From b4549fe5b20cc035b4d0ce4a00d455ca22a06e1c Mon Sep 17 00:00:00 2001 From: Daniel Pozsar Date: Sat, 9 Nov 2024 14:40:53 +0100 Subject: [PATCH] now we have a working documentation --- README.md | 9 +- docs/_build/doctrees/grogupy.doctree | Bin 134083 -> 0 bytes .../doctrees/implementation/index.doctree | Bin 6981 -> 0 bytes docs/_build/html/_sources/environment.rst.txt | 2 - docs/_build/html/_sources/grogupy.rst.txt | 53 -- .../_sources/implementation/index.rst.txt | 11 - docs/_build/html/environment.html | 131 --- docs/_build/html/grogupy.html | 822 ------------------ docs/_build/html/modules.html | 179 ---- docs/_build/html/objects.inv | Bin 1171 -> 0 bytes docs/_build/html/searchindex.js | 1 - docs/environment.rst | 2 - docs/grogupy.rst | 53 -- docs/implementation/index.rst | 11 - docs/{ => source}/Makefile | 0 .../_build/doctrees/bibliography.doctree | Bin .../_build/doctrees/changelog/index.doctree | Bin .../{ => source}/_build/doctrees/cite.doctree | Bin 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(72%) rename docs/{ => source}/index.rst (92%) rename docs/{ => source}/introduction.rst (100%) create mode 100644 docs/source/make.bat rename docs/{ => source}/quickstart/index.rst (100%) rename docs/{ => source}/tutorials/index.rst (100%) diff --git a/README.md b/README.md index fd35883..c355a29 100644 --- a/README.md +++ b/README.md @@ -55,9 +55,16 @@ pre-commit install pre-commit run --all-files ``` -To build the documentation navigate to the `docs/source` folder and run `make clean` and `make html`. After this the html page can be found in `docs/source/_build/html`. +To build the documentation navigate to the `docs/source` folder. Then autogenerate the documentation and build. After this the html page can be found in `docs/source/_build/html`. Follow the commands below. ``` cd docs/source +sphinx-apidoc -o ./implementation/ ../../src/ make clean make html ``` +To build a pdf containing the documentation instead of make, first navigate to the `docs/source` folde, then use the rst2pdf extension. +``` +cd docs/source +sphinx-apidoc -o ./implementation/ ../../src/ +sphinx-build -b pdf . _build/pdf +``` diff --git a/docs/_build/doctrees/grogupy.doctree b/docs/_build/doctrees/grogupy.doctree deleted file mode 100644 index bd66d0938fc9ea47dd0029f962f9850daf88c2cd..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 134083 zcmeHw3!EHBd8hSQNxOPkk|kS~C6DEYM)GQ9%a#Gz0vie2vasw(0u00~vpcPwY0b_I z^N_R(c8tx#BF*arh5rQ$#gphFD|NE+{tGcGU zrh9f*>)ahbyz1$$uj;Gs`|7Lj`&V`KJp->>aMrxD=zqb=X1!Fdo*XF@i`81uYj%Pq z#oBm#(yO*QukCDoQRl8sJ{W8iPBd%n#<5aF_wQ5LS8YnF)ExxmpFAW9*t#Yg48IOXM6OGzLyFQhx7sihjCcF+6MahLnypzO2 zcY&951Xqjd1@O@7lvV|Uqao9!1;HZ8>%m}QrCjwo2is$XV5rb)HOgb{7WzniT2L-F 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-===================== \ No newline at end of file diff --git a/docs/_build/html/_sources/grogupy.rst.txt b/docs/_build/html/_sources/grogupy.rst.txt deleted file mode 100644 index 18af50d..0000000 --- a/docs/_build/html/_sources/grogupy.rst.txt +++ /dev/null @@ -1,53 +0,0 @@ -grogupy package -=============== - -Submodules ----------- - -grogupy.core module -------------------- - -.. automodule:: grogupy.core - :members: - :undoc-members: - :show-inheritance: - -grogupy.grogu module --------------------- - -.. automodule:: grogupy.grogu - :members: - :undoc-members: - :show-inheritance: - -grogupy.io module ------------------ - -.. automodule:: grogupy.io - :members: - :undoc-members: - :show-inheritance: - -grogupy.magnetism module ------------------------- - -.. automodule:: grogupy.magnetism - :members: - :undoc-members: - :show-inheritance: - -grogupy.utilities module ------------------------- - -.. automodule:: grogupy.utilities - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: grogupy - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/_build/html/_sources/implementation/index.rst.txt b/docs/_build/html/_sources/implementation/index.rst.txt deleted file mode 100644 index cca03c6..0000000 --- a/docs/_build/html/_sources/implementation/index.rst.txt +++ /dev/null @@ -1,11 +0,0 @@ -Implementation -============== - -.. autosummary:: - :toctree: generated - :recursive: - - core - magnetism - utilities - io \ No newline at end of file diff --git a/docs/_build/html/environment.html b/docs/_build/html/environment.html deleted file mode 100644 index 2875f2c..0000000 --- a/docs/_build/html/environment.html +++ /dev/null @@ -1,131 +0,0 @@ - - - - - - - - - Environment variables — grogupy 1.0.0 documentation - - - - - - - - - - - - - - - - - - - -
- - -
- -
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- -
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- -
-

Environment variables

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- - -
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-
- - - - \ No newline at end of file diff --git a/docs/_build/html/grogupy.html b/docs/_build/html/grogupy.html deleted file mode 100644 index 5b2878f..0000000 --- a/docs/_build/html/grogupy.html +++ /dev/null @@ -1,822 +0,0 @@ - - - - - - - - - grogupy package — grogupy 1.0.0 documentation - - - - - - - - - - - - - - - - - -
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- -
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grogupy package

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-

Submodules

-
-
-

grogupy.core module

-
-
-grogupy.core.build_hh_ss(dh)[source]
-

It builds the Hamiltonian and Overlap matrix from the sisl.dh class.

