├── .coveragerc ├── .gitignore ├── .travis.yml ├── LICENSE ├── README.md ├── devtools └── travis-ci │ └── install.sh ├── docs ├── Makefile ├── _build │ ├── doctrees │ │ ├── environment.pickle │ │ ├── index.doctree │ │ ├── installation.doctree │ │ ├── modules.doctree │ │ ├── msibi.doctree │ │ ├── msibi.utils.doctree │ │ └── tutorials │ │ │ └── tutorials.doctree │ └── html │ │ ├── .buildinfo │ │ ├── _modules │ │ ├── index.html │ │ ├── msibi.html │ │ └── msibi │ │ │ ├── optimize.html │ │ │ ├── pair.html │ │ │ ├── potentials.html │ │ │ ├── state.html │ │ │ ├── utils │ │ │ ├── error_calculation.html │ │ │ ├── exceptions.html │ │ │ └── general.html │ │ │ └── workers.html │ │ ├── _sources │ │ ├── index.txt │ │ ├── installation.txt │ │ ├── modules.txt │ │ ├── msibi.txt │ │ ├── msibi.utils.txt │ │ └── tutorials │ │ │ └── tutorials.txt │ │ ├── _static │ │ ├── ajax-loader.gif │ │ ├── basic.css │ │ ├── comment-bright.png │ │ ├── comment-close.png │ │ ├── comment.png │ │ ├── css │ │ │ ├── badge_only.css │ │ │ └── theme.css │ │ ├── default.css │ │ ├── doctools.js │ │ ├── down-pressed.png │ │ ├── down.png │ │ ├── file.png │ │ ├── fonts │ │ │ ├── fontawesome-webfont.eot │ │ │ ├── fontawesome-webfont.svg │ │ │ ├── fontawesome-webfont.ttf │ │ │ └── fontawesome-webfont.woff │ │ ├── jquery.js │ │ ├── js │ │ │ └── theme.js │ │ ├── minus.png │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── searchtools.js │ │ ├── sidebar.js │ │ ├── underscore.js │ │ ├── up-pressed.png │ │ ├── up.png │ │ └── websupport.js │ │ ├── genindex.html │ │ ├── index.html │ │ ├── installation.html │ │ ├── modules.html │ │ ├── msibi.html │ │ ├── msibi.utils.html │ │ ├── objects.inv │ │ ├── py-modindex.html │ │ ├── search.html │ │ ├── searchindex.js │ │ └── tutorials │ │ └── tutorials.html ├── conf.py ├── index.rst ├── installation.rst ├── make.bat ├── modules.rst ├── msibi.rst ├── msibi.utils.rst └── tutorials │ └── tutorials.rst ├── environment.yml ├── msibi ├── __init__.py ├── optimize.py ├── pair.py ├── potentials.py ├── state.py ├── tests │ ├── __init__.py │ ├── test_error_calculation.py │ ├── test_msibi.py │ ├── test_pair.py │ ├── test_potentials.py │ ├── test_select_pairs.py │ ├── test_state.py │ ├── test_utils.py │ └── test_workers.py ├── tutorials │ ├── README │ ├── lj │ │ ├── opt.py │ │ ├── rdfs │ │ │ ├── rdf.target0.t1t1.txt │ │ │ ├── rdf.target1.t1t1.txt │ │ │ └── rdf.target2.t1t1.txt │ │ ├── state0 │ │ │ ├── hoomd_run_template.py │ │ │ └── start.hoomdxml │ │ ├── state1 │ │ │ ├── hoomd_run_template.py │ │ │ └── start.hoomdxml │ │ └── state2 │ │ │ ├── hoomd_run_template.py │ │ │ └── start.hoomdxml │ └── propane │ │ ├── .gitignore │ │ ├── opt.py │ │ ├── plot.py │ │ ├── propane.ipynb │ │ ├── rdfs │ │ ├── C3-C3-state_A.txt │ │ ├── C3-C3-state_B.txt │ │ └── C3-C3-state_C.txt │ │ ├── state_A │ │ ├── hoomd_run_template.py │ │ └── start.hoomdxml │ │ ├── state_B │ │ ├── hoomd_run_template.py │ │ └── start.hoomdxml │ │ └── state_C │ │ ├── hoomd_run_template.py │ │ └── start.hoomdxml ├── utils │ ├── __init__.py │ ├── error_calculation.py │ ├── exceptions.py │ ├── find_exclusions.py │ ├── general.py │ ├── reference │ │ ├── 2chains.hoomdxml │ │ ├── final.hoomdxml │ │ ├── state0 │ │ │ ├── err.txt │ │ │ ├── hoomd_run_template.py │ │ │ ├── log.txt │ │ │ ├── query.dcd │ │ │ ├── sys.hoomdxml │ │ │ └── target-rdf.txt │ │ └── state1 │ │ │ ├── hoomd_run_template.py │ │ │ ├── query.dcd │ │ │ ├── sys.hoomdxml │ │ │ └── target-rdf.txt │ └── smoothing.py └── workers.py ├── requirements.txt └── setup.py /.coveragerc: -------------------------------------------------------------------------------- 1 | [report] 2 | omit = */tutorials/* 3 | exclude_lines = 4 | pragma: no cover 5 | 6 | # Don't complain if non-runnable code isn't run: 7 | if 0: 8 | if __name__ == .__main__.: 9 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | # Default files 2 | *.pyc 3 | *.dcd 4 | .DS_Store 5 | *.egg-info 6 | 7 | # Byte-compiled / optimized / DLL files 8 | __pycache__/ 9 | *.py[cod] 10 | *$py.class 11 | 12 | # C extensions 13 | *.so 14 | 15 | # Distribution / packaging 16 | .Python 17 | build/ 18 | develop-eggs/ 19 | dist/ 20 | downloads/ 21 | eggs/ 22 | .eggs/ 23 | lib/ 24 | lib64/ 25 | parts/ 26 | sdist/ 27 | var/ 28 | wheels/ 29 | *.egg-info/ 30 | .installed.cfg 31 | *.egg 32 | 33 | # PyInstaller 34 | # Usually these files are written by a python script from a template 35 | # before PyInstaller builds the exe, so as to inject date/other infos into it. 36 | *.manifest 37 | *.spec 38 | 39 | # Installer logs 40 | pip-log.txt 41 | pip-delete-this-directory.txt 42 | 43 | # Unit test / coverage reports 44 | htmlcov/ 45 | .tox/ 46 | .coverage 47 | .coverage.* 48 | .cache 49 | nosetests.xml 50 | coverage.xml 51 | *.cover 52 | .hypothesis/ 53 | 54 | # Translations 55 | *.mo 56 | *.pot 57 | 58 | # Django stuff: 59 | *.log 60 | local_settings.py 61 | 62 | # Flask stuff: 63 | instance/ 64 | .webassets-cache 65 | 66 | # Scrapy stuff: 67 | .scrapy 68 | 69 | # Sphinx documentation 70 | docs/_build/ 71 | 72 | # PyBuilder 73 | target/ 74 | 75 | # Jupyter Notebook 76 | .ipynb_checkpoints 77 | 78 | # pyenv 79 | .python-version 80 | 81 | # celery beat schedule file 82 | celerybeat-schedule 83 | 84 | # SageMath parsed files 85 | *.sage.py 86 | 87 | # Environments 88 | .env 89 | .venv 90 | env/ 91 | venv/ 92 | ENV/ 93 | 94 | # Spyder project settings 95 | .spyderproject 96 | .spyproject 97 | 98 | # Rope project settings 99 | .ropeproject 100 | 101 | # mkdocs documentation 102 | /site 103 | 104 | # mypy 105 | .mypy_cache/ 106 | -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 1 | language: generic 2 | 3 | sudo: false 4 | 5 | matrix: 6 | include: 7 | - { os: linux, env: PYTHON_VERSION=2.7 } 8 | - { os: linux, env: PYTHON_VERSION=3.5 } 9 | - { os: linux, env: PYTHON_VERSION=3.6 } 10 | - { os: osx, env: PYTHON_VERSION=2.7 } 11 | - { os: osx, env: PYTHON_VERSION=3.5 } 12 | 13 | install: 14 | - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install md5sha1sum; fi 15 | - source devtools/travis-ci/install.sh 16 | - conda config --set always_yes yes --set changeps1 no 17 | - conda env create -n test-environment python=$PYTHON_VERSION -f environment.yml 18 | - source activate test-environment 19 | - pip install -e . 20 | 21 | script: 22 | - pytest -v --cov=msibi --cov-report= --pyargs msibi 23 | 24 | after_success: 25 | - coveralls 26 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | The MIT License (MIT) 2 | 3 | Copyright (c) 2015 Christoph Klein and Timothy C. Moore 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | MultiState Iterative Boltzmann Inversion 2 | ---------------------------------------- 3 | [![Build Status](https://travis-ci.org/mosdef-hub/msibi.svg?branch=master)](https://travis-ci.org/mosdef-hub/msibi) 4 | [![Coverage Status](https://coveralls.io/repos/ctk3b/msibi/badge.svg?branch=master)](https://coveralls.io/r/ctk3b/msibi?branch=master) 5 | 6 | A package to help you manage and run pair potential optimizations using 7 | multistate iterative Boltzmann inversion. 8 | 9 | Install from source: 10 | ```python 11 | git clone https://github.com/mosdef-hub/msibi.git 12 | cd msibi 13 | pip install . 14 | ``` 15 | 16 | 17 | #### Citation [![Citing MSIBI](https://img.shields.io/badge/DOI-10.1063%2F1.4880555-blue.svg)](http://dx.doi.org/10.1063/1.4880555) 18 | Details of the underlying method and its validation can be found [here](http://dx.doi.org/10.1063/1.4880555). 19 | 20 | If you use this package, please cite the above paper. The BibTeX reference is 21 | ``` 22 | @article{Moore2014, 23 | author = "Moore, Timothy C. and Iacovella, Christopher R. and McCabe, Clare", 24 | title = "Derivation of coarse-grained potentials via multistate iterative Boltzmann inversion", 25 | journal = "The Journal of Chemical Physics", 26 | year = "2014", 27 | volume = "140", 28 | number = "22", 29 | doi = "http://dx.doi.org/10.1063/1.4880555" 30 | } 31 | ``` 32 | 33 | 34 | 35 | -------------------------------------------------------------------------------- /devtools/travis-ci/install.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then MINICONDA=Miniconda3-latest-MacOSX-x86_64.sh; fi 4 | if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then MINICONDA=Miniconda3-latest-Linux-x86_64.sh; fi 5 | 6 | MINICONDA_MD5=$(curl -s https://repo.continuum.io/miniconda/ | grep -A3 $MINICONDA | sed -n '4p' | sed -n 's/ *\(.*\)<\/td> */\1/p') 7 | wget https://repo.continuum.io/miniconda/$MINICONDA 8 | if [[ $MINICONDA_MD5 != $(md5sum $MINICONDA | cut -d ' ' -f 1) ]]; then 9 | echo "Miniconda MD5 mismatch" 10 | exit 1 11 | fi 12 | bash $MINICONDA -b 13 | rm -f $MINICONDA 14 | 15 | export PATH=$HOME/miniconda3/bin:$PATH 16 | 17 | conda update -yq conda 18 | -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- 1 | # Makefile for Sphinx documentation 2 | # 3 | 4 | # You can set these variables from the command line. 5 | SPHINXOPTS = 6 | SPHINXBUILD = sphinx-build 7 | PAPER = 8 | BUILDDIR = _build 9 | 10 | # User-friendly check for sphinx-build 11 | ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1) 12 | $(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/) 13 | endif 14 | 15 | # Internal variables. 16 | PAPEROPT_a4 = -D latex_paper_size=a4 17 | PAPEROPT_letter = -D latex_paper_size=letter 18 | ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . 19 | # the i18n builder cannot share the environment and doctrees with the others 20 | I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . 21 | 22 | .PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext 23 | 24 | help: 25 | @echo "Please use \`make ' where is one of" 26 | @echo " html to make standalone HTML files" 27 | @echo " dirhtml to make HTML files named index.html in directories" 28 | @echo " singlehtml to make a single large HTML file" 29 | @echo " pickle to make pickle files" 30 | @echo " json to make JSON files" 31 | @echo " htmlhelp to make HTML files and a HTML help project" 32 | @echo " qthelp to make HTML files and a qthelp project" 33 | @echo " devhelp to make HTML files and a Devhelp project" 34 | @echo " epub to make an epub" 35 | @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" 36 | @echo " latexpdf to make LaTeX files and run them through pdflatex" 37 | @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx" 38 | @echo " text to make text files" 39 | @echo " man to make manual pages" 40 | @echo " texinfo to make Texinfo files" 41 | @echo " info to make Texinfo files and run them through makeinfo" 42 | @echo " gettext to make PO message catalogs" 43 | @echo " changes to make an overview of all changed/added/deprecated items" 44 | @echo " xml to make Docutils-native XML files" 45 | @echo " pseudoxml to make pseudoxml-XML files for display purposes" 46 | @echo " linkcheck to check all external links for integrity" 47 | @echo " doctest to run all doctests embedded in the documentation (if enabled)" 48 | 49 | clean: 50 | rm -rf $(BUILDDIR)/* 51 | 52 | html: 53 | $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html 54 | @echo 55 | @echo "Build finished. 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Source code for msibi

133 | from msibi.optimize import MSIBI
134 | from msibi.pair import Pair
135 | from msibi.potentials import *
136 | from msibi.state import State
137 | 
138 | __all__ = ['MSIBI', 'Pair', 'State',
139 | 
140 |            # Potentials.
