MobileAtoms.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 "Matter.h"
 
#include <string>
 
namespace eonc {

VectorXi freeAtomIndices(const Matter *matter);

bool atomListMeansAll(const std::string &atomList);

VectorXi resolveMobileAtoms(const Matter *matter, const std::string &atomList);

VectorXi resolveMobileAtoms(const Matter *matter, const VectorXi &candidates);

VectorXd packMobileRows(const AtomMatrix &full, const VectorXi &mobile);

void unpackMobileRows(const VectorXd &packed, const VectorXi &mobile,
                      AtomMatrix &full);

VectorXd mobileForces(Matter *matter, const VectorXi &mobile);
 
} // namespace eonc