4
$\begingroup$

I'm trying to do a geometry optimization of a paraquat molecule ontop of a goldbulk consisting of four layers. Two of those layers are fixed. The input file looks like the following:

%cpu=16-31
%mem=120GB
%chk=mychk.chk
#p opt b3lyp/genecp nosymm int=ultrafine

title

2 2
C 0 8.29256346 -1.77584455 6.71957144
N 0 7.01616228 -2.44803618 6.31406805
C 0 6.15166862 -2.90727492 7.26967799
C 0 4.99476528 -3.59917666 6.91326232
C 0 4.69746661 -3.83580056 5.55116288
C 0 5.61233204 -3.34791231 4.58370498
C 0 6.75906414 -2.66573184 4.98812963
H 0 7.49092507 -2.2999946 4.2781678
H 0 5.47355565 -3.52974232 3.52457489
C 0 3.50515803 -4.62098617 5.14441683
C 0 3.03689444 -5.6915301 5.93988213
C 0 1.95600465 -6.46277758 5.51155339
N 0 1.32757473 -6.19245305 4.32995917
C 0 1.76115824 -5.16728842 3.53542831
C 0 2.83888632 -4.37295286 3.92100924
H 0 3.13422947 -3.5616365 3.2653502
H 0 1.22991791 -5.00732082 2.60540607
C 0 0.21761679 -7.08683285 3.87327092
H 0 -0.45556376 -7.2893041 4.70953912
H 0 0.65539728 -8.02329804 3.50851655
H 0 -0.33886341 -6.59914796 3.0713439
H 0 1.59077204 -7.30783464 6.08188303
H 0 3.52243201 -5.9708836 6.86728718
H 0 4.33354916 -3.92830506 7.70670577
H 0 6.4066222 -2.70684036 8.30318156
H 0 8.55449396 -1.01492896 5.98161263
H 0 9.08581616 -2.52876751 6.77856604
H 0 8.16023712 -1.29869759 7.6923691
Au 0 -0.10658791 -0.106921953 -0.106690731
Au 0 1.962673477 -0.108146433 1.967644211
Au 0 -0.104312471 1.962824173 1.96310486
Au 0 1.962220846 1.968008833 -0.108468191
Au 0 4.029052369 -0.113085184 -0.113315722
Au 0 6.100413428 -0.107515425 1.963537211
Au 0 4.027379147 1.957131265 1.956852168
Au 0 6.100891806 1.96315078 -0.107153726
Au -1 -0.108432478 4.029817671 -0.106900538
Au -1 1.966063731 4.035475821 1.957133099
Au -1 -0.107699713 6.10022317 1.963471746
Au -1 1.96334103 6.105285747 -0.113099315
Au -1 4.031227295 4.025096026 -0.108559409
Au -1 6.096793033 4.030440023 1.962747495
Au -1 4.029966357 6.101404983 1.967749875
Au -1 6.099422231 6.100547277 -0.107291631
Au 0 -0.107736128 -0.107293668 4.029462667
Au 0 1.963383929 -0.112698271 6.105685109
Au 0 -0.108455559 1.963028094 6.099907542
Au 0 1.966151805 1.957296424 4.035602077
Au 0 4.030467415 -0.108378488 4.025383791
Au 0 6.099475812 -0.107691576 6.10027262
Au 0 4.030711294 1.968064547 6.101647758
Au 0 6.096755631 1.962292106 4.030192249
Au -1 -0.104246292 4.030229057 4.030157401
Au -1 1.962014634 4.025121721 6.101404005
Au -1 -0.107187056 6.10015712 6.09984544
Au -1 1.962631286 6.101182934 4.025368963
Au -1 4.0272297 4.035507714 4.035779287
Au -1 6.100784367 4.029654954 6.099793808
Au -1 4.029316571 6.105543384 6.105809512
Au -1 6.100357877 6.100269913 4.029261219
Au 0 8.173484232 -0.107257541 -0.106967104
Au 0 10.2426731 -0.10800139 1.967581809
Au 0 8.175595408 1.962573792 1.96288082
Au 0 10.24210072 1.96779256 -0.108506954
Au 0 12.30958154 -0.112865775 -0.113025501
Au 0 14.38050861 -0.107372838 1.963614389
Au 0 12.30746675 1.957538422 1.956915328
Au 0 14.38121226 1.963465707 -0.107028802
Au -1 8.171668329 4.029977538 -0.106926707
Au -1 10.24618233 4.035401227 1.957135362
Au -1 8.172682989 6.100220211 1.963118804
Au -1 10.24383858 6.105431827 -0.113127362
Au -1 12.31113776 4.025295034 -0.108490865
Au -1 14.37675695 4.030834106 1.962942431
Au -1 12.31055328 6.101381386 1.967741887
