[cig-commits] [commit] master's head updated: Merge remote-tracking branch 'origin/devel' (05e7443)
cig_noreply at geodynamics.org
cig_noreply at geodynamics.org
Tue Nov 11 13:07:18 PST 2014
Repository : https://github.com/geodynamics/specfem3d
Branch 'master' now includes:
a672af7 Combine volume data for ADIOS. modified Makefile.in for conditional compilation
9232d96 text formatted.
2dc5012 temporary fix. different targets for combine_vol_data w/ and w/o ADIOS
2836170 Merge pull request #75 from mpbl/devel
41ef047 Merge branch 'master' into QA updates QA with Carl's test commit which was on master branch, but not done in QA
b51a2fa combine_vol_data rely on par_file to use ADIOS.
9df1942 removed adios only version of combine vol_data.
232818c Merge pull request #76 from mpbl/devel
ce90249 added the station name to output_list_stations.txt. also removed an unused variable from src/specfem3D/gravity_perturbation.f90
1fe92c9 Merge pull request #83 from komatits/devel
dbf684c Fix building in serial.
6c327a1 Merge pull request #85 from QuLogic/serial
d801758 build: Make changes to scotch build permanent.
f3c4b21 build: Remove backup Makefile targets.
09910bd build: Remove unnecessary creation/deletion of directories.
122f89e build: Remove extra build script.
7520567 build: Remove forced re-compilation.
c5bc599 build: Remove extra targets from generate_databases.
d5039a3 build: Fix rules for executables.
43a4244 build: Fix scotch dependency of decompose_mesh.F90.
8a7bed3 build: Add module dependencies to rules.
4359ed5 Merge pull request #86 from QuLogic/parallel-make
a8a0044 build: Fix dependencies for ADIOS objects.
076c717 Fix compile with ADIOS enabled.
aff4543 build: Fix rules for xmodel_update.
2800b40 Fix serial build for optional programs.
75a36e4 build: Error if config with ADIOS but without MPI.
160f992 ADIOS: Stop if unable to open or read from file.
d9daf54 build: Use consistent rules for building ADIOS files.
39257a8 ADIOS: Use consistent naming for variables in files.
8e7fca2 Merge pull request #88 from QuLogic/adios-build
8b5d44e User manual: ADIOS + PML + author list updated.
6a53e19 Merge branch 'devel' of github.com:mpbl/specfem3d into mpbl-devel
10e3bb9 uses new Makefiles and rules.mk for configuration and compilation
fd9094b uses top_srcdir instead of top_builddir for bundled scotch directory; cleans up code a bit
dd29b92 parameters string length increased to 512.
353252b Merge remote-tracking branch 'upstream/devel' into devel
56deeb2 ignore latex generated files for doc
6408279 Merge branch 'QA' of https://github.com/geodynamics/specfem3d into devel
7a0c6c0 updates configuration scripts to allow for building binaries in a different directory than the root directory; bug fix in check_mesh_resolution() which speeds it up; adds middle abscissa check into zwgldj() routine and removes the checks in other locations
5a5caf0 adds subdirectory tests/ for compilation and unit testing; deallocates temporary arrays in check_valence(); uses cudaMemcpy2D for padded array copies
e38ba40 code cleanup removes outcommented middle abscissa check
c999b52 updates .gitignore file
20f1434 speeds up mesh resolution check; updates comments and replaces dot_product() call with explicit calculation
890e1ef updates cuda routines, uses better indexing and pointer declarations
2dbb673 adds more tests
b14d8ed adds cuda timing functions and updates cuda kernel_2
4197533 updates .gitignore file; uses cuda d_ibool array with padding; adds wrapper for global memory load function __ldg()
4981f6c fixed overflow of degrees-of-freedom counters when more that 2 gigapoints; added comment about Zlib -lz to the users manual
40388be Merge pull request #97 from komatits/devel
cc878e6 Trick the implicit interface of the adios stub module by calling a dummy function with no interface. Deal with unused variable warnings when not configuring with ADIOS>
1d2434c Vicious bug fix. Multi GPU per nodes implied multiple synchronizations of the same device when checking error after the call to deviceCount.
