[cig-commits] [commit] devel's head updated: Merge branch 'master' into devel (bf10ec8)
cig_noreply at geodynamics.org
cig_noreply at geodynamics.org
Wed Jun 18 15:24:51 PDT 2014
Repository : https://github.com/geodynamics/specfem2d
Branch 'devel' now includes:
3a9a6cd moves examples to SPECFEM2D/EXAMPLES and adds process.sh script for each to run a default simulation
250a0f4 adds USER_T0 capability to SPECFEM2D/ to fix simulation start times
297ae44 updated README files for examples; added print line in checkgrid.F90 for USER_T0 ; added symbolic link for manual
6cfce9a added SOURCE files for Carl Tape's examples
5cf3b18 updates some variable names in SPECFEM2D/ related to sources; adds new source code files compute_normal_vector.f90, prepare_initialfield.F90, initialize_simulation.F90, set_sources.f90, read_databases.f90, prepare_source_time_function.f90, save_openDX_jacobian.f90, prepare_color_image.F90, prepare_absorb.f90
28b2d42 updates source parameters in SPECFEM2D/; adds new file check_stability.F90
8ab5d5f Added Abel_Brest and canyon as formal examples.
6a7322b updates configure script, puts compiled binaries into bin/ subdirectory; fixes problem with MPI deadlocks
a3b4671 updated Par_file for all six examples to reflect recent changes; tested to make sure each one works
078d24a testing output_wavefield_snapshot option
42bd2a1 added "sngl" within output_wavefield_snapshopt format statement to fix bug
a23beca added GMT/perl script for plotting wavefield snapshots; added three example figures; tested all examples.
b6a1334 added kernel example for Tape2007
23b1dfd added kernel example for Tromp2005
e9726cd updated run scripts for examples
593018d added sub-example to Tape2007 to illustrate reading in an external model (with internal mesh).
f938a6e uses directory SEM/ for adjoint sources; removes trailing spaces from source code files
77e25d7 renames precision_mpi.h to precision.h; renames seismogram band codes from BHX/BHY/BHZ to BXX/BXY/BXZ; renames kernel file names to e.g. proc000000_rho_kappa_mu_kernel.dat; adds param_reader.c to handle more flexible parameter file formats
3f8af7f updates version number to 6.2.0 in source code files and manual
049226a removed unused lines in fluid_solid external mesh; changed "negative" error message to "non-positive" when appropriate
4d4416b reduced number of receivers from 100 to 12 in fluid_solid example
9038f69 added Paul Cristini's Gmsh examples
1c258d0 More detailed instructions on how to use initial input plane waves (initialfield=true) an example is checked into EXAMPLES/init_plane prepare_initial_field is modified to allow plane wave incidence from the right (angleforce=negative vals) output snapshots are in jpg files which are easier to convert to avi movie
e3db089 adds NOISE_TOMOGRAPHY flag to Par_file
7e7dd30 adds an example illustrating noise tomography with uniform spatial distribution of noise sources
4634584 adds noise example to EXAMPLES/ directory
b35ddde fixed the QKappa/Qmu bug detected by Julien Barriere (we used to use Qp/Qs instead of QKappa/Qmu in the DATA/Par_file input file due to a confusion in the notations used in a 1988 viscoelasticity article by Jose Carcione). Also removed directory "NOISE_TOMOGRAPHY", which was empty.
e5dac00 Changes EXAMPLES/noise_uniform for improved consistency with the other test cases
9e6c954 adds comment explaining source time functions for noise simulations
44fbb26 fixed the plane wave code and made sure the "EXAMPLES/canyon" example now works fine; also removed useless white spaces in source files.
727ab34 removed some obsolete examples
75e7a36 fixed the script to run the "EXAMPLES/canyon" example
eeafd54 added directory DATA/NOISE_TOMOGRAPHY
9093091 changed processing script for EXAMPLES/noise_uniform so that it computes both kernel contributions instead of just one
48d467d add EXAMPLES/BENCHMARK_CLAERBOUT_ADJOINT
2d0a14a (SPECFEM2D) correct typos in EXAMPLE/BENCHMARK_CLAERBOUT_ADJOINT
725bdb8 (SPECFEM2D) BENCHMARKED
0fa6113 (SPECFEM2D) warning to equivalence in SU corrected
0c4a33c for noise tomography, fixes weighting on ensemble forward wavefield source
de8b0d0 for noise tomography, adds flags "save_everywhere" and "output_wavefields_noise"
27365e8 fixes ensemble forward wavefield during third noise simulation
0337a2c Add NOISE_TOMOGRAPHY = 0 # 0 = earthquake simulation, 1/2/3 = noise simulation to Par_file of various examples.
7e7b86a switch to direct access i/o for writing noise wavefields
940b19c added noise exploration test case
302d05c Added an acoustic-poroelastic example in EXAMPLES/acoustic_poroelastic
b900312 suppressed older versions of Paul Cristini's Python script for Gmsh
2ca9ab2 updated EXAMPLES/canyon/Par_file_canyon to the new Par_file format
f7505d8 done making the periodic boundary conditions more flexible
5d1efce renamed an old directory
40537f7 Paul Cristini converted all the EXAMPLES/Par_files to the new format with more input parameters
0915313 changed Qp Qs to QKappa Qmu in some old EXAMPLES/Par_files
80ed947 changed Qp Qs to QKappa Qmu in more old EXAMPLES/Par_files
3d45bdb updated script for noise_uniform example
fd5fc2e added a cleaned version of the 2D attenuation example from our 1999 GJI paper (Figure 16)
d4880a5 removed an unused (extra) receiver in the 2D attenuation example
f7b9d6d added a Gnuplot script to compare the results to the quasi-analytical solution of Carcione et al. (1988).
3eb7f87 fixed a comment in the attenuation routine, and added more details about how to use EXAMPLES/attenuation
1ec592e improved the README file for EXAMPLES/attenuation
344d449 added EXAMPLES/Rayleigh_wave and fixed a small problem in the horizontal offset of Rayleigh sources
7deafb5 added an example with an incident Rayleigh wave propagating towards a crack; modified the source code in order to "manually" add a crack (i.e., some parameters are hardwired and the crack detection and handling code I added is not very flexible yet)
2565856 fixed the processing scripts for some of the examples
ca30e58 changed "receiverlines" to "receiversets" because each set can now have a single receiver if needed, thus it is not necessarily a line any more
2115a0e moved fluid-solid example to a subdirectory
b856ce5 added two subdirectories for the fluid/solid examples of my 2000 Geophysics paper
5d5aa2d added EXAMPLES/fluid_solid/from_2000_Geophysics_paper_flat_ocean_bottom
d4b8504 added EXAMPLES/fluid_solid/from_2000_Geophysics_paper_sinusoidal_ocean_bottom and improved the parameter file in EXAMPLES/fluid_solid/from_2000_Geophysics_paper_flat_ocean_bottom
b61599b fixed the number of receivers (from 11 to 110)
846f428 renamed two flags to ATTENUATION_VISCOELASTIC_SOLID and ATTENUATION_POROELASTIC_SOLID to avoid confusion; also removed useless white spaces
7438c51 changed ATTENUATION_POROELASTIC_SOLID to ATTENUATION_PORO_FLUID_PART to further clarify
93d2f61 committed new version of Paul Cristini's Python script to convert old Par_files to the new format; and used it to convert old examples that had not been converted before
438572b Xie Zhinan fixed the non-causal attenuation problem of the paper of Carcione et al. (1993). Also updated the BibTeX manual.
f8e4ba7 mentioned the Carcione et al. (1993) attenuation problem in the README file
537d110 added time_stepping_scheme to all the Par_files. added EXAMPLES/semi_infinite_homo
2eb7d1f RK and LDDRK time schemes not supported for adjoint inversion, mixed elastic/poroelastic forword simulations and poroelastic forword simulations with attenuation
dce6ce3 added my scripts to clean all the Par_files. set Cuthill-McKee sorting to .false. by default.
bae684c added the missing C Delta_t / 2 term in the mass matrix for Clayton-Engquist absorbing elements (mentioned by Jean-Paul Ampuero in 2003, see the book of Hughes 1987 chapter 9). Zhinan Xie also added a spring to further stabilize the Clayton-Engquist absorbing conditions.