Au -1 14.37974656 6.100351584 -0.10715489
Au 0 8.17242271 -0.10720197 4.029906451
Au 0 10.24390116 -0.112721363 6.105757939
Au 0 8.172037308 1.962992304 6.099907521
Au 0 10.24624213 1.957509237 4.035546755
Au 0 12.31037637 -0.108185085 4.025464664
Au 0 14.37978242 -0.107527714 6.100084777
Au 0 12.31122283 1.968045494 6.10164273
Au 0 14.37665552 1.962356799 4.030403516
Au -1 8.175757467 4.030101225 4.029869405
Au -1 10.24244723 4.024991727 6.101675348
Au -1 8.173500953 6.100134157 6.099898359
Au -1 10.24296627 6.101136447 4.025207108
Au -1 12.30732913 4.035741234 4.036158699
Au -1 14.38111729 4.02949595 6.099999196
Au -1 12.30997416 6.105689433 6.105867222
Au -1 14.38049004 6.100330203 4.02933331
Au 0 -0.110675599 -0.10692626 8.173385353
Au 0 1.964395467 -0.110650578 10.23303171
Au 0 -0.105337606 1.962681536 10.24274555
Au 0 1.963576452 1.953386788 8.168981444
Au 0 4.033984919 -0.106497996 8.173258141
Au 0 6.098423867 -0.107472902 10.24226983
Au 0 4.027896284 1.963608742 10.24368626
Au 0 6.098687574 1.961927149 8.172900262
Au -1 -0.106356748 4.03031267 8.173012052
Au -1 1.965494778 4.029194988 10.2435807
Au -1 -0.10574068 6.100281467 10.24291691
Au -1 1.957977111 6.099463582 8.173302307
Au -1 4.029169465 4.039905504 8.168828641
Au -1 6.097972078 4.030047441 10.24315388
Au -1 4.02852714 6.103771506 10.23281613
Au -1 6.103955516 6.100017782 8.173392305
Au 0 -0.105742597 -0.107250925 12.31006325
Au 0 1.958219527 -0.106407399 14.37981901
Au 0 -0.106318609 1.962591757 14.37998728
Au 0 1.965496162 1.9640177 12.30950882
Au 0 4.028809863 -0.110936508 12.32041903
Au 0 6.103803063 -0.107126394 14.37978038
Au 0 4.029545447 1.952813846 14.38413203
Au 0 6.097946043 1.962549282 12.31025073
Au -1 -0.10541945 4.030493698 12.30990333
Au -1 1.9636217 4.039699677 14.38397381
Au -1 1.964152272 6.103690334 12.32002979
Au -1 4.027937847 4.029141231 12.309527
Au -1 6.099026591 4.03096867 14.38011203
Au -1 4.034166199 6.099507849 14.37986718
Au -1 6.098221034 6.100471253 12.31074101
Au 0 8.169303897 -0.107088897 8.172998013
Au 0 10.24429637 -0.110818714 10.23312609
Au 0 8.174763135 1.962539691 10.24305171
Au 0 10.24427889 1.953172282 8.169145352
Au 0 12.31443364 -0.106617427 8.173157632
Au 0 14.37859285 -0.107580526 10.24238667
Au 0 12.307872 1.963716285 10.24354675
Au 0 14.37890404 1.961905252 8.172955331
Au -1 8.174068129 4.030284854 8.173192708
Au -1 10.24565854 4.029153839 10.24360727
Au -1 8.174669921 6.100093377 10.24289344
Au -1 10.23886588 6.099407109 8.173367256
Au -1 12.30974664 4.040056972 8.168745349
Au -1 14.3778573 4.030393781 10.2427932
Au -1 12.30896384 6.103801617 10.23270602
Au -1 14.38430447 6.100160741 8.173368684
Au 0 8.174358566 -0.107334796 12.31025502
Au 0 10.23882241 -0.106481136 14.37989878
Au 0 8.17374741 1.962409134 14.38011457
Au 0 10.24562189 1.9638841 12.30971547
Au 0 12.30896575 -0.110907628 12.32012273
Au 0 14.38364416 -0.106773053 14.3794082
Au 0 12.30973836 1.953108318 14.38412088
Au 0 14.37794273 1.962847693 12.30988596
Au -1 8.174772567 4.030251307 12.31001218
Au -1 10.24368676 4.039594667 14.38402548
Au -1 8.169160822 6.100241203 14.3798991
Au -1 10.24475746 6.103654283 12.32021449
Au -1 12.30797253 4.029302002 12.3092692
Au -1 14.37912548 4.030811334 14.38014928
Au -1 12.31462635 6.099478716 14.38002931
Au -1 14.3785305 6.100462042 12.31074091

