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dat.cpp
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dat.cpp
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#include <string>
#include <iostream>
#include <vector>
#include <algorithm>
#include "dat.hpp"
#include "maths.hpp"
/*******
* DAT *
*******/
// CONSTRUCTORS
Dat::Dat(std::string filename, bool loadWork, bool corruption) :
numberParticles(), persistenceLength(), packingFraction(), systemSize(),
torqueParameter(), randomSeed(), timeStep(), framesWork(), dumpParticles(),
dumpPeriod(),
input(filename) {
// HEADER INFORMATION
input.read<const int>(&numberParticles);
input.read<const double>(&persistenceLength);
input.read<const double>(&packingFraction);
input.read<const double>(&systemSize);
input.read<const double>(&torqueParameter);
input.read<const int>(&randomSeed);
input.read<const double>(&timeStep);
input.read<const int>(&framesWork);
input.read<const bool>(&dumpParticles);
input.read<const int>(&dumpPeriod);
// FILE PARTS LENGTHS
headerLength = input.tellg();
particleLength = 5*sizeof(double)*dumpParticles;
frameLength = numberParticles*particleLength;
workLength = 8*sizeof(double);
// ESTIMATION OF NUMBER OF COMPUTED WORK AND ORDER PARAMETER SUMS AND FRAMES
numberWork = (input.getFileSize() - headerLength - frameLength)/(
framesWork*frameLength + workLength);
frames = !dumpParticles ? 0 :
(input.getFileSize() - headerLength - numberWork*workLength)/frameLength;
// FILE CORRUPTION CHECK
if ( !corruption && input.getFileSize() !=
headerLength + frames*frameLength + numberWork*workLength ) {
throw std::invalid_argument("Invalid file size.");
}
// ACTIVE WORK AND ORDER PARAMETER
if ( loadWork ) {
double work;
for (int i=0; i < numberWork; i++) {
input.read<double>(&work,
headerLength // header
+ frameLength // frame with index 0
+ (1 + i)*framesWork*frameLength // all following packs of framesWork frames
+ i*workLength); // previous values of the active work
activeWork.push_back(work);
input.read<double>(&work);
activeWorkForce.push_back(work);
input.read<double>(&work);
activeWorkOri.push_back(work);
input.read<double>(&work);
orderParameter.push_back(work);
input.read<double>(&work);
orderParameter0.push_back(work);
input.read<double>(&work);
orderParameter1.push_back(work);
input.read<double>(&work);
torqueIntegral1.push_back(work);
input.read<double>(&work);
torqueIntegral2.push_back(work);
}
}
}
// DESTRUCTORS
Dat::~Dat() {}
// METHODS
Read* Dat::getInput() { return &input; }
int Dat::getNumberParticles() const { return numberParticles; }
double Dat::getPersistenceLength() const { return persistenceLength; }
double Dat::getPackingFraction() const { return packingFraction; }
double Dat::getSystemSize() const { return systemSize; }
double Dat::getTorqueParameter() const { return torqueParameter; }
int Dat::getRandomSeed() const { return randomSeed; }
double Dat::getTimeStep() const { return timeStep; }
int Dat::getFramesWork() const { return framesWork; }
long int Dat::getNumberWork() const { return numberWork; }
long int Dat::getFrames() const { return frames; }
std::vector<double> Dat::getActiveWork() { return activeWork; }
std::vector<double> Dat::getActiveWorkForce() { return activeWorkForce; }
std::vector<double> Dat::getActiveWorkOri() { return activeWorkOri; }
std::vector<double> Dat::getOrderParameter() { return orderParameter; }
std::vector<double> Dat::getOrderParameter0() { return orderParameter0; }
std::vector<double> Dat::getOrderParameter1() { return orderParameter1; }
std::vector<double> Dat::getTorqueIntegral1() { return torqueIntegral1; }
std::vector<double> Dat::getTorqueIntegral2() { return torqueIntegral2; }
double Dat::getPosition(
int const& frame, int const& particle, int const& dimension) {
// Returns position of a given particle at a given frame.
