ParticleSwarm.h File Reference

Header file for Particle Swarm management functions. More...

#include <petsc.h>
#include <petscdmswarm.h>
#include <stdbool.h>
#include <math.h>
#include "variables.h"
#include "logging.h"
#include "walkingsearch.h"
#include "Metric.h"
#include "io.h"

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Functions
PetscErrorCode	CreateParticleSwarm (UserCtx *user, PetscInt numParticles, PetscInt *particlesPerProcess, BoundingBox *bboxlist)
	Creates and initializes a Particle Swarm.
PetscErrorCode	InitializeSwarm (UserCtx *user)
	Initializes the DMSwarm object within the UserCtx structure.
PetscErrorCode	RegisterSwarmField (DM swarm, const char *fieldName, PetscInt fieldDim, PetscDataType dtype)
	Registers a swarm field without finalizing registration.
PetscErrorCode	RegisterParticleFields (DM swarm)
	Registers necessary particle fields within the DMSwarm.
PetscErrorCode	AssignInitialPropertiesToSwarm (UserCtx *user, PetscInt particlesPerProcess, PetscRandom *rand_phys_x, PetscRandom *rand_phys_y, PetscRandom *rand_phys_z, PetscRandom *rand_logic_i, PetscRandom *rand_logic_j, PetscRandom *rand_logic_k, BoundingBox *bboxlist)
	Initializes all particle properties in the swarm.
PetscErrorCode	DistributeParticles (PetscInt numParticles, PetscMPIInt rank, PetscMPIInt size, PetscInt *particlesPerProcess, PetscInt *remainder)
	Distributes particles evenly across MPI processes, handling any remainders.
PetscErrorCode	FinalizeSwarmSetup (PetscRandom *randx, PetscRandom *randy, PetscRandom *randz, PetscRandom *rand_logic_i, PetscRandom *rand_logic_j, PetscRandom *rand_logic_k)
	Finalizes the swarm setup by destroying random generators and logging completion.
PetscErrorCode	UnpackSwarmFields (PetscInt i, const PetscInt64 *PIDs, const PetscReal *weights, const PetscReal *positions, const PetscInt *cellIndices, PetscReal *velocities, PetscInt *LocStatus, PetscReal *diffusivity, Cmpnts *diffusivitygradient, PetscReal *psi, Particle *particle)
	Initializes a Particle struct with data from DMSwarm fields.
PetscErrorCode	UpdateSwarmFields (PetscInt i, const Particle *particle, PetscReal *positions, PetscReal *velocities, PetscReal *weights, PetscInt *cellIndices, PetscInt *status, PetscReal *diffusivity, Cmpnts *diffusivitygradient, PetscReal *psi)
	Updates DMSwarm data arrays from a Particle struct.
PetscBool	IsParticleInsideBoundingBox (const BoundingBox *bbox, const Particle *particle)
	Checks if a particle's location is within a specified bounding box.
PetscErrorCode	UpdateParticleWeights (PetscReal *d, Particle *particle)
	Updates a particle's interpolation weights based on distances to cell faces.
PetscErrorCode	InitializeParticleSwarm (SimCtx *simCtx)
	High-level particle initialization orchestrator for a simulation run.

Detailed Description

Header file for Particle Swarm management functions.

This file contains declarations of functions responsible for creating, managing, initializing, migrating, and printing particle swarms within a simulation using PETSc's DMSwarm.

Definition in file ParticleSwarm.h.

Function Documentation

CreateParticleSwarm()

PetscErrorCode CreateParticleSwarm	(	UserCtx *	user,
		PetscInt	numParticles,
		PetscInt *	particlesPerProcess,
		BoundingBox *	bboxlist
	)

Creates and initializes a Particle Swarm.

This function sets up a DMSwarm within the provided UserCtx structure, initializes particle fields, and distributes particles across MPI processes. It ensures that the number of particles is evenly divided among the available MPI ranks. If the total number of particles isn't divisible by the number of processes, the remainder is distributed to the first few ranks.

Additionally, it now takes a 'bboxlist' array as an input parameter and passes it on to AssignInitialProperties(), enabling particle initialization at the midpoint of each rank's bounding box if ParticleInitialization is set to 0.

Parameters

[in,out]	user	Pointer to the UserCtx structure containing the simulation context.
[in]	numParticles	Total number of particles to create across all MPI processes.
[out]	particlesPerProcess	Number of particles assigned to the local rank.
[in]	bboxlist	Pointer to an array of BoundingBox structures, one per rank.

Returns

PetscErrorCode Returns 0 on success, non-zero on failure.

Note

• Ensure that numParticles is a positive integer.
• The control.dat file should contain necessary PETSc options.
• The bboxlist array should be properly populated before calling this function.

Creates and initializes a Particle Swarm.

Local to this translation unit.

Definition at line 651 of file ParticleSwarm.c.

                                                                                                                               {
    PetscErrorCode ierr;                      // PETSc error handling variable
    (void)bboxlist;
    PetscMPIInt rank, size;                   // Variables to store MPI rank and size
    PetscInt remainder = 0;                   // Remainder of particles after division
    
    PetscFunctionBeginUser;
    PROFILE_FUNCTION_BEGIN;
    // Validate input parameters
    if (numParticles <= 0) {
    LOG_ALLOW(GLOBAL,LOG_DEBUG, "Number of particles must be positive. Given: %d\n", numParticles);
        return PETSC_ERR_ARG_OUTOFRANGE;
    }
    
