<html><head></head><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px"><div dir="ltr" id="yui_3_16_0_ym19_1_1484770680995_7299">Dear All,</div><div dir="ltr" id="yui_3_16_0_ym19_1_1484770680995_8163"><br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1484770680995_7320">I am absolutely new to the mesh generation, the finite element method and petsc. But I wish to master this platform. <br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1484770680995_7380"><br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1484770680995_7372">I am trying to use gmsh to generate mesh file of a sphere and use the interface, DMPlexCreateGmshFromFile, to create mesh in petsc. The mesh file (sphere.msh, see to the end of the email), created by gmsh, contains 58 nodes and 220 elements of two types, a) type 2, triangle of 3 vertices and b) type 4, tetrahedral with 4 vertices. <br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1484770680995_7596"><br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1484770680995_7566">I have absolute no idea of my setup and could not find examples of this problem to compare with. So could anyone tell me whether the following code is correct or not? This code runs properly on petsc 3.7.5 with -@$(MPIEXEC) -n $(N_CPU) ./a.out -snes_monitor_short, where N_CPU can be any number.</div><div dir="ltr" id="yui_3_16_0_ym19_1_1484770680995_7857"><br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1484770680995_7856">Q1: Corresponding to the given mesh file, are these variables correct?</div><div dir="ltr" id="yui_3_16_0_ym19_1_1484770680995_8340"><br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1484770680995_7873">#define MAX_ELEM 220 /* Maximum number of elements */<br id="yui_3_16_0_ym19_1_1484770680995_7876">#define MAX_VERT 58 /* Maximum number of vertices */<br id="yui_3_16_0_ym19_1_1484770680995_7877">#define MAX_VERT_ELEM 4 /* Vertices per element */</div><div dir="ltr" id="yui_3_16_0_ym19_1_1484770680995_7894"><br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1484770680995_8310">Q2: The data structure AppCtx is copied from src/snes/examples/tutorials/ex10d/ex10.c. Is this structure suitable for this problem? <br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1484770680995_8445"><br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1484770680995_7891">Q3: Before and after calling DMPlexCreateGmshFromFile, did I miss any important steps?</div><div dir="ltr" id="yui_3_16_0_ym19_1_1484770680995_7968"><br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1484770680995_7726">Q4: Also could anyone let me know what the proper way to check the mesh setup by petsc is.</div><div dir="ltr" id="yui_3_16_0_ym19_1_1484770680995_7755"><br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1484770680995_8495">I just started playing around with is package. I found it is really amazing powerful, but also quite hard to get the accurate understanding. I appreciate if someone can give me some further suggestions.<br></div><div dir="ltr"><br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1484770680995_7841">Thank you very much in advance.