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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8289 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2012-06-14 22:17:17 +00:00
parent 5b52b62ff1
commit 0f4be10d4a
7 changed files with 177 additions and 22 deletions
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67
src/domain.cpp
View File

@ -41,6 +41,7 @@ using namespace MathConst;
#define BIG 1.0e20
#define SMALL 1.0e-4
#define DELTA 1
#define BONDSTRETCH 1.1
enum{NO_REMAP,X_REMAP,V_REMAP}; // same as fix_deform.cpp
@ -97,6 +98,12 @@ Domain::~Domain()
void Domain::init()
{
// check for too small a periodic box for molecular system
if (atom->molecular && box_too_small())
error->all(FLERR,"Bond/angle/dihedral extent must be < "
"half of periodic box dimension");
// set box_change if box dimensions/shape ever changes
// due to shrink-wrapping, fixes that change volume (npt, vol/rescale, etc)
@ -515,6 +522,66 @@ void Domain::pbc()
}
}
/* ----------------------------------------------------------------------
check that no pair of atoms in a bonded interaction
are further apart than half a periodic box length
return 1 if any pair is, else 0
------------------------------------------------------------------------- */
int Domain::box_too_small()
{
int i,j,k;
// only need to check if some dimension is periodic
if (!xperiodic && !yperiodic && (dimension == 2 || !zperiodic)) return 0;
// maxbondall = longest current bond length
// NOTE: if box is tiny (less than 2 * bond-length),
// the check itself may compute bad bond lengths
// not sure how to account for that extreme case
int *num_bond = atom->num_bond;
int **bond_atom = atom->bond_atom;
double **x = atom->x;
int nlocal = atom->nlocal;
double delx,dely,delz,rsq,r;
double maxbondme = 0.0;
for (i = 0; i < nlocal; i++)
for (j = 0; j < num_bond[i]; j++) {
k = atom->map(bond_atom[i][j]);
if (k < 0) error->one(FLERR,"Bond atom missing in box size check");
delx = x[i][0] - x[k][0];
dely = x[i][1] - x[k][1];
delz = x[i][2] - x[k][2];
domain->minimum_image(delx,dely,delz);
rsq = delx*delx + dely*dely + delz*delz;
maxbondme = MAX(maxbondme,rsq);
}
double maxbondall;
MPI_Allreduce(&maxbondme,&maxbondall,1,MPI_DOUBLE,MPI_MAX,world);
maxbondall = sqrt(maxbondall);
// maxdelta = furthest apart 2 atoms in a bonded interaction can be
// include BONDSTRETCH factor to account for dynamics
double maxdelta = maxbondall * BONDSTRETCH;
if (atom->nangles) maxdelta = 2.0 * maxbondall * BONDSTRETCH;
if (atom->ndihedrals) maxdelta = 3.0 * maxbondall * BONDSTRETCH;
// maxdelta cannot be more than half a periodic box length,
// else when use minimg() in bond/angle/dihdral compute,
// could calculate incorrect distance between 2 atoms
if (xperiodic && maxdelta > xprd_half) return 1;
if (yperiodic && maxdelta > yprd_half) return 1;
if (dimension == 3 && zperiodic && maxdelta > zprd_half) return 1;
return 0;
}
/* ----------------------------------------------------------------------
minimum image convention check
return 1 if any distance > 1/2 of box size

3
src/domain.h
View File

@ -70,7 +70,7 @@ class Domain : protected Pointers {
// triclinic box
double xy,xz,yz; // 3 tilt factors
double h[6],h_inv[6]; // shape matrix in Voigt notation
double h[6],h_inv[6]; // shape matrix in Voigt notation
double h_rate[6],h_ratelo[3]; // rate of box size/shape change
int box_change; // 1 if box bounds ever change, 0 if fixed
@ -93,6 +93,7 @@ class Domain : protected Pointers {
virtual void set_local_box();
virtual void reset_box();
virtual void pbc();
int box_too_small();
int minimum_image_check(double, double, double);
void minimum_image(double &, double &, double &);
void minimum_image(double *);

