corrected Vij Vji storage

src/grogu_magn/grogu.py

@@ -1,26 +1,16 @@
+import warnings
+from sys import stdout
+from timeit import default_timer as timer
+
+import numpy as np
+import sisl
+from mpi4py import MPI
+from numpy.linalg import inv
+from tqdm import tqdm
 from useful import *
 
 
 def main():
-    import os
-    from sys import stdout
-    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 mpi4py import MPI
-    from numpy.linalg import inv
-
     start_time = timer()
 
     # this cell mimicks an input file
@@ -54,10 +44,36 @@ def main():
     #    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),
+    #    dict(atom=5, l=2),
+    # ]
+
+    # 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=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])),
+    #    dict(ai=0, aj=1, Ruc=np.array([1, 0, 0])),
+    #    dict(ai=0, aj=2, Ruc=np.array([1, 0, 0])),
+    #    dict(ai=0, aj=1, Ruc=np.array([0, -1, 0])),
+    #    dict(ai=0, aj=2, Ruc=np.array([0, -1, 0])),
+    #    dict(ai=0, aj=1, Ruc=np.array([0, 1, 0])),
+    #    dict(ai=0, aj=2, Ruc=np.array([0, 1, 0])),
+    #    dict(ai=1, aj=2, Ruc=np.array([-1, 0, 0])),
+    # ]
     magnetic_entities = [
         dict(atom=3, l=2),
         dict(atom=4, l=2),
         dict(atom=5, l=2),
+        dict(
+            atom=[3, 4],
+        ),
     ]
 
     # pair information
@@ -67,22 +83,15 @@ def main():
             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])),
-        dict(ai=0, aj=1, Ruc=np.array([1, 0, 0])),
-        dict(ai=0, aj=2, Ruc=np.array([1, 0, 0])),
-        dict(ai=0, aj=1, Ruc=np.array([0, -1, 0])),
-        dict(ai=0, aj=2, Ruc=np.array([0, -1, 0])),
-        dict(ai=0, aj=1, Ruc=np.array([0, 1, 0])),
-        dict(ai=0, aj=2, Ruc=np.array([0, 1, 0])),
         dict(ai=1, aj=2, Ruc=np.array([-1, 0, 0])),
     ]
 
     # Brilloun zone sampling and Green function contour integral
-    kset = 20
+    kset = 100
     kdirs = "xy"
     ebot = -30
-    eset = 50
+    eset = 100
     esetp = 1000
 
     # MPI parameters
@@ -250,12 +259,6 @@ def main():
         pair["Gji"] = []
         pair["Gij_tmp"] = []  # Greens function for parallelization
         pair["Gji_tmp"] = []
-
-        pair["Vij"] = [
-            list([]) for _ in range(len(ref_xcf_orientations))
-        ]  # These will be the perturbed potentials from eq. 100
-        pair["Vji"] = [list([]) for _ in range(len(ref_xcf_orientations))]
-
         for i in ref_xcf_orientations:
             pair["Gij"].append(
                 np.zeros((eset, spin_box_shape_i, spin_box_shape_j), dtype="complex128")
@@ -315,16 +318,6 @@ def main():
                     Vu2[:, mag_ent["spin_box_indeces"]][mag_ent["spin_box_indeces"], :]
                 )
 
-            for pair in pairs:
-                ai = magnetic_entities[pair["ai"]][
-                    "spin_box_indeces"
-                ]  # get the pair orbital sizes from the magnetic entities
-                aj = magnetic_entities[pair["aj"]]["spin_box_indeces"]
-                pair["Vij"][i].append(
-                    Vu1[:, ai][aj, :]
-                )  # fill up the perturbed potentials (for now) based on the on-site projections
-                pair["Vji"][i].append(Vu1[:, aj][ai, :])
-
     reference_rotations_time = timer()
 
     if rank == root_node: