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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3951 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2010-04-02 16:53:40 +00:00
parent 02ac8178c5
commit 75c51a178d
30 changed files with 3477 additions and 3896 deletions
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561
src/fix_box_relax.cpp
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@ -27,13 +27,17 @@
#include "modify.h"
#include "compute.h"
#include "error.h"
#include "math_extra.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};
enum{NONE,XYZ,XY,YZ,XZ};
enum{ISO,ANISO,TRICLINIC};
#define MAX_LIFO_DEPTH 2 // 3 box0 arrays in *.h dimensioned to this
/* ---------------------------------------------------------------------- */
@ -42,66 +46,118 @@ FixBoxRelax::FixBoxRelax(LAMMPS *lmp, int narg, char **arg) :
{
if (narg < 4) error->all("Illegal fix box/relax command");
scalar_flag = 1;
extscalar = 1;
global_freq = 1;
box_change = 1;
no_change_box = 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
// default values
pcouple = NONE;
allremap = 1;
vmax = 0.0001;
deviatoric_flag = 0;
nreset_h0 = 0;
int iarg;
if (press_couple == XYZ) iarg = 5;
else iarg = 7;
p_target[0] = p_target[1] = p_target[2] =
p_target[3] = p_target[4] = p_target[5] = 0.0;
// process keywords
dimension = domain->dimension;
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg],"dilate") == 0) {
if (strcmp(arg[iarg],"iso") == 0) {
if (iarg+4 > narg) error->all("Illegal fix box/relax command");
pcouple = XYZ;
p_target[0] = p_target[1] = p_target[2] = atof(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 += 4;
} else if (strcmp(arg[iarg],"aniso") == 0) {
if (iarg+4 > narg) error->all("Illegal fix box/relax command");
pcouple = NONE;
p_target[0] = p_target[1] = p_target[2] = atof(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 += 4;
} else if (strcmp(arg[iarg],"tri") == 0) {
if (iarg+4 > narg) error->all("Illegal fix box/relax command");
pcouple = NONE;
p_target[0] = p_target[1] = p_target[2] = atof(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 += 4;
} else if (strcmp(arg[iarg],"x") == 0) {
if (iarg+4 > narg) error->all("Illegal fix box/relax command");
p_target[0] = atof(arg[iarg+1]);
p_flag[0] = 1;
deviatoric_flag = 1;
iarg += 4;
} else if (strcmp(arg[iarg],"y") == 0) {
if (iarg+4 > narg) error->all("Illegal fix box/relax command");
p_target[1] = atof(arg[iarg+1]);
p_flag[1] = 1;
deviatoric_flag = 1;
iarg += 4;
} else if (strcmp(arg[iarg],"z") == 0) {
if (iarg+4 > narg) error->all("Illegal fix box/relax command");
p_target[2] = atof(arg[iarg+1]);
p_flag[2] = 1;
deviatoric_flag = 1;
iarg += 4;
if (dimension == 2)
error->all("Invalid fix box/relax command for a 2d simulation");
} else if (strcmp(arg[iarg],"yz") == 0) {
if (iarg+4 > narg) error->all("Illegal fix box/relax command");
p_target[3] = atof(arg[iarg+1]);
p_flag[3] = 1;
deviatoric_flag = 1;
iarg += 4;
if (dimension == 2)
error->all("Invalid fix box/relax command for a 2d simulation");
} else if (strcmp(arg[iarg],"xz") == 0) {
if (iarg+4 > narg) error->all("Illegal fix box/relax command");
p_target[4] = atof(arg[iarg+1]);
p_flag[4] = 1;
deviatoric_flag = 1;
iarg += 4;
if (dimension == 2)
error->all("Invalid fix box/relax command for a 2d simulation");
} else if (strcmp(arg[iarg],"xy") == 0) {
if (iarg+4 > narg) error->all("Illegal fix box/relax command");
p_target[5] = atof(arg[iarg+1]);
p_flag[5] = 1;
deviatoric_flag = 1;
iarg += 4;
} else if (strcmp(arg[iarg],"couple") == 0) {
if (iarg+2 > narg) error->all("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("Illegal fix box/relax command");
iarg += 2;
} else 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;
