ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@763 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2007-08-03 19:36:35 +00:00
parent a2d5aa2e1f
commit 72ec2d9204
5 changed files with 67 additions and 94 deletions
Download Patch File Download Diff File Expand all files Collapse all files

132
src/fix_npt.cpp
View File

@ -22,7 +22,6 @@
#include "atom.h"
#include "force.h"
#include "comm.h"
#include "output.h"
#include "modify.h"
#include "compute.h"
#include "kspace.h"
@ -117,7 +116,7 @@ FixNPT::FixNPT(LAMMPS *lmp, int narg, char **arg) :
// process extra keywords
drag = 0.0;
dilate_partial = 0;
allremap = 1;
int iarg;
if (press_couple == 0) iarg = 10;
@ -130,8 +129,8 @@ FixNPT::FixNPT(LAMMPS *lmp, int narg, char **arg) :
iarg += 2;
} else if (strcmp(arg[iarg],"dilate") == 0) {
if (iarg+2 > narg) error->all("Illegal fix npt command");
if (strcmp(arg[iarg+1],"all") == 0) dilate_partial = 0;
else if (strcmp(arg[iarg+1],"partial") == 0) dilate_partial = 1;
if (strcmp(arg[iarg+1],"all") == 0) allremap = 1;
else if (strcmp(arg[iarg+1],"partial") == 0) allremap = 0;
else error->all("Illegal fix npt command");
iarg += 2;
} else error->all("Illegal fix npt command");
@ -284,7 +283,7 @@ void FixNPT::init()
step_respa = ((Respa *) update->integrate)->step;
}
// detect if any rigid fixes exist so rigid bodies move when box is dilated
// detect if any rigid fixes exist so rigid bodies move when box is remapped
// rfix[] = indices to each fix rigid
delete [] rfix;
@ -381,9 +380,9 @@ void FixNPT::initial_integrate()
}
}
// rescale simulation box and all owned atoms by 1/2 step
// remap simulation box and all owned atoms by 1/2 step
box_dilate(0);
remap(0);
// x update by full step only for atoms in NPT group
@ -395,10 +394,10 @@ void FixNPT::initial_integrate()
}
}
// rescale simulation box and all owned atoms by 1/2 step
// remap simulation box and all owned atoms by 1/2 step
// redo KSpace coeffs since volume has changed
box_dilate(0);
remap(0);
if (kspace_flag) force->kspace->setup();
}
@ -468,11 +467,11 @@ void FixNPT::final_integrate()
void FixNPT::initial_integrate_respa(int ilevel, int flag)
{
// if flag = 1, then is 2nd call at outermost level from rRESPA
// perform 2nd half of box dilate on own + ghost atoms and return
// perform 2nd half of box remap on own + ghost atoms and return
// redo KSpace coeffs since volume has changed
if (flag == 1) {
box_dilate(1);
remap(1);
if (kspace_flag) force->kspace->setup();
return;
}
@ -494,7 +493,7 @@ void FixNPT::initial_integrate_respa(int ilevel, int flag)
int *mask = atom->mask;
int nlocal = atom->nlocal;
// outermost level - update eta_dot and omega_dot, apply to v, dilate box
// outermost level - update eta_dot and omega_dot, apply to v, remap box
// all other levels - NVE update of v
// x,v updates only performed for atoms in NPT group
@ -540,9 +539,9 @@ void FixNPT::initial_integrate_respa(int ilevel, int flag)
}
}
// rescale simulation box and all owned atoms by 1/2 step
// remap simulation box and all owned atoms by 1/2 step
box_dilate(0);
remap(0);
} else {
@ -638,89 +637,62 @@ void FixNPT::couple()
}
/* ----------------------------------------------------------------------
dilate the box around center of box
change box size
remap owned or owned+ghost atoms depending on flag
