could not read hamiltonian, tested for a bunch of sisl versions

3 months ago · 8b2afbb555
parent cf0d57d93d
commit 8b2afbb555
5 changed files with 117 additions and 201 deletions
--- a/Fe3GeTe2_3-791lat_short-1.txt
+++ b/Fe3GeTe2_3-791lat_short-1.txt
@ -1,70 +0,0 @@
-========================================
-Cell Angstroms
-3.7910	0.0000	0.0000
-1.8955	3.2831	0.0000
-0.0000	0.0000	20.5700
-========================================
-
-Atom Angstrom
-# Label,        x           y           z          Sx           Sy           Sz         #Q           Lx           Ly           Lz           Jx           Jy           Jz
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-Te1         1.8955      1.0943      13.1698     -0.0000     0.0000      -0.1543    # 5.9345       -0.0000      0.0000       -0.0537      -0.0000      0.0000       -0.2080
-Te2         1.8955      1.0943      7.4002      0.0000      -0.0000     -0.1543    # 5.9345       0.0000       -0.0000      -0.0537      0.0000       -0.0000      -0.2080
-Ge3         -0.0000     2.1887      10.2850     0.0000      0.0000      -0.1605    # 3.1927       -0.0000      0.0000       0.0012       0.0000       0.0000       -0.1593
-Fe4         -0.0000     0.0000      11.6576     0.0001      -0.0001     2.0466     # 8.3044       0.0000       -0.0000      0.1606       0.0001       -0.0001      2.2072
-Fe5         -0.0000     0.0000      8.9124      -0.0001     0.0001      2.0466     # 8.3044       -0.0000      0.0000       0.1606       -0.0001      0.0001       2.2072
-Fe6         1.8955      1.0944      10.2850     0.0000      0.0000      1.5824     # 8.3296       -0.0000      -0.0000      0.0520       -0.0000      0.0000       1.6344
-==================================================================================================================================
-
-Exchange meV
--------------------------------------------------------------------------------
-# at1     at2   i  j  k    #    d (Ang)
--------------------------------------------------------------------------------
-Fe4     Fe5     0  0  0    #    2.7452
-Isotropic -82.0854
-DMI 0.12557 -0.00082199  6.9668e-08
-Symmetric-anisotropy -0.60237    -0.83842 -0.00032278 -1.2166e-05 -3.3923e-05
--------------------------------------------------------------------------------
-Fe4     Fe6     0  0  0    #    2.5835
-Isotropic -41.9627
-DMI 1.1205     -1.9532   0.0018386
-Symmetric-anisotropy 0.26007 -0.00013243     0.12977   -0.069979   -0.042066
--------------------------------------------------------------------------------
-Fe4     Fe4     1  0  0    #    3.791
-Isotropic 11.3817
-DMI -0.027065      5.0079      1.2495
-Symmetric-anisotropy 0.25899     0.61356  0.00018352 -8.2489e-06   -0.059116
--------------------------------------------------------------------------------
-Fe4     Fe5     1  0  0    #    4.6806
-Isotropic -2.9464
-DMI 1.7   0.0069825      6.4657
-Symmetric-anisotropy 0.44323    0.056997  1.7739e-05     0.14942   1.077e-05
--------------------------------------------------------------------------------
-Fe4     Fe6     1  0  0    #    5.9513
-Isotropic -1.9722
-DMI -0.044414     0.34777     0.55124
-Symmetric-anisotropy 0.19364    -0.10179   -0.057654    0.023297    0.033722
--------------------------------------------------------------------------------
-Fe4     Fe4     2  0  0    #    7.582
-Isotropic -2.5085
-DMI 0.015126    0.020638    -0.26104
-Symmetric-anisotropy -0.145   -0.021424   6.948e-05  3.0356e-05    -0.18409
-================================================================================
-
-On-site meV
----------------------------------------
