QuantumATK Forum
QuantumATK => General Questions and Answers => Topic started by: sumitn60 on April 4, 2022, 17:18
-
Hi,
While doing device NEGF-DFT calculation, is it possible to print the Hamiltonian and Overlap matrices?
Please suggest how to print/extract them from a converged NEGF-DFT calculation.
I really appreciate any help you can provide.
Sumit
-
https://docs.quantumatk.com/tutorials/low_level_entities/low_level_entities.html
-
Hi Anders,
Thank you for your response.
I tried to print those matrices for simple molecule_configuration (Benzene), but I didn't find anything. I have attached the input file; please suggest where I'm making a mistake.
Thanks
Sumit
-
Hi Anders,
Adding:
print('Hamiltonian : ', hamiltonian)
print('Overlap : ', overlap)
print('')
I'm able to print the Hamiltonian and Overlap for each SCF cycle. I have added the output below.
Thank You
Sumit
| Calculation Converged in 13 steps |
| |
| Fermi Level = -3.889050 eV |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| DFT Calculation [Finished Wed Apr 6 12:59:52 2022] |
| |
+------------------------------------------------------------------------------+
Hamiltonian : [[-3.59032220e-01-1.29056719e-20j 3.46412440e-12-1.21667632e-12j
8.17982219e-02+1.44061808e-20j ... -7.19852035e-08-4.70211730e-09j
8.39974836e-02-1.84622872e-09j 9.38259570e-08+3.90192286e-09j]
[ 3.46412440e-12+1.21667632e-12j -3.59029030e-01+1.29056719e-20j
4.45180078e-12+1.09713035e-12j ... -7.54532144e-02-4.43759714e-09j
-9.37885388e-08+3.89844158e-09j 8.39971402e-02+1.84622872e-09j]
[ 8.17982219e-02-1.44061808e-20j 4.45180078e-12-1.09713035e-12j
4.59094866e-01-6.82920960e-21j ... 1.76589278e-07+1.09730678e-08j
-9.22280117e-03-9.46961721e-09j -6.39674337e-08-1.41767968e-09j]
...
[-7.19852035e-08+4.70211730e-09j -7.54532144e-02+4.43759714e-09j
1.76589278e-07-1.09730678e-08j ... -4.35606266e-02-2.56545139e-24j
-6.43143228e-07-6.79178074e-10j -1.48253265e-03-3.49468552e-08j]
[ 8.39974836e-02+1.84622872e-09j -9.37885388e-08-3.89844158e-09j
-9.22280117e-03+9.46961721e-09j ... -6.43143228e-07+6.79178074e-10j
1.46149708e-01-3.67281117e-22j -1.01890544e-12-6.57268857e-13j]
[ 9.38259570e-08-3.90192286e-09j 8.39971402e-02-1.84622872e-09j
-6.39674337e-08+1.41767968e-09j ... -1.48253265e-03+3.49468552e-08j
-1.01890544e-12+6.57268857e-13j 1.46155125e-01+3.67281117e-22j]] Hartree
Overlap : [[ 9.99999999e-01+0.j 0.00000000e+00+0.j -8.47863236e-10+0.j ...
0.00000000e+00+0.j -1.51349581e-01+0.j 0.00000000e+00+0.j]
[ 0.00000000e+00+0.j 9.99999999e-01+0.j 0.00000000e+00+0.j ...
8.94296345e-02+0.j 0.00000000e+00+0.j -1.51349581e-01+0.j]
[-8.47863236e-10+0.j 0.00000000e+00+0.j 1.00000000e+00+0.j ...
0.00000000e+00+0.j 1.89803809e-01+0.j 0.00000000e+00+0.j]
...
[ 0.00000000e+00+0.j 8.94296345e-02+0.j 0.00000000e+00+0.j ...
9.99999997e-01+0.j 0.00000000e+00+0.j 0.00000000e+00+0.j]
[-1.51349581e-01+0.j 0.00000000e+00+0.j 1.89803809e-01+0.j ...
0.00000000e+00+0.j 9.99999997e-01+0.j 0.00000000e+00+0.j]
[ 0.00000000e+00+0.j -1.51349581e-01+0.j 0.00000000e+00+0.j ...
0.00000000e+00+0.j 0.00000000e+00+0.j 9.99999997e-01+0.j]]
......................................
Hamiltonian : [[-3.59032220e-01-1.29056719e-20j 3.46412440e-12-1.21667632e-12j
8.17982219e-02+1.44061808e-20j ... -7.19852035e-08-4.70211730e-09j
8.39974836e-02-1.84622872e-09j 9.38259570e-08+3.90192286e-09j]
[ 3.46412440e-12+1.21667632e-12j -3.59029030e-01+1.29056719e-20j
4.45180078e-12+1.09713035e-12j ... -7.54532144e-02-4.43759714e-09j
-9.37885388e-08+3.89844158e-09j 8.39971402e-02+1.84622872e-09j]
[ 8.17982219e-02-1.44061808e-20j 4.45180078e-12-1.09713035e-12j
4.59094866e-01-6.82920960e-21j ... 1.76589278e-07+1.09730678e-08j
-9.22280117e-03-9.46961721e-09j -6.39674337e-08-1.41767968e-09j]
...
