From alexandre.kazantsev at mines-paristech.fr Tue May 2 06:37:46 2017 From: alexandre.kazantsev at mines-paristech.fr (Alexandre KAZANTSEV) Date: Tue, 2 May 2017 15:37:46 +0200 (CEST) Subject: [CIG-SEISMO] SPECFEM2D output files Message-ID: <1025754825.1149068.1493732265983.JavaMail.zimbra@mines-paristech.fr> Good afternoon, I write you by e-mail to avoid a potentially useless issue on github. I have encountered two problems with specfem2D outputs. 1. I wanted to sample the wavefield densly in space. I first tried to use the following options in Par_file : output_wavefield_dumps = .true. use_binary_for_wavefield_dumps = .true. This resulted into a crash. 2. I bypassed this issue by generating a STATIONS file with several thousands stations and using the options : save_ASCII_seismograms = .false. save_binary_seismograms_single = .true. use_existing_STATIONS = .true. This worked, but generated heavy files. To avoid this, I tried to use subsamp_seismos = 50 , But it looks like it works well only with ascii seismograms . The size of the binary file 'Uz_file_single.bin' remains the same (huge) as it was without downsampling. The import of the "downsampled" files with Matlab "fread" produced strange results, while it worked well if no downsampling was used. If you have an idea on why these problems occur and how to handle them, please let me know. You will find enclosed an example of simulation parameters. The executable is ./main.sh, which must be modified to account for the true location of the scripts xspecfem2D, xmeshfem2D and gmsh. Best regards, Alexandre (PhD student in Geophysics at Mines-Paristech, France) -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: export_simu_params.zip Type: application/zip Size: 1057649 bytes Desc: not available URL: From phil.cummins at anu.edu.au Tue May 2 21:22:05 2017 From: phil.cummins at anu.edu.au (Phil Cummins) Date: Wed, 3 May 2017 14:22:05 +1000 Subject: [CIG-SEISMO] Specfem anelasticity Message-ID: <59095AED.3030206@anu.edu.au> Hi, I am wondering if someone could please direct me to which publication gives a detailed treatment of how anelasticity is handled in specfem. From comments in the manual and the input file I believe an absorption band model is used, but I couldn't find anything describing just how this is done. Can someone please tell me, which of the many specfem references might cover this? Many thanks, - Phil From komatitsch at lma.cnrs-mrs.fr Wed May 3 02:05:27 2017 From: komatitsch at lma.cnrs-mrs.fr (Dimitri Komatitsch) Date: Wed, 3 May 2017 11:05:27 +0200 Subject: [CIG-SEISMO] Specfem anelasticity In-Reply-To: <59095AED.3030206@anu.edu.au> References: <59095AED.3030206@anu.edu.au> Message-ID: <84be518d-526e-1daa-3eb1-5473772a7b41@lma.cnrs-mrs.fr> Hi Phil, Yes, you can see http://komatitsch.free.fr/preprints/GJI_Lombard_2016.pdf and http://komatitsch.free.fr/preprints/GJI_1999_figure16_error_fixed_equation3_typo_fixed.pdf . http://komatitsch.free.fr/preprints/GJI_undo_attenuation_2016.pdf can also help if you work on inversion / time reversal with viscoelasticity. Best regards, Dimitri. On 05/03/2017 06:22 AM, Phil Cummins wrote: > Hi, > > I am wondering if someone could please direct me to which publication > gives a detailed treatment of how anelasticity is handled in specfem. > From comments in the manual and the input file I believe an absorption > band model is used, but I couldn't find anything describing just how > this is done. Can someone please tell me, which of the many specfem > references might cover this? > Many thanks, > > - Phil > _______________________________________________ > CIG-SEISMO mailing list > CIG-SEISMO at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo -- Dimitri Komatitsch, CNRS Research Director (DR CNRS) Laboratory of Mechanics and Acoustics, Marseille, France http://komatitsch.free.fr From seckinpolat at hotmail.com.tr Sat May 6 20:28:56 2017 From: seckinpolat at hotmail.com.tr (=?utf-8?B?U2XDp2tpbiBQb2xhdA==?=) Date: Sun, 7 May 2017 03:28:56 +0000 Subject: [CIG-SEISMO] Problem with Absorbing Boundary Condition Message-ID: Hello, My name is Seckin Polat, I am a master’s student in Geophysics, I have been using Specfem2D for a while for my research. I placed a void inside of one layer model whose dimension is 50 m. x 50 m. And I would like to observe the seismic wave propagation while they travel along the void. I am using Gmsh to generate external models then I run them with Specfem2D and I have never encountered this problem before and I decided to ask for it. When I assign absorbing boundary condition for left, right, and bottom boundaries, my model is working fine when there attenuation is zero, however when I assign the attenuation to 30, all my boundary conditions are behaving like free surface that I did not assign. My .geo file for Gmsh is; // Geometry File of Perfect Shape Tunnel With Receiver and Source That is Not Located in Wells cl1=0.25; //Boundary Points of Square Point(1) = {0, 0, 0, cl1}; Point(2) = {50, 0, 0, cl1}; Point(3) = {50, 50, 0, cl1}; Point(14) = {0, 50, 0, cl1}; //Connection Points Point(5) = {25, 50, 0, cl1}; //Points of Boundary of Tunnel Point(7) = {25, 31, 0, cl1}; Point(8) = {24.5 , 30.5, 0, cl1}; Point(9) = {24.5, 29.5, 0, cl1}; Point(10) = {25.5, 29.5, 0, cl1}; Point(11) = {25.5, 30.5, 0, cl1}; //Points of Center of Tunnel and Its Circles Point(12) = {25, 30.5, 0, cl1}; Point(13) = {25, 29.5, 0, cl1}; //Lines of Square Line(1) = {1, 2}; Line(2) = {2, 3}; Line(4) = {3, 5}; Line(14) = {5, 14}; Line(15) = {14, 1}; //Lines of Connection Line(5) = {5, 7}; //Lines of Tunnel Circle(7) = {7,12, 8}; Line(8) = {8, 9}; Circle(9) = {9, 13, 10}; Line(10) = {10, 11}; Circle(11) = {11, 12, 7}; //Loops Line Loop(1) = {1, 2, 4, 5, 7, 8, 9, 10, 11, -5, 14, 15}; Plane Surface(1) = {1}; Physical Line("Top") = {4, 14}; Physical Line("Bottom") = {1}; Physical Line("Left") = {15}; Physical Line("Right") = {2}; //Physical Surfaces Physical Surface("M1") = {1}; Then I mesh this .geo file and saved it as .mesh, then I transfer this files into Specfem2D, and run “process_the_Gmsh_file_once_and_for_all.sh” command line which is written below. #!