debug_Geometry_view_addFracCoordAtom.ipynb 134 KB
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{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2020-06-30T03:33:03.442062Z",
     "start_time": "2020-06-30T03:33:01.594274Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The autoreload extension is already loaded. To reload it, use:\n",
      "  %reload_ext autoreload\n",
      " \n",
      " _    _ _____ _____ _____            \n",
      "| |  | |  ___/  ___|_   _|           \n",
      "| |  | | |__ \\ `--.  | |_ __  _   _  \n",
      "| |/\\| |  __| `--. \\ | | '_ \\| | | | \n",
      "\\  /\\  / |___/\\__/ / | | |_) | |_| | \n",
      " \\/  \\/\\____/\\____/  \\_/ .__/ \\__, | \n",
      "                       | |     __/ | \n",
      "                       |_|    |___/  \n",
      " \n",
      "WEST version     :  4.1.0\n",
      "Today            :  2020-06-29 22:33:03.328128\n"
     ]
    }
   ],
   "source": [
    "from westpy import *\n",
    "\n",
    "def xyz2center(in_xyz,out_xyz,box_length=30):\n",
    "    '''\n",
    "    in_xyz: input xyz file in unit A\n",
    "    out_xyz: output xyz file where coords are centered in simulation box. \n",
    "    box_length:  in unit Bohr\n",
    "    '''\n",
    "    from westpy.units import Angstrom\n",
    "    import pandas as pd\n",
    "    BOHR2A = 1.0 / Angstrom\n",
    "    #convert box length 2 A:\n",
    "    box_length *= BOHR2A\n",
    "    #read in_xyz in unit A\n",
    "    dict_atoms = {'element':[], 'x':[], 'y':[], 'z':[]}\n",
    "    with open(in_xyz,'r') as f:\n",
    "        n_atoms=int(f.readline())\n",
    "        f.readline()\n",
    "        for _ in range(n_atoms):\n",
    "            element, x, y, z = f.readline().split()\n",
    "            dict_atoms['element'].append(element.strip())\n",
    "            dict_atoms['x'].append(float(x))\n",
    "            dict_atoms['y'].append(float(y))\n",
    "            dict_atoms['z'].append(float(z))\n",
    "        assert(len(dict_atoms['x']) == n_atoms)\n",
    "    df_atoms_centered=pd.DataFrame(dict_atoms)\n",
    "    # shift in_xyz coords by [box_length/2,box_length/2,box_length/2]\n",
    "    df_atoms_centered[['x','y','z']] -= df_atoms_centered[['x','y','z']].mean(axis=0)\n",
    "    df_atoms_centered[['x','y','z']] += box_length/2.0\n",
    "    # save to out_xyz\n",
    "    xyz=str(len(df_atoms_centered))+'\\n\\n'\n",
    "    for row in df_atoms_centered.values:\n",
    "        xyz += \" \".join([str(e) for e in row]) + '\\n'    \n",
    "    with open(out_xyz,'w') as f:\n",
    "        f.write(xyz)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Geometry.view()  Si35H36 "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2020-06-30T03:33:21.001332Z",
     "start_time": "2020-06-30T03:33:11.473346Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Downloaded file:  si35h36.xyz , from url:  https://journals.aps.org/prx/supplemental/10.1103/PhysRevX.6.041002/si35h36.xyz\n"
     ]
    },
    {
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       "\tviewer_15934880008848822.addLine({\"color\": \"blue\", \"start\": {\"x\": 0.0, \"y\": 15.875316335825389, \"z\": 15.875316335825389}, \"end\": {\"x\": 0.0, \"y\": 15.875316335825389, \"z\": 0.0}});\n",
       "\tviewer_15934880008848822.addLine({\"color\": \"blue\", \"start\": {\"x\": 0.0, \"y\": 15.875316335825389, \"z\": 15.875316335825389}, \"end\": {\"x\": 0.0, \"y\": 0.0, \"z\": 15.875316335825389}});\n",
