{ "cells": [ { "cell_type": "markdown", "metadata": { "id": "TOqzF3QC_p6U" }, "source": [ "# Tutorial: Analysis\n", "\n", "[![Open in Bohrium](https://cdn.dp.tech/bohrium/web/static/images/open-in-bohrium.svg)](https://bohrium.dp.tech/notebook/52a1b090ba2a4761836b5f19df1814e7)\n", "\n", "In this tutorial, we analyze a simple trajectroy as an example. The trajectory is taken from the real case [the thermal decomposition of CL-20](cl20.md).\n", "\n", "Download this trajectory using `wget`:" ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "8tAra7vQ_JOL", "outputId": "d44cc292-1e6c-4735-88e1-21c685b6d885" }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "--2022-11-05 08:51:40-- https://raw.githubusercontent.com/tongzhugroup/TRAJREAX/f10a5c2cab77d3f3b659d9dd08256ae7b27c2820/cl20/cl20.lammpstrj\n", "Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.109.133, 185.199.110.133, 185.199.111.133, ...\n", "Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.109.133|:443... connected.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 920127 (899K) [text/plain]\n", "Saving to: ‘cl20.lammpstrj’\n", "\n", " 0K .......... .......... .......... .......... .......... 5% 4.24M 0s\n", " 50K .......... .......... .......... .......... .......... 11% 5.15M 0s\n", " 100K .......... .......... .......... .......... .......... 16% 24.7M 0s\n", " 150K .......... .......... .......... .......... .......... 22% 20.2M 0s\n", " 200K .......... .......... .......... .......... .......... 27% 7.99M 0s\n", " 250K .......... .......... .......... .......... .......... 33% 42.7M 0s\n", " 300K .......... .......... .......... .......... .......... 38% 38.7M 0s\n", " 350K .......... .......... .......... .......... .......... 44% 40.9M 0s\n", " 400K .......... .......... .......... .......... .......... 50% 54.6M 0s\n", " 450K .......... .......... .......... .......... .......... 55% 58.8M 0s\n", " 500K .......... .......... .......... .......... .......... 61% 9.66M 0s\n", " 550K .......... .......... .......... .......... .......... 66% 45.7M 0s\n", " 600K .......... .......... .......... .......... .......... 72% 38.5M 0s\n", " 650K .......... .......... .......... .......... .......... 77% 80.2M 0s\n", " 700K .......... .......... .......... .......... .......... 83% 70.4M 0s\n", " 750K .......... .......... .......... .......... .......... 89% 68.7M 0s\n", " 800K .......... .......... .......... .......... .......... 94% 67.0M 0s\n", " 850K .......... .......... .......... .......... ........ 100% 79.9M=0.05s\n", "\n", "2022-11-05 08:51:41 (18.5 MB/s) - ‘cl20.lammpstrj’ saved [920127/920127]\n", "\n" ] } ], "source": [ "%%bash\n", "wget https://raw.githubusercontent.com/tongzhugroup/TRAJREAX/f10a5c2cab77d3f3b659d9dd08256ae7b27c2820/cl20/cl20.lammpstrj -O cl20.lammpstrj" ] }, { "cell_type": "markdown", "metadata": { "id": "PmUV6VDyALqi" }, "source": [ "Then use `reacnetgenerator` to analyze it. Note the order of elements (`H C N O`) MUST map to those in the trajectory." ] }, { "cell_type": "code", "execution_count": 8, "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "AgVDORot8sfl", "outputId": "bd357812-f3f7-4dee-e5cf-6a793b542ee6" }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "2022-11-05 08:51:46,154 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: ReacNetGenerator: an automatic reaction network generator for reactive\n", "molecular dynamics simulation.\n", "\n", "Please cite: ReacNetGenerator: an automatic reaction network generator\n", "for reactive molecular dynamic simulations, Phys. Chem. Chem. Phys.,\n", "2020, 22 (2): 683-691, doi: 10.1039/C9CP05091D\n", "\n", "Jinzhe Zeng (jinzhe.zeng@rutgers.edu), Tong Zhu (tzhu@lps.ecnu.edu.cn)\n", "\n", "==================\n", "Features\n", "==================\n", "* Processing of MD trajectory containing atomic coordinates or bond orders\n", "* Hidden Markov Model (HMM) based noise filtering\n", "* Isomers identifying accoarding to SMILES\n", "* Generation of reaction network for visualization using force-directed\n", " algorithm\n", "* Parallel computing\n", "\n", "==================\n", "Simple example\n", "==================\n", "ReacNetGenerator can process any kind of trajectory files containing \n", "atomic coordinates, e.g. a LAMMPS dump file prepared by running “dump 1\n", "all custom 100 dump.reaxc id type x y z” in LAMMPS:\n", "$ reacnetgenerator --type dump -i dump.reaxc -a C H O --nohmm\n", "where C, H, and O are atomic names in the input file. Analysis report\n", "will be generated automatically.