-

It restructures the data in the SPIN BOX representation, where NS is -the number of supercells and NO is the number of orbitals.

-
-
Parameters:
-

dh – sisl.physics.Hamiltonian -Hamiltonian read in by sisl

-
-
Returns:
-

-
(NS, NO, NO) np.array_like

Hamiltonian in SPIN BOX representation

-
-
ss(NS, NO, NO) np.array_like

Overlap matrix in SPIN BOX representation

-
-
-

-
-
Return type:
-

hh

-
-
-
- -
-
-grogupy.core.calc_Vu(H, Tu)[source]
-

Calculates the local perturbation in case of a spin rotation.

-
-
Parameters:
-
    -

  • H – (NO, NO) np.array_like -Hamiltonian

    • -

  • Tu – (NO, NO) array_like -Rotation around u

    • -
-
-
Returns:
-

-
(NO, NO) np.array_like

First order perturbed matrix

-
-
Vu2(NO, NO) np.array_like

Second order perturbed matrix

-
-
-

-
-
Return type:
-

Vu1

-
-
-
- -
-
-grogupy.core.onsite_projection(matrix, idx1, idx2)[source]
-

It produces the slices of a matrix for the on site projection.

-

The slicing is along the last two axes as these contains the orbital indexing.

-
-
Parameters:
-
    -

  • matrix – (…, :, :) np.array_like -Some matrix

    • -

  • idx – np.array_like -The indexes of the orbitals

    • -
-
-
Returns:
-

-
np.array_like

Reduced matrix based on the projection

-
-
-

-
-
-
- -
-
-grogupy.core.parallel_Gk(HK, SK, eran, eset)[source]
-

Calculates the Greens function by inversion.

-

It calculates the Greens function on all the energy levels at the same time.

-
-
Parameters:
-
    -

  • HK – (NO, NO), np.array_like -Hamiltonian at a given k point

    • -

  • SK – (NO, NO), np.array_like -Overlap Matrix at a given k point

    • -

  • eran – (eset) np.array_like -Energy sample along the contour

    • -

  • eset – int -Number of energy samples along the contour

    • -
-
-
Returns:
-

-
(eset, NO, NO), np.array_like

Green’s function at a given k point

-
-
-

-
-
Return type:
-

Gk

-
-
-
- -
-
-grogupy.core.remove_clutter_for_save(pairs, magnetic_entities)[source]
-

Removes unimportant data from the dictionaries.

-

It is used before saving to throw away data that -is not needed for post processing.

-
-
Parameters:
-
    -

  • pairs – dict -Contains all the pair information

    • -

  • magnetic_entities – dict -Contains all the magnetic entity information

    • -
-
-
Returns:
-

-
dict

Contains all the reduced pair information

-
-
magnetic_entitiesdict

Contains all the reduced magnetic entity information

-
-
-

-
-
Return type:
-

pairs

-
-
-
- -
-
-grogupy.core.sequential_GK(HK, SK, eran, eset)[source]
-

Calculates the Greens function by inversion.

-

It calculates sequentially over the energy levels.

-
-
Parameters:
-
    -

  • HK – (NO, NO), np.array_like -Hamiltonian at a given k point

    • -

  • SK – (NO, NO), np.array_like -Overlap Matrix at a given k point

    • -

  • eran – (eset) np.array_like -Energy sample along the contour

    • -

  • eset – int -Number of energy samples along the contour

    • -
-
-
Returns:
-

-
(eset, NO, NO), np.array_like

Green’s function at a given k point

-
-
-

-
-
Return type:
-

Gk

-
-
-
- -
-
-grogupy.core.setup_pairs_and_magnetic_entities(magnetic_entities, pairs, dh, simulation_parameters)[source]
-

It creates the complete structure of the dictionaries and fills some basic data.

-

It creates orbital indexes, spin box indexes, coordinates and tags for magnetic entities. -Furthermore it creates the structures for the energies, the perturbed potentials and -the Greens function calculation. It dose the same for the pairs.

-
-
Parameters:
-
    -

  • pairs – dict -Contains the initial pair information

    • -

  • magnetic_entities – dict -Contains the initial magnetic entity information

    • -

  • dh – sisl.physics.Hamiltonian -Hamiltonian read in by sisl

    • -

  • simulation_parameters – dict -A set of parameters from the simulation

    • -
-
-
Returns:
-

-
dict

Contains the initial information and the complete structure

-
-
magnetic_entitiesdict

Contains the initial information and the complete structure

-
-
-

-
-
Return type:
-

pairs

-
-
-
- -
-
-

grogupy.grogu module

-
-
-grogupy.grogu.main()[source]
-
- -
-
-

grogupy.io module

-
-
-grogupy.io.load_pickle(infile)[source]
-

Loads the data from the infile with pickle.

-
-
Parameters:
-

infile – str -Path to infile

-
-
Returns:
-

-
dict

A dictionary of data

-
-
-

-
-
Return type:
-

data

-
-
-
- -
-
-grogupy.io.print_atoms_and_pairs(magnetic_entities, pairs)[source]
-

It prints the pair and magnetic entity information for the grogu out.

-
-
Parameters:
-
    -

  • magnetic_entities – dict -It contains the data on the magnetic entities

    • -

  • pairs – dict -It contains the data on the pairs

    • -
-
-
-
- -
-
-grogupy.io.print_job_description(simulation_parameters)[source]
-

It prints the parameters and the description of the job.

-
-
Parameters:
-

simulation_parameters – dict -It contains the simulations parameters

-
-
-
- -
-
-grogupy.io.print_parameters(simulation_parameters)[source]
-

It prints the simulation parameters for the grogu out.

-
-
Parameters:
-

simulation_parameters – dict -It contains the simulations parameters

-
-
-
- -
-
-grogupy.io.print_runtime_information(times)[source]
-

It prints the runtime information for the grogu out.

