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Added triclinic and relative remap functions to press/langevin files

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This commit is contained in:
Germain Clavier
2023-05-19 16:34:42 +02:00
parent 1c33aec5dc
commit ab925000fe
2 changed files with 224 additions and 29 deletions
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235
src/fix_press_langevin.cpp
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@ -26,6 +26,7 @@
#include "fix_deform.h"
#include "force.h"
#include "group.h"
#include "irregular.h"
#include "kspace.h"
#include "modify.h"
#include "random_mars.h"
@ -37,14 +38,17 @@
using namespace LAMMPS_NS;
using namespace FixConst;
#define DELTAFLIP 0.1
#define TILTMAX 1.5
enum{NONE,XYZ,XY,YZ,XZ};
enum{ISO,ANISO};
enum{ISO,ANISO,TRICLINIC};
/* ---------------------------------------------------------------------- */
FixPressLangevin::FixPressLangevin(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
id_press(nullptr), pflag(0), random(nullptr)
id_press(nullptr), pflag(0), random(nullptr), irregular(nullptr)
{
if (narg < 5) error->all(FLERR,"Illegal fix press/langevin command");
@ -58,13 +62,15 @@ FixPressLangevin::FixPressLangevin(LAMMPS *lmp, int narg, char **arg) :
pcouple = NONE;
allremap = 1;
pre_exchange_flag = 0;
flipflag = 1;
// Alpha friction coefficient
p_fric = 1e-4;
// Target temperature
t_start = t_stop = t_target = 0.0;
for (int i = 0; i < 3; i++) {
for (int i = 0; i < 6; i++) {
// Pressure and pistons mass Q
p_start[i] = p_stop[i] = p_period[i] = 0.0;
p_flag[i] = 0;
@ -113,7 +119,28 @@ FixPressLangevin::FixPressLangevin(LAMMPS *lmp, int narg, char **arg) :
p_flag[2] = 0;
}
iarg += 4;
} else if (strcmp(arg[iarg],"tri") == 0) {
if (iarg+4 > narg)
error->all(FLERR,"Illegal fix press/langevin 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;
p_start[3] = p_start[4] = p_start[5] = 0.0;
p_stop[3] = p_stop[4] = p_stop[5] = 0.0;
p_period[3] = p_period[4] = p_period[5] =
utils::numeric(FLERR,arg[iarg+3],false,lmp);
p_flag[3] = p_flag[4] = p_flag[5] = 1;
if (dimension == 2) {
p_start[2] = p_stop[2] = p_period[2] = 0.0;
p_flag[2] = 0;
p_start[3] = p_stop[3] = p_period[3] = 0.0;
p_flag[3] = 0;
p_start[4] = p_stop[4] = p_period[4] = 0.0;
p_flag[4] = 0;
}
iarg += 4;
} else if (strcmp(arg[iarg],"x") == 0) {
if (iarg+4 > narg)
error->all(FLERR,"Illegal fix press/langevin command");
@ -140,6 +167,37 @@ FixPressLangevin::FixPressLangevin(LAMMPS *lmp, int narg, char **arg) :
iarg += 4;
if (dimension == 2)
error->all(FLERR,"Invalid fix press/langevin for a 2d simulation");
} else if (strcmp(arg[iarg],"xy") == 0) {
if (iarg+4 > narg) utils::missing_cmd_args(FLERR, fmt::format("fix {} yz", style), error);
p_start[3] = utils::numeric(FLERR,arg[iarg+1],false,lmp);
p_stop[3] = utils::numeric(FLERR,arg[iarg+2],false,lmp);
p_period[3] = utils::numeric(FLERR,arg[iarg+3],false,lmp);
p_flag[3] = 1;
iarg += 4;
if (dimension == 2) error->all(FLERR,"Invalid fix {} command for a 2d simulation", style);
} else if (strcmp(arg[iarg],"xz") == 0) {
if (iarg+4 > narg) utils::missing_cmd_args(FLERR, fmt::format("fix {} xz", style), error);
p_start[4] = utils::numeric(FLERR,arg[iarg+1],false,lmp);
p_stop[4] = utils::numeric(FLERR,arg[iarg+2],false,lmp);
p_period[4] = utils::numeric(FLERR,arg[iarg+3],false,lmp);
p_flag[4] = 1;
iarg += 4;
if (dimension == 2) error->all(FLERR,"Invalid fix {} command for a 2d simulation", style);
} else if (strcmp(arg[iarg],"yz") == 0) {
if (iarg+4 > narg) utils::missing_cmd_args(FLERR, fmt::format("fix {} xy", style), error);
