PICurv 0.1.0
A Parallel Particle-In-Cell Solver for Curvilinear LES
Loading...
Searching...
No Matches
Macros | Functions
setup.c File Reference

// Setup code for running any simulation More...

#include <ctype.h>
#include <errno.h>
#include "setup.h"
#include "statistics_config.h"
#include "statistics_accumulator.h"
Include dependency graph for setup.c:

Go to the source code of this file.

Macros

#define __FUNCT__   "CreateSimulationContext"
 
#define __FUNCT__   "PetscMkdirRecursive"
 
#define __FUNCT__   "SetupSimulationEnvironment"
 
#define __FUNCT__   "AllocateContextHeirarchy"
 
#define __FUNCT__   "SetupSolverParameters"
 
#define __FUNCT__   "SetupGridAndSolvers"
 
#define __FUNCT__   "CreateAndInitializeAllVectors"
 
#define __FUNCT__   "RepairPeriodicNormalFaceGhosts"
 
#define __FUNCT__   "UpdateLocalGhosts"
 
#define __FUNCT__   "SetupBoundaryConditions"
 
#define __FUNCT__   "GetOwnedCellRange"
 
#define __FUNCT__   "ComputeAndStoreNeighborRanks"
 
#define __FUNCT__   "SetDMDAProcLayout"
 
#define __FUNCT__   "SetupDomainRankInfo"
 
#define __FUNCT__   "Contra2Cart"
 
#define __FUNCT__   "Cart2Contra"
 
#define __FUNCT__   "UniformCart2Contra"
 
#define __FUNCT__   "SetupDomainCellDecompositionMap"
 
#define __FUNCT__   "BinarySearchInt64"
 
#define __FUNCT__   "ComputeDivergence"
 
#define __FUNCT__   "InitializeRandomGenerators"
 
#define __FUNCT__   "InitializeLogicalSpaceRNGs"
 
#define __FUNCT__   "InitializeBrownianRNG"
 
#define __FUNCT__   "TransformScalarDerivativesToPhysical"
 
#define __FUNCT__   "TransformDerivativesToPhysical"
 
#define __FUNCT__   "ComputeScalarFieldDerivatives"
 
#define __FUNCT__   "ComputeVectorFieldDerivatives"
 
#define __FUNCT__   "DestroyUserVectors"
 
#define __FUNCT__   "DestroyUserContext"
 
#define __FUNCT__   "FinalizeSimulation"
 

Functions

PetscBool RuntimeWalltimeGuardParsePositiveSeconds (const char *text, PetscReal *seconds_out)
 Implementation of RuntimeWalltimeGuardParsePositiveSeconds().
 
PetscErrorCode InitializeSolutionConvergenceState (SimCtx *simCtx)
 Implementation of InitializeSolutionConvergenceState().
 
PetscErrorCode DestroySolutionConvergenceState (SimCtx *simCtx)
 Implementation of DestroySolutionConvergenceState().
 
PetscErrorCode CreateSimulationContext (int argc, char **argv, SimCtx **p_simCtx)
 Implementation of CreateSimulationContext().
 
static PetscErrorCode PetscMkdirRecursive (const char *path)
 Create a directory path recursively using PETSc-compatible error handling.
 
PetscErrorCode SetupSimulationEnvironment (SimCtx *simCtx)
 Internal helper implementation: SetupSimulationEnvironment().
 
static PetscErrorCode AllocateContextHierarchy (SimCtx *simCtx)
 Allocate the user-context objects required by every multigrid level.
 
static PetscErrorCode SetupSolverParameters (SimCtx *simCtx)
 Configure solver tolerances, operators, and time-integration controls from the context.
 
PetscErrorCode SetupGridAndSolvers (SimCtx *simCtx)
 Implementation of SetupGridAndSolvers().
 
PetscErrorCode CreateAndInitializeAllVectors (SimCtx *simCtx)
 Internal helper implementation: CreateAndInitializeAllVectors().
 
static PetscErrorCode RepairPeriodicNormalFaceGhosts (UserCtx *user, DM dm, Vec local_vec, PetscInt dof, char face_direction, PetscBool component_staggered)
 Repairs the adjacent normal ghost layer for periodic face-staggered data.
 
PetscErrorCode UpdateLocalGhosts (UserCtx *user, FieldId field_id)
 Updates a catalogued field's local ghost representation.
 
PetscErrorCode SetupBoundaryConditions (SimCtx *simCtx)
 Internal helper implementation: SetupBoundaryConditions().
 
PetscErrorCode Allocate3DArrayScalar (PetscReal ****array, PetscInt nz, PetscInt ny, PetscInt nx)
 Internal helper implementation: Allocate3DArrayScalar().
 
PetscErrorCode Deallocate3DArrayScalar (PetscReal ***array, PetscInt nz, PetscInt ny)
 Internal helper implementation: Deallocate3DArrayScalar().
 
PetscErrorCode Allocate3DArrayVector (Cmpnts ****array, PetscInt nz, PetscInt ny, PetscInt nx)
 Implementation of Allocate3DArrayVector().
 
PetscErrorCode Deallocate3DArrayVector (Cmpnts ***array, PetscInt nz, PetscInt ny)
 Implementation of Deallocate3DArrayVector().
 
PetscErrorCode GetOwnedCellRange (const DMDALocalInfo *info_nodes, PetscInt dim, PetscInt *xs_cell_global_out, PetscInt *xm_cell_local_out)
 Internal helper implementation: GetOwnedCellRange().
 
PetscErrorCode ComputeAndStoreNeighborRanks (UserCtx *user)
 Internal helper implementation: ComputeAndStoreNeighborRanks().
 
PetscErrorCode SetDMDAProcLayout (DM dm, UserCtx *user)
 Internal helper implementation: SetDMDAProcLayout().
 
PetscErrorCode SetupDomainRankInfo (SimCtx *simCtx)
 Implementation of SetupDomainRankInfo().
 
PetscErrorCode Contra2Cart (UserCtx *user)
 Internal helper implementation: Contra2Cart().
 
PetscErrorCode Cart2Contra (UserCtx *user)
 Convert a spatially varying Cartesian velocity field to contravariant fluxes.
 
PetscErrorCode UniformCart2Contra (UserCtx *user, PetscReal u, PetscReal v, PetscReal w)
 Populate contravariant fluxes from one uniform Cartesian velocity.
 
PetscErrorCode SetupDomainCellDecompositionMap (UserCtx *user)
 Internal helper implementation: SetupDomainCellDecompositionMap().
 
PetscErrorCode BinarySearchInt64 (PetscInt n, const PetscInt64 arr[], PetscInt64 key, PetscBool *found)
 Implementation of BinarySearchInt64().
 
static PetscInt Gidx (PetscInt i, PetscInt j, PetscInt k, UserCtx *user)
 Convert logical indices into the flattened global index used by setup helpers.
 
PetscErrorCode ComputeDivergence (UserCtx *user)
 Implementation of ComputeDivergence().
 
PetscErrorCode InitializeRandomGenerators (UserCtx *user, PetscRandom *randx, PetscRandom *randy, PetscRandom *randz)
 Implementation of InitializeRandomGenerators().
 
PetscErrorCode InitializeLogicalSpaceRNGs (PetscRandom *rand_logic_i, PetscRandom *rand_logic_j, PetscRandom *rand_logic_k)
 Internal helper implementation: InitializeLogicalSpaceRNGs().
 
PetscErrorCode InitializeBrownianRNG (SimCtx *simCtx)
 Internal helper implementation: InitializeBrownianRNG().
 
void TransformScalarDerivativesToPhysical (PetscReal jacobian, Cmpnts csi_metrics, Cmpnts eta_metrics, Cmpnts zet_metrics, PetscReal dPhi_dcsi, PetscReal dPhi_deta, PetscReal dPhi_dzet, Cmpnts *gradPhi)
 Implementation of TransformScalarDerivativesToPhysical().
 
static void TransformDerivativesToPhysical (PetscReal jacobian, Cmpnts csi_metrics, Cmpnts eta_metrics, Cmpnts zet_metrics, Cmpnts deriv_csi, Cmpnts deriv_eta, Cmpnts deriv_zet, Cmpnts *dudx, Cmpnts *dvdx, Cmpnts *dwdx)
 Transform contravariant vector derivatives into physical Cartesian derivatives.
 
PetscErrorCode ComputeScalarFieldDerivatives (UserCtx *user, PetscInt i, PetscInt j, PetscInt k, PetscReal ***field_data, Cmpnts *grad)
 Internal helper implementation: ComputeScalarFieldDerivatives().
 
PetscErrorCode ComputeVectorFieldDerivatives (UserCtx *user, PetscInt i, PetscInt j, PetscInt k, Cmpnts ***field_data, Cmpnts *dudx, Cmpnts *dvdx, Cmpnts *dwdx)
 Internal helper implementation: ComputeVectorFieldDerivatives().
 
PetscErrorCode DestroyUserVectors (UserCtx *user)
 Internal helper implementation: DestroyUserVectors().
 
PetscErrorCode DestroyUserContext (UserCtx *user)
 Internal helper implementation: DestroyUserContext().
 
PetscErrorCode FinalizeSimulation (SimCtx *simCtx)
 Implementation of FinalizeSimulation().
 

Detailed Description

// Setup code for running any simulation

Test program for DMSwarm interpolation using the fdf-curvIB method. Provides the setup to start any simulation with DMSwarm and DMDAs.

Definition in file setup.c.

Macro Definition Documentation

◆ __FUNCT__ [1/30]

#define __FUNCT__   "CreateSimulationContext"

Definition at line 152 of file setup.c.

◆ __FUNCT__ [2/30]

#define __FUNCT__   "PetscMkdirRecursive"

Definition at line 152 of file setup.c.

◆ __FUNCT__ [3/30]

#define __FUNCT__   "SetupSimulationEnvironment"

Definition at line 152 of file setup.c.

◆ __FUNCT__ [4/30]

#define __FUNCT__   "AllocateContextHeirarchy"

Definition at line 152 of file setup.c.

◆ __FUNCT__ [5/30]

#define __FUNCT__   "SetupSolverParameters"

Definition at line 152 of file setup.c.

◆ __FUNCT__ [6/30]

#define __FUNCT__   "SetupGridAndSolvers"

Definition at line 152 of file setup.c.

◆ __FUNCT__ [7/30]

#define __FUNCT__   "CreateAndInitializeAllVectors"

Definition at line 152 of file setup.c.

◆ __FUNCT__ [8/30]

#define __FUNCT__   "RepairPeriodicNormalFaceGhosts"

Definition at line 152 of file setup.c.

◆ __FUNCT__ [9/30]

#define __FUNCT__   "UpdateLocalGhosts"

Definition at line 152 of file setup.c.

◆ __FUNCT__ [10/30]

#define __FUNCT__   "SetupBoundaryConditions"

Definition at line 152 of file setup.c.

◆ __FUNCT__ [11/30]

#define __FUNCT__   "GetOwnedCellRange"

Definition at line 152 of file setup.c.

◆ __FUNCT__ [12/30]

#define __FUNCT__   "ComputeAndStoreNeighborRanks"

Definition at line 152 of file setup.c.

◆ __FUNCT__ [13/30]

#define __FUNCT__   "SetDMDAProcLayout"

Definition at line 152 of file setup.c.

◆ __FUNCT__ [14/30]

#define __FUNCT__   "SetupDomainRankInfo"

Definition at line 152 of file setup.c.

◆ __FUNCT__ [15/30]

#define __FUNCT__   "Contra2Cart"

Definition at line 152 of file setup.c.

◆ __FUNCT__ [16/30]

#define __FUNCT__   "Cart2Contra"

Definition at line 152 of file setup.c.

◆ __FUNCT__ [17/30]

#define __FUNCT__   "UniformCart2Contra"

Definition at line 152 of file setup.c.

◆ __FUNCT__ [18/30]

#define __FUNCT__   "SetupDomainCellDecompositionMap"

Definition at line 152 of file setup.c.

◆ __FUNCT__ [19/30]

#define __FUNCT__   "BinarySearchInt64"

Definition at line 152 of file setup.c.

◆ __FUNCT__ [20/30]

#define __FUNCT__   "ComputeDivergence"

Definition at line 152 of file setup.c.

◆ __FUNCT__ [21/30]

#define __FUNCT__   "InitializeRandomGenerators"

Definition at line 152 of file setup.c.

◆ __FUNCT__ [22/30]

#define __FUNCT__   "InitializeLogicalSpaceRNGs"

Definition at line 152 of file setup.c.

◆ __FUNCT__ [23/30]

#define __FUNCT__   "InitializeBrownianRNG"

Definition at line 152 of file setup.c.

◆ __FUNCT__ [24/30]

#define __FUNCT__   "TransformScalarDerivativesToPhysical"

Definition at line 152 of file setup.c.

◆ __FUNCT__ [25/30]

#define __FUNCT__   "TransformDerivativesToPhysical"

Definition at line 152 of file setup.c.

◆ __FUNCT__ [26/30]

#define __FUNCT__   "ComputeScalarFieldDerivatives"

Definition at line 152 of file setup.c.

◆ __FUNCT__ [27/30]

#define __FUNCT__   "ComputeVectorFieldDerivatives"

Definition at line 152 of file setup.c.

◆ __FUNCT__ [28/30]

#define __FUNCT__   "DestroyUserVectors"

Definition at line 152 of file setup.c.

◆ __FUNCT__ [29/30]

#define __FUNCT__   "DestroyUserContext"

Definition at line 152 of file setup.c.

◆ __FUNCT__ [30/30]

#define __FUNCT__   "FinalizeSimulation"

Definition at line 152 of file setup.c.

Function Documentation

◆ RuntimeWalltimeGuardParsePositiveSeconds()

PetscBool RuntimeWalltimeGuardParsePositiveSeconds ( const char *  text,
PetscReal *  seconds_out 
)

Implementation of RuntimeWalltimeGuardParsePositiveSeconds().

Parse a positive floating-point seconds value from runtime metadata.

Full API contract (arguments, ownership, side effects) is documented with the header declaration in include/setup.h.

See also
RuntimeWalltimeGuardParsePositiveSeconds()

Definition at line 20 of file setup.c.

21{
22 char *endptr = NULL;
23 double parsed_value;
24
25 if (seconds_out) *seconds_out = 0.0;
26 if (!text || text[0] == '\0') return PETSC_FALSE;
27
28 errno = 0;
29 parsed_value = strtod(text, &endptr);
30 if (endptr == text || errno == ERANGE || !isfinite(parsed_value) || parsed_value <= 0.0) {
31 return PETSC_FALSE;
32 }
33
34 while (*endptr != '\0' && isspace((unsigned char)*endptr)) {
35 endptr++;
36 }
37 if (*endptr != '\0') return PETSC_FALSE;
38
39 if (seconds_out) *seconds_out = (PetscReal)parsed_value;
40 return PETSC_TRUE;
41}
Here is the caller graph for this function:

◆ InitializeSolutionConvergenceState()

PetscErrorCode InitializeSolutionConvergenceState ( SimCtx *  simCtx)

Implementation of InitializeSolutionConvergenceState().

Allocates any runtime storage required by solution-convergence logging.

Full API contract (arguments, ownership, side effects) is documented with the header declaration in include/setup.h.

See also
InitializeSolutionConvergenceState()

Definition at line 49 of file setup.c.

50{
51 UserCtx *user = NULL;
52 PetscInt history_capacity = 0;
53
54 PetscFunctionBeginUser;
55 if (!simCtx) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_NULL, "SimCtx cannot be NULL.");
56 if (simCtx->exec_mode != EXEC_MODE_SOLVER) PetscFunctionReturn(0);
57 if (!simCtx->solutionConvergenceEnabled) PetscFunctionReturn(0);
58 if (!simCtx->usermg.mgctx) {
59 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE,
60 "Multigrid hierarchy must exist before initializing solution convergence storage.");
61 }
62
63 user = simCtx->usermg.mgctx[simCtx->usermg.mglevels - 1].user;
64 if (!user) {
65 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE,
66 "Finest-level UserCtx must exist before initializing solution convergence storage.");
67 }
68
69 simCtx->solutionConvergenceSamplesRecorded = 0;
70
71 if (simCtx->solutionConvergenceMode == SOLUTION_CONVERGENCE_PERIODIC_DETERMINISTIC) {
72 for (PetscInt bi = 0; bi < simCtx->block_number; ++bi) {
73 PetscCall(PetscCalloc1((size_t)simCtx->solutionConvergencePeriodSteps,
74 &user[bi].solutionConvergencePeriodicUcatRef));
75 PetscCall(PetscCalloc1((size_t)simCtx->solutionConvergencePeriodSteps,
76 &user[bi].solutionConvergencePeriodicPRef));
77 for (PetscInt phase = 0; phase < simCtx->solutionConvergencePeriodSteps; ++phase) {
78 PetscCall(VecDuplicate(user[bi].Ucat, &user[bi].solutionConvergencePeriodicUcatRef[phase]));
79 PetscCall(VecSet(user[bi].solutionConvergencePeriodicUcatRef[phase], 0.0));
80 PetscCall(VecDuplicate(user[bi].P, &user[bi].solutionConvergencePeriodicPRef[phase]));
81 PetscCall(VecSet(user[bi].solutionConvergencePeriodicPRef[phase], 0.0));
82 }
83 }
84 }
85
86 if (simCtx->solutionConvergenceMode == SOLUTION_CONVERGENCE_STATISTICAL_STEADY) {
87 history_capacity = 2 * simCtx->solutionConvergenceWindowSteps;
88 PetscCall(PetscCalloc1((size_t)history_capacity, &simCtx->solutionConvergenceMeanSpeedHistory));
89 PetscCall(PetscCalloc1((size_t)history_capacity, &simCtx->solutionConvergenceMeanKEHistory));
90 }
91
92 PetscFunctionReturn(0);
93}
MGCtx::user
UserCtx * user
Definition variables.h:571
SimCtx::block_number
PetscInt block_number
Definition variables.h:790
SimCtx::solutionConvergenceMeanSpeedHistory
PetscReal * solutionConvergenceMeanSpeedHistory
Definition variables.h:766
SimCtx::usermg
UserMG usermg
Definition variables.h:852
SimCtx::solutionConvergenceSamplesRecorded
PetscInt solutionConvergenceSamplesRecorded
Definition variables.h:765
SimCtx::solutionConvergenceEnabled
PetscBool solutionConvergenceEnabled
Definition variables.h:761
SimCtx::solutionConvergenceMeanKEHistory
PetscReal * solutionConvergenceMeanKEHistory
Definition variables.h:767
SimCtx::solutionConvergencePeriodSteps
PetscInt solutionConvergencePeriodSteps
Definition variables.h:763
UserMG::mglevels
PetscInt mglevels
Definition variables.h:578
SimCtx::solutionConvergenceWindowSteps
PetscInt solutionConvergenceWindowSteps
Definition variables.h:764
EXEC_MODE_SOLVER
@ EXEC_MODE_SOLVER
Definition variables.h:668
UserMG::mgctx
MGCtx * mgctx
Definition variables.h:581
SOLUTION_CONVERGENCE_PERIODIC_DETERMINISTIC
@ SOLUTION_CONVERGENCE_PERIODIC_DETERMINISTIC
Definition variables.h:545
SOLUTION_CONVERGENCE_STATISTICAL_STEADY
@ SOLUTION_CONVERGENCE_STATISTICAL_STEADY
Definition variables.h:546
SimCtx::solutionConvergenceMode
SolutionConvergenceMode solutionConvergenceMode
Definition variables.h:762
SimCtx::exec_mode
ExecutionMode exec_mode
Definition variables.h:714
UserCtx
User-defined context containing data specific to a single computational grid level.
Definition variables.h:906
Here is the caller graph for this function:

◆ DestroySolutionConvergenceState()

PetscErrorCode DestroySolutionConvergenceState ( SimCtx *  simCtx)

Implementation of DestroySolutionConvergenceState().

Frees any runtime storage allocated for solution-convergence logging.

Full API contract (arguments, ownership, side effects) is documented with the header declaration in include/setup.h.

See also
DestroySolutionConvergenceState()

Definition at line 101 of file setup.c.

102{
103 UserCtx *user = NULL;
104
105 PetscFunctionBeginUser;
106 if (!simCtx) PetscFunctionReturn(0);
107 if (simCtx->fieldStatisticsWindows) {
108 PetscCall(PetscFree(simCtx->fieldStatisticsWindows));
109 simCtx->fieldStatisticsWindows = NULL;
110 simCtx->fieldStatisticsWindowCount = 0;
111 }
112 if (!simCtx->usermg.mgctx) PetscFunctionReturn(0);
113
114 user = simCtx->usermg.mgctx[simCtx->usermg.mglevels - 1].user;
115 if (user) {
116 for (PetscInt bi = 0; bi < simCtx->block_number; ++bi) {
117 if (user[bi].solutionConvergencePeriodicUcatRef) {
118 for (PetscInt phase = 0; phase < simCtx->solutionConvergencePeriodSteps; ++phase) {
119 if (user[bi].solutionConvergencePeriodicUcatRef[phase]) {
120 PetscCall(VecDestroy(&user[bi].solutionConvergencePeriodicUcatRef[phase]));
121 }
122 }
123 PetscCall(PetscFree(user[bi].solutionConvergencePeriodicUcatRef));
124 user[bi].solutionConvergencePeriodicUcatRef = NULL;
125 }
126 if (user[bi].solutionConvergencePeriodicPRef) {
127 for (PetscInt phase = 0; phase < simCtx->solutionConvergencePeriodSteps; ++phase) {
128 if (user[bi].solutionConvergencePeriodicPRef[phase]) {
129 PetscCall(VecDestroy(&user[bi].solutionConvergencePeriodicPRef[phase]));
130 }
131 }
132 PetscCall(PetscFree(user[bi].solutionConvergencePeriodicPRef));
133 user[bi].solutionConvergencePeriodicPRef = NULL;
134 }
135 }
136 }
137
138 if (simCtx->solutionConvergenceMeanSpeedHistory) {
139 PetscCall(PetscFree(simCtx->solutionConvergenceMeanSpeedHistory));
140 simCtx->solutionConvergenceMeanSpeedHistory = NULL;
141 }
142 if (simCtx->solutionConvergenceMeanKEHistory) {
143 PetscCall(PetscFree(simCtx->solutionConvergenceMeanKEHistory));
144 simCtx->solutionConvergenceMeanKEHistory = NULL;
145 }
146 simCtx->solutionConvergenceSamplesRecorded = 0;
147
148 PetscFunctionReturn(0);
149}
SimCtx::fieldStatisticsWindowCount
PetscInt fieldStatisticsWindowCount
Definition variables.h:770
UserCtx::solutionConvergencePeriodicPRef
Vec * solutionConvergencePeriodicPRef
Definition variables.h:949
UserCtx::solutionConvergencePeriodicUcatRef
Vec * solutionConvergencePeriodicUcatRef
Definition variables.h:948
SimCtx::fieldStatisticsWindows
struct PicurvWindow * fieldStatisticsWindows
Definition variables.h:771
Here is the caller graph for this function:

◆ CreateSimulationContext()

PetscErrorCode CreateSimulationContext ( int  argc,
char **  argv,
SimCtx **  p_simCtx 
)

Implementation of CreateSimulationContext().

Allocates and populates the master SimulationContext object.

Full API contract (arguments, ownership, side effects) is documented with the header declaration in include/setup.h.

See also
CreateSimulationContext()

Definition at line 160 of file setup.c.