-
-
Parameters:
-

times – dict -It contains the runtime data

-
-
-
- -
-
-grogupy.io.save_pickle(outfile, data)[source]
-

Saves the data in the outfile with pickle.

-
-
Parameters:
-
    -

  • outfile – str -Path to outfile

    • -

  • data – dict -Contains the data

    • -
-
-
-
- -
-
-

grogupy.magnetism module

-
-
-grogupy.magnetism.blow_up_orbindx(orb_indices)[source]
-

Function to blow up orbital indices to make SPIN BOX indices.

-
-
Parameters:
-

orb_indices – np.array_like -These are the indices in ORBITAL BOX

-
-
Returns:
-

-
np.array_like

These are the indices in SPIN BOX

-
-
-

-
-
Return type:
-

orb_indices

-
-
-
- -
-
-grogupy.magnetism.calculate_anisotropy_tensor(mag_ent)[source]
-

Calculates the renormalized anisotropy tensor from the energies.

-

It uses the grogu convention for output.

-
-
Parameters:
-

mag_ent – dict -An element from the magnetic entities

-
-
Returns:
-

-
np.array_like

elements of the anisotropy tensor

-
-
-

-
-
Return type:
-

K

-
-
-
- -
-
-grogupy.magnetism.calculate_exchange_tensor(pair)[source]
-

Calculates the exchange tensor from the energies.

-

It produces the isotropic exchange, the relevant elements -from the Dzyaloshinskii-Morilla (Dm) tensor, the symmetric-anisotropy -and the complete exchange tensor.

-
-
Parameters:
-

pair – dict -An element from the pairs

-
-
Returns:
-

-
float

Isotropic exchange (Tr[J] / 3)

-
-
J_Snp.array_like

Symmetric-anisotropy (J_S = J - J_iso * I ––> Jxx, Jyy, Jxy, Jxz, Jyz)

-
-
Dnp.array_like

DM elements (Dx, Dy, Dz)

-
-
Jnp.array_like

Complete exchange tensor flattened (Jxx, Jxy, Jxz, Jyx, Jyy, Jyz, Jzx, Jzy, Jzz)

-
-
-

-
-
Return type:
-

J_iso

-
-
-
- -
-
-grogupy.magnetism.parse_magnetic_entity(dh, atom=None, l=None, **kwargs)[source]
-

Function to define orbital indexes of a given magnetic entity.

-
-
Parameters:
-
    -

  • dh – sisl.physics.Hamiltonian -Hamiltonian from sisl

    • -

  • atom – integer or list of integers, optional -Defining atom (or atoms) in the unit cell forming the magnetic entity. Defaults to None

    • -

  • l – integer, optional -Defining the angular momentum channel. Defaults to None

    • -
-
-
Returns:
-

-
list

The orbital indexes of the given magnetic entity

-
-
-

-
-
-
- -
-
-grogupy.magnetism.spin_tracer(M)[source]
-

Spin tracer utility.

-

This takes an operator with the orbital-spin sequence: -orbital 1 up, -orbital 1 down, -orbital 2 up, -orbital 2 down, -that is in the SPIN-BOX representation, -and extracts orbital dependent Pauli traces.

-
-
Parameters:
-

M – np.array_like -Traceable matrix

-
-
Returns:
-

-
dict

It contains the traced matrix with “x”, “y”, “z” and “c”

-
-
-

-
-
-
- -
-
-

grogupy.utilities module

-
-
-grogupy.utilities.RotM(theta, u, eps=1e-10)[source]
-

Definition of rotation matrix with angle theta around direction u.

-
-
Parameters:
-
    -

  • theta – float -The angle of rotation

    • -

  • u – np.array_like -The rotation axis

    • -

  • eps – float, optional -Cutoff for small elements in the resulting matrix. Defaults to 1e-10

    • -
-
-
Returns:
-

-
np.array_like

The rotation matrix

-
-
-

-
-
-
- -
-
-grogupy.utilities.RotMa2b(a, b, eps=1e-10)[source]
-

Definition of rotation matrix rotating unit vector a to unit vector b.

-

Function returns array R such that R @ a = b holds.

-
-
Parameters:
-
    -

  • a – np.array_like -First vector

    • -

  • b – np.array_like -Second vector

    • -

  • eps – float, optional -Cutoff for small elements in the resulting matrix. Defaults to 1e-10

    • -
-
-
Returns:
-

-
np.array_like

The rotation matrix with the above property

-
-
-

-
-
-
- -
-
-grogupy.utilities.commutator(a, b)[source]
-

Shorthand for commutator.

-

Commutator of two matrices in the mathematical sense.

-
-
Parameters:
-
    -

  • a – np.array_like -The first matrix

    • -

  • b – np.array_like -The second matrix

    • -
-
-
Returns:
-

-
np.array_like

The commutator of a and b

-
-
-

-
-
-
- -
-
-grogupy.utilities.crossM(u)[source]
-

Definition for the cross-product matrix.

-

It acts as a cross product with vector u.

-
-
Parameters:
-

u – list or np.array_like -The second vector in the cross product

-
-
Returns:
-

-
np.array_like

The matrix that represents teh cross product with a vector

-
-
-

-
-
-
- -
-
-grogupy.utilities.hsk(H, ss, sc_off, k=(0, 0, 0))[source]
-

Speed up Hk and Sk generation.

-

Calculates the Hamiltonian and the Overlap matrix at a given k point. It is faster that the sisl version.

-
-
Parameters:
-
    -

  • H – np.array_like -Hamiltonian in spin box form

    • -

  • ss – np.array_like -Overlap matrix in spin box form

    • -

  • sc_off – list -supercell indexes of the Hamiltonian

    • -

  • k – tuple, optional -The k point where the matrices are set up. Defaults to (0, 0, 0)

    • -
-
-
Returns:
-

-
np.array_like

Hamiltonian at the given k point

-
-
np.array_like

Overlap matrix at the given k point

-
-
-

-
-
-
- -
-
-grogupy.utilities.int_de_ke(traced, we)[source]
-

It numerically integrates the traced matrix.

