24
votes
Accepted
Do we know for sure that all atomic and molecular wavefunctions decay exponentially as r goes to infinity?
I'll answer this question from the theoretical side. The exponential behavior follows simply from the Schrödinger equation. Consider the one-electron Schrödinger equation:
$$
(-\frac{1}{2}\nabla^2 + V(...
- 9,076
8
votes
Accepted
Where can I find this formula?
The formulas that the code is using can be directly read off from the code. The code simulates a two-dimensional periodic box, and calculates the distance of each atom to each other atom, namely d. If ...
- 9,076
8
votes
Accepted
Clustering Algorithms with Periodic Boundary Conditions
First, there is a recent paper in which they proposed a k-means clustering algorithm adapted for periodic boundary conditions. Their Python implementation is available here.
However, the clustering ...
- 1,550
8
votes
Accepted
Python library to obtain atomic orbitals of atoms in the lowest energy state
Mendeleev
You can use a python library called Mendeleev. Below is an example of a Silicon atom.
...
- 2,885
6
votes
Copper FCC structure using ASE (Atomic Simulation Environment) library in python
First, I want to show a general way of checking the minimum bond length of a structure in ASE. Using your structure as an example, you can get the distance matrix in ASE by ...
- 1,550
6
votes
What are some ways to check if a molecular simulation is running properly?
It's a very broad question and there isn't really a clean answer that will apply for all cases but I'll just provide some general advice. I would start by re-creating a known result. Follow a tutorial ...
- 890
6
votes
Effect of System Configuration on MD simulation results
If you are running a particular algorithm, then different codes should in principle give the same results. However, often algorithms require random numbers that are generated with seeds within the ...
- 321
6
votes
Accepted
How might inclusion of a Grimme dispersion correction influence a simulation of a dense liquid that is not water?
Following Tyberius's suggestion, I now turn my comment into an answer.
As always, the most reliable way of estimating the effect of the dispersion correction is to actually do two simulations, one ...
- 9,076
5
votes
Are there any codes to study magnetic materials?
Another option is ALF (Algorithms for Lattice Fermions), an auxiliary-field quantum Monte Carlo package. According to its website:
it can simulate any Hamiltonian that can be written in terms of sums ...
- 796
5
votes
Are there any codes to study magnetic materials?
In addition to those listed, Spin-W is another option:
SpinW is a MATLAB library that can plot and numerically simulate magnetic structures and excitations of given spin Hamiltonian using classical ...
- 1,491
5
votes
Are there any codes to study magnetic materials?
If you already know the electron spatial wavefunctions, then it should be possible to calculate the spin exchange coefficients between electrons on neighboring atoms (by directly integrating them) and ...
- 6,579
5
votes
Accepted
Thermodynamics: System versus Ensemble
The textbook you refer to states (p21):
The time-averaged properties of the real system are related to the ensemble average by ... the ergodic hypothesis.
That is, taking N snapshots of one system ...
- 2,673
5
votes
Accepted
What are some symptoms that could tell me that my simulation is not running properly?
There are generic self-consistency checks (SCCs) that check if a simulation set has converged. The most basic of these is to use block analysis to examine the convergence of standard error in ...
- 2,673
4
votes
In which theoretical framework does the size of an atom depend on the temperature of the gas (Bose-Einstein condensates)
In calculations of the electronic energy/wavefunction, temperature typically is not taken in to account (besides cases of orbital occupation smearing, though this is used more as a computational trick ...
- 15.2k
4
votes
Accepted
What are the more efficient, or easier, methods of handling electromagnetic interactions?
You could simplify long range interaction by reducing precision with range. Useful algorithm for it is:
https://en.wikipedia.org/wiki/Barnes%E2%80%93Hut_simulation
It is usually used for gravity, but ...
4
votes
elastic constants transformation/basis change P21/a -> P21/n
In order to define the matrix transforming the P21/n structure into P21/a it is imperative to know the unique axis of both space groups.
