[cig-commits] [commit] pluggable's head updated: Released v1.0.1. (99d99a4)
cig_noreply at geodynamics.org
cig_noreply at geodynamics.org
Wed Apr 9 08:57:42 PDT 2014
Repository : ssh://geoshell/specfem3d_globe
Branch 'pluggable' now includes:
c36d69a Initial revision
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d88df85 added maximum depth of oceans to suppress problem with trenches
596423c fixed problem with radial mesh on the ES - now uniform from d220 to surface
edb3314 added max of topography = 5000 meters
b0f86cb added AbSoft compiler to Makefile. Fixed deallocate(rmass_oceans) bug found by Jean-Paul Ampuero.
426eafc suppressed low-res movies for Keken, and replaced with high-res
6e0f360 allowed receivers to be buried in global code
40171df added OpenDX f90 routine to compute x y z position of hypocenter
e6f9bc3 fixed i6 bug in movies van Keken
6439710 removed old fluid-solid version with iterations
8af31c2 switched to new fluid-solid version with no iterations
9ccf196 saved backup of older fluid-solid version with iterations
b914bf3 added parallel version of fully anisotropic solver for Sebastien
7692a64 Moved all movie-related parameters to the read_parameters file and updated all related calls.
4b3316f Fixed a bug in create_movie_AVS_DX.f90 related to counting the four corners of an element on the surface.
d73eeb7 Fixed the movie code to work at full resolution. Modified the regular code to display velocity in the outer core for movies.
8e672f5 Added GMT capabilities to the create_movie code.
d7f23c9 merged regional and global codes
c747e49 Updated the README file to reflect the use of finite sources and movie capabilities.
8c3de0a fixed bug in get_attenuation (need fictitious inner core even for regional)
0046e0d Moved the absorbing boundary conditions from compute_forces_crust_mantle to specfem3D. Check that both the inlined and the regular version are stable for 25 minutes and give identical answers
f1de25f Implemented absorbing boundaries in regional code for the outer core and the crust-mantle. Tested that the code is stable. Coupling at the CMB appears to be fine.
9c1f4c7 We now have working versions of the both the regular and the inlined versions with absorbing boundary conditions. The regular and inlined versions give identical results on the cluster and are stable for 10,000 timesteps.
427c9e0 added list of Gurnis's Beowulf nodes in mymachines_gurnis
ee1345f fixed inner core bug detected on the ES in Japan
738d501 removed unused array veloc() from compute_forces_crust_mantle
a5b0ad2 added Funaro routines from Bernhard Schubert removed old anisotropy code from Sebastien
58a11bb fixed bug in ES inlining directives for Stacey absorbing conditions
1ff0e36 added clean backup of anisotropic code for Sebastien (OMP July 2003, serial, for IBM p690 at CNES)
10e2df8 added comments about CMTSOLUTION units to get_cmt.f90
cacc12b added Par_file for 507 nodes (4056 processors) on the ES in Japan
59636f7 fixed version number (now all files have v 3.4 label)
a557992 updated Makefile for Intel ifc v7.1
df93c72 added comment about vectorized loop for NSOURCES
6bb9547 Fixed a mismatch in types between combine_AVS_DX.f90 and write_AVS_DX_global_chunks_data.f90. CV: ----------------------------------------------------------------------
abb36ea vectorized versions of sources and receivers detection for the ES in Japan
470e2d6 modified Makefile for vectorized source and detection routine for ES in Japan. Modified go_* scripts for MPICH compiled with ifc v7.1
767e4d7 more modifications to vectorize the NSOURCES code for the ES in Japan
ad2ad69 changed default value of SUPPRESS_STOPS_INLINE to .true. for ES in Japan
ee39dbf added script show_all_max_amplitudes.csh to monitor max amplitude of results
39d21f0 station name up to 8 characters in write_seismograms.f90
9ce9acf changed code to allow t_cmt(i) = 0 to be for any CMT source, not only first
760fed2 removed unused test from locate_source.f90
8a26fe4 changed hdur(1) to minval(hdur) to save seismograms
e7a45d0 added convention for definition of reference frame in comments and README
5b2ce1e fixed format problem for double precision seismograms
3c9174e added file STATIONS_tsuboi_tokachi-oki from Tsuboi-san
65a8de8 added comment about bug in euler_angles. One of the formulas is not general enough, it does not work (I think) for a chunk of size <> 90 degrees
fa597cc Fixed a bug in crustal_model detected by Brian Savage. The Moho depth was not properly smoothed before placing it on the mesh.
85fac63 added rename_files_IBM_f_2_f90.csh script to DATA/util
ccaf280 added Denali, Alaska, source CMTSOLUTION_DENALI
a737a39 Fixed bug introduced by Jeroen for sign of coupling condition at the CMB. Also removed old inlined loops on NSOURCES for ES in Japan.
8ac4b63 finished removing old inlined NSOURCES loops in inlined version of solver for the ES
cc24450 modified regional code to allow for rectangular slice for Lev Vinnik Sdiff study
c2f1b16 fixed time step problem in some Par_files
defe347 added movie code for Tsuboi for ES in Japan in DATA/util/tsuboi_movie_feb2004
2e22baa modified constants.h to be consistent with Sdiff regional code for Vinnik
f75a97a modified write_seismograms.f90 to handle any length of station and network name
c6dc19e changed Par_file and constants.h not to save movies and OpenDX files by default
fbf2dfa modified movie code in the inlined version of the solver to check that half-duration of the source is ok for movies
7755587 modified go_mesher and go_solver to be more robust in terms of detecting NCHUNKS
1e75060 added Par_file for ES movies based on NEX=320
1c3d1cb modified the code to handle 2 chunks (NCHUNKS = 2). Will still need to improve the code in the future to allow for 2 chunks with angles <> 90 degrees, and to assemble the second corner between chunks (in the current version for simplicity only the first corner is assembled)
3a86f58 added test that dynamic memory allocation goes well in create_movie_AVS_DX.f90
4040afc updated CMTSOLUTION info for multiple sources in README file
85edcc9 fixed small bug related to length of station names
2366b7a converted information printed about distance to single precision in locate_receivers.f90
f22fed8 updated Makefile to take into account new Intel ifort v8.0 compiler options
1a9455a fixed one more detail in Makefile
000127a modified format() statements in read_parameter_file.f90 to suppress fixed length of fields
6b6c0d9 3-D Attenuation added
e2d0dc7 added 3D anisotropic code for copper crystal for Jose Carcione in DATA/util
297b72b updated anisotropy code for Carcione (copper crystal) in DATA/util
1e1e06f updated Makefile options for Intel ifort compiler and updated go_* scripts
8421fb0 fixed non-declared length problem in format() in read_parameter_file.f90
12984c3 updated anisotropic code for Jose Carcione in DATA/util
daefd6d distinguish between scalar and vector MPI buffers in assemble_MPI*.f90 in order to avoid fictitious additional dimension (NDIM,...) when using a scalar buffer
0b68d15 Fixed number of dimensions to factor_common
6410b12 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
9d5c2dc updated the README file for the global code to inform users that values of NEX_XI or ETA below 64 can make the mesher exit with an error message (negative Jacobian)
a8abcaf removed white spaces, cleaned listing and cleaned attenuation_model.f90 to compile without warnings with Intel ifort
77efef4 added test to check that sphere can be cut into slices without getting negative Jacobian (in practice, check that both NEX_XI and NEX_ETA are >= 48)
cfd8da7 added comment about the fact that 3D attenuation model is not included and that currently only PREM attenuation is available
17c642c cleaned attenuation listing
9b90a63 fixed typo in comment
f42e769 added smoothed etopo-4 topo/bathy model, and modified routines accordingly
ce308b5 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)
3952fa5 Cleaned code to have chunk of any size and modified corresponding lines in Par_file. Still need to clean euler_angles.f90
60673b8 released version 3.5 of global code and version 1.2 of basin code
87e9cee fixed small bug in calculation of exact surface of mesh (not correct if NCHUNKS /= 6)
eb8d86b suppressed derive_parameters.f90, which was not used anymore
7ae5df2 added white spaces to align tabs in loops
9e5c9c9 added output of number of time steps to output_mesher.txt
e46d08e fixed problem in default values in constants.h
97dded0 cleaned comments before releasing new versions of both codes (v1.2 and v3.5)
4ac2ae4 fixed vertical edges problem for Stacey found by Qinya in get_absorb.f90
e2b5e31 suppressed obsolete regional/global if statement in get_attenuation_model.f90
05b04a9 modify line-break for absoft compiler (-W132)
647a044 updated Makefile options for Absoft compiler
1966065 added comment in anisotropic_mantle_model.f90
61ba5c8 added line to suppress Montagner's model if needed in anisotropic_mantle_model.f90
fe93ce4 fixed bug in IASPEI radii (R80 and RMIDDLE_CRUST) found by Jeroen (previously set to 1., which was dangerous) in read_parameter_file.f90
7af7b1f moved the check of SAVE_AVS_DX_MESH at the beginning of the file to after the read_parameter_file subroutine since it is no longer in the constants file.
8860234 added deallocate(Qmu_store) and deallocate(tau_e_store) to create_regions_mesh.f90 to fix small bug found by Bernhard Schubert on Hitachi compiler
00f762f ROCEAN now set to PREM value if IASPEI is used to avoid problem with fictitious ROCEAN = 1.0d0 in make_ellipticity.f90
0654c27 added support for g95 compiler in Makefile
92790ac incorporate movie 3-D output statements added by Peter van Keken
547a949 Now the code computes seismograms for a source that is equivalent to a triangle with half duration given in CMT file. Previously the half duration from the CMT file was used directly when computing the Gaussian.
