jochym
commented
10 years ago W dniu 27.06.2014 22:03, lim520 pisze:
Hi Dr. Jochym
I was trying to do structural optimization of BeO with a space group of 186. But i was not able to optimize it to the same space group. Can you please go through the code i have used ( shown below) and guide me to know where i am committing mistake and what things should i do different.
I will try. But I need the notebook in the attachment (maybe in the zip file).
Regards, P.
Paweł T. Jochym Institute of Nuclear Physics, PAN Cracow, Poland
lim520
Hi Dr. Jochym
I was trying to do structural optimization of BeO with a space group of 186. But i was not able to optimize it to the same space group. Can you please go through the code i have used ( shown below) and guide me to know where i am committing mistake and what things should i do different.
{ "metadata": { "name": "", "signature": "sha256:1f946d3105d54e3c0582e10bc0200c4465e0d176d8bbc8d7352cc9625d0ae451" }, "nbformat": 3, "nbformat_minor": 0, "worksheets": [ { "cells": [ { "cell_type": "code", "collapsed": false, "input": [ "# Import the basic libraries\n", "\n", "# ASE system\n", "import ase\n", "from ase import Atom, Atoms\n", "from ase import io\n", "from ase.lattice.spacegroup import crystal\n", "from ase.units import GPa, Bohr, Rydberg\n", "\n", "# Spacegroup/symmetry library\n", "from pyspglib import spglib\n", "\n", "# iPython utility function\n", "from IPython.core.display import Image\n", "\n", "# Import the remote execution tools from the qe-util package\n", "from qeutil import RemoteQE\n", "\n", "import warnings\n", "warnings.filterwarnings('ignore')\n", "\n", "# Access info\n", "import hostp\n", "\n", "qe=RemoteQE(label='BeO-structure', # A name for the project\n", " kpts=[3,3,3], # k-space grid\n", " xc='pw91', # Exchange functional type in the name of the pseudopotentials\n", " pp_type='van', # Variant of the pseudopotential\n", " pp_format='UPF', # Format of the pseudopotential files\n", " ecutwfc=70, # Energy cut-off\n", " pseudo_dir='../pspot',\n", " use_symmetry=False,\n", " procs=16) # Use 8 cores for the calculation\n", "\n", "print qe.directory" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "calc/BeO-structure.f33j3k\n" ] } ], "prompt_number": 1 }, { "cell_type": "code", "collapsed": false, "input": [ "a=2.7\n", "c=4.4199\n", "cryst= crystal(['Be', 'O'],\n", " [(1/3., 2/3., 0), (2/3., 1/3., -1/8.)],\n", " spacegroup=186,\n", " cellpar=[a, a, c, 90, 90, 120])\n", "# Assign the calculator to our system\n", "cryst.set_calculator(qe)\n", "\n", "# Verify the symmetry\n", "print \"Symmetry group:\", spglib.get_spacegroup(cryst)\n" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Symmetry group: P6_3mc (186)\n" ] } ], "prompt_number": 2 }, { "cell_type": "code", "collapsed": false, "input": [ "print \"Stress tensor (Voigt notation, GPa):\n\", cryst.get_stress()/GPa\n" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Stress tensor (Voigt notation, GPa):\n", "[-1.853 -1.853 2.58 -0. -0. -0. ]" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "\n" ] } ], "prompt_number": 3 }, { "cell_type": "code", "collapsed": false, "input": [ "cryst.rattle(stdev=0.05)\n", "cryst.set_cell(diag(1+0.01_randn(3))_cryst.get_cell(), scale_atoms=True)" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 4 }, { "cell_type": "code", "collapsed": false, "input": [ "# Verify that indeed we have a low symmetry structure\n", "print \"Symmetry group:\", spglib.get_spacegroup(cryst)" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Symmetry group: P1 (1)\n" ] } ], "prompt_number": 5 }, { "cell_type": "code", "collapsed": false, "input": [ "# Display the structure\n", "ase.io.write('crystal.png', cryst, format='png', show_unit_cell=2, rotation='115y,25x', scale=30)\n", "Image(filename='crystal.png')" ], "language": "python", "metadata": {}, "outputs": [ { "metadata": {}, "output_type": "pyout", "png": 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QdsQsWbJkyZLlIOf/g9iDbu/M2yUAAAAASUVORK5CYII=\n", "prompt_number": 6, "text": [ "<IPython.core.display.Image at 0xa7f9f0c>" ] } ], "prompt_number": 6 }, { "cell_type": "code", "collapsed": false, "input": [ "print \"Stress tensor (Voigt notation, GPa):\n\", cryst.get_stress()/GPa\n", "\n", "# Print also the forces (eV/A)\n", "\n", "print \"\nForces on atoms (eV/A)\"\n", "print \"======================\"\n", "print cryst.get_forces()" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Stress tensor (Voigt notation, GPa):\n", "[ -8.022 -84.177 -12.79 2.087 -0.245 49.47 ]" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "\n", "\n", "Forces on atoms (eV/A)\n", "======================\n", "[[-0.00456724 0.00399573 0.0021234 ]\n", " [ 0.00512782 -0.00498257 0.00401369]\n", " [ 0.00560462 -0.00496495 -0.00302884]\n", " [-0.0061652 0.00595179 -0.00310826]]\n" ] } ], "prompt_number": 7 }, { "cell_type": "code", "collapsed": false, "input": [ "# Switch to the atomic position relaxation mode\n", "qe.set(calc='relax')\n", "\n", "# Switch off the use of symmetries. \n", "qe.set(use_symmetry=False)\n", "\n", "# Force recalculation by clearing the results from the previous calculation.\n", "qe.reset()" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 8 }, { "cell_type": "code", "collapsed": false, "input": [ "\n", "\n", "# Run the calculation and get the stresses and forces at the end.\n", "# The structure in cryst is not modified\n", "print \"Stress:\n\", cryst.get_stress()/GPa\n", "print \"\nForces:\n\", cryst.get_forces()\n", "\n" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Stress:\n", "[ 14.82 -78.361 38.072 -2.042 2.902 -0.593]" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "\n", "\n", "Forces:\n", "[[-0.0003558 0.00047606 0.00075467]\n", " [-0.00144971 0.00085408 -0.00112689]\n", " [ 0.00055243 -0.00031167 -0.002229 ]\n", " [ 0.00125308 -0.00101846 0.00260122]]\n" ] } ], "prompt_number": 9 }, { "cell_type": "code", "collapsed": false, "input": [ "qe.set(forc_conv_thr=1e-8*Rydberg/Bohr)\n", "qe.reset()\n" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 10 }, { "cell_type": "code", "collapsed": false, "input": [ "\n", "print \"Stress:\n\", cryst.get_stress()/GPa\n", "print \"\nForces:\n\", cryst.get_forces()" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Stress:\n", "[ 1.71940000e+01 -7.72210000e+01 4.11520000e+01 -0.00000000e+00\n", " 1.10000000e-02 0.00000000e+00]" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "\n", "\n", "Forces:\n", "[[ 8.01212231e-07 2.37252165e-07 -8.82889205e-07]\n", " [ 9.80123699e-08 -2.25584026e-07 -2.49892650e-06]\n", " [ 1.32900106e-06 -2.01236509e-06 -2.43202916e-06]\n", " [ -2.22822566e-06 2.00108589e-06 5.81345593e-06]]\n" ] } ], "prompt_number": 11 }, { "cell_type": "code", "collapsed": false, "input": [ "# Update the positions using calculated values\n", "cryst.set_scaled_positions(qe.results['atomic_positions'])\n", "\n", "# Check the symmetry. Probably not the F-43m !\n", "print \"Symmetry group:\", spglib.get_spacegroup(cryst,symprec=1e-4)\n" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Symmetry group: P1 (1)\n" ] } ], "prompt_number": 12 }, { "cell_type": "code", "collapsed": false, "input": [ "qe.set(calc='vc-relax')\n", "qe.reset()" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 13 }, { "cell_type": "code", "collapsed": false, "input": [ "print \"Stress:\n\", cryst.get_stress()/GPa\n", "print \"\nForces:\n\", cryst.get_forces()" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Stress:\n", "[-0.183 -0.304 -0.3 0.001 -0.002 0.002]" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "\n", "\n", "Forces:\n", "[[ -1.50433430e-05 -1.17996003e-05 -1.90416254e-05]\n", " [ 1.54653407e-05 1.14958398e-05 