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Negative value in the SCF of an anion vacancy

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  • Moundefined Offline
    Moundefined Offline
    Mo
    wrote last edited by Mo
    #1

    Hi,

    I am trying to calculate defect formation energies following Bailey's method (10.1103/PhysRevB.81.205214). In the paper they deal with anion vacancies by removing the anion and retaining its basis sets. When I follow this method I end up with a negative value in the SCF on the anion. For example, for Ca2ZnN2 I replaced one of the nitrogens with a 0 basis set (shown below), and using ATOMONLY to optimise (neutral defect). The calculation converged but the value on the anion vacancy was -1.3085951 (shown below) and when checking the geometry I found that the vacancy has merged with a neighbouring Zn atom. I can get the calculation to converge without producing a negative value in the SCF using FRAGMENT to keep the vacancy and the cation it merges with in place, but if I restart the calculation without FRAGMENT it will not converge. For Ca2ZnN2 this happens across all charge states of the anion vacancy I have tried (-2,-1,0,1,2). I have so far looked at five nitride compounds and this behaviour happens in three of them.

    What does the negative value here mean?
    Is there a way around this besides using FRAGMENT?

    I would appreciate any help.
    Thanks!

    0 4
0 0 6 0 1.0
 4150.0 0.001845
 620.1 0.01416
 141.7 0.06863
 40.34 0.2286
 13.03 0.4662
 4.47 0.3657
0 1 2 0 1.0
 5.425 -0.4133 0.238
 1.149 1.224 0.859
0 1 1 0.0 1.0
 0.2832 1.0 1.0
0 3 1 0.0 1.0
 0.8 1.0 1.0

     TOTAL ATOMIC CHARGES:
   8.1376632   8.1212165   8.1248702   8.1206438   8.1229391   8.1124523
   8.1236540   8.1193919   8.1205622   8.1248273   8.1212382   8.1375264
   8.1125477  -1.3072013   8.1125440   8.1257835   8.1206284   8.1377578
   8.1194311   8.1236914   8.1124840   8.1226134   8.1377863   8.1205830
   8.1173933   8.1258681   8.1207059   8.1240065   8.1199368   8.1207339
   8.1194493   8.1236090   8.1239754   8.1207282   8.1258496   8.1174264
   8.1206901   8.1197740   8.1207285   8.1206837   8.1239699   8.1174550
   8.1236610   8.1194374   8.1206695   8.1199530   8.1174242   8.1240181
  29.6808307  29.6816377  29.6812243  29.6819752  29.6710460  29.6849333
  29.6759320  29.6852850  29.6820377  29.6812695  29.6815737  29.6808892
  29.6849531  31.6491331  29.6849573  29.6819626  29.6819686  29.6807771
  29.6852479  29.6759483  29.6849717  29.6711835  29.6807525  29.6819924
  19.0454220  19.0459330  19.0431780  19.0431020  19.0432569  19.0451214
  19.0452198  19.0462440  19.0451348  19.0432244  19.0430908  19.0432040
  19.0459080  19.0452863  19.0925535  19.0432123  19.0444657  19.0432576
  19.0459533  19.0430879  19.0462163  19.0453976  19.0430765  19.0459700
  19.0634872  19.0436933  19.0366981  19.0429866  19.0441015  19.0430915
  19.0628392  19.0436877  19.0430659  19.0443015  19.0429753  19.0368146
  19.0436806  19.0628125  19.0649399  19.0442844  19.0435415  19.0442819
  19.0437081  19.0456880  19.0436812  19.0634794  19.0457099  19.0436711
    1 Reply Last reply
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    • aerbaundefined Offline
      aerbaundefined Offline
      aerba Developer
      wrote last edited by
      #2

      Hi,

      Would you please share your full input file?