       "\tviewer_15934880008848822.addLine({\"color\": \"blue\", \"start\": {\"x\": 0.0, \"y\": 15.875316335825389, \"z\": 15.875316335825389}, \"end\": {\"x\": 15.875316335825389, \"y\": 15.875316335825389, \"z\": 15.875316335825389}});\n",
       "\tviewer_15934880008848822.zoomTo();\n",
       "viewer_15934880008848822.render();\n",
       "});\n",
       "</script>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "#download xyz\n",
    "url = 'https://journals.aps.org/prx/supplemental/10.1103/PhysRevX.6.041002/si35h36.xyz'\n",
    "fname = 'si35h36.xyz'\n",
    "download(url=url, fname='si35h36.xyz')\n",
    "#center it to fit geom.setCell((box_length,0,0),(0,box_length,0),(0,0,box_length))\n",
    "box_length = 30 #Bohr\n",
    "center2box_fname = 'centered_si35h36.xyz' \n",
    "xyz2center(in_xyz=fname,out_xyz=center2box_fname,box_length=box_length)\n",
    "#creat geom\n",
    "geom = Geometry()\n",
    "geom.setCell((box_length,0,0),(0,box_length,0),(0,0,box_length))\n",
    "geom.addAtomsFromXYZFile(center2box_fname)\n",
    "geom.addSpecies( \"Si\", \"http://www.quantum-simulation.org/potentials/sg15_oncv/upf/Si_ONCV_PBE-1.2.upf\")\n",
    "geom.addSpecies( \"H\", \"http://www.quantum-simulation.org/potentials/sg15_oncv/upf/H_ONCV_PBE-1.2.upf\")\n",
    "geom.view()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2020-06-30T03:33:28.829407Z",
     "start_time": "2020-06-30T03:33:28.358677Z"
    }
   },
   "outputs": [
    {
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       "        <p id=\"3dmolwarning_15934880088194125\" style=\"background-color:#ffcccc;color:black\">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the 3dmol extension: <br>\n",
       "        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n",
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     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "geom.view(style='line')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2020-06-30T03:33:33.263955Z",
     "start_time": "2020-06-30T03:33:32.947704Z"
    }
   },
   "outputs": [
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       "$3Dmolpromise.then(function() {\n",
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       "\tviewer_1593488013257959.addModel(\"71\\n\\nSi 7.938911562278893 7.935994660870439 7.944704703123958\\nSi 7.933811562278892 7.941257660870441 13.399227703123959\\nSi 9.237906562278893 6.507230660870441 6.579459703123959\\nSi 7.821957562278893 5.21792166087044 10.66353170312396\\nSi 7.797518562278891 5.220964660870441 5.22088570312396\\nSi 10.528546562278892 5.09011066087044 7.95921070312396\\nSi 6.5230705622788925 6.644192660870441 3.83861570312396\\nSi 6.389611562278892 3.9084506608704412 6.5823287031239595\\nSi 9.098878562278891 3.7777316608704403 9.29985570312396\\nSi 7.6976215622788935 2.4806026608704403 7.92113370312396\\nSi 6.641655562278894 9.36360766087044 6.57582670312396\\nSi 8.050662562278893 10.66016266087044 10.65949870312396\\nSi 8.083912562278893 10.648327660870441 5.216555703123959\\nSi 5.348593562278893 10.78356166087044 7.9513687031239595\\nSi 9.360512562278892 9.22267266087044 3.83869170312396\\nSi 9.48897756227889 11.96368666087044 6.578289703123958\\nSi 6.776402562278893 12.09889566087044 9.29159670312396\\nSi 8.174761562278892 13.394013660870442 7.908066703123959\\nSi 7.937994562278893 7.937623660870441 2.47113870312396\\nSi 6.507352562278892 6.63872266087044 9.30900570312396\\nSi 5.224965562278893 8.05215966087044 5.21535970312396\\nSi 5.216745562278893 8.08618966087044 10.65828170312396\\nSi 5.092996562278893 5.34892766087044 7.924984703123959\\nSi 6.642474562278894 9.36249866087044 12.036764703123957\\nSi 3.902415562278893 9.486385660870441 