changes to the USAGE (fab35881) · Commits · 郑智淋 / GB_code

Usage_of_GB_code.ipynb

+0 −174

Original line number	Diff line number	Diff line
		@@ -2,11 +2,7 @@
		"cells": [
		{
		"cell_type": "code",
		<<<<<<< HEAD
		"execution_count": 1,
		=======
		"execution_count": 55,
		>>>>>>> development
		"metadata": {},
		"outputs": [],
		"source": [
		@@ -58,11 +54,7 @@
		],
		"source": [
		"# for example: [1, 0, 0], [1, 1, 0] or [1, 1, 1]\n",
		<<<<<<< HEAD
		"axis = np.array([1, 1, 2])\n",
		=======
		"axis = np.array([1, 1, 1])\n",
		>>>>>>> development
		"\n",
		"# list Sigma boundaries < 50\n",
		"csl.print_list(axis,50)\n"
		@@ -84,17 +76,6 @@
		"name": "stdout",
		"output_type": "stream",
		"text": [
		<<<<<<< HEAD
		"Angle: 52.200277564572765 \n",
		" Sigma: 31 \n",
		" Minimal cells: \n",
		" [[-1 -3 1]\n",
		" [ 4 -1 1]\n",
		" [ 0 1 2]] \n",
		" [[-3 -1 1]\n",
		" [ 2 -3 1]\n",
		" [ 2 1 2]] \n",
		=======
		"Angle: 27.79577249602797 \n",
		" Sigma: 13 \n",
		" Minimal cells: \n",
		@@ -104,18 +85,13 @@
		" [[ 2 -1 1]\n",
		" [-2 -2 1]\n",
		" [ 1 2 1]] \n",
		>>>>>>> development
		"\n"
		]
		}
		],
		"source": [
		"# pick a sigma for this axis, ex: 19.\n",
		<<<<<<< HEAD
		"sigma = 31\n",
		=======
		"sigma = 13\n",
		>>>>>>> development
		"\n",
		"theta, m, n = csl.get_theta_m_n_list(axis,sigma)[0]\n",
		"\n",
		@@ -138,11 +114,7 @@
		},
		{
		"cell_type": "code",
		<<<<<<< HEAD
		"execution_count": 6,
		=======
		"execution_count": 35,
		>>>>>>> development
		"metadata": {},
		"outputs": [
		{
		@@ -174,57 +146,32 @@
		" <tbody>\n",
		" <tr>\n",
		" <th>0</th>\n",
		<<<<<<< HEAD
		" <td>[3, 1, -1]</td>\n",
		" <td>[1, 3, -1]</td>\n",
		=======
		" <td>[2, 1, -2]</td>\n",
		" <td>[1, 2, -2]</td>\n",
		>>>>>>> development
		" <td>Mixed</td>\n",
		" </tr>\n",
		" <tr>\n",
		" <th>1</th>\n",
		<<<<<<< HEAD
		" <td>[-1, -1, -2]</td>\n",
		" <td>[-1, -1, -2]</td>\n",
		=======
		" <td>[-1, -1, -1]</td>\n",
		" <td>[-1, -1, -1]</td>\n",
		>>>>>>> development
		" <td>Twist</td>\n",
		" </tr>\n",
		" <tr>\n",
		" <th>2</th>\n",
		<<<<<<< HEAD
		" <td>[1, 1, 2]</td>\n",
		" <td>[1, 1, 2]</td>\n",
		=======
		" <td>[1, 1, 1]</td>\n",
		" <td>[1, 1, 1]</td>\n",
		>>>>>>> development
		" <td>Twist</td>\n",
		" </tr>\n",
		" <tr>\n",
		" <th>3</th>\n",
		<<<<<<< HEAD
		" <td>[1, -4, 0]</td>\n",
		" <td>[3, -2, -2]</td>\n",
		=======
		" <td>[-1, 2, -2]</td>\n",
		" <td>[-2, 2, -1]</td>\n",
		>>>>>>> development
		" <td>Mixed</td>\n",
		" </tr>\n",
		" <tr>\n",
		" <th>4</th>\n",
		<<<<<<< HEAD
		" <td>[-3, -1, 1]</td>\n",
		" <td>[-1, -3, 1]</td>\n",
		=======
		" <td>[-2, -1, 2]</td>\n",
		" <td>[-1, -2, 2]</td>\n",
		>>>>>>> development
		" <td>Mixed</td>\n",
		" </tr>\n",
		" </tbody>\n",
		@@ -233,16 +180,6 @@
		],
		"text/plain": [
		" GB1 GB2 Type\n",
		<<<<<<< HEAD
		"0 [3, 1, -1] [1, 3, -1] Mixed\n",
		"1 [-1, -1, -2] [-1, -1, -2] Twist\n",
		"2 [1, 1, 2] [1, 1, 2] Twist\n",
		"3 [1, -4, 0] [3, -2, -2] Mixed\n",
		"4 [-3, -1, 1] [-1, -3, 1] Mixed"
		]
		},
		"execution_count": 6,
		=======
		"0 [2, 1, -2] [1, 2, -2] Mixed\n",
		"1 [-1, -1, -1] [-1, -1, -1] Twist\n",
		"2 [1, 1, 1] [1, 1, 1] Twist\n",
