sym_explore.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "import pickle\n",
    "import pylada.crystal.read as pcread\n",
    "import pylada.crystal.write as pcwrite\n",
    "from copy import deepcopy\n",
    "from util import write_tcl\n",
    "import numpy.linalg as npl\n",
    "from pylada.crystal import supercell, space_group, into_cell\n",
    "from util import rot_euler\n",
    "from copy import deepcopy\n",
    "\n",
    "\n",
    "\n",
    "class Options():\n",
    "    def __init__(self):\n",
    "        self.output_tiles = 1\n",
    "options = Options()\n",
    "\n",
    "\n",
    "def basic_tform_cell(M, A):\n",
    "    # transform cell by a left multiplication\n",
    "    from copy import deepcopy\n",
    "    B = deepcopy(A)\n",
    "    B.cell = np.dot(M, A.cell)\n",
    "    for b in B:\n",
    "        b.pos = into_cell(np.dot(M, b.pos), B.cell)\n",
    "    return B\n",
    "\n",
    "\n",
    "\n",
    "def eq_struct(s1,s2):\n",
    "    eqc = npl.norm(s1.cell-s2.cell) < 1e-6\n",
    "#    vals = [npl.norm(s1[k].pos - s2[k].pos) for k in range(len(s1))]\n",
    "#    print vals\n",
    "    vals = [npl.norm(s1[k].pos - s2[k].pos) < 1e-6 for k in range(len(s1))]\n",
    "#    print vals\n",
    "    eqp = all(vals)\n",
    "    return eqc and eqp\n",
    "    \n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "192\n",
      "Structure( 10, 5, 0,\n",
      "           5, 10, 0,\n",
      "           0, 0, 10,\n",
      "           scale=1, name='icsd_100672.cif' )\\\n",
      "  .add_atom(8.5, 5, 0, 'Al')\\\n",
      "  .add_atom(4.5, 4.5, 0, 'Sn')\n"
     ]
    }
   ],
   "source": [
    "\n",
    "def load_sym_dict(symloc):\n",
    "    with open(symloc,'rb') as handle:\n",
    "        syms=pickle.loads(handle.read())\n",
    "    return syms\n",
    "\n",
    "\n",
    "def load_syms(symloc, space_group):\n",
    "    with open(symloc,'rb') as handle:\n",
    "        syms=pickle.loads(handle.read())[space_group]\n",
    "    return syms\n",
    "\n",
    "def load_all_syms():\n",
    "    ## this is the space group that includes all 192 possible operations\n",
    "    symidx = 227\n",
    "#    symidx = 168\n",
    "    syms = load_syms(\"symmetries.pickle\", symidx)\n",
    "    return syms\n",
    "\n",
    "syms = load_all_syms()\n",
    "symdict = load_sym_dict(\"symmetries.pickle\")\n",
    "\n",
    "print len(syms)\n",
    "\n",
    "s = pcread.poscar(\"symtest.vasp\")\n",
    "print s"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "ename": "NameError",
     "evalue": "name 'syms' is not defined",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-2-48a7d9d0401b>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m \u001b[0ms2\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mbasic_tform_cell\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msyms\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0msymidx\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0ms\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      3\u001b[0m \u001b[0;32mprint\u001b[0m \u001b[0ms2\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      4\u001b[0m \u001b[0mpcwrite\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mposcar\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0ms2\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"sym2.vasp\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvasp5\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mTrue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      5\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mNameError\u001b[0m: name 'syms' is not defined"
     ]
    }
   ],
   "source": [
    "\n",
    "s2 = basic_tform_cell(syms[symidx], s)\n",
    "print s2\n",
    "pcwrite.poscar(s2, \"sym2.vasp\", vasp5=True)\n",
    "\n",
    "write_tcl(options,s,s2,[],\"nb1\")\n",
    "M = np.dot(s.cell, npl.inv(s2.cell))\n",
    "s3 = basic_tform_cell(M, s2)\n",
    "print s3\n",
    "write_tcl(options,s,s3,[],\"nb2\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "192 ARE equal\n"
     ]
    }
   ],
   "source": [
    "eq = []\n",
    "for i in range(len(syms)):\n",
    "    s2 = basic_tform_cell(syms[i], s)\n",
    "    M = np.dot(s.cell, npl.inv(s2.cell))\n",
    "    s3 = basic_tform_cell(M, s2)\n",
    "    if (not eq_struct(s,s3)):\n",
    "        print s\n",
    "        print \"AND\"\n",
    "        print s3\n",
    "        print \"are not equal\"\n",
    "    else:\n",
    "        eq.append(i)\n",
    "print len(eq), \"ARE equal\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "\n",
    "s2 = pcread.poscar(\"symtest.sym.vasp\")\n",
    "s3 = basic_tform_cell(rot_euler(0,0,180), s2)\n",
    "for a in s3:\n",
    "    a.pos = into_cell(a.pos, s2.cell)\n",
    "print s3\n",
    "print s\n",
    "\n",
    "sg = space_group(s)\n",
    "\n",
    "eq = []\n",
    "neq = []\n",
    "for i in range(len(syms)):\n",
    "#    s3 = basic_tform_cell(syms[i], s2)\n",
    "    s3 = deepcopy(s2)\n",
    "    for a in s3:\n",
    "        a.pos = into_cell(np.dot(syms[i],a.pos), s2.cell)\n",
    "#    s3.cell = np.dot(npl.inv(syms[i]),s3.cell)\n",
    "        \n",
    "    if (not eq_struct(s,s3)):\n",
    "        neq.append(i)\n",
    "    else:\n",
    "        eq.append(i)\n",
    "        print syms[i]\n",
    "print len(eq), \"ARE equal\"\n",
    "print len(neq), \"are NOT equal\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "ss=  deepcopy(s)\n",
