
4 GPU(s) detected.

Patched coupled.in -> num_procs = 4 (SLURM_GPUS_ON_NODE='4')
/home/users/sajagbe2/.local/lib/python3.11/site-packages/pyscf/dft/libxc.py:511: UserWarning: Since PySCF-2.3, B3LYP (and B3P86) are changed to the VWN-RPA variant, corresponding to the original definition by Stephens et al. (issue 1480) and the same as the B3LYP functional in Gaussian. To restore the VWN5 definition, you can put the setting "B3LYP_WITH_VWN5 = True" in pyscf_conf.py
  warnings.warn('Since PySCF-2.3, B3LYP (and B3P86) are changed to the VWN-RPA variant, '


============================================================
                   Electrostatic Map Suite
                    By Stephen O. Ajagbe
============================================================

============================================================
              Electrostatic Potential Module
============================================================

Generating VDW surface for potential mapping...
Generating VDW surface (density=0.5, scale=1.0)...
Generated 158 surface points
Surface saved to: _potential_tmp.surf (158 points)
Computed Gauss-law surface charges from APBS potential and dielectric maps
Surface saved to: coupled_triplet.surf (158 points)
Potential map CSV: coupled_triplet.csv
============================================================
============================================================
                  Electrostatic Tuning Maps
             Built on efforts by the Gozem Lab
   See: https://pubs.acs.org/doi/10.1021/acs.jpcb.9b00489
============================================================



4 GPU(s) detected.

Calculating Tuning of:  ['exe']
Using molecular states: {'neutral': True, 'td': True}


============================================================
                Calculation Type: combined
                Number of surface points: 158
                Parallel Processing: True
============================================================


Logging results to: logs_20260905_170737
converged SCF energy = -1896.66490191507
Spin 0 (2S+1=1) converged: E = -1896.664902 Ha

Lowest energy: spin=0 (2S+1=1), E=-1896.664902 Ha
Saving GPU object type: <class 'gpu4pyscf.dft.rks.RKS'>
Saving functional (from parameter): b3lyp
Saved to molecule_alone.chk, Energy: -1896.6649019150746 (GPU)
Multi-GPU detected. Using subprocess for single-GPU TDDFT...
TDDFT completed in subprocess on GPU 0, states: 3


============================================================
                Raw Properties (No Surface)
                Total raw properties calculated: 3
                t1_exe: 0.321239
                t2_exe: 0.473556
                t3_exe: 1.300773
============================================================


Running combined calculation with all 158 surface points...
Summary log initialized: logs_20260905_170737/calculation_summary.out

=== Resurrecting /data/PHO_WORK/sajagbe2/QMMM/LOVCalculations/lf-proto/sog-protein-step0/coupled-combined/SOPP3/triplet/molecule_alone.chk ===
Loaded XC functional: b3lyp
Creating DFT object with xc=b3lyp
Converting <class 'pyscf.dft.rks.RKS'> to GPU...
Successfully converted to GPU: <class 'gpu4pyscf.dft.rks.RKS'>


******** <class 'gpu4pyscf.dft.rks.RKS'> ********
method = RKS
initial guess = chkfile
damping factor = 0
level_shift factor = 0
DIIS = <class 'gpu4pyscf.scf.diis.CDIIS'>
diis_start_cycle = 1
diis_space = 8
diis_damp = 0
SCF conv_tol = 1e-09
SCF conv_tol_grad = None
SCF max_cycles = 50
direct_scf = True
direct_scf_tol = 1e-13
chkfile to save SCF result = /tmp/tmphmtc1vgn.chk
max_memory 4000 MB (current use 1584 MB)
XC library gpu4pyscf.dft.libxc version 7.0.0 (CUDA)
    unable to decode the reference due to https://github.com/NVIDIA/cuda-python/issues/29
XC functionals = b3lyp
small_rho_cutoff = 1e-07
Set gradient conv threshold to 3.16228e-05
init E= -1896.66490191506
  HOMO = 0.0555706516628563  LUMO = 0.06642219940123
cycle= 1 E= -1896.6649018506  delta_E= 6.45e-08  |g|= 0.000376  |ddm|= 0.000695
  HOMO = 0.0556663614627193  LUMO = 0.0664034134316589
cycle= 2 E= -1896.66483071611  delta_E= 7.11e-05  |g|= 0.0125  |ddm|= 0.023
  HOMO = 0.0555737516861222  LUMO = 0.0664214374620543
cycle= 3 E= -1896.66490191433  delta_E= -7.12e-05  |g|= 4.39e-05  |ddm|= 0.0222
  HOMO = 0.0555737289855305  LUMO = 0.0664215151653018
cycle= 4 E= -1896.66490191473  delta_E= -3.96e-10  |g|= 2.76e-05  |ddm|= 2.9e-05
converged SCF energy = -1896.66490191473
Resurrected GPU DFT object: <class 'gpu4pyscf.dft.rks.RKS'>, Energy: -1896.6649019147299
Multi-GPU detected. Using subprocess for single-GPU TDDFT...
TDDFT completed in subprocess on GPU 0, states: 3


