Frequency calculation on an optimized geometry + thermodynamic analysis

I am trying to do a frequency calculation and also get the thermodynamic corrections. This is my input file.

memory 48 Gb

molecule sco {
2 1
Fe -0.8927096298 7.8573022815 14.2264600261
N -0.7386040277 9.6912294368 15.1577449739
H 0.1349346868 9.8803952771 15.6582160656
H -0.7790336546 10.3959795165 14.4146724473
N -2.8753826910 8.2293349715 14.5853548724
N -1.2515212753 5.9761767639 13.5033091293
H -1.8748837923 5.9390026852 12.6906624631
H -0.3694636100 5.5771086727 13.1674937090
N -0.6518062206 6.7848375242 15.9350501554
N 1.1042588792 7.7348595927 13.8298824651
H 1.6580081246 7.7793164514 14.6903144923
H 1.3598340664 6.8421713367 13.3938146262
N -0.8803414777 8.7557336218 12.3992058235
C -1.8976242063 9.8944094131 16.0689605133
H -2.0842620738 10.9598311709 16.2596997333
H -1.6618845365 9.4285580764 17.0350921073
C -3.1147736335 9.2373283577 15.4683654447
C -4.4095526521 9.6389445950 15.8121349800
H -4.5440669407 10.4581597032 16.5167134943
C -5.5065737118 8.9886900334 15.2435406141
H -6.5221309637 9.2851313123 15.5013641467
C -5.2683626313 7.9609855731 14.3255689446
H -6.0835195174 7.4288023263 13.8396142098
C -3.9508279973 7.6213560965 14.0244946307
H -3.7462525072 6.8398576275 13.2972295114
C -1.7742005184 5.1019880874 14.5933664660
H -1.6032140050 4.0384995871 14.3801575104
H -2.8592305412 5.2493086300 14.6697330493
C -1.1099774047 5.5044572180 15.8871410991
C -0.9716288986 4.6237622923 16.9634466996
H -1.3488351380 3.6062589339 16.8743596175
C -0.3439763515 5.0613753303 18.1324824177
H -0.2284054542 4.3914734191 18.9831397958
C 0.1488787105 6.3694590605 18.1771228506
H 0.6625172325 6.7554215391 19.0552540775
C -0.0198940493 7.1900123069 17.0628534747
H 0.3750352502 8.2032182276 17.0684178224
C 1.4891680401 8.8516394796 12.9238133047
H 2.4303896756 8.6523027369 12.3946268686
H 1.6433970400 9.7444140057 13.5457924793
C 0.3604190950 9.0998117462 11.9529025840
C 0.5671498255 9.6704041760 10.6946027202
H 1.5793257378 9.9163790903 10.3774744461
C -0.5300901413 9.9134267338 9.8636826160
H -0.3908333936 10.3581261079 8.8794567454
C -1.8050996840 9.5652461904 10.3200029954
H -2.6918702751 9.7288973344 9.7109070059
C -1.9356136478 8.9896091614 11.5835171545
H -2.9109806057 8.6978171161 11.9608184029
}

b3lyphfx10 = {
“name”: “b3lyp_hfx10”,
“x_functionals”: {“GGA_X_B88”: {“alpha”: 0.81}, “LDA_X”: {“alpha”: 0.09}},
“x_hf”: {“alpha”: 0.10},
“c_functionals”: {“GGA_C_LYP”: {“alpha”: 0.81},“LDA_C_VWN_RPA”: {“alpha”: 0.19}}
}

set globals {
basis def2-tzvp
reference rhf
mp2_type df
maxiter 500
scf_type df
PRINT_MOS True
guess sad
}

set t 300.0
wfn = psi4.core.Wavefunction.from_file(“wfn.180.npy”)
sco_e, sco_wfn = freq(‘scf’, dft_functional=b3lyphfx10, molecule=sco, ref_gradient=wfn.gradient(), return_wfn=True)

print(get_variable(‘enthalpy correction’))
print(get_variable(‘enthalpy’))
print(get_variable(‘thermal energy correction’))
print(get_variable(‘thermal energy’))
print(get_variable(‘gibbs free energy correction’))
print(get_variable(‘gibbs free energy’))
print(get_variable(‘zpve’))

The output file shows this error:

hessian() using ref_gradient to assess stationary point.

