Topics

1

General Questions and Answers / Device configuration for stacked 2D materials

« on: November 15, 2016, 21:58 »

Hello ATK users,
I have a question.
Is it possible to transform multilayers of graphene to device configuration? (along c vector).

Best regards,
Payam

2

General Questions and Answers / Spectral energy density SED

« on: November 8, 2016, 21:35 »

Hello ATK Users,
Does anyone know about the implementation of SED method to calculate phonon lifetimes in the ATK-Classical?
Is there any python file someone provided?
Any suggestion will help.

Best regards,
Payam

3

General Questions and Answers / Green-Kubo or autocorrelation function of velocity

« on: November 7, 2016, 05:11 »

Hello ATK-Classical users,
I have a question and any response will be help.
Is there any tutorial  showing how to calculate thermal conductivity using Green-Kubo method?
Does anyone know how to calculate the autocorrelation function of velocity in a MD run?
Thanks in advance.

Best regards,
Payam

4

General Questions and Answers / Combining new SW potential with LJ interaction between layers

« on: October 31, 2016, 18:06 »

Hello ATK Users,
I have tried to develop  a  new Stillinger-Weber type for WTe2 and calculate the cross-plane thermal conductivity. I want to add Lennard-Jones type potential between layers as well.
The potential I have developed  works for monolayer or bulk material (no LJ intercation). However, It does not work for  the case I add the LJ interaction as it does not recognize the potential I have developed for in-plane structure. Here is my code for calculator:

# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------
potentialSet = TremoloXPotentialSet(name = 'StillingerWeber_WTe_2016')
potentialSet.addParticleType(ParticleType(symbol='W', mass=183.84 * atomic_mass_unit, charge=None, sigma=None, sigma14=None, epsilon=None, epsilon14=None, atomicNumber=74))
potentialSet.addParticleType(ParticleType(symbol='Te', mass=78.96 * atomic_mass_unit, charge=None, sigma=None, sigma14=None, epsilon=None, epsilon14=None, atomicNumber=52))

#----------------------------------   Two Body    -----------------------------------------------------
potential = Stiwe2Potential(particleType1 = 'Te', particleType2 = 'Te', p = 4.0, A = 12.265*eV,   B = 60.4319*Angstrom**4,  gamma = 0.046*Angstrom, r_cut = 4.05735*Angstrom)
potentialSet.addPotential(potential)
potential = Stiwe2Potential(particleType1 = 'W',  particleType2 = 'W',  p = 4.0, A = 26.7*eV,   B = 29.0197*Angstrom**4,  gamma = 2.019346*Angstrom,   r_cut = 4.63325*Angstrom)
potentialSet.addPotential(potential)
potential = Stiwe2Potential(particleType1 = 'W',  particleType2 = 'Te', p = 4.0, A = 35.783*eV,   B = 32*Angstrom**4,  gamma = 2.852*Angstrom, r_cut = 3.49635*Angstrom)

#----------------------------------   Three Body    -----------------------------------------------------
potentialSet.addPotential(potential)
potential = Stiwe3Potential(particleType1 = 'Te', particleType2 = 'W',  particleType3 = 'Te', gamma0 = 0.7*Angstrom, gamma1 = 0.7*Angstrom, l = 24.157*eV, cosTheta0 = 0.1, type = 1, r_0 = 3.29915*Angstrom, r_1 = 3.29915*Angstrom, r_13 = 4.05735*Angstrom)
potentialSet.addPotential(potential)
potential = Stiwe3Potential(particleType1 = 'W',  particleType2 = 'Te', particleType3 = 'W', gamma0 = 2.2*Angstrom, gamma1 = 2.2*Angstrom, l =13.52*eV, cosTheta0 = 0.1, type = 1, r_0 = 3.29915*Angstrom, r_1 = 3.29915*Angstrom, r_13 = 4.63325*Angstrom)
potentialSet.addPotential(potential)
#--------------------------------------------------------------------------------------------------------
sw_layer1 = StillingerWeber_WSe_2016(tags='layer1')
sw_layer2 = StillingerWeber_WSe_2016(tags='layer2')
sw_layer1 = StillingerWeber_WSe_2016(tags='layer3')
sw_layer1 = StillingerWeber_WSe_2016(tags='layer4')
sw_layer1 = StillingerWeber_WSe_2016(tags='layer5')
sw_layer1 = StillingerWeber_WSe_2016(tags='layer6')
sw_layer1 = StillingerWeber_WSe_2016(tags='layer7')
sw_layer1 = StillingerWeber_WSe_2016(tags='layer8')
sw_layer1 = StillingerWeber_WSe_2016(tags='layer9')
sw_layer1 = StillingerWeber_WSe_2016(tags='layer10')
sw_layer1 = StillingerWeber_WSe_2016(tags='layer11')

# Define a new potential for the interlayer interaction.
lj_interlayer_potential = TremoloXPotentialSet(name="InterLayerPotential")

# Add particle type definitions for both types.
lj_interlayer_potential.addParticleType(ParticleType.fromElement(Tungsten))
lj_interlayer_potential.addParticleType(ParticleType.fromElement(Tellurium, sigma=3.5*Angstrom, epsilon=0.0215*eV))

# Add Lennard-Jones potentials between the sulfur atoms of different layers.
lj_interlayer_potential.addPotential(LennardJonesPotential('Te', 'Te', r_cut=10.0 * Angstrom))
lj_interlayer_potential.setTags(['layer1', 'layer2', 'layer3', 'layer4', 'layer5', 'layer6', 'layer7', 'layer8', 'layer9', 'layer10', 'layer11'])

# Combine all 3 potential sets in a single calculator.
calculator = TremoloXCalculator(parameters=[sw_layer1, sw_layer2, sw_layer3, sw_layer4, sw_layer5, sw_layer6, sw_layer7, sw_layer8, sw_layer9, sw_layer10, sw_layer11, lj_interlayer_potential])


bulk_configuration.setCalculator(calculator)
nlprint(bulk_configuration)
bulk_configuration.update()
nlsave('/home/payam/Desktop/CrossPlaneKappa/300K_total.nc', bulk_configuration)


Could anyone help me to modify the calculator?

Best regards,
Payam

5

General Questions and Answers / Fails to start

« on: September 29, 2016, 01:19 »

Dear ATK Users,
The ATK was running and after a while it crashed. Now, it fails to start and after clicking on the VNL icon  nothing happens. Only the logo appears and then it disappears.
Could you please let me know what to do?

Best regards,
Payam

6

General Questions and Answers / harmonic and cubic force constants

« on: September 19, 2016, 21:55 »

Dear ATK users,
Does anyone know how to calculate harmonic and anharmonic (cubic) force constants using ATK-classical module?

Best regards,
Payam

7

General Questions and Answers / SW potential-ATK and Lammps

« on: September 9, 2016, 20:54 »

Dear all,
It seems that there is no one to one correspondence between SW parametrization in ATK and in Lammps. The number of cutoff distances in 3-body interaction terms of ATK is more than that of Lammps. The same thing is true for gammas.
This the list of parameters in Lammps:
Epsilon   Sigma           a           lambda     gamma           costheta0   A           B           p   q   tol

which is less than this list as an example:
potential = Stiwe3Potential(particleType1 = 'Se', particleType2 = 'Mo', particleType3 = 'Se', gamma0 = 0.425*Angstrom, gamma1 = 0.425*Angstrom, l = 8*eV, cosTheta0 = 0.2, type = 1, r_0 = 3.25*Angstrom, r_1 = 3.25*Angstrom, r_13 = 3.85*Angstrom)
Any clarification would be appreciated.

Best  regards,
Payam

8

General Questions and Answers / Cross plane thermal conductivity of 2D materials

« on: September 2, 2016, 06:30 »

Dear all,
Does anyone know the procedure to calculate the cross plane thermal conductivity of 2D materials? is there ant tutorial about it?

Best regards,
Payam

9

General Questions and Answers / Defining new Tersoff potential

« on: July 19, 2016, 18:57 »

Dear All,
I need to define a new Tersoff potential and then combine it with Lenard-Jones potential foe interlayer interaction. Does anyone know how to do that?
In tutorial , the LJ potential can be combined only with available potential. How can I combine LJ interaction with newly created Tersoff potential?

Best regards,
Payam

10

General Questions and Answers / Adding LJ potential between hBN

« on: July 12, 2016, 21:38 »

Hello,
How can I add LJ potential between layers of hBN?
are sigma and epsilon the parameters of LJ potential in the following lines from the python script?
potentialSet.addParticleType(ParticleType(symbol='B', mass=10.811 * atomic_mass_unit, charge=None, sigma=None, sigma14=None, epsilon=None, epsilon14=None, atomicNumber=5))
potentialSet.addParticleType(ParticleType(symbol='N', mass=14.0067 * atomic_mass_unit, charge=None, sigma=None, sigma14=None, epsilon=None, epsilon14=None, atomicNumber=7))

Best regards,
Payam Norouzzadeh