Atoms.h¶

Structures for single and multiple atom positions.

These objects facilitate storage and manipulation of atom positions (and possibly velocities, but not currently), and calculation of non-cartesian components of stored quantities.

struct Atom¶

#include <Atoms.h>

Simple structure to hold information about a single atom.

Public Functions

void calculateRadius()¶: Calculate cylindrical radius \(r\) from \(x\) and \(y\) coordinates.

void print()¶: Print atom type and coordinates.

Public Members

double x¶

double y¶

double z¶

double r¶

int type¶

class AtomArray¶

#include <Atoms.h>

Data structure to hold information about multiple atoms.

Can get and set coordinates from Atom. This object must be instantiated after DatafileReader so that SimData::numAtoms is already defined since this value is used to determine the size of allocated arrays.

Atom positions for all timesteps in a frame are stored, which may lead to memory issues if Options::stepsPerFrame or SimData::numAtoms are very large.

Public Functions

void allocateArrays()¶

Allocate arrays.

Four arrays are allocated: x, y, z, r; each of which are of length numAtoms * stepsPerFrame. Since the last frame may have more steps than other frames, we use stepsPerFrame = simDataPtr->lastFrame.numSteps.

AtomArray(SimData &simData)¶

Sole constructor.

Parameters

simData: SimData object whose numAtoms member is already defined.

~AtomArray()¶

void setSimData(SimData &simData)¶: Set simDataPtr and number of atoms.

void setNumAtoms(int _numAtoms)¶

void setAtom(int atomNum, int stepInFrame, Atom &atom)¶: Copy data for atom atomNum at step stepInFrame to atom.

void getAtom(int atomNum, int stepInFrame, Atom &atom)¶: Copy data for atom atomNum at step stepInFrame from atom.

void printStats()¶: Print min, max, mean, std. of each x, y, z components of positions.

Public Members

int numAtoms¶

SimData *simDataPtr¶

int *type¶

double *x¶

double *y¶

double *z¶

double *r¶

Private Functions

void deallocateArrays()¶

int getIndex(int atomNum, int stepInFrame)¶: Return index of atom position in arrays.

Private Members

bool allocated¶: Whether the position arrays have been allocated.