From 29b987333e157b66bed7bf1fa3b0612770750909 Mon Sep 17 00:00:00 2001 From: Dimitri Komatitsch Date: Thu, 22 Jan 2015 03:00:53 +0100 Subject: [PATCH] ran the code beautifier, which now removes accented letters and cleans text and LaTeX files --- ...he_adjoint_tomography_workflow_dec2014.txt | 14 +- ...nt_adjoint_tomography_workflow_dec2014.txt | 14 +- .../slices.txt | 2 +- .../slices.txt | 2 +- .../slices.txt | 2 +- .../slices.txt | 2 +- .../slices.txt | 2 +- .../slices.txt | 2 +- .../station_for_simulation.txt | 47 + EXAMPLES/Mount_StHelens/convert_lonlat2utm.pl | 4 +- .../slices.txt | 2 +- .../slices.txt | 2 +- .../paper_GJI_2011_about_the_code.tex | 6 +- doc/README_gravityPerturbation_bis.txt | 40 +- list_for_Zhinan_for_SPECFEM3D_PMLs.txt | 24 +- src/cuda/check_fields_cuda.cu | 4 +- .../scotch_5.1.12b/LICENCE_fr.txt | 7 - .../scotch_5.1.12b/LISEZ-MOI.txt | 8 - src/generate_databases/model_1d_prem.f90 | 2 +- src/meshfem3D/earth_chunk_HEX27_Mesher.f90 | 4 +- src/meshfem3D/earth_chunk_HEX8_Mesher.f90 | 4 +- src/meshfem3D/earth_chunk_all_Utils.f90 | 12 +- src/shared/utm_geo.f90 | 4 +- src/specfem3D/make_gravity.f90 | 2 +- src/specfem3D/prepare_timerun.F90 | 2 +- .../HowtoUseToolkit.tex | 6 +- .../measure_adj/measure_adj.f90 | 2 +- ...litting_in_a_isotropic_Earth_from_2010.txt | 38 +- ...E-DONE-for_integration_of_the_coupling.txt | 62 +- ..._with_SPECFEM_and_DSM_on_Curie_apr2014.txt | 2 +- ..._remove_about_DSM_SPECFEM_coupled_code.txt | 26 +- ..._Dimitri_two_different_problems_in_DSM.txt | 10 +- .../notes_Nobuaki_calcul_strain_tensor.txt | 52 +- ...tes_Nobuaki_compute_strain_in_DSM_code.txt | 26 +- ...lises_dans_DSM_et_changement_de_repere.txt | 56 +- ...ute_strain_seismograms_in_the_DSM_code.txt | 10 +- ..._GEMINI_paper_for_source_discontinuity.txt | 26 +- ...uchi_about_how_to_implement_high_order.txt | 58 +- ...ute_strain_seismograms_in_the_DSM_code.txt | 34 +- ...ource_discontinuity_is_already_handled.txt | 4 +- ...on_of_mass_lumping_of_Takeuchi_apr2014.txt | 6 +- ..._deja_traitee_dans_le_code_de_Takeuchi.txt | 8 +- .../mesh_chunk.f90 | 30 +- .../cart2geogr.f90 | 2 +- .../geogr2cart.f90 | 2 +- .../bacchus_run_benchmark_all_process.sh | 2 +- .../shells/msub_compute_coef_process.sh | 2 +- .../shells/msub_setup_process.sh | 2 +- utils/Visualization/GMT/readme.txt | 4 +- utils/Visualization/Paraview/readme.txt | 20 +- .../HOWTO_use_this_tool.txt | 18 +- utils/bathy_sep_to_ascii/CMakeLists.txt | 2 +- utils/clean_listings_specfem.pl | 41 +- ...SVN_version_of_SPECFEM3D_GLOBE_mar2012.txt | 2 +- utils/readme_cuda_cscs.txt | 126 +- utils/seis_process/readme.txt | 6 +- .../timings_comparing_all_versions.txt | 50 +- .../mean_value_slip_Sieh_1857.txt | 2 +- .../raw_data_andreas_1857.txt | 2 +- .../slip_sieh_1857_extracted.txt | 5274 ++++++++--------- .../model_interface_bedrock.f90 | 2 +- .../readme_LA_HR_and_MR_vo.txt | 32 +- .../list_stations_Dave_Wald_names.txt | 76 +- 63 files changed, 3204 insertions(+), 3133 deletions(-) delete mode 100644 src/decompose_mesh/scotch_5.1.12b/LICENCE_fr.txt delete mode 100644 src/decompose_mesh/scotch_5.1.12b/LISEZ-MOI.txt diff --git a/Carl_Tape_his_comments_on_the_adjoint_tomography_workflow_dec2014.txt b/Carl_Tape_his_comments_on_the_adjoint_tomography_workflow_dec2014.txt index ffadaae06..1a0340e3b 100644 --- a/Carl_Tape_his_comments_on_the_adjoint_tomography_workflow_dec2014.txt +++ b/Carl_Tape_his_comments_on_the_adjoint_tomography_workflow_dec2014.txt @@ -10,19 +10,19 @@ Hi Ryan and all, I met with Ebru, Emanuele, Frederica, Elliott, and Lion on Thursday night at AGU. (We scheduled at the last minute and missed Min and Hejun, unfortunately.) Below are some discussion points and questions. -You already have plenty to discuss anyway, so you don’t have to +You already have plenty to discuss anyway, so you don't have to consider any of these, of course. I cced Emanuele and Frederica, -though I don’t think they’ll be back by Monday. +though I don't think they'll be back by Monday. + It seems like those in our discussion were supportive of the move -from “legacy” utilities (perl, sac, flexwin, measure_adj) to +from "legacy" utilities (perl, sac, flexwin, measure_adj) to python-based utilities (obspy, pyflex, pyadj). Lion seemed quite -willing to rewrite measure_adj into python (pyadj) – the multitaper +willing to rewrite measure_adj into python (pyadj) - the multitaper measurement is the key piece, and there are Slepian tapers within python libraries, apparently. + Lion suggested that, in his opinion, the hdf5 file format would be -optimal for seismograms and adjoint sources. I don’t know the details +optimal for seismograms and adjoint sources. I don't know the details about this. But clearly this is an important decision, since it impacts the processing scripts, adjoint sources, the moment tensor inversion codes, etc. @@ -63,10 +63,10 @@ little regarding the adjoint tomography workflow since 2009. But I have several projects that will move forward in 2015, lead by me (southern California), my student Vipul Silwal (Alaska), my postdoc Amir Allam (fault zones up to 5-10 Hz), and Yoshihiro Kaneko (New -Zealand). I’d like to get these folks on the right track and am open +Zealand). I'd like to get these folks on the right track and am open to trying out new things. Hopefully we can help in this effort. -I’ll talk to you soon. Thanks for including me in the call. +I'll talk to you soon. Thanks for including me in the call. Carl diff --git a/Daniel_Peter_his_comments_on_the_current_adjoint_tomography_workflow_dec2014.txt b/Daniel_Peter_his_comments_on_the_current_adjoint_tomography_workflow_dec2014.txt index 2c179f94c..f04cef39d 100644 --- a/Daniel_Peter_his_comments_on_the_current_adjoint_tomography_workflow_dec2014.txt +++ b/Daniel_Peter_his_comments_on_the_current_adjoint_tomography_workflow_dec2014.txt @@ -11,27 +11,27 @@ for 1. i kept the routines very similar, some differences occur when reading in mesh files and e.g. where the maximum of the gradient is taken for the update step length. in future, i want to have them also merged into the same set of SPECFEM function library. for 2. -good point, the jacobian is used for smoothing of the kernels in the global code, but isn’t currently used for the cartesian code. that is one of the differences that has to be checked again (thus smoothing in the cartesian is based solely on point distance, not volume) +good point, the jacobian is used for smoothing of the kernels in the global code, but isn't currently used for the cartesian code. that is one of the differences that has to be checked again (thus smoothing in the cartesian is based solely on point distance, not volume) best wishes, daniel > > On 22 Dec 2014, at 5:50 pm, Carl Tape wrote: -> > +> > > > Hi all, -> > +> > > > Thanks for the call. I wanted to ask two questions. -> > +> > > > 1. Daniel, can you briefly describe the differences between the > > src/tomograhy/ files in SPECFEM3D and SPECFEM3D_GLOBE? Would it be > > simpler to have only one set of files? -> > +> > > > 2. Isn't the jacobian of the mesh needed for many of the optimization > > operations (dot product, integration, etc)? So my impression is that > > you need more than just the kernel name to do something like smoothing > > -- you also need the jacobian. Probably this is already in the > > scripts, but the discussion in the call did not mention it. -> > +> > > > Carl -> > +> > diff --git a/EXAMPLES/CPML_examples/homogeneous_halfspace_HEX8_acoustic_absorbing_CPML_5sides/slices.txt b/EXAMPLES/CPML_examples/homogeneous_halfspace_HEX8_acoustic_absorbing_CPML_5sides/slices.txt index e8c63f701..bc856dafa 100644 --- a/EXAMPLES/CPML_examples/homogeneous_halfspace_HEX8_acoustic_absorbing_CPML_5sides/slices.txt +++ b/EXAMPLES/CPML_examples/homogeneous_halfspace_HEX8_acoustic_absorbing_CPML_5sides/slices.txt @@ -1,4 +1,4 @@ 0 1 2 -3 \ No newline at end of file +3 diff --git a/EXAMPLES/CPML_examples/homogeneous_halfspace_HEX8_acoustic_absorbing_CPML_6sides/slices.txt b/EXAMPLES/CPML_examples/homogeneous_halfspace_HEX8_acoustic_absorbing_CPML_6sides/slices.txt index e8c63f701..bc856dafa 100644 --- a/EXAMPLES/CPML_examples/homogeneous_halfspace_HEX8_acoustic_absorbing_CPML_6sides/slices.txt +++ b/EXAMPLES/CPML_examples/homogeneous_halfspace_HEX8_acoustic_absorbing_CPML_6sides/slices.txt @@ -1,4 +1,4 @@ 0 1 2 -3 \ No newline at end of file +3 diff --git a/EXAMPLES/CPML_examples/homogeneous_halfspace_HEX8_acoustic_elastic_absorbing_CPML_5sides/slices.txt b/EXAMPLES/CPML_examples/homogeneous_halfspace_HEX8_acoustic_elastic_absorbing_CPML_5sides/slices.txt index e8c63f701..bc856dafa 100644 --- a/EXAMPLES/CPML_examples/homogeneous_halfspace_HEX8_acoustic_elastic_absorbing_CPML_5sides/slices.txt +++ b/EXAMPLES/CPML_examples/homogeneous_halfspace_HEX8_acoustic_elastic_absorbing_CPML_5sides/slices.txt @@ -1,4 +1,4 @@ 0 1 2 -3 \ No newline at end of file +3 diff --git a/EXAMPLES/CPML_examples/homogeneous_halfspace_HEX8_acoustic_elastic_absorbing_CPML_6sides/slices.txt b/EXAMPLES/CPML_examples/homogeneous_halfspace_HEX8_acoustic_elastic_absorbing_CPML_6sides/slices.txt index e8c63f701..bc856dafa 100644 --- a/EXAMPLES/CPML_examples/homogeneous_halfspace_HEX8_acoustic_elastic_absorbing_CPML_6sides/slices.txt +++ b/EXAMPLES/CPML_examples/homogeneous_halfspace_HEX8_acoustic_elastic_absorbing_CPML_6sides/slices.txt @@ -1,4 +1,4 @@ 0 1 2 -3 \ No newline at end of file +3 diff --git a/EXAMPLES/CPML_examples/homogeneous_halfspace_HEX8_elastic_absorbing_CPML_5sides/slices.txt b/EXAMPLES/CPML_examples/homogeneous_halfspace_HEX8_elastic_absorbing_CPML_5sides/slices.txt index e8c63f701..bc856dafa 100644 --- a/EXAMPLES/CPML_examples/homogeneous_halfspace_HEX8_elastic_absorbing_CPML_5sides/slices.txt +++ b/EXAMPLES/CPML_examples/homogeneous_halfspace_HEX8_elastic_absorbing_CPML_5sides/slices.txt @@ -1,4 +1,4 @@ 0 1 2 -3 \ No newline at end of file +3 diff --git a/EXAMPLES/CPML_examples/homogeneous_halfspace_HEX8_elastic_absorbing_CPML_6sides/slices.txt b/EXAMPLES/CPML_examples/homogeneous_halfspace_HEX8_elastic_absorbing_CPML_6sides/slices.txt index e8c63f701..bc856dafa 100644 --- a/EXAMPLES/CPML_examples/homogeneous_halfspace_HEX8_elastic_absorbing_CPML_6sides/slices.txt +++ b/EXAMPLES/CPML_examples/homogeneous_halfspace_HEX8_elastic_absorbing_CPML_6sides/slices.txt @@ -1,4 +1,4 @@ 0 1 2 -3 \ No newline at end of file +3 diff --git a/EXAMPLES/DSM_FOR_SPECFEM3D/example_simple_small/station_for_simulation.txt b/EXAMPLES/DSM_FOR_SPECFEM3D/example_simple_small/station_for_simulation.txt index e69de29bb..bf1a0967f 100644 --- a/EXAMPLES/DSM_FOR_SPECFEM3D/example_simple_small/station_for_simulation.txt +++ b/EXAMPLES/DSM_FOR_SPECFEM3D/example_simple_small/station_for_simulation.txt @@ -0,0 +1,47 @@ +PREFIX=velocity_Z_it +OUT=./movie + + +declare -i it itmax istep + + +istep=25 +itmax=3500 #30000 + + +it=0 + +while [ "$it" -le "$itmax" ] ; do + + if [ "$it" -lt 1000000 ]; then + FICHIER=$PREFIX${it} + fi; + + if [ "$it" -lt 100000 ]; then + FICHIER=$PREFIX"0"${it} + fi; + + if [ "$it" -lt 10000 ]; then + FICHIER=$PREFIX"00"${it} + fi; + + if [ "$it" -lt 1000 ]; then + FICHIER=$PREFIX"000"${it} + fi; + + if [ "$it" -lt 100 ]; then + FICHIER=$PREFIX"0000"${it} + fi; + + + echo $FICHIER.mesh + ./mesh2vtu.pl -i $OUT/$FICHIER.mesh -o $FICHIER.vtu + it="$it+$istep" + +done; + +echo $PREFIX + +mv $PREFIX* ./movie_vtu/ + + diff --git a/EXAMPLES/Mount_StHelens/convert_lonlat2utm.pl b/EXAMPLES/Mount_StHelens/convert_lonlat2utm.pl index c6dd65cb3..45ae5790d 100755 --- a/EXAMPLES/Mount_StHelens/convert_lonlat2utm.pl +++ b/EXAMPLES/Mount_StHelens/convert_lonlat2utm.pl @@ -93,9 +93,9 @@ sub geo2utm { #! some extracts about UTM: #! -#! There are 60 longitudinal projection zones numbered 1 to 60 starting at 180°W. +#! There are 60 longitudinal projection zones numbered 1 to 60 starting at 180 degrees W. #! Each of these zones is 6 degrees wide, apart from a few exceptions around Norway and Svalbard. -#! There are 20 latitudinal zones spanning the latitudes 80°S to 84°N and denoted +#! There are 20 latitudinal zones spanning the latitudes 80 degrees S to 84 degrees N and denoted #! by the letters C to X, ommitting the letter O. #! Each of these is 8 degrees south-north, apart from zone X which is 12 degrees south-north. #! diff --git a/EXAMPLES/homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides/slices.txt b/EXAMPLES/homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides/slices.txt index e8c63f701..bc856dafa 100644 --- a/EXAMPLES/homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides/slices.txt +++ b/EXAMPLES/homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides/slices.txt @@ -1,4 +1,4 @@ 0 1 2 -3 \ No newline at end of file +3 diff --git a/EXAMPLES/homogeneous_halfspace_HEX8_elastic_no_absorbing/slices.txt b/EXAMPLES/homogeneous_halfspace_HEX8_elastic_no_absorbing/slices.txt index e8c63f701..bc856dafa 100644 --- a/EXAMPLES/homogeneous_halfspace_HEX8_elastic_no_absorbing/slices.txt +++ b/EXAMPLES/homogeneous_halfspace_HEX8_elastic_no_absorbing/slices.txt @@ -1,4 +1,4 @@ 0 1 2 -3 \ No newline at end of file +3 diff --git a/doc/GJI_2011_paper_about_the_code/paper_GJI_2011_about_the_code.tex b/doc/GJI_2011_paper_about_the_code/paper_GJI_2011_about_the_code.tex index de0398478..88de94e75 100644 --- a/doc/GJI_2011_paper_about_the_code/paper_GJI_2011_about_the_code.tex +++ b/doc/GJI_2011_paper_about_the_code/paper_GJI_2011_about_the_code.tex @@ -378,7 +378,7 @@ \subsection{Acoustic domain}\label{subsec:acoustic} \bv = \rho^{-1}\,\bnabla \partial_t \phi\, , \eequ \bequ - p = \mbox{} - \kappa\, (\bnabla \cdot \bs ) = \mbox{}- \partial_t^2 \phi\, . \label{equ:pressure} + p = \mbox{} - \kappa\, (\bnabla \cdot \bs ) = \mbox{}- \partial_t^2 \phi\, . \label{equ:pressure} \eequ The resulting formulation for pressure $p$ is the reason why we choose to define the potential $\phi$ as in equation (\ref{equ:acousticdisplacement}). Since pressure is continuous across first-order discontinuities, @@ -899,7 +899,7 @@ \section{Conclusions and future work}\label{sec:Conclusions} The goal is to harness the power of forward and adjoint modeling tools, such as \href{http://www.geodynamics.org/cig/software/specfem3d}{SPECFEM3D}, together with modern computers to enhance -the quality of images of Earths interior and the earthquake rupture process. +the quality of images of Earth's interior and the earthquake rupture process. Most traditional tomographic methods utilize traveltime or phase information measured by comparing data with simulations, and interpret such measurements based on ray theory or other approximate methods. Because of the limitations of these approximate theories, only parts of seismograms can be used, @@ -963,7 +963,7 @@ \subsection{Pressure waveform misfit kernels}\label{appendix:acoustickernels1} The corresponding action in the acoustic case is given by \bequ \chi = \frac{1}{2} \sum_i \int || p_i^{\mathrm{syn}} - p_i^{\mathrm{obs}} ||^2 \, \mathrm{d}t - - \int \int_{\Omega} \lambda\, \left[ \kappa^{-1}\, \partial_t^2 \phi - \bnabla \cdot \left( \rho^{-1} \,\bnabla \phi \right) - f \right] \,\mathrm{d}^3\bx \, \mathrm{d}t\,, + - \int \int_{\Omega} \lambda\, \left[ \kappa^{-1}\, \partial_t^2 \phi - \bnabla \cdot \left( \rho^{-1} \,\bnabla \phi \right) - f \right] \,\mathrm{d}^3\bx \, \mathrm{d}t\,, \eequ where $\lambda$ denotes a scalar Lagrange multiplier. Setting $ \Delta p_i = p_i^{\mathrm{syn}} - p_i^{\mathrm{obs}}$ diff --git a/doc/README_gravityPerturbation_bis.txt b/doc/README_gravityPerturbation_bis.txt index 0074d702f..dc04497b9 100644 --- a/doc/README_gravityPerturbation_bis.txt +++ b/doc/README_gravityPerturbation_bis.txt @@ -1,13 +1,13 @@ -SPECFEM3D has the capability to compute the perturbations of gravity -induced by seismic waves at arbitrary locations above the Earth's surface. -The current file documents the usage of this feature and the related code +SPECFEM3D has the capability to compute the perturbations of gravity +induced by seismic waves at arbitrary locations above the Earth's surface. +The current file documents the usage of this feature and the related code modifications. Theory ------ -The computation of gravity perturbations induced by deformation is based on +The computation of gravity perturbations induced by deformation is based on equation 4 of: J. Harms, R. DeSalvo, S. Dorsher and V. Mandic (2009), "Simulation of underground gravity gradients from stochastic seismic fields", Phys. Rev. D, 80, 122001 @@ -16,8 +16,8 @@ gravity gradients from stochastic seismic fields", Phys. Rev. D, 80, 122001 Enabling gravity computations ----------------------------- -Gravity perturbation can be computed in any SPECFEM3D simulation by -placing a file called "gravity_stations" in the DATA directory, in +Gravity perturbation can be computed in any SPECFEM3D simulation by +placing a file called "gravity_stations" in the DATA directory, in addition to the regular input files. @@ -26,15 +26,15 @@ Input file format The format of the "gravity_stations" input file is: -n dt_gap -x1 y1 z1 -x2 y2 z2 -... ... ... -xn yn zn +n dt_gap +x1 y1 z1 +x2 y2 z2 +... ... ... +xn yn zn where n : number of stations where gravity time series are needed - dt_gap : gravity time series are sampled every dt_gap time steps of the + dt_gap : gravity time series are sampled every dt_gap time steps of the SPECFEM3D simulation @@ -44,22 +44,22 @@ Output file format Time series of gravity are output in files named "OUTPUT_FILES/stat*.grav", where * is the station index (one file per station). Their format is four columns: - t ax ay az + t ax ay az (time and acceleration along x, y and z, respectively). Code modifications ------------------ -All the routines related to the gravity perturbation computations are -placed in one module called specfem3d/gravity_perturbation.f90. The module -provides three public subroutines and a flag. Each subroutine is invoked +All the routines related to the gravity perturbation computations are +placed in one module called specfem3d/gravity_perturbation.f90. The module +provides three public subroutines and a flag. Each subroutine is invoked in one of the following stages: - 1. during the initialization, - 2. during the iterative time stepping scheme and + 1. during the initialization, + 2. during the iterative time stepping scheme and 3. at the output stage. -In #1 the code checks for the presence of the input file "gravity_stations". -If the file exists, the flag "GRAVITY_SIMULATION" is turned on and the +In #1 the code checks for the presence of the input file "gravity_stations". +If the file exists, the flag "GRAVITY_SIMULATION" is turned on and the subroutines #2 and #3 are invoked. diff --git a/list_for_Zhinan_for_SPECFEM3D_PMLs.txt b/list_for_Zhinan_for_SPECFEM3D_PMLs.txt index c2c636e74..9fb3910b5 100644 --- a/list_for_Zhinan_for_SPECFEM3D_PMLs.txt +++ b/list_for_Zhinan_for_SPECFEM3D_PMLs.txt @@ -5,7 +5,7 @@ Subject: Re:Re: PML Date: Wed, 17 Dec 2014 19:41:23 +0800 (CST) From: xiezhinan To: Dimitri Komatitsch -CC: Jeroen Tromp , Matthieu Lefebvre , Ryan Modrak , Alexis Bottero , Daniel Peter , Mathilde Griveaux , Paul Cristini , Clément Durochat , Yi Wang , Vadim Monteiller +CC: Jeroen Tromp , Matthieu Lefebvre , Ryan Modrak , Alexis Bottero , Daniel Peter , Mathilde Griveaux , Paul Cristini , Clement Durochat , Yi Wang , Vadim Monteiller Dear Dimitri, dear all, @@ -53,16 +53,16 @@ Zhinan Subject: Re: PML Date: Thu, 22 Jan 2015 01:43:52 +0100 -From: Dimitri Komatitsch +From: Dimitri Komatitsch Organization: CNRS, Marseille, France To: xiezhinan -CC: Jeroen Tromp , Matthieu Lefebvre , Ryan Modrak , Alexis Bottero , Daniel Peter , Mathilde Griveaux , Paul Cristini , Clément Durochat , Yi Wang , Vadim Monteiller +CC: Jeroen Tromp , Matthieu Lefebvre , Ryan Modrak , Alexis Bottero , Daniel Peter , Mathilde Griveaux , Paul Cristini , Clement Durochat , Yi Wang , Vadim Monteiller Dear Zhinan, dear all, -I would add one more thing to the list (we discussed it in the Skype -call of Dec 22): committing the fluid-solid boundary kernels that are -currently implemented in a local version in your account of the +I would add one more thing to the list (we discussed it in the Skype +call of Dec 22): committing the fluid-solid boundary kernels that are +currently implemented in a local version in your account of the Marseille supercomputer but not committed to Git yet. Thanks, @@ -146,7 +146,7 @@ going on. Subject: Re: [specfem3d] Runing both PML and attenuation causes error results (#356) Date: Tue, 20 Jan 2015 23:58:21 +0100 -From: Dimitri Komatitsch +From: Dimitri Komatitsch Organization: CNRS, Marseille, France To: geodynamics/specfem3d , specfem3d-zhang-ksu CC: Zhinan Xie @@ -239,7 +239,7 @@ Hi Zhinan, OK, thank you very much for your answer. I suggest we proceed as you plan below, i.e. in the next few days you can start cleaning the code -(please do a git pull because Clément and Yi as well as Vadim have +(please do a git pull because Clement and Yi as well as Vadim have changed many things in the code) and you can start merging all your contributions from the last few months, which are not committed yet. Then, as soon as all of this is merged Vadim can have a look at how to @@ -305,9 +305,9 @@ On 10/28/2014 01:52 PM, xiezhinan wrote: 3/ add a more flexible function for scale factor and fix one error in create_mass_matrices.f90: Date: Tue, 24 Jun 2014 07:15:03 +0800 -From: 谢志南 NGLOB_AB,(realw*)mp->d_potential_dot_dot_acoustic, incr); diff --git a/src/decompose_mesh/scotch_5.1.12b/LICENCE_fr.txt b/src/decompose_mesh/scotch_5.1.12b/LICENCE_fr.txt deleted file mode 100644 index 89250d526..000000000 --- a/src/decompose_mesh/scotch_5.1.12b/LICENCE_fr.txt +++ /dev/null @@ -1,7 +0,0 @@ -Cette copie de la distribution logicielle Scotch 5.1 est distribue -selon les termes de la licence de logiciel libre CeCILL-C. - -Une copie du texte de cette licence se trouve dans le sous-rpertoire -"doc", dans le fichier appel "CeCILL-C_V1-fr.txt". Veuillez en lire -attentivement les clauses. Vous ne pourrez utiliser cette copie de la -distribution logicielle Scotch 5.1 que si vous les acceptez. diff --git a/src/decompose_mesh/scotch_5.1.12b/LISEZ-MOI.txt b/src/decompose_mesh/scotch_5.1.12b/LISEZ-MOI.txt deleted file mode 100644 index 1dc6dabcd..000000000 --- a/src/decompose_mesh/scotch_5.1.12b/LISEZ-MOI.txt +++ /dev/null @@ -1,8 +0,0 @@ -Les clauses selon lesquelles cette copie de la distribution logicielle -Scotch 5.1 est mise votre disposition sont dfinies dans le fichier -"LICENCE_fr.txt", situ dans le mme rpertoire que le prsent -fichier. - -Si vous les acceptez, veuillez vous rfrer au fichier "INSTALL.txt", -galement situ dans ce rpertoire, pour consulter les instructions -d'installation. diff --git a/src/generate_databases/model_1d_prem.f90 b/src/generate_databases/model_1d_prem.f90 index 51590905f..c0fcc88ac 100644 --- a/src/generate_databases/model_1d_prem.f90 +++ b/src/generate_databases/model_1d_prem.f90 @@ -31,7 +31,7 @@ ! ! A. M. Dziewonski and D. L. Anderson. ! Preliminary reference Earth model. -! Phys. Earth Planet. Inter., 25:297–356, 1981. +! Phys. Earth Planet. Inter., 25:297-356, 1981. ! ! Isotropic (iso) and transversely isotropic (aniso) version of the ! spherically symmetric Preliminary Reference Earth Model diff --git a/src/meshfem3D/earth_chunk_HEX27_Mesher.f90 b/src/meshfem3D/earth_chunk_HEX27_Mesher.f90 index 2cfed0f1c..3e50b31c7 100644 --- a/src/meshfem3D/earth_chunk_HEX27_Mesher.f90 +++ b/src/meshfem3D/earth_chunk_HEX27_Mesher.f90 @@ -587,8 +587,8 @@ subroutine earth_chunk_HEX27_Mesher(NGNOD) if (ilat==nel_lat-1) call write_Igm_file(41,ispec2Dymax,NGLLX,NGLLZ,ilon,iz,izshift,ilayer_current) ! stzmin - if (iz==0) then ! pas besoin du test comme précédemment car je stocke tout dans des tableaux et c'est pas - ! grave si on récrit les memes choses + if (iz==0) then ! pas besoin du test comme precedemment car je stocke tout dans des tableaux et c'est pas + ! grave si on recrit les memes choses call calc_gll_points(xelm,yelm,zelm,xstore,ystore,zstore,shape3D,NGNOD,NGLLX,NGLLY,NGLLZ) call write_Igm_file(42,ispec2Dzmin,NGLLX,NGLLY,ilon,ilat,0,ilayer_current) diff --git a/src/meshfem3D/earth_chunk_HEX8_Mesher.f90 b/src/meshfem3D/earth_chunk_HEX8_Mesher.f90 index 077b0061f..e0624dd0b 100644 --- a/src/meshfem3D/earth_chunk_HEX8_Mesher.f90 +++ b/src/meshfem3D/earth_chunk_HEX8_Mesher.f90 @@ -504,8 +504,8 @@ subroutine earth_chunk_HEX8_Mesher(NGNOD) if (ilat==nel_lat-1) call write_Igm_file(41,ispec2Dymax,NGLLX,NGLLZ,ilon,iz,izshift,ilayer_current) ! stzmin - if (iz==0) then ! pas besoin du test comme précédemment car je stocke tout dans des tableaux et c'est pas - ! grave si on récrit les memes choses + if (iz==0) then ! pas besoin du test comme precedemment car je stocke tout dans des tableaux et c'est pas + ! grave si on recrit les memes choses call calc_gll_points(xelm,yelm,zelm,xstore,ystore,zstore,shape3D,NGNOD,NGLLX,NGLLY,NGLLZ) call write_Igm_file(42,ispec2Dzmin,NGLLX,NGLLY,ilon,ilat,0,ilayer_current) !open(125,file='ggl_elemts') diff --git a/src/meshfem3D/earth_chunk_all_Utils.f90 b/src/meshfem3D/earth_chunk_all_Utils.f90 index 3a76a020a..41ecb5c73 100644 --- a/src/meshfem3D/earth_chunk_all_Utils.f90 +++ b/src/meshfem3D/earth_chunk_all_Utils.f90 @@ -317,7 +317,7 @@ subroutine write_stxmin(xstore,ystore,zstore,NGLLX,NGLLY,NGLLZ,rotation_matrix,t long=atan2(y,x) lati=asin(z/rayon) - ! passage de geocentique à géographique + ! passage de geocentique a geographique !!theta = PI/2.D0 - lati ! convert the geocentric colatitude to a geographic colatitude !!colat = PI/2.0d0 - datan(1.006760466d0*dcos(theta)/dmax1(TINYVAL,dsin(theta))) @@ -375,7 +375,7 @@ subroutine write_stxmax(xstore,ystore,zstore,NGLLX,NGLLY,NGLLZ,rotation_matrix,t long=atan2(y,x) lati=asin(z/rayon) - ! passage de geocentique à géographique + ! passage de geocentique a geographique !!theta = PI/2.D0 - lati ! convert the geocentric colatitude to a geographic colatitude !!colat = PI/2.0d0 - datan(1.006760466d0*dcos(theta)/dmax1(TINYVAL,dsin(theta))) @@ -428,7 +428,7 @@ subroutine write_stymin(xstore,ystore,zstore,NGLLX,NGLLY,NGLLZ,rotation_matrix,t long=atan2(y,x) lati=asin(z/rayon) - ! passage de geocentique à géographique + ! passage de geocentique a geographique !!theta = PI/2.D0 - lati ! convert the geocentric colatitude to a geographic colatitude !!colat = PI/2.0d0 - datan(1.006760466d0*dcos(theta)/dmax1(TINYVAL,dsin(theta))) @@ -481,7 +481,7 @@ subroutine write_stymax(xstore,ystore,zstore,NGLLX,NGLLY,NGLLZ,rotation_matrix,t long=atan2(y,x) lati=asin(z/rayon) - ! passage de geocentique à géographique + ! passage de geocentique a geographique !!theta = PI/2.D0 - lati ! convert the geocentric colatitude to a geographic colatitude !!colat = PI/2.0d0 - datan(1.006760466d0*dcos(theta)/dmax1(TINYVAL,dsin(theta))) @@ -532,7 +532,7 @@ subroutine store_zmin_points(xstore,ystore,zstore,NGLLX,NGLLY,NGLLZ,rotation_mat long=atan2(y,x) lati=asin(z/rayon) - ! passage de geocentique à géographique + ! passage de geocentique a geographique !!theta = PI/2.D0 - lati ! convert the geocentric colatitude to a geographic colatitude !!colat = PI/2.0d0 - datan(1.006760466d0*dcos(theta)/dmax1(TINYVAL,dsin(theta))) @@ -627,7 +627,7 @@ end subroutine compute_rotation_matrix ! Vadim Monteiller Mars 2013 ! !------------------------------------------------------------------------------- -! matrice de rotation 3D d'axe "axe" et d'angle theta (d°) +! matrice de rotation 3D d'axe "axe" et d'angle theta (en degres) ! cette matrice est en complexe ! !======================================================================================================= diff --git a/src/shared/utm_geo.f90 b/src/shared/utm_geo.f90 index bc1b2e536..1446eb50b 100644 --- a/src/shared/utm_geo.f90 +++ b/src/shared/utm_geo.f90 @@ -77,9 +77,9 @@ subroutine utm_geo(rlon4,rlat4,rx4,ry4,UTM_PROJECTION_ZONE,iway,SUPPRESS_UTM_PRO ! Some general information about UTM: ! (for more details see e.g. http://en.wikipedia.org/wiki/Universal_Transverse_Mercator_coordinate_system ) ! -! There are 60 longitudinal projection zones numbered 1 to 60 starting at 180°W. +! There are 60 longitudinal projection zones numbered 1 to 60 starting at 180 degrees W. ! Each of these zones is 6 degrees wide, apart from a few exceptions around Norway and Svalbard. -! There are 20 latitudinal zones spanning the latitudes 80°S to 84°N and denoted +! There are 20 latitudinal zones spanning the latitudes 80 degrees S to 84 degrees N and denoted ! by the letters C to X, ommitting the letter O. ! Each of these is 8 degrees south-north, apart from zone X which is 12 degrees south-north. ! diff --git a/src/specfem3D/make_gravity.f90 b/src/specfem3D/make_gravity.f90 index a6a1f7855..188c53606 100644 --- a/src/specfem3D/make_gravity.f90 +++ b/src/specfem3D/make_gravity.f90 @@ -161,7 +161,7 @@ end subroutine make_gravity ! ! A. M. Dziewonski and D. L. Anderson. ! Preliminary reference Earth model. -! Phys. Earth Planet. Inter., 25:297–356, 1981. +! Phys. Earth Planet. Inter., 25:297-356, 1981. ! ! Isotropic (iso) and transversely isotropic (aniso) version of the ! spherically symmetric Preliminary Reference Earth Model diff --git a/src/specfem3D/prepare_timerun.F90 b/src/specfem3D/prepare_timerun.F90 index d7334b1b8..6bc31f4b0 100644 --- a/src/specfem3D/prepare_timerun.F90 +++ b/src/specfem3D/prepare_timerun.F90 @@ -1190,7 +1190,7 @@ subroutine prepare_timerun_GPU() call memory_eval_gpu() ! prepares general fields on GPU - !§!