9.28853470312396\\nSi 3.7847805622788933 6.773047660870441 6.575218703123959\\nSi 2.480699562278893 8.17510166087044 7.944572703123959\\nSi 9.366810562278893 9.23731066087044 9.308992703123959\\nSi 10.655939562278894 7.816715660870441 5.21976570312396\\nSi 10.655553562278893 7.791960660870441 10.66263670312396\\nSi 10.783121562278891 10.52509666087044 7.925128703123959\\nSi 9.227429562278893 6.5182526608704405 12.040755703123958\\nSi 11.971591562278894 6.389467660870441 9.297189703123959\\nSi 12.093414562278893 9.098875660870439 6.579483703123959\\nSi 13.395204562278893 7.7039096608704405 7.958359703123959\\nH 8.836224562278893 8.76422666087044 14.278886703123959\\nH 5.601936562278892 5.804202660870441 2.9878377031239594\\nH 5.469867562278893 3.0973066608704407 5.702740703123959\\nH 9.933719562278892 2.87880466087044 10.17910970312396\\nH 7.239636562278893 11.55437366087044 4.353334703123959\\nH 7.328198562278892 14.265524660870438 7.01942970312396\\nH 9.056106562278893 14.280857660870442 8.74564470312396\\nH 8.975123562278894 11.48053466087044 11.525873703123958\\nH 4.531539562278892 11.689461660870439 7.06258070312396\\nH 7.029460562278892 7.119788660870441 14.278299703123956\\nH 10.283754562278894 10.06059966087044 2.98819370312396\\nH 10.410364562278891 12.773854660870441 5.699508703123959\\nH 5.9403575622788924 12.99943666087044 10.168155703123958\\nH 8.642225562278893 4.313243660870441 4.360114703123959\\nH 8.539848562278893 1.5982346608704407 7.039363703123959\\nH 6.811044562278893 1.6035436608704403 8.763524703123958\\nH 6.897062562278893 4.398461660870439 11.530331703123961\\nH 11.347385562278893 4.182414660870441 7.074094703123959\\nH 8.754462562278892 7.03996466087044 1.5810257031239594\\nH 5.8078285622788925 10.28033066087044 12.896460703123958\\nH 3.0836145622788926 10.40350866087044 10.164121703123959\\nH 2.8923845622788935 5.93187066087044 5.69558370312396\\nH 11.560714562278893 8.63484066087044 11.52772470312396\\nH 14.270380562278893 8.55129666087044 8.842502703123959\\nH 14.279547562278895 6.82191066087044 7.118952703123959\\nH 11.477410562278893 6.889255660870441 4.35744770312396\\nH 11.691336562278893 11.346644660870442 8.80777470312396\\nH 7.112568562278893 8.84486066087044 1.598922703123959\\nH 10.060353562278893 5.602364660870441 12.904073703123961\\nH 12.789078562278894 5.473744660870441 10.17534570312396\\nH 12.986454562278892 9.938748660870441 5.69927670312396\\nH 4.310589562278892 7.244092660870441 11.52305470312396\\nH 1.5949765622788927 7.33404866087044 8.824268703123957\\nH 1.607909562278893 9.061251660870441 7.097168703123958\\nH 4.4049325622788915 8.978832660870438 4.350565703123959\\nH 4.182525562278894 4.52965966087044 8.80741070312396\\n\",\"xyz\");\n",
       "\tviewer_1593488013257959.setStyle({\"sphere\": {}});\n",
       "\tviewer_1593488013257959.addLine({\"color\": \"blue\", \"start\": {\"x\": 0.0, \"y\": 0.0, \"z\": 0.0}, \"end\": {\"x\": 15.875316335825389, \"y\": 0.0, \"z\": 0.0}});\n",
       "\tviewer_1593488013257959.addLine({\"color\": \"blue\", \"start\": {\"x\": 0.0, \"y\": 0.0, \"z\": 0.0}, \"end\": {\"x\": 0.0, \"y\": 15.875316335825389, \"z\": 0.0}});\n",
       "\tviewer_1593488013257959.addLine({\"color\": \"blue\", \"start\": {\"x\": 0.0, \"y\": 0.0, \"z\": 0.0}, \"end\": {\"x\": 0.0, \"y\": 0.0, \"z\": 15.875316335825389}});\n",
       "\tviewer_1593488013257959.addLine({\"color\": \"blue\", \"start\": {\"x\": 15.875316335825389, \"y\": 15.875316335825389, \"z\": 0.0}, \"end\": {\"x\": 15.875316335825389, \"y\": 0.0, \"z\": 0.0}});\n",
