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lammps/src/USER-ATC/fix_atc.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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.
------------------------------------------------------------------------- */
// LAMMPS
#include "fix_atc.h"
#include "fix_nve.h"
#include "atom.h"
#include "force.h"
#include "update.h"
#include "respa.h"
#include "error.h"
#include "neighbor.h"
#include "neigh_request.h"
#include "pointers.h"
#include "comm.h"
#include "group.h"
// ATC
#include "ATC_Method.h"
#include "ATC_Transfer.h"
#include "ATC_TransferKernel.h"
#include "ATC_TransferPartitionOfUnity.h"
#include "ATC_CouplingEnergy.h"
#include "ATC_CouplingMomentum.h"
#include "ATC_CouplingMass.h"
#include "ATC_CouplingMomentumEnergy.h"
#include "LammpsInterface.h"
// other
#include <stdio.h>
#include <string.h>
#include <sstream>
using namespace LAMMPS_NS;
using namespace FixConst;
using std::string;
#ifdef LAMMPS_BIGBIG
#error "The USER-ATC package is not compatible with -DLAMMPS_BIGBIG"
#endif
// 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),
lammps_(lmp), atc_(NULL)
{
// ID GROUP atc PHYSICSTYPE [PARAMETERFILE]
if (narg < 4 || narg > 5) 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 <fixID> <group> atc <type> <parameter_file>
- fixID = name of fix
- group = name of group fix is to be applied
- type\n
= thermal : thermal coupling with fields: temperature \n
= two_temperature : electron-phonon coupling with field: temperature and electron_temperature \n
= hardy : on-the-fly post-processing using kernel localization functions (see "related" section for possible fields) \n
= field : on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields) \n
- parameter_file = name of the file with material parameters. \n
note: Neither hardy nor field requires a parameter file
\section examples
<TT> fix AtC internal atc thermal Ar_thermal.dat </TT> \n
<TT> fix AtC internal atc two_temperature Ar_ttm.mat </TT> \n
<TT> fix AtC internal atc hardy </TT> \n
<TT> fix AtC internal atc field </TT> \n
\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 /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 mesh create 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 thermal control flux \n \n
# specify the initial values for the empirical field "temperature" \n
# field node_group value \n
fix_modify AtC initial temperature all 30.\n \n
# create an output stream for nodal fields \n
# filename output_frequency \n
fix_modify AtC 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
# for hardy fix, specific kernel function (function type and range) to
# be used as a localization function \n
fix AtC kernel quartic_sphere 10.0 \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 mesh create 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
# add mass density, potential energy density, stress and temperature \n
fix_modify AtC fields add density energy stress temperature \n\n
# create an output stream for nodal fields \n
# filename output_frequency \n
fix_modify AtC output nvtFE 100 text \n
run 1000 \n
</TT>
the mesh's linear interpolation functions can be used as the localization function \n
by using the field option: \n
<TT>
fix AtC internal atc field \n \n
fix_modify AtC mesh create 1 1 1 box p p p \n\n
... \n\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. \n
- 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. \n
- Zimmerman, JA; Jones, RE; Templeton, JA,
<VAR> A material frame approach for evaluating continuum variables in
atomistic simulations. </VAR>
Journal of Computational Physics (2010), 229:2364. \n
- Templeton, JA; Jones, RE; Wagner, GJ, <VAR> Application of a field-based method
to spatially varying thermal transport problems in molecular dynamics. </VAR>
Modelling and Simulation in Materials Science and Engineering (2010), 18:085007. \n
- Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine, JA, <VAR>
Electron transport enhanced molecular dynamics for metals and semi-metals. </VAR>
International Journal for Numerical Methods in Engineering (2010), 83:940. \n
- Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM,
<VAR> A long-range electric field solver for molecular dynamics based on
atomistic-to-continuum modeling. </VAR>
Journal of Chemical Theory and Computation (2011), 7:1736. \n
- Mandadapu, KK; Templeton, JA; Lee, JW, <VAR> Polarization as a field variable
from molecular dynamics simulations. </VAR>
Journal of Chemical Physics (2013), 139:054115. \n
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_mesh_create
- \ref man_mesh_quadrature
- \ref man_mesh_read
- \ref man_mesh_write
- \ref man_mesh_create_nodeset
- \ref man_mesh_add_to_nodeset
- \ref man_mesh_create_faceset_box
- \ref man_mesh_create_faceset_plane
- \ref man_mesh_create_elementset
- \ref man_mesh_delete_elements
- \ref man_mesh_nodeset_to_elementset
- \ref man_boundary
- \ref man_internal_quadrature
- \ref man_thermal_time_integration
- \ref man_momentum_time_integration
- \ref man_electron_integration
- \ref man_internal_element_set
- \ref man_decomposition
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_control
- \ref man_control_thermal
- \ref man_control_thermal_correction_max_iterations
- \ref man_control_momentum
- \ref man_localized_lambda
- \ref man_lumped_lambda_solve
- \ref man_mask_direction
- \ref man_time_filter
- \ref man_filter_scale
- \ref man_filter_type
- \ref man_equilibrium_start
- \ref man_extrinsic_exchange
- \ref man_poisson_solver
fix_modify commands for output: \n
- \ref man_output
- \ref man_output_nodeset
- \ref man_output_elementset
- \ref man_boundary_integral
- \ref man_contour_integral
- \ref man_mesh_output
- \ref man_write_restart
- \ref man_read_restart
fix_modify commands for post-processing: \n
- \ref man_hardy_kernel
- \ref man_hardy_fields
- \ref man_hardy_gradients
- \ref man_hardy_rates
- \ref man_hardy_computes
- \ref man_hardy_on_the_fly
- \ref man_pair_interactions
- \ref man_sample_frequency
- \ref man_set
miscellaneous fix_modify commands: \n
- \ref man_atom_element_map
- \ref man_atom_weight
- \ref man_write_atom_weights
- \ref man_reset_time
- \ref man_reset_atomic_reference_positions
- \ref man_fe_md_boundary
- \ref man_boundary_faceset
- \ref man_consistent_fe_initialization
- \ref man_mass_matrix
- \ref man_material
- \ref man_atomic_charge
- \ref man_source_integration
- \ref man_temperature_definition
- \ref man_track_displacement
- \ref man_boundary_dynamics
- \ref man_add_species
- \ref man_add_molecule
- \ref man_remove_species
- \ref man_remove_molecule
Note: a set of example input files with the attendant material files are
included with this package
\section default
none
*/
// Construct new ATC_Method object
// note use "unfix" to destroy
int me = ATC::LammpsInterface::instance()->comm_rank();
string groupName(arg[1]);
int igroup = group->find(groupName.c_str());
int atomCount = group->count(igroup);
try {
// Postprocessing
if (strcmp(arg[3],"field")==0)
{
if (atomCount == 0) {
if (me==0) printf("ATC: can't construct transfer, no atoms in group \n");
throw;
}
if (narg < 5) {
if (me==0) printf("ATC: constructing shape function field estimate\n");
atc_ = new ATC::ATC_TransferPartitionOfUnity(groupName,
array_atom,
this);
}
else {
if (me==0) printf("ATC: constructing shape function field estimate with parameter file %s\n",arg[4]);
string matParamFile = arg[4];
atc_ = new ATC::ATC_TransferPartitionOfUnity(groupName,
array_atom, this,
matParamFile);
}
}
else if (strcmp(arg[3],"hardy")==0)
{
if (atomCount == 0) {
if (me==0) printf("ATC: Can't construct transfer, no atoms in group \n");
throw;
}
if (narg < 5) {
if (me==0) printf("ATC: constructing kernel field estimate\n");
atc_ = new ATC::ATC_TransferKernel(groupName,
array_atom,
this);
}
else {
if (me==0) printf("ATC: constructing kernel field estimate with parameter file %s\n",arg[4]);
string matParamFile = arg[4];
atc_ = new ATC::ATC_TransferKernel(groupName,
array_atom, this,
matParamFile);
}
}
// PhysicsTypes
else if (strcmp(arg[3],"thermal")==0)
{
string matParamFile = arg[4];
if (me==0) printf("ATC: constructing thermal coupling with parameter file %s\n",arg[4]);
atc_ = new ATC::ATC_CouplingEnergy(groupName,
array_atom, this,
matParamFile);
}
else if (strcmp(arg[3],"two_temperature")==0)
{
string matParamFile = arg[4];
if (me==0) printf("ATC: constructing two_temperature coupling with parameter file %s\n",arg[4]);
atc_ = new ATC::ATC_CouplingEnergy(groupName,
array_atom, this,
matParamFile, ATC::TWO_TEMPERATURE);
}
else if (strcmp(arg[3],"drift_diffusion")==0)
{
string matParamFile = arg[4];
if (me==0) printf("ATC: constructing drift_diffusion coupling with parameter file %s\n",arg[4]);
atc_ = new ATC::ATC_CouplingEnergy(groupName,
array_atom, this,
matParamFile, ATC::DRIFT_DIFFUSION);
}
else if (strcmp(arg[3],"drift_diffusion-equilibrium")==0)
{
string matParamFile = arg[4];
if (me==0) printf("ATC: constructing drift_diffusion-equilibrium coupling with parameter file %s\n",arg[4]);
atc_ = new ATC::ATC_CouplingEnergy(groupName,
array_atom, this,
matParamFile, ATC::DRIFT_DIFFUSION_EQUILIBRIUM);
}
else if (strcmp(arg[3],"drift_diffusion-schrodinger")==0)
{
string matParamFile = arg[4];
if (me==0) printf("ATC: constructing drift_diffusion-schrodinger coupling with parameter file %s\n",arg[4]);
atc_ = new ATC::ATC_CouplingEnergy(groupName,
array_atom, this,
matParamFile, ATC::DRIFT_DIFFUSION_SCHRODINGER);
}
else if (strcmp(arg[3],"drift_diffusion-schrodinger-slice")==0)
{
string matParamFile = arg[4];
if (me==0) printf("Constructing ATC transfer (drift_diffusion-schrodinger-slice) with parameter file %s\n",arg[4]);
atc_ = new ATC::ATC_CouplingEnergy(groupName,
array_atom, this,
matParamFile, ATC::DRIFT_DIFFUSION_SCHRODINGER_SLICE);
}
else if (strcmp(arg[3],"convective_drift_diffusion")==0)
{
string matParamFile = arg[4];
if (me==0) printf("ATC: constructing convective_drift_diffusion coupling with parameter file %s\n",arg[4]);
atc_ = new ATC::ATC_CouplingEnergy(groupName,
array_atom, this,
matParamFile, ATC::CONVECTIVE_DRIFT_DIFFUSION);
}
else if (strcmp(arg[3],"convective_drift_diffusion-equilibrium")==0)
{
string matParamFile = arg[4];
if (me==0) printf("ATC: constructing convective_drift_diffusion-equilibrium coupling with parameter file %s\n",arg[4]);
atc_ = new ATC::ATC_CouplingEnergy(groupName,
array_atom, this,
matParamFile, ATC::CONVECTIVE_DRIFT_DIFFUSION_EQUILIBRIUM);
}
else if (strcmp(arg[3],"convective_drift_diffusion-schrodinger")==0)
{
string matParamFile = arg[4];
if (me==0) printf("ATC: constructing convective_drift_diffusion-schrodinger coupling with parameter file %s\n",arg[4]);
atc_ = new ATC::ATC_CouplingEnergy(groupName,
array_atom, this,
matParamFile, ATC::CONVECTIVE_DRIFT_DIFFUSION_SCHRODINGER);
}
else if (strcmp(arg[3],"elastic")==0)
{
string matParamFile = arg[4];
if (me==0) printf("ATC: constructing elastic coupling with parameter file %s\n",arg[4]);
atc_ = new ATC::ATC_CouplingMomentum(groupName,
array_atom, this,
matParamFile,
ATC::ELASTIC);
}
else if (strcmp(arg[3],"electrostatic")==0)
{
string matParamFile = arg[4];
if (me==0) printf("ATC: constructing electrostatic mechanical coupling with parameter file %s\n",arg[4]);
atc_ = new ATC::ATC_CouplingMomentum(groupName,
array_atom, this,
matParamFile,
ATC::ELASTIC,
ATC::ELECTROSTATIC);
}
else if (strcmp(arg[3],"electrostatic-equilibrium")==0)
{
string matParamFile = arg[4];
if (me==0) printf("ATC: constructing equilibrium electrostatic coupling with parameter file %s\n",arg[4]);
atc_ = new ATC::ATC_CouplingMomentum(groupName,
array_atom, this,
matParamFile,
ATC::ELASTIC,
ATC::ELECTROSTATIC_EQUILIBRIUM);
}
else if (strcmp(arg[3],"shear")==0)
{
string matParamFile = arg[4];
if (me==0) printf("ATC: constructing viscous/shear coupling with parameter file %s\n",arg[4]);
atc_ = new ATC::ATC_CouplingMomentum(groupName,
array_atom, this,
matParamFile,
ATC::SHEAR);
}
else if (strcmp(arg[3],"species")==0)
{
string matParamFile = arg[4];
if (me==0) printf("ATC: constructing species diffusion coupling with parameter file %s\n",arg[4]);
atc_ = new ATC::ATC_CouplingMass(groupName,
array_atom, this,
matParamFile);
}
else if (strcmp(arg[3],"species_electrostatic")==0)
{
string matParamFile = arg[4];
if (me==0) printf("ATC: constructing electrostatic species coupling with parameter file %s\n",arg[4]);
atc_ = new ATC::ATC_CouplingMass(groupName,
array_atom, this,
matParamFile, ATC::FEM_EFIELD);
}
else if (strcmp(arg[3],"thermo_elastic")==0)
{
string matParamFile = arg[4];
if (me==0) printf("ATC: constructing thermo-mechanical coupling with parameter file %s\n",arg[4]);
atc_ = new ATC::ATC_CouplingMomentumEnergy(groupName,
