Questions tagged [quantum-chemistry]
For questions about quantum chemistry.
104
questions
6
votes
1answer
61 views
How to predict protonation state of molecules in water?
I'm interested in predicting the protonation and tautomer state of organic molecules (typically CHNOS) at near pH 7 in water. I've used tools like Schrodinger's Epik / LigPrep before, but they ...
10
votes
3answers
234 views
How to plot molecules with angles and bond lengths
There are many programs out there where you pass an XYZ coordinate file and the program will give you a visualization of the molecule. I want to make a plot like the one in the picture, with bond ...
6
votes
1answer
38 views
Transforming basis functions from Cartesian to speherical
I read the basis set from book
A d-type GTO written in terms of the spherical functions has five
components (Y2,2, Y2,1, Y2,0, Y2,1, Y2,2),but there appear to be six
components in the Cartesian ...
6
votes
1answer
126 views
About LaCrO3 space group stability
I found two space groups of $\ce{LaCrO3}$ material Pnma and Pm-3m. If someone is familiar with this material, please help to understand which phase is more stable. what are the factors that determine ...
5
votes
2answers
138 views
How can I get started on DFT?
This question is simply:
How can we use DFT in the field of electrochemistry?
What are the best resources (Books, reviews, papers, software ...) to learn about using DFT in electrochemistry? ...
5
votes
2answers
140 views
The format and values provided by Basis Set Exchange
In this question and answers, I found that Basis Set Exchange provides information about the orbitals (e.g., the orbital exponents and contraction coefficients). For example, the following example is ...
5
votes
0answers
64 views
What are the electronic steps and ionic steps in VASP?
I am getting confused about what the electronic step and ionic step are in VASP.
I used to think that finishing the following loop one time is called an electronic step. but I am not sure how to ...
10
votes
4answers
666 views
How can I find the parameters in a basis set?
I have a question about the basis functions of Gaussian. When the basis function is set (e.g., 6-31G), I would like to know the specific value of Gaussian's parameters for each atom.
In particular, I ...
5
votes
1answer
114 views
Unrecognized or duplicated keyword error using ORCA
I wanted to run ORCA 5.0.2 with the following input:
...
5
votes
0answers
33 views
Segmentation fault during execution of Orca 4.0.0.1
I would like to use Orca 4.0.0.1 under the following Linux version:
...
7
votes
1answer
259 views
Where to find organic molecules atomic coordinates
I have found many organic molecule databases, such as PubChem or chEMBL. But they don't provide the atomic coordinates of each atom on the structure. I'm especially interested in organic molecules ...
6
votes
0answers
47 views
How do you perform parallelization of NEB-TS in ORCA?
I have tried running a NEB-TS calculation in orca with %pal nprocs 32, but I get an error saying ...
10
votes
2answers
217 views
Calculating the excited state dipole moment
I am trying to calculate the dipole moment of an excited state, using "Gaussian" software. My input commands were:
...
7
votes
1answer
60 views
What are the types of PT applied to electronic structure methods?
The motivation for this question is similar in nature to the series of questions on different methods :
What are the types of SCF?
What are the types of MCSCF?
What are the types of Quantum Monte ...
8
votes
2answers
106 views
Vibrational frequencies results with GAMESS. Is it an equilibrium geometry?
A specific HESSIAN calculation carried out with GAMESS software presents this result:
...
11
votes
0answers
118 views
How may I calculate the "effective transfer integral" in free electronic-structure software?
I would like to calculate the following four quantities in a free electronic structure program:
\begin{alignat}{2}\tag{1}
e_1&=\langle\phi_1|H^{KS}|\phi_1\rangle,\\
e_2&=\langle\phi_2|H^{KS}|\...
8
votes
0answers
45 views
Implementing symmetry in MRCI calculation [closed]
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
140 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
409 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 ...
11
votes
3answers
206 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
294 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
168 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
61 views
Orbital space clustering [closed]
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 ...
6
votes
0answers
71 views
How to calculate energy gradient and Hessian with respect to only a few internal coordinates using Gaussian? [closed]
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
128 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 ...
15
votes
2answers
301 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. ...
7
votes
1answer
160 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
338 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
223 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
64 views
How can I calculate the exchange energy for a molecule in PySCF? [closed]
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
295 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
284 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
62 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 ...
8
votes
1answer
196 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
238 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
106 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
104 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
158 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. ...
9
votes
2answers
250 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
102 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
82 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
86 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
139 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 ...
17
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 ...
11
votes
3answers
252 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
65 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
110 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 ...
32
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
147 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
287 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,
$M = {(\ce{O}, R_\ce{O}), (\ce{H}, R_\ce{H}), (\ce{H}, R_\ce{H})}$,
...
