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fix_nh_uef.cpp
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fix_nh_uef.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.
Contributing author: David Nicholson (MIT)
------------------------------------------------------------------------- */
#include <string.h>
#include <stdlib.h>
#include <math.h>
#include "fix_nh_uef.h"
#include "atom.h"
#include "force.h"
#include "group.h"
#include "comm.h"
#include "citeme.h"
#include "irregular.h"
#include "modify.h"
#include "compute.h"
#include "kspace.h"
#include "update.h"
#include "domain.h"
#include "error.h"
#include "output.h"
#include "timer.h"
#include "neighbor.h"
#include "compute_pressure_uef.h"
#include "compute_temp_uef.h"
#include "uef_utils.h"
using namespace LAMMPS_NS;
using namespace FixConst;
enum{ISO,ANISO,TRICLINIC};
// citation info
static const char cite_user_uef_package[] =
"USER-UEF package:\n\n"
"@Article{NicholsonRutledge16,\n"
"author = {David A. Nicholson and Gregory C. Rutledge},\n"
"title = {Molecular simulation of flow-enhanced nucleation in n-eicosane melts under steady shear and uniaxial extension},\n"
"journal = {The Journal of Chemical Physics},\n"
"volume = {145},\n"
"number = {24},\n"
"pages = {244903},\n"
"year = {2016}\n"
"}\n\n";
/* ----------------------------------------------------------------------
* Parse fix specific keywords, do some error checking, and initalize
* temp/pressure fixes
---------------------------------------------------------------------- */
FixNHUef::FixNHUef(LAMMPS *lmp, int narg, char **arg) :
FixNH(lmp, narg, arg), uefbox(NULL)
{
if (lmp->citeme) lmp->citeme->add(cite_user_uef_package);
//initialization
erate[0] = erate[1] = 0;
// default values
strain[0]=strain[1]= 0;
ext_flags[0]=ext_flags[1]=ext_flags[2] = true;
// need to initialize these
omega_dot[0]=omega_dot[1]=omega_dot[2]=0;
// parse fix nh/uef specific options
bool erate_flag = false;
int iarg = 3;
while (iarg <narg) {
if (strcmp(arg[iarg],"erate")==0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix nvt/npt/uef command");
erate[0] = force->numeric(FLERR,arg[iarg+1]);
erate[1] = force->numeric(FLERR,arg[iarg+2]);
erate_flag = true;
iarg += 3;
} else if (strcmp(arg[iarg],"strain")==0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix nvt/npt/uef command");
strain[0] = force->numeric(FLERR,arg[iarg+1]);
strain[1] = force->numeric(FLERR,arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg],"ext")==0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/uef command");
if (strcmp(arg[iarg+1],"x")==0)
ext_flags[1] = ext_flags[2] = false;
else if (strcmp(arg[iarg+1],"y")==0)
ext_flags[0] = ext_flags[2] = false;
else if (strcmp(arg[iarg+1],"z")==0)
ext_flags[0] = ext_flags[1] = false;
else if (strcmp(arg[iarg+1],"xy")==0)
ext_flags[2] = false;
else if (strcmp(arg[iarg+1],"xz")==0)
ext_flags[1] = false;
else if (strcmp(arg[iarg+1],"yz")==0)
ext_flags[0] = false;
else if (strcmp(arg[iarg+1],"xyz")!=0)
error->all(FLERR,"Illegal fix nvt/npt/uef command");
iarg += 2;
} else {
// skip to next argument; argument check for unknown keywords is done in FixNH
++iarg;
}
}
if (!erate_flag)
error->all(FLERR,"Keyword erate must be set for fix npt/npt/uef command");
if (mtchain_default_flag) mtchain=1;
if (!domain->triclinic)
error->all(FLERR,"Simulation box must be triclinic for fix/nvt/npt/uef");
// check for conditions that impose a deviatoric stress
if (pstyle == TRICLINIC)
error->all(FLERR,"Only normal stresses can be controlled with fix/nvt/npt/uef");
double erate_tmp[3];
erate_tmp[0]=erate[0];
erate_tmp[1]=erate[1];
erate_tmp[2]=-erate[0]-erate[1];
if (pstyle == ANISO) {
if (!(ext_flags[0] & ext_flags[1] & ext_flags[2]))
error->all(FLERR,"The ext keyword may only be used with iso pressure control");
for (int k=0;k<3;k++)
for (int j=0;j<3;j++)
if (p_flag[k] && p_flag[j]) {
double tol = 1e-6;
if ( !nearly_equal(p_start[k],p_start[j],tol)
|| !nearly_equal(p_stop[k],p_stop[j],tol))
error->all(FLERR,"All controlled stresses must have the same "
"value in fix/nvt/npt/uef");
if ( !nearly_equal(erate_tmp[k],erate_tmp[j],tol)
|| !nearly_equal(erate_tmp[k],erate_tmp[j],tol))
error->all(FLERR,"Dimensions with controlled stresses must have"\
" same strain rate in fix/nvt/npt/uef");
}
}
// conditions that produce a deviatoric stress have already been eliminated.