141 |            'mie', 'morse']
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135 | import numpy as np
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138 | 
[docs]def calc_similarity(arr1, arr2):
139 |     f_fit = np.sum(np.absolute(arr1 - arr2))
140 |     f_fit /= np.sum((np.absolute(arr1) + np.absolute(arr2)))
141 |     return 1.0 - f_fit

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Source code for msibi.utils.exceptions

135 | SUPPORTED_ENGINES = ['hoomd']
136 | 
137 | 
138 | 
[docs]class UnsupportedEngine(Exception):
139 |     def __init__(self, engine):
140 |         message = 'Unsupported engine: "{0}". Supported engines are: {1}'.format(
141 |             engine, ', '.join(SUPPORTED_ENGINES))
142 |         super(UnsupportedEngine, self).__init__(message)
143 |
144 | 145 |
146 |
147 | 148 | 149 |
150 | 151 |
152 |

153 | © Copyright 2015, Christoph Klein, Timothy C. Moore. 154 |

155 |
156 | 157 | Built with Sphinx using a theme provided by Read the Docs. 158 | 159 |
160 |
161 |
162 | 163 | 164 | 165 | 166 | 167 | 168 | 169 | 170 | 171 | 180 | 181 | 182 | 183 | 184 | 185 | 186 | 187 | 188 | 189 | 190 | 191 | 192 | 193 | 194 | 199 | 200 | 201 | 202 | -------------------------------------------------------------------------------- /docs/_build/html/_sources/index.txt: -------------------------------------------------------------------------------- 1 | .. Multistate Iterative Boltzmann Inversion documentation master file, created by 2 | sphinx-quickstart on Mon Mar 30 14:37:56 2015. 3 | You can adapt this file completely to your liking, but it should at least 4 | contain the root `toctree` directive. 5 | 6 | MultiState Iterative Boltzmann Inversion 7 | ---------------------------------------- 8 | 9 | A package to help you manage and run pair potential optimizations using the 10 | multistate iterative Boltzmann inversion procedure. 11 | 12 | Installation 13 | ------------ 14 | .. toctree:: 15 | installation 16 | 17 | Tutorials 18 | --------- 19 | .. toctree:: 20 | tutorials/tutorials 21 | 22 | Citation 23 | -------- 24 | Details of the underlying method and its validation can be found here |citation| 25 | 26 | If you use this package please cite the above paper. The BibTeX reference is:: 27 | 28 | @article{Moore2014, 29 | author = "Moore, Timothy C. and Iacovella, Christopher R. and McCabe, Clare", 30 | title = "Derivation of coarse-grained potentials via multistate iterative Boltzmann inversion", 31 | journal = "The Journal of Chemical Physics", 32 | year = "2014", 33 | volume = "140", 34 | number = "22", 35 | doi = "http://dx.doi.org/10.1063/1.4880555" 36 | } 37 | 38 | API Reference 39 | ------------- 40 | .. toctree:: 41 | msibi 42 | msibi.utils 43 | 44 | Indices and tables 45 | ================== 46 | 47 | * :ref:`genindex` 48 | * :ref:`modindex` 49 | * :ref:`search` 50 | 51 | .. |citation| image:: https://img.shields.io/badge/DOI-10.1063%2F1.4880555-blue.svg 52 | :target: http://dx.doi.org/10.1063/1.4880555 53 | -------------------------------------------------------------------------------- /docs/_build/html/_sources/installation.txt: -------------------------------------------------------------------------------- 1 | ============ 2 | Installation 3 | ============ 4 | 5 | Install with pip 6 | ---------------- 7 | Coming soon! 8 | 9 | Install from source 10 | ------------------- 11 | :: 12 | 13 | $ git clone https://github.com/ctk3b/msibi 14 | $ cd msibi 15 | $ python setup.py install 16 | 17 | Dependencies 18 | ------------ 19 | To use mbuild, the following libraries and software will need to be installed. 20 | 21 | Linux, Mac OS X or Windows operating system 22 | We develop mainly on 64-bit OS X Yosemite and Windows 7 machines. 23 | TravisCI is currently only set up to perform testing on Ubuntu 12.04 24 | LTS Server Edition 64 bit 25 | 26 | `Python `_ = 2.7 or 3.3+ 27 | TravisCI currently tests on 2.7, 3.3 and 3.4. 28 | 29 | `MDTraj `_ >=1.0.0 30 | MDTraj is a Python library for reading, writing and analyizing 31 | molecular dynamics trajectories. mBuild uses MDTraj as an entry and 32 | exit point for several types of molecule data formats. See their 33 | installation instructions 34 | `here `_. 35 | 36 | To make your life easier, we recommend that you use a pre-packaged Python 37 | distribution like `Continuum's Anaconda `_ 38 | in order to get all of the dependencies. 39 | 40 | Testing your installation 41 | ------------------------- 42 | 43 | mBuild uses `py.test` for unit testing. To run them simply type run the 44 | following while in the base directory:: 45 | 46 | $ pip install pytest 47 | $ py.test 48 | 49 | We need a LOT more tests so any help here is especially welcome! 50 | -------------------------------------------------------------------------------- /docs/_build/html/_sources/modules.txt: -------------------------------------------------------------------------------- 1 | msibi 2 | ===== 3 | 4 | .. toctree:: 5 | :maxdepth: 4 6 | 7 | msibi 8 | -------------------------------------------------------------------------------- /docs/_build/html/_sources/msibi.txt: -------------------------------------------------------------------------------- 1 | msibi package 2 | ============= 3 | 4 | Subpackages 5 | ----------- 6 | 7 | .. toctree:: 8 | 9 | msibi.utils 10 | 11 | Submodules 12 | ---------- 13 | 14 | msibi.optimize module 15 | --------------------- 16 | 17 | .. automodule:: msibi.optimize 18 | :members: 19 | :undoc-members: 20 | :show-inheritance: 21 | 22 | msibi.pair module 23 | ----------------- 24 | 25 | .. automodule:: msibi.pair 26 | :members: 27 | :undoc-members: 28 | :show-inheritance: 29 | 30 | msibi.potentials module 31 | ----------------------- 32 | 33 | .. automodule:: msibi.potentials 34 | :members: 35 | :undoc-members: 36 | :show-inheritance: 37 | 38 | msibi.state module 39 | ------------------ 40 | 41 | .. automodule:: msibi.state 42 | :members: 43 | :undoc-members: 44 | :show-inheritance: 45 | 46 | msibi.workers module 47 | -------------------- 48 | 49 | .. automodule:: msibi.workers 50 | :members: 51 | :undoc-members: 52 | :show-inheritance: 53 | 54 | 55 | Module contents 56 | --------------- 57 | 58 | .. automodule:: msibi 59 | :members: 60 | :undoc-members: 61 | :show-inheritance: 62 | -------------------------------------------------------------------------------- /docs/_build/html/_sources/msibi.utils.txt: -------------------------------------------------------------------------------- 1 | msibi.utils package 2 | =================== 3 | 4 | Submodules 5 | ---------- 6 | 7 | msibi.utils.error_calculation module 8 | ------------------------------------ 9 | 10 | .. automodule:: msibi.utils.error_calculation 11 | :members: 12 | :undoc-members: 13 | :show-inheritance: 14 | 15 | msibi.utils.exceptions module 16 | ----------------------------- 17 | 18 | .. automodule:: msibi.utils.exceptions 19 | :members: 20 | :undoc-members: 21 | :show-inheritance: 22 | 23 | msibi.utils.general module 24 | -------------------------- 25 | 26 | .. automodule:: msibi.utils.general 27 | :members: 28 | :undoc-members: 29 | :show-inheritance: 30 | 31 | 32 | Module contents 33 | --------------- 34 | 35 | .. automodule:: msibi.utils 36 | :members: 37 | :undoc-members: 38 | :show-inheritance: 39 | -------------------------------------------------------------------------------- /docs/_build/html/_sources/tutorials/tutorials.txt: -------------------------------------------------------------------------------- 1 | Tutorials 2 | --------- 3 | Coming soon! 4 | -------------------------------------------------------------------------------- /docs/_build/html/_static/ajax-loader.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mosdef-hub/msibi/fe2bd543093531740cca4666721b0c0bb5be539f/docs/_build/html/_static/ajax-loader.gif -------------------------------------------------------------------------------- /docs/_build/html/_static/comment-bright.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mosdef-hub/msibi/fe2bd543093531740cca4666721b0c0bb5be539f/docs/_build/html/_static/comment-bright.png -------------------------------------------------------------------------------- /docs/_build/html/_static/comment-close.png: -------------------------------------------------------------------------------- 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98 | 99 | -------------------------------------------------------------------------------- /docs/_build/html/searchindex.js: -------------------------------------------------------------------------------- 1 | Search.setIndex({envversion:42,terms:{all:1,help:[0,1],show:[],queri:[],soon:[1,6],radiu:[],shape:[],paper:0,follow:1,mainli:1,find:[],dynam:1,row:[],yosemit:1,onli:1,depend:[],point:1,except:[],articl:0,window:1,pytest:1,dtype:[],exit:1,save:[],easier:1,them:1,sourc:[],everi:[],format:1,read:1,molecul:1,initi:[],submodul:[],util:[],temperatur:[],volum:0,compute_current_rdf:[],bit:1,associ:[],continuum:1,tail:[],like:1,edit:1,pot_cutoff:[],n_pair:[],list:[],traj:[],separ:[],bool:[],traj_fil:[],each:[],usabl:[],found:0,pot_r:[],page:[4,0],underli:0,upper:[],set:1,specifi:[],analy:1,runscript:[],back:[],procedur:0,status_filenam:[],n_bin:[],see:1,year:0,server:1,todo:[],librari:1,deriv:0,index:[4,0],scale:[],space:[],mbuild:1,"while":1,calc_similar:[],content:[],state:[],moor:0,moore2014:0,chemic:0,method:0,fals:[],machin:1,r_rang:[],full:[],run:[0,1],linear:[],mdtraj:1,whose:[],numer:[],journal:0,hoomd_run_templ:[],here:[0,1],base:1,find_nearest:[],ubuntu:1,path:[],come:[1,6],valu:[],n_iter:[],search:[4,0],iacovella:0,add_stat:[],current:1,simul:[],rdf:[],grain:0,coars:0,gener:[],unsupportedengin:[],com:1,run_query_simul:[],oper:1,pleas:0,via:0,simpli:1,backup:[],christoph:0,clare:0,appli:[],arrai:[],"float":[],number:0,evolut:[],filenam:[],instruct:1,linux:1,constant:[],n_point:[],msibi:[],your:[],unit:1,manag:0,plot:[],git:1,from:[],log:[],script:[],update_potenti:[],mors:[],interact:[],softwar:1,alpha:[],system:1,name:[],compon:[],timothi:0,alpha_form:[],lot:1,recommend:1,save_runscript:[],trajectori:1,molecular:1,type:1,cite:0,more:1,save_current_rdf:[],life:1,table_width:[],option:[],especi:1,save_table_potenti:[],factor:[],worker:[],weight:[],part:[],error_calcul:[],func:[],atom:[],"true":[],hoomd:[],none:[],input:[],"default":[],setup:1,potentials_dir:[],calcul:[],ctk3b:1,can:0,str:[],modul:[],clone:1,pre:1,r_switch:[],comput:[],abov:0,creat:[],give:[],"int":[],anaconda:1,doi:0,ani:1,top_fil:[],repres:[],packag:[],file:[],pip:[],backup_fil:[],f_fit:[],type1:[],sever:1,type2:[],rdf_cutoff:[],develop:1,welcom:[],author:0,perform:1,titl:0,make:1,get:1,mie:[],detail:0,data:1,write:1,python:1,need:1,valid:0,sig:[],state_dir:[],which:[],test:[],you:[0,1],out:[],target:[],singl:[],arr2:[],pair_indic:[],http:[0,1],arr1:[],closest:[],table_potenti:[],optim:[],kelvin:[],org:0,after:[],correct:[],ndarrai:[],mac:1,two:[],distribut:1,thi:0,pair:[],engin:[],cutoff:[],"class":[],physic:0,subpackag:[],target_rdf:[],github:1,orchestr:[],directori:1,entri:1,backup_trajectori:[],object:[],working_dir:[],mccabe:0,travisci:1,bibtex:0,reload_query_trajectori:[],potenti:[],add:[],order:1},objtypes:{},objnames:{},filenames:["index","installation","modules","msibi.utils","index2","msibi","tutorials/tutorials"],titles:["MultiState Iterative Boltzmann Inversion","Installation","msibi","msibi.utils package","Welcome to msibi’s documentation!","msibi package","Tutorials"],objects:{},titleterms:{citat:0,modul:[3,5],submodul:[3,5],indic:[4,0],except:3,packag:[3,5],api:0,tabl:[4,0],pip:1,instal:[0,1],msibi:[4,3,5,2],your:1,from:1,welcom:4,invers:0,content:[3,5],state:5,test:1,document:4,refer:0,sourc:1,optim:5,gener:3,worker:5,util:3,boltzmann:0,error_calcul:3,pair:5,depend:1,subpackag:5,multist:0,iter:0,tutori:[0,6],potenti:5}}) -------------------------------------------------------------------------------- /docs/_build/html/tutorials/tutorials.html: -------------------------------------------------------------------------------- 1 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | Tutorials — msibi 0.1 documentation 10 | 11 | 12 | 13 | 14 | 23 | 24 | 25 | 26 | 27 | 28 | 29 |
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87 | © Copyright 2015, Christoph Klein, Timothy C. Moore. 88 | Created using Sphinx 1.2.3. 89 |
90 | 91 | -------------------------------------------------------------------------------- /docs/index.rst: -------------------------------------------------------------------------------- 1 | .. Multistate Iterative Boltzmann Inversion documentation master file, created by 2 | sphinx-quickstart on Mon Mar 30 14:37:56 2015. 3 | You can adapt this file completely to your liking, but it should at least 4 | contain the root `toctree` directive. 5 | 6 | MultiState Iterative Boltzmann Inversion 7 | ---------------------------------------- 8 | 9 | A package to help you manage and run pair potential optimizations using the 10 | multistate iterative Boltzmann inversion procedure. 11 | 12 | Installation 13 | ------------ 14 | .. toctree:: 15 | installation 16 | 17 | Tutorials 18 | --------- 19 | .. toctree:: 20 | tutorials/tutorials 21 | 22 | Citation 23 | -------- 24 | Details of the underlying method and its validation can be found here |citation| 25 | 26 | If you use this package please cite the above paper. The BibTeX reference is:: 27 | 28 | @article{Moore2014, 29 | author = "Moore, Timothy C. and Iacovella, Christopher R. and McCabe, Clare", 30 | title = "Derivation of coarse-grained potentials via multistate iterative Boltzmann inversion", 31 | journal = "The Journal of Chemical Physics", 32 | year = "2014", 33 | volume = "140", 34 | number = "22", 35 | doi = "http://dx.doi.org/10.1063/1.4880555" 36 | } 37 | 38 | API Reference 39 | ------------- 40 | .. toctree:: 41 | msibi 42 | msibi.utils 43 | 44 | Indices and tables 45 | ================== 46 | 47 | * :ref:`genindex` 48 | * :ref:`modindex` 49 | * :ref:`search` 50 | 51 | .. |citation| image:: https://img.shields.io/badge/DOI-10.1063%2F1.4880555-blue.svg 52 | :target: http://dx.doi.org/10.1063/1.4880555 53 | -------------------------------------------------------------------------------- /docs/installation.rst: -------------------------------------------------------------------------------- 1 | ============ 2 | Installation 3 | ============ 4 | 5 | Install with pip 6 | ---------------- 7 | Coming soon! 8 | 9 | Install from source 10 | ------------------- 11 | :: 12 | 13 | $ git clone https://github.com/ctk3b/msibi 14 | $ cd msibi 15 | $ python setup.py install 16 | 17 | Dependencies 18 | ------------ 19 | To use mbuild, the following libraries and software will need to be installed. 20 | 21 | Linux, Mac OS X or Windows operating system 22 | We develop mainly on 64-bit OS X Yosemite and Windows 7 machines. 23 | TravisCI is currently only set up to perform testing on Ubuntu 12.04 24 | LTS Server Edition 64 bit 25 | 26 | `Python `_ = 2.7 or 3.3+ 27 | TravisCI currently tests on 2.7, 3.3 and 3.4. 28 | 29 | `MDTraj `_ >=1.0.0 30 | MDTraj is a Python library for reading, writing and analyizing 31 | molecular dynamics trajectories. mBuild uses MDTraj as an entry and 32 | exit point for several types of molecule data formats. See their 33 | installation instructions 34 | `here `_. 35 | 36 | To make your life easier, we recommend that you use a pre-packaged Python 37 | distribution like `Continuum's Anaconda `_ 38 | in order to get all of the dependencies. 39 | 40 | Testing your installation 41 | ------------------------- 42 | 43 | mBuild uses `py.test` for unit testing. To run them simply type run the 44 | following while in the base directory:: 45 | 46 | $ pip install pytest 47 | $ py.test 48 | 49 | We need a LOT more tests so any help here is especially welcome! 