Questions tagged [hartree-fock]
For any questions about (or related to) the Hartree-Fock method.
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Locating Symmetry Equivalent Atoms from Distance Matrix?
As a follow up to my previous question here, I am now trying to implement symmetry detection in my code. I am following the paper by Beruski et. al to understand the background required. I am able to ...
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2
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How to use libint with Python
I am trying to write a basic Hartree-Fock code to compute orbital energies and total energy of a molecule at almost all basis sets. I wrote the integral code in Cython/Python and is very slow. I would ...
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How is the zero energy defined for molecular orbitals?
In DFT and Hartree-Fock bonding orbitals have negative energies while antibonding orbitals have positive energies. Why is this the case? It seems this is due to the zero-point energy being defined for ...
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Effective core potential (ECP) calculations
I'm setting up a simple Hartree-Fock problem in pyscf with ECPs to test things out. However, the numbers I get do not make sense to me as the energies are very different. I have never used ECPs before ...
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How to evaluate Hartree--Fock exchange energy density on grids in pyscf?
I am trying to evaluate the Hartree--Fock exchange energy density on grids in pyscf with an instance of class "UKS", in order to test some functionals depending on the exchange energy ...
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How to calculate the forces of attraction between a surface and molecules of a substance at a corrosion affection? [closed]
Previously, a question was asked about an equation that is able to calculate the forces of attraction between a surface and molecules (of another substance). During the discussion of the question a ...
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3
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Is there a simple free working code that implements Hartree–Fock or DFT?
Is there somewhere in the internet a good simple free working code (with a minimal number of lines in its presentation) that implements a calculation of eigenvalues with Hartree–Fock (or DFT) ...
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How to detect an "open shell" molecule?
I feel like this is a really stupid question, and I've been ashamed to ask for a while...
When I'm about to run some electronic structure calculation on a molecule, how do I know if I need to use an ...
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Hartree Fock Algorithm too high values for Molecules
I am working on a high school graduation paper on Hartree Fock and have gotten pretty far already. With help from this community, I managed to generate all the necessary integrals and implement the ...
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Implementation of one-elecron integrals in a Hartree-Fock program
Absolute newbie in quantum chemistry here. I was recently looking through some Fortran libraries from my university to see if I understand all of the mathematics. In a Hartree-Fock library, I found ...
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How to read two electron integrals from pyscf
This is a follow-up question to this one I asked a few days ago. I in the meantime talked to my teacher and generate all the necessary integrals in PySCF. For the one electron integrals that isn't an ...
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What is the best algorithm for ERIs of contracted gaussian atomic orbitals
I am currently working on python script that does Hartree-Fock-Calculations. I try to avoid packages as good as possible. I've figured out how to calculate the one electron integrals when it comes to ...
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What is the physical meaning of the term "non-local interaction"?
This term pops up through out Hartree-Fock and DFT. Does this term have any physical significance to actual(real) system or it is a mathematical by-product?
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Continuously-varying Hartree-Fock transition matrix?
Suppose we have a parametrized molecular Hamiltonian $H(R)$, where $R$ are the nuclear coordinates. If we let $B(R)$ be some chosen atomic basis set (like STO-3G) centred at $R$, then using $B(R)$, we ...
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Molecular orbital values on grid points in PySCF?
I am looking for a way to easily evaluate individual molecular orbitals on a grid(assuming a single determinant method for now) in PySCF.
I am aware on how to generate efficient grids for real-space ...
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Is it possible to obtain the current-voltage characteristic for a crystal using the Hartree–Fock (or DFT) calculation?
In continuation of the question of obtaining an electrical conductivity tensor (ECT) from the “first characteristics”, will my following suggestion be correct? Since a crystal with an applied-to-it ...
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Simple question about Hartree-Fock algorithm
Classically in Hartree-Fock implementations we define the wave-function in term of a basis set:
$$\phi_i = \sum_{\alpha} C_{\alpha i}\chi_\alpha$$
If I understand correctly the problem is reduced to ...
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Can the electrical conductivity tensor of a crystal be obtained from a Hartree-Fock calculation?
Let’s assume that a crystal has been calculated by Hartree–Fock (HF) method (or DFT one), i.d., so to speak, the "first characteristics", which are eigenvalues and eigenvectors, as well as ...
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In which part of the Hartree–Fock algorithm (or DFT one) could a neural network be most effectively used?
I understand that the task of implementing machine learning in DFT and Hartree–Fock (HF) algorithm has already been solved, perhaps to some extent, but it is interesting to think about how to ...
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Rys Quadrature method for integrating over Gaussian basis functions: 1D integral recursion relation
I'm trying to implement the Rys Quadrature method for integrations of Gaussians, from scratch. I'm using this paper as a reference.
So, how does the overall recursion relation for evaluating 1D ...
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Which formalism is better suited to model a crystal with defects: Hartree–Fock, Kohn–Sham, or something else?
Let’s suppose that
(1) it’s required to calculate a crystal with certain parameters of a crystal lattice;
(2) this crystal has some defects (let it be Frenkel defects for simplicity);
(3) these ...
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1
answer
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Hartree-Fock Method: Projection of density matrix onto a larger basis set
I am implementing a Hartree-Fock SCF program with an educational purpose. Although the code works fine using a Core Hamiltonian guess for the SCF iterative process, I want to implement a more accurate ...
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About the order of indices in basis set expansion
In many books, e.g., Szabo and Ostlund, Helgaker Jorgensen and Olsen, etc etc, the expansion of Hartree-Fock orbital by basis set is written as a kind of
$$
\phi_i = \sum_{\mu} C_{\mu i} \chi_{\mu}
$$
...
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What are the physical reasons if the SCF doesn't converge?
