Thu Aug 22 00:40:44 PDT 2013

Author: danielpeter
Date: 2013-08-22 00:40:44 -0700 (Thu, 22 Aug 2013)
New Revision: 22728

Modified:
   seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/
   seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/benchmarks/prem_ani_noocean_Q_Cowling_Bolivia_9s/SEMD/DATA/Par_file
   seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/benchmarks/prem_ani_noocean_Q_Cowling_Vanuatu/SEMD/DATA/Par_file
   seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/benchmarks/prem_iso_noocean_Q_Cowling_Vanuatu/SEMD/DATA/Par_file
   seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/global_PREM_kernels/amplitude/DATA/Par_file
   seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/global_PREM_kernels/traveltime/DATA/Par_file
   seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/global_s362ani/DATA/Par_file
   seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_long/Par_file_NOISE_1_attenuation
   seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_long/Par_file_NOISE_1_noattenuation
   seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_long/Par_file_NOISE_2_attenuation
   seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_long/Par_file_NOISE_2_noattenuation
   seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_long/Par_file_NOISE_3_noattenuation
   seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_short/Par_file_NOISE_1_attenuation
   seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_short/Par_file_NOISE_1_noattenuation
   seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_short/Par_file_NOISE_2_attenuation
   seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_short/Par_file_NOISE_2_noattenuation
   seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_short/Par_file_NOISE_3_noattenuation
   seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/regional/Par_file_NOISE_1_attenuation
   seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/regional/Par_file_NOISE_1_noattenuation
   seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/regional/Par_file_NOISE_2_attenuation
   seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/regional/Par_file_NOISE_2_noattenuation
   seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/regional/Par_file_NOISE_3_noattenuation
   seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/regional_Greece_small/DATA/Par_file
   seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/regional_MiddleEast/DATA/Par_file
   seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/Makefile.in
   seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/src/auxiliaries/create_movie_AVS_DX.f90
   seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/src/meshfem3D/meshfem3D.f90
   seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/src/meshfem3D/model_crustmaps.f90
   seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/src/shared/exit_mpi.f90
   seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/src/specfem3D/save_regular_kernels.f90
   seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/src/specfem3D/specfem3D.F90
Log:
merges commit 22724 to SUNFLOWER branch; updates model_crustmaps routines


Property changes on: seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER
___________________________________________________________________
Modified: svn:ignore
   - 

   + daniel


Modified: seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/benchmarks/prem_ani_noocean_Q_Cowling_Bolivia_9s/SEMD/DATA/Par_file
===================================================================

--- seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/benchmarks/prem_ani_noocean_Q_Cowling_Bolivia_9s/SEMD/DATA/Par_file	2013-08-21 16:56:20 UTC (rev 22727)
+++ seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/benchmarks/prem_ani_noocean_Q_Cowling_Bolivia_9s/SEMD/DATA/Par_file	2013-08-22 07:40:44 UTC (rev 22728)
@@ -57,10 +57,36 @@
 # to undo attenuation for sensitivity kernel calculations or forward runs with SAVE_FORWARD
 # use one (and only one) of the two flags below. UNDO_ATTENUATION is much better (it is exact)
 # but requires a significant amount of disk space for temporary storage.
+ATTENUATION_1D_WITH_3D_STORAGE  = .true.
 PARTIAL_PHYS_DISPERSION_ONLY    = .true.
 UNDO_ATTENUATION                = .false.
 NT_DUMP_ATTENUATION             = 100   # how often we dump restart files to undo attenuation, only needed when using UNDO_ATTENUATION
 
+# three mass matrices instead of one are needed to handle rotation very accurately;
+# otherwise rotation is handled slightly less accurately (but still reasonably well);
+# set to .true. if you are interested in precise effects related to rotation;
+# set to .false. if you are solving very large inverse problems at high frequency and also undoing attenuation exactly
+# using the UNDO_ATTENUATION flag above, in which case saving as much memory as possible can be a good idea.
+# You can also safely set it to .false. if you are not in a period range in which rotation matters, e.g. if you are targetting very short-period body waves.
+# if in doubt, set to .true.
+# Set it to .true. if you have ABSORBING_CONDITIONS above, because in that case the code will use the three mass matrices anyway
+# and thus there is no additional cost.
+# this flag is of course unused if ROTATION above is set to .false.
+EXACT_MASS_MATRIX_FOR_ROTATION  = .false.
+
+# this for LDDRK high-order time scheme instead of Newmark
+USE_LDDRK                       = .false.
+
+# the maximum CFL of LDDRK is significantly higher than that of the Newmark scheme,
+# in a ratio that is theoretically 1.327 / 0.697 = 1.15 / 0.604 = 1.903 for a solid with Poisson's ratio = 0.25
+# and for a fluid (see the manual of the 2D code, SPECFEM2D, Tables 4.1 and 4.2, and that ratio does not
+# depend on whether we are in 2D or in 3D). However in practice a ratio of about 1.5 to 1.7 is often safer
+# (for instance for models with a large range of Poisson's ratio values).
+# Since the code computes the time step using the Newmark scheme, for LDDRK we will simply
+# multiply that time step by this ratio when LDDRK is on and when flag INCREASE_CFL_FOR_LDDRK is true.
+INCREASE_CFL_FOR_LDDRK          = .true.
+RATIO_BY_WHICH_TO_INCREASE_IT   = 1.5d0
+
 # save AVS or OpenDX movies
 #MOVIE_COARSE saves movie only at corners of elements (SURFACE OR VOLUME)
 #MOVIE_COARSE does not work with create_movie_AVS_DX
@@ -125,6 +151,47 @@
 # print source time function
 PRINT_SOURCE_TIME_FUNCTION      = .false.
 
-# output kernels on a regular grid instead of on the mesh points
+#-----------------------------------------------------------
+#
+#  adjoint kernel outputs
+#
+#-----------------------------------------------------------
+
+# this parameter must be set to .true. to compute anisotropic kernels
+# in crust and mantle (related to the 21 Cij in geographical coordinates)
+# default is .false. to compute isotropic kernels (related to alpha and beta)
+ANISOTROPIC_KL                  = .false.
+
+# output only transverse isotropic kernels (alpha_v,alpha_h,beta_v,beta_h,eta,rho)
+# rather than fully anisotropic kernels when ANISOTROPIC_KL above is set to .true.
+# means to save radial anisotropic kernels, i.e., sensitivity kernels for beta_v, beta_h, etc.
+SAVE_TRANSVERSE_KL_ONLY         = .false.
+
+# output approximate Hessian in crust mantle region.
+# means to save the preconditioning for gradients, they are cross correlations between forward and adjoint accelerations.
+APPROXIMATE_HESS_KL             = .false.
+
+# forces transverse isotropy for all mantle elements
+# (default is to use transverse isotropy only between MOHO and 220)
+# means we allow radial anisotropy between the bottom of the crust to the bottom of the transition zone, i.e., 660~km depth.
+USE_FULL_TISO_MANTLE            = .false.
+
+# output kernel mask to zero out source region
+# to remove large values near the sources in the sensitivity kernels
+SAVE_SOURCE_MASK                = .false.
+
+# output kernels on a regular grid instead of on the GLL mesh points (a bit expensive)
 SAVE_REGULAR_KL                 = .false.
 
+#-----------------------------------------------------------
+
+# set to true to use GPUs
+GPU_MODE                        = .false.
+
+# set to true to use the ADIOS library for I/Os
+ADIOS_ENABLED                   = .false.
+ADIOS_FOR_FORWARD_ARRAYS        = .true.
+ADIOS_FOR_MPI_ARRAYS            = .true.
+ADIOS_FOR_ARRAYS_SOLVER         = .true.
+ADIOS_FOR_AVS_DX                = .true.
+

Modified: seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/benchmarks/prem_ani_noocean_Q_Cowling_Vanuatu/SEMD/DATA/Par_file
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/benchmarks/prem_ani_noocean_Q_Cowling_Vanuatu/SEMD/DATA/Par_file	2013-08-21 16:56:20 UTC (rev 22727)
+++ seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/benchmarks/prem_ani_noocean_Q_Cowling_Vanuatu/SEMD/DATA/Par_file	2013-08-22 07:40:44 UTC (rev 22728)
@@ -57,10 +57,36 @@
 # to undo attenuation for sensitivity kernel calculations or forward runs with SAVE_FORWARD
 # use one (and only one) of the two flags below. UNDO_ATTENUATION is much better (it is exact)
 # but requires a significant amount of disk space for temporary storage.
+ATTENUATION_1D_WITH_3D_STORAGE  = .true.
 PARTIAL_PHYS_DISPERSION_ONLY    = .true.
 UNDO_ATTENUATION                = .false.
 NT_DUMP_ATTENUATION             = 100   # how often we dump restart files to undo attenuation, only needed when using UNDO_ATTENUATION
 
+# three mass matrices instead of one are needed to handle rotation very accurately;
+# otherwise rotation is handled slightly less accurately (but still reasonably well);
+# set to .true. if you are interested in precise effects related to rotation;
+# set to .false. if you are solving very large inverse problems at high frequency and also undoing attenuation exactly
+# using the UNDO_ATTENUATION flag above, in which case saving as much memory as possible can be a good idea.
+# You can also safely set it to .false. if you are not in a period range in which rotation matters, e.g. if you are targetting very short-period body waves.
+# if in doubt, set to .true.
+# Set it to .true. if you have ABSORBING_CONDITIONS above, because in that case the code will use the three mass matrices anyway
+# and thus there is no additional cost.
+# this flag is of course unused if ROTATION above is set to .false.
+EXACT_MASS_MATRIX_FOR_ROTATION  = .false.
+
+# this for LDDRK high-order time scheme instead of Newmark
+USE_LDDRK                       = .false.
+
+# the maximum CFL of LDDRK is significantly higher than that of the Newmark scheme,
+# in a ratio that is theoretically 1.327 / 0.697 = 1.15 / 0.604 = 1.903 for a solid with Poisson's ratio = 0.25
+# and for a fluid (see the manual of the 2D code, SPECFEM2D, Tables 4.1 and 4.2, and that ratio does not
+# depend on whether we are in 2D or in 3D). However in practice a ratio of about 1.5 to 1.7 is often safer
+# (for instance for models with a large range of Poisson's ratio values).
+# Since the code computes the time step using the Newmark scheme, for LDDRK we will simply
+# multiply that time step by this ratio when LDDRK is on and when flag INCREASE_CFL_FOR_LDDRK is true.
+INCREASE_CFL_FOR_LDDRK          = .true.
+RATIO_BY_WHICH_TO_INCREASE_IT   = 1.5d0
+
 # save AVS or OpenDX movies
 #MOVIE_COARSE saves movie only at corners of elements (SURFACE OR VOLUME)
 #MOVIE_COARSE does not work with create_movie_AVS_DX
@@ -125,6 +151,47 @@
 # print source time function
 PRINT_SOURCE_TIME_FUNCTION      = .false.
 
-# output kernels on a regular grid instead of on the mesh points
+#-----------------------------------------------------------
+#
+#  adjoint kernel outputs
+#
+#-----------------------------------------------------------
+
+# this parameter must be set to .true. to compute anisotropic kernels
+# in crust and mantle (related to the 21 Cij in geographical coordinates)
+# default is .false. to compute isotropic kernels (related to alpha and beta)
+ANISOTROPIC_KL                  = .false.
+
+# output only transverse isotropic kernels (alpha_v,alpha_h,beta_v,beta_h,eta,rho)
+# rather than fully anisotropic kernels when ANISOTROPIC_KL above is set to .true.
+# means to save radial anisotropic kernels, i.e., sensitivity kernels for beta_v, beta_h, etc.
+SAVE_TRANSVERSE_KL_ONLY         = .false.
+
+# output approximate Hessian in crust mantle region.
+# means to save the preconditioning for gradients, they are cross correlations between forward and adjoint accelerations.
+APPROXIMATE_HESS_KL             = .false.
+
+# forces transverse isotropy for all mantle elements
+# (default is to use transverse isotropy only between MOHO and 220)
+# means we allow radial anisotropy between the bottom of the crust to the bottom of the transition zone, i.e., 660~km depth.
+USE_FULL_TISO_MANTLE            = .false.
+
+# output kernel mask to zero out source region
+# to remove large values near the sources in the sensitivity kernels
+SAVE_SOURCE_MASK                = .false.
+
+# output kernels on a regular grid instead of on the GLL mesh points (a bit expensive)
 SAVE_REGULAR_KL                 = .false.
 
+#-----------------------------------------------------------
+
+# set to true to use GPUs
+GPU_MODE                        = .false.
+
+# set to true to use the ADIOS library for I/Os
+ADIOS_ENABLED                   = .false.
+ADIOS_FOR_FORWARD_ARRAYS        = .true.
+ADIOS_FOR_MPI_ARRAYS            = .true.
+ADIOS_FOR_ARRAYS_SOLVER         = .true.
+ADIOS_FOR_AVS_DX                = .true.
+

Modified: seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/benchmarks/prem_iso_noocean_Q_Cowling_Vanuatu/SEMD/DATA/Par_file
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/benchmarks/prem_iso_noocean_Q_Cowling_Vanuatu/SEMD/DATA/Par_file	2013-08-21 16:56:20 UTC (rev 22727)
+++ seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/benchmarks/prem_iso_noocean_Q_Cowling_Vanuatu/SEMD/DATA/Par_file	2013-08-22 07:40:44 UTC (rev 22728)
@@ -57,10 +57,36 @@
 # to undo attenuation for sensitivity kernel calculations or forward runs with SAVE_FORWARD
 # use one (and only one) of the two flags below. UNDO_ATTENUATION is much better (it is exact)
 # but requires a significant amount of disk space for temporary storage.
+ATTENUATION_1D_WITH_3D_STORAGE  = .true.
 PARTIAL_PHYS_DISPERSION_ONLY    = .true.
 UNDO_ATTENUATION                = .false.
 NT_DUMP_ATTENUATION             = 100   # how often we dump restart files to undo attenuation, only needed when using UNDO_ATTENUATION
 
+# three mass matrices instead of one are needed to handle rotation very accurately;
+# otherwise rotation is handled slightly less accurately (but still reasonably well);
+# set to .true. if you are interested in precise effects related to rotation;
+# set to .false. if you are solving very large inverse problems at high frequency and also undoing attenuation exactly
+# using the UNDO_ATTENUATION flag above, in which case saving as much memory as possible can be a good idea.
+# You can also safely set it to .false. if you are not in a period range in which rotation matters, e.g. if you are targetting very short-period body waves.
+# if in doubt, set to .true.
+# Set it to .true. if you have ABSORBING_CONDITIONS above, because in that case the code will use the three mass matrices anyway
+# and thus there is no additional cost.
+# this flag is of course unused if ROTATION above is set to .false.
+EXACT_MASS_MATRIX_FOR_ROTATION  = .false.
+
+# this for LDDRK high-order time scheme instead of Newmark
+USE_LDDRK                       = .false.
+
+# the maximum CFL of LDDRK is significantly higher than that of the Newmark scheme,
+# in a ratio that is theoretically 1.327 / 0.697 = 1.15 / 0.604 = 1.903 for a solid with Poisson's ratio = 0.25
+# and for a fluid (see the manual of the 2D code, SPECFEM2D, Tables 4.1 and 4.2, and that ratio does not
+# depend on whether we are in 2D or in 3D). However in practice a ratio of about 1.5 to 1.7 is often safer
+# (for instance for models with a large range of Poisson's ratio values).
+# Since the code computes the time step using the Newmark scheme, for LDDRK we will simply
+# multiply that time step by this ratio when LDDRK is on and when flag INCREASE_CFL_FOR_LDDRK is true.
+INCREASE_CFL_FOR_LDDRK          = .true.
+RATIO_BY_WHICH_TO_INCREASE_IT   = 1.5d0
+
 # save AVS or OpenDX movies
 #MOVIE_COARSE saves movie only at corners of elements (SURFACE OR VOLUME)
 #MOVIE_COARSE does not work with create_movie_AVS_DX
@@ -125,6 +151,47 @@
 # print source time function
 PRINT_SOURCE_TIME_FUNCTION      = .false.
 
-# output kernels on a regular grid instead of on the mesh points
+#-----------------------------------------------------------
+#
+#  adjoint kernel outputs
+#
+#-----------------------------------------------------------
+
+# this parameter must be set to .true. to compute anisotropic kernels
+# in crust and mantle (related to the 21 Cij in geographical coordinates)
+# default is .false. to compute isotropic kernels (related to alpha and beta)
+ANISOTROPIC_KL                  = .false.
+
+# output only transverse isotropic kernels (alpha_v,alpha_h,beta_v,beta_h,eta,rho)
+# rather than fully anisotropic kernels when ANISOTROPIC_KL above is set to .true.
+# means to save radial anisotropic kernels, i.e., sensitivity kernels for beta_v, beta_h, etc.
+SAVE_TRANSVERSE_KL_ONLY         = .false.
+
+# output approximate Hessian in crust mantle region.
+# means to save the preconditioning for gradients, they are cross correlations between forward and adjoint accelerations.
+APPROXIMATE_HESS_KL             = .false.
+
+# forces transverse isotropy for all mantle elements
+# (default is to use transverse isotropy only between MOHO and 220)
+# means we allow radial anisotropy between the bottom of the crust to the bottom of the transition zone, i.e., 660~km depth.
+USE_FULL_TISO_MANTLE            = .false.
+
+# output kernel mask to zero out source region
+# to remove large values near the sources in the sensitivity kernels
+SAVE_SOURCE_MASK                = .false.
+
+# output kernels on a regular grid instead of on the GLL mesh points (a bit expensive)
 SAVE_REGULAR_KL                 = .false.
 
