runloop.h File Reference

#include <petscpf.h>
#include <petscdmswarm.h>
#include <stdlib.h>
#include <time.h>
#include <math.h>
#include <petsctime.h>
#include <petscsys.h>
#include <petscdmcomposite.h>
#include <petscsystypes.h>
#include "variables.h"
#include "ParticleSwarm.h"
#include "walkingsearch.h"
#include "grid.h"
#include "logging.h"
#include "io.h"
#include "interpolation.h"
#include "initialcondition.h"
#include "AnalyticalSolutions.h"
#include "ParticleMotion.h"
#include "ParticlePhysics.h"
#include "Boundaries.h"
#include "setup.h"
#include "solvers.h"

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Functions
PetscErrorCode	InitializeRuntimeSignalHandlers (void)
	Installs lightweight signal handlers for graceful shutdown requests.
PetscReal	RuntimeWalltimeGuardUpdateEWMA (PetscBool has_previous, PetscReal previous_ewma_seconds, PetscReal latest_step_seconds, PetscReal alpha)
	Update an EWMA estimate for timestep wall-clock duration.
PetscReal	RuntimeWalltimeGuardConservativeEstimate (PetscReal warmup_average_seconds, PetscReal ewma_seconds, PetscReal latest_step_seconds)
	Return the conservative timestep estimate used by the walltime guard.
PetscReal	RuntimeWalltimeGuardRequiredHeadroom (PetscReal min_seconds, PetscReal multiplier, PetscReal conservative_estimate_seconds)
	Compute the required shutdown headroom from timestep estimate and floor.
PetscBool	RuntimeWalltimeGuardShouldTrigger (PetscInt completed_steps, PetscInt warmup_steps, PetscReal remaining_seconds, PetscReal min_seconds, PetscReal multiplier, PetscReal warmup_average_seconds, PetscReal ewma_seconds, PetscReal latest_step_seconds, PetscReal *required_headroom_seconds_out)
	Decide whether the runtime walltime guard should stop before another step.
PetscErrorCode	UpdateSolverHistoryVectors (UserCtx *user)
	Copies the current time step's solution fields into history vectors (e.g., U(t_n) -> U_o, U_o -> U_rm1) for the next time step's calculations.
PetscErrorCode	AdvanceSimulation (SimCtx *simCtx)
	Executes the main time-marching loop for the particle simulation.
PetscErrorCode	PerformInitializedParticleSetup (SimCtx *simCtx)
	Finalizes the simulation setup at t=0, ensuring a consistent state before time marching.
PetscErrorCode	PerformLoadedParticleSetup (SimCtx *simCtx)
	Finalizes the simulation state after particle and fluid data have been loaded from a restart.
PetscErrorCode	FinalizeRestartState (SimCtx *simCtx)
	Performs post-load/post-init consistency checks for a restarted simulation.

Function Documentation

InitializeRuntimeSignalHandlers()

PetscErrorCode InitializeRuntimeSignalHandlers

(

void

)

Installs lightweight signal handlers for graceful shutdown requests.

The handlers only record that a shutdown signal was received. The actual output flush and exit path happens later at safe checkpoints in the run loop.

Returns

PetscErrorCode 0 on success.

Installs lightweight signal handlers for graceful shutdown requests.

Full API contract (arguments, ownership, side effects) is documented with the matching public header declaration.

See also

InitializeRuntimeSignalHandlers()

Definition at line 123 of file runloop.c.

{
    PetscErrorCode ierr;
 
    PetscFunctionBeginUser;
    g_runtime_shutdown_signal = 0;
    g_runtime_shutdown_auto_requested = PETSC_FALSE;
 
#ifdef SIGTERM
    ierr = RegisterRuntimeSignalHandler(SIGTERM); CHKERRQ(ierr);
#endif
#ifdef SIGUSR1
    ierr = RegisterRuntimeSignalHandler(SIGUSR1); CHKERRQ(ierr);
#endif
#ifdef SIGINT
    ierr = RegisterRuntimeSignalHandler(SIGINT); CHKERRQ(ierr);
#endif
 
    PetscFunctionReturn(0);
}

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RuntimeWalltimeGuardUpdateEWMA()

PetscReal RuntimeWalltimeGuardUpdateEWMA	(	PetscBool	has_previous,
		PetscReal	previous_ewma_seconds,
		PetscReal	latest_step_seconds,
		PetscReal	alpha
	)

Update an EWMA estimate for timestep wall-clock duration.

Parameters

[in]	has_previous	Whether a previous EWMA estimate exists.
[in]	previous_ewma_seconds	Prior EWMA estimate in seconds.
[in]	latest_step_seconds	Latest completed timestep duration in seconds.
[in]	alpha	EWMA weighting factor in (0, 1].

Returns

PetscReal Updated EWMA estimate in seconds.

Update an EWMA estimate for timestep wall-clock duration.

Full API contract (arguments, ownership, side effects) is documented with the matching public header declaration.

See also

RuntimeWalltimeGuardUpdateEWMA()

Definition at line 150 of file runloop.c.

{
    if (!has_previous) return latest_step_seconds;
    return alpha * latest_step_seconds + (1.0 - alpha) * previous_ewma_seconds;
}

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RuntimeWalltimeGuardConservativeEstimate()

PetscReal RuntimeWalltimeGuardConservativeEstimate	(	PetscReal	warmup_average_seconds,
		PetscReal	ewma_seconds,
		PetscReal	latest_step_seconds
	)

Return the conservative timestep estimate used by the walltime guard.