813515a Following modification to the method of determining the stress and strain relaxation times in the standard linear solid system for attenuation implementation. Old method was a SVD inversion , new version is a simplex inversion. Simplex methods contained within attenuation_simplex.f90 Modifications made to attenuation.f90 to mirror attenuation_prem.c output. Added run_attenuation2.sh to make it easier to run the new attenuation code.
518e8e9 Modified the attenuation_conversion code for 3D attenuation to use a simplex method for determining the stress and strain relaxation times in a standard linear solid. The previous version used a SVD inversion which worked well for large values of Q but not for small values of Q (Q < 80). No changes to existing code should be necesary, although meshing may be slightly longer due to the increased compuatation.
5d8e3fa added .keepdir to keep some empty directories such as obj/
47a4a29 Inserted new tau_mu's into get_attenuation_model.f90 based on Brian Savage's simplex inversion for the standard linear solids that will give the nearest to constant Q values.
872e666 changed "nodes" to "processors" in go_* scripts
a8dc3d0 modified compute_arrays_source.f90 to compile much faster under Portland pgf90 (used to take 20 minutes!)
a1c97d7 initialized memory variables before time loop in specfem3D*.f90
67f5782 Changed elat and elon to lat and long in order to be consistent in all the subroutines. fixed small bug in initialization of deviatoric tensor epsilondev for memory variables in global code. Added bak directory.
15b3400 fixed OUTPUT_FILES/timestamp* OUTPUT_FILES/starttime*txt in Makefile
fdd3827 moved inlined version of the solver to DATA/util/scaling_nodes_ES. Won't be maintained anymore.
2005de9 added read_value_parameters.f90 to global code to ignore comments and white lines in Par_file
0037460 fixed small details in two comments
abbbf32 updated run3d.csh scripts and also OpenDX stuff in DATA/util/opendx_AVS_GMT
76a116d clean implementation of Lacq gas field MNT in basin code
90caa33 removed SPECFEM3D_GLOBE/DATA/util/wasiu_code/wasiu_code_26feb03.tar.bz2
f93dcce Fixed subroutine name and allocation deallocation issues Default 3D attenuation now donw by simplex inversion Somewhat slower than SVD inversion but produces better results
323deb5 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
3255ee3 removed old script in bak in Makefile
adc4af3 According to Seiji Tsuboi's Email, they use DT = 0.072 for V3.3 in 1944 processor case. Modify DT from 0.05 to 0.072.
33eeb63 updated Makefiles for IDRIS machines (IBM Power4 machines at www.idris.fr)
facf20a removed rename_files_IBM_f_2_f90.csh and rename_files_IBM_f90_2_f.csh and changed Makefile for IBM accordingly
eb6164f changed Makefiles for IBM Power 4
fad6dad suppressed constraint of aligning values in Par_file on the 34th column
affd0cd fixed portability problem that made reading of Par_file crash on IBM Power4
0a0f08a fixed some comments
e133fea exit_mpi.f90 -- added the if conditions for closing IMAIN
b67232f modify go_solver to run as front job
25c2afb changed details in global code: switched order of parameters in calls to subroutines to use NEX_XI,NEX_ETA instead of NEX_ETA,NEX_XI and NPROC_XI,NPROC_ETA instead of NPROC_ETA,NPROC_XI. Also changed minor details in attenuation code by Brian Savage: suppressed semicolons, changed real(8) to double precision etc.
0bbb3f6 define r_earth and r_ocean differently under gravity = .true. to avoid problems in make_gravity subroutine in the solver
55d6e35 Add full anisotropic tensor (total 21 elements) rotation in the subroutine anisotropic_mantle_model.f90.
00708d3 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.
e4701f2 suppressed old CDIR NODEP directives that remained from Japanese Earth Simulator implementation
efc3371 removed "format(" from 3D global code
b61a48f Add the auxiliary programs to convert the mesh files created by the specfem package into the format known to Paraview (unstructured grid files)
72aa655 renamed save_arrays.f90 to save_arrays_solver.f90
c493718 Added an Output section at the bottom to report various parameters internal to the code, but needed for computing the memory requirements. A new file OUTPUT_FILES/derived_values.h will be created, which is then read in by memory.pl to estimate the memory usage for the solver and mesher.
415fe23 Added in yet another attenuation subroutine describing the PREM attenuation structure. It is called from get_attenuation_model() when the MIN_ and MAX_ATTENUATION_PERIODS are determined automatically. This code conincides with the automatic radial meshing for very dense meshes and CHUNKS less than 90 degrees.
631890f Code to automatically determine the attenuation parameters for period ranges which do not match the current one defined which makes up most of this file. This code will be called for very dense meshes and CHUNKS less than 90 degrees.
f577da0 Brian's subroutine for automatical determination of radial spacing (NER's)
58b2a54 removed mymachines_gurnis
f57f20b moved FIX_UNDERFLOW_PROBLEM to section that should never be modified in constants.h
5ed47a4 renamed SAVE_AVS_DX_MESH_FILES to SAVE_MESH_FILES
9077998 converted solver from static memory allocation to dynamic
302eeaf changed details in statistics that are printed about the mesh
3d9f4db fixed bug introduced by Brian Savage: writing output to IMAIN while it is not open yet
75cf318 write mesh statistics to IMAIN instead of IOUT
17dfef5 suppressed extra white spaces that resulted in "line too long" error
b0bb47e removed old stuff from DATA/util
be40d44 removed old stuff from DATA/util
77a75a6 removed old stuff from DATA/util
c115d48 removed old stuff from DATA/util
0316dfc (Re)Pyrization Part I: Read parameters from a Pyre inventory.
eb0d2d7 Fixed a bug in read_value_string(), and improved the error message.
3e89ec1 (Re)Pyrization Part II: Partition inventory items among various Pyre components which mirror the concepts in the underlying Fortran code.
39861a1 Doh! Sync'd read_value_parameters with my changes to the Pyrized version.
49550ef Improved error reporting for bogus user input; unfortunately this required patching Pyre ("PyrePatches.py"). Incorporated my launchers from CitComS.
079ae28 Added a codec to allow the use of INI-format ".cfg" parameter/preference files, which users will undoubtedly prefer to XML.
bc5f941 Command line overrides .cfg files, and not vice-versa. Allow users to give .cfg/.pml files on the command line. Handle more exceptions in _richCast() (bool, dimensional). Changed RECORD_LENGTH_IN_MINUTES to a dimensional.
41a95cd Added example parameter file and preferences file for the Pyrized version; they are derived from the traditional "Par_file".
2d3ae5e Link Pyrized version with MPICC instead of MPI90: ifort preempts our 'main' with its own.
6f8fc0d Call MPI_Init() from "workers" only -- and from Python instead of main() -- in order to avoid SIGPIPE with MPICH-GM ("<MPICH-GM> Error: Need to obtain the job magic number in GMPI_MAGIC !"). Created a tiny Pyrex MPI module for this purpose.
fa4a694 Running jobs on Pangu: added "bsub-options" to LauncherLSF; added Fortran function check_parameters.
8ed3988 added routines to convert DX files to AVS in DATA/util/opendx_AVS/
712855f Allow the Pyrized version to override the hard-coded pathnames in the code ('DATA', 'OUTPUT_FILES') so that users can specify an alternate location for files, and even effortlessly change the output directory between runs.
013c9f1 Check input/output pathnames from Python.
52aa8e5 Reworked InputPile handling.
a85358e Work-around for bizzare performance hit incurred by mixed-language programming with ifort v9 on Pangu (Pyrized version was 3x+ slower than classic version).
2defef1 Use CIT_FC_MAIN instead AC_FC_MAIN, which doesn't work with ifort v9.
313f504 Validate parameters in Python.
f0b73db Eliminated default time limit for batch jobs (port of fix for CitcomS issue8).
12a39cc Checked-in Pyrex-generated code, so that users don't need to have Pyrex installed to build the Pyrized version. (The Pyrex source is quite stable.)
6557105 Refactored Python scripts so that they can run standalone on a web server (without the Fortran/C code present).
a65c697 Fix for compile-time errors (bugs?) reported by the NAGWare f95 compiler:
397e999 Reference Model inventory items by their Python name, not their Pyre name.
50c0c9c added LaTeX manual under DATA/util/manual
d2b3ca0 added mesh_scaling_processors_ES_japan.xls to DATA/util/scaling_nodes (Excel file to compute mesh size and scaling on large machines)
4f46e31 removed -Mstandard from the Portland pgf90 Makefile because gives errors that are due to a bug in version 6 of pgf90 (the Portland technical support confirmed that the problem comes from their compiler, not from SPECFEM3D)
6ff3369 create the adjoint branch off the 502 version of the global code, and merge the adjoint changes I made into the branch.
72a80f1 Fix the hdur/hdur_gaussian problem according to the newest update
1010438 fix the bug in combine_paraview_data.f90 where arg() should have array length of 6 instead 5
ea50840 update HDUR_MOVIE and IOVTK variables
a1a82bf Fix Makefile, add combine_paraview_data
0bc6d4e Fix for possible bug: initialize 'A_array_rotation' and 'B_array_rotation' to zero.
921c104 combine_paraview_data.f90: fix the strings after stop function to aviod compilation errors for ifort
fa2308b Reverted r517 by komatits ("converted solver from static memory allocation to dynamic").
add8139 fixed problem introduced by Brian Savage: writing output to IMAIN going nowhere
b236fcc fixed order of parameters from NEX_ETA,NEX_XI to NEX_XI,NEX_ETA
2dd9b5a fixed two bugs detected by Bernhard Schubert: AVS point order was incorrect, and one statement was incorrect when using less than 6 chunks
7f673aa Suppress ifort's warning about unused variables with "-warn unused".
3fc9857 added comment about routine handling unused variables
b817682 removed -fast and -Munroll for Portland pgf90, because that compiler is not very stable and these options create problems on some machines
ebd0367 Minor.
