xref: /honee/problems/stg_shur14.c (revision d4e0f297ef2664708bd5ce944b5e7bed1590825e)
1493642f1SJames Wright // Copyright (c) 2017-2022, Lawrence Livermore National Security, LLC and other CEED contributors.
2493642f1SJames Wright // All Rights Reserved. See the top-level LICENSE and NOTICE files for details.
3493642f1SJames Wright //
4493642f1SJames Wright // SPDX-License-Identifier: BSD-2-Clause
5493642f1SJames Wright //
6493642f1SJames Wright // This file is part of CEED:  http://github.com/ceed
7493642f1SJames Wright 
8493642f1SJames Wright /// @file
9493642f1SJames Wright /// Implementation of the Synthetic Turbulence Generation (STG) algorithm
10493642f1SJames Wright /// presented in Shur et al. 2014
11493642f1SJames Wright 
12493642f1SJames Wright #include <stdlib.h>
13493642f1SJames Wright #include <math.h>
14493642f1SJames Wright #include <petsc.h>
15493642f1SJames Wright #include "../navierstokes.h"
16493642f1SJames Wright #include "stg_shur14.h"
17493642f1SJames Wright #include "../qfunctions/stg_shur14.h"
18493642f1SJames Wright 
198085925cSJames Wright STGShur14Context global_stg_ctx;
208085925cSJames Wright 
21493642f1SJames Wright /*
22493642f1SJames Wright  * @brief Perform Cholesky decomposition on array of symmetric 3x3 matrices
23493642f1SJames Wright  *
24493642f1SJames Wright  * This assumes the input matrices are in order [11,22,33,12,13,23]. This
25493642f1SJames Wright  * format is also used for the output.
26493642f1SJames Wright  *
27493642f1SJames Wright  * @param[in]  comm   MPI_Comm
28493642f1SJames Wright  * @param[in]  nprofs Number of matrices in Rij
29493642f1SJames Wright  * @param[in]  Rij    Array of the symmetric matrices [6,nprofs]
30493642f1SJames Wright  * @param[out] Cij    Array of the Cholesky Decomposition matrices, [6,nprofs]
31493642f1SJames Wright  */
32493642f1SJames Wright PetscErrorCode CalcCholeskyDecomp(MPI_Comm comm, PetscInt nprofs,
33493642f1SJames Wright                                   const CeedScalar Rij[6][nprofs], CeedScalar Cij[6][nprofs]) {
34493642f1SJames Wright   PetscFunctionBeginUser;
35493642f1SJames Wright   for (PetscInt i=0; i<nprofs; i++) {
36493642f1SJames Wright     Cij[0][i] = sqrt(Rij[0][i]);
37493642f1SJames Wright     Cij[3][i] = Rij[3][i] / Cij[0][i];
38493642f1SJames Wright     Cij[1][i] = sqrt(Rij[1][i] - pow(Cij[3][i], 2) );
39493642f1SJames Wright     Cij[4][i] = Rij[4][i] / Cij[0][i];
40493642f1SJames Wright     Cij[5][i] = (Rij[5][i] - Cij[3][i]*Cij[4][i]) / Cij[1][i];
41493642f1SJames Wright     Cij[2][i] = sqrt(Rij[2][i] - pow(Cij[4][i], 2) - pow(Cij[5][i], 2));
42493642f1SJames Wright 
43493642f1SJames Wright     if (isnan(Cij[0][i]) || isnan(Cij[1][i]) || isnan(Cij[2][i]))
4445aa3cadSJeremy L Thompson       SETERRQ(comm, -1, "Cholesky decomposition failed at profile point %"
4545aa3cadSJeremy L Thompson               PetscInt_FMT ". Either STGInflow has non-SPD matrix or contains nan.", i+1);
46493642f1SJames Wright   }
47493642f1SJames Wright   PetscFunctionReturn(0);
48493642f1SJames Wright }
49493642f1SJames Wright 
50493642f1SJames Wright 
51493642f1SJames Wright /*
52493642f1SJames Wright  * @brief Open a PHASTA *.dat file, grabbing dimensions and file pointer
53493642f1SJames Wright  *
54493642f1SJames Wright  * This function opens the file specified by `path` using `PetscFOpen` and
55493642f1SJames Wright  * passes the file pointer in `fp`. It is not closed in this function, thus
56493642f1SJames Wright  * `fp` must be closed sometime after this function has been called (using
57493642f1SJames Wright  * `PetscFClose` for example).
58493642f1SJames Wright  *
59493642f1SJames Wright  * Assumes that the first line of the file has the number of rows and columns
60493642f1SJames Wright  * as the only two entries, separated by a single space
61493642f1SJames Wright  *
62493642f1SJames Wright  * @param[in] comm MPI_Comm for the program
63493642f1SJames Wright  * @param[in] path Path to the file
64493642f1SJames Wright  * @param[in] char_array_len Length of the character array that should contain each line
65493642f1SJames Wright  * @param[out] dims Dimensions of the file, taken from the first line of the file
66493642f1SJames Wright  * @param[out] fp File pointer to the opened file
67493642f1SJames Wright  */
68493642f1SJames Wright static PetscErrorCode OpenPHASTADatFile(const MPI_Comm comm,
69493642f1SJames Wright                                         const char path[PETSC_MAX_PATH_LEN], const PetscInt char_array_len,
70493642f1SJames Wright                                         PetscInt dims[2], FILE **fp) {
71493642f1SJames Wright   PetscErrorCode ierr;
72493642f1SJames Wright   PetscInt ndims;
73493642f1SJames Wright   char line[char_array_len];
74493642f1SJames Wright   char **array;
75493642f1SJames Wright 
76493642f1SJames Wright   PetscFunctionBeginUser;
77493642f1SJames Wright   ierr = PetscFOpen(comm, path, "r", fp); CHKERRQ(ierr);
78493642f1SJames Wright   ierr = PetscSynchronizedFGets(comm, *fp, char_array_len, line); CHKERRQ(ierr);
79493642f1SJames Wright   ierr = PetscStrToArray(line, ' ', &ndims, &array); CHKERRQ(ierr);
80493642f1SJames Wright   if (ndims != 2) SETERRQ(comm, -1,
8145aa3cadSJeremy L Thompson                             "Found %" PetscInt_FMT" dimensions instead of 2 on the first line of %s",
82493642f1SJames Wright                             ndims, path);
83493642f1SJames Wright 
84493642f1SJames Wright   for (PetscInt i=0; i<ndims; i++)  dims[i] = atoi(array[i]);
85493642f1SJames Wright   ierr = PetscStrToArrayDestroy(ndims, array); CHKERRQ(ierr);
86493642f1SJames Wright   PetscFunctionReturn(0);
87493642f1SJames Wright }
88493642f1SJames Wright 
89493642f1SJames Wright /*
90493642f1SJames Wright  * @brief Get the number of rows for the PHASTA file at path
91493642f1SJames Wright  *
92493642f1SJames Wright  * Assumes that the first line of the file has the number of rows and columns
93493642f1SJames Wright  * as the only two entries, separated by a single space
94493642f1SJames Wright  *
95493642f1SJames Wright  * @param[in] comm MPI_Comm for the program
96493642f1SJames Wright  * @param[in] path Path to the file
97493642f1SJames Wright  * @param[out] nrows Number of rows
98493642f1SJames Wright  */
99493642f1SJames Wright static PetscErrorCode GetNRows(const MPI_Comm comm,
100493642f1SJames Wright                                const char path[PETSC_MAX_PATH_LEN], PetscInt *nrows) {
101493642f1SJames Wright   PetscErrorCode ierr;
102493642f1SJames Wright   const PetscInt char_array_len = 512;
103493642f1SJames Wright   PetscInt dims[2];
104493642f1SJames Wright   FILE *fp;
105493642f1SJames Wright 
106493642f1SJames Wright   PetscFunctionBeginUser;
107493642f1SJames Wright   ierr = OpenPHASTADatFile(comm, path, char_array_len, dims, &fp); CHKERRQ(ierr);
108493642f1SJames Wright   *nrows = dims[0];
109493642f1SJames Wright   ierr = PetscFClose(comm, fp); CHKERRQ(ierr);
110493642f1SJames Wright   PetscFunctionReturn(0);
111493642f1SJames Wright }
112493642f1SJames Wright 
113493642f1SJames Wright /*
114493642f1SJames Wright  * @brief Read the STGInflow file and load the contents into stg_ctx
115493642f1SJames Wright  *
116493642f1SJames Wright  * Assumes that the first line of the file has the number of rows and columns
117493642f1SJames Wright  * as the only two entries, separated by a single space.
118493642f1SJames Wright  * Assumes there are 14 columns in the file
119493642f1SJames Wright  *
120493642f1SJames Wright  * Function calculates the Cholesky decomposition from the Reynolds stress
121493642f1SJames Wright  * profile found in the file
122493642f1SJames Wright  *
123493642f1SJames Wright  * @param[in] comm MPI_Comm for the program
124493642f1SJames Wright  * @param[in] path Path to the STGInflow.dat file
125493642f1SJames Wright  * @param[inout] stg_ctx STGShur14Context where the data will be loaded into
126493642f1SJames Wright  */
127493642f1SJames Wright static PetscErrorCode ReadSTGInflow(const MPI_Comm comm,
128493642f1SJames Wright                                     const char path[PETSC_MAX_PATH_LEN], STGShur14Context stg_ctx) {
129493642f1SJames Wright   PetscErrorCode ierr;
130493642f1SJames Wright   PetscInt ndims, dims[2];
131493642f1SJames Wright   FILE *fp;
132493642f1SJames Wright   const PetscInt char_array_len=512;
133493642f1SJames Wright   char line[char_array_len];
134493642f1SJames Wright   char **array;
135493642f1SJames Wright 
136493642f1SJames Wright   PetscFunctionBeginUser;
137493642f1SJames Wright 
138493642f1SJames Wright   ierr = OpenPHASTADatFile(comm, path, char_array_len, dims, &fp); CHKERRQ(ierr);
139493642f1SJames Wright 
140493642f1SJames Wright   CeedScalar rij[6][stg_ctx->nprofs];
141c77f3192SJames Wright   CeedScalar *wall_dist = &stg_ctx->data[stg_ctx->offsets.wall_dist];
142493642f1SJames Wright   CeedScalar *eps = &stg_ctx->data[stg_ctx->offsets.eps];
143493642f1SJames Wright   CeedScalar *lt = &stg_ctx->data[stg_ctx->offsets.lt];
144493642f1SJames Wright   CeedScalar (*ubar)[stg_ctx->nprofs] = (CeedScalar (*)[stg_ctx->nprofs])
145493642f1SJames Wright                                         &stg_ctx->data[stg_ctx->offsets.ubar];
146493642f1SJames Wright 
147493642f1SJames Wright   for (PetscInt i=0; i<stg_ctx->nprofs; i++) {
148493642f1SJames Wright     ierr = PetscSynchronizedFGets(comm, fp, char_array_len, line); CHKERRQ(ierr);
149493642f1SJames Wright     ierr = PetscStrToArray(line, ' ', &ndims, &array); CHKERRQ(ierr);
150493642f1SJames Wright     if (ndims < dims[1]) SETERRQ(comm, -1,
