changed pre-commit

.gitignore

@@ -20,7 +20,7 @@ docs/source/api/generated
 
 # Debug
 tmp*
-.coverage
+*.coverage
 
 # Mac stuff
 *.DS_Store*

.pre-commit-config.yaml

@@ -22,16 +22,16 @@ repos:
   hooks:
   - id: isort
     args: ["--profile", "black", "--filter-files"]
-- repo: https://github.com/psf/black-pre-commit-mirror
-  rev: 24.4.2
-  hooks:
-  - id: black
-    language_version: python3.9
-- repo: local
-  hooks:
-    - id: pytest-check
-      name: pytest-check
-      entry: ./.venv/bin/pytest
-      language: system
-      pass_filenames: false
-      always_run: true
+#- repo: https://github.com/psf/black-pre-commit-mirror
+#  rev: 24.4.2
+#  hooks:
+#  - id: black
+#    language_version: python3.9
+#- repo: local
+#  hooks:
+#    - id: pytest-check
+#      name: pytest-check
+#      entry: ./.venv/bin/pytest
+#      language: system
+#      pass_filenames: false
+#      always_run: true

README.md

@@ -2,21 +2,28 @@
 
 # TODO
 
-[x] Definition of magnetic entities:
+- Definition of magnetic entities:
     * Through simple sequence o forbitals in the unit cell
     * Through atom specification
     * Through atom and orbital specification
-[x] Separation of TR and TRB components of the Hamiltonian, Identification of the exchange field.
-[x] Definition of commutator expressions, old projection matrix elements
-[x] Efficient calculation of Green's functions
-[] Calculation of energy and momentum resolved derivatives
-[] Parallel BZ and serial energy integral
+- Separation of TR and TRB components of the Hamiltonian, Identification of the exchange field.
+- Definition of commutator expressions, old projection matrix elements
+- Efficient calculation of Green's functions
+- Calculation of energy and momentum resolved derivatives
+- Parallel BZ and serial energy integral
 
 # Building wheel
-https://packaging.python.org/en/latest/tutorials/packaging-projects/
+See detailed documentation on [PYPI](https://packaging.python.org/en/latest/tutorials/packaging-projects/).
 
+Use the following commands for a quick setup:
 
-Build wheel: python -m build
+- Build wheel
+```
+python -m build
+
+```
+
+Build wheel:
 
 Push to pypi(testpypi for beginners): python3 -m twine upload --repository testpypi dist/*
 
@@ -25,4 +32,3 @@ You will be prompted for a username and password. For the username, use __token_
 
 
 Végfelhasználóknak (egyelőre testpypi): python3 -m pip install --index-url https://test.pypi.org/simple/ example-package-YOUR-USERNAME-HERE
-

lat3_791/Fe.psf

@@ -2829,4 +2829,3 @@
   0.159623499658E-47  0.394685762244E-48  0.959152537476E-49  0.229037992853E-49
   0.537289950000E-50  0.123783348782E-50  0.280097688343E-51  0.624177220781E-52
   0.136516118863E-52  0.292975523658E-53  0.616797664740E-54
-

lat3_791/Fe3GeTe2.ORB_INDX

@@ -6823,4 +6823,3 @@ spec = Atomic species label
  isc = Unit cell indexes to which orbital belongs:
        center(io) = center(iuo) + sum_(i=1:3) cell_vec(i) * isc(i)
  iuo = Equivalent orbital in first unit cell
- 

lat3_791/Fe3GeTe2.bib

@@ -21,4 +21,3 @@
   issue = {086005},
   doi = {10.1088/0953-8984/24/8/086005},
 }
-

lat3_791/Fe3GeTe2.times

@@ -72,4 +72,3 @@ Tot.tot: total CPU time in all programs in one node
 Nod.avg: average calculation time in one program across nodes
 Nod.max: maximum calculation time in one program across nodes
 Calculation time: CPU time excluding communications
-

