/*
* 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.
*
*/
#include "votca/xtp/atom.h"
#include <votca/tools/elements.h>
namespace votca {
namespace xtp {
Atom::Atom(Index resnr, std::string md_atom_name, Index atom_id,
Eigen::Vector3d pos, std::string type)
: _id(atom_id), _name(md_atom_name), _resnr(resnr), _pos(pos) {
std::string elename = GetElementFromString(md_atom_name);
std::string eletype = GetElementFromString(type);
tools::Elements ele;
bool found_element_name = true;
bool found_element_type = true;
try {
ele.getMass(elename);
} catch (std::runtime_error&) {
found_element_name = false;
}
try {
ele.getMass(eletype);
} catch (std::runtime_error&) {
found_element_type = false;
}
if (found_element_name && found_element_type) {
if (elename != eletype) {
throw std::runtime_error("Elements " + elename + " and" + eletype +
" from atom name: " + md_atom_name +
" and atom type:" + type + " do not match.");
}
_element = elename;
} else if (found_element_name) {
_element = elename;
} else if (found_element_type) {
_element = elename;
} else {
throw std::runtime_error("Could not get Element from atom name:" +
md_atom_name + " or atom type:" + type);
}
}
Atom::Atom(Index atom_id, std::string element, Eigen::Vector3d pos)
: Atom(-1, element, atom_id, pos, element) {}
std::string Atom::GetElementFromString(const std::string& MDName) {
std::string element = MDName.substr(0, 1);
if (MDName.size() > 1) {
if (std::islower(MDName[1])) {
element += MDName[1];
}
}
return element;
}
void Atom::Rotate(const Eigen::Matrix3d& R, const Eigen::Vector3d& refPos) {
Eigen::Vector3d dir = _pos - refPos;
dir = R * dir;
_pos = refPos + dir; // Rotated Position
}
void Atom::SetupCptTable(CptTable& table) const {
table.addCol(_id, "index", HOFFSET(data, id));
table.addCol(_element, "element", HOFFSET(data, element));
table.addCol(_name, "name", HOFFSET(data, name));
table.addCol(_pos[0], "pos.x", HOFFSET(data, x));
table.addCol(_pos[1], "pos.y", HOFFSET(data, y));
table.addCol(_pos[2], "pos.z", HOFFSET(data, z));
table.addCol(_resnr, "resnr", HOFFSET(data, resnr));
}
void Atom::WriteData(data& d) const {
d.id = _id;
d.element = const_cast<char*>(_element.c_str());
d.name = const_cast<char*>(_name.c_str());
d.x = _pos[0];
d.y = _pos[1];
d.z = _pos[2];
d.resnr = _resnr;
}
void Atom::ReadData(const data& d) {
_id = d.id;
_element = std::string(d.element);
free(d.element);
_name = std::string(d.name);
free(d.name);
_pos[0] = d.x;
_pos[2] = d.z;
_pos[1] = d.y;
_resnr = d.resnr;
}
} // namespace xtp
} // namespace votca