[cig-commits] r20873 - in seismo/3D/SPECFEM3D/trunk: DATA DATA/meshfem3D_files examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/in_data_files examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/in_data_files/meshfem3D_files examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/in_data_files examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/in_data_files/meshfem3D_files examples/Mount_StHelens examples/Mount_StHelens/in_data_files examples/homogeneous_halfspace_HEX27 examples/homogeneous_halfspace_HEX27/in_data_files examples/homogeneous_halfspace_HEX8 examples/homogeneous_halfspace_HEX8/in_data_files examples/homogeneous_poroelastic examples/homogeneous_poroelastic/in_data_files examples/layered_halfspace examples/layered_halfspace/in_data_files examples/meshfem3D_examples/many_interfaces examples/meshfem3D_examples/simple_model examples/meshfem3D_examples/simple_model/in_data_files examples/meshfem3D_examples/simple_model/in_data_files/meshfem3D_files examples/meshfem3D_examples/socal1D examples/meshfem3D_examples/socal1D/example_deep examples/meshfem3D_examples/socal1D/example_utm examples/meshfem3D_examples/socal1D/in_data_files examples/meshfem3D_examples/socal1D/in_data_files/meshfem3D_files examples/noise_tomography examples/noise_tomography/bin examples/noise_tomography/in_data_files examples/tomographic_model examples/tomographic_model/in_data_files examples/waterlayered_halfspace examples/waterlayered_halfspace/in_data_files src/cuda src/decompose_mesh_SCOTCH src/generate_databases src/shared src/specfem3D utils utils/Cluster utils/Cluster/lsf utils/Cluster/pbs utils/Cluster/sge utils/Visualization/GMT utils/adjoint_sources utils/unused_routines
dkomati1 at geodynamics.org
dkomati1 at geodynamics.org
Mon Oct 22 09:16:57 PDT 2012
Author: dkomati1
Date: 2012-10-22 09:16:57 -0700 (Mon, 22 Oct 2012)
New Revision: 20873
Modified:
seismo/3D/SPECFEM3D/trunk/DATA/Par_file
seismo/3D/SPECFEM3D/trunk/DATA/meshfem3D_files/Mesh_Par_file
seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/adj_seismogram.f90
seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/in_data_files/Par_file
seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/in_data_files/meshfem3D_files/Mesh_Par_file
seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/postprocessing.f90
seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/random_model_generation.f90
seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/run_inhomogeneous.bash
seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/adj_seismogram.f90
seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/in_data_files/Par_file
seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/in_data_files/meshfem3D_files/Mesh_Par_file
seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/postprocessing.f90
seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/random_model_generation.f90
seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/run_inhomogeneous.bash
seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/in_data_files/Par_file
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_HEX27/in_data_files/Par_file
seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/plotall_comparison_seismograms.gnu
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/in_data_files/Par_file
seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8/process.sh
seismo/3D/SPECFEM3D/trunk/examples/homogeneous_poroelastic/README
seismo/3D/SPECFEM3D/trunk/examples/homogeneous_poroelastic/in_data_files/Par_file
seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/README
seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/in_data_files/Par_file
seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/process.sh
seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/many_interfaces/Mesh_Par_file
seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/many_interfaces/Par_file
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/in_data_files/Par_file
seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/simple_model/in_data_files/meshfem3D_files/Mesh_Par_file
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/example_deep/Mesh_Par_file_deep
seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/example_deep/Mesh_Par_file_deep_honor60km
seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/example_utm/Mesh_Par_file_utm
seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/example_utm/Par_file_utm
seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/in_data_files/Par_file
seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/in_data_files/meshfem3D_files/Mesh_Par_file
seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/in_data_files/meshfem3D_files/Mesh_Par_file_001
seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/in_data_files/meshfem3D_files/Mesh_Par_file_042
seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/in_data_files/meshfem3D_files/Mesh_Par_file_168
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/bin/adj_traveltime_filter.f90
seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/in_data_files/Par_file_step1
seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/in_data_files/Par_file_step2
seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/in_data_files/Par_file_step3
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/in_data_files/Par_file
seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/process.sh
seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/README
seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/in_data_files/Par_file
seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/process.sh
seismo/3D/SPECFEM3D/trunk/src/cuda/check_fields_cuda.cu
seismo/3D/SPECFEM3D/trunk/src/cuda/initialize_cuda.cu
seismo/3D/SPECFEM3D/trunk/src/cuda/save_and_compare_cpu_vs_gpu.c
seismo/3D/SPECFEM3D/trunk/src/decompose_mesh_SCOTCH/README
seismo/3D/SPECFEM3D/trunk/src/generate_databases/Makefile.in
seismo/3D/SPECFEM3D/trunk/src/shared/constants.h.in
seismo/3D/SPECFEM3D/trunk/src/shared/create_movie_shakemap_AVS_DX_GMT.f90
seismo/3D/SPECFEM3D/trunk/src/specfem3D/Makefile.in
seismo/3D/SPECFEM3D/trunk/src/specfem3D/model_update.f90
seismo/3D/SPECFEM3D/trunk/utils/Cluster/go_generate_databases
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/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/adjoint_sources/SU_adjoint.f90
seismo/3D/SPECFEM3D/trunk/utils/locate_partition.f90
seismo/3D/SPECFEM3D/trunk/utils/unused_routines/create_header_file.f90
Log:
replaced in_out_files with OUTPUT_FILES in all files and scripts
Modified: seismo/3D/SPECFEM3D/trunk/DATA/Par_file
===================================================================
--- seismo/3D/SPECFEM3D/trunk/DATA/Par_file 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/DATA/Par_file 2012-10-22 16:16:57 UTC (rev 20873)
@@ -2,9 +2,9 @@
#
# forward or adjoint simulation
# 1 = forward, 2 = adjoint, 3 = both simultaneously
-SIMULATION_TYPE = 1
+SIMULATION_TYPE = 1
# 0 = earthquake simulation, 1/2/3 = three steps in noise simulation
-NOISE_TOMOGRAPHY = 0
+NOISE_TOMOGRAPHY = 0
SAVE_FORWARD = .false.
# UTM projection parameters
@@ -21,9 +21,9 @@
# models:
# available options are:
# default (model parameters described by mesh properties)
-# 1D models available are:
+# 1D models available are:
# 1d_prem,1d_socal,1d_cascadia
-# 3D models available are:
+# 3D models available are:
# aniso,external,gll,salton_trough,tomo
MODEL = default
@@ -54,7 +54,7 @@
SAVE_MESH_FILES = .true.
# path to store the local database file on each node
-LOCAL_PATH = ../in_out_files/DATABASES_MPI
+LOCAL_PATH = ../OUTPUT_FILES/DATABASES_MPI
# interval at which we output time step info and max of norm of displacement
NTSTEP_BETWEEN_OUTPUT_INFO = 500
@@ -64,7 +64,7 @@
# interval in time steps for reading adjoint traces
# 0 = read the whole adjoint sources at the same time
-NTSTEP_BETWEEN_READ_ADJSRC = 0
+NTSTEP_BETWEEN_READ_ADJSRC = 0
# use a force source (or several) located exactly at a grid point instead of a CMTSOLUTION source.
# This can be useful e.g. for oil industry foothills simulations or asteroid simulations
@@ -79,13 +79,13 @@
# The direction vector is made unitary internally in the code and thus only its direction matters here;
# its norm is ignored and the norm of the force used is the factor force source times the source time function.
-# set to use a Ricker source time function instead of a gaussian (when using CMTSOLUTION files)
-# or a quasi-Heaviside (when using FORCESOLUTION files)
+# set to use a Ricker source time function instead of a gaussian (when using CMTSOLUTION files)
+# or a quasi-Heaviside (when using FORCESOLUTION files)
USE_RICKER_TIME_FUNCTION = .false.
# print source time function
PRINT_SOURCE_TIME_FUNCTION = .false.
-# set to true to use GPUs
+# set to true to use GPUs
GPU_MODE = .false.
Modified: seismo/3D/SPECFEM3D/trunk/DATA/meshfem3D_files/Mesh_Par_file
===================================================================
--- seismo/3D/SPECFEM3D/trunk/DATA/meshfem3D_files/Mesh_Par_file 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/DATA/meshfem3D_files/Mesh_Par_file 2012-10-22 16:16:57 UTC (rev 20873)
@@ -35,7 +35,7 @@
CREATE_VTK_FILES = .false.
# path to store the databases files
-LOCAL_PATH = ../in_out_files/DATABASES_MPI
+LOCAL_PATH = ../OUTPUT_FILES/DATABASES_MPI
# number of materials
NMATERIALS = 4
Modified: seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/adj_seismogram.f90
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/adj_seismogram.f90 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/adj_seismogram.f90 2012-10-22 16:16:57 UTC (rev 20873)
@@ -28,7 +28,7 @@
!!!! read NSTEP from seismograms
!!!filename=trim(adjustl(procname))//"_dx_SU"
- !!!open(111,file="../in_out_files/OUTPUT_FILES/"//trim(filename),access='direct',recl=240,iostat = ios)
+ !!!open(111,file="../OUTPUT_FILES/"//trim(filename),access='direct',recl=240,iostat = ios)
!!!read(111,rec=1,iostat=ios) r4head
!!!close(111)
!!!header4=r4head(29)
@@ -48,123 +48,123 @@
! read 'syn', 'dat' and then write 'adj'
! x-component
filename=trim(adjustl(procname))//"_dx_SU"
- open(111,file="../in_out_files/SEM/syn/"//trim(filename), &
+ open(111,file="../OUTPUT_FILES/SEM/syn/"//trim(filename), &
status='old',access='direct',action='read',recl=240+4*NSTEP,iostat = ios)
if( ios /= 0 ) stop 'error opening file syn'
- open(112,file="../in_out_files/SEM/dat/"//trim(filename), &
+ open(112,file="../OUTPUT_FILES/SEM/dat/"//trim(filename), &
status='old',access='direct',action='read',recl=240+4*NSTEP,iostat = ios)
if( ios /= 0 ) stop 'error opening file dat'
- open(113,file="../in_out_files/SEM/"//trim(filename)//".adj", &
+ open(113,file="../OUTPUT_FILES/SEM/"//trim(filename)//".adj", &
status='unknown',access='direct',action='write',recl=240+4*NSTEP,iostat = ios)
if( ios /= 0 ) stop 'error opening file .adj'
-
+
irec=1
do while(ios==0)
-
- syn(:) = 0.0
+
+ syn(:) = 0.0
dat(:) = 0.0
-
+
read(111,rec=irec,iostat=ios) r4head,syn
if (ios /= 0) exit
read(112,rec=irec,iostat=ios) r4head,dat
if (ios /= 0) exit
-
+
write(113,rec=irec,iostat=ios) r4head,syn-dat
if (ios /= 0) exit
-
+
!daniel: outputs ascii trace
if( myrank == 0 .and. irec == 196 ) then
- open(221,file="../in_out_files/SEM/syn/"//trim(filename)//".ascii",status='unknown')
+ open(221,file="../OUTPUT_FILES/SEM/syn/"//trim(filename)//".ascii",status='unknown')
do i=1,NSTEP
write(221,*) i,syn(i)
enddo
close(221)
- open(222,file="../in_out_files/SEM/dat/"//trim(filename)//".ascii",status='unknown')
+ open(222,file="../OUTPUT_FILES/SEM/dat/"//trim(filename)//".ascii",status='unknown')
do i=1,NSTEP
write(222,*) i,dat(i)
enddo
close(222)
- open(223,file="../in_out_files/SEM/"//trim(filename)//".adj.ascii",status='unknown')
+ open(223,file="../OUTPUT_FILES/SEM/"//trim(filename)//".adj.ascii",status='unknown')
do i=1,NSTEP
write(223,*) i,syn(i)-dat(i)
enddo
close(223)
- endif
-
+ endif
+
irec=irec+1
enddo
close(111)
close(112)
close(113)
-
+
! y-component
filename=trim(adjustl(procname))//"_dy_SU"
- open(111,file="../in_out_files/SEM/syn/"//trim(filename), &
+ open(111,file="../OUTPUT_FILES/SEM/syn/"//trim(filename), &
status='old',access='direct',action='read',recl=240+4*NSTEP,iostat = ios)
if( ios /= 0 ) stop 'error opening file syn'
- open(112,file="../in_out_files/SEM/dat/"//trim(filename), &
+ open(112,file="../OUTPUT_FILES/SEM/dat/"//trim(filename), &
status='old',access='direct',action='read',recl=240+4*NSTEP,iostat = ios)
if( ios /= 0 ) stop 'error opening file dat'
- open(113,file="../in_out_files/SEM/"//trim(filename)//".adj", &
+ open(113,file="../OUTPUT_FILES/SEM/"//trim(filename)//".adj", &
status='unknown',access='direct',action='write',recl=240+4*NSTEP,iostat = ios)
if( ios /= 0 ) stop 'error opening file .adj'
-
+
irec=1
do while(ios==0)
- syn(:) = 0.0
+ syn(:) = 0.0
dat(:) = 0.0
-
+
read(111,rec=irec,iostat=ios) r4head,syn
if (ios /= 0) exit
read(112,rec=irec,iostat=ios) r4head,dat
if (ios /= 0) exit
write(113,rec=irec,iostat=ios) r4head,syn-dat
if (ios /= 0) exit
-
+
!daniel: outputs ascii trace
if( myrank == 0 .and. irec == 196 ) then
- open(221,file="../in_out_files/SEM/syn/"//trim(filename)//".ascii",status='unknown')
+ open(221,file="../OUTPUT_FILES/SEM/syn/"//trim(filename)//".ascii",status='unknown')
do i=1,NSTEP
write(221,*) i,syn(i)
- enddo
+ enddo
close(221)
- open(222,file="../in_out_files/SEM/dat/"//trim(filename)//".ascii",status='unknown')
+ open(222,file="../OUTPUT_FILES/SEM/dat/"//trim(filename)//".ascii",status='unknown')
do i=1,NSTEP
write(222,*) i,dat(i)
enddo
close(222)
- open(223,file="../in_out_files/SEM/"//trim(filename)//".adj.ascii",status='unknown')
+ open(223,file="../OUTPUT_FILES/SEM/"//trim(filename)//".adj.ascii",status='unknown')
do i=1,NSTEP
write(223,*) i,syn(i)-dat(i)
enddo
close(223)
- endif
-
-
+ endif
+
+
irec=irec+1
enddo
close(111)
close(112)
close(113)
-
+
! z-component
filename=trim(adjustl(procname))//"_dz_SU"
- open(111,file="../in_out_files/SEM/syn/"//trim(filename), &
+ open(111,file="../OUTPUT_FILES/SEM/syn/"//trim(filename), &
status='old',access='direct',action='read',recl=240+4*NSTEP,iostat = ios)
if( ios /= 0 ) stop 'error opening file syn'
- open(112,file="../in_out_files/SEM/dat/"//trim(filename), &
+ open(112,file="../OUTPUT_FILES/SEM/dat/"//trim(filename), &
status='old',access='direct',action='read',recl=240+4*NSTEP,iostat = ios)
if( ios /= 0 ) stop 'error opening file dat'
- open(113,file="../in_out_files/SEM/"//trim(filename)//".adj", &
+ open(113,file="../OUTPUT_FILES/SEM/"//trim(filename)//".adj", &
status='unknown',access='direct',action='write',recl=240+4*NSTEP,iostat = ios)
if( ios /= 0 ) stop 'error opening file .adj'
irec=1
do while(ios==0)
-
- syn(:) = 0.0
+
+ syn(:) = 0.0
dat(:) = 0.0
-
+
read(111,rec=irec,iostat=ios) r4head,syn
if (ios /= 0) exit
read(112,rec=irec,iostat=ios) r4head,dat
@@ -174,24 +174,24 @@
!daniel: outputs ascii trace
if( myrank == 0 .and. irec == 196 ) then
- open(221,file="../in_out_files/SEM/syn/"//trim(filename)//".ascii",status='unknown')
+ open(221,file="../OUTPUT_FILES/SEM/syn/"//trim(filename)//".ascii",status='unknown')
do i=1,NSTEP
write(221,*) i,syn(i)
enddo
close(221)
- open(222,file="../in_out_files/SEM/dat/"//trim(filename)//".ascii",status='unknown')
+ open(222,file="../OUTPUT_FILES/SEM/dat/"//trim(filename)//".ascii",status='unknown')
do i=1,NSTEP
write(222,*) i,dat(i)
enddo
close(222)
- open(223,file="../in_out_files/SEM/"//trim(filename)//".adj.ascii",status='unknown')
+ open(223,file="../OUTPUT_FILES/SEM/"//trim(filename)//".adj.ascii",status='unknown')
do i=1,NSTEP
write(223,*) i,syn(i)-dat(i)
enddo
close(223)
- endif
-
-
+ endif
+
+
irec=irec+1
enddo
close(111)
Modified: seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/in_data_files/Par_file
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/in_data_files/Par_file 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/in_data_files/Par_file 2012-10-22 16:16:57 UTC (rev 20873)
@@ -4,7 +4,7 @@
# 1 = forward, 2 = adjoint, 3 = both simultaneously
SIMULATION_TYPE = 3
# 0 = earthquake simulation, 1/2/3 = three steps in noise simulation
-NOISE_TOMOGRAPHY = 0
+NOISE_TOMOGRAPHY = 0
SAVE_FORWARD = .false.
# UTM projection parameters
@@ -15,15 +15,15 @@
NPROC = 4
# time step parameters
-NSTEP = 10000
+NSTEP = 10000
DT = 0.001
# models:
# available options are:
# default (model parameters described by mesh properties)
-# 1D models available are:
+# 1D models available are:
# 1d_prem,1d_socal,1d_cascadia
-# 3D models available are:
+# 3D models available are:
# aniso,external,gll,salton_trough,tomo
MODEL = default
@@ -53,7 +53,7 @@
SAVE_MESH_FILES = .true.
# path to store the local database file on each node
-LOCAL_PATH = ../in_out_files/DATABASES_MPI/
+LOCAL_PATH = ../OUTPUT_FILES/DATABASES_MPI/
# interval at which we output time step info and max of norm of displacement
NTSTEP_BETWEEN_OUTPUT_INFO = 100
@@ -77,13 +77,13 @@
# The direction vector is made unitary internally in the code and thus only its direction matters here;
# its norm is ignored and the norm of the force used is the factor force source times the source time function.
-# set to use a Ricker source time function instead of a gaussian (when using CMTSOLUTION files)
-# or a quasi-Heaviside (when using FORCESOLUTION files)
+# set to use a Ricker source time function instead of a gaussian (when using CMTSOLUTION files)
+# or a quasi-Heaviside (when using FORCESOLUTION files)
USE_RICKER_TIME_FUNCTION = .false.
# print source time function
PRINT_SOURCE_TIME_FUNCTION = .true.
-# set to true to use GPUs
+# set to true to use GPUs
GPU_MODE = .false.
Modified: seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/in_data_files/meshfem3D_files/Mesh_Par_file
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/in_data_files/meshfem3D_files/Mesh_Par_file 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/in_data_files/meshfem3D_files/Mesh_Par_file 2012-10-22 16:16:57 UTC (rev 20873)
@@ -35,7 +35,7 @@
CREATE_VTK_FILES = .false.
# path to store the databases files
-LOCAL_PATH = ../in_out_files/DATABASES_MPI/
+LOCAL_PATH = ../OUTPUT_FILES/DATABASES_MPI/
# number of materials
NMATERIALS = 3
Modified: seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/postprocessing.f90
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/postprocessing.f90 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/postprocessing.f90 2012-10-22 16:16:57 UTC (rev 20873)
@@ -27,7 +27,7 @@
MODELSPACE=0.0
DATASPACE=0.0
-
+
irec_total = 0
allocate(adj(NSTEP))
@@ -35,30 +35,30 @@
!!! calculate inner product in model space --- <F* F dm, dm>
! processors name
write(prname,'(a,i6.6,a)') 'proc',myrank,'_'
-
+
print*,' ',trim(prname)
-
+
! nspec & nglob
- open(unit=IOUT,file='../in_out_files/DATABASES_MPI/'//trim(adjustl(prname))//'external_mesh.bin',status='old',action='read',form='unformatted',iostat=ier)
+ open(unit=IOUT,file='../OUTPUT_FILES/DATABASES_MPI/'//trim(adjustl(prname))//'external_mesh.bin',status='old',action='read',form='unformatted',iostat=ier)
if( ier /= 0 ) stop 'error opening database proc######_external_mesh.bin'
read(IOUT) nspec
read(IOUT) nglob
close(IOUT)
-
+
! weights
allocate(weights(NGLLX,NGLLY,NGLLZ,nspec),stat=ier); if( ier /= 0 ) stop 'error allocating array weights'
- open(unit=IOUT,file='../in_out_files/DATABASES_MPI/'//trim(adjustl(prname))//'weights_kernel.bin',status='old',action='read',form='unformatted',iostat=ier)
+ open(unit=IOUT,file='../OUTPUT_FILES/DATABASES_MPI/'//trim(adjustl(prname))//'weights_kernel.bin',status='old',action='read',form='unformatted',iostat=ier)
read(IOUT) weights
close(IOUT)
-
- ! kernels
+
+ ! kernels
allocate(krhop(NGLLX,NGLLY,NGLLZ,nspec),stat=ier); if( ier /= 0 ) stop 'error allocating array krhop'
- open(unit=IOUT,file='../in_out_files/DATABASES_MPI/'//trim(adjustl(prname))//'rhop_acoustic_kernel.bin',status='old',action='read',form='unformatted',iostat=ier)
+ open(unit=IOUT,file='../OUTPUT_FILES/DATABASES_MPI/'//trim(adjustl(prname))//'rhop_acoustic_kernel.bin',status='old',action='read',form='unformatted',iostat=ier)
read(IOUT) krhop
close(IOUT)
allocate(kalpha(NGLLX,NGLLY,NGLLZ,nspec),stat=ier); if( ier /= 0 ) stop 'error allocating array kalpha'
- open(unit=IOUT,file='../in_out_files/DATABASES_MPI/'//trim(adjustl(prname))//'alpha_acoustic_kernel.bin',status='old',action='read',form='unformatted',iostat=ier)
+ open(unit=IOUT,file='../OUTPUT_FILES/DATABASES_MPI/'//trim(adjustl(prname))//'alpha_acoustic_kernel.bin',status='old',action='read',form='unformatted',iostat=ier)
read(IOUT) kalpha
close(IOUT)
@@ -94,32 +94,32 @@
sum(weights*(-kalpha)*(vp-vp0)/vp0)
deallocate(rho,rho0,vp,vp0,vs,vs0,weights,krhop,kalpha,kbeta)
-
-
+
+
!!! calculate inner product in data space --- <F dm, F dm>
write(procname,"(i4)") myrank
filename=trim(adjustl(procname))//"_dx_SU"
- open(111,file="../in_out_files/SEM/"//trim(adjustl(filename))//".adj",access='direct',recl=240+4*NSTEP,iostat = ios)
+ open(111,file="../OUTPUT_FILES/SEM/"//trim(adjustl(filename))//".adj",access='direct',recl=240+4*NSTEP,iostat = ios)
if( ios /= 0 ) stop 'error opening adjoint trace'
print*,' ',trim(adjustl(filename))//".adj"
-
+
irec=1
- do while(ios==0)
+ do while(ios==0)
adj(:) = 0.0
-
- read(111,rec=irec,iostat=ios) r4head,adj
+
+ read(111,rec=irec,iostat=ios) r4head,adj
if (ios /= 0) exit
-
+
DATASPACE=DATASPACE+sum(adj(:)*adj(:))*DT
-
+
irec=irec+1
enddo
close(111)
irec_total = irec_total + irec
-
+
!elastic case
! filename=trim(adjustl(procname))//"_dy_SU"
-! open(111,file="../in_out_files/SEM/"//trim(adjustl(filename))//".adj",access='direct',recl=240+4*NSTEP,iostat = ios)
+! open(111,file="../OUTPUT_FILES/SEM/"//trim(adjustl(filename))//".adj",access='direct',recl=240+4*NSTEP,iostat = ios)
! if( ios /= 0 ) stop 'error opening adjoint trace'
! print*,' ',trim(adjustl(filename))//".adj"
!
@@ -137,7 +137,7 @@
! close(111)
!
