forked from lijiext/lammps
Merge pull request #1770 from rbberger/doc_math_changes
Update angle docs
This commit is contained in:
Richard Berger
GitHub
commit
2e6b19ea5f
43
doc/README
43
doc/README
|
|
@ -5,7 +5,7 @@ sub-directories and optionally 2 PDF files and an ePUB file:
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src content files for LAMMPS documentation
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html HTML version of the LAMMPS manual (see html/Manual.html)
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tools tools and settings for building the documentation
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utils utilities and settings for building the documentation
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Manual.pdf large PDF version of entire manual
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Developer.pdf small PDF with info about how LAMMPS is structured
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LAMMPS.epub Manual in ePUB format
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@ -25,17 +25,12 @@ the fetched documentation will include those changes (but your source
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code will not, unless you update your local repository).
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(b) You can build the HTML and PDF files yourself, by typing "make
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html" followed by "make pdf". Note that the PDF make requires the
|
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HTML files already exist. This requires various tools including
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Sphinx, which the build process will attempt to download and install
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on your system, if not already available. See more details below.
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(c) You can genererate an older, simpler, less-fancy style of HTML
|
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documentation by typing "make old". This will create an "old"
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directory. This can be useful if (b) does not work on your box for
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||||
some reason, or you want to quickly view the HTML version of a doc
|
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page you have created or edited yourself within the src directory.
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E.g. if you are planning to submit a new feature to LAMMPS.
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html" or by "make pdf", respectively. This requires various tools
|
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including the Python documentation processing tool Sphinx, which the
|
||||
build process will attempt to download and install on your system into
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a python virtual environment, if not already available. The PDF file
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will require a working LaTeX installation with several add-on packages
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in addition to the Python/Sphinx setup. See more details below.
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----------------
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@ -46,11 +41,10 @@ Options:
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make html # generate HTML in html dir using Sphinx
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make pdf # generate 2 PDF files (Manual.pdf,Developer.pdf)
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# in this dir via htmldoc and pdflatex
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make old # generate old-style HTML pages in old dir via txt2html
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# in this dir via Sphinx and PDFLaTeX
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make fetch # fetch HTML doc pages and 2 PDF files from web site
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# as a tarball and unpack into html dir and 2 PDFs
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make epub # generate LAMMPS.epub in ePUB format using Sphinx
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make epub # generate LAMMPS.epub in ePUB format using Sphinx
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make clean # remove intermediate RST files created by HTML build
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make clean-all # remove entire build folder and any cached data
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@ -94,8 +88,17 @@ This will install virtualenv from the Python Package Index.
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Installing prerequisites for PDF build
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[TBA]
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Same as for HTML plus a compatible LaTeX installation with
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support for PDFLaTeX. Also the following LaTeX packages need
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to be installed (e.g. from texlive):
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- amsmath
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- babel
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- cmap
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- fncychap
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- geometry
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- hyperref
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- hypcap
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- times
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----------------
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Installing prerequisites for epub build
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@ -103,7 +106,11 @@ Installing prerequisites for epub build
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## ePUB
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Same as for HTML. This uses the same tools and configuration
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files as the HTML tree.
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files as the HTML tree. The ePUB format conversion currently
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does not support processing mathematical expressions via MathJAX,
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so there will be limitations on some pages. For the time being
|
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until this is resolved, building and using the PDF format file
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is recommended instead.
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|
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For converting the generated ePUB file to a mobi format file
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(for e-book readers like Kindle, that cannot read ePUB), you
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|
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\documentclass[12pt]{article}
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\begin{document}
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$$
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E = K (\theta - \theta_0)^2 + K_{UB} (r - r_{UB})^2
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$$
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\end{document}
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\documentclass[12pt]{article}
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\begin{document}
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\begin{eqnarray*}
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E & = & E_a + E_{bb} + E_{ba} \\
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E_a & = & K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4 (\theta - \theta_0)^4 \\
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E_{bb} & = & M (r_{ij} - r_1) (r_{jk} - r_2) \\
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E_{ba} & = & N_1 (r_{ij} - r_1) (\theta - \theta_0) + N_2 (r_{jk} - r_2) (\theta - \theta_0)
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\end{eqnarray*}
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\end{document}
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\documentclass[12pt]{article}
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\begin{document}
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$$
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E = K [1 + \cos(\theta)]
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$$
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\end{document}
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\documentclass[12pt]{article}
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\pagestyle{empty}
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\begin{document}
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$$
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E = K \left[ 1 + \cos(n\theta - \theta_0)\right]
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$$
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\end{document}
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%%% Local Variables:
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%%% mode: latex
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%%% TeX-master: t
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%%% End:
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\documentclass[12pt]{article}
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\begin{document}
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$$
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E = K [1 - \cos(\theta - \theta_0)]
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$$
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\end{document}
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\documentstyle[12pt]{article}
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\begin{document}
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$$
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E=C\left[ 1-B(-1)^ncos\left( n\theta\right) \right]
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$$
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\end{document}
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\documentstyle[12pt]{article}
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\begin{document}
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$$
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E=-\frac{Umin}{2} \left[ 1+Cos(\theta-\theta_0) \right]
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$$
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\end{document}
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\documentstyle[12pt]{article}
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\begin{document}
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$$
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E=-U_{min}
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\frac{e^{-a U(\theta,\theta_0)}-1}{e^a-1}
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\quad\mbox{with}\quad
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U(\theta,\theta_0)
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=-0.5 \left(1+\cos(\theta-\theta_0) \right)
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$$
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\end{document}
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\documentclass[12pt]{article}
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\begin{document}
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$$
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E = K [\cos(\theta) - \cos(\theta_0)]^2
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$$
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\end{document}
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\documentclass[12pt]{article}
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\begin{document}
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\thispagestyle{empty}
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$$
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E = K_{SS} \left(r_{12}-r_{12,0}\right)\left(r_{32}-r_{32,0}\right) + K_{BS0}\left(r_{12}-r_{12,0}\right)\left(\theta-\theta_0\right) + K_{BS1}\left(r_{32}-r_{32,0}\right)\left(\theta-\theta_0\right)
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$$
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\end{document}
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\documentclass[12pt]{article}
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\begin{document}
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\begin{eqnarray*}
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-\vec{T_j} & = & \vec{r_{ij}} \times \vec{F_i}\\
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\vec{F_j} & = & -\vec{F_i} \\
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\end{eqnarray*}
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\end{document}
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\documentclass[12pt]{article}
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\begin{document}
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$$
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\cos\gamma = \frac{\vec{\mu_j}\bullet\vec{r_{ij}}}{\mu_j\,r_{ij}}
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$$
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\end{document}
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\documentclass[12pt]{article}
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\begin{document}
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$$
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E = K (\cos\gamma - \cos\gamma_0)^2
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$$
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\end{document}
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@ -1,9 +0,0 @@
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\documentclass[12pt]{article}
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\begin{document}
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$$
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\vec{T_j} = \frac{2K(\cos\gamma - \cos\gamma_0)}{\mu_j\,r_{ij}}\,
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\vec{r_{ij}} \times \vec{\mu_j}
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$$
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\end{document}
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\documentclass[12pt]{article}
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\begin{document}
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$$
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E = K [C_0 + C_1 \cos ( \theta) + C_2 \cos( 2 \theta) ]
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$$
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\end{document}
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\documentclass[12pt]{article}
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\begin{document}
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$$
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E = K [ 1.0 + c \cos ( n \theta) ]
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$$
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\end{document}
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\documentclass[12pt]{article}
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\begin{document}
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$$
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E = K (\theta - \theta_0)^2
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$$
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\end{document}
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\documentclass[12pt]{article}
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\begin{document}
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\thispagestyle{empty}
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$$
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E = K (\theta - \theta_0)^2 \left[ 1 - 0.014(\theta - \theta_0) + 5.6(10)^{-5} (\theta - \theta_0)^2 - 7.0(10)^{-7} (\theta - \theta_0)^3 + 9(10)^{-10} (\theta - \theta_0)^4 \right]
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$$
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\end{document}
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\documentclass[12pt]{article}
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\begin{document}
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$$
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E = K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4 (\theta - \theta_0)^4
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$$
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\end{document}
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@ -32,12 +32,10 @@ install the `openkim-models` package
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If you have problems with the installation you can post issues to
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`this link <conda_forge_lammps_>`_.
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.. _conda_forge_lammps: https://github.com/conda-forge/lammps-feedstock/issues
|
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Thanks to Jan Janssen (Max-Planck-Institut für Eisenforschung) for setting
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Thanks to Jan Janssen (Max-Planck-Institut fuer Eisenforschung) for setting
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up the Conda capability.
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.. _conda_forge_lammps: https://github.com/conda-forge/lammps-feedstock/issues
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.. _openkim: https://openkim.org
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@ -45,9 +43,6 @@ up the Conda capability.
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.. _mini_conda_install: https://docs.conda.io/en/latest/miniconda.html
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Commands_all.html
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|
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@ -1,22 +1,22 @@
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.. index:: angle\_style charmm
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.. index:: angle_style charmm
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angle\_style charmm command
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===========================
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angle_style charmm command
|
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==========================
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|
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angle\_style charmm/intel command
|
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=================================
|
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angle_style charmm/intel command
|
||||
================================
|
||||
|
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angle\_style charmm/kk command
|
||||
angle_style charmm/kk command
|
||||
=============================
|
||||
|
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angle_style charmm/omp command
|
||||
==============================
|
||||
|
||||
angle\_style charmm/omp command
|
||||
===============================
|
||||
|
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Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
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angle_style charmm
|
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|
||||
|
|
@ -24,7 +24,7 @@ Examples
|
|||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style charmm
|
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angle_coeff 1 300.0 107.0 50.0 3.0
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|
@ -34,12 +34,15 @@ Description
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|||
|
||||
The *charmm* angle style uses the potential
|
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|
||||
.. image:: Eqs/angle_charmm.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
with an additional Urey\_Bradley term based on the distance *r* between
|
||||
the 1st and 3rd atoms in the angle. K, theta0, Kub, and Rub are
|
||||
coefficients defined for each angle type.
|
||||
E = K (\theta - \theta_0)^2 + K_{ub} (r - r_{ub})^2
|
||||
|
||||
|
||||
with an additional Urey\_Bradley term based on the distance :math:`r` between
|
||||
the 1st and 3rd atoms in the angle. :math:`K`, :math:`\theta_0`,
|
||||
:math:`K_{ub}`, and :math:`R_{ub}` are coefficients defined for each angle
|
||||
type.
|
||||
|
||||
See :ref:`(MacKerell) <angle-MacKerell>` for a description of the CHARMM force
|
||||
field.
|
||||
|
|
@ -49,13 +52,13 @@ The following coefficients must be defined for each angle type via the
|
|||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* K (energy/radian\^2)
|
||||
* theta0 (degrees)
|
||||
* K\_ub (energy/distance\^2)
|
||||
* r\_ub (distance)
|
||||
* :math:`K` (energy/radian\^2)
|
||||
* :math:`\theta_0` (degrees)
|
||||
* :math:`K_{ub}` (energy/distance\^2)
|
||||
* :math:`r_{ub}` (distance)
|
||||
|
||||
Theta0 is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of K are in energy/radian\^2.
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of :math:`K` are in energy/radian\^2.
|
||||
|
||||
|
||||
----------
|
||||
|
|
@ -108,8 +111,3 @@ Related commands
|
|||
|
||||
**(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
|
||||
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
|
|
|||
|
|
@ -1,22 +1,22 @@
|
|||
.. index:: angle\_style class2
|
||||
.. index:: angle_style class2
|
||||
|
||||
angle\_style class2 command
|
||||
===========================
|
||||
angle_style class2 command
|
||||
==========================
|
||||
|
||||
angle\_style class2/kk command
|
||||
angle_style class2/kk command
|
||||
=============================
|
||||
|
||||
angle_style class2/omp command
|
||||
==============================
|
||||
|
||||
angle\_style class2/omp command
|
||||
===============================
|
||||
|
||||
angle\_style class2/p6 command
|
||||
==============================
|
||||
angle_style class2/p6 command
|
||||
=============================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style class2
|
||||
|
||||
|
|
@ -24,44 +24,49 @@ Examples
|
|||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style class2
|
||||
angle_coeff \* 75.0
|
||||
angle_coeff * 75.0
|
||||
angle_coeff 1 bb 10.5872 1.0119 1.5228
|
||||
angle_coeff \* ba 3.6551 24.895 1.0119 1.5228
|
||||
angle_coeff * ba 3.6551 24.895 1.0119 1.5228
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
The *class2* angle style uses the potential
|
||||
|
||||
.. image:: Eqs/angle_class2.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where Ea is the angle term, Ebb is a bond-bond term, and Eba is a
|
||||
bond-angle term. Theta0 is the equilibrium angle and r1 and r2 are
|
||||
E & = E_a + E_{bb} + E_{ba} \\
|
||||
E_a & = K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4(\theta - \theta_0)^4 \\
|
||||
E_{bb} & = M (r_{ij} - r_1) (r_{jk} - r_2) \\
|
||||
E_{ba} & = N_1 (r_{ij} - r_1) (\theta - \theta_0) + N_2(r_{jk} - r_2)(\theta - \theta_0)
|
||||
|
||||
|
||||
where :math:`E_a` is the angle term, :math:`E_{bb}` is a bond-bond term, and :math:`E_{ba}` is a
|
||||
bond-angle term. :math:`\theta_0` is the equilibrium angle and :math:`r_1` and :math:`r_2` are
|
||||
the equilibrium bond lengths.
|
||||
|
||||
See :ref:`(Sun) <angle-Sun>` for a description of the COMPASS class2 force field.
|
||||
|
||||
Coefficients for the Ea, Ebb, and Eba formulas must be defined for
|
||||
Coefficients for the :math:`E_a`, :math:`E_{bb}`, and :math:`E_{ba}` formulas must be defined for
|
||||
each angle type via the :doc:`angle\_coeff <angle_coeff>` command as in
|
||||
the example above, or in the data file or restart files read by the
|
||||
:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
|
||||
commands.
|
||||
|
||||
These are the 4 coefficients for the Ea formula:
|
||||
These are the 4 coefficients for the :math:`E_a` formula:
|
||||
|
||||
* theta0 (degrees)
|
||||
* K2 (energy/radian\^2)
|
||||
* K3 (energy/radian\^3)
|
||||
* K4 (energy/radian\^4)
|
||||
* :math:`\theta_0` (degrees)
|
||||
* :math:`K_2` (energy/radian\^2)
|
||||
* :math:`K_3` (energy/radian\^3)
|
||||
* :math:`K_4` (energy/radian\^4)
|
||||
|
||||
Theta0 is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of the various K are in per-radian.
