{ "cells": [ { "cell_type": "markdown", "id": "820a1fbe", "metadata": {}, "source": [ "# Reading HDF5 Trajectories" ] }, { "cell_type": "markdown", "id": "01981d4b", "metadata": {}, "source": [ "Reading *narupatools* HDF5 trajectory files is simple." ] }, { "cell_type": "code", "execution_count": 1, "id": "61c0fd40", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "" ] }, "execution_count": 1, "metadata": {}, "output_type": "execute_result" } ], "source": [ "from narupatools.frame.hdf5 import HDF5Trajectory\n", "\n", "# Read in the trajectory with the given filename\n", "trajectory = HDF5Trajectory.load_file(\"nanotube.h5\")\n", "trajectory" ] }, { "cell_type": "markdown", "id": "a7333971", "metadata": {}, "source": [ "## Accessing Trajectory Data" ] }, { "cell_type": "markdown", "id": "960eabdd", "metadata": {}, "source": [ "You can access positions, velocities, forces, times, kinetic energies and potential energies from the trajectory" ] }, { "cell_type": "code", "execution_count": 2, "id": "bfc3ba71", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "array([4.0772214, 3.4326735, 3.706915 ], dtype=float32)" ] }, "execution_count": 2, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# Position of atom 55 at the end of 43rd frame\n", "trajectory.positions[43][55]" ] }, { "cell_type": "code", "execution_count": 3, "id": "910b2574", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "1262.3097" ] }, "execution_count": 3, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# Potential energy at the end of the 123rd frame\n", "trajectory.potential_energies[123]" ] }, { "cell_type": "code", "execution_count": 4, "id": "3858aa30", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "1.257" ] }, "execution_count": 4, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# Duration of the simulation\n", "trajectory.times[-1]" ] }, { "cell_type": "code", "execution_count": 5, "id": "0584cbe3", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "2707.7803" ] }, "execution_count": 5, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# Maximum kinetic energy achieved\n", "max(trajectory.kinetic_energies)" ] }, { "cell_type": "markdown", "id": "1872aa26", "metadata": {}, "source": [ "## Exploring Interactions" ] }, { "cell_type": "markdown", "id": "0b4010da", "metadata": {}, "source": [ "Interactions can be viewed through the `interactions` attribute" ] }, { "cell_type": "code", "execution_count": 6, "id": "afa8a904", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "" ] }, "execution_count": 6, "metadata": {}, "output_type": "execute_result" } ], "source": [ "trajectory.interactions" ] }, { "cell_type": "markdown", "id": "aff1aec0", "metadata": {}, "source": [ "This is a dictionary of interaction IDs to interactions" ] }, { "cell_type": "code", "execution_count": 7, "id": "58633898", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "['interaction.166f117c-f73b-4a66-83f6-d1d233158305',\n", " 'interaction.1d63599b-1174-4fbd-b9a2-bcd9af8205b1',\n", " 'interaction.63ec07ab-5b3e-45a1-aa10-f6f7f85decf0',\n", " 'interaction.75546256-6793-4de2-a333-de80da48259b',\n", " 'interaction.a61a910a-6f2c-41eb-8efd-7a80844cc75e',\n", " 'interaction.e4bbb3de-70cd-42b3-9fa8-e0198c1f4b89',\n", " 'interaction.fa99c0a3-a0c6-41b8-a9b1-5ec9aa35764d']" ] }, "execution_count": 7, "metadata": {}, "output_type": "execute_result" } ], "source": [ "list(trajectory.interactions.keys())" ] }, { "cell_type": "code", "execution_count": 8, "id": "1af8986a", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "[,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ]" ] }, "execution_count": 8, "metadata": {}, "output_type": "execute_result" } ], "source": [ "list(trajectory.interactions.values())" ] }, { "cell_type": "markdown", "id": "2862568a", "metadata": {}, "source": [ "We can access individual interactions and look at their properties" ] }, { "cell_type": "code", "execution_count": 9, "id": "600d88bc", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "" ] }, "execution_count": 9, "metadata": {}, "output_type": "execute_result" } ], "source": [ "interaction = list(trajectory.interactions.values())[0]\n", "interaction" ] }, { "cell_type": "code", "execution_count": 10, "id": "f0193728", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "'spring'" ] }, "execution_count": 10, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# Type used for the interaction\n", "interaction.type" ] }, { "cell_type": "code", "execution_count": 11, "id": "c9752060", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "0.012000084" ] }, "execution_count": 11, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# Duration of the interaction\n", "interaction.duration" ] }, { "cell_type": "code", "execution_count": 12, "id": "a1a204a3", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "array([60])" ] }, "execution_count": 12, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# Particle indices affected by this interaction\n", "interaction.indices" ] }, { "cell_type": "code", "execution_count": 13, "id": "e32290b2", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "array([5000., 5000., 5000., 5000., 5000., 5000., 5000., 5000., 5000.,\n", " 5000., 5000., 5000., 5000.], dtype=float32)" ] }, "execution_count": 13, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# Interaction scales for all the frames it was active\n", "interaction.interaction_scales" ] }, { "cell_type": "code", "execution_count": 22, "id": "3d876a69", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "array([370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382,\n", " 383, 384])" ] }, "execution_count": 22, "metadata": {}, "output_type": "execute_result" } ], "source": [ "interaction.frame_indices" ] }, { "cell_type": "code", "execution_count": 14, "id": "8c423091", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "range(1045, 1058)" ] }, "execution_count": 14, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# Range of frame's this interaction was active\n", "interaction.frame_range" ] }, { "cell_type": "code", "execution_count": 24, "id": "56c7533d", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "-274.0996720147649" ] }, "execution_count": 24, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# Calculate work done by this interaction\n", "interaction.calculate_work() / interaction.duration" ] }, { "cell_type": "code", "execution_count": 32, "id": "0ec61528", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "array([ 3.943864 , 3.7499657, 2.32591 , 1.9871073, 3.4310095,\n", " 13.931385 , 18.887295 , 24.125637 , 38.57629 , 68.2246 ,\n", " 80.72703 , 85.26426 , 94.47824 , 94.30299 , 84.89401 ],\n", " dtype=float32)" ] }, "execution_count": 32, "metadata": {}, "output_type": "execute_result" } ], "source": [ "interaction.potential_energies" ] }, { "cell_type": "code", "execution_count": 29, "id": "435207a5", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "array([0., 0., 0., ..., 0., 0., 0.])" ] }, "execution_count": 29, "metadata": {}, "output_type": "execute_result" } ], "source": [ "trajectory.interactions.potential_energies" ] }, { "cell_type": "markdown", "id": "d6b347dc", "metadata": {}, "source": [ "## Plotting Data" ] }, { "cell_type": "markdown", "id": "58dddfdc", "metadata": {}, "source": [ "The following shows how to use plotly to plot the various energies and work associated with your trajectory.\n", "\n", "It uses the `calculate_cumulative_work` which gives the cumulative work for each frame of the trajectory." ] }, { "cell_type": "code", "execution_count": 16, "id": "28cd25e3", "metadata": {}, "outputs": [ { "data": { "text/html": [ " \n", " " ] }, "metadata": {}, "output_type": "display_data" }, { "data": { 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"" } }, "title": { "x": 0.05 }, "xaxis": { "automargin": true, "gridcolor": "white", "linecolor": "white", "ticks": "", "title": { "standoff": 15 }, "zerolinecolor": "white", "zerolinewidth": 2 }, "yaxis": { "automargin": true, "gridcolor": "white", "linecolor": "white", "ticks": "", "title": { "standoff": 15 }, "zerolinecolor": "white", "zerolinewidth": 2 } } }, "xaxis": { "title": { "text": "Time (ps)" } }, "yaxis": { "title": { "text": "Energy (kJ/mol)" } } } }, "text/html": [ "
" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "import plotly.graph_objects as go\n", "\n", "# Create the figure\n", "fig = go.Figure()\n", "\n", "# Add x and y labels\n", "fig.update_yaxes(title_text=\"Energy (kJ/mol)\")\n", "fig.update_xaxes(title_text=\"Time (ps)\")\n", "\n", "# Add a kinetic energy line\n", "fig.add_trace(go.Scatter(x=trajectory.times, y=trajectory.kinetic_energies,\n", " mode='lines',\n", " name='Kinetic Energy'))\n", "\n", "# Add a potential energy line, removing the potential energy from interactions\n", "fig.add_trace(go.Scatter(x=trajectory.times, y=trajectory.potential_energies - trajectory.interactions.potential_energies,\n", " mode='lines',\n", " name='Potential Energy'))\n", "\n", "# Add a cumulative work line\n", "fig.add_trace(go.Scatter(x=trajectory.times, y=trajectory.interactions.calculate_cumulative_work(),\n", " mode='lines',\n", " name='Cumulative Work'))\n", "\n", "# Add a interaction energy line\n", "fig.add_trace(go.Scatter(x=trajectory.times, y=trajectory.interactions.potential_energies,\n", " mode='lines',\n", " name='Interaction Energies'))\n", "\n", "# Highlight regions in which interactions were applied\n", "for interaction in trajectory.interactions.values():\n", " fig.add_vrect(\n", " x0=interaction.start_time, x1=interaction.end_time,\n", " fillcolor=\"LightSalmon\", opacity=0.5,\n", " layer=\"below\", line_width=0,\n", " )\n", "\n", "# Show the figure\n", "fig.show()" ] }, { "cell_type": "markdown", "id": "452829df", "metadata": {}, "source": [ "## NGLView" ] }, { "cell_type": "markdown", "id": "a6e84411", "metadata": {}, "source": [ "The trajectory can also be visualised in nglview" ] }, { "cell_type": "code", "execution_count": 17, "id": "1c32c385", "metadata": {}, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "8d01b45966bb49d6a9ae9432e965e671", "version_major": 2, "version_minor": 0 }, "text/plain": [] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "587dccf376824c0e9cb2ac92e54a63cd", "version_major": 2, "version_minor": 0 }, "text/plain": [ "NGLWidget(max_frame=1257)" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "from narupatools.nglview.show import show_narupatools_traj\n", "show_narupatools_traj(trajectory)" ] } ], "metadata": { "kernelspec": { "display_name": "Python 3", "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": "3.9.2" }, "widgets": { "application/vnd.jupyter.widget-state+json": { "state": { "0aebe00f9d1f4c418ab1401fa3a7f35a": { "model_module": "@jupyter-widgets/controls", "model_module_version": "1.5.0", "model_name": "SliderStyleModel", "state": { "description_width": "" } }, 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