    // Retrieve MPI rank and size
    ierr = MPI_Comm_rank(PETSC_COMM_WORLD, &rank); CHKERRQ(ierr);
    ierr = MPI_Comm_size(PETSC_COMM_WORLD, &size); CHKERRQ(ierr);
    LOG_ALLOW(GLOBAL,LOG_INFO," Domain dimensions: [%.2f,%.2f],[%.2f,%.2f],[%.2f,%.2f] \n", 
        user->Min_X,user->Max_X,user->Min_Y,user->Max_Y, user->Min_Z,user->Max_Z);
    LOG_ALLOW_SYNC(GLOBAL,LOG_DEBUG, "[Rank %d] Local Bounding Box: [%.2f,%.2f],[%.2f,%.2f],[%.2f,%.2f] \n", 
        rank,user->bbox.min_coords.x,user->bbox.max_coords.x,
        user->bbox.min_coords.y,user->bbox.max_coords.y,
        user->bbox.min_coords.z,user->bbox.max_coords.z);
    // Distribute particles among MPI processes
    ierr = DistributeParticles(numParticles, rank, size, particlesPerProcess, &remainder); CHKERRQ(ierr);
 
    // Initialize the DMSwarm - creates the swarm, sets the type and dimension
    ierr = InitializeSwarm(user); CHKERRQ(ierr);
 
    if (user->da) {
    ierr = DMSwarmSetCellDM(user->swarm, user->da); CHKERRQ(ierr);
    LOG_ALLOW(LOCAL,LOG_INFO,"Associated DMSwarm with Cell DM (user->da).\n");
    } else {
    // If user->da is essential for your simulation logic with particles, this should be a fatal error.
    LOG_ALLOW(GLOBAL, LOG_WARNING, "user->da (Cell DM for Swarm) is NULL. Cell-based swarm operations might fail.\n");
    // SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONGSTATE, "user->da (Cell DM) is NULL but required.");
    }
    
    // Register particle fields (position, velocity, CellID, weight, etc.)
    ierr = RegisterParticleFields(user->swarm); CHKERRQ(ierr);
 
    // Set the local number of particles for this rank and additional buffer for particle migration
    ierr = DMSwarmSetLocalSizes(user->swarm, *particlesPerProcess, numParticles); CHKERRQ(ierr);
    LOG_ALLOW(GLOBAL,LOG_INFO, "Set local swarm size: %d particles.\n", *particlesPerProcess);
 
    // Optionally, LOG_ALLOW detailed DM info in debug mode
    if (get_log_level() == LOG_DEBUG && is_function_allowed(__func__)) {
    LOG_ALLOW(GLOBAL,LOG_DEBUG,"Viewing DMSwarm:\n");
        ierr = DMView(user->swarm, PETSC_VIEWER_STDOUT_WORLD); CHKERRQ(ierr);
    }
 
    LOG_ALLOW(GLOBAL,LOG_INFO, "Particle swarm creation and initialization complete.\n");
 
    PROFILE_FUNCTION_END;
    PetscFunctionReturn(0);
}

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InitializeSwarm()

PetscErrorCode InitializeSwarm

(

UserCtx *

user

)

Initializes the DMSwarm object within the UserCtx structure.

This function creates the DMSwarm, sets its type and dimension, and configures basic swarm properties.

Parameters

[in,out]

user

Pointer to the UserCtx structure containing simulation context.

Returns

PetscErrorCode Returns 0 on success, non-zero on failure.

Initializes the DMSwarm object within the UserCtx structure.

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

See also

InitializeSwarm()

Definition at line 15 of file ParticleSwarm.c.

                                              {
    PetscErrorCode ierr;  // Error code for PETSc functions
 
    PetscFunctionBeginUser;
    PROFILE_FUNCTION_BEGIN;
    // Create the DMSwarm object for particle management
    ierr = DMCreate(PETSC_COMM_WORLD, &user->swarm); CHKERRQ(ierr);
    ierr = DMSetType(user->swarm, DMSWARM); CHKERRQ(ierr);
    ierr = DMSetDimension(user->swarm, 3); CHKERRQ(ierr);
    ierr = DMSwarmSetType(user->swarm, DMSWARM_BASIC); CHKERRQ(ierr);
    LOG_ALLOW(LOCAL,LOG_INFO, "DMSwarm created and configured.\n");
 
    PROFILE_FUNCTION_END;
    PetscFunctionReturn(0);
}

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RegisterSwarmField()

PetscErrorCode RegisterSwarmField	(	DM	swarm,
		const char *	fieldName,
		PetscInt	fieldDim,
		PetscDataType	dtype
	)

Registers a swarm field without finalizing registration.

This function calls DMSwarmRegisterPetscDatatypeField for the given field, but does not finalize the registration. The finalization is deferred until all fields have been registered.

Parameters

swarm	[in] The DMSwarm object.
fieldName	[in] Name of the field to register.
fieldDim	[in] Dimension of the field (1 for scalar, 3 for vector, etc.).
dtype	[in] The datatype of the swarm field being registered.

Returns

PetscErrorCode Returns 0 on success, non-zero on failure.

Registers a swarm field without finalizing registration.

Local to this translation unit.

Definition at line 38 of file ParticleSwarm.c.

{
    PetscErrorCode ierr;
    PetscFunctionBeginUser;
    
    ierr = DMSwarmRegisterPetscDatatypeField(swarm, fieldName, fieldDim, dtype); CHKERRQ(ierr);
    // PetscDataTypes is an extern char* [] defined in petscsystypes.h that gives string names for PetscDataType enums
    LOG_ALLOW(LOCAL,LOG_DEBUG,"Registered field '%s' with dimension=%d, type=%s.\n",
            fieldName, fieldDim, PetscDataTypes[dtype]);
    
    PetscFunctionReturn(0);
}

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RegisterParticleFields()

PetscErrorCode RegisterParticleFields

(

DM

swarm

)

Registers necessary particle fields within the DMSwarm.

This function registers fields such as position, velocity, CellID, and weight for each particle.

Parameters

[in,out]

swarm

The DMSwarm object managing the particle swarm.

Returns

PetscErrorCode Returns 0 on success, non-zero on failure.

Registers necessary particle fields within the DMSwarm.

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

See also

RegisterParticleFields()

Definition at line 61 of file ParticleSwarm.c.