Parameters

[in]	warmup_average_seconds	Average duration across warmup steps.
[in]	ewma_seconds	Current EWMA duration estimate.
[in]	latest_step_seconds	Most recent completed timestep duration.

Returns

PetscReal Conservative timestep estimate in seconds.

Return the conservative timestep estimate used by the walltime guard.

Full API contract (arguments, ownership, side effects) is documented with the matching public header declaration.

See also

RuntimeWalltimeGuardConservativeEstimate()

Definition at line 162 of file runloop.c.

{
    return PetscMax(warmup_average_seconds, PetscMax(ewma_seconds, latest_step_seconds));
}

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RuntimeWalltimeGuardRequiredHeadroom()

PetscReal RuntimeWalltimeGuardRequiredHeadroom	(	PetscReal	min_seconds,
		PetscReal	multiplier,
		PetscReal	conservative_estimate_seconds
	)

Compute the required shutdown headroom from timestep estimate and floor.

Parameters

[in]	min_seconds	Absolute minimum shutdown headroom.
[in]	multiplier	Safety multiplier applied to the timestep estimate.
[in]	conservative_estimate_seconds	Conservative timestep estimate in seconds.

Returns

PetscReal Required headroom in seconds.

Compute the required shutdown headroom from timestep estimate and floor.

Full API contract (arguments, ownership, side effects) is documented with the matching public header declaration.

See also

RuntimeWalltimeGuardRequiredHeadroom()

Definition at line 173 of file runloop.c.

{
    return PetscMax(min_seconds, multiplier * conservative_estimate_seconds);
}

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RuntimeWalltimeGuardShouldTrigger()

PetscBool RuntimeWalltimeGuardShouldTrigger	(	PetscInt	completed_steps,
		PetscInt	warmup_steps,
		PetscReal	remaining_seconds,
		PetscReal	min_seconds,
		PetscReal	multiplier,
		PetscReal	warmup_average_seconds,
		PetscReal	ewma_seconds,
		PetscReal	latest_step_seconds,
		PetscReal *	required_headroom_seconds_out
	)

Decide whether the runtime walltime guard should stop before another step.

Parameters

[in]	completed_steps	Number of completed timesteps observed so far.
[in]	warmup_steps	Minimum completed timesteps required before guarding.
[in]	remaining_seconds	Remaining walltime in seconds.
[in]	min_seconds	Absolute minimum shutdown headroom.
[in]	multiplier	Safety multiplier applied to timestep estimate.
[in]	warmup_average_seconds	Average duration across warmup steps.
[in]	ewma_seconds	Current EWMA duration estimate.
[in]	latest_step_seconds	Latest completed timestep duration.
[out]	required_headroom_seconds_out	Computed required headroom in seconds.

Returns

PetscBool PETSC_TRUE when shutdown should be requested.

Decide whether the runtime walltime guard should stop before another step.

Full API contract (arguments, ownership, side effects) is documented with the matching public header declaration.

See also

RuntimeWalltimeGuardShouldTrigger()

Definition at line 184 of file runloop.c.

{
    PetscReal conservative_estimate = 0.0;
    PetscReal required_headroom     = 0.0;
 
    if (required_headroom_seconds_out) *required_headroom_seconds_out = 0.0;
    if (completed_steps < warmup_steps) return PETSC_FALSE;
 
    conservative_estimate = RuntimeWalltimeGuardConservativeEstimate(warmup_average_seconds, ewma_seconds, latest_step_seconds);
    required_headroom     = RuntimeWalltimeGuardRequiredHeadroom(min_seconds, multiplier, conservative_estimate);
    if (required_headroom_seconds_out) *required_headroom_seconds_out = required_headroom;
    return (PetscBool)(remaining_seconds <= required_headroom);
}

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UpdateSolverHistoryVectors()

PetscErrorCode UpdateSolverHistoryVectors

(

UserCtx *

user

)

Copies the current time step's solution fields into history vectors (e.g., U(t_n) -> U_o, U_o -> U_rm1) for the next time step's calculations.

This function is critical for multi-step time integration schemes (like BDF2) used by the legacy solver. It must be called at the end of every time step, after the new solution has been fully computed.

The order of operations is important to avoid overwriting data prematurely.

Parameters

user	The UserCtx for a single block. The function modifies the history vectors (Ucont_o, Ucont_rm1, etc.) within this context.

Returns

PetscErrorCode 0 on success.

Copies the current time step's solution fields into history vectors (e.g., U(t_n) -> U_o, U_o -> U_rm1) for the next time step's calculations.

Local to this translation unit.

Definition at line 319 of file runloop.c.