§ JC JC here we will need to add GPU support for the new C-PML routines + !! JC JC here we will need to add GPU support for the C-PML routines call prepare_constants_device(Mesh_pointer, & NGLLX, NSPEC_AB, NGLOB_AB, & xix, xiy, xiz, etax,etay,etaz, gammax, gammay, gammaz, & diff --git a/utils/ADJOINT_TOMOGRAPHY_TOOLS/ADJOINT_TOMOGRAPHY_TOOLKIT/HowtoUseToolkit.tex b/utils/ADJOINT_TOMOGRAPHY_TOOLS/ADJOINT_TOMOGRAPHY_TOOLKIT/HowtoUseToolkit.tex index daed3a895..5e6f8812e 100644 --- a/utils/ADJOINT_TOMOGRAPHY_TOOLS/ADJOINT_TOMOGRAPHY_TOOLKIT/HowtoUseToolkit.tex +++ b/utils/ADJOINT_TOMOGRAPHY_TOOLS/ADJOINT_TOMOGRAPHY_TOOLKIT/HowtoUseToolkit.tex @@ -84,7 +84,7 @@ \subsection{ITERATION\_UPDATE} \item X05\_SRC\_UPDATE\_MODELS, update model parameters based on search directions \end{enumerate} -In Step 4 above, one should either 04a, 04b or 04c; in most cases, the best choice is 04c, which approximates the Hessian and thus +In Step 4 above, one should either 04a, 04b or 04c; in most cases, the best choice is 04c, which approximates the Hessian and thus converges much faster. From Wikipedia http://en.wikipedia.org/wiki/Limited-memory\_BFGS, here is a brief description of L-BFGS: @@ -146,7 +146,7 @@ \section{Suggestion by Dimitri Komatitsch, November 2012} - clarify somewhere if and when/why a pseudo-Hessian calculation could or should be done; explain how to use the internal flag "APPROXIMATE\_HESS\_KL" of the code -- mention somewhere that Vadim and Sébastien Chevrot will commit their routines to interpolate back and forth between the SEM mesh and a regular mesh; mention that we should talk to Qinya about this, since she was in the process of implementing that as well (I think that Vadim and Sébastien's routine will be sufficient, but we should doublecheck with Qinya if she had something different (more powerful? or faster?) in mind +- mention somewhere that Vadim and Sebastien Chevrot will commit their routines to interpolate back and forth between the SEM mesh and a regular mesh; mention that we should talk to Qinya about this, since she was in the process of implementing that as well (I think that Vadim and Sebastien's routine will be sufficient, but we should doublecheck with Qinya if she had something different (more powerful? or faster?) in mind - what about boundary kernels, as developed by Qinya a few years ago? we forgot to talk about this yesterday, and they are not mentioned in the document; I guess they are inactive by default, but can one use them, and if so how? and are there scripts to use for that? @@ -175,7 +175,7 @@ \section{Suggestion by Dimitri Komatitsch, November 2012} - clarify somewhere if and when/why a pseudo-Hessian calculation could or should be done; explain how to use the internal flag "APPROXIMATE\_HESS\_KL" of the code -- mention somewhere that Vadim and Sébastien Chevrot will commit their routines to interpolate back and forth between the SEM mesh and a regular mesh; mention that we should talk to Qinya about this, since she was in the process of implementing that as well (I think that Vadim and Sébastien's routine will be sufficient, but we should doublecheck with Qinya if she had something different (more powerful? or faster?) in mind +- mention somewhere that Vadim and Sebastien Chevrot will commit their routines to interpolate back and forth between the SEM mesh and a regular mesh; mention that we should talk to Qinya about this, since she was in the process of implementing that as well (I think that Vadim and Sebastien's routine will be sufficient, but we should doublecheck with Qinya if she had something different (more powerful? or faster?) in mind - what about boundary kernels, as developed by Qinya a few years ago? we forgot to talk about this yesterday, and they are not mentioned in the document; I guess they are inactive by default, but can one use them, and if so how? and are there scripts to use for that? diff --git a/utils/ADJOINT_TOMOGRAPHY_TOOLS/measure_adj/measure_adj.f90 b/utils/ADJOINT_TOMOGRAPHY_TOOLS/measure_adj/measure_adj.f90 index af698c600..408d33681 100644 --- a/utils/ADJOINT_TOMOGRAPHY_TOOLS/measure_adj/measure_adj.f90 +++ b/utils/ADJOINT_TOMOGRAPHY_TOOLS/measure_adj/measure_adj.f90 @@ -6,7 +6,7 @@ program measure_adj ! input parameter: ! 1. imeas = 1, normalized waveform difference. Adjoint source is constructed from the data ! only, with the form -d(t)/ || d(t) || 2 - ! 2. imeas = 2, waveform difference, s(t) − d(t). + ! 2. imeas = 2, waveform difference, s(t) - d(t). ! 3. imeas = 3, cross-correlation traveltime difference for a (banana-doughtnut) sensitivity ker- ! nel. The measurement between data and synthetics is not used in constructing the adjoint ! source. diff --git a/utils/DSM_FOR_SPECFEM3D/NOTE--HOWTO_from_Yi_Wang_to_reproduce_the_DSM_results_from_SHdiff_SVdiff_splitting_in_a_isotropic_Earth_from_2010.txt b/utils/DSM_FOR_SPECFEM3D/NOTE--HOWTO_from_Yi_Wang_to_reproduce_the_DSM_results_from_SHdiff_SVdiff_splitting_in_a_isotropic_Earth_from_2010.txt index 6950cac33..70dec6635 100644 --- a/utils/DSM_FOR_SPECFEM3D/NOTE--HOWTO_from_Yi_Wang_to_reproduce_the_DSM_results_from_SHdiff_SVdiff_splitting_in_a_isotropic_Earth_from_2010.txt +++ b/utils/DSM_FOR_SPECFEM3D/NOTE--HOWTO_from_Yi_Wang_to_reproduce_the_DSM_results_from_SHdiff_SVdiff_splitting_in_a_isotropic_Earth_from_2010.txt @@ -12,32 +12,32 @@ Dimitri Komatitsch , Sebastien Chevrot Dear Laura, > -> Thank you very much for your email. Let me cc our new PhD student, Yi -> Wang, who can send you all the input files and filtering routines -> because he has redone that calculation recently (last month) using the +> Thank you very much for your email. Let me cc our new PhD student, Yi +> Wang, who can send you all the input files and filtering routines +> because he has redone that calculation recently (last month) using the > DSM code. > -> Please note that we did not use the classical IASP91 model, we used a -> filtered / modified version (no crust, and smoothed d410 and d670). I do -> not remember having problems with high frequencies; we did filter very -> low frequencies a little bit (not much) because one of the 1D codes had +> Please note that we did not use the classical IASP91 model, we used a +> filtered / modified version (no crust, and smoothed d410 and d670). I do +> not remember having problems with high frequencies; we did filter very +> low frequencies a little bit (not much) because one of the 1D codes had > small problems computing them (DSM or GEMINI, I do not remember). -> Absolute amplitudes do not matter, i.e. even if they are small the -> calculation is as accurate as if they were high because the wave +> Absolute amplitudes do not matter, i.e. even if they are small the +> calculation is as accurate as if they were high because the wave > equation is linear. > -> Yi, could you please send Laura all the input files and scripts for DSM +> Yi, could you please send Laura all the input files and scripts for DSM > for that calculation? > > Thanks, @@ -46,10 +46,10 @@ Dear Laura, > Dimitri. > > On 29/05/2014 13:19, Laura Parisi (ENV) wrote: ->> Dear Dimitri, my name is Laura Parisi and I am a PhD student in seismology working with Ana Ferreira (in Cc). I hope to not bother you too much with this email where I would like to ask you something about your work published in JGR in 2010 ('SHdiff-SVdiff splitting in a isotropic Earth'). I tried to reproduce your results, in particular figure 2 (left side) and 3, where you used your modified version of IASP91 model without any other perturbation in the D''. I have obtained a good match for figure 2 (seismograms in displacement at epicentral distance of 100°) but I am still struggling with figure 3 (seismograms in velocity at epicentral distance from 90° to 120°). For figure 2, the only processing I did is the convolution with the source function you indicate in the paper and using the script contained in the specfem package. For figure 3, I derivate to obtain the velocity seismograms but for epicentral distance larger than 104° I obtain seismograms containing very high frequencies (I think because the displacement amplitudes are very small). Then, I tried various filters to eliminate this effects but I couldn't obtain your same results. I suppose you did filter the seismograms in figure 3 but guessing exactly how is difficult! If you could advice me regarding the processing to obtain the results shown in figure 3, it would be very appreciated! :) Many thanks. Best regards, Laura --------------------------------------------------------------- --------------------------------------------------------------- Ph.D. student in Seismology School of Environmental Sciences University of East Anglia Norwich Research Park Norwich, NR4 7TJ, UK --------------------------------------------------------------- --------------------------------------------------------------- +>> Dear Dimitri, my name is Laura Parisi and I am a PhD student in seismology working with Ana Ferreira (in Cc). I hope to not bother you too much with this email where I would like to ask you something about your work published in JGR in 2010 ('SHdiff-SVdiff splitting in a isotropic Earth'). I tried to reproduce your results, in particular figure 2 (left side) and 3, where you used your modified version of IASP91 model without any other perturbation in the D''. I have obtained a good match for figure 2 (seismograms in displacement at epicentral distance of 100?) but I am still struggling with figure 3 (seismograms in velocity at epicentral distance from 90? to 120?). For figure 2, the only processing I did is the convolution with the source function you indicate in the paper and using the script contained in the specfem package. For figure 3, I derivate to obtain the velocity seismograms but for epicentral distance larger than 104? I obtain seismograms containing very high frequencies (I think because the displacement amplitudes are very small). Then, I tried various filters to eliminate this effects but I couldn't obtain your same results. I suppose you did filter the seismograms in figure 3 but guessing exactly how is difficult! If you could advice me regarding the processing to obtain the results shown in figure 3, it would be very appreciated! :) Many thanks. Best regards, Laura --------------------------------------------------------------- --------------------------------------------------------------- Ph.D. student in Seismology School of Environmental Sciences University of East Anglia Norwich Research Park Norwich, NR4 7TJ, UK --------------------------------------------------------------- --------------------------------------------------------------- + + - - Attachments: -DSM_cleaned_smooth_model_0_1hz.tar.bz2 3,3 MB \ No newline at end of file +DSM_cleaned_smooth_model_0_1hz.tar.bz2 3,3 MB diff --git a/utils/DSM_FOR_SPECFEM3D/NOTE-DONE-for_integration_of_the_coupling.txt b/utils/DSM_FOR_SPECFEM3D/NOTE-DONE-for_integration_of_the_coupling.txt index 387afce2e..997163cfb 100644 --- a/utils/DSM_FOR_SPECFEM3D/NOTE-DONE-for_integration_of_the_coupling.txt +++ b/utils/DSM_FOR_SPECFEM3D/NOTE-DONE-for_integration_of_the_coupling.txt @@ -1,42 +1,42 @@ -Mail de Vadim : +Mail de Vadim : -Subject: Re: Clément Durochat will contact you tomorrow about SEM - DSM coupling +Subject: Re: Clement Durochat will contact you tomorrow about SEM - DSM coupling Date: Tue, 20 May 2014 19:03:30 +0200 From: Vadim MONTEILLER -To: Clément Durochat, Yi Wang, Dimitri Komatitsch, Sebastien Chevrot +To: Clement Durochat, Yi Wang, Dimitri Komatitsch, Sebastien Chevrot Hi, -the coupled SPECFEM code is SPECFEM3D_HYBRID_VADIM_version_non_official. -Before running it you must run DSM code in order to create the incident -wavefield on the box boundary. DSM consists in 4 steps. Each code is in +the coupled SPECFEM code is SPECFEM3D_HYBRID_VADIM_version_non_official. +Before running it you must run DSM code in order to create the incident +wavefield on the box boundary. DSM consists in 4 steps. Each code is in Part1(2,3,4)_* directory. In the example directory, there is a benchmark to run all process (DSM+ SPECFEM) : bacchus_run_benchmark_all_process.sh. ======================================================== -Liste des fichiers déjà modifiés committés dans GitHub : +Liste des fichiers deja modifies committes dans GitHub : ======================================================== -src/specfem3D/compute_add_sources_viscoelastic.f90 -==> Certains critères d'arrêts qui n'était pas listés ==> demander à Dimitri +src/specfem3D/compute_add_sources_viscoelastic.f90 +==> Certains criteres d'arrets qui n'etait pas listes ==> demander a Dimitri src/generate_databases/get_absorbing_boundary.f90 -==> a priori, enlever fichier xmin_gll... (debuggage only). Cf iboun(:,:)=.true. : laisser ou pas ?? ==> demander à Dimitri +==> a priori, enlever fichier xmin_gll... (debuggage only). Cf iboun(:,:)=.true. : laisser ou pas ?? ==> demander a Dimitri src/specfem3D/compute_stacey_(visco)elastic.f90 ==> mettre commentaire routine read_dsm_file, changer OLD_TEST... en COUPLE_WI..., laisser pour ..._GPU ==> ok a priori -src/specfem3D/prepare_timerun.f90 +src/specfem3D/prepare_timerun.f90 ==> cf truc avec VM STDE ==> Ok, cf commentaire l.288 src/generate_databases/save_arrays_solver.f90 ==> ok, on oublie le src/specfem3D/save_arrays_solver_1---to_check.f90 pour l'instant -src/specfem3D/read_mesh_databases.f90 +src/specfem3D/read_mesh_databases.f90 ==> cf truc avec VM STDE ==> Ok, RAS src/specfem3D/write_movie_output.f90 @@ -49,12 +49,12 @@ src/shared/read_parameter_file.f90 ==> RAS src/specfem3D/initialize_simulation.f90 -==> RAS +==> RAS src/specfem3D/compute_kernels.f90 ==> RAS -src/specfem3D/compute_forces_viscoelastic_calling_routine.F90 +src/specfem3D/compute_forces_viscoelastic_calling_routine.F90 ==> RAS src/specfem3D/iterate_time.f90 @@ -64,56 +64,56 @@ src/specfem3D/specfem3D_par.f90 ==> RAS ----------------------------------------------------------- -Ces deux là, modifiés mais pour l'instant on y touche pas : +Ces deux la, modifies mais pour l'instant on y touche pas : ----------------------------------------------------------- src/generate_databases/get_model.f90 src/generate_databases/model_tomography.f90 -==> Modifiés à partir des ceux de specfem existants. On les mets pas pour l'instant, il faudra peut-être y revenir pour certains modèles, à ne pas oublier +==> Modifies a partir des ceux de specfem existants. On les mets pas pour l'instant, il faudra peut-etre y revenir pour certains modeles, a ne pas oublier -VM a dit : "Il faut réfléchir a ces codes pour qu'il puissent aussi générer des modèles à partir de PREM, AK135 ou IASP91 sans modifier leur comportement habituel" +VM a dit : "Il faut reflechir a ces codes pour qu'il puissent aussi generer des modeles a partir de PREM, AK135 ou IASP91 sans modifier leur comportement habituel" ==> NORMALEMENT C'EST REGLE !! ============================================================== -+++++++++++++++++++ !! Attention !! 4 fichiers à voir encore : ++++++++++++++++++++ !! Attention !! 