Topics

1

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

2

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)

------------------------------------------------------
+------------------------------------------------------------------------------+
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+------------------------------------------------------------------------------+
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

3

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)

4

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.

5

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.

6

General Questions and Answers / Silicene Nanoribbon

« on: December 21, 2021, 11:46 »

i have few questions about the Silicene nanoribbons.
1. I build a silicene nanoribbon from a plugin. Unit cell is a default option i have. Whether it is okay or i have to change it to hexagonal.
2. What is the K_point sampling for the Silicene nanoribbon.What is criteria to choose the value.
3.What is total energy of the system.
4.What is the band gap value for the Both armchair and Zigzag nanoribbon