len=256), parameter :: MF_IN_DATA_FILES_PATH = '../DATA/meshfem3D_files/'
   character(len=256), parameter :: OUTPUT_FILES_PATH = '../in_out_files/OUTPUT_FILES/'
 
 

Modified: seismo/3D/SPECFEM3D/trunk/src/shared/read_value_parameters.f90
===================================================================
--- seismo/3D/SPECFEM3D/trunk/src/shared/read_value_parameters.f90	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/src/shared/read_value_parameters.f90	2012-10-22 16:06:16 UTC (rev 20872)
@@ -255,7 +255,7 @@
 !
 !  include "constants.h"
 !
-!  open(unit=IIN,file='in_data_files/Par_file',status='old',action='read')
+!  open(unit=IIN,file='DATA/Par_file',status='old',action='read')
 !
 !  end subroutine open_parameter_file
 !

Modified: seismo/3D/SPECFEM3D/trunk/utils/Cluster/go_generate_databases
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Cluster/go_generate_databases	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/utils/Cluster/go_generate_databases	2012-10-22 16:06:16 UTC (rev 20872)
@@ -7,10 +7,10 @@
 # name of the file that contains the list of machines
 set machine_file = "mymachines"
 
-set my_local_path = `grep LOCAL_PATH in_data_files/Par_file | cut -d '=' -f 2 `
+set my_local_path = `grep LOCAL_PATH DATA/Par_file | cut -d '=' -f 2 `
 
 # compute total number of processors needed
-set NPROC = `grep NPROC in_data_files/Par_file | cut -d '=' -f 2 `
+set NPROC = `grep NPROC DATA/Par_file | cut -d '=' -f 2 `
 
 # total number of processors is the product of the values read
 @ numprocessors = $NPROC

Modified: seismo/3D/SPECFEM3D/trunk/utils/Cluster/go_solver
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Cluster/go_solver	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/utils/Cluster/go_solver	2012-10-22 16:06:16 UTC (rev 20872)
@@ -7,10 +7,10 @@
 # name of the file that contains the list of machines
 set machine_file = "mymachines"
 
-set my_local_path = `grep LOCAL_PATH in_data_files/Par_file | cut -d '=' -f 2 `
+set my_local_path = `grep LOCAL_PATH DATA/Par_file | cut -d '=' -f 2 `
 
 # compute total number of processors needed
-set NPROC = `grep NPROC in_data_files/Par_file | cut -d '=' -f 2 `
+set NPROC = `grep NPROC DATA/Par_file | cut -d '=' -f 2 `
 
 # total number of processors is the product of the values read
 @ numprocessors = $NPROC

Modified: seismo/3D/SPECFEM3D/trunk/utils/Cluster/lsf/go_generate_databases_lsf.bash
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Cluster/lsf/go_generate_databases_lsf.bash	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/utils/Cluster/lsf/go_generate_databases_lsf.bash	2012-10-22 16:06:16 UTC (rev 20872)
@@ -25,12 +25,12 @@
 # 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
 
-cp in_data_files/Par_file in_out_files/OUTPUT_FILES/
+cp DATA/Par_file in_out_files/OUTPUT_FILES/
 
 # obtain lsf job information
 cat $LSB_DJOB_HOSTFILE > in_out_files/OUTPUT_FILES/compute_nodes

Modified: seismo/3D/SPECFEM3D/trunk/utils/Cluster/lsf/go_mesher_solver_lsf_basin.forward
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Cluster/lsf/go_mesher_solver_lsf_basin.forward	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/utils/Cluster/lsf/go_mesher_solver_lsf_basin.forward	2012-10-22 16:06:16 UTC (rev 20872)
@@ -17,12 +17,12 @@
 shmux -M50 -Sall -c "mkdir -p /scratch/$USER/; mkdir -p $BASEMPIDIR.$LSB_JOBID" - < in_out_files/OUTPUT_FILES/machines >/dev/null
 