4 fichiers a voir encore : ============================================================== ------------------------------------- -Ces deux ci, situation particulière : +Ces deux ci, situation particuliere : ------------------------------------- -src/specfem3D/save_arrays_solver_1---to_check.f90 !! => nom modifié de src/specfem3D/save_arrays_solver_1.f90, quel différence avec src/generate_databases/save_arrays_solver.f90 à part des déclarations ? +src/specfem3D/save_arrays_solver_1---to_check.f90 !! => nom modifie de src/specfem3D/save_arrays_solver_1.f90, quel difference avec src/generate_databases/save_arrays_solver.f90 a part des declarations ? ==> A oublier pour le moment -src/specfem3D/v_model_update.f90 => Attention !! => nom modifié et placé dans auxiliaries (*model_update_Vadim_specific.f90* et *model_update.f90*) par Dimitri, et attention, pas de balise VM pour les modifs dedans (cf *model_update_Vadim_specific.f90* et *model_update.f90* => a remplacer dans auxiliaries ? Dans quel fichier ?) -==> Modifiés à partir des ceux de specfem existants. On les mets pas pour l'instant, il faudra surement y revenir pour faire de l'imagerie (pb inverse). +src/specfem3D/v_model_update.f90 => Attention !! => nom modifie et place dans auxiliaries (*model_update_Vadim_specific.f90* et *model_update.f90*) par Dimitri, et attention, pas de balise VM pour les modifs dedans (cf *model_update_Vadim_specific.f90* et *model_update.f90* => a remplacer dans auxiliaries ? Dans quel fichier ?) +==> Modifies a partir des ceux de specfem existants. On les mets pas pour l'instant, il faudra surement y revenir pour faire de l'imagerie (pb inverse). ---------------- -Et ces deux là : +Et ces deux la : ---------------- src/shared/project_tomo_grid.f90 src/shared/project_sem.f90 -==> Modifiés à partir des ceux de specfem existants. On les mets pas pour l'instant, il faudra surement y revenir pour faire de l'imagerie (pb inverse). +==> Modifies a partir des ceux de specfem existants. On les mets pas pour l'instant, il faudra surement y revenir pour faire de l'imagerie (pb inverse). -VM a dit : "Ce sont deux codes que j'ai ajouté qui permettent de projetter sur la grille d'inversion et vis vera. C'est utile que pour l'inversion. Je ne sais pas si il faut le mettre sous GIT. Cela demande de changer le configure, pour générer un makefile qui prenne en compte ces deux codes." +VM a dit : "Ce sont deux codes que j'ai ajoute qui permettent de projetter sur la grille d'inversion et vis vera. C'est utile que pour l'inversion. Je ne sais pas si il faut le mettre sous GIT. Cela demande de changer le configure, pour generer un makefile qui prenne en compte ces deux codes." ============================================================== -+++++++++++++++++++ !! Attention !! Ce dossier à voir encore : ++++++++++++++++++++ !! Attention !! Ce dossier a voir encore : ============================================================== *Utils_for_WFI* -==> Pour faire de l'imagerie (pb inverse). Pour l'instant, on met pas dans SPECFEM, à utiliser surement plus tard pour imagerie CMB. +==> Pour faire de l'imagerie (pb inverse). Pour l'instant, on met pas dans SPECFEM, a utiliser surement plus tard pour imagerie CMB. -VM a dit : "Il y a aussi tous les utilitaires pour faire de l'inversion *Utils_for_WFI*, il faudra réfléchir où le mettre, peut-être avec DSM?" +VM a dit : "Il y a aussi tous les utilitaires pour faire de l'inversion *Utils_for_WFI*, il faudra reflechir ou le mettre, peut-etre avec DSM?" ============================================================================================================ -Liste initiale de Vadim avec les répertoires (certain .f90 ont été changé en .F90), 14 fichiers à modifier : +Liste initiale de Vadim avec les repertoires (certain .f90 ont ete change en .F90), 14 fichiers a modifier : ============================================================================================================ src/generate_databases/get_absorbing_boundary.f90 @@ -123,10 +123,10 @@ src/specfem3D/initialize_simulation.f90 src/specfem3D/read_mesh_databases.f90 src/specfem3D/prepare_timerun.f90 src/specfem3D/compute_kernels.f90 -src/specfem3D/compute_forces_elastic.f90 ==> Attention !! => cp: cannot stat ‘src/specfem3D/compute_forces_elastic.f90’: No such file or directory => cf ce fichier, à remplacer par : *compute_forces_viscoelastic.f90*, *compute_forces_viscoelastic_Dev.F90* ou *compute_forces_viscoelastic_noDev.f90* +src/specfem3D/compute_forces_elastic.f90 ==> Attention !! => cp: cannot stat 'src/specfem3D/compute_forces_elastic.f90': No such file or directory => cf ce fichier, a remplacer par : *compute_forces_viscoelastic.f90*, *compute_forces_viscoelastic_Dev.F90* ou *compute_forces_viscoelastic_noDev.f90* src/specfem3D/compute_stacey_elastic.f90 src/specfem3D/save_arrays_solver_1.f90 src/specfem3D/iterate_time.f90 src/specfem3D/specfem3D_par.f90 src/specfem3D/write_movie_output.f90 -src/specfem3D/v_model_update.f90 +src/specfem3D/v_model_update.f90 diff --git a/utils/DSM_FOR_SPECFEM3D/NOTE-from_Vadim-HOWTO_use_his_scripts_for_FWI_with_SPECFEM_and_DSM_on_Curie_apr2014.txt b/utils/DSM_FOR_SPECFEM3D/NOTE-from_Vadim-HOWTO_use_his_scripts_for_FWI_with_SPECFEM_and_DSM_on_Curie_apr2014.txt index 1d296262f..846f6720d 100644 --- a/utils/DSM_FOR_SPECFEM3D/NOTE-from_Vadim-HOWTO_use_his_scripts_for_FWI_with_SPECFEM_and_DSM_on_Curie_apr2014.txt +++ b/utils/DSM_FOR_SPECFEM3D/NOTE-from_Vadim-HOWTO_use_his_scripts_for_FWI_with_SPECFEM_and_DSM_on_Curie_apr2014.txt @@ -3,7 +3,7 @@ Subject: scripts for Full Waveform Inversion (FWI) From: Vadim MONTEILLER Date: 09/04/2014 15:39 To: ywang -CC: Sébastien Chevrot, Dimitri Komatitsch +CC: Sebastien Chevrot, Dimitri Komatitsch Hi Yi, diff --git a/utils/DSM_FOR_SPECFEM3D/NOTE-todo_list_please_dont_remove_about_DSM_SPECFEM_coupled_code.txt b/utils/DSM_FOR_SPECFEM3D/NOTE-todo_list_please_dont_remove_about_DSM_SPECFEM_coupled_code.txt index 68935143f..98a6e91b0 100644 --- a/utils/DSM_FOR_SPECFEM3D/NOTE-todo_list_please_dont_remove_about_DSM_SPECFEM_coupled_code.txt +++ b/utils/DSM_FOR_SPECFEM3D/NOTE-todo_list_please_dont_remove_about_DSM_SPECFEM_coupled_code.txt @@ -4,12 +4,12 @@ Remark about the cost of the different parts: Quand je fais le processus complet, la partie 1 (calcul des coefs) prend ~20% du temps et dans cette partie, dcsymbl0 pend 80% du temps. -Ensuite il y a la partie 2 (lecture des coefs) qui prend ~50% du temps, et là les I/O peuvent nous permettre de gagner encore un peu. +Ensuite il y a la partie 2 (lecture des coefs) qui prend ~50% du temps, et la les I/O peuvent nous permettre de gagner encore un peu. -Le reste du temps (qu'on peut nommer partie 3) c'est aussi des I/O, ça consiste à passer de la base de données produite par DSM -à celle de SPECFEM3D. +Le reste du temps (qu'on peut nommer partie 3) c'est aussi des I/O, ca consiste a passer de la base de donnees produite par DSM +a celle de SPECFEM3D. -Si on résume : +Si on resume : + 20% du temps : calcul des coeffs @@ -24,22 +24,22 @@ Things to do: - for Vadim: ------------ - * Je crois que ce qu'il faut faire maintenant c'est rendre les écritures sur disque non bloquantes (d'une part) et parallèles (d'autre part) car c'est dans les MPI_ALLGATHERV() et dans les écritures sur disque pour chaque l qu'on doit perdre beaucoup de temps maintenant je pense -(sachant que l va souvent jusqu'à 20000, i.e. on le fait 20000 fois de suite). + * Je crois que ce qu'il faut faire maintenant c'est rendre les ecritures sur disque non bloquantes (d'une part) et paralleles (d'autre part) car c'est dans les MPI_ALLGATHERV() et dans les ecritures sur disque pour chaque l qu'on doit perdre beaucoup de temps maintenant je pense +(sachant que l va souvent jusqu'a 20000, i.e. on le fait 20000 fois de suite). -Pour faire cela, on va pouvoir supprimer tous les MPI_ALLGATHERV() (complètement) et utiliser un système de fichiers parallèle tel que MPI-IO, HDF5, ParallelNetCDF ou bien ADIOS. +Pour faire cela, on va pouvoir supprimer tous les MPI_ALLGATHERV() (completement) et utiliser un systeme de fichiers parallele tel que MPI-IO, HDF5, ParallelNetCDF ou bien ADIOS. * faire un flag qui permet soit: -- de faire le calcul pour les 6 sources elementaires. - -- de faire le calcul pour 1 tenseur des moments donné. + -- de faire le calcul pour 1 tenseur des moments donne. * fusionner les parties 2 et 3 du code maintenant qu'on a de bonnes perfs - * il faudra aussi ajouter le cas SH, qui d'après Nobuaki est beaucoup plus simple. + * il faudra aussi ajouter le cas SH, qui d'apres Nobuaki est beaucoup plus simple. - * a terme il faudra reformuler le pb en tenant compte de la discontinuite au niveau de la source + * a terme il faudra reformuler le pb en tenant compte de la discontinuite au niveau de la source dans le systeme d'equations (mettre une interface fictive, voir comment sont defini les conditions de raccord) - et non pas seulement dans le terme source. + et non pas seulement dans le terme source. * ecrire un nouveau fichier flags.guess qui prennent en compte les procs nehalem (pour specfem3D) @@ -47,12 +47,12 @@ Pour faire cela, on va pouvoir supprimer tous les MPI_ALLGATHERV() (complètemen * ecrire la deconvolution en fortran -* ajouter la possibilite d'utiliser la forme d'onde et au temps dans les inversions +* ajouter la possibilite d'utiliser la forme d'onde et au temps dans les inversions - for Dimitri: -------------- - * + * ====================================================================== diff --git a/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_Dimitri_two_different_problems_in_DSM.txt b/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_Dimitri_two_different_problems_in_DSM.txt index c897ba9cb..2962a9b01 100644 --- a/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_Dimitri_two_different_problems_in_DSM.txt +++ b/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_Dimitri_two_different_problems_in_DSM.txt @@ -2,7 +2,7 @@ Subject: two different problems in DSM From: Dimitri Komatitsch Date: 01/04/2014 14:41 -To: Sébastien Chevrot, Yi Wang, Vadim Monteiller, Roland Martin +To: Sebastien Chevrot, Yi Wang, Vadim Monteiller, Roland Martin Hi all, @@ -36,8 +36,8 @@ On 01/04/2014 13:25, Dimitri Komatitsch wrote: > Cheers, > Dimitri. > -> On 01/04/2014 07:23, Sébastien Chevrot wrote: ->> Le 01/04/14 01:26, Dimitri Komatitsch a écrit : +> On 01/04/2014 07:23, Sebastien Chevrot wrote: +>> Le 01/04/14 01:26, Dimitri Komatitsch a ecrit : >>> >>> Hi all, >>> @@ -69,10 +69,10 @@ On 01/04/2014 13:25, Dimitri Komatitsch wrote: >> When do you want to do this ? > --- +-- Dimitri Komatitsch CNRS Research Director (DR CNRS), Laboratory of Mechanics and Acoustics, UPR 7051, Marseille, France http://komatitsch.free.fr Attachments: -Takeuchi_Geller_Cummins_GRL_1996.pdf 410 KB +Takeuchi_Geller_Cummins_GRL_1996.pdf 410 KB diff --git a/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_Nobuaki_calcul_strain_tensor.txt b/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_Nobuaki_calcul_strain_tensor.txt index ee3bc4d42..5dfc18ad1 100644 --- a/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_Nobuaki_calcul_strain_tensor.txt +++ b/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_Nobuaki_calcul_strain_tensor.txt @@ -5,35 +5,35 @@ Dimitri Komatitsch Date: Thu, 02 Jul 2009 13:00:49 +0200 To: -冨士延章 +???? CC: -Sébastien Chevrot , Vadim Monteiller +Sebastien Chevrot , Vadim Monteiller Bonjour Nobuaki, -Ce n'est pas comme cela qu'il faut faire. Tu n'as pas besoin de nouveaux polynomes de Legendre locaux comme en SEM. Je te l'ai dit plusieurs fois déjà. Il te suffit de dériver spatialement les fonctions de base de DSM, c'est-à-dire de dériver les fonctions des équations (1), (12) et (13) de +Ce n'est pas comme cela qu'il faut faire. Tu n'as pas besoin de nouveaux polynomes de Legendre locaux comme en SEM. Je te l'ai dit plusieurs fois deja. Il te suffit de deriver spatialement les fonctions de base de DSM, c'est-a-dire de deriver les fonctions des equations (1), (12) et (13) de cet article : http://depot.univ-pau.fr/files/15_days/200972_1246532347CvPRG1/kawai_geller_dsm_2hz_seismograms_gji_2006.pdf -A bientôt, +A bientot, Dimitri. -冨士延章 wrote: +???? wrote: > Cher Dimitri: > -> Ok je vois ça (et puis désolé j'ai oublié ce que tu m'a dit -> parce que pour des dérivées partielles, ça semble marcher... -> donc en ce moment pour moi c'était très réalistique) +> Ok je vois ca (et puis desole j'ai oublie ce que tu m'a dit +> parce que pour des derivees partielles, ca semble marcher... +> donc en ce moment pour moi c'etait tres realistique) > -> Je peux discuter avec Dr. Takeuchi (il est maintenant l'assistant à ERI) -> demain ou la semaine prochaine, après un séminaire. -> Mais voilà ce qu'on a déjà discuté sur ce problème avec Dr. Mizutani +> Je peux discuter avec Dr. Takeuchi (il est maintenant l'assistant a ERI) +> demain ou la semaine prochaine, apres un seminaire. +> Mais voila ce qu'on a deja discute sur ce probleme avec Dr. Mizutani > qui aussi travaille sur le coding de DSM: > > Si on choisit une fonction de Legendre comme une "trial function" comme -> les gens de SEM font, c'est possible à analytiquement dériver le strain tensor. +> les gens de SEM font, c'est possible a analytiquement deriver le strain tensor. > > En fait, je vais discuter profondement avec Dr. Takeuchi, attendez-vous svp > @@ -46,39 +46,39 @@ Dimitri. > > Bonjour Nobuaki, > -> Ce n'est pas du tout une bonne idée d'utiliser une interpolation -> sur trois points pour calculer le strain tensor, comme je te l'ai déjà -> dit quand on a discuté à Toulouse. Car ce ne sera pas précis du tout. -> Ce qu'il faut c'est dériver analytiquement la base de fonctions -> utilisées -> dans le DSM afin de calculer des dérivées consistantes avec la technique +> Ce n'est pas du tout une bonne idee d'utiliser une interpolation +> sur trois points pour calculer le strain tensor, comme je te l'ai deja +> dit quand on a discute a Toulouse. Car ce ne sera pas precis du tout. +> Ce qu'il faut c'est deriver analytiquement la base de fonctions +> utilisees +> dans le DSM afin de calculer des derivees consistantes avec la technique > DSM. Les autres approches (interpolation par exemple) ne sont pas > bonnes. > Donc il faut que tu parles au Prof. Takeuchi pour voir comment faire > cela. > > Merci, -> Amitiés, +> Amities, > > Dimitri. > -> 冨士延章 wrote: +> ???? wrote: > > Cher Dimitri: > > -> > Pour faire des dérivées partielles 3-D, je dois modifier le code +> > Pour faire des derivees partielles 3-D, je dois modifier le code > de DSM > > pour gagner les "strain tensors" aussi. Donc automatiquement > > je suis en train de faire des strains avec l'interpolation des > trois points. > > -> > Amitiés, +> > Amities, > > > > Nobuaki > > > > > > -- > > ***************************************************** -> > FUJI Nobuaki (冨士　延章) +> > FUJI Nobuaki (?? ??) > > seismobassoon@gmail.com > > > (primary) @@ -105,9 +105,9 @@ Dimitri. > > > -> -- +> -- > ***************************************************** -> FUJI Nobuaki (冨士　延章) seismobassoon@gmail.com (primary) +> FUJI Nobuaki (?? ??) seismobassoon@gmail.com (primary) > fuji@eps.s.u-tokyo.ac.jp (will be expired in a year ihope) > Ph.D student 3rd at Lab. of Prof. R.J. Geller > Dept. of Earth and Planetary Science, @@ -118,7 +118,7 @@ Dimitri. > fax: +81-(0)3-5841-8318 > mobile: +81-(0)90-9995-9859 --- +-- Dimitri Komatitsch - dimitri.komatitsch aT univ-pau.fr Professor, University of Pau, Institut universitaire de France, CNRS and INRIA Magique3D, France http://www.univ-pau.fr/~dkomati1 diff --git a/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_Nobuaki_compute_strain_in_DSM_code.txt b/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_Nobuaki_compute_strain_in_DSM_code.txt index 4d8fd82fb..27cc7e9d0 100644 --- a/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_Nobuaki_compute_strain_in_DSM_code.txt +++ b/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_Nobuaki_compute_strain_in_DSM_code.txt @@ -5,7 +5,7 @@ Dimitri Komatitsch Date: Mon, 04 May 2009 18:27:29 +0200 To: -冨士延章 +???? CC: Sebastien Chevrot , Vadim Monteiller @@ -14,27 +14,27 @@ Bonjour, Parfait, merci beaucoup. -Entre temps N. Takeuchi vient de trouver le bug que je lui avais signalé +Entre temps N. Takeuchi vient de trouver le bug que je lui avais signale donc je vais essayer la nouvelle version de son code. -Je suis d'accord qu'il faut calculer dU/dx pour le strain, mais la question est de savoir quelle est la façon simple de le faire dans le code DSM. Le mieux à mon avis serait de dériver les fonctions de base +Je suis d'accord qu'il faut calculer dU/dx pour le strain, mais la question est de savoir quelle est la facon simple de le faire dans le code DSM. Le mieux a mon avis serait de deriver les fonctions de base ("compute the derivative of the basis functions"). Merci, -A bientôt, +A bientot, Dimitri. -冨士延章 wrote: +???? wrote: > Cher Dimitri Komatitsch, > -> C'était vraiment bonne discussion avec vous hier. -> DSM, bien sûr, calcule des displacements pour l'éspace +> C'etait vraiment bonne discussion avec vous hier. +> DSM, bien sur, calcule des displacements pour l'espace > entier, donc c'est facile a calculer: > > strain: dU/dx -> stress: multiplé par le constant élastique -> traction: le produit intérieur avec le vecteur normal +> stress: multiple par le constant elastique +> traction: le produit interieur avec le vecteur normal > > ben, soit moi ou mon collegue ou aussi Vadim peuvent modifier des codes: > @@ -44,12 +44,12 @@ Dimitri. > > Merci de patienter. > -> Amitiés, +> Amities, > > Nobuaki -> -- +> -- > ***************************************************** -> FUJI Nobuaki (冨士　延章) seismobassoon@gmail.com (primary) +> FUJI Nobuaki (?? ??) seismobassoon@gmail.com (primary) > fuji@eps.s.u-tokyo.ac.jp (will be expired in a year ihope) > Ph.D student 3rd at Lab. of Prof. R.J. Geller > Dept. of Earth and Planetary Science, @@ -60,7 +60,7 @@ Dimitri. > fax: +81-(0)3-5841-8318 > mobile: +81-(0)90-9995-9859 --- +-- Dimitri Komatitsch - dimitri.komatitsch aT univ-pau.fr Professor, University of Pau, Institut universitaire de France, CNRS and INRIA Magique3D, France http://www.univ-pau.fr/~dkomati1 diff --git a/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_Nobuaki_definition_de_theta_et_phi_utilises_dans_DSM_et_changement_de_repere.txt b/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_Nobuaki_definition_de_theta_et_phi_utilises_dans_DSM_et_changement_de_repere.txt index 0a134a90d..08230f1a1 100644 --- a/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_Nobuaki_definition_de_theta_et_phi_utilises_dans_DSM_et_changement_de_repere.txt +++ b/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_Nobuaki_definition_de_theta_et_phi_utilises_dans_DSM_et_changement_de_repere.txt @@ -1,5 +1,5 @@ Subject: -Re: Question sur theta et phi utilisé dans DSM +Re: Question sur theta et phi utilise dans DSM From: Nobuaki FUJI Date: @@ -7,41 +7,41 @@ Thu, 17 Nov 2011 00:20:48 +0100 To: Vadim Monteiller CC: -Dimitri Komatitsch , Sébastien Chevrot +Dimitri Komatitsch , Sebastien Chevrot Salut Vadim, -Je m'excuserais si cette explication pourra être un peu répétitive et -un peu trop pédagogique mais +Je m'excuserais si cette explication pourra etre un peu repetitive et +un peu trop pedagogique mais donc -1) tu définis ta source (EVLA, EVLO) et ton récepteur (STLA, STLO) -dans le fichier d'entrée. (latitude, longitude) -1') si tu veux prendre l'effet de l'ellipticité, on convertit EVLA et STLA. -2) on pivote la source à (pi/2,0) (pôle nord) et on redéfinit (STLA*,STLO*) +1) tu definis ta source (EVLA, EVLO) et ton recepteur (STLA, STLO) +dans le fichier d'entree. (latitude, longitude) +1') si tu veux prendre l'effet de l'ellipticite, on convertit EVLA et STLA. +2) on pivote la source a (pi/2,0) (pole nord) et on redefinit (STLA*,STLO*) theta = pi/2 - STLA* phi = STLO* -après ce que tu obtiens comme u(1:3) est +apres ce que tu obtiens comme u(1:3) est u(1): le composant vertical (sens graine -> surface) (PSV) -u(2): le composant radial (sens nord à sud dans les coordonnées*: si +u(2): le composant radial (sens nord a sud dans les coordonnees*: si tu le suis, tu augmentes la valeur de theta) (PSV) -u(3): le composant transverse (sens ouest à est dans les coordonnées*: +u(3): le composant transverse (sens ouest a est dans les coordonnees*: si tu le suis, tu augmentes la valeur de phi) (SH) -ce qui est connu est qu'il y a des petits bruits numériques avant le -temps d'arrivée sur u(2) et u(3) si on ne calcule que PSV ou SH à -cause du mode de rotation et de symétrie -(qui vont être tués quand tu calcule les deux) mais ça n'arrive pas au +ce qui est connu est qu'il y a des petits bruits numeriques avant le +temps d'arrivee sur u(2) et u(3) si on ne calcule que PSV ou SH a +cause du mode de rotation et de symetrie +(qui vont etre tues quand tu calcule les deux) mais ca n'arrive pas au cas de la source explosive. -Et je ne suis pas bien sûr si on a besoin de 'déplacements' et -'tractions' ou ses dérivées temporelles, j'ai laissé comme +Et je ne suis pas bien sur si on a besoin de 'deplacements' et +'tractions' ou ses derivees temporelles, j'ai laisse comme stress (:) = stress (:) / cmplx(0.d0,omega) displacement (:) = displacement (:) mais naturellement ce qu'on obtient dans le code est la vitesse (la -dérivée temporelle). +derivee temporelle). Merci pour l'installation de svn aussi, A+ @@ -57,25 +57,25 @@ Nobuaki > > > > > > le repere 1 est celui que tu utilises pour le calcul des coeffs dans DSM. -> > le repere 2 est un repre local défini que je défini ainsi pour qu'il soit +> > le repere 2 est un repre local defini que je defini ainsi pour qu'il soit > > direct et qu'il corresponde au repere 3 lorsqu'on se trouve au centre du > > chunk. > > le repere 3 est celui de specfem avec (X=Est, Y=Nord, Z=Haut) au centre du > > chunk. > > -> > Visiblement j'ai un pb dans mes changement de reprère, peux-tu me préciser -> > stp la définition de theta et phi. +> > Visiblement j'ai un pb dans mes changement de reprere, peux-tu me preciser +> > stp la definition de theta et phi. > > > > -> > Jusqu'à présent j'ai utilisé: +> > Jusqu'a present j'ai utilise: > > -> > theta : vecteur de direction (source -> récepteur) et sens (source -> -> > récepeur) -> > phi : vecteur orthogonal à theta avec une rotation de pi/2 dans le sens -> > trigonométique direct de manière à ce que (r,theta,phi) soit un repère +> > theta : vecteur de direction (source -> recepteur) et sens (source -> +> > recepeur) +> > phi : vecteur orthogonal a theta avec une rotation de pi/2 dans le sens +> > trigonometique direct de maniere a ce que (r,theta,phi) soit un repere > > direct. > > -> > mais je ne suis plus très sûr de çà. +> > mais je ne suis plus tres sur de ca. > > > > Merci > > @@ -89,4 +89,4 @@ Nobuaki --- ***************************************************** FUJI Nobuaki Nobuaki.Fuji@irap.omp.eu seismobassoon@gmail.com Institut de Recherche en Astrophysique et Planetologie 14 Avenue Edouard Belin 31400 Toulouse, France bureau: +33 (0)5.61.33.29.73 home: +33(0)9.81.03.60.67 mobile: +33 (0)6.67.29.61.09 \ No newline at end of file +-- ***************************************************** FUJI Nobuaki Nobuaki.Fuji@irap.omp.eu seismobassoon@gmail.com Institut de Recherche en Astrophysique et Planetologie 14 Avenue Edouard Belin 31400 Toulouse, France bureau: +33 (0)5.61.33.29.73 home: +33(0)9.81.03.60.67 mobile: +33 (0)6.67.29.61.09 diff --git a/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_Nobuaki_how_can_we_compute_strain_seismograms_in_the_DSM_code.txt b/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_Nobuaki_how_can_we_compute_strain_seismograms_in_the_DSM_code.txt index 480c3a95b..c3b92123c 100644 --- a/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_Nobuaki_how_can_we_compute_strain_seismograms_in_the_DSM_code.txt +++ b/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_Nobuaki_how_can_we_compute_strain_seismograms_in_the_DSM_code.txt @@ -4,10 +4,10 @@ From: Dimitri Komatitsch Organization: University of Pau, France User-Agent: Thunderbird 2.0.0.21 (X11/20090320) MIME-Version: 1.0 -To: =?UTF-8?B?5Yao5aOr5bu256ug?= , +To: =?UTF-8?B?5Yao5aOr5bu256ug?= , seismobassoon@gmail.com CC: Vadim Monteiller , =?UTF-8?B?U8OpYmFz?= - =?UTF-8?B?dGllbiBDaGV2cm90?= , + =?UTF-8?B?dGllbiBDaGV2cm90?= , Dimitri Komatitsch , Nozomu Takeuchi Subject: how can we compute strain "seismograms" in the DSM code? @@ -18,11 +18,11 @@ Content-Transfer-Encoding: 7bit Dear Nobuaki, Did you have time to talk to Prof. Takeuchi or Prof. Kawai -about how to output values of strain instead of displacement or velocity +about how to output values of strain instead of displacement or velocity in the DSM code, i.e. compute strain "seismograms" in addition to more classical velocity or displacement seismograms? Because as we discussed when you came to Toulouse, for some applications -it would be interesting to be able to output the components of the +it would be interesting to be able to output the components of the strain tensor. I copy this email to Prof. Takeuchi for information. @@ -32,7 +32,7 @@ Best regards, Dimitri. --- +-- Dimitri Komatitsch - dimitri.komatitsch aT univ-pau.fr Professor, University of Pau, Institut universitaire de France, CNRS and INRIA Magique3D, France http://www.univ-pau.fr/~dkomati1 diff --git a/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_Vadim_about_eq17_in_GEMINI_paper_for_source_discontinuity.txt b/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_Vadim_about_eq17_in_GEMINI_paper_for_source_discontinuity.txt index 930c08cc9..5d5abbf98 100644 --- a/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_Vadim_about_eq17_in_GEMINI_paper_for_source_discontinuity.txt +++ b/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_Vadim_about_eq17_in_GEMINI_paper_for_source_discontinuity.txt @@ -1,29 +1,29 @@ -------- Original Message -------- -Subject: Re: une question sur la discontinuité de source pour DSM +Subject: Re: une question sur la discontinuite de source pour DSM Date: Sun, 23 Mar 2014 14:05:47 +0100 From: Vadim MONTEILLER -To: Dimitri Komatitsch, Sébastien Chevrot, Yi Wang +To: Dimitri Komatitsch, Sebastien Chevrot, Yi Wang Salut Dimitri, -Dans le papier il faut regarder l'équation (17) juste en dessous il est -mentionné un "JUMP" au niveau de la source. Ensuite dans le reste du -papier ils font la distinction entre les solutions en dessous de la -sources et celles au dessus. Mais c'est pas très détaillé dans ce -papier. Je me souviens de papier de Woodhouse où les équations sont plus -précises. J'ai plus les rèfs ici mais je crois que tu as du les -photocopier en même temps que le papier gemini. En fait, je n'avais -qu'une version papier de tout çà et je n'arrive plus à les retrouver. +Dans le papier il faut regarder l'equation (17) juste en dessous il est +mentionne un "JUMP" au niveau de la source. Ensuite dans le reste du +papier ils font la distinction entre les solutions en dessous de la +sources et celles au dessus. Mais c'est pas tres detaille dans ce +papier. Je me souviens de papier de Woodhouse ou les equations sont plus +precises. J'ai plus les refs ici mais je crois que tu as du les +photocopier en meme temps que le papier gemini. En fait, je n'avais +qu'une version papier de tout ca et je n'arrive plus a les retrouver. Vadim -Le 23/03/2014 01:30, Dimitri Komatitsch a écrit : +Le 23/03/2014 01:30, Dimitri Komatitsch a ecrit : > > Salut Vadim, > -> Stp dans le papier GEMINI de 1995 pourrais-tu nous dire à quel -> endroit du papier est décrite la façon de mettre la discontinuité de +> Stp dans le papier GEMINI de 1995 pourrais-tu nous dire a quel +> endroit du papier est decrite la facon de mettre la discontinuite de > source dont tu me parlais ? > > Merci, diff --git a/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_from_Nozomu_Takeuchi_about_how_to_implement_high_order.txt b/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_from_Nozomu_Takeuchi_about_how_to_implement_high_order.txt index db77d39fb..4540535a8 100644 --- a/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_from_Nozomu_Takeuchi_about_how_to_implement_high_order.txt +++ b/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_from_Nozomu_Takeuchi_about_how_to_implement_high_order.txt @@ -16,7 +16,7 @@ and errors of other operators cancel with each other.) What we meant in the 1996 paper is that we have to modify 0th or 1st derivative operators to achieve optimal accuracy because we have no -way to tune errors of the 2nd derivative operators. +way to tune errors of the 2nd derivative operators. At the moment, I'm not very sure whether higher order basis functions will improve the performance. @@ -69,45 +69,45 @@ Thank you very much. c variables for a source - integer idim_rs_sph,idim_rs_tor,idim_rs_sph0,idim_rs_tor0 + integer idim_rs_sph,idim_rs_tor,idim_rs_sph0,idim_rs_tor0 c variables for stations - integer idim_station_sph,idim_station_tor, - & idim_station_sph0,idim_station_tor0 + integer idim_station_sph,idim_station_tor, + & idim_station_sph0,idim_station_tor0 c variables for matrix elements - real*8 submatrix_I0(4,maxngrid_r) - real*8 submatrix_I1k(4,maxngrid_r),submatrix_I1m(4,maxngrid_r) - real*8 submatrix_I2(4,maxngrid_r) - real*8 submatrix_I3k(4,maxngrid_r),submatrix_I3m(4,maxngrid_r) - real*8 submatrix_I4(4,maxngrid_r) - real*8 submatrix_I5k(4,maxngrid_r),submatrix_I5m(4,maxngrid_r) - real*8 submatrix_I6(4,maxngrid_r) - real*8 submatrix_I7(4,maxngrid_r) - real*8 submatrix_I3k_mod(6,maxngrid_r) - real*8 submatrix_I3m_mod(6,maxngrid_r) - real*8 submatrix_I4_mod(6,maxngrid_r) + real*8 submatrix_I0(4,maxngrid_r) + real*8 submatrix_I1k(4,maxngrid_r),submatrix_I1m(4,maxngrid_r) + real*8 submatrix_I2(4,maxngrid_r) + real*8 submatrix_I3k(4,maxngrid_r),submatrix_I3m(4,maxngrid_r) + real*8 submatrix_I4(4,maxngrid_r) + real*8 submatrix_I5k(4,maxngrid_r),submatrix_I5m(4,maxngrid_r) + real*8 submatrix_I6(4,maxngrid_r) + real*8 submatrix_I7(4,maxngrid_r) + real*8 submatrix_I3k_mod(6,maxngrid_r) + real*8 submatrix_I3m_mod(6,maxngrid_r) + real*8 submatrix_I4_mod(6,maxngrid_r) c variables for wavefield - integer idim0,init_npos_sph,init_npos_tor - complex*16 whole_matrix_sph(4,2*maxngrid_r) - complex*16 whole_matrix_tor(2,maxngrid_r) - complex*16 whole_matrix_dr_sph(2*maxngrid_r) - complex*16 whole_matrix_dr_tor(maxngrid_r) - complex*16 whole_vector_sph(2*maxngrid_r,-2:2) - complex*16 whole_vector_tor(maxngrid_r,-2:2) + integer idim0,init_npos_sph,init_npos_tor + complex*16 whole_matrix_sph(4,2*maxngrid_r) + complex*16 whole_matrix_tor(2,maxngrid_r) + complex*16 whole_matrix_dr_sph(2*maxngrid_r) + complex*16 whole_matrix_dr_tor(maxngrid_r) + complex*16 whole_vector_sph(2*maxngrid_r,-2:2) + complex*16 whole_vector_tor(maxngrid_r,-2:2) -2014-04-01 (火) の 15:36 +0200 に Dimitri Komatitsch さんは書きました: +2014-04-01 (?) ? 15:36 +0200 ? Dimitri Komatitsch ????????: > Dear Nozomu, -> -> PS: I am also not sure if the optimized operators with a 1/12.d0 -> coefficient would also need to change when going to higher-order basis +> +> PS: I am also not sure if the optimized operators with a 1/12.d0 +> coefficient would also need to change when going to higher-order basis > functions. -> +> > Thank you, > Best regards, -> +> > Dimitri. -> +> > On 01/04/2014 15:13, Dimitri Komatitsch wrote: > > > > Dear Nozomu, diff --git a/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_how_can_we_compute_strain_seismograms_in_the_DSM_code.txt b/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_how_can_we_compute_strain_seismograms_in_the_DSM_code.txt index d90d7ded6..c28a3fab6 100644 --- a/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_how_can_we_compute_strain_seismograms_in_the_DSM_code.txt +++ b/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_how_can_we_compute_strain_seismograms_in_the_DSM_code.txt @@ -1,13 +1,13 @@ Subject: Re: how can we compute strain "seismograms" in the DSM code? From: -冨士延章 +???? Date: Tue, 30 Jun 2009 15:15:48 +0900 To: Dimitri Komatitsch CC: -Vadim Monteiller , Sébastien Chevrot , Nozomu Takeuchi +Vadim Monteiller , Sebastien Chevrot , Nozomu Takeuchi Dear Dimitri: @@ -20,22 +20,22 @@ For strains you can calculate those by taking spatial partial derivatives for those wavefields. After completing this project I will let you know how to derive those tensors. -Cher Sébastien: +Cher Sebastien: -J'étais désolé mais j'ai manqué vous répondre la semaine dernière... -Comme vous lisez dans ce mél, je suis maintenant en train de faire du +J'etais desole mais j'ai manque vous repondre la semaine derniere... +Comme vous lisez dans ce mel, je suis maintenant en train de faire du re-coding de DSM pour faciliter la computation, pour l'inversion 3-D. -Pour la décomposition en onglettes, j'ai aussi travaillé mais en ce moment -j'ai pas vraiment réussi: il me semble qu'on doit transformer la matrice A +Pour la decomposition en onglettes, j'ai aussi travaille mais en ce moment +j'ai pas vraiment reussi: il me semble qu'on doit transformer la matrice A dans la domaine du temps... je vais essayer maintenant. -Ce que je vous ai envoyé est le résultat avec la méthode du gradient conjugué: -Avec moins de paramètres que la méthode de SVD, j'ai réussi à expliquer des données. -Je vais écrire sur cette méthode et je veux travailler sur la combination de -onglettes et du gradient conjugué, ça peux faire mieux. -Pour des données de Hi-net, il semble possible à utiiser avec vous, si on met -des noms des staffs là-bas. +Ce que je vous ai envoye est le resultat avec la methode du gradient conjugue: +Avec moins de parametres que la methode de SVD, j'ai reussi a expliquer des donnees. +Je vais ecrire sur cette methode et je veux travailler sur la combination de +onglettes et du gradient conjugue, ca peux faire mieux. +Pour des donnees de Hi-net, il semble possible a utiiser avec vous, si on met +des noms des staffs la-bas. -Amitiés, +Amities, Nobuaki @@ -57,7 +57,7 @@ Nobuaki Dimitri. - -- + -- Dimitri Komatitsch - dimitri.komatitsch aT univ-pau.fr Professor, University of Pau, Institut universitaire de France, CNRS and INRIA Magique3D, France http://www.univ-pau.fr/~dkomati1 @@ -65,9 +65,9 @@ Nobuaki --- +-- ***************************************************** -FUJI Nobuaki (冨士　延章) +FUJI Nobuaki (?? ??) seismobassoon@gmail.com (primary) fuji@eps.s.u-tokyo.ac.jp (will be expired in a year ihope) Ph.D student 3rd at Lab. of Prof. R.J. Geller diff --git a/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_it_could_be_that_the_source_discontinuity_is_already_handled.txt b/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_it_could_be_that_the_source_discontinuity_is_already_handled.txt index dfa865ec0..aa26e0f03 100644 --- a/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_it_could_be_that_the_source_discontinuity_is_already_handled.txt +++ b/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_it_could_be_that_the_source_discontinuity_is_already_handled.txt @@ -3,7 +3,7 @@ Subject: it could be that the source discontinuity is already handled (?) From: Dimitri Komatitsch Date: 24/03/2014 11:54 To: ywang -CC: Sébastien Chevrot, Vadim Monteiller +CC: Sebastien Chevrot, Vadim Monteiller Hi all, @@ -23,7 +23,7 @@ but I am not sure if this just adds a point at the source location (which is *no Thanks, Dimitri. --- +-- Dimitri Komatitsch CNRS Research Director (DR CNRS), Laboratory of Mechanics and Acoustics, UPR 7051, Marseille, France http://komatitsch.free.fr diff --git a/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_my_interpretation_of_mass_lumping_of_Takeuchi_apr2014.txt b/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_my_interpretation_of_mass_lumping_of_Takeuchi_apr2014.txt index 824600882..90e0fbd0a 100644 --- a/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_my_interpretation_of_mass_lumping_of_Takeuchi_apr2014.txt +++ b/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_my_interpretation_of_mass_lumping_of_Takeuchi_apr2014.txt @@ -3,7 +3,7 @@ Subject: Re: More to say about Takeuchi's code From: Dimitri Komatitsch Date: 02/04/2014 13:42 To: martinr -CC: Yi Wang, Sébastien Chevrot, Roland Martin +CC: Yi Wang, Sebastien Chevrot, Roland Martin Hi Roland, Hi all, @@ -33,10 +33,10 @@ On 02/04/2014 13:25, martinr wrote: > ROland > --- +-- Dimitri Komatitsch CNRS Research Director (DR CNRS), Laboratory of Mechanics and Acoustics, UPR 7051, Marseille, France http://komatitsch.free.fr Attachments: -Takeuchi_Geller_Cummins_GRL_1996.pdf 410 KB +Takeuchi_Geller_Cummins_GRL_1996.pdf 410 KB diff --git a/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_pour_voir_si_la_discontinuite_est_deja_traitee_dans_le_code_de_Takeuchi.txt b/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_pour_voir_si_la_discontinuite_est_deja_traitee_dans_le_code_de_Takeuchi.txt index ed7169b36..f8b3491e3 100644 --- a/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_pour_voir_si_la_discontinuite_est_deja_traitee_dans_le_code_de_Takeuchi.txt +++ b/utils/DSM_FOR_SPECFEM3D/OLD--DSM_cleaned/notes_pour_voir_si_la_discontinuite_est_deja_traitee_dans_le_code_de_Takeuchi.txt @@ -1,13 +1,13 @@ -Subject: pour voir si la discontinuité est déjà traitée de la bonne façon dans le code de Takeuchi +Subject: pour voir si la discontinuite est deja traitee de la bonne facon dans le code de Takeuchi From: Dimitri Komatitsch Date: 23/03/2014 19:17 -To: Vadim MONTEILLER, Sébastien Chevrot, Yi Wang +To: Vadim MONTEILLER, Sebastien Chevrot, Yi Wang Salut Vadim, -Si tu veux dans le répertoire 'DSM_cleaned' tu trouveras les fichiers *.f90 du code de Takeuchi (que j'ai commencé à nettoyer et aussi à convertir en F90 au lieu de F77). Son code est super clair et super facile à lire, donc peut-être qu'il a déjà mis le bon traitement de cette discontinuité dedans, faudrait regarder à l'occasion -(Yi va regarder dans les prochaines semaines, si jamais tu ouvres les fichiers *.f90 et que tu vois si la réponse est oui ou non (son code est court, et facile à lire) stp dis-le nous et on le dira à Yi. +Si tu veux dans le repertoire 'DSM_cleaned' tu trouveras les fichiers *.f90 du code de Takeuchi (que j'ai commence a nettoyer et aussi a convertir en F90 au lieu de F77). Son code est super clair et super facile a lire, donc peut-etre qu'il a deja mis le bon traitement de cette discontinuite dedans, faudrait regarder a l'occasion +(Yi va regarder dans les prochaines semaines, si jamais tu ouvres les fichiers *.f90 et que tu vois si la reponse est oui ou non (son code est court, et facile a lire) stp dis-le nous et on le dira a Yi. Merci, Dimitri. diff --git a/utils/DSM_FOR_SPECFEM3D/OLD--VM_mesher_now_handled_by_meshfem3d/mesh_chunk.f90 b/utils/DSM_FOR_SPECFEM3D/OLD--VM_mesher_now_handled_by_meshfem3d/mesh_chunk.f90 index b704dcd10..29926646e 100755 --- a/utils/DSM_FOR_SPECFEM3D/OLD--VM_mesher_now_handled_by_meshfem3d/mesh_chunk.f90 +++ b/utils/DSM_FOR_SPECFEM3D/OLD--VM_mesher_now_handled_by_meshfem3d/mesh_chunk.f90 @@ -6,7 +6,7 @@ ! Vadim Monteiler, Fevrier 2013 ! ! -! J'ai une convention propre pour le mapping de la sphere cubique (a compléter ... ) !!!!!! +! J'ai une convention propre pour le mapping de la sphere cubique (a completer ... ) !!!!!! ! program mesh_chunk implicit none @@ -40,7 +40,7 @@ program mesh_chunk ! nb couches dans modele iasp91 ou ak135 ou prem integer nlayer - parameter (nlayer=12) ! 1 couche de plus que le modèle + parameter (nlayer=12) ! 1 couche de plus que le modele double precision zlayer(nlayer),vpv(nlayer,4),vsv(nlayer,4),density(nlayer,4) double precision, dimension(:,:), allocatable :: ProfForGemini double precision Z_DEPTH_BLOCK,UTM_X_MIN,UTM_X_MAX @@ -57,7 +57,7 @@ program mesh_chunk character(len=250) model1D_file !! CONVENTION : (lon,lat) -> (xi,eta) (k=6 avec -z pour le mapping sphere cubique (cf Chervot 2012) - ! on definit le maillage d'un chunk dans la sphère cubique------------------------------------------------------- + ! on definit le maillage d'un chunk dans la sphere cubique------------------------------------------------------- PI = 3.141592653589793d0 deg2rad = 3.141592653589793d0/180.d0 R_EARTH=6371000.d0 @@ -75,7 +75,7 @@ program mesh_chunk chunk_azi=0.d0 !90.d0 !80.d0 !10.d0 !* deg2rad ! depth chunk_depth = 1000.d0 *1000.d0 ! 250.d0 * 1000.d0 - ! nb d'éléments + ! nb d'elements nel_lat = 20 !120 nel_lon = 40 !96 nel_depth = 20 !100 @@ -99,7 +99,7 @@ program mesh_chunk ANGULAR_WIDTH_XI_RAD = deg2rad * ANGULAR_WIDTH_XI_RAD ANGULAR_WIDTH_ETA_RAD = deg2rad * ANGULAR_WIDTH_ETA_RAD chunk_depth = chunk_depth * 1000.d0 - endif !这里是读入chunk的尺寸和网点间隔，需要ParFileMeshChunk文件 + endif !?????chunk????????,??ParFileMeshChunk?? NX = nel_lon NY = nel_lat @@ -299,12 +299,12 @@ program mesh_chunk y = tan((ANGULAR_WIDTH_ETA_RAD/2.d0) * y) !if (ilat==0.and.iz==0) write(49,*) ia,i,ratio_xi - !mapping sphere cubique (k=5) (Chevrot et al 2012) (il y a un signe opposé) + !mapping sphere cubique (k=5) (Chevrot et al 2012) (il y a un signe oppose) !pz = z/dsqrt(1.d0 + y*y + x*x) !px = x*pz !py = y*pz ! mapping qui permet d'avoir le chunk au pole Nord - ! mapping sphère cubique (k=6, Chevrot at al 2012, avec -z) + ! mapping sphere cubique (k=6, Chevrot at al 2012, avec -z) pz= z/dsqrt(1.d0 + y*y + x*x) !(=r/s) px= pz * x !(tan(xi) * r/s) py= pz * y !(tan(eta) * r/s) @@ -384,8 +384,8 @@ program mesh_chunk if (ilat==nel_lat-1) call write_Igm_file(41,ispec2Dymax,NGLLX,NGLLZ,ilon,iz,izshift,ilayer_current) ! stzmin - if (iz==0) then ! pas besoin du test comme précédemment car je stocke tout dans des tableaux et c'est pas - ! grave si on récrit les memes choses + if (iz==0) then ! pas besoin du test comme precedemment car je stocke tout dans des tableaux et c'est pas + ! grave si on recrit les memes choses call calc_gll_points(xelm,yelm,zelm,xstore,ystore,zstore,shape3D,NGNOD,NGLLX,NGLLY,NGLLZ) call write_Igm_file(42,ispec2Dzmin,NGLLX,NGLLY,ilon,ilat,0,ilayer_current) !open(125,file='ggl_elemts') @@ -749,7 +749,7 @@ subroutine write_stxmin(xstore,ystore,zstore,NGLLX,NGLLY,NGLLZ,rotation_matrix,t long=atan2(y,x) lati=asin(z/rayon) - ! passage de geocentique à géographique + ! passage de geocentique a geographique !!theta = PI/2.D0 - lati ! convert the geocentric colatitude to a geographic colatitude !!colat = PI/2.0d0 - datan(1.006760466d0*dcos(theta)/dmax1(TINYVAL,dsin(theta))) @@ -802,7 +802,7 @@ subroutine write_stxmax(xstore,ystore,zstore,NGLLX,NGLLY,NGLLZ,rotation_matrix,t long=atan2(y,x) lati=asin(z/rayon) - ! passage de geocentique à géographique + ! passage de geocentique a geographique !!theta = PI/2.D0 - lati ! convert the geocentric colatitude to a geographic colatitude !!colat = PI/2.0d0 - datan(1.006760466d0*dcos(theta)/dmax1(TINYVAL,dsin(theta))) @@ -855,7 +855,7 @@ subroutine write_stymin(xstore,ystore,zstore,NGLLX,NGLLY,NGLLZ,rotation_matrix,t long=atan2(y,x) lati=asin(z/rayon) - ! passage de geocentique à géographique + ! passage de geocentique a geographique !!theta = PI/2.D0 - lati ! convert the geocentric colatitude to a geographic colatitude !!colat = PI/2.0d0 - datan(1.006760466d0*dcos(theta)/dmax1(TINYVAL,dsin(theta))) @@ -903,7 +903,7 @@ subroutine write_stymax(xstore,ystore,zstore,NGLLX,NGLLY,NGLLZ,rotation_matrix,t long=atan2(y,x) lati=asin(z/rayon) - ! passage de geocentique à géographique + ! passage de geocentique a geographique !!theta = PI/2.D0 - lati ! convert the geocentric colatitude to a geographic colatitude !!colat = PI/2.0d0 - datan(1.006760466d0*dcos(theta)/dmax1(TINYVAL,dsin(theta))) @@ -954,7 +954,7 @@ subroutine store_zmin_points(xstore,ystore,zstore,NGLLX,NGLLY,NGLLZ,rotation_mat long=atan2(y,x) lati=asin(z/rayon) - ! passage de geocentique à géographique + ! passage de geocentique a geographique !!theta = PI/2.D0 - lati ! convert the geocentric colatitude to a geographic colatitude !!colat = PI/2.0d0 - datan(1.006760466d0*dcos(theta)/dmax1(TINYVAL,dsin(theta))) @@ -1034,7 +1034,7 @@ end subroutine compute_rotation_matrix ! Vadim Monteiller Mars 2013 ! !------------------------------------------------------------------------------- -! matrice de rotation 3D d'axe "axe" et d'angle theta (d°) +! matrice de rotation 3D d'axe "axe" et d'angle theta (d?) ! cette matrice est en complexe subroutine rotation_matrix_axe(R,axe,theta) implicit none diff --git a/utils/DSM_FOR_SPECFEM3D/routines_for_conversion_geogr_cart/cart2geogr.f90 b/utils/DSM_FOR_SPECFEM3D/routines_for_conversion_geogr_cart/cart2geogr.f90 index 9377a7183..e6dff5ed7 100755 --- a/utils/DSM_FOR_SPECFEM3D/routines_for_conversion_geogr_cart/cart2geogr.f90 +++ b/utils/DSM_FOR_SPECFEM3D/routines_for_conversion_geogr_cart/cart2geogr.f90 @@ -100,7 +100,7 @@ subroutine compute_rotation_matrix(rotation_matrix,lon_center_chunk,lat_center_ end subroutine compute_rotation_matrix !-------------------------------------------------------------------------------------------------------------------------------------------------------- -! 