    "ss.clear()\n",
    "ss.add_atom(0,0,0,'Au')\n",
    "print ss\n",
    "sg = space_group(ss)\n",
    "print len(sg)\n",
    "print sg"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "sq = pcread.poscar(\"symtest.square.vasp\")\n",
    "sg = space_group(sq)\n",
    "print len(sg)\n",
    "for g in sg:\n",
    "    print g"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "7.47219219373\n",
      "[[-1.  0.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 0.  1.  0.]]\n",
      "symmetry 0 is not a symmetry for this cell\n",
      "[[ 1.  0.  0.]\n",
      " [ 0.  1.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 1.  0.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 0. -1.  0.]]\n",
      "symmetry 1 is not a symmetry for this cell\n",
      "[[-1.  0.  0.]\n",
      " [ 0. -1.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 0.  1.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [-1.  0.  0.]]\n",
      "symmetry 2 is not a symmetry for this cell\n",
      "[[ 0. -1.  0.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 1.  0.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 0. -1.  0.]]\n",
      "symmetry 3 is not a symmetry for this cell\n",
      "[[-1.  0.  0.]\n",
      " [ 0. -1.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 0.  1.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [-1.  0.  0.]]\n",
      "symmetry 4 is not a symmetry for this cell\n",
      "[[ 0. -1.  0.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 1.  0.  0.]\n",
      " [ 0. -1.  0.]\n",
      " [ 0.  0.  1.]]\n",
      "symmetry 5 is not a symmetry for this cell\n",
      "[[-1.  0.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 0.  1.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 0.  0. -1.]\n",
      " [ 0. -1.  0.]\n",
      " [-1.  0.  0.]]\n",
      "symmetry 6 is not a symmetry for this cell\n",
      "[[ 0. -1.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 1.  0.  0.]\n",
      " [ 0.  1.  0.]\n",
      " [ 0.  0.  1.]]\n",
      "symmetry 7 is not a symmetry for this cell\n",
      "[[-1.  0.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 0.  1.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 0.  0. -1.]\n",
      " [ 0.  1.  0.]\n",
      " [-1.  0.  0.]]\n",
      "symmetry 8 is not a symmetry for this cell\n",
      "[[ 0. -1.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 0.  1.  0.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  0.  1.]]\n",
      "symmetry 9 is not a symmetry for this cell\n",
      "[[ 0.  0. -1.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  1.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 0.  0. -1.]\n",
      " [-1.  0.  0.]\n",
      " [ 0. -1.  0.]]\n",
      "symmetry 10 is not a symmetry for this cell\n",
      "[[ 0.  0. -1.]\n",
      " [ 0. -1.  0.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 0.  1.  0.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  0.  1.]]\n",
      "symmetry 11 is not a symmetry for this cell\n",
      "[[ 0.  0.  1.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  1.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 0.  0. -1.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0. -1.  0.]]\n",
      "symmetry 12 is not a symmetry for this cell\n",
      "[[ 0.  0.  1.]\n",
      " [ 0. -1.  0.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 1.  0.  0.]\n",
      " [ 0. -1.  0.]\n",
      " [ 0.  0. -1.]]\n",
      "symmetry 13 is not a symmetry for this cell\n",
      "[[-1.  0.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 0. -1.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 1.  0.  0.]\n",
      " [ 0.  1.  0.]\n",
      " [ 0.  0. -1.]]\n",
      "symmetry 14 is not a symmetry for this cell\n",
      "[[-1.  0.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 0. -1.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 0.  0.  1.]\n",
      " [ 0. -1.  0.]\n",
      " [-1.  0.  0.]]\n",
      "symmetry 15 is not a symmetry for this cell\n",
      "[[ 0. -1.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 0.  0.  1.]\n",
      " [ 0.  1.  0.]\n",
      " [-1.  0.  0.]]\n",
      "symmetry 16 is not a symmetry for this cell\n",
      "[[ 0. -1.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 1.  0.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 0.  1.  0.]]\n",
      "symmetry 17 is not a symmetry for this cell\n",
      "[[-1.  0.  0.]\n",
      " [ 0.  1.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 1.  0.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 0.  1.  0.]]\n",
      "symmetry 18 is not a symmetry for this cell\n",
      "[[-1.  0.  0.]\n",
      " [ 0.  1.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 0. -1.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [-1.  0.  0.]]\n",
      "symmetry 19 is not a symmetry for this cell\n",
      "[[ 0. -1.  0.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 0. -1.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [-1.  0.  0.]]\n",
      "symmetry 20 is not a symmetry for this cell\n",
      "[[ 0. -1.  0.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 0.  1.  0.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  0. -1.]]\n",
      "symmetry 21 is not a symmetry for this cell\n",
      "[[ 0.  0. -1.]\n",
      " [-1.  0.  0.]\n",
      " [ 0. -1.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 0.  0.  1.]\n",
      " [-1.  0.  0.]\n",
      " [ 0. -1.  0.]]\n",