deviatoric_flag=0;
// need pre_exchange and irregular migration
pre_exchange_flag = 1;
irregular = new Irregular(lmp);
// flag that I change the box here (in case of nvt)
box_change_shape = 1;
// initialize the UEFBox class which computes the box at each step
uefbox = new UEF_utils::UEFBox();
uefbox->set_strain(strain[0],strain[1]);
// reset fixedpoint to the stagnation point. I don't allow fixedpoint
// to be set by the user.
fixedpoint[0] = domain->boxlo[0];
fixedpoint[1] = domain->boxlo[1];
fixedpoint[2] = domain->boxlo[2];
// Create temp and pressure computes for nh/uef
int n = strlen(id) + 6;
id_temp = new char[n];
strcpy(id_temp,id);
strcat(id_temp,"_temp");
char **newarg = new char*[3];
newarg[0] = id_temp;
newarg[1] = (char *) "all";
newarg[2] = (char *) "temp/uef";
modify->add_compute(3,newarg);
delete [] newarg;
tcomputeflag = 1;
n = strlen(id) + 7;
id_press = new char[n];
strcpy(id_press,id);
strcat(id_press,"_press");
newarg = new char*[4];
newarg[0] = id_press;
newarg[1] = (char *) "all";
newarg[2] = (char *) "pressure/uef";
newarg[3] = id_temp;
modify->add_compute(4,newarg);
delete [] newarg;
pcomputeflag = 1;
nevery = 1;
}
/* ----------------------------------------------------------------------
* Erase the UEFBox object and get rid of the pressure compute if the nvt
* version is being used. Everything else will be done in base destructor
* ---------------------------------------------------------------------- */
FixNHUef::~FixNHUef()
{
delete uefbox;
if (pcomputeflag && !pstat_flag)
{
modify->delete_compute(id_press);
delete [] id_press;
}
}
/* ----------------------------------------------------------------------
* Make the end_of_step() routine callable
* ---------------------------------------------------------------------- */
int FixNHUef::setmask()
{
int mask = FixNH::setmask();
mask |= END_OF_STEP;
return mask;
}
/* ----------------------------------------------------------------------
* Run FixNH::init() and do more error checking. Set the pressure
* pointer in the case that the nvt version is used
* ---------------------------------------------------------------------- */
void FixNHUef::init()
{
FixNH::init();
// find conflict with fix/deform or other box chaging fixes
for (int i=0; i < modify->nfix; i++)
{
if (strcmp(modify->fix[i]->id,id) != 0)
if (modify->fix[i]->box_change_shape != 0)
error->all(FLERR,"Can't use another fix which changes box shape with fix/nvt/npt/uef");
}
// this will make the pressure compute for nvt
if (!pstat_flag)
if (pcomputeflag) {
int icomp = modify->find_compute(id_press);
if (icomp<0)
error->all(FLERR,"Pressure ID for fix/nvt/uef doesn't exist");
pressure = modify->compute[icomp];
if (strcmp(pressure->style,"pressure/uef") != 0)
error->all(FLERR,"Using fix nvt/npt/uef without a compute pressure/uef");
}
if (strcmp(temperature->style,"temp/uef") != 0)
error->all(FLERR,"Using fix nvt/npt/uef without a compute temp/uef");
}
/* ----------------------------------------------------------------------
* Run FixNH::setup() make sure the box is OK and set the rotation matrix
* for the first step
* ---------------------------------------------------------------------- */
void FixNHUef::setup(int j)
{
double box[3][3];
double vol = domain->xprd * domain->yprd * domain->zprd;
uefbox->get_box(box,vol);
double tol = 1e-4;
// ensure the box is ok for uef
bool isok = true;
isok &= nearly_equal(domain->h[0],box[0][0],tol);
isok &= nearly_equal(domain->h[1],box[1][1],tol);
isok &= nearly_equal(domain->h[2],box[2][2],tol);
isok &= nearly_equal(domain->xy,box[0][1],tol);
isok &= nearly_equal(domain->yz,box[1][2],tol);
isok &= nearly_equal(domain->xz,box[0][2],tol);