70fe818 Merged Qinya Liu's adjoint code -- r570:600 from the 'adjoint' branch -- to the trunk.
3025e0d renamed file
d0b0fe1 changed copyright information in new files added by Qinya
3c5eb00 added classical files with list of developers, copyright, known bugs etc.
f2240ff moved SIMULATION_TYPE and SAVE_FORWARD to Par_file. Also removed unused variables in several other routines.
1ad3c27 updated BibTeX file and changed citations accordingly in the manual
0fee12c Update the scaling and dimension of the kernel variables. Now output kernel is physically in s/km^3 unit.
d843c0f Fix some minor errors to eliminate the warning messages from ifort compilation
2771454 fix bug of scale_disp
a992622 Added SIMULATION_TYPE and SAVE_FORWARD to Pyre code.
de2594a Added 'simulation-type' and 'save-forward'.
59377ec change back save_arrays() to save_arrays_solver() according to the newest version in the main branch
75d3c54 clean this empty file
16ebaaa fix NPROC_ETA,NPROC_XI for read_parameter_file.f90
811a23c Suppressed NGLLSQUARE and NGLLCUBE. Cleaned extra white spaces at end of lines in listings using a script. Changed length of station and network names in LaTeX manual.
e106811 removed NGLLSQUARE. reduced size of postscript figure in Manual.
502002c changed jtromp at caltech.edu to jtromp AT caltech.edu to avoid scanning of source code by spam engines
dbbd43c Delete PvK MOVIE_VOLUME implementation.
ac313aa added comment about how to report bugs.
d0807a0 added scripts to run on the "pangu" cluster at Caltech.
7c6d5f4 added paragraph about how to define the "machines" file on "pangu"
c3ccf2d removed extra white spaces in listing
e5186a0 fixed important topography bug detected by Bernhard Schubert: longitude blocks were inverted in topography/bathymetry file
169be95 - added details about how to check the mesh in the manual.
700eae4 changed transversly to transversely (there was a typo)
dc90e93 change exit_mpi to exit_MPI in specfem3D.f90 rename the saved array files to start with 'proc'
099e598 Further optimize the loops in the 'it' main loop.
c820b30 get rid of dot_product in the kernel calculations
7ffa04b fix bugs in combine_paraview_data.f90 which fails to treat cases of low-resolution mesh of the inner_core.
44e722a - added section to additionally output SAC format in write_seismograms.f90 (- creates seismogram files named according to ASCII files + label ".sac" - leads to only 50% more disk space for seismogram output as time information is not written explicitly for every station and component)
22b691b moved Users' Manual from DATA/util/manual to USERS_MANUAL
171c86f cleaned white spaces and comments
e6ba805 moved DATA/util/scripts_pangu_Caltech to SCRIPTS_SCHEDULER
6384bf0 committed Jeroen's changes to the manual and my changes to the README and BibTeX files.
7ae0aad Restructured Pyrized version to easily allow running mesher+solver in a single batch (LSF) job.
7c0ef87 Minor bug fix: must set scheduler.nodes in addition to launcher.nodes.
0ad1aba Last-minute fixes before meeting :-)
bda857b A handful of fixes and work-arounds.
22d7d80 Use Cheetah instead of Opal for HTML generation.
9e18c40 More web interface work.
5eb6a94 Whoops -- one more template file.
75ae405 added options for IBM MareNostrum at the Barcelona SuperComputing Center (Spain)
fb4c70e added create_header_file to "make all"
d71e83f suppressed non-standard "call flush(IMAIN)"
e4401ed added program to filter the STATIONS file to include stations located in a given region only
ebeb827 Revamped build system -- standardizing it somewhat -- in anticipation of building and testing Specfem under CIG's BuildBot. Users must now run 'configure' before building for the first time -- 'Makefile', 'constants.h', and 'precision.h' are now generated by 'configure'.
4d86175 - created and added regional_c1_1.html.tmpl, regional_c2_1.html.tmpl, regional_c3_1.html.tmpl - modified global.html.tmpl - modifed regional.html.tmpl
6f70002 Factored-out Fortran-compiler-flag guessing code into 'flags.guess', so that it can be updated without having Autotools installed. Also, svn:ignore all the files which are now generated.
3cefd6b Bug fixes, tabs -> spaces for flags.guess.
fbc6556 Merged r664 by komatits from Basin code:
bcd64e2 Significant re-work of Pyrized version (still in progress).
3e2cb64 changed (i4) to (i5) in Qinya's display of mesh topology, otherwise problem when using more than 999 processors.
64f8e35 added routine to display mesh topology (how processor numbers are assigned in the cubed sphere)
c04a706 Reverted accidental change.
386f47f merged the "do l=1,NGLLY" and "do l=1,NGLLZ" loops because we know that NGLLX = NGLLY = NGLLZ and therefore the compiler can optimize further if we merge the three loops in one.
94cdfdc I'm getting there: currently, it gets to mpirun, and then bombs.
150b470 removed derived_values.h problem introduced by Brian Savage
bea6452 replaced reading of files by all the nodes from directory OUTPUT_FILES with call to MPI_BCAST to avoid bottleneck on very large number of nodes.
4c40d82 changed i3.3 and i4.4 to i6.6 to allow for up to 999,999 processors to be used instead of 999 or 9,999.
9589561 changed "slave" to "worker" in all the source files
5951652 Specfem can launch now! But the output files are still a mess. Need to add scratch dir cleanup and collection of seismos.
4d4efad fixed definition of IASP91 model in the upper mantle and crust, which was completely wrong
e85bb95 added models 1066a and ak135, and changed call structure of iasp91
f9fd72e added tools to display models 1066a and ak135
8b1b300 removed semicolons from source code because they make the code difficult to read
1b6af00 Fixed build under version 8 of the Intel compiler.
4a88401 Silly work-around for hang during compile with ifort v8.1.
a447236 Fixed infinite loop introduced by my previous check-in (it is true that I don't really know Fortran).
3c04c82 The scratch dir is now cleaned-up when the job completes, and a tarball of everything in the output-dir is staged back to the login node.
6bbbbce fixed integer*8 problem in that include file from MPICH
7045a0c Added a codec for Par_files.
bc390f6 moved three of the six loops to a separate subroutine because (although the code was correct) some compilers used to take forever trying to unroll the six levels of loops in that file.
d654ece wrote better version of routines for Earth models 1066a and ak135 (model is now defined and stored once and for all)
a75d3f4 fixed a potential problem: Q values for attenuation could be zero near the CMB and ICB because of possible roundoff errors.
7a30580 fixed potential problem for Vs in outer core in models 1066a and ak135 due to possible roundoff errors on depth
5a4a7e4 fixed radii values for 1066a and ak135, which were incorrect, now uses new values provided by Ying Zhou <yingz at gps.caltech.edu>
4e69bdb added comment about bug for ROCEANS in the case of the 1066a model
8266358 fixed some radii for ak135 in main code, and for PREM in display routine
922c54d changed a comment
d1aa7ee Added CIT_FC_MPI_HEADER, which, if necessary, will automatically generate a 'mpif.h' sanitized for Fortran-9x. (Only works with MPICH at present... not sure if other MPI implementations have a problem.)
7db1656 Reset AC_LANG back to C for Pyrized build.
a33ce1b fixed problem with ROCEAN for model 1066A, which has no oceans
fd37fe0 Added "call system()" calls for MareNostrum in Barcelona. Also added an MPI cascade to avoid overloading the GPFS file system there. Moved statements and comments about beginning of time loop to the right location. Renamed isender to sender and ireceiver to receiver.
2037bf9 Removed the last bottlenecks related to reading files on all the nodes from the remotely-mounted home file system in directory DATA.
e75ee26 fixed deadlocking problem in my MPI implementation of Bernhard Schubert's SAC seismograms routine. added file get_event_info.f90 (which contains both a serial and a parallel version) to get information needed for the SAC headers without deadlocking.
2263931 added non-dimensionalization to models 1066a and ak135 (it had been forgotten)
b245543 modified routines for models 1066a and ak135 to make sure behavior is correct around the ICB and CMB (the previous version had a bug: it could take a point above and a point below and interpolate between them, leading to a wrong value)
04d73c0 removed old trick used to fix a potential roundoff problem in the interpolation code across the CMB and ICB
6c7920e moved creation of central cube buffers from main program to a separate subroutine (create_central_cube_buffers.f90)
fe40c1e fixed bug in scaling of radius for models 1066a and ak135. added flag to avoid saving seismograms to local disks on MareNostrum. removed useless space in create_regions_mesh.f90.
f68fea2 Pyrized version can now collect seismograms. (Finally!)
17cd116 Removed 'values_from_mesher.h' from the repository. Use a Makefile rule instead.
ffcd3ee suppressed old dummy .keepdir files that remained from the conversion from CVS to SubVersion.
2ff3588 Don't archive seismograms during dry runs. Also, the mesher always writes 'values_from_mesher.h', so set its pathname correctly in all cases.
83bcb42 Use OUTPUT_FILES variable instead of hard-coded path (for Pyrized version).
bc932ed The 'local-path' option is now called 'scratch-dir'.
491d73a Final bug fixes: create solver header file if it doesn't exist; minor fix in ParFileCodec.
a5f3573 for model IASP91, following a suggestion by Ying Zhou, changed ROCEAN = 6368000.d0 RMIDDLE_CRUST = 6356000.d0 to ROCEAN = 6371000.d0 RMIDDLE_CRUST = 6351000.d0
98a8495 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
6acad2d Split MPI_GATHER lines in locate_sources routine that generated errors. Removed a variable (iline) from comp_subarrays_adjoint_src that wasn't used.
c43272b Fixed typo.
db340ba New Attenuation Routines for 1D Attenuation Models
f29d4a1 Use eggs for Python dependencies. Also, made some minor tweaks to the Fortran so that it compiles with g95.
