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classPNM.cpp
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classPNM.cpp
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#include "classPNM.h"
///
///ClassPNM functions
///
//classPNM classPNM::poresGeneration(classPNM PNM, classUtils utils)
//{
//
// PNM.poreSizeDist.clear();
// PNM.network.pores.clear();
// PNM.network.diameter_pore.clear();
//
// //variable for holding the array of pore coordinates
// vector<vector<double>> pores;
//
// //converting string into double PSD
// vector<double> temp;
// for (int i = 0; i < PNM.poreSizeDist_raw.size(); i++)
// {
// temp.clear();
// for (int j = 0; j < PNM.poreSizeDist_raw[i].size(); j++)
// {
// if (j == 0) { temp.push_back(stod(PNM.poreSizeDist_raw[i][j])*1e-9); }
// else { temp.push_back(stod(PNM.poreSizeDist_raw[i][j])); }
// }
// PNM.poreSizeDist.push_back(temp);
// }
//
// //calculate number of pores per each poe size with given domain
// vector<int> nPores = PNM.poresPsize(PNM);
//
// //variable definition
// int total_pn, current_psd_index, nCells, xCell, yCell, zCell, cellIndex;
//
// double expected_porosity, cellSize, pores_per_cell;
//
// total_pn = 0;
// expected_porosity = 0;
// //calculate total pore number
// for (int i = 0; i < nPores.size(); i++)
// {
// if (!(nPores[i] < 1))
// {
// total_pn += nPores[i];
// expected_porosity += PNM.poreSizeDist[i][1];
// }
// }
// PNM.expectedP = expected_porosity;
// cout << "Expected network porosity is: " << expected_porosity*100.0 << " %\n";
//
// //define which pore size we are starting generation from
// current_psd_index = 0;
// while (nPores[current_psd_index] < 1)
// {
// current_psd_index++;
// }
//
// //divide donain into cells, just larger than biggest pore radius
// cellSize = PNM.poreSizeDist[current_psd_index][0] / 2;
// nCells = (int)floor(PNM.settings.domain / cellSize);
// cellSize = PNM.settings.domain / nCells;
//
// //variable for storing each cell pore coords+diameter
// vector<vector<vector<double>>> cellCoords(pow(nCells, 3));
//
// int n_generated = 0;
//
// //give seed to the random generation algorithm
// srand(PNM.settings.seed);
//
// //variable for storing randomly generated pore coords plus its diameter before pushing into the Pores array
// vector<double> temp_pore = { ((double)rand() / RAND_MAX) * PNM.settings.domain, ((double)rand() / RAND_MAX) * PNM.settings.domain, ((double)rand() / RAND_MAX) * PNM.settings.domain };
// temp_pore.push_back(PNM.poreSizeDist[current_psd_index][0]);
// pores.push_back(temp_pore);
// PNM.network.diameter_pore.push_back(PNM.poreSizeDist[current_psd_index][0]);
//
//
// n_generated++;
// if (n_generated >= nPores[current_psd_index])
// {
// current_psd_index++;
// n_generated = 0;
// }
//
// //assign pore to a cell
// xCell = (int)floor(temp_pore[0] / cellSize);
// yCell = (int)floor(temp_pore[1] / cellSize);
// zCell = (int)floor(temp_pore[2] / cellSize);
// cellIndex = pow(nCells, 2)*xCell + nCells * yCell + zCell;
// cellCoords[cellIndex].push_back(temp_pore);
//
// //loop for generating the rest of the pores
// int flag;
// for (int i = 1; i < total_pn; i++)
// {
// //V1: assign pores to cells
// flag = 1; //flag is 1 (overlap)to enter the loop, but reset to zero(no overlap) straight after and raised in the overlap loop
// while (flag > 0)
// {
// flag = 0; //flag reset
// //take a random coordinate and calculate its location in the cell grid
// temp_pore.clear();
// double failsafe = 0.999999999;
// temp_pore = { ((double)rand() / RAND_MAX) * PNM.settings.domain * failsafe, ((double)rand() / RAND_MAX) * PNM.settings.domain * failsafe, ((double)rand() / RAND_MAX) * PNM.settings.domain * failsafe };
// temp_pore.push_back(PNM.poreSizeDist[current_psd_index][0]);
// //pore HAS TO BE this diameter, assign now
// PNM.network.diameter_pore.push_back(PNM.poreSizeDist[current_psd_index][0]);
//
// xCell = (int)floor(temp_pore[0] / cellSize);
// yCell = (int)floor(temp_pore[1] / cellSize);
// zCell = (int)floor(temp_pore[2] / cellSize);
// //cellIndex = pow(nCells, 2)*xCell + nCells * yCell + zCell;
// //cellCoords[cellIndex].push_back(temp_pore);
//
// //run search in 25 cells around the cell of interest
// int cellIndexSearch;
// double distance2;
// for (int iCell = max(0, xCell - 2); iCell < min(nCells, xCell + 3); iCell++)
// {
// for (int jCell = max(0, yCell - 2); jCell < min(nCells, yCell + 3); jCell++)
// {
// for (int kCell = max(0, zCell - 2); kCell < min(nCells, zCell + 3); kCell++)
// {
// cellIndexSearch = pow(nCells, 2)*iCell + nCells * jCell + kCell;
