[cig-commits] [commit] devel's head updated: Merge pull request #167 from komatits/devel (47f7038)
cig_noreply at geodynamics.org
cig_noreply at geodynamics.org
Wed Jun 18 16:55:35 PDT 2014
Repository : https://github.com/geodynamics/specfem3d
Branch 'devel' now includes:
53d6a0d important modifications : modified the tree structure of the software package. source code files are located in src/ and binaries are created in bin/. To compile type './configure' in the main folder and then 'make' or 'make generate_databases' for instance.
e62b98b Modified the Makefiles to not always recompile everything for decompose_mesh_SCOTCH and to get rid of unwanted messages, deleted Mesh_Pieyre in examples, other minor modifs
fe885eb updates attenuation handling so that users can directly specify Q_mu values rather than iflags in CUBIT and xmeshfem3D; updates some files referencing old paths to DATA/
afa533e added examples for meshfem3D and updated the manual
ea27d93 Minor updates to instructions for homogeneous example
bb276a2 Noise tomography capability added (./src/shared/noise_tomography.f90). Two new parameters NOISE_TOMOGRAPHY & NTSTEP_BETWEEN_READ_ADJSRC in Par_file.
c98490c updates SPECFEM3D manual and example readme files; bug fixes coupling surface detection for single layer cases
a5c16ef change the position of NTSTEP_BETWEEN_READ_ADJSRC in Par_file. One example of noise sensitivity kernels is added
edf524e Manual updated for noise simulations
706d9fc minor restructuring of examples files; adding flag USE_SOURCES_RECVS_Z in constants.h for locating source/receivers in randomly shaped meshes; updates some files to avoid compiler warnings and unifies character lengths for LOCAL_PATH; updates manual
2917e71 adapts IRIS name convention for seismograms; updates seis_process/ scripts; updates manual
ba44ee8 moves unused/old/deprecated files and routines into SPECFEM3D/utils/unused_routines; updates manual and Makefiles
e174463 updates examples/ files in SPECFEM3D; cleans up code
4207d98 updates SPECFEM3D configure script and manual regarding scotch installation
0e80bb3 updates SPECFEM3D configuration with scotch, manual and examples; further code clean up
c10f535 adds reference solutions to SPECFEM3D examples
de55431 adds USER_T0 to fix start time; bug fix of start time with multiple point force sources; adds kernel smoothing routine smooth_vol_data.f90
ad49ff6 Updated README files for four examples, to reflect current directory structure.
445836a adds a README file to examples/ directory in SPECFEM3D
4d96129 updated README files for examples
7fbec60 updated README files for examples. also added go_decomposer_pbs.bash to remind user not to run huge partition jobs on the head node, but rather on a (high-memory) compute node
f39afdc re-adds TOPOGRAPHY flag to use with ocean load approximation; updates Makefiles; updates layered_halfspace example
887ea00 updates STATIONS files in SPECFEM3D/examples
e7e6b7d updated example README files
e38ab2b updates configure file to bundle with new scotch_5.1.11 version; updates in-house mesher examples meshfem3D_examples/; updates post-processing scripts process_data.pl and process_syn.pl
193e6d5 fixes bug in minimum period calculation in check_mesh_resolution.f90
449c994 minor updates to homogeneous README
3788601 updated README for meshfem3D examples
e66382e updates example reference solution in SPECFEM3D/examples/waterlayered_halfspace/
2ba2150 fix a bug in meshfem3D.f90: line 650--spacing_x_interface_top changed to spacing_y_interface_top
b088b61 added warning message to the README for the "many_interfaces" internal mesh example (>= 1.1 GB memory per core; 415 GB disk space total); this example should not be run by the typical user.
99e98ab added the four-layer socal1D model as an internal mesher example; mesh is comparable to the DT=0.011 s mesh from the old SPECFEM3D_BASIN
bb91a32 added Mesh_Par_file_168 for 1D socal example to give the option of a 168-core simulation for a larger region.
5a37ac9 adds directory utils/adjoint_sources to create traveltime and amplitude adjoint sources
b38f890 new version of NOISE_TOMOGRAPHY in SPECFEM3D_SESAME
8ca8f8e new version of NOISE_TOMOGRAPHY in SPECFEM3D_SESAME benchmarked
228f02f added reference seismograms for socal1D example.
