[cig-commits] [commit] devel's head updated: Merge branch 'master' into devel (1bc4138)
cig_noreply at geodynamics.org
cig_noreply at geodynamics.org
Wed Jun 18 16:20:43 PDT 2014
Repository : https://github.com/geodynamics/specfem3d_globe
Branch 'devel' now includes:
b044fd9 *** empty log message ***
ae6cdb5 *** empty log message ***
b9b8eb9 *** empty log message ***
95d13ab *** empty log message ***
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
0d904cd James' ASDF format for seismograms
70377ac James' ASDF format for seismograms
e5bf8c4 terri test
76f64d8 renamed all process.sh scripts to run_this_example.sh
b8c84cb added a comment to the Par_file
c0bc5ba Merge remote-tracking branch 'origin/devel'
170e5f7 Update submodules in master
cd83b68 submodules updated
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
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
a5f174d compressed the large topo files that are unused by default and added some conversion and display scripts
69b16e7 replaced the old version of ETOPO with the latest one (etopo2v2c), which fixes several issues, and also added ETOPO1 (etopo1_ice_c)
2a11397 done cleaning and adding all the topography files, in particular adding ETOPO1
7f29f8a added a test to check that color palette file GMTglobe.cpt exists
2e38728 better cleaning at the end of the GMT script
cc50b88 convert final output file from PS to PDF
ec7a783 added a color scale to the GMT script
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
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