Comments (11)
zerothi
commented on July 28, 2024
1
@KitchenSong I allowed my-self to add ``` to your comment (this makes it look like code)
from sisl.
zerothi
commented on July 28, 2024
Thanks for your feedback.
I have fixed the code in the latest commit 4e48b7e.
It however shows that your system is not tiled, i.e. the cut structure is not correct.
You have to use tiling in order for cut to work correctly.
from sisl.
KitchenSong
commented on July 28, 2024
I can run the script now. But seems that the final .nc file still contains 3B atoms instead of B, when I do the following.
tmp = sisl.get_sile('DEVICE_gaas.nc')
tmp1 = tmp.read_geometry()
print tmp1.xyz
from sisl.
zerothi
commented on July 28, 2024
Could you post the full script? I.e. as I wrote previously cutting a structure requires the initial structure to be tiled (see Geometry.tile)
from sisl.
KitchenSong
commented on July 28, 2024
Okay.. I find that the final coordinates provided by GULP is changed such that the z transport position is not longer ordered.
#!/usr/bin/env python
# This example relies on GULP being installed.
# It calculates the dynamical matrix for ZZ-oriented graphene
# and afterward it can write the dynamical matrix to be processed by
# PHtrans for transport properties.
import sisl
import os
# opti conv Set flags for constant volume optimisation.
with open('gaas.gin', 'w') as f:
f.write("""opti cellonly dist full nosymmetry phon dynamical_matrix
cutd 3.0
cell
8.324642 4.8062220 188.39512 90 90 90
cartesian 192
Ga core 4.162321 2.403111 0.000000 0 1 0 1 1 1
Ga core 0.000000 0.000000 0.000000 0 1 0 1 1 1
As core 4.162321 2.403111 2.942732 0 1 0 1 1 1
As core 0.000000 0.000000 2.942732 0 1 0 1 1 1
Ga core 1.387468 2.403111 3.924270 0 1 0 1 1 1
Ga core 5.549789 0.000000 3.924270 0 1 0 1 1 1
As core 1.387468 2.403111 6.868886 0 1 0 1 1 1
As core 5.549789 0.000000 6.868886 0 1 0 1 1 1
Ga core 6.937174 2.403111 7.850424 0 1 0 1 1 1
Ga core 2.774853 0.000000 7.850424 0 1 0 1 1 1
As core 6.937174 2.403111 10.793156 0 1 0 1 1 1
As core 2.774853 0.000000 10.793156 0 1 0 1 1 1
Ga core 4.162321 2.403111 11.774695 0 1 0 1 1 1
Ga core 0.000000 0.000000 11.774695 0 1 0 1 1 1
As core 4.162321 2.403111 14.719311 0 1 0 1 1 1
As core 0.000000 0.000000 14.719311 0 1 0 1 1 1
Ga core 1.387468 2.403111 15.698965 0 1 0 1 1 1
Ga core 5.549789 0.000000 15.698965 0 1 0 1 1 1
As core 1.387468 2.403111 18.643581 0 1 0 1 1 1
As core 5.549789 0.000000 18.643581 0 1 0 1 1 1
Ga core 6.937174 2.403111 19.625120 0 1 0 1 1 1
Ga core 2.774853 0.000000 19.625120 0 1 0 1 1 1