array_atom, this,
matParamFile);
}
else
{
lmp->error->all(FLERR,"Unknown physics type in ATC");
}
}
catch (ATC::ATC_Error& atcError) {
ATC::LammpsInterface::instance()->print_msg(atcError.error_description());
throw;
}
lmp->atom->add_callback(0);
// we write our own restart file
restart_global = 0;
// Set output computation data based on transfer info
scalar_flag = atc_->scalar_flag();
vector_flag = atc_->vector_flag();
size_vector = atc_->size_vector();
global_freq = atc_->global_freq();
extscalar = atc_->extscalar();
extvector = atc_->extvector();
extlist = atc_->extlist();
thermo_energy = atc_->thermo_energy_flag();
// set pointer for output
peratom_flag = atc_->peratom_flag();
size_peratom_cols = atc_->size_peratom_cols();
peratom_freq = atc_->peratom_freq();
// set comm size needed by this fix
comm_forward = atc_->comm_forward();
// call this fix every step
nevery = 1;
}
/*----------------------------------------------------------------------- */
FixATC::~FixATC()
{
if (lmp->atom) lmp->atom->delete_callback(id,0);
if (atc_) delete atc_;
}
/* ---------------------------------------------------------------------- */
int FixATC::setmask()
{
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= POST_INTEGRATE;
mask |= FINAL_INTEGRATE;
mask |= PRE_EXCHANGE;
mask |= PRE_NEIGHBOR;
mask |= PRE_FORCE;
mask |= POST_FORCE;
mask |= MIN_PRE_EXCHANGE;
mask |= MIN_PRE_NEIGHBOR;
mask |= MIN_PRE_FORCE;
mask |= MIN_POST_FORCE;
mask |= THERMO_ENERGY;
mask |= POST_RUN;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
int FixATC::modify_param(int narg, char** arg)
{
bool match;
// pass on to transfer layer
try {
match = atc_->modify(narg,arg);
}
catch (ATC::ATC_Error& atcError) {
ATC::LammpsInterface::instance()->print_msg(atcError.error_description());
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(this,instance_me);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->fix = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
// create computes, if necessary
atc_->init_computes();
}
void FixATC::min_setup(int vflag)
{
setup(vflag);
}
void FixATC::setup(int vflag)
{
comm->forward_comm_fix(this);
try {
atc_->initialize();
}
catch (ATC::ATC_Error& atcError) {
ATC::LammpsInterface::instance()->print_msg(atcError.error_description());
throw;
}
}
/* ----------------------------------------------------------------------
pass throughs to atc functions to handle swapping atom data on
when they move processors
------------------------------------------------------------------------- */
void FixATC::pre_exchange()
{
try {
atc_->pre_exchange();
}
catch (ATC::ATC_Error& atcError) {
ATC::LammpsInterface::instance()->print_msg(atcError.error_description());
throw;
}
}
void FixATC::setup_pre_exchange()
{
if (atc_->is_initialized()) {
try {
atc_->setup_pre_exchange();
}
catch (ATC::ATC_Error& atcError) {
ATC::LammpsInterface::instance()->print_msg(atcError.error_description());
throw;
}
}
}
void FixATC::min_pre_exchange()
{
try {
atc_->pre_exchange();
}
catch (ATC::ATC_Error& atcError) {
ATC::LammpsInterface::instance()->print_msg(atcError.error_description());
throw;
}
}
void FixATC::min_setup_pre_exchange()
{
try {
atc_->setup_pre_exchange();
}
catch (ATC::ATC_Error& atcError) {
ATC::LammpsInterface::instance()->print_msg(atcError.error_description());
throw;
}
}
double FixATC::memory_usage()
{
double bytes = (double) atc_->memory_usage() * sizeof(double);
return bytes;
}
void FixATC::grow_arrays(int nmax)
{
atc_->grow_arrays(nmax);
}
void FixATC::copy_arrays(int i, int j, int delflag)
{
atc_->copy_arrays(i,j);
}
int FixATC::pack_exchange(int i, double * buf)
{
int num = atc_->pack_exchange(i,buf);
return num;
}
int FixATC::unpack_exchange(int nlocal, double * buf)
{
int num = atc_->unpack_exchange(nlocal,buf);
return num;
}
int FixATC::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
{
int num = atc_->pack_comm(n, list, buf, pbc_flag, pbc);
return num;
}
void FixATC::unpack_forward_comm(int n, int first, double *buf)
{
atc_->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){
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) {
atc_->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){
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) {
