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testing input.fdf and reading input.fdf

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class-solution
Daniel Pozsar 2 months ago
parent 496732dcd5
commit b6767c68d1
2 changed files with 78 additions and 37 deletions
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36
input.fdf
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@ -1,23 +1,23 @@
InputFile /Users/danielpozsar/Downloads/nojij/Fe3GeTe2/monolayer/soc/lat3_791/Fe3GeTe2.fdf InputFile /Users/danielpozsar/Downloads/nojij/Fe3GeTe2/monolayer/soc/lat3_791/Fe3GeTe2.fdf # comment test
OutputFile ./Fe3GeTe2_notebook OutputFile ./Fe3GeTe2_notebook # comment test
ScfXcfOrientation [ 0 0 1 ] ScfXcfOrientation [ 0 0 1 ] # comment test
# comment test
%block XCF_Rotation # comment test
1 0 0 0 1 0 0 0 1 # comment test
0 1 0 1 0 0 0 0 1 # comment test
0 0 1 1 0 0 0 1 0 # comment test
%endblock XCFRotation # comment test
%block XCF_Rotation %block MagneticEntities # comment test
1 0 0 0 1 0 0 0 1
0 1 0 1 0 0 0 0 1
0 0 1 1 0 0 0 1 0
%endblock XCFRotation
%block MagneticEntities
Cluster 4 5 # this is a list of atoms Cluster 4 5 # this is a list of atoms
AtomShell 3 2 # this is one atom and shell index AtomShell 3 2 # this is one atom and shell index
AtomShell 4 2 # this is one atom and shell index AtomShell 4 2 # this is one atom and shell index
AtomShell 5 2 # this is one atom and shell index AtomShell 5 2 # this is one atom and shell index
AtomOrbital 3 # this is one atom and orbital index AtomOrbital 3 # this is one atom and orbital index
ExplicitOrbital # this is a slice of orbital index Orbitals # this is a slice of orbital index
%endblock MagneticEntities %endblock MagneticEntities
@ -26,19 +26,19 @@ ExplicitOrbital # this is a slice of orbital index
0 1 0 0 0 0 1 0 0 0
0 2 0 0 0 0 2 0 0 0
1 2 0 0 0 1 2 0 0 0
0 2 -1 -1 0 0 2 -1 -1 0 # comment test
1 2 -1 -1 0 1 2 -1 -1 0
0 2 -1 0 0 0 2 -1 0 0
1 2 -1 0 0 1 2 -1 0 0
1 2 -2 0 0 1 2 -2 0 0
1 2 -3 0 0 1 2 -3 0 0 # comment test
%endblock Pairs %endblock Pairs
INTEGRAL.Kset 3 INTEGRAL.Kset 3
INTEGRAL.Kdirs xy INTEGRAL.Kdirs xy
INTEGRAL.Ebot -13 INTEGRAL.Ebot -13 # comment test
INTEGRAL.Eset 300 INTEGRAL.Eset 300 # comment test
INTEGRAL.Esetp 1000 INTEGRAL.Esetp 1000 # comment test
GREEN.ParallelSolver False GREEN.ParallelSolver False # comment test
PadawanMode True PadawanMode True # comment test

57
test.ipynb
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@ -76,10 +76,14 @@
"metadata": {}, "metadata": {},
"outputs": [ "outputs": [
{ {
"name": "stdout", "ename": "TypeError",
"output_type": "stream", "evalue": "'NoneType' object is not iterable",
"text": [ "output_type": "error",
"[{'ai': 0, 'aj': 1, 'Ruc': array([0, 0, 0])}, {'ai': 0, 'aj': 2, 'Ruc': array([0, 0, 0])}, {'ai': 1, 'aj': 2, 'Ruc': array([0, 0, 0])}, {'ai': 0, 'aj': 2, 'Ruc': array([-1, -1, 0])}, {'ai': 1, 'aj': 2, 'Ruc': array([-1, -1, 0])}, {'ai': 0, 'aj': 2, 'Ruc': array([-1, 0, 0])}, {'ai': 1, 'aj': 2, 'Ruc': array([-1, 0, 0])}, {'ai': 1, 'aj': 2, 'Ruc': array([-2, 0, 0])}, {'ai': 1, 'aj': 2, 'Ruc': array([-3, 0, 0])}]\n" "traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mTypeError\u001b[0m Traceback (most recent call last)",
"Cell \u001b[0;32mIn[58], line 28\u001b[0m\n\u001b[1;32m 26\u001b[0m magnetic_entities \u001b[38;5;241m=\u001b[39m fdf\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mMagneticEntities\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 27\u001b[0m fdf_magnetic_entities \u001b[38;5;241m=\u001b[39m []\n\u001b[0;32m---> 28\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m mag_ent \u001b[38;5;129;01min\u001b[39;00m magnetic_entities:\n\u001b[1;32m 29\u001b[0m row \u001b[38;5;241m=\u001b[39m mag_ent\u001b[38;5;241m.\u001b[39msplit()\n\u001b[1;32m 30\u001b[0m dat \u001b[38;5;241m=\u001b[39m []\n",
"\u001b[0;31mTypeError\u001b[0m: 'NoneType' object is not iterable"
] ]
} }
], ],
@ -93,9 +97,12 @@
"fdf_parameters[\"scf_xcf_orientation\"] = np.array(fdf.get(\"ScfXcfOrientation\"))\n", "fdf_parameters[\"scf_xcf_orientation\"] = np.array(fdf.get(\"ScfXcfOrientation\"))\n",
"\n", "\n",
"rotations = fdf.get(\"XCF_Rotation\")\n", "rotations = fdf.get(\"XCF_Rotation\")\n",
"if rotations is None:\n",
" pass\n",
"else:\n",
" fdf_rot = []\n", " fdf_rot = []\n",
" for rot in rotations:\n", " for rot in rotations:\n",
" dat = np.array(rot.split(), dtype=float)\n", " dat = np.array(rot.split()[:9], dtype=float)\n",
" o = dat[:3]\n", " o = dat[:3]\n",
" vw = dat[3:]\n", " vw = dat[3:]\n",
" vw = vw.reshape(2, 3)\n", " vw = vw.reshape(2, 3)\n",
@ -103,14 +110,41 @@
" fdf_parameters[\"ref_xcf_orientations\"] = fdf_rot\n", " fdf_parameters[\"ref_xcf_orientations\"] = fdf_rot\n",
"\n", "\n",
"pairs = fdf.get(\"Pairs\")\n", "pairs = fdf.get(\"Pairs\")\n",
"if pairs in None:\n",
" pass\n",
"else:\n",
" fdf_pairs = []\n", " fdf_pairs = []\n",
" for fdf_pair in pairs:\n", " for fdf_pair in pairs:\n",
" dat = np.array(fdf_pair.split(), dtype=int)\n", " dat = np.array(fdf_pair.split()[:5], dtype=int)\n",
" my_pair = dict(ai=dat[0], aj=dat[1], Ruc=np.array(dat[2:]))\n", " my_pair = dict(ai=dat[0], aj=dat[1], Ruc=np.array(dat[2:]))\n",
" fdf_pairs.append(fdf_pair)\n", " fdf_pairs.append(my_pair)\n",
"\n", "\n",
"pairs = fdf.get(\"Pairs\")\n", "magnetic_entities = fdf.get(\"MagneticEntities\")\n",
"if magnetic_entities is None:\n",
" pass\n",
"else:\n",
" fdf_magnetic_entities = []\n", " fdf_magnetic_entities = []\n",
" for mag_ent in magnetic_entities:\n",
" row = mag_ent.split()\n",
" dat = []\n",
" for string in row:\n",
" if string.find(\"#\") != -1:\n",
" break\n",
" dat.append(string)\n",
" if dat[0] == \"Cluster\" or \"cluster\":\n",
" fdf_magnetic_entities.append(dict(atom=dat[1:]))\n",
" continue\n",
" elif dat[0] == \"AtomShell\" or \"Atomshell\" or \"atomShell\" or \"atomshell\":\n",
" fdf_magnetic_entities.append(dict(atom=dat[1], l=dat[2:]))\n",
" continue\n",
" elif dat[0] == \"AtomOrbital\" or \"Atomorbital\" or \"tomOrbital\" or \"atomorbital\":\n",
" continue\n",
" elif dat[0] == \"Orbitals\" or \"orbitals\":\n",
" continue\n",
" else:\n",
" print(\"Unrecognizable magnetic entity in fdf\")\n",
" break\n",
"\n",
"\n", "\n",
"fdf_parameters[\"kset\"] = fdf.get(\"INTEGRAL.Kset\")\n", "fdf_parameters[\"kset\"] = fdf.get(\"INTEGRAL.Kset\")\n",
"fdf_parameters[\"kdirs\"] = fdf.get(\"INTEGRAL.Kdirs\")\n", "fdf_parameters[\"kdirs\"] = fdf.get(\"INTEGRAL.Kdirs\")\n",
@ -121,6 +155,13 @@
"fdf_parameters[\"padawan_mode\"] = fdf.get(\"PadawanMode\")" "fdf_parameters[\"padawan_mode\"] = fdf.get(\"PadawanMode\")"
] ]
}, },
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": 4, "execution_count": 4,

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