! filename=trim(adjustl(procname))//"_dz_SU"
-! open(111,file="../in_out_files/SEM/"//trim(adjustl(filename))//".adj",access='direct',recl=240+4*NSTEP,iostat = ios)
+! open(111,file="../OUTPUT_FILES/SEM/"//trim(adjustl(filename))//".adj",access='direct',recl=240+4*NSTEP,iostat = ios)
! if( ios /= 0 ) stop 'error opening adjoint trace'
! print*,' ',trim(adjustl(filename))//".adj"
!
Modified: seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/random_model_generation.f90
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/random_model_generation.f90 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/random_model_generation.f90 2012-10-22 16:16:57 UTC (rev 20873)
@@ -6,7 +6,7 @@
integer,parameter :: NGLLX=5,NGLLY=5,NGLLZ=5,IOUT=20
integer,parameter :: CUSTOM_REAL = 4
- character(len=512),parameter :: LOCAL_PATH='../in_out_files/DATABASES_MPI/'
+ character(len=512),parameter :: LOCAL_PATH='../OUTPUT_FILES/DATABASES_MPI/'
integer :: myrank,ier,nspec,nglob,NPROC,ios
double precision :: percent
@@ -25,7 +25,7 @@
!real(kind=CUSTOM_REAL) :: norm_h,norm_v,norm
real(kind=CUSTOM_REAL),parameter :: PI = 3.1415926535897931
integer :: i,j,k,ispec,iglob
-
+
call MPI_Init(ier)
call MPI_Comm_Rank(MPI_COMM_WORLD,myrank,ier)
call MPI_Comm_Size(MPI_COMM_WORLD,NPROC,ier)
@@ -41,7 +41,7 @@
if( ier /= 0 ) stop 'error opening database proc######_external_mesh.bin'
read(IOUT) nspec
read(IOUT) nglob
-
+
! ibool file
allocate(ibool(NGLLX,NGLLY,NGLLZ,nspec),stat=ier)
if( ier /= 0 ) stop 'error allocating array ibool'
@@ -52,15 +52,15 @@
read(IOUT) xstore
read(IOUT) ystore
read(IOUT) zstore
-
+
close(IOUT)
-
+
! rho
allocate( rho_read(NGLLX,NGLLY,NGLLZ,nspec),stat=ier); if( ier /= 0 ) stop 'error allocating array rho_read'
open(unit=IOUT,file=trim(adjustl(prname))//'rho.bin',status='old',action='read',form='unformatted')
read(IOUT) rho_read
close(IOUT)
-
+
! vp
allocate( vp_read(NGLLX,NGLLY,NGLLZ,nspec),stat=ier); if( ier /= 0 ) stop 'error allocating array vp_read'
open(unit=IOUT,file=trim(adjustl(prname))//'vp.bin',status='old',action='read',form='unformatted')
@@ -72,44 +72,44 @@
read(IOUT) vs_read
close(IOUT)
-!-------------------------------------------------
+!-------------------------------------------------
!daniel: this will randomly perturb every GLL point in the model, thus adding like white noise to it.
! question: is the signal sensitive to this perturbation? or is it within numerical noise/artefacts?
! perturb model randomly
allocate( random(NGLLX,NGLLY,NGLLZ,nspec),stat=ier); if( ier /= 0 ) stop 'error allocating array random'
- if( .false. ) then
-
+ if( .false. ) then
+
CALL RANDOM_SEED()
!daniel: re-initialize seed with fixed value to make successive runs repeatable
CALL RANDOM_SEED(size=n)
allocate(myseed(n))
- myseed(1:n) = myrank * 75347
+ myseed(1:n) = myrank * 75347
CALL RANDOM_SEED(put=myseed)
! this should return the same number for repeated runs...
!call random_number(tmpharvest)
!print *,'seed size',n
!print *,'random number: ',tmpharvest
-
- CALL RANDOM_NUMBER(random)
- random=random/maxval(abs(random))*2.0-1.0
+
+ CALL RANDOM_NUMBER(random)
+ random=random/maxval(abs(random))*2.0-1.0
rho_read=rho_read*(1.0+percent*random)
CALL RANDOM_NUMBER(random)
- random=random/maxval(abs(random))*2.0-1.0
+ random=random/maxval(abs(random))*2.0-1.0
vp_read= vp_read*(1.0+percent*random)
CALL RANDOM_NUMBER(random)
random=random/maxval(abs(random))*2.0-1.0
vs_read= vs_read*(1.0+percent*random)
-
+
endif
-
-
-! adds a gaussian perturbation in the middle of the model
+
+
+! adds a gaussian perturbation in the middle of the model
if( .true. ) then
! initializes perturbations
random(:,:,:,:) = 0.0
@@ -130,41 +130,41 @@
!norm_h = 2.0*PI*sigma_h**2
!norm_v = sqrt(2.0*PI) * sigma_v
!norm = norm_h * norm_v
-
- ! sets gaussian perturbation into the middle of model:
+
+ ! sets gaussian perturbation into the middle of model:
! dimension (Width x Length x Depth) : 2640.0 m x 2640.0 m x 1.44 km
do ispec = 1,nspec
do k=1,NGLLZ
do j=1,NGLLY
do i=1,NGLLX
! GLL point location (given in m: dimension 2640 m x 2640 x x 1440 m)
- iglob = ibool(i,j,k,ispec)
+ iglob = ibool(i,j,k,ispec)
x = xstore(iglob)
y = ystore(iglob)
z = zstore(iglob)
-
+
! vertical distance to center: at - 500 m depth
dist_v = sqrt( (-500.0 - z)*(-500.0 - z) )
! horizontal distance to center: at 1320 x 1320 m
dist_h = sqrt( (1320.0 - x)*(1320.0 -x) + (1320.0 - y)*(1320.0 - y) )
! gaussian function: values between [0,1]
- random(i,j,k,ispec) = exp( - (dist_h*dist_h) / sigma_h2 - (dist_v*dist_v) / sigma_v2 )
-
+ random(i,j,k,ispec) = exp( - (dist_h*dist_h) / sigma_h2 - (dist_v*dist_v) / sigma_v2 )
+
!if(myrank == 0 )print*,random(i,j,k,ispec),x,y,z,dist_v,dist_h
enddo
enddo
enddo
- enddo
+ enddo
! adds positive perturbation to model:
!rho_read = rho_read*(1.0+percent*random)
vp_read = vp_read*(1.0+percent*random)
!vs_read = vs_read*(1.0+percent*random)
-
+
endif
-
-!-------------------------------------------------
+!-------------------------------------------------
+
! store perturbed model
! rho
open(unit=IOUT,file=trim(adjustl(prname))//'rho.bin',status='old',action='write',form='unformatted')
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 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/run_inhomogeneous.bash 2012-10-22 16:16:57 UTC (rev 20873)
@@ -28,7 +28,7 @@
bin="$PWD/bin"
DATA="$bin/../DATA"
-in_out_files="$bin/../in_out_files"
+OUTPUT_FILES="$bin/../OUTPUT_FILES"
models="$bin/../models"
SESAME="$bin/../../../../"
@@ -49,8 +49,8 @@
echo "setting up example..."
echo
-rm -rf $in_out_files $models $bin
-mkdir -p $in_out_files/DATABASES_MPI $in_out_files/OUTPUT_FILES $in_out_files/SEM/dat $in_out_files/SEM/syn
+rm -rf $OUTPUT_FILES $models $bin
+mkdir -p $OUTPUT_FILES/DATABASES_MPI $OUTPUT_FILES $OUTPUT_FILES/SEM/dat $OUTPUT_FILES/SEM/syn
mkdir -p $models/initial_model $models/target_model $bin
cd $SESAME
@@ -118,12 +118,12 @@
$MPIRUN ./xspecfem3D
#daniel
-cp -rp $in_out_files/OUTPUT_FILES $in_out_files/OUTPUT_FILES.dat.forward
+cp -rp $OUTPUT_FILES $OUTPUT_FILES.dat.forward
-mv $in_out_files/OUTPUT_FILES/*SU $in_out_files/SEM/dat/
-cp $in_out_files/DATABASES_MPI/*rho.bin $models/target_model/
-cp $in_out_files/DATABASES_MPI/*vp.bin $models/target_model/
-cp $in_out_files/DATABASES_MPI/*vs.bin $models/target_model/
+mv $OUTPUT_FILES/*SU $OUTPUT_FILES/SEM/dat/
+cp $OUTPUT_FILES/DATABASES_MPI/*rho.bin $models/target_model/
+cp $OUTPUT_FILES/DATABASES_MPI/*vp.bin $models/target_model/
+cp $OUTPUT_FILES/DATABASES_MPI/*vs.bin $models/target_model/
########################### syn ########################################
$MPIRUN ./xrandom_model $percent
@@ -134,12 +134,12 @@
$MPIRUN ./xspecfem3D
#daniel
-cp -rp $in_out_files/OUTPUT_FILES $in_out_files/OUTPUT_FILES.syn.forward
+cp -rp $OUTPUT_FILES $OUTPUT_FILES.syn.forward
-mv $in_out_files/OUTPUT_FILES/*SU $in_out_files/SEM/syn/
-cp $in_out_files/DATABASES_MPI/*rho.bin $models/initial_model/
-cp $in_out_files/DATABASES_MPI/*vp.bin $models/initial_model/
-cp $in_out_files/DATABASES_MPI/*vs.bin $models/initial_model/
+mv $OUTPUT_FILES/*SU $OUTPUT_FILES/SEM/syn/
+cp $OUTPUT_FILES/DATABASES_MPI/*rho.bin $models/initial_model/
+cp $OUTPUT_FILES/DATABASES_MPI/*vp.bin $models/initial_model/
+cp $OUTPUT_FILES/DATABASES_MPI/*vs.bin $models/initial_model/
########################### adj sources ################################
$MPIRUN ./xadj $NSTEP $DT
@@ -153,7 +153,7 @@
$MPIRUN ./xspecfem3D
#daniel
-cp -rp $in_out_files/OUTPUT_FILES $in_out_files/OUTPUT_FILES.syn.adjoint
+cp -rp $OUTPUT_FILES $OUTPUT_FILES.syn.adjoint
./xpostprocessing $NSTEP $DT $NPROC
@@ -167,7 +167,7 @@
#cd $bin/../
#rm -f compile.log make.log
-#rm -rf $in_out_files $models $bin
+#rm -rf $OUTPUT_FILES $models $bin
fi
Modified: seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/adj_seismogram.f90
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/adj_seismogram.f90 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/adj_seismogram.f90 2012-10-22 16:16:57 UTC (rev 20873)
@@ -28,7 +28,7 @@
!!!! read NSTEP from seismograms
!!!filename=trim(adjustl(procname))//"_dx_SU"
- !!!open(111,file="../in_out_files/OUTPUT_FILES/"//trim(filename),access='direct',recl=240,iostat = ios)
+ !!!open(111,file="../OUTPUT_FILES/"//trim(filename),access='direct',recl=240,iostat = ios)
!!!read(111,rec=1,iostat=ios) r4head
!!!close(111)
!!!header4=r4head(29)
@@ -48,123 +48,123 @@
! read 'syn', 'dat' and then write 'adj'
! x-component
filename=trim(adjustl(procname))//"_dx_SU"
- open(111,file="../in_out_files/SEM/syn/"//trim(filename), &
+ open(111,file="../OUTPUT_FILES/SEM/syn/"//trim(filename), &
status='old',access='direct',action='read',recl=240+4*NSTEP,iostat = ios)
if( ios /= 0 ) stop 'error opening file syn'
- open(112,file="../in_out_files/SEM/dat/"//trim(filename), &
+ open(112,file="../OUTPUT_FILES/SEM/dat/"//trim(filename), &
status='old',access='direct',action='read',recl=240+4*NSTEP,iostat = ios)
if( ios /= 0 ) stop 'error opening file dat'
- open(113,file="../in_out_files/SEM/"//trim(filename)//".adj", &
+ open(113,file="../OUTPUT_FILES/SEM/"//trim(filename)//".adj", &
status='unknown',access='direct',action='write',recl=240+4*NSTEP,iostat = ios)
if( ios /= 0 ) stop 'error opening file .adj'
-
+
irec=1
do while(ios==0)
-
- syn(:) = 0.0
+
+ syn(:) = 0.0
dat(:) = 0.0
-
+
read(111,rec=irec,iostat=ios) r4head,syn
if (ios /= 0) exit
read(112,rec=irec,iostat=ios) r4head,dat
if (ios /= 0) exit
-
+
write(113,rec=irec,iostat=ios) r4head,syn-dat
if (ios /= 0) exit
-
+
!daniel: outputs ascii trace
if( myrank == 0 .and. irec == 196 ) then
- open(221,file="../in_out_files/SEM/syn/"//trim(filename)//".ascii",status='unknown')
+ open(221,file="../OUTPUT_FILES/SEM/syn/"//trim(filename)//".ascii",status='unknown')
do i=1,NSTEP
write(221,*) i,syn(i)
enddo
close(221)
- open(222,file="../in_out_files/SEM/dat/"//trim(filename)//".ascii",status='unknown')
+ open(222,file="../OUTPUT_FILES/SEM/dat/"//trim(filename)//".ascii",status='unknown')
do i=1,NSTEP
write(222,*) i,dat(i)
enddo
close(222)
- open(223,file="../in_out_files/SEM/"//trim(filename)//".adj.ascii",status='unknown')
+ open(223,file="../OUTPUT_FILES/SEM/"//trim(filename)//".adj.ascii",status='unknown')
do i=1,NSTEP
write(223,*) i,syn(i)-dat(i)
enddo
close(223)
- endif
-
+ endif
+
irec=irec+1
enddo
close(111)
close(112)
close(113)
-
+
! y-component
filename=trim(adjustl(procname))//"_dy_SU"
- open(111,file="../in_out_files/SEM/syn/"//trim(filename), &
+ open(111,file="../OUTPUT_FILES/SEM/syn/"//trim(filename), &
status='old',access='direct',action='read',recl=240+4*NSTEP,iostat = ios)
if( ios /= 0 ) stop 'error opening file syn'
- open(112,file="../in_out_files/SEM/dat/"//trim(filename), &
+ open(112,file="../OUTPUT_FILES/SEM/dat/"//trim(filename), &
status='old',access='direct',action='read',recl=240+4*NSTEP,iostat = ios)
if( ios /= 0 ) stop 'error opening file dat'
- open(113,file="../in_out_files/SEM/"//trim(filename)//".adj", &
+ open(113,file="../OUTPUT_FILES/SEM/"//trim(filename)//".adj", &
status='unknown',access='direct',action='write',recl=240+4*NSTEP,iostat = ios)
if( ios /= 0 ) stop 'error opening file .adj'
-
+
irec=1
do while(ios==0)
- syn(:) = 0.0
+ syn(:) = 0.0
dat(:) = 0.0
-
+
read(111,rec=irec,iostat=ios) r4head,syn
if (ios /= 0) exit
read(112,rec=irec,iostat=ios) r4head,dat
if (ios /= 0) exit
write(113,rec=irec,iostat=ios) r4head,syn-dat
if (ios /= 0) exit
-
+
!daniel: outputs ascii trace
if( myrank == 0 .and. irec == 196 ) then
- open(221,file="../in_out_files/SEM/syn/"//trim(filename)//".ascii",status='unknown')
+ open(221,file="../OUTPUT_FILES/SEM/syn/"//trim(filename)//".ascii",status='unknown')
do i=1,NSTEP
write(221,*) i,syn(i)
- enddo
+ enddo
close(221)
- open(222,file="../in_out_files/SEM/dat/"//trim(filename)//".ascii",status='unknown')
+ open(222,file="../OUTPUT_FILES/SEM/dat/"//trim(filename)//".ascii",status='unknown')
do i=1,NSTEP
write(222,*) i,dat(i)
enddo
close(222)
- open(223,file="../in_out_files/SEM/"//trim(filename)//".adj.ascii",status='unknown')
+ open(223,file="../OUTPUT_FILES/SEM/"//trim(filename)//".adj.ascii",status='unknown')
do i=1,NSTEP
write(223,*) i,syn(i)-dat(i)
enddo
close(223)
- endif
-
-
+ endif
+
+
irec=irec+1
enddo
close(111)
close(112)
close(113)
-
+
! z-component
filename=trim(adjustl(procname))//"_dz_SU"
- open(111,file="../in_out_files/SEM/syn/"//trim(filename), &
+ open(111,file="../OUTPUT_FILES/SEM/syn/"//trim(filename), &
status='old',access='direct',action='read',recl=240+4*NSTEP,iostat = ios)
if( ios /= 0 ) stop 'error opening file syn'
- open(112,file="../in_out_files/SEM/dat/"//trim(filename), &
+ open(112,file="../OUTPUT_FILES/SEM/dat/"//trim(filename), &
status='old',access='direct',action='read',recl=240+4*NSTEP,iostat = ios)
if( ios /= 0 ) stop 'error opening file dat'
- open(113,file="../in_out_files/SEM/"//trim(filename)//".adj", &
+ open(113,file="../OUTPUT_FILES/SEM/"//trim(filename)//".adj", &
status='unknown',access='direct',action='write',recl=240+4*NSTEP,iostat = ios)
if( ios /= 0 ) stop 'error opening file .adj'
irec=1
do while(ios==0)
-
- syn(:) = 0.0
+
+ syn(:) = 0.0
dat(:) = 0.0
-
+
read(111,rec=irec,iostat=ios) r4head,syn
if (ios /= 0) exit
read(112,rec=irec,iostat=ios) r4head,dat
@@ -174,24 +174,24 @@
!daniel: outputs ascii trace
if( myrank == 0 .and. irec == 196 ) then
- open(221,file="../in_out_files/SEM/syn/"//trim(filename)//".ascii",status='unknown')
+ open(221,file="../OUTPUT_FILES/SEM/syn/"//trim(filename)//".ascii",status='unknown')
do i=1,NSTEP
write(221,*) i,syn(i)
enddo
close(221)
- open(222,file="../in_out_files/SEM/dat/"//trim(filename)//".ascii",status='unknown')
+ open(222,file="../OUTPUT_FILES/SEM/dat/"//trim(filename)//".ascii",status='unknown')
do i=1,NSTEP
write(222,*) i,dat(i)
enddo
close(222)
- open(223,file="../in_out_files/SEM/"//trim(filename)//".adj.ascii",status='unknown')
+ open(223,file="../OUTPUT_FILES/SEM/"//trim(filename)//".adj.ascii",status='unknown')
do i=1,NSTEP
write(223,*) i,syn(i)-dat(i)
enddo
close(223)
- endif
-
-
+ endif
+
+
irec=irec+1
enddo
close(111)
Modified: seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/in_data_files/Par_file
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/in_data_files/Par_file 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/in_data_files/Par_file 2012-10-22 16:16:57 UTC (rev 20873)
@@ -4,7 +4,7 @@
# 1 = forward, 2 = adjoint, 3 = both simultaneously
SIMULATION_TYPE = 3
# 0 = earthquake simulation, 1/2/3 = three steps in noise simulation
-NOISE_TOMOGRAPHY = 0
+NOISE_TOMOGRAPHY = 0
SAVE_FORWARD = .false.
# UTM projection parameters
@@ -15,15 +15,15 @@
NPROC = 4
# time step parameters
-NSTEP = 4000
+NSTEP = 4000
DT = 0.0006
# models:
# available options are:
# default (model parameters described by mesh properties)
-# 1D models available are:
+# 1D models available are:
# 1d_prem,1d_socal,1d_cascadia
-# 3D models available are:
+# 3D models available are:
# aniso,external,gll,salton_trough,tomo
MODEL = default
@@ -53,7 +53,7 @@
SAVE_MESH_FILES = .true.
# path to store the local database file on each node
-LOCAL_PATH = ../in_out_files/DATABASES_MPI/
+LOCAL_PATH = ../OUTPUT_FILES/DATABASES_MPI/
# interval at which we output time step info and max of norm of displacement
NTSTEP_BETWEEN_OUTPUT_INFO = 100
@@ -77,13 +77,13 @@
# The direction vector is made unitary internally in the code and thus only its direction matters here;
# its norm is ignored and the norm of the force used is the factor force source times the source time function.
-# set to use a Ricker source time function instead of a gaussian (when using CMTSOLUTION files)
-# or a quasi-Heaviside (when using FORCESOLUTION files)
+# set to use a Ricker source time function instead of a gaussian (when using CMTSOLUTION files)
+# or a quasi-Heaviside (when using FORCESOLUTION files)
USE_RICKER_TIME_FUNCTION = .false.
# print source time function
PRINT_SOURCE_TIME_FUNCTION = .true.
-# set to true to use GPUs
+# set to true to use GPUs
GPU_MODE = .false.
Modified: seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/in_data_files/meshfem3D_files/Mesh_Par_file
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/in_data_files/meshfem3D_files/Mesh_Par_file 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/in_data_files/meshfem3D_files/Mesh_Par_file 2012-10-22 16:16:57 UTC (rev 20873)
@@ -35,7 +35,7 @@
CREATE_VTK_FILES = .false.
# path to store the databases files
-LOCAL_PATH = ../in_out_files/DATABASES_MPI/
+LOCAL_PATH = ../OUTPUT_FILES/DATABASES_MPI/
# number of materials
NMATERIALS = 3
Modified: seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/postprocessing.f90
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/postprocessing.f90 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/postprocessing.f90 2012-10-22 16:16:57 UTC (rev 20873)
@@ -12,7 +12,7 @@
real(kind=4) :: r4head(60)
real(kind=4),dimension(:), allocatable :: adj
-
+
!! input parameters
if( iargc() .ne. 3 ) stop 'Usage: ./xpostprocessing NSTEP DT NPROC'
j=1; call getarg(j, arg); read(arg,*,iostat=ios) NSTEP; if (ios /= 0) stop 'Error reading NSTEP'
@@ -24,7 +24,7 @@
print*,' DT:',DT
print*,' NPROC:',NPROC
print*
-
+
MODELSPACE=0.0
DATASPACE=0.0
@@ -35,38 +35,38 @@
!!! calculate inner product in model space --- <F* F dm, dm>
! processors name
write(prname,'(a,i6.6,a)') 'proc',myrank,'_'
-
+
print*,' ',trim(prname)
-
+
! nspec & nglob
- open(unit=IOUT,file='../in_out_files/DATABASES_MPI/'//trim(adjustl(prname))//'external_mesh.bin',status='old',action='read',form='unformatted',iostat=ier)
+ open(unit=IOUT,file='../OUTPUT_FILES/DATABASES_MPI/'//trim(adjustl(prname))//'external_mesh.bin',status='old',action='read',form='unformatted',iostat=ier)
if( ier /= 0 ) stop 'error opening database proc######_external_mesh.bin'
read(IOUT) nspec
read(IOUT) nglob
close(IOUT)
-
+
! weights
allocate(weights(NGLLX,NGLLY,NGLLZ,nspec),stat=ier); if( ier /= 0 ) stop 'error allocating array weights'
- open(unit=IOUT,file='../in_out_files/DATABASES_MPI/'//trim(adjustl(prname))//'weights_kernel.bin',status='old',action='read',form='unformatted',iostat=ier)
+ open(unit=IOUT,file='../OUTPUT_FILES/DATABASES_MPI/'//trim(adjustl(prname))//'weights_kernel.bin',status='old',action='read',form='unformatted',iostat=ier)
read(IOUT) weights
close(IOUT)
-
+
! kernels
allocate(krhop(NGLLX,NGLLY,NGLLZ,nspec),stat=ier); if( ier /= 0 ) stop 'error allocating array krhop'
- open(unit=IOUT,file='../in_out_files/DATABASES_MPI/'//trim(adjustl(prname))//'rhop_kernel.bin',status='old',action='read',form='unformatted',iostat=ier)
+ open(unit=IOUT,file='../OUTPUT_FILES/DATABASES_MPI/'//trim(adjustl(prname))//'rhop_kernel.bin',status='old',action='read',form='unformatted',iostat=ier)
read(IOUT) krhop
close(IOUT)
-
+
allocate(kalpha(NGLLX,NGLLY,NGLLZ,nspec),stat=ier); if( ier /= 0 ) stop 'error allocating array kalpha'
- open(unit=IOUT,file='../in_out_files/DATABASES_MPI/'//trim(adjustl(prname))//'alpha_kernel.bin',status='old',action='read',form='unformatted',iostat=ier)
+ open(unit=IOUT,file='../OUTPUT_FILES/DATABASES_MPI/'//trim(adjustl(prname))//'alpha_kernel.bin',status='old',action='read',form='unformatted',iostat=ier)
read(IOUT) kalpha
close(IOUT)
-
+
allocate(kbeta(NGLLX,NGLLY,NGLLZ,nspec),stat=ier); if( ier /= 0 ) stop 'error allocating array kbeta'
- open(unit=IOUT,file='../in_out_files/DATABASES_MPI/'//trim(adjustl(prname))//'beta_kernel.bin',status='old',action='read',form='unformatted',iostat=ier)
+ open(unit=IOUT,file='../OUTPUT_FILES/DATABASES_MPI/'//trim(adjustl(prname))//'beta_kernel.bin',status='old',action='read',form='unformatted',iostat=ier)
read(IOUT) kbeta
close(IOUT)
-
+
! rho
allocate(rho(NGLLX,NGLLY,NGLLZ,nspec),stat=ier); if( ier /= 0 ) stop 'error allocating array rho'
allocate(rho0(NGLLX,NGLLY,NGLLZ,nspec),stat=ier); if( ier /= 0 ) stop 'error allocating array rho0'
@@ -76,7 +76,7 @@
open(unit=IOUT,file='../models/initial_model/'//trim(adjustl(prname))//'rho.bin',status='old',action='read',form='unformatted')
read(IOUT) rho0
close(IOUT)
-
+
! vp
allocate(vp(NGLLX,NGLLY,NGLLZ,nspec),stat=ier); if( ier /= 0 ) stop 'error allocating array vp'
allocate(vp0(NGLLX,NGLLY,NGLLZ,nspec),stat=ier); if( ier /= 0 ) stop 'error allocating array vp0'
@@ -86,7 +86,7 @@
open(unit=IOUT,file='../models/initial_model/'//trim(adjustl(prname))//'vp.bin',status='old',action='read',form='unformatted')
read(IOUT) vp0
close(IOUT)
-
+
! vs
allocate(vs(NGLLX,NGLLY,NGLLZ,nspec),stat=ier); if( ier /= 0 ) stop 'error allocating array vs'
allocate(vs0(NGLLX,NGLLY,NGLLZ,nspec),stat=ier); if( ier /= 0 ) stop 'error allocating array vs0'
@@ -104,31 +104,31 @@
sum(weights*(-kbeta)*(vs-vs0)/vs0))
deallocate(rho,rho0,vp,vp0,vs,vs0,weights,krhop,kalpha,kbeta)
-
-
+
+
!!! calculate inner product in data space --- <F dm, F dm>
write(procname,"(i4)") myrank
filename=trim(adjustl(procname))//"_dx_SU"
- open(111,file="../in_out_files/SEM/"//trim(adjustl(filename))//".adj",access='direct',recl=240+4*NSTEP,iostat = ios)
+ open(111,file="../OUTPUT_FILES/SEM/"//trim(adjustl(filename))//".adj",access='direct',recl=240+4*NSTEP,iostat = ios)
if( ios /= 0 ) stop 'error opening adjoint trace'
print*,' ',trim(adjustl(filename))//".adj"
-
+
irec=1
- do while(ios==0)
+ do while(ios==0)
adj(:) = 0.0
-
+
read(111,rec=irec,iostat=ios) r4head,adj
if (ios /= 0) exit
-
+
DATASPACE=DATASPACE+sum(adj(:)*adj(:))*DT
-
+
irec=irec+1
enddo
close(111)
irec_total = irec_total + 1
-
+
filename=trim(adjustl(procname))//"_dy_SU"
- open(111,file="../in_out_files/SEM/"//trim(adjustl(filename))//".adj",access='direct',recl=240+4*NSTEP,iostat = ios)
+ open(111,file="../OUTPUT_FILES/SEM/"//trim(adjustl(filename))//".adj",access='direct',recl=240+4*NSTEP,iostat = ios)
if( ios /= 0 ) stop 'error opening adjoint trace'
print*,' ',trim(adjustl(filename))//".adj"
@@ -146,7 +146,7 @@
close(111)
filename=trim(adjustl(procname))//"_dz_SU"
- open(111,file="../in_out_files/SEM/"//trim(adjustl(filename))//".adj",access='direct',recl=240+4*NSTEP,iostat = ios)
+ open(111,file="../OUTPUT_FILES/SEM/"//trim(adjustl(filename))//".adj",access='direct',recl=240+4*NSTEP,iostat = ios)
if( ios /= 0 ) stop 'error opening adjoint trace'
print*,' ',trim(adjustl(filename))//".adj"
Modified: seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/random_model_generation.f90
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/random_model_generation.f90 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/random_model_generation.f90 2012-10-22 16:16:57 UTC (rev 20873)
@@ -6,7 +6,7 @@
integer,parameter :: NGLLX=5,NGLLY=5,NGLLZ=5,IOUT=20
integer,parameter :: CUSTOM_REAL = 4
- character(len=512),parameter :: LOCAL_PATH='../in_out_files/DATABASES_MPI/'
+ character(len=512),parameter :: LOCAL_PATH='../OUTPUT_FILES/DATABASES_MPI/'
integer :: myrank,ier,nspec,nglob,NPROC,ios
double precision :: percent
@@ -25,7 +25,7 @@
!real(kind=CUSTOM_REAL) :: norm_h,norm_v,norm
real(kind=CUSTOM_REAL),parameter :: PI = 3.1415926535897931
integer :: i,j,k,ispec,iglob
-
+
call MPI_Init(ier)
call MPI_Comm_Rank(MPI_COMM_WORLD,myrank,ier)
call MPI_Comm_Size(MPI_COMM_WORLD,NPROC,ier)
@@ -41,7 +41,7 @@
if( ier /= 0 ) stop 'error opening database proc######_external_mesh.bin'
read(IOUT) nspec
read(IOUT) nglob
-
+
! ibool file
allocate(ibool(NGLLX,NGLLY,NGLLZ,nspec),stat=ier)
if( ier /= 0 ) stop 'error allocating array ibool'
@@ -52,15 +52,15 @@
read(IOUT) xstore
read(IOUT) ystore
read(IOUT) zstore
-
+
close(IOUT)
-
+
! rho
allocate( rho_read(NGLLX,NGLLY,NGLLZ,nspec),stat=ier); if( ier /= 0 ) stop 'error allocating array rho_read'
open(unit=IOUT,file=trim(adjustl(prname))//'rho.bin',status='old',action='read',form='unformatted')
read(IOUT) rho_read
close(IOUT)
-
+
! vp
allocate( vp_read(NGLLX,NGLLY,NGLLZ,nspec),stat=ier); if( ier /= 0 ) stop 'error allocating array vp_read'
open(unit=IOUT,file=trim(adjustl(prname))//'vp.bin',status='old',action='read',form='unformatted')
@@ -72,44 +72,44 @@
read(IOUT) vs_read
close(IOUT)
-!-------------------------------------------------
+!-------------------------------------------------
!daniel: this will randomly perturb every GLL point in the model, thus adding like white noise to it.
! question: is the signal sensitive to this perturbation? or is it within numerical noise/artefacts?
! perturb model randomly
allocate( random(NGLLX,NGLLY,NGLLZ,nspec),stat=ier); if( ier /= 0 ) stop 'error allocating array random'
- if( .false. ) then
-
+ if( .false. ) then
+
CALL RANDOM_SEED()
!daniel: re-initialize seed with fixed value to make successive runs repeatable
CALL RANDOM_SEED(size=n)
allocate(myseed(n))
- myseed(1:n) = myrank * 75347
+ myseed(1:n) = myrank * 75347
CALL RANDOM_SEED(put=myseed)
! this should return the same number for repeated runs...
!call random_number(tmpharvest)
!print *,'seed size',n
!print *,'random number: ',tmpharvest
-
- CALL RANDOM_NUMBER(random)
- random=random/maxval(abs(random))*2.0-1.0
+
+ CALL RANDOM_NUMBER(random)
+ random=random/maxval(abs(random))*2.0-1.0
rho_read=rho_read*(1.0+percent*random)
CALL RANDOM_NUMBER(random)
- random=random/maxval(abs(random))*2.0-1.0
+ random=random/maxval(abs(random))*2.0-1.0
vp_read= vp_read*(1.0+percent*random)
CALL RANDOM_NUMBER(random)
random=random/maxval(abs(random))*2.0-1.0
vs_read= vs_read*(1.0+percent*random)
-
+
endif
-
-
-! adds a gaussian perturbation in the middle of the model
+
+
+! adds a gaussian perturbation in the middle of the model
if( .true. ) then
! initializes perturbations
random(:,:,:,:) = 0.0
@@ -130,41 +130,41 @@
!norm_h = 2.0*PI*sigma_h**2
!norm_v = sqrt(2.0*PI) * sigma_v
!norm = norm_h * norm_v
-
- ! sets gaussian perturbation into the middle of model:
+
+ ! sets gaussian perturbation into the middle of model:
! dimension (Width x Length x Depth) : 2640.0 m x 2640.0 m x 1.44 km
do ispec = 1,nspec
do k=1,NGLLZ
do j=1,NGLLY
do i=1,NGLLX
! GLL point location (given in m: dimension 2640 m x 2640 x x 1440 m)
- iglob = ibool(i,j,k,ispec)
+ iglob = ibool(i,j,k,ispec)
x = xstore(iglob)
y = ystore(iglob)
z = zstore(iglob)
-
+
! vertical distance to center: at - 500 m depth
dist_v = sqrt( (-500.0 - z)*(-500.0 - z) )
! horizontal distance to center: at 1320 x 1320 m
dist_h = sqrt( (1320.0 - x)*(1320.0 -x) + (1320.0 - y)*(1320.0 - y) )
! gaussian function: values between [0,1]
- random(i,j,k,ispec) = exp( - (dist_h*dist_h) / sigma_h2 - (dist_v*dist_v) / sigma_v2 )
-
+ random(i,j,k,ispec) = exp( - (dist_h*dist_h) / sigma_h2 - (dist_v*dist_v) / sigma_v2 )
+
!if(myrank == 0 )print*,random(i,j,k,ispec),x,y,z,dist_v,dist_h
enddo
enddo
enddo
- enddo
+ enddo
! adds positive perturbation to model:
!rho_read = rho_read*(1.0+percent*random)
vp_read = vp_read*(1.0+percent*random)
!vs_read = vs_read*(1.0+percent*random)
-
+
endif
-
-!-------------------------------------------------
+!-------------------------------------------------
+
! store perturbed model
! rho
open(unit=IOUT,file=trim(adjustl(prname))//'rho.bin',status='old',action='write',form='unformatted')
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 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/run_inhomogeneous.bash 2012-10-22 16:16:57 UTC (rev 20873)
@@ -28,7 +28,7 @@
bin="$PWD/bin"
DATA="$bin/../DATA"
-in_out_files="$bin/../in_out_files"
+OUTPUT_FILES="$bin/../OUTPUT_FILES"
models="$bin/../models"
SESAME="$bin/../../../../"
@@ -49,8 +49,8 @@
echo "setting up example..."
echo
-rm -rf $in_out_files $models $bin
-mkdir -p $in_out_files/DATABASES_MPI $in_out_files/OUTPUT_FILES $in_out_files/SEM/dat $in_out_files/SEM/syn
+rm -rf $OUTPUT_FILES $models $bin
+mkdir -p $OUTPUT_FILES/DATABASES_MPI $OUTPUT_FILES $OUTPUT_FILES/SEM/dat $OUTPUT_FILES/SEM/syn
mkdir -p $models/initial_model $models/target_model $bin
cd $SESAME
@@ -118,12 +118,12 @@
$MPIRUN ./xspecfem3D
#daniel
-cp -rp $in_out_files/OUTPUT_FILES $in_out_files/OUTPUT_FILES.dat.forward
+cp -rp $OUTPUT_FILES $OUTPUT_FILES.dat.forward
-mv $in_out_files/OUTPUT_FILES/*SU $in_out_files/SEM/dat/
-cp $in_out_files/DATABASES_MPI/*rho.bin $models/target_model/
-cp $in_out_files/DATABASES_MPI/*vp.bin $models/target_model/
-cp $in_out_files/DATABASES_MPI/*vs.bin $models/target_model/
+mv $OUTPUT_FILES/*SU $OUTPUT_FILES/SEM/dat/
+cp $OUTPUT_FILES/DATABASES_MPI/*rho.bin $models/target_model/
+cp $OUTPUT_FILES/DATABASES_MPI/*vp.bin $models/target_model/
+cp $OUTPUT_FILES/DATABASES_MPI/*vs.bin $models/target_model/
########################### syn ########################################
$MPIRUN ./xrandom_model $percent
@@ -134,12 +134,12 @@
$MPIRUN ./xspecfem3D
#daniel
-cp -rp $in_out_files/OUTPUT_FILES $in_out_files/OUTPUT_FILES.syn.forward
+cp -rp $OUTPUT_FILES $OUTPUT_FILES.syn.forward
-mv $in_out_files/OUTPUT_FILES/*SU $in_out_files/SEM/syn/
-cp $in_out_files/DATABASES_MPI/*rho.bin $models/initial_model/
-cp $in_out_files/DATABASES_MPI/*vp.bin $models/initial_model/
-cp $in_out_files/DATABASES_MPI/*vs.bin $models/initial_model/
+mv $OUTPUT_FILES/*SU $OUTPUT_FILES/SEM/syn/
+cp $OUTPUT_FILES/DATABASES_MPI/*rho.bin $models/initial_model/
+cp $OUTPUT_FILES/DATABASES_MPI/*vp.bin $models/initial_model/
+cp $OUTPUT_FILES/DATABASES_MPI/*vs.bin $models/initial_model/
########################### adj sources ################################
$MPIRUN ./xadj $NSTEP $DT
@@ -153,7 +153,7 @@
$MPIRUN ./xspecfem3D
#daniel
-cp -rp $in_out_files/OUTPUT_FILES $in_out_files/OUTPUT_FILES.syn.adjoint
+cp -rp $OUTPUT_FILES $OUTPUT_FILES.syn.adjoint
./xpostprocessing $NSTEP $DT $NPROC
@@ -167,7 +167,7 @@
#cd $bin/../
#rm -f compile.log make.log
-#rm -rf $in_out_files $models $bin
+#rm -rf $OUTPUT_FILES $models $bin
fi
Modified: seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/in_data_files/Par_file
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/in_data_files/Par_file 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/in_data_files/Par_file 2012-10-22 16:16:57 UTC (rev 20873)
@@ -2,9 +2,9 @@
#
# forward or adjoint simulation
# 1 = forward, 2 = adjoint, 3 = both simultaneously
-SIMULATION_TYPE = 1
+SIMULATION_TYPE = 1
# 0 = earthquake simulation, 1/2/3 = three steps in noise simulation
-NOISE_TOMOGRAPHY = 0
+NOISE_TOMOGRAPHY = 0
SAVE_FORWARD = .false.
# UTM projection parameters
@@ -21,9 +21,9 @@
# models:
# available options are:
# default (model parameters described by mesh properties)
-# 1D models available are:
+# 1D models available are:
# 1d_prem,1d_socal,1d_cascadia
-# 3D models available are:
+# 3D models available are:
# aniso,external,gll,salton_trough,tomo
MODEL = default
@@ -53,7 +53,7 @@
SAVE_MESH_FILES = .true.
# path to store the local database file on each node
-LOCAL_PATH = ../in_out_files/DATABASES_MPI
+LOCAL_PATH = ../OUTPUT_FILES/DATABASES_MPI
# interval at which we output time step info and max of norm of displacement
NTSTEP_BETWEEN_OUTPUT_INFO = 500
@@ -77,13 +77,13 @@
# The direction vector is made unitary internally in the code and thus only its direction matters here;
# its norm is ignored and the norm of the force used is the factor force source times the source time function.
-# set to use a Ricker source time function instead of a gaussian (when using CMTSOLUTION files)
-# or a quasi-Heaviside (when using FORCESOLUTION files)
+# set to use a Ricker source time function instead of a gaussian (when using CMTSOLUTION files)
+# or a quasi-Heaviside (when using FORCESOLUTION files)
USE_RICKER_TIME_FUNCTION = .false.
# print source time function
PRINT_SOURCE_TIME_FUNCTION = .false.
-# set to true to use GPUs
+# set to true to use GPUs
GPU_MODE = .false.
Modified: seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/process.sh
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/process.sh 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/process.sh 2012-10-22 16:16:57 UTC (rev 20873)
@@ -27,11 +27,11 @@
echo
mkdir -p bin
-mkdir -p in_out_files/OUTPUT_FILES
-mkdir -p in_out_files/DATABASES_MPI
+mkdir -p OUTPUT_FILES
+mkdir -p OUTPUT_FILES/DATABASES_MPI
-rm -rf in_out_files/OUTPUT_FILES/*
-rm -rf in_out_files/DATABASES_MPI/*
+rm -rf OUTPUT_FILES/*
+rm -rf OUTPUT_FILES/DATABASES_MPI/*
# compiles executables in root directory
cd ../../
@@ -50,12 +50,12 @@
echo
echo " decomposing mesh..."
echo
-./bin/xdecompose_mesh_SCOTCH $NPROC MESH/ in_out_files/DATABASES_MPI/
+./bin/xdecompose_mesh_SCOTCH $NPROC MESH/ OUTPUT_FILES/DATABASES_MPI/
# stores setup
-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/
+cp DATA/Par_file OUTPUT_FILES/
+cp DATA/CMTSOLUTION OUTPUT_FILES/
+cp DATA/STATIONS OUTPUT_FILES/
# runs database generation
echo
@@ -74,7 +74,7 @@
cd ../
echo
-echo "see results in directory: in_out_files/OUTPUT_FILES/"
+echo "see results in directory: OUTPUT_FILES/"
echo
echo "done"
echo `date`
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 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/HOWTO_run_this_example.txt 2012-10-22 16:16:57 UTC (rev 20873)
@@ -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 DATA/MESH in_out_files/DATABASES_MPI
+./bin/xdecompose_mesh_SCOTCH 2 DATA/MESH OUTPUT_FILES/DATABASES_MPI
mpirun -np 2 ./bin/xgenerate_databases
Modified: seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/in_data_files/Par_file
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/in_data_files/Par_file 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/in_data_files/Par_file 2012-10-22 16:16:57 UTC (rev 20873)
@@ -2,9 +2,9 @@
#
# forward or adjoint simulation
# 1 = forward, 2 = adjoint, 3 = both simultaneously
-SIMULATION_TYPE = 1
+SIMULATION_TYPE = 1
# 0 = earthquake simulation, 1/2/3 = three steps in noise simulation
-NOISE_TOMOGRAPHY = 0
+NOISE_TOMOGRAPHY = 0
SAVE_FORWARD = .false.
# UTM projection parameters
@@ -21,9 +21,9 @@
# models:
# available options are:
# default (model parameters described by mesh properties)
-# 1D models available are:
+# 1D models available are:
# 1d_prem,1d_socal,1d_cascadia
-# 3D models available are:
+# 3D models available are:
# aniso,external,gll,salton_trough,tomo
MODEL = default
@@ -54,7 +54,7 @@
SAVE_MESH_FILES = .true.
# path to store the local database file on each node
-LOCAL_PATH = ../in_out_files/DATABASES_MPI
+LOCAL_PATH = ../OUTPUT_FILES/DATABASES_MPI
# interval at which we output time step info and max of norm of displacement
NTSTEP_BETWEEN_OUTPUT_INFO = 100
@@ -64,7 +64,7 @@
# interval in time steps for reading adjoint traces
# 0 = read the whole adjoint sources at the same time
-NTSTEP_BETWEEN_READ_ADJSRC = 0
+NTSTEP_BETWEEN_READ_ADJSRC = 0
# use a force source (or several) located exactly at a grid point instead of a CMTSOLUTION source.
# This can be useful e.g. for oil industry foothills simulations or asteroid simulations
@@ -79,13 +79,13 @@
# The direction vector is made unitary internally in the code and thus only its direction matters here;
# its norm is ignored and the norm of the force used is the factor force source times the source time function.
-# set to use a Ricker source time function instead of a gaussian (when using CMTSOLUTION files)
-# or a quasi-Heaviside (when using FORCESOLUTION files)
+# set to use a Ricker source time function instead of a gaussian (when using CMTSOLUTION files)
+# or a quasi-Heaviside (when using FORCESOLUTION files)
USE_RICKER_TIME_FUNCTION = .false.
# print source time function
PRINT_SOURCE_TIME_FUNCTION = .false.
-# set to true to use GPUs
+# set to true to use GPUs
GPU_MODE = .false.
Modified: seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/plotall_comparison_seismograms.gnu
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/plotall_comparison_seismograms.gnu 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/plotall_comparison_seismograms.gnu 2012-10-22 16:16:57 UTC (rev 20873)
@@ -2,21 +2,21 @@
set xlabel "time (s)"
set ylabel "displacement (m)"
-plot 'REF_SEIS/X1.DB.BXZ.semd' w l lc 1, 'in_out_files/OUTPUT_FILES/X1.DB.BXZ.semd' w l lc 3
+plot 'REF_SEIS/X1.DB.BXZ.semd' w l lc 1, 'OUTPUT_FILES/X1.DB.BXZ.semd' w l lc 3
pause -1 "hit key..."
-plot 'REF_SEIS/X10.DB.BXZ.semd' w l lc 1, 'in_out_files/OUTPUT_FILES/X10.DB.BXZ.semd' w l lc 3
+plot 'REF_SEIS/X10.DB.BXZ.semd' w l lc 1, 'OUTPUT_FILES/X10.DB.BXZ.semd' w l lc 3
pause -1 "hit key..."
-plot 'REF_SEIS/X20.DB.BXZ.semd' w l lc 1, 'in_out_files/OUTPUT_FILES/X20.DB.BXZ.semd' w l lc 3
+plot 'REF_SEIS/X20.DB.BXZ.semd' w l lc 1, 'OUTPUT_FILES/X20.DB.BXZ.semd' w l lc 3
pause -1 "hit key..."
-plot 'REF_SEIS/X30.DB.BXZ.semd' w l lc 1, 'in_out_files/OUTPUT_FILES/X30.DB.BXZ.semd' w l lc 3
+plot 'REF_SEIS/X30.DB.BXZ.semd' w l lc 1, 'OUTPUT_FILES/X30.DB.BXZ.semd' w l lc 3
pause -1 "hit key..."
-plot 'REF_SEIS/X40.DB.BXZ.semd' w l lc 1, 'in_out_files/OUTPUT_FILES/X40.DB.BXZ.semd' w l lc 3
+plot 'REF_SEIS/X40.DB.BXZ.semd' w l lc 1, 'OUTPUT_FILES/X40.DB.BXZ.semd' w l lc 3
pause -1 "hit key..."
-plot 'REF_SEIS/X50.DB.BXZ.semd' w l lc 1, 'in_out_files/OUTPUT_FILES/X50.DB.BXZ.semd' w l lc 3
+plot 'REF_SEIS/X50.DB.BXZ.semd' w l lc 1, 'OUTPUT_FILES/X50.DB.BXZ.semd' w l lc 3
pause -1 "hit key..."
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 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8/HOWTO_run_this_example.txt 2012-10-22 16:16:57 UTC (rev 20873)
@@ -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 DATA/MESH in_out_files/DATABASES_MPI
+./bin/xdecompose_mesh_SCOTCH 2 DATA/MESH OUTPUT_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 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8/README 2012-10-22 16:16:57 UTC (rev 20873)
@@ -82,14 +82,14 @@
note: this script will need to be tailored to your cluster, e.g.,
> bsub < go_decomposer_lsf.bash
- this creates mesh partitions "proc000***_Database" in directory in_out_files/DATABASES_MPI/.
- the output file in_out_files/OUTPUT_FILES/*.o contains information on the partitioning
+ this creates mesh partitions "proc000***_Database" in directory OUTPUT_FILES/DATABASES_MPI/.
