Energy calculation error

Shreshth · June 26, 2024, 8:24am

I am trying to calculate energy between graphene oxide and water in spi4. But I m getting an error

My input file:

molecule {
0 2
C -4.86976 -6.56484 2.14932
C -3.61171 -5.74443 2.08807
C -2.40021 -6.39187 1.89961
C -1.17743 -5.68727 1.84226
C -1.19745 -4.29375 1.98120
C -2.41564 -3.59902 2.16835
C -3.64606 -4.32297 2.23086
C -4.86347 -3.58351 2.34449
C -4.87109 -2.21751 2.30798
C -3.66712 -1.45070 2.20226
C -2.43659 -2.14712 2.19784
C -1.20818 -1.41762 2.15252
C -1.21311 -0.06072 1.91188
C -2.44018 0.68062 1.91703
C -3.66488 -0.00814 2.11026
C -4.87086 0.75438 2.19888
C -4.86751 2.11436 2.09200
C -3.65783 2.84250 1.88584
C -2.42800 2.12443 1.81039
C -1.21152 2.84385 1.66904
C -1.21591 4.23574 1.59026
C -2.42794 4.94006 1.65653
C -3.62932 4.26465 1.78289
O -4.75756 5.02669 1.82575
C 0.08158 -6.37893 1.61209
C 1.27986 -5.75955 1.76067
C 2.53433 -6.44949 1.60234
C 3.73701 -5.88692 1.86834
C 3.86642 -4.44792 2.33194
C 2.62530 -3.61043 2.03767
C 0.09552 -3.52591 1.70378
H 0.04344 -7.42994 1.33267
H 2.52018 -7.48903 1.28390
C 0.04247 -2.19163 2.47581
C 1.36005 -1.37448 2.56309
C 2.63696 -2.13665 2.15412
C 3.84773 -1.30417 2.42100
C 2.61204 0.68171 1.50437
C 1.33027 -0.04573 1.87588
C 0.06594 0.62584 1.60094
C 0.07348 2.11561 1.50941
C 1.34202 2.82783 1.85148
C 2.52262 2.18011 1.85379
C 3.82270 2.92066 2.02845
C 3.69618 4.41696 2.07119
C 2.51068 5.03355 2.13033
C 1.20744 4.29237 2.25092
C 0.09920 4.96461 1.41556
H 2.43313 6.11992 2.12359
H 4.50511 2.65648 1.20871
H -5.81572 2.63608 2.20337
H -5.81426 0.25173 2.37396
H -5.82939 -1.71365 2.35542
H -5.79470 -4.12674 2.44388
C 4.99063 5.17291 1.97147
O 5.97112 4.72137 1.42684
O 5.02200 6.41352 2.52659
H 4.22712 6.54598 3.06975
O -5.79348 -6.36167 2.90182
O -4.92081 -7.62015 1.28870
H -4.18520 -7.56160 0.65594
H -5.54548 4.46600 1.76736
C 4.94056 -6.76897 1.74333
O 4.89583 -7.91891 1.36777
O 6.14268 -6.23033 2.09415
H 6.04379 -5.30567 2.37137
O 2.69988 -2.78580 0.86868
O 0.09228 1.30901 0.27627
O 2.84229 0.57806 0.07503
H 2.02317 0.92072 -0.33376
O 0.22250 -3.41135 0.30314
H -0.54603 -2.93103 -0.08123
H -2.44427 6.02399 1.59385
H -2.37387 -7.47695 1.82047
O 1.47645 -1.13640 4.00329
H 2.26984 -0.58885 4.13583
O 0.87522 4.39844 3.65490
H -0.04617 4.10178 3.75837
C 3.82610 0.00028 2.12511
H 4.76210 -1.77255 2.77642
H 4.73426 0.58434 2.22420
C 1.29290 -4.32826 2.25356
H 1.15030 -4.38286 3.34678
H -0.00061 6.01066 1.72651
H 0.39460 4.96460 0.35656
H -0.10782 -2.50394 3.51940
H 4.70438 -3.95187 1.82428
H 4.07813 -4.41938 3.41399
H 4.33890 2.59398 2.94424

