Messages

1

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

« on: November 18, 2016, 17:01 »

Dear Daniele,
Thank you for your response. I have attached the configuration  of stacked MoS2 to form a device in z direction.
Thank you for your help.

Best regards,
Payam

2

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

« on: November 16, 2016, 18:59 »

Thank you for your response Daniele.
I tried the device from bulk already but it is not active for my configuration. Am I missing something?

Best regards,
Payam

3

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

« on: November 16, 2016, 18:57 »

Thank you very much Julian for your informative response.

Best regards,
Payam

4

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

5

General Questions and Answers / Re: Spectral energy density SED

« on: November 9, 2016, 21:23 »

Thank you Daniele for your response.

Best regards,
Payam

6

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

7

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

« on: November 8, 2016, 15:24 »

Thank you Petr for your response.
BR,
Payam

8

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

« on: November 7, 2016, 18:18 »

Thank you Petr.
As I noticed, the calculation of thermal conductance in that example is based on NEGF and not Green-Kubo method.
velocity autocorrelation function is available through menu of MD analyzer.
Do you know how to calculate the heat capacity after a MD simulation? Do you know an example by ATK?
Thanks again.

Best regards,
Payam

9

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

10

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

« on: November 1, 2016, 16:40 »

Dear Anders,
You are right. Thank you.
However, it seems that the number of layers should be limited to 2 in ATK. With 2 layers it works.

Best regards,
Payam

11

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

12

General Questions and Answers / Re: Fails to start

« on: September 29, 2016, 17:30 »

Dear Anders,
I resolved it and it works. Thank you very much.

Best regards,
Payam

13

General Questions and Answers / Re: Fails to start

« on: September 29, 2016, 17:26 »

Dear Anders,
Thank you for your response.
Is $home/.vnl an address? I could not find main.ini file. Could you please clarify it?

Best regards,
Payam

14

General Questions and Answers / Re: Fails to start

« on: September 29, 2016, 16:23 »

By the way, this is what I found in crash.log:

Traceback (most recent call last):
  File "./zipdir/NL/GUI/Main/Main.py", line 114, in main
  File "./zipdir/NL/GUI/MainWindow/MainStack.py", line 21, in __init__
  File "./zipdir/NL/GUI/MainWindow/MainStack.py", line 114, in readSettings
UnicodeEncodeError: 'ascii' codec can't encode characters in position 3-4: ordinal not in range(128)

15

General Questions and Answers / Re: Fails to start

« on: September 29, 2016, 16:02 »

Thank you for your attention.
I put VNL in terminal then the VNL logo appeared and disappeared with no message!
I remember it happened once in before and I removed a file and it became healthy. I do not remember that procedure now.

Best regards,
Payam