still looking for bug

README.md

@@ -18,6 +18,8 @@ More on the theoretical background can be seen on [arXiv](https://arxiv.org/abs/
 - Add more tests!!
 - io stuff
 - logging
+- fdf atom input
+- orbital indexing must be correct
 
 # Building wheel
 See detailed documentation on [PYPI](https://packaging.python.org/en/latest/tutorials/packaging-projects/).

input.fdf

@@ -12,6 +12,7 @@ ScfXcfOrientation  [ 0   0   1 ] # comment test
 
 %block MagneticEntities  # comment test
 Cluster 4 5                   # this is a list of atoms
+Atom 3                        # this MUST BE one atom else error
 AtomShell 3 2                 # this is one atom and shell index
 AtomShell 4 2 3               # this is one atom and shell index
 AtomShell 5 2                 # this is one atom and shell index

src/grogupy/__init__.py

@@ -20,3 +20,9 @@
 
 """Docstring in init.
 """
+
+from grogupy.core import *
+from grogupy.globals import *
+from grogupy.io import *
+from grogupy.magnetism import *
+from grogupy.utilities import *

src/grogupy/grogu.py

@@ -48,11 +48,7 @@ except:
     tqdm_imported = False
 
 
-from .core import *
-from .globals import *
-from .io import *
-from .magnetism import *
-from .utilities import *
+from grogupy import *
 
 
 def parse_command_line():
@@ -166,7 +162,7 @@ def main(simulation_parameters, magnetic_entities, pairs):
     if simulation_parameters["ebot"] is None:
         try:
             eigfile = simulation_parameters["infile"][:-3] + "EIG"
-            simulation_parameters["ebot"] = read_siesta_emin(eigfile) - 1
+            simulation_parameters["ebot"] = read_siesta_emin(eigfile) - 0.1
             simulation_parameters["automatic_ebot"] = True
         except:
             print("Could not determine ebot.")
@@ -347,7 +343,7 @@ def main(simulation_parameters, magnetic_entities, pairs):
                 f"Total number of matrix inversions: {kset.shape[0] * len(hamiltonians) * simulation_parameters['eset']}"
             )
             print(
-                f"The shape of the Hamiltonian and the Greens function is {NO}x{NO}={NO*NO}"
+                f"The shape of the Hamiltonian and the Greens function is {2*NO}x{2*NO}={4*NO*NO}"
             )
             # https://stackoverflow.com/questions/70746660/how-to-predict-memory-requirement-for-np-linalg-inv
             # memory is O(64 n**2) for complex matrices
@@ -357,7 +353,7 @@ def main(simulation_parameters, magnetic_entities, pairs):
             )
             print(f"Expected memory usage per matrix inversion: {memory_size * 32} KB")
             print(
-                f"Expected memory usage per k point for parallel inversion: {memory_size * len(hamiltonians) * simulation_parameters['eset'] * 32} KB"
+                f"Expected memory usage per k point for parallel inversion: {memory_size * 32 * len(hamiltonians) * simulation_parameters['eset']} KB"
             )
             print(
                 f"Expected memory usage on root node: {len(np.array_split(kset, size)[0]) * memory_size * len(hamiltonians) * simulation_parameters['eset'] * 32 / 1024} MB"
@@ -549,7 +545,9 @@ if __name__ == "__main__":
         dict(ai=1, aj=2, Ruc=np.array([-3, 0, 0])),
     ]
     simulation_parameters = dict()
-    simulation_parameters["infile"] = ""
+    simulation_parameters["infile"] = (
+        "/Users/danielpozsar/Downloads/nojij/Fe3GeTe2/monolayer/soc/lat3_791/Fe3GeTe2.fdf"
+    )
     simulation_parameters["outfile"] = "./"
     simulation_parameters["scf_xcf_orientation"] = np.array([0, 0, 1])
     simulation_parameters["ref_xcf_orientations"] = [
@@ -557,11 +555,11 @@ if __name__ == "__main__":
         dict(o=np.array([0, 1, 0]), vw=[np.array([1, 0, 0]), np.array([0, 0, 1])]),
         dict(o=np.array([0, 0, 1]), vw=[np.array([1, 0, 0]), np.array([0, 1, 0])]),
     ]
-    simulation_parameters["kset"] = 0
-    simulation_parameters["kdirs"] = ""
+    simulation_parameters["kset"] = 10
+    simulation_parameters["kdirs"] = "xy"
     simulation_parameters["ebot"] = None
-    simulation_parameters["eset"] = 0
-    simulation_parameters["esetp"] = 0
+    simulation_parameters["eset"] = 600
+    simulation_parameters["esetp"] = 1000
     simulation_parameters["parallel_solver_for_Gk"] = False
     simulation_parameters["padawan_mode"] = True
     ####################################################################################################

src/grogupy/io.py

@@ -209,8 +209,8 @@ def load_pickle(infile):
     """
 
     # open and read file
-    with open(infile, "wb") as input_file:
-        data = load(data, input_file)
+    with open(infile, "rb") as input_file:
+        data = load(input_file)
 
     return data
 

test.ipynb

@@ -16,7 +16,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [
     {
@@ -24,14 +24,14 @@
      "output_type": "stream",
      "text": [
       "0.14.3\n",
-      "1.24.4\n"
+      "numpy version unknown.\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "[Mac:30692] shmem: mmap: an error occurred while determining whether or not /var/folders/yh/dx7xl94n3g52ts3td8qcxjcc0000gn/T//ompi.Mac.501/jf.0/6815744/sm_segment.Mac.501.680000.0 could be created.\n"
+      "[Daniels-MacBook-Air.local:40959] shmem: mmap: an error occurred while determining whether or not /var/folders/yh/dx7xl94n3g52ts3td8qcxjcc0000gn/T//ompi.Daniels-MacBook-Air.501/jf.0/3756457984/sm_segment.Daniels-MacBook-Air.501.dfe70000.0 could be created.\n"
      ]
     }
    ],