+#-----------------------------------------------------------
+
+# set to true to use GPUs
+GPU_MODE                        = .false.
+
+# set to true to use the ADIOS library for I/Os
+ADIOS_ENABLED                   = .false.
+ADIOS_FOR_FORWARD_ARRAYS        = .true.
+ADIOS_FOR_MPI_ARRAYS            = .true.
+ADIOS_FOR_ARRAYS_SOLVER         = .true.
+ADIOS_FOR_AVS_DX                = .true.
+

Modified: seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/global_PREM_kernels/amplitude/DATA/Par_file
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/global_PREM_kernels/amplitude/DATA/Par_file	2013-08-21 16:56:20 UTC (rev 22727)
+++ seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/global_PREM_kernels/amplitude/DATA/Par_file	2013-08-22 07:40:44 UTC (rev 22728)
@@ -57,10 +57,36 @@
 # to undo attenuation for sensitivity kernel calculations or forward runs with SAVE_FORWARD
 # use one (and only one) of the two flags below. UNDO_ATTENUATION is much better (it is exact)
 # but requires a significant amount of disk space for temporary storage.
+ATTENUATION_1D_WITH_3D_STORAGE  = .true.
 PARTIAL_PHYS_DISPERSION_ONLY    = .true.
 UNDO_ATTENUATION                = .false.
 NT_DUMP_ATTENUATION             = 100   # how often we dump restart files to undo attenuation, only needed when using UNDO_ATTENUATION
 
+# three mass matrices instead of one are needed to handle rotation very accurately;
+# otherwise rotation is handled slightly less accurately (but still reasonably well);
+# set to .true. if you are interested in precise effects related to rotation;
+# set to .false. if you are solving very large inverse problems at high frequency and also undoing attenuation exactly
+# using the UNDO_ATTENUATION flag above, in which case saving as much memory as possible can be a good idea.
+# You can also safely set it to .false. if you are not in a period range in which rotation matters, e.g. if you are targetting very short-period body waves.
+# if in doubt, set to .true.
+# Set it to .true. if you have ABSORBING_CONDITIONS above, because in that case the code will use the three mass matrices anyway
+# and thus there is no additional cost.
+# this flag is of course unused if ROTATION above is set to .false.
+EXACT_MASS_MATRIX_FOR_ROTATION  = .false.
+
+# this for LDDRK high-order time scheme instead of Newmark
+USE_LDDRK                       = .false.
+
+# the maximum CFL of LDDRK is significantly higher than that of the Newmark scheme,
+# in a ratio that is theoretically 1.327 / 0.697 = 1.15 / 0.604 = 1.903 for a solid with Poisson's ratio = 0.25
+# and for a fluid (see the manual of the 2D code, SPECFEM2D, Tables 4.1 and 4.2, and that ratio does not
+# depend on whether we are in 2D or in 3D). However in practice a ratio of about 1.5 to 1.7 is often safer
+# (for instance for models with a large range of Poisson's ratio values).
+# Since the code computes the time step using the Newmark scheme, for LDDRK we will simply
+# multiply that time step by this ratio when LDDRK is on and when flag INCREASE_CFL_FOR_LDDRK is true.
+INCREASE_CFL_FOR_LDDRK          = .true.
+RATIO_BY_WHICH_TO_INCREASE_IT   = 1.5d0
+
 # save AVS or OpenDX movies
 #MOVIE_COARSE saves movie only at corners of elements (SURFACE OR VOLUME)
 #MOVIE_COARSE does not work with create_movie_AVS_DX
@@ -125,6 +151,47 @@
 # print source time function
 PRINT_SOURCE_TIME_FUNCTION      = .false.
 
-# output kernels on a regular grid instead of on the mesh points
+#-----------------------------------------------------------
+#
+#  adjoint kernel outputs
+#
+#-----------------------------------------------------------
+
+# this parameter must be set to .true. to compute anisotropic kernels
+# in crust and mantle (related to the 21 Cij in geographical coordinates)
+# default is .false. to compute isotropic kernels (related to alpha and beta)
+ANISOTROPIC_KL                  = .false.
+
+# output only transverse isotropic kernels (alpha_v,alpha_h,beta_v,beta_h,eta,rho)
+# rather than fully anisotropic kernels when ANISOTROPIC_KL above is set to .true.
+# means to save radial anisotropic kernels, i.e., sensitivity kernels for beta_v, beta_h, etc.
+SAVE_TRANSVERSE_KL_ONLY         = .false.
+
+# output approximate Hessian in crust mantle region.
+# means to save the preconditioning for gradients, they are cross correlations between forward and adjoint accelerations.
+APPROXIMATE_HESS_KL             = .false.
+
+# forces transverse isotropy for all mantle elements
+# (default is to use transverse isotropy only between MOHO and 220)
+# means we allow radial anisotropy between the bottom of the crust to the bottom of the transition zone, i.e., 660~km depth.
+USE_FULL_TISO_MANTLE            = .false.
+
+# output kernel mask to zero out source region
+# to remove large values near the sources in the sensitivity kernels
+SAVE_SOURCE_MASK                = .false.
+
+# output kernels on a regular grid instead of on the GLL mesh points (a bit expensive)
 SAVE_REGULAR_KL                 = .false.
 
+#-----------------------------------------------------------
+
+# set to true to use GPUs
+GPU_MODE                        = .false.
+
+# set to true to use the ADIOS library for I/Os
+ADIOS_ENABLED                   = .false.
+ADIOS_FOR_FORWARD_ARRAYS        = .true.
+ADIOS_FOR_MPI_ARRAYS            = .true.
+ADIOS_FOR_ARRAYS_SOLVER         = .true.
+ADIOS_FOR_AVS_DX                = .true.
+

Modified: seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/global_PREM_kernels/traveltime/DATA/Par_file
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/global_PREM_kernels/traveltime/DATA/Par_file	2013-08-21 16:56:20 UTC (rev 22727)
+++ seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/global_PREM_kernels/traveltime/DATA/Par_file	2013-08-22 07:40:44 UTC (rev 22728)
@@ -57,10 +57,36 @@
 # to undo attenuation for sensitivity kernel calculations or forward runs with SAVE_FORWARD
 # use one (and only one) of the two flags below. UNDO_ATTENUATION is much better (it is exact)
 # but requires a significant amount of disk space for temporary storage.
+ATTENUATION_1D_WITH_3D_STORAGE  = .true.
 PARTIAL_PHYS_DISPERSION_ONLY    = .true.
 UNDO_ATTENUATION                = .false.
 NT_DUMP_ATTENUATION             = 100   # how often we dump restart files to undo attenuation, only needed when using UNDO_ATTENUATION
 
+# three mass matrices instead of one are needed to handle rotation very accurately;
+# otherwise rotation is handled slightly less accurately (but still reasonably well);
+# set to .true. if you are interested in precise effects related to rotation;
+# set to .false. if you are solving very large inverse problems at high frequency and also undoing attenuation exactly
+# using the UNDO_ATTENUATION flag above, in which case saving as much memory as possible can be a good idea.
+# You can also safely set it to .false. if you are not in a period range in which rotation matters, e.g. if you are targetting very short-period body waves.
+# if in doubt, set to .true.
+# Set it to .true. if you have ABSORBING_CONDITIONS above, because in that case the code will use the three mass matrices anyway
+# and thus there is no additional cost.
+# this flag is of course unused if ROTATION above is set to .false.
+EXACT_MASS_MATRIX_FOR_ROTATION  = .false.
+
+# this for LDDRK high-order time scheme instead of Newmark
+USE_LDDRK                       = .false.
+
+# the maximum CFL of LDDRK is significantly higher than that of the Newmark scheme,
+# in a ratio that is theoretically 1.327 / 0.697 = 1.15 / 0.604 = 1.903 for a solid with Poisson's ratio = 0.25
+# and for a fluid (see the manual of the 2D code, SPECFEM2D, Tables 4.1 and 4.2, and that ratio does not
+# depend on whether we are in 2D or in 3D). However in practice a ratio of about 1.5 to 1.7 is often safer
+# (for instance for models with a large range of Poisson's ratio values).
+# Since the code computes the time step using the Newmark scheme, for LDDRK we will simply
+# multiply that time step by this ratio when LDDRK is on and when flag INCREASE_CFL_FOR_LDDRK is true.
+INCREASE_CFL_FOR_LDDRK          = .true.
+RATIO_BY_WHICH_TO_INCREASE_IT   = 1.5d0
+
 # save AVS or OpenDX movies
 #MOVIE_COARSE saves movie only at corners of elements (SURFACE OR VOLUME)
 #MOVIE_COARSE does not work with create_movie_AVS_DX
@@ -125,6 +151,47 @@
 # print source time function
 PRINT_SOURCE_TIME_FUNCTION      = .false.
 
-# output kernels on a regular grid instead of on the mesh points
+#-----------------------------------------------------------
+#
+#  adjoint kernel outputs
+#
+#-----------------------------------------------------------
+
+# this parameter must be set to .true. to compute anisotropic kernels
+# in crust and mantle (related to the 21 Cij in geographical coordinates)
+# default is .false. to compute isotropic kernels (related to alpha and beta)
+ANISOTROPIC_KL                  = .false.
+
+# output only transverse isotropic kernels (alpha_v,alpha_h,beta_v,beta_h,eta,rho)
+# rather than fully anisotropic kernels when ANISOTROPIC_KL above is set to .true.
+# means to save radial anisotropic kernels, i.e., sensitivity kernels for beta_v, beta_h, etc.
+SAVE_TRANSVERSE_KL_ONLY         = .false.
+
+# output approximate Hessian in crust mantle region.
+# means to save the preconditioning for gradients, they are cross correlations between forward and adjoint accelerations.
+APPROXIMATE_HESS_KL             = .false.
+
+# forces transverse isotropy for all mantle elements
+# (default is to use transverse isotropy only between MOHO and 220)
+# means we allow radial anisotropy between the bottom of the crust to the bottom of the transition zone, i.e., 660~km depth.
+USE_FULL_TISO_MANTLE            = .false.
+
+# output kernel mask to zero out source region
+# to remove large values near the sources in the sensitivity kernels
+SAVE_SOURCE_MASK                = .false.
+
+# output kernels on a regular grid instead of on the GLL mesh points (a bit expensive)
 SAVE_REGULAR_KL                 = .false.
 
+#-----------------------------------------------------------
+
+# set to true to use GPUs
+GPU_MODE                        = .false.
+
+# set to true to use the ADIOS library for I/Os
+ADIOS_ENABLED                   = .false.
+ADIOS_FOR_FORWARD_ARRAYS        = .true.
+ADIOS_FOR_MPI_ARRAYS            = .true.
+ADIOS_FOR_ARRAYS_SOLVER         = .true.
+ADIOS_FOR_AVS_DX                = .true.
+

Modified: seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/global_s362ani/DATA/Par_file
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/global_s362ani/DATA/Par_file	2013-08-21 16:56:20 UTC (rev 22727)
+++ seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/global_s362ani/DATA/Par_file	2013-08-22 07:40:44 UTC (rev 22728)
@@ -57,10 +57,36 @@
 # to undo attenuation for sensitivity kernel calculations or forward runs with SAVE_FORWARD
 # use one (and only one) of the two flags below. UNDO_ATTENUATION is much better (it is exact)
 # but requires a significant amount of disk space for temporary storage.
+ATTENUATION_1D_WITH_3D_STORAGE  = .true.
 PARTIAL_PHYS_DISPERSION_ONLY    = .true.
 UNDO_ATTENUATION                = .false.
 NT_DUMP_ATTENUATION             = 100   # how often we dump restart files to undo attenuation, only needed when using UNDO_ATTENUATION
 
+# three mass matrices instead of one are needed to handle rotation very accurately;
+# otherwise rotation is handled slightly less accurately (but still reasonably well);
+# set to .true. if you are interested in precise effects related to rotation;
+# set to .false. if you are solving very large inverse problems at high frequency and also undoing attenuation exactly
+# using the UNDO_ATTENUATION flag above, in which case saving as much memory as possible can be a good idea.
+# You can also safely set it to .false. if you are not in a period range in which rotation matters, e.g. if you are targetting very short-period body waves.
+# if in doubt, set to .true.
+# Set it to .true. if you have ABSORBING_CONDITIONS above, because in that case the code will use the three mass matrices anyway
+# and thus there is no additional cost.
+# this flag is of course unused if ROTATION above is set to .false.
+EXACT_MASS_MATRIX_FOR_ROTATION  = .false.
+
+# this for LDDRK high-order time scheme instead of Newmark
+USE_LDDRK                       = .false.
+
+# the maximum CFL of LDDRK is significantly higher than that of the Newmark scheme,
+# in a ratio that is theoretically 1.327 / 0.697 = 1.15 / 0.604 = 1.903 for a solid with Poisson's ratio = 0.25
+# and for a fluid (see the manual of the 2D code, SPECFEM2D, Tables 4.1 and 4.2, and that ratio does not
+# depend on whether we are in 2D or in 3D). However in practice a ratio of about 1.5 to 1.7 is often safer
+# (for instance for models with a large range of Poisson's ratio values).
+# Since the code computes the time step using the Newmark scheme, for LDDRK we will simply
+# multiply that time step by this ratio when LDDRK is on and when flag INCREASE_CFL_FOR_LDDRK is true.
+INCREASE_CFL_FOR_LDDRK          = .true.
+RATIO_BY_WHICH_TO_INCREASE_IT   = 1.5d0
+
 # save AVS or OpenDX movies
 #MOVIE_COARSE saves movie only at corners of elements (SURFACE OR VOLUME)
 #MOVIE_COARSE does not work with create_movie_AVS_DX
@@ -125,6 +151,47 @@
 # print source time function
 PRINT_SOURCE_TIME_FUNCTION      = .false.
 
-# output kernels on a regular grid instead of on the mesh points
+#-----------------------------------------------------------
+#
+#  adjoint kernel outputs
+#
+#-----------------------------------------------------------
+
+# this parameter must be set to .true. to compute anisotropic kernels
+# in crust and mantle (related to the 21 Cij in geographical coordinates)
+# default is .false. to compute isotropic kernels (related to alpha and beta)
+ANISOTROPIC_KL                  = .false.
+
+# output only transverse isotropic kernels (alpha_v,alpha_h,beta_v,beta_h,eta,rho)
+# rather than fully anisotropic kernels when ANISOTROPIC_KL above is set to .true.
+# means to save radial anisotropic kernels, i.e., sensitivity kernels for beta_v, beta_h, etc.
+SAVE_TRANSVERSE_KL_ONLY         = .false.
+
+# output approximate Hessian in crust mantle region.
+# means to save the preconditioning for gradients, they are cross correlations between forward and adjoint accelerations.
+APPROXIMATE_HESS_KL             = .false.
+
+# forces transverse isotropy for all mantle elements
+# (default is to use transverse isotropy only between MOHO and 220)
+# means we allow radial anisotropy between the bottom of the crust to the bottom of the transition zone, i.e., 660~km depth.
+USE_FULL_TISO_MANTLE            = .false.
+
+# output kernel mask to zero out source region
+# to remove large values near the sources in the sensitivity kernels
+SAVE_SOURCE_MASK                = .false.
+
+# output kernels on a regular grid instead of on the GLL mesh points (a bit expensive)
 SAVE_REGULAR_KL                 = .false.
 
+#-----------------------------------------------------------
+
+# set to true to use GPUs
+GPU_MODE                        = .false.
+
+# set to true to use the ADIOS library for I/Os
+ADIOS_ENABLED                   = .false.
+ADIOS_FOR_FORWARD_ARRAYS        = .true.
+ADIOS_FOR_MPI_ARRAYS            = .true.
+ADIOS_FOR_ARRAYS_SOLVER         = .true.
+ADIOS_FOR_AVS_DX                = .true.
+

Modified: seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_long/Par_file_NOISE_1_attenuation
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_long/Par_file_NOISE_1_attenuation	2013-08-21 16:56:20 UTC (rev 22727)
+++ seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_long/Par_file_NOISE_1_attenuation	2013-08-22 07:40:44 UTC (rev 22728)
@@ -57,10 +57,36 @@
 # to undo attenuation for sensitivity kernel calculations or forward runs with SAVE_FORWARD
 # use one (and only one) of the two flags below. UNDO_ATTENUATION is much better (it is exact)
 # but requires a significant amount of disk space for temporary storage.
+ATTENUATION_1D_WITH_3D_STORAGE  = .true.
 PARTIAL_PHYS_DISPERSION_ONLY    = .true.
 UNDO_ATTENUATION                = .false.
 NT_DUMP_ATTENUATION             = 100   # how often we dump restart files to undo attenuation, only needed when using UNDO_ATTENUATION
 
+# three mass matrices instead of one are needed to handle rotation very accurately;
+# otherwise rotation is handled slightly less accurately (but still reasonably well);
+# set to .true. if you are interested in precise effects related to rotation;
+# set to .false. if you are solving very large inverse problems at high frequency and also undoing attenuation exactly
+# using the UNDO_ATTENUATION flag above, in which case saving as much memory as possible can be a good idea.
+# You can also safely set it to .false. if you are not in a period range in which rotation matters, e.g. if you are targetting very short-period body waves.
+# if in doubt, set to .true.
+# Set it to .true. if you have ABSORBING_CONDITIONS above, because in that case the code will use the three mass matrices anyway
+# and thus there is no additional cost.
+# this flag is of course unused if ROTATION above is set to .false.
+EXACT_MASS_MATRIX_FOR_ROTATION  = .false.
+
+# this for LDDRK high-order time scheme instead of Newmark
+USE_LDDRK                       = .false.
+
+# the maximum CFL of LDDRK is significantly higher than that of the Newmark scheme,
+# in a ratio that is theoretically 1.327 / 0.697 = 1.15 / 0.604 = 1.903 for a solid with Poisson's ratio = 0.25
+# and for a fluid (see the manual of the 2D code, SPECFEM2D, Tables 4.1 and 4.2, and that ratio does not
+# depend on whether we are in 2D or in 3D). However in practice a ratio of about 1.5 to 1.7 is often safer
+# (for instance for models with a large range of Poisson's ratio values).
+# Since the code computes the time step using the Newmark scheme, for LDDRK we will simply
+# multiply that time step by this ratio when LDDRK is on and when flag INCREASE_CFL_FOR_LDDRK is true.
+INCREASE_CFL_FOR_LDDRK          = .true.
+RATIO_BY_WHICH_TO_INCREASE_IT   = 1.5d0
+
 # save AVS or OpenDX movies
 #MOVIE_COARSE saves movie only at corners of elements (SURFACE OR VOLUME)
 #MOVIE_COARSE does not work with create_movie_AVS_DX
@@ -125,6 +151,47 @@
 # print source time function
 PRINT_SOURCE_TIME_FUNCTION      = .true.
 