8cdb4f0 improves cuda kernel for acoustic simulations; adds file assemble_MPI_scalar_cuda.cu and assemble_MPI_vector_cuda.cu
5168199 updates configuration files to compile CUDA executables without MPI
3390703 adds depedency for locate_receivers.f90 compilation
e7a682a Add scotch 6.061rc2
3c34e23 removed built object for scotch -- add .gitignore
b683d0a Merge pull request #102 from mpbl/devel
fce8e2b Merge branches 'master' and 'devel' of https://github.com/geodynamics/specfem3d into devel
77845b6 better flags.guess for Intel ifort
dd7232c Merge pull request #103 from komatits/devel
9bef9d2 fixed three warnings in scotch_6.0.1rc2
3cc4e18 Merge pull request #104 from komatits/devel
028f1dc changed -gen-interface to -gen-interfaces
8f48c60 updated some comments in README and in configure
f933db6 Merge pull request #105 from komatits/devel
eee700f Fix .gitignore.
9ec3e1f Merge pull request #108 from QuLogic/gitignore
7092627 added -fpe0 for Intel ifort
f1d0da3 directory structure matches 3D_GLOBE and 2D
c413870 Parfiles in DATA/ matches new directory structure
937b89b Merge pull request #110 from mpbl/devel
30a6710 Updates examples with (Mesh_)Par_files matching the new directory structure
13423a5 Merge pull request #111 from mpbl/devel
c542500 examples' process.sh reflect new directory structure
8056d9e Merge pull request #112 from mpbl/devel
4a5d6e7 added run_this_example_external_mesh.sh and run_this_example_internal_mesher.sh
8c0a1d2 Merge pull request #113 from komatits/devel
8d2bf14 fixed a path that was not right in run_this_example_internal_mesher.sh and run_this_example_external_mesh.sh
6ab93c5 Merge pull request #114 from komatits/devel
2293e23 Rename run_this_example_external_mesh.sh to run_default_example_external_mesh.sh
80ce289 Rename run_this_example_internal_mesher.sh to run_default_example_internal_mesher.sh
6f7860b updated the LICENSE files
902d8e8 Merge pull request #115 from komatits/devel
ac0fa0b with the agreement of the GeoCUBIT authors, changed the GeoCUBIT license from GNU GPL v3 to v2+ to avoid potential incompatibility issues with SPECFEM3D
3889f3a Merge pull request #116 from komatits/devel
5e2baaf Update README
c11fbc6 replaced all the GeoCUBIT GNU GPL v3 license headers with v2+
3139c8f Merge pull request #117 from komatits/devel
9f25621 added the logo of the Del Duca Foundation
4af479c Merge pull request #118 from komatits/devel
c664567 removed src/decompose_mesh/scotch_6.0.1rc2, which gives a major warning at compile time (variable used before being assigned a value) and also (independently) refuses to compile on Cray with pgf90. More generally, we should never use Release Candidate (rc) versions of any package, only stable versions
fd49f35 Merge pull request #120 from komatits/devel
6c8aa4e 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)
e4139e0 Merge pull request #121 from komatits/devel
d453e37 Update force_ftz.c
f0ea1b9 improved replace_use_mpi_with_include_mpif_dot_h.pl and improved "use mpi" usage to make it work
b054a4f Merge pull request #123 from komatits/devel
729ab2f fixed smooth_vol_data to agree with order of records in external_mesh.bin
859589a Merge pull request #124 from rmodrak-princeton/devel
10b44e6 added symbolic links to DATA and run_this_example.sh; please do *NOT* remove them
0a40b72 Merge pull request #125 from komatits/devel
007beb3 commented out the "compile a trivial MPI program" test, which is not needed and which makes "configure" crash on several machines
6405469 Merge pull request #126 from komatits/devel
409219b Update PBS scripts and examples.
a668bac Merge pull request #127 from QuLogic/carl-example-updates
553bc35 Remove hard-coded output paths.
dae8154 Fix hard-coded paths in CUDA routines.
aa19d65 Merge pull request #130 from QuLogic/output-paths
6235d33 added a stop statement in src/auxiliaries/smooth_vol_data.f90 and commented out all MPI statements because they break the build system; developers should use routines in src/shared/parallel.f90 only instead of calling MPI directly
251b0d9 Merge pull request #131 from komatits/devel
69178f8 use wrappers from parallel.f90 in smooth_vol_data.f90
4f5e220 Merge pull request #132 from rmodrak-princeton/devel
fd0ed10 improved a comment
1860d74 Merge pull request #133 from komatits/devel
a3068df updated all the copyright header files
7c4dfa7 Merge pull request #134 from komatits/devel
05a7571 added doc/map_projections_Geomatics_Guidance_Note_number7_part2_June2013.pdf
cb32c88 Merge pull request #135 from komatits/devel
eb09601 Cleanup C code slightly.
e2054ba Remove duplicate constants.h file.
