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ref_subcommand.c
3926 lines (3590 loc) · 146 KB
/
ref_subcommand.c
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/* Copyright 2014 United States Government as represented by the
* Administrator of the National Aeronautics and Space
* Administration. No copyright is claimed in the United States under
* Title 17, U.S. Code. All Other Rights Reserved.
*
* The refine platform is licensed under the Apache License, Version
* 2.0 (the "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0.
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
* implied. See the License for the specific language governing
* permissions and limitations under the License.
*/
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "ref_adapt.h"
#include "ref_args.h"
#include "ref_defs.h"
#include "ref_dist.h"
#include "ref_egads.h"
#include "ref_export.h"
#include "ref_gather.h"
#include "ref_geom.h"
#include "ref_grid.h"
#include "ref_import.h"
#include "ref_inflate.h"
#include "ref_iso.h"
#include "ref_malloc.h"
#include "ref_math.h"
#include "ref_matrix.h"
#include "ref_meshlink.h"
#include "ref_metric.h"
#include "ref_mpi.h"
#include "ref_part.h"
#include "ref_phys.h"
#include "ref_shard.h"
#include "ref_split.h"
#include "ref_validation.h"
#ifdef HAVE_CONFIG_H
#include "config.h"
#else
#define VERSION "not available"
#endif
static void usage(const char *name) {
printf("usage: \n %s [--help] <subcommand> [<args>]\n", name);
printf("\n");
printf("ref subcommands:\n");
printf(" adapt Adapt a mesh\n");
printf(" bootstrap Create initial mesh from EGADS file\n");
printf(" collar Inflate surface to create swept mesh\n");
printf(" distance Calculate wall distance (for turbulence model)\n");
printf(" examine Report mesh or solution file meta data.\n");
/*printf(" grow Fills surface mesh with volume to debug
* bootstrap\n");*/
printf(" interpolate Interpolate a field from one mesh to another\n");
printf(" loop Multiscale metric, adapt, and interpolation.\n");
printf(" multiscale Compute a multiscale metric.\n");
/*printf(" node Reports location of a node by index\n");*/
/*printf(" quilt Construct effective EGADS model.\n");*/
printf(" surface Extract mesh surface.\n");
printf(" translate Convert mesh formats.\n");
printf(" visualize Convert solution formats.\n");
printf("\n");
printf("'ref <command> -h' provides details on a specific subcommand.\n");
}
static void option_uniform_help(void) {
printf(
" --uniform box {ceil,floor} h0 decay_distance xmin ymin zmin "
"xmax ymax zmax\n");
printf(
" --uniform cyl {ceil,floor} h0 decay_distance x1 y1 z1 "
"x2 y2 z2 r1 r2\n");
printf(" decay_distance is negative to increase h with distance.\n");
printf(" decay_distance is positive to decrease h with distance.\n");
}
static void option_auto_tprarms_help(void) {
printf(" --auto-tparams {or combination of options} adjust .tParams\n");
printf(" 1:single edge, 2:chord violation, 4:face width (-1:all)\n");
}
static void adapt_help(const char *name) {
printf("usage: \n %s adapt input_mesh.extension [<options>]\n", name);
printf(" -x output_mesh.extension\n");
printf(" -g geometry.egads\n");
printf(" -m metric.solb (geometry feature metric when missing)\n");
printf(" --implied-complexity [complexity] imply metric from input mesh\n");
printf(" and scale to complexity\n");
printf(" --spalding [y+=1] [complexity]\n");
printf(" construct a multiscale metric to control interpolation\n");
printf(" error in u+ of Spalding's Law. Requires boundary conditions\n");
printf(" via the --fun3d-mapbc or --viscous-tags options.\n");
printf(" --stepexp [h0] [h1] [h2] [s1] [s2] [width]\n");
printf(" construct an isotropic metric of constant then exponential\n");
printf(" Requires boundary conditions via the --fun3d-mapbc or\n");
printf(" --viscous-tags options.\n");
option_uniform_help();
printf(" --fun3d-mapbc fun3d_format.mapbc\n");
printf(" --viscous-tags <comma-separated list of viscous boundary tags>\n");
printf(" --partitioner selects domain decomposition method.\n");
printf(" 2: ParMETIS graph partitioning.\n");
printf(" 3: Zoltan graph partitioning.\n");
printf(" 4: Zoltan recursive bisection.\n");
printf(" 5: native recursive bisection.\n");
printf("\n");
}
static void collar_help(const char *name) {
printf(
"usage: \n %s collar input_mesh.extension "
"nlayers first_thickness total_thickness mach\n",
name);
printf(" --fun3d-mapbc fun3d_format.mapbc\n");
printf(" -x output_mesh.extension\n");
printf("\n");
}
static void bootstrap_help(const char *name) {
printf("usage: \n %s bootstrap project.egads [-t]\n", name);
printf(" -t tecplot movie of surface curvature adaptation\n");
printf(" in files ref_gather_movie.tec and ref_gather_histo.tec\n");
printf(" --mesher {tetgen|aflr} volume mesher\n");
printf(" --mesher-options \"<options>\" quoted mesher options.\n");
option_auto_tprarms_help();
printf("\n");
}
static void distance_help(const char *name) {
printf("usage: \n %s distance input_mesh.extension distance.solb\n", name);
printf(" --fun3d-mapbc fun3d_format.mapbc\n");
printf(" --viscous-tags <comma-separated list of viscous boundary tags>\n");
printf("\n");
}
static void examine_help(const char *name) {
printf("usage: \n %s examine input_mesh_or_solb.extension\n", name);
printf("\n");
}
static void grow_help(const char *name) {
printf("usage: \n %s grow surface.meshb volume.meshb\n", name);
printf(" --mesher {tetgen|aflr} volume mesher\n");
printf(" --mesher-options \"<options>\" quoted mesher options.\n");
printf("\n");
}
static void interpolate_help(const char *name) {
printf(
"usage: \n %s interpolate donor.meshb donor.solb receptor.meshb "
"receptor.solb\n",
name);
printf("\n");
printf(" options:\n");
printf(" --extrude receptor.solb data to two planes.\n");
printf(" --face <face id> <persist>.solb\n");
printf(" where persist.solb is copied to receptor.solb\n");
printf(" and face id is replaced with donor.solb.\n");
printf("\n");
}
static void loop_help(const char *name) {
printf(
"usage: \n %s loop <input_project_name> <output_project_name>"
