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domain_md1d.hh
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/**
* @file domain_md1d.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Srinivasa Babu Ramisetti <srinivasa.ramisetti@epfl.ch>
*
* @date Fri Jan 10 20:47:45 2014
*
* @brief This is the domain for 1d atomic chains
*
* @section LICENSE
*
* Copyright INRIA and CEA
*
* The LibMultiScale is a C++ parallel framework for the multiscale
* coupling methods dedicated to material simulations. This framework
* provides an API which makes it possible to program coupled simulations
* and integration of already existing codes.
*
* This Project was initiated in a collaboration between INRIA Futurs Bordeaux
* within ScAlApplix team and CEA/DPTA Ile de France.
* The project is now continued at the Ecole Polytechnique Fédérale de Lausanne
* within the LSMS/ENAC laboratory.
*
* This software is governed by the CeCILL-C license under French law and
* abiding by the rules of distribution of free software. You can use,
* modify and/ or redistribute the software under the terms of the CeCILL-C
* license as circulated by CEA, CNRS and INRIA at the following URL
* "http://www.cecill.info".
*
* As a counterpart to the access to the source code and rights to copy,
* modify and redistribute granted by the license, users are provided only
* with a limited warranty and the software's author, the holder of the
* economic rights, and the successive licensors have only limited
* liability.
*
* In this respect, the user's attention is drawn to the risks associated
* with loading, using, modifying and/or developing or reproducing the
* software by the user in light of its specific status of free software,
* that may mean that it is complicated to manipulate, and that also
* therefore means that it is reserved for developers and experienced
* professionals having in-depth computer knowledge. Users are therefore
* encouraged to load and test the software's suitability as regards their
* requirements in conditions enabling the security of their systems and/or
* data to be ensured and, more generally, to use and operate it in the
* same conditions as regards security.
*
* The fact that you are presently reading this means that you have had
* knowledge of the CeCILL-C license and that you accept its terms.
*
*/
#ifndef __LIBMULTISCALE_DOMAIN_MD1D_HH__
#define __LIBMULTISCALE_DOMAIN_MD1D_HH__
/* -------------------------------------------------------------------------- */
#include "container_md1d.hh"
#include "domain_md.hh"
/* -------------------------------------------------------------------------- */
__BEGIN_LIBMULTISCALE__
/**
* Class DomainAtomic
* domaine atomique
*/
class DomainMD1D : public DomainAtomic<ContainerMD1D, 1> {
public:
using RefDof = RefMD1D;
using ContainerDofs = ContainerMD1D;
using IteratorDofs = ContainerMD1D::iterator;
DomainMD1D(const LMID &ID, CommGroup &group);
~DomainMD1D();
ArrayView getField(FieldType field_type) override;
void updateGradient() override;
void updateAcceleration() override;
ArrayView acceleration() override;
ArrayView gradient() override;
ArrayView primal() override;
ArrayView primalTimeDerivative() override;
ArrayView mass() override;
void init() override;
void declareParams() override;
Cube getDomainBoundingBox() const override;
Cube getSubDomainBoundingBox() const override { LM_TOIMPLEMENT; };
void setDomainBoundingBox(const Cube &) override { LM_TOIMPLEMENT; };
void setSubDomainBoundingBox(const Cube &) override { LM_TOIMPLEMENT; };
Real potentialEnergy() override { LM_TOIMPLEMENT; };
void enforceCompatibility() override;
bool isPeriodic(UInt dir) override;
protected:
//! get the elastic stiffness constant
Real getElasticConstant();
//! get R0
Real getR0();
int getNbDofs();
void p1();
void p3();
//! compute linear force (quadratic potential)
void linearForceComputation();
inline Real computeDistance(const Real &xi, const Real &xj);
void correctPBCPositions();
UInt getDim();
void getNeighborList(RefAtom &atom, UInt count,
std::vector<RefAtom> &neigbhor_list);
void setPeriodicFlag(bool flag);
void setReferenceManagerState(bool state);
Real getEcin() { LM_TOIMPLEMENT; };
Real getDomainSize();
void computeNeighborLists();
Real ljForce(Real rij);
Real ljBondEnergy(Real rij);
private:
//! the neighbor list
std::vector<std::vector<UInt>> neighbor_lists;
//! array for constraints
// std::vector<Real> stress;
//! interatomic distance
Quantity<Length> r0;
//! cutoff radius
Quantity<Length> rcut;
//! epsilon parameter for lennard jones
Quantity<Energy> epsilon;
//! sigma parameter for lennard jones
Quantity<Length> sigma;
//! equivalent stiffness
Real stiffness_parameter;
//! flag to activate periodic boundary conditions
bool periodic_flag;
/* ------------------------------------------------------------------------ */
// old material members
/* --------------------------------------------------------------------------
*/
//! per atom mass
Quantity<Mass> atomic_mass;
//! flag to activate elasticity (linearize LJ)
bool elastic_flag;
//! if a shift is requested for the entire set of atoms
Quantity<Length> shift;
//! the file to read the atomic points from
std::string atom_file;
};
/* -------------------------------------------------------------------------- */
__END_LIBMULTISCALE__
/* -------------------------------------------------------------------------- */
#endif /* __LIBMULTISCALE_DOMAIN_MD1D_HH__ */

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