</div><div dir="ltr" id="yui_3_16_0_ym19_1_1484770680995_7754"><br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1484770680995_7746">Juan<br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1484770680995_7437"><br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1484770680995_8456"><br></div><div dir="ltr"><br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1484770680995_7438">//------------------------------------------------<br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1484770680995_7318">#include <petscsnes.h><br id="yui_3_16_0_ym19_1_1484770680995_7105">#include <petscao.h><br id="yui_3_16_0_ym19_1_1484770680995_7106">#include <petscsys.h><br id="yui_3_16_0_ym19_1_1484770680995_7107">#include <petscvec.h><br id="yui_3_16_0_ym19_1_1484770680995_7108">#include <petscdm.h> </div><div dir="ltr" id="yui_3_16_0_ym19_1_1484770680995_7307"><br id="yui_3_16_0_ym19_1_1484770680995_7269">DM dm; /* problem definition */<br id="yui_3_16_0_ym19_1_1484770680995_7272"><br id="yui_3_16_0_ym19_1_1484770680995_7273">PetscMPIInt ranks, sizes, ierr;<br id="yui_3_16_0_ym19_1_1484770680995_7276"><br id="yui_3_16_0_ym19_1_1484770680995_7277">PetscViewer viewer;<br id="yui_3_16_0_ym19_1_1484770680995_7278"><br id="yui_3_16_0_ym19_1_1484770680995_7279">PetscBool interpolate;<br id="yui_3_16_0_ym19_1_1484770680995_7280"><br id="yui_3_16_0_ym19_1_1484770680995_7281">#define MAX_ELEM 220 /* Maximum number of elements */<br id="yui_3_16_0_ym19_1_1484770680995_7282">#define MAX_VERT 58 /* Maximum number of vertices */<br id="yui_3_16_0_ym19_1_1484770680995_7283">#define MAX_VERT_ELEM 4 /* Vertices per element */<br id="yui_3_16_0_ym19_1_1484770680995_7284"><br id="yui_3_16_0_ym19_1_1484770680995_7285">typedef struct {<br id="yui_3_16_0_ym19_1_1484770680995_7286"> PetscInt Nvglobal,Nvlocal; /* global and local number of vertices */<br id="yui_3_16_0_ym19_1_1484770680995_7287"> PetscInt Neglobal,Nelocal; /* global and local number of vertices */<br id="yui_3_16_0_ym19_1_1484770680995_7288"> PetscInt AdjM[MAX_VERT][50]; /* adjacency list of a vertex */<br id="yui_3_16_0_ym19_1_1484770680995_7289"> PetscInt itot[MAX_VERT]; /* total number of neighbors for a vertex */<br id="yui_3_16_0_ym19_1_1484770680995_7290"> PetscInt icv[MAX_ELEM][MAX_VERT_ELEM]; /* vertices belonging to an element */<br id="yui_3_16_0_ym19_1_1484770680995_7291"> PetscInt v2p[MAX_VERT]; /* processor number for a vertex */<br id="yui_3_16_0_ym19_1_1484770680995_7292"> PetscInt *locInd,*gloInd; /* local and global orderings for a node */<br id="yui_3_16_0_ym19_1_1484770680995_7293"> Vec localX,localF; /* local solution (u) and f(u) vectors */<br id="yui_3_16_0_ym19_1_1484770680995_7294"> PetscReal non_lin_param; /* nonlinear parameter for the PDE */<br id="yui_3_16_0_ym19_1_1484770680995_7295"> PetscReal lin_param; /* linear parameter for the PDE */<br id="yui_3_16_0_ym19_1_1484770680995_7296"> VecScatter scatter; /* scatter context for the local and<br id="yui_3_16_0_ym19_1_1484770680995_7297"> distributed vectors */<br id="yui_3_16_0_ym19_1_1484770680995_7298">} AppCtx;<br id="yui_3_16_0_ym19_1_1484770680995_7112"><br id="yui_3_16_0_ym19_1_1484770680995_7113"><br id="yui_3_16_0_ym19_1_1484770680995_7114">#undef __FUNCT__<br id="yui_3_16_0_ym19_1_1484770680995_7115">#define __FUNCT__ "main"<br id="yui_3_16_0_ym19_1_1484770680995_7116">int main(int argc,char **argv)<br id="yui_3_16_0_ym19_1_1484770680995_7117">{<br id="yui_3_16_0_ym19_1_1484770680995_7118"><br id="yui_3_16_0_ym19_1_1484770680995_7119"> static char help[] = "Define Vector";<br id="yui_3_16_0_ym19_1_1484770680995_7120"> static char filename[] = "./data/sphere.msh";<br id="yui_3_16_0_ym19_1_1484770680995_7121"><br id="yui_3_16_0_ym19_1_1484770680995_7122"> PetscInitialize(&argc,&argv,(char*)0,help);<br