493663d added two sub-examples to handle utm suppression for the socal1D internal mesh example
d026ee8 added socal1D sub-example to illustrate how to extend the identical model downward in depth; because layers are ordered from bottom up, this requires several minor changes to ensure that the meshes are identical in the overlapping region.
214c02e (SPECFEM3D_SESAME) examples/BENCHMARK_CLAERBOUT_ADJOINT added
a746bdc Merging of 3D Biot into SPECFEM3D with CUBIT support... Modify README in examples/ ** NOTE ** Because of the poroelastic implementation, even in an acoustic/elastic case, the file nummaterial_poroelastic_file must be present in the MESH/ directory. Need to had a dummy file in cubit2specfem3d.py [CM - Oct. 2011] For now it can be copied from examples/homogeneous_poro/MESH_coarse.
cb56cbc Merging of 3D Biot into SPECFEM3D with CUBIT support... Added an example in examples/homogeneous_poroelastic
24a0570 updates database creations, coupling interface detection and inner/outer element detection for mesher; adds model update routines from federica; removes obsolete scotch_5.1.10b directory; moves compute_arrays_source.f90, compute_kernels.f90 & compute_boundary_kernel.f90 to src/specfem3D directory and adds write_output_SU.f90 file; updates Makefiles.in
96ec9d9 adds Mount_StHelens CUBIT example; updates some default process.sh scripts
53b7475 updates example Mount_StHelens; adds mesh output for courant and minimum period; updates manual for xcheck_mesh_quality_CUBIT_Abaqus outputs
6de86f7 fixes sign() function for double precision value; updates mesh_mount.py for Mount St.Helens example
8f7a313 adds estimated time output to timestamp files
cbd5de9 adds flag for VTK mesh output files in xmeshfem3D
5cdb277 adds predefined 1D and 3D model options to generate_databases
0b624fe added the coffee mug mesh from our 2011 GJI paper
21c7a08 copy run script as a backup file
1245733 fixed a couple typos in README_kernel
4478d3b updates kernel example in example/homogeneous_halfspace/
8503f02 adds GPU functionality to SPECFEM3D solver (requires to rerun ./configure); merges GPU branch modifications to main trunk; adds src/cuda directory & files; updates Par_files; renames compute_forces_elastic.F90 and prepare_timerun.F90
b71359d updates code file version numbers to version 2.1
b698971 Updated Par_file in example/homogeneous_poroelastic/ Corrected arguments in check_mesh_resolution_poro() in /specfem3D/read_mesh_database.f90 Suppressed stop flag for forward poro calculation in generate_databases/save_arrays_solver.f90
32f1080 add
cd398f4 updates constants.h file for meshfem3D; updates generate_databases and fixes acoustic-elastic coupling detection; updates CUDA declarations
14d284b moves point source flags from constants.h.in to Par_file
2d6496b adds point source flags in Par_file related to the use of an inclined force
a3ace9c moves ABSORB_FREE_SURFACE flag from constants.h.in into ABSORB_INSTEAD_OF_FREE_SURFACE flag in Par_file
2a8f30e adds default mesh files for examples/Mount_StHelens/MESH-default
c83bd25 adds a set of FORCESOLUTION files to set force source parameters, used instead of CMTSOLUTION files if "USE_FORCE_POINT_SOURCE = .true".
33a6fd8 adds the hdur parameter in FORCESOLUTION files and the use of a quasi-Heaviside source time function for runs involving a FORCESOLUTION file
6d74f14 renames the USE_RICKER_IPATI flag in USE_RICKER_TIME_FUNCTION and moves it from constants.h.in to the Par_file
a05ded3 renamed examples/homogeneous_halfspace to examples/homogeneous_halfspace_HEX8
6047e35 added example "homogeneous_halfspace_HEX27"
1916df6 replaced in_data_files with DATA in all files and scripts
4b4814b replaced in_out_files with OUTPUT_FILES in all files and scripts
0a80a8c added Emanuele Casarotti's Python scripts for HEX27
f8b9205 fixed instructions for homogeneous_halfspace_HEX8 example
0849d5d moves parameter 'NGNOD' from constants.h to Par_file, updates the 'simple_model' example
abeb258 cleanup in 'meshfem3D_examples' directories
3bfd19c cleanup in all examples directories
3a0dd55 fixes a bug in NGNOD-related developments; moves parameters MOVIE_SURFACE, CREATE_SHAKEMAP, OLSEN_ATTENUATION_RATIO from constants.h.in to Par_file; gets rid of previous EXTERNAL_MESH_* flags and introduces instead a new parameter MOVIE_TYPE in Par_file. (beware: the activation of movie flags still needs to be tested!)