598d13c Initial Version.
fc315a9 Removed *.pyc files.
81c74b5 Convert seismograms to SAC binary format using asc2sac() (the *.sac files produced by the Fortran code are "alphanumeric" SAC files, which isn't what is wanted).
413c4e0 Fixed typo.
c0aedc1 - Added UserInfo, Mesh, Model, Simulation tables in the database (models.py) - For now, there is no user authentication (e.g. login). Let's use 'test_user' for testing purposes. - Added simulation creation, viewing, deletion functionalities.
3c0d591 Initial Version
7d21197 Minor cleanup of HTML.
501724a More HTML cleanup. Pluralized some URLs and removed references to "mysite".
6e68708 Model clean-up: made 'simulation_type' an integer choice; removed parameters that don't make sense for the web.
aaae6de Split global/regional form template into separate files using template inheritance.
84452f1 Beautified HTML.
9c536d0 Added skeleton code for PML file download.
f3bf3dd - views.py - skipped hdur_movie field when writing to db. hdur_movie valued will be set to 1000 which is default value. - models.py - added ntstep_between_output_info, ntstep_between_output_seismos fields to simulation table. - set 1000 as hdur_movie field's default value. - simulation_base.html - set 100 as timestep's default displayed value. - detail.html - nothing significant. (changed the html table border size) - simulation.pml - now this page displays values read from db.
87cb2f4 - Created [mesh_info,model_info,movie_info,output_format_info].html for user information - Modified [views,urls].py to support user information displays above - Modified [simulation_base,simulation_form_regional].html to have button which will pop up a info window - Created Daemon.py which will read ready records from database, fetch xml files from web server, and finally save it to a local file.
0b51260 - Fixed a bug where cur = conn.cursor() was used twice within the for loop, and it caused only first record to be downloaded.
2f7e1c8 Added an 'events' sub-application for collecting CMTSOLUTION data ('events' is actually a component of the CIG framework).
81afe1f Put most object files into an archive library, 'libspecfem.a', and thereby let the linker decide which object files are needed to link which programs. (That's the linker's job!)
e234e72 Pyrized create_movie_AVS_DX. (Internalized its rank() and swap_all() subroutines to avoid multiply defined symbol conflict.)
4e22408 Changed the url path of http://.../simulations/sid.pml to http://.../simulations/sid/parameters.pml
ed985ff - views.py - Fixed indentation error (replaced spaces -> tabs)
6d5a1a9 - Added stations.txt, events.txt for Daemon interce. - Added userinfo_form.html for user registration interface. - Modified home.html, detail.html, base.html for simpler interface with user login feature.
a5d08ac - Added session (user login) feature with simpler interface.
3612fba Incorporated my new 'stations' mini-app for selecting seismo stations (STATIONS).
30451d8 Got inline editing working for UserInfo's OneToOneField. The "edit registration" page now works again, but the "new registration" page is still broken.
5c37733 Registration is now fully functional. I've given up on inline editing; registration now uses a custom form.
9d2a0ad Added 'simulation_list.py' and made related changes to the daemon.
91bbe2f Reworked the "Mesh" section of the "new simulation" form. There are actually several constraints that vary with the number of chunks; as the number of chunks increases, the more constraints there are. (It is more complicated than simply regional vs. global.)
ad4e93b Consolidated site structure somewhat.
c89fe42 added program to permute point order in a CUBIT mesh to generate an OpenDX file
9df9e48 Replaced templates 'events.txt' and 'stations.txt' with Python code which does precise formatting. Fixed bug where 'absorbing_conditions' wasn't being set.
1bbc692 Added a form for the daemon to change simulation status and upload output. Added a link for the user to download the output.
0e1b175 Completed the sketch of how the daemon will work.
2289257 Gave the daemon the ability to post "multipart/form-data", so that it can upload the simulation output to the web server.
955bb18 Connected the daemon to the Pyrized Specfem code; it did a dry run of a simulation. Moved 'Daemon.py' out of the 'web' subdirectory to avoid a name conflict with 'Specfem3DGlobe'.
14da573 Fixed unclosed HTML comment.
8ccc88b Avoid specific fonts & sizes so that the site is readable in all browsers.
a1e017e Changed response of simulation status form to text/plain Python repr() (either 'OK' or errors) so the Daemon can log/parse it.
9fe7b3b Zero "time shift" of CMTSOLUTION, as required by Specfem. Currently, it is not possible to specify a kinematic rupture from the web portal.
90be348 Changes leading up to the first working run of the daemon.
f81d9ca Archive all output files, not just seismograms. Also fixed glitch in Models.py.
1506301 Trap validation errors, log them, and keep going.
a4da5b5 Fixed mislabeled input.
a03a35d Log & keep going if output tarball is missing.
804ed14 updated the copyright information to release version 3.6
e8149b7 changed comments and updated the copyright information to release version 3.6
9e415b1 more updated comments for release of version 3.6
bfaf567 - models.py - removed some models (iaspei, ak135, 3d isotropic) and changed MODEL_TYPES enum values - renamed 'isotropic prem' -> 'isotropic PREM' - renamed 'transversely isotropic prem' -> 'transversely isotropic PREM' - added 's20rts' model
5bdbce4 - model_info.html - removed description for iasp91 and ak135 models
9867d4c - models.py - removed '3d anisotropic' model
35459a1 - model_info.html - fixed a typo (transverserly -> transversely).
a3abbbe Initial re-work of events & stations, in response to feedback from Tromp's group. Users can now upload events and stations, manage multiple station lists, and create multi-source events (kinematic ruptures).
870a306 - models.py - removed 'adjoint' and 'both forward and adjoint' from SIMULATION_TYPES
bc9d6d5 "Surface" -> "Create movie". Hide 'simulation_type'.
d2063f1 Updated get_type_id() to reflect new MODEL_TYPES.
509a14b Removed random garbage inserted by... Subversion?
286ffa0 Fix the inconsistent naming scheme of save_forward_array file
0fcf504 move the scripts/programs directory name to UTILS/
85af046 add utility programs into UTILS/
8647c0f - Added model types (1066a, iasp91, ak135, crust2.0+PREM) and deleted model types (3d attenuation).
c6c737b Removal of myrank variables and general attenuaiton code cleanups
edf6cf9 model options updated: ------------ isotropic_prem transversely_isotropic_prem crust_2.0_plus_transversely_isotropic_prem iasp91 1066a ak135 s20rts 3D_anisotropic 3D_attenuation -----------
b8f8b33 added a comment about the call to read_aniso_mantle_model
aeb8455 add auxilliary programs for
29e249a remove unnecessary temp.m file
01a0844 Added create_movie_GMT_global, and modified the Makefile.in accordingly. Note that this code is not yet pyrized.
3eb3ea5 Moving web portal to its own project directory......done.
3f1889d
2f3ee27 update the output of sr.vtk for multiple sources and multiple receivers.
c47317c fix usage of change_simulation_type.pl
dcf4e77 for the manual: - add kernel figure - post-processing scripts - simpler scheduler scripts
5d6c5f5 modify globe_slice_number.pl to add the calculation of the normal of the source-receiver plane
609efb3 add more comments for the scripts
86593a6 Remove HOWTO, since everything is documented in the manual now.
89c5afa Version 3.5 -> 3.6 on handful more files.
55e1817 add more utility scripts
fa6e2ac remove binary executables from the SVN sever
a4ddc93 modifications to take care of warning message.
fad9eba remove mesh2vtu under DATA/util
ddf86a1 correct scheduler bash file name
d6101fa more modifications
b91f0ac add lsf scripts for kernel simulation
5725b9b fix plot_source_time_function.txt more changes in the global manual
c4e7070 added KoVi98 to list of possible BibTeX references to cite
2c3877f added DOI information to BibTeX references
8b7c75f add bib
59692b6 fix bug in plot_source_time_function.txt
283dc0b fix kernel comments for UTILS/run_lsf
acdf376 fix bug in run_lsf
8bcc70d fix attenuation_conversion(myrank...) bug
0eb5418 filter stations for 1 chunk run
8f64c11 Improved robustness by adding 'preparing' and 'error' states, forking the launch process (which also builds the solver), and putting a try-except around poll().
ea17c3f fix bug in locate_receiver.f90 (broadcast nu!)
2babe6f Added one more state: 'finishing'. The upload of output data at the end of a simulation can take a long time... the daemon needs to fork.
0b5c6a3 Fixed bug in "move old sim dir out of the way" code.
8ab3939 Brought model names into sync with code. Reaffirms my conviction: one language, one code.
5435c55 small modification in Qinya's code to exclude stations that are outside the mesh: I now print a different message depending if NCHUNKS = 6 or not.
4adafbf use PREM to get the density profile for ellipticity and gravity (fine for other 1D reference models)
4537f01 renamed run_lsf to run_lsf.bash
2ef14e7 added code to suppress trailing carriage return (ASCII code 13) if any (e.g. if input text file coming from Windows/DOS)
5a32592 fix globe go script
011074e added support for GNU gfortran compiler
25c865e Fix for different 'flags.guess' behavior when FC is guessed vs. when it is specified explicitly.
fd854b8 Regenerated 'configure' using the latest version of Autoconf (v2.61) so that 'configure' will search for 'g95', and prefer 'ifort' to 'ifc' when checking for the Intel Fortran driver.
e026608 Updated the Pyrization to use the latest and greatest: the newly released (v0.8.1.x), egg-based "CIG Edition" of Pythia/Pyre; and "merlin". (I have not tested these changes yet.)
f4cc9ca fixed bug: gfortran was not correctly detected by "configure"
654570c fix bug 'cut'
aeea044 added to-do list
feb9bc2 updated the to-do list
5dc63c7 added program to convert AVS files containing "quads" to OpenDX format
e9e652f updated the to-do list
f227cd6 added an item about the way we should set the attenuation absorption band
e7edbed added program to shrink elements in an OpenDX file
cd25bc9 updated the todo list
719d45f updated the todo list
f64d397 task reordering
6862ad0 Major Bug fix for Attenuation Code - Now Uses idoubling flag to determine specific region of attenuation - Scaling of Velocities in the Inner Core now uses correct values
8f67e38 modified the todo list
0c1cad3 added handling of First Touch in Linux to todo list
658a9bc added doubling_brick directory to DATA/util
5f08719 updated the todo list
39f035f have changed data reading method. DM.