if (!isok)
error->all(FLERR,"Initial box is not close enough to the expected uef box");
uefbox->get_rot(rot);
((ComputeTempUef*) temperature)->yes_rot();
((ComputePressureUef*) pressure)->in_fix = true;
((ComputePressureUef*) pressure)->update_rot();
FixNH::setup(j);
}
/* ----------------------------------------------------------------------
* rotate -> initial integration step -> rotate back
* ---------------------------------------------------------------------- */
void FixNHUef::initial_integrate(int vflag)
{
inv_rotate_x(rot);
inv_rotate_v(rot);
inv_rotate_f(rot);
((ComputeTempUef*) temperature)->no_rot();
FixNH::initial_integrate(vflag);
rotate_x(rot);
rotate_v(rot);
rotate_f(rot);
((ComputeTempUef*) temperature)->yes_rot();
}
/* ----------------------------------------------------------------------
* rotate -> initial integration step -> rotate back (RESPA)
* ---------------------------------------------------------------------- */
void FixNHUef::initial_integrate_respa(int vflag, int ilevel, int iloop)
{
inv_rotate_x(rot);
inv_rotate_v(rot);
inv_rotate_f(rot);
((ComputeTempUef*) temperature)->no_rot();
FixNH::initial_integrate_respa(vflag,ilevel,iloop);
rotate_x(rot);
rotate_v(rot);
rotate_f(rot);
((ComputeTempUef*) temperature)->yes_rot();
}
/* ----------------------------------------------------------------------
* rotate -> final integration step -> rotate back
* ---------------------------------------------------------------------- */
void FixNHUef::final_integrate()
{
// update rot here since it must directly follow the virial calculation
((ComputePressureUef*) pressure)->update_rot();
inv_rotate_v(rot);
inv_rotate_f(rot);
((ComputeTempUef*) temperature)->no_rot();
FixNH::final_integrate();
rotate_v(rot);
rotate_f(rot);
((ComputeTempUef*) temperature)->yes_rot();
}
/* ----------------------------------------------------------------------
* at outer level: call this->final_integrate()
* at other levels: rotate -> 2nd verlet step -> rotate back
* ---------------------------------------------------------------------- */
void FixNHUef::final_integrate_respa(int ilevel, int iloop)
{
// set timesteps by level
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
dthalf = 0.5 * step_respa[ilevel];
// outermost level - update eta_dot and omega_dot, apply via final_integrate
// all other levels - NVE update of v
if (ilevel == nlevels_respa-1) final_integrate();
else
{
inv_rotate_v(rot);
inv_rotate_f(rot);
nve_v();
rotate_v(rot);
rotate_f(rot);
}
}
/* ----------------------------------------------------------------------
SLLOD velocity update in time-reversible (i think) increments
v -> exp(-edot*dt/2)*v
v -> v +f/m*dt
v -> exp(-edot*dt/2)*v
-----------------------------------------------------------------------*/
void FixNHUef::nve_v()
{
double dtfm;
double **v = atom->v;
double **f = atom->f;
double *rmass = atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double ex = erate[0]*dtf/2;
double ey = erate[1]*dtf/2;
double ez = -ex-ey;
double e0 = exp(-ex);
double e1 = exp(-ey);
double e2 = exp(-ez);
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
if (rmass) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / rmass[i];
v[i][0] *= e0;
v[i][1] *= e1;
v[i][2] *= e2;
v[i][0] += dtfm*f[i][0];
v[i][1] += dtfm*f[i][1];
v[i][2] += dtfm*f[i][2];
v[i][0] *= e0;
v[i][1] *= e1;
v[i][2] *= e2;
}
}
} else {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / mass[type[i]];
v[i][0] *= e0;
v[i][1] *= e1;
v[i][2] *= e2;
v[i][0] += dtfm*f[i][0];
v[i][1] += dtfm*f[i][1];
v[i][2] += dtfm*f[i][2];
v[i][0] *= e0;
v[i][1] *= e1;
v[i][2] *= e2;
}
}
}
}