 # main parameter file
-sed -e "s:^LOCAL_PATH .*:LOCAL_PATH                      =  $BASEMPIDIR.$LSB_JOBID:" < in_data_files/Par_file > Par_file.tmp
-mv Par_file.tmp in_data_files/Par_file
+sed -e "s:^LOCAL_PATH .*:LOCAL_PATH                      =  $BASEMPIDIR.$LSB_JOBID:" < DATA/Par_file > Par_file.tmp
+mv Par_file.tmp DATA/Par_file
 
 # mesher parameter file
-sed -e "s:^LOCAL_PATH .*:LOCAL_PATH                      =  $BASEMPIDIR.$LSB_JOBID:" < in_data_files/meshfem3D_files/Mesh_Par_file > Par_file.tmp
-mv Par_file.tmp in_data_files/meshfem3D_files/Mesh_Par_file
+sed -e "s:^LOCAL_PATH .*:LOCAL_PATH                      =  $BASEMPIDIR.$LSB_JOBID:" < DATA/meshfem3D_files/Mesh_Par_file > Par_file.tmp
+mv Par_file.tmp DATA/meshfem3D_files/Mesh_Par_file
 
 # run the specfem program
 current_pwd=$PWD
@@ -36,5 +36,5 @@
 cd current_pwd/
 mkdir -p in_out_files/SEM
 cd in_out_files/SEM/
-collect_seismo_lsf_multi.pl ../OUTPUT_FILES/lsf_machines $current_pwd/in_data_files/Par_file
+collect_seismo_lsf_multi.pl ../OUTPUT_FILES/lsf_machines $current_pwd/DATA/Par_file
 cleanbase.pl ../OUTPUT_FILES/machines

Modified: seismo/3D/SPECFEM3D/trunk/utils/Cluster/lsf/go_mesher_solver_lsf_basin.kernel
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Cluster/lsf/go_mesher_solver_lsf_basin.kernel	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/utils/Cluster/lsf/go_mesher_solver_lsf_basin.kernel	2012-10-22 16:06:16 UTC (rev 20872)
@@ -16,12 +16,12 @@
 shmux -M50 -Sall -c "mkdir -p /scratch/$USER/; mkdir -p $BASEMPIDIR.$LSB_JOBID" - < in_out_files/OUTPUT_FILES/machines >/dev/null
 
 # main parameter file
-sed -e "s:^LOCAL_PATH .*:LOCAL_PATH                      =  $BASEMPIDIR.$LSB_JOBID:" < in_data_files/Par_file > Par_file.tmp
-mv Par_file.tmp in_data_files/Par_file
+sed -e "s:^LOCAL_PATH .*:LOCAL_PATH                      =  $BASEMPIDIR.$LSB_JOBID:" < DATA/Par_file > Par_file.tmp
+mv Par_file.tmp DATA/Par_file
 
 # mesher parameter file
-sed -e "s:^LOCAL_PATH .*:LOCAL_PATH                      =  $BASEMPIDIR.$LSB_JOBID:" < in_data_files/meshfem3D_files/Mesh_Par_file > Par_file.tmp
-mv Par_file.tmp in_data_files/meshfem3D_files/Mesh_Par_file
+sed -e "s:^LOCAL_PATH .*:LOCAL_PATH                      =  $BASEMPIDIR.$LSB_JOBID:" < DATA/meshfem3D_files/Mesh_Par_file > Par_file.tmp
+mv Par_file.tmp DATA/meshfem3D_files/Mesh_Par_file
 
 current_pwd=$PWD
 
@@ -35,7 +35,7 @@
 #### this is the part needs to be revised for each kernel simulation #####
 mkdir -p $current_pwd/in_out_files/SEM
 cd $current_pwd/in_out_files/SEM
-collect_seismo_lsf_multi.pl $current_pwd/in_out_files/OUTPUT_FILES/lsf_machines $current_pwd/in_data_files/Par_file
+collect_seismo_lsf_multi.pl $current_pwd/in_out_files/OUTPUT_FILES/lsf_machines $current_pwd/DATA/Par_file
 #xcut_velocity 29.0 32.5 3 GSC*.semd
 xcreate_adjsrc_traveltime 29.0 32.5 3 GSC*.semd
 rename .semd.adj .adj *.semd.ad