{
    PetscErrorCode ierr;
    PetscFunctionBeginUser;
    
    // Register each field using the helper function
    ierr = RegisterSwarmField(swarm, "position", 3 ,PETSC_REAL); CHKERRQ(ierr);
    LOG_ALLOW(LOCAL,LOG_DEBUG, "Registered field 'position'.\n");
    
    ierr = RegisterSwarmField(swarm, "velocity", 3, PETSC_REAL); CHKERRQ(ierr);
    LOG_ALLOW(LOCAL,LOG_DEBUG,"Registered field 'velocity'.\n");
    
    ierr = RegisterSwarmField(swarm, "DMSwarm_CellID", 3, PETSC_INT); CHKERRQ(ierr);
    LOG_ALLOW(LOCAL,LOG_DEBUG,"Registered field 'DMSwarm_CellID'.\n");
    
    ierr = RegisterSwarmField(swarm, "weight", 3,PETSC_REAL); CHKERRQ(ierr);
    LOG_ALLOW(LOCAL,LOG_DEBUG,"Registered field 'weight'.\n");
 
    ierr = RegisterSwarmField(swarm,"Diffusivity", 1,PETSC_REAL); CHKERRQ(ierr);
    LOG_ALLOW(LOCAL,LOG_DEBUG,"Registered field 'Diffusivity' - Scalar.\n");
 
    ierr = RegisterSwarmField(swarm,"DiffusivityGradient", 3,PETSC_REAL); CHKERRQ(ierr);
    LOG_ALLOW(LOCAL,LOG_DEBUG,"Registered field 'DiffusivityGradient' - Vector.\n");
 
    ierr = RegisterSwarmField(swarm,"Psi", 1,PETSC_REAL); CHKERRQ(ierr);
    LOG_ALLOW(LOCAL,LOG_DEBUG,"Registered field 'Psi' - Scalar.\n");
 
    ierr =  RegisterSwarmField(swarm,"DMSwarm_location_status",1,PETSC_INT);CHKERRQ(ierr);
    LOG_ALLOW(LOCAL,LOG_DEBUG,"Registered field 'DMSwarm_location_status' - Status of Location of Particle(located,lost etc).\n");
    
    // Finalize the field registration after all fields have been added
    ierr = DMSwarmFinalizeFieldRegister(swarm); CHKERRQ(ierr);
    LOG_ALLOW(LOCAL,LOG_INFO,"RegisterParticleFields - Finalized field registration.\n");
    
    PetscFunctionReturn(0);
}

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AssignInitialPropertiesToSwarm()

PetscErrorCode AssignInitialPropertiesToSwarm	(	UserCtx *	user,
		PetscInt	particlesPerProcess,
		PetscRandom *	rand_phys_x,
		PetscRandom *	rand_phys_y,
		PetscRandom *	rand_phys_z,
		PetscRandom *	rand_logic_i,
		PetscRandom *	rand_logic_j,
		PetscRandom *	rand_logic_k,
		BoundingBox *	bboxlist
	)

Initializes all particle properties in the swarm.

This function orchestrates the initialization of particle properties. It first determines the inlet face if surface initialization (Mode 0) is selected by parsing "bcs.dat". Then, it initializes basic particle properties (physical position, Particle ID, and placeholder Cell IDs) by calling InitializeParticleBasicProperties. This call uses the provided rand_logic_i/j/k RNGs, which must be pre-initialized for [0,1). The rand_phys_x/y/z RNGs (physically bounded) are passed but may not be used by InitializeParticleBasicProperties for position setting if all initialization paths use logical-to-physical mapping. Finally, it calls helper functions to initialize other registered swarm fields like "velocity", "weight", and "P" (pressure) to default values.

Parameters

[in,out]	user	Pointer to the UserCtx structure.
[in]	particlesPerProcess	Number of particles assigned to this MPI process.
[in]	rand_phys_x	RNG for physical x-coordinates (from InitializeRandomGenerators).
[in]	rand_phys_y	RNG for physical y-coordinates (from InitializeRandomGenerators).
[in]	rand_phys_z	RNG for physical z-coordinates (from InitializeRandomGenerators).
[in]	rand_logic_i	RNG for i-logical dimension tasks [0,1) (from InitializeLogicalSpaceRNGs).
[in]	rand_logic_j	RNG for j-logical dimension tasks [0,1) (from InitializeLogicalSpaceRNGs).
[in]	rand_logic_k	RNG for k-logical dimension tasks [0,1) (from InitializeLogicalSpaceRNGs).
[in]	bboxlist	Array of BoundingBox structures (potentially unused by IPBP).

Returns

PetscErrorCode Returns 0 on success, non-zero on failure.

Initializes all particle properties in the swarm.

Local to this translation unit.

Definition at line 503 of file ParticleSwarm.c.

{
    PetscErrorCode ierr;
    PetscFunctionBeginUser;
 
    PROFILE_FUNCTION_BEGIN;
 
    SimCtx *simCtx = user->simCtx;
    
    // --- 0. Input Validation ---
    if (!user || !bboxlist || !rand_logic_i || !rand_logic_j || !rand_logic_k || !rand_phys_x || !rand_phys_y || !rand_phys_z) {
        // Check all RNGs now as they are passed in
        LOG_ALLOW(GLOBAL, LOG_ERROR, "Null user, bboxlist, or RNG pointer.\n");
        SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_NULL, "Null input detected.");
    }
 
    LOG_ALLOW(GLOBAL, LOG_INFO, "Initializing swarm with %d particles per process. Mode: %s.\n",
            particlesPerProcess, ParticleInitializationToString(simCtx->ParticleInitialization));
 
