Added examples for Exercise 1 (not final)

Exercise_1/exercise9_solution.ipynb

@@ -0,0 +1,126 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "f94243a4378b446689751ca2143e94f2",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": []
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "import numpy as np\n",
+    "from ase import Atom\n",
+    "from ase.io import read\n",
+    "from ase.visualize import view\n",
+    "import matplotlib.pyplot as plt\n",
+    "import nglview as nv"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def view_structure(system):\n",
+    "    t = nv.ASEStructure(system) \n",
+    "    w = nv.NGLWidget(t, gui=True)\n",
+    "   # w.add_spacefill()\n",
+    "    return w"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def view_trajectory(trajectory):\n",
+    "    t2 = nv.ASETrajectory(trajectory)\n",
+    "    w2 = nv.NGLWidget(t2, gui=True)\n",
+    "    w2.add_spacefill()\n",
+    "    return w2"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "ec427b547fc64fe19a5ca976707664a8",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "NGLWidget()"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "9c5a2de3e42a48b7993e952c09b76687",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "Tab(children=(Box(children=(Box(children=(Box(children=(Label(value='step'), IntSlider(value=1, min=-100)), la…"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "struc_38 = read(\"38atoms.xyz\")\n",
+    "traj_38 = read(\"production_38-pos-1.xyz\")\n",
+    "view_structure(struc_38)   #this works\n",
+    "#view_trajectory(traj_38)   #this not"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

Exercise_1/input.lammps

@@ -0,0 +1,46 @@
+# Initialisation
+
+units metal
+atom_style molecular
+boundary p p p
+pair_style airebo 2.5 1 1
+read_data cnt_atom.data
+pair_coeff * * CH.airebo C
+
+change_box all x final -40 40 y final -40 40 z final -80 80
+
+group carbon_atoms type 1
+variable carbon_xcm equal -1*xcm(carbon_atoms,x)
+variable carbon_ycm equal -1*xcm(carbon_atoms,y)
+variable carbon_zcm equal -1*xcm(carbon_atoms,z)
+displace_atoms carbon_atoms move ${carbon_xcm} ${carbon_ycm} ${carbon_zcm}
+
+variable zmax equal bound(carbon_atoms,zmax)+2.5
+variable zmin equal bound(carbon_atoms,zmin)-2.5
+region rtop block INF INF INF INF ${zmax} INF
+region rbot block INF INF INF INF INF ${zmin}
+region rmid block INF INF INF INF ${zmin} ${zmax}
+group carbon_top region rtop
+group carbon_bot region rbot
+group carbon_mid region rmid
+
+# velocity carbon_mid create ${T} 48455 mom yes rot yes
+
+# delete_atoms random fraction 0.005 yes all NULL 482793
+
+fix mynve all nve
+compute Tmid carbon_mid temp
+fix myber carbon_mid temp/berendsen 1 1000 0.1
+fix_modify myber temp Tmid
+
+dump mydmp all atom 1000 dump.lammpstrj
+
+thermo 100
+thermo_modify temp Tmid
+
+timestep 0.0005
+#run 5000
+
+# 0.15 A/ps = 30 m/s
+#velocity carbon_top set NULL NULL 1.5
+run 100000

Exercise_1/inputcu.lammps

@@ -0,0 +1,46 @@
+# Initialisation
+
+units metal
+atom_style molecular
+boundary p p p
+pair_style eam
+read_data cnt_cu.data
+pair_coeff * * Cu_u3.eam
+
+change_box all x final -71.4286 71.4286 y final -71.4286 71.4286 z final -142.8572 142.8572
+
+group carbon_atoms type 1
+variable carbon_xcm equal -1*xcm(carbon_atoms,x)
+variable carbon_ycm equal -1*xcm(carbon_atoms,y)
+variable carbon_zcm equal -1*xcm(carbon_atoms,z)
+displace_atoms carbon_atoms move ${carbon_xcm} ${carbon_ycm} ${carbon_zcm}
+
+variable zmax equal bound(carbon_atoms,zmax)+2.5
+variable zmin equal bound(carbon_atoms,zmin)-2.5
+region rtop block INF INF INF INF ${zmax} INF
+region rbot block INF INF INF INF INF ${zmin}
+region rmid block INF INF INF INF ${zmin} ${zmax}
+group carbon_top region rtop
+group carbon_bot region rbot
+group carbon_mid region rmid
+
+# velocity carbon_mid create ${T} 48455 mom yes rot yes
+
+# delete_atoms random fraction 0.005 yes all NULL 482793
+
+fix mynve all nve
+compute Tmid carbon_mid temp
+fix myber carbon_mid temp/berendsen 1 200 0.1
+fix_modify myber temp Tmid
+
+dump mydmp all atom 1000 dump.lammpstrj
+
+thermo 100
+thermo_modify temp Tmid
+
+timestep 0.0005
+#run 5000
+
+# 0.15 A/ps = 30 m/s
+#velocity carbon_top set NULL NULL 1.5
+run 100000