/* ----------------------------------------------------------------------
Don't actually move atoms in remap(), just change the box
-----------------------------------------------------------------------*/
void FixNHUef::remap()
{
double vol = domain->xprd * domain->yprd * domain->zprd;
double domega = dto*(omega_dot[0]+omega_dot[1]+omega_dot[2])/3.;
// constant volume strain associated with barostat
// box scaling
double ex = dto*omega_dot[0]-domega;
double ey = dto*omega_dot[1]-domega;
uefbox->step_deform(ex,ey);
strain[0] += ex;
strain[1] += ey;
// volume change
vol = vol*exp(3*domega);
double box[3][3];
uefbox->get_box(box,vol);
domain->boxhi[0] = domain->boxlo[0]+box[0][0];
domain->boxhi[1] = domain->boxlo[1]+box[1][1];
domain->boxhi[2] = domain->boxlo[2]+box[2][2];
domain->xy = box[0][1];
domain->xz = box[0][2];
domain->yz = box[1][2];
domain->set_global_box();
domain->set_local_box();
uefbox->get_rot(rot);
}
/* ----------------------------------------------------------------------
SLLOD position update in time-reversible (i think) increments
x -> exp(edot*dt/2)*x
x -> x + v*dt
x -> exp(edot*dt/2)*x
-----------------------------------------------------------------------*/
void FixNHUef::nve_x()
{
double **x = atom->x;
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double ex = erate[0]*dtv;
strain[0] += ex;
double e0 = exp((ex+omega_dot[0]*dtv)/2);
double ey = erate[1]*dtv;
strain[1] += ey;
double e1 = exp((ey+omega_dot[1]*dtv)/2.);
double ez = -ex -ey;
double e2 = exp((ez+omega_dot[2]*dtv)/2.);
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
// x update by full step only for atoms in group
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
x[i][0] *= e0;
x[i][1] *= e1;
x[i][2] *= e2;
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
x[i][0] *= e0;
x[i][1] *= e1;
x[i][2] *= e2;
}
}
uefbox->step_deform(ex,ey);
double box[3][3];
double vol = domain->xprd * domain->yprd * domain->zprd;
uefbox->get_box(box,vol);
domain->boxhi[0] = domain->boxlo[0]+box[0][0];
domain->boxhi[1] = domain->boxlo[1]+box[1][1];
domain->boxhi[2] = domain->boxlo[2]+box[2][2];
domain->xy = box[0][1];
domain->xz = box[0][2];
domain->yz = box[1][2];
domain->set_global_box();
domain->set_local_box();
uefbox->get_rot(rot);
}
/* ----------------------------------------------------------------------
* Do the lattice reduction if necessary.
-----------------------------------------------------------------------*/
void FixNHUef::pre_exchange()
{
// only need to reset things if the lattice needs to be reduced
if (uefbox->reduce())
{
// go to lab frame
inv_rotate_x(rot);
inv_rotate_v(rot);
inv_rotate_f(rot);
// get & set the new box and rotation matrix
double vol = domain->xprd * domain->yprd * domain->zprd;
double box[3][3];
uefbox->get_box(box,vol);
domain->boxhi[0] = domain->boxlo[0]+box[0][0];
domain->boxhi[1] = domain->boxlo[1]+box[1][1];
domain->boxhi[2] = domain->boxlo[2]+box[2][2];
domain->xy = box[0][1];
domain->xz = box[0][2];
domain->yz = box[1][2];
domain->set_global_box();
domain->set_local_box();
uefbox->get_rot(rot);
// rotate to the new upper triangular frame
rotate_v(rot);
rotate_x(rot);
rotate_f(rot);
// put all atoms in the new box
double **x = atom->x;
imageint *image = atom->image;
int nlocal = atom->nlocal;
for (int i=0; i<nlocal; i++) domain->remap(x[i],image[i]);
// move atoms to the right processors
domain->x2lamda(atom->nlocal);
irregular->migrate_atoms();
domain->lamda2x(atom->nlocal);
}
}
/* ----------------------------------------------------------------------
* The following are routines to rotate between the lab and upper triangular
* (UT) frames. For most of the time the simulation is in the UT frame.
* To get to the lab frame, apply the inv_rotate_[..](rot) and to
* get back to the UT frame apply rotate_[..](rot).
*
* Note: the rotate_x() functions also apply a shift to/from the fixedpoint
* to make the integration a little simpler.
* ---------------------------------------------------------------------- */
void FixNHUef::rotate_x(double r[3][3])
{
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
double xn[3];
for (int i=0;i<nlocal;i++)
{
if (mask[i] & groupbit)
{
xn[0]=r[0][0]*x[i][0]+r[0][1]*x[i][1]+r[0][2]*x[i][2];
xn[1]=r[1][0]*x[i][0]+r[1][1]*x[i][1]+r[1][2]*x[i][2];
xn[2]=r[2][0]*x[i][0]+r[2][1]*x[i][1]+r[2][2]*x[i][2];
x[i][0]=xn[0]+domain->boxlo[0];
x[i][1]=xn[1]+domain->boxlo[1];
x[i][2]=xn[2]+domain->boxlo[2];
}
}
}
void FixNHUef::inv_rotate_x(double r[3][3])
{
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
double xn[3];
for (int i=0;i<nlocal;i++)
{
if (mask[i] & groupbit)
{
x[i][0] -= domain->boxlo[0];
x[i][1] -= domain->boxlo[1];
x[i][2] -= domain->boxlo[2];
xn[0]=r[0][0]*x[i][0]+r[1][0]*x[i][1]+r[2][0]*x[i][2];
xn[1]=r[0][1]*x[i][0]+r[1][1]*x[i][1]+r[2][1]*x[i][2];
xn[2]=r[0][2]*x[i][0]+r[1][2]*x[i][1]+r[2][2]*x[i][2];
x[i][0]=xn[0];
x[i][1]=xn[1];
x[i][2]=xn[2];
}
}
}
void FixNHUef::rotate_v(double r[3][3])
{
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
double vn[3];
for (int i=0;i<nlocal;i++)
{
if (mask[i] & groupbit)
{
vn[0]=r[0][0]*v[i][0]+r[0][1]*v[i][1]+r[0][2]*v[i][2];
vn[1]=r[1][0]*v[i][0]+r[1][1]*v[i][1]+r[1][2]*v[i][2];
vn[2]=r[2][0]*v[i][0]+r[2][1]*v[i][1]+r[2][2]*v[i][2];
v[i][0]=vn[0]; v[i][1]=vn[1]; v[i][2]=vn[2];
}
}
}
void FixNHUef::inv_rotate_v(double r[3][3])
{
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
double vn[3];
for (int i=0;i<nlocal;i++)
{
if (mask[i] & groupbit)
{
vn[0]=r[0][0]*v[i][0]+r[1][0]*v[i][1]+r[2][0]*v[i][2];
vn[1]=r[0][1]*v[i][0]+r[1][1]*v[i][1]+r[2][1]*v[i][2];
vn[2]=r[0][2]*v[i][0]+r[1][2]*v[i][1]+r[2][2]*v[i][2];
v[i][0]=vn[0]; v[i][1]=vn[1]; v[i][2]=vn[2];
}
}
}
void FixNHUef::rotate_f(double r[3][3])
{
double **f = atom->f;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
double fn[3];
for (int i=0;i<nlocal;i++)
{
if (mask[i] & groupbit)
{
fn[0]=r[0][0]*f[i][0]+r[0][1]*f[i][1]+r[0][2]*f[i][2];
fn[1]=r[1][0]*f[i][0]+r[1][1]*f[i][1]+r[1][2]*f[i][2];
fn[2]=r[2][0]*f[i][0]+r[2][1]*f[i][1]+r[2][2]*f[i][2];
f[i][0]=fn[0]; f[i][1]=fn[1]; f[i][2]=fn[2];
}
}
}
void FixNHUef::inv_rotate_f(double r[3][3])
{
double **f = atom->f;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
double fn[3];
for (int i=0;i<nlocal;i++)
{
if (mask[i] & groupbit)
{
fn[0]=r[0][0]*f[i][0]+r[1][0]*f[i][1]+r[2][0]*f[i][2];
fn[1]=r[0][1]*f[i][0]+r[1][1]*f[i][1]+r[2][1]*f[i][2];
fn[2]=r[0][2]*f[i][0]+r[1][2]*f[i][1]+r[2][2]*f[i][2];
f[i][0]=fn[0]; f[i][1]=fn[1]; f[i][2]=fn[2];
}
}
}
/* ----------------------------------------------------------------------
* Increase the size of the restart list to add in the strains
* ---------------------------------------------------------------------- */
int FixNHUef::size_restart_global()
{
return FixNH::size_restart_global() +2;
}
/* ----------------------------------------------------------------------
* Pack the strains after packing the default FixNH values
* ---------------------------------------------------------------------- */
int FixNHUef::pack_restart_data(double *list)
{
int n = FixNH::pack_restart_data(list);
list[n++] = strain[0];
list[n++] = strain[1];
return n;
}
