[cig-commits] r20923 - in seismo/3D/SPECFEM3D/trunk/examples: BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/meshfem3D_files BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/meshfem3D_files Mount_StHelens Mount_StHelens/DATA homogeneous_halfspace_HEX27 homogeneous_halfspace_HEX27/DATA homogeneous_poroelastic homogeneous_poroelastic/DATA layered_halfspace layered_halfspace/DATA meshfem3D_examples/many_interfaces meshfem3D_examples/simple_model meshfem3D_examples/socal1D meshfem3D_examples/socal1D/DATA meshfem3D_examples/socal1D/DATA/meshfem3D_files noise_tomography noise_tomography/DATA tomographic_model tomographic_model/DATA waterlayered_halfspace waterlayered_halfspace/DATA

[joseph.charles at geodynamics.org]

Author: joseph.charles
Date: 2012-10-25 07:58:44 -0700 (Thu, 25 Oct 2012)
New Revision: 20923

Added:
   seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/
   seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/CMTSOLUTION
   seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/FORCESOLUTION
   seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/Par_file
   seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/STATIONS
   seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/STATIONS_ADJOINT
   seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/meshfem3D_files/
   seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/meshfem3D_files/Mesh_Par_file
   seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/meshfem3D_files/interface3.dat
   seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/meshfem3D_files/interfaces.dat
   seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/
   seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/CMTSOLUTION
   seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/FORCESOLUTION
   seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/Par_file
   seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/STATIONS
   seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/STATIONS_ADJOINT
   seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/meshfem3D_files/
   seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/meshfem3D_files/Mesh_Par_file
   seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/meshfem3D_files/interface3.dat
   seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/meshfem3D_files/interfaces.dat
   seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/DATA/
   seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/DATA/CMTSOLUTION
   seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/DATA/FORCESOLUTION
   seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/DATA/Par_file
   seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/DATA/STATIONS
   seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/DATA/
   seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/DATA/CMTSOLUTION
   seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/DATA/FORCESOLUTION
   seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/DATA/Par_file
   seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/DATA/STATIONS
   seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/DATA/STATIONS_ADJOINT
   seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/README
   seismo/3D/SPECFEM3D/trunk/examples/homogeneous_poroelastic/DATA/
   seismo/3D/SPECFEM3D/trunk/examples/homogeneous_poroelastic/DATA/CMTSOLUTION
   seismo/3D/SPECFEM3D/trunk/examples/homogeneous_poroelastic/DATA/FORCESOLUTION
   seismo/3D/SPECFEM3D/trunk/examples/homogeneous_poroelastic/DATA/Par_file
   seismo/3D/SPECFEM3D/trunk/examples/homogeneous_poroelastic/DATA/STATIONS
   seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/DATA/
   seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/DATA/CMTSOLUTION
   seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/DATA/FORCESOLUTION
   seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/DATA/Par_file
   seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/DATA/STATIONS
   seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/DATA/STATIONS_X
   seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/DATA/STATIONS_Y
   seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/
   seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/CMTSOLUTION
   seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/FORCESOLUTION
   seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/Par_file
   seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/STATIONS
   seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/
   seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/Mesh_Par_file
   seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/Mesh_Par_file_001
   seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/Mesh_Par_file_042
   seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/Mesh_Par_file_168
   seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/interface1.dat
   seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/interface2.dat
   seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/interface3.dat
   seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/interface4.dat
   seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/interfaces.dat
   seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/DATA/
   seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/DATA/CMTSOLUTION
   seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/DATA/FORCESOLUTION
   seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/DATA/Par_file_step1
   seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/DATA/Par_file_step2
   seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/DATA/Par_file_step3
   seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/DATA/STATIONS
   seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/DATA/STATIONS_ADJOINT
   seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/DATA/
   seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/DATA/CMTSOLUTION
   seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/DATA/FORCESOLUTION
   seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/DATA/Par_file
   seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/DATA/STATIONS
   seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/DATA/
   seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/DATA/CMTSOLUTION
   seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/DATA/FORCESOLUTION
   seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/DATA/Par_file
   seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/DATA/STATIONS
Removed:
   seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/in_data_files/
   seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/in_data_files/
   seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/in_data_files/
   seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/HOWTO_run_this_example.txt
   seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/in_data_files/
   seismo/3D/SPECFEM3D/trunk/examples/homogeneous_poroelastic/in_data_files/
   seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/in_data_files/
   seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/in_data_files/
   seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/in_data_files/
   seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/in_data_files/
   seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/in_data_files/
Modified:
   seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/process.sh
   seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/README
   seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/process.sh
   seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/many_interfaces/README
   seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/simple_model/README
   seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/README
   seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/process.sh
   seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/README
   seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/pre-processing.sh
   seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/README
   seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/process.sh
   seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/README
   seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/process.sh
Log:
cleanup in all examples directories


Added: seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/CMTSOLUTION
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/CMTSOLUTION	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/CMTSOLUTION	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,13 @@
+PDE  1999 01 01 00 00 00.00  67000 67000 -25000 4.2 4.2 hom_explosion
+event name:       hom_explosion
+time shift:       0.0000
+half duration:    0.5
+latitude:       1320.0
+longitude:      1320.0
+depth:           1.0
+Mrr:       1.000000e+23
+Mtt:       1.000000e+23
+Mpp:       1.000000e+23
+Mrt:       0.000000
+Mrp:       0.000000
+Mtp:       0.000000

Added: seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/FORCESOLUTION
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/FORCESOLUTION	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/FORCESOLUTION	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,10 @@
+FORCE  001
+time shift:     0.0000
+hdur:           0.5
+latitude:       1320.0
+longitude:      1320.0
+depth:          1.0
+factor force source:             1.d15
+component dir vect source E:     1.d0
+component dir vect source N:     -2.d0
+component dir vect source Z_UP:  -1.d0

Added: seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/Par_file
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/Par_file	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/Par_file	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,96 @@
+# simulation input parameters
+#
+# forward or adjoint simulation
+# 1 = forward, 2 = adjoint, 3 = both simultaneously
+SIMULATION_TYPE                 = 3
+# 0 = earthquake simulation,  1/2/3 = three steps in noise simulation
+NOISE_TOMOGRAPHY                = 0
+SAVE_FORWARD                    = .false.
+
+# UTM projection parameters
+UTM_PROJECTION_ZONE             = 11
+SUPPRESS_UTM_PROJECTION         = .true.
+
+# number of MPI processors
+NPROC                           = 4
+
+# time step parameters
+NSTEP                           = 10000
+DT                              = 0.001
+
+# number of nodes for 2D and 3D shape functions for hexahedra
+# we use either 8-node mesh elements (bricks) or 27-node elements.
+# If you use our internal mesher, the only option is 8-node bricks (27-node elements are not supported)
+# CUBIT does not support HEX27 elements either (it can generate them, but they are flat, i.e. identical to HEX8).
+# To generate HEX27 elements with curvature properly taken into account, you can use Gmsh http://geuz.org/gmsh/
+NGNOD 	      	    	     	= 8
+
+# models:
+# available options are:
+#   default (model parameters described by mesh properties)
+# 1D models available are:
+#   1d_prem,1d_socal,1d_cascadia
+# 3D models available are:
+#   aniso,external,gll,salton_trough,tomo
+MODEL                           = default
+
+# parameters describing the model
+OCEANS                          = .false.
+TOPOGRAPHY                      = .false.
+ATTENUATION                     = .false.
+USE_OLSEN_ATTENUATION           = .false.
+ANISOTROPY                      = .false.
+
+# absorbing boundary conditions for a regional simulation
+ABSORBING_CONDITIONS            = .true.
+
+# absorbing top surface (defined in mesh as 'free_surface_file')
+ABSORB_INSTEAD_OF_FREE_SURFACE  = .false.
+
+# save AVS or OpenDX movies
+MOVIE_SURFACE                   = .false.
+MOVIE_VOLUME                    = .false.
+NTSTEP_BETWEEN_FRAMES           = 100
+CREATE_SHAKEMAP                 = .false.
+SAVE_DISPLACEMENT               = .true.
+USE_HIGHRES_FOR_MOVIES          = .false.
+HDUR_MOVIE                      = 0.0
+
+# save AVS or OpenDX mesh files to check the mesh
+SAVE_MESH_FILES                 = .true.
+
+# path to store the local database file on each node
+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
+
+# interval in time steps for writing of seismograms
+NTSTEP_BETWEEN_OUTPUT_SEISMOS   = 10000
+
+# interval in time steps for reading adjoint traces
+NTSTEP_BETWEEN_READ_ADJSRC      = 0      # 0 = read the whole adjoint sources at the same time
+
+# 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
+# in which the source is a vertical force, normal force, inclined force, impact etc.
+# If this flag is turned on, the FORCESOLUTION file must be edited by precising:
+# - the corresponding time-shift parameter,
+# - the half duration parameter of the source,
+# - the coordinates of the source,
+# - the magnitude of the force source,
+# - the components of a (non-unitary) direction vector for the force source in the E/N/Z_UP basis.
+# 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.
+USE_FORCE_POINT_SOURCE          = .false.
+
+# 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
+GPU_MODE                        = .false.
+

