[cig-commits] [commit] master's head updated: fixed a typo in the manual and in my notes (8430778)

[cig_noreply at geodynamics.org]

Repository : https://github.com/geodynamics/specfem2d

Branch 'master' now includes:

     ca0d66a added another comment about 2D sources to the manual
     b57ef60 Merge pull request #19 from komatits/devel
     a766a0d fixed test on N_SLS when attenuation is off to use 2 instead of 1
     24dca31 Merge pull request #20 from komatits/devel
     1958ca1 doc: Remove broken LaTeX commands.
     f056c19 doc: Remove unused commands and packages.
     c5eeb87 doc: Really center front page figure.
     19bc806 doc: Convert workflow figure to vector format.
     66e7126 doc: Convert PML figure to vector format.
     ae96bca doc: Cleanup some LaTeX oddities.
     82b08d5 doc: Turn Carcione reference into a real quotation.
     5fdd862 doc: Replace lyxcode environment with verbatim.
     73e795f doc: Remove some TeX style formatting.
     02e4ff9 doc: Itemize example citation list.
     35bb3c2 doc: Remove extra newlines and unindentations.
     96d47dc doc: Remove mention of old todo list.
     b45869a doc: Re-establish some sections in the ToC.
     c11f41c doc: Use AMS's align instead of eqnarray.
     538db8c Update Inria spelling.
     fcd0a23 doc: Remove duplicate/unused logos.
     700dd71 doc: Spelling and grammar fixes.
     6642e1d doc: Try to use consistent formatting everywhere.
     ec60437 doc: Remove reference to old SVN location.
     a388031 Merge pull request #21 from QuLogic/docs
     88b981f better scan of Pilant (1979); can go into master branch as well because source code unchanged
     d1837bc Merge pull request #22 from komatits/devel
     a8d9a61 added a sentence about Zlib -lz to the users manual
     5729b51 Merge pull request #23 from komatits/devel
     57a15de renamed QUART to QUARTER
     594a714 Merge pull request #24 from komatits/devel
     84cb404 - added a print statement to prepare_color_image if the code detects that the image is too big - increased the image size limit to 10000 pixels in each direction - added a small Fortran program to create a pseudo plane wave source based on tapering with a Hamming window - fixed the "Number of absorbing elements" print statement bug: this should not be printed when PML is on
     3bae725 Merge pull request #25 from komatits/devel
     037544b removed USE_GUENNEAU
     d1a2dd7 removed USE_GUENNEAU
     cdb75e3 Merge pull request #26 from komatits/devel
     5db0729 suppressed ipass, PERFORM_CUTHILL_MCKEE, ACTUALLY_IMPLEMENT_PERM* and FURTHER_REDUCE_CACHE_MISSES, which were making the code too complex with no significant performance improvement. Also suppressed GENERATE_PARAVER_TRACES, which is not used any more.
     51f3e6f Merge pull request #27 from komatits/devel
     bde4bf2 removed CUTHILL_MCKEE from DATA/Par_file, removed unused variables at the end of setup/constants.h.in, and created an empty OUTPUT_FILES/ directory because it is required by the solver
     bb0020b Merge pull request #28 from komatits/devel
     df613b7 fixed some typos found by Alexis Bottero
     7c3de41 Merge pull request #29 from komatits/devel
     ac69638 better (more general) implementation of periodic boundary conditions; currently work fine for elastic media and serial simulations only, will add support for acoustic media and for MPI later
     b662f42 Merge pull request #30 from komatits/devel
     6c1775f added support for acoustic media for periodic boundary conditions
     6031c13 Merge pull request #31 from komatits/devel
     9a04018 added a comment in DATA/Par_file, and fixed a typo in src/specfem2D/specfem2D.F90
     6c511ae Merge pull request #32 from komatits/devel
     733fd3a updated the README file
     83fd4ee Merge pull request #33 from komatits/devel
     c3c2646 fixed some typos
     6022c48 Merge pull request #34 from komatits/devel
     63606af swapped two sections of the global point numbering code to avoid potential problems
     f9d070c Merge pull request #35 from komatits/devel
     022fc27 improved some comments
     29e6a86 Merge pull request #36 from komatits/devel
     52aa46b done implementing support for acoustic elements in periodic boundary conditions
     e8507f7 Merge pull request #37 from komatits/devel
     fbc32aa made the implementation of periodic boundary conditions more general (more flexible). They work fine in the serial case. I will add MPI support tomorrow.