" complexity [<options>]\n",
name);
printf("\n");
printf(" expects:\n");
printf(
" <input_project_name>.meshb is"
" mesh with geometry association and model.\n");
printf(
" <input_project_name>_volume.solb is"
" [rho,u,v,w,p] or [rho,u,v,w,p,turb1]\n");
printf(" in FUN3D nondimensionalization.\n");
printf(" complexity is half of the target number of vertices.\n");
printf("\n");
printf(" creates:\n");
printf(
" <output_project_name>.meshb is"
" mesh with geometry association and model.\n");
printf(
" <output_project_name>.lb8.ugrid is"
" FUN3D compatible little-endian mesh.\n");
printf(
" <output_project_name>-restart.solb is"
" an interpolated solution.\n");
printf("\n");
printf(" options:\n");
printf(" --norm-power <power> multiscale metric norm power.\n");
printf(" Default power is 2 (1 for goal-based metrics)\n");
printf(" --gradation <gradation> (default -1)\n");
printf(" positive: metric-space gradation stretching ratio.\n");
printf(" negative: mixed-space gradation.\n");
printf(" --partitioner <id> selects domain decomposition method.\n");
printf(" 2: ParMETIS graph partitioning.\n");
printf(" 3: Zoltan graph partitioning.\n");
printf(" 4: Zoltan recursive bisection.\n");
printf(" 5: native recursive bisection.\n");
printf(" --mesh-extension <output mesh extension> (replaces lb8.ugrid).\n");
printf(" --fixed-point <middle-string> \\\n");
printf(" <first_timestep> <timestep_increment> <last_timestep>\n");
printf(" where <input_project_name><middle-string>N.solb are\n");
printf(" scalar fields and N is the timestep index.\n");
printf(" --interpolant <type or file.solb> multiscale scalar field.\n");
printf(
" Type is mach (default), "
"incomp (incompressible vel magnitude),\n");
printf(" htot, pressure, density, or temperature.\n");
printf(" Read from file.solb, if not a recognized type.\n");
printf(" --export-metric writes <input_project_name>-metric.solb.\n");
printf(" --opt-goal metric of Loseille et al. AIAA 2007--4186.\n");
printf(" Include flow and adjoint information in volume.solb.\n");
printf(" Use --fun3d-mapbc or --viscous-tags with strong BCs.\n");
printf(" --cons-visc <mach> <re> <temperature> see AIAA 2019--2947.\n");
printf(" <mach> is reference Mach nubmer.\n");
printf(" <re> is reference Reylonds number in grid units.\n");
printf(" <temperature> is reference temperature in K.\n");
printf(" Include flow and adjoint information in volume.solb.\n");
printf(" Use --fun3d-mapbc or --viscous-tags with strong BCs.\n");
printf(" --fun3d-mapbc fun3d_format.mapbc\n");
printf(" --viscous-tags <comma-separated list of viscous boundary tags>\n");
printf(" --deforming mesh flow solve, include xyz in *_volume.solb.\n");
printf(" --buffer coarsens the metric approaching the x max boundary.\n");
option_uniform_help();
printf("\n");
}
static void multiscale_help(const char *name) {
printf(
"usage: \n %s multiscale input_mesh.extension scalar.{solb,snap} "
"complexity metric.solb\n",
name);
printf(" complexity is approximately half the target number of vertices\n");
printf("\n");
printf(" options:\n");
printf(" --norm-power <power> multiscale metric norm power (default 2)\n");
printf(" --gradation <gradation> (default -1)\n");
printf(" positive: metric-space gradation stretching ratio.\n");
printf(" negative: mixed-space gradation.\n");
printf(" --buffer coarsens the metric approaching the x max boundary.\n");
option_uniform_help();
printf(" --hessian expects hessian.* in place of scalar.{solb,snap}.\n");
printf(" --pcd <project.pcd> exports isotropic spacing.\n");
printf(" --combine <scalar2.solb> <scalar2 ratio>.\n");
printf("\n");
}
static void node_help(const char *name) {
printf("usage: \n %s node input.meshb node_index node_index ...\n", name);
printf(" node_index is zero-based\n");
printf("\n");
}
static void quilt_help(const char *name) {
printf("usage: \n %s quilt original.egads\n", name);
printf(" originaleff.egads is output EGADS model with EBODY\n");
option_auto_tprarms_help();
printf("\n");
}
static void surface_help(const char *name) {
printf("usage: \n %s surface input_mesh.extension [surface_mesh.tec] \n",
name);
printf("\n");
}
static void translate_help(const char *name) {
printf("usage: \n %s translate input_mesh.extension output_mesh.extension \n",
name);
printf("\n");
printf(" options:\n");
printf(" --extrude a 2D mesh to single layer of prisms.\n");
printf(" extrusion added implicitly for ugrid output files\n");
printf(" --planes <N> extrude a 2D mesh to N layers of prisms.\n");
printf(" --zero-y-face [face id] explicitly set y=0 on face id.\n");
printf(" --shard converts mixed-elments to simplicies.\n");
printf(" --surface extracts surface elements (deletes volume).\n");
printf("\n");
}
static void visualize_help(const char *name) {
printf(
"usage: \n %s visualize input_mesh.extension input_solution.extension "
"output_solution.extension\n",
name);
printf("\n");
printf(" --surface extracts surface elements (deletes volume).\n");
printf(
" --subtract <baseline_solution.extension> "
"computes (input-baseline).\n");
printf(
" --iso <0-based variable index> <threshold> "
"extracts an isosurface.\n");
printf("\n");
}
static REF_STATUS spalding_metric(REF_GRID ref_grid, REF_DICT ref_dict_bcs,
REF_DBL spalding_yplus, REF_DBL complexity,
int argc, char *argv[]) {
REF_MPI ref_mpi = ref_grid_mpi(ref_grid);
REF_DBL *metric;
REF_DBL *distance, *uplus, yplus;
REF_INT node;
REF_RECON_RECONSTRUCTION reconstruction = REF_RECON_L2PROJECTION;
REF_DBL gradation = 10.0;
REF_INT pos;
ref_malloc(metric, 6 * ref_node_max(ref_grid_node(ref_grid)), REF_DBL);
ref_malloc(distance, ref_node_max(ref_grid_node(ref_grid)), REF_DBL);
ref_malloc(uplus, ref_node_max(ref_grid_node(ref_grid)), REF_DBL);
RSS(ref_phys_wall_distance(ref_grid, ref_dict_bcs, distance), "wall dist");
ref_mpi_stopwatch_stop(ref_mpi, "wall distance");
each_ref_node_valid_node(ref_grid_node(ref_grid), node) {
RAS(ref_math_divisible(distance[node], spalding_yplus),
"\nare viscous boundarys set with --viscous-tags or --fun3d-mapbc?"
