Adaptive intermolecular reactive empirical bond order potential (AIREBO)¶

AIREBO method was realized according to article: Steven J. Stuart, Alan B. Tutein and Judith A. Harrison. “A reactive potential for hydrocarbons with intermolecular interactions” // Journ. of Chem. Phys., V 112,14 (2000), p. 6472-6486.

AIREBO potential can be represented by a sum over pairwise interactions, including covalent bonding REBO interactions, LJ terms, and torsion interactions:

(1) $E = \frac{1}{2}\sum_{i}\sum_{j\neq{i}}\left(E_{ij}^{REBO} + E_{ij}^{LJ} +\sum_{k\neq{i,j}}\sum_{l\neq{i,j,k}}E_{kijl}^{tors} \right)$

Van-der-Vaals interaction is described through the using of the Lennard-Jones potential:

(2) $E_{ij}^{LJ} = S(t_r (r_{ij}))S(t_b (b_{ij}^* ))C_{ij}V_{ij}^{LJ}(r_{ij}) + [1 - S(t_r(r_{ij}))]C_{ij}V_{ij}^{LJ}(r_{ij})$

$V_{ij}^{LJ}$ is the traditional LJ term:

(3) $V_{ij}^{LJ} = 4\epsilon_{ij}\left( \left(\frac{\sigma_{ij}}{r_{ij}}\right)^{12} - \left(\frac{\sigma_{ij}}{r_{ij}}\right)^6 \right)$

It was modified by several sets of switching functions. S(t) can be represented in the next form:

(4) $S(t) = \Theta(-t)+\Theta(t)\Theta(1-t)[1 - t^2(3-2t)]$

Magnitude of LJ interactions depends on bonding environment. Gradual exclusion of Lennard-Jones interactions with changings of $r_{ij}$ is controlled by scalling function $t_{b}$ :

(5) $t_b(b_{ij}) = \frac{b_{ij} - b_{ij}^{min}}{b_{ij}^{max} - b_{ij}^{min}}$

If atoms $i$ and $j$ are not connected by two or fewer intermediate atoms, LJ interactions between them are controlled by next switching function:

(6) $C_{ij} = 1 - max\{w_{ij}(r_{ij}),w_{ik}(r_{ik})w_{kj}(r_{kj}), \forall k, \\ w_{ik}(r_{ik})w_{kl}(r_{kl})w_{lj}(r_{lj}), \forall k,l \}$

where:

$w_{ij}(r_{ij}) = S^\prime(t_c(r_{ij}))$

$S^\prime(t_c(r_{ij})) = \Theta(-t)+\Theta(t)\Theta(1-t)\frac{1}{2}[1+cos(\pi t)]$

The torsional part of equation (1) for the dihedral angle determined by atoms i, j, k, l has the next form:

(7) $E^{tors}_{kijl} = w_{ki}(r_{ki})w_{ij}(r_{ij})w_{jl}(r_{jl})V^{tors}(\omega_{kijl})$

where $V^{tors}(\omega_{kijl})$ is the torsional potential:

(8) $V^{tors}(\omega_{kijl}) = \frac{256}{405}\epsilon_{kijl}cos^{10}(\omega_{kijl}/2)-\frac{1}{10}\epsilon_{kijl}$

class kvazar.core.airebo.AIREBO(struct, ff_params, comm=None)[source]¶

This class is the successor of class MM

Constructor of class AIREBO:

Args:

struct(structure): nanostructure

ff_params(list): list of names of potentials functions

init_cutoff(r_in, r_out, cutoff_neighbours)[source]¶: Args:

r_in(float): internal cutoff radius

r_out(float): external cutoff radius

cutoff_neighbours(list): list of neighbours get into the field with r_out radius

preprocessing(struct)[source]¶: It corrects atom type and atom boxnames, group them and find out. Masses are taken from parameters.

update_cutoff(cutoff_neighbours)[source]¶

Updates list of neighbours in cutoff area

Args:

cutoff_neighbours(list): list of neighbours

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