-Fe4
-0.16339	0.16068	0	0	0	0
-========================================
-
-# ----------------------GROGU INFORMATION----------------------
-# Grogu calculation was performed with a k-grid equal to  100  100    1
-# On-site Projection is performed over l = 2
-# Original DFT calculation with quantization axis along the z direction
-
-Notation
-Double-counting  true
-Spin-normalized  true
-Exchange-factor  0.5
-On-site-factor   1
-========================================
--- a/pyproject.toml
+++ b/pyproject.toml
@ -20,8 +20,8 @@ kewords = [
 requires-python = ">=3.9"
 dependencies = [
  "numpy==1.24.4",
-  "scipy",
-  "sisl==0.14.3",
+  "scipy==1.10.1",
+  "sisl==0.13",
  "netcdf4==1.6.2",
  "openmpi",
  "mpi4py",
--- a/requirements.txt
+++ b/requirements.txt
@ -1,7 +1,7 @@
 # Package dependencies
 numpy==1.24.4
 scipy==1.10.1
-sisl==0.14.1
+sisl==0.13
 netcdf4==1.6.2
 openmpi
 mpi4py
--- a/simmetries.txt
+++ b/simmetries.txt
@ -1,120 +0,0 @@
-Number of nodes in the parallel cluster:  4
-
k loop:   0% 0/100 [00:00<?, ?it/s]
k loop:   0% 0/100 [00:00<?, ?it/s]
k loop:   0% 0/100 [00:00<?, ?it/s]
k loop:   0% 0/100 [00:00<?, ?it/s]Number of magnetic entities being calculated:  3
-We have to calculate the Greens function for three reference direction and we are going to calculate 15 energy integrals per site.
-The shape of the Hamiltonian and the Greens function is 84x84.
-
k loop:   1% 1/100 [00:00<01:34,  1.05it/s]
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k loop: 100% 100/100 [00:37<00:00,  2.65it/s]
k loop: 100% 100/100 [00:37<00:00,  2.69it/s]
-############################### GROGU OUTPUT ###################################
-================================================================================
-Input file:
-Not yet specified.
-Number of nodes in the parallel cluster:  4
-================================================================================
-Cell [Ang]:
-[[ 3.79100000e+00  0.00000000e+00  0.00000000e+00]
- [-1.89550000e+00  3.28310231e+00  0.00000000e+00]
- [ 1.25954923e-15  2.18160327e-15  2.05700000e+01]]
-================================================================================
-DFT axis:
-[0 0 1]
-Quantization axis and perpendicular rotation directions:
-[1 0 0]  --»  [array([0, 1, 0]), array([0, 0, 1])]
-[0 1 0]  --»  [array([1, 0, 0]), array([0, 0, 1])]
-[0 0 1]  --»  [array([1, 0, 0]), array([0, 1, 0])]
-================================================================================
-number of k points:  20
-k point directions:  xy
-================================================================================
-Parameters for the contour integral:
-Ebot:  -30
-Eset:  50
-Esetp:  1000
-================================================================================
-Atomic informations:
-
-
-Not yet specified.
-
-
-================================================================================
-Exchange [meV]
--------------------------------------------------------------------------------
-Atom1    Atom2   [i  j  k]   d [Ang]
--------------------------------------------------------------------------------
-[3]Fe(2)    [4]Fe(2)    [0 0 0]    d [Ang] Not yet.
-Isotropic:  -59.460784608983374
-DMI:  [-7.73155890e+00  1.05962615e+01  2.21680365e-03 -8.54205178e-04
-  1.44527058e-04]
-Symmetric-anisotropy:  [-9.33132578e-01 -1.02533215e-03 -3.10751832e-06]
-
-[3]Fe(2)    [5]Fe(2)    [0 0 0]    d [Ang] Not yet.
-Isotropic:  -60.569416473077176
-DMI:  [-0.38257071  0.66548096  0.07063389 -6.22368411 -0.04236017]
-Symmetric-anisotropy:  [ 3.78638786 -6.13074804  0.00644632]
-
-[4]Fe(2)    [5]Fe(2)    [0 0 0]    d [Ang] Not yet.
