Questions tagged [pyscf]
For questions about or related to the PySCF electronic structure package for Python
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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 ...
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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 ...
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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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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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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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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
After finishing the orthonormalization of IAOs basis, and the LO.boys localization I am building my hamiltonian:
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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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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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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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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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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
...
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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 ...
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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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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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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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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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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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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:
$$\chi = \sum_i c_i \...
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How can I change the mass of an electron in the hamiltonian on a PySCF calculation?
I have been looking for a way to change some parameters included in the calculations of PySCF (e.g., changing the mass of the electron to the mass of a muon, so forming an exotic molecule). I know the ...
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Convert reduced density matrix in A.O. basis from GAMESS to pyscf [closed]
I want pyscf to read the single-particle reduced density matrix computed by GAMESS.
However, I am having trouble because the matrix sizes in GAMESS and pyscf are different.
For example, the AO-...
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How to evaluate Hartree--Fock exchange energy density on grids in pyscf?
I am trying to evaluate the Hartree--Fock exchange energy density on grids in pyscf with an instance of class "UKS", in order to test some functionals depending on the exchange energy ...
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Neural network as a customised XC functional in PySCF?
I've been trying to implement neural network as a customised exchange-correlation functional in PySCF but with no success. Below is the example code for customised XC functional. Anyone has any idea ...
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How does pyscf's internal basis format distinguish between 1s and 2s orbitals?
For example: gto.basis.load("6-31g", "Li") will show:
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Restarting an FCI calculation in PySCF
My question is, if there is a way to continue an earlier FCI calculation in PySCF.
Imagine you initially just need energies converged up to a certain threshold:
...
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How to get a two-electron expectation value for atoms in PySCF?
I am interested in calculating the following expectation value for atoms using a converged Slater deteminant from in DFT
$$ \left< \Psi \left| \sum_{i,j=1}^N r_i^a r_j^b\right| \Psi \right> \; ,\...
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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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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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Interface between PySCF and Molpro
I am currently interested in using pySCF to generate density matrices (first order single particle density matrices) and then using them in Molpro. In principle, this should be possible if the matrix ...
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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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What information does the 1RDM contain?
The one-electron reduced density matrix (1RDM) contains information useful for the prediction of molecular properties (for instance, dipole moments). As an example, the 1RDM can be easily obtained in ...
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Generate grid coordinates from PySCF DFT package for plotting grid points
As can be read in the pyscf.dft documentation, there should be the possibility of generating the coordinates of the grid for numerical integration. According to the documentation, one can generate the ...
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How to add confining potentials in PySCF? [closed]
I want to try to model the electornic structure of atoms in a confining potential, eg. add a term to the Hamiltonian either of a constant value $V$ after certain distance from the origin or just the ...
user5418
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Is the 4-index tensor in the coupled cluster code of PySCF stored in memory or on disk? [closed]
In the coupled cluster code of PySCF, is the four index tensor stored in memory or in disk?
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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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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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How to visualize natural atomic orbitals from PySCF [closed]
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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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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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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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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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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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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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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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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