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Structural characterization of deformed crystals by analysis of common

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 Computer Physics Communications 177 (2007) 518–523
www.elsevier.com/locate/cpc

Structural characterization of deformed crystals by analysis

of common atomic neighborhood
Helio Tsuzuki ∗ , Paulo S. Branicio, José P. Rino
Departamento de Física, Universidade Federal de São Carlos, São Carlos, SP 13565, Brazil
Received 27 April 2007; accepted 28 May 2007
Available online 12 June 2007

Abstract
Simulations of crystal deformation and structural transformation may generate complex datasets involving networks with million to billion
chemical bonds which makes local structure analysis a challenge. An ideal analysis method must recognize perfect crystal structures, such as
face-centered cubic, body-centered cubic and hexagonal close packed, and differentiate structural defects such as dislocations, stacking faults,
grain boundaries, cracks and surfaces. Currently a few methods are used for this purpose, e.g., the Common Neighbor Analysis (CNA) and the
Centrosymmetry Parameter (CSP). This paper proposes an alternative method based on the calculation of a single parameter that depends on
the common atomic neighborhood. We validate the method characterizing local structures in complex molecular-dynamics datasets, clarifying its
advantages over the CNA and the CSP methods.
© 2007 Elsevier B.V. All rights reserved.

PACS: 07.05.Kf; 61.43.Bn; 82.20.Wt

Keywords: Topological network; Molecular dynamics simulation; Structural data analysis

1. Introduction
The analysis of atomic chemical bonds is widely used to
characterize the state of a local crystal structure in simulations
of solid materials. Because of the unique atomic arrangement
of a given crystal phase its presence within a simulated mate-
rial can be attested by a topological analysis of the chemical
bond network. In such analysis, the structure of a material is
considered as a topological network of chemical bonds. Bonds
here are typically defined between a pair of atoms, for which
Pauling’s bond order has a value larger than a threshold value.
Usually though a bond is defined in simulations when the pair
distance is less than a cutoff radius. Most local structure analy-
sis methods such as the Common Neighbor Analysis (CNA)
and the Centrosymmetry Parameter (CSP) use such abstractions
to characterize the local state of solid materials. The popu-
larity of these methods has soared in recent years due to the
ever-increasing size and complexity of the chemical networks
* Corresponding author.
E-mail address: helio@df.ufscar.br (H. Tsuzuki).
0010-4655/$ – see front matter © 2007 Elsevier B.V. All rights reserved.
doi:10.1016/j.cpc.2007.05.018
that are simulated [1]. For such large systems, structural analy-
sis algorithms demand low computational complexity. Large
datasets are commonly found in molecular dynamics (MD) sim-
ulations, which model materials as a set of atoms. Currently,
state-of-the-art MD simulations may involve hundred-billion
atoms [2]. Efficient algorithms for structural characterization
with near linear scaling are therefore vital for such analysis, es-
pecially if the analysis is to be performed in real time during
the simulation.
Among the most used methods for structure analysis the
CNA, proposed by Honeycutt and Andersen [3], is based on
nearest neighbor atoms. It is a generalization of the method
proposed by Blaisten-Farojas and Andersen [4], in order to de-
termine the equilibrium structure of small clusters of Lennard-
Jones atoms. With that method Honeycutt and Andersen could
describe the structural transition in small clusters with increas-
ing size from icosahedral structure, to polyicosahedral to fcc
(face-centered cubic). Jonsson and Andersen [5], used the same
technique to study the structures produced by cooling Lennard-
Jones fluids to below the glass transition. Clarke and Jonsson
[6], used a slight different version of the CNA to investigate the
 H. Tsuzuki et al. / Computer Physics Communications 177 (2007) 518–523 519

