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lammps/src/USER-ATC/fix_atc.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Reese Jones, Jon Zimmerman, Jeremy Templeton (SNL)
------------------------------------------------------------------------- */
#include "stdio.h"
#include "string.h"
#include "fix_atc.h"
#include "ATC_TransferHardy.h"
#include "ATC_TransferThermal.h"
#include "ExtrinsicModel.h"
#include "LammpsInterface.h"
#include "fix_nve.h"
#include "atom.h"
#include "force.h"
#include "update.h"
#include "respa.h"
#include "neighbor.h"
#include "neigh_request.h"
#include "pointers.h"
#include "comm.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
// main page of doxygen documentation
/*! \mainpage AtC : Atom-to-Continuum methods
fix commands:
- \ref man_fix_atc (links to all related commands)
*/
/* ------------------------------------------------------------------------- */
FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
{
// ID GROUP atc PHYSICSTYPE [PARAMETERFILE]
// can have either 4 or 5 args, only arg[3] and arg[4] are used by this class
if (narg > 5 || narg < 4) lmp->error->all(FLERR,"Illegal fix atc command");
// Set LAMMPS pointer on LammpsInterface
ATC::LammpsInterface::instance()->set_lammps(lmp);
/*! \page man_fix_atc fix atc command
\section syntax
fix AtC transfer <type> <parameter_file>
- type\n
= thermal : thermal coupling with fields: temperature \n
= two_temperature : electron-phonon coupling with field: temperature and electron_temperature \n
= hardy : Hardy on-the-fly post-processing (see "related" section for possible fields) \n
- parameter_file = name of the file with material parameters. \n
note: hardy does not require a parameter file
\section examples
<TT> fix_modify AtC transfer thermal Ar_thermal.dat </TT> \n
<TT> fix_modify AtC transfer hardy </TT>
\section description
This fix is the beginning to creating a coupled FE/MD simulation and/or
an on-the-fly estimation of continuum fields. The coupled versions of this
fix do Verlet integration and the Hardy/post-processing does not.
After instantiating this fix, several other fix_modify commands will be
needed to set up the problem, e.g. define the finite element mesh and
prescribe initial and boundary conditions.
The following coupling example is typical, but non-exhaustive:\n
<TT>
# ... commands to create and initialize the MD system \n
# initial fix to designate coupling type and group to apply it to \n
# tag group physics material_file \n
fix AtC internal atc thermal Ar_thermal.mat\n \n
# create a uniform 12 x 2 x 2 mesh that covers region contain the group \n
# nx ny nz region periodicity \n
fix_modify AtC fem create mesh 12 2 2 mdRegion f p p\n \n
# specify the control method for the type of coupling \n
# physics control_type \n
fix_modify AtC transfer thermal control flux \n \n
# specify the initial values for the empirical field "temperature" \n
# field node_group value \n
fix_modify AtC transfer initial temperature all 30.\n \n
# create an output stream for nodal fields \n
# filename output_frequency \n
fix_modify AtC transfer output atc_fe_output 100\n \n
run 1000 \n
</TT>
likewise for this post-processing example: \n
<TT>
# ... commands to create and initialize the MD system \n
# initial fix to designate post-processing and the group to apply it to \n
# no material file is allowed nor required \n
fix AtC internal atc hardy \n \n
# create a uniform 1 x 1 x 1 mesh that covers region contain the group \n
# with periodicity this effectively creats a system average \n
fix_modify AtC fem create mesh 1 1 1 box p p p \n\n
# change from default lagrangian map to eulerian \n
# refreshed every 100 steps \n
fix_modify AtC atom_element_map eulerian 100 \n \n
# start with no field defined \n
fix_modify AtC transfer fields none \n \n
# add mass density, potential energy density, stress and temperature \n
fix_modify AtC transfer fields add density energy stress temperature \n\n
# create an output stream for nodal fields \n
# filename output_frequency \n
fix_modify AtC transfer output nvtFE 100 text \n
run 1000 \n
</TT>
Note coupling and post-processing can be combined in the same simulations
using separate fixes.
\n
For detailed exposition of the theory and algorithms please see:\n
- Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA. <VAR> An
atomistic-to-continuum coupling method for heat transfer in solids. </VAR>
Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351.
- Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ,
<VAR> Calculation of stress in atomistic simulation </VAR>
Special Issue of Modelling and Simulation in Materials Science and
Engineering (2004), 12:S319
Please refer to the standard
finite element (FE) texts, e.g. T.J.R Hughes <VAR> The finite element
method </VAR>, Dover 2003, for the basics of FE simulation.
\section restrictions
Thermal and two_temperature (coupling) types use a Verlet time-integration
algorithm.
The hardy type does not contain its own time-integrator and must be used
with a separate fix that does contain one, e.g. nve, nvt, etc.
Currently,
- the coupling is restricted to thermal physics
- the FE computations are done in serial on each processor.
\section related
fix_modify commands for setup: \n
- \ref man_fem_mesh
- \ref man_mesh_nodeset
- \ref man_mesh_faceset
- \ref man_mesh_elemset
- \ref man_transfer_internal
- \ref man_transfer_boundary
- \ref man_internal_quadrature
- \ref man_time_integration
- \ref man_electron_integration
fix_modify commands for boundary and initial conditions:\n
- \ref man_initial
- \ref man_fix_nodes
- \ref man_unfix_nodes
- \ref man_fix_flux
- \ref man_unfix_flux
- \ref man_source
- \ref man_remove_source
fix_modify commands for control and filtering: \n
- \ref man_thermal_control
- \ref man_time_filter
- \ref man_filter_scale
- \ref man_equilibrium_start
- \ref man_extrinsic_exchange
fix_modify commands for output: \n
- \ref man_transfer_output
- \ref man_transfer_atomic_output
- \ref man_mesh_output
- \ref man_write_restart
- \ref man_read_restart
fix_modify commands for post-processing: \n
- \ref man_hardy_fields
- \ref man_hardy_gradients
- \ref man_hardy_rates
- \ref man_hardy_computes
- \ref man_hardy_set
- \ref man_hardy_on_the_fly
- \ref man_boundary_integral
- \ref man_contour_integral
miscellaneous fix_modify commands: \n
- \ref man_atom_element_map
- \ref man_neighbor_reset_frequency
Note: a set of example input files with the attendant material files are
included with this package
\section default
none
*/
// Construct new ATC_Transfer object
// note use "unfix" to destroy
int me = ATC::LammpsInterface::instance()->comm_rank();
string groupName(arg[1]);
// Postprocessing
try {
if (strcmp(arg[3],"hardy")==0)
{
if (narg < 5) {
if (me==0) printf("Constructing ATC transfer (hardy)\n");
atcTransfer_ = new ATC::ATC_TransferHardy(groupName);
}
else {
if (me==0) printf("Constructing ATC transfer (hardy) with parameter file %s\n",arg[4]);
std::string matParamFile = arg[4];
atcTransfer_ = new ATC::ATC_TransferHardy(groupName,matParamFile);
}
}
// PhysicsTypes
else if (strcmp(arg[3],"thermal")==0)
{
std::string matParamFile = arg[4];
if (me==0) printf("Constructing ATC transfer (thermal) with parameter file %s\n",arg[4]);
atcTransfer_ = new ATC::ATC_TransferThermal(groupName,matParamFile);
lmp->atom->add_callback(0); // NOTE what is this?
}
else if (strcmp(arg[3],"two_temperature")==0)
{
std::string matParamFile = arg[4];
if (me==0) printf("Constructing ATC transfer (two_temperature) with parameter file %s\n",arg[4]);
atcTransfer_ = new ATC::ATC_TransferThermal(groupName,matParamFile,
ATC::TWO_TEMPERATURE);
}
else
{
lmp->error->all(FLERR,"Unknown physics type in ATC");
}
}
catch (ATC::ATC_Error& atcError) {
cout << "ATC ERROR: " << atcError.get_error_description() << " processor: " << atcError.get_id() << endl;
throw;
}
lmp->atom->add_callback(0);
// Tell LAMMPS we want to write_restart to be called (writes fix state)
//restart_global = 1;
restart_global = 0; // NOTE : turning off ATC restart
// Tell LAMMPS we want to pack_restart to be called (writes per-atom data)
//restart_peratom = 1;
// Set output computation data based on transfer info
scalar_flag = atcTransfer_->scalar_flag();
vector_flag = atcTransfer_->vector_flag();
size_vector = atcTransfer_->size_vector();
global_freq = atcTransfer_->global_freq();
extscalar = atcTransfer_->extscalar();
extvector = atcTransfer_->extvector();
extlist = atcTransfer_->extlist();
// set comm size needed by this fix
comm_forward = 3;
}
/*----------------------------------------------------------------------- */
FixATC::~FixATC()
{
if (lmp->atom) lmp->atom->delete_callback(id,0);
if (atcTransfer_) delete atcTransfer_;
}
/* ---------------------------------------------------------------------- */
int FixATC::setmask()
{
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= FINAL_INTEGRATE;
mask |= PRE_EXCHANGE;
mask |= MIN_PRE_EXCHANGE;
return mask;
}
/* ---------------------------------------------------------------------- */
int FixATC::modify_param(int narg, char** arg)
{
bool match;
// pass on to transfer layer
try {
match = atcTransfer_->modify(narg,arg);
}
catch (ATC::ATC_Error& atcError) {
cout << "ATC ERROR: " << atcError.get_error_description() << " processor: " << atcError.get_id() << endl;
throw;
}
if (!match) return 0;
return narg;
}
/* ----------------------------------------------------------------------
create initial list of neighbor partners via call to neighbor->build()
must be done in setup (not init) since fix init comes before neigh init
------------------------------------------------------------------------- */
void FixATC::init()
{
// Guarantee construction of full neighborlist
int irequest = neighbor->request((void *) this);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->fix = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
void FixATC::setup(int vflag)
{
try {
atcTransfer_->initialize();
}
catch (ATC::ATC_Error& atcError) {
cout << "ATC ERROR: " << atcError.get_error_description() << " processor: " << atcError.get_id() << endl;
throw;
}
groupbit = atcTransfer_->get_groupbit();
}
/* ----------------------------------------------------------------------