50 | -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- 1 | @ECHO OFF 2 | 3 | REM Command file for Sphinx documentation 4 | 5 | if "%SPHINXBUILD%" == "" ( 6 | set SPHINXBUILD=sphinx-build 7 | ) 8 | set BUILDDIR=_build 9 | set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% . 10 | set I18NSPHINXOPTS=%SPHINXOPTS% . 11 | if NOT "%PAPER%" == "" ( 12 | set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS% 13 | set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS% 14 | ) 15 | 16 | if "%1" == "" goto help 17 | 18 | if "%1" == "help" ( 19 | :help 20 | echo.Please use `make ^` where ^ is one of 21 | echo. html to make standalone HTML files 22 | echo. dirhtml to make HTML files named index.html in directories 23 | echo. singlehtml to make a single large HTML file 24 | echo. pickle to make pickle files 25 | echo. json to make JSON files 26 | echo. htmlhelp to make HTML files and a HTML help project 27 | echo. qthelp to make HTML files and a qthelp project 28 | echo. devhelp to make HTML files and a Devhelp project 29 | echo. epub to make an epub 30 | echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter 31 | echo. text to make text files 32 | echo. man to make manual pages 33 | echo. texinfo to make Texinfo files 34 | echo. gettext to make PO message catalogs 35 | echo. changes to make an overview over all changed/added/deprecated items 36 | echo. xml to make Docutils-native XML files 37 | echo. pseudoxml to make pseudoxml-XML files for display purposes 38 | echo. linkcheck to check all external links for integrity 39 | echo. doctest to run all doctests embedded in the documentation if enabled 40 | goto end 41 | ) 42 | 43 | if "%1" == "clean" ( 44 | for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i 45 | del /q /s %BUILDDIR%\* 46 | goto end 47 | ) 48 | 49 | 50 | %SPHINXBUILD% 2> nul 51 | if errorlevel 9009 ( 52 | echo. 53 | echo.The 'sphinx-build' command was not found. Make sure you have Sphinx 54 | echo.installed, then set the SPHINXBUILD environment variable to point 55 | echo.to the full path of the 'sphinx-build' executable. Alternatively you 56 | echo.may add the Sphinx directory to PATH. 57 | echo. 58 | echo.If you don't have Sphinx installed, grab it from 59 | echo.http://sphinx-doc.org/ 60 | exit /b 1 61 | ) 62 | 63 | if "%1" == "html" ( 64 | %SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html 65 | if errorlevel 1 exit /b 1 66 | echo. 67 | echo.Build finished. The HTML pages are in %BUILDDIR%/html. 68 | goto end 69 | ) 70 | 71 | if "%1" == "dirhtml" ( 72 | %SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml 73 | if errorlevel 1 exit /b 1 74 | echo. 75 | echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml. 76 | goto end 77 | ) 78 | 79 | if "%1" == "singlehtml" ( 80 | %SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml 81 | if errorlevel 1 exit /b 1 82 | echo. 83 | echo.Build finished. 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The XML files are in %BUILDDIR%/xml. 231 | goto end 232 | ) 233 | 234 | if "%1" == "pseudoxml" ( 235 | %SPHINXBUILD% -b pseudoxml %ALLSPHINXOPTS% %BUILDDIR%/pseudoxml 236 | if errorlevel 1 exit /b 1 237 | echo. 238 | echo.Build finished. The pseudo-XML files are in %BUILDDIR%/pseudoxml. 239 | goto end 240 | ) 241 | 242 | :end 243 | -------------------------------------------------------------------------------- /docs/modules.rst: -------------------------------------------------------------------------------- 1 | msibi 2 | ===== 3 | 4 | .. toctree:: 5 | :maxdepth: 4 6 | 7 | msibi 8 | -------------------------------------------------------------------------------- /docs/msibi.rst: -------------------------------------------------------------------------------- 1 | msibi package 2 | ============= 3 | 4 | Subpackages 5 | ----------- 6 | 7 | .. toctree:: 8 | 9 | msibi.utils 10 | 11 | Submodules 12 | ---------- 13 | 14 | msibi.optimize module 15 | --------------------- 16 | 17 | .. automodule:: msibi.optimize 18 | :members: 19 | :undoc-members: 20 | :show-inheritance: 21 | 22 | msibi.pair module 23 | ----------------- 24 | 25 | .. automodule:: msibi.pair 26 | :members: 27 | :undoc-members: 28 | :show-inheritance: 29 | 30 | msibi.potentials module 31 | ----------------------- 32 | 33 | .. automodule:: msibi.potentials 34 | :members: 35 | :undoc-members: 36 | :show-inheritance: 37 | 38 | msibi.state module 39 | ------------------ 40 | 41 | .. automodule:: msibi.state 42 | :members: 43 | :undoc-members: 44 | :show-inheritance: 45 | 46 | msibi.workers module 47 | -------------------- 48 | 49 | .. automodule:: msibi.workers 50 | :members: 51 | :undoc-members: 52 | :show-inheritance: 53 | 54 | 55 | Module contents 56 | --------------- 57 | 58 | .. automodule:: msibi 59 | :members: 60 | :undoc-members: 61 | :show-inheritance: 62 | -------------------------------------------------------------------------------- /docs/msibi.utils.rst: -------------------------------------------------------------------------------- 1 | msibi.utils package 2 | =================== 3 | 4 | Submodules 5 | ---------- 6 | 7 | msibi.utils.error_calculation module 8 | ------------------------------------ 9 | 10 | .. automodule:: msibi.utils.error_calculation 11 | :members: 12 | :undoc-members: 13 | :show-inheritance: 14 | 15 | msibi.utils.exceptions module 16 | ----------------------------- 17 | 18 | .. automodule:: msibi.utils.exceptions 19 | :members: 20 | :undoc-members: 21 | :show-inheritance: 22 | 23 | msibi.utils.general module 24 | -------------------------- 25 | 26 | .. automodule:: msibi.utils.general 27 | :members: 28 | :undoc-members: 29 | :show-inheritance: 30 | 31 | 32 | Module contents 33 | --------------- 34 | 35 | .. automodule:: msibi.utils 36 | :members: 37 | :undoc-members: 38 | :show-inheritance: 39 | -------------------------------------------------------------------------------- /docs/tutorials/tutorials.rst: -------------------------------------------------------------------------------- 1 | Tutorials 2 | --------- 3 | Coming soon! 4 | -------------------------------------------------------------------------------- /environment.yml: -------------------------------------------------------------------------------- 1 | name: test-environment 2 | channels: 3 | - omnia 4 | - glotzer 5 | - defaults 6 | dependencies: 7 | - numpy 8 | - mdtraj 9 | - hoomd 10 | - pytest >=3.0 11 | - pytest-cov 12 | -------------------------------------------------------------------------------- /msibi/__init__.py: -------------------------------------------------------------------------------- 1 | from msibi.optimize import MSIBI 2 | from msibi.pair import Pair 3 | from msibi.potentials import * 4 | from msibi.state import State 5 | 6 | __all__ = ['MSIBI', 'Pair', 'State', 7 | 8 | # Potentials. 9 | 'mie', 'morse'] 10 | -------------------------------------------------------------------------------- /msibi/potentials.py: -------------------------------------------------------------------------------- 1 | ############################################################################## 2 | # MSIBI: A package for optimizing coarse-grained force fields using multistate 3 | # iterative Boltzmann inversion. 4 | # Copyright (c) 2017 Vanderbilt University and the Authors 5 | # 6 | # Authors: Christoph Klein, Timothy C. Moore 7 | # 8 | # Permission is hereby granted, free of charge, to any person obtaining a copy 9 | # of this software and associated documentation files, to deal 10 | # in MSIBI without restriction, including without limitation the rights 11 | # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 12 | # # copies of MSIBI, and to permit persons to whom MSIBI is 13 | # furnished to do so, subject to the following conditions: 14 | # 15 | # The above copyright notice and this permission notice shall be included in all 16 | # copies or substantial portions of MSIBI. 17 | # 18 | # MSIBI IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 19 | # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 20 | # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 21 | # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 22 | # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 23 | # OUT OF OR IN CONNECTION WITH MSIBI OR THE USE OR OTHER DEALINGS ALONG WITH 24 | # MSIBI. 25 | # 26 | # You should have received a copy of the MIT license. 27 | # If not, see . 28 | ############################################################################## 29 | 30 | from __future__ import division 31 | 32 | import numpy as np 33 | 34 | from msibi.utils.general import find_nearest 35 | 36 | __all__ = ['mie', 'morse'] 37 | 38 | 39 | def mie(r, eps, sig, m=12, n=6): 40 | """Mie pair potential. """ 41 | prefactor = (m / (m - n)) * (m / n)**(n / (m - n)) 42 | return prefactor * eps * ((sig / r) ** m - (sig / r) ** n) 43 | 44 | 45 | def morse(r, D, alpha, r0): 46 | """Morse pair potential. """ 47 | return D * (np.exp(-2 * alpha * (r - r0)) - 2 * np.exp(-alpha * (r - r0))) 48 | 49 | 50 | def tail_correction(r, V, r_switch): 51 | """Apply a tail correction to a potential making it go to zero smoothly. 52 | 53 | Parameters 54 | ---------- 55 | r : np.ndarray, shape=(n_points,), dtype=float 56 | The radius values at which the potential is given. 57 | V : np.ndarray, shape=r.shape, dtype=float 58 | The potential values at each radius value. 59 | r_switch : float, optional, default=pot_r[-1] - 5 * dr 60 | The radius after which a tail correction is applied. 61 | 62 | References 63 | ---------- 64 | .. [1] https://codeblue.umich.edu/hoomd-blue/doc/classhoomd__script_1_1pair_1_1pair.html 65 | 66 | """ 67 | r_cut = r[-1] 68 | idx_r_switch, r_switch = find_nearest(r, r_switch) 69 | 70 | S_r = np.ones_like(r) 71 | r = r[idx_r_switch:] 72 | S_r[idx_r_switch:] = ((r_cut ** 2 - r ** 2) ** 2 * 73 | (r_cut ** 2 + 2 * r ** 2 - 3 * r_switch ** 2) / 74 | (r_cut ** 2 - r_switch ** 2) ** 3) 75 | return V * S_r 76 | 77 | 78 | def head_correction(r, V, previous_V, form='linear'): 79 | """Apply head correction to V making it go to a finite value at V(0). 80 | 81 | Parameters 82 | ---------- 83 | r : np.ndarray, shape=(n_points,), dtype=float 84 | The radius values at which the potential is given. 85 | V : np.ndarray, shape=r.shape, dtype=float 86 | The potential values at each radius value. 87 | previous_V : np.ndarray, shape=r.shape, dtype=float 88 | The potential from the previous iteration. 89 | form : str, optional, default='linear' 90 | The form of the smoothing function used. 91 | 92 | """ 93 | if form == 'linear': 94 | correction_function = linear_head_correction 95 | elif form == 'exponential': 96 | correction_function = exponential_head_correction 97 | else: 98 | raise ValueError('Unsupported head correction form: "{0}"'.format(form)) 99 | 100 | for i, pot_value in enumerate(V[::-1]): 101 | # Apply correction function because either of the following is true: 102 | # * both current and target RDFs are 0 --> nan values in potential. 103 | # * current rdf > 0, target rdf = 0 --> +inf values in potential. 104 | if np.isnan(pot_value) or np.isposinf(pot_value): 105 | last_real = V.shape[0] - i - 1 106 | if last_real > len(V) - 2: 107 | raise RuntimeError('Undefined values in tail of potential.' 108 | 'This probably means you need better ' 109 | 'sampling at this state point.') 110 | return correction_function(r, V, last_real) 111 | # Retain old potential at small r because: 112 | # * current rdf = 0, target rdf > 0 --> -inf values in potential. 113 | elif np.isneginf(pot_value): 114 | last_neginf = V.shape[0] - i - 1 115 | for i, pot_value in enumerate(V[:last_neginf+1]): 116 | V[i] = previous_V[i] 117 | return V 118 | else: 119 | # TODO: Raise error? 120 | # This means that all potential values are well behaved. 121 | pass 122 | 123 | 124 | def linear_head_correction(r, V, cutoff): 125 | """Use a linear function to smoothly force V to a finite value at V(0). """ 126 | slope = ((V[cutoff+1] - V[cutoff+2]) / (r[cutoff+1] - r[cutoff+2])) 127 | V[:cutoff + 1] = slope * (r[:cutoff + 1] - r[cutoff + 1]) + V[cutoff + 1] 128 | return V 129 | 130 | 131 | def exponential_head_correction(r, V, cutoff): 132 | """Use an exponential function to smoothly force V to a finite value at V(0) 133 | 134 | Parameters 135 | ---------- 136 | r : np.ndarray 137 | Separation values 138 | V : np.ndarray 139 | Potential at each of the separation values 140 | cutoff : int 141 | The last real value of V when iterating backwards 142 | 143 | This function fits the small part of the potential to the form: 144 | V(r) = A*exp(-Br) 145 | """ 146 | dr = r[cutoff+2] - r[cutoff+1] 147 | B = np.log(V[cutoff+1] / V[cutoff+2]) / dr 148 | A = V[cutoff+1] * np.exp(B * r[cutoff+1]) 149 | V[:cutoff+1] = A * np.exp(-B * r[:cutoff+1]) 150 | 151 | 152 | def alpha_array(alpha0, pot_r, form='linear'): 153 | """Generate an array of alpha values used for scaling in the IBI step. """ 154 | if form == 'linear': 155 | return alpha0 * (1.0 - pot_r / pot_r[-1]) 156 | else: 157 | raise ValueError('Unsupported alpha form') 158 | -------------------------------------------------------------------------------- /msibi/state.py: -------------------------------------------------------------------------------- 1 | ############################################################################## 2 | # MSIBI: A package for optimizing coarse-grained force fields using multistate 3 | # iterative Boltzmann inversion. 4 | # Copyright (c) 2017 Vanderbilt University and the Authors 5 | # 6 | # Authors: Christoph Klein, Timothy C. Moore 7 | # Contributors: Davy Yue 8 | # 9 | # Permission is hereby granted, free of charge, to any person obtaining a copy 10 | # of this software and associated documentation files, to deal 11 | # in MSIBI without restriction, including without limitation the rights 12 | # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 13 | # # copies of MSIBI, and to permit persons to whom MSIBI is 14 | # furnished to do so, subject to the following conditions: 15 | # 16 | # The above copyright notice and this permission notice shall be included in all 17 | # copies or substantial portions of MSIBI. 18 | # 19 | # MSIBI IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 20 | # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 21 | # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 22 | # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 23 | # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 24 | # OUT OF OR IN CONNECTION WITH MSIBI OR THE USE OR OTHER DEALINGS ALONG WITH 25 | # MSIBI. 26 | # 27 | # You should have received a copy of the MIT license. 28 | # If not, see . 29 | ############################################################################## 30 | 31 | import os 32 | 33 | import mdtraj as md 34 | 35 | 36 | HOOMD1_HEADER = """ 37 | from hoomd_script import * 38 | 39 | system = init.read_xml(filename="{0}", wrap_coordinates=True) 40 | 41 | T_final = {1:.1f} 42 | 43 | pot_width = {2:d} 44 | table = pair.table(width=pot_width) 45 | """ 46 | 47 | HOOMD2_HEADER = """ 48 | import hoomd 49 | import hoomd.md 50 | from hoomd.deprecated.init import read_xml 51 | 52 | hoomd.context.initialize("") 53 | system = read_xml(filename="{0}", wrap_coordinates=True) 54 | T_final = {1:.1f} 55 | 56 | pot_width = {2:d} 57 | nl = hoomd.md.nlist.cell() 58 | table = hoomd.md.pair.table(width=pot_width, nlist=nl) 59 | 60 | """ 61 | 62 | HOOMD_TABLE_ENTRY = """ 63 | table.set_from_file('{type1}', '{type2}', filename='{potential_file}') 64 | """ 65 | 66 | 67 | class State(object): 68 | """A single state used as part of a multistate optimization. 69 | 70 | Attributes 71 | ---------- 72 | k : float 73 | Boltzmann's constant in specified units. 74 | T : float 75 | Temperature in kelvin. 