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of the various :math:`K` are in per-radian.
|
||||
|
||||
For the Ebb formula, each line in a :doc:`angle\_coeff <angle_coeff>`
|
||||
For the :math:`E_{bb}` formula, each line in a :doc:`angle\_coeff <angle_coeff>`
|
||||
command in the input script lists 4 coefficients, the first of which
|
||||
is "bb" to indicate they are BondBond coefficients. In a data file,
|
||||
these coefficients should be listed under a "BondBond Coeffs" heading
|
||||
|
|
@ -69,11 +74,11 @@ and you must leave out the "bb", i.e. only list 3 coefficients after
|
|||
the angle type.
|
||||
|
||||
* bb
|
||||
* M (energy/distance\^2)
|
||||
* r1 (distance)
|
||||
* r2 (distance)
|
||||
* :math:`M` (energy/distance\^2)
|
||||
* :math:`r_1` (distance)
|
||||
* :math:`r_2` (distance)
|
||||
|
||||
For the Eba formula, each line in a :doc:`angle\_coeff <angle_coeff>`
|
||||
For the :math:`E_{ba}` formula, each line in a :doc:`angle\_coeff <angle_coeff>`
|
||||
command in the input script lists 5 coefficients, the first of which
|
||||
is "ba" to indicate they are BondAngle coefficients. In a data file,
|
||||
these coefficients should be listed under a "BondAngle Coeffs" heading
|
||||
|
|
@ -81,13 +86,13 @@ and you must leave out the "ba", i.e. only list 4 coefficients after
|
|||
the angle type.
|
||||
|
||||
* ba
|
||||
* N1 (energy/distance\^2)
|
||||
* N2 (energy/distance\^2)
|
||||
* r1 (distance)
|
||||
* r2 (distance)
|
||||
* :math:`N_1` (energy/distance\^2)
|
||||
* :math:`N_2` (energy/distance\^2)
|
||||
* :math:`r_1` (distance)
|
||||
* :math:`r_2` (distance)
|
||||
|
||||
The theta0 value in the Eba formula is not specified, since it is the
|
||||
same value from the Ea formula.
|
||||
The :math:`\theta_0` value in the :math:`E_{ba}` formula is not specified,
|
||||
since it is the same value from the :math:`E_a` formula.
|
||||
|
||||
|
||||
----------
|
||||
|
|
@ -117,17 +122,19 @@ instructions on how to use the accelerated styles effectively.
|
|||
|
||||
The *class2/p6* angle style uses the *class2* potential expanded to sixth order:
|
||||
|
||||
.. image:: Eqs/angle_class2_p6.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
In this expanded term 6 coefficients for the Ea formula need to be set:
|
||||
E_{a} = K_2\left(\theta - \theta_0\right)^2 + K_3\left(\theta - \theta_0\right)^3 + K_4\left(\theta - \theta_0\right)^4 + K_5\left(\theta - \theta_0\right)^5 + K_6\left(\theta - \theta_0\right)^6
|
||||
|
||||
* theta0 (degrees)
|
||||
* K2 (energy/radian\^2)
|
||||
* K3 (energy/radian\^3)
|
||||
* K4 (energy/radian\^4)
|
||||
* K5 (energy/radian\^5)
|
||||
* K6 (energy/radian\^6)
|
||||
|
||||
In this expanded term 6 coefficients for the :math:`E_a` formula need to be set:
|
||||
|
||||
* :math:`\theta_0` (degrees)
|
||||
* :math:`K_2` (energy/radian\^2)
|
||||
* :math:`K_3` (energy/radian\^3)
|
||||
* :math:`K_4` (energy/radian\^4)
|
||||
* :math:`K_5` (energy/radian\^5)
|
||||
* :math:`K_6` (energy/radian\^6)
|
||||
|
||||
The bond-bond and bond-angle terms remain unchanged.
|
||||
|
||||
|
|
@ -160,8 +167,3 @@ Related commands
|
|||
|
||||
|
||||
**(Sun)** Sun, J Phys Chem B 102, 7338-7364 (1998).
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
|
|
|||
|
|
@ -1,13 +1,13 @@
|
|||
.. index:: angle\_coeff
|
||||
.. index:: angle_coeff
|
||||
|
||||
angle\_coeff command
|
||||
====================
|
||||
angle_coeff command
|
||||
===================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_coeff N args
|
||||
|
||||
|
|
@ -18,11 +18,11 @@ Examples
|
|||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_coeff 1 300.0 107.0
|
||||
angle_coeff \* 5.0
|
||||
angle_coeff 2\*10 5.0
|
||||
angle_coeff * 5.0
|
||||
angle_coeff 2*10 5.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
|
@ -30,7 +30,7 @@ Description
|
|||
Specify the angle force field coefficients for one or more angle types.
|
||||
The number and meaning of the coefficients depends on the angle style.
|
||||
Angle coefficients can also be set in the data file read by the
|
||||
:doc:`read\_data <read_data>` command or in a restart file.
|
||||
:doc:`read_data <read_data>` command or in a restart file.
|
||||
|
||||
N can be specified in one of two ways. An explicit numeric value can
|
||||
be used, as in the 1st example above. Or a wild-card asterisk can be
|
||||
|
|
@ -41,18 +41,18 @@ leading asterisk means all types from 1 to n (inclusive). A trailing
|
|||
asterisk means all types from n to N (inclusive). A middle asterisk
|
||||
means all types from m to n (inclusive).
|
||||
|
||||
Note that using an angle\_coeff command can override a previous setting
|
||||
Note that using an :doc:`angle_coeff <angle_coeff>` command can override a previous setting
|
||||
for the same angle type. For example, these commands set the coeffs
|
||||
for all angle types, then overwrite the coeffs for just angle type 2:
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_coeff \* 200.0 107.0 1.2
|
||||
angle_coeff * 200.0 107.0 1.2
|
||||
angle_coeff 2 50.0 107.0
|
||||
|
||||
A line in a data file that specifies angle coefficients uses the exact
|
||||
same format as the arguments of the angle\_coeff command in an input
|
||||
same format as the arguments of the :doc:`angle_coeff <angle_coeff>` command in an input
|
||||
script, except that wild-card asterisks should not be used since
|
||||
coefficients for all N types must be listed in the file. For example,
|
||||
under the "Angle Coeffs" section of a data file, the line that
|
||||
|
|
@ -63,7 +63,7 @@ corresponds to the 1st example above would be listed as
|
|||
|
||||
1 300.0 107.0
|
||||
|
||||
The :doc:`angle\_style class2 <angle_class2>` is an exception to this
|
||||
The :doc:`angle_style class2 <angle_class2>` is an exception to this
|
||||
rule, in that an additional argument is used in the input script to
|
||||
allow specification of the cross-term coefficients. See its
|
||||
doc page for details.
|
||||
|
|
@ -73,13 +73,13 @@ doc page for details.
|
|||
|
||||
|
||||
The list of all angle styles defined in LAMMPS is given on the
|
||||
:doc:`angle\_style <angle_style>` doc page. They are also listed in more
|
||||
:doc:`angle_style <angle_style>` doc page. They are also listed in more
|
||||
compact form on the :ref:`Commands angle <angle>` doc
|
||||
page.
|
||||
|
||||
On either of those pages, click on the style to display the formula it
|
||||
computes and its coefficients as specified by the associated
|
||||
angle\_coeff command.
|
||||
:doc:`angle_coeff <angle_coeff>` command.
|
||||
|
||||
|
||||
----------
|
||||
|
|
@ -90,8 +90,8 @@ Restrictions
|
|||
|
||||
|
||||
This command must come after the simulation box is defined by a
|
||||
:doc:`read\_data <read_data>`, :doc:`read\_restart <read_restart>`, or
|
||||
:doc:`create\_box <create_box>` command.
|
||||
:doc:`read_data <read_data>`, :doc:`read_restart <read_restart>`, or
|
||||
:doc:`create_box <create_box>` command.
|
||||
|
||||
An angle style must be defined before any angle coefficients are
|
||||
set, either in the input script or in a data file.
|
||||
|
|
@ -99,11 +99,6 @@ set, either in the input script or in a data file.
|
|||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`angle\_style <angle_style>`
|
||||
:doc:`angle_style <angle_style>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
|
|
|||
|
|
@ -1,19 +1,19 @@
|
|||
.. index:: angle\_style cosine
|
||||
.. index:: angle_style cosine
|
||||
|
||||
angle\_style cosine command
|
||||
===========================
|
||||
angle_style cosine command
|
||||
==========================
|
||||
|
||||
angle\_style cosine/omp command
|
||||
===============================
|
||||
|
||||
angle\_style cosine/kk command
|
||||
angle_style cosine/omp command
|
||||
==============================
|
||||
|
||||
angle_style cosine/kk command
|
||||
=============================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style cosine
|
||||
|
||||
|
|
@ -21,27 +21,29 @@ Examples
|
|||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style cosine
|
||||
angle_coeff \* 75.0
|
||||
angle_coeff * 75.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
The *cosine* angle style uses the potential
|
||||
|
||||
.. image:: Eqs/angle_cosine.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where K is defined for each angle type.
|
||||
E = K [1 + \cos(\theta)]
|
||||
|
||||
|
||||
where :math:`K` is defined for each angle type.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
|
||||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* K (energy)
|
||||
* :math:`K` (energy)
|
||||
|
||||
|
||||
----------
|
||||
|
|
@ -83,8 +85,3 @@ Related commands
|
|||
:doc:`angle\_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
|
|
|||
|
|
@ -1,13 +1,13 @@
|
|||
.. index:: angle\_style cosine/buck6d
|
||||
.. index:: angle_style cosine/buck6d
|
||||
|
||||
angle\_style cosine/buck6d command
|
||||
==================================
|
||||
angle_style cosine/buck6d command
|
||||
=================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style cosine/buck6d
|
||||
|
||||
|
|
@ -15,7 +15,7 @@ Examples
|
|||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style cosine/buck6d
|
||||
angle_coeff 1 cosine/buck6d 1.978350 4 180.000000
|
||||
|
|
@ -25,22 +25,23 @@ Description
|
|||
|
||||
The *cosine/buck6d* angle style uses the potential
|
||||
|
||||
.. image:: Eqs/angle_cosine_buck6d.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where K is the energy constant, n is the periodic multiplicity and
|
||||
Theta0 is the equilibrium angle.
|
||||
E = K \left[ 1 + \cos(n\theta - \theta_0)\right]
|
||||
|
||||
where :math:`K` is the energy constant, :math:`n` is the periodic multiplicity and
|
||||
:math:`\theta_0` is the equilibrium angle.
|
||||
|
||||
The coefficients must be defined for each angle type via the
|
||||
:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
|
||||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands in the following order:
|
||||
|
||||
* K (energy)
|
||||
* n
|
||||
* Theta0 (degrees)
|
||||
* :math:`K` (energy)
|
||||
* :math:`n`
|
||||
* :math:`\theta_0` (degrees)
|
||||
|
||||
Theta0 is specified in degrees, but LAMMPS converts it to radians
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
|
||||
internally.
|
||||
|
||||
Additional to the cosine term the *cosine/buck6d* angle style computes
|
||||
|
|
@ -73,8 +74,3 @@ Related commands
|
|||
:doc:`angle\_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
|
|
|||
|
|
@ -1,16 +1,16 @@
|
|||
.. index:: angle\_style cosine/delta
|
||||
.. index:: angle_style cosine/delta
|
||||
|
||||
angle\_style cosine/delta command
|
||||
=================================
|
||||
angle_style cosine/delta command
|
||||
================================
|
||||
|
||||
angle\_style cosine/delta/omp command
|
||||
=====================================
|
||||
angle_style cosine/delta/omp command
|
||||
====================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style cosine/delta
|
||||
|
||||
|
|
@ -18,31 +18,33 @@ Examples
|
|||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style cosine/delta
|
||||
angle_coeff 2\*4 75.0 100.0
|
||||
angle_coeff 2*4 75.0 100.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
The *cosine/delta* angle style uses the potential
|
||||
|
||||
.. image:: Eqs/angle_cosine_delta.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where theta0 is the equilibrium value of the angle, and K is a
|
||||
prefactor. Note that the usual 1/2 factor is included in K.
|
||||
E = K [1 - \cos(\theta - \theta_0)]
|
||||
|
||||
|
||||
where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a
|
||||
prefactor. Note that the usual 1/2 factor is included in :math:`K`.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
|
||||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* K (energy)
|
||||
* theta0 (degrees)
|
||||
* :math:`K` (energy)
|
||||
* :math:`\theta_0` (degrees)
|
||||
|
||||
Theta0 is specified in degrees, but LAMMPS converts it to radians
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
|
||||
internally.
|
||||
|
||||
|
||||
|
|
@ -85,8 +87,3 @@ Related commands
|
|||
:doc:`angle\_coeff <angle_coeff>`, :doc:`angle\_style cosine/squared <angle_cosine_squared>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
|
|
|||
|
|
@ -1,16 +1,16 @@
|
|||
.. index:: angle\_style cosine/periodic
|
||||
.. index:: angle_style cosine/periodic
|
||||
|
||||
angle\_style cosine/periodic command
|
||||
====================================
|
||||
angle_style cosine/periodic command
|
||||
===================================
|
||||
|
||||
angle\_style cosine/periodic/omp command
|
||||
========================================
|
||||
angle_style cosine/periodic/omp command
|
||||
=======================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style cosine/periodic
|
||||
|
||||
|
|
@ -18,24 +18,26 @@ Examples
|
|||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style cosine/periodic
|
||||
angle_coeff \* 75.0 1 6
|
||||
angle_coeff * 75.0 1 6
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
The *cosine/periodic* angle style uses the following potential, which
|
||||
is commonly used in the :doc:`DREIDING <Howto_bioFF>` force field,
|
||||
particularly for organometallic systems where *n* = 4 might be used
|
||||
for an octahedral complex and *n* = 3 might be used for a trigonal
|
||||
particularly for organometallic systems where :math:`n` = 4 might be used
|
||||
for an octahedral complex and :math:`n` = 3 might be used for a trigonal
|
||||
center:
|
||||
|
||||
.. image:: Eqs/angle_cosine_periodic.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where C, B and n are coefficients defined for each angle type.
|
||||
E = C \left[ 1 - B(-1)^n\cos\left( n\theta\right) \right]
|
||||
|
||||
|
||||
where :math:`C`, :math:`B` and :math:`n` are coefficients defined for each angle type.
|
||||
|
||||
See :ref:`(Mayo) <cosine-Mayo>` for a description of the DREIDING force field
|
||||
|
||||
|
|
@ -44,13 +46,13 @@ The following coefficients must be defined for each angle type via the
|
|||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* C (energy)
|
||||
* B = 1 or -1
|
||||
* n = 1, 2, 3, 4, 5 or 6 for periodicity
|
||||
* :math:`C` (energy)
|
||||
* :math:`B` = 1 or -1
|
||||
* :math:`n` = 1, 2, 3, 4, 5 or 6 for periodicity
|
||||
|
||||
Note that the prefactor C is specified and not the overall force
|
||||
constant K = C / n\^2. When B = 1, it leads to a minimum for the
|
||||
linear geometry. When B = -1, it leads to a maximum for the linear
|
||||
Note that the prefactor :math:`C` is specified and not the overall force
|
||||
constant :math:`K = \frac{C}{n^2}`. When :math:`B = 1`, it leads to a minimum for the
|
||||
linear geometry. When :math:`B = -1`, it leads to a maximum for the linear
|
||||
geometry.
|
||||
|
||||
|
||||
|
|
@ -104,8 +106,3 @@ Related commands
|
|||
|
||||
**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
|
||||
(1990).
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
|
|
|||
|
|
@ -1,16 +1,16 @@
|
|||
.. index:: angle\_style cosine/shift
|
||||
.. index:: angle_style cosine/shift
|
||||
|
||||
angle\_style cosine/shift command
|
||||
angle_style cosine/shift command
|
||||
=================================
|
||||
|
||||
angle\_style cosine/shift/omp command
|
||||
=====================================
|
||||
angle_style cosine/shift/omp command
|
||||
====================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style cosine/shift
|
||||
|
||||
|
|
@ -18,30 +18,33 @@ Examples
|
|||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style cosine/shift
|
||||
angle_coeff \* 10.0 45.0
|
||||
angle_coeff * 10.0 45.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
The *cosine/shift* angle style uses the potential
|
||||
|
||||
.. image:: Eqs/angle_cosine_shift.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where theta0 is the equilibrium angle. The potential is bounded
|
||||
between -Umin and zero. In the neighborhood of the minimum E=- Umin +
|
||||
Umin/4(theta-theta0)\^2 hence the spring constant is umin/2.
|
||||
E = -\frac{U_{\text{min}}}{2} \left[ 1 + \cos(\theta-\theta_0) \right]
|
||||
|
||||
|
||||
where :math:`\theta_0` is the equilibrium angle. The potential is bounded
|
||||
between :math:`-U_{\text{min}}` and zero. In the neighborhood of the minimum
|
||||
:math:`E = - U_{\text{min}} + U_{\text{min}}/4(\theta - \theta_0)^2` hence
|
||||
the spring constant is :math:`\frac{U_{\text{min}}}{2}`.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
|
||||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* umin (energy)
|
||||
* theta (angle)
|
||||
* :math:`U_{\text{min}}` (energy)
|
||||
* :math:`\theta` (angle)
|
||||
|
||||
|
||||
----------
|
||||
|
|
@ -83,8 +86,3 @@ Related commands
|
|||
:doc:`angle\_cosine\_shift\_exp <angle_cosine_shift_exp>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
|
|
|||
|
|
@ -1,16 +1,16 @@
|
|||
.. index:: angle\_style cosine/shift/exp
|
||||
.. index:: angle_style cosine/shift/exp
|
||||
|
||||
angle\_style cosine/shift/exp command
|
||||
=====================================
|
||||
angle_style cosine/shift/exp command
|
||||
====================================
|
||||
|
||||
angle\_style cosine/shift/exp/omp command
|
||||
=========================================
|
||||
angle_style cosine/shift/exp/omp command
|
||||
========================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style cosine/shift/exp
|
||||
|
||||
|
|
@ -18,32 +18,33 @@ Examples
|
|||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style cosine/shift/exp
|
||||
angle_coeff \* 10.0 45.0 2.0
|
||||
angle_coeff * 10.0 45.0 2.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
The *cosine/shift/exp* angle style uses the potential
|
||||
|
||||
.. image:: Eqs/angle_cosine_shift_exp.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where Umin, theta, and a are defined for each angle type.
