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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5708 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2011-02-22 22:16:07 +00:00
parent d7ce656741
commit 49f5603f7f
4 changed files with 45 additions and 27 deletions
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23
src/PERI/fix_peri_neigh.cpp
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@ -120,6 +120,15 @@ void FixPeriNeigh::init_list(int id, NeighList *ptr)
list = ptr;
}
/* ----------------------------------------------------------------------
For minimization: setup as with dynamics
------------------------------------------------------------------------- */
void FixPeriNeigh::min_setup(int vflag)
{
setup(vflag);
}
/* ----------------------------------------------------------------------
create initial list of neighbor partners via call to neighbor->build()
must be done in setup (not init) since fix init comes before neigh init
@ -231,6 +240,20 @@ void FixPeriNeigh::setup(int vflag)
}
}
// Sanity check: Does any atom appear twice in any neigborlist?
// Should only be possible if using pbc and domain not at least of width 2 \delta
if (domain->xperiodic || domain->yperiodic || domain->zperiodic) {
for (i = 0; i < nlocal; i++) {
jnum = npartner[i];
for (jj = 0; jj < jnum; jj++) {
for (int kk = jj+1; kk < jnum; kk++) {
if (partner[i][jj] == partner[i][kk]) error->one("Duplicate particle in bond family. Check that box is greater than size 2*delta in periodic dimensions.");
}
}
}
}
// compute wvolume for each atom
double **x0 = atom->x0;

1
src/PERI/fix_peri_neigh.h
View File

@ -36,6 +36,7 @@ class FixPeriNeigh : public Fix {
void init();
void init_list(int, class NeighList *);
void setup(int);
void min_setup(int);
double memory_usage();
void grow_arrays(int);

26
src/PERI/pair_peri_lps.cpp
View File

@ -44,6 +44,7 @@ using namespace LAMMPS_NS;
PairPeriLPS::PairPeriLPS(LAMMPS *lmp) : Pair(lmp)
{
for (int i = 0; i < 6; i++) virial[i] = 0.0;
no_virial_compute=1;
ifix_peri = -1;
@ -120,7 +121,7 @@ void PairPeriLPS::compute(int eflag, int vflag)
int nall = atom->nlocal + atom->nghost;
int newton_pair = force->newton_pair;
int nonperiodic = domain->nonperiodic;
int periodic = domain->xperiodic || domain->yperiodic || domain->zperiodic;
inum = list->inum;
ilist = list->ilist;
@ -156,7 +157,7 @@ void PairPeriLPS::compute(int eflag, int vflag)
delx0 = xtmp0 - x0[j][0];
dely0 = ytmp0 - x0[j][1];
delz0 = ztmp0 - x0[j][2];
if (nonperiodic == 0) domain->minimum_image(delx0,dely0,delz0);
if (periodic) domain->minimum_image(delx0,dely0,delz0);
rsq0 = delx0*delx0 + dely0*dely0 + delz0*delz0;
jtype = type[j];
@ -194,8 +195,7 @@ void PairPeriLPS::compute(int eflag, int vflag)
}
if (eflag) evdwl = 0.5*rk*dr;
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair*vfrac[i],delx,dely,delz);
}
}
}
@ -265,12 +265,12 @@ void PairPeriLPS::compute(int eflag, int vflag)
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
if (nonperiodic == 0) domain->minimum_image(delx,dely,delz);
if (periodic) domain->minimum_image(delx,dely,delz);
rsq = delx*delx + dely*dely + delz*delz;
delx0 = xtmp0 - x0[j][0];
dely0 = ytmp0 - x0[j][1];
delz0 = ztmp0 - x0[j][2];
if (nonperiodic == 0) domain->minimum_image(delx0,dely0,delz0);
if (periodic) domain->minimum_image(delx0,dely0,delz0);
jtype = type[j];
delta = sqrt(cutsq[itype][jtype]);
r = sqrt(rsq);
@ -309,8 +309,7 @@ void PairPeriLPS::compute(int eflag, int vflag)
if (eflag) evdwl = 0.5 * 15 * (shearmodulus[itype][itype]/wvolume[i]) *
omega_plus*(deviatoric_extension * deviatoric_extension) *
vfrac[j] * vfrac_scale;
if (evflag) ev_tally(i,i,nlocal,0,
0.5*evdwl,0.0,0.5*fbond,delx,dely,delz);
if (evflag) ev_tally(i,i,nlocal,0,0.5*evdwl,0.0,0.5*fbond*vfrac[i],delx,dely,delz);
// find stretch in bond I-J and break if necessary
// use s0 from previous timestep
@ -330,8 +329,6 @@ void PairPeriLPS::compute(int eflag, int vflag)
}
}
if (vflag_fdotr) virial_compute();
// store new s0
for (i = 0; i < nlocal; i++) s0[i] = s0_new[i];
@ -542,7 +539,8 @@ double PairPeriLPS::single(int i, int j, int itype, int jtype,
delx0 = x0[i][0] - x0[j][0];
dely0 = x0[i][1] - x0[j][1];
delz0 = x0[i][2] - x0[j][2];
if (domain->nonperiodic == 0) domain->minimum_image(delx0,dely0,delz0);
int periodic = domain->xperiodic || domain->yperiodic || domain->zperiodic;
if (periodic) domain->minimum_image(delx0,dely0,delz0);
rsq0 = delx0*delx0 + dely0*dely0 + delz0*delz0;
d_ij = MIN(0.9*sqrt(rsq0),1.35*lc);
@ -663,7 +661,7 @@ void PairPeriLPS::compute_dilatation()
int *npartner = ((FixPeriNeigh *) modify->fix[ifix_peri])->npartner;
double *wvolume = ((FixPeriNeigh *) modify->fix[ifix_peri])->wvolume;
int nonperiodic = domain->nonperiodic;
int periodic = domain->xperiodic || domain->yperiodic || domain->zperiodic;
// compute the dilatation theta
@ -693,12 +691,12 @@ void PairPeriLPS::compute_dilatation()
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
if (nonperiodic == 0) domain->minimum_image(delx,dely,delz);
if (periodic) domain->minimum_image(delx,dely,delz);
rsq = delx*delx + dely*dely + delz*delz;
delx0 = xtmp0 - x0[j][0];
dely0 = ytmp0 - x0[j][1];
delz0 = ztmp0 - x0[j][2];
if (nonperiodic == 0) domain->minimum_image(delx0,dely0,delz0);
if (periodic) domain->minimum_image(delx0,dely0,delz0);
r = sqrt(rsq);
dr = r - r0[i][jj];

