1
General Questions and Answers / Re: Brodening in LCAO calculator
« on: September 24, 2024, 07:21 »
Thanks for your kind reply. If I change the broadening to 300K, how much change will occur in my results? and it is correct.
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2
General Questions and Answers / Brodening in LCAO calculator
« on: September 23, 2024, 07:21 »
Dear all,
I have a doubt regarding the default broadening value in the LCAO calculator which is 1000 K. What does it mean?
I have a doubt regarding the default broadening value in the LCAO calculator which is 1000 K. What does it mean?
3
General Questions and Answers / Re: Calculating UV Vis spectra
« on: September 4, 2024, 06:31 »
Thanks for your suggestion.
4
General Questions and Answers / Re: Calculating UV Vis spectra
« on: August 28, 2024, 07:30 »
Optical spectrum enables only in the bulk configuration, not the molecular configuration.
5
General Questions and Answers / Calculating UV Vis spectra
« on: August 23, 2024, 15:56 »
Dear all,
Is there a way to calculate the UV Vis spectra like in Gaussian or any other spectral studies for molecules in our quantum ATK?
Is there a way to calculate the UV Vis spectra like in Gaussian or any other spectral studies for molecules in our quantum ATK?
6
General Questions and Answers / Cosmo solvation for 1D materials
« on: August 22, 2024, 07:04 »
Dear all,
I am trying to calculate the solvation energy for 1D materials, but how can I fix the boundary conditions?
I am trying to calculate the solvation energy for 1D materials, but how can I fix the boundary conditions?
7
General Questions and Answers / protonation and deprotonation
« on: June 21, 2024, 12:58 »
Dear experts,
How can I perform protonation and deprotonation in a particular molecule?
Thanks in advance
How can I perform protonation and deprotonation in a particular molecule?
Thanks in advance
8
General Questions and Answers / Dipole calculation
« on: March 16, 2024, 08:19 »
I am trying to calculate the dipole as per the tutorial code for the silicene nanoribbon system. But I am getting some error. I herewith attached the py file and the error message.
Thanks in advance
error message
Mi = sum([ i*abs(grid_data[i,:,:]).sum() for i in range(ni)])/density_abs_sum
TypeError: 'PhysicalQuantity' object is not callable
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1
Thanks in advance
error message
Mi = sum([ i*abs(grid_data[i,:,:]).sum() for i in range(ni)])/density_abs_sum
TypeError: 'PhysicalQuantity' object is not callable
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1
9
General Questions and Answers / Re: Name error in Cosmosolvationparameter
« on: December 28, 2023, 06:43 »
Thank you. Now I have the solvation energy.
10
General Questions and Answers / Name error in Cosmosolvationparameter
« on: December 21, 2023, 14:25 »
Hello everyone,
I am trying to run the py file given in the tutorials for solvation energy in 2023 version [( https://docs.quantumatk.com/manual/Types/SolvationEnergy/SolvationEnergy.html#NL.Analysis.SolvationEnergy.SolvationEnergy ) and I am getting name error. So What I do to solve the error?
# Set minimal log verbosity
setVerbosity(MinimalLog)
# Define elements
elements = [Nitrogen, Hydrogen, Hydrogen, Hydrogen]
# Define coordinates
cartesian_coordinates = [[ 0. , 0. , 0. ],
[ 1.06999992324 , 0. , 0. ],
[-0.35666664108 , 0. , -1.008805602123],
[-0.35666664108 , -0.873651278919, 0.504402801062]]*Angstrom
# Set up configuration
configuration = MoleculeConfiguration(
elements=elements,
cartesian_coordinates=cartesian_coordinates
)
#----------------------------------------
# Basis Set
#----------------------------------------
basis_set = [
BasisGGAPseudoDojo.Hydrogen_High,
BasisGGAPseudoDojo.Nitrogen_High,
]
solvation_parameters = CosmoSolvationParameters(
solvent_dielectric_constant=2.3741,
solvent_surface_tension=27.9*dyne/cm
)
calculator = LCAOCalculator(
basis_set=basis_set,
solvation_parameters=solvation_parameters
)
# Set the calculator
configuration.setCalculator(calculator)
configuration.update()
nlsave('ammonia_toluene.hdf5', configuration)
# Optimize the geometry
optimized_configuration = OptimizeGeometry(
configuration=configuration,
trajectory_filename='ammonia_toluene.hdf5'
)
nlsave('ammonia_toluene.hdf5', optimized_configuration)
# Calculate the solvation energy
solvation_energy = SolvationEnergy(
configuration=optimized_configuration
)
nlsave('ammonia_toluene.hdf5', solvation_energy)
------------------------------------------------------
+------------------------------------------------------------------------------+
| |
| QuantumATK® |
| |
| Version: T-2022.03 for Windows and Linux [Build 17f5b1eb610] |
| |
| Copyright © 2004-2023 Synopsys, Inc. |
| |
| This software and all associated documentation are proprietary to |
| Synopsys, Inc. This software may only be used pursuant to the |
| terms and conditions of a written license agreement with Synopsys, |
| Inc. All other use, reproduction, modification, or distribution of |
| this software is strictly prohibited. |
| |
+------------------------------------------------------------------------------+
Traceback (most recent call last):
File "/opt/home/Akash/Zigzag/dd_chk/dd_chk.py", line 27, in <module>
solvation_parameters = CosmoSolvationParameters(
NameError: name 'CosmoSolvationParameters' is not defined
Traceback (most recent call last):
File "/opt/home/Akash/Zigzag/dd_chk/dd_chk.py", line 27, in <module>
solvation_parameters = CosmoSolvationParameters(
NameError: name 'CosmoSolvationParameters' is not defined
Traceback (most recent call last):
File "/opt/home/Akash/Zigzag/dd_chk/dd_chk.py", line 27, in <module>
solvation_parameters = CosmoSolvationParameters(
NameError: name 'CosmoSolvationParameters' is not defined
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6
I am trying to run the py file given in the tutorials for solvation energy in 2023 version [( https://docs.quantumatk.com/manual/Types/SolvationEnergy/SolvationEnergy.html#NL.Analysis.SolvationEnergy.SolvationEnergy ) and I am getting name error. So What I do to solve the error?
# Set minimal log verbosity
setVerbosity(MinimalLog)
# Define elements
elements = [Nitrogen, Hydrogen, Hydrogen, Hydrogen]
# Define coordinates
cartesian_coordinates = [[ 0. , 0. , 0. ],
[ 1.06999992324 , 0. , 0. ],
[-0.35666664108 , 0. , -1.008805602123],
[-0.35666664108 , -0.873651278919, 0.504402801062]]*Angstrom
# Set up configuration
configuration = MoleculeConfiguration(
elements=elements,
cartesian_coordinates=cartesian_coordinates
)
#----------------------------------------
# Basis Set
#----------------------------------------
basis_set = [
BasisGGAPseudoDojo.Hydrogen_High,
BasisGGAPseudoDojo.Nitrogen_High,
]
solvation_parameters = CosmoSolvationParameters(
solvent_dielectric_constant=2.3741,
solvent_surface_tension=27.9*dyne/cm
)
calculator = LCAOCalculator(
basis_set=basis_set,
solvation_parameters=solvation_parameters
)
# Set the calculator
configuration.setCalculator(calculator)
configuration.update()
nlsave('ammonia_toluene.hdf5', configuration)
# Optimize the geometry
optimized_configuration = OptimizeGeometry(
configuration=configuration,
trajectory_filename='ammonia_toluene.hdf5'
)
nlsave('ammonia_toluene.hdf5', optimized_configuration)
# Calculate the solvation energy
solvation_energy = SolvationEnergy(
configuration=optimized_configuration
)
nlsave('ammonia_toluene.hdf5', solvation_energy)
------------------------------------------------------
+------------------------------------------------------------------------------+
| |
| QuantumATK® |
| |
| Version: T-2022.03 for Windows and Linux [Build 17f5b1eb610] |
| |
| Copyright © 2004-2023 Synopsys, Inc. |
| |
| This software and all associated documentation are proprietary to |
| Synopsys, Inc. This software may only be used pursuant to the |
| terms and conditions of a written license agreement with Synopsys, |
| Inc. All other use, reproduction, modification, or distribution of |
| this software is strictly prohibited. |
| |
+------------------------------------------------------------------------------+
Traceback (most recent call last):
File "/opt/home/Akash/Zigzag/dd_chk/dd_chk.py", line 27, in <module>
solvation_parameters = CosmoSolvationParameters(
NameError: name 'CosmoSolvationParameters' is not defined
Traceback (most recent call last):
File "/opt/home/Akash/Zigzag/dd_chk/dd_chk.py", line 27, in <module>
solvation_parameters = CosmoSolvationParameters(
NameError: name 'CosmoSolvationParameters' is not defined
Traceback (most recent call last):
File "/opt/home/Akash/Zigzag/dd_chk/dd_chk.py", line 27, in <module>
solvation_parameters = CosmoSolvationParameters(
NameError: name 'CosmoSolvationParameters' is not defined
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6
11
General Questions and Answers / Re: regarding calculation of PhononTransmissionSpectra and TE coefficients
« on: June 19, 2023, 16:09 »
In the dynamical matrix, in repetitions choose the custom option with default values. First, try it. Maybe you can get it.
12
General Questions and Answers / Error in Adsorption energy values
« on: June 8, 2023, 12:11 »
Greetings everyone,
As per the literature survey, for NO, NO2, and NH3 adsorption on pristine WS2, the adsorption energy range stated between -0.1 to -0.4 eV. But in our case, we are getting nearly -3 eV. So what will be the reason and what I can do?
Ref. J. Chem. Phys. 142, 214704 (2015)
As per the literature survey, for NO, NO2, and NH3 adsorption on pristine WS2, the adsorption energy range stated between -0.1 to -0.4 eV. But in our case, we are getting nearly -3 eV. So what will be the reason and what I can do?
Ref. J. Chem. Phys. 142, 214704 (2015)
13
General Questions and Answers / Re: Bond distance
« on: May 31, 2023, 12:14 »
Thanks for your suggestion.
14
General Questions and Answers / Bond distance
« on: May 30, 2023, 06:31 »
The Covalent radii in the literature are Si(116 pm) and O(63 pm). But in my case, the covalent bond is formed around (199 pm) between Si and O atoms. Generally, the literature's are mentioning the bond distance must be less than or equal to the sum of covalent radii. Whether the bond I get is considered to be a covalent or van der Waals interaction.
15
General Questions and Answers / Bader analysis
« on: March 18, 2022, 11:11 »
How can i calculate charge transfer through bader analysis for a Silicene nanoribbon.
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