EpiCenters.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 "Matter.h"
#include <vector>
 
namespace eonc {
 
namespace EpiCenters {
 
const char DISP_LOAD[] = "load";
const char DISP_NOT_FCC_OR_HCP[] = "not_fcc_hcp_coordinated";
const char DISP_MIN_COORDINATED[] = "least_coordinated";
const char DISP_LAST_ATOM[] = "last_atom";
const char DISP_RANDOM[] = "random";
const char DISP_LISTED_ATOMS[] = "listed_atoms";
 
// index of random atom that is free and neither FCC nor HCP coordinated
long cnaEpiCenter(const Matter *matter, double neighborCutoff);
 
// index of a random atom that is free and minimally coordinated
long minCoordinatedEpiCenter(const Matter *matter, double neighborCutoff);
 
// index of last atom -- assumed to be free
long lastAtom(const Matter *matter);
 
// index of a random atom that is free
long randomFreeAtomEpiCenter(const Matter *matter);
 
// index of a random free atom from a user-provided list
long listedAtomEpiCenter(const Matter *matter,
                         const std::vector<long> &atomList);
 
// do a common neighbor analysis
void cna(long *cna, const Matter *matter, double neighborCutoff);
 
// determine the coordination for individual atoms
void coordination(long *coordinationVal, const Matter *matter,
                  double neighborCutoff);
 
// determine atoms with coordination <= coordinationMaxVal
void coordinationLessOrEqual(bool *result, long coordinationMaxVal,
                             const Matter *matter, double neighborCutoff);
 
// determine first minimally coordinated atom
long minCoordination(const Matter *matter, double neighborCutoff);
} // namespace EpiCenters
 
} // namespace eonc