available online - Computational Infrastructure for Geodynamics
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1. 19 56 57 58 59 60 61 62 errrrere 2 3 7 3 24 4 51 8379 0 0 159 5407 0 0 0 0 0 0 594 38 39 40 41 42 43 44 45 46 erererrrrrrre 3 2 7 Material list file matfile This file contains material properties of each material regions Material properties must be listed in a sequential order of the unique material IDs In addition this data file optionally contains the information on the water condition of material regions Material regions or material IDs must be consistent with the Material IDs Element IDs defined in idfile The matfile has the following format comment line number of material regions unique material IDs materialID domainID y E v 0 c Y materialID domainID y E v P c Y materialID domainID y E v 0 c Y number of submerged material regions submerged materiall D submerged materiall D The materilID must be in a sequential order starting from 1 The doaminID represents 20 the material domain e g isotropic or anisotropic and it is currently irrelevant there fore always use 1 Similarly y represents the unit weight in kN m E the Young s modulus of elasticity in kN m the angle of internal friction in degrees c the cohesion in kN m and y the angle of dilation in degrees Example The following data defines four material regions No region is submerged in water material properties id domain gamma ym nu phi coh psi 1 18 8 1e5 1 19 0 1e5 1 18 1 1e52. converted to the input files required by SPECFEM3D GEOTECH Output data can be visualized and processed using the open source visualization application ParaView www paraview org 1 2 Status summary Slope stability analysis Yes Multistage excavation Yes Gravity loading Yes Surface loading Yes point load uniformly distributed load linearly distributed load Experimental Water table Yes Experimental Pseudo static earthquake loading Yes Experimental Automatic factor of safety No Revisions HNG Jan 12 2012 HNG Sep 08 2011 HNG Jul 12 2011 HNG May 20 2011 HNG Jan 17 2011 Chapter 2 Getting started 2 1 Package structure The original SPECFEM3D_GEOTECH package comes in a single compressed file SPECFEM3D_GEOTECH tar gz which can be extracted using tar command tar zxvf SPECFEM3D_GEOTECH tar gz or using for example 7 zip www 7 zip org under WINDOWS The package has the following structure SPECFEM3D_GEOTECH COPYING License README brief description of the package CMakeLists txt CMake configuration file bin all object files and executables are stored in this folder doc documentation files for the SPECFEM3D_GEOTECH package If built this file is created input contains input files partition contains partition files for parallel processing output default output folder All output files are stored in this folder unless the different output path is de
3. 0 porep pore water pressure integer optional 0 No 1 Yes default 0 11 3 1 3 Examples of main input file Input file for a simple elastic simulation 12 Serial input file for slope stability 13 Parallel input file for slope stability 14 Serial input file for excavation 15 Parallel input file for excavation input file excavation_3d psem pre information preinfo nproc 8 ngllx 3 nglly 3 ngllz 3 nenod 8 ngnod 8 inp_path input out_path output mesh information mesh xfile excavation_3d_coord_x yfile excavation_3d_coord_y amp zfile excavation 3d coord z confile excavation_3d_connectivity idfile excavation 3d material id gfile excavation Sd ghost boundary conditions bc uxfile excavation 3d ssbcux uyfile excavation_3d_ssbcuy amp uzfile excavation 3d ssbcuz initial stress stress0 type 0 z0 0 s0 0 k0 0 5 usek0 1 material list material matfile excavation_3d_material_list control parameters control cg_tol 1e 8 cg_maxiter 5000 nl tol 0 0005 nl_maxiter 3000 amp nexcav 3 excavid 2 3 4 ninc 10 There are only two additional pieces of information i e number of processors nproc in line preinfo and file name for ghost partition interfaces gfile in line mesh in parallel input file 3 2 Input files detail All local element face edge node numbering follows the EXODUS II convention 3 2 1 Coordinates fil
