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Engineering

Using Simulated Annealing with Parallel Tempering to Create Low-Defect Silica Surfaces

&

Aerospace

Paul Norman and Thomas Schwartzentruber

Mechanics

University of Minnesota

1

1.1

Introduction

1.4

Simulated Annealing

**The LAMMPS molecular dynamics code
**

allows for massively parallel simulations

with billions of atoms[1]. However, as

with all molecular dynamics (MD) simulations, the practical timescales of simulations are relatively short (10-100 ns). Of

special interest in this work are MD simulations of systems with ’rugged’ potential energy surfaces, which are characterized by numerous local (metastable) minima separated by high energetic barriers.

Due to the limited timescales of MD simulations, simulations of such systems can

suffer from inadequate sampling because

they are trapped in these local minima.

One common method to enhance the samFigure 1.1: Simulated Annealing

pling of phase space is simulated annealing. In simulated annealing simulations, a system is given an initially high temperature, allowing

it to overcome high energy barriers, and then gradually cooled to the desired temperature[2]. The

simulated annealing technique is guaranteed to reach the global optimum of a system as the time

taken to cool the system approaches infinity[3]. However, actual MD simulations cannot be infinite in length. During simulated annealing simulations, the system can become trapped in local

energy minimum, escape from which is unlikely as the system is further cooled. The extent to

which this occurs is specific to the system being simulated. Examples of a simulated annealing

simulations using linear and stepped cooling are shown in Fig 1.1.

1.2

Parallel Tempering

**The goal of parallel tempering (or replica
**

exchange) MD simulations is to increase

the efficiency of the sampling of the phase

space of a system. In parallel tempering molecular dynamics simulations, several replicas of a system are simulated independently and simultaneously at different temperatures[4]. At specified intervals, replicas with neighboring temperatures are exchanged with the the Boltzmann weighted metropolis criterion:

P swap(i, j) = min(1, e(β j−βi)(Ui−U j )

(1)

**The random walk in temperature allows
**

systems trapped in metastable states to esFigure 1.2 Parallel Tempering

cape by exchanging replicas with systems

at higher temperatures. Systems at high temperatures are able to efficiently overcome large potential barriers, while systems at low temperatures selectively gain access to low energy structures. An advantage of parallel tempering simulations over simulated annealing is that exchange

between low and high temperatures is possible throughout the entire simulation. However, one

drawback to parallel tempering is the large number of replicas needed to cover the desired temperature interval. Efficient exchanges between replicas can only take place if there is some overlap

between the potential energy of neighboring replicas over the course of a simulation. It has been

shown that the number of replicas needed in a parallel tempering simulations scales approximately

with the square root of the number of particles[5]. Additionally, simulations with a large number

replicas require increased simulation times for replicas to ’diffuse’ over the range of temperatures

and effectively cross barriers. An example of a parallel tempering simulation is shown in Fig. 1.2.

1.3

**Department of Aerospace Engineering and Mechanics
**

University of Minnesota, Twin Cities Campus, Minneapolis, MN, 55455 USA

contact email: norma198@umn.edu

Simulated Annealing combined with Parallel Tempering

**By combining simulated annealing with
**

parallel tempering, a method that shares

the advantages of both techniques is

created[6]. A small set of replicas are

given a temperature distribution around

a high temperature, and simulated via parallel tempering. At specified time intervals, each replica is cooled to a lower

temperature, until the replicas are at the

desired final temperature. This method

keeps the efficient sampling of parallel

tempering while relaxing the constraints

on the large number of replicas needed. It

has been shown to be more computationally efficient than simulated annealing for

simulations of protein model structures,

Fig 1.3: Simulated Annealing combined with

and requires fewer replicas than parallel

Parallel Tempering

tempering[6]. However, to fully realize

the benefits of parallel tempering there must be a sufficient number of replica exchanges between

temperature shifts, placing an upper bound on the cooling rate of the simulated annealing. An

example of a simulation using simulated annealing combined with parallel tempering is shown in

Fig. 1.3.

Implementation in LAMMPS

The capability to run both simulated annealing and parallel tempering simulations already exists in LAMMPS. Simulated annealing combined with parallel tempering was implemented in

LAMMPS, and can be executed with the anneal_temper command in a typical input script. To

run simulations the following syntax is used:

anneal_temper N X Y W fix-ID seed1 seed2 T1 T2 T3 ... TN

• N = Total number of timesteps to run

• X = Attempt tempering swap every this many steps

• Y = Shift temperature of Ti to Ti+1 every this many steps

• W = Which entry on the temperature list (T1 T2 T3 ... TN) I am in simulations

2.2

Results And Discussion

We will compare the results of simulated annealing to simulated annealing with parallel tempering. To perform a relevant comparison, simulated annealing simulations are run with a linear

cooling schedule with the same temperature list as simulated annealing with parallel tempering

simulations. Four pairs of simulations were run, each with different starting a-SiO2 surfaces

cleaved from the bulk. We will use two metrics to determine the efficacy of the techniques: surface energy and defect concentration. The surface energy is defined as the difference between the

energy of the slab exposed to vacuum and the the energy of the slab in the bulk, divided by area

of the slab. There are several types of defects predicted by the BKS potential on a-SiO2 surfaces:

under-coordinated silicon atoms (≡Si· as shown in Fig. 2.2(b)), non-bridging oxygen (≡Si-O· and

=Si-O·, as shown in Fig. 2.2(c) and (d) respectively), and Si2O2 rings (shown in Fig 2.2(e)). These

defects can be uniquely identified by their connectivity to other atoms in the slab. An annealed

a-SiO2 surface with ≡Si· defects highlighted is shown in Fig. 2.2(a).

**• ID of the fix that will control temperature during the run
**

• seed1 = random number seed used to decide on adjacent temperature to partner with

• seed2 = = random number seed for Boltzmann factor in Metropolis swap

• T1 T2 T3 ... TN List of temperatures to descend through.

**The number of timesteps between temperature shifts (Y) must be a multiple of the number of
**

timesteps between attempted swaps (X). If any individual world has a temperature of Tn, no more

temperature shifts will occur. The method was validated by checking that it reproduced typical

parallel tempering simulations before shifting occurred, and that it reproduced typical simulated

annealing simulations when no swaps were allowed.

2

2.1

.

(b)≡Si·

(c)≡Si-O·

.

(e)=Si·

(f) Si2O2 Ring

Application

Amorphous Silica Surfaces

**We will consider the application of simulated annealing and simulated annealing with parallel
**

tempering to dry amorphous silica surfaces. Amorphous silica (a-SiO2) surfaces can be created

by simply cleaving bulk a-SiO2 along a desired plane. However, this creates an unrealistic surface covered with highly reactive broken bonds that could only be produced experimentally with

infinitely high strain rates. Simulated annealing has previously been applied to a-SiO2 surfaces to

create more realistic surfaces[7]. Previous annealing simulations of a-SiO2 surfaces have shown

that short annealing simulations tend to leave a surface covered with more defects, while longer

simulations annealing simulations decrease number of defects on the surface[8]. Experimental

evidence suggests that real a-SiO2 surfaces annealed over long timescales (hours) have very few

defects and are primarily terminated with bridging oxygen atoms (Si-O-Si)[9]. Our goal is to

approach realistic, defect free surfaces by accelerating annealing simulations with parallel tempering. Realistic a-SiO2 surfaces are important for numerous applications, including simulations

of the chemical reaction occurring on silica heat shields during reentry[8].

Typical annealing simulations of a-SiO2 surfaces have a temperature range from 4000 K - 300

K[7]. To run parallel tempering simulations, it is necessary to create a list of temperatures spanning this range. These temperatures must be chosen such that there is a reasonable swapping

probability between replicas. It has been shown that for parallel tempering simulations of model

proteins that a swapping probability of 20-40% is desirable[6].

For the purpose of our simulations, we will

use a 20 Å x 35 Å x 35 Å slab of a-SiO2

(∼1600 atoms), created by cleaving a previously annealed bulk along the (001) plane. For

all simulations we will use the the BKS interatomic potential[10] with the modifications

suggested by Jee et al.[11]. To check how the

swapping probability varies with the temperature difference, we ran parallel tempering simulations with two replicas. A total of 200 exchanges were attempted with at a frequency

of 1 attempt/ps. In all cases the temperature

of the higher replica was 4000 K. As shown

in Fig. 2.1, the exchange probability decreases

with the temperature difference. For simulations with this slab, we will use ∆T= 50 K

Fig 2.1: Swapping Probability vs. T

at 4000 K, which corresponds to a swapping

probability of ∼20%. The list of temperatures used in the simulated annealing with parallel tempering simulations is generated with the equation:

T i = Aek∗i

(2)

The exchange probability between replicas remains constant over the temperature list created by

this equation. Using the parameters A = 1000 K and k = 0.011, this produces a list of 128 temperatures between 4000 K - 1000 K, with ∆T = 50K near 4000 K. A parallel tempering simulation

using this temperature list would require 128 individual replicas.

The three additional parameters that are

needed for simulations are: the time between

swap attempts, the time between temperature shifts, and the number of local replicas. The time between swap attempts must

be large enough that replicas undergo appreciable conformational changes between exchange

attempts. Figure. 2.1 shows the mean square

displacement of atoms in the slab at different

temperatures. It might be optimal to adjust

the shift attempt frequency with temperature so

it corresponds directly to a constant value of

mean square displacement, however this goes

beyond the capabilities of current implementation of the method. We will attempt temperature swaps every 1 ps, which gives a mean

Fig 2.2: MSD vs. T

square diffusion of about 1 Å per swap attempt

at 4000 K. The number of replicas used must be large enough to span a temperature range that

allows replicas to overcome whatever potential barriers exist in the system, and the time between

shifts must allow sufficient time for individual replicas to overcome these barriers via exchange.