       "\tviewer_1593488013257959.addLine({\"color\": \"blue\", \"start\": {\"x\": 15.875316335825389, \"y\": 15.875316335825389, \"z\": 0.0}, \"end\": {\"x\": 0.0, \"y\": 15.875316335825389, \"z\": 0.0}});\n",
       "\tviewer_1593488013257959.addLine({\"color\": \"blue\", \"start\": {\"x\": 15.875316335825389, \"y\": 15.875316335825389, \"z\": 0.0}, \"end\": {\"x\": 15.875316335825389, \"y\": 15.875316335825389, \"z\": 15.875316335825389}});\n",
       "\tviewer_1593488013257959.addLine({\"color\": \"blue\", \"start\": {\"x\": 15.875316335825389, \"y\": 0.0, \"z\": 15.875316335825389}, \"end\": {\"x\": 15.875316335825389, \"y\": 0.0, \"z\": 0.0}});\n",
       "\tviewer_1593488013257959.addLine({\"color\": \"blue\", \"start\": {\"x\": 15.875316335825389, \"y\": 0.0, \"z\": 15.875316335825389}, \"end\": {\"x\": 0.0, \"y\": 0.0, \"z\": 15.875316335825389}});\n",
       "\tviewer_1593488013257959.addLine({\"color\": \"blue\", \"start\": {\"x\": 15.875316335825389, \"y\": 0.0, \"z\": 15.875316335825389}, \"end\": {\"x\": 15.875316335825389, \"y\": 15.875316335825389, \"z\": 15.875316335825389}});\n",
       "\tviewer_1593488013257959.addLine({\"color\": \"blue\", \"start\": {\"x\": 0.0, \"y\": 15.875316335825389, \"z\": 15.875316335825389}, \"end\": {\"x\": 0.0, \"y\": 15.875316335825389, \"z\": 0.0}});\n",
       "\tviewer_1593488013257959.addLine({\"color\": \"blue\", \"start\": {\"x\": 0.0, \"y\": 15.875316335825389, \"z\": 15.875316335825389}, \"end\": {\"x\": 0.0, \"y\": 0.0, \"z\": 15.875316335825389}});\n",
       "\tviewer_1593488013257959.addLine({\"color\": \"blue\", \"start\": {\"x\": 0.0, \"y\": 15.875316335825389, \"z\": 15.875316335825389}, \"end\": {\"x\": 15.875316335825389, \"y\": 15.875316335825389, \"z\": 15.875316335825389}});\n",
       "\tviewer_1593488013257959.zoomTo();\n",
       "viewer_1593488013257959.render();\n",
       "});\n",
       "</script>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "geom.view(style='sphere')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2020-06-30T03:33:35.916789Z",
     "start_time": "2020-06-30T03:33:35.605968Z"
    }
   },
   "outputs": [
    {
     "data": {
      "application/3dmoljs_load.v0": "<div id=\"3dmolviewer_15934880159087925\"  style=\"position: relative; width: 800px; height: 800px\">\n        <p id=\"3dmolwarning_15934880159087925\" style=\"background-color:#ffcccc;color:black\">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the 3dmol extension: <br>\n        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n        </div>\n<script>\n\nvar loadScriptAsync = function(uri){\n  return new Promise((resolve, reject) => {\n    var tag = document.createElement('script');\n    tag.src = uri;\n    tag.async = true;\n    tag.onload = () => {\n      resolve();\n    };\n  var firstScriptTag = document.getElementsByTagName('script')[0];\n  firstScriptTag.parentNode.insertBefore(tag, firstScriptTag);\n});\n};\n\nif(typeof $3Dmolpromise === 'undefined') {\n$3Dmolpromise = null;\n  $3Dmolpromise = loadScriptAsync('https://3dmol.csb.pitt.edu/build/3Dmol.js');\n}\n\nvar viewer_15934880159087925 = null;\nvar warn = document.getElementById(\"3dmolwarning_15934880159087925\");\nif(warn) {\n    warn.parentNode.removeChild(warn);\n}\n$3Dmolpromise.then(function() {\nviewer_15934880159087925 = $3Dmol.createViewer($(\"#3dmolviewer_15934880159087925\"),{backgroundColor:\"white\"});\n\tviewer_15934880159087925.addModel(\"284\\n\\nSi 7.938911562278893 7.935994660870439 7.944704703123958\\nSi 7.938911562278893 23.811310996695827 7.944704703123958\\nSi 23.81422789810428 7.935994660870439 7.944704703123958\\nSi 23.81422789810428 