161{
162 PetscErrorCode ierr;
163 (void)argc;
164 (void)argv;
165 SimCtx *simCtx;
166 char control_filename[PETSC_MAX_PATH_LEN] = ""; // Temporary placeholder for control file name.
167 PetscBool control_flg; // Temporary placeholder for control file tag existence check flag.
168 PetscBool particle_console_output_freq_flg = PETSC_FALSE;
169
170 PetscFunctionBeginUser;
171
172 PROFILE_FUNCTION_BEGIN;
173
174 // === 1. Allocate the Context Struct and Set ALL Defaults ==================
175 ierr = PetscNew(p_simCtx); CHKERRQ(ierr);
176 simCtx = *p_simCtx;
177
178 // --- Group 1: Parallelism & MPI ---
179 simCtx->rank = 0; simCtx->size = 1;
180
181 // --- Group 2: Simulation Control, Time, and I/O ---
182 simCtx->step = 0; simCtx->ti = 0.0; simCtx->StartStep = 0; simCtx->StepsToRun = 10;
183 simCtx->tiout = 10; simCtx->particleConsoleOutputFreq = simCtx->tiout;
184 simCtx->StartTime = 0.0; simCtx->dt = 0.001;
185 simCtx->OnlySetup = PETSC_FALSE;
186 simCtx->continueMode = PETSC_FALSE;
187 simCtx->logviewer = NULL;
188 strcpy(simCtx->eulerianSource,"solve");
189 strcpy(simCtx->restart_dir,"restart");
190 strcpy(simCtx->output_dir,"output");
191 strcpy(simCtx->log_dir,"logs");
192 simCtx->_io_context_buffer[0] = '\0';
193 simCtx->current_io_directory = NULL;
194 simCtx->checkpointGeometrySHA256[0] = '\0';
195 simCtx->checkpointGeometryHashReady = PETSC_FALSE;
196 simCtx->restartHistoryAvailable = PETSC_FALSE;
197
198 // --- Group 3: High-Level Physics & Model Selection Flags ---
199 simCtx->immersed = 0; simCtx->movefsi = 0; simCtx->rotatefsi = 0;
200 simCtx->sediment = 0; simCtx->rheology = 0; simCtx->invicid = 0;
201 simCtx->TwoD = 0; simCtx->thin = 0; simCtx->moveframe = 0;
202 simCtx->rotateframe = 0; simCtx->blank = 0;
203 simCtx->dgf_x = 0; simCtx->dgf_y = 1; simCtx->dgf_z = 0;
204 simCtx->dgf_ax = 1; simCtx->dgf_ay = 0; simCtx->dgf_az = 0;
205 strcpy(simCtx->AnalyticalSolutionType,"TGV3D");
206
207 // --- Group 4: Specific Simulation Case Flags --- (DEPRICATED)
208 simCtx->cop=0; simCtx->fish=0; simCtx->fish_c=0; simCtx->fishcyl=0;
209 simCtx->eel=0; simCtx->pizza=0; simCtx->turbine=0; simCtx->Pipe=0;
210 simCtx->wing=0; simCtx->hydro=0; simCtx->MHV=0; simCtx->LV=0;
211 simCtx->channelz = 0;
212
213 // --- Group 5: Solver & Numerics Parameters ---
214 simCtx->mom_solver_type = MOMENTUM_SOLVER_DUALTIME_PICARD_JAMESON_RK; simCtx->mom_max_pseudo_steps = 50;
215 simCtx->mom_dt_jameson_residual_norm_noise_allowance_factor = 1.1; // raised from 1.05; less aggressive rejection
216 simCtx->mom_atol = 1e-7; simCtx->mom_rtol = 1e-4;
217 /* Residual-based convergence is the default. Leaving both at 0.0 selected the
218 * update-only branch, where |dU| <= mom_atol can pass purely because dtau collapsed
219 * (|dU| ~ dtau*|R|), converging on a state that does not satisfy the equations.
220 * Shipped configs all set these explicitly; these defaults protect a minimal
221 * user-written config. Set both non-positive to opt back out deliberately. */
222 simCtx->mom_resid_atol = 1e-8; simCtx->mom_resid_rtol = 1e-3;
223 simCtx->imp_stol = 1.e-8;
224 simCtx->mglevels = 3; simCtx->mg_MAX_IT = 30; simCtx->mg_idx = 1;
225 simCtx->mg_preItr = 1; simCtx->mg_poItr = 1;
226 simCtx->poisson = 0; simCtx->poisson_tol = 5.e-9;
227 simCtx->STRONG_COUPLING = 0;simCtx->central=0;
228 /* pseudo_cfl and its bounds are now dimensionless Courant numbers: CFL = dtau * lambda_max,
229 where lambda_max is the global spectral radius computed at each physical timestep.
230 Stable range for 4-stage Jameson RK: ~0–2.83. Initial 0.5 gives a comfortable margin. */
231 simCtx->ren = 100.0; simCtx->pseudo_cfl = 0.5;
232 simCtx->max_pseudo_cfl = 2.0; simCtx->min_pseudo_cfl = 0.001;
233 simCtx->pseudo_cfl_reduction_factor = 0.75;
234 simCtx->pseudo_cfl_growth_factor = 1.1; // raised from 1.0; controller can now increase CFL
235 simCtx->no_pseudo_cfl_backtrack = PETSC_FALSE;
236 simCtx->mom_ratio_ema_alpha = 0.3; /* moderate smoothing; set to 1.0 to recover original raw-ratio behavior */
237 simCtx->mom_last_converged = PETSC_TRUE;
238 simCtx->mom_last_lambda_max = 0.0; /* populated after first momentum solve */
239 simCtx->mom_nk_monitor_history = PETSC_FALSE;
240 simCtx->ps_ksp_pic_monitor_true_residual = PETSC_FALSE;
241 simCtx->cdisx = 0.0; simCtx->cdisy = 0.0; simCtx->cdisz = 0.0;
242 simCtx->initialConditionMode = IC_MODE_ZERO;
243 simCtx->initialConditionField = IC_FIELD_UCAT;
244 strcpy(simCtx->initialConditionDirectory, "config/initial_condition");
245 simCtx->InitialConstantContra.x = 0.0;
246 simCtx->InitialConstantContra.y = 0.0;
247 simCtx->InitialConstantContra.z = 0.0;
248 simCtx->flowDirection = FLOW_DIR_UNSET;
249 simCtx->icVelocityPhysical = 0.0;
250 simCtx->AnalyticalUniformVelocity.x = 0.0;
251 simCtx->AnalyticalUniformVelocity.y = 0.0;
252 simCtx->AnalyticalUniformVelocity.z = 0.0;
253 simCtx->fieldStatisticsEnabled = PETSC_FALSE;
254 simCtx->fieldStatisticsWindowCount = 0;
255 simCtx->fieldStatisticsWindows = NULL;
256 simCtx->statisticsConsoleOutputFreq = 0;
257 simCtx->fieldStatisticsContinue = PETSC_FALSE;
258 simCtx->solutionConvergenceEnabled = PETSC_TRUE;
259 simCtx->solutionConvergenceMode = SOLUTION_CONVERGENCE_STEADY_DETERMINISTIC;
260 simCtx->solutionConvergencePeriodSteps = 0;
261 simCtx->solutionConvergenceWindowSteps = 0;
262 simCtx->solutionConvergenceSamplesRecorded = 0;
263 simCtx->solutionConvergenceMeanSpeedHistory = NULL;
264 simCtx->solutionConvergenceMeanKEHistory = NULL;
265 simCtx->verificationDiffusivity.enabled = PETSC_FALSE;
266 strcpy(simCtx->verificationDiffusivity.mode, "");
267 strcpy(simCtx->verificationDiffusivity.profile, "");
268 simCtx->verificationDiffusivity.gamma0 = 0.0;
269 simCtx->verificationDiffusivity.slope_x = 0.0;
270
271 // --- Group 6: Physical & Geometric Parameters ---
272 simCtx->NumberOfBodies = 1; simCtx->Flux_in = 1.0; simCtx->angle = 0.0;
273 simCtx->max_angle = -54. * 3.1415926 / 180.;
274 simCtx->CMx_c=0.0; simCtx->CMy_c=0.0; simCtx->CMz_c=0.0;
275 simCtx->wall_roughness_height = 1e-16;
276 simCtx->schmidt_number = 1.0; simCtx->Turbulent_schmidt_number = 0.7;
277
278 // --- Group 7: Grid, Domain, and Boundary Condition Settings ---
279 simCtx->block_number = 1; simCtx->inletprofile = 1;
280 simCtx->grid1d = 0; simCtx->Ogrid = 0;
281 simCtx->i_periodic = 0; simCtx->j_periodic = 0; simCtx->k_periodic = 0;
282 simCtx->blkpbc = 10; simCtx->pseudo_periodic = 0;
283 strcpy(simCtx->grid_file, "config/grid.run");
284 simCtx->generate_grid = PETSC_FALSE;
285 simCtx->da_procs_x = PETSC_DECIDE;
286 simCtx->da_procs_y = PETSC_DECIDE;
287 simCtx->da_procs_z = PETSC_DECIDE;
288 simCtx->grid_rotation_angle = 0.0;
289 simCtx->Croty = 0.0; simCtx->Crotz = 0.0;
290 simCtx->num_bcs_files = 1;
291 ierr = PetscMalloc1(1, &simCtx->bcs_files); CHKERRQ(ierr);
292 ierr = PetscStrallocpy("config/bcs.run", &simCtx->bcs_files[0]); CHKERRQ(ierr);
293 simCtx->FluxInSum = 0.0; simCtx->FluxOutSum = 0.0; simCtx->Fluxsum = 0.0;
294 simCtx->drivingForceMagnitude = 0.0, simCtx->forceScalingFactor = 1.8;
295 simCtx->drivingForceStep = -1;
296 simCtx->targetVolumetricFlux = 0.0;
297 simCtx->drivenFluxTargetLatched = PETSC_FALSE;
298 simCtx->bulkVelocityCorrection = 0.0;
299 simCtx->boundaryVelocityCorrection = 0.0;
300 simCtx->AreaInSum = 0.0; simCtx->AreaOutSum = 0.0;
301 simCtx->U_bc = 0.0; simCtx->ccc = 0;
302 simCtx->ratio = 0.0;
303
304
305 // --- Group 8: Turbulence Modeling (LES/RANS) ---
306 simCtx->les = NO_LES_MODEL; simCtx->rans = 0;
307 simCtx->wallfunction = 0; simCtx->mixed = 0; simCtx->clark = 0;
308 simCtx->dynamic_freq = 1; simCtx->max_cs = 0.5;
309 simCtx->Const_CS = 0.03;
310 simCtx->testfilter_ik = 0; simCtx->testfilter_1d = 0;
311 simCtx->i_homo_filter = 0; simCtx->j_homo_filter = 0; simCtx->k_homo_filter = 0;
312
313 // --- Group 9: Particle / DMSwarm Data & Settings ---
314 simCtx->np = 0; simCtx->readFields = PETSC_FALSE;
315 simCtx->dm_swarm = NULL; simCtx->bboxlist = NULL;
316 simCtx->ParticleInitialization = PARTICLE_INIT_SURFACE_RANDOM;
317 simCtx->interpolationMethod = INTERP_TRILINEAR;
318 strcpy(simCtx->particleRestartMode,"load");
319 simCtx->particlesLostLastStep = 0;
320 simCtx->particlesLostCumulative = 0;
321 simCtx->particlesMigratedLastStep = 0;
322 simCtx->occupiedCellCount = 0;
323 simCtx->particleLoadImbalance = 0.0;
324 simCtx->migrationPassesLastStep = 0;
325 simCtx->searchMetrics.searchAttempts = 0;
326 simCtx->searchMetrics.searchPopulation = 0;
327 simCtx->searchMetrics.searchLocatedCount = 0;
328 simCtx->searchMetrics.searchLostCount = 0;
329 simCtx->searchMetrics.traversalStepsSum = 0;
330 simCtx->searchMetrics.reSearchCount = 0;
331 simCtx->searchMetrics.maxTraversalSteps = 0;
332 simCtx->searchMetrics.maxTraversalFailCount = 0;
333 simCtx->searchMetrics.tieBreakCount = 0;
334 simCtx->searchMetrics.boundaryClampCount = 0;
335 simCtx->searchMetrics.bboxGuessSuccessCount = 0;
336 simCtx->searchMetrics.bboxGuessFallbackCount = 0;
337 simCtx->searchMetrics.maxParticlePassDepth = 0;
338 simCtx->searchMetrics.currentSettlementPass = 0;
339 simCtx->BrownianMotionRNG = NULL;
340 simCtx->C_IEM = 2.0;
341
342 // --- Group 10: Immersed Boundary & FSI Data Object Pointers ---
343 simCtx->ibm = NULL; simCtx->ibmv = NULL; simCtx->fsi = NULL;
344 simCtx->rstart_fsi = PETSC_FALSE; simCtx->duplicate = 0;
345
346 // --- Group 11: Logging and Custom Configuration ---
347 strcpy(simCtx->allowedFile, "config/whitelist.run");
348 simCtx->useCfg = PETSC_FALSE;
349 simCtx->allowedFuncs = NULL;
350 simCtx->nAllowed = 0;
351 simCtx->LoggingFrequency = 10;
352 simCtx->summationRHS = 0.0;
353 simCtx->MaxDiv = 0.0;
354 simCtx->MaxDivFlatArg = 0; simCtx->MaxDivx = 0; simCtx->MaxDivy = 0; simCtx->MaxDivz = 0;
355 strcpy(simCtx->profilingSelectedFuncsFile, "config/profile.run");
356 simCtx->useProfilingSelectedFuncsCfg = PETSC_FALSE;
357 simCtx->profilingSelectedFuncs = NULL;
358 simCtx->nProfilingSelectedFuncs = 0;
359 strcpy(simCtx->profilingTimestepMode, "selected");
360 strcpy(simCtx->profilingTimestepFile, "Profiling_Timestep_Summary.csv");
361 simCtx->profilingFinalSummary = PETSC_TRUE;
362 simCtx->walltimeGuardEnabled = PETSC_FALSE;
363 simCtx->walltimeGuardActive = PETSC_FALSE;
364 simCtx->walltimeGuardWarmupSteps = 10;
365 simCtx->walltimeGuardMultiplier = 2.0;
366 simCtx->walltimeGuardMinSeconds = 60.0;
367 simCtx->walltimeGuardEstimatorAlpha = 0.35;
368 simCtx->walltimeGuardJobStartEpochSeconds = 0.0;
369 simCtx->walltimeGuardLimitSeconds = 0.0;
370 simCtx->walltimeGuardCompletedSteps = 0;
371 simCtx->walltimeGuardWarmupTotalSeconds = 0.0;
372 simCtx->walltimeGuardWarmupAverageSeconds = 0.0;
373 simCtx->walltimeGuardHasEWMA = PETSC_FALSE;
374 simCtx->walltimeGuardEWMASeconds = 0.0;
375 simCtx->walltimeGuardLatestStepSeconds = 0.0;
376 simCtx->runtimeMemoryLogEnabled = PETSC_TRUE;
377 strcpy(simCtx->runtimeMemoryLogFile, "Runtime_Memory.log");
378 simCtx->runtimeMemoryLogStarted = PETSC_FALSE;
379 simCtx->runtimeMemoryLogHasPrevious = PETSC_FALSE;
380 simCtx->runtimeMemoryLogPreviousProcessMB = 0.0;
381 // --- Group 11: Post-Processing Information ---
382 strcpy(simCtx->PostprocessingControlFile, "config/post.run");
383 ierr = PetscNew(&simCtx->pps); CHKERRQ(ierr);
384
385 // === 2. Get MPI Info and Handle Config File =============================
386 // -- Group 1: Parallelism & MPI Information
387 ierr = MPI_Comm_rank(PETSC_COMM_WORLD, &simCtx->rank); CHKERRQ(ierr);
388 ierr = MPI_Comm_size(PETSC_COMM_WORLD, &simCtx->size); CHKERRQ(ierr);
389
390 // First, check if the -control_file argument was provided by the user/script.
391 ierr = PetscOptionsGetString(NULL, NULL, "-control_file", control_filename, sizeof(control_filename), &control_flg); CHKERRQ(ierr);
392
393 // If the flag is NOT present or the filename is empty, abort with a helpful error.
394 if (!control_flg || strlen(control_filename) == 0) {
395 SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG,
396 "\n\n*** MANDATORY ARGUMENT MISSING ***\n"
397 "The -control_file argument was not provided.\n"
398 "This program must be launched with a configuration file.\n"
399 "Example: mpiexec -n 4 ./simulator -control_file /path/to/your/config.control\n"
400 "This is typically handled automatically by the 'picurv' script.\n");
401 }
402
403 // At this point, we have a valid filename. Attempt to load it.
404 LOG(GLOBAL, LOG_INFO, "Loading mandatory configuration from: %s\n", control_filename);
405 ierr = PetscOptionsInsertFile(PETSC_COMM_WORLD, NULL, control_filename, PETSC_FALSE);
406 if (ierr == PETSC_ERR_FILE_OPEN) {
407 SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_FILE_OPEN, "The specified control file was not found or could not be opened: %s", control_filename);
408 }
409 CHKERRQ(ierr);
410
411 {
412 PetscBool legacy_averaging = PETSC_FALSE;
413 ierr = PetscOptionsHasName(NULL, NULL, "-averaging", &legacy_averaging); CHKERRQ(ierr);
414 PetscCheck(!legacy_averaging, PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG,
415 "Legacy -averaging was removed. Use instantaneous output and offline "
416 "postprocessing until the replacement field-statistics pipeline is available.");
417 }
418
419 // === 3. A Configure Logging System ========================================
420 // This logic determines the logging configuration and STORES it in simCtx for
421 // later reference and cleanup.
422 ierr = PetscOptionsGetString(NULL, NULL, "-whitelist_config_file", simCtx->allowedFile, PETSC_MAX_PATH_LEN, &simCtx->useCfg); CHKERRQ(ierr);
423
424 if (simCtx->useCfg) {
425 ierr = LoadAllowedFunctionsFromFile(simCtx->allowedFile, &simCtx->allowedFuncs, &simCtx->nAllowed);
426 if (ierr) {
427 // Use direct PetscPrintf as logging system isn't fully active yet.
428 PetscPrintf(PETSC_COMM_SELF, "[%s] WARNING: Failed to load allowed functions from '%s'. Falling back to default list.\n", __func__, simCtx->allowedFile);
429 simCtx->useCfg = PETSC_FALSE; // Mark as failed.
430 ierr = 0; // Clear the error to allow fallback.
431 } else if (simCtx->nAllowed == 0) {
432 SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG,
433 "Whitelist config file '%s' is empty. Omit -whitelist_config_file to use the default allow-list, or list at least one function.",
434 simCtx->allowedFile);
435 }
436 }
437 if (!simCtx->useCfg) {
438 // Fallback to default logging functions if no file was used or if loading failed.
439 simCtx->nAllowed = 2;
440 ierr = PetscMalloc1(simCtx->nAllowed, &simCtx->allowedFuncs); CHKERRQ(ierr);
441 ierr = PetscStrallocpy("main", &simCtx->allowedFuncs[0]); CHKERRQ(ierr);
442 ierr = PetscStrallocpy("CreateSimulationContext", &simCtx->allowedFuncs[1]); CHKERRQ(ierr);
443 }
444
445 // Activate the configuration by passing it to the logging module's setup function.
446 set_allowed_functions((const char**)simCtx->allowedFuncs, (size_t)simCtx->nAllowed);
447
448 // Now that the logger is configured, we can use it.
449 LOG_ALLOW_SYNC(LOCAL, LOG_INFO, "Context created. Initializing on rank %d of %d.\n", simCtx->rank, simCtx->size);
450 print_log_level(); // This will now correctly reflect the LOG_LEVEL environment variable.
451
452 // === 3.B Configure Profiling System ========================================
453 ierr = PetscOptionsGetString(NULL, NULL, "-profiling_timestep_mode", simCtx->profilingTimestepMode, sizeof(simCtx->profilingTimestepMode), NULL); CHKERRQ(ierr);
454 ierr = PetscOptionsGetString(NULL, NULL, "-profiling_timestep_file", simCtx->profilingTimestepFile, PETSC_MAX_PATH_LEN, NULL); CHKERRQ(ierr);
455 ierr = PetscOptionsGetBool(NULL, NULL, "-profiling_final_summary", &simCtx->profilingFinalSummary, NULL); CHKERRQ(ierr);
456 if (strcmp(simCtx->profilingTimestepMode, "off") != 0 &&
457 strcmp(simCtx->profilingTimestepMode, "selected") != 0 &&
458 strcmp(simCtx->profilingTimestepMode, "all") != 0) {
459 PetscPrintf(PETSC_COMM_SELF, "[%s] WARNING: Unknown profiling timestep mode '%s'. Falling back to 'selected'.\n", __func__, simCtx->profilingTimestepMode);
460 strcpy(simCtx->profilingTimestepMode, "selected");
461 }
462
463 if (strcmp(simCtx->profilingTimestepMode, "selected") == 0) {
464 ierr = PetscOptionsGetString(NULL, NULL, "-profile_config_file", simCtx->profilingSelectedFuncsFile, PETSC_MAX_PATH_LEN, &simCtx->useProfilingSelectedFuncsCfg); CHKERRQ(ierr);
465 if (simCtx->useProfilingSelectedFuncsCfg) {
466 ierr = LoadAllowedFunctionsFromFile(simCtx->profilingSelectedFuncsFile, &simCtx->profilingSelectedFuncs, &simCtx->nProfilingSelectedFuncs);
467 if (ierr) {
468 PetscPrintf(PETSC_COMM_SELF, "[%s] WARNING: Failed to load selected profiling functions from '%s'. Falling back to default list.\n", __func__, simCtx->profilingSelectedFuncsFile);
469 simCtx->useProfilingSelectedFuncsCfg = PETSC_FALSE;
470 ierr = 0;
471 }
472 }
473 if (!simCtx->useProfilingSelectedFuncsCfg) {
474 // Fallback to a hardcoded default list if no file was provided or loading failed.
475 simCtx->nProfilingSelectedFuncs = 4;
476 ierr = PetscMalloc1(simCtx->nProfilingSelectedFuncs, &simCtx->profilingSelectedFuncs); CHKERRQ(ierr);
477 ierr = PetscStrallocpy("FlowSolver", &simCtx->profilingSelectedFuncs[0]); CHKERRQ(ierr);
478 ierr = PetscStrallocpy("AdvanceSimulation", &simCtx->profilingSelectedFuncs[1]); CHKERRQ(ierr);
479 ierr = PetscStrallocpy("LocateAllParticlesInGrid", &simCtx->profilingSelectedFuncs[2]); CHKERRQ(ierr);
480 ierr = PetscStrallocpy("InterpolateAllFieldsToSwarm", &simCtx->profilingSelectedFuncs[3]); CHKERRQ(ierr);
481 }
482 }
483
484 // Initialize the profiling system with the current updated simulation context.
485 ierr = ProfilingInitialize(simCtx); CHKERRQ(ierr);
486
487 // === 4. Parse All Command Line Options ==================================
488 LOG_ALLOW(GLOBAL, LOG_INFO, "Parsing command-line options...\n");
489
490 // --- Group 2
491 LOG_ALLOW(GLOBAL,LOG_DEBUG, "Parsing Group 2: Simulation Control,Time and I/O.\n");
492 // Read the physical time to start from.
493 // The default is already 0.0, so this will only be non-zero if the user provides it.
494 ierr = PetscOptionsGetInt(NULL, NULL, "-start_step", &simCtx->StartStep, NULL); CHKERRQ(ierr);
495 ierr = PetscOptionsGetInt(NULL,NULL, "-totalsteps", &simCtx->StepsToRun, NULL); CHKERRQ(ierr);
496 ierr = PetscOptionsGetBool(NULL, NULL, "-only_setup", &simCtx->OnlySetup, NULL); CHKERRQ(ierr);
497 ierr = PetscOptionsGetBool(NULL, NULL, "-continue_mode", &simCtx->continueMode, NULL); CHKERRQ(ierr);
498 /* Resuming in the same run directory continues accumulated statistics by
499 * default; branching with --restart-from must opt in, because the branch may
500 * follow a different physical trajectory than the samples already collected. */
501 simCtx->fieldStatisticsContinue = simCtx->continueMode;
502 ierr = PetscOptionsGetReal(NULL, NULL, "-dt", &simCtx->dt, NULL); CHKERRQ(ierr);
503 ierr = PetscOptionsGetInt(NULL, NULL, "-tio", &simCtx->tiout, NULL); CHKERRQ(ierr);
504 ierr = PetscOptionsGetInt(NULL, NULL, "-particle_console_output_freq", &simCtx->particleConsoleOutputFreq, &particle_console_output_freq_flg); CHKERRQ(ierr);
505 if (!particle_console_output_freq_flg) {
506 simCtx->particleConsoleOutputFreq = simCtx->tiout;
507 }
508 ierr = PetscOptionsGetString(NULL,NULL,"-euler_field_source",simCtx->eulerianSource,sizeof(simCtx->eulerianSource),NULL);CHKERRQ(ierr);
509 ierr = PetscOptionsGetString(NULL,NULL,"-output_dir",simCtx->output_dir,sizeof(simCtx->output_dir),NULL);CHKERRQ(ierr);
510 ierr = PetscOptionsGetString(NULL,NULL,"-restart_dir",simCtx->restart_dir,sizeof(simCtx->restart_dir),NULL);CHKERRQ(ierr);
511 ierr = PetscOptionsGetString(NULL,NULL,"-log_dir",simCtx->log_dir,sizeof(simCtx->log_dir),NULL);CHKERRQ(ierr);
512 ierr = PetscOptionsGetBool(NULL, NULL, "-walltime_guard_enabled", &simCtx->walltimeGuardEnabled, NULL); CHKERRQ(ierr);
513 ierr = PetscOptionsGetInt(NULL, NULL, "-walltime_guard_warmup_steps", &simCtx->walltimeGuardWarmupSteps, NULL); CHKERRQ(ierr);
514 ierr = PetscOptionsGetReal(NULL, NULL, "-walltime_guard_multiplier", &simCtx->walltimeGuardMultiplier, NULL); CHKERRQ(ierr);
515 ierr = PetscOptionsGetBool(NULL, NULL, "-runtime_memory_log_enabled", &simCtx->runtimeMemoryLogEnabled, NULL); CHKERRQ(ierr);
516 ierr = PetscOptionsGetString(NULL, NULL, "-runtime_memory_log_file", simCtx->runtimeMemoryLogFile, PETSC_MAX_PATH_LEN, NULL); CHKERRQ(ierr);
517 ierr = PetscOptionsGetReal(NULL, NULL, "-walltime_guard_min_seconds", &simCtx->walltimeGuardMinSeconds, NULL); CHKERRQ(ierr);
518 ierr = PetscOptionsGetReal(NULL, NULL, "-walltime_guard_estimator_alpha", &simCtx->walltimeGuardEstimatorAlpha, NULL); CHKERRQ(ierr);
519
520 if (simCtx->walltimeGuardWarmupSteps <= 0) {
521 SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG, "Invalid value for -walltime_guard_warmup_steps: %d. Must be > 0.", simCtx->walltimeGuardWarmupSteps);
522 }
523 if (simCtx->walltimeGuardMultiplier <= 0.0 || simCtx->walltimeGuardMultiplier > 5.0) {
524 SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG, "Invalid value for -walltime_guard_multiplier: %.6f. Must be in (0, 5].", (double)simCtx->walltimeGuardMultiplier);
525 }
526 if (simCtx->walltimeGuardMinSeconds <= 0.0) {
527 SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG, "Invalid value for -walltime_guard_min_seconds: %.6f. Must be > 0.", (double)simCtx->walltimeGuardMinSeconds);
528 }
529 if (simCtx->walltimeGuardEstimatorAlpha <= 0.0 || simCtx->walltimeGuardEstimatorAlpha > 1.0) {
530 SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG, "Invalid value for -walltime_guard_estimator_alpha: %.6f. Must be in (0, 1].", (double)simCtx->walltimeGuardEstimatorAlpha);
531 }
532
533 if(strcmp(simCtx->eulerianSource,"solve")!= 0 && strcmp(simCtx->eulerianSource,"load") != 0 && strcmp(simCtx->eulerianSource,"analytical")!=0){
534 SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"Invalid value for -euler_field_source. Must be 'load','analytical' or 'solve'. You provided '%s'.",simCtx->eulerianSource);
535 }
536 if (simCtx->walltimeGuardEnabled) {
537 const char *job_start_env = getenv("PICURV_JOB_START_EPOCH");
538 const char *limit_env = getenv("PICURV_WALLTIME_LIMIT_SECONDS");
539 PetscBool job_start_ok = RuntimeWalltimeGuardParsePositiveSeconds(job_start_env, &simCtx->walltimeGuardJobStartEpochSeconds);
540 PetscBool limit_ok = RuntimeWalltimeGuardParsePositiveSeconds(limit_env, &simCtx->walltimeGuardLimitSeconds);
541
542 if (!job_start_ok || !limit_ok) {
543 simCtx->walltimeGuardActive = PETSC_FALSE;
544 simCtx->walltimeGuardJobStartEpochSeconds = 0.0;
545 simCtx->walltimeGuardLimitSeconds = 0.0;
546 LOG_ALLOW(
547 GLOBAL,
548 LOG_WARNING,
549 "Runtime walltime guard enabled but %s/%s are missing or invalid. Falling back to external shutdown signals only.\n",
550 "PICURV_JOB_START_EPOCH",
551 "PICURV_WALLTIME_LIMIT_SECONDS"
552 );
553 } else {
554 simCtx->walltimeGuardActive = PETSC_TRUE;
555 }
556 }
557
558 // --- Group 3
559 LOG_ALLOW(GLOBAL,LOG_DEBUG, "Parsing Group 3: High-Level Physics & Model Selection Flags\n");
560 ierr = PetscOptionsGetInt(NULL, NULL, "-imm", &simCtx->immersed, NULL); CHKERRQ(ierr);
561 ierr = PetscOptionsGetInt(NULL, NULL, "-fsi", &simCtx->movefsi, NULL); CHKERRQ(ierr);
562 ierr = PetscOptionsGetInt(NULL, NULL, "-rfsi", &simCtx->rotatefsi, NULL); CHKERRQ(ierr);
563 ierr = PetscOptionsGetInt(NULL, NULL, "-sediment", &simCtx->sediment, NULL); CHKERRQ(ierr);
564 ierr = PetscOptionsGetInt(NULL, NULL, "-rheology", &simCtx->rheology, NULL); CHKERRQ(ierr);
565 ierr = PetscOptionsGetInt(NULL, NULL, "-inv", &simCtx->invicid, NULL); CHKERRQ(ierr);
566 ierr = PetscOptionsGetInt(NULL, NULL, "-TwoD", &simCtx->TwoD, NULL); CHKERRQ(ierr);
567 ierr = PetscOptionsGetInt(NULL, NULL, "-thin", &simCtx->thin, NULL); CHKERRQ(ierr);
568 ierr = PetscOptionsGetInt(NULL, NULL, "-mframe", &simCtx->moveframe, NULL); CHKERRQ(ierr);
569 ierr = PetscOptionsGetInt(NULL, NULL, "-rframe", &simCtx->rotateframe, NULL); CHKERRQ(ierr);
570 ierr = PetscOptionsGetInt(NULL, NULL, "-blk", &simCtx->blank, NULL); CHKERRQ(ierr);
571 ierr = PetscOptionsGetInt(NULL, NULL, "-dgf_z", &simCtx->dgf_z, NULL); CHKERRQ(ierr);
572 ierr = PetscOptionsGetInt(NULL, NULL, "-dgf_y", &simCtx->dgf_y, NULL); CHKERRQ(ierr);
573 ierr = PetscOptionsGetInt(NULL, NULL, "-dgf_x", &simCtx->dgf_x, NULL); CHKERRQ(ierr);
574 ierr = PetscOptionsGetInt(NULL, NULL, "-dgf_az", &simCtx->dgf_az, NULL); CHKERRQ(ierr);
575 ierr = PetscOptionsGetInt(NULL, NULL, "-dgf_ay", &simCtx->dgf_ay, NULL); CHKERRQ(ierr);
576 ierr = PetscOptionsGetInt(NULL, NULL, "-dgf_ax", &simCtx->dgf_ax, NULL); CHKERRQ(ierr);
577 ierr = PetscOptionsGetString(NULL,NULL,"-analytical_type",simCtx->AnalyticalSolutionType,sizeof(simCtx->AnalyticalSolutionType),NULL);CHKERRQ(ierr);
578
579 // --- Group 4
580 LOG_ALLOW(GLOBAL,LOG_DEBUG, "Parsing Group 4: Specific Simulation Case Flags \n");
581 ierr = PetscOptionsGetInt(NULL, NULL, "-cop", &simCtx->cop, NULL); CHKERRQ(ierr);
582 ierr = PetscOptionsGetInt(NULL, NULL, "-fish", &simCtx->fish, NULL); CHKERRQ(ierr);
583 ierr = PetscOptionsGetInt(NULL, NULL, "-pizza", &simCtx->pizza, NULL); CHKERRQ(ierr);
584 ierr = PetscOptionsGetInt(NULL, NULL, "-turbine", &simCtx->turbine, NULL); CHKERRQ(ierr);
585 ierr = PetscOptionsGetInt(NULL, NULL, "-fishcyl", &simCtx->fishcyl, NULL); CHKERRQ(ierr);
586 ierr = PetscOptionsGetInt(NULL, NULL, "-eel", &simCtx->eel, NULL); CHKERRQ(ierr);
587 ierr = PetscOptionsGetInt(NULL, NULL, "-cstart", &simCtx->fish_c, NULL); CHKERRQ(ierr);
588 ierr = PetscOptionsGetInt(NULL, NULL, "-wing", &simCtx->wing, NULL); CHKERRQ(ierr);
589 ierr = PetscOptionsGetInt(NULL, NULL, "-mhv", &simCtx->MHV, NULL); CHKERRQ(ierr);
590 ierr = PetscOptionsGetInt(NULL, NULL, "-hydro", &simCtx->hydro, NULL); CHKERRQ(ierr);
591 ierr = PetscOptionsGetInt(NULL, NULL, "-lv", &simCtx->LV, NULL); CHKERRQ(ierr);
592 ierr = PetscOptionsGetInt(NULL, NULL, "-Pipe", &simCtx->Pipe, NULL); CHKERRQ(ierr);
593 ierr = PetscOptionsGetInt(NULL, NULL, "-Turbulent_Channel_z", &simCtx->channelz, NULL); CHKERRQ(ierr);
594 ierr = PetscOptionsGetReal(NULL,NULL,"-driven_flow_initial_force",&simCtx->drivingForceMagnitude,NULL);CHKERRQ(ierr);
595 ierr = PetscOptionsGetReal(NULL,NULL,"-driven_flow_scaling_factor",&simCtx->forceScalingFactor,NULL);CHKERRQ(ierr);
596 // --- Group 5
597 LOG_ALLOW(GLOBAL,LOG_DEBUG, "Parsing Group 5: Solver & Numerics Parameters \n");
598 char mom_solver_type_char[PETSC_MAX_PATH_LEN];
599 char solution_convergence_mode_char[PETSC_MAX_PATH_LEN];
600 PetscBool mom_solver_type_flg = PETSC_FALSE;
601 PetscBool solution_convergence_mode_flg = PETSC_FALSE;
602 ierr = PetscOptionsGetString(NULL, NULL, "-mom_solver_type", mom_solver_type_char, sizeof(mom_solver_type_char), &mom_solver_type_flg); CHKERRQ(ierr);
603 ierr = PetscOptionsGetInt(NULL, NULL, "-mom_max_pseudo_steps", &simCtx->mom_max_pseudo_steps, NULL); CHKERRQ(ierr);
604 ierr = PetscOptionsGetReal(NULL, NULL, "-mom_atol", &simCtx->mom_atol, NULL); CHKERRQ(ierr);
605 ierr = PetscOptionsGetReal(NULL, NULL, "-mom_rtol", &simCtx->mom_rtol, NULL); CHKERRQ(ierr);
606 ierr = PetscOptionsGetReal(NULL, NULL, "-mom_resid_atol", &simCtx->mom_resid_atol, NULL); CHKERRQ(ierr);
607 ierr = PetscOptionsGetReal(NULL, NULL, "-mom_resid_rtol", &simCtx->mom_resid_rtol, NULL); CHKERRQ(ierr);
608 ierr = PetscOptionsGetReal(NULL, NULL, "-imp_stol", &simCtx->imp_stol, NULL); CHKERRQ(ierr);
609 ierr = PetscOptionsGetInt(NULL, NULL, "-central", &simCtx->central, NULL); CHKERRQ(ierr);
610 ierr = PetscOptionsGetString(NULL, NULL, "-solution_convergence_mode",
611 solution_convergence_mode_char, sizeof(solution_convergence_mode_char),
612 &solution_convergence_mode_flg); CHKERRQ(ierr);
613 ierr = PetscOptionsGetBool(NULL, NULL, "-solution_convergence_enabled", &simCtx->solutionConvergenceEnabled, NULL); CHKERRQ(ierr);
614 ierr = PetscOptionsGetInt(NULL, NULL, "-solution_convergence_period_steps", &simCtx->solutionConvergencePeriodSteps, NULL); CHKERRQ(ierr);
615 ierr = PetscOptionsGetInt(NULL, NULL, "-solution_convergence_window_steps", &simCtx->solutionConvergenceWindowSteps, NULL); CHKERRQ(ierr);
616 /* Field statistics resolve here rather than inline, because a variable-arity
617 * window list needs its own parse site; see statistics_config.c. It must
618 * precede CreateAndInitializeAllVectors, which sizes the per-window
619 * accumulators from the window count resolved here. */
620 ierr = ParseFieldStatisticsConfig(simCtx); CHKERRQ(ierr);
621
622 // Keep parser acceptance aligned with the enum and FlowSolver dispatch.
623 if (mom_solver_type_flg) {
624 if(strcmp(mom_solver_type_char, "DUALTIME_PICARD_JAMESON_RK") == 0 ||
625 strcmp(mom_solver_type_char, "DUALTIME_PICARD_RK4") == 0) {
626 simCtx->mom_solver_type = MOMENTUM_SOLVER_DUALTIME_PICARD_JAMESON_RK;
627 } else if (strcmp(mom_solver_type_char, "EXPLICIT_RK") == 0) {
628 simCtx->mom_solver_type = MOMENTUM_SOLVER_EXPLICIT_RK;
629 } else if (strcmp(mom_solver_type_char, "newton_krylov") == 0) {
630 simCtx->mom_solver_type = MOMENTUM_SOLVER_NEWTON_KRYLOV;
631 } else {
632 LOG(GLOBAL, LOG_ERROR, "Invalid value for -mom_solver_type: '%s'. Valid options are: 'DUALTIME_PICARD_JAMESON_RK', 'EXPLICIT_RK', 'newton_krylov'.\n", mom_solver_type_char);
633 SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG, "Invalid value for -mom_solver_type: '%s'.", mom_solver_type_char);
634 }
635 }
636
637 if (solution_convergence_mode_flg) {
638 if (strcmp(solution_convergence_mode_char, "STEADY_DETERMINISTIC") == 0) {
639 simCtx->solutionConvergenceMode = SOLUTION_CONVERGENCE_STEADY_DETERMINISTIC;
640 } else if (strcmp(solution_convergence_mode_char, "PERIODIC_DETERMINISTIC") == 0) {
641 simCtx->solutionConvergenceMode = SOLUTION_CONVERGENCE_PERIODIC_DETERMINISTIC;
642 } else if (strcmp(solution_convergence_mode_char, "STATISTICAL_STEADY") == 0) {
643 simCtx->solutionConvergenceMode = SOLUTION_CONVERGENCE_STATISTICAL_STEADY;
644 } else if (strcmp(solution_convergence_mode_char, "TRANSIENT") == 0) {
645 simCtx->solutionConvergenceMode = SOLUTION_CONVERGENCE_TRANSIENT;
646 } else {
647 SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG,
648 "Invalid value for -solution_convergence_mode: '%s'.", solution_convergence_mode_char);
649 }
650 }
651
652 if (simCtx->solutionConvergenceMode == SOLUTION_CONVERGENCE_PERIODIC_DETERMINISTIC &&
653 simCtx->solutionConvergencePeriodSteps <= 0) {
654 SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG,
655 "solution convergence mode PERIODIC_DETERMINISTIC requires -solution_convergence_period_steps > 0.");
656 }
657 if (simCtx->solutionConvergenceMode == SOLUTION_CONVERGENCE_STATISTICAL_STEADY &&
658 simCtx->solutionConvergenceWindowSteps <= 0) {
659 SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG,
660 "solution convergence mode STATISTICAL_STEADY requires -solution_convergence_window_steps > 0.");
661 }
662
663 // --- Multigrid Options ---
664 ierr = PetscOptionsGetInt(NULL, NULL, "-mg_level", &simCtx->mglevels, NULL); CHKERRQ(ierr);
665 ierr = PetscOptionsGetInt(NULL, NULL, "-mg_max_it", &simCtx->mg_MAX_IT, NULL); CHKERRQ(ierr);
666 ierr = PetscOptionsGetInt(NULL, NULL, "-mg_idx", &simCtx->mg_idx, NULL); CHKERRQ(ierr);
667 ierr = PetscOptionsGetInt(NULL, NULL, "-mg_pre_it", &simCtx->mg_preItr, NULL); CHKERRQ(ierr);
668 ierr = PetscOptionsGetInt(NULL, NULL, "-mg_post_it", &simCtx->mg_poItr, NULL); CHKERRQ(ierr);
669
670 // --- Other Solver Options ---
671 ierr = PetscOptionsGetInt(NULL, NULL, "-poisson", &simCtx->poisson, NULL); CHKERRQ(ierr);
672 ierr = PetscOptionsGetReal(NULL, NULL, "-poisson_tol", &simCtx->poisson_tol, NULL); CHKERRQ(ierr);
673 ierr = PetscOptionsGetInt(NULL, NULL, "-str", &simCtx->STRONG_COUPLING, NULL); CHKERRQ(ierr);
674 ierr = PetscOptionsGetReal(NULL, NULL, "-ren", &simCtx->ren, NULL); CHKERRQ(ierr);
675 ierr = PetscOptionsGetReal(NULL, NULL, "-pseudo_cfl", &simCtx->pseudo_cfl, NULL); CHKERRQ(ierr);
676 ierr = PetscOptionsGetReal(NULL, NULL, "-max_pseudo_cfl", &simCtx->max_pseudo_cfl, NULL); CHKERRQ(ierr);
677 ierr = PetscOptionsGetReal(NULL, NULL, "-min_pseudo_cfl", &simCtx->min_pseudo_cfl, NULL); CHKERRQ(ierr);
678 ierr = PetscOptionsGetReal(NULL, NULL, "-pseudo_cfl_reduction_factor", &simCtx->pseudo_cfl_reduction_factor, NULL); CHKERRQ(ierr);
679 ierr = PetscOptionsGetReal(NULL, NULL, "-pseudo_cfl_growth_factor", &simCtx->pseudo_cfl_growth_factor, NULL); CHKERRQ(ierr);
680 // Read the deprecated RK4 spelling first so the canonical Jameson option wins if both are present.
681 ierr = PetscOptionsGetReal(NULL,NULL, "-mom_dt_rk4_residual_norm_noise_allowance_factor",&simCtx->mom_dt_jameson_residual_norm_noise_allowance_factor,NULL);CHKERRQ(ierr);
682 ierr = PetscOptionsGetReal(NULL,NULL, "-mom_dt_jameson_residual_norm_noise_allowance_factor",&simCtx->mom_dt_jameson_residual_norm_noise_allowance_factor,NULL);CHKERRQ(ierr);
683 ierr = PetscOptionsGetBool(NULL, NULL, "-no_pseudo_cfl_backtrack", &simCtx->no_pseudo_cfl_backtrack, NULL); CHKERRQ(ierr);
684 ierr = PetscOptionsGetReal(NULL, NULL, "-mom_ratio_ema_alpha", &simCtx->mom_ratio_ema_alpha, NULL); CHKERRQ(ierr);
685 if (simCtx->min_pseudo_cfl <= 0.0 ||
686 simCtx->pseudo_cfl < simCtx->min_pseudo_cfl ||
687 simCtx->pseudo_cfl > simCtx->max_pseudo_cfl) {
688 SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE,
689 "Pseudo-CFL controls require 0 < minimum <= initial <= maximum.");
690 }
691 if (simCtx->pseudo_cfl_growth_factor < 1.0 ||
692 simCtx->pseudo_cfl_reduction_factor <= 0.0 ||
693 simCtx->pseudo_cfl_reduction_factor >= 1.0 ||
694 simCtx->mom_dt_jameson_residual_norm_noise_allowance_factor < 1.0) {
695 SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE,
696 "Pseudo-CFL controls require growth_factor >= 1, 0 < reduction_factor < 1, and noise allowance >= 1.");
697 }
698 if (simCtx->mom_ratio_ema_alpha < 0.0 || simCtx->mom_ratio_ema_alpha > 1.0) {
699 SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE,
700 "-mom_ratio_ema_alpha must be in [0, 1].");
701 }
702 ierr = PetscOptionsHasName(NULL, NULL, "-ps_ksp_pic_monitor_true_residual", &simCtx->ps_ksp_pic_monitor_true_residual); CHKERRQ(ierr);
703 ierr = PetscOptionsGetBool(NULL, NULL, "-mom_nk_pic_monitor", &simCtx->mom_nk_monitor_history, NULL); CHKERRQ(ierr);
704 {
705 PetscInt ic_mode = (PetscInt)simCtx->initialConditionMode;
706 PetscInt ic_field = (PetscInt)simCtx->initialConditionField;
707 ierr = PetscOptionsGetInt(NULL, NULL, "-finit", &ic_mode, NULL); CHKERRQ(ierr);
708 ierr = PetscOptionsGetInt(NULL, NULL, "-ic_field", &ic_field, NULL); CHKERRQ(ierr);
709 simCtx->initialConditionMode = (InitialConditionMode)ic_mode;
710 simCtx->initialConditionField = (InitialConditionField)ic_field;
711 }
712 ierr = PetscOptionsGetString(NULL, NULL, "-ic_dir", simCtx->initialConditionDirectory,
713 sizeof(simCtx->initialConditionDirectory), NULL); CHKERRQ(ierr);
714 if (simCtx->initialConditionMode < IC_MODE_ZERO || simCtx->initialConditionMode > IC_MODE_FILE) {
715 SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE,
716 "Invalid value for -finit. Expected an initial-condition mode in [0,4], got %d.",
717 simCtx->initialConditionMode);
718 }
719 if (simCtx->initialConditionField < IC_FIELD_UCAT || simCtx->initialConditionField > IC_FIELD_UCONT) {
720 SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE,
721 "Invalid value for -ic_field. Expected 0 (Ucat) or 1 (Ucont), got %d.",
722 simCtx->initialConditionField);
723 }
724 ierr = PetscOptionsGetReal(NULL, NULL, "-ucont_x", &simCtx->InitialConstantContra.x, NULL); CHKERRQ(ierr);
725 ierr = PetscOptionsGetReal(NULL, NULL, "-ucont_y", &simCtx->InitialConstantContra.y, NULL); CHKERRQ(ierr);
726 ierr = PetscOptionsGetReal(NULL, NULL, "-ucont_z", &simCtx->InitialConstantContra.z, NULL); CHKERRQ(ierr);
727 {
728 PetscInt fd_int = (PetscInt)FLOW_DIR_UNSET;
729 PetscBool fd_set = PETSC_FALSE;
730 ierr = PetscOptionsGetInt(NULL, NULL, "-flow_direction", &fd_int, &fd_set); CHKERRQ(ierr);
731 if (fd_set) simCtx->flowDirection = (FlowDirection)fd_int;
732 }
733 ierr = PetscOptionsGetReal(NULL, NULL, "-ic_velocity_physical", &simCtx->icVelocityPhysical, NULL); CHKERRQ(ierr);
734 ierr = PetscOptionsGetReal(NULL, NULL, "-analytical_uniform_u", &simCtx->AnalyticalUniformVelocity.x, NULL); CHKERRQ(ierr);
735 ierr = PetscOptionsGetReal(NULL, NULL, "-analytical_uniform_v", &simCtx->AnalyticalUniformVelocity.y, NULL); CHKERRQ(ierr);
736 ierr = PetscOptionsGetReal(NULL, NULL, "-analytical_uniform_w", &simCtx->AnalyticalUniformVelocity.z, NULL); CHKERRQ(ierr);
737 PetscBool verification_scalar_value_set = PETSC_FALSE;
738 PetscBool verification_scalar_phi0_set = PETSC_FALSE;
739 PetscBool verification_scalar_slope_x_set = PETSC_FALSE;
740 PetscBool verification_scalar_amplitude_set = PETSC_FALSE;
741 PetscBool verification_scalar_kx_set = PETSC_FALSE;
742 PetscBool verification_scalar_ky_set = PETSC_FALSE;
743 PetscBool verification_scalar_kz_set = PETSC_FALSE;
744 ierr = PetscOptionsGetString(NULL, NULL, "-verification_diffusivity_mode",
745 simCtx->verificationDiffusivity.mode,
746 sizeof(simCtx->verificationDiffusivity.mode), NULL); CHKERRQ(ierr);
747 ierr = PetscOptionsGetString(NULL, NULL, "-verification_diffusivity_profile",
748 simCtx->verificationDiffusivity.profile,
749 sizeof(simCtx->verificationDiffusivity.profile), NULL); CHKERRQ(ierr);
750 ierr = PetscOptionsGetReal(NULL, NULL, "-verification_diffusivity_gamma0",
751 &simCtx->verificationDiffusivity.gamma0, NULL); CHKERRQ(ierr);
752 ierr = PetscOptionsGetReal(NULL, NULL, "-verification_diffusivity_slope_x",
753 &simCtx->verificationDiffusivity.slope_x, NULL); CHKERRQ(ierr);
754 ierr = PetscOptionsGetString(NULL, NULL, "-verification_scalar_mode",
755 simCtx->verificationScalar.mode,
756 sizeof(simCtx->verificationScalar.mode), NULL); CHKERRQ(ierr);
757 ierr = PetscOptionsGetString(NULL, NULL, "-verification_scalar_profile",
758 simCtx->verificationScalar.profile,
759 sizeof(simCtx->verificationScalar.profile), NULL); CHKERRQ(ierr);
760 ierr = PetscOptionsGetReal(NULL, NULL, "-verification_scalar_value",
761 &simCtx->verificationScalar.value, &verification_scalar_value_set); CHKERRQ(ierr);
762 ierr = PetscOptionsGetReal(NULL, NULL, "-verification_scalar_phi0",