-Isotropic:  -60.55753389874924
-DMI:  [-0.36873857  0.65357935  0.07063401  6.23608252  0.03586405]
-Symmetric-anisotropy:  [-3.79781231  6.14756367  0.0064464 ]
-
-[3]Fe(2)    [4]Fe(2)    [-1  0  0]    d [Ang] Not yet.
-Isotropic:  -2.8126561936571113
-DMI:  [-2.13036930e+00  2.12113650e+00 -1.15876881e-03  1.21597832e-03
- -3.82889721e-04]
-Symmetric-anisotropy:  [ 6.06216550e-01  1.65863149e-04 -7.08970077e-06]
-
-[3]Fe(2)    [5]Fe(2)    [-1  0  0]    d [Ang] Not yet.
-Isotropic:  -6.632424073374205
-DMI:  [-0.67789101  0.73512516 -0.03120852  7.69153574  0.03112759]
-Symmetric-anisotropy:  [5.94798961 7.6408739  6.50853286]
-
-[3]Fe(2)    [4]Fe(2)    [1 0 0]    d [Ang] Not yet.
-Isotropic:  -4.7207835764097394
-DMI:  [-2.11695855e-01 -1.88028223e+00  1.05835226e-05 -1.03316787e-03
-  8.36865493e-04]
-Symmetric-anisotropy:  [ 7.63450180e-01 -3.81117143e-04  5.86749095e-06]
-
-[3]Fe(2)    [5]Fe(2)    [1 0 0]    d [Ang] Not yet.
-Isotropic:  -6.214233340151194
-DMI:  [ 4.11507584e-01 -3.77553764e-03 -2.48385400e-02 -4.29528744e+00
-  1.08981268e-01]
-Symmetric-anisotropy:  [-6.15499102 -4.29890748 -6.16472834]
-
-[3]Fe(2)    [4]Fe(2)    [ 0 -1  0]    d [Ang] Not yet.
-Isotropic:  -3.4636353917354374
-DMI:  [ 0.1019479   2.85695253 -0.03948534  0.3670612   0.04783194]
-Symmetric-anisotropy:  [-1.37861735e-02  3.40298270e-01  6.43031013e-06]
-
-[3]Fe(2)    [5]Fe(2)    [ 0 -1  0]    d [Ang] Not yet.
-Isotropic:  -0.16440230179059723
-DMI:  [0.03598949 0.18262092 0.00868944 0.35936314 0.00610426]
-Symmetric-anisotropy:  [-0.34092127  0.35586356  0.00589118]
-
-[3]Fe(2)    [4]Fe(2)    [0 1 0]    d [Ang] Not yet.
-Isotropic:  -5.582632299818422
-DMI:  [ 2.18039489 -1.25058397  0.13106217  0.45989655 -0.05702247]
-Symmetric-anisotropy:  [-9.37614656e-02  4.95671083e-01 -5.31876420e-06]
-
-[3]Fe(2)    [5]Fe(2)    [0 1 0]    d [Ang] Not yet.
-Isotropic:  -0.2565503383305444
-DMI:  [ 0.23312087 -0.42413096 -0.02052235  0.2509258  -0.02076644]
-Symmetric-anisotropy:  [-0.32690519  0.27669077 -0.00562126]
-
-[4]Fe(2)    [5]Fe(2)    [-1  0  0]    d [Ang] Not yet.
-Isotropic:  -6.128256753571549
-DMI:  [ 0.31014172  0.23111069 -0.03120608  4.2460402  -0.09698692]
-Symmetric-anisotropy:  [6.19497698 4.23351577 6.50855465]
-
-================================================================================
-Runtime information:
-Total runtime:  38.489369708
--------------------------------------------------------------------------------
-Initial setup:  0.141595916
-Hamiltonian conversion and XC field extraction: 0.812 s
-Pair and site datastructure creatrions: 0.016 s
-k set cration and distribution: 0.023 s
-Rotating XC potential: 0.509 s
-Greens function inversion: 36.922 s
-Calculate energies and magnetic components: 0.065 s
-
k loop:   0% 0/100 [00:37<?, ?it/s]
-
k loop:   0% 0/100 [00:37<?, ?it/s]
-
k loop:   0% 0/100 [00:37<?, ?it/s]
--- a/test.ipynb
+++ b/test.ipynb
@ -2,9 +2,27 @@
 "cells": [
  {
   "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
   "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "[Mac:83105] shmem: mmap: an error occurred while determining whether or not /var/folders/yh/dx7xl94n3g52ts3td8qcxjcc0000gn/T//ompi.Mac.501/jf.0/3811770368/sm_segment.Mac.501.e3330000.0 could be created.\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "'0.13.0'"
+      ]
+     },
+     "execution_count": 1,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
   "source": [
    "import os\n",
    "from sys import stdout\n",
@ -26,14 +44,49 @@
    "\n",
    "# runtime information\n",
    "times = dict()\n",
-    "times[\"start_time\"] = timer()"
+    "times[\"start_time\"] = timer()\n",
+    "########################\n",
+    "# doesnt work with sisl\n",
+    "#\n",
+    "#\n",
+    "#\n",
+    "#'0.13.0'\n",
+    "#'0.14.1'\n",
+    "#'0.14.2'\n",
+    "#'0.14.3'\n",
+    "#'0.15.0'\n",
+    "#'0.15.1'\n",
+    "########################\n",
+    "sisl.__version__"
   ]
  },
  {
   "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
   "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Number of nodes in the parallel cluster:  1\n"
+     ]
+    },
+    {
+     "ename": "TypeError",
+     "evalue": "function takes exactly 5 arguments (1 given)",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[2], line 104\u001b[0m\n\u001b[1;32m     90\u001b[0m simulation_parameters \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mdict\u001b[39m(\n\u001b[1;32m     91\u001b[0m     path\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mNot yet specified.\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m     92\u001b[0m     scf_xcf_orientation\u001b[38;5;241m=\u001b[39mscf_xcf_orientation,\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m     99\u001b[0m     parallel_size\u001b[38;5;241m=\u001b[39msize,\n\u001b[1;32m    100\u001b[0m )\n\u001b[1;32m    102\u001b[0m \u001b[38;5;66;03m# digestion of the input\u001b[39;00m\n\u001b[1;32m    103\u001b[0m \u001b[38;5;66;03m# read in hamiltonian\u001b[39;00m\n\u001b[0;32m--> 104\u001b[0m dh \u001b[38;5;241m=\u001b[39m \u001b[43mfdf\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mread_hamiltonian\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    105\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m    106\u001b[0m     simulation_parameters[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mgeom\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m=\u001b[39m fdf\u001b[38;5;241m.\u001b[39mread_geometry()\n",
+      "File \u001b[0;32m~/Documents/oktatás/elte/phd/grogu_project/.venv/lib/python3.9/site-packages/sisl/io/siesta/fdf.py:2062\u001b[0m, in \u001b[0;36mfdfSileSiesta.read_hamiltonian\u001b[0;34m(self, *args, **kwargs)\u001b[0m\n\u001b[1;32m   2060\u001b[0m order \u001b[38;5;241m=\u001b[39m _listify_str(kwargs\u001b[38;5;241m.\u001b[39mpop(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124morder\u001b[39m\u001b[38;5;124m\"\u001b[39m, [\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mnc\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mTSHS\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mHSX\u001b[39m\u001b[38;5;124m\"\u001b[39m]))\n\u001b[1;32m   2061\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m f \u001b[38;5;129;01min\u001b[39;00m order:\n\u001b[0;32m-> 2062\u001b[0m     H \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mgetattr\u001b[39;49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43mf\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m_r_hamiltonian_\u001b[39;49m\u001b[38;5;132;43;01m{\u001b[39;49;00m\u001b[43mf\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mlower\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;132;43;01m}\u001b[39;49;00m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m   2063\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m H \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m   2064\u001b[0m         _track(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mread_hamiltonian, \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mfound file \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mf\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m)\n",
+      "File \u001b[0;32m~/Documents/oktatás/elte/phd/grogu_project/.venv/lib/python3.9/site-packages/sisl/io/siesta/fdf.py:2094\u001b[0m, in \u001b[0;36mfdfSileSiesta._r_hamiltonian_hsx\u001b[0;34m(self, *args, **kwargs)\u001b[0m\n\u001b[1;32m   2092\u001b[0m H \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m   2093\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m f\u001b[38;5;241m.\u001b[39mis_file():\n\u001b[0;32m-> 2094\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m \u001b[43mhsxSileSiesta\u001b[49m\u001b[43m(\u001b[49m\u001b[43mf\u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mversion\u001b[49m \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m0\u001b[39m:\n\u001b[1;32m   2095\u001b[0m         \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mgeometry\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;129;01min\u001b[39;00m kwargs:\n\u001b[1;32m   2096\u001b[0m             \u001b[38;5;66;03m# to ensure we get the correct orbital count\u001b[39;00m\n\u001b[1;32m   2097\u001b[0m             kwargs[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mgeometry\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mread_geometry(\u001b[38;5;28;01mTrue\u001b[39;00m, order\u001b[38;5;241m=\u001b[39m[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mnc\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mTSHS\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mfdf\u001b[39m\u001b[38;5;124m\"\u001b[39m])\n",
+      "File \u001b[0;32m~/Documents/oktatás/elte/phd/grogu_project/.venv/lib/python3.9/site-packages/sisl/io/siesta/binaries.py:663\u001b[0m, in \u001b[0;36mhsxSileSiesta.version\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    660\u001b[0m \u001b[38;5;129m@property\u001b[39m\n\u001b[1;32m    661\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mversion\u001b[39m(\u001b[38;5;28mself\u001b[39m) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m \u001b[38;5;28mint\u001b[39m:\n\u001b[1;32m    662\u001b[0m \u001b[38;5;250m    \u001b[39m\u001b[38;5;124;03m\"\"\" The version of the file \"\"\"\u001b[39;00m\n\u001b[0;32m--> 663\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43m_siesta\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mread_hsx_version\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mfile\u001b[49m\u001b[43m)\u001b[49m\n",
+      "\u001b[0;31mTypeError\u001b[0m: function takes exactly 5 arguments (1 given)"
+     ]
+    }
+   ],
   "source": [
    "# this cell mimicks an input file\n",
    "fdf = sisl.get_sile(\"./lat3_791/Fe3GeTe2.fdf\")  # ./Jij_for_Marci_6p45ang/CrBr.fdf\n",
@ -61,6 +114,23 @@
    "pairs = [\n",
    "    # isotropic should be -82 meV\n",
    "    dict(ai=0, aj=1, Ruc=np.array([0, 0, 0])),\n",
+    "    dict(ai=0, aj=1, Ruc=np.array([1, 0, 0])),\n",
+    "    dict(ai=0, aj=1, Ruc=np.array([-1, 0, 0])),\n",
+    "    dict(ai=0, aj=1, Ruc=np.array([2, 0, 0])),\n",
+    "    dict(ai=0, aj=1, Ruc=np.array([-2, 0, 0])),\n",
+    "    dict(ai=0, aj=1, Ruc=np.array([0, 1, 0])),\n",
+    "    dict(ai=0, aj=1, Ruc=np.array([0, -1, 0])),\n",
