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Questions tagged [pyscf]

For questions about or related to the PySCF electronic structure package for Python

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FCIDUMP file from UHF calculation in PySCF

Background In PySCF, one can use from_chkfile() to Read SCF results from PySCF chkfile and transform 1e, 2e integrals using the SCF orbitals. The transformed integrals are then written to FCIDUMP file....
Jaafar Mehrez's user avatar
0 votes
1 answer
45 views

In which irreducible representations shall I put the electrons in an F atom in PySCF?

I’m looking to complete ROHF energy calculations in PySCF for the F atom. I need to update the irrep_nelec dictionary for F. I know that the one for the O atom is: ...
TheorVHP's user avatar
6 votes
1 answer
78 views

May I use a DFTB+ result as initial guess for HF or DFT in PySCF?

I would like to use the result of a DFTB+ calculation as an SCF initial guess calculation in PySCF. Is there a way to generate the density matrix of the converged calculation and read it with PySCF to ...
rbw's user avatar
  • 273
15 votes
2 answers
2k views

Why is my hydrogen energy not equal to -0.5 hartrees?

I'm trying to calculate the HOMO of various molecules in water solution. I first tried to see how PySCF calculates the HOMO of hydrogen. I ran the following code: ...
nkam's user avatar
  • 153
12 votes
2 answers
186 views

Are there any free or free quantum chemistry codes which can apply an external field gradient?

I wanted to apply a field gradient on my molecule and study some associated property. I'm able use MM point charges w.r.t a QM/MM scheme of doing things to produce a field gradient. But I was ...
Atom's user avatar
  • 1,005
3 votes
1 answer
105 views

Orthonormality of AOs and MOs in PySCF

I have a basic question about how to calculate molecular-orbitals from atomic-orbitals in PySCF using the self-consistent field approach. My understanding mathematically is as follows: we start with a ...
Solarflare0's user avatar
5 votes
0 answers
78 views

Can PySCF generate FCIDUMPs in native MOLPRO format? [closed]

I am working on a C++ project that entails reading FCIDUMP files and feeding it into some post-HF calculation. For practical reasons, it is more preferable to stick with the native FCIDUMP format of ...
Izzy Vang's user avatar
6 votes
0 answers
69 views

What are the parameters in PySCF's Selected Configuration Interaction code

Dear StackExchange Members, I'm using the native PySCF implementation of selected configuration interaction (SCI). However, I can't seem to find any documentation detailing the algorithm or various ...
AWPrentice's user avatar
4 votes
0 answers
62 views

CCSD calculation between two orbitals

I am trying to calculate the CCSD energies between two orbitals. Suppose I have a system, ...
Pro's user avatar
  • 1,056
7 votes
1 answer
584 views

pyscf: Why should the choice of pseudopotential determine the total energy, and not the physics?

I have limited experience with DFT, but as an exercise I have written a DFT program of an atom (from scratch using nothing more than python built in functions and numpy) by following Richard Martin's ...
Mikke Mus's user avatar
  • 263
3 votes
0 answers
46 views

Reproduce Dissociation Energy of BH molecule with PySCF

I want to reproduce the bond dissociation energy of the BH molecule as stated in the book 'Molecular Electronic Structure Theory' by Helgaker et al, (chapter 8.3.1), using FCI with 1 frozen core ...
jakg's user avatar
  • 31
3 votes
1 answer
109 views

How may I verify that my A matrix for TDA (Tamm-Dancoff Approximation of TD-DFT) from PySCF is correct?

This is a follow-up to a series of questions that I have asked here: Is a D-Wave quantum computer able to do TD-DFT calculations? (answer was "yes, but it might not be efficient") Inquiry ...
Hadeel Moustafa's user avatar
5 votes
1 answer
59 views

A matrix form used in the Quantum Annealer Eigensolver (QAE)

In the paper "Computing molecular excited states on a D‑Wave quantum annealer", PySCF is employed to compute the TDA matrix. Then a few of the lowest eigenvalues and eigenvectors of a TDA ...
Hadeel Moustafa's user avatar
7 votes
0 answers
109 views

Coupled cluster and periodic systems

I recently found that PySCF supports coupled cluster calculations for periodic systems (link to the documentation: https://pyscf.org/user/pbc/mix_mol.html). That seems pretty unique: of course DFT in ...
Alex I's user avatar
  • 1,070
4 votes
1 answer
115 views

Inquiry about A Matrix Output in 21-matrix_A_B.py

I'm trying to use the pyscf library for some calculations, specifically the 21-matrix_A_B.py example script for obtaining the A matrix. https://github.com/tepl/pyscf/blob/master/examples/tddft/21-...
Hadeel Moustafa's user avatar
4 votes
2 answers
172 views

