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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8392 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2012-06-25 17:13:30 +00:00
parent e8ff810ee7
commit da1c864eab
2 changed files with 48 additions and 25 deletions
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1
src/MC/fix_bond_break.cpp
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@ -204,7 +204,6 @@ void FixBondBreak::post_integrate()
delx = x[i1][0] - x[i2][0];
dely = x[i1][1] - x[i2][1];
delz = x[i1][2] - x[i2][2];
domain->minimum_image(delx,dely,delz);
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutsq) continue;

72
src/neigh_bond.cpp
View File

@ -48,13 +48,14 @@ void Neighbor::bond_all()
tag[i],bond_atom[i][m],me,update->ntimestep);
error->one(FLERR,str);
}
atom1 = domain->closest_image(i,atom1);
if (newton_bond || i < atom1) {
if (nbondlist == maxbond) {
maxbond += BONDDELTA;
memory->grow(bondlist,maxbond,3,"neighbor:bondlist");
}
bondlist[nbondlist][0] = i;
bondlist[nbondlist][1] = domain->closest_image(i,atom1);
bondlist[nbondlist][1] = atom1;
bondlist[nbondlist][2] = bond_type[i][m];
nbondlist++;
}
@ -87,13 +88,14 @@ void Neighbor::bond_partial()
tag[i],bond_atom[i][m],me,update->ntimestep);
error->one(FLERR,str);
}
atom1 = domain->closest_image(i,atom1);
if (newton_bond || i < atom1) {
if (nbondlist == maxbond) {
maxbond += BONDDELTA;
memory->grow(bondlist,maxbond,3,"neighbor:bondlist");
}
bondlist[nbondlist][0] = i;
bondlist[nbondlist][1] = domain->closest_image(i,atom1);
bondlist[nbondlist][1] = atom1;
bondlist[nbondlist][2] = bond_type[i][m];
nbondlist++;
}
@ -130,14 +132,17 @@ void Neighbor::angle_all()
me,update->ntimestep);
error->one(FLERR,str);
}
atom1 = domain->closest_image(i,atom1);
atom2 = domain->closest_image(i,atom2);
atom3 = domain->closest_image(i,atom3);
if (newton_bond || (i <= atom1 && i <= atom2 && i <= atom3)) {
if (nanglelist == maxangle) {
maxangle += BONDDELTA;
memory->grow(anglelist,maxangle,4,"neighbor:anglelist");
}
anglelist[nanglelist][0] = domain->closest_image(i,atom1);
anglelist[nanglelist][1] = domain->closest_image(i,atom2);
anglelist[nanglelist][2] = domain->closest_image(i,atom3);
anglelist[nanglelist][0] = atom1;
anglelist[nanglelist][1] = atom2;
anglelist[nanglelist][2] = atom3;
anglelist[nanglelist][3] = angle_type[i][m];
nanglelist++;
}
@ -175,14 +180,17 @@ void Neighbor::angle_partial()
me,update->ntimestep);
error->one(FLERR,str);
}
atom1 = domain->closest_image(i,atom1);
atom2 = domain->closest_image(i,atom2);
atom3 = domain->closest_image(i,atom3);
if (newton_bond || (i <= atom1 && i <= atom2 && i <= atom3)) {
if (nanglelist == maxangle) {
maxangle += BONDDELTA;
memory->grow(anglelist,maxangle,4,"neighbor:anglelist");
}
anglelist[nanglelist][0] = domain->closest_image(i,atom1);
anglelist[nanglelist][1] = domain->closest_image(i,atom2);
anglelist[nanglelist][2] = domain->closest_image(i,atom3);
anglelist[nanglelist][0] = atom1;
anglelist[nanglelist][1] = atom2;
anglelist[nanglelist][2] = atom3;
anglelist[nanglelist][3] = angle_type[i][m];
nanglelist++;
}
@ -222,16 +230,20 @@ void Neighbor::dihedral_all()
me,update->ntimestep);
error->one(FLERR,str);
}
atom1 = domain->closest_image(i,atom1);
atom2 = domain->closest_image(i,atom2);
atom3 = domain->closest_image(i,atom3);
atom4 = domain->closest_image(i,atom4);
if (newton_bond ||
(i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
if (ndihedrallist == maxdihedral) {