// for (int pore_in_cell = 0; pore_in_cell < cellCoords[cellIndexSearch].size(); pore_in_cell++)
// {
// distance2 = pow((temp_pore[0] - cellCoords[cellIndexSearch][pore_in_cell][0]), 2) + pow((temp_pore[1] - cellCoords[cellIndexSearch][pore_in_cell][1]), 2) + pow((temp_pore[2] - cellCoords[cellIndexSearch][pore_in_cell][2]), 2);
// if (distance2 <= pow(cellCoords[cellIndexSearch][pore_in_cell][3] / 2 + temp_pore[3] / 2, 2))
// {
// flag = 1;
// }
// if (flag > 0) { break; }
// }
// if (flag > 0) { break; }
// }
// if (flag > 0) { break; }
// }
// if (flag > 0) { break; }
// }
// }
//
//
// cellIndex = pow(nCells, 2)*xCell + nCells * yCell + zCell;
// cellCoords[cellIndex].push_back(temp_pore);
// pores.push_back(temp_pore);
//
// n_generated++;
// if (n_generated >= nPores[current_psd_index])
// {
// current_psd_index++;
// n_generated = 0;
// }
//
// if (i % 1000 == 0)
// {
// //cout << i << "\n";
// }
//
// }
//
// cout << "Number of pores generated: " << pores.size() << endl;
// PNM.network.pores = pores;
//
// return PNM;
//}
//
//classPNM classPNM::poresGeneration2(classPNM PNM, classUtils utils)
//{
// chrono::steady_clock::time_point begin = chrono::steady_clock::now();
//
// PNM.poreSizeDist.clear();
// PNM.network.pores.clear();
// PNM.network.diameter_pore.clear();
//
// //variable for holding the array of pore coordinates
// vector<vector<double>> pores;
//
// //converting string into double PSD
// vector<double> temp;
// for (int i = 0; i < PNM.poreSizeDist_raw.size(); i++)
// {
// temp.clear();
// for (int j = 0; j < PNM.poreSizeDist_raw[i].size(); j++)
// {
// if (j == 0) { temp.push_back(stod(PNM.poreSizeDist_raw[i][j])*1e-9); }
// else { temp.push_back(stod(PNM.poreSizeDist_raw[i][j])); }
// }
// PNM.poreSizeDist.push_back(temp);
// }
//
// //calculate number of pores per each poe size with given domain
// vector<int> nPores = PNM.poresPsize(PNM);
//
// //variable definition
// int total_pn, current_psd_index, nCells, xCell, yCell, zCell, cellIndex, nCellsSmall, xCellSmall, yCellSmall, zCellSmall, cellIndexSmall;
// double expected_porosity, cellSize, pores_per_cell, cellSizeSmall;
// int nCellsMicro, xCellMicro, yCellMicro, zCellMicro, cellIndexMicro;
// double cellSizeMicro;
//
// total_pn = 0;
// expected_porosity = 0;
// //calculate total pore number
// for (int i = 0; i < nPores.size(); i++)
// {
// if (!(nPores[i] < 1))
// {
// total_pn += nPores[i];
// expected_porosity += PNM.poreSizeDist[i][1];
// }
// }
// PNM.expectedP = expected_porosity;
// cout << "Expected network porosity is: " << expected_porosity * 100.0 << " %\n";
//
// //define which pore size we are starting generation from
// current_psd_index = 0;
// while (nPores[current_psd_index] < 1)
// {
// current_psd_index++;
// }
//
// //define how many pores we want to generate as a "large" grid:
// double fraction = 0.0;
// double cut_off = current_psd_index; //everything up to but NOT including THIS entry into PSD to be generated as "large" grid
// double cut_off_micro = current_psd_index; ////everything up to but NOT including THIS entry into PSD to be generated as "small" grid
// int large_pores = 0; //number of large pores to be generated
// int small_pores = 0;
// while (fraction < 0.001)
// {
// fraction += (double)nPores[cut_off] / total_pn;
// large_pores += nPores[cut_off];
// cut_off++;
//
// };
// cout << "Cut-off: " << cut_off << endl;
//
// //divide donain into "large" cells, just larger than biggest pore radius
// cellSize = PNM.poreSizeDist[current_psd_index][0] / 2;
// nCells = (int)floor(PNM.settings.domain / cellSize);
// cellSize = PNM.settings.domain / nCells;
//
// //divide domain into "small" cells, based on the cut-off pore size
// cellSizeSmall = PNM.poreSizeDist[cut_off][0] / 2;
// nCellsSmall = (int)floor(PNM.settings.domain / cellSizeSmall);
// cellSizeSmall = PNM.settings.domain / nCellsSmall;
//
// //variable for storing each "large" cell pore coords+diameter
// vector<vector<vector<double>>> cellCoords(pow(nCells, 3));
//
// //variable for storing each "small" cell pore coords+diameter
// vector<vector<vector<double>>> cellCoordsSmall(pow(nCellsSmall, 3));
//
//
// int n_generated = 0;
//
// //give seed to the random generation algorithm
// srand(PNM.settings.seed);
//
// //generate the first pore
// //variable for storing randomly generated pore coords plus its diameter before pushing into the Pores array
// vector<double> temp_pore = { ((double)rand() / RAND_MAX) * PNM.settings.domain, ((double)rand() / RAND_MAX) * PNM.settings.domain, ((double)rand() / RAND_MAX) * PNM.settings.domain };