"\nwall distance not divisible by y+=1");
yplus = distance[node] / spalding_yplus;
RSS(ref_phys_spalding_uplus(yplus, &(uplus[node])), "uplus");
}
RSS(ref_recon_hessian(ref_grid, uplus, metric, reconstruction), "hess");
RSS(ref_recon_roundoff_limit(metric, ref_grid),
"floor metric eigenvalues based on grid size and solution jitter");
RSS(ref_metric_local_scale(metric, NULL, ref_grid, 4),
"local lp=4 norm scaling");
RXS(ref_args_find(argc, argv, "--aspect-ratio", &pos), REF_NOT_FOUND,
"arg search");
if (REF_EMPTY != pos && pos < argc - 1) {
REF_DBL aspect_ratio = atof(argv[pos + 1]);
if (ref_mpi_once(ref_mpi))
printf("limit --aspect-ratio to %f\n", aspect_ratio);
RSS(ref_metric_limit_aspect_ratio(metric, ref_grid, aspect_ratio),
"limit aspect ratio");
}
ref_mpi_stopwatch_stop(ref_mpi, "spalding metric");
RSS(ref_metric_gradation_at_complexity(metric, ref_grid, gradation,
complexity),
"set complexity");
RSS(ref_metric_parse(metric, ref_grid, argc, argv), "parse metric");
RSS(ref_metric_to_node(metric, ref_grid_node(ref_grid)), "node metric");
ref_free(uplus);
ref_free(distance);
ref_free(metric);
ref_mpi_stopwatch_stop(ref_mpi, "spalding gradation");
if (ref_geom_model_loaded(ref_grid_geom(ref_grid)) ||
ref_geom_meshlinked(ref_grid_geom(ref_grid))) {
RSS(ref_metric_constrain_curvature(ref_grid), "crv const");
ref_mpi_stopwatch_stop(ref_mpi, "crv const");
}
return REF_SUCCESS;
}
static REF_STATUS stepexp_metric_fill(REF_GRID ref_grid, REF_DICT ref_dict_bcs,
int argc, char *argv[]) {
REF_MPI ref_mpi = ref_grid_mpi(ref_grid);
REF_NODE ref_node = ref_grid_node(ref_grid);
REF_DBL *distance;
REF_INT node;
REF_INT pos;
REF_DBL h0, h1, h2, s1, s2, width;
RSS(ref_args_find(argc, argv, "--stepexp", &pos), "arg search");
RAS(pos + 6 < argc, "not enough --stepexp args");
h0 = atof(argv[pos + 1]);
h1 = atof(argv[pos + 2]);
h2 = atof(argv[pos + 3]);
s1 = atof(argv[pos + 4]);
s2 = atof(argv[pos + 5]);
width = atof(argv[pos + 6]);
if (ref_mpi_once(ref_mpi))
printf("h0 %f h1 %f h2 %f s1 %f s2 %f width %f\n", h0, h1, h2, s1, s2,
width);
RAS(h0 > 0.0, "positive h0");
RAS(h1 > 0.0, "positive h1");
RAS(h2 > 0.0, "positive h2");
RAS(s1 > 0.0, "positive s1");
RAS(s2 > 0.0, "positive s2");
RAS(width > 0.0, "positive width");
ref_malloc(distance, ref_node_max(ref_grid_node(ref_grid)), REF_DBL);
RSS(ref_phys_wall_distance(ref_grid, ref_dict_bcs, distance), "wall dist");
ref_mpi_stopwatch_stop(ref_mpi, "wall distance");
each_ref_node_valid_node(ref_grid_node(ref_grid), node) {
REF_DBL m[6];
REF_DBL h;
REF_DBL s = distance[node];
RSS(ref_metric_step_exp(s, &h, h0, h1, h2, s1, s2, width), "step exp");
m[0] = 1.0 / (h * h);
m[1] = 0.0;
m[2] = 0.0;
m[3] = 1.0 / (h * h);
m[4] = 0.0;
m[5] = 1.0 / (h * h);
if (ref_grid_twod(ref_grid)) m[5] = 1.0;
RSS(ref_node_metric_set(ref_node, node, m), "set");
}
ref_free(distance);
return REF_SUCCESS;
}
static REF_STATUS adapt(REF_MPI ref_mpi_orig, int argc, char *argv[]) {
char *in_mesh = NULL;
char *in_metric = NULL;
char *in_egads = NULL;
REF_GRID ref_grid = NULL;
REF_MPI ref_mpi = ref_mpi_orig;
REF_BOOL stepexp_metric = REF_FALSE;
REF_BOOL curvature_metric = REF_TRUE;
REF_BOOL all_done = REF_FALSE;
REF_BOOL all_done0 = REF_FALSE;
REF_BOOL all_done1 = REF_FALSE;
REF_INT pass, passes = 30;
REF_INT opt, pos;
REF_LONG ntet;
REF_DICT ref_dict_bcs = NULL;
REF_DBL spalding_yplus = -1.0;
REF_DBL complexity = -1.0;
if (argc < 3) goto shutdown;
in_mesh = argv[2];
if (ref_mpi_para(ref_mpi)) {
if (ref_mpi_once(ref_mpi)) printf("part %s\n", in_mesh);
RSS(ref_part_by_extension(&ref_grid, ref_mpi, in_mesh), "part");
ref_mpi = ref_grid_mpi(ref_grid); /* ref_grid made a deep copy */
ref_mpi_stopwatch_stop(ref_mpi, "part");
} else {
if (ref_mpi_once(ref_mpi)) printf("import %s\n", in_mesh);
RSS(ref_import_by_extension(&ref_grid, ref_mpi, in_mesh), "import");
ref_mpi = ref_grid_mpi(ref_grid); /* ref_grid made a deep copy */
ref_mpi_stopwatch_stop(ref_mpi, "import");
}
if (ref_mpi_once(ref_mpi))
