jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
lammps/src/fix_box_relax.cpp

975 lines
32 KiB
C++
Raw Blame History

/* ----------------------------------------------------------------------
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 author: Aidan Thompson (SNL)
------------------------------------------------------------------------- */
#include "fix_box_relax.h"
#include <cmath>
#include <cstring>
#include "atom.h"
#include "domain.h"
#include "update.h"
#include "comm.h"
#include "force.h"
#include "kspace.h"
#include "modify.h"
#include "compute.h"
#include "error.h"
#include "math_extra.h"
using namespace LAMMPS_NS;
using namespace FixConst;
enum{NONE,XYZ,XY,YZ,XZ};
enum{ISO,ANISO,TRICLINIC};
#define MAX_LIFO_DEPTH 2 // 3 box0 arrays in *.h dimensioned to this
/* ---------------------------------------------------------------------- */
FixBoxRelax::FixBoxRelax(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
id_temp(NULL), id_press(NULL), tflag(0), pflag(0)
{
if (narg < 5) error->all(FLERR,"Illegal fix box/relax command");
scalar_flag = 1;
extscalar = 1;
global_freq = 1;
no_change_box = 1;
// default values
pcouple = NONE;
allremap = 1;
vmax = 0.0001;
deviatoric_flag = 0;
nreset_h0 = 0;
p_target[0] = p_target[1] = p_target[2] =
p_target[3] = p_target[4] = p_target[5] = 0.0;
p_flag[0] = p_flag[1] = p_flag[2] =
p_flag[3] = p_flag[4] = p_flag[5] = 0;
// turn on tilt factor scaling, whenever applicable
dimension = domain->dimension;
scaleyz = scalexz = scalexy = 0;
if (domain->yperiodic && domain->xy != 0.0) scalexy = 1;
if (domain->zperiodic && dimension == 3) {
if (domain->yz != 0.0) scaleyz = 1;
if (domain->xz != 0.0) scalexz = 1;
}
// set fixed-point to default = center of cell
fixedpoint[0] = 0.5*(domain->boxlo[0]+domain->boxhi[0]);
fixedpoint[1] = 0.5*(domain->boxlo[1]+domain->boxhi[1]);
fixedpoint[2] = 0.5*(domain->boxlo[2]+domain->boxhi[2]);
// process keywords
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg],"iso") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix box/relax command");
pcouple = XYZ;
p_target[0] = p_target[1] = p_target[2] = force->numeric(FLERR,arg[iarg+1]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (dimension == 2) {
p_target[2] = 0.0;
p_flag[2] = 0;
}
iarg += 2;
} else if (strcmp(arg[iarg],"aniso") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix box/relax command");
pcouple = NONE;
p_target[0] = p_target[1] = p_target[2] = force->numeric(FLERR,arg[iarg+1]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (dimension == 2) {
p_target[2] = 0.0;
p_flag[2] = 0;
}
iarg += 2;
} else if (strcmp(arg[iarg],"tri") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix box/relax command");
pcouple = NONE;
scalexy = scalexz = scaleyz = 0;
p_target[0] = p_target[1] = p_target[2] = force->numeric(FLERR,arg[iarg+1]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
p_target[3] = p_target[4] = p_target[5] = 0.0;
p_flag[3] = p_flag[4] = p_flag[5] = 1;
if (dimension == 2) {
p_target[2] = p_target[3] = p_target[4] = 0.0;
p_flag[2] = p_flag[3] = p_flag[4] = 0;
}
iarg += 2;
} else if (strcmp(arg[iarg],"x") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix box/relax command");
p_target[0] = force->numeric(FLERR,arg[iarg+1]);
p_flag[0] = 1;
deviatoric_flag = 1;
iarg += 2;
} else if (strcmp(arg[iarg],"y") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix box/relax command");
p_target[1] = force->numeric(FLERR,arg[iarg+1]);
p_flag[1] = 1;
deviatoric_flag = 1;
iarg += 2;
} else if (strcmp(arg[iarg],"z") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix box/relax command");
p_target[2] = force->numeric(FLERR,arg[iarg+1]);
p_flag[2] = 1;
deviatoric_flag = 1;
iarg += 2;
if (dimension == 2)
error->all(FLERR,"Invalid fix box/relax command for a 2d simulation");
} else if (strcmp(arg[iarg],"yz") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix box/relax command");
p_target[3] = force->numeric(FLERR,arg[iarg+1]);
p_flag[3] = 1;
deviatoric_flag = 1;
scaleyz = 0;
iarg += 2;
if (dimension == 2)
error->all(FLERR,"Invalid fix box/relax command for a 2d simulation");
} else if (strcmp(arg[iarg],"xz") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix box/relax command");
p_target[4] = force->numeric(FLERR,arg[iarg+1]);
p_flag[4] = 1;
deviatoric_flag = 1;
scalexz = 0;
iarg += 2;
if (dimension == 2)
error->all(FLERR,"Invalid fix box/relax command for a 2d simulation");
} else if (strcmp(arg[iarg],"xy") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix box/relax command");
p_target[5] = force->numeric(FLERR,arg[iarg+1]);
p_flag[5] = 1;
deviatoric_flag = 1;
scalexy = 0;
iarg += 2;
} else if (strcmp(arg[iarg],"couple") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix box/relax command");
if (strcmp(arg[iarg+1],"xyz") == 0) pcouple = XYZ;
else if (strcmp(arg[iarg+1],"xy") == 0) pcouple = XY;
else if (strcmp(arg[iarg+1],"yz") == 0) pcouple = YZ;
else if (strcmp(arg[iarg+1],"xz") == 0) pcouple = XZ;
else if (strcmp(arg[iarg+1],"none") == 0) pcouple = NONE;
else error->all(FLERR,"Illegal fix box/relax command");
iarg += 2;
} else if (strcmp(arg[iarg],"dilate") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix box/relax command");
if (strcmp(arg[iarg+1],"all") == 0) allremap = 1;
else if (strcmp(arg[iarg+1],"partial") == 0) allremap = 0;
else error->all(FLERR,"Illegal fix box/relax command");
iarg += 2;
} else if (strcmp(arg[iarg],"vmax") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix box/relax command");
vmax = force->numeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"nreset") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix box/relax command");
nreset_h0 = force->inumeric(FLERR,arg[iarg+1]);
if (nreset_h0 < 0) error->all(FLERR,"Illegal fix box/relax command");
iarg += 2;
} else if (strcmp(arg[iarg],"scalexy") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix box/relax command");
if (strcmp(arg[iarg+1],"yes") == 0) scalexy = 1;
else if (strcmp(arg[iarg+1],"no") == 0) scalexy = 0;
else error->all(FLERR,"Illegal fix box/relax command");
iarg += 2;
} else if (strcmp(arg[iarg],"scalexz") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix box/relax command");
if (strcmp(arg[iarg+1],"yes") == 0) scalexz = 1;
else if (strcmp(arg[iarg+1],"no") == 0) scalexz = 0;
else error->all(FLERR,"Illegal fix box/relax command");
iarg += 2;
} else if (strcmp(arg[iarg],"scaleyz") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix box/relax command");
if (strcmp(arg[iarg+1],"yes") == 0) scaleyz = 1;
else if (strcmp(arg[iarg+1],"no") == 0) scaleyz = 0;
else error->all(FLERR,"Illegal fix box/relax command");
iarg += 2;
} else if (strcmp(arg[iarg],"fixedpoint") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix box/relax command");
fixedpoint[0] = force->numeric(FLERR,arg[iarg+1]);
fixedpoint[1] = force->numeric(FLERR,arg[iarg+2]);
fixedpoint[2] = force->numeric(FLERR,arg[iarg+3]);
iarg += 4;
} else error->all(FLERR,"Illegal fix box/relax command");
}
if (p_flag[0] || p_flag[1] || p_flag[2]) box_change_size = 1;
if (p_flag[3] || p_flag[4] || p_flag[5]) box_change_shape = 1;
if (allremap == 0) restart_pbc = 1;
// error checks
if (dimension == 2 && (p_flag[2] || p_flag[3] || p_flag[4]))
error->all(FLERR,"Invalid fix box/relax command for a 2d simulation");
