From 8b2afbb555684eefabbfb49edcde6009c8f7e01c Mon Sep 17 00:00:00 2001
From: Daniel Pozsar <danielpozsar@student.elte.hu>
Date: Fri, 1 Nov 2024 10:55:54 +0100
Subject: [PATCH] could not read hamiltonian, tested for a bunch of sisl
 versions

---
 Fe3GeTe2_3-791lat_short-1.txt |  70 -------------------
 pyproject.toml                |   4 +-
 requirements.txt              |   2 +-
 simmetries.txt                | 120 ---------------------------------
 test.ipynb                    | 122 +++++++++++++++++++++++++++++++---
 5 files changed, 117 insertions(+), 201 deletions(-)
 delete mode 100644 Fe3GeTe2_3-791lat_short-1.txt
 delete mode 100644 simmetries.txt

diff --git a/Fe3GeTe2_3-791lat_short-1.txt b/Fe3GeTe2_3-791lat_short-1.txt
deleted file mode 100644
index 99d4228..0000000
--- a/Fe3GeTe2_3-791lat_short-1.txt
+++ /dev/null
@@ -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
-========================================
diff --git a/pyproject.toml b/pyproject.toml
index 187cb8e..8dc1b11 100644
--- 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",
diff --git a/requirements.txt b/requirements.txt
index 81c9cc2..6d0475e 100644
--- 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
diff --git a/simmetries.txt b/simmetries.txt
deleted file mode 100644
index 36444de..0000000
--- a/simmetries.txt
+++ /dev/null
@@ -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]
k loop:   2% 2/100 [00:01<00:57,  1.71it/s]
k loop:   3% 3/100 [00:01<00:44,  2.17it/s]
k loop:   4% 4/100 [00:01<00:38,  2.51it/s]
k loop:   5% 5/100 [00:02<00:35,  2.71it/s]
k loop:   6% 6/100 [00:02<00:33,  2.83it/s]
k loop:   7% 7/100 [00:02<00:31,  2.92it/s]
k loop:   8% 8/100 [00:03<00:30,  2.98it/s]
k loop:   9% 9/100 [00:03<00:29,  3.07it/s]
k loop:  10% 10/100 [00:03<00:28,  3.12it/s]
k loop:  11% 11/100 [00:04<00:28,  3.17it/s]
k loop:  12% 12/100 [00:04<00:27,  3.21it/s]
k loop:  13% 13/100 [00:04<00:27,  3.22it/s]
k loop:  14% 14/100 [00:05<00:26,  3.24it/s]
k loop:  15% 15/100 [00:05<00:28,  2.99it/s]
k loop:  16% 16/100 [00:05<00:32,  2.59it/s]
k loop:  17% 17/100 [00:06<00:31,  2.63it/s]
k loop:  18% 18/100 [00:06<00:31,  2.62it/s]
k loop:  19% 19/100 [00:07<00:30,  2.67it/s]
k loop:  20% 20/100 [00:07<00:29,  2.75it/s]
k loop:  21% 21/100 [00:07<00:29,  2.72it/s]
k loop:  22% 22/100 [00:08<00:28,  2.75it/s]
k loop:  23% 23/100 [00:08<00:26,  2.86it/s]
k loop:  24% 24/100 [00:08<00:26,  2.92it/s]
k loop:  25% 25/100 [00:09<00:25,  2.97it/s]
k loop:  26% 26/100 [00:09<00:24,  3.01it/s]
k loop:  27% 27/100 [00:09<00:24,  3.04it/s]
k loop:  28% 28/100 [00:10<00:23,  3.07it/s]
k loop:  29% 29/100 [00:10<00:22,  3.10it/s]
k loop:  30% 30/100 [00:10<00:22,  3.13it/s]
k loop:  31% 31/100 [00:10<00:22,  3.12it/s]
k loop:  32% 32/100 [00:11<00:21,  3.10it/s]
k loop:  33% 33/100 [00:11<00:21,  3.11it/s]
k loop:  34% 34/100 [00:11<00:21,  3.11it/s]
k loop:  35% 35/100 [00:12<00:20,  3.12it/s]
k loop:  36% 36/100 [00:12<00:20,  3.11it/s]
k loop:  37% 37/100 [00:12<00:20,  3.11it/s]
