[cig-commits] [commit] master's head updated: Merge remote-tracking branch 'origin/devel' (1300e56)
cig_noreply at geodynamics.org
cig_noreply at geodynamics.org
Thu Nov 6 08:33:36 PST 2014
Repository : https://github.com/geodynamics/specfem3d_globe
Branch 'master' now includes:
b044fd9 *** empty log message ***
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2e696a1 improved topo file filtering routine
801780e Moved all movie-related parameters to the read_parameters file and updated all related calls.
53a104b merged regional and global codes
326e945 added Par_file for 507 nodes (4056 processors) on the ES in Japan
65555f5 added file STATIONS_tsuboi_tokachi-oki from Tsuboi-san
1f5ee2d added Denali, Alaska, source CMTSOLUTION_DENALI
ac0bf90 modified regional code to allow for rectangular slice for Lev Vinnik Sdiff study
f64a9a1 fixed time step problem in some Par_files
7e1ede6 changed Par_file and constants.h not to save movies and OpenDX files by default
dd7f674 added Par_file for ES movies based on NEX=320
8133ad6 3-D Attenuation added
3275095 changed NSEIS to large values in all the Par_file* in order to save seismograms only once at the end of the simulation to avoid NFS problems
88e40a4 added smoothed etopo-4 topo/bathy model, and modified routines accordingly
2d93bd8 fixed bug in smoothing of topography (periodic conditions between South and North pole...)
2d185ac cleaned the code for 3D attenuation and better topo/bathy model (etopo-4) in order to release version 3.5 in a few days (still need to fix the code for any chunk size)
ae1bdbb changed Par_file
5c11e14 released version 3.5 of global code and version 1.2 of basin code
a974e33 changed default value in Par_file
a4bedbc Added FUNA, DGAR, TRIS
65b22db added read_value_parameters.f90 to global code to ignore comments and white lines in Par_file
f6c6b04 Modified Files: anisotropic_mantle_model.f90: in line 555 change the reading format from (21f5.3) to (21f7.3) DATA/Montagner_model/Adrem119 Added Files: DATA/Montagner_model/Adrem119_old
245d6b8 suppressed constraint of aligning values in Par_file on the 34th column
d1d2936 Vala: Added HDUR_MOVIE to parameter file, and modified all files that call read_parameter_file. If HDUR_MOVIE=0.d0 in Par_file, a HDUR_MOVIE appropriate for the resolution of the run is computed in read_parameters_file.f90. Also fixed the bug where hdur(1) is being called, by introducing the variable t0 that is the start time of the simulation. The source decay rate was changed in constants.h and the 5/3 to convert to gaussian hdur was removed from compute_source_time_function and the division by source decay rate was moved to specfem3D.f90.
cface1d renamed SAVE_AVS_DX_MESH_FILES to SAVE_MESH_FILES
d4ee587 removed old stuff from DATA/util
f22be17 removed old stuff from DATA/util
56cf9e4 Added example parameter file and preferences file for the Pyrized version; they are derived from the traditional "Par_file".
966e2b1 Validate parameters in Python.
5a47e4c correct the format for NEX_XI, NEX_ETA, so that '=' is after column 34.
70d1a8b same changes for NCHUNKS
06c9b13 moved SIMULATION_TYPE and SAVE_FORWARD to Par_file. Also removed unused variables in several other routines.
bbbf540 Added 'simulation-type' and 'save-forward'.
6a567c2 fixed important topography bug detected by Bernhard Schubert: longitude blocks were inverted in topography/bathymetry file
4a2875e added JPEG pictures of new topography files with longitude bug fixed
fbe83ab changed transversly to transversely (there was a typo)
6478292 A handful of fixes and work-arounds.
deb89b8 added program to filter the STATIONS file to include stations located in a given region only
864827e Significant re-work of Pyrized version (still in progress).
3a2e99c Reverted accidental change.
cbb5fab switched to new convention on Caltech's "pangu" cluster: /scratch/komatits/DATABASES_MPI
8dd3644 changed NTSTEP_BETWEEN_OUTPUT_INFO to 100
2a985ff changed iaspei to iasp91
bca586b added models 1066a and ak135, and changed call structure of iasp91
9e52913 The 'local-path' option is now called 'scratch-dir'.
03a4c2a Modified code to use less memory for large adjoint runs (large meaning many adjoint sources and receivers and many processors). Changes involve: *reading adjoint sources in in chunks *writing seismograms out in chunks for adjoint runs (not storing the entire trace *locating sources in chunks
aea3d5c Fixing that I added a Par_file with non-standard options in last commit
d2cb3e0 model options updated: ------------ isotropic_prem transversely_isotropic_prem crust_2.0_plus_transversely_isotropic_prem iasp91 1066a ak135 s20rts 3D_anisotropic 3D_attenuation -----------
22b69c6 Added 6 new stations to STATIONS file
ef2bfd8 moved DATA/oldstuff to UTILS and suppressed DATA/util
2636d3b moved filter_station_list.f90 to UTILS
f2da092 release of version 4.0:
6d30d9b Updated the Pyrization for v4.0 and Pythia v0.8.1.3b4; successful run.
b0bcd9c make EXAMPLES dir
937e922 mv PDF to EXAMPLES
fc4c63b mv readme to EXAMPLES
73daaec mv readme.stations to EXAMPLES
13454d5 renamed model name : 3D_crust_2.0_plus_transversely_isotropic_prem by transversely_isotropic_prem_plus_3D_crust_2.0
3fcd5f0 - added possibility of writing SAC binary format in write_seismograms.f90 this involved adding a new function in write_c_binary.c - added flags OUTPUT_SEISMOS_ASCII_TEXT, OUTPUT_SEISMOS_SAC_ALPHANUM, and OUTPUT_SEISMOS_SAC_BINARY to Par_file, which are used to decide on the output format - added flag ROTATE_SEISMOGRAMS_RT which is used to decide whether the horizontal components of the seismograms are rotated to radial and transverse directions - added file get_backazimuth.f90 which computes the backazimuth from source and receiver coordinates needed to rotate the horizontal components - added get_backazimuth.f90 as object and target in Makefile.in - changed read_compute_parameters.f90 according to the new flags in Par_file - updated all calls to read_compute_parameters.f90 and the respective MPI_BAST call in specfem3D.f90 (not in meshfem3D.f90, the new flags are not used there) - Added information on new output flags to the manual
45c66b5 main commit of modifications done during our stay at the BSC to optimize the code.
48c614b
260578d Jeroen added a new integer variable THREE_D_MODEL which enables us to distinguish between various 3D model. The new 1D Harvard model "REF" is now available as "1Dref", and the 3D models s362ani, s362wmani, s362ani_prem and s29EA will soon be available.
d80bf3d I have tested the new 1D model REF, which is working fine. The 3D Harvard models S362ANI, S362WMANI, S362ANI_PREM and S2.9EA have also been incorporated. I will continue to test these, including the topographic variations on the 410 km and 650 km discontinuities. I needed to add the new REF models to the write_AVS_DX_global_chunks_data.f90 routine.
db9713e Added the routine DATA/s362ani/src/read_model_s362ani.f. Currently this routine is called by all CPUs, and we should change it to be called only by the master and broadcast to the other nodes, as we do with read_mantle_model.f90.
1119a11 Minor modifications to the Par_file, read_compute_parameters.f90 and add_topography_410_650.f90.
da57ff9 converted Harvard model s362ani Fortran77 source code to Fortran90
fe4d291 updated a comment
1be8b31 suppressed useless /plevel/ common
dd25438 Moved the new f90 source code for the 3D model S362ANI to s362ani.f90 and fixed the Makefile.
a336d52 Minor modifications to ensure that the define_model_* routines get called only when the appropriate REFERENCE_1D_MODEL is on. Also made the real(kind=4) in s362ani.f90 consistent with the type inthe calls to this routine.
7de89a6 deleted useless examples; kept only one
eca464f moved some example files
7202119 Added a routine moho_stretching.f90 to slightly squish the mesh underneath the oceans and stretch it underneath the continents to get better sampling of the crust. This is accomplished based upon a degree-12 Moho map. Once paraview reads the new file structure we should make some mesh crss sections with the wave speeds superimposed to make sure we want to use this stretching. Tests suggests the stretched mesh gives slightly better dispersion.