4. and solid mechanics Computer Methods in Applied Mechanics and Engineering 36 2 241 254 King R B and V Sonnad 1987 Implementation of an element by element solution al gorithm for the finite element method on a coarse grained parallel computer Computer Methods in Applied Mechanics and Engineering 65 1 47 59 Komatitsch D and J Tromp 1999 Introduction to the spectral element method for three dimensional seismic wave propagation Geophysical Journal International 139 806 822 26 Komatitsch D and J P Vilotte 1998 The spectral element method An efficient tool to simulate the seismic response of 2D and 3D geological structures Bulletin of the Seismological Society of America 88 2 368 392 Larsen S and C A Schultz 1995 ELAS3D 2D 3D elastic finite difference wave propagation code Technical Report No UCRL MA 121792 Technical report Law K H 1986 A parallel finite element solution method Computers amp Struc tures 23 6 845 858 Pacheco P 1997 Parallel Programming with MPI Morgan Kaufmann Patera A T 1984 A spectral element method for fluid dynamics laminar flow in a channel expansion Journal of Computational Physics 54 468 488 Pellegrini F and J Roman 1996 SCOTCH A software package for static mapping by dual recursive bipartitioning of process and architecture graphs Lecture Notes in Computer Science 1067 493 498 Peter D D Komatitsch Y Luo R Martin N Le G
5. displacement boundary conditions along y axis string file name of displacement boundary conditions along z axis string file name of traction specification string type of initial stress integer optional 0 compute using SEM itself 1 compute using simple vertical lithostatic relation default 0 datum free surface coordinate real m Only required if type 1 datum free surface vertical stress real kN m Only required if type 1 lateral earth pressure coefficient real file name of material list string flag to indicate whether the material file is partitioned integer optional 0 No 1 Yes default 1 Only required for parallel processing path to material file string optional default gt input for serial or unpartitioned material file in parallel and partition for partitioned material file in parallel assume all entire domain as elastic integer optional 0 No 1 Yes default gt 0 pseudo static earthquake loading coefficient along x axis real 0 lt eqkx lt 1 0 default gt 0 0 pseudo static earthquake loading coefficient along y axis real 0 lt eqky lt 1 0 default gt 0 0 10 egkz pseudo static earthquake loading coefficient along z axis real 0 lt eqkz lt 1 0 default gt 0 0 Note For the stability analysis purpose these coefficients should be cho sen carefully For example if the slope face is po
6. follows the format in put file name header case for serial run and input file name header procprocessor ID case for parallel run 23 4 1 6 SOS file This is an EnSight Gold server of server file for parallel visualization The write_sos f90 program provided in the utilities may be used to generate this file See Chapter 5 Section 5 2 for more detail All above EnSight Gold files correspond to the model with spectral element mesh Ad ditionally the CASE file s and mesh file s are written for the original model These file names follow the similar conventions and they have the tag original in the file name headers 4 2 Visualization 4 2 1 Serial visualization Requirement ParaView version later than 3 7 Precompiled binaries available from Par aView web www paraview org may be installed directly or it can be build from the source e open a session e open paraview client paraview e In ParaView client File gt Open select appropriate serial CASE file case file see ParaView wiki paraview org Wiki ParaView for more detail 4 2 2 Parallel visualization Requirement ParaView version later than 3 7 It should be built enabling MPI An appropriate MPI library is necessary e open a session e open paraview client paraview e start ParaView server mpirun np 8 pvserver display 0 e In ParaView client File gt Connect and connect to the appropriate server e In ParaView client gt Open select appropri
