git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2609 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2009-02-27 21:24:57 +00:00
parent 00ea6e394e
commit 99f2b70e24
2 changed files with 76 additions and 81 deletions

View File

@ -11,6 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Aidan Thompson (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "string.h"
#include "stdlib.h"
@ -96,18 +100,18 @@ FixBoxRelax::FixBoxRelax(LAMMPS *lmp, int narg, char **arg) :
// error checks
if (press_couple == XY && (p_flag[0] == 0 || p_flag[1] == 0))
error->all("Invalid fix npt command");
error->all("Invalid fix box/relax command");
if (press_couple == YZ && (p_flag[1] == 0 || p_flag[2] == 0))
error->all("Invalid fix npt command");
error->all("Invalid fix box/relax command");
if (press_couple == XZ && (p_flag[0] == 0 || p_flag[2] == 0))
error->all("Invalid fix npt command");
error->all("Invalid fix box/relax command");
if (press_couple == XY && p_target[0] != p_target[1])
error->all("Invalid fix npt command");
error->all("Invalid fix box/relax command");
if (press_couple == YZ && p_target[1] != p_target[2])
error->all("Invalid fix npt command");
error->all("Invalid fix box/relax command");
if (press_couple == XZ && p_target[0] != p_target[2])
error->all("Invalid fix npt command");
error->all("Invalid fix box/relax command");
if (p_flag[0] && domain->xperiodic == 0)
error->all("Cannot use fix box/relax on a non-periodic dimension");
@ -152,6 +156,7 @@ FixBoxRelax::FixBoxRelax(LAMMPS *lmp, int narg, char **arg) :
delete [] newarg;
pflag = 1;
dimension = domain->dimension;
nrigid = 0;
rfix = 0;
}
@ -186,11 +191,11 @@ void FixBoxRelax::init()
// set temperature and pressure ptrs
int icompute = modify->find_compute(id_temp);
if (icompute < 0) error->all("Temp ID for fix npt does not exist");
if (icompute < 0) error->all("Temp ID for fix box/relax does not exist");
temperature = modify->compute[icompute];
icompute = modify->find_compute(id_press);
if (icompute < 0) error->all("Press ID for fix npt does not exist");
if (icompute < 0) error->all("Press ID for fix box/relax does not exist");
pressure = modify->compute[icompute];
// initial box dimensions
@ -198,7 +203,7 @@ void FixBoxRelax::init()
xprdinit = domain->xprd;
yprdinit = domain->yprd;
zprdinit = domain->zprd;
if (domain->dimension == 3) volinit = domain->xprd*domain->yprd*domain->zprd;
if (dimension == 3) volinit = domain->xprd*domain->yprd*domain->zprd;
else volinit = domain->xprd*domain->yprd;
pv2e = 1.0 / force->nktv2p;
@ -225,7 +230,7 @@ void FixBoxRelax::init()
double FixBoxRelax::min_energy(double *fextra)
{
double scale, scalex, scaley, scalez;
double eng,scale,scalex,scaley,scalez;
double t_current = temperature->compute_scalar();
if (press_couple == XYZ) {
@ -240,53 +245,54 @@ double FixBoxRelax::min_energy(double *fextra)
pressure->addstep(update->ntimestep+1);
// compute new energy, forces for each extra degree of freedom
// PV must be in units of energy
double eng;
// compute energy, forces for each extra degree of freedom
// returned eng = PV must be in units of energy
// returned force = Ptarget - Pcurrent must be in units of
if (press_couple == XYZ) {
scale = domain->xprd/xprdinit;
if (domain->dimension == 3) {
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*volinit*scale*scale;
} else {
eng = pv2e * p_target[0] * (scale*scale-1.0)*volinit;
fextra[0] = pv2e * (p_current[0] - p_target[0])*2.0*volinit*scale;
}
}
if (press_couple == ANISO) {
} else if (press_couple == XY) {
scale = domain->xprd/xprdinit;
eng = pv2e * p_target[0] * (scale*scale-1.0)*volinit;
fextra[0] = pv2e * (p_current[0] - p_target[0])*scale*volinit;
if (p_flag[2]) {
scale = domain->zprd/zprdinit;
eng = pv2e * p_target[2] * (scale*scale-1.0)*volinit;
fextra[1] = pv2e * (p_current[1] - p_target[1])*scale*volinit;
}
} else if (press_couple == YZ) {
scale = domain->yprd/yprdinit;
eng = pv2e * p_target[1] * (scale*scale-1.0)*volinit;
fextra[1] = pv2e * (p_current[1] - p_target[1])*scale*volinit;
fextra[0] = 0.0;
} else if (press_couple == XZ) {
scale = domain->xprd/xprdinit;
eng = pv2e * p_target[0] * (scale*scale-1.0)*volinit;
fextra[0] = pv2e * (p_current[0] - p_target[0])*scale*volinit;
fextra[1] = 0.0;
} else if (press_couple == ANISO) {
scalex = domain->xprd/xprdinit;
scaley = domain->yprd/yprdinit;
scalez = domain->zprd/zprdinit;
eng = pv2e * p_target[0] * (scalex*scaley*scalez-1.0)*volinit;
fextra[0] = fextra[1] = fextra[2] = 0.0;
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;
}
}
if (press_couple == XY) {
scale = domain->xprd/xprdinit;
eng = pv2e * p_target[0] * (scale*scale-1.0)*volinit;
fextra[0] = fextra[1] = pv2e * (p_current[0] - p_target[0])*scale*volinit;
fextra[2] = 0.0;
}
if (press_couple == YZ) {
scale = domain->yprd/yprdinit;
eng = pv2e * p_target[1] * (scale*scale-1.0)*volinit;
fextra[1] = fextra[2] = pv2e * (p_current[1] - p_target[1])*scale*volinit;
fextra[0] = 0.0;
}
if (press_couple == XZ) {
scale = domain->xprd/xprdinit;
eng = pv2e * p_target[0] * (scale*scale-1.0)*volinit;
fextra[0] = fextra[2] = pv2e * (p_current[0] - p_target[0])*scale*volinit;
fextra[1] = 0.0;
int i = 0;
if (p_flag[0])
fextra[i++] = pv2e * (p_current[0] - p_target[0])*scaley*scalez*volinit;
if (p_flag[1])
fextra[i++] = pv2e * (p_current[1] - p_target[1])*scalex*scalez*volinit;
if (p_flag[2])
fextra[i++] = pv2e * (p_current[2] - p_target[2])*scalex*scaley*volinit;
}
return eng;
@ -294,6 +300,8 @@ double FixBoxRelax::min_energy(double *fextra)
/* ----------------------------------------------------------------------
store extra dof values for linesearch starting point
boxlo0,boxhi0 = box dimensions
s0 = ratio of current boxsize to initial boxsize
------------------------------------------------------------------------- */
void FixBoxRelax::min_store()
@ -308,36 +316,27 @@ void FixBoxRelax::min_store()
}
/* ----------------------------------------------------------------------
change the box dimensions by alpha from
x0extra along linesearch direction fextra
change the box dimensions by fraction ds = alpha*fextra
------------------------------------------------------------------------- */
void FixBoxRelax::min_step(double alpha, double *fextra)
{
double htmp;
if (press_couple == XYZ) {
ds[0] = alpha*fextra[0];
ds[1] = alpha*fextra[0];
ds[2] = alpha*fextra[0];
}
if (press_couple == ANISO) {
ds[0] = ds[1] = ds[2] = 0.0;
ds[0] = ds[1] = ds[2] = alpha*fextra[0];
} else if (press_couple == XY) {
ds[0] = ds[1] = alpha*fextra[0];
if (p_flag[2]) ds[2] = alpha*fextra[1];
} else if (press_couple == YZ) {
ds[1] = ds[2] = alpha*fextra[0];
if (p_flag[0]) ds[0] = alpha*fextra[1];
} else if (press_couple == XZ) {
ds[0] = ds[2] = alpha*fextra[0];
if (p_flag[1]) ds[1] = alpha*fextra[1];
} else if (press_couple == ANISO) {
if (p_flag[0]) ds[0] = alpha*fextra[0];
if (p_flag[1]) ds[1] = alpha*fextra[1];
if (p_flag[2]) ds[2] = alpha*fextra[2];
}
if (press_couple == XY) {
ds[0] = ds[1] = alpha*fextra[0];
ds[2] = 0.0;
}
if (press_couple == XZ) {
ds[0] = ds[2] = alpha*fextra[0];
ds[1] = 0.0;
}
if (press_couple == YZ) {
ds[1] = ds[2] = alpha*fextra[1];
ds[0] = 0.0;
}
remap();
}
@ -349,7 +348,11 @@ void FixBoxRelax::min_step(double alpha, double *fextra)
int FixBoxRelax::min_dof()
{
if (press_couple == XYZ) return 1;
else return 3;
else if (press_couple == XY) return (1 + p_flag[2]);
else if (press_couple == YZ) return (1 + p_flag[0]);
else if (press_couple == XZ) return (1 + p_flag[1]);
else if (press_couple == ANISO) return (p_flag[0] + p_flag[1] + p_flag[2]);
return 0;
}
/* ----------------------------------------------------------------------
@ -364,11 +367,6 @@ void FixBoxRelax::remap()
// 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
// don't do anything if non-periodic or style is constant volume
// we assume initially the atoms positions and box dimensions
// are at linesearch starting point.
// If not, atom positions will not be scaled correctly.
double **x = atom->x;
int *mask = atom->mask;
@ -389,13 +387,12 @@ void FixBoxRelax::remap()
// reset global and local box to new size/shape
for (i = 0; i < 3; i++) {
for (i = 0; i < 3; i++)
if (p_flag[i]) {
ctr = 0.5 * ( boxlo0[i] + boxhi0[i]);
ctr = 0.5 * (boxlo0[i] + boxhi0[i]);
domain->boxlo[i] = boxlo0[i] + (boxlo0[i]-ctr)*ds[i]/s0[i];
domain->boxhi[i] = boxhi0[i] + (boxhi0[i]-ctr)*ds[i]/s0[i];
}
}
domain->set_global_box();
domain->set_local_box();
@ -412,8 +409,6 @@ void FixBoxRelax::remap()
if (nrigid)
for (i = 0; i < nrigid; i++)
modify->fix[rfix[i]]->deform(1);
}
/* ---------------------------------------------------------------------- */

View File

@ -32,15 +32,15 @@ class FixBoxRelax : public Fix {
private:
int p_flag[3];
int press_couple,allremap;
int dimension;
double p_target[3],p_current[3];
double dilation[3];
double volinit,xprdinit,yprdinit,zprdinit;
double pv2e;
// These variables are for linesearch
double boxlo0[3],boxhi0[3]; // x0extra box bounds
double s0[6]; // x0extra scale matrix in Voigt notation
double ds[6]; // increment in scale matrix in Voigt notation
double boxlo0[3],boxhi0[3]; // box bounds at start of line search
double s0[6]; // scale matrix in Voigt notation
double ds[6]; // increment in scale matrix
char *id_temp,*id_press;
class Compute *temperature,*pressure;