From istoneuw at gmail.com Thu Aug 9 15:41:28 2018 From: istoneuw at gmail.com (Ian Stone) Date: Thu, 9 Aug 2018 15:41:28 -0700 Subject: [CIG-SEISMO] Reflections off of C-PML Boundaries in Specfem3D Cartesian Message-ID: Hello, I am attempting to simulate an earthquake using Specfem3D, but keep running into issues with reflections off the absorbing boundaries, even with C-PML layers along the edges. I was wondering if anyone else had experienced a similar problem and had recommendations on how to fix it. Some information about my simulation: - The x/y/z dimensions of my model area are 15X12X9.9km, respectively. The mesh has 2 triplication layers, transitioning from 300m to 100m, and from 100m to 33.3m near the surface. To accommodate the PML layers, I simply extruded the mesh 2400m in each direction (except for the free surface); so on each side, there are 8, 300m-thick PML layers. - I use a CMTSOLUTION for a M4 thrust earthquake as a source. In the Par_file, I set f0_FOR_PML=1.0Hz, as this seems to be the frequency range with the most energy. - The reflections off the absorbing boundaries are most prominent with the longer period S-waves, though other waves and periods do produce some smaller reflections as well. Reflections are generated regardless of where the source is located in the model. - I have checked to make sure all the min/max absorbing boundary files correspond to the actual outer surface of the model, and not the PML/non-PML boundary. Everything looks ok. I have attached a few screenshots of my model setup. The first is a small-scale version of my large mesh, showing 4 extruded layers on each of the bounding surfaces. The last 3 images show the cpml damping profile in the x, y, and z directions, respectively; these were generated using the .vtk files output during the simulation. Thank you, Ian Stone -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: small_mesh_pml.png Type: image/png Size: 120810 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: cpml_damping_x.png Type: image/png Size: 214340 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: cpml_damping_y.png Type: image/png Size: 235473 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: cpml_damping_z.png Type: image/png Size: 234536 bytes Desc: not available URL: From cristini at lma.cnrs-mrs.fr Fri Aug 17 14:18:55 2018 From: cristini at lma.cnrs-mrs.fr (cristini paul) Date: Fri, 17 Aug 2018 23:18:55 +0200 Subject: [CIG-SEISMO] Model error in mesh In-Reply-To: References: Message-ID: Dear Ed, Please could you provide more information on the type of error you are getting. If it is connected to the quality of the mesh (too distorted) then depending on the geometry, it is sometimes difficult to get a good mesh with Gmsh without dividing the geometry into several elementary parts. Let me also remind you that you need to define your line loops in a counter clockwise manner as it is done in the Gmsh example provided with Sepcfem2D otherwise you will get negative jacobians. Thank you Best regards Paul Le 17/07/2018 à 00:20, ed cas a écrit : > Dear developers and users, > > > I have been trying to produce a readable mesh file > for specfem2d by using gmsh. > > I produced the mesh inside gmsh, I saved the mesh and then paste it to > the MESH directory > > and then run the command > > python LibGmsh2Specfem_convert_Gmsh_to_Specfem2D_official.py > model_shallow_v42 -t A -b A -r A -l A > That produced the five files in the same directory. > > Please find attached the file I have been trying to run > (model_shallow_v42). > > However, when running specfem2d gives error telling me about Jacobians, > I have been trying for a couple of days and cannot get with the error, > I checked the > line loops and seems  fine , I have resized the elements and with no > success. > > I was hoping you could help me with this. > Could you please check my file and indicate me what is wrong with it, > and any solution. > > I would really appreciate your help, > > Thank you for your time and help, > > Sincerely, > > ------------------------------------------- > Edwin Castillo > > > > _______________________________________________ > CIG-SEISMO mailing list > CIG-SEISMO at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo -- *--------------------------------------------------------------------------* Paul CRISTINI Charge de Recherche CNRS (HDR) / CNRS Research Scientist *--------------------------------------------------------------------------* CNRS - Laboratoire de Mecanique et d'Acoustique (UMR 7031) Bureau 119 4 Impasse Nikola Tesla, CS 40006, F-13453 Marseille Cedex 13 - France mailto: cristini at lma.cnrs-mrs.fr phone number: +33 (0)4 84 52 42 51 http://www.lma.cnrs-mrs.fr/ *--------------------------------------------------------------------------* -------------- next part -------------- An HTML attachment was scrubbed... URL: From komatitsch at lma.cnrs-mrs.fr Mon Aug 20 09:46:20 2018 From: komatitsch at lma.cnrs-mrs.fr (Dimitri Komatitsch) Date: Mon, 20 Aug 2018 18:46:20 +0200 Subject: [CIG-SEISMO] Model error in mesh In-Reply-To: References: Message-ID: Dear Ed, dear all, If your Jacobians are all negative, your mesh is likely good, it is just that you export the points in reverse order (clockwise instead of counterclockwise). What is not good is positive and negative in the same mesh; all positive or all negative is OK. (in the latter case, you need to flip them once and for all before importing the mesh in SPECFEM) Best wishes, Dimitri. On 08/17/2018 11:18 PM, cristini paul wrote: > Dear Ed, > > Please could you provide more information on the type of error you are > getting. > > If it is connected to the quality of the mesh (too distorted) then > depending on the geometry, it is sometimes difficult to get a good mesh > with Gmsh without dividing the geometry into several elementary parts. > > Let me also remind you that you need to define your line loops in a > counter clockwise manner as it is done in the Gmsh example provided with > Sepcfem2D otherwise you will get negative jacobians. > > Thank you > > Best regards > > Paul > > > > Le 17/07/2018 à 00:20, ed cas a écrit : >> Dear developers and users, >> >> >> I have been trying to produce a readable mesh file >> for specfem2d by using gmsh. >> >> I produced the mesh inside gmsh, I saved the mesh and then paste it to >> the MESH directory >> >> and then run the command >> >> python LibGmsh2Specfem_convert_Gmsh_to_Specfem2D_official.py >> model_shallow_v42 -t A -b A -r A -l A >> That produced the five files in the same directory. >> >> Please find attached the file I have been trying to run >> (model_shallow_v42). >> >> However, when running specfem2d gives error telling me about Jacobians, >> I have been trying for a couple of days and cannot get with the error, >> I checked the >> line loops and seems  fine , I have resized the elements and with no >> success. >> >> I was hoping you could help me with this. >> Could you please check my file and indicate me what is wrong with it, >> and any solution. >> >> I would really appreciate your help, >> >> Thank you for your time and help, >> >> Sincerely, >> >> ------------------------------------------- >> Edwin Castillo >> >> >> >> _______________________________________________ >> CIG-SEISMO mailing list >> CIG-SEISMO at geodynamics.org >> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo > > -- > *--------------------------------------------------------------------------* > Paul CRISTINI Charge de Recherche CNRS (HDR) / CNRS Research Scientist > *--------------------------------------------------------------------------* > CNRS - Laboratoire de Mecanique et d'Acoustique (UMR 7031) > Bureau 119 > 4 Impasse Nikola Tesla, CS 40006, F-13453 Marseille Cedex 13 - France > mailto:cristini at lma.cnrs-mrs.fr > phone number: +33 (0)4 84 52 42 51 > http://www.lma.cnrs-mrs.fr/ > *--------------------------------------------------------------------------* > > > > _______________________________________________ > 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 yang.zhao at mq.edu.au Wed Aug 22 05:43:11 2018 From: yang.zhao at mq.edu.au (Yang Zhao) Date: Wed, 22 Aug 2018 12:43:11 +0000 Subject: [CIG-SEISMO] Compilation Problem with the SPECFEM3D, asking for your help Message-ID: Dear Sir or Madam, I am currently a visiting scholar at the Department of Earth and Planetary Sciences, Macquarie University, collaborating with the seismology group. I am working on the ambient noise adjoint tomography based on SPECFEM3D_Cartesian. Recently i've downloaded the SPECFEM3D program from your website. But some problems came to me when I was trying to compile this program. After the configuration, when i input the command "make", it shows this error: "ld: cannot find -lpciaccess" and the compilation failed. A screenshot of this error is attached for your reference. Could you please help me to figure out how to solve this problem and how to make it successfully? I am looking forward to your reply. Best Regards, Yang Zhao Department of Earth and Planetary Sciences, Macquarie University, RM 121, 12 Wally's walk, North Ryde, NSW, 2109 Australia email: yang.zhao at mq.edu.au -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: WeChat Image_20180822203941.jpg Type: image/jpeg Size: 10229 bytes Desc: WeChat Image_20180822203941.jpg URL: From komatitsch at lma.cnrs-mrs.fr Wed Aug 22 16:48:03 2018 From: komatitsch at lma.cnrs-mrs.fr (Dimitri Komatitsch) Date: Thu, 23 Aug 2018 01:48:03 +0200 Subject: [CIG-SEISMO] Compilation Problem with the SPECFEM3D, asking for your help In-Reply-To: References: Message-ID: Dear Yang, This is unrelated to SPECFEM, it is a Linux package that is missing on your machine. If you have Ubuntu or similar, you can type this: sudo apt-get install libpciaccess-dev libpciaccess0 Best regards, Dimitri. On 08/22/2018 02:43 PM, Yang Zhao wrote: > Dear Sir or Madam, > > I am currently a visiting scholar at the Department of Earth and > Planetary Sciences, Macquarie University, collaborating with the > seismology group. > > I am working on the ambient noise adjoint tomography based on > SPECFEM3D_Cartesian. > Recently i've downloaded the SPECFEM3D program from your website. > > But some problems came to me when I was trying to compile this program. > After the configuration, when i input the command "make",  it shows this > error: "ld: cannot find -lpciaccess" and the compilation failed. > A screenshot of this error is attached for your reference. > > Could you please help me to figure out how to solve this problem and how > to make it successfully? > I am looking forward to your reply. > > > Best Regards, > > Yang Zhao > > Department of Earth and Planetary Sciences, > > Macquarie University, RM 121, 12 Wally's walk, North Ryde, NSW, 2109 > Australia > > email: yang.zhao at mq.edu.au > > > > _______________________________________________ > 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 sysun at vt.edu Tue Aug 28 11:13:49 2018 From: sysun at vt.edu (Shuyang Sun) Date: Tue, 28 Aug 2018 14:13:49 -0400 Subject: [CIG-SEISMO] problem about Spheroidal mode calculation Message-ID: Hi, How are you? I am Booker from Virginia Tech. I used your mineos to calculate the eigenfunction but encountered one problem. I would like to calculate the Spheroidal modes with program minos_bran. But this program would get stuck when the parameter wmax was set at a higher frequency (like >80mHZ). Could you help give a hint about how to fix this problem? I really appreciate it. Thanks. Kind regards Booker -------------- next part -------------- An HTML attachment was scrubbed... URL: From jattanayake at yahoo.com Tue Aug 28 20:10:38 2018 From: jattanayake at yahoo.com (Januka Attanayake) Date: Wed, 29 Aug 2018 03:10:38 +0000 (UTC) Subject: [CIG-SEISMO] problem about Spheroidal mode calculation In-Reply-To: References: Message-ID: <1069286222.62880.1535512238544@mail.yahoo.com> Are you sure it's stuck? What nmax do you use? Increasing nmax exponentially increases your computing time. Also, effectively wmax ≤ 166. Januka Attanayake Research Fellow | Earthquake Seismology Homepage: http://sites.google.com/site/janukaattanayake School of Earth Sciences | McCoy Bldg. 200 University of Melbourne | Parkville 3010 VIC Australia On Wednesday, August 29, 2018, 4:47:06 AM GMT+10, Shuyang Sun wrote: Hi, How are you? I am Booker from Virginia Tech. I used your mineos to calculate the eigenfunction but encountered one problem. I would like to calculate the Spheroidal modes with program minos_bran. But this program would get stuck when the parameter wmax was set at a higher frequency (like >80mHZ). Could you help give a hint about how to fix this problem? I really appreciate it. Thanks. Kind regards Booker _______________________________________________ CIG-SEISMO mailing list CIG-SEISMO at geodynamics.org http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo -------------- next part -------------- An HTML attachment was scrubbed... URL: From bruckued at gmail.com Fri Aug 31 09:47:34 2018 From: bruckued at gmail.com (kued bruc) Date: Fri, 31 Aug 2018 12:47:34 -0400 Subject: [CIG-SEISMO] Viewing Specfem3D Globe Mesh Message-ID: Greetings, I am interested in viewing the SPECFEM3DGlobe Mesh created for the simulations I run, and in particular, extracting the dvs values in a form that will easily let me open it in other programs. Section 10.1 of the manual tells us to use the command xcombine_AVS_DX to view the mesh When run, this only appears to have options to generate a mesh of the model surface, or along chunk edges or slices. When I view the AVS output in Paraview or when I read it into other programs, it seems that none of these options appear to generate a file that contains information about *every* cell in the mesh, such as that needed to make Figure 5.1 in the SPECFEM3DGLOBE manual. Could you point me in the right direction here? I'd like to be able to extract information about the velocity of every cell in the final mesh. Sorry if I've missed something obvious here. Thank you for your help. Regards, -------------- next part -------------- An HTML attachment was scrubbed... URL: