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Added tilt factor scaling and fixed-point features to fix box/relax 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8472 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
athomps 2012-07-03 22:50:34 +00:00
parent 959f12463b
commit c89a12ff71
2 changed files with 85 additions and 19 deletions
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97
src/fix_box_relax.cpp
View File

@ -64,10 +64,25 @@ FixBoxRelax::FixBoxRelax(LAMMPS *lmp, int narg, char **arg) :
p_flag[0] = p_flag[1] = p_flag[2] =
p_flag[3] = p_flag[4] = p_flag[5] = 0;
// process keywords
// turn on tilt factor scaling, whenever applicable
dimension = domain->dimension;
scaleyz = scalexz = scalexy = 0;
if (domain->yperiodic && domain->xy != 0.0) scalexy = 1;
if (domain->zperiodic && dimension == 3) {
if (domain->yz != 0.0) scaleyz = 1;
if (domain->xz != 0.0) scalexz = 1;
}
// set fixed-point to default = center of cell
fixedpoint[0] = 0.5*(domain->boxlo[0]+domain->boxhi[0]);
fixedpoint[1] = 0.5*(domain->boxlo[1]+domain->boxhi[1]);
fixedpoint[2] = 0.5*(domain->boxlo[2]+domain->boxhi[2]);
// process keywords
int iarg = 3;
while (iarg < narg) {
@ -94,6 +109,7 @@ FixBoxRelax::FixBoxRelax(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"tri") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix box/relax command");
pcouple = NONE;
scalexy = scalexz = scaleyz = 0;
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;
@ -130,6 +146,7 @@ FixBoxRelax::FixBoxRelax(LAMMPS *lmp, int narg, char **arg) :
p_target[3] = atof(arg[iarg+1]);
p_flag[3] = 1;
deviatoric_flag = 1;
scaleyz = 0;
iarg += 2;
if (dimension == 2)
error->all(FLERR,"Invalid fix box/relax command for a 2d simulation");
@ -138,6 +155,7 @@ FixBoxRelax::FixBoxRelax(LAMMPS *lmp, int narg, char **arg) :
p_target[4] = atof(arg[iarg+1]);
p_flag[4] = 1;
deviatoric_flag = 1;
scalexz = 0;
iarg += 2;
if (dimension == 2)
error->all(FLERR,"Invalid fix box/relax command for a 2d simulation");
@ -146,6 +164,7 @@ FixBoxRelax::FixBoxRelax(LAMMPS *lmp, int narg, char **arg) :
p_target[5] = atof(arg[iarg+1]);
p_flag[5] = 1;
deviatoric_flag = 1;
scalexy = 0;
iarg += 2;
} else if (strcmp(arg[iarg],"couple") == 0) {
@ -173,6 +192,30 @@ FixBoxRelax::FixBoxRelax(LAMMPS *lmp, int narg, char **arg) :
nreset_h0 = atoi(arg[iarg+1]);
if (nreset_h0 < 0) error->all(FLERR,"Illegal fix box/relax command");
iarg += 2;
} else if (strcmp(arg[iarg],"scalexy") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix box/relax command");
if (strcmp(arg[iarg+1],"yes") == 0) scalexy = 1;
else if (strcmp(arg[iarg+1],"no") == 0) scalexy = 0;
else error->all(FLERR,"Illegal fix box/relax command");
iarg += 2;
} else if (strcmp(arg[iarg],"scalexz") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix box/relax command");
if (strcmp(arg[iarg+1],"yes") == 0) scalexz = 1;
else if (strcmp(arg[iarg+1],"no") == 0) scalexz = 0;
else error->all(FLERR,"Illegal fix box/relax command");
iarg += 2;
} else if (strcmp(arg[iarg],"scaleyz") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix box/relax command");
if (strcmp(arg[iarg+1],"yes") == 0) scaleyz = 1;
else if (strcmp(arg[iarg+1],"no") == 0) scaleyz = 0;
else error->all(FLERR,"Illegal fix box/relax command");
iarg += 2;
} else if (strcmp(arg[iarg],"fixedpoint") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix box/relax command");
fixedpoint[0] = atof(arg[iarg+1]);
fixedpoint[1] = atof(arg[iarg+2]);
fixedpoint[2] = atof(arg[iarg+3]);
iarg += 4;
} else error->all(FLERR,"Illegal fix box/relax command");
}
@ -217,7 +260,27 @@ FixBoxRelax::FixBoxRelax(LAMMPS *lmp, int narg, char **arg) :
"Cannot use fix box/relax on a 2nd non-periodic dimension");