pass throughs to atc functions to handle swapping atom data on
when they move processors
------------------------------------------------------------------------- */
void FixATC::pre_exchange()
{
atcTransfer_->pre_exchange();
}
void FixATC::min_pre_exchange()
{
atcTransfer_->pre_exchange();
}
double FixATC::memory_usage()
{
double bytes = (double) atcTransfer_->memory_usage() * sizeof(double);
return bytes;
}
void FixATC::grow_arrays(int nmax)
{
atcTransfer_->grow_arrays(nmax);
}
void FixATC::copy_arrays(int i, int j)
{
atcTransfer_->copy_arrays(i,j);
}
int FixATC::pack_exchange(int i, double * buf)
{
int num = atcTransfer_->pack_exchange(i,buf);
return num;
}
int FixATC::unpack_exchange(int nlocal, double * buf)
{
int num = atcTransfer_->unpack_exchange(nlocal,buf);
return num;
}
int FixATC::pack_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
{
int num = atcTransfer_->pack_comm(n, list, buf, pbc_flag, pbc);
return num;
}
void FixATC::unpack_comm(int n, int first, double *buf)
{
atcTransfer_->unpack_comm(n, first, buf);
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for restart file
------------------------------------------------------------------------- */
int FixATC::pack_restart(int i, double *buf){
return 0;
}
/* ----------------------------------------------------------------------
unpack values from atom->extra array to restart the fix
------------------------------------------------------------------------- */
void FixATC::unpack_restart(int nlocal, int nth){
}
/* ----------------------------------------------------------------------
maxsize of any atom's restart data
------------------------------------------------------------------------- */
int FixATC::maxsize_restart(){
return 0;
}
/* ----------------------------------------------------------------------
size of atom nlocal's restart data
------------------------------------------------------------------------- */
int FixATC::size_restart(int nlocal){
return 0;
}
/* ----------------------------------------------------------------------
pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixATC::write_restart(FILE *fp){
// hardcode filename for now
char ** args = new char*[2];
args[0] = new char[50];
args[1] = new char[50];
sprintf(args[0],"write_restart");
sprintf(args[1],"ATC.restart");
// Then call all objects I own to write their data
if (comm->me == 0) {
atcTransfer_->modify(2,args);
}
delete [] args[0];
delete [] args[1];
delete [] args;
}
/* ----------------------------------------------------------------------
use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixATC::restart(char *buf){
// hardcode filename for now
char ** args = new char*[2];
args[0] = new char[50];
args[1] = new char[50];
sprintf(args[0],"read_restart");
sprintf(args[1],"ATC.restart");
// Then call all objects I own to write their data
if (comm->me == 0) {
atcTransfer_->modify(2,args);
}
delete [] args[0];
delete [] args[1];
delete [] args;
}
/* ----------------------------------------------------------------------
allow for both per-type and per-atom mass
------------------------------------------------------------------------- */
void FixATC::initial_integrate(int vflag)
{
try {
atcTransfer_->pre_init_integrate();
}
catch (ATC::ATC_Error& atcError) {
cout << "ATC ERROR: " << atcError.get_error_description() << " processor: " << atcError.get_id() << endl;
throw;
}
try {
atcTransfer_->init_integrate_velocity();
}
catch (ATC::ATC_Error& atcError) {
cout << "ATC ERROR: " << atcError.get_error_description() << " processor: " << atcError.get_id() << endl;
throw;
}
try {
atcTransfer_->mid_init_integrate();
}
catch (ATC::ATC_Error& atcError) {
cout << "ATC ERROR: " << atcError.get_error_description() << " processor: " << atcError.get_id() << endl;
throw;
}
try {
atcTransfer_->init_integrate_position();
}
catch (ATC::ATC_Error& atcError) {
cout << "ATC ERROR: " << atcError.get_error_description() << " processor: " << atcError.get_id() << endl;
throw;
}
try {
atcTransfer_->post_init_integrate();
}
catch (ATC::ATC_Error& atcError) {
cout << "ATC ERROR: " << atcError.get_error_description() << " processor: " << atcError.get_id() << endl;
throw;
}
}
/* ---------------------------------------------------------------------- */
void FixATC::final_integrate()
{
// need updated ghost atom positions
comm->forward_comm_fix(this);
try {
atcTransfer_->pre_final_integrate();
}
catch (ATC::ATC_Error& atcError) {
cout << "ATC ERROR: " << atcError.get_error_description() << " processor: " << atcError.get_id() << endl;
throw;
}
try {
atcTransfer_->final_integrate();
}
catch (ATC::ATC_Error& atcError) {
cout << "ATC ERROR: " << atcError.get_error_description() << " processor: " << atcError.get_id() << endl;
throw;
}
try {
atcTransfer_->post_final_integrate();
}
catch (ATC::ATC_Error& atcError) {
cout << "ATC ERROR: " << atcError.get_error_description() << " processor: " << atcError.get_id() << endl;
throw;
}
}
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