      "symmetry 22 is not a symmetry for this cell\n",
      "[[ 0.  0. -1.]\n",
      " [ 0. -1.  0.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 0.  1.  0.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  0. -1.]]\n",
      "symmetry 23 is not a symmetry for this cell\n",
      "[[ 0.  0.  1.]\n",
      " [-1.  0.  0.]\n",
      " [ 0. -1.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 0.  0.  1.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0. -1.  0.]]\n",
      "symmetry 24 is not a symmetry for this cell\n",
      "[[ 0.  0.  1.]\n",
      " [ 0. -1.  0.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 0.  0. -1.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  1.  0.]]\n",
      "symmetry 25 is not a symmetry for this cell\n",
      "[[ 0.  0. -1.]\n",
      " [ 0.  1.  0.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 0. -1.  0.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  0.  1.]]\n",
      "symmetry 26 is not a symmetry for this cell\n",
      "[[ 0.  0. -1.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  1.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 0.  0. -1.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  1.  0.]]\n",
      "symmetry 27 is not a symmetry for this cell\n",
      "[[ 0.  0.  1.]\n",
      " [ 0.  1.  0.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 0. -1.  0.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  0.  1.]]\n",
      "symmetry 28 is not a symmetry for this cell\n",
      "[[ 0.  0.  1.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  1.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 0.  1.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 1.  0.  0.]]\n",
      "symmetry 29 is not a symmetry for this cell\n",
      "[[ 0.  1.  0.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 0.  1.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 1.  0.  0.]]\n",
      "symmetry 30 is not a symmetry for this cell\n",
      "[[ 0.  1.  0.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[-1.  0.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 0. -1.  0.]]\n",
      "symmetry 31 is not a symmetry for this cell\n",
      "[[ 1.  0.  0.]\n",
      " [ 0. -1.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[-1.  0.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 0. -1.  0.]]\n",
      "symmetry 32 is not a symmetry for this cell\n",
      "[[ 1.  0.  0.]\n",
      " [ 0. -1.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 0.  0. -1.]\n",
      " [ 0. -1.  0.]\n",
      " [ 1.  0.  0.]]\n",
      "symmetry 33 is not a symmetry for this cell\n",
      "[[ 0.  1.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 0.  0. -1.]\n",
      " [ 0.  1.  0.]\n",
      " [ 1.  0.  0.]]\n",
      "symmetry 34 is not a symmetry for this cell\n",
      "[[ 0.  1.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[-1.  0.  0.]\n",
      " [ 0. -1.  0.]\n",
      " [ 0.  0.  1.]]\n",
      "symmetry 35 is not a symmetry for this cell\n",
      "[[ 1.  0.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 0.  1.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[-1.  0.  0.]\n",
      " [ 0.  1.  0.]\n",
      " [ 0.  0.  1.]]\n",
      "symmetry 36 is not a symmetry for this cell\n",
      "[[ 1.  0.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 0.  1.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 0.  0.  1.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  1.  0.]]\n",
      "symmetry 37 is not a symmetry for this cell\n",
      "[[ 0.  0. -1.]\n",
      " [ 0.  1.  0.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 0. -1.  0.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  0. -1.]]\n",
      "symmetry 38 is not a symmetry for this cell\n",
      "[[ 0.  0. -1.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0. -1.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 0.  0.  1.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  1.  0.]]\n",
      "symmetry 39 is not a symmetry for this cell\n",
      "[[ 0.  0.  1.]\n",
      " [ 0.  1.  0.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 0. -1.  0.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  0. -1.]]\n",
      "symmetry 40 is not a symmetry for this cell\n",
      "[[ 0.  0.  1.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0. -1.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 0.  0.  1.]\n",
      " [ 0. -1.  0.]\n",
      " [ 1.  0.  0.]]\n",
      "symmetry 41 is not a symmetry for this cell\n",
      "[[ 0.  1.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[-1.  0.  0.]\n",
      " [ 0. -1.  0.]\n",
      " [ 0.  0. -1.]]\n",
      "symmetry 42 is not a symmetry for this cell\n",
      "[[ 1.  0.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 0. -1.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 0.  0.  1.]\n",
      " [ 0.  1.  0.]\n",
      " [ 1.  0.  0.]]\n",
      "symmetry 43 is not a symmetry for this cell\n",
      "[[ 0.  1.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[-1.  0.  0.]\n",
      " [ 0.  1.  0.]\n",
      " [ 0.  0. -1.]]\n",
      "symmetry 44 is not a symmetry for this cell\n",
      "[[ 1.  0.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 0. -1.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 0. -1.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 1.  0.  0.]]\n",
      "symmetry 45 is not a symmetry for this cell\n",
