[gpaw-users] An error occurs when performing STM simulation using GPAW

[kgd]

Dear gpaw-users,
    An error occurs when we perform STM simulation using GPAW(see attachment). First,we run surface.py and it works.Then,we run mystm.py and an error occurs during "stm.initialize()"(see error_CuO). The error is as following:
 
Traceback (most recent call last):
  File "mystm.py", line 28, in ?
    stm.initialize() 
  File "/usr/lib64/python2.4/site-packages/gpaw/transport/jstm.py", line 360, in initialize
    f = AtomCenteredFunctions(self.srf.wfs.gd, [phit], spos_c, j)
  File "/usr/lib64/python2.4/site-packages/gpaw/transport/jstm.py", line 156, in __init__
    lfc.set_positions((spos_c[np.newaxis, :] * gd.N_c - corner_c + 1) /
  File "/usr/lib64/python2.4/site-packages/gpaw/lfc.py", line 262, in set_positions
    movement |= sphere.set_position(spos_c, self.gd, self.cut)
  File "/usr/lib64/python2.4/site-packages/gpaw/lfc.py", line 89, in set_position
    for beg_c, end_c, sdisp_c in gd.get_boxes(spos_c, rcut, cut):
  File "/usr/lib64/python2.4/site-packages/gpaw/grid_descriptor.py", line 259, in get_boxes
    raise RuntimeError(('Atom at %.3f %.3f %.3f ' +
RuntimeError: Atom at 0.500 0.500 0.504 too close to boundary (beg. of box [-2  1  1], end of box [23 24 25])

 
 
   It is strange that the atom at ( 0.500 0.500 0.504) is not found. "Atom at 0.500 0.500 0.504 too close to boundary (beg. of box [-2  1  1], end of box [23 24 25])" , we set pbc= (1, 1, 0), that is the systerm has periodicity on X,Y,but not on Z. The negative value [-2 1 1] of beg. of box appears on X, we don't know where is the error considering periodicity. Any reply is appreciated.
Best regards!
 
Xianxin Wu
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