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lammps/src/fix_press_berendsen.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.
------------------------------------------------------------------------- */
#include "string.h"
#include "stdlib.h"
#include "math.h"
#include "fix_press_berendsen.h"
#include "atom.h"
#include "force.h"
#include "comm.h"
#include "modify.h"
#include "fix_deform.h"
#include "compute.h"
#include "kspace.h"
#include "update.h"
#include "respa.h"
#include "domain.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{NOBIAS,BIAS};
enum{NONE,XYZ,XY,YZ,XZ};
enum{ISO,ANISO};
/* ---------------------------------------------------------------------- */
FixPressBerendsen::FixPressBerendsen(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 5) error->all("Illegal fix press/berendsen command");
box_change = 1;
box_change_size = 1;
// Berendsen barostat applied every step
nevery = 1;
// default values
pcouple = NONE;
bulkmodulus = 10.0;
allremap = 1;
for (int i = 0; i < 3; i++) {
p_start[i] = p_stop[i] = p_period[i] = 0.0;
p_flag[i] = 0;
p_period[i] = 0.0;
}
// process keywords
dimension = domain->dimension;
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg],"iso") == 0) {
if (iarg+4 > narg) error->all("Illegal fix press/berendsen command");
pcouple = XYZ;
p_start[0] = p_start[1] = p_start[2] = atof(arg[iarg+1]);
p_stop[0] = p_stop[1] = p_stop[2] = atof(arg[iarg+2]);
p_period[0] = p_period[1] = p_period[2] = atof(arg[iarg+3]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (dimension == 2) {
p_start[2] = p_stop[2] = p_period[2] = 0.0;
p_flag[2] = 0;
}
iarg += 4;
} else if (strcmp(arg[iarg],"aniso") == 0) {
if (iarg+4 > narg) error->all("Illegal fix press/berendsen command");
pcouple = NONE;
p_start[0] = p_start[1] = p_start[2] = atof(arg[iarg+1]);
p_stop[0] = p_stop[1] = p_stop[2] = atof(arg[iarg+2]);
p_period[0] = p_period[1] = p_period[2] = atof(arg[iarg+3]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (dimension == 2) {
p_start[2] = p_stop[2] = p_period[2] = 0.0;
p_flag[2] = 0;
}
iarg += 4;
} else if (strcmp(arg[iarg],"x") == 0) {
if (iarg+4 > narg) error->all("Illegal fix press/berendsen command");
p_start[0] = atof(arg[iarg+1]);
p_stop[0] = atof(arg[iarg+2]);
p_period[0] = atof(arg[iarg+3]);
p_flag[0] = 1;
iarg += 4;
} else if (strcmp(arg[iarg],"y") == 0) {
if (iarg+4 > narg) error->all("Illegal fix press/berendsen command");
p_start[1] = atof(arg[iarg+1]);
p_stop[1] = atof(arg[iarg+2]);
p_period[1] = atof(arg[iarg+3]);
p_flag[1] = 1;
iarg += 4;
} else if (strcmp(arg[iarg],"z") == 0) {
if (iarg+4 > narg) error->all("Illegal fix press/berendsen command");
p_start[2] = atof(arg[iarg+1]);
p_stop[2] = atof(arg[iarg+2]);
p_period[2] = atof(arg[iarg+3]);
p_flag[2] = 1;
iarg += 4;
if (dimension == 2)
error->all("Invalid fix press/berendsen for a 2d simulation");
} else if (strcmp(arg[iarg],"couple") == 0) {
if (iarg+2 > narg) error->all("Illegal fix press/berendsen 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("Illegal fix press/berendsen command");
iarg += 2;
} else if (strcmp(arg[iarg],"modulus") == 0) {
if (iarg+2 > narg) error->all("Illegal fix press/berendsen command");
bulkmodulus = atof(arg[iarg+1]);
if (bulkmodulus <= 0.0)
error->all("Illegal fix press/berendsen command");
iarg += 2;
} else if (strcmp(arg[iarg],"dilate") == 0) {
if (iarg+2 > narg) error->all("Illegal fix press/berendsen 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 press/berendsen command");
iarg += 2;
} else error->all("Illegal fix press/berendsen command");
}
if (allremap == 0) restart_pbc = 1;
// error checks
if (dimension == 2 && p_flag[2])
error->all("Invalid fix press/berendsen for a 2d simulation");
if (dimension == 2 && (pcouple == YZ || pcouple == XZ))
error->all("Invalid fix press/berendsen for a 2d simulation");
if (pcouple == XYZ && (p_flag[0] == 0 || p_flag[1] == 0))
error->all("Invalid fix press/berendsen pressure settings");
if (pcouple == XYZ && dimension == 3 && p_flag[2] == 0)
error->all("Invalid fix press/berendsen pressure settings");
if (pcouple == XY && (p_flag[0] == 0 || p_flag[1] == 0))
error->all("Invalid fix press/berendsen pressure settings");
if (pcouple == YZ && (p_flag[1] == 0 || p_flag[2] == 0))
error->all("Invalid fix press/berendsen pressure settings");
if (pcouple == XZ && (p_flag[0] == 0 || p_flag[2] == 0))
error->all("Invalid fix press/berendsen pressure settings");
if (p_flag[0] && domain->xperiodic == 0)
error->all("Cannot use fix press/berendsen on a non-periodic dimension");
if (p_flag[1] && domain->yperiodic == 0)
error->all("Cannot use fix press/berendsen on a non-periodic dimension");
if (p_flag[2] && domain->zperiodic == 0)
error->all("Cannot use fix press/berendsen on a non-periodic dimension");
if (pcouple == XYZ && dimension == 3 &&
(p_start[0] != p_start[1] || p_start[0] != p_start[2] ||
p_stop[0] != p_stop[1] || p_stop[0] != p_stop[2] ||
p_period[0] != p_period[1] || p_period[0] != p_period[2]))
error->all("Invalid fix press/berendsen pressure settings");
if (pcouple == XYZ && dimension == 2 &&
(p_start[0] != p_start[1] || p_stop[0] != p_stop[1] ||