******** <class 'gpu4pyscf.dft.rks.RKS'> ********
method = RKS
initial guess = chkfile
damping factor = 0
level_shift factor = 0
DIIS = <class 'gpu4pyscf.scf.diis.CDIIS'>
diis_start_cycle = 1
diis_space = 8
diis_damp = 0
SCF conv_tol = 1e-09
SCF conv_tol_grad = None
SCF max_cycles = 50
direct_scf = True
direct_scf_tol = 1e-13
chkfile to save SCF result = molecule_alone.chk
max_memory 4000 MB (current use 1686 MB)
XC library gpu4pyscf.dft.libxc version 7.0.0 (CUDA)
    unable to decode the reference due to https://github.com/NVIDIA/cuda-python/issues/29
XC functionals = b3lyp
small_rho_cutoff = 1e-07
Overwritten attributes  energy_nuc get_hcore  of <class 'gpu4pyscf.dft.rks.RKS'>
<class 'gpu4pyscf.dft.rks.RKS'> does not have attributes  basis spin charge
Set gradient conv threshold to 3.16228e-05
init E= -1896.70330980776
  HOMO = 0.0353469484620101  LUMO = 0.0545029437800625
cycle= 1 E= -1896.66963831883  delta_E= 0.0337  |g|= 0.248  |ddm|= 0.642
  HOMO = 0.0984181672097266  LUMO = 0.110184361495147
cycle= 2 E= -1888.81983098549  delta_E= 7.85  |g|= 3.11  |ddm|= 4.62
  HOMO = 0.0420428756050618  LUMO = 0.0502966681793522
cycle= 3 E= -1896.28213265498  delta_E= -7.46  |g|= 0.916  |ddm|= 4.12
  HOMO = 0.0433475729544087  LUMO = 0.0517821779455503
cycle= 4 E= -1896.68850157552  delta_E= -0.406  |g|= 0.171  |ddm|= 1.77
  HOMO = 0.0451408904517475  LUMO = 0.0517357460021638
cycle= 5 E= -1896.6421110643  delta_E= 0.0464  |g|= 0.376  |ddm|= 0.962
  HOMO = 0.0437293775992769  LUMO = 0.0510127724157148
cycle= 6 E= -1896.6669469366  delta_E= -0.0248  |g|= 0.295  |ddm|= 0.154
  HOMO = 0.0436212019880067  LUMO = 0.0518670204512181
cycle= 7 E= -1896.65389692024  delta_E= 0.0131  |g|= 0.343  |ddm|= 0.0955
  HOMO = 0.0436283621987054  LUMO = 0.0521719785013047
cycle= 8 E= -1896.65661219544  delta_E= -0.00272  |g|= 0.333  |ddm|= 0.0406
  HOMO = 0.0435168883128043  LUMO = 0.0522098840696234
cycle= 9 E= -1896.64399894001  delta_E= 0.0126  |g|= 0.374  |ddm|= 0.0697
  HOMO = 0.0435189892057565  LUMO = 0.0529929032187181
cycle= 10 E= -1896.59997586541  delta_E= 0.044  |g|= 0.488  |ddm|= 0.191
  HOMO = 0.043513817484023  LUMO = 0.0524162507136212
cycle= 11 E= -1896.61285008021  delta_E= -0.0129  |g|= 0.457  |ddm|= 0.0657
  HOMO = 0.0436309065074687  LUMO = 0.0530574696525752
cycle= 12 E= -1896.55879922371  delta_E= 0.0541  |g|= 0.569  |ddm|= 0.194
  HOMO = 0.0419210606208759  LUMO = 0.0533788160056134
cycle= 13 E= -1896.69036415898  delta_E= -0.132  |g|= 0.176  |ddm|= 0.636
  HOMO = 0.0417038390654242  LUMO = 0.0527088435542072
cycle= 14 E= -1896.68148057048  delta_E= 0.00888  |g|= 0.224  |ddm|= 0.123
  HOMO = 0.0393848868459682  LUMO = 0.052723682611612
cycle= 15 E= -1896.6998235062  delta_E= -0.0183  |g|= 0.0893  |ddm|= 0.549
  HOMO = 0.0413532532901076  LUMO = 0.0522631411571296
cycle= 16 E= -1896.70368092328  delta_E= -0.00386  |g|= 0.00344  |ddm|= 0.172
  HOMO = 0.0415044517533353  LUMO = 0.0521757735031787
cycle= 17 E= -1896.70357571822  delta_E= 0.000105  |g|= 0.0156  |ddm|= 0.0324
  HOMO = 0.0413997764509234  LUMO = 0.0521830358786619
cycle= 18 E= -1896.70366325548  delta_E= -8.75e-05  |g|= 0.00685  |ddm|= 0.016
  HOMO = 0.0414248948236809  LUMO = 0.0522134016774899
cycle= 19 E= -1896.7036525094  delta_E= 1.07e-05  |g|= 0.00835  |ddm|= 0.00404
  HOMO = 0.0413556236039389  LUMO = 0.0522419770869133
cycle= 20 E= -1896.70368380291  delta_E= -3.13e-05  |g|= 0.00193  |ddm|= 0.0186
  HOMO = 0.041349725416367  LUMO = 0.0522171779170079
cycle= 21 E= -1896.70368487556  delta_E= -1.07e-06  |g|= 0.000964  |ddm|= 0.0017
  HOMO = 0.0413650235754751  LUMO = 0.0522087850686054
cycle= 22 E= -1896.70368489168  delta_E= -1.61e-08  |g|= 0.000964  |ddm|= 0.00359
  HOMO = 0.0413602527807555  LUMO = 0.0522147580275034
cycle= 23 E= -1896.70368532559  delta_E= -4.34e-07  |g|= 5.44e-05  |ddm|= 0.00175
  HOMO = 0.0413578303106078  LUMO = 0.0522142336643522
cycle= 24 E= -1896.70368531344  delta_E= 1.22e-08  |g|= 0.00017  |ddm|= 0.000405
  HOMO = 0.0413592515195318  LUMO = 0.052214015571338
cycle= 25 E= -1896.70368532737  delta_E= -1.39e-08  |g|= 3.35e-05  |ddm|= 0.000318
  HOMO = 0.0413589707859178  LUMO = 0.0522139495042522
cycle= 26 E= -1896.70368532702  delta_E= 3.47e-10  |g|= 3.97e-05  |ddm|= 7.85e-05
  HOMO = 0.0413592564980778  LUMO = 0.0522140239105933
cycle= 27 E= -1896.70368532757  delta_E= -5.49e-10  |g|= 2.01e-05  |ddm|= 3.81e-05
converged SCF energy = -1896.70368532757
Running TDDFT in current process (force_single_gpu=True)


******** <class 'gpu4pyscf.tdscf.rks.TDDFT'> for <class 'gpu4pyscf.dft.rks.RKS'> ********
nstates = 3 triplet
deg_eia_thresh = 1.000e-03
wfnsym = None
conv_tol = 1e-05
eigh lindep = 1e-12
eigh level_shift = 0
eigh max_cycle = 100
chkfile = molecule_alone.chk
max_memory 4000 MB (current use 1659 MB)


Excited State energies (eV)
[0.37755165 0.49352608 1.3313899 ]
Combined effects: {'t1_exe_effect': 0.05626439761386509, 't2_exe_effect': 0.019927342191196074, 't3_exe_effect': 0.030564453379080092}

Final statistics written to: logs_20260905_170737/calculation_summary.out
Raw properties appended to: logs_20260905_170737/calculation_summary.out
Created: ligand_t1_exe.mol2
Created: ligand_t2_exe.mol2
Created: ligand_t3_exe.mol2
Created: ligand_t1_exe_normalized.mol2
Created: ligand_t2_exe_normalized.mol2
Created: ligand_t3_exe_normalized.mol2

Created: ligand_tuning_summary.csv

Organizing results into: results_ligand_2026-09-05_17-10-20/
  Moved: ligand_tuning_summary.csv
  Moved 6 MOL2 files
  Added normalization parameters to summary
  Moved: logs_20260905_170737/ -> logs/
All expected output files were created.