We will use four local replicas, which span as much as 175 K in temperature, and perform temperature shifts every 10 ps.

**(a): Defects Highlighted on Surface.
**

≡Si-O·(blue). ≡Si-O·(green)

**Fig 2.2: a-SiO2 Surface with Defects
**

Defect Concentration (/Å2)

Method

Total Si2O2 ≡Si· ≡Si-O· =Si-O· Surface Energy

(meV/Å2)

Parallel Tempering with 0.726 0.552 0.112 0.127 0.008 18.89

Simulated Annealing

Simulated Annealing

0.7811 0.482 0.165 0.132 0.002 21.7

Simulated Annealing (2x 0.676 0.388 0.149 0.129 0.009 19.2

slower)

Table 1: Comparison of a-SiO2 Surfaces created with different methods

As shown in Table 1 the surfaces created by simulated annealing with parallel tempering have

slightly fewer defects and slightly lower surface energies than those created with simulated annealing. An additional simulated annealing simulation run at half the cooling rate (and thus twice

the CPU time) creates a surfaces with fewer defects but a higher surface energy than simulated annealing with parallel tempering. These results demonstrate that simulated annealing with parallel

tempering is faster than simulated annealing alone for this system, and even has the potential to

be more efficient in terms of total CPU time used. It has been shown that this method, when finely

tuned for certain systems, can be more efficient than simulated annealing alone[6]. However,

additional annealing simulations would need to be needed to confirm this.

3

Conclusions

**The hybrid method of simulated annealing with parallel tempering was implemented in
**

LAMMPS. This method shares the advantages of simulated annealing and parallel tempering,

and uses fewer replicas than parallel tempering alone. We applied this method to a-SiO2 silica

surfaces and found that it was more effective than simulated annealing at creating low-defect surfaces. However, to successfully apply this method to a general system, care must be taken in

choosing the parameters to suit the specific needs of the system. The primary limitation of this

method is that as the total number of atoms in a system increases, the maximum cooling rate

decreases. This method would be most effective when applied to smaller systems of atoms, or

simulations with computationally expensive interatomic potentials.

REFERENCES

[1] Plimpton, S., “Fast Parallel Algorithms for Short-Range Molecular Dynamics,” J. Computational Physics, Vol. 117,

1995, pp. 1–19, lammps.sandia.gov.

[2] Kirkpatrick, S., C.D. Gelatt, J., and Vecchi, M. P., “Optimization by Simulated Annealing,” Science, Vol. 220, No.

4598, 1983.

[3] Mitra, D., Romeo, F., and Sangiovanni-Vincentelli, A., “Convergence and Finite-Time Behavoir of Simulated Annealing,” Advanced Applied Probability, Vol. 18, 1986, pp. 747–771.

[4] Fukunishi, H., WWatanabe, O., and Takda, S., “On the Hamiltonian replica exchange method for efficient samping

of biomolecular systems: application to protein structure prediction,” Journal of Chemical Physics, Vol. 116, 2002,

pp. 9058–9067.

[5] Tathore, N., Chopra, M., and de Pablo, J., “Optimal allocation of replicas in parallel tempering simulations,” Journal

of Chemical Physics, Vol. 122, 2005.

[6] Kannan, S. and Zacharias, M., “Simulated annealing coupled replica exchange molecular dynamics – An efficient

conformational sampling method,” Journal of Structural Biology, 2009, pp. 288–294.

[7] Fogarty, J., Aktulga, H., Grama, A., and van Duin, A., “A reactive molecular dynamics simulation of the silica water

interface,” The Journal of Chemical Physics, Vol. 132, 2010, pp. 174704.

[8] Norman, P., Schwartzentruber, T., and Cozmuta, I., “A computational Chemistry Methodology for Developing an

Oxygen-Silica Finite Rate Catalytic Model for Hypersonic Flows,” 42nd AIAA Thermophysics Conference. Honolulu, Hawaii. June 27-30, 2011.

[9] Sneh, O. and George, S., “Thermal Stability of Hydroxyl Groups on a Well-Defined Silica Surface,” The Journal of

Chemical Physics, 1995, pp. 4639–4647.

[10] Beest, B., Kramer, G., and van Santen, R., “Force Fields fo Silicas and Aluminophosphates Based on Ab Initio

Calculations,” Physical Review Letters, Vol. 64, No. 16, 1990.

[11] Jee, S., McGaughey, A., and Sholl, D., “Molecular simulations of hydrogen and methane permeation through pore

moth modified zeolite membranes,” Molecular Simulation, Vol. 35, 2009.

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