return input.read<double>(
headerLength // header
+ frame*frameLength // other frames
+ particle*particleLength // other particles
+ (std::max(frame - 1, 0)/framesWork)*workLength // active work sums (taking into account the frame with index 0)
+ dimension*sizeof(double)); // dimension
}
double Dat::getOrientation(int const& frame, int const& particle){
// Returns orientation of a given particle at a given frame.
return input.read<double>(
headerLength // header
+ frame*frameLength // other frames
+ particle*particleLength // other particles
+ (std::max(frame - 1, 0)/framesWork)*workLength // active work sums (taking into account the frame with index 0)
+ 2*sizeof(double)); // positions
}
double Dat::getVelocity(
int const& frame, int const& particle, int const& dimension) {
// Returns velocity of a given particle at a given frame.
return input.read<double>(
headerLength // header
+ frame*frameLength // other frames
+ particle*particleLength // other particles
+ (std::max(frame - 1, 0)/framesWork)*workLength // active work sums (taking into account the frame with index 0)
+ 3*sizeof(double) // positions and orientation
+ dimension*sizeof(double)); // dimension
}
/********
* DAT0 *
********/
// CONSTRUCTORS
Dat0::Dat0(std::string filename, bool loadWork, bool corruption) :
numberParticles(), potentialParameter(), propulsionVelocity(),
transDiffusivity(), rotDiffusivity(), persistenceLength(),
packingFraction(), systemSize(), randomSeed(), timeStep(), framesWork(),
dumpParticles(), dumpPeriod(),
input(filename) {
// HEADER INFORMATION
input.read<const int>(&numberParticles);
input.read<const double>(&potentialParameter);
input.read<const double>(&propulsionVelocity);
input.read<const double>(&transDiffusivity);
input.read<const double>(&rotDiffusivity);
input.read<const double>(&persistenceLength);
input.read<const double>(&packingFraction);
input.read<const double>(&systemSize);
input.read<const int>(&randomSeed);
input.read<const double>(&timeStep);
input.read<const int>(&framesWork);
input.read<const bool>(&dumpParticles);
input.read<const int>(&dumpPeriod);
// DIAMETERS
double diameter;
for (int i=0; i < numberParticles; i++) {
input.read<double>(&diameter);
diameters.push_back(diameter);
}
// FILE PARTS LENGTHS
headerLength = input.tellg();
particleLength = 9*sizeof(double)*dumpParticles;
frameLength = numberParticles*particleLength;
workLength = 4*sizeof(double);
// ESTIMATION OF NUMBER OF COMPUTED WORK AND ORDER PARAMETER SUMS AND FRAMES
numberWork = (input.getFileSize() - headerLength - frameLength)/(
framesWork*frameLength + workLength);
frames = !dumpParticles ? 0 :
(input.getFileSize() - headerLength - numberWork*workLength)/frameLength;
// FILE CORRUPTION CHECK
if ( !corruption && input.getFileSize() !=
headerLength + frames*frameLength + numberWork*workLength ) {
throw std::invalid_argument("Invalid file size.");
}
// ACTIVE WORK AND ORDER PARAMETER
if ( loadWork ) {
double work;
for (int i=0; i < numberWork; i++) {
input.read<double>(&work,
headerLength // header
+ frameLength // frame with index 0
+ (1 + i)*framesWork*frameLength // all following packs of framesWork frames
+ i*workLength); // previous values of the active work
activeWork.push_back(work);
input.read<double>(&work);
activeWorkForce.push_back(work);
input.read<double>(&work);
activeWorkOri.push_back(work);
input.read<double>(&work);
orderParameter.push_back(work);
}
}
}
// DESTRUCTORS
Dat0::~Dat0() {}
// METHODS
Read* Dat0::getInput() { return &input; }
int Dat0::getNumberParticles() const { return numberParticles; }
double Dat0::getPotentialParameter() const { return potentialParameter; }