-# output kernels on a regular grid instead of on the mesh points
+#-----------------------------------------------------------
+#
+#  adjoint kernel outputs
+#
+#-----------------------------------------------------------
+
+# this parameter must be set to .true. to compute anisotropic kernels
+# in crust and mantle (related to the 21 Cij in geographical coordinates)
+# default is .false. to compute isotropic kernels (related to alpha and beta)
+ANISOTROPIC_KL                  = .false.
+
+# output only transverse isotropic kernels (alpha_v,alpha_h,beta_v,beta_h,eta,rho)
+# rather than fully anisotropic kernels when ANISOTROPIC_KL above is set to .true.
+# means to save radial anisotropic kernels, i.e., sensitivity kernels for beta_v, beta_h, etc.
+SAVE_TRANSVERSE_KL_ONLY         = .false.
+
+# output approximate Hessian in crust mantle region.
+# means to save the preconditioning for gradients, they are cross correlations between forward and adjoint accelerations.
+APPROXIMATE_HESS_KL             = .false.
+
+# forces transverse isotropy for all mantle elements
+# (default is to use transverse isotropy only between MOHO and 220)
+# means we allow radial anisotropy between the bottom of the crust to the bottom of the transition zone, i.e., 660~km depth.
+USE_FULL_TISO_MANTLE            = .false.
+
+# output kernel mask to zero out source region
+# to remove large values near the sources in the sensitivity kernels
+SAVE_SOURCE_MASK                = .false.
+
+# output kernels on a regular grid instead of on the GLL mesh points (a bit expensive)
 SAVE_REGULAR_KL                 = .false.
 
+#-----------------------------------------------------------
+
+# set to true to use GPUs
+GPU_MODE                        = .false.
+
+# set to true to use the ADIOS library for I/Os
+ADIOS_ENABLED                   = .false.
+ADIOS_FOR_FORWARD_ARRAYS        = .true.
+ADIOS_FOR_MPI_ARRAYS            = .true.
+ADIOS_FOR_ARRAYS_SOLVER         = .true.
+ADIOS_FOR_AVS_DX                = .true.
+

Modified: seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_long/Par_file_NOISE_1_noattenuation
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_long/Par_file_NOISE_1_noattenuation	2013-08-21 16:56:20 UTC (rev 22727)
+++ seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_long/Par_file_NOISE_1_noattenuation	2013-08-22 07:40:44 UTC (rev 22728)
@@ -57,10 +57,36 @@
 # to undo attenuation for sensitivity kernel calculations or forward runs with SAVE_FORWARD
 # use one (and only one) of the two flags below. UNDO_ATTENUATION is much better (it is exact)
 # but requires a significant amount of disk space for temporary storage.
+ATTENUATION_1D_WITH_3D_STORAGE  = .true.
 PARTIAL_PHYS_DISPERSION_ONLY    = .false.
 UNDO_ATTENUATION                = .false.
 NT_DUMP_ATTENUATION             = 100   # how often we dump restart files to undo attenuation, only needed when using UNDO_ATTENUATION
 
+# three mass matrices instead of one are needed to handle rotation very accurately;
+# otherwise rotation is handled slightly less accurately (but still reasonably well);
+# set to .true. if you are interested in precise effects related to rotation;
+# set to .false. if you are solving very large inverse problems at high frequency and also undoing attenuation exactly
+# using the UNDO_ATTENUATION flag above, in which case saving as much memory as possible can be a good idea.
+# You can also safely set it to .false. if you are not in a period range in which rotation matters, e.g. if you are targetting very short-period body waves.
+# if in doubt, set to .true.
+# Set it to .true. if you have ABSORBING_CONDITIONS above, because in that case the code will use the three mass matrices anyway
+# and thus there is no additional cost.
+# this flag is of course unused if ROTATION above is set to .false.
+EXACT_MASS_MATRIX_FOR_ROTATION  = .false.
+
+# this for LDDRK high-order time scheme instead of Newmark
+USE_LDDRK                       = .false.
+
+# the maximum CFL of LDDRK is significantly higher than that of the Newmark scheme,
+# in a ratio that is theoretically 1.327 / 0.697 = 1.15 / 0.604 = 1.903 for a solid with Poisson's ratio = 0.25
+# and for a fluid (see the manual of the 2D code, SPECFEM2D, Tables 4.1 and 4.2, and that ratio does not
+# depend on whether we are in 2D or in 3D). However in practice a ratio of about 1.5 to 1.7 is often safer
+# (for instance for models with a large range of Poisson's ratio values).
+# Since the code computes the time step using the Newmark scheme, for LDDRK we will simply
+# multiply that time step by this ratio when LDDRK is on and when flag INCREASE_CFL_FOR_LDDRK is true.
+INCREASE_CFL_FOR_LDDRK          = .true.
+RATIO_BY_WHICH_TO_INCREASE_IT   = 1.5d0
+
 # save AVS or OpenDX movies
 #MOVIE_COARSE saves movie only at corners of elements (SURFACE OR VOLUME)
 #MOVIE_COARSE does not work with create_movie_AVS_DX
@@ -125,6 +151,47 @@
 # print source time function
 PRINT_SOURCE_TIME_FUNCTION      = .true.
 
-# output kernels on a regular grid instead of on the mesh points
+#-----------------------------------------------------------
+#
+#  adjoint kernel outputs
+#
+#-----------------------------------------------------------
+
+# this parameter must be set to .true. to compute anisotropic kernels
+# in crust and mantle (related to the 21 Cij in geographical coordinates)
+# default is .false. to compute isotropic kernels (related to alpha and beta)
+ANISOTROPIC_KL                  = .false.
+
+# output only transverse isotropic kernels (alpha_v,alpha_h,beta_v,beta_h,eta,rho)
+# rather than fully anisotropic kernels when ANISOTROPIC_KL above is set to .true.
+# means to save radial anisotropic kernels, i.e., sensitivity kernels for beta_v, beta_h, etc.
+SAVE_TRANSVERSE_KL_ONLY         = .false.
+
+# output approximate Hessian in crust mantle region.
+# means to save the preconditioning for gradients, they are cross correlations between forward and adjoint accelerations.
+APPROXIMATE_HESS_KL             = .false.
+
+# forces transverse isotropy for all mantle elements
+# (default is to use transverse isotropy only between MOHO and 220)
+# means we allow radial anisotropy between the bottom of the crust to the bottom of the transition zone, i.e., 660~km depth.
+USE_FULL_TISO_MANTLE            = .false.
+
+# output kernel mask to zero out source region
+# to remove large values near the sources in the sensitivity kernels
+SAVE_SOURCE_MASK                = .false.
+
+# output kernels on a regular grid instead of on the GLL mesh points (a bit expensive)
 SAVE_REGULAR_KL                 = .false.
 
+#-----------------------------------------------------------
+
+# set to true to use GPUs
+GPU_MODE                        = .false.
+
+# set to true to use the ADIOS library for I/Os
+ADIOS_ENABLED                   = .false.
+ADIOS_FOR_FORWARD_ARRAYS        = .true.
+ADIOS_FOR_MPI_ARRAYS            = .true.
+ADIOS_FOR_ARRAYS_SOLVER         = .true.
+ADIOS_FOR_AVS_DX                = .true.
+

Modified: seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_long/Par_file_NOISE_2_attenuation
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_long/Par_file_NOISE_2_attenuation	2013-08-21 16:56:20 UTC (rev 22727)
+++ seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_long/Par_file_NOISE_2_attenuation	2013-08-22 07:40:44 UTC (rev 22728)
@@ -57,10 +57,36 @@
 # to undo attenuation for sensitivity kernel calculations or forward runs with SAVE_FORWARD
 # use one (and only one) of the two flags below. UNDO_ATTENUATION is much better (it is exact)
 # but requires a significant amount of disk space for temporary storage.
+ATTENUATION_1D_WITH_3D_STORAGE  = .true.
 PARTIAL_PHYS_DISPERSION_ONLY    = .true.
 UNDO_ATTENUATION                = .false.
 NT_DUMP_ATTENUATION             = 100   # how often we dump restart files to undo attenuation, only needed when using UNDO_ATTENUATION
 
+# three mass matrices instead of one are needed to handle rotation very accurately;
+# otherwise rotation is handled slightly less accurately (but still reasonably well);
+# set to .true. if you are interested in precise effects related to rotation;
+# set to .false. if you are solving very large inverse problems at high frequency and also undoing attenuation exactly
+# using the UNDO_ATTENUATION flag above, in which case saving as much memory as possible can be a good idea.
+# You can also safely set it to .false. if you are not in a period range in which rotation matters, e.g. if you are targetting very short-period body waves.
+# if in doubt, set to .true.
+# Set it to .true. if you have ABSORBING_CONDITIONS above, because in that case the code will use the three mass matrices anyway
+# and thus there is no additional cost.
+# this flag is of course unused if ROTATION above is set to .false.
+EXACT_MASS_MATRIX_FOR_ROTATION  = .false.
+
+# this for LDDRK high-order time scheme instead of Newmark
+USE_LDDRK                       = .false.
+
+# the maximum CFL of LDDRK is significantly higher than that of the Newmark scheme,
+# in a ratio that is theoretically 1.327 / 0.697 = 1.15 / 0.604 = 1.903 for a solid with Poisson's ratio = 0.25
+# and for a fluid (see the manual of the 2D code, SPECFEM2D, Tables 4.1 and 4.2, and that ratio does not
+# depend on whether we are in 2D or in 3D). However in practice a ratio of about 1.5 to 1.7 is often safer
+# (for instance for models with a large range of Poisson's ratio values).
+# Since the code computes the time step using the Newmark scheme, for LDDRK we will simply
+# multiply that time step by this ratio when LDDRK is on and when flag INCREASE_CFL_FOR_LDDRK is true.
+INCREASE_CFL_FOR_LDDRK          = .true.
+RATIO_BY_WHICH_TO_INCREASE_IT   = 1.5d0
+
 # save AVS or OpenDX movies
 #MOVIE_COARSE saves movie only at corners of elements (SURFACE OR VOLUME)
 #MOVIE_COARSE does not work with create_movie_AVS_DX
@@ -125,6 +151,47 @@
 # print source time function
 PRINT_SOURCE_TIME_FUNCTION      = .true.
 
-# output kernels on a regular grid instead of on the mesh points
+#-----------------------------------------------------------
+#
+#  adjoint kernel outputs
+#
+#-----------------------------------------------------------
+
+# this parameter must be set to .true. to compute anisotropic kernels
+# in crust and mantle (related to the 21 Cij in geographical coordinates)
+# default is .false. to compute isotropic kernels (related to alpha and beta)
+ANISOTROPIC_KL                  = .false.
+
+# output only transverse isotropic kernels (alpha_v,alpha_h,beta_v,beta_h,eta,rho)
+# rather than fully anisotropic kernels when ANISOTROPIC_KL above is set to .true.
+# means to save radial anisotropic kernels, i.e., sensitivity kernels for beta_v, beta_h, etc.
+SAVE_TRANSVERSE_KL_ONLY         = .false.
+
+# output approximate Hessian in crust mantle region.
+# means to save the preconditioning for gradients, they are cross correlations between forward and adjoint accelerations.
+APPROXIMATE_HESS_KL             = .false.
+
+# forces transverse isotropy for all mantle elements
+# (default is to use transverse isotropy only between MOHO and 220)
+# means we allow radial anisotropy between the bottom of the crust to the bottom of the transition zone, i.e., 660~km depth.
+USE_FULL_TISO_MANTLE            = .false.
+
+# output kernel mask to zero out source region
+# to remove large values near the sources in the sensitivity kernels
+SAVE_SOURCE_MASK                = .false.
+
+# output kernels on a regular grid instead of on the GLL mesh points (a bit expensive)
 SAVE_REGULAR_KL                 = .false.
 
+#-----------------------------------------------------------
+
+# set to true to use GPUs
+GPU_MODE                        = .false.
+
+# set to true to use the ADIOS library for I/Os
+ADIOS_ENABLED                   = .false.
+ADIOS_FOR_FORWARD_ARRAYS        = .true.
+ADIOS_FOR_MPI_ARRAYS            = .true.
+ADIOS_FOR_ARRAYS_SOLVER         = .true.
+ADIOS_FOR_AVS_DX                = .true.
+

Modified: seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_long/Par_file_NOISE_2_noattenuation
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_long/Par_file_NOISE_2_noattenuation	2013-08-21 16:56:20 UTC (rev 22727)
+++ seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_long/Par_file_NOISE_2_noattenuation	2013-08-22 07:40:44 UTC (rev 22728)
@@ -57,10 +57,36 @@
 # to undo attenuation for sensitivity kernel calculations or forward runs with SAVE_FORWARD
 # use one (and only one) of the two flags below. UNDO_ATTENUATION is much better (it is exact)
 # but requires a significant amount of disk space for temporary storage.
+ATTENUATION_1D_WITH_3D_STORAGE  = .true.
 PARTIAL_PHYS_DISPERSION_ONLY    = .false.
 UNDO_ATTENUATION                = .false.
 NT_DUMP_ATTENUATION             = 100   # how often we dump restart files to undo attenuation, only needed when using UNDO_ATTENUATION
 
+# three mass matrices instead of one are needed to handle rotation very accurately;
+# otherwise rotation is handled slightly less accurately (but still reasonably well);
+# set to .true. if you are interested in precise effects related to rotation;
+# set to .false. if you are solving very large inverse problems at high frequency and also undoing attenuation exactly
+# using the UNDO_ATTENUATION flag above, in which case saving as much memory as possible can be a good idea.
+# You can also safely set it to .false. if you are not in a period range in which rotation matters, e.g. if you are targetting very short-period body waves.
+# if in doubt, set to .true.
+# Set it to .true. if you have ABSORBING_CONDITIONS above, because in that case the code will use the three mass matrices anyway
+# and thus there is no additional cost.
+# this flag is of course unused if ROTATION above is set to .false.
+EXACT_MASS_MATRIX_FOR_ROTATION  = .false.
+
+# this for LDDRK high-order time scheme instead of Newmark
+USE_LDDRK                       = .false.
+
+# the maximum CFL of LDDRK is significantly higher than that of the Newmark scheme,
+# in a ratio that is theoretically 1.327 / 0.697 = 1.15 / 0.604 = 1.903 for a solid with Poisson's ratio = 0.25
+# and for a fluid (see the manual of the 2D code, SPECFEM2D, Tables 4.1 and 4.2, and that ratio does not
+# depend on whether we are in 2D or in 3D). However in practice a ratio of about 1.5 to 1.7 is often safer
+# (for instance for models with a large range of Poisson's ratio values).
+# Since the code computes the time step using the Newmark scheme, for LDDRK we will simply
+# multiply that time step by this ratio when LDDRK is on and when flag INCREASE_CFL_FOR_LDDRK is true.
+INCREASE_CFL_FOR_LDDRK          = .true.
+RATIO_BY_WHICH_TO_INCREASE_IT   = 1.5d0
+
 # save AVS or OpenDX movies
 #MOVIE_COARSE saves movie only at corners of elements (SURFACE OR VOLUME)
 #MOVIE_COARSE does not work with create_movie_AVS_DX
@@ -125,6 +151,47 @@
 # print source time function
 PRINT_SOURCE_TIME_FUNCTION      = .true.
 
-# output kernels on a regular grid instead of on the mesh points
+#-----------------------------------------------------------
+#
+#  adjoint kernel outputs
+#
+#-----------------------------------------------------------
+
+# this parameter must be set to .true. to compute anisotropic kernels
+# in crust and mantle (related to the 21 Cij in geographical coordinates)
+# default is .false. to compute isotropic kernels (related to alpha and beta)
+ANISOTROPIC_KL                  = .false.
+
+# output only transverse isotropic kernels (alpha_v,alpha_h,beta_v,beta_h,eta,rho)
+# rather than fully anisotropic kernels when ANISOTROPIC_KL above is set to .true.
+# means to save radial anisotropic kernels, i.e., sensitivity kernels for beta_v, beta_h, etc.
+SAVE_TRANSVERSE_KL_ONLY         = .false.
+
+# output approximate Hessian in crust mantle region.
+# means to save the preconditioning for gradients, they are cross correlations between forward and adjoint accelerations.
+APPROXIMATE_HESS_KL             = .false.
+
+# forces transverse isotropy for all mantle elements
+# (default is to use transverse isotropy only between MOHO and 220)
+# means we allow radial anisotropy between the bottom of the crust to the bottom of the transition zone, i.e., 660~km depth.
+USE_FULL_TISO_MANTLE            = .false.
+
+# output kernel mask to zero out source region
+# to remove large values near the sources in the sensitivity kernels
+SAVE_SOURCE_MASK                = .false.
+
+# output kernels on a regular grid instead of on the GLL mesh points (a bit expensive)
 SAVE_REGULAR_KL                 = .false.
 