     065f6d2 Merge pull request #38 from komatits/devel
     cf40549 fixed an important bug in the call to compute_pressure_whole_medium()
     def0803 added a test to check that the CPML flags read from an external file make sense, and call a stop statement otherwise. Also improved a few print statements and a few comments.
     9231451 Merge pull request #39 from komatits/devel
     15a0c3b added an option (in setup/constants.h.in for now) to display the PMLs in a different color in Postscript vector plots. This option could/should be moved to DATA/Par_file one day.
     3601a7a Merge pull request #40 from komatits/devel
     7b5d519 avoid an edge effect if the PML color number is too high for the display
     199590f Merge pull request #41 from komatits/devel
     4943efb improved a comment
     55fb671 Merge pull request #42 from komatits/devel
     c4113dc removed three unused routines (Alexis Bottero had noticed that they were unused)
     1ce526c Merge pull request #43 from komatits/devel
     3e66632 avoided a potential side effect for array "rmemory_fsb_displ_elastic" owing to some "if" statements: the array was sometimes unallocated
     f553d8d Merge pull request #44 from komatits/devel
     8219b7f updated and cleaned some comments
     be22c3f Merge pull request #45 from komatits/devel
     d927f9d done porting periodic boundary conditions to MPI
     9fff280 Merge pull request #46 from komatits/devel
     e76402e fixed all the warnings found by the new Intel compiler option -gen-interface -warn all
     ab3e0a1 Merge pull request #47 from komatits/devel
     4a31b45 changed -gen-interface to -gen-interfaces
     0ce656a added removal of *__genmod.f90 to "make clean"
     cf6e274 put two erroneous statements in Zhinan Xie's PML code back purposely because otherwise the PML code blows up; I am going to contact Zhinan to see if he could fix that
     e1f096d Merge pull request #48 from komatits/devel
     5bc7e3a fixed a bug I had introduced in src/specfem2D/enforce_acoustic_free_surface.f90 when I added a logical flag to check that the edge does not also belong to a periodic interface: the array was declared of size 1 but used with size NGLOB when periodic conditions were off
     b42d70c Merge pull request #50 from komatits/devel
     cdc6cb7 Zhinan fixed the real(kind=CUSTOM_REAL) vs double precision problems that remained in his CPML code and made the CPML code become unstable in some cases
     de5c111 Merge pull request #51 from komatits/devel
     c1cef4c updated some comments in configure
     b53b82d Merge pull request #52 from komatits/devel
     2f63f43 updated EXAMPLES to the right version
     bc218de Merge pull request #53 from komatits/devel
     3ba6b0e switched to the current version of the EXAMPLES submodule
     a894e25 Merge pull request #54 from komatits/devel
     2337e21 switched to the right version of the EXAMPLES; and fixed a small bug in the allocation of is_PML(), which is used in plotpost.f90 even when the PMLs are off
     9e800f8 Merge pull request #55 from komatits/devel
     ed3167e updated some comments in src/specfem2D/specfem2D.F90, and switched to the right version of the EXAMPLES
     3d0000c Merge pull request #56 from komatits/devel
     1ea8fc3 added Alexis Bottero's axisymmetric formulation; also removed useless white spaces
     bf29d05 Merge pull request #57 from komatits/devel
     fda426b switched to the right new version of the EXAMPLES
     22a6b73 Merge pull request #58 from komatits/devel
     af88b4b fixed a warning in src/specfem2D/read_databases.F90 and a file name that was not right in the default DATA/Par_file
     fdabe51 Merge pull request #59 from komatits/devel
     10039a1 removed Alexis Bottero's "axisym" comments at the end of his new lines
     f36f97e Merge pull request #60 from komatits/devel
     320c8ca switched to the right version of the EXAMPLES
     c07b113 Merge pull request #61 from komatits/devel
     ca7a283 Alexis Bottero fixed a small issue for AXISYM Gmsh meshes in src/meshfem2D/meshfem2D.F90
     130867d Merge pull request #62 from komatits/devel
     2e882cf got rid of ugly !axisym comments at the end of lines
     4668df8 Merge pull request #63 from komatits/devel
     2fc1616 Alexis Bottero added a stop statement for some unsupported PML cases in the axisymmetric case
     ec794d4 Merge pull request #64 from komatits/devel
     b8b558e Modified indentation in pml_init.F90
     7d83b85 Merge pull request #65 from bottero/devel
     2bc7d87 committed Quentin Brissaud's modifications to handle gravitoacoustic media
     22eda3d Merge pull request #66 from komatits/devel
     9662ffc This commit fixes PMLs and external meshes for axisymmetric runs.