// temp_pore.push_back(PNM.poreSizeDist[current_psd_index][0]);
// pores.push_back(temp_pore);
// PNM.network.diameter_pore.push_back(PNM.poreSizeDist[current_psd_index][0]);
//
//
// n_generated++;
// if (n_generated >= nPores[current_psd_index])
// {
// current_psd_index++;
// n_generated = 0;
// }
//
// //assign pore to a cell
// xCell = (int)floor(temp_pore[0] / cellSize);
// yCell = (int)floor(temp_pore[1] / cellSize);
// zCell = (int)floor(temp_pore[2] / cellSize);
// cellIndex = pow(nCells, 2)*xCell + nCells * yCell + zCell;
// cellCoords[cellIndex].push_back(temp_pore);
//
// cout << "Pore generation progress:\n";
// cout << setprecision(2) << std::fixed;
//
// //loop for generating the rest of the LARGE pores
// int flag;
// double progress;
// for (int i = 1; i < large_pores; i++)
// {
// //V1: assign pores to cells
// flag = 1; //flag is 1 (overlap)to enter the loop, but reset to zero(no overlap) straight after and raised in the overlap loop
// while (flag > 0)
// {
// flag = 0; //flag reset
// //take a random coordinate and calculate its location in the cell grid
// temp_pore.clear();
// double failsafe = 0.999999999;
// temp_pore = { ((double)rand() / RAND_MAX) * PNM.settings.domain * failsafe, ((double)rand() / RAND_MAX) * PNM.settings.domain * failsafe, ((double)rand() / RAND_MAX) * PNM.settings.domain * failsafe };
// temp_pore.push_back(PNM.poreSizeDist[current_psd_index][0]);
// //pore HAS TO BE this diameter, assign now
// PNM.network.diameter_pore.push_back(PNM.poreSizeDist[current_psd_index][0]);
//
// xCell = (int)floor(temp_pore[0] / cellSize);
// yCell = (int)floor(temp_pore[1] / cellSize);
// zCell = (int)floor(temp_pore[2] / cellSize);
// //cellIndex = pow(nCells, 2)*xCell + nCells * yCell + zCell;
// //cellCoords[cellIndex].push_back(temp_pore);
//
// //run search in 25 cells around the cell of interest
// int cellIndexSearch;
// double distance2;
// for (int iCell = max(0, xCell - 2); iCell < min(nCells, xCell + 3); iCell++)
// {
// for (int jCell = max(0, yCell - 2); jCell < min(nCells, yCell + 3); jCell++)
// {
// for (int kCell = max(0, zCell - 2); kCell < min(nCells, zCell + 3); kCell++)
// {
// cellIndexSearch = pow(nCells, 2)*iCell + nCells * jCell + kCell;
// for (int pore_in_cell = 0; pore_in_cell < cellCoords[cellIndexSearch].size(); pore_in_cell++)
// {
// distance2 = pow((temp_pore[0] - cellCoords[cellIndexSearch][pore_in_cell][0]), 2) + pow((temp_pore[1] - cellCoords[cellIndexSearch][pore_in_cell][1]), 2) + pow((temp_pore[2] - cellCoords[cellIndexSearch][pore_in_cell][2]), 2);
// if (distance2 <= pow(cellCoords[cellIndexSearch][pore_in_cell][3] / 2 + temp_pore[3] / 2, 2))
// {
// flag = 1;
// }
// if (flag > 0) { break; }
// }
// if (flag > 0) { break; }
// }
// if (flag > 0) { break; }
// }
// if (flag > 0) { break; }
// }
// }
//
//
// cellIndex = pow(nCells, 2)*xCell + nCells * yCell + zCell;
// cellCoords[cellIndex].push_back(temp_pore);
// pores.push_back(temp_pore);
//
// n_generated++;
// if (n_generated >= nPores[current_psd_index])
// {
// current_psd_index++;
// n_generated = 0;
// }
//
// if (i % 10000 == 0)
// {
// progress = 100 * (i + 1) / (double)total_pn;
// cout << "\r" << progress << "%" << flush;
// }
//
// }
//
// //loop for generating SMALL pores
// for (int i = large_pores; i < total_pn; i++)
// {
// //V1: assign pores to cells
// flag = 1; //flag is 1 (overlap)to enter the loop, but reset to zero(no overlap) straight after and raised in the overlap loop
// while (flag > 0)
// {
// flag = 0; //flag reset
// //take a random coordinate and calculate its location in the cell grid
// temp_pore.clear();
// double failsafe = 0.999999999;
// temp_pore = { ((double)rand() / RAND_MAX) * PNM.settings.domain * failsafe, ((double)rand() / RAND_MAX) * PNM.settings.domain * failsafe, ((double)rand() / RAND_MAX) * PNM.settings.domain * failsafe };
// temp_pore.push_back(PNM.poreSizeDist[current_psd_index][0]);
// //pore HAS TO BE this diameter, assign now
// PNM.network.diameter_pore.push_back(PNM.poreSizeDist[current_psd_index][0]);
//
// //TEST LARGE GRID FIRST
// xCell = (int)floor(temp_pore[0] / cellSize);
// yCell = (int)floor(temp_pore[1] / cellSize);
// zCell = (int)floor(temp_pore[2] / cellSize);
// //cellIndex = pow(nCells, 2)*xCell + nCells * yCell + zCell;
// //cellCoords[cellIndex].push_back(temp_pore);
//
// //run search in 25 cells around the cell of interest
// int cellIndexSearch;
// double distance2;
// for (int iCell = max(0, xCell - 2); iCell < min(nCells, xCell + 3); iCell++)
// {
// for (int jCell = max(0, yCell - 2); jCell < min(nCells, yCell + 3); jCell++)
// {
// for (int kCell = max(0, zCell - 2); kCell < min(nCells, zCell + 3); kCell++)
// {
// cellIndexSearch = pow(nCells, 2)*iCell + nCells * jCell + kCell;
// for (int pore_in_cell = 0; pore_in_cell < cellCoords[cellIndexSearch].size(); pore_in_cell++)
// {
// distance2 = pow((temp_pore[0] - cellCoords[cellIndexSearch][pore_in_cell][0]), 2) + pow((temp_pore[1] - cellCoords[cellIndexSearch][pore_in_cell][1]), 2) + pow((temp_pore[2] - cellCoords[cellIndexSearch][pore_in_cell][2]), 2);
// if (distance2 <= pow(cellCoords[cellIndexSearch][pore_in_cell][3] / 2 + temp_pore[3] / 2, 2))
// {
// flag = 1;
// }
// if (flag > 0) { break; }
// }
// if (flag > 0) { break; }
// }
// if (flag > 0) { break; }
// }
// if (flag > 0) { break; }
// }
// //if fist check exits with flag > 0, it will exit instantly in the next loop, loss of efficiency is minimal
//
// //TEST SMALL GRID
// xCellSmall = (int)floor(temp_pore[0] / cellSizeSmall);
// yCellSmall = (int)floor(temp_pore[1] / cellSizeSmall);
// zCellSmall = (int)floor(temp_pore[2] / cellSizeSmall);
// //cellIndex = pow(nCells, 2)*xCell + nCells * yCell + zCell;
// //cellCoords[cellIndex].push_back(temp_pore);
//
// //run search in 25 cells around the cell of interest
// /*int cellIndexSearch;
// double distance2;*/
// for (int iCell = max(0, xCellSmall - 2); iCell < min(nCellsSmall, xCellSmall + 3); iCell++)
// {
// for (int jCell = max(0, yCellSmall - 2); jCell < min(nCellsSmall, yCellSmall + 3); jCell++)
// {
// for (int kCell = max(0, zCellSmall - 2); kCell < min(nCellsSmall, zCellSmall + 3); kCell++)
// {
// cellIndexSearch = pow(nCellsSmall, 2)*iCell + nCellsSmall * jCell + kCell;
// for (int pore_in_cell = 0; pore_in_cell < cellCoordsSmall[cellIndexSearch].size(); pore_in_cell++)
// {
// distance2 = pow((temp_pore[0] - cellCoordsSmall[cellIndexSearch][pore_in_cell][0]), 2) + pow((temp_pore[1] - cellCoordsSmall[cellIndexSearch][pore_in_cell][1]), 2) + pow((temp_pore[2] - cellCoordsSmall[cellIndexSearch][pore_in_cell][2]), 2);
// if (distance2 <= pow(cellCoordsSmall[cellIndexSearch][pore_in_cell][3] / 2 + temp_pore[3] / 2, 2))
// {
// flag = 1;
// }
// if (flag > 0) { break; }
// }
// if (flag > 0) { break; }
// }
// if (flag > 0) { break; }
// }
// if (flag > 0) { break; }
// }
// }
//
// //push back generated pore into the small grid storage
// cellIndexSmall = pow(nCellsSmall, 2)*xCellSmall + nCellsSmall * yCellSmall + zCellSmall;
// cellCoordsSmall[cellIndexSmall].push_back(temp_pore);
// pores.push_back(temp_pore);
//
// n_generated++;
// if (n_generated >= nPores[current_psd_index])
// {
// current_psd_index++;
// n_generated = 0;
// }
//
// if (i % 10000 == 0)
// {
// progress = 100 * (i + 1) / (double)total_pn;
// cout << "\r" << progress << "%" << flush;
// }
//
// }
// progress = 100;
// cout << "\r" << progress << "%" << flush;
//
// cout << "\nNumber of pores generated: " << pores.size() << endl;
// PNM.network.pores = pores;
//
// return PNM;
//
// chrono::steady_clock::time_point end = chrono::steady_clock::now();
// string elapsedTime = "Elapsed time: " + to_string(chrono::duration_cast<std::chrono::seconds>(end - begin).count()) + " [s]";
// cout << elapsedTime << endl;
//}
//
//classPNM classPNM::poresGeneration3(classPNM PNM, classUtils utils)
//{
//
// PNM.poreSizeDist.clear();
// PNM.network.pores.clear();
// PNM.network.diameter_pore.clear();
//
// //variable for holding the array of pore coordinates
// vector<vector<double>> pores;
//
// //converting string into double PSD
// vector<double> temp;
// for (int i = 0; i < PNM.poreSizeDist_raw.size(); i++)
// {
// temp.clear();
// for (int j = 0; j < PNM.poreSizeDist_raw[i].size(); j++)
// {
// if (j == 0) { temp.push_back(stod(PNM.poreSizeDist_raw[i][j])*1e-9); }
// else { temp.push_back(stod(PNM.poreSizeDist_raw[i][j])); }
// }
// PNM.poreSizeDist.push_back(temp);
// }
//
// //calculate number of pores per each poe size with given domain
// vector<int> nPores = PNM.poresPsize(PNM);
//
// //variable definition
// int total_pn, current_psd_index, nCells, xCell, yCell, zCell, cellIndex;
// int nCellsSmall, xCellSmall, yCellSmall, zCellSmall, cellIndexSmall;
// double expected_porosity, cellSize, pores_per_cell;
// double cellSizeSmall;
// int nCellsMicro, xCellMicro, yCellMicro, zCellMicro, cellIndexMicro;
// double cellSizeMicro;
//
// total_pn = 0;
// expected_porosity = 0;
// //calculate total pore number
// for (int i = 0; i < nPores.size(); i++)
// {
