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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14440 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2016-01-14 22:33:46 +00:00
parent cd1f4ae7f0
commit 09fb68df71
10 changed files with 588 additions and 117 deletions
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200
src/dump_image.cpp
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@ -18,7 +18,8 @@
#include "dump_image.h"
#include "image.h"
#include "atom.h"
#include "atom_vec.h"
#include "atom_vec_line.h"
#include "atom_vec_tri.h"
#include "atom_vec_body.h"
#include "body.h"
#include "molecule.h"
@ -29,6 +30,7 @@
#include "input.h"
#include "variable.h"
#include "math_const.h"
#include "math_extra.h"
#include "error.h"
#include "memory.h"
@ -106,7 +108,7 @@ DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) :
// set defaults for optional args
atomflag = YES;
bodyflag = NO;
lineflag = triflag = bodyflag = NO;
if (atom->nbondtypes == 0) bondflag = NO;
else {
bondflag = YES;
@ -132,28 +134,19 @@ DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) :
int iarg = ioptional;
while (iarg < narg) {
if (strcmp(arg[iarg],"adiam") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump image command");
adiam = NUMERIC;
adiamvalue = force->numeric(FLERR,arg[iarg+1]);
if (adiamvalue <= 0.0) error->all(FLERR,"Illegal dump image command");
iarg += 2;
} else if (strcmp(arg[iarg],"atom") == 0) {
if (strcmp(arg[iarg],"atom") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump image command");
if (strcmp(arg[iarg+1],"yes") == 0) atomflag = YES;
else if (strcmp(arg[iarg+1],"no") == 0) atomflag = NO;
else error->all(FLERR,"Illegal dump image command");
iarg += 2;
} else if (strcmp(arg[iarg],"body") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal dump image command");
if (strcmp(arg[iarg+1],"yes") == 0) bodyflag = YES;
else if (strcmp(arg[iarg+1],"no") == 0) bodyflag = NO;
else error->all(FLERR,"Illegal dump image command");
bodyflag1 = force->numeric(FLERR,arg[iarg+2]);
bodyflag2 = force->numeric(FLERR,arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"adiam") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump image command");
adiam = NUMERIC;
adiamvalue = force->numeric(FLERR,arg[iarg+1]);
if (adiamvalue <= 0.0) error->all(FLERR,"Illegal dump image command");
iarg += 2;
} else if (strcmp(arg[iarg],"bond") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal dump image command");
@ -174,6 +167,32 @@ DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) :
else error->all(FLERR,"Illegal dump image command");
iarg += 3;
} else if (strcmp(arg[iarg],"line") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal dump image command");
lineflag = YES;
if (strcmp(arg[iarg+1],"type") == 0) lcolor = TYPE;
else error->all(FLERR,"Illegal dump image command");
ldiam = NUMERIC;
ldiamvalue = force->numeric(FLERR,arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg],"tri") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump image command");
triflag = YES;
if (strcmp(arg[iarg+1],"type") == 0) tcolor = TYPE;
else error->all(FLERR,"Illegal dump image command");
iarg += 2;
} else if (strcmp(arg[iarg],"body") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal dump image command");
bodyflag = YES;
if (strcmp(arg[iarg+1],"type") == 0) bodycolor = TYPE;
else error->all(FLERR,"Illegal dump image command");
bodyflag1 = force->numeric(FLERR,arg[iarg+2]);
bodyflag2 = force->numeric(FLERR,arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"size") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal dump image command");
int width = force->inumeric(FLERR,arg[iarg+1]);
@ -333,13 +352,26 @@ DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) :
} else error->all(FLERR,"Illegal dump image command");
}
// error check for bodyflag
// error checks and setup for lineflag, triflag, bodyflag
