WIP: Model based on new temgym_core

.github/workflows/ci.yml

@@ -16,12 +16,10 @@ concurrency:
 jobs:
   tests:
     strategy:
+      fail-fast: false
       matrix:
-        python_version: ["3.9", "3.10", "3.11", "3.12"]
+        python_version: ["3.10", "3.11", "3.12"]
         os: [ubuntu-latest, windows-latest, macos-14]
-        exclude:
-          - os: macos-14
-            python_version: "3.9"
     runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v5
@@ -39,6 +37,7 @@ jobs:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
   pinned-requirements:
+    if: false  # skip job
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v5
@@ -52,6 +51,7 @@ jobs:
         run: pytest --cov=microscope_calibration --cov-report=xml --cov-report=term tests/
 
   numba_coverage:
+    if: false  # skip job
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v5

.pre-commit-config.yaml

@@ -8,6 +8,7 @@ repos:
   - id: end-of-file-fixer
   - id: check-yaml
   - id: check-added-large-files
+    exclude: prototypes/clcalib.ipynb
 - repo: https://github.com/pycqa/flake8
   rev: 7.3.0
   hooks:

prototypes/.gitignore

@@ -0,0 +1 @@
+*.npy

prototypes/BiFeO3EntryWithCollCode29921.cif

@@ -0,0 +1,85 @@
+
+#(C) 2025 by FIZ Karlsruhe - Leibniz Institute for Information Infrastructure.  All rights reserved.
+data_29921-ICSD
+_database_code_ICSD 29921
+_audit_creation_date 2021-08-01
+_chemical_name_common 'Bismuth ferrite'
+_chemical_formula_structural 'Bi Fe O3'
+_chemical_formula_sum 'Bi1 Fe1 O3'
+_chemical_name_structure_type LiNbO3
+_exptl_crystal_density_diffrn 8.34
+_citation_title
+
+;
+Rietveld study of the changes of phase composition, crystal structure, and
+morphology of BiFeO$_3$ by partial substitution of bismuth with rare-earth
+ions
+;
+loop_
+_citation_id
+_citation_journal_full
+_citation_year
+_citation_journal_volume
+_citation_page_first
+_citation_page_last
+_citation_journal_id_ASTM
+primary 'Minerals (Basel, Switzerland)' 2021 11 1 11 MBSIBI
+loop_
+_citation_author_citation_id
+_citation_author_name
+primary 'Kireva, Maria'
+primary 'Tumbalev, Ventsislav'
+primary 'Kostov-Kytin, Vladislav'
+primary 'Tzvetkov, Peter'
+primary 'Kovacheva, Daniela'
+_cell_length_a 5.5785(2)
+_cell_length_b 5.5785(2)
+_cell_length_c 13.8696(5)
+_cell_angle_alpha 90.
+_cell_angle_beta 90.
+_cell_angle_gamma 120.
+_cell_volume 373.79
+_cell_formula_units_Z 6
+_space_group_name_H-M_alt 'R 3 c H'
+_space_group_IT_number 161
+loop_
+_space_group_symop_id
+_space_group_symop_operation_xyz
+1 '-x+y, y, z+1/2'
+2 'x, x-y, z+1/2'
+3 '-y, -x, z+1/2'
+4 '-x+y, -x, z'
+5 '-y, x-y, z'
+6 'x, y, z'
+7 '-x+y+2/3, y+1/3, z+5/6'
+8 'x+2/3, x-y+1/3, z+5/6'
+9 '-y+2/3, -x+1/3, z+5/6'
+10 '-x+y+2/3, -x+1/3, z+1/3'
+11 '-y+2/3, x-y+1/3, z+1/3'
+12 'x+2/3, y+1/3, z+1/3'
+13 '-x+y+1/3, y+2/3, z+1/6'
+14 'x+1/3, x-y+2/3, z+1/6'
+15 '-y+1/3, -x+2/3, z+1/6'
+16 '-x+y+1/3, -x+2/3, z+2/3'
+17 '-y+1/3, x-y+2/3, z+2/3'
+18 'x+1/3, y+2/3, z+2/3'
+loop_
+_atom_type_symbol
+_atom_type_oxidation_number
+Bi3+ 3
+Fe3+ 3
+O2- -2
+loop_
+_atom_site_label
+_atom_site_type_symbol
+_atom_site_symmetry_multiplicity
+_atom_site_Wyckoff_symbol
+_atom_site_fract_x
+_atom_site_fract_y
+_atom_site_fract_z
+_atom_site_B_iso_or_equiv
+_atom_site_occupancy
+Bi1 Bi3+ 6 a 0 0 0 1.30(1) 1.
+Fe1 Fe3+ 6 a 0 0 0.2206(1) 1.41(1) 1.
+O1 O2- 18 b 0.446(4) 0.021(1) 0.9504(3) 1.3(1) 1.
+#End of TTdata_29921-ICSD

