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particle.cpp
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#include <cmath>
#include <math.h>
#include <vector>
#include <string>
#include <algorithm>
#include "dat.hpp"
#include "particle.hpp"
#include "maths.hpp"
/////////////
// CLASSES //
/////////////
/************
* PARTICLE *
************/
// CONSTRUCTORS
Particle::Particle(double d) :
r{0, 0}, theta(0), v{0, 0}, sigma(d), f{0, 0}, gamma (0) {}
Particle::Particle(double x, double y, double ang, double d) :
r{x, y}, theta(ang), v{0, 0}, sigma(d), f{0, 0}, gamma (0) {}
// METHODS
double* Particle::position() { return &r[0]; } // returns pointer to position
double* Particle::orientation() { return θ } // returns pointer to orientation
double* Particle::velocity() { return &v[0]; } // returns pointer to velocity
double Particle::diameter() const { return sigma; } // returns pointer to diameter
double* Particle::force() { return &f[0]; }; // returns pointer to force
double* Particle::torque() { return γ } // returns pointer to aligning torque
/*************
* CELL LIST *
*************/
// CONSTRUCTORS
CellList::CellList() {}
// DESTRUCTORS
CellList::~CellList() {}
// METHODS
int CellList::getNumberBoxes() { return numberBoxes; } // return number of boxes in each dimension
std::vector<int>* CellList::getCell(int const &index) {
return &cellList[index]; } // return pointer to vector of indexes in cell
int CellList::index(Particle *particle) {
// Index of the box corresponding to a given particle.
int x = (int) ((particle->position())[0]/sizeBox);
int y = (int) ((particle->position())[1]/sizeBox);
return (x == numberBoxes ? 0 : x) + numberBoxes*(y == numberBoxes ? 0 : y);
}
std::vector<int> CellList::getNeighbours(Particle *particle) {
// Returns vector of indexes of neighbouring particles.
std::vector<int> neighbours; // vector of neighbouring particles
int indexParticle = index(particle);
int x = indexParticle%numberBoxes;
int y = indexParticle/numberBoxes;
int neighbourIndex;
for (int dx=dmin; dx < 2; dx++) {
for (int dy=dmin; dy < 2; dy++) {
neighbourIndex =
(numberBoxes + (x + dx))%numberBoxes
+ numberBoxes*((numberBoxes + (y + dy))%numberBoxes); // index of neighbouring cell
neighbours.insert(
std::end(neighbours),
std::begin(cellList[neighbourIndex]),
std::end(cellList[neighbourIndex])); // add particle indexes of neighbouring cell
}
}
return neighbours;
}
/**************
* PARAMETERS *
**************/
// CONSTRUCTORS
Parameters::Parameters() :
numberParticles(0), potentialParameter(0), propulsionVelocity(0),
transDiffusivity(0), rotDiffusivity(0), persistenceLength(0),
packingFraction(0), systemSize(0), torqueParameter(0), timeStep(0) {}
Parameters::Parameters(int N, double lp, double phi, double dt, double g) :
numberParticles(N), potentialParameter(1.0), propulsionVelocity(1.0),
transDiffusivity(1.0/(3.0*lp)), rotDiffusivity(1.0/lp),
persistenceLength(lp), packingFraction(phi),
systemSize(sqrt(M_PI*N/phi)/2.0), torqueParameter(g), timeStep(dt) {}
Parameters::Parameters(
int N, double epsilon, double v0, double D, double Dr, double phi, double L,
double dt) :
numberParticles(N), potentialParameter(epsilon), propulsionVelocity(v0),
transDiffusivity(D), rotDiffusivity(Dr), persistenceLength(v0/Dr),
packingFraction(phi), systemSize(L), torqueParameter(0), timeStep(dt) {}
Parameters::Parameters(Parameters const& parameters) :
numberParticles(parameters.getNumberParticles()),
potentialParameter(parameters.getPotentialParameter()),
propulsionVelocity(parameters.getPropulsionVelocity()),
transDiffusivity(parameters.getTransDiffusivity()),
rotDiffusivity(parameters.getRotDiffusivity()),
persistenceLength(parameters.getPersistenceLength()),
packingFraction(parameters.getPackingFraction()),
systemSize(parameters.getSystemSize()),
torqueParameter(parameters.getTorqueParameter()),
timeStep(parameters.getTimeStep()) {}
Parameters::Parameters(Parameters* parameters) :
numberParticles(parameters->getNumberParticles()),
potentialParameter(parameters->getPotentialParameter()),
propulsionVelocity(parameters->getPropulsionVelocity()),
transDiffusivity(parameters->getTransDiffusivity()),
rotDiffusivity(parameters->getRotDiffusivity()),
persistenceLength(parameters->getPersistenceLength()),
