z2packdev/tbmodels

A tool for creating and manipulating tight-binding models.

tbmodels's Issues

band selection in construct_kdotp part

In the function MODEL_TB.construct_kdotp(k_star, order=2), the program will construct the kp model with same band number as the given TB model.

Is it possible to construct a kp model with much less band number, for example 3 bands around Gamma from a multy-band W90 model?

Thank you very much,
Yang

Check if per-matrix sparsity (automatic) makes sense

Currently, the hopping matrices can either all be stored as dense matrices, or all sparse. It might make sense to mix sparse and dense matrices though.

Since there's anyway a compatibility layer in the form of _array_cast and empty_matrix, it might not be too hard to implement.

What's more difficult is probably adjusting the sparsity dynamically. A good starting point could be analyzing the matrices in set_sparse, and then set each according to some heuristic for the filling factor (adjustable?).

To be checked:

• Find some models where mixed sparse / dense provides measurable benefit.
• Find cut-off where storing dense / sparse is more efficient
• Check impact on Hamiltonian evaluation
• Are there places where matrix manipulation relies on it all being the same data type?

Make 'pos=None' handling consistent

Currently, setting pos=None in the constructor will set all positions to the origin. There are few places in the code that rely on this behavior, but also some places where pos is not None is explicitly checked.

We need to decide if pos=None should be possible, and then either remove the pos is None checks or add them where they are missing.

Make position tolerance when symmetrizing configurable

Add function to create k.p model

TODO: documentation

Add exception marker for symmetrizing a model that does not match the symmetry

Add method to parse from Wannier90 _tb.dat file

Test against pythtb

Running pytest from base directory gives errors

I'm not sure if that's the desired behavior, but running pytest from the base directory gives many test failures as the sample data from tests/samples is not found.

Fix tests for Python 3.6

Add documentation for symmetrization procedure

Related to #11.

Converting WANNIERT_HR.dat for unit cell to that of SUPPERCELL

Hi,
By using the following commands I have tried to produce wannier_hr.dat file for silicon supercell. the file is produced in model3.
But the values are different. The model2 file is differing from wannier_hr.dat file of the silicon unit cell, too.
The next problem is belonging to model4, this command does not run.
I would appreciate your comments.
import tbmodels
import numpy as np
model = tbmodels.Model.from_wannier_folder(folder='/d......./TBmodels-trunk/examples/silicon/build/', prefix='silicon')
supercell_model = model.supercell((4, 4, 1))
model2=model.to_hr_file('model_hr.dat')
model3=supercell_model.to_hr_file('supercell_model_hr.dat')
model4 = tbmodels.Model.from_hr_file('model_hr.dat')

Add public API for obtainin the "full" hopping matrices

Allow cutting off small hoppings after model is created

Add dependabot configuration

Use 'pytest-regressions' for test output check.

Needs checking if the more complicated "comparison" features are easily portable.

win parser should properly consider units

Now, if units are specified, the win parser fails.

E.g. with this in the .win:

begin atoms_cart
ang
W 0. 0. 0.
end atoms_cart

it fails. The same for begin unit_cell_cart.

For now, as we only use ang (that anyway is the default) we just strip in the parser the following lines:

lines = (l for l in lines if 'ang' != l)

but of course it is subideal.
One should read the first line after 'begin', that could be already a value, or contain either bohr or ang.
If specified, one should use this as units (and convert the values where needed).
If not specified, one should check the global flag that specifies units for the whole file, and if not specified, assume the default is angstrom.

Evaluate HDF5 or SQLite for saving Models

JSON / msgpack is sub-optimal because the complex data type has a lot of overhead. Write generic from_file and to_file functions that dispatch according to the file ending.

Check unit cell convention

Use unit cell vectors as rows. This will become important when implementing the new features (from full_feature branch).

Use periodic distance in 'nearest_atom' xyz parsing

The returned position should be close to the Wannier position (not the original atomic position), so that the overlap matrices are still correct.