@ -111,24 +167,29 @@ FixBoxRelax::FixBoxRelax(LAMMPS *lmp, int narg, char **arg) :
if (iarg+2 > narg) error->all("Illegal fix box/relax command");
vmax = atof(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"nreset") == 0) {
if (iarg+2 > narg) error->all("Illegal fix box/relax command");
nreset_h0 = atoi(arg[iarg+1]);
if (nreset_h0 < 0) error->all("Illegal fix box/relax command");
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 (dimension == 2 && (p_flag[2] || p_flag[3] || p_flag[4]))
error->all("Invalid fix box/relax command for a 2d simulation");
if (dimension == 2 && (pcouple == YZ || pcouple == XZ))
error->all("Invalid fix box/relax command for a 2d simulation");
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 (pcouple == XYZ && (p_flag[0] == 0 || p_flag[1] == 0 || p_flag[2] == 0))
error->all("Invalid fix box/relax command pressure settings");
if (pcouple == XY && (p_flag[0] == 0 || p_flag[1] == 0))
error->all("Invalid fix box/relax command pressure settings");
if (pcouple == YZ && (p_flag[1] == 0 || p_flag[2] == 0))
error->all("Invalid fix box/relax command pressure settings");
if (pcouple == XZ && (p_flag[0] == 0 || p_flag[2] == 0))
error->all("Invalid fix box/relax command pressure settings");
if (p_flag[0] && domain->xperiodic == 0)
error->all("Cannot use fix box/relax on a non-periodic dimension");
@ -136,9 +197,37 @@ FixBoxRelax::FixBoxRelax(LAMMPS *lmp, int narg, char **arg) :
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 (p_flag[3] && domain->zperiodic == 0)
error->all("Cannot use fix box/relax on a 2nd non-periodic dimension");
if (p_flag[4] && domain->zperiodic == 0)
error->all("Cannot use fix box/relax on a 2nd non-periodic dimension");
if (p_flag[5] && domain->yperiodic == 0)
error->all("Cannot use fix box/relax on a 2nd non-periodic dimension");
if (!domain->triclinic && (p_flag[3] || p_flag[4] || p_flag[5]))
error->all("Can not specify Pxy/Pxz/Pyz in "
"fix box/relax with non-triclinic box");
if (pcouple == XYZ &&
(p_target[0] != p_target[1] || p_target[0] != p_target[2]))
error->all("Invalid fix box/relax pressure settings");
if (pcouple == XY && p_target[0] != p_target[1])
error->all("Invalid fix box/relax pressure settings");
if (pcouple == YZ && p_target[1] != p_target[2])
error->all("Invalid fix box/relax pressure settings");
if (pcouple == XZ && p_target[0] != p_target[2])
error->all("Invalid fix box/relax pressure settings");
if (vmax <= 0.0) error->all("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)
@ -221,13 +310,6 @@ void FixBoxRelax::init()
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
@ -245,6 +327,19 @@ void FixBoxRelax::init()
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;
// hydrostatic target pressure and deviatoric target stress
compute_press_target();
if (deviatoric_flag) compute_sigma();
}
/* ----------------------------------------------------------------------
@ -253,12 +348,11 @@ void FixBoxRelax::init()
double FixBoxRelax::min_energy(double *fextra)
{
double eng,scale,scalex,scaley,scalez;
double eng,scale,scalex,scaley,scalez,scalevol;
double t_current = temperature->compute_scalar();
if (press_couple == XYZ) {
double tmp = pressure->compute_scalar();
} else {
if (pstyle == ISO) double tmp = pressure->compute_scalar();
else {
temperature->compute_vector();
pressure->compute_vector();
}
@ -272,14 +366,14 @@ double FixBoxRelax::min_energy(double *fextra)
// returned eng = PV must be in units of energy
// returned fextra must likewise be in units of energy
if (press_couple == XYZ) {
if (pstyle == ISO) {
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;
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)*volinit;