7. was funded in part by the Research Council of Norway and supported by in dustry partners BP Statoil and Total Some of the routines were imported and modified from the Programming the finite element method Smith and Griffiths 2004 and the original SPECFEM3D package e g Komatitsch and Vilotte 1998 Komatitsch and Tromp 1999 Peter et al 2011 Contents Licensing Acknowledgments 1 Introduction LI ACES TO Und de one ul eke yo et ake te Hols a Brees Se abe oe ae ed Status at fe at Bae Re knee eR me He oR me Be le HR 2 Getting started 221 P ck g struct te sane we eae Boe ED Be at Ee a RS 2 2 a rene UISIOS E Gin Pos GE a A eR ae See ee ee Si ha 23s C nfic re so dc e ee ee Re RAR AA BD Cat ed Back i 2A ONIN Ue a A sis A AAA AS AS a 2o A e td o e Ave Se e O de a 3 Input 3 1 Main input A E ES EA Maks tA oes UN WMO yes tee n o pat leao a ped Ee E eee ee Re e ee eo 3 1 2 Arguments add A eR oe oe Ne oe Rd 3 1 3 Examples of main input file 0 3 2 input Hes detail o salas dak eos tye Se as Bek ee eo Ce e 3 2 1 Coordinates files xfile yfile zfile 3 2 2 Connectivity file confile do mei DM cde dios Logado 3 2 3 Element IDs or Material IDs file idfile 3 2 4 Ghost partition interfaces file gfile 3 2 5 Displacement boundary conditions files uxfile uyfile uzfile 3 20 Traction files TELLO q ei DEE a O DH AR a 3 2 7
8. write sos program writes a EnSight SOS file necessary for the parallel visualization see also Chapter 5 ENABLE MPI If ON the main parallel program psemgeotech is built otherwise main serial program semgeotech is built The default is OFF SCOTCH_LIBRARY_PATH This is required if BUILD_PARTMESH is ON If not found automatically it can be set manually CMAKE_Fortran_COMPILER This defines the Fortran compiler If not found au tomatically or the automatically found compiler is not correct it can be set manually Note 1 If CMAKE_Fortran_COMPILER has to be changed first change this and configure and then change other variables if necessary and configure Note 2 Even if some of the above variables are set ON if appropriate working compilers are not found corresponding variables are internally set OFF with WARNING messages 2 4 Compile Once configuration and generation are successful the necessary build files are created Now to build the main program type make On multi processor systems let s say eight processors type make j 8 To clean type make clean Note If reconfiguration is necessary it 1s better to delete all Cache files of the build directory 2 5 Run Serial run To run the serial program type bin semgeotech input file name Example bin semgeotech input validation1 sem Parallel run To partition the mesh type bin partmesh input_file_ name Example bin partmesh i
9. 1 18 5 1e5 PUNE The following data defines four material regions with two of them submerged material properties id domain gamma ym nu phi coh psi 4 1 1 18 8 1e5 0 3 20 0 0 0 0 0 2 1 19 0 1e5 0 3 20 0 27 0 0 0 3 1 18 1 1e5 0 3 20 0 0 0 0 0 4 1 18 5 1e5 0 3 20 0 29 0 0 0 2 1 3 3 2 8 Water surface file wsfile This file contains the water table information on the model in the format as number of water surfaces water surface type integer O horizontal surface 1 inclined surface 2 meshed surface if wstype 0 can be reconstructed by sweeping a horizontal line relevant axis z La 2 if wstype 1 can be reconstructed by sweeping a inclined line relevant axis La 21 22 if wstype 2 meshed surface attached to the model number of faces elelemetID facelD elelemetID facelD elelemetID facelD 21 The relevant axis denotes the axis along which the line is defined and it is taken as 1 x axis 2 y axis and 3 z axis The variables z and x2 denote the coordinates only relevant axis of point 1 and 2 that define the line Similarly z denotes a z coordinate of a horizontal water surface and z and z denote the z coordinates of the two points that define the line on the water surface Example Following data specify the two water surfaces a horizontal surface and an inclined surface 2 0 1 42 7 50 0 6 1 1 1 0 0 42 7 12 2 6 1 22 Chapter 4 Output and Visualization 4 1 Ou
