diff --git a/docs/source/jupyter/quantum-espresso.ipynb b/docs/source/jupyter/quantum-espresso.ipynb
index a412a50..bd30ba4 100644
--- a/docs/source/jupyter/quantum-espresso.ipynb
+++ b/docs/source/jupyter/quantum-espresso.ipynb
@@ -1,4 +1,25 @@
 {
+ "metadata": {
+  "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
+  },
+  "orig_nbformat": 2,
+  "kernelspec": {
+   "name": "python_defaultSpec_1597048081738",
+   "display_name": "Python 3.8.2 64-bit"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2,
  "cells": [
   {
    "cell_type": "markdown",
@@ -34,7 +55,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -54,7 +75,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -71,7 +92,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -92,9 +113,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "output_type": "execute_result",
+     "data": {
+      "text/plain": "<qe.Celldm1: be8f3915-3eb7-4221-a441-345eda51832b,  CoreSession: @0x7feae9717370>"
+     },
+     "metadata": {},
+     "execution_count": 4
+    }
+   ],
    "source": [
     "Si.add(SiPseudo, Si1)\n",
     "Si.add(QE.Mass(value = 28.085, unit = \"amu\"))\n",
@@ -112,9 +142,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "output_type": "execute_result",
+     "data": {
+      "text/plain": "[<qe.CellParameterX: 0ebdeed9-1d8a-498d-94c9-bafccb05d652,  CoreSession: @0x7feae9717370>,\n <qe.CellParameterY: fea8789c-8c07-49f9-9971-8d42bdd6ba3f,  CoreSession: @0x7feae9717370>,\n <qe.CellParameterZ: 1474d106-4204-428d-827b-2d5e2cb4af51,  CoreSession: @0x7feae9717370>]"
+     },
+     "metadata": {},
+     "execution_count": 5
+    }
+   ],
    "source": [
     "SiParams.add(QE.CellParameterX(vector = (0.5, 0.5, 0), unit = \"\"),\n",
     "             QE.CellParameterY(vector = (0.5, 0, 0.5), unit = \"\"),\n",
@@ -130,9 +169,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 6,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "output_type": "execute_result",
+     "data": {
+      "text/plain": "<qe.K_POINTS: 6847a5f0-8d20-4f73-9eb3-043e78053182,  CoreSession: @0x7feae9717370>"
+     },
+     "metadata": {},
+     "execution_count": 6
+    }
+   ],
    "source": [
     "sim.add(SiCell)\n",
     "sim.add(Si)\n",
@@ -148,9 +196,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 7,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "output_type": "execute_result",
+     "data": {
+      "text/plain": "<qe.StressTensor: 2f302f8b-89b8-4d7a-a2a7-4f6e19737f00,  CoreSession: @0x7feae9717370>"
+     },
+     "metadata": {},
+     "execution_count": 7
+    }
+   ],
    "source": [
     "sim.add(QE.Pressure(value = 100, unit = \"kbar\"))\n",
     "sim.add(QE.StressTensor(tensor2 = np.zeros((3, 3)), unit = \"kbar\"))"
@@ -165,9 +222,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
+   "execution_count": 8,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [
+    {
+     "output_type": "stream",
+     "name": "stdout",
+     "text": "- Cuds object:\n  uuid: 903145ad-50e3-46fc-9d28-1aa1ec364e8a\n  type: qe.Simulation\n  superclasses: cuba.Class, cuba.Entity, qe.Simulation\n  description: \n    All components of the simulation that are needed to run the model\n\n   |_Relationship qe.HAS_PART:\n     -  qe.Cell cuds object:\n     .  uuid: 67a0fcb4-4977-49df-9bcb-13bca17b2763\n     .   |_Relationship qe.HAS_PART:\n     .     -  qe.Atom cuds object:\n     .     .  uuid: 1bad1c25-609a-4bc0-8c65-3c0167cfdbe2\n     .     .   |_Relationship qe.HAS_PART:\n     .     .     -  qe.Position cuds object:\n     .     .        uuid: c70afbb3-0012-488d-8059-b44d775c6b23\n     .     .        vector: [0. 0. 0.]\n     .     .        unit: \n     .     -  qe.CellParams cuds object:\n     .     .  uuid: f444899a-e850-4ab2-b79e-c91026523eb3\n     .     .   |_Relationship qe.HAS_PART:\n     .     .     -  qe.CellParameterX cuds object:\n     .     .     .  uuid: 0ebdeed9-1d8a-498d-94c9-bafccb05d652\n     .     .     .  vector: [0.5 0.5 0. ]\n     .     .     .  unit: \n     .     .     -  qe.CellParameterY cuds object:\n     .     .     .  uuid: fea8789c-8c07-49f9-9971-8d42bdd6ba3f\n     .     .     .  vector: [0.5 0.  0.5]\n     .     .     .  unit: \n     .     .     -  qe.CellParameterZ cuds object:\n     .     .        uuid: 1474d106-4204-428d-827b-2d5e2cb4af51\n     .     .        vector: [0.  0.5 0.5]\n     .     .        unit: \n     .     -  qe.Celldm1 cuds object:\n     .        