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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9398 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2013-02-08 16:35:58 +00:00
parent 6ab4ee064b
commit 6bdbde76da
2 changed files with 37 additions and 11 deletions
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46
src/neigh_bond.cpp
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@ -246,10 +246,13 @@ void Neighbor::angle_check()
double **x = atom->x; double **x = atom->x;
int flag = 0; int flag = 0;
for (int m = 0; m < nbondlist; m++) { // check all 3 distances
// in case angle potential computes any of them
for (int m = 0; m < nanglelist; m++) {
i = anglelist[m][0]; i = anglelist[m][0];
j = anglelist[m][1]; j = anglelist[m][1];
k = anglelist[m][1]; k = anglelist[m][2];
dxstart = dx = x[i][0] - x[j][0]; dxstart = dx = x[i][0] - x[j][0];
dystart = dy = x[i][1] - x[j][1]; dystart = dy = x[i][1] - x[j][1];
dzstart = dz = x[i][2] - x[j][2]; dzstart = dz = x[i][2] - x[j][2];
@ -260,6 +263,11 @@ void Neighbor::angle_check()
dzstart = dz = x[i][2] - x[k][2]; dzstart = dz = x[i][2] - x[k][2];
domain->minimum_image(dx,dy,dz); domain->minimum_image(dx,dy,dz);
if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1; if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
dxstart = dx = x[j][0] - x[k][0];
dystart = dy = x[j][1] - x[k][1];
dzstart = dz = x[j][2] - x[k][2];
domain->minimum_image(dx,dy,dz);
if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
} }
int flag_all; int flag_all;
@ -319,7 +327,7 @@ void Neighbor::dihedral_all()
} }
} }
if (cluster_check) dihedral_check(dihedrallist); if (cluster_check) dihedral_check(ndihedrallist,dihedrallist);
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -375,12 +383,12 @@ void Neighbor::dihedral_partial()
} }
} }
if (cluster_check) dihedral_check(dihedrallist); if (cluster_check) dihedral_check(ndihedrallist,dihedrallist);
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
void Neighbor::dihedral_check(int **list) void Neighbor::dihedral_check(int nlist, int **list)
{ {
int i,j,k,l; int i,j,k,l;
double dx,dy,dz,dxstart,dystart,dzstart; double dx,dy,dz,dxstart,dystart,dzstart;
@ -388,11 +396,14 @@ void Neighbor::dihedral_check(int **list)
double **x = atom->x; double **x = atom->x;
int flag = 0; int flag = 0;
for (int m = 0; m < nbondlist; m++) { // check all 6 distances
// in case dihedral/improper potential computes any of them
for (int m = 0; m < nlist; m++) {
i = list[m][0]; i = list[m][0];
j = list[m][1]; j = list[m][1];
k = list[m][1]; k = list[m][2];
l = list[m][1]; l = list[m][3];
dxstart = dx = x[i][0] - x[j][0]; dxstart = dx = x[i][0] - x[j][0];
dystart = dy = x[i][1] - x[j][1]; dystart = dy = x[i][1] - x[j][1];
dzstart = dz = x[i][2] - x[j][2]; dzstart = dz = x[i][2] - x[j][2];
@ -408,6 +419,21 @@ void Neighbor::dihedral_check(int **list)
dzstart = dz = x[i][2] - x[l][2]; dzstart = dz = x[i][2] - x[l][2];
domain->minimum_image(dx,dy,dz); domain->minimum_image(dx,dy,dz);
if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1; if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
dxstart = dx = x[j][0] - x[k][0];
dystart = dy = x[j][1] - x[k][1];
dzstart = dz = x[j][2] - x[k][2];
domain->minimum_image(dx,dy,dz);
if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
dxstart = dx = x[j][0] - x[l][0];
dystart = dy = x[j][1] - x[l][1];
dzstart = dz = x[j][2] - x[l][2];
domain->minimum_image(dx,dy,dz);
if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
dxstart = dx = x[k][0] - x[l][0];
dystart = dy = x[k][1] - x[l][1];
dzstart = dz = x[k][2] - x[l][2];
domain->minimum_image(dx,dy,dz);
if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
} }
int flag_all; int flag_all;
@ -468,7 +494,7 @@ void Neighbor::improper_all()
} }
} }
if (cluster_check) dihedral_check(improperlist); if (cluster_check) dihedral_check(nimproperlist,improperlist);
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -524,5 +550,5 @@ void Neighbor::improper_partial()
} }
} }
if (cluster_check) dihedral_check(improperlist); if (cluster_check) dihedral_check(nimproperlist,improperlist);
} }

2
src/neighbor.h
View File

@ -266,7 +266,7 @@ class Neighbor : protected Pointers {
BondPtr dihedral_build; // ptr to dihedral list functions BondPtr dihedral_build; // ptr to dihedral list functions
void dihedral_all(); // dihedral list with all dihedrals void dihedral_all(); // dihedral list with all dihedrals
void dihedral_partial(); // exclude certain dihedrals void dihedral_partial(); // exclude certain dihedrals
void dihedral_check(int **); void dihedral_check(int, int **);
BondPtr improper_build; // ptr to improper list functions BondPtr improper_build; // ptr to improper list functions
void improper_all(); // improper list with all impropers void improper_all(); // improper list with all impropers