=Paper= {{Paper |id=Vol-2426/paper7 |storemode=property |title=Multiscale Modeling of Clusters of Point Defects in Semiconductor Structures |pdfUrl=https://ceur-ws.org/Vol-2426/paper7.pdf |volume=Vol-2426 |authors=Karine K. Abgaryan,Ilya V. Mutigullin,Sergey I. Uvarov,Olga V. Uvarova }} ==Multiscale Modeling of Clusters of Point Defects in Semiconductor Structures== https://ceur-ws.org/Vol-2426/paper7.pdf
    Multiscale Modeling of Clusters of Point Defects in Semiconductor
                               Structures

                   Karine K. Abgaryan1,2, Ilya V. Mutigullin1, Sergey I. Uvarov1, Olga V. Uvarova1,2
                            1
                          Dorodnitsyn Computing Center FRC CSC RAS, Moscow, Russia
                    2
                     Moscow Aviation Institute (NRU) (MAI), Moscow, Russia, kristal83@mail.ru


                                                         Abstract
                        Clusters of point and extended defects, arising in semiconductors as a
                        result of radiation exposure, allow structures to acquire various properties
                        that can be used in the manufacture of new generation devices for
                        nanoelectronics. Numerical simulation of semiconductor materials used to
                        research such processes is a resource-intensive and multifaceted task. To
                        solve it, the multiscale modeling complex was created and the multiscale
                        composition containing instances of basic composition models was set.
                        An algorithm was developed that allows speeding up calculations for
                        systems of large dimensions and accounting for a large number of
                        interacting atoms. The structure of silicon with a complex of point defects
                        was considered as a model. Molecular dynamics simulation was
                        performed using the multiparameter potential of Tersoff. For the
                        calculations, an effective approach to the implementation of parallel
                        computing was presented, and software for parallel computations was
                        used, placed on the hybrid high-performance computing complex of the
                        FRC β€œComputer Science and Control" of Russian Academy of Science.
                        To implement the parallel algorithm, the OpenMP standard was used.
                        This approach has significantly reduced the computational complexity of
                        the calculations. It was shown that the developed high-performance
                        software can significantly accelerate molecular dynamics calculations,
                        such as the calculation of divacancy communication energy, due to the
                        parallel algorithm.

1        Introduction
   Conducting theoretical studies of the formation of clusters of point defects in semiconductor structures is an
important task on the way to improving technologies for obtaining new materials. One of the reasons for the
formation of various defects in the semiconductor structure, including point, extended, their clusters and complexes is
the radiative forcing. As is known from a number of experimental studies [1, 2], as a result of irradiation, such
structures acquire various properties that can be used in the manufacture of new generation devices for
nanoelectronics. In this work, the multiscale approach is used to calculate defects that form in semiconductor
structures as a result of radiation exposure [3, 4]. It is based on:
    - selection of the main scale levels, including atomic-crystalline and molecular-dynamic;
   - development and application for solving the set tasks of mathematical models and algorithms specific for each
level;
   - combining models and algorithms in the general computing process.
   Due to the large labor-intensiveness and versatility of the methods used for numerical simulation of semiconductor
materials, a software package was created for multiscale modeling of their structural features, which allowed studying
the formation of clusters of point and extended defects in a computational experiment. The paper presents the results
of calculations obtained using the software for paralleling the computations placed on the hybrid high-performance
computing complex of the FIC "Informatics and Control" of the Russian Academy of Sciences.
   At present, a theoretical study of the processes occurring in complex defect structures is a very urgent task. One of
the common approaches to conducting such research, which provides a compromise between the speed of calculations
and the accuracy of the results, is the method of molecular-dynamic calculations. However, the problem of molecular


     Copyright Β© 2019 for the individual papers by the papers' authors. Copyright Β© 2019 for the volume as a collection by its
editors. This volume and its papers are published under the Creative Commons License Attribution 4.0 International (CC BY 4.0).
   In: Sergey I. Smagin, Alexander A. Zatsarinnyy (eds.): V International Conference Information Technologies and High-
Performance Computing (ITHPC-2019), Khabarovsk, Russia, 16-19 Sep, 2019, published at http://ceur-ws.org

