def energy_density_plot(storage):
rho=[]
ener=[]
for minimum in storage.data:
ca = CoordsAdapter(nrigid=2, nlattice=6, coords=minimum.coords)
ml = lattice.lowerTriangular(ca.lattice)
volume = np.dot(ml[:,0],np.cross(ml[:,1], ml[:,2]))
rho.append(1./volume)
ener.append(minimum.energy)
return rho, ener
def draw(self, coords_rigid, index):
from OpenGL import GL,GLUT
coords=np.zeros([GMIN.getNAtoms(), 3])
GMIN.toAtomistic(coords.reshape(coords.size), coords_rigid)
#coords = coords.reshape(GMIN.getNAtoms, 3)
com=np.mean(coords, axis=0)
if index == 1:
color = [[0.65, 0.0, 0.0, 1.], [0.35, 0.0, 0.0, 1.]]
else:
color = [[0.00, 0.65, 0., 1.], [0.00, 0.35, 0., 1.]]
i=0
for xx in coords[:-2]:
GL.glMaterialfv(GL.GL_FRONT_AND_BACK, GL.GL_DIFFUSE, color[i%2])
i+=1
x = xx-com
GL.glPushMatrix()
GL.glTranslate(x[0],x[1],x[2])
GLUT.glutSolidSphere(0.5,30,30)
GL.glPopMatrix()
GL.glMaterialfv(GL.GL_FRONT_AND_BACK, GL.GL_DIFFUSE, [0.,0.,1.,1.])
from pygmin.utils import lattice
l = lattice.lowerTriangular(coords_rigid[-6:])
mb = l[:,0] + l[:,1] + l[:,2]
GL.glPushMatrix()
GL.glTranslate(-0.5*mb[0],-0.5*mb[1],-0.5*mb[2])
for i in xrange(3):
self.drawCylinder([0.,0.,0.], l[:,i])
for i in xrange(1,3):
self.drawCylinder(l[:,0], l[:,0] + l[:,i])
mb = l[:,0] + l[:,1] + l[:,2]
for i in xrange(0,3):
self.drawCylinder(mb, mb - l[:,i])
for i in xrange(1,3):
self.drawCylinder(mb-l[:,0], mb - l[:,i]-l[:,0])
self.drawCylinder(l[:,1], l[:,1] + l[:,0])
self.drawCylinder(l[:,2], l[:,2] + l[:,0])
GL.glPopMatrix()