29ecd9a added scripts used for implementation of the new doubling brick. DM.
abc802d updated the todo list
b96279d moved DATA/util to UTILS
04dd872 moved DATA/oldstuff to UTILS and suppressed DATA/util
3e6016d suppressed a line cut in source code
81e3c46 added scripts to run at IDRIS in Paris (France) using MPI or OpenMP
a34036d updated the todo list
6aa7fa3 added simpler Makefile that does not use "configure", in case "configure" does not give a fully functional Makefile (e.g. at IDRIS in Paris, France)
7040d55 cleaned and improved the LoadLeveler script for MPI runs at IDRIS in Paris (France)
d101c26 added copy of seismograms to LoadLeveler script
49bb737 moved filter_station_list.f90 to UTILS
838cfc1 added data and stack memory limits to the script
55a88ad added automatic handling of current submission path to LoadLeveler script
41d60f3 added serial version of LoadLeveler script
36ffd34 thread-safe modification of the code : all modules have been removed.
ff92e85 improved the LoadLeveler script and added comments
3613f4f fix VTK output bug on the NSOURCES + nrec
b53de39 added some scripts in UTILS
e90e44b changed 3 to NDIM
de317f6 updated BibTeX information
57b5a12 fixed bug in scaling of non-dimensional velocity vector for surface movies
ecaccff updated the todo list
0c5c32c updated options for IBM xlf
5f4bc4c changed options for IBM xlf
468b380 AM_V%Qs is now an integer in place of a double precision
80d9837 MAJ des tâches effectuées par David Michéa au 05/03/2007.
520bfb4 deleted debug lines that i had forgotten. DM.
3412e76 added central_cube directory in UTILS and IC_analyse.pl in central_cube. DM.
db51c0c added two little scripts to visualize inflated central cube. DM.
9017c66 renamed file
479d8ce updated the todo list
4959e8c i have modified define_superbrick.pl in order to add boundaries detection for the superbrick. DM.
2bc1e4b updated the todo list
3a3df35 suppressed an old (and false) version of count_nglob_analytical.pl
74daa84 EXAMPLES/readme
e831524 EXAMPLES/NEX_480/Q
2d8ac45 NEX_480 del
ced9f07 MAJ todo_list
2f63877 deleted the huge EXAMPLES directory (more than 7 gigabytes, including very large binary files) committed by Ying and which made local copies crash
8c81ecf reverted wrong version committed by David following the crash resulting from the huge binary files committed by Ying. The bug was: double precision, dimension(:), pointer :: Qr ! Radius integer, dimension(:), pointer :: Qs ! Steps instead of: double precision, dimension(:), pointer :: Qr, Qs ! Radius and Steps
a35130a changed order of BibTeX information in header of main programs
6a58702 cleaned some Numerical Recipes routines (suppressed some goto's etc)
9037ed3 updated the todo list
622dcff archived scripts and programs used to create the new doubling brick; suppressed old versions
bdbc3c9 again suppressed old versions of scripts and programs used to create the new doubling brick
b9483af added a routine to study radial thickness of the elements in the new mesh; also updated the todo list
1e9e5ef I have changed : double precision :: Qs to integer :: interval_Q in type attenuation_model_variables to avoid confusion with a real attenuation factor.
40544ee updated the todo list
40da6ba updated the todo list
c641b49 committed Jeroen's modifications for gravity in the fluid outer core to fix the small problem found by Tarje Nissen-Meyer
cef0808 added a test to exit if user tries to turn rotation on with gravity off
db2eec0 fixed a bug (undeclared variable) introduced by Jeroen in compute_forces_outer_core.f90 when he fixed the gravity/rotation problem found by Tarje Nissen-Meyer.
9bd0e72 updated comment about displacement potential used in the outer core
fbaaf28 committed new changes made by Jeroen in the fluid outer core with gravity, following a discussion with Tarje about a problem he found.
7ba557e Updated the Pyrization to Pythia v0.8.1.3b2; successful dry run.
92d94d5 release of version 4.0:
f7a6376 Updated the Pyrization for v4.0 and Pythia v0.8.1.3b4; successful run.
a397395 correct values of dT updated for the following cases :
3a96f56 updated DT for 3D case with NEX=320
6aa8f5e added comments to the routine
4cbbca8 changed the first two sections of Brian's 3D attenuation code (out of four sections that need to change)
0d806f3 finished fixing Brian Savage's 3D attenuation code to get rid of the old way of detecting the d80 discontinuity for attenuation
6cda9b3 EXAMPLES directory added
dbc8e96 mv PDF to EXAMPLES
8616a19 mv readme to EXAMPLES
d1ddbf6 mv readme.stations to EXAMPLES
a46ad12 removed unused variables from modified 3D attenuation routines
2ff8bbb suppressed attenuation_lookup_index subroutine by Brian Savage, now unused.
9c98858 updated values of Dt with an additional security margin of 5%. Also updated values of Dt for NEX > 480.
b21af13 Updated for newly-released Pythia v0.8.1.3.
e7914bf fixed bug in specfem3D.f90 : NSOURCES was read by all processes.
cea4641 cleaned the arrays before the gather to fix a problem detected in Vala's NSOURCES_SUB modification
15ee9f8 updated the todo list
716196b updated the todo list
8deace0 added one more comment in the todo list
fdf5d93 changed limit of 100000 sources to 1 million for adjoint simulations
d8e65c4 added files with location of CMB and ICB for gnuplot scripts
bab4e03 added code to display old mesh sampling in v3.6, in order to be able to compare with v4.0
7091f28 values of DT updated.
2b2e882 Removed program 'create_movie_GMT_global' from library.
2f7b40f deleted simpler_Makefile since Leif has now improved the "configure" script
49f7be1 updated the todo list
9521b27 fixed bug in the solver memory size calculation : static_size & dynamic_size are now in double precision.
439e190 fixed bug : declaration of NUMBER_OF_MESH_LAYER in place of NUMBER_OF_MESH_LAYERS
f184f3c added program to test the cache size of a processor and its effect on CPU time
dbbf6ab - suppressed AB, AC and BC chunks in solver - removed old comments left by David - fixed a bug for PREM transverse anisotropy in new d80 mesh layer
c3e0a23 - fixed a small bug (variable used before being assigned a value, but then multiplied by zero therefore no big deal) - suppressed old comments left by David
1a6cf45 fixed a few other small bugs (other variables used before being assigned a value, but then multiplied by zero therefore no big deal)
765d256 removed the redundant calculation of the memory needed for the solver from save_header_file. static_size & dynamic_size are now passed as parameters to save_header_file by create_header_file. Call to save_header_file from meshfem3D use 0.d0,0.d0 as value for static_size,dynamic_size.
934d8c7 added SUPPRESS_CRUSTALMESH flag.
cdd85d3 back to the revision 1345 (r1346 & r1347 overwrite Dimitri's previous modifications)
77f1453 readded SUPPRESS_CRUSTALMESH flag
be81a10 suppressed useless files saved to the disk (and which were not used anywhere anymore)
df9f36e set the flag SUPPRESS_CRUSTAL_MESH to .false. by default.
61064fe added routine memory_eval to compute the amount of memory needed to run the solver. severals dynamic arrays in the solver set to static allocation. modified calculation of NER_80_MOHO in case of SUPPRESS_CRUSTLAMESH = .true. in read_compute_parameters.f90
382d4ad fixed a bug : pasted spaces instead of a tab in a rule
96d4fc5 read_compute_parameters is now called by the master and results are broadcasted to the other MPI processes. removed an unused variable from get_absorb.
d84a84d fixed a minor bug in create_regions_mesh
2c29a9f fixed bug detected at IDRIS in Paris on an IBM / AIX machine: name aliasing such as create_movie_AVS_DX: xcreate_movie_AVS_DX did not work and made "make all" crash, therefore I got rid of the aliases.
9178a44 fixed 2 bugs
a27f453 added parameter ATTENUATION_3D_VAL in values_from_mesher.h, replaced ATTENUATION_3D by ATTENUATION_3D_VAL in the solver.
e8f78b5 renamed parameters from save_header_file : PARAMETER_ become PARAMETER_VAL yet.
f5319c0 renamed model name : 3D_crust_2.0_plus_transversely_isotropic_prem by transversely_isotropic_prem_plus_3D_crust_2.0
01dfe0b replaced variables in if statements by precalculated parameters of values_from_mesher.h for code which belong to the critical part of the code (time loop).
97f6117 fixed bug in specfem3D.
91ec140 Fixed Pyrized build w.r.t. recent Makefile changes.
731a9d1 changed -O2 to -O3 for pgf90
09b58df Removed old html templates.
de39dc4 Bumped version number in configure script.
acbfc81 changed some default options in flags.guess
cdbf816 changed some default options in flags.guess
054ac4d Regenerated 'configure' (it was bogus).
fe4d28a better versions of LoadLeveler submission scripts for MareNostrum (IBM Power in Barcelona, Spain)
54207c2 added a system call to clean the local scratch space on MareNostrum (Barcelona, Spain)
d3f1fc4 modified prompt in bash_profile
1aba85e Turned the 'flags.guess' case statement inside-out so that it switches on compiler, then on OS/platform (instead of vice-versa). This allows e.g., xlf95 to be recognized on both AIX and Linux. (The only ambiguous compiler command name is 'f90', which is assumed to be different compilers depending upon the platform.)
