Questions tagged [quantum-chemistry]
For questions about quantum chemistry.
62
questions
7
votes
1answer
81 views
Avogadro for Linux — Input Generators and Submitting Job to QM software?
Regarding input generators for a Linux (Linux Mint 20.1 Xfce) version of Avogadro2, I have managed to get this working using the Flatpak version and copying the input generator python scripts from ...
15
votes
3answers
2k views
What does “strongly correlated” mean?
For quantum many body problem, there is a common terminology “strong correlated systems” that appears in different context. However, it seems that the definition of it is ambiguous and sometimes ...
10
votes
3answers
147 views
CCSD and CISD size-consistency problem
I have performed a Gaussian16 calculation to explore the size-consistency problem for the CISD method. The system I am studying is the water dimer and the results are not what I expected at first. I ...
6
votes
1answer
39 views
Vibrational frequency analysis for NEB result through Maestro
I have ran a Nudged Elastic Band (NEB) calculation using QuantumEspresso through Maestro to find the potential transition state. Within Maestro there is an option where you can select for NEB type ...
7
votes
1answer
92 views
How is the error in a wavefunction related to the error in energy?
While studying the variational method in McQuarrie's Quantum Chemistry, I came across the following problem: to relate the difference between an approximation $\phi$ and the exact ground-state wave ...
30
votes
5answers
2k views
What is a good replacement for Gaussian?
When I started studying computational chemistry (circa 2007), my supervisor used to tell me about the controversy surrounding Gaussian, Inc. regarding the banning of researchers involved in the ...
10
votes
1answer
69 views
How to determine occupied and closed orbitals for a Molpro CASSCF calculation?
I am currently working with Molpro, to which I am completely new, trying to run some calculations on $\ce{PdO}$. From literature I have gathered that the ground state is given by $^3\Sigma^-$ state, ...
9
votes
1answer
209 views
How can I implement the Cartesian harmonics?
I'm studying the quantum chemistry calculation and now trying to implement the basic methods.
For example, given a water molecule,
$M = {(\ce{O}, R_\ce{O}), (\ce{H}, R_\ce{H}), (\ce{H}, R_\ce{H})}$,
...
7
votes
0answers
64 views
What are some examples where TD-DFT was successful and where it fell short in describing photophysical or photochemical processes?
Time-dependent Density Functional Theory has been around for quite a while now, seeing Density-Functional Theory for Time-Dependent Systems, and so it has been developed extensively, implemented in ...
10
votes
0answers
82 views
How does one project out the translations and rotations from a hessian?
I've recently written a simple code to numerically compute the hessian of some function (at a point). Most electronic structure packages will compute the hessian and then project out the translations ...
12
votes
2answers
64 views
What are some of the advantages and disadvantages when using shape consistent pseudopotentials as compared to energy consistent pseduopotentials
From the literature as well as the answer to the question What is the meaning of energy-consistent and shape-consistent in the context of pseudopotentials? I can see that the key difference between ...
13
votes
1answer
89 views
What is a good practical way to determine whether or not I need to use a multiconfigurational method?
I’m planning to run a calculation of single electron transfer where my system goes from singlet to triplet biradical (presumably). So I’m wondering how to decide if I need to use milticonfigurational ...
14
votes
1answer
99 views
Why are Norm-conserving Pseudopotentials considered so important?
So I am aware that a norm-conserving pseudopotential enforces the conditions that:
Inside the cut-off radius, the norm of each pseudo-wavefunction is identical to its corresponding all-electron ...
13
votes
1answer
181 views
Gaussian-type orbitals vs Slater-type orbitals in terms of computational efficiency
When creating molecular orbitals via the linear combination of atomic orbitals method I am told that Slater orbitals provide a more accurate representation whilst Gaussian orbitals are computationally ...
6
votes
1answer
94 views
What is the meaning of energy-consistent and shape-consistent in the context of pseudopotentials?
I am trying to use pseudopotentials to model scattering from heavy molecules.
However, I am confused by some of the terminologies of pseudopotentials/ECPs:
Norm-conserving according to Wikipedia and ...
6
votes
0answers
55 views
Two-stage unbinding & binding energies with DFT
I'm trying to calculate the stability of the product of a coordinate bonding process of molecules A and B in the polarizable continuum solvent model (PCM, solvent set to water).
I'm getting energies ...
8
votes
1answer
106 views
How to get the .47 file from ORCA for natural bonding orbital analysis
I am trying to perform NBO analysis with relaxed density matrix with the open-source program JANPA. I am following the guide here. The first step is to get the NBO input .47 file from Orca v4.2.1. The ...