I've been mostly using ab initio methods as a routine calculation tool, so even though I know some things from the theoretical side, I still have mostly hands-on experience. One of the things that I ...
user4626
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Evaluating Coulomb and exchange integrals in practice using cartesian coordinates [closed]
Many software packages provide means to calculate the Coulomb and exchange integrals, for example, the exchange
$$\int \phi^*(1) \, \psi^*(2) \frac{1}{|\mathbf{r_1} - \mathbf{r_2}|} \, \psi(1) \, \phi(...
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Exploiting 8-fold symmetry of ERI tensor for building Coulomb and Exchange matrices
I'm trying to write a restricted Hartree Fock code in Fortran that reads in a file of zeroth-iteration 1 and 2 electron integrals (FCIDUMP format) and uses them to do the SCF procedure from an initial ...
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What do size-extensivity and size-consistency mean?
I have heard both terms in various lectures and books on quantum chemistry, however, I have not found a proper explanation of them. As I understand now, size consistency of a method means for example, ...
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How to compute the overlap matrix in Python
I want to calculate the overlap integral (S), I made the code, but it is only worked when I use a basis function that describe 1s and when I include 2s orbital, I start to get error.
The First Problem ...
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Is the formula of a Dyson orbital independent of whether there is degeneracy or not in the HOMO of the neutral?
A Dyson orbital is defined as:
$$
\textrm{Dy}(x) = \int dx_1 \ldots dx_{N-1} \, (\Psi^+(x_1,\ldots,x_{N-1}))^* \, \Psi^0(x_1,\ldots,x_{N-1}, x),\tag{1}
$$
where $\Psi^0$ and $\Psi^+$ are the total ...
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How to read data from an input and form two-electrons integral?
I am doing a code that can calculate the hartree-fock energy. I want to form the two-electrons integral by reading the data from the input like this one below. The first four number are the indices ...
- 1,031
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Differences between DFTB3 energy and HF energy
I was performing DFTB3 calculation with DFTB+ on water monomer. This is my input.
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Why is uncertainty not a big problem in computational chemistry?
The molecular Hamiltonian (or, for simplicity, the Fock operator) contains coulomb potentials as well as momentum operators. To evaluate the coulomb potential, we need to know where the electrons are. ...
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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 ...
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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 ...
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Visualize electron density using pyscf
I found the following example of code which uses density functional theory to compute the electron density $\rho$:
...
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1
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'Exchange' in Hartree-Fock and Kohn-Sham DFT
I am a bit confused about the notions of exchange in the Hartree-Fock and Kohn-Sham Density Functional Theory schemes.
In Hartree-Fock, one just writes down the many-electron wavefunction as a hartree-...
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Does Kohn-Sham DFT use Slater determinants?
In the Hartree method, it is known that the wavefunction of the system does not obey the antisymmetry principle of fermions - that is when you swap two particles, they don't up a negative sign. ...
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Why is CPHF/CPKS necessary for calculating second derivatives?
This question is coming from an answer to one of my previous questions. During optimizations, QM programs usually compute the gradient(first derivative) analytically, and take a guess of the hessian (...
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2
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Optimization of Gaussian basis sets within the Hartree-Fock Method
I am revisiting some exercises in Thijssen's Computational Physics book, particularly chapter 4 on the Hartree-Fock method. I am interested in the method of nonlinear optimisation for its own purposes,...
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Why is my quantum chemistry software not printing as many 2e- integrals as I expect?
Background:
In Hartree-Fock theory, the two-electron integral is given by:
$[ij|kl]$ = $\int dx_{1}dx_{2}(\chi_{i}(x_{1})\chi_{j}(x_{1})\frac{1}{r_{12}}\chi_{k}^{*}(x_2)\chi_{l}(x_{2})$
I am ...
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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):
...
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Semi-canonicalisation vs canonicalisation of the Fock matrix and orbitals
I have seen the terms semi-canonicalized and canonicalized used in relation to the Fock matrix, density matrices, and orbitals; however, I am unsure what these terms actually describe.
For instance:
...
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Muonic Modeling
I have seen an article[1] that describes a HF approach to working with exotic muonic atoms. I am curious about how far DFT has been extended for modeling muonic chemistry. Are there psuedopotentials ...
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What are the types of SCF?
Many of us know the most common types of SCF
(though we can do better than Wikipedia at explaining them):
RHF (Restricted Hartree-Fock), RKS (Restricted Kohn-Sham) [link to answer]
UHF (Unrestricted ...
- 30.4k
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Analog computing in matter modeling today: Any applications?
When we think about computers and computing today, almost invariably we think about digital computers, the ever-present objects today. But reading this question in the Chemistry stackexchange, How are ...
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How to calculate the Fock matrix in the molecular orbital basis PySCF?
I am interested in calculating the Fock matrix in the molecular orbital basis with PySCF, though I am not clear on the methodology behind this task.
In my attempt, I use the following script (for the ...
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What do the rows and columns of a Fock matrix represent?
I am using the pyscf code, where the Fock matrix can be obtained by:
...
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Hartree-Fock density vs Kohn-Sham density
Hartree-Fock density is free of self-interaction but lacks electron correlation effects, while the density from KS-DFT (using an xc functional or potential, both which are explicitly density-dependent ...
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One-center two-electron integrals between 1s STO
As per @user1271772 's suggestion I am asking this question here again.
I am trying to understand SCF cycle by trying to code up solved example from Quantum Chemistry by Levine (page 443, 5th edition)...
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What is the mathematical condition that ensure that the self-consistent field (SCF) procedure must converge?
We know that there is convergence issue of DFT method on study real molecular system. It would be conducive if people could pre-determine if the SCF procedure is converge analytically before starting ...
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