On Thu, Mar 9, 2023 at 3:38 PM Blaise Bourdin <bour...@mcmaster.ca> wrote:
> Hi, > > I am encountering an issue with the GMSH reader which seems to ignore > vertex sets. I am attaching a small c example, as well as two meshes, both > contain cell, face, and vertex sets, but somehow the vertex sets are not > read by the GMSH reader. > I am particularly confused since the plexgmsh.c seems to have code to > handle vertex sets. > I will run this, but could you quickly test whether -dm_plex_gmsh_mark_vertices fixes this? The old behavior was to ignore vertex sets (for reasons I do not understand but Lisandro might). I put this in to keep them. Thanks, Matt > Regards, > Blaise > > > > > For reference, I am attaching the .geo file for the GMSH file and a dump > of the exodus version: > bblaptop:Tests (dmplex)$ ncdump ../TestMeshes/SquareFaceSet.gen > netcdf SquareFaceSet { > dimensions: > len_name = 256 ; > time_step = UNLIMITED ; // (0 currently) > num_dim = 2 ; > num_nodes = 9 ; > num_elem = 8 ; > num_el_blk = 1 ; > num_node_sets = 2 ; > num_side_sets = 3 ; > num_el_in_blk1 = 8 ; > num_nod_per_el1 = 3 ; > num_side_ss1 = 2 ; > num_df_ss1 = 4 ; > num_side_ss2 = 2 ; > num_df_ss2 = 4 ; > num_side_ss3 = 4 ; > num_df_ss3 = 8 ; > num_qa_rec = 1 ; > four = 4 ; > len_string = 33 ; > num_nod_ns1 = 3 ; > num_nod_ns2 = 3 ; > variables: > double time_whole(time_step) ; > int eb_status(num_el_blk) ; > int eb_prop1(num_el_blk) ; > eb_prop1:name = "ID" ; > int ns_status(num_node_sets) ; > int ns_prop1(num_node_sets) ; > ns_prop1:name = "ID" ; > int ss_status(num_side_sets) ; > int ss_prop1(num_side_sets) ; > ss_prop1:name = "ID" ; > double coordx(num_nodes) ; > double coordy(num_nodes) ; > char eb_names(num_el_blk, len_name) ; > char ns_names(num_node_sets, len_name) ; > char ss_names(num_side_sets, len_name) ; > char coor_names(num_dim, len_name) ; > int connect1(num_el_in_blk1, num_nod_per_el1) ; > connect1:elem_type = "TRI3" ; > int elem_ss1(num_side_ss1) ; > int side_ss1(num_side_ss1) ; > double dist_fact_ss1(num_df_ss1) ; > int elem_ss2(num_side_ss2) ; > int side_ss2(num_side_ss2) ; > double dist_fact_ss2(num_df_ss2) ; > int elem_ss3(num_side_ss3) ; > int side_ss3(num_side_ss3) ; > double dist_fact_ss3(num_df_ss3) ; > char qa_records(num_qa_rec, four, len_string) ; > int elem_map(num_elem) ; > int elem_num_map(num_elem) ; > int node_num_map(num_nodes) ; > int node_ns1(num_nod_ns1) ; > double dist_fact_ns1(num_nod_ns1) ; > int node_ns2(num_nod_ns2) ; > double dist_fact_ns2(num_nod_ns2) ; > > // global attributes: > :api_version = 8.03f ; > :version = 8.03f ; > :floating_point_word_size = 8 ; > :file_size = 1 ; > :maximum_name_length = 32 ; > :int64_status = 0 ; > :title = "cubit(SquareFaceSet.gen): 07/22/2022: 16:01:07" ; > data: > > eb_status = 1 ; > > eb_prop1 = 1 ; > > ns_status = 1, 1 ; > > ns_prop1 = 10, 20 ; > > ss_status = 1, 1, 1 ; > > ss_prop1 = 20, 21, 22 ; > > coordx = 0, 0.5, -0.166666666666667, 0, 0.5, -0.5, -0.5, -0.5, 0.5 ; > > coordy = -0.5, 0, 0, 0.5, 0.5, 0, 0.5, -0.5, -0.5 ; > > eb_names = > "" ; > > ns_names = > "", > "" ; > > ss_names = > "", > "", > "" ; > > coor_names = > "x", > "y" ; > > connect1 = > 1, 2, 3, > 2, 4, 3, > 5, 4, 2, > 6, 3, 7, > 1, 3, 8, > 9, 2, 1, > 3, 6, 8, > 3, 4, 7 ; > > elem_ss1 = 5, 6 ; > > side_ss1 = 3, 3 ; > > dist_fact_ss1 = 1, 1, 1, 1 ; > > elem_ss2 = 3, 8 ; > > side_ss2 = 1, 2 ; > > dist_fact_ss2 = 1, 1, 1, 1 ; > > elem_ss3 = 6, 3, 4, 7 ; > > side_ss3 = 1, 3, 3, 2 ; > > dist_fact_ss3 = 1, 1, 1, 1, 1, 1, 1, 1 ; > > qa_records = > "CUBIT", > "2021.11", > "07/22/2022", > "16:01:07" ; > > elem_map = 1, 2, 3, 4, 5, 6, 7, 8 ; > > elem_num_map = 1, 2, 3, 4, 5, 6, 7, 8 ; > > node_num_map = 8, 3, 9, 5, 2, 7, 4, 6, 1 ; > > node_ns1 = 5, 7, 4 ; > > dist_fact_ns1 = 1, 1, 1 ; > > node_ns2 = 8, 9, 1 ; > > dist_fact_ns2 = 1, 1, 1 ; > } > > — > Canada Research Chair in Mathematical and Computational Aspects of Solid > Mechanics (Tier 1) > Professor, Department of Mathematics & Statistics > Hamilton Hall room 409A, McMaster University > 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada > https://www.math.mcmaster.ca/bourdin | +1 (905) 525 9140 ext. 27243 > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>