Added: seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/STATIONS
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/STATIONS	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/STATIONS	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,729 @@
+X1 Y1 0 0 10 10
+X2 Y1 0 100 10 10
+X3 Y1 0 200 10 10
+X4 Y1 0 300 10 10
+X5 Y1 0 400 10 10
+X6 Y1 0 500 10 10
+X7 Y1 0 600 10 10
+X8 Y1 0 700 10 10
+X9 Y1 0 800 10 10
+X10 Y1 0 900 10 10
+X11 Y1 0 1000 10 10
+X12 Y1 0 1100 10 10
+X13 Y1 0 1200 10 10
+X14 Y1 0 1300 10 10
+X15 Y1 0 1400 10 10
+X16 Y1 0 1500 10 10
+X17 Y1 0 1600 10 10
+X18 Y1 0 1700 10 10
+X19 Y1 0 1800 10 10
+X20 Y1 0 1900 10 10
+X21 Y1 0 2000 10 10
+X22 Y1 0 2100 10 10
+X23 Y1 0 2200 10 10
+X24 Y1 0 2300 10 10
+X25 Y1 0 2400 10 10
+X26 Y1 0 2500 10 10
+X27 Y1 0 2600 10 10
+X1 Y2 100 0 10 10
+X2 Y2 100 100 10 10
+X3 Y2 100 200 10 10
+X4 Y2 100 300 10 10
+X5 Y2 100 400 10 10
+X6 Y2 100 500 10 10
+X7 Y2 100 600 10 10
+X8 Y2 100 700 10 10
+X9 Y2 100 800 10 10
+X10 Y2 100 900 10 10
+X11 Y2 100 1000 10 10
+X12 Y2 100 1100 10 10
+X13 Y2 100 1200 10 10
+X14 Y2 100 1300 10 10
+X15 Y2 100 1400 10 10
+X16 Y2 100 1500 10 10
+X17 Y2 100 1600 10 10
+X18 Y2 100 1700 10 10
+X19 Y2 100 1800 10 10
+X20 Y2 100 1900 10 10
+X21 Y2 100 2000 10 10
+X22 Y2 100 2100 10 10
+X23 Y2 100 2200 10 10
+X24 Y2 100 2300 10 10
+X25 Y2 100 2400 10 10
+X26 Y2 100 2500 10 10
+X27 Y2 100 2600 10 10
+X1 Y3 200 0 10 10
+X2 Y3 200 100 10 10
+X3 Y3 200 200 10 10
+X4 Y3 200 300 10 10
+X5 Y3 200 400 10 10
+X6 Y3 200 500 10 10
+X7 Y3 200 600 10 10
+X8 Y3 200 700 10 10
+X9 Y3 200 800 10 10
+X10 Y3 200 900 10 10
+X11 Y3 200 1000 10 10
+X12 Y3 200 1100 10 10
+X13 Y3 200 1200 10 10
+X14 Y3 200 1300 10 10
+X15 Y3 200 1400 10 10
+X16 Y3 200 1500 10 10
+X17 Y3 200 1600 10 10
+X18 Y3 200 1700 10 10
+X19 Y3 200 1800 10 10
+X20 Y3 200 1900 10 10
+X21 Y3 200 2000 10 10
+X22 Y3 200 2100 10 10
+X23 Y3 200 2200 10 10
+X24 Y3 200 2300 10 10
+X25 Y3 200 2400 10 10
+X26 Y3 200 2500 10 10
+X27 Y3 200 2600 10 10
+X1 Y4 300 0 10 10
+X2 Y4 300 100 10 10
+X3 Y4 300 200 10 10
+X4 Y4 300 300 10 10
+X5 Y4 300 400 10 10
+X6 Y4 300 500 10 10
+X7 Y4 300 600 10 10
+X8 Y4 300 700 10 10
+X9 Y4 300 800 10 10
+X10 Y4 300 900 10 10
+X11 Y4 300 1000 10 10
+X12 Y4 300 1100 10 10
+X13 Y4 300 1200 10 10
+X14 Y4 300 1300 10 10
+X15 Y4 300 1400 10 10
+X16 Y4 300 1500 10 10
+X17 Y4 300 1600 10 10
+X18 Y4 300 1700 10 10
+X19 Y4 300 1800 10 10
+X20 Y4 300 1900 10 10
+X21 Y4 300 2000 10 10
+X22 Y4 300 2100 10 10
+X23 Y4 300 2200 10 10
+X24 Y4 300 2300 10 10
+X25 Y4 300 2400 10 10
+X26 Y4 300 2500 10 10
+X27 Y4 300 2600 10 10
+X1 Y5 400 0 10 10
+X2 Y5 400 100 10 10
+X3 Y5 400 200 10 10
+X4 Y5 400 300 10 10
+X5 Y5 400 400 10 10
+X6 Y5 400 500 10 10
+X7 Y5 400 600 10 10
+X8 Y5 400 700 10 10
+X9 Y5 400 800 10 10
+X10 Y5 400 900 10 10
+X11 Y5 400 1000 10 10
+X12 Y5 400 1100 10 10
+X13 Y5 400 1200 10 10
+X14 Y5 400 1300 10 10
+X15 Y5 400 1400 10 10
+X16 Y5 400 1500 10 10
+X17 Y5 400 1600 10 10
+X18 Y5 400 1700 10 10
+X19 Y5 400 1800 10 10
+X20 Y5 400 1900 10 10
+X21 Y5 400 2000 10 10
+X22 Y5 400 2100 10 10
+X23 Y5 400 2200 10 10
+X24 Y5 400 2300 10 10
+X25 Y5 400 2400 10 10
+X26 Y5 400 2500 10 10
+X27 Y5 400 2600 10 10
+X1 Y6 500 0 10 10
+X2 Y6 500 100 10 10
+X3 Y6 500 200 10 10
+X4 Y6 500 300 10 10
+X5 Y6 500 400 10 10
+X6 Y6 500 500 10 10
+X7 Y6 500 600 10 10
+X8 Y6 500 700 10 10
+X9 Y6 500 800 10 10
+X10 Y6 500 900 10 10
+X11 Y6 500 1000 10 10
+X12 Y6 500 1100 10 10
+X13 Y6 500 1200 10 10
+X14 Y6 500 1300 10 10
+X15 Y6 500 1400 10 10
+X16 Y6 500 1500 10 10
+X17 Y6 500 1600 10 10
+X18 Y6 500 1700 10 10
+X19 Y6 500 1800 10 10
+X20 Y6 500 1900 10 10
+X21 Y6 500 2000 10 10
+X22 Y6 500 2100 10 10
+X23 Y6 500 2200 10 10
+X24 Y6 500 2300 10 10
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Added: seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/STATIONS_ADJOINT
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/STATIONS_ADJOINT	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/STATIONS_ADJOINT	2012-10-25 14:58:44 UTC (rev 20923)
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Added: seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/meshfem3D_files/Mesh_Par_file
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/meshfem3D_files/Mesh_Par_file	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/meshfem3D_files/Mesh_Par_file	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,54 @@
+
+# coordinates of mesh block in latitude/longitude and depth in km
+LATITUDE_MIN                    = 0.0d0
+LATITUDE_MAX                    = 2640.0d0
+LONGITUDE_MIN                   = 0.0d0
+LONGITUDE_MAX                   = 2640.0d0
+DEPTH_BLOCK_KM                  = 1.440d0
+UTM_PROJECTION_ZONE             = 11
+SUPPRESS_UTM_PROJECTION         = .true.
+
+# file that contains the interfaces of the model / mesh
+INTERFACES_FILE                 = interfaces.dat
+
+# number of elements at the surface along edges of the mesh at the surface
+# (must be 8 * multiple of NPROC below if mesh is not regular and contains mesh doublings)
+# (must be multiple of NPROC below if mesh is regular)
+NEX_XI                          = 32
+NEX_ETA                         = 32
+
+# number of MPI processors along xi and eta (can be different)
+NPROC_XI                        = 2
+NPROC_ETA                       = 2
+
+# Regular/irregular mesh
+USE_REGULAR_MESH                = .true.
+# Only for irregular meshes, number of doubling layers (1 or 2) and their position
+NDOUBLINGS                      = 1
+# NZ_DOUGLING_1 is the parameter to set up if there is only one doubling layer
+NZ_DOUGLING_1                   = 11
+NZ_DOUGLING_2                   = 0
+
+# create mesh files for visualisation or further checking
+CREATE_ABAQUS_FILES             = .false.
+CREATE_DX_FILES                 = .false.
+CREATE_VTK_FILES                = .false.
+
+# path to store the databases files
+LOCAL_PATH                      = ../OUTPUT_FILES/DATABASES_MPI/
+
+# number of materials
+NMATERIALS                      = 3
+# define the different materials in the model as :
+# #material_id  #rho  #vp  #vs  #Q  #anisotropy_flag #domain_id
+#     Q                : quality factor
+#     anisotropy_flag  : 0=no anisotropy/ 1,2,.. check with implementation in aniso_model.f90
+#     domain_id        : 1=acoustic / 2=elastic
+1  2000  2000  1500  0.0   0  2
+2  2000  2000  0     0.0   0  1
+3  2000  2000  0.001 0.0   0  2
+# number of regions
+NREGIONS                        = 1
+# define the different regions of the model as :
+#NEX_XI_BEGIN  #NEX_XI_END  #NEX_ETA_BEGIN  #NEX_ETA_END  #NZ_BEGIN #NZ_END  #material_id
+1              32            1               32             1         8        2

Added: seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/meshfem3D_files/interface3.dat
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/meshfem3D_files/interface3.dat	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/meshfem3D_files/interface3.dat	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,4 @@
+0.0
+0.0
+0.0
+0.0

Added: seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/meshfem3D_files/interfaces.dat
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/meshfem3D_files/interfaces.dat	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/meshfem3D_files/interfaces.dat	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,22 @@
+# number of interfaces
+ 1
+#
+# We describe each interface below, structured as a 2D-grid, with several parameters : 
+# number of points along XI and ETA, minimal XI ETA coordinates 
+# and spacing between points which must be constant.
+# Then the records contain the Z coordinates of the NXI x NETA points.
+#
+# interface number 1 
+# SUPPRESS_UTM_PROJECTION  NXI  NETA LONG_MIN   LAT_MIN    SPACING_XI SPACING_ETA
+# .true.                    161  144  316000.d0  3655000.d0 20000.d0    20000.d0
+# interface1.dat
+# interface number 2 (topography, top of the mesh)
+ .true. 2 2 0.d0 0.d0 2640.00d0 2640.00d0
+ interface3.dat
+#
+# for each layer, we give the number of spectral elements in the vertical direction
+# layer number 1 (bottom layer)
+# 11
+# layer number 2 (top layer)
+# 4
+8

Added: seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/CMTSOLUTION
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/CMTSOLUTION	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/CMTSOLUTION	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,13 @@
+PDE  1999 01 01 00 00 00.00  67000 67000 -25000 4.2 4.2 hom_explosion
+event name:       hom_explosion
+time shift:       0.0000
+half duration:    0.5
+latitude:       1320.0
+longitude:      1320.0
+depth:           1.0
+Mrr:       1.000000e+23
+Mtt:       1.000000e+23
+Mpp:       1.000000e+23
+Mrt:       0.000000
+Mrp:       0.000000
+Mtp:       0.000000

Added: seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/FORCESOLUTION
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/FORCESOLUTION	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/FORCESOLUTION	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,10 @@
+FORCE  001
+time shift:     0.0000
+hdur:           0.5
+latitude:       1320.0
+longitude:      1320.0
+depth:          1.0
+factor force source:             1.d15
+component dir vect source E:     1.d0
+component dir vect source N:     -2.d0
+component dir vect source Z_UP:  -1.d0

Added: seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/Par_file
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/Par_file	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/Par_file	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,96 @@
+# simulation input parameters
+#
+# forward or adjoint simulation
+# 1 = forward, 2 = adjoint, 3 = both simultaneously
+SIMULATION_TYPE                 = 3
+# 0 = earthquake simulation,  1/2/3 = three steps in noise simulation
+NOISE_TOMOGRAPHY                = 0
+SAVE_FORWARD                    = .false.
+
+# UTM projection parameters
+UTM_PROJECTION_ZONE             = 11
+SUPPRESS_UTM_PROJECTION         = .true.
+
+# number of MPI processors
+NPROC                           = 4
+
+# time step parameters
+NSTEP                           = 4000
+DT                              = 0.0006
+
+# number of nodes for 2D and 3D shape functions for hexahedra
+# we use either 8-node mesh elements (bricks) or 27-node elements.
+# If you use our internal mesher, the only option is 8-node bricks (27-node elements are not supported)
+# CUBIT does not support HEX27 elements either (it can generate them, but they are flat, i.e. identical to HEX8).
+# To generate HEX27 elements with curvature properly taken into account, you can use Gmsh http://geuz.org/gmsh/
+NGNOD 	      	    	     	= 8
+
+# models:
+# available options are:
+#   default (model parameters described by mesh properties)
+# 1D models available are:
+#   1d_prem,1d_socal,1d_cascadia
+# 3D models available are:
+#   aniso,external,gll,salton_trough,tomo
+MODEL                           = default
+
+# parameters describing the model
+OCEANS                          = .false.
+TOPOGRAPHY                      = .false.
+ATTENUATION                     = .false.
+USE_OLSEN_ATTENUATION           = .false.
+ANISOTROPY                      = .false.
+
+# absorbing boundary conditions for a regional simulation
+ABSORBING_CONDITIONS            = .true.
+
+# absorbing top surface (defined in mesh as 'free_surface_file')
+ABSORB_INSTEAD_OF_FREE_SURFACE  = .false.
+
+# save AVS or OpenDX movies
+MOVIE_SURFACE                   = .false.
+MOVIE_VOLUME                    = .false.
+NTSTEP_BETWEEN_FRAMES           = 100
+CREATE_SHAKEMAP                 = .false.
+SAVE_DISPLACEMENT               = .true.
+USE_HIGHRES_FOR_MOVIES          = .false.
+HDUR_MOVIE                      = 0.0
+
+# save AVS or OpenDX mesh files to check the mesh
+SAVE_MESH_FILES                 = .true.
+
+# path to store the local database file on each node
+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
+
+# interval in time steps for writing of seismograms
+NTSTEP_BETWEEN_OUTPUT_SEISMOS   = 10000
+
+# interval in time steps for reading adjoint traces
+NTSTEP_BETWEEN_READ_ADJSRC      = 0      # 0 = read the whole adjoint sources at the same time
+
+# 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
+# in which the source is a vertical force, normal force, inclined force, impact etc.
+# If this flag is turned on, the FORCESOLUTION file must be edited by precising:
+# - the corresponding time-shift parameter,
+# - the half duration parameter of the source,
+# - the coordinates of the source,
+# - the magnitude of the force source,
+# - the components of a (non-unitary) direction vector for the force source in the E/N/Z_UP basis.
+# 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.
+USE_FORCE_POINT_SOURCE          = .false.
+
+# 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
+GPU_MODE                        = .false.
+

Added: seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/STATIONS
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/STATIONS	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/STATIONS	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,729 @@
+X1 Y1 0 0 10 10
+X2 Y1 0 100 10 10
+X3 Y1 0 200 10 10
+X4 Y1 0 300 10 10
+X5 Y1 0 400 10 10
+X6 Y1 0 500 10 10
+X7 Y1 0 600 10 10
+X8 Y1 0 700 10 10
+X9 Y1 0 800 10 10
+X10 Y1 0 900 10 10
+X11 Y1 0 1000 10 10
+X12 Y1 0 1100 10 10
+X13 Y1 0 1200 10 10
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+X19 Y1 0 1800 10 10
+X20 Y1 0 1900 10 10
+X21 Y1 0 2000 10 10
+X22 Y1 0 2100 10 10
+X23 Y1 0 2200 10 10
+X24 Y1 0 2300 10 10
+X25 Y1 0 2400 10 10
+X26 Y1 0 2500 10 10
+X27 Y1 0 2600 10 10
+X1 Y2 100 0 10 10
+X2 Y2 100 100 10 10
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+X4 Y2 100 300 10 10
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Added: seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/STATIONS_ADJOINT
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/STATIONS_ADJOINT	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/STATIONS_ADJOINT	2012-10-25 14:58:44 UTC (rev 20923)
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+X5 Y22 2100 400 10 10
+X6 Y22 2100 500 10 10
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+X8 Y22 2100 700 10 10
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+X11 Y23 2200 1000 10 10
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+X16 Y23 2200 1500 10 10
+X17 Y23 2200 1600 10 10
+X18 Y23 2200 1700 10 10
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+X20 Y23 2200 1900 10 10
+X21 Y23 2200 2000 10 10
+X22 Y23 2200 2100 10 10
+X23 Y23 2200 2200 10 10
+X24 Y23 2200 2300 10 10
+X25 Y23 2200 2400 10 10
+X26 Y23 2200 2500 10 10
+X27 Y23 2200 2600 10 10
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+X3 Y24 2300 200 10 10
+X4 Y24 2300 300 10 10
+X5 Y24 2300 400 10 10
+X6 Y24 2300 500 10 10
+X7 Y24 2300 600 10 10
+X8 Y24 2300 700 10 10
+X9 Y24 2300 800 10 10
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+X3 Y26 2500 200 10 10
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+X21 Y26 2500 2000 10 10
+X22 Y26 2500 2100 10 10
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+X1 Y27 2600 0 10 10
+X2 Y27 2600 100 10 10
+X3 Y27 2600 200 10 10
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+X12 Y27 2600 1100 10 10
+X13 Y27 2600 1200 10 10
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+X16 Y27 2600 1500 10 10
+X17 Y27 2600 1600 10 10
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+X20 Y27 2600 1900 10 10
+X21 Y27 2600 2000 10 10
+X22 Y27 2600 2100 10 10
+X23 Y27 2600 2200 10 10
+X24 Y27 2600 2300 10 10
+X25 Y27 2600 2400 10 10
+X26 Y27 2600 2500 10 10
+X27 Y27 2600 2600 10 10