763 &simCtx->verificationScalar.phi0, &verification_scalar_phi0_set); CHKERRQ(ierr);
764 ierr = PetscOptionsGetReal(NULL, NULL, "-verification_scalar_slope_x",
765 &simCtx->verificationScalar.slope_x, &verification_scalar_slope_x_set); CHKERRQ(ierr);
766 ierr = PetscOptionsGetReal(NULL, NULL, "-verification_scalar_amplitude",
767 &simCtx->verificationScalar.amplitude, &verification_scalar_amplitude_set); CHKERRQ(ierr);
768 ierr = PetscOptionsGetReal(NULL, NULL, "-verification_scalar_kx",
769 &simCtx->verificationScalar.kx, &verification_scalar_kx_set); CHKERRQ(ierr);
770 ierr = PetscOptionsGetReal(NULL, NULL, "-verification_scalar_ky",
771 &simCtx->verificationScalar.ky, &verification_scalar_ky_set); CHKERRQ(ierr);
772 ierr = PetscOptionsGetReal(NULL, NULL, "-verification_scalar_kz",
773 &simCtx->verificationScalar.kz, &verification_scalar_kz_set); CHKERRQ(ierr);
774 simCtx->verificationDiffusivity.enabled =
775 (PetscBool)(simCtx->verificationDiffusivity.mode[0] != '\0' ||
776 simCtx->verificationDiffusivity.profile[0] != '\0');
777 simCtx->verificationScalar.enabled =
778 (PetscBool)(simCtx->verificationScalar.mode[0] != '\0' ||
779 simCtx->verificationScalar.profile[0] != '\0');
780 if (simCtx->verificationDiffusivity.enabled) {
781 if (strcmp(simCtx->eulerianSource, "analytical") != 0) {
782 SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONGSTATE,
783 "verification diffusivity overrides require -euler_field_source \"analytical\".");
784 }
785 if (strcmp(simCtx->verificationDiffusivity.mode, "analytical") != 0) {
786 SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG,
787 "Unsupported -verification_diffusivity_mode '%s'. Only 'analytical' is supported.",
788 simCtx->verificationDiffusivity.mode);
789 }
790 if (strcmp(simCtx->verificationDiffusivity.profile, "LINEAR_X") != 0) {
791 SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG,
792 "Unsupported -verification_diffusivity_profile '%s'. Only 'LINEAR_X' is supported.",
793 simCtx->verificationDiffusivity.profile);
794 }
795 }
796 if (simCtx->verificationScalar.enabled) {
797 if (strcmp(simCtx->eulerianSource, "analytical") != 0) {
798 SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONGSTATE,
799 "verification scalar overrides require -euler_field_source \"analytical\".");
800 }
801 if (strcmp(simCtx->verificationScalar.mode, "analytical") != 0) {
802 SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG,
803 "Unsupported -verification_scalar_mode '%s'. Only 'analytical' is supported.",
804 simCtx->verificationScalar.mode);
805 }
806 if (strcmp(simCtx->verificationScalar.profile, "CONSTANT") == 0) {
807 if (!verification_scalar_value_set) {
808 SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG,
809 "verification scalar profile CONSTANT requires -verification_scalar_value.");
810 }
811 } else if (strcmp(simCtx->verificationScalar.profile, "LINEAR_X") == 0) {
812 if (!verification_scalar_phi0_set || !verification_scalar_slope_x_set) {
813 SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG,
814 "verification scalar profile LINEAR_X requires -verification_scalar_phi0 and -verification_scalar_slope_x.");
815 }
816 } else if (strcmp(simCtx->verificationScalar.profile, "SIN_PRODUCT") == 0) {
817 if (!verification_scalar_amplitude_set || !verification_scalar_kx_set ||
818 !verification_scalar_ky_set || !verification_scalar_kz_set) {
819 SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG,
820 "verification scalar profile SIN_PRODUCT requires -verification_scalar_amplitude, -verification_scalar_kx, -verification_scalar_ky, and -verification_scalar_kz.");
821 }
822 } else {
823 SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG,
824 "Unsupported -verification_scalar_profile '%s'. Supported profiles: CONSTANT, LINEAR_X, SIN_PRODUCT.",
825 simCtx->verificationScalar.profile);
826 }
827 }
828 // NOTE: cdisx,cdisy,cdisz haven't been parsed, add if necessary.
829
830 // --- Group 6
831 LOG_ALLOW(GLOBAL,LOG_DEBUG, "Parsing Group 6: Physical & Geometric Parameters \n");
832 ierr = PetscOptionsGetReal(NULL,NULL,"-schmidt_number",&simCtx->schmidt_number,NULL);CHKERRQ(ierr);
833 ierr = PetscOptionsGetReal(NULL,NULL,"-turb_schmidt_number",&simCtx->Turbulent_schmidt_number,NULL);CHKERRQ(ierr);
834 ierr = PetscOptionsGetInt(NULL, NULL, "-no_of_bodies", &simCtx->NumberOfBodies, NULL); CHKERRQ(ierr);
835 ierr = PetscOptionsGetReal(NULL,NULL,"-wall_roughness",&simCtx->wall_roughness_height,NULL);CHKERRQ(ierr);
836 // NOTE: angle is not parsed in the original code, it set programmatically. We will follow that.
837 // NOTE: max_angle is calculated based on other flags (like MHV) in the legacy code.
838 // We will defer that logic to a later setup stage and not parse them directly.
839 // The Scaling Information is calculated here
840 ierr = ParseScalingInformation(simCtx); CHKERRQ(ierr);
841
842 // --- Group 7
843 LOG_ALLOW(GLOBAL,LOG_DEBUG, "Parsing Group 7: Grid, Domain, and Boundary Condition Settings \n");
844 ierr = PetscOptionsGetInt(NULL, NULL, "-nblk", &simCtx->block_number, NULL); CHKERRQ(ierr); // This is also a modern option
845 ierr = PetscOptionsGetInt(NULL, NULL, "-inlet", &simCtx->inletprofile, NULL); CHKERRQ(ierr);
846 ierr = PetscOptionsGetInt(NULL, NULL, "-Ogrid", &simCtx->Ogrid, NULL); CHKERRQ(ierr);
847 // NOTE: channelz was not parsed, likely set programmatically. We will omit its parsing call.
848 ierr = PetscOptionsGetInt(NULL, NULL, "-grid1d", &simCtx->grid1d, NULL); CHKERRQ(ierr);
849 ierr = PetscOptionsGetBool(NULL, NULL, "-grid", &simCtx->generate_grid, NULL); CHKERRQ(ierr);
850 ierr = PetscOptionsGetString(NULL, NULL, "-grid_file", simCtx->grid_file, PETSC_MAX_PATH_LEN, NULL); CHKERRQ(ierr);
851 ierr = PetscOptionsGetInt(NULL, NULL, "-da_processors_x", &simCtx->da_procs_x, NULL); CHKERRQ(ierr);
852 ierr = PetscOptionsGetInt(NULL, NULL, "-da_processors_y", &simCtx->da_procs_y, NULL); CHKERRQ(ierr);
853 ierr = PetscOptionsGetInt(NULL, NULL, "-da_processors_z", &simCtx->da_procs_z, NULL); CHKERRQ(ierr);
854 ierr = PetscOptionsGetInt(NULL, NULL, "-pbc_domain", &simCtx->blkpbc, NULL); CHKERRQ(ierr);
855 // NOTE: pseudo_periodic was not parsed. We will omit its parsing call.
856 ierr = PetscOptionsGetReal(NULL, NULL, "-grid_rotation_angle", &simCtx->grid_rotation_angle, NULL); CHKERRQ(ierr);
857 ierr = PetscOptionsGetReal(NULL, NULL, "-Croty", &simCtx->Croty, NULL); CHKERRQ(ierr);
858 ierr = PetscOptionsGetReal(NULL, NULL, "-Crotz", &simCtx->Crotz, NULL); CHKERRQ(ierr);
859 PetscBool bcs_flg;
860 char file_list_str[PETSC_MAX_PATH_LEN * 10]; // Buffer for comma-separated list
861
862 ierr = PetscOptionsGetString(NULL, NULL, "-bcs_files", file_list_str, sizeof(file_list_str), &bcs_flg); CHKERRQ(ierr);
863 ierr = PetscOptionsGetReal(NULL, NULL, "-U_bc", &simCtx->U_bc, NULL); CHKERRQ(ierr);
864
865 if (bcs_flg) {
866 LOG_ALLOW(GLOBAL, LOG_DEBUG, "Found -bcs_files option, overriding default.\n");
867
868 // A. Clean up the default memory we allocated in Phase 1.
869 ierr = PetscFree(simCtx->bcs_files[0]); CHKERRQ(ierr);
870 ierr = PetscFree(simCtx->bcs_files); CHKERRQ(ierr);
871 simCtx->num_bcs_files = 0;
872 simCtx->bcs_files = NULL;
873
874 // B. Parse the user-provided comma-separated list.
875 char *token;
876 char *str_copy;
877 ierr = PetscStrallocpy(file_list_str, &str_copy); CHKERRQ(ierr);
878
879 // First pass: count the number of files.
880 token = strtok(str_copy, ",");
881 while (token) {
882 simCtx->num_bcs_files++;
883 token = strtok(NULL, ",");
884 }
885 ierr = PetscFree(str_copy); CHKERRQ(ierr);
886
887 // Second pass: allocate memory and store the filenames.
888 ierr = PetscMalloc1(simCtx->num_bcs_files, &simCtx->bcs_files); CHKERRQ(ierr);
889 ierr = PetscStrallocpy(file_list_str, &str_copy); CHKERRQ(ierr);
890 token = strtok(str_copy, ",");
891 for (PetscInt i = 0; i < simCtx->num_bcs_files; i++) {
892 ierr = PetscStrallocpy(token, &simCtx->bcs_files[i]); CHKERRQ(ierr);
893 token = strtok(NULL, ",");
894 }
895 ierr = PetscFree(str_copy); CHKERRQ(ierr);
896 }
897
898
899 // --- Group 8
900 LOG_ALLOW(GLOBAL,LOG_DEBUG, "Parsing Group 8: Turbulence Modeling (LES/RANS) \n");
901 PetscInt temp_les_model;
902 ierr = PetscOptionsGetInt(NULL, NULL, "-les", &temp_les_model, NULL); CHKERRQ(ierr);
903 simCtx->les = (LESModelType)temp_les_model;
904 ierr = PetscOptionsGetInt(NULL, NULL, "-rans", &simCtx->rans, NULL); CHKERRQ(ierr);
905 ierr = PetscOptionsGetInt(NULL, NULL, "-wallfunction", &simCtx->wallfunction, NULL); CHKERRQ(ierr);
906 ierr = PetscOptionsGetInt(NULL, NULL, "-mixed", &simCtx->mixed, NULL); CHKERRQ(ierr);
907 ierr = PetscOptionsGetInt(NULL, NULL, "-clark", &simCtx->clark, NULL); CHKERRQ(ierr);
908 ierr = PetscOptionsGetInt(NULL, NULL, "-dynamic_freq", &simCtx->dynamic_freq, NULL); CHKERRQ(ierr);
909 ierr = PetscOptionsGetReal(NULL, NULL, "-max_cs", &simCtx->max_cs, NULL); CHKERRQ(ierr);
910 ierr = PetscOptionsGetReal(NULL, NULL, "-const_cs", &simCtx->Const_CS, NULL); CHKERRQ(ierr);
911 ierr = PetscOptionsGetInt(NULL, NULL, "-testfilter_ik", &simCtx->testfilter_ik, NULL); CHKERRQ(ierr);
912 ierr = PetscOptionsGetInt(NULL, NULL, "-testfilter_1d", &simCtx->testfilter_1d, NULL); CHKERRQ(ierr);
913 ierr = PetscOptionsGetInt(NULL, NULL, "-i_homo_filter", &simCtx->i_homo_filter, NULL); CHKERRQ(ierr);
914 ierr = PetscOptionsGetInt(NULL, NULL, "-j_homo_filter", &simCtx->j_homo_filter, NULL); CHKERRQ(ierr);
915 ierr = PetscOptionsGetInt(NULL, NULL, "-k_homo_filter", &simCtx->k_homo_filter, NULL); CHKERRQ(ierr);
916
917 // --- Group 9
918 LOG_ALLOW(GLOBAL,LOG_DEBUG, "Parsing Group 9: Particle / DMSwarm Data & Settings \n");
919 ierr = PetscOptionsGetInt(NULL, NULL, "-numParticles", &simCtx->np, NULL); CHKERRQ(ierr);
920 ierr = PetscOptionsGetBool(NULL, NULL, "-read_fields", &simCtx->readFields, NULL); CHKERRQ(ierr);
921 PetscInt temp_pinit = (PetscInt)PARTICLE_INIT_SURFACE_RANDOM;
922 ierr = PetscOptionsGetInt(NULL, NULL, "-pinit", &temp_pinit, NULL); CHKERRQ(ierr);
923 simCtx->ParticleInitialization = (ParticleInitializationType)temp_pinit;
924 PetscInt temp_interp = (PetscInt)INTERP_TRILINEAR;
925 ierr = PetscOptionsGetInt(NULL, NULL, "-interpolation_method", &temp_interp, NULL); CHKERRQ(ierr);
926 simCtx->interpolationMethod = (InterpolationMethod)temp_interp;
927 LOG_ALLOW(GLOBAL, LOG_DEBUG, "Interpolation method: %s\n",
928 simCtx->interpolationMethod == INTERP_TRILINEAR ? "Trilinear (direct cell-center)" : "CornerAveraged (legacy)");
929 ierr = PetscOptionsGetReal(NULL, NULL, "-psrc_x", &simCtx->psrc_x, NULL); CHKERRQ(ierr);
930 ierr = PetscOptionsGetReal(NULL, NULL, "-psrc_y", &simCtx->psrc_y, NULL); CHKERRQ(ierr);
931 ierr = PetscOptionsGetReal(NULL, NULL, "-psrc_z", &simCtx->psrc_z, NULL); CHKERRQ(ierr);
932 LOG_ALLOW(GLOBAL, LOG_DEBUG, "Particle initialization mode: %s. Point source: (%.6f, %.6f, %.6f)\n",
933 ParticleInitializationToString(simCtx->ParticleInitialization),
934 simCtx->psrc_x, simCtx->psrc_y, simCtx->psrc_z);
935 ierr = PetscOptionsGetString(NULL,NULL,"-particle_restart_mode",simCtx->particleRestartMode,sizeof(simCtx->particleRestartMode),NULL); CHKERRQ(ierr);
936 // Validation for Particle Restart Mode
937 if (strcmp(simCtx->particleRestartMode, "load") != 0 && strcmp(simCtx->particleRestartMode, "init") != 0) {
938 SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG, "Invalid value for -particle_restart_mode. Must be 'load' or 'init'. You provided '%s'.", simCtx->particleRestartMode);
939 }
940 ierr = InitializeBrownianRNG(simCtx); CHKERRQ(ierr);
941 // --- Group 10
942 LOG_ALLOW(GLOBAL,LOG_DEBUG, "Parsing Group 10: Immersed Boundary & FSI Data Object Pointers \n");
943 ierr = PetscOptionsGetBool(NULL, NULL, "-rs_fsi", &simCtx->rstart_fsi, NULL); CHKERRQ(ierr);
944 ierr = PetscOptionsGetInt(NULL, NULL, "-duplicate", &simCtx->duplicate, NULL); CHKERRQ(ierr);
945
946 // --- Group 11
947 LOG_ALLOW(GLOBAL,LOG_DEBUG, "Parsing Group 11: Top-Level Managers & Custom Configuration \n");
948 ierr = PetscOptionsGetInt(NULL, NULL, "-logfreq", &simCtx->LoggingFrequency, NULL); CHKERRQ(ierr);
949
950 if (simCtx->num_bcs_files != simCtx->block_number) {
951 SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_INCOMP, "Number of BC files (%d) does not match number of blocks (%d). Use -bcs_files \"file1.dat,file2.dat,...\".", simCtx->num_bcs_files, simCtx->block_number);
952 }
953
954 // --- Group 12
955 LOG_ALLOW(GLOBAL,LOG_DEBUG, "Parsing Group 12: Post-Processing Information.\n");
956 // This logic determines the Post Processing configuration and STORES it in simCtx for later reference and cleanup.
957 ierr = PetscOptionsGetString(NULL,NULL,"-postprocessing_config_file",simCtx->PostprocessingControlFile,PETSC_MAX_PATH_LEN,NULL); CHKERRQ(ierr);
958 /* Parse post settings for both solver and post-processor binaries using the single pre-allocated pps object. */
959 ierr = ParsePostProcessingSettings(simCtx);
960
961 // === 5. Dependent Parameter Calculations ================================
962 // Some parameters depend on others, so we calculate them here.
963 simCtx->StartTime = (PetscReal)simCtx->StartStep*simCtx->dt;
964 simCtx->ti = simCtx->StartTime;
965 simCtx->step = simCtx->StartStep;
966
967 // === 5. Log Summary and Finalize Setup ==================================
968 LOG_ALLOW(GLOBAL, LOG_DEBUG, "-- Console Output Functions [Total : %d] : --\n", simCtx->nAllowed);
969 for (PetscInt i = 0; i < simCtx->nAllowed; ++i) {
970 LOG_ALLOW(GLOBAL, LOG_DEBUG, " [%2d] «%s»\n", i, simCtx->allowedFuncs[i]);
971 }
972
973 LOG_ALLOW(GLOBAL, LOG_INFO, "Configuration complete. Key parameters:\n");
974 LOG_ALLOW(GLOBAL, LOG_INFO, " - Run mode: %s\n", simCtx->OnlySetup ? "SETUP ONLY" : "Full Simulation");
975 LOG_ALLOW(GLOBAL, LOG_INFO, " - Time steps: %d (from %d to %d)\n", simCtx->StepsToRun, simCtx->StartStep, simCtx->StartStep + simCtx->StepsToRun);
976 LOG_ALLOW(GLOBAL, LOG_INFO, " - Time step size (dt): %g\n", simCtx->dt);
977 if (simCtx->tiout > 0) {
978 LOG_ALLOW(GLOBAL, LOG_INFO, " - Field/restart output cadence: every %d step(s)\n", simCtx->tiout);
979 } else {
980 LOG_ALLOW(GLOBAL, LOG_INFO, " - Field/restart output cadence: DISABLED\n");
981 }
982 LOG_ALLOW(GLOBAL, LOG_INFO, " - Immersed Boundary: %s\n", simCtx->immersed ? "ENABLED" : "DISABLED");
983 LOG_ALLOW(GLOBAL, LOG_INFO, " - Particles: %d\n", simCtx->np);
984 if (simCtx->np > 0) {
985 if (simCtx->particleConsoleOutputFreq > 0) {
986 LOG_ALLOW(GLOBAL, LOG_INFO, " - Particle console cadence: every %d step(s)\n", simCtx->particleConsoleOutputFreq);
987 } else {
988 LOG_ALLOW(GLOBAL, LOG_INFO, " - Particle console cadence: DISABLED\n");
989 }
990 LOG_ALLOW(GLOBAL, LOG_INFO, " - Particle console row subsampling: every %d particle(s)\n", simCtx->LoggingFrequency);
991 }
992 if (simCtx->StartStep > 0 && simCtx->np > 0) {
993 LOG_ALLOW(GLOBAL, LOG_INFO, " - Particle Restart Mode: %s\n", simCtx->particleRestartMode);
994 }
995
996 // --- Initialize PETSc's internal performance logging stage ---
997 ierr = PetscLogDefaultBegin(); CHKERRQ(ierr); // REDUNDANT but safe.
998 ierr = PetscMemorySetGetMaximumUsage(); CHKERRQ(ierr);
999
1000 LOG_ALLOW(GLOBAL, LOG_DEBUG, "Finished CreateSimulationContext successfully on rank %d.\n", simCtx->rank);
1001
1002 PROFILE_FUNCTION_END;
1003 PetscFunctionReturn(0);
1004}
ParsePostProcessingSettings
PetscErrorCode ParsePostProcessingSettings(SimCtx *simCtx)
Initializes post-processing settings from a config file and command-line overrides.
Definition io.c:3076
ParseScalingInformation
PetscErrorCode ParseScalingInformation(SimCtx *simCtx)
Parses physical scaling parameters from command-line options.
Definition io.c:3242
set_allowed_functions
void set_allowed_functions(const char **functionList, int count)
Sets the global list of function names that are allowed to log.
Definition logging.c:155
LOG_ALLOW_SYNC
#define LOG_ALLOW_SYNC(scope, level, fmt,...)
Synchronized logging macro that checks both the log level and whether the calling function is in the ...
Definition logging.h:253
LOCAL
#define LOCAL
Logging scope definitions for controlling message output.
Definition logging.h:45
GLOBAL
#define GLOBAL
Scope for global logging across all processes.
Definition logging.h:46
LOG_ALLOW
#define LOG_ALLOW(scope, level, fmt,...)
Logging macro that checks both the log level and whether the calling function is in the allowed-funct...
Definition logging.h:200
print_log_level
PetscErrorCode print_log_level(void)
Prints the current logging level to the console.
Definition logging.c:119
PROFILE_FUNCTION_END
#define PROFILE_FUNCTION_END
Marks the end of a profiled code block.
Definition logging.h:859
LOG
#define LOG(scope, level, fmt,...)
Logging macro for PETSc-based applications with scope control.
Definition logging.h:84
LoadAllowedFunctionsFromFile
PetscErrorCode LoadAllowedFunctionsFromFile(const char filename[], char ***funcsOut, PetscInt *nOut)
Load function names from a text file.
Definition logging.c:598
ProfilingInitialize
PetscErrorCode ProfilingInitialize(SimCtx *simCtx)
Initializes the custom profiling system using configuration from SimCtx.
Definition logging.c:1928
LOG_ERROR
@ LOG_ERROR
Critical errors that may halt the program.
Definition logging.h:29
LOG_INFO
@ LOG_INFO
Informational messages about program execution.
Definition logging.h:31
LOG_WARNING
@ LOG_WARNING
Non-critical issues that warrant attention.
Definition logging.h:30
LOG_DEBUG
@ LOG_DEBUG
Detailed debugging information.
Definition logging.h:32
PROFILE_FUNCTION_BEGIN
#define PROFILE_FUNCTION_BEGIN
Marks the beginning of a profiled code block (typically a function).
Definition logging.h:850
ParticleInitializationToString
const char * ParticleInitializationToString(ParticleInitializationType ParticleInitialization)
Returns the canonical log token for a particle-initialization mode.
Definition logging.c:724
InitializeBrownianRNG
PetscErrorCode InitializeBrownianRNG(SimCtx *simCtx)
Internal helper implementation: InitializeBrownianRNG().
Definition setup.c:3285
RuntimeWalltimeGuardParsePositiveSeconds
PetscBool RuntimeWalltimeGuardParsePositiveSeconds(const char *text, PetscReal *seconds_out)
Implementation of RuntimeWalltimeGuardParsePositiveSeconds().
Definition setup.c:20
ParseFieldStatisticsConfig
PetscErrorCode ParseFieldStatisticsConfig(SimCtx *simCtx)
Resolves field-statistics configuration from the control file.
Definition statistics_config.c:291
LESModelType
LESModelType
Identifies the six logical faces of a structured computational block.
Definition variables.h:520
NO_LES_MODEL
@ NO_LES_MODEL
Definition variables.h:521
SimCtx::icVelocityPhysical
PetscReal icVelocityPhysical
Definition variables.h:759
SimCtx::MHV
PetscInt MHV
Definition variables.h:732
SimCtx::turbine
PetscInt turbine
Definition variables.h:732
SimCtx::mom_nk_monitor_history
PetscBool mom_nk_monitor_history
Definition variables.h:752
SimCtx::fishcyl
PetscInt fishcyl
Definition variables.h:732
SimCtx::clark
PetscInt clark
Definition variables.h:822
SimCtx::movefsi
PetscInt movefsi
Definition variables.h:726
SimCtx::continueMode
PetscBool continueMode
Definition variables.h:712
SimCtx::moveframe
PetscInt moveframe
Definition variables.h:727
SimCtx::TwoD
PetscInt TwoD
Definition variables.h:727
SimCtx::pseudo_periodic
PetscInt pseudo_periodic
Definition variables.h:791
SimCtx::fish_c
PetscInt fish_c
Definition variables.h:732
SimCtx::dgf_z
PetscInt dgf_z
Definition variables.h:728
SimCtx::poisson_tol
PetscReal poisson_tol
Definition variables.h:741
SimCtx::profilingFinalSummary
PetscBool profilingFinalSummary
Definition variables.h:868
SimCtx::schmidt_number
PetscReal schmidt_number
Definition variables.h:787
SimCtx::rank
PetscMPIInt rank
Definition variables.h:698
SimCtx::profilingTimestepFile
char profilingTimestepFile[PETSC_MAX_PATH_LEN]
Definition variables.h:867
SimCtx::fish
PetscInt fish
Definition variables.h:732
SimCtx::LV
PetscInt LV
Definition variables.h:732
SimCtx::angle
PetscReal angle
Definition variables.h:782
SimCtx::Turbulent_schmidt_number
PetscReal Turbulent_schmidt_number
Definition variables.h:787
SearchMetricsState::searchLocatedCount
PetscInt64 searchLocatedCount
Definition variables.h:241
SimCtx::thin
PetscInt thin
Definition variables.h:727
SimCtx::statisticsConsoleOutputFreq
PetscInt statisticsConsoleOutputFreq
Definition variables.h:772
SimCtx::grid1d
PetscInt grid1d
Definition variables.h:790
SimCtx::mom_rtol
PetscReal mom_rtol
Definition variables.h:738
SearchMetricsState::searchLostCount
PetscInt64 searchLostCount
Definition variables.h:242
SimCtx::da_procs_z
PetscInt da_procs_z
Definition variables.h:796
SimCtx::blkpbc
PetscInt blkpbc
Definition variables.h:791
SimCtx::sediment
PetscInt sediment
Definition variables.h:726
SimCtx::targetVolumetricFlux
PetscReal targetVolumetricFlux
Definition variables.h:807
SimCtx::walltimeGuardActive
PetscBool walltimeGuardActive
Definition variables.h:870
SimCtx::mom_last_lambda_max
PetscReal mom_last_lambda_max
Definition variables.h:751
SimCtx::channelz
PetscInt channelz
Definition variables.h:733
SimCtx::walltimeGuardWarmupTotalSeconds
PetscReal walltimeGuardWarmupTotalSeconds
Definition variables.h:878
SimCtx::forceScalingFactor
PetscReal forceScalingFactor
Definition variables.h:801
SimCtx::pseudo_cfl_reduction_factor
PetscReal pseudo_cfl_reduction_factor
Definition variables.h:745
SimCtx::initialConditionMode
InitialConditionMode initialConditionMode
Definition variables.h:754
SimCtx::rans
PetscInt rans
Definition variables.h:821
ParticleInitializationType
ParticleInitializationType
Enumerator to identify the particle initialization strategy.
Definition variables.h:551
PARTICLE_INIT_SURFACE_RANDOM
@ PARTICLE_INIT_SURFACE_RANDOM
Random placement on the inlet face.
Definition variables.h:552
SimCtx::StartTime
PetscReal StartTime
Definition variables.h:709
SimCtx::dgf_az
PetscInt dgf_az
Definition variables.h:728
SimCtx::FluxOutSum
PetscReal FluxOutSum
Definition variables.h:799
SimCtx::walltimeGuardHasEWMA
PetscBool walltimeGuardHasEWMA
Definition variables.h:880
SimCtx::CMy_c
PetscReal CMy_c
Definition variables.h:783
SimCtx::flowDirection
FlowDirection flowDirection
Definition variables.h:758
SimCtx::runtimeMemoryLogEnabled
PetscBool runtimeMemoryLogEnabled
Enable the rank-reduced runtime memory log.
Definition variables.h:883
SimCtx::bcs_files
char ** bcs_files
Definition variables.h:798
SimCtx::boundaryVelocityCorrection
PetscReal boundaryVelocityCorrection
Definition variables.h:814
SimCtx::max_angle
PetscReal max_angle
Definition variables.h:782
SimCtx::min_pseudo_cfl
PetscReal min_pseudo_cfl
Definition variables.h:746
SearchMetricsState::boundaryClampCount
PetscInt64 boundaryClampCount
Definition variables.h:248
SimCtx::particlesLostLastStep
PetscInt particlesLostLastStep
Definition variables.h:834
SimCtx::duplicate
PetscInt duplicate
Definition variables.h:849
SimCtx::tiout
PetscInt tiout
Definition variables.h:707
SimCtx::walltimeGuardMinSeconds
PetscReal walltimeGuardMinSeconds
Definition variables.h:873
SimCtx::allowedFile
char allowedFile[PETSC_MAX_PATH_LEN]
Definition variables.h:853
SimCtx::da_procs_y
PetscInt da_procs_y
Definition variables.h:796
SearchMetricsState::traversalStepsSum
PetscInt64 traversalStepsSum
Definition variables.h:243
SimCtx::mom_last_converged
PetscBool mom_last_converged
Definition variables.h:750
SimCtx::testfilter_1d
PetscInt testfilter_1d
Definition variables.h:824
SimCtx::psrc_x
PetscReal psrc_x
Definition variables.h:784
SimCtx::ren
PetscReal ren
Definition variables.h:744
SimCtx::Crotz
PetscReal Crotz
Definition variables.h:794
SimCtx::mixed
PetscInt mixed
Definition variables.h:822
SimCtx::drivenFluxTargetLatched
PetscBool drivenFluxTargetLatched
Definition variables.h:812
SimCtx::ibmv
IBMVNodes * ibmv
Definition variables.h:846
SearchMetricsState::searchPopulation
PetscInt64 searchPopulation
Definition variables.h:240
SimCtx::output_dir
char output_dir[PETSC_MAX_PATH_LEN]
Definition variables.h:717
SimCtx::walltimeGuardLatestStepSeconds
PetscReal walltimeGuardLatestStepSeconds
Definition variables.h:882
SimCtx::dt
PetscReal dt
Definition variables.h:710
SimCtx::runtimeMemoryLogFile
char runtimeMemoryLogFile[PETSC_MAX_PATH_LEN]
File name written under log_dir.
Definition variables.h:884
SimCtx::runtimeMemoryLogStarted
PetscBool runtimeMemoryLogStarted
True after rank 0 writes the log header.
Definition variables.h:885
SimCtx::occupiedCellCount
PetscInt occupiedCellCount
Definition variables.h:838
SimCtx::StepsToRun
PetscInt StepsToRun
Definition variables.h:706
SimCtx::profilingTimestepMode
char profilingTimestepMode[32]
Definition variables.h:866
SimCtx::k_periodic
PetscInt k_periodic
Definition variables.h:791
SimCtx::inletprofile
PetscInt inletprofile
Definition variables.h:790
SimCtx::bulkVelocityCorrection
PetscReal bulkVelocityCorrection
Definition variables.h:813
SimCtx::cdisy
PetscReal cdisy
Definition variables.h:744
SimCtx::mom_atol
PetscReal mom_atol
Definition variables.h:738
SimCtx::rstart_fsi
PetscBool rstart_fsi
Definition variables.h:848
SearchMetricsState::currentSettlementPass
PetscInt currentSettlementPass
Definition variables.h:252
SimCtx::np
PetscInt np
Definition variables.h:827
SimCtx::fieldStatisticsEnabled
PetscBool fieldStatisticsEnabled
Definition variables.h:769
SimCtx::no_pseudo_cfl_backtrack
PetscBool no_pseudo_cfl_backtrack
Definition variables.h:748
SimCtx::C_IEM
PetscReal C_IEM
Definition variables.h:842
SimCtx::ccc
PetscInt ccc
Definition variables.h:817
SimCtx::ratio
PetscReal ratio
Definition variables.h:818
SimCtx::mg_idx
PetscInt mg_idx
Definition variables.h:739
SimCtx::StartStep
PetscInt StartStep
Definition variables.h:705
SimCtx::mg_MAX_IT
PetscInt mg_MAX_IT
Definition variables.h:739
SimCtx::OnlySetup
PetscBool OnlySetup
Definition variables.h:711
SimCtx::rotatefsi
PetscInt rotatefsi
Definition variables.h:726
MOMENTUM_SOLVER_DUALTIME_PICARD_JAMESON_RK
@ MOMENTUM_SOLVER_DUALTIME_PICARD_JAMESON_RK
Definition variables.h:536
MOMENTUM_SOLVER_EXPLICIT_RK
@ MOMENTUM_SOLVER_EXPLICIT_RK
Definition variables.h:535
MOMENTUM_SOLVER_NEWTON_KRYLOV
@ MOMENTUM_SOLVER_NEWTON_KRYLOV
Definition variables.h:537
SimCtx::cdisz
PetscReal cdisz
Definition variables.h:744
Cmpnts::x
PetscScalar x
Definition variables.h:103
SearchMetricsState::reSearchCount
PetscInt64 reSearchCount
Definition variables.h:244
SimCtx::dgf_x
PetscInt dgf_x
Definition variables.h:728
SimCtx::current_io_directory
char * current_io_directory
Definition variables.h:720
SimCtx::pizza
PetscInt pizza
Definition variables.h:732
SimCtx::MaxDiv
PetscReal MaxDiv
Definition variables.h:859
SimCtx::grid_file
char grid_file[PETSC_MAX_PATH_LEN]
Definition variables.h:795
SimCtx::max_cs
PetscReal max_cs
Definition variables.h:823
SimCtx::invicid
PetscInt invicid
Definition variables.h:727
SimCtx::allowedFuncs
char ** allowedFuncs
Definition variables.h:855
SearchMetricsState::bboxGuessFallbackCount
PetscInt64 bboxGuessFallbackCount
Definition variables.h:250
SimCtx::interpolationMethod
InterpolationMethod interpolationMethod
Definition variables.h:832
SimCtx::psrc_z
PetscReal psrc_z
Point source location for PARTICLE_INIT_POINT_SOURCE.
Definition variables.h:784
SimCtx::mg_poItr
PetscInt mg_poItr
Definition variables.h:739
SimCtx::STRONG_COUPLING
PetscInt STRONG_COUPLING
Definition variables.h:742
SimCtx::verificationScalar
VerificationScalarConfig verificationScalar
Definition variables.h:778
SimCtx::max_pseudo_cfl
PetscReal max_pseudo_cfl
Definition variables.h:746
SimCtx::MaxDivx
PetscInt MaxDivx
Definition variables.h:860
SimCtx::poisson
PetscInt poisson
Definition variables.h:740
SimCtx::k_homo_filter
PetscInt k_homo_filter
Definition variables.h:824
SimCtx::profilingSelectedFuncsFile
char profilingSelectedFuncsFile[PETSC_MAX_PATH_LEN]
Definition variables.h:862
SimCtx::MaxDivy
PetscInt MaxDivy
Definition variables.h:860
SimCtx::NumberOfBodies
PetscInt NumberOfBodies
Definition variables.h:781
SimCtx::particleRestartMode
char particleRestartMode[16]
Definition variables.h:833
SimCtx::Ogrid
PetscInt Ogrid
Definition variables.h:790
SearchMetricsState::bboxGuessSuccessCount
PetscInt64 bboxGuessSuccessCount
Definition variables.h:249
SimCtx::MaxDivz
PetscInt MaxDivz
Definition variables.h:860
SimCtx::bboxlist
BoundingBox * bboxlist
Definition variables.h:830
SimCtx::j_homo_filter
PetscInt j_homo_filter
Definition variables.h:824
SimCtx::eel
PetscInt eel
Definition variables.h:732
SimCtx::log_dir
char log_dir[PETSC_MAX_PATH_LEN]
Definition variables.h:718
SimCtx::MaxDivFlatArg
PetscInt MaxDivFlatArg
Definition variables.h:860
SimCtx::FluxInSum
PetscReal FluxInSum
Definition variables.h:799
SimCtx::walltimeGuardCompletedSteps
PetscInt walltimeGuardCompletedSteps
Definition variables.h:877
SearchMetricsState::maxParticlePassDepth
PetscInt64 maxParticlePassDepth
Definition variables.h:251
SimCtx::CMz_c
PetscReal CMz_c
Definition variables.h:783
SearchMetricsState::maxTraversalSteps
PetscInt64 maxTraversalSteps
Definition variables.h:245
SimCtx::generate_grid
PetscBool generate_grid
Definition variables.h:792
SimCtx::AnalyticalUniformVelocity
Cmpnts AnalyticalUniformVelocity
Definition variables.h:760
SimCtx::eulerianSource
char eulerianSource[PETSC_MAX_PATH_LEN]
Definition variables.h:715
SimCtx::imp_stol
PetscReal imp_stol
Definition variables.h:738
SimCtx::nAllowed
PetscInt nAllowed
Definition variables.h:856
SimCtx::walltimeGuardEnabled
PetscBool walltimeGuardEnabled
Definition variables.h:869
SimCtx::checkpointGeometryHashReady
PetscBool checkpointGeometryHashReady
Definition variables.h:722
SimCtx::wall_roughness_height
PetscReal wall_roughness_height
Definition variables.h:786
SimCtx::useProfilingSelectedFuncsCfg
PetscBool useProfilingSelectedFuncsCfg
Definition variables.h:863
SimCtx::walltimeGuardWarmupSteps
PetscInt walltimeGuardWarmupSteps
Definition variables.h:871
SimCtx::ParticleInitialization
ParticleInitializationType ParticleInitialization
Definition variables.h:831
SimCtx::mom_dt_jameson_residual_norm_noise_allowance_factor
PetscReal mom_dt_jameson_residual_norm_noise_allowance_factor
Definition variables.h:747
Cmpnts::z
PetscScalar z
Definition variables.h:103
InterpolationMethod
InterpolationMethod
Selects the grid-to-particle interpolation method.
Definition variables.h:564
INTERP_TRILINEAR
@ INTERP_TRILINEAR
Definition variables.h:565
SimCtx::Const_CS
PetscReal Const_CS
Definition variables.h:823
SimCtx::i_homo_filter
PetscInt i_homo_filter
Definition variables.h:824
SimCtx::wallfunction
PetscInt wallfunction
Definition variables.h:822
SimCtx::drivingForceStep
PetscInt drivingForceStep
Definition variables.h:806
SimCtx::rheology
PetscInt rheology
Definition variables.h:726
SimCtx::Flux_in
PetscReal Flux_in
Definition variables.h:782
SimCtx::runtimeMemoryLogHasPrevious
PetscBool runtimeMemoryLogHasPrevious
True after the first process-memory sample.
Definition variables.h:886
SimCtx::profilingSelectedFuncs
char ** profilingSelectedFuncs
Definition variables.h:864
SimCtx::cdisx
PetscReal cdisx
Definition variables.h:744
SimCtx::dgf_ax
PetscInt dgf_ax
Definition variables.h:728
SimCtx::mglevels
PetscInt mglevels
Definition variables.h:739
SimCtx::num_bcs_files
PetscInt num_bcs_files
Definition variables.h:797
SimCtx::dm_swarm
DM dm_swarm
Definition variables.h:829
SimCtx::useCfg
PetscBool useCfg
Definition variables.h:854
SimCtx::psrc_y
PetscReal psrc_y
Definition variables.h:784
SimCtx::readFields
PetscBool readFields
Definition variables.h:828
SimCtx::central
PetscInt central
Definition variables.h:742
SimCtx::Fluxsum
PetscReal Fluxsum
Definition variables.h:799
FlowDirection
FlowDirection
Primary flow direction for streamwise IC and Poiseuille modes.
Definition variables.h:272
FLOW_DIR_UNSET
@ FLOW_DIR_UNSET
Definition variables.h:279
SimCtx::pseudo_cfl_growth_factor
PetscReal pseudo_cfl_growth_factor
Definition variables.h:745
SimCtx::Croty
PetscReal Croty
Definition variables.h:794
SimCtx::particlesLostCumulative
PetscInt particlesLostCumulative
Definition variables.h:835
SimCtx::nProfilingSelectedFuncs
PetscInt nProfilingSelectedFuncs
Definition variables.h:865
SimCtx::particlesMigratedLastStep
PetscInt particlesMigratedLastStep
Definition variables.h:837
SimCtx::initialConditionDirectory
char initialConditionDirectory[PETSC_MAX_PATH_LEN]
Definition variables.h:756
SimCtx::grid_rotation_angle
PetscReal grid_rotation_angle
Definition variables.h:793
SimCtx::dynamic_freq
PetscInt dynamic_freq
Definition variables.h:822
SimCtx::AnalyticalSolutionType
char AnalyticalSolutionType[PETSC_MAX_PATH_LEN]
Definition variables.h:729
SimCtx::da_procs_x
PetscInt da_procs_x
Definition variables.h:796
SimCtx::U_bc
PetscReal U_bc
Definition variables.h:816
SimCtx::walltimeGuardWarmupAverageSeconds
PetscReal walltimeGuardWarmupAverageSeconds
Definition variables.h:879
InitialConditionMode
InitialConditionMode
Selects the algorithm used to populate a fresh Eulerian velocity field.
Definition variables.h:151
IC_MODE_FILE
@ IC_MODE_FILE
Definition variables.h:156
IC_MODE_ZERO
@ IC_MODE_ZERO
Definition variables.h:152
SimCtx::particleConsoleOutputFreq
PetscInt particleConsoleOutputFreq
Definition variables.h:708
SimCtx::InitialConstantContra
Cmpnts InitialConstantContra
Definition variables.h:757
SimCtx::searchMetrics
SearchMetricsState searchMetrics
Definition variables.h:840
SimCtx::i_periodic
PetscInt i_periodic
Definition variables.h:791
SimCtx::mom_resid_rtol
PetscReal mom_resid_rtol
Definition variables.h:738
SimCtx::checkpointGeometrySHA256
char checkpointGeometrySHA256[65]
Definition variables.h:721
SimCtx::runtimeMemoryLogPreviousProcessMB
PetscReal runtimeMemoryLogPreviousProcessMB
Previous local process memory sample in MB.
Definition variables.h:887
SimCtx::step
PetscInt step
Definition variables.h:703
SimCtx::walltimeGuardEWMASeconds
PetscReal walltimeGuardEWMASeconds
Definition variables.h:881
SimCtx::AreaOutSum
PetscReal AreaOutSum
Definition variables.h:815
SimCtx::dgf_ay
PetscInt dgf_ay
Definition variables.h:728
SimCtx::mom_max_pseudo_steps
PetscInt mom_max_pseudo_steps
Definition variables.h:737
SimCtx::BrownianMotionRNG
PetscRandom BrownianMotionRNG
Definition variables.h:841
SimCtx::testfilter_ik
PetscInt testfilter_ik
Definition variables.h:824
SimCtx::hydro
PetscInt hydro
Definition variables.h:732
SimCtx::pps
PostProcessParams * pps
Definition variables.h:890
SimCtx::migrationPassesLastStep
PetscInt migrationPassesLastStep
Definition variables.h:836
Cmpnts::y
PetscScalar y
Definition variables.h:103
InitialConditionField
InitialConditionField
Selects the authoritative velocity representation in a staged file IC.
Definition variables.h:160
IC_FIELD_UCONT
@ IC_FIELD_UCONT
Definition variables.h:162
IC_FIELD_UCAT
@ IC_FIELD_UCAT
Definition variables.h:161
SimCtx::size
PetscMPIInt size
Definition variables.h:699
SimCtx::_io_context_buffer
char _io_context_buffer[PETSC_MAX_PATH_LEN]
Definition variables.h:719
SimCtx::walltimeGuardLimitSeconds
PetscReal walltimeGuardLimitSeconds
Definition variables.h:876
SimCtx::ps_ksp_pic_monitor_true_residual
PetscBool ps_ksp_pic_monitor_true_residual
Definition variables.h:753
SimCtx::walltimeGuardEstimatorAlpha
PetscReal walltimeGuardEstimatorAlpha
Definition variables.h:874
SimCtx::les
PetscInt les
Definition variables.h:821
SOLUTION_CONVERGENCE_TRANSIENT
@ SOLUTION_CONVERGENCE_TRANSIENT
Definition variables.h:547
SOLUTION_CONVERGENCE_STEADY_DETERMINISTIC
@ SOLUTION_CONVERGENCE_STEADY_DETERMINISTIC
Definition variables.h:544
SimCtx::mg_preItr
PetscInt mg_preItr
Definition variables.h:739
SimCtx::mom_ratio_ema_alpha
PetscReal mom_ratio_ema_alpha
Definition variables.h:749
SimCtx::logviewer
PetscViewer logviewer
Definition variables.h:713
SearchMetricsState::searchAttempts
PetscInt64 searchAttempts
Definition variables.h:239
SimCtx::initialConditionField
InitialConditionField initialConditionField
Definition variables.h:755
SearchMetricsState::tieBreakCount
PetscInt64 tieBreakCount
Definition variables.h:247
SimCtx::mom_resid_atol
PetscReal mom_resid_atol
Definition variables.h:738
SimCtx::restartHistoryAvailable
PetscBool restartHistoryAvailable
Definition variables.h:723
SimCtx::cop
PetscInt cop
Definition variables.h:732
SimCtx::ti
PetscReal ti
Definition variables.h:704
SimCtx::walltimeGuardMultiplier
PetscReal walltimeGuardMultiplier
Definition variables.h:872
SimCtx::Pipe
PetscInt Pipe
Definition variables.h:732
SimCtx::rotateframe
PetscInt rotateframe
Definition variables.h:727
SimCtx::ibm
IBMNodes * ibm
Definition variables.h:845
SimCtx::AreaInSum
PetscReal AreaInSum
Definition variables.h:815
SimCtx::mom_solver_type
MomentumSolverType mom_solver_type
Definition variables.h:736
SimCtx::summationRHS
PetscReal summationRHS
Definition variables.h:858
SimCtx::immersed
PetscInt immersed
Definition variables.h:726
SearchMetricsState::maxTraversalFailCount
PetscInt64 maxTraversalFailCount
Definition variables.h:246
SimCtx::PostprocessingControlFile
char PostprocessingControlFile[PETSC_MAX_PATH_LEN]
Definition variables.h:889
SimCtx::restart_dir
char restart_dir[PETSC_MAX_PATH_LEN]
Definition variables.h:716
SimCtx::verificationDiffusivity
VerificationDiffusivityConfig verificationDiffusivity
Definition variables.h:777
SimCtx::blank
PetscInt blank
Definition variables.h:727
SimCtx::dgf_y
PetscInt dgf_y
Definition variables.h:728
SimCtx::walltimeGuardJobStartEpochSeconds
PetscReal walltimeGuardJobStartEpochSeconds
Definition variables.h:875
SimCtx::pseudo_cfl
PetscReal pseudo_cfl
Definition variables.h:744
SimCtx::LoggingFrequency
PetscInt LoggingFrequency
Definition variables.h:857
SimCtx::CMx_c
PetscReal CMx_c
Definition variables.h:783
SimCtx::drivingForceMagnitude
PetscReal drivingForceMagnitude
Definition variables.h:801
SimCtx::particleLoadImbalance
PetscReal particleLoadImbalance
Definition variables.h:839
SimCtx::fieldStatisticsContinue
PetscBool fieldStatisticsContinue
Definition variables.h:776
SimCtx::j_periodic
PetscInt j_periodic
Definition variables.h:791
SimCtx::wing
PetscInt wing
Definition variables.h:732
SimCtx::fsi
FSInfo * fsi
Definition variables.h:847
SimCtx
The master context for the entire simulation.
Definition variables.h:695
Here is the call graph for this function:
Here is the caller graph for this function:

◆ PetscMkdirRecursive()

static PetscErrorCode PetscMkdirRecursive ( const char *  path)
static

Create a directory path recursively using PETSc-compatible error handling.

Definition at line 1011 of file setup.c.

1012{
1013 PetscErrorCode ierr;
1014 char tmp_path[PETSC_MAX_PATH_LEN];
1015 char *p = NULL;
1016 size_t len;
1017 PetscBool exists;
1018
1019 PetscFunctionBeginUser;
1020
1021 // Create a mutable copy of the path
1022 len = strlen(path);
1023 if (len >= sizeof(tmp_path)) {
1024 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Path is too long to process: %s", path);
1025 }
1026 strcpy(tmp_path, path);
1027
1028 // If the path ends with a separator, remove it
1029 if (tmp_path[len - 1] == '/') {
1030 tmp_path[len - 1] = 0;
1031 }
1032
1033 // Iterate through the path, creating each directory level
1034 for (p = tmp_path + 1; *p; p++) {
1035 if (*p == '/') {
1036 *p = 0; // Temporarily terminate the string
1037
1038 // Check if this directory level exists
1039 ierr = PetscTestDirectory(tmp_path, 'r', &exists); CHKERRQ(ierr);
1040 if (!exists) {
1041 ierr = PetscMkdir(tmp_path); CHKERRQ(ierr);
1042 }
1043
1044 *p = '/'; // Restore the separator
1045 }
1046 }
1047
1048 // Create the final, full directory path
1049 ierr = PetscTestDirectory(tmp_path, 'r', &exists); CHKERRQ(ierr);
1050 if (!exists) {
1051 ierr = PetscMkdir(tmp_path); CHKERRQ(ierr);
1052 }
1053
1054 PetscFunctionReturn(0);
1055}
Here is the caller graph for this function:

◆ SetupSimulationEnvironment()

PetscErrorCode SetupSimulationEnvironment ( SimCtx *  simCtx)

Internal helper implementation: SetupSimulationEnvironment().

Verifies and prepares the complete I/O environment for a simulation run.

Local to this translation unit.

Definition at line 1063 of file setup.c.

1064{
1065 PetscErrorCode ierr;
1066 PetscMPIInt rank;
1067 PetscBool exists;
1068
1069 PetscFunctionBeginUser;
1070 ierr = MPI_Comm_rank(PETSC_COMM_WORLD, &rank); CHKERRQ(ierr);
1071
1072 LOG_ALLOW(GLOBAL, LOG_INFO, "--- Setting up simulation environment ---\n");
1073
1074 /* =====================================================================
1075 * Phase 1: Check for all required and optional INPUT files.
1076 * ===================================================================== */
1077 LOG_ALLOW(GLOBAL, LOG_DEBUG, "Phase 1: Verifying input files...\n");
1078
1079 // --- Mandatory Inputs ---
1080 if (!simCtx->generate_grid) {
1081 ierr = VerifyPathExistence(simCtx->grid_file, PETSC_FALSE, PETSC_FALSE, "Grid file", &exists); CHKERRQ(ierr);
1082 }
1083 for (PetscInt i = 0; i < simCtx->num_bcs_files; i++) {
1084 char desc[128];
1085 ierr = PetscSNPrintf(desc, sizeof(desc), "BCS file #%d", i + 1); CHKERRQ(ierr);
1086 ierr = VerifyPathExistence(simCtx->bcs_files[i], PETSC_FALSE, PETSC_FALSE, desc, &exists); CHKERRQ(ierr);
1087 }
1088
1089 // --- Optional Inputs (these produce warnings if missing) ---
1090 if (simCtx->useCfg) {
1091 ierr = VerifyPathExistence(simCtx->allowedFile, PETSC_FALSE, PETSC_TRUE, "Whitelist config file", &exists); CHKERRQ(ierr);
1092 }
1093 if (simCtx->useProfilingSelectedFuncsCfg) {
1094 ierr = VerifyPathExistence(simCtx->profilingSelectedFuncsFile, PETSC_FALSE, PETSC_TRUE, "Profiling config file", &exists); CHKERRQ(ierr);
1095 }
1096 if (simCtx->exec_mode == EXEC_MODE_POSTPROCESSOR) {
1097 ierr = VerifyPathExistence(simCtx->PostprocessingControlFile, PETSC_FALSE, PETSC_TRUE, "Post-processing control file", &exists); CHKERRQ(ierr);
1098 }
1099
1100
1101 /* =====================================================================
1102 * Phase 2: Validate directories specific to the execution mode.
1103 * ===================================================================== */
1104 LOG_ALLOW(GLOBAL, LOG_DEBUG, "Phase 2: Verifying execution mode directories...\n");
1105 // The data source directory must exist if we intend to load any data from it.
1106 // This is true if:
1107 // 1. We are restarting from a previous time step (StartStep > 0), which implies
1108 // loading Eulerian fields and/or particle fields.
1109 // 2. We are starting from t=0 but are explicitly told to load the initial
1110 // Eulerian fields from a file (eulerianSource == "load").
1111 if (simCtx->StartStep > 0 || strcmp(simCtx->eulerianSource,"load")== 0){ // If this is a restart run
1112 ierr = VerifyPathExistence(simCtx->restart_dir, PETSC_TRUE, PETSC_FALSE, "Restart source directory", &exists); CHKERRQ(ierr);
1113 }
1114 if (simCtx->StartStep == 0 && strcmp(simCtx->eulerianSource, "solve") == 0 &&
1115 simCtx->initialConditionMode == IC_MODE_FILE) {
1116 ierr = VerifyPathExistence(simCtx->initialConditionDirectory, PETSC_TRUE, PETSC_FALSE,
1117 "Initial-condition source directory", &exists); CHKERRQ(ierr);
1118 }
1119 if (simCtx->exec_mode == EXEC_MODE_POSTPROCESSOR) {
1120 ierr = VerifyPathExistence(simCtx->pps->source_dir, PETSC_TRUE, PETSC_FALSE, "Post-processing source directory", &exists); CHKERRQ(ierr);
1121 }
1122
1123 /* =====================================================================
1124 * Phase 3: Create and prepare all OUTPUT directories.
1125 * ===================================================================== */
1126 LOG_ALLOW(GLOBAL, LOG_DEBUG, "Phase 3: Preparing output directories...\n");
1127
1128 if (rank == 0){
1129 if(simCtx->exec_mode == EXEC_MODE_SOLVER){
1130 // --- Prepare Log Directory ---
1131 if (!simCtx->continueMode) {
1132 // Only wipe logs on fresh runs; continue mode appends to existing logs.
1133 LOG_ALLOW(GLOBAL, LOG_DEBUG, "Creating/cleaning log directory: %s\n", simCtx->log_dir);
1134 ierr = PetscRMTree(simCtx->log_dir); // Wipes the directory and its contents
1135 if (ierr) { /* Ignore file-not-found error, but fail on others */
1136 PetscError(PETSC_COMM_SELF, __LINE__, __FUNCT__, __FILE__, ierr, PETSC_ERROR_INITIAL, "Could not remove existing log directory '%s'. Check permissions.", simCtx->log_dir);
1137 }
1138 ierr = PetscMkdir(simCtx->log_dir); CHKERRQ(ierr);
1139 } else {
1140 // In continue mode, ensure log directory exists but don't wipe it.
1141 LOG_ALLOW(GLOBAL, LOG_DEBUG, "Continue mode: preserving existing log directory: %s\n", simCtx->log_dir);
1142 ierr = PetscMkdir(simCtx->log_dir); CHKERRQ(ierr);
1143 }
1144
1145 // --- Prepare Output Directory ---
1146 // The checkpoint coordinator creates its fixed internal hierarchy
1147 // transactionally when a checkpoint is due.
1148 LOG_ALLOW(GLOBAL, LOG_DEBUG, "Verifying main output directory: %s\n", simCtx->output_dir);
1149 ierr = PetscTestDirectory(simCtx->output_dir, 'r', &exists); CHKERRQ(ierr);
1150 if (!exists) {
1151 LOG_ALLOW(GLOBAL, LOG_INFO, "Output directory not found. Creating: %s\n", simCtx->output_dir);
1152 ierr = PetscMkdir(simCtx->output_dir); CHKERRQ(ierr);
1153 }
1154 } else if(simCtx->exec_mode == EXEC_MODE_POSTPROCESSOR){
1155 LOG_ALLOW(GLOBAL, LOG_DEBUG, "Preparing post-processing output directories ...\n");
1156
1157 PostProcessParams *pps = simCtx->pps;
1158 char path_buffer[PETSC_MAX_PATH_LEN];
1159
1160 const char *last_slash_euler = strrchr(pps->output_prefix, '/');
1161 if(last_slash_euler){
1162 size_t dir_len = last_slash_euler - pps->output_prefix;
1163 if(dir_len > 0){
1164 if(dir_len >= sizeof(path_buffer)) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"Post-processing output prefix path is too long.");
1165 strncpy(path_buffer, pps->output_prefix, dir_len);
1166 path_buffer[dir_len] = '\0';
1167
1168 ierr = PetscTestDirectory(path_buffer, 'r', &exists); CHKERRQ(ierr);
1169 if (!exists){
1170 LOG_ALLOW(GLOBAL, LOG_INFO, "Creating post-processing Eulerian output directory: %s\n", path_buffer);
1171 ierr = PetscMkdirRecursive(path_buffer); CHKERRQ(ierr);
1172 }
1173 }
1174 }
1175
1176 // Particle output directory
1177 if(pps->outputParticles){
1178 const char *last_slash_particle = strrchr(pps->particle_output_prefix, '/');
1179 if(last_slash_particle){
1180 size_t dir_len = last_slash_particle - pps->particle_output_prefix;
1181 if(dir_len > 0){
1182 if(dir_len > sizeof(path_buffer)) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"Post-processing particle output prefix path is too long.");
1183 strncpy(path_buffer, pps->particle_output_prefix, dir_len);
1184 path_buffer[dir_len] = '\0';
1185
1186 ierr = PetscTestDirectory(path_buffer, 'r', &exists); CHKERRQ(ierr);
1187
1188 if (!exists){
1189 LOG_ALLOW(GLOBAL, LOG_INFO, "Creating post-processing Particle output directory: %s\n", path_buffer);
1190 ierr = PetscMkdirRecursive(path_buffer); CHKERRQ(ierr);
1191 }
1192 }
1193 }
1194 }
1195
1196 // Statistics output directory
1197 if(pps->statistics_pipeline[0] != '\0'){
1198 const char *last_slash_stats = strrchr(pps->statistics_output_prefix, '/');
1199 if(last_slash_stats){
1200 size_t dir_len = last_slash_stats - pps->statistics_output_prefix;
1201 if(dir_len > 0){
1202 if(dir_len >= sizeof(path_buffer)) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"Post-processing statistics output prefix path is too long.");
1203 strncpy(path_buffer, pps->statistics_output_prefix, dir_len);
1204 path_buffer[dir_len] = '\0';
1205
1206 ierr = PetscTestDirectory(path_buffer, 'r', &exists); CHKERRQ(ierr);
1207 if (!exists){
1208 LOG_ALLOW(GLOBAL, LOG_INFO, "Creating post-processing Statistics output directory: %s\n", path_buffer);
1209 ierr = PetscMkdirRecursive(path_buffer); CHKERRQ(ierr);
1210 }
1211 }
1212 }
1213 }
1214 }
1215 }
1216
1217 // Synchronize all processes before proceeding
1218 ierr = MPI_Barrier(PETSC_COMM_WORLD); CHKERRMPI(ierr);
1219
1220 LOG_ALLOW(GLOBAL, LOG_INFO, "--- Environment setup complete ---\n");
1221
1222 PetscFunctionReturn(0);
1223}
VerifyPathExistence
PetscErrorCode VerifyPathExistence(const char *path, PetscBool is_dir, PetscBool is_optional, const char *description, PetscBool *exists)
A parallel-safe helper to verify the existence of a generic file or directory path.
Definition io.c:1128
PetscMkdirRecursive
static PetscErrorCode PetscMkdirRecursive(const char *path)
Create a directory path recursively using PETSc-compatible error handling.
Definition setup.c:1011
__FUNCT__
#define __FUNCT__
Definition setup.c:152
PostProcessParams::statistics_output_prefix
char statistics_output_prefix[256]
basename for CSV output, e.g.
Definition variables.h:617
PostProcessParams::particle_output_prefix
char particle_output_prefix[256]
Definition variables.h:612
PostProcessParams::output_prefix
char output_prefix[256]
Definition variables.h:609
PostProcessParams::statistics_pipeline
char statistics_pipeline[1024]
e.g.
Definition variables.h:616
PostProcessParams::source_dir
char source_dir[PETSC_MAX_PATH_LEN]
Definition variables.h:598
PostProcessParams::outputParticles
PetscBool outputParticles
Definition variables.h:604
EXEC_MODE_POSTPROCESSOR
@ EXEC_MODE_POSTPROCESSOR
Definition variables.h:669
PostProcessParams
Holds all configuration parameters for a post-processing run.
Definition variables.h:596
Here is the call graph for this function:
Here is the caller graph for this function:

◆ AllocateContextHierarchy()

static PetscErrorCode AllocateContextHierarchy ( SimCtx *  simCtx)
static

Allocate the user-context objects required by every multigrid level.

Definition at line 1230 of file setup.c.

1231{
1232 PetscErrorCode ierr;
1233 UserMG *usermg = &simCtx->usermg;
1234 MGCtx *mgctx;
1235 PetscInt nblk = simCtx->block_number;
1236 PetscBool found;
1237 PetscFunctionBeginUser;
1238 PROFILE_FUNCTION_BEGIN;
1239
1240 LOG_ALLOW(GLOBAL, LOG_INFO, "Allocating context hierarchy for %d levels and %d blocks...\n", simCtx->mglevels, nblk);
1241
1242 // Store the number of levels in the UserMG struct itself
1243 usermg->mglevels = simCtx->mglevels;
1244
1245 // --- 1. Allocate the array of MGCtx structs ---
1246 ierr = PetscMalloc(usermg->mglevels * sizeof(MGCtx), &usermg->mgctx); CHKERRQ(ierr);
1247 // Zero-initialize to ensure all pointers (especially packer) are NULL
1248 ierr = PetscMemzero(usermg->mgctx, usermg->mglevels * sizeof(MGCtx)); CHKERRQ(ierr);
1249 mgctx = usermg->mgctx;
1250 LOG_ALLOW(LOCAL, LOG_DEBUG, "Rank %d: Allocated MGCtx array of size %d.\n", simCtx->rank, usermg->mglevels);
1251
1252 // --- 2. Parse semi-coarsening options (logic from MG_Initial) ---
1253 // These flags determine if a dimension is coarsened in the multigrid hierarchy.
1254 PetscInt *isc, *jsc, *ksc;
1255 ierr = PetscMalloc3(nblk, &isc, nblk, &jsc, nblk, &ksc); CHKERRQ(ierr);
1256 // Set defaults to FALSE (full coarsening)
1257 for (PetscInt i = 0; i < nblk; ++i) {
1258 isc[i] = 0; jsc[i] = 0; ksc[i] = 0;
1259 }
1260
1261// Use a temporary variable for the 'count' argument to the parsing function.
1262 // This protects the original 'nblk' which is needed for the loop bounds.
1263 PetscInt n_opts_found = nblk;
1264 ierr = PetscOptionsGetIntArray(NULL, NULL, "-mg_i_semi", isc, &n_opts_found, &found); CHKERRQ(ierr);
1265
1266 n_opts_found = nblk; // Reset the temp variable before the next call
1267 ierr = PetscOptionsGetIntArray(NULL, NULL, "-mg_j_semi", jsc, &n_opts_found, &found); CHKERRQ(ierr);
1268
1269 n_opts_found = nblk; // Reset the temp variable before the next call
1270 ierr = PetscOptionsGetIntArray(NULL, NULL, "-mg_k_semi", ksc, &n_opts_found, &found); CHKERRQ(ierr);
1271
1272 // --- 3. Loop over levels and blocks to allocate UserCtx arrays ---
1273 for (PetscInt level = 0; level < simCtx->mglevels; level++) {
1274
1275 LOG_ALLOW(LOCAL, LOG_DEBUG, "Rank %d: Setting up MG Level %d...\n", simCtx->rank, level);
1276 // Allocate the array of UserCtx structs for this level
1277 ierr = PetscMalloc(nblk * sizeof(UserCtx), &mgctx[level].user); CHKERRQ(ierr);
1278 // It's good practice to zero out the memory to avoid uninitialized values
1279 ierr = PetscMemzero(mgctx[level].user, nblk * sizeof(UserCtx)); CHKERRQ(ierr);
1280 mgctx[level].thislevel = level;
1281
1282 for (PetscInt bi = 0; bi < nblk; bi++) {
1283 UserCtx *currentUser = &mgctx[level].user[bi];
1284 LOG_ALLOW(LOCAL, LOG_DEBUG, "Rank %d: Initializing UserCtx for Level %d, Block %d.\n", simCtx->rank, level, bi);
1285
1286 // --- CRITICAL STEP: Set the back-pointer to the master context ---
1287 currentUser->simCtx = simCtx;
1288
1289 // Initialize other per-context values
1290 currentUser->thislevel = level;
1291 currentUser->_this = bi; //
1292 currentUser->mglevels = usermg->mglevels;
1293
1294 // Assign semi-coarsening flags
1295 currentUser->isc = isc[bi];
1296 currentUser->jsc = jsc[bi];
1297 currentUser->ksc = ksc[bi];
1298
1299 // Link to finer/coarser contexts for multigrid operations
1300 if (level > 0) {
1301 currentUser->user_c = &mgctx[level-1].user[bi];
1302 LOG_ALLOW_SYNC(GLOBAL, LOG_DEBUG, "Rank %d: -> Linked to coarser context (user_c).\n", simCtx->rank);
1303 }
1304 if (level < usermg->mglevels - 1) {
1305 currentUser->user_f = &mgctx[level+1].user[bi];
1306 LOG_ALLOW_SYNC(GLOBAL, LOG_DEBUG, "Rank %d: -> Linked to finer context (user_f).\n", simCtx->rank);
1307 }
1308 }
1309 }
1310
1311 // Log a summary of the parsed flags on each rank.
1312 if (get_log_level() >= LOG_DEBUG && nblk > 0) {
1313 LOG_ALLOW(LOCAL, LOG_DEBUG, "Rank %d: Final semi-coarsening configuration view:\n", simCtx->rank);
1314 for (PetscInt bi = 0; bi < nblk; ++bi) {
1315 LOG_ALLOW(LOCAL, LOG_DEBUG, "Rank %d: Block %d: i-semi=%d, j-semi=%d, k-semi=%d\n", simCtx->rank, bi, isc[bi], jsc[bi], ksc[bi]);
1316 }
1317 }
1318
1319 // Clean up temporary arrays
1320 ierr = PetscFree3(isc, jsc, ksc); CHKERRQ(ierr);
1321
1322 LOG_ALLOW(GLOBAL, LOG_INFO, "Context hierarchy allocation complete.\n");
1323 PROFILE_FUNCTION_END;
1324 PetscFunctionReturn(0);
1325}
get_log_level
LogLevel get_log_level()
Retrieves the current logging level from the environment variable LOG_LEVEL.
Definition logging.c:87
UserCtx::isc
PetscInt isc
Definition variables.h:924
UserCtx::mglevels
PetscInt mglevels
Definition variables.h:988
UserCtx::user_f
UserCtx * user_f
Definition variables.h:989
UserCtx::simCtx
SimCtx * simCtx
Back-pointer to the master simulation context.
Definition variables.h:909
UserCtx::ksc
PetscInt ksc
Definition variables.h:924
UserCtx::_this
PetscInt _this
Definition variables.h:924
UserCtx::jsc
PetscInt jsc
Definition variables.h:924
MGCtx::thislevel
PetscInt thislevel
Definition variables.h:572
UserCtx::user_c
UserCtx * user_c
Definition variables.h:989
UserCtx::thislevel
PetscInt thislevel
Definition variables.h:988
MGCtx
Context for Multigrid operations.
Definition variables.h:570
UserMG
User-level context for managing the entire multigrid hierarchy.
Definition variables.h:577
Here is the call graph for this function:
Here is the caller graph for this function:

◆ SetupSolverParameters()

static PetscErrorCode SetupSolverParameters ( SimCtx *  simCtx)
static

Configure solver tolerances, operators, and time-integration controls from the context.

Definition at line 1332 of file setup.c.

1332 {
1333
1334 PetscFunctionBeginUser;
1335 PROFILE_FUNCTION_BEGIN;
1336
1337 LOG_ALLOW(GLOBAL,LOG_INFO, " -- Setting up solver parameters -- .\n");
1338
1339 UserMG *usermg = &simCtx->usermg;
1340 MGCtx *mgctx = usermg->mgctx;
1341 PetscInt nblk = simCtx->block_number;
1342
1343 for (PetscInt level = usermg->mglevels-1; level >=0; level--) {
1344 for (PetscInt bi = 0; bi < nblk; bi++) {
1345 UserCtx *user = &mgctx[level].user[bi];
1346 LOG_ALLOW_SYNC(LOCAL, LOG_DEBUG, "Rank %d: Setting up parameters for level %d, block %d\n", simCtx->rank, level, bi);
1347
1348 user->assignedA = PETSC_FALSE;
1349 user->multinullspace = PETSC_FALSE;
1350 }
1351 }
1352 PROFILE_FUNCTION_END;
1353 PetscFunctionReturn(0);
1354}
UserCtx::assignedA
PetscBool assignedA
Definition variables.h:970
UserCtx::multinullspace
PetscBool multinullspace
Definition variables.h:967
Here is the caller graph for this function:

◆ SetupGridAndSolvers()

PetscErrorCode SetupGridAndSolvers ( SimCtx *  simCtx)

Implementation of SetupGridAndSolvers().

The main orchestrator for setting up all grid-related components.

Full API contract (arguments, ownership, side effects) is documented with the header declaration in include/setup.h.

See also
SetupGridAndSolvers()

Definition at line 1364 of file setup.c.

1365{
1366 PetscErrorCode ierr;
1367 PetscFunctionBeginUser;
1368
1369 PROFILE_FUNCTION_BEGIN;
1370
1371 LOG_ALLOW(GLOBAL, LOG_INFO, "--- Starting Grid and Solvers Setup ---\n");
1372
1373 // Phase 1: Allocate the UserMG and UserCtx hierarchy
1374 ierr = AllocateContextHierarchy(simCtx); CHKERRQ(ierr);
1375
1376 ierr = DefineAllGridDimensions(simCtx); CHKERRQ(ierr);
1377 ierr = InitializeAllGridDMs(simCtx); CHKERRQ(ierr);
1378 ierr = AssignAllGridCoordinates(simCtx); CHKERRQ(ierr);
1379 ierr = CreateAndInitializeAllVectors(simCtx); CHKERRQ(ierr);
1380 ierr = SetupSolverParameters(simCtx); CHKERRQ(ierr);
1381
1382 // NOTE: CalculateAllGridMetrics is now called inside SetupBoundaryConditions (not here) to ensure:
1383 // 1. Boundary condition configuration data (boundary_faces) is available for periodic BC corrections
1384 // 2. Computed metrics are available for inlet/outlet area calculations
1385 // This resolves the circular dependency between BC setup and metric calculations.
1386
1387 LOG_ALLOW(GLOBAL, LOG_INFO, "--- Grid and Solvers Setup Complete ---\n");
1388
1389 PROFILE_FUNCTION_END;
1390 PetscFunctionReturn(0);
1391}
DefineAllGridDimensions
PetscErrorCode DefineAllGridDimensions(SimCtx *simCtx)
Orchestrates the parsing and setting of grid dimensions for all blocks.
Definition grid.c:57
InitializeAllGridDMs
PetscErrorCode InitializeAllGridDMs(SimCtx *simCtx)
Orchestrates the creation of DMDA objects for every block and multigrid level.
Definition grid.c:276
AssignAllGridCoordinates
PetscErrorCode AssignAllGridCoordinates(SimCtx *simCtx)
Orchestrates the assignment of physical coordinates to all DMDA objects.
Definition grid.c:358
SetupSolverParameters
static PetscErrorCode SetupSolverParameters(SimCtx *simCtx)
Configure solver tolerances, operators, and time-integration controls from the context.
Definition setup.c:1332
CreateAndInitializeAllVectors
PetscErrorCode CreateAndInitializeAllVectors(SimCtx *simCtx)
Internal helper implementation: CreateAndInitializeAllVectors().
Definition setup.c:1400
AllocateContextHierarchy
static PetscErrorCode AllocateContextHierarchy(SimCtx *simCtx)
Allocate the user-context objects required by every multigrid level.
Definition setup.c:1230
Here is the call graph for this function:
Here is the caller graph for this function:

◆ CreateAndInitializeAllVectors()

PetscErrorCode CreateAndInitializeAllVectors ( SimCtx *  simCtx)

Internal helper implementation: CreateAndInitializeAllVectors().

Creates and initializes all PETSc Vec objects for all fields.

Local to this translation unit.

Definition at line 1400 of file setup.c.

