UFFPotentialBuilder

Included in QATK.Calculators.ForceField

class UFFPotentialBuilder(use_bonds=None, include_bond_stretching=None, include_bond_angles=None, include_torsions=None, include_inversions=None, include_lennard_jones=None, include_electrostatic=None, lennard_jones_cutoff=None, lennard_jones_smoothing_length=None, use_long_range_correction=None, electrostatic_pairwise_cutoff=None, electrostatic_smoothing_length=None, electrostatic_spme_cutoff=None, electrostatic_accuracy=None, electrostatic_scale=None, use_electrostatic_direct_sum=None, ignore_untyped_molecules=None, add_missing_potentials=None)

This object builds a Universal potential using TremoloX.

Parameters:

• use_bonds – Controls if any bonding (stretching, angle, torsion, inversion and hydrogen bond) terms are to be included.
  Default: True.

• include_bond_stretching (bool) – Controls if bonding stretching terms are included.
  Default: use_bonds.

• include_bond_angles (bool) – Controls if angle bending terms are included.
  Default: use_bonds.

• include_torsions (bool) – Controls if bond torsion terms are included.
  Default: use_bonds.

• include_inversions (bool) – Controls if bond inversion torsion terms are included.
  Default: use_bonds.

• include_lennard_jones (bool) – Controls if Lennard-Jones terms are included.
  Default: use_bonds.

• include_electrostatic (bool) – Controls if electrostatic terms are included.
  Default: use_bonds.

• lennard_jones_cutoff (PhysicalQuantity of type distance) – Distance beyond which the Lennard-Jones terms are truncated.
  Default: 10.0 * Angstrom.

• lennard_jones_smoothing_length (PhysicalQuantity of type distance) – Distance over which the Lennard-Jones terms are brought to zero at the cutoff.
  Default: 2.0 * Angstrom.

• use_long_range_correction (bool) – Whether to use the long-range correction for the Lennard-Jones terms.
  Default: True

• electrostatic_pairwise_cutoff (PhysicalQuantity of type distance) – Distance at which the pairwise electrostatic terms are brought to zero in pairwise summation.
  Default: 12 * Angstrom

• electrostatic_smoothing_length (PhysicalQuantity of type distance) – Distance over which the electrostatic terms are brought to zero at the cutoff when using the direct electrostatic sum.
  Default: 2.0 * Angstrom

• electrostatic_spme_cutoff (PhysicalQuantity of type distance) – Distance at which the pairwise electrostatic terms are brought to zero in SPME summation.
  Default: 7.5 * Angstrom

• electrostatic_accuracy (float) – Sets the relative accuracy of the SPME summation.
  Default: 0.0001

• electrostatic_scale (float) – Set the relative strength of the electrostatic terms.
  Default: 1.0

• use_electrostatic_direct_sum (bool) – Use the direct Coulomb sum to calculate the electrostatic terms in MoleculeConfigurations.
  Default: False

• ignore_untyped_molecules (bool) – Whether whole bonded structures are ignored if they do not have potential atom types.
  Default: False

• add_missing_potentials (bool) – Whether to add potentials for terms that are missing parameters. All types starting with the potential prefix (UFF_, DREI_, OPLS_, etc.) will be considered as potential types.
  Default: False

addCustomBondChargeIncrement(label_a, label_b, q_a, q_b)

Add a custom charge increments. Charge increments are used to calculate atomic charges. Atoms have their charge adjusted by the charge increments on the bonds attached to them. If opposite charges are added to each atom in the increment the whole configuration charge remains the same.

Parameters:

• label_a (str) – The first particle label. This can be either a type or a class.

• label_b (str) – The second particle label. This can be either a type or a class.

• q_a (PhysicalQuantity of type charge.) – The charge added to particle type_a.

• q_b (PhysicalQuantity of type charge.) – The charge added to particle type_b.

addCustomConstrainedAngle(class_a, class_b, class_c, theta_0)

Add a custom constrained angle between three bonded particle classes.

Parameters:

• class_a (str) – The first particle class.

• class_b (str) – The second particle class.

• class_c (str) – The third particle class.

