Finite difference non-linear susceptibility gives zero

pfons · September 25, 2023, 9:27am

I have been trying to calculate chi2 for a NV center in diamond. As the number of bands is odd, I have included a single hydrogen atom to result in an even number of electrons. The relaxation process went fine. I then tried to calculate chi2 based upon the non-DFPT finite-difference example given in the tutorial. The calculation runs until the end, but gives an error stating that “chkph3 : WARNING -
The dynamical matrix was incomplete : phonon frequencies may be wrong …” and later “dfptnl_doutput: WARNING - matrix of third-order energies incomplete, non-linear optical coefficients may be wrong.”

I would be grateful for any advice that can be offered. I am trying to calculate chi2 to analyze some ultrafast optical results for my colleague and the process is taking far longer than I hoped. Thanks for any help. I tried the same calculated (same relaxed structure) with DFPT and I will include that in a different post. Note that the diamond input lattice was maintained and only ions were relaxed after introducing the NV center.

All of the calculated elements of the non-linear optical susceptibility tensor d are zero. Unfortunately, I don’t have the ability to upload files yet, so I shall upload the last bit of the abo file.

 -outvars: echo values of variables after computation  --------
-          iomode1          1
-          iomode2          1
-          iomode3          0
-          iomode4          0
-          iomode5          0
            acell      1.0000000000E+00  1.0000000000E+00  1.0000000000E+00 Bohr
              amu      1.00794000E+00  1.20110000E+01  1.40067400E+01
        autoparal1          1
        autoparal2          1
        autoparal3          0
        autoparal4          0
        autoparal5          0
     densfor_pred1          6
     densfor_pred2          6
     densfor_pred3          2
     densfor_pred4          2
     densfor_pred5          2
          dilatmx      1.05000000E+00
  d3e_pert1_atpol1          1       1
  d3e_pert1_atpol2          1       1
  d3e_pert1_atpol3          1       1
  d3e_pert1_atpol4          1       1
  d3e_pert1_atpol5          1      63
   d3e_pert1_elfd1          0
   d3e_pert1_elfd2          0
   d3e_pert1_elfd3          0
   d3e_pert1_elfd4          0
   d3e_pert1_elfd5          1
   d3e_pert1_phon1          0
   d3e_pert1_phon2          0
   d3e_pert1_phon3          0
   d3e_pert1_phon4          0
   d3e_pert1_phon5          1
   d3e_pert2_elfd1          0
   d3e_pert2_elfd2          0
   d3e_pert2_elfd3          0
   d3e_pert2_elfd4          0
   d3e_pert2_elfd5          1
   d3e_pert3_elfd1          0
   d3e_pert3_elfd2          0
   d3e_pert3_elfd3          0
   d3e_pert3_elfd4          0
   d3e_pert3_elfd5          1
             ecut      4.50000000E+01 Hartree
           ecutsm      5.00000000E-01 Hartree
           etotal1    -3.8455031143E+02
           etotal3    -5.6336988035E+01
           etotal4     4.5498801849E+01
           etotal5     0.0000000000E+00
            fcart1    -7.7445707783E-04 -1.5309135004E-03  7.7098594616E-04
                      -3.7743958984E-04  7.1134296716E-05 -7.8391714291E-06
                      -1.5670599478E-04 -4.2681366138E-04 -7.6588771161E-05
                      -3.1333380522E-04 -9.4653745393E-06 -9.6247588485E-04
                      -1.3617774820E-04  4.9550624141E-05  1.1177587059E-05
                       4.6283643436E-04 -1.7492402814E-03 -1.8930773091E-03
                       1.0036996176E-04  5.9993499997E-05  2.0580372847E-04
                       9.6534584677E-05  2.5506505994E-04 -1.1312435852E-05
                      -1.6665548082E-04 -1.7481675017E-04 -2.5501574332E-04
                      -8.5354290299E-05  6.5225071203E-05  2.1913322890E-04
                       2.3329401714E-03 -6.9224907674E-04  7.8552303186E-04
                       2.1385035530E-03  5.3819195492E-04 -6.9580425062E-04
                       3.8627611074E-03  2.2069776734E-03  2.0657376543E-04
                       8.7346116378E-05 -3.1962895673E-06  7.2922149886E-05
                       1.1053310521E-04 -7.1447525336E-05  2.7491050688E-04
                      -1.4121741819E-04 -3.3362537549E-04  7.7270849694E-05
                       4.1724666406E-05  6.6767055019E-05  3.1296987524E-05
                      -4.8965869930E-04 -9.0478063620E-05  1.5012141104E-04
                      -5.0248829893E-04 -2.6783531277E-05  1.3629673240E-04
                       1.1932218202E-03 -2.6919110988E-04 -6.2831742171E-05
                      -1.2856209836E-04 -2.3954724239E-05  6.9738891500E-07
                       3.7202228013E-04 -1.4170046276E-04 -3.4601669513E-05
                       4.4280255348E-04 -1.7622091370E-04 -8.5283402300E-05
                      -2.4044673306E-05  4.2927441722E-05  2.0297678163E-05
                       2.5176172024E-04 -2.3352015447E-04 -5.3260973997E-06
                      -6.4098264178E-05 -6.3462257371E-05 -4.0534015992E-05
                      -9.6796240781E-04 -1.0137353475E-03 -1.1573329320E-04
                       3.7002709427E-06  2.1118661062E-04  1.5637962046E-04
                       2.0529688963E-04 -4.5187416526E-05 -4.7380603812E-05
                      -4.5285565898E-05  1.1735223501E-04  2.7078188862E-05
                       8.4627326442E-04 -4.5562211875E-04 -1.2927366362E-03
                      -5.2240173641E-05 -2.1623430339E-04  2.0912262959E-04
                       2.5284804621E-04  1.8230057180E-04 -1.8942058544E-04
                      -6.5567364730E-05 -4.7884682537E-04  5.9060344438E-05
                      -8.6269703997E-05  1.9653338566E-05 -8.2930457907E-05
                      -5.4806364224E-05 -9.7566541652E-05  5.3810361303E-04
                       1.0798378397E-04 -6.5376425706E-05 -5.4273024422E-06
                      -5.0882629411E-04  2.3959988771E-04  6.5426747633E-04
                       5.9577084447E-05  5.8327568365E-05  1.4148417955E-04
                      -3.5101819125E-05 -3.9010030346E-05 -2.4857205948E-04
                      -2.8606804717E-04 -4.2892843281E-05 -1.6549361982E-04
                      -2.7941259144E-04  5.1363384115E-04  7.3474422792E-05
                      -3.8593725263E-04  9.1464459938E-04  2.8445753557E-04
                      -5.8182711228E-05 -1.8660979117E-04 -1.0282055336E-04
                       1.8127342732E-04 -2.5398991355E-04  7.1046119414E-05
                       2.1539401024E-06 -6.0054753831E-06 -1.5643097827E-04
                      -1.1037678768E-03 -6.1259004787E-04  7.1993904271E-04
                      -3.8772701751E-03 -7.5961640681E-04  3.2135157390E-03
                       3.8572304440E-04  9.2973728620E-05 -1.3941090464E-04
                       9.0913132252E-04  8.5006344007E-04 -1.2062576755E-04
                      -1.1622728926E-03  9.7863017403E-05 -5.7926579126E-05
                      -1.7633110623E-04  8.9400884590E-05 -4.1769421209E-04
                      -6.9433717958E-05  6.6475521800E-06  3.0820916498E-06
                       2.3652687198E-05 -1.2072113103E-05  5.9190997456E-04
                      -2.9030065065E-05  1.2676508251E-04 -3.4096922299E-05
                      -2.1316352498E-03  2.8671544001E-03 -1.1031926835E-03
                       1.0296047492E-03  4.3814675612E-04 -5.7346630967E-04
                       5.7035324350E-04  2.1431588731E-06 -5.1371815406E-05
                      -1.2791729430E-03  5.7392185667E-05  1.0902153433E-04
                      -1.4018664677E-04 -1.7671749803E-04 -9.3501327305E-05
                       1.7312727740E-04  3.4181921468E-04 -2.0373088645E-04
                      -8.0372107045E-05  7.2469250613E-05 -9.4087317566E-05
                      -4.6453382511E-05  3.7676781936E-05  1.4098459826E-05
                       3.7722792425E-05 -2.1389463233E-04 -4.0231065520E-04
            fcart3     all zero
                       0.0000000000E+00  0.0000000000E+00  0.0000000000E+00
            fcart4     0.0000000000E+00  0.0000000000E+00  0.0000000000E+00
                      
