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fix_box_relax.cpp
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Sat, Aug 10, 05:15

fix_box_relax.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 author: Aidan Thompson (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "string.h"
#include "stdlib.h"
#include "fix_box_relax.h"
#include "atom.h"
#include "domain.h"
#include "update.h"
#include "comm.h"
#include "force.h"
#include "modify.h"
#include "compute.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
enum{XYZ,XY,YZ,XZ,ANISO};
/* ---------------------------------------------------------------------- */
FixBoxRelax::FixBoxRelax(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 4) error->all("Illegal fix box/relax command");
box_change = 1;
if (strcmp(arg[3],"xyz") == 0) {
if (narg < 5) error->all("Illegal fix box/relax command");
press_couple = XYZ;
p_target[0] = p_target[1] = p_target[2] = atof(arg[4]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (domain->dimension == 2) p_flag[2] = 0;
} else {
if (strcmp(arg[3],"xy") == 0) press_couple = XY;
else if (strcmp(arg[3],"yz") == 0) press_couple = YZ;
else if (strcmp(arg[3],"xz") == 0) press_couple = XZ;
else if (strcmp(arg[3],"aniso") == 0) press_couple = ANISO;
else error->all("Illegal fix box/relax command");
if (narg < 7) error->all("Illegal fix box/relax command");
if (domain->dimension == 2 &&
(press_couple == XY || press_couple == YZ || press_couple == XZ))
error->all("Invalid fix box/relax command for a 2d simulation");
if (strcmp(arg[4],"NULL") == 0) {
p_target[0] = 0.0;
p_flag[0] = 0;
} else {
p_target[0] = atof(arg[4]);
p_flag[0] = 1;
}
if (strcmp(arg[5],"NULL") == 0) {
p_target[1] = 0.0;
p_flag[1] = 0;
} else {
p_target[1] = atof(arg[5]);
p_flag[1] = 1;
}
if (strcmp(arg[6],"NULL") == 0) {
p_target[2] = 0.0;
p_flag[2] = 0;
} else {
if (domain->dimension == 2)
error->all("Invalid fix box/relax command for a 2d simulation");
p_target[2] = atof(arg[6]);
p_flag[2] = 1;
}
}
pflagsum = p_flag[0] + p_flag[1] + p_flag[2];
// process extra keywords
allremap = 1;
vmax = 0.0001;
int iarg;
if (press_couple == XYZ) iarg = 5;
else iarg = 7;
while (iarg < narg) {
if (strcmp(arg[iarg],"dilate") == 0) {
if (iarg+2 > narg) error->all("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("Illegal fix box/relax command");
iarg += 2;
} else if (strcmp(arg[iarg],"vmax") == 0) {
if (iarg+2 > narg) error->all("Illegal fix box/relax command");
vmax = atof(arg[iarg+1]);
iarg += 2;
} else error->all("Illegal fix box/relax command");
}
// error checks
if (press_couple == XY && (p_flag[0] == 0 || p_flag[1] == 0))
error->all("Illegal fix box/relax command");
if (press_couple == YZ && (p_flag[1] == 0 || p_flag[2] == 0))
error->all("Illegal fix box/relax command");
if (press_couple == XZ && (p_flag[0] == 0 || p_flag[2] == 0))
error->all("Illegal fix box/relax command");
if (press_couple == XY && p_target[0] != p_target[1])
error->all("Illegal fix box/relax command");
if (press_couple == YZ && p_target[1] != p_target[2])
error->all("Illegal fix box/relax command");
if (press_couple == XZ && p_target[0] != p_target[2])
error->all("Illegal fix box/relax command");
if (p_flag[0] && domain->xperiodic == 0)
error->all("Cannot use fix box/relax on a non-periodic dimension");
if (p_flag[1] && domain->yperiodic == 0)
error->all("Cannot use fix box/relax on a non-periodic dimension");
if (p_flag[2] && domain->zperiodic == 0)
error->all("Cannot use fix box/relax on a non-periodic dimension");
if (vmax <= 0.0) error->all("Illegal fix box/relax command");
// 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("Temperature ID for fix box/relax does not exist");
temperature = modify->compute[icompute];
icompute = modify->find_compute(id_press);
if (icompute < 0) error->all("Pressure ID for fix box/relax does not exist");
pressure = modify->compute[icompute];
// initial box dimensions
xprdinit = domain->xprd;
yprdinit = domain->yprd;
zprdinit = domain->zprd;
if (dimension == 3) volinit = domain->xprd*domain->yprd*domain->zprd;
else volinit = domain->xprd*domain->yprd;
pv2e = 1.0 / force->nktv2p;
// 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;
}
}
/* ----------------------------------------------------------------------
compute energy and force due to extra degrees of freedom
------------------------------------------------------------------------- */
double FixBoxRelax::min_energy(double *fextra)
{
double eng,scale,scalex,scaley,scalez;
double t_current = temperature->compute_scalar();
if (press_couple == XYZ) {
double tmp = 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 (press_couple == XYZ) {
scale = domain->xprd/xprdinit;
if (dimension == 3) {