8c33685 Added routines add_topography_cmb and add_topography_icb that accommodate topography on the CMB and ICB, respectively. The user will have to provide the subroutines subtopo_cmb and subtopo_icb that assign the topography. I tested the routines by putting the smooth Moho variations from read_smooth_moho on both boundaries, and saw sensible results, e.g., changes in the ScS and sScS traveltimes. These Moho variations involve larger topography than is believe to exist on the CMB or ICB, so we should be all set.
ab3594b moved files to UTILS/s362ani
2d59a6b suppressed non alphanumerical characters and changed one incorrect comment
6ac7e8c Fixed a small bug in the assignment of REF radii near the ICB and CMB in model_ref.f90.
fa8d3a5 put back the old STATIONS file that includes 765 stations
e356ede Fixed a bug assocaited with adjoint simulations. The arrays epsilondev_crust_mantle and epsilondev_crust_inner_core were not properly being allocated. I also set the Max and Min attenuation periods to better values in read_compute_parameters.
dee82c3 added STATIONS_SUBSET_35
b179eb2 suppressed non alphanumeric characters again because someone had mistakenly committed the wrong Par_file again
8d934bb replaced Ying Zhou's v3.6 examples with Anne Sieminski's v4.0 examples
040bf53 - added size of static arrays for adjoint runs to memory size estimate - added more details in timing information - general definition and calculation of ratio to use to divide the central cube, to allow for easier suppression of the crustal mesh - added more debugging options for the Intel ifort compiler - added a full STATIONS file called STATIONS_FULL_758
397bcd6 - fixed truncated station names bug - updated some comments and information messages - better code to generate artificial stations along the equator - better CMT file for Sdiff runs for Lev Vinnik
ed5d0d7 Updated notes on using the synthetics held in the EXAMPLES directory CMTSOLUTION and half duration Post Processing Long Records and those with Small Epicentral Distances
6045e3b modifications for cutting the doublingbrick in 4 sub-blocks. Allows NEX_XI to be a multiple of 16*NPROC_XI instead of 32*NPROC_XI. NEX_XI must still be a multiple of 32. user's manual has been modified too.
8c179a1 Change the license to GPL v2+
4779ebc - moved variables SAVE_ALL_SEISMOS_IN_ONE_FILE and USE_BINARY_FOR_LARGE_FILE from constants.h to DATA/Par_file - added a new variable called WRITE_SEISMOGRAMS_BY_MASTER to DATA/Par_file. This new variable allows the user to choose between two modes of seismogram output. Either only the master writes all the time series files, or if set to .false. all processes write the time series of their local receivers (like in V3.6). - changed write_seismograms.f90 to incorporate the above option - adding new variables to DATA/Par_file results in changes in all subroutines calling read_compute_parameters.f90
b5b14ee Modified the way MOVIE_VOLUME is done. Added several new parameters to the Par_file to allow saving movie in sub volume. Moved all movie writing to subroutines in write_movie_volume.f90 (similarly to write_seismograms). Added new parameter MOVIE_VOLUME_TYPE to allow for adding new output values/formats without modifying par_file and by simply adding new sub routines.
f5aab5a - Suppressed number of stations at the beginning of the STATIONS file - Suppressed old VINNIK files - Removed useless white spaces at the end of some lines
9a653a4 Fixed a bug with how 1D_ref was being read and added models 1D_ref_iso and s362iso. The elastic constants in the models are the Voight averages of the transversely isotropic models 1D_ref and s362ani respectively.
011a8b1 Add the possibility of computing 21 anisotropic kernels instead of the isotropic (P-wave, S-wave) kernels. This done by setting the new parameter ANISOTROPIC_KL in constants.h to .true.
822a2cc Added the option to output displacement and velocity in volume
6127748 changed comment to "must be multiple of 16 and 8 * multiple of NPROC below"
8aa6850 changed default value for WRITE_SEISMOGRAMS_BY_MASTER
c9c4b19 Removed the Pyrized version of the code.
7a486ff Implement the regional models of Japan.
7e6fcb0 declared a parameter (which has been moved to DATA/Par_file)
85258a8 Modified parameter MOVIE_VOLUME_COARSE to MOVIE_COARSE. This parameter will now work for both MOVIE_VOLUME and MOVIE_SURFACE to output only values at corners of elements. Note that this options so far only works for surface movies with create_movie_GMT_global, not with create_movie_AVS_DX.
e48f803 Added mantle heterogeneity model 'heterogen', where the user can specify an arbitrary density anomaly field. See for more information on implementation and use, DATA/heterogen/README_heterogen.
c984d8d Set the default parameters in DATA/Par_file to what they were
82c5498 Some minor fixes: -fixed bug in subroutine write_movie_volume_vector -set eta_ani=1.0 when inside crust 2.0 (in get_model.f90). -added a smaller time step for NEX = 80 (was unstable, at least for s362ani) -added a new stations file. This one includes all stations recording LHZ components, requested from IRIS June 20th, 2008.
910f6f0 Added 3D mantle model QRFSI12. This is the new default when choosing ATTENUATION_3D = .true. There are two options in the Par_file to choose this model: s362ani_3DQ and s362iso_3DQ
f2c3a21 removed the duplicates from the STATIONS files
198f118 fixed some incorrect stations in Jeroen's station file
86d2494 suppressed useless topo/bathy pictures
ae4ffc4 Add SeismiQuery directory to update IRIS station file: readme_STATIONS_LH Default STATIONS file now is set to STATIONS_II_IU, because for usual runs, it does not make sense to use 1800+ stations For data query and corresponding synthetics calculation, use STATIONS_LH
ac60ec9 In order to use ETOPO1 as new topography, we describe a small step-by-step procedure how to create the needed file 'ETOPO1.xyz' (rather than upload the file to this package because of its file size ~4.7GB). however, the scripts are based on MATLAB, a numerical computing environment, with the Mapping Toolbox, which has to be purchased (http://www.mathworks.com/) in order to use the script files. these files have been added to DATA/topo_bathy: - readme_etopo1.txt - xprocess_ETOPO1.m - xread_ETOPO1.m
4ba5014 further changes to move towards the new version 'Tiger':
f3d4fc7 these are the main changes for the new "Tiger" version. you will have to re-configure in order to compile executables.
c6c69e5 updated the version number and header information to 5.0 in the source code files
4b5cb96 added DATA/Par_file, DATA/CMTSOLUTION and DATA/STATIONS (which are the same as the *.default files) to have the compilation of the package work as it comes out-of-the-box
db41831 updated the configure script to create DATA/Par_file, DATA/CMTSOLUTION and DATA/STATIONS
8586e0a updated header information; added new lsf-scripts; changed default CMTSOLUTION to be identical with the GlobalCMT.org solution
1db8550 added a readme.txt to DATA/crustmap/ (by Matthias Meschede)
12af148 removed an old Pyre configuration file
aaf8a95 the changes here include: - improved backward/reconstruction of forward wavefield
692fd6a bug fix for no gravity case and non-Deville routine (compute_forces_outer_core.f90)
e10c6fc added mantle model s40rts
15ed3b7 adding one more parameter NOISE_TOMOGRAPHY in default DATA/Par_files
fc57175 updates model S40RTS; adds calculations for an approximate hessian for kernel simulations; updates mesh2vtu files
564a028 moves source files in SPECFEM3D_GLOBE/ into corresponding subdirectories for mesher and solver; updates Makefiles and configure
2f6b4e8 fixes bugs for adjoint simulations in specfem3D.f90; updates example scripts
ec60183 updates scripts in EXAMPLES/global_s362ani
6922300 adds EPcrust from Irene Molinari & Andrea Morelli (2011)
cfee3ec fix EXAMPLES/noise_tomography to fit updates made in other subroutines. write SURFACE_MOVIE using the same c rountine for absorbing boundaries (presumably much faster and more effective, since there is only one file on each PROC for the whole simulation instead of one file for each time step)
02fee70 NOISE minor changes
d773215 change number of files defined in src/shared/write_c_binary.c (from 9 to 10), new index 9 corresponds to SURFACE_MOVIE used in NOISE_TOMOGRAPHY
7e4a0be NOISE GLOBAL bugs fixed
e421fd9 another update on NOISE_TOMOGRAPHY in SPECFEM3D_GLOBE
eb3bc9c clean up EXAMPLES/noise_examples
6b400df two very short tests for NOISE_TOMOGRAPHY, just to make sure scripts work before submitting the real jobs
8a70aa4 two very short tests for NOISE_TOMOGRAPHY, just to make sure scripts work before submitting the real jobs
035814f minor changes in scripts for NOISE_TOMOGRAPHY
0de98e1 new version of NOISE_TOMOGRAPHY in SPECFEM3D_GLOBE benchemarked
133caac updates Makefiles for UTILS/adjoint_sources; adds a check in routine read_parameters_noise()
7ee6e60 updates EXAMPLES/ folder and adds new traveltime/amplitude kernel example
ecb3e02 removes trailing spaces from source code files; adds transverse isotropy for STW 1D reference models to have tiso between moho and 670km depth
385f4d2 adds small regional example for Greece to run on a desktop machine
d005fe3 updates EXAMPLES/ with new reference solution for s362ani
6f4f4ba updates reference solutions for regional_MiddleEast example
84209a1 adds a PPM model file (mediterranean_Vs-model-born.txt) as example to DATA/PPM/
58c5960 improved the Gnuplot script to compare seismograms
bb08adb suppressed DATA/Par_file.in and DATA/SOURCE.in handled by "configure", since it was both useless and dangerous (modifications made by the user would be erased by another "configure" run in the future)
d084ef9 fixed a few minor details
7bc6808 centered the first chunk on the North pole by default
73cb95b fixed model ak135f_no_mud, which was not correct
6463d96 Update Par_file for previous change.