|
||||
E = -U_{\text{min}} \frac{e^{-a U(\theta,\theta_0)}-1}{e^a-1} \quad \text{with} \quad U(\theta,\theta_0) = -0.5 \left(1+\cos(\theta-\theta_0) \right)
|
||||
|
||||
The potential is bounded between [-Umin:0] and the minimum is
|
||||
located at the angle theta0. The a parameter can be both positive or
|
||||
where :math:`U_{\text{min}}`, :math:`\theta`, and :math:`a` are defined for each angle type.
|
||||
|
||||
The potential is bounded between :math:`[-U_{\text{min}}, 0]` and the minimum is
|
||||
located at the angle :math:`\theta_0`. The a parameter can be both positive or
|
||||
negative and is used to control the spring constant at the
|
||||
equilibrium.
|
||||
|
||||
The spring constant is given by k = A exp(A) Umin / [2 (Exp(a)-1)].
|
||||
For a > 3, k/Umin = a/2 to better than 5% relative error. For negative
|
||||
values of the a parameter, the spring constant is essentially zero,
|
||||
The spring constant is given by :math:`k = A \exp(A) U_{\text{min}} / [2 (\exp(a)-1)]`.
|
||||
For :math:`a > 3`, :math:`\frac{k}{U_{\text{min}}} = \frac{a}{2}` to better than 5% relative error. For negative
|
||||
values of the :math:`a` parameter, the spring constant is essentially zero,
|
||||
and anharmonic terms takes over. The potential is furthermore well
|
||||
behaved in the limit a -> 0, where it has been implemented to linear
|
||||
order in a for a < 0.001. In this limit the potential reduces to the
|
||||
behaved in the limit :math:`a \rightarrow 0`, where it has been implemented to linear
|
||||
order in :math:`a` for :math:`a < 0.001`. In this limit the potential reduces to the
|
||||
cosineshifted potential.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
|
|
@ -51,9 +52,9 @@ The following coefficients must be defined for each angle type via the
|
|||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* umin (energy)
|
||||
* theta (angle)
|
||||
* A (real number)
|
||||
* :math:`U_min` (energy)
|
||||
* :math:`\theta` (angle)
|
||||
* :math:`A` (real number)
|
||||
|
||||
|
||||
----------
|
||||
|
|
@ -97,8 +98,3 @@ Related commands
|
|||
:doc:`dihedral\_cosine\_shift\_exp <dihedral_cosine_shift_exp>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
|
|
|||
|
|
@ -1,16 +1,16 @@
|
|||
.. index:: angle\_style cosine/squared
|
||||
.. index:: angle_style cosine/squared
|
||||
|
||||
angle\_style cosine/squared command
|
||||
===================================
|
||||
angle_style cosine/squared command
|
||||
==================================
|
||||
|
||||
angle\_style cosine/squared/omp command
|
||||
=======================================
|
||||
angle_style cosine/squared/omp command
|
||||
======================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style cosine/squared
|
||||
|
||||
|
|
@ -18,31 +18,33 @@ Examples
|
|||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style cosine/squared
|
||||
angle_coeff 2\*4 75.0 100.0
|
||||
angle_coeff 2*4 75.0 100.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
The *cosine/squared* angle style uses the potential
|
||||
|
||||
.. image:: Eqs/angle_cosine_squared.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where theta0 is the equilibrium value of the angle, and K is a
|
||||
prefactor. Note that the usual 1/2 factor is included in K.
|
||||
E = K [\cos(\theta) - \cos(\theta_0)]^2
|
||||
|
||||
|
||||
where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a
|
||||
prefactor. Note that the usual 1/2 factor is included in :math:`K`.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
|
||||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* K (energy)
|
||||
* theta0 (degrees)
|
||||
* :math:`K` (energy)
|
||||
* :math:`\theta_0` (degrees)
|
||||
|
||||
Theta0 is specified in degrees, but LAMMPS converts it to radians
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
|
||||
internally.
|
||||
|
||||
|
||||
|
|
@ -85,8 +87,3 @@ Related commands
|
|||
:doc:`angle\_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
|
|
|||
|
|
@ -1,13 +1,13 @@
|
|||
.. index:: angle\_style cross
|
||||
.. index:: angle_style cross
|
||||
|
||||
angle\_style cross command
|
||||
angle_style cross command
|
||||
==========================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style cross
|
||||
|
||||
|
|
@ -15,7 +15,7 @@ Examples
|
|||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style cross
|
||||
angle_coeff 1 200.0 100.0 100.0 1.25 1.25 107.0
|
||||
|
|
@ -26,13 +26,14 @@ Description
|
|||
The *cross* angle style uses a potential that couples the bond stretches of
|
||||
a bend with the angle stretch of that bend:
|
||||
|
||||
.. image:: Eqs/angle_cross.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where r12,0 is the rest value of the bond length between atom 1 and 2,
|
||||
r32,0 is the rest value of the bond length between atom 2 and 2,
|
||||
and theta0 is the rest value of the angle. KSS is the force constant of
|
||||
the bond stretch-bond stretch term and KBS0 and KBS1 are the force constants
|
||||
E = K_{SS} \left(r_{12}-r_{12,0}\right)\left(r_{32}-r_{32,0}\right) + K_{BS0}\left(r_{12}-r_{12,0}\right)\left(\theta-\theta_0\right) + K_{BS1}\left(r_{32}-r_{32,0}\right)\left(\theta-\theta_0\right)
|
||||
|
||||
where :math:`r_{12,0}` is the rest value of the bond length between atom 1 and 2,
|
||||
:math:`r_{32,0}` is the rest value of the bond length between atom 3 and 2,
|
||||
and :math:`\theta_0` is the rest value of the angle. :math:`K_{SS}` is the force constant of
|
||||
the bond stretch-bond stretch term and :math:`K_{BS0}` and :math:`K_{BS1}` are the force constants
|
||||
of the bond stretch-angle stretch terms.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
|
|
@ -40,15 +41,15 @@ The following coefficients must be defined for each angle type via the
|
|||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* KSS (energy/distance\^2)
|
||||
* KBS0 (energy/distance/rad)
|
||||
* KBS1 (energy/distance/rad)
|
||||
* r12,0 (distance)
|
||||
* r32,0 (distance)
|
||||
* theta0 (degrees)
|
||||
* :math:`K_{SS}` (energy/distance\^2)
|
||||
* :math:`K_{BS0}` (energy/distance/rad)
|
||||
* :math:`K_{BS1}` (energy/distance/rad)
|
||||
* :math:`r_{12,0}` (distance)
|
||||
* :math:`r_{32,0}` (distance)
|
||||
* :math:`\theta_0` (degrees)
|
||||
|
||||
Theta0 is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of KBS0 and KBS1 are in energy/distance/radian.
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of :math:`K_{BS0}` and :math:`K_{BS1}` are in energy/distance/radian.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
|
@ -64,12 +65,3 @@ Related commands
|
|||
:doc:`angle\_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
----------
|
||||
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
|
|
|||
|
|
@ -1,16 +1,16 @@
|
|||
.. index:: angle\_style dipole
|
||||
.. index:: angle_style dipole
|
||||
|
||||
angle\_style dipole command
|
||||
===========================
|
||||
angle_style dipole command
|
||||
==========================
|
||||
|
||||
angle\_style dipole/omp command
|
||||
===============================
|
||||
angle_style dipole/omp command
|
||||
==============================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style dipole
|
||||
|
||||
|
|
@ -18,7 +18,7 @@ Examples
|
|||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style dipole
|
||||
angle_coeff 6 2.1 180.0
|
||||
|
|
@ -28,53 +28,63 @@ Description
|
|||
|
||||
The *dipole* angle style is used to control the orientation of a dipolar
|
||||
atom within a molecule :ref:`(Orsi) <Orsi>`. Specifically, the *dipole* angle
|
||||
style restrains the orientation of a point dipole mu\_j (embedded in atom
|
||||
'j') with respect to a reference (bond) vector r\_ij = r\_i - r\_j, where 'i'
|
||||
is another atom of the same molecule (typically, 'i' and 'j' are also
|
||||
covalently bonded).
|
||||
style restrains the orientation of a point dipole :math:`\mu_j` (embedded in atom
|
||||
:math:`j`) with respect to a reference (bond) vector
|
||||
:math:`\vec{r_{ij}} = \vec{r_i} - \vec{r_j}`, where :math:`i` is another atom of
|
||||
the same molecule (typically, :math:`i` and :math:`j` are also covalently bonded).
|
||||
|
||||
It is convenient to define an angle gamma between the 'free' vector mu\_j
|
||||
and the reference (bond) vector r\_ij:
|
||||
It is convenient to define an angle gamma between the 'free' vector :math:`\vec{\mu_j}`
|
||||
and the reference (bond) vector :math:`\vec{r_{ij}}`:
|
||||
|
||||
.. math::
|
||||
|
||||
\cos\gamma = \frac{\vec{\mu_j}\cdot\vec{r_{ij}}}{\mu_j\,r_{ij}}
|
||||
|
||||
.. image:: Eqs/angle_dipole_gamma.jpg
|
||||
:align: center
|
||||
|
||||
The *dipole* angle style uses the potential:
|
||||
|
||||
.. image:: Eqs/angle_dipole_potential.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where K is a rigidity constant and gamma0 is an equilibrium (reference)
|
||||
E = K (\cos\gamma - \cos\gamma_0)^2
|
||||
|
||||
|
||||
where :math:`K` is a rigidity constant and gamma0 is an equilibrium (reference)
|
||||
angle.
|
||||
|
||||
The torque on the dipole can be obtained by differentiating the
|
||||
potential using the 'chain rule' as in appendix C.3 of
|
||||
:ref:`(Allen) <Allen1>`:
|
||||
|
||||
.. image:: Eqs/angle_dipole_torque.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
Example: if gamma0 is set to 0 degrees, the torque generated by
|
||||
\vec{T_j} = \frac{2K(\cos\gamma - \cos\gamma_0)}{\mu_j\,r_{ij}}\, \vec{r_{ij}} \times \vec{\mu_j}
|
||||
|
||||
|
||||
Example: if :math:`\gamma_0` is set to 0 degrees, the torque generated by
|
||||
the potential will tend to align the dipole along the reference
|
||||
direction defined by the (bond) vector r\_ij (in other words, mu\_j is
|
||||
restrained to point towards atom 'i').
|
||||
direction defined by the (bond) vector :math:`\vec{r_{ij}}` (in other words, :math:`\vec{\mu_j}` is
|
||||
restrained to point towards atom :math:`i`).
|
||||
|
||||
The dipolar torque T\_j must be counterbalanced in order to conserve
|
||||
The dipolar torque :math:`\vec{T_j}` must be counterbalanced in order to conserve
|
||||
the local angular momentum. This is achieved via an additional force
|
||||
couple generating a torque equivalent to the opposite of T\_j:
|
||||
couple generating a torque equivalent to the opposite of :math:`\vec{T_j}`:
|
||||
|
||||
.. image:: Eqs/angle_dipole_couple.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where F\_i and F\_j are applied on atoms i and j, respectively.
|
||||
-\vec{T_j} & = \vec{r_{ij}} \times \vec{F_i} \\
|
||||
\vec{F_j} & = -\vec{F_i}
|
||||
|
||||
|
||||
where :math:`\vec{F_i}` and :math:`\vec{F_j}` are applied on atoms :math:`i`
|
||||
and :math:`j`, respectively.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
|
||||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* K (energy)
|
||||
* gamma0 (degrees)
|
||||
* :math:`K` (energy)
|
||||
* :math:`\gamma_0` (degrees)
|
||||
|
||||
|
||||
----------
|
||||
|
|
@ -108,17 +118,17 @@ page for more info.
|
|||
|
||||
.. note::
|
||||
|
||||
In the "Angles" section of the data file, the atom ID 'j'
|
||||
In the "Angles" section of the data file, the atom ID :math:`j`
|
||||
defining the direction of the dipole vector to restrain must come
|
||||
before the atom ID of the reference atom 'i'. A third atom ID 'k' must
|
||||
before the atom ID of the reference atom :math:`i`. A third atom ID :math:`k` must
|
||||
also be provided to comply with the requirement of a valid angle
|
||||
definition. This atom ID k should be chosen to be that of an atom
|
||||
bonded to atom 'i' to avoid errors with "lost angle atoms" when running
|
||||
definition. This atom ID :math:`k` should be chosen to be that of an atom
|
||||
bonded to atom :math:`i` to avoid errors with "lost angle atoms" when running
|
||||
in parallel. Since the LAMMPS code checks for valid angle definitions,
|
||||
cannot use the same atom ID of either 'i' or 'j' (this was allowed
|
||||
cannot use the same atom ID of either :math:`i` or :math:`j` (this was allowed
|
||||
and recommended with older LAMMPS versions).
|
||||
|
||||
The "newton" command for intramolecular interactions must be "on"
|
||||
The :doc:`newton <newton>` command for intramolecular interactions must be "on"
|
||||
(which is the default except when using some accelerator packages).
|
||||
|
||||
This angle style should not be used with SHAKE.
|
||||
|
|
@ -147,8 +157,3 @@ lipid membranes, PloS ONE 6(12): e28637, 2011.
|
|||
|
||||
**(Allen)** Allen & Tildesley, Computer Simulation of Liquids,
|
||||
Clarendon Press, Oxford, 1987.
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
|
|
|||
|
|
@ -1,42 +1,46 @@
|
|||
.. index:: angle\_style fourier
|
||||
.. index:: angle_style fourier
|
||||
|
||||
angle\_style fourier command
|
||||
============================
|
||||
angle_style fourier command
|
||||
===========================
|
||||
|
||||
angle\_style fourier/omp command
|
||||
================================
|
||||
angle_style fourier/omp command
|
||||
===============================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style fourier
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
angle\_style fourier
|
||||
angle\_coeff 75.0 1.0 1.0 1.0
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style fourier
|
||||
angle_coeff 75.0 1.0 1.0 1.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
The *fourier* angle style uses the potential
|
||||
|
||||
.. image:: Eqs/angle_fourier.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
E = K [C_0 + C_1 \cos ( \theta) + C_2 \cos( 2 \theta) ]
|
||||
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
|
||||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* K (energy)
|
||||
* C0 (real)
|
||||
* C1 (real)
|
||||
* C2 (real)
|
||||
* :math:`K` (energy)
|
||||
* :math:`C_0` (real)
|
||||
* :math:`C_1` (real)
|
||||
* :math:`C_2` (real)
|
||||
|
||||
|
||||
----------
|
||||
|
|
@ -78,8 +82,3 @@ Related commands
|
|||
:doc:`angle\_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
|
|
|||
|
|
@ -1,41 +1,45 @@
|
|||
.. index:: angle\_style fourier/simple
|
||||
.. index:: angle_style fourier/simple
|
||||
|
||||
angle\_style fourier/simple command
|
||||
===================================
|
||||
angle_style fourier/simple command
|
||||
==================================
|
||||
|
||||
angle\_style fourier/simple/omp command
|
||||
=======================================
|
||||
angle_style fourier/simple/omp command
|
||||
======================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style fourier/simple
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
angle\_style fourier/simple
|
||||
angle\_coeff 100.0 -1.0 1.0
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style fourier/simple
|
||||
angle_coeff 100.0 -1.0 1.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
The *fourier/simple* angle style uses the potential
|
||||
|
||||
.. image:: Eqs/angle_fourier_simple.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
E = K [ 1.0 + c \cos ( n \theta) ]
|
||||
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
|
||||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* K (energy)
|
||||
* c (real)
|
||||
* n (real)
|
||||
* :math:`K` (energy)
|
||||
* :math:`c` (real)
|
||||
* :math:`n` (real)
|
||||
|
||||
|
||||
----------
|
||||
|
|
@ -77,8 +81,3 @@ Related commands
|
|||
:doc:`angle\_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
|
|
|||
|
|
@ -1,22 +1,22 @@
|
|||
.. index:: angle\_style harmonic
|
||||
.. index:: angle_style harmonic
|
||||
|
||||
angle\_style harmonic command
|
||||
=============================
|
||||
angle_style harmonic command
|
||||
============================
|
||||
|
||||
angle\_style harmonic/intel command
|
||||
===================================
|
||||
angle_style harmonic/intel command
|
||||
==================================
|
||||
|
||||
angle\_style harmonic/kk command
|
||||
angle_style harmonic/kk command
|
||||
===============================
|
||||
|
||||
angle_style harmonic/omp command
|
||||
================================
|
||||
|
||||
angle\_style harmonic/omp command
|
||||
=================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style harmonic
|
||||
|
||||
|
|
@ -24,7 +24,7 @@ Examples
|
|||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style harmonic
|
||||
angle_coeff 1 300.0 107.0
|
||||
|
|
@ -34,22 +34,24 @@ Description
|
|||
|
||||
The *harmonic* angle style uses the potential
|
||||
|
||||
.. image:: Eqs/angle_harmonic.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where theta0 is the equilibrium value of the angle, and K is a
|
||||
prefactor. Note that the usual 1/2 factor is included in K.
|
||||
E = K (\theta - \theta_0)^2
|
||||
|
||||
|
||||
where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a
|
||||
prefactor. Note that the usual 1/2 factor is included in :math:`K`.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
|
||||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* K (energy/radian\^2)
|
||||
* theta0 (degrees)
|
||||
* :math:`K` (energy/radian\^2)
|
||||
* :math:`\theta_0` (degrees)
|
||||
|
||||
Theta0 is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of K are in energy/radian\^2.
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of :math:`K` are in energy/radian\^2.
|
||||
|
||||
|
||||
----------
|
||||
|
|
@ -91,8 +93,3 @@ Related commands
|
|||
:doc:`angle\_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
|
|
|||
|
|
@ -1,13 +1,13 @@
|
|||
.. index:: angle\_style hybrid
|
||||
.. index:: angle_style hybrid
|
||||
|
||||
angle\_style hybrid command
|
||||
===========================
|
||||
angle_style hybrid command
|
||||
==========================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style hybrid style1 style2 ...
|
||||
|
||||
|
|
@ -17,11 +17,11 @@ Examples
|
|||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style hybrid harmonic cosine
|
||||
angle_coeff 1 harmonic 80.0 30.0
|
||||
angle_coeff 2\* cosine 50.0
|
||||
angle_coeff 2* cosine 50.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
|
@ -31,19 +31,19 @@ simulation. An angle style is assigned to each angle type. For
|
|||
example, angles in a polymer flow (of angle type 1) could be computed
|
||||
with a *harmonic* potential and angles in the wall boundary (of angle
|
||||
type 2) could be computed with a *cosine* potential. The assignment
|
||||
of angle type to style is made via the :doc:`angle\_coeff <angle_coeff>`
|
||||
of angle type to style is made via the :doc:`angle_coeff <angle_coeff>`
|
||||
command or in the data file.
|
||||
|
||||
In the angle\_coeff commands, the name of an angle style must be added
|
||||
In the :doc:`angle_coeff <angle_coeff>` commands, the name of an angle style must be added
|
||||
after the angle type, with the remaining coefficients being those
|
||||
appropriate to that style. In the example above, the 2 angle\_coeff
|
||||
commands set angles of angle type 1 to be computed with a *harmonic*
|
||||
potential with coefficients 80.0, 30.0 for K, theta0. All other angle
|
||||
types (2-N) are computed with a *cosine* potential with coefficient
|
||||
50.0 for K.
|
||||
potential with coefficients 80.0, 30.0 for :math:`K`, :math:`\theta_0`. All other angle
|
||||
types :math:`(2 - N)` are computed with a *cosine* potential with coefficient
|
||||
50.0 for :math:`K`.
|
||||
|
||||
If angle coefficients are specified in the data file read via the
|
||||
:doc:`read\_data <read_data>` command, then the same rule applies.
|
||||
:doc:`read_data <read_data>` command, then the same rule applies.
|
||||
E.g. "harmonic" or "cosine", must be added after the angle type, for each
|
||||
line in the "Angle Coeffs" section, e.g.
|
||||
|
||||
|
|
@ -77,7 +77,7 @@ input script, since BondBond (or BondAngle) coefficients need not be
|
|||
specified at all for angle types that are not *class2*\ .
|
||||
|
||||
An angle style of *none* with no additional coefficients can be used
|
||||
in place of an angle style, either in a input script angle\_coeff
|
||||
in place of an angle style, either in a input script :doc:`angle_coeff <angle_coeff>`
|
||||
command or in the data file, if you desire to turn off interactions
|
||||
for specific angle types.
|
||||
|
||||
|
|
@ -95,16 +95,11 @@ for more info.
|
|||
|
||||
Unlike other angle styles, the hybrid angle style does not store angle
|
||||
coefficient info for individual sub-styles in a :doc:`binary restart files <restart>`. Thus when restarting a simulation from a restart
|
||||
file, you need to re-specify angle\_coeff commands.
|
||||
file, you need to re-specify :doc:`angle_coeff <angle_coeff>` commands.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`angle\_coeff <angle_coeff>`
|
||||
:doc:`angle_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
|
|
|||
|
|
@ -1,13 +1,13 @@
|
|||
.. index:: angle\_style mm3
|
||||
.. index:: angle_style mm3
|
||||
|
||||
angle\_style mm3 command
|
||||
========================
|
||||
angle_style mm3 command
|
||||
=======================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style mm3
|
||||
|
||||
|
|
@ -15,7 +15,7 @@ Examples
|
|||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style mm3
|
||||
angle_coeff 1 100.0 107.0
|
||||
|
|
@ -26,23 +26,25 @@ Description
|
|||
The *mm3* angle style uses the potential that is anharmonic in the angle
|
||||
as defined in :ref:`(Allinger) <mm3-allinger1989>`
|
||||
|
||||
.. image:: Eqs/angle_mm3.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where theta0 is the equilibrium value of the angle, and K is a
|
||||
prefactor. The anharmonic prefactors have units deg\^(-n), for example
|
||||
-0.014 deg\^(-1), 5.6(10)\^(-5) deg\^(-2), ...
|
||||
E = K (\theta - \theta_0)^2 \left[ 1 - 0.014(\theta - \theta_0) + 5.6(10)^{-5} (\theta - \theta_0)^2 - 7.0(10)^{-7} (\theta - \theta_0)^3 + 9(10)^{-10} (\theta - \theta_0)^4 \right]
|
||||
|
||||
|
||||
where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a
|
||||
prefactor. The anharmonic prefactors have units :math:`\deg^{-n}`, for example
|
||||
:math:`-0.014 \deg^{-1}`, :math:`5.6 \cdot 10^{-5} \deg^{-2}`, ...
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
|
||||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* K (energy/radian\^2)
|
||||
* theta0 (degrees)
|
||||
* :math:`K` (energy/radian\^2)
|
||||
* :math:`\theta_0` (degrees)
|
||||
|
||||
Theta0 is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of K are in energy/radian\^2.
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of :math:`K` are in energy/radian\^2.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
|
@ -58,12 +60,3 @@ Related commands
|
|||
:doc:`angle\_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
----------
|
||||
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
|
|
|||
|
|
@ -1,13 +1,13 @@
|
|||
.. index:: angle\_style none
|
||||
.. index:: angle_style none
|
||||
|
||||
angle\_style none command
|
||||
=========================
|
||||
angle_style none command
|
||||
========================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style none
|
||||
|
||||
|
|
@ -15,7 +15,7 @@ Examples
|
|||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style none
|
||||
|
||||
|
|
@ -24,23 +24,19 @@ Description
|
|||
|
||||
Using an angle style of none means angle forces and energies are not
|
||||
computed, even if triplets of angle atoms were listed in the data file
|
||||
read by the :doc:`read\_data <read_data>` command.
|
||||
read by the :doc:`read_data <read_data>` command.
|
||||
|
||||
See the :doc:`angle\_style zero <angle_zero>` command for a way to
|
||||
See the :doc:`angle_style zero <angle_zero>` command for a way to
|
||||
calculate angle statistics, but compute no angle interactions.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
none
|
||||
|
||||
none
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`angle\_style zero <angle_zero>`
|
||||
:doc:`angle_style zero <angle_zero>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
|
|
|||
|
|
@ -1,16 +1,16 @@
|
|||
.. index:: angle\_style quartic
|
||||
.. index:: angle_style quartic
|
||||
|
||||
angle\_style quartic command
|
||||
============================
|
||||
angle_style quartic command
|
||||
===========================
|
||||
|
||||
angle\_style quartic/omp command
|
||||
================================
|
||||
angle_style quartic/omp command
|
||||
===============================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style quartic
|
||||
|
||||
|
|
@ -18,7 +18,7 @@ Examples
|
|||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style quartic
|
||||
angle_coeff 1 129.1948 56.8726 -25.9442 -14.2221
|
||||
|
|
@ -28,24 +28,26 @@ Description
|
|||
|
||||
The *quartic* angle style uses the potential
|
||||
|
||||
.. image:: Eqs/angle_quartic.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where theta0 is the equilibrium value of the angle, and K is a
|
||||
prefactor. Note that the usual 1/2 factor is included in K.
|
||||
E = K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4 (\theta - \theta_0)^4
|
||||
|
||||
|
||||
where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a
|
||||
prefactor. Note that the usual 1/2 factor is included in :math:`K`.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
|
||||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* theta0 (degrees)
|
||||
* K2 (energy/radian\^2)
|
||||
* K3 (energy/radian\^3)
|
||||
* K4 (energy/radian\^4)
|
||||
* :math:`\theta_0` (degrees)
|
||||
* :math:`K_2` (energy/radian\^2)
|
||||
* :math:`K_3` (energy/radian\^3)
|
||||
* :math:`K_4` (energy/radian\^4)
|
||||
|
||||
Theta0 is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of K are in energy/radian\^2.
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of :math:`K` are in energy/radian\^2.
|
||||
|
||||
|
||||
----------
|
||||
|
|
@ -87,8 +89,3 @@ Related commands
|
|||
:doc:`angle\_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
|
|
|||
|
|
@ -1,16 +1,16 @@
|
|||
.. index:: angle\_style sdk
|
||||
.. index:: angle_style sdk
|
||||
|
||||
angle\_style sdk command
|
||||
========================
|
||||
angle_style sdk command
|
||||
=======================
|
||||
|
||||
angle\_style sdk/omp command
|
||||
============================
|
||||
angle_style sdk/omp command
|
||||
===========================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style sdk
|
||||
|
||||
|
|
@ -20,7 +20,7 @@ Examples
|
|||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style sdk
|
||||
angle_coeff 1 300.0 107.0
|
||||
|
|
@ -30,25 +30,27 @@ Description
|
|||
|
||||
The *sdk* angle style is a combination of the harmonic angle potential,
|
||||
|
||||
.. image:: Eqs/angle_harmonic.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where theta0 is the equilibrium value of the angle and K a prefactor,
|
||||
E = K (\theta - \theta_0)^2
|
||||
|
||||
|
||||
where :math:`\theta_0` is the equilibrium value of the angle and :math:`K` a prefactor,
|
||||
with the *repulsive* part of the non-bonded *lj/sdk* pair style
|
||||
between the atoms 1 and 3. This angle potential is intended for
|
||||
coarse grained MD simulations with the CMM parameterization using the
|
||||
:doc:`pair\_style lj/sdk <pair_sdk>`. Relative to the pair\_style
|
||||
*lj/sdk*\ , however, the energy is shifted by *epsilon*\ , to avoid sudden
|
||||
jumps. Note that the usual 1/2 factor is included in K.
|
||||
jumps. Note that the usual 1/2 factor is included in :math:`K`.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
:doc:`angle\_coeff <angle_coeff>` command as in the example above:
|
||||
|
||||
* K (energy/radian\^2)
|
||||
* theta0 (degrees)
|
||||
* :math:`K` (energy/radian\^2)
|
||||
* :math:`\theta_0` (degrees)
|
||||
|
||||
Theta0 is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of K are in energy/radian\^2.
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of :math:`K` are in energy/radian\^2.
|
||||
The also required *lj/sdk* parameters will be extracted automatically
|
||||
from the pair\_style.
|
||||
|
||||
|
|
@ -93,8 +95,3 @@ Related commands
|
|||
:doc:`pair\_style lj/sdk/coul/long <pair_sdk>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
|
|
|||
|
|
@ -1,13 +1,13 @@
|
|||
.. index:: angle\_style
|
||||
.. index:: angle_style
|
||||
|
||||
angle\_style command
|
||||
====================
|
||||
angle_style command
|
||||
===================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style style
|
||||
|
||||
|
|
@ -17,7 +17,7 @@ Examples
|
|||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style harmonic
|
||||
angle_style charmm
|
||||
|
|
@ -29,19 +29,19 @@ Description
|
|||
Set the formula(s) LAMMPS uses to compute angle interactions between
|
||||
triplets of atoms, which remain in force for the duration of the
|
||||
simulation. The list of angle triplets is read in by a
|
||||
:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>` command
|
||||
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>` command
|
||||
from a data or restart file.
|
||||
|
||||
Hybrid models where angles are computed using different angle
|
||||
potentials can be setup using the *hybrid* angle style.
|
||||
|
||||
The coefficients associated with a angle style can be specified in a
|
||||
data or restart file or via the :doc:`angle\_coeff <angle_coeff>` command.
|
||||
data or restart file or via the :doc:`angle_coeff <angle_coeff>` command.
|
||||
|
||||
All angle potentials store their coefficient data in binary restart
|
||||
files which means angle\_style and :doc:`angle\_coeff <angle_coeff>`
|
||||
files which means angle_style and :doc:`angle_coeff <angle_coeff>`
|
||||
commands do not need to be re-specified in an input script that
|
||||
restarts a simulation. See the :doc:`read\_restart <read_restart>`
|
||||
restarts a simulation. See the :doc:`read_restart <read_restart>`
|
||||
command for details on how to do this. The one exception is that
|
||||
angle\_style *hybrid* only stores the list of sub-styles in the restart
|
||||
file; angle coefficients need to be re-specified.
|
||||
|
|
@ -49,7 +49,7 @@ file; angle coefficients need to be re-specified.
|
|||
.. note::
|
||||
|
||||
When both an angle and pair style is defined, the
|
||||
:doc:`special\_bonds <special_bonds>` command often needs to be used to
|
||||
:doc:`special_bonds <special_bonds>` command often needs to be used to
|
||||
turn off (or weight) the pairwise interaction that would otherwise
|
||||
exist between 3 bonded atoms.
|
||||
|
||||
|
|
@ -62,11 +62,11 @@ between the 3 atoms in the angle.
|
|||
|
||||
Here is an alphabetic list of angle styles defined in LAMMPS. Click on
|
||||
the style to display the formula it computes and coefficients
|
||||
specified by the associated :doc:`angle\_coeff <angle_coeff>` command.
|
||||
specified by the associated :doc:`angle_coeff <angle_coeff>` command.
|
||||
|
||||
Click on the style to display the formula it computes, any additional
|
||||
arguments specified in the angle\_style command, and coefficients
|
||||
specified by the associated :doc:`angle\_coeff <angle_coeff>` command.
|
||||
specified by the associated :doc:`angle_coeff <angle_coeff>` command.
|
||||
|
||||
There are also additional accelerated pair styles included in the
|
||||
LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
|
||||
|
|
@ -115,17 +115,12 @@ individual bond potentials tell if it is part of a package.
|
|||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`angle\_coeff <angle_coeff>`
|
||||
:doc:`angle_coeff <angle_coeff>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
|
|
|||
|
|
@ -1,16 +1,16 @@
|
|||
.. index:: angle\_style table
|
||||
.. index:: angle_style table
|
||||
|
||||
angle\_style table command
|
||||
==========================
|
||||
angle_style table command
|
||||
=========================
|
||||
|
||||
angle\_style table/omp command
|
||||
==============================
|
||||
angle_style table/omp command
|
||||
=============================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style table style N
|
||||
|
||||
|
|
@ -21,7 +21,7 @@ Examples
|
|||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style table linear 1000
|
||||
angle_coeff 3 file.table ENTRY1
|
||||
|
|
@ -31,7 +31,7 @@ Description
|
|||
|
||||
Style *table* creates interpolation tables of length *N* from angle
|
||||
potential and derivative values listed in a file(s) as a function of
|
||||
angle The files are read by the :doc:`angle\_coeff <angle_coeff>`
|
||||
angle The files are read by the :doc:`angle_coeff <angle_coeff>`
|
||||
command.
|
||||
|
||||
The interpolation tables are created by fitting cubic splines to the
|
||||
|
|
@ -50,7 +50,7 @@ find the appropriate set of coefficients which are used to evaluate a
|
|||
cubic polynomial which computes the energy or derivative.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
:doc:`angle\_coeff <angle_coeff>` command as in the example above.
|
||||
:doc:`angle_coeff <angle_coeff>` command as in the example above.
|
||||
|
||||
* filename
|
||||
* keyword
|
||||
|
|
@ -85,13 +85,13 @@ A section begins with a non-blank line whose 1st character is not a
|
|||
between sections. The first line begins with a keyword which
|
||||
identifies the section. The line can contain additional text, but the
|
||||
initial text must match the argument specified in the
|
||||
:doc:`angle\_coeff <angle_coeff>` command. The next line lists (in any
|
||||
:doc:`angle_coeff <angle_coeff>` command. The next line lists (in any
|
||||
order) one or more parameters for the table. Each parameter is a
|
||||
keyword followed by one or more numeric values.
|
||||
|
||||
The parameter "N" is required and its value is the number of table
|
||||
entries that follow. Note that this may be different than the *N*
|
||||
specified in the :doc:`angle\_style table <angle_style>` command. Let
|
||||
specified in the :doc:`angle_style table <angle_style>` command. Let
|
||||
Ntable = *N* in the angle\_style command, and Nfile = "N" in the
|
||||
tabulated file. What LAMMPS does is a preliminary interpolation by
|
||||
creating splines using the Nfile tabulated values as nodal points. It
|
||||
|
|
@ -176,11 +176,6 @@ for more info.
|
|||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`angle\_coeff <angle_coeff>`
|
||||
:doc:`angle_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
|
|
|||
|
|
@ -1,13 +1,13 @@
|
|||
.. index:: angle\_style zero
|
||||
.. index:: angle_style zero
|
||||
|
||||
angle\_style zero command
|
||||
=========================
|
||||
angle_style zero command
|
||||
========================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style zero *nocoeff*
|
||||
|
||||
|
|
@ -15,12 +15,12 @@ Examples
|
|||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style zero
|
||||
angle_style zero nocoeff
|
||||
angle_coeff \*
|
||||
angle_coeff \* 120.0
|
||||
angle_coeff *
|
||||
angle_coeff * 120.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
|
@ -32,14 +32,14 @@ other commands.
|
|||
As an example, the :doc:`compute angle/local <compute_angle_local>`
|
||||
command can be used to compute the theta values for the list of
|
||||
triplets of angle atoms listed in the data file read by the
|
||||
:doc:`read\_data <read_data>` command. If no angle style is defined,
|
||||
:doc:`read_data <read_data>` command. If no angle style is defined,
|
||||
this command cannot be used.
|
||||
|
||||
The optional *nocoeff* flag allows to read data files with AngleCoeff
|
||||
section for any angle style. Similarly, any angle\_coeff commands
|
||||
section for any angle style. Similarly, any :doc:`angle_coeff <angle_coeff>` commands
|
||||
will only be checked for the angle type number and the rest ignored.
|
||||
|
||||
Note that the :doc:`angle\_coeff <angle_coeff>` command must be used for
|
||||
Note that the :doc:`angle_coeff <angle_coeff>` command must be used for
|
||||
all angle types. If specified, there can be only one value, which is
|
||||
going to be used to assign an equilibrium angle, e.g. for use with
|
||||
:doc:`fix shake <fix_shake>`.
|
||||
|
|
@ -51,11 +51,6 @@ Restrictions
|
|||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`angle\_style none <angle_none>`
|
||||
:doc:`angle_style none <angle_none>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
|
|
|||
|
|
@ -7,7 +7,7 @@ Syntax
|
|||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix ID group-ID restrain keyword args ...
|
||||
|
||||
|
|
@ -39,7 +39,7 @@ Examples
|
|||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix holdem all restrain bond 45 48 2000.0 2000.0 2.75
|
||||
fix holdem all restrain dihedral 1 2 3 4 2000.0 2000.0 120.0
|
||||
|
|
@ -98,7 +98,7 @@ conventional force field terms. If the restraint is applied during a
|
|||
dynamics run (as opposed to during an energy minimization), a large
|
||||
restraint coefficient can significantly reduce the stable timestep
|
||||
size, especially if the atoms are initially far from the preferred
|
||||
conformation. You may need to experiment to determine what value of K
|
||||
conformation. You may need to experiment to determine what value of :math:`K`
|
||||
works best for a given application.
|
||||
|
||||
For the case of finding a minimum energy structure for a single
|
||||
|
|
@ -107,7 +107,7 @@ parameters or constructing a potential energy surface), commands such
|
|||
as the following may be useful:
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
# minimize molecule energy with restraints
|
||||
velocity all create 600.0 8675309 mom yes rot yes dist gaussian
|
||||
|
|
@ -134,16 +134,18 @@ The *bond* keyword applies a bond restraint to the specified atoms
|
|||
using the same functional form used by the :doc:`bond\_style harmonic <bond_harmonic>` command. The potential associated with
|
||||
the restraint is
|
||||
|
||||
.. image:: Eqs/bond_harmonic.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
E = K (r - r_0)^2
|
||||
|
||||
|
||||
with the following coefficients:
|
||||
|
||||
* K (energy/distance\^2)
|
||||
* r0 (distance)
|
||||
* :math:`K` (energy/distance\^2)
|
||||
* :math:`r_0` (distance)
|
||||
|
||||
K and r0 are specified with the fix. Note that the usual 1/2 factor
|
||||
is included in K.
|
||||
:math:`K` and :math:`r_0` are specified with the fix. Note that the usual 1/2 factor
|
||||
is included in :math:`K`.
|
||||
|
||||
|
||||
----------
|
||||
|
|
@ -153,16 +155,17 @@ The *angle* keyword applies an angle restraint to the specified atoms
|
|||
using the same functional form used by the :doc:`angle\_style harmonic <angle_harmonic>` command. The potential associated with
|
||||
the restraint is
|
||||
|
||||
.. image:: Eqs/angle_harmonic.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
E = K (\theta - \theta_0)^2
|
||||
|
||||
with the following coefficients:
|
||||
|
||||
* K (energy/radian\^2)
|
||||
* theta0 (degrees)
|
||||
* :math:`K` (energy/radian\^2)
|
||||
* :math:`\theta_0` (degrees)
|
||||
|
||||
K and theta0 are specified with the fix. Note that the usual 1/2
|
||||
factor is included in K.
|
||||
:math:`K` and :math:`\theta_0` are specified with the fix. Note that the usual 1/2
|
||||
factor is included in :math:`K`.
|
||||
|
||||
|
||||
----------
|
||||
|
|
@ -173,20 +176,22 @@ atoms using a simplified form of the function used by the
|
|||
:doc:`dihedral\_style charmm <dihedral_charmm>` command. The potential
|
||||
associated with the restraint is
|
||||
|
||||
.. image:: Eqs/dihedral_charmm.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
E = K [ 1 + \cos (n \phi - d) ]
|
||||
|
||||
|
||||
with the following coefficients:
|
||||
|
||||
* K (energy)
|
||||
* n (multiplicity, >= 0)
|
||||
* d (degrees) = phi0 + 180
|
||||
* :math:`K` (energy)
|
||||
* :math:`n` (multiplicity, >= 0)
|
||||
* :math:`d` (degrees) = :math:`\phi_0 + 180`
|
||||
|
||||
K and phi0 are specified with the fix. Note that the value of the
|
||||
dihedral multiplicity *n* is set by default to 1. You can use the
|
||||
:math:`K` and :math:`\phi_0` are specified with the fix. Note that the value of the
|
||||
dihedral multiplicity :math:`n` is set by default to 1. You can use the
|
||||
optional *mult* keyword to set it to a different positive integer.
|
||||
Also note that the energy will be a minimum when the
|
||||
current dihedral angle phi is equal to phi0.
|
||||
current dihedral angle :math:`\phi` is equal to :math:`\phi_0`.
|
||||
|
||||
|
||||
----------
|
||||
|
|
@ -233,8 +238,3 @@ Restrictions
|
|||
**Related commands:** none
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
|
|
|||
|
|
@ -1,89 +0,0 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
angle_style charmm command :h3
|
||||
angle_style charmm/intel command :h3
|
||||
angle_style charmm/kk command :h3
|
||||
angle_style charmm/omp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
angle_style charmm :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
angle_style charmm
|
||||
angle_coeff 1 300.0 107.0 50.0 3.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {charmm} angle style uses the potential
|
||||
|
||||
:c,image(Eqs/angle_charmm.jpg)
|
||||
|
||||
with an additional Urey_Bradley term based on the distance {r} between
|
||||
the 1st and 3rd atoms in the angle. K, theta0, Kub, and Rub are
|
||||
coefficients defined for each angle type.
|
||||
|
||||
See "(MacKerell)"_#angle-MacKerell for a description of the CHARMM force
|
||||
field.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
"angle_coeff"_angle_coeff.html command as in the example above, or in
|
||||
the data file or restart files read by the "read_data"_read_data.html
|
||||
or "read_restart"_read_restart.html commands:
|
||||
|
||||
K (energy/radian^2)
|
||||
theta0 (degrees)
|
||||
K_ub (energy/distance^2)
|
||||
r_ub (distance) :ul
|
||||
|
||||
Theta0 is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of K are in energy/radian^2.
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Run_options.html when you invoke LAMMPS, or you can use the
|
||||
"suffix"_suffix.html command in your input script.
|
||||
|
||||
See "Speed packages"_Speed_packages.html doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This angle style can only be used if LAMMPS was built with the
|
||||
MOLECULE package. See the "Build package"_Build_package.html doc page
|
||||
for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"angle_coeff"_angle_coeff.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(angle-MacKerell)
|
||||
[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
|
||||
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
|
||||
|
|
@ -1,138 +0,0 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
angle_style class2 command :h3
|
||||
angle_style class2/kk command :h3
|
||||
angle_style class2/omp command :h3
|
||||
angle_style class2/p6 command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
angle_style class2 :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
angle_style class2
|
||||
angle_coeff * 75.0
|
||||
angle_coeff 1 bb 10.5872 1.0119 1.5228
|
||||
angle_coeff * ba 3.6551 24.895 1.0119 1.5228 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {class2} angle style uses the potential
|
||||
|
||||
:c,image(Eqs/angle_class2.jpg)
|
||||
|
||||
where Ea is the angle term, Ebb is a bond-bond term, and Eba is a
|
||||
bond-angle term. Theta0 is the equilibrium angle and r1 and r2 are
|
||||
the equilibrium bond lengths.
|
||||
|
||||
See "(Sun)"_#angle-Sun for a description of the COMPASS class2 force field.
|
||||
|
||||
Coefficients for the Ea, Ebb, and Eba formulas must be defined for
|
||||
each angle type via the "angle_coeff"_angle_coeff.html command as in
|
||||
the example above, or in the data file or restart files read by the
|
||||
"read_data"_read_data.html or "read_restart"_read_restart.html
|
||||
commands.
|
||||
|
||||
These are the 4 coefficients for the Ea formula:
|
||||
|
||||
theta0 (degrees)
|
||||
K2 (energy/radian^2)
|
||||
K3 (energy/radian^3)
|
||||
K4 (energy/radian^4) :ul
|
||||
|
||||
Theta0 is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of the various K are in per-radian.
|
||||
|
||||
For the Ebb formula, each line in a "angle_coeff"_angle_coeff.html
|
||||
command in the input script lists 4 coefficients, the first of which
|
||||
is "bb" to indicate they are BondBond coefficients. In a data file,
|
||||
these coefficients should be listed under a "BondBond Coeffs" heading
|
||||
and you must leave out the "bb", i.e. only list 3 coefficients after
|
||||
the angle type.
|
||||
|
||||
bb
|
||||
M (energy/distance^2)
|
||||
r1 (distance)
|
||||
r2 (distance) :ul
|
||||
|
||||
For the Eba formula, each line in a "angle_coeff"_angle_coeff.html
|
||||
command in the input script lists 5 coefficients, the first of which
|
||||
is "ba" to indicate they are BondAngle coefficients. In a data file,
|
||||
these coefficients should be listed under a "BondAngle Coeffs" heading
|
||||
and you must leave out the "ba", i.e. only list 4 coefficients after
|
||||
the angle type.
|
||||
|
||||
ba
|
||||
N1 (energy/distance^2)
|
||||
N2 (energy/distance^2)
|
||||
r1 (distance)
|
||||
r2 (distance) :ul
|
||||
|
||||
The theta0 value in the Eba formula is not specified, since it is the
|
||||
same value from the Ea formula.
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Run_options.html when you invoke LAMMPS, or you can use the
|
||||
"suffix"_suffix.html command in your input script.
|
||||
|
||||
See the "Speed packages"_Speed_packages.html doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
The {class2/p6} angle style uses the {class2} potential expanded to sixth order:
|
||||
|
||||
:c,image(Eqs/angle_class2_p6.jpg)
|
||||
|
||||
In this expanded term 6 coefficients for the Ea formula need to be set:
|
||||
|
||||
theta0 (degrees)
|
||||
K2 (energy/radian^2)
|
||||
K3 (energy/radian^3)
|
||||
K4 (energy/radian^4)
|
||||
K5 (energy/radian^5)
|
||||
K6 (energy/radian^6) :ul
|
||||
|
||||
The bond-bond and bond-angle terms remain unchanged.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This angle style can only be used if LAMMPS was built with the CLASS2
|
||||
package. For the {class2/p6} style LAMMPS needs to be built with the
|
||||
USER-MOFFF package. See the "Build package"_Build_package.html doc
|
||||
page for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"angle_coeff"_angle_coeff.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(angle-Sun)
|
||||
[(Sun)] Sun, J Phys Chem B 102, 7338-7364 (1998).
|
||||
|
|
@ -1,87 +0,0 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
angle_coeff command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
angle_coeff N args :pre
|
||||
|
||||
N = angle type (see asterisk form below)
|
||||
args = coefficients for one or more angle types :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
angle_coeff 1 300.0 107.0
|
||||
angle_coeff * 5.0
|
||||
angle_coeff 2*10 5.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Specify the angle force field coefficients for one or more angle types.
|
||||
The number and meaning of the coefficients depends on the angle style.
|
||||
Angle coefficients can also be set in the data file read by the
|
||||
"read_data"_read_data.html command or in a restart file.
|
||||
|
||||
N can be specified in one of two ways. An explicit numeric value can
|
||||
be used, as in the 1st example above. Or a wild-card asterisk can be
|
||||
used to set the coefficients for multiple angle types. This takes the
|
||||
form "*" or "*n" or "n*" or "m*n". If N = the number of angle types,
|
||||
then an asterisk with no numeric values means all types from 1 to N. A
|
||||
leading asterisk means all types from 1 to n (inclusive). A trailing
|
||||
asterisk means all types from n to N (inclusive). A middle asterisk
|
||||
means all types from m to n (inclusive).
|
||||
|
||||
Note that using an angle_coeff command can override a previous setting
|
||||
for the same angle type. For example, these commands set the coeffs
|
||||
for all angle types, then overwrite the coeffs for just angle type 2:
|
||||
|
||||
angle_coeff * 200.0 107.0 1.2
|
||||
angle_coeff 2 50.0 107.0 :pre
|
||||
|
||||
A line in a data file that specifies angle coefficients uses the exact
|
||||
same format as the arguments of the angle_coeff command in an input
|
||||
script, except that wild-card asterisks should not be used since
|
||||
coefficients for all N types must be listed in the file. For example,
|
||||
under the "Angle Coeffs" section of a data file, the line that
|
||||
corresponds to the 1st example above would be listed as
|
||||
|
||||
1 300.0 107.0 :pre
|
||||
|
||||
The "angle_style class2"_angle_class2.html is an exception to this
|
||||
rule, in that an additional argument is used in the input script to
|
||||
allow specification of the cross-term coefficients. See its
|
||||
doc page for details.
|
||||
|
||||
:line
|
||||
|
||||
The list of all angle styles defined in LAMMPS is given on the
|
||||
"angle_style"_angle_style.html doc page. They are also listed in more
|
||||
compact form on the "Commands angle"_Commands_bond.html#angle doc
|
||||
page.
|
||||
|
||||
On either of those pages, click on the style to display the formula it
|
||||
computes and its coefficients as specified by the associated
|
||||
angle_coeff command.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This command must come after the simulation box is defined by a
|
||||
"read_data"_read_data.html, "read_restart"_read_restart.html, or
|
||||
"create_box"_create_box.html command.
|
||||
|
||||
An angle style must be defined before any angle coefficients are
|
||||
set, either in the input script or in a data file.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"angle_style"_angle_style.html
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -1,71 +0,0 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
angle_style cosine command :h3
|
||||
angle_style cosine/omp command :h3
|
||||
angle_style cosine/kk command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
angle_style cosine :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
angle_style cosine
|
||||
angle_coeff * 75.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {cosine} angle style uses the potential
|
||||
|
||||
:c,image(Eqs/angle_cosine.jpg)
|
||||
|
||||
where K is defined for each angle type.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
"angle_coeff"_angle_coeff.html command as in the example above, or in
|
||||
the data file or restart files read by the "read_data"_read_data.html
|
||||
or "read_restart"_read_restart.html commands:
|
||||
|
||||
K (energy) :ul
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Run_options.html when you invoke LAMMPS, or you can use the
|
||||
"suffix"_suffix.html command in your input script.
|
||||
|
||||
See the "Speed packages"_Speed_packages.html doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This angle style can only be used if LAMMPS was built with the
|
||||
MOLECULE package. See the "Build package"_Build_package.html doc page
|
||||
for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"angle_coeff"_angle_coeff.html
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -1,65 +0,0 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
angle_style cosine/buck6d command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
angle_style cosine/buck6d :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
angle_style cosine/buck6d
|
||||
angle_coeff 1 cosine/buck6d 1.978350 4 180.000000 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {cosine/buck6d} angle style uses the potential
|
||||
|
||||
:c,image(Eqs/angle_cosine_buck6d.jpg)
|
||||
|
||||
where K is the energy constant, n is the periodic multiplicity and
|
||||
Theta0 is the equilibrium angle.
|
||||
|
||||
The coefficients must be defined for each angle type via the
|
||||
"angle_coeff"_angle_coeff.html command as in the example above, or in
|
||||
the data file or restart files read by the "read_data"_read_data.html
|
||||
or "read_restart"_read_restart.html commands in the following order:
|
||||
|
||||
K (energy)
|
||||
n
|
||||
Theta0 (degrees) :ul
|
||||
|
||||
Theta0 is specified in degrees, but LAMMPS converts it to radians
|
||||
internally.
|
||||
|
||||
Additional to the cosine term the {cosine/buck6d} angle style computes
|
||||
the short range (vdW) interaction belonging to the
|
||||
"pair_buck6d"_pair_buck6d_coul_gauss.html between the end atoms of the
|
||||
angle. For this reason this angle style only works in combination
|
||||
with the "pair_buck6d"_pair_buck6d_coul_gauss.html styles and needs
|
||||
the "special_bonds"_special_bonds.html 1-3 interactions to be weighted
|
||||
0.0 to prevent double counting.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
{cosine/buck6d} can only be used in combination with the
|
||||
"pair_buck6d"_pair_buck6d_coul_gauss.html style and with a
|
||||
"special_bonds"_special_bonds.html 0.0 weighting of 1-3 interactions.
|
||||
|
||||
This angle style can only be used if LAMMPS was built with the
|
||||
USER-MOFFF package. See the "Build package"_Build_package.html doc
|
||||
page for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"angle_coeff"_angle_coeff.html
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -1,76 +0,0 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
angle_style cosine/delta command :h3
|
||||
angle_style cosine/delta/omp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
angle_style cosine/delta :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
angle_style cosine/delta
|
||||
angle_coeff 2*4 75.0 100.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {cosine/delta} angle style uses the potential
|
||||
|
||||
:c,image(Eqs/angle_cosine_delta.jpg)
|
||||
|
||||
where theta0 is the equilibrium value of the angle, and K is a
|
||||
prefactor. Note that the usual 1/2 factor is included in K.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
"angle_coeff"_angle_coeff.html command as in the example above, or in
|
||||
the data file or restart files read by the "read_data"_read_data.html
|
||||
or "read_restart"_read_restart.html commands:
|
||||
|
||||
K (energy)
|
||||
theta0 (degrees) :ul
|
||||
|
||||
Theta0 is specified in degrees, but LAMMPS converts it to radians
|
||||
internally.
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Run_options.html when you invoke LAMMPS, or you can use the
|
||||
"suffix"_suffix.html command in your input script.
|
||||
|
||||
See the "Speed packages"_Speed_packages.html doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This angle style can only be used if LAMMPS was built with the
|
||||
MOLECULE package. See the "Build package"_Build_package.html doc page
|
||||
for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"angle_coeff"_angle_coeff.html, "angle_style
|
||||
cosine/squared"_angle_cosine_squared.html
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -1,89 +0,0 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
angle_style cosine/periodic command :h3
|
||||
angle_style cosine/periodic/omp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
angle_style cosine/periodic :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
angle_style cosine/periodic
|
||||
angle_coeff * 75.0 1 6 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {cosine/periodic} angle style uses the following potential, which
|
||||
is commonly used in the "DREIDING"_Howto_bioFF.html force field,
|
||||
particularly for organometallic systems where {n} = 4 might be used
|
||||
for an octahedral complex and {n} = 3 might be used for a trigonal
|
||||
center:
|
||||
|
||||
:c,image(Eqs/angle_cosine_periodic.jpg)
|
||||
|
||||
where C, B and n are coefficients defined for each angle type.
|
||||
|
||||
See "(Mayo)"_#cosine-Mayo for a description of the DREIDING force field
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
"angle_coeff"_angle_coeff.html command as in the example above, or in
|
||||
the data file or restart files read by the "read_data"_read_data.html
|
||||
or "read_restart"_read_restart.html commands:
|
||||
|
||||
C (energy)
|
||||
B = 1 or -1
|
||||
n = 1, 2, 3, 4, 5 or 6 for periodicity :ul
|
||||
|
||||
Note that the prefactor C is specified and not the overall force
|
||||
constant K = C / n^2. When B = 1, it leads to a minimum for the
|
||||
linear geometry. When B = -1, it leads to a maximum for the linear
|
||||
geometry.
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Run_options.html when you invoke LAMMPS, or you can use the
|
||||
"suffix"_suffix.html command in your input script.
|
||||
|
||||
See the "Speed packages"_Speed_packages.html doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This angle style can only be used if LAMMPS was built with the
|
||||
MOLECULE package. See the "Build package"_Build_package.html doc page
|
||||
for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"angle_coeff"_angle_coeff.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(cosine-Mayo)
|
||||
[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
|
||||
(1990).
|
||||
|
|
@ -1,73 +0,0 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
angle_style cosine/shift command :h3
|
||||
angle_style cosine/shift/omp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
angle_style cosine/shift :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
angle_style cosine/shift
|
||||
angle_coeff * 10.0 45.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {cosine/shift} angle style uses the potential
|
||||
|
||||
:c,image(Eqs/angle_cosine_shift.jpg)
|
||||
|
||||
where theta0 is the equilibrium angle. The potential is bounded
|
||||
between -Umin and zero. In the neighborhood of the minimum E=- Umin +
|
||||
Umin/4(theta-theta0)^2 hence the spring constant is umin/2.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
"angle_coeff"_angle_coeff.html command as in the example above, or in
|
||||
the data file or restart files read by the "read_data"_read_data.html
|
||||
or "read_restart"_read_restart.html commands:
|
||||
|
||||
umin (energy)
|
||||
theta (angle) :ul
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Run_options.html when you invoke LAMMPS, or you can use the
|
||||
"suffix"_suffix.html command in your input script.
|
||||
|
||||
See the "Speed packages"_Speed_packages.html doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This angle style can only be used if LAMMPS was built with the
|
||||
USER-MISC package.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"angle_coeff"_angle_coeff.html,
|
||||
"angle_cosine_shift_exp"_angle_cosine_shift_exp.html
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -1,87 +0,0 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
angle_style cosine/shift/exp command :h3
|
||||
angle_style cosine/shift/exp/omp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
angle_style cosine/shift/exp :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
angle_style cosine/shift/exp
|
||||
angle_coeff * 10.0 45.0 2.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {cosine/shift/exp} angle style uses the potential
|
||||
|
||||
:c,image(Eqs/angle_cosine_shift_exp.jpg)
|
||||
|
||||
where Umin, theta, and a are defined for each angle type.
|
||||
|
||||
The potential is bounded between \[-Umin:0\] and the minimum is
|
||||
located at the angle theta0. The a parameter can be both positive or
|
||||
negative and is used to control the spring constant at the
|
||||
equilibrium.
|
||||
|
||||
The spring constant is given by k = A exp(A) Umin / \[2 (Exp(a)-1)\].
|
||||
For a > 3, k/Umin = a/2 to better than 5% relative error. For negative
|
||||
values of the a parameter, the spring constant is essentially zero,
|
||||
and anharmonic terms takes over. The potential is furthermore well
|
||||
behaved in the limit a -> 0, where it has been implemented to linear
|
||||
order in a for a < 0.001. In this limit the potential reduces to the
|
||||
cosineshifted potential.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
"angle_coeff"_angle_coeff.html command as in the example above, or in
|
||||
the data file or restart files read by the "read_data"_read_data.html
|
||||
or "read_restart"_read_restart.html commands:
|
||||
|
||||
umin (energy)
|
||||
theta (angle)
|
||||
A (real number) :ul
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Run_options.html when you invoke LAMMPS, or you can use the
|
||||
"suffix"_suffix.html command in your input script.
|
||||
|
||||
See the "Speed packages"_Speed_packages.html doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This angle style can only be used if LAMMPS was built with the
|
||||
USER-MISC package. See the "Build package"_Build_package.html doc
|
||||
page for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"angle_coeff"_angle_coeff.html,
|
||||
"angle_cosine_shift"_angle_cosine_shift.html,
|
||||
"dihedral_cosine_shift_exp"_dihedral_cosine_shift_exp.html
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -1,75 +0,0 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
angle_style cosine/squared command :h3
|
||||
angle_style cosine/squared/omp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
angle_style cosine/squared :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
angle_style cosine/squared
|
||||
angle_coeff 2*4 75.0 100.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {cosine/squared} angle style uses the potential
|
||||
|
||||
:c,image(Eqs/angle_cosine_squared.jpg)
|
||||
|
||||
where theta0 is the equilibrium value of the angle, and K is a
|
||||
prefactor. Note that the usual 1/2 factor is included in K.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
"angle_coeff"_angle_coeff.html command as in the example above, or in
|
||||
the data file or restart files read by the "read_data"_read_data.html
|
||||
or "read_restart"_read_restart.html commands:
|
||||
|
||||
K (energy)
|
||||
theta0 (degrees) :ul
|
||||
|
||||
Theta0 is specified in degrees, but LAMMPS converts it to radians
|
||||
internally.
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Run_options.html when you invoke LAMMPS, or you can use the
|
||||
"suffix"_suffix.html command in your input script.
|
||||
|
||||
See the "Speed packages"_Speed_packages.html doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This angle style can only be used if LAMMPS was built with the
|
||||
MOLECULE package. See the "Build package"_Build_package.html doc page
|
||||
for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"angle_coeff"_angle_coeff.html
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -1,62 +0,0 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
angle_style cross command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
angle_style cross :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
angle_style cross
|
||||
angle_coeff 1 200.0 100.0 100.0 1.25 1.25 107.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {cross} angle style uses a potential that couples the bond stretches of
|
||||
a bend with the angle stretch of that bend:
|
||||
|
||||
:c,image(Eqs/angle_cross.jpg)
|
||||
|
||||
where r12,0 is the rest value of the bond length between atom 1 and 2,
|
||||
r32,0 is the rest value of the bond length between atom 2 and 2,
|
||||
and theta0 is the rest value of the angle. KSS is the force constant of
|
||||
the bond stretch-bond stretch term and KBS0 and KBS1 are the force constants
|
||||
of the bond stretch-angle stretch terms.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
"angle_coeff"_angle_coeff.html command as in the example above, or in
|
||||
the data file or restart files read by the "read_data"_read_data.html
|
||||
or "read_restart"_read_restart.html commands:
|
||||
|
||||
KSS (energy/distance^2)
|
||||
KBS0 (energy/distance/rad)
|
||||
KBS1 (energy/distance/rad)
|
||||
r12,0 (distance)
|
||||
r32,0 (distance)
|
||||
theta0 (degrees) :ul
|
||||
|
||||
Theta0 is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of KBS0 and KBS1 are in energy/distance/radian.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This angle style can only be used if LAMMPS was built with the
|
||||
USER_YAFF package. See the "Build package"_Build_package.html doc
|
||||
page for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"angle_coeff"_angle_coeff.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
|
||||
|
|
@ -1,126 +0,0 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
angle_style dipole command :h3
|
||||
angle_style dipole/omp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
angle_style dipole :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
angle_style dipole
|
||||
angle_coeff 6 2.1 180.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {dipole} angle style is used to control the orientation of a dipolar
|
||||
atom within a molecule "(Orsi)"_#Orsi. Specifically, the {dipole} angle
|
||||
style restrains the orientation of a point dipole mu_j (embedded in atom
|
||||
'j') with respect to a reference (bond) vector r_ij = r_i - r_j, where 'i'
|
||||
is another atom of the same molecule (typically, 'i' and 'j' are also
|
||||
covalently bonded).
|
||||
|
||||
It is convenient to define an angle gamma between the 'free' vector mu_j
|
||||
and the reference (bond) vector r_ij:
|
||||
|
||||
:c,image(Eqs/angle_dipole_gamma.jpg)
|
||||
|
||||
The {dipole} angle style uses the potential:
|
||||
|
||||
:c,image(Eqs/angle_dipole_potential.jpg)
|
||||
|
||||
where K is a rigidity constant and gamma0 is an equilibrium (reference)
|
||||
angle.
|
||||
|
||||
The torque on the dipole can be obtained by differentiating the
|
||||
potential using the 'chain rule' as in appendix C.3 of
|
||||
"(Allen)"_#Allen1:
|
||||
|
||||
:c,image(Eqs/angle_dipole_torque.jpg)
|
||||
|
||||
Example: if gamma0 is set to 0 degrees, the torque generated by
|
||||
the potential will tend to align the dipole along the reference
|
||||
direction defined by the (bond) vector r_ij (in other words, mu_j is
|
||||
restrained to point towards atom 'i').
|
||||
|
||||
The dipolar torque T_j must be counterbalanced in order to conserve
|
||||
the local angular momentum. This is achieved via an additional force
|
||||
couple generating a torque equivalent to the opposite of T_j:
|
||||
|
||||
:c,image(Eqs/angle_dipole_couple.jpg)
|
||||
|
||||
where F_i and F_j are applied on atoms i and j, respectively.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
"angle_coeff"_angle_coeff.html command as in the example above, or in
|
||||
the data file or restart files read by the "read_data"_read_data.html
|
||||
or "read_restart"_read_restart.html commands:
|
||||
|
||||
K (energy)
|
||||
gamma0 (degrees) :ul
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Run_options.html when you invoke LAMMPS, or you can use the
|
||||
"suffix"_suffix.html command in your input script.
|
||||
|
||||
See the "Speed packages"_Speed_packages.html doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This angle style can only be used if LAMMPS was built with the
|
||||
USER-MISC package. See the "Build package"_Build_package.html doc
|
||||
page for more info.
|
||||
|
||||
NOTE: In the "Angles" section of the data file, the atom ID 'j'
|
||||
defining the direction of the dipole vector to restrain must come
|
||||
before the atom ID of the reference atom 'i'. A third atom ID 'k' must
|
||||
also be provided to comply with the requirement of a valid angle
|
||||
definition. This atom ID k should be chosen to be that of an atom
|
||||
bonded to atom 'i' to avoid errors with "lost angle atoms" when running
|
||||
in parallel. Since the LAMMPS code checks for valid angle definitions,
|
||||
cannot use the same atom ID of either 'i' or 'j' (this was allowed
|
||||
and recommended with older LAMMPS versions).
|
||||
|
||||
The "newton" command for intramolecular interactions must be "on"
|
||||
(which is the default except when using some accelerator packages).
|
||||
|
||||
This angle style should not be used with SHAKE.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"angle_coeff"_angle_coeff.html, "angle_hybrid"_angle_hybrid.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Orsi)
|
||||
[(Orsi)] Orsi & Essex, The ELBA force field for coarse-grain modeling of
|
||||
lipid membranes, PloS ONE 6(12): e28637, 2011.
|
||||
|
||||
:link(Allen1)
|
||||
[(Allen)] Allen & Tildesley, Computer Simulation of Liquids,
|
||||
Clarendon Press, Oxford, 1987.
|
||||
|
|
@ -1,71 +0,0 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
angle_style fourier command :h3
|
||||
angle_style fourier/omp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
angle_style fourier :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
angle_style fourier
|
||||
angle_coeff 75.0 1.0 1.0 1.0
|
||||
|
||||
[Description:]
|
||||
|
||||
The {fourier} angle style uses the potential
|
||||
|
||||
:c,image(Eqs/angle_fourier.jpg)
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
"angle_coeff"_angle_coeff.html command as in the example above, or in
|
||||
the data file or restart files read by the "read_data"_read_data.html
|
||||
or "read_restart"_read_restart.html commands:
|
||||
|
||||
K (energy)
|
||||
C0 (real)
|
||||
C1 (real)
|
||||
C2 (real) :ul
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Run_options.html when you invoke LAMMPS, or you can use the
|
||||
"suffix"_suffix.html command in your input script.
|
||||
|
||||
See the "Speed packages"_Speed_packages.html doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This angle style can only be used if LAMMPS was built with the
|
||||
USER_MISC package. See the "Build package"_Build_package.html doc
|
||||
page for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"angle_coeff"_angle_coeff.html
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -1,70 +0,0 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
angle_style fourier/simple command :h3
|
||||
angle_style fourier/simple/omp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
angle_style fourier/simple :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
angle_style fourier/simple
|
||||
angle_coeff 100.0 -1.0 1.0
|
||||
|
||||
[Description:]
|
||||
|
||||
The {fourier/simple} angle style uses the potential
|
||||
|
||||
:c,image(Eqs/angle_fourier_simple.jpg)
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
"angle_coeff"_angle_coeff.html command as in the example above, or in
|
||||
the data file or restart files read by the "read_data"_read_data.html
|
||||
or "read_restart"_read_restart.html commands:
|
||||
|
||||
K (energy)
|
||||
c (real)
|
||||
n (real) :ul
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Run_options.html when you invoke LAMMPS, or you can use the
|
||||
"suffix"_suffix.html command in your input script.
|
||||
|
||||
See the "Speed packages"_Speed_packages.html doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This angle style can only be used if LAMMPS was built with the
|
||||
USER_MISC package. See the "Build package"_Build_package.html doc
|
||||
page for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"angle_coeff"_angle_coeff.html
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -1,77 +0,0 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
angle_style harmonic command :h3
|
||||
angle_style harmonic/intel command :h3
|
||||
angle_style harmonic/kk command :h3
|
||||
angle_style harmonic/omp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
angle_style harmonic :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
angle_style harmonic
|
||||
angle_coeff 1 300.0 107.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {harmonic} angle style uses the potential
|
||||
|
||||
:c,image(Eqs/angle_harmonic.jpg)
|
||||
|
||||
where theta0 is the equilibrium value of the angle, and K is a
|
||||
prefactor. Note that the usual 1/2 factor is included in K.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
"angle_coeff"_angle_coeff.html command as in the example above, or in
|
||||
the data file or restart files read by the "read_data"_read_data.html
|
||||
or "read_restart"_read_restart.html commands:
|
||||
|
||||
K (energy/radian^2)
|
||||
theta0 (degrees) :ul
|
||||
|
||||
Theta0 is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of K are in energy/radian^2.
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Run_options.html when you invoke LAMMPS, or you can use the
|
||||
"suffix"_suffix.html command in your input script.
|
||||
|
||||
See the "Speed packages"_Speed_packages.html doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This angle style can only be used if LAMMPS was built with the
|
||||
MOLECULE package. See the "Build package"_Build_package.html doc
|
||||
page for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"angle_coeff"_angle_coeff.html
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -1,91 +0,0 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
angle_style hybrid command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
angle_style hybrid style1 style2 ... :pre
|
||||
|
||||
style1,style2 = list of one or more angle styles :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
angle_style hybrid harmonic cosine
|
||||
angle_coeff 1 harmonic 80.0 30.0
|
||||
angle_coeff 2* cosine 50.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {hybrid} style enables the use of multiple angle styles in one
|
||||
simulation. An angle style is assigned to each angle type. For
|
||||
example, angles in a polymer flow (of angle type 1) could be computed
|
||||
with a {harmonic} potential and angles in the wall boundary (of angle
|
||||
type 2) could be computed with a {cosine} potential. The assignment
|
||||
of angle type to style is made via the "angle_coeff"_angle_coeff.html
|
||||
command or in the data file.
|
||||
|
||||
In the angle_coeff commands, the name of an angle style must be added
|
||||
after the angle type, with the remaining coefficients being those
|
||||
appropriate to that style. In the example above, the 2 angle_coeff
|
||||
commands set angles of angle type 1 to be computed with a {harmonic}
|
||||
potential with coefficients 80.0, 30.0 for K, theta0. All other angle
|
||||
types (2-N) are computed with a {cosine} potential with coefficient
|
||||
50.0 for K.
|
||||
|
||||
If angle coefficients are specified in the data file read via the
|
||||
"read_data"_read_data.html command, then the same rule applies.
|
||||
E.g. "harmonic" or "cosine", must be added after the angle type, for each
|
||||
line in the "Angle Coeffs" section, e.g.
|
||||
|
||||
Angle Coeffs :pre
|
||||
|
||||
1 harmonic 80.0 30.0
|
||||
2 cosine 50.0
|
||||
... :pre
|
||||
|
||||
If {class2} is one of the angle hybrid styles, the same rule holds for
|
||||
specifying additional BondBond (and BondAngle) coefficients either via
|
||||
the input script or in the data file. I.e. {class2} must be added to
|
||||
each line after the angle type. For lines in the BondBond (or
|
||||
BondAngle) section of the data file for angle types that are not
|
||||
{class2}, you must use an angle style of {skip} as a placeholder, e.g.
|
||||
|
||||
BondBond Coeffs :pre
|
||||
|
||||
1 skip
|
||||
2 class2 3.6512 1.0119 1.0119
|
||||
... :pre
|
||||
|
||||
Note that it is not necessary to use the angle style {skip} in the
|
||||
input script, since BondBond (or BondAngle) coefficients need not be
|
||||
specified at all for angle types that are not {class2}.
|
||||
|
||||
An angle style of {none} with no additional coefficients can be used
|
||||
in place of an angle style, either in a input script angle_coeff
|
||||
command or in the data file, if you desire to turn off interactions
|
||||
for specific angle types.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This angle style can only be used if LAMMPS was built with the
|
||||
MOLECULE package. See the "Build package"_Build_package.html doc page
|
||||
for more info.
|
||||
|
||||
Unlike other angle styles, the hybrid angle style does not store angle
|
||||
coefficient info for individual sub-styles in a "binary restart
|
||||
files"_restart.html. Thus when restarting a simulation from a restart
|
||||
file, you need to re-specify angle_coeff commands.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"angle_coeff"_angle_coeff.html
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -1,55 +0,0 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
angle_style mm3 command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
angle_style mm3 :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
angle_style mm3
|
||||
angle_coeff 1 100.0 107.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {mm3} angle style uses the potential that is anharmonic in the angle
|
||||
as defined in "(Allinger)"_#mm3-allinger1989
|
||||
|
||||
:c,image(Eqs/angle_mm3.jpg)
|
||||
|
||||
where theta0 is the equilibrium value of the angle, and K is a
|
||||
prefactor. The anharmonic prefactors have units deg^(-n), for example
|
||||
-0.014 deg^(-1), 5.6(10)^(-5) deg^(-2), ...
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
"angle_coeff"_angle_coeff.html command as in the example above, or in
|
||||
the data file or restart files read by the "read_data"_read_data.html
|
||||
or "read_restart"_read_restart.html commands:
|
||||
|
||||
K (energy/radian^2)
|
||||
theta0 (degrees) :ul
|
||||
|
||||
Theta0 is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of K are in energy/radian^2.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This angle style can only be used if LAMMPS was built with the
|
||||
USER_YAFF package. See the "Build package"_Build_package.html doc
|
||||
page for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"angle_coeff"_angle_coeff.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -1,34 +0,0 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
angle_style none command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
angle_style none :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
angle_style none :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Using an angle style of none means angle forces and energies are not
|
||||
computed, even if triplets of angle atoms were listed in the data file
|
||||
read by the "read_data"_read_data.html command.
|
||||
|
||||
See the "angle_style zero"_angle_zero.html command for a way to
|
||||
calculate angle statistics, but compute no angle interactions.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"angle_style zero"_angle_zero.html
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -1,77 +0,0 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
angle_style quartic command :h3
|
||||
angle_style quartic/omp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
angle_style quartic :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
angle_style quartic
|
||||
angle_coeff 1 129.1948 56.8726 -25.9442 -14.2221 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {quartic} angle style uses the potential
|
||||
|
||||
:c,image(Eqs/angle_quartic.jpg)
|
||||
|
||||
where theta0 is the equilibrium value of the angle, and K is a
|
||||
prefactor. Note that the usual 1/2 factor is included in K.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
"angle_coeff"_angle_coeff.html command as in the example above, or in
|
||||
the data file or restart files read by the "read_data"_read_data.html
|
||||
or "read_restart"_read_restart.html commands:
|
||||
|
||||
theta0 (degrees)
|
||||
K2 (energy/radian^2)
|
||||
K3 (energy/radian^3)
|
||||
K4 (energy/radian^4) :ul
|
||||
|
||||
Theta0 is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of K are in energy/radian^2.
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Run_options.html when you invoke LAMMPS, or you can use the
|
||||
"suffix"_suffix.html command in your input script.
|
||||
|
||||
See the "Speed packages"_Speed_packages.html doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This angle style can only be used if LAMMPS was built with the
|
||||
USER_MISC package. See the "Build package"_Build_package.html doc
|
||||
page for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"angle_coeff"_angle_coeff.html
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -1,83 +0,0 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
angle_style sdk command :h3
|
||||
angle_style sdk/omp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
angle_style sdk :pre
|
||||
angle_style sdk/omp :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
angle_style sdk
|
||||
angle_coeff 1 300.0 107.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {sdk} angle style is a combination of the harmonic angle potential,
|
||||
|
||||
:c,image(Eqs/angle_harmonic.jpg)
|
||||
|
||||
where theta0 is the equilibrium value of the angle and K a prefactor,
|
||||
with the {repulsive} part of the non-bonded {lj/sdk} pair style
|
||||
between the atoms 1 and 3. This angle potential is intended for
|
||||
coarse grained MD simulations with the CMM parameterization using the
|
||||
"pair_style lj/sdk"_pair_sdk.html. Relative to the pair_style
|
||||
{lj/sdk}, however, the energy is shifted by {epsilon}, to avoid sudden
|
||||
jumps. Note that the usual 1/2 factor is included in K.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
"angle_coeff"_angle_coeff.html command as in the example above:
|
||||
|
||||
K (energy/radian^2)
|
||||
theta0 (degrees) :ul
|
||||
|
||||
Theta0 is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of K are in energy/radian^2.
|
||||
The also required {lj/sdk} parameters will be extracted automatically
|
||||
from the pair_style.
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Run_options.html when you invoke LAMMPS, or you can use the
|
||||
"suffix"_suffix.html command in your input script.
|
||||
|
||||
See the "Speed packages"_Speed_packages.html doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This angle style can only be used if LAMMPS was built with the
|
||||
USER-CGSDK package. See the "Build package"_Build_package.html doc
|
||||
page for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"angle_coeff"_angle_coeff.html, "angle_style
|
||||
harmonic"_angle_harmonic.html, "pair_style lj/sdk"_pair_sdk.html,
|
||||
"pair_style lj/sdk/coul/long"_pair_sdk.html
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -1,112 +0,0 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
angle_style command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
angle_style style :pre
|
||||
|
||||
style = {none} or {hybrid} or {charmm} or {class2} or {cosine} or \
|
||||
{cosine/squared} or {harmonic} :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
angle_style harmonic
|
||||
angle_style charmm
|
||||
angle_style hybrid harmonic cosine :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Set the formula(s) LAMMPS uses to compute angle interactions between
|
||||
triplets of atoms, which remain in force for the duration of the
|
||||
simulation. The list of angle triplets is read in by a
|
||||
"read_data"_read_data.html or "read_restart"_read_restart.html command
|
||||
from a data or restart file.
|
||||
|
||||
Hybrid models where angles are computed using different angle
|
||||
potentials can be setup using the {hybrid} angle style.
|
||||
|
||||
The coefficients associated with a angle style can be specified in a
|
||||
data or restart file or via the "angle_coeff"_angle_coeff.html command.
|
||||
|
||||
All angle potentials store their coefficient data in binary restart
|
||||
files which means angle_style and "angle_coeff"_angle_coeff.html
|
||||
commands do not need to be re-specified in an input script that
|
||||
restarts a simulation. See the "read_restart"_read_restart.html
|
||||
command for details on how to do this. The one exception is that
|
||||
angle_style {hybrid} only stores the list of sub-styles in the restart
|
||||
file; angle coefficients need to be re-specified.
|
||||
|
||||
NOTE: When both an angle and pair style is defined, the
|
||||
"special_bonds"_special_bonds.html command often needs to be used to
|
||||
turn off (or weight) the pairwise interaction that would otherwise
|
||||
exist between 3 bonded atoms.
|
||||
|
||||
In the formulas listed for each angle style, {theta} is the angle
|
||||
between the 3 atoms in the angle.
|
||||
|
||||
:line
|
||||
|
||||
Here is an alphabetic list of angle styles defined in LAMMPS. Click on
|
||||
the style to display the formula it computes and coefficients
|
||||
specified by the associated "angle_coeff"_angle_coeff.html command.
|
||||
|
||||
Click on the style to display the formula it computes, any additional
|
||||
arguments specified in the angle_style command, and coefficients
|
||||
specified by the associated "angle_coeff"_angle_coeff.html command.
|
||||
|
||||
There are also additional accelerated pair styles included in the
|
||||
LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
|
||||
The individual style names on the "Commands
|
||||
angle"_Commands_bond.html#angle doc page are followed by one or more
|
||||
of (g,i,k,o,t) to indicate which accelerated styles exist.
|
||||
|
||||
"none"_angle_none.html - turn off angle interactions
|
||||
"zero"_angle_zero.html - topology but no interactions
|
||||
"hybrid"_angle_hybrid.html - define multiple styles of angle interactions :ul
|
||||
|
||||
"charmm"_angle_charmm.html - CHARMM angle
|
||||
"class2"_angle_class2.html - COMPASS (class 2) angle
|
||||
"class2/p6"_angle_class2.html - COMPASS (class 2) angle expanded to 6th order
|
||||
"cosine"_angle_cosine.html - angle with cosine term
|
||||
"cosine/buck6d"_angle_cosine_buck6d.html - same as cosine with Buckingham term between 1-3 atoms
|
||||
"cosine/delta"_angle_cosine_delta.html - angle with difference of cosines
|
||||
"cosine/periodic"_angle_cosine_periodic.html - DREIDING angle
|
||||
"cosine/shift"_angle_cosine_shift.html - angle cosine with a shift
|
||||
"cosine/shift/exp"_angle_cosine_shift_exp.html - cosine with shift and exponential term in spring constant
|
||||
"cosine/squared"_angle_cosine_squared.html - angle with cosine squared term
|
||||
"cross"_angle_cross.html - cross term coupling angle and bond lengths
|
||||
"dipole"_angle_dipole.html - angle that controls orientation of a point dipole
|
||||
"fourier"_angle_fourier.html - angle with multiple cosine terms
|
||||
"fourier/simple"_angle_fourier_simple.html - angle with a single cosine term
|
||||
"harmonic"_angle_harmonic.html - harmonic angle
|
||||
"mm3"_angle_mm3.html - anharmonic angle
|
||||
"quartic"_angle_quartic.html - angle with cubic and quartic terms
|
||||
"sdk"_angle_sdk.html - harmonic angle with repulsive SDK pair style between 1-3 atoms
|
||||
"table"_angle_table.html - tabulated by angle :ul
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
Angle styles can only be set for atom_styles that allow angles to be
|
||||
defined.