if (dimension == 2 && (pcouple == YZ || pcouple == XZ))
error->all(FLERR,"Invalid fix box/relax command for a 2d simulation");
if (pcouple == XYZ && (p_flag[0] == 0 || p_flag[1] == 0))
error->all(FLERR,"Invalid fix box/relax command pressure settings");
if (pcouple == XYZ && dimension == 3 && p_flag[2] == 0)
error->all(FLERR,"Invalid fix box/relax command pressure settings");
if (pcouple == XY && (p_flag[0] == 0 || p_flag[1] == 0))
error->all(FLERR,"Invalid fix box/relax command pressure settings");
if (pcouple == YZ && (p_flag[1] == 0 || p_flag[2] == 0))
error->all(FLERR,"Invalid fix box/relax command pressure settings");
if (pcouple == XZ && (p_flag[0] == 0 || p_flag[2] == 0))
error->all(FLERR,"Invalid fix box/relax command pressure settings");
// require periodicity in tensile dimension
if (p_flag[0] && domain->xperiodic == 0)
error->all(FLERR,"Cannot use fix box/relax on a non-periodic dimension");
if (p_flag[1] && domain->yperiodic == 0)
error->all(FLERR,"Cannot use fix box/relax on a non-periodic dimension");
if (p_flag[2] && domain->zperiodic == 0)
error->all(FLERR,"Cannot use fix box/relax on a non-periodic dimension");
// require periodicity in 2nd dim of off-diagonal tilt component
if (p_flag[3] && domain->zperiodic == 0)
error->all(FLERR,
"Cannot use fix box/relax on a 2nd non-periodic dimension");
if (p_flag[4] && domain->zperiodic == 0)
error->all(FLERR,
"Cannot use fix box/relax on a 2nd non-periodic dimension");
if (p_flag[5] && domain->yperiodic == 0)
error->all(FLERR,
"Cannot use fix box/relax on a 2nd non-periodic dimension");
if (scaleyz == 1 && domain->zperiodic == 0)
error->all(FLERR,"Cannot use fix box/relax "
"with tilt factor scaling on a 2nd non-periodic dimension");
if (scalexz == 1 && domain->zperiodic == 0)
error->all(FLERR,"Cannot use fix box/relax "
"with tilt factor scaling on a 2nd non-periodic dimension");
if (scalexy == 1 && domain->yperiodic == 0)
error->all(FLERR,"Cannot use fix box/relax "
"with tilt factor scaling on a 2nd non-periodic dimension");
if (p_flag[3] && scaleyz == 1)
error->all(FLERR,"Cannot use fix box/relax with "
"both relaxation and scaling on a tilt factor");
if (p_flag[4] && scalexz == 1)
error->all(FLERR,"Cannot use fix box/relax with "
"both relaxation and scaling on a tilt factor");
if (p_flag[5] && scalexy == 1)
error->all(FLERR,"Cannot use fix box/relax with "
"both relaxation and scaling on a tilt factor");
if (!domain->triclinic && (p_flag[3] || p_flag[4] || p_flag[5]))
error->all(FLERR,"Can not specify Pxy/Pxz/Pyz in "
"fix box/relax with non-triclinic box");
if (pcouple == XYZ && dimension == 3 &&
(p_target[0] != p_target[1] || p_target[0] != p_target[2]))
error->all(FLERR,"Invalid fix box/relax pressure settings");
if (pcouple == XYZ && dimension == 2 && p_target[0] != p_target[1])
error->all(FLERR,"Invalid fix box/relax pressure settings");
if (pcouple == XY && p_target[0] != p_target[1])
error->all(FLERR,"Invalid fix box/relax pressure settings");
if (pcouple == YZ && p_target[1] != p_target[2])
error->all(FLERR,"Invalid fix box/relax pressure settings");
if (pcouple == XZ && p_target[0] != p_target[2])
error->all(FLERR,"Invalid fix box/relax pressure settings");
if (vmax <= 0.0) error->all(FLERR,"Illegal fix box/relax command");
// pstyle = TRICLINIC if any off-diagonal term is controlled -> 6 dof
// else pstyle = ISO if XYZ coupling or XY coupling in 2d -> 1 dof
// else pstyle = ANISO -> 3 dof
if (p_flag[3] || p_flag[4] || p_flag[5]) pstyle = TRICLINIC;
else if (pcouple == XYZ || (dimension == 2 && pcouple == XY)) pstyle = ISO;
else pstyle = ANISO;
// create a new compute temp style
// id = fix-ID + temp
