Dynamic Monte Carlo

Methods:
Theory and Applications

By
Daniela S. Mainardi

1
 Outline

1. Theoretical Introduction

DMC Method
Program Carlos 4.0

2. Applications

Temperature Programmed Simulations

Lateral Interactions
Voltammetric Scans

2
THEORY

3
 Introduction to DMC Methods
Quantum Mechanical Laws of Quantum Mechanics
(Ab Initio, DFT) ∧
H ψ = Eψ

Quantum effects determine all the chemistry

Hardware and software not enough to fully treat

relatively large systems!!!

Classical
(Monte Carlo, Molecular Dynamics)
1. Do not explicitly include the presence of electrons
2. Effective force fields represent the electronic effects
3. Physical and thermodynamic properties obtained using
classical statistical mechanics and Newton’s Law (MD). 4
Introduction to DMC Methods
MD simulations provide dynamic phenomena to
the order of nanoseconds.

For phenomena taking place in the range of

seconds,

Coarse-Grained methods

Dynamic Monte Carlo

5
 DMC Methods
Advantages:
1. treatment of non-equilibrium systems in which
conditions change over time
Importance reaction mechanisms for
heterogeneous catalysis

2. It is able to simultaneously simulate many different

transitions or reaction types covering events that
span time scales up to the orders of seconds
3. The real-time behavior of a system is simulated

6
 DMC Methods
Main Challenge:
Reaction rates are needed as input

experiments or ab initio calculations

7
How can we implement the
DMC method?

If we want to study chemical

reactions on crystal surfaces

Carlos 4.0
© Copyright Johan J. Lukkien
October 1995

8
 What is Carlos useful for?
Systems not at equilibrium like
1. Temperature Programmed systems 2. Voltammetric
scans
3. Oscillating systems, spatio-temporal pattern
formation
4. Epitaxial growth
Non-homogeneous systems
1. Surface steps/defects
2. Lateral interactions
Systems with slow relaxation

9
 What do we need?
1. Specify the chemical System we want to
study

2. A stochastic model is built:

* crystal surface,
* the adsorbates,
* a law to describe the microscopic
reaction steps that change the surface
configuration over time.

The behavior of this system over time is

determined by the rates of these reactions
(specified as probabilities). 10
 Elements in the model
The crystal surface

– The surface is represented by a lattice: each

lattice point corresponds to a surface site
Top
fcc (111) surface Bridge Unit cell
Hollow
Atom

11
 Elements in the model
The adsorbates
– The lattice together with “values for all its
points” is called a configuration

“values for all its points” means information about

the state of the adsorption sites: empty or filled
by the adsorbates

– A reaction changes a configuration into a new one

– If in a certain configuration a reaction is possible

we say that it is enable
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 Elements in the model
The “law”
– The evolution of the system over time is described by the chemical master equation

dP (c, t )
= ∑ ( kc 'c P(c' , t ) − kcc ' P (c, t ) )
dt c '≠ c

kA
A →*
P(c,t) ≡ probability of
dθ A
finding the system in dt
= −k Aθ A = − rA
configuration kc 'c ~ r ≡ reaction rate
c at time t.
kcc’ ≡ microscopic rate of  Eact 
the reaction that transfer c r = υ exp − 
Arrhenius Law  k BT  13
into c’
 How Carlos works?
We could either give Carlos the macroscopic rates or
Eact and ν , and Carlos will compute the microscopic
ones to solve the Master equation

There are methods which are used internally to solve

this equation:
 First-Reaction Method (FRM)
 Variable Step Size Method (VSSM)
 Random Selection Method (RSM)
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Solving the Master equation...

 tα β ' 
exp − ∫ dt rβ α(t ' ) = δ
 t 
rβα = the time dependent rate of a reaction
δ = a random number selected uniformly (0,1)

The way in which this equation is

solved gives rise to the different
methods
R.J. Gelten, R.A. VanSanten, A.P.J. Jansen, in: P.B. Balbuena, 15
J.M. Seminario (Eds.), Molecular dynamics: From classical to
quantum methods, Elsevier Science, Amsterdam, 1999, p. 737
 FRM

– It can be used for BOTH time-dependent or time-

independent rate constants.