+#-----------------------------------------------------------
+
+# set to true to use GPUs
+GPU_MODE                        = .false.
+
+# set to true to use the ADIOS library for I/Os
+ADIOS_ENABLED                   = .false.
+ADIOS_FOR_FORWARD_ARRAYS        = .true.
+ADIOS_FOR_MPI_ARRAYS            = .true.
+ADIOS_FOR_ARRAYS_SOLVER         = .true.
+ADIOS_FOR_AVS_DX                = .true.
+

Modified: seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_long/Par_file_NOISE_3_noattenuation
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_long/Par_file_NOISE_3_noattenuation	2013-08-21 16:56:20 UTC (rev 22727)
+++ seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_long/Par_file_NOISE_3_noattenuation	2013-08-22 07:40:44 UTC (rev 22728)
@@ -57,10 +57,36 @@
 # to undo attenuation for sensitivity kernel calculations or forward runs with SAVE_FORWARD
 # use one (and only one) of the two flags below. UNDO_ATTENUATION is much better (it is exact)
 # but requires a significant amount of disk space for temporary storage.
+ATTENUATION_1D_WITH_3D_STORAGE  = .true.
 PARTIAL_PHYS_DISPERSION_ONLY    = .false.
 UNDO_ATTENUATION                = .false.
 NT_DUMP_ATTENUATION             = 100   # how often we dump restart files to undo attenuation, only needed when using UNDO_ATTENUATION
 
+# three mass matrices instead of one are needed to handle rotation very accurately;
+# otherwise rotation is handled slightly less accurately (but still reasonably well);
+# set to .true. if you are interested in precise effects related to rotation;
+# set to .false. if you are solving very large inverse problems at high frequency and also undoing attenuation exactly
+# using the UNDO_ATTENUATION flag above, in which case saving as much memory as possible can be a good idea.
+# You can also safely set it to .false. if you are not in a period range in which rotation matters, e.g. if you are targetting very short-period body waves.
+# if in doubt, set to .true.
+# Set it to .true. if you have ABSORBING_CONDITIONS above, because in that case the code will use the three mass matrices anyway
+# and thus there is no additional cost.
+# this flag is of course unused if ROTATION above is set to .false.
+EXACT_MASS_MATRIX_FOR_ROTATION  = .false.
+
+# this for LDDRK high-order time scheme instead of Newmark
+USE_LDDRK                       = .false.
+
+# the maximum CFL of LDDRK is significantly higher than that of the Newmark scheme,
+# in a ratio that is theoretically 1.327 / 0.697 = 1.15 / 0.604 = 1.903 for a solid with Poisson's ratio = 0.25
+# and for a fluid (see the manual of the 2D code, SPECFEM2D, Tables 4.1 and 4.2, and that ratio does not
+# depend on whether we are in 2D or in 3D). However in practice a ratio of about 1.5 to 1.7 is often safer
+# (for instance for models with a large range of Poisson's ratio values).
+# Since the code computes the time step using the Newmark scheme, for LDDRK we will simply
+# multiply that time step by this ratio when LDDRK is on and when flag INCREASE_CFL_FOR_LDDRK is true.
+INCREASE_CFL_FOR_LDDRK          = .true.
+RATIO_BY_WHICH_TO_INCREASE_IT   = 1.5d0
+
 # save AVS or OpenDX movies
 #MOVIE_COARSE saves movie only at corners of elements (SURFACE OR VOLUME)
 #MOVIE_COARSE does not work with create_movie_AVS_DX
@@ -125,6 +151,47 @@
 # print source time function
 PRINT_SOURCE_TIME_FUNCTION      = .true.
 
-# output kernels on a regular grid instead of on the mesh points
+#-----------------------------------------------------------
+#
+#  adjoint kernel outputs
+#
+#-----------------------------------------------------------
+
+# this parameter must be set to .true. to compute anisotropic kernels
+# in crust and mantle (related to the 21 Cij in geographical coordinates)
+# default is .false. to compute isotropic kernels (related to alpha and beta)
+ANISOTROPIC_KL                  = .false.
+
+# output only transverse isotropic kernels (alpha_v,alpha_h,beta_v,beta_h,eta,rho)
+# rather than fully anisotropic kernels when ANISOTROPIC_KL above is set to .true.
+# means to save radial anisotropic kernels, i.e., sensitivity kernels for beta_v, beta_h, etc.
+SAVE_TRANSVERSE_KL_ONLY         = .false.
+
+# output approximate Hessian in crust mantle region.
+# means to save the preconditioning for gradients, they are cross correlations between forward and adjoint accelerations.
+APPROXIMATE_HESS_KL             = .false.
+
+# forces transverse isotropy for all mantle elements
+# (default is to use transverse isotropy only between MOHO and 220)
+# means we allow radial anisotropy between the bottom of the crust to the bottom of the transition zone, i.e., 660~km depth.
+USE_FULL_TISO_MANTLE            = .false.
+
+# output kernel mask to zero out source region
+# to remove large values near the sources in the sensitivity kernels
+SAVE_SOURCE_MASK                = .false.
+
+# output kernels on a regular grid instead of on the GLL mesh points (a bit expensive)
 SAVE_REGULAR_KL                 = .false.
 
+#-----------------------------------------------------------
+
+# set to true to use GPUs
+GPU_MODE                        = .false.
+
+# set to true to use the ADIOS library for I/Os
+ADIOS_ENABLED                   = .false.
+ADIOS_FOR_FORWARD_ARRAYS        = .true.
+ADIOS_FOR_MPI_ARRAYS            = .true.
+ADIOS_FOR_ARRAYS_SOLVER         = .true.
+ADIOS_FOR_AVS_DX                = .true.
+

Modified: seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_short/Par_file_NOISE_1_attenuation
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_short/Par_file_NOISE_1_attenuation	2013-08-21 16:56:20 UTC (rev 22727)
+++ seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_short/Par_file_NOISE_1_attenuation	2013-08-22 07:40:44 UTC (rev 22728)
@@ -57,10 +57,36 @@
 # to undo attenuation for sensitivity kernel calculations or forward runs with SAVE_FORWARD
 # use one (and only one) of the two flags below. UNDO_ATTENUATION is much better (it is exact)
 # but requires a significant amount of disk space for temporary storage.
+ATTENUATION_1D_WITH_3D_STORAGE  = .true.
 PARTIAL_PHYS_DISPERSION_ONLY    = .true.
 UNDO_ATTENUATION                = .false.
 NT_DUMP_ATTENUATION             = 100   # how often we dump restart files to undo attenuation, only needed when using UNDO_ATTENUATION
 
+# three mass matrices instead of one are needed to handle rotation very accurately;
+# otherwise rotation is handled slightly less accurately (but still reasonably well);
+# set to .true. if you are interested in precise effects related to rotation;
+# set to .false. if you are solving very large inverse problems at high frequency and also undoing attenuation exactly
+# using the UNDO_ATTENUATION flag above, in which case saving as much memory as possible can be a good idea.
+# You can also safely set it to .false. if you are not in a period range in which rotation matters, e.g. if you are targetting very short-period body waves.
+# if in doubt, set to .true.
+# Set it to .true. if you have ABSORBING_CONDITIONS above, because in that case the code will use the three mass matrices anyway
+# and thus there is no additional cost.
+# this flag is of course unused if ROTATION above is set to .false.
+EXACT_MASS_MATRIX_FOR_ROTATION  = .false.
+
+# this for LDDRK high-order time scheme instead of Newmark
+USE_LDDRK                       = .false.
+
+# the maximum CFL of LDDRK is significantly higher than that of the Newmark scheme,
+# in a ratio that is theoretically 1.327 / 0.697 = 1.15 / 0.604 = 1.903 for a solid with Poisson's ratio = 0.25
+# and for a fluid (see the manual of the 2D code, SPECFEM2D, Tables 4.1 and 4.2, and that ratio does not
+# depend on whether we are in 2D or in 3D). However in practice a ratio of about 1.5 to 1.7 is often safer
+# (for instance for models with a large range of Poisson's ratio values).
+# Since the code computes the time step using the Newmark scheme, for LDDRK we will simply
+# multiply that time step by this ratio when LDDRK is on and when flag INCREASE_CFL_FOR_LDDRK is true.
+INCREASE_CFL_FOR_LDDRK          = .true.
+RATIO_BY_WHICH_TO_INCREASE_IT   = 1.5d0
+
 # save AVS or OpenDX movies
 #MOVIE_COARSE saves movie only at corners of elements (SURFACE OR VOLUME)
 #MOVIE_COARSE does not work with create_movie_AVS_DX
@@ -125,6 +151,47 @@
 # print source time function
 PRINT_SOURCE_TIME_FUNCTION      = .true.
 
-# output kernels on a regular grid instead of on the mesh points
+#-----------------------------------------------------------
+#
+#  adjoint kernel outputs
+#
+#-----------------------------------------------------------
+
+# this parameter must be set to .true. to compute anisotropic kernels
+# in crust and mantle (related to the 21 Cij in geographical coordinates)
+# default is .false. to compute isotropic kernels (related to alpha and beta)
+ANISOTROPIC_KL                  = .false.
+
+# output only transverse isotropic kernels (alpha_v,alpha_h,beta_v,beta_h,eta,rho)
+# rather than fully anisotropic kernels when ANISOTROPIC_KL above is set to .true.
+# means to save radial anisotropic kernels, i.e., sensitivity kernels for beta_v, beta_h, etc.
+SAVE_TRANSVERSE_KL_ONLY         = .false.
+
+# output approximate Hessian in crust mantle region.
+# means to save the preconditioning for gradients, they are cross correlations between forward and adjoint accelerations.
+APPROXIMATE_HESS_KL             = .false.
+
+# forces transverse isotropy for all mantle elements
+# (default is to use transverse isotropy only between MOHO and 220)
+# means we allow radial anisotropy between the bottom of the crust to the bottom of the transition zone, i.e., 660~km depth.
+USE_FULL_TISO_MANTLE            = .false.
+
+# output kernel mask to zero out source region
+# to remove large values near the sources in the sensitivity kernels
+SAVE_SOURCE_MASK                = .false.
+
+# output kernels on a regular grid instead of on the GLL mesh points (a bit expensive)
 SAVE_REGULAR_KL                 = .false.
 
+#-----------------------------------------------------------
+
+# set to true to use GPUs
+GPU_MODE                        = .false.
+
+# set to true to use the ADIOS library for I/Os
+ADIOS_ENABLED                   = .false.
+ADIOS_FOR_FORWARD_ARRAYS        = .true.
+ADIOS_FOR_MPI_ARRAYS            = .true.
+ADIOS_FOR_ARRAYS_SOLVER         = .true.
+ADIOS_FOR_AVS_DX                = .true.
+

Modified: seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_short/Par_file_NOISE_1_noattenuation
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_short/Par_file_NOISE_1_noattenuation	2013-08-21 16:56:20 UTC (rev 22727)
+++ seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_short/Par_file_NOISE_1_noattenuation	2013-08-22 07:40:44 UTC (rev 22728)
@@ -57,10 +57,36 @@
 # to undo attenuation for sensitivity kernel calculations or forward runs with SAVE_FORWARD
 # use one (and only one) of the two flags below. UNDO_ATTENUATION is much better (it is exact)
 # but requires a significant amount of disk space for temporary storage.
+ATTENUATION_1D_WITH_3D_STORAGE  = .true.
 PARTIAL_PHYS_DISPERSION_ONLY    = .false.
 UNDO_ATTENUATION                = .false.
 NT_DUMP_ATTENUATION             = 100   # how often we dump restart files to undo attenuation, only needed when using UNDO_ATTENUATION
 
+# three mass matrices instead of one are needed to handle rotation very accurately;
+# otherwise rotation is handled slightly less accurately (but still reasonably well);
+# set to .true. if you are interested in precise effects related to rotation;
+# set to .false. if you are solving very large inverse problems at high frequency and also undoing attenuation exactly
+# using the UNDO_ATTENUATION flag above, in which case saving as much memory as possible can be a good idea.
+# You can also safely set it to .false. if you are not in a period range in which rotation matters, e.g. if you are targetting very short-period body waves.
+# if in doubt, set to .true.
+# Set it to .true. if you have ABSORBING_CONDITIONS above, because in that case the code will use the three mass matrices anyway
+# and thus there is no additional cost.
+# this flag is of course unused if ROTATION above is set to .false.
+EXACT_MASS_MATRIX_FOR_ROTATION  = .false.
+
+# this for LDDRK high-order time scheme instead of Newmark
+USE_LDDRK                       = .false.
+
+# the maximum CFL of LDDRK is significantly higher than that of the Newmark scheme,
+# in a ratio that is theoretically 1.327 / 0.697 = 1.15 / 0.604 = 1.903 for a solid with Poisson's ratio = 0.25
+# and for a fluid (see the manual of the 2D code, SPECFEM2D, Tables 4.1 and 4.2, and that ratio does not
+# depend on whether we are in 2D or in 3D). However in practice a ratio of about 1.5 to 1.7 is often safer
+# (for instance for models with a large range of Poisson's ratio values).
+# Since the code computes the time step using the Newmark scheme, for LDDRK we will simply
+# multiply that time step by this ratio when LDDRK is on and when flag INCREASE_CFL_FOR_LDDRK is true.
+INCREASE_CFL_FOR_LDDRK          = .true.
+RATIO_BY_WHICH_TO_INCREASE_IT   = 1.5d0
+
 # save AVS or OpenDX movies
 #MOVIE_COARSE saves movie only at corners of elements (SURFACE OR VOLUME)
 #MOVIE_COARSE does not work with create_movie_AVS_DX
@@ -125,6 +151,47 @@
 # print source time function
 PRINT_SOURCE_TIME_FUNCTION      = .true.
 
-# output kernels on a regular grid instead of on the mesh points
+#-----------------------------------------------------------
+#
+#  adjoint kernel outputs
+#
+#-----------------------------------------------------------
+
+# this parameter must be set to .true. to compute anisotropic kernels
+# in crust and mantle (related to the 21 Cij in geographical coordinates)
+# default is .false. to compute isotropic kernels (related to alpha and beta)
+ANISOTROPIC_KL                  = .false.
+
+# output only transverse isotropic kernels (alpha_v,alpha_h,beta_v,beta_h,eta,rho)
+# rather than fully anisotropic kernels when ANISOTROPIC_KL above is set to .true.
+# means to save radial anisotropic kernels, i.e., sensitivity kernels for beta_v, beta_h, etc.
+SAVE_TRANSVERSE_KL_ONLY         = .false.
+
+# output approximate Hessian in crust mantle region.
+# means to save the preconditioning for gradients, they are cross correlations between forward and adjoint accelerations.
+APPROXIMATE_HESS_KL             = .false.
+
+# forces transverse isotropy for all mantle elements
+# (default is to use transverse isotropy only between MOHO and 220)
+# means we allow radial anisotropy between the bottom of the crust to the bottom of the transition zone, i.e., 660~km depth.
+USE_FULL_TISO_MANTLE            = .false.
+
+# output kernel mask to zero out source region
+# to remove large values near the sources in the sensitivity kernels
+SAVE_SOURCE_MASK                = .false.
+
+# output kernels on a regular grid instead of on the GLL mesh points (a bit expensive)
 SAVE_REGULAR_KL                 = .false.
 
+#-----------------------------------------------------------
+
+# set to true to use GPUs
+GPU_MODE                        = .false.
+
+# set to true to use the ADIOS library for I/Os
+ADIOS_ENABLED                   = .false.
+ADIOS_FOR_FORWARD_ARRAYS        = .true.
+ADIOS_FOR_MPI_ARRAYS            = .true.
+ADIOS_FOR_ARRAYS_SOLVER         = .true.
+ADIOS_FOR_AVS_DX                = .true.
+

Modified: seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_short/Par_file_NOISE_2_attenuation
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_short/Par_file_NOISE_2_attenuation	2013-08-21 16:56:20 UTC (rev 22727)
+++ seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_short/Par_file_NOISE_2_attenuation	2013-08-22 07:40:44 UTC (rev 22728)
@@ -57,10 +57,36 @@
 # to undo attenuation for sensitivity kernel calculations or forward runs with SAVE_FORWARD
 # use one (and only one) of the two flags below. UNDO_ATTENUATION is much better (it is exact)
 # but requires a significant amount of disk space for temporary storage.
+ATTENUATION_1D_WITH_3D_STORAGE  = .true.
 PARTIAL_PHYS_DISPERSION_ONLY    = .true.
 UNDO_ATTENUATION                = .false.
 NT_DUMP_ATTENUATION             = 100   # how often we dump restart files to undo attenuation, only needed when using UNDO_ATTENUATION
 
+# three mass matrices instead of one are needed to handle rotation very accurately;
+# otherwise rotation is handled slightly less accurately (but still reasonably well);
+# set to .true. if you are interested in precise effects related to rotation;
+# set to .false. if you are solving very large inverse problems at high frequency and also undoing attenuation exactly
+# using the UNDO_ATTENUATION flag above, in which case saving as much memory as possible can be a good idea.
+# You can also safely set it to .false. if you are not in a period range in which rotation matters, e.g. if you are targetting very short-period body waves.
+# if in doubt, set to .true.
+# Set it to .true. if you have ABSORBING_CONDITIONS above, because in that case the code will use the three mass matrices anyway
+# and thus there is no additional cost.
+# this flag is of course unused if ROTATION above is set to .false.
+EXACT_MASS_MATRIX_FOR_ROTATION  = .false.
+
+# this for LDDRK high-order time scheme instead of Newmark
+USE_LDDRK                       = .false.
+
+# the maximum CFL of LDDRK is significantly higher than that of the Newmark scheme,
+# in a ratio that is theoretically 1.327 / 0.697 = 1.15 / 0.604 = 1.903 for a solid with Poisson's ratio = 0.25
+# and for a fluid (see the manual of the 2D code, SPECFEM2D, Tables 4.1 and 4.2, and that ratio does not
+# depend on whether we are in 2D or in 3D). However in practice a ratio of about 1.5 to 1.7 is often safer
+# (for instance for models with a large range of Poisson's ratio values).
+# Since the code computes the time step using the Newmark scheme, for LDDRK we will simply
+# multiply that time step by this ratio when LDDRK is on and when flag INCREASE_CFL_FOR_LDDRK is true.
+INCREASE_CFL_FOR_LDDRK          = .true.
+RATIO_BY_WHICH_TO_INCREASE_IT   = 1.5d0
+
 # save AVS or OpenDX movies
 #MOVIE_COARSE saves movie only at corners of elements (SURFACE OR VOLUME)
 #MOVIE_COARSE does not work with create_movie_AVS_DX
@@ -125,6 +151,47 @@
 # print source time function
 PRINT_SOURCE_TIME_FUNCTION      = .true.
 