aeade6d adds automatic detection of NGNOD and NGNOD2D values in program_decompose_mesh_SCOTCH
fc275ab updates the user manual; modifies all parameter files
85bead6 renamed decompose_mesh_SCOTCH to decompose_mesh because METIS is now supported as well, in addition to SCOTCH (and ZOLTAN may also be added in the future).
70a37e1 renamed src/decompose_mesh_SCOTCH to src/decompose_mesh
3f7f569 now mention the fact that element imbalance can be normal if fluid, elastic and poro elements are mixed (also with CPML elements). also added a gnuplot script for the HEX27 example.
b072e54 adds a (pseudo) Dirac delta source time function set by default when FORCESOLUTION is used; adds calculation of source arrays for interpolated locations of force point sources; corrects source time function factors used in GPU code; updates the user manual in Par_file and FORCESOLUTION related pages.
52b12a3 fixes a small bug in the setup_sources_precompute_arrays() subroutine
3771760 allows the use of multiple user-defined tomographic files instead of having the same and only "tomography_model.xyz" file, moves the TOMOGRAPHY_PATH flag in Par_file, organises the "done" items of the todo list
9267add Merged fault kinematics/dynamics routines
25d4c46 Updated Par_file of fault-examples to new format
d9cf6d8 fixed documentation of fault side 1/2 conventions
a324b48 adds C-PML boundary conditions in CPU code for elastic and acoustic domains. BEWARE!!! runs ok but no fully tested -> desactivated by default in all examples.
58b0a5e fixes a small bug in specfem3D/Makefile.in by removing an old routine that has been deleted with the new C-PML implementation
0cfa327 added two simple CPML examples
1364e08 replaced the OCEANS flag with APPROXIMATE_OCEAN_LOAD to avoid confusion
f9cc77f added examples/CPML/HOMO8_FREE_SURFACE/HOWTO_run_this_example.txt
1f7373c fixes one small bug in pml_compute_memory_variables.f90 related to acoustic C-PML elements
fa8af37 updated process.sh and HOWTO_run_this_example.txt for examples/homogeneous_halfspace_HEX8
b5d43ec added examples/homogeneous_halfspace_HEX27/HOWTO_run_this_example.txt
aaa32ab switched to 4 processors
ff2d661 converted both PML examples to purely elastic models
3a6a766 added three new CPML example directories
abdeae2 moved CPML/HOMO8_NOFREESURFACE and CPML/HOMO8_FREE_SURFACE to CPML/purely_elastic
4da997d fixed the problems in the nummaterial_velocity_file of all the CPML examples
29fce2f typed svn add in examples/CPML/purely_acoustic (I had forgotten)
e2b8a5d fixes a bug for runs without C-PML conditions; creates bash scripts for both CPML/purely_elastic/ examples; modifies loops using the CPML_mask_ibool array; comments out boundary conditions for acoustic pml elements
a7e24ea updates process.sh file for running homogeneous_halfspace_HEX8 example
70798f2 fixes bugs in acoustic C-PML simulations; create bash scripts for both C-PML examples
021010f added PML_CUBIT_notes_from_Emanuele_Casarotti_16oct2012.pdf
f2f9f14 fixed hdur and f0_for_PML in all the CPML examples; switched to a source that creates S waves as well for the elastic example
0c053b4 added examples/CPML/purely_elastic/geometrical_properties_of_this_PML_mesh.txt
10a18ce added examples/CPML/acoustic_elastic_two_layers/image_of_this_CPML_mesh_with_PML_colors_not_displayed_only_acoustic_and_elastic.jpg
184dc43 fixed the source location in all CMTSOLUTION files; also renamed some directories for clarity
237028c added directory examples/CPML/purely_elastic/HOMO8_FREE_SURFACE_without_CPML
19374d3 suppressed PML_WIDTH_MIN and PML_WIDTH_MAX
211b355 renamed ABSORBING_CONDITIONS to STACEY_ABSORBING_CONDITIONS
e8a861c renamed ABSORB_INSTEAD_OF_FREE_SURFACE to STACEY_INSTEAD_OF_FREE_SURFACE
a8af962 suppressed the "examples/CPML" directory because we are going to replace it with a better example
2a0b1e9 renamed two directories for clarity
7fb29db no need to store database files
435286a removed homogeneous_halfspace_HEX8_no_absorbing/DATABASES-default
