Questions tagged [quantum-chemistry]
For questions about quantum chemistry.
74
questions
9
votes
2answers
142 views
DFT functionals from MP2 methods
I have heard people talk about DFT functionals built starting from MP2 corrections. Do you happen to have a reference I read about that from?
6
votes
1answer
142 views
Convert reduced density matrix from M.O. to A.O. basis
I am interested in converting the one-particle reduced matrix (rdm1) from the molecular orbital (M.O.) basis to the atomic orbital (A.O.) basis. Is the following method correct (in an identical ...
8
votes
2answers
53 views
Are there efficient open source implementations of electrostatic potential integrals?
We've had several questions regarding calculation and plotting of electron density.
The electrostatic potential represents the interaction between a point charge at a given point $\mathbf{r}$ in a ...
7
votes
1answer
64 views
Visualize electron density using pyscf
I found the following example of code which uses density functional theory to compute the electron density $\rho$:
...
11
votes
2answers
136 views
Critical difference and roles of Slater- and Gaussian-type orbitals
I was very interested in the following question and answer about the Slater- and Gaussian-type orbitals (STO and GTO) used in quantum chemistry and a practical calculation.
Gaussian-type orbitals vs ...
7
votes
1answer
83 views
Computing analytic derivatives of molecular Hamiltonians obtained from solving Hartree-Fock equations
I'm currently working on a quantum chemistry project, I am dealing with a second-quantized electronic Hamiltonian (corresponding to some molecule), written in terms of fermionic creation and ...
5
votes
1answer
84 views
Calculating first and second derivatives of a molecular Hamiltonian?
I'm interested in computing first and second derivatives of molecular Hamiltonians with respect to nuclear coordinates. I've been using Psi4 and PySCF to perform Hartree-Fock calculations, and I was ...
13
votes
1answer
130 views
Generating numpy-compatible electron density from Molden / QC calculation
I'd like to use a variety of Python tools (e.g., matplotlib and Mayavi) to analyze orbitals plot electron density contours, etc. ...
8
votes
3answers
109 views
How do you generate 3D electron density from fchk file without the Gaussian software?
I'm trying to reproduce some results from a paper with fchk output files containing DFT calculations. The paper details how to produce the 3D electron density using Gaussian software, but since I don'...
7
votes
2answers
94 views
What quantity to perform CBS extrapolation on for adsorption/binding energies?
When calculating complete basis set extrapolations for quantities, such as adsorption energies or binding energies, which depend on the difference between three quantities (i.e. $E_\textrm{prop} = E_\...
8
votes
1answer
66 views
Excited states using ORMAS flag in GAMESS
I am trying to calculate the excited states using single reference CISD on $\ce{CH3OH},$ using ORMAS' CI-X option in GAMESS. As a test example I am using the $\ce{CH3OH}$ that has 2 core, 7 occ. ...
6
votes
0answers
71 views
Calculating excited states using GAMESS CISD module [closed]
I am trying to compare the energies of the excited states of $\ce{C12H9N}$ molecule using the CIS and CISD module implemented in the quantum chemistry package in GAMESS.
While I can easily obtain the ...
8
votes
1answer
123 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
180 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
42 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
101 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 ...
31
votes
5answers
3k 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
100 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
240 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
66 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
98 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
68 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
94 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
110 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 ...
14
votes
1answer
283 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
95 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
57 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
146 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
537 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
306 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
91 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
77 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
7k 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
400 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
111 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
120 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
267 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
108 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
183 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
187 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
390 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:
$$\lambda_0 \approx -2....
9
votes
1answer
43 views
How can I determine the maximum value of a spin orbital and its derivative in any direction?
I'd like to be able to recover the maximum value that any of the basis functions can take, as well as their maximum derivative. How can I do this?
For context, I need it because I want to calculate ...
10
votes
2answers
102 views
Analytic Hessians for meta-GGA functionals
In many of the free/open-source QM programs like GAMESS, ORCA, NWChem, the calculation of analytic hessians is not possible when a meta-GGA density functional is used, like M06-2X. My first question ...
9
votes
2answers
252 views
Normalization constant and Roothaan Equations
Roothaan Hall Equations:
The Hartree-Fock equations are a set of modified Schrodinger equations:
$f_{i}\psi_{m}=\epsilon_{m}\psi_{m}$
where:
The Fock operator ($f_{i}$) is given by (restricted case):
...
8
votes
1answer
1k views
How to fix Error Link9999 in Gaussian
I have a problem with geometry optimization in Gaussian software with M062X method. The structure was smoothly optimized using M062X/Gen. Nevertheless, I need very accurate results so afterwards the ...
5
votes
1answer
105 views
What are the other matrix elements in singlet symmetry-adapted CISD?
Szabo/Ostlund list the CI matrix elements between singlet symmetry-adapted configurations (SAC) in Table 4.1 of their book:
$$
\langle ^1\Psi^r_ a \lvert \mathcal{H} - E_ 0 \rvert ^1\Psi^r_ a \rangle,
...