12
votes
1answer
521 views
When do we abandon ab initio methods?
This question is related to (and was originally asked in) another post about "quantum protectorates" I made here.
Ab initio methods are nice because they directly solve a sort of "...
0
votes
1answer
277 views
Has there been any research on the stability of buckminsterfullerene?
C60 can refer to any substance composed of molecules with 60 carbon atoms. Buckminsterfullerene on the other hand is specifically the substance composed of soccer ball shape molecules with 60 carbon ...
6
votes
1answer
88 views
Is it possible to get complex numbers as solutions for a secular determinant in simple Hückel method (SHM)?
Past semester we revisited the Hückel molecular orbital theory at class. One day I was trying to solve some problems with SymPy, a Python module that is a computer algebra system (CAS), and noticed ...
8
votes
1answer
56 views
Error running psi4 on charged molecules
I am running a simple energy calculation on a conformer of 3-Sulfopropyl methacrylate, which is given my C=C(C)C(=O)OCCCS(=O)(=O)[O-].
This is my workflow:
...
16
votes
12answers
6k views
Is it better for me to study chemistry or physics?
I might decide to pursue material science.
Aptitude and background
I am from the UK, and for A-levels, I am studying Maths, Further Maths, Physics and Chemistry, and I am predicted decent grades in ...
12
votes
1answer
399 views
Are there examples of ab initio predictions on small molecules without the “major approximations”?
In most textbooks the precise Schrödinger euqation of a molecule is given (and the "beautiful thing" stops here), then born oppenheimer approximation is made, then layers of other ...
9
votes
1answer
103 views
Energy decomposition analysis (EDA) at transition state
I am trying to understand the interaction between the nucleophile and the substrate for some SN2 reactions (e.g. $\ce{I- +CH3Cl->CH3I + Cl-}$) at the transition states. Now, it seems that EDA would ...
10
votes
1answer
116 views
What are the trade-offs setting DIRSCF to either .TRUE. or .FALSE. (the default) in GAMESS (US)?
The first software I used to run calculations was Gaussian09. When submitting a input, I used to see a pattern of resource usage where the allocated CPU quickly maxed out, remaining high most of the ...
10
votes
1answer
67 views
How to understand the formation of covalent bond from the viewpoint of wavefunction interaction?
The formation of the covalent bond is usually understood from the electron sharing, like explained by the following figure:
However, this simple physical picture seemingly hinders many things. In ...
11
votes
3answers
1k views
What does “level of theory” mean?
I was reading this paper on the QM9 synthetic molecular database and their computed properties. It is stated that
All properties were calculated at the B3LYP/6-31G(2df,p) level of
quantum chemistry.
...
10
votes
1answer
265 views
Does One-to-One Correspondence of Hohenberg Kohn Theorem Mean Bijective or Injective and How to Prove it?
I have asked a similar question but after thinking about it I have a more specific question.
According to Ullrich, Carsten A.. Time-Dependent Density-Functional Theory : Concepts and Applications, the ...
15
votes
2answers
96 views
What is the difference between orbital localisation and NBO?
I am new to computational chemistry, I have used mainly GAMESS and Orca. In GAMESS, there are orbital localisation schemes like Pipek-Mezey, Ruedenberg-Edminston, etc. which generate orbitals that ...
16
votes
1answer
1k views
Does the Schrödinger equation have unique solutions?
I am learning DFT and the Hohenberg Kohn Theorem of Existence. It says that there is a one-to-one correspondence between the external potential and the density.
However the proofs that I have seen ...
8
votes
0answers
130 views
How to interpret second order perturbation theory analysis from NBO calculations? [closed]
The question is quite simple — how to interpret NBO results of second order perturbation theory analysis? As I have read several papers the most important interactions are $\pi\rightarrow\pi^{*}$, $LP\...
12
votes
1answer
184 views
How to explain Density Functional Theory results to an experimentalist?
When we present our Density Functional Theory simulation results e.g. lattice parameters, stacking fault energies, band gaps, etc. to people who are experimentalists then the very first question ...
9
votes
1answer
382 views
High precision helium energy
In the paper "High Precision Theory of Atomic Helium", Drake lists the then best-known ground state energy of the Schrödinger equation for helium to 22 digits as:
$$\lambda_0 \approx -2....
9
votes
1answer
42 views
How can I determine the maximum value of a spin orbital and its derivative in any direction?
I'd like to be able to recover the maximum value that any of the basis functions can take, as well as their maximum derivative. How can I do this?
For context, I need it because I want to calculate ...
