" ValueError: operands could not be broadcast together with shapes (0,0) (3,3) (0,0)" when using siesta2J.py

[Sucitto Teh]

Good day. I am trying to use siesta2J to calculate exchange constant of Fe but the error messages appear:

"

Starting to calculate exchange.

Green's function Calculation started.

/cluster/tb2j/lib/python3.6/site-packages/TB2J/exchangeCL2.py:134: RuntimeWarning: invalid value encountered in double_scalars

  np.dot(self.spinat[iatom], self.spinat[jatom]))

/cluster/tb2j/lib/python3.6/site-packages/TB2J/exchangeCL2.py:136: RuntimeWarning: invalid value encountered in true_divide

  np.dot(self.spinat[iatom], self.spinat[jatom]))

 [Elapsed Time: 0:00:29] |##################################################################################| (Time: 0:00:29)

/cluster/tb2j/lib/python3.6/site-packages/TB2J/io_exchange/io_tomsasd.py:30: RuntimeWarning: invalid value encountered in true_divide

  spin = np.array(cls.spinat[i]) / ms

/cluster/tb2j/lib/python3.6/site-packages/TB2J/io_exchange/io_vampire.py:91: RuntimeWarning: invalid value encountered in true_divide

  spin = np.array(cls.spinat[i]) / ms

Traceback (most recent call last):

  File "/cluster/tb2j/bin/siesta2J.py", line 107, in <module>

    run_siesta2J()

  File "/cluster/tb2j/bin/siesta2J.py", line 103, in run_siesta2J

    exclude_orbs=args.exclude_orbs)

  File "/cluster/tb2j/lib/python3.6/site-packages/TB2J/manager.py", line 229, in gen_exchange_siesta

    exchange.run()

  File "/cluster/tb2j/lib/python3.6/site-packages/TB2J/exchange.py", line 568, in run

    self.write_output(path=path)

  File "/cluster/tb2j/lib/python3.6/site-packages/TB2J/exchangeCL2.py", line 222, in write_output

    output.write_all()

  File "/cluster/tb2j/lib/python3.6/site-packages/TB2J/io_exchange/io_exchange.py", line 181, in write_all

    self.write_Jq(kmesh=[9, 9, 9], path=path)

  File "/cluster/tb2j/lib/python3.6/site-packages/TB2J/io_exchange/io_exchange.py", line 201, in write_Jq

    evals, evecs = m.ham.solve_k(kpts, Jq=True)

  File "/cluster/tb2j/lib/python3.6/site-packages/TB2J/spinham/hamiltonian.py", line 297, in solve_k

    evals, evecs = qsolver.solve_all(kpts, eigen_vectors=True, Jq=Jq)

  File "/cluster/tb2j/lib/python3.6/site-packages/TB2J/spinham/qsolver.py", line 53, in solve_all

    evals, evecs = self.solve_k(kpt, eigen_vectors=True, Jq=Jq)

  File "/cluster/tb2j/lib/python3.6/site-packages/TB2J/spinham/qsolver.py", line 33, in solve_k

    2.0j * math.pi * np.dot(kpt, R))

ValueError: operands could not be broadcast together with shapes (0,0) (3,3) (0,0)

"

I had also attached the input of siesta. Thank you.

[Xu He]

Could you send the command to run siesta2J.py as well?

HeXu

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[Sucitto Teh]

sure.

siesta2J.py --fdf_fname siesta.fdf --elements Fe --kmesh 5 5 5 --rcut 7 --emin -10 --nz=50

[Xu He]

Hi,

The SCF.Spin.Fix option is siesta input is to True.  Can you check if the total magnetizatoin is 0, and try to set that option to False?

Best wishes,

HeXu

On 2/11/20 15:11, Sucitto Teh wrote:

[Sucitto Teh]

Thanks for the suggestion. 

I just tried to change it to "False" but the the problem persists (the initial result has non zero spin anyway). I'm using the same input as provided in the github examples folder, what could possible go wrong here?

best regards,
sukhito teh

[Xu He]

Hi,

That is probably because it reuse the density matrix of the previous run. Try to run in an empty directory with no previous result so things don't get mixed. 

Also please try with the updated examples on github.

Best wishes,

HeXu

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[Sucitto Teh]

Hi, thanks for the reply. I just checked and realized the problem is I didn't compile the siesta with NETCDF support, so I'm not even providing the required input files to tb2j.

best regards,

sukhito teh