ReadFile.h

#pragma once

#include <math.h>
#include <array>
#include <string>
#include <vector>
#include <iostream>
#include <fstream>

// Temp read file class. This class will be integrated/changed
// into a larger read file class that uses
// readxyz as a function. Can be expanded to include other
// file types.

namespace SSAGES
{

    class ReadFile
    {
    public:

        ReadFile()
        {

        }

        ~ReadFile()
        {

        }


        static std::vector<std::array<double,4>> ReadXYZ(std::string FileName)
        {
            std::vector<std::array<double,4>> refcoord;
            int numatoms = 0;
            std::string comments = "";
            std::ifstream infile;
            infile.open(FileName, std::ios::in);
            if(!infile.is_open())
                throw std::runtime_error("File " + FileName + " does not exist.");
            
            std::string ignore;
            
            std::getline(infile, ignore); // Get number of atoms

            numatoms = std::atoi(ignore.c_str());
            if(numatoms <= 0)
                throw std::runtime_error("Must be more than 0 atoms or invalid number atoms defined.");

            refcoord.resize(numatoms);

            std::getline(infile, comments); // Get comments

            int i = 0;
            std::string line;

            while (i < numatoms)
            {
                std::getline(infile,line);
                std::istringstream iss(line);
                if (!(iss >> refcoord[i][0] >> refcoord[i][1] >> refcoord[i][2] >> refcoord[i][3])) 
                    throw std::runtime_error("Bad file format for " + FileName + " for atom " + std::to_string(i+1)); 
                i++;
            }

            if(std::getline(infile, line) && !line.empty())
                throw std::runtime_error("Bad end line, possibly too many atoms defined.");

            if(i != numatoms)
                throw std::runtime_error("Number atoms specified does not match number of atoms defined");

            return refcoord;
        }
    };
}