76 | traj : md.Trajectory 77 | The trajectory associated with this state. 78 | backup_trajectory : bool 79 | True if each query trajectory is backed up (default=False) 80 | 81 | """ 82 | 83 | def __init__(self, kT, state_dir='', traj_file=None, top_file=None, 84 | name=None, backup_trajectory=False): 85 | self.kT = kT 86 | self.state_dir = state_dir 87 | 88 | if not traj_file: 89 | self.traj_path = os.path.join(state_dir, 'query.dcd') 90 | if top_file: 91 | self.top_path = os.path.join(state_dir, top_file) 92 | 93 | self.traj = None 94 | if not name: 95 | name = 'state-{0:.3f}'.format(self.kT) 96 | self.name = name 97 | 98 | self.backup_trajectory = backup_trajectory 99 | 100 | def reload_query_trajectory(self): 101 | """Reload the query trajectory. """ 102 | if self.top_path: 103 | self.traj = md.load(self.traj_path, top=self.top_path) 104 | else: 105 | self.traj = md.load(self.traj_path) 106 | 107 | def save_runscript(self, table_potentials, table_width, engine='hoomd', 108 | runscript='hoomd_run_template.py'): 109 | """Save the input script for the MD engine. """ 110 | 111 | header = list() 112 | 113 | if self.HOOMD_VERSION == 1: 114 | HOOMD_HEADER = HOOMD1_HEADER 115 | elif self.HOOMD_VERSION == 2: 116 | HOOMD_HEADER = HOOMD2_HEADER 117 | 118 | header.append(HOOMD_HEADER.format('start.hoomdxml', self.kT, table_width)) 119 | for type1, type2, potential_file in table_potentials: 120 | header.append(HOOMD_TABLE_ENTRY.format(**locals())) 121 | header = ''.join(header) 122 | with open(os.path.join(self.state_dir, runscript)) as fh: 123 | body = ''.join(fh.readlines()) 124 | 125 | runscript_file = os.path.join(self.state_dir, 'run.py') 126 | with open(runscript_file, 'w') as fh: 127 | fh.write(header) 128 | fh.write(body) 129 | -------------------------------------------------------------------------------- /msibi/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mosdef-hub/msibi/fe2bd543093531740cca4666721b0c0bb5be539f/msibi/tests/__init__.py -------------------------------------------------------------------------------- /msibi/tests/test_error_calculation.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | 3 | from msibi.utils.error_calculation import calc_similarity 4 | 5 | 6 | def test_calc_similarity(): 7 | arr1 = np.ones(10) 8 | arr2 = np.ones(10) 9 | f_fit = calc_similarity(arr1, arr2) 10 | assert f_fit == 1.0 11 | 12 | arr2 = np.zeros(10) 13 | f_fit = calc_similarity(arr1, arr2) 14 | assert f_fit == 0.0 15 | 16 | arr1 = np.random.random(10) 17 | arr2 = np.random.random(10) 18 | assert calc_similarity(arr1, arr2) == calc_similarity(arr2, arr1) 19 | -------------------------------------------------------------------------------- /msibi/tests/test_msibi.py: -------------------------------------------------------------------------------- 1 | import pytest 2 | 3 | from msibi.optimize import MSIBI 4 | from msibi.tests.test_pair import init_state 5 | 6 | 7 | n_bins = 151 8 | 9 | def test_msibi_init_single_cutoff(): 10 | opt = MSIBI(2.5, n_bins) 11 | assert opt.pot_cutoff == opt.rdf_cutoff 12 | assert opt.n_rdf_points == n_bins 13 | assert opt.rdf_n_bins == n_bins 14 | assert opt.r_switch == 14.6/6.0 15 | assert opt.dr == 0.1/6.0 16 | assert opt.smooth_rdfs is False 17 | assert opt.rdf_r_range.shape[0] == 2 18 | assert opt.pot_r.shape[0] == n_bins 19 | 20 | 21 | def test_msibi_init_multiple_cutoff(): 22 | opt = MSIBI(2.5, n_bins, pot_cutoff=2.0) 23 | assert opt.pot_cutoff != opt.rdf_cutoff 24 | assert opt.n_rdf_points == n_bins 25 | assert opt.rdf_n_bins == n_bins 26 | assert opt.r_switch == 11.6/6.0 27 | assert opt.dr == 0.1/6.0 28 | assert opt.smooth_rdfs is False 29 | assert opt.rdf_r_range.shape[0] == 2 30 | assert opt.pot_r.shape[0] != n_bins 31 | assert opt.pot_r.shape[0] == 121 32 | 33 | 34 | def test_msibi_optimize_states(): 35 | pair, state0, rdf = init_state(0) 36 | opt = MSIBI(2.5, n_bins, pot_cutoff=2.5) 37 | opt.optimize([state0], [pair], n_iterations=0, engine='hoomd') 38 | 39 | 40 | def test_rdf_length(): 41 | pair, state0, rdf = init_state(0) 42 | opt = MSIBI(2.5, n_bins + 1, pot_cutoff=2.5) 43 | with pytest.raises(ValueError): 44 | opt.optimize([state0], [pair], n_iterations=0, engine='hoomd') 45 | -------------------------------------------------------------------------------- /msibi/tests/test_pair.py: -------------------------------------------------------------------------------- 1 | import os 2 | import pytest 3 | import tempfile 4 | 5 | import mdtraj as md 6 | import numpy as np 7 | 8 | from msibi.potentials import mie 9 | from msibi.pair import Pair 10 | from msibi.state import State 11 | from msibi.utils.general import get_fn 12 | 13 | 14 | dr = 0.1/6.0 15 | r = np.arange(0, 2.5+dr, dr) 16 | pot_r = np.arange(0, 2.0+dr, dr) 17 | r_range = np.asarray([0.0, 2.5+dr]) 18 | n_bins = 151 19 | k_B = 1.9872041e-3 # kcal/mol-K 20 | T = 298.0 # K 21 | 22 | 23 | @pytest.fixture 24 | def init_state(state_number): 25 | pair = Pair('0', '1', potential=mie(r, 1.0, 1.0)) 26 | topology_filename = get_fn('final.hoomdxml') 27 | traj_filename = get_fn('state{0}/query.dcd'.format(state_number)) 28 | t = md.load(traj_filename, top=topology_filename) 29 | pair_list = t.top.select_pairs('name "0"', 'name "1"') 30 | rdf_filename = get_fn('state{0}/target-rdf.txt'.format(state_number)) 31 | rdf = np.loadtxt(rdf_filename) 32 | alpha = 0.5 33 | state_dir = get_fn('state{0}/'.format(state_number)) 34 | state = State(k_B*T, state_dir=state_dir, 35 | top_file='sys.hoomdxml', name='state0') 36 | pair.add_state(state, rdf, alpha, pair_list) 37 | return pair, state, rdf 38 | 39 | 40 | def test_pair_name(): 41 | pair, state, rdf = init_state(0) 42 | assert pair.name == '0-1' 43 | 44 | 45 | def test_save_table_potential(): 46 | pair = Pair('A', 'B', potential=mie(r, 1.0, 1.0)) 47 | pair.potential_file = tempfile.mkstemp()[1] 48 | pair.save_table_potential(r, dr) 49 | assert os.path.isfile(pair.potential_file) 50 | 51 | 52 | def test_add_state(): 53 | pair, state, rdf = init_state(0) 54 | assert np.array_equal(pair.states[state]['target_rdf'], rdf) 55 | assert pair.states[state]['current_rdf'] is None 56 | assert pair.states[state]['alpha'] == 0.5 57 | assert len(pair.states[state]['pair_indices']) == 145152 58 | assert len(pair.states[state]['f_fit']) == 0 59 | 60 | 61 | def test_calc_current_rdf_no_smooth(): 62 | pair, state, rdf = init_state(0) 63 | state.reload_query_trajectory() 64 | pair.compute_current_rdf(state, r_range, n_bins, smooth=False, max_frames=1e3) 65 | assert pair.states[state]['current_rdf'] is not None 66 | assert len(pair.states[state]['f_fit']) > 0 67 | 68 | 69 | def test_calc_current_rdf_smooth(): 70 | pair, state, rdf = init_state(0) 71 | state.reload_query_trajectory() 72 | pair.compute_current_rdf(state, r_range, n_bins, smooth=True, max_frames=1e3) 73 | assert pair.states[state]['current_rdf'] is not None 74 | assert len(pair.states[state]['f_fit']) > 0 75 | 76 | 77 | def test_save_current_rdf(): 78 | pair, state, rdf = init_state(0) 79 | state.reload_query_trajectory() 80 | pair.compute_current_rdf(state, r_range, n_bins, smooth=True, max_frames=1e3) 81 | pair.save_current_rdf(state, 0, 0.1/6.0) 82 | if not os.path.isdir('rdfs'): 83 | os.system('mkdir rdfs') 84 | assert os.path.isfile('rdfs/pair_0-1-state_state0-step0.txt') 85 | 86 | 87 | def test_update_potential(): 88 | """Make sure the potential changes after calculating RDF""" 89 | pair, state, rdf = init_state(0) 90 | state.reload_query_trajectory() 91 | pair.compute_current_rdf(state, r_range, n_bins, smooth=True, max_frames=1e3) 92 | pair.update_potential(np.arange(0, 2.5+dr, dr), r_switch=1.8) 93 | assert not np.array_equal(pair.potential, pair.previous_potential) 94 | 95 | 96 | def test_select_pairs(): 97 | """Test selecting pairs with exclusions""" 98 | pair = Pair('tail', 'tail', potential=mie(r, 1.0, 1.0)) 99 | alpha = 0.5 100 | state_dir = get_fn('state0/') 101 | state = State(k_B*T, state_dir=state_dir, 102 | top_file=get_fn('2chains.hoomdxml'), name='state0') 103 | rdf_filename = get_fn('state0/target-rdf.txt') 104 | rdf = np.loadtxt(rdf_filename) 105 | pair.add_state(state, rdf, alpha) 106 | pair.select_pairs(state, exclude_up_to=3) 107 | assert pair.states[state]['pair_indices'].shape[0] == 162 108 | -------------------------------------------------------------------------------- /msibi/tests/test_potentials.py: -------------------------------------------------------------------------------- 1 | import pytest 2 | import numpy as np 3 | 4 | from msibi.potentials import tail_correction, mie, alpha_array 5 | 6 | 7 | def test_tail_correction(): 8 | dr = 0.05 9 | r = np.arange(0, 2.5, dr) 10 | V = mie(r, 1, 1) 11 | smooth_V = tail_correction(r, V, r_switch=2.25) 12 | assert smooth_V[-1] == 0.0 13 | 14 | 15 | def test_calc_alpha_array(): 16 | alpha0 = 1.0 17 | dr = 0.1 18 | r = np.arange(0, 2.5, dr) 19 | form = 'linear' 20 | alpha = alpha_array(alpha0, r, form) 21 | assert alpha[0] == alpha0 22 | assert alpha[-1] == 0.0 23 | 24 | form = 'margaret-thatcher' 25 | with pytest.raises(ValueError): 26 | alpha = alpha_array(alpha0, r, form) 27 | 28 | -------------------------------------------------------------------------------- /msibi/tests/test_select_pairs.py: -------------------------------------------------------------------------------- 1 | import mdtraj as md 2 | import networkx as nx 3 | import numpy as np 4 | 5 | from msibi.utils.general import get_fn 6 | from msibi.utils.find_exclusions import find_1_n_exclusions 7 | from msibi.utils.find_exclusions import is_1_n 8 | 9 | 10 | def test_select_pair_no_exclusions(): 11 | """Test pair selection without exclusions""" 12 | top = md.load(get_fn('2chains.hoomdxml')).top 13 | pairs = top.select_pairs("name 'tail'", "name 'tail'") 14 | assert pairs.shape[0] == 190 15 | 16 | 17 | def test_find_1_n_exclusions(): 18 | top = md.load(get_fn('2chains.hoomdxml')).top 19 | pairs = top.select_pairs("name 'tail'", "name 'tail'") 20 | to_delete = find_1_n_exclusions(top, pairs, 3) 21 | assert to_delete.shape[0] == 28 22 | 23 | 24 | def test_select_pair_with_exclusions(): 25 | traj = md.load(get_fn('2chains.hoomdxml')) 26 | pairs = traj.top.select_pairs("name 'tail'", "name 'tail'") 27 | to_delete = find_1_n_exclusions(traj.top, pairs, 3) 28 | pairs = np.delete(pairs, to_delete, axis=0) 29 | assert pairs.shape[0] == 162 30 | 31 | 32 | def test_is_exclusion(): 33 | top = md.load(get_fn('2chains.hoomdxml')).top 34 | G = nx.Graph() 35 | G.add_nodes_from([a.index for a in top.atoms]) 36 | bonds = [b for b in top.bonds] 37 | bonds_by_index = [(b[0].index, b[1].index) for b in bonds] 38 | G.add_edges_from(bonds_by_index) 39 | tail_tail = top.select_pairs("name 'tail'", "name 'tail'") 40 | assert is_1_n(tail_tail[0], 3, G) 41 | assert is_1_n(tail_tail[0], 2, G) 42 | assert is_1_n(tail_tail[0], 4, G) 43 | assert is_1_n(tail_tail[2], 4, G) 44 | assert not is_1_n(tail_tail[2], 3, G) 45 | 46 | -------------------------------------------------------------------------------- /msibi/tests/test_state.py: -------------------------------------------------------------------------------- 1 | import pytest 2 | 3 | from msibi.state import State 4 | from msibi.utils.general import get_fn 5 | 6 | 7 | @pytest.mark.skipif(True, reason='Needs implementing!') 8 | def test_init(): 9 | pass 10 | 11 | 12 | def test_reload_query_trajectory(): 13 | state_dir = get_fn('state0/') 14 | state = State(1.987e-3*500.0, state_dir=state_dir, top_file='sys.hoomdxml', 15 | name='state0') 16 | state.reload_query_trajectory() 17 | assert(state.traj) 18 | assert(state.traj.top) 19 | 20 | @pytest.mark.skipif(True, reason='Needs implementing!') 21 | def test_save_runscript(): 22 | pass 23 | -------------------------------------------------------------------------------- /msibi/tests/test_utils.py: -------------------------------------------------------------------------------- 1 | import pytest 2 | 3 | import numpy as np 4 | 5 | from msibi.utils.error_calculation import calc_similarity 6 | from msibi.utils.general import find_nearest 7 | from msibi.utils.smoothing import savitzky_golay 8 | 9 | 10 | def test_calc_similarity(): 11 | a = np.arange(0.0, 5.0, 0.05) 12 | b = np.arange(0.0, 5.0, 0.05) 13 | assert calc_similarity(a, b) == 1.0 14 | b *= -1 15 | assert calc_similarity(a, b) == 0.0 16 | 17 | 18 | def test_find_nearest(): 19 | a = np.arange(10) 20 | idx, nearest = find_nearest(a, 2.1) 21 | assert idx == 2 22 | assert nearest == 2 23 | 24 | 25 | def test_savitzky_golay(): 26 | x = np.arange(0, 1, 0.01) 27 | y = 2 * x + 1 28 | y2 = savitzky_golay(y, 3, 1) 29 | assert y.shape == y2.shape 30 | assert np.allclose(y, y2) 31 | 32 | y = x**3.0 33 | y2 = savitzky_golay(y, 3, 1) 34 | assert calc_similarity(y, y2) > 0.99 35 | 36 | with pytest.raises(ValueError): 37 | y2 = savitzky_golay(y, 3.1, 1) 38 | with pytest.raises(TypeError): 39 | y2 = savitzky_golay(y, 2, 1) 40 | with pytest.raises(TypeError): 41 | y2 = savitzky_golay(y, 4, 1) 42 | with pytest.raises(TypeError): 43 | y2 = savitzky_golay(y, 3, 3) 44 | with pytest.raises(TypeError): 45 | y2 = savitzky_golay(y, 3, 2) 46 | -------------------------------------------------------------------------------- /msibi/tests/test_workers.py: -------------------------------------------------------------------------------- 1 | import os 2 | import pytest 3 | 4 | from msibi.tests.test_pair import init_state 5 | from msibi.utils.exceptions import UnsupportedEngine 6 | from msibi.workers import run_query_simulations 7 | from msibi.workers import _post_query 8 | 9 | 10 | def test_unsupported_engine(): 11 | engine = 'crammps' 12 | with pytest.raises(UnsupportedEngine): 13 | run_query_simulations(['margaret', 'thatcher'], engine=engine) 14 | 15 | 16 | def test_post_query(): 17 | pair, state0, rdf = init_state(0) 18 | _post_query(state0) 19 | assert state0.traj is not None 20 | assert os.path.isfile(os.path.join(state0.state_dir, '_.0.log.txt')) 21 | assert os.path.isfile(os.path.join(state0.state_dir, '_.0.err.txt')) 22 | -------------------------------------------------------------------------------- /msibi/tutorials/README: -------------------------------------------------------------------------------- 1 | This directory contains several tests. 2 | It is advisable, at the minimum, to run the LJ test to make sure the 3 | code works as expected. To run plot.py, downloading and installing msibi_utils 4 | is highly recommended to visualize the results. 5 | 6 | LJ : recover known LJ potential 7 | - This test, as described in the original paper, is recovering a 8 | known potential to show that the methodology works. The target 9 | data was derived from LJ fluids at three different states. 10 | 11 | PROPANE : optimize pair potentials for a single-site propane model 12 | - This test, as described in the original 2014 paper, performs further 13 | optimizations on propane using a coarse-graining 3-1 mapping. The 3-site 14 | propane is mapped to the single-site propane and the generated data can be 15 | compared to known LJ potentials from literature [1]. 16 | 17 | [1] Q. Pu et al., “Molecular simulations of stretching gold nanowires in 18 | solvents,” Nanotechnology 18, 424007 (2007). 19 | -------------------------------------------------------------------------------- /msibi/tutorials/lj/opt.py: -------------------------------------------------------------------------------- 1 | import itertools 2 | import os 3 | 4 | import numpy as np 5 | 6 | from msibi import MSIBI, State, Pair, mie 7 | 8 | 9 | os.system('rm state*/_* rdfs/pair* potentials/* f_fits.log state*/log.txt') 10 | os.system('rm state*/err.txt') 11 | os.system('rm state*/query.dcd') 12 | 13 | # Set up global parameters. 