/* ----------------------------------------------------------------------
* read and set the strains after the default FixNH values
* ---------------------------------------------------------------------- */
void FixNHUef::restart(char *buf)
{
int n = size_restart_global();
FixNH::restart(buf);
double *list = (double *) buf;
strain[0] = list[n-2];
strain[1] = list[n-1];
uefbox->set_strain(strain[0],strain[1]);
}
/* ----------------------------------------------------------------------
* If the step writes a restart, reduce the box beforehand. This makes sure
* the unique box shape can be found once the restart is read and that
* all of the atoms lie within the box.
* This may only be necessary for RESPA runs, but I'm leaving it in anyway.
* ---------------------------------------------------------------------- */
void FixNHUef::end_of_step()
{
if (update->ntimestep==output->next_restart)
{
pre_exchange();
domain->x2lamda(atom->nlocal);
domain->pbc();
timer->stamp();
comm->exchange();
comm->borders();
domain->lamda2x(atom->nlocal+atom->nghost);
timer->stamp(Timer::COMM);
neighbor->build();
timer->stamp(Timer::NEIGH);
}
}
/* ----------------------------------------------------------------------
* reduce the simulation box after a run is complete. otherwise it won't
* be possible to resume from a write_restart since the initialization of
* the simulation box requires reduced simulation box
* ---------------------------------------------------------------------- */
void FixNHUef::post_run()
{
pre_exchange();
domain->x2lamda(atom->nlocal);
domain->pbc();
timer->stamp();
comm->exchange();
comm->borders();
domain->lamda2x(atom->nlocal+atom->nghost);
timer->stamp(Timer::COMM);
neighbor->build();
timer->stamp(Timer::NEIGH);
}
/* ----------------------------------------------------------------------
* public read for rotation matrix
* ---------------------------------------------------------------------- */
void FixNHUef::get_rot(double r[3][3])
{
r[0][0] = rot[0][0];
r[0][1] = rot[0][1];
r[0][2] = rot[0][2];
r[1][0] = rot[1][0];
r[1][1] = rot[1][1];
r[1][2] = rot[1][2];
r[2][0] = rot[2][0];
r[2][1] = rot[2][1];
r[2][2] = rot[2][2];
}
/* ----------------------------------------------------------------------
* public read for ext flags
* ---------------------------------------------------------------------- */
void FixNHUef::get_ext_flags(bool* e)
{
e[0] = ext_flags[0];
e[1] = ext_flags[1];
e[2] = ext_flags[2];
}
/* ----------------------------------------------------------------------
* public read for simulation box
* ---------------------------------------------------------------------- */
void FixNHUef::get_box(double b[3][3])
{
double box[3][3];
double vol = domain->xprd * domain->yprd * domain->zprd;
uefbox->get_box(box,vol);
b[0][0] = box[0][0];
b[0][1] = box[0][1];
b[0][2] = box[0][2];
b[1][0] = box[1][0];
b[1][1] = box[1][1];
b[1][2] = box[1][2];
b[2][0] = box[2][0];
b[2][1] = box[2][1];
b[2][2] = box[2][2];
}
/* ----------------------------------------------------------------------
* comparing floats
* it's imperfect, but should work provided no infinities
* ---------------------------------------------------------------------- */
bool FixNHUef::nearly_equal(double a, double b, double epsilon)
{
double absa = fabs(a);
double absb = fabs(b);
double diff = fabs(a-b);
if (a == b) return true;
else if ( (absa+absb) < epsilon)
return diff < epsilon*epsilon;
else
return diff/(absa+absb) < epsilon;
}

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