1401{
1402 PetscErrorCode ierr;
1403 UserMG *usermg = &simCtx->usermg;
1404 MGCtx *mgctx = usermg->mgctx;
1405 PetscInt nblk = simCtx->block_number;
1406
1407 PetscFunctionBeginUser;
1408
1409 PROFILE_FUNCTION_BEGIN;
1410
1411 LOG_ALLOW(GLOBAL, LOG_INFO, "Creating and initializing all simulation vectors...\n");
1412
1413 for (PetscInt level = usermg->mglevels-1; level >=0; level--) {
1414 for (PetscInt bi = 0; bi < nblk; bi++) {
1415 UserCtx *user = &mgctx[level].user[bi];
1416
1417 if(!user->da || !user->fda) {
1418 SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONGSTATE, "DMs not properly initialized in UserCtx before vector creation.");
1419 }
1420
1421 LOG_ALLOW_SYNC(LOCAL, LOG_DEBUG, "Rank %d: Creating vectors for level %d, block %d\n", simCtx->rank, level, bi);
1422
1423 // --- Group A: Primary Flow Fields (Global and Local) ---
1424 // These are the core solution variables.
1425 ierr = DMCreateGlobalVector(user->fda, &user->Ucont); CHKERRQ(ierr); ierr = VecSet(user->Ucont, 0.0); CHKERRQ(ierr);
1426 ierr = DMCreateGlobalVector(user->fda, &user->Ucat); CHKERRQ(ierr); ierr = VecSet(user->Ucat, 0.0); CHKERRQ(ierr);
1427 ierr = DMCreateGlobalVector(user->da, &user->P); CHKERRQ(ierr); ierr = VecSet(user->P, 0.0); CHKERRQ(ierr);
1428 ierr = DMCreateGlobalVector(user->da, &user->Nvert); CHKERRQ(ierr); ierr = VecSet(user->Nvert, 0.0); CHKERRQ(ierr);
1429
1430 ierr = DMCreateLocalVector(user->fda, &user->lUcont); CHKERRQ(ierr); ierr = VecSet(user->lUcont, 0.0); CHKERRQ(ierr);
1431 ierr = DMCreateLocalVector(user->fda, &user->lUcat); CHKERRQ(ierr); ierr = VecSet(user->lUcat, 0.0); CHKERRQ(ierr);
1432 ierr = DMCreateLocalVector(user->da, &user->lP); CHKERRQ(ierr); ierr = VecSet(user->lP, 0.0); CHKERRQ(ierr);
1433 ierr = DMCreateLocalVector(user->da, &user->lNvert); CHKERRQ(ierr); ierr = VecSet(user->lNvert, 0.0); CHKERRQ(ierr);
1434
1435 // -- Group A2: Derived Flow Fields (Global and Local) ---
1436 ierr = VecDuplicate(user->P,&user->Diffusivity); CHKERRQ(ierr); ierr = VecSet(user->Diffusivity, 0.0); CHKERRQ(ierr);
1437 ierr = VecDuplicate(user->lP,&user->lDiffusivity); CHKERRQ(ierr); ierr = VecSet(user->lDiffusivity, 0.0); CHKERRQ(ierr);
1438 ierr = VecDuplicate(user->Ucat,&user->DiffusivityGradient); CHKERRQ(ierr); ierr = VecSet(user->DiffusivityGradient, 0.0); CHKERRQ(ierr);
1439 ierr = VecDuplicate(user->lUcat,&user->lDiffusivityGradient); CHKERRQ(ierr); ierr = VecSet(user->lDiffusivityGradient, 0.0); CHKERRQ(ierr);
1440
1441 // -- Group B: Solver Work Vectors (Global and Local) ---
1442 ierr = VecDuplicate(user->P, &user->Phi); CHKERRQ(ierr); ierr = VecSet(user->Phi, 0.0); CHKERRQ(ierr);
1443 ierr = VecDuplicate(user->lP, &user->lPhi); CHKERRQ(ierr); ierr = VecSet(user->lPhi, 0.0); CHKERRQ(ierr);
1444
1445 // --- Group C: Time-Stepping & Workspace Fields (Finest Level Only) ---
1446 if (level == usermg->mglevels - 1) {
1447 ierr = VecDuplicate(user->Ucont, &user->Ucont_o); CHKERRQ(ierr); ierr = VecSet(user->Ucont_o, 0.0); CHKERRQ(ierr);
1448 ierr = VecDuplicate(user->Ucont, &user->Ucont_rm1); CHKERRQ(ierr); ierr = VecSet(user->Ucont_rm1, 0.0); CHKERRQ(ierr);
1449 ierr = VecDuplicate(user->Ucat, &user->Ucat_o); CHKERRQ(ierr); ierr = VecSet(user->Ucat_o, 0.0); CHKERRQ(ierr);
1450 ierr = VecDuplicate(user->P, &user->P_o); CHKERRQ(ierr); ierr = VecSet(user->P_o, 0.0); CHKERRQ(ierr);
1451 ierr = VecDuplicate(user->lUcont, &user->lUcont_o); CHKERRQ(ierr); ierr = VecSet(user->lUcont_o, 0.0); CHKERRQ(ierr);
1452 ierr = VecDuplicate(user->lUcont, &user->lUcont_rm1); CHKERRQ(ierr); ierr = VecSet(user->lUcont_rm1, 0.0); CHKERRQ(ierr);
1453 ierr = DMCreateLocalVector(user->da, &user->lNvert_o); CHKERRQ(ierr); ierr = VecSet(user->lNvert_o, 0.0); CHKERRQ(ierr);
1454 ierr = VecDuplicate(user->Nvert, &user->Nvert_o); CHKERRQ(ierr); ierr = VecSet(user->Nvert_o, 0.0); CHKERRQ(ierr);
1455 }
1456
1457 // --- Group D: Grid Metrics (Face-Centered) ---
1458 ierr = DMCreateGlobalVector(user->fda, &user->Csi); CHKERRQ(ierr); ierr = VecSet(user->Csi, 0.0); CHKERRQ(ierr);
1459 ierr = VecDuplicate(user->Csi, &user->Eta); CHKERRQ(ierr); ierr = VecSet(user->Eta, 0.0); CHKERRQ(ierr);
1460 ierr = VecDuplicate(user->Csi, &user->Zet); CHKERRQ(ierr); ierr = VecSet(user->Zet, 0.0); CHKERRQ(ierr);
1461 ierr = DMCreateGlobalVector(user->da, &user->Aj); CHKERRQ(ierr); ierr = VecSet(user->Aj, 0.0); CHKERRQ(ierr);
1462
1463 ierr = DMCreateLocalVector(user->fda, &user->lCsi); CHKERRQ(ierr); ierr = VecSet(user->lCsi, 0.0); CHKERRQ(ierr);
1464 ierr = VecDuplicate(user->lCsi, &user->lEta); CHKERRQ(ierr); ierr = VecSet(user->lEta, 0.0); CHKERRQ(ierr);
1465 ierr = VecDuplicate(user->lCsi, &user->lZet); CHKERRQ(ierr); ierr = VecSet(user->lZet, 0.0); CHKERRQ(ierr);
1466 ierr = DMCreateLocalVector(user->da, &user->lAj); CHKERRQ(ierr); ierr = VecSet(user->lAj, 0.0); CHKERRQ(ierr);
1467
1468
1469 // --- Group E: Grid Metrics (Face-Centered) ---
1470 // Vector metrics are duplicated from Csi (DOF=3, fda-based)
1471 ierr = VecDuplicate(user->Csi, &user->ICsi); CHKERRQ(ierr); ierr = VecSet(user->ICsi, 0.0); CHKERRQ(ierr);
1472 ierr = VecDuplicate(user->Csi, &user->IEta); CHKERRQ(ierr); ierr = VecSet(user->IEta, 0.0); CHKERRQ(ierr);
1473 ierr = VecDuplicate(user->Csi, &user->IZet); CHKERRQ(ierr); ierr = VecSet(user->IZet, 0.0); CHKERRQ(ierr);
1474 ierr = VecDuplicate(user->Csi, &user->JCsi); CHKERRQ(ierr); ierr = VecSet(user->JCsi, 0.0); CHKERRQ(ierr);
1475 ierr = VecDuplicate(user->Csi, &user->JEta); CHKERRQ(ierr); ierr = VecSet(user->JEta, 0.0); CHKERRQ(ierr);
1476 ierr = VecDuplicate(user->Csi, &user->JZet); CHKERRQ(ierr); ierr = VecSet(user->JZet, 0.0); CHKERRQ(ierr);
1477 ierr = VecDuplicate(user->Csi, &user->KCsi); CHKERRQ(ierr); ierr = VecSet(user->KCsi, 0.0); CHKERRQ(ierr);
1478 ierr = VecDuplicate(user->Csi, &user->KEta); CHKERRQ(ierr); ierr = VecSet(user->KEta, 0.0); CHKERRQ(ierr);
1479 ierr = VecDuplicate(user->Csi, &user->KZet); CHKERRQ(ierr); ierr = VecSet(user->KZet, 0.0); CHKERRQ(ierr);
1480 // Scalar metrics are duplicated from Aj (DOF=1, da-based)
1481 ierr = VecDuplicate(user->Aj, &user->IAj); CHKERRQ(ierr); ierr = VecSet(user->IAj, 0.0); CHKERRQ(ierr);
1482 ierr = VecDuplicate(user->Aj, &user->JAj); CHKERRQ(ierr); ierr = VecSet(user->JAj, 0.0); CHKERRQ(ierr);
1483 ierr = VecDuplicate(user->Aj, &user->KAj); CHKERRQ(ierr); ierr = VecSet(user->KAj, 0.0); CHKERRQ(ierr);
1484
1485 ierr = VecDuplicate(user->lCsi, &user->lICsi); CHKERRQ(ierr); ierr = VecSet(user->lICsi, 0.0); CHKERRQ(ierr);
1486 ierr = VecDuplicate(user->lCsi, &user->lIEta); CHKERRQ(ierr); ierr = VecSet(user->lIEta, 0.0); CHKERRQ(ierr);
1487 ierr = VecDuplicate(user->lCsi, &user->lIZet); CHKERRQ(ierr); ierr = VecSet(user->lIZet, 0.0); CHKERRQ(ierr);
1488 ierr = VecDuplicate(user->lCsi, &user->lJCsi); CHKERRQ(ierr); ierr = VecSet(user->lJCsi, 0.0); CHKERRQ(ierr);
1489 ierr = VecDuplicate(user->lCsi, &user->lJEta); CHKERRQ(ierr); ierr = VecSet(user->lJEta, 0.0); CHKERRQ(ierr);
1490 ierr = VecDuplicate(user->lCsi, &user->lJZet); CHKERRQ(ierr); ierr = VecSet(user->lJZet, 0.0); CHKERRQ(ierr);
1491 ierr = VecDuplicate(user->lCsi, &user->lKCsi); CHKERRQ(ierr); ierr = VecSet(user->lKCsi, 0.0); CHKERRQ(ierr);
1492 ierr = VecDuplicate(user->lCsi, &user->lKEta); CHKERRQ(ierr); ierr = VecSet(user->lKEta, 0.0); CHKERRQ(ierr);
1493 ierr = VecDuplicate(user->lCsi, &user->lKZet); CHKERRQ(ierr); ierr = VecSet(user->lKZet, 0.0); CHKERRQ(ierr);
1494
1495 ierr = VecDuplicate(user->lAj, &user->lIAj); CHKERRQ(ierr); ierr = VecSet(user->lIAj, 0.0); CHKERRQ(ierr);
1496 ierr = VecDuplicate(user->lAj, &user->lJAj); CHKERRQ(ierr); ierr = VecSet(user->lJAj, 0.0); CHKERRQ(ierr);
1497 ierr = VecDuplicate(user->lAj, &user->lKAj); CHKERRQ(ierr); ierr = VecSet(user->lKAj, 0.0); CHKERRQ(ierr);
1498
1499 // --- Group F: Cell/Face Center Coordinates and Grid Spacing ---
1500 ierr = DMCreateGlobalVector(user->fda, &user->Cent); CHKERRQ(ierr); ierr = VecSet(user->Cent, 0.0); CHKERRQ(ierr);
1501 ierr = DMCreateLocalVector(user->fda, &user->lCent); CHKERRQ(ierr); ierr = VecSet(user->lCent, 0.0); CHKERRQ(ierr);
1502
1503 ierr = VecDuplicate(user->Cent, &user->GridSpace); CHKERRQ(ierr); ierr = VecSet(user->GridSpace, 0.0); CHKERRQ(ierr);
1504 ierr = VecDuplicate(user->lCent, &user->lGridSpace); CHKERRQ(ierr); ierr = VecSet(user->lGridSpace, 0.0); CHKERRQ(ierr);
1505
1506 ierr = VecDuplicate(user->Cent, &user->Centx); CHKERRQ(ierr); ierr = VecSet(user->Centx, 0.0); CHKERRQ(ierr);
1507 ierr = VecDuplicate(user->Cent, &user->Centy); CHKERRQ(ierr); ierr = VecSet(user->Centy, 0.0); CHKERRQ(ierr);
1508 ierr = VecDuplicate(user->Cent, &user->Centz); CHKERRQ(ierr); ierr = VecSet(user->Centz, 0.0); CHKERRQ(ierr);
1509 ierr = VecDuplicate(user->lCent, &user->lCentx); CHKERRQ(ierr); ierr = VecSet(user->lCentx, 0.0); CHKERRQ(ierr);
1510 ierr = VecDuplicate(user->lCent, &user->lCenty); CHKERRQ(ierr); ierr = VecSet(user->lCenty, 0.0); CHKERRQ(ierr);
1511 ierr = VecDuplicate(user->lCent, &user->lCentz); CHKERRQ(ierr); ierr = VecSet(user->lCentz, 0.0); CHKERRQ(ierr);
1512
1513 if(level == usermg->mglevels -1){
1514 // --- Group G: Turbulence Models (Finest Level Only) ---
1515 if (simCtx->les || simCtx->rans) {
1516 ierr = DMCreateGlobalVector(user->da, &user->Nu_t); CHKERRQ(ierr); ierr = VecSet(user->Nu_t, 0.0); CHKERRQ(ierr);
1517 ierr = DMCreateLocalVector(user->da, &user->lNu_t); CHKERRQ(ierr); ierr = VecSet(user->lNu_t, 0.0); CHKERRQ(ierr);
1518 LOG_ALLOW(GLOBAL, LOG_DEBUG, "Turbulence viscosity (Nu_t) vectors created for LES/RANS model.\n");
1519 if(simCtx->les){
1520 ierr = DMCreateGlobalVector(user->da,&user->CS); CHKERRQ(ierr); ierr = VecSet(user->CS,0.0); CHKERRQ(ierr);
1521 ierr = DMCreateLocalVector(user->da,&user->lCs); CHKERRQ(ierr); ierr = VecSet(user->lCs,0.0); CHKERRQ(ierr);
1522 LOG_ALLOW(GLOBAL, LOG_DEBUG, "Smagorinsky constant (CS) vectors created for LES model.\n");
1523 }
1524
1525 if(simCtx->wallfunction){
1526 ierr = DMCreateLocalVector(user->fda,&user->lFriction_Velocity); CHKERRQ(ierr); ierr = VecSet(user->lFriction_Velocity,0.0);
1527 }
1528 // Add K_Omega etc. here as needed
1529
1530 // Note: Add any other vectors from the legacy MG_Initial here as needed.
1531 // For example: Rhs, Forcing, turbulence Vecs (K_Omega, Nu_t)...
1532
1533 }
1534 // --- Group H: Particle Methods
1535 if(simCtx->np>0){
1536 ierr = DMCreateGlobalVector(user->da,&user->ParticleCount); CHKERRQ(ierr); ierr = VecSet(user->ParticleCount,0.0); CHKERRQ(ierr);
1537 ierr = DMCreateLocalVector(user->da,&user->lParticleCount); CHKERRQ(ierr); ierr = VecSet(user->lParticleCount,0.0); CHKERRQ(ierr);
1538 // Scalar field to hold particle scalar property (e.g., temperature, concentration)
1539 ierr = DMCreateGlobalVector(user->da,&user->Psi); CHKERRQ(ierr); ierr = VecSet(user->Psi,0.0); CHKERRQ(ierr);
1540 ierr = DMCreateLocalVector(user->da,&user->lPsi); CHKERRQ(ierr); ierr = VecSet(user->lPsi,0.0); CHKERRQ(ierr);
1541 LOG_ALLOW(GLOBAL,LOG_DEBUG,"ParticleCount & Scalar(Psi) created for %d particles.\n",simCtx->np);
1542 }
1543 }
1544 // --- Group I: Boundary Condition vectors ---
1545 ierr = DMCreateGlobalVector(user->fda, &user->Bcs.Ubcs); CHKERRQ(ierr);
1546 ierr = VecSet(user->Bcs.Ubcs, 0.0); CHKERRQ(ierr);
1547 ierr = DMCreateGlobalVector(user->fda, &user->Bcs.Uch); CHKERRQ(ierr);
1548 ierr = VecSet(user->Bcs.Uch, 0.0); CHKERRQ(ierr);
1549
1550 // --- Group J: Coarsest-Level Immersed-Boundary Workspace ---
1551 // Sized from the coarsest-level DMDA, which is fixed once the DMs exist,
1552 // so this is allocated once here rather than on every Poisson solve.
1553 // FullyBlocked() guards every read with its own Blocked[] flag, so the
1554 // buffer carries no state between solves.
1555 if (level == 0 && simCtx->immersed) {
1556 ierr = PetscCalloc1((size_t)(user->info.mx * user->info.my * 2), &user->KSKE); CHKERRQ(ierr);
1557 LOG_ALLOW(LOCAL, LOG_DEBUG, "Coarsest-level KSKE workspace allocated for immersed boundaries.\n");
1558 }
1559
1560 // --- Group L: Field-Statistics Accumulators (Finest Level Only) ---
1561 // Config-counted, like the convergence-state reference fields: the window
1562 // count is resolved before this factory runs, and each accumulator is
1563 // duplicated from a vector created above so it inherits DM and layout.
1564 if (level == usermg->mglevels - 1 && FieldStatisticsIsActive(simCtx)) {
1565 ierr = PetscCalloc1((size_t)simCtx->fieldStatisticsWindowCount,
1566 &user->fieldStatisticsStorage); CHKERRQ(ierr);
1567 for (PetscInt w = 0; w < simCtx->fieldStatisticsWindowCount; ++w) {
1568 ierr = PicurvWindowStorageCreate(user,
1569 &simCtx->fieldStatisticsWindows[w].definition,
1570 &user->fieldStatisticsStorage[w]); CHKERRQ(ierr);
1571 }
1572 LOG_ALLOW(LOCAL, LOG_INFO,
1573 "Allocated accumulators for %d statistics window(s).\n",
1574 simCtx->fieldStatisticsWindowCount);
1575 }
1576
1577 // --- Group K: Corner-Staging Workspace (Finest Level Only) ---
1578 // One pair per block size. Previously these were created lazily inside
1579 // the interpolation routine and rebuilt whenever the block size changed;
1580 // allocating both here removes that churn and the cached-size check.
1581 if (level == usermg->mglevels - 1) {
1582 ierr = DMCreateGlobalVector(user->da, &user->CellScalarAtCorner); CHKERRQ(ierr);
1583 ierr = VecSet(user->CellScalarAtCorner, 0.0); CHKERRQ(ierr);
1584 ierr = DMCreateLocalVector(user->da, &user->lCellScalarAtCorner); CHKERRQ(ierr);
1585 ierr = VecSet(user->lCellScalarAtCorner, 0.0); CHKERRQ(ierr);
1586 ierr = DMCreateGlobalVector(user->fda, &user->CellVectorAtCorner); CHKERRQ(ierr);
1587 ierr = VecSet(user->CellVectorAtCorner, 0.0); CHKERRQ(ierr);
1588 ierr = DMCreateLocalVector(user->fda, &user->lCellVectorAtCorner); CHKERRQ(ierr);
1589 ierr = VecSet(user->lCellVectorAtCorner, 0.0); CHKERRQ(ierr);
1590 }
1591
1592 /* --- Group N: Statistics Output Staging (Finest Level Only) ---
1593 * The same kind of object as the corner workspace: a named buffer the
1594 * shared kernels can address, rather than simulation state. It exists only
1595 * to carry derived statistics to the nodal and VTK paths, so a run without
1596 * statistics allocates none of it. */
1597 if (level == usermg->mglevels - 1 && FieldStatisticsIsActive(simCtx)) {
1598 ierr = DMCreateGlobalVector(user->da, &user->PostScalar); CHKERRQ(ierr);
1599 ierr = VecSet(user->PostScalar, 0.0); CHKERRQ(ierr);
1600 ierr = DMCreateLocalVector(user->da, &user->lPostScalar); CHKERRQ(ierr);
1601 ierr = VecSet(user->lPostScalar, 0.0); CHKERRQ(ierr);
1602 ierr = DMCreateGlobalVector(user->da, &user->PostScalarNodal); CHKERRQ(ierr);
1603 ierr = VecSet(user->PostScalarNodal, 0.0); CHKERRQ(ierr);
1604 ierr = DMCreateGlobalVector(user->fda, &user->PostVector); CHKERRQ(ierr);
1605 ierr = VecSet(user->PostVector, 0.0); CHKERRQ(ierr);
1606 ierr = DMCreateLocalVector(user->fda, &user->lPostVector); CHKERRQ(ierr);
1607 ierr = VecSet(user->lPostVector, 0.0); CHKERRQ(ierr);
1608 ierr = DMCreateGlobalVector(user->fda, &user->PostVectorNodal); CHKERRQ(ierr);
1609 ierr = VecSet(user->PostVectorNodal, 0.0); CHKERRQ(ierr);
1610 }
1611
1612 if(level == usermg->mglevels - 1){
1613 if(simCtx->exec_mode == EXEC_MODE_POSTPROCESSOR){
1614 LOG_ALLOW(LOCAL, LOG_DEBUG, "Post-processor mode detected. Allocating derived field vectors.\n");
1615
1616 ierr = VecDuplicate(user->P, &user->P_nodal); CHKERRQ(ierr);
1617 ierr = VecSet(user->P_nodal, 0.0); CHKERRQ(ierr);
1618
1619 ierr = VecDuplicate(user->Ucat, &user->Ucat_nodal); CHKERRQ(ierr);
1620 ierr = VecSet(user->Ucat_nodal, 0.0); CHKERRQ(ierr);
1621
1622 ierr = VecDuplicate(user->P, &user->Qcrit); CHKERRQ(ierr);
1623 ierr = VecSet(user->Qcrit, 0.0); CHKERRQ(ierr);
1624
1625 LOG_ALLOW(LOCAL, LOG_DEBUG, "Derived field vectors P_nodal, Ucat_nodal, and Qcrit created.\n");
1626
1627 if(simCtx->np>0){
1628 ierr = VecDuplicate(user->Psi, &user->Psi_nodal); CHKERRQ(ierr);
1629 ierr = VecSet(user->Psi_nodal, 0.0); CHKERRQ(ierr);
1630
1631 LOG_ALLOW(LOCAL, LOG_DEBUG, "Derived field vector Psi_nodal created for particle scalar property.\n");
1632
1633 }
1634 }else{
1635 user->P_nodal = NULL;
1636 user->Ucat_nodal = NULL;
1637 user->Qcrit = NULL;
1638 user->Psi_nodal = NULL;
1639 }
1640 }
1641
1642 }
1643}
1644
1645 /* Config-counted vectors belong to this factory too. The convergence state
1646 * allocates a Vec array whose length comes from configuration, so it is
1647 * invoked here rather than by the caller, keeping every vector this run
1648 * owns created in one place. It depends only on option-parsed configuration
1649 * and on the vectors created above. */
1650 ierr = InitializeSolutionConvergenceState(simCtx); CHKERRQ(ierr);
1651
1652 LOG_ALLOW(GLOBAL, LOG_INFO, "All simulation vectors created and initialized.\n");
1653
1654 PROFILE_FUNCTION_END;
1655 PetscFunctionReturn(0);
1656}
InitializeSolutionConvergenceState
PetscErrorCode InitializeSolutionConvergenceState(SimCtx *simCtx)
Implementation of InitializeSolutionConvergenceState().
Definition setup.c:49
PicurvWindowStorageCreate
PetscErrorCode PicurvWindowStorageCreate(UserCtx *user, const PicurvWindowDefinition *definition, PicurvWindowStorage *storage)
Allocates the accumulator state one window owns on one block.
Definition statistics_accumulator.c:124
PicurvWindow::definition
PicurvWindowDefinition definition
Definition statistics_window.h:76
FieldStatisticsIsActive
PetscBool FieldStatisticsIsActive(const struct SimCtx *simCtx)
Reports whether this run has live field-statistics state.
UserCtx::lFriction_Velocity
Vec lFriction_Velocity
Definition variables.h:935
UserCtx::lDiffusivityGradient
Vec lDiffusivityGradient
Definition variables.h:943
UserCtx::lPostScalar
Vec lPostScalar
Definition variables.h:959
UserCtx::lCent
Vec lCent
Definition variables.h:974
UserCtx::GridSpace
Vec GridSpace
Definition variables.h:974
UserCtx::P_nodal
Vec P_nodal
Definition variables.h:1001
UserCtx::JCsi
Vec JCsi
Definition variables.h:978
UserCtx::KAj
Vec KAj
Definition variables.h:979
UserCtx::JEta
Vec JEta
Definition variables.h:978
UserCtx::Zet
Vec Zet
Definition variables.h:974
UserCtx::lIEta
Vec lIEta
Definition variables.h:977
UserCtx::KSKE
PetscInt * KSKE
Definition variables.h:966
UserCtx::lIZet
Vec lIZet
Definition variables.h:977
UserCtx::lNvert
Vec lNvert
Definition variables.h:939
UserCtx::Phi
Vec Phi
Definition variables.h:939
UserCtx::IZet
Vec IZet
Definition variables.h:977
UserCtx::Centz
Vec Centz
Definition variables.h:975
UserCtx::IEta
Vec IEta
Definition variables.h:977
UserCtx::lZet
Vec lZet
Definition variables.h:974
UserCtx::Csi
Vec Csi
Definition variables.h:974
UserCtx::lUcont_rm1
Vec lUcont_rm1
Definition variables.h:947
UserCtx::lIAj
Vec lIAj
Definition variables.h:977
UserCtx::lKEta
Vec lKEta
Definition variables.h:979
UserCtx::Ucat_nodal
Vec Ucat_nodal
Definition variables.h:1002
UserCtx::lPsi
Vec lPsi
Definition variables.h:997
UserCtx::PostScalarNodal
Vec PostScalarNodal
Definition variables.h:959
UserCtx::DiffusivityGradient
Vec DiffusivityGradient
Definition variables.h:943
UserCtx::lJCsi
Vec lJCsi
Definition variables.h:978
UserCtx::lCs
Vec lCs
Definition variables.h:982
UserCtx::Ucont
Vec Ucont
Definition variables.h:939
UserCtx::PostScalar
Vec PostScalar
Definition variables.h:959
BCS::Ubcs
Vec Ubcs
Physical Cartesian velocity at boundary faces. Full 3D array but only boundary-face entries are meani...
Definition variables.h:123
UserCtx::Qcrit
Vec Qcrit
Definition variables.h:1003
UserCtx::JZet
Vec JZet
Definition variables.h:978
UserCtx::CellScalarAtCorner
Vec CellScalarAtCorner
Definition variables.h:952
UserCtx::Centx
Vec Centx
Definition variables.h:975
UserCtx::Bcs
BCS Bcs
Definition variables.h:934
UserCtx::lPhi
Vec lPhi
Definition variables.h:939
UserCtx::lParticleCount
Vec lParticleCount
Definition variables.h:996
UserCtx::lUcont_o
Vec lUcont_o
Definition variables.h:946
UserCtx::CellVectorAtCorner
Vec CellVectorAtCorner
Definition variables.h:953
UserCtx::Ucat_o
Vec Ucat_o
Definition variables.h:946
UserCtx::lKZet
Vec lKZet
Definition variables.h:979
UserCtx::Eta
Vec Eta
Definition variables.h:974
UserCtx::lNu_t
Vec lNu_t
Definition variables.h:982
UserCtx::Nu_t
Vec Nu_t
Definition variables.h:982
UserCtx::lCellScalarAtCorner
Vec lCellScalarAtCorner
Definition variables.h:952
UserCtx::lJEta
Vec lJEta
Definition variables.h:978
UserCtx::lCsi
Vec lCsi
Definition variables.h:974
UserCtx::lGridSpace
Vec lGridSpace
Definition variables.h:974
UserCtx::ICsi
Vec ICsi
Definition variables.h:977
UserCtx::lKCsi
Vec lKCsi
Definition variables.h:979
UserCtx::Ucat
Vec Ucat
Definition variables.h:939
UserCtx::ParticleCount
Vec ParticleCount
Definition variables.h:996
UserCtx::Ucont_o
Vec Ucont_o
Definition variables.h:946
UserCtx::lCenty
Vec lCenty
Definition variables.h:976
UserCtx::PostVectorNodal
Vec PostVectorNodal
Definition variables.h:960
UserCtx::lJZet
Vec lJZet
Definition variables.h:978
UserCtx::Nvert_o
Vec Nvert_o
Definition variables.h:946
UserCtx::IAj
Vec IAj
Definition variables.h:977
UserCtx::lCellVectorAtCorner
Vec lCellVectorAtCorner
Definition variables.h:953
UserCtx::fieldStatisticsStorage
struct PicurvWindowStorage * fieldStatisticsStorage
Definition variables.h:962
UserCtx::Psi_nodal
Vec Psi_nodal
Definition variables.h:1004
UserCtx::JAj
Vec JAj
Definition variables.h:978
UserCtx::lPostVector
Vec lPostVector
Definition variables.h:960
UserCtx::KEta
Vec KEta
Definition variables.h:979
UserCtx::lCentx
Vec lCentx
Definition variables.h:976
UserCtx::Ucont_rm1
Vec Ucont_rm1
Definition variables.h:947
UserCtx::lUcont
Vec lUcont
Definition variables.h:939
UserCtx::Diffusivity
Vec Diffusivity
Definition variables.h:942
UserCtx::lAj
Vec lAj
Definition variables.h:974
UserCtx::lICsi
Vec lICsi
Definition variables.h:977
UserCtx::info
DMDALocalInfo info
Definition variables.h:918
UserCtx::lUcat
Vec lUcat
Definition variables.h:939
UserCtx::lEta
Vec lEta
Definition variables.h:974
UserCtx::PostVector
Vec PostVector
Definition variables.h:960
UserCtx::KZet
Vec KZet
Definition variables.h:979
UserCtx::Cent
Vec Cent
Definition variables.h:974
UserCtx::Nvert
Vec Nvert
Definition variables.h:939
UserCtx::KCsi
Vec KCsi
Definition variables.h:979
UserCtx::lDiffusivity
Vec lDiffusivity
Definition variables.h:942
UserCtx::lNvert_o
Vec lNvert_o
Definition variables.h:946
UserCtx::Centy
Vec Centy
Definition variables.h:975
UserCtx::lCentz
Vec lCentz
Definition variables.h:976
UserCtx::lJAj
Vec lJAj
Definition variables.h:978
UserCtx::lKAj
Vec lKAj
Definition variables.h:979
UserCtx::Psi
Vec Psi
Definition variables.h:997
UserCtx::P_o
Vec P_o
Definition variables.h:946
BCS::Uch
Vec Uch
Characteristic velocity for boundary conditions.
Definition variables.h:124
Here is the call graph for this function:
Here is the caller graph for this function:

◆ RepairPeriodicNormalFaceGhosts()

static PetscErrorCode RepairPeriodicNormalFaceGhosts ( UserCtx *  user,
DM  dm,
Vec  local_vec,
PetscInt  dof,
char  face_direction,
PetscBool  component_staggered 
)
static

Repairs the adjacent normal ghost layer for periodic face-staggered data.

PETSc wraps every component with cell-style indexing. A face family instead needs its adjacent normal ghost shifted by one additional physical face. With the width-three periodic DMDA, the required value is available in the deeper PETSc ghost at -3 or n+2. Tangential ghosts retain PETSc's native wraparound.

Definition at line 1668 of file setup.c.

1671{
1672 DMDALocalInfo info;
1673 PetscInt xs, xe, ys, ye, zs, ze;
1674 PetscInt gxs, gxe, gys, gye, gzs, gze;
1675 PetscInt mx, my, mz;
1676
1677 PetscFunctionBeginUser;
1678 if (!face_direction && !component_staggered) PetscFunctionReturn(0);
1679
1680 PetscCall(DMDAGetLocalInfo(dm, &info));
1681 xs = info.xs; xe = info.xs + info.xm;
1682 ys = info.ys; ye = info.ys + info.ym;
1683 zs = info.zs; ze = info.zs + info.zm;
1684 gxs = info.gxs; gxe = info.gxs + info.gxm;
1685 gys = info.gys; gye = info.gys + info.gym;
1686 gzs = info.gzs; gze = info.gzs + info.gzm;
1687 mx = info.mx; my = info.my; mz = info.mz;
1688
1689 if (component_staggered) {
1690 Cmpnts ***array;
1691 PetscCall(DMDAVecGetArray(dm, local_vec, &array));
1692
1693 if (user->boundary_faces[BC_FACE_NEG_X].mathematical_type == PERIODIC && xs == 0) {
1694 PetscCheck(gxs <= -3, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ,
1695 "Periodic Ucont.x ghost repair requires DMDA stencil width at least 3.");
1696 for (PetscInt k = gzs; k < gze; k++) for (PetscInt j = gys; j < gye; j++)
1697 array[k][j][-1].x = array[k][j][-3].x;
1698 }
1699 if (user->boundary_faces[BC_FACE_POS_X].mathematical_type == PERIODIC && xe == mx) {
1700 PetscCheck(gxe > mx + 2, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ,
1701 "Periodic Ucont.x ghost repair requires DMDA stencil width at least 3.");
1702 for (PetscInt k = gzs; k < gze; k++) for (PetscInt j = gys; j < gye; j++)
1703 array[k][j][mx].x = array[k][j][mx + 2].x;
1704 }
1705 if (user->boundary_faces[BC_FACE_NEG_Y].mathematical_type == PERIODIC && ys == 0) {
1706 PetscCheck(gys <= -3, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ,
1707 "Periodic Ucont.y ghost repair requires DMDA stencil width at least 3.");
1708 for (PetscInt k = gzs; k < gze; k++) for (PetscInt i = gxs; i < gxe; i++)
1709 array[k][-1][i].y = array[k][-3][i].y;
1710 }
1711 if (user->boundary_faces[BC_FACE_POS_Y].mathematical_type == PERIODIC && ye == my) {
1712 PetscCheck(gye > my + 2, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ,
1713 "Periodic Ucont.y ghost repair requires DMDA stencil width at least 3.");
1714 for (PetscInt k = gzs; k < gze; k++) for (PetscInt i = gxs; i < gxe; i++)
1715 array[k][my][i].y = array[k][my + 2][i].y;
1716 }
1717 if (user->boundary_faces[BC_FACE_NEG_Z].mathematical_type == PERIODIC && zs == 0) {
1718 PetscCheck(gzs <= -3, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ,
1719 "Periodic Ucont.z ghost repair requires DMDA stencil width at least 3.");
1720 for (PetscInt j = gys; j < gye; j++) for (PetscInt i = gxs; i < gxe; i++)
1721 array[-1][j][i].z = array[-3][j][i].z;
1722 }
1723 if (user->boundary_faces[BC_FACE_POS_Z].mathematical_type == PERIODIC && ze == mz) {
1724 PetscCheck(gze > mz + 2, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ,
1725 "Periodic Ucont.z ghost repair requires DMDA stencil width at least 3.");
1726 for (PetscInt j = gys; j < gye; j++) for (PetscInt i = gxs; i < gxe; i++)
1727 array[mz][j][i].z = array[mz + 2][j][i].z;
1728 }
1729
1730 PetscCall(DMDAVecRestoreArray(dm, local_vec, &array));
1731 PetscFunctionReturn(0);
1732 }
1733
1734 if (dof == 1) {
1735 PetscReal ***array;
1736 PetscCall(DMDAVecGetArray(dm, local_vec, &array));
1737
1738 if (face_direction == 'i') {
1739 if (user->boundary_faces[BC_FACE_NEG_X].mathematical_type == PERIODIC && xs == 0) {
1740 PetscCheck(gxs <= -3, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ,
1741 "Periodic I-face ghost repair requires DMDA stencil width at least 3.");
1742 for (PetscInt k = gzs; k < gze; k++) for (PetscInt j = gys; j < gye; j++)
1743 array[k][j][-1] = array[k][j][-3];
1744 }
1745 if (user->boundary_faces[BC_FACE_POS_X].mathematical_type == PERIODIC && xe == mx) {
1746 PetscCheck(gxe > mx + 2, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ,
1747 "Periodic I-face ghost repair requires DMDA stencil width at least 3.");
1748 for (PetscInt k = gzs; k < gze; k++) for (PetscInt j = gys; j < gye; j++)
1749 array[k][j][mx] = array[k][j][mx + 2];
1750 }
1751 } else if (face_direction == 'j') {
1752 if (user->boundary_faces[BC_FACE_NEG_Y].mathematical_type == PERIODIC && ys == 0) {
1753 PetscCheck(gys <= -3, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ,
1754 "Periodic J-face ghost repair requires DMDA stencil width at least 3.");
1755 for (PetscInt k = gzs; k < gze; k++) for (PetscInt i = gxs; i < gxe; i++)
1756 array[k][-1][i] = array[k][-3][i];
1757 }
1758 if (user->boundary_faces[BC_FACE_POS_Y].mathematical_type == PERIODIC && ye == my) {
1759 PetscCheck(gye > my + 2, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ,
1760 "Periodic J-face ghost repair requires DMDA stencil width at least 3.");
1761 for (PetscInt k = gzs; k < gze; k++) for (PetscInt i = gxs; i < gxe; i++)
1762 array[k][my][i] = array[k][my + 2][i];
1763 }
1764 } else if (face_direction == 'k') {
1765 if (user->boundary_faces[BC_FACE_NEG_Z].mathematical_type == PERIODIC && zs == 0) {
1766 PetscCheck(gzs <= -3, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ,
1767 "Periodic K-face ghost repair requires DMDA stencil width at least 3.");
1768 for (PetscInt j = gys; j < gye; j++) for (PetscInt i = gxs; i < gxe; i++)
1769 array[-1][j][i] = array[-3][j][i];
1770 }
1771 if (user->boundary_faces[BC_FACE_POS_Z].mathematical_type == PERIODIC && ze == mz) {
1772 PetscCheck(gze > mz + 2, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ,
1773 "Periodic K-face ghost repair requires DMDA stencil width at least 3.");
1774 for (PetscInt j = gys; j < gye; j++) for (PetscInt i = gxs; i < gxe; i++)
1775 array[mz][j][i] = array[mz + 2][j][i];
1776 }
1777 }
1778
1779 PetscCall(DMDAVecRestoreArray(dm, local_vec, &array));
1780 } else {
1781 Cmpnts ***array;
1782 PetscCall(DMDAVecGetArray(dm, local_vec, &array));
1783
1784 if (face_direction == 'i') {
1785 if (user->boundary_faces[BC_FACE_NEG_X].mathematical_type == PERIODIC && xs == 0) {
1786 PetscCheck(gxs <= -3, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ,
1787 "Periodic I-face ghost repair requires DMDA stencil width at least 3.");
1788 for (PetscInt k = gzs; k < gze; k++) for (PetscInt j = gys; j < gye; j++)
1789 array[k][j][-1] = array[k][j][-3];
1790 }
1791 if (user->boundary_faces[BC_FACE_POS_X].mathematical_type == PERIODIC && xe == mx) {
1792 PetscCheck(gxe > mx + 2, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ,
1793 "Periodic I-face ghost repair requires DMDA stencil width at least 3.");
1794 for (PetscInt k = gzs; k < gze; k++) for (PetscInt j = gys; j < gye; j++)
1795 array[k][j][mx] = array[k][j][mx + 2];
1796 }
1797 } else if (face_direction == 'j') {
1798 if (user->boundary_faces[BC_FACE_NEG_Y].mathematical_type == PERIODIC && ys == 0) {
1799 PetscCheck(gys <= -3, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ,
1800 "Periodic J-face ghost repair requires DMDA stencil width at least 3.");
1801 for (PetscInt k = gzs; k < gze; k++) for (PetscInt i = gxs; i < gxe; i++)
1802 array[k][-1][i] = array[k][-3][i];
1803 }
1804 if (user->boundary_faces[BC_FACE_POS_Y].mathematical_type == PERIODIC && ye == my) {
1805 PetscCheck(gye > my + 2, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ,
1806 "Periodic J-face ghost repair requires DMDA stencil width at least 3.");
1807 for (PetscInt k = gzs; k < gze; k++) for (PetscInt i = gxs; i < gxe; i++)
1808 array[k][my][i] = array[k][my + 2][i];
1809 }
1810 } else if (face_direction == 'k') {
1811 if (user->boundary_faces[BC_FACE_NEG_Z].mathematical_type == PERIODIC && zs == 0) {
1812 PetscCheck(gzs <= -3, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ,
1813 "Periodic K-face ghost repair requires DMDA stencil width at least 3.");
1814 for (PetscInt j = gys; j < gye; j++) for (PetscInt i = gxs; i < gxe; i++)
1815 array[-1][j][i] = array[-3][j][i];
1816 }
1817 if (user->boundary_faces[BC_FACE_POS_Z].mathematical_type == PERIODIC && ze == mz) {
1818 PetscCheck(gze > mz + 2, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ,
1819 "Periodic K-face ghost repair requires DMDA stencil width at least 3.");
1820 for (PetscInt j = gys; j < gye; j++) for (PetscInt i = gxs; i < gxe; i++)
1821 array[mz][j][i] = array[mz + 2][j][i];
1822 }
1823 }
1824
1825 PetscCall(DMDAVecRestoreArray(dm, local_vec, &array));
1826 }
1827
1828 PetscFunctionReturn(0);
1829}
PERIODIC
@ PERIODIC
Definition variables.h:292
UserCtx::boundary_faces
BoundaryFaceConfig boundary_faces[6]
Definition variables.h:931
BoundaryFaceConfig::mathematical_type
BCType mathematical_type
Definition variables.h:368
BC_FACE_NEG_X
@ BC_FACE_NEG_X
Definition variables.h:262
BC_FACE_POS_Z
@ BC_FACE_POS_Z
Definition variables.h:264
BC_FACE_POS_Y
@ BC_FACE_POS_Y
Definition variables.h:263
BC_FACE_NEG_Z
@ BC_FACE_NEG_Z
Definition variables.h:264
BC_FACE_POS_X
@ BC_FACE_POS_X
Definition variables.h:262
BC_FACE_NEG_Y
@ BC_FACE_NEG_Y
Definition variables.h:263
Cmpnts
A 3D point or vector with PetscScalar components.
Definition variables.h:102
Here is the caller graph for this function:

◆ UpdateLocalGhosts()

PetscErrorCode UpdateLocalGhosts ( UserCtx *  user,
FieldId  field_id 
)

Updates a catalogued field's local ghost representation.

Updates the local vector (including ghost points) from its corresponding global vector.

Resolves the typed field view, performs the existing PETSc scatter, and applies the established periodic normal-face repair when needed.

Definition at line 1838 of file setup.c.

1839{
1840 PetscErrorCode ierr;
1841 PetscMPIInt rank;
1842 FieldView field_view;
1843 const char *field_name;
1844 Vec globalVec;
1845 Vec localVec;
1846 DM dm;
1847 PetscInt dof;
1848 char face_direction = '\0';
1849 PetscBool component_staggered = PETSC_FALSE;
1850
1851 PetscFunctionBeginUser; // Use User version for application code
1852 PROFILE_FUNCTION_BEGIN;
1853 ierr = MPI_Comm_rank(PETSC_COMM_WORLD, &rank); CHKERRQ(ierr);
1854 ierr = FieldGetView(user, field_id, &field_view); CHKERRQ(ierr);
1855 PetscCheck((field_view.descriptor->capabilities & FIELD_CAPABILITY_GHOST_UPDATE) != 0u,
1856 PETSC_COMM_SELF, PETSC_ERR_SUP,
1857 "Field '%s' does not support ghost updates.",
1858 field_view.descriptor->canonical_name);
1859 field_name = field_view.descriptor->canonical_name;
1860 globalVec = field_view.global_vec;
1861 localVec = field_view.local_vec;
1862 dm = field_view.dm;
1863 dof = field_view.descriptor->dof;
1864
1865 switch (field_view.descriptor->sync_class) {
1866 case FIELD_SYNC_I_FACE:
1867 face_direction = 'i';
1868 break;
1869 case FIELD_SYNC_J_FACE:
1870 face_direction = 'j';
1871 break;
1872 case FIELD_SYNC_K_FACE:
1873 face_direction = 'k';
1874 break;
1875 case FIELD_SYNC_COMPONENT_STAGGERED:
1876 component_staggered = PETSC_TRUE;
1877 break;
1878 case FIELD_SYNC_STANDARD:
1879 break;
1880 default:
1881 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB,
1882 "Field '%s' has an invalid ghost synchronization class.", field_name);
1883 }
1884
1885 LOG_ALLOW(GLOBAL, LOG_INFO, "Rank %d: Starting ghost update for field '%s'.\n", rank, field_name);
1886
1887 LOG_ALLOW(LOCAL, LOG_DEBUG, "Rank %d: Identified components for '%s': DM=%p, GlobalVec=%p, LocalVec=%p.\n",
1888 rank, field_name, (void*)dm, (void*)globalVec, (void*)localVec);
1889
1890 // --- 3. Optional Debugging: Norm Before Update ---
1891 // Use your logging convention check
1892 // if (get_log_level() >= LOG_LEVEL_DEBUG && is_function_allowed("UpdateLocalGhosts")) { // Example check
1893 if(get_log_level() == LOG_DEBUG && is_function_allowed(__func__)){
1894 PetscReal norm_global_before;
1895 ierr = VecNorm(globalVec, NORM_INFINITY, &norm_global_before); CHKERRQ(ierr);
1896 LOG_ALLOW(GLOBAL, LOG_INFO,"Max norm '%s' (Global) BEFORE Ghost Update: %g\n", field_name, norm_global_before);
1897 // Optional: Norm of local vector before update (might contain old ghost values)
1898 // PetscReal norm_local_before;
1899 // ierr = VecNorm(localVec, NORM_INFINITY, &norm_local_before); CHKERRQ(ierr);
1900 // LOG_ALLOW(GLOBAL, LOG_DEBUG,"Max norm '%s' (Local) BEFORE Ghost Update: %g\n", field_name, norm_local_before);
1901 }
1902
1903 // --- 4. Perform the Global-to-Local Transfer (Ghost Update) ---
1904 LOG_ALLOW(LOCAL, LOG_DEBUG, "Rank %d: Calling DMGlobalToLocalBegin/End for '%s'.\n", rank, field_name);
1905 ierr = DMGlobalToLocalBegin(dm, globalVec, INSERT_VALUES, localVec); CHKERRQ(ierr);
1906 ierr = DMGlobalToLocalEnd(dm, globalVec, INSERT_VALUES, localVec); CHKERRQ(ierr);
1907 ierr = RepairPeriodicNormalFaceGhosts(user, dm, localVec, dof, face_direction,
1908 component_staggered); CHKERRQ(ierr);
1909 LOG_ALLOW(LOCAL, LOG_DEBUG, "Rank %d: Completed DMGlobalToLocalBegin/End for '%s'.\n", rank, field_name);
1910
1911 // --- 5. Optional Debugging: Norm After Update ---
1912 // Use your logging convention check
1913 // if (get_log_level() >= LOG_LEVEL_DEBUG && is_function_allowed("UpdateLocalGhosts")) { // Example check
1914 if(get_log_level() == LOG_DEBUG && is_function_allowed(__func__)){ // Using your specific check
1915 PetscReal norm_local_after;
1916 ierr = VecNorm(localVec, NORM_INFINITY, &norm_local_after); CHKERRQ(ierr);
1917 LOG_ALLOW(GLOBAL, LOG_INFO,"Max norm '%s' (Local) AFTER Ghost Update: %g\n", field_name, norm_local_after);
1918
1919 // --- 6. Optional Debugging: Specific Point Checks (Example for Ucat on Rank 0/1) ---
1920 // (Keep this conditional if it's only for specific debug scenarios)
1921 if (field_id == FIELD_ID_UCAT) { // Only do detailed checks for Ucat for now
1922 PetscMPIInt rank_test;
1923 MPI_Comm_rank(PETSC_COMM_WORLD, &rank_test);
1924
1925 // Get Local Info needed for indexing checks
1926 DMDALocalInfo info_check;
1927 ierr = DMDAGetLocalInfo(dm, &info_check); CHKERRQ(ierr); // Use the correct dm
1928
1929 // Buffer for array pointer
1930 Cmpnts ***lUcat_arr_test = NULL;
1931 PetscErrorCode ierr_test = 0;
1932
1933 LOG_ALLOW(LOCAL, LOG_DEBUG, "Rank %d: Testing '%s' access immediately after ghost update...\n", rank_test, field_name);
1934 ierr_test = DMDAVecGetArrayDOFRead(dm, localVec, &lUcat_arr_test); // Use correct dm and localVec
1935
1936 if (ierr_test) {
1937 LOG_ALLOW(LOCAL, LOG_ERROR, "Rank %d: ERROR %d getting '%s' array after ghost update!\n", rank_test, ierr_test, field_name);
1938 } else if (!lUcat_arr_test) {
1939 LOG_ALLOW(LOCAL, LOG_ERROR, "Rank %d: ERROR NULL pointer getting '%s' array after ghost update!\n", rank_test, field_name);
1940 }
1941 else {
1942 // Check owned interior point (e.g., first interior point)
1943 PetscInt k_int = info_check.zs + (info_check.zm > 1 ? 1 : 0); // Global k index (at least zs+1 if possible)
1944 PetscInt j_int = info_check.ys + (info_check.ym > 1 ? 1 : 0); // Global j index
1945 PetscInt i_int = info_check.xs + (info_check.xm > 1 ? 1 : 0); // Global i index
1946 // Ensure indices are within global bounds if domain is very small
1947 //if (k_int >= info_check.mz-1) k_int = info_check.mz-2; if (k_int < 1) k_int = 1;
1948 //if (j_int >= info_check.my-1) j_int = info_check.my-2; if (j_int < 1) j_int = 1;
1949 // if (i_int >= info_check.mx-1) i_int = info_check.mx-2; if (i_int < 1) i_int = 1;
1950 // clamp k_int to [1 .. mz-2]
1951 if (k_int >= info_check.mz - 1) {
1952 k_int = info_check.mz - 2;
1953 }
1954 if (k_int < 1) {
1955 k_int = 1;
1956 }
1957
1958 // clamp j_int to [1 .. my-2]
1959 if (j_int >= info_check.my - 1) {
1960 j_int = info_check.my - 2;
1961 }
1962 if (j_int < 1) {
1963 j_int = 1;
1964 }
1965
1966 // clamp i_int to [1 .. mx-2]
1967 if (i_int >= info_check.mx - 1) {
1968 i_int = info_check.mx - 2;
1969 }
1970 if (i_int < 1) {
1971 i_int = 1;
1972 }
1973
1974 // Only attempt read if indices are actually owned (relevant for multi-rank)
1975 if (k_int >= info_check.zs && k_int < info_check.zs + info_check.zm &&
1976 j_int >= info_check.ys && j_int < info_check.ys + info_check.ym &&
1977 i_int >= info_check.xs && i_int < info_check.xs + info_check.xm)
1978 {
1979 LOG_ALLOW(LOCAL, LOG_DEBUG, "Rank %d: Attempting test read OWNED INTERIOR [%d][%d][%d] (Global)\n", rank_test, k_int, j_int, i_int);
1980 Cmpnts test_val_owned_interior = lUcat_arr_test[k_int][j_int][i_int];
1981 LOG_ALLOW(LOCAL, LOG_DEBUG, "Rank %d: SUCCESS reading owned interior: x=%g\n", rank_test, test_val_owned_interior.x);
1982 } else {
1983 LOG_ALLOW(LOCAL, LOG_DEBUG, "Rank %d: Skipping interior test read for non-owned index [%d][%d][%d].\n", rank_test, k_int, j_int, i_int);
1984 }
1985
1986
1987 // Check owned boundary point (e.g., first owned point)
1988 PetscInt k_bnd = info_check.zs; // Global k index
1989 PetscInt j_bnd = info_check.ys; // Global j index
1990 PetscInt i_bnd = info_check.xs; // Global i index
1991 LOG_ALLOW(LOCAL, LOG_DEBUG, "Rank %d: Attempting test read OWNED BOUNDARY [%d][%d][%d] (Global)\n", rank_test, k_bnd, j_bnd, i_bnd);
1992 Cmpnts test_val_owned_boundary = lUcat_arr_test[k_bnd][j_bnd][i_bnd];
1993 LOG_ALLOW(LOCAL, LOG_DEBUG, "Rank %d: SUCCESS reading owned boundary: x=%g\n", rank_test, test_val_owned_boundary.x);
1994
1995
1996 // Check ghost point (e.g., one layer below in k, if applicable)
1997 if (info_check.zs > 0) { // Only if there's a rank below
1998 PetscInt k_ghost = info_check.zs - 1;
1999 PetscInt j_ghost = info_check.ys; // Use start of owned y, simple example
2000 PetscInt i_ghost = info_check.xs; // Use start of owned x, simple example
2001 LOG_ALLOW(LOCAL, LOG_DEBUG, "Rank %d: Attempting test read GHOST [%d][%d][%d] (Global)\n", rank_test, k_ghost, j_ghost, i_ghost);
2002 Cmpnts test_val_ghost = lUcat_arr_test[k_ghost][j_ghost][i_ghost];
2003 LOG_ALLOW(LOCAL, LOG_DEBUG, "Rank %d: SUCCESS reading ghost: x=%g\n", rank_test, test_val_ghost.x);
2004 } else {
2005 LOG_ALLOW(LOCAL, LOG_DEBUG, "Rank %d: Skipping ghost test read (zs=0).\n", rank_test);
2006 }
2007
2008 // Restore the array
2009 ierr_test = DMDAVecRestoreArrayDOFRead(dm, localVec, &lUcat_arr_test);
2010 if(ierr_test){ LOG_ALLOW(LOCAL, LOG_ERROR, "Rank %d: ERROR %d restoring '%s' array after test read!\n", rank_test, ierr_test, field_name); }
2011 LOG_ALLOW(LOCAL, LOG_DEBUG, "Rank %d: Finished testing '%s' access.\n", rank_test, field_name);
2012 }
2013 } // end if Ucat
2014 } // end debug logging check
2015
2016 LOG_ALLOW(GLOBAL, LOG_INFO, "Rank %d: Completed ghost update for field '%s'.\n", rank, field_name);
2017 PROFILE_FUNCTION_END;
2018 PetscFunctionReturn(0);
2019}
FIELD_CAPABILITY_GHOST_UPDATE
@ FIELD_CAPABILITY_GHOST_UPDATE
Definition field_catalog.h:110
FIELD_SYNC_STANDARD
@ FIELD_SYNC_STANDARD
Definition field_catalog.h:90
FIELD_SYNC_K_FACE
@ FIELD_SYNC_K_FACE
Definition field_catalog.h:93
FIELD_SYNC_J_FACE
@ FIELD_SYNC_J_FACE
Definition field_catalog.h:92
FIELD_SYNC_COMPONENT_STAGGERED
@ FIELD_SYNC_COMPONENT_STAGGERED
Definition field_catalog.h:94
FIELD_SYNC_I_FACE
@ FIELD_SYNC_I_FACE
Definition field_catalog.h:91
FieldDescriptor::capabilities
unsigned int capabilities
Definition field_catalog.h:129
FieldView::descriptor
const FieldDescriptor * descriptor
Definition field_catalog.h:136
FieldGetView
PetscErrorCode FieldGetView(UserCtx *user, FieldId field_id, FieldView *view)
Resolve the existing DM and global/local vectors for one field.
Definition field_catalog.c:259
FieldView::local_vec
Vec local_vec
Definition field_catalog.h:139
FieldView::dm
DM dm
Definition field_catalog.h:137
FieldDescriptor::dof
PetscInt dof
Definition field_catalog.h:124
FieldView::global_vec
Vec global_vec
Definition field_catalog.h:138
FieldDescriptor::canonical_name
const char * canonical_name
Definition field_catalog.h:121
FieldDescriptor::sync_class
FieldSyncClass sync_class
Definition field_catalog.h:127
FIELD_ID_UCAT
@ FIELD_ID_UCAT
Definition field_catalog.h:26
FieldView
Non-owning runtime objects resolved for one field and UserCtx.
Definition field_catalog.h:135
is_function_allowed
PetscBool is_function_allowed(const char *functionName)
Checks if a given function is in the allow-list.
Definition logging.c:186
RepairPeriodicNormalFaceGhosts
static PetscErrorCode RepairPeriodicNormalFaceGhosts(UserCtx *user, DM dm, Vec local_vec, PetscInt dof, char face_direction, PetscBool component_staggered)
Repairs the adjacent normal ghost layer for periodic face-staggered data.
Definition setup.c:1668
Here is the call graph for this function:
Here is the caller graph for this function:

◆ SetupBoundaryConditions()

PetscErrorCode SetupBoundaryConditions ( SimCtx *  simCtx)

Internal helper implementation: SetupBoundaryConditions().