k loop:  38% 38/100 [00:13<00:20,  3.10it/s]
k loop:  39% 39/100 [00:13<00:19,  3.11it/s]
k loop:  40% 40/100 [00:13<00:19,  3.10it/s]
k loop:  41% 41/100 [00:14<00:19,  3.09it/s]
k loop:  42% 42/100 [00:14<00:18,  3.07it/s]
k loop:  43% 43/100 [00:14<00:18,  3.06it/s]
k loop:  44% 44/100 [00:15<00:21,  2.62it/s]
k loop:  45% 45/100 [00:16<00:29,  1.85it/s]
k loop:  46% 46/100 [00:16<00:28,  1.87it/s]
k loop:  47% 47/100 [00:17<00:26,  2.04it/s]
k loop:  48% 48/100 [00:17<00:24,  2.11it/s]
k loop:  49% 49/100 [00:18<00:23,  2.14it/s]
k loop:  50% 50/100 [00:18<00:23,  2.15it/s]
k loop:  51% 51/100 [00:18<00:22,  2.17it/s]
k loop:  52% 52/100 [00:19<00:20,  2.29it/s]
k loop:  53% 53/100 [00:19<00:19,  2.37it/s]
k loop:  54% 54/100 [00:20<00:19,  2.36it/s]
k loop:  55% 55/100 [00:20<00:18,  2.42it/s]
k loop:  56% 56/100 [00:20<00:17,  2.46it/s]
k loop:  57% 57/100 [00:21<00:16,  2.60it/s]
k loop:  58% 58/100 [00:21<00:15,  2.70it/s]
k loop:  59% 59/100 [00:21<00:14,  2.77it/s]
k loop:  60% 60/100 [00:22<00:14,  2.82it/s]
k loop:  61% 61/100 [00:22<00:13,  2.86it/s]
k loop:  62% 62/100 [00:23<00:13,  2.85it/s]
k loop:  63% 63/100 [00:23<00:13,  2.83it/s]
k loop:  64% 64/100 [00:23<00:12,  2.82it/s]
k loop:  65% 65/100 [00:24<00:12,  2.85it/s]
k loop:  66% 66/100 [00:24<00:11,  2.84it/s]
k loop:  67% 67/100 [00:24<00:11,  2.85it/s]
k loop:  68% 68/100 [00:25<00:11,  2.83it/s]
k loop:  69% 69/100 [00:25<00:10,  2.87it/s]
k loop:  70% 70/100 [00:25<00:10,  2.84it/s]
k loop:  71% 71/100 [00:26<00:10,  2.69it/s]
k loop:  72% 72/100 [00:26<00:10,  2.69it/s]
k loop:  73% 73/100 [00:26<00:09,  2.74it/s]
k loop:  74% 74/100 [00:27<00:09,  2.80it/s]
k loop:  75% 75/100 [00:27<00:08,  2.83it/s]
k loop:  76% 76/100 [00:27<00:08,  2.83it/s]
k loop:  77% 77/100 [00:28<00:08,  2.80it/s]
k loop:  78% 78/100 [00:28<00:07,  2.76it/s]
k loop:  79% 79/100 [00:29<00:07,  2.79it/s]
k loop:  80% 80/100 [00:29<00:07,  2.76it/s]
k loop:  81% 81/100 [00:29<00:06,  2.79it/s]
k loop:  82% 82/100 [00:30<00:06,  2.80it/s]
k loop:  83% 83/100 [00:30<00:06,  2.68it/s]
k loop:  84% 84/100 [00:30<00:05,  2.75it/s]
k loop:  85% 85/100 [00:31<00:05,  2.81it/s]
k loop:  86% 86/100 [00:31<00:04,  2.82it/s]
k loop:  87% 87/100 [00:31<00:04,  2.78it/s]
k loop:  88% 88/100 [00:32<00:04,  2.77it/s]
k loop:  89% 89/100 [00:32<00:04,  2.64it/s]
k loop:  90% 90/100 [00:33<00:04,  2.41it/s]
k loop:  91% 91/100 [00:33<00:03,  2.45it/s]
k loop:  92% 92/100 [00:34<00:03,  2.45it/s]
k loop:  93% 93/100 [00:34<00:02,  2.53it/s]
k loop:  94% 94/100 [00:34<00:02,  2.50it/s]
k loop:  95% 95/100 [00:35<00:02,  2.46it/s]
k loop:  96% 96/100 [00:35<00:01,  2.50it/s]
k loop:  97% 97/100 [00:36<00:01,  2.52it/s]
k loop:  98% 98/100 [00:36<00:00,  2.55it/s]
k loop:  99% 99/100 [00:36<00:00,  2.59it/s]
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]
diff --git a/test.ipynb b/test.ipynb
index 598c74f..792b6f8 100644
--- 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",