Defining new Tersoff potential

[payam]

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

[payam]

Dear ATK users,
I have a quick question. Here is part of script to calculate phonon properties of graphite.
Are sigma and epsilon the same as LJ interaction parameters?
potentialSet = TremoloXPotentialSet(name = 'Tersoff_CH_2010')
potentialSet.addParticleType(ParticleType(symbol='H', mass=1.00794 * atomic_mass_unit, charge=0.0, sigma=1.0*Angstrom, sigma14=1.0*Angstrom, epsilon=0.0*eV, epsilon14=0.0*eV, atomicNumber=None))
potentialSet.addParticleType(ParticleType(symbol='C', mass=12.0107 * atomic_mass_unit, charge=0.0, sigma=1.0*Angstrom, sigma14=1.0*Angstrom, epsilon=0.0*eV, epsilon14=0.0*eV, atomicNumber=None))

best regards,
Payam

[Anders Blom]

Yes, see http://www.quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.lennardjonespotential.html

[payam]

Thank you for your response Anders.
Do we have REBO potential for graphite? I did not see it in the list.

Best regards,
Payam

[payam]

Dear ATK users
I have one more question:
How can I add my own potential to the available potential database?
For example, there is no potential available for MoSe2 and I want to add my own potential to the database. What is the procedure?

Thanks in advance.

Best regards,
Payam

[Anders Blom]

No Brenner/REBO, coming a bit later.
You can in principle add a Python script to lib/python2.7/site-packages which you then can import in any script. However, it will not appear in VNL, there is currently no mechanism for that.
But you can also just keep the definition of the new potential in a separate Python file that you import in each script that uses it.

[payam]

Thank you very much Anders.

Best regards,
Payam

[payam]

Dear All,
I tried to define my own potential for hBN which includes interlayer LJ potential and intra-layer Tersoff potential according to Lindsay's parameters (PRB 2011). Here is the section related to potential definition:

# Add tags
bulk_configuration.addTags('layer1', [0, 3])
bulk_configuration.addTags('layer2', [1, 2])
# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------
#-------------------- Definition ------------------------------
potentialSet = TremoloXPotentialSet(name = 'hBN_Tersoff_Lindsay_2011')

#-------------------- Add Particle ------------------------------
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))

#-------------------- Single Potential ------------------------------
potential = TersoffSingleTypePotential(particleType = 'B', A = 1433.0*eV, B = 417.3*eV, R = 1.95*Angstrom, S = 2.1*Angstrom, l = 3.4661*1/Angstrom, mu = 2.2288*1/Angstrom, alpha = 0.0*1/Angstrom, beta = 1.0239e-07, omega = 1.0, chi = 1.0, chiR = 1.0, m = 0, n = 0.72674, c = 30692.4, d = 4.7295, h = -0.98578)
potentialSet.addPotential(potential)
potential = TersoffSingleTypePotential(particleType = 'N', A = 1433.0*eV, B = 417.3*eV, R = 1.95*Angstrom, S = 2.1*Angstrom, l = 3.4661*1/Angstrom, mu = 2.2288*1/Angstrom, alpha = 0.0*1/Angstrom, beta = 1.0239e-07, omega = 1.0, chi = 1.0, chiR = 1.0, m = 0, n = 0.72674, c = 30692.4, d = 4.7295, h = -0.98578)
potentialSet.addPotential(potential)

#-------------------- Mix Potential ------------------------------
potential = TersoffMixitPotential(particleType1 = 'B', particleType2 = 'N', alpha = 0.0*1/Angstrom, omega = 1.0, chi = 1.0, chiR = 1.0, m = 0)
potentialSet.addPotential(potential)

#-------------------- Intra-layer potential ------------------------------
#tf_layer1 = hBN_Tersoff_Lindsay_2011(tags='layer1')
#tf_layer2 = hBN_Tersoff_Lindsay_2011(tags='layer2')