packingFraction(parameters->getPackingFraction()),
systemSize(parameters->getSystemSize()),
torqueParameter(parameters->getTorqueParameter()),
timeStep(parameters->getTimeStep()) {}
// METHODS
int Parameters::getNumberParticles() const { return numberParticles; }
double Parameters::getPotentialParameter() const { return potentialParameter; }
double Parameters::getPropulsionVelocity() const { return propulsionVelocity; }
double Parameters::getTransDiffusivity() const { return transDiffusivity; }
double Parameters::getRotDiffusivity() const { return rotDiffusivity; }
double Parameters::getPersistenceLength() const { return persistenceLength; }
double Parameters::getPackingFraction() const {return packingFraction; }
double Parameters::getSystemSize() const { return systemSize; }
double Parameters::getTorqueParameter() const { return torqueParameter; }
double Parameters::getTimeStep() const { return timeStep; }
/**********
* SYSTEM *
**********/
// CONSTRUCTORS
System::System() :
param(new Parameters()),
randomSeed(0), randomGenerator(),
particles(0),
cellList(),
output(""), velocitiesDumps(),
framesWork(0), dumpParticles(0), dumpPeriod(0),
torqueParameter(0),
biasingParameter(0),
dumpFrame(-1),
workSum {0, 0, 0}, workForceSum {0, 0, 0}, workOrientationSum {0, 0, 0},
orderSum {0, 0, 0}, order0Sum {0, 0, 0}, order1Sum {0, 0, 0},
torqueIntegral1 {0, 0, 0}, torqueIntegral2 {0, 0, 0}
{}
System::System(
Parameters* parameters, int seed, std::string filename,
int nWork, bool dump, int period) :
param(parameters),
randomSeed(seed), randomGenerator(randomSeed),
particles(parameters->getNumberParticles()),
cellList(),
output(filename), velocitiesDumps(parameters->getNumberParticles()),
framesWork(nWork > 0 ? nWork : (int)
parameters->getPersistenceLength()/(parameters->getTimeStep()*period)),
dumpParticles(dump), dumpPeriod(period),
torqueParameter(parameters->getTorqueParameter()),
biasingParameter(0),
dumpFrame(-1),
workSum {0, 0, 0}, workForceSum {0, 0, 0}, workOrientationSum {0, 0, 0},
orderSum {0, 0, 0}, order0Sum {0, 0, 0}, order1Sum {0, 0, 0},
torqueIntegral1 {0, 0, 0}, torqueIntegral2 {0, 0, 0}
{
// write header with system parameters to output file
output.write<int>(getNumberParticles());
output.write<double>(getPersistenceLength());
output.write<double>(getPackingFraction());
output.write<double>(getSystemSize());
output.write<double>(getTorqueParameter());
output.write<int>(randomSeed);
output.write<double>(getTimeStep());
output.write<int>(framesWork);
output.write<bool>(dumpParticles);
output.write<int>(dumpPeriod);
output.close();
// put particles on a grid with random orientation
int gridSize = ceil(sqrt(getNumberParticles())); // size of the grid on which to put the particles
double gridSpacing = getSystemSize()/gridSize;
for (int i=0; i < getNumberParticles(); i++) { // loop over particles
// position on the grid
particles[i].position()[0] = (i%gridSize)*gridSpacing;
particles[i].position()[1] = (i/gridSize)*gridSpacing;
// random orientation
particles[i].orientation()[0] = 2*M_PI*randomGenerator.random01();
}
// initialise cell list
cellList.initialise<System>(this, pow(2., 1./6.));
}
System::System(
System* system, int seed, std::string filename,
int nWork, bool dump, int period) :
param(system->getParameters()),
randomSeed(seed), randomGenerator(randomSeed),
particles(system->getNumberParticles()),
cellList(),
output(filename), velocitiesDumps(system->getNumberParticles()),
framesWork(nWork > 0 ? nWork : (int)
system->getPersistenceLength()/(system->getTimeStep()*period)),
dumpParticles(dump), dumpPeriod(period),
torqueParameter((system->getParameters())->getTorqueParameter()),
biasingParameter(0),
dumpFrame(-1),
workSum {0, 0, 0}, workForceSum {0, 0, 0}, workOrientationSum {0, 0, 0},
orderSum {0, 0, 0}, order0Sum {0, 0, 0}, order1Sum {0, 0, 0},
torqueIntegral1 {0, 0, 0}, torqueIntegral2 {0, 0, 0}
{
// write header with system parameters to output file
output.write<int>(getNumberParticles());
output.write<double>(getPersistenceLength());
output.write<double>(getPackingFraction());
output.write<double>(getSystemSize());
output.write<double>(getTorqueParameter());
output.write<int>(randomSeed);
output.write<double>(getTimeStep());
output.write<int>(framesWork);
output.write<bool>(dumpParticles);
output.write<int>(dumpPeriod);
output.close();
// initialise cell list
cellList.initialise<System>(this, pow(2., 1./6.));
// copy positions and orientations and update cell list
copyState(system);
// copy dumps
copyDump(system);
}
System::System(
std::string inputFilename, int inputFrame, double dt,
int seed, std::string filename,
int nWork, bool dump, int period) :
param(
[&]{ // necessary initialisation with a lambda function due to const attributes
Dat inputDat(inputFilename, false); // data object
Parameters param(
inputDat.getNumberParticles(),
inputDat.getPersistenceLength(),
inputDat.getPackingFraction(),
dt > 0 ? dt : inputDat.getTimeStep(),
inputDat.getTorqueParameter());
return param;
}()),
randomSeed(seed), randomGenerator(randomSeed),
particles(0),
cellList(),
output(filename), velocitiesDumps(0),
framesWork(nWork > 0 ? nWork : (int)
getPersistenceLength()/(getTimeStep()*period)),
dumpParticles(dump), dumpPeriod(period),
torqueParameter(0),
biasingParameter(0),
dumpFrame(-1),
workSum {0, 0, 0}, workForceSum {0, 0, 0}, workOrientationSum {0, 0, 0},
orderSum {0, 0, 0}, order0Sum {0, 0, 0}, order1Sum {0, 0, 0},
torqueIntegral1 {0, 0, 0}, torqueIntegral2 {0, 0, 0}
{
// load data
Dat inputDat(inputFilename, false); // data object
// set torque parameter
double g = inputDat.getTorqueParameter();
setTorqueParameter(g);
// resize vector of particles
particles.resize(getNumberParticles());
// resize velocity dumps
velocitiesDumps.resize(2*getNumberParticles()); // resize vector of locations of velocity dumps
// set positions and orientations
for (int i=0; i < getNumberParticles(); i++) {
// positions
for (int dim=0; dim < 2; dim++) {
particles[i].position()[dim] = inputDat.getPosition(inputFrame, i, dim);
}
// orientations
particles[i].orientation()[0] = inputDat.getOrientation(inputFrame, i);
}
// write header with system parameters to output file
output.write<int>(getNumberParticles());
output.write<double>(getPersistenceLength());
output.write<double>(getPackingFraction());
output.write<double>(getSystemSize());
output.write<double>(getTorqueParameter());
output.write<int>(randomSeed);
output.write<double>(getTimeStep());
output.write<int>(framesWork);
output.write<bool>(dumpParticles);
output.write<int>(dumpPeriod);
output.close();
// initialise cell list
cellList.initialise<System>(this, pow(2., 1./6.));
}
// DESTRUCTORS
System::~System() {}
// METHODS
Parameters* System::getParameters() { return ¶m; }
int System::getNumberParticles() const {
return param.getNumberParticles(); }
double System::getPersistenceLength() const {
return param.getPersistenceLength(); }
double System::getPackingFraction() const {
return param.getPackingFraction(); }
double System::getSystemSize() const {
return param.getSystemSize(); }
double System::getTimeStep() const {
return param.getTimeStep(); }
int System::getRandomSeed() const { return randomSeed; }
Random* System::getRandomGenerator() { return &randomGenerator; }
void System::setGenerator(std::default_random_engine rndeng) {
randomGenerator.setGenerator(rndeng);
}
Particle* System::getParticle(int const& index) { return &(particles[index]); }
std::vector<Particle> System::getParticles() { return particles; }
CellList* System::getCellList() { return &cellList; }
void System::flushOutputFile() { output.flush(); }
std::string System::getOutputFile() const { return output.getOutputFile(); }
void System::setTorqueParameter(double& g) { torqueParameter = g; }
double System::getTorqueParameter() { return torqueParameter; }
double System::getBiasingParameter() { return biasingParameter; }
void System::setBiasingParameter(double s) { biasingParameter = s; }
int* System::getDump() { return &dumpFrame; }
void System::resetDump() {
// Reset time-extensive quantities over trajectory.
dumpFrame = 0;
workSum[0] = 0;
workForceSum[0] = 0;
workOrientationSum[0] = 0;
orderSum[0] = 0;
order0Sum[0] = 0;
order1Sum[0] = 0;
torqueIntegral1[0] = 0;
torqueIntegral2[0] = 0;
workSum[2] = 0;
workForceSum[2] = 0;
workOrientationSum[2] = 0;
orderSum[2] = 0;
order0Sum[2] = 0;
order1Sum[2] = 0;
torqueIntegral1[2] = 0;
torqueIntegral2[2] = 0;
}
void System::copyDump(System* system) {
// Copy dumps from other system.
// WARNING: This also copies the index of last frame dumped. Consistency
// has to be checked.
dumpFrame = system->getDump()[0];
workSum[2] = system->getTotalWork()[0];
workForceSum[2] = system->getTotalWorkForce()[0];
workOrientationSum[2] = system->getTotalWorkOrientation()[0];
orderSum[2] = system->getTotalOrder()[0];
order0Sum[2] = system->getTotalOrder0()[0];
order1Sum[2] = system->getTotalOrder1()[0];
torqueIntegral1[2] = system->getTotalTorqueIntegral1()[0];
torqueIntegral2[2] = system->getTotalTorqueIntegral2()[0];
}
double System::getWork() { return workSum[1]; }
double System::getWorkForce() { return workForceSum[1]; }
double System::getWorkOrientation() { return workOrientationSum[1]; }
double System::getOrder() { return orderSum[1]; }
double System::getOrder0() { return order0Sum[1]; }
double System::getOrder1() { return order1Sum[1]; }
double System::getTorqueIntegral1() { return torqueIntegral1[1]; }
double System::getTorqueIntegral2() { return torqueIntegral2[1]; }
double* System::getTotalWork() { return &(workSum[2]); }
double* System::getTotalWorkForce() { return &(workForceSum[2]); }
double* System::getTotalWorkOrientation() { return &(workOrientationSum[2]); }
double* System::getTotalOrder() { return &(orderSum[2]); }
double* System::getTotalOrder0() { return &(order0Sum[2]); }
double* System::getTotalOrder1() { return &(order1Sum[2]); }
double* System::getTotalTorqueIntegral1() { return &(torqueIntegral1[2]); }
double* System::getTotalTorqueIntegral2() { return &(torqueIntegral2[2]); }
double System::diffPeriodic(double const& x1, double const& x2) {
// Returns algebraic distance from `x1' to `x2' on a line taking into account
// periodic boundary condition of the system.
return _diffPeriodic<System>(this, x1, x2);
}
double System::getDistance(int const& index1, int const& index2) {
// Returns distance between two particles in a given system.
return _getDistance<System>(this, index1, index2);
}
void System::WCA_force(int const& index1, int const& index2) {
// Compute WCA forces between particles[index1] and particles[index2],
// and add to particles[index1].force() and particles[index2].force().
if ( index1 != index2 ) { // only consider different particles
double force[2];
_WCA_force(this, index1, index2, &force[0]);
for (int dim=0; dim < 2; dim++) {
if ( force[dim] != 0 ) {
// update force arrays
particles[index1].force()[dim] += force[dim];
particles[index2].force()[dim] -= force[dim];
}
}
}
}
void System::copyState(std::vector<Particle>& newParticles) {
// Copy positions and orientations.
for (int i=0; i < getNumberParticles(); i++) {
for (int dim=0; dim < 2; dim++) {
// POSITIONS
particles[i].position()[dim] = newParticles[i].position()[dim];
}
// ORIENTATIONS
particles[i].orientation()[0] = newParticles[i].orientation()[0];
}
// UPDATING CELL LIST
cellList.update<System>(this);
}
void System::copyState(System* system) {
// Copy positions and orientations.
for (int i=0; i < getNumberParticles(); i++) {
for (int dim=0; dim < 2; dim++) {
// POSITIONS
particles[i].position()[dim] = (system->getParticle(i))->position()[dim];
}
// ORIENTATIONS
particles[i].orientation()[0] = (system->getParticle(i))->orientation()[0];
}
// UPDATING CELL LIST
cellList.update<System>(this);
}
void System::saveInitialState() {
// Saves initial state of particles to output file.
// output
if ( dumpParticles ) {
output.open();
for (int i=0; i < getNumberParticles(); i++) { // output all particles
// POSITIONS
for (int dim=0; dim < 2; dim++) { // output position in each dimension
output.write<double>(particles[i].position()[dim]);
}
// ORIENTATIONS
output.write<double>(particles[i].orientation()[0]); // output orientation
// VELOCITIES
velocitiesDumps[i] = output.tellp(); // location to dump velocities at next time step
for (int dim=0; dim < 2; dim++) { // output velocity in each dimension
output.write<double>(0.0); // zero by default for initial frame
}
}
output.close();
}
// reset dump
resetDump();
}
void System::saveNewState(std::vector<Particle>& newParticles) {
// Saves new state of particles to output file then copy it.