– According to this method, when the system is in a

given configuration α , the set of all possible
reactions is determined, and a time of occurrence
tαβ is generated for EACH reaction

– Carlos lists all the reactions from the one with

the smallest tαβ to the one with the largest time

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 FRM

- Then, the reaction with the SMALLEST tα β

is selected, the configuration is changed
accordingly, and the time t is incremented
in tα β

- Finally, the set of possible reactions is

generated according to the new
configuration β , and the procedure is
repeated

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 VSSM
– It can be used for time-independent rate
constants ONLY

– According to this method, when the system is in a

given configuration α , the set of all possible
reactions is determined, and ONLY ONE time of
occurrence t is generated for ALL reactions

– Then, ONE reaction is selected with a probability

proportional to its rate, the configuration is
changed accordingly, the procedure is repeated

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 RSM
– It can be used for BOTH time-dependent or time-
independent rate constants.

– A SITE is selected with a probability 1/N, being N the

total number of sites. Then, a given reaction is
selected with probability proportional to its rate

– When this reaction is possible on the site, it is

executed. After each selection of a site, time is
incremented by t which is selected RAMDOMLY from
a FIXED distribution
 
1 − exp − Nt ∑ ri 
 i 

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– the configuration is changed accordingly, the

 Comments
– FRM and VSSM can be implemented very efficiently
because information generated at some time step can
be re-used at subsequent steps.
– The advantage of VSSM and RSM over FRM is that the
cost per generated transition (reaction) is independent
of the size of the grid used in the simulation, whereas
in FRM it scales as the logarithm of the number of grid
points. Due to this, VSSM and RSM are more efficient
in memory use and execution time.
– The advantage of FRM over VSSM is that it is a
suitable method to simulate reactions with time-
dependent transition probabilities.
– The advantage of RSM is that is easy to implement and
for some models (or reaction types) it is a very fast
method. 20
Preparing Input Files...
CARLOS needs two input files to run a
simulation:

1. Initial Configuration: can be made by CARLOS, as a

.con file, or can be constructed directly using a text
editor
name.init

2. System File: contains a complete description of the

simulation model
name.sim

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 Geting outputs...
The logfile: name
(information recorded during the simulation)

The parameter file: name.par

(describing both the simulation model and relevant information
about the simulation such as timing, memory and methods)

The graph file: name.xxxx.gif

(pictures of the lattice in gif format, if –g option is not given)

The configuration file: name.con

(the final configuration if the -C option is given)

The system file: name.sys

(a copy of the system file if the -S option is present )
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APPLICATIONS

23
Temperature Programmed
simulations

O2 desorption from Pt (111)

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Initial configuration: full, i.e, 1 O2 ML is adsorbed on the surface

O O O2
O2 O2 2 O2 2 O2

1 O2 ML
ONLY O2 desorption reaction is
investigated:

O2 desorption O2(ads_b) → O2 + b b = empty bridge

Prefactor: 1.0 x 1013 s-1

Activation energy: 0.36 eV

I increased T from 100K to 190 K: T = 100.0 + 2.0 *25t

RESULTS 0.6
O2_des

Initial configuration

Reactions/unit cell/sec
0.4

0.2

0
100 120 140 160 180
T (K)
1

0.8
O2 Concentration

0.6

0.4

0.2

0
100 120 140 160 180
T (K)

A. Winkler et al.,
Surface Science 201
(1988), 419 - 443

Final configuration
26
Temperature Programmed
simulations

O2 adsorption, dissociation,
desorption, and O diffusion
on Pt (111)

27
 Initial configuration: empty Pt surface

O2 Top
O2 Bridge
Hollow
Pt atom

Pt(111) surface
64 x 64 lattice
O2 adsorption O2 + b → O2(ads_b)
O2 dissociation O2(ads_b) + 2h → 2O(ads_h) + b b = empty bridge
h = empty hollow
O diffusion O(ads_hhcp ) + hfcc → hhcp + O(ads_hfcc )
O2 desorption O2(ads_b) → O2 + b

• O2 adsorption on Pt(111) occurs on bridge sites (b).