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dynamic modeling of complex defective structures remains resource-intensive due to the need to consider systems of
high dimensionality and to take into account the interaction of a huge number of atoms with each other. In this regard,
it is necessary to develop algorithms that allow accelerating such calculations without sacrificing the size of the
simulated atomic structures.
    The task of developing a new computational algorithm for molecular dynamics calculations was solved in the
framework of the study of clusters of point defects in single-crystal silicon. Crystal defects call any violation of the
translational symmetry of a crystal - the ideal periodicity of the crystal lattice. There are several types of defects:
point, linear, flat, bulk. Point defects are a local violation of the crystal structure, the dimensions of which in all three
dimensions are comparable with one or several interatomic distances. These are defects associated with impurities,
with displacement or with the replacement of a small group of atoms. Such defects usually occur during heating
during crystal growth, during radiation exposure, and also as a result of the addition of impurities. One type of point
defects is a vacancy - a free, unoccupied atom, a lattice site.
    The occurrence of radiation defects is an inevitable side effect of such a method of modifying materials as ion
implantation. Radiation defects occur due to exposure to the material of neutrons or gamma rays. Such an effect is
characteristic of materials found in a nuclear reactor. In space, the impact on materials of electrons and protons, as
well as heavy ions with low energy, is characteristic.
    Theoretical and experimental studies show that defects in silicon can form complex extended structures. For
numerical simulation of such structures and the study of their stability, it is necessary to take into account in the
calculations a large number of interacting atoms. This, in turn, leads to an increase in the computational complexity of
the problem and an increase in the time required to solve it. The use of new approaches to the parallelization of
molecular dynamic calculations on high-performance computer clusters allows us to solve such problems today.
    In this paper, a new efficient approach is proposed for parallel computations when solving the problem of the
molecular dynamic description of the structure of silicon with interacting vacancy defects.

2        Multiscale Modeling of Clusters of Point Defects in Silicon
   Multiscale approach was applied to calculations of ordered cluster configurations of vacancies and the interstitial
atoms in Si [3.4]. Two large-scale levels (apart from zero) - atomic and crystal and molecular and dynamic were
selected. Within set-theoretic representations it can be set by means of multiscale composition in which are involved:
                                           (0,14;1,1;1,2;2,1;2,2)       (𝑆𝑖)
                                         𝐾0,1,2                     = 𝐾0,1,2                                             (1)
such copies of basic models compositions:
                         𝑆𝑖      𝑆𝑖    𝑆𝑖     𝑆𝑖
                       𝑬𝒍01 : {𝑉01  , 𝑋01 , 𝑀𝐴01 };                                                                      (2)
                        𝑆𝑖      𝑆𝑖    𝑆𝑖     𝑆𝑖
                       π‘ͺ11 : {𝑉11  , 𝑋11 , 𝑀𝐴11 };π‘ͺ11 (Β«CRYSTAL βˆ’ CHEMICAL FORMULAΒ»)                                     (3)
                        𝑆𝑖      𝑆𝑖    𝑆𝑖     𝑆𝑖
                       π‘ͺ12 : {𝑉12  , 𝑋12 , 𝑀𝐴12 };π‘ͺ12 (Β«QUANTUM βˆ’ MECHANICAL CELLΒ»)                                      (4)
                        𝑆𝑖      𝑆𝑖    𝑆𝑖     𝑆𝑖
                       π‘ͺ21 : {𝑉21  , 𝑋21 , 𝑀𝐴21 }-π‘ͺ12 (Β«NUCLEAR CLUSTER – STATICΒ»)                                       (5)
                        𝑆𝑖      𝑆𝑖    𝑆𝑖     𝑆𝑖
                       π‘ͺ22 : {𝑉22  , 𝑋22 , 𝑀𝐴22 }-π‘ͺ22 (Β«NUCLEAR CLUSTER – DYNAMICSΒ»)                                     (6)
   In Figure 1 shows the structure of a multiscale composition for calculating ordered cluster configurations of
vacancies and interstitial atoms in Si. Specimens of basic compositions and the sequence of their use in the
computational process are indicated.