// DUMP FRAME
dumpFrame++;
////////////
// SAVING //
////////////
// OPEN FILE
if ( ( dumpParticles && dumpFrame % dumpPeriod == 0 ) ||
( dumpParticles && (dumpFrame - 1) % dumpPeriod == 0 ) ||
( dumpFrame % (framesWork*dumpPeriod) == 0 ) ) {
output.open();
}
for (int i=0; i < getNumberParticles(); i++) { // output all particles
// ACTIVE WORK and ORDER PARAMETER (computation)
for (int dim=0; dim < 2; dim++) {
// active work
workSum[0] +=
(cos(newParticles[i].orientation()[0] - dim*M_PI/2)
+ cos(particles[i].orientation()[0] - dim*M_PI/2))
*(newParticles[i].position()[dim] - particles[i].position()[dim]) // NOTE: at this stage, newParticles[i].position() are not rewrapped, so this difference is the actual displacement
/2;
// force part of the active work
workForceSum[0] +=
(cos(newParticles[i].orientation()[0] - dim*M_PI/2)
+ cos(particles[i].orientation()[0] - dim*M_PI/2))
*getTimeStep()*particles[i].force()[dim]/3/getPersistenceLength()
/2;
// orientation part of the active work
workOrientationSum[0] +=
(cos(newParticles[i].orientation()[0] - dim*M_PI/2)
+ cos(particles[i].orientation()[0] - dim*M_PI/2))
*getTimeStep()*cos(particles[i].orientation()[0] - dim*M_PI/2)
/2;
}
// WRAPPED COORDINATES
for (int dim=0; dim < 2; dim++) {
// keep particles in the box
newParticles[i].position()[dim] =
_wrapCoordinate<System>(this, newParticles[i].position()[dim]);
// output wrapped position in each dimension
if ( dumpParticles && dumpFrame % dumpPeriod == 0 ) {
output.write<double>(newParticles[i].position()[dim]);
}
}
if ( dumpParticles && (dumpFrame - 1) % dumpPeriod == 0 ) {
// VELOCITIES
for (int dim=0; dim < 2; dim++) {
output.write<double>(
particles[i].velocity()[dim],
velocitiesDumps[i] + dim*sizeof(double));
}
}
if ( dumpParticles && dumpFrame % dumpPeriod == 0 ) {
// ORIENTATION
output.write<double>(newParticles[i].orientation()[0]);
// VELOCITIES
velocitiesDumps[i] = output.tellp(); // location to dump velocities at next time step
for (int dim=0; dim < 2; dim++) {
output.write<double>(0.0); // zero by default until rewrite at next time step
}
}
}
// ORDER PARAMETER
std::vector<double> orderOld = getOrderParameter(particles);
double orderNormSqOld = pow(orderOld[0], 2) + pow(orderOld[1], 2);
std::vector<double> orderNew = getOrderParameter(newParticles);
double orderNormSqNew = pow(orderNew[0], 2) + pow(orderNew[1], 2);
orderSum[0] += (sqrt(orderNormSqOld) + sqrt(orderNormSqNew))/2;
order0Sum[0] += (orderOld[0] + orderNew[0])/2;
order1Sum[0] += (orderOld[1] + orderNew[1])/2;
// GLOBAL PHASE
double globalPhaseOld = getGlobalPhase(particles);
double globalPhaseNew = getGlobalPhase(newParticles);
// FIRST TORQUE INTEGRAL
torqueIntegral1[0] += (orderNormSqOld + orderNormSqNew)/2;
// SECOND TORQUE INTEGRAL
for (int i=0; i < getNumberParticles(); i++) {
#if 1 // method with global phase
torqueIntegral2[0] += orderNormSqOld
*pow(sin(particles[i].orientation()[0] - globalPhaseOld), 2)/2.0;
torqueIntegral2[0] += orderNormSqNew
*pow(sin(newParticles[i].orientation()[0] - globalPhaseNew), 2)/2.0;
#else // method with double sum
double sumSinOld (0.0), sumSinNew (0.0);
for (int j=0; j < getNumberParticles(); j++) {
sumSinOld += sin(
particles[i].orientation()[0] - particles[j].orientation()[0]);
sumSinNew += sin(
newParticles[i].orientation()[0] - newParticles[j].orientation()[0]);
}
torqueIntegral2[0] += (pow(sumSinOld, 2) + pow(sumSinNew, 2))
/2.0/pow(getNumberParticles(), 2);
#endif
}
// ACTIVE WORK and ORDER PARAMETER (output)
if ( dumpFrame % (framesWork*dumpPeriod) == 0 ) {
// compute normalised rates since last dump
workSum[1] = workSum[0]/(
getNumberParticles()*getTimeStep()*framesWork*dumpPeriod);
workForceSum[1] = workForceSum[0]/(
getNumberParticles()*getTimeStep()*framesWork*dumpPeriod);
workOrientationSum[1] = workOrientationSum[0]/(
getNumberParticles()*getTimeStep()*framesWork*dumpPeriod);
orderSum[1] = orderSum[0]/(
framesWork*dumpPeriod);
order0Sum[1] = order0Sum[0]/(
framesWork*dumpPeriod);