2e00583 Correct licence in several files.
af5c543 Remove todo file after moving issues to GitHub.
772f41d Remove commented code for absorbing boundary snapshots.
033ef46 Remove irrelevant comments.
5ae80c7 Remove code-duplicating comments.
6c6003f build: Remove Pyre checks.
92088a5 Fix some of the simpler warnings.
a27c27c Use MPI_STATUS_IGNORE in MPI calls.
1c22a2a Combine duplicate get_global subroutines.
a918633 Combine duplicates of sort_array_coordinates.
ee7076f Replace Numerical Routines sorting code.
8c28984 Remove unused constants.
c6c3649 build: Remove unnecessary cleanup.
5584041 Remove get_value_* subroutines.
672fb62 Remove another unused constants file.
d396f2a Remove more dead code.
9cbcd40 Normalize case of Fortran keywords.
aefc970 Fix inconsistent indenting.
e0a6ee1 Fix up Par_file reading.
df49c7f Fix up mesher Par_file reading slightly.
87283b5 Add -ggdb to recommended gfortran debug flags.
ff0d5a3 Remove unnecessary allocated array.
37cbf64 Fix grammar mistake.
3ccbe15 Remove unnecessary adjustl calls.
50e16a2 Remove duplicate create_name_database file.
320d29f Fix a couple more licenses.
7952d3f Remove unused parameters.
756db1c Remove Par_file variable prefixes.
129d6b0 build: Fix scotch header dependency.
50aa953 Merge pull request #136 from QuLogic/cleanup
e1bd242 turned -DFORCE_VECTORIZATION off by default in flags.guess to be safe (see https://github.com/geodynamics/specfem3d/issues/81 for more details). Also removed a few unused variables in src/shared/get_global.f90
4027bee Merge pull request #137 from komatits/devel
9dec754 Move constants module to shared directory.
017e23b Make maximum string length configurable.
f89cea5 Increase size of some strings likely to overflow.
f5b7671 Merge pull request #140 from QuLogic/short-strings
32510e7 Fix lists of auxiliaries objects.
8a98c87 Fix module list in auxiliaries directory.
f1cc124 Merge pull request #141 from QuLogic/fix-auxiliaries-clean
1e40049 more complete gfortran options
f3d4ff7 Merge pull request #142 from komatits/devel
e5846a7 changed the definition of LOCAL_PATH_Q in constants.h to use len=MAX_STRING_LEN instead of len=*
2696d80 Merge pull request #144 from komatits/devel
14f0a7b Fix string length with ifort.
0f4879d Fix typo in mesher dependencies.
519949c Remove constants module from solver list.
7f75746 Add arguments to ADIOS stubs.
e0ac5aa Swap order of mpi and constants usage.
68e4d79 Remove dimitrize_args subroutine.
d28c9f5 Add a module to hide unused variables.
5596530 Add dependencies to constants module in solver.
85b1db7 Fix ifort 13 bug with constants module.
1a2f0a3 Also silence unused variables in serial code.
f1f936a added section "multiple external tomography files for SPECFEM3D" from Carl Tape
a6b2cfa Merge pull request #146 from komatits/devel
22a04a2 added doc/call_trees_of_the_source_code/Doxyfile_complete_call_tree and doc/call_trees_of_the_source_code/Doxyfile_truncated_call_tree from Clement Durochat
67bd919 Merge pull request #147 from komatits/devel
da9c26c added CUBIT_GEOCUBIT/geocubitlib/block_mesh.py
4e5603b Merge pull request #148 from komatits/devel
6de0c30 added CUBIT_GEOCUBIT/geocubitlib/boundary_definition.py and CUBIT_GEOCUBIT/geocubitlib/cubit2specfem3d.py
0c1575c Merge pull request #149 from komatits/devel
c75667d increased MAX_STRING_LEN to 512
bbbfcc0 Merge pull request #150 from komatits/devel
5ade6fa add examples in geocubit
2d162d7 Merge pull request #151 from casarotti/devel
2f72cad add irregular topography option...
