Questions tagged [pyscf]
For questions about or related to the PySCF electronic structure package for Python
80
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PySCF CASSCF wavefunction symmetry not consistent during iteration
I'm tring to use symmetry adapted CASSCF to scan an energy curve of a carbon dimer. Yet with a slightly larger bond length, the SCF iteration always raises a RuntimeError. Here is a sample code:
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0
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How to start a unrestricted hartree fock (UHF) calculation with a custom guess in PySCF?
At first I want to do a UHF calculation of Li$_2$ dimer with spin=6 which shall give a sequence of $\sigma_{1s} \sigma^*_{1s} \sigma_{2s} \pi_{2p_x} \pi_{2p_y} \pi_{2p_z}$ (ordering might be wrong) ...
3
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Parsing Numbers as Basis Sets directly into PySCF
I was just wondering, and I bet others have come across this before, whether there is a way to parse numpy arrays as basis into PySCF. Let's say I want the exponents corresponding to numpy.losgcale(-...
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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....
3
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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 ...
0
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1
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57
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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:
...
8
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355
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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
...
6
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1
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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 ...
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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:
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12
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2
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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 ...
3
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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 ...
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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 ...
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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 ...
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63
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CCSD calculation between two orbitals
I am trying to calculate the CCSD energies between two orbitals. Suppose I have a system,
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7
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1
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601
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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 ...
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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 ...
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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 ...
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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 ...
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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-...
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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 ...
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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 ...
4
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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 ...
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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 ...
4
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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 ...
6
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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.
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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 <...
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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 ...
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3
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323
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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 ...
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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 ...
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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:
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2
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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 ...
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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 ...
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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')
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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
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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 ...
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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 ...
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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 $\...
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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, ...
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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 ...
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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 ...
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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?
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Why does CCSD work, but not CCSD(T), after reading an FCIDUMP in PySCF?
CCSD(T) works after an RHF calculation:
Input:
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Print chemical formula from list of atoms in Python?
Lets consider the following code which uses the Mole object:
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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 \...
4
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2
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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:
...
7
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3
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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 ...
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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-...
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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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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 ...
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