Traceback (most recent call last):
File “/home/miniconda/envs/psi4_1.3.2/bin/psi4”, line 287, in
exec(content)
File “”, line 88, in
File “/home/miniconda/envs/psi4_1.3.2/lib//python3.7/site-packages/psi4/driver/driver.py”, line 1464, in frequency
H, wfn = hessian(name, return_wfn=True, molecule=molecule, **kwargs)
File “/home/miniconda/envs/psi4_1.3.2/lib//python3.7/site-packages/psi4/driver/driver.py”, line 1259, in hessian
translations_projection_sound, rotations_projection_sound = _energy_is_invariant(G0)
File “/home/miniconda/envs/psi4_1.3.2/lib//python3.7/site-packages/psi4/driver/driver.py”, line 118, in _energy_is_invariant
stationary_point = gradient.rms() < stationary_criterion # 1.e-2 pulled out of a hat

AttributeError: ‘NoneType’ object has no attribute ‘rms’

Printing out the relevant lines from the Psithon → Python processed input file:
core.set_global_option(“SCF_TYPE”, “df”)
core.set_global_option(“PRINT_MOS”, “True”)
core.set_global_option(“GUESS”, “sad”)
core.set_global_option(“T”, 300.0)
wfn = psi4.core.Wavefunction.from_file(“wfn.180.npy”)
→ sco_e, sco_wfn = freq(‘scf’, dft_functional=b3lyphfx10, molecule=sco, ref_gradient=wfn.gradient(), return_wfn=True)
print(get_variable(‘enthalpy correction’))
print(get_variable(‘enthalpy’))
print(get_variable(‘thermal energy correction’))
print(get_variable(‘thermal energy’))
print(get_variable(‘gibbs free energy correction’))

Psi4 stopped on: Friday, 17 February 2023 03:37PM
Psi4 wall time for execution: 0:00:00.61

*** 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.

Could someone please help me fix this error? Thank you so much!

  1. Please follow our guidelines for posting help topics. In particular, your input and output files are very difficult to read because you haven’t enclosed them in triple backticks.
  2. Why are you using Psi4 1.3.2? That’s nearly three years old.
  3. The crash is happening because you are passing in a value for ref_gradient, but Psi is not finding a gradient on that wavefunction. The most likely explanation is that there is no gradient on that wavefunction, though I would need a copy of the wfn.180.npy to confirm that. Either don’t pass in an argument for ref_gradient, or pass in a new wavefunction that actually does have a gradient.

Hi, sorry about not posting the input and output files according to the guidelines. I changed my input file and now have this instead.


molecule sco {
  2 1
    Fe    -0.8927096298    7.8573022815   14.2264600261
     N    -0.7386040277    9.6912294368   15.1577449739
     H     0.1349346868    9.8803952771   15.6582160656
     H    -0.7790336546   10.3959795165   14.4146724473
     N    -2.8753826910    8.2293349715   14.5853548724
     N    -1.2515212753    5.9761767639   13.5033091293
     H    -1.8748837923    5.9390026852   12.6906624631
     H    -0.3694636100    5.5771086727   13.1674937090
     N    -0.6518062206    6.7848375242   15.9350501554
     N     1.1042588792    7.7348595927   13.8298824651
     H     1.6580081246    7.7793164514   14.6903144923
     H     1.3598340664    6.8421713367   13.3938146262
     N    -0.8803414777    8.7557336218   12.3992058235
     C    -1.8976242063    9.8944094131   16.0689605133
     H    -2.0842620738   10.9598311709   16.2596997333
     H    -1.6618845365    9.4285580764   17.0350921073
     C    -3.1147736335    9.2373283577   15.4683654447
     C    -4.4095526521    9.6389445950   15.8121349800
     H    -4.5440669407   10.4581597032   16.5167134943
     C    -5.5065737118    8.9886900334   15.2435406141
     H    -6.5221309637    9.2851313123   15.5013641467
     C    -5.2683626313    7.9609855731   14.3255689446
     H    -6.0835195174    7.4288023263   13.8396142098
     C    -3.9508279973    7.6213560965   14.0244946307
     H    -3.7462525072    6.8398576275   13.2972295114
     C    -1.7742005184    5.1019880874   14.5933664660
     H    -1.6032140050    4.0384995871   14.3801575104
     H    -2.8592305412    5.2493086300   14.6697330493
     C    -1.1099774047    5.5044572180   15.8871410991
     C    -0.9716288986    4.6237622923   16.9634466996
     H    -1.3488351380    3.6062589339   16.8743596175
     C    -0.3439763515    5.0613753303   18.1324824177
     H    -0.2284054542    4.3914734191   18.9831397958
     C     0.1488787105    6.3694590605   18.1771228506
     H     0.6625172325    6.7554215391   19.0552540775
     C    -0.0198940493    7.1900123069   17.0628534747
     H     0.3750352502    8.2032182276   17.0684178224
     C     1.4891680401    8.8516394796   12.9238133047
     H     2.4303896756    8.6523027369   12.3946268686
     H     1.6433970400    9.7444140057   13.5457924793
     C     0.3604190950    9.0998117462   11.9529025840
     C     0.5671498255    9.6704041760   10.6946027202
     H     1.5793257378    9.9163790903   10.3774744461
     C    -0.5300901413    9.9134267338    9.8636826160
     H    -0.3908333936   10.3581261079    8.8794567454
     C    -1.8050996840    9.5652461904   10.3200029954
     H    -2.6918702751    9.7288973344    9.7109070059
     C    -1.9356136478    8.9896091614   11.5835171545
     H    -2.9109806057    8.6978171161   11.9608184029
}


