mirror of
https://github.com/triqs/dft_tools
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![Alexander Hampel](/assets/img/avatar_default.png)
* adapted all occurences of the converter script file names including the doc files * fixed one failing test: Py_basis_transformation.py
357 lines
12 KiB
Plaintext
357 lines
12 KiB
Plaintext
{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": 1,
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"metadata": {
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"nbsphinx": "hidden"
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},
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"outputs": [],
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"source": [
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"import matplotlib\n",
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"matplotlib.use(\"Pdf\")\n",
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"import matplotlib.pyplot as plt\n",
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"%matplotlib inline\n",
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"%config InlineBackend.figure_format = 'svg'\n",
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"\n",
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"# set matplotlib parameters\n",
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"params = {'backend': 'ps',\n",
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" 'axes.labelsize': 13,\n",
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" 'font.size': 13,\n",
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" 'legend.fontsize': 13,\n",
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" 'xtick.labelsize': 13,\n",
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" 'ytick.labelsize': 13,\n",
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" 'text.usetex': False,\n",
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" 'text.latex.preamble': \"\\\\usepackage{mathpazo}, \\\\usepackage{amsmath}\",\n",
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" 'font.family': 'sans-serif',\n",
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" 'font.sans-serif': ['Computer Modern Sans serif']}\n",
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"plt.rcParams.update(params)\n",
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"\n",
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"import warnings \n",
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"warnings.filterwarnings(\"ignore\") #ignore some matplotlib warnings\n",
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"\n",
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"# numpy\n",
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"import numpy as np"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"In this basic example we will perform a VASP calculation for SrVO$_3$, build PLOs for the Vanadium t$_{2g}$ orbitals, and load them as SumK object, which can be then used to perform a DMFT calculation.\n",
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"\n",
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"## VASP setup\n",
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"\n",
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"First we setup the VASP [INCAR link](INCAR) file by specifing the LOCPROJ, EMIN, EMAX and LORBIT flags:"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"```\n",
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"SYSTEM = SrVO3\n",
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"NCORE = 4\n",
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"LMAXMIX=6\n",
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"EDIFF = 1.E-10\n",
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"\n",
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"# DOS energy window\n",
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"NEDOS = 2001\n",
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"\n",
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"! switch off symmetries\n",
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"ISYM=-1\n",
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"\n",
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"# Smearing procedure\n",
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"ISMEAR = -5\n",
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"\n",
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"# the energy window to optimize projector channels\n",
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"EMIN = 3.9\n",
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"EMAX = 7.1\n",
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"\n",
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"# use the PAW channel optimization\n",
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"LORBIT=14\n",
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"\n",
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"# project to V d\n",
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"LOCPROJ = 2 : d : Pr\n",
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"```\n",
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"Moreover we prepare a [KPOINTS link](KPOINTS), [POSCAR link](POSCAR), and a POTCAR file. For the POTCAR file please use the VASP provided PBE pseudopotentials: `Sr_sv`, `V`, and `O`. \n",
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"\n",
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"Now VASP is executed, which should converge in roughly 27 iterations. Afterwards you should find the files LOCPROJ and PROJCAR in you directory. \n",
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"\n",
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"## PLOVASP\n",
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"\n",
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"First import the PLOVASP module of DFTTools:"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"metadata": {},
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"outputs": [
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"Starting run with 1 MPI rank(s) at : 2019-12-05 16:12:52.689539\n"
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]
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}
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],
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"source": [
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"# import plovasp converter\n",
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"import triqs_dft_tools.converters.plovasp.converter as plo_converter"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Next, create a configuration file for plovasp [plo.cfg link](plo.cfg):\n",
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"\n",
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"```\n",
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"[General]\n",
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"DOSMESH = -3.0 3.0 2001\n",
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"\n",
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"[Shell 1]\n",
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"LSHELL = 2\n",
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"IONS = 2\n",
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"EWINDOW = -1.4 2.0\n",
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"\n",
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"TRANSFORM = 1.0 0.0 0.0 0.0 0.0\n",
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" 0.0 1.0 0.0 0.0 0.0\n",
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" 0.0 0.0 0.0 1.0 0.0\n",
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"\n",
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"```\n",
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"where the energy window of the t$_{2g}$ bands is specified by `EWINDOW` and the `TRANSFORM` flag picks the correct three orbitals out of the five Vanadium $d$ orbitals [see the guide for the ordering of orbitals](../../guide/conv_vasp.html). Before running PLOVASP, make sure that the Fermi energy is written in the first line of the `LOCPROJ` file, or copy it there (see the VASP [interface guide](../../guide/conv_vasp.html) for more information). The first line should look like\n",
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"```\n",
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"1 729 21 5 5.3834262 # of spin, # of k-points, # of bands, # of proj, Efermi\n",
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"```\n",
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"\n",
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"Now run PLOVASP:"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Read parameters:\n",
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"0 -> {'m': 0, 'l': 2, 'isite': 2, 'label': 'dxy'}\n",
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"1 -> {'m': 1, 'l': 2, 'isite': 2, 'label': 'dyz'}\n",
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"2 -> {'m': 2, 'l': 2, 'isite': 2, 'label': 'dz2'}\n",
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"3 -> {'m': 3, 'l': 2, 'isite': 2, 'label': 'dxz'}\n",
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"4 -> {'m': 4, 'l': 2, 'isite': 2, 'label': 'dx2-y2'}\n",
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" Found POSCAR, title line: SrVO3\n",
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" Total number of ions: 5\n",
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" Number of types: 3\n",
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" Number of ions for each type: [1, 1, 3]\n",
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"\n",
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" Total number of k-points: 729\n",
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" Total number of tetrahedra: 4374\n",
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"eigvals from LOCPROJ\n",
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"\n",
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" Unorthonormalized density matrices and overlaps:\n",
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" Spin: 1\n",
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" Site: 2\n",
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" Density matrix Overlap\n",
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" 0.5875772 0.0015679 -0.0003707 0.0015674 0.0000000 0.9294791 -0.0000080 -0.0000078 -0.0000080 -0.0000001\n",
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" 0.0015679 0.5876177 -0.0001854 -0.0016078 0.0003240 -0.0000080 0.9294790 -0.0000042 0.0000080 0.0000070\n",
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" -0.0003707 -0.0001854 0.5815486 -0.0001854 -0.0000000 -0.0000078 -0.0000042 0.9715751 -0.0000038 0.0000003\n",
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" 0.0015674 -0.0016078 -0.0001854 0.5876172 -0.0003240 -0.0000080 0.0000080 -0.0000038 0.9294791 -0.0000066\n",
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" 0.0000000 0.0003240 -0.0000000 -0.0003240 0.5815487 -0.0000001 0.0000070 0.0000003 -0.0000066 0.9715748\n",
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"\n",
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" Generating 1 shell...\n",
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"\n",
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" Shell : 1\n",
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" Orbital l : 2\n",
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" Number of ions: 1\n",
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" Dimension : 3\n",
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" Correlated : True\n",
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" Ion sort : [1]\n",
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"Density matrix:\n",
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" Shell 1\n",
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" Site 1\n",
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" 0.3332630 0.0021719 0.0021714\n",
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" 0.0021719 0.3333128 -0.0022211\n",
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" 0.0021714 -0.0022211 0.3333123\n",
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" trace: 0.9998880790966638\n",
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"\n",
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" Impurity density: 0.9998880790966638\n",
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"\n",
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"Overlap:\n",
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" Site 1\n",
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"[[ 1. -0. 0.]\n",
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" [-0. 1. 0.]\n",
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" [ 0. 0. 1.]]\n",
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"\n",
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"Local Hamiltonian:\n",
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" Shell 1\n",
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" Site 1\n",
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" 0.5633806 0.0007563 0.0007563\n",
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" 0.0007563 0.5633801 -0.0007559\n",
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" 0.0007563 -0.0007559 0.5633801\n",
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"\n",
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"Evaluating DOS...\n",
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" Shell 1\n",
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" Total number of states: [[[7.33737319 7.48285647 7.28002405]]]\n",
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" Storing ctrl-file...\n",
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" Storing PLO-group file 'vasp.pg1'...\n",
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" Density within window: 0.9999741659673522\n"
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]
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}
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],
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"source": [
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"# Generate and store PLOs\n",
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"plo_converter.generate_and_output_as_text('plo.cfg', vasp_dir='./')"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"PLOVASP created one shell with three orbitals, which are equally filled by 1/3, one electron in total. Additionally we calculated the density of states. Both in VASP and PLOVASP. The later stores the data in the file pdos_x.dat, which can be simply plotted with [matplotlib](https://matplotlib.org/). The result should look similar to:\n",
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"\n",
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"![](svo_dos.svg)\n",
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"\n",
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"Here the gray area highlights the energy window for the PLOs. The total DOS of VASP (blue) coincides with the PLO DOS in the window, as we re-orthonormalized the projector functions in the given window, picking up also Oxygen weight. This setting is closed to the result of maximally localized Wannier functions created with [wannier90](http://www.wannier.org/) without running the actual minimization of the spread. Note, for a proper comparison one can use the hydrogen projector in VASP by using the the line `LOCPROJ= 2 : d : Hy`, instead of `Pr`. \n",
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"\n",
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"\n",
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"## Converting to hdf5 file\n",
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"\n",
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"Finally we can run the VASP converter to create a h5 file:"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Reading input from vasp.ctrl...\n",
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"{\n",
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" \"ngroups\": 1,\n",
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" \"nk\": 729,\n",
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" \"ns\": 1,\n",
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" \"nc_flag\": 0\n",
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"}\n",
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"\n",
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" No. of inequivalent shells: 1\n"
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]
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}
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],
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"source": [
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"# import VASPconverter\n",
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"from triqs_dft_tools.converters.vasp import *\n",
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"\n",
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"\n",
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"# create Converter\n",
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"Converter = VaspConverter(filename = 'vasp')\n",
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"# run the converter\n",
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"Converter.convert_dft_input()"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"The resulting h5 file `vasp.h5` can now be loaded as sumk object via:"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"metadata": {},
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"outputs": [],
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"source": [
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"# SumK\n",
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"from triqs_dft_tools.sumk_dft_tools import SumkDFTTools\n",
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"\n",
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"SK = SumkDFTTools(hdf_file='vasp.h5', use_dft_blocks = False)"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Here one should carefully determine the block structure manually. This is important to find degenerate orbitals and spin-channels:"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"found 1 blocks of degenerate orbitals in shell 0\n",
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"block 0 consists of orbitals:\n",
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" up_2\n",
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" up_0\n",
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" up_1\n",
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" down_2\n",
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" down_1\n",
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" down_0\n"
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]
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}
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],
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"source": [
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"Sigma = SK.block_structure.create_gf(beta=40)\n",
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"SK.put_Sigma([Sigma])\n",
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"G = SK.extract_G_loc()\n",
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"SK.analyse_block_structure_from_gf(G, threshold = 1e-3)\n",
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"for i_sh in range(len(SK.deg_shells)):\n",
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" num_block_deg_orbs = len(SK.deg_shells[i_sh])\n",
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" mpi.report('found {0:d} blocks of degenerate orbitals in shell {1:d}'.format(num_block_deg_orbs, i_sh))\n",
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" for iblock in range(num_block_deg_orbs):\n",
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" mpi.report('block {0:d} consists of orbitals:'.format(iblock))\n",
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" for keys in list(SK.deg_shells[i_sh][iblock].keys()):\n",
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" mpi.report(' '+keys)"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"This minimal example extracts the block structure by calculating once the local Green's functions and then finds degenerate orbitals with a certain threshold in `Gloc`. Afterwards the result is reported, where 1 block is found with size 6 (3x2 orbitals for spin), where a all 6 orbitals are marked as degenerate. This is indeed correct in cubic SrVO$_3$, as all 3 t$_{2g}$ orbitals are degenerate. Note: for a magnetic calculation one has to break the symmetry between up and down at this point manually. Moreover, one can reduce the threshold for example to `1e-5` and finds that then the degeneracy of the 3 t$_{2g}$ orbitals is not found anymore, resulting in only two degenerate blocks for spin up and down, each with size 3x3.\n",
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"\n",
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"Afterwards the exact same DMFT script as in the [Wien2k tutorial](../srvo3.html) can be used. For a more elaborate example including charge self-consistency take a look at the [VASP NiO example](../nio_csc.html)."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 2
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}
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