Modified: seismo/3D/SPECFEM3D/trunk/utils/Cluster/lsf/go_solver_lsf.bash
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Cluster/lsf/go_solver_lsf.bash	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/utils/Cluster/lsf/go_solver_lsf.bash	2012-10-22 16:06:16 UTC (rev 20872)
@@ -25,16 +25,16 @@
 # 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
 
 rm -r -f in_out_files/OUTPUT_FILES
 mkdir 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/Par_file in_out_files/OUTPUT_FILES/
+cp DATA/CMTSOLUTION in_out_files/OUTPUT_FILES/
+cp DATA/STATIONS in_out_files/OUTPUT_FILES/
 
 # obtain lsf job information
 cat $BSUB_DJOB_NODEFILE > in_out_files/OUTPUT_FILES/compute_nodes

Modified: seismo/3D/SPECFEM3D/trunk/utils/Cluster/lsf/run_lsf.bash
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Cluster/lsf/run_lsf.bash	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/utils/Cluster/lsf/run_lsf.bash	2012-10-22 16:06:16 UTC (rev 20872)
@@ -25,11 +25,11 @@
 echo "Finished compilation $d"
 
 # get total number of nodes needed for solver
-NPROC=`grep NPROC in_data_files/Par_file | cut -d = -f 2 `
+NPROC=`grep NPROC DATA/Par_file | cut -d = -f 2 `
 
 # compute total number of nodes needed for mesher
-NPROC_XI=`grep NPROC_XI in_data_files/meshfem3D_files/Mesh_Par_file | cut -d = -f 2 `
-NPROC_ETA=`grep NPROC_ETA in_data_files/meshfem3D_files/Mesh_Par_file | cut -d = -f 2 `
+NPROC_XI=`grep NPROC_XI DATA/meshfem3D_files/Mesh_Par_file | cut -d = -f 2 `
+NPROC_ETA=`grep NPROC_ETA DATA/meshfem3D_files/Mesh_Par_file | cut -d = -f 2 `
 # total number of nodes is the product of the values read
 numnodes=$(( $NPROC_XI * $NPROC_ETA ))
 

Modified: seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_decomposer_pbs.bash
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_decomposer_pbs.bash	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_decomposer_pbs.bash	2012-10-22 16:06:16 UTC (rev 20872)
@@ -20,7 +20,7 @@
 # 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

Modified: seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_generate_databases_pbs.bash
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_generate_databases_pbs.bash	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_generate_databases_pbs.bash	2012-10-22 16:06:16 UTC (rev 20872)
@@ -20,7 +20,7 @@
 # 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
@@ -29,7 +29,7 @@
 
 # backup files used for this simulation
 cp go_generate_databases_pbs.bash in_out_files/OUTPUT_FILES/
-cp in_data_files/Par_file in_out_files/OUTPUT_FILES/
+cp DATA/Par_file in_out_files/OUTPUT_FILES/
 
 # save a complete copy of source files
 #rm -rf in_out_files/OUTPUT_FILES/src

Modified: seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_mesher_pbs.bash
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_mesher_pbs.bash	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_mesher_pbs.bash	2012-10-22 16:06:16 UTC (rev 20872)
@@ -18,7 +18,7 @@
 cd $PBS_O_WORKDIR
 