                          all zero
            fcart5   
                          all zero
-          fftalg1        401
-          fftalg2        401
-          fftalg3        512
-          fftalg4        512
-          fftalg5        512
           getddk1          0
           getddk2          0
           getddk3          0
           getddk4          3
           getddk5          0
           getden1          0
           getden2          1
           getden3          0
           getden4          0
           getden5          0
           getwfk1          0
           getwfk2          1
           getwfk3          2
           getwfk4          2
           getwfk5          2
          get1den1          0
          get1den2          0
          get1den3          0
          get1den4          0
          get1den5          4
           get1wf1          0
           get1wf2          0
           get1wf3          0
           get1wf4          0
           get1wf5          4
             iscf1          7
             iscf2         -2
             iscf3          7
             iscf4          7
             iscf5          7
              ixc       -1012
           jdtset        1    2    3    4    5
              kpt      1.25000000E-01  1.25000000E-01  1.25000000E-01
                       3.75000000E-01  1.25000000E-01  1.25000000E-01
                      -3.75000000E-01  1.25000000E-01  1.25000000E-01
                      -1.25000000E-01  1.25000000E-01  1.25000000E-01
                       1.25000000E-01  3.75000000E-01  1.25000000E-01
                       3.75000000E-01  3.75000000E-01  1.25000000E-01
                      -3.75000000E-01  3.75000000E-01  1.25000000E-01
                      -1.25000000E-01  3.75000000E-01  1.25000000E-01
                       1.25000000E-01 -3.75000000E-01  1.25000000E-01
                       3.75000000E-01 -3.75000000E-01  1.25000000E-01
                      -3.75000000E-01 -3.75000000E-01  1.25000000E-01
                      -1.25000000E-01 -3.75000000E-01  1.25000000E-01
                       1.25000000E-01 -1.25000000E-01  1.25000000E-01
                       3.75000000E-01 -1.25000000E-01  1.25000000E-01
                      -3.75000000E-01 -1.25000000E-01  1.25000000E-01
                      -1.25000000E-01 -1.25000000E-01  1.25000000E-01
                       1.25000000E-01  1.25000000E-01  3.75000000E-01
                       3.75000000E-01  1.25000000E-01  3.75000000E-01
                      -3.75000000E-01  1.25000000E-01  3.75000000E-01
                      -1.25000000E-01  1.25000000E-01  3.75000000E-01
                       1.25000000E-01  3.75000000E-01  3.75000000E-01
                       3.75000000E-01  3.75000000E-01  3.75000000E-01
                      -3.75000000E-01  3.75000000E-01  3.75000000E-01
                      -1.25000000E-01  3.75000000E-01  3.75000000E-01
                       1.25000000E-01 -3.75000000E-01  3.75000000E-01
                       3.75000000E-01 -3.75000000E-01  3.75000000E-01
                      -3.75000000E-01 -3.75000000E-01  3.75000000E-01
                      -1.25000000E-01 -3.75000000E-01  3.75000000E-01
                       1.25000000E-01 -1.25000000E-01  3.75000000E-01
                       3.75000000E-01 -1.25000000E-01  3.75000000E-01
                      -3.75000000E-01 -1.25000000E-01  3.75000000E-01
                      -1.25000000E-01 -1.25000000E-01  3.75000000E-01
                       1.25000000E-01  1.25000000E-01 -3.75000000E-01
                       3.75000000E-01  1.25000000E-01 -3.75000000E-01
                      -3.75000000E-01  1.25000000E-01 -3.75000000E-01
                      -1.25000000E-01  1.25000000E-01 -3.75000000E-01
                       1.25000000E-01  3.75000000E-01 -3.75000000E-01
                       3.75000000E-01  3.75000000E-01 -3.75000000E-01
                      -3.75000000E-01  3.75000000E-01 -3.75000000E-01
                      -1.25000000E-01  3.75000000E-01 -3.75000000E-01
                       1.25000000E-01 -3.75000000E-01 -3.75000000E-01
                       3.75000000E-01 -3.75000000E-01 -3.75000000E-01
                      -3.75000000E-01 -3.75000000E-01 -3.75000000E-01
                      -1.25000000E-01 -3.75000000E-01 -3.75000000E-01
                       1.25000000E-01 -1.25000000E-01 -3.75000000E-01
                       3.75000000E-01 -1.25000000E-01 -3.75000000E-01
                      -3.75000000E-01 -1.25000000E-01 -3.75000000E-01
                      -1.25000000E-01 -1.25000000E-01 -3.75000000E-01
                       1.25000000E-01  1.25000000E-01 -1.25000000E-01
                       3.75000000E-01  1.25000000E-01 -1.25000000E-01
                       outvar_i_n : Printing only first  50 k-points.
           kptopt           3
         kptrlatt        4    0    0      0    4    0      0    0    4
          kptrlen      5.38148647E+01
P           mkmem1          2
P           mkmem2          2
P           mkmem3          1
P           mkmem4          1
P           mkmem5          1
P          mkqmem1          2
P          mkqmem2          2
P          mkqmem3          1
P          mkqmem4          1
P          mkqmem5          1
P          mk1mem1          2
P          mk1mem2          2
P          mk1mem3          1
P          mk1mem4          1
P          mk1mem5          1
            natom          64
            nband         127
           ndtset           5
            ngfft          90      90      90