26
src/neigh_full.cpp
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@ -14,6 +14,7 @@
#include "neighbor.h"
#include "neigh_list.h"
#include "atom.h"
#include "domain.h"
#include "group.h"
#include "error.h"
@ -89,7 +90,10 @@ void Neighbor::full_nsq(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
@ -173,7 +177,10 @@ void Neighbor::full_nsq_ghost(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
@ -281,7 +288,10 @@ void Neighbor::full_bin(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
@ -379,7 +389,10 @@ void Neighbor::full_bin_ghost(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
@ -507,7 +520,10 @@ void Neighbor::full_multi(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}

23
src/neigh_half_bin.cpp
View File

@ -14,6 +14,7 @@
#include "neighbor.h"
#include "neigh_list.h"
#include "atom.h"
#include "domain.h"
#include "error.h"
using namespace LAMMPS_NS;
@ -98,7 +99,10 @@ void Neighbor::half_bin_no_newton(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
@ -196,7 +200,11 @@ void Neighbor::half_bin_newton(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
// OLD: if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
@ -217,7 +225,11 @@ void Neighbor::half_bin_newton(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
// OLD: if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
@ -320,7 +332,10 @@ void Neighbor::half_bin_newton_tri(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}

21
src/neigh_half_multi.cpp
View File

@ -14,6 +14,7 @@
#include "neighbor.h"
#include "neigh_list.h"
#include "atom.h"
#include "domain.h"
#include "error.h"
using namespace LAMMPS_NS;
@ -106,7 +107,10 @@ void Neighbor::half_multi_no_newton(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
@ -207,7 +211,10 @@ void Neighbor::half_multi_newton(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
@ -235,7 +242,10 @@ void Neighbor::half_multi_newton(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
@ -348,7 +358,10 @@ void Neighbor::half_multi_newton_tri(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}

11
src/neigh_half_nsq.cpp
View File

@ -14,6 +14,7 @@
#include "neighbor.h"
#include "neigh_list.h"
#include "atom.h"
#include "domain.h"
#include "group.h"
#include "error.h"
@ -89,7 +90,10 @@ void Neighbor::half_nsq_no_newton(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
@ -193,7 +197,10 @@ void Neighbor::half_nsq_newton(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}