uuid: be8f3915-3eb7-4221-a441-345eda51832b\n     .        unit: au\n     .        value: 5.4307\n     -  qe.Element cuds object named <Si>:\n     .  uuid: 8628ceb7-1c02-4014-95a4-d9450aab4753\n     .   |_Relationship qe.HAS_PART:\n     .     -  qe.Atom cuds object:\n     .     .  uuid: 1bad1c25-609a-4bc0-8c65-3c0167cfdbe2\n     .     .  (already printed)\n     .     -  qe.Mass cuds object:\n     .     .  uuid: 1aee515a-4e12-40e6-bbd6-23bf5c95fe84\n     .     .  unit: amu\n     .     .  value: 28.085\n     .     -  qe.PSEUDOPOTENTIAL cuds object named <Si.pbe-n-kjpaw_psl.1.0.0.UPF>:\n     .        uuid: cb27bcb9-27c6-48a9-8f1e-8977b16567c5\n     -  qe.K_POINTS cuds object:\n     .  uuid: 6847a5f0-8d20-4f73-9eb3-043e78053182\n     .  vector: [7. 7. 7.]\n     .  unit: \n     -  qe.Pressure cuds object:\n     .  uuid: d281d93d-fd10-41fd-868c-0cda3b510431\n     .  unit: kbar\n     .  value: 100.0\n     -  qe.StressTensor cuds object:\n        uuid: 2f302f8b-89b8-4d7a-a2a7-4f6e19737f00\n        unit: kbar\n        tensor2: [[0. 0. 0.]\n [0. 0. 0.]\n [0. 0. 0.]]\n"
+    }
+   ],
    "source": [
     "pretty_print(sim)"
    ]
@@ -181,16 +246,24 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
+   "execution_count": 12,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [
+    {
+     "output_type": "stream",
+     "name": "stdout",
+     "text": "Running calculation...\n/mnt/c/iwm/docs/si.pwscf.in\npw.x -i /mnt/c/iwm/docs/si.pwscf.in > /mnt/c/iwm/docs/si.pwscf.out\n"
+    }
+   ],
    "source": [
-    "session = qeSession(root = \"\")\n",
+    "session = qeSession()\n",
     "quantum_espresso_wrapper = QE.QEWrapper(session = session)\n",
     "quantum_espresso_wrapper.add(sim)\n",
     "print(\"Running calculation...\")\n",
     "\n",
-    "quantum_espresso_wrapper.session._run(prefix = \"si\", command_type = \"pw.x\", calculation_type = \"scf\")"
+    "quantum_espresso_wrapper.session._run(simulation = sim, prefix = \"si\", command_type = \"pw.x\", calculation_type = \"scf\", root = \"\", CONTROL = {'pseudo_dir': \"'.'\"})"
    ]
   },
   {
@@ -202,9 +275,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
+   "execution_count": 10,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [
+    {
+     "output_type": "stream",
+     "name": "stdout",
+     "text": "- Cuds object:\n  uuid: 903145ad-50e3-46fc-9d28-1aa1ec364e8a\n  type: qe.Simulation\n  superclasses: cuba.Class, cuba.Entity, qe.Simulation\n  description: \n    All components of the simulation that are needed to run the model\n\n   |_Relationship qe.HAS_PART:\n     -  qe.Cell cuds object:\n     .  uuid: 67a0fcb4-4977-49df-9bcb-13bca17b2763\n     .   |_Relationship qe.HAS_PART:\n     .     -  qe.Atom cuds object:\n     .     .  uuid: 1bad1c25-609a-4bc0-8c65-3c0167cfdbe2\n     .     .   |_Relationship qe.HAS_PART:\n     .     .     -  qe.Position cuds object:\n     .     .        uuid: c70afbb3-0012-488d-8059-b44d775c6b23\n     .     .        vector: [0. 0. 0.]\n     .     .        unit: \n     .     -  qe.CellParams cuds object:\n     .     .  uuid: f444899a-e850-4ab2-b79e-c91026523eb3\n     .     .   |_Relationship qe.HAS_PART:\n     .     .     -  qe.CellParameterX cuds object:\n     .     .     .  uuid: 0ebdeed9-1d8a-498d-94c9-bafccb05d652\n     .     .     .  vector: [0.5 0.5 0. ]\n     .     .     .  unit: \n     .     .     -  qe.CellParameterY cuds object:\n     .     .     .  uuid: fea8789c-8c07-49f9-9971-8d42bdd6ba3f\n     .     .     .  vector: [0.5 0.  0.5]\n     .     .     .  unit: \n     .     .     -  qe.CellParameterZ cuds object:\n     .     .        uuid: 1474d106-4204-428d-827b-2d5e2cb4af51\n     .     .        vector: [0.  0.5 0.5]\n     .     .        unit: \n     .     -  qe.Celldm1 cuds object:\n     .        uuid: be8f3915-3eb7-4221-a441-345eda51832b\n     .        unit: au\n     .        value: 5.4307\n     -  qe.Element cuds object named <Si>:\n     .  uuid: 8628ceb7-1c02-4014-95a4-d9450aab4753\n     .   |_Relationship qe.HAS_PART:\n     .     -  qe.Atom cuds object:\n     .     .  uuid: 1bad1c25-609a-4bc0-8c65-3c0167cfdbe2\n     .     .  (already printed)\n     .     -  qe.Mass cuds object:\n     .     .  uuid: 1aee515a-4e12-40e6-bbd6-23bf5c95fe84\n     .     .  unit: amu\n     .     .  value: 28.085\n     .     -  qe.PSEUDOPOTENTIAL cuds object named <Si.pbe-n-kjpaw_psl.1.0.0.UPF>:\n     .        uuid: cb27bcb9-27c6-48a9-8f1e-8977b16567c5\n     -  qe.K_POINTS cuds object:\n     .  uuid: 6847a5f0-8d20-4f73-9eb3-043e78053182\n     .  vector: [7. 7. 7.]\n     .  unit: \n     -  qe.Pressure cuds object:\n     .  uuid: d281d93d-fd10-41fd-868c-0cda3b510431\n     .  unit: kbar\n     .  value: 100.0\n     -  qe.PwOut cuds object:\n     .  uuid: 15c6637e-9124-44dd-a1d3-f225203c1bfc\n     .  path: /mnt/c/iwm/docs/si.pwscf.out\n     -  qe.StressTensor cuds object:\n        uuid: 2f302f8b-89b8-4d7a-a2a7-4f6e19737f00\n        unit: kbar\n        tensor2: [[0. 0. 0.]\n [0. 0. 0.]\n [0. 0. 0.]]\n"
