replaced in_data_files with DATA in all files and scripts

Makefile.in

@@ -84,7 +84,7 @@ all: default \
 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
 

examples/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
 

src/generate_databases/model_tomography.f90

@@ -39,7 +39,7 @@ module tomography_par
   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'

src/shared/constants.h.in

@@ -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/'
 
 

src/shared/read_value_parameters.f90

@@ -255,7 +255,7 @@ end function err_occurred
 !
 !  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
 !

utils/Cluster/go_generate_databases

@@ -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

utils/Cluster/go_solver

@@ -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

utils/Cluster/lsf/go_generate_databases_lsf.bash

@@ -25,12 +25,12 @@ fi
 # 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

utils/Cluster/lsf/go_mesher_solver_lsf_basin.forward

@@ -17,12 +17,12 @@ remap_lsf_machines.pl in_out_files/OUTPUT_FILES/lsf_machines > in_out_files/OUTP
 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 @@ mpirun.lsf --gm-no-shmem --gm-copy-env ./xspecfem3D
 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

utils/Cluster/lsf/go_mesher_solver_lsf_basin.kernel

@@ -16,12 +16,12 @@ remap_lsf_machines.pl in_out_files/OUTPUT_FILES/lsf_machines > in_out_files/OUTP
 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 @@ mpirun.lsf --gm-no-shmem --gm-copy-env ./xspecfem3D
 #### 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

utils/Cluster/lsf/go_solver_lsf.bash

@@ -25,16 +25,16 @@ fi
 # 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

utils/Cluster/lsf/run_lsf.bash

@@ -25,11 +25,11 @@ d=`date`
 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 ))
 

utils/Cluster/pbs/go_decomposer_pbs.bash

@@ -20,7 +20,7 @@ cd $PBS_O_WORKDIR
 # 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

utils/Cluster/pbs/go_generate_databases_pbs.bash

@@ -20,7 +20,7 @@ cd $PBS_O_WORKDIR
 # 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 @@ mkdir -p in_out_files/OUTPUT_FILES
 
 # 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

utils/Cluster/pbs/go_mesher_pbs.bash

@@ -18,16 +18,16 @@
 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
 mkdir -p in_out_files/DATABASES_MPI
 
 # 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

utils/Cluster/pbs/go_solver_pbs.bash

@@ -20,7 +20,7 @@ cd $PBS_O_WORKDIR
 # 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 @@ mkdir -p in_out_files/OUTPUT_FILES
 
 # 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

utils/Cluster/pbs/valgrind_go_solver_pbs.bash

@@ -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
 
 ###########################################################
@@ -35,17 +35,17 @@ cd $PBS_O_WORKDIR
 # 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
 
 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

utils/Cluster/run3d.csh

@@ -21,7 +21,7 @@ if (! -d $OUTDIR) then
    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 .
 

utils/Cluster/sge/go_generate_databases_sge.bash

@@ -20,17 +20,17 @@
 # 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
 
 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/

utils/Cluster/sge/go_solver_sge.bash

@@ -20,17 +20,17 @@
 # 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
 
 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/

utils/Visualization/GMT/movie2gif.gmt.pl

@@ -89,11 +89,11 @@ sub Usage {
 #   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 @@ sub Usage {
 
 } 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];
 
 }

utils/Visualization/GMT/plot_shakemap.gmt.pl

@@ -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