BoxConfiguration.cpp

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/*
 * BoxConfiguration.cpp
 *
 *  Created on: Nov 4, 2019
 *      Author: Nikhil
 */

#include <fstream>
#include "BoxConfiguration.h"
#include "Configuration.h"
#include "typedef.h"
#include "neighbor_list.h"
#include "helper.hpp"


BoxConfiguration::BoxConfiguration(int numberOfParticles, int referenceAndFinal):
        Configuration(numberOfParticles,referenceAndFinal)
{
    MY_HEADING("Initializing a box configuration");
    if (referenceAndFinal)
        std::cout << "Creating a configuration of " << numberOfParticles << " particles" <<
                     " along with reference coordinates in a box of size zero" << std::endl;
    else
        std::cout << "Creating a configuration of " << numberOfParticles << " particles" <<
                     " in a box of size zero" << std::endl;
    // Default to zero box sizes and no pbc
    box.setZero();
    reference_box.setZero();
    pbc.setZero();
}


void BoxConfiguration::read(std::string configFileName, int referenceAndFinal)
{
    // Read in the atomistic system
    std::cout << "Reading the box configuration from file " << configFileName << std::endl;
    std::ifstream file(configFileName);
    if(!file)
    {
    // Print an error and exit
        std::cerr << "ERROR: " << configFileName << " could not be opened for reading!" << std::endl;
        exit(1);
    }

    int numberOfParticlesInFile;
    file >> numberOfParticlesInFile;
    if (numberOfParticles != numberOfParticlesInFile)
        MY_ERROR("Error: Number of particles in file does not equal to that of BoxConfiguration");

    for(int i=0;i<DIM*DIM;++i)
        if(!(file >> reference_box(i)))  MY_ERROR("ERROR: Reference box size.");
    for(int i=0;i<DIM*DIM;++i)
        if(!(file >> box(i)))            MY_ERROR("ERROR: Box size.");
    for(int i=0;i<DIM;++i)
        if(!(file >> pbc(i)))            MY_ERROR("ERROR: PBC.");


    std::string speciesTemp;
    for(int i=0;i<numberOfParticles;++i)
    {
        if(!(file >> speciesTemp))           MY_ERROR("ERROR: Species code of particle " + std::to_string(i));
        species.push_back(speciesTemp);
        for(int j=0;j<DIM;++j)
            if(!(file >> coordinates[Current](i,j)))  MY_ERROR("ERROR: Coordinate of particle " + std::to_string(i));
        for(int j=0;j<DIM;++j)
            if(!(file >> velocities(i,j)))   MY_ERROR("ERROR: Velocity of particle " + std::to_string(i));
        if (referenceAndFinal == true)
        {
            for(int j=0;j<DIM;++j)
                if(!(file >> coordinates[Reference](i,j)))
                    MY_ERROR("ERROR: Reference coordinate of particle " + std::to_string(i) + "\n");
        }
        else
        {
            file.ignore(32767, '\n');
        }
    }
    std::cout << std::endl;
    std::cout << "Box size = " << std::endl;
    std::cout << box << std::endl;
    std::cout << std::endl;
    std::cout << "Reference box size = " << std::endl;
    std::cout << reference_box << std::endl;
    std::cout << std::endl;
    std::cout << "Periodic boundary conditions = " << pbc << std::endl;


}

Configuration* BoxConfiguration::getConfiguration(double padding) const
{
    // Build padding atoms
    int numberOfPaddings{0};
    std::vector<double> reference_coordinatesOfPaddings,coordinatesOfPaddings;
    std::vector<std::string> speciesOfPaddings;
    std::vector<int> masterOfPaddings;
    int referenceAndFinal= (coordinates.at(Reference).rows()>0);

    nbl_create_paddings(numberOfParticles,
                        padding,
                        reference_box.data(),
                        box.data(),
                        pbc.data(),
                        coordinates.at(Reference).data(),
                        coordinates.at(Current).data(),
                        species,
                        numberOfPaddings,
                        reference_coordinatesOfPaddings,
                        coordinatesOfPaddings,
                        speciesOfPaddings,
                        masterOfPaddings,
                        referenceAndFinal);

    int total= numberOfParticles + numberOfPaddings;

    Configuration* config_ptr(new Configuration{total,referenceAndFinal});

    // copy the coordinates, particleContributing and species
    // of contributing atoms from BoxConfiguration to Configuration
    if (referenceAndFinal) (config_ptr->coordinates.at(Reference)).topRows(numberOfParticles)= coordinates.at(Reference);
    (config_ptr->coordinates.at(Current)).topRows(numberOfParticles)= coordinates.at(Current);
    for (auto it= species.begin();it!= species.end();it++)
        config_ptr->species.push_back(*it);

    if (numberOfPaddings)
    {
        if (referenceAndFinal) config_ptr->coordinates.at(Reference).bottomRows(numberOfPaddings)=
        *new Eigen::Map<MatrixXd> (reference_coordinatesOfPaddings.data(),numberOfPaddings,DIM);
        config_ptr->coordinates.at(Current).bottomRows(numberOfPaddings)=
        *new Eigen::Map<MatrixXd> (coordinatesOfPaddings.data(),numberOfPaddings,DIM);
        for (auto it= speciesOfPaddings.begin();it!= speciesOfPaddings.end();it++)
            config_ptr->species.push_back(*it);
    }

    return config_ptr;
}
BoxConfiguration::~BoxConfiguration() {
    // TODO Auto-generated destructor stub
}