6e4a6fd removed FLAGS_NO_CHECK
e9fca3c Allow setting an unlimited NUMBER_OF_RUNS.
c7c07d1 Fix example Par_files.
80cb452 Fix example Par_files.
d640884 rename EXAMPLES/small_benchmark_run_to_test_a_new_machine to EXAMPLES/small_benchmark_run_to_test_more_complex_Earth
c0d9db0 added small_benchmark_run_to_test_very_simple_Earth
eae8839 correct values_from_mesher.h for this example
82e5440 new values_from_mesher.h (the version I committed a few minutes ago was not the right one)
104c76b added all reference seismograms in EXAMPLES/small_benchmark_run_to_test_very_simple_Earth/OUTPUT_FILES_reference_OK
a23fa5c done merging undoing of attenuation into the trunk; three new parameters have been added to the Par_file for that
2a8739d added the three new parameters to undo attenuation to all the Par_files in EXAMPLES
05a807c added the three new parameters to undo attenuation to all the Par_files in EXAMPLES
896af09 done merging all the easy changes in src/auxiliaries
d493b3a fixed all compilation warnings that resulted from the changes I made in the last two days (merging some straightforward modifications and small bug fixes from the GPU version back into the trunk)
3d18e90 added all the new and future parameters to the Par_file; modified all the routines that read it accordingly; also renamed broadcast_compute_parameters() to broadcast_computed_parameters()
54a73cd added missing parameters to the Par_files
ed8834b renamed SAVE_TRANSVERSE_KL to SAVE_TRANSVERSE_KL_ONLY for clarity
2fb5592 renamed SAVE_TRANSVERSE_KL to SAVE_TRANSVERSE_KL_ONLY for clarity
8f74bbf set NT_DUMP_ATTENUATION = 77 instead of 100 according to the new estimates after fixing memory_eval() and optimizing total memory size in the new code
7aa4632 added more precise comments for the new parameters added to the Par_files
d199ef8 added more precise comments for the new parameters added to the Par_files
910e8aa added two new flags RECOMPUTE_STRAIN_DO_NOT_STORE and EXACT_MASS_MATRIX_FOR_ROTATION to the Par_file
c6e13dd added two new flags RECOMPUTE_STRAIN_DO_NOT_STORE and EXACT_MASS_MATRIX_FOR_ROTATION to the Par_file
87d478f completely removed flag RECOMPUTE_STRAIN_DO_NOT_STORE, which turned out not to be a good idea
7d0df13 completely removed flag RECOMPUTE_STRAIN_DO_NOT_STORE, which turned out not to be a good idea
8e4325c renamed some files in the EXAMPLES directory for clarity
462df23 changed 3300 to 2200 in Gnuplot scripts for seismograms
feeee6e fixed a wrong value for PARTIAL_PHYS_DISPERSION_ONLY
0eca21f set PARTIAL_PHYS_DISPERSION_ONLY to .false.
fa274db added ATTENUATION_1D_WITH_3D_STORAGE to the Par_files of the EXAMPLES
8c3b15a added ATTENUATION_1D_WITH_3D_STORAGE to the Par_files of the EXAMPLES
0300c65 adds missing flags to all example's Par_file; bug fixes
6d59894 renamed branches/SPECFEM3D_GLOBE_SUNFLOWER to trunk, i.e. made the GPU branch become the new trunk
ab88c4b renamed branches/SPECFEM3D_GLOBE_SUNFLOWER to trunk, i.e. made the GPU branch become the new trunk
16e8ba8 added EXAMPLES/benchmarks/attenuation_benchmark_GJI_2002_versus_normal_modes
aafe7bb removed ATTENUATION_NEW from EXAMPLES/benchmarks/attenuation_benchmark_GJI_2002_versus_normal_modes/Par_file because now unused
5f60cb4 replaced all the reference seismograms in EXAMPLES/small_benchmark_run_to_test_more_complex_Earth/OUTPUT_FILES_reference_OK with a version that is correct for the new merged version of the code
3525fcd improved the readme
0bc3c36 done adding the new GPU and ADIOS parameters into all the Parfiles for the EXAMPLES; also fixed all the STATIONS files that were still using the old format (with the number of stations on the first line of the file)
3d85f01 fixed LOCAL_PATH in the examples
82f4d89 removed _new
ae4d11c added symbolic link to process_syn.pl
5801357 renamed the old reference files from LH? to MX? and from semd to sem, which is the current convention
0faa0e3 done cleaning all the processing and plotting scripts in EXAMPLES/benchmarks/prem_* from Anne Sieminski
9a50ef1 put a print statement back into the processing scripts
d25ff97 changed NTSTEP_BETWEEN_OUTPUT_INFO from 100 to 500 in the Par_files
4bd0cf8 updates adios routines and configuration
3ba32b6 updates adios routines and configuration
1422bfc re-adds 410/660 topography routine for s362ani models
95ac2c7 adds (preliminary) crustal model CRUST1.0 (see: http://igppweb.ucsd.edu/~gabi/crust1.html) which can be selected in constants.h
70377ac James' ASDF format for seismograms
0d904cd James' ASDF format for seismograms
5b53f58 explicit interface in write_seismograms.f90 to be able to use optional arguments as requested by DK
9ad95ce Merge pull request #2 from mpbl/devel
553861c Merge pull request #2 from mpbl/devel
14a5045 Merge pull request #3 from mpbl/devel
8e6616f Updated ASDF headers for scale factor, azimuth, and incident angle
a2ed28e Merge remote-tracking branch 'upstream/devel' into devel
1a6a6eb Merge pull request #4 from jas11/devel
f2c60d7 updated some comments in README and in configure
ae74771 Merge pull request #5 from komatits/devel
9221b3e Fixed call of write_seismograms in iterate_time and an allocate issue with ASDF that was causing the output to hang when more than 6 processors were used to run the solver.
3a17ce8 Fixes bug with ASDF where the sovler hangs when too many processors were used.
32290d1 Removed print statements used for debugging the ASDF output
0b6766c Merge pull request #6 from jas11/devel
486137b reverted changes to flags.guess unintentionally made by James
38bf62f Merge pull request #7 from komatits/devel
e5bf8c4 terri test
76f64d8 renamed all process.sh scripts to run_this_example.sh
81b8b05 switched to the right version of EXAMPLES
59cf4ee Merge pull request #8 from komatits/devel
74fa36e save_arrays_solver_adios bug corrected: local dimensions vary along interfaces.
91ee696 Merge remote-tracking branch 'upstream/devel' into devel
e01ed88 Merge pull request #9 from mpbl/devel
f3ab45b added the logo of the Del Duca Foundation
64c52e0 Merge pull request #10 from komatits/devel
7082777 double precision literals in correct format, use myrank from specfem3d_par module added.