      Alessandro Erba
      Professor of Physical Chemistry
      Department of Chemistry, University of Torino
      [email protected]

      Moundefined 1 Reply Last reply
      0
      • Moundefined Offline
        Moundefined Offline
        Mo
        replied to aerba last edited by
        #3

        aerba Hi, this is the pristine supercell (120 atoms)

        Ca2ZnN2
CRYSTAL
0 0 0
139
3.584 12.665
3
7 0 0 0.15221
30 0 0 0
20 0 0 0.33550
supercon
4 0 0
0 3 0
0 0 1
optgeom
fulloptg
END
END

20 9
0 0 6 2 1
  35138.713929      0.003948252074
  5276.4111348      0.030234243552
  1200.4692589      0.149520196810
  338.71810542      0.515973457130
  109.85385922      1.033951029600
  37.608880299      0.769379335260
0 0 3 2 1
  73.107977555     -0.282685250110
  8.2407705688      1.679609214200
  3.2959812993      1.280376601600
0 0 3 2 1
  5.23418009140    -0.007686860456
  0.84187220515     0.025382375978
  0.36510294029     0.016512171511
0 0 1 2 1
  0.3207089200      1.000000000000
0 0 1 0 1
  0.1400001600      1.000000000000
0 2 5 6 1
  413.11313893      0.020327135354
  96.935786224      0.147302763620
  30.372154659      0.548871673220
  10.684776830      1.044065981800
  3.8821258350      0.686534906840
0 2 3 6 1
  1.7993016295      0.754102468710
  0.6918905653      1.340929659900
  0.2636402410      0.563919894350
0 2 1 0 1
  0.1400000000      1.000000000000
0 3 1 0 1
  0.5251112100      1.000000000000

7 4
0 0 6 2.0 1.0
 4150.0 0.001845
 620.1 0.01416
 141.7 0.06863
 40.34 0.2286
 13.03 0.4662
 4.47 0.3657
0 1 2 5.0 1.0
 5.425 -0.4133 0.238
 1.149 1.224 0.859
0 1 1 0.0 1.0
 0.2832 1.0 1.0
0 3 1 0.0 1.0
 0.8 1.0 1.0
 
30 14
0 0 8 2.0 1.0
 405924.31028 0.00022442017483
 60846.955735 0.00174020866260
 13847.343092 0.00905133395650
 3919.6158551 0.03681734144500
 1276.3594167 0.12004850256000
 458.67254435 0.28576057621000
 178.28725246 0.41087462062000
 70.612192837 0.21816962456000
0 0 4 2.0 1.0
 443.88077950 -0.02493427498400
 137.55875267 -0.11817955766000
 22.268083479 0.55367318468000
 9.5217310606 0.52628934936000
0 0 2 2.0 1.0
 14.874114065 -0.22929955254000
 2.4647517612 0.71135484742000
0 0 1 2.0 1.0
 1.0113272200 1.00000000000000
0 0 1 0.0 1.0
 0.322980200 1.00000000000000
0 0 1 0.0 1.0
 0.1016731100 1.00000000000000
0 2 6 6.0 1.0
 2205.3508534 0.00233562404480
 522.35300699 0.01903102263400
 167.73055542 0.08995575867500
 62.670045373 0.26113248631000
 25.109749456 0.42348448173000
 10.225142681 0.24618926885000
0 2 3 6.0 1.0
 40.713442521 -0.03002966759200
 5.6247090696 0.55575254864000
 2.2279949116 0.95581013442000
0 2 1 0.0 1.0
 1.1601141800 1.00000000000000
0 2 1 0.0 1.0
 0.2624550000 1.00000000000000
0 3 4 10.0 1.0
 88.554315311 0.01272817001500
 25.721525557 0.07939449984300
 9.1278367624 0.24491506805000
 3.4312364064 0.40390526479000
0 3 1 0.0 1.0
 1.1861283200 1.00000000000000
0 3 1 0.0 1.0
 0.4308920600 1.00000000000000
0 4 1 0.0 1.0
 2.6140000000 1.00000000000000

99 0
END
dft
HSE06
end
MAXCYCLE
2000
shrink
6 6
END

        This is the input file for the neutral defective supercell. Atom 14 is nitrogen.