Post-hartree fock calculation with localized Molecular orbitals in PySCF

I have localized the canonical Hartree-Fock orbitals for a molecule in PySCF. Now I want to perform ccsd calculations with these localized orbitals. Is it possible with pyscf? Example with CCSD with ...
Pro's user avatar
  • 1,056
4 votes
0 answers
43 views

Carbon Capture Research - Force Constants & Basis Sets

Greetings Matter Modeling, I'm researching carbon capture dynamics in the context of sorbent regeneration. The UN IPCC Net-Zero goal requires 75 Mt-CO₂/year captured by 2030. According to the IEA, we ...
Phill McGee's user avatar
1 vote
1 answer
114 views

Spin Configuration of Active Space in PySCF

I was running a state averaged CASSCF (4,4) calculation for the first 3 roots of the TMM biradical in PySCF. I wanted to get the spin configuration of the active space but the only information I could ...
Abhishek R Nath's user avatar
4 votes
1 answer
78 views

Table of Largest CI Components in PySCF CASSCF Calculation

I was running a simple CASSCF calculation in PySCF on the TMM biradical. It was a CASSCF (4,4) state averaged calculation where the energies of the first 3 roots were calculated. The simulation output ...
Abhishek R Nath's user avatar
3 votes
1 answer
138 views

Verifying periodicity of crystalline orbital modulus in PySCF

I'm trying to verify that the modulus of the crystalline atomic/molecular orbitals computed by PySCF satisfy the correct periodicity condition for the supercell. I'm considering a hydrogen chain ...
phonon's user avatar
  • 61
3 votes
1 answer
281 views

Comparison between the ordering of Molecular Orbital coefficients between Gaussian and PySCF

I am trying to compare the Molecular Orbital coefficients obtained from PySCF and G09 program. Below is the PySCF and Gaussian input and output. I am using 3-21G basis and RHF method for both the ...
Pro's user avatar
  • 1,056
4 votes
1 answer
363 views

What's the best code for getting 1-particle and 2-particle density matrices with CCSD(T) in Python?

I have been using PySCF to calculate the 1-particle and 2-particle density matrix from ccsd(T) wavefunction using these modules in-built in PySCF make_rdm1() and <...
Pro's user avatar
  • 1,056
3 votes
1 answer
79 views

Change the density threshold for functional evaluation in PySCF

I'm testing some scaling properties of various density functional approximations, which involves evaluating the functionals on model systems with very low density. I am using the funcition ...
Lex Lee's user avatar
  • 123
1 vote
0 answers
58 views

Restoring MO from ao2mo using PYSCF module [closed]

After finishing the orthonormalization of IAOs basis, and the LO.boys localization I am building my hamiltonian: ...
Ruben Alfonso Casillas Pacheco's user avatar
2 votes
0 answers
48 views

PySCF two-electron integrals between two fragments

I am trying to compute integrals of the form $(pq|rs)$ where the orbitals $p$ and $q$ are orthogonalized atomic orbitals for a fragment $A$ and $r,s$ are orthogonalized on fragment $B$. I was thinking ...
Szgoger's user avatar
  • 624
5 votes
1 answer
304 views

Error in UCCSD(T) Calculation in PySCF for S atom?

I am trying to calculate the UCCSD energy and UCCSD(T) correction for the S atom using PySCF. Using sto-3g basis set, I found that the UCCSD calculation would be completed successfully, but the ...
Hemanth Haridas's user avatar
8 votes
1 answer
427 views

Does PySCF use chemist's or physicist's notation for 1- and 2-electron integrals?

I am trying to evaluate 1- and 2-electron integrals using PySCF trough this code: Hij = mol.intor('int1e_kin') + mol.intor('int1e_nuc') Vijkl = mol.intor('int2e') ...
Rodrigo Sánchez Martínez's user avatar
7 votes
1 answer
291 views

Start a CI calculation from HF/DFT chkfile in PySCF

I am trying to perform a CISD calculation in PySCF using the starting orbitals from an old DFT result. The DFT result was saved on a chkfile, mf.hdf5. The code that ...
David Sousa's user avatar
5 votes
0 answers
52 views

How can I get 2c2e and 3c2e integrals using the erf kernel in PySCF? [closed]

I want to reproduce the calculation procedure of density fitting in PySCF. I know how to get the 2c2e/3c2e integrals matrix/tensor with $1/r_{12}$ kernel by using ...
Gaelthorn's user avatar
6 votes
1 answer
144 views

Has non-orthogonal CI (NOCI) been implemented in PySCF?