• Upon dissociation of O2, O atoms occupy hollow sites
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(h).
 Reaction Eact Eact/KB (K) ν
(eV) (s-1 )
O2 ads 0.09 1044.4 F(T)

O2 diss 0.3 3481.33 1.20E+12

O2 des 0.36 4177.6 1.00E+13

O diff 0.13 1508.58 2.60E+12

Prefactor calculated using Hertz-

Knudsen formula:

+
Ea P
F=
ν = A site FS0 e KT
2πMkT
[P] = Pa
[k] = J/K
[M] = kg (= 0.032 kg/NA)
[T] = K 29
[F] = molecules/m2.sec
 For my simulations I will consider:
Assuming a flat surface: rPt = 1.387 Ǻ = 1.387 x 10-8 cm2

...
DPt = 2.774 x 10-8 cm2
W = 64 x DPt = 1.775 x 10-6 cm2
... ...
Area = W2 = 3.151 x 10-12 cm2
In a lattice with 64x64 Pt atoms we have
64x64 unit cells (due to the periodic
...

boundary conditions)
W
There are 3 bridge, 2 hollow, and 1 top
sites per unit cell, therefore,
N° sites per unit cell = 6
64 x 64 Pt atoms
Total N° of sites = 6 x 64 x 64 = 24576

assuming that all sites have the same area

24576 sites have an area of 3.151 x 10-12 cm2
1 site 1.282 x 10-16 cm2

Asite = Area of 1 adsorption site = 1.28 x 10-16 cm2 = 1.28 x 10-20 m2 30

 P= 0.001 Pa

T A=
S01.28E-20m2

PEa
F=+
ν =A
86.3801091 2.97E-01
FS e KT
site 0 2πMkT
values used in Carlos’ input

92.3057527 2.95E-01
T range (K)
100 - 108
ν O2ads

4.80 E+03
( s-1 )

96.4545828 2.85E-01
108 - 111
111 - 120
120 - 135
5.72 E+02
2.46 E+02
7.88 E+01

98.3604058 2.71E-01
135 - 148
148 - 154
154 - 162
1.94 E+01
7.42 E+00
2.47 E+00

100.272093 2.55E-01
162 - 170 1.18 E+00
A. Winkler et al., 31
Surface Science 201
(1988), 419 - 443
 Ea
+
Prefactor for O2 ads calculated using ν = A site FS0e KT

Prefactor used in Carlos at each T range

6.00E+03 3.00E+02

5.00E+03

Prefactor (O2 ads)

Prefactor (O2 ads)

4.00E+03 2.00E+02

3.00E+03

2.00E+03 1.00E+02

1.00E+03

0.00E+00 0.00E+00
100 105 110 115 120 120 130 140 150 160 170
T T

32
 0.2
Heating rate = 2K/s
0.18 O2_des
P=10-3 Pa
Reactions/unit cell/sec

0.16 O2_ads
O2_diss
0.14
O_diff
0.12
0.1
0.08
0.06
Results with the previous
0.04
0.02
approximation
0
100 120 140 160
T (K)

1
0.9 O2
0.8
O
0.7
Concentration
0.6
0.5
0.4
0.3
0.2
0.1
0
100 120 140 160
T (K)

