# CoulombDSF¶

class CoulombDSF(r_cut=None, alpha=None, bonded_mode=None)

Constructor of the Coulomb solver.

Parameters: r_cut (PhysicalQuantity of type length) – The cutoff radius of this Coulomb solver. alpha (PhysicalQuantity of type length**-1) – Damping parameter in the DSF method. It determines how fast the Coulomb interactions decay with the particle distance. bonded_mode – Either CoulombDSF.evaluateAll or CoulombDSF.evaluate4. If evaluateAll is chosen, interactions between all particles - even those that are connected by bonds - are evaluated, using the sigma and epsilon parameters. If evaluate4 is chosen, interactions between particles that are connected by a path of bonds of length less than four are omitted.
getAllParameterNames()

Return the names of all used parameters as a list.

getAllParameters()

Return all parameters of this potential and their current values as a <parameterName / parameterValue> dictionary.

static getDefaults()

Get the default parameters of this potential and return them in form of a dictionary of <parameter name, default value> key-value pairs.

getInteractionMode()

Return the currently used interaction mode.

getParameter(parameterName)

Get the current value of the parameter parameterName.

setBondedMode(bonded_mode)

Set the way how particles that are connected by bonds are treated.

Parameters: bonded_mode – Either self.evaluateAll or self.evaluate4. If evaluateAll is chosen, interactions between all particles - even those that are connected by bonds - are evaluated, using the sigma and epsilon parameters. If evaluate4 is chosen, interactions between particles that are connected by a path of bonds of length less than four are omitted.
setCutoff(r_cut)

Set the cutoff radius of the Coulomb solver.

Parameters: r_cut (PhysicalQuantity of type length) – The cutoff radius of this Coulomb solver.
setParameter(parameterName, value)

Set the parameter parameterName to the given value.

Parameters: parameterName (str) – The name of the parameter that will be modified. value – The new value that will be assigned to the parameter parameterName.

## Usage Examples¶

Define a potential for Quartz by adding particle types and interaction functions to the TremoloXPotentialSet.

# -------------------------------------------------------------
# Set up a SiO2 Quartz crystal
# -------------------------------------------------------------

# Set up lattice
lattice = Hexagonal(4.916*Angstrom, 5.4054*Angstrom)

# Define elements
elements = [Silicon, Silicon, Silicon, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen,
Oxygen]

# Define coordinates
fractional_coordinates = [[ 0.4697,  0.0000,  0.0000    ],
[ 0.0000,  0.4697,  0.66666667],
[ 0.5303,  0.5303,  0.33333333],
[ 0.4135,  0.2669,  0.1191    ],
[ 0.2669,  0.4135,  0.547567  ],
[ 0.7331,  0.1466,  0.785767  ],
[ 0.5865,  0.8534,  0.214233  ],
[ 0.8534,  0.5865,  0.452433  ],
[ 0.1466,  0.7331,  0.8809    ]]

# Set up configuration
bulk_configuration = BulkConfiguration(
bravais_lattice=lattice,
elements=elements,
fractional_coordinates=fractional_coordinates
)

# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------

# Create the Pedone_2006Fe2 potential by hand, by adding the individual components

potentialSet = TremoloXPotentialSet(name='Pedone_2006Fe2')

# Add the particle types to the potential set
mass=28.0855*atomic_mass_unit,
charge=2.4))
mass=15.9994*atomic_mass_unit,
charge=-1.2))

# Add the pair potentials to the potential set
r_0=2.1*Angstrom,
k=2.0067*1/Ang,
E_0=0.340554*eV,
r_i=6.0*Angstrom,
r_cut=7.5*Angstrom))
r_cut=7.5*Angstrom,
c=1.0*Ang**12*eV))
r_0=3.618701*Angstrom,
k=1.379316*1/Ang,
E_0=0.042395*eV,
r_i=6.0*Angstrom,
r_cut=7.5*Angstrom))
r_cut=7.5*Angstrom,
c=22.0*Ang**12*eV))

# Add the coulomb solver to the potential set
potentialSet.setCoulombSolver(CoulombDSF(r_cut=9.0*Angstrom, alpha=0.2))

# Create the calculator from the potential set
calculator = TremoloXCalculator(parameters=potentialSet)

bulk_configuration.setCalculator(calculator)
bulk_configuration.update()


## Notes¶

The damped shifted force (DSF) solver [FG06] represents an efficient method to calculate the electrostatic interactions between particles with partial charges, as defined in ParticleType.

The Coulomb interactions between two particles $$i$$ and $$j$$ are approximated by the following expression for the potential energy:

$V_{ij}(r) = q_i q_j \left[ \frac{\mathrm{erfc}(\alpha r)}{r} - \frac{\mathrm{erfc}(\alpha R_c)}{R_c} + \left (\frac{\mathrm{erfc}(\alpha R_c)}{R_c^2} + \frac{2\alpha}{\pi^{1/2}} \frac{\exp(-\alpha^2 R_c^2)}{R_c} \right ) ( r - R_c ) \right ] \, .$

When using bonded force fields the bonded_mode parameter can be used to modify how this potential acts between atoms that are connected by less than 4 bonds. If CoulombSolver.evaluateAll (or “mode_bondless”) is chosen, the potential acts between all selected atoms independent of the bonds between them. If CoulombSolver.evaluate4 (or “mode_14”) is chosen, the potential is switched off for all atoms that are connected via one, two, or three consecutive bonds.

 [FG06] C. J. Fennell and J. D. Gezelter. Is the Ewald summation still necessary? Pairwise alternatives to the accepted standard for long-range electrostatics. J. Chem. Phys., 2006. doi:http://dx.doi.org/10.1063/1.2206581.