[Wien] Problem with BerryPI 1.3
aaaa bbbb cccc
ccaabb12345 at gmail.com
Tue Nov 24 15:34:03 CET 2015
Dear Wien2k users,
I am a new BerryPi 1.3 program user and want to reproduce the example in
the manual with compound GaAs. I got an error such as:
$ berrypi -p -k6:6:6
[ BerryPI ] Parallel calculation is activated
it is assumed that you have .machines file ready
[ BerryPI ] Proceed with the k-mesh [6, 6, 6]
[ BerryPI ] Starting BerryPI Automation for berry
[ BerryPI ] New working directory: /home/upetralanda001/BFO/berry/berry
[ BerryPI ] w2kpath = /software/WIEN2k
[ BerryPI ] pypath = /software/python-2.7.9/bin/python2.7
[ BerryPI ] bppath = /software/WIEN2k/BerryPI-1.3
[ BerryPI ] +++Version 1.3 (Mar 17, 2015)
[ BerryPI ] Python version: 2.7.9
[ BerryPI ] Numpy version: 1.10.2rc1
[ BerryPI ] Calling command: rm -f berry.broyd*
[ BerryPI ] Copied berry.struct to berry.ksym
[ BerryPI ] Calling command: echo "0 6 6 6 0" | x kgen -fbz
1 symmetry operations without inversion
NUMBER OF K-POINTS IN WHOLE CELL: (0 allows to specify 3 divisions of G)
length of reciprocal lattice vectors: 1.019 1.019 1.019 0.000
0.000 0.000
Specify 3 mesh-divisions (n1,n2,n3):
Shift of k-mesh allowed. Do you want to shift: (0=no, 1=shift)
216 k-points generated, ndiv= 6 6 6
KGEN ENDS
0.010u 0.020s 0:00.11 27.2% 0+0k 0+0io 0pf+0w
[ BerryPI ] Calling command: cp berry.klist berry.klist_w90
[ BerryPI ] Calling command: x lapw1 -p
running lapw1c in single mode
LAPW1 END
7.300u 0.550s 0:08.29 94.6% 0+0k 0+0io 0pf+0w
[ BerryPI ] Determine number of bloch bands in non-sp mode
[ BerryPI ] Number of bloch bands is [[1, 14]]
[ BerryPI ] Calling command: /software/python-2.7.9/bin/python2.7
/software/WIEN2k/write_inwf -mode MMN -bands 1 14
[ BerryPI ] berry.win is present and will be removed
... done
[ BerryPI ] Calling command: write_win
/software/WIEN2k/write_win: line 2: setenv: command not found
write_win: template file `/software/WIEN2k/SRC_templates/case.win' not
found, will use empty template
[ BerryPI ] Calling command: /software/python-2.7.9/bin/python2.7
/software/WIEN2k/BerryPI-1.3/win2nnkp.py berry
[ BerryPI ] file berry.scf2 found; will extract the Fermi energy
:FER : F E R M I - ENERGY(TETRAH.M.)= 0.3185071614
[ BerryPI ] Ef = 0.3185071614 Ry
[ BerryPI ] berry.fermi is present and will be removed
... done
[ BerryPI ] Fermi energy is written to berry.fermi
[ BerryPI ] Calling command: x w2w -p
grep: .processes: No such file or directory
grep: .processes: No such file or directory
W2W END
6.240u 0.060s 0:07.21 87.3% 0+0k 0+0io 0pf+0w
[ BerryPI ] Finished Berry phase computation for berry
[ BerryPI ] Performing main calculation on berry
[ BerryPI ] Checking existance of berry.outputst
[ BerryPI ] -- OK
[ BerryPI ] Checking existance of berry.scf
[ BerryPI ] -- OK
[ BerryPI ] Checking existance of berry.struct
[ BerryPI ] -- OK
[ BerryPI ] Checking existance of berry.outputd
[ BerryPI ] -- OK
Initial Berry phases and their wrapped values in the range [-pi ... +pi]
=======================================================================================