• theta_0 (PhysicalQuantity of type length.) – The equilibrium bond angle.

addCustomConstrainedBond(class_a, class_b, r_0)

Add a custom constrained bond between two bonded particle classes.

Parameters:

• class_a (str) – The first particle class.

• class_b (str) – The second particle class.

• r_0 (PhysicalQuantity of type length.) – The equilibrium bond length.

addCustomCosinePowerTorsion(class_a, class_b, class_c, class_d, k, c_list)

Add a custom power-series torsion potential between four bonded particle classes. The torsion potential is of the form:

\[V(\theta) = k \left[c_0 + \sum_{i=1} c_i \cos^i(\phi) \right]\]

Parameters:

• class_a (str) – The first particle class.

• class_b (str) – The second particle class.

• class_c (str) – The third particle class.

• class_d (str) – The fourth particle class.

• k (PhysicalQuantity of type energy per square angle.) – The strength of the potential.

• c_list (sequence of float) – The list of coefficients in the power series.

addCustomCosineTorsion(class_a, class_b, class_c, class_d, k_list, n_list, delta_list)

Add a custom Cosine torsion between four bonded particle classes. The torsion potential is of the form:

\[V(\phi) = \sum_{i=1}^n k_i \left[1 + \cos(n_i \phi - \delta_i)\right]\]

Parameters:

• class_a (str) – The first particle class.

• class_b (str) – The second particle class.

• class_c (str) – The third particle class.

• class_d (str) – The fourth particle class.

• k_list (Sequence of PhysicalQuantity of type energy.) – The size of the cosine potentials. This must have the same number of elements and n_list and delta_list.

• n_list (Sequence of int.) – The period of each cosine function. This must have the same number of elements and k_list and delta_list.

• delta_list (Sequence of PhysicalQuantity of type angle.) – The offset of the cosine potentials. This must have the same number of elements and k_list and n_list.

addCustomDreidingHydrogenBond(donor_class, hydrogen_class, acceptor_class, a, b)

Add a custom Fourier improper torsion between four bonded particle types. The improper torsion potential is of the form:

\[V(\r, \theta) = a \left[5(r/b)^{12} - 6(r/b)^{10}\right] \cos^4 \theta\]

The distance is measured between the hydrogen donor and acceptor, while the angle is measured with the hydrogen in the center. When the angle is less than 90 degrees the potential is zero.

Parameters:

• donor_class (str) – The donor particle class, which is bonded to the hydrogen.

• hydrogen_class (str) – The hydrogen particle class.

• acceptor_class (str) – The acceptor particle class, which is not bonded to the hydrogen.

• a (PhysicalQuantity of type energy.) – The strength of the hydrogen bond potential.

• b (PhysicalQuantity of type distance.) – The equilibrium hydrogen bond distance.

addCustomFourierAngle(class_a, class_b, class_c, k, c_list)

Add a custom Fourier angle potential between three bonded particle classes. The angle potential is of the form:

\[V(\theta) = k \left[c_0 + \sum_{i=1}^4 c_i \cos(i \theta) \right]\]

Parameters:

• class_a (str) – The first particle class.

• class_b (str) – The second particle class.

• class_c (str) – The third particle class.

• k (PhysicalQuantity of type energy per square angle.) – The strength of the potential.

• c_list (sequence of float) – The list of coefficients in the Fourier series.

addCustomFourierImproperTorsion(class_a, class_b, class_c, class_d, k, c_list)

Add a custom Fourier improper torsion between four bonded particle classes. The improper torsion potential is of the form:

\[V(\chi) = \frac{k}{3} \sum_{i=0}^n \cos(i \chi)\]

Parameters:

• class_a (str) – The central particle class.

• class_b (str) – The first bonded particle class.

• class_c (str) – The second bonded particle class.

• class_d (str) – The third bonded particle class.

• k (PhysicalQuantity of type energy per square angle.) – The strength of the potential.

• c_list (sequence of float) – The list of coefficients in the Fourier series.

addCustomFourierTorsion(class_a, class_b, class_c, class_d, k, c_list)

Add a custom Fourier torsion potential between four bonded particle classes. The torsion potential is of the form:

\[V(\theta) = k \left[c_0 + \sum_{i=1} c_i \cos(i \phi) \right]\]

Parameters:

• class_a (str) – The first particle class.