[-7.19852035e-08+4.70211730e-09j -7.54532144e-02+4.43759714e-09j
1.76589278e-07-1.09730678e-08j ... -4.35606266e-02-2.56545139e-24j
-6.43143228e-07-6.79178074e-10j -1.48253265e-03-3.49468552e-08j]
[ 8.39974836e-02+1.84622872e-09j -9.37885388e-08-3.89844158e-09j
-9.22280117e-03+9.46961721e-09j ... -6.43143228e-07+6.79178074e-10j
1.46149708e-01-3.67281117e-22j -1.01890544e-12-6.57268857e-13j]
[ 9.38259570e-08-3.90192286e-09j 8.39971402e-02-1.84622872e-09j
-6.39674337e-08+1.41767968e-09j ... -1.48253265e-03+3.49468552e-08j
-1.01890544e-12+6.57268857e-13j 1.46155125e-01+3.67281117e-22j]] Hartree
Overlap : [[ 9.99999999e-01+0.j 0.00000000e+00+0.j -8.47863236e-10+0.j ...
0.00000000e+00+0.j -1.51349581e-01+0.j 0.00000000e+00+0.j]
[ 0.00000000e+00+0.j 9.99999999e-01+0.j 0.00000000e+00+0.j ...
8.94296345e-02+0.j 0.00000000e+00+0.j -1.51349581e-01+0.j]
[-8.47863236e-10+0.j 0.00000000e+00+0.j 1.00000000e+00+0.j ...
0.00000000e+00+0.j 1.89803809e-01+0.j 0.00000000e+00+0.j]
...
[ 0.00000000e+00+0.j 8.94296345e-02+0.j 0.00000000e+00+0.j ...
9.99999997e-01+0.j 0.00000000e+00+0.j 0.00000000e+00+0.j]
[-1.51349581e-01+0.j 0.00000000e+00+0.j 1.89803809e-01+0.j ...
0.00000000e+00+0.j 9.99999997e-01+0.j 0.00000000e+00+0.j]
[ 0.00000000e+00+0.j -1.51349581e-01+0.j 0.00000000e+00+0.j ...
0.00000000e+00+0.j 0.00000000e+00+0.j 9.99999997e-01+0.j]]
Hamiltonian : [[-3.59032220e-01-1.29056719e-20j 3.46412440e-12-1.21667632e-12j
8.17982219e-02+1.44061808e-20j ... -7.19852035e-08-4.70211730e-09j
8.39974836e-02-1.84622872e-09j 9.38259570e-08+3.90192286e-09j]
[ 3.46412440e-12+1.21667632e-12j -3.59029030e-01+1.29056719e-20j
4.45180078e-12+1.09713035e-12j ... -7.54532144e-02-4.43759714e-09j
-9.37885388e-08+3.89844158e-09j 8.39971402e-02+1.84622872e-09j]
[ 8.17982219e-02-1.44061808e-20j 4.45180078e-12-1.09713035e-12j
4.59094866e-01-6.82920960e-21j ... 1.76589278e-07+1.09730678e-08j
-9.22280117e-03-9.46961721e-09j -6.39674337e-08-1.41767968e-09j]
...
[-7.19852035e-08+4.70211730e-09j -7.54532144e-02+4.43759714e-09j
1.76589278e-07-1.09730678e-08j ... -4.35606266e-02-2.56545139e-24j
-6.43143228e-07-6.79178074e-10j -1.48253265e-03-3.49468552e-08j]
[ 8.39974836e-02+1.84622872e-09j -9.37885388e-08-3.89844158e-09j
-9.22280117e-03+9.46961721e-09j ... -6.43143228e-07+6.79178074e-10j
1.46149708e-01-3.67281117e-22j -1.01890544e-12-6.57268857e-13j]
[ 9.38259570e-08-3.90192286e-09j 8.39971402e-02-1.84622872e-09j
-6.39674337e-08+1.41767968e-09j ... -1.48253265e-03+3.49468552e-08j
-1.01890544e-12+6.57268857e-13j 1.46155125e-01+3.67281117e-22j]] Hartree
Overlap : [[ 9.99999999e-01+0.j 0.00000000e+00+0.j -8.47863236e-10+0.j ...
0.00000000e+00+0.j -1.51349581e-01+0.j 0.00000000e+00+0.j]
[ 0.00000000e+00+0.j 9.99999999e-01+0.j 0.00000000e+00+0.j ...