prototypes/EntryWithCollCode163723.cif

@@ -0,0 +1,250 @@
+
+#(C) 2025 by FIZ Karlsruhe - Leibniz Institute for Information Infrastructure.  All rights reserved.
+data_163723-ICSD
+_database_code_ICSD 163723
+_audit_creation_date 2009-08-01
+_chemical_name_common Gold
+_chemical_formula_structural Au
+_chemical_formula_sum Au1
+_chemical_name_structure_type Cu
+_exptl_crystal_density_diffrn 19.39
+_citation_title 'Isothermal section of the Ce - Au - Sb system at 870 K'
+loop_
+_citation_id
+_citation_journal_full
+_citation_year
+_citation_journal_volume
+_citation_page_first
+_citation_page_last
+_citation_journal_id_ASTM
+primary 'Journal of Alloys and Compounds' 2009 479 184 188 JALCEU
+loop_
+_citation_author_citation_id
+_citation_author_name
+primary 'Salamakha, L.P.'
+primary 'Bauer, E.'
+primary 'Mudryi, S.I.'
+primary 'Goncalves, A.P.'
+primary 'Almeida, M.'
+primary 'Noel, H.'
+_cell_length_a 4.0709(2)
+_cell_length_b 4.0709(2)
+_cell_length_c 4.0709(2)
+_cell_angle_alpha 90.
+_cell_angle_beta 90.
+_cell_angle_gamma 90.
+_cell_volume 67.46
+_cell_formula_units_Z 4
+_space_group_name_H-M_alt 'F m -3 m'
+_space_group_IT_number 225
+loop_
+_space_group_symop_id
+_space_group_symop_operation_xyz
+1 'z, y, -x'
+2 'y, x, -z'
+3 'x, z, -y'
+4 'z, x, -y'
+5 'y, z, -x'
+6 'x, y, -z'
+7 'z, -y, x'
+8 'y, -x, z'
+9 'x, -z, y'
+10 'z, -x, y'
+11 'y, -z, x'
+12 'x, -y, z'
+13 '-z, y, x'
+14 '-y, x, z'
+15 '-x, z, y'
+16 '-z, x, y'
+17 '-y, z, x'
+18 '-x, y, z'
+19 '-z, -y, -x'
+20 '-y, -x, -z'
+21 '-x, -z, -y'
+22 '-z, -x, -y'
+23 '-y, -z, -x'
+24 '-x, -y, -z'
+25 '-z, -y, x'
+26 '-y, -x, z'
+27 '-x, -z, y'
+28 '-z, -x, y'
+29 '-y, -z, x'
+30 '-x, -y, z'
+31 '-z, y, -x'
+32 '-y, x, -z'
+33 '-x, z, -y'
+34 '-z, x, -y'
+35 '-y, z, -x'
+36 '-x, y, -z'
+37 'z, -y, -x'
+38 'y, -x, -z'
+39 'x, -z, -y'
+40 'z, -x, -y'
+41 'y, -z, -x'
+42 'x, -y, -z'
+43 'z, y, x'
+44 'y, x, z'
+45 'x, z, y'
+46 'z, x, y'
+47 'y, z, x'
+48 'x, y, z'
+49 'z, y+1/2, -x+1/2'
+50 'y, x+1/2, -z+1/2'
+51 'x, z+1/2, -y+1/2'
+52 'z, x+1/2, -y+1/2'
+53 'y, z+1/2, -x+1/2'
+54 'x, y+1/2, -z+1/2'
+55 'z, -y+1/2, x+1/2'
+56 'y, -x+1/2, z+1/2'
+57 'x, -z+1/2, y+1/2'
+58 'z, -x+1/2, y+1/2'
+59 'y, -z+1/2, x+1/2'
+60 'x, -y+1/2, z+1/2'
+61 '-z, y+1/2, x+1/2'
+62 '-y, x+1/2, z+1/2'
+63 '-x, z+1/2, y+1/2'
+64 '-z, x+1/2, y+1/2'
+65 '-y, z+1/2, x+1/2'
+66 '-x, y+1/2, z+1/2'
+67 '-z, -y+1/2, -x+1/2'
+68 '-y, -x+1/2, -z+1/2'
+69 '-x, -z+1/2, -y+1/2'
+70 '-z, -x+1/2, -y+1/2'
+71 '-y, -z+1/2, -x+1/2'
+72 '-x, -y+1/2, -z+1/2'
+73 '-z, -y+1/2, x+1/2'
+74 '-y, -x+1/2, z+1/2'
+75 '-x, -z+1/2, y+1/2'
+76 '-z, -x+1/2, y+1/2'
+77 '-y, -z+1/2, x+1/2'
+78 '-x, -y+1/2, z+1/2'
+79 '-z, y+1/2, -x+1/2'
+80 '-y, x+1/2, -z+1/2'
+81 '-x, z+1/2, -y+1/2'
+82 '-z, x+1/2, -y+1/2'
+83 '-y, z+1/2, -x+1/2'
+84 '-x, y+1/2, -z+1/2'
+85 'z, -y+1/2, -x+1/2'
+86 'y, -x+1/2, -z+1/2'
+87 'x, -z+1/2, -y+1/2'
+88 'z, -x+1/2, -y+1/2'
+89 'y, -z+1/2, -x+1/2'
+90 'x, -y+1/2, -z+1/2'
+91 'z, y+1/2, x+1/2'
+92 'y, x+1/2, z+1/2'
+93 'x, z+1/2, y+1/2'
+94 'z, x+1/2, y+1/2'
+95 'y, z+1/2, x+1/2'
+96 'x, y+1/2, z+1/2'
+97 'z+1/2, y, -x+1/2'
+98 'y+1/2, x, -z+1/2'
+99 'x+1/2, z, -y+1/2'
+100 'z+1/2, x, -y+1/2'
+101 'y+1/2, z, -x+1/2'
+102 'x+1/2, y, -z+1/2'
+103 'z+1/2, -y, x+1/2'
+104 'y+1/2, -x, z+1/2'
+105 'x+1/2, -z, y+1/2'
+106 'z+1/2, -x, y+1/2'
+107 'y+1/2, -z, x+1/2'
+108 'x+1/2, -y, z+1/2'
+109 '-z+1/2, y, x+1/2'
+110 '-y+1/2, x, z+1/2'
+111 '-x+1/2, z, y+1/2'
+112 '-z+1/2, x, y+1/2'
+113 '-y+1/2, z, x+1/2'
+114 '-x+1/2, y, z+1/2'
+115 '-z+1/2, -y, -x+1/2'
+116 '-y+1/2, -x, -z+1/2'
+117 '-x+1/2, -z, -y+1/2'
+118 '-z+1/2, -x, -y+1/2'
+119 '-y+1/2, -z, -x+1/2'
+120 '-x+1/2, -y, -z+1/2'
+121 '-z+1/2, -y, x+1/2'
+122 '-y+1/2, -x, z+1/2'
+123 '-x+1/2, -z, y+1/2'
+124 '-z+1/2, -x, y+1/2'
+125 '-y+1/2, -z, x+1/2'
+126 '-x+1/2, -y, z+1/2'
+127 '-z+1/2, y, -x+1/2'