4a2914d modified USER_T0 in the Tromp2005 and Tape2007 examples; also updated the instructions for these examples. added a few 'quick test' lines to the main README
7cd17b5 capital letter to interfaces_Rayleigh_flat.dat
ab45008 used Paul Cristini's script to process all the Par_files to convert them to the new format
72950cc turned PostScript output off in EXAMPLES/Tromp2005/Par_file_Tromp2005 because PostScript vector plots cannot be drawn in the SH case
058c6c1 adds Zhinan's pml routines
3616a41 used Paul Cristini's script to add the new PML parameters to all the Par_files
fa05b2e updated the list of all Par_files
7a2bc13 fixed two bugs in my scripts to change parameter values in the Par_files in directory "EXAMPLES" automatically
490860e renamed STATIONS_target_noise to STATIONS_noise
41608cf updated all the process.sh to take the new STATIONS and SOURCE file names into account
7db41a8 Paul changed the old Par_file by adding on term with CPML_element_file
58325a0 Paul fixed problems in Par_file when using PML with external mesh
3a78ad3 set STACEY_ABSORBING_CONDITIONS to .true., otherwise Bielak conditions are inactive
8b932c0 added "typeabs()" to prepare for handling of rotated absorbing elements in the Stacey absorbing boundary conditions
15ef5e6 switched from angleforce to anglesource; added flexible reading of DATA/SOURCE; added possibility to use the incident field only for a plane wave
10c13d8 fix the wrong output the file name of PML_ELEMENT_FILE in specfem2D.F90 and two small bugs in other two files
e5d70d8 removed obsolete Gmsh files
d271f7d updated UTILS/Gmsh/LibGmsh2Specfem_convert_Gmsh_to_Specfem2D_official.py and added EXAMPLES/Gmsh_example_serial/process_the_Gmsh_file_once_and_for_all.sh
6016c44 added EXAMPLES/Gmsh_example_MPI/process_the_Gmsh_file_once_and_for_all.sh
3a23e3f added salt dome example; fixed the height of element numbers in PostScript display
2f18e6d Use Paul's script to add in Par_file about how to choose time step
911bdcc fixed the manual and also comments in the different Par_files about how to choose the time step
2739be5 added Gmsh_example_titled_CPMLs
6e3b020 added CUBIT and ACIS files for the salt dome model with CPML
a3e0bde added the geometry of the salt dome in two more formats
83689ce converted the salt dome geometry model from the (x,z) plane to the (x,y) plane
eff7c47 improved the salt dome mesh manually (one element on the right edge has a strange shape) and made sure we have only 8 materials instead of 11
3b19d1e changed the name of the CPML file name to make it clearer
3f280b7 add the process file for this example
3ef80f5 modify the process file for example of salt_dome
f0349ab minor change
fb7abb5 added salt dome mesh with CPML
d2470f4 added EXAMPLES/salt_dome/CPML_homogeneous
1f5055d committed the right version of EXAMPLES/salt_dome/CPML_normal/modelY1_materials_file
69fddc0 added the original "grep" statement
3dbba07 removed an extra comment
4e9f13d added EXAMPLES/global_Earth_ak135f
d6b2f9d new version of Paul Cristini's script
2d68b73 initial version of titled PML commited, please becarful to use it, since the current pml_init.F90 code using to define the pml parameter do not support titled mesh.
e0d07fc change default time scheme to newmark
4cb086f changed generate_STATIONS to use_existing_STATIONS
be6512c New version of python script for updating Par_files
5b9c9b0 change the par_file to reproduce the same original pdf file presented in this example
d5f0734 Fixed viscous attenuation for poroelastic media to suppress the error on inversion of the permeability matrix in specfem2D.f90. Modified some parameters in Par_file_acoustic_poroelastic so users can turn ATTENUATION_PORO_FLUID_PART on or off to use or not viscous attenuation.