// if (!(nPores[i] < 1))
// {
// total_pn += nPores[i];
// expected_porosity += PNM.poreSizeDist[i][1];
// }
// }
// PNM.expectedP = expected_porosity;
// cout << "Expected network porosity is: " << expected_porosity * 100.0 << " %\n";
//
// //define which pore size we are starting generation from
// current_psd_index = 0;
// while (nPores[current_psd_index] < 1)
// {
// current_psd_index++;
// }
//
// //define how many pores we want to generate as a "large" grid:
// double fraction = 0.0;
// double cut_off = current_psd_index; //everything up to but NOT including THIS entry into PSD to be generated as "large" grid
// double cut_off_micro = current_psd_index; ////everything up to but NOT including THIS entry into PSD to be generated as "small" grid
// int large_pores = 0; //number of large pores to be generated
// int small_pores = 0;
// while (fraction < 0.0001)
// {
// fraction += (double)nPores[cut_off] / total_pn;
// large_pores += nPores[cut_off];
// cut_off++;
//
// };
// cout << "Cut-off: " << cut_off << endl;
//
// fraction = 0.0;
// while (fraction < 0.001)
// {
// fraction += (double)nPores[cut_off_micro] / total_pn;
// small_pores += nPores[cut_off_micro];
// cut_off_micro++;
//
// };
// cout << "Cut-off_micro: " << cut_off_micro << endl;
//
// //divide donain into "large" cells, just larger than biggest pore radius
// cellSize = PNM.poreSizeDist[current_psd_index][0] / 2;
// nCells = (int)floor(PNM.settings.domain / cellSize);
// cellSize = PNM.settings.domain / nCells;
//
// //divide domain into "small" cells, based on the cut-off pore size
// cellSizeSmall = PNM.poreSizeDist[cut_off][0] / 2;
// nCellsSmall = (int)floor(PNM.settings.domain / cellSizeSmall);
// cellSizeSmall = PNM.settings.domain / nCellsSmall;
//
// //divide domain into "micro" cells, based on the cut-off_micro pore size
// cellSizeMicro = PNM.poreSizeDist[cut_off_micro][0] / 2;
// nCellsMicro = (int)floor(PNM.settings.domain / cellSizeMicro);
// cellSizeMicro = PNM.settings.domain / nCellsSmall;
//
// //variable for storing each "large" cell pore coords+diameter
// vector<vector<vector<double>>> cellCoords(pow(nCells, 3));
//
// //variable for storing each "small" cell pore coords+diameter
// vector<vector<vector<double>>> cellCoordsSmall(pow(nCellsSmall, 3));
//
// //variable for storing each "micro" cell pore coords+diameter
// vector<vector<vector<double>>> cellCoordsMicro(pow(nCellsMicro, 3));
//
//
// int n_generated = 0;
//
// //give seed to the random generation algorithm
// srand(PNM.settings.seed);
//
// //generate the first pore
// //variable for storing randomly generated pore coords plus its diameter before pushing into the Pores array
// vector<double> temp_pore = { ((double)rand() / RAND_MAX) * PNM.settings.domain, ((double)rand() / RAND_MAX) * PNM.settings.domain, ((double)rand() / RAND_MAX) * PNM.settings.domain };
// temp_pore.push_back(PNM.poreSizeDist[current_psd_index][0]);
// pores.push_back(temp_pore);
// PNM.network.diameter_pore.push_back(PNM.poreSizeDist[current_psd_index][0]);
//
//
// n_generated++;
// if (n_generated >= nPores[current_psd_index])
// {
// current_psd_index++;
// n_generated = 0;
// }
//
// //assign pore to a cell
// xCell = (int)floor(temp_pore[0] / cellSize);
// yCell = (int)floor(temp_pore[1] / cellSize);
// zCell = (int)floor(temp_pore[2] / cellSize);
// cellIndex = pow(nCells, 2)*xCell + nCells * yCell + zCell;
// cellCoords[cellIndex].push_back(temp_pore);
//
// //loop for generating the rest of the LARGE pores
// int flag;
// for (int i = 1; i < large_pores; i++)
// {
// //V1: assign pores to cells
// flag = 1; //flag is 1 (overlap)to enter the loop, but reset to zero(no overlap) straight after and raised in the overlap loop
// while (flag > 0)
// {
// flag = 0; //flag reset
// //take a random coordinate and calculate its location in the cell grid
// temp_pore.clear();
// double failsafe = 0.999999999;
// temp_pore = { ((double)rand() / RAND_MAX) * PNM.settings.domain * failsafe, ((double)rand() / RAND_MAX) * PNM.settings.domain * failsafe, ((double)rand() / RAND_MAX) * PNM.settings.domain * failsafe };
// temp_pore.push_back(PNM.poreSizeDist[current_psd_index][0]);
// //pore HAS TO BE this diameter, assign now
// PNM.network.diameter_pore.push_back(PNM.poreSizeDist[current_psd_index][0]);
//
// xCell = (int)floor(temp_pore[0] / cellSize);
// yCell = (int)floor(temp_pore[1] / cellSize);
// zCell = (int)floor(temp_pore[2] / cellSize);
// //cellIndex = pow(nCells, 2)*xCell + nCells * yCell + zCell;
// //cellCoords[cellIndex].push_back(temp_pore);
//