I'm kinda new to Pyscf and was wondering if there is a way to do non-orthogonal CI calculations with it. I would appreciate any help.
master_disaster's user avatar
4 votes
0 answers
139 views

PySCF calcuation of 'one-index' electrostatic (Hartree) potential [closed]

I'm trying to calculate the electrostatic (Hartree) potential corresponding to a single (auxiliary) GTO: $$v_i({\bf r_1}) = \int d{\bf r}_2~ \frac{\phi_i ({\bf r}_2)}{r_{12}}$$ [Please note that $\...
stefan_chem's user avatar
8 votes
1 answer
342 views

How can I build the wheels necessary for a quick installation of PySCFad on a "compute node"?

The following is the procedure I have been following: Install PySCFad ...
Nike Dattani - No Free Time's user avatar
3 votes
1 answer
118 views

Why is my CISD restart failing in PySCF?

A case that works In my answer to Restarting an FCI calculation in PySCF, I provided a folder full of input and output files that demonstrates saving (as a numpy ...
Nike Dattani - No Free Time's user avatar
3 votes
1 answer
185 views

Is PySCF able to print checkpoint files during a CISD calculation?

The problem I've described how to restart a CISD calculation in my answer to the question: Restarting an FCI calculation in PySCF, but this requires all iterations of the CISD calculation to finish, ...
Nike Dattani - No Free Time's user avatar
2 votes
1 answer
337 views

How may I calculate free energy using PySCF?

I want to calculate the thermodynamic parameters for a single molecule at a certain temperature. How may I do it with PySCF?
greg pits's user avatar
1 vote
1 answer
425 views

PySCF: How to do CCSD calculations from an FCIDUMP file in HDF5 format?

Recently my question: Why does CCSD work, but not CCSD(T), after reading an FCIDUMP in PySCF? lead to a bug fix that allows users to do CCSD(T) calculations from an FCIDUMP file in PySCF. That was ...
Nike Dattani - No Free Time's user avatar
2 votes
0 answers
74 views

PySCF: Two electron integrals, translate between aosym=s8 and full tensor [closed]

...
alex math's user avatar
2 votes
1 answer
264 views

Why does CCSD work, but not CCSD(T), after reading an FCIDUMP in PySCF?

CCSD(T) works after an RHF calculation: Input: ...
Nike Dattani - No Free Time's user avatar
7 votes
3 answers
1k views

Print chemical formula from list of atoms in Python?

Lets consider the following code which uses the Mole object: ...
Nike Dattani - No Free Time's user avatar
4 votes
1 answer
158 views

Check whether a simple molecule is Raman-active or IR-active using PySCF

I am trying to write a python code that checks the dipole moment and the polarisability of a certain molecule in order to determine if it will be Raman-active or IR-active. Raman-active molecules are ...
Joan Grebol's user avatar
4 votes
1 answer
400 views

Inputting custom STO-3G basis into PySCF

A simple question about PySCF, but nonetheless I could not find out how to do it: I have a system of atoms for which I already calculated a STO-3G basis in the usual form of MOs: $$\chi = \sum_i c_i \...
greilchri's user avatar
7 votes
3 answers
311 views

How can I change the mass of an electron in the hamiltonian on a PySCF calculation?

I have been looking for a way to change some parameters included in the calculations of PySCF (e.g., changing the mass of the electron to the mass of a muon, so forming an exotic molecule). I know the ...
Joan Grebol's user avatar
4 votes
0 answers
173 views

Convert reduced density matrix in A.O. basis from GAMESS to pyscf [closed]

I want pyscf to read the single-particle reduced density matrix computed by GAMESS. However, I am having trouble because the matrix sizes in GAMESS and pyscf are different. For example, the AO-...
user2436's user avatar
5 votes
2 answers
299 views

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 ...
Lex Lee's user avatar
  • 123
3 votes
1 answer
192 views

Neural network as a customised XC functional in PySCF?

I've been trying to implement neural network as a customised exchange-correlation functional in PySCF but with no success. Below is the example code for customised XC functional. Anyone has any idea ...
Ken.WS's user avatar
  • 31
7 votes
2 answers
248 views

How does pyscf's internal basis format distinguish between 1s and 2s orbitals?

For example: gto.basis.load("6-31g", "Li") will show: ...
theQman's user avatar
  • 231
4 votes
2 answers
279 views

Restarting an FCI calculation in PySCF

My question is, if there is a way to continue an earlier FCI calculation in PySCF. Imagine you initially just need energies converged up to a certain threshold: ...
Jannis Erhard's user avatar
3 votes
1 answer
193 views

How to get a two-electron expectation value for atoms in PySCF?

I am interested in calculating the following expectation value for atoms using a converged Slater deteminant from in DFT $$ \left< \Psi \left| \sum_{i,j=1}^N r_i^a r_j^b\right| \Psi \right> \; ,\...
Szgoger's user avatar
  • 624
5 votes
1 answer
355 views

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 ...
lela2011's user avatar
  • 125
2 votes
0 answers
562 views

How to read two electron integrals from pyscf [closed]

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 ...
lela2011's user avatar
  • 125