I get the following error when running my tddft job:
=> Iterations <=
Max[D[value]] Max[|R|] # vectors
Traceback (most recent call last):
File "/data/Apps/anaconda3/envs/psi4env/bin/psi4", line 387, in <module>
exec(content)
File "<string>", line 144, in <module>
File "/data/Apps/anaconda3/envs/psi4env_1-9-1/lib/python3.12/site-packages/psi4/driver/procrouting/response/scf_response.py", line 761, in tdscf_excitations
res_1 = _solve_loop(wfn, ptype, solve_function, singlets_per_irrep, maxiter, restricted, "singlet")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/data/Apps/anaconda3/envs/psi4env_1-9-1/lib/python3.12/site-packages/psi4/driver/procrouting/response/scf_response.py", line 332, in _solve_loop
ret = solve_function(engine, nstates, guess_, maxiter)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/data/Apps/anaconda3/envs/psi4env_1-9-1/lib/python3.12/site-packages/psi4/driver/procrouting/response/scf_response.py", line 728, in rpa_solver
return solvers.hamiltonian_solver(engine=e,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/data/Apps/anaconda3/envs/psi4env_1-9-1/lib/python3.12/site-packages/psi4/driver/p4util/solvers.py", line 985, in hamiltonian_solver
H1x, H2x, nprod = engine.compute_products(vecs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/data/Apps/anaconda3/envs/psi4env_1-9-1/lib/python3.12/site-packages/psi4/driver/procrouting/response/scf_products.py", line 264, in compute_products
twoel = self.wfn.twoel_Hx_full(compute_vectors, False, "SO", self.singlet)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
RuntimeError:
Fatal Error: READ failed. Error description from the OS: Bad address
Error reading the first partial page, unit 97.
Error occurred in file: /home/conda/feedstock_root/build_artifacts/psi4_1720499718168/work/psi4/src/psi4/libpsio/error.cc on line: 135
The most recent 5 function calls were:
psi::PsiException::PsiException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char const*, int)
psi::PSIO::rw(unsigned long, char*, psi::psio_address, unsigned long, int)
psi::DiskDFJK::manage_JK_disk()
psi::DiskDFJK::compute_JK()
Printing out the relevant lines from the Psithon --> Python processed input file:
set_num_threads(32)
import psi4
from psi4.driver.procrouting.response.scf_response import tdscf_excitations
core.set_global_option("SAVE_JK", "true")
e, wfn = energy('b3lyp-d3bj/aug-cc-pVTZ', return_wfn=True)
--> res = tdscf_excitations(wfn, states=100, tdm_print=['E_TDM_LEN', 'E_TDM_VEL'], coeff_cutoff=0.01)
for state in range(10):
nto_wfn = psi4.driver.nto(wfn, states=[state+1])
psi4.cubeprop(nto_wfn)
from psi4.driver.p4util import spectrum
poles = [r["EXCITATION ENERGY"] for r in res]
!----------------------------------------------------------------------------------!
! !
! Fatal Error: READ failed. Error description from the OS: Bad address !
! Error reading the first partial page, unit 97. !
! Error occurred in file: /home/conda/feedstock_root/build_artifacts/psi4_17204997 !
! 18168/work/psi4/src/psi4/libpsio/error.cc on line: 135 !
! The most recent 5 function calls were: !
! psi::PsiException::PsiException(std::__cxx11::basic_string<char, !
! std::char_traits<char>, std::allocator<char> >, char const*, int) !
! psi::PSIO::rw(unsigned long, char*, psi::psio_address, unsigned long, int) !
! psi::DiskDFJK::manage_JK_disk() !
! psi::DiskDFJK::compute_JK() !
! !
!----------------------------------------------------------------------------------!