21e5885 Merge pull request #11 from mpbl/devel
a38b4a5 tried to patch
26b149a changed a file
ed8f2b4 Merge pull request #13 from komatits/devel
398ae1b fixed all the warnings given by the Portland and Cray compilers on a Cray at ORNL. In particular, renamed all the variables or functions that had the same name as Fortran intrinsics (although that is correct in Fortran, it can be confusing and it also confuses syntax highlighting, and the Portland compiler prints a warning for each of them)
98bda06 Merge pull request #15 from komatits/devel
f32b71b Update flags.guess
026de77 fixed three warnings / errors from the gfortran compiler about undefined behavior when aggressive loop vectorization is used by the compiler
82f4981 Merge pull request #16 from komatits/devel
3e83caf added a return statement after phtread_exit to please the copmiler.
64e1b38 Merge pull request #17 from mpbl/devel
c8b107d fixes solver_data_mpi.bp read in adios.
099a4d3 Merge pull request #18 from mpbl/devel
0e1fa7d improved replace_use_mpi_with_include_mpif_dot_h.pl and improved "use mpi" usage to make it work
92f6f46 Merge pull request #19 from komatits/devel
8142b71 added directory "IMPORTANT_BUG_benchmark_Ebru_Par_file"
7ca3f38 Merge pull request #20 from komatits/devel
08ae020 Update README_current_conclusions_from_Dimitri_about_the_bug.txt
d70688a Update README_current_conclusions_from_Dimitri_about_the_bug.txt
e87c874 Update gnuplot_script_plotall_curves.gnu
3887afd Update README_current_conclusions_from_Dimitri_about_the_bug.txt
bacdb30 Update README_current_conclusions_from_Dimitri_about_the_bug.txt
1651cb3 Update README_current_conclusions_from_Dimitri_about_the_bug.txt
316c065 Update README_current_conclusions_from_Dimitri_about_the_bug.txt
7c5bffa added Par_file for each of the examples in IMPORTANT_BUG_benchmark_Ebru_Par_file (in each sub-directory)
edef443 Merge pull request #22 from komatits/devel
c37c9ce Update README_current_conclusions_from_Dimitri_about_the_bug.txt
41abb48 added IMPORTANT_BUG_benchmark_Ebru_Par_file/s40rts_with_attenuation_for_Ebru_s_Par_file_is_OK
fc7c0a7 Merge pull request #23 from komatits/devel
a6310e3 added s40rts_with_attenuation for GNU gfortran and for Portland pgf90; both work fine and give the same seismograms as Intel ifort with or without mcmodel=medium
7a3aa53 Merge pull request #30 from komatits/devel
c246cf5 cosmetic changes to be able to use "meld" more efficiency to apply an old but useful change sent by a colleague last October
34432ca Merge pull request #31 from komatits/devel
b38ab36 final cosmetic changes
5ae76f7 Merge pull request #32 from komatits/devel
9cfa414 added a hash table to drastically speed up src/meshfem3D/model_crust.f90, which in turn drastically speeds up the mesher in the case of 3D models
b9ed1dc Merge pull request #33 from komatits/devel
a0a2875 fixed a typo in a comment
a56548e Merge pull request #34 from komatits/devel
e715f9c added IMPORTANT_BUG_benchmark_Ebru_Par_file/Ebru_s_runs_are_NOT_OK/the_bug_is_NOT_in_the_two_DK_DK_July_2013_restored_lines and IMPORTANT_BUG_benchmark_Ebru_Par_file/s40rts_with_attenuation_for_Ebru_s_Par_file_is_OK/specfem3d_globe_ifort_s40RTS_with_new_Th_Gilet_crustal_hash_table
0ea7c2c Merge pull request #35 from komatits/devel
b7d1c98 better comments in src/meshfem3D/model_crust.f90
fffd8ea Merge pull request #36 from komatits/devel
80f9d27 added IMPORTANT_BUG_benchmark_Ebru_Par_file/Ebru_s_runs_are_NOT_OK/the_bug_is_NOT_in_how_we_MPI_Bcast_the_s362ani_model
73ad1d4 Merge pull request #37 from komatits/devel
9daa3eb cosmetic changes in src/meshfem3D/model_s362ani.f90
0440bda Merge pull request #38 from komatits/devel
2f1f00c minor cosmetic change to be able to later fix the s362ani bug
c58836e Merge pull request #39 from komatits/devel
ee103b1 build: Fix some module dependencies in mesher.
eb3759e build: Fix module dependencies in solver.
bbc5532 build: Fix module dependencies in auxiliaries.
d36048c build: Simplify linker rules using automatic vars.
46b00e6 Merge pull request #40 from QuLogic/parallel-build
41f2c30 improved the source code for attenuation models: fixed a double to single precision conversion statement, replaced Qmu = 0 with Qmu = 4999 in model_1dref.f90 because Qmu = 0 makes no sense
9419f59 Merge pull request #41 from komatits/devel
b19fbb4 commented out the call to meshfem3D_models_getatten_val(), which was making the code unreliable at least in the case of s362ani + attenuation (see https://github.com/geodynamics/specfem3d/issues/8 )
573eae5 Merge pull request #42 from komatits/devel
a629b85 removed directory "IMPORTANT_BUG_benchmark_Ebru_Par_file"
9970030 Merge pull request #43 from komatits/devel
f0c3e2a fixed two warnings from gfortran
4e0c67e Merge pull request #44 from komatits/devel
d9f7f36 commented out the "compile a trivial MPI program" test, which is not needed and which makes "configure" crash on several machines
a353ab5 Merge pull request #45 from komatits/devel
908d430 my initial idea of not calling meshfem3D_models_getatten_val() at all does not work because that routine calls another routine to compute tau values; I thus now only avoid the problematic lines in that routine
bbdf11e Merge pull request #46 from komatits/devel
f5a3132 added a new comment about the s362ani + ATTENUATION bug
1a5b4a1 Merge pull request #47 from komatits/devel
40002cb cosmetic changes to be able to later apply an old patch from Thomas Gillet to significantly speed up the mesher for model s362ani
9f9faf7 Merge pull request #48 from komatits/devel
567cb26 added a comment about -DFORCE_VECTORIZATION
01a32b6 Merge pull request #49 from komatits/devel
c15e7e2 added a patch from Thomas Gillet to drastically speed up mesh creation when model s362ani is used
e776b18 fixed a typo in a comment
cc9dcb8 Merge pull request #50 from komatits/devel
b8c84cb added a comment to the Par_file
7611ad3 updated the copyright headers and the users manual to version 6.0
8b96932 Merge pull request #51 from komatits/devel
607038b updated three headers that I had forgotten
73e65c6 Merge pull request #52 from komatits/devel
86b5dab - added a routine to compute the total mass of the Earth - fixed double precision compilation support, which was broken - changed USE_VERSION_5_1_5 to USE_OLD_VERSION_5_1_5_FORMAT (in the process it seems my script also removed all white spaces at the end of lines, if any) - added support for ROLAND_SYLVAIN simulations
bd213f2 Merge pull request #53 from komatits/devel
1d38110 cosmetic changes
b6ad89b Merge pull request #54 from komatits/devel
f0ab85a added constant SECONDS_PER_HOUR = 3600.d0
2c74a0d Merge pull request #55 from komatits/devel
a7e8590 added doc/Melchior_1991_about_ellipticity_see_in_particular_page77.pdf and doc/map_projections_Geomatics_Guidance_Note_number7_part2_June2013_geographic_geocentric_conversion_pages_94_and_95.pdf
2385088 Merge pull request #56 from komatits/devel
719b654 clarified the definition of the reference ellipsoid and left some notes about this in the users manual and in the conversion routine
124baaa Merge pull request #57 from komatits/devel
fe1cc1c added a comment about Radau's approximation of Clairaut's equation for first-order terms of ellipticity.
6079475 Merge pull request #58 from komatits/devel
253b728 Fix off-by-one in regular layer count.
c4704bc Fix calculation of regular grid point order.
638b0ef fixed a significant bug in the calculation of the total volume of the mesh: some central cube elements were counted several times because IFLAG_IN_FICTITIOUS_CUBE elements were not excluded. This volume is computed in the mesher for information purposes only and thus seismograms were not affected.
e27d871 Merge pull request #59 from komatits/devel
32686e3 Fix allocation of regular kernel arrays.
163240c simpler implementation of volume and area calculations in the mesher (merged two routines)
811ae11 Merge pull request #60 from komatits/devel
672b5e6 Use specfem modules to reduce subroutine arguments.
eeeeb36 Round chunk_map output to the nearest EPS.
433edf7 Use addressing to find regular grid slices.