p_period[0] != p_period[1]))
error->all("Invalid fix press/berendsen pressure settings");
if (pcouple == XY &&
(p_start[0] != p_start[1] || p_stop[0] != p_stop[1] ||
p_period[0] != p_period[1]))
error->all("Invalid fix press/berendsen pressure settings");
if (pcouple == YZ &&
(p_start[1] != p_start[2] || p_stop[1] != p_stop[2] ||
p_period[1] != p_period[2]))
error->all("Invalid fix press/berendsen pressure settings");
if (pcouple == XZ &&
(p_start[0] != p_start[2] || p_stop[0] != p_stop[2] ||
p_period[0] != p_period[2]))
error->all("Invalid fix press/berendsen pressure settings");
if ((p_flag[0] && p_period[0] <= 0.0) ||
(p_flag[1] && p_period[1] <= 0.0) ||
(p_flag[2] && p_period[2] <= 0.0))
error->all("Fix press/berendsen damping parameters must be > 0.0");
// pstyle = ISO if XYZ coupling or XY coupling in 2d -> 1 dof
// else pstyle = ANISO -> 3 dof
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
// 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*[4];
newarg[0] = id_press;
newarg[1] = (char *) "all";
newarg[2] = (char *) "pressure";
newarg[3] = id_temp;
modify->add_compute(4,newarg);
delete [] newarg;
pflag = 1;
nrigid = 0;
rfix = NULL;
}
/* ---------------------------------------------------------------------- */
FixPressBerendsen::~FixPressBerendsen()
{
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 FixPressBerendsen::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixPressBerendsen::init()
{
if (domain->triclinic)
error->all("Cannot use fix press/berendsen with triclinic box");
// insure no conflict with fix deform
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"deform") == 0) {
int *dimflag = ((FixDeform *) modify->fix[i])->dimflag;
if ((p_flag[0] && dimflag[0]) || (p_flag[1] && dimflag[1]) ||
(p_flag[2] && dimflag[2]))
error->all("Cannot use fix press/berendsen and "
"fix deform on same component of stress tensor");
}
// set temperature and pressure ptrs
int icompute = modify->find_compute(id_temp);
if (icompute < 0)
error->all("Temperature ID for fix press/berendsen does not exist");
temperature = modify->compute[icompute];
if (temperature->tempbias) which = BIAS;
else which = NOBIAS;
icompute = modify->find_compute(id_press);
if (icompute < 0)
error->all("Pressure ID for fix press/berendsen does not exist");
pressure = modify->compute[icompute];
// Kspace setting
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;
}
}
/* ----------------------------------------------------------------------
compute T,P before integrator starts
------------------------------------------------------------------------- */
void FixPressBerendsen::setup(int vflag)
{
// trigger virial computation on next timestep
pressure->addstep(update->ntimestep+1);
}
/* ---------------------------------------------------------------------- */
void FixPressBerendsen::end_of_step()
{
// compute new T,P
if (pstyle == ISO) {
double tmp = temperature->compute_scalar();
tmp = pressure->compute_scalar();
} else {
temperature->compute_vector();
pressure->compute_vector();
}
couple();
double delta = update->ntimestep - update->beginstep;
delta /= update->endstep - update->beginstep;
for (int i = 0; i < 3; i++) {
if (p_flag[i]) {
p_target[i] = p_start[i] + delta * (p_stop[i]-p_start[i]);
dilation[i] =
pow(1.0 - update->dt/p_period[i] *
(p_target[i]-p_current[i])/bulkmodulus,1.0/3.0);
}
}
// remap simulation box and atoms
// redo KSpace coeffs since volume has changed
remap();
if (kspace_flag) force->kspace->setup();
// trigger virial computation on next timestep
pressure->addstep(update->ntimestep+1);
}
/* ---------------------------------------------------------------------- */
void FixPressBerendsen::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];
}
}
/* ----------------------------------------------------------------------
change box size
remap all atoms or fix group atoms depending on allremap flag
if rigid bodies exist, scale rigid body centers-of-mass
------------------------------------------------------------------------- */
void FixPressBerendsen::remap()
{
int i;
double oldlo,oldhi,ctr;
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
// convert pertinent atoms and rigid bodies to lamda coords
if (allremap) domain->x2lamda(nlocal);
else {
for (i = 0; i < nlocal; 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]) {
oldlo = domain->boxlo[i];
oldhi = domain->boxhi[i];
ctr = 0.5 * (oldlo + oldhi);
domain->boxlo[i] = (oldlo-ctr)*dilation[i] + ctr;
domain->boxhi[i] = (oldhi-ctr)*dilation[i] + ctr;
}
}
domain->set_global_box();
domain->set_local_box();
// convert pertinent atoms and rigid bodies back to box coords
if (allremap) domain->lamda2x(nlocal);
else {
for (i = 0; i < nlocal; 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);
}
/* ---------------------------------------------------------------------- */
int FixPressBerendsen::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 NPT 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 press/berendsen 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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