{
    PetscErrorCode ierr;
    SimCtx         *simCtx = user->simCtx; // Access global settings if needed
 
    PetscFunctionBeginUser;
    LOG_ALLOW(LOCAL, LOG_DEBUG, "Rank %d, Block %d: Updating solver history vectors.\n",
              simCtx->rank, user->_this);
 
    // --- Primary Contravariant Velocity History ---
    // The order is critical here.
    // 1. First, move the n-1 state (Ucont_o) to the n-2 slot (Ucont_rm1).
    ierr = VecCopy(user->Ucont_o, user->Ucont_rm1); CHKERRQ(ierr);
    // 2. Then, move the new n state (Ucont) to the n-1 slot (Ucont_o).
    ierr = VecCopy(user->Ucont, user->Ucont_o); CHKERRQ(ierr);
 
    LOG_ALLOW(LOCAL,LOG_DEBUG, "Rank %d, Block %d, Ucont history updated.\n",simCtx->rank,user->_this); 
    
    // --- Update History for Other Fields ---
    // These are typically only needed at the n-1 state.
    ierr = VecCopy(user->Ucat, user->Ucat_o); CHKERRQ(ierr);
    ierr = VecCopy(user->P, user->P_o); CHKERRQ(ierr);
    LOG_ALLOW(LOCAL,LOG_DEBUG, "Rank %d, Block %d, Ucat & P  history updated.\n",simCtx->rank,user->_this); 
    
    if (simCtx->immersed) {
        ierr = VecCopy(user->Nvert, user->Nvert_o); CHKERRQ(ierr);
    }
 
    // --- Update History for Turbulence Models (if active) ---
    if (simCtx->rans) {
       ierr = VecCopy(user->K_Omega, user->K_Omega_o); CHKERRQ(ierr);
    }
    
    // --- Synchronize Local Ghost Regions for the new history vectors ---
    // This is essential so that stencils in the next time step's calculations
    // have correct values from neighboring processes.
    ierr = DMGlobalToLocalBegin(user->fda, user->Ucont_o, INSERT_VALUES, user->lUcont_o); CHKERRQ(ierr);
    ierr = DMGlobalToLocalEnd(user->fda, user->Ucont_o, INSERT_VALUES, user->lUcont_o); CHKERRQ(ierr);
 
    ierr = DMGlobalToLocalBegin(user->fda, user->Ucont_rm1, INSERT_VALUES, user->lUcont_rm1); CHKERRQ(ierr);
    ierr = DMGlobalToLocalEnd(user->fda, user->Ucont_rm1, INSERT_VALUES, user->lUcont_rm1); CHKERRQ(ierr);
    
    if (simCtx->immersed) {
        ierr = DMGlobalToLocalBegin(user->da, user->Nvert_o, INSERT_VALUES, user->lNvert_o); CHKERRQ(ierr);
        ierr = DMGlobalToLocalEnd(user->da, user->Nvert_o, INSERT_VALUES, user->lNvert_o); CHKERRQ(ierr);
    }
    
    if (simCtx->rans) {
       ierr = DMGlobalToLocalBegin(user->fda2, user->K_Omega_o, INSERT_VALUES, user->lK_Omega_o); CHKERRQ(ierr);
       ierr = DMGlobalToLocalEnd(user->fda2, user->K_Omega_o, INSERT_VALUES, user->lK_Omega_o); CHKERRQ(ierr);
    }
    
    PetscFunctionReturn(0);
}

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AdvanceSimulation()

PetscErrorCode AdvanceSimulation

(

SimCtx *

simCtx

)

Executes the main time-marching loop for the particle simulation.

This version uses the new, integrated LocateAllParticlesInGrid orchestrator and the ResetAllParticleStatuses helper for a clean, robust, and understandable workflow.

For each timestep, it performs:

1. Sets the background fluid velocity field (Ucat) for the current step.
2. Updates particle positions using velocity from the previous step's interpolation.
3. Removes any particles that have left the global domain.
4. A single call to ‘LocateAllParticlesInGrid’, which handles all particle location and migration until the swarm is fully settled.
5. Interpolates the current fluid velocity to the newly settled particle locations.
6. Scatters particle data back to Eulerian fields.
7. Outputs data at specified intervals.

Parameters

simCtx

Pointer to the master simulation context.

Returns

PetscErrorCode 0 on success, non-zero on failure.

Executes the main time-marching loop for the particle simulation.

Local to this translation unit.

Definition at line 572 of file runloop.c.

{
    PetscErrorCode ierr;
    PetscReal      step_start_seconds = 0.0;
    PetscReal      step_elapsed_local = 0.0;
    PetscReal      step_elapsed_max = 0.0;
    // Get the master context from the first block. All blocks share it.
    UserCtx *user = simCtx->usermg.mgctx[simCtx->usermg.mglevels-1].user;
 
    // Retrieve control parameters from SimCtx for clarity
    const PetscInt  StartStep = simCtx->StartStep;
    const PetscInt  StepsToRun = simCtx->StepsToRun;
    const PetscReal dt = simCtx->dt;
    
    // Variables for particle removal statistics
    //PetscInt removed_local_ob, removed_global_ob;
    PetscInt removed_local_lost, removed_global_lost;
    PetscBool terminated_early = PETSC_FALSE;
    PetscInt  last_completed_loop_index = StartStep - 1;
 
    PetscFunctionBeginUser;
    PROFILE_FUNCTION_BEGIN;
    LOG_ALLOW(GLOBAL, LOG_INFO, "Starting main time-marching loop: %d steps from step %d (t=%.4f), dt=%.4f\n",
              StepsToRun, StartStep, simCtx->StartTime, dt);
 
    // --- Main Time-Marching Loop ---
    for (PetscInt step = StartStep; step < StartStep + StepsToRun; step++) {
        ierr = MaybeRequestRuntimeWalltimeGuardShutdown(simCtx, "pre-step checkpoint"); CHKERRQ(ierr);
        if (RuntimeShutdownRequested()) {
            ierr = WriteForcedTerminationOutput(simCtx, user, "pre-step checkpoint"); CHKERRQ(ierr);
            terminated_early = PETSC_TRUE;
            break;
        }
 
        step_start_seconds = MPI_Wtime();
        