6cea702 Save some memory on addressing array.
fedf291 Merge pull request #61 from QuLogic/regular-kernel-grid
2f0c52e Fix some small typos.
2878904 Merge pull request #62 from QuLogic/typos
413d5c6 renamed my new gatherv_all_cr_single_prec() to gatherv_all_r() to be consistent with Daniel Peter's notations
a583c06 Merge pull request #63 from komatits/devel
9e5dcc4 added Roland_Sylvain integrals; also fixed a few typos in comments
5fb4808 Merge pull request #64 from komatits/devel
9f01b3a removed accented letters: we prefer to keep using standard ASCII for the source code
39f00c5 Merge pull request #65 from komatits/devel
cb1e8f4 fixed physical units of Roland_Sylvain integrals
7cb4737 Merge pull request #66 from komatits/devel
e347ecc faster way of computing the Roland_Sylvain integrals by pre-computing many common terms
2b70a18 Merge pull request #67 from komatits/devel
5babcb0 Add links to submodules in readme.
eb6066e Change to Markdown so GitHub linkifies stuff.
e2f2928 Section-ify readme file.
40bcfdd Merge pull request #68 from QuLogic/readme
754300e Update README.md
c0bc5ba Merge remote-tracking branch 'origin/devel'
170e5f7 Update submodules in master
cd83b68 submodules updated
b173684 fixed a bug in Matthias Meschede's crustal model smoothing routines: latitude was used instead of longitude
bed4deb Merge pull request #69 from komatits/devel
9a28612 added a remark about ellipticity to the users manual.
1e48348 Merge pull request #70 from komatits/devel
cdbee0f switched the default to FORCE_VECTORIZATION = .true.
a2b53e8 Merge pull request #71 from komatits/devel
47332f7 switched from a single observation point to a whole surface around the Earth for Roland_Sylvain integrals
7be81d6 Merge pull request #72 from komatits/devel
25bd1b9 add OpenCL support to Specfem3D-globe
32268ae add OpenCL configuration backend
47badd5 point m4 module to our repository
a9b5683 fix bugs
c6d2aa9 improve speed with clFlush instead of clFinish and fix bugs
d321da5 fix bugs
6895f34 cosmetics
8934464 satellite clipart added to the cover of the manual to prepare for the release of Roland_Sylvain gravity integrals
b399bb5 Merge pull request #73 from komatits/devel
c33bf42 better format for the output of Roland_Sylvain gravity integrals, added output of the norm of the g vector, and added an exit message if the solver is run with ROLAND_SYLVAIN = .true. (only the mesher is needed in that case, since we compute some integrals on the mesh and then we are done, no need for a time-domain solver)
1fce2e1 Merge pull request #75 from komatits/devel
68fd046 put http:// at the beginning of all \url{} addresses. It seems many had been missing for months. Although the result in the PDF is really ugly, it seems to be the only way of making the clickable URL work.
c45b60b Merge pull request #76 from komatits/devel
c38411c fix bugs
5997858 better TOPO_MINIMUM and TOPO_MAXIMUM
6509705 Merge pull request #77 from komatits/devel
bde5c50 added more precise comments and doc about ellipticity calculations
90f8a21 Merge pull request #78 from komatits/devel
49bb85f added a comment referring to eq (14.21) in Dahlen and Tromp (1998) regarding ellipticity
7cbcde8 Merge pull request #79 from komatits/devel
8e77f34 improved a variable declaration
d2496e9 Merge pull request #80 from komatits/devel
5b48368 moved some old files from DATA to utils/oldstuff
63d2961 Merge pull request #81 from komatits/devel
a2e0657 deleted topo_bathy/convert_etopo2_bin2ascii_Sun.f90 and topo_bathy/swap_topo_bathy_Sun.f90 and updated the header file of topo_bathy/smooth_topo_bathy_PPM_image.f90
385bfa7 cleaned DATA/topo_bathy
b8d6a16 Merge pull request #82 from komatits/devel
5304f2e added topo_bathy/topo_bathy_etopo2_original_unmodified_unsmoothed.dat and topo_bathy/topo_bathy_etopo2_smoothed_window_3.dat and updated topo_bathy/smooth_topo_bathy_PPM_image.f90
06dd1c2 updated DATA/topo_bathy
0e84408 Merge pull request #83 from komatits/devel
a5f174d compressed the large topo files that are unused by default and added some conversion and display scripts
85124e8 compressed the large topo files that are unused by default and added some conversion and display scripts
97da690 Merge pull request #84 from komatits/devel
69b16e7 replaced the old version of ETOPO with the latest one (etopo2v2c), which fixes several issues, and also added ETOPO1 (etopo1_ice_c)
04ab1bc replaced the old version of ETOPO with the latest one (etopo2v2c), which fixes several issues, and also added ETOPO1 (etopo1_ice_c)
ba3f67c Merge pull request #85 from komatits/devel
2a11397 done cleaning and adding all the topography files, in particular adding ETOPO1
2614dd9 done cleaning and adding all the topography files, in particular adding ETOPO1
e63245c Merge pull request #86 from komatits/devel
ffd536a renamed model_crust to model_crust_2_0 to be consistent with existing model_crust_1_0
f2de2cd Merge pull request #87 from komatits/devel
a5dde6d added an email from Daniel Peter about ellipticity as a comment in src/shared/rthetaphi_xyz.f90
f218984 Merge pull request #88 from komatits/devel
5cfc0d4 use ocl events for async dependencies
b2c7b97 add events around copy queue operations
589f129 Merge branch 'devel' into opencl
3bcafda add restrict to boast kernels
d08fd18 enable MANUALLY UNROLL LOOPS by default
62b2186 Merge branch 'opencl' of github.com:Nanosim-LIG/specfem3d_globe into opencl
66a0592 import last version of the kernel references from boast
32bcdea pass launch_bounds macros to OCL processor
9f9ceca add launch bounds qualifiers in gpu kernels
e45b2ec remove reqd_work_group_size from OpenCL kernels (inefficient)
6acd7dc Merge pull request #89 from Nanosim-LIG/opencl
78dfa42 switched back to the right version of DATA (it seems Kevin Pouget's commit of the OpenCL modifications had changed it to an older version)
d561fb7 Merge pull request #90 from komatits/devel
99c106b added Kevin Pouget's description of the new OpenCL routines to the manual
e51b41c Merge pull request #91 from komatits/devel
ec1a33c update git submodules
54fc581 Merge branch 'devel' of https://github.com/geodynamics/specfem3d_globe into opencl
466344f translate OpenCL note in English and regenerate the PDF
b2c09ee Merge pull request #92 from Nanosim-LIG/opencl
3730a2f added the two suggestions made by Elliott
d696d58 Merge pull request #93 from komatits/devel
7582c07 fixed a compilation problem introduced by Kevin Pouget's OpenCL modification: the solver did not compile without GPUs any more. My modification works fine for CPUs, regarding GPUs I am not sure (I am not familiar enough with how the Makefile works for GPU routines)
69ca609 Merge pull request #94 from komatits/devel
198182e updated some comments
cd5bc89 Merge pull request #95 from komatits/devel
615d1f7 tried to use the same notations in model_crust_1_0.f90 and model_crust_2_0.f90; also cleaned useless white spaces in all source files using a script
e1ce7fe Merge pull request #96 from komatits/devel
d03666b renamed INCLUDE_SEDIMENTS_CRUST to INCLUDE_SEDIMENTS_IN_CRUST
a4fbfb9 Merge pull request #97 from komatits/devel
1260874 made source code of model_crust_2_0.f90 closer to that of model_crust_1_0.f90
6e4a1ea Merge pull request #98 from komatits/devel
80bfee7 improved a comment
5ad7f5f Merge pull request #99 from komatits/devel
2e95185 added support (off by default) for the ice layer in crustal models model_crust_1_0.f90 and model_crust_2_0.f90
6df1df1 Merge pull request #100 from komatits/devel
412b039 got rid of MAXIMUM_HEIGHT_TOPO and MAXIMUM_DEPTH_BATHY, which had become useless
9d3a086 Merge pull request #101 from komatits/devel
178f39e also output a timestamp file for ispec == nspec
eb990f2 Merge pull request #102 from komatits/devel
7f29f8a added a test to check that color palette file GMTglobe.cpt exists
918596c added a test to check that color palette file GMTglobe.cpt exists
d736762 Merge pull request #103 from komatits/devel
2e38728 better cleaning at the end of the GMT script
8b12737 better cleaning at the end of the GMT script
fdeb613 Merge pull request #104 from komatits/devel
cc50b88 convert final output file from PS to PDF
b0ce31f convert final output file from PS to PDF
0fddd2b Merge pull request #105 from komatits/devel
ec7a783 added a color scale to the GMT script
f4e8641 added a color scale to the GMT script
7ccf1c6 Merge pull request #106 from komatits/devel
3cae917 Fix out-of-bounds array access warning.
