corrected DM and simmetric exchange in printing

src/grogu_magn/useful.py

@@ -223,7 +223,7 @@ 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, np.concatenate([J_ii[:2] - J_ii.sum() / 3, J_S]).flatten(), D
 
 
 def print_atomic_indices(pair, magnetic_entities, dh):

test.ipynb

@@ -9,7 +9,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "[Mac:47146] shmem: mmap: an error occurred while determining whether or not /var/folders/yh/dx7xl94n3g52ts3td8qcxjcc0000gn/T//ompi.Mac.501/jf.0/4070375424/sm_segment.Mac.501.f29d0000.0 could be created.\n"
+      "[Mac:47319] shmem: mmap: an error occurred while determining whether or not /var/folders/yh/dx7xl94n3g52ts3td8qcxjcc0000gn/T//ompi.Mac.501/jf.0/1258881024/sm_segment.Mac.501.4b090000.0 could be created.\n"
      ]
     }
    ],
@@ -61,7 +61,7 @@
     "# we can have some default for this\n",
     "ref_xcf_orientations = [\n",
     "    dict(o=np.array([1, 0, 0]), vw=[np.array([0, 1, 0]), np.array([0, 0, 1])]),\n",
-    "    dict(o=np.array([0, 1, 0]), vw=[np.array([0, 0, 1]), np.array([1, 0, 0])]),\n",
+    "    dict(o=np.array([0, 1, 0]), vw=[np.array([1, 0, 1]), np.array([0, 0, 1])]),\n",
     "    dict(o=np.array([0, 0, 1]), vw=[np.array([1, 0, 0]), np.array([0, 1, 0])]),\n",
     "]\n",
     "\n",
@@ -122,7 +122,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -213,6 +213,46 @@
     "H_and_XCF_time = timer()"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "84"
+      ]
+     },
+     "execution_count": 7,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "NO"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "(3, 81, 84, 84)"
+      ]
+     },
+     "execution_count": 6,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "XCF.shape"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 4,
@@ -223,25 +263,29 @@
     "for i, mag_ent in enumerate(magnetic_entities):\n",
     "    parsed = parse_magnetic_entity(dh, **mag_ent)  # parse orbital indexes\n",
     "    magnetic_entities[i][\"orbital_indeces\"] = parsed\n",
+    "    # calculate spin box indexes\n",
     "    magnetic_entities[i][\"spin_box_indeces\"] = blow_up_orbindx(\n",
     "        parsed\n",
-    "    )  # calculate spin box indexes\n",
+    "    )\n",
+    "    # calculate size for Greens function generation\n",
     "    spin_box_shape = len(\n",
     "        mag_ent[\"spin_box_indeces\"]\n",
-    "    )  # calculate size for Greens function generation\n",
+    "    )\n",
     "\n",
     "    mag_ent[\"energies\"] = []  # we will store the second order energy derivations here\n",
     "\n",
     "    mag_ent[\"Gii\"] = []  # Greens function\n",
     "    mag_ent[\"Gii_tmp\"] = []  # Greens function for parallelization\n",
+    "    # These will be the perturbed potentials from eq. 100\n",
     "    mag_ent[\"Vu1\"] = [\n",
     "        list([]) for _ in range(len(ref_xcf_orientations))\n",
-    "    ]  # These will be the perturbed potentials from eq. 100\n",
+    "    ]\n",
     "    mag_ent[\"Vu2\"] = [list([]) for _ in range(len(ref_xcf_orientations))]\n",
     "    for i in ref_xcf_orientations:\n",
+    "        # Greens functions for every quantization axis\n",
     "        mag_ent[\"Gii\"].append(\n",
     "            np.zeros((eset, spin_box_shape, spin_box_shape), dtype=\"complex128\")\n",
-    "        )  # Greens functions for every quantization axis\n",
+    "        )\n",
     "        mag_ent[\"Gii_tmp\"].append(\n",
     "            np.zeros((eset, spin_box_shape, spin_box_shape), dtype=\"complex128\")\n",
     "        )\n",
@@ -249,11 +293,13 @@
     "# for every site we have to store 2x3 Greens function (and the associated _tmp-s)\n",
     "# in the 3 reference directions, because G_ij and G_ji are both needed\n",
     "for pair in pairs:\n",
-    "    spin_box_shape_i, spin_box_shape_j = len(\n",
+    "    # calculate size for Greens function generation\n",
+    "    spin_box_shape_i = len(\n",
     "        magnetic_entities[pair[\"ai\"]][\"spin_box_indeces\"]\n",
-    "    ), len(\n",
+    "    )\n",
+    "    spin_box_shape_j = len(\n",
     "        magnetic_entities[pair[\"aj\"]][\"spin_box_indeces\"]\n",
-    "    )  # calculate size for Greens function generation\n",
+    "    )\n",
     "\n",
     "    pair[\"energies\"] = []  # we will store the second order energy derivations here\n",
     "\n",