Added: seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/meshfem3D_files/Mesh_Par_file
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/meshfem3D_files/Mesh_Par_file	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/meshfem3D_files/Mesh_Par_file	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,54 @@
+
+# coordinates of mesh block in latitude/longitude and depth in km
+LATITUDE_MIN                    = 0.0d0
+LATITUDE_MAX                    = 2640.0d0
+LONGITUDE_MIN                   = 0.0d0
+LONGITUDE_MAX                   = 2640.0d0
+DEPTH_BLOCK_KM                  = 1.440d0
+UTM_PROJECTION_ZONE             = 11
+SUPPRESS_UTM_PROJECTION         = .true.
+
+# file that contains the interfaces of the model / mesh
+INTERFACES_FILE                 = interfaces.dat
+
+# number of elements at the surface along edges of the mesh at the surface
+# (must be 8 * multiple of NPROC below if mesh is not regular and contains mesh doublings)
+# (must be multiple of NPROC below if mesh is regular)
+NEX_XI                          = 32
+NEX_ETA                         = 32
+
+# number of MPI processors along xi and eta (can be different)
+NPROC_XI                        = 2
+NPROC_ETA                       = 2
+
+# Regular/irregular mesh
+USE_REGULAR_MESH                = .true.
+# Only for irregular meshes, number of doubling layers (1 or 2) and their position
+NDOUBLINGS                      = 1
+# NZ_DOUGLING_1 is the parameter to set up if there is only one doubling layer
+NZ_DOUGLING_1                   = 11
+NZ_DOUGLING_2                   = 0
+
+# create mesh files for visualisation or further checking
+CREATE_ABAQUS_FILES             = .false.
+CREATE_DX_FILES                 = .false.
+CREATE_VTK_FILES                = .false.
+
+# path to store the databases files
+LOCAL_PATH                      = ../OUTPUT_FILES/DATABASES_MPI/
+
+# number of materials
+NMATERIALS                      = 3
+# define the different materials in the model as :
+# #material_id  #rho  #vp  #vs  #Q  #anisotropy_flag #domain_id
+#     Q                : quality factor
+#     anisotropy_flag  : 0=no anisotropy/ 1,2,.. check with implementation in aniso_model.f90
+#     domain_id        : 1=acoustic / 2=elastic
+1  2000  5000  3000  0.0   0  2
+2  2000  2000  0     0.0   0  1
+3  2000  2000  0.001 0.0   0  2
+# number of regions
+NREGIONS                        = 1
+# define the different regions of the model as :
+#NEX_XI_BEGIN  #NEX_XI_END  #NEX_ETA_BEGIN  #NEX_ETA_END  #NZ_BEGIN #NZ_END  #material_id
+1              32            1               32             1         8        1

Added: seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/meshfem3D_files/interface3.dat
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/meshfem3D_files/interface3.dat	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/meshfem3D_files/interface3.dat	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,4 @@
+0.0
+0.0
+0.0
+0.0

Added: seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/meshfem3D_files/interfaces.dat
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/meshfem3D_files/interfaces.dat	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/meshfem3D_files/interfaces.dat	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,22 @@
+# number of interfaces
+ 1
+#
+# We describe each interface below, structured as a 2D-grid, with several parameters : 
+# number of points along XI and ETA, minimal XI ETA coordinates 
+# and spacing between points which must be constant.
+# Then the records contain the Z coordinates of the NXI x NETA points.
+#
+# interface number 1 
+# SUPPRESS_UTM_PROJECTION  NXI  NETA LONG_MIN   LAT_MIN    SPACING_XI SPACING_ETA
+# .true.                    161  144  316000.d0  3655000.d0 20000.d0    20000.d0
+# interface1.dat
+# interface number 2 (topography, top of the mesh)
+ .true. 2 2 0.d0 0.d0 2640.00d0 2640.00d0
+ interface3.dat
+#
+# for each layer, we give the number of spectral elements in the vertical direction
+# layer number 1 (bottom layer)
+# 11
+# layer number 2 (top layer)
+# 4
+8

Added: seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/DATA/CMTSOLUTION
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/DATA/CMTSOLUTION	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/DATA/CMTSOLUTION	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,13 @@
+PDE  1999 01 01 00 00 00.00  67000 67000 -25000 4.2 4.2 hom_explosion
+event name:       hom_explosion
+time shift:       0.0000
+half duration:    1.5
+latitude:       46.197
+longitude:      -122.186
+depth:            5.0
+Mrr:       1.000000e+23
+Mtt:       1.000000e+23
+Mpp:       1.000000e+23
+Mrt:       0.000000
+Mrp:       0.000000
+Mtp:       0.000000

Added: seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/DATA/FORCESOLUTION
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/DATA/FORCESOLUTION	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/DATA/FORCESOLUTION	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,10 @@
+FORCE  001
+time shift:     0.0000
+hdur:           0.5
+latitude:       46.197
+longitude:      -122.186
+depth:          5.0
+factor force source:             1.d15
+component dir vect source E:     1.d0
+component dir vect source N:     -2.d0
+component dir vect source Z_UP:  -1.d0

Added: seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/DATA/Par_file
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/DATA/Par_file	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/DATA/Par_file	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,96 @@
+# simulation input parameters
+#
+# forward or adjoint simulation
+# 1 = forward, 2 = adjoint, 3 = both simultaneously
+SIMULATION_TYPE                 = 1
+# 0 = earthquake simulation,  1/2/3 = three steps in noise simulation
+NOISE_TOMOGRAPHY                = 0
+SAVE_FORWARD                    = .false.
+
+# UTM projection parameters
+UTM_PROJECTION_ZONE             = 10
+SUPPRESS_UTM_PROJECTION         = .false.
+
+# number of MPI processors
+NPROC                           = 4
+
+# time step parameters
+NSTEP                           = 2500
+DT                              = 0.005d0
+
+# number of nodes for 2D and 3D shape functions for hexahedra
+# we use either 8-node mesh elements (bricks) or 27-node elements.
+# If you use our internal mesher, the only option is 8-node bricks (27-node elements are not supported)
+# CUBIT does not support HEX27 elements either (it can generate them, but they are flat, i.e. identical to HEX8).
+# To generate HEX27 elements with curvature properly taken into account, you can use Gmsh http://geuz.org/gmsh/
+NGNOD 	      	    	     	= 8
+
+# models:
+# available options are:
+#   default (model parameters described by mesh properties)
+# 1D models available are:
+#   1d_prem,1d_socal,1d_cascadia
+# 3D models available are:
+#   aniso,external,gll,salton_trough,tomo
+MODEL                           = default
+
+# parameters describing the model
+OCEANS                          = .false.
+TOPOGRAPHY                      = .false.
+ATTENUATION                     = .false.
+USE_OLSEN_ATTENUATION           = .false.
+ANISOTROPY                      = .false.
+
+# absorbing boundary conditions for a regional simulation
+ABSORBING_CONDITIONS            = .true.
+
+# absorbing top surface (defined in mesh as 'free_surface_file')
+ABSORB_INSTEAD_OF_FREE_SURFACE  = .false.
+
+# save AVS or OpenDX movies
+MOVIE_SURFACE                   = .false.
+MOVIE_VOLUME                    = .false.
+NTSTEP_BETWEEN_FRAMES           = 200
+CREATE_SHAKEMAP                 = .false.
+SAVE_DISPLACEMENT               = .false.
+USE_HIGHRES_FOR_MOVIES          = .false.
+HDUR_MOVIE                      = 0.0
+
+# save AVS or OpenDX mesh files to check the mesh
+SAVE_MESH_FILES                 = .true.
+
+# path to store the local database file on each node
+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
+
+# interval in time steps for writing of seismograms
+NTSTEP_BETWEEN_OUTPUT_SEISMOS   = 10000
+
+# interval in time steps for reading adjoint traces
+NTSTEP_BETWEEN_READ_ADJSRC      = 0      # 0 = read the whole adjoint sources at the same time
+
+# 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
+# in which the source is a vertical force, normal force, inclined force, impact etc.
+# If this flag is turned on, the FORCESOLUTION file must be edited by precising:
+# - the corresponding time-shift parameter,
+# - the half duration parameter of the source,
+# - the coordinates of the source,
+# - the magnitude of the force source,
+# - the components of a (non-unitary) direction vector for the force source in the E/N/Z_UP basis.
+# 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.
+USE_FORCE_POINT_SOURCE          = .false.
+
+# 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
+GPU_MODE                        = .false.
+

Added: seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/DATA/STATIONS
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/DATA/STATIONS	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/DATA/STATIONS	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,8 @@
+X10 DB 46.197 -122.186 0.0 0.0
+X20 DB 46.2 -122.2 0.0 0.0
+X30 DB 46.29 -122.2 0.0 0.0
+X40 DB 46.11 -122.2 0.0 0.0
+Y10 DB 46.197 -122.186 0.0 0.0
+Y20 DB 46.2 -122.2 0.0 0.0
+Y30 DB 46.2 -122.29 0.0 0.0
+Y40 DB 46.2 -122.11 0.0 0.0

Modified: seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/process.sh
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/process.sh	2012-10-25 14:18:46 UTC (rev 20922)
+++ seismo/3D/SPECFEM3D/trunk/examples/Mount_StHelens/process.sh	2012-10-25 14:58:44 UTC (rev 20923)
@@ -27,15 +27,15 @@
 echo
 
 mkdir -p bin
-mkdir -p OUTPUT_FILES
 mkdir -p OUTPUT_FILES/DATABASES_MPI
 
-rm -rf OUTPUT_FILES/*
+rm -f OUTPUT_FILES/*
 rm -rf OUTPUT_FILES/DATABASES_MPI/*
 
 # compiles executables in root directory
 cd ../../
-make >& $currentdir/tmp.log
+make clean
+make > $currentdir/tmp.log
 cd $currentdir
 
 # links executables

Added: seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/DATA/CMTSOLUTION
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/DATA/CMTSOLUTION	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/DATA/CMTSOLUTION	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,13 @@
+PDE  1999 01 01 00 00 00.00  67000 67000 -25000 4.2 4.2 hom_explosion
+event name:       hom_explosion
+time shift:       0.0000
+half duration:    5.0
+latitude:       67000.0
+longitude:      67000.0
+depth:          25.0
+Mrr:       1.000000e+23
+Mtt:       1.000000e+23
+Mpp:       1.000000e+23
+Mrt:       0.000000
+Mrp:       0.000000
+Mtp:       0.000000

Added: seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/DATA/FORCESOLUTION
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/DATA/FORCESOLUTION	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/DATA/FORCESOLUTION	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,10 @@
+FORCE  001
+time shift:     0.0000
+hdur:           0.5
+latitude:       67000.0
+longitude:      67000.0
+depth:          25.0
+factor force source:             1.d15
+component dir vect source E:     1.d0
+component dir vect source N:     -2.d0
+component dir vect source Z_UP:  -1.d0

Added: seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/DATA/Par_file
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/DATA/Par_file	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/DATA/Par_file	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,98 @@
+# simulation input parameters
+#
+# forward or adjoint simulation
+# 1 = forward, 2 = adjoint, 3 = both simultaneously
+SIMULATION_TYPE                 = 1
+# 0 = earthquake simulation,  1/2/3 = three steps in noise simulation
+NOISE_TOMOGRAPHY                = 0
+SAVE_FORWARD                    = .false.
+
+# UTM projection parameters
+UTM_PROJECTION_ZONE             = 11
+SUPPRESS_UTM_PROJECTION         = .true.
+
+# number of MPI processors
+NPROC                           = 4
+
+# time step parameters
+NSTEP                           = 1000
+DT                              = 0.05
+
+# number of nodes for 2D and 3D shape functions for hexahedra
+# we use either 8-node mesh elements (bricks) or 27-node elements.
+# If you use our internal mesher, the only option is 8-node bricks (27-node elements are not supported)
+# CUBIT does not support HEX27 elements either (it can generate them, but they are flat, i.e. identical to HEX8).
+# To generate HEX27 elements with curvature properly taken into account, you can use Gmsh http://geuz.org/gmsh/
+NGNOD 	      	    	     	= 8
+
+# models:
+# available options are:
+#   default (model parameters described by mesh properties)
+# 1D models available are:
+#   1d_prem,1d_socal,1d_cascadia
+# 3D models available are:
+#   aniso,external,gll,salton_trough,tomo
+MODEL                           = default
+
+# parameters describing the model
+OCEANS                          = .false.
+TOPOGRAPHY                      = .false.
+ATTENUATION                     = .false.
+USE_OLSEN_ATTENUATION           = .false.
+ANISOTROPY                      = .false.
+GRAVITY                         = .false.
+
+# absorbing boundary conditions for a regional simulation
+ABSORBING_CONDITIONS            = .false.
+
+# absorbing top surface (defined in mesh as 'free_surface_file')
+ABSORB_INSTEAD_OF_FREE_SURFACE  = .false.
+
+# save AVS or OpenDX movies
+MOVIE_SURFACE                   = .false.
+MOVIE_VOLUME                    = .false.
+NTSTEP_BETWEEN_FRAMES           = 200
+CREATE_SHAKEMAP                 = .false.
+SAVE_DISPLACEMENT               = .false.
+USE_HIGHRES_FOR_MOVIES          = .false.
+HDUR_MOVIE                      = 0.0
+
+# save AVS or OpenDX mesh files to check the mesh
+SAVE_MESH_FILES                 = .true.
+
+# path to store the local database file on each node
+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
+
+# interval in time steps for writing of seismograms
+NTSTEP_BETWEEN_OUTPUT_SEISMOS   = 10000
+
+# interval in time steps for reading adjoint traces
+# 0 = read the whole adjoint sources at the same time
+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
+# in which the source is a vertical force, normal force, inclined force, impact etc.
+# If this flag is turned on, the FORCESOLUTION file must be edited by precising:
+# - the corresponding time-shift parameter,
+# - the half duration parameter of the source,
+# - the coordinates of the source,
+# - the magnitude of the force source,
+# - the components of a (non-unitary) direction vector for the force source in the E/N/Z_UP basis.
+# 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.
+USE_FORCE_POINT_SOURCE          = .false.
+
+# 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
+GPU_MODE                        = .false.
+