|
||||
|
||||
Most angle styles are part of the MOLECULE package. They are only
|
||||
enabled if LAMMPS was built with that package. See the "Build
|
||||
package"_Build_package.html doc page for more info. The doc pages for
|
||||
individual bond potentials tell if it is part of a package.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"angle_coeff"_angle_coeff.html
|
||||
|
||||
[Default:]
|
||||
|
||||
angle_style none :pre
|
||||
|
|
@ -1,166 +0,0 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
angle_style table command :h3
|
||||
angle_style table/omp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
angle_style table style N :pre
|
||||
|
||||
style = {linear} or {spline} = method of interpolation
|
||||
N = use N values in table :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
angle_style table linear 1000
|
||||
angle_coeff 3 file.table ENTRY1 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Style {table} creates interpolation tables of length {N} from angle
|
||||
potential and derivative values listed in a file(s) as a function of
|
||||
angle The files are read by the "angle_coeff"_angle_coeff.html
|
||||
command.
|
||||
|
||||
The interpolation tables are created by fitting cubic splines to the
|
||||
file values and interpolating energy and derivative values at each of
|
||||
{N} angles. During a simulation, these tables are used to interpolate
|
||||
energy and force values on individual atoms as needed. The
|
||||
interpolation is done in one of 2 styles: {linear} or {spline}.
|
||||
|
||||
For the {linear} style, the angle is used to find 2 surrounding table
|
||||
values from which an energy or its derivative is computed by linear
|
||||
interpolation.
|
||||
|
||||
For the {spline} style, a cubic spline coefficients are computed and
|
||||
stored at each of the {N} values in the table. The angle is used to
|
||||
find the appropriate set of coefficients which are used to evaluate a
|
||||
cubic polynomial which computes the energy or derivative.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
"angle_coeff"_angle_coeff.html command as in the example above.
|
||||
|
||||
filename
|
||||
keyword :ul
|
||||
|
||||
The filename specifies a file containing tabulated energy and
|
||||
derivative values. The keyword specifies a section of the file. The
|
||||
format of this file is described below.
|
||||
|
||||
:line
|
||||
|
||||
The format of a tabulated file is as follows (without the
|
||||
parenthesized comments):
|
||||
|
||||
# Angle potential for harmonic (one or more comment or blank lines) :pre
|
||||
|
||||
HAM (keyword is the first text on line)
|
||||
N 181 FP 0 0 EQ 90.0 (N, FP, EQ parameters)
|
||||
(blank line)
|
||||
N 181 FP 0 0 (N, FP parameters)
|
||||
1 0.0 200.5 2.5 (index, angle, energy, derivative)
|
||||
2 1.0 198.0 2.5
|
||||
...
|
||||
181 180.0 0.0 0.0 :pre
|
||||
|
||||
A section begins with a non-blank line whose 1st character is not a
|
||||
"#"; blank lines or lines starting with "#" can be used as comments
|
||||
between sections. The first line begins with a keyword which
|
||||
identifies the section. The line can contain additional text, but the
|
||||
initial text must match the argument specified in the
|
||||
"angle_coeff"_angle_coeff.html command. The next line lists (in any
|
||||
order) one or more parameters for the table. Each parameter is a
|
||||
keyword followed by one or more numeric values.
|
||||
|
||||
The parameter "N" is required and its value is the number of table
|
||||
entries that follow. Note that this may be different than the {N}
|
||||
specified in the "angle_style table"_angle_style.html command. Let
|
||||
Ntable = {N} in the angle_style command, and Nfile = "N" in the
|
||||
tabulated file. What LAMMPS does is a preliminary interpolation by
|
||||
creating splines using the Nfile tabulated values as nodal points. It
|
||||
uses these to interpolate as needed to generate energy and derivative
|
||||
values at Ntable different points. The resulting tables of length
|
||||
Ntable are then used as described above, when computing energy and
|
||||
force for individual angles and their atoms. This means that if you
|
||||
want the interpolation tables of length Ntable to match exactly what
|
||||
is in the tabulated file (with effectively no preliminary
|
||||
interpolation), you should set Ntable = Nfile.
|
||||
|
||||
The "FP" parameter is optional. If used, it is followed by two values
|
||||
fplo and fphi, which are the 2nd derivatives at the innermost and
|
||||
outermost angle settings. These values are needed by the spline
|
||||
construction routines. If not specified by the "FP" parameter, they
|
||||
are estimated (less accurately) by the first two and last two
|
||||
derivative values in the table.
|
||||
|
||||
The "EQ" parameter is also optional. If used, it is followed by a the
|
||||
equilibrium angle value, which is used, for example, by the "fix
|
||||
shake"_fix_shake.html command. If not used, the equilibrium angle is
|
||||
set to 180.0.
|
||||
|
||||
Following a blank line, the next N lines list the tabulated values.
|
||||
On each line, the 1st value is the index from 1 to N, the 2nd value is
|
||||
the angle value (in degrees), the 3rd value is the energy (in energy
|
||||
units), and the 4th is -dE/d(theta) (also in energy units). The 3rd
|
||||
term is the energy of the 3-atom configuration for the specified
|
||||
angle. The last term is the derivative of the energy with respect to
|
||||
the angle (in degrees, not radians). Thus the units of the last term
|
||||
are still energy, not force. The angle values must increase from one
|
||||
line to the next. The angle values must also begin with 0.0 and end
|
||||
with 180.0, i.e. span the full range of possible angles.
|
||||
|
||||
Note that one file can contain many sections, each with a tabulated
|
||||
potential. LAMMPS reads the file section by section until it finds
|
||||
one that matches the specified keyword.
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Run_options.html when you invoke LAMMPS, or you can use the
|
||||
"suffix"_suffix.html command in your input script.
|
||||
|
||||
See the "Speed packages"_Speed_packages.html doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restart info:]
|
||||
|
||||
This angle style writes the settings for the "angle_style table"
|
||||
command to "binary restart files"_restart.html, so a angle_style
|
||||
command does not need to specified in an input script that reads a
|
||||
restart file. However, the coefficient information is not stored in
|
||||
the restart file, since it is tabulated in the potential files. Thus,
|
||||
angle_coeff commands do need to be specified in the restart input
|
||||
script.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This angle style can only be used if LAMMPS was built with the
|
||||
MOLECULE package. See the "Build package"_Build_package.html doc page
|
||||
for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"angle_coeff"_angle_coeff.html
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -1,49 +0,0 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
angle_style zero command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
angle_style zero {nocoeff} :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
angle_style zero
|
||||
angle_style zero nocoeff
|
||||
angle_coeff *
|
||||
angle_coeff * 120.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Using an angle style of zero means angle forces and energies are not
|
||||
computed, but the geometry of angle triplets is still accessible to
|
||||
other commands.
|
||||
|
||||
As an example, the "compute angle/local"_compute_angle_local.html
|
||||
command can be used to compute the theta values for the list of
|
||||
triplets of angle atoms listed in the data file read by the
|
||||
"read_data"_read_data.html command. If no angle style is defined,
|
||||
this command cannot be used.
|
||||
|
||||
The optional {nocoeff} flag allows to read data files with AngleCoeff
|
||||
section for any angle style. Similarly, any angle_coeff commands
|
||||
will only be checked for the angle type number and the rest ignored.
|
||||
|
||||
Note that the "angle_coeff"_angle_coeff.html command must be used for
|
||||
all angle types. If specified, there can be only one value, which is
|
||||
going to be used to assign an equilibrium angle, e.g. for use with
|
||||
"fix shake"_fix_shake.html.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"angle_style none"_angle_none.html
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -1,209 +0,0 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
fix restrain command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID restrain keyword args ... :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
restrain = style name of this fix command :l
|
||||
one or more keyword/arg pairs may be appended :l
|
||||
keyword = {bond} or {angle} or {dihedral} :l
|
||||
{bond} args = atom1 atom2 Kstart Kstop r0
|
||||
atom1,atom2 = IDs of 2 atoms in bond
|
||||
Kstart,Kstop = restraint coefficients at start/end of run (energy units)
|
||||
r0 = equilibrium bond distance (distance units)
|
||||
{angle} args = atom1 atom2 atom3 Kstart Kstop theta0
|
||||
atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom
|
||||
Kstart,Kstop = restraint coefficients at start/end of run (energy units)
|
||||
theta0 = equilibrium angle theta (degrees)
|
||||
{dihedral} args = atom1 atom2 atom3 atom4 Kstart Kstop phi0 keyword/value
|
||||
atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order
|
||||
Kstart,Kstop = restraint coefficients at start/end of run (energy units)
|
||||
phi0 = equilibrium dihedral angle phi (degrees)
|
||||
keyword/value = optional keyword value pairs. supported keyword/value pairs:
|
||||
{mult} n = dihedral multiplicity n (integer >= 0, default = 1) :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix holdem all restrain bond 45 48 2000.0 2000.0 2.75
|
||||
fix holdem all restrain dihedral 1 2 3 4 2000.0 2000.0 120.0
|
||||
fix holdem all restrain bond 45 48 2000.0 2000.0 2.75 dihedral 1 2 3 4 2000.0 2000.0 120.0
|
||||
fix texas_holdem all restrain dihedral 1 2 3 4 0.0 2000.0 120.0 dihedral 1 2 3 5 0.0 2000.0 -120.0 dihedral 1 2 3 6 0.0 2000.0 0.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Restrain the motion of the specified sets of atoms by making them part
|
||||
of a bond or angle or dihedral interaction whose strength can vary
|
||||
over time during a simulation. This is functionally similar to
|
||||
creating a bond or angle or dihedral for the same atoms in a data
|
||||
file, as specified by the "read_data"_read_data.html command, albeit
|
||||
with a time-varying pre-factor coefficient, and except for exclusion
|
||||
rules, as explained below.
|
||||
|
||||
For the purpose of force field parameter-fitting or mapping a molecular
|
||||
potential energy surface, this fix reduces the hassle and risk
|
||||
associated with modifying data files. In other words, use this fix to
|
||||
temporarily force a molecule to adopt a particular conformation. To
|
||||
create a permanent bond or angle or dihedral, you should modify the
|
||||
data file.
|
||||
|
||||
NOTE: Adding a bond/angle/dihedral with this command does not apply
|
||||
the exclusion rules and weighting factors specified by the
|
||||
"special_bonds"_special_bonds.html command to atoms in the restraint
|
||||
that are now bonded (1-2,1-3,1-4 neighbors) as a result. If they are
|
||||
close enough to interact in a "pair_style"_pair_style.html sense
|
||||
(non-bonded interaction), then the bond/angle/dihedral restraint
|
||||
interaction will simply be superposed on top of that interaction.
|
||||
|
||||
The group-ID specified by this fix is ignored.
|
||||
|
||||
The second example above applies a restraint to hold the dihedral
|
||||
angle formed by atoms 1, 2, 3, and 4 near 120 degrees using a constant
|
||||
restraint coefficient. The fourth example applies similar restraints
|
||||
to multiple dihedral angles using a restraint coefficient that
|
||||
increases from 0.0 to 2000.0 over the course of the run.
|
||||
|
||||
NOTE: Adding a force to atoms implies a change in their potential
|
||||
energy as they move due to the applied force field. For dynamics via
|
||||
the "run"_run.html command, this energy can be added to the system's
|
||||
potential energy for thermodynamic output (see below). For energy
|
||||
minimization via the "minimize"_minimize.html command, this energy
|
||||
must be added to the system's potential energy to formulate a
|
||||
self-consistent minimization problem (see below).
|
||||
|
||||
In order for a restraint to be effective, the restraint force must
|
||||
typically be significantly larger than the forces associated with
|
||||
conventional force field terms. If the restraint is applied during a
|
||||
dynamics run (as opposed to during an energy minimization), a large
|
||||
restraint coefficient can significantly reduce the stable timestep
|
||||
size, especially if the atoms are initially far from the preferred
|
||||
conformation. You may need to experiment to determine what value of K
|
||||
works best for a given application.
|
||||
|
||||
For the case of finding a minimum energy structure for a single
|
||||
molecule with particular restraints (e.g. for fitting force field
|
||||
parameters or constructing a potential energy surface), commands such
|
||||
as the following may be useful:
|
||||
|
||||
# minimize molecule energy with restraints
|
||||
velocity all create 600.0 8675309 mom yes rot yes dist gaussian
|
||||
fix NVE all nve
|
||||
fix TFIX all langevin 600.0 0.0 100 24601
|
||||
fix REST all restrain dihedral 2 1 3 8 0.0 5000.0 $\{angle1\} dihedral 3 1 2 9 0.0 5000.0 $\{angle2\}
|
||||
fix_modify REST energy yes
|
||||
run 10000
|
||||
fix TFIX all langevin 0.0 0.0 100 24601
|
||||
fix REST all restrain dihedral 2 1 3 8 5000.0 5000.0 $\{angle1\} dihedral 3 1 2 9 5000.0 5000.0 $\{angle2\}
|
||||
fix_modify REST energy yes
|
||||
run 10000
|
||||
# sanity check for convergence
|
||||
minimize 1e-6 1e-9 1000 100000
|
||||
# report unrestrained energies
|
||||
unfix REST
|
||||
run 0 :pre
|
||||
|
||||
:line
|
||||
|
||||
The {bond} keyword applies a bond restraint to the specified atoms
|
||||
using the same functional form used by the "bond_style
|
||||
harmonic"_bond_harmonic.html command. The potential associated with
|
||||
the restraint is
|
||||
|
||||
:c,image(Eqs/bond_harmonic.jpg)
|
||||
|
||||
with the following coefficients:
|
||||
|
||||
K (energy/distance^2)
|
||||
r0 (distance) :ul
|
||||
|
||||
K and r0 are specified with the fix. Note that the usual 1/2 factor
|
||||
is included in K.
|
||||
|
||||
:line
|
||||
|
||||
The {angle} keyword applies an angle restraint to the specified atoms
|
||||
using the same functional form used by the "angle_style
|
||||
harmonic"_angle_harmonic.html command. The potential associated with
|
||||
the restraint is
|
||||
|
||||
:c,image(Eqs/angle_harmonic.jpg)
|
||||
|
||||
with the following coefficients:
|
||||
|
||||
K (energy/radian^2)
|
||||
theta0 (degrees) :ul
|
||||
|
||||
K and theta0 are specified with the fix. Note that the usual 1/2
|
||||
factor is included in K.
|
||||
|
||||
:line
|
||||
|
||||
The {dihedral} keyword applies a dihedral restraint to the specified
|
||||
atoms using a simplified form of the function used by the
|
||||
"dihedral_style charmm"_dihedral_charmm.html command. The potential
|
||||
associated with the restraint is
|
||||
|
||||
:c,image(Eqs/dihedral_charmm.jpg)
|
||||
|
||||
with the following coefficients:
|
||||
|
||||
K (energy)
|
||||
n (multiplicity, >= 0)
|
||||
d (degrees) = phi0 + 180 :ul
|
||||
|
||||
K and phi0 are specified with the fix. Note that the value of the
|
||||
dihedral multiplicity {n} is set by default to 1. You can use the
|
||||
optional {mult} keyword to set it to a different positive integer.
|
||||
Also note that the energy will be a minimum when the
|
||||
current dihedral angle phi is equal to phi0.
|
||||
|
||||
:line
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
files"_restart.html.
|
||||
|
||||
The "fix_modify"_fix_modify.html {energy} option is supported by this
|
||||
fix to add the potential energy associated with this fix to the
|
||||
system's potential energy as part of "thermodynamic
|
||||
output"_thermo_style.html.
|
||||
|
||||
The "fix_modify"_fix_modify.html {respa} option is supported by this
|
||||
fix. This allows to set at which level of the "r-RESPA"_run_style.html
|
||||
integrator the fix is adding its forces. Default is the outermost level.
|
||||
|
||||
NOTE: If you want the fictitious potential energy associated with the
|
||||
added forces to be included in the total potential energy of the
|
||||
system (the quantity being minimized), you MUST enable the
|
||||
"fix_modify"_fix_modify.html {energy} option for this fix.
|
||||
|
||||
This fix computes a global scalar and a global vector of length 3,
|
||||
which can be accessed by various "output commands"_Howto_output.html.
|
||||
The scalar is the total potential energy for {all} the restraints as
|
||||
discussed above. The vector values are the sum of contributions to the
|
||||
following individual categories:
|
||||
|
||||
1 = bond energy
|
||||
2 = angle energy
|
||||
3 = dihedral energy :ul
|
||||
|
||||
The scalar and vector values calculated by this fix are "extensive".
|
||||
|
||||
No parameter of this fix can be used with the {start/stop} keywords of
|
||||
the "run"_run.html command.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:] none
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -933,7 +933,7 @@ funcs
|
|||
functionalities
|
||||
functionals
|
||||
funroll
|
||||
für
|
||||
fuer
|
||||
fx
|
||||
fy
|
||||
fz
|
||||
|
|
|
|||
Loading…
Reference in New Issue