        // =================================================================
        //     1. PRE-STEP SETUP
        // =================================================================
        
        // Update simulation time and step counters in the master context
        simCtx->step = step + 1;
        simCtx->ti   += simCtx->dt; //simCtx->StartTime + step * simCtx->dt;
 
        LOG_ALLOW(GLOBAL, LOG_INFO, "--- Advancing Step %d (To t=%.4f) ---\n", simCtx->step, simCtx->ti);
        
 
        // For particles, reset their status to prepare for the new advection/location cycle
        if (simCtx->np > 0) {
            LOG_ALLOW(GLOBAL, LOG_DEBUG, "Resetting all particle statuses to NEEDS_LOCATION.\n");
            ierr = ResetAllParticleStatuses(user); CHKERRQ(ierr);
        }
 
        // =================================================================
        //     2. EULERIAN SOLVER STEP
        // =================================================================
        if(get_log_level() == LOG_VERBOSE && is_function_allowed(__FUNCT__)==true){
            ierr = LOG_FIELD_ANATOMY(&user[0],"Coordinates","PreFlowSolver"); CHKERRQ(ierr);
            ierr = LOG_FIELD_ANATOMY(&user[0],"Csi","PreFlowSolver"); CHKERRQ(ierr);
            ierr = LOG_FIELD_ANATOMY(&user[0],"Eta","PreFlowSolver"); CHKERRQ(ierr);
            ierr = LOG_FIELD_ANATOMY(&user[0],"Zet","PreFlowSolver"); CHKERRQ(ierr);
            ierr = LOG_FIELD_ANATOMY(&user[0],"Center-Coordinates","PreFlowSolver"); CHKERRQ(ierr);
            ierr = LOG_FIELD_ANATOMY(&user[0],"X-Face-Centers","PreFlowSolver"); CHKERRQ(ierr);
            ierr = LOG_FIELD_ANATOMY(&user[0],"Y-Face-Centers","PreFlowSolver"); CHKERRQ(ierr);
            ierr = LOG_FIELD_ANATOMY(&user[0],"Z-Face-Centers","PreFlowSolver"); CHKERRQ(ierr);
            ierr = LOG_FIELD_ANATOMY(&user[0],"Ucat","PreFlowSolver"); CHKERRQ(ierr);
        }
        LOG_ALLOW(GLOBAL, LOG_INFO, "Updating Eulerian Field ...\n");
        if(strcmp(simCtx->eulerianSource,"load")==0){
            //LOAD mode: Read pre-computed fields for the current step.
            LOG_ALLOW(GLOBAL,LOG_INFO,"Eulerian Source 'load': Reading fields (t=%.4f,step=%d)...\n",simCtx->ti,simCtx->step);
            for(PetscInt bi = 0; bi < simCtx->block_number;bi++){
                ierr = ReadSimulationFields(&user[bi],simCtx->step); CHKERRQ(ierr);
            }
        }else if(strcmp(simCtx->eulerianSource,"analytical")==0){
            // ANALYTICAL mode:Call the Analytical Solution Prescription Engine to enable a variety of analytical functions
            LOG_ALLOW(GLOBAL,LOG_INFO,"Eulerian Source 'analytical'. Updating Eulerian field via the Analytical Solution Engine ...\n");
            ierr = AnalyticalSolutionEngine(simCtx); CHKERRQ(ierr);
        }else if(strcmp(simCtx->eulerianSource,"solve")==0){
            // SOLVE mode:Call the refactored, high-level legacy solver. This single function
            // advances the entire multi-block fluid field from t_n to t_{n+1}.
            LOG_ALLOW(GLOBAL,LOG_INFO,"Eulerian Source 'solve'. Updating Eulerian field via Solver...\n");
            ierr = FlowSolver(simCtx); CHKERRQ(ierr);
        }
        LOG_ALLOW(GLOBAL, LOG_INFO, "Eulerian Field Updated ...\n");
        if(get_log_level() == LOG_VERBOSE && is_function_allowed(__FUNCT__)==true){
            LOG_ALLOW(GLOBAL, LOG_VERBOSE, "Post FlowSolver field states:\n");
            ierr = LOG_FIELD_ANATOMY(&user[0],"Ucat","PostFlowSolver"); CHKERRQ(ierr);
            ierr = LOG_FIELD_ANATOMY(&user[0],"P","PostFlowSolver"); CHKERRQ(ierr);
            ierr = LOG_FIELD_ANATOMY(&user[0],"Ucont","PostFlowSolver"); CHKERRQ(ierr);
        }
 
 
        // =================================================================
        //     3. LAGRANGIAN PARTICLE STEP
        // =================================================================
        
        if (simCtx->np > 0) {
            LOG_ALLOW(GLOBAL, LOG_INFO, "Updating Lagrangian particle system...\n");
            simCtx->particlesLostLastStep = 0;
 