double Dat0::getPropulsionVelocity() const { return propulsionVelocity; }
double Dat0::getTransDiffusivity() const { return transDiffusivity; }
double Dat0::getRotDiffusivity() const { return rotDiffusivity; }
double Dat0::getPersistenceLength() const { return persistenceLength; }
double Dat0::getPackingFraction() const { return packingFraction; }
double Dat0::getSystemSize() const { return systemSize; }
int Dat0::getRandomSeed() const { return randomSeed; }
double Dat0::getTimeStep() const { return timeStep; }
int Dat0::getFramesWork() const { return framesWork; }
long int Dat0::getNumberWork() const { return numberWork; }
long int Dat0::getFrames() const { return frames; }
std::vector<double> Dat0::getDiameters() const { return diameters; }
std::vector<double> Dat0::getActiveWork() { return activeWork; }
std::vector<double> Dat0::getActiveWorkForce() { return activeWorkForce; }
std::vector<double> Dat0::getActiveWorkOri() { return activeWorkOri; }
std::vector<double> Dat0::getOrderParameter() { return orderParameter; }
double Dat0::getPosition(
int const& frame, int const& particle, int const& dimension,
bool const& unfolded) {
// Returns position of a given particle at a given frame.
return input.read<double>(
headerLength // header
+ frame*frameLength // other frames
+ particle*particleLength // other particles
+ (std::max(frame - 1, 0)/framesWork)*workLength // active work sums (taking into account the frame with index 0)
+ 7*unfolded*sizeof(double) // unfolded positions
+ dimension*sizeof(double)); // dimension
}
double Dat0::getOrientation(int const& frame, int const& particle){
// Returns orientation of a given particle at a given frame.
return input.read<double>(
headerLength // header
+ frame*frameLength // other frames
+ particle*particleLength // other particles
+ (std::max(frame - 1, 0)/framesWork)*workLength // active work sums (taking into account the frame with index 0)
+ 2*sizeof(double)); // positions
}
double Dat0::getVelocity(
int const& frame, int const& particle, int const& dimension) {
// Returns velocity of a given particle at a given frame.
return input.read<double>(
headerLength // header
+ frame*frameLength // other frames
+ particle*particleLength // other particles
+ (std::max(frame - 1, 0)/framesWork)*workLength // active work sums (taking into account the frame with index 0)
+ 3*sizeof(double) // positions and orientation
+ dimension*sizeof(double)); // dimension
}
double Dat0::getPropulsion(
int const& frame, int const& particle, int const& dimension) {
// Returns self-propulsion vector of a given particle at a given frame.
return input.read<double>(
headerLength // header
+ frame*frameLength // other frames
+ particle*particleLength // other particles
+ (std::max(frame - 1, 0)/framesWork)*workLength // active work sums (taking into account the frame with index 0)
+ 5*sizeof(double) // positions, orientation, and velocities
+ dimension*sizeof(double)); // dimension
}
/********
* DATN *
********/
// CONSTRUCTORS
DatN::DatN(std::string filename, bool loadWork, bool corruption) :
numberParticles(), potentialParameter(), propulsionVelocity(),
transDiffusivity(), rotDiffusivity(), persistenceLength(),
packingFraction(), systemSize(), randomSeed(), timeStep(),
initialTimes(), lagTimes(), frames(),
input(filename) {
// HEADER INFORMATION
input.read<const int>(&numberParticles);
input.read<const double>(&potentialParameter);
input.read<const double>(&propulsionVelocity);
input.read<const double>(&transDiffusivity);
input.read<const double>(&rotDiffusivity);
input.read<const double>(&persistenceLength);