As core 6.937174 2.403111 22.567852 0 1 0 1 1 1
As core 2.774853 0.000000 22.567852 0 1 0 1 1 1
Ga core 4.162321 2.403111 23.549390 0 1 0 1 1 1
Ga core 0.000000 0.000000 23.549390 0 1 0 1 1 1
As core 4.162321 2.403111 26.492120 0 1 0 1 1 1
As core 0.000000 0.000000 26.492120 0 1 0 1 1 1
Ga core 1.387468 2.403111 27.473661 0 1 0 1 1 1
Ga core 5.549789 0.000000 27.473661 0 1 0 1 1 1
As core 1.387468 2.403111 30.418276 0 1 0 1 1 1
As core 5.549789 0.000000 30.418276 0 1 0 1 1 1
Ga core 6.937174 2.403111 31.399814 0 1 0 1 1 1
Ga core 2.774853 0.000000 31.399814 0 1 0 1 1 1
As core 6.937174 2.403111 34.342547 0 1 0 1 1 1
As core 2.774853 0.000000 34.342547 0 1 0 1 1 1
Ga core 4.162321 2.403111 35.324085 0 1 0 1 1 1
Ga core 0.000000 0.000000 35.324085 0 1 0 1 1 1
As core 4.162321 2.403111 38.266815 0 1 0 1 1 1
As core 0.000000 0.000000 38.266815 0 1 0 1 1 1
Ga core 1.387468 2.403111 39.248356 0 1 0 1 1 1
Ga core 5.549789 0.000000 39.248356 0 1 0 1 1 1
As core 1.387468 2.403111 42.192971 0 1 0 1 1 1
As core 5.549789 0.000000 42.192971 0 1 0 1 1 1
Ga core 6.937174 2.403111 43.174509 0 1 0 1 1 1
Ga core 2.774853 0.000000 43.174509 0 1 0 1 1 1
As core 6.937174 2.403111 46.117242 0 1 0 1 1 1
As core 2.774853 0.000000 46.117242 0 1 0 1 1 1
Ga core 4.162321 2.403111 47.098780 0 1 0 1 1 1
Ga core 0.000000 0.000000 47.098780 0 1 0 1 1 1
As core 4.162321 2.403111 50.041510 0 1 0 1 1 1
As core 0.000000 0.000000 50.041510 0 1 0 1 1 1
Ga core 1.387468 2.403111 51.023051 0 1 0 1 1 1
Ga core 5.549789 0.000000 51.023051 0 1 0 1 1 1
As core 1.387468 2.403111 53.967668 0 1 0 1 1 1
As core 5.549789 0.000000 53.967668 0 1 0 1 1 1
Ga core 6.937174 2.403111 54.949204 0 1 0 1 1 1
Ga core 2.774853 0.000000 54.949204 0 1 0 1 1 1
As core 6.937174 2.403111 57.891934 0 1 0 1 1 1
As core 2.774853 0.000000 57.891934 0 1 0 1 1 1
Ga core 4.162321 2.403111 58.873475 0 1 0 1 1 1
Ga core 0.000000 0.000000 58.873475 0 1 0 1 1 1
As core 4.162321 2.403111 61.816205 0 1 0 1 1 1
As core 0.000000 0.000000 61.816205 0 1 0 1 1 1
Ga core 1.387468 2.403111 62.797746 0 1 0 1 1 1
Ga core 5.549789 0.000000 62.797746 0 1 0 1 1 1
As core 1.387468 2.403111 65.742363 0 1 0 1 1 1
As core 5.549789 0.000000 65.742363 0 1 0 1 1 1
Ga core 6.937174 2.403111 66.723899 0 1 0 1 1 1
Ga core 2.774853 0.000000 66.723899 0 1 0 1 1 1
As core 6.937174 2.403111 69.666629 0 1 0 1 1 1
As core 2.774853 0.000000 69.666629 0 1 0 1 1 1
Ga core 4.162321 2.403111 70.648170 0 1 0 1 1 1
Ga core 0.000000 0.000000 70.648170 0 1 0 1 1 1
As core 4.162321 2.403111 73.590900 0 1 0 1 1 1