• class_b (str) – The second particle class.

• class_c (str) – The third particle class.

• class_d (str) – The fourth particle class.

• k (PhysicalQuantity of type energy per square angle.) – The strength of the potential.

• c_list (sequence of float) – The list of coefficients in the Fourier series.

addCustomHarmonicAngle(class_a, class_b, class_c, k, theta_0)

Add a custom harmonic angle potential between three bonded particle classes. The angle potential is of the form:

\[V(\theta) = k(\theta - \theta_0)^2\]

Parameters:

• class_a (str) – The first particle class.

• class_b (str) – The second particle class.

• class_c (str) – The third particle class.

• k (PhysicalQuantity of type energy per square angle.) – The steepness of the harmonic potential.

• theta_0 (PhysicalQuantity of type length.) – The equilibrium bond angle.

addCustomHarmonicBond(class_a, class_b, k, r_0)

Add a custom harmonic bond potential between two bonded particle classes. The bond potential is of the form:

\[V(r) = k(r - r_0)^2\]

Parameters:

• class_a (str) – The first particle class.

• class_b (str) – The second particle class.

• k (PhysicalQuantity of type energy per square distance.) – The steepness of the harmonic potential.

• r_0 (PhysicalQuantity of type length.) – The equilibrium bond length.

addCustomHarmonicCisTransTorsion(class_a, class_b, class_c, class_d, cis_k, trans_k, cis_torsion)

Add a custom harmonic torsion potential with optionally different parameters for torsions that are originally in the cis or trans orientation. This is most commonly applied to molecules that have double bonds. If the cis and trans parameters are the same, the same potential is used regardless of the initial torsion angle.

Parameters:

• class_a (str) – The first particle class.

• class_b (str) – The second particle class.

• class_c (str) – The third particle class.

• class_d (str) – The fourth particle class.

• cis_k (PhysicalQuantity of type energy per angle squared.) – The strength of the harmonic potential for a cis torsion.

• trans_k (PhysicalQuantity of type energy per angle squared.) – The strength of the harmonic potential for a trans torsion.

• cis_torsion (PhysicalQuantity of type angle.) – The equilibrium torsion angle of the cis configuration. The trans equilibrium angle is 180 degrees plus this angle.

addCustomHarmonicImproperTorsion(class_a, class_b, class_c, class_d, k, psi_0)

Add a custom harmonic improper torsion potential between four bonded particle classes. The bond potential is of the form:

\[V(\psi) = k(\psi - \psi_0)^2\]

Parameters:

• class_a (str) – The central particle class.

• class_b (str) – The first bonded particle class.

• class_c (str) – The second bonded particle class.

• class_d (str) – The third bonded particle class.

• k (PhysicalQuantity of type energy per square angle.) – The steepness of the harmonic potential.

• psi_0 (PhysicalQuantity of type length.) – The equilibrium improper torsion angle.

addCustomLennardJonesNonbond(type_a, type_b, epsilon, sigma)

Add a custom Lennard-Jones potential between two non-bonded atoms. These potentials are used instead of the potentials defined by the single atom parameters and combination rule.

Parameters:

• type_a (str) – The first particle type.

• type_b (str) – The second particle type.

• epsilon (PhysicalQuantity of type energy.) – The well depth of the potential.

• sigma (PhysicalQuantity of type length.) – The distance where the potential is zero.

addCustomOplsTorsion(class_a, class_b, class_c, class_d, k_1=PhysicalQuantity(0.0, eV), k_2=PhysicalQuantity(0.0, eV), k_3=PhysicalQuantity(0.0, eV), k_4=PhysicalQuantity(0.0, eV))

Add a custom OPLS torsion between four bonded particle classes. The torsion potential is of the form:

\[V(\phi) = \sum_{i=1}^4 \frac{k_i}{2}\left[1 + (-1)^{i+1} \cos(i \phi)\right]\]

Parameters:

• class_a (str) – The first particle class.

• class_b (str) – The second particle class.

• class_c (str) – The third particle class.

• class_d (str) – The fourth particle class.

• k_1 (PhysicalQuantity of type energy.) – The first cosine potential size.

• k_2 (PhysicalQuantity of type energy.) – The second cosine potential size.

• k_3 (PhysicalQuantity of type energy.) – The third cosine potential size.

• k_4 (PhysicalQuantity of type energy.) – The fourth cosine potential size.

addCustomParticleType(type_label, class_label, description, particle_symbol, sigma, epsilon, charge, bond_number, type_filter=None, necessary_elements=None, definitions=None, overrides=None)

Add a new particle type to the potential.

Parameters:

• type_label (str) – The label for the new particle types. This is specified without the forcefield prefix.

• class_label (str) – The class for the new particle type. Classes are used to group types together that use the same valence potentials such as bond or angle potentials.

• description (str) – A description of the particle type.

• particle_symbol (str) – The chemical symbol for the particle that the type refers to. Can be either an element symbol or a symbol from a UnitedAtom or Particle

• sigma (PhysicalQuantity of type length.) – The Lennard-Jones sigma parameter for the type. This should correspond to where the Lennard-Jones potential is zero.

• epsilon (PhysicalQuantity of type energy.) – The Lennard-Jones epsilon parameter for the type. This should correspond to the well depth in the potential.

• charge (PhysicalQuantity of type charge.) – The charge of the particle type. This charge is assigned to the particle before charge increments are added to the particle charges.

• bond_number (int) – The bond coordination number of the particle.

• type_filter (str) – A label used to describe the chemical class that the type is found in. This can also be used to select types that generally work together.

• necessary_elements (list of PeriodicTableElement) – A list of elements that must be present in the structure for the type to be found. This is used to speed atom typing by not searching for types for which the necessary atoms are not present. All types are assumed to require carbon, hydrogen and the element represented by the type.

• definitions (str | list of str) – A SMARTS string defining the local bond graph of the atom type. This definition should be unique amongst the other user defined types. Multiple definitions, specified as a list of str, can also be given.

• overrides (list of str) – A list of atom types that this type takes precedence over. This is used to resolve cases where an atom matches one ore more types, and allows some type definitions to be quite general. All user defined types are assumed to take precedence over pre-defined types.

addCustomRepulsionShortRange(class_a, class_b, a)

Add a custom short-range repulsion potential between two bonded particle classes. The bond potential is of the form:

\[V(r) = \frac{a}{r^{12}}\]

Parameters:

• class_a (str) – The first particle class.

• class_b (str) – The second particle class.

• a (PhysicalQuantity of type energy distance to the 12th power.) – The strength of the repulsion potential.

addMissingPotentials()

Returns:

Whether default potentials are added for terms that are missing explicit terms.

Return type:

bool

assignAtomCharges(configuration)

Assign the atomic partial charges to the given configuration. This only includes charges defined by the potential, which in some cases are zero.

Parameters:

configuration (MoleculeConfiguration | BulkConfiguration | DeviceConfiguration | SurfaceConfiguration) – The configuration to assign partial charges to.

assignAtomTypes(configuration, search_types=None, overwrite=False, progress_widget=None)

Automatically assign OPLS atom tags to a configuration.

Parameters:

• configuration (AtomicConfiguration) – The configuration on which to assign tags.

• search_types (list of str | None) – List of types to assign onto the configuration. If specified only these types will be assigned, with UNKNOWN assigned to atoms that don’t match any of the given types. The default argument None means that all available types are assigned.
  Default: None.

• overwrite (bool) – Whether to assign new types if the configuration already has a valid set of types.
  Default: False.

• progress_widget (ForcefieldTypesWidget) – The progress bar / cancel button widget.

checkAtomTypes(configuration)

Function that tests that each atom has only one valid type.

Parameters:

configuration (AtomicConfiguration) – The configuration whose types are being checked.

combinationRule()

Returns:

The combination rule used for the Lennard-Jones potential.

Return type:

str

createCalculator(configuration, check_types=True, atomic_charges=None, charge_averaging=None)

Create and return a calculator with the potential.