10. Material list file matfile 3 2 8 Water surface file wsfile su grs pg pia E a a4 bs 4 Output and Visualization E Output DAS a d de EA ah has ag re day ae Saad ah ae Beal he ATL Summary MeS ta Se ol ae the BA Se Rs eRe eee Sd 4 1 2 Mesh files op tras nr oy Ore any oe ae eek eG ae ae ee 4 1 3 Displacement field fle o 0 o 4 1 4 Pore pressure file xs Sey o a ee RR oe Ro PR Rw Ae MOSER EOS ss go eS ihe do si ite th ih the sit dl Mtge MR R dh GAR So DA dd GAS cel OE 416 coy ard le E Ma do E Boao ae oF COR ah A are CS ee ese 42 AAA BIO erri A Kone Gee te Sra da a PORE Se do ee E eS ili li NE a NDR WWW 4 2 1 Serial visualization 0 0 0 0 0 0 00000 08 2G 4 2 2 Parallel visualization 0 00008 88 5 Utilities 5 1 Convert EXODUS mesh into SEM files 5 2 Generate SOS file iv Chapter 1 Introduction 1 1 Background SPECFEM3D_GEOTECH is a free and open source command driven software for 3D slope stability analysis for more details see Gharti et al 2012 and simulation of 3D multistage excavation for more details see Gharti et al 2012 based on the spectral element method e g Patera 1984 Canuto et al 1988 Seriani 1994 Faccioli et al 1997 Komatitsch and Vilotte 1998 Komatitsch and Tromp 1999 Peter et al 2011 The slope stability and the excavation routines were originally started from the routines found in the
11. User Manual Version 1 1 Beta 0 0 0030 0 0040 0 0020 Hom Nath Gharti tri Komatitsch imi D Volker Oye Roland Martin Jeroen Tromp LECT ESTUDEI ALTA LO LLL Lag ada 0 0010 Multistage excavation Displacement magnitude m Es le T Q as E O as O OLAS RELE RR Peta eet eee PERILS RRA PERO EA rte PRP RR a Cofee too aaa vee oe EY NE a en gt aa L O aa A N Slope stability SPECFEM3D GEOTECH 1 1 Beta User Manual Hom Nath Gharti Princeton University USA Dimitri Komatitsch Aix Marseille University France Volker Oye NORSAR Norway Roland Martin University of Toulouse France Jeroen Tromp Princeton University USA April 23 2012 Previously at NORSAR Norway Licensing SPECFEM3D_GEOTECH 1 1 Beta is free software you can redistribute it and or mod ify it under the terms of the GNU General Public License as published by the Free Soft ware Foundation either version 3 of the License or at your option any later version SPECFEM3D_GEOTECH 1 1 Beta is distributed in the hope that it will be useful but WITHOUT ANY WARRANTY without even the implied warranty of MERCHANTABIL ITY or FITNESS FOR A PARTICULAR PURPOSE See the GNU General Public Li cense for more details You should have received a copy of the GNU General Public License along with SPECFEM3D_GEOTECH 1 1 Beta If not see lt http www gnu org licenses gt Acknowledgments This work
12. Y Hussaini A Quarteroni and T A Zang 1988 Spectral methods in fluid dynamics Springer CUBIT 2011 CUBIT 13 0 User Documentation Sandia National Laboratories Online accessed 27 May 2011 EnSight 2008 EnSight User Manual Version 9 0 ed Salem Street Suite 101 Apex NC 27523 USA Computational Engineering International Inc Online accessed 11 July 2011 Faccioli E F Maggio R Paolucci and A Quarteroni 1997 2D and 3D elastic wave propagation by a pseudo spectral domain decomposition method Journal of Seismology 1 237 251 Geuzaine C and J F Remacle 2009 Gmsh a three dimensional finite element mesh generator with built in pre and post processing facilities International Journal for Numerical Methods in Engineering 79 11 1309 1331 Gharti H N D Komatitsch V Oye R Martin and J Tromp 2012 Application of an elastoplastic spectral element method to 3D slope stability analysis International Journal for Numerical Methods in Engineering in press Gharti H N V Oye D Komatitsch and J Tromp 2012 Simulation of multistage excavation based on a 3d spectral element method Computers amp Structures 100 101 54 69 Gropp W E Lusk and A Skjellum 1994 Using MPI portable parallel programming with the Message Passing Interface Cambridge USA MIT Press Hughes T J R I Levit and J Winget 1983 An element by element solution algo rithm for problems of structural
13. al argg valo OF 9n val Example preinfo nproc 8 ngllx 3 nglly 3 ngllz 3 nenod 8 ngnod 8 amp inp_path input part_path partition out_path output All legitimate input lines should be written in lower case Line type and argument value pairs must be separated by a space Each argument value pair must be separated by a comma and a space s No space s are recommended before line type and in between argument name and or and argument value If argument value is a string the FORTRAN 90 string i e enclosed within single quotes should be used for example inp_path input If the argument value is a vector i e multi valued a list of values separated