Change unit cell: Test impact of skipping shape / offset part when not used

Test the performance impact of skipping the unused parts of the change_unit_cell method when either the unit cell shape does not change, or there is no offset. Especially the former could be important, because it involves solving a few matrix equations.

Factor out parsing functions into separate submodule

Fix behavior of symmetrize for full_group=False

Right now, it only considers the first power of the generators. However, this does not necessarily produce all symmetries in the group. Instead, all powers up to the order of the symmetry should be included.

Allow for symmetrizing the positions

Match the closest possible position when symmetrizing, to avoid having to set the positions manually (or to zero) for symmetrization to work.

Factor out unit cell / structure code

In many places, there is now code which deals with unit cells / structures (related to the uc and pos parameters), and how they transform. This should be factored out to a separate module, since it is not specific to TBmodels.

Examples:

• Model.__add__: checks if the UC / positions match
• reciprocal_lattice
• Reading from Wannier90 output. Here it might pay off to use pymatgen as an intermediate parsing step, and then go from there to our type.

pymatgen.Lattice and pymatgen.Structure unfortunately only support 3D systems, so they are not an option to simply use.

Extend Wannier90 interface

Read the positions from the .xyz file (see the PythTB Wannier90 interface).

Add '-v' option in command-line.

To easily print the current version.

Add custom exceptions, handle in CLI

Add custom exceptions for known errors, and handle them in the CLI in a way that makes it easy to parse.

Add --sparse option to parsing command

Add an option to store the parsed tight-binding model in sparse format, since this can be significantly cheaper in terms of storage.

Is it possible that the Kwant-interface can deal with Polyatomic

Hi Dominik,

I just found that your Tbmodels code group all the orbitals into one site when interfacing with kwant.

Is there a way to deal with Polyatomic case that simulate the real system which has different sites and different orbitals on each site?

Thanks
Xiangru

Parsing the _r file to obtain dipole elements

I have written a little modification that can read wannier90's *_r.dat output and create the transition dipole elements. If this is relevant, I could try to match the style of the project and create a pull request. I might need some help with the proper implementation, since I'am unsure if I should also go for the possibility of sparse matrices and how to deal with iterators properly.

Create separate files for each serialization method

For example, some of the serialization code might warrant being moved to a separate (hidden) module.

Add regression test for tabs in .win

Regression test for merge #30.

Add sanity check for new unit cell / positions when folding model.

Currently, it is possible to select a nonsensical new unit cell without feedback. The code will just not populate the hoppings.

The sanity check should be configurable, such that inexact supercells can still be folded.

H5py version 3.3.0 produces an incompatibility

Improve import time

This is mostly due to explicit sympy imports (via symmetry-representation, I believe). To create a profile (py3.7+):

python -X importtime -c "import tbmodels" 2> out.log
tuna out.log

Requires https://pypi.org/project/tuna/

Use only upper half of matrix in R=zero

Might not be worth it (most probably a very small improvement).

Check what can be done with the position operator information

Check if _array_cast should be before or after the multiplication with the exponential factor

Add function to return the reciprocal lattice vectors.

Add non-utf8 locale test on Travis

Implement pos_kind='atom'

Implement reading the orbital positions from the atomic positions. For this, the orbital - atom correspondence needs to be made from the projections in the .win file.

Add a function to compute the group average

Improve performance of "listable" hamilton evaluation for large models

When using the new "listable" mode of the Hamiltonian evaluation for large matrices, the multiplication between the exponential and hopping matrices seems to scale badly.

This needs to be investigated and fixed, without affecting the performance for many k-points on small models too much.

Factor out HDF5 serialization

Can use fsc.hdf5_io once it is published.

Real space Eigenfunctions

Dear Developers,
Thanks for making the code available for users.

May I ask if it is possible to obtain real-space eigenfunctions from wannier90 output using TB models?

Thanks in advance!