-# output kernels on a regular grid instead of on the mesh points
+#-----------------------------------------------------------
+#
+#  adjoint kernel outputs
+#
+#-----------------------------------------------------------
+
+# this parameter must be set to .true. to compute anisotropic kernels
+# in crust and mantle (related to the 21 Cij in geographical coordinates)
+# default is .false. to compute isotropic kernels (related to alpha and beta)
+ANISOTROPIC_KL                  = .false.
+
+# output only transverse isotropic kernels (alpha_v,alpha_h,beta_v,beta_h,eta,rho)
+# rather than fully anisotropic kernels when ANISOTROPIC_KL above is set to .true.
+# means to save radial anisotropic kernels, i.e., sensitivity kernels for beta_v, beta_h, etc.
+SAVE_TRANSVERSE_KL_ONLY         = .false.
+
+# output approximate Hessian in crust mantle region.
+# means to save the preconditioning for gradients, they are cross correlations between forward and adjoint accelerations.
+APPROXIMATE_HESS_KL             = .false.
+
+# forces transverse isotropy for all mantle elements
+# (default is to use transverse isotropy only between MOHO and 220)
+# means we allow radial anisotropy between the bottom of the crust to the bottom of the transition zone, i.e., 660~km depth.
+USE_FULL_TISO_MANTLE            = .false.
+
+# output kernel mask to zero out source region
+# to remove large values near the sources in the sensitivity kernels
+SAVE_SOURCE_MASK                = .false.
+
+# output kernels on a regular grid instead of on the GLL mesh points (a bit expensive)
 SAVE_REGULAR_KL                 = .false.
 
+#-----------------------------------------------------------
+
+# set to true to use GPUs
+GPU_MODE                        = .false.
+
+# set to true to use the ADIOS library for I/Os
+ADIOS_ENABLED                   = .false.
+ADIOS_FOR_FORWARD_ARRAYS        = .true.
+ADIOS_FOR_MPI_ARRAYS            = .true.
+ADIOS_FOR_ARRAYS_SOLVER         = .true.
+ADIOS_FOR_AVS_DX                = .true.
+

Modified: seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_short/Par_file_NOISE_2_noattenuation
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_short/Par_file_NOISE_2_noattenuation	2013-08-21 16:56:20 UTC (rev 22727)
+++ seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_short/Par_file_NOISE_2_noattenuation	2013-08-22 07:40:44 UTC (rev 22728)
@@ -57,10 +57,36 @@
 # to undo attenuation for sensitivity kernel calculations or forward runs with SAVE_FORWARD
 # use one (and only one) of the two flags below. UNDO_ATTENUATION is much better (it is exact)
 # but requires a significant amount of disk space for temporary storage.
+ATTENUATION_1D_WITH_3D_STORAGE  = .true.
 PARTIAL_PHYS_DISPERSION_ONLY    = .false.
 UNDO_ATTENUATION                = .false.
 NT_DUMP_ATTENUATION             = 100   # how often we dump restart files to undo attenuation, only needed when using UNDO_ATTENUATION
 
+# three mass matrices instead of one are needed to handle rotation very accurately;
+# otherwise rotation is handled slightly less accurately (but still reasonably well);
+# set to .true. if you are interested in precise effects related to rotation;
+# set to .false. if you are solving very large inverse problems at high frequency and also undoing attenuation exactly
+# using the UNDO_ATTENUATION flag above, in which case saving as much memory as possible can be a good idea.
+# You can also safely set it to .false. if you are not in a period range in which rotation matters, e.g. if you are targetting very short-period body waves.
+# if in doubt, set to .true.
+# Set it to .true. if you have ABSORBING_CONDITIONS above, because in that case the code will use the three mass matrices anyway
+# and thus there is no additional cost.
+# this flag is of course unused if ROTATION above is set to .false.
+EXACT_MASS_MATRIX_FOR_ROTATION  = .false.
+
+# this for LDDRK high-order time scheme instead of Newmark
+USE_LDDRK                       = .false.
+
+# the maximum CFL of LDDRK is significantly higher than that of the Newmark scheme,
+# in a ratio that is theoretically 1.327 / 0.697 = 1.15 / 0.604 = 1.903 for a solid with Poisson's ratio = 0.25
+# and for a fluid (see the manual of the 2D code, SPECFEM2D, Tables 4.1 and 4.2, and that ratio does not
+# depend on whether we are in 2D or in 3D). However in practice a ratio of about 1.5 to 1.7 is often safer
+# (for instance for models with a large range of Poisson's ratio values).
+# Since the code computes the time step using the Newmark scheme, for LDDRK we will simply
+# multiply that time step by this ratio when LDDRK is on and when flag INCREASE_CFL_FOR_LDDRK is true.
+INCREASE_CFL_FOR_LDDRK          = .true.
+RATIO_BY_WHICH_TO_INCREASE_IT   = 1.5d0
+
 # save AVS or OpenDX movies
 #MOVIE_COARSE saves movie only at corners of elements (SURFACE OR VOLUME)
 #MOVIE_COARSE does not work with create_movie_AVS_DX
@@ -125,6 +151,47 @@
 # print source time function
 PRINT_SOURCE_TIME_FUNCTION      = .true.
 
-# output kernels on a regular grid instead of on the mesh points
+#-----------------------------------------------------------
+#
+#  adjoint kernel outputs
+#
+#-----------------------------------------------------------
+
+# this parameter must be set to .true. to compute anisotropic kernels
+# in crust and mantle (related to the 21 Cij in geographical coordinates)
+# default is .false. to compute isotropic kernels (related to alpha and beta)
+ANISOTROPIC_KL                  = .false.
+
+# output only transverse isotropic kernels (alpha_v,alpha_h,beta_v,beta_h,eta,rho)
+# rather than fully anisotropic kernels when ANISOTROPIC_KL above is set to .true.
+# means to save radial anisotropic kernels, i.e., sensitivity kernels for beta_v, beta_h, etc.
+SAVE_TRANSVERSE_KL_ONLY         = .false.
+
+# output approximate Hessian in crust mantle region.
+# means to save the preconditioning for gradients, they are cross correlations between forward and adjoint accelerations.
+APPROXIMATE_HESS_KL             = .false.
+
+# forces transverse isotropy for all mantle elements
+# (default is to use transverse isotropy only between MOHO and 220)
+# means we allow radial anisotropy between the bottom of the crust to the bottom of the transition zone, i.e., 660~km depth.
+USE_FULL_TISO_MANTLE            = .false.
+
+# output kernel mask to zero out source region
+# to remove large values near the sources in the sensitivity kernels
+SAVE_SOURCE_MASK                = .false.
+
+# output kernels on a regular grid instead of on the GLL mesh points (a bit expensive)
 SAVE_REGULAR_KL                 = .false.
 
+#-----------------------------------------------------------
+
+# set to true to use GPUs
+GPU_MODE                        = .false.
+
+# set to true to use the ADIOS library for I/Os
+ADIOS_ENABLED                   = .false.
+ADIOS_FOR_FORWARD_ARRAYS        = .true.
+ADIOS_FOR_MPI_ARRAYS            = .true.
+ADIOS_FOR_ARRAYS_SOLVER         = .true.
+ADIOS_FOR_AVS_DX                = .true.
+

Modified: seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_short/Par_file_NOISE_3_noattenuation
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_short/Par_file_NOISE_3_noattenuation	2013-08-21 16:56:20 UTC (rev 22727)
+++ seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/global_short/Par_file_NOISE_3_noattenuation	2013-08-22 07:40:44 UTC (rev 22728)
@@ -57,10 +57,36 @@
 # to undo attenuation for sensitivity kernel calculations or forward runs with SAVE_FORWARD
 # use one (and only one) of the two flags below. UNDO_ATTENUATION is much better (it is exact)
 # but requires a significant amount of disk space for temporary storage.
+ATTENUATION_1D_WITH_3D_STORAGE  = .true.
 PARTIAL_PHYS_DISPERSION_ONLY    = .false.
 UNDO_ATTENUATION                = .false.
 NT_DUMP_ATTENUATION             = 100   # how often we dump restart files to undo attenuation, only needed when using UNDO_ATTENUATION
 
+# three mass matrices instead of one are needed to handle rotation very accurately;
+# otherwise rotation is handled slightly less accurately (but still reasonably well);
+# set to .true. if you are interested in precise effects related to rotation;
+# set to .false. if you are solving very large inverse problems at high frequency and also undoing attenuation exactly
+# using the UNDO_ATTENUATION flag above, in which case saving as much memory as possible can be a good idea.
+# You can also safely set it to .false. if you are not in a period range in which rotation matters, e.g. if you are targetting very short-period body waves.
+# if in doubt, set to .true.
+# Set it to .true. if you have ABSORBING_CONDITIONS above, because in that case the code will use the three mass matrices anyway
+# and thus there is no additional cost.
+# this flag is of course unused if ROTATION above is set to .false.
+EXACT_MASS_MATRIX_FOR_ROTATION  = .false.
+
+# this for LDDRK high-order time scheme instead of Newmark
+USE_LDDRK                       = .false.
+
+# the maximum CFL of LDDRK is significantly higher than that of the Newmark scheme,
+# in a ratio that is theoretically 1.327 / 0.697 = 1.15 / 0.604 = 1.903 for a solid with Poisson's ratio = 0.25
+# and for a fluid (see the manual of the 2D code, SPECFEM2D, Tables 4.1 and 4.2, and that ratio does not
+# depend on whether we are in 2D or in 3D). However in practice a ratio of about 1.5 to 1.7 is often safer
+# (for instance for models with a large range of Poisson's ratio values).
+# Since the code computes the time step using the Newmark scheme, for LDDRK we will simply
+# multiply that time step by this ratio when LDDRK is on and when flag INCREASE_CFL_FOR_LDDRK is true.
+INCREASE_CFL_FOR_LDDRK          = .true.
+RATIO_BY_WHICH_TO_INCREASE_IT   = 1.5d0
+
 # save AVS or OpenDX movies
 #MOVIE_COARSE saves movie only at corners of elements (SURFACE OR VOLUME)
 #MOVIE_COARSE does not work with create_movie_AVS_DX
@@ -125,6 +151,47 @@
 # print source time function
 PRINT_SOURCE_TIME_FUNCTION      = .true.
 
-# output kernels on a regular grid instead of on the mesh points
+#-----------------------------------------------------------
+#
+#  adjoint kernel outputs
+#
+#-----------------------------------------------------------
+
+# this parameter must be set to .true. to compute anisotropic kernels
+# in crust and mantle (related to the 21 Cij in geographical coordinates)
+# default is .false. to compute isotropic kernels (related to alpha and beta)
+ANISOTROPIC_KL                  = .false.
+
+# output only transverse isotropic kernels (alpha_v,alpha_h,beta_v,beta_h,eta,rho)
+# rather than fully anisotropic kernels when ANISOTROPIC_KL above is set to .true.
+# means to save radial anisotropic kernels, i.e., sensitivity kernels for beta_v, beta_h, etc.
+SAVE_TRANSVERSE_KL_ONLY         = .false.
+
+# output approximate Hessian in crust mantle region.
+# means to save the preconditioning for gradients, they are cross correlations between forward and adjoint accelerations.
+APPROXIMATE_HESS_KL             = .false.
+
+# forces transverse isotropy for all mantle elements
+# (default is to use transverse isotropy only between MOHO and 220)
+# means we allow radial anisotropy between the bottom of the crust to the bottom of the transition zone, i.e., 660~km depth.
+USE_FULL_TISO_MANTLE            = .false.
+
+# output kernel mask to zero out source region
+# to remove large values near the sources in the sensitivity kernels
+SAVE_SOURCE_MASK                = .false.
+
+# output kernels on a regular grid instead of on the GLL mesh points (a bit expensive)
 SAVE_REGULAR_KL                 = .false.
 
+#-----------------------------------------------------------
+
+# set to true to use GPUs
+GPU_MODE                        = .false.
+
+# set to true to use the ADIOS library for I/Os
+ADIOS_ENABLED                   = .false.
+ADIOS_FOR_FORWARD_ARRAYS        = .true.
+ADIOS_FOR_MPI_ARRAYS            = .true.
+ADIOS_FOR_ARRAYS_SOLVER         = .true.
+ADIOS_FOR_AVS_DX                = .true.
+

Modified: seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/regional/Par_file_NOISE_1_attenuation
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/regional/Par_file_NOISE_1_attenuation	2013-08-21 16:56:20 UTC (rev 22727)
+++ seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/regional/Par_file_NOISE_1_attenuation	2013-08-22 07:40:44 UTC (rev 22728)
@@ -57,10 +57,36 @@
 # to undo attenuation for sensitivity kernel calculations or forward runs with SAVE_FORWARD
 # use one (and only one) of the two flags below. UNDO_ATTENUATION is much better (it is exact)
 # but requires a significant amount of disk space for temporary storage.
+ATTENUATION_1D_WITH_3D_STORAGE  = .true.
 PARTIAL_PHYS_DISPERSION_ONLY    = .true.
 UNDO_ATTENUATION                = .false.
 NT_DUMP_ATTENUATION             = 100   # how often we dump restart files to undo attenuation, only needed when using UNDO_ATTENUATION
 
+# three mass matrices instead of one are needed to handle rotation very accurately;
+# otherwise rotation is handled slightly less accurately (but still reasonably well);
+# set to .true. if you are interested in precise effects related to rotation;
+# set to .false. if you are solving very large inverse problems at high frequency and also undoing attenuation exactly
+# using the UNDO_ATTENUATION flag above, in which case saving as much memory as possible can be a good idea.
+# You can also safely set it to .false. if you are not in a period range in which rotation matters, e.g. if you are targetting very short-period body waves.
+# if in doubt, set to .true.
+# Set it to .true. if you have ABSORBING_CONDITIONS above, because in that case the code will use the three mass matrices anyway
+# and thus there is no additional cost.
+# this flag is of course unused if ROTATION above is set to .false.
+EXACT_MASS_MATRIX_FOR_ROTATION  = .false.
+
+# this for LDDRK high-order time scheme instead of Newmark
+USE_LDDRK                       = .false.
+
+# the maximum CFL of LDDRK is significantly higher than that of the Newmark scheme,
+# in a ratio that is theoretically 1.327 / 0.697 = 1.15 / 0.604 = 1.903 for a solid with Poisson's ratio = 0.25
+# and for a fluid (see the manual of the 2D code, SPECFEM2D, Tables 4.1 and 4.2, and that ratio does not
+# depend on whether we are in 2D or in 3D). However in practice a ratio of about 1.5 to 1.7 is often safer
+# (for instance for models with a large range of Poisson's ratio values).
+# Since the code computes the time step using the Newmark scheme, for LDDRK we will simply
+# multiply that time step by this ratio when LDDRK is on and when flag INCREASE_CFL_FOR_LDDRK is true.
+INCREASE_CFL_FOR_LDDRK          = .true.
+RATIO_BY_WHICH_TO_INCREASE_IT   = 1.5d0
+
 # save AVS or OpenDX movies
 #MOVIE_COARSE saves movie only at corners of elements (SURFACE OR VOLUME)
 #MOVIE_COARSE does not work with create_movie_AVS_DX
@@ -125,6 +151,47 @@
 # print source time function
 PRINT_SOURCE_TIME_FUNCTION      = .true.
 
-# output kernels on a regular grid instead of on the mesh points
+#-----------------------------------------------------------
+#
+#  adjoint kernel outputs
+#
+#-----------------------------------------------------------
+
+# this parameter must be set to .true. to compute anisotropic kernels
+# in crust and mantle (related to the 21 Cij in geographical coordinates)
+# default is .false. to compute isotropic kernels (related to alpha and beta)
+ANISOTROPIC_KL                  = .false.
+
+# output only transverse isotropic kernels (alpha_v,alpha_h,beta_v,beta_h,eta,rho)
+# rather than fully anisotropic kernels when ANISOTROPIC_KL above is set to .true.
+# means to save radial anisotropic kernels, i.e., sensitivity kernels for beta_v, beta_h, etc.
+SAVE_TRANSVERSE_KL_ONLY         = .false.
+
+# output approximate Hessian in crust mantle region.
+# means to save the preconditioning for gradients, they are cross correlations between forward and adjoint accelerations.
+APPROXIMATE_HESS_KL             = .false.
+
+# forces transverse isotropy for all mantle elements
+# (default is to use transverse isotropy only between MOHO and 220)
+# means we allow radial anisotropy between the bottom of the crust to the bottom of the transition zone, i.e., 660~km depth.
+USE_FULL_TISO_MANTLE            = .false.
+
+# output kernel mask to zero out source region
+# to remove large values near the sources in the sensitivity kernels
+SAVE_SOURCE_MASK                = .false.
+
+# output kernels on a regular grid instead of on the GLL mesh points (a bit expensive)
 SAVE_REGULAR_KL                 = .false.
 