+ the output file OUTPUT_FILES/*.o contains information on the partitioning
note 1: the program xdecompose_mesh_SCOTCH is a serial program (runs on 1 core)
note 2: for small jobs (like this one), you can simply launch the job on
the local node from directory SPECFEM3D:
- > ./bin/xdecompose_mesh_SCOTCH 4 examples/homogeneous_halfspace/MESH/ in_out_files/DATABASES_MPI/
+ > ./bin/xdecompose_mesh_SCOTCH 4 examples/homogeneous_halfspace/MESH/ OUTPUT_FILES/DATABASES_MPI/
5. generate databases:
@@ -104,7 +104,7 @@
> bsub < go_generate_databases_lsf.bash
this will create binary mesh files, e.g. "proc000***_external_mesh.bin"
- in directory in_out_files/DATABASES_MPI/.
+ in directory OUTPUT_FILES/DATABASES_MPI/.
6. run simulation:
@@ -119,11 +119,11 @@
> bsub < go_solver_lsf.bash
note 2: the simulation runs on 4 cores and should take about 5 minutes,
and you can track the progress with the timestamp files
- generated in in_out_files/OUTPUT_FILES/
+ generated in OUTPUT_FILES/
- the job should take a couple minutes
- when the job is complete, you should have 3 sets (semd,semv,sema)
- of 18 (ls -1 *semd | wc) seismogram files in the directory in_out_files/OUTPUT_FILES,
+ of 18 (ls -1 *semd | wc) seismogram files in the directory OUTPUT_FILES,
as well as 3 timestamp****** files
@@ -133,7 +133,7 @@
- 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 &
+ > xmgrace OUTPUT_FILES/*Z.semd &
- option 2: generate ps files using gnuplot:
@@ -157,7 +157,7 @@
gnuplot> replot
gnuplot> quit
- - copy gnuplot script X1-50.BXZ.gnuplot to in_out_files/OUTPUT_FILES/
+ - copy gnuplot script X1-50.BXZ.gnuplot to OUTPUT_FILES/
- execute same commands as above
- you should see the same image as generated from the reference seismograms
Modified: seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8/README_kernel
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8/README_kernel 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8/README_kernel 2012-10-22 16:16:57 UTC (rev 20873)
@@ -33,11 +33,11 @@
- run the forward simulation, submitting the job script:
> qsub go_solver_pbs.bash
- you should have now the necessary seismograms in directory in_out_files/OUTPUT_FILES/:
+ you should have now the necessary seismograms in directory OUTPUT_FILES/:
...
- in_out_files/OUTPUT_FILES/X20.BXX.semd
- in_out_files/OUTPUT_FILES/X20.BXY.semd
- in_out_files/OUTPUT_FILES/X20.BXZ.semd
+ OUTPUT_FILES/X20.BXX.semd
+ OUTPUT_FILES/X20.BXY.semd
+ OUTPUT_FILES/X20.BXZ.semd
...
@@ -51,24 +51,24 @@
e.g. using the seismograms from station X20, and create the
corresponding adjoint source files:
> cd /SPECFEM3D
- > ./utils/adjoint_sources/traveltime/xcreate_adjsrc_traveltime 10. 25. 3 in_out_files/OUTPUT_FILES/X20.DB.BX*.semd
+ > ./utils/adjoint_sources/traveltime/xcreate_adjsrc_traveltime 10. 25. 3 OUTPUT_FILES/X20.DB.BX*.semd
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:
- > mkdir in_out_files/SEM/
- > mv in_out_files/OUTPUT_FILES/*.adj in_out_files/SEM/
- > cd in_out_files/SEM/
+ > mkdir OUTPUT_FILES/SEM/
+ > mv OUTPUT_FILES/*.adj OUTPUT_FILES/SEM/
+ > cd OUTPUT_FILES/SEM/
> rename .semd.adj .adj *.adj
this should create the files:
- in_out_files/SEM/X20.DB.BXX.adj
- in_out_files/SEM/X20.DB.BXY.adj
- in_out_files/SEM/X20.DB.BXZ.adj
+ OUTPUT_FILES/SEM/X20.DB.BXX.adj
+ OUTPUT_FILES/SEM/X20.DB.BXY.adj
+ OUTPUT_FILES/SEM/X20.DB.BXZ.adj
- setup adjoint stations file STATIONS_ADJOINT containing the receiver stations locations
- which will have adjoint source files in in_out_files/SEM/:
+ which will have adjoint source files in OUTPUT_FILES/SEM/:
> cd /SPECFEM3D
> cp examples/homogeneous_halfspace/DATA/STATIONS_ADJOINT DATA/
@@ -88,23 +88,23 @@
> qsub go_solver_pbs.bash
- this will create adjoint kernel files in directory in_out_files/DATABASES_MPI/
+ this will create adjoint kernel files in directory OUTPUT_FILES/DATABASES_MPI/
according to travel-time kernels as e.g. defined in Tromp et al. (2005) :
- in_out_files/DATABASES_MPI/proc000***_alpha_kernel.bin
- in_out_files/DATABASES_MPI/proc000***_beta_kernel.bin
- in_out_files/DATABASES_MPI/proc000***_kappa_kernel.bin
- in_out_files/DATABASES_MPI/proc000***_mu_kernel.bin
- in_out_files/DATABASES_MPI/proc000***_rho_kernel.bin
- in_out_files/DATABASES_MPI/proc000***_rhop_kernel.bin
+ OUTPUT_FILES/DATABASES_MPI/proc000***_alpha_kernel.bin
+ OUTPUT_FILES/DATABASES_MPI/proc000***_beta_kernel.bin
+ OUTPUT_FILES/DATABASES_MPI/proc000***_kappa_kernel.bin
+ OUTPUT_FILES/DATABASES_MPI/proc000***_mu_kernel.bin
+ OUTPUT_FILES/DATABASES_MPI/proc000***_rho_kernel.bin
+ OUTPUT_FILES/DATABASES_MPI/proc000***_rhop_kernel.bin
- visualize with Paraview, e.g. :
> cd /SPECFEM3D
> make xcombine_vol_data
> cd bin/
- > ./xcombine_vol_data 0 3 alpha_kernel ../in_out_files/DATABASES_MPI/ ../in_out_files/OUTPUT_FILES/ 1
+ > ./xcombine_vol_data 0 3 alpha_kernel ../OUTPUT_FILES/DATABASES_MPI/ ../OUTPUT_FILES/ 1
where we use the partitions with id 0 to 3 to include all 4 processor partitions.
- By default, this will produce the vtk file /SPECFEM3D/in_out_files/OUTPUT_FILES/alpha_kernel.vtk
+ By default, this will produce the vtk file /SPECFEM3D/OUTPUT_FILES/alpha_kernel.vtk
This file can be visualized using Paraview (see image alpha_kernel.png for reference).
OPTIONAL:
@@ -114,7 +114,7 @@
> make
the modify the paths to your mesh2vtu installation in the utils/Visualization/Paraview/mesh2vtu.pl file,
and run:
- > mesh2vtu.pl -i in_out_files/OUTPUT_FILES/alpha_kernel.mesh -o in_out_files/OUTPUT_FILES/alpha_kernel.vtu
+ > mesh2vtu.pl -i OUTPUT_FILES/alpha_kernel.mesh -o OUTPUT_FILES/alpha_kernel.vtu
which creates the *.vtu file: Paraview -> Menu File -> Open ...
(and choose the alpha_kernel.vtu)
Modified: seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8/in_data_files/Par_file
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8/in_data_files/Par_file 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8/in_data_files/Par_file 2012-10-22 16:16:57 UTC (rev 20873)
@@ -2,9 +2,9 @@
#
# forward or adjoint simulation
# 1 = forward, 2 = adjoint, 3 = both simultaneously
-SIMULATION_TYPE = 1
+SIMULATION_TYPE = 1
# 0 = earthquake simulation, 1/2/3 = three steps in noise simulation
-NOISE_TOMOGRAPHY = 0
+NOISE_TOMOGRAPHY = 0
SAVE_FORWARD = .false.
# UTM projection parameters
@@ -21,9 +21,9 @@
# models:
# available options are:
# default (model parameters described by mesh properties)
-# 1D models available are:
+# 1D models available are:
# 1d_prem,1d_socal,1d_cascadia
-# 3D models available are:
+# 3D models available are:
# aniso,external,gll,salton_trough,tomo
MODEL = default
@@ -54,7 +54,7 @@
SAVE_MESH_FILES = .true.
# path to store the local database file on each node
-LOCAL_PATH = ../in_out_files/DATABASES_MPI
+LOCAL_PATH = ../OUTPUT_FILES/DATABASES_MPI
# interval at which we output time step info and max of norm of displacement
NTSTEP_BETWEEN_OUTPUT_INFO = 100
@@ -64,7 +64,7 @@
# interval in time steps for reading adjoint traces
# 0 = read the whole adjoint sources at the same time
-NTSTEP_BETWEEN_READ_ADJSRC = 0
+NTSTEP_BETWEEN_READ_ADJSRC = 0
# use a force source (or several) located exactly at a grid point instead of a CMTSOLUTION source.
# This can be useful e.g. for oil industry foothills simulations or asteroid simulations
@@ -79,13 +79,13 @@
# The direction vector is made unitary internally in the code and thus only its direction matters here;
# its norm is ignored and the norm of the force used is the factor force source times the source time function.
-# set to use a Ricker source time function instead of a gaussian (when using CMTSOLUTION files)
-# or a quasi-Heaviside (when using FORCESOLUTION files)
+# set to use a Ricker source time function instead of a gaussian (when using CMTSOLUTION files)
+# or a quasi-Heaviside (when using FORCESOLUTION files)
USE_RICKER_TIME_FUNCTION = .false.
# print source time function
PRINT_SOURCE_TIME_FUNCTION = .false.
-# set to true to use GPUs
+# set to true to use GPUs
GPU_MODE = .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 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8/process.sh 2012-10-22 16:16:57 UTC (rev 20873)
@@ -27,11 +27,11 @@
echo
mkdir -p bin
-mkdir -p in_out_files/OUTPUT_FILES
-mkdir -p in_out_files/DATABASES_MPI
+mkdir -p OUTPUT_FILES
+mkdir -p OUTPUT_FILES/DATABASES_MPI
-rm -rf in_out_files/OUTPUT_FILES/*
-rm -rf in_out_files/DATABASES_MPI/*
+rm -rf OUTPUT_FILES/*
+rm -rf OUTPUT_FILES/DATABASES_MPI/*
# compiles executables in root directory
cd ../../
@@ -50,12 +50,12 @@
echo
echo " decomposing mesh..."
echo
-./bin/xdecompose_mesh_SCOTCH $NPROC MESH/ in_out_files/DATABASES_MPI/
+./bin/xdecompose_mesh_SCOTCH $NPROC MESH/ OUTPUT_FILES/DATABASES_MPI/
# stores setup
-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/
+cp DATA/Par_file OUTPUT_FILES/
+cp DATA/CMTSOLUTION OUTPUT_FILES/
+cp DATA/STATIONS OUTPUT_FILES/
# runs database generation
echo
@@ -74,7 +74,7 @@
cd ../
echo
-echo "see results in directory: in_out_files/OUTPUT_FILES/"
+echo "see results in directory: OUTPUT_FILES/"
echo
echo "done"
echo `date`
Modified: seismo/3D/SPECFEM3D/trunk/examples/homogeneous_poroelastic/README
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/homogeneous_poroelastic/README 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/homogeneous_poroelastic/README 2012-10-22 16:16:57 UTC (rev 20873)
@@ -59,10 +59,10 @@
- run decomposer in directory
(example assumes 16 partitions with mesh files in ../examples/homogeneous_poro/MESH/)
- > ./bin/xdecompose_mesh_SCOTCH 16 ../examples/homogeneous_poro/MESH/ ../in_out_files/DATABASES_MPI/
+ > ./bin/xdecompose_mesh_SCOTCH 16 ../examples/homogeneous_poro/MESH/ ../OUTPUT_FILES/DATABASES_MPI/
- this creates mesh partitions "proc000***_Database" in directory in_out_files/DATABASES_MPI/.
- (you can then specify "../in_out_files/DATABASES_MPI" in "Par_file" for your "LOCAL_PATH")
+ this creates mesh partitions "proc000***_Database" in directory OUTPUT_FILES/DATABASES_MPI/.
+ (you can then specify "../OUTPUT_FILES/DATABASES_MPI" in "Par_file" for your "LOCAL_PATH")
4. generate databases:
@@ -78,7 +78,7 @@
> bsub < go_generate_databases_lsf.bash
this will create binary mesh files, e.g. "proc000***_external_mesh.bin"
- in directory in_out_files/DATABASES_MPI/.
+ in directory OUTPUT_FILES/DATABASES_MPI/.
5. run simulation:
@@ -102,7 +102,7 @@
as well as 3 timestamp****** files
-6. plot your output seismograms in SPECFEM3D/in_out_files/OUTPUT_FILES/
+6. plot your output seismograms in SPECFEM3D/OUTPUT_FILES/
using xmgrace for example.
===========================================================
Modified: seismo/3D/SPECFEM3D/trunk/examples/homogeneous_poroelastic/in_data_files/Par_file
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/homogeneous_poroelastic/in_data_files/Par_file 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/homogeneous_poroelastic/in_data_files/Par_file 2012-10-22 16:16:57 UTC (rev 20873)
@@ -2,9 +2,9 @@
#
# forward or adjoint simulation
# 1 = forward, 2 = adjoint, 3 = both simultaneously
-SIMULATION_TYPE = 1
+SIMULATION_TYPE = 1
# 0 = earthquake simulation, 1/2/3 = three steps in noise simulation
-NOISE_TOMOGRAPHY = 0
+NOISE_TOMOGRAPHY = 0
SAVE_FORWARD = .true.
# UTM projection parameters
@@ -21,9 +21,9 @@
# models:
# available options are:
# default (model parameters described by mesh properties)
-# 1D models available are:
+# 1D models available are:
# 1d_prem,1d_socal,1d_cascadia
-# 3D models available are:
+# 3D models available are:
# aniso,external,gll,salton_trough,tomo
MODEL = default
@@ -54,7 +54,7 @@
SAVE_MESH_FILES = .true.
# path to store the local database file on each node
-LOCAL_PATH = ../in_out_files/DATABASES_MPI
+LOCAL_PATH = ../OUTPUT_FILES/DATABASES_MPI
# interval at which we output time step info and max of norm of displacement
NTSTEP_BETWEEN_OUTPUT_INFO = 250
@@ -79,12 +79,12 @@
# The direction vector is made unitary internally in the code and thus only its direction matters here;
# its norm is ignored and the norm of the force used is the factor force source times the source time function.
-# set to use a Ricker source time function instead of a gaussian (when using CMTSOLUTION files)
-# or a quasi-Heaviside (when using FORCESOLUTION files)
+# set to use a Ricker source time function instead of a gaussian (when using CMTSOLUTION files)
+# or a quasi-Heaviside (when using FORCESOLUTION files)
USE_RICKER_TIME_FUNCTION = .false.
# print source time function
PRINT_SOURCE_TIME_FUNCTION = .true.
-# set to true to use GPUs
+# set to true to use GPUs
GPU_MODE = .false.
Modified: seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/README
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/README 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/README 2012-10-22 16:16:57 UTC (rev 20873)
@@ -85,7 +85,7 @@
> qsub go_decomposer_pbs.bash
which creates mesh partitions "proc0000***_Database" in directory "DATABASES_MPI".
- you can then specify "../in_out_files/DATABASES_MPI" in "Par_file" for your "LOCAL_PATH"
+ you can then specify "../OUTPUT_FILES/DATABASES_MPI" in "Par_file" for your "LOCAL_PATH"
4. generate databases:
@@ -97,7 +97,7 @@
> qsub go_generate_databases_pbs.bash
this will create binary mesh files, e.g. "proc000***_external_mesh.bin"
- in directory in_out_files/DATABASES_MPI/.
+ in directory OUTPUT_FILES/DATABASES_MPI/.
(note: if execution fails due to memory shortage - most likely fails when calling routine to
create regional mesh - then try to increase process memory stack size: ulimit -s 2000000 (2GB) )
@@ -114,12 +114,12 @@
> qsub go_solver_pbs.bash
note: simulation will take about 25 minutes and generate
- 3 sets (semd,semv,sema) of 6 seismogram files in in_out_files/OUTPUT_FILES,
+ 3 sets (semd,semv,sema) of 6 seismogram files in OUTPUT_FILES,
as well as 7 timestamp****** files
Optional:
Compare the solution traces in the directory
- in_out_files/OUTPUT_FILES/:
+ OUTPUT_FILES/:
X55.DB.HXZ.semd
X31.DB.HXZ.semd
Modified: seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/in_data_files/Par_file
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/in_data_files/Par_file 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/in_data_files/Par_file 2012-10-22 16:16:57 UTC (rev 20873)
@@ -2,9 +2,9 @@
#
# forward or adjoint simulation
# 1 = forward, 2 = adjoint, 3 = both simultaneously
-SIMULATION_TYPE = 1
+SIMULATION_TYPE = 1
# 0 = earthquake simulation, 1/2/3 = three steps in noise simulation
-NOISE_TOMOGRAPHY = 0
+NOISE_TOMOGRAPHY = 0
SAVE_FORWARD = .false.
# UTM projection parameters
@@ -21,9 +21,9 @@
# models:
# available options are:
# default (model parameters described by mesh properties)
-# 1D models available are:
+# 1D models available are:
# 1d_prem,1d_socal,1d_cascadia
-# 3D models available are:
+# 3D models available are:
# aniso,external,gll,salton_trough,tomo
MODEL = default
@@ -54,7 +54,7 @@
SAVE_MESH_FILES = .true.
# path to store the local database file on each node
-LOCAL_PATH = ../in_out_files/DATABASES_MPI
+LOCAL_PATH = ../OUTPUT_FILES/DATABASES_MPI
# interval at which we output time step info and max of norm of displacement
NTSTEP_BETWEEN_OUTPUT_INFO = 500
@@ -78,13 +78,13 @@
# The direction vector is made unitary internally in the code and thus only its direction matters here;
# its norm is ignored and the norm of the force used is the factor force source times the source time function.
-# set to use a Ricker source time function instead of a gaussian (when using CMTSOLUTION files)
-# or a quasi-Heaviside (when using FORCESOLUTION files)
+# set to use a Ricker source time function instead of a gaussian (when using CMTSOLUTION files)
+# or a quasi-Heaviside (when using FORCESOLUTION files)
USE_RICKER_TIME_FUNCTION = .false.
# print source time function
PRINT_SOURCE_TIME_FUNCTION = .false.
-# set to true to use GPUs
+# set to true to use GPUs
GPU_MODE = .false.
Modified: seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/process.sh
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/process.sh 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/process.sh 2012-10-22 16:16:57 UTC (rev 20873)
@@ -28,11 +28,11 @@
echo
mkdir -p bin
-mkdir -p in_out_files/OUTPUT_FILES
-mkdir -p in_out_files/DATABASES_MPI
+mkdir -p OUTPUT_FILES
+mkdir -p OUTPUT_FILES/DATABASES_MPI
-rm -rf in_out_files/OUTPUT_FILES/*
-rm -rf in_out_files/DATABASES_MPI/*
+rm -rf OUTPUT_FILES/*
+rm -rf OUTPUT_FILES/DATABASES_MPI/*
cd $currentdir
@@ -48,12 +48,12 @@
echo
echo " decomposing mesh..."
echo
-./bin/xdecompose_mesh_SCOTCH $NPROC MESH/ in_out_files/DATABASES_MPI/
+./bin/xdecompose_mesh_SCOTCH $NPROC MESH/ OUTPUT_FILES/DATABASES_MPI/
# stores setup
-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/
+cp DATA/Par_file OUTPUT_FILES/
+cp DATA/CMTSOLUTION OUTPUT_FILES/
+cp DATA/STATIONS OUTPUT_FILES/
# runs database generation
echo
@@ -72,7 +72,7 @@
cd ../
echo
-echo "see results in directory: in_out_files/OUTPUT_FILES/"
+echo "see results in directory: OUTPUT_FILES/"
echo
echo "done"
echo `date`
Modified: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/many_interfaces/Mesh_Par_file
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/many_interfaces/Mesh_Par_file 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/many_interfaces/Mesh_Par_file 2012-10-22 16:16:57 UTC (rev 20873)
@@ -35,7 +35,7 @@
CREATE_VTK_FILES = .false.
# path to store the databases files
-LOCAL_PATH = ../in_out_files/DATABASES_MPI
+LOCAL_PATH = ../OUTPUT_FILES/DATABASES_MPI
# number of materials
NMATERIALS = 4
Modified: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/many_interfaces/Par_file
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/many_interfaces/Par_file 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/many_interfaces/Par_file 2012-10-22 16:16:57 UTC (rev 20873)
@@ -2,9 +2,9 @@
#
# forward or adjoint simulation
# 1 = forward, 2 = adjoint, 3 = both simultaneously
-SIMULATION_TYPE = 1
+SIMULATION_TYPE = 1
# 0 = earthquake simulation, 1/2/3 = three steps in noise simulation
-NOISE_TOMOGRAPHY = 0
+NOISE_TOMOGRAPHY = 0
SAVE_FORWARD = .false.
# UTM projection parameters
@@ -21,9 +21,9 @@
# models:
# available options are:
# default (model parameters described by mesh properties)
-# 1D models available are:
+# 1D models available are:
# 1d_prem,1d_socal,1d_cascadia
-# 3D models available are:
+# 3D models available are:
# aniso,external,gll,salton_trough,tomo
MODEL = default
@@ -54,7 +54,7 @@
SAVE_MESH_FILES = .true.
# path to store the local database file on each node
-LOCAL_PATH = ../in_out_files/DATABASES_MPI
+LOCAL_PATH = ../OUTPUT_FILES/DATABASES_MPI
# interval at which we output time step info and max of norm of displacement
NTSTEP_BETWEEN_OUTPUT_INFO = 500
@@ -78,13 +78,13 @@
# The direction vector is made unitary internally in the code and thus only its direction matters here;
# its norm is ignored and the norm of the force used is the factor force source times the source time function.
-# set to use a Ricker source time function instead of a gaussian (when using CMTSOLUTION files)
-# or a quasi-Heaviside (when using FORCESOLUTION files)
+# set to use a Ricker source time function instead of a gaussian (when using CMTSOLUTION files)
+# or a quasi-Heaviside (when using FORCESOLUTION files)
USE_RICKER_TIME_FUNCTION = .false.
# print source time function
PRINT_SOURCE_TIME_FUNCTION = .false.
-# set to true to use GPUs
+# set to true to use GPUs
GPU_MODE = .false.
Modified: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/many_interfaces/README
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/many_interfaces/README 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/many_interfaces/README 2012-10-22 16:16:57 UTC (rev 20873)
@@ -36,10 +36,10 @@
> qsub go_mesher_pbs.bash
- - this should generate "proc000***_Database" files in in_out_files/DATABASES_MPI/.
+ - this should generate "proc000***_Database" files in OUTPUT_FILES/DATABASES_MPI/.
- save output file
- > cp in_out_files/OUTPUT_FILES/output_mesher.txt in_out_files/OUTPUT_FILES/output_meshfem3D.txt
+ > cp OUTPUT_FILES/output_mesher.txt OUTPUT_FILES/output_meshfem3D.txt
3. generate databases:
@@ -50,7 +50,7 @@
> qsub go_generate_databases_pbs.bash
this job will take about XX minutes and will create binary mesh files,
- e.g. "proc000***_external_mesh.bin", in directory in_out_files/DATABASES_MPI/.
+ e.g. "proc000***_external_mesh.bin", in directory OUTPUT_FILES/DATABASES_MPI/.
Optional: If you have paraview, load the .vtk files (see simple_model.png).