    // --- 1. Parse BCS File for Inlet Information (if surface initialization) ---
    if (simCtx->ParticleInitialization == PARTICLE_INIT_SURFACE_RANDOM ||
        simCtx->ParticleInitialization == PARTICLE_INIT_SURFACE_EDGES) { // Surface initialization
    if(user->inletFaceDefined == PETSC_FALSE){
    LOG_ALLOW(GLOBAL, LOG_ERROR, "Particle Initialization on inlet surface selected, but no INLET face was identified from bcs.dat. Cannot proceed.\n");
        SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONGSTATE, "ParticleInitialization Mode 0 requires an INLET face to be defined in bcs.dat.");
    }else{
    LOG_ALLOW(GLOBAL, LOG_INFO, "After Parsing BCS file for Inlet, Inlet face = %s\n", BCFaceToString((BCFace)user->identifiedInletBCFace));
    }
    }
 
    // --- 2. Initialize Basic Particle Properties (Position, PID, Cell IDs placeholder) ---
    // The rand_logic_i/j/k are now passed directly.
    // The rand_phys_x/y/z are passed but InitializeParticleBasicProperties (refactored version)
    // will not use them for setting positions if all its paths use logical-to-physical mapping.
    LOG_ALLOW(GLOBAL, LOG_DEBUG, "Calling InitializeParticleBasicProperties.\n");
    ierr = InitializeParticleBasicProperties(user, particlesPerProcess,
                                            rand_logic_i, rand_logic_j, rand_logic_k,
                                            bboxlist); // bboxlist passed along
    CHKERRQ(ierr);
    LOG_ALLOW(GLOBAL, LOG_INFO, "Successfully initialized basic particle properties.\n");
 
    // Note: The logical RNGs (rand_logic_i/j/k) are NOT destroyed here.
    // They were created externally (e.g., by InitializeLogicalSpaceRNGs) and
    // should be destroyed externally (e.g., in FinalizeSwarmSetup).
    // Same for rand_phys_x/y/z.
 
    // --- 3. Initialize Other Swarm Fields (Velocity, Weight, Pressure, etc.) ---
    LOG_ALLOW(GLOBAL, LOG_DEBUG, "Initializing 'velocity' field.\n");
    ierr = AssignInitialFieldToSwarm(user, "velocity", 3); CHKERRQ(ierr);
    LOG_ALLOW(LOCAL, LOG_INFO, "'velocity' field initialization complete.\n");
 
    LOG_ALLOW(GLOBAL, LOG_DEBUG, "Initializing 'weight' field.\n");
    ierr = AssignInitialFieldToSwarm(user, "weight", 3); CHKERRQ(ierr); // Assuming weight is vec3
    LOG_ALLOW(LOCAL, LOG_INFO, "'weight' field initialization complete.\n");
 
    LOG_ALLOW(GLOBAL, LOG_DEBUG, "Initializing 'Diffusivity' field.\n");
    ierr = AssignInitialFieldToSwarm(user, "Diffusivity", 1); CHKERRQ(ierr);
    LOG_ALLOW(GLOBAL, LOG_INFO, "'Diffusivity' field initialization complete.\n");
 
    LOG_ALLOW(GLOBAL, LOG_DEBUG, "Initializing 'DiffusivityGradient' field.\n");
    ierr = AssignInitialFieldToSwarm(user, "DiffusivityGradient", 3); CHKERRQ(ierr);
    LOG_ALLOW(GLOBAL, LOG_INFO, "'DiffusivityGradient' field initialization complete.\n");
 
    LOG_ALLOW(GLOBAL, LOG_DEBUG, "Initializing 'Psi' (Scalar) field.\n");
    ierr = AssignInitialFieldToSwarm(user, "Psi", 1); CHKERRQ(ierr);
    LOG_ALLOW(GLOBAL, LOG_INFO, "'P' field initialization complete.\n");
    
    LOG_ALLOW(GLOBAL, LOG_INFO, "Successfully completed all swarm property initialization.\n");
 
 
    PROFILE_FUNCTION_END;
 
    PetscFunctionReturn(0);
}

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DistributeParticles()

PetscErrorCode DistributeParticles	(	PetscInt	numParticles,
		PetscMPIInt	rank,
		PetscMPIInt	size,
		PetscInt *	particlesPerProcess,
		PetscInt *	remainder
	)

Distributes particles evenly across MPI processes, handling any remainders.

This function calculates the number of particles each MPI process should handle, distributing the remainder particles to the first few ranks if necessary.

Parameters

[in]	numParticles	Total number of particles to create across all MPI processes.
[in]	rank	MPI rank of the current process.
[in]	size	Total number of MPI processes.
[out]	particlesPerProcess	Number of particles assigned to the current MPI process.
[out]	remainder	Remainder particles when dividing numParticles by size.

Returns

PetscErrorCode Returns 0 on success, non-zero on failure.

Distributes particles evenly across MPI processes, handling any remainders.

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

See also

DistributeParticles()

Definition at line 595 of file ParticleSwarm.c.

                                                                                                                                                  {
 
    PetscFunctionBeginUser;
 
    PROFILE_FUNCTION_BEGIN;
    // Calculate the base number of particles per process
    *particlesPerProcess = numParticles / size;
    *remainder = numParticles % size;
 
    // Distribute the remainder particles to the first 'remainder' ranks
    if (rank < *remainder) {
        *particlesPerProcess += 1;
        LOG_ALLOW_SYNC(GLOBAL,LOG_INFO,"Rank %d receives an extra particle. Total: %d\n", rank, *particlesPerProcess);
    } else {
        LOG_ALLOW_SYNC(GLOBAL,LOG_INFO, "Rank %d receives %d particles.\n", rank, *particlesPerProcess);
    }
 
    PROFILE_FUNCTION_END;
    PetscFunctionReturn(0);
}

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FinalizeSwarmSetup()

PetscErrorCode FinalizeSwarmSetup	(	PetscRandom *	randx,
		PetscRandom *	randy,
		PetscRandom *	randz,
		PetscRandom *	rand_logic_i,
		PetscRandom *	rand_logic_j,
		PetscRandom *	rand_logic_k
	)

Finalizes the swarm setup by destroying random generators and logging completion.

This function cleans up resources by destroying random number generators and LOG_ALLOWs the completion of swarm setup.

Parameters

[in]	randx	Random number generator for the x-coordinate.
[in]	randy	Random number generator for the y-coordinate.
[in]	randz	Random number generator for the z-coordinate.
[in]	rand_logic_i	Random number generator for the xi-coordinate.
[in]	rand_logic_j	Random number generator for the eta-coordinate.
[in]	rand_logic_k	Random number generator for the zeta-coordinate.

Returns

PetscErrorCode Returns 0 on success, non-zero on failure.

Finalizes the swarm setup by destroying random generators and logging completion.

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

See also

FinalizeSwarmSetup()

Definition at line 625 of file ParticleSwarm.c.

                                                                                                                                                                               {
    PetscErrorCode ierr;  // Error code for PETSc functions
    PetscFunctionBeginUser;
    PROFILE_FUNCTION_BEGIN;
    // Destroy random number generators to free resources
    // Physical space
    ierr = PetscRandomDestroy(randx); CHKERRQ(ierr);
    ierr = PetscRandomDestroy(randy); CHKERRQ(ierr);
    ierr = PetscRandomDestroy(randz); CHKERRQ(ierr);
    // Logical space
    ierr = PetscRandomDestroy(rand_logic_i); CHKERRQ(ierr);
    ierr = PetscRandomDestroy(rand_logic_j); CHKERRQ(ierr);
    ierr = PetscRandomDestroy(rand_logic_k); CHKERRQ(ierr);      
    
    LOG_ALLOW(LOCAL,LOG_DEBUG,"Destroyed all random number generators.\n");
 
    PROFILE_FUNCTION_END;
    PetscFunctionReturn(0);
}

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UnpackSwarmFields()

PetscErrorCode UnpackSwarmFields	(	PetscInt	i,
		const PetscInt64 *	PIDs,
		const PetscReal *	weights,
		const PetscReal *	positions,
		const PetscInt *	cellIndices,
		PetscReal *	velocities,
		PetscInt *	LocStatus,
		PetscReal *	diffusivity,
		Cmpnts *	diffusivitygradient,
		PetscReal *	psi,
		Particle *	particle
	)

Initializes a Particle struct with data from DMSwarm fields.

This helper function populates a Particle structure using data retrieved from DMSwarm fields.

Parameters

[in]	i	Index of the particle in the DMSwarm.
[in]	PIDs	Pointer to the array of particle IDs.
[in]	weights	Pointer to the array of particle weights.
[in]	positions	Pointer to the array of particle positions.
[in]	cellIndices	Pointer to the array of particle cell indices.
[in]	velocities	Pointer to the array of particle velocities.
[in]	LocStatus	Pointer to the array of cell location status indicators.
[in]	diffusivity	Pointer to the array of particle diffusivities.
[in]	diffusivitygradient	Pointer to the array of particle diffusivity gradients.
[in]	psi	Pointer to the array of particle psi values.
[out]	particle	Pointer to the Particle struct to initialize.

Returns

PetscErrorCode Returns 0 on success, non-zero on failure.

Initializes a Particle struct with data from DMSwarm fields.

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

See also

UnpackSwarmFields()

Definition at line 722 of file ParticleSwarm.c.

                                                                                                                                                   {
    PetscFunctionBeginUser;
 
    PROFILE_FUNCTION_BEGIN;
 
    PetscMPIInt rank;
    PetscErrorCode ierr;
 
    ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank); CHKERRQ(ierr);
    
    if (particle == NULL) {
        SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_NULL, "Output Particle pointer is NULL. \n");
    }
    
    // logging the start of particle initialization
    LOG_ALLOW(LOCAL,LOG_DEBUG, "[Rank %d]Unpacking Particle [%d] with PID: %ld.\n",rank, i, PIDs[i]);
    
    // Initialize PID
    if(PIDs == NULL){
        SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_NULL, "Input PIDs pointer is NULL.\n");
    }
    particle->PID = PIDs[i];
    LOG_ALLOW(LOCAL,LOG_VERBOSE, "[Rank %d]Particle [%d] PID set to: %ld.\n", rank,i, particle->PID);
    
    // Initialize weights
    if(weights == NULL){
        particle->weights.x = 1.0;
        particle->weights.y = 1.0;
        particle->weights.z = 1.0;
        LOG_ALLOW(LOCAL,LOG_WARNING, "[Rank %d]Particle [%d] weights pointer is NULL. Defaulting weights to (1.0, 1.0, 1.0).\n", rank,i);
    }else{
    particle->weights.x = weights[3 * i];
    particle->weights.y = weights[3 * i + 1];
    particle->weights.z = weights[3 * i + 2];
    LOG_ALLOW(LOCAL,LOG_VERBOSE, "[Rank %d]Particle [%d] weights set to: (%.6f, %.6f, %.6f).\n", 
        rank,i, particle->weights.x, particle->weights.y, particle->weights.z);
    }
    // Initialize locations
    if(positions == NULL){
        SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_NULL, "Input positions pointer is NULL.\n");
    }
    particle->loc.x = positions[3 * i];
    particle->loc.y = positions[3 * i + 1];
    particle->loc.z = positions[3 * i + 2];
    LOG_ALLOW(LOCAL,LOG_VERBOSE, "[Rank %d]Particle [%d] location set to: (%.6f, %.6f, %.6f).\n", 
        rank,i, particle->loc.x, particle->loc.y, particle->loc.z);
    
