# Tag Info

14

I wrote the following simple Python function that allows one to use any distribution from scipy.stats for peak broadening (the scale parameter determines how broad peaks will be): import numpy as np from scipy.stats import cauchy, norm def broaden_spectrum(x, x0, y0, distribution="gaussian", scale=1.0, fit_points=True, *args, **kwargs)...

13

Incidentally, I initiated some discussions along these lines in these questions for HF-DFT (also called 'density-corrected' DFT) here, and here. I'm familiar with Quantum ESPRESSO, so I can detail a procedure with QE. If you want to generate a Hartree-Fock density, you can just turn on a hybrid functional (say HSE06) and turn up the fraction of exact ...

13

VMD Normal Mode Wizard If you're goal is to create high quality visualizations of vibrations I recommend VMD. It's highly customizable in terms of colors, resolution, and representation. The setup however, is a little bit painful as the normal mode (NMD) input file has to be specially prepared in atomic units and has a special format (see below). The ...

12

I think the way this question is asked is a little too simplistic. In order to execute a computational project, there is always more than one calculation required. Even if you are happy with the lowest level of theory (say, B3LYP/6-31G*), it does not mean that any package that lists B3LYP in the list of the available features would be useful. Possible ...

11

Many thanks to Felipe, the code is very useful! I know this is just a simple editing, but this is how I adjusted part of the code for Raman spectra: import cclib data = cclib.ccopen("molecule.out").parse() x = np.linspace(data.vibfreqs.min() - 100., data.vibfreqs.max() + 100., num=1000) y = broaden_spectrum(x, data.vibfreqs, data.vibramans, ...

11

Multi-reference or single-reference? While it is appreciated that near dissociation there will be a near-degeneracy of orbitals, requiring a multi-reference treatment, fortunately we don't have to worry about this when calculating dissociation energies. For example, the N$_2%$ molecule has profound multi-reference character as you approach the dissociation ...

9

While I am not completely familiar with all the details in Q-Chem's SCFs, I am aware that there are in fact multiple SCF implementations and multiple implementations for computing two-electron integrals in Q-Chem. I could therefore imagine that -nt and -np triggers different code branches (for all cases but 1 thread, where the same is used). This explains ...

9

Jmol The Jmol package is able to do what you want. You can produce the animations below just using point & click with your mouse. But you can also use its scripting capabilities to work with batch files, and make the process all automatic. As it is coded in Java, you can used in any operative system. Here are some examples. Below the results for $CH_4$ ($... 8 Supplementing Nike's answer above.. This is actually quite elementary math. Let's say I have an orbital in a basis$|\psi\rangle = \sum_i c_i |i\rangle$and I want to find the expansion in some other basis set$|J\rangle$. How do I do this? In the new basis set, one has the resolution of the identity$\sum_{JK} |J\rangle \langle J|K\rangle^{-1} \langle K|\...

8

BDEs are calculated by the below procedure: Calculate initial energy Perform homolytic bond cleavage and separate fragments Calculate energies of the fragments, add the energies together Calculate BDE by comparing the fragment energies to the initial energy The level of theory and basis set is dependent on how accurate you want the results to be. B3LYP ...

8

What you're describing is very common, and is not limited to GAMESS and Q-Chem. First, here's how to do it in MOLPRO, MRCC, GAMESS, Q-Chem (in fact the only electronic structure software that I regularly use which doesn't allow this type of projection into a bigger basis set, is CFOUR): 1) MOLPRO: basis=cc-pVDZ hf basis=cc-pVQZ hf The HF ...

8

Yes, this is correct explanation. There are three SCF codes and two integral libraries and which ones are executed depends on the job parameters (single core, multicore, multi-node). If accurate scaling benchmarks are desired, I would use execution with 2 threads as the base. One should also pay attention to the current defaults re: integral and scf engines -...

8

One can also pose the opposite question, which may be more interesting: what significant matter modelling methods are implemented in open source software, for which there is no commercial alternative? Anna's answer above had a lot of important considerations, but also this reverse question is important to keep in mind; commercial software is not always free ...

7

Explicit solvent can be of importance, like you mention, whenever strong coordination or hydrogen bonding is involved. For example, transition metals often coordinate to solvent and not including them in the calculation would give very poor results. Similarly hydrogen bonding can affect the electrostatics and result in poor properties like reaction paths, ...

7

iMos iMos is Ion Mobility Software based on MATLAB parallelized code that can model Collisional Cross-Section. Tool is available for macOS, Linux and Windows and developed by Carlos Larriba-Andaluz. Installer, code comments and tutorials can be found here.

7

Generally you want to use the same settings when trying to combine results from different jobs. However, below is the general procedure that I have seen performed for a basic, publishable PES. 1) Perform geometry optimization 2) Perform solvent/frequency calculations 3) Combine solvent energy and enthalpy (from frequency calculation "Total Enthalp...") 4)...

6

One thing the other answers haven't mentioned is the zero point and thermal corrections to the BDE. As mentioned in the Wikipedia Morse potential article, a geometry optimization will take you, by definition to the equilibrium bond length ($r_e$). If you use this as the low energy state, you're calculating $D_e$. The problem is that a quantum harmonic ...

6

I think the easiest way to parse multiple-job files from Q-Chem is if you just manually split the output file into the parts that pertain to the individual jobs. Just locate where the first job ends and the second one starts and save the output in individual files. If you have lots of those jobs to split, then I am sure this could be done with the head and ...

5

Note: I have corrected some omissions from my initial answer to avoid any confusion. For a rigorous explanation of the process, I would recommend looking at Susi's answer. The projection process for MOs is actually fairly straightforward. In the following, let $m$ be the dimension of the new basis, $n$ the dimension of the old. Even though getting a guess ...

4

So this question is related to the recent discussion in Procedure to classify errors in Kohn-Sham DFT where I already gave the general procedure: get the density from some level of theory, and use it to run a single-point DFT calculation. This question was about how to do this in Q-Chem; it's actually quite simple. Here's an example input for a calculation ...

4

I do not think the server setup is the problem per se. By default, IQmol is setup to submit jobs to a server that is owned by Q-Chem and those jobs are time-limited at 5-10 min. (The precise limit has varied over time.) The job failed to finish error reflects this limit. That said, I am a bit surprised that $\ce{H2}$ frequencies failed to finish. Is it ...

4

I am not at all surprised that using 16 cores on one node with OpenMP is faster than using 16 cores spread across 4 different computers (nodes). The 16 cores on a single node are usually part of the same "chip" and are definitely attached to the same motherboard. The 16 cores spread across 4 computers will not be able to communicate with each other nearly as ...

3

The Q-Chem manual edition 5.2 is much better at describing QM/MM However, to answer your main question there are no angles and torsions across a link atom. The link atom is a fictitious hydrogen that is added when you break the QM and MM region at a bond. This is done to maintain the proper valency/avoid dangling bonds in the QM region. The MM region is ...

2

I really don't know the output structure of Q-Chem, but in SIESTA, we have the following information: siesta: Final energy (eV): siesta: Band Struct. = -6333.862502 siesta: Kinetic = 15927.632813 siesta: Hartree = 72644.682988 siesta: Eldau = 0.000000 siesta: Eso = 0.000000 siesta: Ext. field = 0....

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