// compute group = all since pressure is always global (group all)
// and thus its KE/temperature contribution should use group all
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";
modify->add_compute(3,newarg);
delete [] newarg;
tflag = 1;
// create a new compute pressure style (virial only)
// id = fix-ID + press, compute group = all
// pass id_temp as 4th arg to pressure constructor
n = strlen(id) + 7;
id_press = new char[n];
strcpy(id_press,id);
strcat(id_press,"_press");
newarg = new char*[5];
newarg[0] = id_press;
newarg[1] = (char *) "all";
newarg[2] = (char *) "pressure";
newarg[3] = id_temp;
newarg[4] = (char *) "virial";
modify->add_compute(5,newarg);
delete [] newarg;
pflag = 1;
dimension = domain->dimension;
nrigid = 0;
rfix = 0;
current_lifo = 0;
}
/* ---------------------------------------------------------------------- */
FixBoxRelax::~FixBoxRelax()
{
delete [] rfix;
// delete temperature and pressure if fix created them
if (tflag) modify->delete_compute(id_temp);
if (pflag) modify->delete_compute(id_press);
delete [] id_temp;
delete [] id_press;
}
/* ---------------------------------------------------------------------- */
int FixBoxRelax::setmask()
{
int mask = 0;
mask |= MIN_ENERGY;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixBoxRelax::init()
{
// set temperature and pressure ptrs
int icompute = modify->find_compute(id_temp);
if (icompute < 0)
error->all(FLERR,"Temperature ID for fix box/relax does not exist");
temperature = modify->compute[icompute];
icompute = modify->find_compute(id_press);
if (icompute < 0)
error->all(FLERR,"Pressure ID for fix box/relax does not exist");
pressure = modify->compute[icompute];
pv2e = 1.0 / force->nktv2p;
if (force->kspace) kspace_flag = 1;
else kspace_flag = 0;
// detect if any rigid fixes exist so rigid bodies move when box is remapped
// rfix[] = indices to each fix rigid
delete [] rfix;
nrigid = 0;
rfix = NULL;
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->rigid_flag) nrigid++;
if (nrigid) {
rfix = new int[nrigid];
nrigid = 0;
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->rigid_flag) rfix[nrigid++] = i;
}
// initial box dimensions
xprdinit = domain->xprd;
yprdinit = domain->yprd;
zprdinit = domain->zprd;
if (dimension == 2) zprdinit = 1.0;
vol0 = xprdinit * yprdinit * zprdinit;
h0[0] = domain->h[0];
h0[1] = domain->h[1];
h0[2] = domain->h[2];
h0[3] = domain->h[3];
h0[4] = domain->h[4];
h0[5] = domain->h[5];
// hydrostatic target pressure and deviatoric target stress
compute_press_target();
if (deviatoric_flag) compute_sigma();
}
/* ----------------------------------------------------------------------
compute energy and force due to extra degrees of freedom
------------------------------------------------------------------------- */
double FixBoxRelax::min_energy(double *fextra)
{
double eng,scale,scalex,scaley,scalez,scalevol;
temperature->compute_scalar();
if (pstyle == ISO) pressure->compute_scalar();
else {
temperature->compute_vector();
pressure->compute_vector();
}
couple();
// trigger virial computation on every iteration of minimizer
pressure->addstep(update->ntimestep+1);
// compute energy, forces for each extra degree of freedom
// returned eng = PV must be in units of energy
// returned fextra must likewise be in units of energy
if (pstyle == ISO) {
scale = domain->xprd/xprdinit;
if (dimension == 3) {
eng = pv2e * p_target[0] * (scale*scale*scale-1.0)*vol0;
fextra[0] = pv2e * (p_current[0] - p_target[0])*3.0*scale*scale*vol0;
} else {
eng = pv2e * p_target[0] * (scale*scale-1.0)*vol0;
fextra[0] = pv2e * (p_current[0] - p_target[0])*2.0*scale*vol0;
}
} else {
fextra[0] = fextra[1] = fextra[2] = 0.0;
scalex = scaley = scalez = 1.0;
if (p_flag[0]) scalex = domain->xprd/xprdinit;
if (p_flag[1]) scaley = domain->yprd/yprdinit;
if (p_flag[2]) scalez = domain->zprd/zprdinit;
scalevol = scalex*scaley*scalez;
eng = pv2e * p_hydro * (scalevol-1.0)*vol0;
if (p_flag[0])
fextra[0] = pv2e * (p_current[0] - p_hydro)*scaley*scalez*vol0;
if (p_flag[1])
fextra[1] = pv2e * (p_current[1] - p_hydro)*scalex*scalez*vol0;
if (p_flag[2])
fextra[2] = pv2e * (p_current[2] - p_hydro)*scalex*scaley*vol0;
if (pstyle == TRICLINIC) {
fextra[3] = fextra[4] = fextra[5] = 0.0;
if (p_flag[3])
fextra[3] = pv2e*p_current[3]*scaley*yprdinit*scalex*xprdinit*yprdinit;
if (p_flag[4])
fextra[4] = pv2e*p_current[4]*scalex*xprdinit*scaley*yprdinit*xprdinit;
if (p_flag[5])
fextra[5] = pv2e*p_current[5]*scalex*xprdinit*scalez*zprdinit*xprdinit;
}
if (deviatoric_flag) {
compute_deviatoric();
if (p_flag[0]) fextra[0] -= fdev[0]*xprdinit;
if (p_flag[1]) fextra[1] -= fdev[1]*yprdinit;
if (p_flag[2]) fextra[2] -= fdev[2]*zprdinit;
if (pstyle == TRICLINIC) {
if (p_flag[3]) fextra[3] -= fdev[3]*yprdinit;
if (p_flag[4]) fextra[4] -= fdev[4]*xprdinit;
if (p_flag[5]) fextra[5] -= fdev[5]*xprdinit;
}
eng += compute_strain_energy();
}
}
return eng;
}
/* ----------------------------------------------------------------------
store extra dof values for minimization linesearch starting point
boxlo0,boxhi0 = box dimensions
box values are pushed onto a LIFO stack so nested calls can be made
values are popped by calling min_step(0.0)
------------------------------------------------------------------------- */
void FixBoxRelax::min_store()
{
for (int i = 0; i < 3; i++) {
boxlo0[current_lifo][i] = domain->boxlo[i];
boxhi0[current_lifo][i] = domain->boxhi[i];
}
if (pstyle == TRICLINIC) {
boxtilt0[current_lifo][0] = domain->yz;
boxtilt0[current_lifo][1] = domain->xz;
boxtilt0[current_lifo][2] = domain->xy;
}
}
/* ----------------------------------------------------------------------
clear the LIFO stack for min_store
------------------------------------------------------------------------- */
void FixBoxRelax::min_clearstore()
{
current_lifo = 0;
}
/* ----------------------------------------------------------------------
push the LIFO stack for min_store
------------------------------------------------------------------------- */
void FixBoxRelax::min_pushstore()
{
if (current_lifo >= MAX_LIFO_DEPTH) {
error->all(FLERR,"Attempt to push beyond stack limit in fix box/relax");
return;
}
current_lifo++;
}
/* ----------------------------------------------------------------------
pop the LIFO stack for min_store
------------------------------------------------------------------------- */
void FixBoxRelax::min_popstore()
{
if (current_lifo <= 0) {
error->all(FLERR,"Attempt to pop empty stack in fix box/relax");
return;
}
current_lifo--;
}
/* ----------------------------------------------------------------------
check if time to reset reference state. If so, do so.
------------------------------------------------------------------------- */
int FixBoxRelax::min_reset_ref()
{
int itmp = 0;
// if nreset_h0 > 0, reset reference box
// every nreset_h0 timesteps
// only needed for deviatoric external stress
if (deviatoric_flag && nreset_h0 > 0) {
int delta = update->ntimestep - update->beginstep;
if (delta % nreset_h0 == 0) {
compute_sigma();
itmp = 1;
}
}
return itmp;
}
/* ----------------------------------------------------------------------
change the box dimensions by fraction ds = alpha*hextra
------------------------------------------------------------------------- */
void FixBoxRelax::min_step(double alpha, double *hextra)
{
if (pstyle == ISO) {
ds[0] = ds[1] = ds[2] = alpha*hextra[0];
} else {
ds[0] = ds[1] = ds[2] = 0.0;
if (p_flag[0]) ds[0] = alpha*hextra[0];
if (p_flag[1]) ds[1] = alpha*hextra[1];
if (p_flag[2]) ds[2] = alpha*hextra[2];
if (pstyle == TRICLINIC) {
ds[3] = ds[4] = ds[5] = 0.0;
if (p_flag[3]) ds[3] = alpha*hextra[3];
if (p_flag[4]) ds[4] = alpha*hextra[4];
if (p_flag[5]) ds[5] = alpha*hextra[5];
}
}
remap();
if (kspace_flag) force->kspace->setup();
}
/* ----------------------------------------------------------------------
max allowed step size along hextra
------------------------------------------------------------------------- */
double FixBoxRelax::max_alpha(double *hextra)
{
double alpha = 1.0;
if (pstyle == ISO) alpha = vmax/fabs(hextra[0]);
else {
if (p_flag[0]) alpha = MIN(alpha,vmax/fabs(hextra[0]));
if (p_flag[1]) alpha = MIN(alpha,vmax/fabs(hextra[1]));
if (p_flag[2]) alpha = MIN(alpha,vmax/fabs(hextra[2]));
if (pstyle == TRICLINIC) {
if (p_flag[3]) alpha = MIN(alpha,vmax/fabs(hextra[3]));
if (p_flag[4]) alpha = MIN(alpha,vmax/fabs(hextra[4]));
if (p_flag[5]) alpha = MIN(alpha,vmax/fabs(hextra[5]));
}
}
return alpha;
}
/* ----------------------------------------------------------------------
return number of degrees of freedom added by this fix
------------------------------------------------------------------------- */
int FixBoxRelax::min_dof()
{
if (pstyle == ISO) return 1;
if (pstyle == TRICLINIC) return 6;
return 3;
}
/* ----------------------------------------------------------------------
dilate the box and owned/ghost atoms around center of box
------------------------------------------------------------------------- */
void FixBoxRelax::remap()
{
int i,n;
// rescale simulation box from linesearch starting point
// scale atom coords for all atoms or only for fix group atoms
double **x = atom->x;
int *mask = atom->mask;
n = atom->nlocal + atom->nghost;
// convert pertinent atoms and rigid bodies to lamda coords
if (allremap) domain->x2lamda(n);
else {
for (i = 0; i < n; i++)
if (mask[i] & groupbit)
domain->x2lamda(x[i],x[i]);
}
if (nrigid)
for (i = 0; i < nrigid; i++)
modify->fix[rfix[i]]->deform(0);
// reset global and local box to new size/shape
for (i = 0; i < 3; i++)
if (p_flag[i]) {
double currentBoxLo0 = boxlo0[current_lifo][i];
double currentBoxHi0 = boxhi0[current_lifo][i];
domain->boxlo[i] = currentBoxLo0 + (currentBoxLo0 - fixedpoint[i])/domain->h[i]*ds[i]*h0[i];
domain->boxhi[i] = currentBoxHi0 + (currentBoxHi0 - fixedpoint[i])/domain->h[i]*ds[i]*h0[i];
if (domain->boxlo[i] >= domain->boxhi[i])
error->all(FLERR,"Fix box/relax generated negative box length");
}
// scale tilt factors with cell, if set
if (scaleyz) domain->yz = (domain->boxhi[2] - domain->boxlo[2])*h0[3]/h0[2];
if (scalexz) domain->xz = (domain->boxhi[2] - domain->boxlo[2])*h0[4]/h0[2];
if (scalexy) domain->xy = (domain->boxhi[1] - domain->boxlo[1])*h0[5]/h0[1];
if (pstyle == TRICLINIC) {
if (p_flag[3]) domain->yz = boxtilt0[current_lifo][0]+ds[3]*yprdinit;
if (p_flag[4]) domain->xz = boxtilt0[current_lifo][1]+ds[4]*xprdinit;
if (p_flag[5]) domain->xy = boxtilt0[current_lifo][2]+ds[5]*xprdinit;
}
domain->set_global_box();
domain->set_local_box();
// convert pertinent atoms and rigid bodies back to box coords
if (allremap) domain->lamda2x(n);
else {
for (i = 0; i < n; i++)
if (mask[i] & groupbit)
domain->lamda2x(x[i],x[i]);
}
if (nrigid)
for (i = 0; i < nrigid; i++)
modify->fix[rfix[i]]->deform(1);
}
/* ---------------------------------------------------------------------- */
void FixBoxRelax::couple()
{
double *tensor = pressure->vector;
if (pstyle == ISO)
p_current[0] = p_current[1] = p_current[2] = pressure->scalar;
else if (pcouple == XYZ) {