    // Initialize velocities (assuming default zero; modify if necessary)
    if(velocities == NULL){
        particle->vel.x = 0.0;
        particle->vel.y = 0.0;
        particle->vel.z = 0.0;
        LOG_ALLOW(LOCAL,LOG_WARNING, "[Rank %d]Particle [%d] velocities pointer is NULL. Defaulting velocities to (0.0, 0.0, 0.0).\n", rank,i);
    }else{
    particle->vel.x = velocities[3 * i];
    particle->vel.y = velocities[3 * i + 1];
    particle->vel.z = velocities[3 * i + 2];
    LOG_ALLOW(LOCAL,LOG_VERBOSE,"[Rank %d]Particle [%d] velocities unpacked to: [%.6f,%.6f,%.6f].\n",rank, i,particle->vel.x,particle->vel.y,particle->vel.z);
    }
    
    // Initialize diffusivity
    if(diffusivity == NULL){
        particle->diffusivity = 1.0; // Default diffusivity
    }else{
        particle->diffusivity = diffusivity[i];
    }
    LOG_ALLOW(LOCAL,LOG_VERBOSE,"[Rank %d]Particle [%d] diffusivity set to: %.6f.\n",rank,i, particle->diffusivity);
    
    // Initialize diffusivity gradient
    if(diffusivitygradient == NULL){
        particle->diffusivitygradient.x = 0.0;
        particle->diffusivitygradient.y = 0.0;
        particle->diffusivitygradient.z = 0.0;
        LOG_ALLOW(LOCAL,LOG_WARNING, "[Rank %d]Particle [%d] diffusivity gradient pointer is NULL. Defaulting to (0.0, 0.0, 0.0).\n", rank,i);
    }else{
        particle->diffusivitygradient.x = diffusivitygradient[i].x;
        particle->diffusivitygradient.y = diffusivitygradient[i].y;
        particle->diffusivitygradient.z = diffusivitygradient[i].z;
    }
    LOG_ALLOW(LOCAL,LOG_VERBOSE,"[Rank %d]Particle [%d] diffusivity gradient set to: (%.6f, %.6f, %.6f).\n", rank,i,particle->diffusivitygradient.x,particle->diffusivitygradient.y,particle->diffusivitygradient.z);
 
    // Initialize psi
    if(psi == NULL){
        particle->psi = 0.0; // Default psi
    }else{
    particle->psi = psi[i];
    }        
    LOG_ALLOW(LOCAL,LOG_VERBOSE,"[Rank %d]Particle [%d] psi set to: %.6f.\n",rank,i, particle->psi);
    
    // Initialize cell indices
    if(cellIndices == NULL){
        SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_NULL, "Input cellIndices pointer is NULL.\n");
    }
    particle->cell[0] = cellIndices[3 * i];
    particle->cell[1] = cellIndices[3 * i + 1];
    particle->cell[2] = cellIndices[3 * i + 2];
    LOG_ALLOW(LOCAL,LOG_VERBOSE,"[Rank %d]Particle [%d] cell indices set to: [%d, %d, %d].\n",rank,i, particle->cell[0], particle->cell[1], particle->cell[2]);
 
    if(LocStatus == NULL){
        SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_NULL, "Input LocStatus pointer is NULL.\n");
    }
    // Initialize location status
    particle->location_status = (ParticleLocationStatus)LocStatus[i];
    LOG_ALLOW(LOCAL,LOG_VERBOSE, "[Rank %d]Particle [%d] Status set to: %d.\n",rank, i, particle->location_status);
 
    // The destination_rank is only set by the location search, not read from the swarm,
    // so we initialize it to a known invalid state.
    particle->destination_rank = MPI_PROC_NULL;
    
    // logging the completion of particle initialization
    LOG_ALLOW(LOCAL,LOG_DEBUG,"[Rank %d]Completed initialization of Particle [%d]. \n", rank,i);
    
 
    PROFILE_FUNCTION_END;
 
    PetscFunctionReturn(0);
}

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UpdateSwarmFields()

PetscErrorCode UpdateSwarmFields	(	PetscInt	i,
		const Particle *	particle,
		PetscReal *	positions,
		PetscReal *	velocities,
		PetscReal *	weights,
		PetscInt *	cellIndices,
		PetscInt *	status,
		PetscReal *	diffusivity,
		Cmpnts *	diffusivitygradient,
		PetscReal *	psi
	)

Updates DMSwarm data arrays from a Particle struct.

This function writes data from the Particle struct back into the raw DMSwarm arrays. It is robust: if any array pointer is NULL, that specific field is skipped. This allows selective updating (e.g., update position but not velocity).

Parameters

[in]	i	Index of the particle in the local swarm arrays.
[in]	particle	Pointer to the Particle struct containing updated data.
[in,out]	positions	(Optional) Array of particle positions (size 3*n).
[in,out]	velocities	(Optional) Array of particle velocities (size 3*n).
[in,out]	weights	(Optional) Array of particle weights (size 3*n).
[in,out]	cellIndices	(Optional) Array of particle cell indices (size 3*n).
[in,out]	status	(Optional) Array of location status (size 1*n).
[in,out]	diffusivity	(Optional) Array of diffusivity values (size 1*n).
[in,out]	diffusivitygradient	(Optional) Array of diffusivity gradient values (size 3*n).
[in,out]	psi	(Optional) Array of scalar Psi values (size 1*n).

Returns

PetscErrorCode Returns 0 on success.

Updates DMSwarm data arrays from a Particle struct.

Local to this translation unit.

Definition at line 848 of file ParticleSwarm.c.