\n", "\n", "Also, ReacNetGenerator can process files containing bond information, \n", "e.g. LAMMPS bond file:\n", "$ reacnetgenerator --type bond -i bonds.reaxc -a C H O --nohmm\n", "\n", "You can running the following script for help:\n", "$ reacnetgenerator -h\n", "\n", "2022-11-05 08:51:46,154 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: Version: 1.6.6.dev24+g068dac4 Creation date: 2018-03-11\n", "\rRead bond information and Detect molecules: 0timestep [00:00, ?timestep/s]\rRead bond information and Detect molecules: 2timestep [00:01, 1.40timestep/s]\rRead bond information and Detect molecules: 101timestep [00:01, 70.84timestep/s]\n", "\rSave molecules: 0%| | 0/11 [00:00C+D): 0%| | 0/100 [00:00C+D): 100%|██████████| 100/100 [00:00<00:00, 12790.24timestep/s]\n", "2022-11-05 08:51:48,583 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: Step 4: Done! Time consumed (s): 0.444 (Indentify isomers and collect reaction paths)\n", "2022-11-05 08:51:48,651 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: Step 5: Done! Time consumed (s): 0.068 (Reaction matrix generation)\n", "2022-11-05 08:51:48,667 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: Species are:\n", "2022-11-05 08:51:48,667 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: 1 [H]C12N(N(=O)=O)C3([H])N(N(=O)=O)C1([H])N(N(=O)=O)C1([H])N(N(=O)=O)C3([H])N(N(=O)=O)C1([H])N2N(=O)=O\n", "2022-11-05 08:51:48,667 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: 2 [H]C12NC3([H])N(N(=O)=O)C1([H])N(N(=O)=O)C1([H])N(N(=O)=O)C3([H])N(N(=O)=O)C1([H])N2N(=O)=O\n", "2022-11-05 08:51:48,667 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: 3 O=NO\n", "2022-11-05 08:51:48,672 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: The position of the species in the network is:\n", "2022-11-05 08:51:48,672 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: {1: array([-5.95629110e-05, -1.00129074e-04]), 2: array([-0.59480018, -0.99989987]), 3: array([0.59485974, 1. ])}\n", "2022-11-05 08:51:48,855 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: Step 6: Done! Time consumed (s): 0.204 (Draw reaction network)\n", "2022-11-05 08:51:48,878 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: Report is generated. Please see cl20.lammpstrj.html for more details.\n", "2022-11-05 08:51:48,942 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: Step 7: Done! Time consumed (s): 0.087 (Generate analysis report)\n", "2022-11-05 08:51:48,942 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: ====== Summary ======\n", "2022-11-05 08:51:48,942 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: Total time(s): 2.787 s\n" ] } ], "source": [ "%%bash\n", "reacnetgenerator -i cl20.lammpstrj -a H C N O --type dump --nohmm" ] }, { "cell_type": "markdown", "metadata": { "id": "PO14aadxA4Cy" }, "source": [ "The results are shown in `cl20.lammpstrj.html`. In addition, we can view an overview of reactions in the trajectory in the command line:" ] }, { "cell_type": "code", "execution_count": 9, "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "GQNtq6mLAoJK", "outputId": "1fcc9399-5b5b-4fa6-b0aa-f753fcfb9fd2" }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1 [H]C12N(N(=O)=O)C3([H])N(N(=O)=O)C1([H])N(N(=O)=O)C1([H])N(N(=O)=O)C3([H])N(N(=O)=O)C1([H])N2N(=O)=O->O=NO+[H]C12NC3([H])N(N(=O)=O)C1([H])N(N(=O)=O)C1([H])N(N(=O)=O)C3([H])N(N(=O)=O)C1([H])N2N(=O)=O\n" ] } ], "source": [ "%%bash\n", "cat cl20.lammpstrj.reactionabcd" ] }, { "cell_type": "markdown", "metadata": { "id": "4xL87CdoBPQz" }, "source": [ "Here we can clearly see that the CL-20 molecule is decomposited into a nitrogen dioxide molecule.\n" ] } ], "metadata": { "colab": { "authorship_tag": "ABX9TyN2IDYefbmLYArmNHl2104Q", "include_colab_link": true, "provenance": [] }, "kernelspec": { "display_name": "Python 3.10.6 64-bit", "language": "python", "name": "python3" }, "language_info": { "name": "python", "version": "3.10.6" }, "vscode": { "interpreter": { "hash": "916dbcbb3f70747c44a77c7bcd40155683ae19c65e1c03b4aa3499c5328201f1" } } }, "nbformat": 4, "nbformat_minor": 0 }