                          Figure 1: Large-scale composition for the calculation of defects in Si



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   At the first level, data on the chemical composition and atomic crystal structure of Si (diamond structure), obtained
using the basic composition π‘ͺ11 ("CRYSTAL CHEMICAL FORMULA"), were used. Further, they were used as input
data in the base composition π‘ͺ12 (β€œQUANTUM-MECHANICAL CELL”) during the first-principle calculations in the
framework of the electron density functional theory using the VASP software package [5]. In the first-principle
modeling of the structure of ideal silicon, a periodic cell consisting of 64 atoms of dimension (2 Γ— 2 Γ— 2) was used.
   Refined the atomic-crystalline and electronic structure of silicon with defects, was calculated πΈπ‘π‘œβ„Ž . The
computational resources of the Interdepartmental Supercomputer Center of the Russian Academy of Sciences and
Moscow State University of M. V. Lomonosov were used for the calculations.
   At the second scale level, questions were studied of the time variation of the structure of silicon with defects and
with defective clusters. A composition of computational models consisting of basic compositions π‘ͺ12 (β€œNUCLEAR
CLUSTER – STATIC”) and π‘ͺ22 (β€œNUCLEAR CLUSTER - DYNAMICS”) was used. Moreover, when forming the
input data π‘ͺ12 we used the results of first-principle calculations [5], obtained using the basic composition π‘ͺ12 . They
were used as reference. The cohesive energy of the system was the global parameter transmitted from the first to the
second scale πΈπ‘π‘œβ„Ž .

3       Model Description
    For the numerical simulation of silicon single crystal, an elementary silicon cell consisting of 8 atoms was used
(Figure 2). Further, using parallel transfers, the unit cell multiplied to silicon structures containing 616, 1160, and
4504 atoms. A structure was simulated with a complex of point defects, two vacancies located in neighboring lattice
sites (Figure 3), with a selected frequency of defect recurrence β€” through a cell.




                                       Figure 2: Si crystal lattice without defects




                                        Figure 3: Silicon lattice with divacancy

4       The Solution of the Problem
   Molecular dynamics modeling was carried out using the multiparameter potential of Tersoff [6], which proved
well in solving problems of modeling compounds with covalent bonds. The calculation of the cohesive energy of the
system of atoms was carried out as follows:
                                                 1
                                       𝐸 = βˆ‘ 𝐸𝑖 = βˆ‘ 𝑉𝑖𝑗                                                       (7)
                                                 2
                                               𝑖            𝑖

                                   𝑉𝑖𝑗 = 𝑓𝐢 (π‘Ÿπ‘–π‘— )[𝑓𝑅 (π‘Ÿπ‘–π‘— ) + 𝑏𝑖𝑗 𝑓𝐴 (π‘Ÿπ‘–π‘— )]                                       (8)




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                            1, π‘Ÿπ‘–π‘— < 𝑅 βˆ’ 𝑅𝑐𝑒𝑑
                                      1            πœ‹(π‘Ÿπ‘–π‘— βˆ’ 𝑅)
                    𝑓𝐢 (π‘Ÿπ‘–π‘— ) =         [1 + π‘π‘œπ‘  [           ]], 𝑅 βˆ’ 𝑅𝑐𝑒𝑑 < π‘Ÿπ‘–π‘— < 𝑅 + 𝑅𝑐𝑒𝑑                                            (9)
                                      2              2𝑅𝑐𝑒𝑑
                                  {      0, π‘Ÿπ‘–π‘— > 𝑅 + 𝑅𝑐𝑒𝑑                                              }
                                        𝑓𝑅 (π‘Ÿπ‘–π‘— ) = 𝐴𝑖𝑗 𝑒π‘₯𝑝(βˆ’πœ…π‘–π‘— (π‘Ÿπ‘–π‘— βˆ’ 𝑅𝑒 ))                                                        (10)
                                          𝑓𝐴 (π‘Ÿπ‘–π‘— ) = 𝐡𝑖𝑗 𝑒π‘₯𝑝(βˆ’πœ‡π‘–π‘— (π‘Ÿπ‘–π‘— βˆ’ 𝑅𝑒 ))                                                      (11)
                                                                              𝑛𝑖
                                                                          βˆ’
                                             𝑏𝑖𝑗 = πœ’π‘–π‘— (1 + 𝛾𝑖𝑛𝑖 πœπ‘–π‘—π‘›π‘– ) 2                                                           (12)
   Potential parameters were selected as a result of solving the optimization problem [7]:
                                              𝑓𝑝𝑐
               𝐹(πœ‰) = πœ”1 (πΈπ‘π‘œβ„Ž (πœ‰) βˆ’ πΈπ‘π‘œβ„Ž )2 + πœ”2 (π‘Ž(πœ‰) βˆ’ π‘Ž 𝑓𝑝𝑐 )2 + πœ”3 (𝐡(πœ‰) βˆ’ 𝐡 𝑓𝑝𝑐 )2 +

                                                                𝑓𝑝𝑐                                                                  (13)
               +πœ”4 (𝐢′(πœ‰) βˆ’ 𝐢′𝑓𝑝𝑐 )2 + πœ”5 (𝐢44 (πœ‰) βˆ’ 𝐢44 )2 + πœ”6 (𝜁(πœ‰) βˆ’ πœπ‘“π‘π‘ )2 β†’ π‘šπ‘–π‘›

where πœ‰ = (πœ‰1 … πœ‰π‘š ) - parameters of Tersoff potential
    𝑓𝑝𝑐                           𝑓𝑝𝑐
  πΈπ‘π‘œβ„Ž , π‘Ž 𝑓𝑝𝑐 , 𝐡 𝑓𝑝𝑐 , 𝐢′𝑓𝑝𝑐 , 𝐢44 , 𝜁 𝑓𝑝𝑐 - reference values obtained using ab initio calculations and from
publication [8]. Selected values of the potential parameters are given in Table 1.

                                  Table 1: Parameters of Tersoff potential for silicon structure

   𝑫𝒆         𝑺         𝜷              𝑹𝒆              𝒄                  𝒅                   𝒏         𝒉            𝜸           𝝀
 2,3631    1,4864 1,4637            2,3436      113074,1153           14,2474              0,9388     -0,4239   1,2466βˆ— 10βˆ’6   0,2993

  Molecular dynamics modeling was a solution to the Cauchy problem for the equation of motion described below.
The coordinates and velocities of each particle were set as the initial conditions for such problem.
                                              𝑑𝑒𝑛
                                         π‘šπ‘›        = 𝐹𝑛 (π‘₯1 , . . , π‘₯𝑁 ),
                                               𝑑𝑑
                                              π‘‘π‘žπ‘›
                                         π‘šπ‘›        = 𝐹𝑛 (𝑦1 , . . , 𝑦𝑁 ),
                                               𝑑𝑑
                                              𝑑𝑀𝑛
                                         π‘šπ‘›         = 𝐹𝑛 (𝑧1 , . . , 𝑧𝑁 ),
                                               𝑑𝑑                                                         (14)
                                                  𝑑π‘₯𝑛
                                                      = 𝑒𝑛 ,
                                                   𝑑𝑑
                                                  𝑑𝑦𝑛
                                                      = π‘žπ‘› ,
                                                   𝑑𝑑
                                                  𝑑𝑧𝑛
                                       {              = 𝑀𝑛 ,
                                                  𝑑𝑑
where π‘›πœ–[1, 𝑁];
   π‘šπ‘› – mass of the n-th atom, π‘›πœ–[1, 𝑁];
   𝐹𝑛 – force acting on the particle n.

To integrate the Cauchy problem, we used the Verlet velocity method [9]:
                                                                  πœπ‘˜2 πœ•π‘ˆπ‘›π‘˜
                                           π‘Ÿπ‘›π‘˜+1 = π‘Ÿπ‘›π‘˜ + πœπ‘˜ π‘£π‘›π‘˜ βˆ’
                                                                  2 πœ•π‘Ÿπ‘›π‘˜                                                             (15)


                                                                      𝜏     π‘˜+1
                                                                          πœ•π‘ˆπ‘›                π‘˜
                                                                                           πœ•π‘ˆπ‘›
                                                    π‘£π‘›π‘˜+1 = π‘£π‘›π‘˜ + π‘˜ (                  +          )
                                                                      2       πœ•π‘Ÿπ‘›π‘˜+1       πœ•π‘Ÿπ‘›π‘˜                                      (16)

This method is a compromise between accuracy and speed of implementation. The method is stable and accurate, as
well as self-starting due to the fact that its velocity is taken into account to obtain the next position of the particle.




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                           Figure 4: Block diagram of the molecular dynamics algorithm.




                               Figure 5: The block diagram of the parallel algorithm.

   Two algorithms were developed to simulate defects: serial, which was run on a personal computer (Intel Core i7 4-
core 4 GHz CPU, 16 GB OP), and parallelized to run on the IBM supercomputer (two 8-core IBM Power 8 CPUs, OP

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512 GB) Features of the implementation are associated with the use of the potential of Tersoff, which is difficult to
parallelize due to its complex structure, and is also resource-intensive from the point of view of computation.
    To implement the parallelized algorithm, the OpenMP standard was used. To do this, we determined the maximum
available number of threads for the program instance being started, after which the input data were divided into the
number of blocks equal to the number of available threads. Each input block was launched in its own stream. During
the molecular dynamics simulation, at the end of each time step, the blocks exchanged data in order to synchronize
the parameters of atoms that are common to different blocks (Figure 5). This approach has reduced the computational
complexity by reducing the number of atoms processed in each stream. In turn, this made it possible to significantly
accelerate the process of modeling, thanks to which it became possible to take into account a larger number of atoms
in the calculations.
    For a visual comparison of the speed of the parallel and sequential algorithms, the modeling process was limited to
10 time steps. The results of the calculations are presented in Table 2. According to the obtained results, the
application of the developed algorithm on a personal computer allows you to significantly speed up the calculations,
and the demonstrated result of acceleration on a supercomputer is more significant than on a quad-core processor.

             Table 2: Comparison of the running time of the algorithm on PC and IBM for different amount

Number of atoms              Personal              Personal                 IBM                IBM supercomputer,
                            Computer,             Computer,            supercomputer,             128 threads,
                             1 thread             4 threads               1 thread,                    sec
                                sec                  sec                     sec
          864                 991.664              358.496                1990.230                    65.585
         1152                 1995.660             707.852                3830.310                   125.255
         2048                 7010.740             2873.040              14231.100                   464.480

   The results obtained using the developed software package were also compared with the results obtained using the
LAMMPS package. A separate program was written to obtain results within the LAMMPS package. In it, the
elementary cell of silicon was modeled from 16 atoms with the help of the Tersoff potential at different temperatures.
The obtained data were compared with a similar experiment set in the developed software package. The bond energy
(E_pair) and system temperature (Temp) were compared.

     Table 3: Calculation results for a cell of 16 silicon atoms with a divacancy (the temperature at the beginning of the
                                                       simulation is 0 K)

    Number of time          E_pair MD             E_pair                 Temp MD,               Temp LAMMPS,
       steps                   eV                LAMMPS,                    K                         К
                                                   eV
0                       -74.0808               -74.0866            0                     0
100                     -74.0808               -74.0866                5.8324 βˆ— 10βˆ’34    9.8751βˆ— 10βˆ’25
1000                    -74.0808               -74.0866            6.0933βˆ— 10βˆ’32         9.1005βˆ— 10βˆ’25
10000                   -74.0808               -74.0866            7.0054βˆ— 10βˆ’34         3.1961βˆ— 10βˆ’25

     Table 4: Calculation results for a cell of 16 silicon atoms with a divacancy (the temperature at the beginning of the
                                                     simulation is 100 K)

    Number of time          E_pair MD             E_pair                 Temp MD,               Temp LAMMPS,
       steps                   eV                LAMMPS,                    K                         К
                                                   eV
0                       -74.0808               -74.0866            100                   100

100                     -73.5437               -73.9947            87.5567               52.6309
1000                    -74.0808               -74.0120            87.5872               61.5911
10000                   -74.0808               -73.9978            87.5872               54.2501
     Table 5: Calculation results for a cell of 16 silicon atoms with a divacancy (the temperature at the beginning of the
                                                      simulation is 500 K)

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    Number of time          E_pair MD              E_pair                   Temp MD,            Temp LAMMPS,
       steps                   eV                 LAMMPS,                      K                      К
                                                    eV
0                       -74.0808               -74.0866            500                   500

100                     -70.9716               -73.6818            437.8505              291.3985
1000                    -74.0808               -73.6169            437.9358              258.1365
10000                   -74.0808               -73.6535            437.9360              276.9892

     Table 6: Calculation results for a cell of 16 silicon atoms with a divacancy (the temperature at the beginning of the
                                                     simulation is 1000 K)

    Number of time          E_pair MD              E_pair                Temp MD,              Temp LAMMPS,
       steps                   eV                 LAMMPS,                   K                        К
                                                    eV
0                       -74.0808               -74.0866            1000                 1000
100                     -67.8394               -73.1538            875.6751             519.4458
1000                    -74.0808               -73.1616            875.8718             523.6768
10000                   -74.0808               -73.0931            875.8721             488.4341

   From the comparison performed, it can be seen that the binding energy is close to the energy values obtained using
the LAMMPS software, and the temperature is comparable to the results obtained in LAMMPS.
The implemented algorithm made it possible to calculate the characteristics of monocrystalline silicon, in particular,
the value of the binding energy for monocrystalline silicon was calculated (πΈπ‘π‘œβ„Ž (πœ‰) = βˆ’4.6314С𝑉). The obtained
                                                                                                     𝑓𝑝𝑐
value turned out to be close to the value obtained earlier with the help of ab initio calculations (πΈπ‘π‘œβ„Ž = βˆ’4.6305С𝑉)
[10]. Thus, the developed software using the selected parameters of the Tersof potential allows one to fairly
accurately describe the geometric and energy properties of monocrystalline silicon. This approach can be further
applied to the study of more complex structures of vacancy clusters in a silicon single crystal.

5         Conclusion
   In this paper, software was developed that enables molecular dynamics modeling, effectively parallelizing
computational flows. As part of the task of studying the stability of defective clusters in monocrystalline silicon, the
developed software was used to calculate the divacancy binding energy in the structure of monocrystalline silicon.
The proposed algorithm allows us to significantly accelerate molecular dynamics calculations, making it possible to
take into account a larger number of interacting atoms in the simulation. In turn, this will allow us to study the
properties of more complex defective structures in silicon. This approach can be applied further to simulate
interacting atomic systems described by different potentials.
   The calculations were performed by Hybrid high-performance computing cluster of FRC CS RAS) [19,20] and
Shared Facility Center β€œData Center of FEB RAS” (Khabarovsk) [21].

6         Application

The designation of variables used in formulas.

𝑬 - total energy of the system, (eV);
π‘½π’Šπ’‹ - potential energy of the interaction of two particles i and j, (eV);
𝒇π‘ͺ (π’“π’Šπ’‹ ) - cutoff-function
π’“π’Šπ’‹ -distance between two particles i and j, (Γ…);
𝑹𝒄𝒖𝒕 - cutoff distance (Γ…);
𝒇𝑹 – repulsive potential between two atoms, (eV);
𝒇𝑨 – potential of attraction between two atoms, (eV);
Π’π’Šπ’‹ -parameter of attraction between two atoms, (eV);


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π‘¨π’Šπ’‹ -repulsive parameter between two atoms, (eV);
R – parameter of Tersoff potential, (Γ…);
ππ’Šπ’‹ – parameter of Tersoff potential, (Γ…);
πœΏπ’Šπ’‹ – parameter of Tersoff potential, (Γ…);
Ξ³ – parameter of Tersoff potential, (dimensionless);
Re – parameter of Tersoff potential, (Γ…);
Ξ» – parameter of Tersoff potential, (Γ…);
n – parameter of Tersoff potential, (dimensionless);
ΞΆ – parameter of Tersoff potential, (dimensionless);
𝝌 - parameter of Tersoff potential, (dimensionless);
𝑬𝒄𝒐𝒉 - cohesive energy of the system, (eV);
𝒂 - lattice constant, (Γ…);
𝑩 - bulk modulus, (Mbar);
π‘ͺβ€² - shear modulus, (Mbar);
π‘ͺπŸ’πŸ’ - elastic constant, (Mbar);
𝜻 - Kleinman's constant, (dimensionless);
𝝎 = (𝝎𝟏 … πŽπŸ” ) βˆ’ weights;
𝝃 = (πƒπŸ … πƒπ’Ž ) - parameter of Tersoff potential;
m – atom mass, (1.66054 * 10-27 kg);
F – the force acting on the molecule, (N);
𝒙𝒏 , π’šπ’ , 𝒛𝒏 – coordinates of the n-th atom, (Γ…);
𝒖𝒏 , 𝒒𝒏 , π’˜π’ – the speed of the n-th atom (m/s);
r – atomic coordinates, (Γ…);
v – atom speeds (m/s);
t – time, (s);
U - interaction potential between two atoms, (J);

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