a417482 delete block_mesh.py
23b46f1 bug fix
7dfb8ad Merge pull request #152 from casarotti/devel
1612ea8 switched to the cleaned version of the "examples" directory
11139bf Merge pull request #153 from komatits/devel
463e742 Fix some more short strings.
e55f95d replaced block_mesh.py with create_mesh.py
adadc99 Merge pull request #155 from komatits/devel
addf93b added instructions for Python paths and GeoCUBIT to the manual
12e0fdd Merge pull request #156 from komatits/devel
cd64165 removed the Python header I had added to homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides/create_mesh.py, since it is unneeded and was leading to warnings at run time
6e7cdf9 Merge pull request #157 from komatits/devel
de94597 added utils/DSM_FOR_SPECFEM3D (permanently moved from an old SVN server to here in Git)
d29a156 Merge pull request #158 from komatits/devel
d2e6f20 added Roland_Sylvain gravity integrals; also simplified run_this_example.sh
2b6a417 Merge pull request #159 from komatits/devel
53582fd Rename README to README.md
6f401a2 Update README.md
48d1318 Update README.md
528a2a6 Merge pull request #160 from casarotti/devel
d8ca344 added a link to the developers' wiki
e010a3b Merge pull request #161 from komatits/devel
3679c83 replaced DATA, which used to be a symbolic link, with a real directory (following a suggestion by Carl Tape, to make it much easier to run other cases or other examples)
2e7c97b Merge pull request #162 from komatits/devel
a794012 removed white spaces from the examples using a script, to reduce their size before we move them to GitHub
ed82eef Merge pull request #163 from komatits/devel
40407ea in the internal mesher, removed some unnecessary checks on NEX_XI being a multiple of 8 in the case of USE_REGULAR = .true.
ef9ac84 Merge pull request #164 from komatits/devel
e879ce3 add a more flexible function for scale factor and fix one error in create_mass_matrices.f90
25553a6 Remove submodule
f85e215 Merge branch 'master' into devel
162be97 Merge pull request #165 from xiezhinan/devel
fa40b98 Test
fa2bafd Test
64e54da Coupling with DSM
610cc8a Coupling with DSM
1c07758 updated README_SPECFEM3D_FAULT
ba49c5d Merge pull request #166 from komatits/devel
6026e36 Merge branch 'devel' of https://github.com/geodynamics/specfem3d into devel
a011602 updated the symbolic links that were pointing to "examples", which is now called "EXAMPLES"
cbc549f changed 'examples' to 'EXAMPLES' in the users manual, and removed the obsolete file README_SPECFEM3D_FAULT
47f7038 Merge pull request #167 from komatits/devel
3b988e5 Merge branch 'devel' of git://github.com/geodynamics/specfem3d into devel
55a6501 Coupling with DSM
63f289f Updated for coupling with DSM
b2e4f00 Updated for coupling with DSM
7f63787 Updated for coupling with DSM
0eddb0a Updated for coupling with DSM
b513776 Updated for coupling with DSM
f316cd0 Update write_VTK_data.f90
c14a59b Merge branch 'devel' of git://github.com/geodynamics/specfem3d into devel
7c85c3d Updated for coupling with DSM
cb1e09a Updated for coupling with DSM
e676e9d commit recent change inside pml involved codes
e6a0ddf Merge branch 'devel' of github.com:xiezhinan/specfem3d into devel
d8ee135 Updated for coupling with DSM
53b3fa8 Updated for coupling with DSM
18c368a Updated flags for coupling with DSM
e793f3b Update for coupling with DSM
cd8e1a3 changed i1 and i2 to i7.7 following a request from Carl Tape
15f6ee4 Merge branch 'devel' of git://github.com/geodynamics/specfem3d into devel
7720ed9 corrected job name; mainly a trivial change to test github
f93e607 Merge branch 'devel' of git://github.com/geodynamics/specfem3d into devel
b09e4e9 Update for couple with DSM
8447c9a update comments for homogeneous_halfspace README (github test)
3afd771 Merge branch 'devel' of git://github.com/geodynamics/specfem3d into devel
d29cbc8 added a stop statement if the first time step entered by the user is negative
c6e41a6 Merge branch 'devel' of git://github.com/geodynamics/specfem3d into devel
a11837a added Can Kangchen Bai to the list of developers
fbd64d2 changed Can Kangchen Bai to Kangchen Bai
c01fc25 Merge branch 'devel' of git://github.com/geodynamics/specfem3d into devel
5510605 Conflicts temporary commented
d6cf045 Fix conflict
16bebb7 improved a stop statement
8bb89ba Merge pull request #177 from komatits/devel
064754b Merge branch 'devel' of git://github.com/geodynamics/specfem3d into devel
01063d6 merged Vadim's support for coupling with DSM, cleaned and improved by Clément Durochat
7fd4b96 parallel fault fix:Add sychronizations at every timestep to ensure thet the displacement and velocity values at nodes on MPI interface stay equal on all processors that share the node. This have to be done because of the nolinearity introduced by dynamic fault solver. Will be activated only when dynamic fault simulation is turned on.
db2fc8a parallel fault fix:Add sychronizations at every timestep to ensure that the displacement and velocity values at nodes on MPI interface stay equal on all processors that share the node. This have to be done because of the nolinearity introduced by dynamic fault solver. Will be activated only when dynamic fault simulation is turned on.
35ff4e4 parallel fault fix:Add sychronizations at every timestep to ensure that the displacement and velocity values at nodes on MPI interface stay equal on all processors that share the node. This have to be done because of the nonlinearity introduced by dynamic fault solver. Will be activated only when dynamic fault simulation is turned on.
271c1ec Merge pull request #178 from komatits/devel
357e5da cut a line that was too long
09df28d Merge pull request #180 from komatits/devel
d1b916c fix one error in pml_compute_memory_variables.f90, answer one commit from Dimitri in compute_forces_viscoelastic_noDev.f90
3141b3e Merge pull request #181 from xiezhinan/devel
a4bc7b6 Updates for coupling with DSM
6d70f0d Merge branch 'devel' of git://github.com/geodynamics/specfem3d into devel
6608495 Last updates
c990e78 added a comment to do a test to see if I can commit changes using Hub
8b9384e Change benchmark for coupling w DSM
d266339 temporary fix for a dependency problem in the Makefile detected by BuildBot
0b126d1 Merge pull request #182 from komatits/devel
a15ab90 Merge branch 'devel' of git://github.com/geodynamics/specfem3d into devel
1b0834d moved COUPLE_WITH_DSM from setup/constants.h.in to DATA/Par_file. There are thus two new parameters in the Par_file to couple with DSM: COUPLE_WITH_DSM = .false. TRACTION_PATH = ./DATA/DSM_traction_files/ Also removed useless white spaces, and deleted two broken symbolic links.
c080d14 CD modif.
57c11d9 Correct module dependencies in auxiliaries.
8af99fb fix mesh sandwich
4e452ef fix vol sandwich
efca0f4 acknowledge Geza Seriani and Enrico Priolo in the users manual
45d9069 Merge branch 'devel' of git://github.com/geodynamics/specfem3d into devel
8b0c03c Modif comment
f470392 Modif comments
c9dfcea renamed in_data_files to DATA
72288c1 Merge pull request #187 from komatits/devel
3b561c1 Merge branch 'devel' of git://github.com/geodynamics/specfem3d into devel
2d6ee63 added directories OUTPUT_FILES and OUTPUT_FILES/DATABASES_MPI
7869d8b changed in_data_files to DATA and in_out_files to OUTPUT_FILES in all the scripts
a11d1f6 updated utils/DSM_FOR_SPECFEM3D/example/DATA/Par_file to the current format of Par_files (it was obsolete)
d843be6 added and cleaned utils/DSM_FOR_SPECFEM3D/example_pyrope
c955f01 Merge pull request #191 from komatits/devel
bd417fb moved the DSM_FOR_SPECFEM3D/examples to EXAMPLES/DSM_FOR_SPECFEM3D in order to maintain them in the same directory as all other examples
84afeb0 Merge pull request #192 from komatits/devel
f838c33 DSM changes
f39919c Merge branch 'devel' of git://github.com/geodynamics/specfem3d into devel
821b6e6 Change for DSM
e17359b Change for DSM
9d406f8 Change for DSM
5ab8d7a Change for DSM
a3de4f9 Changes for DSM
260b3e6 Changes for DSM
29a5267 Changes for DSM
276d4cc Last modif DSM
29ddcde For DSM
859403f changed i4 to i6 to avoid overflow for very slow runs with full range-checking options
cf015a6 Merge branch 'devel' of git://github.com/geodynamics/specfem3d into devel
08f6677 Last changes
a5856d0 added the framework for the future option NUMBER_OF_SIMULTANEOUS_RUNS that I will add to setup/constants.h.in (off by default, i.e. equal to 1 by default) to have the ability to run several independent earthquakes in parallel from the same big job
98a6f2f Merge pull request #194 from komatits/devel
b6ea28a forced old LaTeX syntax (only) for accented letters
1fff88f Merge branch 'devel' of git://github.com/geodynamics/specfem3d into devel
b4aa078 done adding support for new option NUMBER_OF_SIMULTANEOUS_RUNS. Also fixed a dependency issue that was in the code when compiling without MPI.
