
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 153 surface points
Surface saved to: _potential_tmp.surf (153 points)
Computed Gauss-law surface charges from APBS potential and dielectric maps
Surface saved to: coupled_triplet.surf (153 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: 153
                Parallel Processing: True
============================================================


Logging results to: logs_20260905_163539
converged SCF energy = -1896.64637740258
Spin 0 (2S+1=1) converged: E = -1896.646377 Ha

Lowest energy: spin=0 (2S+1=1), E=-1896.646377 Ha
Saving GPU object type: <class 'gpu4pyscf.dft.rks.RKS'>
Saving functional (from parameter): b3lyp
Saved to molecule_alone.chk, Energy: -1896.6463774025765 (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: 0.394274
                t2_exe: 0.546711
                t3_exe: 1.464071
============================================================


Running combined calculation with all 153 surface points...
Summary log initialized: logs_20260905_163539/calculation_summary.out

=== Resurrecting /data/PHO_WORK/sajagbe2/QMMM/LOVCalculations/lf-proto/sog-protein/coupled-combined/MSOG/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/tmpjxf4xcij.chk
max_memory 4000 MB (current use 1708 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= -1896.64637740257
  HOMO = 0.0673432831337837  LUMO = 0.0781764606597102
cycle= 1 E= -1896.64637737526  delta_E= 2.73e-08  |g|= 0.000244  |ddm|= 0.000472
  HOMO = 0.0674106337225933  LUMO = 0.0781601069873263
cycle= 2 E= -1896.64634953206  delta_E= 2.78e-05  |g|= 0.00781  |ddm|= 0.015
  HOMO = 0.0673453893240857  LUMO = 0.0781756880018083
cycle= 3 E= -1896.64637740224  delta_E= -2.79e-05  |g|= 2.9e-05  |ddm|= 0.0145
  HOMO = 0.06734542592757  LUMO = 0.0781758552348288
cycle= 4 E= -1896.64637740245  delta_E= -2.1e-10  |g|= 1.24e-05  |ddm|= 2.88e-05
converged SCF energy = -1896.64637740245
Resurrected GPU DFT object: <class 'gpu4pyscf.dft.rks.RKS'>, Energy: -1896.646377402452
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 1838 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  get_hcore energy_nuc  of <class 'gpu4pyscf.dft.rks.RKS'>
<class 'gpu4pyscf.dft.rks.RKS'> does not have attributes  spin charge basis
Set gradient conv threshold to 3.16228e-05
init E= -1896.68144265013
  HOMO = 0.0526410743427909  LUMO = 0.0645633423856437
cycle= 1 E= -1896.67863841199  delta_E= 0.0028  |g|= 0.0803  |ddm|= 0.201
  HOMO = 0.0545037151805998  LUMO = 0.0904916953168906
cycle= 2 E= -1896.07697723126  delta_E= 0.602  |g|=    1  |ddm|= 2.03
  HOMO = 0.0547552286859736  LUMO = 0.0648612610104562
cycle= 3 E= -1896.6790789602  delta_E= -0.602  |g|= 0.0826  |ddm|= 2.01
  HOMO = 0.0547064644861339  LUMO = 0.0644724758918846
cycle= 4 E= -1896.68123532608  delta_E= -0.00216  |g|= 0.0303  |ddm|= 0.0903
  HOMO = 0.0533525444369532  LUMO = 0.0643066181579636
cycle= 5 E= -1896.6811842612  delta_E= 5.11e-05  |g|= 0.0359  |ddm|= 0.037
  HOMO = 0.0537826404340575  LUMO = 0.0647062882077638
cycle= 6 E= -1896.68162372321  delta_E= -0.000439  |g|= 0.00721  |ddm|= 0.0494
  HOMO = 0.053925419206228  LUMO = 0.0647944018084181
cycle= 7 E= -1896.68164265588  delta_E= -1.89e-05  |g|= 0.00235  |ddm|= 0.0124
  HOMO = 0.0539118866316878  LUMO = 0.0647514761909231
cycle= 8 E= -1896.68164381824  delta_E= -1.16e-06  |g|= 0.000771  |ddm|= 0.00336
  HOMO = 0.053925662418499  LUMO = 0.0647508742061421
cycle= 9 E= -1896.681643894  delta_E= -7.58e-08  |g|= 0.000558  |ddm|= 0.000814
  HOMO = 0.0539236604832229  LUMO = 0.0647412876082838
cycle= 10 E= -1896.68164394363  delta_E= -4.96e-08  |g|= 0.000425  |ddm|= 0.000376
  HOMO = 0.0539247352159899  LUMO = 0.0647440337069453
cycle= 11 E= -1896.68164399419  delta_E= -5.06e-08  |g|= 0.000261  |ddm|= 0.000311
  HOMO = 0.0539241566394535  LUMO = 0.0647452203976325
cycle= 12 E= -1896.68164401844  delta_E= -2.42e-08  |g|= 0.000121  |ddm|= 0.000268
  HOMO = 0.0539206481303952  LUMO = 0.0647444532655247
cycle= 13 E= -1896.68164401728  delta_E= 1.16e-09  |g|= 0.000138  |ddm|= 0.000458
  HOMO = 0.0539219091241818  LUMO = 0.0647445075751796
cycle= 14 E= -1896.68164402481  delta_E= -7.53e-09  |g|= 1.42e-05  |ddm|= 0.000235
  HOMO = 0.0539221314274673  LUMO = 0.0647447382989656
cycle= 15 E= -1896.68164402496  delta_E= -1.49e-10  |g|= 4.73e-06  |ddm|= 1.73e-05
converged SCF energy = -1896.68164402496
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 1861 MB)


Excited State energies (eV)
[0.40854891 0.53457145 1.48634341]
Combined effects: {'t1_exe_effect': 0.014312959096924704, 't2_exe_effect': -0.012110000425170409, 't3_exe_effect': 0.022291030564790315}

Final statistics written to: logs_20260905_163539/calculation_summary.out
Raw properties appended to: logs_20260905_163539/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_16-38-44/
  Moved: ligand_tuning_summary.csv
  Moved 6 MOL2 files
  Added normalization parameters to summary
  Moved: logs_20260905_163539/ -> logs/
All expected output files were created.
