Merge branch 'master' into zeeman-rework
This commit is contained in:
Axel Kohlmeyer
@ -9,9 +9,7 @@ if(BUILD_DOC)
|
||||
|
||||
set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv)
|
||||
|
||||
file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.txt)
|
||||
file(GLOB PDF_EXTRA_SOURCES ${LAMMPS_DOC_DIR}/src/lammps_commands*.txt ${LAMMPS_DOC_DIR}/src/lammps_support.txt ${LAMMPS_DOC_DIR}/src/lammps_tutorials.txt)
|
||||
list(REMOVE_ITEM DOC_SOURCES ${PDF_EXTRA_SOURCES})
|
||||
file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
|
||||
|
||||
add_custom_command(
|
||||
OUTPUT docenv
|
||||
@ -28,25 +26,10 @@ if(BUILD_DOC)
|
||||
COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
|
||||
)
|
||||
|
||||
set(RST_FILES "")
|
||||
set(RST_DIR ${CMAKE_BINARY_DIR}/rst)
|
||||
file(MAKE_DIRECTORY ${RST_DIR})
|
||||
foreach(TXT_FILE ${DOC_SOURCES})
|
||||
get_filename_component(FILENAME ${TXT_FILE} NAME_WE)
|
||||
set(RST_FILE ${RST_DIR}/${FILENAME}.rst)
|
||||
list(APPEND RST_FILES ${RST_FILE})
|
||||
add_custom_command(
|
||||
OUTPUT ${RST_FILE}
|
||||
DEPENDS requirements.txt docenv ${TXT_FILE}
|
||||
COMMAND ${DOCENV_BINARY_DIR}/txt2rst -o ${RST_DIR} ${TXT_FILE}
|
||||
)
|
||||
endforeach()
|
||||
|
||||
add_custom_command(
|
||||
OUTPUT html
|
||||
DEPENDS ${RST_FILES}
|
||||
COMMAND ${CMAKE_COMMAND} -E copy_directory ${LAMMPS_DOC_DIR}/src ${RST_DIR}
|
||||
COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -j ${NPROCS} -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${RST_DIR} html
|
||||
DEPENDS ${DOC_SOURCES} docenv requirements.txt
|
||||
COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -j ${NPROCS} -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${LAMMPS_DOC_DIR}/src html
|
||||
)
|
||||
|
||||
add_custom_target(
|
||||
|
||||
43
doc/README
43
doc/README
@ -5,7 +5,7 @@ sub-directories and optionally 2 PDF files and an ePUB file:
|
||||
|
||||
src content files for LAMMPS documentation
|
||||
html HTML version of the LAMMPS manual (see html/Manual.html)
|
||||
tools tools and settings for building the documentation
|
||||
utils utilities and settings for building the documentation
|
||||
Manual.pdf large PDF version of entire manual
|
||||
Developer.pdf small PDF with info about how LAMMPS is structured
|
||||
LAMMPS.epub Manual in ePUB format
|
||||
@ -25,17 +25,12 @@ the fetched documentation will include those changes (but your source
|
||||
code will not, unless you update your local repository).
|
||||
|
||||
(b) You can build the HTML and PDF files yourself, by typing "make
|
||||
html" followed by "make pdf". Note that the PDF make requires the
|
||||
HTML files already exist. This requires various tools including
|
||||
Sphinx, which the build process will attempt to download and install
|
||||
on your system, if not already available. See more details below.
|
||||
|
||||
(c) You can genererate an older, simpler, less-fancy style of HTML
|
||||
documentation by typing "make old". This will create an "old"
|
||||
directory. This can be useful if (b) does not work on your box for
|
||||
some reason, or you want to quickly view the HTML version of a doc
|
||||
page you have created or edited yourself within the src directory.
|
||||
E.g. if you are planning to submit a new feature to LAMMPS.
|
||||
html" or by "make pdf", respectively. This requires various tools
|
||||
including the Python documentation processing tool Sphinx, which the
|
||||
build process will attempt to download and install on your system into
|
||||
a python virtual environment, if not already available. The PDF file
|
||||
will require a working LaTeX installation with several add-on packages
|
||||
in addition to the Python/Sphinx setup. See more details below.