(Orchestrator) Sets up all boundary conditions for the simulation.

Local to this translation unit.

Definition at line 2027 of file setup.c.

2028{
2029 PetscErrorCode ierr;
2030 PetscFunctionBeginUser;
2031
2032 PROFILE_FUNCTION_BEGIN;
2033
2034 LOG_ALLOW(GLOBAL,LOG_INFO, "--- Setting up Boundary Conditions ---\n");
2035 // --- Phase 1: Parse and initialize BC configuration for all blocks ---
2036 LOG_ALLOW(GLOBAL,LOG_INFO,"Parsing BC configuration files and initializing boundary condition data structures.\n");
2037 UserCtx *user_finest = simCtx->usermg.mgctx[simCtx->usermg.mglevels-1].user;
2038 for (PetscInt bi = 0; bi < simCtx->block_number; bi++) {
2039 LOG_ALLOW(GLOBAL,LOG_DEBUG, " -> Processing Block %d:\n", bi);
2040
2041 // --- Generate the filename for the current block ---
2042 const char *current_bc_filename = simCtx->bcs_files[bi];
2043 LOG_ALLOW(GLOBAL,LOG_DEBUG," -> Processing Block %d using config file '%s'\n", bi, current_bc_filename);
2044 // This will populate user_finest[bi].boundary_faces
2045
2046 //ierr = ParseAllBoundaryConditions(&user_finest[bi],current_bc_filename); CHKERRQ(ierr);
2047
2048 ierr = BoundarySystem_Initialize(&user_finest[bi], current_bc_filename); CHKERRQ(ierr);
2049 }
2050
2051 // Propogate BC Configuration to coarser levels.
2052 ierr = PropagateBoundaryConfigToCoarserLevels(simCtx); CHKERRQ(ierr);
2053
2054 // Validate the geometric contract before any metric consumes periodic geometry.
2055 for (PetscInt level = simCtx->usermg.mglevels - 1; level >= 0; level--) {
2056 UserCtx *level_users = simCtx->usermg.mgctx[level].user;
2057 for (PetscInt bi = 0; bi < simCtx->block_number; bi++) {
2058 ierr = ValidatePeriodicGeometry(&level_users[bi]); CHKERRQ(ierr);
2059 }
2060 }
2061
2062 // --- Calculate Grid Metrics (requires BC configuration) ---
2063 // NOTE: This MUST be called here (after BC initialization but before inlet/outlet calculations) because:
2064 // 1. Periodic BC corrections in metric calculations need boundary_faces data to be populated
2065 // 2. Inlet/Outlet area calculations (below) require computed metrics (Csi, Eta, Zet) to be available
2066 // Previously this was in SetupGridAndSolvers, but that caused metrics to be computed without BC info.
2067 LOG_ALLOW(GLOBAL,LOG_INFO,"Computing grid metrics with boundary condition information.\n");
2068 ierr = CalculateAllGridMetrics(simCtx); CHKERRQ(ierr);
2069
2070 // --- Phase 2: Calculate inlet/outlet properties (requires computed metrics) ---
2071 LOG_ALLOW(GLOBAL,LOG_INFO,"Calculating inlet and outlet face properties.\n");
2072 for (PetscInt bi = 0; bi < simCtx->block_number; bi++) {
2073 // Call the function to calculate the center of the inlet face & the inlet area, which may be used to calculate Boundary values.
2074 ierr = CalculateInletProperties(&user_finest[bi]); CHKERRQ(ierr);
2075
2076 // Call the function to calculate the center of the outlet face & the outlet area, which may be used to calculate Boundary values.
2077 ierr = CalculateOutletProperties(&user_finest[bi]); CHKERRQ(ierr);
2078 }
2079
2080 LOG_ALLOW(GLOBAL,LOG_INFO, "--- Boundary Conditions setup complete ---\n");
2081
2082
2083 PROFILE_FUNCTION_END;
2084 PetscFunctionReturn(0);
2085}
BoundarySystem_Initialize
PetscErrorCode BoundarySystem_Initialize(UserCtx *user, const char *bcs_filename)
Initializes the entire boundary system.
Definition Boundaries.c:850
PropagateBoundaryConfigToCoarserLevels
PetscErrorCode PropagateBoundaryConfigToCoarserLevels(SimCtx *simCtx)
Propagates boundary condition configuration from finest to all coarser multigrid levels.
Definition Boundaries.c:947
CalculateAllGridMetrics
PetscErrorCode CalculateAllGridMetrics(SimCtx *simCtx)
Orchestrates the calculation of all grid metrics.
Definition Metric.c:1940
CalculateOutletProperties
PetscErrorCode CalculateOutletProperties(UserCtx *user)
Calculates the center and area of the primary OUTLET face.
Definition grid.c:1164
ValidatePeriodicGeometry
PetscErrorCode ValidatePeriodicGeometry(UserCtx *user)
Validates that configured geometric periodic seams match by translation.
Definition grid.c:421
CalculateInletProperties
PetscErrorCode CalculateInletProperties(UserCtx *user)
Calculates the center and area of the primary INLET face.
Definition grid.c:1111
Here is the call graph for this function:
Here is the caller graph for this function:

◆ Allocate3DArrayScalar()

PetscErrorCode Allocate3DArrayScalar ( PetscReal ****  array,
PetscInt  nz,
PetscInt  ny,
PetscInt  nx 
)

Internal helper implementation: Allocate3DArrayScalar().

Allocates a 3D array of PetscReal values using PetscCalloc.

Local to this translation unit.

Definition at line 2091 of file setup.c.

2092{
2093 PetscErrorCode ierr;
2094 PetscReal ***data;
2095 PetscReal *dataContiguous;
2096 PetscInt k, j;
2097
2098 PetscFunctionBegin;
2099 /* Step 1: Allocate memory for an array of nz layer pointers (zero-initialized) */
2100 ierr = PetscCalloc1(nz, &data); CHKERRQ(ierr);
2101
2102 /* Step 2: Allocate memory for all row pointers (nz * ny pointers) */
2103 ierr = PetscCalloc1(nz * ny, &data[0]); CHKERRQ(ierr);
2104 for (k = 1; k < nz; k++) {
2105 data[k] = data[0] + k * ny;
2106 }
2107
2108 /* Step 3: Allocate one contiguous block for all data elements (nz*ny*nx) */
2109 ierr = PetscCalloc1(nz * ny * nx, &dataContiguous); CHKERRQ(ierr);
2110
2111 /* Build the 3D pointer structure: each row pointer gets the correct segment of data */
2112 for (k = 0; k < nz; k++) {
2113 for (j = 0; j < ny; j++) {
2114 data[k][j] = dataContiguous + (k * ny + j) * nx;
2115 /* Memory is already zeroed by PetscCalloc1, so no manual initialization is needed */
2116 }
2117 }
2118 *array = data;
2119 PetscFunctionReturn(0);
2120}

◆ Deallocate3DArrayScalar()

PetscErrorCode Deallocate3DArrayScalar ( PetscReal ***  array,
PetscInt  nz,
PetscInt  ny 
)

Internal helper implementation: Deallocate3DArrayScalar().

Deallocates a 3D array of PetscReal values allocated by Allocate3DArrayScalar.

Local to this translation unit.

Definition at line 2126 of file setup.c.

2127{
2128 PetscErrorCode ierr;
2129 (void)nz;
2130 (void)ny;
2131
2132 PetscFunctionBegin;
2133 if (!array || !array[0] || !array[0][0] ) { // Added more robust check
2134 LOG_ALLOW(GLOBAL, LOG_WARNING, "Deallocate3DArrayScalar called with potentially unallocated or NULL array.\n");
2135 if (array) {
2136 if (array[0]) { // Check if row pointers might exist
2137 // Cannot safely access array[0][0] if array[0] might be invalid/freed
2138 // Standard deallocation below assumes valid pointers.
2139 ierr = PetscFree(array[0]); CHKERRQ(ierr); // Free row pointers if they exist
2140 }
2141 ierr = PetscFree(array); CHKERRQ(ierr); // Free layer pointers if they exist
2142 }
2143 PetscFunctionReturn(0);
2144 }
2145
2146 // --- Standard Deallocation (assuming valid allocation) ---
2147
2148 /* 1. Free the contiguous block of PetscReal values.
2149 The starting address was stored in array[0][0]. */
2150 ierr = PetscFree(array[0][0]); CHKERRQ(ierr); // Free the ACTUAL DATA
2151
2152 /* 2. Free the contiguous block of row pointers.
2153 The starting address was stored in array[0]. */
2154 ierr = PetscFree(array[0]); CHKERRQ(ierr); // Free the ROW POINTERS
2155
2156 /* 3. Free the layer pointer array.
2157 The starting address is 'array' itself. */
2158 ierr = PetscFree(array); CHKERRQ(ierr); // Free the LAYER POINTERS
2159
2160 PetscFunctionReturn(0);
2161}

◆ Allocate3DArrayVector()

PetscErrorCode Allocate3DArrayVector ( Cmpnts ****  array,
PetscInt  nz,
PetscInt  ny,
PetscInt  nx 
)

Implementation of Allocate3DArrayVector().

Allocates a contiguous 3D array of Cmpnts values.

Full API contract (arguments, ownership, side effects) is documented with the header declaration in include/setup.h.

See also
Allocate3DArrayVector()

Definition at line 2169 of file setup.c.

2170{
2171 PetscErrorCode ierr;
2172 Cmpnts ***data;
2173 Cmpnts *dataContiguous;
2174 PetscInt k, j;
2175 PetscMPIInt rank;
2176
2177 PetscFunctionBegin;
2178
2179 ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);
2180
2181 /* Step 1: Allocate memory for nz layer pointers (zeroed) */
2182 ierr = PetscCalloc1(nz, &data); CHKERRQ(ierr);
2183
2184 LOG_ALLOW(LOCAL,LOG_DEBUG," [Rank %d] memory allocated for outermost layer (%d k-layer pointers).\n",rank,nz);
2185
2186 /* Step 2: Allocate memory for all row pointers (nz * ny pointers) */
2187 ierr = PetscCalloc1(nz * ny, &data[0]); CHKERRQ(ierr);
2188 for (k = 1; k < nz; k++) {
2189 data[k] = data[0] + k * ny;
2190 }
2191
2192 LOG_ALLOW(LOCAL,LOG_DEBUG,"[Rank %d] memory allocated for %dx%d row pointers.\n",rank,nz,ny);
2193
2194 /* Step 3: Allocate one contiguous block for nz*ny*nx Cmpnts structures (zeroed) */
2195 ierr = PetscCalloc1(nz * ny * nx, &dataContiguous); CHKERRQ(ierr);
2196
2197 LOG_ALLOW(GLOBAL,LOG_DEBUG,"[Rank %d] memory allocated for contigous block of %dx%dx%d Cmpnts structures).\n",rank,nz,ny,nx);
2198
2199 /* Build the 3D pointer structure for vector data */
2200 for (k = 0; k < nz; k++) {
2201 for (j = 0; j < ny; j++) {
2202 data[k][j] = dataContiguous + (k * ny + j) * nx;
2203 /* The PetscCalloc1 call has already initialized each Cmpnts to zero. */
2204 }
2205 }
2206
2207 LOG_ALLOW(GLOBAL,LOG_DEBUG,"[Rank %d] 3D pointer structure for vector data created. \n",rank);
2208
2209 *array = data;
2210 PetscFunctionReturn(0);
2211}

◆ Deallocate3DArrayVector()

PetscErrorCode Deallocate3DArrayVector ( Cmpnts ***  array,
PetscInt  nz,
PetscInt  ny 
)

Implementation of Deallocate3DArrayVector().

Deallocates a 3D array of Cmpnts structures allocated by Allocate3DArrayVector.

Full API contract (arguments, ownership, side effects) is documented with the header declaration in include/setup.h.

See also
Deallocate3DArrayVector()

Definition at line 2219 of file setup.c.

2220{
2221 PetscErrorCode ierr;
2222 (void)nz;
2223 (void)ny;
2224
2225 PetscFunctionBegin;
2226 // If array is NULL or hasn't been allocated properly, just return.
2227 if (!array || !array[0] || !array[0][0] ) {
2228 LOG_ALLOW(GLOBAL, LOG_WARNING, "Deallocate3DArrayVector called with potentially unallocated or NULL array.\n");
2229 // Attempt to free what might exist, but be cautious
2230 if (array) {
2231 if (array[0]) { // Check if row pointers were allocated
2232 // We don't have a direct pointer to the contiguous data block
2233 // saved separately in this allocation scheme. The allocation relies
2234 // on array[0][0] pointing to it. If array[0] was freed first,
2235 // accessing array[0][0] is unsafe.
2236 // The allocation scheme where the contiguous data block is not
2237 // stored separately makes safe deallocation tricky if freeing
2238 // happens out of order or if parts are NULL.
2239
2240 // A SAFER ALLOCATION/DEALLOCATION would store the data pointer separately.
2241 // Given the current allocation scheme, the order MUST be:
2242 // 1. Free the data block (pointed to by array[0][0])
2243 // 2. Free the row pointer block (pointed to by array[0])
2244 // 3. Free the layer pointer block (pointed to by array)
2245
2246 // Let's assume the allocation was successful and pointers are valid.
2247 // Get pointer to the contiguous data block *before* freeing row pointers
2248 Cmpnts *dataContiguous = array[0][0];
2249 ierr = PetscFree(dataContiguous); CHKERRQ(ierr); // Free data block
2250
2251 // Now free the row pointers block
2252 ierr = PetscFree(array[0]); CHKERRQ(ierr); // Free row pointers
2253
2254 }
2255 // Finally, free the array of layer pointers
2256 ierr = PetscFree(array); CHKERRQ(ierr);
2257 }
2258 PetscFunctionReturn(0); // Return gracefully if input was NULL initially
2259 }
2260
2261
2262 // --- Standard Deallocation (assuming valid allocation) ---
2263
2264 /* 1. Free the contiguous block of Cmpnts structures.
2265 The starting address was stored in array[0][0] by Allocate3DArrayVector. */
2266 ierr = PetscFree(array[0][0]); CHKERRQ(ierr); // Free the ACTUAL DATA
2267
2268 /* 2. Free the contiguous block of row pointers.
2269 The starting address was stored in array[0]. */
2270 ierr = PetscFree(array[0]); CHKERRQ(ierr); // Free the ROW POINTERS
2271
2272 /* 3. Free the layer pointer array.
2273 The starting address is 'array' itself. */
2274 ierr = PetscFree(array); CHKERRQ(ierr); // Free the LAYER POINTERS
2275
2276 PetscFunctionReturn(0);
2277}

◆ GetOwnedCellRange()

PetscErrorCode GetOwnedCellRange ( const DMDALocalInfo *  info_nodes,
PetscInt  dim,
PetscInt *  xs_cell_global_out,
PetscInt *  xm_cell_local_out 
)

Internal helper implementation: GetOwnedCellRange().

Determines the global starting index and number of CELLS owned by the current processor in a specified dimension.

Local to this translation unit.

Definition at line 2285 of file setup.c.

2289{
2290 PetscErrorCode ierr = 0; // Standard PETSc error code, not explicitly set here but good practice.
2291 PetscInt xs_node_global_rank; // Global index of the first node owned by this rank in the specified dimension.
2292 PetscInt num_nodes_owned_rank; // Number of nodes owned by this rank in this dimension (local count, excluding ghosts).
2293 PetscInt GlobalNodesInDim_from_info; // Total number of DA points in this dimension, from DMDALocalInfo.
2294
2295 PetscFunctionBeginUser;
2296
2297 // --- 1. Input Validation ---
2298 if (!info_nodes || !xs_cell_global_out || !xm_cell_local_out) {
2299 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_NULL, "Null pointer passed to GetOwnedCellRange.");
2300 }
2301
2302 // --- 2. Extract Node Ownership and Global Dimension Information from DMDALocalInfo ---
2303 if (dim == 0) { // I-direction
2304 xs_node_global_rank = info_nodes->xs;
2305 num_nodes_owned_rank = info_nodes->xm;
2306 GlobalNodesInDim_from_info = info_nodes->mx;
2307 } else if (dim == 1) { // J-direction
2308 xs_node_global_rank = info_nodes->ys;
2309 num_nodes_owned_rank = info_nodes->ym;
2310 GlobalNodesInDim_from_info = info_nodes->my;
2311 } else if (dim == 2) { // K-direction
2312 xs_node_global_rank = info_nodes->zs;
2313 num_nodes_owned_rank = info_nodes->zm;
2314 GlobalNodesInDim_from_info = info_nodes->mz;
2315 } else {
2316 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid dimension %d in GetOwnedCellRange. Must be 0, 1, or 2.", dim);
2317 }
2318
2319 // --- 3. Correct for User-Defined Ghost Node ---
2320 // Per the function's contract (@warning), the DA size includes an extra, non-physical
2321 // node. We subtract 1 to get the true number of physical nodes for cell calculations.
2322 const PetscInt physical_nodes_in_dim = GlobalNodesInDim_from_info - 1;
2323
2324 // --- 4. Handle Edge Cases for Physical Domain Size ---
2325 // If the physical domain has 0 or 1 node, no cells can be formed.
2326 if (physical_nodes_in_dim <= 1) {
2327 *xs_cell_global_out = xs_node_global_rank; // Still report the rank's starting node
2328 *xm_cell_local_out = 0; // But 0 cells
2329 PetscFunctionReturn(0);
2330 }
2331
2332 // --- 5. Determine Cell Ownership Based on Corrected Node Ownership ---
2333 // The first cell this rank *could* define has its origin at the first node this rank owns.
2334 *xs_cell_global_out = xs_node_global_rank;
2335
2336 // If the rank owns no nodes in this dimension, it can't form any cell origins.
2337 if (num_nodes_owned_rank == 0) {
2338 *xm_cell_local_out = 0;
2339 } else {
2340 // --- BUG FIX APPLIED HERE ---
2341 // The previous logic incorrectly assumed a cell's end node (N_{k+1}) must be on the
2342 // same rank as its origin node (N_k). The correct logic is to find the intersection
2343 // between the nodes this rank owns and the nodes that are valid origins globally.
2344
2345 // The first node owned by the rank is its first potential origin.
2346 PetscInt first_owned_origin = xs_node_global_rank;
2347
2348 // The absolute last node owned by this rank. Any node up to and including this one
2349 // is a potential cell origin from this rank's perspective.
2350 PetscInt last_node_owned_by_rank = xs_node_global_rank + num_nodes_owned_rank - 1;
2351
2352 // The absolute last node in the entire PHYSICAL domain that can serve as a cell origin.
2353 // If there are `N` physical nodes (0 to N-1), this index is `N-2`.
2354 PetscInt last_possible_origin_global_idx = physical_nodes_in_dim - 2;
2355
2356 // The actual last origin this rank can provide is the *minimum* of what it owns
2357 // and what is globally possible. This correctly handles both ranks in the middle of
2358 // the domain and the very last rank.
2359 PetscInt actual_last_origin_this_rank_can_form = PetscMin(last_node_owned_by_rank, last_possible_origin_global_idx);
2360
2361 // If the first potential origin this rank owns is already beyond the actual last
2362 // origin it can form, then this rank forms no valid cell origins. This happens if
2363 // the rank only owns the very last physical node.
2364 if (first_owned_origin > actual_last_origin_this_rank_can_form) {
2365 *xm_cell_local_out = 0;
2366 } else {
2367 // The number of cells is the count of valid origins this rank owns.
2368 // (Count = Last Index - First Index + 1)
2369 *xm_cell_local_out = actual_last_origin_this_rank_can_form - first_owned_origin + 1;
2370 }
2371 }
2372
2373 PetscFunctionReturn(ierr);
2374}
Here is the caller graph for this function:

◆ ComputeAndStoreNeighborRanks()

PetscErrorCode ComputeAndStoreNeighborRanks ( UserCtx *  user)

Internal helper implementation: ComputeAndStoreNeighborRanks().

Computes and stores the Cartesian neighbor ranks for the DMDA decomposition.

Local to this translation unit.

Definition at line 2382 of file setup.c.

2383{
2384 PetscErrorCode ierr;
2385 PetscMPIInt rank;
2386 PetscMPIInt size; // MPI communicator size
2387 const PetscMPIInt *neighbor_ranks_ptr; // Pointer to raw neighbor data from PETSc
2388
2389 PetscFunctionBeginUser;
2390 PROFILE_FUNCTION_BEGIN;
2391 ierr = MPI_Comm_rank(PETSC_COMM_WORLD, &rank); CHKERRQ(ierr);
2392 ierr = MPI_Comm_size(PETSC_COMM_WORLD, &size); CHKERRQ(ierr); // Get MPI size for validation
2393
2394 LOG_ALLOW(GLOBAL, LOG_INFO, "Rank %d: Computing DMDA neighbor ranks.\n", rank);
2395
2396 if (!user || !user->da) {
2397 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_NULL, "UserCtx or user->da is NULL in ComputeAndStoreNeighborRanks.");
2398 }
2399
2400 // Get the neighbor information from the DMDA
2401 // neighbor_ranks_ptr will point to an internal PETSc array of 27 ranks.
2402 ierr = DMDAGetNeighbors(user->da, &neighbor_ranks_ptr); CHKERRQ(ierr);
2403
2404 // Log the raw values from DMDAGetNeighbors for boundary-relevant directions for debugging
2405 LOG_ALLOW_SYNC(GLOBAL, LOG_DEBUG, "[Rank %d]Raw DMDAGetNeighbors: xm_raw=%d, xp_raw=%d, ym_raw=%d, yp_raw=%d, zm_raw=%d, zp_raw=%d. MPI_PROC_NULL is %d.\n",
2406 rank,
2407 neighbor_ranks_ptr[12], neighbor_ranks_ptr[14],
2408 neighbor_ranks_ptr[10], neighbor_ranks_ptr[16],
2409 neighbor_ranks_ptr[4], neighbor_ranks_ptr[22],
2410 (int)MPI_PROC_NULL);
2411
2412 // PETSc standard indices for 3D face neighbors from the 27-point stencil:
2413 // Index = k_offset*9 + j_offset*3 + i_offset (where offsets -1,0,1 map to 0,1,2)
2414 // Center: (i_off=1, j_off=1, k_off=1) => 1*9 + 1*3 + 1 = 13
2415 // X-min: (i_off=0, j_off=1, k_off=1) => 1*9 + 1*3 + 0 = 12
2416 // X-plus: (i_off=2, j_off=1, k_off=1) => 1*9 + 1*3 + 2 = 14
2417 // Y-min: (i_off=1, j_off=0, k_off=1) => 1*9 + 0*3 + 1 = 10
2418 // Y-plus: (i_off=1, j_off=2, k_off=1) => 1*9 + 2*3 + 1 = 16
2419 // Z-min: (i_off=1, j_off=1, k_off=0) => 0*9 + 1*3 + 1 = 4
2420 // Z-plus: (i_off=1, j_off=1, k_off=2) => 2*9 + 1*3 + 1 = 22
2421
2422 if (neighbor_ranks_ptr[13] != rank) {
2423 LOG_ALLOW(GLOBAL, LOG_WARNING, "Rank %d: DMDAGetNeighbors center index (13) is %d, expected current rank %d. Neighbor indexing might be non-standard or DMDA small.\n",
2424 rank, neighbor_ranks_ptr[13], rank);
2425 // This warning is important. If the center isn't the current rank, the offsets are likely wrong.
2426 // However, PETSc should ensure this unless the DM is too small for a 3x3x3 stencil.
2427 }
2428
2429 // Assign and sanitize each neighbor rank
2430 PetscMPIInt temp_neighbor;
2431
2432 temp_neighbor = neighbor_ranks_ptr[12]; // xm
2433 if (temp_neighbor < 0 || temp_neighbor >= size) {
2434 LOG_ALLOW(GLOBAL, LOG_WARNING, "[Rank %d] Correcting invalid xm neighbor %d to MPI_PROC_NULL (%d).\n", rank, temp_neighbor, (int)MPI_PROC_NULL);
2435 user->neighbors.rank_xm = MPI_PROC_NULL;
2436 } else {
2437 user->neighbors.rank_xm = temp_neighbor;
2438 }
2439
2440 temp_neighbor = neighbor_ranks_ptr[14]; // xp
2441 if (temp_neighbor < 0 || temp_neighbor >= size) {
2442 LOG_ALLOW(GLOBAL, LOG_WARNING, "[Rank %d] Correcting invalid xp neighbor %d to MPI_PROC_NULL (%d).\n", rank, temp_neighbor, (int)MPI_PROC_NULL);
2443 user->neighbors.rank_xp = MPI_PROC_NULL;
2444 } else {
2445 user->neighbors.rank_xp = temp_neighbor;
2446 }
2447
2448 temp_neighbor = neighbor_ranks_ptr[10]; // ym
2449 if (temp_neighbor < 0 || temp_neighbor >= size) {
2450 LOG_ALLOW(GLOBAL, LOG_WARNING, "[Rank %d] Correcting invalid ym neighbor %d to MPI_PROC_NULL (%d).\n", rank, temp_neighbor, (int)MPI_PROC_NULL);
2451 user->neighbors.rank_ym = MPI_PROC_NULL;
2452 } else {
2453 user->neighbors.rank_ym = temp_neighbor;
2454 }
2455
2456 temp_neighbor = neighbor_ranks_ptr[16]; // yp
2457 if (temp_neighbor < 0 || temp_neighbor >= size) {
2458 // The log for index 16 was "zm" in your output, should be yp
2459 LOG_ALLOW(GLOBAL, LOG_WARNING, "[Rank %d] Correcting invalid yp neighbor (raw index 16) %d to MPI_PROC_NULL (%d).\n", rank, temp_neighbor, (int)MPI_PROC_NULL);
2460 user->neighbors.rank_yp = MPI_PROC_NULL;
2461 } else {
2462 user->neighbors.rank_yp = temp_neighbor;
2463 }
2464
2465 temp_neighbor = neighbor_ranks_ptr[4]; // zm
2466 if (temp_neighbor < 0 || temp_neighbor >= size) {
2467 LOG_ALLOW(GLOBAL, LOG_WARNING, "[Rank %d] Correcting invalid zm neighbor %d to MPI_PROC_NULL (%d).\n", rank, temp_neighbor, (int)MPI_PROC_NULL);
2468 user->neighbors.rank_zm = MPI_PROC_NULL;
2469 } else {
2470 user->neighbors.rank_zm = temp_neighbor;
2471 }
2472
2473 temp_neighbor = neighbor_ranks_ptr[22]; // zp
2474 if (temp_neighbor < 0 || temp_neighbor >= size) {
2475 LOG_ALLOW(GLOBAL, LOG_WARNING, "[Rank %d] Correcting invalid zp neighbor %d to MPI_PROC_NULL (%d).\n", rank, temp_neighbor, (int)MPI_PROC_NULL);
2476 user->neighbors.rank_zp = MPI_PROC_NULL;
2477 } else {
2478 user->neighbors.rank_zp = temp_neighbor;
2479 }
2480
2481 LOG_ALLOW_SYNC(GLOBAL, LOG_DEBUG, "[Rank %d] Stored user->neighbors: xm=%d, xp=%d, ym=%d, yp=%d, zm=%d, zp=%d\n", rank,
2482 user->neighbors.rank_xm, user->neighbors.rank_xp,
2483 user->neighbors.rank_ym, user->neighbors.rank_yp,
2484 user->neighbors.rank_zm, user->neighbors.rank_zp);
2485 PetscSynchronizedFlush(PETSC_COMM_WORLD, PETSC_STDOUT); // Ensure logs are flushed
2486
2487 // Note: neighbor_ranks_ptr memory is managed by PETSc, do not free it.
2488 PROFILE_FUNCTION_END;
2489 PetscFunctionReturn(0);
2490}
RankNeighbors::rank_zm
PetscMPIInt rank_zm
Definition variables.h:199
RankNeighbors::rank_yp
PetscMPIInt rank_yp
Definition variables.h:198
RankNeighbors::rank_ym
PetscMPIInt rank_ym
Definition variables.h:198
RankNeighbors::rank_xp
PetscMPIInt rank_xp
Definition variables.h:197
UserCtx::neighbors
RankNeighbors neighbors
Definition variables.h:923
RankNeighbors::rank_xm
PetscMPIInt rank_xm
Definition variables.h:197
RankNeighbors::rank_zp
PetscMPIInt rank_zp
Definition variables.h:199
Here is the caller graph for this function:

◆ SetDMDAProcLayout()

PetscErrorCode SetDMDAProcLayout ( DM  dm,
UserCtx *  user 
)

Internal helper implementation: SetDMDAProcLayout().

Sets the processor layout for a given DMDA based on PETSc options.

Local to this translation unit.

Definition at line 2498 of file setup.c.

2499{
2500 PetscErrorCode ierr;
2501 PetscMPIInt size, rank;
2502 PetscInt px = PETSC_DECIDE, py = PETSC_DECIDE, pz = PETSC_DECIDE;
2503 PetscBool px_set = PETSC_FALSE, py_set = PETSC_FALSE, pz_set = PETSC_FALSE;
2504 SimCtx *simCtx = user->simCtx;
2505
2506 // Set no.of processors in direction 1
2507 if(simCtx->da_procs_x) {
2508 px_set = PETSC_TRUE;
2509 px = simCtx->da_procs_x;
2510 }
2511 // Set no.of processors in direction 2
2512 if(simCtx->da_procs_y) {
2513 py_set = PETSC_TRUE;
2514 py = simCtx->da_procs_y;
2515 }
2516 // Set no.of processors in direction 1
2517 if(simCtx->da_procs_z) {
2518 pz_set = PETSC_TRUE;
2519 pz = simCtx->da_procs_z;
2520 }
2521
2522 PetscFunctionBeginUser;
2523 PROFILE_FUNCTION_BEGIN;
2524 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)dm), &size); CHKERRQ(ierr);
2525 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank); CHKERRQ(ierr);
2526 LOG_ALLOW(GLOBAL, LOG_INFO, "Rank %d: Configuring DMDA processor layout for %d total processes.\n", rank, size);
2527
2528 // --- Validate User Input (Optional but Recommended) ---
2529 // Check if specified processor counts multiply to the total MPI size
2530 if (px_set && py_set && pz_set) {
2531 if (px * py * pz != size) {
2532 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_INCOMP,
2533 "Specified processor layout %d x %d x %d = %d does not match MPI size %d",
2534 px, py, pz, px * py * pz, size);
2535 }
2536 LOG_ALLOW(GLOBAL, LOG_INFO, "Using specified processor layout: %d x %d x %d\n", px, py, pz);
2537 } else if (px_set || py_set || pz_set) {
2538 // If only some are set, PETSC_DECIDE will be used for others
2539 LOG_ALLOW(GLOBAL, LOG_INFO, "Using partially specified processor layout: %d x %d x %d (PETSC_DECIDE for unspecified)\n", px, py, pz);
2540 } else {
2541 LOG_ALLOW(GLOBAL, LOG_INFO, "Using fully automatic processor layout (PETSC_DECIDE x PETSC_DECIDE x PETSC_DECIDE)\n");
2542 }
2543 // Additional checks: Ensure px, py, pz are positive if set
2544 if ((px_set && px <= 0) || (py_set && py <= 0) || (pz_set && pz <= 0)) {
2545 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Specified processor counts must be positive.");
2546 }
2547
2548
2549 // --- Apply the layout to the DMDA ---
2550 ierr = DMDASetNumProcs(dm, px, py, pz); CHKERRQ(ierr);
2551 LOG_ALLOW(GLOBAL, LOG_DEBUG, "Rank %d: DMDASetNumProcs called with px=%d, py=%d, pz=%d.\n", rank, px, py, pz);
2552
2553 // --- Store the values in UserCtx (Optional) ---
2554 // Note: If PETSC_DECIDE was used, PETSc calculates the actual values during DMSetUp.
2555 // We store the *requested* values here. To get the *actual* values used,
2556 // you would need to call DMDAGetInfo after DMSetUp.
2557 /*
2558 if (user) {
2559 user->procs_x = px;
2560 user->procs_y = py;
2561 user->procs_z = pz;
2562 }
2563 */
2564 PROFILE_FUNCTION_END;
2565 PetscFunctionReturn(0);
2566}

◆ SetupDomainRankInfo()

PetscErrorCode SetupDomainRankInfo ( SimCtx *  simCtx)

Implementation of SetupDomainRankInfo().

Sets up the full rank communication infrastructure, including neighbor ranks and bounding box exchange.

Full API contract (arguments, ownership, side effects) is documented with the header declaration in include/setup.h.

See also
SetupDomainRankInfo()

Definition at line 2576 of file setup.c.

2577{
2578 PetscErrorCode ierr;
2579 PetscInt nblk = simCtx->block_number;
2580 PetscInt size = simCtx->size;
2581 BoundingBox *final_bboxlist = NULL;
2582
2583 PetscFunctionBeginUser;
2584 PROFILE_FUNCTION_BEGIN;
2585
2586 LOG_ALLOW(GLOBAL, LOG_INFO, "Starting full rank communication setup for %d block(s).\n", nblk);
2587
2588 UserCtx *user_finest = simCtx->usermg.mgctx[simCtx->usermg.mglevels - 1].user;
2589
2590 // --- Step 1: Compute neighbor ranks (unchanged) ---
2591 for (int bi = 0; bi < nblk; bi++) {
2592 ierr = ComputeAndStoreNeighborRanks(&user_finest[bi]); CHKERRQ(ierr);
2593 }
2594 LOG_ALLOW(GLOBAL, LOG_INFO, "Neighbor ranks computed and stored for all blocks.\n");
2595
2596 // --- Step 2: Allocate the final, unified list on ALL ranks ---
2597 // Every rank will build this list in parallel.
2598 ierr = PetscMalloc1(size * nblk, &final_bboxlist); CHKERRQ(ierr);
2599
2600 // --- Step 3: Loop through each block, gather then broadcast its bbox list ---
2601 for (int bi = 0; bi < nblk; bi++) {
2602 // This is a temporary pointer for the current block's list.
2603 BoundingBox *block_bboxlist = NULL;
2604
2605 LOG_ALLOW(GLOBAL, LOG_INFO, "Processing bounding boxes for block %d...\n", bi);
2606
2607 // A) GATHER: On rank 0, block_bboxlist is allocated and filled. On others, it's NULL.
2608 ierr = GatherAllBoundingBoxes(&user_finest[bi], &block_bboxlist); CHKERRQ(ierr);
2609 LOG_ALLOW(GLOBAL, LOG_DEBUG, " -> Gather complete for block %d.\n", bi);
2610
2611 // B) BROADCAST: On non-root ranks, block_bboxlist is allocated. Then, the data
2612 // from rank 0 is broadcast to all ranks. After this call, ALL ranks have
2613 // an identical, complete copy of the bounding boxes for the current block.
2614 ierr = BroadcastAllBoundingBoxes(&user_finest[bi], &block_bboxlist); CHKERRQ(ierr);
2615 LOG_ALLOW(GLOBAL, LOG_DEBUG, " -> Broadcast complete for block %d.\n", bi);
2616
2617 // C) ASSEMBLE: Every rank now copies the data for this block into the
2618 // correct segment of its final, unified list.
2619 for (int r = 0; r < size; r++) {
2620 // The layout is [r0b0, r1b0, ..., r(size-1)b0, r0b1, r1b1, ...]
2621 final_bboxlist[bi * size + r] = block_bboxlist[r];
2622 }
2623 LOG_ALLOW(GLOBAL, LOG_DEBUG, " -> Assembly into final list complete for block %d.\n", bi);
2624
2625 // D) CLEANUP: Free the temporary list for this block on ALL ranks before the next iteration.
2626 // Your helper functions use malloc, so we must use free.
2627 free(block_bboxlist);
2628 }
2629
2630 // --- Step 4: Assign the final pointer and run the last setup step ---
2631 simCtx->bboxlist = final_bboxlist;
2632 LOG_ALLOW(GLOBAL, LOG_INFO, "Final unified bboxlist created on all ranks and stored in SimCtx.\n");
2633
2634 ierr = SetupDomainCellDecompositionMap(&user_finest[0]); CHKERRQ(ierr);
2635 LOG_ALLOW(GLOBAL, LOG_INFO, "Domain Cell Composition set and broadcasted.\n");
2636
2637 LOG_ALLOW(GLOBAL, LOG_INFO, "SetupDomainRankInfo: Completed successfully.\n");
2638
2639 PROFILE_FUNCTION_END;
2640 PetscFunctionReturn(0);
2641}
BroadcastAllBoundingBoxes
PetscErrorCode BroadcastAllBoundingBoxes(UserCtx *user, BoundingBox **bboxlist)
Broadcasts the bounding box information collected on rank 0 to all other ranks.
Definition grid.c:1061
GatherAllBoundingBoxes
PetscErrorCode GatherAllBoundingBoxes(UserCtx *user, BoundingBox **allBBoxes)
Gathers local bounding boxes from all MPI processes to rank 0.
Definition grid.c:999
ComputeAndStoreNeighborRanks
PetscErrorCode ComputeAndStoreNeighborRanks(UserCtx *user)
Internal helper implementation: ComputeAndStoreNeighborRanks().
Definition setup.c:2382
SetupDomainCellDecompositionMap
PetscErrorCode SetupDomainCellDecompositionMap(UserCtx *user)
Internal helper implementation: SetupDomainCellDecompositionMap().
Definition setup.c:2900
BoundingBox
Defines a 3D axis-aligned bounding box.
Definition variables.h:171
Here is the call graph for this function:
Here is the caller graph for this function:

◆ Contra2Cart()

PetscErrorCode Contra2Cart ( UserCtx *  user)

Internal helper implementation: Contra2Cart().

Reconstructs Cartesian velocity (Ucat) at cell centers from contravariant velocity (Ucont) defined on cell faces.

Local to this translation unit.

Definition at line 2649 of file setup.c.