lat3_791/TIMES

@@ -72,4 +72,3 @@ Tot.tot: total CPU time in all programs in one node
 Nod.avg: average calculation time in one program across nodes
 Nod.max: maximum calculation time in one program across nodes
 Calculation time: CPU time excluding communications
- 

src/grogu/useful.py

@@ -223,7 +223,8 @@ def calculate_exchange_tensor(pair):
     J_ii = np.array([o2[-1], o3[0], o1[0]])  # xx, yy, zz
     J_S = -0.5 * np.array([o3[1] + o3[2], o2[1] + o2[1], o1[1] + o1[2]])  # yz, zx, xy
     D = 0.5 * np.array([o1[1] - o1[2], o2[2] - o2[1], o3[1] - o3[2]])  # x, y, z
-    return J_ii.sum() / 3, D, np.concatenate([J_ii[:2] - J_ii.sum()/3, J_S]).flatten()
+    return J_ii.sum() / 3, D, np.concatenate([J_ii[:2] - J_ii.sum() / 3, J_S]).flatten()
+
 
 def print_atomic_indices(pair, magnetic_entities, dh):
     atomic_indices = ""
@@ -231,17 +232,27 @@ def print_atomic_indices(pair, magnetic_entities, dh):
     if "l" not in atoms.keys():
         atoms["l"] = "all"
     if isinstance(atoms["atom"], int):
-        atomic_indices += f"[{atoms['atom']}]{dh.atoms[atoms['atom']].tag}({atoms['l']})"
+        atomic_indices += (
+            f"[{atoms['atom']}]{dh.atoms[atoms['atom']].tag}({atoms['l']})"
+        )
     if isinstance(atoms, list):
-        atomic_indices += [f"[{atoms['atom']}]{dh.atoms[atom['atom']].tag}({atom['l']})" for atom in atoms["atom"]]
+        atomic_indices += [
+            f"[{atoms['atom']}]{dh.atoms[atom['atom']].tag}({atom['l']})"
+            for atom in atoms["atom"]
+        ]
     atoms = magnetic_entities[pair["aj"]]
     if "l" not in atoms.keys():
         atoms["l"] = "all"
     atomic_indices += "    "
     if isinstance(atoms["atom"], int):
-        atomic_indices += f"[{atoms['atom']}]{dh.atoms[atoms['atom']].tag}({atoms['l']})"
+        atomic_indices += (
+            f"[{atoms['atom']}]{dh.atoms[atoms['atom']].tag}({atoms['l']})"
+        )
     if isinstance(atoms, list):
-        atomic_indices += [f"[{atoms['atom']}]{dh.atoms[atom['atom']].tag}({atom['l']})" for atom in atoms["atom"]]
+        atomic_indices += [
+            f"[{atoms['atom']}]{dh.atoms[atom['atom']].tag}({atom['l']})"
+            for atom in atoms["atom"]
+        ]
 
     atomic_indices += f"    {pair['Ruc']}    d [Ang] Not yet."
     return atomic_indices

test.py

@@ -1,27 +1,28 @@
 import os
 from sys import stdout
-from tqdm import tqdm
 from timeit import default_timer as timer
 
+from tqdm import tqdm
+
 os.environ["OMP_NUM_THREADS"] = "1"  # export OMP_NUM_THREADS=4
 os.environ["OPENBLAS_NUM_THREADS"] = "1"  # export OPENBLAS_NUM_THREADS=4
 os.environ["MKL_NUM_THREADS"] = "1"  # export MKL_NUM_THREADS=6
 os.environ["VECLIB_MAXIMUM_THREADS"] = "1"  # export VECLIB_MAXIMUM_THREADS=4
 os.environ["NUMEXPR_NUM_THREADS"] = "1"  # export NUMEXPR_NUM_THREADS=6
 
+import warnings
+
 import numpy as np
 import sisl
-from grogu.useful import *
 from mpi4py import MPI
 from numpy.linalg import inv
-import warnings
+
+from grogu.useful import *
 
 start_time = timer()
 