             nkpt          64
-           npfft1          3
-           npfft2          3
-           npfft3          1
-           npfft4          1
-           npfft5          1
-        np_spkpt1         32
-        np_spkpt2         32
-        np_spkpt3          1
-        np_spkpt4          1
-        np_spkpt5          1
            nstep         200
             nsym           1
           ntypat           3
              occ      2.000000  2.000000  2.000000  2.000000  2.000000  2.000000
                       2.000000  2.000000  2.000000  2.000000  2.000000  2.000000
                       2.000000  2.000000  2.000000  2.000000  2.000000  2.000000
                       2.000000  2.000000  2.000000  2.000000  2.000000  2.000000
                       2.000000  2.000000  2.000000  2.000000  2.000000  2.000000
                       2.000000  2.000000  2.000000  2.000000  2.000000  2.000000
                       2.000000  2.000000  2.000000  2.000000  2.000000  2.000000
                       2.000000  2.000000  2.000000  2.000000  2.000000  2.000000
                       2.000000  2.000000  2.000000  2.000000  2.000000  2.000000
                       2.000000  2.000000  2.000000  2.000000  2.000000  2.000000
                       2.000000  2.000000  2.000000  2.000000  2.000000  2.000000
                       2.000000  2.000000  2.000000  2.000000  2.000000  2.000000
                       2.000000  2.000000  2.000000  2.000000  2.000000  2.000000
                       2.000000  2.000000  2.000000  2.000000  2.000000  2.000000
                       2.000000  2.000000  2.000000  2.000000  2.000000  2.000000
                       2.000000  2.000000  2.000000  2.000000  2.000000  2.000000
                       2.000000  2.000000  2.000000  2.000000  2.000000  2.000000
                       2.000000  2.000000  2.000000  2.000000  2.000000  2.000000
                       2.000000  2.000000  2.000000  2.000000  2.000000  2.000000
                       2.000000  2.000000  2.000000  2.000000  2.000000  2.000000
                       2.000000  2.000000  2.000000  2.000000  2.000000  2.000000
                       2.000000
        optdriver1          0
        optdriver2          0
        optdriver3          1
        optdriver4          1
        optdriver5          5
           ortalg1         -2
           ortalg2         -2
           ortalg3          2
           ortalg4          2
           ortalg5          2
        paral_kgb1          1
        paral_kgb2          1
        paral_kgb3          0
        paral_kgb4          0
        paral_kgb5          0
          prepanl1          0
          prepanl2          0
          prepanl3          0
          prepanl4          1
          prepanl5          0
           prtden1          1
           prtden2          0
           prtden3          0
           prtden4          1
           prtden5          0
           prteig           0
            prtwf1          1
            prtwf2          1
            prtwf3          1
            prtwf4          1
            prtwf5          0
            rfdir1          0       0       0
            rfdir2          0       0       0
            rfdir3          1       1       1
            rfdir4          1       1       1
            rfdir5          0       0       0
           rfelfd1          0
           rfelfd2          0
           rfelfd3          2
           rfelfd4          3
           rfelfd5          0
           rfphon1          0
           rfphon2          0
           rfphon3          0
           rfphon4          1
           rfphon5          0
           rfstrs1          0
           rfstrs2          0
           rfstrs3          0
           rfstrs4          3
           rfstrs5          0
            rprim      1.3453716172E+01  0.0000000000E+00  0.0000000000E+00
                       0.0000000000E+00  1.3453716172E+01  0.0000000000E+00
                       0.0000000000E+00  0.0000000000E+00  1.3453716172E+01
           shiftk      5.00000000E-01  5.00000000E-01  5.00000000E-01
          spgroup           1
           strten1     3.3934954646E-05  8.5690835393E-05  1.3182698875E-04
                       2.9900704248E-05  1.0297908406E-04 -2.0135670299E-04
           strten3     0.0000000000E+00  0.0000000000E+00  0.0000000000E+00
                       0.0000000000E+00  0.0000000000E+00  0.0000000000E+00
           strten4     0.0000000000E+00  0.0000000000E+00  0.0000000000E+00
                       0.0000000000E+00  0.0000000000E+00  0.0000000000E+00
           strten5     0.0000000000E+00  0.0000000000E+00  0.0000000000E+00
                       0.0000000000E+00  0.0000000000E+00  0.0000000000E+00
           toldfe1     1.00000000E-12 Hartree
           toldfe2     0.00000000E+00 Hartree
           toldfe3     0.00000000E+00 Hartree
           toldfe4     0.00000000E+00 Hartree
           toldfe5     0.00000000E+00 Hartree
           tolvrs1     0.00000000E+00
           tolvrs2     0.00000000E+00
           tolvrs3     0.00000000E+00
           tolvrs4     1.00000000E-12
           tolvrs5     0.00000000E+00
           tolwfr1     0.00000000E+00
           tolwfr2     1.00000000E-22
           tolwfr3     1.00000000E-22
           tolwfr4     0.00000000E+00
           tolwfr5     0.00000000E+00
            typat      1  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2
                       2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2
                       2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2
                       2  2  2  3
         wfoptalg1        114
         wfoptalg2        114
         wfoptalg3          0
         wfoptalg4          0
         wfoptalg5          0
              wtk        0.01563    0.01563    0.01563    0.01563    0.01563    0.01563
                         0.01563    0.01563    0.01563    0.01563    0.01563    0.01563
                         0.01563    0.01563    0.01563    0.01563    0.01563    0.01563
                         0.01563    0.01563    0.01563    0.01563    0.01563    0.01563
                         0.01563    0.01563    0.01563    0.01563    0.01563    0.01563
                         0.01563    0.01563    0.01563    0.01563    0.01563    0.01563
                         0.01563    0.01563    0.01563    0.01563    0.01563    0.01563
                         0.01563    0.01563    0.01563    0.01563    0.01563    0.01563
                         0.01563    0.01563
                       outvars : Printing only first  50 k-points.
           xangst      3.9593296320E+00  6.0905092690E-01  1.4886369880E+00
                       1.7667667421E+00  1.7489468128E+00  1.7684252063E+00
                       1.7742995656E+00  1.7677558403E+00  5.3312678363E+00
                       1.7443582171E+00  5.3001863871E+00  1.7775073537E+00
                       1.7751834391E+00  5.3228755588E+00  5.3404735052E+00
                       5.4639204122E+00  1.7317363041E+00  1.6241361136E+00
                       5.3330518867E+00  1.7960067585E+00  5.2915298375E+00
                       5.3135353332E+00  5.3113566544E+00  1.7894692271E+00
                       5.3347402524E+00  5.3432670154E+00  5.3359714103E+00
                       4.4833349834E+00  4.4294614160E+00  4.4406647173E+00
                       4.4407079321E+00  4.4079562716E+00  9.0671958945E-01
                       4.4390794406E+00  9.0589452218E-01  4.3997103690E+00
                       4.6792800218E+00  1.0757407657E+00  6.7145090136E-01
                       8.8821278042E-01  4.4388387336E+00  4.4431429805E+00
                       8.7821479346E-01  4.4297268984E+00  8.8978310647E-01
                       8.6367249350E-01  8.8266071635E-01  4.4475461870E+00
                       8.8418476631E-01  8.7680956630E-01  8.7419866875E-01
                       4.4540333130E+00  2.6961737234E+00  6.1772698367E+00
                       4.4135465669E+00  6.1755705071E+00  2.6972315239E+00
                       4.4430612498E+00  6.2187188409E+00  6.2223705948E+00
                       8.8147405477E-01  2.6550296431E+00  2.6534472141E+00
                       8.9913308564E-01  2.6615913093E+00  6.2136666299E+00
                       8.6831227766E-01  6.2047987053E+00  2.6687124179E+00
                       8.8640153387E-01  6.2226303817E+00  6.2243929315E+00
                       2.6710011626E+00  4.3970932776E+00  2.6660004249E+00
                       2.6734055975E+00  4.4337000219E+00  6.2191567552E+00
                       2.5963930547E+00  8.4433072125E-01  2.7154048602E+00
                       2.6845023215E+00  8.8007623178E-01  6.2172733892E+00
                       6.2185330958E+00  4.4394039428E+00  2.7017120470E+00
                       6.2299632212E+00  4.4526021000E+00  6.2202329237E+00
                       6.2163055067E+00  8.8588701484E-01  2.6217975655E+00
                       6.2424866018E+00  8.9560043938E-01  6.1877943745E+00
                       2.6725628742E+00  2.6519705081E+00  4.4161452191E+00
                       2.6859901337E+00  2.6429220355E+00  8.8846822449E-01
                       2.6606167346E+00  6.2008546289E+00  4.4554394657E+00
                       2.6285782244E+00  6.1798360956E+00  9.0094155562E-01
                       6.2257543032E+00  2.7009763994E+00  4.4233471329E+00
                       6.2460413182E+00  2.7129341436E+00  8.7626037578E-01
                       6.2163856712E+00  6.2345604314E+00  4.4353164105E+00
                       6.2179697377E+00  6.2107436179E+00  8.8778255508E-01
                       1.7689272664E+00  3.5375661971E+00  3.5500875842E+00
                       1.7764683484E+00  3.5376622378E+00  7.1058346642E+00
                       1.7214055564E+00  7.0866224650E+00  3.5852772120E+00
                       1.7813979634E+00  7.1093613302E+00  7.1174291766E+00
                       5.3416591701E+00  3.5684466657E+00  7.1011126510E+00
                       5.3164248129E+00  1.9223091856E-03  3.5289848996E+00
                       5.3527138896E+00  7.0937814489E+00  7.0774434938E+00
                       3.4796696703E+00  3.5667405727E+00  1.7230238672E+00
                       3.5726404906E+00  3.5514676799E+00  5.3012726651E+00
                       3.3670555711E+00  6.9279165161E+00  1.9495094227E+00
                       3.5540178489E+00  7.1025530480E+00  5.3293385501E+00
                       7.1103899411E+00  3.5587205686E+00  1.7819727837E+00
                       8.4803444670E-03  3.5531478583E+00  5.3365134102E+00
                       7.1164550291E+00  7.0953304879E+00  1.7685306446E+00
                       7.1114582782E+00  7.1170277136E+00  5.3254842494E+00
                       3.4594146926E+00  1.6989372284E+00  3.5805081395E+00
                       3.5989073032E+00  1.8132820537E+00  7.0542643650E+00
                       3.5639995325E+00  5.2803405613E+00  3.5727331852E+00