p_start[5] = utils::numeric(FLERR,arg[iarg+1],false,lmp);
p_stop[5] = utils::numeric(FLERR,arg[iarg+2],false,lmp);
p_period[5] = utils::numeric(FLERR,arg[iarg+3],false,lmp);
p_flag[5] = 1;
iarg += 4;
if (dimension == 2) error->all(FLERR,"Invalid fix {} command for a 2d simulation", style);
} else if (strcmp(arg[iarg],"flip") == 0) {
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, fmt::format("fix {} flip", style), error);
flipflag = utils::logical(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"couple") == 0) {
if (iarg+2 > narg)
@ -212,6 +270,17 @@ FixPressLangevin::FixPressLangevin(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,
"Cannot use fix press/langevin 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 {} on a 2nd non-periodic dimension", style);
if (p_flag[4] && domain->zperiodic == 0)
error->all(FLERR, "Cannot use fix {} on a 2nd non-periodic dimension", style);
if (p_flag[5] && domain->yperiodic == 0)
error->all(FLERR, "Cannot use fix {} on a 2nd non-periodic dimension", style);
if (!domain->triclinic && (p_flag[3] || p_flag[4] || p_flag[5]))
error->all(FLERR,"Can not specify Pxy/Pxz/Pyz in fix {} with non-triclinic box", style);
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] ||
@ -234,26 +303,35 @@ FixPressLangevin::FixPressLangevin(LAMMPS *lmp, int narg, char **arg) :
p_period[0] != p_period[2]))
error->all(FLERR,"Invalid fix press/langevin pressure settings");
if (t_start < 0.0)
error->all(FLERR,"Fix press/langevin temperature parameters must be >= 0.0");
if (t_stop < 0.0)
if (t_start < 0.0 || t_stop < 0.0)
error->all(FLERR,"Fix press/langevin temperature parameters must be >= 0.0");
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))
(p_flag[2] && p_period[2] <= 0.0) ||
(p_flag[3] && p_period[3] <= 0.0) ||
(p_flag[4] && p_period[4] <= 0.0) ||
(p_flag[5] && p_period[5] <= 0.0))
error->all(FLERR,"Fix press/langevin 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;
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;
// pre_exchange only required if flips can occur due to shape changes
if (flipflag && (p_flag[3] || p_flag[4] || p_flag[5]))
pre_exchange_flag = pre_exchange_migrate = 1;
if (flipflag && (domain->yz != 0.0 || domain->xz != 0.0 ||
domain->xy != 0.0))
pre_exchange_flag = pre_exchange_migrate = 1;
if (pre_exchange_flag) irregular = new Irregular(lmp);
else irregular = nullptr;
// C1
// Langevin GJF dynamics does NOT need a temperature compute
// This is stated explicitely in their paper.
@ -278,7 +356,7 @@ FixPressLangevin::FixPressLangevin(LAMMPS *lmp, int narg, char **arg) :
modify->add_compute(fmt::format("{} all pressure NULL virial",id_press, id_temp));
pflag = 1;
for (int i = 0; i < 3; i++) {
for (int i = 0; i < 6; i++) {
gjfa[i] = (1.0 - update->dt / 2.0 / p_period[i]) / (1.0 + update->dt / 2.0 / p_period[i]);
gjfb[i] = 1./(1.0 + update->dt / 2.0 / p_period[i]);
}
@ -293,6 +371,8 @@ FixPressLangevin::~FixPressLangevin()
{
delete random;
delete[] rfix;
delete irregular;
// delete temperature and pressure if fix created them
@ -308,6 +388,7 @@ int FixPressLangevin::setmask()
mask |= INITIAL_INTEGRATE;
mask |= POST_FORCE;
mask |= END_OF_STEP;
if (pre_exchange_flag) mask |= PRE_EXCHANGE;
return mask;
}
@ -315,16 +396,14 @@ int FixPressLangevin::setmask()
void FixPressLangevin::init()
{
if (domain->triclinic)
error->all(FLERR,"Cannot use fix press/langevin with triclinic box");
// ensure no conflict with fix deform
for (const auto &ifix : modify->get_fix_list())
if (strcmp(ifix->style, "^deform") == 0) {