if (p_flag[5] && domain->yperiodic == 0)
error->all(FLERR,
"Cannot use fix box/relax on a 2nd non-periodic dimension");
"Cannot use fix box/relax on a 2nd non-periodic dimensio");
if (scaleyz == 1 && domain->zperiodic == 0)
error->all(FLERR,"Cannot use fix box/relax "
"with tilt factor scaling on a 2nd non-periodic dimension");
if (scalexz == 1 && domain->zperiodic == 0)
error->all(FLERR,"Cannot use fix box/relax "
"with tilt factor scaling on a 2nd non-periodic dimension");
if (scalexy == 1 && domain->yperiodic == 0)
error->all(FLERR,"Cannot use fix box/relax "
"with tilt factor scaling on a 2nd non-periodic dimension");
if (p_flag[3] && scaleyz == 1)
error->all(FLERR,"Cannot use fix box/relax with "
"both relaxation and scaling on a tilt factor");
if (p_flag[4] && scalexz == 1)
error->all(FLERR,"Cannot use fix box/relax with "
"both relaxation and scaling on a tilt factor");
if (p_flag[5] && scalexy == 1)
error->all(FLERR,"Cannot use fix box/relax with "
"both relaxation and scaling on a tilt factor");
if (!domain->triclinic && (p_flag[3] || p_flag[4] || p_flag[5]))
error->all(FLERR,"Can not specify Pxy/Pxz/Pyz in "
@ -356,6 +419,12 @@ void FixBoxRelax::init()
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];
// hydrostatic target pressure and deviatoric target stress
@ -443,7 +512,6 @@ double FixBoxRelax::min_energy(double *fextra)
/* ----------------------------------------------------------------------
store extra dof values for minimization linesearch starting point
boxlo0,boxhi0 = box dimensions
s0 = ratio of current boxsize to initial boxsize
box values are pushed onto a LIFO stack so nested calls can be made
values are popped by calling min_step(0.0)
------------------------------------------------------------------------- */
@ -454,9 +522,6 @@ void FixBoxRelax::min_store()
boxlo0[current_lifo][i] = domain->boxlo[i];
boxhi0[current_lifo][i] = domain->boxhi[i];
}
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;
@ -585,9 +650,7 @@ int FixBoxRelax::min_dof()
void FixBoxRelax::remap()
{
int i,n;
double ctr;
// 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
@ -614,13 +677,18 @@ void FixBoxRelax::remap()
if (p_flag[i]) {
double currentBoxLo0 = boxlo0[current_lifo][i];
double currentBoxHi0 = boxhi0[current_lifo][i];
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];
domain->boxlo[i] = currentBoxLo0 + (currentBoxLo0 - fixedpoint[i])/domain->h[i]*ds[i]*h0[i];
domain->boxhi[i] = currentBoxHi0 + (currentBoxHi0 - fixedpoint[i])/domain->h[i]*ds[i]*h0[i];
if (domain->boxlo[i] >= domain->boxhi[i])
error->all(FLERR,"Fix box/relax generated negative box length");
}
// scale tilt factors with cell, if set
if (scaleyz) domain->yz = (domain->boxhi[2] - domain->boxlo[2])*h0[3]/h0[2];
if (scalexz) domain->xz = (domain->boxhi[2] - domain->boxlo[2])*h0[4]/h0[2];
if (scalexy) domain->xy = (domain->boxhi[1] - domain->boxlo[1])*h0[5]/h0[1];
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;
@ -756,13 +824,6 @@ void FixBoxRelax::compute_sigma()
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];

7
src/fix_box_relax.h
View File

@ -56,9 +56,14 @@ class FixBoxRelax : public Fix {
double boxlo0[2][3]; // box bounds at start of line search
double boxhi0[2][3];
double boxtilt0[2][3]; // xy,xz,yz tilts at start of line search
double s0[3]; // scale matrix at start of line search
double ds[6]; // increment in scale matrix
int scaleyz; // 1 if yz scaled with lz
int scalexz; // 1 if xz scaled with lz
int scalexy; // 1 if xy scaled with ly
double fixedpoint[3]; // Location of dilation fixed-point
char *id_temp,*id_press;
class Compute *temperature,*pressure;
int tflag,pflag;