by space no comma shoud be used e g srf 1 0 1 2 1 3 1 4 3 1 1 Line types Only the following line types are permitted preinfo preliminary information of the simulation mesh mesh information be traction stress0 material eqload water control save boundary conditions information traction information optional initial stress information optional It is generally necessary for multistage excavation material properties pseudo static earthquake loading optional water table information optional control of the simulation options to save data 3 1 2 Arguments Only the following arguments under the specified line types are permitted preinfo nproc ngllx nglly ngllz inp_path pa
14. ate SOS file sos file see ParaView wiki paraview org Wiki ParaView for more detail Note Each CASE file obtained from the parallel processing can also be visualized in a serial 24 Chapter 5 Utilities 5 1 Convert EXODUS mesh into SEM files The program exodus2sem c contained in the utilities directory can be used to convert the mesh file in EXODUS II format to input files required by the SPECFEM3D_GEOTECH Compile gcc o exodus2sem exodus2sem c Run exodus2sem EXODUS mesh file OPTIONS For more details see utilities README exodus2sem It can also be compiled au tomatically during the build process of main package SPECFEM3D GEOTECH see Section 2 3 5 2 Generate SOS file The program write sos f90 contained in the utilities directory can be used to write EnSight Gold server of server file sos file see EnSight 2008 to visualize the multi processors data in parallel This file does not contain the actual data but only information on the data location and parallel processing Compile gfortran o write sos write sos f90 Run exodus2sem input file For more details see utilities README write sos It can also be compiled auto matically during the build process of main package SPECFEM3D_GEOTECH see Sec tion 2 3 25 Bibliography Barragy E and G F Carey 1988 A parallel element by element solution scheme International Journal for Numerical Methods in Engineering 26 2367 2382 Canuto C M
15. book Programming the finite element method Smith and Griffiths 2004 The software can run on a single processor as well as multi core machines or large clusters It is written mainly in FORTRAN 90 and parallelized using MPI Gropp et al 1994 Pacheco 1997 based on domain decomposition For the domain decomposition the open source graph partitioning library SCOTCH Pellegrini and Roman 1996 is used The element by element preconditioned conjugate gradient method e g Hughes et al 1983 Law 1986 King and Sonnad 1987 Barragy and Carey 1988 is implemented to solve the linear equations For elastoplastic failure a Mohr coulomb failure criterion is used with a viscoplastic strain method Zienkiewicz and Cormeau 1974 This program does not automatically determine the factor of safety of slope stability Simulations can be performed for a series of safety factors After plotting the safety factor verses maximum displacement curve one can determine the factor of safety of the given slope Although the software is optimized for slope stability analysis and multistage excavation other relevant simulations of quasistatic problems in solid geo mechanics can also be performed with this software The software currently does not include an inbuilt mesher Existing tools such as Gmsh Geuzaine and Remacle 2009 CUBIT CUBIT 2011 TrueGrid Rainsberger 2006 etc can be used for hexahedral meshing and the resulting mesh file can be
16. cement boundary conditions files uxfile uyfile uzfile This file contains information on the displacement boundary conditions currently only the zero displacement is implemented and has the following format number of element faces elementID facelD elementID facelD elementID facelD 18 Example 849 O ON DOW N Rhin 3 2 6 Traction file trfile This file contains the traction information on the model in the following format traction type integer 0 point 1 uniformly distributed 2 linearly distributed if traction type 0 de qy qz load vector in kN if traction type 1 de dy qz load vector in kN m if traction type 2 relevant axis 21 2 Qui Wi Ga qz2 Qy2 Q22 number of entities points for point load or faces for distributed load elementID