fextra[0] = pv2e * (p_current[0] - p_target[0])*2.0*scale*volinit;
eng = pv2e * p_target[0] * (scale*scale-1.0)*vol0;
fextra[0] = pv2e * (p_current[0] - p_target[0])*2.0*scale*vol0;
}
} else {
@ -288,15 +382,38 @@ double FixBoxRelax::min_energy(double *fextra)
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;
scalevol = scalex*scaley*scalez;
eng = pv2e * p_hydro * (scalevol-1.0)*vol0;
if (p_flag[0])
fextra[0] = pv2e * (p_current[0] - p_target[0])*scaley*scalez*volinit;
fextra[0] = pv2e * (p_current[0] - p_hydro)*scaley*scalez*vol0;
if (p_flag[1])
fextra[1] = pv2e * (p_current[1] - p_target[1])*scalex*scalez*volinit;
fextra[1] = pv2e * (p_current[1] - p_hydro)*scalex*scalez*vol0;
if (p_flag[2])
fextra[2] = pv2e * (p_current[2] - p_target[2])*scalex*scaley*volinit;
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;
@ -319,6 +436,11 @@ void FixBoxRelax::min_store()
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;
if (pstyle == TRICLINIC) {
boxtilt0[current_lifo][0] = domain->yz;
boxtilt0[current_lifo][1] = domain->xz;
boxtilt0[current_lifo][2] = domain->xy;
}
}
/* ----------------------------------------------------------------------
@ -340,7 +462,6 @@ void FixBoxRelax::min_pushstore()
error->all("Attempt to push beyond stack limit in fix box/relax");
return;
}
current_lifo++;
}
@ -355,24 +476,51 @@ void FixBoxRelax::min_popstore()
error->all("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 (press_couple == XYZ) {
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();
}
@ -382,12 +530,17 @@ void FixBoxRelax::min_step(double alpha, double *hextra)
double FixBoxRelax::max_alpha(double *hextra)
{
double alpha = 0.0;
if (press_couple == XYZ) alpha = vmax/fabs(hextra[0]);
double alpha = 1.0;
if (pstyle == ISO) 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]));
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;
}
@ -398,7 +551,8 @@ double FixBoxRelax::max_alpha(double *hextra)
int FixBoxRelax::min_dof()
{
if (press_couple == XYZ) return 1;
if (pstyle == ISO) return 1;
if (pstyle == TRICLINIC) return 6;
return 3;
}
@ -441,8 +595,16 @@ void FixBoxRelax::remap()
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];
if (domain->boxlo[i] >= domain->boxhi[i])
error->all("fix box/relax generated negative dimension");
}
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();
@ -466,25 +628,36 @@ void FixBoxRelax::couple()
{
double *tensor = pressure->vector;
if (press_couple == XYZ)
if (pstyle == ISO)
p_current[0] = p_current[1] = p_current[2] = pressure->scalar;
else if (press_couple == XY) {
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 (press_couple == YZ) {
} 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 (press_couple == XZ) {
} 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 if (press_couple == ANISO) {
} 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];
}
}
/* ---------------------------------------------------------------------- */
@ -540,3 +713,187 @@ int FixBoxRelax::modify_param(int narg, char **arg)
}
return 0;
}
/* ----------------------------------------------------------------------
compute sigma tensor (needed whenever reference box is reset)
-----------------------------------------------------------------------*/
void FixBoxRelax::compute_sigma()
{
double pdevmod[3][3],pdeviatoric[3][3],htmp[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[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];
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];
htmp[0][0] = h0[0];
htmp[1][1] = h0[1];
htmp[2][2] = h0[2];
htmp[1][2] = h0[3];
htmp[0][2] = h0[4];
htmp[0][1] = h0[5];
htmp[2][1] = 0.0;
htmp[2][0] = 0.0;
htmp[1][0] = 0.0;
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);
}