Here is my input file:
memory 102400 mb
molecule mol {
0 1
F -13.28560 -1.56730 1.43140
F -11.77120 -3.12310 1.39200
F -12.76100 -2.52150 -0.43810
F -12.21880 2.97400 0.18350
F -11.16620 2.81060 -1.69960
F -10.13070 3.54970 0.05080
N -7.01230 -3.31370 0.62840
C -2.83640 1.09600 0.18950
C -4.20550 1.12730 0.19860
C -4.98910 -0.05190 0.19840
C -6.43820 0.11480 0.20320
C -7.44310 -0.78220 0.30920
C -7.18850 -2.18560 0.48880
C -8.87020 -0.40350 0.26800
C -9.85900 -1.36680 0.50380
C -11.20220 -1.01850 0.48000
C -11.60340 0.28210 0.20510
C -10.62210 1.24230 -0.03000
C -9.27550 0.91440 -0.00480
C -12.25660 -2.06840 0.71930
C -11.03580 2.65160 -0.37240
F 6.15750 1.37160 -1.05920
F 4.64220 2.92960 -1.01890
F 5.63070 2.32550 0.80940
F 5.08940 -3.16920 0.18880
F 4.03660 -3.00540 2.07090
F 3.00260 -3.74430 0.31960
N -0.11630 3.12620 -0.26000
C -4.29350 -1.29090 0.17810
C -2.92410 -1.32290 0.17050
C -2.14060 -0.14350 0.17120
C -0.69030 -0.30930 0.16870
C 0.31420 0.58960 0.06290
C 0.06190 1.98630 -0.11390
C 1.74100 0.20950 0.10420
C 2.73100 1.17160 -0.13130
C 4.07330 0.82500 -0.10760
C 4.47440 -0.47490 0.16760
C 3.49300 -1.43570 0.40010
C 2.14550 -1.10960 0.37430
C 5.12690 1.87480 -0.35070
C 3.90620 -2.84360 0.74520
F -9.17930 -4.39490 -1.70440
F -7.66380 -5.95290 -1.74410
F -8.65220 -5.34940 -3.57280
F -8.11080 0.14570 -2.95170
F -7.05820 -0.01810 -4.83380
F -6.02410 0.72080 -3.08260
N -2.90610 -6.14550 -2.50360
C 1.27190 -1.73270 -2.94090
C -0.09740 -1.70070 -2.93330
C -0.88110 -2.88010 -2.93420
C -2.33120 -2.71410 -2.93220
C -3.33590 -3.61240 -2.82660
C -3.08270 -5.01480 -2.64900
C -4.76270 -3.23280 -2.86780
C -5.75260 -4.19520 -2.63220
C -7.09490 -3.84850 -2.65610
C -7.49590 -2.54850 -2.93090
C -6.51450 -1.58780 -3.16310
C -5.16700 -1.91400 -3.13770
C -8.14830 -4.89830 -2.41310
C -6.92770 -0.17990 -3.50820
F 10.26380 -1.45590 -4.19500
F 8.74960 0.09980 -4.15490
F 9.73940 -0.50230 -2.32510
F 9.19720 -5.99750 -2.94630
F 8.14470 -5.83410 -1.06330
F 7.10930 -6.57320 -2.81370
N 3.99080 0.29010 -3.39160
C -0.18510 -4.11950 -2.95240
C 1.18410 -4.15080 -2.96150
C 1.96760 -2.97180 -2.96150
C 3.41670 -3.13830 -2.96670
C 4.42160 -2.24130 -3.07280
C 4.16690 -0.83790 -3.25250
C 5.84860 -2.61990 -3.03150
C 6.83740 -1.65680 -3.26730
C 8.18050 -2.00500 -3.24350
C 8.58180 -3.30550 -2.96840
C 7.60050 -4.26590 -2.73310
C 6.25390 -3.93800 -2.75830
C 9.23480 -0.95490 -3.48300
C 8.01420 -5.67510 -2.39040
H -2.28450 2.01600 0.20570
H -4.69800 2.08390 0.20820
H -6.73010 1.13770 0.10830
H -9.57530 -2.39000 0.71150
H -12.65680 0.54690 0.18070
H -8.54800 1.69180 -0.20580
H -4.84570 -2.21030 0.16670
H -2.43140 -2.27880 0.16400
H -0.39870 -1.33300 0.26040
H 2.44690 2.19390 -0.34240
H 5.52770 -0.73980 0.19100
H 1.41770 -1.88670 0.57470
H 1.82420 -0.81340 -2.92960
H -0.59010 -0.74470 -2.92690
H -2.62290 -1.69070 -3.02380
H -5.46850 -5.21730 -2.42070
H -8.54920 -2.28350 -2.95410
H -4.43890 -1.13710 -3.33800
H -0.73700 -5.03960 -2.96860
H 1.67660 -5.10750 -2.97120
H 3.70890 -4.16130 -2.87220
H 6.55370 -0.63350 -3.47460
H 9.63510 -3.57030 -2.94390
H 5.52650 -4.71520 -2.55700
symmetry c1
no_reorient
no_com
}
psi4_io.set_default_path('/data/sbembenek/FB/1_FB_Denovicon2/2025/11_26_24/Tetra_CF3_Di_Nitrile_Tri_Phenyl/Packing/Mer_Systems/1_Native/Dimer_Systems/Dimer_F2F_Native_v1/5_TDDFT/2_Output/1_Raw/Scratch')
# Standard Options
set scf_type df
set reference rks
set s_tolerance 1e-9
set_num_threads(32)
#TDDFT Setup
import psi4
from psi4.driver.procrouting.response.scf_response import tdscf_excitations
set save_jk true
