Show Posts

1

General Questions and Answers / how to use COSMO solvent in 1D systems?

« on: April 10, 2024, 17:34 »

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)

2

General Questions and Answers / Re: QuantumATK-R-2020.09:JobManager does not start

« on: October 1, 2020, 14:10 »

I solved the problem by removing two files from '.vnl/job_manager_2020.09' : 'state.hdf5' and 'machines.hdf5' (I am not sure which was causing the problem) However, this removes all history of previous jobs. The restored Job Manager does not show any jobs that were run before.

3

General Questions and Answers / QuantumATK-R-2020.09:JobManager does not start

« on: October 1, 2020, 13:41 »

I have encountered strange problem with launching JobManager in QuantumATK-R-2020.09 which was working normally up to now. I am not able to open the Job Manager from the left menu nor send prepared input from Script Generator to the Job Manager. As I checked, this error appears in all projects including example project.

I am getting the following error message:
Traceback (most recent call last):
File "zipdir/NL/GUI/MainWindow/MainWindow.py", line 1011, in jobManager
File "zipdir/NL/GUI/MainWindow/MainWindow.py", line 1026, in jobManagerReference
File "zipdir/NL/GUI/MainWindow/MainWindow.py", line 1043, in singletonTool
File "zipdir/NL/GUI/Tools/JobManager/JobManager.py", line 272, in __init__
File "zipdir/NL/GUI/Tools/JobManager/JobManager.py", line 454, in loadSettings
File "zipdir/NL/GUI/Tools/JobManager/JobManager.py", line 491, in loadSettingsPre2019_12
TypeError: argument of type 'int' is not iterable

QuantumATK Forum

News:

Messages - karolina

General Questions and Answers / how to use COSMO solvent in 1D systems?

General Questions and Answers / Re: QuantumATK-R-2020.09:JobManager does not start

General Questions and Answers / QuantumATK-R-2020.09:JobManager does not start