|
||||
|
||||
----------------
|
||||
|
||||
@ -46,11 +41,10 @@ Options:
|
||||
|
||||
make html # generate HTML in html dir using Sphinx
|
||||
make pdf # generate 2 PDF files (Manual.pdf,Developer.pdf)
|
||||
# in this dir via htmldoc and pdflatex
|
||||
make old # generate old-style HTML pages in old dir via txt2html
|
||||
# in this dir via Sphinx and PDFLaTeX
|
||||
make fetch # fetch HTML doc pages and 2 PDF files from web site
|
||||
# as a tarball and unpack into html dir and 2 PDFs
|
||||
make epub # generate LAMMPS.epub in ePUB format using Sphinx
|
||||
make epub # generate LAMMPS.epub in ePUB format using Sphinx
|
||||
make clean # remove intermediate RST files created by HTML build
|
||||
make clean-all # remove entire build folder and any cached data
|
||||
|
||||
@ -94,8 +88,17 @@ This will install virtualenv from the Python Package Index.
|
||||
|
||||
Installing prerequisites for PDF build
|
||||
|
||||
[TBA]
|
||||
|
||||
Same as for HTML plus a compatible LaTeX installation with
|
||||
support for PDFLaTeX. Also the following LaTeX packages need
|
||||
to be installed (e.g. from texlive):
|
||||
- amsmath
|
||||
- babel
|
||||
- cmap
|
||||
- fncychap
|
||||
- geometry
|
||||
- hyperref
|
||||
- hypcap
|
||||
- times
|
||||
----------------
|
||||
|
||||
Installing prerequisites for epub build
|
||||
@ -103,7 +106,11 @@ Installing prerequisites for epub build
|
||||
## ePUB
|
||||
|
||||
Same as for HTML. This uses the same tools and configuration
|
||||
files as the HTML tree.
|
||||
files as the HTML tree. The ePUB format conversion currently
|
||||
does not support processing mathematical expressions via MathJAX,
|
||||
so there will be limitations on some pages. For the time being
|
||||
until this is resolved, building and using the PDF format file
|
||||
is recommended instead.
|
||||
|
||||
For converting the generated ePUB file to a mobi format file
|
||||
(for e-book readers like Kindle, that cannot read ePUB), you
|
||||
|
||||
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|
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@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = K (\theta - \theta_0)^2 + K_{UB} (r - r_{UB})^2
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
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|
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@ -1,12 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
\begin{eqnarray*}
|
||||
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)
|
||||
\end{eqnarray*}
|
||||
|
||||
\end{document}
|
||||
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|
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@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = K [1 + \cos(\theta)]
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
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|
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@ -1,15 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\pagestyle{empty}
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = K \left[ 1 + \cos(n\theta - \theta_0)\right]
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
|
||||
%%% Local Variables:
|
||||
%%% mode: latex
|
||||
%%% TeX-master: t
|
||||
%%% End:
|
||||
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|
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@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = K [1 - \cos(\theta - \theta_0)]
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
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|
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@ -1,9 +0,0 @@
|
||||
\documentstyle[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E=C\left[ 1-B(-1)^ncos\left( n\theta\right) \right]
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
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|
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@ -1,9 +0,0 @@
|
||||
\documentstyle[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E=-\frac{Umin}{2} \left[ 1+Cos(\theta-\theta_0) \right]
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
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|
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@ -1,13 +0,0 @@
|
||||
\documentstyle[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E=-U_{min}
|
||||
\frac{e^{-a U(\theta,\theta_0)}-1}{e^a-1}
|
||||
\quad\mbox{with}\quad
|
||||
U(\theta,\theta_0)
|
||||
=-0.5 \left(1+\cos(\theta-\theta_0) \right)
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
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|
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@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = K [\cos(\theta) - \cos(\theta_0)]^2
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
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|
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@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
\thispagestyle{empty}
|
||||
$$
|
||||
E = K_{SS} \left(r_{12}-r_{12,0}\right)\left(r_{32}-r_{32,0}\right) + K_{BS0}\left(r_{12}-r_{12,0}\right)\left(\theta-\theta_0\right) + K_{BS1}\left(r_{32}-r_{32,0}\right)\left(\theta-\theta_0\right)
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
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|
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@ -1,10 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
\begin{eqnarray*}
|
||||
-\vec{T_j} & = & \vec{r_{ij}} \times \vec{F_i}\\
|
||||
\vec{F_j} & = & -\vec{F_i} \\
|
||||
\end{eqnarray*}
|
||||
|
||||
\end{document}
|
||||
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|
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@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
\cos\gamma = \frac{\vec{\mu_j}\bullet\vec{r_{ij}}}{\mu_j\,r_{ij}}
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
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|
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@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = K (\cos\gamma - \cos\gamma_0)^2
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
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|