Parameters:

• configuration (AtomicConfiguration) – The configuration the potential is to be used with.

• check_types (bool) – Whether the types are checked for basic consistency.
  Default: True

• atomic_charges (PhysicalQuantity of type charge) – Custom atomic charges to be used in the potential.

• charge_averaging (NLFlag | None) – The type of averaging of charges to be used, if any. Accepted values are None, AtomConnectivity to average over atoms bonded to the same elements and AtomTypes to average over atoms of the same forcefield type.
  Default: None

Returns:

The calculator containing the potential.

Return type:

TremoloXCalculator

electrostaticAccuracy()

Returns:

The relative accuracy of the electrostatic summation for SPME.

Return type:

float

electrostaticPairwiseCutoff()

Returns:

The cutoff used in pairwise electrostatic summation.

Return type:

PhysicalQuantity (length)

electrostaticScale()

Returns:

Scaling factor for the electrostatic terms.

Return type:

float

electrostaticSmoothingLength()

Returns:

Distance at which electrostatic terms are splined when using direct summation.

Return type:

PhysicalQuantity (length)

electrostaticSpmeCutoff()

Returns:

The cutoff used in SPME electrostatic summation.

Return type:

PhysicalQuantity (length)

hBondCutoff()

Returns:

The cutoff used in hydrogen bond summation.

Return type:

PhysicalQuantity of type length

hBondScale()

Returns:

Scaling factor for the hydrogen bond terms.

Return type:

float

ignoreUntypedMolecules()

Returns:

Whether bonded structures missing atom types are ignored in setting potentials.

Return type:

bool

includeBondAngles()

Returns:

Whether bond angle terms are included in the potential set.

Return type:

bool

includeBondStretching()

Returns:

Whether bond stretching terms are included in the potential set.

Return type:

bool

includeElectrostatic()

Returns:

Whether electrostatic terms are included in the potential set.

Return type:

bool

includeHBonds()

Returns:

Whether hydrogen bond terms are included in the potential set.

Return type:

bool

includeInversions()

Returns:

Whether bond inversion terms are included in the potential set.

Return type:

bool

includeLennardJones()

Returns:

Whether Lennard Jones terms are included in the potential set.

Return type:

bool

includeShortRange()

Returns:

Whether short-range terms are included in the potential set.

Return type:

bool

includeTorsions()

Returns:

Whether bond torsion terms are included in the potential set.

Return type:

bool

isUniversalType(type_label)

Function that tests if a type is in the potential

Parameters:

type_label (str) – The type being tested.

Returns:

Whether the tag follows the convention.

Return type:

bool

lennardJonesCutoff()

Returns:

Distance at which Lennard Jones terms are ignored.

Return type:

PhysicalQuantity (length)

lennardJonesSmoothingLength()

Returns:

Distance at which Lennard Jones terms are splined.

Return type:

PhysicalQuantity (length)

potentialName()

Returns:

The name used to identify the potential.

Return type:

str

printTotalTypes(type_class=None)

Print a table of available atom types. This provides a list of types and descriptions which can be useful when doing manual type assignment.

Parameters:

type_class (str | None) – Display only atom types with this class label. None displays all types.
Default: None

printUsedTypes(configuration)

Print a table of the types used on the configuration.

Parameters:

configuration (AtomicConfiguration) – The configuration whose types are being displayed.

removeCustomAngle(class_a, class_b, class_c)

Remove a user-defined angle potential from the builder. When a custom potential overrides a standard potential, removing it restores the original standard potential parameters.

Parameters:

• class_a (str) – The first particle class.

• class_b (str) – The second particle class.

• class_c (str) – The third particle class.

removeCustomBond(class_a, class_b)

Remove a user-defined bond potential from the builder. When a custom potential overrides a standard bond potential, removing it restores the original standard potential parameters.

Parameters:

• class_a (str) – The first particle class.

• class_b (str) – The second particle class.

removeCustomChargeIncrement(label_a, label_b)

Remove a user-defined charge increment from the builder. When a custom increment overrides a standard increment, removing it restores the original standard increment parameters.