0 1
O -1.65486 -1.79724 -1.05222
H -1.12444 -0.98623 -1.11751
H -2.41939 -1.53436 -0.51583
units angstrom
}
set {
basis 6-311G(2DF,P)
}

energy(‘b3lyp’)

The ouput I get is: It’s an error

==> Geometry <==

Molecular point group: c1
Full point group: C1

Geometry (in Angstrom), charge = 0, multiplicity = 2:

   Center              X                  Y                   Z               Mass       
------------   -----------------  -----------------  -----------------  -----------------
     C           -4.961726394750    -5.669200251827     0.291461747997    12.000000000000
     C           -3.703676394750    -4.848790251827     0.230211747997    12.000000000000
     C           -2.492176394750    -5.496230251827     0.041751747997    12.000000000000
     C           -1.269396394750    -4.791630251827    -0.015598252003    12.000000000000
     C           -1.289416394750    -3.398110251827     0.123341747997    12.000000000000
     C           -2.507606394750    -2.703380251827     0.310491747997    12.000000000000
     C           -3.738026394750    -3.427330251827     0.373001747997    12.000000000000
     C           -4.955436394750    -2.687870251827     0.486631747997    12.000000000000
     C           -4.963056394750    -1.321870251827     0.450121747997    12.000000000000
     C           -3.759086394750    -0.555060251827     0.344401747997    12.000000000000
     C           -2.528556394750    -1.251480251827     0.339981747997    12.000000000000
     C           -1.300146394750    -0.521980251827     0.294661747997    12.000000000000
     C           -1.305076394750     0.834919748173     0.054021747997    12.000000000000
     C           -2.532146394750     1.576259748173     0.059171747997    12.000000000000
     C           -3.756846394750     0.887499748173     0.252401747997    12.000000000000
     C           -4.962826394750     1.650019748173     0.341021747997    12.000000000000
     C           -4.959476394750     3.009999748173     0.234141747997    12.000000000000
     C           -3.749796394750     3.738139748173     0.027981747997    12.000000000000
     C           -2.519966394750     3.020069748173    -0.047468252003    12.000000000000
     C           -1.303486394750     3.739489748173    -0.188818252003    12.000000000000
     C           -1.307876394750     5.131379748173    -0.267598252003    12.000000000000
     C           -2.519906394750     5.835699748173    -0.201328252003    12.000000000000
     C           -3.721286394750     5.160289748173    -0.074968252003    12.000000000000
     O           -4.849526394750     5.922329748173    -0.032108252003    15.994914619570
     C           -0.010386394750    -5.483290251827    -0.245768252003    12.000000000000
     C            1.187893605250    -4.863910251827    -0.097188252003    12.000000000000
     C            2.442363605250    -5.553850251827    -0.255518252003    12.000000000000
     C            3.645043605250    -4.991280251827     0.010481747997    12.000000000000
     C            3.774453605250    -3.552280251827     0.474081747997    12.000000000000
     C            2.533333605250    -2.714790251827     0.179811747997    12.000000000000
     C            0.003553605250    -2.630270251827    -0.154078252003    12.000000000000
     H           -0.048526394750    -6.534300251827    -0.525188252003     1.007825032230
     H            2.428213605250    -6.593390251827    -0.573958252003     1.007825032230
     C           -0.049496394750    -1.295990251827     0.617951747997    12.000000000000
     C            1.268083605250    -0.478840251827     0.705231747997    12.000000000000
     C            2.544993605250    -1.241010251827     0.296261747997    12.000000000000
     C            3.755763605250    -0.408530251827     0.563141747997    12.000000000000
     C            2.520073605250     1.577349748173    -0.353488252003    12.000000000000
     C            1.238303605250     0.849909748173     0.018021747997    12.000000000000
     C           -0.026026394750     1.521479748173    -0.256918252003    12.000000000000
     C           -0.018486394750     3.011249748173    -0.348448252003    12.000000000000
     C            1.250053605250     3.723469748173    -0.006378252003    12.000000000000
     C            2.430653605250     3.075749748173    -0.004068252003    12.000000000000