int *dimflag = static_cast<FixDeform *>(ifix)->dimflag;
if ((p_flag[0] && dimflag[0]) || (p_flag[1] && dimflag[1]) ||
(p_flag[2] && dimflag[2]))
(p_flag[2] && dimflag[2]) || (p_flag[3] && dimflag[3]) ||
(p_flag[4] && dimflag[4]) || (p_flag[5] && dimflag[5]))
error->all(FLERR,"Cannot use fix press/langevin and "
"fix deform on same component of stress tensor");
}
@ -386,14 +465,15 @@ void FixPressLangevin::initial_integrate(int /* vflag */)
dt = update->dt;
for (int i = 0; i < 3; i++) {
for (int i = 0; i < 6; i++) {
if (p_flag[i]) {
// See equation 13
displacement = dt*p_deriv[i]*gjfb[i];
displacement += 0.5*dt*dt*f_piston[i]*gjfb[i]/p_period[i];
displacement += 0.5*dt*fran[i]*gjfb[i]/p_period[i];
dl = domain->boxhi[i] - domain->boxlo[i];
dilation[i] = (dl + displacement)/dl;
if (i < 3) dilation[i] = (dl + displacement)/dl;
else dilation[i] = displacement;
}
}
@ -423,7 +503,7 @@ void FixPressLangevin::post_force(int /*vflag*/)
couple_pressure();
couple_kinetic(t_target);
for (int i = 0; i < 3; i++) {
for (int i = 0; i < 6; i++) {
if (p_flag[i]) {
f_old_piston[i] = f_piston[i];
p_target[i] = p_start[i] + delta * (p_stop[i]-p_start[i]);
@ -445,7 +525,7 @@ void FixPressLangevin::end_of_step()
double dt;
dt = update->dt;
for (int i = 0; i < 3; i++) {
for (int i = 0; i < 6; i++) {
if (p_flag[i]) {
p_deriv[i] *= gjfa[i];
p_deriv[i] += 0.5*dt*(gjfa[i]*f_old_piston[i]+f_piston[i])/p_period[i];
@ -483,6 +563,9 @@ void FixPressLangevin::couple_pressure()
p_current[1] = tensor[1];
p_current[2] = tensor[2];
}
p_current[3] = tensor[3];
p_current[4] = tensor[4];
p_current[5] = tensor[5];
}
/* ---------------------------------------------------------------------- */
@ -511,6 +594,7 @@ void FixPressLangevin::couple_beta(double t_target)
gamma = sqrt(2.0*force->boltz*update->dt*p_fric*t_target);
fran[0] = fran[1] = fran[2] = 0.0;
fran[3] = fran[4] = fran[5] = 0.0;
if (me == 0) {
if (pstyle == ISO)
fran[0] = fran[1] = fran[2] = gamma*random->gaussian();
@ -530,8 +614,11 @@ void FixPressLangevin::couple_beta(double t_target)
fran[1] = gamma*random->gaussian();
fran[2] = gamma*random->gaussian();
}
fran[3] = gamma*random->gaussian();
fran[4] = gamma*random->gaussian();
fran[5] = gamma*random->gaussian();
}
MPI_Bcast(&fran, 3, MPI_DOUBLE, 0, world);
MPI_Bcast(&fran, 6, MPI_DOUBLE, 0, world);
}
/* ----------------------------------------------------------------------
@ -574,6 +661,19 @@ void FixPressLangevin::remap()
}
}
if (p_flag[3]) domain->xy += dilation[3];
if (p_flag[4]) domain->xz += dilation[4];
if (p_flag[5]) domain->yz += dilation[5];
if (domain->yz < -TILTMAX*domain->yprd ||
domain->yz > TILTMAX*domain->yprd ||
domain->xz < -TILTMAX*domain->xprd ||
domain->xz > TILTMAX*domain->xprd ||
domain->xy < -TILTMAX*domain->xprd ||
domain->xy > TILTMAX*domain->xprd)
error->all(FLERR,"Fix {} has tilted box too far in one step - "
"periodic cell is too far from equilibrium state", style);
domain->set_global_box();
domain->set_local_box();
@ -591,6 +691,85 @@ void FixPressLangevin::remap()
modify->fix[rfix[i]]->deform(1);
}
/* ----------------------------------------------------------------------
if any tilt ratios exceed limits, set flip = 1 and compute new tilt values
do not flip in x or y if non-periodic (can tilt but not flip)
this is b/c the box length would be changed (dramatically) by flip
if yz tilt exceeded, adjust C vector by one B vector
if xz tilt exceeded, adjust C vector by one A vector
if xy tilt exceeded, adjust B vector by one A vector
check yz first since it may change xz, then xz check comes after
