Messages

1

General Questions and Answers / Re: class STM

« on: September 20, 2022, 18:07 »

Dear Anders,

Thank you. As far as I see, in the TAMR case study the STM tip structure is not considered. However,  class STM for which there is no usage example in the 2022 manual seems to have tip_configuration parameter that allows to read bulk configuration.

So l am wondering whether tip and sample configuration should be stored in separate
 files and then somehow read.

2

General Questions and Answers / class STM

« on: September 5, 2022, 18:59 »

Dear All,

I am wondering how to use STM class. There is no usage example in the manual.

The STM image can be simply calculated using LDOS of bulk configuration in Tersoff-Hamann approximation but it seems that STM class enables also to take into account tip  structure.

Could you kindly explain how to use STM class?

3

General Questions and Answers / DREIDING Calculator error

« on: August 14, 2022, 03:51 »

I encountered the following error while trying to run Time-Stamped Force-Bias Monte Carlo calculations using DREIDING Calculator:

Traceback (most recent call last):
  File "n73_p3_175toluene_175tetralin_NPT_MC.py", line 23441, in <module>
    calculator = potential_builder.createCalculator(bulk_configuration)
  File "zipdir/NL/Calculators/ExternalCalculators/ClassicalCalculators/DreidingPotentialBuilder.py", line 1240, in createCalculator
  File "zipdir/NL/Calculators/ExternalCalculators/ClassicalCalculators/EEMAtomicCharges.py", line 594, in charges
  File "zipdir/NL/CommonConcepts/PhysicalQuantity.py", line 1915, in __setitem__
ValueError: shape mismatch: value array of shape (316,) could not be broadcast to indexing result of shape (1,)

I am wondering what is wrong and how to fix it.

The system contains cnt, few units of polymer, and solvent. The initial configuration was created using packmol and optimized and equilibrated using ReaxFF. I defined the static bonds in the system.

This is how my input looks like below static bonds definitions:


bond_constraint = BondConstraint([[ Nitrogen,  Sulfur],
                     [ Nitrogen,  Carbon]],  inversion_order=8, rotation_order=5)

com_constraint = FixCenterOfMass()

# -------------------------------------------------------------
# DREIDING Calculator
# -------------------------------------------------------------
potential_builder = DreidingPotentialBuilder()
potential_builder.assignAtomTypes(bulk_configuration)
calculator = potential_builder.createCalculator(bulk_configuration)
bulk_configuration.setCalculator(calculator)

bulk_configuration.update()
nlsave('test6.hdf5', bulk_configuration)

# -------------------------------------------------------------
# Time-Stamped Force-Bias Monte Carlo
# -------------------------------------------------------------

method = ForceBiasMonteCarloNPTBerendsen(
    temperature=300*Kelvin,
    max_atom_displacement=0.05*Angstrom,
    heating_rate=0*Kelvin,
    pressure=1*bar,
    barostat_factor=500,
    compressibility=0.0001*bar**-1,
)

tfmc_trajectory = TimeStampedForceBiasMonteCarlo(
    bulk_configuration,
    constraints=[com_constraint],
    trajectory_filename='test6.hdf5',
    steps=100000,
    log_interval=5000,
    method=method,
)

bulk_configuration = tfmc_trajectory.lastImage()
nlsave('test6.hdf5', tfmc_trajectory)

The MC calculation runs when I delete solvent molecules from system.

4

General Questions and Answers / Re: 'Compare Data' Analyzer in T-2022.03 version

« on: June 7, 2022, 11:40 »

Yes, it would be fantastic if you could add step-by-step instructions!

5

General Questions and Answers / Re: 'Compare Data' Analyzer in T-2022.03 version

« on: June 7, 2022, 02:14 »

I have already tried to select two transmission spectra and click on the 'Open all with Transmission Analyzer (Ctrl+O)'. In result I am getting two new windows. In each I see only one spectrum. But I would like to have both plots on one graph - as the old 'Compare Data' worked. How may I do that (except for using 'Compare Data' in the previous version of ATK?)?

6

General Questions and Answers / 'Compare Data' Analyzer in T-2022.03 version

« on: April 16, 2022, 12:24 »

Where can I find the 'Compare Data' Analyzer in the T-2022.03 version?

I would like to plot on one graph the transmission spectra from few files.

In previous ATK NanoLab versions, the 'Compare Data' Analyzer was on the right panel under Compare category (together with 'Compare Configurations'). But in the new version of ATK, the right panel does not contain the complete list of Analyzers; only the supplementary tools list.