printf(" read " REF_GLOB_FMT " vertices\n",
ref_node_n_global(ref_grid_node(ref_grid)));
RXS(ref_args_find(argc, argv, "--meshlink", &pos), REF_NOT_FOUND,
"arg search");
if (REF_EMPTY != pos && pos < argc - 1) {
if (ref_mpi_once(ref_mpi)) printf("meshlink with %s\n", argv[pos + 1]);
RSS(ref_meshlink_open(ref_grid, argv[pos + 1]), "meshlink init");
RSS(ref_meshlink_infer_orientation(ref_grid), "meshlink orient");
} else {
RXS(ref_args_char(argc, argv, "-g", &in_egads), REF_NOT_FOUND,
"egads arg search");
if (NULL != in_egads) {
if (ref_mpi_once(ref_mpi)) printf("load egads from %s\n", in_egads);
RSS(ref_egads_load(ref_grid_geom(ref_grid), in_egads), "load egads");
if (ref_mpi_once(ref_mpi) && ref_geom_effective(ref_grid_geom(ref_grid)))
printf("EBody Effective Body loaded\n");
ref_mpi_stopwatch_stop(ref_mpi, "load egads");
} else {
if (0 < ref_geom_cad_data_size(ref_grid_geom(ref_grid))) {
if (ref_mpi_once(ref_mpi))
printf("load egadslite from .meshb byte stream\n");
RSS(ref_egads_load(ref_grid_geom(ref_grid), NULL), "load egads");
if (ref_mpi_once(ref_mpi) &&
ref_geom_effective(ref_grid_geom(ref_grid)))
printf("EBody Effective Body loaded\n");
ref_mpi_stopwatch_stop(ref_mpi, "load egads");
} else {
if (ref_mpi_once(ref_mpi))
printf("warning: no geometry loaded, assuming planar faces.\n");
}
}
}
if (ref_geom_model_loaded(ref_grid_geom(ref_grid))) {
RSS(ref_cell_ncell(ref_grid_tet(ref_grid), ref_grid_node(ref_grid), &ntet),
"global tets");
if (0 == ntet) ref_grid_surf(ref_grid) = REF_TRUE;
RSS(ref_egads_mark_jump_degen(ref_grid), "T and UV jumps; UV degen");
}
if (ref_geom_model_loaded(ref_grid_geom(ref_grid)) ||
ref_geom_meshlinked(ref_grid_geom(ref_grid))) {
RSS(ref_geom_verify_topo(ref_grid), "geom topo");
RSS(ref_geom_verify_param(ref_grid), "geom param");
ref_mpi_stopwatch_stop(ref_mpi, "geom assoc");
}
RXS(ref_args_find(argc, argv, "--facelift", &pos), REF_NOT_FOUND,
"arg search");
if (REF_EMPTY != pos && pos < argc - 1) {
if (ref_mpi_once(ref_mpi)) printf("--facelift %s import\n", argv[pos + 1]);
RSS(ref_facelift_import(ref_grid, argv[pos + 1]), "attach");
ref_mpi_stopwatch_stop(ref_mpi, "facelift loaded");
}
RXS(ref_args_find(argc, argv, "--surrogate", &pos), REF_NOT_FOUND,
"arg search");
if (REF_EMPTY != pos && pos < argc - 1) {
if (ref_mpi_once(ref_mpi)) printf("--surrogate %s import\n", argv[pos + 1]);
RSS(ref_facelift_surrogate(ref_grid, argv[pos + 1]), "attach");
ref_mpi_stopwatch_stop(ref_mpi, "facelift loaded");
if (ref_mpi_once(ref_mpi)) printf("constrain all\n");
RSS(ref_geom_constrain_all(ref_grid), "constrain");
ref_mpi_stopwatch_stop(ref_mpi, "constrain param");
if (ref_mpi_once(ref_mpi)) printf("verify constrained param\n");
RSS(ref_geom_verify_param(ref_grid), "constrained params");
ref_mpi_stopwatch_stop(ref_mpi, "verify param");
}
RXS(ref_args_find(argc, argv, "-t", &pos), REF_NOT_FOUND, "arg search");
if (REF_EMPTY != pos)
RSS(ref_gather_tec_movie_record_button(ref_grid_gather(ref_grid), REF_TRUE),
"movie on");
RXS(ref_args_find(argc, argv, "-s", &pos), REF_NOT_FOUND, "arg search");
if (REF_EMPTY != pos && pos < argc - 1) {
passes = atoi(argv[pos + 1]);
if (ref_mpi_once(ref_mpi)) printf("-s %d adaptation passes\n", passes);
}
RXS(ref_args_find(argc, argv, "--partitioner", &pos), REF_NOT_FOUND,
"arg search");
if (REF_EMPTY != pos && pos < argc - 1) {
REF_INT part_int = atoi(argv[pos + 1]);
ref_grid_partitioner(ref_grid) = (REF_MIGRATE_PARTIONER)part_int;
if (ref_mpi_once(ref_mpi))
printf("--partitioner %d partitioner\n",
(int)ref_grid_partitioner(ref_grid));
}
RXS(ref_args_find(argc, argv, "--ratio-method", &pos), REF_NOT_FOUND,
"arg search");
if (REF_EMPTY != pos && pos < argc - 1) {
ref_grid_node(ref_grid)->ratio_method = atoi(argv[pos + 1]);
if (ref_mpi_once(ref_mpi))
printf("--ratio-method %d\n", ref_grid_node(ref_grid)->ratio_method);
}
RXS(ref_args_find(argc, argv, "--zip-pcurve", &pos), REF_NOT_FOUND,
"arg search");
if (REF_EMPTY != pos) {
ref_geom_zip_pcurve(ref_grid_geom(ref_grid)) = REF_TRUE;