/bin/bash # # create the absorbing and free surface files from the Gmsh file # ##cd MESH/ python /home/spolat/specfem2d/utils/Gmsh/LibGmsh2Specfem_convert_Gmsh_to_Specfem2D_official.py perfectshape.msh -t F -b A -r A -l A cd ../ And my source file is written below as; #source 1. The components of a moment tensor source must be given in N.m, not in dyne.cm as in the DATA/CMTSOLUTION source file of the 3D version of the code. source_surf = .false. # source inside the medium or at the surface xs = 10.395 # source location x in meters zs = ABCD # source location z in meters source_type = 1 # elastic force or acoustic pressure = 1 or moment tensor = 2 time_function_type = 1 # Ricker = 1, first derivative = 2, Gaussian = 3, Dirac = 4, Heaviside = 5 # time function_type == 8 source read from file, if time function_type == 9 : burst # If time_function_type == 8, enter below the custom source file to read (two columns file with time and amplitude) : # (For the moment dt must be equal to the dt of the simulation. File name can't exceed 150 characters) name_of_source_file = "" # Only for option 8 : file containing the source wavelet burst_band_width = 0. # Only for option 9 : band width of the burst f0 = 4000 # dominant source frequency (Hz) if not Dirac or Heaviside tshift = 0.0 # time shift when multi sources (if one source, must be zero) anglesource = 90.0 # angle of the source (for a force only) Mxx = 1. # Mxx component (for a moment tensor source only) Mzz = 1. # Mzz component (for a moment tensor source only) Mxz = 0. # Mxz component (for a moment tensor source only) factor = 1.d10 # amplification factor In this example, I designed the model as the top as free surface, and other surfaces have absorbing boundary condition. However, when I run Specfem2D, absorbing boundaries are acting like free surfaces. My Par_file is written below. #----------------------------------------------------------------------------- # # simulation input parameters # #----------------------------------------------------------------------------- # title of job title = Subsurface Modeling for Detection of a Tunnel with One Receiver Set # forward or adjoint simulation # 1 = forward, 2 = adjoint, 3 = both simultaneously # note: 2 is purposely UNUSED (for compatibility with the numbering of our 3D codes) SIMULATION_TYPE = 1 # 0 = regular wave propagation simulation, 1/2/3 = noise simulation NOISE_TOMOGRAPHY = 0 # save the last frame, needed for adjoint simulation SAVE_FORWARD = .false. # parameters concerning partitioning NPROC = 256 # number of processes partitioning_method = 3 # SCOTCH = 3, ascending order (very bad idea) = 1 # number of control nodes per element (4 or 9) ngnod = 4 # time step parameters # total number of time steps NSTEP =65000 # duration of a time step (see section "How to choose the time step" of the manual for how to do this) DT = 5.d-7 # time stepping # 1 = Newmark (2nd order), 2 = LDDRK4-6 (4th-order 6-stage low storage Runge-Kutta), 3 = classical RK4 4th-order 4-stage Runge-Kutta time_stepping_scheme = 1 # axisymmetric (2.5D) or Cartesian planar (2D) simulation AXISYM = .false. # set the type of calculation (P-SV or SH/membrane waves) P_SV = .true. # set to true to use GPUs GPU_MODE = .false. # available models # default - define model using nbmodels below # ascii - read model from ascii database file # binary - read model from binary databse file # binary_voigt - read Voigt model from binary database file # external - define model using define_external_model subroutine # gll - read GLL model from binary database file # legacy - read model from model_velocity.dat_input MODEL = default # Output the model with the requested type, does not save if turn to default or .false. # (available output formats: ascii,binary,gll,legacy) SAVE_MODEL = default #----------------------------------------------------------------------------- # # attenuation # #----------------------------------------------------------------------------- # attenuation parameters ATTENUATION_VISCOELASTIC = .true. # turn attenuation (viscoelasticity) on or off for non-poroelastic solid parts of the model ATTENUATION_PORO_FLUID_PART = .false. # turn viscous attenuation on or off for the fluid part of poroelastic parts of the model Q0 = 30 # quality factor for viscous attenuation freq0 = 4000 # frequency for viscous attenuation # for viscoelastic attenuation N_SLS = 2 # number of standard linear solids for attenuation (3 is usually the minimum) f0_attenuation = 4000 # (Hz) relevant only if source is a Dirac or a Heaviside, otherwise it is f0 the dominant frequency of the source in the DATA/SOURCE file READ_VELOCITIES_AT_f0 = .false. # shift velocities to account for physical dispersion (see user manual for more information) # to undo attenuation for sensitivity kernel calculations or forward runs with SAVE_FORWARD # use the flag below. It performs undoing of attenuation in an exact way for sensitivity kernel calculations # but requires disk space for temporary storage, and uses a significant amount of memory used as buffers