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@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
\vec{T_j} = \frac{2K(\cos\gamma - \cos\gamma_0)}{\mu_j\,r_{ij}}\,
|
||||
\vec{r_{ij}} \times \vec{\mu_j}
|
||||
$$
|
||||
\end{document}
|
||||
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|
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@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = K [C_0 + C_1 \cos ( \theta) + C_2 \cos( 2 \theta) ]
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
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|
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@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = K [ 1.0 + c \cos ( n \theta) ]
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
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|
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@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = K (\theta - \theta_0)^2
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
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|
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@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
\thispagestyle{empty}
|
||||
$$
|
||||
E = K (\theta - \theta_0)^2 \left[ 1 - 0.014(\theta - \theta_0) + 5.6(10)^{-5} (\theta - \theta_0)^2 - 7.0(10)^{-7} (\theta - \theta_0)^3 + 9(10)^{-10} (\theta - \theta_0)^4 \right]
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
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|
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@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4 (\theta - \theta_0)^4
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
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|
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@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = K_2 (r - r_0)^2 + K_3 (r - r_0)^3 + K_4 (r - r_0)^4
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
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|
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@ -1,11 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = -0.5 K R_0^2 \ln \left[ 1 - \left(\frac{r}{R_0}\right)^2\right] +
|
||||
4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
|
||||
\left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
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|
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@ -1,13 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = -0.5 K R_0^2
|
||||
\ln \left[1 -\left( \frac{\left(r - \Delta\right)}{R_0}\right)^2 \right] +
|
||||
4 \epsilon \left[ \left(\frac{\sigma}{\left(r -
|
||||
\Delta\right)}\right)^{12} - \left(\frac{\sigma}{\left(r -
|
||||
\Delta\right)}\right)^6 \right] + \epsilon
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
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|
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@ -1,10 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
\pagestyle{empty}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = K (r^2 - r_0^2)^2
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
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|
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@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = K (r - r_0)^2
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
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|
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@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = \frac{Umin}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right]
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
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|
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@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = \frac{Umin}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right]
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
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|
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@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
\thispagestyle{empty}
|
||||
$$
|
||||
E = K (r - r_0)^2 \left[ 1 - 2.55(r-r_0) + (7/12) 2.55^2(r-r_0)^2 \right]
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
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|
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@ -1,10 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
% E = D \left[ 1 - \exp \left( -\alpha (r - r_0) \right) \right]^2
|
||||
E = D \left[ 1 - e^{-\alpha (r - r_0)} \right]^2
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
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|
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@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = \frac{\epsilon (r - r_0)^2}{ [ \lambda^2 - (r - r_0)^2 ]}
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
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|
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@ -1,10 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
\pagestyle{empty}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = - \frac{\epsilon}{2} \ln \left[ 1 - \left(\frac{r-r0}{\Delta}\right)^2\right]
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 9.3 KiB |
@ -1,11 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = K (r - R_c)^ 2 (r - R_c - B_1) (r - R_c - B_2) + U_0 +
|
||||
4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
|
||||
\left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
@ -32,12 +32,10 @@ install the `openkim-models` package
|
||||
|
||||
If you have problems with the installation you can post issues to
|
||||
`this link <conda_forge_lammps_>`_.
|
||||
|
||||
.. _conda_forge_lammps: https://github.com/conda-forge/lammps-feedstock/issues
|
||||
|
||||
Thanks to Jan Janssen (Max-Planck-Institut für Eisenforschung) for setting
|
||||
Thanks to Jan Janssen (Max-Planck-Institut fuer Eisenforschung) for setting
|
||||
up the Conda capability.
|
||||
|
||||
.. _conda_forge_lammps: https://github.com/conda-forge/lammps-feedstock/issues
|
||||
|
||||
.. _openkim: https://openkim.org
|
||||
|
||||
@ -45,9 +43,6 @@ up the Conda capability.