Added: seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/DATA/STATIONS
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/DATA/STATIONS	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/DATA/STATIONS	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,6 @@
+X1 DB 67000.00 0.000000 0.0 0.0
+X10 DB 67000.00 10767.86 0.0 0.0
+X20 DB 67000.00 22732.14 0.0 0.0
+X30 DB 67000.00 34696.43 0.0 0.0
+X40 DB 67000.00 46660.71 0.0 0.0
+X50 DB 67000.00 58625.00 0.0 0.0

Added: seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/DATA/STATIONS_ADJOINT
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/DATA/STATIONS_ADJOINT	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/DATA/STATIONS_ADJOINT	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1 @@
+X20 DB 67000.00 22732.14 0.0 0.0

Deleted: 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	2012-10-25 14:18:46 UTC (rev 20922)
+++ seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/HOWTO_run_this_example.txt	2012-10-25 14:58:44 UTC (rev 20923)
@@ -1,10 +0,0 @@
-
-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 OUTPUT_FILES/DATABASES_MPI
-
-mpirun -np 2 ./bin/xgenerate_databases
-
-mpirun -np 2 ./bin/xspecfem3D
-

Added: seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/README
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/README	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX27/README	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,10 @@
+
+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 OUTPUT_FILES/DATABASES_MPI
+
+mpirun -np 2 ./bin/xgenerate_databases
+
+mpirun -np 2 ./bin/xspecfem3D
+

Added: seismo/3D/SPECFEM3D/trunk/examples/homogeneous_poroelastic/DATA/CMTSOLUTION
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/homogeneous_poroelastic/DATA/CMTSOLUTION	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/homogeneous_poroelastic/DATA/CMTSOLUTION	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,13 @@
+PDE  1999 01 01 00 00 00.00  100 150 -150 4.2 4.2 hom_explosion
+event name:       hom_explosion
+time shift:       0.0000
+half duration:  0.003  
+latitude:       100.0
+longitude:      150.0
+depth:          0.150
+Mrr:       1.000000e+24
+Mtt:       1.000000e+24
+Mpp:       1.000000e+24
+Mrt:       0.000000
+Mrp:       0.000000
+Mtp:       0.000000

Added: seismo/3D/SPECFEM3D/trunk/examples/homogeneous_poroelastic/DATA/FORCESOLUTION
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/homogeneous_poroelastic/DATA/FORCESOLUTION	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/homogeneous_poroelastic/DATA/FORCESOLUTION	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,10 @@
+FORCE  001
+time shift:     0.0000
+hdur:           0.5
+latitude:       100.0
+longitude:      150.0
+depth:          0.150
+factor force source:             1.d15
+component dir vect source E:     1.d0
+component dir vect source N:     -2.d0
+component dir vect source Z_UP:  -1.d0

Added: seismo/3D/SPECFEM3D/trunk/examples/homogeneous_poroelastic/DATA/Par_file
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/homogeneous_poroelastic/DATA/Par_file	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/homogeneous_poroelastic/DATA/Par_file	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,97 @@
+*# simulation input parameters
+#
+# forward or adjoint simulation
+# 1 = forward, 2 = adjoint, 3 = both simultaneously
+SIMULATION_TYPE                 = 1
+# 0 = earthquake simulation,  1/2/3 = three steps in noise simulation
+NOISE_TOMOGRAPHY                = 0
+SAVE_FORWARD                    = .true.
+
+# UTM projection parameters
+UTM_PROJECTION_ZONE             = 11
+SUPPRESS_UTM_PROJECTION         = .true.
+
+# number of MPI processors
+NPROC                           = 14
+
+# time step parameters
+NSTEP                           = 4000
+DT                              = 5.d-5 #0.5d-3
+
+# number of nodes for 2D and 3D shape functions for hexahedra
+# we use either 8-node mesh elements (bricks) or 27-node elements.
+# If you use our internal mesher, the only option is 8-node bricks (27-node elements are not supported)
+# CUBIT does not support HEX27 elements either (it can generate them, but they are flat, i.e. identical to HEX8).
+# To generate HEX27 elements with curvature properly taken into account, you can use Gmsh http://geuz.org/gmsh/
+NGNOD 	      	    	     	= 8
+
+# models:
+# available options are:
+#   default (model parameters described by mesh properties)
+# 1D models available are:
+#   1d_prem,1d_socal,1d_cascadia
+# 3D models available are:
+#   aniso,external,gll,salton_trough,tomo
+MODEL                           = default
+
+# parameters describing the model
+OCEANS                          = .false.
+TOPOGRAPHY                      = .false.
+ATTENUATION                     = .false.
+USE_OLSEN_ATTENUATION           = .false.
+ANISOTROPY                      = .false.
+GRAVITY                         = .false.
+
+# absorbing boundary conditions for a regional simulation
+ABSORBING_CONDITIONS            = .false.
+
+# absorbing top surface (defined in mesh as 'free_surface_file')
+ABSORB_INSTEAD_OF_FREE_SURFACE  = .false.
+
+# save AVS or OpenDX movies
+MOVIE_SURFACE                   = .false.
+MOVIE_VOLUME                    = .false.
+NTSTEP_BETWEEN_FRAMES           = 100
+CREATE_SHAKEMAP                 = .false.
+SAVE_DISPLACEMENT               = .false.
+USE_HIGHRES_FOR_MOVIES          = .false.
+HDUR_MOVIE                      = 0.0
+
+# save AVS or OpenDX mesh files to check the mesh
+SAVE_MESH_FILES                 = .true.
+
+# path to store the local database file on each node
+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
+
+# interval in time steps for writing of seismograms
+NTSTEP_BETWEEN_OUTPUT_SEISMOS   = 10000
+
+# interval in time steps for reading adjoint traces
+# # 0 = read the whole adjoint sources at the same time
+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
+# in which the source is a vertical force, normal force, inclined force, impact etc.
+# If this flag is turned on, the FORCESOLUTION file must be edited by precising:
+# - the corresponding time-shift parameter,
+# - the half duration parameter of the source,
+# - the coordinates of the source,
+# - the magnitude of the force source,
+# - the components of a (non-unitary) direction vector for the force source in the E/N/Z_UP basis.
+# 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.
+USE_FORCE_POINT_SOURCE          = .false.
+
+# 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
+GPU_MODE                        = .false.

Added: seismo/3D/SPECFEM3D/trunk/examples/homogeneous_poroelastic/DATA/STATIONS
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/homogeneous_poroelastic/DATA/STATIONS	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/homogeneous_poroelastic/DATA/STATIONS	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,5 @@
+X1 DB 150.00 240.000000 0.0 150.0
+X2 DB 150.00 220.000000 0.0 150.0
+X3 DB 150.00 200.000000 0.0 150.0
+X4 DB 150.00 180.000000 0.0 150.0
+X5 DB 150.00 160.000000 0.0 150.0

Added: seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/DATA/CMTSOLUTION
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/DATA/CMTSOLUTION	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/DATA/CMTSOLUTION	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,13 @@
+PDE  1999 01 01 00 00 00.00  67000 67000 -25000 4.2 4.2 FIG8
+event name:       FIG8_vertical
+time shift:       0.0000
+half duration:    0.4
+latitude:       67000.0
+longitude:      67000.0
+depth:         25.05
+Mrr:       1.000000e+23
+Mtt:       0.000000
+Mpp:       0.000000
+Mrt:       0.000000
+Mrp:       0.000000
+Mtp:       0.000000

Added: seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/DATA/FORCESOLUTION
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/DATA/FORCESOLUTION	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/DATA/FORCESOLUTION	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,10 @@
+FORCE  001
+time shift:     0.0000
+hdur:           0.5
+latitude:       67000.0
+longitude:      67000.0
+depth:          25.05
+factor force source:             1.d15
+component dir vect source E:     1.d0
+component dir vect source N:     -2.d0
+component dir vect source Z_UP:  -1.d0

Added: seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/DATA/Par_file
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/DATA/Par_file	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/DATA/Par_file	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,97 @@
+# simulation input parameters
+#
+# forward or adjoint simulation
+# 1 = forward, 2 = adjoint, 3 = both simultaneously
+SIMULATION_TYPE                 = 1
+# 0 = earthquake simulation,  1/2/3 = three steps in noise simulation
+NOISE_TOMOGRAPHY                = 0
+SAVE_FORWARD                    = .false.
+
+# UTM projection parameters
+UTM_PROJECTION_ZONE             = 11
+SUPPRESS_UTM_PROJECTION         = .true.
+
+# number of MPI processors
+NPROC                           = 4
+
+# time step parameters
+NSTEP                           = 3000
+DT                              = 0.0075
+
+# number of nodes for 2D and 3D shape functions for hexahedra
+# we use either 8-node mesh elements (bricks) or 27-node elements.
+# If you use our internal mesher, the only option is 8-node bricks (27-node elements are not supported)
+# CUBIT does not support HEX27 elements either (it can generate them, but they are flat, i.e. identical to HEX8).
+# To generate HEX27 elements with curvature properly taken into account, you can use Gmsh http://geuz.org/gmsh/
+NGNOD 	      	    	     	= 8
+
+# models:
+# available options are:
+#   default (model parameters described by mesh properties)
+# 1D models available are:
+#   1d_prem,1d_socal,1d_cascadia
+# 3D models available are:
+#   aniso,external,gll,salton_trough,tomo
+MODEL                           = default
+
+# parameters describing the model
+OCEANS                          = .false.
+TOPOGRAPHY                      = .false.
+ATTENUATION                     = .false.
+USE_OLSEN_ATTENUATION           = .false.
+ANISOTROPY                      = .false.
+GRAVITY                         = .false.
+
+# absorbing boundary conditions for a regional simulation
+ABSORBING_CONDITIONS            = .true.
+
+# absorbing top surface (defined in mesh as 'free_surface_file')
+ABSORB_INSTEAD_OF_FREE_SURFACE  = .false.
+
+# save AVS or OpenDX movies
+MOVIE_SURFACE                   = .false.
+MOVIE_VOLUME                    = .false.
+NTSTEP_BETWEEN_FRAMES           = 200
+CREATE_SHAKEMAP                 = .false.
+SAVE_DISPLACEMENT               = .false.
+USE_HIGHRES_FOR_MOVIES          = .false.
+HDUR_MOVIE                      = 0.0
+
+# save AVS or OpenDX mesh files to check the mesh
+SAVE_MESH_FILES                 = .true.
+
+# path to store the local database file on each node
+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
+
+# interval in time steps for writing of seismograms
+NTSTEP_BETWEEN_OUTPUT_SEISMOS   = 10000
+
+# interval in time steps for reading adjoint traces
+NTSTEP_BETWEEN_READ_ADJSRC      = 0      # 0 = read the whole adjoint sources at the same time
+
+# 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
+# in which the source is a vertical force, normal force, inclined force, impact etc.
+# If this flag is turned on, the FORCESOLUTION file must be edited by precising:
+# - the corresponding time-shift parameter,
+# - the half duration parameter of the source,
+# - the coordinates of the source,
+# - the magnitude of the force source,
+# - the components of a (non-unitary) direction vector for the force source in the E/N/Z_UP basis.
+# 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.
+USE_FORCE_POINT_SOURCE          = .false.
+
+# 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
+GPU_MODE                        = .false.
+

Added: seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/DATA/STATIONS
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/DATA/STATIONS	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/DATA/STATIONS	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,2 @@
+X31 DB 67000.00 35892.86 0.0 0.0
+X55 DB 67000.00 64607.14 0.0 0.0

Added: seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/DATA/STATIONS_X
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/DATA/STATIONS_X	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/DATA/STATIONS_X	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,112 @@
+X1 DB 67000.00 0.000000 0.0 0.0
+X2 DB 67000.00 1196.429 0.0 0.0
+X3 DB 67000.00 2392.857 0.0 0.0
+X4 DB 67000.00 3589.286 0.0 0.0
+X5 DB 67000.00 4785.714 0.0 0.0
+X6 DB 67000.00 5982.143 0.0 0.0
+X7 DB 67000.00 7178.571 0.0 0.0
+X8 DB 67000.00 8375.000 0.0 0.0
+X9 DB 67000.00 9571.429 0.0 0.0
+X10 DB 67000.00 10767.86 0.0 0.0
+X11 DB 67000.00 11964.29 0.0 0.0
+X12 DB 67000.00 13160.71 0.0 0.0
+X13 DB 67000.00 14357.14 0.0 0.0
+X14 DB 67000.00 15553.57 0.0 0.0
+X15 DB 67000.00 16750.00 0.0 0.0
+X16 DB 67000.00 17946.43 0.0 0.0
+X17 DB 67000.00 19142.86 0.0 0.0
+X18 DB 67000.00 20339.29 0.0 0.0
+X19 DB 67000.00 21535.71 0.0 0.0
+X20 DB 67000.00 22732.14 0.0 0.0
+X21 DB 67000.00 23928.57 0.0 0.0
+X22 DB 67000.00 25125.00 0.0 0.0
+X23 DB 67000.00 26321.43 0.0 0.0
+X24 DB 67000.00 27517.86 0.0 0.0
+X25 DB 67000.00 28714.29 0.0 0.0
+X26 DB 67000.00 29910.71 0.0 0.0
+X27 DB 67000.00 31107.14 0.0 0.0
+X28 DB 67000.00 32303.57 0.0 0.0
+X29 DB 67000.00 33500.00 0.0 0.0
+X30 DB 67000.00 34696.43 0.0 0.0
+X31 DB 67000.00 35892.86 0.0 0.0
+X32 DB 67000.00 37089.29 0.0 0.0
+X33 DB 67000.00 38285.71 0.0 0.0
+X34 DB 67000.00 39482.14 0.0 0.0
+X35 DB 67000.00 40678.57 0.0 0.0
+X36 DB 67000.00 41875.00 0.0 0.0
+X37 DB 67000.00 43071.43 0.0 0.0
+X38 DB 67000.00 44267.86 0.0 0.0
+X39 DB 67000.00 45464.29 0.0 0.0
+X40 DB 67000.00 46660.71 0.0 0.0
+X41 DB 67000.00 47857.14 0.0 0.0
+X42 DB 67000.00 49053.57 0.0 0.0
+X43 DB 67000.00 50250.00 0.0 0.0
+X44 DB 67000.00 51446.43 0.0 0.0
+X45 DB 67000.00 52642.86 0.0 0.0
+X46 DB 67000.00 53839.29 0.0 0.0
+X47 DB 67000.00 55035.71 0.0 0.0
+X48 DB 67000.00 56232.14 0.0 0.0
+X49 DB 67000.00 57428.57 0.0 0.0
+X50 DB 67000.00 58625.00 0.0 0.0
+X51 DB 67000.00 59821.43 0.0 0.0
+X52 DB 67000.00 61017.86 0.0 0.0
+X53 DB 67000.00 62214.29 0.0 0.0
+X54 DB 67000.00 63410.71 0.0 0.0
+X55 DB 67000.00 64607.14 0.0 0.0
+X56 DB 67000.00 65803.57 0.0 0.0
+X57 DB 67000.00 67000.00 0.0 0.0
+X58 DB 67000.00 68196.43 0.0 0.0
+X59 DB 67000.00 69392.86 0.0 0.0
+X60 DB 67000.00 70589.29 0.0 0.0
+X61 DB 67000.00 71785.71 0.0 0.0
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Added: seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/DATA/STATIONS_Y
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/DATA/STATIONS_Y	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/DATA/STATIONS_Y	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,112 @@
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Modified: seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/README
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/README	2012-10-25 14:18:46 UTC (rev 20922)
+++ seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/README	2012-10-25 14:58:44 UTC (rev 20923)
@@ -107,10 +107,8 @@
 