            // a. Update Eulerian Transport Properties:
            // Optimization: Only recalculate if turbulence is active (Nu_t changes).
            // For Laminar flow, the value calculated at Setup is constant.
            if (simCtx->les || simCtx->rans) {
                for (PetscInt bi = 0; bi < simCtx->block_number; bi++) {
                    ierr = ComputeEulerianDiffusivity(&user[bi]); CHKERRQ(ierr);
                    ierr = ComputeEulerianDiffusivityGradient(&user[bi]); CHKERRQ(ierr);
                }
            }
 
            // a.1 (Optional) Log Eulerian Diffusivity min/max and anatomy for debugging.
            if(get_log_level() == LOG_VERBOSE && is_function_allowed(__FUNCT__)==true){
                LOG_ALLOW(GLOBAL, LOG_VERBOSE, "Updated Diffusivity Min/Max:\n");
                ierr = LOG_FIELD_MIN_MAX(&user[0],"Diffusivity"); CHKERRQ(ierr);
                ierr = LOG_FIELD_MIN_MAX(&user[0],"DiffusivityGradient"); CHKERRQ(ierr);
                //LOG_ALLOW(GLOBAL, LOG_VERBOSE, "Updated Diffusivity Anatomy:\n");
                ierr = LOG_FIELD_ANATOMY(&user[0],"Diffusivity","PostDiffusivityUpdate"); CHKERRQ(ierr);
            }
            // b. Advect particles using the velocity interpolated from the *previous* step.
            //    P(t_{n+1}) = P(t_n) + V_p(t_n) * dt
            ierr = UpdateAllParticlePositions(user); CHKERRQ(ierr);
 
            // c. Settle all particles: find their new host cells and migrate them across ranks.
            ierr = LocateAllParticlesInGrid(user, simCtx->bboxlist); CHKERRQ(ierr);
 
            // d. Remove any particles that are now lost or out of the global domain.
            ierr = CheckAndRemoveLostParticles(user, &removed_local_lost, &removed_global_lost); CHKERRQ(ierr);
            //ierr = CheckAndRemoveOutOfBoundsParticles(user, &removed_local_ob, &removed_global_ob, simCtx->bboxlist); CHKERRQ(ierr);
            simCtx->particlesLostLastStep = removed_global_lost;
            simCtx->particlesLostCumulative += removed_global_lost;
            if (removed_global_lost> 0) { // if(removed_global_lost + removed_global_ob > 0){
                LOG_ALLOW(GLOBAL, LOG_INFO, "Removed %d particles globally this step.\n", removed_global_lost); // removed_global_lost + removed_global_ob;
            }
 
            // e. Interpolate the NEW fluid velocity (just computed by FlowSolver) onto the
            //    particles' new positions. This gives them V_p(t_{n+1}) for the *next* advection step.
            ierr = InterpolateAllFieldsToSwarm(user); CHKERRQ(ierr);
 
            // f. Update the Particle Fields (e.g., temperature, concentration) if applicable.
            //    This can be extended to include reactions, growth, etc.
            ierr = UpdateAllParticleFields(user); CHKERRQ(ierr);
            
            // g. (For Two-Way Coupling) Scatter particle data back to the grid to act as a source term.
            ierr = CalculateParticleCountPerCell(user); CHKERRQ(ierr);
            ierr = ScatterAllParticleFieldsToEulerFields(user); CHKERRQ(ierr);
            
            // h. (Optional) Calculate advanced particle metrics for logging/debugging.
            ierr = CalculateAdvancedParticleMetrics(user); CHKERRQ(ierr);
            ierr = LOG_SEARCH_METRICS(user); CHKERRQ(ierr);
 
            ierr = LOG_PARTICLE_METRICS(user, "Timestep Metrics"); CHKERRQ(ierr);
 
 
            if(get_log_level() == LOG_VERBOSE && is_function_allowed(__FUNCT__)==true){
                LOG_ALLOW(GLOBAL, LOG_VERBOSE, "Post Lagrangian update field states:\n");
                ierr = LOG_FIELD_MIN_MAX(&user[0],"Psi"); CHKERRQ(ierr);
            }
        }
 
        // =================================================================
        //     4. UPDATE HISTORY & I/O
        // =================================================================
        
        // Copy the newly computed fields (Ucont, P, etc.) to the history vectors
        // (_o, _rm1) to prepare for the next time step.
        for (PetscInt bi = 0; bi < simCtx->block_number; bi++) {
            ierr = UpdateSolverHistoryVectors(&user[bi]); CHKERRQ(ierr);
        }
        
        //ierr = LOG_UCAT_ANATOMY(&user[0],"Final"); CHKERRQ(ierr);
        
        // Handle periodic file output
        if (ShouldWriteDataOutput(simCtx, simCtx->step)) {
            LOG_ALLOW(GLOBAL, LOG_INFO, "Writing output for step %d.\n",simCtx->step);
            for (PetscInt bi = 0; bi < simCtx->block_number; bi++) {
                ierr = WriteSimulationFields(&user[bi]); CHKERRQ(ierr);
            }
            if (simCtx->np > 0) {
                ierr = WriteAllSwarmFields(user); CHKERRQ(ierr);
                if (strcmp(simCtx->eulerianSource, "analytical") == 0 &&
                    AnalyticalTypeSupportsInterpolationError(simCtx->AnalyticalSolutionType)) {
                    LOG_INTERPOLATION_ERROR(user);
                }
                ierr = LOG_SCATTER_METRICS(user); CHKERRQ(ierr);
            }
        }
 
        if (ShouldEmitPeriodicParticleConsoleSnapshot(simCtx, simCtx->step)) {
            ierr = EmitParticleConsoleSnapshot(user, simCtx, simCtx->step); CHKERRQ(ierr);
        }
 