entitylD elementID entitylD elementID entitylD This can be repeated as many times as there are tractions The relevant axis denotes the axis along which the load is varying and is represented by an integer as 1 x axis 2 y axis and 3 z axis The variables x and x2 denote the coordinates only the relevant axis of two points between which the linearly distributed load is applied Similarly q 1 dy and Q 1 and q 2 qy2 and q denote the load vectors in kN m at the point 1 and 2 respectively Example The following data specify the two tractions a uniformly distributed traction and a lin early distributed traction 1 0 0 0 0 167 751 363
17. es xfile yfile zfile Each of the coordinates files contains a list of corresponding coordinates in the following format number of points coordinate of point 1 coordinate of point 2 coordinate of point 3 16 Example 2354 40 230394465164999 40 759090909090901 42 700000000000003 40 957142857142898 40 230394465164999 40 759090909090901 42 700000000000003 40 957142857142898 3 2 2 Connectivity file confile The connectivity file contains the connectivity lists of elements in the following format number of elements Ny Na N3 N4 Ng Ne Ny Ng Of element 1 n N2 Ng N4 Ns Ne Ny Ng Of element 2 n N2 Ng N4 Ng Ne Ny Ng Of element 3 n Na Ng N4 Ns Ne Ny Ng Of element 4 Example 1800 123456768 91021111265 914131158 14 15 16 10 9 17 18 12 11 15 9 13 19 17 11 14 20 21 22 16 15 23 24 18 17 21 15 19 25 23 17 20 26 27 28 22 21 29 30 24 23 27 21 25 31 29 23 26 32 33 34 28 27 35 36 30 29 33 27 31 37 35 29 32 38 34 33 39 40 36 35 41 42 33 37 43 39 35 38 44 41 17 3 2 3 Element IDs or Material IDs file idfile This file contains the IDs of elements This ID will be used in the program mainly to identify the material regions This file has the following format number of elements ID of element 1 ID of element 2 ID of element 3 ID of element 4 Example 1800 BPRPRPRPPrRPP RPP BE 3 2 4 Ghost partition interfaces file gfile This file will be generated automatically by a program partmesh 3 2 5 Displa
18. fined in the main input file src contains all source files 2 2 Prerequisites CMake build system The CMake version gt 2 8 4 is necessary to configure the software It is free and open source and can be downloaded from www cmake org Make utility The make utility is necessary to build the software using Makefile This utility is usually installed by default in most LINUX systems Under WINDOWS one can use Cygwin www cygwin com or MinGW www mingw org to install the make utility A recent FORTRAN compiler The software is written mainly in FORTRAN 90 but it also uses a few FORTRAN 2003 features e g streaming IO These features are already available in most of the FORTRAN compilers e g gfortran version gt 4 2 gcc gnu org wiki GFortran and g95 www g95 org Following libraries are necessary for parallel processing A recent MPI library It should be built with the same FORTRAN compiler used to compile the software Please see www open mpi org or www mcs anl gov research projects mpich2 for details on how to install MPI li brary and how to run MPI programs SCOTCH graph partitioning library This library should be compiled with the same FORTRAN compiler used to compile the software Please see www labri fr perso pelegrin scotch for details on how to install SCOTCH Finally the following compiler is necessary to build the documentation this file BTE X compiler This is necessary to c
19. inting towards the negative x axis value of eqkx is taken negative water wsfile file name of water surface file control cg_tol tolerance for conjugate gradient method real cg_maxiter maximum iterations for conjugate gradient method integer gt 0 nl_tol tolerance for nonlinear iterations real nl maxiter maximum iterations for nonlinear iterations integer gt 0 ninc number of load increments for the plastic iterations integer gt 0 default 1 This is currently not used for slope stability analysis Arguments specific to slope stability analysis nsrf number of strength reduction factors to try integer gt 0 optional default gt 1 srf values of strength reduction factors real vector optional default 1 0 Number of srfs must be equal to nsrf phinu force v Friction angle Poisson s ratio inequality sing gt 1 2v see Zheng et al 2005 integer 0 No 1 Yes default 0 Only for TESTING purpose Arguments specific to multistage excavation nexcav number of excavation stages integer gt 0 optional default 1 nexcavid number of excavation IDs in each excavation stage integer vector default gt 1 excavid IDs of blocks regions in the mesh to be excavated in each stage integer vector default 1 Note Do not mix arguments for slope stability and excavation save disp displacement field integer optional 0 No 1 Yes default
