Questions tagged [pyscf]

For questions about the PySCF electronic structure module for Python

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Is the 4-index tensor in the coupled cluster code of PySCF stored in memory or on disk?

In the coupled cluster code of PySCF, is the four index tensor stored in memory or in disk?
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7 votes
1 answer
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Molecular geometry optimization for cyclooctatetraene with pyscf

I am trying to reproduce the cyclooctatetraene isometrization process pulished here. In figure 3 of the paper, it shows the potential energy surface as a variable of the polar angle using the CAS(8,8) ...
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7 votes
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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10 votes
0 answers
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How to visualize natural atomic orbitals from PySCF

I'm trying to visualize the different methods of getting localized orbital (LO) given in the User Guide. I went through the example, saved the orbitals as cube files, then opened the files in ...
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9 votes
2 answers
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How to get atomic orbital coefficients in PySCF

I'm new to quantum chemistry software, so I'll try my best to explain my thought process. When running a DFT calculation, the software uses a linear combination of basis functions to approximate the ...
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6 votes
1 answer
208 views

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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8 votes
0 answers
101 views

Interacting with pyscf integral library from Fortran [closed]

I would like to use libcint, the integral library in pyscf from Fortran. Its webpage has a Fortran API and developer manual, but ...
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6 votes
1 answer
83 views

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 ...
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7 votes
0 answers
87 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?
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8 votes
1 answer
485 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 ...
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7 votes
1 answer
129 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 ...
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5 votes
1 answer
125 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 ...
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11 votes
2 answers
667 views

How are 1-electron and 2-electron integrals done in PySCF?

I am right now using the PySCF for some quantum chemistry problems. I need to get the parameters, which are labeled $h_{ij}$ and $V_{ijkl}$. How can I get this done with PySCF?
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4 votes
1 answer
110 views

PySCF: 2-index and 3-index matrix

The 4-index 2-electron integral can be obtained for the He atom with the following code: ...
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7 votes
1 answer
326 views

PySCF: Implementing SHCI frozen argument

I am trying to run a SHCI calculation in PYSCF with DICE; however, I want to freeze the first two core orbitals and the highest 3 virtual orbitals in a calculation. In other parts of PySCF this can ...
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5 votes
1 answer
241 views

PySCF: atomic basis Fock matrix changes after mo_coeff update

I've noted a curious thing with PySCF when updating the molecular orbital coefficients of the mean-field object. If one prints out the Fock matrix in the atomic basis (...
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6 votes
1 answer
403 views

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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9 votes
1 answer
179 views

PySCF: eigenvalues, non-integer occupation, CISD calculations, and frozen lists

I have been performing CISD calculations with PySCF and I have a query surrounding the occupation of the orbitals. Here, the occupancies are calculated from the eigenvalues of the 1-electron ...
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10 votes
4 answers
982 views

Codes for post-processing Gaussian cube files?

I have generated MOs of a molecular system and I need to recreate its electronic density via $\rho(r)=\sum_{A_i}|\psi_i(\mathbf{r})|^2$ where $A$ is a set of occupied MOs. I am trying to do this via ...
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9 votes
1 answer
531 views

What unit of energy does PySCF use?

The documentation for PySCF can be found here: https://sunqm.github.io/pyscf/ However, it does not explicitly state in the documentation what unit of energy is used. Is there a way to find this out?
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11 votes
1 answer
554 views

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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12 votes
2 answers
747 views

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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