8686aaf removed call to MPI_FINALIZE
fb3894f modified the todo list
dc27efe added -qflttrap=en:ov:zero:inv to the IBM options
b1f8d8f changed -qnostrict to -qstrict for IBM
9006004 added -mcmodel=medium for Intel ifort, Portland pgf90 and gfortran
20e9046 suppressed -mcmodel=medium as a default (because may be slower), but left it as a comment; added -i-dynamic for Intel ifort
e42be79 updated the todo list
7446af0 bug temporary fixed : anisotropic elements are created first again yet, should write something more general later because of the problem of cuthill McKee sorting.
457de7e fixed bug in specfem3D : source line truncated l1643
745ab47 Fixed r1433.
7d45d58 removed useless UNUSED_compute_field_gradient subroutine
fbdef6a added system call to suppress local directory at the end of the simulation on MareNostrum
99c3d9a added output of information if it == NSTEP
aab9a1c - added sorting of ibool to reduce cache misses; performance improvement is very significant (factor between 1.5 on most machines and 3.3 on some) - added cleaning of /scratch disk space on MareNostrum in Barcelona - suppressed MPI_FINALIZE from exit_MPI
af395b9 added -q64 for xlf
c0929b1 modified access to /scratch on MareNostrum in Barcelona
b742fde Addition of radial meshing for single chunk widths less than 90 degrees and for chunks greater than 1248 elements wide.
3a1a1e7 correction of the bugs announced by Qinya, adaptation of the DT for NEX=160 (simulation became unstable with the topography flag on)
f5c69ed updated the todo list
fa4456c updated the todo list
fa1ab0c updated the todo list
095c67c updated the todo list
aa9b5c3 updated the todo list
36f1bf5 fixed compiler warning in Qinya's code to display the mesh topology when NCHUNKS < 6
60f6fbb converted single precision to double precision everywhere, and %g to %lf in scanf statements
3ecd77b converted hprime derivation matrix to its transpose to conform to usual definition as in Deville et al. (2002)
9380011 - 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
5513037 Updated Pyrized version w.r.t. bernhard's r1529 changes.
b2f6592 main commit of modifications done during our stay at the BSC to optimize the code.
b3d3208
e6f8a4e 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.
9c9dd69 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.
ce66fbd Minor modifications to the Par_file, read_compute_parameters.f90 and add_topography_410_650.f90.
3447737 converted Harvard model s362ani Fortran77 source code to Fortran90
9ca78fc Moved the new f90 source code for the 3D model S362ANI to s362ani.f90 and fixed the Makefile.
cb1e840 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.
499beac deleted useless examples; kept only one
b4611ee moved some example files
ad95cb7 updated the todo list
9706a0d updated the todo list again
9f13b13 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.
9474706 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.
0b1b772 renamed IFLAG_IN_CENTRAL_CUBE to IFLAG_MIDDLE_CENTRAL_CUBE everywhere. Also removed useless white spaces at the end of all the lines.
9f87ec8 updated the todo list
8d91def Renamed add_topography_moho.f90 moh-Stretching.f90, since what the routine does is stretch th moho, not honor it.
4402f4c changed the name or spelling of some flags in constants.h, changed some comments as well, and updated the todo list
cae4f37 suppressed 3dmodl.h and mod.h because they contained "common" blocks; now use regular subroutine arguments instead
aecc053 moved program_test_s362ani.f90 to UTILS/s362ani
7a6a96b added MPI_BCAST to Jeroen's routine to read the new Harvard model, and inlined some model definition statements
eb7fab7 moved files to UTILS/s362ani
bcfdc29 renamed file
40a3bee changed program name and path to data file
22505b2 updated the Makefile
1b7b3b9 updated the todo list
4733775 removed unused variables
57927fa used array constructors instead of inlined array indices to define the model in order for the code to compile much faster
97c8537 reverted Jeroen's changes for points at the ICB or the CMB because my original code was correct; added a more precise comment about this
a35cf5a added #include <stdlib.h> to suppress a warning about "exit" being undeclared
a71bd1f merged calls to assemble_MPI_vector for crust_mantle and for the inner core in one call in order to divide the number of MPI messages by 2; updated the todo list
4640db6 changed some variable names that were longer than 31 characters
8a1f17b suppressed unused getcurrmodels subroutine, which produced compilation errors with IBM xlf
a7fe66e also suppressed unused putcurrmodels subroutine, which produced a compilation error with IBM xlf
3f8aa05 fixed bug in second call to assemble_MPI_vector in specfem3D.f90; updated copyright information in write_c_binary.c; added comment about options for the C compiler on IBM in flags.guess
bd08107 made a comment for IBM xlf with xlc or gcc more precise
fc65ff1 Fixed a small bug in the assignment of REF radii near the ICB and CMB in model_ref.f90.
2956d37 Converted read_compute_parameters.f90 to its previous state.
deff806 updated the todo list
9c7a4c9 updated the README file and deleted obsolete text files
1f0e86f added a test in create_regions_mesh.f90 to completely suppress Cuthill-McKee sorting if needed; updated some comments; removed useless white spaces in C codes
1ded4f9 renamed a few variables and updated several comments
ada8a31 fixed a bug introduced by David Michea about dummy variables to call read_arrays_solver that were declared with a real size (i.e. large arrays wasting memory) instead of a small fictitious dummy size.
1c662ac - fixed bug in David Michea's routine to compute static memory size: all the numbers needed to be in double precision to avoid integer overflow - removed dynamic memory size calculation (which was too complex and not crucial) - converted all memory sizes displayed to gigabytes rather than megabytes - updated some comments - updated the todo list
71018f5 cleaner implementation to assign mesh parameters in the case of PREM, PREM_one_crust or a 3D model
f943212 fixed a bug in one of the static memory size estimates
fe93d59 rho_vp_crust_mantle, rho_vs_crust_mantle and vp_outer_core are now allocated only if absorbing conditions are used; rmass_ocean_load and updated_dof_ocean_load are now allocated only if oceans are used
1bff810 reverted attenuation routines back to v3.6 because new routines in v4.0 did not work
6b7dc7a - went back to attenuation v4.0 even if it has a bug, because switching back to attenuation v3.6 did not work either - suppressed dead code and dead routine in Brian Savage's attenuation routines - removed unused variables - added the LSF scripts to the main directory
a41bae9 - fixed incorrect index flag calculation in get_attenuation_index - fixed missing parentheses around IFLAG_220_80, which induced incorrect comparison - suppressed useless external read_crustal_model,read_mantle_model, crustal_model etc. - use f90 syntax everywhere instead of f77 syntax for comparison operators
6b73f96 updated a comment
02cb8de fixed the allocation size of eps_trace_over_3_inner_core and b_eps_trace_over_3_inner_core, which was NSPEC_CRUST_MANTLE instead of NSPEC_INNER_CORE, thus wasting a lot of memory
bc6b903 removed unused commented lines
2c134e2 removed a comment
73c5fa1 updated the todo list
4718b3a updated the todo list
14b594b removed a useless print statement left by David Michea
34efa21 suppressed two problems with variables used before being assigned a value
4e4e51c avoided automatic creation of a dynamic array when calling pspline() with a sub-array
956cd21 removed FINAL argument
6537ac1 fixed a misplaced if statement that created a deadlock when intermediate seismograms were saved to disk; also used a local variable to make RECV statement clearer
85c1896 updated the todo list
48352e7 added output of more detailed information about memory consumption per node, and added output of total number of time steps
bb02aee added comments about the (chi/rho)grad(rho) term added by Jeroen in the fluid when gravity is turned off
163d4f6 added missing spaces for arguments of shmux command
1936bb5 Fixed a mismatch between types in gt3dmodl and rd3dmodl.
a62aafe replaced nspec_reg with NSPEC(iregion_code) for clarity
fa11659 added more options for IBM xlf
9d0a0b3 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.
0231e1c added STATIONS_SUBSET_35
9f2b789 added more details about optimal memory size at Caltech and BSC
0d2bbda changed /scratch/komatits to /scratch/komatits_new because of write permissions related to new account on MareNostrum in Barcelona
5ea7354 moved these lines:
d7108ab now create the mesh in each region in two passes to save memory and use approximately the same amount of memory in the mesher as in the solver (the mesher used to use a lot more than the solver and be the main limitation in terms of memory on a given machine)
64ca2fc removed storage of the determinant of the Jacobian matrix (array jacobianstore); it is now recomputed every time it is needed in order to save memory
f77f640 added more precise timing information
3c54513 added a few white lines to the output of timing information
a1f4f57 changed "total time" to "total run time" in output
58b1d3b Properly initialized "gamma" in add_topography_410_650.f90. Moved to static memory allocation for the SAVE_STRAIN arrays.
2c685fd replaced Ying Zhou's v3.6 examples with Anne Sieminski's v4.0 examples
bd19dba fixed the bug I introduced in one of Brian Savage's attenuation routines in release 1688: one of his parameters was used as both input and output, not input only
406d962 Changed the adjoint arrays from dynamic to static. Needs to be carefully tested by Qinya & Anne.
153fa8f More modifications associated with the (static) adjoint simulations. Now the code combine_paraview_data.f90 still needs to be fixed to read the new *_solver_data_1.bin files.
00a7d86 Modified combine_paraview_data.f90 to accommodate the new *solver_data_1.bin files written by the mesher and solver. This meant getting access to ibool and xstore, ystore & zstore is a bit more tricky. Qinya should check carefully...