|
||||
|
||||
.. _mini_conda_install: https://docs.conda.io/en/latest/miniconda.html
|
||||
|
||||
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,22 +1,22 @@
|
||||
.. index:: angle\_style charmm
|
||||
.. index:: angle_style charmm
|
||||
|
||||
angle\_style charmm command
|
||||
===========================
|
||||
angle_style charmm command
|
||||
==========================
|
||||
|
||||
angle\_style charmm/intel command
|
||||
=================================
|
||||
angle_style charmm/intel command
|
||||
================================
|
||||
|
||||
angle\_style charmm/kk command
|
||||
angle_style charmm/kk command
|
||||
=============================
|
||||
|
||||
angle_style charmm/omp command
|
||||
==============================
|
||||
|
||||
angle\_style charmm/omp command
|
||||
===============================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style charmm
|
||||
|
||||
@ -24,7 +24,7 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style charmm
|
||||
angle_coeff 1 300.0 107.0 50.0 3.0
|
||||
@ -34,12 +34,15 @@ Description
|
||||
|
||||
The *charmm* angle style uses the potential
|
||||
|
||||
.. 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
|
||||
|
||||
@ -1,13 +1,13 @@
|
||||
.. index:: atom\_modify
|
||||
.. index:: atom_modify
|
||||
|
||||
atom\_modify command
|
||||
====================
|
||||
atom_modify command
|
||||
===================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
atom_modify keyword values ...
|
||||
|
||||
@ -29,7 +29,7 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
atom_modify map yes
|
||||
atom_modify map hash sort 10000 2.0
|
||||
@ -188,8 +188,3 @@ defined, sorting will be turned off.
|
||||
|
||||
|
||||
**(Meloni)** Meloni, Rosati and Colombo, J Chem Phys, 126, 121102 (2007).
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,13 +1,13 @@
|
||||
.. index:: atom\_style
|
||||
.. index:: atom_style
|
||||
|
||||
atom\_style command
|
||||
===================
|
||||
atom_style command
|
||||
==================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
atom_style style args
|
||||
|
||||
@ -33,7 +33,7 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
atom_style atomic
|
||||
atom_style bond
|
||||
@ -371,8 +371,3 @@ atom\_style atomic
|
||||
|
||||
**(Grime)** Grime and Voth, to appear in J Chem Theory & Computation
|
||||
(2014).
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,19 +1,19 @@
|
||||
.. index:: bond\_style class2
|
||||
.. index:: bond_style class2
|
||||
|
||||
bond\_style class2 command
|
||||
==========================
|
||||
bond_style class2 command
|
||||
=========================
|
||||
|
||||
bond\_style class2/omp command
|
||||
==============================
|
||||
|
||||
bond\_style class2/kk command
|
||||
bond_style class2/omp command
|
||||
=============================
|
||||
|
||||
bond_style class2/kk command
|
||||
============================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_style class2
|
||||
|
||||
@ -21,7 +21,7 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_style class2
|
||||
bond_coeff 1 1.0 100.0 80.0 80.0
|
||||
@ -31,10 +31,12 @@ Description
|
||||
|
||||
The *class2* bond style uses the potential
|
||||
|
||||
.. image:: Eqs/bond_class2.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where r0 is the equilibrium bond distance.
|
||||
E = K_2 (r - r_0)^2 + K_3 (r - r_0)^3 + K_4 (r - r_0)^4
|
||||
|
||||
|
||||
where :math:`r_0` is the equilibrium bond distance.
|
||||
|
||||
See :ref:`(Sun) <bond-Sun>` for a description of the COMPASS class2 force field.
|
||||
|
||||
@ -43,10 +45,10 @@ The following coefficients must be defined for each bond type via the
|
||||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* R0 (distance)
|
||||
* K2 (energy/distance\^2)
|
||||
* K3 (energy/distance\^3)
|
||||
* K4 (energy/distance\^4)
|
||||
* :math:`r_0` (distance)
|
||||
* :math:`K_2` (energy/distance\^2)
|
||||
* :math:`K_3` (energy/distance\^3)
|
||||
* :math:`K_4` (energy/distance\^4)
|
||||
|
||||
|
||||
----------
|
||||
@ -98,8 +100,3 @@ 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:: bond\_coeff
|
||||
.. index:: bond_coeff
|
||||
|
||||
bond\_coeff command
|
||||
===================
|
||||
bond_coeff command
|
||||
==================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_coeff N args
|
||||
|
||||
