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fix_press_berendsen.cpp
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fix_press_berendsen.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: [email protected]
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 "fix_press_berendsen.h"
#include "atom.h"
#include "comm.h"
#include "compute.h"
#include "domain.h"
#include "error.h"
#include "fix_deform.h"
#include "force.h"
#include "group.h"
#include "kspace.h"
#include "modify.h"
#include "update.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace FixConst;
enum { NOBIAS, BIAS };
enum { NONE, XYZ, XY, YZ, XZ };
enum { ISO, ANISO };
/* ---------------------------------------------------------------------- */
FixPressBerendsen::FixPressBerendsen(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), id_temp(nullptr), id_press(nullptr), tflag(0), pflag(0)
{
if (narg < 5) error->all(FLERR, "Illegal fix press/berendsen command");
// 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(FLERR, "Illegal fix press/berendsen command");
pcouple = XYZ;
p_start[0] = p_start[1] = p_start[2] = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
p_stop[0] = p_stop[1] = p_stop[2] = utils::numeric(FLERR, arg[iarg + 2], false, lmp);
p_period[0] = p_period[1] = p_period[2] = utils::numeric(FLERR, arg[iarg + 3], false, lmp);
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(FLERR, "Illegal fix press/berendsen command");
pcouple = NONE;
p_start[0] = p_start[1] = p_start[2] = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
p_stop[0] = p_stop[1] = p_stop[2] = utils::numeric(FLERR, arg[iarg + 2], false, lmp);
p_period[0] = p_period[1] = p_period[2] = utils::numeric(FLERR, arg[iarg + 3], false, lmp);
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(FLERR, "Illegal fix press/berendsen command");
p_start[0] = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
p_stop[0] = utils::numeric(FLERR, arg[iarg + 2], false, lmp);
p_period[0] = utils::numeric(FLERR, arg[iarg + 3], false, lmp);
p_flag[0] = 1;
iarg += 4;
} else if (strcmp(arg[iarg], "y") == 0) {
if (iarg + 4 > narg) error->all(FLERR, "Illegal fix press/berendsen command");
p_start[1] = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
p_stop[1] = utils::numeric(FLERR, arg[iarg + 2], false, lmp);
p_period[1] = utils::numeric(FLERR, arg[iarg + 3], false, lmp);
p_flag[1] = 1;
iarg += 4;
} else if (strcmp(arg[iarg], "z") == 0) {
if (iarg + 4 > narg) error->all(FLERR, "Illegal fix press/berendsen command");
p_start[2] = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
p_stop[2] = utils::numeric(FLERR, arg[iarg + 2], false, lmp);
p_period[2] = utils::numeric(FLERR, arg[iarg + 3], false, lmp);
p_flag[2] = 1;
iarg += 4;
if (dimension == 2) error->all(FLERR, "Invalid fix press/berendsen for a 2d simulation");
} else if (strcmp(arg[iarg], "couple") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "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(FLERR, "Illegal fix press/berendsen command");
iarg += 2;
} else if (strcmp(arg[iarg], "modulus") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal fix press/berendsen command");
bulkmodulus = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
if (bulkmodulus <= 0.0) error->all(FLERR, "Illegal fix press/berendsen command");
iarg += 2;
} else if (strcmp(arg[iarg], "dilate") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "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(FLERR, "Illegal fix press/berendsen command");
iarg += 2;
} else
error->all(FLERR, "Illegal fix press/berendsen command");
}
if (allremap == 0) restart_pbc = 1;
// error checks
if (dimension == 2 && p_flag[2])
error->all(FLERR, "Invalid fix press/berendsen for a 2d simulation");
if (dimension == 2 && (pcouple == YZ || pcouple == XZ))
error->all(FLERR, "Invalid fix press/berendsen for a 2d simulation");
if (pcouple == XYZ && (p_flag[0] == 0 || p_flag[1] == 0))
error->all(FLERR, "Invalid fix press/berendsen pressure settings");
if (pcouple == XYZ && dimension == 3 && p_flag[2] == 0)
error->all(FLERR, "Invalid fix press/berendsen pressure settings");
if (pcouple == XY && (p_flag[0] == 0 || p_flag[1] == 0))
error->all(FLERR, "Invalid fix press/berendsen pressure settings");
if (pcouple == YZ && (p_flag[1] == 0 || p_flag[2] == 0))
error->all(FLERR, "Invalid fix press/berendsen pressure settings");