| init k-point | phase raw (rad) | phase
wrap. (rad)
---------------------------------------------------------------------------------------
direction(1)
spin(1)
path( 1) 1 -8.117735e+00
-1.834549e+00
path( 2) 2 -1.609796e+00
-1.609796e+00
path( 3) 3 4.707841e+00
-1.575344e+00
path( 4) 4 -1.576636e+00
-1.576636e+00
path( 5) 5 -1.575344e+00
-1.575344e+00
path( 6) 6 -7.892981e+00
-1.609796e+00
path( 7) 7 4.673390e+00
-1.609796e+00
path( 8) 8 -1.609796e+00
-1.609796e+00
path( 9) 9 4.759751e+00
-1.523434e+00
path( 10) 10 4.762531e+00
-1.520654e+00
path( 11) 11 -1.520654e+00
-1.520654e+00
path( 12) 12 -1.523434e+00
-1.523434e+00
path( 13) 13 -1.575344e+00
-1.575344e+00
path( 14) 14 -1.523434e+00
-1.523434e+00
path( 15) 15 4.707841e+00
-1.575344e+00
path( 16) 16 -1.520654e+00
-1.520654e+00
path( 17) 17 -1.508676e+00
-1.508676e+00
path( 18) 18 4.762531e+00
-1.520654e+00
path( 19) 19 -7.859822e+00
-1.576636e+00
path( 20) 20 4.762531e+00
-1.520654e+00
path( 21) 21 -1.520654e+00
-1.520654e+00
path( 22) 22 -1.576636e+00
-1.576636e+00
path( 23) 23 4.762531e+00
-1.520654e+00
path( 24) 24 -1.520654e+00
-1.520654e+00
path( 25) 25 4.707841e+00
-1.575344e+00
path( 26) 26 -1.520654e+00
-1.520654e+00
path( 27) 27 -1.508676e+00
-1.508676e+00
path( 28) 28 -1.520654e+00
-1.520654e+00
path( 29) 29 -7.858529e+00
-1.575344e+00
path( 30) 30 4.759751e+00
-1.523434e+00
path( 31) 31 -1.609796e+00
-1.609796e+00
path( 32) 32 -1.523434e+00
-1.523434e+00
path( 33) 33 -1.520654e+00
-1.520654e+00
path( 34) 34 -7.803840e+00
-1.520654e+00
path( 35) 35 -7.806619e+00
-1.523434e+00
path( 36) 36 -1.609796e+00
-1.609796e+00
---------------------------------------------------------------------------------------
direction(2)
spin(1)
path( 1) 1 4.448636e+00
-1.834549e+00
path( 2) 2 4.673390e+00
-1.609796e+00
path( 3) 3 1.099103e+01
-1.575344e+00
path( 4) 4 -1.576636e+00
-1.576636e+00
path( 5) 5 4.707841e+00
-1.575344e+00
path( 6) 6 -1.609796e+00
-1.609796e+00
path( 7) 37 -7.892981e+00
-1.609796e+00
path( 8) 38 4.673390e+00
-1.609796e+00
path( 9) 39 1.104294e+01
-1.523434e+00
path( 10) 40 -1.520654e+00
-1.520654e+00
path( 11) 41 -1.520654e+00
-1.520654e+00
path( 12) 42 4.759751e+00
-1.523434e+00
path( 13) 73 4.707841e+00
-1.575344e+00
path( 14) 74 -1.523434e+00
-1.523434e+00
path( 15) 75 -1.575344e+00
-1.575344e+00
path( 16) 76 -1.520654e+00
-1.520654e+00
path( 17) 77 4.774509e+00
-1.508676e+00
path( 18) 78 4.762531e+00
-1.520654e+00
path( 19) 109 -1.576636e+00
-1.576636e+00
path( 20) 110 -1.520654e+00
-1.520654e+00
path( 21) 111 -1.520654e+00
-1.520654e+00
path( 22) 112 -1.576636e+00
-1.576636e+00
path( 23) 113 -1.520654e+00
-1.520654e+00
path( 24) 114 -1.520654e+00
-1.520654e+00
path( 25) 145 4.707841e+00
-1.575344e+00
path( 26) 146 4.762531e+00
-1.520654e+00
path( 27) 147 1.105769e+01
-1.508676e+00
path( 28) 148 -1.520654e+00
-1.520654e+00
path( 29) 149 -1.575344e+00
-1.575344e+00
path( 30) 150 4.759751e+00
-1.523434e+00
path( 31) 181 1.095657e+01
-1.609796e+00
path( 32) 182 4.759751e+00
-1.523434e+00
path( 33) 183 -1.520654e+00
-1.520654e+00
path( 34) 184 -1.520654e+00