1.40694423e-05]\n", " [ 1.89762838e-06 -7.93044533e-07 2.59032692e-06]\n", " [ -2.31962609e-06 1.09680509e-06 2.38146723e-06]]\n" ] } ], "prompt_number": 14 }, { "cell_type": "code", "collapsed": false, "input": [ "# Update the crystal\n", "cryst.set_cell(qe.results['cell'])\n", "cryst.set_scaled_positions(qe.results['atomic_positions'])\n", "\n", "# Check the symmetry\n", "print \"Symmetry group:\", spglib.get_spacegroup(cryst,symprec=1e-4)" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Symmetry group: Pm (6)\n" ] } ], "prompt_number": 15 }, { "cell_type": "code", "collapsed": false, "input": [ "qe.set(calc='vc-relax')\n", "qe.reset()" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 16 }, { "cell_type": "code", "collapsed": false, "input": [ "print \"Stress:\n\", cryst.get_stress()/GPa\n", "print \"\nForces:\n\", cryst.get_forces()" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Stress:\n", "[ 0.048 0.052 0.06 0. -0.001 0. ]" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "\n", "\n", "Forces:\n", "[[ -6.22300762e-07 -1.26793780e-07 -7.16034814e-07]\n", " [ 3.67935325e-07 3.77269837e-07 2.17921948e-06]\n", " [ 2.12749073e-07 -2.85480474e-07 -7.25758263e-07]\n", " [ 4.16163634e-08 3.53933558e-08 -7.37815340e-07]]\n" ] } ], "prompt_number": 17 }, { "cell_type": "code", "collapsed": false, "input": [ "# Update the crystal\n", "cryst.set_cell(qe.results['cell'])\n", "cryst.set_scaled_positions(qe.results['atomic_positions'])\n", "\n", "# Check the symmetry\n", "print \"Symmetry group:\", spglib.get_spacegroup(cryst,symprec=1e-4)" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Symmetry group: P2_1 (4)\n" ] } ], "prompt_number": 18 }, { "cell_type": "code", "collapsed": false, "input": [ "qe.set(calc='vc-relax')\n", "qe.reset()" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 19 }, { "cell_type": "code", "collapsed": false, "input": [ "print \"Stress:\n\", cryst.get_stress()/GPa\n", "print \"\nForces:\n\", cryst.get_forces()" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Stress:\n", "[ 0.195 0.197 0.199 0. -0. 0. ]" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "\n", "\n", "Forces:\n", "[[ -4.46111858e-07 -1.12403075e-07 -2.17416329e-07]\n", " [ 3.03760559e-07 2.69534017e-07 1.11858562e-06]\n", " [ 1.51685811e-07 -2.11193321e-07 -4.56224246e-07]\n", " [ -8.94557345e-09 5.36734407e-08 -4.44945045e-07]]\n" ] } ], "prompt_number": 20 }, { "cell_type": "code", "collapsed": false, "input": [ "# Update the crystal\n", "cryst.set_cell(qe.results['cell'])\n", "cryst.set_scaled_positions(qe.results['atomic_positions'])\n", "\n", "# Check the symmetry\n", "print \"Symmetry group:\", spglib.get_spacegroup(cryst,symprec=1e-4)" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Symmetry group: P2_1 (4)\n" ] } ], "prompt_number": 21 }, { "cell_type": "code", "collapsed": false, "input": [ "qe.set(calc='vc-relax')\n", "qe.reset()" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 22 }, { "cell_type": "code", "collapsed": false, "input": [ "print \"Stress:\n\", cryst.get_stress()/GPa\n", "print \"\nForces:\n\", cryst.get_forces()" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Stress:\n", "[ 0.276 0.278 0.28 0. -0. 0. ]" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "\n", "\n", "Forces:\n", "[[ -4.65169819e-07 -7.50650294e-08 -1.61798198e-07]\n", " [ 3.07649939e-07 2.03025623e-07 9.29950701e-07]\n", " [ 1.80856159e-07 -1.59075632e-07 -3.99050363e-07]\n", " [ -2.29473406e-08 3.11150381e-08 -3.69102139e-07]]\n" ] } ], "prompt_number": 23 }, { "cell_type": "code", "collapsed": false, "input": [ "# Update the crystal\n", "cryst.set_cell(qe.results['cell'])\n", "cryst.set_scaled_positions(qe.results['atomic_positions'])\n", "\n", "# Check the symmetry\n", "print \"Symmetry group:\", spglib.get_spacegroup(cryst,symprec=1e-4)" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Symmetry group: P2_1 (4)\n" ] } ], "prompt_number": 24 }, { "cell_type": "code", "collapsed": false, "input": [ "qe.set(calc='vc-relax')\n", "qe.reset()" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 25 }, { "cell_type": "code", "collapsed": false, "input": [ "print \"Stress:\n\", cryst.get_stress()/GPa\n", "print \"\nForces:\n\", cryst.get_forces()" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Stress:\n", "[ 0.011 0.011 0.014 0. 0. 0. ]" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "\n", "\n", "Forces:\n", "[[ -1.87079166e-07 -8.40106028e-08 7.00088357e-08]\n", " [ 1.52463687e-07 1.23682276e-07 1.77744655e-07]\n", " [ 7.38982154e-08 -8.47884788e-08 -1.22126524e-07]\n", " [ -3.96716736e-08 4.51168052e-08 -1.25626966e-07]]\n" ] } ], "prompt_number": 26 }, { "cell_type": "code", "collapsed": false, "input": [ "# Update the crystal\n", "cryst.set_cell(qe.results['cell'])\n", "cryst.set_scaled_positions(qe.results['atomic_positions'])\n", "\n", "# Check the symmetry\n", "print \"Symmetry group:\", spglib.get_spacegroup(cryst,symprec=1e-4)" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Symmetry group: P2_1 (4)\n" ] } ], "prompt_number": 27 }, { "cell_type": "code", "collapsed": false, "input": [ "qe.set(calc='vc-relax')\n", "qe.reset()" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 28 }, { "cell_type": "code", "collapsed": false, "input": [ "print \"Stress:\n\", cryst.get_stress()/GPa\n", "print \"\nForces:\n\", cryst.get_forces()" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Stress:\n", "[ 0.068 0.069 0.067 0. 0. 0. ]" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "\n", "\n", "Forces:\n", "[[ -8.63442307e-08 -6.41747660e-08 3.96716736e-08]\n", " [ 7.07867116e-08 7.23424635e-08 3.07261001e-08]\n", " [ 4.58946812e-08 -3.65601697e-08 -3.65601697e-08]\n", " [ -3.03371621e-08 2.83924722e-08 -3.38376039e-08]]\n" ] } ], "prompt_number": 29 }, { "cell_type": "code", "collapsed": false, "input": [ "# Update the crystal\n", "cryst.set_cell(qe.results['cell'])\n", "cryst.set_scaled_positions(qe.results['atomic_positions'])\n", "\n", "# Check the symmetry\n", "print \"Symmetry group:\", spglib.get_spacegroup(cryst,symprec=1e-4)" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Symmetry group: C222_1 (20)\n" ] } ], "prompt_number": 30 }, { "cell_type": "code", "collapsed": false, "input": [ "qe.set(calc='vc-relax')\n", "qe.reset()" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 31 }, { "cell_type": "code", "collapsed": false, "input": [ "print \"Stress:\n\", cryst.get_stress()/GPa\n", "print \"\nForces:\n\", cryst.get_forces()" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Stress:\n", "[ 0.438 0.438 0.433 0. -0. 0. ]" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "\n", "\n", "Forces:\n", "[[ -6.10632622e-08 -4.04495495e-08 2.52809684e-08]\n", " [ 7.97322851e-08 5.56181306e-08 -5.05619369e-09]\n", " [ 2.02247748e-08 -1.82800849e-08 -1.28349532e-08]\n", " [ -3.88937976e-08 3.11150381e-09 -7.77875952e-09]]\n" ] } ], "prompt_number": 32 }, { "cell_type": "code", "collapsed": false, "input": [ "# Update the crystal\n", "cryst.set_cell(qe.results['cell'])\n", "cryst.set_scaled_positions(qe.results['atomic_positions'])\n", "\n", "# Check the symmetry\n", "print \"Symmetry group:\", spglib.get_spacegroup(cryst,symprec=1e-4)" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Symmetry group: C222_1 (20)\n" ] } ], "prompt_number": 33 }, { "cell_type": "code", "collapsed": false, "input": [ "qe.set(calc='vc-relax')\n", "qe.reset()" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 34 }, { "cell_type": "code", "collapsed": false, "input": [ "print \"Stress:\n\", cryst.get_stress()/GPa\n", "print \"\nForces:\n\", cryst.get_forces()" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Stress:\n", "[ 0.394 0.394 0.387 0. 0. 