for temporary storage. # When that option is on the second parameter indicates how often the code dumps restart files to disk (if in doubt, use something between 100 and 1000). UNDO_ATTENUATION = .false. NT_DUMP_ATTENUATION = 500 #----------------------------------------------------------------------------- # # sources # #----------------------------------------------------------------------------- # source parameters NSOURCES = 1 # number of sources (source information is then read from the DATA/SOURCE file) force_normal_to_surface = .false. # angleforce normal to surface (external mesh and curve file needed) # use an existing initial wave field as source or start from zero (medium initially at rest) initialfield = .false. add_Bielak_conditions_bottom = .false. # add Bielak conditions or not if initial plane wave add_Bielak_conditions_right = .false. add_Bielak_conditions_top = .false. add_Bielak_conditions_left = .false. # acoustic forcing ACOUSTIC_FORCING = .false. # acoustic forcing of an acoustic medium with a rigid interface #----------------------------------------------------------------------------- # # receivers # #----------------------------------------------------------------------------- # receiver set parameters for recording stations (i.e. recording points) seismotype = 1 # record 1=displ 2=veloc 3=accel 4=pressure 5=curl of displ 6=the fluid potential # subsampling of the seismograms to create smaller files (but less accurately sampled in time) subsamp_seismos = 1 # so far, this option can only be used if all the receivers are in acoustic elements USE_TRICK_FOR_BETTER_PRESSURE = .false. # every how many time steps we save the seismograms # (costly, do not use a very small value; if you use a very large value that is larger than the total number # of time steps of the run, the seismograms will automatically be saved once at the end of the run anyway) NSTEP_BETWEEN_OUTPUT_SEISMOS = 5000000 # Compute the field int_0^t v^2 dt for a set of GLL points and write it to file. Use # the script utils/visualisation/plotIntegratedEnergyFile.py to watch. It is refreshed at the same time than the seismograms COMPUTE_INTEGRATED_ENERGY_FIELD = .false. # use this t0 as earliest starting time rather than the automatically calculated one USER_T0 = 0.0d0 # seismogram formats save_ASCII_seismograms = .true. # save seismograms in ASCII format or not save_binary_seismograms_single = .true. # save seismograms in single precision binary format or not (can be used jointly with ASCII above to save both) save_binary_seismograms_double = .false. # save seismograms in double precision binary format or not (can be used jointly with both flags above to save all) SU_FORMAT = .true. # output single precision binary seismograms in Seismic Unix format (adjoint traces will be read in the same format) # use an existing STATION file found in ./DATA or create a new one from the receiver positions below in this Par_file use_existing_STATIONS = .false. # number of receiver sets (i.e. number of receiver lines to create below) nreceiversets = 1 # orientation anglerec = 0.d0 # angle to rotate components at receivers rec_normal_to_surface = .false. # base anglerec normal to surface (external mesh and curve file needed) # first receiver set (repeat these 6 lines and adjust nreceiversets accordingly) nrec = 39 # number of receivers xdeb = 10.395 # first receiver x in meters zdeb = 49 # first receiver z in meters xfin = 10.395 # last receiver x in meters (ignored if only one receiver) zfin = 11 # last receiver z in meters (ignored if only one receiver) record_at_surface_same_vertical = .false. # receivers inside the medium or at the surface #----------------------------------------------------------------------------- # # adjoint kernel outputs # #----------------------------------------------------------------------------- # save sensitivity kernels in ASCII format (much bigger files, but compatible with current GMT scripts) or in binary format save_ASCII_kernels = .true. #----------------------------------------------------------------------------- # # boundary conditions # #----------------------------------------------------------------------------- # Perfectly Matched Layer (PML) boundaries # absorbing boundary active or not PML_BOUNDARY_CONDITIONS = .false. NELEM_PML_THICKNESS = 3 ROTATE_PML_ACTIVATE = .false. ROTATE_PML_ANGLE = 30. # Stacey ABC STACEY_ABSORBING_CONDITIONS = .true. # periodic boundaries ADD_PERIODIC_CONDITIONS = .false. PERIODIC_HORIZ_DIST = 0.3597d0 #----------------------------------------------------------------------------- # # velocity and density models # #----------------------------------------------------------------------------- nbmodels = 1 # available material types (see user manual for more information) # acoustic: model_number 1 rho Vp 0 0 0 QKappa Qmu 0 0 0 0 0 0 # elastic: model_number 1 rho Vp Vs 0 0 QKappa Qmu 0 0 0 0 0 0 # anistoropic: model_number 2 rho c11 c13 c15 c33 c35 c55 c12 c23 c25 0 0 0 # poroelastic: model_number 3 rhos rhof phi c kxx kxz kzz Ks Kf Kfr etaf mufr Qmu # tomo: model_number -1 0 0 A 0 0 0 0 0 0 0 0 0 0 1 1 2600.d0 3000.d0 1500.0d0 0 0 10.d0 10.d0 0 0 0 0 0 0 #2 1 2400.d0 2500.d0 800.0d0 0 0 10.d0 10.d0 0 0 0 0 0 0 #1 1 2600.d0 3000.d0 1500.0d0 0 0 10.d0 10.d0 0 0 0 0 0 0 #2 1 1000.d0 1477.d0 0 0 0 10.d0 10.d0 0 0 0 0 0 0 # external tomography file TOMOGRAPHY_FILE = dummy # use an external mesh created by an external meshing tool or use the internal mesher read_external_mesh = .true. #----------------------------------------------------------------------------- # # PARAMETERS FOR EXTERNAL