#-------------------- Finalizing ------------------------------
# Define a new potential for the interlayer interaction.
lj_interlayer_potential = TremoloXPotentialSet(name="InterLayerPotential")
lj_interlayer_potential.setTags(['layer1', 'layer2'])
# Add particle type definitions for both types.
lj_interlayer_potential.addParticleType(ParticleType.fromElement(Boron,))
lj_interlayer_potential.addParticleType(ParticleType.fromElement(Nitrogen, sigma=3.212*Angstrom, epsilon=0.004*eV))

# Add Lennard-Jones potentials between the sulfur atoms of different layers.
lj_interlayer_potential.addPotential(LennardJonesPotential('layer1', 'layer2', r_cut=10.0 * Angstrom))

# Combine all 3 potential sets in a single calculator.
calculator = TremoloXCalculator(parameters=potentialSet)
calculator.setInternalOrdering("default")


However, ATK does not include the interlayer potential in calculations. Does anyone have any solution?

Best regards,
Payam

[Anders Blom]

You never add the interlayer potential to the potentialSet

[payam]

Dear Anders,
I added LJ to potentialset and it looks like this but still it does not include the LJ interaction:

# Add tags
bulk_configuration.addTags('layer1', [0, 3])
bulk_configuration.addTags('layer2', [1, 2])
# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------
#-------------------- Definition ------------------------------
potentialSet = TremoloXPotentialSet(name = 'hBN_Tersoff_Lindsay_2011')

#-------------------- Add Particle ------------------------------
potentialSet.addParticleType(ParticleType(symbol='B', mass=10.811 * atomic_mass_unit, charge=None, sigma=3.212*Angstrom, sigma14=None, epsilon=0.004*eV, epsilon14=None, atomicNumber=5))
potentialSet.addParticleType(ParticleType(symbol='N', mass=14.0067 * atomic_mass_unit, charge=None, sigma=3.212*Angstrom, sigma14=None, epsilon=0.004*eV, epsilon14=None, atomicNumber=7))

#-------------------- Single Potential ------------------------------
potential = TersoffSingleTypePotential(particleType = 'B', A = 1433.0*eV, B = 417.3*eV, R = 1.95*Angstrom, S = 2.1*Angstrom, l = 3.4661*1/Angstrom, mu = 2.2288*1/Angstrom, alpha = 0.0*1/Angstrom, beta = 1.0239e-07, omega = 1.0, chi = 1.0, chiR = 1.0, m = 0, n = 0.72674, c = 30692.4, d = 4.7295, h = -0.98578)
potentialSet.addPotential(potential)
potential = TersoffSingleTypePotential(particleType = 'N', A = 1433.0*eV, B = 417.3*eV, R = 1.95*Angstrom, S = 2.1*Angstrom, l = 3.4661*1/Angstrom, mu = 2.2288*1/Angstrom, alpha = 0.0*1/Angstrom, beta = 1.0239e-07, omega = 1.0, chi = 1.0, chiR = 1.0, m = 0, n = 0.72674, c = 30692.4, d = 4.7295, h = -0.98578)
potentialSet.addPotential(potential)

#-------------------- Mix Potential ------------------------------
potential = TersoffMixitPotential(particleType1 = 'B', particleType2 = 'N', alpha = 0.0*1/Angstrom, omega = 1.0, chi = 1.0, chiR = 1.0, m = 0)
potentialSet.addPotential(potential)

#-------------------- Finalizing ------------------------------
# Define a new potential for the interlayer interaction.
lj_interlayer_potential = TremoloXPotentialSet(name="InterLayerPotential")
lj_interlayer_potential.setTags(['layer1', 'layer2'])

# Add particle type definitions for both types.
lj_interlayer_potential.addParticleType(ParticleType.fromElement(Boron,))
lj_interlayer_potential.addParticleType(ParticleType.fromElement(Nitrogen, sigma=3.212*Angstrom, epsilon=0.004*eV))

# Add Lennard-Jones potentials between the sulfur atoms of different layers.
potentialSet.addPotential(LennardJonesPotential('layer1', 'layer2', r_cut=10.0 * Angstrom))

# Combine all 3 potential sets in a single calculator.
calculator = TremoloXCalculator(parameters=potentialSet)
calculator.setInternalOrdering("default")


Could you please let me know what I am missing?

Best regards,
Payam

[Anders Blom]

How can you tell it's not using it?
Shouldn't there be sigma and epsilon for Boron?
I'm going on vacation, you can email support@ for more help

[payam]

Because, adding or removing LJ interaction has no effect on phonon dispersion in z direction (A-Gamma k-path).

[Anders Blom]

No = 0, or perhaps just very small? The LJ interaction is quite weak...

[payam]

Yes. The LJ interaction is weak. However, Lindsay in PHYSICAL REVIEW B 84, 155421 (2011) Figure 1
shows that the LJ effect is not negligible and adding LJ causes dispersion in the z-axis.

[Julian Schneider]

What you need to do is

Code

# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------
#-------------------- Definition ------------------------------
potentialSet = TremoloXPotentialSet(name = 'hBN_Tersoff_Lindsay_2011')

#-------------------- Add Particle ------------------------------
potentialSet.addParticleType(ParticleType(symbol='B', mass=10.811 * atomic_mass_unit, charge=None, sigma=3.212*Angstrom, sigma14=None, epsilon=0.004*eV, epsilon14=None, atomicNumber=5))
potentialSet.addParticleType(ParticleType(symbol='N', mass=14.0067 * atomic_mass_unit, charge=None, sigma=3.212*Angstrom, sigma14=None, epsilon=0.004*eV, epsilon14=None, atomicNumber=7))

#-------------------- Single Potential ------------------------------
potential = TersoffSingleTypePotential(particleType = 'B', A = 1433.0*eV, B = 417.3*eV, R = 1.95*Angstrom, S = 2.1*Angstrom, l = 3.4661*1/Angstrom, mu = 2.2288*1/Angstrom, alpha = 0.0*1/Angstrom, beta = 1.0239e-07, omega = 1.0, chi = 1.0, chiR = 1.0, m = 0, n = 0.72674, c = 30692.4, d = 4.7295, h = -0.98578)
potentialSet.addPotential(potential)
potential = TersoffSingleTypePotential(particleType = 'N', A = 1433.0*eV, B = 417.3*eV, R = 1.95*Angstrom, S = 2.1*Angstrom, l = 3.4661*1/Angstrom, mu = 2.2288*1/Angstrom, alpha = 0.0*1/Angstrom, beta = 1.0239e-07, omega = 1.0, chi = 1.0, chiR = 1.0, m = 0, n = 0.72674, c = 30692.4, d = 4.7295, h = -0.98578)
potentialSet.addPotential(potential)

#-------------------- Mix Potential ------------------------------
potential = TersoffMixitPotential(particleType1 = 'B', particleType2 = 'N', alpha = 0.0*1/Angstrom, omega = 1.0, chi = 1.0, chiR = 1.0, m = 0)
potentialSet.addPotential(potential)

# 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(Boron,))
lj_interlayer_potential.addParticleType(ParticleType.fromElement(Nitrogen, sigma=3.212*Angstrom, epsilon=0.004*eV))

# Add Lennard-Jones potentials between the nitrogen atoms of different layers.
lj_interlayer_potential.addPotential(LennardJonesPotential(' N', 'N', r_cut=10.0 * Angstrom))
lj_interlayer_potential.setTags(['layer1', 'layer2'])

# Combine all potential sets in a single calculator.
calculator = TremoloXCalculator(parameters=[potential, lj_interlayer_potential])

This adds LJ-interaction between nitrogen atoms in layer1 and layer2. IF you want to add LJ-interactions for Boron-Boron or Nitrogen-Boron as well, you need to specify the epsilon and sigma parameters for Boron in the line

Code

lj_interlayer_potential.addParticleType(ParticleType.fromElement(Boron,))

and then add LennardJones-potentials for the desired element interactions, e.g.

Code

lj_interlayer_potential.addPotential(LennardJonesPotential(' B', 'B', r_cut=10.0 * Angstrom))