order1Sum[1] = order1Sum[0]/(
framesWork*dumpPeriod);
torqueIntegral1[1] = torqueIntegral1[0]/(
framesWork*dumpPeriod);
torqueIntegral2[1] = torqueIntegral2[0]/(
getNumberParticles()*framesWork*dumpPeriod);
// output normalised rates
output.write<double>(workSum[1]);
output.write<double>(workForceSum[1]);
output.write<double>(workOrientationSum[1]);
output.write<double>(orderSum[1]);
output.write<double>(order0Sum[1]);
output.write<double>(order1Sum[1]);
output.write<double>(torqueIntegral1[1]);
output.write<double>(torqueIntegral2[1]);
// update time extensive quantities over trajectory since last reset
workSum[2] += workSum[0]/getNumberParticles();
workForceSum[2] += workForceSum[0]/getNumberParticles();
workOrientationSum[2] += workOrientationSum[0]/getNumberParticles();
orderSum[2] += orderSum[0];
order0Sum[2] += order0Sum[0];
order1Sum[2] += order1Sum[0];
torqueIntegral1[2] += torqueIntegral1[0];
torqueIntegral2[2] += torqueIntegral2[0]/getNumberParticles();
// reset sums
workSum[0] = 0;
workForceSum[0] = 0;
workOrientationSum[0] = 0;
orderSum[0] = 0;
order0Sum[0] = 0;
order1Sum[0] = 0;
torqueIntegral1[0] = 0;
torqueIntegral2[0] = 0;
}
// CLOSE FILE
if ( output.is_open() ) { output.close(); }
/////////////
// COPYING //
/////////////
copyState(newParticles);
}
/***********
* SYSTEM0 *
***********/
// CONSTRUCTORS
System0::System0() :
param(new Parameters()),
randomSeed(0), randomGenerator(),
particles(0),
cellList(),
output(""), velocitiesDumps(),
framesWork(0), dumpParticles(0), dumpPeriod(0),
dumpFrame(-1),
workSum {0, 0, 0}, workForceSum {0, 0, 0}, workOrientationSum {0, 0, 0},
orderSum {0, 0, 0} {}
System0::System0(
Parameters* parameters, int seed, std::string filename,
int nWork, bool dump, int period) :
param(parameters),
randomSeed(seed), randomGenerator(randomSeed),
particles(0),
cellList(),
output(filename), velocitiesDumps(parameters->getNumberParticles()),
framesWork(nWork > 0 ? nWork : (int)
1/(parameters->getRotDiffusivity()*parameters->getTimeStep()*period)),
dumpParticles(dump), dumpPeriod(period),
dumpFrame(-1),
workSum {0, 0, 0}, workForceSum {0, 0, 0}, workOrientationSum {0, 0, 0},
orderSum {0, 0, 0} {
// set diameters
// CAUTION: consistence between packing fraction and system size has to be checked before
for (int i=0; i < getNumberParticles(); i++) {
particles.push_back(Particle(1.0));
}
// write header with system parameters to output file
output.write<int>(getNumberParticles());
output.write<double>(getPotentialParameter());
output.write<double>(getPropulsionVelocity());
output.write<double>(getTransDiffusivity());
output.write<double>(getRotDiffusivity());
output.write<double>(getPersistenceLength());
output.write<double>(getPackingFraction());
output.write<double>(getSystemSize());
output.write<int>(randomSeed);
output.write<double>(getTimeStep());
output.write<int>(framesWork);
output.write<bool>(dumpParticles);
output.write<int>(dumpPeriod);
// write particles' diameters
for (int i=0; i < getNumberParticles(); i++) {
output.write<double>(getParticle(i)->diameter());
}
// put particles on a grid with random orientation
int gridSize = ceil(sqrt(getNumberParticles())); // size of the grid on which to put the particles
double gridSpacing = getSystemSize()/gridSize;
for (int i=0; i < getNumberParticles(); i++) { // loop over particles
// position on the grid
particles[i].position()[0] = (i%gridSize)*gridSpacing;
particles[i].position()[1] = (i/gridSize)*gridSpacing;
// random orientation
particles[i].orientation()[0] = 2*M_PI*randomGenerator.random01();
}
// initialise cell list
double maxDiameter = 1.0; // maximum diameter
cellList.initialise<System0>(this, pow(2.0*maxDiameter, 1./6.));
}
System0::System0(
Parameters* parameters, std::vector<double>& diameters, int seed,
std::string filename, int nWork, bool dump, int period) :
param(parameters),
randomSeed(seed), randomGenerator(randomSeed),
particles(0),
cellList(),
output(filename), velocitiesDumps(parameters->getNumberParticles()),