if (ref_mpi_once(ref_mpi)) printf("--zip-pcurve pcurve zipping\n");
}
RXS(ref_args_find(argc, argv, "--topo", &pos), REF_NOT_FOUND, "arg search");
if (REF_EMPTY != pos) {
ref_grid_adapt(ref_grid, watch_topo) = REF_TRUE;
if (ref_mpi_once(ref_mpi)) printf("--topo checks active\n");
}
RXS(ref_args_char(argc, argv, "-m", &in_metric), REF_NOT_FOUND,
"metric arg search");
if (NULL != in_metric) {
if (ref_mpi_once(ref_mpi)) printf("part metric %s\n", in_metric);
RSS(ref_part_metric(ref_grid_node(ref_grid), in_metric), "part metric");
curvature_metric = REF_FALSE;
ref_mpi_stopwatch_stop(ref_mpi, "part metric");
}
RSS(ref_dict_create(&ref_dict_bcs), "make dict");
RXS(ref_args_find(argc, argv, "--av", &pos), REF_NOT_FOUND, "arg search");
if (REF_EMPTY != pos) {
if (ref_mpi_once(ref_mpi)) {
printf("parse AV bcs from EGADS attributes\n");
RSS(ref_phys_av_tag_attributes(ref_dict_bcs, ref_grid_geom(ref_grid)),
"unable to parse AV bcs from EGADS attribute");
}
RSS(ref_dict_bcast(ref_dict_bcs, ref_mpi), "bcast");
}
RXS(ref_args_find(argc, argv, "--fun3d-mapbc", &pos), REF_NOT_FOUND,
"arg search");
if (REF_EMPTY != pos && pos < argc - 1) {
const char *mapbc;
mapbc = argv[pos + 1];
if (ref_mpi_once(ref_mpi)) {
printf("reading fun3d bc map %s\n", mapbc);
RSS(ref_phys_read_mapbc(ref_dict_bcs, mapbc),
"unable to read fun3d formatted mapbc");
}
RSS(ref_dict_bcast(ref_dict_bcs, ref_mpi), "bcast");
}
RXS(ref_args_find(argc, argv, "--viscous-tags", &pos), REF_NOT_FOUND,
"arg search");
if (REF_EMPTY != pos && pos < argc - 1) {
const char *tags;
tags = argv[pos + 1];
if (ref_mpi_once(ref_mpi)) {
printf("parsing viscous tags\n");
RSS(ref_phys_parse_tags(ref_dict_bcs, tags),
"unable to parse viscous tags");
printf(" %d viscous tags parsed\n", ref_dict_n(ref_dict_bcs));
}
RSS(ref_dict_bcast(ref_dict_bcs, ref_mpi), "bcast");
}
RXS(ref_args_find(argc, argv, "--spalding", &pos), REF_NOT_FOUND,
"metric arg search");
if (REF_EMPTY != pos && pos < argc - 2) {
if (0 == ref_dict_n(ref_dict_bcs)) {
if (ref_mpi_once(ref_mpi))
printf(
"\nset viscous boundaries via --fun3d-mapbc or --viscous-tags "
"to use --spalding\n\n");
goto shutdown;
}
spalding_yplus = atof(argv[pos + 1]);
complexity = atof(argv[pos + 2]);
if (ref_mpi_once(ref_mpi))
printf(" --spalding %e %f law of the wall metric\n", spalding_yplus,
complexity);
curvature_metric = REF_TRUE;
}
RXS(ref_args_find(argc, argv, "--stepexp", &pos), REF_NOT_FOUND,
"metric arg search");
if (REF_EMPTY != pos && pos < argc - 6) {
if (0 == ref_dict_n(ref_dict_bcs)) {
if (ref_mpi_once(ref_mpi))
printf(
"\nset viscous boundaries via --fun3d-mapbc or --viscous-tags "
"to use --stepexp\n\n");
goto shutdown;
}
if (ref_mpi_once(ref_mpi)) printf(" --stepexp metric\n");
stepexp_metric = REF_TRUE;
curvature_metric = REF_TRUE;
}
RXS(ref_args_find(argc, argv, "--implied-complexity", &pos), REF_NOT_FOUND,
"metric arg search");
if (REF_EMPTY != pos && pos < argc - 1) {
REF_DBL *metric;
complexity = atof(argv[pos + 1]);
if (ref_mpi_once(ref_mpi))
printf(" --implied-complexity %f implied metric scaled to complexity\n",
complexity);
ref_malloc(metric, 6 * ref_node_max(ref_grid_node(ref_grid)), REF_DBL);
RSS(ref_metric_imply_from(metric, ref_grid), "imply metric");
ref_mpi_stopwatch_stop(ref_mpi, "imply metric");
RSS(ref_metric_set_complexity(metric, ref_grid, complexity),
"scale metric");
RSS(ref_metric_parse(metric, ref_grid, argc, argv), "parse metric");
RSS(ref_metric_to_node(metric, ref_grid_node(ref_grid)), "node metric");
ref_free(metric);
curvature_metric = REF_FALSE;
}
if (curvature_metric) {
if (stepexp_metric) {
RSS(stepexp_metric_fill(ref_grid, ref_dict_bcs, argc, argv), "stepexp");
} else {
if (spalding_yplus > 0.0) {
RSS(spalding_metric(ref_grid, ref_dict_bcs, spalding_yplus, complexity,
argc, argv),
"spalding");
} else {
RSS(ref_metric_interpolated_curvature(ref_grid), "interp curve");
ref_mpi_stopwatch_stop(ref_mpi, "curvature metric");