      "[[ 0.  1.  0.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[ 0. -1.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 1.  0.  0.]]\n",
      "symmetry 46 is not a symmetry for this cell\n",
      "[[ 0.  1.  0.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "7.47219219373\n",
      "[[-1.  0.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 0.  1.  0.]]\n",
      "symmetry 47 is not a symmetry for this cell\n",
      "[[ 1.  0.  0.]\n",
      " [ 0.  1.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 0.  0.  0.]]\n",
      "\n",
      "Found 0 syms that could produce matching cells and 48 that cannot\n"
     ]
    }
   ],
   "source": [
    "s1 = pcread.poscar(\"symtest.vasp\")\n",
    "s2 = pcread.poscar(\"symtest.sym.vasp\")\n",
    "#s1 = pcread.poscar(\"symtest.square.vasp\")\n",
    "#s2 = basic_tform_cell(rot_euler(0,0,90), s1)\n",
    "\n",
    "s1 = pcread.poscar(\"badsns_a\")\n",
    "s2 = pcread.poscar(\"badsns_b\")\n",
    "\n",
    "fcc = Structure([[0.5,0.5,0],[0.5,0,0.5],[0,0.5,0.5]])\n",
    "fcc.add_atom(0,0,0,\"Au\")\n",
    "grp = space_group(fcc)\n",
    "\n",
    "def eq_latt(A,B):\n",
    "    mind = 1e10\n",
    "    eps = 1e-1\n",
    "    goodP = []\n",
    "    perms = [[0,1,2],[0,2,1],[1,0,2],[1,2,0],[2,0,1],[2,1,0]]  ## permute a,b,c in case there are other orders also good\n",
    "    for i in range(-1,2,2):\n",
    "        for j in range(-1,2,2):\n",
    "            for k in range(-1,2,2):\n",
    "                for p in perms:\n",
    "                    P = np.zeros((3,3))\n",
    "                    for m in range(3):\n",
    "                        P[p[0],0] = i\n",
    "                        P[p[1],1] = j\n",
    "                        P[p[2],2] = k\n",
    "                    diff = npl.norm(np.dot(P,A) - B)\n",
    "                    if (diff < mind):\n",
    "                        minP = P\n",
    "                        mind = diff\n",
    "\n",
    "                    if diff < eps:\n",
    "                        print \"eq enough latt\"\n",
    "                        print diff\n",
    "#                        print A\n",
    "#                        print B\n",
    "#                        print np.dot(P,A)\n",
    "\n",
    "                        print P\n",
    "                        goodP.append(P)\n",
    "    print mind\n",
    "    print minP\n",
    "    return (goodP)\n",
    "                    \n",
    "eq = []\n",
    "neq = []\n",
    "#for i in range(len(syms)):\n",
    "#for i in range(10):\n",
    "for i in range(len(grp)):\n",
    "    g = grp[i]\n",
    "    test_cell = np.dot(g[0:3,0:3], s2.cell)\n",
    "    gp = eq_latt(test_cell, s1.cell)\n",
    "    if (len(gp) > 0):\n",
    "        print \"symmetry %d has %d perms that look good\" % (i, len(gp))\n",
    "        print g\n",
    "        print \n",
    "        eq.append(i)\n",
    "    else:\n",
    "        print \"symmetry %d is not a symmetry for this cell\" % (i)\n",
    "        print g\n",
    "        print \n",
    "        neq.append(i)\n",
    "        \n",
    "#    for a in s3:\n",
    "#        a.pos = into_cell(np.dot(syms[i],a.pos), s2.cell)\n",
    "#    s3.cell = np.dot(npl.inv(syms[i]),s3.cell)\n",
    "        \n",
    "print \"Found %d syms that could produce matching cells and %d that cannot\" % (len(eq),len(neq))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "ename": "NameError",
     "evalue": "name 'symdict' is not defined",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-3-905ce7ca708b>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mset_printoptions\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mprecision\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m3\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      2\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mset_printoptions\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msuppress\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mTrue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 3\u001b[0;31m \u001b[0;32mfor\u001b[0m \u001b[0msym\u001b[0m \u001b[0;32min\u001b[0m \u001b[0msymdict\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mkeys\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      4\u001b[0m     \u001b[0;32mprint\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      5\u001b[0m     \u001b[0;32mprint\u001b[0m \u001b[0msym\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mNameError\u001b[0m: name 'symdict' is not defined"
     ]
    }
   ],
   "source": [
    "np.set_printoptions(precision=3)\n",
    "np.set_printoptions(suppress=True)\n",
    "for sym in symdict.keys():\n",
    "    print \n",
    "    print sym\n",
    "    for s in symdict[sym]:\n",
    "        print s\n",
    "    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "def eq_sym(s,t):\n",
    "    eps = 1e-15\n",
    "    return (npl.norm(s-t) < eps)\n",
    "\n",
    "def find_sym(s, symset):\n",
    "    for sym in symset:\n",
    "        if eq_sym(s, sym):\n",
    "            return True\n",
    "    return False\n",
    "\n",
    "def get_sym_set(symdict):\n",
    "    symset = []\n",
    "    for k in symdict.keys():\n",
    "        for s in symdict[k]:\n",
    "            if not find_sym(s,symset):\n",
    "                symset.append(s)\n",
    "    return symset"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[[ 1.  0.  0.]\n",
      " [ 0.  1.  0.]\n",
      " [ 0.  0.  1.]]\n",