// //run search in 25 cells around the cell of interest
// int cellIndexSearch;
// double distance2;
// for (int iCell = max(0, xCell - 2); iCell < min(nCells, xCell + 3); iCell++)
// {
// for (int jCell = max(0, yCell - 2); jCell < min(nCells, yCell + 3); jCell++)
// {
// for (int kCell = max(0, zCell - 2); kCell < min(nCells, zCell + 3); kCell++)
// {
// cellIndexSearch = pow(nCells, 2)*iCell + nCells * jCell + kCell;
// for (int pore_in_cell = 0; pore_in_cell < cellCoords[cellIndexSearch].size(); pore_in_cell++)
// {
// distance2 = pow((temp_pore[0] - cellCoords[cellIndexSearch][pore_in_cell][0]), 2) + pow((temp_pore[1] - cellCoords[cellIndexSearch][pore_in_cell][1]), 2) + pow((temp_pore[2] - cellCoords[cellIndexSearch][pore_in_cell][2]), 2);
// if (distance2 <= pow(cellCoords[cellIndexSearch][pore_in_cell][3] / 2 + temp_pore[3] / 2, 2))
// {
// flag = 1;
// }
// if (flag > 0) { break; }
// }
// if (flag > 0) { break; }
// }
// if (flag > 0) { break; }
// }
// if (flag > 0) { break; }
// }
// }
//
//
// cellIndex = pow(nCells, 2)*xCell + nCells * yCell + zCell;
// cellCoords[cellIndex].push_back(temp_pore);
// pores.push_back(temp_pore);
//
// n_generated++;
// if (n_generated >= nPores[current_psd_index])
// {
// current_psd_index++;
// n_generated = 0;
// }
//
// if (i % 1000 == 0)
// {
// //cout << i << "\n";
// }
//
// }
//
// //loop for generating SMALL pores
// for (int i = large_pores; i < small_pores; i++)
// {
// //V1: assign pores to cells
// flag = 1; //flag is 1 (overlap)to enter the loop, but reset to zero(no overlap) straight after and raised in the overlap loop
// while (flag > 0)
// {
// flag = 0; //flag reset
// //take a random coordinate and calculate its location in the cell grid
// temp_pore.clear();
// double failsafe = 0.999999999;
// temp_pore = { ((double)rand() / RAND_MAX) * PNM.settings.domain * failsafe, ((double)rand() / RAND_MAX) * PNM.settings.domain * failsafe, ((double)rand() / RAND_MAX) * PNM.settings.domain * failsafe };
// temp_pore.push_back(PNM.poreSizeDist[current_psd_index][0]);
// //pore HAS TO BE this diameter, assign now
// PNM.network.diameter_pore.push_back(PNM.poreSizeDist[current_psd_index][0]);
//
// //TEST LARGE GRID FIRST
// xCell = (int)floor(temp_pore[0] / cellSize);
// yCell = (int)floor(temp_pore[1] / cellSize);
// zCell = (int)floor(temp_pore[2] / cellSize);
// //cellIndex = pow(nCells, 2)*xCell + nCells * yCell + zCell;
// //cellCoords[cellIndex].push_back(temp_pore);
//
// //run search in 25 cells around the cell of interest
// int cellIndexSearch;
// double distance2;
// for (int iCell = max(0, xCell - 2); iCell < min(nCells, xCell + 3); iCell++)
// {
// for (int jCell = max(0, yCell - 2); jCell < min(nCells, yCell + 3); jCell++)
// {
// for (int kCell = max(0, zCell - 2); kCell < min(nCells, zCell + 3); kCell++)
// {
// cellIndexSearch = pow(nCells, 2)*iCell + nCells * jCell + kCell;
// for (int pore_in_cell = 0; pore_in_cell < cellCoords[cellIndexSearch].size(); pore_in_cell++)
// {
// distance2 = pow((temp_pore[0] - cellCoords[cellIndexSearch][pore_in_cell][0]), 2) + pow((temp_pore[1] - cellCoords[cellIndexSearch][pore_in_cell][1]), 2) + pow((temp_pore[2] - cellCoords[cellIndexSearch][pore_in_cell][2]), 2);
// if (distance2 <= pow(cellCoords[cellIndexSearch][pore_in_cell][3] / 2 + temp_pore[3] / 2, 2))
// {
// flag = 1;
// }
// if (flag > 0) { break; }
// }
// if (flag > 0) { break; }
// }
// if (flag > 0) { break; }
// }
// if (flag > 0) { break; }
// }
// //if fist check exits with flag > 0, it will exit instantly in the next loop, loss of efficiency is minimal
//
// //TEST SMALL GRID
// xCellSmall = (int)floor(temp_pore[0] / cellSizeSmall);
// yCellSmall = (int)floor(temp_pore[1] / cellSizeSmall);
// zCellSmall = (int)floor(temp_pore[2] / cellSizeSmall);
// //cellIndex = pow(nCells, 2)*xCell + nCells * yCell + zCell;
// //cellCoords[cellIndex].push_back(temp_pore);
//
// //run search in 25 cells around the cell of interest
// /*int cellIndexSearch;
// double distance2;*/
// for (int iCell = max(0, xCellSmall - 2); iCell < min(nCellsSmall, xCellSmall + 3); iCell++)
// {
// for (int jCell = max(0, yCellSmall - 2); jCell < min(nCellsSmall, yCellSmall + 3); jCell++)
// {
// for (int kCell = max(0, zCellSmall - 2); kCell < min(nCellsSmall, zCellSmall + 3); kCell++)
// {
// cellIndexSearch = pow(nCellsSmall, 2)*iCell + nCellsSmall * jCell + kCell;
// for (int pore_in_cell = 0; pore_in_cell < cellCoordsSmall[cellIndexSearch].size(); pore_in_cell++)
// {