id="yui_3_16_0_ym19_1_1484770680995_7129"><br></div><div id="yui_3_16_0_ym19_1_1484770680995_6918" dir="ltr"> ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&ranks);CHKERRQ(ierr);<br id="yui_3_16_0_ym19_1_1484770680995_7145"> ierr = MPI_Comm_size(PETSC_COMM_WORLD,&sizes);CHKERRQ(ierr);<br id="yui_3_16_0_ym19_1_1484770680995_7146"><br id="yui_3_16_0_ym19_1_1484770680995_7147"> ierr=DMPlexCreateGmshFromFile(PETSC_COMM_WORLD, filename, interpolate, &dm);</div><div id="yui_3_16_0_ym19_1_1484770680995_6916" dir="ltr"> <br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1484770680995_7185"> PetscFinalize();<br id="yui_3_16_0_ym19_1_1484770680995_7182"><br id="yui_3_16_0_ym19_1_1484770680995_7183"> return 0;<br id="yui_3_16_0_ym19_1_1484770680995_7184">};<br></div><div id="yui_3_16_0_ym19_1_1484770680995_6915"><br></div><div id="yui_3_16_0_ym19_1_1484770680995_7315">-------------- Mesh file ----------<br></div><div id="yui_3_16_0_ym19_1_1484770680995_6914"><br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1484770680995_6901">$MeshFormat<br id="yui_3_16_0_ym19_1_1484770680995_6614">2.2 0 8<br id="yui_3_16_0_ym19_1_1484770680995_6615">$EndMeshFormat<br id="yui_3_16_0_ym19_1_1484770680995_6616">$Nodes<br id="yui_3_16_0_ym19_1_1484770680995_6617">58<br id="yui_3_16_0_ym19_1_1484770680995_6618">1 0 1 0<br id="yui_3_16_0_ym19_1_1484770680995_6619">2 -1 0 0<br id="yui_3_16_0_ym19_1_1484770680995_6620">3 0 0 1<br id="yui_3_16_0_ym19_1_1484770680995_6621">4 -0.4999999999988097 0.8660254037851258 0<br id="yui_3_16_0_ym19_1_1484770680995_6622">5 -0.8660254037838017 0.5000000000011033 0<br id="yui_3_16_0_ym19_1_1484770680995_6623">6 0 0.4999999999988097 0.8660254037851258<br id="yui_3_16_0_ym19_1_1484770680995_6624">7 0 0.8660254037838017 0.5000000000011033<br id="yui_3_16_0_ym19_1_1484770680995_6625">8 -0.4999999999988097 0 0.8660254037851258<br id="yui_3_16_0_ym19_1_1484770680995_6626">9 -0.8660254037838017 0 0.5000000000011033<br id="yui_3_16_0_ym19_1_1484770680995_6627">10 -0.6339745962178445 0.4428909829273233 0.633974596172505<br id="yui_3_16_0_ym19_1_1484770680995_6628">11 -0.4822994153869866 0.7506004041478795 0.4516484331982243<br id="yui_3_16_0_ym19_1_1484770680995_6629">12 -0.3493897428766589 0.3546301510880328 0.8672740417606545<br id="yui_3_16_0_ym19_1_1484770680995_6630">13 -0.8378218522221577 0.4012601404060589 0.3701956829304511<br id="yui_3_16_0_ym19_1_1484770680995_6631">14 0 -1 0<br id="yui_3_16_0_ym19_1_1484770680995_6632">15 -0.8660254037851258 -0.4999999999988097 0<br id="yui_3_16_0_ym19_1_1484770680995_6633">16 -0.5000000000011033 -0.8660254037838017 0<br id="yui_3_16_0_ym19_1_1484770680995_6634">17 0 -0.8660254037851258 0.4999999999988097<br id="yui_3_16_0_ym19_1_1484770680995_6635">18 0 -0.5000000000011033 0.8660254037838017<br id="yui_3_16_0_ym19_1_1484770680995_6636">19 -0.4428909828654145 -0.6339745962336311 0.6339745961999673<br id="yui_3_16_0_ym19_1_1484770680995_6637">20 -0.7198886675198282 -0.4906852283660827 0.4909056050197959<br id="yui_3_16_0_ym19_1_1484770680995_6638">21 -0.3594838238878847 -0.383951782616808 0.8505012692455668<br id="yui_3_16_0_ym19_1_1484770680995_6639">22 -0.358692803375615 -0.8508569143149735 0.3839036131230655<br id="yui_3_16_0_ym19_1_1484770680995_6640">23 1 0 0<br id="yui_3_16_0_ym19_1_1484770680995_6641">24 0.8660254037851258 0.4999999999988097 0<br id="yui_3_16_0_ym19_1_1484770680995_6642">25 0.5000000000011033 0.8660254037838017 0<br id="yui_3_16_0_ym19_1_1484770680995_6643">26 0.8660254037851258 0 0.4999999999988097<br id="yui_3_16_0_ym19_1_1484770680995_6644">27 0.5000000000011033 0 0.8660254037838017<br id="yui_3_16_0_ym19_1_1484770680995_6645">28 0.5108386809150948 0.5108386789440059 0.6914388520872029<br id="yui_3_16_0_ym19_1_1484770680995_6646">29 0.8481866372316714 0.374552685492926 0.3745526854952001<br id="yui_3_16_0_ym19_1_1484770680995_6647">30 0.4487154446450166 0.8265947249299238 0.3396992941633065<br id="yui_3_16_0_ym19_1_1484770680995_6648">31 0 0 -1<br id="yui_3_16_0_ym19_1_1484770680995_6649">32 0 0.8660254037851258 -0.4999999999988097<br id="yui_3_16_0_ym19_1_1484770680995_6650">33 0 0.5000000000011033 -0.8660254037838017<br id="yui_3_16_0_ym19_1_1484770680995_6651">34 -0.8660254037851258 0 -0.4999999999988097<br id="yui_3_16_0_ym19_1_1484770680995_6652">35 -0.5000000000011033 0 -0.8660254037838017<br id="yui_3_16_0_ym19_1_1484770680995_6653">36 -0.6339745962178445 0.633974596172505 -0.4428909829273234<br id="yui_3_16_0_ym19_1_1484770680995_6654">37 -0.5097746217363811 0.4676776035922022 -0.7220855171873929<br id="yui_3_16_0_ym19_1_1484770680995_6655">38 -0.3545204312296736 0.868050272320611 -0.3475686817951805<br id="yui_3_16_0_ym19_1_1484770680995_6656">39 -0.8398086783581998 0.3742446117737876 -0.3932713494682021<br id="yui_3_16_0_ym19_1_1484770680995_6657">40 0.4999999999988097 0 -0.8660254037851258<br id="yui_3_16_0_ym19_1_1484770680995_6658">41 0.8660254037838017 0 -0.5000000000011033<br id="yui_3_16_0_ym19_1_1484770680995_6659">42 0.5314152505108283 0.5314152505101392 -0.6596936130127075<br id="yui_3_16_0_ym19_1_1484770680995_6660">43 0.3745526855885761 0.8481866371475475 -0.3745526855900513<br id="yui_3_16_0_ym19_1_1484770680995_6661">44 0.8166239656466456 0.4593780018327371 -0.3494240263114541<br id="yui_3_16_0_ym19_1_1484770680995_6662">45 0 -0.4999999999988097 -0.8660254037851258<br id="yui_3_16_0_ym19_1_1484770680995_6663">46 0 -0.8660254037838017 -0.5000000000011033<br id="yui_3_16_0_ym19_1_1484770680995_6664">47 -0.693625367376466 -0.4647476149317986 -0.5503576147806688<br id="yui_3_16_0_ym19_1_1484770680995_6665">48 -0.3745526897803909 -0.3745526897775885 -0.8481866334472902<br id="yui_3_16_0_ym19_1_1484770680995_6666">49 -0.4411747191846568 -0.7694084839919415 -0.4619258078020342<br id="yui_3_16_0_ym19_1_1484770680995_6667">50 0.4999999999988097 -0.8660254037851258 0<br id="yui_3_16_0_ym19_1_1484770680995_6668">51 0.8660254037838017 -0.5000000000011033 0<br id="yui_3_16_0_ym19_1_1484770680995_6669">52 0.4835428142572408 -0.7296387419233323 0.4835428140968744<br id="yui_3_16_0_ym19_1_1484770680995_6670">53 0.8051246928456837 -0.4546444607248049 0.38088402867854<br id="yui_3_16_0_ym19_1_1484770680995_6671">54 0.4212799396792105 -0.4355246816538718 0.7955133336998031<br id="yui_3_16_0_ym19_1_1484770680995_6672">55 0.4835428133498502 -0.7296387419932698 -0.483542814898733<br id="yui_3_16_0_ym19_1_1484770680995_6673">56 0.3808840285417322 -0.4546444603984627 -0.8051246930946855<br id="yui_3_16_0_ym19_1_1484770680995_6674">57 0.7955133341574981 -0.4355246806022939 -0.4212799399020684<br id="yui_3_16_0_ym19_1_1484770680995_6675">58 -1.110223024625157e-15 1.110223024625157e-15 -6.106226635438361e-16<br id="yui_3_16_0_ym19_1_1484770680995_6676">$EndNodes<br id="yui_3_16_0_ym19_1_1484770680995_6677">$Elements<br id="yui_3_16_0_ym19_1_1484770680995_6678">220<br id="yui_3_16_0_ym19_1_1484770680995_6679">1 2 2 1 14 1 4 11<br 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