maxdihedral += BONDDELTA;
memory->grow(dihedrallist,maxdihedral,5,"neighbor:dihedrallist");
}
dihedrallist[ndihedrallist][0] = domain->closest_image(i,atom1);
dihedrallist[ndihedrallist][1] = domain->closest_image(i,atom2);
dihedrallist[ndihedrallist][2] = domain->closest_image(i,atom3);
dihedrallist[ndihedrallist][3] = domain->closest_image(i,atom4);
dihedrallist[ndihedrallist][0] = atom1;
dihedrallist[ndihedrallist][1] = atom2;
dihedrallist[ndihedrallist][2] = atom3;
dihedrallist[ndihedrallist][3] = atom4;
dihedrallist[ndihedrallist][4] = dihedral_type[i][m];
ndihedrallist++;
}
@ -272,16 +284,20 @@ void Neighbor::dihedral_partial()
me,update->ntimestep);
error->one(FLERR,str);
}
atom1 = domain->closest_image(i,atom1);
atom2 = domain->closest_image(i,atom2);
atom3 = domain->closest_image(i,atom3);
atom4 = domain->closest_image(i,atom4);
if (newton_bond ||
(i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
if (ndihedrallist == maxdihedral) {
maxdihedral += BONDDELTA;
memory->grow(dihedrallist,maxdihedral,5,"neighbor:dihedrallist");
}
dihedrallist[ndihedrallist][0] = domain->closest_image(i,atom1);
dihedrallist[ndihedrallist][1] = domain->closest_image(i,atom2);
dihedrallist[ndihedrallist][2] = domain->closest_image(i,atom3);
dihedrallist[ndihedrallist][3] = domain->closest_image(i,atom4);
dihedrallist[ndihedrallist][0] = atom1;
dihedrallist[ndihedrallist][1] = atom2;
dihedrallist[ndihedrallist][2] = atom3;
dihedrallist[ndihedrallist][3] = atom4;
dihedrallist[ndihedrallist][4] = dihedral_type[i][m];
ndihedrallist++;
}
@ -321,16 +337,20 @@ void Neighbor::improper_all()
me,update->ntimestep);
error->one(FLERR,str);
}
atom1 = domain->closest_image(i,atom1);
atom2 = domain->closest_image(i,atom2);
atom3 = domain->closest_image(i,atom3);
atom4 = domain->closest_image(i,atom4);
if (newton_bond ||
(i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
if (nimproperlist == maximproper) {
maximproper += BONDDELTA;
memory->grow(improperlist,maximproper,5,"neighbor:improperlist");
}
improperlist[nimproperlist][0] = domain->closest_image(i,atom1);
improperlist[nimproperlist][1] = domain->closest_image(i,atom2);
improperlist[nimproperlist][2] = domain->closest_image(i,atom3);
improperlist[nimproperlist][3] = domain->closest_image(i,atom4);
improperlist[nimproperlist][0] = atom1;
improperlist[nimproperlist][1] = atom2;
improperlist[nimproperlist][2] = atom3;
improperlist[nimproperlist][3] = atom4;
improperlist[nimproperlist][4] = improper_type[i][m];
nimproperlist++;
}
@ -371,16 +391,20 @@ void Neighbor::improper_partial()
me,update->ntimestep);
error->one(FLERR,str);
}
atom1 = domain->closest_image(i,atom1);
atom2 = domain->closest_image(i,atom2);
atom3 = domain->closest_image(i,atom3);
atom4 = domain->closest_image(i,atom4);
if (newton_bond ||
(i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
if (nimproperlist == maximproper) {
maximproper += BONDDELTA;
memory->grow(improperlist,maximproper,5,"neighbor:improperlist");
}
improperlist[nimproperlist][0] = domain->closest_image(i,atom1);
improperlist[nimproperlist][1] = domain->closest_image(i,atom2);
improperlist[nimproperlist][2] = domain->closest_image(i,atom3);
improperlist[nimproperlist][3] = domain->closest_image(i,atom4);
improperlist[nimproperlist][0] = atom1;
improperlist[nimproperlist][1] = atom2;
improperlist[nimproperlist][2] = atom3;
improperlist[nimproperlist][3] = atom4;
improperlist[nimproperlist][4] = improper_type[i][m];
nimproperlist++;
}