MESHING # #----------------------------------------------------------------------------- # data concerning mesh, when generated using third-party app (more info in README) # (see also absorbing_conditions above) mesh_file = Mesh_perfectshape # file containing the mesh nodes_coords_file = Nodes_perfectshape # file containing the nodes coordinates materials_file = Material_perfectshape # file containing the material number for each element free_surface_file = Surf_free_perfectshape # file containing the free surface axial_elements_file = dummy # file containing the axial elements if AXISYM is true absorbing_surface_file = Surf_abs_perfectshape # file containing the absorbing surface acoustic_forcing_surface_file = dummy # file containing the acoustic forcing surface absorbing_cpml_file = dummy # file containing the CPML element numbers tangential_detection_curve_file = dummy # file containing the curve delimiting the velocity model #----------------------------------------------------------------------------- # # PARAMETERS FOR INTERNAL MESHING # #----------------------------------------------------------------------------- # file containing interfaces for internal mesh interfacesfile = dummy # geometry of the model (origin lower-left corner = 0,0) and mesh description xmin = -1.d0 # abscissa of left side of the model xmax = 4.d0 # abscissa of right side of the model nx = 835 # number of elements along X # absorbing boundary parameters (see absorbing_conditions above) absorbbottom = .true. absorbright = .true. absorbtop = .true. absorbleft = .true. # define the different regions of the model in the (nx,nz) spectral-element mesh nbregions = 2 # then set below the different regions and model number for each region 1 835 1 71 1 1 835 72 96 2 #----------------------------------------------------------------------------- # # display parameters # #----------------------------------------------------------------------------- # every how many time steps we display information about the simulation (costly, do not use a very small value) NSTEP_BETWEEN_OUTPUT_INFO = 300 # meshing output output_grid_Gnuplot = .false. # generate a GNUPLOT file containing the grid, and a script to plot it output_grid_ASCII = .false. # dump the grid in an ASCII text file consisting of a set of X,Y,Z points or not # compute and output total acoustic and elastic energy curves (slows down the code significantly) OUTPUT_ENERGY = .false. # every how many time steps we compute energy (which is a bit expensive to compute) NTSTEP_BETWEEN_OUTPUT_ENERGY = 10 #----------------------------------------------------------------------------- # # movies/images/snaphots # #----------------------------------------------------------------------------- # every how many time steps we draw JPEG or PostScript pictures of the simulation (costly, do not use a very small value) NSTEP_BETWEEN_OUTPUT_IMAGES = 100 # every how many time steps we dump results of the simulation as ASCII or binary files (costly, do not use a very small value) NSTEP_BETWEEN_OUTPUT_WAVE_DUMPS = 100 # minimum amplitude kept in % for the JPEG and PostScript snapshots; amplitudes below that are muted cutsnaps = 1. #### for JPEG color images #### output_color_image = .true. # output JPEG color image of the results every NSTEP_BETWEEN_OUTPUT_IMAGES time steps or not imagetype_JPEG = 10 # display 1=displ_Ux 2=displ_Uz 3=displ_norm 4=veloc_Vx 5=veloc_Vz 6=veloc_norm 7=accel_Ax 8=accel_Az 9=accel_norm 10=pressure factor_subsample_image = 1.0d0 # (double precision) factor to subsample color images output by the code (useful for very large models) USE_CONSTANT_MAX_AMPLITUDE = .false. # by default the code normalizes each image independently to its maximum; use this option to use the global maximum below instead CONSTANT_MAX_AMPLITUDE_TO_USE = 1.17d4 # constant maximum amplitude to use for all color images if the above USE_CONSTANT_MAX_AMPLITUDE option is true POWER_DISPLAY_COLOR = 0.30d0 # non linear display to enhance small amplitudes in JPEG color images DRAW_SOURCES_AND_RECEIVERS = .true. # display sources as orange crosses and receivers as green squares in JPEG images or not DRAW_WATER_IN_BLUE = .true. # display acoustic layers as constant blue in JPEG images, because they likely correspond to water in the case of ocean acoustics or in the case of offshore oil industry experiments (if off, display them as greyscale, as for elastic or poroelastic elements, for instance for acoustic-only oil industry models of solid media) USE_SNAPSHOT_NUMBER_IN_FILENAME = .false. # use snapshot number in the file name of JPEG color snapshots instead of the time step (for instance to create movies in an easier way later) #### for PostScript snapshots #### output_postscript_snapshot = .false. # output Postscript snapshot of the results every NSTEP_BETWEEN_OUTPUT_IMAGES time steps or not imagetype_postscript = 1 # display 1=displ vector 2=veloc vector 3=accel vector; small arrows are displayed for the vectors meshvect = .true. # display mesh on PostScript plots or not modelvect = .false. # display velocity model on PostScript plots or not boundvect = .true. # display boundary conditions on PostScript plots or not interpol = .true. # interpolation of the PostScript display on a regular grid inside each spectral element, or use the non-evenly spaced GLL points pointsdisp = 6 # number of points in each direction for interpolation of PostScript snapshots (set to 1 for lower-left corner only) subsamp_postscript = 1 # subsampling of background velocity model in PostScript snapshots sizemax_arrows = 1.d0 # maximum size of arrows