23.811310996695827 7.944704703123958\\nSi 7.933811562278892 7.941257660870441 13.399227703123959\\nSi 7.933811562278892 23.81657399669583 13.399227703123959\\nSi 23.80912789810428 7.941257660870441 13.399227703123959\\nSi 23.80912789810428 23.81657399669583 13.399227703123959\\nSi 9.237906562278893 6.507230660870441 6.579459703123959\\nSi 9.237906562278893 22.38254699669583 6.579459703123959\\nSi 25.113222898104283 6.507230660870441 6.579459703123959\\nSi 25.113222898104283 22.38254699669583 6.579459703123959\\nSi 7.821957562278893 5.21792166087044 10.66353170312396\\nSi 7.821957562278893 21.093237996695827 10.66353170312396\\nSi 23.69727389810428 5.21792166087044 10.66353170312396\\nSi 23.69727389810428 21.093237996695827 10.66353170312396\\nSi 7.797518562278891 5.220964660870441 5.22088570312396\\nSi 7.797518562278891 21.096280996695832 5.22088570312396\\nSi 23.67283489810428 5.220964660870441 5.22088570312396\\nSi 23.67283489810428 21.096280996695832 5.22088570312396\\nSi 10.528546562278892 5.09011066087044 7.95921070312396\\nSi 10.528546562278892 20.96542699669583 7.95921070312396\\nSi 26.40386289810428 5.09011066087044 7.95921070312396\\nSi 26.40386289810428 20.96542699669583 7.95921070312396\\nSi 6.5230705622788925 6.644192660870441 3.83861570312396\\nSi 6.5230705622788925 22.51950899669583 3.83861570312396\\nSi 22.39838689810428 6.644192660870441 3.83861570312396\\nSi 22.39838689810428 22.51950899669583 3.83861570312396\\nSi 6.389611562278892 3.9084506608704412 6.5823287031239595\\nSi 6.389611562278892 19.78376699669583 6.5823287031239595\\nSi 22.264927898104283 3.9084506608704412 6.5823287031239595\\nSi 22.264927898104283 19.78376699669583 6.5823287031239595\\nSi 9.098878562278891 3.7777316608704403 9.29985570312396\\nSi 9.098878562278891 19.65304799669583 9.29985570312396\\nSi 24.97419489810428 3.7777316608704403 9.29985570312396\\nSi 24.97419489810428 19.65304799669583 9.29985570312396\\nSi 7.6976215622788935 2.4806026608704403 7.92113370312396\\nSi 7.6976215622788935 18.355918996695827 7.92113370312396\\nSi 23.572937898104282 2.4806026608704403 7.92113370312396\\nSi 23.572937898104282 18.355918996695827 7.92113370312396\\nSi 6.641655562278894 9.36360766087044 6.57582670312396\\nSi 6.641655562278894 25.238923996695828 6.57582670312396\\nSi 22.51697189810428 9.36360766087044 6.57582670312396\\nSi 22.51697189810428 25.238923996695828 6.57582670312396\\nSi 8.050662562278893 10.66016266087044 10.65949870312396\\nSi 8.050662562278893 26.53547899669583 10.65949870312396\\nSi 23.925978898104283 10.66016266087044 10.65949870312396\\nSi 23.925978898104283 26.53547899669583 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12.09889566087044 9.29159670312396\\nSi 6.776402562278893 27.97421199669583 9.29159670312396\\nSi 22.65171889810428 12.09889566087044 9.29159670312396\\nSi 22.65171889810428 27.97421199669583 9.29159670312396\\nSi 8.174761562278892 13.394013660870442 7.908066703123959\\nSi 8.174761562278892 29.26932999669583 7.908066703123959\\nSi 24.05007789810428 13.394013660870442 7.908066703123959\\nSi 24.05007789810428 29.26932999669583 7.908066703123959\\nSi 7.937994562278893 7.937623660870441 2.47113870312396\\nSi 7.937994562278893 23.81293999669583 2.47113870312396\\nSi 23.813310898104284 7.937623660870441 2.47113870312396\\nSi 23.813310898104284 23.81293999669583 2.47113870312396\\nSi 6.507352562278892 6.63872266087044 9.30900570312396\\nSi 6.507352562278892 22.514038996695827 9.30900570312396\\nSi 22.38266889810428 6.63872266087044 9.30900570312396\\nSi 22.38266889810428 22.514038996695827 9.30900570312396\\nSi 5.224965562278893 