22
src/PERI/pair_peri_pmb.cpp
View File

@ -45,6 +45,7 @@ using namespace LAMMPS_NS;
PairPeriPMB::PairPeriPMB(LAMMPS *lmp) : Pair(lmp)
{
for (int i = 0; i < 6; i++) virial[i] = 0.0;
no_virial_compute=1;
ifix_peri = -1;
@ -112,7 +113,7 @@ void PairPeriPMB::compute(int eflag, int vflag)
int nall = atom->nlocal + atom->nghost;
int newton_pair = force->newton_pair;
int nonperiodic = domain->nonperiodic;
int periodic = (domain->xperiodic || domain->yperiodic || domain->zperiodic);
inum = list->inum;
ilist = list->ilist;
@ -145,7 +146,7 @@ void PairPeriPMB::compute(int eflag, int vflag)
delx0 = xtmp0 - x0[j][0];
dely0 = ytmp0 - x0[j][1];
delz0 = ztmp0 - x0[j][2];
if (nonperiodic == 0) domain->minimum_image(delx0,dely0,delz0);
if (periodic) domain->minimum_image(delx0,dely0,delz0);
rsq0 = delx0*delx0 + dely0*dely0 + delz0*delz0;
jtype = type[j];
@ -178,8 +179,7 @@ void PairPeriPMB::compute(int eflag, int vflag)
}
if (eflag) evdwl = 0.5*rk*dr;
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair*vfrac[i],delx,dely,delz);
}
}
}
@ -224,7 +224,7 @@ void PairPeriPMB::compute(int eflag, int vflag)
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
if (nonperiodic == 0) domain->minimum_image(delx,dely,delz);
if (periodic) domain->minimum_image(delx,dely,delz);
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
delta = sqrt(cutsq[itype][jtype]);
@ -254,8 +254,7 @@ void PairPeriPMB::compute(int eflag, int vflag)
// since I-J is double counted, set newton off & use 1/2 factor and I,I
if (eflag) evdwl = 0.5*rk*dr;
if (evflag) ev_tally(i,i,nlocal,0,
0.5*evdwl,0.0,0.5*fbond,delx,dely,delz);
if (evflag) ev_tally(i,i,nlocal,0,0.5*evdwl,0.0,0.5*fbond*vfrac[i],delx,dely,delz);
// find stretch in bond I-J and break if necessary
// use s0 from previous timestep
@ -267,16 +266,12 @@ void PairPeriPMB::compute(int eflag, int vflag)
if (first)
s0_new[i] = s00[itype][jtype] - (alpha[itype][jtype] * stretch);
else
s0_new[i] = MAX(s0_new[i],
s00[itype][jtype] - (alpha[itype][jtype] * stretch));
s0_new[i] = MAX(s0_new[i],s00[itype][jtype] - (alpha[itype][jtype] * stretch));
first = false;
}
}
if (vflag_fdotr) virial_compute();
// store new s0
for (i = 0; i < nlocal; i++) s0[i] = s0_new[i];
}
@ -474,7 +469,8 @@ double PairPeriPMB::single(int i, int j, int itype, int jtype, double rsq,
delx0 = x0[i][0] - x0[j][0];
dely0 = x0[i][1] - x0[j][1];
delz0 = x0[i][2] - x0[j][2];
if (domain->nonperiodic == 0) domain->minimum_image(delx0,dely0,delz0);
int periodic = domain->xperiodic || domain->yperiodic || domain->zperiodic;
if (periodic) domain->minimum_image(delx0,dely0,delz0);
rsq0 = delx0*delx0 + dely0*dely0 + delz0*delz0;
d_ij = MIN(0.9*sqrt(rsq0),1.35*lc);