on PostScript plots in centimeters US_LETTER = .false. # use US letter or European A4 paper for PostScript plots #### for wavefield dumps #### output_wavefield_dumps = .false. # output wave field to a text file every NSTEP_BETWEEN_OUTPUT_TEXT_DUMPS time steps (creates very big files) imagetype_wavefield_dumps = 1 # display 1=displ vector 2=veloc vector 3=accel vector 4=pressure use_binary_for_wavefield_dumps = .false. # use ASCII or single-precision binary format for the wave field dumps Is there any ideas that why my model is not working as it was assigned as absorbing boundary condition? Thank you very much for your help. Sincerely, Seckin -------------- next part -------------- An HTML attachment was scrubbed... URL: From Lili.Feng at colorado.edu Mon May 15 13:54:45 2017 From: Lili.Feng at colorado.edu (Lili Feng) Date: Mon, 15 May 2017 14:54:45 -0600 Subject: [CIG-SEISMO] Question about anisotropy for SW4 Message-ID: Hi, I'm trying to run sw4 for anisotropic media, but the code just stuck and does not output anything. Here is the output information: "*----------------------------------------------------------------* * sw4 version 1.1* * This program comes with ABSOLUTELY NO WARRANTY; released under GPL.* * This is free software, and you are welcome to redistribute * * it under certain conditions, see LICENSE.txt for more details * *----------------------------------------------------------------* * Compiled on: Tue Apr 4 16:03:04 MDT 2017* * By user: life9360* * Machine: shas0137* * Compiler: /projects/life9360/anaconda2/bin/mpicxx* * 3rd party include dir: /include, and library dir: /lib* *----------------------------------------------------------------* *Input file: ak135_aniso_001.in *" The code stuck here and did not output any more information... And below is my input file: *fileio path=ak135_aniso_001 pfs=1 verbose=1* *grid h=1000 nx=2001 ny=2001 nz=201 proj=utm ellps=WGS84* *time t=500* *source x=1000000 y=1000000 z=0 fz=1 t0=13.5 type=Dirac* *prefilter fc1=0.01 fc2=0.1* *rec x=1500000.000 y=1500000.000 depth=0.000 file=SW4.AAA sta=AAA writeEvery=1000 usgsformat=0 sacformat=1 nsew=1 variables=displacement* *anisotropy* *#------------------- ablock models -------------------* *ablock z1=0.000000 z2=20000.000000 rho=2730.000000 c11=1.076668e+11 c12=3.520350e+10 c13=3.458358e+10 c14=7.671698e+08 c22=1.033435e+11 c23=3.484267e+10 c24=2.942917e+09 c33=9.909447e+10 c34=2.315423e+09 c44=3.383794e+10 c55=3.397182e+10 c56=1.349769e+09 c66=3.506251e+10* *ablock z1=20000.000000 z2=35000.000000 rho=2920.000000 c11=1.233700e+11 c12=3.680660e+10 c13=3.680660e+10 c22=1.233700e+11 c23=3.680660e+10 c33=1.233700e+11 c44=4.328170e+10 c55=4.328170e+10 c66=4.328170e+10* *ablock z1=35000.000000 z2=77000.000000 rho=3332.600000 c11=2.155586e+11 c12=8.148659e+10 c13=8.148659e+10 c22=2.155586e+11 c23=8.148659e+10 c33=2.155586e+11 c44=6.703600e+10 c55=6.703600e+10 c66=6.703600e+10* *ablock z1=77000.000000 z2=120000.000000 rho=3358.400000 c11=2.174976e+11 c12=8.178445e+10 c13=8.178445e+10 c22=2.174976e+11 c23=8.178445e+10 c33=2.174976e+11 c44=6.785656e+10 c55=6.785656e+10 c66=6.785656e+10* *ablock z1=120000.000000 z2=165000.000000 rho=3399.000000 c11=2.236862e+11 c12=8.575123e+10 c13=8.575123e+10 c22=2.236862e+11 c23=8.575123e+10 c33=2.236862e+11 c44=6.896748e+10 c55=6.896748e+10 c66=6.896748e+10* *ablock z1=165000.000000 z2=200000.000000 rho=3347.700000 c11=2.271574e+11 c12=9.074873e+10 c13=9.074873e+10 c22=2.271574e+11 c23=9.074873e+10 c33=2.271574e+11 c44=6.820432e+10 c55=6.820432e+10 c66=6.820432e+10* I ran the code with 120 cores and waited for two days. The code is still running now without any warning or error messages, but no output at all... Lili -- Leon(Lili) Feng Ph.D Candidate Center for Imaging the Earth's Interior Department of Physics University of Colorado Boulder +1-(720)-412-4379 -------------- next part -------------- An HTML attachment was scrubbed... URL: From petersson1 at llnl.gov Tue May 16 12:34:26 2017 From: petersson1 at llnl.gov (Petersson, Anders) Date: Tue, 16 May 2017 19:34:26 +0000 Subject: [CIG-SEISMO] Anisotropy in SW4 Message-ID: <7A10CC16-1879-4472-8DC6-634477170844@llnl.gov> Hi Lili, Please provide your input file. Thanks, Anders On 5/16/17, 12:00 PM, "CIG-SEISMO on behalf of cig-seismo-request at geodynamics.org" wrote: Send CIG-SEISMO mailing list submissions to cig-seismo at geodynamics.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo or, via email, send a message with subject or body 'help' to cig-seismo-request at geodynamics.org You can reach the person managing the list at cig-seismo-owner at geodynamics.org When replying, please edit your Subject line so it is more specific than "Re: Contents of CIG-SEISMO digest..." Today's Topics: 1. Question about anisotropy for SW4 (Lili Feng) ---------------------------------------------------------------------- Message: 1 Date: Mon, 15 May 2017 14:54:45 -0600 From: Lili Feng To: cig-seismo at geodynamics.org Subject: [CIG-SEISMO] Question about anisotropy for SW4 Message-ID: Content-Type: text/plain; charset="utf-8" Hi, I'm trying to run sw4 for anisotropic media, but the code just stuck and does not output anything. Here is the output information: "*----------------------------------------------------------------* * sw4 version 1.1* * This program comes with ABSOLUTELY NO WARRANTY; released under GPL.