{
    PetscFunctionBeginUser;
    PROFILE_FUNCTION_BEGIN;
    
    if (!particle) {
        SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_NULL, "Input Particle pointer is NULL.\n");
    }
    
    // --- 1. Position (x, y, z) ---
    if (positions) {
        positions[3 * i + 0] = particle->loc.x;
        positions[3 * i + 1] = particle->loc.y;
        positions[3 * i + 2] = particle->loc.z;
    }
 
    // --- 2. Velocity (u, v, w) ---
    if (velocities) {
        velocities[3 * i + 0] = particle->vel.x;
        velocities[3 * i + 1] = particle->vel.y;
        velocities[3 * i + 2] = particle->vel.z;
    }
 
    // --- 3. Weights (i, j, k) ---
    if (weights) {
        weights[3 * i + 0] = particle->weights.x;
        weights[3 * i + 1] = particle->weights.y;
        weights[3 * i + 2] = particle->weights.z;
    }
    
    // --- 4. Cell Indices (i, j, k) ---
    if (cellIndices) {
        cellIndices[3 * i + 0] = particle->cell[0];
        cellIndices[3 * i + 1] = particle->cell[1];
        cellIndices[3 * i + 2] = particle->cell[2];
    }
 
    // --- 5. Status ---
    if (status) {
        status[i] = (PetscInt)particle->location_status;
    }
 
    // --- 6. Diffusivity ---
    if (diffusivity) {
        diffusivity[i] = particle->diffusivity;
    }
 
    if(diffusivitygradient){
        diffusivitygradient[i].x = particle->diffusivitygradient.x;
        diffusivitygradient[i].y = particle->diffusivitygradient.y;
        diffusivitygradient[i].z = particle->diffusivitygradient.z;
    }
    // --- 7. Psi ---
    if (psi) {
        psi[i] = particle->psi;
    }
 
    // LOG_LOOP_ALLOW(LOCAL, LOG_VERBOSE, i, 1000, "Updated fields for Particle [%d].\n", i);
 
    PROFILE_FUNCTION_END;
    PetscFunctionReturn(0);
}

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IsParticleInsideBoundingBox()

PetscBool IsParticleInsideBoundingBox	(	const BoundingBox *	bbox,
		const Particle *	particle
	)

Checks if a particle's location is within a specified bounding box.

This function determines whether the given particle's location lies inside the provided bounding box. It performs an axis-aligned bounding box (AABB) check by comparing the particle's coordinates to the minimum and maximum coordinates of the bounding box in each dimension (x, y, z).

Logging statements are included to provide detailed information about the function's execution.

Parameters

[in]	bbox	Pointer to the BoundingBox structure containing minimum and maximum coordinates.
[in]	particle	Pointer to the Particle structure containing the particle's location and identifier.

Returns

PetscBool Returns PETSC_TRUE if the particle is inside the bounding box, PETSC_FALSE otherwise.

Note

• The function assumes that the bbox and particle pointers are valid and non-NULL.
• The function includes logging statements that start with the function name.
• Be cautious when logging in performance-critical code sections, especially if the function is called frequently.

Checks if a particle's location is within a specified bounding box.

Local to this translation unit.

Definition at line 925 of file ParticleSwarm.c.

{
    PetscFunctionBeginUser;
    PROFILE_FUNCTION_BEGIN;
 
    // Validate input pointers
    if (!bbox) {
        // LOG_ALLOW error message and return PETSC_FALSE
    LOG_ALLOW(LOCAL,LOG_ERROR, "Error - 'bbox' pointer is NULL.");
        PROFILE_FUNCTION_END;
        return PETSC_FALSE;
    }
    if (!particle) {
    LOG_ALLOW(LOCAL,LOG_ERROR,"Error - 'particle' pointer is NULL.");
        PROFILE_FUNCTION_END;
        return PETSC_FALSE;
    }
 
    // Extract particle location and bounding box coordinates
    const Cmpnts loc = particle->loc;
    const Cmpnts min_coords = bbox->min_coords;
    const Cmpnts max_coords = bbox->max_coords;
 
    // LOG_ALLOW the particle location and bounding box coordinates for debugging
    LOG_ALLOW_SYNC(LOCAL, LOG_VERBOSE, "Particle PID %ld location: (%.6f, %.6f, %.6f).\n",particle->PID, loc.x, loc.y, loc.z);
    LOG_ALLOW_SYNC(LOCAL, LOG_VERBOSE, "BoundingBox min_coords: (%.6f, %.6f, %.6f), max_coords: (%.6f, %.6f, %.6f).\n", 
    min_coords.x, min_coords.y, min_coords.z, max_coords.x, max_coords.y, max_coords.z);
 
    // Check if the particle's location is within the bounding box
    if ((loc.x >= min_coords.x && loc.x <= max_coords.x) &&
        (loc.y >= min_coords.y && loc.y <= max_coords.y) &&
        (loc.z >= min_coords.z && loc.z <= max_coords.z)) {
        // Particle is inside the bounding box
        LOG_ALLOW_SYNC(LOCAL,LOG_VERBOSE, "Particle PID %ld is inside the bounding box.\n",particle->PID);
        PROFILE_FUNCTION_END;
        return PETSC_TRUE;
    }
 
    // Particle is outside the bounding box
    LOG_ALLOW_SYNC(LOCAL, LOG_VERBOSE,"Particle PID %ld is outside the bounding box.\n",particle->PID);
    PROFILE_FUNCTION_END;
    return PETSC_FALSE;
}

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UpdateParticleWeights()

PetscErrorCode UpdateParticleWeights	(	PetscReal *	d,
		Particle *	particle
	)

Updates a particle's interpolation weights based on distances to cell faces.

This function computes interpolation weights using distances to the six cell faces (d) and updates the weight field of the provided particle.

Parameters

[in]	d	Pointer to an array of distances to the six cell faces.
[out]	particle	Pointer to the Particle structure whose weights are to be updated.

Returns

PetscErrorCode Returns 0 on success, or a non-zero error code on failure.

Updates a particle's interpolation weights based on distances to cell faces.

Local to this translation unit.

Definition at line 976 of file ParticleSwarm.c.