b3lyphfx10 = {
    "name": "b3lyp_hfx10",
    "x_functionals": {"GGA_X_B88": {"alpha": 0.81}, "LDA_X": {"alpha": 0.09}},
    "x_hf": {"alpha": 0.10},
    "c_functionals": {"GGA_C_LYP": {"alpha": 0.81},"LDA_C_VWN_RPA": {"alpha": 0.19}}
}

set globals {
	basis def2-tzvp
	reference rhf
	mp2_type df
	maxiter 500
	scf_type df
        PRINT_MOS True
        guess sad
}

set t 300.0
frequency('scf', dft_functional=b3lyphfx10)

However, I get a different error this time in the output file.

  Nuclear repulsion = 2888.128317592217627

  ==> Basis Set <==

  Basis Set: DEF2-TZVP
    Blend: DEF2-TZVP
    Number of shells: 375
    Number of basis function: 933
    Number of Cartesian functions: 1060
    Spherical Harmonics?: true
    Max angular momentum: 3


Traceback (most recent call last):
  File "/home/miniconda/envs/psi4_1.3.2/bin/psi4", line 287, in <module>
    exec(content)
  File "<string>", line 87, in <module>
  File "/home/miniconda/envs/psi4_1.3.2/lib//python3.7/site-packages/psi4/driver/driver.py", line 1464, in frequency
    H, wfn = hessian(name, return_wfn=True, molecule=molecule, **kwargs)
  File "/home/miniconda/envs/psi4_1.3.2/lib//python3.7/site-packages/psi4/driver/driver.py", line 1272, in hessian
    wfn = procedures['hessian'][lowername](lowername, molecule=molecule, **kwargs)
  File "/home/miniconda/envs/psi4_1.3.2/lib//python3.7/site-packages/psi4/driver/procrouting/proc.py", line 2141, in run_scf_hessian
    H = core.scfhess(ref_wfn)

RuntimeError:
Fatal Error: Missing XC derivatives for Hessians
Error occurred in file: /scratch/psilocaluser/conda-builds/psi4-multiout_1563933640427/work/psi4/src/psi4/scfgrad/scf_grad.cc on line: 360
The most recent 5 function calls were:




Printing out the relevant lines from the Psithon --> Python processed input file:
    core.set_global_option("MAXITER", 500)
    core.set_global_option("SCF_TYPE", "df")
    core.set_global_option("PRINT_MOS", "True")
    core.set_global_option("GUESS", "sad")
    core.set_global_option("T", 300.0)
--> frequency('scf', dft_functional=b3lyphfx10)

    Psi4 stopped on: Friday, 17 February 2023 05:53PM
    Psi4 wall time for execution: 2:03:33.69

*** Psi4 encountered an error. Buy a developer more coffee!
*** Resources and help at github.com/psi4/psi4.

Could you please let me know what the problem might be? Thank you so much!

I already answered that in item 3 of my previous post.

Hi, I changed my input file as shown in my previouus reply, and I get a different error (also shown in my previous reply). I did not read in a wfn file this time but ended up with an error. Could you please let me know how this new error can be resolved? Thank you.

Add dertype = 1 as an argument to your frequency call. That the user needs to supply that keyword is a bug. That Psi4 doesn’t yet have analytic GGA hessians is a missing feature. That’s #4 on my DFT to-do list, after TDDFT singlets, UKS LDA hessians, and RKS stability analysis.