* * This is free software, and you are welcome to redistribute * * it under certain conditions, see LICENSE.txt for more details * *----------------------------------------------------------------* * Compiled on: Tue Apr 4 16:03:04 MDT 2017* * By user: life9360* * Machine: shas0137* * Compiler: /projects/life9360/anaconda2/bin/mpicxx* * 3rd party include dir: /include, and library dir: /lib* *----------------------------------------------------------------* *Input file: ak135_aniso_001.in *" The code stuck here and did not output any more information... And below is my input file: *fileio path=ak135_aniso_001 pfs=1 verbose=1* *grid h=1000 nx=2001 ny=2001 nz=201 proj=utm ellps=WGS84* *time t=500* *source x=1000000 y=1000000 z=0 fz=1 t0=13.5 type=Dirac* *prefilter fc1=0.01 fc2=0.1* *rec x=1500000.000 y=1500000.000 depth=0.000 file=SW4.AAA sta=AAA writeEvery=1000 usgsformat=0 sacformat=1 nsew=1 variables=displacement* *anisotropy* *#------------------- ablock models -------------------* *ablock z1=0.000000 z2=20000.000000 rho=2730.000000 c11=1.076668e+11 c12=3.520350e+10 c13=3.458358e+10 c14=7.671698e+08 c22=1.033435e+11 c23=3.484267e+10 c24=2.942917e+09 c33=9.909447e+10 c34=2.315423e+09 c44=3.383794e+10 c55=3.397182e+10 c56=1.349769e+09 c66=3.506251e+10* *ablock z1=20000.000000 z2=35000.000000 rho=2920.000000 c11=1.233700e+11 c12=3.680660e+10 c13=3.680660e+10 c22=1.233700e+11 c23=3.680660e+10 c33=1.233700e+11 c44=4.328170e+10 c55=4.328170e+10 c66=4.328170e+10* *ablock z1=35000.000000 z2=77000.000000 rho=3332.600000 c11=2.155586e+11 c12=8.148659e+10 c13=8.148659e+10 c22=2.155586e+11 c23=8.148659e+10 c33=2.155586e+11 c44=6.703600e+10 c55=6.703600e+10 c66=6.703600e+10* *ablock z1=77000.000000 z2=120000.000000 rho=3358.400000 c11=2.174976e+11 c12=8.178445e+10 c13=8.178445e+10 c22=2.174976e+11 c23=8.178445e+10 c33=2.174976e+11 c44=6.785656e+10 c55=6.785656e+10 c66=6.785656e+10* *ablock z1=120000.000000 z2=165000.000000 rho=3399.000000 c11=2.236862e+11 c12=8.575123e+10 c13=8.575123e+10 c22=2.236862e+11 c23=8.575123e+10 c33=2.236862e+11 c44=6.896748e+10 c55=6.896748e+10 c66=6.896748e+10* *ablock z1=165000.000000 z2=200000.000000 rho=3347.700000 c11=2.271574e+11 c12=9.074873e+10 c13=9.074873e+10 c22=2.271574e+11 c23=9.074873e+10 c33=2.271574e+11 c44=6.820432e+10 c55=6.820432e+10 c66=6.820432e+10* I ran the code with 120 cores and waited for two days. The code is still running now without any warning or error messages, but no output at all... Lili -- Leon(Lili) Feng Ph.D Candidate Center for Imaging the Earth's Interior Department of Physics University of Colorado Boulder +1-(720)-412-4379 -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Subject: Digest Footer _______________________________________________ CIG-SEISMO mailing list CIG-SEISMO at geodynamics.org http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo ------------------------------ End of CIG-SEISMO Digest, Vol 112, Issue 4 ****************************************** From sunjunping at mail.ioa.ac.cn Wed May 17 01:59:26 2017 From: sunjunping at mail.ioa.ac.cn (=?GBK?B?y+++/Ma9?=) Date: Wed, 17 May 2017 16:59:26 +0800 (GMT+08:00) Subject: [CIG-SEISMO] SPECFEM3D Cartesian and SPECFEM2D Message-ID: <5f40ef.32dd2.15c15a224b9.Coremail.sunjunping@mail.ioa.ac.cn> Dear Sir/Madam I am from the Institute of Acoustics, Chinese Academy of Sciences. I wish to use 'SPECFEM3D Cartesian' and 'SPECFEM2D' to compute sound field in ocean, but i can not download them from the CIG website. Are they free or not? I am looking forward to your reply. Thank you very much for your time. Sincerely, Sun Junping -------------- next part -------------- An HTML attachment was scrubbed... URL: From komatitsch at lma.cnrs-mrs.fr Wed May 17 07:35:04 2017 From: komatitsch at lma.cnrs-mrs.fr (Dimitri Komatitsch) Date: Wed, 17 May 2017 16:35:04 +0200 Subject: [CIG-SEISMO] SPECFEM3D Cartesian and SPECFEM2D In-Reply-To: <5f40ef.32dd2.15c15a224b9.Coremail.sunjunping@mail.ioa.ac.cn> References: <5f40ef.32dd2.15c15a224b9.Coremail.sunjunping@mail.ioa.ac.cn> Message-ID: <99dfe998-1b11-bf1b-1be2-b1af8816e65b@lma.cnrs-mrs.fr> Dear Sun Junping, Sure, they are free and open source, you can get them from https://geodynamics.org/cig/software/specfem3d/ and https://geodynamics.org/cig/software/specfem2d/ by typing the Git command that we give on these pages. Best regards, Dimitri. On 05/17/2017 10:59 AM, 孙军平 wrote: > > Dear Sir/Madam > > I am from the Institute of Acoustics, Chinese Academy of Sciences. I > wish to use 'SPECFEM3D Cartesian' and 'SPECFEM2D' to compute sound field > in ocean, but i can not download them from the CIG website. Are they > free or not? I am looking forward to your reply. Thank you very much for > your time. > > Sincerely, > > Sun Junping > > > > > > > _______________________________________________ > CIG-SEISMO mailing list > CIG-SEISMO at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo > -- Dimitri Komatitsch, CNRS Research Director (DR CNRS) Laboratory of Mechanics and Acoustics, Marseille, France http://komatitsch.free.fr From komatitsch at lma.cnrs-mrs.fr Wed May 17 07:37:45 2017 From: komatitsch at lma.cnrs-mrs.fr (Dimitri Komatitsch) Date: Wed, 17 May 2017 16:37:45 +0200 Subject: [CIG-SEISMO] Sun Junping is right, the "current release" sections have vanished from the CIG Web site for some reason In-Reply-To: <99dfe998-1b11-bf1b-1be2-b1af8816e65b@lma.cnrs-mrs.fr> References: <5f40ef.32dd2.15c15a224b9.Coremail.sunjunping@mail.ioa.ac.cn> <99dfe998-1b11-bf1b-1be2-b1af8816e65b@lma.cnrs-mrs.fr> Message-ID: <47f8c03e-5ca5-f8f2-46c8-27f886e7b721@lma.cnrs-mrs.fr> Hi all, Sun Junping is right, the "current release" sections have vanished from the CIG Web site for some reason. See e.g. https://geodynamics.org/cig/software/specfem3d/ and https://geodynamics.org/cig/software/specfem2d/ , they are empty. Best