ff927de now use 5000 time steps instead of 1000
e517de0 changed the source in order to use a real CMT source, i.e. to generate S waves in addition to P waves, to make this validation test more complete
15a92ec modified the HEX27 example to use the same as the nex HEX8
81461f0 added the right reference seismograms
f980998 added examples/homogeneous_halfspace_HEX8_absorbing_Stacey_5sides
4eb5cbf added this_regular_mesh_contains_36x36x16_elements.txt
8298bb6 switched back from 20 processors to 4 for this example
96cc8ef removed useless directories
85da54a better description of the size of the mesh
00ff9c1 even better description of the size of the mesh
80c67c1 added examples/homogeneous_halfspace_HEX8_absorbing_CPML_5sides
a09b0a8 renamed four examples for clarity
530e026 added Emanuele Casarotti's realistic CPML example with topography in examples/CPML_realistic_mesh_with_topography (slightly modified it in order to reduce the total number of PML elements)
f24a85f removed a temporary comment about Q_Kappa
c366b2e added several new CPML examples
bdbcd81 added examples/homogeneous_halfspace_HEX8_acoustic_elastic_absorbing_CPML_5sides
a327d5f added examples/homogeneous_halfspace_HEX8_acoustic_elastic_absorbing_CPML_6sides
836b44c added examples/CPML_realistic_mesh_with_topography/picture_of_this_two_layer_mesh_with_topography.jpg
b5f63db removed the now unused -2001 ... -2007 flags from the material file
98181b0 added examples/CPML_realistic_mesh_with_topography/size_of_this_mesh.txt
33fbc0b added nummaterial_velocity_file and CMTSOLUTION for examples/CPML_realistic_mesh_with_topography
eb7a30d moved the Stacey parameters to after the PML parameters in the Par_file, since using CPML is much better
95eb92f started to move FULL_ATTENUATION_SOLID to the Par_file
4c30b64 set the PML_INSTEAD_OF_FREE_SURFACE to .true. to include computation of top CPML layer
c73adc4 fixed PML_INSTEAD_OF_FREE_SURFACE in the case of 6 sides
9d50f2b renamed free_surface_file to free_or_absorbing_surface_file_zmax for clarity
3fdd7dd now read Q_kappa as an input model parameter instead of a constant in constants.h.in. Updated the manual and the example files accordingly. Also removed old -2001 ... -2007 CPML flags from Joseph Charles. Also removed useless white spaces.
cd30c11 added Postscript output to the Gnuplot script (commented out by default)
115f575 removed all old binary database files; such output files should never be stored in SVN
d10a015 removed the X1 and X10 recording stations, which were located inside the CPML layers
58fe08a better DATA/FORCESOLUTION file for the homogeneous_halfspace examples
0b8defb fixed the moment tensor source to be pure compression in the case of a source located in an acoustic medium
f2a53f3 updated examples/README
23c3751 minor edits to instructions for default example
1e2c807 updated homogeneous_halfspace python scripts for cubit, based on the extra Qkappa column that is needed in nummaterial_velocity_file
41c260c added $NPROC variable to process.sh in homogeneous_halfspace example
4fa715e moves CPML examples to subdirectory examples/CPML_examples/; moves fault examples to examples/fault_examples/; updates scripts cubit2specfem3d.py and boundary_definition.py in CUBIT/ directory to be usable with Q_kappa; links examples scripts cubit2specfem3d.py and boundary_definition.py to the ones in CUBIT/ directory; adds some README files to example subdirectories
44ed292 updates README file in examples/; adds links cubit2specfem3d.py and boundary_definition.py in examples/layered_halfspace/
efcaf1c ** Fix process.sh and update README for examples/layered_halfspace ** Update manual: fix small formatting problems; add a note on 'decompose_mesh has to be run in bin/'
1d52c42 Update instructions on kernel computations for homogeneous_halfspace model
8649866 Add kernel visualization png file for examples/homogenous_halfspace.
549e6a4 switched to the newest version of cubit2specfem3d.py from GEOCUBIT; fixed a symbolic link; added two README files.