As core 0.000000 0.000000 73.590900 0 1 0 1 1 1
Ga core 1.387468 2.403111 74.572441 0 1 0 1 1 1
Ga core 5.549789 0.000000 74.572441 0 1 0 1 1 1
As core 1.387468 2.403111 77.517058 0 1 0 1 1 1
As core 5.549789 0.000000 77.517058 0 1 0 1 1 1
Ga core 6.937174 2.403111 78.498594 0 1 0 1 1 1
Ga core 2.774853 0.000000 78.498594 0 1 0 1 1 1
As core 6.937174 2.403111 81.441324 0 1 0 1 1 1
As core 2.774853 0.000000 81.441324 0 1 0 1 1 1
Ga core 4.162321 2.403111 82.422865 0 1 0 1 1 1
Ga core 0.000000 0.000000 82.422865 0 1 0 1 1 1
As core 4.162321 2.403111 85.365595 0 1 0 1 1 1
As core 0.000000 0.000000 85.365595 0 1 0 1 1 1
Ga core 1.387468 2.403111 86.347136 0 1 0 1 1 1
Ga core 5.549789 0.000000 86.347136 0 1 0 1 1 1
As core 1.387468 2.403111 89.291753 0 1 0 1 1 1
As core 5.549789 0.000000 89.291753 0 1 0 1 1 1
Ga core 6.937174 2.403111 90.273289 0 1 0 1 1 1
Ga core 2.774853 0.000000 90.273289 0 1 0 1 1 1
As core 6.937174 2.403111 93.216019 0 1 0 1 1 1
As core 2.774853 0.000000 93.216019 0 1 0 1 1 1
Ga core 4.162321 2.403111 94.197560 0 1 0 1 1 1
Ga core 0.000000 0.000000 94.197560 0 1 0 1 1 1
As core 4.162321 2.403111 97.140290 0 1 0 1 1 1
As core 0.000000 0.000000 97.140290 0 1 0 1 1 1
Ga core 6.937174 2.403111 98.121826 0 1 0 1 1 1
Ga core 2.774853 0.000000 98.121826 0 1 0 1 1 1
As core 6.937174 2.403111 101.066443 0 1 0 1 1 1
As core 2.774853 0.000000 101.066443 0 1 0 1 1 1
Ga core 1.387468 2.403111 102.047989 0 1 0 1 1 1
Ga core 5.549789 0.000000 102.047989 0 1 0 1 1 1
As core 1.387468 2.403111 104.990720 0 1 0 1 1 1
As core 5.549789 0.000000 104.990720 0 1 0 1 1 1
Ga core 4.162321 2.403111 105.972255 0 1 0 1 1 1
Ga core 0.000000 0.000000 105.972255 0 1 0 1 1 1
As core 4.162321 2.403111 108.914985 0 1 0 1 1 1
As core 0.000000 0.000000 108.914985 0 1 0 1 1 1
Ga core 6.937174 2.403111 109.896521 0 1 0 1 1 1
Ga core 2.774853 0.000000 109.896521 0 1 0 1 1 1
As core 6.937174 2.403111 112.841138 0 1 0 1 1 1
As core 2.774853 0.000000 112.841138 0 1 0 1 1 1
Ga core 1.387468 2.403111 113.822684 0 1 0 1 1 1
Ga core 5.549789 0.000000 113.822684 0 1 0 1 1 1
As core 1.387468 2.403111 116.765415 0 1 0 1 1 1
As core 5.549789 0.000000 116.765415 0 1 0 1 1 1
Ga core 4.162321 2.403111 117.746950 0 1 0 1 1 1
Ga core 0.000000 0.000000 117.746950 0 1 0 1 1 1
As core 4.162321 2.403111 120.689680 0 1 0 1 1 1
As core 0.000000 0.000000 120.689680 0 1 0 1 1 1
Ga core 6.937174 2.403111 121.671216 0 1 0 1 1 1
Ga core 2.774853 0.000000 121.671216 0 1 0 1 1 1
As core 6.937174 2.403111 124.615833 0 1 0 1 1 1
As core 2.774853 0.000000 124.615833 0 1 0 1 1 1
