Messages

1

General Questions and Answers / query regarding molecular polarizability and electric field calculations

« on: March 1, 2024, 12:08 »

Dear Sir/Madam,
Could you please tell me the procedure for calculating the following properties for the fullerene:
1. How to calculate the magnitude of molecular polarizability (ALPHA) using QuantumATK?
2. How to apply electric field for a molecule for performing only eigen value calculation (energy gap calculation)?
The structure is attached herewith.
Waiting for your kind reply.

2

General Questions and Answers / Unable to run molecular dynamics simulation using semi-empirical calculator

« on: February 16, 2024, 10:45 »

I am trying to run a semi-empirical molecular dynamics calculation on a carbon nanotube. But when I submit the job, I get the error message

  File "CNT.py", line 111, in <module>
    method=method
  File "zipdir/NL/Dynamics/MolecularDynamics/MolecularDynamics.py", line 677, in MolecularDynamics
  File "zipdir/NL/Dynamics/MolecularDynamics/DynamicsEnergyForcesStress.py", line 31, in wrapped_analysis
  File "zipdir/NL/Calculators/DensityFunctionalTheory/LCAOCalculator/Analysis/FastEnergyForcesStress.py", line 45, in forcesFunction
  File "zipdir/NL/Calculators/DensityFunctionalTheory/LCAOCalculator/Analysis/FastEnergyForcesStress.py", line 71, in _checkAndUpdate
  File "zipdir/NL/Calculators/DensityFunctionalTheory/LCAOCalculator/Analysis/FastEnergyForcesStress.py", line 108, in _update
  File "zipdir/NL/Calculators/SemiEmpirical/HuckelCalculator/Analysis/EnergyForcesStress.py", line 34, in calculateHuckelEnergyForcesStress
  File "zipdir/NL/Calculators/SemiEmpirical/HuckelCalculator/Analysis/EnergyForcesStressUtilities.py", line 216, in setupEnergyForcesStress
NL.ComputerScienceUtilities.Exceptions.NLValueError: No PairPotential given, which is required in order to calculate forces or stress.

Attached with this message is the input file that I am trying to run.

3

General Questions and Answers / How to perform calculation in solvent medium in ATK (Version: ATK-R-2020.09-SP1)

« on: July 1, 2023, 13:38 »

I am using the QuantumATK-R-2020.09-SP1 version and I wish to run a system where solvation effects in a medium such as formaldehyde is considered. Is there any way to perform solvation effects in ATK?

4

General Questions and Answers / Problem related to PDOS of fullerene

« on: July 1, 2023, 13:30 »

I am trying to produce the projected density of states (PDOS) of a fullerene comprising of 80 atoms inside a box. But after running the calculation, only a single line is obtained (all the lines seem to coincide with the Fermi level). But when the calculation is performed for molecular system of the same fullerene, Though different states are obtained, some state are obtained on the fermi level also. Please note that we have performed bandstructure calculations and no states are found on the fermi level and with a considerable energy gap between the VBM and CBM.

1. So how to solve the problem where we are getting the coinciding PDOS lines in the bulk structure.
2. How to solve the problems related to the states being present in the fermi level in the molecular system.

5

General Questions and Answers / Solution calculation in quantumATK

« on: June 15, 2023, 11:41 »

How to take into account the effect of the solution on the interaction energy of the carrier with the drug (within the framework of the PCM, COSMO or similar model) in  QuantumATK-R-2020.09-SP1 version?

6

General Questions and Answers / Re: How to get the spring constant for NEB calculations

« on: March 22, 2023, 12:35 »

Thank you Anders Blom for your reply!
But how do you know that the Default value is 5 eV/A. From where you get this information? If it is in the ATK manual kindly give me the link of that page please. 

7

General Questions and Answers / How to get the spring constant for NEB calculations

« on: March 13, 2023, 10:31 »

I am running an NEB calculation where an atom is moved by a distance of about 2.54 angstrom and created 9 images in the linear method with maximum distance between images set to 0.4 angstrom. But I am unable to find the spring constant for the ion movement images in the NEB calculation. How to know the spring constant?

8

General Questions and Answers / How to resume an NEB calculation in QuantumATK?

« on: September 18, 2022, 13:25 »

I wish to perform an CI-NEB calculation in QuantumATK with about 41 images. But due to power related issues, the machine got shut-down in the middle of the calculation. How can I resume the calculation?

9

General Questions and Answers / How to print stress and forces (fx, fy, fz) at each step of AIMD run

« on: March 28, 2022, 11:39 »

I am running an AIMD simulation in ATK and I want to print the stress as well as the forces fx, fy and fz at each step of the AIMD run in the output log file. How to do that?

10

General Questions and Answers / Question related to charge calculation

« on: February 12, 2022, 17:09 »

I am trying to calculate Fukui Function for periodic system using quantumATK inspired from the work J. Phys. Chem. A 2020, 124, 2826−2833 (using VASP code). As in the mentioned paper they have generated the CHGCAR file (the total charge density multiplied by the volume) for different fractional charges as well as neutral charges. Now, I want to generate the same using ATK. I have generated electron density but I am not understanding how to make this file similar as that of CHGCAR file and also I am not understanding what are the different values in electron density file represents. Another point is that how to give fractional charges during calculation.

11

General Questions and Answers / How to get Coordinates, Energy from AIMD run at each step

« on: December 12, 2021, 07:25 »

I have prepared an input for AIMD run of 20 steps. In the output file, I want to get the following information
lattice vector, coordinates, energy and stress tensor for each step.
However, from the input that I am running, I am not getting these information. And it seems a tedious task to get the coordinates and corresponding values from the movie tool at each snapshot. So kindly tell me how to obtain these values from the AIMD run. Attached with this message is the input file that I am running.

12

General Questions and Answers / Job termination problem during HSE calculation

« on: November 22, 2021, 12:52 »

I am trying to optimize one nanotube having 182 atoms using HSE functional with the help of LCAO calculator. Initially, I have submitted the job using m_file with two nodes (8 proc each. One node having 128 GB RAM and other node having 96 GB RAM). However, the job terminated with the following message "=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES=   PID 244987 RUNNING AT compute-0-1 =   EXIT CODE: 9 =   CLEANING UP REMAINING PROCESSES=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES". After that we have submitted the Job using four nodes with four processor each and RAMs are 128 GB, 96 GB, 64 GB and 64 GB and this time also the job terminated with the same error. Next, I have submitted the using three nodes except compute-0-1 and this time the job stopped without showing any error. I am attaching all the log files for your reference. Kindly help me in this regard.