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12

I know it is easy to get the PES tabulated very neatly in MOLPRO with a command like: {table,r,scf,ccsd,ccsd_t head, R,HF-SCF,CCSD,CCSD(T) sort,1,2,3} which for a diatomic molecule like yours, gives the following output: R HF-SCF CCSD CCSD(T) 1.5 -108.3566620 -108.6007993 -108.6060512 1.6 -108.6053845 -108.8602358 -108.8662569 1.7 -...


10

Note: This was a response I've originally written on Chemistry Stack Exchange, so it was intended to be very brief. Natural Bond Orbital Theory is basically (among plenty of other uses) providing an orbital localisation scheme to achieve similarity to Lewis structures. In some of my answers you have probably read the term 'Lewis-like' structures for these ...


8

Firstly, a minor correction: a non-linear molecule has 3N-6 normal modes, not 3N-5 modes. Linear molecules have 3N-5 normal modes. GAMESS automatically prints out some values in normal coordinate analysis section with the labels TRANS. SAYVETZ and ROT. SAYVETZ. If the total value of ROT SAYVETZ is high, that mode can be identified as a rotation. You will ...


8

Things are more clear to me when I look at the basis set in CFOUR format, because of the information at the top which tells me how many primitives and how many contractions there are for each type of orbital: O:MIDI Huzinaga MIDI 2 0 1 3 2 6 3 281.86658 42.416000 9.0956200 11.46603 0.887860 0.278800 0.069060 0.000000 0.00000000 0.393159 0.000000 0....


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

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

It's not the simplest alternative, but sometimes to learn a bit of regular expressions and one scripting language can help a lot in tasks like this. It's a really worth time investment, if you have a little time to spare. For example, I ran your input in my machine, saving the results to PES_scan_oxygen.log, and in Python 3 wrote a script to read this log ...


8

LocVib (part of MoViPac) I have never used VEDA before, but according to the paper, it decomposes the normal modes into vibrations of atomic groups, bond stretching, bending or something else. Something similar is LocVib, which localizes normal modes to localized vibrational modes by maximizing the "distances" between vibrational modes and "...


8

General vs segmented contraction Unless one is using a fully decontracted a.k.a "primitive" basis set, one uses contracted Gaussian-type orbitals (cGTOs), which are given as a linear combination of the primitive Gaussian-type orbitals (pGTOs): $\chi_i^\text{cGTO}({\bf r}) = \sum_{\alpha} d_{\alpha i} \chi_\alpha^\text{pGTO}({\bf r}) $. ...


8

Integral Screening It is possible to place upper bounds on integrals based on the Cauchy-Schwartz inequality: $$ \left( a a | b b \right) \ge \left( a c | b d \right) $$ If the first integral is computed and deemed insignificant, the latter is as well. One can further combine this with the appropriate density matrix element and decide that the resulting ...


7

In short, natural atomic orbitals are the orbitals you get from diagonalizing the one-particle reduced density matrix. One can then localize this set of orbitals via some maximization criteria. Natural bond orbitals are the orbitals you get when maximizing the occupancy of orbitals such that electrons occupy the space between two atoms or on a single atom. ...


6

I cannot see your output file, but I am pretty sure that the program is running into an error when starting the optimization i.e. when it is trying to generate the guess hessian. You are using Cartesian coordinates for optimization, and GAMESS by default will attempt to eliminate the rotational and translational modes from the guess hessian, before the ...


6

MOLPRO Continuing Susi's excellent benchmarking for $\ce{Zn}$ and $\ce{Zn_2}$, MOLPRO 2012 gives for $\ce{Zn}$: RHF-SCF energy: -1777.84665521 CPU time for INT: 0.42 SEC CPU time for RHF: 0.01 SEC Disk used for INT: 12.87 MB However the RHF energy was converged already at iteration 1, so there wasn't much work to do: ITERATION DDIFF ...


5

This is not a full answer, because it does not solve the problem. But I hope to shed some light on why you are not getting the correct frequencies. Short answer: I suspect there is a bug in GAMESS Long answer: First of all I would advise you to go through the manual of GAMESS. There are lots of problems in the input file, and most of them can be easily ...


5

I can see two major problems: CCD != CC2 and I'm not certain if CC2 is available in GAMESS. CC2 is an approximation of CCSD, which is available in GAMESS. You may be able to use this since $\ce{NH3}$ is a fairly small molecule, though I don't know how time consuming this will be relative to your initial CCD calculation. TZV != TZVPP. The def2-TZVPP basis ...


5

I was able to figure out what was going wrong, but forgot to check back here and leave an answer if none were give. @ShoubhikRMaiti should be credited with helping me figure this out. From this comment Also, may I ask why you are using fully numeric differentiation? U-BLYP has analytic hessian programmed into the code. I was curious to try removing this from ...


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 ...


5

I would say the reason that they default to storing the integrals is because there is no obvious choice to make one way or the other as it depends a lot on what resources are available and how large of a calculation you are doing. I have encountered this same situation while using Molpro before. In fact, every electronic structure package I'm aware of has an ...


5

Based on your input file, I tried to run the calculation in my machine. As you didn't specified how did you obtain the original structure (assembled by hand or downloaded from structure database), I first generated a SDF file of your structure with Avogadro, and did a conformer search with obconformer from Open Babel, just to be sure to pick a initial ...


5

If you look at your last five iterations, you will see that the density change (which is what matters most for SCF convergence) is getting smaller in each iteration, meaning that the calculation is still converging, and will converge if you give it more iterations: Iteration SCF Energy Energy change Density Change 26 -2246.3335762326 0.0000000384 0....


5

PySCF and Psi4 both implement analytical geometric Hessians for Hartree-Fock calculations. The computation of the geometric Hessian indeed requires solving the coupled perturbed Hartree-Fock equations: while one can evaluate the force acting on the nuclei just with the SCF wave function and the integral derivatives, the second derivative also contains a ...


3

As specified in the GAMESS Documentation: nspace=n means the active space will be split into $n$ groups. mstart sets the starting orbital for each of the $n$ groups. In your case, the first group extends from orbital 3 to orbital 9, while the second is from orbital 10 to NCORE+NACT (the number of core and active space orbitals). They mention that in this ...


3

Very interesting question. I have no experience doing EDA, but as I'll probably need to do it in the future, I used your question as a starting point to learn more about it. I did some research, but unfortunately could not find clear guidance on how to set the charges. In the Gamess (US) user group, a user called Marcela Tormena posted a small but detailed ...


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