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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> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DomainMD1D(DomainID ID, CommGroup GID);
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
typedef RefMD1D RefDof;
typedef ContainerMD1D ContainerDofs;
typedef ContainerMD1D::iterator IteratorDofs;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
void performStep1();
void performStep3();
void performStep2();
void init();
//! get the elastic stiffness constant
Real getElasticConstant();
//! get R0
Real getR0();
int getNbDofs();
virtual bool isPeriodic(UInt dir);
protected:
void performMigration(){};
void p1();
void p3();
//! compute quadratic potential force
void quadraticForceComputation();
void declareParams();
inline Real computeDistance(const Real &xi, const Real &xj);
void correctPBCPositions();
/* --------------------------------------------------------------------------
*/
// functions for AMELCG
/* --------------------------------------------------------------------------
*/
public:
//! return product of force by descent direction (for AMELCG)
Real getFdotDir() { return 0; };
//! return max of forces (for AMELCG)
Real getFMax() { return 0; };
//! return max of direction vector (for AMELCG)
Real getDirMax() { return 0; };
//! return norm 2 of forces (for AMELCG)
Real getFNorm2() { return 0; };
//! return stuff for AMELCG
Real getFdotOldF() { return 0; };
//! update direction AMELCG
void updateDirection(Real beta){};
//! return stuff for AMELCG
void saveForceVector(){};
//! displace in descent direction with given magnitude
void displaceTowardsDirection(Real alpha){};
//! get amount of work done by external forces
Real getExternalWork() { return 0; };
//! set amount of work done by external forces
void setExternalWork(Real work){};
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
UInt getDim();
void getNeighborList(RefAtom &atom, UInt count,
std::vector<RefAtom> &neigbhor_list);
void getDomainDimensions(Real *xmin, Real *xmax);
void getSubDomainDimensions(Real *xmin, Real *xmax);
//! set current step to a given value
void setCurrentStep(UInt ts);
//! get current step to a given value
UInt getCurrentStep();
//! set timestep to a given value
void setTimeStep(Real ts);
//! GetTimeStep
Real getTimeStep();
void setPeriodicFlag(bool flag);
void setReferenceManagerState(bool state);
Real getEcin();
Real getEpot();
private:
Real getDomainSize();
void computeNeighborLists();
void computeContribution(UInt i, UInt j);
/* ------------------------------------------------------------------------ */
/* Friends */
/* ------------------------------------------------------------------------ */
// friend class DomainAtomicInterface;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
//! the neighbor list
std::vector<std::vector<UInt>> neighbor_lists;
//! array to atoms
std::vector<DOF> dofs;
// timestep
Quantity<Time> timeStep;
//! array for constraints
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> 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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