def test_contour_sphere(npts):
"Test example using POVRay module"
from numpy import arange,array
from Pistol.POVRay import Scene,TriangleMesh
def sphere(x,y,z): return x*x+y*y+z*z
# The goal here was to see whether MC would work when there weren't cubes,
# e.g. when yvec = 0.1,1.0,0.0. It doesn't appear to.
origin = array([-5.0,-5.0,-5.0])
length = 10
xvec = length*array([1.0,0.0,0.0])
yvec = length*array([0.0,1.0,0.0])
zvec = length*array([0.0,0.0,1.0])
nx=ny=nz=npts
triangles = []
for i in range(nx-1):
ifrac = i/(nx-1.)
ifracp = (i+1.)/(nx-1.)
for j in range(ny-1):
jfrac = j/(ny-1.)
jfracp = (j+1.)/(ny-1.)
for k in range(nz-1):
kfrac = k/(nz-1.)
kfracp = (k+1.)/(nz-1.)
x,y,z = origin + ifrac*xvec + jfrac*yvec + kfrac*zvec
xp,yp,zp = origin + ifracp*xvec + jfracp*yvec + kfracp*zvec
newtris = contour(3.0,
(x,y,z),(x,y,zp),(x,yp,zp),(x,yp,z),
(xp,y,z),(xp,y,zp),(xp,yp,zp),(xp,yp,z),
sphere(x,y,z),sphere(x,y,zp),
sphere(x,yp,zp),sphere(x,yp,z),
sphere(xp,y,z),sphere(xp,y,zp),
sphere(xp,yp,zp),sphere(xp,yp,z))
if newtris:
for tri in newtris: triangles.append(tri)
pov = Scene('test_sphere')
tmesh = TriangleMesh(triangles,(0,0,1))
pov.add(tmesh)
pov.write_pov()
pov.render()
pov.display()
return
def write_svg(self,filename,atoms):
from Pistol.SVG import Scene,Circle,Line
# recompute the name from the filename: this will
# have the _0001 on it, if applicable:
basename = os.path.basename(filename)
name = os.path.splitext(basename)[0]
atoms = rotate_2d(atoms,self.camera)
if self.iframe == 0:
# need to recompute bbox for rotated mol
xmin,xmax,ymin,ymax,zmin,zmax = get_bbox(atoms)
self.bbox = xmin,xmax,ymin,ymax,zmin,zmax
else:
xmin,xmax,ymin,ymax,zmin,zmax = self.bbox
height,width = 800,800 # in pixels
# readjust heigh and width based upon bbox.
dx = xmax - xmin
dy = ymax - ymin
if dx > dy:
height = height*dy/dx
else:
width = width*dy/dx
scale = get_2d_scale(xmin,xmax,ymin,ymax,height,width)
scene = Scene(name,height,width)
for i,j in get_bonds_from_distance(atoms):
atnoi,(xi,yi,zi) = atoms[i]
atnoj,(xj,yj,zj) = atoms[j]
Xi = int(scale*(xi-xmin))
Yi = int(scale*(yi-ymin))
Xj = int(scale*(xj-xmin))
Yj = int(scale*(yj-ymin))
scene.add(Line((Xi,Yi),(Xj,Yj)))
for atno,(x,y,z) in atoms:
X = int(scale*(x-xmin))
Y = int(scale*(y-ymin))
scene.add(Circle((X,Y),rscale*scale*radius[atno],color[atno]))
scene.write_svg(filename)
if self.nframes == 1: scene.display()
return
def main(outname,pltname):
mol_info = read_output_as_dict(outname)
plt_info = read_plt(pltname)
name = mol_info['name']
scene = Scene(name)
#scene.set_camera((0,4,0.5),(0,0,0.5))
scene.set_camera((0,10,0))
atoms = mol_info['structure']
for i,j in get_bonds_from_distance(atoms):
atnoi,xyzi = atoms[i]
atnoj,xyzj = atoms[j]
scene.add(Cylinder(xyzi,xyzj,0.1))
for atno,xyz in atoms:
r,g,b = color[atno]
sphere = Sphere(xyz,rscale*radius[atno],(r/255.,g/255.,b/255.))
scene.add(sphere)
ptris = mcube_contour(plt_info,0.1)
ntris = mcube_contour(plt_info,-0.1)
# if desired, compute normals at each vertex
ptris = smooth_tris(ptris)
ntris = smooth_tris(ntris)
if ptris: scene.add(TriangleMesh(ptris,(1,0,0)))
if ntris: scene.add(TriangleMesh(ntris,(0,0,1)))
scene.write_pov()
scene.render()
scene.display()
return
def write_pov(self,filename,atoms):
from Pistol.POVRay import Scene,Sphere,Cylinder
# recompute the name from the filename: this will
# have the _0001 on it, if applicable:
basename = os.path.basename(filename)
name = os.path.splitext(basename)[0]
scene = Scene(name,self.camera,self.light,bgcolor=(1,1,1))
for i,j in get_bonds_from_distance(atoms):
atnoi,xyzi = atoms[i]
atnoj,xyzj = atoms[j]
scene.add(Cylinder(xyzi,xyzj,0.1))
for atno,xyz in atoms:
r,g,b = color[atno]
sphere = Sphere(xyz,rscale*radius[atno],(r/255.,g/255.,b/255.))
scene.add(sphere)
scene.write_pov(filename)
scene.render()
if self.nframes == 1: scene.display()
return