14 | rdf_cutoff = 5.0 15 | opt = MSIBI(rdf_cutoff=rdf_cutoff, n_rdf_points=101, pot_cutoff=3.0, 16 | smooth_rdfs=True) 17 | 18 | # Specify states. 19 | state0 = State(kT=0.5, state_dir='./state0', top_file='start.hoomdxml', 20 | name='state0', backup_trajectory=True) 21 | state1 = State(kT=1.5, state_dir='./state1', top_file='start.hoomdxml', 22 | name='state1', backup_trajectory=True) 23 | state2 = State(kT=2.0, state_dir='./state2', top_file='start.hoomdxml', 24 | name='state2', backup_trajectory=True) 25 | states = [state0, state1, state2] 26 | 27 | # Specify pairs. 28 | indices = list(itertools.combinations(range(1468), 2)) # all-all for 1468 atoms 29 | initial_guess = mie(opt.pot_r, 1.0, 1.0) # 1-D array of potential values. 30 | rdf_targets = [np.loadtxt('rdfs/rdf.target{0:d}.t1t1.txt'.format(i)) 31 | for i in range(3)] 32 | 33 | pair0 = Pair('1', '1', initial_guess) 34 | alphas = [1.0, 1.0, 1.0] 35 | 36 | # Add targets to pair. 37 | for state, target, alpha in zip(states, rdf_targets, alphas): 38 | pair0.add_state(state, target, alpha, indices) 39 | pairs = [pair0] # optimize() expects a list of pairs 40 | 41 | # Do magic. 42 | opt.optimize(states, pairs, n_iterations=5, engine='hoomd') 43 | -------------------------------------------------------------------------------- /msibi/tutorials/lj/rdfs/rdf.target0.t1t1.txt: -------------------------------------------------------------------------------- 1 | 0 0 2 | 0.05 0 3 | 0.1 0 4 | 0.15 0 5 | 0.2 0 6 | 0.25 0 7 | 0.3 0 8 | 0.35 0 9 | 0.4 0 10 | 0.45 0 11 | 0.5 0 12 | 0.55 0 13 | 0.6 0 14 | 0.65 0 15 | 0.7 0 16 | 0.75 0 17 | 0.8 0 18 | 0.85 0 19 | 0.9 0.00343199 20 | 0.95 0.25661 21 | 1 1.70286 22 | 1.05 3.13567 23 | 1.1 3.10826 24 | 1.15 2.37586 25 | 1.2 1.68615 26 | 1.25 1.19868 27 | 1.3 0.905337 28 | 1.35 0.715035 29 | 1.4 0.609764 30 | 1.45 0.543081 31 | 1.5 0.51985 32 | 1.55 0.518761 33 | 1.6 0.553223 34 | 1.65 0.611436 35 | 1.7 0.707678 36 | 1.75 0.839403 37 | 1.8 0.977983 38 | 1.85 1.10835 39 | 1.9 1.20238 40 | 1.95 1.25224 41 | 2 1.28504 42 | 2.05 1.30419 43 | 2.1 1.30097 44 | 2.15 1.25637 45 | 2.2 1.17699 46 | 2.25 1.06703 47 | 2.3 0.968362 48 | 2.35 0.884896 49 | 2.4 0.81879 50 | 2.45 0.788498 51 | 2.5 0.781656 52 | 2.55 0.796351 53 | 2.6 0.828547 54 | 2.65 0.881824 55 | 2.7 0.946627 56 | 2.75 1.0153 57 | 2.8 1.07573 58 | 2.85 1.11632 59 | 2.9 1.13682 60 | 2.95 1.14071 61 | 3 1.12151 62 | 3.05 1.10168 63 | 3.1 1.07506 64 | 3.15 1.04158 65 | 3.2 1.01435 66 | 3.25 0.981591 67 | 3.3 0.953676 68 | 3.35 0.928868 69 | 3.4 0.91361 70 | 3.45 0.905935 71 | 3.5 0.913247 72 | 3.55 0.92847 73 | 3.6 0.949367 74 | 3.65 0.981483 75 | 3.7 1.00953 76 | 3.75 1.03721 77 | 3.8 1.05739 78 | 3.85 1.06761 79 | 3.9 1.069 80 | 3.95 1.05941 81 | 4 1.04634 82 | 4.05 1.02815 83 | 4.1 1.01618 84 | 4.15 0.998816 85 | 4.2 0.981874 86 | 4.25 0.97311 87 | 4.3 0.964823 88 | 4.35 0.961271 89 | 4.4 0.958939 90 | 4.45 0.96255 91 | 4.5 0.969203 92 | 4.55 0.981393 93 | 4.6 0.993913 94 | 4.65 1.00835 95 | 4.7 1.0183 96 | 4.75 1.02735 97 | 4.8 1.03295 98 | 4.85 1.03346 99 | 4.9 1.03082 100 | 4.95 1.02326 101 | 5 1.01477 102 | -------------------------------------------------------------------------------- /msibi/tutorials/lj/rdfs/rdf.target1.t1t1.txt: -------------------------------------------------------------------------------- 1 | 0 0 2 | 0.05 0 3 | 0.1 0 4 | 0.15 0 5 | 0.2 0 6 | 0.25 0 7 | 0.3 0 8 | 0.35 0 9 | 0.4 0 10 | 0.45 0 11 | 0.5 0 12 | 0.55 0 13 | 0.6 0 14 | 0.65 0 15 | 0.7 0 16 | 0.75 0 17 | 0.8 0 18 | 0.85 0.00419783 19 | 0.9 0.179927 20 | 0.95 0.933757 21 | 1 1.7965 22 | 1.05 2.12968 23 | 1.1 2.02124 24 | 1.15 1.76298 25 | 1.2 1.50654 26 | 1.25 1.28046 27 | 1.3 1.10959 28 | 1.35 0.994047 29 | 1.4 0.905181 30 | 1.45 0.849052 31 | 1.5 0.818728 32 | 1.55 0.791253 33 | 1.6 0.785798 34 | 1.65 0.794944 35 | 1.7 0.813936 36 | 1.75 0.854724 37 | 1.8 0.905149 38 | 1.85 0.947861 39 | 1.9 1.00115 40 | 1.95 1.06015 41 | 2 1.09604 42 | 2.05 1.11635 43 | 2.1 1.11768 44 | 2.15 1.10942 45 | 2.2 1.08775 46 | 2.25 1.06184 47 | 2.3 1.03587 48 | 2.35 1.00724 49 | 2.4 0.987037 50 | 2.45 0.968469 51 | 2.5 0.959016 52 | 2.55 0.950442 53 | 2.6 0.955028 54 | 2.65 0.955511 55 | 2.7 0.961311 56 | 2.75 0.97273 57 | 2.8 0.98225 58 | 2.85 0.997133 59 | 2.9 1.007 60 | 2.95 1.01668 61 | 3 1.02303 62 | 3.05 1.02556 63 | 3.1 1.02454 64 | 3.15 1.02506 65 | 3.2 1.0172 66 | 3.25 1.01363 67 | 3.3 1.00662 68 | 3.35 0.998155 69 | 3.4 0.996059 70 | 3.45 0.993227 71 | 3.5 0.992487 72 | 3.55 0.988348 73 | 3.6 0.988808 74 | 3.65 0.990113 75 | 3.7 0.993798 76 | 3.75 0.995855 77 | 3.8 0.997494 78 | 3.85 1.00021 79 | 3.9 1.00321 80 | 3.95 1.00573 81 | 4 1.00682 82 | 4.05 1.00402 83 | 4.1 1.00852 84 | 4.15 1.00458 85 | 4.2 1.00321 86 | 4.25 1.00055 87 | 4.3 1.00034 88 | 4.35 0.99851 89 | 4.4 1.00097 90 | 4.45 0.997601 91 | 4.5 0.999584 92 | 4.55 0.998182 93 | 4.6 0.997278 94 | 4.65 1.0018 95 | 4.7 1.00001 96 | 4.75 0.998586 97 | 4.8 1.00024 98 | 4.85 1.00015 99 | 4.9 1.00053 100 | 4.95 1.00254 101 | 5 1.00049 102 | -------------------------------------------------------------------------------- /msibi/tutorials/lj/rdfs/rdf.target2.t1t1.txt: -------------------------------------------------------------------------------- 1 | 0 0 2 | 0.05 0 3 | 0.1 0 4 | 0.15 0 5 | 0.2 0 6 | 0.25 0 7 | 0.3 0 8 | 0.35 0 9 | 0.4 0 10 | 0.45 0 11 | 0.5 0 12 | 0.55 0 13 | 0.6 0 14 | 0.65 0 15 | 0.7 0 16 | 0.75 0 17 | 0.8 0 18 | 0.85 0.00895525 19 | 0.9 0.172014 20 | 0.95 0.719421 21 | 1 1.29325 22 | 1.05 1.5901 23 | 1.1 1.61558 24 | 1.15 1.55716 25 | 1.2 1.45771 26 | 1.25 1.35727 27 | 1.3 1.26668 28 | 1.35 1.20882 29 | 1.4 1.15728 30 | 1.45 1.10923 31 | 1.5 1.06256 32 | 1.55 1.04378 33 | 1.6 1.01623 34 | 1.65 1.00287 35 | 1.7 1.00196 36 | 1.75 0.991572 37 | 1.8 0.98435 38 | 1.85 0.98909 39 | 1.9 0.992431 40 | 1.95 0.99902 41 | 2 1.0103 42 | 2.05 1.01935 43 | 2.1 1.01052 44 | 2.15 1.0247 45 | 2.2 1.03272 46 | 2.25 1.02417 47 | 2.3 1.01708 48 | 2.35 1.02181 49 | 2.4 1.02312 50 | 2.45 1.02258 51 | 2.5 1.01355 52 | 2.55 1.01791 53 | 2.6 1.01454 54 | 2.65 1.00772 55 | 2.7 1.01094 56 | 2.75 1.00267 57 | 2.8 1.00448 58 | 2.85 1.00337 59 | 2.9 1.00168 60 | 2.95 1.00182 61 | 3 1.00441 62 | 3.05 1.00288 63 | 3.1 1.00277 64 | 3.15 1.00897 65 | 3.2 1.0099 66 | 3.25 1.00403 67 | 3.3 1.0071 68 | 3.35 1.00727 69 | 3.4 0.995851 70 | 3.45 1.00373 71 | 3.5 1.00183 72 | 3.55 0.999256 73 | 3.6 1.00526 74 | 3.65 1.00322 75 | 3.7 0.994496 76 | 3.75 1.00761 77 | 3.8 0.99495 78 | 3.85 0.995781 79 | 3.9 1.00257 80 | 3.95 1.00232 81 | 4 0.999494 82 | 4.05 1.00209 83 | 4.1 0.997951 84 | 4.15 1.00455 85 | 4.2 0.99336 86 | 4.25 0.996347 87 | 4.3 0.994082 88 | 4.35 0.993397 89 | 4.4 0.995942 90 | 4.45 0.997825 91 | 4.5 0.997754 92 | 4.55 0.998684 93 | 4.6 0.997661 94 | 4.65 0.997053 95 | 4.7 0.997254 96 | 4.75 0.998877 97 | 4.8 1.00133 98 | 4.85 0.997903 99 | 4.9 1.00021 100 | 4.95 0.997446 101 | 5 0.997648 102 | -------------------------------------------------------------------------------- /msibi/tutorials/lj/state0/hoomd_run_template.py: -------------------------------------------------------------------------------- 1 | all = hoomd.group.all() 2 | nvt_int = hoomd.md.integrate.langevin(group=all, kT=T_final, seed=1) 3 | hoomd.md.integrate.mode_standard(dt=0.001) 4 | 5 | hoomd.run(1e2) 6 | output_dcd = hoomd.dump.dcd(filename='query.dcd', period=100, overwrite=True) 7 | hoomd.run(1e4) 8 | -------------------------------------------------------------------------------- /msibi/tutorials/lj/state1/hoomd_run_template.py: -------------------------------------------------------------------------------- 1 | all = hoomd.group.all() 2 | nvt_int = hoomd.md.integrate.langevin(group=all, kT=T_final, seed=1) 3 | hoomd.md.integrate.mode_standard(dt=0.001) 4 | 5 | hoomd.run(1e2) 6 | output_dcd = hoomd.dump.dcd(filename='query.dcd', period=100, overwrite=True) 7 | hoomd.run(1e4) 8 | -------------------------------------------------------------------------------- /msibi/tutorials/lj/state2/hoomd_run_template.py: -------------------------------------------------------------------------------- 1 | all = hoomd.group.all() 2 | nvt_int = hoomd.md.integrate.langevin(group=all, kT=T_final, seed=1) 3 | hoomd.md.integrate.mode_standard(dt=0.001) 4 | 5 | hoomd.run(1e2) 6 | output_dcd = hoomd.dump.dcd(filename='query.dcd', period=100, overwrite=True) 7 | hoomd.run(1e4) 8 | -------------------------------------------------------------------------------- /msibi/tutorials/propane/.gitignore: -------------------------------------------------------------------------------- 1 | rdfs/pair* 2 | potentials/ 3 | state*/*.txt 4 | state*/run.py 5 | -------------------------------------------------------------------------------- /msibi/tutorials/propane/opt.py: -------------------------------------------------------------------------------- 1 | import itertools 2 | import string 3 | import os 4 | 5 | import numpy as np 6 | 7 | from msibi import MSIBI, State, Pair, mie 8 | 9 | os.system('rm rdfs/pair_C3*_state*-step*.txt f_fits.log') 10 | os.system('rm state_*/*.txt state*/run.py state*/*query.dcd') 11 | 12 | 13 | # Set up global parameters. 14 | rdf_cutoff = 5.0 15 | opt = MSIBI(rdf_cutoff=rdf_cutoff, n_rdf_points=201, pot_cutoff=3.0, 16 | smooth_rdfs=True) 17 | 18 | # Specify states. 19 | stateA = State(kT=0.5, state_dir='./state_A', top_file='start.hoomdxml', 20 | name='stateA', backup_trajectory=True) 21 | stateB = State(kT=1.5, state_dir='./state_B', top_file='start.hoomdxml', 22 | name='stateB', backup_trajectory=True) 23 | stateC = State(kT=2.0, state_dir='./state_C', top_file='start.hoomdxml', 24 | name='stateC', backup_trajectory=True) 25 | states = [stateA, stateB, stateC] 26 | 27 | # Specify pairs. 28 | indices = list(itertools.combinations(range(1024), 2)) # all-all for 1024 atoms 29 | 30 | initial_guess = mie(opt.pot_r, 1.0, 1.0) # 1-D array of potential values. 31 | alphabet = ['A', 'B', 'C'] 32 | rdf_targets = [np.loadtxt('rdfs/C3-C3-state_{0}.txt'.format(i)) 33 | for i in alphabet] 34 | 35 | pair0 = Pair('C3', 'C3', initial_guess) 36 | alphas = [1.0, 1.0, 1.0] 37 | 38 | # Add targets to pair. 39 | for state, target, alpha in zip(states, rdf_targets, alphas): 40 | pair0.add_state(state, target, alpha, indices) 41 | pairs = [pair0] # optimize() expects a list of pairs 42 | 43 | # Do magic. 44 | opt.optimize(states, pairs, n_iterations=5, engine='hoomd') 45 | -------------------------------------------------------------------------------- /msibi/tutorials/propane/plot.py: -------------------------------------------------------------------------------- 1 | from msibi_utils.plot_fit import plot_all_fits 2 | from msibi_utils.plot_rdfs import plot_all_rdfs 3 | from msibi_utils.animate_rdf import animate_all_pairs_states 4 | 5 | plot_all_fits('opt.out', ylims=(0.5, 1)) 6 | plot_all_rdfs('opt.out', 'rdfs', step=4) 7 | animate_all_pairs_states('opt.out', 'rdfs', step=4, n_skip=0) 8 | -------------------------------------------------------------------------------- /msibi/tutorials/propane/propane.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "cells": [ 3 | { 4 | "cell_type": "markdown", 5 | "metadata": {}, 6 | "source": [ 7 | "# Propane Tutorial\n", 8 | "\n", 9 | "Created by Davy Yue 2017-06-14\n", 10 | "\n", 11 | "\n", 12 | "### Imports" 13 | ] 14 | }, 15 | { 16 | "cell_type": "code", 17 | "execution_count": null, 18 | "metadata": { 19 | "collapsed": true 20 | }, 21 | "outputs": [], 22 | "source": [ 23 | "import itertools\n", 24 | "import string\n", 25 | "import os\n", 26 | "\n", 27 | "import numpy as np\n", 28 | "\n", 29 | "from msibi import MSIBI, State, Pair, mie" 30 | ] 31 | }, 32 | { 33 | "cell_type": "markdown", 34 | "metadata": {}, 35 | "source": [ 36 | "### Remove files generated during CG simulation" 37 | ] 38 | }, 39 | { 40 | "cell_type": "code", 41 | "execution_count": null, 42 | "metadata": {}, 43 | "outputs": [], 44 | "source": [ 45 | "os.system('rm rdfs/pair_C3*_state*-step*.txt f_fits.log')\n", 46 | "os.system('rm state_*/*.txt state*/run.py state*/*query.dcd')" 47 | ] 48 | }, 49 | { 50 | "cell_type": "markdown", 51 | "metadata": {}, 52 | "source": [ 53 | "### Set up global parameters\n", 54 | "Cutoff radius set to 5.0 units. Parameters including number of data points and potential cutoff are passed to `MSIBI`." 55 | ] 56 | }, 57 | { 58 | "cell_type": "code", 59 | "execution_count": null, 60 | "metadata": { 61 | "collapsed": true 62 | }, 63 | "outputs": [], 64 | "source": [ 65 | "rdf_cutoff = 5.0\n", 66 | "opt = MSIBI(rdf_cutoff=rdf_cutoff, n_rdf_points=201, pot_cutoff=3.0,\n", 67 | " smooth_rdfs=True)" 68 | ] 69 | }, 70 | { 71 | "cell_type": "markdown", 72 | "metadata": {}, 73 | "source": [ 74 | "### Specify states\n", 75 | "States each are initialized with different temperatures, directories, and start.hoomdxml files. \n", 76 | "\n", 77 | "A list `states` contains all the individual states: `stateA`, `stateB`, `stateC`." 78 | ] 79 | }, 80 | { 81 | "cell_type": "code", 82 | "execution_count": null, 83 | "metadata": { 84 | "collapsed": true 85 | }, 86 | "outputs": [], 87 | "source": [ 88 | "stateA = State(kT=0.5, state_dir='./state_A', top_file='start.hoomdxml',\n", 89 | " name='stateA', backup_trajectory=True)\n", 90 | "stateB = State(kT=1.5, state_dir='./state_B', top_file='start.hoomdxml',\n", 91 | " name='stateB', backup_trajectory=True)\n", 92 | "stateC = State(kT=2.0, state_dir='./state_C', top_file='start.hoomdxml',\n", 93 | " name='stateC', backup_trajectory=True)\n", 94 | "states = [stateA, stateB, stateC]" 95 | ] 96 | }, 97 | { 98 | "cell_type": "markdown", 99 | "metadata": {}, 100 | "source": [ 101 | "### Specify pairs\n", 102 | "\n", 103 | "Creates a list of all the possible indices for the 1024 atoms. \n", 104 | "\n", 105 | "Passes the type of interaction to be optimized, a `C3` to itself, to `Pair`. Sets the alpha values to `1.0`" 106 | ] 107 | }, 108 | { 109 | "cell_type": "code", 110 | "execution_count": null, 111 | "metadata": {}, 112 | "outputs": [], 113 | "source": [ 114 | "indices = list(itertools.combinations(range(1024), 2)) # all-all for 1024 atoms\n", 115 | "\n", 116 | "initial_guess = mie(opt.pot_r, 1.0, 1.0) # 1-D array of potential values.\n", 117 | "alphabet = ['A', 'B', 'C']\n", 118 | "rdf_targets = [np.loadtxt('rdfs/C3-C3-state_{0}.txt'.format(i))\n", 119 | " for i in alphabet]\n", 120 | "\n", 121 | "pair0 = Pair('C3', 'C3', initial_guess)\n", 122 | "alphas = [1.0, 1.0, 1.0]" 123 | ] 124 | }, 125 | { 126 | "cell_type": "markdown", 127 | "metadata": {}, 128 | "source": [ 129 | "### Add targets to pair\n", 130 | "\n", 131 | "Loops through each `state`, `target`, and `alpha` in `zip`. Adds the appropriate states, and converts `pair0` into a list for the `optimize()` function." 132 | ] 133 | }, 134 | { 135 | "cell_type": "code", 136 | "execution_count": null, 137 | "metadata": { 138 | "collapsed": true 139 | }, 140 | "outputs": [], 141 | "source": [ 142 | "for state, target, alpha in zip(states, rdf_targets, alphas):\n", 143 | " pair0.add_state(state, target, alpha, indices)\n", 144 | "pairs = [pair0]" 145 | ] 146 | }, 147 | { 148 | "cell_type": "markdown", 149 | "metadata": {}, 150 | "source": [ 151 | "### Do magic\n", 152 | "\n", 153 | "Sprinkle fairy dust over the code.\n", 154 | "\n", 155 | "\n", 156 | "Calls the `optimize` function with the parameters given. \n", 157 | "Performs five iterations, with each successive iteration usually producing finer, better output. \n", 158 | "Uses the `hoomd` engine to run the simulations." 159 | ] 160 | }, 161 | { 162 | "cell_type": "code", 163 | "execution_count": null, 164 | "metadata": {}, 165 | "outputs": [], 166 | "source": [ 167 | "opt.optimize(states, pairs, n_iterations=5, engine='hoomd')" 168 | ] 169 | }, 170 | { 171 | "cell_type": "code", 172 | "execution_count": null, 173 | "metadata": { 174 | "collapsed": true 175 | }, 176 | "outputs": [], 177 | "source": [] 178 | } 179 | ], 180 | "metadata": { 181 | "kernelspec": { 182 | "display_name": "Python 3", 183 | "language": "python", 184 | "name": "python3" 185 | }, 186 | "language_info": { 187 | "codemirror_mode": { 188 | "name": "ipython", 189 | "version": 3 190 | }, 191 | "file_extension": ".py", 192 | "mimetype": "text/x-python", 193 | "name": "python", 194 | "nbconvert_exporter": "python", 195 | "pygments_lexer": "ipython3", 196 | "version": "3.5.3" 197 | }, 198 | "widgets": { 199 | "state": { 200 | "0167551767ac4299a760fb1f479ad1b1": { 201 | "views": [ 202 | { 203 | "cell_index": 2 204 | } 205 | ] 206 | }, 207 | "0c7a72e241b341ab8ca29ce3292b3ea3": { 208 | "views": [ 209 | { 210 | "cell_index": 2 211 | } 212 | ] 213 | }, 214 | "1fca05dfeb3d4987893759f4cc0520ea": { 215 | "views": [ 216 | { 217 | "cell_index": 3 218 | } 219 | ] 220 | }, 221 | "56215d591c034eff8b0899b7e18d5cba": { 222 | "views": [ 223 | { 224 | "cell_index": 3 225 | } 226 | ] 227 | } 228 | }, 229 | "version": "1.2.0" 230 | } 231 | }, 232 | "nbformat": 4, 233 | "nbformat_minor": 1 234 | } 235 | -------------------------------------------------------------------------------- /msibi/tutorials/propane/rdfs/C3-C3-state_A.txt: -------------------------------------------------------------------------------- 1 | 0 0 2 | 0.025 0 3 | 0.05 0 4 | 0.075 0 5 | 0.1 0 6 | 0.125 0 7 | 0.15 0 8 | 0.175 0 9 | 0.2 0 10 | 0.225 0 11 | 0.25 0 12 | 0.275 0 13 | 0.3 0 14 | 0.325 0 15 | 0.35 0 16 | 0.375 0 17 | 0.4 0 18 | 0.425 0 19 | 0.45 0 20 | 0.475 0 21 | 0.5 0 22 | 0.525 0 23 | 0.55 0 24 | 0.575 0 25 | 0.6 0 26 | 0.625 0 27 | 0.65 0 28 | 0.675 0 29 | 0.7 0 30 | 0.725 0 31 | 0.75 0 32 | 0.775 0 33 | 0.8 0 34 | 0.825 0 35 | 0.85 0 36 | 0.875 0 37 | 0.9 0 38 | 0.925 0 39 | 0.95 0.000144115 40 | 0.975 0.000547643 41 | 1 0.00169303 42 | 1.025 0.0121552 43 | 1.05 0.0501444 44 | 1.075 0.122938 45 | 1.1 0.261594 46 | 1.125 0.471037 47 | 1.15 0.720606 48 | 1.175 1.00672 49 | 1.2 1.28503 50 | 1.225 1.54392 51 | 1.25 1.7639 52 | 1.275 1.96846 53 | 1.3 2.09609 54 | 1.325 2.16646 55 | 1.35 2.20974 56 | 1.375 2.23375 57 | 1.4 2.1875 58 | 1.425 2.11498 59 | 1.45 2.02195 60 | 1.475 1.91865 61 | 1.5 1.76103 62 | 1.525 1.6286 63 | 1.55 1.47759 64 | 1.575 1.34798 65 | 1.6 1.2129 66 | 1.625 1.07562 67 | 1.65 0.963757 68 | 1.675 0.875166 69 | 1.7 0.784106 70 | 1.725 0.709739 71 | 1.75 0.637311 72 | 1.775 0.58593 73 | 1.8 0.558539 74 | 1.825 0.523949 75 | 1.85 0.501472 76 | 1.875 0.498544 77 | 1.9 0.499577 78 | 1.925 0.504871 79 | 1.95 0.515455 80 | 1.975 0.535119 81 | 2 0.562982 82 | 2.025 0.590418 83 | 2.05 0.645273 84 | 2.075 0.699583 85 | 2.1 0.741972 86 | 2.125 0.808908 87 | 2.15 0.848957 88 | 2.175 0.92252 89 | 2.2 0.986616 90 | 2.225 1.03662 91 | 2.25 1.07654 92 | 2.275 1.12029 93 | 2.3 1.16658 94 | 2.325 1.19948 95 | 2.35 1.22069 96 | 2.375 1.2414 97 | 2.4 1.25684 98 | 2.425 1.27803 99 | 2.45 1.26927 100 | 2.475 1.26756 101 | 2.5 1.25481 102 | 2.525 1.23782 103 | 2.55 1.23436 104 | 2.575 1.20045 105 | 2.6 1.19355 106 | 2.625 1.16264 107 | 2.65 1.14071 108 | 2.675 1.11648 109 | 2.7 1.10066 110 | 2.725 1.07295 111 | 2.75 1.04931 112 | 2.775 1.01796 113 | 2.8 0.989396 114 | 2.825 0.975405 115 | 2.85 0.954841 116 | 2.875 0.928418 117 | 2.9 0.906819 118 | 2.925 0.896277 119 | 2.95 0.880408 120 | 2.975 0.857058 121 | 3 0.856589 122 | 3.025 0.84602 123 | 3.05 0.844549 124 | 3.075 0.840522 125 | 3.1 0.842606 126 | 3.125 0.85214 127 | 3.15 0.853192 128 | 3.175 0.868522 129 | 3.2 0.885085 130 | 3.225 0.90618 131 | 3.25 0.920494 132 | 3.275 0.93758 133 | 3.3 0.957528 134 | 3.325 0.978968 135 | 3.35 0.996503 136 | 3.375 1.01699 137 | 3.4 1.03399 138 | 3.425 1.05251 139 | 3.45 1.06703 140 | 3.475 1.08176 141 | 3.5 1.08419 142 | 3.525 1.09654 143 | 3.55 1.10207 144 | 3.575 1.10333 145 | 3.6 1.09967 146 | 3.625 1.09822 147 | 3.65 1.0893 148 | 3.675 1.08512 149 | 3.7 1.0874 150 | 3.725 1.07274 151 | 3.75 1.06293 152 | 3.775 1.05613 153 | 3.8 1.04845 154 | 3.825 1.03628 155 | 3.85 1.02356 156 | 3.875 1.01704 157 | 3.9 1.00752 158 | 3.925 0.995554 159 | 3.95 0.991526 160 | 3.975 0.980938 161 | 4 0.966381 162 | 4.025 0.968382 163 | 4.05 0.956258 164 | 4.075 0.951557 165 | 4.1 0.950104 166 | 4.125 0.944795 167 | 4.15 0.94601 168 | 4.175 0.942964 169 | 4.2 0.944521 170 | 4.225 0.948882 171 | 4.25 0.942759 172 | 4.275 0.948713 173 | 4.3 0.95107 174 | 4.325 0.960172 175 | 4.35 0.963644 176 | 4.375 0.971281 177 | 4.4 0.973871 178 | 4.425 0.988009 179 | 4.45 0.990748 180 | 4.475 1.00135 181 | 4.5 1.00679 182 | 4.525 1.00726 183 | 4.55 1.01578 184 | 4.575 1.02861 185 | 4.6 1.02607 186 | 4.625 1.03425 187 | 4.65 1.03473 188 | 4.675 1.03698 189 | 4.7 1.03563 190 | 4.725 1.03737 191 | 4.75 1.04003 192 | 4.775 1.03881 193 | 4.8 1.03667 194 | 4.825 1.03565 195 | 4.85 1.03125 196 | 4.875 1.02937 197 | 4.9 1.02547 198 | 4.925 1.01571 199 | 4.95 1.01456 200 | 4.975 1.01306 201 | 5 1.00527 202 | -------------------------------------------------------------------------------- /msibi/tutorials/propane/rdfs/C3-C3-state_B.txt: -------------------------------------------------------------------------------- 1 | 0 0 2 | 0.025 0 3 | 0.05 0 4 | 0.075 0 5 | 0.1 0 6 | 0.125 0 7 | 0.15 0 8 | 0.175 0 9 | 0.2 0 10 | 0.225 0 11 | 0.25 0 12 | 0.275 0 13 | 0.3 0 14 | 0.325 0 15 | 0.35 0 16 | 0.375 0 17 | 0.4 0 18 | 0.425 0 19 | 0.45 0 20 | 0.475 0 21 | 0.5 0 22 | 0.525 0 23 | 0.55 0 24 | 0.575 0 25 | 0.6 0 26 | 0.625 0 27 | 0.65 0 28 | 0.675 0 29 | 0.7 0 30 | 0.725 0 31 | 0.75 0 32 | 0.775 0 33 | 0.8 0 34 | 0.825 0 35 | 0.85 0 36 | 0.875 0 37 | 0.9 0 38 | 0.925 0 39 | 0.95 0 40 | 0.975 0.000255251 41 | 1 0.00169961 42 | 1.025 0.00485609 43 | 1.05 0.0143318 44 | 1.075 0.039989 45 | 1.1 0.0774296 46 | 1.125 0.151013 47 | 1.15 0.232077 48 | 1.175 0.350029 49 | 1.2 0.470177 50 | 1.225 0.631954 51 | 1.25 0.782237 52 | 1.275 0.955022 53 | 1.3 1.07692 54 | 1.325 1.22071 55 | 1.35 1.31282 56 | 1.375 1.40248 57 | 1.4 1.49962 58 | 1.425 1.56042 59 | 1.45 1.63426 60 | 1.475 1.65258 61 | 1.5 1.65248 62 | 1.525 1.66015 63 | 1.55 1.63467 64 | 1.575 1.61026 65 | 1.6 1.61279 66 | 1.625 1.53515 67 | 1.65 1.49644 68 | 1.675 1.41886 69 | 1.7 1.3684 70 | 1.725 1.31307 71 | 1.75 1.26262 72 | 1.775 1.21345 73 | 1.8 1.15694 74 | 1.825 1.10054 75 | 1.85 1.05648 76 | 1.875 1.03189 77 | 1.9 0.982227 78 | 1.925 0.952203 79 | 1.95 0.925125 80 | 1.975 0.90477 81 | 2 0.884706 82 | 2.025 0.866786 83 | 2.05 0.851869 84 | 2.075 0.854722 85 | 2.1 0.830429 86 | 2.125 0.832093 87 | 2.15 0.818714 88 | 2.175 0.833712 89 | 2.2 0.829927 90 | 2.225 0.831175 91 | 2.25 0.845731 92 | 2.275 0.839667 93 | 2.3 0.86234 94 | 2.325 0.875564 95 | 2.35 0.89223 96 | 2.375 0.899582 97 | 2.4 0.913197 98 | 2.425 0.93675 99 | 2.45 0.93675 100 | 2.475 0.965808 101 | 2.5 0.968371 102 | 2.525 0.986767 103 | 2.55 1.00093 104 | 2.575 0.995883 105 | 2.6 1.01663 106 | 2.625 1.0327 107 | 2.65 1.03906 108 | 2.675 1.04684 109 | 2.7 1.04485 110 | 2.725 1.06558 111 | 2.75 1.05131 112 | 2.775 1.07229 113 | 2.8 1.06216 114 | 2.825 1.06612 115 | 2.85 1.06778 116 | 2.875 1.04973 117 | 2.9 1.05321 118 | 2.925 1.06046 119 | 2.95 1.05682 120 | 2.975 1.06079 121 | 3 1.04611 122 | 3.025 1.04423 123 | 3.05 1.03256 124 | 3.075 1.03311 125 | 3.1 1.03401 126 | 3.125 1.02275 127 | 3.15 1.02165 128 | 3.175 1.0128 129 | 3.2 1.00631 130 | 3.225 0.999732 131 | 3.25 0.995858 132 | 3.275 0.997422 133 | 3.3 0.993471 134 | 3.325 0.992834 135 | 3.35 0.992568 136 | 3.375 0.980184 137 | 3.4 0.982292 138 | 3.425 0.979832 139 | 3.45 0.980662 140 | 3.475 0.974942 141 | 3.5 0.987442 142 | 3.525 0.975922 143 | 3.55 0.979807 144 | 3.575 0.982175 145 | 3.6 0.978966 146 | 3.625 0.986024 147 | 3.65 0.981646 148 | 3.675 0.979987 149 | 3.7 0.982654 150 | 3.725 0.978498 151 | 3.75 0.983104 152 | 3.775 0.995 153 | 3.8 0.98475 154 | 3.825 0.999378 155 | 3.85 1.00454 156 | 3.875 1.0036 157 | 3.9 0.994945 158 | 3.925 1.00486 159 | 3.95 1.00237 160 | 3.975 1.00196 161 | 4 1.0103 162 | 4.025 1.01528 163 | 4.05 1.00907 164 | 4.075 1.01096 165 | 4.1 1.00708 166 | 4.125 1.00403 167 | 4.15 1.00802 168 | 4.175 1.01443 169 | 4.2 1.01285 170 | 4.225 1.00767 171 | 4.25 1.00745 172 | 4.275 1.01301 173 | 4.3 1.01036 174 | 4.325 1.00657 175 | 4.35 1.00384 176 | 4.375 1.00371 177 | 4.4 1.00044 178 | 4.425 1.00326 179 | 4.45 1.00137 180 | 4.475 1.00545 181 | 4.5 1.00006 182 | 4.525 1.00315 183 | 4.55 1.00036 184 | 4.575 1.00028 185 | 4.6 0.999741 186 | 4.625 1.00937 187 | 4.65 0.9978 188 | 4.675 0.999239 189 | 4.7 1.0039 190 | 4.725 1.00128 191 | 4.75 0.998765 192 | 4.775 0.991327 193 | 4.8 1.00171 194 | 4.825 0.99314 195 | 4.85 0.994734 196 | 4.875 0.994286 197 | 4.9 0.998199 198 | 4.925 1.0024 199 | 4.95 1.0009 200 | 4.975 1.0005 201 | 5 1.00046 202 | -------------------------------------------------------------------------------- /msibi/tutorials/propane/rdfs/C3-C3-state_C.txt: -------------------------------------------------------------------------------- 1 | 0 0 2 | 0.025 0 3 | 0.05 0 4 | 0.075 0 5 | 0.1 0 6 | 0.125 0 7 | 0.15 0 8 | 0.175 0 9 | 0.2 0 10 | 0.225 0 11 | 0.25 0 12 | 0.275 0 13 | 0.3 0 14 | 0.325 0 15 | 0.35 0 16 | 0.375 0 17 | 0.4 0 18 | 0.425 0 19 | 0.45 0 20 | 0.475 0 21 | 0.5 0 22 | 0.525 0 23 | 0.55 0 24 | 0.575 0 25 | 0.6 0 26 | 0.625 0 27 | 0.65 0 28 | 0.675 0 29 | 0.7 0 30 | 0.725 0 31 | 0.75 0 32 | 0.775 0 33 | 0.8 0 34 | 0.825 0 35 | 0.85 0 36 | 0.875 0 37 | 0.9 0 38 | 0.925 0 39 | 0.95 0 40 | 0.975 0 41 | 1 0.00296389 42 | 1.025 0.00423417 43 | 1.05 0.0107661 44 | 1.075 0.0475301 45 | 1.1 0.0969736 46 | 1.125 0.190213 47 | 1.15 0.272055 48 | 1.175 0.392159 49 | 1.2 0.535298 50 | 1.225 0.72123 51 | 1.25 0.943632 52 | 1.275 1.09614 53 | 1.3 1.3467 54 | 1.325 1.52698 55 | 1.35 1.61222 56 | 1.375 1.82533 57 | 1.4 1.89303 58 | 1.425 1.96745 59 | 1.45 2.08757 60 | 1.475 2.16356 61 | 1.5 2.13115 62 | 1.525 2.08426 63 | 1.55 2.1718 64 | 1.575 2.1594 65 | 1.6 2.10173 66 | 1.625 2.09924 67 | 1.65 2.05417 68 | 1.675 1.97082 69 | 1.7 1.90074 70 | 1.725 1.86204 71 | 1.75 1.8497 72 | 1.775 1.78501 73 | 1.8 1.67691 74 | 1.825 1.65679 75 | 1.85 1.56925 76 | 1.875 1.58382 77 | 1.9 1.48204 78 | 1.925 1.46266 79 | 1.95 1.44299 80 | 1.975 1.37461 81 | 2 1.33579 82 | 2.025 1.31017 83 | 2.05 1.27967 84 | 2.075 1.275 85 | 2.1 1.24126 86 | 2.125 1.23667 87 | 2.15 1.21929 88 | 2.175 1.19983 89 | 2.2 1.18529 90 | 2.225 1.17078 91 | 2.25 1.14565 92 | 2.275 1.14484 93 | 2.3 1.1242 94 | 2.325 1.10807 95 | 2.35 1.13237 96 | 2.375 1.076 97 | 2.4 1.09375 98 | 2.425 1.06837 99 | 2.45 1.08812 100 | 2.475 1.08134 101 | 2.5 1.06257 102 | 2.525 1.08044 103 | 2.55 1.03609 104 | 2.575 1.06178 105 | 2.6 1.07895 106 | 2.625 1.042 107 | 2.65 1.04652 108 | 2.675 1.0425 109 | 2.7 1.06157 110 | 2.725 1.06052 111 | 2.75 1.03683 112 | 2.775 1.00619 113 | 2.8 1.03141 114 | 2.825 1.04785 115 | 2.85 1.04705 116 | 2.875 1.03301 117 | 2.9 1.02932 118 | 2.925 1.0441 119 | 2.95 1.02118 120 | 2.975 1.02748 121 | 3 1.0331 122 | 3.025 1.01699 123 | 3.05 1.02621 124 | 3.075 1.03373 125 | 3.1 1.04008 126 | 3.125 1.0015 127 | 3.15 1.03343 128 | 3.175 1.03179 129 | 3.2 1.03066 130 | 3.225 1.00205 131 | 3.25 1.00531 132 | 3.275 1.01749 133 | 3.3 1.00607 134 | 3.325 1.02488 135 | 3.35 1.01628 136 | 3.375 1.01974 137 | 3.4 1.01737 138 | 3.425 1.01073 139 | 3.45 1.01659 140 | 3.475 1.00232 141 | 3.5 1.03022 142 | 3.525 0.99543 143 | 3.55 0.995634 144 | 3.575 1.01498 145 | 3.6 1.0281 146 | 3.625 1.01184 147 | 3.65 0.997846 148 | 3.675 1.00738 149 | 3.7 0.998266 150 | 3.725 1.0289 151 | 3.75 0.99316 152 | 3.775 1.00371 153 | 3.8 0.998534 154 | 3.825 1.00424 155 | 3.85 1.0089 156 | 3.875 0.999082 157 | 3.9 1.02278 158 | 3.925 1.00346 159 | 3.95 0.996261 160 | 3.975 0.999478 161 | 4 0.999141 162 | 4.025 1.00629 163 | 4.05 1.0187 164 | 4.075 0.995549 165 | 4.1 1.00899 166 | 4.125 0.99382 167 | 4.15 1.00209 168 | 4.175 1.00246 169 | 4.2 1.00387 170 | 4.225 1.00619 171 | 4.25 1.00914 172 | 4.275 0.998725 173 | 4.3 1.00621 174 | 4.325 1.00305 175 | 4.35 0.989747 176 | 4.375 0.983472 177 | 4.4 1.00607 178 | 4.425 1.00132 179 | 4.45 0.992959 180 | 4.475 1.01233 181 | 4.5 1.01778 182 | 4.525 0.998039 183 | 4.55 0.993919 184 | 4.575 1.01567 185 | 4.6 0.982628 186 | 4.625 0.989017 187 | 4.65 1.00528 188 | 4.675 0.992508 189 | 4.7 0.995893 190 | 4.725 0.995767 191 | 4.75 0.999742 192 | 4.775 0.993372 193 | 4.8 0.992983 194 | 4.825 1.00489 195 | 4.85 0.997149 196 | 4.875 1.00122 197 | 4.9 0.996219 198 | 4.925 0.995193 199 | 4.95 1.00247 200 | 4.975 1.00844 201 | 5 1.0125 202 | -------------------------------------------------------------------------------- /msibi/tutorials/propane/state_A/hoomd_run_template.py: -------------------------------------------------------------------------------- 1 | all = hoomd.group.all() 2 | nvt_int = hoomd.md.integrate.langevin(group=all, kT=T_final, seed=1) 3 | hoomd.md.integrate.mode_standard(dt=0.001) 4 | 5 | hoomd.run(1e2) 6 | output_dcd = hoomd.dump.dcd(filename='query.dcd', period=100, overwrite=True) 7 | hoomd.run(1e4) 8 | -------------------------------------------------------------------------------- /msibi/tutorials/propane/state_B/hoomd_run_template.py: -------------------------------------------------------------------------------- 1 | all = hoomd.group.all() 2 | nvt_int = hoomd.md.integrate.langevin(group=all, kT=T_final, seed=1) 3 | hoomd.md.integrate.mode_standard(dt=0.001) 4 | 5 | hoomd.run(1e2) 6 | output_dcd = hoomd.dump.dcd(filename='query.dcd', period=100, overwrite=True) 7 | hoomd.run(1e4) 8 | -------------------------------------------------------------------------------- /msibi/tutorials/propane/state_C/hoomd_run_template.py: -------------------------------------------------------------------------------- 1 | all = hoomd.group.all() 2 | nvt_int = hoomd.md.integrate.langevin(group=all, kT=T_final, seed=1) 3 | hoomd.md.integrate.mode_standard(dt=0.001) 4 | 5 | hoomd.run(1e2) 6 | output_dcd = hoomd.dump.dcd(filename='query.dcd', period=100, overwrite=True) 7 | hoomd.run(1e4) 8 | -------------------------------------------------------------------------------- /msibi/utils/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mosdef-hub/msibi/fe2bd543093531740cca4666721b0c0bb5be539f/msibi/utils/__init__.py -------------------------------------------------------------------------------- /msibi/utils/error_calculation.py: -------------------------------------------------------------------------------- 1 | ############################################################################## 2 | # MSIBI: A package for optimizing coarse-grained force fields using multistate 3 | # iterative Boltzmann inversion. 4 | # Copyright (c) 2017 Vanderbilt University and the Authors 5 | # 6 | # Authors: Christoph Klein, Timothy C. Moore 7 | # 8 | # Permission is hereby granted, free of charge, to any person obtaining a copy 9 | # of this software and associated documentation files, to deal 10 | # in MSIBI without restriction, including without limitation the rights 11 | # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 12 | # # copies of MSIBI, and to permit persons to whom MSIBI is 13 | # furnished to do so, subject to the following conditions: 14 | # 15 | # The above copyright notice and this permission notice shall be included in all 16 | # copies or substantial portions of MSIBI. 17 | # 18 | # MSIBI IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 19 | # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 20 | # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 21 | # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 22 | # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 23 | # OUT OF OR IN CONNECTION WITH MSIBI OR THE USE OR OTHER DEALINGS ALONG WITH 24 | # MSIBI. 25 | # 26 | # You should have received a copy of the MIT license. 27 | # If not, see . 