 5. run simulation:
 
-    - compile specfem3D:
+    - compile and run specfem3D:
       > make xspecfem3D
-
-    - submit job script:
       > qsub go_solver_pbs.bash
 
     note: simulation will take about 25 minutes and generate

Modified: seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/process.sh
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/process.sh	2012-10-25 14:18:46 UTC (rev 20922)
+++ seismo/3D/SPECFEM3D/trunk/examples/layered_halfspace/process.sh	2012-10-25 14:58:44 UTC (rev 20923)
@@ -28,12 +28,15 @@
 echo
 
 mkdir -p bin
-mkdir -p OUTPUT_FILES
 mkdir -p OUTPUT_FILES/DATABASES_MPI
 
-rm -rf OUTPUT_FILES/*
+rm -f OUTPUT_FILES/*
 rm -rf OUTPUT_FILES/DATABASES_MPI/*
 
+# compiles executables in root directory
+cd ../../
+make clean
+make > $currentdir/tmp.log
 cd $currentdir
 
 # links executables
@@ -44,17 +47,17 @@
 cp ../../../bin/xspecfem3D ./
 cd ../
 
+# stores setup
+cp DATA/Par_file OUTPUT_FILES/
+cp DATA/CMTSOLUTION OUTPUT_FILES/
+cp DATA/STATIONS OUTPUT_FILES/
+
 # decomposes mesh
 echo
 echo "  decomposing mesh..."
 echo
 ./bin/xdecompose_mesh_SCOTCH $NPROC MESH/ OUTPUT_FILES/DATABASES_MPI/
 
-# stores setup
-cp DATA/Par_file OUTPUT_FILES/
-cp DATA/CMTSOLUTION OUTPUT_FILES/
-cp DATA/STATIONS OUTPUT_FILES/
-
 # runs database generation
 echo
 echo "  running database generation..."

Modified: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/many_interfaces/README
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/many_interfaces/README	2012-10-25 14:18:46 UTC (rev 20922)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/many_interfaces/README	2012-10-25 14:58:44 UTC (rev 20923)
@@ -29,7 +29,6 @@
 2. compile and run internal mesher
 
    > make xmeshfem3D
-
    > qsub go_mesher_pbs.bash
 
    - this should generate "proc000***_Database" files in OUTPUT_FILES/DATABASES_MPI/.
@@ -39,23 +38,19 @@
 
 3. generate databases:
 
-   - compile generate_databases in directory SPECFEM3D/:
+   - compile and run generate_databases in directory SPECFEM3D/:
      > make xgenerate_databases
-
-   - submit job script:
      > qsub go_generate_databases_pbs.bash
 
-     this job will take about XX minutes and will create binary mesh files,
-     e.g. "proc000***_external_mesh.bin", in directory OUTPUT_FILES/DATABASES_MPI/.
+     this will create binary mesh files, e.g. "proc000***_external_mesh.bin"
+     in directory OUTPUT_FILES/DATABASES_MPI/.
 
-     Optional: If you have paraview, load the .vtk files (see simple_model.png).
+     optional: If you have paraview, load the .vtk files (see simple_model.png).
 
 4. run simulation:
 
-   - compile specfem3D:
+   - compile and run specfem3D:
      > make xspecfem3D
-
-   - submit job script:
      > qsub go_solver_pbs.bash
 
    - the job should take about 70 minutes

Modified: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/simple_model/README
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/simple_model/README	2012-10-25 14:18:46 UTC (rev 20922)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/simple_model/README	2012-10-25 14:58:44 UTC (rev 20923)
@@ -15,12 +15,8 @@
 1. Set up input files.
 
    > cd SPECFEM3D
-   > rsync -av examples/meshfem3D_examples/simple_model/ DATA/meshfem3D_files/
+   > rsync -av examples/meshfem3D_examples/simple_model/DATA DATA
 
-   > cd DATA/meshfem3D_files/
-   > cp Par_file CMTSOLUTION STATIONS ..
-   > cd SPECFEM3D
-
    - adapt the submission scripts for the appropriate queues and number of cores:
      go_mesher_pbs.bash, go_generate_databases_pbs.bash, go_solver_pbs.bash
 
@@ -29,7 +25,6 @@
 2. compile and run internal mesher
 
    > make xmeshfem3D
-
    > qsub go_mesher_pbs.bash
 
    This should generate these files in OUTPUT_FILES/DATABASES_MPI/:
@@ -52,23 +47,19 @@
 
 3. generate databases:
 
-   - compile generate_databases in directory SPECFEM3D/:
+   - compile and run generate_databases in directory SPECFEM3D/:
      > make xgenerate_databases
-
-   - submit job script:
      > qsub go_generate_databases_pbs.bash
 
      this will create binary mesh files, e.g. "proc000***_external_mesh.bin"
      in directory OUTPUT_FILES/DATABASES_MPI/.
 
-     Optional: If you have paraview, load the .vtk files (see simple_model.png).
+     optional: If you have paraview, load the .vtk files (see simple_model.png).
 
 4. run simulation:
 
-   - compile specfem3D:
+   - compile and run specfem3D:
      > make xspecfem3D
-
-   - submit job script:
      > qsub go_solver_pbs.bash
 
    - the job should take about 10 minutes

Added: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/CMTSOLUTION
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/CMTSOLUTION	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/CMTSOLUTION	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,13 @@
+PDE 2001  9  9 23 59 17.78  34.0745 -118.3792   6.4 4.2 4.2 HOLLYWOOD POLET SEM
+event name:     9703873
+time shift:      0.0000
+half duration:   0.3114
+latitude:       34.0745
+longitude:    -118.3792
+depth:           5.4000
+Mrr:      -0.002000e+23
+Mtt:      -0.064000e+23
+Mpp:       0.066000e+23
+Mrt:      -0.090000e+23
+Mrp:      -0.002000e+23
+Mtp:       0.188000e+23

Added: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/FORCESOLUTION
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/FORCESOLUTION	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/FORCESOLUTION	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,10 @@
+FORCE  001
+time shift:     0.0000
+hdur:           0.5
+latitude:       34.0745
+longitude:      -118.3792
+depth:          5.4000
+factor force source:             1.d15
+component dir vect source E:     1.d0
+component dir vect source N:     -2.d0
+component dir vect source Z_UP:  -1.d0

Added: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/Par_file
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/Par_file	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/Par_file	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,97 @@
+# simulation input parameters
+#
+# forward or adjoint simulation
+# 1 = forward, 2 = adjoint, 3 = both simultaneously
+SIMULATION_TYPE                 = 1
+# 0 = earthquake simulation,  1/2/3 = three steps in noise simulation
+NOISE_TOMOGRAPHY                = 0
+SAVE_FORWARD                    = .false.
+
+# UTM projection parameters
+UTM_PROJECTION_ZONE             = 11
+SUPPRESS_UTM_PROJECTION         = .false.
+
+# number of MPI processors
+NPROC                           = 1
+
+# time step parameters
+NSTEP                           = 840
+DT                              = 0.012
+
+# number of nodes for 2D and 3D shape functions for hexahedra
+# we use either 8-node mesh elements (bricks) or 27-node elements.
+# If you use our internal mesher, the only option is 8-node bricks (27-node elements are not supported)
+# CUBIT does not support HEX27 elements either (it can generate them, but they are flat, i.e. identical to HEX8).
+# To generate HEX27 elements with curvature properly taken into account, you can use Gmsh http://geuz.org/gmsh/
+NGNOD 	      	    	     	= 8
+
+# models:
+# available options are:
+#   default (model parameters described by mesh properties)
+# 1D models available are:
+#   1d_prem,1d_socal,1d_cascadia
+# 3D models available are:
+#   aniso,external,gll,salton_trough,tomo
+MODEL                           = default
+
+# parameters describing the model
+OCEANS                          = .false.
+TOPOGRAPHY                      = .false.
+ATTENUATION                     = .false.
+USE_OLSEN_ATTENUATION           = .false.
+ANISOTROPY                      = .false.
+GRAVITY                         = .false.
+
+# absorbing boundary conditions for a regional simulation
+ABSORBING_CONDITIONS            = .true.
+
+# absorbing top surface (defined in mesh as 'free_surface_file')
+ABSORB_INSTEAD_OF_FREE_SURFACE  = .false.
+
+# save AVS or OpenDX movies
+MOVIE_SURFACE                   = .false.
+MOVIE_VOLUME                    = .false.
+NTSTEP_BETWEEN_FRAMES           = 200
+CREATE_SHAKEMAP                 = .false.
+SAVE_DISPLACEMENT               = .false.
+USE_HIGHRES_FOR_MOVIES          = .false.
+HDUR_MOVIE                      = 0.0
+
+# save AVS or OpenDX mesh files to check the mesh
+SAVE_MESH_FILES                 = .true.
+
+# path to store the local database file on each node
+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
+
+# interval in time steps for writing of seismograms
+NTSTEP_BETWEEN_OUTPUT_SEISMOS   = 10000
+
+# interval in time steps for reading adjoint traces
+NTSTEP_BETWEEN_READ_ADJSRC      = 0      # 0 = read the whole adjoint sources at the same time
+
+# 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
+# in which the source is a vertical force, normal force, inclined force, impact etc.
+# If this flag is turned on, the FORCESOLUTION file must be edited by precising:
+# - the corresponding time-shift parameter,
+# - the half duration parameter of the source,
+# - the coordinates of the source,
+# - the magnitude of the force source,
+# - the components of a (non-unitary) direction vector for the force source in the E/N/Z_UP basis.
+# 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.
+USE_FORCE_POINT_SOURCE          = .false.
+
+# 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
+GPU_MODE                        = .false.
+

Added: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/STATIONS
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/STATIONS	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/STATIONS	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,30 @@
+24851 CE       34.070000     -118.346000        0.000000        0.000000
+24853 CE       34.077000     -118.286000        0.000000        0.000000
+K851 CE       34.070000     -118.346000        0.000000        0.000000
+K853 CE       34.077000     -118.286000        0.000000        0.000000
+BVH CI       34.076180     -118.395900        0.000000        0.000000
+CAB CI       34.155730     -118.640930        0.000000        0.000000
+DJJ CI       34.106180     -118.455050        0.000000        0.000000
+DJJB CI       34.106180     -118.455050        0.000000        0.000000
+GR2 CI       34.118300     -118.299400        0.000000        0.000000
+GRF CI       34.119200     -118.300400        0.000000        0.000000
+LAF CI       33.868890     -118.331430        0.000000        0.000000
+LAX CI       33.943820     -118.413900        0.000000        0.000000
+LCG CI       34.000330     -118.377940        0.000000        0.000000
+PDR CI       33.962730     -118.437020        0.000000        0.000000
+SMF CI       34.021590     -118.446750        0.000000        0.000000
+SMS CI       34.014380     -118.456170        0.000000        0.000000
+SPF CI       34.059330     -118.646140        0.000000        0.000000
+TCF CI       34.083770     -118.599000        0.000000        0.000000
+USC CI       34.019190     -118.286310        0.000000        0.000000
+WNS CI       34.115000     -118.380000        0.000000        0.000000
+WTT CI       33.948690     -118.255470        0.000000        0.000000
+FABS FA       34.066670     -118.571113        0.000000        0.000000
+5081 NP       34.084000     -118.600000        0.000000        0.000000
+5399 NP       33.943000     -118.411000        0.000000        0.000000
+5402 NP       34.076000     -118.395000        0.000000        0.000000
+5404 NP       34.155000     -118.641000        0.000000        0.000000
+BVH NP       34.076180     -118.395900        0.000000        0.000000
+GRF NP       34.119200     -118.300400        0.000000        0.000000
+LAX NP       33.943820     -118.413900        0.000000        0.000000
+TCF NP       34.083770     -118.599000        0.000000        0.000000

Added: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/Mesh_Par_file
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/Mesh_Par_file	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/Mesh_Par_file	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,59 @@
+
+# coordinates of mesh block in latitude/longitude and depth in km
+LATITUDE_MIN                    = 33.790d0
+LATITUDE_MAX                    = 34.157d0
+LONGITUDE_MIN                   = -118.728d0
+LONGITUDE_MAX                   = -118.237d0
+DEPTH_BLOCK_KM                  = 60.d0
+UTM_PROJECTION_ZONE             = 11
+SUPPRESS_UTM_PROJECTION         = .false.
+
+# file that contains the interfaces of the model / mesh
+INTERFACES_FILE                 = interfaces.dat
+
+# number of elements at the surface along edges of the mesh at the surface
+# (must be 8 * multiple of NPROC below if mesh is not regular and contains mesh doublings)
+# (must be multiple of NPROC below if mesh is regular)
+NEX_XI                          = 24
+NEX_ETA                         = 24
+
+# number of MPI processors along xi and eta (can be different)
+NPROC_XI                        = 1
+NPROC_ETA                       = 1
+
+# Regular/irregular mesh
+USE_REGULAR_MESH                = .false.
+# Only for irregular meshes, number of doubling layers (1 or 2) and their position
+NDOUBLINGS                      = 2
+# NZ_DOUGLING_1 is the parameter to set up if there is only one doubling layer
+NZ_DOUGLING_1                   = 6
+NZ_DOUGLING_2                   = 9
+
+# create mesh files for visualisation or further checking
+CREATE_ABAQUS_FILES             = .true.
+CREATE_DX_FILES                 = .true.
+CREATE_VTK_FILES                = .false.
+
+# path to store the databases files
+LOCAL_PATH                      = ../OUTPUT_FILES/DATABASES_MPI
+
+# number of materials
+NMATERIALS                      = 4
+# define the different materials in the model as :
+# #material_id  #rho  #vp  #vs  #Q  #anisotropy_flag #domain_id
+#     Q                : quality factor
+#     anisotropy_flag  : 0=no anisotropy/ 1,2,.. check with implementation in aniso_model.f90
+#     domain_id        : 1=acoustic / 2=elastic
+1  3000  7800  4500 0.0  0  2
+2  2800  6700  3870 0.0  0  2
+3  2670  6300  3640 0.0  0  2
+4  2400  5500  3180 0.0  0  2
+# number of regions
+NREGIONS                        = 4
+# define the different regions of the model as :
+#NEX_XI_BEGIN  #NEX_XI_END  #NEX_ETA_BEGIN  #NEX_ETA_END  #NZ_BEGIN #NZ_END  #material_id
+1              24            1               24             1          3       1
+1              24            1               24             4          6       2
+1              24            1               24             7          9       3
+1              24            1               24             10        12       4
+

Added: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/Mesh_Par_file_001
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/Mesh_Par_file_001	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/Mesh_Par_file_001	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,59 @@
+
+# coordinates of mesh block in latitude/longitude and depth in km
+LATITUDE_MIN                    = 33.790d0
+LATITUDE_MAX                    = 34.157d0
+LONGITUDE_MIN                   = -118.728d0
+LONGITUDE_MAX                   = -118.237d0
+DEPTH_BLOCK_KM                  = 60.d0
+UTM_PROJECTION_ZONE             = 11
+SUPPRESS_UTM_PROJECTION         = .false.
+
+# file that contains the interfaces of the model / mesh
+INTERFACES_FILE                 = interfaces.dat
+
+# number of elements at the surface along edges of the mesh at the surface
+# (must be 8 * multiple of NPROC below if mesh is not regular and contains mesh doublings)
+# (must be multiple of NPROC below if mesh is regular)
+NEX_XI                          = 24
+NEX_ETA                         = 24
+
+# number of MPI processors along xi and eta (can be different)
+NPROC_XI                        = 1
+NPROC_ETA                       = 1
+
+# Regular/irregular mesh
+USE_REGULAR_MESH                = .false.
+# Only for irregular meshes, number of doubling layers (1 or 2) and their position
+NDOUBLINGS                      = 2
+# NZ_DOUGLING_1 is the parameter to set up if there is only one doubling layer
+NZ_DOUGLING_1                   = 6
+NZ_DOUGLING_2                   = 9
+
+# create mesh files for visualisation or further checking
+CREATE_ABAQUS_FILES             = .true.
+CREATE_DX_FILES                 = .true.
+CREATE_VTK_FILES                = .false.
+
+# path to store the databases files
+LOCAL_PATH                      = ../OUTPUT_FILES/DATABASES_MPI
+
+# number of materials
+NMATERIALS                      = 4
+# define the different materials in the model as :
+# #material_id  #rho  #vp  #vs  #Q  #anisotropy_flag #domain_id
+#     Q                : quality factor
+#     anisotropy_flag  : 0=no anisotropy/ 1,2,.. check with implementation in aniso_model.f90
+#     domain_id        : 1=acoustic / 2=elastic
+1  3000  7800  4500 0.0  0  2
+2  2800  6700  3870 0.0  0  2
+3  2670  6300  3640 0.0  0  2
+4  2400  5500  3180 0.0  0  2
+# number of regions
+NREGIONS                        = 4
+# define the different regions of the model as :
+#NEX_XI_BEGIN  #NEX_XI_END  #NEX_ETA_BEGIN  #NEX_ETA_END  #NZ_BEGIN #NZ_END  #material_id
+1              24            1               24             1          3       1
+1              24            1               24             4          6       2
+1              24            1               24             7          9       3
+1              24            1               24             10        12       4
+

Added: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/Mesh_Par_file_042
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/Mesh_Par_file_042	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/Mesh_Par_file_042	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,59 @@
+
+# coordinates of mesh block in latitude/longitude and depth in km
+LATITUDE_MIN                    = 32.2d0
+LATITUDE_MAX                    = 36.8d0
+LONGITUDE_MIN                   = -121.6d0
+LONGITUDE_MAX                   = -114.7d0
+DEPTH_BLOCK_KM                  = 60.d0
+UTM_PROJECTION_ZONE             = 11
+SUPPRESS_UTM_PROJECTION         = .false.
+
+# file that contains the interfaces of the model / mesh
+INTERFACES_FILE                 = interfaces.dat
+
+# number of elements at the surface along edges of the mesh at the surface
+# (must be 8 * multiple of NPROC below if mesh is not regular and contains mesh doublings)
+# (must be multiple of NPROC below if mesh is regular)
+NEX_XI                          = 336
+NEX_ETA                         = 288
+
+# number of MPI processors along xi and eta (can be different)
+NPROC_XI                        = 7
+NPROC_ETA                       = 6
+
+# Regular/irregular mesh
+USE_REGULAR_MESH                = .false.
+# Only for irregular meshes, number of doubling layers (1 or 2) and their position
+NDOUBLINGS                      = 2
+# NZ_DOUGLING_1 is the parameter to set up if there is only one doubling layer
+NZ_DOUGLING_1                   = 6
+NZ_DOUGLING_2                   = 9
+
+# create mesh files for visualisation or further checking
+CREATE_ABAQUS_FILES             = .true.
+CREATE_DX_FILES                 = .true.
+CREATE_VTK_FILES                = .false.
+
+# path to store the databases files
+LOCAL_PATH                      = ../OUTPUT_FILES/DATABASES_MPI
+
+# number of materials
+NMATERIALS                      = 4
+# define the different materials in the model as :
+# #material_id  #rho  #vp  #vs  #Q  #anisotropy_flag #domain_id
+#     Q                : quality factor
+#     anisotropy_flag  : 0=no anisotropy/ 1,2,.. check with implementation in aniso_model.f90
+#     domain_id        : 1=acoustic / 2=elastic
+1  3000  7800  4500 0.0  0  2
+2  2800  6700  3870 0.0  0  2
+3  2670  6300  3640 0.0  0  2
+4  2400  5500  3180 0.0  0  2
+# number of regions
+NREGIONS                        = 4
+# define the different regions of the model as :
+#NEX_XI_BEGIN  #NEX_XI_END  #NEX_ETA_BEGIN  #NEX_ETA_END  #NZ_BEGIN #NZ_END  #material_id
+1              336            1               288             1          3       1
+1              336            1               288             4          6       2
+1              336            1               288             7          9       3
+1              336            1               288             10        12       4
+

Added: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/Mesh_Par_file_168
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/Mesh_Par_file_168	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/Mesh_Par_file_168	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,59 @@
+
+# coordinates of mesh block in latitude/longitude and depth in km
+LATITUDE_MIN                    = 32.2d0
+LATITUDE_MAX                    = 36.8d0
+LONGITUDE_MIN                   = -121.6d0
+LONGITUDE_MAX                   = -114.7d0
+DEPTH_BLOCK_KM                  = 60.d0
+UTM_PROJECTION_ZONE             = 11
+SUPPRESS_UTM_PROJECTION         = .false.
+
+# file that contains the interfaces of the model / mesh
+INTERFACES_FILE                 = interfaces.dat
+
+# number of elements at the surface along edges of the mesh at the surface
+# (must be 8 * multiple of NPROC below if mesh is not regular and contains mesh doublings)
+# (must be multiple of NPROC below if mesh is regular)
+NEX_XI                          = 336
+NEX_ETA                         = 288
+
+# number of MPI processors along xi and eta (can be different)
+NPROC_XI                        = 14
+NPROC_ETA                       = 12
+
+# Regular/irregular mesh
+USE_REGULAR_MESH                = .false.
+# Only for irregular meshes, number of doubling layers (1 or 2) and their position
+NDOUBLINGS                      = 2
+# NZ_DOUGLING_1 is the parameter to set up if there is only one doubling layer
+NZ_DOUGLING_1                   = 6
+NZ_DOUGLING_2                   = 9
+
+# create mesh files for visualisation or further checking
+CREATE_ABAQUS_FILES             = .true.
+CREATE_DX_FILES                 = .true.
+CREATE_VTK_FILES                = .false.
+
+# path to store the databases files
+LOCAL_PATH                      = ../OUTPUT_FILES/DATABASES_MPI
+
+# number of materials
+NMATERIALS                      = 4
+# define the different materials in the model as :
+# #material_id  #rho  #vp  #vs  #Q  #anisotropy_flag #domain_id
+#     Q                : quality factor
+#     anisotropy_flag  : 0=no anisotropy/ 1,2,.. check with implementation in aniso_model.f90
+#     domain_id        : 1=acoustic / 2=elastic
+1  3000  7800  4500 0.0  0  2
+2  2800  6700  3870 0.0  0  2
+3  2670  6300  3640 0.0  0  2
+4  2400  5500  3180 0.0  0  2
+# number of regions
+NREGIONS                        = 4
+# define the different regions of the model as :
+#NEX_XI_BEGIN  #NEX_XI_END  #NEX_ETA_BEGIN  #NEX_ETA_END  #NZ_BEGIN #NZ_END  #material_id
+1              336            1               288             1          3       1
+1              336            1               288             4          6       2
+1              336            1               288             7          9       3
+1              336            1               288             10        12       4
+

Added: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/interface1.dat
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/interface1.dat	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/interface1.dat	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,4 @@
+-32000
+-32000
+-32000
+-32000

Added: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/interface2.dat
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/interface2.dat	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/interface2.dat	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,4 @@
+-16000
+-16000
+-16000
+-16000

Added: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/interface3.dat
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/interface3.dat	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/interface3.dat	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,4 @@
+-5500
+-5500
+-5500
+-5500

Added: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/interface4.dat
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/interface4.dat	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/interface4.dat	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,4 @@
+0
+0
+0
+0

Added: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/interfaces.dat
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/interfaces.dat	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/DATA/meshfem3D_files/interfaces.dat	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,30 @@
+# number of interfaces
+ 4
+#
+# We describe each interface below, structured as a 2D-grid, with several parameters : 
+# number of points along XI and ETA, minimal XI ETA coordinates 
+# and spacing between points which must be constant.
+# Then the records contain the Z coordinates of the NXI x NETA points.
+#
+# interface number 1 (moho)
+ .false. 2 2 -121.d0 32.d0 6.0d0 6.0d0
+ interface1.dat
+# interface number 2
+ .false. 2 2 -121.d0 32.d0 6.0d0 6.0d0
+ interface2.dat
+# interface number 3
+ .false. 2 2 -121.d0 32.d0 6.0d0 6.0d0
+ interface3.dat
+# interface number 4 (topography, top of the mesh)
+ .false. 2 2 -121.d0 32.d0 6.0d0 6.0d0
+ interface4.dat
+#
+# for each layer, we give the number of spectral elements in the vertical direction
+# layer number 1 (bottom layer)
+ 3
+# layer number 2
+ 3
+# layer number 4
+ 3
+# layer number 5 (top layer)
+ 3
\ No newline at end of file

Modified: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/README
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/README	2012-10-25 14:18:46 UTC (rev 20922)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/README	2012-10-25 14:58:44 UTC (rev 20923)
@@ -24,24 +24,19 @@
 1. set up input files:
 
    > cd SPECFEM3D
-   > rsync -av examples/meshfem3D_examples/socal1D/ DATA/meshfem3D_files/
+   > rsync -av examples/meshfem3D_examples/socal1D/DATA/ DATA
 
-   > cd DATA/meshfem3D_files/
-   > cp Par_file CMTSOLUTION STATIONS ..
-   > cd SPECFEM3D
-
    - adapt the submission scripts for the appropriate queues (-q) and number of cores (-l):
      go_mesher_pbs.bash, go_generate_databases_pbs.bash, go_solver_pbs.bash
 