remap all atoms or fix group atoms depending on allremap flag
if rigid bodies exist, scale rigid body centers-of-mass
------------------------------------------------------------------------- */
void FixNPT::box_dilate(int flag)
void FixNPT::remap(int flag)
{
int i,n;
// ctr = geometric center of box in a dimension
// scale owned or owned+ghost atoms depending on flag
// re-define simulation box via xprd/yprd/zprd
// scale atom coords for all atoms or only for fix group atoms
// if fix rigid exists, scale rigid body centers-of-mass
// don't do anything if non-periodic or press style is constant volume
double oldlo,oldhi,ctr;
double **x = atom->x;
int *mask = atom->mask;
if (flag) n = atom->nlocal + atom->nghost;
else n = atom->nlocal;
double oldlo,oldhi,ctr;
// convert pertinent atoms and rigid bodies to lamda coords
if (domain->xperiodic && p_flag[0]) {
oldlo = domain->boxlo[0];
oldhi = domain->boxhi[0];
ctr = 0.5 * (oldlo + oldhi);
domain->boxlo[0] = (oldlo-ctr)*dilation[0] + ctr;
domain->boxhi[0] = (oldhi-ctr)*dilation[0] + ctr;
domain->prd[0] = domain->xprd = domain->boxhi[0] - domain->boxlo[0];
if (dilate_partial) {
for (i = 0; i < n; i++)
if (mask[i] & groupbit)
x[i][0] = ctr + (x[i][0]-ctr)*dilation[0];
} else {
for (i = 0; i < n; i++)
x[i][0] = ctr + (x[i][0]-ctr)*dilation[0];
}
if (nrigid)
for (i = 0; i < nrigid; i++)
modify->fix[rfix[i]]->
dilate(0,oldlo,oldhi,domain->boxlo[0],domain->boxhi[0]);
if (allremap) domain->x2lamda(n);
else {
for (i = 0; i < n; i++)
if (mask[i] & groupbit)
domain->x2lamda(x[i],x[i]);
}
if (domain->yperiodic && p_flag[1]) {
oldlo = domain->boxlo[1];
oldhi = domain->boxhi[1];
ctr = 0.5 * (oldlo + oldhi);
domain->boxlo[1] = (oldlo-ctr)*dilation[1] + ctr;
domain->boxhi[1] = (oldhi-ctr)*dilation[1] + ctr;
domain->prd[1] = domain->yprd = domain->boxhi[1] - domain->boxlo[1];
if (dilate_partial) {
for (i = 0; i < n; i++)
if (mask[i] & groupbit)
x[i][1] = ctr + (x[i][1]-ctr)*dilation[1];
} else {
for (i = 0; i < n; i++)
x[i][1] = ctr + (x[i][1]-ctr)*dilation[1];
if (nrigid)
for (i = 0; i < nrigid; i++)
modify->fix[rfix[i]]->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;
}
if (nrigid)
for (i = 0; i < nrigid; i++)
modify->fix[rfix[i]]->
dilate(1,oldlo,oldhi,domain->boxlo[1],domain->boxhi[1]);
}
if (domain->zperiodic && p_flag[2]) {
oldlo = domain->boxlo[2];
oldhi = domain->boxhi[2];
ctr = 0.5 * (oldlo + oldhi);
domain->boxlo[2] = (oldlo-ctr)*dilation[2] + ctr;
domain->boxhi[2] = (oldhi-ctr)*dilation[2] + ctr;
domain->prd[2] = domain->zprd = domain->boxhi[2] - domain->boxlo[2];
if (dilate_partial) {
for (i = 0; i < n; i++)
if (mask[i] & groupbit)
x[i][2] = ctr + (x[i][2]-ctr)*dilation[2];
} else {
for (i = 0; i < n; i++)
x[i][2] = ctr + (x[i][2]-ctr)*dilation[2];
}
if (nrigid)
for (i = 0; i < nrigid; i++)
modify->fix[rfix[i]]->
dilate(2,oldlo,oldhi,domain->boxlo[2],domain->boxhi[2]);
domain->set_global_box();
domain->set_local_box();
// convert pertinent atoms and rigid bodies back to box coords
if (allremap) domain->lamda2x(n);
else {
for (i = 0; i < n; i++)
if (mask[i] & groupbit)
domain->lamda2x(x[i],x[i]);
}
if (nrigid)
for (i = 0; i < nrigid; i++)
modify->fix[rfix[i]]->deform(1);
}
/* ----------------------------------------------------------------------