potential Module

class potential.BasePotential

Bases: object

Abstract base class for inter-atomic potentials.

Inter-atomic potentials can be described by a scalar function \(V(r)\) which depends on the distance \(r=|\vec{r}_i-\vec{r}_j|\) between two atoms i and j. In MD simulations we need this potential and the force \(\vec{F}(r) = -\nabla V(r)\).

class potential.Buckingham(a=1.0, b=1.0, c=1.0, rc=2.5)

Bases: potential.BasePotential

datdict(input_state)

Map between state variables and kernel variables, returns required dictonary.

Parameters:input_state (state) – state with containing variables.
get_data_map(positions=None, forces=None, potential_energy=None)
kernel

Returns a kernel class for the potential.

class potential.BuckinghamSymmetric(a=1.0, b=1.0, c=1.0, rc=2.5)

Bases: potential.Buckingham

kernel

Returns a kernel class for the potential.

class potential.LennardJones(epsilon=1.0, sigma=1.0, rc=None)

Bases: potential.LennardJonesShifted

Lennard Jones potential.

for \(r>r_c=(5/2) \sigma\) the potential (and force) is set to zero.

Parameters:
  • epsilon – Potential parameter \(\epsilon\)
  • sigma – Potential parameter \(\sigma\)
kernel

Returns a kernel class for the potential.

class potential.LennardJonesCounter(epsilon=1.0, sigma=1.0, rc=None)

Bases: potential.LennardJones

Lennard Jones potential.

for \(r>r_c=(5/2) \sigma\) the potential (and force) is set to zero.

Parameters:
  • epsilon – Potential parameter \(\epsilon\)
  • sigma – Potential parameter \(\sigma\)
datdict(input_state)

Map between state variables and kernel variables, returns required dictonary.

Parameters:input_state (state) – state with containing variables.
kernel

Returns a kernel class for the potential.

class potential.LennardJonesShifted(epsilon=1.0, sigma=1.0)

Bases: potential.BasePotential

Shifted Lennard Jones potential.

for \(r>r_c=2^{1/6}\) the potential (and force) is set to zero.

Parameters:
  • epsilon – Potential parameter \(\epsilon\)
  • sigma – Potential parameter \(\sigma\)
datdict(input_state)

Map between state variables and kernel variables, returns required dictonary.

Parameters:input_state (state) – state with containing variables.
get_data_map(positions=None, forces=None, potential_energy=None)
kernel

Returns a kernel class for the potential.

rc

Value of cufoff distance \(r_c\)

class potential.NULL(rc=None)

Bases: object

NULL potential

static datdict(input_state)

Map between state variables and kernel variables, returns required dictonary.

Parameters:input_state (state) – state with containing variables.
kernel

Returns a kernel class for the potential.

rc

Value of cufoff distance \(r_c\)

rn

Value of cufoff distance \(r_c\)

class potential.NoVLennardJones(epsilon=1.0, sigma=1.0, rc=None)

Bases: potential.LennardJones

kernel

Returns a kernel class for the potential.

class potential.TestPotential1(epsilon=1.0, sigma=1.0, rc=None)

Bases: potential.LennardJones

Lennard Jones potential.

for \(r>r_c=(5/2) \sigma\) the potential (and force) is set to zero.

Parameters:
  • epsilon – Potential parameter \(\epsilon\)
  • sigma – Potential parameter \(\sigma\)
kernel

Returns a kernel class for the potential.

class potential.TestPotential2(epsilon=1.0, sigma=1.0, rc=None)

Bases: potential.LennardJones

Lennard Jones potential.

for \(r>r_c=(5/2) \sigma\) the potential (and force) is set to zero.

Parameters:
  • epsilon – Potential parameter \(\epsilon\)
  • sigma – Potential parameter \(\sigma\)
kernel

Returns a kernel class for the potential.

class potential.TestPotential3(epsilon=1.0, sigma=1.0, rc=None)

Bases: potential.LennardJones

Lennard Jones potential.

for \(r>r_c=(5/2) \sigma\) the potential (and force) is set to zero.

Parameters:
  • epsilon – Potential parameter \(\epsilon\)
  • sigma – Potential parameter \(\sigma\)
kernel

Returns a kernel class for the potential.

class potential.TestPotential4(epsilon=1.0, sigma=1.0, rc=None)

Bases: potential.LennardJones

Lennard Jones potential.

for \(r>r_c=(5/2) \sigma\) the potential (and force) is set to zero.

Parameters:
  • epsilon – Potential parameter \(\epsilon\)
  • sigma – Potential parameter \(\sigma\)
kernel

Returns a kernel class for the potential.

class potential.TestPotential4p(epsilon=1.0, sigma=1.0, rc=None)

Bases: potential.LennardJones

Lennard Jones potential.

for \(r>r_c=(5/2) \sigma\) the potential (and force) is set to zero.

Parameters:
  • epsilon – Potential parameter \(\epsilon\)
  • sigma – Potential parameter \(\sigma\)
kernel

Returns a kernel class for the potential.

class potential.VLennardJones(epsilon=1.0, sigma=1.0, rc=None)

Bases: potential.LennardJones

kernel

Returns a kernel class for the potential.

class potential.VLennardJones2(epsilon=1.0, sigma=1.0, rc=None)

Bases: potential.LennardJones

kernel

Returns a kernel class for the potential.

class potential.VLennardJonesNoU(epsilon=1.0, sigma=1.0, rc=None)

Bases: potential.LennardJones

get_data_map(positions=None, forces=None, potential_energy=None)
kernel

Returns a kernel class for the potential.

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