                       3.5521849594E+00  5.3242537323E+00  1.4044440319E-03
                       7.0956203899E+00  1.7812532972E+00  3.5312166891E+00
                       1.6741197833E-02  1.7819807574E+00  7.0901155274E+00
                       7.1118521234E+00  5.3373864622E+00  3.5570161842E+00
                       7.1153893261E+00  5.3296411958E+00  7.1157369664E+00
                       5.4154845000E+00  3.6267452962E+00  3.6248278994E+00
            xcart      7.4820486743E+00  1.1509394528E+00  2.8131162186E+00
                       deleted for space
             xred      5.5613249000E-01  8.5548070000E-02  2.0909585000E-01
                       2.4816231000E-01  2.4565930000E-01  2.4839526000E-01
                       2.4922038000E-01  2.4830124000E-01  7.4883668000E-01
                       2.4501478000E-01  7.4447094000E-01  2.4967095000E-01
                       2.4934453000E-01  7.4765789000E-01  7.5012972000E-01
                       7.6746923000E-01  2.4324189000E-01  2.2812823000E-01
                       7.4908727000E-01  2.5226940000E-01  7.4325503000E-01
                       7.4634595000E-01  7.4603993000E-01  2.5135113000E-01
                       7.4932442000E-01  7.5052210000E-01  7.4949735000E-01
                       6.2973495000E-01  6.2216780000E-01  6.2374143000E-01
                       6.2374750000E-01  6.1914716000E-01  1.2735899000E-01
                       6.2351876000E-01  1.2724310000E-01  6.1798893000E-01
                       6.5725764000E-01  1.5109992000E-01  9.4312850000E-02
                       1.2475950000E-01  6.2348495000E-01  6.2408953000E-01
                       1.2335517000E-01  6.2220509000E-01  1.2498007000E-01
                       1.2131254000E-01  1.2397965000E-01  6.2470801000E-01
                       1.2419372000E-01  1.2315779000E-01  1.2279106000E-01
                       6.2561920000E-01  3.7870800000E-01  8.6766720000E-01
                       6.1993238000E-01  8.6742851000E-01  3.7885658000E-01
                       6.2407805000E-01  8.7348918000E-01  8.7400211000E-01
                       1.2381297000E-01  3.7292885000E-01  3.7270658000E-01
                       1.2629338000E-01  3.7385051000E-01  8.7277954000E-01
                       1.2196425000E-01  8.7153394000E-01  3.7485075000E-01
                       1.2450509000E-01  8.7403860000E-01  8.7428617000E-01
                       3.7517223000E-01  6.1762133000E-01  3.7446982000E-01
                       3.7550996000E-01  6.2276316000E-01  8.7355069000E-01
                       3.6469268000E-01  1.1859577000E-01  3.8140923000E-01
                       3.7706862000E-01  1.2361663000E-01  8.7328615000E-01
                       8.7346309000E-01  6.2356434000E-01  3.7948592000E-01
                       8.7506858000E-01  6.2541817000E-01  8.7370185000E-01
                       8.7315020000E-01  1.2443282000E-01  3.6826103000E-01
                       8.7682763000E-01  1.2579718000E-01  8.6914549000E-01
                       3.7539159000E-01  3.7249916000E-01  6.2029739000E-01
                       3.7727760000E-01  3.7122820000E-01  1.2479538000E-01
                       3.7371362000E-01  8.7097995000E-01  6.2581671000E-01
                       3.6921345000E-01  8.6802766000E-01  1.2654740000E-01
                       8.7447739000E-01  3.7938259000E-01  6.2130898000E-01
                       8.7732693000E-01  3.8106219000E-01  1.2308065000E-01
                       8.7316146000E-01  8.7571431000E-01  6.2299020000E-01
                       8.7338396000E-01  8.7236897000E-01  1.2469907000E-01
                       2.4846578000E-01  4.9689106000E-01  4.9864983000E-01
                       2.4952501000E-01  4.9690455000E-01  9.9809460000E-01
                       2.4179082000E-01  9.9539603000E-01  5.0359261000E-01
                       2.5021743000E-01  9.9858996000E-01  9.9972318000E-01
                       7.5029626000E-01  5.0122857000E-01  9.9743134000E-01
                       7.4675181000E-01  2.7001000000E-04  4.9568572000E-01
                       7.5184902000E-01  9.9640159000E-01  9.9410674000E-01
                       4.8875884000E-01  5.0098893000E-01  2.4201813000E-01
                       5.0181764000E-01  4.9884368000E-01  7.4462352000E-01
                       4.7294092000E-01  9.7310399000E-01  2.7383058000E-01
                       4.9920188000E-01  9.9763366000E-01  7.4856569000E-01
                       9.9873444000E-01  4.9986243000E-01  2.5029817000E-01
                       1.1911600000E-03  4.9907968000E-01  7.4957348000E-01
                       9.9958635000E-01  9.9661917000E-01  2.4841007000E-01
                       9.9888450000E-01  9.9966679000E-01  7.4802431000E-01
                       4.8591380000E-01  2.3863489000E-01  5.0292274000E-01
                       5.0550711000E-01  2.5469591000E-01  9.9085097000E-01
                       5.0060392000E-01  7.4168337000E-01  5.0183066000E-01
                       4.9894443000E-01  7.4785147000E-01  1.9727000000E-04
                       9.9665989000E-01  2.5019711000E-01  4.9599920000E-01
                       2.3514900000E-03  2.5029929000E-01  9.9588667000E-01
                       9.9893982000E-01  7.4969611000E-01  4.9962303000E-01
                       9.9943666000E-01  7.4860820000E-01  9.9948549000E-01
                       7.6066586000E-01  5.0941727000E-01  5.0914795000E-01
            znucl        1.00000    6.00000    7.00000