8.94296345e-02+0.j 0.00000000e+00+0.j -1.51349581e-01+0.j]
[-8.47863236e-10+0.j 0.00000000e+00+0.j 1.00000000e+00+0.j ...
0.00000000e+00+0.j 1.89803809e-01+0.j 0.00000000e+00+0.j]
...
[ 0.00000000e+00+0.j 8.94296345e-02+0.j 0.00000000e+00+0.j ...
9.99999997e-01+0.j 0.00000000e+00+0.j 0.00000000e+00+0.j]
[-1.51349581e-01+0.j 0.00000000e+00+0.j 1.89803809e-01+0.j ...
0.00000000e+00+0.j 9.99999997e-01+0.j 0.00000000e+00+0.j]
[ 0.00000000e+00+0.j -1.51349581e-01+0.j 0.00000000e+00+0.j ...
0.00000000e+00+0.j 0.00000000e+00+0.j 9.99999997e-01+0.j]]
Hamiltonian : [[-3.59032220e-01-1.29056719e-20j 3.46412440e-12-1.21667632e-12j
8.17982219e-02+1.44061808e-20j ... -7.19852035e-08-4.70211730e-09j
8.39974836e-02-1.84622872e-09j 9.38259570e-08+3.90192286e-09j]
[ 3.46412440e-12+1.21667632e-12j -3.59029030e-01+1.29056719e-20j
4.45180078e-12+1.09713035e-12j ... -7.54532144e-02-4.43759714e-09j
-9.37885388e-08+3.89844158e-09j 8.39971402e-02+1.84622872e-09j]
[ 8.17982219e-02-1.44061808e-20j 4.45180078e-12-1.09713035e-12j
4.59094866e-01-6.82920960e-21j ... 1.76589278e-07+1.09730678e-08j
-9.22280117e-03-9.46961721e-09j -6.39674337e-08-1.41767968e-09j]
...
[-7.19852035e-08+4.70211730e-09j -7.54532144e-02+4.43759714e-09j
1.76589278e-07-1.09730678e-08j ... -4.35606266e-02-2.56545139e-24j
-6.43143228e-07-6.79178074e-10j -1.48253265e-03-3.49468552e-08j]
[ 8.39974836e-02+1.84622872e-09j -9.37885388e-08-3.89844158e-09j
-9.22280117e-03+9.46961721e-09j ... -6.43143228e-07+6.79178074e-10j
1.46149708e-01-3.67281117e-22j -1.01890544e-12-6.57268857e-13j]
[ 9.38259570e-08-3.90192286e-09j 8.39971402e-02-1.84622872e-09j
-6.39674337e-08+1.41767968e-09j ... -1.48253265e-03+3.49468552e-08j
-1.01890544e-12+6.57268857e-13j 1.46155125e-01+3.67281117e-22j]] Hartree
Overlap : [[ 9.99999999e-01+0.j 0.00000000e+00+0.j -8.47863236e-10+0.j ...
0.00000000e+00+0.j -1.51349581e-01+0.j 0.00000000e+00+0.j]
[ 0.00000000e+00+0.j 9.99999999e-01+0.j 0.00000000e+00+0.j ...
8.94296345e-02+0.j 0.00000000e+00+0.j -1.51349581e-01+0.j]
[-8.47863236e-10+0.j 0.00000000e+00+0.j 1.00000000e+00+0.j ...
0.00000000e+00+0.j 1.89803809e-01+0.j 0.00000000e+00+0.j]
...
[ 0.00000000e+00+0.j 8.94296345e-02+0.j 0.00000000e+00+0.j ...
9.99999997e-01+0.j 0.00000000e+00+0.j 0.00000000e+00+0.j]
[-1.51349581e-01+0.j 0.00000000e+00+0.j 1.89803809e-01+0.j ...
0.00000000e+00+0.j 9.99999997e-01+0.j 0.00000000e+00+0.j]
[ 0.00000000e+00+0.j -1.51349581e-01+0.j 0.00000000e+00+0.j ...
0.00000000e+00+0.j 0.00000000e+00+0.j 9.99999997e-01+0.j]]
-
Looks like you got it to work. Now the main question of course is what to use this for :-)
The ordering of the matrix follows that of the MullikenPopulation output, and also note that we use cubic harmonics, not spherical ones, so for d-shells the basis functions are
xy zy zz-rr zx xx-yy
and for p the ordering is not xyz but rather
y z x
-
Hi,
I wanted to plot the Im(H), which will sufficiently modify with spin-orbit calculations ( I mean, there will be more non-trivial terms at the off-diagonal, including spin-orbit interactions)...
I needed the whole matrix, but the format is not so straightforward; I want the matrix in square form. Is there some way to do that? Any help is very much appreciated.
Thank you
Sumit
-
The matrix should be square already