8.05215966087044 5.21535970312396\\nSi 5.224965562278893 23.92747599669583 5.21535970312396\\nSi 21.10028189810428 8.05215966087044 5.21535970312396\\nSi 21.10028189810428 23.92747599669583 5.21535970312396\\nSi 5.216745562278893 8.08618966087044 10.65828170312396\\nSi 5.216745562278893 23.961505996695827 10.65828170312396\\nSi 21.092061898104284 8.08618966087044 10.65828170312396\\nSi 21.092061898104284 23.961505996695827 10.65828170312396\\nSi 5.092996562278893 5.34892766087044 7.924984703123959\\nSi 5.092996562278893 21.22424399669583 7.924984703123959\\nSi 20.96831289810428 5.34892766087044 7.924984703123959\\nSi 20.96831289810428 21.22424399669583 7.924984703123959\\nSi 6.642474562278894 9.36249866087044 12.036764703123957\\nSi 6.642474562278894 25.23781499669583 12.036764703123957\\nSi 22.51779089810428 9.36249866087044 12.036764703123957\\nSi 22.51779089810428 25.23781499669583 12.036764703123957\\nSi 3.902415562278893 9.486385660870441 9.28853470312396\\nSi 3.902415562278893 25.361701996695828 9.28853470312396\\nSi 19.777731898104282 9.486385660870441 9.28853470312396\\nSi 19.777731898104282 25.361701996695828 9.28853470312396\\nSi 3.7847805622788933 6.773047660870441 6.575218703123959\\nSi 3.7847805622788933 22.648363996695828 6.575218703123959\\nSi 19.660096898104282 6.773047660870441 6.575218703123959\\nSi 19.660096898104282 22.648363996695828 6.575218703123959\\nSi 2.480699562278893 8.17510166087044 7.944572703123959\\nSi 2.480699562278893 24.050417996695828 7.944572703123959\\nSi 18.356015898104282 8.17510166087044 7.944572703123959\\nSi 18.356015898104282 24.050417996695828 7.944572703123959\\nSi 9.366810562278893 9.23731066087044 9.308992703123959\\nSi 9.366810562278893 25.11262699669583 9.308992703123959\\nSi 25.24212689810428 9.23731066087044 9.308992703123959\\nSi 25.24212689810428 25.11262699669583 9.308992703123959\\nSi 10.655939562278894 7.816715660870441 5.21976570312396\\nSi 10.655939562278894 23.69203199669583 5.21976570312396\\nSi 26.531255898104284 7.816715660870441 5.21976570312396\\nSi 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       "        <p id=\"3dmolwarning_15934880159087925\" style=\"background-color:#ffcccc;color:black\">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the 3dmol extension: <br>\n",
       "        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n",
       "        </div>\n",
       "<script>\n",
       "\n",
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       "\tviewer_15934880159087925.zoomTo();\n",
       "viewer_15934880159087925.render();\n",
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       "</script>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "geom.view(ix=2,iy=2,iz=1)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Geometry.view()  HBN"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2020-06-30T03:45:12.638959Z",
     "start_time": "2020-06-30T03:45:12.323122Z"
    }
   },
   "outputs": [],
   "source": [
    "from westpy.units import Angstrom\n",
    "import numpy as np\n",
    "A2BOHR = Angstrom"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2020-06-30T03:45:48.928561Z",
     "start_time": "2020-06-30T03:45:48.461759Z"
    }
   },
   "outputs": [],
   "source": [
    "geom = Geometry()\n",
    "#define unit cell\n",
    "#>>    ibrav = 4           ,\n",
    "#>>    celldm(1) = 4.695926777902829 ,\n",
    "#>>    celldm(3) = 8.048362859199854 ,\n",
    "# 4     Hexagonal and Trigonal P   celldm(3)=c/a\n",
    "#       v1 = a(1,0,0),  v2 = a(-1/2,sqrt(3)/2,0),  v3 = a(0,0,c/a)\n",
    "#https://materialsproject.org/materials/mp-984/\n",