		@@ -251,7 +188,6 @@
		]
		},
		"execution_count": 35,
		>>>>>>> development
		"metadata": {},
		"output_type": "execute_result"
		}
		@@ -285,11 +221,7 @@
		},
		{
		"cell_type": "code",
		<<<<<<< HEAD
		"execution_count": 7,
		=======
		"execution_count": 36,
		>>>>>>> development
		"metadata": {},
		"outputs": [
		{
		@@ -320,17 +252,6 @@
		" </thead>\n",
		" <tbody>\n",
		" <tr>\n",
		<<<<<<< HEAD
		" <th>27</th>\n",
		" <td>[-3, 7, -2]</td>\n",
		" <td>[-7, 3, 2]</td>\n",
		" <td>Symmetric Tilt</td>\n",
		" </tr>\n",
		" <tr>\n",
		" <th>43</th>\n",
		" <td>[3, -7, 2]</td>\n",
		" <td>[7, -3, -2]</td>\n",
		=======
		" <th>13</th>\n",
		" <td>[-1, -3, 4]</td>\n",
		" <td>[1, -4, 3]</td>\n",
		@@ -358,7 +279,6 @@
		" <th>71</th>\n",
		" <td>[3, -4, 1]</td>\n",
		" <td>[4, -3, -1]</td>\n",
		>>>>>>> development
		" <td>Symmetric Tilt</td>\n",
		" </tr>\n",
		" </tbody>\n",
		@@ -367,13 +287,6 @@
		],
		"text/plain": [
		" GB1 GB2 Type\n",
		<<<<<<< HEAD
		"27 [-3, 7, -2] [-7, 3, 2] Symmetric Tilt\n",
		"43 [3, -7, 2] [7, -3, -2] Symmetric Tilt"
		]
		},
		"execution_count": 7,
		=======
		"13 [-1, -3, 4] [1, -4, 3] Symmetric Tilt\n",
		"15 [1, 3, -4] [-1, 4, -3] Symmetric Tilt\n",
		"64 [-3, 4, -1] [-4, 3, 1] Symmetric Tilt\n",
		@@ -382,7 +295,6 @@
		]
		},
		"execution_count": 36,
		>>>>>>> development
		"metadata": {},
		"output_type": "execute_result"
		}
		@@ -405,11 +317,7 @@
		},
		{
		"cell_type": "code",
		<<<<<<< HEAD
		"execution_count": 8,
		=======
		"execution_count": 37,
		>>>>>>> development
		"metadata": {},
		"outputs": [],
		"source": [
		@@ -616,11 +524,7 @@
		"\n",
		"df['Number'] = Number_atoms \n",
		"\n",
		<<<<<<< HEAD
		"max_num_atoms = 500\n",
		=======
		"max_num_atoms = 300\n",
		>>>>>>> development
		"df[df['Number'] < max_num_atoms]"
		]
		},
		@@ -637,11 +541,7 @@
		},
		{
		"cell_type": "code",
		<<<<<<< HEAD
		"execution_count": null,
		=======
		"execution_count": 44,
		>>>>>>> development
		"metadata": {},
		"outputs": [],
		"source": [
		@@ -650,15 +550,9 @@
		" if str(Gb[i]) == 'Symmetric Tilt':\n",
		" SymmTiltGbs.append(V1[i])\n",
		"\n",
		<<<<<<< HEAD
		"# Find GBs less than Delta (here 5) degrees from any of the symmetric tilt boundaries in this system\n",
		"\n",
		"Delta = 5\n",
		=======
		"# Find GBs less than Delta (here 4) degrees from any of the symmetric tilt boundaries in this system\n",
		"\n",
		"Delta = 4\n",
		>>>>>>> development
		"Min_angles = []\n",
		"for i in range(len(V1)):\n",
		" angles = []\n",
		@@ -669,11 +563,6 @@
		},
		{
		"cell_type": "code",
		<<<<<<< HEAD
		"execution_count": null,
		"metadata": {},
		"outputs": [],
		=======
		"execution_count": 43,
		"metadata": {},
		"outputs": [
		@@ -917,7 +806,6 @@
		"output_type": "execute_result"
		}
		],
		>>>>>>> development
		"source": [
		"df['Angles'] = Min_angles\n",
		"\n",
		@@ -934,19 +822,11 @@
		},
		{
		"cell_type": "code",
		<<<<<<< HEAD
		"execution_count": null,
		"metadata": {},
		"outputs": [],
		"source": [
		"GB_plane = [-7, 18, -4]\n",
		=======
		"execution_count": 59,
		"metadata": {},
		"outputs": [],
		"source": [
		"GB_plane = [-7, 5, 2]\n",
		>>>>>>> development
		"# lattice parameter\n",