b93f992 Merge branch 'devel' of git://github.com/geodynamics/specfem3d into devel
157d91f Change coupling
30d6bd7 Couple
6260094 added MAKE_HOOKE_LAW_WEAKLY_NONLINEAR option
7616dfa fixed two compilation errors detected by David Luet when configuring with --enable-double-precision
aa9b457 fixed a typo in a comment
a6815a4 Merge branch 'devel' of git://github.com/geodynamics/specfem3d into devel
06fc814 Uncommented the FCFLAGS in Makefile.in
955ba32 added ADJOINT_TOMOGRAPHY_TOOLS (moved from the old and unused SVN repository to here)
8a3f14d fixed the OpenMP compilation problem detected by David Luet
04a8fe2 Merge branch 'devel' of git://github.com/geodynamics/specfem3d into devel
d14dbf0 Old DSM delete
4e83e1d Add new DSM_FOR_SPECFEM3D
9cd84b8 Delete example for DSM
b707dc2 Add new example for DSM
1c030e2 Change in specfem for DSM
d759e09 Modif for specfem-DSM
f88679e added OpenMP compiler flags as comments to flags.guess
58f61af added a symbol of gravity calculations on the cover of the manual (now that we can compute the gravity vector and gradiometric tensor in the code)
5b7671d switched to the new version of src/shared/utm_geo.f90 in order to have support for the Southern hemisphere. Also switched to the WGS84 ellipsoid instead of Clarke 1866. Updated the users manual accordingly.
59a4485 changed "zone" from double precision to integer (the code worked fine anyway because the value was then used in a double-precision expression)
32f16f6 update instructions for default example based on file name changes
0db93d6 added a warning about versions dot zero of a compiler
cfaa568 cray flags to keep module information
17fbe27 Merge branch 'devel' of github.com:casarotti/specfem3d into devel
d364e44 adds flop count to compute_forces_viscoelastic_Dev_5p() routine
1999c62 removes header files from repository which are created automatically by scotch compilation
ed52090 added doc/SEM_class_from_Yvon_Maday_to_Dimitri_Komatitsch_and_Jean_Pierre_Vilotte_04apr1995.pdf
3704c88 fixed a typo in the manual and in my notes
978df47 Modif maillage Vadim
6d9ce8d performance optimization for acoustic & elastic CUDA kernels
4f11e7d merges with upstream/devel
fba8797 updates configuration files and m4/ version for CUDA compilation
bbc1e25 updates meshing to be able to use tomographic models with Par_file setting (MODEL = tomo); fixes geocubit scripts to be able to use python-scripts within CUBIT; updates unit testing which can be run by: make tests; moves module tomography_par into file model_tomography.f90; updates use-statements
e84e7ba removes trailing spaces
6d674d5 fixes compilation of xmodel_update when configured with ADIOS
8251184 removes obsolete links in README file
5c57f77 Merge branch 'devel' of git://github.com/geodynamics/specfem3d into devel
a305b99 Modif CD
633036a added mkdir -p bin
b57460b Merge branch 'devel' of git://github.com/geodynamics/specfem3d into devel
f1bbebf Modfi manual visu Paraview
6975b16 fixed a typo
b8df327 Reverted commit of wrong version of submodule m4
27634e9 adds error checking when reading of Par_file parameters; updates user output in model_tomography.f90
31e57e0 renames output from xmeshfem3D to output_meshfem3D.txt (to avoid overwriting by xgenerate_databases); updates error messages
27c70c5 Merge branch 'devel' of https://github.com/geodynamics/specfem3d into devel
aad4eb9 added calculation of the estimated day and time at which the run will finish; taken from SPECFEM3D_GLOBE; useful for large runs
afa264d fixed confusing sentences about the number of elements and points in the mesh (problem detected by Vadim Monteiller)
9cddf01 removed two useless lines in src/specfem3D/rules.mk
61ecf41 renamed the existing read_mesh_for_init() to read_mesh_for_init_ADIOS(), and created a new one called read_mesh_for_init() for the non-ADIOS case
aa38229 added a link to the GitHub discussion about tomography tools
1157b47 better compiler options for Portland pgfortran
68b5fcc revert pgfortan to pgf90 (although in principle pgfortan is the standard name these days, but it seems to break BuildBot)
4e768ab got rid of compiler option -Mipa=fast,inline for pgf90 because it creates problems with some older versions of that compiler
428a004 changed pgf90 back to pgfortran, since the problem detected by BuildBot was not coming from that
01fb7e7 framework for the future broadcast of the mesh and model databases in the case of simultaneous runs for the same mesh and model (but different source and/or receivers)
f693910 Merge pull request #235 from komatits/devel
a4d3a42 committed a change I had forgotten to make in my previous commit
49ec9de updates get_cmt() and get_force(); only master process reads in source files
4865c1e updates configuration and m4/ scripts
bd8f2a0 updates cuda file includes
b89f008 added option to broadcast the database between simultaneous runs for identical mesh and model (but different source and/or receiver).
