def scale_bounds(self,bounds):
if bounds is None:
return None
else:
boundsnew = np.empty(np.shape(bounds))
for i in range(3): # dimensions
boundsnew[i,:] = Mmath.rescale_coords(bounds[i,:],self.boxdims[i,:],[0,1])
return boundsnew
def dilate_points(self,pts):
colother = self.colother
coordsold = pts[:,colother]
linelimsold = min(coordsold), max(coordsold)
linelimsnew = self.linelims
coordsnew = Mmath.rescale_coords(coordsold,linelimsold,linelimsnew)
ptsnew = np.copy(pts)
ptsnew[:,colother] = coordsnew
return ptsnew
def getArrayOut(xyarray, typesarray, boxbounds):
natoms = xyarray.shape[0]
xyscaled = np.empty((natoms, 3))
xyarraynew = np.zeros((natoms, 3))
xyarraynew[:, :2] = xyarray[:, :2]
for i in range(3):
vec = xyarraynew[:, i]
bounds = boxbounds[i, :]
xyscaled[:, i] = Mmath.rescale_coords(vec, bounds, [0, 1])
atomvec = np.arange(1, natoms + 1, 1)
return np.column_stack((atomvec, typesarray[:, 0], xyscaled))
def getArrayOut(xyarray,typesarray,boxbounds):
natoms = xyarray.shape[0]
xyscaled = np.empty((natoms,3))
xyarraynew = np.zeros((natoms,3))
xyarraynew[:,:2] = xyarray[:,:2]
for i in range(3):
vec = xyarraynew[:,i]
bounds = boxbounds[i,:]
xyscaled[:,i] = Mmath.rescale_coords(vec,bounds,[0,1])
atomvec = np.arange(1,natoms+1,1)
return np.column_stack((atomvec,typesarray[:,0],xyscaled))
def unscale_coords(self,dumparray,indexstart=2):
for i in range(3):
dumparray[:,i+indexstart] = Mmath.rescale_coords(dumparray[:,i+indexstart],[0,1],self.boxdims[i,:])
return dumparray