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First design of MD capability in Magpie (idaholab#367)
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Sebastian Schunert committed Jan 31, 2019
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14 changes: 14 additions & 0 deletions doc/content/source/auxkernels/MDNParticleAux.md
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# MDNParticleAux

!syntax description /AuxKernels/MDNParticleAux

Injects the number of MD particles per element computed by
MD runner object into an auxiliary variable.

!syntax parameters /AuxKernels/MDNParticleAux

!syntax inputs /AuxKernels/MDNParticleAux

!syntax children /AuxKernels/MDNParticleAux

!bibtex bibliography
21 changes: 21 additions & 0 deletions doc/content/source/userobjects/LAMMPSFileRunner.md
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# LAMMPSFileRunner

`LAMMPSFileRunner` reads in LAMMPS dumps file and maps them on an FEM mesh.
The `time_sequence` parameter determines if a sequence of LAMMPS files is read
or a single file is loaded and used throughout. If a sequence of files is used,
the `lammps_file` parameter should contain the file base, e.g. `path/to/file/filebase`
if the files are called `path/to/file/filebase.<time>.xyz`.

Time conversion from FEM time to LAMMPS time is facilitated by the `time_conversion`
parameter that accepts a MOOSE function object. Denoting FEM time by `t` and LAMMPS time
by `T`, `time_conversion` is a function `T = F(t)`.

!syntax description /UserObjects/LAMMPSFileRunner

!syntax parameters /UserObjects/LAMMPSFileRunner

!syntax inputs /UserObjects/LAMMPSFileRunner

!syntax children /UserObjects/LAMMPSFileRunner

!bibtex bibliography
33 changes: 33 additions & 0 deletions include/auxkernels/MDNParticleAux.h
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/**********************************************************************/
/* DO NOT MODIFY THIS HEADER */
/* MAGPIE - Mesoscale Atomistic Glue Program for Integrated Execution */
/* */
/* Copyright 2017 Battelle Energy Alliance, LLC */
/* ALL RIGHTS RESERVED */
/**********************************************************************/

#ifndef MDNPARTICLEAUX_H
#define MDNPARTICLEAUX_H

#include "AuxKernel.h"

// forward declarations
class MDRunBase;
class MDNParticleAux;

template <>
InputParameters validParams<MDNParticleAux>();

class MDNParticleAux : public AuxKernel
{
public:
MDNParticleAux(const InputParameters & params);
virtual ~MDNParticleAux() {}

virtual Real computeValue();

protected:
const MDRunBase & _md_uo;
};

#endif // MDNPARTICLEAUX_H
61 changes: 61 additions & 0 deletions include/userobjects/LAMMPSFileRunner.h
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/**********************************************************************/
/* DO NOT MODIFY THIS HEADER */
/* MAGPIE - Mesoscale Atomistic Glue Program for Integrated Execution */
/* */
/* Copyright 2017 Battelle Energy Alliance, LLC */
/* ALL RIGHTS RESERVED */
/**********************************************************************/

#ifndef LAMMPSFILERUNNER_H
#define LAMMPSFILERUNNER_H

#include "MDRunBase.h"

class LAMMPSFileRunner;

template <>
InputParameters validParams<LAMMPSFileRunner>();

/**
* Reads lammps dump files to emulate MD simulation
*/
class LAMMPSFileRunner : public MDRunBase
{
public:
LAMMPSFileRunner(const InputParameters & parameters);

virtual void initialize() override {}
virtual void execute() override {}
virtual void finalize() override {}
virtual void initialSetup() override;

virtual void updateParticleList() override;

protected:
/// reads a LAMMPS file
void readLAMMPSFile(FileName filename);

/// reads two LAMMPS files and interpolates times
void readLAMMPSFileHistory(std::pair<FileName, FileName> filenames,
std::pair<Real, Real> timestamps,
Real current_time);

/// helper function that finds two files, one right before and one right after md_time
void findBracketingLAMMPSFiles(Real md_time,
std::pair<std::string, std::string> & filenames,
std::pair<Real, Real> & timestamps);

/// whether a sequence of input files or a single input file is read
bool _time_sequence;

/// name of LAMMPS file or file base if _time_sequence == true
FileName _lammps_file;

/// column of x, y, z coordinate in LAMMPS files
std::vector<unsigned int> _pos_columns;

/// Conversion from FEM time to MD time_stamp
Function * _time_conversion;
};

#endif // LAMMPSFILERUNNER_H
96 changes: 96 additions & 0 deletions include/userobjects/MDRunBase.h
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/**********************************************************************/
/* DO NOT MODIFY THIS HEADER */
/* MAGPIE - Mesoscale Atomistic Glue Program for Integrated Execution */
/* */
/* Copyright 2017 Battelle Energy Alliance, LLC */
/* ALL RIGHTS RESERVED */
/**********************************************************************/

#ifndef MDRUNBASE_H
#define MDRUNBASE_H

#include "GeneralUserObject.h"
#include "KDTree.h"
#include "libmesh/bounding_box.h"

class MDRunBase;
class MooseMesh;

template <>
InputParameters validParams<MDRunBase>();

/**
* Base class for molecular dynamics runs in Magpie
*/
class MDRunBase : public GeneralUserObject
{
public:
MDRunBase(const InputParameters & parameters);

void initialSetup() override;
void timestepSetup() override;

class MDParticles
{
public:
/// particle's position
std::vector<Point> pos;

/// particle's velocity
std::vector<Point> vel;

/// the id of particle in the MD calculation
std::vector<unsigned int> id;

/// the mesh element the particles are in
std::vector<unique_id_type> elem_id;
};

/// access to the MDParticles
const MDParticles & particles() const { return _md_particles; }

/// access to the element to particle map
const std::vector<unsigned int> elemParticles(unique_id_type elem_id) const;

/// List of quantities to get from MD simulation
MultiMooseEnum getMDQuantities() const;

protected:
/// call back function to update the particle list
virtual void updateParticleList() = 0;

/// updates the KDTree object
void updateKDTree();

/// map MDParticles to elements
void mapMDParticles();

/// The Mesh we're using
MooseMesh & _mesh;

/// dimension of the mesh
const unsigned int _dim;

/// dimension of the mesh
const unsigned int _nproc;

/// stores bounding boxes of all other processors
std::vector<BoundingBox> _bbox;

/// total number of particles
unsigned int _n_particles;

/// number of local particles
unsigned int _n_local_particles;

/// stores the location of
MDParticles _md_particles;

/// a map from elem pointer to particles in this element
std::map<unique_id_type, std::vector<unsigned int>> _elem_particles;

/// A KDTree object to handle md_particles
std::unique_ptr<KDTree> _kd_tree;
};

#endif // MDRUNBASE_H
34 changes: 34 additions & 0 deletions src/auxkernels/MDNParticleAux.C
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/**********************************************************************/
/* DO NOT MODIFY THIS HEADER */
/* MAGPIE - Mesoscale Atomistic Glue Program for Integrated Execution */
/* */
/* Copyright 2017 Battelle Energy Alliance, LLC */
/* ALL RIGHTS RESERVED */
/**********************************************************************/

#include "MDNParticleAux.h"
#include "MDRunBase.h"

registerMooseObject("MagpieApp", MDNParticleAux);

template <>
InputParameters
validParams<MDNParticleAux>()
{
InputParameters params = validParams<AuxKernel>();
params.addRequiredParam<UserObjectName>("user_object", "Name of MD runner UserObject");
params.addClassDescription("Injects the number of MD particles from MDRunBase object user_object "
"into auxiliary variable.");
return params;
}

MDNParticleAux::MDNParticleAux(const InputParameters & parameters)
: AuxKernel(parameters), _md_uo(getUserObject<MDRunBase>("user_object"))
{
}

Real
MDNParticleAux::computeValue()
{
return _md_uo.elemParticles(_current_elem->unique_id()).size();
}
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