-

It is a wrapper from numpy.trapz and it contains the -relevant constants to calculate the energy integral from -equation 93 or 96.

-
-
Parameters:
-
    -

  • traced – np.array_like -The trace of a matrix or a matrix product

    • -

  • we – float -The weight of a point on the contour

    • -
-
-
Returns:
-

-
float

The energy calculated from the integral formula

-
-
-

-
-
-
- -
-
-grogupy.utilities.make_contour(emin=-20, emax=0.0, enum=42, p=150)[source]
-

A more sophisticated contour generator.

-

Calculates the parameters for the complex contour integral. It uses the -Legendre-Gauss quadrature method. It returns a class that contains -the information for the contour integral.

-
-
Parameters:
-
    -

  • emin – int, optional -Energy minimum of the contour. Defaults to -20

    • -

  • emax – float, optional -Energy maximum of the contour. Defaults to 0.0, so the Fermi level

    • -

  • enum – int, optional -Number of sample points along the contour. Defaults to 42

    • -

  • p – int, optional -Shape parameter that describes the distribution of the sample points. Defaults to 150

    • -
-
-
Returns:
-

-
ccont

Contains all the information for the contour integral

-
-
-

-
-
-
- -
-
-grogupy.utilities.make_kset(dirs='xyz', NUMK=20)[source]
-

Simple k-grid generator to sample the Brillouin zone.

-

Depending on the value of the dirs -argument k sampling in 1,2 or 3 dimensions is generated. -If dirs argument does not contain either of x, y or z -a kset of a single k-pont at the origin is returned. The total number of k points is the NUMK**(dimensions)

-
-
Parameters:
-
    -

  • dirs – str, optional -Directions of the k points in the Brillouin zone. They are the three lattice vectors. Defaults to “xyz”

    • -

  • NUMK – int, optional -The number of k points in a direction. Defaults to 20

    • -
-
-
Returns:
-

-
np.array_like

An array of k points that uniformly sample the Brillouin zone in the given directions

-
-
-

-
-
-
- -
-
-grogupy.utilities.read_siesta_emin(eigfile)[source]
-

It reads the lowest energy level from the siesta run.

-

It uses the .EIG file from siesta that contains the eigenvalues.

-
-
Parameters:
-

eigfile – str -The path to the .EIG file

-
-
Returns:
-

-
float

The energy minimum

-
-
-

-
-
-
- -
-
-grogupy.utilities.tau_u(u)[source]
-

Pauli matrix in direction u.

-

Returns the vector u in the basis of the Pauli matrices.

-
-
Parameters:
-

u – list or np.array_like -The direction

-
-
Returns:
-

-
np.array_like

Arbitrary direction in the base of the Pauli matrices

-
-
-

-
-
-
- -
-
-

Module contents

-
-
- - -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/docs/_build/html/modules.html b/docs/_build/html/modules.html deleted file mode 100644 index 188f37d..0000000 --- a/docs/_build/html/modules.html +++ /dev/null @@ -1,179 +0,0 @@ - - - - - - - - - grogupy — grogupy 1.0.0 documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
- -
- -
-
-
-
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"Environment variables", "grogupy package", "core", "io", "magnetism", "utilities", "Implementation", "grogupy: Script for calculating magnetic interactions", "Introduction", "grogupy", "Quickstart", "Tutorials"], "titleterms": {"bibliographi": 0, "calcul": 11, "changelog": 1, "cite": 2, "command": 12, "content": 5, "contribut": 3, "core": [5, 6], "environ": 4, "grogu": 5, "grogupi": [2, 3, 5, 11, 13], "implement": 10, "indic": 11, "instal": 14, "interact": 11, "introduct": 12, "io": [5, 7], "line": 12, "magnet": [5, 8, 11], "modul": 5, "packag": [5, 12], "quickstart": 14, "script": 11, "submodul": 5, "tabl": 11, "tutori": 15, "usag": 12, "util": [5, 9], "variabl": 4}}) \ No newline at end of file diff --git a/docs/environment.rst b/docs/environment.rst deleted file mode 100644 index 73ff15a..0000000 --- a/docs/environment.rst +++ /dev/null @@ -1,2 +0,0 @@ -Environment variables -===================== \ No newline at end of file diff --git a/docs/grogupy.rst b/docs/grogupy.rst deleted file mode 100644 index 18af50d..0000000 --- a/docs/grogupy.rst +++ /dev/null @@ -1,53 +0,0 @@ -grogupy package -=============== - -Submodules ----------- - -grogupy.core module -------------------- - -.. automodule:: grogupy.core - :members: - :undoc-members: - :show-inheritance: - -grogupy.grogu module --------------------- - -.. automodule:: grogupy.grogu - :members: - :undoc-members: - :show-inheritance: - -grogupy.io module ------------------ - -.. automodule:: grogupy.io - :members: - :undoc-members: - :show-inheritance: - -grogupy.magnetism module ------------------------- - -.. automodule:: grogupy.magnetism - :members: - :undoc-members: - :show-inheritance: - -grogupy.utilities module ------------------------- - -.. automodule:: grogupy.utilities - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: grogupy - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/implementation/index.rst b/docs/implementation/index.rst deleted file mode 100644 index cca03c6..0000000 --- a/docs/implementation/index.rst +++ /dev/null @@ -1,11 +0,0 @@ -Implementation -============== - -.. autosummary:: - :toctree: generated - :recursive: - - core - magnetism - utilities - io \ No newline at end of file diff --git a/docs/Makefile b/docs/source/Makefile similarity index 100% rename from docs/Makefile rename to docs/source/Makefile diff --git a/docs/_build/doctrees/bibliography.doctree b/docs/source/_build/doctrees/bibliography.doctree similarity index 100% rename from docs/_build/doctrees/bibliography.doctree rename to docs/source/_build/doctrees/bibliography.doctree diff --git a/docs/_build/doctrees/changelog/index.doctree b/docs/source/_build/doctrees/changelog/index.doctree similarity index 100% rename from docs/_build/doctrees/changelog/index.doctree rename to docs/source/_build/doctrees/changelog/index.doctree diff --git a/docs/_build/doctrees/cite.doctree 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similarity index 100% rename from docs/_build/doctrees/introduction.doctree rename to docs/source/_build/doctrees/introduction.doctree diff --git a/docs/_build/doctrees/quickstart/index.doctree b/docs/source/_build/doctrees/quickstart/index.doctree similarity index 100% rename from docs/_build/doctrees/quickstart/index.doctree rename to docs/source/_build/doctrees/quickstart/index.doctree diff --git a/docs/_build/doctrees/tutorials/index.doctree b/docs/source/_build/doctrees/tutorials/index.doctree similarity index 100% rename from docs/_build/doctrees/tutorials/index.doctree rename to docs/source/_build/doctrees/tutorials/index.doctree diff --git a/docs/_build/html/.buildinfo b/docs/source/_build/html/.buildinfo similarity index 100% rename from docs/_build/html/.buildinfo rename to docs/source/_build/html/.buildinfo diff --git a/docs/_build/html/_modules/grogupy/core.html b/docs/source/_build/html/_modules/grogupy/core.html similarity index 98% rename from docs/_build/html/_modules/grogupy/core.html rename to docs/source/_build/html/_modules/grogupy/core.html index 8ff4288..5ebd162 100644 --- a/docs/_build/html/_modules/grogupy/core.html +++ b/docs/source/_build/html/_modules/grogupy/core.html @@ -53,8 +53,9 @@