+    }
+   ],
    "source": [
     "pretty_print(sim)"
    ]
@@ -234,9 +315,21 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 21,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "output_type": "error",
+     "ename": "TypeError",
+     "evalue": "_run() missing 1 required positional argument: 'simulation'",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
+      "\u001b[0;32m<ipython-input-21-51324d6941c1>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mquantum_espresso_wrapper\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msession\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_run\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mprefix\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"si\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcommand_type\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"pw.x\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcalculation_type\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"bands\"\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      2\u001b[0m \u001b[0mquantum_espresso_wrapper\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msession\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_run\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mprefix\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"si\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcommand_type\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"bands.x\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcalculation_type\u001b[0m \u001b[0;34m=\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[0;31mTypeError\u001b[0m: _run() missing 1 required positional argument: 'simulation'"
+     ]
+    }
+   ],
    "source": [
     "quantum_espresso_wrapper.session._run(prefix = \"si\", command_type = \"pw.x\", calculation_type = \"bands\")\n",
     "quantum_espresso_wrapper.session._run(prefix = \"si\", command_type = \"bands.x\", calculation_type = \"\")"
@@ -253,18 +346,38 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 22,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "output_type": "error",
+     "ename": "TypeError",
+     "evalue": "_run() missing 1 required positional argument: 'simulation'",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
+      "\u001b[0;32m<ipython-input-22-8a4fa9c53f25>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mquantum_espresso_wrapper\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msession\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_run\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mprefix\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"si\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcommand_type\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"pw.x\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcalculation_type\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"relax\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mIONS\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m{\u001b[0m\u001b[0;34m'ion_dynamics'\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0;34m\"'bfgs'\"\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[0;31mTypeError\u001b[0m: _run() missing 1 required positional argument: 'simulation'"
+     ]
+    }
+   ],
    "source": [
     "quantum_espresso_wrapper.session._run(prefix = \"si\", command_type = \"pw.x\", calculation_type = \"relax\", IONS = {'ion_dynamics': \"'bfgs'\"})"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
+   "execution_count": 23,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [
+    {
+     "output_type": "stream",
+     "name": "stdout",