Ga core 1.387468 2.403111 125.597379 0 1 0 1 1 1
Ga core 5.549789 0.000000 125.597379 0 1 0 1 1 1
As core 1.387468 2.403111 128.540110 0 1 0 1 1 1
As core 5.549789 0.000000 128.540110 0 1 0 1 1 1
Ga core 4.162321 2.403111 129.521645 0 1 0 1 1 1
Ga core 0.000000 0.000000 129.521645 0 1 0 1 1 1
As core 4.162321 2.403111 132.464375 0 1 0 1 1 1
As core 0.000000 0.000000 132.464375 0 1 0 1 1 1
Ga core 6.937174 2.403111 133.445911 0 1 0 1 1 1
Ga core 2.774853 0.000000 133.445911 0 1 0 1 1 1
As core 6.937174 2.403111 136.390528 0 1 0 1 1 1
As core 2.774853 0.000000 136.390528 0 1 0 1 1 1
Ga core 1.387468 2.403111 137.372074 0 1 0 1 1 1
Ga core 5.549789 0.000000 137.372074 0 1 0 1 1 1
As core 1.387468 2.403111 140.314805 0 1 0 1 1 1
As core 5.549789 0.000000 140.314805 0 1 0 1 1 1
Ga core 4.162321 2.403111 141.296340 0 1 0 1 1 1
Ga core 0.000000 0.000000 141.296340 0 1 0 1 1 1
As core 4.162321 2.403111 144.239070 0 1 0 1 1 1
As core 0.000000 0.000000 144.239070 0 1 0 1 1 1
Ga core 6.937174 2.403111 145.220606 0 1 0 1 1 1
Ga core 2.774853 0.000000 145.220606 0 1 0 1 1 1
As core 6.937174 2.403111 148.165223 0 1 0 1 1 1
As core 2.774853 0.000000 148.165223 0 1 0 1 1 1
Ga core 1.387468 2.403111 149.146769 0 1 0 1 1 1
Ga core 5.549789 0.000000 149.146769 0 1 0 1 1 1
As core 1.387468 2.403111 152.089500 0 1 0 1 1 1
As core 5.549789 0.000000 152.089500 0 1 0 1 1 1
Ga core 4.162321 2.403111 153.071035 0 1 0 1 1 1
Ga core 0.000000 0.000000 153.071035 0 1 0 1 1 1
As core 4.162321 2.403111 156.013765 0 1 0 1 1 1
As core 0.000000 0.000000 156.013765 0 1 0 1 1 1
Ga core 6.937174 2.403111 156.995301 0 1 0 1 1 1
Ga core 2.774853 0.000000 156.995301 0 1 0 1 1 1
As core 6.937174 2.403111 159.939918 0 1 0 1 1 1
As core 2.774853 0.000000 159.939918 0 1 0 1 1 1
Ga core 1.387468 2.403111 160.921464 0 1 0 1 1 1
Ga core 5.549789 0.000000 160.921464 0 1 0 1 1 1
As core 1.387468 2.403111 163.864195 0 1 0 1 1 1
As core 5.549789 0.000000 163.864195 0 1 0 1 1 1
Ga core 4.162321 2.403111 164.845730 0 1 0 1 1 1
Ga core 0.000000 0.000000 164.845730 0 1 0 1 1 1
As core 4.162321 2.403111 167.788460 0 1 0 1 1 1
As core 0.000000 0.000000 167.788460 0 1 0 1 1 1
Ga core 6.937174 2.403111 168.769996 0 1 0 1 1 1
Ga core 2.774853 0.000000 168.769996 0 1 0 1 1 1
As core 6.937174 2.403111 171.714613 0 1 0 1 1 1
As core 2.774853 0.000000 171.714613 0 1 0 1 1 1
Ga core 1.387468 2.403111 172.696159 0 1 0 1 1 1
Ga core 5.549789 0.000000 172.696159 0 1 0 1 1 1
As core 1.387468 2.403111 175.638890 0 1 0 1 1 1
As core 5.549789 0.000000 175.638890 0 1 0 1 1 1