                                                                       {
 
    PetscFunctionBeginUser;
    PROFILE_FUNCTION_BEGIN;
 
    // Validate input pointers
    if (!d || !particle) {
        SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_NULL,
                "Null pointer argument (d or particle).");
    }
 
 
    // Validate distances
    for (PetscInt i = LEFT; i < NUM_FACES; i++) {
        if (d[i] <= INTERPOLATION_DISTANCE_TOLERANCE) {
            LOG_ALLOW(LOCAL, LOG_WARNING,
                "face distance d[%d] = %f <= %f; "
                "clamping to 1e-14 to avoid zero/negative.\n",
                i, (double)d[i], INTERPOLATION_DISTANCE_TOLERANCE);
            d[i] = INTERPOLATION_DISTANCE_TOLERANCE;
        }
    }
 
    // LOG_ALLOW the input distances
    LOG_ALLOW(LOCAL, LOG_VERBOSE,
        "Calculating weights with distances: "
        "[LEFT=%f, RIGHT=%f, BOTTOM=%f, TOP=%f, FRONT=%f, BACK=%f].\n",
        d[LEFT], d[RIGHT], d[BOTTOM], d[TOP], d[FRONT], d[BACK]);
 
    // Compute and update the particle's weights
    particle->weights.x = d[LEFT] / (d[LEFT] + d[RIGHT]);
    particle->weights.y = d[BOTTOM] / (d[BOTTOM] + d[TOP]);
    particle->weights.z = d[BACK] / (d[FRONT] + d[BACK]);
 
    // LOG_ALLOW the updated weights
    LOG_ALLOW(LOCAL,LOG_VERBOSE,
        "Updated particle weights: x=%f, y=%f, z=%f.\n",
        particle->weights.x, particle->weights.y, particle->weights.z);
 
 
    PROFILE_FUNCTION_END;
    PetscFunctionReturn(0);
}

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InitializeParticleSwarm()

PetscErrorCode InitializeParticleSwarm

(

SimCtx *

simCtx

)

High-level particle initialization orchestrator for a simulation run.

This routine drives end-to-end swarm setup from the top-level simulation context: creation/registration of particle fields, initial placement according to configured mode, initial localization on the Eulerian grid, and startup interpolation needed before entering the main run loop.

Parameters

[in,out]

simCtx

Master simulation context containing all blocks and run settings.

Returns

PetscErrorCode Returns 0 on success, non-zero on failure.

High-level particle initialization orchestrator for a simulation run.

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

See also

InitializeParticleSwarm()

Definition at line 1049 of file ParticleSwarm.c.

{
    PetscErrorCode ierr;
    PetscInt       particlesPerProcess = 0;
    UserCtx       *user = simCtx->usermg.mgctx[simCtx->usermg.mglevels - 1].user;
 
    PetscFunctionBeginUser;
    PROFILE_FUNCTION_BEGIN;
 
    LOG_ALLOW(GLOBAL, LOG_INFO, "Starting particle swarm setup for %d particles.\n", simCtx->np);
 
    // --- Phase 1: Create the DMSwarm Object (Always required) ---
    // This creates the container and registers the fields. It does not add particles yet.
    ierr = CreateParticleSwarm(user, simCtx->np, &particlesPerProcess, simCtx->bboxlist); CHKERRQ(ierr);
    LOG_ALLOW(GLOBAL, LOG_INFO, "DMSwarm object and fields created successfully.\n");
 
 
    // --- Phase 2: Decide whether to Initialize new particles or Load existing ones ---
    PetscBool should_initialize_new_particles = PETSC_FALSE;
    if(simCtx->exec_mode == EXEC_MODE_POSTPROCESSOR){
        should_initialize_new_particles = PETSC_TRUE;
    }else{
        if (simCtx->StartStep == 0) {
            should_initialize_new_particles = PETSC_TRUE; // Standard fresh start
        } else {
        // It's a restart, so check the user's requested particle mode.
            if (strcmp(simCtx->particleRestartMode, "init") == 0) {
                should_initialize_new_particles = PETSC_TRUE; // User wants to re-initialize particles in a restarted flow.
            }
        }
    }
 
    // --- Phase 3: Execute the chosen particle setup path ---
    if (should_initialize_new_particles) {
        // --- PATH A: Generate a fresh population of particles ---
        LOG_ALLOW(GLOBAL, LOG_INFO, "Mode: INITIALIZE. Generating new particle population.\n");
        PetscRandom randx, randy, randz;
        PetscRandom rand_logic_i, rand_logic_j, rand_logic_k;
 
        ierr = InitializeRandomGenerators(user, &randx, &randy, &randz); CHKERRQ(ierr);
        ierr = InitializeLogicalSpaceRNGs(&rand_logic_i, &rand_logic_j, &rand_logic_k); CHKERRQ(ierr);
        ierr = AssignInitialPropertiesToSwarm(user, particlesPerProcess, &randx, &randy, &randz, &rand_logic_i, &rand_logic_j, &rand_logic_k, simCtx->bboxlist); CHKERRQ(ierr);
        ierr = FinalizeSwarmSetup(&randx, &randy, &randz, &rand_logic_i, &rand_logic_j, &rand_logic_k); CHKERRQ(ierr);
 
    } else {
        // --- PATH B: Load particle population from restart files ---
        // This path is only taken if simCtx->StartStep > 0 AND simCtx->particleRestartMode == "load"
        LOG_ALLOW(GLOBAL, LOG_INFO, "Mode: LOAD. Loading particle population from files for step %d.\n", simCtx->StartStep);
 
        ierr = PreCheckAndResizeSwarm(user, simCtx->StartStep, "dat"); CHKERRQ(ierr);
 
        ierr = ReadAllSwarmFields(user, simCtx->StartStep); CHKERRQ(ierr);
        // Note: We check for file-open errors inside ReadAllSwarmFields now.
 
        LOG_ALLOW(GLOBAL, LOG_INFO, "Particle data loaded. CellID and status are preserved from file.\n");
    }
 
    LOG_ALLOW_SYNC(GLOBAL, LOG_INFO, "Particle swarm setup complete.\n");
 
    PROFILE_FUNCTION_END;
    PetscFunctionReturn(0);
}

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