@@ -64,7 +64,7 @@
- the job should take about 70 minutes
- when the job is complete, you should have 3 sets (semd,semv,sema)
- of XX (ls -1 *semd | wc) seismogram files in the directory in_out_files/OUTPUT_FILES,
+ of XX (ls -1 *semd | wc) seismogram files in the directory OUTPUT_FILES,
as well as XX timestamp****** files
- view seismograms, for example, using xmgrace:
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 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/many_interfaces/go_process_pbs.bash 2012-10-22 16:16:57 UTC (rev 20873)
@@ -8,7 +8,7 @@
## job name and output file
#PBS -N go_process
#PBS -j oe
-#PBS -o in_out_files/OUTPUT_FILES/$PBS_JOBID.o
+#PBS -o OUTPUT_FILES/$PBS_JOBID.o
## PBS -q test
###########################################################
@@ -36,11 +36,11 @@
# setup
mkdir -p bin
-mkdir -p in_out_files/OUTPUT_FILES
-mkdir -p in_out_files/DATABASES_MPI
+mkdir -p OUTPUT_FILES
+mkdir -p OUTPUT_FILES/DATABASES_MPI
-rm -rf in_out_files/OUTPUT_FILES/*
-rm -rf in_out_files/DATABASES_MPI/*
+rm -rf OUTPUT_FILES/*
+rm -rf OUTPUT_FILES/DATABASES_MPI/*
mkdir -p DATA
mkdir -p DATA/meshfem3D_files/
@@ -75,12 +75,12 @@
cd bin/
mpiexec -np $numnodes ./xmeshfem3D
cd ../
-mv in_out_files/OUTPUT_FILES/output_mesher.txt in_out_files/OUTPUT_FILES/output_meshfem3D.txt
+mv OUTPUT_FILES/output_mesher.txt OUTPUT_FILES/output_meshfem3D.txt
# stores setup
-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/
+cp DATA/Par_file OUTPUT_FILES/
+cp DATA/CMTSOLUTION OUTPUT_FILES/
+cp DATA/STATIONS OUTPUT_FILES/
# runs database generation
echo
@@ -99,7 +99,7 @@
cd ../
echo
-echo "see results in directory: in_out_files/OUTPUT_FILES/"
+echo "see results in directory: OUTPUT_FILES/"
echo
echo "done"
echo `date`
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 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/many_interfaces/process.sh 2012-10-22 16:16:57 UTC (rev 20873)
@@ -24,11 +24,11 @@
echo
mkdir -p bin
-mkdir -p in_out_files/OUTPUT_FILES
-mkdir -p in_out_files/DATABASES_MPI
+mkdir -p OUTPUT_FILES
+mkdir -p OUTPUT_FILES/DATABASES_MPI
-rm -rf in_out_files/OUTPUT_FILES/*
-rm -rf in_out_files/DATABASES_MPI/*
+rm -rf OUTPUT_FILES/*
+rm -rf OUTPUT_FILES/DATABASES_MPI/*
mkdir -p DATA
mkdir -p DATA/meshfem3D_files/
@@ -60,12 +60,12 @@
cd bin/
mpirun -np $NPROC ./xmeshfem3D
cd ../
-mv in_out_files/OUTPUT_FILES/output_mesher.txt in_out_files/OUTPUT_FILES/output_meshfem3D.txt
+mv OUTPUT_FILES/output_mesher.txt OUTPUT_FILES/output_meshfem3D.txt
# stores setup
-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/
+cp DATA/Par_file OUTPUT_FILES/
+cp DATA/CMTSOLUTION OUTPUT_FILES/
+cp DATA/STATIONS OUTPUT_FILES/
# runs database generation
echo
@@ -84,7 +84,7 @@
cd ../
echo
-echo "see results in directory: in_out_files/OUTPUT_FILES/"
+echo "see results in directory: OUTPUT_FILES/"
echo
echo "done"
echo `date`
Modified: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/simple_model/README
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/simple_model/README 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/simple_model/README 2012-10-22 16:16:57 UTC (rev 20873)
@@ -32,7 +32,7 @@
> qsub go_mesher_pbs.bash
- This should generate these files in in_out_files/DATABASES_MPI/:
+ This should generate these files in OUTPUT_FILES/DATABASES_MPI/:
proc000000_Database
proc000000_.dx
@@ -48,7 +48,7 @@
proc000003_.INP
- save output file
- > cp in_out_files/OUTPUT_FILES/output_mesher.txt in_out_files/OUTPUT_FILES/output_meshfem3D.txt
+ > cp OUTPUT_FILES/output_mesher.txt OUTPUT_FILES/output_meshfem3D.txt
3. generate databases:
@@ -59,7 +59,7 @@
> qsub go_generate_databases_pbs.bash
this will create binary mesh files, e.g. "proc000***_external_mesh.bin"
- in directory in_out_files/DATABASES_MPI/.
+ in directory OUTPUT_FILES/DATABASES_MPI/.
Optional: If you have paraview, load the .vtk files (see simple_model.png).
@@ -73,7 +73,7 @@
- the job should take about 10 minutes
- when the job is complete, you should have 3 sets (semd,semv,sema)
- of 27 (ls -1 *semd | wc) seismogram files in the directory in_out_files/OUTPUT_FILES,
+ of 27 (ls -1 *semd | wc) seismogram files in the directory OUTPUT_FILES,
as well as 5 timestamp****** files
- view seismograms, for example, using xmgrace:
Modified: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/simple_model/in_data_files/Par_file
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/simple_model/in_data_files/Par_file 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/simple_model/in_data_files/Par_file 2012-10-22 16:16:57 UTC (rev 20873)
@@ -2,9 +2,9 @@
#
# forward or adjoint simulation
# 1 = forward, 2 = adjoint, 3 = both simultaneously
-SIMULATION_TYPE = 1
+SIMULATION_TYPE = 1
# 0 = earthquake simulation, 1/2/3 = three steps in noise simulation
-NOISE_TOMOGRAPHY = 0
+NOISE_TOMOGRAPHY = 0
SAVE_FORWARD = .false.
# UTM projection parameters
@@ -21,9 +21,9 @@
# models:
# available options are:
# default (model parameters described by mesh properties)
-# 1D models available are:
+# 1D models available are:
# 1d_prem,1d_socal,1d_cascadia
-# 3D models available are:
+# 3D models available are:
# aniso,external,gll,salton_trough,tomo
MODEL = default
@@ -54,7 +54,7 @@
SAVE_MESH_FILES = .true.
# path to store the local database file on each node
-LOCAL_PATH = ../in_out_files/DATABASES_MPI
+LOCAL_PATH = ../OUTPUT_FILES/DATABASES_MPI
# interval at which we output time step info and max of norm of displacement
NTSTEP_BETWEEN_OUTPUT_INFO = 100
@@ -78,13 +78,13 @@
# The direction vector is made unitary internally in the code and thus only its direction matters here;
# its norm is ignored and the norm of the force used is the factor force source times the source time function.
-# set to use a Ricker source time function instead of a gaussian (when using CMTSOLUTION files)
-# or a quasi-Heaviside (when using FORCESOLUTION files)
+# set to use a Ricker source time function instead of a gaussian (when using CMTSOLUTION files)
+# or a quasi-Heaviside (when using FORCESOLUTION files)
USE_RICKER_TIME_FUNCTION = .false.
# print source time function
PRINT_SOURCE_TIME_FUNCTION = .false.
-# set to true to use GPUs
+# set to true to use GPUs
GPU_MODE = .false.
Modified: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/simple_model/in_data_files/meshfem3D_files/Mesh_Par_file
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/simple_model/in_data_files/meshfem3D_files/Mesh_Par_file 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/simple_model/in_data_files/meshfem3D_files/Mesh_Par_file 2012-10-22 16:16:57 UTC (rev 20873)
@@ -35,7 +35,7 @@
CREATE_VTK_FILES = .false.
# path to store the databases files
-LOCAL_PATH = ../in_out_files/DATABASES_MPI
+LOCAL_PATH = ../OUTPUT_FILES/DATABASES_MPI
# number of materials
NMATERIALS = 4
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 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/simple_model/process.sh 2012-10-22 16:16:57 UTC (rev 20873)
@@ -24,11 +24,11 @@
echo
mkdir -p bin
-mkdir -p in_out_files/OUTPUT_FILES
-mkdir -p in_out_files/DATABASES_MPI
+mkdir -p OUTPUT_FILES
+mkdir -p OUTPUT_FILES/DATABASES_MPI
-rm -rf in_out_files/OUTPUT_FILES/*
-rm -rf in_out_files/DATABASES_MPI/*
+rm -rf OUTPUT_FILES/*
+rm -rf OUTPUT_FILES/DATABASES_MPI/*
# compiles executables in root directory
@@ -42,9 +42,9 @@
if [ ! -e bin/xspecfem3D ]; then echo "compilation failed, please check..."; exit 1; fi
# stores setup
-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/
+cp DATA/Par_file OUTPUT_FILES/
+cp DATA/CMTSOLUTION OUTPUT_FILES/
+cp DATA/STATIONS OUTPUT_FILES/
# creates and decomposes mesh
echo
@@ -53,7 +53,7 @@
cd bin/
mpirun -np $NPROC ./xmeshfem3D
cd ../
-mv in_out_files/OUTPUT_FILES/output_mesher.txt in_out_files/OUTPUT_FILES/output_meshfem3D.txt
+mv OUTPUT_FILES/output_mesher.txt OUTPUT_FILES/output_meshfem3D.txt
# runs database generation
echo
@@ -72,7 +72,7 @@
cd ../
echo
-echo "see results in directory: in_out_files/OUTPUT_FILES/"
+echo "see results in directory: OUTPUT_FILES/"
echo
echo "done"
echo `date`
Modified: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/README
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/README 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/README 2012-10-22 16:16:57 UTC (rev 20873)
@@ -41,14 +41,14 @@
> make xmeshfem3D
> qsub go_mesher_pbs.bash
- this should generate these files in in_out_files/DATABASES_MPI/:
+ this should generate these files in OUTPUT_FILES/DATABASES_MPI/:
proc000000_Database
proc000000_.dx
proc000000_.INP
- save output file:
- > cp in_out_files/OUTPUT_FILES/output_mesher.txt in_out_files/OUTPUT_FILES/output_meshfem3D.txt
+ > cp OUTPUT_FILES/output_mesher.txt OUTPUT_FILES/output_meshfem3D.txt
3. generate databases:
@@ -57,7 +57,7 @@
> qsub go_generate_databases_pbs.bash
this will create binary mesh files, e.g. "proc000***_external_mesh.bin"
- in directory in_out_files/DATABASES_MPI/.
+ in directory OUTPUT_FILES/DATABASES_MPI/.
optional: If you have paraview, load the .vtk files (see socal1D_sesame.png).
@@ -69,7 +69,7 @@
- the job should take about 2 minutes
- when the job is complete, you should have 3 sets (semd,semv,sema)
- of 84 (ls -1 *semd | wc) seismogram files in the directory in_out_files/OUTPUT_FILES,
+ of 84 (ls -1 *semd | wc) seismogram files in the directory OUTPUT_FILES,
as well as 9 timestamp****** files
- view seismograms, for example, using xmgrace:
Modified: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/example_deep/Mesh_Par_file_deep
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/example_deep/Mesh_Par_file_deep 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/example_deep/Mesh_Par_file_deep 2012-10-22 16:16:57 UTC (rev 20873)
@@ -35,7 +35,7 @@
CREATE_VTK_FILES = .false.
# path to store the databases files
-LOCAL_PATH = ../in_out_files/DATABASES_MPI
+LOCAL_PATH = ../OUTPUT_FILES/DATABASES_MPI
# number of materials
NMATERIALS = 4
@@ -55,4 +55,4 @@
1 24 1 24 1 17 1
1 24 1 24 18 20 2
1 24 1 24 21 23 3
-1 24 1 24 24 26 4
\ No newline at end of file
+1 24 1 24 24 26
Modified: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/example_deep/Mesh_Par_file_deep_honor60km
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/example_deep/Mesh_Par_file_deep_honor60km 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/example_deep/Mesh_Par_file_deep_honor60km 2012-10-22 16:16:57 UTC (rev 20873)
@@ -35,7 +35,7 @@
CREATE_VTK_FILES = .false.
# path to store the databases files
-LOCAL_PATH = ../in_out_files/DATABASES_MPI
+LOCAL_PATH = ../OUTPUT_FILES/DATABASES_MPI
# number of materials
NMATERIALS = 4
@@ -56,4 +56,4 @@
1 24 1 24 15 17 1
1 24 1 24 18 20 2
1 24 1 24 21 23 3
-1 24 1 24 24 26 4
\ No newline at end of file
+1 24 1 24 24 26
Modified: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/example_utm/Mesh_Par_file_utm
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/example_utm/Mesh_Par_file_utm 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/example_utm/Mesh_Par_file_utm 2012-10-22 16:16:57 UTC (rev 20873)
@@ -35,7 +35,7 @@
CREATE_VTK_FILES = .false.
# path to store the databases files
-LOCAL_PATH = ../in_out_files/DATABASES_MPI
+LOCAL_PATH = ../OUTPUT_FILES/DATABASES_MPI
# number of materials
NMATERIALS = 4
Modified: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/example_utm/Par_file_utm
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/example_utm/Par_file_utm 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/example_utm/Par_file_utm 2012-10-22 16:16:57 UTC (rev 20873)
@@ -2,9 +2,9 @@
#
# forward or adjoint simulation
# 1 = forward, 2 = adjoint, 3 = both simultaneously
-SIMULATION_TYPE = 1
+SIMULATION_TYPE = 1
# 0 = earthquake simulation, 1/2/3 = three steps in noise simulation
-NOISE_TOMOGRAPHY = 0
+NOISE_TOMOGRAPHY = 0
SAVE_FORWARD = .false.
# UTM projection parameters
@@ -21,9 +21,9 @@
# models:
# available options are:
# default (model parameters described by mesh properties)
-# 1D models available are:
+# 1D models available are:
# 1d_prem,1d_socal,1d_cascadia
-# 3D models available are:
+# 3D models available are:
# aniso,external,gll,salton_trough,tomo
MODEL = default
@@ -51,7 +51,7 @@
SAVE_MESH_FILES = .true.
# path to store the local database file on each node
-LOCAL_PATH = ../in_out_files/DATABASES_MPI
+LOCAL_PATH = ../OUTPUT_FILES/DATABASES_MPI
# interval at which we output time step info and max of norm of displacement
NTSTEP_BETWEEN_OUTPUT_INFO = 100
@@ -65,6 +65,6 @@
# print source time function
PRINT_SOURCE_TIME_FUNCTION = .true.
-# set to true to use GPUs
+# set to true to use GPUs
GPU_MODE = .false.
Modified: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/in_data_files/Par_file
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/in_data_files/Par_file 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/in_data_files/Par_file 2012-10-22 16:16:57 UTC (rev 20873)
@@ -2,9 +2,9 @@
#
# forward or adjoint simulation
# 1 = forward, 2 = adjoint, 3 = both simultaneously
-SIMULATION_TYPE = 1
+SIMULATION_TYPE = 1
# 0 = earthquake simulation, 1/2/3 = three steps in noise simulation
-NOISE_TOMOGRAPHY = 0
+NOISE_TOMOGRAPHY = 0
SAVE_FORWARD = .false.
# UTM projection parameters
@@ -21,9 +21,9 @@
# models:
# available options are:
# default (model parameters described by mesh properties)
-# 1D models available are:
+# 1D models available are:
# 1d_prem,1d_socal,1d_cascadia
-# 3D models available are:
+# 3D models available are:
# aniso,external,gll,salton_trough,tomo
MODEL = default
@@ -54,7 +54,7 @@
SAVE_MESH_FILES = .true.
# path to store the local database file on each node
-LOCAL_PATH = ../in_out_files/DATABASES_MPI
+LOCAL_PATH = ../OUTPUT_FILES/DATABASES_MPI
# interval at which we output time step info and max of norm of displacement
NTSTEP_BETWEEN_OUTPUT_INFO = 100
@@ -78,13 +78,13 @@
# The direction vector is made unitary internally in the code and thus only its direction matters here;
# its norm is ignored and the norm of the force used is the factor force source times the source time function.
-# set to use a Ricker source time function instead of a gaussian (when using CMTSOLUTION files)
-# or a quasi-Heaviside (when using FORCESOLUTION files)
+# set to use a Ricker source time function instead of a gaussian (when using CMTSOLUTION files)
+# or a quasi-Heaviside (when using FORCESOLUTION files)
USE_RICKER_TIME_FUNCTION = .false.
# print source time function
PRINT_SOURCE_TIME_FUNCTION = .true.
-# set to true to use GPUs
+# set to true to use GPUs
GPU_MODE = .false.
Modified: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/in_data_files/meshfem3D_files/Mesh_Par_file
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/in_data_files/meshfem3D_files/Mesh_Par_file 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/in_data_files/meshfem3D_files/Mesh_Par_file 2012-10-22 16:16:57 UTC (rev 20873)
@@ -35,7 +35,7 @@
CREATE_VTK_FILES = .false.
# path to store the databases files
-LOCAL_PATH = ../in_out_files/DATABASES_MPI
+LOCAL_PATH = ../OUTPUT_FILES/DATABASES_MPI
# number of materials
NMATERIALS = 4
Modified: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/in_data_files/meshfem3D_files/Mesh_Par_file_001
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/in_data_files/meshfem3D_files/Mesh_Par_file_001 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/in_data_files/meshfem3D_files/Mesh_Par_file_001 2012-10-22 16:16:57 UTC (rev 20873)
@@ -35,7 +35,7 @@
CREATE_VTK_FILES = .false.
# path to store the databases files
-LOCAL_PATH = ../in_out_files/DATABASES_MPI
+LOCAL_PATH = ../OUTPUT_FILES/DATABASES_MPI
# number of materials
NMATERIALS = 4
Modified: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/in_data_files/meshfem3D_files/Mesh_Par_file_042
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/in_data_files/meshfem3D_files/Mesh_Par_file_042 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/in_data_files/meshfem3D_files/Mesh_Par_file_042 2012-10-22 16:16:57 UTC (rev 20873)
@@ -35,7 +35,7 @@
CREATE_VTK_FILES = .false.
# path to store the databases files
-LOCAL_PATH = ../in_out_files/DATABASES_MPI
+LOCAL_PATH = ../OUTPUT_FILES/DATABASES_MPI
# number of materials
NMATERIALS = 4
Modified: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/in_data_files/meshfem3D_files/Mesh_Par_file_168
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/in_data_files/meshfem3D_files/Mesh_Par_file_168 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/in_data_files/meshfem3D_files/Mesh_Par_file_168 2012-10-22 16:16:57 UTC (rev 20873)
@@ -35,7 +35,7 @@
CREATE_VTK_FILES = .false.
# path to store the databases files
-LOCAL_PATH = ../in_out_files/DATABASES_MPI
+LOCAL_PATH = ../OUTPUT_FILES/DATABASES_MPI
# number of materials
NMATERIALS = 4
Modified: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/process.sh
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/process.sh 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/process.sh 2012-10-22 16:16:57 UTC (rev 20873)
@@ -24,11 +24,11 @@
echo
mkdir -p bin
-mkdir -p in_out_files/OUTPUT_FILES
-mkdir -p in_out_files/DATABASES_MPI
+mkdir -p OUTPUT_FILES
+mkdir -p OUTPUT_FILES/DATABASES_MPI
-rm -rf in_out_files/OUTPUT_FILES/*
-rm -rf in_out_files/DATABASES_MPI/*
+rm -rf OUTPUT_FILES/*
+rm -rf OUTPUT_FILES/DATABASES_MPI/*
mkdir -p DATA
mkdir -p DATA/meshfem3D_files/
@@ -45,10 +45,10 @@
if [ ! -e bin/xspecfem3D ]; then echo "compilation failed, please check..."; exit 1; fi
# stores setup
-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/
+cp DATA/meshfem3D_files/Mesh_Par_file OUTPUT_FILES/
+cp DATA/Par_file OUTPUT_FILES/
+cp DATA/CMTSOLUTION OUTPUT_FILES/
+cp DATA/STATIONS OUTPUT_FILES/
# decomposes mesh
echo
@@ -57,7 +57,7 @@
cd bin/
mpirun -np $NPROC ./xmeshfem3D
cd ../
-mv in_out_files/OUTPUT_FILES/output_mesher.txt in_out_files/OUTPUT_FILES/output_meshfem3D.txt
+mv OUTPUT_FILES/output_mesher.txt OUTPUT_FILES/output_meshfem3D.txt
# runs database generation
@@ -80,15 +80,15 @@
cd ../
echo
-echo "see results in directory: in_out_files/OUTPUT_FILES/"
+echo "see results in directory: OUTPUT_FILES/"
echo
echo "done"
echo `date`
# To make a full mesh using combine_vol_data:
# cd bin
-# xcombine_vol_data 0 0 vs ../in_out_files/DATABASES_MPI/ ../in_out_files/DATABASES_MPI/ 1
-# cd ../in_out_files/DATABASES_MPI/
+# xcombine_vol_data 0 0 vs ../OUTPUT_FILES/DATABASES_MPI/ ../OUTPUT_FILES/DATABASES_MPI/ 1
+# cd ../OUTPUT_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 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/NOISE_TOMOGRAPHY.m 2012-10-22 16:16:57 UTC (rev 20873)
@@ -39,7 +39,7 @@
% the source time function has been saved in:
% /data2/yangl/3D_NOISE/S_squared
% S_squared should be put into directory:
-% in_out_files/NOISE_TOMOGRAPHY/ in the SPECFEM3D package
+% OUTPUT_FILES/NOISE_TOMOGRAPHY/ in the SPECFEM3D package
clf;
@@ -159,5 +159,5 @@
fprintf('the source time function has been saved in:\n');
fprintf([DIR '/S_squared\n']);
fprintf('S_squared should be put into directory:\n');
-fprintf('in_out_files/NOISE_TOMOGRAPHY/ in the SPECFEM3D package\n');
+fprintf('OUTPUT_FILES/NOISE_TOMOGRAPHY/ in the SPECFEM3D package\n');
fprintf('*************************************************************\n');
Modified: seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/README
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/README 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/README 2012-10-22 16:16:57 UTC (rev 20873)
@@ -80,6 +80,6 @@
4. Results
**************
- At the end of those simulations, kernel files will be saved in SPECFEM3D/in_out_files/NOISE_TOMOGRAPHY/1st/ & SPECFEM3D/in_out_files/NOISE_TOMOGRAPHY/2nd/
- If mesh2vtu.pl works, you will have 1st_beta_kernel.vtu & 2nd_beta_kernel.vtu in SPECFEM3D/in_out_files/NOISE_TOMOGRAPHY/, which can be directly viewed in Paraview
+ At the end of those simulations, kernel files will be saved in SPECFEM3D/OUTPUT_FILES/NOISE_TOMOGRAPHY/1st/ & SPECFEM3D/OUTPUT_FILES/NOISE_TOMOGRAPHY/2nd/
+ If mesh2vtu.pl works, you will have 1st_beta_kernel.vtu & 2nd_beta_kernel.vtu in SPECFEM3D/OUTPUT_FILES/NOISE_TOMOGRAPHY/, which can be directly viewed in Paraview
Once you visualize them in Paraview, you should see pictures similar to those in SPECFEM3D/examples/noise_tomography/REF_KERNELS/
Modified: seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/bin/adj_traveltime_filter.f90
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/bin/adj_traveltime_filter.f90 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/bin/adj_traveltime_filter.f90 2012-10-22 16:16:57 UTC (rev 20873)
@@ -45,7 +45,7 @@
nfreq=size(freq_low)
-file_misfit = '../in_out_files/SEM/misfit_traveltime_delay'
+file_misfit = '../OUTPUT_FILES/SEM/misfit_traveltime_delay'
open(unit=1111,file=trim(file_misfit),status='unknown')
DELT=dt*1.0d3
@@ -53,7 +53,7 @@
misfit_traveltime = 0.0d0
!!!! loading data and synthetics !!!!
do irec = 1,nrec
- file_data = '../in_out_files/SEM/X2.DB.BXZ.semd'
+ file_data = '../OUTPUT_FILES/SEM/X2.DB.BXZ.semd'
open(unit=1001,file=trim(file_data),status='old',action='read')
do itime = 1,nstep
read(1001,*) t(itime),data_origin(nstep-itime+1,irec) ! the reversed seismogram involves $C^\alpha\beta(t)=C^\beta\alpha(-t)$
@@ -150,13 +150,13 @@
end do !do ifreq=1,nfreq
!!!! output !!!!