8f92288 - 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
e4eece4 updated the todo list
87d1693 Changed the convolution for a Gaussian to be consistent with the new convention.
eb2caa8 better explanations about the decay rate when convolving with a Gaussian
5d82c1d made the convolution routine run faster
4890c93 fixed a small bug: N_j was too small in the case of a Gaussian
3bfe83d updated the todo list
db2a59b commented out an option for IBM xlf that slowed down the code
64a047e added a program to generate a list of stations every half degree along a great circle
d8c0c34 updated the todo list
93f5b21 better programs to create a station list for a great circle
a1f94a4 updated the todo list
d4cce27 removed two obsolete lines that were commented out
81bfa37 - 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
6910d89 added option to save all the seismograms in one large combined file to avoid overloading of shared non-local file systems such as GPFS
6f21050 updated the todo list
908b8fd added programs to convert from strike dip rake to CMTSOLUTION or Aki/Richards convention for moment tensors
db395f1 fixed a bug in save_arrays_solver.f90 for simulations with NCHUNK=1
f63c26f added control of multilevel cuthill mckee by the flag MULTI_LEVEL_CUTHILL in get_perm_cuthill_mckee.f90
f42607d removed debug lines i had forgotten.
45cd00a todo_list updated
c16b923 added calculation of the average size of a spectral element along the surface
1397b7d changed 1.6 GB to 1.7 GB in memory estimate for MareNostrum
7c87105 added program to extract individual seismograms when they are stored in one large file
2d78230 updated copyright information for future release of v4.0 on October 9, 2007
013603d added cleanup for the nodes before and after the run
94d10c0 added SUPPRESS_CRUSTAL_MESH flag. Supported by models : prem, ref, 1066a, iasp91, ak135
adaae34 put correct copyright information again (it had been erased by David Michéa)
4da938e updated the todo list
a9fba20 fixed some minors problems in read_compute_parameters.f90 : DT & NER_CRUST for 3D models
51d08bf added references in which the formula to scale mu to the right reference frequency can be found
2bd2f53 added references in which the formula to scale mu to the right reference frequency can be found in a second routine
67776b6 Update of the 3D Attenuation routines for Version 4.0
1bff9ce fixed a small mistake in a print statement
9e9c6d4 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
e8e58c0 fixed a bug i had introduced in read_compute_parameters.f90.
7e2724c fixed a bug for absorbing conditions : file (prname)_stacey.bin read by the solver was not created by the mesher. bug introduced when I have gathered the small *.bin files in larger files in the r1300 (first release of v4.0)
b92d5d6 Update of the Radial Auto Meshing for Version 4.0 This should affect runs with Single Chunks less than 90 degrees and Chunks with NEX > 1248
4049b2b Forgot to remove a write statment, oops
e15e0e1 Min and Max Attenuation periods should now be computed using the routine auto_attenuation_periods() in auto_ner.f90 The value of ATTENUATION_RANGE_PREDEFINED will determine if the older pre calculated period will be used (.true.) as opposed to those computed on the fly (.false.). Values are computed on the fly as the current default.
07b71da Changed model_ref.f90 to replace the ocean layer with upper crust. This solves a problem associated with attenuation.
958973e added a program to plot seismograms as record sections with "Grace" (formerly "xmgr")
d2ad06b changed grace to xmgrace
11257d6 updated the todo list
d0ff126 - updated the manual - added a program to create the table with NEX values in the manual automatically - updated the todo list - added comments to read_compute_parameters.f90 - removed "collect_seismograms" from the LSF scripts
3dd607d added program to draw regular 2D GLL element using Gnuplot for articles or presentations
9e6cd4e fix A bug in ACTUALLY_COUPLE_FLUID_ICB, and change vx,vy,vz to displ_x, displ_y, displ_z.
dde0c13 Added small single chunks for specfem v 4.0 Attenuation periods now are computed automatically for all chunk sizes and chunk numbers
a4b8111 improved the test to check that the block size is a multiple of 32: can now be 16 when one suppresses the crust with flag SUPPRESS_CRUSTAL_MESH
ded627b the seismograms are now appended and not rewritten entirely each time.
d8f66f1 Fix a bug in the process of reading adjoint source by blocks: giving the right dimension to adj_sourcearray in compute_arrays_source.f90 adj_sourcearray(NTSTEP_BETWEEN_READ_ADJSRC,NDIM,NGLLX,NGLLY,NGLLZ) instead of adj_sourcearray(NSTEP,NDIM,NGLLX,NGLLY,NGLLZ) where NSTEP=iadjsrc_len(iadj_block)
be17cfb fixed the bug about rho_vp & rho_vs calculation (both are passed in the argument list of compute_element_properties())
ee1078a Write out DT information after NSTEP to output_mesher.txt.
9ef421f added program to generate the STATIONS file to include stations every 0.1 degree along one-fourth of a great circle
8fa4f21 changed from formatted to unformatted input
cfcd019 cleaner way of storing all the seismograms in one large file, and added option to store them either in binary or in ASCII
3ee09f2 added more details to output of text messages
bbff963 fixed a bug in read_compute_parameters.f90 when auto_ner is called and NER_CRUST<2
3a8f2f0 removed element sorting in get_MPI_1D_buffers.f90 get_MPI_cutplanes_*.f90 get_jacobian_boundaries.f90.
c878b6a updated the todo list
980e48d 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.
40ac345 updated the todo list
f38ebff Change the license to GPL v2+
c6bc43a updated the copyright information from October 2007 to November 2007
0cea276 updated the todo list
0e3d022 fixed a bug in the path of the large seismogram file when SAVE_ALL_SEISMOS_IN_ONE_FILE is used
763e64a Adding boundary kernel computations: constants.h.in -- add logical SAVE_BOUNDARY_MESH create_regions_mesh.f90, get_jacobian_discontinuities.f90 -- compute mesh info for Moho, 400, 670 save_header_file.f90 -- save NSPEC2D_Moho/400/670/CMB/ICB to values_from_mesher.h specfem3D.f90, compute_boundary_kernel.f90 -- compute boundary kernels for Moho, 400, 670, CMB, ICB read_compute_parameters.f90, create_movie_AVS_DX/GMT_global.f90, check_buffer_faces/corners_chunks.f90, create_buffer_1D/2D.f90, combine_AVS_DX.f90 create_regions_mesh.f90, create_header_file.f90 -- add HONOR_1D_SPHERICAL_MOHO to read_compute_parameters(), therefore update all the subroutines that call it.
0d8ceb1 updated copyright information
e739c47 Clean up the utilities and organize them into directories, such as Paraview, collect_database, seis_process.
1517dbe - 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
53cb50b broadcast of SAVE_ALL_SEISMOS_IN_ONE_FILE from the master to the nodes : needed if RUN_ON_MARENOSTRUM_BARCELONA = .true.
468edc5 update of todo_list
306f6a6 fixed an error i have introduced in the last commit
4d93995 Set SAVE_BOUNDARY_MESH to be false by default.
ae31eaa added a command to clean the local /scratch space before starting the simulation when one submits a job
02367dd recommit of bug correction previously committed in R1884.
3e6fab8 replaced erf() from Numerical Recipes with erf() from Netlib.
2dd74f3 added CNRS to copyright information
41cee36 added CNRS to copyright information
4c6f063 renamed numerical_recipes.f90 to spline_routines.f90 to avoid copyright problem
3a1408a combined the two shmux commands
b696ced removed an empty line in the script
8824a23 modified the spline routines in order not to use the copyrighted version from "Numerical Recipes"
ef3fc9e added email from Jack Dongarra as a comment at the end of the Netlib routine
19a258f fixed naming of end subroutine call away from pspline and psplint to match the previous fix by dimitri
4888ac8 updated the README file
d533075 created an explicit copy before argument passing to avoid warning in create_header_file.
2645626 - modified clean_sac_headers_after_crash.sh to also run with alphanumeric SAC files.
e220869 fixed bug found by Qinya when NEX_XI/NPROC_XI = n*16 with (n>2 and mod(n,2)!=0). reduced DT for NEX_XI<=480 : 0.12 -> 0.11 because simulation was unstable.
48cf09e Fix the bug at checking the top and bottom of discontinuities: save the radii of the nodes before entering compute_element_properties()
d411700 updated the todo list
c34733c update combine_vol_data.f90 to allow different dirs for topology files and kernel files.
f55a248 todolist updated
da7e957 Delete testing comments in combine_vol_data.f90 and combine_surf_data.f90
b7f6fd9 Added an opendx program with an example file to visualize the valency in term of MPI procs of the central cube points. It was used to debug the assembly of the new shared central cube.
56ee166 merged writing of temporary and final seismograms
27d6669 updated the todo list
3bec317 suppressed the "DONE" section in the todo list
a5652ec fixed bug in syntax of MPI_ABORT. also removed some white spaces in the Makefile.
53196da fixed a small problem for the pgf90 linker
2e99ac8 quick fix by Brian Savage to solve the ScS bug; change committed by Dimitri; Brian will implement a cleaner solution in the next few weeks
ba82953 fixing the bug of calculating the div_s and b_div_s in the outer core.
c38f51d 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.
410438c added a trick to try to avoid slow runs on "pangu" at Caltech
bf81bdf better version of the trick to try to avoid slow runs on "pangu" at Caltech
87651e1 changed "sleep 300" to "sleep 30" because 300 does not prevent slow runs from occurring on "pangu"
ffbb433 added calculation of approximate date and time at which the run will finish
8502545 improved the output format
698e259 put "sleep 200" back
e2f87a4 updated comments and added indentations
c488edc change NSPEC_STRAIN_ATT to NSPEC_STR_OR_ATT
ae55ff9 added date and time estimate of end of run at a remote location, in addition to local time
2982d78 changed 9 to +9 for time difference to illustrate the fact that it can be positive or negative
b914f8c removed empty line
98ce12c suppressed output of date and time estimate of end of run if last time step
eea76f4 added "in remote time" to print statement
94f2dd4 added correct (complete) detection of leap years
3546c0e - 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
97c3836 suppressed nrec_dummy
f71a95b In order to reduce the bottleneck it occurs in the MPI communication pattern, the central cube is now split and shared between chunk AB & chunk AB_ANTIPODE.