     C            3.730733605250     3.816299748173     0.170591747997    12.000000000000
     C            3.604213605250     5.312599748173     0.213331747997    12.000000000000
     C            2.418713605250     5.929189748173     0.272471747997    12.000000000000
     C            1.115473605250     5.188009748173     0.393061747997    12.000000000000
     C            0.007233605250     5.860249748173    -0.442298252003    12.000000000000
     H            2.341163605250     7.015559748173     0.265731747997     1.007825032230
     H            4.413143605250     3.552119748173    -0.649148252003     1.007825032230
     H           -5.907686394750     3.531719748173     0.345511747997     1.007825032230
     H           -5.906226394750     1.147369748173     0.516101747997     1.007825032230
     H           -5.921356394750    -0.818010251827     0.497561747997     1.007825032230
     H           -5.886666394750    -3.231100251827     0.586021747997     1.007825032230
     C            4.898663605250     6.068549748173     0.113611747997    12.000000000000
     O            5.879153605250     5.617009748173    -0.431018252003    15.994914619570
     O            4.930033605250     7.309159748173     0.668731747997    15.994914619570
     H            4.135153605250     7.441619748173     1.211891747997     1.007825032230
     O           -5.885446394750    -5.466030251827     1.043961747997    15.994914619570
     O           -5.012776394750    -6.724510251827    -0.569158252003    15.994914619570
     H           -4.277166394750    -6.665960251827    -1.201918252003     1.007825032230
     H           -5.637446394750     5.361639748173    -0.090498252003     1.007825032230
     C            4.848593605250    -5.873330251827    -0.114528252003    12.000000000000
     O            4.803863605250    -7.023270251827    -0.490088252003    15.994914619570
     O            6.050713605250    -5.334690251827     0.236291747997    15.994914619570
     H            5.951823605250    -4.410030251827     0.513511747997     1.007825032230
     O            2.607913605250    -1.890160251827    -0.989178252003    15.994914619570
     O            0.000313605250     2.204649748173    -1.581588252003    15.994914619570
     O            2.750323605250     1.473699748173    -1.782828252003    15.994914619570
     H            1.931203605250     1.816359748173    -2.191618252003     1.007825032230
     O            0.130533605250    -2.515710251827    -1.554718252003    15.994914619570
     H           -0.637996394750    -2.035390251827    -1.939088252003     1.007825032230
     H           -2.536236394750     6.919629748173    -0.264008252003     1.007825032230
     H           -2.465836394750    -6.581310251827    -0.037388252003     1.007825032230
     O            1.384483605250    -0.240760251827     2.145431747997    15.994914619570
     H            2.177873605250     0.306789748173     2.277971747997     1.007825032230
     O            0.783253605250     5.294079748173     1.797041747997    15.994914619570
     H           -0.138136394750     4.997419748173     1.900511747997     1.007825032230
     C            3.734133605250     0.895919748173     0.267251747997    12.000000000000
     H            4.670133605250    -0.876910251827     0.918561747997     1.007825032230
     H            4.642293605250     1.479979748173     0.366341747997     1.007825032230
     C            1.200933605250    -3.432620251827     0.395701747997    12.000000000000
     H            1.058333605250    -3.487220251827     1.488921747997     1.007825032230
     H           -0.092576394750     6.906299748173    -0.131348252003     1.007825032230
     H            0.302633605250     5.860239748173    -1.501298252003     1.007825032230
     H           -0.199786394750    -1.608300251827     1.661541747997     1.007825032230
     H            4.612413605250    -3.056230251827    -0.033578252003     1.007825032230
     H            3.986163605250    -3.523740251827     1.556131747997     1.007825032230
     H            4.246933605250     3.489619748173     1.086381747997     1.007825032230
     O           -1.746826394750    -0.901600251827    -2.910078252003    15.994914619570
     H           -1.216406394750    -0.090590251827    -2.975368252003     1.007825032230
     H           -2.511356394750    -0.638720251827    -2.373688252003     1.007825032230

Running in c1 symmetry.