H C N 0
def2TZVP
****
Au 0
LANL2DZ
****

Au 0
LANL2DZ

After 128 cycles the calculation terminated due to an error. The ending of the .log file looks like this:

Cycle 127  Pass 1  IDiag  1:
 RMSU=  1.40D-06    CP:  1.00D+00 -2.25D+00 -2.73D-01  2.44D+00 -3.00D+00
                    CP:  7.55D-01
 E= -17784.2869983765     Delta-E=       -0.000000032014 Rises=F Damp=F
 DIIS: error= 6.70D-06 at cycle 127 NSaved=  14.
 NSaved=14 IEnMin= 9 EnMin= -17784.2870124687     IErMin=14 ErrMin= 6.70D-06
 ErrMax= 6.70D-06  0.00D+00 EMaxC= 1.00D-01 BMatC= 3.40D-07 BMatP= 2.30D-07
 IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00
 Large coefficients: NSaved= 14 BigCof=   13.54 CofMax=   10.00 Det=-3.94D-11
 Inversion failed.  Reducing to 13 matrices.
 Large coefficients: NSaved= 13 BigCof=   10.03 CofMax=   10.00 Det=-4.35D-11
 Inversion failed.  Reducing to 12 matrices.
 Coeff-Com:  0.166D+00 0.282D+00 0.433D+00 0.348D+00 0.160D+01 0.988D+00
 Coeff-Com: -0.604D+01 0.266D+01 0.198D+00 0.131D+00 0.175D+00 0.573D-01
 Coeff:      0.166D+00 0.282D+00 0.433D+00 0.348D+00 0.160D+01 0.988D+00
 Coeff:     -0.604D+01 0.266D+01 0.198D+00 0.131D+00 0.175D+00 0.573D-01
 Gap=     0.014 Goal=   None    Shift=    0.000
 Gap=     0.016 Goal=   None    Shift=    0.000
 RMSDP=1.23D-04 MaxDP=2.26D-02 DE=-3.20D-08 OVMax= 1.36D-02

