/*
* Copyright 2009-2019 The VOTCA Development Team
* (http://www.votca.org)
*
* Licensed under the Apache License, Version 2.0 (the "License")
*
* You may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*/
/// For earlier commit history see ctp commit
/// 77795ea591b29e664153f9404c8655ba28dc14e9
#pragma once
#ifndef VOTCA_XTP_ATOM_H
#define VOTCA_XTP_ATOM_H
#include <exception>
#include <map>
#include <string>
#include <votca/xtp/checkpointreader.h>
#include <votca/xtp/checkpointwriter.h>
namespace votca {
namespace xtp {
class Atom {
public:
struct data {
Index id;
char* element;
char* name;
double x;
double y;
double z;
Index resnr;
};
Atom(Index resnr, std::string md_atom_name, Index atom_id,
Eigen::Vector3d pos, std::string element);
Atom(Index atom_id, std::string element, Eigen::Vector3d pos);
Atom(data& d) { ReadData(d); }
static std::string GetElementFromString(const std::string& MDName);
Index getId() const { return _id; }
const std::string& getName() const { return _name; }
std::string getElement() const { return _element; }
Index getResnr() const { return _resnr; }
void setResnr(Index resnr) { _resnr = resnr; }
void Translate(const Eigen::Vector3d& shift) { _pos = _pos + shift; }
void Rotate(const Eigen::Matrix3d& R, const Eigen::Vector3d& refPos);
const Eigen::Vector3d& getPos() const { return _pos; }
void setPos(const Eigen::Vector3d& r) { _pos = r; }
std::string identify() const { return "atom"; }
friend std::ostream& operator<<(std::ostream& out, const Atom& atom) {
out << atom.getId() << " " << atom.getName() << " " << atom.getElement()
<< " " << atom.getResnr();
out << " " << atom.getPos().x() << "," << atom.getPos().y() << ","
<< atom.getPos().z() << "\n";
return out;
}
void SetupCptTable(CptTable& table) const;
void WriteData(data& d) const;
void ReadData(const data& d);
private:
Index _id = -1;
std::string _name = "";
std::string _element = "";
Index _resnr = -1;
Eigen::Vector3d _pos = Eigen::Vector3d::Zero();
};
} // namespace xtp
} // namespace votca
#endif // VOTCA_XTP_ATOM_H