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docs: add analysis.ipynb (#1771)
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225 changes: 225 additions & 0 deletions docs/tutorial/analysis.ipynb
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{
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"source": [
"# Tutorial: Analysis\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`:"
]
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"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",
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" 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"
]
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"source": [
"%%bash\n",
"wget https://raw.githubusercontent.com/tongzhugroup/TRAJREAX/f10a5c2cab77d3f3b659d9dd08256ae7b27c2820/cl20/cl20.lammpstrj -O cl20.lammpstrj"
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"source": [
"Then use `reacnetgenerator` to analyze it. Note the order of elements (`H C N O`) MUST map to those in the trajectory."
]
},
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"execution_count": 8,
"metadata": {
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"base_uri": "https://localhost:8080/"
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"outputId": "bd357812-f3f7-4dee-e5cf-6a793b542ee6"
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"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 ([email protected]), Tong Zhu ([email protected])\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 [00:00<?, ?molecule/s]\rSave molecules: 100%|██████████| 11/11 [00:00<00:00, 3376.31molecule/s]\n",
"2022-11-05 08:51:47,881 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: Step 1: Done! Time consumed (s): 1.726 (Read bond information and detect molecules)\n",
"2022-11-05 08:51:47,941 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: Step 2: Done! Time consumed (s): 0.060 (Merge isomers)\n",
"\rHMM filter: 0molecule [00:00, ?molecule/s]\rHMM filter: 11molecule [00:00, 2628.61molecule/s]\n",
"2022-11-05 08:51:48,139 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: Step 3: Done! Time consumed (s): 0.198 (HMM filter)\n",
"\rIndentify isomers: 0%| | 0/11 [00:00<?, ?molecule/s]\rIndentify isomers: 100%|██████████| 11/11 [00:00<00:00, 585.62molecule/s]\n",
"\rAnalyze atoms: 0%| | 0/11 [00:00<?, ?molecule/s]\rAnalyze atoms: 100%|██████████| 11/11 [00:00<00:00, 7775.08molecule/s]\n",
"\rCollect reaction paths: 0%| | 0/288 [00:00<?, ?atom/s]\rCollect reaction paths: 100%|██████████| 288/288 [00:00<00:00, 11114.42atom/s]\n",
"\rAnalyze reactions (A+B->C+D): 0%| | 0/100 [00:00<?, ?timestep/s]\rAnalyze reactions (A+B->C+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"
]
},
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"cell_type": "markdown",
"metadata": {
"id": "PO14aadxA4Cy"
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"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:"
]
},
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"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"
]
},
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"cell_type": "markdown",
"metadata": {
"id": "4xL87CdoBPQz"
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"source": [
"Here we can clearly see that the CL-20 molecule is decomposited into a nitrogen dioxide molecule.\n"
]
}
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1 change: 1 addition & 0 deletions docs/tutorial/index.rst
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Expand Up @@ -6,6 +6,7 @@ Examples
:caption: Tutorials

install.ipynb
analysis.ipynb

.. toctree::
:maxdepth: 2
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