- file_adj_BXZ = '../in_out_files/SEM/adj_sources_contribution1'
+ file_adj_BXZ = '../OUTPUT_FILES/SEM/adj_sources_contribution1'
open(unit=1002,file=trim(file_adj_BXZ),status='unknown')
do itime = 1,nstep
write(1002,*) t(itime), adj(nstep-itime+1,irec)
end do
close(1002)
- file_adj_zeros = '../in_out_files/SEM/adj_sources_contribution2'
+ file_adj_zeros = '../OUTPUT_FILES/SEM/adj_sources_contribution2'
open(unit=1002,file=trim(file_adj_zeros),status='unknown')
do itime = 1,nstep
write(1002,*) t(itime), adj(itime,irec)
@@ -168,7 +168,7 @@
close(1111)
-file_misfit = '../in_out_files/SEM/misfit_traveltime'
+file_misfit = '../OUTPUT_FILES/SEM/misfit_traveltime'
open(unit=1001,file=trim(file_misfit),status='unknown')
write(1001,*) misfit_traveltime, traveltime_delay
close(1001)
Modified: seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/in_data_files/Par_file_step1
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/in_data_files/Par_file_step1 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/in_data_files/Par_file_step1 2012-10-22 16:16:57 UTC (rev 20873)
@@ -2,7 +2,7 @@
#
# forward or adjoint simulation
# 1 = forward, 2 = adjoint, 3 = both simultaneously
-SIMULATION_TYPE = 1
+SIMULATION_TYPE = 1
# 0 = earthquake simulation, 1/2/3 = three steps in noise simulation
NOISE_TOMOGRAPHY = 1
SAVE_FORWARD = .true.
@@ -22,9 +22,9 @@
# models:
# available options are:
# default (model parameters described by mesh properties)
-# 1D models available are:
+# 1D models available are:
# 1d_prem,1d_socal,1d_cascadia
-# 3D models available are:
+# 3D models available are:
# aniso,external,gll,salton_trough,tomo
MODEL = default
@@ -52,7 +52,7 @@
SAVE_MESH_FILES = .false.
# path to store the local database file on each node
-LOCAL_PATH = ../in_out_files/DATABASES_MPI
+LOCAL_PATH = ../OUTPUT_FILES/DATABASES_MPI
# interval at which we output time step info and max of norm of displacement
NTSTEP_BETWEEN_OUTPUT_INFO = 1000
@@ -63,6 +63,6 @@
# print source time function
PRINT_SOURCE_TIME_FUNCTION = .true.
-# set to true to use GPUs
+# set to true to use GPUs
GPU_MODE = .false.
Modified: seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/in_data_files/Par_file_step2
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/in_data_files/Par_file_step2 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/in_data_files/Par_file_step2 2012-10-22 16:16:57 UTC (rev 20873)
@@ -2,7 +2,7 @@
#
# forward or adjoint simulation
# 1 = forward, 2 = adjoint, 3 = both simultaneously
-SIMULATION_TYPE = 1
+SIMULATION_TYPE = 1
# 0 = earthquake simulation, 1/2/3 = three steps in noise simulation
NOISE_TOMOGRAPHY = 2
SAVE_FORWARD = .true.
@@ -22,9 +22,9 @@
# models:
# available options are:
# default (model parameters described by mesh properties)
-# 1D models available are:
+# 1D models available are:
# 1d_prem,1d_socal,1d_cascadia
-# 3D models available are:
+# 3D models available are:
# aniso,external,gll,salton_trough,tomo
MODEL = default
@@ -52,7 +52,7 @@
SAVE_MESH_FILES = .false.
# path to store the local database file on each node
-LOCAL_PATH = ../in_out_files/DATABASES_MPI
+LOCAL_PATH = ../OUTPUT_FILES/DATABASES_MPI
# interval at which we output time step info and max of norm of displacement
NTSTEP_BETWEEN_OUTPUT_INFO = 1000
@@ -63,6 +63,6 @@
# print source time function
PRINT_SOURCE_TIME_FUNCTION = .true.
-# set to true to use GPUs
+# set to true to use GPUs
GPU_MODE = .false.
Modified: seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/in_data_files/Par_file_step3
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/in_data_files/Par_file_step3 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/in_data_files/Par_file_step3 2012-10-22 16:16:57 UTC (rev 20873)
@@ -2,9 +2,9 @@
#
# forward or adjoint simulation
# 1 = forward, 2 = adjoint, 3 = both simultaneously
-SIMULATION_TYPE = 3
+SIMULATION_TYPE = 3
# 0 = earthquake simulation, 1/2/3 = three steps in noise simulation
-NOISE_TOMOGRAPHY = 3
+NOISE_TOMOGRAPHY = 3
SAVE_FORWARD = .false.
# UTM projection parameters
@@ -22,9 +22,9 @@
# models:
# available options are:
# default (model parameters described by mesh properties)
-# 1D models available are:
+# 1D models available are:
# 1d_prem,1d_socal,1d_cascadia
-# 3D models available are:
+# 3D models available are:
# aniso,external,gll,salton_trough,tomo
MODEL = default
@@ -52,7 +52,7 @@
SAVE_MESH_FILES = .false.
# path to store the local database file on each node
-LOCAL_PATH = ../in_out_files/DATABASES_MPI
+LOCAL_PATH = ../OUTPUT_FILES/DATABASES_MPI
# interval at which we output time step info and max of norm of displacement
NTSTEP_BETWEEN_OUTPUT_INFO = 1000
@@ -63,5 +63,5 @@
# print source time function
PRINT_SOURCE_TIME_FUNCTION = .true.
-# set to true to use GPUs
+# set to true to use GPUs
GPU_MODE = .false.
Modified: seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/pre-processing.sh
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/pre-processing.sh 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/pre-processing.sh 2012-10-22 16:16:57 UTC (rev 20873)
@@ -28,7 +28,7 @@
# specify directories for executables, input files and output files
# those values are default for SPECFEM3D
bin="$script_dir/bin"
-in_out_files="$script_dir/in_out_files"
+OUTPUT_FILES="$script_dir/OUTPUT_FILES"
DATA="$script_dir/DATA"
# specify which kernel we want to visualize
@@ -38,23 +38,23 @@
# create directories for noise simulations and adjoint simulations
# they are also default in SPECFEM3D
-mkdir -p $in_out_files
-mkdir -p $in_out_files/SEM
-mkdir -p $in_out_files/NOISE_TOMOGRAPHY
-mkdir -p $in_out_files/DATABASES_MPI
-mkdir -p $in_out_files/OUTPUT_FILES
+mkdir -p $OUTPUT_FILES
+mkdir -p $OUTPUT_FILES/SEM
+mkdir -p $OUTPUT_FILES/NOISE_TOMOGRAPHY
+mkdir -p $OUTPUT_FILES/DATABASES_MPI
+mkdir -p $OUTPUT_FILES
# create directories for storing kernels (first contribution and second contribution)
-mkdir -p $in_out_files/NOISE_TOMOGRAPHY/1st
-mkdir -p $in_out_files/NOISE_TOMOGRAPHY/2nd
+mkdir -p $OUTPUT_FILES/NOISE_TOMOGRAPHY/1st
+mkdir -p $OUTPUT_FILES/NOISE_TOMOGRAPHY/2nd
# copy noise input files
-cp $script_dir/NOISE_TOMOGRAPHY/S_squared $in_out_files/NOISE_TOMOGRAPHY/
-cp $script_dir/NOISE_TOMOGRAPHY/irec_master_noise* $in_out_files/NOISE_TOMOGRAPHY/
-cp $script_dir/NOISE_TOMOGRAPHY/nu_master $in_out_files/NOISE_TOMOGRAPHY/
+cp $script_dir/NOISE_TOMOGRAPHY/S_squared $OUTPUT_FILES/NOISE_TOMOGRAPHY/
+cp $script_dir/NOISE_TOMOGRAPHY/irec_master_noise* $OUTPUT_FILES/NOISE_TOMOGRAPHY/
+cp $script_dir/NOISE_TOMOGRAPHY/nu_master $OUTPUT_FILES/NOISE_TOMOGRAPHY/
# copy model information
-cp $script_dir/DATABASES_MPI/proc* $in_out_files/DATABASES_MPI/
+cp $script_dir/DATABASES_MPI/proc* $OUTPUT_FILES/DATABASES_MPI/
# copy simulation parameter files
#cp $script_dir/DATA/Par_file* $DATA/
@@ -87,7 +87,7 @@
echo "1. contribution..."
echo
# the master receiver is receiver 1
-cp $in_out_files/NOISE_TOMOGRAPHY/irec_master_noise_contribution1 $in_out_files/NOISE_TOMOGRAPHY/irec_master_noise
+cp $OUTPUT_FILES/NOISE_TOMOGRAPHY/irec_master_noise_contribution1 $OUTPUT_FILES/NOISE_TOMOGRAPHY/irec_master_noise
# step 1 of noise simulation
cp $DATA/Par_file_step1 $DATA/Par_file
@@ -97,7 +97,7 @@
# step 2 of noise simulation
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/
+mv $OUTPUT_FILES/X2.DB.BXZ.semd $OUTPUT_FILES/SEM/
# calculating adjoint source
# note that "a.out" is compiled from "ifort adj_traveltime_filter.f90"
@@ -106,14 +106,14 @@
# since it's 1st contribution, we inject adjoint source 1 at receiver 2
# pay attention to "adj_sources_contribution1" & "X2.DB.BXZ.adj"
# we will be using "adj_sources_contribution2" & "X1.DB.BXZ.adj" for the 2nd contribution in next part
-rm -f $in_out_files/SEM/*.adj
-cp $in_out_files/SEM/adj_sources_contribution1 $in_out_files/SEM/X2.DB.BXZ.adj
-awk '{print $1,0.0}' $in_out_files/SEM/X2.DB.BXZ.adj > $in_out_files/SEM/X2.DB.BXX.adj
-awk '{print $1,0.0}' $in_out_files/SEM/X2.DB.BXZ.adj > $in_out_files/SEM/X2.DB.BXY.adj
+rm -f $OUTPUT_FILES/SEM/*.adj
+cp $OUTPUT_FILES/SEM/adj_sources_contribution1 $OUTPUT_FILES/SEM/X2.DB.BXZ.adj
+awk '{print $1,0.0}' $OUTPUT_FILES/SEM/X2.DB.BXZ.adj > $OUTPUT_FILES/SEM/X2.DB.BXX.adj
+awk '{print $1,0.0}' $OUTPUT_FILES/SEM/X2.DB.BXZ.adj > $OUTPUT_FILES/SEM/X2.DB.BXY.adj
-awk '{print $1,0.0}' $in_out_files/SEM/X2.DB.BXZ.adj > $in_out_files/SEM/X1.DB.BXX.adj
-awk '{print $1,0.0}' $in_out_files/SEM/X2.DB.BXZ.adj > $in_out_files/SEM/X1.DB.BXY.adj
-awk '{print $1,0.0}' $in_out_files/SEM/X2.DB.BXZ.adj > $in_out_files/SEM/X1.DB.BXZ.adj
+awk '{print $1,0.0}' $OUTPUT_FILES/SEM/X2.DB.BXZ.adj > $OUTPUT_FILES/SEM/X1.DB.BXX.adj
+awk '{print $1,0.0}' $OUTPUT_FILES/SEM/X2.DB.BXZ.adj > $OUTPUT_FILES/SEM/X1.DB.BXY.adj
+awk '{print $1,0.0}' $OUTPUT_FILES/SEM/X2.DB.BXZ.adj > $OUTPUT_FILES/SEM/X1.DB.BXZ.adj
# step 3 of noise simulation
@@ -121,19 +121,19 @@
mpirun -np 4 ./xspecfem3D
# store kernels
-cp $in_out_files/DATABASES_MPI/*kernel* $in_out_files/NOISE_TOMOGRAPHY/1st/
+cp $OUTPUT_FILES/DATABASES_MPI/*kernel* $OUTPUT_FILES/NOISE_TOMOGRAPHY/1st/
# visualization (refer to other examples, if you don't know the visualization process very well)
# note that "xcombine_vol_data" is compiled by "make combine_vol_data"
-# this program generates a file "$in_out_files/OUTPUT_FILES/$kernel.mesh"
-./xcombine_vol_data 0 3 $kernel $in_out_files/DATABASES_MPI/ $in_out_files/OUTPUT_FILES/ 1
+# this program generates a file "$OUTPUT_FILES/$kernel.mesh"
+./xcombine_vol_data 0 3 $kernel $OUTPUT_FILES/DATABASES_MPI/ $OUTPUT_FILES/ 1
# you may need to install "mesh2vtu" package first, before you can use "mesh2vtu.pl"
-# convert "$in_out_files/OUTPUT_FILES/$kernel.mesh" to "$in_out_files/NOISE_TOMOGRAPHY/1st_$kernel.vtu"
+# convert "$OUTPUT_FILES/$kernel.mesh" to "$OUTPUT_FILES/NOISE_TOMOGRAPHY/1st_$kernel.vtu"
# which can be loaded and visualized in Paraview
-mesh2vtu.pl -i $in_out_files/OUTPUT_FILES/$kernel.mesh -o $in_out_files/NOISE_TOMOGRAPHY/1st_$kernel.vtu
+mesh2vtu.pl -i $OUTPUT_FILES/$kernel.mesh -o $OUTPUT_FILES/NOISE_TOMOGRAPHY/1st_$kernel.vtu
# 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
+# $OUTPUT_FILES/NOISE_TOMOGRAPHY/1st_$kernel.vtu
echo
@@ -145,7 +145,7 @@
echo
# the master receiver is receiver 2
-cp $in_out_files/NOISE_TOMOGRAPHY/irec_master_noise_contribution2 $in_out_files/NOISE_TOMOGRAPHY/irec_master_noise
+cp $OUTPUT_FILES/NOISE_TOMOGRAPHY/irec_master_noise_contribution2 $OUTPUT_FILES/NOISE_TOMOGRAPHY/irec_master_noise
# step 1 of noise simulation
cp $DATA/Par_file_step1 $DATA/Par_file
@@ -159,14 +159,14 @@
# since it's 2nd contribution, we inject adjoint source 2 at receiver 1
# pay attention to "adj_sources_contribution2" & "X1.DB.BXZ.adj"
# we have been using "adj_sources_contribution1" & "X2.DB.BXZ.adj" for the 1st contribution in previous part
-rm -f $in_out_files/SEM/*.adj
-cp $in_out_files/SEM/adj_sources_contribution2 $in_out_files/SEM/X1.DB.BXZ.adj
-awk '{print $1,0.0}' $in_out_files/SEM/X1.DB.BXZ.adj > $in_out_files/SEM/X1.DB.BXX.adj
-awk '{print $1,0.0}' $in_out_files/SEM/X1.DB.BXZ.adj > $in_out_files/SEM/X1.DB.BXY.adj
+rm -f $OUTPUT_FILES/SEM/*.adj
+cp $OUTPUT_FILES/SEM/adj_sources_contribution2 $OUTPUT_FILES/SEM/X1.DB.BXZ.adj
+awk '{print $1,0.0}' $OUTPUT_FILES/SEM/X1.DB.BXZ.adj > $OUTPUT_FILES/SEM/X1.DB.BXX.adj
+awk '{print $1,0.0}' $OUTPUT_FILES/SEM/X1.DB.BXZ.adj > $OUTPUT_FILES/SEM/X1.DB.BXY.adj
-awk '{print $1,0.0}' $in_out_files/SEM/X1.DB.BXZ.adj > $in_out_files/SEM/X2.DB.BXX.adj
-awk '{print $1,0.0}' $in_out_files/SEM/X1.DB.BXZ.adj > $in_out_files/SEM/X2.DB.BXY.adj
-awk '{print $1,0.0}' $in_out_files/SEM/X1.DB.BXZ.adj > $in_out_files/SEM/X2.DB.BXZ.adj
+awk '{print $1,0.0}' $OUTPUT_FILES/SEM/X1.DB.BXZ.adj > $OUTPUT_FILES/SEM/X2.DB.BXX.adj
+awk '{print $1,0.0}' $OUTPUT_FILES/SEM/X1.DB.BXZ.adj > $OUTPUT_FILES/SEM/X2.DB.BXY.adj
+awk '{print $1,0.0}' $OUTPUT_FILES/SEM/X1.DB.BXZ.adj > $OUTPUT_FILES/SEM/X2.DB.BXZ.adj
# step 3 of noise simulation
@@ -174,18 +174,18 @@
mpirun -np 4 ./xspecfem3D
# store kernels
-cp $in_out_files/DATABASES_MPI/*kernel* $in_out_files/NOISE_TOMOGRAPHY/2nd/
+cp $OUTPUT_FILES/DATABASES_MPI/*kernel* $OUTPUT_FILES/NOISE_TOMOGRAPHY/2nd/
# visualization (refer to other examples, if you don't know the visualization process very well)
-# this program generates a file "$in_out_files/OUTPUT_FILES/$kernel.mesh"
-./xcombine_vol_data 0 3 $kernel $in_out_files/DATABASES_MPI/ $in_out_files/OUTPUT_FILES/ 1
+# this program generates a file "$OUTPUT_FILES/$kernel.mesh"
+./xcombine_vol_data 0 3 $kernel $OUTPUT_FILES/DATABASES_MPI/ $OUTPUT_FILES/ 1
# you may need to install "mesh2vtu" package first, before you can use "mesh2vtu.pl"
-# convert "$in_out_files/OUTPUT_FILES/$kernel.mesh" to "$in_out_files/NOISE_TOMOGRAPHY/1st_$kernel.vtu"
+# convert "$OUTPUT_FILES/$kernel.mesh" to "$OUTPUT_FILES/NOISE_TOMOGRAPHY/1st_$kernel.vtu"
# which can be loaded and visualized in Paraview
-mesh2vtu.pl -i $in_out_files/OUTPUT_FILES/$kernel.mesh -o $in_out_files/NOISE_TOMOGRAPHY/2nd_$kernel.vtu
+mesh2vtu.pl -i $OUTPUT_FILES/$kernel.mesh -o $OUTPUT_FILES/NOISE_TOMOGRAPHY/2nd_$kernel.vtu
# at the end of this part, we obtain the 2nd contribution of the noise sensitivity kernel, stored as:
-# $in_out_files/NOISE_TOMOGRAPHY/2nd_$kernel.vtu
+# $OUTPUT_FILES/NOISE_TOMOGRAPHY/2nd_$kernel.vtu
echo
echo `date`
Modified: seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/README
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/README 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/README 2012-10-22 16:16:57 UTC (rev 20873)
@@ -52,7 +52,7 @@
> qsub go_decomposer_pbs.bash
which creates mesh partitions "proc0000***_Database" in directory "DATABASES_MPI".
- you can then specify "../in_out_files/DATABASES_MPI" in "Par_file" for your "LOCAL_PATH"
+ you can then specify "../OUTPUT_FILES/DATABASES_MPI" in "Par_file" for your "LOCAL_PATH"
5. generate databases:
@@ -74,7 +74,7 @@
the simulation will take about 10 minutes
when the job is complete, you should have 3 sets (semd,semv,sema)
- of 18 (ls -1 *semd | wc) seismogram files in directory in_out_files/OUTPUT_FILES,
+ of 18 (ls -1 *semd | wc) seismogram files in directory OUTPUT_FILES,
as well as 9 timestamp****** files
===========================================================
Modified: seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/in_data_files/Par_file
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/in_data_files/Par_file 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/in_data_files/Par_file 2012-10-22 16:16:57 UTC (rev 20873)
@@ -2,9 +2,9 @@
#
# forward or adjoint simulation
# 1 = forward, 2 = adjoint, 3 = both simultaneously
-SIMULATION_TYPE = 1
+SIMULATION_TYPE = 1
# 0 = earthquake simulation, 1/2/3 = three steps in noise simulation
-NOISE_TOMOGRAPHY = 0
+NOISE_TOMOGRAPHY = 0
SAVE_FORWARD = .false.
# UTM projection parameters
@@ -21,9 +21,9 @@
# models:
# available options are:
# default (model parameters described by mesh properties)
-# 1D models available are:
+# 1D models available are:
# 1d_prem,1d_socal,1d_cascadia
-# 3D models available are:
+# 3D models available are:
# aniso,external,gll,salton_trough,tomo
MODEL = default
@@ -54,7 +54,7 @@
SAVE_MESH_FILES = .true.
# path to store the local database file on each node
-LOCAL_PATH = ../in_out_files/DATABASES_MPI
+LOCAL_PATH = ../OUTPUT_FILES/DATABASES_MPI
# interval at which we output time step info and max of norm of displacement
NTSTEP_BETWEEN_OUTPUT_INFO = 500
@@ -78,13 +78,13 @@
# The direction vector is made unitary internally in the code and thus only its direction matters here;
# its norm is ignored and the norm of the force used is the factor force source times the source time function.
-# set to use a Ricker source time function instead of a gaussian (when using CMTSOLUTION files)
-# or a quasi-Heaviside (when using FORCESOLUTION files)
+# set to use a Ricker source time function instead of a gaussian (when using CMTSOLUTION files)
+# or a quasi-Heaviside (when using FORCESOLUTION files)
USE_RICKER_TIME_FUNCTION = .false.
# print source time function
PRINT_SOURCE_TIME_FUNCTION = .false.
-# set to true to use GPUs
+# set to true to use GPUs
GPU_MODE = .false.
Modified: seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/process.sh
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/process.sh 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/process.sh 2012-10-22 16:16:57 UTC (rev 20873)
@@ -27,11 +27,11 @@
echo
mkdir -p bin
-mkdir -p in_out_files/OUTPUT_FILES
-mkdir -p in_out_files/DATABASES_MPI
+mkdir -p OUTPUT_FILES
+mkdir -p OUTPUT_FILES/DATABASES_MPI
-rm -rf in_out_files/OUTPUT_FILES/*
-rm -rf in_out_files/DATABASES_MPI/*
+rm -rf OUTPUT_FILES/*
+rm -rf OUTPUT_FILES/DATABASES_MPI/*
# sets up tomography model file
./create_tomography_model_file.sh
@@ -55,12 +55,12 @@
echo
echo " decomposing mesh..."
echo
-./bin/xdecompose_mesh_SCOTCH $NPROC MESH/ in_out_files/DATABASES_MPI/
+./bin/xdecompose_mesh_SCOTCH $NPROC MESH/ OUTPUT_FILES/DATABASES_MPI/
# stores setup
-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/
+cp DATA/Par_file OUTPUT_FILES/
+cp DATA/CMTSOLUTION OUTPUT_FILES/
+cp DATA/STATIONS OUTPUT_FILES/
# runs database generation
echo
@@ -79,7 +79,7 @@
cd ../
echo
-echo "see results in directory: in_out_files/OUTPUT_FILES/"
+echo "see results in directory: OUTPUT_FILES/"
echo
echo "done"
echo `date`
Modified: seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/README
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/README 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/README 2012-10-22 16:16:57 UTC (rev 20873)
@@ -39,7 +39,7 @@
> qsub go_decomposer_pbs.bash
which creates mesh partitions "proc0000***_Database" in directory "DATABASES_MPI".
- you can then specify "../in_out_files/DATABASES_MPI" in "Par_file" for your "LOCAL_PATH"
+ you can then specify "../OUTPUT_FILES/DATABASES_MPI" in "Par_file" for your "LOCAL_PATH"
4. generate databases:
@@ -51,7 +51,7 @@
> qsub go_generate_databases_pbs.bash
this will create binary mesh files, e.g. "proc000***_external_mesh.bin"
- in directory in_out_files/DATABASES_MPI/.
+ in directory OUTPUT_FILES/DATABASES_MPI/.
(note: if execution fails due to memory shortage - most likely fails when calling routine to
create regional mesh - then try to increase process memory stack size: ulimit -s 2000000 (2GB) )
@@ -65,6 +65,6 @@
> qsub go_solver_pbs.bash
note: simulation will take about 1 h 45 minutes and generate
- 3 sets (semd,semv,sema) of 9 seismogram files in in_out_files/OUTPUT_FILES,
+ 3 sets (semd,semv,sema) of 9 seismogram files in OUTPUT_FILES,
as well as 10 timestamp****** files
Modified: seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/in_data_files/Par_file
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/in_data_files/Par_file 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/in_data_files/Par_file 2012-10-22 16:16:57 UTC (rev 20873)
@@ -2,9 +2,9 @@
#
# forward or adjoint simulation
# 1 = forward, 2 = adjoint, 3 = both simultaneously
-SIMULATION_TYPE = 1
+SIMULATION_TYPE = 1
# 0 = earthquake simulation, 1/2/3 = three steps in noise simulation
-NOISE_TOMOGRAPHY = 0
+NOISE_TOMOGRAPHY = 0
SAVE_FORWARD = .false.