15145aa3cadSJeremy L Thompson                                    "Line %" PetscInt_FMT" of %s does not contain enough columns (%"
15245aa3cadSJeremy L Thompson                                    PetscInt_FMT" instead of %" PetscInt_FMT")", i,
153493642f1SJames Wright                                    path, ndims, dims[1]);
154493642f1SJames Wright 
155c77f3192SJames Wright     wall_dist[i] = (CeedScalar) atof(array[0]);
156493642f1SJames Wright     ubar[0][i]   = (CeedScalar) atof(array[1]);
157493642f1SJames Wright     ubar[1][i]   = (CeedScalar) atof(array[2]);
158493642f1SJames Wright     ubar[2][i]   = (CeedScalar) atof(array[3]);
159493642f1SJames Wright     rij[0][i]    = (CeedScalar) atof(array[4]);
160493642f1SJames Wright     rij[1][i]    = (CeedScalar) atof(array[5]);
161493642f1SJames Wright     rij[2][i]    = (CeedScalar) atof(array[6]);
162493642f1SJames Wright     rij[3][i]    = (CeedScalar) atof(array[7]);
163493642f1SJames Wright     rij[4][i]    = (CeedScalar) atof(array[8]);
164493642f1SJames Wright     rij[5][i]    = (CeedScalar) atof(array[9]);
165493642f1SJames Wright     lt[i]        = (CeedScalar) atof(array[12]);
166493642f1SJames Wright     eps[i]       = (CeedScalar) atof(array[13]);
167493642f1SJames Wright 
168c77f3192SJames Wright     if (wall_dist[i] < 0) SETERRQ(comm, -1,
169493642f1SJames Wright                                     "Distance to wall in %s cannot be negative", path);
170493642f1SJames Wright     if (lt[i] < 0) SETERRQ(comm, -1,
171493642f1SJames Wright                              "Turbulent length scale in %s cannot be negative", path);
172493642f1SJames Wright     if (eps[i] < 0) SETERRQ(comm, -1,
173493642f1SJames Wright                               "Turbulent dissipation in %s cannot be negative", path);
174493642f1SJames Wright 
175493642f1SJames Wright   }
176493642f1SJames Wright   CeedScalar (*cij)[stg_ctx->nprofs]  = (CeedScalar (*)[stg_ctx->nprofs])
177493642f1SJames Wright                                         &stg_ctx->data[stg_ctx->offsets.cij];
178493642f1SJames Wright   ierr = CalcCholeskyDecomp(comm, stg_ctx->nprofs, rij, cij); CHKERRQ(ierr);
179493642f1SJames Wright   ierr = PetscFClose(comm, fp); CHKERRQ(ierr);
180493642f1SJames Wright   PetscFunctionReturn(0);
181493642f1SJames Wright }
182493642f1SJames Wright 
183493642f1SJames Wright /*
184493642f1SJames Wright  * @brief Read the STGRand file and load the contents into stg_ctx
185493642f1SJames Wright  *
186493642f1SJames Wright  * Assumes that the first line of the file has the number of rows and columns
187493642f1SJames Wright  * as the only two entries, separated by a single space.
188493642f1SJames Wright  * Assumes there are 7 columns in the file
189493642f1SJames Wright  *
190493642f1SJames Wright  * @param[in]    comm    MPI_Comm for the program
191493642f1SJames Wright  * @param[in]    path    Path to the STGRand.dat file
192493642f1SJames Wright  * @param[inout] stg_ctx STGShur14Context where the data will be loaded into
193493642f1SJames Wright  */
194493642f1SJames Wright static PetscErrorCode ReadSTGRand(const MPI_Comm comm,
195493642f1SJames Wright                                   const char path[PETSC_MAX_PATH_LEN],
196493642f1SJames Wright                                   STGShur14Context stg_ctx) {
197493642f1SJames Wright   PetscErrorCode ierr;
198493642f1SJames Wright   PetscInt ndims, dims[2];
199493642f1SJames Wright   FILE *fp;
200493642f1SJames Wright   const PetscInt char_array_len = 512;
201493642f1SJames Wright   char line[char_array_len];
202493642f1SJames Wright   char **array;
203493642f1SJames Wright 
204493642f1SJames Wright   PetscFunctionBeginUser;
205493642f1SJames Wright   ierr = OpenPHASTADatFile(comm, path, char_array_len, dims, &fp); CHKERRQ(ierr);
206493642f1SJames Wright 
207493642f1SJames Wright   CeedScalar *phi = &stg_ctx->data[stg_ctx->offsets.phi];
208493642f1SJames Wright   CeedScalar (*d)[stg_ctx->nmodes]     = (CeedScalar (*)[stg_ctx->nmodes])
209493642f1SJames Wright                                          &stg_ctx->data[stg_ctx->offsets.d];
210493642f1SJames Wright   CeedScalar (*sigma)[stg_ctx->nmodes] = (CeedScalar (*)[stg_ctx->nmodes])
211493642f1SJames Wright                                          &stg_ctx->data[stg_ctx->offsets.sigma];
212493642f1SJames Wright 
213493642f1SJames Wright   for (PetscInt i=0; i<stg_ctx->nmodes; i++) {
214493642f1SJames Wright     ierr = PetscSynchronizedFGets(comm, fp, char_array_len, line); CHKERRQ(ierr);
215493642f1SJames Wright     ierr = PetscStrToArray(line, ' ', &ndims, &array); CHKERRQ(ierr);
216493642f1SJames Wright     if (ndims < dims[1]) SETERRQ(comm, -1,
21745aa3cadSJeremy L Thompson                                    "Line %" PetscInt_FMT" of %s does not contain enough columns (%"
21845aa3cadSJeremy L Thompson                                    PetscInt_FMT" instead of %" PetscInt_FMT")", i,
219493642f1SJames Wright                                    path, ndims, dims[1]);
220493642f1SJames Wright 
221493642f1SJames Wright     d[0][i]     = (CeedScalar) atof(array[0]);
222493642f1SJames Wright     d[1][i]     = (CeedScalar) atof(array[1]);
223493642f1SJames Wright     d[2][i]     = (CeedScalar) atof(array[2]);
224493642f1SJames Wright     phi[i]      = (CeedScalar) atof(array[3]);
225493642f1SJames Wright     sigma[0][i] = (CeedScalar) atof(array[4]);
226493642f1SJames Wright     sigma[1][i] = (CeedScalar) atof(array[5]);
227493642f1SJames Wright     sigma[2][i] = (CeedScalar) atof(array[6]);
228493642f1SJames Wright   }
229493642f1SJames Wright   ierr = PetscFClose(comm, fp); CHKERRQ(ierr);
230493642f1SJames Wright   PetscFunctionReturn(0);
231493642f1SJames Wright }
232493642f1SJames Wright 
233493642f1SJames Wright /*
234493642f1SJames Wright  * @brief Read STG data from input paths and put in STGShur14Context
235493642f1SJames Wright  *
236493642f1SJames Wright  * Reads data from input paths and puts them into a STGShur14Context object.
237493642f1SJames Wright  * Data stored initially in `*pstg_ctx` will be copied over to the new
238493642f1SJames Wright  * STGShur14Context instance.
239493642f1SJames Wright  *
240493642f1SJames Wright  * @param[in]    comm            MPI_Comm for the program
241493642f1SJames Wright  * @param[in]    dm              DM for the program
242493642f1SJames Wright  * @param[in]    stg_inflow_path Path to STGInflow.dat file
243493642f1SJames Wright  * @param[in]    stg_rand_path   Path to STGRand.dat file
244493642f1SJames Wright  * @param[inout] pstg_ctx        Pointer to STGShur14Context where the data will be loaded into
245493642f1SJames Wright  */
246493642f1SJames Wright PetscErrorCode GetSTGContextData(const MPI_Comm comm, const DM dm,
247493642f1SJames Wright                                  char stg_inflow_path[PETSC_MAX_PATH_LEN],
248493642f1SJames Wright                                  char stg_rand_path[PETSC_MAX_PATH_LEN],
249e6098bcdSJames Wright                                  STGShur14Context *pstg_ctx,
250e6098bcdSJames Wright                                  const CeedScalar ynodes[]) {
251493642f1SJames Wright   PetscErrorCode ierr;
252493642f1SJames Wright   PetscInt nmodes, nprofs;
253493642f1SJames Wright   STGShur14Context stg_ctx;
254493642f1SJames Wright   PetscFunctionBeginUser;
255493642f1SJames Wright 
256493642f1SJames Wright   // Get options
257493642f1SJames Wright   ierr = GetNRows(comm, stg_rand_path, &nmodes); CHKERRQ(ierr);
258493642f1SJames Wright   ierr = GetNRows(comm, stg_inflow_path, &nprofs); CHKERRQ(ierr);
259493642f1SJames Wright   if (nmodes > STG_NMODES_MAX)
26045aa3cadSJeremy L Thompson     SETERRQ(comm, 1, "Number of wavemodes in %s (%"
26145aa3cadSJeremy L Thompson             PetscInt_FMT") exceeds STG_NMODES_MAX (%" PetscInt_FMT"). "
262493642f1SJames Wright             "Change size of STG_NMODES_MAX and recompile", stg_rand_path, nmodes,
263493642f1SJames Wright             STG_NMODES_MAX);
264493642f1SJames Wright 
265493642f1SJames Wright   {
266493642f1SJames Wright     STGShur14Context s;
267493642f1SJames Wright     ierr = PetscCalloc1(1, &s); CHKERRQ(ierr);
268493642f1SJames Wright     *s = **pstg_ctx;
269493642f1SJames Wright     s->nmodes = nmodes;
270493642f1SJames Wright     s->nprofs = nprofs;
271493642f1SJames Wright     s->offsets.sigma   = 0;
272493642f1SJames Wright     s->offsets.d       = nmodes*3;
273493642f1SJames Wright     s->offsets.phi       = s->offsets.d         + nmodes*3;
274493642f1SJames Wright     s->offsets.kappa     = s->offsets.phi       + nmodes;
275c77f3192SJames Wright     s->offsets.wall_dist = s->offsets.kappa     + nmodes;
276c77f3192SJames Wright     s->offsets.ubar      = s->offsets.wall_dist + nprofs;
277493642f1SJames Wright     s->offsets.cij       = s->offsets.ubar      + nprofs*3;
278493642f1SJames Wright     s->offsets.eps       = s->offsets.cij       + nprofs*6;
279493642f1SJames Wright     s->offsets.lt        = s->offsets.eps       + nprofs;
280e6098bcdSJames Wright     s->offsets.ynodes    = s->offsets.lt        + nprofs;
281e6098bcdSJames Wright     PetscInt total_num_scalars = s->offsets.ynodes + s->nynodes;
282493642f1SJames Wright     s->total_bytes = sizeof(*stg_ctx) + total_num_scalars*sizeof(stg_ctx->data[0]);
283493642f1SJames Wright     ierr = PetscMalloc(s->total_bytes, &stg_ctx); CHKERRQ(ierr);
284493642f1SJames Wright     *stg_ctx = *s;
285493642f1SJames Wright     ierr = PetscFree(s); CHKERRQ(ierr);
286493642f1SJames Wright   }
287493642f1SJames Wright 
288493642f1SJames Wright   ierr = ReadSTGInflow(comm, stg_inflow_path, stg_ctx); CHKERRQ(ierr);
289493642f1SJames Wright   ierr = ReadSTGRand(comm, stg_rand_path, stg_ctx); CHKERRQ(ierr);
290493642f1SJames Wright 
291e6098bcdSJames Wright   if (stg_ctx->nynodes > 0) {
292e6098bcdSJames Wright     CeedScalar *ynodes_ctx = &stg_ctx->data[stg_ctx->offsets.ynodes];
293e6098bcdSJames Wright     for (PetscInt i=0; i<stg_ctx->nynodes; i++) ynodes_ctx[i] = ynodes[i];
294e6098bcdSJames Wright   }
295e6098bcdSJames Wright 
296493642f1SJames Wright   // -- Calculate kappa
297493642f1SJames Wright   {
298493642f1SJames Wright     CeedScalar *kappa = &stg_ctx->data[stg_ctx->offsets.kappa];