framesWork(nWork > 0 ? nWork : (int)
1/(parameters->getRotDiffusivity()*parameters->getTimeStep()*period)),
dumpParticles(dump), dumpPeriod(period),
dumpFrame(-1),
workSum {0, 0, 0}, workForceSum {0, 0, 0}, workOrientationSum {0, 0, 0},
orderSum {0, 0, 0} {
// set diameters
// CAUTION: consistence between packing fraction and system size has to be checked before
for (int i=0; i < getNumberParticles(); i++) {
particles.push_back(Particle(diameters[i]));
}
// write header with system parameters to output file
output.write<int>(getNumberParticles());
output.write<double>(getPotentialParameter());
output.write<double>(getPropulsionVelocity());
output.write<double>(getTransDiffusivity());
output.write<double>(getRotDiffusivity());
output.write<double>(getPersistenceLength());
output.write<double>(getPackingFraction());
output.write<double>(getSystemSize());
output.write<int>(randomSeed);
output.write<double>(getTimeStep());
output.write<int>(framesWork);
output.write<bool>(dumpParticles);
output.write<int>(dumpPeriod);
// write particles' diameters
for (int i=0; i < parameters->getNumberParticles(); i++) {
output.write<double>(getParticle(i)->diameter());
}
// put particles on a grid with random orientation
int gridSize = ceil(sqrt(getNumberParticles())); // size of the grid on which to put the particles
double gridSpacing = getSystemSize()/gridSize;
for (int i=0; i < getNumberParticles(); i++) { // loop over particles
// position on the grid
particles[i].position()[0] = (i%gridSize)*gridSpacing;
particles[i].position()[1] = (i/gridSize)*gridSpacing;
// random orientation
particles[i].orientation()[0] = 2*M_PI*randomGenerator.random01();
}
// initialise cell list
double maxDiameter = *std::max_element(diameters.begin(), diameters.end()); // maximum diameter
cellList.initialise<System0>(this, pow(2.0*maxDiameter, 1./6.));
}
System0::System0(
System0* system, int seed, std::string filename,
int nWork, bool dump, int period) :
param(system->getParameters()),
randomSeed(seed), randomGenerator(randomSeed),
particles(0),
cellList(),
output(filename), velocitiesDumps(system->getNumberParticles()),
framesWork(nWork > 0 ? nWork : (int)
1/(system->getRotDiffusivity()*system->getTimeStep()*period)),
dumpParticles(dump), dumpPeriod(period),
dumpFrame(-1),
workSum {0, 0, 0}, workForceSum {0, 0, 0}, workOrientationSum {0, 0, 0},
orderSum {0, 0, 0} {
// set diameters
// CAUTION: consistence between packing fraction and system size has to be checked before
std::vector<double> diameters(0);
for (int i=0; i < getNumberParticles(); i++) {
diameters.push_back((system->getParticle(i))->diameter());
particles.push_back(Particle(diameters[i]));
}
// write header with system parameters to output file
output.write<int>(getNumberParticles());
output.write<double>(getPotentialParameter());
output.write<double>(getPropulsionVelocity());
output.write<double>(getTransDiffusivity());
output.write<double>(getRotDiffusivity());
output.write<double>(getPersistenceLength());
output.write<double>(getPackingFraction());
output.write<double>(getSystemSize());
output.write<int>(randomSeed);
output.write<double>(getTimeStep());
output.write<int>(framesWork);
output.write<bool>(dumpParticles);
output.write<int>(dumpPeriod);
// write particles' diameters
for (int i=0; i < getNumberParticles(); i++) {
output.write<double>(getParticle(i)->diameter());
}
// initialise cell list
double maxDiameter = *std::max_element(diameters.begin(), diameters.end()); // maximum diameter
cellList.initialise<System0>(this, pow(2.0*maxDiameter, 1./6.));
// copy positions and orientations and update cell list
copyState(system);
// copy dumps
copyDump(system);
}
System0::System0(
System0* system, std::vector<double>& diameters, int seed,
std::string filename, int nWork, bool dump, int period) :
param(system->getParameters()),
randomSeed(seed), randomGenerator(randomSeed),
particles(0),
cellList(),
output(filename), velocitiesDumps(system->getNumberParticles()),
framesWork(nWork > 0 ? nWork : (int)
