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@11328 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2014-01-25 22:46:08 +00:00
parent 2f6a46a2be
commit 0ce16af78b
63 changed files with 2943 additions and 798 deletions
Download Patch File Download Diff File Expand all files Collapse all files

35
src/dump_image.cpp
View File

@ -18,6 +18,8 @@
#include "dump_image.h"
#include "image.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "domain.h"
#include "group.h"
#include "force.h"
@ -646,7 +648,8 @@ void DumpImage::view_params()
void DumpImage::create_image()
{
int i,j,m,itype,atom1,atom2;
int i,j,m,n,itype,atom1,atom2,imol,iatom,btype;
tagint tagprev;
double diameter,delx,dely,delz;
double *color,*color1,*color2;
double xmid[3];
@ -700,10 +703,14 @@ void DumpImage::create_image()
tagint **bond_atom = atom->bond_atom;
int **bond_type = atom->bond_type;
int *num_bond = atom->num_bond;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
int newton_bond = force->newton_bond;
int molecular = atom->molecular;
Molecule **onemols = atom->avec->onemols;
// communicate choose flag for ghost atoms to know if they are selected
// if bcolor/bdiam = ATOM, setup bufcopy to comm atom color/diam attributes
@ -735,11 +742,27 @@ void DumpImage::create_image()
for (i = 0; i < nchoose; i++) {
atom1 = clist[i];
for (m = 0; m < num_bond[atom1]; m++) {
atom2 = atom->map(bond_atom[atom1][m]);
if (molecular == 1) n = num_bond[atom1];
else {
if (molindex[atom1] < 0) continue;
imol = molindex[atom1];
iatom = molatom[atom1];
n = onemols[imol]->num_bond[iatom];
}
for (m = 0; m < n; m++) {
if (molecular == 1) {
btype = bond_type[atom1][m];
atom2 = atom->map(bond_atom[atom1][m]);
} else {
tagprev = tag[i] - iatom - 1;
btype = atom->map(onemols[imol]->bond_type[atom1][m]);
atom2 = atom->map(onemols[imol]->bond_atom[iatom][m]+tagprev);
}
if (atom2 < 0 || !chooseghost[atom2]) continue;
if (newton_bond == 0 && tag[atom1] > tag[atom2]) continue;
if (bond_type[atom1][m] == 0) continue;
if (btype == 0) continue;
if (bcolor == ATOM) {
if (acolor == TYPE) {
@ -753,7 +776,7 @@ void DumpImage::create_image()
color2 = image->map_value2color(0,bufcopy[atom2][0]);
}
} else if (bcolor == TYPE) {
itype = bond_type[atom1][m];
itype = btype;
if (itype < 0) itype = -itype;
color = bcolortype[itype];
}
@ -771,7 +794,7 @@ void DumpImage::create_image()
diameter = MIN(bufcopy[atom1][1],bufcopy[atom2][1]);
}
} else if (bdiam == TYPE) {
itype = bond_type[atom1][m];
itype = btype;
if (itype < 0) itype = -itype;
diameter = bdiamtype[itype];
}