pfons · September 25, 2023, 9:29am

Here is the input file for the above post as it was too big to include)

##### DATASET 1 #####
#####################
##############################################
####                SECTION: basic               
##############################################
 kptopt1 3
 toldfe1 1e-12
##############################################
####                SECTION: files               
##############################################
 prtden1 1
 prtwf1 1
##############################################
####                SECTION: paral               
##############################################
 autoparal1 1


#####################
##### DATASET 2 #####
#####################
##############################################
####                SECTION: basic               
##############################################
 kptopt2 3
 iscf2 -2
 tolwfr2 1e-22
##############################################
####                SECTION: files               
##############################################
 getden2 1
 getwfk2 1
 prtwf2 1
##############################################
####                SECTION: paral               
##############################################
 autoparal2 1


#####################
##### DATASET 3 #####
#####################
##############################################
####                SECTION: basic               
##############################################
 kptopt3 3
 tolwfr3 1e-22
##############################################
####                SECTION: dfpt                
##############################################
 optdriver3 1
 rfelfd3 2
##############################################
####                SECTION: files               
##############################################
 getwfk3 2
 prtwf3 1


#####################
##### DATASET 4 #####
#####################
##############################################
####                SECTION: basic               
##############################################
 kptopt4 3
 tolvrs4 1e-12
##############################################
####                SECTION: dfpt                
##############################################
 optdriver4 1
 rfphon4 1
 rfelfd4 3
 rfstrs4 3
 prepanl4 1
##############################################
####                SECTION: files               
##############################################
 getwfk4 2
 getddk4 3
 prtwf4 1
 prtden4 1


#####################
##### DATASET 5 #####
#####################
##############################################
####                SECTION: basic               
##############################################
 kptopt5 3
##############################################
####                SECTION: dfpt                
##############################################
 optdriver5 5
 d3e_pert1_elfd5    1     # activate electric field for 1st perturbation...
 d3e_pert1_phon5    1     # ...and also atomic displacements...
 d3e_pert1_atpol5   1 63  # ...for all atoms 
 d3e_pert2_elfd5    1     # activate electric field for 2nd perturbation...
 d3e_pert3_elfd5    1     # activate electric field for 3rd perturbation...

##############################################
####                SECTION: files               
##############################################
 getwfk5 2
 get1den5 4
 get1wf5 4

mverstra · September 25, 2023, 11:34am

Hi Paul,

it’s important we get more complete info, as in a whole input file and some specs on your machine, in case it can influence the output. I have tried to piece together your full input (is atom 1 H or N??) and run it with minimal convergence parameters (below) and it does seem to run indeed (churning through a ton of perturbations right now, and succeeded with no “The dynamical matrix was incomplete” in the log).

One thing I noticed: you set rfatpol to 63 instead of 64 in dtset 5. Could be as simple as that. The warning means not all of the needed derivatives are present in the full DDB file, and in that case 0 is returned (does not mean some symmetry is killing your chi2).

With the latest version of abinit the atpol variables are set to 1 natom automatically, so you may have to “unset” them in DTSET 4 if you don’t want it to do the full dynamical matrix. This could be the other problem, if you think you actually have all of the 2DTE from the phonons at gamma but you don’t. With abinit 9.10 this should be automatic.

The same issues are probably arising in your other full DFPT calculation - do check which DDB are really needed by comparison with the tutorial: if you can get away with only E derivatives at the dtset 4 level then great, but at the dtset 5 level everything should be present and just multiplied up.