 Cycle 128  Pass 1  IDiag  1:
 RMSU=  9.96D-07    CP:  1.00D+00  4.61D-01  6.36D-01  5.27D-01 -1.83D+00
                    CP:  3.23D-01  7.69D-01
 E= -17784.2870030630     Delta-E=       -0.000004686532 Rises=F Damp=F
 DIIS: error= 7.00D-06 at cycle 128 NSaved=  13.
 NSaved=13 IEnMin= 9 EnMin= -17784.2870124687     IErMin=12 ErrMin= 6.70D-06
 ErrMax= 7.00D-06  0.00D+00 EMaxC= 1.00D-01 BMatC= 4.72D-07 BMatP= 2.30D-07
 IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00
 Large coefficients: NSaved= 13 BigCof=   10.76 CofMax=   10.00 Det=-5.44D-11
 Inversion failed.  Reducing to 12 matrices.
 Coeff-Com:  0.218D+00 0.291D+00 0.398D+00 0.325D+00 0.190D+01 0.117D+01
 Coeff-Com: -0.702D+01 0.314D+01 0.194D+00 0.150D+00 0.986D-01 0.137D+00
 Coeff:      0.218D+00 0.291D+00 0.398D+00 0.325D+00 0.190D+01 0.117D+01
 Coeff:     -0.702D+01 0.314D+01 0.194D+00 0.150D+00 0.986D-01 0.137D+00
 Gap=     0.014 Goal=   None    Shift=    0.000
 Gap=     0.016 Goal=   None    Shift=    0.000
 RMSDP=8.66D-06 MaxDP=1.38D-03 DE=-4.69D-06 OVMax= 9.27D-04

 >>>>>>>>>> Convergence criterion not met.
SCF Done:  E(UB3LYP) =  -17784.2870031     A.U. after  129 cycles
            NFock=128  Conv=0.87D-05     -V/T= 3.9415
 <Sx>= 0.0000 <Sy>= 0.0000 <Sz>= 0.5000 <S**2>= 1.7335 S= 0.9084
 <L.S>=  0.00000000000    
 KE= 6.045904443211D+03 PE=-4.699311015858D+05 EE= 2.294861147025D+05
 Annihilation of the first spin contaminant:
 S**2 before annihilation     1.7335,   after     0.7928
 Convergence failure -- run terminated.
 Error termination via Lnk1e in /opt/g16/l502.exe at Fri Nov  4 12:04:39 2022.
 Job cpu time:     139 days 18 hours 50 minutes 34.0 seconds.
 Elapsed time:       8 days 17 hours 44 minutes 29.2 seconds.
 File lengths (MBytes):  RWF=  11366 Int=      0 D2E=      0 Chk=    334 Scr=      1
Error: segmentation violation
   rax 0000000000000000, rbx ffffffffffffffff, rcx 00002b90b86e5577
   rdx 000000000000ff77, rsp 00007fff42825978, rbp 00007fff42825ef0
   rsi 000000000000000b, rdi 000000000000ff77, r8  0000000000000020
   r9  0000000000000401, r10 000000007c998911, r11 0000000000000206
   r12 00007fff42825f38, r13 0000000000000000, r14 0000000000000000
   r15 00000000000003e6
  /lib64/libpthread.so.0(+0x11c00) [0x2b90b81a4c00]
  /lib64/libc.so.6(kill+0x7) [0x2b90b86e5577]
  /opt/g16/l502.exe() [0x4747c5]
  /opt/g16/l502.exe() [0x499bda]
  /opt/g16/l502.exe() [0x51679b]
  /opt/g16/l502.exe() [0x4f58bf]
  /opt/g16/l502.exe() [0x41df52]
  /opt/g16/l502.exe() [0x412b1b]
  /opt/g16/l502.exe() [0x412a24]
  /lib64/libc.so.6(__libc_start_main+0xf5) [0x2b90b86d0a35]
  /opt/g16/l502.exe() [0x40d169]

I am now trying to restart the calculation at this point but can't seem to make it work. I tried different methods shown at this website.