0. ]" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "\n", "\n", "Forces:\n", "[[ -5.25066268e-08 -4.23942394e-08 2.52809684e-08]\n", " [ 4.74504331e-08 5.71738825e-08 -1.94468988e-09]\n", " [ 3.30597280e-08 -2.02247748e-08 -1.43907051e-08]\n", " [ -2.80035343e-08 5.05619369e-09 -8.55663547e-09]]\n" ] } ], "prompt_number": 35 }, { "cell_type": "code", "collapsed": false, "input": [ "# Update the crystal\n", "cryst.set_cell(qe.results['cell'])\n", "cryst.set_scaled_positions(qe.results['atomic_positions'])\n", "\n", "# Check the symmetry\n", "print \"Symmetry group:\", spglib.get_spacegroup(cryst,symprec=1e-4)" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Symmetry group: C222_1 (20)\n" ] } ], "prompt_number": 36 }, { "cell_type": "code", "collapsed": false, "input": [ "qe.set(calc='vc-relax')\n", "qe.reset()" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 37 }, { "cell_type": "code", "collapsed": false, "input": [ "print \"Stress:\n\", cryst.get_stress()/GPa\n", "print \"\nForces:\n\", cryst.get_forces()" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Stress:\n", "[ 0.396 0.396 0.389 0. 0. 0. ]" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "\n", "\n", "Forces:\n", "[[ -5.25066268e-08 -4.20053014e-08 3.07261001e-08]\n", " [ 4.74504331e-08 5.71738825e-08 -4.27831774e-09]\n", " [ 3.30597280e-08 -2.02247748e-08 -1.59464570e-08]\n", " [ -2.80035343e-08 5.05619369e-09 -1.05013254e-08]]\n" ] } ], "prompt_number": 38 }, { "cell_type": "code", "collapsed": false, "input": [ "# Update the crystal\n", "cryst.set_cell(qe.results['cell'])\n", "cryst.set_scaled_positions(qe.results['atomic_positions'])\n", "\n", "# Check the symmetry\n", "print \"Symmetry group:\", spglib.get_spacegroup(cryst,symprec=1e-4)" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Symmetry group: C222_1 (20)\n" ] } ], "prompt_number": 39 }, { "cell_type": "code", "collapsed": false, "input": [ "qe.set(calc='vc-relax')\n", "qe.reset()" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 40 }, { "cell_type": "code", "collapsed": false, "input": [ "print \"Stress:\n\", cryst.get_stress()/GPa\n", "print \"\nForces:\n\", cryst.get_forces()" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Stress:\n", "[ 0.141 0.141 0.137 0. -0. 0. ]" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "\n", "\n", "Forces:\n", "[[ -6.96198977e-08 -1.20570773e-08 1.24460152e-08]\n", " [ 6.22300762e-08 2.45030925e-08 4.66725571e-09]\n", " [ 6.02853863e-08 8.55663547e-09 -2.87814102e-08]\n", " [ -5.28955647e-08 -2.10026507e-08 1.16681393e-08]]\n" ] } ], "prompt_number": 41 }, { "cell_type": "code", "collapsed": false, "input": [ "# Update the crystal\n", "cryst.set_cell(qe.results['cell'])\n", "cryst.set_scaled_positions(qe.results['atomic_positions'])\n", "\n", "# Check the symmetry\n", "print \"Symmetry group:\", spglib.get_spacegroup(cryst,symprec=1e-4)" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Symmetry group: C222_1 (20)\n" ] } ], "prompt_number": 42 }, { "cell_type": "code", "collapsed": false, "input": [ "\n", "\n", "# Round the sizes and positions to get to the high-symmetry structure\n", "cryst.set_cell(np.round(qe.results['cell'],4))\n", "cryst.set_scaled_positions(np.round(qe.results['atomic_positions'],3))\n", "\n", "# See the structure\n", "print \"Unit cell:\n\", cryst.get_cell()\n", "print \"\nAtomic positions:\n\", cryst.get_scaled_positions()\n", "\n" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Unit cell:\n", "[[ 2.7155 -0. 0. ]\n", " [-0. 2.7155 -0. ]\n", " [-0. 0. 3.7903]]\n", "\n", "Atomic positions:\n", "[[ 0.769 0.749 0.061]\n", " [ 0.269 0.25 0.561]\n", " [ 0.769 0.25 0.811]\n", " [ 0.269 0.75 0.311]]\n" ] } ], "prompt_number": 43 }, { "cell_type": "code", "collapsed": false, "input": [], "language": "python", "metadata": {}, "outputs": [] } ], "metadata": {} } ] }
Regards Linu