+#-----------------------------------------------------------
+
+# set to true to use GPUs
+GPU_MODE                        = .false.
+
+# set to true to use the ADIOS library for I/Os
+ADIOS_ENABLED                   = .false.
+ADIOS_FOR_FORWARD_ARRAYS        = .true.
+ADIOS_FOR_MPI_ARRAYS            = .true.
+ADIOS_FOR_ARRAYS_SOLVER         = .true.
+ADIOS_FOR_AVS_DX                = .true.
+

Modified: seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/regional/Par_file_NOISE_1_noattenuation
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/regional/Par_file_NOISE_1_noattenuation	2013-08-21 16:56:20 UTC (rev 22727)
+++ seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/regional/Par_file_NOISE_1_noattenuation	2013-08-22 07:40:44 UTC (rev 22728)
@@ -57,10 +57,36 @@
 # to undo attenuation for sensitivity kernel calculations or forward runs with SAVE_FORWARD
 # use one (and only one) of the two flags below. UNDO_ATTENUATION is much better (it is exact)
 # but requires a significant amount of disk space for temporary storage.
+ATTENUATION_1D_WITH_3D_STORAGE  = .true.
 PARTIAL_PHYS_DISPERSION_ONLY    = .false.
 UNDO_ATTENUATION                = .false.
 NT_DUMP_ATTENUATION             = 100   # how often we dump restart files to undo attenuation, only needed when using UNDO_ATTENUATION
 
+# three mass matrices instead of one are needed to handle rotation very accurately;
+# otherwise rotation is handled slightly less accurately (but still reasonably well);
+# set to .true. if you are interested in precise effects related to rotation;
+# set to .false. if you are solving very large inverse problems at high frequency and also undoing attenuation exactly
+# using the UNDO_ATTENUATION flag above, in which case saving as much memory as possible can be a good idea.
+# You can also safely set it to .false. if you are not in a period range in which rotation matters, e.g. if you are targetting very short-period body waves.
+# if in doubt, set to .true.
+# Set it to .true. if you have ABSORBING_CONDITIONS above, because in that case the code will use the three mass matrices anyway
+# and thus there is no additional cost.
+# this flag is of course unused if ROTATION above is set to .false.
+EXACT_MASS_MATRIX_FOR_ROTATION  = .false.
+
+# this for LDDRK high-order time scheme instead of Newmark
+USE_LDDRK                       = .false.
+
+# the maximum CFL of LDDRK is significantly higher than that of the Newmark scheme,
+# in a ratio that is theoretically 1.327 / 0.697 = 1.15 / 0.604 = 1.903 for a solid with Poisson's ratio = 0.25
+# and for a fluid (see the manual of the 2D code, SPECFEM2D, Tables 4.1 and 4.2, and that ratio does not
+# depend on whether we are in 2D or in 3D). However in practice a ratio of about 1.5 to 1.7 is often safer
+# (for instance for models with a large range of Poisson's ratio values).
+# Since the code computes the time step using the Newmark scheme, for LDDRK we will simply
+# multiply that time step by this ratio when LDDRK is on and when flag INCREASE_CFL_FOR_LDDRK is true.
+INCREASE_CFL_FOR_LDDRK          = .true.
+RATIO_BY_WHICH_TO_INCREASE_IT   = 1.5d0
+
 # save AVS or OpenDX movies
 #MOVIE_COARSE saves movie only at corners of elements (SURFACE OR VOLUME)
 #MOVIE_COARSE does not work with create_movie_AVS_DX
@@ -125,6 +151,47 @@
 # print source time function
 PRINT_SOURCE_TIME_FUNCTION      = .true.
 
-# output kernels on a regular grid instead of on the mesh points
+#-----------------------------------------------------------
+#
+#  adjoint kernel outputs
+#
+#-----------------------------------------------------------
+
+# this parameter must be set to .true. to compute anisotropic kernels
+# in crust and mantle (related to the 21 Cij in geographical coordinates)
+# default is .false. to compute isotropic kernels (related to alpha and beta)
+ANISOTROPIC_KL                  = .false.
+
+# output only transverse isotropic kernels (alpha_v,alpha_h,beta_v,beta_h,eta,rho)
+# rather than fully anisotropic kernels when ANISOTROPIC_KL above is set to .true.
+# means to save radial anisotropic kernels, i.e., sensitivity kernels for beta_v, beta_h, etc.
+SAVE_TRANSVERSE_KL_ONLY         = .false.
+
+# output approximate Hessian in crust mantle region.
+# means to save the preconditioning for gradients, they are cross correlations between forward and adjoint accelerations.
+APPROXIMATE_HESS_KL             = .false.
+
+# forces transverse isotropy for all mantle elements
+# (default is to use transverse isotropy only between MOHO and 220)
+# means we allow radial anisotropy between the bottom of the crust to the bottom of the transition zone, i.e., 660~km depth.
+USE_FULL_TISO_MANTLE            = .false.
+
+# output kernel mask to zero out source region
+# to remove large values near the sources in the sensitivity kernels
+SAVE_SOURCE_MASK                = .false.
+
+# output kernels on a regular grid instead of on the GLL mesh points (a bit expensive)
 SAVE_REGULAR_KL                 = .false.
 
+#-----------------------------------------------------------
+
+# set to true to use GPUs
+GPU_MODE                        = .false.
+
+# set to true to use the ADIOS library for I/Os
+ADIOS_ENABLED                   = .false.
+ADIOS_FOR_FORWARD_ARRAYS        = .true.
+ADIOS_FOR_MPI_ARRAYS            = .true.
+ADIOS_FOR_ARRAYS_SOLVER         = .true.
+ADIOS_FOR_AVS_DX                = .true.
+

Modified: seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/regional/Par_file_NOISE_2_attenuation
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/regional/Par_file_NOISE_2_attenuation	2013-08-21 16:56:20 UTC (rev 22727)
+++ seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/regional/Par_file_NOISE_2_attenuation	2013-08-22 07:40:44 UTC (rev 22728)
@@ -57,10 +57,36 @@
 # to undo attenuation for sensitivity kernel calculations or forward runs with SAVE_FORWARD
 # use one (and only one) of the two flags below. UNDO_ATTENUATION is much better (it is exact)
 # but requires a significant amount of disk space for temporary storage.
+ATTENUATION_1D_WITH_3D_STORAGE  = .true.
 PARTIAL_PHYS_DISPERSION_ONLY    = .true.
 UNDO_ATTENUATION                = .false.
 NT_DUMP_ATTENUATION             = 100   # how often we dump restart files to undo attenuation, only needed when using UNDO_ATTENUATION
 
+# three mass matrices instead of one are needed to handle rotation very accurately;
+# otherwise rotation is handled slightly less accurately (but still reasonably well);
+# set to .true. if you are interested in precise effects related to rotation;
+# set to .false. if you are solving very large inverse problems at high frequency and also undoing attenuation exactly
+# using the UNDO_ATTENUATION flag above, in which case saving as much memory as possible can be a good idea.
+# You can also safely set it to .false. if you are not in a period range in which rotation matters, e.g. if you are targetting very short-period body waves.
+# if in doubt, set to .true.
+# Set it to .true. if you have ABSORBING_CONDITIONS above, because in that case the code will use the three mass matrices anyway
+# and thus there is no additional cost.
+# this flag is of course unused if ROTATION above is set to .false.
+EXACT_MASS_MATRIX_FOR_ROTATION  = .false.
+
+# this for LDDRK high-order time scheme instead of Newmark
+USE_LDDRK                       = .false.
+
+# the maximum CFL of LDDRK is significantly higher than that of the Newmark scheme,
+# in a ratio that is theoretically 1.327 / 0.697 = 1.15 / 0.604 = 1.903 for a solid with Poisson's ratio = 0.25
+# and for a fluid (see the manual of the 2D code, SPECFEM2D, Tables 4.1 and 4.2, and that ratio does not
+# depend on whether we are in 2D or in 3D). However in practice a ratio of about 1.5 to 1.7 is often safer
+# (for instance for models with a large range of Poisson's ratio values).
+# Since the code computes the time step using the Newmark scheme, for LDDRK we will simply
+# multiply that time step by this ratio when LDDRK is on and when flag INCREASE_CFL_FOR_LDDRK is true.
+INCREASE_CFL_FOR_LDDRK          = .true.
+RATIO_BY_WHICH_TO_INCREASE_IT   = 1.5d0
+
 # save AVS or OpenDX movies
 #MOVIE_COARSE saves movie only at corners of elements (SURFACE OR VOLUME)
 #MOVIE_COARSE does not work with create_movie_AVS_DX
@@ -125,6 +151,47 @@
 # print source time function
 PRINT_SOURCE_TIME_FUNCTION      = .true.
 
-# output kernels on a regular grid instead of on the mesh points
+#-----------------------------------------------------------
+#
+#  adjoint kernel outputs
+#
+#-----------------------------------------------------------
+
+# this parameter must be set to .true. to compute anisotropic kernels
+# in crust and mantle (related to the 21 Cij in geographical coordinates)
+# default is .false. to compute isotropic kernels (related to alpha and beta)
+ANISOTROPIC_KL                  = .false.
+
+# output only transverse isotropic kernels (alpha_v,alpha_h,beta_v,beta_h,eta,rho)
+# rather than fully anisotropic kernels when ANISOTROPIC_KL above is set to .true.
+# means to save radial anisotropic kernels, i.e., sensitivity kernels for beta_v, beta_h, etc.
+SAVE_TRANSVERSE_KL_ONLY         = .false.
+
+# output approximate Hessian in crust mantle region.
+# means to save the preconditioning for gradients, they are cross correlations between forward and adjoint accelerations.
+APPROXIMATE_HESS_KL             = .false.
+
+# forces transverse isotropy for all mantle elements
+# (default is to use transverse isotropy only between MOHO and 220)
+# means we allow radial anisotropy between the bottom of the crust to the bottom of the transition zone, i.e., 660~km depth.
+USE_FULL_TISO_MANTLE            = .false.
+
+# output kernel mask to zero out source region
+# to remove large values near the sources in the sensitivity kernels
+SAVE_SOURCE_MASK                = .false.
+
+# output kernels on a regular grid instead of on the GLL mesh points (a bit expensive)
 SAVE_REGULAR_KL                 = .false.
 
+#-----------------------------------------------------------
+
+# set to true to use GPUs
+GPU_MODE                        = .false.
+
+# set to true to use the ADIOS library for I/Os
+ADIOS_ENABLED                   = .false.
+ADIOS_FOR_FORWARD_ARRAYS        = .true.
+ADIOS_FOR_MPI_ARRAYS            = .true.
+ADIOS_FOR_ARRAYS_SOLVER         = .true.
+ADIOS_FOR_AVS_DX                = .true.
+

Modified: seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/regional/Par_file_NOISE_2_noattenuation
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/regional/Par_file_NOISE_2_noattenuation	2013-08-21 16:56:20 UTC (rev 22727)
+++ seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/regional/Par_file_NOISE_2_noattenuation	2013-08-22 07:40:44 UTC (rev 22728)
@@ -57,10 +57,36 @@
 # to undo attenuation for sensitivity kernel calculations or forward runs with SAVE_FORWARD
 # use one (and only one) of the two flags below. UNDO_ATTENUATION is much better (it is exact)
 # but requires a significant amount of disk space for temporary storage.
+ATTENUATION_1D_WITH_3D_STORAGE  = .true.
 PARTIAL_PHYS_DISPERSION_ONLY    = .false.
 UNDO_ATTENUATION                = .false.
 NT_DUMP_ATTENUATION             = 100   # how often we dump restart files to undo attenuation, only needed when using UNDO_ATTENUATION
 
+# three mass matrices instead of one are needed to handle rotation very accurately;
+# otherwise rotation is handled slightly less accurately (but still reasonably well);
+# set to .true. if you are interested in precise effects related to rotation;
+# set to .false. if you are solving very large inverse problems at high frequency and also undoing attenuation exactly
+# using the UNDO_ATTENUATION flag above, in which case saving as much memory as possible can be a good idea.
+# You can also safely set it to .false. if you are not in a period range in which rotation matters, e.g. if you are targetting very short-period body waves.
+# if in doubt, set to .true.
+# Set it to .true. if you have ABSORBING_CONDITIONS above, because in that case the code will use the three mass matrices anyway
+# and thus there is no additional cost.
+# this flag is of course unused if ROTATION above is set to .false.
+EXACT_MASS_MATRIX_FOR_ROTATION  = .false.
+
+# this for LDDRK high-order time scheme instead of Newmark
+USE_LDDRK                       = .false.
+
+# the maximum CFL of LDDRK is significantly higher than that of the Newmark scheme,
+# in a ratio that is theoretically 1.327 / 0.697 = 1.15 / 0.604 = 1.903 for a solid with Poisson's ratio = 0.25
+# and for a fluid (see the manual of the 2D code, SPECFEM2D, Tables 4.1 and 4.2, and that ratio does not
+# depend on whether we are in 2D or in 3D). However in practice a ratio of about 1.5 to 1.7 is often safer
+# (for instance for models with a large range of Poisson's ratio values).
+# Since the code computes the time step using the Newmark scheme, for LDDRK we will simply
+# multiply that time step by this ratio when LDDRK is on and when flag INCREASE_CFL_FOR_LDDRK is true.
+INCREASE_CFL_FOR_LDDRK          = .true.
+RATIO_BY_WHICH_TO_INCREASE_IT   = 1.5d0
+
 # save AVS or OpenDX movies
 #MOVIE_COARSE saves movie only at corners of elements (SURFACE OR VOLUME)
 #MOVIE_COARSE does not work with create_movie_AVS_DX
@@ -125,6 +151,47 @@
 # print source time function
 PRINT_SOURCE_TIME_FUNCTION      = .true.
 
-# output kernels on a regular grid instead of on the mesh points
+#-----------------------------------------------------------
+#
+#  adjoint kernel outputs
+#
+#-----------------------------------------------------------
+
+# this parameter must be set to .true. to compute anisotropic kernels
+# in crust and mantle (related to the 21 Cij in geographical coordinates)
+# default is .false. to compute isotropic kernels (related to alpha and beta)
+ANISOTROPIC_KL                  = .false.
+
+# output only transverse isotropic kernels (alpha_v,alpha_h,beta_v,beta_h,eta,rho)
+# rather than fully anisotropic kernels when ANISOTROPIC_KL above is set to .true.
+# means to save radial anisotropic kernels, i.e., sensitivity kernels for beta_v, beta_h, etc.
+SAVE_TRANSVERSE_KL_ONLY         = .false.
+
+# output approximate Hessian in crust mantle region.
+# means to save the preconditioning for gradients, they are cross correlations between forward and adjoint accelerations.
+APPROXIMATE_HESS_KL             = .false.
+
+# forces transverse isotropy for all mantle elements
+# (default is to use transverse isotropy only between MOHO and 220)
+# means we allow radial anisotropy between the bottom of the crust to the bottom of the transition zone, i.e., 660~km depth.
+USE_FULL_TISO_MANTLE            = .false.
+
+# output kernel mask to zero out source region
+# to remove large values near the sources in the sensitivity kernels
+SAVE_SOURCE_MASK                = .false.
+
+# output kernels on a regular grid instead of on the GLL mesh points (a bit expensive)
 SAVE_REGULAR_KL                 = .false.
 
+#-----------------------------------------------------------
+
+# set to true to use GPUs
+GPU_MODE                        = .false.
+
+# set to true to use the ADIOS library for I/Os
+ADIOS_ENABLED                   = .false.
+ADIOS_FOR_FORWARD_ARRAYS        = .true.
+ADIOS_FOR_MPI_ARRAYS            = .true.
+ADIOS_FOR_ARRAYS_SOLVER         = .true.
+ADIOS_FOR_AVS_DX                = .true.
+

Modified: seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/regional/Par_file_NOISE_3_noattenuation
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/regional/Par_file_NOISE_3_noattenuation	2013-08-21 16:56:20 UTC (rev 22727)
+++ seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/noise_examples/regional/Par_file_NOISE_3_noattenuation	2013-08-22 07:40:44 UTC (rev 22728)
@@ -57,10 +57,36 @@
 # to undo attenuation for sensitivity kernel calculations or forward runs with SAVE_FORWARD
 # use one (and only one) of the two flags below. UNDO_ATTENUATION is much better (it is exact)
 # but requires a significant amount of disk space for temporary storage.
+ATTENUATION_1D_WITH_3D_STORAGE  = .true.
 PARTIAL_PHYS_DISPERSION_ONLY    = .false.
 UNDO_ATTENUATION                = .false.
 NT_DUMP_ATTENUATION             = 100   # how often we dump restart files to undo attenuation, only needed when using UNDO_ATTENUATION
 
+# three mass matrices instead of one are needed to handle rotation very accurately;
+# otherwise rotation is handled slightly less accurately (but still reasonably well);
+# set to .true. if you are interested in precise effects related to rotation;
+# set to .false. if you are solving very large inverse problems at high frequency and also undoing attenuation exactly
+# using the UNDO_ATTENUATION flag above, in which case saving as much memory as possible can be a good idea.
+# You can also safely set it to .false. if you are not in a period range in which rotation matters, e.g. if you are targetting very short-period body waves.
+# if in doubt, set to .true.
+# Set it to .true. if you have ABSORBING_CONDITIONS above, because in that case the code will use the three mass matrices anyway
+# and thus there is no additional cost.
+# this flag is of course unused if ROTATION above is set to .false.
+EXACT_MASS_MATRIX_FOR_ROTATION  = .false.
+
+# this for LDDRK high-order time scheme instead of Newmark
+USE_LDDRK                       = .false.
+
+# the maximum CFL of LDDRK is significantly higher than that of the Newmark scheme,
+# in a ratio that is theoretically 1.327 / 0.697 = 1.15 / 0.604 = 1.903 for a solid with Poisson's ratio = 0.25
+# and for a fluid (see the manual of the 2D code, SPECFEM2D, Tables 4.1 and 4.2, and that ratio does not
+# depend on whether we are in 2D or in 3D). However in practice a ratio of about 1.5 to 1.7 is often safer
+# (for instance for models with a large range of Poisson's ratio values).
+# Since the code computes the time step using the Newmark scheme, for LDDRK we will simply
+# multiply that time step by this ratio when LDDRK is on and when flag INCREASE_CFL_FOR_LDDRK is true.
+INCREASE_CFL_FOR_LDDRK          = .true.
+RATIO_BY_WHICH_TO_INCREASE_IT   = 1.5d0
+
 # save AVS or OpenDX movies
 #MOVIE_COARSE saves movie only at corners of elements (SURFACE OR VOLUME)
 #MOVIE_COARSE does not work with create_movie_AVS_DX
@@ -125,6 +151,47 @@
 # print source time function
 PRINT_SOURCE_TIME_FUNCTION      = .true.
 