a5db7e8 Merge pull request #107 from QuLogic/warning-fix
b316cb7 fixed a minor range problem when Roland_Sylvain conditions are off
b119f58 added Julien Derouillat's (from Maison de la Simulation, France) OpenMP support
eb90220 Merge pull request #108 from komatits/devel
be02546 more complete gfortran options
d45fd44 Merge pull request #110 from komatits/devel
a378188 added flag REUSE_EXISTING_OBSERVATION_SURF to be able to reuse an existing observation surface from a previous run. Also added directory utils/Roland_Sylvain_gravity.
ae22573 Merge pull request #111 from komatits/devel
293d10f added a comment
d462ac4 Merge pull request #112 from komatits/devel
86b9b4d folded OpenMP lines that were longer than the standard
c45144d Merge pull request #113 from komatits/devel
ac73846 cosmetic change to an OpenMP statement
349757e Merge pull request #114 from komatits/devel
6fcc510 added the calculation of longitude and latitude of the observation grid for GMT display purposes when the observation grid is read back from a saved file on the disk
e96c78a Merge pull request #115 from komatits/devel
1cb1024 added "blockmedian" to GMT script; added output of time stamp file for ispec == 1
4c2fe25 Merge pull request #116 from komatits/devel
121972c uncommented a line that was commented out by mistake
cbd301f Merge pull request #117 from komatits/devel
ebc9e2c changed blockmedian to blockmean (according to the GMT manual)
f11fa7f Merge pull request #118 from komatits/devel
e6f8bd7 added the calculation of the location of the center of mass of the Earth model and mesh
9c54f7d Merge pull request #119 from komatits/devel
d02f73b removed extra white spaces
c5007a6 Merge pull request #120 from komatits/devel
3027b17 removed "blockmean", which was smoothing out the results way too much
0c658eb Merge pull request #121 from komatits/devel
76b1524 fixed a typo in convert_all_result_files_to_GRD_format.sh and improved the color scale in display_g_vector_norm_SPECFEM3D_GLOBE_with_GMT.sh
f16203a Merge pull request #122 from komatits/devel
70b3411 added Vittorio Ruggiero's additional OpenMP support, and in particular added a new compiler option -DUSE_OPENMP_ATOMIC_INSTEAD_OF_CRITICAL to use OpenMP ATOMIC statements for some critical loops instead of OpenMP CRITICAL regions.
44a503f Merge pull request #123 from komatits/devel
66411e2 initialize moho to zero
dd7f9ad Merge pull request #124 from hejunzhu/devel
72f95ad fixed the problem introduced by Hejun Zhu's commit: the version of DATA and m4 had been changed
b1e1a79 Merge pull request #125 from komatits/devel
dc6d421 removed the "goto 777" that was used to avoid the s362ani + attenuation bug in Hejun Zhu's routine
046ab6a Merge pull request #126 from komatits/devel
b5fe28d fixed a bug I had introduced in OMP END CRITICAL
3c9d5b6 Merge pull request #127 from komatits/devel
02ccaa1 added flags SHIFT_TO_THIS_CENTER_OF_MASS and ONLY_COMPUTE_CENTER_OF_MASS for Roland_Sylvain gravity integrals
1610204 Merge pull request #128 from komatits/devel
f6f55ce left a comment about the fact that it is crucial to leave "moho = 0" to avoid the s362ani + attenuation bug
d296a23 Merge pull request #129 from komatits/devel
a63cd7b added utils/Roland_Sylvain_gravity/output_file_of_the_code.txt and utils/Roland_Sylvain_gravity/saved_observation_grid_real_x_y_z_used_by_the_code.txt.bz2 and updated utils/Roland_Sylvain_gravity/constants.h.in
f3b5ba3 Merge pull request #130 from komatits/devel
a4eba40 added utils/Roland_Sylvain_gravity/HOWTO_use_the_code_for_Roland_Sylvain.txt and renamed the two submission scripts for 600 cores
a77c84d Merge pull request #131 from komatits/devel
47ecff9 start working on better OCL cleanups
1ae63dd update DATA submodule
724fa2d Fix array dimensions of movie volumes.
0cb72f2 Merge pull request #133 from QuLogic/fix-ifort
ba2c480 Fix make clean from subdirectories.
862ac9a Remove backup target.
4fc56a1 Correct license in several files.
7db6445 Clean up C code slightly.
4c0e111 Remove comment about s362ani + attenuation.
911ac0e Remove some commented and unused code.
a9fd39a Use real(..,kind=CUSTOM_REAL) for type conversion.
672c799 Use MPI_STATUS_IGNORE in MPI calls.
180110a Remove explicitly imported but unused module vars.
7607904 Fix real-to-integer conversion warnings.
3a2cf6a Make SAC type conversion explicit.
0d652ae Remove unused constants.
38469fd Fix spelling of some constants.
0d35ab5 Combine duplicate get_global subroutines.
2419de2 Combine duplicates of sort_array_coordinates.
55b14dc Replace Numerical Routines sorting code.
0705089 Remove get_value_string subroutine.
e504052 Normalize case of some Fortran keywords.
88864c7 Remove err_occurred function and commented code.
9fa2185 Remove unnecessary string trimming.
4c04d81 Remove Par_file variable prefixes.
8711be6 Small spelling fixes in comments.
f10c4ab Remove scripts that do nothing.
eefe3ac Change a misleading filename.
bc156ed Fix script executable bits.
968b09a Replace bubble sort with heap sort.
8222716 Remove specific subroutines from inlining on XLF.
5bec0e8 Fix warning about doubly-defined macro.
ab8a7ce Correct definition of Fortran preprocessor macros.
6099212 Fix definition of FORCE_VECTORIZATION macro.
ce0e08f Merge pull request #135 from QuLogic/fix-xlf
e0db75e added utils/Roland_Sylvain_gravity/display_g_vector_norm_SPECFEM3D_GLOBE_with_GMT_absolute.sh utils/Roland_Sylvain_gravity/display_g_vector_components_SPECFEM3D_GLOBE_with_GMT_absolute.sh utils/Roland_Sylvain_gravity/display_G_tensor_components_SPECFEM3D_GLOBE_with_GMT_absolute.sh
ad18112 Merge pull request #136 from komatits/devel
f12a92e Reduce DT for AK135F_NO_MUD.
fcaf7ee Merge branch 'cleanup' of github.com:QuLogic/specfem3d_globe into devel
35fef95 Fix model_attenuation sorting.
e5ae7c2 fix div by 0 bug: OpenCL gpu backend can't provide information about memory usage
a35d9a3 improve OCL cleanups
677d61e Merge branch 'devel' into opencl
6e100c2 last DATA commit
dceb26a cosmetics changes
0ddd37a revert to efficient version, without OCL kernel qualifiers
5525ec3 Merge pull request #137 from QuLogic/ak135-timestep
22e808a added a link to the developers' wiki
fe780c1 Merge pull request #140 from komatits/devel
c34e165 removed white spaces from the examples using a script, to reduce their size before we move them to GitHub; also suppressed the seismograms for s362ani + attenuation that were affected by the s362ani + Q bug, since the reference seismograms were wrong.
c02fafd Merge pull request #141 from komatits/devel
0b8177e removed a few old files in the DATA directory
2f567d8 Merge pull request #142 from komatits/devel
52d1523 merged compute_optimized_dumping_undo_att.f90 as a subroutine into the main code instead as a separate program
88c7688 Merge pull request #144 from komatits/devel
70b7397 fixed a declaration problem in src/meshfem3D/compute_volumes_and_areas.F90 when configuring with --disable-vectorization Also created empty directory DATABASES_MPI/, since it is required by the default example in DATA/Par_file
e3cd687 Merge pull request #145 from komatits/devel
6d7da3d Merge pull request #146 from Nanosim-LIG/opencl
c4e38d5 added comment about total memory size per core to undo attenuation on the TGCC Curie machi ne in Paris
23b1b22 Merge pull request #147 from komatits/devel
089c229 Dimitri changes
2e952e3 Dimitri changes
db9d2a4 Remove submodule
51f0d99 Add 'EXAMPLES/' from commit '2e952e3d967c9579a2565995c1b7b46b06e83c2c'
80e63a5 Add 'DATA/' from commit '089c22968a5de0b8aefaa4deb899413ff59ad0d4'
88ad6ff Remove submodule
1bc4138 Merge branch 'master' into devel
c672433 Fix ADIOS routine that was not compiling because of module changes
d7e975d Fix parallel compilation as a dependency was added
c285e06 par_file has options that were created by the opencl dev.
fa9148d moved ATTENUATION_1D_WITH_3D_STORAGE from the Par_file to setup/constants.h.in
10a92ce fixed a gfortran warning
c75d818 Merge pull request #155 from komatits/devel
d396c8a Re-update m4 submodule.