2650{
2651 PetscErrorCode ierr;
2652 DMDALocalInfo info;
2653 Cmpnts ***lcsi_arr, ***leta_arr, ***lzet_arr; // Local metric arrays
2654 Cmpnts ***lucont_arr; // Local contravariant velocity array
2655 Cmpnts ***gucat_arr; // Global Cartesian velocity array
2656 PetscReal ***lnvert_arr; // Local Nvert array
2657 PetscReal ***laj_arr; // Local Jacobian Determinant inverse array
2658
2659 PetscFunctionBeginUser;
2660 PROFILE_FUNCTION_BEGIN;
2661 LOG_ALLOW(GLOBAL, LOG_DEBUG, "Starting Contravariant-to-Cartesian velocity transformation.\n");
2662
2663 // --- 1. Get DMDA Info and Check for Valid Inputs ---
2664 // All inputs (lUcont, lCsi, etc.) and outputs (Ucat) are on DMs from the UserCtx.
2665 // We get local info from fda, which governs the layout of most arrays here.
2666 ierr = DMDAGetLocalInfo(user->fda, &info); CHKERRQ(ierr);
2667 if (!user->lUcont || !user->lCsi || !user->lEta || !user->lZet || !user->lNvert || !user->Ucat) {
2668 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Contra2Cart requires lUcont, lCsi/Eta/Zet, lNvert, and Ucat to be non-NULL.");
2669 }
2670
2671
2672 // --- 2. Get Read-Only Array Access to Local Input Vectors (with ghosts) ---
2673 ierr = DMDAVecGetArrayRead(user->fda, user->lUcont, &lucont_arr); CHKERRQ(ierr);
2674 ierr = DMDAVecGetArrayRead(user->fda, user->lCsi, &lcsi_arr); CHKERRQ(ierr);
2675 ierr = DMDAVecGetArrayRead(user->fda, user->lEta, &leta_arr); CHKERRQ(ierr);
2676 ierr = DMDAVecGetArrayRead(user->fda, user->lZet, &lzet_arr); CHKERRQ(ierr);
2677 ierr = DMDAVecGetArrayRead(user->da, user->lNvert, &lnvert_arr); CHKERRQ(ierr);
2678 ierr = DMDAVecGetArrayRead(user->da, user->lAj, &laj_arr); CHKERRQ(ierr);
2679
2680 // --- 3. Get Write-Only Array Access to the Global Output Vector ---
2681 // We compute for local owned cells and write into the global vector.
2682 // PETSc handles mapping the global indices to the correct local memory locations.
2683 ierr = DMDAVecGetArray(user->fda, user->Ucat, &gucat_arr); CHKERRQ(ierr);
2684
2685
2686 // --- 4. Define Loop Bounds for INTERIOR Cells ---
2687 // We use adjusted bounds to avoid calculating Ucat on the physical domain boundaries,
2688 // as these are typically set explicitly by boundary condition functions.
2689 // The stencils use indices like i-1, j-1, k-1, so we must start loops at least at index 1.
2690 PetscInt i_start = (info.xs == 0) ? info.xs + 1 : info.xs;
2691 PetscInt i_end = (info.xs + info.xm == info.mx) ? info.xs + info.xm - 1 : info.xs + info.xm;
2692
2693 PetscInt j_start = (info.ys == 0) ? info.ys + 1 : info.ys;
2694 PetscInt j_end = (info.ys + info.ym == info.my) ? info.ys + info.ym - 1 : info.ys + info.ym;
2695
2696 PetscInt k_start = (info.zs == 0) ? info.zs + 1 : info.zs;
2697 PetscInt k_end = (info.zs + info.zm == info.mz) ? info.zs + info.zm - 1 : info.zs + info.zm;
2698
2699 // --- 5. Main Computation Loop ---
2700 // Loops over the GLOBAL indices of interior cells owned by this rank.
2701 for (PetscInt k_cell = k_start; k_cell < k_end; ++k_cell) {
2702 for (PetscInt j_cell = j_start; j_cell < j_end; ++j_cell) {
2703 for (PetscInt i_cell = i_start; i_cell < i_end; ++i_cell) {
2704
2705 // Check if the cell is a fluid cell (not solid/blanked)
2706 // if (lnvert_arr[k_cell][j_cell][i_cell] > 0.1) continue; // Skip solid/blanked cells
2707
2708 // Transformation matrix [mat] is the metric tensor at the cell center,
2709 // estimated by averaging metrics from adjacent faces.
2710 PetscReal mat[3][3];
2711
2712 // PetscReal aj_center = laj_arr[k_cell+1][j_cell+1][i_cell+1];
2713
2714 mat[0][0] = 0.5 * (lcsi_arr[k_cell][j_cell][i_cell-1].x + lcsi_arr[k_cell][j_cell][i_cell].x); //* aj_center;
2715 mat[0][1] = 0.5 * (lcsi_arr[k_cell][j_cell][i_cell-1].y + lcsi_arr[k_cell][j_cell][i_cell].y); //* aj_center;
2716 mat[0][2] = 0.5 * (lcsi_arr[k_cell][j_cell][i_cell-1].z + lcsi_arr[k_cell][j_cell][i_cell].z); //* aj_center;
2717
2718 mat[1][0] = 0.5 * (leta_arr[k_cell][j_cell-1][i_cell].x + leta_arr[k_cell][j_cell][i_cell].x); //* aj_center;
2719 mat[1][1] = 0.5 * (leta_arr[k_cell][j_cell-1][i_cell].y + leta_arr[k_cell][j_cell][i_cell].y); //* aj_center;
2720 mat[1][2] = 0.5 * (leta_arr[k_cell][j_cell-1][i_cell].z + leta_arr[k_cell][j_cell][i_cell].z); //* aj_center;
2721
2722 mat[2][0] = 0.5 * (lzet_arr[k_cell-1][j_cell][i_cell].x + lzet_arr[k_cell][j_cell][i_cell].x); //* aj_center;
2723 mat[2][1] = 0.5 * (lzet_arr[k_cell-1][j_cell][i_cell].y + lzet_arr[k_cell][j_cell][i_cell].y); //* aj_center;
2724 mat[2][2] = 0.5 * (lzet_arr[k_cell-1][j_cell][i_cell].z + lzet_arr[k_cell][j_cell][i_cell].z); //* aj_center;
2725
2726 // Contravariant velocity vector `q` at the cell center,
2727 // estimated by averaging face-based contravariant velocities.
2728 PetscReal q[3];
2729 q[0] = 0.5 * (lucont_arr[k_cell][j_cell][i_cell-1].x + lucont_arr[k_cell][j_cell][i_cell].x); // U¹ at cell center
2730 q[1] = 0.5 * (lucont_arr[k_cell][j_cell-1][i_cell].y + lucont_arr[k_cell][j_cell][i_cell].y); // U² at cell center
2731 q[2] = 0.5 * (lucont_arr[k_cell-1][j_cell][i_cell].z + lucont_arr[k_cell][j_cell][i_cell].z); // U³ at cell center
2732
2733 // Solve the 3x3 system `mat * ucat = q` using Cramer's rule.
2734 PetscReal det = mat[0][0] * (mat[1][1] * mat[2][2] - mat[1][2] * mat[2][1]) -
2735 mat[0][1] * (mat[1][0] * mat[2][2] - mat[1][2] * mat[2][0]) +
2736 mat[0][2] * (mat[1][0] * mat[2][1] - mat[1][1] * mat[2][0]);
2737
2738 if (PetscAbsReal(det) < 1.0e-18) {
2739 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_FLOP_COUNT, "Transformation matrix determinant is near zero at cell (%d,%d,%d) \n", i_cell, j_cell, k_cell);
2740 }
2741
2742 PetscReal det_inv = 1.0 / det;
2743
2744 PetscReal det0 = q[0] * (mat[1][1] * mat[2][2] - mat[1][2] * mat[2][1]) -
2745 q[1] * (mat[0][1] * mat[2][2] - mat[0][2] * mat[2][1]) +
2746 q[2] * (mat[0][1] * mat[1][2] - mat[0][2] * mat[1][1]);
2747
2748 PetscReal det1 = -q[0] * (mat[1][0] * mat[2][2] - mat[1][2] * mat[2][0]) +
2749 q[1] * (mat[0][0] * mat[2][2] - mat[0][2] * mat[2][0]) -
2750 q[2] * (mat[0][0] * mat[1][2] - mat[0][2] * mat[1][0]);
2751
2752 PetscReal det2 = q[0] * (mat[1][0] * mat[2][1] - mat[1][1] * mat[2][0]) -
2753 q[1] * (mat[0][0] * mat[2][1] - mat[0][1] * mat[2][0]) +
2754 q[2] * (mat[0][0] * mat[1][1] - mat[0][1] * mat[1][0]);
2755
2756 // Store computed Cartesian velocity in the GLOBAL Ucat array at the
2757 // array index corresponding to the cell's origin node.
2758 gucat_arr[k_cell][j_cell][i_cell].x = det0 * det_inv;
2759 gucat_arr[k_cell][j_cell][i_cell].y = det1 * det_inv;
2760 gucat_arr[k_cell][j_cell][i_cell].z = det2 * det_inv;
2761 }
2762 }
2763 }
2764
2765 // --- 6. Restore Array Access ---
2766 ierr = DMDAVecRestoreArrayRead(user->fda, user->lUcont, &lucont_arr); CHKERRQ(ierr);
2767 ierr = DMDAVecRestoreArrayRead(user->fda, user->lCsi, &lcsi_arr); CHKERRQ(ierr);
2768 ierr = DMDAVecRestoreArrayRead(user->fda, user->lEta, &leta_arr); CHKERRQ(ierr);
2769 ierr = DMDAVecRestoreArrayRead(user->fda, user->lZet, &lzet_arr); CHKERRQ(ierr);
2770 ierr = DMDAVecRestoreArrayRead(user->da, user->lNvert, &lnvert_arr); CHKERRQ(ierr);
2771 ierr = DMDAVecRestoreArrayRead(user->da, user->lAj, &laj_arr); CHKERRQ(ierr);
2772 ierr = DMDAVecRestoreArray(user->fda, user->Ucat, &gucat_arr); CHKERRQ(ierr);
2773
2774 LOG_ALLOW(GLOBAL, LOG_INFO, "Completed Contravariant-to-Cartesian velocity transformation. \n");
2775 PROFILE_FUNCTION_END;
2776 PetscFunctionReturn(0);
2777}
Here is the caller graph for this function:

◆ Cart2Contra()

PetscErrorCode Cart2Contra ( UserCtx *  user)

Convert a spatially varying Cartesian velocity field to contravariant fluxes.

Convert the ghosted Cartesian velocity field to contravariant face fluxes.

Definition at line 2784 of file setup.c.

2785{
2786 PetscErrorCode ierr;
2787 DMDALocalInfo info;
2788 const Cmpnts ***ucat_arr, ***csi_arr, ***eta_arr, ***zet_arr;
2789 Cmpnts ***ucont_arr;
2790
2791 PetscFunctionBeginUser;
2792 PROFILE_FUNCTION_BEGIN;
2793
2794 ierr = DMDAGetLocalInfo(user->fda, &info); CHKERRQ(ierr);
2795 ierr = DMDAVecGetArrayRead(user->fda, user->lUcat, &ucat_arr); CHKERRQ(ierr);
2796 ierr = DMDAVecGetArrayRead(user->fda, user->lCsi, &csi_arr); CHKERRQ(ierr);
2797 ierr = DMDAVecGetArrayRead(user->fda, user->lEta, &eta_arr); CHKERRQ(ierr);
2798 ierr = DMDAVecGetArrayRead(user->fda, user->lZet, &zet_arr); CHKERRQ(ierr);
2799 ierr = DMDAVecGetArray(user->fda, user->Ucont, &ucont_arr); CHKERRQ(ierr);
2800
2801 const PetscInt i_start = PetscMax(info.xs, 1);
2802 const PetscInt j_start = PetscMax(info.ys, 1);
2803 const PetscInt k_start = PetscMax(info.zs, 1);
2804 const PetscInt i_end = PetscMin(info.xs + info.xm, info.mx - 1);
2805 const PetscInt j_end = PetscMin(info.ys + info.ym, info.my - 1);
2806 const PetscInt k_end = PetscMin(info.zs + info.zm, info.mz - 1);
2807
2808 for (PetscInt k = k_start; k < k_end; k++) {
2809 for (PetscInt j = j_start; j < j_end; j++) {
2810 for (PetscInt i = i_start; i < i_end; i++) {
2811 const Cmpnts u_xi = {
2812 0.5 * (ucat_arr[k][j][i].x + ucat_arr[k][j][i + 1].x),
2813 0.5 * (ucat_arr[k][j][i].y + ucat_arr[k][j][i + 1].y),
2814 0.5 * (ucat_arr[k][j][i].z + ucat_arr[k][j][i + 1].z)
2815 };
2816 const Cmpnts u_eta = {
2817 0.5 * (ucat_arr[k][j][i].x + ucat_arr[k][j + 1][i].x),
2818 0.5 * (ucat_arr[k][j][i].y + ucat_arr[k][j + 1][i].y),
2819 0.5 * (ucat_arr[k][j][i].z + ucat_arr[k][j + 1][i].z)
2820 };
2821 const Cmpnts u_zeta = {
2822 0.5 * (ucat_arr[k][j][i].x + ucat_arr[k + 1][j][i].x),
2823 0.5 * (ucat_arr[k][j][i].y + ucat_arr[k + 1][j][i].y),
2824 0.5 * (ucat_arr[k][j][i].z + ucat_arr[k + 1][j][i].z)
2825 };
2826 ucont_arr[k][j][i].x = csi_arr[k][j][i].x * u_xi.x + csi_arr[k][j][i].y * u_xi.y + csi_arr[k][j][i].z * u_xi.z;
2827 ucont_arr[k][j][i].y = eta_arr[k][j][i].x * u_eta.x + eta_arr[k][j][i].y * u_eta.y + eta_arr[k][j][i].z * u_eta.z;
2828 ucont_arr[k][j][i].z = zet_arr[k][j][i].x * u_zeta.x + zet_arr[k][j][i].y * u_zeta.y + zet_arr[k][j][i].z * u_zeta.z;
2829 }
2830 }
2831 }
2832
2833 ierr = DMDAVecRestoreArray(user->fda, user->Ucont, &ucont_arr); CHKERRQ(ierr);
2834 ierr = DMDAVecRestoreArrayRead(user->fda, user->lZet, &zet_arr); CHKERRQ(ierr);
2835 ierr = DMDAVecRestoreArrayRead(user->fda, user->lEta, &eta_arr); CHKERRQ(ierr);
2836 ierr = DMDAVecRestoreArrayRead(user->fda, user->lCsi, &csi_arr); CHKERRQ(ierr);
2837 ierr = DMDAVecRestoreArrayRead(user->fda, user->lUcat, &ucat_arr); CHKERRQ(ierr);
2838
2839 PROFILE_FUNCTION_END;
2840 PetscFunctionReturn(0);
2841}
Here is the caller graph for this function:

◆ UniformCart2Contra()

PetscErrorCode UniformCart2Contra ( UserCtx *  user,
PetscReal  u,
PetscReal  v,
PetscReal  w 
)

Populate contravariant fluxes from one uniform Cartesian velocity.

Parameters
[in,out]userUserCtx for the block; Ucont is written in place.
[in]uPhysical x-velocity component.
[in]vPhysical y-velocity component.
[in]wPhysical z-velocity component.
Returns
PetscErrorCode 0 on success.

Definition at line 2853 of file setup.c.

2854{
2855 PetscErrorCode ierr;
2856 PetscFunctionBeginUser;
2857 PROFILE_FUNCTION_BEGIN;
2858
2859 DMDALocalInfo info;
2860 Cmpnts ***ucont_arr;
2861 const Cmpnts ***csi_arr, ***eta_arr, ***zet_arr;
2862
2863 ierr = DMDAGetLocalInfo(user->fda, &info); CHKERRQ(ierr);
2864 ierr = DMDAVecGetArray(user->fda, user->Ucont, &ucont_arr); CHKERRQ(ierr);
2865 ierr = DMDAVecGetArrayRead(user->fda, user->lCsi, &csi_arr); CHKERRQ(ierr);
2866 ierr = DMDAVecGetArrayRead(user->fda, user->lEta, &eta_arr); CHKERRQ(ierr);
2867 ierr = DMDAVecGetArrayRead(user->fda, user->lZet, &zet_arr); CHKERRQ(ierr);
2868
2869 const PetscInt xs = info.xs, xe = info.xs + info.xm;
2870 const PetscInt ys = info.ys, ye = info.ys + info.ym;
2871 const PetscInt zs = info.zs, ze = info.zs + info.zm;
2872
2873 for (PetscInt k = zs; k < ze; k++) {
2874 for (PetscInt j = ys; j < ye; j++) {
2875 for (PetscInt i = xs; i < xe; i++) {
2876 ucont_arr[k][j][i].x = csi_arr[k][j][i].x * u + csi_arr[k][j][i].y * v + csi_arr[k][j][i].z * w;
2877 ucont_arr[k][j][i].y = eta_arr[k][j][i].x * u + eta_arr[k][j][i].y * v + eta_arr[k][j][i].z * w;
2878 ucont_arr[k][j][i].z = zet_arr[k][j][i].x * u + zet_arr[k][j][i].y * v + zet_arr[k][j][i].z * w;
2879 }
2880 }
2881 }
2882
2883 ierr = DMDAVecRestoreArrayRead(user->fda, user->lZet, &zet_arr); CHKERRQ(ierr);
2884 ierr = DMDAVecRestoreArrayRead(user->fda, user->lEta, &eta_arr); CHKERRQ(ierr);
2885 ierr = DMDAVecRestoreArrayRead(user->fda, user->lCsi, &csi_arr); CHKERRQ(ierr);
2886 ierr = DMDAVecRestoreArray(user->fda, user->Ucont, &ucont_arr); CHKERRQ(ierr);
2887
2888 LOG_ALLOW(GLOBAL, LOG_DEBUG, "Cart2Contra: set Ucont from Cartesian (%.3f, %.3f, %.3f).\n",
2889 (double)u, (double)v, (double)w);
2890 PROFILE_FUNCTION_END;
2891 PetscFunctionReturn(0);
2892}
Here is the caller graph for this function:

◆ SetupDomainCellDecompositionMap()

PetscErrorCode SetupDomainCellDecompositionMap ( UserCtx *  user)

Internal helper implementation: SetupDomainCellDecompositionMap().

Creates and distributes a map of the domain's cell decomposition to all ranks.

Local to this translation unit.

Definition at line 2900 of file setup.c.

2901{
2902 PetscErrorCode ierr;
2903 DMDALocalInfo local_node_info;
2904 RankCellInfo my_cell_info;
2905 PetscMPIInt rank, size;
2906
2907 PetscFunctionBeginUser;
2908 PROFILE_FUNCTION_BEGIN;
2909
2910 // --- 1. Input Validation and MPI Info ---
2911 if (!user) {
2912 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_NULL, "UserCtx pointer is NULL in SetupDomainCellDecompositionMap.");
2913 }
2914 if (!user->da) {
2915 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "user->da is not initialized in SetupDomainCellDecompositionMap.");
2916 }
2917
2918 ierr = MPI_Comm_rank(PETSC_COMM_WORLD, &rank); CHKERRQ(ierr);
2919 ierr = MPI_Comm_size(PETSC_COMM_WORLD, &size); CHKERRQ(ierr);
2920
2921 LOG_ALLOW(GLOBAL, LOG_INFO, "Setting up domain cell decomposition map for %d ranks.\n", size);
2922
2923 // --- 2. Determine Local Cell Ownership ---
2924 // Get the local node ownership information from the primary DMDA.
2925 ierr = DMDAGetLocalInfo(user->da, &local_node_info); CHKERRQ(ierr);
2926
2927 // Use the robust helper function to convert node ownership to cell ownership.
2928 // A cell's index is defined by its origin node.
2929
2930 ierr = GetOwnedCellRange(&local_node_info, 0, &my_cell_info.xs_cell, &my_cell_info.xm_cell); CHKERRQ(ierr);
2931 ierr = GetOwnedCellRange(&local_node_info, 1, &my_cell_info.ys_cell, &my_cell_info.ym_cell); CHKERRQ(ierr);
2932 ierr = GetOwnedCellRange(&local_node_info, 2, &my_cell_info.zs_cell, &my_cell_info.zm_cell); CHKERRQ(ierr);
2933
2934 // Log the calculated local ownership for debugging purposes.
2935 LOG_ALLOW(LOCAL, LOG_DEBUG, "[Rank %d] Owns cells: i[%d, %d), j[%d, %d), k[%d, %d)\n",
2936 rank, my_cell_info.xs_cell, my_cell_info.xs_cell + my_cell_info.xm_cell,
2937 my_cell_info.ys_cell, my_cell_info.ys_cell + my_cell_info.ym_cell,
2938 my_cell_info.zs_cell, my_cell_info.zs_cell + my_cell_info.zm_cell);
2939
2940 // --- 3. Allocate and Distribute the Global Map ---
2941 // Allocate memory for the global map that will hold information from all ranks.
2942 ierr = PetscMalloc1(size, &user->RankCellInfoMap); CHKERRQ(ierr);
2943
2944 // Perform the collective communication to gather the `RankCellInfo` struct from every rank.
2945 // Each rank sends its `my_cell_info` and receives the complete array in `user->RankCellInfoMap`.
2946 // We use MPI_BYTE to ensure portability across different systems and struct padding.
2947 ierr = MPI_Allgather(&my_cell_info, sizeof(RankCellInfo), MPI_BYTE,
2948 user->RankCellInfoMap, sizeof(RankCellInfo), MPI_BYTE,
2949 PETSC_COMM_WORLD); CHKERRQ(ierr);
2950
2951 LOG_ALLOW(GLOBAL, LOG_INFO, "Domain cell decomposition map created and distributed successfully.\n");
2952
2953 PROFILE_FUNCTION_END;
2954 PetscFunctionReturn(0);
2955}
GetOwnedCellRange
PetscErrorCode GetOwnedCellRange(const DMDALocalInfo *info_nodes, PetscInt dim, PetscInt *xs_cell_global_out, PetscInt *xm_cell_local_out)
Internal helper implementation: GetOwnedCellRange().
Definition setup.c:2285
RankCellInfo::ys_cell
PetscInt ys_cell
Definition variables.h:204
RankCellInfo::xs_cell
PetscInt xs_cell
Definition variables.h:204
RankCellInfo::zm_cell
PetscInt zm_cell
Definition variables.h:205
RankCellInfo::zs_cell
PetscInt zs_cell
Definition variables.h:204
RankCellInfo::xm_cell
PetscInt xm_cell
Definition variables.h:205
UserCtx::RankCellInfoMap
RankCellInfo * RankCellInfoMap
Definition variables.h:995
RankCellInfo::ym_cell
PetscInt ym_cell
Definition variables.h:205
RankCellInfo
A lean struct to hold the global cell ownership range for a single MPI rank.
Definition variables.h:203
Here is the call graph for this function:
Here is the caller graph for this function:

◆ BinarySearchInt64()

PetscErrorCode BinarySearchInt64 ( PetscInt  n,
const PetscInt64  arr[],
PetscInt64  key,
PetscBool *  found 
)

Implementation of BinarySearchInt64().

Performs a binary search for a key in a sorted array of PetscInt64.

Full API contract (arguments, ownership, side effects) is documented with the header declaration in include/setup.h.

See also
BinarySearchInt64()

Definition at line 2965 of file setup.c.

2966{
2967 PetscInt low = 0, high = n - 1;
2968
2969 PetscFunctionBeginUser;
2970 PROFILE_FUNCTION_BEGIN;
2971
2972 // --- 1. Input Validation ---
2973 if (!found) {
2974 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_NULL, "Output pointer 'found' is NULL in PetscBinarySearchInt64.");
2975 }
2976 if (n > 0 && !arr) {
2977 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_NULL, "Input array 'arr' is NULL for n > 0.");
2978 }
2979
2980 // Initialize output
2981 *found = PETSC_FALSE;
2982
2983 // --- 2. Binary Search Algorithm ---
2984 while (low <= high) {
2985 // Use this form to prevent potential integer overflow on very large arrays
2986 PetscInt mid = low + (high - low) / 2;
2987
2988 if (arr[mid] == key) {
2989 *found = PETSC_TRUE; // Key found!
2990 break; // Exit the loop
2991 }
2992
2993 if (arr[mid] < key) {
2994 low = mid + 1; // Search in the right half
2995 } else {
2996 high = mid - 1; // Search in the left half
2997 }
2998 }
2999
3000 PROFILE_FUNCTION_END;
3001 PetscFunctionReturn(0);
3002}
Here is the caller graph for this function:

◆ Gidx()

static PetscInt Gidx ( PetscInt  i,
PetscInt  j,
PetscInt  k,
UserCtx *  user 
)
static

Convert logical indices into the flattened global index used by setup helpers.

Definition at line 3008 of file setup.c.

3009{
3010 PetscInt nidx;
3011 DMDALocalInfo info = user->info;
3012
3013 PetscInt mx = info.mx, my = info.my;
3014
3015 AO ao;
3016 DMDAGetAO(user->da, &ao);
3017 nidx=i+j*mx+k*mx*my;
3018
3019 AOApplicationToPetsc(ao,1,&nidx);
3020
3021 return (nidx);
3022}
Here is the caller graph for this function:

◆ ComputeDivergence()

PetscErrorCode ComputeDivergence ( UserCtx *  user)

Implementation of ComputeDivergence().

Computes the discrete divergence of the contravariant velocity field.

Full API contract (arguments, ownership, side effects) is documented with the header declaration in include/setup.h.

See also
ComputeDivergence()

Definition at line 3034 of file setup.c.

3035{
3036 DM da = user->da, fda = user->fda;
3037 DMDALocalInfo info = user->info;
3038
3039 PetscInt ti = user->simCtx->step;
3040
3041 PetscInt xs = info.xs, xe = info.xs + info.xm;
3042 PetscInt ys = info.ys, ye = info.ys + info.ym;
3043 PetscInt zs = info.zs, ze = info.zs + info.zm;
3044 PetscInt mx = info.mx, my = info.my, mz = info.mz;
3045
3046 PetscInt lxs, lys, lzs, lxe, lye, lze;
3047 PetscInt i, j, k;
3048
3049 Vec Div;
3050 PetscReal ***div, ***aj, ***nvert,***p;
3051 Cmpnts ***ucont;
3052 PetscReal maxdiv;
3053
3054 lxs = xs; lxe = xe;
3055 lys = ys; lye = ye;
3056 lzs = zs; lze = ze;
3057
3058 if (xs==0) lxs = xs+1;
3059 if (ys==0) lys = ys+1;
3060 if (zs==0) lzs = zs+1;
3061
3062 if (xe==mx) lxe = xe-1;
3063 if (ye==my) lye = ye-1;
3064 if (ze==mz) lze = ze-1;
3065
3066 PetscFunctionBeginUser;
3067 PROFILE_FUNCTION_BEGIN;
3068
3069 DMDAVecGetArray(fda,user->lUcont, &ucont);
3070 DMDAVecGetArray(da, user->lAj, &aj);
3071 VecDuplicate(user->P, &Div);
3072 DMDAVecGetArray(da, Div, &div);
3073 DMDAVecGetArray(da, user->lNvert, &nvert);
3074 DMDAVecGetArray(da, user->P, &p);
3075 for (k=lzs; k<lze; k++) {
3076 for (j=lys; j<lye; j++){
3077 for (i=lxs; i<lxe; i++) {
3078 if (k==10 && j==10 && i==1){
3079 LOG_ALLOW(LOCAL,LOG_INFO,"Pressure[10][10][1] = %f | Pressure[10][10][0] = %f \n ",p[k][j][i],p[k][j][i-1]);
3080 }
3081
3082 if (k==10 && j==10 && i==mx-3)
3083 LOG_ALLOW(LOCAL,LOG_INFO,"Pressure[10][10][%d] = %f | Pressure[10][10][%d] = %f \n ",mx-2,p[k][j][mx-2],mx-1,p[k][j][mx-1]);
3084 }
3085 }
3086 }
3087 DMDAVecRestoreArray(da, user->P, &p);
3088
3089
3090 for (k=lzs; k<lze; k++) {
3091 for (j=lys; j<lye; j++) {
3092 for (i=lxs; i<lxe; i++) {
3093 maxdiv = fabs((ucont[k][j][i].x - ucont[k][j][i-1].x +
3094 ucont[k][j][i].y - ucont[k][j-1][i].y +
3095 ucont[k][j][i].z - ucont[k-1][j][i].z)*aj[k][j][i]);
3096 if (nvert[k][j][i] + nvert[k+1][j][i] + nvert[k-1][j][i] +
3097 nvert[k][j+1][i] + nvert[k][j-1][i] +
3098 nvert[k][j][i+1] + nvert[k][j][i-1] > 0.1) maxdiv = 0.;
3099 div[k][j][i] = maxdiv;
3100
3101 }
3102 }
3103 }
3104
3105 if (zs==0) {
3106 k=0;
3107 for (j=ys; j<ye; j++) {
3108 for (i=xs; i<xe; i++) {
3109 div[k][j][i] = 0.;
3110 }
3111 }
3112 }
3113
3114 if (ze == mz) {
3115 k=mz-1;
3116 for (j=ys; j<ye; j++) {
3117 for (i=xs; i<xe; i++) {
3118 div[k][j][i] = 0.;
3119 }
3120 }
3121 }
3122
3123 if (xs==0) {
3124 i=0;
3125 for (k=zs; k<ze; k++) {
3126 for (j=ys; j<ye; j++) {
3127 div[k][j][i] = 0.;
3128 }
3129 }
3130 }
3131
3132 if (xe==mx) {
3133 i=mx-1;
3134 for (k=zs; k<ze; k++) {
3135 for (j=ys; j<ye; j++) {
3136 div[k][j][i] = 0;
3137 }
3138 }
3139 }
3140
3141 if (ys==0) {
3142 j=0;
3143 for (k=zs; k<ze; k++) {
3144 for (i=xs; i<xe; i++) {
3145 div[k][j][i] = 0.;
3146 }
3147 }
3148 }
3149
3150 if (ye==my) {
3151 j=my-1;
3152 for (k=zs; k<ze; k++) {
3153 for (i=xs; i<xe; i++) {
3154 div[k][j][i] = 0.;
3155 }
3156 }
3157 }
3158 DMDAVecRestoreArray(da, Div, &div);
3159 PetscInt MaxFlatIndex;
3160
3161 VecMax(Div, &MaxFlatIndex, &maxdiv);
3162
3163 LOG_ALLOW(GLOBAL,LOG_INFO,"[Step %d]] The Maximum Divergence is %e at flat index %d.\n",ti,maxdiv,MaxFlatIndex);
3164
3165 user->simCtx->MaxDivFlatArg = MaxFlatIndex;
3166 user->simCtx->MaxDiv = maxdiv;
3167
3168 for (k=zs; k<ze; k++) {
3169 for (j=ys; j<ye; j++) {
3170 for (i=xs; i<xe; i++) {
3171 if (Gidx(i,j,k,user) == MaxFlatIndex) {
3172 LOG_ALLOW(GLOBAL,LOG_INFO,"[Step %d] The Maximum Divergence(%e) is at location [%d][%d][%d]. \n", ti, maxdiv,k,j,i);
3173 user->simCtx->MaxDivz = k;
3174 user->simCtx->MaxDivy = j;
3175 user->simCtx->MaxDivx = i;
3176 }
3177 }
3178 }
3179 }
3180
3181
3182 DMDAVecRestoreArray(da, user->lNvert, &nvert);
3183 DMDAVecRestoreArray(fda, user->lUcont, &ucont);
3184 DMDAVecRestoreArray(da, user->lAj, &aj);
3185 VecDestroy(&Div);
3186
3187 PROFILE_FUNCTION_END;
3188 PetscFunctionReturn(0);
3189}
Gidx
static PetscInt Gidx(PetscInt i, PetscInt j, PetscInt k, UserCtx *user)
Convert logical indices into the flattened global index used by setup helpers.
Definition setup.c:3008
Here is the call graph for this function:
Here is the caller graph for this function:

◆ InitializeRandomGenerators()

PetscErrorCode InitializeRandomGenerators ( UserCtx *  user,
PetscRandom *  randx,
PetscRandom *  randy,
PetscRandom *  randz 
)

Implementation of InitializeRandomGenerators().

Initializes random number generators for assigning particle properties.

Full API contract (arguments, ownership, side effects) is documented with the header declaration in include/setup.h.

See also
InitializeRandomGenerators()

Definition at line 3200 of file setup.c.

3200 {
3201 PetscErrorCode ierr; // Error code for PETSc functions
3202 PetscMPIInt rank;
3203 PetscFunctionBeginUser;
3204 PROFILE_FUNCTION_BEGIN;
3205 MPI_Comm_rank(PETSC_COMM_WORLD, &rank);
3206
3207 // Initialize RNG for x-coordinate
3208 ierr = PetscRandomCreate(PETSC_COMM_SELF, randx); CHKERRQ(ierr);
3209 ierr = PetscRandomSetType((*randx), PETSCRAND48); CHKERRQ(ierr);
3210 ierr = PetscRandomSetInterval(*randx, user->bbox.min_coords.x, user->bbox.max_coords.x); CHKERRQ(ierr);
3211 ierr = PetscRandomSetSeed(*randx, rank + 12345); CHKERRQ(ierr); // Unique seed per rank
3212 ierr = PetscRandomSeed(*randx); CHKERRQ(ierr);
3213 LOG_ALLOW_SYNC(LOCAL,LOG_VERBOSE, "[Rank %d]Initialized RNG for X-axis.\n",rank);
3214
3215 // Initialize RNG for y-coordinate
3216 ierr = PetscRandomCreate(PETSC_COMM_SELF, randy); CHKERRQ(ierr);
3217 ierr = PetscRandomSetType((*randy), PETSCRAND48); CHKERRQ(ierr);
3218 ierr = PetscRandomSetInterval(*randy, user->bbox.min_coords.y, user->bbox.max_coords.y); CHKERRQ(ierr);
3219 ierr = PetscRandomSetSeed(*randy, rank + 67890); CHKERRQ(ierr); // Unique seed per rank
3220 ierr = PetscRandomSeed(*randy); CHKERRQ(ierr);
3221 LOG_ALLOW_SYNC(LOCAL,LOG_VERBOSE, "[Rank %d]Initialized RNG for Y-axis.\n",rank);
3222
3223 // Initialize RNG for z-coordinate
3224 ierr = PetscRandomCreate(PETSC_COMM_SELF, randz); CHKERRQ(ierr);
3225 ierr = PetscRandomSetType((*randz), PETSCRAND48); CHKERRQ(ierr);
3226 ierr = PetscRandomSetInterval(*randz, user->bbox.min_coords.z, user->bbox.max_coords.z); CHKERRQ(ierr);
3227 ierr = PetscRandomSetSeed(*randz, rank + 54321); CHKERRQ(ierr); // Unique seed per rank
3228 ierr = PetscRandomSeed(*randz); CHKERRQ(ierr);
3229 LOG_ALLOW_SYNC(LOCAL,LOG_VERBOSE, "[Rank %d]Initialized RNG for Z-axis.\n",rank);
3230
3231 PROFILE_FUNCTION_END;
3232 PetscFunctionReturn(0);
3233}
LOG_VERBOSE
@ LOG_VERBOSE
Extremely detailed logs, typically for development use only.
Definition logging.h:34
BoundingBox::max_coords
Cmpnts max_coords
Maximum x, y, z coordinates of the bounding box.
Definition variables.h:173
BoundingBox::min_coords
Cmpnts min_coords
Minimum x, y, z coordinates of the bounding box.
Definition variables.h:172
UserCtx::bbox
BoundingBox bbox
Definition variables.h:922
Here is the caller graph for this function:

◆ InitializeLogicalSpaceRNGs()

PetscErrorCode InitializeLogicalSpaceRNGs ( PetscRandom *  rand_logic_i,
PetscRandom *  rand_logic_j,
PetscRandom *  rand_logic_k 
)

Internal helper implementation: InitializeLogicalSpaceRNGs().

Initializes random number generators for logical space operations [0.0, 1.0).

Local to this translation unit.

Definition at line 3241 of file setup.c.

3241 {
3242 PetscErrorCode ierr;
3243 PetscMPIInt rank;
3244 PetscFunctionBeginUser;
3245
3246 PROFILE_FUNCTION_BEGIN;
3247
3248 ierr = MPI_Comm_rank(PETSC_COMM_WORLD, &rank); CHKERRQ(ierr);
3249
3250 // --- RNG for i-logical dimension ---
3251 ierr = PetscRandomCreate(PETSC_COMM_SELF, rand_logic_i); CHKERRQ(ierr);
3252 ierr = PetscRandomSetType((*rand_logic_i), PETSCRAND48); CHKERRQ(ierr);
3253 ierr = PetscRandomSetInterval(*rand_logic_i, 0.0, 1.0); CHKERRQ(ierr); // Key change: [0,1)
3254 ierr = PetscRandomSetSeed(*rand_logic_i, rank + 202401); CHKERRQ(ierr); // Unique seed
3255 ierr = PetscRandomSeed(*rand_logic_i); CHKERRQ(ierr);
3256 LOG_ALLOW(LOCAL,LOG_VERBOSE, "[Rank %d] Initialized RNG for i-logical dimension [0,1).\n",rank);
3257
3258 // --- RNG for j-logical dimension ---
3259 ierr = PetscRandomCreate(PETSC_COMM_SELF, rand_logic_j); CHKERRQ(ierr);
3260 ierr = PetscRandomSetType((*rand_logic_j), PETSCRAND48); CHKERRQ(ierr);
3261 ierr = PetscRandomSetInterval(*rand_logic_j, 0.0, 1.0); CHKERRQ(ierr); // Key change: [0,1)
3262 ierr = PetscRandomSetSeed(*rand_logic_j, rank + 202402); CHKERRQ(ierr);
3263 ierr = PetscRandomSeed(*rand_logic_j); CHKERRQ(ierr);
3264 LOG_ALLOW(LOCAL,LOG_VERBOSE, "[Rank %d] Initialized RNG for j-logical dimension [0,1).\n",rank);
3265
3266 // --- RNG for k-logical dimension ---
3267 ierr = PetscRandomCreate(PETSC_COMM_SELF, rand_logic_k); CHKERRQ(ierr);
3268 ierr = PetscRandomSetType((*rand_logic_k), PETSCRAND48); CHKERRQ(ierr);
3269 ierr = PetscRandomSetInterval(*rand_logic_k, 0.0, 1.0); CHKERRQ(ierr); // Key change: [0,1)
3270 ierr = PetscRandomSetSeed(*rand_logic_k, rank + 202403); CHKERRQ(ierr);
3271 ierr = PetscRandomSeed(*rand_logic_k); CHKERRQ(ierr);
3272 LOG_ALLOW(LOCAL,LOG_VERBOSE, "[Rank %d] Initialized RNG for k-logical dimension [0,1).\n",rank);
3273
3274
3275 PROFILE_FUNCTION_END;
3276 PetscFunctionReturn(0);
3277}
Here is the caller graph for this function:

◆ InitializeBrownianRNG()

PetscErrorCode InitializeBrownianRNG ( SimCtx *  simCtx)

Internal helper implementation: InitializeBrownianRNG().

Initializes a single master RNG for time-stepping physics (Brownian motion).

Local to this translation unit.

Definition at line 3285 of file setup.c.

3285 {
3286 PetscErrorCode ierr;
3287 PetscMPIInt rank;
3288
3289 PetscFunctionBeginUser;
3290 PROFILE_FUNCTION_BEGIN;
3291
3292 ierr = MPI_Comm_rank(PETSC_COMM_WORLD, &rank); CHKERRQ(ierr);
3293
3294 // 1. Create the generator (stored in SimCtx, not UserCtx, as it is global physics)
3295 ierr = PetscRandomCreate(PETSC_COMM_WORLD, &simCtx->BrownianMotionRNG); CHKERRQ(ierr);
3296 ierr = PetscRandomSetType(simCtx->BrownianMotionRNG, PETSCRAND48); CHKERRQ(ierr);
3297
3298 // 2. CRITICAL: Set interval to [0, 1).
3299 // This is required for the Gaussian math to work.
3300 ierr = PetscRandomSetInterval(simCtx->BrownianMotionRNG, 0.0, 1.0); CHKERRQ(ierr);
3301
3302 // 3. Seed based on Rank to ensure spatial randomness
3303 // Multiplying by a large prime helps separate the streams significantly
3304 unsigned long seed = (unsigned long)rank * 987654321 + (unsigned long)time(NULL);
3305 ierr = PetscRandomSetSeed(simCtx->BrownianMotionRNG, seed); CHKERRQ(ierr);
3306 ierr = PetscRandomSeed(simCtx->BrownianMotionRNG); CHKERRQ(ierr);
3307
3308 LOG_ALLOW(LOCAL, LOG_VERBOSE, "[Rank %d] Initialized Brownian Physics RNG.\n", rank);
3309
3310 PROFILE_FUNCTION_END;
3311 PetscFunctionReturn(0);
3312}
Here is the caller graph for this function:

◆ TransformScalarDerivativesToPhysical()

void TransformScalarDerivativesToPhysical ( PetscReal  jacobian,
Cmpnts  csi_metrics,
Cmpnts  eta_metrics,
Cmpnts  zet_metrics,
PetscReal  dPhi_dcsi,
PetscReal  dPhi_deta,
PetscReal  dPhi_dzet,
Cmpnts *  gradPhi 
)

Implementation of TransformScalarDerivativesToPhysical().

Transforms scalar derivatives from computational space to physical space.

Full API contract (arguments, ownership, side effects) is documented with the header declaration in include/setup.h.

See also
TransformScalarDerivativesToPhysical()

Definition at line 3324 of file setup.c.