Advanced usage

Development

    @@ -119,7 +120,7 @@
    -[docs] +[docs] def parallel_Gk(HK, SK, eran, eset): """Calculates the Greens function by inversion. @@ -146,7 +147,7 @@
    -[docs] +[docs] def sequential_GK(HK, SK, eran, eset): """Calculates the Greens function by inversion. @@ -178,7 +179,7 @@
    -[docs] +[docs] def calc_Vu(H, Tu): """Calculates the local perturbation in case of a spin rotation. @@ -203,7 +204,7 @@
    -[docs] +[docs] def remove_clutter_for_save(pairs, magnetic_entities): """Removes unimportant data from the dictionaries. @@ -240,7 +241,7 @@
    -[docs] +[docs] def build_hh_ss(dh): """It builds the Hamiltonian and Overlap matrix from the sisl.dh class. @@ -299,7 +300,7 @@ [ U.T
    -[docs] +[docs] @ np.block([[h11[:, :, i], h12[:, :, i]], [h21[:, :, i], h22[:, :, i]]]) @ U for i in range(dh.lattice.nsc.prod()) @@ -474,7 +475,7 @@
    -[docs] +[docs] def onsite_projection(matrix, idx1, idx2): """It produces the slices of a matrix for the on site projection. diff --git a/docs/_build/html/_modules/grogupy/grogu.html b/docs/source/_build/html/_modules/grogupy/grogu.html similarity index 99% rename from docs/_build/html/_modules/grogupy/grogu.html rename to docs/source/_build/html/_modules/grogupy/grogu.html index bad6d5c..233f699 100644 --- a/docs/_build/html/_modules/grogupy/grogu.html +++ b/docs/source/_build/html/_modules/grogupy/grogu.html @@ -53,8 +53,9 @@

Advanced usage

Development

    @@ -140,7 +141,7 @@
    -[docs] +[docs] def main(): # runtime information times = dict() diff --git a/docs/_build/html/_modules/grogupy/io.html b/docs/source/_build/html/_modules/grogupy/io.html similarity index 98% rename from docs/_build/html/_modules/grogupy/io.html rename to docs/source/_build/html/_modules/grogupy/io.html index 5794a71..96ec00d 100644 --- a/docs/_build/html/_modules/grogupy/io.html +++ b/docs/source/_build/html/_modules/grogupy/io.html @@ -53,8 +53,9 @@

Advanced usage

Development

    @@ -149,7 +150,7 @@
    -[docs] +[docs] def save_pickle(outfile, data): """Saves the data in the outfile with pickle. @@ -167,7 +168,7 @@
    -[docs] +[docs] def load_pickle(infile): """Loads the data from the infile with pickle. @@ -189,7 +190,7 @@

Advanced usage

Development

    @@ -115,7 +116,7 @@
    -[docs] +[docs] def blow_up_orbindx(orb_indices): """Function to blow up orbital indices to make SPIN BOX indices. @@ -135,7 +136,7 @@
    -[docs] +[docs] def spin_tracer(M): """Spin tracer utility. @@ -172,7 +173,7 @@
    -[docs] +[docs] def parse_magnetic_entity(dh, atom=None, l=None, **kwargs): """Function to define orbital indexes of a given magnetic entity. @@ -214,7 +215,7 @@
    -[docs] +[docs] def calculate_anisotropy_tensor(mag_ent): """Calculates the renormalized anisotropy tensor from the energies. @@ -247,7 +248,7 @@
    -[docs] +[docs] def calculate_exchange_tensor(pair): """Calculates the exchange tensor from the energies. diff --git a/docs/_build/html/_modules/grogupy/utilities.html b/docs/source/_build/html/_modules/grogupy/utilities.html similarity index 96% rename from docs/_build/html/_modules/grogupy/utilities.html rename to docs/source/_build/html/_modules/grogupy/utilities.html index c7f9775..54e615b 100644 --- a/docs/_build/html/_modules/grogupy/utilities.html +++ b/docs/source/_build/html/_modules/grogupy/utilities.html @@ -53,8 +53,9 @@