regards, Dimitri. On 05/17/2017 04:35 PM, Dimitri Komatitsch wrote: > > Dear Sun Junping, > > Sure, they are free and open source, you can get them from > https://geodynamics.org/cig/software/specfem3d/ and > https://geodynamics.org/cig/software/specfem2d/ by typing the Git > command that we give on these pages. > > Best regards, > Dimitri. > > On 05/17/2017 10:59 AM, 孙军平 wrote: >> >> Dear Sir/Madam >> >> I am from the Institute of Acoustics, Chinese Academy of Sciences. I >> wish to use 'SPECFEM3D Cartesian' and 'SPECFEM2D' to compute sound field >> in ocean, but i can not download them from the CIG website. Are they >> free or not? I am looking forward to your reply. Thank you very much for >> your time. >> >> Sincerely, >> >> Sun Junping >> >> >> >> >> >> >> _______________________________________________ >> CIG-SEISMO mailing list >> CIG-SEISMO at geodynamics.org >> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo >> > -- Dimitri Komatitsch, CNRS Research Director (DR CNRS) Laboratory of Mechanics and Acoustics, Marseille, France http://komatitsch.free.fr From baagaard at usgs.gov Wed May 17 07:53:58 2017 From: baagaard at usgs.gov (Brad Aagaard) Date: Wed, 17 May 2017 07:53:58 -0700 Subject: [CIG-SEISMO] Sun Junping is right, the "current release" sections have vanished from the CIG Web site for some reason In-Reply-To: <47f8c03e-5ca5-f8f2-46c8-27f886e7b721@lma.cnrs-mrs.fr> References: <5f40ef.32dd2.15c15a224b9.Coremail.sunjunping@mail.ioa.ac.cn> <99dfe998-1b11-bf1b-1be2-b1af8816e65b@lma.cnrs-mrs.fr> <47f8c03e-5ca5-f8f2-46c8-27f886e7b721@lma.cnrs-mrs.fr> Message-ID: <5b677ffb-2dfa-8634-d9c7-f7f1cb04a952@usgs.gov> Items under "Current Release" show up there as a result of flags in the software release database that are part of the Admin Tools within the CIG website. There are check boxes for whether it is recent or active. For SPECFEM3D Cartesian, the most recent version listed is 2.0.2 (SPECFEM3D_Cartesian_V2.0.2.tar.gz) released on 2012-07-05 and the "active" flag is "no". My guess is that at some point it was set to "no" because it was so far behind the repository. I think CIG is willing to set the flags, etc to meet the developers wishes for what shows up as current and previous releases, so if you need changes, let them know (send email to cig-help at geodynamics.org). Regards, Brad On 05/17/2017 07:37 AM, Dimitri Komatitsch wrote: > > Hi all, > > Sun Junping is right, the "current release" sections have vanished from > the CIG Web site for some reason. See e.g. > https://geodynamics.org/cig/software/specfem3d/ and > https://geodynamics.org/cig/software/specfem2d/ , they are empty. > > Best regards, > Dimitri. > > On 05/17/2017 04:35 PM, Dimitri Komatitsch wrote: >> >> Dear Sun Junping, >> >> Sure, they are free and open source, you can get them from >> https://geodynamics.org/cig/software/specfem3d/ and >> https://geodynamics.org/cig/software/specfem2d/ by typing the Git >> command that we give on these pages. >> >> Best regards, >> Dimitri. >> >> On 05/17/2017 10:59 AM, 孙军平 wrote: >>> >>> Dear Sir/Madam >>> >>> I am from the Institute of Acoustics, Chinese Academy of Sciences. I >>> wish to use 'SPECFEM3D Cartesian' and 'SPECFEM2D' to compute sound field >>> in ocean, but i can not download them from the CIG website. Are they >>> free or not? I am looking forward to your reply. Thank you very much for >>> your time. >>> >>> Sincerely, >>> >>> Sun Junping >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> CIG-SEISMO mailing list >>> CIG-SEISMO at geodynamics.org >>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo >>> >> > From komatitsch at lma.cnrs-mrs.fr Wed May 17 08:34:43 2017 From: komatitsch at lma.cnrs-mrs.fr (Dimitri Komatitsch) Date: Wed, 17 May 2017 17:34:43 +0200 Subject: [CIG-SEISMO] Sun Junping is right, the "current release" sections have vanished from the CIG Web site for some reason In-Reply-To: <5b677ffb-2dfa-8634-d9c7-f7f1cb04a952@usgs.gov> References: <5f40ef.32dd2.15c15a224b9.Coremail.sunjunping@mail.ioa.ac.cn> <99dfe998-1b11-bf1b-1be2-b1af8816e65b@lma.cnrs-mrs.fr> <47f8c03e-5ca5-f8f2-46c8-27f886e7b721@lma.cnrs-mrs.fr> <5b677ffb-2dfa-8634-d9c7-f7f1cb04a952@usgs.gov> Message-ID: Hi Brad, Hi all, Thanks a lot. We should just remove the old version and put this instead: "To get the current version, just type: git clone --recursive https://github.com/geodynamics/specfem3d.git " (this is for SPECFEM3D_Cartesian, for 2D and 3D_globe it would be git clone --recursive https://github.com/geodynamics/specfem2d.git or git clone --recursive https://github.com/geodynamics/specfem3d_globe.git Could somebody do it? (I do not have the password to do it) Thanks, Best regards, Dimitri. On 05/17/2017 04:53 PM, Brad Aagaard wrote: > Items under "Current Release" show up there as a result of flags in the > software release database that are part of the Admin Tools within the > CIG website. There are check boxes for whether it is recent or active. > > For SPECFEM3D Cartesian, the most recent version listed is 2.0.2 > (SPECFEM3D_Cartesian_V2.0.2.tar.gz) released on 2012-07-05 and the > "active" flag is "no". My guess is that at some point it was set to "no" > because it was so far behind the repository. > > I think CIG is willing to set the flags, etc to meet the developers > wishes for what shows up as current and previous releases, so if you > need changes, let them know (send email to cig-help at geodynamics.org). > > Regards, > Brad > > > On 05/17/2017 07:37 AM, Dimitri Komatitsch wrote: >> >> Hi all, >> >> Sun Junping is right, the "current release" sections have vanished >> from the CIG Web site