299c77f3192SJames Wright     CeedScalar *wall_dist = &stg_ctx->data[stg_ctx->offsets.wall_dist];
300493642f1SJames Wright     CeedScalar *lt = &stg_ctx->data[stg_ctx->offsets.lt];
301493642f1SJames Wright     CeedScalar le, le_max=0;
302493642f1SJames Wright 
303493642f1SJames Wright     CeedPragmaSIMD
304493642f1SJames Wright     for (PetscInt i=0; i<stg_ctx->nprofs; i++) {
305c77f3192SJames Wright       le = PetscMin(2*wall_dist[i], 3*lt[i]);
306493642f1SJames Wright       if (le_max < le) le_max = le;
307493642f1SJames Wright     }
308493642f1SJames Wright     CeedScalar kmin = M_PI/le_max;
309493642f1SJames Wright 
310493642f1SJames Wright     CeedPragmaSIMD
311493642f1SJames Wright     for (PetscInt i=0; i<stg_ctx->nmodes; i++) {
312493642f1SJames Wright       kappa[i] = kmin*pow(stg_ctx->alpha, i);
313493642f1SJames Wright     }
314493642f1SJames Wright   } //end calculate kappa
315493642f1SJames Wright 
31676a21e77SJames Wright   ierr = PetscFree(*pstg_ctx); CHKERRQ(ierr);
317493642f1SJames Wright   *pstg_ctx = stg_ctx;
318493642f1SJames Wright   PetscFunctionReturn(0);
319493642f1SJames Wright }
320493642f1SJames Wright 
321493642f1SJames Wright PetscErrorCode SetupSTG(const MPI_Comm comm, const DM dm, ProblemData *problem,
322493642f1SJames Wright                         User user, const bool prescribe_T,
323e6098bcdSJames Wright                         const CeedScalar theta0, const CeedScalar P0,
324e6098bcdSJames Wright                         const CeedScalar ynodes[], const CeedInt nynodes) {
325493642f1SJames Wright   PetscErrorCode ierr;
326493642f1SJames Wright   char stg_inflow_path[PETSC_MAX_PATH_LEN] = "./STGInflow.dat";
327493642f1SJames Wright   char stg_rand_path[PETSC_MAX_PATH_LEN]   = "./STGRand.dat";
328e6098bcdSJames Wright   PetscBool  mean_only          = PETSC_FALSE,
329*d4e0f297SJames Wright              use_stgstrong      = PETSC_FALSE,
330*d4e0f297SJames Wright              use_fluctuating_IC = PETSC_FALSE;
331e6098bcdSJames Wright   CeedScalar u0            = 0.0,
332e6098bcdSJames Wright              alpha         = 1.01;
333493642f1SJames Wright   CeedQFunctionContext stg_context;
334493642f1SJames Wright   NewtonianIdealGasContext newtonian_ig_ctx;
335493642f1SJames Wright   PetscFunctionBeginUser;
336493642f1SJames Wright 
337493642f1SJames Wright   // Get options
338493642f1SJames Wright   PetscOptionsBegin(comm, NULL, "STG Boundary Condition Options", NULL);
339493642f1SJames Wright   ierr = PetscOptionsString("-stg_inflow_path", "Path to STGInflow.dat", NULL,
340493642f1SJames Wright                             stg_inflow_path, stg_inflow_path,
341493642f1SJames Wright                             sizeof(stg_inflow_path), NULL); CHKERRQ(ierr);
342493642f1SJames Wright   ierr = PetscOptionsString("-stg_rand_path", "Path to STGInflow.dat", NULL,
343493642f1SJames Wright                             stg_rand_path,stg_rand_path,
344493642f1SJames Wright                             sizeof(stg_rand_path), NULL); CHKERRQ(ierr);
345493642f1SJames Wright   ierr = PetscOptionsReal("-stg_alpha", "Growth rate of the wavemodes", NULL,
346493642f1SJames Wright                           alpha, &alpha, NULL); CHKERRQ(ierr);
347493642f1SJames Wright   ierr = PetscOptionsReal("-stg_u0", "Advective velocity for the fluctuations",
348493642f1SJames Wright                           NULL, u0, &u0, NULL); CHKERRQ(ierr);
349493642f1SJames Wright   ierr = PetscOptionsBool("-stg_mean_only", "Only apply mean profile",
350493642f1SJames Wright                           NULL, mean_only, &mean_only, NULL); CHKERRQ(ierr);
351e6098bcdSJames Wright   ierr = PetscOptionsBool("-stg_strong", "Enforce STG inflow strongly",
352e6098bcdSJames Wright                           NULL, use_stgstrong, &use_stgstrong, NULL); CHKERRQ(ierr);
353*d4e0f297SJames Wright   PetscCall(PetscOptionsBool("-stg_fluctuating_IC",
354*d4e0f297SJames Wright                              "\"Extrude\" the fluctuations through the domain as an initial condition",
355*d4e0f297SJames Wright                              NULL, use_fluctuating_IC, &use_fluctuating_IC, NULL));
356493642f1SJames Wright   PetscOptionsEnd();
357493642f1SJames Wright 