+128 '-y+1/2, x, -z+1/2'
+129 '-x+1/2, z, -y+1/2'
+130 '-z+1/2, x, -y+1/2'
+131 '-y+1/2, z, -x+1/2'
+132 '-x+1/2, y, -z+1/2'
+133 'z+1/2, -y, -x+1/2'
+134 'y+1/2, -x, -z+1/2'
+135 'x+1/2, -z, -y+1/2'
+136 'z+1/2, -x, -y+1/2'
+137 'y+1/2, -z, -x+1/2'
+138 'x+1/2, -y, -z+1/2'
+139 'z+1/2, y, x+1/2'
+140 'y+1/2, x, z+1/2'
+141 'x+1/2, z, y+1/2'
+142 'z+1/2, x, y+1/2'
+143 'y+1/2, z, x+1/2'
+144 'x+1/2, y, z+1/2'
+145 'z+1/2, y+1/2, -x'
+146 'y+1/2, x+1/2, -z'
+147 'x+1/2, z+1/2, -y'
+148 'z+1/2, x+1/2, -y'
+149 'y+1/2, z+1/2, -x'
+150 'x+1/2, y+1/2, -z'
+151 'z+1/2, -y+1/2, x'
+152 'y+1/2, -x+1/2, z'
+153 'x+1/2, -z+1/2, y'
+154 'z+1/2, -x+1/2, y'
+155 'y+1/2, -z+1/2, x'
+156 'x+1/2, -y+1/2, z'
+157 '-z+1/2, y+1/2, x'
+158 '-y+1/2, x+1/2, z'
+159 '-x+1/2, z+1/2, y'
+160 '-z+1/2, x+1/2, y'
+161 '-y+1/2, z+1/2, x'
+162 '-x+1/2, y+1/2, z'
+163 '-z+1/2, -y+1/2, -x'
+164 '-y+1/2, -x+1/2, -z'
+165 '-x+1/2, -z+1/2, -y'
+166 '-z+1/2, -x+1/2, -y'
+167 '-y+1/2, -z+1/2, -x'
+168 '-x+1/2, -y+1/2, -z'
+169 '-z+1/2, -y+1/2, x'
+170 '-y+1/2, -x+1/2, z'
+171 '-x+1/2, -z+1/2, y'
+172 '-z+1/2, -x+1/2, y'
+173 '-y+1/2, -z+1/2, x'
+174 '-x+1/2, -y+1/2, z'
+175 '-z+1/2, y+1/2, -x'
+176 '-y+1/2, x+1/2, -z'
+177 '-x+1/2, z+1/2, -y'
+178 '-z+1/2, x+1/2, -y'
+179 '-y+1/2, z+1/2, -x'
+180 '-x+1/2, y+1/2, -z'
+181 'z+1/2, -y+1/2, -x'
+182 'y+1/2, -x+1/2, -z'
+183 'x+1/2, -z+1/2, -y'
+184 'z+1/2, -x+1/2, -y'
+185 'y+1/2, -z+1/2, -x'
+186 'x+1/2, -y+1/2, -z'
+187 'z+1/2, y+1/2, x'
+188 'y+1/2, x+1/2, z'
+189 'x+1/2, z+1/2, y'
+190 'z+1/2, x+1/2, y'
+191 'y+1/2, z+1/2, x'
+192 'x+1/2, y+1/2, z'
+loop_
+_atom_type_symbol
+_atom_type_oxidation_number
+Au0+ 0
+loop_
+_atom_site_label
+_atom_site_type_symbol
+_atom_site_symmetry_multiplicity
+_atom_site_Wyckoff_symbol
+_atom_site_fract_x
+_atom_site_fract_y
+_atom_site_fract_z
+_atom_site_B_iso_or_equiv
+_atom_site_occupancy
+Au1 Au0+ 4 a 0 0 0 . 1.
+#End of TTdata_163723-ICSD