for some reason. See e.g. >> https://geodynamics.org/cig/software/specfem3d/ and >> https://geodynamics.org/cig/software/specfem2d/ , they are empty. >> >> Best regards, >> Dimitri. >> >> On 05/17/2017 04:35 PM, Dimitri Komatitsch wrote: >>> >>> Dear Sun Junping, >>> >>> Sure, they are free and open source, you can get them from >>> https://geodynamics.org/cig/software/specfem3d/ and >>> https://geodynamics.org/cig/software/specfem2d/ by typing the Git >>> command that we give on these pages. >>> >>> Best regards, >>> Dimitri. >>> >>> On 05/17/2017 10:59 AM, 孙军平 wrote: >>>> >>>> Dear Sir/Madam >>>> >>>> I am from the Institute of Acoustics, Chinese Academy of Sciences. I >>>> wish to use 'SPECFEM3D Cartesian' and 'SPECFEM2D' to compute sound >>>> field >>>> in ocean, but i can not download them from the CIG website. Are they >>>> free or not? I am looking forward to your reply. Thank you very much >>>> for >>>> your time. >>>> >>>> Sincerely, >>>> >>>> Sun Junping >>>> >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> CIG-SEISMO mailing list >>>> CIG-SEISMO at geodynamics.org >>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo >>>> >>> >> > > _______________________________________________ > CIG-SEISMO mailing list > CIG-SEISMO at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo -- Dimitri Komatitsch, CNRS Research Director (DR CNRS) Laboratory of Mechanics and Acoustics, Marseille, France http://komatitsch.free.fr From mzhao at cea-igp.ac.cn Fri May 19 02:26:16 2017 From: mzhao at cea-igp.ac.cn (=?gbk?B?1dTD9w==?=) Date: Fri, 19 May 2017 17:26:16 +0800 Subject: [CIG-SEISMO] A update of the mesh2vtu program under vtk7.1 Message-ID: <900376249938adeb2a4f5f06f451f6f9@cea-igp.ac.cn> Hi everyone, I found the current mesh2vtu program under the directory specfem3d/utils/Visualization/Paraview is outdated,so I made a few change to make it compile with VTK 7.1(the newest version).To use it,one need to: 1.download VTK 7.1 and install 2.set the correct VTK dir. Cheers Dr. Ming Zhao -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: mesh2vtu.tar Type: application/x-tar Size: 112640 bytes Desc: not available URL: From mzhao at cea-igp.ac.cn Fri May 19 02:28:30 2017 From: mzhao at cea-igp.ac.cn (=?gbk?B?1dTD9w==?=) Date: Fri, 19 May 2017 17:28:30 +0800 Subject: [CIG-SEISMO] A update of the mesh2vtu program under vtk7.1 Message-ID: <0752ff00d9c46f561f387e4b158fe761@cea-igp.ac.cn> Hi everyone, I found the current mesh2vtu program under the directory specfem3d/utils/Visualization/Paraview is outdated,so I made a few change to make it compile with VTK 7.1(the newest version).To use it,one need to: 1.download VTK 7.1 and install 2.set the correct VTK dir. Cheers Dr. Ming Zhao -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: mesh2vtu.tar Type: application/x-tar Size: 112640 bytes Desc: not available URL: From tuxiang2016 at outlook.com Tue May 30 00:15:34 2017 From: tuxiang2016 at outlook.com (tu xiang) Date: Tue, 30 May 2017 07:15:34 +0000 Subject: [CIG-SEISMO] Some problems Message-ID: Good afternoon I alse cannot download SPECFEM3D Cartesian from the CIG website. I have tried this command : git clone --recursive https://github.com/geodynamics/specfem3d.git The output of this command is : $ git clone --recursive https://github.com/geodynamics/specfem3d.git Initialized empty Git repository in /home/specfem3d/.git/ remote: Counting objects: 38298, done. remote: Compressing objects: 100% (25/25), done. remote: Total 38298 (delta 12), reused 23 (delta 11), pack-reused 38261 Receiving objects: 100% (38298/38298), 372.06 MiB | 2.38 MiB/s, done. Resolving deltas: 100% (29156/29156), done. Submodule 'm4' (https://github.com/geodynamics/autoconf_cig.git) registered for path 'm4' Submodule 'utils/ADJOINT_TOMOGRAPHY_TOOLS/flexwin' (https://github.com/geodynamics/flexwin.git) registered for path 'utils/ADJOINT_TOMOGRAPHY_TOOLS/flexwin' Initialized empty Git repository in /home/specfem3d/m4/.git/ remote: Counting objects: 403, done. remote: Total 403 (delta 0), reused 0 (delta 0), pack-reused 403 Receiving objects: 100% (403/403), 127.11 KiB | 201 KiB/s, done. Resolving deltas: 100% (224/224), done. Submodule path 'm4': checked out '9912ff1c7f7e66577d849160c4169c0c3be4806f' Initialized empty Git repository in /home/specfem3d/utils/ADJOINT_TOMOGRAPHY_TOOLS/flexwin/.git/ remote: Counting objects: 830, done. remote: Total 830 (delta 0), reused 0 (delta 0), pack-reused 830 Receiving objects: 100% (830/830), 2.40 MiB | 577 KiB/s, done. Resolving deltas: 100% (517/517), done. Submodule path 'utils/ADJOINT_TOMOGRAPHY_TOOLS/flexwin': checked out 'fde3e0993c1853d98bd564e0cf13d796afe16cbe' I don't know why, and I tried many times on different computers. Then I download one version of SPECFEM3D Cartesian from github I do not have ifort compiler on my computer, so I want to compile the software with gfortran. I installed gfortran and openmpi. Then, I run next command: ./configure FC=gfortran MPIFC=mpif90 Next, I run: $ make xcheck_mesh_quality_CUBIT_Abaqus output: make: *** No rule to make target `xcheck_mesh_quality_CUBIT_Abaqus'. Stop. But the command: make xdecompose_mesh and make xgenerate_databases can run successfully. However, the command: make xspecfem3D cannot, the errors are: ATTENUATION,deltat,PML_CONDITIONS, & 1 Warning: Unused dummy argument 'pml_conditions' at (1) make: *** [obj/compute_forces_viscoelastic.spec.o] Error 1 I do not know how to deal with these problems. Hope someone give me a hand. Best regards Yours sincerely, Tu Xiang -------------- next part -------------- An HTML attachment was scrubbed... URL: