New Bending Algorithm for Field-Driven Molecular Dynamics
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- Chen, DL., Chen, TC. & Lai, YS. Nanoscale Res Lett (2010) 5: 315. doi:10.1007/s11671-009-9482-8
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A field-driven bending method is introduced in this paper according to the coordinate transformation between straight and curved coordinates. This novel method can incorporate with the periodic boundary conditions in analysis along axial, bending, and transverse directions. For the case of small bending, the bending strain can be compatible with the beam theory. Consequently, it can be regarded as a generalized SLLOD algorithm. In this work, the bulk copper beam under bending is analyzed first by the novel bending method. The bending stress estimated here is well consistent to the results predicted by the beam theory. Moreover, a hollow nanowire is also analyzed. The zigzag traces of atomic stress and the corresponding 422 common neighbor type can be observed near the inner surface of the hollow nanowire, which values are increased with an increase of time. It can be seen that the novel bending method with periodic boundary condition along axial direction can provide a more physical significance than the traditional method with fixed boundary condition.
KeywordsMolecular dynamicsField-drivenHollow nanowireBendingSLLOD algorithm
The nano-scale mechanical properties become important since the size of electrical components is successively reduced for the portable convenience [1, 2]. Most of studies focused on mechanical properties related to the tension and compression. The problems of bending are actually met more frequently although it is composed by tension and compression. The bending tests of nanomaterials by using atomic simulation were widely applied. Liu et al.  simulated the pure bending of defect-free Al single crystals to investigate dislocation nucleation from free surfaces. They found that dislocation nucleation is not well represented by a critical value of the resolved shear stress but is reasonably well represented by the critical stress-gradient criterion. On the other hand, the size effects were also discussed widely. Miller and Shenoy  found that the surface elastic constant is the same order as the bulk elastic constant. The surface effect was also discussed in the bending case.
Unlike the case of tensile or compression tests of nanowire (NW) or nanofilm (NF) where the periodic boundary conditions (PBCs) were applied along the axial direction to remove the size effect, almost all the bending simulations took the ends of nanowire or nanofilm as fixed boundary conditions (FxBCs) . The FxBC is essentially inducing the size effects into the simulated objects. From the viewpoint of thermodynamics, the fixed atoms are viewed as zero velocities, and, thus, zero temperature at the fixed ends. In other words, all thermodynamic variables involving atom velocities are not well defined at the fixed boundary.
For the purpose of the computational efficiency, there are many methods to improve the computational speed. One of the methods is to use the synthetic system instead of real system. For example, Nose–Hoover algorithm [5–7], the synthetic thermostat variable generates the NVT ensemble more stably and efficiently than the rescaled velocity method , the latter cannot generate the NVT ensemble exactly. Moreover, the synthetic system usually combines the physical response into the equations of motion, thus can prevent the discontinuous trajectory of atoms and save the time to do the local equilibrium.
Non-equilibrium molecular dynamics (NEMD) can be described as two representations . One is the boundary-driven (BD) representation, the other is the field-driven (FD) representation. The FD method is belonging to the synthetic system. The BD method was used to calculate the thermal transport coefficients while the FD method was used to calculate the mechanical ones. One can mathematically transform the non-equilibrium boundary conditions for a thermal transport process into a mechanical field. The two representations of the system are said to be “congruent”. Almost all FD methods can combine with PBC while BD methods usually combine with FxBCs. In addition, since the non-equilibrium response is reflected in the equations of motion for FD method, it is no need to use the stepwise equilibrium-non-equilibrium cyclic driven that usually used in the BD method. Thus the FD method can be more efficient than BD method.
From the above reasons, a novel-bending algorithm is proposed and investigated in this paper. Based on the coordinate transformation from flat coordinate to curved one, the straight material is transformed to the curved one. The method belongs to FD method, and can be viewed as the generalized SLLOD algorithm . It also removes the fixed atoms generally used at FxBCs so that all thermodynamic variables involving atom velocities can be defined everywhere. The method for the bending algorithm is introduced in “Methodology” section. “Numerical Tests” section shows some numerical tests for both macroscopic and microscopic systems. Finally, it is concluded in “Conclusion” section.
The Coordinate Transformation
For D < 0, there are three different real roots; for D = 0, there are triple or double real roots; and for D > 0, there is only one real root and two imaginary roots. The geometrical condition requests that the distance d is a real root, thus D must be greater than zero. One can see that if we set Open image in new window then D must be greater than zero. Thus the condition Open image in new window is selected as a limit range of the coordinate transformation.
It can be seen thatOpen image in new window
The Bending Strain
where L,b, and c are the length, width, and depth of the beam, respectively. Thus the volume of the beam can be viewed as no change after bending. At y = 0, the axial strain εxx = 0, thus the axis x′ can be considered as centroid axis or neutral surface. The linear relation between εxx and y is also consistent with the assumption of beam theory . For εxy = 0, it is also conformed to the assumption that plane sections initially normal to the beam axis remain plane and normal to that axis after bending. The transverse strain Open image in new window also meets the assumption of beam theory. Thus the model can be used to verify the suitability of beam theory in the nanoscale model with slight bending.
The SLOOD Algorithm
where Open image in new window
where Ci and Di are the phase variables coupling of the field Fe(t) to the system. Equations 25 and 26 can be reduced to original SLLOD algorithm if the rate of displacement gradient tensor is independent of coordinate . Thus Eqs. 25 and 26 can be viewed as the generalized SLLOD algorithm. Note that Eqs. 25 and 26 can also be used in the case with large deformation.
Periodic Boundary Conditions
The minimum image criteria (MIC) can also be implemented. As shown in Fig. 4, the curved cell can be transformed to rectangular one by J−1. After building the image cells, the neighbor list can be built up , and then the rectangular cell is restored to the curved cell by J. The forces between any neighbor atoms thus are calculated according to the neighbor list and the curved positions.
Equation 29 then serves the equation of motion for the primary cell.
Bulk Copper Beam
The system is equilibrated first in the NσT ensemble with GGMT thermostat method (with five thermostat variables)  at 300 K and MTK barostat method  at 0 GPa during 0.1 ns. Then the system is bended with bending rate Open image in new window fs−1 Å−1, which equals to the bending rate at the beam end of Open image in new window rad ns−1, and the temperature is controlled at 300 K with GGMT method.
The simulated values with the bending algorithm are σmax = 7.81 GPa and σmin = −6.79 GPa which take the average among the top and bottom atomic layers, respectively. The values of atomic simulation are close to the one estimated by continuous mechanical beam theory.
The values of the axial stress obtained in this work are distributed just in between. The possible cause is that the lattice constant is stretched/compressed so that the elastic moduli are no longer the same as reference . Thus the axial stresses at top and bottom are not symmetric, and deviate from Eq. 36.
Once the model is compatible with macroscopic bulk, it is confident to use the bending method to simulate the microscopic nano-system.
Hollow Copper Nanowire
Nanowires (NWs) exhibit an interesting quantum conductance behavior even at room temperature. Electron transport properties for NWs have been investigated extensively due to their significant importance in a variety of applications . Diao et al.  investigated the elastic properties of Au NWs by molecular statics, and found that due to the surface effects, the smaller the cross-sectional area the higher the Young’s modulus in the NWs without undergoing the phase transformation. Chen and Chen  studied the Au NWs subjected to uniaxial tension at high strain-rate under different temperatures. They found the microstructures of NWs were transformed first from FCC to face-centred-orthorhombic-like crystalline, and then changed to the amorphous state. Moreover, it was predicted that the conductance at high strain-rate deformation may be no longer quantized. Recent research has revealed that geometry, including surface orientation and the hollowness of nanomaterials, can also greatly affect their behavior [24–28].
The works of Jiang and Zheng [27, 28] are referred here to compare the effect induced by different boundaries. The system size studied in this paper is same as Zheng’s work (outer and inner cross-section parameters are 10aLattice and 4alattice, respectively), except the PBC is applied here along the axial direction instead of FxBC used in Zheng’s work. Other settings remain the same as previous sub-section. The system is equilibrated in NVT ensemble with GGMT method at 10 K before bending.
Since the PBC is applied here, the atoms at the boundary are movable so that the stress trace can grow through the ends. On the contrary, if the FxBC is applied, the atoms at the ends will be fixed, and the interface between movable and fixed atoms will lead to an artificially induced crack, obviously violating the physical phenomenon.
In this study, the synthetic, field-driven bending method is introduced by using the coordinate transformation between straight and curved coordinates. The new method can incorporate with PBCs along axial, bending, and transverse directions. For problem with small bending effect, the bending strains evaluated by this method are well consistent with those predicted by the beam theory. Furthermore, it can be regarded as the generalized SLLOD algorithm. The accuracy and reliability of this novel bending method are verified by two examples, which are the bulk copper beam and the hollow NW under bending, respectively. The bending stress of the bulk copper beam estimated here is quite close to those predicted by the beam theory; while the atomic stress and the corresponding microstructure of 422 CN type near the inner surface of the hollow NW are increased with an increase of time. These results are well consistent with the earlier work. Moreover, the performance of this novel bending method can be significantly enhanced by using PBC along axial direction in the bending model by eliminating the artificial crack which is easily created by using traditional method with FxBC.