28 | ############################################################################## 29 | 30 | from __future__ import division 31 | 32 | import numpy as np 33 | 34 | 35 | def calc_similarity(arr1, arr2): 36 | f_fit = np.sum(np.absolute(arr1 - arr2)) 37 | f_fit /= np.sum((np.absolute(arr1) + np.absolute(arr2))) 38 | return 1.0 - f_fit 39 | -------------------------------------------------------------------------------- /msibi/utils/exceptions.py: -------------------------------------------------------------------------------- 1 | ############################################################################## 2 | # MSIBI: A package for optimizing coarse-grained force fields using multistate 3 | # iterative Boltzmann inversion. 4 | # Copyright (c) 2017 Vanderbilt University and the Authors 5 | # 6 | # Authors: Christoph Klein, Timothy C. Moore 7 | # 8 | # Permission is hereby granted, free of charge, to any person obtaining a copy 9 | # of this software and associated documentation files, to deal 10 | # in MSIBI without restriction, including without limitation the rights 11 | # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 12 | # # copies of MSIBI, and to permit persons to whom MSIBI is 13 | # furnished to do so, subject to the following conditions: 14 | # 15 | # The above copyright notice and this permission notice shall be included in all 16 | # copies or substantial portions of MSIBI. 17 | # 18 | # MSIBI IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 19 | # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 20 | # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 21 | # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 22 | # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 23 | # OUT OF OR IN CONNECTION WITH MSIBI OR THE USE OR OTHER DEALINGS ALONG WITH 24 | # MSIBI. 25 | # 26 | # You should have received a copy of the MIT license. 27 | # If not, see . 28 | ############################################################################## 29 | 30 | SUPPORTED_ENGINES = ['hoomd'] 31 | 32 | 33 | class UnsupportedEngine(Exception): 34 | def __init__(self, engine): 35 | message = 'Unsupported engine: "{0}". Supported engines are: {1}'.format( 36 | engine, ', '.join(SUPPORTED_ENGINES)) 37 | super(UnsupportedEngine, self).__init__(message) 38 | -------------------------------------------------------------------------------- /msibi/utils/find_exclusions.py: -------------------------------------------------------------------------------- 1 | ############################################################################## 2 | # MSIBI: A package for optimizing coarse-grained force fields using multistate 3 | # iterative Boltzmann inversion. 4 | # Copyright (c) 2017 Vanderbilt University and the Authors 5 | # 6 | # Authors: Christoph Klein, Timothy C. Moore 7 | # 8 | # Permission is hereby granted, free of charge, to any person obtaining a copy 9 | # of this software and associated documentation files, to deal 10 | # in MSIBI without restriction, including without limitation the rights 11 | # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 12 | # # copies of MSIBI, and to permit persons to whom MSIBI is 13 | # furnished to do so, subject to the following conditions: 14 | # 15 | # The above copyright notice and this permission notice shall be included in all 16 | # copies or substantial portions of MSIBI. 17 | # 18 | # MSIBI IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 19 | # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 20 | # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 21 | # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 22 | # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 23 | # OUT OF OR IN CONNECTION WITH MSIBI OR THE USE OR OTHER DEALINGS ALONG WITH 24 | # MSIBI. 25 | # 26 | # You should have received a copy of the MIT license. 27 | # If not, see . 28 | ############################################################################## 29 | 30 | import networkx as nx 31 | from networkx import NetworkXNoPath 32 | import numpy as np 33 | 34 | def find_1_n_exclusions(top, pairs, n): 35 | """Find exclusions in a trajectory based on an exculsion principle 36 | 37 | Parameters 38 | ---------- 39 | top : mdtraj.Topology 40 | Topology object containing the types and list of bonds 41 | pairs : array-like, shape=(n_pairs, 2), dtype=int 42 | Each row gives the indices of two atoms. 43 | n : int 44 | Exclude particles in pairs separated by n or fewer bonds 45 | """ 46 | G = nx.Graph() 47 | G.add_nodes_from([a.index for a in top.atoms]) 48 | bonds = [b for b in top.bonds] 49 | bonds_by_index = [(b[0].index, b[1].index) for b in bonds] 50 | G.add_edges_from(bonds_by_index) 51 | to_exclude = [] 52 | # TODO: make faster by looping over bonds instead of pairs 53 | for i, pair in enumerate(pairs): 54 | if is_1_n(pair, n, G) == True: 55 | to_exclude.append(i) 56 | return np.asarray(to_exclude) 57 | 58 | 59 | def is_1_n(pair, n, G): 60 | """Find if atoms in a pair are separated by n or less bonds 61 | 62 | Parameters 63 | ---------- 64 | n : int 65 | Return false atoms in pair are separated by n or fewer bonds 66 | pair : [int, int] 67 | Pair of atom indices 68 | G : networkx.Graph 69 | A graph with atoms and nodes and bonds as edges 70 | 71 | Returns 72 | ------- 73 | answer : bool 74 | answer == True if atoms are separated by n or fewer bonds, False otherwise 75 | 76 | The graph is expected to have atom indices as nodes, and tuples of atom indices as 77 | edges. Ideally, the nodes would be MDTraj.Atom-s and edges a list of tuples of 78 | MDTraj.Atom-s 79 | try: 80 | return n > len(nx.shortest_path(G, pair[0], pair[1])) - 1 81 | except: # no path between pair[0] and pair[1] 82 | return False 83 | """ 84 | try: 85 | return n > len(nx.shortest_path(G, pair[0], pair[1])) - 1 86 | except NetworkXNoPath: 87 | return False 88 | -------------------------------------------------------------------------------- /msibi/utils/general.py: -------------------------------------------------------------------------------- 1 | ############################################################################## 2 | # MSIBI: A package for optimizing coarse-grained force fields using multistate 3 | # iterative Boltzmann inversion. 4 | # Copyright (c) 2017 Vanderbilt University and the Authors 5 | # 6 | # Authors: Christoph Klein, Timothy C. Moore 7 | # 8 | # Permission is hereby granted, free of charge, to any person obtaining a copy 9 | # of this software and associated documentation files, to deal 10 | # in MSIBI without restriction, including without limitation the rights 11 | # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 12 | # # copies of MSIBI, and to permit persons to whom MSIBI is 13 | # furnished to do so, subject to the following conditions: 14 | # 15 | # The above copyright notice and this permission notice shall be included in all 16 | # copies or substantial portions of MSIBI. 17 | # 18 | # MSIBI IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 19 | # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 20 | # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 21 | # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 22 | # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 23 | # OUT OF OR IN CONNECTION WITH MSIBI OR THE USE OR OTHER DEALINGS ALONG WITH 24 | # MSIBI. 25 | # 26 | # You should have received a copy of the MIT license. 27 | # If not, see . 28 | ############################################################################## 29 | 30 | import glob 31 | import os 32 | from pkg_resources import resource_filename 33 | import shutil 34 | 35 | import numpy as np 36 | 37 | 38 | def get_fn(name): 39 | """Get the full path to one of the reference files shipped for testing. 40 | 41 | This function is taken straight from MDTraj (see https://github.com/mdtraj/mdtraj). 42 | In the source distribution, these files are in ``msibi/utils/reference``, 43 | but on istallation, they're moved to somewhere in the user's python 44 | site-packages directory. 45 | 46 | Parameters 47 | ---------- 48 | name : str 49 | Name of the file ot load (with respecto to the reference/ directory). 50 | 51 | Examples 52 | ________ 53 | >>> import mdtraj as md 54 | >>> t = md.load(get_fun('final.hoomdxml')) 55 | """ 56 | 57 | fn = resource_filename('msibi', os.path.join('utils', 'reference', name)) 58 | 59 | if not os.path.exists(fn): 60 | raise ValueError('Sorry! %s does not exist. If you just ' 61 | 'added it, you\'ll have to re install' % fn) 62 | 63 | return fn 64 | 65 | 66 | def find_nearest(array, target): 67 | """Find array component whose numeric value is closest to 'target'. """ 68 | idx = np.abs(array - target).argmin() 69 | return idx, array[idx] 70 | 71 | 72 | def _count_backups(filename): 73 | """Count the number of backups of a file in a directory. """ 74 | head, tail = os.path.split(filename) 75 | backup_files = ''.join(['_.*.', tail]) 76 | return len(glob.glob(os.path.join(head, backup_files))) 77 | 78 | 79 | def _backup_name(filename, n_backups): 80 | """Return backup filename based on the number of existing backups. 81 | 82 | Parameters 83 | ---------- 84 | filename : str 85 | Full path to file to make backup of. 86 | n_backups : int 87 | Number of existing backups. 88 | 89 | """ 90 | head, tail = os.path.split(filename) 91 | new_backup = ''.join(['_.{0:d}.'.format(n_backups), tail]) 92 | return os.path.join(head, new_backup) 93 | 94 | 95 | def backup_file(filename): 96 | """Backup a file based on the number of backups in the file's directory. 97 | 98 | Parameters 99 | ---------- 100 | filename : str 101 | Full path to file to make backup of. 102 | 103 | """ 104 | n_backups = _count_backups(filename) 105 | new_backup = _backup_name(filename, n_backups) 106 | shutil.copy(filename, new_backup) 107 | -------------------------------------------------------------------------------- /msibi/utils/reference/2chains.hoomdxml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | -2.7333316803 -2.46567463875 0.55542576313 7 | -2.72046780586 -2.46154713631 1.02677297592 8 | -2.80130243301 -2.46441173553 1.56453490257 9 | -2.91316199303 -2.44769048691 2.08861136436 10 | -2.87734794617 -2.27416229248 2.58729457855 11 | -2.7680990696 -2.2819275856 3.07851672173 12 | -2.29131817818 -2.29085230827 3.05982160568 13 | -2.05989289284 -2.20904803276 2.53355431557 14 | -2.03481507301 -2.22300314903 1.9820330143 15 | -2.00645232201 -2.20227694511 1.38646674156 16 | -1.92186760902 -2.39061784744 0.853813171387 17 | -1.97674882412 -2.21867656708 0.322696864605 18 | -2.20922231674 -2.5525393486 3.35658693314 19 | -2.02347803116 -2.05300593376 3.07850694656 20 | -1.35115528107 -3.29404234886 -0.347912281752 21 | -1.3077236414 -3.2197394371 -0.885239481926 22 | -1.36111533642 -3.08145642281 -1.37002539635 23 | -1.36416041851 -3.004601717 -1.94559442997 24 | -1.28880751133 -2.95457053185 -2.45670771599 25 | -1.4447606802 -3.07918691635 -2.91643261909 26 | -1.78900539875 -3.41477632523 -2.93149352074 27 | -2.04393744469 -3.44978022575 -2.4506289959 28 | -2.09815168381 -3.3438911438 -1.89779162407 29 | -1.97417390347 -3.43454241753 -1.38360655308 30 | -1.98977410793 -3.61914563179 -0.832499086857 31 | -2.03277039528 -3.73046851158 -0.282502353191 32 | -1.83023786545 -3.12718200684 -3.19096660614 33 | -1.74684906006 -3.72490954399 -2.80147957802 34 | 35 | 36 | 0.597922980785 37 | 0.583921015263 38 | 0.583921015263 39 | 0.583921015263 40 | 0.583921015263 41 | 0.597075998783 42 | 0.555985987186 43 | 0.555971980095 44 | 0.583921015263 45 | 0.583921015263 46 | 0.583921015263 47 | 0.597922980785 48 | 0.236021995544 49 | 0.236021995544 50 | 0.597922980785 51 | 0.583921015263 52 | 0.583921015263 53 | 0.583921015263 54 | 0.583921015263 55 | 0.597075998783 56 | 0.555985987186 57 | 0.555971980095 58 | 0.583921015263 59 | 0.583921015263 60 | 0.583921015263 61 | 0.597922980785 62 | 0.236021995544 63 | 0.236021995544 64 | 65 | 66 | tail 67 | tail 68 | tail 69 | tail 70 | tail 71 | amide 72 | mhead2 73 | tail 74 | tail 75 | tail 76 | tail 77 | tail 78 | stick1 79 | stick2 80 | tail 81 | tail 82 | tail 83 | tail 84 | tail 85 | amide 86 | mhead2 87 | tail 88 | tail 89 | tail 90 | tail 91 | tail 92 | stick1 93 | stick2 94 | 95 | 96 | bond0 0 1 97 | bond0 1 2 98 | bond0 2 3 99 | bond0 3 4 100 | bond1 4 5 101 | bond2 5 6 102 | bond3 6 7 103 | bond0 7 8 104 | bond0 8 9 105 | bond0 9 10 106 | bond0 10 11 107 | bond4 6 12 108 | bond5 6 13 109 | bond0 14 15 110 | bond0 15 16 111 | bond0 16 17 112 | bond0 17 18 113 | bond1 18 19 114 | bond2 19 20 115 | bond3 20 21 116 | bond0 21 22 117 | bond0 22 23 118 | bond0 23 24 119 | bond0 24 25 120 | bond4 20 26 121 | bond5 20 27 122 | 123 | 124 | angle0 0 1 2 125 | angle0 1 2 3 126 | angle0 2 3 4 127 | angle0 3 4 5 128 | angle1 4 5 6 129 | angle2 5 6 7 130 | angle0 6 7 8 131 | angle0 7 8 9 132 | angle0 8 9 10 133 | angle0 9 10 11 134 | angle3 5 6 12 135 | angle4 5 6 13 136 | angle5 7 6 12 137 | angle6 7 6 13 138 | angle7 12 6 13 139 | angle0 14 15 16 140 | angle0 15 16 17 141 | angle0 16 17 18 142 | angle0 17 18 19 143 | angle1 18 19 20 144 | angle2 19 20 21 145 | angle0 20 21 22 146 | angle0 21 22 23 147 | angle0 22 23 24 148 | angle0 23 24 25 149 | angle3 19 20 26 150 | angle4 19 20 27 151 | angle5 21 20 26 152 | angle6 21 20 27 153 | angle7 26 20 27 154 | 155 | 156 | 157 | 158 | 159 | 160 | 0 161 | 0 162 | 0 163 | 0 164 | 0 165 | 0 166 | 0 167 | 0 168 | 0 169 | 0 170 | 0 171 | 0 172 | 0 173 | 0 174 | 0 175 | 0 176 | 0 177 | 0 178 | 0 179 | 0 180 | 0 181 | 0 182 | 0 183 | 0 184 | 0 185 | 0 186 | 0 187 | 0 188 | 189 | 190 | 191 | -------------------------------------------------------------------------------- /msibi/utils/reference/state0/err.txt: -------------------------------------------------------------------------------- 1 | [vmp840:19487] mca: base: component_find: unable to open /usr/local/openmpi/1.4.4/x86_64/gcc46/lib/openmpi/mca_plm_tm: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored) 2 | [vmp840:19487] mca: base: component_find: unable to open /usr/local/openmpi/1.4.4/x86_64/gcc46/lib/openmpi/mca_ras_tm: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored) 3 | *Warning*: Syntax bond.harmonic.set_coeff deprecated. 4 | *Warning*: Syntax bond.harmonic.set_coeff deprecated. 5 | *Warning*: Syntax bond.harmonic.set_coeff deprecated. 6 | *Warning*: Syntax bond.harmonic.set_coeff deprecated. 7 | *Warning*: Syntax bond.harmonic.set_coeff deprecated. 8 | *Warning*: Syntax bond.harmonic.set_coeff deprecated. 9 | *Warning*: Syntax bond.harmonic.set_coeff deprecated. 