if (pcouple == XZ && (p_flag[0] == 0 || p_flag[2] == 0))
error->all(FLERR, "Invalid fix press/berendsen pressure settings");
if (p_flag[0] && domain->xperiodic == 0)
error->all(FLERR, "Cannot use fix press/berendsen on a non-periodic dimension");
if (p_flag[1] && domain->yperiodic == 0)
error->all(FLERR, "Cannot use fix press/berendsen on a non-periodic dimension");
if (p_flag[2] && domain->zperiodic == 0)
error->all(FLERR, "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(FLERR, "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(FLERR, "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(FLERR, "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(FLERR, "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(FLERR, "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(FLERR, "Fix press/berendsen damping parameters must be > 0.0");
if (p_flag[0]) box_change |= BOX_CHANGE_X;
if (p_flag[1]) box_change |= BOX_CHANGE_Y;
if (p_flag[2]) box_change |= BOX_CHANGE_Z;
// 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
id_temp = utils::strdup(std::string(id) + "_temp");
modify->add_compute(fmt::format("{} all temp", id_temp));
tflag = 1;
// create a new compute pressure style
// id = fix-ID + press, compute group = all
// pass id_temp as 4th arg to pressure constructor
id_press = utils::strdup(std::string(id) + "_press");
modify->add_compute(fmt::format("{} all pressure {}", id_press, id_temp));
pflag = 1;
}
/* ---------------------------------------------------------------------- */
FixPressBerendsen::~FixPressBerendsen()
{
// 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(FLERR, "Cannot use fix press/berendsen with triclinic box");
// ensure no conflict with fix deform
for (const auto &ifix : modify->get_fix_by_style("^deform")) {
int *dimflag = static_cast<FixDeform *>(ifix)->dimflag;
if (!dimflag) continue;
if ((p_flag[0] && dimflag[0]) || (p_flag[1] && dimflag[1]) || (p_flag[2] && dimflag[2]))
error->all(FLERR,
"Cannot use fix press/berendsen and "
"fix deform on same component of stress tensor");
}
// set temperature and pressure ptrs
temperature = modify->get_compute_by_id(id_temp);
if (!temperature)
error->all(FLERR, "Temperature compute ID {} for fix press/berendsen does not exist", id_temp);
if (temperature->tempbias)
which = BIAS;
else
which = NOBIAS;
pressure = modify->get_compute_by_id(id_press);
if (!pressure)
error->all(FLERR, "Pressure compute ID {} for fix press/berendsen does not exist", id_press);
// 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.clear();
for (auto &ifix : modify->get_fix_list())
if (ifix->rigid_flag) rfix.push_back(ifix);
}
/* ----------------------------------------------------------------------
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) {
temperature->compute_scalar();
pressure->compute_scalar();
} else {
temperature->compute_vector();
pressure->compute_vector();
}
couple();
double delta = update->ntimestep - update->beginstep;
if (delta != 0.0) 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]);
}
for (auto &ifix : rfix) ifix->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]);
}
for (auto &ifix : rfix) ifix->deform(1);
}
/* ---------------------------------------------------------------------- */
int FixPressBerendsen::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;
id_temp = utils::strdup(arg[1]);
temperature = modify->get_compute_by_id(arg[1]);
if (!temperature)
error->all(FLERR, "Could not find fix_modify temperature compute ID: ", arg[1]);
if (temperature->tempflag == 0)
error->all(FLERR, "Fix_modify temperature compute {} does not compute temperature", arg[1]);
if (temperature->igroup != 0 && comm->me == 0)
error->warning(FLERR, "Temperature compute {} for fix {} is not for group all: {}", arg[1],
style, group->names[temperature->igroup]);
// reset id_temp of pressure to new temperature ID
auto icompute = modify->get_compute_by_id(id_press);
if (!icompute)
error->all(FLERR, "Pressure compute ID {} for fix {} does not exist", id_press, style);
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;
id_press = utils::strdup(arg[1]);
pressure = modify->get_compute_by_id(arg[1]);
if (!pressure) error->all(FLERR, "Could not find fix_modify pressure compute ID: {}", arg[1]);
if (pressure->pressflag == 0)
error->all(FLERR, "Fix_modify pressure compute {} does not compute pressure", arg[1]);
return 2;
}
return 0;
}