    - note: go_decomposer_pbs.bash is not used with the internal mesher
 
-2. generate internal mesh:
+2. compile and run internal mesher
 
-   - compile and run meshfem3D:
     > make xmeshfem3D
     > qsub go_mesher_pbs.bash
 
-    this should generate these files in OUTPUT_FILES/DATABASES_MPI/:
+    - this should generate these files in OUTPUT_FILES/DATABASES_MPI/:
 
     proc000000_Database
     proc000000_.dx
@@ -52,7 +47,7 @@
 
 3. generate databases:
 
-   - compile and run generate_databases:
+   - compile and run generate_databases in directory SPECFEM3D/:
      > make xgenerate_databases
      > qsub go_generate_databases_pbs.bash
 

Modified: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/process.sh
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/process.sh	2012-10-25 14:18:46 UTC (rev 20922)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/socal1D/process.sh	2012-10-25 14:58:44 UTC (rev 20923)
@@ -32,7 +32,7 @@
 # compiles executables in root directory
 cd ../../../
 make clean
-make
+make > $currentdir/tmp.log
 #make combine_vol_data
 cd $currentdir
 

Added: seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/DATA/CMTSOLUTION
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/DATA/CMTSOLUTION	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/DATA/CMTSOLUTION	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,13 @@
+PDE  1999 01 01 00 00 00.00  67000 67000 -25000 4.2 4.2 hom_explosion
+event name:       hom_explosion
+time shift:       0.0000
+half duration:    5.0
+latitude:       67000.0
+longitude:      67000.0
+depth:          25.0
+Mrr:       0.000000
+Mtt:       0.000000
+Mpp:       0.000000
+Mrt:       0.000000
+Mrp:       0.000000
+Mtp:       0.000000

Added: seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/DATA/FORCESOLUTION
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/DATA/FORCESOLUTION	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/DATA/FORCESOLUTION	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,10 @@
+FORCE  001
+time shift:     0.0000
+hdur:           0.5
+latitude:       46.197
+longitude:      -122.186
+depth:          5.0
+factor force source:             1.d15
+component dir vect source E:     1.d0
+component dir vect source N:     -2.d0
+component dir vect source Z_UP:  -1.d0

Added: seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/DATA/Par_file_step1
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/DATA/Par_file_step1	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/DATA/Par_file_step1	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,68 @@
+# simulation input parameters
+#
+# forward or adjoint simulation
+# 1 = forward, 2 = adjoint, 3 = both simultaneously
+SIMULATION_TYPE                 = 1
+# 0 = earthquake simulation,  1/2/3 = three steps in noise simulation
+NOISE_TOMOGRAPHY                = 1
+SAVE_FORWARD                    = .true.
+
+# UTM projection parameters
+UTM_PROJECTION_ZONE             = 11
+SUPPRESS_UTM_PROJECTION         = .true.
+
+# number of MPI processors
+NPROC                           = 4
+
+# time step parameters
+NSTEP                           = 1500
+DT                              = 0.05d0
+NTSTEP_BETWEEN_READ_ADJSRC      = 0
+
+# models:
+# available options are:
+#   default (model parameters described by mesh properties)
+# 1D models available are:
+#   1d_prem,1d_socal,1d_cascadia
+# 3D models available are:
+#   aniso,external,gll,salton_trough,tomo
+MODEL                           = default
+
+# parameters describing the model
+OCEANS                          = .false.
+TOPOGRAPHY                      = .false.
+ATTENUATION                     = .false.
+USE_OLSEN_ATTENUATION           = .false.
+ANISOTROPY                      = .false.
+GRAVITY                         = .false.
+
+# absorbing boundary conditions for a regional simulation
+ABSORBING_CONDITIONS            = .true.
+
+# save AVS or OpenDX movies
+MOVIE_SURFACE                   = .true.
+MOVIE_VOLUME                    = .false.
+NTSTEP_BETWEEN_FRAMES           = 100
+CREATE_SHAKEMAP                 = .false.
+SAVE_DISPLACEMENT               = .false.
+USE_HIGHRES_FOR_MOVIES          = .true.
+HDUR_MOVIE                      = 0.0
+
+# save AVS or OpenDX mesh files to check the mesh
+SAVE_MESH_FILES                 = .false.
+
+# path to store the local database file on each node
+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
+
+# interval in time steps for writing of seismograms
+NTSTEP_BETWEEN_OUTPUT_SEISMOS   = 10000
+
+# print source time function
+PRINT_SOURCE_TIME_FUNCTION      = .true.
+
+# set to true to use GPUs
+GPU_MODE                        = .false.
+

Added: seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/DATA/Par_file_step2
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/DATA/Par_file_step2	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/DATA/Par_file_step2	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,68 @@
+# simulation input parameters
+#
+# forward or adjoint simulation
+# 1 = forward, 2 = adjoint, 3 = both simultaneously
+SIMULATION_TYPE                 = 1
+# 0 = earthquake simulation,  1/2/3 = three steps in noise simulation
+NOISE_TOMOGRAPHY                = 2
+SAVE_FORWARD                    = .true.
+
+# UTM projection parameters
+UTM_PROJECTION_ZONE             = 11
+SUPPRESS_UTM_PROJECTION         = .true.
+
+# number of MPI processors
+NPROC                           = 4
+
+# time step parameters
+NSTEP                           = 1500
+DT                              = 0.05d0
+NTSTEP_BETWEEN_READ_ADJSRC      = 0
+
+# models:
+# available options are:
+#   default (model parameters described by mesh properties)
+# 1D models available are:
+#   1d_prem,1d_socal,1d_cascadia
+# 3D models available are:
+#   aniso,external,gll,salton_trough,tomo
+MODEL                           = default
+
+# parameters describing the model
+OCEANS                          = .false.
+TOPOGRAPHY                      = .false.
+ATTENUATION                     = .false.
+USE_OLSEN_ATTENUATION           = .false.
+ANISOTROPY                      = .false.
+GRAVITY                         = .false.
+
+# absorbing boundary conditions for a regional simulation
+ABSORBING_CONDITIONS            = .true.
+
+# save AVS or OpenDX movies
+MOVIE_SURFACE                   = .true.
+MOVIE_VOLUME                    = .false.
+NTSTEP_BETWEEN_FRAMES           = 100
+CREATE_SHAKEMAP                 = .false.
+SAVE_DISPLACEMENT               = .false.
+USE_HIGHRES_FOR_MOVIES          = .true.
+HDUR_MOVIE                      = 0.0
+
+# save AVS or OpenDX mesh files to check the mesh
+SAVE_MESH_FILES                 = .false.
+
+# path to store the local database file on each node
+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
+
+# interval in time steps for writing of seismograms
+NTSTEP_BETWEEN_OUTPUT_SEISMOS   = 10000
+
+# print source time function
+PRINT_SOURCE_TIME_FUNCTION      = .true.
+
+# set to true to use GPUs
+GPU_MODE                        = .false.
+

Added: seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/DATA/Par_file_step3
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/DATA/Par_file_step3	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/DATA/Par_file_step3	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,67 @@
+# simulation input parameters
+#
+# forward or adjoint simulation
+# 1 = forward, 2 = adjoint, 3 = both simultaneously
+SIMULATION_TYPE                 = 3
+# 0 = earthquake simulation,  1/2/3 = three steps in noise simulation
+NOISE_TOMOGRAPHY                = 3
+SAVE_FORWARD                    = .false.
+
+# UTM projection parameters
+UTM_PROJECTION_ZONE             = 11
+SUPPRESS_UTM_PROJECTION         = .true.
+
+# number of MPI processors
+NPROC                           = 4
+
+# time step parameters
+NSTEP                           = 1500
+DT                              = 0.05d0
+NTSTEP_BETWEEN_READ_ADJSRC      = 0
+
+# models:
+# available options are:
+#   default (model parameters described by mesh properties)
+# 1D models available are:
+#   1d_prem,1d_socal,1d_cascadia
+# 3D models available are:
+#   aniso,external,gll,salton_trough,tomo
+MODEL                           = default
+
+# parameters describing the model
+OCEANS                          = .false.
+TOPOGRAPHY                      = .false.
+ATTENUATION                     = .false.
+USE_OLSEN_ATTENUATION           = .false.
+ANISOTROPY                      = .false.
+GRAVITY                         = .false.
+
+# absorbing boundary conditions for a regional simulation
+ABSORBING_CONDITIONS            = .true.
+
+# save AVS or OpenDX movies
+MOVIE_SURFACE                   = .true.
+MOVIE_VOLUME                    = .false.
+NTSTEP_BETWEEN_FRAMES           = 100
+CREATE_SHAKEMAP                 = .false.
+SAVE_DISPLACEMENT               = .false.
+USE_HIGHRES_FOR_MOVIES          = .true.
+HDUR_MOVIE                      = 0.0
+
+# save AVS or OpenDX mesh files to check the mesh
+SAVE_MESH_FILES                 = .false.
+
+# path to store the local database file on each node
+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
+
+# interval in time steps for writing of seismograms
+NTSTEP_BETWEEN_OUTPUT_SEISMOS   = 10000
+
+# print source time function
+PRINT_SOURCE_TIME_FUNCTION      = .true.
+
+# set to true to use GPUs
+GPU_MODE                        = .false.

Added: seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/DATA/STATIONS
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/DATA/STATIONS	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/DATA/STATIONS	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,2 @@
+X1 DB 67000.00 35500.00 0.0 0.0
+X2 DB 67000.00 100500.0 0.0 0.0

Added: seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/DATA/STATIONS_ADJOINT
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/DATA/STATIONS_ADJOINT	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/DATA/STATIONS_ADJOINT	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,2 @@
+X1 DB 67000.00 35500.00 0.0 0.0
+X2 DB 67000.00 100500.0 0.0 0.0

Modified: seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/README
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/README	2012-10-25 14:18:46 UTC (rev 20922)
+++ seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/README	2012-10-25 14:58:44 UTC (rev 20923)
@@ -56,9 +56,9 @@
          Refer to '../examples/homogeneous_halfspace', if you don't know how to get them from CUBIT and SCOTCH.
 
    3.2 - Source and Receivers
-         Since NO earthquakes are allowed for noise simulations, we have a ZERO moment tensor in "./in_data_file/CMTSOLUTION"
+         Since NO earthquakes are allowed for noise simulations, we have a ZERO moment tensor in "./DATA/CMTSOLUTION"
          As for receivers, instead of having a lot of stations in '../examples/homogeneous_halfspace',
-         we have only two receivers in "./in_data_file/STATIONS" and "./in_data_file/STATIONS_ADJOINT"
+         we have only two receivers in "./DATA/STATIONS" and "./DATA/STATIONS_ADJOINT"
 
    3.3 - Noise statistics
          "./NOISE_TOMOGRAPHY" contains:

Modified: seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/pre-processing.sh
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/pre-processing.sh	2012-10-25 14:18:46 UTC (rev 20922)
+++ seismo/3D/SPECFEM3D/trunk/examples/noise_tomography/pre-processing.sh	2012-10-25 14:58:44 UTC (rev 20923)
@@ -15,14 +15,11 @@
 echo "(will take about 3 h 30 min)"
 echo
 
-
-# return to the main SPECFEM3D directory
+# compile the package in root directory
 cd ../../
-
-# compile the package
-make > tmp.log
-make combine_vol_data >> tmp.log
-
+make clean
+make > $script_dir/tmp.log
+make combine_vol_data >> $script_dir/tmp.log
 cd $script_dir
 
 # specify directories for executables, input files and output files
@@ -190,4 +187,3 @@
 echo
 echo `date`
 echo "done"
-

Added: seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/DATA/CMTSOLUTION
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/DATA/CMTSOLUTION	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/DATA/CMTSOLUTION	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,13 @@
+PDE  1999 01 01 00 00 00.00  67000 67000 -25000 4.2 4.2 hom_explosion
+event name:       hom_explosion
+time shift:       0.0000
+half duration:    5.0
+latitude:       67000.0
+longitude:      67000.0
+depth:          25.0
+Mrr:       1.000000e+23
+Mtt:       1.000000e+23
+Mpp:       1.000000e+23
+Mrt:       0.000000
+Mrp:       0.000000
+Mtp:       0.000000

Added: seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/DATA/FORCESOLUTION
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/DATA/FORCESOLUTION	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/DATA/FORCESOLUTION	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,10 @@
+FORCE  001
+time shift:     0.0000
+hdur:           0.5
+latitude:       67000.0
+longitude:      67000.0
+depth:          25.0
+factor force source:             1.d15
+component dir vect source E:     1.d0
+component dir vect source N:     -2.d0
+component dir vect source Z_UP:  -1.d0