Parameters:

• label_a – The first particle type.

• type_b – The second particle type.

removeCustomHydrogenBond(donor_class, hydrogen_class, acceptor_class)

Remove a user-defined hydrogen bond potential from the builder. When a custom potential overrides a standard potential, removing it restores the original standard potential parameters.

Parameters:

• donor_class (str) – The donor particle class, which is bonded to the hydrogen.

• hydrogen_class (str) – The hydrogen particle class.

• acceptor_class (str) – The acceptor particle class, which is not bonded to the hydrogen.

removeCustomImproperTorsion(class_a, class_b, class_c, class_d)

Remove a user-defined improper torsion potential from the builder. When a custom potential overrides a standard potential, removing it restores the original standard potential parameters.

Parameters:

• class_a (str) – The first particle class.

• class_b (str) – The second particle class.

• class_c (str) – The third particle class.

• class_d (str) – The fourth particle class.

removeCustomNonbond(type_a, type_b)

Remove a user-defined Lennard-Jones potential from the builder. When a custom potential overrides a standard potential, removing it restores the original standard potential parameters.

Parameters:

• type_a (str) – The first particle type.

• type_b (str) – The second particle type.

removeCustomParticleType(type_label)

Remove a user-defined particle type from the builder. When a custom type overrides a standard particle type, removing it restores the original standard potential parameters.

Parameters:

type_label (str) – The particle type.

removeCustomShortRange(class_a, class_b)

Remove a user-defined short-range potential from the builder. When a custom potential overrides a standard potential, removing it restores the original standard potential parameters.

Parameters:

• class_a (str) – The first particle class.

• class_b (str) – The second particle class.

removeCustomTorsion(class_a, class_b, class_c, class_d)

Remove a user-defined torsion potential from the builder. In cases where the standard potential is over-written, this returns the standard potential.

Parameters:

• class_a (str) – The first particle class.

• class_b (str) – The second particle class.

• class_c (str) – The third particle class.

• class_d (str) – The fourth particle class.

scaleCoulomb()

Returns:

The scaling factor for 1-4 interactions.

Return type:

float

scaleLennardJones()

Returns:

The scaling factor for 1-4 interactions.

Return type:

float

scaleLennardJonesNonbond(type_a, type_b, epsilon_scale=1, sigma_scale=1)

Scale a Lennard-Jones potential by a given factor. This creates a user entry for this potential pair that over-writes the standard value.

Parameters:

• type_a (str) – The first particle type.

• type_b (str) – The second particle type

• epsilon_scale (float) – The scaling factor to apply to the well depth.

• sigma_scale (float) – The scaling factor to apply to the particle size.

tagPrefix()

Returns:

The tag prefix used to identify the potential.

Return type:

str

totalCharge(configuration, verbose=True)

Return the total charge of the configuration according to the atom types on the molecule.

Parameters:

• configuration (AtomicConfiguration) – The configuration whose charges are being reported.

• verbose (bool) – Flag as to whether or not additional information about charges is printed.
  Default: False

Returns:

The total charge of the configuration according to the atom types on the molecule.

Return type:

PhysicalQuantity with units of charge.

uniqueString()

Return a unique string representing the state of the object.

universalType(index, configuration)

Gives the Universal type on an atom in a configuration, ignoring other tags.

Parameters:

• index (int) – Index of the atom for which the type is sought.

• configuration (AtomicConfiguration) – The configuration containing the atom.

Returns:

The type of the atom.

Return type:

str

useBonds()

Returns:

Whether bond terms are included in the potential set.

Return type:

bool

useElectrostaticDirectSum()

Returns:

Whether direct Coulomb sums are used for molecules.

Return type:

bool

useLongRangeCorrection()

Returns:

Whether the long-range correction is used for the Lennard-Jones terms.

Return type:

bool

Usage Examples

Investigate the diffusion of chloroform molecules in LTA zeolites using the UFF potential.