input.read<const double>(&packingFraction);
input.read<const double>(&systemSize);
input.read<const int>(&randomSeed);
input.read<const double>(&timeStep);
// FRAMES
input.read<const int>(&initialTimes);
int t0;
for (int i=0; i < initialTimes; i++) {
input.read<int>(&t0);
time0.push_back(t0);
}
input.read<const int>(&lagTimes);
int t;
for (int i=0; i < lagTimes; i++) {
input.read<int>(&t);
time0.push_back(t);
}
input.read<const int>(&frames);
frameIndices.push_back(0);
int frame;
for (int i=0; i < frames; i++) {
input.read<int>(&frame);
frameIndices.push_back(frame);
}
// DIAMETERS
double diameter;
for (int i=0; i < numberParticles; i++) {
input.read<double>(&diameter);
diameters.push_back(diameter);
}
// FILE PARTS LENGTHS
headerLength = input.tellg();
particleLength = 9*sizeof(double);
frameLength = numberParticles*particleLength;
// FILE CORRUPTION CHECK
if ( !corruption && input.getFileSize() !=
headerLength + (frames + 1)*frameLength ) {
throw std::invalid_argument("Invalid file size.");
}
}
// DESTRUCTORS
DatN::~DatN() {}
// METHODS
Read* DatN::getInput() { return &input; }
int DatN::getNumberParticles() const { return numberParticles; }
double DatN::getPotentialParameter() const { return potentialParameter; }
double DatN::getPropulsionVelocity() const { return propulsionVelocity; }
double DatN::getTransDiffusivity() const { return transDiffusivity; }
double DatN::getRotDiffusivity() const { return rotDiffusivity; }
double DatN::getPersistenceLength() const { return persistenceLength; }
double DatN::getPackingFraction() const { return packingFraction; }
double DatN::getSystemSize() const { return systemSize; }
int DatN::getRandomSeed() const { return randomSeed; }
double DatN::getTimeStep() const { return timeStep; }
std::vector<int>* DatN::getTime0() { return &time0; }
std::vector<int>* DatN::getDt() { return &dt; }
std::vector<int>* DatN::getFrames() { return &frameIndices; }
std::vector<double> DatN::getDiameters() const { return diameters; }
double DatN::getPosition(
int const& frame, int const& particle, int const& dimension,
bool const& unfolded) {
// Returns position of a given particle at a given frame.
return input.read<double>(
headerLength // header
+ getFrameIndex(frame)*frameLength // other frames
+ particle*particleLength // other particles
+ 7*unfolded*sizeof(double) // unfolded positions
+ dimension*sizeof(double)); // dimension
}
double DatN::getOrientation(int const& frame, int const& particle){
// Returns orientation of a given particle at a given frame.
return input.read<double>(
headerLength // header
+ getFrameIndex(frame)*frameLength // other frames
+ particle*particleLength // other particles
+ 2*sizeof(double)); // positions
}
double DatN::getVelocity(
int const& frame, int const& particle, int const& dimension) {
// Returns velocity of a given particle at a given frame.
return input.read<double>(
headerLength // header
+ getFrameIndex(frame)*frameLength // other frames
+ particle*particleLength // other particles
+ 3*sizeof(double) // positions and orientation
+ dimension*sizeof(double)); // dimension
}
double DatN::getPropulsion(
int const& frame, int const& particle, int const& dimension) {
// Returns self-propulsion vector of a given particle at a given frame.
return input.read<double>(
headerLength // header
+ getFrameIndex(frame)*frameLength // other frames
+ particle*particleLength // other particles
+ 5*sizeof(double) // positions, orientation, and velocities
+ dimension*sizeof(double)); // dimension
}
int DatN::getFrameIndex(int const& frame) {
// Returns index of frame in file.