        ProfilingLogTimestepSummary(simCtx, simCtx->step);
 
        // Update Progress Bar
        if(simCtx->rank == 0) {
            PrintProgressBar(step,StartStep,StepsToRun,simCtx->ti);
            if(get_log_level()>=LOG_WARNING) PetscPrintf(PETSC_COMM_SELF,"\n");
        }
 
        last_completed_loop_index = step;
 
        step_elapsed_local = MPI_Wtime() - step_start_seconds;
        step_elapsed_max   = step_elapsed_local;
        ierr               = MPI_Allreduce(&step_elapsed_local, &step_elapsed_max, 1, MPIU_REAL, MPI_MAX, PETSC_COMM_WORLD); CHKERRMPI(ierr);
        if (simCtx->walltimeGuardActive) {
            UpdateRuntimeWalltimeGuardEstimator(simCtx, step_elapsed_max);
            ierr = MaybeRequestRuntimeWalltimeGuardShutdown(simCtx, "post-step checkpoint"); CHKERRQ(ierr);
        }
 
        if (RuntimeShutdownRequested()) {
            ierr = WriteForcedTerminationOutput(simCtx, user, "post-step checkpoint"); CHKERRQ(ierr);
            terminated_early = PETSC_TRUE;
            break;
        }
    } // --- End of Time-Marching Loop ---
 
    // After the loop, print the final progress state on rank 0 and add a newline
    // to ensure subsequent terminal output starts on a fresh line.
    if (simCtx->rank == 0 && StepsToRun > 0) {
        if (!terminated_early && last_completed_loop_index >= StartStep) {
            PrintProgressBar(StartStep + StepsToRun - 1, StartStep, StepsToRun, simCtx->ti);
        } else if (terminated_early && last_completed_loop_index >= StartStep) {
            PrintProgressBar(last_completed_loop_index, StartStep, StepsToRun, simCtx->ti);
        }
        PetscPrintf(PETSC_COMM_SELF, "\n");
        fflush(stdout);
    }
 
    if (terminated_early) {
        LOG_ALLOW(GLOBAL, LOG_WARNING,
                  "Time marching stopped early after %s. Final retained state is step %d at t=%.4f.\n",
                  RuntimeShutdownReasonName(), simCtx->step, simCtx->ti);
    } else {
        LOG_ALLOW(GLOBAL, LOG_INFO, "Time marching completed. Final time t=%.4f.\n", simCtx->ti);
    }
    PROFILE_FUNCTION_END;
    PetscFunctionReturn(0);
}

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PerformInitializedParticleSetup()

PetscErrorCode PerformInitializedParticleSetup

(

SimCtx *

simCtx

)

Finalizes the simulation setup at t=0, ensuring a consistent state before time marching.

This function is called from main() after the initial Eulerian and Lagrangian states have been created but before the main time loop begins. Its responsibilities are:

1. Settling the particle swarm: Migrates particles to their correct owner ranks and finds their initial host cells. This includes handling special surface initializations.
2. Coupling the fields: Interpolates the initial Eulerian fields to the settled particle locations.
3. Preparing for the first step: Scatters particle data back to the grid.
4. Writing the initial output for step 0.

Parameters

simCtx

Pointer to the main simulation context structure.

Returns

PetscErrorCode 0 on success, non-zero on failure.

Finalizes the simulation setup at t=0, ensuring a consistent state before time marching.

Local to this translation unit.

Definition at line 380 of file runloop.c.

{
    PetscErrorCode ierr;
    // --- Get pointers from SimCtx instead of passing them as arguments ---
    UserCtx     *user     = simCtx->usermg.mgctx[simCtx->usermg.mglevels-1].user;
    BoundingBox *bboxlist = simCtx->bboxlist;
 
    PetscFunctionBeginUser;
    
    LOG_ALLOW(GLOBAL, LOG_INFO, "[T=%.4f, Step=%d] Performing initial particle setup procedures.\n", simCtx->ti, simCtx->step);
 
    // --- 0. Loop over all blocks to compute Eulerian diffusivity.
    for (PetscInt bi = 0; bi < simCtx->block_number; bi++) {
        ierr = ComputeEulerianDiffusivity(&user[bi]); CHKERRQ(ierr);
        ierr = ComputeEulerianDiffusivityGradient(&user[bi]); CHKERRQ(ierr);
    }
 
    // --- 1. Initial Particle Settlement (Location and Migration) ---
    LOG_ALLOW(GLOBAL, LOG_INFO, "[T=%.4f, Step=%d] Initial Settlement: Locating and migrating all particles...\n", simCtx->ti, simCtx->step);
    ierr = LocateAllParticlesInGrid(user, bboxlist); CHKERRQ(ierr);
 
    if(get_log_level() >= LOG_DEBUG && is_function_allowed(__FUNCT__)==true){
        LOG_ALLOW(GLOBAL, LOG_DEBUG, "[T=%.4f, Step=%d] Particle field states after Initial settlement...\n", simCtx->ti, simCtx->step);
        ierr = LOG_PARTICLE_FIELDS(user,simCtx->LoggingFrequency); CHKERRQ(ierr);
    }
 