e, wfn = energy('b3lyp-d3bj/aug-cc-pVTZ', return_wfn=True)
res = tdscf_excitations(wfn, states=100, tdm_print=['E_TDM_LEN', 'E_TDM_VEL'], coeff_cutoff=0.01)
#NTOs
# Generate NTOs for first 10 states
for state in range(10):
nto_wfn = psi4.driver.nto(wfn, states=[state+1])
psi4.cubeprop(nto_wfn)
#----------------------------------------------Spectra ----------------------------------------
#Poles
from psi4.driver.p4util import spectrum
poles = [r["EXCITATION ENERGY"] for r in res]
#OPA Spectra
import numpy as np
import matplotlib.pyplot as plt
#----------------------------------------------------------------------------------------------
#----------------------------------------------------------------------------------------------
# Residues & Poles
opa_residues = [np.linalg.norm(r["ELECTRIC DIPOLE TRANSITION MOMENT (LEN)"])**2 for r in res]
opa_spectrum = spectrum(poles=poles, residues=opa_residues, gamma=0.01, out_units="nm")
#----------------------------------------------------------------------------------------------
#Spectrum (Broadening)
data_x_opa = opa_spectrum["convolution"]["x"]
data_y_opa = opa_spectrum["convolution"]["y"]
#----------------------------------------------------------------------------------------------
#Save (PNG)
plt.clf()
plt.plot(data_x_opa, data_y_opa, "r-")
plt.savefig("opa.png")
#----------------------------------------------------------------------------------------------
#Save (CSV via Matplotlib)
# transpose because numpy treats (array_1, array_2) as a 2 x N matrix
# and I want a N x 2 matrix
np.savetxt("opa.csv", np.transpose((data_x_opa, data_y_opa)), delimiter=",")
#----------------------------------------------------------------------------------------------
#Spectrum (Sticks & Broadening)
opa_stick_poles = opa_spectrum["sticks"]["poles"]
opa_stick_residues = opa_spectrum["sticks"]["residues"]
#Save (PNG)
#plt.clf()
plt.vlines(
opa_stick_poles,
np.zeros(len(poles)),
opa_stick_residues, "black"
)
# scaling the min. and max. x range by a little bit
# because I think it looks better that way
plt.hlines(
[0, 0],
0.9 * min(opa_stick_poles),
1.1 * max(opa_stick_poles)
)
plt.savefig("opa_combo.png")
#----------------------------------------------------------------------------------------------
#Spectrum (Sticks Only)
#opa_stick_poles = opa_spectrum["sticks"]["poles"]
#opa_stick_residues = opa_spectrum["sticks"]["residues"]
#Save (PNG)
plt.clf()
plt.vlines(
opa_stick_poles,
np.zeros(len(poles)),
opa_stick_residues, "black"
)
# scaling the min. and max. x range by a little bit
# because I think it looks better that way
plt.hlines(
[0, 0],
0.9 * min(opa_stick_poles),
1.1 * max(opa_stick_poles)
)
plt.savefig("opa_sticks.png")
#----------------------------------------------------------------------------------------------
#Save (CSV via Matplotlib)
np.savetxt("opa_sticks.csv", np.transpose((opa_stick_poles, opa_stick_residues)), delimiter=",")
#----------------------------------------------------------------------------------------------
#----------------------------------------------------------------------------------------------
And I am running 1.9.1 And I also tried under an older version → 1.4 since some of these inputs have not been change since then. But it does not run under there as well. Under 1.4 these inputs have run successfully with a different system. So, I am thinking it has something to do with the system, or the size of the system – this current system is a dimer consisting of 108 atoms in total.
Let me know if I can provide more info.