Ga core 4.162321 2.403111 176.620425 0 1 0 1 1 1
Ga core 0.000000 0.000000 176.620425 0 1 0 1 1 1
As core 4.162321 2.403111 179.563155 0 1 0 1 1 1
As core 0.000000 0.000000 179.563155 0 1 0 1 1 1
Ga core 6.937174 2.403111 180.544691 0 1 0 1 1 1
Ga core 2.774853 0.000000 180.544691 0 1 0 1 1 1
As core 6.937174 2.403111 183.489308 0 1 0 1 1 1
As core 2.774853 0.000000 183.489308 0 1 0 1 1 1
Ga core 1.387468 2.403111 184.470854 0 1 0 1 1 1
Ga core 5.549789 0.000000 184.470854 0 1 0 1 1 1
As core 1.387468 2.403111 187.413585 0 1 0 1 1 1
As core 5.549789 0.000000 187.413585 0 1 0 1 1 1
sw2
Ga As 4.6264 1.0 35.7999 0.0 3.8416
sw3
Ga As As 30.0402 109.4712 2.5610 2.5610 4.8830 4.8830
As Ga Ga 30.0402 109.4712 2.5610 2.5610 4.8830 4.8830
""")
# https://journals.aps.org/prb/pdf/10.1103/PhysRevB.83.174304
with open('gaas_s.gin', 'w') as f:
f.write("""opti cellonly dist full nosymmetry phon dynamical_matrix
cutd 3.0
cell
8.324642 4.8062220 35.3240850000000 90 90 90
cartesian 36
Ga core 4.162321 2.403111 47.098780 0 1 0 1 1 1
Ga core 0.000000 0.000000 47.098780 0 1 0 1 1 1
As core 4.162321 2.403111 50.041510 0 1 0 1 1 1
As core 0.000000 0.000000 50.041510 0 1 0 1 1 1
Ga core 1.387468 2.403111 51.023051 0 1 0 1 1 1
Ga core 5.549789 0.000000 51.023051 0 1 0 1 1 1
As core 1.387468 2.403111 53.967668 0 1 0 1 1 1
As core 5.549789 0.000000 53.967668 0 1 0 1 1 1
Ga core 6.937174 2.403111 54.949204 0 1 0 1 1 1
Ga core 2.774853 0.000000 54.949204 0 1 0 1 1 1
As core 6.937174 2.403111 57.891934 0 1 0 1 1 1
As core 2.774853 0.000000 57.891934 0 1 0 1 1 1
Ga core 4.162321 2.403111 58.873475 0 1 0 1 1 1
Ga core 0.000000 0.000000 58.873475 0 1 0 1 1 1
As core 4.162321 2.403111 61.816205 0 1 0 1 1 1
As core 0.000000 0.000000 61.816205 0 1 0 1 1 1
Ga core 1.387468 2.403111 62.797746 0 1 0 1 1 1
Ga core 5.549789 0.000000 62.797746 0 1 0 1 1 1
As core 1.387468 2.403111 65.742363 0 1 0 1 1 1
As core 5.549789 0.000000 65.742363 0 1 0 1 1 1
Ga core 6.937174 2.403111 66.723899 0 1 0 1 1 1
Ga core 2.774853 0.000000 66.723899 0 1 0 1 1 1
As core 6.937174 2.403111 69.666629 0 1 0 1 1 1
As core 2.774853 0.000000 69.666629 0 1 0 1 1 1
Ga core 4.162321 2.403111 70.648170 0 1 0 1 1 1
Ga core 0.000000 0.000000 70.648170 0 1 0 1 1 1
As core 4.162321 2.403111 73.590900 0 1 0 1 1 1
As core 0.000000 0.000000 73.590900 0 1 0 1 1 1
Ga core 1.387468 2.403111 74.572441 0 1 0 1 1 1
Ga core 5.549789 0.000000 74.572441 0 1 0 1 1 1
As core 1.387468 2.403111 77.517058 0 1 0 1 1 1
As core 5.549789 0.000000 77.517058 0 1 0 1 1 1
Ga core 6.937174 2.403111 78.498594 0 1 0 1 1 1