RXS(ref_args_find(argc, argv, "--facelift-metric", &pos), REF_NOT_FOUND,
"arg search");
if (REF_EMPTY != pos && pos < argc - 1) {
complexity = atof(argv[pos + 1]);
if (ref_mpi_once(ref_mpi))
printf("--facelift-metric %f\n", complexity);
RSS(ref_facelift_multiscale(ref_grid, complexity), "metric");
ref_mpi_stopwatch_stop(ref_mpi, "facelift metric");
}
}
}
} else {
if (ref_geom_model_loaded(ref_grid_geom(ref_grid)) ||
ref_geom_meshlinked(ref_grid_geom(ref_grid))) {
RSS(ref_metric_constrain_curvature(ref_grid), "crv const");
RSS(ref_validation_cell_volume(ref_grid), "vol");
ref_mpi_stopwatch_stop(ref_mpi, "crv const");
}
RSS(ref_grid_cache_background(ref_grid), "cache");
ref_mpi_stopwatch_stop(ref_mpi, "cache background metric");
}
RSS(ref_validation_cell_volume(ref_grid), "vol");
RSS(ref_migrate_to_balance(ref_grid), "balance");
RSS(ref_grid_pack(ref_grid), "pack");
ref_mpi_stopwatch_stop(ref_mpi, "pack");
for (pass = 0; !all_done && pass < passes; pass++) {
if (ref_mpi_once(ref_mpi))
printf("\n pass %d of %d with %d ranks\n", pass + 1, passes,
ref_mpi_n(ref_mpi));
all_done1 = all_done0;
RSS(ref_adapt_pass(ref_grid, &all_done0), "pass");
all_done = all_done0 && all_done1 && (pass > MIN(5, passes));
if (curvature_metric) {
if (stepexp_metric) {
RSS(stepexp_metric_fill(ref_grid, ref_dict_bcs, argc, argv), "stepexp");
} else {
if (spalding_yplus > 0.0) {
RSS(spalding_metric(ref_grid, ref_dict_bcs, spalding_yplus,
complexity, argc, argv),
"spalding");
} else {
RSS(ref_metric_interpolated_curvature(ref_grid), "interp curve");
ref_mpi_stopwatch_stop(ref_mpi, "curvature metric");
if (REF_EMPTY != pos && pos < argc - 1) {
complexity = atof(argv[pos + 1]);
if (ref_mpi_once(ref_mpi))
printf("--facelift-metric %f\n", complexity);
RSS(ref_facelift_multiscale(ref_grid, complexity), "metric");
ref_mpi_stopwatch_stop(ref_mpi, "facelift metric");
}
}
}
} else {
RSS(ref_metric_synchronize(ref_grid), "sync with background");
ref_mpi_stopwatch_stop(ref_mpi, "metric sync");
}
RSS(ref_validation_cell_volume(ref_grid), "vol");
RSS(ref_adapt_tattle_faces(ref_grid), "tattle");
ref_mpi_stopwatch_stop(ref_grid_mpi(ref_grid), "tattle faces");
RSS(ref_migrate_to_balance(ref_grid), "balance");
RSS(ref_grid_pack(ref_grid), "pack");
ref_mpi_stopwatch_stop(ref_mpi, "pack");
}
RSS(ref_node_implicit_global_from_local(ref_grid_node(ref_grid)),
"implicit global");
ref_mpi_stopwatch_stop(ref_mpi, "implicit global");
RSS(ref_geom_verify_param(ref_grid), "final params");
ref_mpi_stopwatch_stop(ref_mpi, "verify final params");
/* export via -x grid.ext and -f final-surf.tec and -q final-vol.plt */
for (opt = 0; opt < argc - 1; opt++) {
if (strcmp(argv[opt], "-x") == 0) {
if (ref_mpi_para(ref_mpi)) {
if (ref_mpi_once(ref_mpi))
printf("gather " REF_GLOB_FMT " nodes to %s\n",
ref_node_n_global(ref_grid_node(ref_grid)), argv[opt + 1]);
RSS(ref_gather_by_extension(ref_grid, argv[opt + 1]), "gather -x");
} else {
if (ref_mpi_once(ref_mpi))
printf("export " REF_GLOB_FMT " nodes to %s\n",
ref_node_n_global(ref_grid_node(ref_grid)), argv[opt + 1]);
RSS(ref_export_by_extension(ref_grid, argv[opt + 1]), "export -x");
}
}
if (strcmp(argv[opt], "-f") == 0) {
if (ref_mpi_once(ref_mpi))
printf("gather final surface status %s\n", argv[opt + 1]);
RSS(ref_gather_surf_status_tec(ref_grid, argv[opt + 1]), "gather -f");
}
if (strcmp(argv[opt], "-q") == 0) {
if (ref_mpi_once(ref_mpi))
printf("gather final volume status %s\n", argv[opt + 1]);
RSS(ref_gather_volume_status_tec(ref_grid, argv[opt + 1]), "gather -f");
}
}
RSS(ref_dict_free(ref_dict_bcs), "free");
RSS(ref_grid_free(ref_grid), "free");
return REF_SUCCESS;
shutdown:
if (ref_mpi_once(ref_mpi)) adapt_help(argv[0]);
return REF_FAILURE;
}
static REF_STATUS fossilize(REF_GRID ref_grid, const char *fossil_filename,
const char *project, const char *mesher,
const char *mesher_options) {
REF_MPI ref_mpi = ref_grid_mpi(ref_grid);
REF_GRID fossil_grid;
REF_NODE ref_node, fossil_node;
REF_CELL ref_cell, fossil_cell;
REF_INT node, new_node, *f2g;
