Questions tagged [quantum-chemistry]
For questions about quantum chemistry.
89
questions
5
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Calculations of the charge transfer in GAMESS US
I'm trying to calculate the effective transfer integrals $J_{\text{eff}}$ from monomer A to monomer B within dimer AB by using GAMESS US:
$$J_{\text{eff}}=\frac{J-S\cdot (e_1+e_2)/2}{1-S^2},$$
where $...
6
votes
0answers
35 views
Implementing symmetry in MRCI calculation
I am running Multi Reference Configuration Interaction calculations for Aluminium Flouride molecule in its $A^1\Pi$ state interacting with Helium. For a complete Potential energy surface, I am doing ...
8
votes
2answers
119 views
Why are method developments and new implementations not done much in Gaussian?
While I have seen many papers in which Gaussian is used in calculations, I have not seen any paper in recent times where new methods are implemented in Gaussian. The latest paper I could find ...
9
votes
1answer
387 views
Why is the planewave codes ecosystem healthier on free/opensource software adoption, when compared to codes supporting atom-centered orbitals?
Regarding the branch of matter modeling that deals with electronic structure methods, I think we can divide it in two camps: Those who work mostly with planewave-based software, geared towards ...
10
votes
2answers
112 views
Quantum chemistry in external electrostatic field?
Which quantum chemistry methods can be used in an external electrostatic field? Also which software supports that? I'm interested in anything from semiempirical (eg XTB) to DFT (eg ωB97, B3LYP-D3) ...
12
votes
1answer
218 views
Comparing GAMESS, OpenMOLCAS and Psi4
Over the years many open-source ab initio packages have been developed and the diversity in subroutines, methods and portability (ability to interface with other software) is quite varied for ...
5
votes
2answers
151 views
SCF not converging during RHF/STO-3G geometry optimisation
I'm new in the field of QM methods and I've run into a problem for which I can't find a solution online.
I have tried with different basis sets, I've raised the maximum number of iterations and number ...
6
votes
0answers
50 views
Orbital space clustering
I am interested in how the orbital space of a system can be partitioned into clusters.
I read reading 'Cluster many-body expansion: A many-body expansion of the electron correlation energy about a ...
5
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0answers
54 views
How to calculate energy gradient and Hessian with respect to only a few internal coordinates using Gaussian?
I would like to form the (numerical) gradient and the Hessian of the total electronic energy with respect only to a few internal coordinates (namely, the six intermolecular coordinates of a weakly ...
8
votes
1answer
103 views
Molecular orbitals and active space
During the same minute as asking this question, I also asked this at Quantum Computing SE.
In Qiskit, each qubit corresponds to one spin orbital. For example, the $\ce{N2}$ molecule would have 10 ...
14
votes
2answers
252 views
What's the best quantum chemistry output parser for the command line?
This question is about tools like Open Babel. Are there any good command-line parsers for quantum chemistry program outputs? A good Python library could come in as a close second.
I am interested e.g. ...
6
votes
1answer
90 views
How to extract transition density cube from .fch file in Gaussian?
I have been trying to extract the transition density cube of a simple molecule, $\ce{H_2O}$. I did a regular geometry optimization and then TD-DFT calculation with a keyword ...
12
votes
2answers
305 views
For DFT and Hartree-Fock, how can we know that we have a true minimum? Is there an equivalent to the "frequency analysis" for geometry optimization?
In a geometry optimisation, one can check if they have reached a minimum by checking the phonons. And to a certain extent, the global minimum can be confirmed by relaxing from different starting ...
12
votes
2answers
204 views
What are the references in multi-reference methods?
After reading What exactly is meant by 'multi-configurational' and 'multireference'?
I still don't understand what the multiple "references" are. I understand that you can for example use a ...
7
votes
0answers
46 views
How can I calculate the exchange energy for a molecule in PySCF?
I am trying to generate exchange energy separately in pyscf but didn't see a way to do that. For correlation energy, it's fairly simple but do you have any idea how to calculate exchange energy?
11
votes
2answers
284 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?
7
votes
1answer
185 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
57 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
94 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
171 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
89 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
93 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
142 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
139 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
97 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
72 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
75 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
126 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 ...
16
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
197 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
45 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
103 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
117 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
262 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,
$M = {(\ce{O}, R_\ce{O}), (\ce{H}, R_\ce{H}), (\ce{H}, R_\ce{H})}$,
...
8
votes
0answers
69 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 ...
12
votes
1answer
156 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
75 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
102 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
121 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
335 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
99 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
65 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
178 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
556 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
307 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 ...
7
votes
1answer
108 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
93 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
8k 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
404 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 ...