3588085925cSJames Wright   ierr = PetscCalloc1(1, &global_stg_ctx); CHKERRQ(ierr);
3598085925cSJames Wright   global_stg_ctx->alpha              = alpha;
3608085925cSJames Wright   global_stg_ctx->u0                 = u0;
3618085925cSJames Wright   global_stg_ctx->is_implicit        = user->phys->implicit;
3628085925cSJames Wright   global_stg_ctx->prescribe_T        = prescribe_T;
3638085925cSJames Wright   global_stg_ctx->mean_only          = mean_only;
364*d4e0f297SJames Wright   global_stg_ctx->use_fluctuating_IC = use_fluctuating_IC;
3658085925cSJames Wright   global_stg_ctx->theta0             = theta0;
3668085925cSJames Wright   global_stg_ctx->P0                 = P0;
3678085925cSJames Wright   global_stg_ctx->nynodes            = nynodes;
368493642f1SJames Wright 
369493642f1SJames Wright   {
370493642f1SJames Wright     // Calculate dx assuming constant spacing
371493642f1SJames Wright     PetscReal domain_min[3], domain_max[3], domain_size[3];
372493642f1SJames Wright     ierr = DMGetBoundingBox(dm, domain_min, domain_max); CHKERRQ(ierr);
373493642f1SJames Wright     for (PetscInt i=0; i<3; i++) domain_size[i] = domain_max[i] - domain_min[i];
374493642f1SJames Wright 
375493642f1SJames Wright     PetscInt nmax = 3, faces[3];
376493642f1SJames Wright     ierr = PetscOptionsGetIntArray(NULL, NULL, "-dm_plex_box_faces", faces, &nmax,
377493642f1SJames Wright                                    NULL); CHKERRQ(ierr);
3788085925cSJames Wright     global_stg_ctx->dx = domain_size[0]/faces[0];
3798085925cSJames Wright     global_stg_ctx->dz = domain_size[2]/faces[2];
380493642f1SJames Wright   }
381493642f1SJames Wright 
382493642f1SJames Wright   CeedQFunctionContextGetData(problem->apply_vol_rhs.qfunction_context,
383493642f1SJames Wright                               CEED_MEM_HOST, &newtonian_ig_ctx);
3848085925cSJames Wright   global_stg_ctx->newtonian_ctx = *newtonian_ig_ctx;
385493642f1SJames Wright   CeedQFunctionContextRestoreData(problem->apply_vol_rhs.qfunction_context,
386493642f1SJames Wright                                   &newtonian_ig_ctx);
387493642f1SJames Wright 
3888085925cSJames Wright   ierr = GetSTGContextData(comm, dm, stg_inflow_path, stg_rand_path,
3898085925cSJames Wright                            &global_stg_ctx, ynodes); CHKERRQ(ierr);
390493642f1SJames Wright 
391493642f1SJames Wright   CeedQFunctionContextCreate(user->ceed, &stg_context);
392493642f1SJames Wright   CeedQFunctionContextSetData(stg_context, CEED_MEM_HOST,
3938085925cSJames Wright                               CEED_USE_POINTER, global_stg_ctx->total_bytes, global_stg_ctx);
394493642f1SJames Wright   CeedQFunctionContextSetDataDestroy(stg_context, CEED_MEM_HOST,
395493642f1SJames Wright                                      FreeContextPetsc);
396493642f1SJames Wright   CeedQFunctionContextRegisterDouble(stg_context, "solution time",
397493642f1SJames Wright                                      offsetof(struct STGShur14Context_, time), 1,
3982c498363SJed Brown                                      "Physical time of the solution");
399493642f1SJames Wright 
40043bff553SJames Wright   CeedQFunctionContextDestroy(&problem->ics.qfunction_context);
40143bff553SJames Wright   problem->ics.qfunction         = ICsSTG;
40243bff553SJames Wright   problem->ics.qfunction_loc     = ICsSTG_loc;
40343bff553SJames Wright   problem->ics.qfunction_context = stg_context;
40443bff553SJames Wright 
405e6098bcdSJames Wright   if (use_stgstrong) {
4068085925cSJames Wright     // Use default boundary integral QF (BoundaryIntegral) in newtonian.h
4076d0190e2SJames Wright     problem->use_dirichlet_ceed = PETSC_TRUE;
408d7244455SJames Wright     problem->bc_from_ics        = PETSC_FALSE;
409e6098bcdSJames Wright   } else {
410493642f1SJames Wright     problem->apply_inflow.qfunction              = STGShur14_Inflow;
411493642f1SJames Wright     problem->apply_inflow.qfunction_loc          = STGShur14_Inflow_loc;
412a6e8f989SJames Wright     problem->apply_inflow_jacobian.qfunction     = STGShur14_Inflow_Jacobian;
413a6e8f989SJames Wright     problem->apply_inflow_jacobian.qfunction_loc = STGShur14_Inflow_Jacobian_loc;