For example the contracted P21/n symbol can be used for the ...
- 651
4
votes
How to calculate the exchange matrix of a bilayer magentic system?
But in order to do that I need the exchange matrix of Co-CoO system
which should include the constant which represents the interaction
between spins in the Co part, spins in the CoO part and a ...
- 4,448
4
votes
Accepted
What is the relationship between periodic boundary and the simulation box?
Some pseudo-code
...
- 4,306
4
votes
Accepted
Why do we even need periodic boundary conditions?
In (Metropolis) Monte Carlo one should be generating random changes in coordinates such that
\begin{equation}
X_{new} = X_{old} + \Delta X
\end{equation}
and we used a random number to generate $\...
- 4,306
4
votes
What formula should I use to calculate the total energy of a linear polymer chain?
The difference between total potential energy and total energy is just the kinetic energy, which is the sum of the kinetic energies of your particles, $$E_K = \frac{1}{2}\sum_{i=1}^3 m_i v_i^2$$
where ...
- 890
3
votes
Accepted
How should I calculate total potential in a polymer chain?
You'll want to add up all interactions that you can, up to some appropriately chosen cutoff distance. Choose the VDW cutoff such that the total energy doesn't change much if you further increase this ...
- 890
3
votes
When should I use Charge-Charge Interactions, Charge-Dipole Interactions, and Dipole-Dipole Interactions in molecular simulation?
Let's say you are trying to study the formation of hydration shells around ions or something like Antifreeze Glycoproteins (AFGPs). In such cases, it is important that you include charge-dipole and ...
- 2,742
3
votes
Accepted
Definition of the terms "modeling" and "simulation" in the context of biomolecules and/or proteins
You simply cannot go past Allen and Tildesley's Computer Simulation of Liquids as a standard textbook on molecular dynamics. Here is a particularly illuminating diagram:
As the diagram says: (italics ...
- 2,673
2
votes
Thermodynamics: System versus Ensemble
I like how this book starts by defining all the concepts to be used after:
THERMODYNAMICS AND INTRODUCTORY STATISTICAL MECHANICS. Bruno Linder. John Wiley & Sons, Inc., 2004.
He defines ...
2
votes
Accepted
What is the purpose of a kinetically resolved activation barrier in cluster-based kinetic Monte Carlo simulations?
For any reaction, the forward barrier height must be equal to the reverse barrier height plus free energy change (or minus, depending on signs). Violating this would break detailed balance.
However, ...
- 2,673
2
votes
Accepted
What is the minimum number of atoms required to run a Monte Carlo simulation meaningfully?
I used a Monte Carlo method called FCIQMC to calculate the ionization energy of the carbon atom with unprecedented precision. Therefore, MC methods can be used for a single isolated atom.
The answer ...
- 33.6k
2
votes
What is the minimum number of atoms required to run a Monte Carlo simulation meaningfully?
The literal answer to the question you asked is zero. That might not be the answer you were looking for, but then again, you're asking too general a question to get a meaningfully specific answer. ...
- 4,696
2
votes
How to Create a 2D Structure of Boron (Brophene) using ASE?
As you said, borophene has the same structure as graphene. Then you can first build a graphene structure in ASE, then change every atom to boron, and scale the lattice parameters to be that of a ...
- 1,550
2
votes
How to Create a 2D Structure of Boron (Brophene) using ASE?
You could define the formula for a graphene-like structure. For example, ase.build.graphene(formula='B2', a=2.46, thickness=0.0, size=(1, 1, 1), vacuum=None)
- 21
1
vote
Copper FCC structure using ASE (Atomic Simulation Environment) library in python
Since you perform DFT calculations under periodic boundary condition(PBC), you should check your structure carefully. The first two atoms (0, 0, 0) and ...
- 71
Only top scored, non community-wiki answers of a minimum length are eligible