# UTM projection parameters
@@ -21,9 +21,9 @@
# models:
# available options are:
# default (model parameters described by mesh properties)
-# 1D models available are:
+# 1D models available are:
# 1d_prem,1d_socal,1d_cascadia
-# 3D models available are:
+# 3D models available are:
# aniso,external,gll,salton_trough,tomo
MODEL = default
@@ -54,7 +54,7 @@
SAVE_MESH_FILES = .true.
# path to store the local database file on each node
-LOCAL_PATH = ../in_out_files/DATABASES_MPI
+LOCAL_PATH = ../OUTPUT_FILES/DATABASES_MPI
# interval at which we output time step info and max of norm of displacement
NTSTEP_BETWEEN_OUTPUT_INFO = 500
@@ -78,13 +78,13 @@
# The direction vector is made unitary internally in the code and thus only its direction matters here;
# its norm is ignored and the norm of the force used is the factor force source times the source time function.
-# set to use a Ricker source time function instead of a gaussian (when using CMTSOLUTION files)
-# or a quasi-Heaviside (when using FORCESOLUTION files)
+# set to use a Ricker source time function instead of a gaussian (when using CMTSOLUTION files)
+# or a quasi-Heaviside (when using FORCESOLUTION files)
USE_RICKER_TIME_FUNCTION = .false.
# print source time function
PRINT_SOURCE_TIME_FUNCTION = .false.
-# set to true to use GPUs
+# set to true to use GPUs
GPU_MODE = .false.
Modified: seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/process.sh
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/process.sh 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/process.sh 2012-10-22 16:16:57 UTC (rev 20873)
@@ -27,11 +27,11 @@
echo
mkdir -p bin
-mkdir -p in_out_files/OUTPUT_FILES
-mkdir -p in_out_files/DATABASES_MPI
+mkdir -p OUTPUT_FILES
+mkdir -p OUTPUT_FILES/DATABASES_MPI
-rm -rf in_out_files/OUTPUT_FILES/*
-rm -rf in_out_files/DATABASES_MPI/*
+rm -rf OUTPUT_FILES/*
+rm -rf OUTPUT_FILES/DATABASES_MPI/*
# compiles executables in root directory
cd ../../
@@ -50,12 +50,12 @@
echo
echo " decomposing mesh..."
echo
-./bin/xdecompose_mesh_SCOTCH $NPROC MESH/ in_out_files/DATABASES_MPI/
+./bin/xdecompose_mesh_SCOTCH $NPROC MESH/ OUTPUT_FILES/DATABASES_MPI/
# stores setup
-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/
+cp DATA/Par_file OUTPUT_FILES/
+cp DATA/CMTSOLUTION OUTPUT_FILES/
+cp DATA/STATIONS OUTPUT_FILES/
# runs database generation
echo
@@ -74,7 +74,7 @@
cd ../
echo
-echo "see results in directory: in_out_files/OUTPUT_FILES/"
+echo "see results in directory: OUTPUT_FILES/"
echo
echo "done"
echo `date`
Modified: seismo/3D/SPECFEM3D/trunk/src/cuda/check_fields_cuda.cu
===================================================================
--- seismo/3D/SPECFEM3D/trunk/src/cuda/check_fields_cuda.cu 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/src/cuda/check_fields_cuda.cu 2012-10-22 16:16:57 UTC (rev 20873)
@@ -111,7 +111,7 @@
#else
myrank = 0;
#endif
- sprintf(filename,"../in_out_files/OUTPUT_FILES/error_message_%06d.txt",myrank);
+ sprintf(filename,"../OUTPUT_FILES/error_message_%06d.txt",myrank);
fp = fopen(filename,"a+");
if (fp != NULL){
fprintf(fp,"Error after %s: %s\n", kernel_name, cudaGetErrorString(err));
@@ -142,7 +142,7 @@
#else
myrank = 0;
#endif
- sprintf(filename,"../in_out_files/OUTPUT_FILES/error_message_%06d.txt",myrank);
+ sprintf(filename,"../OUTPUT_FILES/error_message_%06d.txt",myrank);
fp = fopen(filename,"a+");
if (fp != NULL){
fprintf(fp,"ERROR: %s\n",info);
@@ -175,7 +175,7 @@
#else
myrank = 0;
#endif
- sprintf(filename,"../in_out_files/OUTPUT_FILES/error_message_%06d.txt",myrank);
+ sprintf(filename,"../OUTPUT_FILES/error_message_%06d.txt",myrank);
fp = fopen(filename,"a+");
if (fp != NULL){
fprintf(fp,"\nCUDA error !!!!! <%s> !!!!! \nat CUDA call error code: # %d\n",cudaGetErrorString(err),num);
@@ -221,7 +221,7 @@
get_free_memory(&free_db,&used_db,&total_db);
- sprintf(filename,"../in_out_files/OUTPUT_FILES/gpu_device_mem_usage_proc_%06d.txt",myrank);
+ sprintf(filename,"../OUTPUT_FILES/gpu_device_mem_usage_proc_%06d.txt",myrank);
fp = fopen(filename,"a+");
if (fp != NULL){
fprintf(fp,"%d: @%s GPU memory usage: used = %f MB, free = %f MB, total = %f MB\n", myrank, info_str,
Modified: seismo/3D/SPECFEM3D/trunk/src/cuda/initialize_cuda.cu
===================================================================
--- seismo/3D/SPECFEM3D/trunk/src/cuda/initialize_cuda.cu 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/src/cuda/initialize_cuda.cu 2012-10-22 16:16:57 UTC (rev 20873)
@@ -129,7 +129,7 @@
// outputs device infos to file
char filename[BUFSIZ];
FILE* fp;
- sprintf(filename,"../in_out_files/OUTPUT_FILES/gpu_device_info_proc_%06d.txt",myrank);
+ sprintf(filename,"../OUTPUT_FILES/gpu_device_info_proc_%06d.txt",myrank);
fp = fopen(filename,"a+");
if (fp != NULL){
// display device properties
Modified: seismo/3D/SPECFEM3D/trunk/src/cuda/save_and_compare_cpu_vs_gpu.c
===================================================================
--- seismo/3D/SPECFEM3D/trunk/src/cuda/save_and_compare_cpu_vs_gpu.c 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/src/cuda/save_and_compare_cpu_vs_gpu.c 2012-10-22 16:16:57 UTC (rev 20873)
@@ -95,7 +95,7 @@
#else
procid = 0;
#endif
- sprintf(filename,"/scratch/eiger/rietmann/SPECFEM3D_AIGLE/in_out_files/DATABASES_MPI/proc%06d_surface_movie",procid);
+ sprintf(filename,"/scratch/eiger/rietmann/SPECFEM3D_AIGLE/OUTPUT_FILES/DATABASES_MPI/proc%06d_surface_movie",procid);
FILE* fp; int it;
printf("Opening %s for analysis\n",filename);
@@ -174,8 +174,8 @@
void compare_surface_files_(int* bytes_per_iteration, int* number_of_iterations) {
- char* cpu_file = "/scratch/eiger/rietmann/SPECFEM3D/in_out_files/DATABASES_MPI/cpu_proc000001_surface_movie";
- char* gpu_file = "/scratch/eiger/rietmann/SPECFEM3D/in_out_files/DATABASES_MPI/cpu_v2_proc000001_surface_movie";
+ char* cpu_file = "/scratch/eiger/rietmann/SPECFEM3D/OUTPUT_FILES/DATABASES_MPI/cpu_proc000001_surface_movie";
+ char* gpu_file = "/scratch/eiger/rietmann/SPECFEM3D/OUTPUT_FILES/DATABASES_MPI/cpu_v2_proc000001_surface_movie";
FILE* fp_cpu;
fp_cpu = fopen(cpu_file,"rb");
Modified: seismo/3D/SPECFEM3D/trunk/src/decompose_mesh_SCOTCH/README
===================================================================
--- seismo/3D/SPECFEM3D/trunk/src/decompose_mesh_SCOTCH/README 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/src/decompose_mesh_SCOTCH/README 2012-10-22 16:16:57 UTC (rev 20873)
@@ -35,7 +35,7 @@
for example, a call could look like:
- > ./xdecompose_mesh_SCOTCH 4 ../examples/homogeneous_halfspace/MESH/ ../in_out_files/DATABASES_MPI/
+ > ./xdecompose_mesh_SCOTCH 4 ../examples/homogeneous_halfspace/MESH/ ../OUTPUT_FILES/DATABASES_MPI/
Modified: seismo/3D/SPECFEM3D/trunk/src/generate_databases/Makefile.in
===================================================================
--- seismo/3D/SPECFEM3D/trunk/src/generate_databases/Makefile.in 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/src/generate_databases/Makefile.in 2012-10-22 16:16:57 UTC (rev 20873)
@@ -46,7 +46,7 @@
# L : libraries directory
L = ../../lib
# Output files directory
-OUTPUT=../../in_out_files/OUTPUT_FILES
+OUTPUT=../../OUTPUT_FILES
FCCOMPILE_CHECK =@FCENV@ ${FC} ${FCFLAGS} $(FLAGS_CHECK) -I${SHARED}
FCCOMPILE_NO_CHECK =@FCENV@ ${FC} ${FCFLAGS} $(FLAGS_NO_CHECK) -I${SHARED}
Modified: seismo/3D/SPECFEM3D/trunk/src/shared/constants.h.in
===================================================================
--- seismo/3D/SPECFEM3D/trunk/src/shared/constants.h.in 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/src/shared/constants.h.in 2012-10-22 16:16:57 UTC (rev 20873)
@@ -164,7 +164,7 @@
! paths for inputs and outputs 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/'
+ character(len=256), parameter :: OUTPUT_FILES_PATH = '../OUTPUT_FILES/'
! ---------------------------------------------------------------------------------------
@@ -184,7 +184,7 @@
! the scratch disk to save the state variables saved in the forward
! simulation, this can be a global scratch disk in case you run out of
! space on the local scratch disk, e.g. '/ibrixfs1/scratch/lqy/DATABASES_MPI_Q/'
- character(len=256), parameter :: LOCAL_PATH_Q = '../in_out_files/DATABASES_MPI'
+ character(len=256), parameter :: LOCAL_PATH_Q = '../OUTPUT_FILES/DATABASES_MPI'
!------------------------------------------------------
! nlegoff -- Variables that should be read/computed elsewhere.
Modified: seismo/3D/SPECFEM3D/trunk/src/shared/create_movie_shakemap_AVS_DX_GMT.f90
===================================================================
--- seismo/3D/SPECFEM3D/trunk/src/shared/create_movie_shakemap_AVS_DX_GMT.f90 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/src/shared/create_movie_shakemap_AVS_DX_GMT.f90 2012-10-22 16:16:57 UTC (rev 20873)
@@ -35,7 +35,7 @@
implicit none
include "constants.h"
- include "../../in_out_files/OUTPUT_FILES/surface_from_mesher.h"
+ include "../../OUTPUT_FILES/surface_from_mesher.h"
!-------------------------------------------------------------------------------------------------
! user parameters
Modified: seismo/3D/SPECFEM3D/trunk/src/specfem3D/Makefile.in
===================================================================
--- seismo/3D/SPECFEM3D/trunk/src/specfem3D/Makefile.in 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/src/specfem3D/Makefile.in 2012-10-22 16:16:57 UTC (rev 20873)
@@ -34,8 +34,8 @@
# default cuda libraries
# runtime library -lcudart needed, others are optional -lcuda -lcublas
- at COND_CUDA_TRUE@CUDA_LIBS = -lcudart
- at COND_CUDA_FALSE@CUDA_LIBS =
+ at COND_CUDA_TRUE@CUDA_LIBS = -lcudart
+ at COND_CUDA_FALSE@CUDA_LIBS =
CUDA_LIB_LOCATION = @CUDA_LIB@
CUDA_LINK = $(CUDA_LIB_LOCATION) $(CUDA_LIBS)
@@ -51,9 +51,9 @@
@COND_CUDA_FALSE at NVCCLINK = $(NVCC) $(NVCC_FLAGS)
# OpenMP
-# with configure: ./configure --with-openmp FLAGS_NO_CHECK="-openmp .." OPENMP_LIB=..
+# with configure: ./configure --with-openmp FLAGS_NO_CHECK="-openmp .." OPENMP_LIB=..
@COND_OPENMP_TRUE at OPENMP_LIBS = $(OPENMP_LIB)
- at COND_OPENMP_FALSE@OPENMP_LIBS =
+ at COND_OPENMP_FALSE@OPENMP_LIBS =
@COND_OPENMP_TRUE at COND_OPENMP_FFLAGS = -DOPENMP_MODE
@COND_OPENMP_FALSE at COND_OPENMP_FFLAGS =
@@ -77,7 +77,7 @@
# L : libraries directory
L = ../../lib
# Output files directory
-OUTPUT=../../in_out_files/OUTPUT_FILES
+OUTPUT=../../OUTPUT_FILES
FCCOMPILE_CHECK =@FCENV@ ${FC} ${FCFLAGS} $(FLAGS_CHECK) $(COND_OPENMP_FFLAGS) -I$(SHARED)
FCCOMPILE_NO_CHECK =@FCENV@ ${FC} ${FCFLAGS} $(FLAGS_NO_CHECK) $(COND_OPENMP_FFLAGS) -I$(SHARED)
@@ -318,7 +318,7 @@
${FCLINK} -o ${E}/xsmooth_vol_data $O/smooth_vol_data.o $O/read_parameter_file.shared.o $O/read_value_parameters.shared.o $O/get_value_parameters.shared.o $O/param_reader.cc.o $O/gll_library.shared.o $O/exit_mpi.shared.o $(COND_MPI_OBJECTS) $(MPILIBS)
xsum_kernels: $(SUM_KERNELS_OBJECTS) $(COND_MPI_OBJECTS)
- ${FCLINK} -o ${E}/xsum_kernels $(SUM_KERNELS_OBJECTS) $(COND_MPI_OBJECTS) $(MPILIBS)
+ ${FCLINK} -o ${E}/xsum_kernels $(SUM_KERNELS_OBJECTS) $(COND_MPI_OBJECTS) $(MPILIBS)
xmodel_update: $(MODEL_UPD_OBJECTS) $(COND_MPI_OBJECTS) $(CUDA_STUBS)
${FCLINK} -o ${E}/xmodel_update $(MODEL_UPD_OBJECTS) $(COND_MPI_OBJECTS) $(MPILIBS) $(CUDA_STUBS)
@@ -395,7 +395,7 @@
$O/serial.o: $(SHARED)constants.h $(SHARED)serial.f90
${FCCOMPILE_CHECK} -c -o $O/serial.o $(SHARED)serial.f90
-
+
$O/smooth_vol_data.o: $(SHARED)constants.h $(SHARED)smooth_vol_data.f90
${MPIFCCOMPILE_NO_CHECK} -c -o $O/smooth_vol_data.o $(SHARED)smooth_vol_data.f90
Modified: seismo/3D/SPECFEM3D/trunk/src/specfem3D/model_update.f90
===================================================================
--- seismo/3D/SPECFEM3D/trunk/src/specfem3D/model_update.f90 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/src/specfem3D/model_update.f90 2012-10-22 16:16:57 UTC (rev 20873)
@@ -41,7 +41,7 @@
! root file directory
character (len=256), parameter :: &
- ROOT_PATH = '/lscratch/users/magnoni/SPECFEM3D/trunk_update/in_out_files'
+ ROOT_PATH = '/lscratch/users/magnoni/SPECFEM3D/trunk_update/OUTPUT_FILES'
! directory where the mesh files for the NEW model will be written
character (len=256), parameter :: &
Modified: seismo/3D/SPECFEM3D/trunk/utils/Cluster/go_generate_databases
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Cluster/go_generate_databases 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/utils/Cluster/go_generate_databases 2012-10-22 16:16:57 UTC (rev 20873)
@@ -15,8 +15,8 @@
# total number of processors is the product of the values read
@ numprocessors = $NPROC
-rm -r -f in_out_files/OUTPUT_FILES
-mkdir in_out_files/OUTPUT_FILES
+rm -r -f OUTPUT_FILES
+mkdir OUTPUT_FILES
rm -f sources timestamp* PI* error_message* starttimeloop*
Modified: seismo/3D/SPECFEM3D/trunk/utils/Cluster/lsf/go_generate_databases_lsf.bash
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Cluster/lsf/go_generate_databases_lsf.bash 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/utils/Cluster/lsf/go_generate_databases_lsf.bash 2012-10-22 16:16:57 UTC (rev 20873)
@@ -2,8 +2,8 @@
## job name and output file
#BSUB -J go_mesher
-#BSUB -o in_out_files/OUTPUT_FILES/%J.o
-#BSUB -e in_out_files/OUTPUT_FILES/%J.e
+#BSUB -o OUTPUT_FILES/%J.o
+#BSUB -e OUTPUT_FILES/%J.e
###########################################################
# USER PARAMETERS
@@ -30,11 +30,11 @@
# total number of nodes is the product of the values read
numnodes=$NPROC
-cp DATA/Par_file in_out_files/OUTPUT_FILES/
+cp DATA/Par_file OUTPUT_FILES/
# obtain lsf job information
-cat $LSB_DJOB_HOSTFILE > in_out_files/OUTPUT_FILES/compute_nodes
-echo "$LSB_JOBID" > in_out_files/OUTPUT_FILES/jobid
+cat $LSB_DJOB_HOSTFILE > OUTPUT_FILES/compute_nodes
+echo "$LSB_JOBID" > OUTPUT_FILES/jobid
echo starting MPI mesher on $numnodes processors
echo " "
Modified: seismo/3D/SPECFEM3D/trunk/utils/Cluster/lsf/go_mesher_solver_lsf_basin.forward
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Cluster/lsf/go_mesher_solver_lsf_basin.forward 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/utils/Cluster/lsf/go_mesher_solver_lsf_basin.forward 2012-10-22 16:16:57 UTC (rev 20873)
@@ -1,5 +1,5 @@
#!/bin/bash -v
-#BSUB -o in_out_files/OUTPUT_FILES/%J.o
+#BSUB -o OUTPUT_FILES/%J.o
#BSUB -a mpich_gm
#BSUB -J go_mesher_solver_forward
@@ -7,14 +7,14 @@
# Qinya Liu, May 2007, Caltech
BASEMPIDIR=/scratch/$USER/DATABASES_MPI
-mkdir -p in_out_files/OUTPUT_FILES
+mkdir -p OUTPUT_FILES
-echo "$LSB_MCPU_HOSTS" > in_out_files/OUTPUT_FILES/lsf_machines
-echo "$LSB_JOBID" > in_out_files/OUTPUT_FILES/jobid
+echo "$LSB_MCPU_HOSTS" > OUTPUT_FILES/lsf_machines
+echo "$LSB_JOBID" > OUTPUT_FILES/jobid
-remap_lsf_machines.pl in_out_files/OUTPUT_FILES/lsf_machines > in_out_files/OUTPUT_FILES/machines
+remap_lsf_machines.pl OUTPUT_FILES/lsf_machines > OUTPUT_FILES/machines
-shmux -M50 -Sall -c "mkdir -p /scratch/$USER/; mkdir -p $BASEMPIDIR.$LSB_JOBID" - < in_out_files/OUTPUT_FILES/machines >/dev/null
+shmux -M50 -Sall -c "mkdir -p /scratch/$USER/; mkdir -p $BASEMPIDIR.$LSB_JOBID" - < OUTPUT_FILES/machines >/dev/null
# main parameter file
sed -e "s:^LOCAL_PATH .*:LOCAL_PATH = $BASEMPIDIR.$LSB_JOBID:" < DATA/Par_file > Par_file.tmp
@@ -34,7 +34,7 @@
# collect seismograms and clean up
cd current_pwd/
-mkdir -p in_out_files/SEM
-cd in_out_files/SEM/
+mkdir -p OUTPUT_FILES/SEM
+cd OUTPUT_FILES/SEM/
collect_seismo_lsf_multi.pl ../OUTPUT_FILES/lsf_machines $current_pwd/DATA/Par_file
cleanbase.pl ../OUTPUT_FILES/machines
Modified: seismo/3D/SPECFEM3D/trunk/utils/Cluster/lsf/go_mesher_solver_lsf_basin.kernel
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Cluster/lsf/go_mesher_solver_lsf_basin.kernel 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/utils/Cluster/lsf/go_mesher_solver_lsf_basin.kernel 2012-10-22 16:16:57 UTC (rev 20873)
@@ -1,5 +1,5 @@
#!/bin/bash -v
-#BSUB -o in_out_files/OUTPUT_FILES/%J.o
+#BSUB -o OUTPUT_FILES/%J.o
#BSUB -a mpich_gm
#BSUB -J specfem_kernel
@@ -8,12 +8,12 @@
BASEMPIDIR=/scratch/$USER/DATABASES_MPI
-echo "$LSB_MCPU_HOSTS" > in_out_files/OUTPUT_FILES/lsf_machines
-echo "$LSB_JOBID" > in_out_files/OUTPUT_FILES/jobid
+echo "$LSB_MCPU_HOSTS" > OUTPUT_FILES/lsf_machines
+echo "$LSB_JOBID" > OUTPUT_FILES/jobid
-remap_lsf_machines.pl in_out_files/OUTPUT_FILES/lsf_machines > in_out_files/OUTPUT_FILES/machines
+remap_lsf_machines.pl OUTPUT_FILES/lsf_machines > OUTPUT_FILES/machines
-shmux -M50 -Sall -c "mkdir -p /scratch/$USER/; mkdir -p $BASEMPIDIR.$LSB_JOBID" - < in_out_files/OUTPUT_FILES/machines >/dev/null
+shmux -M50 -Sall -c "mkdir -p /scratch/$USER/; mkdir -p $BASEMPIDIR.$LSB_JOBID" - < OUTPUT_FILES/machines >/dev/null
# main parameter file
sed -e "s:^LOCAL_PATH .*:LOCAL_PATH = $BASEMPIDIR.$LSB_JOBID:" < DATA/Par_file > Par_file.tmp
@@ -33,9 +33,9 @@
#### 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/DATA/Par_file
+mkdir -p $current_pwd/OUTPUT_FILES/SEM
+cd $current_pwd/OUTPUT_FILES/SEM
+collect_seismo_lsf_multi.pl $current_pwd/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
@@ -46,5 +46,5 @@
cd bin/
mpirun.lsf --gm-no-shmem --gm-copy-env ./xspecfem3D
-shmux -M50 -Sall -c "cp $BASEMPIDIR.$LSB_JOBID/*alpha_kernel.bin $current_pwd/MESH" - < in_out_files/OUTPUT_FILES/machines >/dev/null
+shmux -M50 -Sall -c "cp $BASEMPIDIR.$LSB_JOBID/*alpha_kernel.bin $current_pwd/MESH" - < OUTPUT_FILES/machines >/dev/null
Modified: seismo/3D/SPECFEM3D/trunk/utils/Cluster/lsf/go_solver_lsf.bash
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Cluster/lsf/go_solver_lsf.bash 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/utils/Cluster/lsf/go_solver_lsf.bash 2012-10-22 16:16:57 UTC (rev 20873)
@@ -2,8 +2,8 @@
## job name and output file
#BSUB -J go_solver
-#BSUB -o in_out_files/OUTPUT_FILES/%J.o
-#BSUB -e in_out_files/OUTPUT_FILES/%J.e
+#BSUB -o OUTPUT_FILES/%J.o
+#BSUB -e OUTPUT_FILES/%J.e
###########################################################
# USER PARAMETERS
@@ -30,15 +30,15 @@
# total number of nodes is the product of the values read
numnodes=$NPROC
-rm -r -f in_out_files/OUTPUT_FILES
-mkdir in_out_files/OUTPUT_FILES
-cp DATA/Par_file in_out_files/OUTPUT_FILES/
-cp DATA/CMTSOLUTION in_out_files/OUTPUT_FILES/
-cp DATA/STATIONS in_out_files/OUTPUT_FILES/
+rm -r -f OUTPUT_FILES
+mkdir OUTPUT_FILES
+cp DATA/Par_file OUTPUT_FILES/
+cp DATA/CMTSOLUTION OUTPUT_FILES/
+cp DATA/STATIONS OUTPUT_FILES/
# obtain lsf job information
-cat $BSUB_DJOB_NODEFILE > in_out_files/OUTPUT_FILES/compute_nodes
-echo "$LSB_JOBID" > in_out_files/OUTPUT_FILES/jobid
+cat $BSUB_DJOB_NODEFILE > OUTPUT_FILES/compute_nodes
+echo "$LSB_JOBID" > OUTPUT_FILES/jobid
echo starting run in current directory $PWD
echo " "
Modified: seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_decomposer_pbs.bash
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_decomposer_pbs.bash 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_decomposer_pbs.bash 2012-10-22 16:16:57 UTC (rev 20873)
@@ -4,7 +4,7 @@
## job name and output file
#PBS -N go_decomposer
#PBS -j oe
-#PBS -o in_out_files/OUTPUT_FILES/$PBS_JOBID.o
+#PBS -o OUTPUT_FILES/$PBS_JOBID.o
