
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 154 surface points
Surface saved to: _potential_tmp.surf (154 points)
Computed Gauss-law surface charges from APBS potential and dielectric maps
Surface saved to: coupled_singlet.surf (154 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: 154
                Parallel Processing: True
============================================================


Logging results to: logs_20260905_170734

WARN: SCF failed to converge

SCF not converged.
SCF energy = -1896.66485107473
converged SCF energy = -1896.66485107812
Spin 0 (2S+1=1) converged: E = -1896.664851 Ha

Lowest energy: spin=0 (2S+1=1), E=-1896.664851 Ha
Saving GPU object type: <class 'gpu4pyscf.scf.soscf.SecondOrderRKS'>
Saving functional (from parameter): b3lyp
Saved to molecule_alone.chk, Energy: -1896.6648510781247 (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: 0.148865
                s2_exe: 0.626014
                s3_exe: 0.718349
============================================================


Running combined calculation with all 154 surface points...
Summary log initialized: logs_20260905_170734/calculation_summary.out

=== Resurrecting /data/PHO_WORK/sajagbe2/QMMM/LOVCalculations/lf-proto/sog-protein-step0/coupled-combined/MSOG/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/tmpdpi21b2q.chk
max_memory 4000 MB (current use 1901 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= -1896.66485107838
  HOMO = 0.055556729779532  LUMO = 0.0664039943770513
cycle= 1 E= -1896.66485107819  delta_E= 1.92e-10  |g|= 2.9e-05  |ddm|= 4.03e-05
converged SCF energy = -1896.66485107819
Resurrected GPU DFT object: <class 'gpu4pyscf.dft.rks.RKS'>, Energy: -1896.6648510781893
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 2004 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= -1896.71443752597
  HOMO = 0.0316692530029751  LUMO = 0.0488115724472498
cycle= 1 E= -1896.68663627177  delta_E= 0.0278  |g|= 0.228  |ddm|= 0.57
  HOMO = 0.0964879711994115  LUMO = 0.0985897712376664
cycle= 2 E= -1893.04120870742  delta_E= 3.65  |g|= 2.36  |ddm|=  3.5
  HOMO = 0.0362817512138182  LUMO = 0.0555538674602441
cycle= 3 E= -1896.16759940768  delta_E= -3.13  |g|= 0.974  |ddm|= 2.78
  HOMO = 0.0376981281979854  LUMO = 0.0479039584610428
cycle= 4 E= -1896.68528751889  delta_E= -0.518  |g|= 0.231  |ddm|=  2.1
  HOMO = 0.0399368498516908  LUMO = 0.0465788125631278
cycle= 5 E= -1896.71269556161  delta_E= -0.0274  |g|= 0.0773  |ddm|= 0.454
  HOMO = 0.0371118891075855  LUMO = 0.0472473183456023
cycle= 6 E= -1896.71098640511  delta_E= 0.00171  |g|= 0.0947  |ddm|= 0.116
  HOMO = 0.0358987962547101  LUMO = 0.0479569389904449
cycle= 7 E= -1896.71174458089  delta_E= -0.000758  |g|= 0.0796  |ddm|= 0.0634
  HOMO = 0.0356517223256993  LUMO = 0.0481413344805606
cycle= 8 E= -1896.71154945868  delta_E= 0.000195  |g|= 0.0827  |ddm|= 0.021
  HOMO = 0.0355701981207138  LUMO = 0.0481655541692249
cycle= 9 E= -1896.71124865157  delta_E= 0.000301  |g|= 0.0863  |ddm|= 0.00804
  HOMO = 0.036085309371529  LUMO = 0.0480159165302758
cycle= 10 E= -1896.7134614804  delta_E= -0.00221  |g|= 0.0546  |ddm|= 0.0694
  HOMO = 0.0365034252927629  LUMO = 0.047761082386798
cycle= 11 E= -1896.71458614953  delta_E= -0.00112  |g|= 0.0228  |ddm|= 0.0648
  HOMO = 0.036859418545337  LUMO = 0.0477613257348066
cycle= 12 E= -1896.71478471215  delta_E= -0.000199  |g|= 0.00401  |ddm|= 0.0342
  HOMO = 0.0367544503376822  LUMO = 0.0478125806771321
cycle= 13 E= -1896.71466693164  delta_E= 0.000118  |g|= 0.0162  |ddm|= 0.0262
  HOMO = 0.0368433972823991  LUMO = 0.0477491643310662
cycle= 14 E= -1896.71478333469  delta_E= -0.000116  |g|= 0.00388  |ddm|= 0.0232
  HOMO = 0.0368850548512806  LUMO = 0.0477613514106566
cycle= 15 E= -1896.71478843549  delta_E= -5.1e-06  |g|= 0.0019  |ddm|= 0.0038
  HOMO = 0.0368895242094131  LUMO = 0.0477502622989322
cycle= 16 E= -1896.71478976124  delta_E= -1.33e-06  |g|= 0.0008  |ddm|= 0.00222
  HOMO = 0.0368821918543848  LUMO = 0.0477487944174142
cycle= 17 E= -1896.71478920041  delta_E= 5.61e-07  |g|= 0.00131  |ddm|= 0.00136
  HOMO = 0.0368911375300996  LUMO = 0.047746482131499
cycle= 18 E= -1896.71478994388  delta_E= -7.43e-07  |g|= 0.000354  |ddm|= 0.00179
  HOMO = 0.0368947269032332  LUMO = 0.047746723050094
cycle= 19 E= -1896.71478999929  delta_E= -5.54e-08  |g|= 8.43e-05  |ddm|= 0.000522
  HOMO = 0.0368945578172173  LUMO = 0.0477463302439198
cycle= 20 E= -1896.71479000055  delta_E= -1.26e-09  |g|= 6.22e-05  |ddm|= 6.3e-05
  HOMO = 0.0368950352209533  LUMO = 0.0477458542374249
cycle= 21 E= -1896.71479000173  delta_E= -1.18e-09  |g|= 3.56e-05  |ddm|= 0.00016
  HOMO = 0.0368950426207591  LUMO = 0.0477460259731408
cycle= 22 E= -1896.71479000214  delta_E= -4.13e-10  |g|= 8.62e-06  |ddm|= 4.48e-05
converged SCF energy = -1896.71479000214
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 2015 MB)


Excited State energies (eV)
[0.14841559 0.63466822 0.71514932]
Combined effects: {'s1_exe_effect': -0.00046506293066048143, 's2_exe_effect': 0.00868181291355874, 's3_exe_effect': -0.003229791098825263}

Final statistics written to: logs_20260905_170734/calculation_summary.out
Raw properties appended to: logs_20260905_170734/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_17-11-19/
  Moved: ligand_tuning_summary.csv
  Moved 6 MOL2 files
  Added normalization parameters to summary
  Moved: logs_20260905_170734/ -> logs/
All expected output files were created.