     16bd156 Merge remote-tracking branch 'upstream/devel' into devel
     298c495 Merge pull request #67 from bottero/devel
     8b52cb7 merged Quentin Brissaud's new modifications; he also got rid of unused variables
     b87b2a2 Merge pull request #68 from komatits/devel
     4d57f33 added the logo of the Del Duca Foundation
     fb480e7 Merge pull request #69 from komatits/devel
     24d334e fixed all the warnings given by the Portland and Cray compilers on a Cray at ORNL. In particular, renamed all the variables or functions that had the same name as Fortran intrinsics (although that is correct in Fortran, it can be confusing and it also confuses syntax highlighting, and the Portland compiler prints a warning for each of them)
     db407f7 Merge pull request #70 from komatits/devel
     dbf3bf9 fixed a warning from the Cray compiler about an implicit (hidden) memory copy in a subroutine call that contained an arithmetic operation
     35e0e37 Merge pull request #71 from komatits/devel
     bd53bae Quentin Brissaud fixed two minor bugs in his gravity routines
     80fabb7 Merge pull request #72 from komatits/devel
     5820374 improved replace_use_mpi_with_include_mpif_dot_h.pl and improved "use mpi" usage to make it work
     42bc2da Merge pull request #73 from komatits/devel
     2be198c renamed FLAGS_CHECK to DEF_FFLAGS in configure and Makefiles to be consistent with the name used in the 3D and 3D_GLOBE codes
     8e867a1 Merge pull request #84 from komatits/devel
     cffa1be commented out the "compile a trivial MPI program" test, which is not needed and which makes "configure" crash on several machines
     32bed13 Merge pull request #85 from komatits/devel
     dae5895 removed an unused variable
     2a7e7fc Merge pull request #86 from komatits/devel
     b886e9f updated all the copyright headers
     b78c2db Merge pull request #87 from komatits/devel
     e85cb6b updated three headers that I had forgotten
     0d5625f Merge pull request #88 from komatits/devel
     fba25c1 updated a sentence about how to report bugs
     4c7bbf8 Merge pull request #89 from komatits/devel
     aa44400 updated the download link in the users manual
     8668abf Merge pull request #90 from komatits/devel
     73695ba added a quick hack to remove the PMLs from JPEG images if needed: set the vector or pressure field to zero there
     26c0b04 Merge pull request #91 from komatits/devel
     3109657 added explanations from Zhinan Xie about how to select PML damping parameters
     83c3f8b Merge pull request #92 from komatits/devel
     f2250b8 added USE_CONSTANT_MAX_AMPLITUDE and CONSTANT_MAX_AMPLITUDE_TO_USE for movies
     43d6015 Merge pull request #93 from komatits/devel
     05c828b changed call read_value_double_precision_p to call read_value_logical_p for the new parameter USE_CONSTANT_MAX_AMPLITUDE
     967f9b9 Merge pull request #94 from komatits/devel
     38c73cd added parameter READ_VELOCITIES_AT_f0 and implemented a shift of velocities read from the Par_file if needed when viscoelasticity is on
     34914dd Merge pull request #95 from komatits/devel
     38559d5 added Paul Cristini's new version of process_DATA_Par_files_to_update_their_format_when_new_parameters_are_added.py; also added a comment in flags.guess
     a7b59ef Merge pull request #96 from komatits/devel