if any flip occurs, create new box in domain
image_flip() adjusts image flags due to box shape change induced by flip
remap() puts atoms outside the new box back into the new box
perform irregular on atoms in lamda coords to migrate atoms to new procs
important that image_flip comes before remap, since remap may change
image flags to new values, making eqs in doc of Domain:image_flip incorrect
------------------------------------------------------------------------- */
void FixPressLangevin::pre_exchange()
{
double xprd = domain->xprd;
double yprd = domain->yprd;
// flip is only triggered when tilt exceeds 0.5 by DELTAFLIP
// this avoids immediate re-flipping due to tilt oscillations
double xtiltmax = (0.5+DELTAFLIP)*xprd;
double ytiltmax = (0.5+DELTAFLIP)*yprd;
int flipxy,flipxz,flipyz;
flipxy = flipxz = flipyz = 0;
if (domain->yperiodic) {
if (domain->yz < -ytiltmax) {
domain->yz += yprd;
domain->xz += domain->xy;
flipyz = 1;
} else if (domain->yz >= ytiltmax) {
domain->yz -= yprd;
domain->xz -= domain->xy;
flipyz = -1;
}
}
if (domain->xperiodic) {
if (domain->xz < -xtiltmax) {
domain->xz += xprd;
flipxz = 1;
} else if (domain->xz >= xtiltmax) {
domain->xz -= xprd;
flipxz = -1;
}
if (domain->xy < -xtiltmax) {
domain->xy += xprd;
flipxy = 1;
} else if (domain->xy >= xtiltmax) {
domain->xy -= xprd;
flipxy = -1;
}
}
int flip = 0;
if (flipxy || flipxz || flipyz) flip = 1;
if (flip) {
domain->set_global_box();
domain->set_local_box();
domain->image_flip(flipxy,flipxz,flipyz);
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]);
domain->x2lamda(atom->nlocal);
irregular->migrate_atoms();
domain->lamda2x(atom->nlocal);
}
}
/* ---------------------------------------------------------------------- */
int FixPressLangevin::modify_param(int narg, char **arg)
@ -612,3 +791,13 @@ int FixPressLangevin::modify_param(int narg, char **arg)
}
return 0;
}
/* ---------------------------------------------------------------------- */
void FixPressLangevin::reset_dt()
{
for (int i=0; i<6; i++) {
gjfa[i] = (1.0 - update->dt / 2.0 / p_period[i]) / (1.0 + update->dt / 2.0 / p_period[i]);
gjfb[i] = sqrt(1.0 + update->dt / 2.0 / p_period[i]);
}
}

18
src/fix_press_langevin.h
View File

@ -31,23 +31,25 @@ class FixPressLangevin : public Fix {
int setmask() override;
void init() override;
void setup(int) override;
void pre_exchange() override;
void initial_integrate(int) override;
void post_force(int) override;
void end_of_step() override;
void reset_dt() override;
int modify_param(int, char **) override;
protected:
int dimension, which;
int pstyle, pcouple, allremap;
int p_flag[3]; // 1 if control P on this dim, 0 if not
int p_flag[6]; // 1 if control P on this dim, 0 if not
double t_start, t_stop, t_target;
double p_fric;
double p_start[3], p_stop[3], p_current[3];
double p_period[3], p_target[3];
double p_deriv[3], dilation[3];
double f_piston[3], f_old_piston[3];
double gjfa[3], gjfb[3], fran[3];
double p_start[6], p_stop[6], p_current[6];
double p_period[6], p_target[6];
double p_deriv[6], dilation[6];
double f_piston[6], f_old_piston[6];
double gjfa[6], gjfb[6], fran[6];
int kspace_flag; // 1 if KSpace invoked, 0 if not
int nrigid; // number of rigid fixes
int *rfix; // indices of rigid fixes
@ -56,6 +58,10 @@ class FixPressLangevin : public Fix {
class Compute *temperature, *pressure;
int pflag;
int flipflag;
int pre_exchange_flag; // set if pre_exchange needed for box flips
class Irregular *irregular; // for migrating atoms after box flips
class RanMars *random;
int seed;