e8f0b0d Merge pull request #237 from komatits/devel
705302c added test of size(array) > 0 before broadcasting them (arrays of size 0 are legal in Fortran for some reason, but can create problems in the call to our broadcast routines because we call them with array(1) as argument). Swapped two "use module" statements in src/specfem3D/fault_solver_*.f90 because the first used the second, which led to an internal compiler error with some versions of GNU gfortran.
69d1a6f added a more precise comment about the new option BROADCAST_SAME_MESH_AND_MODEL
fdd2ff1 moves summation, smoothing and model update tools of global versions from ADJOINT_TOMOGRAPHY_TOOLS/iterate_adj/cluster/ to SPECFEM3D_GLOBE/ package
63b33a6 solves merge conflict in serioal.f90
abc7aef removed an old comment that I had forgotten to delete
505df37 removed a second copy of my old comment
189b4e4 the manual had been compiled without the compiling script and thus without the references; I fixed that
c6e79a8 replaced latitude with latorUTM and longitude with longorUTM in CMTSOLUTION and FORCESOLUTION (as mentioned by Alexis Bottero the original names did not make sense in the cause of SUPPRESS_UTM_PROJECTION = .true. because the values are then given in UTM rather than longitude and latitude). The code still accepts the old format for back-compatibility reasons. That is also why I kept the same length as before for the new names.
858a86e fixed a bug (uninitialized array hdur_tiny) in the case of USE_FORCE_POINT_SOURCE
f17ddfa Adds initial files for SEP models
16596a7 Adds enum value for SEP model
10d194f parse parameter file for SEP_MODEL_DIRECTORY
7117d2e Adds argument to read_parameter_file for SEP models
ab8a468 Adds SEP model to compilation chain
db88fd8 Fixes sep model after testing it.
3b65012 Adds example for sep model
3dfac48 Updates SEP example coarser mesh and stations
fead8a7 Adds routine for SEP model in case of no MPI
620f77a Updates SEP Stations list
c9c7951 Cleans SEP model reader and adds a couple of comments
d04b5f0 Adds CUSTOM_REAL to arguments to pass double precision test
fe8c945 Revert m4
7ef78c5 Merge pull request #244 from mpbl/devel
9473eea Revert "Devel"
2f4e18b Adds initial files for SEP models
bbae9ab Adds enum value for SEP model
edcd062 parse parameter file for SEP_MODEL_DIRECTORY
1552a3c Adds argument to read_parameter_file for SEP models
4498737 Adds SEP model to compilation chain
14c1b3a Fixes sep model after testing it.