7486c15 added creation of absorbing_surface_file_* to utils/CPML/convert_external_layers_of_a_given_mesh_to_CPML_layers.f90
dfa6016 fixed unallocated CPML arrays when PML_CONDITIONS is off. Also fixed examples/meshfem3D_examples/many_interfaces.
c8a6c3b moved "configure" before "make clean"
7a6eba0 moved "configure" before "make clean" in another example
30991eb adds acoustic example to examples/homogeneous_acoustic/; adds create_adjoint_sources.sh and create_alpha_kernel_vtk.sh scripts to example homogeneous_halfspace/
97ac63c Added adios parameters in all Par_file: find . -name 'Par_file' -exec sh -c "cat Par_ext >> {}" \;
19f0f4e deleted old boundary_definition.py
47be174 fixed all links to boundary_definition.py and cubit2specfem3d.py
6f9d11e removed an old version of run_cubit2specfem3d.py and run_boundary_definition.py
eaff854 converted all the export2SESAME() names in CUBIT scripts to the new GEOCUBIT name, which is export2SPECFEM3D()
eca55d7 fixed links to save_fault_nodes_elements.py
50579f8 fixed examples/fault_examples/tpv15/absorbing_boundary.py (now use examples/fault_examples/tpv15/boundary_definition.py instead)
8631eff fixed a typo in a link
6b24365 updated homogeneous_halfspace example to run with latest GEOCUBIT; the new method read in the configuration file homogeneous_halfspace.cfg
e404eaf changed the vertical layers from 17 to 16 to match the previous homogeneous_halfspace mesh
94a7022 updated homogeneous_acoustic example; nummaterial_velocity_file.reference needs to be updated still
426e001 updated homogeneous_acoustic example, which has identical mesh to homogeneous_halfspace
88ad0a9 updated layered_halfspace example
ffb4675 updated waterlayered_halfspace example; did not delete the old .py scripts
d9bf10e corrected nummaterial_velocity_file for homogeneous_halfspace example
09cae29 updated homogeneous_halfspace example
d29d6b6 add end of line to nummaterial_velocity_file reference in homogeneous_halfspace
f41bc89 updated instructions for homogeneous_halfspace example; tested process.sh with gfortran
06f7b71 updated homogeneous_halfspace README
81beb70 updated nummaterial_velocity_file for homogeneous_acoustic
150ad3b parameters string length increased to 512.
6bc492c Merge pull request #101 from mpbl/master
dfc3e20 terri test
d83a9cb terri test
b594041 Eric test
6a822dd Eric test undo
35853eb examples (Mesh_)Par_files updated to reflect the new directory structure.
ceb555e examples' process.sh reflect new directory structure
3342a03 renamed all process.sh scripts to run_this_example.sh
8bc7d4e Update README
1e6f3ac Update homogeneous halfspace readme.
c8fd15a converted block_mesh.py to symbolic links to the GEOCUBIT library
f95e593 added missing homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides/block_mesh.py homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides/boundary_definition.py homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides/cubit2specfem3d.py
2715072 added Surendra's cleaned version of CPML_examples/homogeneous_halfspace_HEX8_acoustic_absorbing_CPML_5sides/block_mesh.py and removed old symbolic links; also updated the README (added a few paragraphs sent by Emanuele Casarotti)
1800307 replaced block_mesh.py with create_mesh.py
e1bcf45 removed the Python header I had added to homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides/create_mesh.py, since it is unneeded and was leading to warnings at run time
30bc235 Dimitri changes
374a97b Remove submodule
2431e45 Add 'EXAMPLES/' from commit '30bc23568e80268a76b012fde2413a0a53abacd5'
25553a6 Remove submodule
f85e215 Merge branch 'master' into devel
6026e36 Merge branch 'devel' of https://github.com/geodynamics/specfem3d into devel
a011602 updated the symbolic links that were pointing to "examples", which is now called "EXAMPLES"
cbc549f changed 'examples' to 'EXAMPLES' in the users manual, and removed the obsolete file README_SPECFEM3D_FAULT
47f7038 Merge pull request #167 from komatits/devel
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