
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 151 surface points
Surface saved to: _potential_tmp.surf (151 points)
Computed Gauss-law surface charges from APBS potential and dielectric maps
Surface saved to: coupled_triplet.surf (151 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: 151
                Parallel Processing: True
============================================================


Logging results to: logs_20260905_163538
converged SCF energy = -1896.64188333725
Spin 0 (2S+1=1) converged: E = -1896.641883 Ha

Lowest energy: spin=0 (2S+1=1), E=-1896.641883 Ha
Saving GPU object type: <class 'gpu4pyscf.dft.rks.RKS'>
Saving functional (from parameter): b3lyp
Saved to molecule_alone.chk, Energy: -1896.641883337255 (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: 0.339821
                t2_exe: 0.588840
                t3_exe: 1.487431
============================================================


Running combined calculation with all 151 surface points...
Summary log initialized: logs_20260905_163538/calculation_summary.out

=== Resurrecting /data/PHO_WORK/sajagbe2/QMMM/LOVCalculations/lf-proto/sog-protein/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/tmp6zcuna0n.chk
max_memory 4000 MB (current use 1621 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= -1896.6418833369
  HOMO = 0.0678057632949532  LUMO = 0.078601859162788
cycle= 1 E= -1896.64188333288  delta_E= 4.02e-09  |g|= 9.37e-05  |ddm|= 0.000182
  HOMO = 0.067832134200938  LUMO = 0.0785964626657445
cycle= 2 E= -1896.6418791578  delta_E= 4.18e-06  |g|= 0.00303  |ddm|= 0.00579
  HOMO = 0.067807084810298  LUMO = 0.0786020808567921
cycle= 3 E= -1896.64188333676  delta_E= -4.18e-06  |g|= 2.21e-05  |ddm|= 0.00559
  HOMO = 0.067806712678351  LUMO = 0.0786017918297346
cycle= 4 E= -1896.64188333686  delta_E= -1.01e-10  |g|= 4.52e-06  |ddm|= 2.54e-05
converged SCF energy = -1896.64188333686
Resurrected GPU DFT object: <class 'gpu4pyscf.dft.rks.RKS'>, Energy: -1896.641883336862
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 1752 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  charge basis spin
Set gradient conv threshold to 3.16228e-05
init E= -1896.68141496652
  HOMO = 0.0525987333086544  LUMO = 0.0642442409664118
cycle= 1 E= -1896.67885496211  delta_E= 0.00256  |g|= 0.0896  |ddm|= 0.225
  HOMO = 0.0491234215737307  LUMO = 0.0851785680904455
cycle= 2 E= -1896.08554528167  delta_E= 0.593  |g|= 0.998  |ddm|= 2.02
  HOMO = 0.0493928126271457  LUMO = 0.0628141372429727
cycle= 3 E= -1896.65972647119  delta_E= -0.574  |g|= 0.219  |ddm|= 2.16
  HOMO = 0.0525108234736902  LUMO = 0.0627941536131268
cycle= 4 E= -1896.67572927906  delta_E= -0.016  |g|= 0.115  |ddm|= 0.231
  HOMO = 0.0518881235017153  LUMO = 0.0629229091367241
cycle= 5 E= -1896.6793175228  delta_E= -0.00359  |g|= 0.0787  |ddm|= 0.0911
  HOMO = 0.0520999167014311  LUMO = 0.063874861991843
cycle= 6 E= -1896.68044544449  delta_E= -0.00113  |g|= 0.0627  |ddm|= 0.0614
  HOMO = 0.051186472904108  LUMO = 0.0641298633353618
cycle= 7 E= -1896.67592063157  delta_E= 0.00452  |g|= 0.112  |ddm|= 0.127
  HOMO = 0.0507874508852247  LUMO = 0.0639959894844986
cycle= 8 E= -1896.67406511134  delta_E= 0.00186  |g|= 0.126  |ddm|= 0.043
  HOMO = 0.0508575637033779  LUMO = 0.0640808918979479
cycle= 9 E= -1896.6733300225  delta_E= 0.000735  |g|= 0.132  |ddm|= 0.0143
  HOMO = 0.0511495345446478  LUMO = 0.0640038239769445
cycle= 10 E= -1896.67563283977  delta_E= -0.0023  |g|= 0.114  |ddm|= 0.0422
  HOMO = 0.0512944134996512  LUMO = 0.0638211973765131
cycle= 11 E= -1896.67664331732  delta_E= -0.00101  |g|= 0.105  |ddm|= 0.0232
  HOMO = 0.0509936750778905  LUMO = 0.063944112462716