3639fc1 Modify UTILS/Paraview/global_slices_number[2].pl to reflect the recent changes Dimitri made on the format of the STATIONS file.
582eb80 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.
79c34ce fixed small bug: missing parentheses
958dd93 updated the todo list
735fb88 fixed minor typos and removed old comments, useless white lines and white spaces
86e1917 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.
29767ad Suppressed the fourth doubling layer. Added a flag SUPPRESS_4TH_DOUBLING = .true. by default in constants.h to do so.
dc8b165 updated generate_table_NEX_manual.f90 in order to take into account the 3 or 4 doubling cases.
1f778f6 minor correction
82ba428 replaced SUPPRESS_4TH_DOUBLING by .not. ADD_4TH_DOUBLING
65c7d34 removed an old irrelevant test.
1ce2f8a made several changes in the manual and created a better table with more values
40c4b1e better algorithm to compute the loop on variable "c"
d8e1c3f improved output about positive or negative time difference for estimate of date and time of end of run
06b29f6 fixed a typo in a comment about the definition of the potential in the fluid when the Cowling approximation is used
905152c added test for negative maximum value to detect if the simulation became unstable, because can happen with some compilers
8a121c3 Fixed NSOURCES_SUB "gather failed" bug in Vala's code, detected by Jeannot Trampert. Also removed useless empty white spaces.
9d7510e cut lines that were too long
ae22f0a moved the line that cleans a temporary array to after allocating it (!!)
e0e5657 updated section 9 of the manual (about changing the crustal, isotropic mantle and anisotropic mantle models), and updated some comments in the code accordingly
db0b397 Added the option to output displacement and velocity in volume
c1c606b fixed the last small problems detected by Vala (including an allocate statement that was far too big for the seismograms, and a problem for station H2O in RECORDHEADERS)
197a15c added comments about MPI_BCAST of model structures in the code and in the manual
f903c34 use dynamic allocation for array one_seismogram
75693b1 changing output file name for movie volume, displacement and velocity
4ac67d0 added test about modified NTSTEP_BETWEEN_OUTPUT_SEISMOS
a94f03d updated the todo list for a future version 4.1
b1315d9 added test to allocate statements for seismograms to detect if out of memory
d26c1b7 - committed the new PKP figure - moved the scripts to directory UTILS and suppressed duplicates - updated the manual accordingly
cb8d782 updated some job submission scripts
dd053b8 added INRIA to copyright
c2dced0 updated the copyright header, which was obsolete for this file
9af76da removed a useless comment
1059245 Created snapshot of svn:externals.
308022d Created SPECFEM3D GLOBE v4.0.1 tag by diffing with the tarball. The release appears to be a backport of r11780 (which can't simply be merged because of conflicts).
651823f Merged my post-v4-release portal-related Makefile/build changes (r11183, r11236, r11263, r11271) to create the "v4.0.1-portal" tag. This is the version of SPECFEM3D GLOBE used by the portal.
fac8c40 Created SPECFEM3D GLOBE v4.0.2 tag, which incorporates the attenuation fix described by Vala.
17a6145 Created SPECFEM3D GLOBE v4.0.2-portal tag.
a74bccd fixed the CASE_3D flag for the OCEANS; also improved the compiler options
e23cc36 Created SPECFEM3D GLOBE v4.0.3-portal tag.
5553c0d fixed a small bug I had introduced in flags.guess: one line had been removed for NEC SX
52e4daf Merged r13128 from v4.0.3.
e0e894f Began the "pluggable earth models" project. This is based upon the v4.0.3 snapshot.
93686cb Partitioned models into subdirectories. Corrected a mistake I made in get_model().
3500df5 Factored-out 'anisotropic_mantle_model.f90' into a third 3D mantle model, 'Montagner', after discovering that ISOTROPIC_3D_MANTLE and ANISOTROPIC_3D_MANTLE really are mutually exclusive, as one would expect.
3135e94 Eliminated most remaining references to THREE_D_MODEL. Resurrected data files for models s362ani_prem, s362wmani, s29ea. Pushed s362ea code into a 'common' subdirectory, so that I can use svn:externals to create mirror reflections of it. Created a dummy mantle model, '3D_mantle/none', to be used when there is no 3D mantle model.
654811c Added get_model_properties(), thus eliminating the last remaining references to REFERENCE_1D_MODEL and THREE_D_MODEL, and also eliminating MODEL. The selection of a 3D mantle model determines the 1D reference model; updated the makefiles to reflect this. Added "mirrors" for s362ani models, and prepared s362ani for mitosis. Added 'blank' model to document the interface.
3ab0a83 Cloned & specialized s362ani.f90 to create s29ea.f90, s362ani_prem.f90, s362iso.f90, and s362wmani.f90. Thanks to the mirrored 'common' directory, the code duplication here is minimal.
a83e179 Resurrected the model 'transversely_isotropic_prem_plus_3D_crust_2.0', because it is offered as an option by the portal (under the name "crust2.0+prem"). From the plug-in perspective, this particular 3D model is basically a no-op, since it sets both ISOTROPIC_3D_MANTLE and ANISOTROPIC_3D_MANTLE to false.
3524a85 Updated the code to use downloaded 3D earth models. Added symlinks to 1D ref models. Wrote a makefile which creates the predefined models.
c9c28b9 Allow users to define their own crustal model.
e6acd58 First draft of generic model data broadcasting routine.
ed172c5 Changed Fortran code to use generic model data broadcasting routine.
3a94f3e Fixed bugs: SIGSEGV caused by bogo proto; trim whitespace from LOCAL_PATH; bad permissions on local copy of broadcasted "model.tgz".
cabf219 Allow this portal-centric version code to be configured normally, for debugging purposes. E.g.:
ef0fe5a Allow C source files in pluggable Earth models. Wrote blank C versions of read_3d_mantle_model() and iso_mantle_model() as examples.
494f617 Added "intent" attribute to subroutine arguments, so that I can safely reuse compute_coord_main_mesh() to get domain bound of current processor before the mesh is created.
94d54c9 Moved the computation of rotation matrix forward. The rotation matrix is needed when calling compute_coord_main_mesh().
276f696 Cleanly separate the subset of model plug-ins which is a dependency of the serial codes. The three plug-in routines called from read_compute_parameters() -- get_model_properties(), get_reference_1d_model_radii(), and reference_1d_model_adjust_time_step() -- must reside in a source file that ends with ".serial.f90" or ".serial.c". The code in "*.serial.*" source files cannot use MPI.
518b6fa Removed unused 'build.mk' files.
943369b Added model plugin support API.
cfc20f7 MODEL can now point to a '.tgz' file.
f6af102 Added model API routine finalize_mantle_model().
669a62f Here is a solution to the "huge model file MPI_Bcast problem", based upon a suggestion from Eh. The "prepare-model.py" script now constructs a special "tgz" file specifically for MPI_Bcast: "bcast_model.tgz". This "tgz" file is basically a copy of the original. However, any subdirectory named "shared" in the original "model.tgz" file is excluded from "bcast_model.tgz". In "bcast_model.tgz", the "shared" subdirectories are replaced with symbolic links which point to the corresponding original subdirectory (from the initial extraction) on the global, shared filesystem.
1845627 Fixed a bug of acessing uninit'd variable
738a60b Merged r13698 bug fix from tags/v4.0.3-portal:
8d1548a translating @THIS_DIR@ in .h file as well.
af1ef2f Incredibly, Fortran 90/95 limits identifiers to 31 characters. Intel's ifort enforces this when given "-e03", which is included in FLAGS_(NO_)CHECK by 'flags.guess'. I renamed various pluggable earth model API routines accordingly.
bb6971b Add my replacement of asc2sac
384ec0e saving as evenly spaced SAC file
ff3481c add get_Sac_header.c to read SAC header from command line
6acef25 Add convolve_stf.c, not working yet.
7d89cb3 Replacement for convolve(). Uses fft() from SAC.
65cbb76 No need for undef, eps.
fa4caa5 Initial configure script generated by 'autoscan'.
08b5b73 Created proper Automake makefile and configure script.
c973ab5 Add license and usage
aa807d5 deleted get_sac_header.c
cb2d619 deleted get_sac_header.c
499e78b removing hard-coded path. sac2000 -> sac
8a65149 Removed most hard-coded paths from Perl scripts.
51df396 Using long int instead of int to be compatible with SAC. Scaling the result.
6cf4045 Removed silly shell script ascii2sac.csh (its functionality has been incorporated into "asc2sac.c").
d7a8c07 Added a configure test to check whether SAC uses 'int' instead of 'long' in function prototypes. The current v101.3 (and later?) uses 'int'. This was probably the most recent change listed in CHANGES:
0a0011a Code to C89 for portability. Avoid fixed-length buffers. Take advantage of realloc(), everybody! [Standard says, realloc(NULL, n) is equivalent to malloc(n), and free(NULL) is a no-op.]
ec3cf48 Several fixes, mostly having to do with SACAUX.
8374c62 Removed phtimes
1e01579 Assuming origin time is 0 if undefined in SAC file. SAC will still print an ugly error message though.
acb2ea9 Add HDUR to -h. This allows me to always convolve with finite duration while my CMTSOLUTION is a step function. Fix the usage string.
d329eb8 Better message
30afc3d add simple installation instruction and usage
a89fc17 Metioned that programs are installed in bin/
94deefb calling convolution program after closing sac to avoid racing condition
1ec5904 update end time in header
77d3ff8 Fixed a scaling error in convolution.
8fdcd5b Partly revert r14964. Added example usage.
99d99a4 Released v1.0.1.
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