3cfb525 added utils/BOAST_framework_to_develop_the_CUDA_and_OpenCL_routines_of_SPECFEM/tutorials_BOAST_for_OpenCL_and_CUDA_programming_of_SPECFEM3D_kernels_Brice_Videau_Kevin_Pouget_Jean_Francois_Mehaut_jun2014.pdf
f002db5 added utils/BOAST_web_site_official_URL.txt
57fe9f3 Merge pull request #158 from komatits/devel
4be3008 moved a file
e70ef6f updated the URL of BOAST
3ed9e4f first kernel test data
d6f39eb put Matthieu Lefebvre's support for ADIOS_FOR_UNDO_ATTENUATION back (they had been lost when CIG got rid of the Git submodules)
bc58688 Merge pull request #161 from komatits/devel
b88f853 added a stop statement if the first time step entered by the user is negative
346cc77 added utils/trick_that_can_be_used_to_easily_create_weak_scaling_curves.txt
02e5ac1 don't forget NULL pointers in the unit test files
4cfe039 add output file for unit test
be24c31 test data for kernel crust_mantle_impl_kernel_forward
c9ffe4d Reference checking working
efef89c Added platform selection to kernels.rb
70aee3f test data for all kernels
7186841 working non regression tests. Inputs are WRONG\!
fd5af76 added the script download_the_whole_topography_database_if_you_want_other_topographic_models.bash
22de8b7 acknowledge Geza Seriani and Enrico Priolo in the users manual
dba0bc5 Add binary version of topography file.
df73113 Modify topography loader to use binary.
657aad2 Tell git to treat topography files as binary.
741ee67 Merge pull request #167 from QuLogic/binary-topography
ad54dd9 regenerate test data
c1cff1e working nopn regression testing
9b7ff79 stupid commit
6c2a930 Optimize ascii2bin script a bit.
0cc3848 Merge pull request #168 from QuLogic/faster-binary-conversion
ef85836 renamed DATA/topo_bathy/ascii2bin.py to DATA/topo_bathy/convert_etopo_files_from_specfem_ASCII_to_binary_topo_format_ascii2bin.py
bac1d1c improved a print statement in download_the_whole_topography_database_if_you_want_other_topographic_models.bash
01408eb fixed a print statement in download_the_whole_topography_database_if_you_want_other_topographic_models.bash
ffeb7b6 now that the s362ani bug has been fixed, re-added EXAMPLES/small_benchmark_run_to_test_more_complex_Earth with new (clean) reference seismograms
b79c294 added directory OUTPUT_FILES
b17a1fe Fix warning about BOZ constant outside of DATA.
2f03d94 better kernel selection
069be26 new set of data after bug fixed in tracer
4e3f2c6 added option EXACT_UNDOING_TO_DISK, which saves the forward run to disk in order to compute exact sensitivity kernels without having to undo the forward run numerically; it will read it back from disk instead. This is for validation purposes only, since the disk files will typically require tens of terabytes (yes, tera). However this will become affordable uin a few years.
32685b6 Merge remote-tracking branch 'origin/devel'
bbdb65f do not call the routine to compute UNDO_ATTENUATION parameters if UNDO_ATTENUATION is off
9fae3b1 Merge pull request #177 from komatits/devel
6faf52b put display of NSTEP back in src/shared/save_header_file.F90
3b4e393 Merge pull request #178 from komatits/devel
0cab2d2 put call to save_header_file() back in src/meshfem3D/finalize_mesher.f90, following a request by Ebru Bozdag (she uses that file in her post-processing scripts)
352fd4e added doc/where_to_put_the_adjoint_sources_and_how_to_name_them.txt
0bbd95a changed i4 to i6 to avoid overflow for very slow runs with full range-checking options
79a78c0 add GPU tracer
19ecfec forced old LaTeX syntax (only) for accented letters
ea5725a improve portability for Python includes
50aed8d Merge branch 'devel' of github.com:Nanosim-LIG/specfem3d_globe into devel
e21ea2f added utils/BuildBot/test_suite_for_BuildBot.py
4467068 Added a README for BOAST kernels.
399c54d Removed test data
e3fe755 removed submodules to avoid conflicts
1fe1f9a Merge branch 'devel' into unit-testing-nodata
9b74895 Merge branch 'unit-testing-nodata' of github.com:Nanosim-LIG/specfem3d_globe into devel
3ecbc57 added a test to check that the center of mass of the model is located in zero when computing Roland_Sylvain integrals
fa5eb6e got rid of the two-chunk option in the users manual (but not in the code), and also mentioned that one-chunk simulations can use a mesh chunk larger than 90 degrees, following suggestions made by Lion Krischer
9469cd0 added for_ADJOINT_TOMOGRAPHY_TOOLS_see_in_the_SPECFEM3D_package.txt
ca6316f Uncommented the FCFLAGS in Makefile.in
c97ba5d fixed the OpenMP compilation issue detected by BuildBot
9870921 do not print the total number of time steps NSTEP in the mesher for information anymore because it may slightly change in the solver depending on the t0 of the source and also on whether UNDO_ATTENUATION is used or not
2a2b330 Merge pull request #200 from komatits/devel
44dfdda removed an old comment
1febe0d fixes a new line issue
f0e2531 updates error checking for adios and asdf; removes unused variables; moves mpi commands in asdf routines to parallel.f90; fixes array allocations in asdf routine
81e9c32 updates asdf routines to be compilable with older gfortran versions used on titan; adds specific adios routines for asdf to adios helpers file and outcomments them in asdf files
57deab8 renames constants for JP3D models to be more specific; moves USE_1D_REFERENCE flag to constants.h; updates movie volume routines
be6b472 updates program combine_paraview_movie_data to take movie files from DATABASES_MPI/ directory by default
f9bb4cc removes prefix vtk/ from include file names in mesh2vtu source files for easier compilation of mesh2vtu
88051d6 bug fix for model s362ani; bug fix for writing AVS_DX files in adios format; updates cuda reference files; adds OpenCL routines for transferring attenuation memory variables; adds gpu support for isotropic kernels w/ undo_att set
b422465 bug fix for gpu attenuation routines; adds header info to gpu kernel file generation; updates file outputs to unit 10, fix in adios AVS_DX routine
9cb66c4 bug fix for gpu output infos for displacement and strain when checking norm of arrays
9b6fbed Rename C I/O file to better indicate its usage.
fcb79a1 Fix file mode in open_file_abs_r_fbin.
3095918 added comments about the fact that one needs to run "configure" with option --disable-vectorization when debugging the code with range checking on
95124e5 bug fix for gpu simulations with stacey absorbing boundaries; updates gpu kernel headers
3f2103d updates rules.mk in src/specfem3D to compile adios files without mpif90
ad40aec added a warning about versions dot zero of a compiler
750737e bug fix for backward/reconstructed wavefield in OpenCL simulations; updates code reformatting
9824e89 Merge branch 'devel' of https://github.com/geodynamics/specfem3d_globe into devel
0dc6d51 bug fix for kernel simulations on OpenCL devices (multiple processes and asynchronuous copy); updates Makefile and rules for OpenCL flags
a84869d adds file check_opencl_device.c in utils/ directory for OpenCL device testing
67792d9 updates configuration script based on newest autoconf functions in m4/
f69b6e3 removes trailing spaces
b9cffa1 bug fix in gpu simulations for writing out strains; adds file helper_functions_gpu.c; makes use of gpu wrapper functions for similar CUDA/OpenCL functions (avoids many ifdef-statements, improves readability)
0ebb7f4 bug fixes combine_vol_data.F90 to be usable again with adios
468c376 prettifies code (space formatting in a slightly more consistent way)
ae70510 some more code formatting; adds additional gpu wrapper functions
c28216c adds preprocessor function GPU_ERROR_CHECKING for ENABLE_VERY_SLOW_ERROR_CHECKING
4063bb9 Added the option to use an external source time function. The parameter EXTERNAL_SOURCE_TIME_FUNCTION has been set in constants.h.in. If this is set to true (it is false by default), a text file called stf is looked for in the data directory. This file should contain a normalized source time function, with the correct number of timesteps, which will be multiplied by the moment tensor at each timestep. Also, if the external stf is specified, the halfduration is set to 0 (not needed), and the simulation start time is set to 0 as well.