      "[[-1.  0.  0.]\n",
      " [ 0. -1.  0.]\n",
      " [ 0.  0. -1.]]\n",
      "[[-1.  0.  0.]\n",
      " [ 0.  1. -0.]\n",
      " [ 0.  0. -1.]]\n",
      "[[ 1. -0.  0.]\n",
      " [ 0. -1.  0.]\n",
      " [ 0.  0.  1.]]\n",
      "[[ 1. -0. -0.]\n",
      " [ 0. -1.  0.]\n",
      " [ 0.  0. -1.]]\n",
      "[[-1.  0.  0.]\n",
      " [ 0. -1.  0.]\n",
      " [ 0.  0.  1.]]\n",
      "[[-1.  0.  0.]\n",
      " [ 0.  1.  0.]\n",
      " [ 0.  0.  1.]]\n",
      "[[ 1.  0. -0.]\n",
      " [ 0.  1. -0.]\n",
      " [ 0.  0. -1.]]\n",
      "[[ 0. -1.  0.]\n",
      " [ 1. -0.  0.]\n",
      " [ 0.  0.  1.]]\n",
      "[[-0.  1.  0.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  0.  1.]]\n",
      "[[ 0. -1.  0.]\n",
      " [ 1. -0. -0.]\n",
      " [ 0.  0. -1.]]\n",
      "[[-0.  1. -0.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  0. -1.]]\n",
      "[[ 0.  1. -0.]\n",
      " [ 1. -0. -0.]\n",
      " [ 0.  0. -1.]]\n",
      "[[-0. -1.  0.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  0. -1.]]\n",
      "[[-0. -1.  0.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  0.  1.]]\n",
      "[[ 0.  1.  0.]\n",
      " [ 1. -0.  0.]\n",
      " [ 0.  0.  1.]]\n",
      "[[-0.5    0.866  0.   ]\n",
      " [-0.866 -0.5    0.   ]\n",
      " [ 0.     0.     1.   ]]\n",
      "[[-0.5   -0.866  0.   ]\n",
      " [ 0.866 -0.5    0.   ]\n",
      " [ 0.     0.     1.   ]]\n",
      "[[ 0.5   -0.866 -0.   ]\n",
      " [ 0.866  0.5   -0.   ]\n",
      " [ 0.     0.    -1.   ]]\n",
      "[[ 0.5    0.866 -0.   ]\n",
      " [-0.866  0.5   -0.   ]\n",
      " [ 0.     0.    -1.   ]]\n",
      "[[ 0.5    0.866 -0.   ]\n",
      " [ 0.866 -0.5   -0.   ]\n",
      " [ 0.     0.    -1.   ]]\n",
      "[[ 0.5   -0.866 -0.   ]\n",
      " [-0.866 -0.5    0.   ]\n",
      " [ 0.     0.    -1.   ]]\n",
      "[[-0.5   -0.866  0.   ]\n",
      " [-0.866  0.5   -0.   ]\n",
      " [ 0.     0.    -1.   ]]\n",
      "[[-0.5    0.866 -0.   ]\n",
      " [ 0.866  0.5   -0.   ]\n",
      " [ 0.     0.    -1.   ]]\n",
      "[[ 0.013  0.013 -1.   ]\n",
      " [ 0.013 -1.    -0.013]\n",
      " [-1.    -0.013 -0.013]]\n",
      "[[-0.013 -0.013  1.   ]\n",
      " [ 1.    -0.     0.013]\n",
      " [ 0.     1.     0.013]]\n",
      "[[-1.     0.     0.   ]\n",
      " [ 0.     0.013 -1.   ]\n",
      " [ 0.    -1.    -0.013]]\n",
      "[[-0.013  1.    -0.   ]\n",
      " [-0.013 -0.     1.   ]\n",
      " [ 1.     0.013  0.013]]\n",
      "[[ 0.013 -1.     0.   ]\n",
      " [-1.    -0.013  0.   ]\n",
      " [ 0.     0.    -1.   ]]\n",
      "[[ 0.5    0.866 -0.   ]\n",
      " [ 0.866 -0.5    0.   ]\n",
      " [ 0.     0.     1.   ]]\n",
      "[[ 0.5   -0.866  0.   ]\n",
      " [-0.866 -0.5    0.   ]\n",
      " [ 0.     0.     1.   ]]\n",
      "[[-0.5   -0.866  0.   ]\n",
      " [-0.866  0.5    0.   ]\n",
      " [ 0.     0.     1.   ]]\n",
      "[[-0.5    0.866 -0.   ]\n",
      " [ 0.866  0.5    0.   ]\n",
      " [ 0.     0.     1.   ]]\n",
      "[[ 0.5   -0.866  0.   ]\n",
      " [ 0.866  0.5    0.   ]\n",
      " [ 0.     0.     1.   ]]\n",
      "[[ 0.5    0.866 -0.   ]\n",
      " [-0.866  0.5    0.   ]\n",
      " [ 0.     0.     1.   ]]\n",
      "[[-0.5    0.866 -0.   ]\n",
      " [-0.866 -0.5   -0.   ]\n",
      " [ 0.     0.    -1.   ]]\n",
      "[[-0.5   -0.866  0.   ]\n",
      " [ 0.866 -0.5   -0.   ]\n",
      " [ 0.     0.    -1.   ]]\n",
      "[[-0.5    0.866 -0.   ]\n",
      " [-0.866 -0.5   -0.   ]\n",
      " [ 0.     0.    -1.   ]]\n",
      "[[-0.5   -0.866  0.   ]\n",
      " [ 0.866 -0.5   -0.   ]\n",
      " [ 0.     0.    -1.   ]]\n",
      "[[ 0.5   -0.866  0.   ]\n",
      " [ 0.866  0.5   -0.   ]\n",
      " [ 0.     0.    -1.   ]]\n",
      "[[ 0.5    0.866 -0.   ]\n",
      " [-0.866  0.5   -0.   ]\n",
      " [ 0.     0.    -1.   ]]\n",
      "[[ 0.5   -0.866  0.   ]\n",
      " [ 0.866  0.5    0.   ]\n",
      " [ 0.     0.     1.   ]]\n",
      "[[ 0.5    0.866 -0.   ]\n",
      " [-0.866  0.5    0.   ]\n",
      " [ 0.     0.     1.   ]]\n",
      "[[-0.5    0.866 -0.   ]\n",
      " [-0.866 -0.5    0.   ]\n",
      " [ 0.     0.     1.   ]]\n",
      "[[-0.5   -0.866  0.   ]\n",
      " [ 0.866 -0.5    0.   ]\n",
      " [ 0.     0.     1.   ]]\n",
      "[[-0.  0. -1.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  1. -0.]]\n",
      "[[ 0. -1. -0.]\n",
      " [ 0. -0. -1.]\n",
      " [ 1. -0. -0.]]\n",
      "[[ 0. -0. -1.]\n",
      " [ 1. -0. -0.]\n",
      " [ 0. -1.  0.]]\n",
      "[[-0. -1.  0.]\n",
      " [-0.  0.  1.]\n",
      " [-1.  0.  0.]]\n",
      "[[-0. -0.  1.]\n",
      " [-1.  0.  0.]\n",
      " [ 0. -1.  0.]]\n",
      "[[-0.  1. -0.]\n",
      " [-0.  0. -1.]\n",
      " [-1.  0.  0.]]\n",
      "[[ 0.  0.  1.]\n",
      " [ 1.  0. -0.]\n",
      " [ 0.  1. -0.]]\n",
      "[[ 0.  1. -0.]\n",
      " [ 0. -0.  1.]\n",
      " [ 1. -0. -0.]]\n",
      "[[ 0.  0. -1.]\n",
      " [ 1.  0. -0.]\n",
      " [ 0.  1. -0.]]\n",
      "[[ 0. -0.  1.]\n",
      " [ 1. -0. -0.]\n",
      " [ 0. -1.  0.]]\n",
      "[[-0.  0.  1.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  1. -0.]]\n",
      "[[-0. -0. -1.]\n",
      " [-1.  0.  0.]\n",
      " [ 0. -1.  0.]]\n",
      "[[ 0.  1. -0.]\n",
      " [ 0. -0. -1.]\n",
      " [ 1. -0. -0.]]\n",
      "[[ 0. -1.  0.]\n",
      " [ 0. -0.  1.]\n",
      " [ 1. -0. -0.]]\n",
      "[[-0.  1.  0.]\n",
      " [-0.  0.  1.]\n",