 # number of cores for the job
-NPROC=`grep NPROC in_data_files/Par_file | cut -d = -f 2 `
+NPROC=`grep NPROC DATA/Par_file | cut -d = -f 2 `
 numnodes=$NPROC
 
 mkdir -p in_out_files/OUTPUT_FILES
@@ -26,8 +26,8 @@
 
 # backup files used for this simulation
 cp go_mesher_pbs.bash in_out_files/OUTPUT_FILES/
-cp in_data_files/Par_file in_out_files/OUTPUT_FILES/
-cp in_data_files/meshfem3D_files/Mesh_Par_file in_out_files/OUTPUT_FILES/
+cp DATA/Par_file in_out_files/OUTPUT_FILES/
+cp DATA/meshfem3D_files/Mesh_Par_file in_out_files/OUTPUT_FILES/
 
 # save a complete copy of source files
 #rm -rf in_out_files/OUTPUT_FILES/src

Modified: seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_solver_pbs.bash
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_solver_pbs.bash	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_solver_pbs.bash	2012-10-22 16:06:16 UTC (rev 20872)
@@ -20,7 +20,7 @@
 # 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
@@ -29,9 +29,9 @@
 
 # backup files used for this simulation
 cp go_solver_pbs.bash in_out_files/OUTPUT_FILES/
-cp in_data_files/Par_file in_out_files/OUTPUT_FILES/
-cp in_data_files/STATIONS in_out_files/OUTPUT_FILES/
-cp in_data_files/CMTSOLUTION in_out_files/OUTPUT_FILES/
+cp DATA/Par_file in_out_files/OUTPUT_FILES/
+cp DATA/STATIONS in_out_files/OUTPUT_FILES/
+cp DATA/CMTSOLUTION in_out_files/OUTPUT_FILES/
 cp src/shared/constants.h in_out_files/OUTPUT_FILES/
 
 # save a complete copy of source files

Modified: seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/valgrind_go_solver_pbs.bash
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/valgrind_go_solver_pbs.bash	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/valgrind_go_solver_pbs.bash	2012-10-22 16:06:16 UTC (rev 20872)
@@ -7,7 +7,7 @@
 # bash script
 #PBS -S /bin/bash
 
-# job name 
+# job name
 #PBS -N valgrind_go_solver
 
 # joins output and error information
@@ -25,7 +25,7 @@
 # 150 CPUs ( 18*8+6 ), walltime 15 hour
 #PBS -l nodes=18:ppn=8+1:ppn=6,walltime=15:00:00
 
-# valgrind mpi library 
+# valgrind mpi library
 PRELOAD_LIB=/my_valgrind_path/valgrind/lib/valgrind/libmpiwrap-x86-linux.so
 
 ###########################################################
@@ -35,7 +35,7 @@
 # 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
@@ -43,9 +43,9 @@
 mkdir -p in_out_files/OUTPUT_FILES
 
 # backup files used for this simulation
-cp in_data_files/Par_file in_out_files/OUTPUT_FILES/
-cp in_data_files/STATIONS in_out_files/OUTPUT_FILES/
-cp in_data_files/CMTSOLUTION in_out_files/OUTPUT_FILES/
+cp DATA/Par_file in_out_files/OUTPUT_FILES/
+cp DATA/STATIONS in_out_files/OUTPUT_FILES/
+cp DATA/CMTSOLUTION in_out_files/OUTPUT_FILES/
 
 # obtain job information
 cat $PBS_NODEFILE > in_out_files/OUTPUT_FILES/compute_nodes

Modified: seismo/3D/SPECFEM3D/trunk/utils/Cluster/run3d.csh
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Cluster/run3d.csh	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/utils/Cluster/run3d.csh	2012-10-22 16:06:16 UTC (rev 20872)
@@ -21,7 +21,7 @@
    mkdir $OUTDIR
 endif
 cd $OUTDIR
-cp ../../in_data_files/CMTSOLUTION .
-cp ../../in_data_files/STATIONS .
-cp ../../in_data_files/Par_file .
+cp ../../DATA/CMTSOLUTION .
+cp ../../DATA/STATIONS .
+cp ../../DATA/Par_file .
 