// distance2 = pow((temp_pore[0] - cellCoordsSmall[cellIndexSearch][pore_in_cell][0]), 2) + pow((temp_pore[1] - cellCoordsSmall[cellIndexSearch][pore_in_cell][1]), 2) + pow((temp_pore[2] - cellCoordsSmall[cellIndexSearch][pore_in_cell][2]), 2);
// if (distance2 <= pow(cellCoordsSmall[cellIndexSearch][pore_in_cell][3] / 2 + temp_pore[3] / 2, 2))
// {
// flag = 1;
// }
// if (flag > 0) { break; }
// }
// if (flag > 0) { break; }
// }
// if (flag > 0) { break; }
// }
// if (flag > 0) { break; }
// }
// }
//
// //push back generated pore into the small grid storage
// cellIndexSmall = pow(nCellsSmall, 2)*xCellSmall + nCellsSmall * yCellSmall + zCellSmall;
// cellCoordsSmall[cellIndexSmall].push_back(temp_pore);
// pores.push_back(temp_pore);
//
// n_generated++;
// if (n_generated >= nPores[current_psd_index])
// {
// current_psd_index++;
// n_generated = 0;
// }
//
// if (i % 1000 == 0)
// {
// //cout << i << "\n";
// }
//
// }
//
// //loop for generating MICRO pores
// for (int i = small_pores; i < total_pn; i++)
// {
// //V1: assign pores to cells
// flag = 1; //flag is 1 (overlap)to enter the loop, but reset to zero(no overlap) straight after and raised in the overlap loop
// while (flag > 0)
// {
// flag = 0; //flag reset
// //take a random coordinate and calculate its location in the cell grid
// temp_pore.clear();
// double failsafe = 0.999999999;
// temp_pore = { ((double)rand() / RAND_MAX) * PNM.settings.domain * failsafe, ((double)rand() / RAND_MAX) * PNM.settings.domain * failsafe, ((double)rand() / RAND_MAX) * PNM.settings.domain * failsafe };
// temp_pore.push_back(PNM.poreSizeDist[current_psd_index][0]);
// //pore HAS TO BE this diameter, assign now
// PNM.network.diameter_pore.push_back(PNM.poreSizeDist[current_psd_index][0]);
//
// //TEST LARGE GRID FIRST
// xCell = (int)floor(temp_pore[0] / cellSize);
// yCell = (int)floor(temp_pore[1] / cellSize);
// zCell = (int)floor(temp_pore[2] / cellSize);
// //cellIndex = pow(nCells, 2)*xCell + nCells * yCell + zCell;
// //cellCoords[cellIndex].push_back(temp_pore);
//
// //run search in 25 cells around the cell of interest
// int cellIndexSearch;
// double distance2;
// for (int iCell = max(0, xCell - 2); iCell < min(nCells, xCell + 3); iCell++)
// {
// for (int jCell = max(0, yCell - 2); jCell < min(nCells, yCell + 3); jCell++)
// {
// for (int kCell = max(0, zCell - 2); kCell < min(nCells, zCell + 3); kCell++)
// {
// cellIndexSearch = pow(nCells, 2)*iCell + nCells * jCell + kCell;
// for (int pore_in_cell = 0; pore_in_cell < cellCoords[cellIndexSearch].size(); pore_in_cell++)
// {
// distance2 = pow((temp_pore[0] - cellCoords[cellIndexSearch][pore_in_cell][0]), 2) + pow((temp_pore[1] - cellCoords[cellIndexSearch][pore_in_cell][1]), 2) + pow((temp_pore[2] - cellCoords[cellIndexSearch][pore_in_cell][2]), 2);
// if (distance2 <= pow(cellCoords[cellIndexSearch][pore_in_cell][3] / 2 + temp_pore[3] / 2, 2))
// {
// flag = 1;
// }
// if (flag > 0) { break; }
// }
// if (flag > 0) { break; }
// }
// if (flag > 0) { break; }
// }
// if (flag > 0) { break; }
// }
// //if fist check exits with flag > 0, it will exit instantly in the next loop, loss of efficiency is minimal
//
// //TEST SMALL GRID
// xCellSmall = (int)floor(temp_pore[0] / cellSizeSmall);
// yCellSmall = (int)floor(temp_pore[1] / cellSizeSmall);
// zCellSmall = (int)floor(temp_pore[2] / cellSizeSmall);
// //cellIndex = pow(nCells, 2)*xCell + nCells * yCell + zCell;
// //cellCoords[cellIndex].push_back(temp_pore);
//
// //run search in 25 cells around the cell of interest
// /*int cellIndexSearch;
// double distance2;*/
// for (int iCell = max(0, xCellSmall - 2); iCell < min(nCellsSmall, xCellSmall + 3); iCell++)
// {
// for (int jCell = max(0, yCellSmall - 2); jCell < min(nCellsSmall, yCellSmall + 3); jCell++)
// {
// for (int kCell = max(0, zCellSmall - 2); kCell < min(nCellsSmall, zCellSmall + 3); kCell++)
// {
// cellIndexSearch = pow(nCellsSmall, 2)*iCell + nCellsSmall * jCell + kCell;
// for (int pore_in_cell = 0; pore_in_cell < cellCoordsSmall[cellIndexSearch].size(); pore_in_cell++)
// {
// distance2 = pow((temp_pore[0] - cellCoordsSmall[cellIndexSearch][pore_in_cell][0]), 2) + pow((temp_pore[1] - cellCoordsSmall[cellIndexSearch][pore_in_cell][1]), 2) + pow((temp_pore[2] - cellCoordsSmall[cellIndexSearch][pore_in_cell][2]), 2);
// if (distance2 <= pow(cellCoordsSmall[cellIndexSearch][pore_in_cell][3] / 2 + temp_pore[3] / 2, 2))
// {
// flag = 1;
// }
// if (flag > 0) { break; }
// }
// if (flag > 0) { break; }
// }
// if (flag > 0) { break; }
// }
// if (flag > 0) { break; }
// }
//
// //TEST MICRO GRID