    "celldm_1 = 2.51242804*A2BOHR         #bohr\n",
    "celldm_3 = 7.70726501/2.0/2.512      #c/a\n",
    "geom.addSpecies( \"B\", \"http://www.quantum-simulation.org/potentials/sg15_oncv/upf/B_ONCV_PBE-1.2.upf\")\n",
    "geom.addSpecies( \"N\", \"http://www.quantum-simulation.org/potentials/sg15_oncv/upf/N_ONCV_PBE-1.2.upf\")\n",
    "geom.setCell(a1=(1,0,0), a2=(-1/2,np.sqrt(3)/2,0), a3=(0,0,celldm_3), units=celldm_1)\n",
    "geom.addFracCoordAtom('B', (1.0/3,2.0/3,0.5) )\n",
    "geom.addFracCoordAtom('N', (2.0/3,1.0/3,0.5) )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2020-06-30T03:45:50.593250Z",
     "start_time": "2020-06-30T03:45:50.282429Z"
    }
   },
   "outputs": [
    {
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       "        <p id=\"3dmolwarning_15934887505872521\" style=\"background-color:#ffcccc;color:black\">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the 3dmol extension: <br>\n",
       "        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n",
       "        </div>\n",
       "<script>\n",
       "\n",
       "var loadScriptAsync = function(uri){\n",
       "  return new Promise((resolve, reject) => {\n",
       "    var tag = document.createElement('script');\n",
       "    tag.src = uri;\n",
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       "  firstScriptTag.parentNode.insertBefore(tag, firstScriptTag);\n",
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       "};\n",
       "\n",
       "if(typeof $3Dmolpromise === 'undefined') {\n",
       "$3Dmolpromise = null;\n",
       "  $3Dmolpromise = loadScriptAsync('https://3dmol.csb.pitt.edu/build/3Dmol.js');\n",
       "}\n",
       "\n",
       "var viewer_15934887505872521 = null;\n",
       "var warn = document.getElementById(\"3dmolwarning_15934887505872521\");\n",
       "if(warn) {\n",
       "    warn.parentNode.removeChild(warn);\n",
       "}\n",
       "$3Dmolpromise.then(function() {\n",
       "viewer_15934887505872521 = $3Dmol.createViewer($(\"#3dmolviewer_15934887505872521\"),{backgroundColor:\"white\"});\n",
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       "</script>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "geom.view(style='stick')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2020-06-30T03:45:54.460859Z",
     "start_time": "2020-06-30T03:45:54.155035Z"
    }
   },
   "outputs": [
    {
     "data": {
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You need to install the 3dmol extension: <br>\n        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n        </div>\n<script>\n\nvar loadScriptAsync = function(uri){\n  return new Promise((resolve, reject) => {\n    var tag = document.createElement('script');\n    tag.src = uri;\n    tag.async = true;\n    tag.onload = () => {\n      resolve();\n    };\n  var firstScriptTag = document.getElementsByTagName('script')[0];\n  firstScriptTag.parentNode.insertBefore(tag, firstScriptTag);\n});\n};\n\nif(typeof $3Dmolpromise === 'undefined') {\n$3Dmolpromise = null;\n  $3Dmolpromise = loadScriptAsync('https://3dmol.csb.pitt.edu/build/3Dmol.js');\n}\n\nvar viewer_15934887544558609 = null;\nvar warn = document.getElementById(\"3dmolwarning_15934887544558609\");\nif(warn) {\n    warn.parentNode.removeChild(warn);\n}\n$3Dmolpromise.then(function() {\nviewer_15934887544558609 = 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   "metadata": {
    "ExecuteTime": {
     "end_time": "2020-06-30T03:45:56.984028Z",
     "start_time": "2020-06-30T03:45:56.675204Z"
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