REF_INT nodes[REF_CELL_MAX_SIZE_PER], tempnode, cell, new_cell;
REF_GLOB global;
char filename[1024];
REF_INT self_intersections;
REF_INT group, cell_node;
if (ref_mpi_para(ref_mpi)) {
if (ref_mpi_once(ref_mpi)) printf("part %s\n", fossil_filename);
RSS(ref_part_by_extension(&fossil_grid, ref_mpi, fossil_filename), "part");
ref_mpi_stopwatch_stop(ref_mpi, "part");
ref_grid_partitioner(ref_grid) = REF_MIGRATE_SINGLE;
RSS(ref_migrate_to_balance(ref_grid), "migrate to single part");
RSS(ref_grid_pack(ref_grid), "pack");
ref_mpi_stopwatch_stop(ref_mpi, "pack");
} else {
if (ref_mpi_once(ref_mpi)) printf("import %s\n", fossil_filename);
RSS(ref_import_by_extension(&fossil_grid, ref_mpi, fossil_filename),
"import");
ref_mpi_stopwatch_stop(ref_mpi, "import");
}
fossil_node = ref_grid_node(fossil_grid);
ref_node = ref_grid_node(ref_grid);
ref_malloc_init(f2g, ref_node_max(fossil_node), REF_INT, REF_EMPTY);
each_ref_node_valid_node(fossil_node, node) {
if (!ref_cell_node_empty(ref_grid_tri(fossil_grid), node)) {
RSS(ref_node_next_global(ref_node, &global), "next global");
RSS(ref_node_add(ref_node, global, &new_node), "new_node");
f2g[node] = new_node;
ref_node_xyz(ref_node, 0, new_node) = ref_node_xyz(fossil_node, 0, node);
ref_node_xyz(ref_node, 1, new_node) = ref_node_xyz(fossil_node, 1, node);
ref_node_xyz(ref_node, 2, new_node) = ref_node_xyz(fossil_node, 2, node);
}
}
fossil_cell = ref_grid_tri(fossil_grid);
ref_cell = ref_grid_tri(ref_grid);
each_ref_cell_valid_cell_with_nodes(fossil_cell, cell, nodes) {
tempnode = nodes[0];
nodes[0] = nodes[1];
nodes[1] = tempnode;
nodes[0] = f2g[nodes[0]];
nodes[1] = f2g[nodes[1]];
nodes[2] = f2g[nodes[2]];
nodes[3] = REF_EMPTY;
RSS(ref_cell_add(ref_cell, nodes, &new_cell), "insert tri");
}
if (strncmp(mesher, "t", 1) == 0) {
if (ref_mpi_once(ref_mpi)) {
printf("fill volume with TetGen\n");
RSB(ref_geom_tetgen_volume(ref_grid, project, mesher_options),
"tetgen surface to volume", {
printf("probing adapted tessellation self-intersections\n");
RSS(ref_dist_collisions(ref_grid, REF_TRUE, &self_intersections),
"bumps");
printf("%d segment-triangle intersections detected.\n",
self_intersections);
});
}
ref_mpi_stopwatch_stop(ref_mpi, "tetgen volume");
} else if (strncmp(mesher, "a", 1) == 0) {
if (ref_mpi_once(ref_mpi)) {
printf("fill volume with AFLR3\n");
RSB(ref_geom_aflr_volume(ref_grid, project, mesher_options),
"aflr surface to volume", {
printf("probing adapted tessellation self-intersections\n");
RSS(ref_dist_collisions(ref_grid, REF_TRUE, &self_intersections),
"bumps");
printf("%d segment-triangle intersections detected.\n",
self_intersections);
});
}
ref_mpi_stopwatch_stop(ref_mpi, "aflr volume");
} else {
if (ref_mpi_once(ref_mpi)) printf("mesher '%s' not implemented\n", mesher);
return REF_FAILURE;
}
ref_grid_surf(ref_grid) = REF_FALSE; /* needed until vol mesher para */
RSS(ref_validation_boundary_face(ref_grid), "boundary-interior connectivity");
ref_mpi_stopwatch_stop(ref_grid_mpi(ref_grid), "boundary-volume check");
RSS(ref_split_edge_geometry(ref_grid), "split geom");
ref_mpi_stopwatch_stop(ref_grid_mpi(ref_grid), "split geom");
RSS(ref_node_synchronize_globals(ref_grid_node(ref_grid)), "sync glob");
ref_cell = ref_grid_tri(ref_grid);
each_ref_cell_valid_cell_with_nodes(ref_cell, cell, nodes) {
if (REF_EMPTY == nodes[3]) RSS(ref_cell_remove(ref_cell, cell), "rm tri");
}
each_ref_node_valid_node(fossil_node, node) {
if (ref_cell_node_empty(ref_grid_tri(fossil_grid), node)) {
RSS(ref_node_next_global(ref_node, &global), "next global");
RSS(ref_node_add(ref_node, global, &new_node), "new_node");
f2g[node] = new_node;
ref_node_xyz(ref_node, 0, new_node) = ref_node_xyz(fossil_node, 0, node);
ref_node_xyz(ref_node, 1, new_node) = ref_node_xyz(fossil_node, 1, node);
ref_node_xyz(ref_node, 2, new_node) = ref_node_xyz(fossil_node, 2, node);
}
}
each_ref_grid_3d_ref_cell(ref_grid, group, ref_cell) {
fossil_cell = ref_grid_cell(fossil_grid, group);