My header looked like this:

%cpu=16-31
%mem=120GB
%chk=mychk.chk
#p Opt=Restart b3lyp/genecp nosymm int=ultrafine

title

...

or this:

%cpu=0-15
%mem=120GB
%oldchk=mychk.chk
%Chk=newchk.chk
#p opt b3lyp/genecp nosymm int=ultrafine Geom=(AllCheck,Step=128) Guess=Read

No matter what I try I'm getting an error looking like this:

...
 dumping /fiocom/, unit = 3 NFiles =     1 SizExt =    524288 WInBlk =       512
                   defal = F LstWrd =       65536 FType=2 FMxFil=10000

 Number              0
 Base            40448
 End             65536
 End1            65536
 Wr Pntr         40448
 Rd Pntr         40448
 Length          25088
 Int.Num             1
 FileIO operation on non-existent file.
 FileIO: IOper= 2 IFilNo(1)=  -997 Len=          20 IPos=           0 Q=  140725376322144
 Error termination in NtrErr:
 NtrErr Called from FileIO.
Error: segmentation violation
   rax 0000000000000000, rbx 0000000006070a30, rcx 00002b18d0862577
   rdx 0000000000001437, rsp 00007ffd2e1105f8, rbp 00007ffd2e110630
   rsi 000000000000000b, rdi 0000000000001437, r8  0000000000000020
   r9  0000000000000401, r10 000000007c998911, r11 0000000000000202
   r12 00007ffd2e110a00, r13 00007ffd2e110968, r14 00007ffd2e110a60
   r15 000000000608d710
  /lib64/libpthread.so.0(+0x11c00) [0x2b18d0321c00]
  /lib64/libc.so.6(kill+0x7) [0x2b18d0862577]
  /opt/g16/l103.exe() [0x474e65]
  /opt/g16/l103.exe() [0x4f3f19]
  /opt/g16/l103.exe() [0x4a7625]
  /opt/g16/l103.exe() [0x53d1a8]
  /opt/g16/l103.exe() [0x53cc31]
  /opt/g16/l103.exe() [0x4928cf]
  /opt/g16/l103.exe() [0x4922ee]
  /opt/g16/l103.exe() [0x412c3b]
  /opt/g16/l103.exe() [0x4126a2]
  /opt/g16/l103.exe() [0x4125a4]
  /lib64/libc.so.6(__libc_start_main+0xf5) [0x2b18d084da35]
  /opt/g16/l103.exe() [0x40cce9]

I don't understand what I am doing wrong and I would much appreciate any tips or input from the community.

Thank you very much in advance.

$\endgroup$
2
  • 2
    $\begingroup$ From the link you shared, two things get my attention: (1) If a geometry optimization is terminated before completion due to an external factor (e.g., due to a machine crash, a power failure, manually killing the job), you can restart the job. (2) If the required file(s) have been deleted, then the job cannot be restarted. In your case, the job stopped no due "external factors", but instead, due to bad convergence. $\endgroup$
    – Camps
    Nov 6, 2022 at 21:30
  • $\begingroup$ Thank you for your answer. I'm gonna restart the job file with a different starting geometry. $\endgroup$ Nov 7, 2022 at 8:33

1 Answer 1

2
$\begingroup$

The excerpt you pasted states that the SCF calculation failed, and one cannot tell when this happened. Was it at the initial geometry? You may get the calculation to work with SCF=XQC.

However, I have further comments on the input.

  1. Why do you not use def2TZVP for gold as well? def2TZVP is available for the whole periodic table up to $Z=86$.

  2. Usually it helps to preoptimize with a smaller basis set, if the initial geometry is bad. The xtb program is often very useful as well, as the tight binding calculations run very quickly and rarely have convergence issues, and the geometries are much improved if you start from a poor guess. Alternatively, you could preoptimize the geometry with def2SVP, or def2-SV(P) on all atoms. These are available in Gaussian as def2SVP and def2SVPP. SCF convergence should likewise be less of an issue in the smaller basis, and you should be able to afford the quadratic convergence procedure. The preoptimized geometry will likewise work a lot better in the TZVP calculation.

$\endgroup$

You must log in to answer this question.

Not the answer you're looking for? Browse other questions tagged .