10
votes
2answers
87 views
Analytic Hessians for meta-GGA functionals
In many of the free/open-source QM programs like GAMESS, ORCA, NWChem, the calculation of analytic hessians is not possible when a meta-GGA density functional is used, like M06-2X. My first question ...
9
votes
2answers
238 views
Normalization constant and Roothaan Equations
Roothaan Hall Equations:
The Hartree-Fock equations are a set of modified Schrodinger equations:
$f_{i}\psi_{m}=\epsilon_{m}\psi_{m}$
where:
The Fock operator ($f_{i}$) is given by (restricted case):
...
8
votes
1answer
841 views
How to fix Error Link9999 in Gaussian
I have a problem with geometry optimization in Gaussian software with M062X method. The structure was smoothly optimized using M062X/Gen. Nevertheless, I need very accurate results so afterwards the ...
5
votes
1answer
102 views
What are the other matrix elements in singlet symmetry-adapted CISD?
Szabo/Ostlund list the CI matrix elements between singlet symmetry-adapted configurations (SAC) in Table 4.1 of their book:
$$
\langle ^1\Psi^r_ a \lvert \mathcal{H} - E_ 0 \rvert ^1\Psi^r_ a \rangle,
...
15
votes
3answers
133 views
Candidate structures for global minimum determination
What are the best packages that can generate candidate structures for quantum chemical optimization (DFT or CCSD) to find the global minimum? I am working on the gas-phase small inorganic clusters (...
8
votes
1answer
122 views
Is this G16 molecular hyperpolarizability error reproducible in other software?
I was trying to calculate the hyperpolarizability $\beta$ of a cluster of two water molecules in Gaussian16 using the route card:
...
9
votes
1answer
72 views
What are some good ways to model radicals and similar intermediates of reactions
Calculations in the ground electronic state are probably the simplest cases where defaults in terms of charge (typically zero) and spin (singlet) are chosen by the calculation software. However, when ...
6
votes
1answer
138 views
I get an error 'Conversion from Z-matrix to cartesian coordinates failed' in Gaussian09. Any suggestions?
I'm doing my calculations using G09W. My OS is Windows 7 (64-bit). This error occurs in the frequency calculation. What's even weirder is that it seems to happen right after everything is already ...
14
votes
1answer
103 views
Why are single excitations ignored in the MP2 component of double hybrid functional calculations?
In the original paper by Grimme introducing double hybrid functionals (also summarized in just 3 paragraphs here), it says:
"[As] opposed to nonempirical versions of KS-PT2 [19],
the single ...
6
votes
1answer
224 views
I get this error in Gaussian09 even though I have enough memory. “Error termination in NtrErr: NtrErr called from FIOCnC.” Any suggestions?
Whenever read-write files get to about 20Gb, I get this error. I know that, in G09, one rw file is limited to 16Gb. So I have set the software to write several RWFs. But it still keeps producing this ...
10
votes
1answer
85 views
Regarding oscillatory strength theoretical units to experimental ones
The output of Gaussian rotatory and oscillatory strength intensities, plus a gaussian/lorentzian fit, translates to a theoretical CD/UV-vis spectra.
In order to try and compare with experimental ...
9
votes
1answer
57 views
Is there an anisotropy factor (g factor) for TDDFT absorption and circular dichroism calculations?
Experimentally, anisotropy factor is calculated by dividing the CD (circular dichroism) spectra by the absorbance spectra and multiplying by a factor of 32980 (in order to get a dimensionless quantity)...
7
votes
1answer
97 views
Bond Order: When and how is it used today?
We all learned about single vs double vs triple bonds in high school chemistry and biology. We learned that unsaturated fats have double bonds whereas saturated fats have only single bonds, which ...
6
votes
2answers
139 views
How is MCTDH derived?
In the multi-configurational time-dependent Hartree (MCTDH) method, the equation of motion is derived from the time-dependent Schrödinger equation by substituting the wavefunction ansatz expanded in a ...
13
votes
2answers
166 views
A CCSD(T) geometry optimization in Gaussian09 is deviating too far from the minimum. How do I deal with it?
I am doing a CCSD(T) geometry optimization on a series of molecules. One of the geometry optimizations took about 2 weeks even though an analogous molecule with the same number of basis functions took ...
32
votes
1answer
2k views
Was Walter Kohn wrong about this?
In Kohn's Nobel Lecture, he claimed that:
"In general the many-electron wave function $\Psi(\mathbf{r}_1,\ldots,\mathbf{r}_N)$ for a system of $N$ electrons is not a legitimate scientific concept,...