3332{
3333 // Gradient X component
3334 gradPhi->x = jacobian * (dPhi_dcsi * csi_metrics.x + dPhi_deta * eta_metrics.x + dPhi_dzet * zet_metrics.x);
3335
3336 // Gradient Y component
3337 gradPhi->y = jacobian * (dPhi_dcsi * csi_metrics.y + dPhi_deta * eta_metrics.y + dPhi_dzet * zet_metrics.y);
3338
3339 // Gradient Z component
3340 gradPhi->z = jacobian * (dPhi_dcsi * csi_metrics.z + dPhi_deta * eta_metrics.z + dPhi_dzet * zet_metrics.z);
3341}
Here is the caller graph for this function:

◆ TransformDerivativesToPhysical()

static void TransformDerivativesToPhysical ( PetscReal  jacobian,
Cmpnts  csi_metrics,
Cmpnts  eta_metrics,
Cmpnts  zet_metrics,
Cmpnts  deriv_csi,
Cmpnts  deriv_eta,
Cmpnts  deriv_zet,
Cmpnts *  dudx,
Cmpnts *  dvdx,
Cmpnts *  dwdx 
)
static

Transform contravariant vector derivatives into physical Cartesian derivatives.

Definition at line 3348 of file setup.c.

3351{
3352 // Derivatives of the first component (u)
3353 dudx->x = jacobian * (deriv_csi.x * csi_metrics.x + deriv_eta.x * eta_metrics.x + deriv_zet.x * zet_metrics.x);
3354 dudx->y = jacobian * (deriv_csi.x * csi_metrics.y + deriv_eta.x * eta_metrics.y + deriv_zet.x * zet_metrics.y);
3355 dudx->z = jacobian * (deriv_csi.x * csi_metrics.z + deriv_eta.x * eta_metrics.z + deriv_zet.x * zet_metrics.z);
3356 // Derivatives of the second component (v)
3357 dvdx->x = jacobian * (deriv_csi.y * csi_metrics.x + deriv_eta.y * eta_metrics.x + deriv_zet.y * zet_metrics.x);
3358 dvdx->y = jacobian * (deriv_csi.y * csi_metrics.y + deriv_eta.y * eta_metrics.y + deriv_zet.y * zet_metrics.y);
3359 dvdx->z = jacobian * (deriv_csi.y * csi_metrics.z + deriv_eta.y * eta_metrics.z + deriv_zet.y * zet_metrics.z);
3360 // Derivatives of the third component (w)
3361 dwdx->x = jacobian * (deriv_csi.z * csi_metrics.x + deriv_eta.z * eta_metrics.x + deriv_zet.z * zet_metrics.x);
3362 dwdx->y = jacobian * (deriv_csi.z * csi_metrics.y + deriv_eta.z * eta_metrics.y + deriv_zet.z * zet_metrics.y);
3363 dwdx->z = jacobian * (deriv_csi.z * csi_metrics.z + deriv_eta.z * eta_metrics.z + deriv_zet.z * zet_metrics.z);
3364}
Here is the caller graph for this function:

◆ ComputeScalarFieldDerivatives()

PetscErrorCode ComputeScalarFieldDerivatives ( UserCtx *  user,
PetscInt  i,
PetscInt  j,
PetscInt  k,
PetscReal ***  field_data,
Cmpnts *  grad 
)

Internal helper implementation: ComputeScalarFieldDerivatives().

Computes the gradient of a cell-centered SCALAR field at a specific grid point.

Local to this translation unit.

Definition at line 3372 of file setup.c.

3374{
3375 PetscErrorCode ierr;
3376 Cmpnts ***csi, ***eta, ***zet;
3377 PetscReal ***jac;
3378 PetscReal d_csi, d_eta, d_zet;
3379
3380 PetscFunctionBeginUser;
3381
3382 // 1. Get read-only access to metrics
3383 ierr = DMDAVecGetArrayRead(user->fda, user->lCsi, &csi); CHKERRQ(ierr);
3384 ierr = DMDAVecGetArrayRead(user->fda, user->lEta, &eta); CHKERRQ(ierr);
3385 ierr = DMDAVecGetArrayRead(user->fda, user->lZet, &zet); CHKERRQ(ierr);
3386 ierr = DMDAVecGetArrayRead(user->da, user->lAj, &jac); CHKERRQ(ierr);
3387
3388 // 2. Compute derivatives in computational space (Central Difference)
3389 // Assumes ghosts are available at i+/-1
3390 d_csi = 0.5 * (field_data[k][j][i+1] - field_data[k][j][i-1]);
3391 d_eta = 0.5 * (field_data[k][j+1][i] - field_data[k][j-1][i]);
3392 d_zet = 0.5 * (field_data[k+1][j][i] - field_data[k-1][j][i]);
3393
3394 // 3. Transform to physical space
3395 TransformScalarDerivativesToPhysical(jac[k][j][i],
3396 csi[k][j][i], eta[k][j][i], zet[k][j][i],
3397 d_csi, d_eta, d_zet,
3398 grad);
3399
3400 // 4. Restore arrays
3401 ierr = DMDAVecRestoreArrayRead(user->fda, user->lCsi, &csi); CHKERRQ(ierr);
3402 ierr = DMDAVecRestoreArrayRead(user->fda, user->lEta, &eta); CHKERRQ(ierr);
3403 ierr = DMDAVecRestoreArrayRead(user->fda, user->lZet, &zet); CHKERRQ(ierr);
3404 ierr = DMDAVecRestoreArrayRead(user->da, user->lAj, &jac); CHKERRQ(ierr);
3405
3406 PetscFunctionReturn(0);
3407}
TransformScalarDerivativesToPhysical
void TransformScalarDerivativesToPhysical(PetscReal jacobian, Cmpnts csi_metrics, Cmpnts eta_metrics, Cmpnts zet_metrics, PetscReal dPhi_dcsi, PetscReal dPhi_deta, PetscReal dPhi_dzet, Cmpnts *gradPhi)
Implementation of TransformScalarDerivativesToPhysical().
Definition setup.c:3324
Here is the call graph for this function:

◆ ComputeVectorFieldDerivatives()

PetscErrorCode ComputeVectorFieldDerivatives ( UserCtx *  user,
PetscInt  i,
PetscInt  j,
PetscInt  k,
Cmpnts ***  field_data,
Cmpnts *  dudx,
Cmpnts *  dvdx,
Cmpnts *  dwdx 
)

Internal helper implementation: ComputeVectorFieldDerivatives().

Computes the derivatives of a cell-centered vector field at a specific grid point.

Local to this translation unit.

Definition at line 3415 of file setup.c.

3417{
3418 PetscErrorCode ierr;
3419 Cmpnts ***csi, ***eta, ***zet;
3420 PetscReal ***jac;
3421 PetscFunctionBeginUser;
3422
3423 // 1. Get read-only access to the necessary metric data arrays
3424 ierr = DMDAVecGetArrayRead(user->fda, user->lCsi, &csi); CHKERRQ(ierr);
3425 ierr = DMDAVecGetArrayRead(user->fda, user->lEta, &eta); CHKERRQ(ierr);
3426 ierr = DMDAVecGetArrayRead(user->fda, user->lZet, &zet); CHKERRQ(ierr);
3427 ierr = DMDAVecGetArrayRead(user->da, user->lAj, &jac); CHKERRQ(ierr);
3428
3429 // 2. Calculate derivatives in computational space using central differencing
3430 Cmpnts deriv_csi, deriv_eta, deriv_zet;
3431 deriv_csi.x = (field_data[k][j][i+1].x - field_data[k][j][i-1].x) * 0.5;
3432 deriv_csi.y = (field_data[k][j][i+1].y - field_data[k][j][i-1].y) * 0.5;
3433 deriv_csi.z = (field_data[k][j][i+1].z - field_data[k][j][i-1].z) * 0.5;
3434
3435 deriv_eta.x = (field_data[k][j+1][i].x - field_data[k][j-1][i].x) * 0.5;
3436 deriv_eta.y = (field_data[k][j+1][i].y - field_data[k][j-1][i].y) * 0.5;
3437 deriv_eta.z = (field_data[k][j+1][i].z - field_data[k][j-1][i].z) * 0.5;
3438
3439 deriv_zet.x = (field_data[k+1][j][i].x - field_data[k-1][j][i].x) * 0.5;
3440 deriv_zet.y = (field_data[k+1][j][i].y - field_data[k-1][j][i].y) * 0.5;
3441 deriv_zet.z = (field_data[k+1][j][i].z - field_data[k-1][j][i].z) * 0.5;
3442
3443 // 3. Transform derivatives to physical space
3444 TransformDerivativesToPhysical(jac[k][j][i], csi[k][j][i], eta[k][j][i], zet[k][j][i],
3445 deriv_csi, deriv_eta, deriv_zet,
3446 dudx, dvdx, dwdx);
3447
3448 // 4. Restore access to the PETSc data arrays
3449 ierr = DMDAVecRestoreArrayRead(user->fda, user->lCsi, &csi); CHKERRQ(ierr);
3450 ierr = DMDAVecRestoreArrayRead(user->fda, user->lEta, &eta); CHKERRQ(ierr);
3451 ierr = DMDAVecRestoreArrayRead(user->fda, user->lZet, &zet); CHKERRQ(ierr);
3452 ierr = DMDAVecRestoreArrayRead(user->da, user->lAj, &jac); CHKERRQ(ierr);
3453
3454 PetscFunctionReturn(0);
3455}
TransformDerivativesToPhysical
static void TransformDerivativesToPhysical(PetscReal jacobian, Cmpnts csi_metrics, Cmpnts eta_metrics, Cmpnts zet_metrics, Cmpnts deriv_csi, Cmpnts deriv_eta, Cmpnts deriv_zet, Cmpnts *dudx, Cmpnts *dvdx, Cmpnts *dwdx)
Transform contravariant vector derivatives into physical Cartesian derivatives.
Definition setup.c:3348
Here is the call graph for this function:
Here is the caller graph for this function:

◆ DestroyUserVectors()

PetscErrorCode DestroyUserVectors ( UserCtx *  user)

Internal helper implementation: DestroyUserVectors().

Destroys all PETSc Vec objects within a single UserCtx structure.

Local to this translation unit.

Definition at line 3469 of file setup.c.

3470{
3471 PetscErrorCode ierr;
3472 PetscFunctionBeginUser;
3473
3474 // --- Group A: Primary Flow Fields (Always allocated at all levels) ---
3475 if (user->Ucont) { ierr = VecDestroy(&user->Ucont); CHKERRQ(ierr); }
3476 if (user->lUcont) { ierr = VecDestroy(&user->lUcont); CHKERRQ(ierr); }
3477 if (user->Ucat) { ierr = VecDestroy(&user->Ucat); CHKERRQ(ierr); }
3478 if (user->lUcat) { ierr = VecDestroy(&user->lUcat); CHKERRQ(ierr); }
3479 if (user->P) { ierr = VecDestroy(&user->P); CHKERRQ(ierr); }
3480 if (user->lP) { ierr = VecDestroy(&user->lP); CHKERRQ(ierr); }
3481 if (user->Nvert) { ierr = VecDestroy(&user->Nvert); CHKERRQ(ierr); }
3482 if (user->lNvert) { ierr = VecDestroy(&user->lNvert); CHKERRQ(ierr); }
3483
3484 // --- Group A2: Derived Flow Fields (Conditional) ---
3485 if(user->Diffusivity) {ierr = VecDestroy(&user->Diffusivity); CHKERRQ(ierr);}
3486 if(user->lDiffusivity){ierr = VecDestroy(&user->lDiffusivity); CHKERRQ(ierr);}
3487 if(user->DiffusivityGradient){ierr = VecDestroy(&user->DiffusivityGradient); CHKERRQ(ierr);}
3488 if(user->lDiffusivityGradient){ierr = VecDestroy(&user->lDiffusivityGradient); CHKERRQ(ierr);}
3489
3490 // --- Group B: Solver Work Vectors (All levels) ---
3491 if (user->Phi) { ierr = VecDestroy(&user->Phi); CHKERRQ(ierr); }
3492 if (user->lPhi) { ierr = VecDestroy(&user->lPhi); CHKERRQ(ierr); }
3493
3494 // --- Group C: Time-Stepping Vectors (Finest level only) ---
3495 if (user->Ucont_o) { ierr = VecDestroy(&user->Ucont_o); CHKERRQ(ierr); }
3496 if (user->Ucont_rm1) { ierr = VecDestroy(&user->Ucont_rm1); CHKERRQ(ierr); }
3497 if (user->Ucat_o) { ierr = VecDestroy(&user->Ucat_o); CHKERRQ(ierr); }
3498 if (user->P_o) { ierr = VecDestroy(&user->P_o); CHKERRQ(ierr); }
3499 if (user->Nvert_o) { ierr = VecDestroy(&user->Nvert_o); CHKERRQ(ierr); }
3500 if (user->lUcont_o) { ierr = VecDestroy(&user->lUcont_o); CHKERRQ(ierr); }
3501 if (user->lUcont_rm1) { ierr = VecDestroy(&user->lUcont_rm1); CHKERRQ(ierr); }
3502 if (user->lNvert_o) { ierr = VecDestroy(&user->lNvert_o); CHKERRQ(ierr); }
3503
3504 // --- Group D: Grid Metrics - Face Centered (All levels) ---
3505 if (user->Csi) { ierr = VecDestroy(&user->Csi); CHKERRQ(ierr); }
3506 if (user->Eta) { ierr = VecDestroy(&user->Eta); CHKERRQ(ierr); }
3507 if (user->Zet) { ierr = VecDestroy(&user->Zet); CHKERRQ(ierr); }
3508 if (user->Aj) { ierr = VecDestroy(&user->Aj); CHKERRQ(ierr); }
3509 if (user->lCsi) { ierr = VecDestroy(&user->lCsi); CHKERRQ(ierr); }
3510 if (user->lEta) { ierr = VecDestroy(&user->lEta); CHKERRQ(ierr); }
3511 if (user->lZet) { ierr = VecDestroy(&user->lZet); CHKERRQ(ierr); }
3512 if (user->lAj) { ierr = VecDestroy(&user->lAj); CHKERRQ(ierr); }
3513
3514 // --- Group E: Grid Metrics - Face Centered (All levels) ---
3515 if (user->ICsi) { ierr = VecDestroy(&user->ICsi); CHKERRQ(ierr); }
3516 if (user->IEta) { ierr = VecDestroy(&user->IEta); CHKERRQ(ierr); }
3517 if (user->IZet) { ierr = VecDestroy(&user->IZet); CHKERRQ(ierr); }
3518 if (user->JCsi) { ierr = VecDestroy(&user->JCsi); CHKERRQ(ierr); }
3519 if (user->JEta) { ierr = VecDestroy(&user->JEta); CHKERRQ(ierr); }
3520 if (user->JZet) { ierr = VecDestroy(&user->JZet); CHKERRQ(ierr); }
3521 if (user->KCsi) { ierr = VecDestroy(&user->KCsi); CHKERRQ(ierr); }
3522 if (user->KEta) { ierr = VecDestroy(&user->KEta); CHKERRQ(ierr); }
3523 if (user->KZet) { ierr = VecDestroy(&user->KZet); CHKERRQ(ierr); }
3524 if (user->IAj) { ierr = VecDestroy(&user->IAj); CHKERRQ(ierr); }
3525 if (user->JAj) { ierr = VecDestroy(&user->JAj); CHKERRQ(ierr); }
3526 if (user->KAj) { ierr = VecDestroy(&user->KAj); CHKERRQ(ierr); }
3527 if (user->lICsi) { ierr = VecDestroy(&user->lICsi); CHKERRQ(ierr); }
3528 if (user->lIEta) { ierr = VecDestroy(&user->lIEta); CHKERRQ(ierr); }
3529 if (user->lIZet) { ierr = VecDestroy(&user->lIZet); CHKERRQ(ierr); }
3530 if (user->lJCsi) { ierr = VecDestroy(&user->lJCsi); CHKERRQ(ierr); }
3531 if (user->lJEta) { ierr = VecDestroy(&user->lJEta); CHKERRQ(ierr); }
3532 if (user->lJZet) { ierr = VecDestroy(&user->lJZet); CHKERRQ(ierr); }
3533 if (user->lKCsi) { ierr = VecDestroy(&user->lKCsi); CHKERRQ(ierr); }
3534 if (user->lKEta) { ierr = VecDestroy(&user->lKEta); CHKERRQ(ierr); }
3535 if (user->lKZet) { ierr = VecDestroy(&user->lKZet); CHKERRQ(ierr); }
3536 if (user->lIAj) { ierr = VecDestroy(&user->lIAj); CHKERRQ(ierr); }
3537 if (user->lJAj) { ierr = VecDestroy(&user->lJAj); CHKERRQ(ierr); }
3538 if (user->lKAj) { ierr = VecDestroy(&user->lKAj); CHKERRQ(ierr); }
3539
3540 // --- Group F: Cell/Face Coordinates and Grid Spacing (All levels) ---
3541 if (user->Cent) { ierr = VecDestroy(&user->Cent); CHKERRQ(ierr); }
3542 if (user->lCent) { ierr = VecDestroy(&user->lCent); CHKERRQ(ierr); }
3543 if (user->GridSpace) { ierr = VecDestroy(&user->GridSpace); CHKERRQ(ierr); }
3544 if (user->lGridSpace) { ierr = VecDestroy(&user->lGridSpace); CHKERRQ(ierr); }
3545 if (user->Centx) { ierr = VecDestroy(&user->Centx); CHKERRQ(ierr); }
3546 if (user->Centy) { ierr = VecDestroy(&user->Centy); CHKERRQ(ierr); }
3547 if (user->Centz) { ierr = VecDestroy(&user->Centz); CHKERRQ(ierr); }
3548 if (user->lCentx) { ierr = VecDestroy(&user->lCentx); CHKERRQ(ierr); }
3549 if (user->lCenty) { ierr = VecDestroy(&user->lCenty); CHKERRQ(ierr); }
3550 if (user->lCentz) { ierr = VecDestroy(&user->lCentz); CHKERRQ(ierr); }
3551
3552 // --- Group G: Turbulence Model Vectors (Finest level, conditional on les/rans) ---
3553 if (user->Nu_t) { ierr = VecDestroy(&user->Nu_t); CHKERRQ(ierr); }
3554 if (user->lNu_t) { ierr = VecDestroy(&user->lNu_t); CHKERRQ(ierr); }
3555 if (user->CS) { ierr = VecDestroy(&user->CS); CHKERRQ(ierr); }
3556 if (user->lCs) { ierr = VecDestroy(&user->lCs); CHKERRQ(ierr); }
3557 if (user->lFriction_Velocity) { ierr = VecDestroy(&user->lFriction_Velocity); CHKERRQ(ierr); }
3558 if (user->K_Omega) { ierr = VecDestroy(&user->K_Omega); CHKERRQ(ierr); }
3559 if (user->lK_Omega) { ierr = VecDestroy(&user->lK_Omega); CHKERRQ(ierr); }
3560 if (user->K_Omega_o) { ierr = VecDestroy(&user->K_Omega_o); CHKERRQ(ierr); }
3561 if (user->lK_Omega_o) { ierr = VecDestroy(&user->lK_Omega_o); CHKERRQ(ierr); }
3562
3563 // --- Group H: Particle Vectors (Finest level, conditional on np > 0) ---
3564 if (user->ParticleCount) { ierr = VecDestroy(&user->ParticleCount); CHKERRQ(ierr); }
3565 if (user->lParticleCount) { ierr = VecDestroy(&user->lParticleCount); CHKERRQ(ierr); }
3566 if (user->Psi) { ierr = VecDestroy(&user->Psi); CHKERRQ(ierr); }
3567 if (user->lPsi) { ierr = VecDestroy(&user->lPsi); CHKERRQ(ierr); }
3568
3569 // --- Group I: Boundary Condition Vectors (All levels) ---
3570 if (user->Bcs.Ubcs) { ierr = VecDestroy(&user->Bcs.Ubcs); CHKERRQ(ierr); }
3571 if (user->Bcs.Uch) { ierr = VecDestroy(&user->Bcs.Uch); CHKERRQ(ierr); }
3572
3573 // --- Group J: Post-Processing Vectors (Finest level, postprocessor mode) ---
3574 if (user->P_nodal) { ierr = VecDestroy(&user->P_nodal); CHKERRQ(ierr); }
3575 if (user->Ucat_nodal) { ierr = VecDestroy(&user->Ucat_nodal); CHKERRQ(ierr); }
3576 if (user->Qcrit) { ierr = VecDestroy(&user->Qcrit); CHKERRQ(ierr); }
3577 if (user->Psi_nodal) { ierr = VecDestroy(&user->Psi_nodal); CHKERRQ(ierr); }
3578
3579 // --- Group K: Interpolation Vectors (Lazy allocation) ---
3580 if (user->fieldStatisticsStorage) {
3581 SimCtx *stats_ctx = user->simCtx;
3582 const PetscInt window_count = stats_ctx ? stats_ctx->fieldStatisticsWindowCount : 0;
3583 for (PetscInt w = 0; w < window_count; ++w) {
3584 ierr = PicurvWindowStorageDestroy(&user->fieldStatisticsStorage[w]); CHKERRQ(ierr);
3585 }
3586 ierr = PetscFree(user->fieldStatisticsStorage); CHKERRQ(ierr);
3587 user->fieldStatisticsStorage = NULL;
3588 }
3589 if (user->CellScalarAtCorner) { ierr = VecDestroy(&user->CellScalarAtCorner); CHKERRQ(ierr); }
3590 if (user->lCellScalarAtCorner) { ierr = VecDestroy(&user->lCellScalarAtCorner); CHKERRQ(ierr); }
3591 if (user->CellVectorAtCorner) { ierr = VecDestroy(&user->CellVectorAtCorner); CHKERRQ(ierr); }
3592 if (user->PostScalar) { ierr = VecDestroy(&user->PostScalar); CHKERRQ(ierr); }
3593 if (user->lPostScalar) { ierr = VecDestroy(&user->lPostScalar); CHKERRQ(ierr); }
3594 if (user->PostScalarNodal) { ierr = VecDestroy(&user->PostScalarNodal); CHKERRQ(ierr); }
3595 if (user->PostVector) { ierr = VecDestroy(&user->PostVector); CHKERRQ(ierr); }
3596 if (user->lPostVector) { ierr = VecDestroy(&user->lPostVector); CHKERRQ(ierr); }
3597 if (user->PostVectorNodal) { ierr = VecDestroy(&user->PostVectorNodal); CHKERRQ(ierr); }
3598 if (user->lCellVectorAtCorner) { ierr = VecDestroy(&user->lCellVectorAtCorner); CHKERRQ(ierr); }
3599
3600 // --- Group L: Implicit Solver Temporary Vectors (Destroyed after use, but check anyway) ---
3601 if (user->Rhs) { ierr = VecDestroy(&user->Rhs); CHKERRQ(ierr); }
3602 if (user->dUcont) { ierr = VecDestroy(&user->dUcont); CHKERRQ(ierr); }
3603 if (user->pUcont) { ierr = VecDestroy(&user->pUcont); CHKERRQ(ierr); }
3604
3605 // --- Group M: Poisson Solver Vectors (Destroyed after solve, but check anyway) ---
3606 if (user->B) { ierr = VecDestroy(&user->B); CHKERRQ(ierr); }
3607 if (user->R) { ierr = VecDestroy(&user->R); CHKERRQ(ierr); }
3608
3609 LOG_ALLOW(LOCAL, LOG_DEBUG, "All vectors destroyed for UserCtx.\n");
3610 PetscFunctionReturn(0);
3611}
PicurvWindowStorageDestroy
PetscErrorCode PicurvWindowStorageDestroy(PicurvWindowStorage *storage)
Releases accumulator state previously created for one window.
Definition statistics_accumulator.c:204
UserCtx::Rhs
Vec Rhs
Definition variables.h:947
UserCtx::K_Omega_o
Vec K_Omega_o
Definition variables.h:982
UserCtx::K_Omega
Vec K_Omega
Definition variables.h:982
UserCtx::pUcont
Vec pUcont
Definition variables.h:947
UserCtx::lK_Omega_o
Vec lK_Omega_o
Definition variables.h:982
UserCtx::lK_Omega
Vec lK_Omega
Definition variables.h:982
UserCtx::dUcont
Vec dUcont
Definition variables.h:947
Here is the call graph for this function:
Here is the caller graph for this function:

◆ DestroyUserContext()

PetscErrorCode DestroyUserContext ( UserCtx *  user)

Internal helper implementation: DestroyUserContext().

Destroys all resources allocated within a single UserCtx structure.

Local to this translation unit.

Definition at line 3618 of file setup.c.

3619{
3620 PetscErrorCode ierr;
3621 PetscFunctionBeginUser;
3622
3623 if (!user) {
3624 LOG_ALLOW(LOCAL, LOG_WARNING, "DestroyUserContext called with NULL user pointer.\n");
3625 PetscFunctionReturn(0);
3626 }
3627
3628 LOG_ALLOW(LOCAL, LOG_INFO, "Destroying UserCtx at level %d...\n", user->thislevel);
3629
3630 // --- Step 1: Destroy Boundary Condition System ---
3631 // This handles all BC handlers and their private data.
3632 ierr = BoundarySystem_Destroy(user); CHKERRQ(ierr);
3633 LOG_ALLOW(LOCAL, LOG_DEBUG, " Boundary system destroyed.\n");
3634
3635 // --- Step 2: Destroy All Vectors ---
3636 // Handles ~74 Vec objects with proper NULL checking.
3637 ierr = DestroyUserVectors(user); CHKERRQ(ierr);
3638 LOG_ALLOW(LOCAL, LOG_DEBUG, " All vectors destroyed.\n");
3639
3640 // --- Step 3: Destroy Matrix and Solver Objects ---
3641 // Destroy pressure-Poisson matrices and solver.
3642 if (user->A) {
3643 ierr = MatDestroy(&user->A); CHKERRQ(ierr);
3644 LOG_ALLOW(LOCAL, LOG_DEBUG, " Matrix A destroyed.\n");
3645 }
3646 if (user->C) {
3647 ierr = MatDestroy(&user->C); CHKERRQ(ierr);
3648 LOG_ALLOW(LOCAL, LOG_DEBUG, " Matrix C destroyed.\n");
3649 }
3650 if (user->MR) {
3651 ierr = MatDestroy(&user->MR); CHKERRQ(ierr);
3652 LOG_ALLOW(LOCAL, LOG_DEBUG, " Matrix MR destroyed.\n");
3653 }
3654 if (user->MP) {
3655 ierr = MatDestroy(&user->MP); CHKERRQ(ierr);
3656 LOG_ALLOW(LOCAL, LOG_DEBUG, " Matrix MP destroyed.\n");
3657 }
3658 if (user->ksp) {
3659 ierr = KSPDestroy(&user->ksp); CHKERRQ(ierr);
3660 LOG_ALLOW(LOCAL, LOG_DEBUG, " KSP solver destroyed.\n");
3661 }
3662 if (user->nullsp) {
3663 ierr = MatNullSpaceDestroy(&user->nullsp); CHKERRQ(ierr);
3664 LOG_ALLOW(LOCAL, LOG_DEBUG, " MatNullSpace destroyed.\n");
3665 }
3666
3667 // --- Step 4: Destroy Application Ordering ---
3668 if (user->ao) {
3669 ierr = AODestroy(&user->ao); CHKERRQ(ierr);
3670 LOG_ALLOW(LOCAL, LOG_DEBUG, " AO destroyed.\n");
3671 }
3672
3673 // --- Step 5: Destroy DM Objects ---
3674 // Destroy in reverse order of dependency: post_swarm, swarm, fda6, fda2, fda, da
3675 if (user->post_swarm) {
3676 ierr = DMDestroy(&user->post_swarm); CHKERRQ(ierr);
3677 LOG_ALLOW(LOCAL, LOG_DEBUG, " post_swarm DM destroyed.\n");
3678 }
3679 if (user->swarm) {
3680 ierr = DMDestroy(&user->swarm); CHKERRQ(ierr);
3681 LOG_ALLOW(LOCAL, LOG_DEBUG, " swarm DM destroyed.\n");
3682 }
3683 if (user->fda6) {
3684 ierr = DMDestroy(&user->fda6); CHKERRQ(ierr);
3685 LOG_ALLOW(LOCAL, LOG_DEBUG, " fda6 DM destroyed.\n");
3686 }
3687 if (user->fda2) {
3688 ierr = DMDestroy(&user->fda2); CHKERRQ(ierr);
3689 LOG_ALLOW(LOCAL, LOG_DEBUG, " fda2 DM destroyed.\n");
3690 }
3691 if (user->da) {
3692 ierr = DMDestroy(&user->da); CHKERRQ(ierr);
3693 LOG_ALLOW(LOCAL, LOG_DEBUG, " da DM destroyed.\n");
3694 }
3695
3696 // --- Step 6: Free PetscMalloc'd Arrays ---
3697 // Free arrays allocated with PetscMalloc1
3698 if (user->RankCellInfoMap) {
3699 ierr = PetscFree(user->RankCellInfoMap); CHKERRQ(ierr);
3700 user->RankCellInfoMap = NULL;
3701 LOG_ALLOW(LOCAL, LOG_DEBUG, " RankCellInfoMap freed.\n");
3702 }
3703 if (user->KSKE) {
3704 ierr = PetscFree(user->KSKE); CHKERRQ(ierr);
3705 user->KSKE = NULL;
3706 LOG_ALLOW(LOCAL, LOG_DEBUG, " KSKE array freed.\n");
3707 }
3708
3709 LOG_ALLOW(LOCAL, LOG_INFO, "UserCtx at level %d fully destroyed.\n", user->thislevel);
3710 PetscFunctionReturn(0);
3711}
BoundarySystem_Destroy
PetscErrorCode BoundarySystem_Destroy(UserCtx *user)
Cleans up and destroys all boundary system resources.
Definition Boundaries.c:1490
DestroyUserVectors
PetscErrorCode DestroyUserVectors(UserCtx *user)
Internal helper implementation: DestroyUserVectors().
Definition setup.c:3469
UserCtx::nullsp
MatNullSpace nullsp
Definition variables.h:965
UserCtx::post_swarm
DM post_swarm
Definition variables.h:1000
UserCtx::ksp
KSP ksp
Definition variables.h:965
Here is the call graph for this function:
Here is the caller graph for this function:

◆ FinalizeSimulation()

PetscErrorCode FinalizeSimulation ( SimCtx *  simCtx)

Implementation of FinalizeSimulation().

Main cleanup function for the entire simulation context.

Full API contract (arguments, ownership, side effects) is documented with the header declaration in include/setup.h.

See also
FinalizeSimulation()

Definition at line 3721 of file setup.c.

3722{
3723 PetscErrorCode ierr;
3724 PetscFunctionBeginUser;
3725
3726 if (!simCtx) {
3727 LOG_ALLOW(GLOBAL, LOG_WARNING, "FinalizeSimulation called with NULL SimCtx pointer.\n");
3728 PetscFunctionReturn(0);
3729 }
3730
3731 LOG_ALLOW(GLOBAL, LOG_INFO, "========================================\n");
3732 LOG_ALLOW(GLOBAL, LOG_INFO, "Beginning simulation memory cleanup...\n");
3733 LOG_ALLOW(GLOBAL, LOG_INFO, "========================================\n");
3734
3735 // ============================================================================
3736 // PHASE 1: DESTROY MULTIGRID HIERARCHY (All UserCtx structures)
3737 // ============================================================================
3738
3739 ierr = DestroySolutionConvergenceState(simCtx); CHKERRQ(ierr);
3740 ierr = DestroyFieldStatisticsConfig(simCtx); CHKERRQ(ierr);
3741
3742 if (simCtx->usermg.mgctx) {
3743 LOG_ALLOW(GLOBAL, LOG_INFO, "Destroying multigrid hierarchy (%d levels)...\n",
3744 simCtx->usermg.mglevels);
3745
3746 // Destroy each UserCtx from finest to coarsest (reverse order is safer)
3747 for (PetscInt level = simCtx->usermg.mglevels - 1; level >= 0; level--) {
3748 UserCtx *user = simCtx->usermg.mgctx[level].user;
3749 if (user) {
3750 LOG_ALLOW(LOCAL, LOG_INFO, " Destroying level %d of %d...\n",
3751 level, simCtx->usermg.mglevels - 1);
3752 ierr = DestroyUserContext(user); CHKERRQ(ierr);
3753
3754 // Free the UserCtx structure itself
3755 ierr = PetscFree(user); CHKERRQ(ierr);
3756 simCtx->usermg.mgctx[level].user = NULL;
3757 }
3758
3759 // Destroy the MGCtx-level packer DM
3760 if (simCtx->usermg.mgctx[level].packer) {
3761 ierr = DMDestroy(&simCtx->usermg.mgctx[level].packer); CHKERRQ(ierr);
3762 LOG_ALLOW(LOCAL, LOG_DEBUG, " MGCtx[%d].packer destroyed.\n", level);
3763 }
3764 }
3765
3766 // Free the MGCtx array itself
3767 ierr = PetscFree(simCtx->usermg.mgctx); CHKERRQ(ierr);
3768 simCtx->usermg.mgctx = NULL;
3769 LOG_ALLOW(GLOBAL, LOG_INFO, "All multigrid levels destroyed.\n");
3770 }
3771
3772 // ============================================================================
3773 // PHASE 2: DESTROY USERMG-LEVEL OBJECTS
3774 // ============================================================================
3775
3776 if (simCtx->usermg.packer) {
3777 ierr = DMDestroy(&simCtx->usermg.packer); CHKERRQ(ierr);
3778 LOG_ALLOW(LOCAL, LOG_DEBUG, "UserMG.packer DM destroyed.\n");
3779 }
3780
3781 if (simCtx->usermg.snespacker) {
3782 ierr = SNESDestroy(&simCtx->usermg.snespacker); CHKERRQ(ierr);
3783 LOG_ALLOW(LOCAL, LOG_DEBUG, "UserMG.snespacker SNES destroyed.\n");
3784 }
3785
3786 // ============================================================================
3787 // PHASE 3: DESTROY SIMCTX-LEVEL OBJECTS
3788 // ============================================================================
3789
3790 LOG_ALLOW(GLOBAL, LOG_INFO, "Destroying SimCtx-level objects...\n");
3791
3792 // --- PetscViewer for logging ---
3793 if (simCtx->logviewer) {
3794 ierr = PetscViewerDestroy(&simCtx->logviewer); CHKERRQ(ierr);
3795 LOG_ALLOW(LOCAL, LOG_DEBUG, " logviewer destroyed.\n");
3796 }
3797
3798 // --- Particle System DM ---
3799 if (simCtx->dm_swarm) {
3800 ierr = DMDestroy(&simCtx->dm_swarm); CHKERRQ(ierr);
3801 LOG_ALLOW(LOCAL, LOG_DEBUG, " dm_swarm destroyed.\n");
3802 }
3803
3804 // --- BoundingBox List (Array of BoundingBox structs) ---
3805 if (simCtx->bboxlist) {
3806 ierr = PetscFree(simCtx->bboxlist); CHKERRQ(ierr);
3807 simCtx->bboxlist = NULL;
3808 LOG_ALLOW(LOCAL, LOG_DEBUG, " bboxlist freed.\n");
3809 }
3810
3811 // --- Boundary Condition Files (Array of strings) ---
3812 if (simCtx->bcs_files) {
3813 for (PetscInt i = 0; i < simCtx->num_bcs_files; i++) {
3814 if (simCtx->bcs_files[i]) {
3815 ierr = PetscFree(simCtx->bcs_files[i]); CHKERRQ(ierr);
3816 }
3817 }
3818 ierr = PetscFree(simCtx->bcs_files); CHKERRQ(ierr);
3819 simCtx->bcs_files = NULL;
3820 LOG_ALLOW(LOCAL, LOG_DEBUG, " bcs_files array freed (%d files).\n", simCtx->num_bcs_files);
3821 }
3822
3823 // --- Brownian Motion RNG ---
3824 if (simCtx->BrownianMotionRNG) {
3825 ierr = PetscRandomDestroy(&simCtx->BrownianMotionRNG); CHKERRQ(ierr);
3826 LOG_ALLOW(LOCAL, LOG_DEBUG, " BrownianMotionRNG destroyed.\n");
3827 }
3828 // --- Post-Processing Parameters ---
3829 // pps is allocated with PetscNew and contains only static char arrays and basic types.
3830 // No internal dynamic allocations need to be freed.
3831 if (simCtx->pps) {
3832 ierr = PetscFree(simCtx->pps); CHKERRQ(ierr);
3833 simCtx->pps = NULL;
3834 LOG_ALLOW(LOCAL, LOG_DEBUG, " PostProcessParams freed.\n");
3835 }
3836
3837 // --- IBM/FSI Objects ---
3838 // Note: These are initialized to NULL and currently have no dedicated destroy functions.
3839 // If these modules are extended with cleanup routines, call them here.
3840 if (simCtx->ibm != NULL) {
3841 LOG_ALLOW(GLOBAL, LOG_WARNING, " WARNING: simCtx->ibm is non-NULL but no destroy function exists. Potential memory leak.\n");
3842 }
3843 if (simCtx->ibmv != NULL) {
3844 LOG_ALLOW(GLOBAL, LOG_WARNING, " WARNING: simCtx->ibmv is non-NULL but no destroy function exists. Potential memory leak.\n");
3845 }
3846 if (simCtx->fsi != NULL) {
3847 LOG_ALLOW(GLOBAL, LOG_WARNING, " WARNING: simCtx->fsi is non-NULL but no destroy function exists. Potential memory leak.\n");
3848 }
3849
3850 // --- Logging Allowed Functions (Array of strings) ---
3851 // Note: The logging system maintains its own copy via set_allowed_functions(),
3852 // so freeing simCtx->allowedFuncs will NOT affect LOG_ALLOW functionality.
3853 if (simCtx->allowedFuncs) {
3854 for (PetscInt i = 0; i < simCtx->nAllowed; i++) {
3855 if (simCtx->allowedFuncs[i]) {
3856 ierr = PetscFree(simCtx->allowedFuncs[i]); CHKERRQ(ierr);
3857 }
3858 }
3859 ierr = PetscFree(simCtx->allowedFuncs); CHKERRQ(ierr);
3860 simCtx->allowedFuncs = NULL;
3861 LOG_ALLOW(LOCAL, LOG_DEBUG, " allowedFuncs array freed (%d functions).\n", simCtx->nAllowed);
3862 }
3863
3864 // --- Profiling Critical Functions (Array of strings) ---
3865 if (simCtx->profilingSelectedFuncs) {
3866 for (PetscInt i = 0; i < simCtx->nProfilingSelectedFuncs; i++) {
3867 if (simCtx->profilingSelectedFuncs[i]) {
3868 ierr = PetscFree(simCtx->profilingSelectedFuncs[i]); CHKERRQ(ierr);
3869 }
3870 }
3871 ierr = PetscFree(simCtx->profilingSelectedFuncs); CHKERRQ(ierr);
3872 simCtx->profilingSelectedFuncs = NULL;
3873 LOG_ALLOW(LOCAL, LOG_DEBUG, " profilingSelectedFuncs array freed (%d functions).\n", simCtx->nProfilingSelectedFuncs);
3874 }
3875
3876 // ============================================================================
3877 // PHASE 4: FINAL SUMMARY
3878 // ============================================================================
3879
3880 LOG_ALLOW(GLOBAL, LOG_INFO, "========================================\n");
3881 LOG_ALLOW(GLOBAL, LOG_INFO, "Simulation cleanup completed successfully.\n");
3882 LOG_ALLOW(GLOBAL, LOG_INFO, "All PETSc objects have been destroyed.\n");
3883 LOG_ALLOW(GLOBAL, LOG_INFO, "========================================\n");
3884
3885 ierr = PetscFree(simCtx); CHKERRQ(ierr);
3886 PetscFunctionReturn(0);
3887}
DestroyUserContext
PetscErrorCode DestroyUserContext(UserCtx *user)
Internal helper implementation: DestroyUserContext().
Definition setup.c:3618
DestroySolutionConvergenceState
PetscErrorCode DestroySolutionConvergenceState(SimCtx *simCtx)
Implementation of DestroySolutionConvergenceState().
Definition setup.c:101
DestroyFieldStatisticsConfig
PetscErrorCode DestroyFieldStatisticsConfig(SimCtx *simCtx)
Releases the window definitions resolved by ParseFieldStatisticsConfig().
Definition statistics_config.c:358
UserMG::packer
DM packer
Definition variables.h:582
UserMG::snespacker
SNES snespacker
Definition variables.h:583
MGCtx::packer
DM packer
Definition variables.h:573
Here is the call graph for this function:
Here is the caller graph for this function:
Generated by doxygen 1.9.8