3D rotation matrix with axis "axe" and angle theta (d°) +! 3D rotation matrix with axis "axe" and angle theta (d?) ! subroutine rotation_matrix_axe(R,axe,theta) implicit none diff --git a/utils/DSM_FOR_SPECFEM3D/routines_for_conversion_geogr_cart/geogr2cart.f90 b/utils/DSM_FOR_SPECFEM3D/routines_for_conversion_geogr_cart/geogr2cart.f90 index 0808999ab..94cd4b1ea 100755 --- a/utils/DSM_FOR_SPECFEM3D/routines_for_conversion_geogr_cart/geogr2cart.f90 +++ b/utils/DSM_FOR_SPECFEM3D/routines_for_conversion_geogr_cart/geogr2cart.f90 @@ -102,7 +102,7 @@ subroutine compute_rotation_matrix(rotation_matrix,lon_center_chunk,lat_center_ end subroutine compute_rotation_matrix !-------------------------------------------------------------------------------------------------------------------------------------------------------- -! 3D rotation matrix with axis "axe" and angle theta (d°) +! 3D rotation matrix with axis "axe" and angle theta (d?) ! subroutine rotation_matrix_axe(R,axe,theta) implicit none diff --git a/utils/DSM_FOR_SPECFEM3D/shells/bacchus_run_benchmark_all_process.sh b/utils/DSM_FOR_SPECFEM3D/shells/bacchus_run_benchmark_all_process.sh index 60ea17565..c36b5acda 100755 --- a/utils/DSM_FOR_SPECFEM3D/shells/bacchus_run_benchmark_all_process.sh +++ b/utils/DSM_FOR_SPECFEM3D/shells/bacchus_run_benchmark_all_process.sh @@ -53,7 +53,7 @@ ## ------------------ INPUTS ----------------------------- -# DSM BINARY : (to do supprimer peut-être çà de params.in??) +# DSM BINARY : (to do supprimer peut-etre ca de params.in??) BIN_DSM=$HOME_SPECFEM3D/utils/DSM_FOR_SPECFEM3D/bin # NBPROC is declared as integer (important do not change) declare -i NPROC NPROC_MINUS_ONE diff --git a/utils/DSM_FOR_SPECFEM3D/shells/msub_compute_coef_process.sh b/utils/DSM_FOR_SPECFEM3D/shells/msub_compute_coef_process.sh index e2c06eb54..e1d92b4ee 100755 --- a/utils/DSM_FOR_SPECFEM3D/shells/msub_compute_coef_process.sh +++ b/utils/DSM_FOR_SPECFEM3D/shells/msub_compute_coef_process.sh @@ -62,7 +62,7 @@ cd $BRIDGE_MSUB_PWD ## ------------------ INPUTS ----------------------------- -# DSM BINARY : (to do supprimer peut-être çà de params.in??) +# DSM BINARY : (to do supprimer peut-etre ca de params.in??) # NBPROC is declared as integer (important do not change) declare -i NPROC NPROC_MINUS_ONE diff --git a/utils/DSM_FOR_SPECFEM3D/shells/msub_setup_process.sh b/utils/DSM_FOR_SPECFEM3D/shells/msub_setup_process.sh index 48aefe321..40151b5a4 100755 --- a/utils/DSM_FOR_SPECFEM3D/shells/msub_setup_process.sh +++ b/utils/DSM_FOR_SPECFEM3D/shells/msub_setup_process.sh @@ -63,7 +63,7 @@ cd $BRIDGE_MSUB_PWD ## ------------------ INPUTS ----------------------------- -# DSM BINARY : (to do supprimer peut-être çà de params.in??) +# DSM BINARY : (to do supprimer peut-etre ca de params.in??) BIN_DSM=$HOME_SPECFEM3D/utils/DSM_FOR_SPECFEM3D/bin # NBPROC is declared as integer (important do not change) declare -i NPROC NPROC_MINUS_ONE diff --git a/utils/Visualization/GMT/readme.txt b/utils/Visualization/GMT/readme.txt index 20389bfa7..f57d4b91c 100644 --- a/utils/Visualization/GMT/readme.txt +++ b/utils/Visualization/GMT/readme.txt @@ -2,8 +2,8 @@ readme -------------------------------- -GMT, the Generic Mapping Tools -http://www.soest.hawaii.edu/GMT/ +GMT, the Generic Mapping Tools +http://www.soest.hawaii.edu/GMT/ - various files provided to create your visualizations diff --git a/utils/Visualization/Paraview/readme.txt b/utils/Visualization/Paraview/readme.txt index bf1f5cf91..8a43466e4 100644 --- a/utils/Visualization/Paraview/readme.txt +++ b/utils/Visualization/Paraview/readme.txt @@ -10,27 +10,27 @@ http://www.paraview.org/ - contains mesh2vtu/: - mesh2vtu/ -- it requires the installation of vtk package. - once vtk is installed, you can set the vars + mesh2vtu/ -- it requires the installation of vtk package. + once vtk is installed, you can set the vars in the Makefile and compile all the programs How to collect and visualize 3D/2D data generated by the parallel simulation? - - figure out the slices you need to collect + - figure out the slices you need to collect - combine all the databases using the program 'combine_vol_data.f90' or 'combine_surf_data.f90' - - convert the mesh file to vtu file using mesh2vtu/, that is, - compile mesh2vtu/mesh2vtu by using `make` + - convert the mesh file to vtu file using mesh2vtu/, that is, + compile mesh2vtu/mesh2vtu by using `make` and call the provided script > mesh2vtu.pl -i my_input.mesh -o my_output.vtu - - visualize the .vtu files in Paraview + - visualize the .vtu files in Paraview - contains visualize_gold/: - creates file formats for Paraview and - - Ensight Gold, parallel processing and rendering visualization + creates file formats for Paraview and + + Ensight Gold, parallel processing and rendering visualization http://www.ensight.com/ensight-gold.html - + please see the manual 'visualize_gold/visualize_manual' for further details diff --git a/utils/Visualization/visualize_chunk_of_the_earth_with_MEDIT/HOWTO_use_this_tool.txt b/utils/Visualization/visualize_chunk_of_the_earth_with_MEDIT/HOWTO_use_this_tool.txt index 66d9229f5..bbe167855 100644 --- a/utils/Visualization/visualize_chunk_of_the_earth_with_MEDIT/HOWTO_use_this_tool.txt +++ b/utils/Visualization/visualize_chunk_of_the_earth_with_MEDIT/HOWTO_use_this_tool.txt @@ -2,7 +2,7 @@ This tool allows to visualize a chunk of the earth (with HEX8 or HEX27 elements) with the software Medit -Reminder : to create a mesh of a earth chunk (in the case of coupling with DSM), the parameter MESH_A_CHUNK_OF_THE_EARTH +Reminder : to create a mesh of a earth chunk (in the case of coupling with DSM), the parameter MESH_A_CHUNK_OF_THE_EARTH in DATA/Par_file have to set .true., and this will be call a specific internal for that in meshfem3D.f90 !======================================================================================================================! @@ -18,17 +18,17 @@ The Medit documentation (Caution : it is in French, and the HTML links in the pa !======================================================================================================================! -a/ HEX8 case (for HEX27 case, go l. 65) : +a/ HEX8 case (for HEX27 case, go l. 65) : !======================================================================================================================! Step 2a : Run the earth chunk mesher with NGNOD=8, for coupling with DSM ------------------------------------------------------------------------ -In the case of coupling with DSM, when you run xmeshfem3D, a subdirectory MESH is created in the directory of -the concerned example, and several files appears. +In the case of coupling with DSM, when you run xmeshfem3D, a subdirectory MESH is created in the directory of +the concerned example, and several files appears. -Among them, copy the files below in utils/Visualization/visualize_chunk_of_the_earth_with_MEDIT/HEX8 +Among them, copy the files below in utils/Visualization/visualize_chunk_of_the_earth_with_MEDIT/HEX8 (path from the specfem3d main directory) : - nodes_coords_file @@ -63,17 +63,17 @@ $ medit test_out_HEX8.mesh & !======================================================================================================================! -b/ HEX27 case : +b/ HEX27 case : !======================================================================================================================! Step 2b : Run the earth chunk mesher with NGNOD=27, for coupling with DSM ------------------------------------------------------------------------- -In the case of coupling with DSM, when you run xmeshfem3D, a subdirectory MESH is created in the directory of -the concerned example, and several files appears. +In the case of coupling with DSM, when you run xmeshfem3D, a subdirectory MESH is created in the directory of +the concerned example, and several files appears. -Among them, copy the files below in utils/Visualization/visualize_chunk_of_the_earth_with_MEDIT/HEX27 +Among them, copy the files below in utils/Visualization/visualize_chunk_of_the_earth_with_MEDIT/HEX27 (path from the specfem3d main directory) : - nodes_coords_file diff --git a/utils/bathy_sep_to_ascii/CMakeLists.txt b/utils/bathy_sep_to_ascii/CMakeLists.txt index f84c5f2e2..f6993d3b8 100644 --- a/utils/bathy_sep_to_ascii/CMakeLists.txt +++ b/utils/bathy_sep_to_ascii/CMakeLists.txt @@ -24,5 +24,5 @@ set(sources add_executable( create_ascii_bathy_from_sep_vs src/create_ascii_bathy_from_sep_vs.c - ${sources} + ${sources} ) diff --git a/utils/clean_listings_specfem.pl b/utils/clean_listings_specfem.pl index 499b4d221..cdad1f09c 100755 --- a/utils/clean_listings_specfem.pl +++ b/utils/clean_listings_specfem.pl @@ -172,13 +172,52 @@ ################################################################################################ ################################################################################################ +# +# Clean spaces in text and LaTeX files +# +# Author : Dimitri Komatitsch, EPS - Harvard University, USA, January 1998 +# + + @objects = `ls *.txt */*.txt */*/*.txt */*/*/*.txt */*.tex */*/*.tex */*/*/*.tex `; + + foreach $name (@objects) { + chop $name; +# change tabs to white spaces + system("expand -2 < $name > _____temp08_____"); + $cname = $name; + print STDOUT "Cleaning $cname ...\n"; + + open(FILEDEPART,"<_____temp08_____"); + open(FILEC,">$cname"); + +# open the input C file + while($line = ) { + +# suppress trailing white spaces and carriage return + $line =~ s/\s*$//; + + print FILEC "$line\n"; + + } + + close(FILEDEPART); + close(FILEC); + + } + + system("rm -f _____temp08_____"); + +################################################################################################ +################################################################################################ +################################################################################################ + # # Clean all accented letters and non-ASCII characters to remain portable # # Authors : David Luet, Princeton University, USA and Dimitri Komatitsch, CNRS, France, January 2015 # - @objects = `ls *.c *.cu *.h *.h.in *.fh */*.c */*.cu */*.h */*.h.in */*.fh */*/*.c */*/*.cu */*/*.h */*/*.h.in */*/*.fh */*/*/*.c */*/*/*.cu */*/*/*.h */*/*/*.h.in */*/*/*.fh *.f90 *.F90 *.h *.h.in *.fh */*.f90 */*.F90 */*.h */*.h.in */*.fh */*/*.f90 */*/*.F90 */*/*.h */*/*.h.in */*/*.fh */*/*/*.f90 */*/*/*.F90 */*/*/*.h */*/*/*.h.in */*/*/*.fh */*.txt */*/*.txt */*/*/*.txt */*.tex */*/*.tex */*/*/*.tex */*.sh */*/*.sh */*/*/*.sh */*.csh */*/*.csh */*/*/*.csh */*.bash */*/*.bash */*/*/*.bash */*.pl */*/*.pl */*/*/*.pl `; + @objects = `ls *.txt *.c *.cu *.h *.h.in *.fh */*.c */*.cu */*.h */*.h.in */*.fh */*/*.c */*/*.cu */*/*.h */*/*.h.in */*/*.fh */*/*/*.c */*/*/*.cu */*/*/*.h */*/*/*.h.in */*/*/*.fh *.f90 *.F90 *.h *.h.in *.fh */*.f90 */*.F90 */*.h */*.h.in */*.fh */*/*.f90 */*/*.F90 */*/*.h */*/*.h.in */*/*.fh */*/*/*.f90 */*/*/*.F90 */*/*/*.h */*/*/*.h.in */*/*/*.fh */*.txt */*/*.txt */*/*/*.txt */*.tex */*/*.tex */*/*/*.tex */*.sh */*/*.sh */*/*/*.sh */*.csh */*/*.csh */*/*/*.csh */*.bash */*/*.bash */*/*/*.bash */*.pl */*/*.pl */*/*/*.pl `; foreach $name (@objects) { chop $name; diff --git a/utils/fault_tolerance/Leonardo_Bautista_email_answer_about_adding_fault_tolerance_to_the_official_SVN_version_of_SPECFEM3D_GLOBE_mar2012.txt b/utils/fault_tolerance/Leonardo_Bautista_email_answer_about_adding_fault_tolerance_to_the_official_SVN_version_of_SPECFEM3D_GLOBE_mar2012.txt index c824ed18f..a0ac972e5 100644 --- a/utils/fault_tolerance/Leonardo_Bautista_email_answer_about_adding_fault_tolerance_to_the_official_SVN_version_of_SPECFEM3D_GLOBE_mar2012.txt +++ b/utils/fault_tolerance/Leonardo_Bautista_email_answer_about_adding_fault_tolerance_to_the_official_SVN_version_of_SPECFEM3D_GLOBE_mar2012.txt @@ -66,7 +66,7 @@ Mpi_tag: 2612 ======================================================== -El 5 de marzo de 2012 05:06, Dimitri Komatitsch escribió: +El 5 de marzo de 2012 05:06, Dimitri Komatitsch escribio: Hi Leonardo, diff --git a/utils/readme_cuda_cscs.txt b/utils/readme_cuda_cscs.txt index 025321244..230e55d1c 100644 --- a/utils/readme_cuda_cscs.txt +++ b/utils/readme_cuda_cscs.txt @@ -1,63 +1,63 @@ - -GPU_MODE Notes (by Max Rietmann) - -src/shared/constants.h: - -Change the following settings (for NOISE simulations): - -! sources and receivers Z coordinates given directly instead of with depth - logical, parameter :: USE_SOURCES_RECVS_Z = .true. - -! the seismograms are normal to surface -! Z record corresponds to the normal, while E and N are two tangent vectors -! that completes an orthonormal. - logical, parameter :: EXT_MESH_RECV_NORMAL = .true. - -Settings for Eiger -./configure --with-cuda FC=mpif90 MPIFC=mpif90 CUDA_LIB=-L/apps/eiger/Cuda-4.0/cuda/lib64 MPI_INC=-I/apps/eiger/mvapich2/1.5.1p1/mvapich2-gnu/include -./configure --with-cuda FC=mpif90 MPIFC=mpif90 FLAGS_CHECK="-O3 -ffree-line-length-none -fopenmp" FLAGS_NO_CHECK="-Ofast -mfpmath=sse -funroll-loops -ffree-line-length-none -fopenmp" CUDA_LIB=-L/apps/eiger/Cuda-4.0/cuda/lib64 MPI_INC=-I/apps/eiger/mvapich2/1.5.1p1/mvapich2-gnu/include - -./configure --with-cuda FC=mpif90 MPIFC=mpif90 FLAGS_CHECK="`echo $ICC_CHECK`" FLAGS_NO_CHECK='`echo $ICC_FCFLAGS`' CUDA_LIB=-L/apps/eiger/Cuda-4.0/cuda/lib64 MPI_INC=-I/apps/eiger/mvapich2/1.5.1p1/mvapich2-gnu/include - -NOTE: Need to add below to get nvcc to use the older version of gcc, as it doesn't support gcc4.5 or above. ---compiler-bindir /usr/bin/gcc-4.3 - - CUDA_LIB=-L$CUDA_HOME/lib64 MPI_INC=-I$MPICH_DIR/include - - -Settings for todi.cscs.ch -export GNU_FCFLAGS="-Ofast -mfpmath=sse -funroll-loops -ffree-line-length-none" -export GNU_CHECK="-O3 -ffree-line-length-none" -export DEBUG_FLAGS="-g -fbacktrace" -export ICC_FCFLAGS="-O3 -fp-model fast=2 -x SSE4.2 -ftz -funroll-loops -unroll5" -export ICC_FCFLAGS="-O3 -fp-model fast=2 -funroll-loops -unroll5 -msse3 -ftree-vectorize" -export ICC_CHECK="-O2" -export CRAY_FCFLAGS="-eF -em -rm -O3,fp3" -export CRAY_CHECK="-eF -em -rm" - -# Cray configure -./configure --with-cuda CC=cc FC=ftn MPIFC=ftn MPICC=cc FLAGS_CHECK="`echo $CRAY_CHECK`" FLAGS_NO_CHECK='`echo $CRAY_FCFLAGS`' CUDA_LIB=-L$CUDA_HOME/lib64 MPI_INC=-I$MPICH_DIR/include -# GNU configure -./configure --with-cuda CC=cc FC=ftn MPIFC=ftn MPICC=cc FLAGS_CHECK="`echo $GNU_CHECK`" FLAGS_NO_CHECK='`echo $GNU_FCFLAGS`' CUDA_LIB=-L$CUDA_HOME/lib64 MPI_INC=-I$MPICH_DIR/include -# Intel convifugre -./configure --with-cuda CC=cc FC=ftn MPIFC=ftn MPICC=cc FLAGS_CHECK="`echo $ICC_CHECK`" FLAGS_NO_CHECK='`echo $ICC_FCFLAGS`' CUDA_LIB=-L$CUDA_HOME/lib64 MPI_INC=-I$MPICH_DIR/include - -./configure CC=cc FC=ftn MPIFC=ftn MPICC=cc FLAGS_CHECK="`echo $CRAY_CHECK`" FLAGS_NO_CHECK='`echo $CRAY_FCFLAGS`' MPI_INC=-I$MPICH_DIR/include - -suggested compiler options: -intel: -O3 -fp-model fast=2 -x SSE4.2 -ftz -funroll-loops -unroll5 -gnu: -Ofast -mfpmath=sse -funroll-loops -pgi: -#################################### -Notes from Jeff Poznanovic: - -Configure and build with: - -module load cuda cudatools cudasdk -module load PrgEnv-cray -./configure --with-cuda --with-mpi MPIFC=ftn MPICC=cc FC=ftn CC=cc FCFLAGS="-eF -em -rm" CFLAGS="-h list=m" MPI_INC=-I/opt/cray/mpt/default/xt/gemini/mpich2-cray/73/include - - -make - - + +GPU_MODE Notes (by Max Rietmann) + +src/shared/constants.h: + +Change the following settings (for NOISE simulations): + +! sources and receivers Z coordinates given directly instead of with depth + logical, parameter :: USE_SOURCES_RECVS_Z = .true. + +! the seismograms are normal to surface +! Z record corresponds to the normal, while E and N are two tangent vectors +! that completes an orthonormal. + logical, parameter :: EXT_MESH_RECV_NORMAL = .true. + +Settings for Eiger +./configure --with-cuda FC=mpif90 MPIFC=mpif90 CUDA_LIB=-L/apps/eiger/Cuda-4.0/cuda/lib64 MPI_INC=-I/apps/eiger/mvapich2/1.5.1p1/mvapich2-gnu/include +./configure --with-cuda FC=mpif90 MPIFC=mpif90 FLAGS_CHECK="-O3 -ffree-line-length-none -fopenmp" FLAGS_NO_CHECK="-Ofast -mfpmath=sse -funroll-loops -ffree-line-length-none -fopenmp" CUDA_LIB=-L/apps/eiger/Cuda-4.0/cuda/lib64 MPI_INC=-I/apps/eiger/mvapich2/1.5.1p1/mvapich2-gnu/include + +./configure --with-cuda FC=mpif90 MPIFC=mpif90 FLAGS_CHECK="`echo $ICC_CHECK`" FLAGS_NO_CHECK='`echo $ICC_FCFLAGS`' CUDA_LIB=-L/apps/eiger/Cuda-4.0/cuda/lib64 MPI_INC=-I/apps/eiger/mvapich2/1.5.1p1/mvapich2-gnu/include + +NOTE: Need to add below to get nvcc to use the older version of gcc, as it doesn't support gcc4.5 or above. +--compiler-bindir /usr/bin/gcc-4.3 + + CUDA_LIB=-L$CUDA_HOME/lib64 MPI_INC=-I$MPICH_DIR/include + + +Settings for todi.cscs.ch +export GNU_FCFLAGS="-Ofast -mfpmath=sse -funroll-loops -ffree-line-length-none" +export GNU_CHECK="-O3 -ffree-line-length-none" +export DEBUG_FLAGS="-g -fbacktrace" +export ICC_FCFLAGS="-O3 -fp-model fast=2 -x SSE4.2 -ftz -funroll-loops -unroll5" +export ICC_FCFLAGS="-O3 -fp-model fast=2 -funroll-loops -unroll5 -msse3 -ftree-vectorize" +export ICC_CHECK="-O2" +export CRAY_FCFLAGS="-eF -em -rm -O3,fp3" +export CRAY_CHECK="-eF -em -rm" + +# Cray configure +./configure --with-cuda CC=cc FC=ftn MPIFC=ftn MPICC=cc FLAGS_CHECK="`echo $CRAY_CHECK`" FLAGS_NO_CHECK='`echo $CRAY_FCFLAGS`' CUDA_LIB=-L$CUDA_HOME/lib64 MPI_INC=-I$MPICH_DIR/include +# GNU configure +./configure --with-cuda CC=cc FC=ftn MPIFC=ftn MPICC=cc FLAGS_CHECK="`echo $GNU_CHECK`" FLAGS_NO_CHECK='`echo $GNU_FCFLAGS`' CUDA_LIB=-L$CUDA_HOME/lib64 MPI_INC=-I$MPICH_DIR/include +# Intel convifugre +./configure --with-cuda CC=cc FC=ftn MPIFC=ftn MPICC=cc FLAGS_CHECK="`echo $ICC_CHECK`" FLAGS_NO_CHECK='`echo $ICC_FCFLAGS`' CUDA_LIB=-L$CUDA_HOME/lib64 MPI_INC=-I$MPICH_DIR/include + +./configure CC=cc FC=ftn MPIFC=ftn MPICC=cc FLAGS_CHECK="`echo $CRAY_CHECK`" FLAGS_NO_CHECK='`echo $CRAY_FCFLAGS`' MPI_INC=-I$MPICH_DIR/include + +suggested compiler options: +intel: -O3 -fp-model fast=2 -x SSE4.2 -ftz -funroll-loops -unroll5 +gnu: -Ofast -mfpmath=sse -funroll-loops +pgi: +#################################### +Notes from Jeff Poznanovic: + +Configure and build with: + +module load cuda cudatools cudasdk +module load PrgEnv-cray +./configure --with-cuda --with-mpi MPIFC=ftn MPICC=cc FC=ftn CC=cc FCFLAGS="-eF -em -rm" CFLAGS="-h list=m" MPI_INC=-I/opt/cray/mpt/default/xt/gemini/mpich2-cray/73/include + + +make + + diff --git a/utils/seis_process/readme.txt b/utils/seis_process/readme.txt index 66244b254..f9b03784c 100644 --- a/utils/seis_process/readme.txt +++ b/utils/seis_process/readme.txt @@ -8,7 +8,7 @@ To compare synthetics and data, the following steps are recommended: correct station/event and timing information. 2. Convolve synthetic seismograms with a source time function with the - half duration specified in the CMTSOLUTION file, provided, as recommended, + half duration specified in the CMTSOLUTION file, provided, as recommended, you used a zero half duration in the SEM simulations. 3. Resample both observed and synthetic seismograms to a common sampling rate. @@ -20,8 +20,8 @@ To compare synthetics and data, the following steps are recommended: 6. Remove the instrument response from the observed seismograms (recommended) or convolve the synthetic seismograms with the instrument response. -7. Make sure that you apply the same filters to both observed and synthetic seismograms. - Preferably, avoid filtering your records more than once. +7. Make sure that you apply the same filters to both observed and synthetic seismograms. + Preferably, avoid filtering your records more than once. 8. Now, you are ready to compare your synthetic and observed seismograms. diff --git a/utils/solver_classical_serial_Fortran_or_C_no_MPI/slower_versions_not_so_good/timings_comparing_all_versions.txt b/utils/solver_classical_serial_Fortran_or_C_no_MPI/slower_versions_not_so_good/timings_comparing_all_versions.txt index e17403ebc..6bee65923 100644 --- a/utils/solver_classical_serial_Fortran_or_C_no_MPI/slower_versions_not_so_good/timings_comparing_all_versions.txt +++ b/utils/solver_classical_serial_Fortran_or_C_no_MPI/slower_versions_not_so_good/timings_comparing_all_versions.txt @@ -1,10 +1,10 @@ original : - + Time step # 2200 out of 2200 Time = 554.1480 seconds out of 554.1480 seconds - Max norm displacement vector U in the solid (m) = 3.036692 - Elapsed time in seconds = 90.7499999998864 + Max norm displacement vector U in the solid (m) = 3.036692 + Elapsed time in seconds = 90.7499999998864 Elapsed time in hh:mm:ss = 0 h 01 m 30 s Mean elapsed time per time step in seconds = 4.124999999994836E-002 @@ -12,14 +12,14 @@ original : new version NGLOB : - + Time step # 2200 out of 2200 Time = 554.1480 seconds out of 554.1480 seconds - Max norm displacement vector U in the solid (m) = 3.036692 - Elapsed time in seconds = 95.5060000000130 + Max norm displacement vector U in the solid (m) = 3.036692 + Elapsed time in seconds = 95.5060000000130 Elapsed time in hh:mm:ss = 0 h 01 m 35 s Mean elapsed time per time step in seconds = 4.341181818182410E-002 - + ----------------- new version NSPEC *seulement partielle* sans les sommes internes du GATHER : @@ -28,57 +28,57 @@ bonne voie rapide) Time step # 2200 out of 2200 Time = 554.1480 seconds out of 554.1480 seconds - Max norm displacement vector U in the solid (m) = 60.49087 - Elapsed time in seconds = 100.840000000104 + Max norm displacement vector U in the solid (m) = 60.49087 + Elapsed time in seconds = 100.840000000104 Elapsed time in hh:mm:ss = 0 h 01 m 40 s Mean elapsed time per time step in seconds = 4.583636363641105E-002 - + ----------------- avec inlining de Deville, partie 1 : - + Time step # 2200 out of 2200 Time = 554.1480 seconds out of 554.1480 seconds - Max norm displacement vector U in the solid (m) = 3.036692 - Elapsed time in seconds = 67.4950000000000 + Max norm displacement vector U in the solid (m) = 3.036692 + Elapsed time in seconds = 67.4950000000000 Elapsed time in hh:mm:ss = 0 h 01 m 07 s Mean elapsed time per time step in seconds = 3.067954545454546E-002 - + ------------------------------- avec inlining de Deville, parties 1 et 2 : - + Time step # 2200 out of 2200 Time = 554.1480 seconds out of 554.1480 seconds - Max norm displacement vector U in the solid (m) = 3.036693 - Elapsed time in seconds = 46.8210000001416 + Max norm displacement vector U in the solid (m) = 3.036693 + Elapsed time in seconds = 46.8210000001416 Elapsed time in hh:mm:ss = 0 h 00 m 46 s Mean elapsed time per time step in seconds = 2.128227272733707E-002 - + ------------------------------- avec separation de displ, veloc, accel en trois tableaux chacun : (only 2% better, not worth the change) Time step # 2200 out of 2200 Time = 554.1480 seconds out of 554.1480 seconds - Max norm displacement vector U in the solid (m) = 3.036693 - Elapsed time in seconds = 45.8600000001565 + Max norm displacement vector U in the solid (m) = 3.036693 + Elapsed time in seconds = 45.8600000001565 Elapsed time in hh:mm:ss = 0 h 00 m 45 s Mean elapsed time per time step in seconds = 2.084545454552567E-002 - + -------------------------- avec passage de fac1, fac2 et fac3 dans des matrices constantes (ce qui prendrait beaucoup de memoire car il faudrait stocker trois versions differentes) de "jacobian" : pas de gain significatif de performance donc pas du tout la peine d'implementer cela : - + Time step # 2200 out of 2200 Time = 554.1480 seconds out of 554.1480 seconds - Max norm displacement vector U in the solid (m) = 3.036693 - Elapsed time in seconds = 46.9840000000261 + Max norm displacement vector U in the solid (m) = 3.036693 + Elapsed time in seconds = 46.9840000000261 Elapsed time in hh:mm:ss = 0 h 00 m 46 s Mean elapsed time per time step in seconds = 2.135636363637549E-002 - + ------------------- diff --git a/utils/unused_routines/Sieh_1857_digitized_slip_map/mean_value_slip_Sieh_1857.txt b/utils/unused_routines/Sieh_1857_digitized_slip_map/mean_value_slip_Sieh_1857.txt index fcd13b61b..0a43e7247 100644 --- a/utils/unused_routines/Sieh_1857_digitized_slip_map/mean_value_slip_Sieh_1857.txt +++ b/utils/unused_routines/Sieh_1857_digitized_slip_map/mean_value_slip_Sieh_1857.txt @@ -1 +1 @@ - mean value of slip (m) = 4.90080192813231 + mean value of slip (m) = 4.90080192813231 diff --git a/utils/unused_routines/Sieh_1857_digitized_slip_map/raw_data_andreas_1857.txt b/utils/unused_routines/Sieh_1857_digitized_slip_map/raw_data_andreas_1857.txt index f2abb74e2..1197ed41b 100644 --- a/utils/unused_routines/Sieh_1857_digitized_slip_map/raw_data_andreas_1857.txt +++ b/utils/unused_routines/Sieh_1857_digitized_slip_map/raw_data_andreas_1857.txt @@ -29,4 +29,4 @@ 265.215 4.356 292.695 2.7846 295.805 2.7846 -327.95 0.742 \ No newline at end of file +327.95 0.742 diff --git a/utils/unused_routines/Sieh_1857_digitized_slip_map/slip_sieh_1857_extracted.txt b/utils/unused_routines/Sieh_1857_digitized_slip_map/slip_sieh_1857_extracted.txt index f0abcff57..f7670d464 100644 --- a/utils/unused_routines/Sieh_1857_digitized_slip_map/slip_sieh_1857_extracted.txt +++ b/utils/unused_routines/Sieh_1857_digitized_slip_map/slip_sieh_1857_extracted.txt @@ -1,2637 +1,2637 @@ - -34.4500007629395 3.51800000667572 - -34.3125197218112 3.51800000667572 - -34.1750386806830 3.51800000667572 - -34.0375576395547 3.54562189745073 - -33.9000765984265 3.53181095206322 - -33.7625955572982 3.51800000667572 - -33.6251145161700 3.51800000667572 - -33.4876334750417 3.51800000667572 - -33.3501524339135 3.51800000667572 - -33.2126713927852 3.51800000667572 - -33.0751903516570 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--- a/utils/unused_routines/model_interface_bedrock.f90 +++ b/utils/unused_routines/model_interface_bedrock.f90 @@ -126,7 +126,7 @@ ! utm_x_station(6) = 817099.3750000d0 ! utm_y_station(6) = -24430.2871094d0 -! print*,myrank,'après store the position of the six stations' +! print*,myrank,'apres store the position of the six stations' ! call flush(6) ! print*, myrank,minval(nodes_coords_ext_mesh(1,:)) diff --git a/utils/unused_routines/readme_LA_HR_and_MR_vo.txt b/utils/unused_routines/readme_LA_HR_and_MR_vo.txt index 7c61a96e6..20251e8d7 100644 --- a/utils/unused_routines/readme_LA_HR_and_MR_vo.txt +++ b/utils/unused_routines/readme_LA_HR_and_MR_vo.txt @@ -1,26 +1,26 @@ High-res model: -AXIS_O 371052.25 3774000 400 -AXIS_U 46000 0 0 -AXIS_V 0 -48750 0 -AXIS_W 0 0 -9900 -AXIS_MIN 0 0 0 -AXIS_MAX 1 1 1 -AXIS_N 185 196 100 -AXIS_NAME " axis-1" " axis-2" " axis-3" +AXIS_O 371052.25 3774000 400 +AXIS_U 46000 0 0 +AXIS_V 0 -48750 0 +AXIS_W 0 0 -9900 +AXIS_MIN 0 0 0 +AXIS_MAX 1 1 1 +AXIS_N 185 196 100 +AXIS_NAME " axis-1" " axis-2" " axis-3" Medium-res model: -AXIS_O 283000 3655000 -15000 -AXIS_U 193000 0 0 -AXIS_V 0 195000 0 -AXIS_W 0 0 19800 -AXIS_MIN 0 0 0 -AXIS_MAX 1 1 1 -AXIS_N 194 196 100 -AXIS_NAME " axis-1" " axis-2" " axis-3" +AXIS_O 283000 3655000 -15000 +AXIS_U 193000 0 0 +AXIS_V 0 195000 0 +AXIS_W 0 0 19800 +AXIS_MIN 0 0 0 +AXIS_MAX 1 1 1 +AXIS_N 194 196 100 +AXIS_NAME " axis-1" " axis-2" " axis-3" diff --git a/utils/unused_routines/source_models/list_stations_Dave_Wald_names.txt b/utils/unused_routines/source_models/list_stations_Dave_Wald_names.txt index 8f63d06ab..6e37b0e41 100644 --- a/utils/unused_routines/source_models/list_stations_Dave_Wald_names.txt +++ b/utils/unused_routines/source_models/list_stations_Dave_Wald_names.txt @@ -1,38 +1,38 @@ - ALHF Alhambra 34.070 118.150 - ARL Arleta 34.236 118.439 - BLD LA - Baldwin Hills 34.009 118.361 - CAS Castaic 34.564 118.642 - ECC ???????? 34.259 118.336 - ENR Encino 34.15 118.51 - GRF Griffith Park 34.118 118.299 - HYSB Los Angeles 34.090 118.339 - JFP Granada Hills 34.312 118.496 - MNG Monte Nido 34.078 118.693 - MOR Moorpark 34.288 118.881 - NHL Newhall 34.387 118.530 - NH20 North Hollywood 34.138 118.359 - PARD Santa Clarita 34.435 118.582 - PDM Pacoima Dam 34.334 118.396 - PIRU Lake Piru 34.460 118.753 - PKC Pacoima 34.288 118.375 - PTMG Point Mugu 34.109 119.065 - RRS Sylmar 34.281 118.479 - RSE San Fernando 34.17 118,36 - SCC Sepulvada Canyon 34.097 118.478 - SCR Stone Canyon 34.106 118.454 - SCS Sylmar 34.312 118.481 - SHR Sherman Oaks 34.154 118.465 - SMC Santa Monica 34.011 118.490 - SSU Santa Susanna 34.230 118.713 - SVA Supulveda 34.312 118.475 - SYL Sylmar 34.326 118.444 - TPG Topanga 34.084 118.600 - U03 Canoga Park 34.209 118.517 - U53 Canoga Park 34.212 118.506 - U55 Santa Susana 34.264 118.666 - U56 Newhall 34.391 118.622 - U57 Mint Canyon 34.419 118.426 - VNY Van Nuys 34.221 118.471 - VSQZ Vasquez Rocks Park 34.490 118.320 - WOOD Wood Ranch Dam 34.240 118.820 - WVA Wadsworth 34.052 118.451 + ALHF Alhambra 34.070 118.150 + ARL Arleta 34.236 118.439 + BLD LA - Baldwin Hills 34.009 118.361 + CAS Castaic 34.564 118.642 + ECC ???????? 34.259 118.336 + ENR Encino 34.15 118.51 + GRF Griffith Park 34.118 118.299 + HYSB Los Angeles 34.090 118.339 + JFP Granada Hills 34.312 118.496 + MNG Monte Nido 34.078 118.693 + MOR Moorpark 34.288 118.881 + NHL Newhall 34.387 118.530 + NH20 North Hollywood 34.138 118.359 + PARD Santa Clarita 34.435 118.582 + PDM Pacoima Dam 34.334 118.396 + PIRU Lake Piru 34.460 118.753 + PKC Pacoima 34.288 118.375 + PTMG Point Mugu 34.109 119.065 + RRS Sylmar 34.281 118.479 + RSE San Fernando 34.17 118,36 + SCC Sepulvada Canyon 34.097 118.478 + SCR Stone Canyon 34.106 118.454 + SCS Sylmar 34.312 118.481 + SHR Sherman Oaks 34.154 118.465 + SMC Santa Monica 34.011 118.490 + SSU Santa Susanna 34.230 118.713 + SVA Supulveda 34.312 118.475 + SYL Sylmar 34.326 118.444 + TPG Topanga 34.084 118.600 + U03 Canoga Park 34.209 118.517 + U53 Canoga Park 34.212 118.506 + U55 Santa Susana 34.264 118.666 + U56 Newhall 34.391 118.622 + U57 Mint Canyon 34.419 118.426 + VNY Van Nuys 34.221 118.471 + VSQZ Vasquez Rocks Park 34.490 118.320 + WOOD Wood Ranch Dam 34.240 118.820 + WVA Wadsworth 34.052 118.451