ndtset 2
jdtset 4 5
ecut 2. # 4.50000000E+01
dilatmx 1.05
ecutsm 5.00000000E-01
ngkpt 1 1 1 #2 2 2
#kptrlatt 4 0 0 0 4 0 0 0 4
natom 64
nband 127 #!!!
rprim 1.3453716172E+01 0.0000000000E+00 0.0000000000E+00
0.0000000000E+00 1.3453716172E+01 0.0000000000E+00
0.0000000000E+00 0.0000000000E+00 1.3453716172E+01
ntypat 3
typat 1 62*2 3
pseudos= “H/H.psp8, C/C.psp8, N/N.psp8”
pp_dirpath = “/Users/mverstra/WorkSpace/pspfiles/ONCVPSP/github_matteo/pseudo_dojo/pseudo_dojo/pseudos/ONCVPSP-PW-PDv0.4/”
xred 5.5613249000E-01 8.5548070000E-02 2.0909585000E-01
2.4816231000E-01 2.4565930000E-01 2.4839526000E-01
2.4922038000E-01 2.4830124000E-01 7.4883668000E-01
2.4501478000E-01 7.4447094000E-01 2.4967095000E-01
2.4934453000E-01 7.4765789000E-01 7.5012972000E-01
7.6746923000E-01 2.4324189000E-01 2.2812823000E-01
7.4908727000E-01 2.5226940000E-01 7.4325503000E-01
7.4634595000E-01 7.4603993000E-01 2.5135113000E-01
7.4932442000E-01 7.5052210000E-01 7.4949735000E-01
6.2973495000E-01 6.2216780000E-01 6.2374143000E-01
6.2374750000E-01 6.1914716000E-01 1.2735899000E-01
6.2351876000E-01 1.2724310000E-01 6.1798893000E-01
6.5725764000E-01 1.5109992000E-01 9.4312850000E-02
1.2475950000E-01 6.2348495000E-01 6.2408953000E-01
1.2335517000E-01 6.2220509000E-01 1.2498007000E-01
1.2131254000E-01 1.2397965000E-01 6.2470801000E-01
1.2419372000E-01 1.2315779000E-01 1.2279106000E-01
6.2561920000E-01 3.7870800000E-01 8.6766720000E-01
6.1993238000E-01 8.6742851000E-01 3.7885658000E-01
6.2407805000E-01 8.7348918000E-01 8.7400211000E-01
1.2381297000E-01 3.7292885000E-01 3.7270658000E-01
1.2629338000E-01 3.7385051000E-01 8.7277954000E-01
1.2196425000E-01 8.7153394000E-01 3.7485075000E-01
1.2450509000E-01 8.7403860000E-01 8.7428617000E-01
3.7517223000E-01 6.1762133000E-01 3.7446982000E-01
3.7550996000E-01 6.2276316000E-01 8.7355069000E-01
3.6469268000E-01 1.1859577000E-01 3.8140923000E-01
3.7706862000E-01 1.2361663000E-01 8.7328615000E-01
8.7346309000E-01 6.2356434000E-01 3.7948592000E-01
8.7506858000E-01 6.2541817000E-01 8.7370185000E-01
8.7315020000E-01 1.2443282000E-01 3.6826103000E-01
8.7682763000E-01 1.2579718000E-01 8.6914549000E-01
3.7539159000E-01 3.7249916000E-01 6.2029739000E-01
3.7727760000E-01 3.7122820000E-01 1.2479538000E-01
3.7371362000E-01 8.7097995000E-01 6.2581671000E-01
3.6921345000E-01 8.6802766000E-01 1.2654740000E-01
8.7447739000E-01 3.7938259000E-01 6.2130898000E-01
8.7732693000E-01 3.8106219000E-01 1.2308065000E-01
8.7316146000E-01 8.7571431000E-01 6.2299020000E-01
8.7338396000E-01 8.7236897000E-01 1.2469907000E-01
2.4846578000E-01 4.9689106000E-01 4.9864983000E-01
2.4952501000E-01 4.9690455000E-01 9.9809460000E-01
2.4179082000E-01 9.9539603000E-01 5.0359261000E-01
2.5021743000E-01 9.9858996000E-01 9.9972318000E-01
7.5029626000E-01 5.0122857000E-01 9.9743134000E-01
7.4675181000E-01 2.7001000000E-04 4.9568572000E-01
7.5184902000E-01 9.9640159000E-01 9.9410674000E-01
4.8875884000E-01 5.0098893000E-01 2.4201813000E-01
5.0181764000E-01 4.9884368000E-01 7.4462352000E-01
4.7294092000E-01 9.7310399000E-01 2.7383058000E-01
4.9920188000E-01 9.9763366000E-01 7.4856569000E-01
9.9873444000E-01 4.9986243000E-01 2.5029817000E-01
1.1911600000E-03 4.9907968000E-01 7.4957348000E-01
9.9958635000E-01 9.9661917000E-01 2.4841007000E-01
9.9888450000E-01 9.9966679000E-01 7.4802431000E-01
4.8591380000E-01 2.3863489000E-01 5.0292274000E-01
5.0550711000E-01 2.5469591000E-01 9.9085097000E-01
5.0060392000E-01 7.4168337000E-01 5.0183066000E-01
4.9894443000E-01 7.4785147000E-01 1.9727000000E-04
9.9665989000E-01 2.5019711000E-01 4.9599920000E-01
2.3514900000E-03 2.5029929000E-01 9.9588667000E-01
9.9893982000E-01 7.4969611000E-01 4.9962303000E-01
9.9943666000E-01 7.4860820000E-01 9.9948549000E-01
7.6066586000E-01 5.0941727000E-01 5.0914795000E-01
znucl 1.00000 6.00000 7.00000

DATASET 1

kptopt1 3
toldfe1 1e-12
prtden1 1
prtwf1 1
autoparal1 1

DATASET 2

kptopt2 3
iscf2 -2
tolwfr2 1e-22
getden2 1
getwfk2 1
prtwf2 1
autoparal2 1

DATASET 3

kptopt3 3
tolwfr3 1e-22
optdriver3 1
rfelfd3 2
getwfk3 2
prtwf3 1

DATASET 4

kptopt4 3
tolvrs4 1e-12
optdriver4 1
rfphon4 1
rfelfd4 3
rfstrs4 3
prepanl4 1
getwfk4 2
getddk4 3
prtwf4 1
prtden4 1

DATASET 5

kptopt5 3
optdriver5 5
d3e_pert1_elfd5 1 # activate electric field for 1st perturbation…
d3e_pert1_phon5 1 # …and also atomic displacements…
d3e_pert1_atpol5 1 63 # …for all atoms
!!! 64 atoms…
d3e_pert2_elfd5 1 # activate electric field for 2nd perturbation…
d3e_pert3_elfd5 1 # activate electric field for 3rd perturbation…
getwfk5 2
get1den5 4
get1wf5 4

beuken · September 25, 2023, 12:23pm

I’ve upgraded you to “basic user” status: you can use extensions : tar.gz, tgz,…
jmb