		"LatP = 4\n",
		"basis = 'fcc'"
		@@ -954,11 +834,6 @@
		},
		{
		"cell_type": "code",
		<<<<<<< HEAD
		"execution_count": null,
		"metadata": {},
		"outputs": [],
		=======
		"execution_count": 60,
		"metadata": {},
		"outputs": [
		@@ -970,7 +845,6 @@
		]
		}
		],
		>>>>>>> development
		"source": [
		"# just a piece of info, how much of this mixed boundary is tilt or twist?\n",
		"csl.Tilt_Twist_comp(GB_plane, axis, m, n)"
		@@ -978,11 +852,6 @@
		},
		{
		"cell_type": "code",
		<<<<<<< HEAD
		"execution_count": null,
		"metadata": {},
		"outputs": [],
		=======
		"execution_count": 65,
		"metadata": {
		"scrolled": true
		@@ -997,7 +866,6 @@
		]
		}
		],
		>>>>>>> development
		"source": [
		"# instantiate a GB:\n",
		"my_gb = gbc.GB_character()\n",
		@@ -1008,33 +876,6 @@
		"# Create the bicrystal\n",
		"my_gb.CSL_Bicrystal_Atom_generator()\n",
		"\n",
		<<<<<<< HEAD
		"# NOW CREATE MY GB, CONSIDER MICROSCOPIC DEGREES OF FREEDOM:\n",
		"\n",
		"# remove atoms closer than this 'my_gb.overD' fraction of the lattice parameter. If put to 0 no atoms will be removed.\n",
		"# if greater than 0, you must immediately input either g1 (grain 1) or g2 (grain 2) from which atoms shall \n",
		"# be removed.\n",
		"\n",
		"my_gb.overD = 0.3\n",
		"\n",
		"# put in the rigib body translation to False: it shows the as constructed GB after atom removal, put it to True: \n",
		"# you must input two integers a and b to create a grid. by default a= 10 and b= 5 and you will produce 50 initial\n",
		"# structures. For mor info, read the README.\n",
		"\n",
		"rigid = True\n",
		"\n",
		"# supercell dimensions [x,y,z], with x along GB normal and y and z in the GB plane\n",
		"\n",
		"dim = [3, 4, 5]\n",
		"\n",
		"#several possible scenarios:\n",
		" \n",
		"# my_gb.WriteGBT(my_gb.overD,'g1', False, dim[0], dim[1], dim[2])\n",
		"# my_gb.WriteGBT(0, True, 10, 5, dim[0], dim[1], dim[2])\n",
		"# my_gb.WriteGB(0, False ,dim[0], dim[1], dim[2])\n",
		"\n",
		"my_gb.WriteGB(my_gb.overD,'g1', rigid, 10, 5, dim[0], dim[1], dim[2])\n"
		=======
		"# Write a GB :\n",
		"# by default overlap = 0.0, rigid = False, \n",
		"# dim1, dim2, dim3 = [1, 1, 1]\n",
		@@ -1048,16 +889,11 @@
		"#my_gb.WriteGB(overlap= 0.3, whichG= 'g1', rigid= True,a = 3, b= 2, dim2=5 , file='VASP')\n",
		"\n",
		"my_gb.WriteGB(overlap=0.3, whichG='g1', dim1=3, dim2=3, dim3= 2,file='VASP')"
		>>>>>>> development
		]
		},
		{
		"cell_type": "code",
		<<<<<<< HEAD
		"execution_count": null,
		=======
		"execution_count": 66,
		>>>>>>> development
		"metadata": {},
		"outputs": [],
		"source": [
		@@ -1069,11 +905,7 @@
		},
		{
		"cell_type": "code",
		<<<<<<< HEAD
		"execution_count": null,
		=======
		"execution_count": 63,
		>>>>>>> development
		"metadata": {},
		"outputs": [],
		"source": [
		@@ -1100,11 +932,6 @@
		},
		{
		"cell_type": "code",
		<<<<<<< HEAD
		"execution_count": null,
		"metadata": {},
		"outputs": [],
		=======
		"execution_count": 67,
		"metadata": {},
		"outputs": [
		@@ -1901,7 +1728,6 @@
		"output_type": "display_data"
		}
		],
		>>>>>>> development
		"source": [
		"%matplotlib notebook\n",
		"plot_gb(X,Y,[0,1,0])"

Admin message