# -------------------------------------------------------------
# Bulk Configuration
# -------------------------------------------------------------
bulk_configuration = nlread('LTA_Chloroform.hdf5')[-1]

# -------------------------------------------------------------
# UFF Calculator
# -------------------------------------------------------------
potential_builder = UFFPotentialBuilder()
potential_builder.assignAtomTypes(bulk_configuration)
calculator = potential_builder.createCalculator(bulk_configuration)
bulk_configuration.setCalculator(calculator)

# -------------------------------------------------------------
# Molecular Dynamics
# -------------------------------------------------------------
initial_velocity = MaxwellBoltzmannDistribution(
    temperature=300.0*Kelvin,
    remove_center_of_mass_momentum=True
)

method = NVTNoseHoover(
    time_step=1*femtoSecond,
    reservoir_temperature=300*Kelvin,
    thermostat_timescale=100*femtoSecond,
    heating_rate=0*Kelvin/picoSecond,
    chain_length=3,
    initial_velocity=initial_velocity,
)

constraints = [FixCenterOfMass()]

md_trajectory = MolecularDynamics(
    bulk_configuration,
    constraints=constraints,
    trajectory_filename='LTA_Chloroform_Trajectory.hdf5',
    steps=100000,
    log_interval=500,
    method=method
)

bulk_configuration = md_trajectory.lastImage()

LTA_Chloroform.py LTA_Chloroform.hdf5

Notes

The UFFPotentialBuilder class enables the creation of a TremoloXCalculator that implements the UFF potential of Rappe, Casewit, Colwell, Goddard and Skiff[1]. This is a bonded valence forcefield that represents the potential energy of a molecule as a collection of simple functions based on bond lengths, bond angles, torsion angles, inversion angles and inter-atomic distances. One of the main advantages of the UFF potential is that it contains data for every atom in the periodic table, so that appropriate potentials can be approximated for any system. The overall mathematical form of the UFF potential can be given as:

\[ \begin{align}\begin{aligned}E(\mathbf{x}) = \sum_i^{bonds} k_i(r_i-r_0)^2 + \sum_i^{angles} k_i\sum_n^m C_n\cos(n\theta_i) + \sum_i^{torsions} k_i(1-\cos(n_i\phi_i-\delta_i))\\+ \sum_i^{inversions} k_i\sum_n^m C_n\cos(n\chi_i)\\+ \sum_{ij}^{atoms} 4\varepsilon_{ij}\left[\left(\frac{\sigma_{ij}}{r_{ij}}\right)^{12} - \left(\frac{\sigma_{ij}}{r_{ij}}\right)^6\right] + \sum_{ij}^{atoms} \frac{q_iq_j}{4\pi \epsilon_0 r_{ij}}\end{aligned}\end{align} \]

Here \(r\), \(\theta\), \(\phi\) and \(\chi\) represent inter-atomic and bond distances, angles, torsions and inversions respectively in the configuration.

Note

While the UFF potential contains data for atoms across the periodic table, in many cases specific types of atoms are assumed by the potential. This means that the generated potentials may not be suitable for specific cases. For instance transition metals are often parameterized based on complexed metal ions, and therefore the generated potential may not be suitable for simulating a pure metal or metal alloy. As in all simulations, care should be taken to ensure that the potential is an appropriate choice for the system at hand by reading the original paper.

To create a UFF calculator, an instance of the UFFPotentialBuilder must first be created. The constructor for this class has a number of options that controls the way in which the calculator is built. Individual types of interactions can be excluded by setting the include_ options to False. By default all possible terms are included. All valence terms can also be excluded by setting the argument use_bonds to False. This is appropriate for configurations consisting of single atoms that are not bonded to each other.

As the UFFPotentialBuilder class uses the bonding in the configuration to determine appropriate potentials, bonds should be set on the configuration. This can be done with the findBonds() method in either the MoleculeConfiguration or BulkConfiguration class. This automatically assigns bonds between atoms that are within the covalent radii of each other. Specific bonds can also be assigned with the setBonds()method, which takes a list of the indices of pairs of atoms that are to be considered bonded.

There are then a number of options that control the non-bonding interactions. The parameter lennard_jones_cutoff sets the distance beyond which Lennard-Jones interactions are truncated. To avoid integration problems in molecular dynamics, Lennard-Jones interactions are brought to zero at the cutoff using a spline function. The width of this spline can be set using the lennard_jones_smoothing_length parameter.

