
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_singlet.surf (158 points)
Potential map CSV: coupled_singlet.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: -1896.6649019150727 (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
                s1_exe: 0.148922
                s2_exe: 0.626368
                s3_exe: 0.718576
============================================================


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/singlet/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/tmp0wn3sb1j.chk
max_memory 4000 MB (current use 1716 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 = 0.0555706516628259  LUMO = 0.0664221994012204
cycle= 1 E= -1896.66490185059  delta_E= 6.45e-08  |g|= 0.000376  |ddm|= 0.000695
  HOMO = 0.0556663614632068  LUMO = 0.0664034134315344
cycle= 2 E= -1896.66483071611  delta_E= 7.11e-05  |g|= 0.0125  |ddm|= 0.023
  HOMO = 0.0555737516860934  LUMO = 0.0664214374620305
cycle= 3 E= -1896.66490191433  delta_E= -7.12e-05  |g|= 4.39e-05  |ddm|= 0.0222
  HOMO = 0.0555737289855275  LUMO = 0.0664215151653043
cycle= 4 E= -1896.66490191473  delta_E= -3.97e-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 1853 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 charge spin
Set gradient conv threshold to 3.16228e-05
init E= -1896.70330980776
  HOMO = 0.0353469484622385  LUMO = 0.0545029437799689
cycle= 1 E= -1896.66963831883  delta_E= 0.0337  |g|= 0.248  |ddm|= 0.642
  HOMO = 0.0984181672105578  LUMO = 0.110184361493587
cycle= 2 E= -1888.8198309855  delta_E= 7.85  |g|= 3.11  |ddm|= 4.62
  HOMO = 0.0420428756050236  LUMO = 0.0502966681793959
cycle= 3 E= -1896.28213265498  delta_E= -7.46  |g|= 0.916  |ddm|= 4.12
  HOMO = 0.0433475729544795  LUMO = 0.0517821779455094
cycle= 4 E= -1896.68850157553  delta_E= -0.406  |g|= 0.171  |ddm|= 1.77
  HOMO = 0.0451408904516199  LUMO = 0.0517357460021671
cycle= 5 E= -1896.6421110643  delta_E= 0.0464  |g|= 0.376  |ddm|= 0.962
  HOMO = 0.0437293775991377  LUMO = 0.051012772415737
cycle= 6 E= -1896.6669469366  delta_E= -0.0248  |g|= 0.295  |ddm|= 0.154
  HOMO = 0.0436212019879118  LUMO = 0.0518670204511895
cycle= 7 E= -1896.65389692025  delta_E= 0.0131  |g|= 0.343  |ddm|= 0.0955
  HOMO = 0.0436283621985848  LUMO = 0.0521719785012723
cycle= 8 E= -1896.65661219545  delta_E= -0.00272  |g|= 0.333  |ddm|= 0.0406
  HOMO = 0.04351688831259  LUMO = 0.0522098840695645
cycle= 9 E= -1896.64399894002  delta_E= 0.0126  |g|= 0.374  |ddm|= 0.0697
  HOMO = 0.0435189892056297  LUMO = 0.0529929032187378
cycle= 10 E= -1896.59997586539  delta_E= 0.044  |g|= 0.488  |ddm|= 0.191
  HOMO = 0.0435138174862017  LUMO = 0.0524162507170866
cycle= 11 E= -1896.61285007977  delta_E= -0.0129  |g|= 0.457  |ddm|= 0.0657
  HOMO = 0.0436309065046493  LUMO = 0.053057469663311
cycle= 12 E= -1896.55879922276  delta_E= 0.0541  |g|= 0.569  |ddm|= 0.194
  HOMO = 0.0419210606419922  LUMO = 0.0533788160110169
cycle= 13 E= -1896.69036415831  delta_E= -0.132  |g|= 0.176  |ddm|= 0.636
  HOMO = 0.0417038390676287  LUMO = 0.0527088435639278
cycle= 14 E= -1896.68148057019  delta_E= 0.00888  |g|= 0.224  |ddm|= 0.123
  HOMO = 0.0393848868497563  LUMO = 0.0527236826141428
cycle= 15 E= -1896.69982350629  delta_E= -0.0183  |g|= 0.0893  |ddm|= 0.549
  HOMO = 0.0413532532876567  LUMO = 0.0522631411613527
cycle= 16 E= -1896.70368092328  delta_E= -0.00386  |g|= 0.00344  |ddm|= 0.172
  HOMO = 0.041504451761694  LUMO = 0.0521757734997013
cycle= 17 E= -1896.7035757182  delta_E= 0.000105  |g|= 0.0156  |ddm|= 0.0324
  HOMO = 0.0413997764564063  LUMO = 0.0521830358759924
cycle= 18 E= -1896.70366325548  delta_E= -8.75e-05  |g|= 0.00685  |ddm|= 0.016
  HOMO = 0.0414248948254719  LUMO = 0.0522134016771712
cycle= 19 E= -1896.7036525094  delta_E= 1.07e-05  |g|= 0.00835  |ddm|= 0.00404
  HOMO = 0.041355623602677  LUMO = 0.0522419770877554
cycle= 20 E= -1896.70368380291  delta_E= -3.13e-05  |g|= 0.00193  |ddm|= 0.0186
  HOMO = 0.041349725415711  LUMO = 0.0522171779171021
cycle= 21 E= -1896.70368487556  delta_E= -1.07e-06  |g|= 0.000964  |ddm|= 0.0017
  HOMO = 0.0413650235758176  LUMO = 0.0522087850684745
cycle= 22 E= -1896.70368489168  delta_E= -1.61e-08  |g|= 0.000964  |ddm|= 0.00359
  HOMO = 0.0413602527806215  LUMO = 0.0522147580275673
cycle= 23 E= -1896.70368532559  delta_E= -4.34e-07  |g|= 5.44e-05  |ddm|= 0.00175
  HOMO = 0.0413578303103544  LUMO = 0.052214233664407
cycle= 24 E= -1896.70368531344  delta_E= 1.22e-08  |g|= 0.00017  |ddm|= 0.000405
  HOMO = 0.0413592515195435  LUMO = 0.0522140155713607
cycle= 25 E= -1896.70368532737  delta_E= -1.39e-08  |g|= 3.35e-05  |ddm|= 0.000318
  HOMO = 0.0413589707859198  LUMO = 0.0522139495042378
cycle= 26 E= -1896.70368532702  delta_E= 3.44e-10  |g|= 3.97e-05  |ddm|= 7.85e-05
  HOMO = 0.0413592564980811  LUMO = 0.0522140239105883
cycle= 27 E= -1896.70368532757  delta_E= -5.46e-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 singlet
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 1880 MB)


Excited State energies (eV)
[0.14851565 0.65948834 0.7216019 ]
Combined effects: {'s1_exe_effect': -0.0005280640308074902, 's2_exe_effect': 0.03309393068006172, 's3_exe_effect': 0.0029998357626802585}

Final statistics written to: logs_20260905_170737/calculation_summary.out
Raw properties appended to: logs_20260905_170737/calculation_summary.out
Created: ligand_s1_exe.mol2
Created: ligand_s2_exe.mol2
Created: ligand_s3_exe.mol2
Created: ligand_s1_exe_normalized.mol2
Created: ligand_s2_exe_normalized.mol2
Created: ligand_s3_exe_normalized.mol2

Created: ligand_tuning_summary.csv

Organizing results into: results_ligand_2026-09-05_17-11-01/
  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.