1/(system->getRotDiffusivity()*system->getTimeStep()*period)),
dumpParticles(dump), dumpPeriod(period),
dumpFrame(-1),
workSum {0, 0, 0}, workForceSum {0, 0, 0}, workOrientationSum {0, 0, 0},
orderSum {0, 0, 0} {
// set diameters
// CAUTION: consistence between packing fraction and system size has to be checked before
for (int i=0; i < getNumberParticles(); i++) {
particles.push_back(Particle(diameters[i]));
}
// write header with system parameters to output file
output.write<int>(getNumberParticles());
output.write<double>(getPotentialParameter());
output.write<double>(getPropulsionVelocity());
output.write<double>(getTransDiffusivity());
output.write<double>(getRotDiffusivity());
output.write<double>(getPersistenceLength());
output.write<double>(getPackingFraction());
output.write<double>(getSystemSize());
output.write<int>(randomSeed);
output.write<double>(getTimeStep());
output.write<int>(framesWork);
output.write<bool>(dumpParticles);
output.write<int>(dumpPeriod);
// write particles' diameters
for (int i=0; i < getNumberParticles(); i++) {
output.write<double>(getParticle(i)->diameter());
}
// initialise cell list
double maxDiameter = *std::max_element(diameters.begin(), diameters.end()); // maximum diameter
cellList.initialise<System0>(this, pow(2.0*maxDiameter, 1./6.));
// copy positions and orientations and update cell list
copyState(system);
// copy dumps
copyDump(system);
}
System0::System0(
std::string inputFilename, int inputFrame, double dt,
int seed, std::string filename,
int nWork, bool dump, int period) :
param(
[&]{ // necessary initialisation with a lambda function due to const attributes
Dat0 inputDat(inputFilename, false); // data object
Parameters param(
inputDat.getNumberParticles(),
inputDat.getPotentialParameter(),
inputDat.getPropulsionVelocity(),
inputDat.getTransDiffusivity(),
inputDat.getRotDiffusivity(),
inputDat.getPackingFraction(),
inputDat.getSystemSize(),
dt > 0 ? dt : inputDat.getTimeStep());
return param;
}()),
randomSeed(seed), randomGenerator(randomSeed),
particles(0),
cellList(),
output(filename), velocitiesDumps(0),
framesWork(nWork > 0 ? nWork : (int)
1/(getRotDiffusivity()*getTimeStep()*period)),
dumpParticles(dump), dumpPeriod(period),
dumpFrame(-1),
workSum {0, 0, 0}, workForceSum {0, 0, 0}, workOrientationSum {0, 0, 0},
orderSum {0, 0, 0} {
// load data
Dat0 inputDat(inputFilename, false); // data object
// set diameters
// CAUTION: consistence between packing fraction and system size has to be checked before
std::vector<double> diameters = inputDat.getDiameters(); // diameters of particles
for (int i=0; i < getNumberParticles(); i++) {
particles.push_back(Particle(diameters[i]));
}
// resize velocity dumps
velocitiesDumps.resize(2*getNumberParticles()); // resize vector of locations of velocity dumps
// set positions and orientations
for (int i=0; i < getNumberParticles(); i++) {
// positions
for (int dim=0; dim < 2; dim++) {
particles[i].position()[dim] = inputDat.getPosition(inputFrame, i, dim);
}
// orientations
particles[i].orientation()[0] = inputDat.getOrientation(inputFrame, i);
}
// write header with system parameters to output file
output.write<int>(getNumberParticles());
output.write<double>(getPotentialParameter());
output.write<double>(getPropulsionVelocity());
output.write<double>(getTransDiffusivity());
output.write<double>(getRotDiffusivity());
output.write<double>(getPersistenceLength());
output.write<double>(getPackingFraction());
output.write<double>(getSystemSize());
output.write<int>(randomSeed);
output.write<double>(getTimeStep());
output.write<int>(framesWork);
output.write<bool>(dumpParticles);
output.write<int>(dumpPeriod);
// write particles' diameters
for (int i=0; i < getNumberParticles(); i++) {
output.write<double>(getParticle(i)->diameter());
}
// initialise cell list
double maxDiameter = *std::max_element(diameters.begin(), diameters.end()); // maximum diameter
cellList.initialise<System0>(this, pow(2.0*maxDiameter, 1./6.));