Modified: seismo/3D/SPECFEM3D/trunk/utils/Cluster/sge/go_generate_databases_sge.bash
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Cluster/sge/go_generate_databases_sge.bash	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/utils/Cluster/sge/go_generate_databases_sge.bash	2012-10-22 16:06:16 UTC (rev 20872)
@@ -20,7 +20,7 @@
 # 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
@@ -28,9 +28,9 @@
 mkdir -p in_out_files/OUTPUT_FILES
 
 # backup for files used for this simulation
-cp in_data_files/Par_file in_out_files/OUTPUT_FILES/
-cp in_data_files/STATIONS in_out_files/OUTPUT_FILES/
-cp in_data_files/CMTSOLUTION in_out_files/OUTPUT_FILES/
+cp DATA/Par_file in_out_files/OUTPUT_FILES/
+cp DATA/STATIONS in_out_files/OUTPUT_FILES/
+cp DATA/CMTSOLUTION in_out_files/OUTPUT_FILES/
 
 rm -rf in_out_files/OUTPUT_FILES/src
 cp -rp ./src in_out_files/OUTPUT_FILES/

Modified: seismo/3D/SPECFEM3D/trunk/utils/Cluster/sge/go_solver_sge.bash
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Cluster/sge/go_solver_sge.bash	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/utils/Cluster/sge/go_solver_sge.bash	2012-10-22 16:06:16 UTC (rev 20872)
@@ -20,7 +20,7 @@
 # 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
@@ -28,9 +28,9 @@
 mkdir -p in_out_files/OUTPUT_FILES
 
 # backup for files used for this simulation
-cp in_data_files/Par_file in_out_files/OUTPUT_FILES/
-cp in_data_files/STATIONS in_out_files/OUTPUT_FILES/
-cp in_data_files/CMTSOLUTION in_out_files/OUTPUT_FILES/
+cp DATA/Par_file in_out_files/OUTPUT_FILES/
+cp DATA/STATIONS in_out_files/OUTPUT_FILES/
+cp DATA/CMTSOLUTION in_out_files/OUTPUT_FILES/
 
 rm -rf in_out_files/OUTPUT_FILES/src
 cp -rp ./src in_out_files/OUTPUT_FILES/

Modified: seismo/3D/SPECFEM3D/trunk/utils/Visualization/GMT/movie2gif.gmt.pl
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Visualization/GMT/movie2gif.gmt.pl	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/utils/Visualization/GMT/movie2gif.gmt.pl	2012-10-22 16:06:16 UTC (rev 20872)
@@ -89,11 +89,11 @@
 #   convert from movie data to gmt xyz files
 if ($tran_to_gmt) {
 
-  if (not -f "../in_data_files/Par_file") {die(" Check if ../in_data_files/Par_file exist or not\n");}
-  (@junk) = split(" ", `grep '^DT' ../in_data_files/Par_file`);
+  if (not -f "../DATA/Par_file") {die(" Check if ../DATA/Par_file exist or not\n");}
+  (@junk) = split(" ", `grep '^DT' ../DATA/Par_file`);
   $dt = $junk[2];
 
-  (@junk) = split(" ", `grep '^NTSTEP_BETWEEN_FRAMES' ../in_data_files/Par_file`);
+  (@junk) = split(" ", `grep '^NTSTEP_BETWEEN_FRAMES' ../DATA/Par_file`);
   $nframe = $junk[2];
 
   # start and end time
@@ -107,11 +107,11 @@
 
 } else {
 
-  if (not -f "../in_data_files/Par_file") {die(" Check if ../in_data_files/Par_file exist or not\n");}
-  (@junk) = split(" ", `grep '^DT' ../in_data_files/Par_file`);
+  if (not -f "../DATA/Par_file") {die(" Check if ../DATA/Par_file exist or not\n");}
+  (@junk) = split(" ", `grep '^DT' ../DATA/Par_file`);
   $dt = $junk[2];
 