1c85f03 Adds example for sep model
bb11664 Updates SEP example coarser mesh and stations
269e53e Adds routine for SEP model in case of no MPI
970a30c Updates SEP Stations list
5bc2995 Cleans SEP model reader and adds a couple of comments
8b76757 Adds CUSTOM_REAL to arguments to pass double precision test
f320687 Removed C __attribute__ keyword, unknown to PGI
dc85103 Fixes dimension in rho SEP header
e47893d Removes trailing underscore
95b3179 Revert m4
41b02e9 Wrap parse_sep C function in FC_FUNC_
81e6e91 reverted my changes for hdur_tiny(), which did not fix the bug when FORCE_SOLUTION is used
da8e86e cleaned useless white spaces
e0b7c32 temporarily patched Matthieu's model_SEP() source code, which had broken the package
2f28100 fixed the "hdur_tiny" bug detected by Alexis Bottero in the case of FORCE_SOURCESOLUTION with a Dirac source time function (hdur_tiny was not sent as a subroutine argument)
31aed1a removed my patch to Matthieu's MPI-IO routines: it was a false positive on our side, MPI had been installed without MPI-IO support on our machine
f1e2052 Adds note on MPI-IO
f337032 merged Clement Durochat's modifications to merge Vadim Monteiller's mesher for a chunk of the Earth (for coupling with DSM)
a5b6706 renamed flag COUPLE_WITH_DSM to COUPLE_WITH_EXTERNAL_CODE, and added a new parameter called EXTERNAL_CODE_TYPE to determine the type of external code to couple with
ba16a65 removed useless white spaces using a script
302f9a3 updates adios helper function to be consistent with global version ones; removes unused variables; checks for adios database setting in xdecompose_mesh
c290682 fixed problems (missing argument in subroutine calls) that were not detected by a parallel make
c0c43b1 Modif scripts DSM
d0ed80d Merge branch 'devel' of https://github.com/geodynamics/specfem3d into devel
758dcb5 updates formatting of example Par_files; bug fix for parse_sep.c to avoid segmentation faults on buffer reallocation
69581f6 Modif paths in Par files
62d217d Modif conflict
acc6906 removed *~ files (useless backup files from an editor (emacs, vi or similar)); please do not commit such extra files
3d4c7cc Merge branch 'devel' of https://github.com/geodynamics/specfem3d into devel
da796d6 fixed a typo in three file names ("scrpits")
ee16718 Better path handling for SEP binary files
42e2a44 Ignores bck files from vi and emacs
0d644a9 Adds a section about SEP models in the manual
bd0537f updated an old comment
4566d0f Corrects english errors
cf28691 Merge branch 'devel' of github.com:mpbl/specfem3d into devel
8611007 Fix typo Par_file
3a650de Merge branch 'devel' of https://github.com/geodynamics/specfem3d into devel
f000de1 Modif Parfile DSM
878e8bd Modif for DSM
c074b0d adds capability of using negative material ids in xmeshfem3D for tomographic models
bc64b62 fixes compilation error on cray for mpi status in read_sep_binary_mpiio; removes trailing spaces and warning about unused function
7c7afa6 Adds a tool to create ascii file for bathymetry from sep files
7197500 Adds readme for the bathy_sep_to_ascii tool
48bfcf0 Removed Makefile -- generated by cmake
15e7693 adds src/tomography directory with summation, smoothing and model update tools
79fa689 Modif to fix problem of generate databases with DSM
186efbb Modif coupling
99d8198 Modif coupling
192e230 adds and updates tomography tools
9068773 updates m4/ and configuration script (fixes configuration with CUDA and intel ifort compilers)
fdc626e redirects file output of mesh resolutions checks in xmodel_update
0479069 fixed the timing routine of SCOTCH that did not compile on MacOS
beeb92a Merge branch 'devel' of https://github.com/geodynamics/specfem3d into devel
b4e3c80 Last modif to validate new coupling with DSM
57f2934 Very last modification for coupling with DSM
00db226 Remove comment in mesh chunk
de447bf Fixed problem 1 and 4 from DK (no change needed for 4)
ae876fe removed white spaces
d8f2bcb Clean DSM directory + change TRACTION_PATH + rename 2 mesh-chunk subroutines
c497ce0 Change in mesh-chunk subroutines
73f4ef6 fix : use pinned buffer to transfer to GPU
7859081 Clean version of convolve_source_timefunction.csh
bf83cf9 added README_inversion_package_list_of_things_to_do.txt
c7475fd fixed a Makefile issue in Scotch that prevented the use of the --always-make compiler option
cb7bfc5 updates naming convention for adjoint seismograms and NSOURCES limit to 999,999 for adjoint simulations
270a6f1 updates ier usage and prettifies code
247c68a adds line breaks to avoid warnings about too long lines
ed36498 updates use statements
f545393 improved a few print statements and comments
19433d6 added Ryan's lists of items and to-do list, and some answers from me
9e2aad4 added a comment from Daniel Peter
05e7443 Merge remote-tracking branch 'origin/devel'
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