20. nput validation1 psem To run the parallel program type mpirun n number of nodes bin psemgeotech input file name OR mpirun n number of nodes hostfile host file bin psemgeotech input file name Example mpirun n 8 bin psemgeotech input validation1 psem Note see Chapter 3 for details on input and input files Try to run one or more examples included in input By default example files included in the package are not copied to build directory during build process If necessary copy files within input folder of source directory to the input folder of build directory Chapter 3 Input 3 1 Main input file The main input file structure is motivated by the E3D Larsen and Schultz 1995 software package The main input file consists of legitimate input lines defined in the specified formats Any number of blank lines or comment lines can be placed for user friendly input structure The blank lines contain no or only white space characters and the comment lines contain as the first character Each legitimate input line consists of a line type and list of arguments and corresponding values All argument value pair are separated by comma If necessary any legitimate input line can be continued to next line using FORTRAN 90 continuation character amp as an absolute last character of a line to be continued Repetition of same line type is not allowed Legitimate input lines have the format line type arg v
21. off E Casarotti P Le Loher F Magnoni Q Liu C Blitz T Nissen Meyer P Basini and J Tromp 2011 Forward and adjoint simulations of seismic wave propagation on fully unstructured hexahedral meshes Geophysical Journal International 186 2 721 739 Rainsberger R 2006 TrueGrid User s Manual version 2 3 0 ed Livermore CA XYZ Scientific Applications Inc Seriani G 1994 3 D large scale wave propagation modeling by spectral element method on Cray T3E multiprocessor Computer Methods in Applied Mechanics and Engineer ing 164 235 247 Smith I M and D V Griffiths 2004 Programming the finite element method John Wiley amp Sons Zheng H D F Liu and C G Li 2005 Slope stability analysis based on elasto plastic finite element method International Journal for Numerical Methods in Engineering 64 1871 1888 Zienkiewicz O and I Cormeau 1974 Visco plasticity plasticity and creep in elastic solids a unified numerical solution approach International Journal for Numerical Methods in Engineering 8 4 821 845 27
22. ompile the documentation files 2 3 Configure Software package SPECFEM3D_GEOTECH is configured using CMake and the package uses an out of source build Hence DO NOT build in the same source directory Let s say the full path to the package source directory is HOME download SPECFEM3D_GEOTECH e Create a separate build directory e g mkdir HOME work SPECFEM3D_GEOTECH e Go to the build directory cd HOME work SPECFEM3D_GEOTECH e Type the cmake command ccmake HOME projects SPECFEM3D_GEOTECH CMake configuration is an iterative process See Figure 2 1 e Configure c key or Configure button e Change variables values if necessary e Configure c key or Configure button E Terminal File Edit View Terminal Tabs Help Page 1 of 1 BUILD DOCUMENTATION BUILD PARTMESH BUILD UTILITIES EXODUS2SEM BUILD UTILITIES WRITE SOS CMAKE BUILD TYPE CMAKE INSTALL PREFIX usr local ENABLE_MPI ON MPI_EXTRA_LIBRARY staff homnath openmpi 1 4 3 lib libopen MPI_LIBRARY staff homnath openmpi 1 4 3 lib libmpi s file_cmd usr bin file BUILD DOCUMENTATION Build documentation for Press enter to edit option CMake Version 2 8 5 Press c to configure Press g to generate and exit Press h for help Press q to quit without generating Press t to toggle advanced mode Currently Off Figure 2 1 CMake configuration of SPECFEM3D_GEOTECH If WARNINGS or ERRORS occur press the e key or the OK bu