6271dcd Changed print source time function back to false by default
94bbd45 adds GPU support for UNDO_ATTENUATION
38846e0 Merge branch 'devel' of https://github.com/geodynamics/specfem3d_globe into devel
d73e17b removes trailing spaces
4420cac updates m4/ version
8f81cfe adds configuration option --with-cem; adds file src/meshfem3D/model_cem.f90 for comprehensive earth model
b7062d6 updates gpu code routines for forward and adjoint runs
afc569e sorts station list in output_solver.txt by epicentral distance
a44a8e9 updates output format in create_movie_GMT_global.f90 to avoid cray compiler separator issues; rewrites if-elseif as select-case statement in write_seismograms()
2daa4d3 updates reading in CMTSOLUTION and station files to be less stringent about formatting and spacing
0a011ec Added initial comprehensive earth model functionality to mesher
fd9c452 Switched default model back to 1D_isotropic_prem
8c5d25d adds scalar moment and moment magnitude information to source output
4f7e397 Fixed passing of ispec from get_model.f90
e893513 added doc/SEM_class_from_Yvon_Maday_to_Dimitri_Komatitsch_and_Jean_Pierre_Vilotte_04apr1995.pdf
1eaaa62 updated BOAST sources to support version 0.9995+
73fec64 Added a preprocessor directive to get_model_parameters to fail out if a CEM model is specified, but configure was run witout CEM
012f8f0 fixed a typo in the manual and in my notes
6f85594 Merge branch 'devel' of https://github.com/geodynamics/specfem3d_globe into devel
d635170 Merge branch 'devel' of github.com:Nanosim-LIG/specfem3d_globe into devel
b60514e removed src/auxiliaries/combine_vol_data_shared.f90, which contained routines duplicated from other files of the code (that is dangerous, and very uneady to maintain the same routines twice, in two different files of the code). Thus temporarily had to comment out xcombine_vol_data* from Makefile.in and from src/auxiliaries/rules.mk because I do not know how to fix the Makefile (probably not difficult, but I am not familiar with that). Also removed unused variables introduced by the CEM modification a few days ago. Added comments for ellipticity. Removed useless white spaces using a cleaning script.
d2ec161 Merge pull request #222 from komatits/devel
558dbe7 build: Update rules for auxiliaries without duplicate code.
0aedbeb build: Split auxiliaries rules by executable.
e91fce8 build: Add ellipticity files to xcombine_vol* programs.
ed6dac2 Merge pull request #224 from QuLogic/auxiliaries-build-rules
857351f build: Split regular and optimized compiler flags.
5c369ff build: Add --enable-debug option to configure.
7015fbf build: Automatically disable vectorization with debug.
b506c88 Merge pull request #225 from QuLogic/debug-config
c1c4e4f build: Add shared module to auxiliaries compile.
cba41c8 Merge remote-tracking branch 'origin/devel'
06d6397 Removed direct usage of BOAST state
6994fe6 Added function declarations
760ea4d Prevent possible out-of-bounds write.
d9d5568 Fix unused variable warning without CEM.
31c4e16 Hard fail if resolution is set to invalid value.
ca6bfa6 Stop if doubling elements cannot be determined.
2d2cce8 Fix a couple type-conversion warnings.
d4ead38 Fix some set-but-unused variables.
b9d571a Fix an unnecessarily inverted condition.
2afaf00 Move force_ftz to the solver directory.
d8c9c45 Move make_gravity into specfem3D directory.
cc79a55 Remove extra shared object from mesher compile.
c53c771 Re-factor band_instrument_code to be clearer.
6b339cf Remove euler_angles from specfem3d compile.
9875814 Remove memory_eval from specfem3D.
76d7cc9 Remove unnecessary consistency check.
9539187 Print solver initialization errors to stdout.
c90b60c Fix intent of get_global arguments.
01e6b37 Fix a couple minor typos.
300803e updates configuration and m4/ scripts
0aa2df0 Fixed a small bug with CEM compilation.
d2dff12 updates user output for undo_attenuation buffers
753122f merges with upstream version
6034d34 updates gpu stubs for calling prepare_lddrk_device() routine
c6e8e9a added explanations from Jeroen about the steps to follow when using PARTIAL_PHYS_DISPERSION_ONLY instead of UNDO_ATTENUATION
44c2c95 Merge branch 'static-analysis' of github.com:QuLogic/specfem3d_globe into devel
957c705 updates geocentric_2_geographic_dble() routine to account for new flattening constant
9df6dd5 bug fix for gpu anisotropic kernels; bug fix in strain product on gpus; adds output directory check in kernels.rb and updates generated files in kernels.gen/ directory
65bcff0 updates configuration to take new m4/ cuda checks
8087d34 clarified the way to define memory sizes for UNDO_ATTENUATION on Titan at Oak Ridge
4cf4cfc allow the code to use up to 100% of the memory instead of 92% when using UNDO_ATTENUATION on GPUs because UNDO_ATTENUATION buffers are then stored on another machine (the host) instead of on the GPU itself
301191e added Jeroen's second set of explanations about how to use PARTIAL_PHYS_DISPERSION_ONLY right to the users manual.
2b030e9 Safe compilation of solver with CEM workflow netcdf kernel output
f90eb91 Added parallel netcdf kernel write for CEM.
782728a Added coordinate netcdf write.
8a794a6 better compiler options for Portland pgfortran
edc57b9 Merge pull request #241 from komatits/devel
7a3a2bc revert pgfortan to pgf90 (although in principle pgfortan is the standard name these days, but it seems to break BuildBot)
afaf5b7 got rid of compiler option -Mipa=fast,inline for pgf90 because it creates problems with some older versions of that compiler
7ff74ed changed pgf90 back to pgfortran, since the problem detected by BuildBot was not coming from that
c97050b Merge pull request #243 from komatits/devel
7e52bb1 adds convert_model_file_adios.f90 to src/tomography/; updates make files
7c95636 adds model interpolation tool to src/tomography
c25bd40 adds tomography tools for summation,smoothing and model updates
ed24ef0 updates Makefile.in to add model update executables to make help informations
46435b2 added missing headers
af7e4b9 removed useless white spaces using a script
4be5f11 Merge pull request #246 from komatits/devel
7a6acc2 updates tomography tools to use common subroutines
5958372 renames constants_tomography.h to constants_tomography.h.in to allow out-of-source builds; small updates in tomo rules and files
efc1238 updates tomography tool routines; adds MAX_STRING_LEN parameter for strings
ca6ec64 updates configuration and m4/ scripts (fixes configuration with CUDA and intel ifort compilers)
60d065d updates smoothing tool and adds mesh geometry to values_from_mesher.h
12a1de4 fixes parameter output to values_from_mesher.h file for mesh geometry (avoids line breaks)
72d3705 updates interpolation tool and rules.mk in src/tomography
7e26ef7 adds difference tool to src/tomography
ccdee4f Textures no longer appear in function declaration when not needed
92e5c5e remove texture definition when not used
eb0800a remove duplicated function
2db7be0 Protect multiline macro function definitions
ad8193f finish removing unused textures from kernels calls
c1bfb4d revert src/gpu/initialize_gpu.c to original state
71b75c4 fix compilation bugs (cudacc stricter than gccwq)
eecbe6b removed white spaces
1956d2e Adds initilization for backward trace arrays
0d9b194 updates interpolation tool; removes redundant asdf helper files; adds new flush_system.f90 file; renames long function names
70fbc91 added see_also_README_inversion_package_list_of_things_to_do_in_the_SPECFEM3D_package.txt
1300e56 Merge remote-tracking branch 'origin/devel'
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