10 | -------------------------------------------------------------------------------- /msibi/utils/reference/state0/hoomd_run_template.py: -------------------------------------------------------------------------------- 1 | all = group.all() 2 | nvt_int = integrate.bdnvt(group=all, T=T_final) 3 | integrate.mode_standard(dt=0.001) 4 | 5 | 6 | run(5000) 7 | output_dcd = dump.dcd(filename="query.dcd", period=1e3, overwrite=True) 8 | run(50000) 9 | 10 | output_xml = dump.xml() 11 | output_xml.set_params(all=True) 12 | output_xml.write(filename="final.xml") 13 | -------------------------------------------------------------------------------- /msibi/utils/reference/state0/query.dcd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mosdef-hub/msibi/fe2bd543093531740cca4666721b0c0bb5be539f/msibi/utils/reference/state0/query.dcd -------------------------------------------------------------------------------- /msibi/utils/reference/state0/target-rdf.txt: -------------------------------------------------------------------------------- 1 | 0 0 2 | 0.0166667 0 3 | 0.0333333 0 4 | 0.05 0 5 | 0.0666667 0 6 | 0.0833333 0 7 | 0.1 0 8 | 0.116667 0 9 | 0.133333 0 10 | 0.15 0 11 | 0.166667 0 12 | 0.183333 0 13 | 0.2 0 14 | 0.216667 0 15 | 0.233333 0 16 | 0.25 0 17 | 0.266667 0 18 | 0.283333 0 19 | 0.3 0 20 | 0.316667 0 21 | 0.333333 0 22 | 0.35 0 23 | 0.366667 0 24 | 0.383333 0 25 | 0.4 0 26 | 0.416667 0 27 | 0.433333 0 28 | 0.45 0 29 | 0.466667 0 30 | 0.483333 0 31 | 0.5 0 32 | 0.516667 0 33 | 0.533333 0 34 | 0.55 0 35 | 0.566667 8.63518e-05 36 | 0.583333 0.000883521 37 | 0.6 0.00452604 38 | 0.616667 0.019198 39 | 0.633333 0.0549186 40 | 0.65 0.131981 41 | 0.666667 0.254326 42 | 0.683333 0.414561 43 | 0.7 0.609593 44 | 0.716667 0.802999 45 | 0.733333 0.978938 46 | 0.75 1.12114 47 | 0.766667 1.23726 48 | 0.783333 1.33056 49 | 0.8 1.4215 50 | 0.816667 1.49667 51 | 0.833333 1.56309 52 | 0.85 1.62478 53 | 0.866667 1.67197 54 | 0.883333 1.69845 55 | 0.9 1.67672 56 | 0.916667 1.61493 57 | 0.933333 1.53568 58 | 0.95 1.46078 59 | 0.966667 1.38933 60 | 0.983333 1.33482 61 | 1 1.26782 62 | 1.01667 1.19002 63 | 1.03333 1.1061 64 | 1.05 1.02777 65 | 1.06667 0.959775 66 | 1.08333 0.91451 67 | 1.1 0.878737 68 | 1.11667 0.855217 69 | 1.13333 0.83591 70 | 1.15 0.822076 71 | 1.16667 0.796467 72 | 1.18333 0.783877 73 | 1.2 0.771965 74 | 1.21667 0.763578 75 | 1.23333 0.761449 76 | 1.25 0.764973 77 | 1.26667 0.773438 78 | 1.28333 0.786288 79 | 1.3 0.798328 80 | 1.31667 0.813496 81 | 1.33333 0.832485 82 | 1.35 0.854556 83 | 1.36667 0.877693 84 | 1.38333 0.910023 85 | 1.4 0.935884 86 | 1.41667 0.969893 87 | 1.43333 0.990216 88 | 1.45 1.01735 89 | 1.46667 1.03598 90 | 1.48333 1.05744 91 | 1.5 1.06812 92 | 1.51667 1.07721 93 | 1.53333 1.08528 94 | 1.55 1.09663 95 | 1.56667 1.11161 96 | 1.58333 1.12913 97 | 1.6 1.14936 98 | 1.61667 1.17015 99 | 1.63333 1.17594 100 | 1.65 1.16913 101 | 1.66667 1.14929 102 | 1.68333 1.12217 103 | 1.7 1.09748 104 | 1.71667 1.07495 105 | 1.73333 1.05946 106 | 1.75 1.04446 107 | 1.76667 1.0368 108 | 1.78333 1.03066 109 | 1.8 1.02137 110 | 1.81667 1.00934 111 | 1.83333 0.990898 112 | 1.85 0.973054 113 | 1.86667 0.955302 114 | 1.88333 0.94063 115 | 1.9 0.931843 116 | 1.91667 0.922475 117 | 1.93333 0.919237 118 | 1.95 0.924236 119 | 1.96667 0.925599 120 | 1.98333 0.934766 121 | 2 0.943183 122 | 2.01667 0.948543 123 | 2.03333 0.952103 124 | 2.05 0.948398 125 | 2.06667 0.943758 126 | 2.08333 0.936261 127 | 2.1 0.93156 128 | 2.11667 0.927669 129 | 2.13333 0.925554 130 | 2.15 0.924349 131 | 2.16667 0.928554 132 | 2.18333 0.931112 133 | 2.2 0.931848 134 | 2.21667 0.934322 135 | 2.23333 0.935492 136 | 2.25 0.93166 137 | 2.26667 0.929361 138 | 2.28333 0.925228 139 | 2.3 0.920542 140 | 2.31667 0.915891 141 | 2.33333 0.907846 142 | 2.35 0.905299 143 | 2.36667 0.902062 144 | 2.38333 0.901072 145 | 2.4 0.900012 146 | 2.41667 0.90475 147 | 2.43333 0.906202 148 | 2.45 0.902537 149 | 2.46667 0.892637 150 | 2.48333 0.876248 151 | 2.5 0.861465 152 | -------------------------------------------------------------------------------- /msibi/utils/reference/state1/hoomd_run_template.py: -------------------------------------------------------------------------------- 1 | all = group.all() 2 | nvt_int = integrate.bdnvt(group=all, T=T_final) 3 | integrate.mode_standard(dt=0.001) 4 | 5 | 6 | run(5000) 7 | output_dcd = dump.dcd(filename="query.dcd", period=1e3, overwrite=True) 8 | run(50000) 9 | 10 | output_xml = dump.xml() 11 | output_xml.set_params(all=True) 12 | output_xml.write(filename="final.xml") 13 | -------------------------------------------------------------------------------- /msibi/utils/reference/state1/query.dcd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mosdef-hub/msibi/fe2bd543093531740cca4666721b0c0bb5be539f/msibi/utils/reference/state1/query.dcd -------------------------------------------------------------------------------- /msibi/utils/reference/state1/target-rdf.txt: -------------------------------------------------------------------------------- 1 | 0 0 2 | 0.0166667 0 3 | 0.0333333 0 4 | 0.05 0 5 | 0.0666667 0 6 | 0.0833333 0 7 | 0.1 0 8 | 0.116667 0 9 | 0.133333 0 10 | 0.15 0 11 | 0.166667 0 12 | 0.183333 0 13 | 0.2 0 14 | 0.216667 0 15 | 0.233333 0 16 | 0.25 0 17 | 0.266667 0 18 | 0.283333 0 19 | 0.3 0 20 | 0.316667 0 21 | 0.333333 0 22 | 0.35 0 23 | 0.366667 0 24 | 0.383333 0 25 | 0.4 0 26 | 0.416667 0 27 | 0.433333 0 28 | 0.45 0 29 | 0.466667 0 30 | 0.483333 0 31 | 0.5 0 32 | 0.516667 0 33 | 0.533333 0 34 | 0.55 0 35 | 0.566667 8.63518e-05 36 | 0.583333 0.000883521 37 | 0.6 0.00452604 38 | 0.616667 0.019198 39 | 0.633333 0.0549186 40 | 0.65 0.131981 41 | 0.666667 0.254326 42 | 0.683333 0.414561 43 | 0.7 0.609593 44 | 0.716667 0.802999 45 | 0.733333 0.978938 46 | 0.75 1.12114 47 | 0.766667 1.23726 48 | 0.783333 1.33056 49 | 0.8 1.4215 50 | 0.816667 1.49667 51 | 0.833333 1.56309 52 | 0.85 1.62478 53 | 0.866667 1.67197 54 | 0.883333 1.69845 55 | 0.9 1.67672 56 | 0.916667 1.61493 57 | 0.933333 1.53568 58 | 0.95 1.46078 59 | 0.966667 1.38933 60 | 0.983333 1.33482 61 | 1 1.26782 62 | 1.01667 1.19002 63 | 1.03333 1.1061 64 | 1.05 1.02777 65 | 1.06667 0.959775 66 | 1.08333 0.91451 67 | 1.1 0.878737 68 | 1.11667 0.855217 69 | 1.13333 0.83591 70 | 1.15 0.822076 71 | 1.16667 0.796467 72 | 1.18333 0.783877 73 | 1.2 0.771965 74 | 1.21667 0.763578 75 | 1.23333 0.761449 76 | 1.25 0.764973 77 | 1.26667 0.773438 78 | 1.28333 0.786288 79 | 1.3 0.798328 80 | 1.31667 0.813496 81 | 1.33333 0.832485 82 | 1.35 0.854556 83 | 1.36667 0.877693 84 | 1.38333 0.910023 85 | 1.4 0.935884 86 | 1.41667 0.969893 87 | 1.43333 0.990216 88 | 1.45 1.01735 89 | 1.46667 1.03598 90 | 1.48333 1.05744 91 | 1.5 1.06812 92 | 1.51667 1.07721 93 | 1.53333 1.08528 94 | 1.55 1.09663 95 | 1.56667 1.11161 96 | 1.58333 1.12913 97 | 1.6 1.14936 98 | 1.61667 1.17015 99 | 1.63333 1.17594 100 | 1.65 1.16913 101 | 1.66667 1.14929 102 | 1.68333 1.12217 103 | 1.7 1.09748 104 | 1.71667 1.07495 105 | 1.73333 1.05946 106 | 1.75 1.04446 107 | 1.76667 1.0368 108 | 1.78333 1.03066 109 | 1.8 1.02137 110 | 1.81667 1.00934 111 | 1.83333 0.990898 112 | 1.85 0.973054 113 | 1.86667 0.955302 114 | 1.88333 0.94063 115 | 1.9 0.931843 116 | 1.91667 0.922475 117 | 1.93333 0.919237 118 | 1.95 0.924236 119 | 1.96667 0.925599 120 | 1.98333 0.934766 121 | 2 0.943183 122 | 2.01667 0.948543 123 | 2.03333 0.952103 124 | 2.05 0.948398 125 | 2.06667 0.943758 126 | 2.08333 0.936261 127 | 2.1 0.93156 128 | 2.11667 0.927669 129 | 2.13333 0.925554 130 | 2.15 0.924349 131 | 2.16667 0.928554 132 | 2.18333 0.931112 133 | 2.2 0.931848 134 | 2.21667 0.934322 135 | 2.23333 0.935492 136 | 2.25 0.93166 137 | 2.26667 0.929361 138 | 2.28333 0.925228 139 | 2.3 0.920542 140 | 2.31667 0.915891 141 | 2.33333 0.907846 142 | 2.35 0.905299 143 | 2.36667 0.902062 144 | 2.38333 0.901072 145 | 2.4 0.900012 146 | 2.41667 0.90475 147 | 2.43333 0.906202 148 | 2.45 0.902537 149 | 2.46667 0.892637 150 | 2.48333 0.876248 151 | 2.5 0.861465 152 | -------------------------------------------------------------------------------- /msibi/utils/smoothing.py: -------------------------------------------------------------------------------- 1 | ############################################################################## 2 | # MSIBI: A package for optimizing coarse-grained force fields using multistate 3 | # iterative Boltzmann inversion. 4 | # Copyright (c) 2017 Vanderbilt University and the Authors 5 | # 6 | # Authors: Christoph Klein, Timothy C. Moore 7 | # 8 | # Permission is hereby granted, free of charge, to any person obtaining a copy 9 | # of this software and associated documentation files, to deal 10 | # in MSIBI without restriction, including without limitation the rights 11 | # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 12 | # # copies of MSIBI, and to permit persons to whom MSIBI is 13 | # furnished to do so, subject to the following conditions: 14 | # 15 | # The above copyright notice and this permission notice shall be included in all 16 | # copies or substantial portions of MSIBI. 17 | # 18 | # MSIBI IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 19 | # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 20 | # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 21 | # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 22 | # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 23 | # OUT OF OR IN CONNECTION WITH MSIBI OR THE USE OR OTHER DEALINGS ALONG WITH 24 | # MSIBI. 25 | # 26 | # You should have received a copy of the MIT license. 27 | # If not, see . 28 | ############################################################################## 29 | 30 | from __future__ import division 31 | 32 | from math import factorial 33 | 34 | import numpy as np 35 | 36 | 37 | def savitzky_golay(y, window_size, order, deriv=0, rate=1): 38 | """ 39 | 40 | Parameters 41 | ---------- 42 | y: 43 | window_size: 44 | order: 45 | deriv: 46 | rate: 47 | 48 | Returns 49 | ------- 50 | 51 | """ 52 | if not (isinstance(window_size, int) and isinstance(order, int)): 53 | raise ValueError("window_size and order must be of type int") 54 | if window_size % 2 != 1 or window_size < 1: 55 | raise TypeError('window_size must be a positive odd number') 56 | if window_size < order + 2: 57 | raise TypeError('window_size is too small for the polynomials order') 58 | 59 | order_range = range(order+1) 60 | half_window = (window_size - 1) // 2 61 | b = np.mat([[k**i for i in order_range] for k in range(-half_window, 62 | half_window +1)]) 63 | m = np.linalg.pinv(b).A[deriv] * rate**deriv * factorial(deriv) 64 | firstvals = y[0] - np.abs(y[1:half_window+1][::-1] - y[0]) 65 | lastvals = y[-1] + np.abs(y[-half_window-1:-1][::-1] - y[-1]) 66 | y = np.concatenate((firstvals, y, lastvals)) 67 | return np.convolve(m[::-1], y, mode='valid') 68 | -------------------------------------------------------------------------------- /msibi/workers.py: -------------------------------------------------------------------------------- 1 | ############################################################################## 2 | # MSIBI: A package for optimizing coarse-grained force fields using multistate 3 | # iterative Boltzmann inversion. 4 | # Copyright (c) 2017 Vanderbilt University and the Authors 5 | # 6 | # Authors: Christoph Klein, Timothy C. Moore 7 | # Contributors: Davy Yue 8 | # 9 | # Permission is hereby granted, free of charge, to any person obtaining a copy 10 | # of this software and associated documentation files, to deal 11 | # in MSIBI without restriction, including without limitation the rights 12 | # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 13 | # # copies of MSIBI, and to permit persons to whom MSIBI is 14 | # furnished to do so, subject to the following conditions: 15 | # 16 | # The above copyright notice and this permission notice shall be included in all 17 | # copies or substantial portions of MSIBI. 18 | # 19 | # MSIBI IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 20 | # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 21 | # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 22 | # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 23 | # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 24 | # OUT OF OR IN CONNECTION WITH MSIBI OR THE USE OR OTHER DEALINGS ALONG WITH 25 | # MSIBI. 26 | # 27 | # You should have received a copy of the MIT license. 28 | # If not, see . 29 | ############################################################################## 30 | 31 | from __future__ import print_function, division 32 | 33 | from distutils.spawn import find_executable 34 | import itertools 35 | import logging 36 | from math import ceil 37 | from multiprocessing import cpu_count 38 | from multiprocessing.dummy import Pool 39 | import os 40 | from subprocess import Popen 41 | 42 | from msibi.utils.general import backup_file 43 | from msibi.utils.exceptions import UnsupportedEngine 44 | 45 | logging.basicConfig(level=logging.DEBUG, format='[%(levelname)s] %(message)s') 46 | 47 | 48 | def run_query_simulations(states, engine='hoomd'): 49 | """Run all query simulations for a single iteration. """ 50 | 51 | # Gather hardware info. 52 | gpus = _get_gpu_info() 53 | if gpus is None: 54 | n_procs = cpu_count() 55 | gpus = [] 56 | logging.info("Launching {n_procs} CPU threads...".format(**locals())) 57 | else: 58 | n_procs = len(gpus) 59 | logging.info("Launching {n_procs} GPU threads...".format(**locals())) 60 | 61 | if engine.lower() == 'hoomd': 62 | worker = _hoomd_worker 63 | else: 64 | raise UnsupportedEngine(engine) 65 | 66 | n_states = len(states) 67 | worker_args = zip(states, range(n_states), itertools.repeat(gpus)) 68 | chunk_size = ceil(n_states / n_procs) 69 | 70 | pool = Pool(n_procs) 71 | pool.imap(worker, worker_args, chunk_size) 72 | pool.close() 73 | pool.join() 74 | 75 | 76 | def _hoomd_worker(args): 77 | """Worker for managing a single HOOMD-blue simulation. """ 78 | 79 | state, idx, gpus = args 80 | log_file = os.path.join(state.state_dir, 'log.txt') 81 | err_file = os.path.join(state.state_dir, 'err.txt') 82 | 83 | if state.HOOMD_VERSION == 1: 84 | executable = 'hoomd' 85 | elif state.HOOMD_VERSION == 2: 86 | executable = 'python' 87 | with open(log_file, 'w') as log, open(err_file, 'w') as err: 88 | if gpus: 89 | card = gpus[idx % len(gpus)] 90 | cmds = [executable, 'run.py', '--gpu={card}'.format(**locals())] 91 | else: 92 | logging.info(' Running state {state.name} on CPU'.format(**locals())) 93 | cmds = [executable, 'run.py'] 94 | 95 | proc = Popen(cmds, cwd=state.state_dir, stdout=log, stderr=err, 96 | universal_newlines=True) 97 | logging.info(" Launched HOOMD in {state.state_dir}".format(**locals())) 98 | proc.communicate() 99 | logging.info(" Finished in {state.state_dir}.".format(**locals())) 100 | _post_query(state) 101 | 102 | def _post_query(state): 103 | """Reload the query trajectory and make backups. """ 104 | 105 | state.reload_query_trajectory() 106 | backup_file(os.path.join(state.state_dir, 'log.txt')) 107 | backup_file(os.path.join(state.state_dir, 'err.txt')) 108 | if state.backup_trajectory: 109 | backup_file(state.traj_path) 110 | 111 | def _get_gpu_info(): 112 | """ """ 113 | nvidia_smi = find_executable('nvidia-smi') 114 | if not nvidia_smi: 115 | return 116 | else: 117 | gpus = [line.split()[1].replace(':', '') for 118 | line in os.popen('nvidia-smi -L').readlines()] 119 | return gpus 120 | -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- 1 | numpy 2 | six 3 | networkx 4 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | """"MSIBI: A package for optimizing coarse-grained force fields using multistate 2 | iterative Boltzmann inversion. 3 | 4 | """ 5 | 6 | from setuptools import setup 7 | from setuptools.command.test import test as TestCommand 8 | import sys 9 | 10 | try: 11 | import mdtraj 12 | except ImportError: 13 | print('Building and running msibi requires mdtraj. See ' 14 | 'http://mdtraj.org/latest/installation.html for help!') 15 | sys.exit(1) 16 | 17 | requirements = [line.strip() for line in open('requirements.txt').readlines()] 18 | 19 | 20 | class PyTest(TestCommand): 21 | def finalize_options(self): 22 | TestCommand.finalize_options(self) 23 | self.test_args = [] 24 | self.test_suite = True 25 | 26 | def run_tests(self): 27 | import pytest 28 | errcode = pytest.main(['msibi']) 29 | sys.exit(errcode) 30 | 31 | 32 | setup(name='msibi', 33 | version='0.1', 34 | description='', 35 | url='http://github.com/mosdef-hub/misibi', 36 | author='Christoph Klein, Timothy C. Moore', 37 | author_email='christoph.klein@vanderbilt.edu, timothy.c.moore@vanderbilt.edu', 38 | license='MIT', 39 | packages=['msibi'], 40 | install_requires=requirements, 41 | zip_safe=False, 42 | test_suite='tests', 43 | cmdclass={'test': PyTest}, 44 | extras_require={'utils': ['pytest']}, 45 | ) 46 | --------------------------------------------------------------------------------