Advanced usage

Development

    @@ -123,7 +124,7 @@
    -[docs] +[docs] def commutator(a, b): """Shorthand for commutator. @@ -146,7 +147,7 @@ # define some useful functions
    -[docs] +[docs] def hsk(H, ss, sc_off, k=(0, 0, 0)): """Speed up Hk and Sk generation. @@ -185,7 +186,7 @@
    -[docs] +[docs] def make_kset(dirs="xyz", NUMK=20): """Simple k-grid generator to sample the Brillouin zone. @@ -226,7 +227,7 @@
    -[docs] +[docs] def make_contour(emin=-20, emax=0.0, enum=42, p=150): """A more sophisticated contour generator. @@ -275,7 +276,7 @@
    -[docs] +[docs] def tau_u(u): """Pauli matrix in direction u. @@ -299,7 +300,7 @@ #
    -[docs] +[docs] def crossM(u): """Definition for the cross-product matrix. @@ -318,7 +319,7 @@
    -[docs] +[docs] def RotM(theta, u, eps=1e-10): """Definition of rotation matrix with angle theta around direction u. @@ -351,7 +352,7 @@
    -[docs] +[docs] def RotMa2b(a, b, eps=1e-10): """Definition of rotation matrix rotating unit vector a to unit vector b. @@ -381,7 +382,7 @@
    -[docs] +[docs] def read_siesta_emin(eigfile): """It reads the lowest energy level from the siesta run. @@ -404,7 +405,7 @@
    -[docs] +[docs] def int_de_ke(traced, we): """It numerically integrates the traced matrix. diff --git a/docs/_build/html/_modules/index.html b/docs/source/_build/html/_modules/index.html similarity index 94% rename from docs/_build/html/_modules/index.html rename to docs/source/_build/html/_modules/index.html index 420bb05..a4ed5c4 100644 --- a/docs/_build/html/_modules/index.html +++ b/docs/source/_build/html/_modules/index.html @@ -53,8 +53,9 @@

Advanced usage

Development

    diff --git a/docs/_build/html/_sources/bibliography.rst.txt b/docs/source/_build/html/_sources/bibliography.rst.txt similarity index 100% rename from docs/_build/html/_sources/bibliography.rst.txt rename to docs/source/_build/html/_sources/bibliography.rst.txt diff --git a/docs/_build/html/_sources/changelog/index.rst.txt b/docs/source/_build/html/_sources/changelog/index.rst.txt similarity index 100% rename from docs/_build/html/_sources/changelog/index.rst.txt rename to docs/source/_build/html/_sources/changelog/index.rst.txt diff --git a/docs/_build/html/_sources/cite.rst.txt b/docs/source/_build/html/_sources/cite.rst.txt similarity index 100% rename from docs/_build/html/_sources/cite.rst.txt rename to docs/source/_build/html/_sources/cite.rst.txt diff --git a/docs/_build/html/_sources/dev/index.rst.txt b/docs/source/_build/html/_sources/dev/index.rst.txt similarity index 100% rename from docs/_build/html/_sources/dev/index.rst.txt rename to docs/source/_build/html/_sources/dev/index.rst.txt diff --git a/docs/source/_build/html/_sources/implementation/environment.rst.txt b/docs/source/_build/html/_sources/implementation/environment.rst.txt new file mode 100644 index 0000000..d1d7b99 --- /dev/null +++ b/docs/source/_build/html/_sources/implementation/environment.rst.txt @@ -0,0 +1,4 @@ +Environment variables +===================== + +Coming soon... \ No newline at end of file diff --git a/docs/source/_build/html/_sources/implementation/grogupy.core.rst.txt b/docs/source/_build/html/_sources/implementation/grogupy.core.rst.txt new file mode 100644 index 0000000..0634729 --- /dev/null +++ b/docs/source/_build/html/_sources/implementation/grogupy.core.rst.txt @@ -0,0 +1,7 @@ +grogupy.core module +=================== + +.. automodule:: grogupy.core + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/_build/html/_sources/implementation/grogupy.grogu.rst.txt b/docs/source/_build/html/_sources/implementation/grogupy.grogu.rst.txt new file mode 100644 index 0000000..c51783a --- /dev/null +++ b/docs/source/_build/html/_sources/implementation/grogupy.grogu.rst.txt @@ -0,0 +1,7 @@ +grogupy.grogu module +==================== + +.. automodule:: grogupy.grogu + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/_build/html/_sources/implementation/grogupy.io.rst.txt b/docs/source/_build/html/_sources/implementation/grogupy.io.rst.txt new file mode 100644 index 0000000..b0f4f60 --- /dev/null +++ b/docs/source/_build/html/_sources/implementation/grogupy.io.rst.txt @@ -0,0 +1,7 @@ +grogupy.io module +================= + +.. automodule:: grogupy.io + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/_build/html/_sources/implementation/grogupy.magnetism.rst.txt b/docs/source/_build/html/_sources/implementation/grogupy.magnetism.rst.txt new file mode 100644 index 0000000..a510e36 --- /dev/null +++ b/docs/source/_build/html/_sources/implementation/grogupy.magnetism.rst.txt @@ -0,0 +1,7 @@ +grogupy.magnetism module +======================== + +.. automodule:: grogupy.magnetism + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/_build/html/_sources/implementation/grogupy.rst.txt b/docs/source/_build/html/_sources/implementation/grogupy.rst.txt new file mode 100644 index 0000000..211bd28 --- /dev/null +++ b/docs/source/_build/html/_sources/implementation/grogupy.rst.txt @@ -0,0 +1,22 @@ +grogupy package +=============== + +Submodules +---------- + +.. toctree:: + :maxdepth: 4 + + grogupy.core + grogupy.grogu + grogupy.io + grogupy.magnetism + grogupy.utilities + +Module contents +--------------- + +.. automodule:: grogupy + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/_build/html/_sources/implementation/grogupy.utilities.rst.txt b/docs/source/_build/html/_sources/implementation/grogupy.utilities.rst.txt new file mode 100644 index 0000000..d4b00f7 --- /dev/null +++ b/docs/source/_build/html/_sources/implementation/grogupy.utilities.rst.txt @@ -0,0 +1,7 @@ +grogupy.utilities module +======================== + +.. automodule:: grogupy.utilities + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/_build/html/_sources/modules.rst.txt b/docs/source/_build/html/_sources/implementation/modules.rst.txt similarity index 72% rename from docs/_build/html/_sources/modules.rst.txt rename to docs/source/_build/html/_sources/implementation/modules.rst.txt index c13cb18..b5811a9 100644 --- a/docs/_build/html/_sources/modules.rst.txt +++ b/docs/source/_build/html/_sources/implementation/modules.rst.txt @@ -1,5 +1,5 @@ -grogupy -======= +src +=== .. toctree:: :maxdepth: 4 diff --git a/docs/_build/html/_sources/index.rst.txt b/docs/source/_build/html/_sources/index.rst.txt similarity index 92% rename from docs/_build/html/_sources/index.rst.txt rename to docs/source/_build/html/_sources/index.rst.txt index e4aad29..8e9e8ea 100644 --- a/docs/_build/html/_sources/index.rst.txt +++ b/docs/source/_build/html/_sources/index.rst.txt @@ -28,7 +28,7 @@ More on the theoretical background can be seen `here