23. rt_path out_path mesh xfile yfile zfile number of processors to be used for the parallel processing integer gt 1 Only required for parallel processing number of Gauss Lobatto Legendre GLL points along x axis integer gt 1 number of GLL points along y axis integer gt 1 number of GLL points along z axis integer gt 1 Note Although the program can use different values of ngllx nglly and ngllz it is recommended to use same number of GLL points along all azes input path where the input data are located string optional default gt input partition path where the partitioned data will be or are located string optional default gt partition Only required for parallel processing output path where the output data will be stored string optional default gt output file name of x coordinates string file name of y coordinates string file name of z coordinates string confile idfile efile be uxfile uyfile uzfile traction trfile stress0 type z0 s0 KO material matfile ispart matpath allelastic eqload eqkx eqky file name of mesh connectivity string file name of element IDs string file name of ghost interfaces i e partition interfaces string Only re quired for parallel processing file name of displacement boundary conditions along x axis string file name of
24. tput files 4 1 1 Summary file This file is self explanatory and it contains a summary of the results including control parameters maximum displacement at each step and elapsed time The file is written in ASCII format and its name follows the convention input file name header summary for serial run and input file name header summary procprocessor ID for parallel run 4 1 2 Mesh files This file contains the mesh information of the model including coordinates connec tivity element types etc in EnSight Gold binary format see EnSight 2008 The file name follows the format input file name header summary for serial run and in put file name header summary procprocessor ID for parallel run 4 1 3 Displacement field file This file contains the nodal displacement field in the model written in EnSight Gold binary format The file name follows the format input file name header stepstep dis for serial run and input fle name header stepstep procprocessor ID dis for parallel runs 4 1 4 Pore pressure file This file contains the hydrostatic pore pressure field in the model written in EnSight Gold binary format The file name follows the format input file name header stepstep por for serial run and input fle name header stepstep procprocessor ID por for parallel run 4 1 5 CASE file This is an EnSight Gold CASE file written in ASCII format This file contain the in formation on the mesh files other files time steps etc The file name
25. tton to return to config uration These steps have to be repeated until successful configuration Then press the g key or the Generate button to generate build files Check carefully that all necessary variables are set properly Unless configuration is successful generate is not enabled Sometimes the c key or Configure button has to be pressed repeatedly until generate is enabled Initially all variables may not be visible To see all variables toggle advanced mode by pressing the t key or the Advanced button To set or change a variable move the cursor to the variable and press Enter key If the variable is a boolean ON OFF it will flip the value on pressing the Enter key If the variable is a string or a file it can be edited For more details please see the CMake documentation www cmake org Following are the main CMake variables for the SPECFEM3D_GEOTECH See Fig ure 2 1 BUILD_DOCUMENTATION If ON the user manual this file is created The default is OFF BUILD_PARTMESH If ON the partmesh program is built The default is OFF The partmesh program is necessary to partition the mesh for parallel processing BUILD_UTILITIES_EXODUS2SEM If ON the exodus2sem program is built The default is OFF The exodus2sem program convert exodus mesh file to input files required by the SPECFEM3D_GEOTECH package see also Chap ter 5 BUILD UTILITIES WRITE SOS If ON the write sos program is built The default is OFF The
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