densification and the icosahedral ordering of hard-sphere pack-

ings. Faken and Jonsson [7], used the same version of CNA
in combination with 3D computer graphics to study the crystal
nucleation in a molten copper slab. The CNA has been useful
in the investigation of several other systems such as the mi-
crostructure of liquid and amorphous Ni [8], small Au clusters
[9,10], metallic nanocontacts [11], grain boundaries [12,13],
dislocation processes in nanocrystalline aluminum [14], liquid
and supercooled tantalum [15], liquid and supercooled copper
[16], and metallic glasses [17].
Another frequently used method for structure analysis is the
CSP which is based on the spatial arrangement formed by the
nearest neighbor atoms. Different from the CNA the CSP is
however well defined only in a centrosymmetric crystal such as
fcc and bcc (body-centered cubic). The CSP method was orig-
inally proposed by Kelchner, Plimpton, and Hamilton [18] to
identify dislocations and stacking faults created during indenta-
tion of gold surface and to distinguish them from purely elasti-
cally deformed regions. A slightly different version of the CSP
was proposed by Li [19,20] and implemented in a 3D computer
visualization package. The CSP was applied successfully to ad-
dress different problems such as the scaling of small indentation
results in Au to the experimental range [21], incipient plasticity
during indentation [22], deformation of metallic nanowires dur- Fig. 1. Illustrations of diagrams constructed from the classification of local
ing compressive and tensile loading [23,24], impact dynamics structures defined in the CNA method. Brown (i) and yellow (j ) atoms indicate
one pair of nearest neighbor atoms, light-blue (k) atoms are common neigh-
of copper clusters [25], deformation in nanocrystalline metals
bors of the brown-yellow pair. (a) shows a 1421 diagram, indicating that brown
[26,27], dislocation nucleation close to copper interfaces [28], (i) and yellow (j ) atoms are nearest neighbors, have 4 common neighbors (k)
shock deformation of metals [29], and defaceting phase transi- which in turn have two bonds. The 1421 is the only diagram present in the fcc
tions in grain boundaries [30]. The calculation of the CSP has structure. (b)–(d) show the 1422, 1441, and 1661 diagrams which are found in
also been included in molecular dynamics standard codes such the hcp and bcc structures. (For interpretation of the references to color in this
figure legend, the reader is referred to the web version of this article.)
as the SPaSM [31].
Apart from the popular CNA and CSP methods a few other
techniques have been used to distinguish among atomic struc- (iii) indicates the number of bonds among the common neigh-
tures and identify the location and type of different structural bors;
defects [32–38]. This paper proposes an alternative method (iv) differentiates diagrams with same (i), (ii), and (iii) indexes
that could be used in place of the CNA and CSP methods. It and different bonding among common neighbors.
is in one hand of simple implementation and interpretation,
like the CSP method, because it is based on a single parame- Here two atoms are nearest neighbors if the distance between
ter calculation. On the other hand it is well defined in non- them is less or equal to a cutoff distance, which is in general
centrosymmetric crystals and it has a broad range of possible defined as the first minimum in the pair distribution function
applications, like the CNA method. In the next section details [39]. Fig. 1 (a)–(d) shows diagrams for a few selected crystal
of these two approaches—CNA and CSP—are briefly reviewed structures, and exemplify the four indexes CNA classification.
and the alternative method presented and analyzed. Fig. 1(a) shows the 1421 diagram, present in the fcc structure,
formed when a pair of nearest neighbors atoms share 4 com-
2. Structural analysis methods mon neighbors, which have two bonds. Fig. 1(b) shows the dia-
gram 1422 which is present in the hcp (hexagonal close packed)
2.1. The Common Neighbor Analysis (CNA)
structure in the same amount as the 1421 diagram. Fig. 1 (c) and
(d) shows the 1441 and 1661 diagrams which are found in the
In the original CNA method proposed by Honeycutt and An-
dersen [3] a structure is represented by diagrams. Starting with bcc structure.
a pair of atoms, α and β, the diagram is classified by a set of For a given perfect crystal structure, the presence of CNA
four indexes: (i), (ii), (iii), and (iv), where diagrams is well determined as shown in Table 1 and can be
used to distinguish them. All pairs of nearest neighbor atoms