double ave = 1.0/3.0 * (tensor[0] + tensor[1] + tensor[2]);
p_current[0] = p_current[1] = p_current[2] = ave;
} else if (pcouple == XY) {
double ave = 0.5 * (tensor[0] + tensor[1]);
p_current[0] = p_current[1] = ave;
p_current[2] = tensor[2];
} else if (pcouple == YZ) {
double ave = 0.5 * (tensor[1] + tensor[2]);
p_current[1] = p_current[2] = ave;
p_current[0] = tensor[0];
} else if (pcouple == XZ) {
double ave = 0.5 * (tensor[0] + tensor[2]);
p_current[0] = p_current[2] = ave;
p_current[1] = tensor[1];
} else {
p_current[0] = tensor[0];
p_current[1] = tensor[1];
p_current[2] = tensor[2];
}
// switch order from xy-xz-yz to Voigt
if (pstyle == TRICLINIC) {
p_current[3] = tensor[5];
p_current[4] = tensor[4];
p_current[5] = tensor[3];
}
}
/* ---------------------------------------------------------------------- */
int FixBoxRelax::modify_param(int narg, char **arg)
{
if (strcmp(arg[0],"temp") == 0) {
if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
if (tflag) {
modify->delete_compute(id_temp);
tflag = 0;
}
delete [] id_temp;
int n = strlen(arg[1]) + 1;
id_temp = new char[n];
strcpy(id_temp,arg[1]);
int icompute = modify->find_compute(arg[1]);
if (icompute < 0)
error->all(FLERR,"Could not find fix_modify temperature ID");
temperature = modify->compute[icompute];
if (temperature->tempflag == 0)
error->all(FLERR,
"Fix_modify temperature ID does not compute temperature");
if (temperature->igroup != 0 && comm->me == 0)
error->warning(FLERR,"Temperature for fix modify is not for group all");
// reset id_temp of pressure to new temperature ID
icompute = modify->find_compute(id_press);
if (icompute < 0)
error->all(FLERR,"Pressure ID for fix modify does not exist");
modify->compute[icompute]->reset_extra_compute_fix(id_temp);
return 2;
} else if (strcmp(arg[0],"press") == 0) {
if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
if (pflag) {
modify->delete_compute(id_press);
pflag = 0;
}
delete [] id_press;
int n = strlen(arg[1]) + 1;
id_press = new char[n];
strcpy(id_press,arg[1]);
int icompute = modify->find_compute(arg[1]);
if (icompute < 0) error->all(FLERR,"Could not find fix_modify pressure ID");
pressure = modify->compute[icompute];
if (pressure->pressflag == 0)
error->all(FLERR,"Fix_modify pressure ID does not compute pressure");
return 2;
}
return 0;
}
/* ----------------------------------------------------------------------
compute sigma tensor (needed whenever reference box is reset)
-----------------------------------------------------------------------*/
void FixBoxRelax::compute_sigma()
{
double pdeviatoric[3][3];
double tmp1[3][3],sigma_tensor[3][3],h_invtmp[3][3];
// reset reference box dimensions
xprdinit = domain->xprd;
yprdinit = domain->yprd;
zprdinit = domain->zprd;
if (dimension == 2) zprdinit = 1.0;
vol0 = xprdinit * yprdinit * zprdinit;
h0_inv[0] = domain->h_inv[0];
h0_inv[1] = domain->h_inv[1];
h0_inv[2] = domain->h_inv[2];
h0_inv[3] = domain->h_inv[3];
h0_inv[4] = domain->h_inv[4];
h0_inv[5] = domain->h_inv[5];
h_invtmp[0][0] = h0_inv[0];
h_invtmp[1][1] = h0_inv[1];
h_invtmp[2][2] = h0_inv[2];
h_invtmp[1][2] = h0_inv[3];
h_invtmp[0][2] = h0_inv[4];
h_invtmp[0][1] = h0_inv[5];
h_invtmp[2][1] = 0.0;
h_invtmp[2][0] = 0.0;
h_invtmp[1][0] = 0.0;
// compute target deviatoric stress tensor pdevmod
pdeviatoric[0][0] = pdeviatoric[1][1] = pdeviatoric[2][2] = 0.0;
if (p_flag[0]) pdeviatoric[0][0] = p_target[0] - p_hydro;
if (p_flag[1]) pdeviatoric[1][1] = p_target[1] - p_hydro;
if (p_flag[2]) pdeviatoric[2][2] = p_target[2] - p_hydro;
pdeviatoric[1][2] = pdeviatoric[2][1] = p_target[3];
pdeviatoric[0][2] = pdeviatoric[2][0] = p_target[4];