+     "text": "- Cuds object:\n  uuid: 90361daa-6905-4566-979e-11b3b0dd4e85\n  type: qe.Simulation\n  superclasses: cuba.Class, cuba.Entity, qe.Simulation\n  description: \n    All components of the simulation that are needed to run the model\n\n   |_Relationship qe.HAS_PART:\n     -  qe.Cell cuds object:\n     .  uuid: f7548873-28e9-4d76-86da-6fddb687d29e\n     .   |_Relationship qe.HAS_PART:\n     .     -  qe.Atom cuds object:\n     .     .  uuid: 53114a1f-ebbb-4e4b-a115-080925d9eaa8\n     .     .   |_Relationship qe.HAS_PART:\n     .     .     -  qe.Position cuds object:\n     .     .        uuid: 48d4483b-7c72-4454-8041-581dc73fd216\n     .     .        vector: [0. 0. 0.]\n     .     .        unit: \n     .     -  qe.CellParams cuds object:\n     .     .  uuid: 9d61e990-2509-474b-935e-618ca11bb40d\n     .     .   |_Relationship qe.HAS_PART:\n     .     .     -  qe.CellParameterX cuds object:\n     .     .     .  uuid: f2655054-efa7-4b39-9f0a-cf6453be68ec\n     .     .     .  vector: [0.5 0.5 0. ]\n     .     .     .  unit: \n     .     .     -  qe.CellParameterY cuds object:\n     .     .     .  uuid: 55647575-ea8f-4ef7-aee8-2a3333a4ec71\n     .     .     .  vector: [0.5 0.  0.5]\n     .     .     .  unit: \n     .     .     -  qe.CellParameterZ cuds object:\n     .     .        uuid: 92be9c63-ee80-46d9-8853-ccb562e94a5b\n     .     .        vector: [0.  0.5 0.5]\n     .     .        unit: \n     .     -  qe.Celldm1 cuds object:\n     .     .  uuid: db776c65-9d2e-448e-bc55-5fe0f9c7ee75\n     .     .  unit: au\n     .     .  value: 5.4307\n     .     -  qe.Element cuds object named <Si>:\n     .        uuid: 14dacecb-023c-4ace-9e83-35b0ecaa1032\n     .         |_Relationship qe.HAS_PART:\n     .           -  qe.Atom cuds object:\n     .           .  uuid: 53114a1f-ebbb-4e4b-a115-080925d9eaa8\n     .           .  (already printed)\n     .           -  qe.Atom cuds object:\n     .           .  uuid: c2094a19-8769-4298-a50a-be1f8befe5bf\n     .           .   |_Relationship qe.HAS_PART:\n     .           .     -  qe.Position cuds object:\n     .           .        uuid: 4087ce47-16f0-4449-b8c4-4577e6d265e2\n     .           .        vector: [0.25 0.25 0.26]\n     .           .        unit: \n     .           -  qe.Mass cuds object:\n     .           .  uuid: 5d57a768-d315-4f91-84a8-fcfad9aae382\n     .           .  unit: amu\n     .           .  value: 28.085\n     .           -  qe.PSEUDOPOTENTIAL cuds object named <Si.pbe-n-kjpaw_psl.1.0.0.UPF>:\n     .              uuid: ab064983-5cc9-418e-a9e7-3357c04388f5\n     -  qe.Element cuds object named <Si>:\n     .  uuid: 14dacecb-023c-4ace-9e83-35b0ecaa1032\n     .  (already printed)\n     -  qe.K_POINTS cuds object:\n     .  uuid: 38385f3b-128c-491f-91f4-44de15055d56\n     .  vector: [7. 7. 7.]\n     .  unit: \n     -  qe.Pressure cuds object:\n     .  uuid: 57f47fa8-4588-488f-8c89-fa8a0f37f567\n     .  unit: kbar\n     .  value: 100.0\n     -  qe.Pressure cuds object:\n     .  uuid: beac6977-01cf-4b4d-b89b-1b4d4eecf5c0\n     .  unit: kbar\n     .  value: 100.0\n     -  qe.PwOut cuds object:\n     .  uuid: 7890c86c-9f6f-42b3-a02c-cd57f5307c75\n     .  path: si.pwscf.out\n     -  qe.PwOut cuds object:\n     .  uuid: 5c7e31f9-6e55-4ddf-af62-5a3e58811464\n     .  path: si.pwscf.out\n     -  qe.StressTensor cuds object:\n     .  uuid: 16b33d51-0f6d-4451-a919-da494a13082f\n     .  unit: kbar\n     .  tensor2: [[0. 0. 0.]\n [0. 0. 0.]\n [0. 0. 0.]]\n     -  qe.StressTensor cuds object:\n        uuid: 590ad64e-d110-4711-90c6-0986bb53dafc\n        unit: kbar\n        tensor2: [[0. 0. 0.]\n [0. 0. 0.]\n [0. 0. 0.]]\n"
+    }
+   ],
    "source": [
     "pretty_print(sim)"
    ]
@@ -278,9 +391,24 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
+   "execution_count": 24,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [
+    {
+     "output_type": "error",
+     "ename": "ValueError",
+     "evalue": "<qe.Element: 14dacecb-023c-4ace-9e83-35b0ecaa1032,  CoreSession: @0x7f3d2d38bfa0> is already in the container",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mValueError\u001b[0m                                Traceback (most recent call last)",