-1.520654e+00
path( 35) 185 -1.523434e+00
-1.523434e+00
path( 36) 186 -1.609796e+00
-1.609796e+00
---------------------------------------------------------------------------------------
direction(3)
spin(1)
path( 1) 1 4.448636e+00
-1.834549e+00
path( 2) 7 4.673390e+00
-1.609796e+00
path( 3) 13 -1.575344e+00
-1.575344e+00
path( 4) 19 4.706549e+00
-1.576636e+00
path( 5) 25 -1.575344e+00
-1.575344e+00
path( 6) 31 4.673390e+00
-1.609796e+00
path( 7) 37 4.673390e+00
-1.609796e+00
path( 8) 43 4.673390e+00
-1.609796e+00
path( 9) 49 4.759751e+00
-1.523434e+00
path( 10) 55 -1.520654e+00
-1.520654e+00
path( 11) 61 -1.520654e+00
-1.520654e+00
path( 12) 67 4.759751e+00
-1.523434e+00
path( 13) 73 -1.575344e+00
-1.575344e+00
path( 14) 79 4.759751e+00
-1.523434e+00
path( 15) 85 -7.858529e+00
-1.575344e+00
path( 16) 91 4.762531e+00
-1.520654e+00
path( 17) 97 -7.791862e+00
-1.508676e+00
path( 18) 103 4.762531e+00
-1.520654e+00
path( 19) 109 4.706549e+00
-1.576636e+00
path( 20) 115 -1.520654e+00
-1.520654e+00
path( 21) 121 -1.520654e+00
-1.520654e+00
path( 22) 127 -1.576636e+00
-1.576636e+00
path( 23) 133 -1.520654e+00
-1.520654e+00
path( 24) 139 -1.520654e+00
-1.520654e+00
path( 25) 145 4.707841e+00
-1.575344e+00
path( 26) 151 4.762531e+00
-1.520654e+00
path( 27) 157 -1.508676e+00
-1.508676e+00
path( 28) 163 -1.520654e+00
-1.520654e+00
path( 29) 169 4.707841e+00
-1.575344e+00
path( 30) 175 -1.523434e+00
-1.523434e+00
path( 31) 181 -1.609796e+00
-1.609796e+00
path( 32) 187 -7.806619e+00
-1.523434e+00
path( 33) 193 -7.803840e+00
-1.520654e+00
path( 34) 199 4.762531e+00
-1.520654e+00
path( 35) 205 4.759751e+00
-1.523434e+00
path( 36) 211 4.673390e+00
-1.609796e+00
=======================================================================================
CALCULATION OF ELECTRONIC POLARIZATION
=======================================================================================
Value | spin | dir(1) | dir(2) |
dir(3)
---------------------------------------------------------------------------------------
Traceback (most recent call last):
File "/software/WIEN2k/BerryPI-1.3/berrypi", line 906, in <module>
theCalc = postProcBerryPhase(configFile,phasesRaw,spCalc)
File "/software/WIEN2k/BerryPI-1.3/berrypi", line 73, in
postProcBerryPhase
file_outputst = structName + structFileExtensions['outputst'],
File "/software/WIEN2k_14.2/BerryPI-1.3/calculations.py", line 292, in
__init__
phaseDirSpinWrp11 = self.wrp11(phaseDirSpinWrp11);
File "/software/WIEN2k_14.2/BerryPI-1.3/calculations.py", line 372, in
wrp11
numpy.round(numpy.absolute(x)/2)*2, lambda x: x]);
File
"/software/python-2.7.9/lib/python2.7/site-packages/numpy/lib/function_base.py",
line 771, in piecewise
condlist = np.vstack([condlist, ~totlist])
File
"/software/python-2.7.9/lib/python2.7/site-packages/numpy/core/shape_base.py",
line 230, in vstack
return _nx.concatenate([atleast_2d(_m) for _m in tup], 0)
ValueError: all the input arrays must have same number of dimensions
Any suggestion on what could be going on?
Thanks in advance
M.
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