-# output kernels on a regular grid instead of on the mesh points
+#-----------------------------------------------------------
+#
+#  adjoint kernel outputs
+#
+#-----------------------------------------------------------
+
+# this parameter must be set to .true. to compute anisotropic kernels
+# in crust and mantle (related to the 21 Cij in geographical coordinates)
+# default is .false. to compute isotropic kernels (related to alpha and beta)
+ANISOTROPIC_KL                  = .false.
+
+# output only transverse isotropic kernels (alpha_v,alpha_h,beta_v,beta_h,eta,rho)
+# rather than fully anisotropic kernels when ANISOTROPIC_KL above is set to .true.
+# means to save radial anisotropic kernels, i.e., sensitivity kernels for beta_v, beta_h, etc.
+SAVE_TRANSVERSE_KL_ONLY         = .false.
+
+# output approximate Hessian in crust mantle region.
+# means to save the preconditioning for gradients, they are cross correlations between forward and adjoint accelerations.
+APPROXIMATE_HESS_KL             = .false.
+
+# forces transverse isotropy for all mantle elements
+# (default is to use transverse isotropy only between MOHO and 220)
+# means we allow radial anisotropy between the bottom of the crust to the bottom of the transition zone, i.e., 660~km depth.
+USE_FULL_TISO_MANTLE            = .false.
+
+# output kernel mask to zero out source region
+# to remove large values near the sources in the sensitivity kernels
+SAVE_SOURCE_MASK                = .false.
+
+# output kernels on a regular grid instead of on the GLL mesh points (a bit expensive)
 SAVE_REGULAR_KL                 = .false.
 
+#-----------------------------------------------------------
+
+# set to true to use GPUs
+GPU_MODE                        = .false.
+
+# set to true to use the ADIOS library for I/Os
+ADIOS_ENABLED                   = .false.
+ADIOS_FOR_FORWARD_ARRAYS        = .true.
+ADIOS_FOR_MPI_ARRAYS            = .true.
+ADIOS_FOR_ARRAYS_SOLVER         = .true.
+ADIOS_FOR_AVS_DX                = .true.
+

Modified: seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/regional_Greece_small/DATA/Par_file
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/regional_Greece_small/DATA/Par_file	2013-08-21 16:56:20 UTC (rev 22727)
+++ seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/regional_Greece_small/DATA/Par_file	2013-08-22 07:40:44 UTC (rev 22728)
@@ -57,10 +57,36 @@
 # to undo attenuation for sensitivity kernel calculations or forward runs with SAVE_FORWARD
 # use one (and only one) of the two flags below. UNDO_ATTENUATION is much better (it is exact)
 # but requires a significant amount of disk space for temporary storage.
+ATTENUATION_1D_WITH_3D_STORAGE  = .true.
 PARTIAL_PHYS_DISPERSION_ONLY    = .true.
 UNDO_ATTENUATION                = .false.
 NT_DUMP_ATTENUATION             = 100   # how often we dump restart files to undo attenuation, only needed when using UNDO_ATTENUATION
 
+# three mass matrices instead of one are needed to handle rotation very accurately;
+# otherwise rotation is handled slightly less accurately (but still reasonably well);
+# set to .true. if you are interested in precise effects related to rotation;
+# set to .false. if you are solving very large inverse problems at high frequency and also undoing attenuation exactly
+# using the UNDO_ATTENUATION flag above, in which case saving as much memory as possible can be a good idea.
+# You can also safely set it to .false. if you are not in a period range in which rotation matters, e.g. if you are targetting very short-period body waves.
+# if in doubt, set to .true.
+# Set it to .true. if you have ABSORBING_CONDITIONS above, because in that case the code will use the three mass matrices anyway
+# and thus there is no additional cost.
+# this flag is of course unused if ROTATION above is set to .false.
+EXACT_MASS_MATRIX_FOR_ROTATION  = .false.
+
+# this for LDDRK high-order time scheme instead of Newmark
+USE_LDDRK                       = .false.
+
+# the maximum CFL of LDDRK is significantly higher than that of the Newmark scheme,
+# in a ratio that is theoretically 1.327 / 0.697 = 1.15 / 0.604 = 1.903 for a solid with Poisson's ratio = 0.25
+# and for a fluid (see the manual of the 2D code, SPECFEM2D, Tables 4.1 and 4.2, and that ratio does not
+# depend on whether we are in 2D or in 3D). However in practice a ratio of about 1.5 to 1.7 is often safer
+# (for instance for models with a large range of Poisson's ratio values).
+# Since the code computes the time step using the Newmark scheme, for LDDRK we will simply
+# multiply that time step by this ratio when LDDRK is on and when flag INCREASE_CFL_FOR_LDDRK is true.
+INCREASE_CFL_FOR_LDDRK          = .true.
+RATIO_BY_WHICH_TO_INCREASE_IT   = 1.5d0
+
 # save AVS or OpenDX movies
 #MOVIE_COARSE saves movie only at corners of elements (SURFACE OR VOLUME)
 #MOVIE_COARSE does not work with create_movie_AVS_DX
@@ -97,7 +123,7 @@
 LOCAL_PATH                      = ./DATABASES_MPI
 
 # interval at which we output time step info and max of norm of displacement
-NTSTEP_BETWEEN_OUTPUT_INFO      = 50
+NTSTEP_BETWEEN_OUTPUT_INFO      = 500
 
 # interval in time steps for temporary writing of seismograms
 NTSTEP_BETWEEN_OUTPUT_SEISMOS   = 5000000
@@ -125,6 +151,47 @@
 # print source time function
 PRINT_SOURCE_TIME_FUNCTION      = .false.
 
-# output kernels on a regular grid instead of on the mesh points
+#-----------------------------------------------------------
+#
+#  adjoint kernel outputs
+#
+#-----------------------------------------------------------
+
+# this parameter must be set to .true. to compute anisotropic kernels
+# in crust and mantle (related to the 21 Cij in geographical coordinates)
+# default is .false. to compute isotropic kernels (related to alpha and beta)
+ANISOTROPIC_KL                  = .false.
+
+# output only transverse isotropic kernels (alpha_v,alpha_h,beta_v,beta_h,eta,rho)
+# rather than fully anisotropic kernels when ANISOTROPIC_KL above is set to .true.
+# means to save radial anisotropic kernels, i.e., sensitivity kernels for beta_v, beta_h, etc.
+SAVE_TRANSVERSE_KL_ONLY         = .false.
+
+# output approximate Hessian in crust mantle region.
+# means to save the preconditioning for gradients, they are cross correlations between forward and adjoint accelerations.
+APPROXIMATE_HESS_KL             = .false.
+
+# forces transverse isotropy for all mantle elements
+# (default is to use transverse isotropy only between MOHO and 220)
+# means we allow radial anisotropy between the bottom of the crust to the bottom of the transition zone, i.e., 660~km depth.
+USE_FULL_TISO_MANTLE            = .false.
+
+# output kernel mask to zero out source region
+# to remove large values near the sources in the sensitivity kernels
+SAVE_SOURCE_MASK                = .false.
+
+# output kernels on a regular grid instead of on the GLL mesh points (a bit expensive)
 SAVE_REGULAR_KL                 = .false.
 
+#-----------------------------------------------------------
+
+# set to true to use GPUs
+GPU_MODE                        = .false.
+
+# set to true to use the ADIOS library for I/Os
+ADIOS_ENABLED                   = .false.
+ADIOS_FOR_FORWARD_ARRAYS        = .true.
+ADIOS_FOR_MPI_ARRAYS            = .true.
+ADIOS_FOR_ARRAYS_SOLVER         = .true.
+ADIOS_FOR_AVS_DX                = .true.
+

Modified: seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/regional_MiddleEast/DATA/Par_file
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/regional_MiddleEast/DATA/Par_file	2013-08-21 16:56:20 UTC (rev 22727)
+++ seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/EXAMPLES/regional_MiddleEast/DATA/Par_file	2013-08-22 07:40:44 UTC (rev 22728)
@@ -57,10 +57,36 @@
 # to undo attenuation for sensitivity kernel calculations or forward runs with SAVE_FORWARD
 # use one (and only one) of the two flags below. UNDO_ATTENUATION is much better (it is exact)
 # but requires a significant amount of disk space for temporary storage.
+ATTENUATION_1D_WITH_3D_STORAGE  = .true.
 PARTIAL_PHYS_DISPERSION_ONLY    = .true.
 UNDO_ATTENUATION                = .false.
 NT_DUMP_ATTENUATION             = 100   # how often we dump restart files to undo attenuation, only needed when using UNDO_ATTENUATION
 
+# three mass matrices instead of one are needed to handle rotation very accurately;
+# otherwise rotation is handled slightly less accurately (but still reasonably well);
+# set to .true. if you are interested in precise effects related to rotation;
+# set to .false. if you are solving very large inverse problems at high frequency and also undoing attenuation exactly
+# using the UNDO_ATTENUATION flag above, in which case saving as much memory as possible can be a good idea.
+# You can also safely set it to .false. if you are not in a period range in which rotation matters, e.g. if you are targetting very short-period body waves.
+# if in doubt, set to .true.
+# Set it to .true. if you have ABSORBING_CONDITIONS above, because in that case the code will use the three mass matrices anyway
+# and thus there is no additional cost.
+# this flag is of course unused if ROTATION above is set to .false.
+EXACT_MASS_MATRIX_FOR_ROTATION  = .false.
+
+# this for LDDRK high-order time scheme instead of Newmark
+USE_LDDRK                       = .false.
+
+# the maximum CFL of LDDRK is significantly higher than that of the Newmark scheme,
+# in a ratio that is theoretically 1.327 / 0.697 = 1.15 / 0.604 = 1.903 for a solid with Poisson's ratio = 0.25
+# and for a fluid (see the manual of the 2D code, SPECFEM2D, Tables 4.1 and 4.2, and that ratio does not
+# depend on whether we are in 2D or in 3D). However in practice a ratio of about 1.5 to 1.7 is often safer
+# (for instance for models with a large range of Poisson's ratio values).
+# Since the code computes the time step using the Newmark scheme, for LDDRK we will simply
+# multiply that time step by this ratio when LDDRK is on and when flag INCREASE_CFL_FOR_LDDRK is true.
+INCREASE_CFL_FOR_LDDRK          = .true.
+RATIO_BY_WHICH_TO_INCREASE_IT   = 1.5d0
+
 # save AVS or OpenDX movies
 #MOVIE_COARSE saves movie only at corners of elements (SURFACE OR VOLUME)
 #MOVIE_COARSE does not work with create_movie_AVS_DX
@@ -125,6 +151,47 @@
 # print source time function
 PRINT_SOURCE_TIME_FUNCTION      = .false.
 
-# output kernels on a regular grid instead of on the mesh points
+#-----------------------------------------------------------
+#
+#  adjoint kernel outputs
+#
+#-----------------------------------------------------------
+
+# this parameter must be set to .true. to compute anisotropic kernels
+# in crust and mantle (related to the 21 Cij in geographical coordinates)
+# default is .false. to compute isotropic kernels (related to alpha and beta)
+ANISOTROPIC_KL                  = .false.
+
+# output only transverse isotropic kernels (alpha_v,alpha_h,beta_v,beta_h,eta,rho)
+# rather than fully anisotropic kernels when ANISOTROPIC_KL above is set to .true.
+# means to save radial anisotropic kernels, i.e., sensitivity kernels for beta_v, beta_h, etc.
+SAVE_TRANSVERSE_KL_ONLY         = .false.
+
+# output approximate Hessian in crust mantle region.
+# means to save the preconditioning for gradients, they are cross correlations between forward and adjoint accelerations.
+APPROXIMATE_HESS_KL             = .false.
+
+# forces transverse isotropy for all mantle elements
+# (default is to use transverse isotropy only between MOHO and 220)
+# means we allow radial anisotropy between the bottom of the crust to the bottom of the transition zone, i.e., 660~km depth.
+USE_FULL_TISO_MANTLE            = .false.
+
+# output kernel mask to zero out source region
+# to remove large values near the sources in the sensitivity kernels
+SAVE_SOURCE_MASK                = .false.
+
+# output kernels on a regular grid instead of on the GLL mesh points (a bit expensive)
 SAVE_REGULAR_KL                 = .false.
 
+#-----------------------------------------------------------
+
+# set to true to use GPUs
+GPU_MODE                        = .false.
+
+# set to true to use the ADIOS library for I/Os
+ADIOS_ENABLED                   = .false.
+ADIOS_FOR_FORWARD_ARRAYS        = .true.
+ADIOS_FOR_MPI_ARRAYS            = .true.
+ADIOS_FOR_ARRAYS_SOLVER         = .true.
+ADIOS_FOR_AVS_DX                = .true.
+

Modified: seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/Makefile.in
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/Makefile.in	2013-08-21 16:56:20 UTC (rev 22727)
+++ seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/Makefile.in	2013-08-22 07:40:44 UTC (rev 22728)
@@ -94,6 +94,14 @@
 
 default: change_date_of_calling_code $(DEFAULT)
 
+required: bin obj
+
+bin:
+	mkdir -p $E
+
+obj:
+	mkdir -p $O
+
 backup:
 	cp -rp src setup DATA/Par_file* Makefile go_mesher* go_solver* mymachines bak
 
@@ -139,15 +147,15 @@
 
 # Shortcut for: <prog>/<xprog> -> bin/<xprog>
 define target_shortcut
-$(patsubst $E/%, %, $(1)): $(1)
+$(patsubst $E/%, %, $(1)): required $(1)
 .PHONY: $(patsubst $E/%, %, $(1))
-$(patsubst $E/x%, %, $(1)): $(1)
+$(patsubst $E/x%, %, $(1)): required $(1)
 .PHONY: $(patsubst $E/x%, %, $(1))
 endef
 
 # Shortcut for: dir -> src/dir/<targets in here>
 define shortcut
-$(1): $($(1)_TARGETS)
+$(1): required $($(1)_TARGETS)
 .PHONY: $(1)
 $$(foreach target, $$(filter $E/%,$$($(1)_TARGETS)), $$(eval $$(call target_shortcut,$$(target))))
 endef

Modified: seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/src/auxiliaries/create_movie_AVS_DX.f90
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/src/auxiliaries/create_movie_AVS_DX.f90	2013-08-21 16:56:20 UTC (rev 22727)
+++ seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/src/auxiliaries/create_movie_AVS_DX.f90	2013-08-22 07:40:44 UTC (rev 22728)
@@ -333,7 +333,12 @@
 
 ! read all the elements from the same file
   write(outputname,"('/moviedata',i6.6)") it
-  open(unit=IOUT,file=trim(OUTPUT_FILES)//outputname,status='old',action='read',form='unformatted')
+  open(unit=IOUT,file=trim(OUTPUT_FILES)//outputname, &
+       status='old',action='read',form='unformatted',iostat=ierror)
+  if(ierror /= 0 ) then
+    print*,'error opening file: ',trim(OUTPUT_FILES)//outputname
+    stop 'error opening moviedata file'
+  endif
 
   ! reads in point locations
   ! (given as r theta phi for geocentric coordinate system)
@@ -348,6 +353,13 @@
 
   close(IOUT)
 
+  !debug
+  print*
+  print*,"data ux min/max: ",minval(store_val_ux),maxval(store_val_ux)
+  print*,"data uy min/max: ",minval(store_val_uy),maxval(store_val_uy)
+  print*,"data uz min/max: ",minval(store_val_uz),maxval(store_val_uz)
+  print*
+
 ! clear number of elements kept
   ispec = 0
 
@@ -529,6 +541,18 @@
     ! map field to [0:255] for AVS color scale
     field_display(:) = 255. * field_display(:)
 
+  else
+
+    ! compute min and max of data value
+    min_field_current = minval(field_display(:))
+    max_field_current = maxval(field_display(:))
+
+    ! print minimum and maximum amplitude in current snapshot
+    print *
+    print *,'minimum amplitude in current snapshot = ',min_field_current
+    print *,'maximum amplitude in current snapshot = ',max_field_current
+    print *
+
   endif
 
 !---------------------------------
@@ -714,10 +738,18 @@
       do ilocnum = 1,NGNOD2D_AVS_DX
         ibool_number = iglob(ilocnum+ieoff)
         if(.not. mask_point(ibool_number)) then
-          if(USE_OPENDX) then
-            write(11,"(f7.2)") field_display(ilocnum+ieoff)
+          if( .not. ALL_THRESHOLD_OFF ) then
+            if(USE_OPENDX) then
+              write(11,"(f7.2)") field_display(ilocnum+ieoff)
+            else
+              write(11,"(i10,1x,f7.2)") ireorder(ibool_number),field_display(ilocnum+ieoff)
+            endif
           else
-            write(11,"(i10,1x,f7.2)") ireorder(ibool_number),field_display(ilocnum+ieoff)
+            if(USE_OPENDX) then
+              write(11,"(e7.4)") field_display(ilocnum+ieoff)
+            else
+              write(11,"(i10,1x,e7.4)") ireorder(ibool_number),field_display(ilocnum+ieoff)
+            endif
           endif
         endif
         mask_point(ibool_number) = .true.