pdeviatoric[0][1] = pdeviatoric[1][0] = p_target[5];
// Modify to account for off-diagonal terms
// These equations come from the stationarity relation:
// Pdev,sys = Pdev,targ*hinv^t*hdiag
// where:
// Pdev,sys is the system deviatoric stress tensor,
// Pdev,targ = pdeviatoric, effective target deviatoric stress
// hinv^t is the transpose of the inverse h tensor
// hdiag is the diagonal part of the h tensor
pdeviatoric[1][1] -= pdeviatoric[1][2]*h0_inv[3]*h0[1];
pdeviatoric[0][1] -= pdeviatoric[0][2]*h0_inv[3]*h0[1];
pdeviatoric[1][0] = pdeviatoric[0][1];
pdeviatoric[0][0] -= pdeviatoric[0][1]*h0_inv[5]*h0[0] +
pdeviatoric[0][2]*h0_inv[4]*h0[0];
// compute symmetric sigma tensor
MathExtra::times3(h_invtmp,pdeviatoric,tmp1);
MathExtra::times3_transpose(tmp1,h_invtmp,sigma_tensor);
MathExtra::scalar_times3(vol0,sigma_tensor);
sigma[0] = sigma_tensor[0][0];
sigma[1] = sigma_tensor[1][1];
sigma[2] = sigma_tensor[2][2];
sigma[3] = sigma_tensor[1][2];
sigma[4] = sigma_tensor[0][2];
sigma[5] = sigma_tensor[0][1];
}
/* ----------------------------------------------------------------------
compute strain energy
-----------------------------------------------------------------------*/
double FixBoxRelax::compute_strain_energy()
{
// compute strain energy = 0.5*Tr(sigma*h*h^t) in energy units
double* h = domain->h;
double d0,d1,d2;
if (dimension == 3) {
d0 =
sigma[0]*(h[0]*h[0]+h[5]*h[5]+h[4]*h[4]) +
sigma[5]*( h[1]*h[5]+h[3]*h[4]) +
sigma[4]*( h[2]*h[4]);
d1 =
sigma[5]*( h[5]*h[1]+h[4]*h[3]) +
sigma[1]*( h[1]*h[1]+h[3]*h[3]) +
sigma[3]*( h[2]*h[3]);
d2 =
sigma[4]*( h[4]*h[2]) +
sigma[3]*( h[3]*h[2]) +
sigma[2]*( h[2]*h[2]);
} else {
d0 = sigma[0]*(h[0]*h[0]+h[5]*h[5]) + sigma[5]*h[1]*h[5];
d1 = sigma[5]*h[5]*h[1] + sigma[1]*h[1]*h[1];
d2 = 0.0;
}
double energy = 0.5*(d0+d1+d2)*pv2e;
return energy;
}
/* ----------------------------------------------------------------------
compute deviatoric barostat force = h*sigma*h^t
-----------------------------------------------------------------------*/
void FixBoxRelax::compute_deviatoric()
{
double* h = domain->h;
// [ 0 5 4 ] [ 0 5 4 ] [ 0 5 4 ]
// [ 5 1 3 ] = [ - 1 3 ] [ 5 1 3 ]
// [ 4 3 2 ] [ - - 2 ] [ 4 3 2 ]
if (dimension == 3) {
fdev[0] = pv2e*(h[0]*sigma[0]+h[5]*sigma[5]+h[4]*sigma[4]);
fdev[1] = pv2e*(h[1]*sigma[1]+h[3]*sigma[3]);
fdev[2] = pv2e*(h[2]*sigma[2]);
fdev[3] = pv2e*(h[1]*sigma[3]+h[3]*sigma[2]);
fdev[4] = pv2e*(h[0]*sigma[4]+h[5]*sigma[3]+h[4]*sigma[2]);
fdev[5] = pv2e*(h[0]*sigma[5]+h[5]*sigma[1]+h[4]*sigma[3]);
} else {
fdev[0] = pv2e*(h[0]*sigma[0]+h[5]*sigma[5]);
fdev[1] = pv2e*(h[1]*sigma[1]);
fdev[5] = pv2e*(h[0]*sigma[5]+h[5]*sigma[1]);
}
}
/* ----------------------------------------------------------------------
compute hydrostatic target pressure
-----------------------------------------------------------------------*/
void FixBoxRelax::compute_press_target()
{
pflagsum = p_flag[0] + p_flag[1] + p_flag[2];
p_hydro = 0.0;
for (int i = 0; i < 3; i++)
if (p_flag[i]) p_hydro += p_target[i];
if (pflagsum) p_hydro /= pflagsum;
for (int i = 0; i < 3; i++) {
if (p_flag[i] && fabs(p_hydro - p_target[i]) > 1.0e-6) deviatoric_flag = 1;
}
if (pstyle == TRICLINIC) {
for (int i = 3; i < 6; i++)
if (p_flag[i] && fabs(p_target[i]) > 1.0e-6) deviatoric_flag = 1;
}
}
/* ----------------------------------------------------------------------
compute PV and strain energy for access to the user
---------------------------------------------------------------------- */
double FixBoxRelax::compute_scalar()
{
double ftmp[6] = {0.0,0.0,0.0,0.0,0.0,0.0};
if (update->ntimestep == 0) return 0.0;
return min_energy(ftmp);
}
Reference in New Issue View Git Blame Copy Permalink