atc_->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 {
atc_->pre_init_integrate();
}
catch (ATC::ATC_Error& atcError) {
ATC::LammpsInterface::instance()->print_msg(atcError.error_description());
throw;
}
// integration of atoms, if desired
try {
atc_->init_integrate();
}
catch (ATC::ATC_Error& atcError) {
ATC::LammpsInterface::instance()->print_msg(atcError.error_description());
throw;
}
}
void FixATC::post_integrate()
{
try {
atc_->post_init_integrate();
}
catch (ATC::ATC_Error& atcError) {
ATC::LammpsInterface::instance()->print_msg(atcError.error_description());
throw;
}
}
/* ---------------------------------------------------------------------- */
void FixATC::final_integrate()
{
try {
atc_->pre_final_integrate();
}
catch (ATC::ATC_Error& atcError) {
ATC::LammpsInterface::instance()->print_msg(atcError.error_description());
throw;
}
try {
atc_->final_integrate();
}
catch (ATC::ATC_Error& atcError) {
ATC::LammpsInterface::instance()->print_msg(atcError.error_description());
throw;
}
}
void FixATC::end_of_step()
{
try {
atc_->post_final_integrate();
}
catch (ATC::ATC_Error& atcError) {
ATC::LammpsInterface::instance()->print_msg(atcError.error_description());
throw;
}
try {
atc_->end_of_step();
}
catch (ATC::ATC_Error& atcError) {
ATC::LammpsInterface::instance()->print_msg(atcError.error_description());
throw;
}
}
/* ---------------------------------------------------------------------- */
void FixATC::init_list(int id, NeighList *ptr) {
ATC::LammpsInterface::instance()->set_list(id,ptr);
}
/* ---------------------------------------------------------------------- */
void FixATC::pre_neighbor()
{
try {
atc_->pre_neighbor();
comm->forward_comm_fix(this);
}
catch (ATC::ATC_Error& atcError) {
ATC::LammpsInterface::instance()->print_msg(atcError.error_description());
throw;
}
}
/* ---------------------------------------------------------------------- */
void FixATC::pre_force(int vflag)
{
try {
atc_->pre_force();
}
catch (ATC::ATC_Error& atcError) {
ATC::LammpsInterface::instance()->print_msg(atcError.error_description());
throw;
}
}
/* ---------------------------------------------------------------------- */
void FixATC::post_force(int vflag)
{
try {
atc_->post_force();
}
catch (ATC::ATC_Error& atcError) {
ATC::LammpsInterface::instance()->print_msg(atcError.error_description());
throw;
}
}
/* ---------------------------------------------------------------------- */
void FixATC::post_run()
{
try {
atc_->finish();
}
catch (ATC::ATC_Error& atcError) {
ATC::LammpsInterface::instance()->print_msg(atcError.error_description());
throw;
}
}
/* ---------------------------------------------------------------------- */
void FixATC::setup_pre_neighbor()
{
if (atc_->is_initialized()) {
try {
atc_->pre_neighbor();
}
catch (ATC::ATC_Error& atcError) {
ATC::LammpsInterface::instance()->print_msg(atcError.error_description());
throw;
}
}
}
/* ---------------------------------------------------------------------- */
void FixATC::min_setup_pre_neighbor()
{
if (atc_->is_initialized()) {
try {
atc_->pre_neighbor();
}
catch (ATC::ATC_Error& atcError) {
ATC::LammpsInterface::instance()->print_msg(atcError.error_description());
throw;
}
}
}
/* ---------------------------------------------------------------------- */
void FixATC::min_pre_force(int vflag)
{
try {
atc_->min_pre_force();
}
catch (ATC::ATC_Error& atcError) {
ATC::LammpsInterface::instance()->print_msg(atcError.error_description());
throw;
}
}
/* ---------------------------------------------------------------------- */
void FixATC::min_post_force(int vflag)
{
try {
atc_->min_post_force();
}
catch (ATC::ATC_Error& atcError) {
ATC::LammpsInterface::instance()->print_msg(atcError.error_description());
throw;
}
}
/* ---------------------------------------------------------------------- */
double FixATC::compute_scalar()
{
return atc_->compute_scalar();
}
/* ---------------------------------------------------------------------- */
double FixATC::compute_vector(int n)
{
return atc_->compute_vector(n);
}
/* ---------------------------------------------------------------------- */
double FixATC::compute_array(int irow, int icol)
{
return atc_->compute_array(irow,icol);
}
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