auto

dimonaks · Nov 24, 2016 · 1713e7d · 1713e7d
1 parent dacbdbf
commit 1713e7d
Showing 1 changed file with 44 additions and 11 deletions.
diff --git a/tutorials/create_vasp_calculation.ipynb b/tutorials/create_vasp_calculation.ipynb
@@ -1,7 +1,7 @@
 {
  "metadata": {
   "name": "",
-  "signature": "sha256:87f5b8b062d9e98df79dddb8eda92a535301608bee8212f8f791f0900c3ff38d"
+  "signature": "sha256:97126c9dbbd1e1781dbc3be5fb4ce7ed564aa7a67aa226273dbcc1fab1d87481"
  },
  "nbformat": 3,
  "nbformat_minor": 0,
@@ -85,14 +85,14 @@
       "1. Read crystall structure from Bi2Se3_mp-541837_computed.POSCAR\n",
       "2. Create all VASP files in folder 'Bi2Se3/Bi2Se3.static'\n",
       "3. Copy files to CEE cluster into 'topologic/Bi2Se3/Bi2Se3.static' folder\n",
-      "4. If run = 1 the calculation will be submitted"
+      "4. Use run = 1 to submit the calculation"
      ]
     },
     {
      "cell_type": "code",
      "collapsed": false,
      "input": [
-      "add_loop('Bi2Se3', 'static', 1, input_geo_file = 'Bi2Se3_mp-541837_computed.POSCAR', it_folder = 'Bi2Se3', run = 0)\n"
+      "add_loop('Bi2Se3', 'static', 1, input_geo_file = 'Bi2Se3_mp-541837_computed.POSCAR', it_folder = 'Bi2Se3', run = 0)"
      ],
      "language": "python",
      "metadata": {},
@@ -111,7 +111,6 @@
      "cell_type": "code",
      "collapsed": false,
      "input": [
-      "# header.calc['Bi2Se3', 'static', 1].read_results()\n",
       "res_loop('Bi2Se3', 'static', 1)"
      ],
      "language": "python",
@@ -145,11 +144,45 @@
      ]
     },
     {
-     "cell_type": "markdown",
-     "metadata": {},
-     "source": [
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
       "header.varset['static'].printme()"
-     ]
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": [
+      {
+       "output_type": "stream",
+       "stream": "stdout",
+       "text": [
+        "-- s.vasp_params['PREC']          = Normal  \n",
+        "-- s.vasp_params['NELM']          = 50  \n",
+        "-- s.vasp_params['KSPACING']      = 0.235  \n",
+        "-- s.vasp_params['LSCALU']        = .FALSE.  \n",
+        "-- s.vasp_params['NSW']           = 0  \n",
+        "-- s.vasp_params['ISMEAR']        = 2  \n",
+        "-- s.vasp_params['LREAL']         = Auto  \n",
+        "-- s.vasp_params['ENAUG']         = 776.16  \n",
+        "-- s.vasp_params['SIGMA']         = 0.2  \n",
+        "-- s.vasp_params['NELMIN']        = 4  \n",
+        "-- s.vasp_params['ALGO']          = Normal  \n",
+        "-- s.vasp_params['NPAR']          = 1  \n",
+        "-- s.vasp_params['LPLANE']        = .TRUE.  \n",
+        "-- s.vasp_params['NSIM']          = 4  \n",
+        "-- s.vasp_params['ENCUT']         = 441.0  \n",
+        "-- s.vasp_params['ISIF']          = 2  \n",
+        "-- s.vasp_params['EDIFFG']        = 0  \n",
+        "-- s.vasp_params['IBRION']        = 1  \n",
+        "-- s.vasp_params['KGAMMA']        = .TRUE.  \n",
+        "-- s.vasp_params['MAXMIX']        = 40  \n",
+        "-- s.vasp_params['ISTART']        = 0  \n",
+        "-- s.vasp_params['EDIFF']         = 6e-06  \n",
+        "-- POTDIR: {34: 'Se', 83: 'Bi_pv'} \n"
+       ]
+      }
+     ],
+     "prompt_number": 29
     },
     {
      "cell_type": "code",
@@ -248,7 +281,7 @@
      "input": [
       "calc = header.calc\n",
       "res_loop('Bi2Se3', 'ion_relax', 1)\n",
-      "print('Relaxation energy = ',calc['Bi2Se3', 'ion_relax', 1].energy_sigma0 - calc['Bi2Se3', 'static', 1].energy_sigma0)"
+      "print('Relaxation energy = {:.6} meV'.format(1000*(calc['Bi2Se3','ion_relax', 1].energy_sigma0 - calc['Bi2Se3', 'static', 1].energy_sigma0)))"
      ],
      "language": "python",
      "metadata": {},
@@ -259,11 +292,11 @@
        "text": [
         "-- name                          |  energy(eV)|    Vector lenghts (A)   | Stresses (MPa)     | N MD, N SCF    \n",
         "-- Bi2Se3.ion_relax.1            |  -20.1552  |    10.27;10.27;10.27    |  -521,-526,-367    |  20, 4, 89    \n",
-        "Relaxation energy =  -0.0009354500000000598\n"
+        "Relaxation energy = -0.93545 meV\n"
        ]
       }
      ],
-     "prompt_number": 25
+     "prompt_number": 28
     },
     {
      "cell_type": "markdown",