        CaZn2N2
EXTERNAL
ATOMSUBS
1
14   0
optgeom
ATOMONLY
END
END

20 9
0 0 6 2 1
  35138.713929      0.003948252074
  5276.4111348      0.030234243552
  1200.4692589      0.149520196810
  338.71810542      0.515973457130
  109.85385922      1.033951029600
  37.608880299      0.769379335260
0 0 3 2 1
  73.107977555     -0.282685250110
  8.2407705688      1.679609214200
  3.2959812993      1.280376601600
0 0 3 2 1
  5.23418009140    -0.007686860456
  0.84187220515     0.025382375978
  0.36510294029     0.016512171511
0 0 1 2 1
  0.3207089200      1.000000000000
0 0 1 0 1
  0.1400001600      1.000000000000
0 2 5 6 1
  413.11313893      0.020327135354
  96.935786224      0.147302763620
  30.372154659      0.548871673220
  10.684776830      1.044065981800
  3.8821258350      0.686534906840
0 2 3 6 1
  1.7993016295      0.754102468710
  0.6918905653      1.340929659900
  0.2636402410      0.563919894350
0 2 1 0 1
  0.1400000000      1.000000000000
0 3 1 0 1
  0.5251112100      1.000000000000

7 4
0 0 6 2.0 1.0
 4150.0 0.001845
 620.1 0.01416
 141.7 0.06863
 40.34 0.2286
 13.03 0.4662
 4.47 0.3657
0 1 2 5.0 1.0
 5.425 -0.4133 0.238
 1.149 1.224 0.859
0 1 1 0.0 1.0
 0.2832 1.0 1.0
0 3 1 0.0 1.0
 0.8 1.0 1.0
 
30 14
0 0 8 2.0 1.0
 405924.31028 0.00022442017483
 60846.955735 0.00174020866260
 13847.343092 0.00905133395650
 3919.6158551 0.03681734144500
 1276.3594167 0.12004850256000
 458.67254435 0.28576057621000
 178.28725246 0.41087462062000
 70.612192837 0.21816962456000
0 0 4 2.0 1.0
 443.88077950 -0.02493427498400
 137.55875267 -0.11817955766000
 22.268083479 0.55367318468000
 9.5217310606 0.52628934936000
0 0 2 2.0 1.0
 14.874114065 -0.22929955254000
 2.4647517612 0.71135484742000
0 0 1 2.0 1.0
 1.0113272200 1.00000000000000
0 0 1 0.0 1.0
 0.322980200 1.00000000000000
0 0 1 0.0 1.0
 0.1016731100 1.00000000000000
0 2 6 6.0 1.0
 2205.3508534 0.00233562404480
 522.35300699 0.01903102263400
 167.73055542 0.08995575867500
 62.670045373 0.26113248631000
 25.109749456 0.42348448173000
 10.225142681 0.24618926885000
0 2 3 6.0 1.0
 40.713442521 -0.03002966759200
 5.6247090696 0.55575254864000
 2.2279949116 0.95581013442000
0 2 1 0.0 1.0
 1.1601141800 1.00000000000000
0 2 1 0.0 1.0
 0.2624550000 1.00000000000000
0 3 4 10.0 1.0
 88.554315311 0.01272817001500
 25.721525557 0.07939449984300
 9.1278367624 0.24491506805000
 3.4312364064 0.40390526479000
0 3 1 0.0 1.0
 1.1861283200 1.00000000000000
0 3 1 0.0 1.0
 0.4308920600 1.00000000000000
0 4 1 0.0 1.0
 2.6140000000 1.00000000000000

0 4
0 0 6 0 1.0
 4150.0 0.001845
 620.1 0.01416
 141.7 0.06863
 40.34 0.2286
 13.03 0.4662
 4.47 0.3657
0 1 2 0 1.0
 5.425 -0.4133 0.238
 1.149 1.224 0.859
0 1 1 0.0 1.0
 0.2832 1.0 1.0
0 3 1 0.0 1.0
 0.8 1.0 1.0


99 0
END
dft
HSE06
spin
end
MAXCYCLE
2000
shrink
6 6
END

        Thank you!

        1 Reply Last reply
        0
        • GiacomoAmbrogioundefined Offline
          GiacomoAmbrogioundefined Offline
          GiacomoAmbrogio Developer
          wrote last edited by
          #4

          Hi Mo,

          I believe the correct way to remove an atom while keeping the basis set is to use the GHOSTS keyword (see page 82 of the User manual) instead of ATOMSUBS, without modifying the original basis set.

          Could you try that and check if the energy makes sense afterward?

          Giacomo Ambrogio, PhD Student
          Department of Chemistry - University of Torino
          V. Giuria 5, 10125 Torino (Italy)

          1 Reply Last reply
          0

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