25
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(...
- 9,981
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 ...
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8
votes
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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 ...
- 1,970
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.
...
- 3,145
8
votes
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Which properties can be directly obtained from Electron Charge Density (obtained from CHGCAR in VASP, etc.) and no other info?
I've never used VASP, but I'll answer this as best I can. There are essentially two parts to this:
What properties are computable from the charge density in principle
What properties are computable ...
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8
votes
How to get 192 of CeO2 atoms coordinates using Vesta?
The paper you link to identifies 4 Ce atoms and 8 O atoms per unit cell, which has the correct stoichiometry and seems a reasonable density for CeO2, so what is going wrong? The issue is that you have ...
- 8,257
8
votes
What's the temperature of the output electronic properties get from Quantum Espresso/VASP, even if we use 298 K cell info (atom position) as an input?
This is slightly difficult to answer, since temperature has several effects and in DFT these can be accounted for in different ways. Probably the main four direct effects are:
Thermal expansion (or ...
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7
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 ...
- 1,970
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 ...
- 950
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 ...
- 390
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 ...
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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 ...
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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 ...
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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 ...
- 6,794
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 ...
- 2,952
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 ...
- 2,952
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 ...
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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 ...
- 671
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 ...
- 4,526
4
votes
Accepted
What is the relationship between periodic boundary and the simulation box?
Some pseudo-code
...
- 4,406
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 $\...
- 4,406
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 ...
- 950
4
votes
Accepted
OpenMPI not running under SLURM in UBUNTU with ORCA?
In order for Orca to launch an 8-task MPI run, Slurm must assign 8 tasks. This is achieved by the --ntasks-per-node flag. So you need the following settings in your ...
- 1,401
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 ...
- 950
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 ...
- 4,036
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 ...
- 2,952
3
votes
Creating 1M NaCl solution using PACKMOL
You don't need it calculate it manually. If you use the latest packmol version, it already has a script for adding ions automatically. (solvate.tcl)
The default ...
- 63
3
votes
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, ...
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