414a6e8f989SJames Wright     CeedQFunctionContextReferenceCopy(stg_context,
415a6e8f989SJames Wright                                       &problem->apply_inflow.qfunction_context);
416a6e8f989SJames Wright     CeedQFunctionContextReferenceCopy(stg_context,
417a6e8f989SJames Wright                                       &problem->apply_inflow_jacobian.qfunction_context);
418d7244455SJames Wright     problem->bc_from_ics = PETSC_TRUE;
419e6098bcdSJames Wright   }
420493642f1SJames Wright 
421493642f1SJames Wright   PetscFunctionReturn(0);
422493642f1SJames Wright }
423e6098bcdSJames Wright 
424e6098bcdSJames Wright static inline PetscScalar FindDy(const PetscScalar ynodes[],
425e6098bcdSJames Wright                                  const PetscInt nynodes, const PetscScalar y) {
4266dd99bedSLeila Ghaffari 
427e6098bcdSJames Wright   const PetscScalar half_mindy = 0.5 * (ynodes[1] - ynodes[0]);
428e6098bcdSJames Wright   // ^^assuming min(dy) is first element off the wall
429e6098bcdSJames Wright   PetscInt idx = -1; // Index
430e6098bcdSJames Wright 
431e6098bcdSJames Wright   for (PetscInt i=0; i<nynodes; i++) {
432e6098bcdSJames Wright     if (y < ynodes[i] + half_mindy) {
433e6098bcdSJames Wright       idx = i; break;
434e6098bcdSJames Wright     }
435e6098bcdSJames Wright   }
436e6098bcdSJames Wright   if      (idx == 0)          return ynodes[1] - ynodes[0];
437e6098bcdSJames Wright   else if (idx == nynodes-1)  return ynodes[nynodes-2] - ynodes[nynodes-1];
438e6098bcdSJames Wright   else                        return 0.5 * (ynodes[idx+1] - ynodes[idx-1]);
439e6098bcdSJames Wright }
440e6098bcdSJames Wright 
441e6098bcdSJames Wright // Function passed to DMAddBoundary
4426d0190e2SJames Wright // NOTE: Not used in favor of QFunction-based method
443e6098bcdSJames Wright PetscErrorCode StrongSTGbcFunc(PetscInt dim, PetscReal time,
444e6098bcdSJames Wright                                const PetscReal x[], PetscInt Nc, PetscScalar bcval[], void *ctx) {
445e6098bcdSJames Wright   PetscFunctionBeginUser;
446e6098bcdSJames Wright 
447e6098bcdSJames Wright   const STGShur14Context stg_ctx = (STGShur14Context) ctx;
448e6098bcdSJames Wright   PetscScalar qn[stg_ctx->nmodes], u[3], ubar[3], cij[6], eps, lt;
449e6098bcdSJames Wright   const bool mean_only      = stg_ctx->mean_only;
450e6098bcdSJames Wright   const PetscScalar dx      = stg_ctx->dx;
451e6098bcdSJames Wright   const PetscScalar dz      = stg_ctx->dz;
452e6098bcdSJames Wright   const PetscScalar mu      = stg_ctx->newtonian_ctx.mu;
453e6098bcdSJames Wright   const PetscScalar theta0  = stg_ctx->theta0;
454e6098bcdSJames Wright   const PetscScalar P0      = stg_ctx->P0;
455e6098bcdSJames Wright   const PetscScalar cv      = stg_ctx->newtonian_ctx.cv;
456e6098bcdSJames Wright   const PetscScalar cp      = stg_ctx->newtonian_ctx.cp;
457e6098bcdSJames Wright   const PetscScalar Rd      = cp - cv;
458e6098bcdSJames Wright 
459e6098bcdSJames Wright   const CeedScalar rho = P0 / (Rd * theta0);
460e6098bcdSJames Wright   InterpolateProfile(x[1], ubar, cij, &eps, &lt, stg_ctx);
461e6098bcdSJames Wright   if (!mean_only) {
462e6098bcdSJames Wright     const PetscInt    nynodes = stg_ctx->nynodes;
463e6098bcdSJames Wright     const PetscScalar *ynodes = &stg_ctx->data[stg_ctx->offsets.ynodes];
464e6098bcdSJames Wright     const PetscScalar h[3]    = {dx, FindDy(ynodes, nynodes, x[1]), dz};
465e6098bcdSJames Wright     CalcSpectrum(x[1], eps, lt, h, mu/rho, qn, stg_ctx);
466e6098bcdSJames Wright     STGShur14_Calc(x, time, ubar, cij, qn, u, stg_ctx);
467e6098bcdSJames Wright   } else {
468e6098bcdSJames Wright     for (CeedInt j=0; j<3; j++) u[j] = ubar[j];
469e6098bcdSJames Wright   }
470e6098bcdSJames Wright 
471e6098bcdSJames Wright   bcval[0] = rho;
472e6098bcdSJames Wright   bcval[1] = rho * u[0];
473e6098bcdSJames Wright   bcval[2] = rho * u[1];
474e6098bcdSJames Wright   bcval[3] = rho * u[2];
475e6098bcdSJames Wright   PetscFunctionReturn(0);
476e6098bcdSJames Wright }
477e6098bcdSJames Wright 
478d374fb47SJames Wright PetscErrorCode SetupStrongSTG(DM dm, SimpleBC bc, ProblemData *problem,
479d374fb47SJames Wright                               Physics phys) {
480e6098bcdSJames Wright   PetscErrorCode ierr;
