ppmd.utility.potential.c_potential module

class ppmd.utility.potential.c_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 ppmd.utility.potential.c_potential.Buckingham(a=1.0, b=1.0, c=1.0, rc=2.5)

Bases: ppmd.utility.potential.c_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)

property kernel

Returns a kernel class for the potential.

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

Bases: ppmd.utility.potential.c_potential.Buckingham

property kernel

Returns a kernel class for the potential.

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

Bases: ppmd.utility.potential.c_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 \(\sigma\)

property kernel

Returns a kernel class for the potential.

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

Bases: ppmd.utility.potential.c_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.

property kernel

Returns a kernel class for the potential.

class ppmd.utility.potential.c_potential.LennardJonesShifted(epsilon=1.0, sigma=1.0)

Bases: ppmd.utility.potential.c_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)

property kernel

Returns a kernel class for the potential.

property rc

Value of cufoff distance \(r_c\)

class ppmd.utility.potential.c_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.

property kernel

Returns a kernel class for the potential.

property rc

Value of cufoff distance \(r_c\)

property rn

Value of cufoff distance \(r_c\)

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

Bases: ppmd.utility.potential.c_potential.LennardJones

property kernel

Returns a kernel class for the potential.

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

Bases: ppmd.utility.potential.c_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 \(\sigma\)

property kernel

Returns a kernel class for the potential.

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

Bases: ppmd.utility.potential.c_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 \(\sigma\)

property kernel

Returns a kernel class for the potential.

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

Bases: ppmd.utility.potential.c_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 \(\sigma\)

property kernel

Returns a kernel class for the potential.

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

Bases: ppmd.utility.potential.c_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 \(\sigma\)

property kernel

Returns a kernel class for the potential.

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

Bases: ppmd.utility.potential.c_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 \(\sigma\)

property kernel

Returns a kernel class for the potential.

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

Bases: ppmd.utility.potential.c_potential.LennardJones

property kernel

Returns a kernel class for the potential.

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

Bases: ppmd.utility.potential.c_potential.LennardJones

property kernel

Returns a kernel class for the potential.

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

Bases: ppmd.utility.potential.c_potential.LennardJones

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

property kernel

Returns a kernel class for the potential.