Hi,
I am struggling with adding COSMO solvent to 1D system. I modified the 'COSMO for slab' template available in ATK-V-2023.12 version's workflows templates for my system. My system is periodic in X-direction. I added an additional vacuum in Y- and Z- directions making sure that there won't be any interactions between images. Unfortunately calculations in V-2023.12-SP1 version crash with the following error:
Traceback (most recent call last):
File "/u/rscratch/kzm21/codes/QuantumWise/quantumatk/V-2023.12-SP1/atkpython/bin/atkpython", line 8, in <module>
sys.exit(__run_atkpython())
^^^^^^^^^^^^^^^^^
File "zipdir/ATKExecutables/atkwrappers/__init__.py", line 783, in __run_atkpython
File "PFON_solvent_dft_UP_corr.py", line 407, in <module>
pfon_dft_sp_opt.update()
File "zipdir/NL/CommonConcepts/Configurations/AtomicConfiguration.py", line 3080, in update
File "zipdir/NL/Calculators/Interfaces/BulkCalculatorInterface.py", line 167, in _update
File "zipdir/NL/Calculators/Interfaces/BulkCalculatorInterface.py", line 224, in _performUpdate
File "zipdir/NL/Calculators/DensityFunctionalTheory/LCAOCalculator/LCAOCalculator.py", line 1086, in scfLoop
File "zipdir/NL/Calculators/DensityFunctionalTheory/LCAOCalculator/SCFLoop.py", line 676, in scfLoopHamiltonian
File "zipdir/NL/ComputerScienceUtilities/Flowchart.py", line 685, in execute
File "zipdir/NL/ComputerScienceUtilities/Flowchart.py", line 671, in executeBlock
File "zipdir/NL/Calculators/DensityFunctionalTheory/LCAOCalculator/Blocks/CosmoSolvationModel.py", line 47, in beforeFirstExecute
File "zipdir/NL/Calculators/DensityFunctionalTheory/LCAOCalculator/SolvationModel/CosmoFundamentalEquation.py", line 137, in __init__
File "zipdir/NL/Calculators/DensityFunctionalTheory/LCAOCalculator/SolvationModel/CosmoSolventSurface.py", line 642, in constructSurface
File "zipdir/NL/Calculators/DensityFunctionalTheory/LCAOCalculator/SolvationModel/CosmoSolventSurface.py", line 1039, in _mapBasisToCosmoGrid
File "zipdir/NL/CommonConcepts/PhysicalQuantity.py", line 437, in __new__
AttributeError: 'list' object has no attribute 'unit'
Does anyone have idea how to fix that/add properly COSMO solvation model to 1D system?
This is my input:
# %% PFON_dft_SP_opt
# Set up lattice
vector_a = [8.49393, 0.0, 0.0]*Angstrom
vector_b = [0.0, 100.0, 0.0]*Angstrom
vector_c = [0.0, 0.0, 100.0]*Angstrom
lattice = UnitCell(vector_a, vector_b, vector_c)
# Define elements
elements = [Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Hydrogen, Hydrogen,
Hydrogen, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Hydrogen,
Hydrogen, Hydrogen, Hydrogen, Carbon, Hydrogen, Hydrogen, Carbon,
Hydrogen, Hydrogen, Carbon, Hydrogen, Hydrogen, Carbon, Hydrogen,
Hydrogen, Carbon, Hydrogen, Hydrogen, Carbon, Hydrogen, Hydrogen,
Carbon, Hydrogen, Hydrogen, Carbon, Hydrogen, Hydrogen, Hydrogen,
Carbon, Hydrogen, Hydrogen, Carbon, Hydrogen, Hydrogen, Carbon,
Hydrogen, Hydrogen, Carbon, Hydrogen, Hydrogen, Carbon, Hydrogen,
Hydrogen, Carbon, Hydrogen, Hydrogen, Carbon, Hydrogen, Hydrogen,
Carbon, Hydrogen, Hydrogen, Carbon]
# Define coordinates
fractional_coordinates = [[ 0.483852701046, 0.119636242633, 0.10307053107 ],
[ 0.626307579003, 0.129516959822, 0.103117489046],
[ 0.56882264541 , 0.142780927709, 0.102392674738],
[ 0.667873550708, 0.153678983126, 0.099638993485],
[ 0.829389475263, 0.15130457815 , 0.098914078206],
[ 0.791275136104, 0.127511455289, 0.103899709013],
[ 0.619339472103, 0.163719720939, 0.097740247574],
[ 0.907420249346, 0.159494676852, 0.095829139155],
[ 0.840492497578, 0.117543598606, 0.106076276456],
[ 0.137872314815, 0.151290334352, 0.107526877178],
[ 0.077934105328, 0.138569696117, 0.104999404482],
[ 0.175965815584, 0.127481990737, 0.102554893925],
[ 0.340966962957, 0.129480732912, 0.103329581382],
[ 0.398340538247, 0.142760121151, 0.104048881045],
[ 0.29936783279 , 0.153660843147, 0.106795091046],
[ 0.059813620566, 0.159485908572, 0.110590317534],
[ 0.126628876245, 0.117522513102, 0.100357003415],
[ 0.34796366517 , 0.163704261185, 0.108667061082],
[-0.024823133934, 0.039440720236, 0.169810889627],
[-0.020925643797, 0.044243926523, 0.159812428013],
[-0.139219516463, 0.048518080954, 0.157777544939],
[ 0.000867835392, 0.036280279061, 0.152293947051],
[ 0.107453473185, 0.055137217166, 0.159190044084],
[ 0.223958664493, 0.050615187103, 0.161538886759],
[ 0.084978427468, 0.062722856234, 0.167108666019],
[ 0.115921563714, 0.062200108258, 0.145476096404],
[-0.001069747721, 0.066679165383, 0.143171096619],
[ 0.138389172062, 0.054637246355, 0.1375224722 ],
[ 0.243292642395, 0.073213685504, 0.144782927838],
[ 0.361352803016, 0.068671434547, 0.146471536072],
[ 0.224613422524, 0.080452651366, 0.153097033436],
[ 0.242725299815, 0.080840487397, 0.13134564222 ],
[ 0.124591664786, 0.085439441256, 0.129842612033],
[ 0.258678418908, 0.073594037126, 0.122993135075],
[ 0.369889319108, 0.091848562291, 0.130315722375],
[ 0.488767110434, 0.087218664903, 0.131121248691],
[ 0.358668028787, 0.098792038172, 0.138968585291],
[ 0.358393424818, 0.099937900458, 0.117163378208],
[ 0.24055780469 , 0.104739428259, 0.116691341189],
[ 0.365371133557, 0.092905440016, 0.108565709313],
[ 0.487714375094, 0.110742132705, 0.115947791511],
[ 0.604943677477, 0.105832966038, 0.116548599603],
[ 0.4808447953 , 0.1175819344 , 0.12469697221 ],
[ 1.025386268399, 0.046804194892, 0.030189110373],
[ 1.034465763821, 0.052377300824, 0.039755337662],
[ 1.139219516463, 0.058992679427, 0.039106200887],
[ 1.056626413198, 0.044987214425, 0.047830424666],
[ 0.883778806144, 0.060527301844, 0.042541184039],
[ 0.780498222033, 0.053680572071, 0.042781207652],
[ 0.86269145579 , 0.067584860681, 0.034122444356],
[ 0.891633608498, 0.068453885168, 0.05578137744 ],
[ 0.995622048808, 0.075237873461, 0.055534736592],
[ 0.912275545135, 0.061379976491, 0.064207384102],
[ 0.741949915245, 0.076755788806, 0.058616320836],
[ 0.637784438396, 0.069996059008, 0.058910537137],
[ 0.721481203945, 0.083791299193, 0.050157938645],
[ 0.751539754811, 0.084755478467, 0.071800596914],
[ 0.85826984398 , 0.09122344284 , 0.071576355819],
[ 0.768273727959, 0.077708961879, 0.080310438722],
[ 0.605605776864, 0.093578324883, 0.074451106147],
[ 0.498236051722, 0.08719778431 , 0.074853695518],
[ 0.588683842635, 0.100542348268, 0.065879427161],
[ 0.6202843238 , 0.101736447894, 0.087512469367],
[ 0.731605273666, 0.107553132139, 0.087170305935],
[ 0.630670319916, 0.094688160725, 0.096075106203],
[ 0.481174575507, 0.111439186983, 0.089735997374],
[ 0.368600194391, 0.10578612029 , 0.089260401918],
[ 0.477334690635, 0.118748072444, 0.08136160612 ],
[ 0.895725710806, 0.138615586328, 0.102302952886]]
# Set up configuration
pfon_dft_sp_opt = BulkConfiguration(
bravais_lattice=lattice,
elements=elements,
fractional_coordinates=fractional_coordinates
)
# Add tags
pfon_dft_sp_opt.addTags('C_chain', [19, 22, 25, 28, 31, 34, 37, 40, 44, 47, 50, 53, 56,
59, 62, 65])
pfon_dft_sp_opt.addTags('C_ring', [0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 68])
# Add bonds
bonds = [[ 0, 1],
[ 0, 12],
[ 0, 40],
[ 0, 65],
[ 1, 2],
[ 1, 5],
[ 2, 3],
[ 2, 13],
[ 3, 4],
[ 3, 6],
[ 4, 7],
[ 4, 68],
[ 5, 8],
[ 5, 68],
[ 9, 10],
[ 9, 14],
[ 9, 15],
[10, 11],
[10, 68],
[11, 12],
[11, 16],
[12, 13],
[13, 14],
[14, 17],
[18, 19],
[19, 20],
[19, 21],
[19, 22],
[22, 23],
[22, 24],
[22, 25],
[25, 26],
[25, 27],
[25, 28],
[28, 29],
[28, 30],
[28, 31],
[31, 32],
[31, 33],
[31, 34],
[34, 35],
[34, 36],
[34, 37],
[37, 38],
[37, 39],
[37, 40],
[40, 41],
[40, 42],
[43, 44],
[44, 45],
[44, 46],
[44, 47],
[47, 48],
[47, 49],
[47, 50],
[50, 51],
[50, 52],
[50, 53],
[53, 54],
[53, 55],
[53, 56],
[56, 57],
[56, 58],
[56, 59],
[59, 60],
[59, 61],
[59, 62],
[62, 63],
[62, 64],
[62, 65],
[65, 66],
[65, 67]]
pfon_dft_sp_opt.setBonds(bonds)
pfon_dft_sp_opt_name = "pfon_dft_sp_opt"
nlsave('PFON_dft_SP_opt_1_corr.hdf5', pfon_dft_sp_opt)
# %% COSMO for slab
# %% Set LCAOCalculator
# %% LCAOCalculator
#----------------------------------------
# Exchange-Correlation
#----------------------------------------
exchange_correlation = HybridGGA.B3LYP
#----------------------------------------
# Basis Set
#----------------------------------------
basis_set = [
GGABasis.Hydrogen_DoubleZetaPolarized,
GGABasis.Carbon_DoubleZetaPolarized,
]
poisson_solver = FastFourier2DSolver(
boundary_conditions=[
[PeriodicBoundaryCondition(), PeriodicBoundaryCondition()],
[PeriodicBoundaryCondition(), PeriodicBoundaryCondition()],
[DirichletBoundaryCondition(), NeumannBoundaryCondition()]
]
)
k_point_sampling = MonkhorstPackGrid(
na=7,
nb=1,
nc=1
)
numerical_accuracy_parameters = NumericalAccuracyParameters(
density_mesh_cutoff=150.0*Hartree,
k_point_sampling=k_point_sampling
)
solvation_parameters = CosmoSolvationParameters(
solvent_dielectric_constant=2.3741,
solvent_surface_tension=27.9*dyne/cm
)
calculator = LCAOCalculator(
basis_set=basis_set,
exchange_correlation=exchange_correlation,
numerical_accuracy_parameters=numerical_accuracy_parameters,
poisson_solver=poisson_solver,
checkpoint_handler=NoCheckpointHandler,
solvation_parameters=solvation_parameters
)
nlsave('PFON_dft_SP_opt_1_corr.hdf5', calculator)
# %% Set Calculator
pfon_dft_sp_opt.setCalculator(calculator)
pfon_dft_sp_opt.update()
nlsave('PFON_dft_SP_opt_1_corr.hdf5', pfon_dft_sp_opt)
# %% OptimizeGeometry
restart_strategy = RestartFromTrajectory(
trajectory_filename='PFON_dft_SP_opt_1_corr.hdf5',
object_id='optimize_trajectory'
)
optimized_configuration = OptimizeGeometry(
configuration=pfon_dft_sp_opt,
max_forces=0.002*eV/Angstrom,
constraints=[
FixStrain(False, True, True)
],
trajectory_filename='PFON_dft_SP_opt_1_corr.hdf5',
trajectory_object_id='optimize_trajectory',
optimize_cell=False,
restart_strategy=restart_strategy
)
nlsave('PFON_dft_SP_opt_1_corr.hdf5', optimized_configuration)
# %% SolventSurface
solvent_surface = SolventSurface(
configuration=optimized_configuration
)
nlsave('PFON_dft_SP_opt_1_corr.hdf5', solvent_surface)
# %% SolvationEnergy
solvation_energy = SolvationEnergy(
configuration=optimized_configuration
)
nlsave('PFON_dft_SP_opt_1_corr.hdf5', solvation_energy)