+      "\u001b[0;32m<ipython-input-24-6957eba14ddb>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0mSi2\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mQE\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mAtom\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[1;32m      2\u001b[0m \u001b[0mSi2\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0madd\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mQE\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mPosition\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mvector\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0;36m0.25\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m0.25\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m0.26\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0munit\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"\"\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[0;32m----> 3\u001b[0;31m \u001b[0mSiCell\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0madd\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mSi\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[0mSi\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0madd\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mSi2\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      5\u001b[0m \u001b[0mpretty_print\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msim\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m/mnt/c/IWM/osp-core-3.4.0-dev/osp/core/cuds.py\u001b[0m in \u001b[0;36madd\u001b[0;34m(self, rel, *args)\u001b[0m\n\u001b[1;32m    161\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0mrel\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_neighbors\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0marg\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0muid\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_neighbors\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mrel\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[1;32m    162\u001b[0m                 \u001b[0mmessage\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'{!r} is already in the container'\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 163\u001b[0;31m                 \u001b[0;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmessage\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0marg\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    164\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msession\u001b[0m \u001b[0;34m!=\u001b[0m \u001b[0marg\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msession\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    165\u001b[0m                 \u001b[0marg\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_recursive_store\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0marg\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnext\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mold_objects\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[0;31mValueError\u001b[0m: <qe.Element: 14dacecb-023c-4ace-9e83-35b0ecaa1032,  CoreSession: @0x7f3d2d38bfa0> is already in the container"
+     ]
+    }
+   ],
    "source": [
     "Si2 = QE.Atom()\n",
     "Si2.add(QE.Position(vector = (0.25, 0.25, 0.26), unit = \"\"))\n",
@@ -291,9 +419,21 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 25,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "output_type": "error",
+     "ename": "TypeError",
+     "evalue": "_run() missing 1 required positional argument: 'simulation'",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
+      "\u001b[0;32m<ipython-input-25-8eda2c089407>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mquantum_espresso_wrapper\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msession\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_run\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mprefix\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"si\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcommand_type\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"pw.x\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcalculation_type\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"relax\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mIONS\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m{\u001b[0m\u001b[0;34m'ion_dynamics'\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0;34m\"'bfgs'\"\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      2\u001b[0m \u001b[0mpretty_print\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msim\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;31mTypeError\u001b[0m: _run() missing 1 required positional argument: 'simulation'"
+     ]
+    }
+   ],
    "source": [
     "quantum_espresso_wrapper.session._run(prefix = \"si\", command_type = \"pw.x\", calculation_type = \"relax\", IONS = {'ion_dynamics': \"'bfgs'\"})\n",
     "pretty_print(sim)"