seams_input.hpp

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//-----------------------------------------------------------------------------------
// d-SEAMS - Deferred Structural Elucidation Analysis for Molecular Simulations
//
// Copyright (c) 2018--present d-SEAMS core team
//
// This program is free software: you can redistribute it and/or modify
// it under the terms of the MIT License as published by
// the Open Source Initiative.
//
// A copy of the MIT License is included in the LICENSE file of this repository.
// You should have received a copy of the MIT License along with this program.
// If not, see <https://opensource.org/licenses/MIT>.
//-----------------------------------------------------------------------------------
 
#ifndef SEAMS_SEAMS_INPUT_H_
#define SEAMS_SEAMS_INPUT_H_
 
#include <cstdint>
#include <functional>
#include <iostream>
#include <memory>
#include <mol_sys.hpp>
#include <ring.hpp>
#include <string>
 
#include <filesystem>



 
namespace sinp {

std::vector<std::string> getInpFileList(std::string inputFolder);

int nLammpsFrames(const std::string &filename);

void dropLammpsDumpIndex(const std::string &filename);

void forEachLammpsFrame(
    const std::string &filename, int first, int last, int typeFilter,
    const std::function<void(
        int, molSys::PointCloud<molSys::Point<double>, double> &)> &fn,
    int nThreads = 0, int part = 0, int parts = 1);

molSys::PointCloud<molSys::Point<double>, double>
readLammpsTrj(std::string filename, int targetFrame,
              molSys::PointCloud<molSys::Point<double>, double> &yCloud,
              bool isSlice = false,
              std::array<double, 3> coordLow = std::array<double, 3>{0, 0, 0},
              std::array<double, 3> coordHigh = std::array<double, 3>{0, 0, 0});

molSys::PointCloud<molSys::Point<double>, double> readLammpsTrjO(
    std::string filename, int targetFrame,
    molSys::PointCloud<molSys::Point<double>, double> &yCloud, int typeO,
    bool isSlice = false,
    std::array<double, 3> coordLow = std::array<double, 3>{0, 0, 0},
    std::array<double, 3> coordHigh = std::array<double, 3>{0, 0, 0});

molSys::PointCloud<molSys::Point<double>, double> readLammpsTrjreduced(
    std::string filename, int targetFrame,
    molSys::PointCloud<molSys::Point<double>, double> &yCloud, int typeI,
    bool isSlice = false,
    std::array<double, 3> coordLow = std::array<double, 3>{0, 0, 0},
    std::array<double, 3> coordHigh = std::array<double, 3>{0, 0, 0});

molSys::PointCloud<molSys::Point<double>, double> readXYZ(std::string filename);

std::vector<std::vector<int>> readBonds(std::string filename);
 
#ifdef SEAMS_HAS_CHEMFILES
molSys::PointCloud<molSys::Point<double>, double>
readChemfiles(std::string filename, int targetFrame,
              molSys::PointCloud<molSys::Point<double>, double> &yCloud,
              int typeFilter = -1);
#endif
 
#ifdef SEAMS_HAS_READCON
molSys::PointCloud<molSys::Point<double>, double>
readCon(std::string filename, int targetFrame,
        molSys::PointCloud<molSys::Point<double>, double> &yCloud);
 
#ifdef SEAMS_HAS_READCON_DB
int ingestConCorpus(const std::string &corpus, std::uint64_t trajId,
                    const std::string &conPath);

molSys::PointCloud<molSys::Point<double>, double>
readConCorpus(const std::string &corpus, const std::string &symbol,
              const std::string &formula, int targetFrame,
              molSys::PointCloud<molSys::Point<double>, double> &yCloud);
#endif
#endif

inline bool atomInSlice(double x, double y, double z,
                        std::array<double, 3> coordLow,
                        std::array<double, 3> coordHigh) {
  int flag = 0; 
 
  if (((x >= coordLow[0]) && (x <= coordHigh[0])) ||
      coordLow[0] == coordHigh[0]) {
    flag++;
  }
  if (((y >= coordLow[1]) && (y <= coordHigh[1])) ||
      coordLow[1] == coordHigh[1]) {
    flag++;
  }
  if (((z >= coordLow[2]) && (z <= coordHigh[2])) ||
      coordLow[2] == coordHigh[2]) {
    flag++;
  }
 
  if (flag == 3) {
    return true;
  } else {
    return false;
  }
}
 
} // namespace sinp
 
#endif