 # this cell mimicks an input file
-fdf = sisl.get_sile(
-    "./lat3_791/Fe3GeTe2.fdf"
-)
+fdf = sisl.get_sile("./lat3_791/Fe3GeTe2.fdf")
 # this information needs to be given at the input!!
 scf_xcf_orientation = np.array([0, 0, 1])  # z
 # list of reference directions for around which we calculate the derivatives
@@ -35,22 +36,22 @@ ref_xcf_orientations = [
 ]
 
 # human readable definition of magnetic entities
-#magnetic_entities = [
+# magnetic_entities = [
 #    dict(atom=0, ),
 #    dict(atom=1, ),
 #    dict(atom=2, ),
 #    dict(atom=3, l=2),
 #    dict(atom=4, l=2),
 #    dict(atom=5, l=2),
-#]
-#pairs = [
+# ]
+# pairs = [
 #    dict(ai=3, aj=4, Ruc=np.array([0, 0, 0])),  # isotropic should be -82 meV
 #    dict(ai=3, aj=5, Ruc=np.array([0, 0, 0])),  # these should all be around -41.9 in the isotropic part
 #    dict(ai=4, aj=5, Ruc=np.array([0, 0, 0])),
 #    dict(ai=3, aj=0, Ruc=np.array([0, 0, 0])),
 #    dict(ai=3, aj=1, Ruc=np.array([0, 0, 0])),
 #    dict(ai=3, aj=2, Ruc=np.array([0, 0, 0])),
-#]
+# ]
 magnetic_entities = [
     dict(atom=3, l=2),
     dict(atom=4, l=2),
@@ -60,7 +61,9 @@ magnetic_entities = [
 # pair information
 pairs = [
     dict(ai=0, aj=1, Ruc=np.array([0, 0, 0])),  # isotropic should be -82 meV
-    dict(ai=0, aj=2, Ruc=np.array([0, 0, 0])),  # these should all be around -41.9 in the isotropic part
+    dict(
+        ai=0, aj=2, Ruc=np.array([0, 0, 0])
+    ),  # these should all be around -41.9 in the isotropic part
     dict(ai=1, aj=2, Ruc=np.array([0, 0, 0])),
     dict(ai=0, aj=1, Ruc=np.array([-1, 0, 0])),
     dict(ai=0, aj=2, Ruc=np.array([-1, 0, 0])),
@@ -89,15 +92,17 @@ root_node = 0
 if rank == root_node:
     print("Number of nodes in the parallel cluster: ", size)
 
-simulation_parameters = dict(path="Not yet specified.",
-                             scf_xcf_orientation=scf_xcf_orientation, 
-                             ref_xcf_orientations=ref_xcf_orientations,
-                             kset=kset,
-                             kdirs=kdirs, 
-                             ebot=ebot,
-                             eset=eset, 
-                             esetp=esetp,
-                             parallel_size=size)
+simulation_parameters = dict(
+    path="Not yet specified.",
+    scf_xcf_orientation=scf_xcf_orientation,
+    ref_xcf_orientations=ref_xcf_orientations,
+    kset=kset,
+    kdirs=kdirs,
+    ebot=ebot,
+    eset=eset,
+    esetp=esetp,
+    parallel_size=size,
+)
 
 # digestion of the input
 # read in hamiltonian
@@ -265,7 +270,7 @@ site_and_pair_dictionaries_time = timer()
 kset = make_kset(dirs=kdirs, NUMK=kset)  # generate k space sampling
 wkset = np.ones(len(kset)) / len(kset)  # generate weights for k points
 kpcs = np.array_split(kset, size)  # split the k points based on MPI size
-kpcs[root_node] = tqdm(kpcs[root_node], desc='k loop', file=stdout)
+kpcs[root_node] = tqdm(kpcs[root_node], desc="k loop", file=stdout)
 
 k_set_time = timer()
 
@@ -411,43 +416,66 @@ if rank == root_node:
 
     end_time = timer()
 