    Advanced usage

    Development

      diff --git a/docs/_build/html/changelog/index.html b/docs/source/_build/html/changelog/index.html similarity index 95% rename from docs/_build/html/changelog/index.html rename to docs/source/_build/html/changelog/index.html index d08fe18..9a8a458 100644 --- a/docs/_build/html/changelog/index.html +++ b/docs/source/_build/html/changelog/index.html @@ -56,8 +56,9 @@

    Advanced usage

    Development

      diff --git a/docs/_build/html/cite.html b/docs/source/_build/html/cite.html similarity index 95% rename from docs/_build/html/cite.html rename to docs/source/_build/html/cite.html index 665370d..c3d7bdb 100644 --- a/docs/_build/html/cite.html +++ b/docs/source/_build/html/cite.html @@ -56,8 +56,9 @@

    Advanced usage

    Development

      diff --git a/docs/_build/html/dev/index.html b/docs/source/_build/html/dev/index.html similarity index 89% rename from docs/_build/html/dev/index.html rename to docs/source/_build/html/dev/index.html index e525ccb..9b5adfb 100644 --- a/docs/_build/html/dev/index.html +++ b/docs/source/_build/html/dev/index.html @@ -22,7 +22,7 @@ - + @@ -56,8 +56,9 @@

    Advanced usage

    Development

      @@ -102,7 +103,7 @@
      diff --git a/docs/_build/html/genindex.html b/docs/source/_build/html/genindex.html similarity index 59% rename from docs/_build/html/genindex.html rename to docs/source/_build/html/genindex.html index 2171a36..7e8d1b9 100644 --- a/docs/_build/html/genindex.html +++ b/docs/source/_build/html/genindex.html @@ -53,8 +53,9 @@

    Advanced usage

    Development

    @@ -175,21 +168,21 @@ grogupy.io
  • grogupy.magnetism
  • grogupy.utilities
@@ -198,7 +191,7 @@

H

@@ -206,24 +199,15 @@

I

-

L

@@ -231,42 +215,27 @@

M

@@ -275,7 +244,7 @@

O

@@ -283,19 +252,19 @@

P

@@ -303,15 +272,15 @@

R

@@ -319,15 +288,15 @@

S

@@ -335,24 +304,11 @@

T

-

U

- - -
    -
  • - utilities - -
    • -
- diff --git a/docs/source/_build/html/implementation/environment.html b/docs/source/_build/html/implementation/environment.html new file mode 100644 index 0000000..8be167f --- /dev/null +++ b/docs/source/_build/html/implementation/environment.html @@ -0,0 +1,133 @@ + + + + + + + + + Environment variables — grogupy 1.0.0 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Environment variables

+

Coming soon…

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/docs/source/_build/html/implementation/grogupy.core.html b/docs/source/_build/html/implementation/grogupy.core.html new file mode 100644 index 0000000..eee07d1 --- /dev/null +++ b/docs/source/_build/html/implementation/grogupy.core.html @@ -0,0 +1,322 @@ + + + + + + + + + grogupy.core module — grogupy 1.0.0 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

grogupy.core module

+
+
+grogupy.core.build_hh_ss(dh)[source]
+

It builds the Hamiltonian and Overlap matrix from the sisl.dh class.

+

It restructures the data in the SPIN BOX representation, where NS is +the number of supercells and NO is the number of orbitals.

+
+
Args:
+
dhsisl.physics.Hamiltonian

Hamiltonian read in by sisl

+
+
+
+
Returns:
+
hh(NS, NO, NO) np.array_like

Hamiltonian in SPIN BOX representation

+
+
ss(NS, NO, NO) np.array_like

Overlap matrix in SPIN BOX representation

+
+
+
+
+
+ +
+
+grogupy.core.calc_Vu(H, Tu)[source]
+

Calculates the local perturbation in case of a spin rotation.

+
+
Args:
+
H(NO, NO) np.array_like

Hamiltonian

+
+
Tu(NO, NO) array_like

Rotation around u

+
+
+
+
Returns:
+
Vu1(NO, NO) np.array_like

First order perturbed matrix

+
+
Vu2(NO, NO) np.array_like

Second order perturbed matrix

+
+
+
+
+
+ +
+
+grogupy.core.onsite_projection(matrix, idx1, idx2)[source]
+

It produces the slices of a matrix for the on site projection.

+

The slicing is along the last two axes as these contains the orbital indexing.

+
+
Args:
+
matrix(…, :, :) np.array_like

Some matrix

+
+
idxnp.array_like

The indexes of the orbitals

+
+
+
+
Returns:
+
np.array_like

Reduced matrix based on the projection

+
+
+
+
+
+ +
+
+grogupy.core.parallel_Gk(HK, SK, eran, eset)[source]
+

Calculates the Greens function by inversion.