cycle= 12 E= -1896.67502636555  delta_E= 0.00162  |g|= 0.119  |ddm|= 0.033
  HOMO = 0.052217501432321  LUMO = 0.0635072501684245
cycle= 13 E= -1896.68146962339  delta_E= -0.00644  |g|= 0.0418  |ddm|= 0.195
  HOMO = 0.0515603689177161  LUMO = 0.0636889666824011
cycle= 14 E= -1896.67896060362  delta_E= 0.00251  |g|= 0.0809  |ddm|= 0.11
  HOMO = 0.0515554948061689  LUMO = 0.0641095608904422
cycle= 15 E= -1896.67701281469  delta_E= 0.00195  |g|= 0.102  |ddm|= 0.0497
  HOMO = 0.051279587417065  LUMO = 0.0637484910882294
cycle= 16 E= -1896.67744512767  delta_E= -0.000432  |g|= 0.0981  |ddm|= 0.0143
  HOMO = 0.0514923536922547  LUMO = 0.0637909493136928
cycle= 17 E= -1896.67814440833  delta_E= -0.000699  |g|= 0.0907  |ddm|= 0.0184
  HOMO = 0.0513873997010757  LUMO = 0.0637258938967168
cycle= 18 E= -1896.6779358092  delta_E= 0.000209  |g|= 0.0926  |ddm|= 0.00943
  HOMO = 0.0514227846699089  LUMO = 0.0638601897274808
cycle= 19 E= -1896.67743795805  delta_E= 0.000498  |g|= 0.0979  |ddm|= 0.0124
  HOMO = 0.0513894891888416  LUMO = 0.0638741669475028
cycle= 20 E= -1896.67721122396  delta_E= 0.000227  |g|= 0.101  |ddm|= 0.00849
  HOMO = 0.0538081005516225  LUMO = 0.0636410306307403
cycle= 21 E= -1896.67196110486  delta_E= 0.00525  |g|= 0.155  |ddm|= 0.458
  HOMO = 0.0532480762547502  LUMO = 0.0633241632106233
cycle= 22 E= -1896.67976509786  delta_E= -0.0078  |g|= 0.0749  |ddm|= 0.154
  HOMO = 0.0530993450365332  LUMO = 0.0631807666052667
cycle= 23 E= -1896.68003244592  delta_E= -0.000267  |g|= 0.0678  |ddm|= 0.0271
  HOMO = 0.0530259421291013  LUMO = 0.0632251763970934
cycle= 24 E= -1896.68075804832  delta_E= -0.000726  |g|= 0.0544  |ddm|= 0.0253
  HOMO = 0.0530083677109829  LUMO = 0.0632713618589591
cycle= 25 E= -1896.68102441669  delta_E= -0.000266  |g|= 0.0482  |ddm|= 0.0112
  HOMO = 0.0526982202292618  LUMO = 0.063278807335611
cycle= 26 E= -1896.68190698868  delta_E= -0.000883  |g|= 0.0182  |ddm|= 0.0537
  HOMO = 0.0526708303243565  LUMO = 0.063375355089017
cycle= 27 E= -1896.68203243184  delta_E= -0.000125  |g|= 0.00713  |ddm|= 0.02
  HOMO = 0.0525555921532451  LUMO = 0.0633654327529144
cycle= 28 E= -1896.68205364551  delta_E= -2.12e-05  |g|= 0.00191  |ddm|= 0.0168
  HOMO = 0.0525609093755892  LUMO = 0.0633592904763002
cycle= 29 E= -1896.68205466417  delta_E= -1.02e-06  |g|= 0.00127  |ddm|= 0.0017
  HOMO = 0.0525764976088045  LUMO = 0.063354361104241
cycle= 30 E= -1896.68205521431  delta_E= -5.5e-07  |g|= 0.000472  |ddm|= 0.00299
  HOMO = 0.0525752726449047  LUMO = 0.0633573917210122
cycle= 31 E= -1896.68205530974  delta_E= -9.54e-08  |g|= 9.99e-05  |ddm|= 0.000682
  HOMO = 0.0525750112089642  LUMO = 0.0633577238464681
cycle= 32 E= -1896.68205531302  delta_E= -3.29e-09  |g|= 5.32e-05  |ddm|= 0.000103
  HOMO = 0.0525741110753586  LUMO = 0.0633579269982423
cycle= 33 E= -1896.68205531358  delta_E= -5.57e-10  |g|= 3.89e-05  |ddm|= 0.000168
  HOMO = 0.0525743168891595  LUMO = 0.0633577772178735
cycle= 34 E= -1896.68205531418  delta_E= -6.03e-10  |g|= 1.16e-05  |ddm|= 5.72e-05
converged SCF energy = -1896.68205531418
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 1773 MB)


Excited State energies (eV)
[0.31631461 0.59537642 1.49418977]
Combined effects: {'t1_exe_effect': -0.02350337472984343, 't2_exe_effect': 0.006535798402962367, 't3_exe_effect': 0.006760598304024645}

Final statistics written to: logs_20260905_163538/calculation_summary.out
Raw properties appended to: logs_20260905_163538/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_16-39-00/
  Moved: ligand_tuning_summary.csv
  Moved 6 MOL2 files
  Added normalization parameters to summary
  Moved: logs_20260905_163538/ -> logs/
All expected output files were created.
