Questions tagged [monte-carlo]

For questions related to Monte Carlo methods, which solve deterministic numerical problems via a probabilistic sampling approach.

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Layer detection in a crystal structure

The situation here, I have two images from a Monte-Carlo Basin hopping where Silicone (in yellow) is getting replaced by Germanium (in blue). Both have 32 Germanium atoms at Si/Ge = 2.5; only the Ge ...
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4 votes
2 answers
489 views

Python script for Metropolis Monte Carlo (global optimisation)

I have written a python script to do global optimisation on interatomic potential (IP) using Metropolis Monte Carlo. I have attached the part of the script which is the Metropolis MC part. I have ...
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2 votes
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how to incorporate size polydispersity in colloidal suspensions

Basically, I'm working on spherical colloids and investigating the phase behavior of these monodisperse colloids using Monte Carlo simulations (Fortran 77 coding). Now I want to introduce size ...
5 votes
1 answer
41 views

Generalization of always accepting box upscaling moves in Monte Carlo for a triclinic box

When you are using Monte Carlo scheme to simulate equilibrium phases of convex hard-core molecules, namely, whose energy is infinite when in contact and 0 otherwise in a standard, cubic simulation box,...
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1 vote
1 answer
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How do I initialize the lattice/grid in a Potts Model?

I am studying the Cellular Potts Model Tutorial. However, this doesn't say anything about the grid/lattice initialization. How do I initialize the lattice/grid in a Potts Model? I.e., how do I assign ...
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3 votes
1 answer
25 views

How do I calculate the acceptance criterion for configuration bias sampling of my polymer?

I am running a lattice simulation of a single chain polymer on a lattice with every other site occupied by solvent. The additional wrinkle is that every particle on the lattice has a number/spin ...
  • 4,091
6 votes
0 answers
41 views

How to rigorously prove the existence of a coil-globule transition of polymers in an on-lattice simulation? [closed]

I am running on-lattice simulations of polymers. I am testing out different Hamiltonians and testing different regimes to test if they yield interesting behavior. My question is, how do I rigorously ...
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3 votes
0 answers
74 views

What are the similarities between MD and MC in the case of protein simulation? [closed]

As far as I understand, both MD and MC simulation methods use Force Fields. Are there any other similarities between them?
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4 votes
0 answers
154 views

Regarding use of GCMC to add water molecules

I am working on a goethite system, and wish to fill the unit cell with water molecules for AIMD simulation using quantum espresso. For this, some papers[1],[2] indicated the use of Grand Canonical ...
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2 votes
1 answer
267 views

Why do we even need periodic boundary conditions?

According to Wikipedia - Periodic boundary conditions (PBCs) are a set of boundary conditions that are often chosen for approximating a large (infinite) system by using a small part called a unit ...
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3 votes
0 answers
125 views

Molecular MC simulation is not equilibrating [closed]

Suppose, a polymer has N monomers in its chain. I want to simulate its movement using the bead-spring model. So, I wrote the following program in Python. Polymer chain simulation with Monte Carlo ...
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3 votes
1 answer
57 views

What formula should I use to calculate the total energy of a linear polymer chain?

I am using the Bead-spring model to model a polymer chain. Suppose, the polymer has 3 monomers in its chain: $$\ce{A1-A2-A3}$$ And, I can use the following formula to calculate the total Lennard-Jones ...
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4 votes
0 answers
58 views

Where should I apply the harmonic spring function in the case of polymer simulation? [closed]

I need to simulate the off-lattice movement of a polymer chain in a 3D space using Monte Carlo simulation. Note this is not a simulation of polymer growth; rather this is about polymer movement/motion....
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3 votes
1 answer
56 views

How should I calculate total potential in a polymer chain?

Suppose, a polymer has 3 monomers in its chain: $$\ce{A1-A2-A3}$$ When calculating total LJ potential, do I need to calculate like this: $$E(r_{12})+E(r_{23})+E(r_{31})$$ Or, do I calculate: $$E(r_{12}...
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4 votes
0 answers
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What does it mean by pruning and enrichment in the case of Rosenbluth method? [closed]

As far as I understand: Pruning means deleting something. Enrich means to enhance/increase weight. Now my question is, in the case of pruned-enriched Rosenbluth method (PERM): For pruning/enriching, ...
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1 vote
0 answers
39 views

Polymer simulation [closed]

I am absolutely new to Polymer simulation. I am trying to understand the simulation by analyzing source code written by others. Can anyone tell me what are the differences between the following three ...
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4 votes
0 answers
38 views

How to construct spinodal and binodal curves from a molecular simulation?

Pretty much what the title states: what is a procedure to construct a binodal and spinodal curve (temperature against composition)? I am running an on-lattice polymer solution Monte Carlo simulation ...
  • 4,091
6 votes
1 answer
70 views

End-to-end correlation of polymers not decorrelating

I am running Monte Carlo simulations of polymers with nearest neighbor interactions only. For benchmarking purposes, I decided to run some excluded volume simulations (no overlaps) allowed on a 3D ...
  • 4,091
9 votes
1 answer
117 views

Some questions about implementing Swendsen-Wang algorithm

I have a lattice system with two types of sites, namely A and B. Both A and B have a possible up or down spin orientation. There exists $J_\textrm{aa,align}/J_\textrm{aa,mis}$, $J_\textrm{bb,align}/...
  • 4,091
12 votes
1 answer
124 views

Benchmarking Monte Carlo simulations of polymers

I have written a simulation engine in C++ to run a Monte Carlo simulation of polymers on a lattice. My code basically plants a polymer on a lattice, and performs certain Monte Carlo moves, including ...
  • 4,091
8 votes
1 answer
90 views

How often does one have to run polymer Monte Carlo moves to effectively sample phase space?