// xCellMicro = (int)floor(temp_pore[0] / cellSizeMicro);
// yCellMicro = (int)floor(temp_pore[1] / cellSizeMicro);
// zCellMicro = (int)floor(temp_pore[2] / cellSizeMicro);
// //cellIndex = pow(nCells, 2)*xCell + nCells * yCell + zCell;
// //cellCoords[cellIndex].push_back(temp_pore);
//
// //run search in 25 cells around the cell of interest
// /*int cellIndexSearch;
// double distance2;*/
// for (int iCell = max(0, xCellMicro - 2); iCell < min(nCellsMicro, xCellMicro + 3); iCell++)
// {
// for (int jCell = max(0, yCellMicro - 2); jCell < min(nCellsMicro, yCellMicro + 3); jCell++)
// {
// for (int kCell = max(0, zCellMicro - 2); kCell < min(nCellsMicro, zCellMicro + 3); kCell++)
// {
// cellIndexSearch = pow(nCellsMicro, 2)*iCell + nCellsMicro * jCell + kCell;
// for (int pore_in_cell = 0; pore_in_cell < cellCoordsMicro[cellIndexSearch].size(); pore_in_cell++)
// {
// distance2 = pow((temp_pore[0] - cellCoordsMicro[cellIndexSearch][pore_in_cell][0]), 2) + pow((temp_pore[1] - cellCoordsMicro[cellIndexSearch][pore_in_cell][1]), 2) + pow((temp_pore[2] - cellCoordsMicro[cellIndexSearch][pore_in_cell][2]), 2);
// if (distance2 <= pow(cellCoordsMicro[cellIndexSearch][pore_in_cell][3] / 2 + temp_pore[3] / 2, 2))
// {
// flag = 1;
// }
// if (flag > 0) { break; }
// }
// if (flag > 0) { break; }
// }
// if (flag > 0) { break; }
// }
// if (flag > 0) { break; }
// }
// }
//
// //push back generated pore into the small grid storage
// cellIndexMicro = pow(nCellsMicro, 2)*xCellMicro + nCellsMicro * yCellMicro + zCellMicro;
// cellCoordsMicro[cellIndexMicro].push_back(temp_pore);
// pores.push_back(temp_pore);
//
// n_generated++;
// if (n_generated >= nPores[current_psd_index])
// {
// current_psd_index++;
// n_generated = 0;
// }
//
// if (i % 1000 == 0)
// {
// //cout << i << "\n";
// }
//
// }
//
// cout << "Number of pores generated: " << pores.size() << endl;
// PNM.network.pores = pores;
//
// return PNM;
//}
//
//classPNM classPNM::throatsGeneration(classPNM PNM, classUtils utils)
//{
// chrono::steady_clock::time_point begin = chrono::steady_clock::now();
//
// PNM.network.throats.clear();
// PNM.network.diameter_throat.clear();
//
// //vector of throat connectivities {start pore index; end pore index; throat diameter}
// vector<vector<double>> throats;
//
// double running_z = 0;
// int n_nearest = 10; //randomly connect to Z/2 out of nearest N pores, to provide some variability
// srand(PNM.settings.seed);
//
// //converting string into double PSD
// vector<double> temp;
// PNM.poreSizeDist.clear();
// for (int i = 0; i < PNM.poreSizeDist_raw.size(); i++)
// {
// temp.clear();
// for (int j = 0; j < PNM.poreSizeDist_raw[i].size(); j++)
// {
// if (j == 0) { temp.push_back(stod(PNM.poreSizeDist_raw[i][j])*1e-9); }
// else { temp.push_back(stod(PNM.poreSizeDist_raw[i][j])); }
// }
// PNM.poreSizeDist.push_back(temp);
// }
//
// //calculate number of pores per each poe size with given domain
// vector<int> nPores = PNM.poresPsize(PNM);
//
// //variable definition
// int total_pn, current_psd_index;
// double expected_porosity;
//
// total_pn = 0;
// //calculate total pore number
// for (int i = 0; i < nPores.size(); i++)
// {
// if (!(nPores[i] < 1))
// {
// total_pn += nPores[i];
// }
// }
//
// //define which pore size we are starting generation from
// current_psd_index = 0;
// while (nPores[current_psd_index] < 1)
// {
// current_psd_index++;
// }
//
// //define how many pores we want to generate as a "large" grid:
// double fraction = 0.0;
// int cut_off = current_psd_index; //everything up to but NOT including THIS entry into PSD to be generated as "large" grid
// int large_pores = 0; //number of large pores to be generated
// while (fraction < 0.001)
// {
// fraction += (double)nPores[cut_off] / total_pn;
// large_pores += nPores[cut_off];
// cut_off++;
//
// };
// cout << "Cut-off: " << cut_off << endl;
//
//
// //assign large pores into cells:
// //divide donain into cells, just larger than biggest pore radius
// double cellSize = PNM.network.pores[0][3] / 2;
// int nCells = (int)floor(PNM.settings.domain / cellSize);
// cellSize = PNM.settings.domain / nCells;
//
// vector<vector<int>> cellCoords(pow(nCells, 3));
// int xCell, yCell, zCell, cellIndex;
// for (int i = 0; i < large_pores; i++)
// {
// xCell = (int)floor(PNM.network.pores[i][0] / cellSize);
// yCell = (int)floor(PNM.network.pores[i][1] / cellSize);
// zCell = (int)floor(PNM.network.pores[i][2] / cellSize);
// cellIndex = pow(nCells, 2)*xCell + nCells * yCell + zCell;
// cellCoords[cellIndex].push_back(i);
// }