@ -18,11 +18,11 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_coeff 5 80.0 1.2
|
||||
bond_coeff \* 30.0 1.5 1.0 1.0
|
||||
bond_coeff 1\*4 30.0 1.5 1.0 1.0
|
||||
bond_coeff * 30.0 1.5 1.0 1.0
|
||||
bond_coeff 1*4 30.0 1.5 1.0 1.0
|
||||
bond_coeff 1 harmonic 200.0 1.0
|
||||
|
||||
Description
|
||||
@ -47,9 +47,9 @@ for the same bond type. For example, these commands set the coeffs
|
||||
for all bond types, then overwrite the coeffs for just bond type 2:
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_coeff \* 100.0 1.2
|
||||
bond_coeff * 100.0 1.2
|
||||
bond_coeff 2 200.0 1.2
|
||||
|
||||
A line in a data file that specifies bond coefficients uses the exact
|
||||
@ -97,8 +97,3 @@ Related commands
|
||||
:doc:`bond\_style <bond_style>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,22 +1,22 @@
|
||||
.. index:: bond\_style fene
|
||||
.. index:: bond_style fene
|
||||
|
||||
bond\_style fene command
|
||||
========================
|
||||
bond_style fene command
|
||||
=======================
|
||||
|
||||
bond\_style fene/intel command
|
||||
==============================
|
||||
bond_style fene/intel command
|
||||
=============================
|
||||
|
||||
bond\_style fene/kk command
|
||||
bond_style fene/kk command
|
||||
==========================
|
||||
|
||||
bond_style fene/omp command
|
||||
===========================
|
||||
|
||||
bond\_style fene/omp command
|
||||
============================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_style fene
|
||||
|
||||
@ -24,7 +24,7 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_style fene
|
||||
bond_coeff 1 30.0 1.5 1.0 1.0
|
||||
@ -34,24 +34,26 @@ Description
|
||||
|
||||
The *fene* bond style uses the potential
|
||||
|
||||
.. image:: Eqs/bond_fene.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
E = -0.5 K R_0^2 \ln \left[ 1 - \left(\frac{r}{R_0}\right)^2\right] + 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
|
||||
|
||||
|
||||
to define a finite extensible nonlinear elastic (FENE) potential
|
||||
:ref:`(Kremer) <fene-Kremer>`, used for bead-spring polymer models. The first
|
||||
term is attractive, the 2nd Lennard-Jones term is repulsive. The
|
||||
first term extends to R0, the maximum extent of the bond. The 2nd
|
||||
term is cutoff at 2\^(1/6) sigma, the minimum of the LJ potential.
|
||||
first term extends to :math:`R_0`, the maximum extent of the bond. The 2nd
|
||||
term is cutoff at :math:`2^\frac{1}{6} \sigma`, the minimum of the LJ potential.
|
||||
|
||||
The following coefficients must be defined for each bond type via the
|
||||
:doc:`bond\_coeff <bond_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/distance\^2)
|
||||
* R0 (distance)
|
||||
* epsilon (energy)
|
||||
* sigma (distance)
|
||||
* :math:`K` (energy/distance\^2)
|
||||
* :math:`R_0` (distance)
|
||||
* :math:`\epsilon` (energy)
|
||||
* :math:`\sigma` (distance)
|
||||
|
||||
|
||||
----------
|
||||
@ -107,8 +109,3 @@ Related commands
|
||||
|
||||
|
||||
**(Kremer)** Kremer, Grest, J Chem Phys, 92, 5057 (1990).
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,16 +1,16 @@
|
||||
.. index:: bond\_style fene/expand
|
||||
.. index:: bond_style fene/expand
|
||||
|
||||
bond\_style fene/expand command
|
||||
===============================
|
||||
bond_style fene/expand command
|
||||
==============================
|
||||
|
||||
bond\_style fene/expand/omp command
|
||||
===================================
|
||||
bond_style fene/expand/omp command
|
||||
==================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_style fene/expand
|
||||
|
||||
@ -18,7 +18,7 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_style fene/expand
|
||||
bond_coeff 1 30.0 1.5 1.0 1.0 0.5
|
||||
@ -28,29 +28,30 @@ Description
|
||||
|
||||
The *fene/expand* bond style uses the potential
|
||||
|
||||
.. image:: Eqs/bond_fene_expand.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
E = -0.5 K R_0^2 \ln \left[1 -\left( \frac{\left(r - \Delta\right)}{R_0}\right)^2 \right] + 4 \epsilon \left[ \left(\frac{\sigma}{\left(r - \Delta\right)}\right)^{12} - \left(\frac{\sigma}{\left(r - \Delta\right)}\right)^6 \right] + \epsilon
|
||||
|
||||
|
||||
to define a finite extensible nonlinear elastic (FENE) potential
|
||||
:ref:`(Kremer) <feneexpand-Kremer>`, used for bead-spring polymer models. The first
|
||||
term is attractive, the 2nd Lennard-Jones term is repulsive.