      " [-1.  0.  0.]]\n",
      "[[-0. -1.  0.]\n",
      " [-0.  0. -1.]\n",
      " [-1.  0.  0.]]\n",
      "[[ 0.  0. -1.]\n",
      " [ 0.  1. -0.]\n",
      " [ 1. -0. -0.]]\n",
      "[[ 0. -0.  1.]\n",
      " [ 0. -1.  0.]\n",
      " [ 1. -0. -0.]]\n",
      "[[-0.  0.  1.]\n",
      " [-0.  1. -0.]\n",
      " [-1.  0.  0.]]\n",
      "[[-0. -0. -1.]\n",
      " [-0. -1.  0.]\n",
      " [-1.  0.  0.]]\n",
      "[[ 1.  0. -0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 0.  1. -0.]]\n",
      "[[ 1. -0.  0.]\n",
      " [ 0. -0.  1.]\n",
      " [ 0. -1.  0.]]\n",
      "[[-1.  0.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 0.  1. -0.]]\n",
      "[[-1.  0.  0.]\n",
      " [ 0. -0. -1.]\n",
      " [ 0. -1.  0.]]\n",
      "[[ 0. -0. -1.]\n",
      " [ 0. -1.  0.]\n",
      " [ 1. -0. -0.]]\n",
      "[[-1.  0. -0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 0.  1. -0.]]\n",
      "[[-0.  0. -1.]\n",
      " [-0.  1. -0.]\n",
      " [-1.  0.  0.]]\n",
      "[[-1.  0.  0.]\n",
      " [ 0. -0.  1.]\n",
      " [ 0. -1.  0.]]\n",
      "[[-0. -0.  1.]\n",
      " [-0. -1.  0.]\n",
      " [-1.  0.  0.]]\n",
      "[[ 1. -0. -0.]\n",
      " [ 0. -0. -1.]\n",
      " [ 0. -1.  0.]]\n",
      "[[ 0.  0.  1.]\n",
      " [ 0.  1. -0.]\n",
      " [ 1. -0. -0.]]\n",
      "[[ 1.  0. -0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 0.  1. -0.]]\n",
      "77\n",
      "229\n"
     ]
    }
   ],
   "source": [
    "symset = get_sym_set(symdict)\n",
    "for s in symset:\n",
    "    print s\n",
    "print len(symset)\n",
    "print len(symdict)\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "30.002910931188026"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from math import acos,pi\n",
    "acos (.866) * 180./pi"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "192\n",
      "229\n"
     ]
    }
   ],
   "source": [
    "print len(syms)\n",
    "print len(symdict)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Ccmm (63)\n",
      "Pnma (62)\n",
      "P-1 (2)\n",
      "Structure( -4.148, 2.55767e-16, 2.074,\n",
      "           0, 2.55767e-16, 5.74,\n",
      "           0, 4.177, 0,\n",
      "           scale=1, name='icsd_100672.cif' )\\\n",
      "  .add_atom(-3.80147e-16, 4.00652, 1.04425, 'Al')\\\n",
      "  .add_atom(-2.074, 1.73348, 3.13275, 'Al')\\\n",
      "  .add_atom(2.85986e-16, 1.3776, 1.04425, 'Sn')\\\n",
      "  .add_atom(-2.074, 4.3624, 3.13275, 'Sn')\n",
      "Structure( 11.1827, 2.43503e-16, 2.64769e-16,\n",
      "           0, 3.9767, 2.64769e-16,\n",
      "           0, 0, 4.324,\n",
      "           scale=1, name='icsd_651025.cif' )\\\n",
      "  .add_atom(9.5053, 0.994175, 2.15335, 'Al')\\\n",
      "  .add_atom(3.91395, 0.994175, 0.008648, 'Al')\\\n",
      "  .add_atom(1.67741, 2.98252, 2.17065, 'Al')\\\n",
      "  .add_atom(7.26876, 2.98253, 4.31535, 'Al')\\\n",
      "  .add_atom(6.96682, 0.994175, 1.82905, 'Sn')\\\n",
      "  .add_atom(1.37547, 0.994175, 0.332948, 'Sn')\\\n",
      "  .add_atom(4.21588, 2.98252, 2.49495, 'Sn')\\\n",
      "  .add_atom(9.80723, 2.98253, 3.99105, 'Sn')\n",
      "Structure( 3.9767, -2.64769e-16, 0,\n",
      "           0, 4.324, 0,\n",
      "           2.43503e-16, 2.64769e-16, 11.1827,\n",
      "           scale=1, name='supercell of supercell of supercell of supercell of icsd_651025.cif' )\\\n",
      "  .add_atom(0.985527, 3.32983, 3.91395, 'Al')\\\n",
      "  .add_atom(2.81752, 3.32983, 9.5053, 'Al')\\\n",
      "  .add_atom(1.00282, 0.994175, 7.26876, 'Al')\\\n",
      "  .add_atom(3.14753, 0.994175, 1.67741, 'Al')\\\n",
      "  .add_atom(0.661227, 3.32983, 1.37547, 'Sn')\\\n",
      "  .add_atom(3.14182, 3.32983, 6.96682, 'Sn')\\\n",
      "  .add_atom(1.32712, 0.994175, 9.80723, 'Sn')\\\n",
      "  .add_atom(2.82323, 0.994175, 4.21588, 'Sn')\n"
     ]
    }
   ],
   "source": [
    "from pyspglib import spglib\n",
    "s = pcread.poscar(\"traj0.vasp\")\n",
    "a = pcread.poscar(\"badsns_a\")\n",
    "b = pcread.poscar(\"badsns_b\")\n",
    "\n",
    "\n",
    "sg = spglib.get_spacegroup(a, symprec=1e-4, angle_tolerance=2.0)\n",
    "print sg\n",
    "\n",
    "sg = spglib.get_spacegroup(b, symprec=1e-4, angle_tolerance=2.0)\n",
    "print sg\n",
    "\n",
    "sg = spglib.get_spacegroup(s, symprec=1e-3, angle_tolerance=3.0)\n",
    "print sg\n",
    "\n",
    "print a\n",
    "print b\n",
    "print s"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Structure( 10, 5, 0,\n",
      "           5, 10, 0,\n",
      "           0, 0, 10,\n",
      "           scale=1, name='icsd_100672.cif' )\\\n",
      "  .add_atom(8.5, 5, 0, 'Al')\\\n",
      "  .add_atom(4.5, 4.5, 0, 'Sn')\n",
      "Structure( 10, 5, 0,\n",
      "           5, 10, 0,\n",
      "           0, 0, 10,\n",
      "           scale=1, name='icsd_100672.cif' )\\\n",
      "  .add_atom(6.5, 10, 0, 'Al')\\\n",
      "  .add_atom(10.5, 10.5, 0, 'Sn')\n",
      "[[ 1.  0.  0.]\n",
      " [ 0.  1.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 0.  0.  0.]]\n",
      "False\n",
      "[[-1.  0.  0.]\n",
      " [ 0. -1.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 0.  0.  0.]]\n",
      "True\n",
      "[[-1.  0.  0.]\n",
      " [ 0. -1.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 0.  0.  0.]]\n",
      "True\n",
      "[[ 0. -1.  0.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 0.  0.  0.]]\n",
      "False\n",