48
src/neigh_respa.cpp
View File

@ -14,6 +14,7 @@
#include "neighbor.h"
#include "neigh_list.h"
#include "atom.h"
#include "domain.h"
#include "group.h"
#include "error.h"
@ -81,6 +82,7 @@ void Neighbor::respa_nsq_no_newton(NeighList *list)
int npnt_middle = 0;
int which = 0;
int minchange = 0;
for (i = 0; i < nlocal; i++) {
@ -132,16 +134,21 @@ void Neighbor::respa_nsq_no_newton(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
if (which == 0) neighptr[n++] = j;
else if (minchange = domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
if (rsq < cut_inner_sq) {
if (which == 0) neighptr_inner[n_inner++] = j;
else if (minchange) neighptr_inner[n_inner++] = j;
else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
}
if (respamiddle && rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
if (which == 0) neighptr_middle[n_middle++] = j;
else if (minchange) neighptr_middle[n_middle++] = j;
else if (which > 0)
neighptr_middle[n_middle++] = j ^ (which << SBBITS);
}
@ -242,6 +249,7 @@ void Neighbor::respa_nsq_newton(NeighList *list)
int npnt_middle = 0;
int which = 0;
int minchange = 0;
for (i = 0; i < nlocal; i++) {
@ -310,17 +318,22 @@ void Neighbor::respa_nsq_newton(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
if (which == 0) neighptr[n++] = j;
else if (minchange = domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
if (rsq < cut_inner_sq) {
if (which == 0) neighptr_inner[n_inner++] = j;
else if (minchange) neighptr_inner[n_inner++] = j;
else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
}
if (respamiddle &&
rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
if (which == 0) neighptr_middle[n_middle++] = j;
else if (minchange) neighptr_middle[n_middle++] = j;
else if (which > 0)
neighptr_middle[n_middle++] = j ^ (which << SBBITS);
}
@ -423,6 +436,7 @@ void Neighbor::respa_bin_no_newton(NeighList *list)
int npnt_middle = 0;
int which = 0;
int minchange = 0;
for (i = 0; i < nlocal; i++) {
@ -480,11 +494,15 @@ void Neighbor::respa_bin_no_newton(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
if (which == 0) neighptr[n++] = j;
else if (minchange = domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
if (rsq < cut_inner_sq) {
if (which == 0) neighptr_inner[n_inner++] = j;
else if (minchange) neighptr_inner[n_inner++] = j;
else if (which > 0)
neighptr_inner[n_inner++] = j ^ (which << SBBITS);
}
@ -492,6 +510,7 @@ void Neighbor::respa_bin_no_newton(NeighList *list)
if (respamiddle &&
rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
if (which == 0) neighptr_middle[n_middle++] = j;
else if (minchange) neighptr_middle[n_middle++] = j;
else if (which > 0)
neighptr_middle[n_middle++] = j ^ (which << SBBITS);
}
@ -594,6 +613,7 @@ void Neighbor::respa_bin_newton(NeighList *list)
int npnt_middle = 0;
int which = 0;
int minchange = 0;
for (i = 0; i < nlocal; i++) {
@ -654,17 +674,22 @@ void Neighbor::respa_bin_newton(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
if (which == 0) neighptr[n++] = j;
else if (minchange = domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
if (rsq < cut_inner_sq) {
if (which == 0) neighptr_inner[n_inner++] = j;
else if (minchange) neighptr_inner[n_inner++] = j;
else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
}
if (respamiddle &&
rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
if (which == 0) neighptr_middle[n_middle++] = j;
else if (minchange) neighptr_middle[n_middle++] = j;
else if (which > 0)
neighptr_middle[n_middle++] = j ^ (which << SBBITS);
}
@ -687,11 +712,15 @@ void Neighbor::respa_bin_newton(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
if (which == 0) neighptr[n++] = j;
else if (minchange = domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
if (rsq < cut_inner_sq) {
if (which == 0) neighptr_inner[n_inner++] = j;
else if (minchange) neighptr_inner[n_inner++] = j;
else if (which > 0)
neighptr_inner[n_inner++] = j ^ (which << SBBITS);
}
@ -699,6 +728,7 @@ void Neighbor::respa_bin_newton(NeighList *list)
if (respamiddle &&
rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
if (which == 0) neighptr_middle[n_middle++] = j;
else if (minchange) neighptr_middle[n_middle++] = j;
else if (which > 0)
neighptr_middle[n_middle++] = j ^ (which << SBBITS);
}
@ -801,6 +831,7 @@ void Neighbor::respa_bin_newton_tri(NeighList *list)
int npnt_middle = 0;
int which = 0;
int minchange = 0;
for (i = 0; i < nlocal; i++) {
@ -866,11 +897,15 @@ void Neighbor::respa_bin_newton_tri(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
if (which == 0) neighptr[n++] = j;
else if (minchange = domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
if (rsq < cut_inner_sq) {
if (which == 0) neighptr_inner[n_inner++] = j;
else if (minchange) neighptr_inner[n_inner++] = j;
else if (which > 0)
neighptr_inner[n_inner++] = j ^ (which << SBBITS);
}
@ -878,6 +913,7 @@ void Neighbor::respa_bin_newton_tri(NeighList *list)
if (respamiddle &&
rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
if (which == 0) neighptr_middle[n_middle++] = j;
else if (minchange) neighptr_middle[n_middle++] = j;
else if (which > 0)
neighptr_middle[n_middle++] = j ^ (which << SBBITS);
}