    // --- 2. Re-initialize Particles on Inlet Surface (if applicable) ---
    if ((simCtx->ParticleInitialization == PARTICLE_INIT_SURFACE_RANDOM ||
         simCtx->ParticleInitialization == PARTICLE_INIT_SURFACE_EDGES) && user->inletFaceDefined) {
        LOG_ALLOW(GLOBAL, LOG_INFO, "[T=%.4f, Step=%d] Re-initializing particles on inlet surface...\n", simCtx->ti, simCtx->step);
        ierr = ReinitializeParticlesOnInletSurface(user, simCtx->ti, simCtx->step); CHKERRQ(ierr);
 
        LOG_ALLOW(GLOBAL, LOG_INFO, "[T=%.4f, Step=%d] Resetting statuses for post-reinitialization settlement.\n", simCtx->ti, simCtx->step);
        ierr = ResetAllParticleStatuses(user); CHKERRQ(ierr);
    
        LOG_ALLOW(GLOBAL, LOG_INFO, "[T=%.4f, Step=%d] Post-Reinitialization Settlement...\n", simCtx->ti, simCtx->step);
        ierr = LocateAllParticlesInGrid(user, bboxlist); CHKERRQ(ierr);
 
    }
    
    // --- 3. Finalize State for t=0 ---
    LOG_ALLOW(GLOBAL, LOG_INFO, "[T=%.4f, Step=%d] Interpolating initial fields to settled particles.\n", simCtx->ti, simCtx->step);
    ierr = InterpolateAllFieldsToSwarm(user); CHKERRQ(ierr);
    ierr = RefreshVerificationScalarScatterState(user); CHKERRQ(ierr);
 
    // --- 4. Initial History and Output ---
    // Update solver history vectors with the t=0 state before the first real step
    for (PetscInt bi = 0; bi < simCtx->block_number; bi++) {
        ierr = UpdateSolverHistoryVectors(&user[bi]); CHKERRQ(ierr);
    }
 
    if (simCtx->tiout > 0 || (simCtx->StepsToRun == 0 && simCtx->StartStep == 0)) {
        LOG_ALLOW(GLOBAL, LOG_INFO, "[T=%.4f, Step=%d] Writing initial simulation data.\n", simCtx->ti, simCtx->step);
        ierr = WriteAllSwarmFields(user); CHKERRQ(ierr);
        
        // --- Eulerian Field Output (MUST loop over all blocks) --- // <<< CHANGED/FIXED
        for (PetscInt bi = 0; bi < simCtx->block_number; bi++) {
            ierr = WriteSimulationFields(&user[bi]); CHKERRQ(ierr);
        }
        ierr = LOG_SCATTER_METRICS(user); CHKERRQ(ierr);
    }
 
    if (IsParticleConsoleSnapshotEnabled(simCtx)) {
        ierr = EmitParticleConsoleSnapshot(user, simCtx, simCtx->step); CHKERRQ(ierr);
    }
 
    LOG_ALLOW(GLOBAL, LOG_INFO, "--- Initial setup complete. Ready for time marching. ---\n");
    PetscFunctionReturn(0);
}

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PerformLoadedParticleSetup()

PetscErrorCode PerformLoadedParticleSetup

(

SimCtx *

simCtx

)

Finalizes the simulation state after particle and fluid data have been loaded from a restart.

This helper function performs the critical sequence of operations required to ensure the loaded Lagrangian and Eulerian states are fully consistent and the solver is ready to proceed. This includes:

1. Verifying particle locations in the grid and building runtime links.
2. Synchronizing particle velocity with the authoritative grid velocity via interpolation.
3. Scattering particle source terms (e.g., volume fraction) back to the grid.
4. Updating the solver's history vectors with the final, fully-coupled state.
5. Writing the complete, consistent state to output files for the restart step.

Parameters

simCtx

The main simulation context.

Returns

PetscErrorCode 0 on success.

Finalizes the simulation state after particle and fluid data have been loaded from a restart.

Local to this translation unit.

Definition at line 456 of file runloop.c.

{
    PetscErrorCode ierr;
    PetscFunctionBeginUser;
    UserCtx     *user     = simCtx->usermg.mgctx[simCtx->usermg.mglevels-1].user;
 
    // --- 0. Re-compute Eulerian Diffusivity from loaded fields.
    LOG_ALLOW(GLOBAL, LOG_INFO, "Re-computing Eulerian Diffusivity from loaded fields...\n");
    for (PetscInt bi = 0; bi < simCtx->block_number; bi++) {
        ierr = ComputeEulerianDiffusivity(&user[bi]); CHKERRQ(ierr);
        ierr = ComputeEulerianDiffusivityGradient(&user[bi]); CHKERRQ(ierr);
    }
 
    // 0.1 This moves particles to their correct ranks immediately using the loaded Cell ID.
    LOG_ALLOW(GLOBAL, LOG_INFO, "Performing fast restart migration using preloaded Cell IDs...\n");
    ierr = MigrateRestartParticlesUsingCellID(user); CHKERRQ(ierr);
 
    // 1. To catch any edge cases (particles with invalid CellIDs or newcomers).
    // Because we kept the statuses, this function will now SKIP all the particles 
    // that are already on the correct rank,
    ierr = LocateAllParticlesInGrid(user, simCtx->bboxlist); CHKERRQ(ierr);
 
    if(get_log_level() == LOG_DEBUG){
        LOG(GLOBAL, LOG_DEBUG, "[T=%.4f, Step=%d] Particle field states after locating loaded particles...\n", simCtx->ti, simCtx->step);
        ierr = LOG_PARTICLE_FIELDS(user,simCtx->LoggingFrequency); CHKERRQ(ierr);
    }
 