(i) with values 1 or 2 indicates that α and β are nearest- in the fcc structure form diagrams of the type 1421. In the hcp
neighbors (i = 1) or not (i = 2); structure half the pairs of nearest neighbor atoms form 1421
(ii) indicates the number of nearest neighbors shared by the while the other half form 1422 diagrams. The bcc structure has
(α, β) pair (common neighbors); an unbalanced distribution of diagrams with 3/7 of the nearest
520 H. Tsuzuki et al. / Computer Physics Communications 177 (2007) 518–523
Table 1
Relative presence of different CNA diagrams in the fcc, bcc, and hcp crystal
structures
CNA diagram fcc bcc
1421 1 0
1422 0 0
1441 0 3/7
1661 0 4/7
neighbor atoms pairs forming 1441 diagrams while the rest 4/7
forming 1661 diagrams.
2.2. The Centrosymmetry Parameter (CSP)
The CSP method proposed by Kelchner, Plimpton, and
Hamilton [18] quantifies local deviations from centrosymmetry
in a given centrosymmetric structure such as fcc and bcc. Based
on that, defects are effectively identified and distinguished from
elastically deformed regions. The calculation of the parameter
exploits the fact that a centrosymmetric material will remain
centrosymmetric under a homogeneous elastic deformation. In
such materials each atom has a certain number of pairs of oppo-
site bonds formed by the nearest neighbor atoms. Fig. 2 (a)–(c)
show the opposite pairs in the fcc, bcc, and hcp crystals. In an
fcc structure, Fig. 2(a), each atom has 6 pairs of opposite near-
est neighbor atoms, and therefore 6 pairs of opposite bonds. In
a bcc structure the first and second shell of nearest neighbors
are close so we consider both as a single shell. Together this
combined shell has 7 pairs of opposite neighbors, see Fig. 2(b).
Under deformation or on a defect these bonds will change in
length and direction and that change is quantified in a parame-
ter. For an fcc structure the CSP is defined as follows:
 fined in a centrosymmetric crystal. The advantages of these two
P= |Ri + Ri+6 |2 ,
i=1,6
where Ri and Ri+6 are bond vectors corresponding to the six
pairs of opposite nearest neighbors. In a perfect undeformed
structure the calculation is trivial. However, in a deformed
structure the 12 vectors Ri for each atom must be determined
by finding those neighbors with vectors close in distance to the
undistorted nearest neighbor vectors. Each, equal and opposite,
pair of vectors is added together, and the sum of the square of
the six resulting vectors is then finally performed. The CSP is
Fig. 2. Illustrations of opposite pairs in the fcc, bcc and hcp structures. Atoms with same colors form opposite pairs from the central (brown) atom. (a) fcc structure
with six opposite pairs. (b) bcc structure with 7 opposite pairs. (c) hcp structure formed with three opposite pairs. Three other pairs, shown in dark blue, do not form
opposite pairs. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
then a measure of the departure from the centrosymmetry in the
vicinity of a given atom. In the bulk of a perfect fcc structure
2
P = 0 [18], at the surface P = 24.9 Å , in an intrinsic stacking
hcp 2
fault P = 8.3 Å , and for atoms halfway between fcc and hcp
0.5 2
0.5 structures (partial dislocation) P = 2.1 Å .
0 An alternative CSP definition was proposed by Li [19,20]
0 and implemented in the “Atomeye” visualization package. This
definition follows
mi /2
Dk
ci = mk=1 ,
j =1 |Rj |
i 2
where ci is the centrosymmetry parameter for the ith atom,
mi the number of its neighbors, Rj are bond vectors and the
function Dk = |Rk + Rk  |2 is minimized by the bond Rk  . This
parameter is dimensionless with a maximum value of 1. In one
perfect fcc structure, for example, atoms at an intrinsic stacking
faults has ci = 0.0416. This implementation has the advantage
of finding dynamically the best opposite pairs of atoms as it is
required for a real time analysis of an arbitrary structure being
visualized.
2.3. A Common Neighborhood Parameter (CNP)
The way the CNA and CSP methods characterize structures
makes them suitable for specific kinds of applications. The
CNA characterizes by using the statistics of diagrams formed
from a given arbitrary local atomic configuration. That is a
powerful method but it may be intricate to implement and to
interpret. The CSP on the other hand gives a measure of the de-
viation from the centrosymmetry in the vicinity of a given atom.
It is of easy implementation and interpretation but it is only de-
methods can be put together through the definition of a para-
meter Qi , for each atom i in the structure, which will be called
from here on as the Common Neighborhood Parameter (CNP).
The definition of Qi follows
 nij
ni 
2
1  
 
Qi =  (Rik + Rj k ) ,
ni  
j =1 k=1
where the index j goes over the ni nearest neighbors of atom
i, and the index k goes over the nij common nearest neighbors
 H. Tsuzuki et al. / Computer Physics Communications 177 (2007) 518–523 521

example is shown in Fig. 4 (a)–(d), which compares the ability

of the CNA and CNP methods to describe the defect distribution
created on a copper nanowire subjected to a high tensile strain
rate of 1.5 × 1011 s−1 . Strained atomic configurations at ε =
0.13 and ε = 0.39 are visualized with atoms colored following
the values of CNA and CNP methods.
With CNA analysis one can distinguish atoms in fcc and
hcp regions by calculating the statistics of diagrams formed
from the nearest neighbors of each atom and comparing it with
those previously known from standard crystals, e.g., fcc, bcc,
etc. Fig. 4 (a) and (b) shows atoms in fcc and hcp local re-
gions that were selected by the presence of 1421 and 1422 CNA
diagrams. Atoms with only 1421 diagrams are in fcc regions
and those atoms with 50% 1421 and 50% 1422 diagrams are
in hcp regions. All atoms with other kinds of diagrams were
eliminated. While powerful this analysis needs attention in the
Fig. 3. Illustration of the common neighborhood used in the calculation of the calculation and interpretation of the statistics of diagrams dis-
Qi parameter for the hcp structure, which has ni = 12 nearest neighbors for any tribution along the system. The CNP analysis provides similar
atom i. The atom i, in brown, and its nearest neighbor j , shown in yellow, have
nij = 4 common nearest neighbors (k1 , k2 , k3 , and k4 ), shown in light-blue.
information about the phases, see Fig. 4 (c) and (d), but use
In the calculation of the Qi parameter the bonds indicated by red and yellow instead a simpler procedure with the calculation of a single pa-
arrows are summed and the result squared. The procedure is repeated for all rameter for each atom what provides a direct interpretation. The
nearest neighbors of the i atom. Finally the total sum of the squares is divided fcc crystal can be identified when CNP values are close to 0 Å2 ,
by ni = 12 to obtain Qi . (For interpretation of the references to color in this see Table 1. Values around 4.4 Å2 indicate atoms in hcp local
figure legend, the reader is referred to the web version of this article.)
crystals.
In Fig. 5 (a)–(c) part of a simulated copper crystal, at 10 K, is
Table 2
Values of the CNP, CSP1 (Kelchner et al.), and CSP2 (Li) for different structures visualized showing a dissociated dislocation, which is formed
and surfaces by two partial dislocations surrounding a stacking fault. Visu-
Structure CNP CSP1 CSP2 alized atoms in Fig. 5(a) are colored by coordination number
2 2 (number of bonds per atom), which indicates the presence of
fcc 0Å 0Å 0
2 2 the partial dislocations delimiting the intrinsic stacking fault.
bcc 0Å 0Å 0
2 2 Fig. 5 (b) and (c) shows the same structure with atoms colored
hcp 4.4 Å 6.6 Å 0.042
2 2
by the CSP (Li) and CNP atomic values. As can be seen by us-
fcc{111} 13.0 Å 19.5 Å 0.186 ing the CNP method one can obtain a higher resolution than by
2 2
fcc{100} 26.5 Å 26.2 Å 0.254 using CSP. Atoms at the intrinsic stacking fault and partial dis-
locations can be better identified and distinguished. In Fig. 5(c)
between atom i and atom j . Rik is the vector connecting atom CNP values around 10 Å2 indicate atoms in dislocations which
i to atom k, see Fig. 3. have coordination 11 and 13. The stacking fault which has a
For instance, in perfect fcc and bcc structures Qi = 0. Ta- CNP value around 4.4 Å2 is better identified than in Fig. 5(b)
ble 2 shows CNP Qi values compared with values from the two using the CSP. One of the reasons for the better accuracy of the
CSP methods discussed. CNP method over the CSP is the need to always find the correct
While the CNA method analyze the nearest neighbors of an opposite neighbors in the later, which in a dynamic simulation
atom i and the configuration of their common neighbors the of a deforming structure are not accurately defined. In the case
CSP monitor the state of the bonds formed by opposite nearest of the hcp crystal that can be further complicated because the
neighbors. The vectors (bonds) formed to the common neigh- three not opposite pairs may cause trouble in finding the best
bors do not form opposite vectors but their sum depends on the opposite pairs, see Fig. 2(c).
state of the local structure and can be used to characterize the lo-
cal environment. The CNP explores this intrinsic characteristic 4. Summary
of the common neighbors with the advantage of not requiring
explicit knowledge about what are the opposite neighbor pairs. In summary an alternative method for structural characteri-
The only information the CNP method requires is the nearest zation based on the common atomic neighborhood is proposed
neighbor list for each atom, what is usually known beforehand for the analysis of complex data sets of deformed simulated
in a simulation. materials. The method is compared to the Common Neighbor
Analysis and the Centrosymmetry Parameter methods. The ef-
3. Discussion ficiency of the proposed method is validated and its advantages
are clarified. For instance the method combines the advantages
The application of the CNP may be advantageous in several of the CNA and CSP methods. It is of easy implementation and
situations over the application of CNA or CSP methods. One interpretation and may be applied in an arbitrary crystal. It is
522 H. Tsuzuki et al. / Computer Physics Communications 177 (2007) 518–523

Fig. 4. Strained copper nanowires at T = 300 K with the 110 direction (along z) stretched at the strain rate 1.5 × 1011 s−1 . Nanowires at ε = 0.13 are showed in
(a) and (c), and at ε = 0.39 in (b) and (d). Atoms in (a)–(b) are colored following CNA analysis while atoms in (c)–(d) are colored by CNP values. Atoms in fcc and
hcp local regions can be distinguished equivalently using both methods. (For interpretation of the references to color in this figure legend, the reader is referred to
the web version of this article.)

Fig. 5. Partial dislocations in copper (fcc structure) at T = 10 K surrounding an intrinsic stacking fault (local hcp structure). (a) Atoms are colored by coordination
number. Atoms with coordination 11 are violet, coordination 12 golden, and coordination 13 blue. (b) Atoms colored by CSP (Li) values ranging from 0 to 0.25.
(c) Atoms colored by the CNP values from 0 Å2 in the fcc structure, to 4.4 Å2 in the stacking fault, to 11 Å2 at the dislocation core. (For interpretation of the
references to color in this figure legend, the reader is referred to the web version of this article.)

sensitive to structural deformations and can be used to char- à Pesquisa do Estado de São Paulo). Numerical tests were
acterize in real time local structures of undeformed and elasti- performed at the Universidade Federal de São Carlos using
cally deformed crystals as well as to distinguish defects such as the 46-processor Linux cluster of the Computer Simulation
stacking faults, dislocations, disordered regions, surfaces, etc. Group.

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