efb71be replaced SIMULATION_TYPE == 2 with SIMULATION_TYPE == 3 in the whole code, to remain consistent with the numbering convention used in our 3D codes
678b92a added EXAMPLES/CPML_absorbing_layers/CPML_layers_added_to_simple_square_with_Gmsh.geo
fcdb155 fixed the name of the Gmsh include file
9a75eb5 update the Par_file and process.sh file in salt_dome_cubit_mesh example
4e9f71f provide process.sh files for examples in salt_dome_cubit_mesh
d703590 commit one example fluid_solid kernel example provided by Luo Yang
72cfeab add one line in LuoYang_fluid_soild_kernel/README file
07fc44c updated (simplified) the CPML flags in the manual; also fixed a typo in a directory name
2aa4e29 added "Stacey" to the name of current CPML examples
290e945 created empty directory EXAMPLES/Gmsh_example_MPI_CPML for Paul and Zhinan next week
d059a59 added flag save_ASCII_kernels to all the Par_files
124f840 unified syntax for endif, enddo and else if; alse removed useless white spaces
9119d4c new version of python script which updates Par_files
c7faac0 renamed two directories
9a122c1 added EXAMPLES/salt_dome_CUBIT_mesh/CPML_normal_solid_only
e1af10d removed the unused fluid material in EXAMPLES/salt_dome_CUBIT_mesh/CPML_normal_solid_only
51d6810 change the old flag of pml into new flag
f7f374b commit one example modified from CPML_normal_solid_only by reducing the thickness of the topest layer
b8469b9 remove the example EXAMPLES/salt_dome_CUBIT_mesh/CPML_normal_solid_only, then rename the name of exampel EXAMPLES/salt_dome_CUBIT_mesh/CPML_normal_solid_only_new to EXAMPLES/salt_dome_CUBIT_mesh/CPML_normal_solid_only
6a411c2 put bach the only example of salt_dome_CUBIT_mesh/CPML_normal_solid_only
ca0ebca fixed the calculation of pressure in the case of an anisotropic material (it is then necessary to compute sigma_yy using additional c_IJ anisotropic parameters); updated the manual and the Par_file accordingly; added a new example: EXAMPLES/anisotropic_zinc_crystal; also removed useless white spaces
e6297d1 reduced the total number of time steps in EXAMPLES/anisotropic_zinc_crystal/Par_file
f31621f readd benchmark data
b87b332 In examples in fluid_solid, the process.sh scripts cd to ../.. to get to the executables but they are in ../../.. This commit fixes that bug.
934db61 Merge pull request #18 from geodynamics/devel
356aeae added removal of *__genmod.f90 to "make clean"
9b7618e Update README
4fe2212 reverted a change made to master instead of devel
568840e reverted a change made to master instead of devel
b5d3a3a Revert "reverted a change made to master instead of devel"
e4fa9d0 Revert "reverted a change made to master instead of devel"
2e83e21 Revert "Update README"
db078e9 Revert "added removal of *__genmod.f90 to "make clean""
fc67e6f Merge pull request #49 from komatits/master
9f699ba test to see if I can commit to the EXAMPLES submodule
2279b1b moved noise_layered and noise_uniform to new directory "broken_or_obsolete_examples_but_do_not_remove"
2a1958f moved some broken examples to "currently_broken_or_obsolete_examples_but_do_not_remove" directory
6622907 renamed process.sh to run_this_example.sh and updated README_EXAMPLES
e2607c1 moved CPML_absorbing_layers to ZZZ_currently_broken_or_obsolete_examples_but_do_not_remove
34fc68e fixed all the broken examples
9fe2773 added Rayleigh_wave_with_crack/README_this_example_requires_changing_one_line_in_the_source_code.txt and renamed process_this_example.sh to run_this_example.sh
f4027ab fixed the last broken examples, and renamed Gmsh_example_MPI_Stacey to Gmsh_example_Stacey_MPI and Gmsh_example_serial_Stacey to Gmsh_example_Stacey_serial
933af0a updated vi_all_2D_Par_files.csh
2fc96fc added the new axisymmetric parameters to all the Par_files of the EXAMPLES; also translated some comments from French to English in global_Earth_ak135f/create_mesh_AK135F_2D_with_central_cube_no_PML.F90
e8e5429 updated process_DATA_Par_files_to_update_their_format_when_new_parameters_are_added.py to handle the two new parameters in the Par_file
a52eab7 added a dummy white space to test
c0cc276 added the two new gravitoacoustic parameters to the Par_files
eac5e30 added USE_CONSTANT_MAX_AMPLITUDE and CONSTANT_MAX_AMPLITUDE_TO_USE for movies
583a76b added parameter READ_VELOCITIES_AT_f0 and implemented a shift of velocities read from the Par_file if needed when viscoelasticity is on
cfda3d6 added Paul Cristini's new version of process_DATA_Par_files_to_update_their_format_when_new_parameters_are_added.py
7394d43 added attenuation/params_carcione.dat renamed attenuation/older_analytical_solution_viscoelastic_Carcione_ori_with_causality_problem.f
485933a fixed the Carcione 1988 1_over_N problem in "attenuation", and kept "older_attenuation_with_Carcione_1988_1_over_N_problem" as a reference
543190f moved older_attenuation_with_Carcione_1988_1_over_N_problem to ZZZ_currently_broken_or_obsolete_examples_but_do_not_remove
cd27e16 Dimitri's changes
5cfa05a Remove submodule
e9ca46c Add 'EXAMPLES/' from commit 'cd27e168bc1a71d83214bc6d2342560ca825aa17'
f1cad83 Remove submodule
bf10ec8 Merge branch 'master' into devel
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