-  (@junk) = split(" ", `grep '^NTSTEP_BETWEEN_FRAMES' ../in_data_files/Par_file`);
+  (@junk) = split(" ", `grep '^NTSTEP_BETWEEN_FRAMES' ../DATA/Par_file`);
   $nframe = $junk[2];
 
 }

Modified: seismo/3D/SPECFEM3D/trunk/utils/Visualization/GMT/plot_shakemap.gmt.pl
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Visualization/GMT/plot_shakemap.gmt.pl	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/utils/Visualization/GMT/plot_shakemap.gmt.pl	2012-10-22 16:06:16 UTC (rev 20872)
@@ -4,7 +4,7 @@
 #
 # copy this script into your bin/ folder and run for example:
 #
-#  ./plot_shakemap.gmt.pl ../in_data_files/ 2 ../in_data_files/CMTSOLUTION
+#  ./plot_shakemap.gmt.pl ../DATA/ 2 ../DATA/CMTSOLUTION
 #
 # will create shakemap file ../in_out_files/OUTPUT_FILES/gmt_shaking_map.ps for peak ground velocity
 

Modified: seismo/3D/SPECFEM3D/trunk/utils/change_simulation_type.pl
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/change_simulation_type.pl	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/utils/change_simulation_type.pl	2012-10-22 16:06:16 UTC (rev 20872)
@@ -1,6 +1,6 @@
 #!/usr/bin/perl
 
-# this script changes the simulation_type in in_data_files/Par_file
+# this script changes the simulation_type in DATA/Par_file
 # Qinya Liu, May 2007, Caltech
 
 use Time::Local;
@@ -11,7 +11,7 @@
 print STDERR <<END;
 
 Usage:   change_simulation_type.pl  [-a|-f|-b|-F]
-         Changes SIMULATION_TYPE in in_data_files/Par_file
+         Changes SIMULATION_TYPE in DATA/Par_file
          -a -- change type to run adjoint calculation(2)
          -f -- change type to run forward calculation(1)
          -b -- change type to run both simultaneously(3)
@@ -23,7 +23,7 @@
 @ARGV == 1 or Usage();
 if(!getopts('abfF')) {die(" check input arguments\n");}
 
-open(IN,"in_data_files/Par_file");
+open(IN,"DATA/Par_file");
 @vfm=<IN>;
 close(IN);
 
@@ -57,7 +57,7 @@
   }
 }
 
-open(OUT,">in_data_files/Par_file");
+open(OUT,">DATA/Par_file");
 foreach $vfm (@vfm){
   print OUT "$vfm";
 }

Modified: seismo/3D/SPECFEM3D/trunk/utils/cmt_frechet/cmt_frechet.csh
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/cmt_frechet/cmt_frechet.csh	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/utils/cmt_frechet/cmt_frechet.csh	2012-10-22 16:06:16 UTC (rev 20872)
@@ -15,8 +15,8 @@
 
 # save the CMTSOLUTION and the STATIONS file
 mkdir -p CMT_FRECHET
-cp in_data_files/CMTSOLUTION CMT_FRECHET
-cp in_data_files/STATIONS CMT_FRECHET
+cp DATA/CMTSOLUTION CMT_FRECHET
+cp DATA/STATIONS CMT_FRECHET
 
 # calculate synthetics
 sleep 180
@@ -32,7 +32,7 @@
 cd ..
 
 # make the CMTSOLUTION files needed for the calculation of Frechet derivatives
-cd in_data_files
+cd DATA
 # backup the CMTSOLUTION file
 cp CMTSOLUTION CMTSOLUTION_BACKUP
 ./xmake_cmtsolution_files
@@ -41,8 +41,8 @@
 foreach extension (Mrr Mtt Mpp Mrt Mrp Mtp depth latitude longitude)
 