+    "    dict(ai=0, aj=1, Ruc=np.array([0, 2, 0])),\n",
+    "    dict(ai=0, aj=1, Ruc=np.array([0, -2, 0])),\n",
+    "    dict(ai=1, aj=0, Ruc=np.array([0, 0, 0])),\n",
+    "    dict(ai=1, aj=0, Ruc=np.array([1, 0, 0])),\n",
+    "    dict(ai=1, aj=0, Ruc=np.array([-1, 0, 0])),\n",
+    "    dict(ai=1, aj=0, Ruc=np.array([2, 0, 0])),\n",
+    "    dict(ai=1, aj=0, Ruc=np.array([-2, 0, 0])),\n",
+    "    dict(ai=1, aj=0, Ruc=np.array([0, 1, 0])),\n",
+    "    dict(ai=1, aj=0, Ruc=np.array([0, -1, 0])),\n",
+    "    dict(ai=1, aj=0, Ruc=np.array([0, 2, 0])),\n",
+    "    dict(ai=1, aj=0, Ruc=np.array([0, -2, 0])),\n",
    "    # these should all be around -41.9 in the isotropic part\n",
    "    #    dict(ai=0, aj=2, Ruc=np.array([0, 0, 0])),\n",
    "    #    dict(ai=1, aj=2, Ruc=np.array([0, 0, 0])),\n",
@ -137,7 +207,19 @@
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "ename": "NameError",
+     "evalue": "name 'dh' is not defined",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[4], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m NO \u001b[38;5;241m=\u001b[39m \u001b[43mdh\u001b[49m\u001b[38;5;241m.\u001b[39mno  \u001b[38;5;66;03m# shorthand for number of orbitals in the unit cell\u001b[39;00m\n\u001b[1;32m      3\u001b[0m \u001b[38;5;66;03m# preprocessing Hamiltonian and overlap matrix elements\u001b[39;00m\n\u001b[1;32m      4\u001b[0m h11 \u001b[38;5;241m=\u001b[39m dh\u001b[38;5;241m.\u001b[39mtocsr(dh\u001b[38;5;241m.\u001b[39mM11r)\n",
+      "\u001b[0;31mNameError\u001b[0m: name 'dh' is not defined"
+     ]
+    }
+   ],
   "source": [
    "NO = dh.no  # shorthand for number of orbitals in the unit cell\n",
    "\n",
@ -230,7 +312,19 @@
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "ename": "NameError",
+     "evalue": "name 'dh' is not defined",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[5], line 3\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[38;5;66;03m# for every site we have to store 3 Greens function (and the associated _tmp-s) in the 3 reference directions\u001b[39;00m\n\u001b[1;32m      2\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m i, mag_ent \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28menumerate\u001b[39m(magnetic_entities):\n\u001b[0;32m----> 3\u001b[0m     parsed \u001b[38;5;241m=\u001b[39m parse_magnetic_entity(\u001b[43mdh\u001b[49m, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mmag_ent)  \u001b[38;5;66;03m# parse orbital indexes\u001b[39;00m\n\u001b[1;32m      4\u001b[0m     magnetic_entities[i][\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124morbital_indeces\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m=\u001b[39m parsed\n\u001b[1;32m      5\u001b[0m     \u001b[38;5;66;03m# calculate spin box indexes\u001b[39;00m\n",
+      "\u001b[0;31mNameError\u001b[0m: name 'dh' is not defined"
+     ]
+    }
+   ],
   "source": [
    "# for every site we have to store 3 Greens function (and the associated _tmp-s) in the 3 reference directions\n",
    "for i, mag_ent in enumerate(magnetic_entities):\n",
@ -684,7 +778,19 @@
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "ename": "NameError",
+     "evalue": "name 'dh' is not defined",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[1], line 3\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mmatplotlib\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mpyplot\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m \u001b[38;5;21;01mplt\u001b[39;00m\n\u001b[0;32m----> 3\u001b[0m coords \u001b[38;5;241m=\u001b[39m \u001b[43mdh\u001b[49m\u001b[38;5;241m.\u001b[39mxyz[\u001b[38;5;241m-\u001b[39m\u001b[38;5;241m3\u001b[39m:]\n\u001b[1;32m      6\u001b[0m plt\u001b[38;5;241m.\u001b[39mfigure(figsize\u001b[38;5;241m=\u001b[39m(\u001b[38;5;241m15\u001b[39m, \u001b[38;5;241m5\u001b[39m))\n\u001b[1;32m      7\u001b[0m plt\u001b[38;5;241m.\u001b[39msubplot(\u001b[38;5;241m131\u001b[39m)\n",
+      "\u001b[0;31mNameError\u001b[0m: name 'dh' is not defined"
+     ]
+    }
+   ],
   "source": [
    "import matplotlib.pyplot as plt\n",
    "\n",