Rotational constants: A = 0.00178 B = 0.00114 C = 0.00073 [cm^-1]
Rotational constants: A = 53.42050 B = 34.31560 C = 21.87572 [MHz]
Nuclear repulsion = 9595.354118558645496

Charge = 0
Multiplicity = 2
Electrons = 435
Nalpha = 218
Nbeta = 217

==> Algorithm <==

SCF Algorithm Type is DF.
DIIS enabled.
MOM disabled.
Fractional occupation disabled.
Guess Type is SAD.
Energy threshold = 1.00e-06
Density threshold = 1.00e-06
Integral threshold = 1.00e-12

==> Primary Basis <==

Basis Set: 6-311G(2DF,P)
Blend: 6-311G(2DF,P)
Number of shells: 746
Number of basis functions: 2064
Number of Cartesian functions: 2379
Spherical Harmonics?: true
Max angular momentum: 3

==> DFT Potential <==

=> LibXC <=

Version 5.1.5
S. Lehtola, C. Steigemann, M. J. Oliveira, and M. A. Marques, SoftwareX 7, 1 (2018) (10.1016/j.softx.2017.11.002)

=> Composite Functional: B3LYP <=

B3LYP Hyb-GGA Exchange-Correlation Functional

P. J. Stephens, F. J. Devlin, C. F. Chabalowski, and M. J. Frisch, J. Phys. Chem. 98, 11623 (1994) (10.1021/j100096a001)

Deriv               =              1
GGA                 =           TRUE
Meta                =          FALSE

Exchange Hybrid     =           TRUE
MP2 Hybrid          =          FALSE

=> Exchange Functionals <=

0.0800   Slater exchange
0.7200         Becke 88

=> Exact (HF) Exchange <=

0.2000               HF

=> Correlation Functionals <=

0.1900   Vosko, Wilk & Nusair (VWN5_RPA)
0.8100   Lee, Yang & Parr

=> LibXC Density Thresholds <==

XC_HYB_GGA_XC_B3LYP:  1.00E-15

=> Molecular Quadrature <=

Radial Scheme          =       TREUTLER
Pruning Scheme         =           NONE
Nuclear Scheme         =       TREUTLER

BS radius alpha        =              1
Pruning alpha          =              1
Radial Points          =             75
Spherical Points       =            302
Total Points           =        1819580
Total Blocks           =          12418
Max Points             =            256
Max Functions          =            915
Weights Tolerance      =       1.00E-15

Traceback (most recent call last):
File “/usr/local/bin/psi4”, line 333, in
exec(content)
File “”, line 118, in
File “/usr/local/lib//python3.8/site-packages/psi4/driver/driver.py”, line 597, in energy
wfn = procedures[‘energy’][lowername](lowername, molecule=molecule, **kwargs)
File “/usr/local/lib//python3.8/site-packages/psi4/driver/procrouting/proc.py”, line 2390, in run_scf
scf_wfn = scf_helper(name, post_scf=False, **kwargs)
File “/usr/local/lib//python3.8/site-packages/psi4/driver/procrouting/proc.py”, line 1513, in scf_helper
scf_wfn = scf_wavefunction_factory(name, base_wfn, core.get_option(‘SCF’, ‘REFERENCE’), **kwargs)
File “/usr/local/lib//python3.8/site-packages/psi4/driver/procrouting/proc.py”, line 1186, in scf_wavefunction_factory
wfn = core.RHF(ref_wfn, superfunc)

RuntimeError:
Fatal Error: RHF: RHF reference is only for singlets.
Error occurred in file: /scratch/psilocaluser/conda-builds/psi4-multiout_1628017372763/work/psi4/src/psi4/libscf_solver/rhf.cc on line: 94
The most recent 5 function calls were:

Printing out the relevant lines from the Psithon → Python processed input file:
H -2.41939 -1.53436 -0.51583
units angstrom
“”“)
core.IO.set_default_namespace(”")
core.set_global_option(“BASIS”, “6-311G(2DF,P)”)
→ energy(‘b3lyp’)

!----------------------------------------------------------------------------------!
! !
! Fatal Error: RHF: RHF reference is only for singlets. !
! Error occurred in file: /scratch/psilocaluser/conda- !
! builds/psi4-multiout_1628017372763/work/psi4/src/psi4/libscf_solver/rhf.cc !
! on line: 94 !
! The most recent 5 function calls were: !
! !
!----------------------------------------------------------------------------------!

Psi4 stopped on: Wednesday, 26 June 2024 01:19AM
Psi4 wall time for execution: 0:00:20.30

*** Psi4 encountered an error. Buy a developer more coffee!
*** Resources and help at GitHub - psi4/psi4: Open-Source Quantum Chemistry – an electronic structure package in C++ driven by Python.

jmisiewicz · June 26, 2024, 12:16pm

Please follow our best practices for posting topics. I specifically refer you to backticks.
Have you been able to identify the error message? If so, do you understand the error message?

Shreshth · June 26, 2024, 12:48pm

I understand this aspect
Fatal Error: RHF: RHF reference is only for singlets.

but I haven’t used rhf as an reference

But I didn’t understand the error completely.

jmisiewicz · June 26, 2024, 1:25pm

Psi4 defaults to an RHF reference. Reference “RHF” and “RKS” are the same for Psi4’s purposes, if you’re hung up on that.

Shreshth · June 26, 2024, 2:04pm

I updated the input file and used reference as uhf

I m gettiing this error,
Traceback (most recent call last):
File “/usr/local/bin/psi4”, line 333, in
exec(content)
File “”, line 119, in
File “/usr/local/lib//python3.8/site-packages/psi4/driver/driver.py”, line 597, in energy
wfn = procedures[‘energy’][lowername](lowername, molecule=molecule, **kwargs)
File “/usr/local/lib//python3.8/site-packages/psi4/driver/procrouting/proc.py”, line 2390, in run_scf
scf_wfn = scf_helper(name, post_scf=False, **kwargs)
File “/usr/local/lib//python3.8/site-packages/psi4/driver/procrouting/proc.py”, line 1607, in scf_helper
e_scf = scf_wfn.compute_energy()
File “/usr/local/lib//python3.8/site-packages/psi4/driver/procrouting/scf_proc/scf_iterator.py”, line 83, in scf_compute_energy
self.initialize()
File “/usr/local/lib//python3.8/site-packages/psi4/driver/procrouting/scf_proc/scf_iterator.py”, line 193, in scf_initialize
self.initialize_jk(self.memory_jk_, jk=jk)
File “/usr/local/lib//python3.8/site-packages/psi4/driver/procrouting/scf_proc/scf_iterator.py”, line 128, in initialize_jk
jk.initialize()

RuntimeError:
Fatal Error: SCF::DF: Disk based algorithm requires 2 (A|B) fitting metrics and an (A|mn) chunk on core.
This is 2Q^2 + QNP doubles, where Q is the auxiliary basis size, N is the
primary basis size, and P is the maximum number of functions in a primary shell.
For this problem, that is 543495968 bytes before taxes,776422811 bytes after taxes.

