61
General Questions and Answers / Re: Constraints_data parameter in function "writePOSCAR"
« Last post by sukhito teh on April 15, 2024, 11:48 »Thanks for your reply.
Recent Posts
62
General Questions and Answers / Re: how to generate a file *.nc from hdf5 or py
« Last post by gloria.cardenas on April 13, 2024, 20:46 »Dear Dr. Blom,
Thanks for your reply.
I am working the tutorial of boron difussion on silicon surface, and the script for AKMC shows that it need to read a file *.nc with the optimized structure. I tried with a file *.py without success.
Thanks for your reply.
I am working the tutorial of boron difussion on silicon surface, and the script for AKMC shows that it need to read a file *.nc with the optimized structure. I tried with a file *.py without success.
63
General Questions and Answers / Re: How is Defect Diffusivity Calculated with calculateDiffusivity method?
« Last post by Anders Blom on April 12, 2024, 23:51 »64
General Questions and Answers / Re: LDA+U in noncollinear spin
« Last post by Anders Blom on April 12, 2024, 23:46 »Should be possible for Normconserving LCAO, yes.
65
General Questions and Answers / Re: Constraints_data parameter in function "writePOSCAR"
« Last post by Anders Blom on April 12, 2024, 23:44 »It requires 2 steps.
1) Define constraints via tags. Supported tags are "constrain" and "constrain_x" (y, z) in order to constrain each atom fully or only in x/y/z
2) Use a few lines of code
Example config attached, with the resulting POSCAR.
Note that you can also do this directly from the Builder, using Export and choosing the VASP format.
1) Define constraints via tags. Supported tags are "constrain" and "constrain_x" (y, z) in order to constrain each atom fully or only in x/y/z
2) Use a few lines of code
Code: python
from AddOns.VASPPlugins.Scripter.VASPConstraintsWidget import extractConstraintsFromTags
from AddOns.VASPPlugins.IO import writePOSCAR
vasp_constraints = extractConstraintsFromTags(configuration)
writePOSCAR(configuration, "POSCAR", vasp_constraints)
Example config attached, with the resulting POSCAR.
Note that you can also do this directly from the Builder, using Export and choosing the VASP format.
66
General Questions and Answers / Re: how to generate a file *.nc from hdf5 or py
« Last post by Anders Blom on April 12, 2024, 23:17 »Why do you need to do that? In general I would say it's not possible, these are not standard file formats you can just convert between.
67
General Questions and Answers / Re: Phonon dispersion is senstitive to "processes_per_displacement" paramter of DM?
« Last post by Anders Blom on April 12, 2024, 23:15 »From these files it is at least clear that the self-consistent loops proceeds very differently in the two cases for some displacements (but not all), and in the end of course this makes a big difference for the dynamical matrix.
Now, when I submit this to our bug fixing team, the first thing they will ask is if it was tested in the latest version. I personally don't have a machine with 168 cores at hand to test on, but you do, so it would be really helpful if you could rerun this with V-2023.12-SP1 (which has many new features compared to U anyway), since in theory it could have been fixed since the version you used. This should only take you 7-8 hours :-)
Second, I find your choice of processes_per_displacement=28 odd when you run on 24-core machines. This gives at the very least odd load-balancing and unnecessary network communications.
So, please check using processes_per_displacement=24 instead. One can argue that any value should work numerically, so we might still look into it, but only if it appears in V-version also.
The nice news, once we resolve this, is that the speedup using a large processes_per_displacement is substantial, basically linear!
Now, when I submit this to our bug fixing team, the first thing they will ask is if it was tested in the latest version. I personally don't have a machine with 168 cores at hand to test on, but you do, so it would be really helpful if you could rerun this with V-2023.12-SP1 (which has many new features compared to U anyway), since in theory it could have been fixed since the version you used. This should only take you 7-8 hours :-)
Second, I find your choice of processes_per_displacement=28 odd when you run on 24-core machines. This gives at the very least odd load-balancing and unnecessary network communications.
So, please check using processes_per_displacement=24 instead. One can argue that any value should work numerically, so we might still look into it, but only if it appears in V-version also.
The nice news, once we resolve this, is that the speedup using a large processes_per_displacement is substantial, basically linear!
68
General Questions and Answers / how to generate a file *.nc from hdf5 or py
« Last post by gloria.cardenas on April 12, 2024, 03:19 »Dear All,
Does someone know how to generate a file *.nc from hdf5 or py?
Thank you
Gloria
Does someone know how to generate a file *.nc from hdf5 or py?
Thank you
Gloria
69
General Questions and Answers / Re: How is Defect Diffusivity Calculated with calculateDiffusivity method?
« Last post by pshinyeong on April 11, 2024, 15:03 »Thank you for your response.
In that case, is the calculatediffusivity method proceed to adaptive kinetic monte carlo? or does it only calculate the diffusivity of diffusion between the specified initial and final state.
If it's the latter, is there an equation or specific link to the document describing how defectdiffusivity is calculated?
Thank you,
Shinyeong
In that case, is the calculatediffusivity method proceed to adaptive kinetic monte carlo? or does it only calculate the diffusivity of diffusion between the specified initial and final state.
If it's the latter, is there an equation or specific link to the document describing how defectdiffusivity is calculated?
Thank you,
Shinyeong
70
General Questions and Answers / how to use COSMO solvent in 1D systems?
« Last post by karolina 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)
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)