-    print("############################### GROGU OUTPUT ###################################")
-    print("================================================================================")
+    print(
+        "############################### GROGU OUTPUT ###################################"
+    )
+    print(
+        "================================================================================"
+    )
     print("Input file: ")
     print(simulation_parameters["path"])
-    print("Number of nodes in the parallel cluster: ", simulation_parameters["parallel_size"])
-    print("================================================================================")
+    print(
+        "Number of nodes in the parallel cluster: ",
+        simulation_parameters["parallel_size"],
+    )
+    print(
+        "================================================================================"
+    )
     try:
         print("Cell [Ang]: ")
         print(simulation_parameters["geom"].cell)
     except:
         print("Geometry could not be read.")
-    print("================================================================================")
+    print(
+        "================================================================================"
+    )
     print("DFT axis: ")
     print(simulation_parameters["scf_xcf_orientation"])
     print("Quantization axis and perpendicular rotation directions:")
     for ref in ref_xcf_orientations:
         print(ref["o"], " --» ", ref["vw"])
-    print("================================================================================")
+    print(
+        "================================================================================"
+    )
     print("number of k points: ", simulation_parameters["kset"])
     print("k point directions: ", simulation_parameters["kdirs"])
-    print("================================================================================")
+    print(
+        "================================================================================"
+    )
     print("Parameters for the contour integral:")
     print("Ebot: ", simulation_parameters["ebot"])
     print("Eset: ", simulation_parameters["eset"])
     print("Esetp: ", simulation_parameters["esetp"])
-    print("================================================================================")
+    print(
+        "================================================================================"
+    )
     print("Atomic informations: ")
     print("")
     print("")
     print("Not yet specified.")
     print("")
     print("")
-    print("================================================================================")
+    print(
+        "================================================================================"
+    )
     print("Exchange [meV]")
-    print("--------------------------------------------------------------------------------")
+    print(
+        "--------------------------------------------------------------------------------"
+    )
     print("Atom1    Atom2   [i  j  k]   d [Ang]")
-    print("--------------------------------------------------------------------------------")
+    print(
+        "--------------------------------------------------------------------------------"
+    )
     for pair in pairs:
         J_iso, J_S, D = calculate_exchange_tensor(pair)
         J_iso = J_iso * sisl.unit_convert("eV", "meV")
@@ -460,14 +488,28 @@ if rank == root_node:
         print("Symmetric-anisotropy: ", J_S)
         print("")
 
-    print("================================================================================")
+    print(
+        "================================================================================"
+    )
     print("Runtime information: ")
     print("Total runtime: ", end_time - start_time)
-    print("--------------------------------------------------------------------------------")
+    print(
+        "--------------------------------------------------------------------------------"
+    )
     print("Initial setup: ", setup_time - start_time)
-    print(f"Hamiltonian conversion and XC field extraction: {H_and_XCF_time - setup_time:.3f} s")
-    print(f"Pair and site datastructure creatrions: {site_and_pair_dictionaries_time - H_and_XCF_time:.3f} s")
-    print(f"k set cration and distribution: {k_set_time - site_and_pair_dictionaries_time:.3f} s")
+    print(
+        f"Hamiltonian conversion and XC field extraction: {H_and_XCF_time - setup_time:.3f} s"
+    )
+    print(
+        f"Pair and site datastructure creatrions: {site_and_pair_dictionaries_time - H_and_XCF_time:.3f} s"
+    )
+    print(
+        f"k set cration and distribution: {k_set_time - site_and_pair_dictionaries_time:.3f} s"
+    )
     print(f"Rotating XC potential: {reference_rotations_time - k_set_time:.3f} s")
-    print(f"Greens function inversion: {green_function_inversion_time - reference_rotations_time:.3f} s")
-    print(f"Calculate energies and magnetic components: {end_time - green_function_inversion_time:.3f} s")
+    print(
+        f"Greens function inversion: {green_function_inversion_time - reference_rotations_time:.3f} s"
+    )
+    print(
+        f"Calculate energies and magnetic components: {end_time - green_function_inversion_time:.3f} s"
+    )