Added: seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/DATA/Par_file
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/DATA/Par_file	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/DATA/Par_file	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,97 @@
+# simulation input parameters
+#
+# forward or adjoint simulation
+# 1 = forward, 2 = adjoint, 3 = both simultaneously
+SIMULATION_TYPE                 = 1
+# 0 = earthquake simulation,  1/2/3 = three steps in noise simulation
+NOISE_TOMOGRAPHY                = 0
+SAVE_FORWARD                    = .false.
+
+# UTM projection parameters
+UTM_PROJECTION_ZONE             = 11
+SUPPRESS_UTM_PROJECTION         = .true.
+
+# number of MPI processors
+NPROC                           = 4
+
+# time step parameters
+NSTEP                           = 4000
+DT                              = 0.01
+
+# number of nodes for 2D and 3D shape functions for hexahedra
+# we use either 8-node mesh elements (bricks) or 27-node elements.
+# If you use our internal mesher, the only option is 8-node bricks (27-node elements are not supported)
+# CUBIT does not support HEX27 elements either (it can generate them, but they are flat, i.e. identical to HEX8).
+# To generate HEX27 elements with curvature properly taken into account, you can use Gmsh http://geuz.org/gmsh/
+NGNOD 	      	    	     	= 8
+
+# models:
+# available options are:
+#   default (model parameters described by mesh properties)
+# 1D models available are:
+#   1d_prem,1d_socal,1d_cascadia
+# 3D models available are:
+#   aniso,external,gll,salton_trough,tomo
+MODEL                           = default
+
+# parameters describing the model
+OCEANS                          = .false.
+TOPOGRAPHY                      = .false.
+ATTENUATION                     = .false.
+USE_OLSEN_ATTENUATION           = .false.
+ANISOTROPY                      = .false.
+GRAVITY                         = .false.
+
+# absorbing boundary conditions for a regional simulation
+ABSORBING_CONDITIONS            = .true.
+
+# absorbing top surface (defined in mesh as 'free_surface_file')
+ABSORB_INSTEAD_OF_FREE_SURFACE  = .false.
+
+# save AVS or OpenDX movies
+MOVIE_SURFACE                   = .false.
+MOVIE_VOLUME                    = .false.
+NTSTEP_BETWEEN_FRAMES           = 200
+CREATE_SHAKEMAP                 = .false.
+SAVE_DISPLACEMENT               = .false.
+USE_HIGHRES_FOR_MOVIES          = .false.
+HDUR_MOVIE                      = 0.0
+
+# save AVS or OpenDX mesh files to check the mesh
+SAVE_MESH_FILES                 = .true.
+
+# path to store the local database file on each node
+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
+
+# interval in time steps for writing of seismograms
+NTSTEP_BETWEEN_OUTPUT_SEISMOS   = 10000
+
+# interval in time steps for reading adjoint traces
+NTSTEP_BETWEEN_READ_ADJSRC      = 0      # 0 = read the whole adjoint sources at the same time
+
+# 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
+# in which the source is a vertical force, normal force, inclined force, impact etc.
+# If this flag is turned on, the FORCESOLUTION file must be edited by precising:
+# - the corresponding time-shift parameter,
+# - the half duration parameter of the source,
+# - the coordinates of the source,
+# - the magnitude of the force source,
+# - the components of a (non-unitary) direction vector for the force source in the E/N/Z_UP basis.
+# 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.
+USE_FORCE_POINT_SOURCE          = .false.
+
+# 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
+GPU_MODE                        = .false.
+

Added: seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/DATA/STATIONS
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/DATA/STATIONS	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/DATA/STATIONS	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,6 @@
+X1 DB 67000.00 0.000000 0.0 0.0
+X10 DB 67000.00 10767.86 0.0 0.0
+X20 DB 67000.00 22732.14 0.0 0.0
+X30 DB 67000.00 34696.43 0.0 0.0
+X40 DB 67000.00 46660.71 0.0 0.0
+X50 DB 67000.00 58625.00 0.0 0.0

Modified: seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/README
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/README	2012-10-25 14:18:46 UTC (rev 20922)
+++ seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/README	2012-10-25 14:58:44 UTC (rev 20923)
@@ -57,19 +57,15 @@
 
 5. generate databases:
 
-   - compile generate_databases from SPECFEM3D/ :
+   - compile and run generate_databases in directory SPECFEM3D/:
      > make xgenerate_databases
-
-   - submit job script
      > qsub go_generate_databases_pbs.bash
 
 
 6. run simulation:
 
-   - compile specfem3D:
+   - compile and run specfem3D:
      > make xspecfem3D
-
-   - submit job script:
      > qsub go_solver_pbs.bash
 
      the simulation will take about 10 minutes

Modified: seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/process.sh
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/process.sh	2012-10-25 14:18:46 UTC (rev 20922)
+++ seismo/3D/SPECFEM3D/trunk/examples/tomographic_model/process.sh	2012-10-25 14:58:44 UTC (rev 20923)
@@ -27,10 +27,9 @@
 echo
 
 mkdir -p bin
-mkdir -p OUTPUT_FILES
 mkdir -p OUTPUT_FILES/DATABASES_MPI
 
-rm -rf OUTPUT_FILES/*
+rm -f OUTPUT_FILES/*
 rm -rf OUTPUT_FILES/DATABASES_MPI/*
 
 # sets up tomography model file
@@ -40,7 +39,8 @@
 
 # compiles executables in root directory
 cd ../../
-make > tmp.log
+make clean
+make > $currentdir/tmp.log
 cd $currentdir
 
 # links executables
@@ -51,17 +51,17 @@
 cp ../../../bin/xspecfem3D ./
 cd ../
 
+# stores setup
+cp DATA/Par_file OUTPUT_FILES/
+cp DATA/CMTSOLUTION OUTPUT_FILES/
+cp DATA/STATIONS OUTPUT_FILES/
+
 # decomposes mesh
 echo
 echo "  decomposing mesh..."
 echo
 ./bin/xdecompose_mesh_SCOTCH $NPROC MESH/ OUTPUT_FILES/DATABASES_MPI/
 
-# stores setup
-cp DATA/Par_file OUTPUT_FILES/
-cp DATA/CMTSOLUTION OUTPUT_FILES/
-cp DATA/STATIONS OUTPUT_FILES/
-
 # runs database generation
 echo
 echo "  running database generation..."

Added: seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/DATA/CMTSOLUTION
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/DATA/CMTSOLUTION	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/DATA/CMTSOLUTION	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,13 @@
+PDE  1999 01 01 00 00 00.00  67000 67000 -25000 4.2 4.2 water_vertical
+event name:       water_vertical
+time shift:       0.0000
+half duration:    2.0
+latitude:       67000.0
+longitude:      66999.9
+depth:           1.0
+Mrr:       1.000000e+23
+Mtt:       1.000000e+23
+Mpp:       1.000000e+23
+Mrt:       0.000000
+Mrp:       0.000000
+Mtp:       0.000000

Added: seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/DATA/FORCESOLUTION
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/DATA/FORCESOLUTION	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/DATA/FORCESOLUTION	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,10 @@
+FORCE  001
+time shift:     0.0000
+hdur:           0.5
+latitude:       67000.0
+longitude:      66999.9
+depth:          1.0
+factor force source:             1.d15
+component dir vect source E:     1.d0
+component dir vect source N:     -2.d0
+component dir vect source Z_UP:  -1.d0

Added: seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/DATA/Par_file
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/DATA/Par_file	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/DATA/Par_file	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,97 @@
+# simulation input parameters
+#
+# forward or adjoint simulation
+# 1 = forward, 2 = adjoint, 3 = both simultaneously
+SIMULATION_TYPE                 = 1
+# 0 = earthquake simulation,  1/2/3 = three steps in noise simulation
+NOISE_TOMOGRAPHY                = 0
+SAVE_FORWARD                    = .false.
+
+# UTM projection parameters
+UTM_PROJECTION_ZONE             = 11
+SUPPRESS_UTM_PROJECTION         = .true.
+
+# number of MPI processors
+NPROC                           = 4
+
+# time step parameters
+NSTEP                           = 4500
+DT                              = 0.005
+
+# number of nodes for 2D and 3D shape functions for hexahedra
+# we use either 8-node mesh elements (bricks) or 27-node elements.
+# If you use our internal mesher, the only option is 8-node bricks (27-node elements are not supported)
+# CUBIT does not support HEX27 elements either (it can generate them, but they are flat, i.e. identical to HEX8).
+# To generate HEX27 elements with curvature properly taken into account, you can use Gmsh http://geuz.org/gmsh/
+NGNOD 	      	    	     	= 8
+
+# models:
+# available options are:
+#   default (model parameters described by mesh properties)
+# 1D models available are:
+#   1d_prem,1d_socal,1d_cascadia
+# 3D models available are:
+#   aniso,external,gll,salton_trough,tomo
+MODEL                           = default
+
+# parameters describing the model
+OCEANS                          = .false.
+TOPOGRAPHY                      = .false.
+ATTENUATION                     = .false.
+USE_OLSEN_ATTENUATION           = .false.
+ANISOTROPY                      = .false.
+GRAVITY                         = .false.
+
+# absorbing boundary conditions for a regional simulation
+ABSORBING_CONDITIONS            = .true.
+
+# absorbing top surface (defined in mesh as 'free_surface_file')
+ABSORB_INSTEAD_OF_FREE_SURFACE  = .false.
+
+# save AVS or OpenDX movies
+MOVIE_SURFACE                   = .false.
+MOVIE_VOLUME                    = .false.
+NTSTEP_BETWEEN_FRAMES           = 100
+CREATE_SHAKEMAP                 = .false.
+SAVE_DISPLACEMENT               = .false.
+USE_HIGHRES_FOR_MOVIES          = .false.
+HDUR_MOVIE                      = 0.0
+
+# save AVS or OpenDX mesh files to check the mesh
+SAVE_MESH_FILES                 = .true.
+
+# path to store the local database file on each node
+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
+
+# interval in time steps for writing of seismograms
+NTSTEP_BETWEEN_OUTPUT_SEISMOS   = 10000
+
+# interval in time steps for reading adjoint traces
+NTSTEP_BETWEEN_READ_ADJSRC      = 0      # 0 = read the whole adjoint sources at the same time
+
+# 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
+# in which the source is a vertical force, normal force, inclined force, impact etc.
+# If this flag is turned on, the FORCESOLUTION file must be edited by precising:
+# - the corresponding time-shift parameter,
+# - the half duration parameter of the source,
+# - the coordinates of the source,
+# - the magnitude of the force source,
+# - the components of a (non-unitary) direction vector for the force source in the E/N/Z_UP basis.
+# 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.
+USE_FORCE_POINT_SOURCE          = .false.
+
+# 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
+GPU_MODE                        = .false.
+

Added: seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/DATA/STATIONS
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/DATA/STATIONS	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/DATA/STATIONS	2012-10-25 14:58:44 UTC (rev 20923)
@@ -0,0 +1,22 @@
+X10 DB 67000.00 10767.86 0.0 100.0
+X20 DB 67000.00 22732.14 0.0 100.0
+X30 DB 67000.00 34696.43 0.0 100.0
+X40 DB 67000.00 46660.71 0.0 100.0
+X50 DB 67000.00 58625.00 0.0 100.0
+X55 DB 67000.00 67000.00 0.0 100.0
+X60 DB 67000.00 75375.00 0.0 100.0
+X70 DB 67000.00 87339.29 0.0 100.0
+X80 DB 67000.00 99303.57 0.0 100.0
+X90 DB 67000.00 111269.86 0.0 100.0
+X1 DB 67000.00 0.0 0.0 100.0
+X2 DB 67000.00 67000.0 0.0 25000.0
+X3 DB 67000.00 134000.0 0.0 100.0
+X4 DB 67000.00 67000.0 0.0 3500.0
+X5 DB 67000.00 67000.0 0.0 3000.2
+X6 DB 67000.00 67000.0 0.0 3000.1
+X7 DB 67000.00 67000.0 0.0 2999.9
+X8 DB 67000.00 67000.0 0.0 2999.8
+Y1 DB 67000.00 58625.0 0.0 2999.9
+Y2 DB 67000.00 58625.0 0.0 3000.1
+Y3 DB 67000.00 46660.71 0.0 2999.9
+Y4 DB 67000.00 46660.71 0.0 3000.1

Modified: seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/README
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/README	2012-10-25 14:18:46 UTC (rev 20922)
+++ seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/README	2012-10-25 14:58:44 UTC (rev 20923)
@@ -6,7 +6,6 @@
 with a water layer on top and an elastic layer below, using CUBIT.
 It then runs a forward simulation which couples acoustic & elastic waves.
 
-
 step-by-step tutorial:
 
 0. run the example in the directory homogeneous_halfspace
@@ -44,10 +43,8 @@
 
 4. generate databases:
 
-    - compile generate_databases:
+    - compile and run generate_databases in directory SPECFEM3D/:
       > make xgenerate_databases
-
-    - submit job script:
       > qsub go_generate_databases_pbs.bash
 
       this will create binary mesh files, e.g. "proc000***_external_mesh.bin"
@@ -58,10 +55,8 @@
 
 5. run simulation:
 
-    - compile specfem3D:
+    - compile and run specfem3D:
       > make xspecfem3D
-
-    - submit job script:
       > qsub go_solver_pbs.bash
 
     note: simulation will take about 1 h 45 minutes and generate

Modified: seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/process.sh
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/process.sh	2012-10-25 14:18:46 UTC (rev 20922)
+++ seismo/3D/SPECFEM3D/trunk/examples/waterlayered_halfspace/process.sh	2012-10-25 14:58:44 UTC (rev 20923)
@@ -27,15 +27,15 @@
 echo
 
 mkdir -p bin
-mkdir -p OUTPUT_FILES
 mkdir -p OUTPUT_FILES/DATABASES_MPI
 
-rm -rf OUTPUT_FILES/*
+rm -f OUTPUT_FILES/*
 rm -rf OUTPUT_FILES/DATABASES_MPI/*
 
 # compiles executables in root directory
 cd ../../
-make > tmp.log
+make clean
+make > $currentdir/tmp.log
 cd $currentdir
 
 # links executables
@@ -46,17 +46,17 @@
 cp ../../../bin/xspecfem3D ./
 cd ../
 
+# stores setup
+cp DATA/Par_file OUTPUT_FILES/
+cp DATA/CMTSOLUTION OUTPUT_FILES/
+cp DATA/STATIONS OUTPUT_FILES/
+
 # decomposes mesh
 echo
 echo "  decomposing mesh..."
 echo
 ./bin/xdecompose_mesh_SCOTCH $NPROC MESH/ OUTPUT_FILES/DATABASES_MPI/
 
-# stores setup
-cp DATA/Par_file OUTPUT_FILES/
-cp DATA/CMTSOLUTION OUTPUT_FILES/
-cp DATA/STATIONS OUTPUT_FILES/
-
 # runs database generation
 echo
 echo "  running database generation..."