481e6098bcdSJames Wright   DMLabel label;
482e6098bcdSJames Wright   PetscFunctionBeginUser;
483e6098bcdSJames Wright 
484d374fb47SJames Wright   PetscInt comps[5], num_comps=4;
4853636f6a4SJames Wright   switch (phys->state_var) {
4863636f6a4SJames Wright   case STATEVAR_CONSERVATIVE:
487d374fb47SJames Wright     // {0,1,2,3} for rho, rho*u, rho*v, rho*w
488d374fb47SJames Wright     for(int i=0; i<4; i++) comps[i] = i;
4893636f6a4SJames Wright     break;
4903636f6a4SJames Wright 
4913636f6a4SJames Wright   case STATEVAR_PRIMITIVE:
4923636f6a4SJames Wright     // {1,2,3,4} for u, v, w, T
4933636f6a4SJames Wright     for(int i=0; i<4; i++) comps[i] = i+1;
4943636f6a4SJames Wright     break;
495d374fb47SJames Wright   }
496d374fb47SJames Wright 
497e6098bcdSJames Wright   ierr = DMGetLabel(dm, "Face Sets", &label); CHKERRQ(ierr);
498e6098bcdSJames Wright   // Set wall BCs
499e6098bcdSJames Wright   if (bc->num_inflow > 0) {
500e6098bcdSJames Wright     ierr = DMAddBoundary(dm, DM_BC_ESSENTIAL, "STG", label,
501e6098bcdSJames Wright                          bc->num_inflow, bc->inflows, 0, num_comps,
502e6098bcdSJames Wright                          comps, (void(*)(void))StrongSTGbcFunc,
5038085925cSJames Wright                          NULL, global_stg_ctx, NULL);  CHKERRQ(ierr);
504e6098bcdSJames Wright   }
505e6098bcdSJames Wright 
506e6098bcdSJames Wright   PetscFunctionReturn(0);
507e6098bcdSJames Wright }
5086d0190e2SJames Wright 
5096d0190e2SJames Wright PetscErrorCode SetupStrongSTG_QF(Ceed ceed, ProblemData *problem,
5109eeef72bSJames Wright                                  CeedInt num_comp_x, CeedInt num_comp_q, CeedInt stg_data_size,
5119eeef72bSJames Wright                                  CeedInt q_data_size_sur, CeedQFunction *pqf_strongbc) {
5126d0190e2SJames Wright 
5136d0190e2SJames Wright   CeedQFunction qf_strongbc;
5146d0190e2SJames Wright   PetscFunctionBeginUser;
5156d0190e2SJames Wright   CeedQFunctionCreateInterior(ceed, 1, STGShur14_Inflow_StrongQF,
5166d0190e2SJames Wright                               STGShur14_Inflow_StrongQF_loc, &qf_strongbc);
5176d0190e2SJames Wright   CeedQFunctionAddInput(qf_strongbc, "surface qdata", q_data_size_sur,
5186d0190e2SJames Wright                         CEED_EVAL_NONE);
5196d0190e2SJames Wright   CeedQFunctionAddInput(qf_strongbc,  "x",        num_comp_x,    CEED_EVAL_NONE);
5206d0190e2SJames Wright   CeedQFunctionAddInput(qf_strongbc,  "scale",    1,             CEED_EVAL_NONE);
5219eeef72bSJames Wright   CeedQFunctionAddInput(qf_strongbc,  "stg data", stg_data_size, CEED_EVAL_NONE);
5226d0190e2SJames Wright   CeedQFunctionAddOutput(qf_strongbc, "q",        num_comp_q,    CEED_EVAL_NONE);
5236d0190e2SJames Wright 
5246d0190e2SJames Wright   CeedQFunctionSetContext(qf_strongbc, problem->ics.qfunction_context);
5256d0190e2SJames Wright   *pqf_strongbc = qf_strongbc;
5266d0190e2SJames Wright   PetscFunctionReturn(0);
5276d0190e2SJames Wright }
5289eeef72bSJames Wright 
5299eeef72bSJames Wright PetscErrorCode SetupStrongSTG_PreProcessing(Ceed ceed, ProblemData *problem,
5309eeef72bSJames Wright     CeedInt num_comp_x, CeedInt stg_data_size, CeedInt q_data_size_sur,
5319eeef72bSJames Wright     CeedQFunction *pqf_strongbc) {
5329eeef72bSJames Wright 
5339eeef72bSJames Wright   CeedQFunction qf_strongbc;
5349eeef72bSJames Wright   PetscFunctionBeginUser;
5359eeef72bSJames Wright   CeedQFunctionCreateInterior(ceed, 1, Preprocess_STGShur14,
5369eeef72bSJames Wright                               Preprocess_STGShur14_loc, &qf_strongbc);
5379eeef72bSJames Wright   CeedQFunctionAddInput(qf_strongbc, "surface qdata", q_data_size_sur,
5389eeef72bSJames Wright                         CEED_EVAL_NONE);
5399eeef72bSJames Wright   CeedQFunctionAddInput(qf_strongbc,  "x",        num_comp_x,    CEED_EVAL_NONE);
5409eeef72bSJames Wright   CeedQFunctionAddOutput(qf_strongbc, "stg data", stg_data_size, CEED_EVAL_NONE);
5419eeef72bSJames Wright 
5429eeef72bSJames Wright   CeedQFunctionSetContext(qf_strongbc, problem->ics.qfunction_context);
5439eeef72bSJames Wright   *pqf_strongbc = qf_strongbc;
5449eeef72bSJames Wright   PetscFunctionReturn(0);
5459eeef72bSJames Wright }
546