if (bodyflag) {
AtomVecBody *avec = (AtomVecBody *) atom->style_match("body");
if (!avec) error->all(FLERR,"Dump image body yes requires atom style body");
bptr = avec->bptr;
if (lineflag) {
avec_line = (AtomVecLine *) atom->style_match("line");
if (!avec_line)
error->all(FLERR,"Dump image line requires atom style line");
}
if (triflag) {
avec_tri = (AtomVecTri *) atom->style_match("tri");
if (!avec_tri)
error->all(FLERR,"Dump image tri requires atom style tri");
}
if (bodyflag) {
avec_body = (AtomVecBody *) atom->style_match("body");
if (!avec_body)
error->all(FLERR,"Dump image body yes requires atom style body");
}
extraflag = 0;
if (lineflag || triflag || bodyflag) extraflag = 1;
// allocate image buffer now that image size is known
@ -679,18 +711,21 @@ void DumpImage::view_params()
void DumpImage::create_image()
{
int i,j,k,m,n,itype,atom1,atom2,imol,iatom,btype,ibonus;
int i,j,k,m,n,itype,atom1,atom2,imol,iatom,btype,ibonus,drawflag;
tagint tagprev;
double diameter,delx,dely,delz;
int *bodyvec;
double **bodyarray;
double *color,*color1,*color2;
double xmid[3];
double xmid[3],pt1[3],pt2[3],pt3[3];
double mat[3][3];
// render my atoms
if (atomflag) {
double **x = atom->x;
int *line = atom->line;
int *tri = atom->tri;
int *body = atom->body;
m = 0;
@ -719,18 +754,109 @@ void DumpImage::create_image()
diameter = buf[m+1];
}
if (!body || !bodyflag || body[j] < 0)
image->draw_sphere(x[j],color,diameter);
else {
ibonus = body[i];
n = bptr->image(ibonus,bodyflag1,bodyflag2,bodyvec,bodyarray);
for (k = 0; k < n; k++) {
if (bodyvec[k] == SPHERE)
image->draw_sphere(bodyarray[k],color,bodyarray[k][3]);
else if (bodyvec[k] == LINE)
image->draw_cylinder(&bodyarray[k][0],&bodyarray[k][3],
color,bodyarray[k][6],3);
}
// do not draw if line,tri,body keywords enabled and atom is one of those
drawflag = 1;
if (extraflag) {
if (lineflag && line[j] >= 0) drawflag = 0;
if (triflag && tri[j] >= 0) drawflag = 0;
if (bodyflag && body[j] >= 0) drawflag = 0;
}
if (drawflag) image->draw_sphere(x[j],color,diameter);
m += size_one;
}
}
// render atoms that are lines
if (lineflag) {
double length,theta,dx,dy;
double **x = atom->x;
int *line = atom->line;
int *type = atom->type;
for (i = 0; i < nchoose; i++) {
j = clist[i];
if (line[j] < 0) continue;
if (lcolor == TYPE) {
color = colortype[type[j]];
}
if (ldiam == NUMERIC) {
diameter = ldiamvalue;
}
length = avec_line->bonus[line[j]].length;
theta = avec_line->bonus[line[j]].theta;
dx = 0.5*length*cos(theta);
dy = 0.5*length*sin(theta);
pt1[0] = x[j][0] + dx;
pt1[1] = x[j][1] + dy;
pt1[2] = 0.0;
pt2[0] = x[j][0] - dx;
pt2[1] = x[j][1] - dy;
pt2[2] = 0.0;
image->draw_cylinder(pt1,pt2,color,ldiamvalue,3);
}
}
// render atoms that are triangles
if (triflag) {
double **x = atom->x;
int *tri = atom->tri;
int *type = atom->type;
for (i = 0; i < nchoose; i++) {
j = clist[i];
if (tri[j] < 0) continue;
if (tcolor == TYPE) {
color = colortype[type[j]];
}
MathExtra::quat_to_mat(avec_tri->bonus[tri[i]].quat,mat);
MathExtra::matvec(mat,avec_tri->bonus[tri[i]].c1,pt1);
MathExtra::matvec(mat,avec_tri->bonus[tri[i]].c2,pt2);
MathExtra::matvec(mat,avec_tri->bonus[tri[i]].c3,pt3);
MathExtra::add3(pt1,x[i],pt1);
MathExtra::add3(pt2,x[i],pt2);
MathExtra::add3(pt3,x[i],pt3);
image->draw_triangle(pt1,pt2,pt3,color);
}
}
// render atoms that are bodies
if (bodyflag) {
Body *bptr = avec_body->bptr;
double **x = atom->x;
int *body = atom->body;
m = 0;
for (i = 0; i < nchoose; i++) {
j = clist[i];
if (body[j] < 0) continue;
if (bodycolor == TYPE) {
itype = static_cast<int> (buf[m]);
color = colortype[itype];
}
ibonus = body[i];
n = bptr->image(ibonus,bodyflag1,bodyflag2,bodyvec,bodyarray);
for (k = 0; k < n; k++) {
if (bodyvec[k] == SPHERE)
image->draw_sphere(bodyarray[k],color,bodyarray[k][3]);
else if (bodyvec[k] == LINE)
image->draw_cylinder(&bodyarray[k][0],&bodyarray[k][3],
color,bodyarray[k][6],3);
}
m += size_one;