|
||||
|
||||
The *fene/expand* bond style is similar to *fene* except that an extra
|
||||
shift factor of delta (positive or negative) is added to *r* to
|
||||
shift factor of :math:`\Delta` (positive or negative) is added to :math:`r` to
|
||||
effectively change the bead size of the bonded atoms. The first term
|
||||
now extends to R0 + delta and the 2nd term is cutoff at 2\^(1/6) sigma
|
||||
+ delta.
|
||||
now extends to :math:`R_0 + \Delta` and the 2nd term is cutoff at :math:`2^\frac{1}{6} \sigma + \Delta`.
|
||||
|
||||
The following coefficients must be defined for each bond type via the
|
||||
:doc:`bond\_coeff <bond_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/distance\^2)
|
||||
* R0 (distance)
|
||||
* epsilon (energy)
|
||||
* sigma (distance)
|
||||
* delta (distance)
|
||||
* :math:`K` (energy/distance\^2)
|
||||
* :math:`R_0` (distance)
|
||||
* :math:`\epsilon` (energy)
|
||||
* :math:`\sigma` (distance)
|
||||
* :math:`\Delta` (distance)
|
||||
|
||||
|
||||
----------
|
||||
@ -106,8 +107,3 @@ Related commands
|
||||
|
||||
|
||||
**(Kremer)** Kremer, Grest, J Chem Phys, 92, 5057 (1990).
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,16 +1,16 @@
|
||||
.. index:: bond\_style gromos
|
||||
.. index:: bond_style gromos
|
||||
|
||||
bond\_style gromos command
|
||||
==========================
|
||||
bond_style gromos command
|
||||
=========================
|
||||
|
||||
bond\_style gromos/omp command
|
||||
==============================
|
||||
bond_style gromos/omp command
|
||||
=============================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_style gromos
|
||||
|
||||
@ -18,7 +18,7 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_style gromos
|
||||
bond_coeff 5 80.0 1.2
|
||||
@ -28,19 +28,21 @@ Description
|
||||
|
||||
The *gromos* bond style uses the potential
|
||||
|
||||
.. image:: Eqs/bond_gromos.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where r0 is the equilibrium bond distance. Note that the usual 1/4
|
||||
factor is included in K.
|
||||
E = K (r^2 - r_0^2)^2
|
||||
|
||||
|
||||
where :math:`r_0` is the equilibrium bond distance. Note that the usual 1/4
|
||||
factor is included in :math:`K`.
|
||||
|
||||
The following coefficients must be defined for each bond type via the
|
||||
:doc:`bond\_coeff <bond_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/distance\^4)
|
||||
* r0 (distance)
|
||||
* :math:`K` (energy/distance\^4)
|
||||
* :math:`r_0` (distance)
|
||||
|
||||
|
||||
----------
|
||||
@ -82,8 +84,3 @@ Related commands
|
||||
:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,22 +1,22 @@
|
||||
.. index:: bond\_style harmonic
|
||||
.. index:: bond_style harmonic
|
||||
|
||||
bond\_style harmonic command
|
||||
============================
|
||||
bond_style harmonic command
|
||||
===========================
|
||||
|
||||
bond\_style harmonic/intel command
|
||||
==================================
|
||||
bond_style harmonic/intel command
|
||||
=================================
|
||||
|
||||
bond\_style harmonic/kk command
|
||||
bond_style harmonic/kk command
|
||||
==============================
|
||||
|
||||
bond_style harmonic/omp command
|
||||
===============================
|
||||
|
||||
bond\_style harmonic/omp command
|
||||
================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_style harmonic
|
||||
|
||||
@ -24,7 +24,7 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 5 80.0 1.2
|
||||
@ -34,19 +34,21 @@ Description
|
||||
|
||||
The *harmonic* bond style uses the potential
|
||||
|
||||
.. image:: Eqs/bond_harmonic.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where r0 is the equilibrium bond distance. Note that the usual 1/2
|
||||
factor is included in K.
|
||||
E = K (r - r_0)^2
|
||||
|
||||
|
||||
where :math:`r_0` is the equilibrium bond distance. Note that the usual 1/2
|
||||
factor is included in :math:`K`.
|
||||
|
||||
The following coefficients must be defined for each bond type via the
|
||||
:doc:`bond\_coeff <bond_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/distance\^2)
|
||||
* r0 (distance)
|
||||
* :math:`K` (energy/distance\^2)
|
||||
* :math:`r_0` (distance)
|
||||
|
||||
|
||||
----------
|
||||
@ -88,8 +90,3 @@ Related commands
|
||||
:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
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Reference in New Issue
Block a user