    LOG_ALLOW(GLOBAL, LOG_INFO, "[T=%.4f, Step=%d] Interpolating initial fields to settled particles.\n", simCtx->ti, simCtx->step);
 
    // 2. Ensure particles have velocity from the authoritative loaded grid for consistency.
    ierr = InterpolateAllFieldsToSwarm(user); CHKERRQ(ierr);
 
    // 3. Update Eulerian source terms from the loaded particle data.
    if (VerificationScalarOverrideActive(simCtx)) {
        ierr = RefreshVerificationScalarScatterState(user); CHKERRQ(ierr);
    } else {
        ierr = ScatterAllParticleFieldsToEulerFields(user); CHKERRQ(ierr);
    }
 
    // --- 4. Initial History and Output ---
    // Update solver history vectors with the t=0 state before the first real step
    for (PetscInt bi = 0; bi < simCtx->block_number; bi++) {
        ierr = UpdateSolverHistoryVectors(&user[bi]); CHKERRQ(ierr);
    }
 
    if (simCtx->tiout > 0 || (simCtx->StepsToRun == 0 && simCtx->StartStep == 0)) {
        LOG_ALLOW(GLOBAL, LOG_INFO, "[T=%.4f, Step=%d] Writing initial simulation data.\n", simCtx->ti, simCtx->step);
        ierr = WriteAllSwarmFields(user); CHKERRQ(ierr);
        
        // --- Eulerian Field Output (MUST loop over all blocks) --- // <<< CHANGED/FIXED
        for (PetscInt bi = 0; bi < simCtx->block_number; bi++) {
            ierr = WriteSimulationFields(&user[bi]); CHKERRQ(ierr);
        }
        ierr = LOG_SCATTER_METRICS(user); CHKERRQ(ierr);
    }
 
    if (IsParticleConsoleSnapshotEnabled(simCtx)) {
        ierr = EmitParticleConsoleSnapshot(user, simCtx, simCtx->step); CHKERRQ(ierr);
    }
 
    LOG_ALLOW(GLOBAL, LOG_INFO, "--- Initial setup complete. Ready for time marching. ---\n");
    PetscFunctionReturn(0);
}

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FinalizeRestartState()

PetscErrorCode FinalizeRestartState

(

SimCtx *

simCtx

)

Performs post-load/post-init consistency checks for a restarted simulation.

This function is called from main() ONLY when a restart is being performed (i.e., StartStep > 0). It inspects the particle restart mode to determine the correct finalization procedure for the Lagrangian swarm.

• If particles were loaded from a file (mode == "load"), it verifies their locations within the grid to establish necessary runtime links.
• If new particles were initialized into the restarted flow (mode == "init"), it runs the full PerformInitialSetup sequence to migrate, locate, and couple the new particles with the existing fluid state.

Parameters

simCtx

The main simulation context.

Returns

PetscErrorCode 0 on success.

Performs post-load/post-init consistency checks for a restarted simulation.

Local to this translation unit.

Definition at line 526 of file runloop.c.

{
    PetscErrorCode ierr;
    UserCtx       *user = simCtx->usermg.mgctx[simCtx->usermg.mglevels - 1].user;
 
    PetscFunctionBeginUser;
 
    LOG_ALLOW(GLOBAL, LOG_INFO, "--- Finalizing RESTART from state (step=%d, t=%.4f) ---\n", simCtx->StartStep, simCtx->ti);
 
    // This function only needs to handle the particle finalization logic.
    // The Eulerian state is assumed to be fully loaded and consistent at this point.
    if (simCtx->np > 0) {
 
        // Use the particle restart mode to decide the workflow.
        if (strcmp(simCtx->particleRestartMode, "load") == 0) {
            // PARTICLES WERE LOADED: The state is complete, but we must verify
            // the loaded CellIDs and build the in-memory grid-to-particle links.
            LOG_ALLOW(GLOBAL, LOG_INFO, "Particle Mode 'load': Verifying particle locations and building grid links...\n");
            ierr = PerformLoadedParticleSetup(simCtx); CHKERRQ(ierr);
 
        } else { // Mode must be "init"
            // PARTICLES WERE RE-INITIALIZED: They need to be fully settled and coupled
            // to the surrounding (restarted) fluid state.
            LOG_ALLOW(GLOBAL, LOG_INFO, "Particle Mode 'init': Running full initial setup for new particles in restarted flow.\n");
            ierr = PerformInitializedParticleSetup(simCtx); CHKERRQ(ierr);
        }
    } else {
        LOG_ALLOW(GLOBAL, LOG_INFO, "No particles in simulation, restart finalization is complete.\n");
 
        // Write the initial eulerian fields (this is done in PerformInitialSetup if particles exist.)
        for(PetscInt bi = 0; bi < simCtx->block_number; bi ++){
            ierr = WriteSimulationFields(&user[bi]); CHKERRQ(ierr);
        }
    }
 
    LOG_ALLOW(GLOBAL, LOG_INFO, "--- Restart state successfully finalized. --\n");
 
    PetscFunctionReturn(0);
}

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