Ga core 2.774853 0.000000 78.498594 0 1 0 1 1 1
As core 6.937174 2.403111 81.441324 0 1 0 1 1 1
As core 2.774853 0.000000 81.441324 0 1 0 1 1 1
sw2
Ga As 4.6264 1.0 35.7999 0.0 3.8416
sw3
Ga As As 30.0402 109.4712 2.5610 2.5610 4.8830 4.8830
As Ga Ga 30.0402 109.4712 2.5610 2.5610 4.8830 4.8830""")
with open('gaas_d.gin', 'w') as f:
f.write("""opti cellonly dist full nosymmetry phon dynamical_matrix
cutd 3.0
cell
8.324642 4.8062220 35.3240850000000 90 90 90
cartesian 36
Ga core 4.162321 2.403111 105.972255 0 1 0 1 1 1
Ga core 0.000000 0.000000 105.972255 0 1 0 1 1 1
As core 4.162321 2.403111 108.914985 0 1 0 1 1 1
As core 0.000000 0.000000 108.914985 0 1 0 1 1 1
Ga core 6.937174 2.403111 109.896521 0 1 0 1 1 1
Ga core 2.774853 0.000000 109.896521 0 1 0 1 1 1
As core 6.937174 2.403111 112.841138 0 1 0 1 1 1
As core 2.774853 0.000000 112.841138 0 1 0 1 1 1
Ga core 1.387468 2.403111 113.822684 0 1 0 1 1 1
Ga core 5.549789 0.000000 113.822684 0 1 0 1 1 1
As core 1.387468 2.403111 116.765415 0 1 0 1 1 1
As core 5.549789 0.000000 116.765415 0 1 0 1 1 1
Ga core 4.162321 2.403111 117.746950 0 1 0 1 1 1
Ga core 0.000000 0.000000 117.746950 0 1 0 1 1 1
As core 4.162321 2.403111 120.689680 0 1 0 1 1 1
As core 0.000000 0.000000 120.689680 0 1 0 1 1 1
Ga core 6.937174 2.403111 121.671216 0 1 0 1 1 1
Ga core 2.774853 0.000000 121.671216 0 1 0 1 1 1
As core 6.937174 2.403111 124.615833 0 1 0 1 1 1
As core 2.774853 0.000000 124.615833 0 1 0 1 1 1
Ga core 1.387468 2.403111 125.597379 0 1 0 1 1 1
Ga core 5.549789 0.000000 125.597379 0 1 0 1 1 1
As core 1.387468 2.403111 128.540110 0 1 0 1 1 1
As core 5.549789 0.000000 128.540110 0 1 0 1 1 1
Ga core 4.162321 2.403111 129.521645 0 1 0 1 1 1
Ga core 0.000000 0.000000 129.521645 0 1 0 1 1 1
As core 4.162321 2.403111 132.464375 0 1 0 1 1 1
As core 0.000000 0.000000 132.464375 0 1 0 1 1 1
Ga core 6.937174 2.403111 133.445911 0 1 0 1 1 1
Ga core 2.774853 0.000000 133.445911 0 1 0 1 1 1
As core 6.937174 2.403111 136.390528 0 1 0 1 1 1
As core 2.774853 0.000000 136.390528 0 1 0 1 1 1
Ga core 1.387468 2.403111 137.372074 0 1 0 1 1 1
Ga core 5.549789 0.000000 137.372074 0 1 0 1 1 1
As core 1.387468 2.403111 140.314805 0 1 0 1 1 1
As core 5.549789 0.000000 140.314805 0 1 0 1 1 1
sw2
Ga As 4.6264 1.0 35.7999 0.0 3.8416
sw3
Ga As As 30.0402 109.4712 2.5610 2.5610 4.8830 4.8830
As Ga Ga 30.0402 109.4712 2.5610 2.5610 4.8830 4.8830
""")
# Create PHtrans input
with open('ZZ.fdf', 'w') as f:
f.write("""SystemLabel gaas
TBT.DOS.Gf T
TBT.Elecs.Coord.EPS 8e-3 Bohr
TBT.k [1 1 1]
ForceAuxCell .true.