if ( ! isInSortedVec(&frameIndices, frame) ) {
throw std::invalid_argument(
"Frame " + std::to_string(frame) + " not in file.");
}
return (int) std::distance(
frameIndices.begin(),
std::lower_bound(frameIndices.begin(), frameIndices.end(), frame));
}
/********
* DATM *
********/
// CONSTRUCTORS
DatM::DatM(std::string filename, bool loadWork, bool corruption) :
numberParticles(), potentialParameter(), propulsionVelocity(),
transDiffusivity(), rotDiffusivity(), persistenceLength(),
packingFraction(), systemSize(), systemSizes(), randomSeed(), timeStep(),
initialTimes(), lagTimes(), frames(),
input(filename) {
// HEADER INFORMATION
input.read<const int>(&numberParticles);
input.read<const double>(&potentialParameter);
input.read<const double>(&propulsionVelocity);
input.read<const double>(&transDiffusivity);
input.read<const double>(&rotDiffusivity);
input.read<const double>(&persistenceLength);
input.read<const double>(&packingFraction);
input.read<const double>(&systemSize);
input.read<const int>(&randomSeed);
input.read<const double>(&timeStep);
// FRAMES
input.read<const int>(&initialTimes);
int t0;
for (int i=0; i < initialTimes; i++) {
input.read<int>(&t0);
time0.push_back(t0);
}
input.read<const int>(&lagTimes);
int t;
for (int i=0; i < lagTimes; i++) {
input.read<int>(&t);
time0.push_back(t);
}
input.read<const int>(&frames);
frameIndices.push_back(0);
int frame;
for (int i=0; i < frames; i++) {
input.read<int>(&frame);
frameIndices.push_back(frame);
}
// DIAMETERS
double diameter;
for (int i=0; i < numberParticles; i++) {
input.read<double>(&diameter);
diameters.push_back(diameter);
}
// SYSTEM SIZE
input.read<const double>(&systemSizes[0]);
input.read<const double>(&systemSizes[1]);
// FILE PARTS LENGTHS
headerLength = input.tellg();
particleLength = 9*sizeof(double);
frameLength = numberParticles*particleLength;
// FILE CORRUPTION CHECK
if ( !corruption && input.getFileSize() !=
headerLength + (frames + 1)*frameLength ) {
throw std::invalid_argument("Invalid file size.");
}
}
// DESTRUCTORS
DatM::~DatM() {}
// METHODS
Read* DatM::getInput() { return &input; }
int DatM::getNumberParticles() const { return numberParticles; }
double DatM::getPotentialParameter() const { return potentialParameter; }
double DatM::getPropulsionVelocity() const { return propulsionVelocity; }
double DatM::getTransDiffusivity() const { return transDiffusivity; }
double DatM::getRotDiffusivity() const { return rotDiffusivity; }
double DatM::getPersistenceLength() const { return persistenceLength; }
double DatM::getPackingFraction() const { return packingFraction; }
double DatM::getSystemSize() const { return systemSize; }
const double* DatM::getSystemSizes() { return &systemSizes[0]; }
int DatM::getRandomSeed() const { return randomSeed; }
double DatM::getTimeStep() const { return timeStep; }
std::vector<int>* DatM::getTime0() { return &time0; }
std::vector<int>* DatM::getDt() { return &dt; }
std::vector<int>* DatM::getFrames() { return &frameIndices; }
std::vector<double> DatM::getDiameters() const { return diameters; }
double DatM::getPosition(
int const& frame, int const& particle, int const& dimension,
bool const& unfolded) {
// Returns position of a given particle at a given frame.
return input.read<double>(
headerLength // header
+ getFrameIndex(frame)*frameLength // other frames
+ particle*particleLength // other particles
+ 7*unfolded*sizeof(double) // unfolded positions
+ dimension*sizeof(double)); // dimension
}
double DatM::getOrientation(int const& frame, int const& particle){
// Returns orientation of a given particle at a given frame.
return input.read<double>(
headerLength // header
+ getFrameIndex(frame)*frameLength // other frames
+ particle*particleLength // other particles
+ 2*sizeof(double)); // positions
}
double DatM::getVelocity(
int const& frame, int const& particle, int const& dimension) {
// Returns velocity of a given particle at a given frame.