I have a polymer and solvent on a lattice, and I am performing an NVT Monte Carlo simulation. I am performing the following moves on it: My question is, how should these moves be conducted to ...
  • 4,091
14 votes
2 answers
541 views

How do you incorporate hydrogen bonding into molecular simulations?

How do computer simulations of liquid hydrogen-bonding systems incorporate hydrogen bonding? Since I think hydrogen bonding has mixed covalent and electrostatic character, wouldn't you need something ...
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4 votes
1 answer
58 views

Discrete lattice polymer simulations

I am trying to develop phase coexistence curves for generic polymers. Of course, I can use standard Flory theory free energy functionals to do this, but I want to define my nearest neighbor polymer-...
  • 4,091
4 votes
1 answer
87 views

Simulating polymers using cellular automata?

I am a physics student, and I am working on my final year project, I am planning to simulate polymers using cellular automata. I am really struggling with this project, if someone can give me any ...
12 votes
1 answer
185 views

Metropolis algorithm reduces energy in molecular simulation, but does not decrease euclidean distance

I am using an open source python package openmmtools to run a simple molecular simulation problem using the metropolis algorithm. I first load a default system of particles (alanine-dipeptide in ...
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11 votes
2 answers
236 views

Starting configuration for a molecular simulation

When doing a computer simulation, what’s the best way to prepare a starting configuration to avoid biasing your results? The book Computer Simulation of Liquids suggests putting the molecules on an ...
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9 votes
1 answer
523 views

Why is specific heat not zero at absolute zero?

In this old paper on Monte Carlo simulations of Lennard-Jones solid, specific heat behaviour (both $c_p$ and $c_v$) have been reported. As you can see from the picture below, both $c_p$ and $c_v$ goes ...
16 votes
3 answers
2k views

Is there a more efficient hard sphere packing algorithm?

I am trying to pack hard-spheres in a unit cubical box, such that these spheres cannot overlap on each other. This is being done in Python. I am given some packing fraction ...
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12 votes
1 answer
460 views

Are there examples of ab initio predictions on small molecules without the "major approximations"?

In most textbooks the precise Schrödinger euqation of a molecule is given (and the "beautiful thing" stops here), then born oppenheimer approximation is made, then layers of other ...
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15 votes
2 answers
4k views

Classical Monte Carlo vs. Molecular Dynamics

Both Classical Monte Carlo (MC) and Classical Molecular Dynamics (MD) simulations are used to perform simulations of ensembles of molecules. These MC calculations are calculating thermodynamic ...
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11 votes
1 answer
344 views

How does one compute the boiling point of a liquid made of a particular molecule?

This question is in relation to Anomalous boiling point of "iso-" alkanes on Chemistry SE. I want to compute the boiling point of the different isomers of an n-carbon alkane to check what ...
9 votes
0 answers
102 views

Coupling between 1st and 2nd order phase transitions? [closed]

I am seeking some models or references on how to couple, or what to take into consideration, while coupling first-order phase transitions (for magnetic systems) and second-order phase transitions, in ...
15 votes
0 answers
227 views

Why does the Wolff algorithm slow down in a 4-body Ising model?

In the paper that introduced "Self-learning MC" (an ML-inspired MC technique, as I understand) the authors consider a many-body Ising model as an example to show the efficiency of their ...
13 votes
3 answers
388 views

What are the types of Quantum Monte Carlo?

Similar to: What are the types of SCF? What are the types of MCSCF? What are the types of ab initio Molecular Dynamics? What are the types of pseudopotentials? What are the types of DFT? What are the ...
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20 votes
1 answer
138 views

How can very small lattices be sufficient for Quantum Monte Carlo simulations?

Quantum Monte Carlo simulations are often performed with very modest lattice sizes (such as [e-print], $64$ sites), due to their computational cost increasing exponentially with the system volume; ...
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12 votes
2 answers
701 views

Autocorrelation function problem in Monte Carlo simulation of 2D Ising model

Currently, I did a Monte Carlo simulation with the local update and Wolff cluster updated in 2D classical Ising model. I use the autocorrelation function to compare 2 different algorithm in critical ...
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12 votes
2 answers
92 views

In Monte Carlo: does nonequilibrium imply stationary state?

I'm currently responding to referees about a manuscript on the dynamics of the Ising model. I have been using the term nonequilibrium to refer to any state that is not characteristic of the ...
17 votes
2 answers
174 views

How to simulate atomic scattering from solid walls at finite temperature for a particles in a box simulation?

I'm not sure if this will be considered on-topic, let's see what happens. I've asked this previously in Physics SE and it was closed as needing focus. It is now past 30 days and too late to consider ...
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15 votes
1 answer
104 views

What are the modelling techniques that can be used for simulating microstructure evolution in materials?

I am aware that the Potts Model can be used to simulate grain growth, and that Phase Field Models have also been very successful. What are the advantages and limitations of these models? What are the ...
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15 votes
1 answer
265 views

What is the definition of ergodicity in Monte Carlo?

I've been writing a manuscript about the breakdown of ergodicity in single spin flip Metropolis algorithm Monte Carlo arXiv:2001.09268. The definition I have been using is: a Markov process is ...