Modified: seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/src/meshfem3D/meshfem3D.f90
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/src/meshfem3D/meshfem3D.f90	2013-08-21 16:56:20 UTC (rev 22727)
+++ seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/src/meshfem3D/meshfem3D.f90	2013-08-22 07:40:44 UTC (rev 22728)
@@ -29,14 +29,8 @@
 
   program xmeshfem3D
 
-  use meshfem3D_par
-  use mpi
-
   implicit none
 
-  ! local parameters
-  integer :: ier
-
 !=====================================================================!
 !                                                                     !
 !  meshfem3D produces a spectral element grid for the Earth.          !
@@ -362,7 +356,7 @@
 !-------------------------------------------------------------------------------------------------
 
   ! initialize the MPI communicator and start the NPROCTOT MPI processes.
-  call MPI_INIT(ier)
+  call init_mpi()
 
   ! initializes parameters
   call initialize_mesher()
@@ -377,7 +371,7 @@
   call finalize_mesher()
 
   ! stop all the MPI processes, and exit
-  call MPI_FINALIZE(ier)
+  call finalize_mpi()
 
   end program xmeshfem3D
 

Modified: seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/src/meshfem3D/model_crustmaps.f90
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/src/meshfem3D/model_crustmaps.f90	2013-08-21 16:56:20 UTC (rev 22727)
+++ seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/src/meshfem3D/model_crustmaps.f90	2013-08-22 07:40:44 UTC (rev 22728)
@@ -79,7 +79,10 @@
           density(180*CRUSTMAP_RESOLUTION,360*CRUSTMAP_RESOLUTION,NLAYERS_CRUSTMAP), &
           velocp(180*CRUSTMAP_RESOLUTION,360*CRUSTMAP_RESOLUTION,NLAYERS_CRUSTMAP), &
           velocs(180*CRUSTMAP_RESOLUTION,360*CRUSTMAP_RESOLUTION,NLAYERS_CRUSTMAP), &
-          thicknessnp(NLAYERS_CRUSTMAP), &
+          stat=ier)
+  if( ier /= 0 ) call exit_MPI(myrank,'error allocating crustmaps arrays')
+
+  allocate(thicknessnp(NLAYERS_CRUSTMAP), &
           densitynp(NLAYERS_CRUSTMAP), &
           velocpnp(NLAYERS_CRUSTMAP), &
           velocsnp(NLAYERS_CRUSTMAP), &
@@ -88,7 +91,7 @@
           velocpsp(NLAYERS_CRUSTMAP), &
           velocssp(NLAYERS_CRUSTMAP), &
           stat=ier)
-  if( ier /= 0 ) call exit_MPI(myrank,'error allocating model_crustmaps arrays')
+  if( ier /= 0 ) call exit_MPI(myrank,'error allocating crustmaps np/sp arrays')
 
   ! master reads in crust maps
   if(myrank == 0) call read_general_crustmap()
@@ -132,158 +135,19 @@
   implicit none
   include "constants.h"
 
-  integer :: ila,iln,i,l
+  integer :: i,l
 
-  character(len=150) :: eucrustt3,eucrustt4,eucrustt5,eucrustt6,eucrustt7,&
-                        eucrustr3,eucrustr4,eucrustr5,eucrustr6,eucrustr7,&
-                        eucrustp3,eucrustp4,eucrustp5,eucrustp6,eucrustp7,&
-                        eucrusts3,eucrusts4,eucrusts5,eucrusts6,eucrusts7
+  do l=1,NLAYERS_CRUSTMAP
+    ! file index: from 3 to 7
+    i = l + 2
 
-! Matthias Meschede
-  call get_value_string(eucrustt3, 'model.eucrustt3','DATA/crustmap/eucrustt3.cmap')
-  call get_value_string(eucrustt4, 'model.eucrustt4','DATA/crustmap/eucrustt4.cmap')
-  call get_value_string(eucrustt5, 'model.eucrustt5','DATA/crustmap/eucrustt5.cmap')
-  call get_value_string(eucrustt6, 'model.eucrustt6','DATA/crustmap/eucrustt6.cmap')
-  call get_value_string(eucrustt7, 'model.eucrustt7','DATA/crustmap/eucrustt7.cmap')
-
-  call get_value_string(eucrustr3, 'model.eucrustr3','DATA/crustmap/eucrustr3.cmap')
-  call get_value_string(eucrustr4, 'model.eucrustr4','DATA/crustmap/eucrustr4.cmap')
-  call get_value_string(eucrustr5, 'model.eucrustr5','DATA/crustmap/eucrustr5.cmap')
-  call get_value_string(eucrustr6, 'model.eucrustr6','DATA/crustmap/eucrustr6.cmap')
-  call get_value_string(eucrustr7, 'model.eucrustr7','DATA/crustmap/eucrustr7.cmap')
-
-  call get_value_string(eucrustp3, 'model.eucrustp3','DATA/crustmap/eucrustp3.cmap')
-  call get_value_string(eucrustp4, 'model.eucrustp4','DATA/crustmap/eucrustp4.cmap')
-  call get_value_string(eucrustp5, 'model.eucrustp5','DATA/crustmap/eucrustp5.cmap')
-  call get_value_string(eucrustp6, 'model.eucrustp6','DATA/crustmap/eucrustp6.cmap')
-  call get_value_string(eucrustp7, 'model.eucrustp7','DATA/crustmap/eucrustp7.cmap')
-
-  call get_value_string(eucrusts3, 'model.eucrusts3','DATA/crustmap/eucrusts3.cmap')
-  call get_value_string(eucrusts4, 'model.eucrusts4','DATA/crustmap/eucrusts4.cmap')
-  call get_value_string(eucrusts5, 'model.eucrusts5','DATA/crustmap/eucrusts5.cmap')
-  call get_value_string(eucrusts6, 'model.eucrusts6','DATA/crustmap/eucrusts6.cmap')
-  call get_value_string(eucrusts7, 'model.eucrusts7','DATA/crustmap/eucrusts7.cmap')
-
-  open(unit=1,file=eucrustt3,status='old',action='read')
-  do ila=1,180*CRUSTMAP_RESOLUTION
-    read(1,*) (thickness(ila,iln,1),iln=1,360*CRUSTMAP_RESOLUTION)
+    call read_general_crustmap_layer(thickness(:,:,l), 't', i)
+    call read_general_crustmap_layer(density(:,:,l),   'r', i)
+    call read_general_crustmap_layer(velocp(:,:,l),    'p', i)
+    call read_general_crustmap_layer(velocs(:,:,l),    's', i)
   enddo
-  close(1)
 
-  open(unit=1,file=eucrustt4,status='old',action='read')
-  do ila=1,180*CRUSTMAP_RESOLUTION
-    read(1,*) (thickness(ila,iln,2),iln=1,360*CRUSTMAP_RESOLUTION)
-  enddo
-  close(1)
-
-  open(unit=1,file=eucrustt5,status='old',action='read')
-  do ila=1,180*CRUSTMAP_RESOLUTION
-    read(1,*) (thickness(ila,iln,3),iln=1,360*CRUSTMAP_RESOLUTION)
-  enddo
-  close(1)
-
-  open(unit=1,file=eucrustt6,status='old',action='read')
-  do ila=1,180*CRUSTMAP_RESOLUTION
-    read(1,*) (thickness(ila,iln,4),iln=1,360*CRUSTMAP_RESOLUTION)
-  enddo
-  close(1)
-
-  open(unit=1,file=eucrustt7,status='old',action='read')
-  do ila=1,180*CRUSTMAP_RESOLUTION
-    read(1,*) (thickness(ila,iln,5),iln=1,360*CRUSTMAP_RESOLUTION)
-  enddo
-  close(1)
-
- open(unit=1,file=eucrustr3,status='old',action='read')
-  do ila=1,180*CRUSTMAP_RESOLUTION
-    read(1,*) (density(ila,iln,1),iln=1,360*CRUSTMAP_RESOLUTION)
-  enddo
-  close(1)
-
- open(unit=1,file=eucrustr4,status='old',action='read')
-  do ila=1,180*CRUSTMAP_RESOLUTION
-    read(1,*) (density(ila,iln,2),iln=1,360*CRUSTMAP_RESOLUTION)
-  enddo
-  close(1)
-
-  open(unit=1,file=eucrustr5,status='old',action='read')
-  do ila=1,180*CRUSTMAP_RESOLUTION
-    read(1,*) (density(ila,iln,3),iln=1,360*CRUSTMAP_RESOLUTION)
-  enddo
-  close(1)
-
-  open(unit=1,file=eucrustr6,status='old',action='read')
-  do ila=1,180*CRUSTMAP_RESOLUTION
-    read(1,*) (density(ila,iln,4),iln=1,360*CRUSTMAP_RESOLUTION)
-  enddo
-  close(1)
-
-  open(unit=1,file=eucrustr7,status='old',action='read')
-  do ila=1,180*CRUSTMAP_RESOLUTION
-    read(1,*) (density(ila,iln,5),iln=1,360*CRUSTMAP_RESOLUTION)
-  enddo
-  close(1)
-
-  open(unit=1,file=eucrustp3,status='old',action='read')
-  do ila=1,180*CRUSTMAP_RESOLUTION
-    read(1,*) (velocp(ila,iln,1),iln=1,360*CRUSTMAP_RESOLUTION)
-  enddo
-  close(1)
-
-  open(unit=1,file=eucrustp4,status='old',action='read')
-  do ila=1,180*CRUSTMAP_RESOLUTION
-    read(1,*) (velocp(ila,iln,2),iln=1,360*CRUSTMAP_RESOLUTION)
-  enddo
-  close(1)
-
-  open(unit=1,file=eucrustp5,status='old',action='read')
-  do ila=1,180*CRUSTMAP_RESOLUTION
-    read(1,*) (velocp(ila,iln,3),iln=1,360*CRUSTMAP_RESOLUTION)
-  enddo
-  close(1)
-
-  open(unit=1,file=eucrustp6,status='old',action='read')
-  do ila=1,180*CRUSTMAP_RESOLUTION
-    read(1,*) (velocp(ila,iln,4),iln=1,360*CRUSTMAP_RESOLUTION)
-  enddo
-  close(1)
-
-  open(unit=1,file=eucrustp7,status='old',action='read')
-  do ila=1,180*CRUSTMAP_RESOLUTION
-    read(1,*) (velocp(ila,iln,5),iln=1,360*CRUSTMAP_RESOLUTION)
-  enddo
-  close(1)
-
-  open(unit=1,file=eucrusts3,status='old',action='read')
-  do ila=1,180*CRUSTMAP_RESOLUTION
-    read(1,*) (velocs(ila,iln,1),iln=1,360*CRUSTMAP_RESOLUTION)
-  enddo
-  close(1)
-
-  open(unit=1,file=eucrusts4,status='old',action='read')
-  do ila=1,180*CRUSTMAP_RESOLUTION
-    read(1,*) (velocs(ila,iln,2),iln=1,360*CRUSTMAP_RESOLUTION)
-  enddo
-  close(1)
-
-  open(unit=1,file=eucrusts5,status='old',action='read')
-  do ila=1,180*CRUSTMAP_RESOLUTION
-    read(1,*) (velocs(ila,iln,3),iln=1,360*CRUSTMAP_RESOLUTION)
-  enddo
-  close(1)
-
-  open(unit=1,file=eucrusts6,status='old',action='read')
-  do ila=1,180*CRUSTMAP_RESOLUTION
-    read(1,*) (velocs(ila,iln,4),iln=1,360*CRUSTMAP_RESOLUTION)
-  enddo
-  close(1)
-
-  open(unit=1,file=eucrusts7,status='old',action='read')
-  do ila=1,180*CRUSTMAP_RESOLUTION
-    read(1,*) (velocs(ila,iln,5),iln=1,360*CRUSTMAP_RESOLUTION)
-  enddo
-  close(1)
-
+  ! north pole / south pole
   thicknessnp(:) = ZERO
   thicknesssp(:) = ZERO
   densitynp(:) = ZERO
@@ -323,6 +187,47 @@
 !-------------------------------------------------------------------------------------------------
 !
 
+  subroutine read_general_crustmap_layer(var,var_letter,ind)
+
+  implicit none
+  include "constants.h"
+
+  double precision, intent(out), &
+    dimension(180*CRUSTMAP_RESOLUTION,360*CRUSTMAP_RESOLUTION)&
+    :: var
+  character(len=1), intent(in) :: var_letter
+  integer, intent(in) :: ind
+
+  ! local variables
+  character(len=50) :: config_name
+  character(len=150) :: default_name
+  character(len=150) :: eucrust
+  integer :: ier, ila, iln
+
+  write(config_name,'(a,a1,i1)') 'model.eucrust', var_letter, ind
+  write(default_name,'(a,a1,i1)') 'DATA/crustmap/eucrust', var_letter, ind
+
+  call get_value_string(eucrust, config_name, default_name)
+
+  open(unit=1,file=trim(eucrust),status='old',action='read',iostat=ier)
+  if ( ier /= 0 ) then
+    write(IMAIN,*) 'error opening "', trim(eucrust), '": ', ier
+    call exit_MPI(0, 'error model crustmap')
+  endif
+
+  do ila=1,180*CRUSTMAP_RESOLUTION
+    read(1,*) (var(ila,iln),iln=1,360*CRUSTMAP_RESOLUTION)
+  enddo
+  close(1)
+
+  end subroutine read_general_crustmap_layer
+
+
+
+!
+!-------------------------------------------------------------------------------------------------
+!
+
   subroutine model_crustmaps(lat,lon,x,vp,vs,rho,moho,found_crust,elem_in_crust)
 
 ! Matthias Meschede

Modified: seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/src/shared/exit_mpi.f90
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/src/shared/exit_mpi.f90	2013-08-21 16:56:20 UTC (rev 22727)
+++ seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/src/shared/exit_mpi.f90	2013-08-22 07:40:44 UTC (rev 22728)
@@ -135,7 +135,42 @@
 !
 !-------------------------------------------------------------------------------------------------
 
+  subroutine init_mpi()
 
+  use mpi
+
+  implicit none
+
+  integer :: ier
+
+  call MPI_INIT(ier)
+  if( ier /= 0 ) stop 'error initializing MPI'
+
+  end subroutine init_mpi
+
+!
+!-------------------------------------------------------------------------------------------------
+!
+
+  subroutine finalize_mpi()
+
+  use mpi
+
+  implicit none
+
+  integer :: ier
+
+  call MPI_FINALIZE(ier)
+  if( ier /= 0 ) stop 'error finalizing MPI'
+
+  end subroutine finalize_mpi
+
+
+
+!
+!-------------------------------------------------------------------------------------------------
+!
+
   subroutine sync_all()
 
   use mpi

Modified: seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/src/specfem3D/save_regular_kernels.f90
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/src/specfem3D/save_regular_kernels.f90	2013-08-21 16:56:20 UTC (rev 22727)
+++ seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/src/specfem3D/save_regular_kernels.f90	2013-08-22 07:40:44 UTC (rev 22728)
@@ -137,6 +137,10 @@
     ! allocates temporary isotropic kernel arrays for file output
     allocate(bulk_c_kl_crust_mantle(npoints_slice), &
              bulk_beta_kl_crust_mantle(npoints_slice))
+
+    allocate(kappa_kl_crust_mantle(npoints_slice), &
+             mu_kl_crust_mantle(npoints_slice), &
+             rhonotprime_kl_crust_mantle(npoints_slice))
   endif
 
   ! crust_mantle
@@ -164,6 +168,7 @@
       rhonotprime_kl_crust_mantle(ipoint) = 0.0
       kappa_kl_crust_mantle(ipoint) = 0.0
       mu_kl_crust_mantle(ipoint) = 0.0
+
       rho_kl_crust_mantle_reg(ipoint) = 0.0
       alpha_kl_crust_mantle_reg(ipoint) = 0.0
       beta_kl_crust_mantle_reg(ipoint) = 0.0
@@ -292,7 +297,7 @@
 
               ! K_rho (primary kernel, for a parameterization (A,C,L,N,F,rho) )
               rhonotprime_kl = rhol * rho_kl / scale_kl_rho
-              rhonotprime_kl_crust_mantle(ipoint) = rhonotprime_kl_crust_mantle(ipoint) + rhonotprime_kl
+              !rhonotprime_kl_crust_mantle(ipoint) = rhonotprime_kl_crust_mantle(ipoint) + rhonotprime_kl
 
               ! note: transverse isotropic kernels are calculated for ALL elements,
               !          and not just transverse elements
@@ -397,7 +402,7 @@
     if (ANISOTROPIC_KL) then
       if (SAVE_TRANSVERSE_KL_ONLY) then
         ! write the kernel in physical units
-        rhonotprime_kl_crust_mantle(ipoint) = - rhonotprime_kl_crust_mantle(ipoint) * scale_kl
+        !rhonotprime_kl_crust_mantle(ipoint) = - rhonotprime_kl_crust_mantle(ipoint) * scale_kl
 
         alphav_kl_crust_mantle(ipoint) = - alphav_kl_crust_mantle(ipoint) * scale_kl
         alphah_kl_crust_mantle(ipoint) = - alphah_kl_crust_mantle(ipoint) * scale_kl
@@ -531,9 +536,12 @@
     deallocate(bulk_c_kl_crust_mantle,bulk_betah_kl_crust_mantle, &
                bulk_betav_kl_crust_mantle,bulk_beta_kl_crust_mantle)
   endif
+
   if (.not. ANISOTROPIC_KL) then
     deallocate(bulk_c_kl_crust_mantle,bulk_beta_kl_crust_mantle)
+    deallocate(kappa_kl_crust_mantle,mu_kl_crust_mantle,rhonotprime_kl_crust_mantle)
   endif
+
   deallocate(cijkl_kl_crust_mantle_reg, &
              rho_kl_crust_mantle_reg, &
              beta_kl_crust_mantle_reg, &

Modified: seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/src/specfem3D/specfem3D.F90
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/src/specfem3D/specfem3D.F90	2013-08-21 16:56:20 UTC (rev 22727)
+++ seismo/3D/SPECFEM3D_GLOBE/branches/SPECFEM3D_GLOBE_SUNFLOWER/src/specfem3D/specfem3D.F90	2013-08-22 07:40:44 UTC (rev 22728)
@@ -29,18 +29,8 @@
 
   program xspecfem3D
 
-  use mpi
-  use specfem_par
-  use specfem_par_crustmantle
-  use specfem_par_innercore
-  use specfem_par_outercore
-  use specfem_par_movie
-
   implicit none
 
-  ! local parameters
-  integer :: ier
-
 !=======================================================================!
 !                                                                       !
 !   specfem3D is a 3-D spectral-element solver for the Earth.           !
@@ -447,7 +437,7 @@
 !-------------------------------------------------------------------------------------------------
 !
   ! initialize the MPI communicator and start the NPROCTOT MPI processes.
-  call MPI_INIT(ier)
+  call init_mpi()
 
   ! force Flush-To-Zero if available to avoid very slow Gradual Underflow trapping
   call force_ftz()
@@ -457,6 +447,7 @@
 
   ! starts reading the databases
   call read_mesh_databases()
+
   ! sets up reference element GLL points/weights/derivatives
   call setup_GLL_points()
 
@@ -476,7 +467,7 @@
   call finalize_simulation()
 
   ! stop all the MPI processes, and exit
-  call MPI_FINALIZE(ier)
+  call finalize_mpi()
 
   end program xspecfem3D
 