33
 Using Discrete Steps
(DS)...
and the following fitting for S0(T) given by Winkler et al...

0.16
0 .16
ReactRate
W [O 2ads ]given by
S 0 = 1.7526 − 1.49 x10 −2 T
0.14
0 .14 Carlos
m athem atic al fitting
0.12
0 .12 W[O
W [O2ads]
2ads ] (1/s ec )
100 K < T < 111 K
(1/s)
O2_ads(1/s)

mathematical fitting
using S0 Exp.
0.1
0.1
RateO2_ads

0 .08
0.08
0 .06
0.06
0 .04 −2  100 
Rate

0.04 S 0 = 3.12 x10 exp 

0 .02
0.02  T 
0
0 T > 111K
100 150 2 00 25 0 30 0
100 150 200 250 300 34

T (K)
Using DS I gave Carlos the functional form
of the rate for O2 ads as S0FAsite
Heating rate = 2K/s
P = 10-3 Pa

0.5
1
0.9 O
0.8
O2
0.7

O2_des

Concentration
0.6
0.5
/unit cell/sec

O2_ads
0.4

0.4 0.3
0.2

O2_diss
0.1
0
0.2 100 120 140 160 180 200

O_diff
1
0.18 O2_des
0.9 O2 T (K)
Reactions/unit cell/sec

0.16 O2_ads
O2_diss 0.8 O
0.14

0.3
O_diff 0.7

Concentration
0.12 0.6
0.1 0.5
0.08 0.4
0.06 0.3
0.04 0.2
0.02 0.1
0 0
100 120 140 160 100 120 140 160
T (K) T (K) 35
Voltammetric scans

O2 electroreduction on Pt
(111)

36
 Proposed Mechanism
I O2(gas) + e- + H+ + b ↔ HO2(ads_b)
II HO2(ads_b) + 2h + e- + H+ → 2OH(ads_h) + b
III O2(gas) + b + e- ↔ O2-(ads_b)
IV O2-(ads_b) + 2h → O-(ads_h) + O(ads_h) + b
V O(ads_hhcp ) + hfcc → hhcp + O(ads_hfcc )
VI O- (ads_h) + H+ → OH (ads_h)
VII O (ads_h) + e- + H+ → OH (ads_h)
VIII OH (ads_h) + t → h + OH (ads_t)
IX OH (ads_t) + H+ + e- → H2O(ads_t)
X OH(ads_h) + H+ + e- → H2O(liq) + h
XI H2O(ads_t) → H2O (liq) + t 37
 Lateral Interactions

HO2 st H 2O
1 neighbors repulsions
O2 -

Model 1 Model 2
Up to 3rd neighbors repulsions for O 38

Model 3
 Results
Model 1 Model 2

1 1
O2-
tion

tion
0.8 0.8
OH
39
 Voltammetric Scans
In the presence of an overpotential V (defined as the
difference between the actual and the equilibrium
potential), the rate of a reaction ri is given by:
V is taken with respect to

ri = ν exp −
0
(
 Eai + αe0V )  the standard reversible
potential for O2
i
K BT  reduction, 1.23 V, on the
 
hydrogen scale.
e0 = charge of an electron Eai = activation energy at V=0
V = overpotential ν i0 = pre-exponential factor
α = transfer coefficient α = 0.5 if the reaction consumes
electrons α = –0.5 if it produces e-

Current = Σ (e- production rate) – Σ (e- consumption rate)

The overpotential was decreased linearly from 0 until -1.12 V with 40

a rate of 50 mV/sec starting from a clean Pt(111) surface.

 Tafel plot

1.1
-1
Model V≠0 Tafel Slope 1
0
(V) (mA/cm2)
1 -0.36 53 ± 18

HE)
2 -0.39 34 ± 12
3 -0.39 41 ± 15 41
 Acknowledments
 Dr. Perla Balbuena
 Molecular modeling group:
– Dr. Wang
– Dr. Martinez-limia
– Yingchun Zhang
– Sergio Calvo
– Zhihui Gu
– Francisco Tarazona Vasquez
– Eduardo Lamas
– Tyler Watt
– Kyle Corbin
– Charlotte Cooper

– Diego Altomare

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