Hessian.h

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/*
** This file is part of eOn.
**
** SPDX-License-Identifier: BSD-3-Clause
**
** Copyright (c) 2010--present, eOn Development Team
** All rights reserved.
**
** Repo:
** https://github.com/TheochemUI/eOn
*/
#pragma once
#include "Eigen.h"
#include "EonLogger.h"
 
#include "FiniteDifference.h"
#include "Matter.h"
#include "Parameters.h"
 
#include <vector>
 
namespace eonc {

bool trivialModeCountIsPhysical(long removed, long fixedAtoms);

inline constexpr double kEvToWavenumber = 8065.543937349212;

std::vector<double> cartesianMode(const Matter &matter, const VectorXi &atoms,
                                  const Eigen::Ref<const VectorXd> &mode);

bool writeNormalModes(Matter &matter, const VectorXi &atoms,
                      const VectorXd &eigenvalues, const MatrixXd &modes,
                      const std::string &path);
 
class Hessian {
public:
  Hessian(const Parameters &params, Matter *matter);
  ~Hessian() = default;
 
  MatrixXd getHessian(Matter *matterIn, const VectorXi &atomsIn);
  VectorXd getFreqs(Matter *matterIn, const VectorXi &atomsIn);
  VectorXd removeZeroFreqs(const VectorXd &freqs);
  [[nodiscard]] const MatrixXd &getModes() const noexcept { return modes; }
  void writeHessianFile(bool on) noexcept { writeFile = on; }
 
private:
  Matter *matter;
  const Parameters &parameters;
 
  MatrixXd hessian;
  VectorXd freqs;
  MatrixXd modes;
  bool writeFile = true;
 
  VectorXi atoms;
  bool calculate();
  bool finalizeHessian(int size);
  bool calculateColored(double cutoff, double dr, FdScheme scheme);
  bool calculateSerial(double dr, FdScheme scheme);
  bool calculateBatched(double dr, FdScheme scheme);
  eonc::log::Scoped log;
};

std::vector<int>
greedyColorCutoffGraph(const std::vector<std::vector<int>> &adj);

std::vector<int> colorMobileCutoffGraph(const Matter &matter,
                                        const VectorXi &atoms, double cutoff);
 
} // namespace eonc