TBT.HS DEVICE_gaas.nc
%block TBT.Contour.line
part line
from 0. eV to .33 eV
points 500
method mid-rule
%endblock TBT.Contour.line
%block TBT.Elec.Left
HS ELEC_gaas.nc
semi-inf-direction -a3
electrode-position 49
%endblock
%block TBT.Elec.Right
HS ELEC_gaas1.nc
semi-inf-direction +a3
electrode-position end -49
%endblock
%block TBT.Atoms.Buffer
atom [ 1 -- 48 ]
atom [ 145 -- 192 ]
%endblock
""")
##
#%block TBT.Atoms.Buffer
#atom [ 1 -- 12 ]
#atom [ 181 -- 192 ]
#%endblock TBT.Atoms.Buffer
os.system("~/epw/gulp-5.0/Src/gulp <gaas_s.gin>gaas_s.gout")
os.system("~/epw/gulp-5.0/Src/gulp <gaas_d.gin>gaas_d.gout")
os.system("~/epw/gulp-5.0/Src/gulp <gaas.gin>gaas.gout")
if not os.path.exists('gaas.gout'):
raise ValueError("gaas.gin has not been runned by GULP")
print('Reading output')
gout = sisl.get_sile('gaas.gout')
gout1 = sisl.get_sile('gaas_s.gout')
gout2 = sisl.get_sile('gaas_d.gout')
# Correct what to read from the gulp output
#gout.set_supercell_key("Cartesian lattice vectors")
#gout1.set_supercell_key("Cartesian lattice vectors")
#gout2.set_supercell_key("Cartesian lattice vectors")
geo = gout.read_geometry()
print geo
geo1 = gout1.read_geometry()
print geo1
geo2 = gout2.read_geometry()
print geo2
dyn = gout.read_hessian()
dyn1 = gout1.read_hessian()
dyn2 = gout2.read_hessian()
# In GULP correcting for Newtons second law is already obeyed
# So this need not be used, however, the precision of output
# may require this anyway.
dyn.correct_Newton()
dyn1.correct_Newton()
dyn2.correct_Newton()
dev = dyn
#dev = dyn.cut(4, 2)
dev = dyn #.cut(2,2)
#dev1 = dev.cut(3,2,seg=1)
dev.write('DEVICE_gaas.nc')
tmp = sisl.get_sile('DEVICE_gaas.nc')
tmp1 = tmp.read_geometry()
print tmp1.xyz
#el = dyn1
#el = dev.cut(2, 2,seg=0) # second arg is the axis 0,1,2-->x,y,z
el = dyn1.cut(3,2,seg=1)
el.write('ELEC_gaas.nc')
tmp2 = sisl.get_sile('ELEC_gaas.nc')
tmp3 = tmp2.read_geometry()
print tmp3.xyz
#el2 = dev.cut(3,2,seg=1)
el2 = dyn2.cut(3,2,seg=1)
el2.write('ELEC_gaas1.nc')
tmp4 = sisl.get_sile('ELEC_gaas1.nc')
tmp5 = tmp4.read_geometry()
print tmp5.xyz
#el2 = dev.cut(3,2,seg=2)
#el2 = dyn2 #.cut(4,2)
#el2.write('dev.nc')
os.system("mpirun -np 4 ~/epw/siesta-4.1-new/bin/phtrans < ZZ.fdf > ZZ.out")from sisl.
zerothi
commented on July 28, 2024
It is a bit unclear what you expect and what you get, I can succesfully run the calculation (script + gulp + PHtrans), by adding this to the PHtrans input: TBT.Elecs.Neglect.Principal true
from sisl.
zerothi
commented on July 28, 2024
You may, however, wish to limit the energy range investigated to say, 0.03 meV
from sisl.
KitchenSong
commented on July 28, 2024
It is a twin boundary so the two electrodes have to be specified separately. I do want to know why the k mesh cannot be larger than 1 1 1 in this calculation.
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zerothi
commented on July 28, 2024
In order to calculate dispersion along the transverse directions you need the dynamical matrix that connects super-cells. GULP does not save the supercell dynamical matrix. This is why one needs the cut method to cut the system while retaining the supercell dynamical matrix.
I.e. if you want to have periodicity along both transverse directions you need to extend your initial gulp calculations just as you did for the electrodes, in both the directions.
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KitchenSong
commented on July 28, 2024
I will have a try asap.
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zerothi
commented on July 28, 2024
@KitchenSong I will mark this question as resolved.
If you have other questions, please open a new issue! 👍
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