eng = pv2e * p_target[0] * (scale*scale*scale-1.0)*volinit;
fextra[0] = pv2e * (p_current[0] - p_target[0])*3.0*scale*scale*volinit;
} else {
eng = pv2e * p_target[0] * (scale*scale-1.0)*volinit;
fextra[0] = pv2e * (p_current[0] - p_target[0])*2.0*scale*volinit;
}
} 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;
eng = pv2e * (p_flag[0]*p_target[0] + p_flag[1]*p_target[1] +
p_flag[2]*p_target[2])/pflagsum *
(scalex*scaley*scalez-1.0)*volinit;
if (p_flag[0])
fextra[0] = pv2e * (p_current[0] - p_target[0])*scaley*scalez*volinit;
if (p_flag[1])
fextra[1] = pv2e * (p_current[1] - p_target[1])*scalex*scalez*volinit;
if (p_flag[2])
fextra[2] = pv2e * (p_current[2] - p_target[2])*scalex*scaley*volinit;
}
return eng;
}
/* ----------------------------------------------------------------------
store extra dof values for minimization linesearch starting point
boxlo0,boxhi0 = box dimensions
s0 = ratio of current boxsize to initial boxsize
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];
}
s0[0] = (boxhi0[current_lifo][0]-boxlo0[current_lifo][0])/xprdinit;
s0[1] = (boxhi0[current_lifo][1]-boxlo0[current_lifo][1])/yprdinit;
s0[2] = (boxhi0[current_lifo][2]-boxlo0[current_lifo][2])/zprdinit;
}
/* ----------------------------------------------------------------------
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("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("Attempt to pop empty stack in fix box/relax");
return;
}
current_lifo--;
}
/* ----------------------------------------------------------------------
change the box dimensions by fraction ds = alpha*hextra
------------------------------------------------------------------------- */
void FixBoxRelax::min_step(double alpha, double *hextra)
{
if (press_couple == XYZ) {
ds[0] = ds[1] = ds[2] = alpha*hextra[0];
} else {
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];
}
remap();
}
/* ----------------------------------------------------------------------
max allowed step size along hextra
------------------------------------------------------------------------- */
double FixBoxRelax::max_alpha(double *hextra)
{
double alpha = 0.0;
if (press_couple == XYZ) alpha = vmax/fabs(hextra[0]);
else {
alpha = vmax/fabs(hextra[0]);
alpha = MIN(alpha,vmax/fabs(hextra[1]));
alpha = MIN(alpha,vmax/fabs(hextra[2]));
}
return alpha;
}
/* ----------------------------------------------------------------------
return number of degrees of freedom added by this fix
------------------------------------------------------------------------- */
int FixBoxRelax::min_dof()
{
if (press_couple == XYZ) return 1;
return 3;
}
/* ----------------------------------------------------------------------
dilate the box and owned/ghost atoms around center of box
------------------------------------------------------------------------- */
void FixBoxRelax::remap()
{
int i,n;
double ctr;
// ctr = geometric center of box in a dimension
// 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];
ctr = 0.5 * (currentBoxLo0 + currentBoxHi0);
domain->boxlo[i] = currentBoxLo0 + (currentBoxLo0-ctr)*ds[i]/s0[i];
domain->boxhi[i] = currentBoxHi0 + (currentBoxHi0-ctr)*ds[i]/s0[i];
}
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 (press_couple == XYZ)
p_current[0] = p_current[1] = p_current[2] = pressure->scalar;
else if (press_couple == XY) {
double ave = 0.5 * (tensor[0] + tensor[1]);
p_current[0] = p_current[1] = ave;
p_current[2] = tensor[2];
} else if (press_couple == YZ) {
double ave = 0.5 * (tensor[1] + tensor[2]);
p_current[1] = p_current[2] = ave;
p_current[0] = tensor[0];
} else if (press_couple == XZ) {
double ave = 0.5 * (tensor[0] + tensor[2]);
p_current[0] = p_current[2] = ave;
p_current[1] = tensor[1];
} else if (press_couple == ANISO) {
p_current[0] = tensor[0];
p_current[1] = tensor[1];
p_current[2] = tensor[2];
}
}
/* ---------------------------------------------------------------------- */
int FixBoxRelax::modify_param(int narg, char **arg)
{
if (strcmp(arg[0],"temp") == 0) {
if (narg < 2) error->all("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("Could not find fix_modify temperature ID");
temperature = modify->compute[icompute];
if (temperature->tempflag == 0)
error->all("Fix_modify temperature ID does not compute temperature");
if (temperature->igroup != 0 && comm->me == 0)
error->warning("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("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("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("Could not find fix_modify pressure ID");
pressure = modify->compute[icompute];
if (pressure->pressflag == 0)
error->all("Fix_modify pressure ID does not compute pressure");
return 2;
}
return 0;
}

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