Error with NetCDF: Index exceeds bounds when using ypp
Posted: Tue Jul 12, 2016 2:39 pm
Dear all!
First of all thank you for accepting me on this board.
I am currently starting using YAMBO and I have encountered an error that I cannot understand.
I am here on Ubuntu 16.04, espresso 5.4.0 and yambo-4.0.3-rev.104;
making yambo (and interfaces, ypp, ypp_ph etc) with iotk and p2y (5.0) worked like a charm; p2y works when called in the prefix.save directory as in the tutorial; however running the tutorials on yambopy (http://yambopy.readthedocs.io/en/latest ... raction-si) gives me the following error:
I interpret this that q-points were not generated because some index exceeded its bounds, thereby killing NetCDF. But I am unable to find the actual culprit. Has anyone encountered this before?
any help is greatly appreciated!
Yours,
Chris
First of all thank you for accepting me on this board.
I am currently starting using YAMBO and I have encountered an error that I cannot understand.
I am here on Ubuntu 16.04, espresso 5.4.0 and yambo-4.0.3-rev.104;
making yambo (and interfaces, ypp, ypp_ph etc) with iotk and p2y (5.0) worked like a charm; p2y works when called in the prefix.save directory as in the tutorial; however running the tutorials on yambopy (http://yambopy.readthedocs.io/en/latest ... raction-si) gives me the following error:
Code: Select all
/si$ python elph_pw_si.py
nscf calculation found!
creating random list of q-points
___ __ _____ __ __ _____ _____
| Y || _ || Y || _ \ | _ |
| | ||. | ||. ||. | / |. | |
\_ _/ |. _ ||.\_/ ||. _ \ |. | |
|: | |: | ||: | ||: | \|: | |
|::| |:.|:.||:.|:.||::. /|::. |
`--" `-- --"`-- --"`-----" `-----"
<---> [01] CPU structure, Files & I/O Directories
<---> [02] Y(ambo) P(ost)/(re) P(rocessor)
<---> [03] Core DB
<---> :: Electrons : 8.000000
<---> :: Temperature [ev]: 0.000000
<---> :: Lattice factors [a.u.]: 5.150000 5.150000 5.150000
<---> :: K points : 13
<---> :: Bands : 20
<---> :: Symmetries : 12
<---> :: RL vectors : 5985
<---> [04] K-point grid
[ERROR] STOP signal received while in :[04] K-point grid
[ERROR][NetCDF] NetCDF: Index exceeds dimension bound
Traceback (most recent call last):
File "elph_pw_si.py", line 72, in <module>
qlist = qpoint_generation(nq)
File "elph_pw_si.py", line 59, in qpoint_generation
q[:,:-1] = loadtxt('database/o.random_k_pts')
File "/home/chris/.local/lib/python2.7/site-packages/numpy/lib/npyio.py", line 803, in loadtxt
fh = iter(open(fname, 'U'))
IOError: [Errno 2] No such file or directory: 'database/o.random_k_pts'
chris@dft:~/Downloads/yambopy-master/tutorial/si$
any help is greatly appreciated!
Yours,
Chris