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The simplest correct answer is that DFT is in $O(N_e^3)$. This comes from the idea that you are ultimately diagonalizing a Hamiltonian with dimension proportional to the number of elections and diagonalization is technically $O(n^3)$. In reality, DFT is a bunch of steps and different steps are rate-limiting in different context. If we restrict ourselves ...


6

Any numerical differences between A and B will become exponentially larger with time (i.e. the Lyapunov instability, as discussed in Frenkel and Smit). Even a small difference due to basis set size could result in dramatic differences in the trajectory over time. So I'm not sure that a comparison between individual trajectories will be meaningful. It may be ...


6

To specifically answer the question: The main shortcoming of Density Functional Theory is that even though it is a formally exact reformulation of quantum theory, in the current state of the theory, approximations are required for the Exchange-Correlation energy functional. All the Density-Functional approximations that we have so far fail to exactly ...


3

NWChem's built-in B3LYP is supposed to agree with Gaussian's, modulo the grid and tolerance issues noted in Thom's answer. You can prescribe any functional form for which the constituents are supported using the explicit XC interface: http://www.nwchem-sw.org/index.php/Density_Functional_Theory_for_Molecules#XC_and_DECOMP_--_Exchange-Correlation_Potentials. ...


2

First thought is to use A and B on standard validation test cases. I'm not sure what's available for validation on MD (googling "molecular dynamics validation" turned up a lot), but in CFD there's plenty of databases. If you need to validate something very specific (it sounds like you are), then you'll need to compile some statistics to convince me that A ...


2

There is no universal answer to this. You will have to find publications that have similar set-ups and already did the benchmarking, or you will have to do it yourself. Once you understand how the methods work, and any quantum/ computational chemistry book is sufficient for that, you have a very general understanding of what might go wrong. It is also very ...


2

Quantum Chemistry codes can get very complicated very fast. Even if you limit yourself to DFT, there are many functionals to support. There's going to be a trade off here for you. You can get a simple, smaller code base, but you'll end up with very few features. Or you can go with a larger, more mature code base, but it will be more complicated for you to ...


2

I don't fully understand where the problem is. Where the bonds are supposed to be, S-Se bonds? Like this, those distances don't seem much longer than Cd-S. In any case, you should not be troubled by the "sticks" connecting atoms in the visual representation: there are thresholds telling the program when to show them, and when not to show them. Actually, in ...


2

In the standard form, KS-DFT is solved variationally, which means that additional degrees of freedom in the basis set must lead to a lower (or equal) energy. This is a very basic property of the variational method and the math is almost certainly explained on Wikipedia or equivalent. I am assuming the same functional is used. Each DFT functional provides ...


1

In planewave calculations, we use a regularly spaced grid that fills the entire unit cell to perform calculations. The number of planewaves is proportional to the number of grid points used (as well as other system dependent parameters). Thus, when you add vacuum to your unit cell, you increase the number of planewave basis functions. With this in mind, you ...


1

Not aware of any CPU benchmarks for DFT. This might be due to different programs being built to take advantage of different architectures etc. If you are truly looking for pure computational power and do not intend to use the computer in any other way (gaming, movies etc.) then it might be worthwhile to look into buying a server computer. A quick search in ...


1

after a short (say 10 ps) equilibration period You say yourself that the re-equilibration period is 'short'. Have you tried waiting longer to see if the two re-initialized systems converge, and if so at what rate? Velocity-rescaling is a notoriously naive thermostat. Maybe you could replace it with something more realistic? (Berendsen, Nose-Hoover, etc.) If ...


1

I think that the problem encountered in this question is not specificly for DFT. But more in general for QM methods. You say that $E(r\rightarrow \infty) \neq0$. Now let us consider the molecular Hamiltonian: $$\hat{H}=\hat{T}_N+\hat{T}_e+\hat{U}_{NN}+\hat{U}_{Ne}+\hat{U}_{ee}$$ Here: The kinetic energy of the nucleis: $$\hat{T}_N=-\sum_i\frac{\hbar^2}{...


1

I assume you are asking about the total energy which is printed as the final result of your DFT calculation. This energy represents the kinetic energy of all your particles (atoms and electrons) and their coulomb interaction. It does not have much physical meaning by itself. Usually, the more particles and the larger your basis set, the smaller (more ...


1

To answer your question, the most popular right now is phonopy. If you are having a technical problem you can post it on GitHub, usage issues are better suited for the mailing list. My opinion is that, if possible, using phonopy and getting it working would probably be best for the community if it is a technical problem in the code or best for you if it's ...


1

Problem can be fixed by adding this around line 395 in the config.py file, inside the build_interpreter function: define_macros.append(('_GNU_SOURCE', '1')) where the other define_macros.append commands reside.


1

Most of your answers look good. For the geometry optimization of single-reference organic systems, B3LYP/big should be fine. MPn is bad for open-shell systems in general. MCSCF is the way to go if one has truly pathological multireference effects. CCSD(T)/huge is good any time you want to treat dispersion, but you'll find in the literature that (He)2 ...


1

Density functional theory optimizes the total energy with respect to the (possibly constrained) electronic density. The usual numerical procedure for this optimization is embodied by the KS method. The KS procedure will give you the optimal total energy and the ground-state (gs) density for which this optimal energy is achieved. This optimization procedure ...


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