Electrostatic interactions are a little more complicated. By default the UFFPotentialBuilder adds a CoulombSPME electrostatic solver for calculators to be used with a bulk configuration, and a CoulombDSF electrostatic solver to calculators to be used with a molecule configuration. When adding an CoulombSPME solver the cutoff used for calculating the real-space interactions can be set using the electrostatic_spme_cutoff argument. Likewise the accuracy of the smoothed particle mesh Ewald solver can be set using the electrostatic_accuracy argument. In the case where a CoulombDSF solver is added to the potential, the cutoff used can be set using the electrostatic_pairwise_cutoff argument. In cases where molecular electrostatics are to be compared with values calculated in a bulk configuration, an explicit splined Coulomb potential can be used for molecules instead of the damped shifted force potential. In this case a CoulombN2Spline electrostatic solver can be added by using use_electrostatic_direct_sum argument. As with the damped shifted force potential the cutoff is controlled using the electrostatic_pairwise_cutoff argument, and like the Lennard-Jones potential is brought to zero with a spline whose length is defined by the electrostatic_smoothing_length argument. For all Coulomb solvers the total electrostatic energies and forces can be scaled up or down using the electrostatic_scale argument.

Once the UFFPotentialBuilder object is instantiated, a calculator is created using the createCalculator method. This takes a configuration and returns the appropriate UFF calculator for that configuration. To use electrostatic potentials in the calculator, atomic partial charges have to be assigned to each atom. As the UFF forcefield does not define specific charges, by default charges are calculated with the QEqAtomicCharges class. This implements the QEq charge equilibration method of Rappe and Goddard[2]. These charges are then added to the calculator. It is also possible to add pre-calculated charges from different sources using the atomic_charges argument. This argument takes a list of charges that have the same ordering as the atoms in the configuration. The partial atomic charges can also be averaged according to a few different schemes. This is controlled by the charge_averaging parameter, which takes an NLFlag which indicates the type of averaging. The flag AtomConnectivity averages charges on each atom based on the element and the other elements it is bonded to. The flag AtomType averages according to the assigned UFF type.

When creating a UFF calculator for a configuration, the configuration must have the appropriate tags for each atom type. Tags used by the UFF forcefield all begin with the prefix UFF_. The next two characters in the tag are for the atomic symbol, followed by a possible character to indicate the hybridization of the atom. In cases where there are atom types with the same geometry, further characters can indicate the oxidation state of the atoms. Tags can be assigned manually, or they can be assigned automatically. Automatic typing can be done with the assignAtomTypes method. This takes the configuration to have types added, as well as a possible flag to overwrite existing types. The atom types are determined by the element and in some cases the bonding of the atom. The validity of the existing types on a configuration can be checked by calling the checkAtomTypes method. This method raises a NLValueError if a problem is found with the tags on the given configuration. The UFF type of a specific atom can also be found using the universalType method.

Two additional types from the set originally specified in the UFF reference have been added to allow the implementation of some special cases. As amides in the UFF potential are treated as a special case, the type UFF_C_R_a has been added to specifically refer to resonant carbons in an amide group. A similar addition has been made to correctly model aromatic nitrogens. Aromatic nitrogens can be bonded to either two or three other atoms, as in the case of imidazole. The original UFF_N_R type for aromatic nitrogens has therefore been split into the two types UFF_N_R2 and UFF_N_R3 which represent aromatic nitrogens bonded to two and three other atoms respectively.

[1]

A. K. Rappe, C. J. Casewit, K. S. Colwell, W. A. Goddard III, and W. M. Skiff. UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations. J. Am. Chem. Soc., 114(25):10024–10035, 1992. URL: https://pubs.acs.org/doi/abs/10.1021/ja00051a040, doi:10.1021/ja00051a040.

[2]

Anthony K. Rappe and Willian A. Goddard III. Charge equilibration for molecular dynamics simulations. J. Phys. Chem., 95:3358, April 1991. URL: https://pubs.acs.org/doi/10.1021/j100161a070, doi:10.1021/j100161a070.