      "[[ 0. -1.  0.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 0.  0.  0.]]\n",
      "False\n",
      "[[ 0.  1.  0.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 0.  0.  0.]]\n",
      "False\n",
      "[[ 0.  1.  0.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 0.  0.  0.]]\n",
      "False\n",
      "[[ 1.  0.  0.]\n",
      " [ 0.  1.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 0.  0.  0.]]\n",
      "False\n"
     ]
    }
   ],
   "source": [
    "s1 = pcread.poscar(\"symtest.vasp\")\n",
    "s2 = pcread.poscar(\"symtest.sym.vasp\")\n",
    "\n",
    "print s1\n",
    "print s2\n",
    "from pylada.crystal import Structure\n",
    "s3 = Structure(s2.cell)\n",
    "s3.add_atom(0,0,0, 'Au')\n",
    "grp = space_group(s3)\n",
    "for g in grp:\n",
    "    print g\n",
    "    stest = deepcopy(s2)\n",
    "    for a in stest:\n",
    "        a.pos = into_cell(np.dot(g[0:3,0:3], a.pos), stest.cell)\n",
    "    print eq_struct(stest, s1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[[-4.148  0.     2.074]\n",
      " [ 0.     0.     5.74 ]\n",
      " [ 0.     4.177  0.   ]]\n",
      "[[ 11.183   0.      0.   ]\n",
      " [  0.      3.977   0.   ]\n",
      " [  0.      0.      4.324]]\n",
      "sns_A\n",
      "8\n",
      "sns_B\n",
      "8\n"
     ]
    }
   ],
   "source": [
    "s1 = pcread.poscar(\"badsns_a\")\n",
    "s2 = pcread.poscar(\"badsns_b\")\n",
    "print s1.cell\n",
    "print s2.cell\n",
    "s3 = Structure(s1.cell)\n",
    "s3.add_atom(0,0,0, 'Au')\n",
    "tol = 10.\n",
    "grp = space_group(s3,tol)\n",
    "print \"sns_A\"\n",
    "print len(grp)\n",
    "s3 = Structure(s2.cell)\n",
    "s3.add_atom(0,0,0, 'Au')\n",
    "grp = space_group(s3, tol)\n",
    "print \"sns_B\"\n",
    "print len(grp)\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "48\n",
      "[[ 1.  0.  0.]\n",
      " [ 0.  1.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 0.  0.  0.]]\n",
      "[[-1.  0.  0.]\n",
      " [ 0. -1.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 0. -1.  0.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 0.  0.  0.]]\n",
      "[[-1.  0.  0.]\n",
      " [ 0. -1.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 0. -1.  0.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 0.  0.  0.]]\n",
      "[[-1.  0.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 0.  1.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 0. -1.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "[[-1.  0.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 0.  1.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 0. -1.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 0.  0. -1.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  1.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 0.  0. -1.]\n",
      " [ 0. -1.  0.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 0.  0.  1.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  1.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 0.  0.  1.]\n",
      " [ 0. -1.  0.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "[[-1.  0.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 0. -1.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "[[-1.  0.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 0. -1.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 0. -1.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 0. -1.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "[[-1.  0.  0.]\n",
      " [ 0.  1.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 0.  0.  0.]]\n",
      "[[-1.  0.  0.]\n",
      " [ 0.  1.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 0. -1.  0.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 0. -1.  0.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 0.  0. -1.]\n",
      " [-1.  0.  0.]\n",
      " [ 0. -1.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 0.  0. -1.]\n",
      " [ 0. -1.  0.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 0.  0.  1.]\n",
      " [-1.  0.  0.]\n",
      " [ 0. -1.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 0.  0.  1.]\n",
      " [ 0. -1.  0.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 0.  0. -1.]\n",
      " [ 0.  1.  0.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 0.  0. -1.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  1.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 0.  0.  1.]\n",
      " [ 0.  1.  0.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 0.  0.  1.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  1.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 0.  1.  0.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 0.  1.  0.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 1.  0.  0.]\n",
      " [ 0. -1.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 1.  0.  0.]\n",
      " [ 0. -1.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 0.  1.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 0.  1.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 1.  0.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 0.  1.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 1.  0.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 0.  1.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 0.  0. -1.]\n",
      " [ 0.  1.  0.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 0.  0. -1.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0. -1.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 0.  0.  1.]\n",