return input.read<double>(
headerLength // header
+ getFrameIndex(frame)*frameLength // other frames
+ particle*particleLength // other particles
+ 3*sizeof(double) // positions and orientation
+ dimension*sizeof(double)); // dimension
}
double DatM::getPropulsion(
int const& frame, int const& particle, int const& dimension) {
// Returns self-propulsion vector of a given particle at a given frame.
return input.read<double>(
headerLength // header
+ getFrameIndex(frame)*frameLength // other frames
+ particle*particleLength // other particles
+ 5*sizeof(double) // positions, orientation, and velocities
+ dimension*sizeof(double)); // dimension
}
int DatM::getFrameIndex(int const& frame) {
// Returns index of frame in file.
if ( ! isInSortedVec(&frameIndices, frame) ) {
throw std::invalid_argument(
"Frame " + std::to_string(frame) + " not in file.");
}
return (int) std::distance(
frameIndices.begin(),
std::lower_bound(frameIndices.begin(), frameIndices.end(), frame));
}
/********
* DATR *
********/
// CONSTRUCTORS
DatR::DatR(std::string filename, bool loadOrder) :
numberParticles(), rotDiffusivity(), torqueParameter(), timeStep(),
framesOrder(), dumpRotors(), dumpPeriod(), randomSeed(),
input(filename) {
// HEADER INFORMATION
input.read<const int>(&numberParticles);
input.read<const double>(&rotDiffusivity);
input.read<const double>(&torqueParameter);
input.read<const double>(&timeStep);
input.read<const int>(&framesOrder);
input.read<const bool>(&dumpRotors);
input.read<const int>(&dumpPeriod);
input.read<const int>(&randomSeed);
// FILE PARTS LENGTHS
headerLength = input.tellg();
rotorLength = 1*sizeof(double);
frameLength = numberParticles*rotorLength;
orderLength = 2*sizeof(double);
// ESTIMATION OF NUMBER OF COMPUTED ORDER PARAMETER SUMS AND FRAMES
numberOrder = (input.getFileSize() - headerLength - frameLength)/(
framesOrder*frameLength + orderLength);
frames = !dumpRotors ? 0 :
(input.getFileSize() - headerLength - numberOrder*orderLength)/frameLength;
// FILE CORRUTION CHECK
if ( input.getFileSize() !=
headerLength + frames*frameLength + numberOrder*orderLength ) {
throw std::invalid_argument("Invalid file size.");
}
// ORDER PARAMETER
if ( loadOrder ) {
double order;
for (int i=0; i < numberOrder; i++) {
input.read<double>(&order,
headerLength // header
+ frameLength // frame with index 0
+ (1 + i)*framesOrder*frameLength // all following packs of framesOrder frames
+ i*orderLength); // previous values of the order parameter
orderParameter.push_back(order);
input.read<double>(&order);
orderParameterSq.push_back(order);
}
}
}
// DESTRUCTORS
DatR::~DatR() {}
// METHODS
Read* DatR::getInput() { return &input; }
int DatR::getNumberParticles() const { return numberParticles; }
double DatR::getRotDiffusivity() const { return rotDiffusivity; }
double DatR::getTorqueParameter() const { return torqueParameter; }
double DatR::getTimeStep() const { return timeStep; }
int DatR::getDumpPeriod() const { return dumpPeriod; }
int DatR::getRandomSeed() const { return randomSeed; }
long int DatR::getFrames() const { return frames; }
std::vector<double> DatR::getOrderParameter() { return orderParameter; }
std::vector<double> DatR::getOrderParameterSq() { return orderParameterSq; }
double DatR::getOrientation(int const& frame, int const& rotor) {
// Returns position of a given rotor at a given frame.
return input.read<double>(
headerLength // header
+ frame*frameLength // other frames
+ rotor*rotorLength // other rotors
+ (std::max(frame - 1, 0)/framesOrder)*orderLength); // order parameter sums (taking into account the frame with index 0)
}