def cms(s, sel):
at = getAtomtypes()
if at is None:
msg().error(
"Atom-types information not available, calculating average.")
if s is None:
return None
s = Structure(s)
s.setCarthesian()
w = Vector(0.0, 0.0, 0.0)
M = 0.0
try:
for i, nx, ny, nz in sel:
if i < len(s) and i >= 0:
try:
m = float(s.info.getRecordForAtom(i).mass)
except:
m = float(
at.getRecordForElement(
s.info.getRecordForAtom(i).element).mass)
w = w + m * (s[i] + nx * s.basis[0] + ny * s.basis[1] +
nz * s.basis[2])
M = M + m
w = (1.0 / M) * w
return w
except:
msg().exception()
msg().error("CMS not aplicable, calculating an average.")
return average(s, sel)
def showStructureWindow(self):
if self.swin is None:
self.swin = StructureWindow(title="p4vasp Structure",
atomtypes=getAtomtypes())
self.swin.structure_drawer.setRadiusFactor(0.5 *
self.radius_factor)
self.swin.show()
def __init__(self):
Applet.__init__(self)
self.win = None
self.a = None
self.dir = 2
self.n = 0
self.value = 0.0
# self.sigmax=0
# self.sigmay=0
# self.sigmaz=0
self.sh = 0
self.sv = 0
self.n1 = 0
self.n2 = 0
self.n3 = 0
self.chgname = "PARCHG"
self.sd = None
self.lo = 0
self.hi = 1
self.inv = 0
self.navigator = None
self.clamp_type = 0
self.charge = None
self.smooth_charge = None
self.structure = None
self.minimum = 0
self.maximum = 0
self.average = 0
self.sigma = 0
self.src = 0
self.mode = 0
self.interpolation = 0
self.postinterpolation = 0
self.postsigma = 0
self.postn = 0
self.atomtypes = getAtomtypes()
self.structure_offset = 0.0
self.brightness = 0.0
self.contrast = 1.0
self.multiple = (1, 1, 1)
self.hide_atoms = []
self.b1 = cmatrix.Vector(0, 0, 0)
self.b2 = cmatrix.Vector(0, 0, 0)
self.bz = cmatrix.Vector(0, 0, 0)
#DUMMY ATTRIBUTES -for compatibility with StructureWindowControlApplet
self.chgcar = None
self.index = 0
self.sequencetype = self.INITIAL_SEQUENCE
self.arrowstype = 0
self.cell_centering = 0
def showStructureWindow(self):
if self.swin is None:
l = [(0, 0, 0, 0)]
for a in applets():
if isinstance(a, StructureWindowApplet):
if a.swin is not None:
w = a.swin.win
if w is not None:
l.append((w.x, w.y, w.w, w.h))
xx = max(map(lambda x: x[0] + x[2], l))
yy = max(map(lambda x: x[1] + x[3], l))
if yy <= 600:
xx = 0
else:
yy = 0
self.swin = StructureWindow(x=xx,
y=yy,
w=500,
h=400,
title="p4vasp Structure",
atomtypes=getAtomtypes())
self.swin.setRadiusFactor(0.5 * self.radius_factor)
# self.swin.setBackground(1,1,1)
self.swin.show()
def __init__(self,name,file_extension,paintCreator):
self._name=name
self._file_extension=file_extension
self.paint=[paintCreator]
self.atomtypes=getAtomtypes()