each_ref_cell_valid_cell_with_nodes(fossil_cell, cell, nodes) {
each_ref_cell_cell_node(ref_cell, cell_node) {
nodes[cell_node] = f2g[nodes[cell_node]];
}
RSS(ref_cell_add(ref_cell, nodes, &new_cell), "insert vol cell");
}
}
sprintf(filename, "%s-vol.plt", project);
if (ref_mpi_once(ref_mpi))
printf("gather " REF_GLOB_FMT " nodes to %s\n",
ref_node_n_global(ref_grid_node(ref_grid)), filename);
RSS(ref_gather_by_extension(ref_grid, filename), "vol export");
ref_mpi_stopwatch_stop(ref_mpi, "export volume");
RSS(ref_validation_boundary_face(ref_grid), "boundary-interior connectivity");
ref_mpi_stopwatch_stop(ref_grid_mpi(ref_grid), "boundary-volume check");
sprintf(filename, "%s-vol.meshb", project);
if (ref_mpi_once(ref_mpi))
printf("gather " REF_GLOB_FMT " nodes to %s\n",
ref_node_n_global(ref_grid_node(ref_grid)), filename);
RSS(ref_gather_by_extension(ref_grid, filename), "vol export");
ref_mpi_stopwatch_stop(ref_mpi, "export volume");
ref_free(f2g);
return REF_SUCCESS;
}
static REF_STATUS bootstrap(REF_MPI ref_mpi, int argc, char *argv[]) {
size_t end_of_string;
char project[1000];
char filename[1024];
REF_GRID ref_grid = NULL;
REF_INT t_pos = REF_EMPTY;
REF_INT s_pos = REF_EMPTY;
REF_INT facelift_pos = REF_EMPTY;
REF_INT pos = REF_EMPTY;
REF_INT auto_tparams = REF_EGADS_RECOMMENDED_TPARAM;
const char *mesher = "tetgen";
const char *mesher_options = NULL;
REF_INT passes = 15;
REF_INT self_intersections;
REF_DBL *global_params = NULL;
if (!ref_egads_allows_construction()) {
if (ref_mpi_once(ref_mpi))
printf("bootstrap requires EGADS(full) use ref or refmpifull\n");
goto shutdown;
}
if (argc < 3) goto shutdown;
end_of_string = MIN(1023, strlen(argv[2]));
if (7 > end_of_string ||
strncmp(&(argv[2][end_of_string - 6]), ".egads", 6) != 0)
goto shutdown;
strncpy(project, argv[2], end_of_string - 6);
project[end_of_string - 6] = '\0';
RSS(ref_grid_create(&ref_grid, ref_mpi), "create");
RXS(ref_args_find(argc, argv, "--zip-pcurve", &pos), REF_NOT_FOUND,
"arg search");
if (REF_EMPTY != pos) {
ref_geom_zip_pcurve(ref_grid_geom(ref_grid)) = REF_TRUE;
if (ref_mpi_once(ref_mpi)) printf("--zip-pcurve pcurve zipping\n");
}
RXS(ref_args_find(argc, argv, "--partitioner", &pos), REF_NOT_FOUND,
"arg search");
if (REF_EMPTY != pos && pos < argc - 1) {
REF_INT part_int = atoi(argv[pos + 1]);
ref_grid_partitioner(ref_grid) = (REF_MIGRATE_PARTIONER)part_int;
if (ref_mpi_once(ref_mpi))
printf("--partitioner %d partitioner\n",
(int)ref_grid_partitioner(ref_grid));
}
if (ref_mpi_once(ref_mpi)) {
printf("loading %s.egads\n", project);
}
RSS(ref_egads_load(ref_grid_geom(ref_grid), argv[2]), "ld egads");
if (ref_mpi_once(ref_mpi) && ref_geom_effective(ref_grid_geom(ref_grid)))
printf("EBody Effective Body loaded\n");
ref_mpi_stopwatch_stop(ref_mpi, "egads load");
if (ref_mpi_once(ref_mpi)) {
sprintf(filename, "%s-vol.mapbc", project);
printf("extracting %s from 'bc_name' attributes\n", filename);
if (REF_SUCCESS ==
ref_egads_extract_mapbc(ref_grid_geom(ref_grid), filename)) {
printf("%s extracted\n", filename);
} else {
printf("one or more 'bc_name' attributes not set, mapbc not written\n");
printf(
" All faces (or edges for 2D) should have bc_name attributes "
"like so:\n");
printf(" select face # all faces\n");
printf(" attribute bc_name $4000_wall\n");
printf(" select face 5\n");
printf(" attribute bc_name $5000_farfield\n");
}
}
RXS(ref_args_find(argc, argv, "--auto-tparams", &pos), REF_NOT_FOUND,
"arg search");
if (REF_EMPTY != pos && pos < argc - 1) {
auto_tparams = atoi(argv[pos + 1]);
if (ref_mpi_once(ref_mpi))
printf("--auto-tparams %d requested\n", auto_tparams);
if (auto_tparams < 0) {
auto_tparams = REF_EGADS_ALL_TPARAM;
if (ref_mpi_once(ref_mpi))
printf("--auto-tparams %d set to all\n", auto_tparams);
}
}
RXS(ref_args_find(argc, argv, "--global", &pos), REF_NOT_FOUND, "arg search");
if (REF_EMPTY != pos && pos < argc - 3) {
ref_malloc(global_params, 3, REF_DBL);
global_params[0] = atof(argv[pos + 1]);