      " [ 0.  1.  0.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 0.  0.  1.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0. -1.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 0.  1.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 1.  0.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 0. -1.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 0.  1.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [-1.  0.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 1.  0.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 0. -1.  0.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 0.  1.  0.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  0.  1.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 0.  1.  0.]\n",
      " [ 1.  0.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 0.  0.  0.]]\n",
      "[[ 1.  0.  0.]\n",
      " [ 0.  1.  0.]\n",
      " [ 0.  0. -1.]\n",
      " [ 0.  0.  0.]]\n"
     ]
    }
   ],
   "source": [
    "fcc = Structure([[0.5,0.5,0],[0.5,0,0.5],[0,0.5,0.5]])\n",
    "fcc.add_atom(0,0,0,\"Au\")\n",
    "grp = space_group(fcc)\n",
    "print len(grp)\n",
    "for g in grp:\n",
    "    print g"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Structure( -4.148, 2.55767e-16, 2.074,\n",
      "           0, 2.55767e-16, 5.74,\n",
      "           0, 4.177, 0,\n",
      "           scale=1, name='icsd_100672.cif' )\\\n",
      "  .add_atom(-3.80147e-16, 4.00652, 1.04425, 'Al')\\\n",
      "  .add_atom(-2.074, 1.73348, 3.13275, 'Al')\\\n",
      "  .add_atom(2.85986e-16, 1.3776, 1.04425, 'Sn')\\\n",
      "  .add_atom(-2.074, 4.3624, 3.13275, 'Sn')\n",
      "Structure( 11.1827, 2.43503e-16, 2.64769e-16,\n",
      "           0, 3.9767, 2.64769e-16,\n",
      "           0, 0, 4.324,\n",
      "           scale=1, name='icsd_651025.cif' )\\\n",
      "  .add_atom(9.5053, 0.994175, 2.15335, 'Al')\\\n",
      "  .add_atom(3.91395, 0.994175, 0.008648, 'Al')\\\n",
      "  .add_atom(1.67741, 2.98252, 2.17065, 'Al')\\\n",
      "  .add_atom(7.26876, 2.98253, 4.31535, 'Al')\\\n",
      "  .add_atom(6.96682, 0.994175, 1.82905, 'Sn')\\\n",
      "  .add_atom(1.37547, 0.994175, 0.332948, 'Sn')\\\n",
      "  .add_atom(4.21588, 2.98252, 2.49495, 'Sn')\\\n",
      "  .add_atom(9.80723, 2.98253, 3.99105, 'Sn')\n"
     ]
    }
   ],
   "source": [
    "print s1\n",
    "print s2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Help on built-in function neighbors in module pylada.crystal.cppwrappers:\n",
      "\n",
      "neighbors(...)\n",
      "    Returns list of neighbors to input position \n",
      "    \n",
      "    Creates a list referencing neighbors of a given position in a structure.\n",
      "    In order to make this function well defined, it may return more\n",
      "    atoms that actually requested. For instance, in an fcc structure\n",
      "    with center at the origin, if asked for the 6 first neighbors,\n",
      "    actually the first twelve are returned since they are equidistant.\n",
      "    The input tolerance is the judge of equidistance.\n",
      "    \n",
      "    :param structure:\n",
      "        :class:`Structure` from which to determine neighbors.\n",
      "    :param nmax:\n",
      "        Integer number of first neighbors to search for.\n",
      "    :param center:\n",
      "        Position for which to determine first neighbors.\n",
      "    :param tolerance:\n",
      "        Tolerance criteria for judging equidistance.\n",
      "    \n",
      "    :returns: A list of 3-tuples. The first item is a refence to the\n",
      "              neighboring atom, the second is the position of its\n",
      "              relevant periodic image *relative* to the center, the\n",
      "              third is its distance from the center.\n",
      "\n"
     ]
    }
   ],
   "source": [
    "from pylada.crystal import neighbors\n",
    "help(neighbors)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Help on built-in function coordination_shells in module pylada.crystal.cppwrappers:\n",
      "\n",
      "coordination_shells(...)\n",
      "    Creates list of coordination shells up to given order.\n",
      "    \n",
      "    :param structure:\n",
      "        :class:`Structure` from which to determine neighbors.\n",
      "    :param nshells:\n",
      "        Integer number of shells to compute.\n",
      "    :param center:\n",
      "        Position for which to determine first neighbors.\n",
      "    :param tolerance:\n",
      "        Tolerance criteria for judging equidistance.\n",
      "    \n",
      "    :param natoms:\n",
      "        Integer number of neighbors to consider. Defaults to fcc + some\n",
      "        security.\n",
      "    \n",
      "    :returns: A list of lists of tuples. The outer list is over\n",
      "              coordination shells.  The inner list references the atoms\n",
      "              in a shell.  Each innermost tuple contains a reference to\n",
      "              the atom in question, a vector from the center to the\n",
      "              relevant periodic image of the atom, and finally, the\n",
      "              associated distance.\n",
      "\n"
     ]
    }
   ],
   "source": [
    "from pylada.crystal import coordination_shells as coord\n",
    "help(coord)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
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