###########################################################
# USER PARAMETERS
@@ -29,11 +29,11 @@
echo " "
# save a copy
-cp go_decomposer_pbs.bash in_out_files/OUTPUT_FILES/
+cp go_decomposer_pbs.bash OUTPUT_FILES/
# USER CHANGE MESH DIRECTORY
MESHDIR=examples/homogeneous_halfspace/MESH/
-./bin/xdecompose_mesh_SCOTCH $numnodes $MESHDIR in_out_files/DATABASES_MPI/
+./bin/xdecompose_mesh_SCOTCH $numnodes $MESHDIR OUTPUT_FILES/DATABASES_MPI/
echo "done "
Modified: seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_generate_databases_pbs.bash
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_generate_databases_pbs.bash 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_generate_databases_pbs.bash 2012-10-22 16:16:57 UTC (rev 20873)
@@ -4,7 +4,7 @@
## job name and output file
#PBS -N go_database
#PBS -j oe
-#PBS -o in_out_files/OUTPUT_FILES/$PBS_JOBID.o
+#PBS -o OUTPUT_FILES/$PBS_JOBID.o
###########################################################
# USER PARAMETERS
@@ -25,19 +25,19 @@
# total number of nodes is the product of the values read
numnodes=$NPROC
-mkdir -p in_out_files/OUTPUT_FILES
+mkdir -p OUTPUT_FILES
# backup files used for this simulation
-cp go_generate_databases_pbs.bash in_out_files/OUTPUT_FILES/
-cp DATA/Par_file in_out_files/OUTPUT_FILES/
+cp go_generate_databases_pbs.bash OUTPUT_FILES/
+cp DATA/Par_file OUTPUT_FILES/
# save a complete copy of source files
-#rm -rf in_out_files/OUTPUT_FILES/src
-#cp -rp ./src in_out_files/OUTPUT_FILES/
+#rm -rf OUTPUT_FILES/src
+#cp -rp ./src OUTPUT_FILES/
# obtain job information
-cat $PBS_NODEFILE > in_out_files/OUTPUT_FILES/compute_nodes
-echo "$PBS_JOBID" > in_out_files/OUTPUT_FILES/jobid
+cat $PBS_NODEFILE > OUTPUT_FILES/compute_nodes
+echo "$PBS_JOBID" > OUTPUT_FILES/jobid
echo starting MPI mesher on $numnodes processors
echo " "
@@ -51,6 +51,6 @@
# per instructions in manual, view low-res mesh with these commands (replace 143 with nproc-1):
# > make xcombine_vol_data
# > cd bin/
-# > ./xcombine_vol_data 0 143 vs ../in_out_files/DATABASES_MPI/ ../in_out_files/OUTPUT_FILES 0
-# > cd ../in_out_files/OUTPUT_FILES
+# > ./xcombine_vol_data 0 143 vs ../OUTPUT_FILES/DATABASES_MPI/ ../OUTPUT_FILES 0
+# > cd ../OUTPUT_FILES
# > paraview &
Modified: seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_mesher_pbs.bash
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_mesher_pbs.bash 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_mesher_pbs.bash 2012-10-22 16:16:57 UTC (rev 20873)
@@ -4,7 +4,7 @@
## job name and output file
#PBS -N go_mesher
#PBS -j oe
-#PBS -o in_out_files/OUTPUT_FILES/$PBS_JOBID.o
+#PBS -o OUTPUT_FILES/$PBS_JOBID.o
###########################################################
# USER PARAMETERS
@@ -21,21 +21,21 @@
NPROC=`grep NPROC DATA/Par_file | cut -d = -f 2 `
numnodes=$NPROC
-mkdir -p in_out_files/OUTPUT_FILES
-mkdir -p in_out_files/DATABASES_MPI
+mkdir -p OUTPUT_FILES
+mkdir -p OUTPUT_FILES/DATABASES_MPI
# backup files used for this simulation
-cp go_mesher_pbs.bash 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/
+cp go_mesher_pbs.bash OUTPUT_FILES/
+cp DATA/Par_file OUTPUT_FILES/
+cp DATA/meshfem3D_files/Mesh_Par_file OUTPUT_FILES/
# save a complete copy of source files
-#rm -rf in_out_files/OUTPUT_FILES/src
-#cp -rp ./src in_out_files/OUTPUT_FILES/
+#rm -rf OUTPUT_FILES/src
+#cp -rp ./src OUTPUT_FILES/
# obtain pbs job information
-cat $PBS_NODEFILE > in_out_files/OUTPUT_FILES/compute_nodes
-echo "$PBS_JOBID" > in_out_files/OUTPUT_FILES/jobid
+cat $PBS_NODEFILE > OUTPUT_FILES/compute_nodes
+echo "$PBS_JOBID" > OUTPUT_FILES/jobid
echo starting MPI internal mesher on $numnodes processors
echo " "
Modified: seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_solver_pbs.bash
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_solver_pbs.bash 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_solver_pbs.bash 2012-10-22 16:16:57 UTC (rev 20873)
@@ -4,7 +4,7 @@
## job name and output file
#PBS -N go_solver
#PBS -j oe
-#PBS -o in_out_files/OUTPUT_FILES/$PBS_JOBID.o
+#PBS -o OUTPUT_FILES/$PBS_JOBID.o
###########################################################
# USER PARAMETERS
@@ -25,22 +25,22 @@
# total number of nodes is the product of the values read
numnodes=$NPROC
-mkdir -p in_out_files/OUTPUT_FILES
+mkdir -p OUTPUT_FILES
# backup files used for this simulation
-cp go_solver_pbs.bash 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/
+cp go_solver_pbs.bash OUTPUT_FILES/
+cp DATA/Par_file OUTPUT_FILES/
+cp DATA/STATIONS OUTPUT_FILES/
+cp DATA/CMTSOLUTION OUTPUT_FILES/
+cp src/shared/constants.h OUTPUT_FILES/
# save a complete copy of source files
-#rm -rf in_out_files/OUTPUT_FILES/src
-#cp -rp ./src in_out_files/OUTPUT_FILES/
+#rm -rf OUTPUT_FILES/src
+#cp -rp ./src OUTPUT_FILES/
# obtain job information
-cat $PBS_NODEFILE > in_out_files/OUTPUT_FILES/compute_nodes
-echo "$PBS_JOBID" > in_out_files/OUTPUT_FILES/jobid
+cat $PBS_NODEFILE > OUTPUT_FILES/compute_nodes
+echo "$PBS_JOBID" > OUTPUT_FILES/jobid
echo starting run in current directory $PWD
echo " "
Modified: seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/valgrind_go_solver_pbs.bash
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/valgrind_go_solver_pbs.bash 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/valgrind_go_solver_pbs.bash 2012-10-22 16:16:57 UTC (rev 20873)
@@ -14,7 +14,7 @@
#PBS -j oe
# job output file
-#PBS -o in_out_files/OUTPUT_FILES/job.o
+#PBS -o OUTPUT_FILES/job.o
###########################################################
# USER PARAMETERS
@@ -40,16 +40,16 @@
# total number of nodes is the product of the values read
numnodes=$NPROC
-mkdir -p in_out_files/OUTPUT_FILES
+mkdir -p OUTPUT_FILES
# backup files used for this simulation
-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 DATA/Par_file OUTPUT_FILES/
+cp DATA/STATIONS OUTPUT_FILES/
+cp DATA/CMTSOLUTION OUTPUT_FILES/
# obtain job information
-cat $PBS_NODEFILE > in_out_files/OUTPUT_FILES/compute_nodes
-echo "$PBS_JOBID" > in_out_files/OUTPUT_FILES/jobid
+cat $PBS_NODEFILE > OUTPUT_FILES/compute_nodes
+echo "$PBS_JOBID" > OUTPUT_FILES/jobid
echo starting run in current directory $PWD
cd bin/
@@ -60,7 +60,7 @@
sleep 2
# memory leaks
-LD_PRELOAD=$PRELOAD_LIB mpiexec -np $numnodes valgrind --leak-check=full ./xspecfem3D >& ../in_out_files/OUTPUT_FILES/output.memory-leaks.log
+LD_PRELOAD=$PRELOAD_LIB mpiexec -np $numnodes valgrind --leak-check=full ./xspecfem3D >& ../OUTPUT_FILES/output.memory-leaks.log
sleep 2
echo " "
@@ -68,9 +68,9 @@
echo " "
# cache misses
-LD_PRELOAD=$PRELOAD_LIB mpiexec -np $numnodes valgrind --tool=cachegrind ./xspecfem3D >& ../in_out_files/OUTPUT_FILES/output.cache-misses.log
+LD_PRELOAD=$PRELOAD_LIB mpiexec -np $numnodes valgrind --tool=cachegrind ./xspecfem3D >& ../OUTPUT_FILES/output.cache-misses.log
-cp cachegrind.out.* ../in_out_files/OUTPUT_FILES/
+cp cachegrind.out.* ../OUTPUT_FILES/
echo " "
echo "finished successfully"
Modified: seismo/3D/SPECFEM3D/trunk/utils/Cluster/run3d.csh
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Cluster/run3d.csh 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/utils/Cluster/run3d.csh 2012-10-22 16:16:57 UTC (rev 20873)
@@ -2,7 +2,7 @@
# compile and run the database generator and then the solver
-set OUTDIR="in_out_files/OUTPUT_FILES"
+set OUTDIR="OUTPUT_FILES"
sleep 1
make clean
Modified: seismo/3D/SPECFEM3D/trunk/utils/Cluster/sge/go_generate_databases_sge.bash
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Cluster/sge/go_generate_databases_sge.bash 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/utils/Cluster/sge/go_generate_databases_sge.bash 2012-10-22 16:16:57 UTC (rev 20873)
@@ -6,7 +6,7 @@
# merge error output into standard output stream
#$ -j yes
-#$ -o in_out_files/OUTPUT_FILES/job.o
+#$ -o OUTPUT_FILES/job.o
###########################################################
# USER PARAMETERS
@@ -25,15 +25,15 @@
# total number of nodes is the product of the values read
numnodes=$NPROC
-mkdir -p in_out_files/OUTPUT_FILES
+mkdir -p OUTPUT_FILES
# backup for files used for this simulation
-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 DATA/Par_file OUTPUT_FILES/
+cp DATA/STATIONS OUTPUT_FILES/
+cp DATA/CMTSOLUTION OUTPUT_FILES/
-rm -rf in_out_files/OUTPUT_FILES/src
-cp -rp ./src in_out_files/OUTPUT_FILES/
+rm -rf OUTPUT_FILES/src
+cp -rp ./src OUTPUT_FILES/
echo starting run in current directory $PWD
echo " "
Modified: seismo/3D/SPECFEM3D/trunk/utils/Cluster/sge/go_solver_sge.bash
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Cluster/sge/go_solver_sge.bash 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/utils/Cluster/sge/go_solver_sge.bash 2012-10-22 16:16:57 UTC (rev 20873)
@@ -6,7 +6,7 @@
# merge error output into standard output stream
#$ -j yes
-#$ -o in_out_files/OUTPUT_FILES/job.o
+#$ -o OUTPUT_FILES/job.o
###########################################################
# USER PARAMETERS
@@ -25,15 +25,15 @@
# total number of nodes is the product of the values read
numnodes=$NPROC
-mkdir -p in_out_files/OUTPUT_FILES
+mkdir -p OUTPUT_FILES
# backup for files used for this simulation
-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 DATA/Par_file OUTPUT_FILES/
+cp DATA/STATIONS OUTPUT_FILES/
+cp DATA/CMTSOLUTION OUTPUT_FILES/
-rm -rf in_out_files/OUTPUT_FILES/src
-cp -rp ./src in_out_files/OUTPUT_FILES/
+rm -rf OUTPUT_FILES/src
+cp -rp ./src OUTPUT_FILES/
echo starting run in current directory $PWD
echo " "
Modified: seismo/3D/SPECFEM3D/trunk/utils/Visualization/GMT/movie2gif.gmt.pl
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Visualization/GMT/movie2gif.gmt.pl 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/utils/Visualization/GMT/movie2gif.gmt.pl 2012-10-22 16:16:57 UTC (rev 20873)
@@ -6,7 +6,7 @@
#
# /movie2gif.gmt.pl -R -118.9/-117.9/33.1/34.1 -g -f 1/10 -n -x
#
-# will create gif files ../in_out_files/OUTPUT_FILES/gmt_movie_000***.gif
+# will create gif files ../OUTPUT_FILES/gmt_movie_000***.gif
use Getopt::Std;
@@ -79,7 +79,7 @@
$csh_file = "movie2gif.csh";
$big_grd_file = "$datalib/big_sc.grd";
$bin = ".";
-$outdir = "../in_out_files/OUTPUT_FILES";
+$outdir = "../OUTPUT_FILES";
$factor = 10000;
$power = 1; #no distortion
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 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/utils/Visualization/GMT/plot_shakemap.gmt.pl 2012-10-22 16:16:57 UTC (rev 20873)
@@ -6,7 +6,7 @@
#
# ./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
+# will create shakemap file ../OUTPUT_FILES/gmt_shaking_map.ps for peak ground velocity
# USERS: change this to point to SPECFEM3D/utils/lib/
use lib '../utils/lib';
@@ -24,7 +24,7 @@
@name = ("Displacement", "Velocity", "Acceleration");
$power = 0.5;
-$file = "../in_out_files/OUTPUT_FILES/gmt_shaking_map";
+$file = "../OUTPUT_FILES/gmt_shaking_map";
$xyz_file = "${file}.xyz";
$grd_file = "${file}.grd";
$cpt_file = "${file}.cpt";
Modified: seismo/3D/SPECFEM3D/trunk/utils/adjoint_sources/SU_adjoint.f90
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/adjoint_sources/SU_adjoint.f90 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/utils/adjoint_sources/SU_adjoint.f90 2012-10-22 16:16:57 UTC (rev 20873)
@@ -8,21 +8,21 @@
! for example, compile with:
! > gfortran -o ../../example/homogeneous/halfspace/bin/xSU_adjoint SU_adjoint.f90
!
-! call in example directory example/homogeneous_halfspace/ by:
+! call in example directory example/homogeneous_halfspace/ by:
! > ./bin/xSU_adjoint 4
!
!-------------------------------------------------------------------------------------------------
module SU_adjoint_var
-
+
implicit none
real(kind=4),dimension(:),allocatable :: syn,dat,adj
-
+
character(len=128) :: DATA_PATH = "./DATA/"
- character(len=128) :: SYN_PATH = "./in_out_files/OUTPUT_FILES/"
- character(len=128) :: ADJ_PATH = "./in_out_files/SEM/"
-
+ character(len=128) :: SYN_PATH = "./OUTPUT_FILES/"
+ character(len=128) :: ADJ_PATH = "./OUTPUT_FILES/SEM/"
+
end module
!-------------------------------------------------------------------------------------------------
@@ -47,11 +47,11 @@
equivalence(header2,header4)
integer :: NSTEP
- double precision :: DT
+ double precision :: DT
! reads in file arguments
i = 1
- do while (1 == 1)
+ do while (1 == 1)
call getarg(i,arg(i))
if (i <= 1 .and. trim(arg(i)) == '') then
print*,'Usage: '
@@ -61,14 +61,14 @@
stop
endif
if (trim(arg(i)) == '') exit
- if (i == 1) then
+ if (i == 1) then
read(arg(i),*,iostat=ios) NPROC
if (ios /= 0) stop 'Error reading NPROC'
endif
i = i+1
enddo
-
- ! user output
+
+ ! user output
print*, "SU adjoint "
print*
print*, "number of partitions : ",NPROC
@@ -87,7 +87,7 @@
if( ios /= 0 ) then
print*,'error opening file: ',trim(filename)
stop 'error opening data file'
- endif
+ endif
! reads in header
read(11,rec=1,iostat=ios) r4head
@@ -103,17 +103,17 @@
print*, "NSTEP = ",NSTEP
print*, "DT = ",DT
print*
-
+
! allocates arrays
allocate(syn(NSTEP),dat(NSTEP),adj(NSTEP))
-
+
! loops over all partitions
do iproc = 0, NPROC - 1
-
+
! partition name
- write(procname,"(i4)") iproc
+ write(procname,"(i4)") iproc
print*,"...reading partition: ",iproc
-
+
! loops over components
do icomp = 1,3
! user output
@@ -125,10 +125,10 @@
open(11,file=trim(filename),access='direct',status='old', &
recl=240+4*NSTEP,iostat=ios)
if( ios /= 0 ) then
- print*,'error opening file: ',trim(filename)
+ print*,'error opening file: ',trim(filename)
stop 'error opening input data file '
endif
-
+
! synthetics
filename = trim(SYN_PATH)//trim(adjustl(procname))//"_d"//compstr(icomp)//"_SU"
open(22,file=trim(filename),access='direct',status='old', &
@@ -137,16 +137,16 @@
print*,'error opening file: ',trim(filename)
stop 'error opening input file '
endif
-
+
! adjoint sources
- filename = trim(ADJ_PATH)//trim(adjustl(procname))//"_d"//compstr(icomp)//"_SU"//".adj"
+ filename = trim(ADJ_PATH)//trim(adjustl(procname))//"_d"//compstr(icomp)//"_SU"//".adj"
open(33,file=trim(filename),access='direct',status='unknown', &
recl=240+4*NSTEP,iostat = ios)
if( ios /= 0 ) then
- print*,'error opening file: ',trim(filename)
+ print*,'error opening file: ',trim(filename)
stop 'error opening output file '
endif
-
+
! loops over all records
irec=1
do while(ios==0)
@@ -160,18 +160,18 @@
! creates adjoint trace
call create_adjoint_trace()
-
+
! writes out adjoint source
write(33,rec=irec,iostat=ios) r4head,adj
if (ios /= 0) cycle
-
+
irec=irec+1
enddo
close(11)
close(22)
close(33)
enddo
-
+
! user output
print*, " receivers read: ",irec
enddo
@@ -188,10 +188,10 @@
use SU_adjoint_var
implicit none
-
+
! MODIFY THIS according to your misfit function
! waveform misfit:
adj(:) = syn(:) - dat(:)
-
+
end subroutine
Modified: seismo/3D/SPECFEM3D/trunk/utils/locate_partition.f90
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/locate_partition.f90 2012-10-22 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/utils/locate_partition.f90 2012-10-22 16:16:57 UTC (rev 20873)
@@ -32,9 +32,9 @@
! > pgf90 -I src/shared -o bin/xlocate_partition utils/locate_partition.f90
!
! specify a target (x,y) may be in UTM, not lon-lat, then run with:
-! > ./bin/xlocate_partition 70000.0 11000.0 -3000.0 ./in_out_files/DATABASES_MPI/
+! > ./bin/xlocate_partition 70000.0 11000.0 -3000.0 ./OUTPUT_FILES/DATABASES_MPI/
!
-! this will generate the output file in_out_files/DATABASES_MPI/partition_bounds.dat
+! this will generate the output file OUTPUT_FILES/DATABASES_MPI/partition_bounds.dat
program locate_partition
@@ -65,7 +65,7 @@
print *
print *,'locate partition'
print *,'----------------------------'
-
+
do i = 1, 4
call getarg(i,arg(i))
if (i <= 4 .and. trim(arg(i)) == '') then
@@ -86,7 +86,7 @@
print *,'in directory: ',trim(LOCAL_PATH)
print *,'----------------------------'
print *
-
+
! open a text file to list the maximal bounds of each partition
open(11,file=trim(LOCAL_PATH)//'partition_bounds.dat',status='unknown')
@@ -98,7 +98,7 @@
total_z = 0.0
iproc = -1
do while( iproc < 10000000 )
- ! starts with 0
+ ! starts with 0
iproc = iproc + 1
! gets number of elements and global points for this partition
@@ -106,7 +106,7 @@
open(unit=27,file=prname_lp(1:len_trim(prname_lp))//'external_mesh.bin',&
status='old',action='read',form='unformatted',iostat=ios)
if( ios /= 0 ) exit
-
+
read(27,iostat=ier) NSPEC_AB
if( ier /= 0 ) stop 'please check your compilation, use the same compiler & flags as for SPECFEM3D'
read(27,iostat=ier) NGLOB_AB
@@ -122,11 +122,11 @@
allocate(xstore(NGLOB_AB),ystore(NGLOB_AB),zstore(NGLOB_AB),stat=ier)
if( ier /= 0 ) stop 'error allocating array xstore etc.'
read(27,iostat=ier) xstore
- if( ier /= 0 ) stop 'please check your compilation, use the same compiler & flags as for SPECFEM3D'
+ if( ier /= 0 ) stop 'please check your compilation, use the same compiler & flags as for SPECFEM3D'
read(27,iostat=ier) ystore
- if( ier /= 0 ) stop 'please check your compilation, use the same compiler & flags as for SPECFEM3D'
+ if( ier /= 0 ) stop 'please check your compilation, use the same compiler & flags as for SPECFEM3D'
read(27,iostat=ier) zstore
- if( ier /= 0 ) stop 'please check your compilation, use the same compiler & flags as for SPECFEM3D'
+ if( ier /= 0 ) stop 'please check your compilation, use the same compiler & flags as for SPECFEM3D'
close(27)
print*,'partition: ',iproc
@@ -134,7 +134,7 @@
print*,' min/max y = ',minval(ystore),maxval(ystore)
print*,' min/max z = ',minval(zstore),maxval(zstore)
print*
-
+
write(11,'(i10,6e18.6)') iproc,minval(xstore),maxval(xstore),minval(ystore),maxval(ystore),minval(zstore),maxval(zstore)
! gets distance to target location
@@ -154,7 +154,7 @@
deallocate(ibool,xstore,ystore,zstore)
enddo ! all slices for points
-
+
close(11)
! checks
@@ -162,7 +162,7 @@
print*,'Error: partition not found among ',iproc,'partitions searched'
stop 'Error: partition not found'
endif
-
+
! output
print*,'number of partitions searched: ',iproc
print*
@@ -187,7 +187,7 @@
implicit none
include 'constants.h'
-
+
real(kind=CUSTOM_REAL),intent(in) :: target_x,target_y,target_z
integer,intent(in) :: NSPEC_AB,NGLOB_AB
@@ -205,16 +205,16 @@
x_found = 0.0
y_found = 0.0
z_found = 0.0
-
+
do ispec=1,NSPEC_AB
do k=1,NGLLZ
- do j=1,NGLLY
+ do j=1,NGLLY
do i=1,NGLLX
iglob = ibool(i,j,k,ispec)
dist = (target_x - xstore(iglob))*(target_x - xstore(iglob)) &
+ (target_y - ystore(iglob))*(target_y - ystore(iglob)) &
- + (target_z - zstore(iglob))*(target_z - zstore(iglob))
-
+ + (target_z - zstore(iglob))*(target_z - zstore(iglob))
+
if( dist < distance ) then
distance = dist
x_found = xstore(iglob)
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 16:06:16 UTC (rev 20872)
+++ seismo/3D/SPECFEM3D/trunk/utils/unused_routines/create_header_file.f90 2012-10-22 16:16:57 UTC (rev 20873)
@@ -24,7 +24,7 @@
!
!=====================================================================
-! create file in_out_files/OUTPUT_FILES/values_from_mesher.h based upon DATA/Par_file
+! create file 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
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