+

It calculates the Greens function on all the energy levels at the same time.

+
+
Args:
+
HK(NO, NO), np.array_like

Hamiltonian at a given k point

+
+
SK(NO, NO), np.array_like

Overlap Matrix at a given k point

+
+
eran(eset) np.array_like

Energy sample along the contour

+
+
esetint

Number of energy samples along the contour

+
+
+
+
Returns:
+
Gk(eset, NO, NO), np.array_like

Green’s function at a given k point

+
+
+
+
+
+ +
+
+grogupy.core.remove_clutter_for_save(pairs, magnetic_entities)[source]
+

Removes unimportant data from the dictionaries.

+

It is used before saving to throw away data that +is not needed for post processing.

+
+
Args:
+
pairsdict

Contains all the pair information

+
+
magnetic_entitiesdict

Contains all the magnetic entity information

+
+
+
+
Returns:
+
pairsdict

Contains all the reduced pair information

+
+
magnetic_entitiesdict

Contains all the reduced magnetic entity information

+
+
+
+
+
+ +
+
+grogupy.core.sequential_GK(HK, SK, eran, eset)[source]
+

Calculates the Greens function by inversion.

+

It calculates sequentially over the energy levels.

+
+
Args:
+
HK(NO, NO), np.array_like

Hamiltonian at a given k point

+
+
SK(NO, NO), np.array_like

Overlap Matrix at a given k point

+
+
eran(eset) np.array_like

Energy sample along the contour

+
+
esetint

Number of energy samples along the contour

+
+
+
+
Returns:
+
Gk(eset, NO, NO), np.array_like

Green’s function at a given k point

+
+
+
+
+
+ +
+
+grogupy.core.setup_pairs_and_magnetic_entities(magnetic_entities, pairs, dh, simulation_parameters)[source]
+

It creates the complete structure of the dictionaries and fills some basic data.

+

It creates orbital indexes, spin box indexes, coordinates and tags for magnetic entities. +Furthermore it creates the structures for the energies, the perturbed potentials and +the Greens function calculation. It dose the same for the pairs.

+
+
Args:
+
pairsdict

Contains the initial pair information

+
+
magnetic_entitiesdict

Contains the initial magnetic entity information

+
+
dhsisl.physics.Hamiltonian

Hamiltonian read in by sisl

+
+
simulation_parametersdict

A set of parameters from the simulation

+
+
+
+
Returns:
+
pairsdict

Contains the initial information and the complete structure

+
+
magnetic_entitiesdict

Contains the initial information and the complete structure

+
+
+
+
+
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/docs/_build/html/implementation/index.html b/docs/source/_build/html/implementation/grogupy.grogu.html similarity index 60% rename from docs/_build/html/implementation/index.html rename to docs/source/_build/html/implementation/grogupy.grogu.html index f93de93..4b837a4 100644 --- a/docs/_build/html/implementation/index.html +++ b/docs/source/_build/html/implementation/grogupy.grogu.html @@ -6,7 +6,7 @@ - Implementation — grogupy 1.0.0 documentation + grogupy.grogu module — grogupy 1.0.0 documentation @@ -21,8 +21,8 @@ - - + + @@ -56,14 +56,23 @@

Advanced usage

    -
  • Implementation

    Development

    Advanced usage

    Development

      @@ -116,7 +117,7 @@ More on the theoretical background can be seen

      Detailed description of the implementation.

      -      Implementation +src diff --git a/docs/_build/html/introduction.html b/docs/source/_build/html/introduction.html similarity index 95% rename from docs/_build/html/introduction.html rename to docs/source/_build/html/introduction.html index 7b18686..aca00ec 100644 --- a/docs/_build/html/introduction.html +++ b/docs/source/_build/html/introduction.html @@ -60,8 +60,9 @@

    Advanced usage

    Development

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    Advanced usage

    Development

    Advanced usage

    Development

      diff --git a/docs/_build/html/search.html b/docs/source/_build/html/search.html similarity index 94% rename from docs/_build/html/search.html rename to docs/source/_build/html/search.html index f37e780..7c8a514 100644 --- a/docs/_build/html/search.html +++ b/docs/source/_build/html/search.html @@ -56,8 +56,9 @@

    Advanced usage

    Development

      diff --git a/docs/source/_build/html/searchindex.js b/docs/source/_build/html/searchindex.js new file mode 100644 index 0000000..3a44374 --- /dev/null +++ b/docs/source/_build/html/searchindex.js @@ -0,0 +1 @@ +Search.setIndex({"alltitles": {"Bibliography": [[0, null]], "Changelog": [[1, null]], "Citing grogupy": [[2, null]], "Command line usage": [[13, "command-line-usage"]], "Contributing to grogupy": [[3, null]], "Environment variables": [[4, null]], "Indices and tables": [[12, "indices-and-tables"]], "Introduction": [[13, null]], "Module contents": [[5, "module-grogupy"]], "Package": [[13, "package"]], "Quickstart": [[14, null]], "Submodules": [[5, "submodules"]], "Tutorials": [[15, null]], "grogupy package": [[5, null]], "grogupy.core module": [[6, null]], "grogupy.grogu module": [[7, null]], "grogupy.io module": [[8, null]], "grogupy.magnetism module": [[9, null]], "grogupy.utilities module": [[10, null]], "grogupy: Script for calculating magnetic interactions": [[12, 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similarity index 90% rename from docs/_build/html/tutorials/index.html rename to docs/source/_build/html/tutorials/index.html index e86f153..2460333 100644 --- a/docs/_build/html/tutorials/index.html +++ b/docs/source/_build/html/tutorials/index.html @@ -21,7 +21,7 @@ - + @@ -56,8 +56,9 @@

    Advanced usage

    Development

      @@ -103,7 +104,7 @@