Error occurred in file: /scratch/psilocaluser/conda-builds/psi4-multiout_1628017372763/work/psi4/src/psi4/libfock/DiskDFJK.cc on line: 727
The most recent 5 function calls were:

psi::DiskDFJK::preiterations()

Printing out the relevant lines from the Psithon → Python processed input file:
units angstrom
“”“)
core.IO.set_default_namespace(”")
core.set_global_option(“BASIS”, “6-31G(d)”)
core.set_global_option(“REFERENCE”, “uhf”)
→ energy(‘b3lyp’)

!----------------------------------------------------------------------------------!
! !
! Fatal Error: SCF::DF: Disk based algorithm requires 2 (A|B) fitting metrics and !
! an (A|mn) chunk on core. !
! This is 2Q^2 + QNP doubles, where Q is the auxiliary basis size, N is !
! the !
! primary basis size, and P is the maximum number of functions in a !
! primary shell. !
! For this problem, that is 543495968 bytes before taxes,776422811 bytes !
! after taxes. !
! Error occurred in file: /scratch/psilocaluser/conda- !
! builds/psi4-multiout_1628017372763/work/psi4/src/psi4/libfock/DiskDFJK.cc on !
! line: 727 !
! The most recent 5 function calls were: !
! psi::DiskDFJK::preiterations() !
! !
!----------------------------------------------------------------------------------!

Psi4 stopped on: Wednesday, 26 June 2024 10:01AM
Psi4 wall time for execution: 0:00:13.64

*** Psi4 encountered an error. Buy a developer more coffee!
*** Resources and help at GitHub - psi4/psi4: Open-Source Quantum Chemistry – an electronic structure package in C++ driven by Python.

P.S. I m using PSI4 server on chemcompute

Shreshth · June 26, 2024, 2:43pm

I updated the input file and set memory 60 GB. and it’s running right now.

jmisiewicz · June 26, 2024, 4:03pm

60 GB is much much more than you would need, by the way.

Shreshth · June 27, 2024, 11:22am

Thanks. I encountered another error though. All same in input file except i m calculation sapto and using basis set as 6-31G(d).

Error
Fatal Error: Monomer A: A Matrix is not SPD !
! Error occurred in file: /scratch/psilocaluser/conda- !
! builds/psi4-multiout_1628017372763/work/psi4/src/psi4/libsapt_solver/usapt0. !
! cc on line: 1609

jmisiewicz · June 27, 2024, 1:15pm

This is a common error with SAPT0 and means that SCF is not finding the correct ground state. Technically, it means it has not found a local minimum in orbital-space, probably related to ghost atoms. Use stability_analysis: follow.

Shreshth · July 4, 2024, 12:23pm

I used some updated file : Just typing import part
memory 64 gb

no_reorient
symmetry c1
}

set globals {
basis jun-cc-pVDZ
scf_type DF
reference ROHF
freeze_core True
soscf true
soscf_max_iter 150
}

energy(‘sapt0’)

I got this error:
Fatal Error: DFHelper:get_tensor: read error !
! Error occurred in file: /scratch/psilocaluser/conda- !
! builds/psi4-multiout_1628017372763/work/psi4/src/psi4/lib3index/dfhelper.cc !
! on line: 1041 !
! The most recent 5 function calls were: !
! psi::DFHelper::get_tensor_(std::_cxx11::basic_string, std::allocator >, double*, unsigned long, !
! unsigned long, unsigned long, unsigned long) !
! psi::DFHelper::get_tensor(std::__cxx11::basic_string, std::allocator >, double*, std::pair, std::pair, !
! std::pair) !
! psi::DFHelper::fill_tensor(std::__cxx11::basic_string, std::allocator >, !
! std::shared_ptr, std::vector >) !
!

I have searched on internet and it tells they should be increased memory. I have provided 64 gb which should be more than enough

jmisiewicz · July 8, 2024, 1:39pm

This isn’t enough information. Please follow the guidelines here. If you can’t share your molecule, I at least need to know the number of basis functions, Psi4 version number, and the last part of the output file before the error message.