     736465c updated comments about Carcione 2007
     67d3f24 Merge pull request #97 from komatits/devel
     870eeef added doc/here_is_how_viscoelastic_attenuation_is_implemented_in_SPECFEM2D_Generalized_Zener_Body_may2014.pdf
     4cdd383 Merge pull request #98 from komatits/devel
     c9f16d3 added a test for negative relaxation times for attenuation memory variables
     9d9b2de Merge pull request #99 from komatits/devel
     9633d06 switched to SolvOpt for the calculation of attenuation relaxation constants
     03e1843 Merge pull request #100 from komatits/devel
     c36aabc fixed the Carcione 1988 1_over_N problem in "EXAMPLES/attenuation"
     9ff6f71 Merge pull request #101 from komatits/devel
     f4001a1 added a test to check that the relaxation times found for viscoelastic materials are positive
     9bc9f1b Merge pull request #102 from komatits/devel
     0a438e8 added a link to the developers' wiki
     3e32e57 Merge pull request #103 from komatits/devel
     75ebe88 improved my new section title
     d7aa3da Merge pull request #104 from komatits/devel
     bdec83a removed ZZZ_currently_broken_or_obsolete_examples_but_do_not_remove/BENCHMARK_CLAERBOUT_ADJOINT, which contained big obsolete binary files (now that we are going to move the examples to GitHub, this was problematic)
     d19ac05 Merge pull request #105 from komatits/devel
     f1cad83 Remove submodule
     bf10ec8 Merge branch 'master' into devel
     4d5e352 set USE_NEW_SOLVOPT_ROUTINE to false instead of true by default, following a bug report by Paul Cristini (not fixed yet, we will investigate)
     372efe6 Merge pull request #106 from komatits/devel
     814a482 did a simple test of a Git commit through Hub
     a771b4d reverted the change in a comment that I had done as a test of committing to Git through Hub
     4ee2f13 acknowledge Geza Seriani and Enrico Priolo in the users manual
     38da483 fixed the attenuation bug detected by Paul Cristini: attenuation factors were computed in acoustic (fluid) layers even though attenuation is not implemented there, resulting in meaningless attenuation parameters that in turn could make the code become unstable in some cases
     6cdae0e changed i4 to i6 to avoid overflow for very slow runs with full range-checking options
     3d4464a forced old LaTeX syntax (only) for accented letters
     5490b25 added for_ADJOINT_TOMOGRAPHY_TOOLS_see_in_the_SPECFEM3D_package.txt
     fa07ed2 updated a comment
     6445827 added "UTILS/sample_code_to_compute_SEM_derivatives_on_a_mesh"
     1e74fc1 added the Makefile for UTILS/sample_code_to_compute_SEM_derivatives_on_a_mesh
     64a2a90 Add the new PML formulation for fluid-solid simulation
     2e2f304 Merge pull request #118 from xiezhinan/devel
     d238a13 changed the name of NXE and NZE for clarity
     7e3133f added a warning about versions dot zero of a compiler
     ee89692 removed an unused variable
     f92dac0 fix the PML fluid-solid implementation with LDDRK time scheme
     af86745 Merge branch 'devel' of github.com:xiezhinan/specfem2d into devel
     7d20599 added doc/SEM_class_from_Yvon_Maday_to_Dimitri_Komatitsch_and_Jean_Pierre_Vilotte_04apr1995.pdf
     99937ce Merge pull request #123 from komatits/devel
     8430778 fixed a typo in the manual and in my notes