 # setup the calculation for the Frechet derivative with respect to ${extension}
-rm in_data_files/CMTSOLUTION
-mv in_data_files/CMTSOLUTION_${extension} in_data_files/CMTSOLUTION
+rm DATA/CMTSOLUTION
+mv DATA/CMTSOLUTION_${extension} DATA/CMTSOLUTION
 
 sleep 180
 go_solver_cmt
@@ -58,6 +58,6 @@
 end
 
 # put the backup CMTSOLUTION file back
-rm in_data_files/CMTSOLUTION
-mv in_data_files/CMTSOLUTION_BACKUP in_data_files/CMTSOLUTION
+rm DATA/CMTSOLUTION
+mv DATA/CMTSOLUTION_BACKUP DATA/CMTSOLUTION
 

Modified: seismo/3D/SPECFEM3D/trunk/utils/cmt_frechet/cmt_frechet1.csh
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/cmt_frechet/cmt_frechet1.csh	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/utils/cmt_frechet/cmt_frechet1.csh	2012-10-22 16:06:16 UTC (rev 20872)
@@ -10,8 +10,8 @@
 foreach extension (Mrr Mtt Mpp Mrt Mrp Mtp depth latitude longitude)
 
 # setup the calculation for the Frechet derivative with respect to ${extension}
-rm in_data_files/CMTSOLUTION
-mv in_data_files/CMTSOLUTION_${extension} in_data_files/CMTSOLUTION
+rm DATA/CMTSOLUTION
+mv DATA/CMTSOLUTION_${extension} DATA/CMTSOLUTION
 
 sleep 180
 go_solver_cmt
@@ -27,6 +27,6 @@
 end
 
 # put the backup CMTSOLUTION file back
-rm in_data_files/CMTSOLUTION
-mv in_data_files/CMTSOLUTION_BACKUP in_data_files/CMTSOLUTION
+rm DATA/CMTSOLUTION
+mv DATA/CMTSOLUTION_BACKUP DATA/CMTSOLUTION
 

Modified: seismo/3D/SPECFEM3D/trunk/utils/cmt_frechet/go_solver_cmt
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/cmt_frechet/go_solver_cmt	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/utils/cmt_frechet/go_solver_cmt	2012-10-22 16:06:16 UTC (rev 20872)
@@ -3,13 +3,13 @@
 # script to run the solver
 
 # name of the file that contains the list of machines
-set list_of_machines = `grep MACHINE_FILE in_data_files/Par_file | cut -c 27- `
-set my_local_path = `grep LOCAL_PATH in_data_files/Par_file | cut -c 27- `
+set list_of_machines = `grep MACHINE_FILE DATA/Par_file | cut -c 27- `
+set my_local_path = `grep LOCAL_PATH DATA/Par_file | cut -c 27- `
 
 # read Par_file to get total number of processors needed
 
-set NPROC_XI = `grep NPROC_XI in_data_files/Par_file | cut -c 27- `
-set NPROC_ETA = `grep NPROC_ETA in_data_files/Par_file | cut -c 27- `
+set NPROC_XI = `grep NPROC_XI DATA/Par_file | cut -c 27- `
+set NPROC_ETA = `grep NPROC_ETA DATA/Par_file | cut -c 27- `
 
 # total number of processors is product of values read
 @ numprocessors = $NPROC_XI * $NPROC_ETA

Modified: seismo/3D/SPECFEM3D/trunk/utils/unused_routines/create_header_file.f90
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/unused_routines/create_header_file.f90	2012-10-22 15:30:36 UTC (rev 20871)
+++ seismo/3D/SPECFEM3D/trunk/utils/unused_routines/create_header_file.f90	2012-10-22 16:06:16 UTC (rev 20872)
@@ -24,7 +24,7 @@
 !
 !=====================================================================
 
-! create file in_out_files/OUTPUT_FILES/values_from_mesher.h based upon in_data_files/Par_file
+! create file in_out_files/OUTPUT_FILES/values_from_mesher.h based upon DATA/Par_file
 ! in order to compile the solver with the right array sizes
 
   subroutine create_header_file

