diff --git a/cmake/Modules/Documentation.cmake b/cmake/Modules/Documentation.cmake index 99f570820a..feff66a9b2 100644 --- a/cmake/Modules/Documentation.cmake +++ b/cmake/Modules/Documentation.cmake @@ -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( diff --git a/doc/README b/doc/README index 6db4ba3ca7..1416584eed 100644 --- a/doc/README +++ b/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 diff --git a/doc/txt/Developer/.gitignore b/doc/src/Developer/.gitignore similarity index 100% rename from doc/txt/Developer/.gitignore rename to doc/src/Developer/.gitignore diff --git a/doc/txt/Developer/classes.fig b/doc/src/Developer/classes.fig similarity index 100% rename from doc/txt/Developer/classes.fig rename to doc/src/Developer/classes.fig diff --git a/doc/txt/Developer/classes.pdf b/doc/src/Developer/classes.pdf similarity index 100% rename from doc/txt/Developer/classes.pdf rename to doc/src/Developer/classes.pdf diff --git a/doc/txt/Developer/developer.tex b/doc/src/Developer/developer.tex similarity index 100% rename from doc/txt/Developer/developer.tex rename to doc/src/Developer/developer.tex diff --git a/doc/src/Eqs/angle_charmm.jpg b/doc/src/Eqs/angle_charmm.jpg deleted file mode 100644 index c6e6c297d2..0000000000 Binary files a/doc/src/Eqs/angle_charmm.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_charmm.tex b/doc/src/Eqs/angle_charmm.tex deleted file mode 100644 index 00b37ba335..0000000000 --- a/doc/src/Eqs/angle_charmm.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = K (\theta - \theta_0)^2 + K_{UB} (r - r_{UB})^2 -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/angle_class2.jpg b/doc/src/Eqs/angle_class2.jpg deleted file mode 100644 index f0f2a5152e..0000000000 Binary files a/doc/src/Eqs/angle_class2.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_class2.tex b/doc/src/Eqs/angle_class2.tex deleted file mode 100644 index e5a542e87a..0000000000 --- a/doc/src/Eqs/angle_class2.tex +++ /dev/null @@ -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} \ No newline at end of file diff --git a/doc/src/Eqs/angle_cosine.jpg b/doc/src/Eqs/angle_cosine.jpg deleted file mode 100644 index 23b9b64310..0000000000 Binary files a/doc/src/Eqs/angle_cosine.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_cosine.tex b/doc/src/Eqs/angle_cosine.tex deleted file mode 100644 index e766676099..0000000000 --- a/doc/src/Eqs/angle_cosine.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = K [1 + \cos(\theta)] -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/angle_cosine_buck6d.jpg b/doc/src/Eqs/angle_cosine_buck6d.jpg deleted file mode 100644 index 69b668c086..0000000000 Binary files a/doc/src/Eqs/angle_cosine_buck6d.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_cosine_buck6d.tex b/doc/src/Eqs/angle_cosine_buck6d.tex deleted file mode 100644 index 49be2fc8c2..0000000000 --- a/doc/src/Eqs/angle_cosine_buck6d.tex +++ /dev/null @@ -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: diff --git a/doc/src/Eqs/angle_cosine_delta.jpg b/doc/src/Eqs/angle_cosine_delta.jpg deleted file mode 100644 index c6e90bb2c5..0000000000 Binary files a/doc/src/Eqs/angle_cosine_delta.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_cosine_delta.tex b/doc/src/Eqs/angle_cosine_delta.tex deleted file mode 100644 index 918e9e5046..0000000000 --- a/doc/src/Eqs/angle_cosine_delta.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = K [1 - \cos(\theta - \theta_0)] -$$ - -\end{document} diff --git a/doc/src/Eqs/angle_cosine_periodic.jpg b/doc/src/Eqs/angle_cosine_periodic.jpg deleted file mode 100644 index a9d7d50cb3..0000000000 Binary files a/doc/src/Eqs/angle_cosine_periodic.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_cosine_periodic.tex b/doc/src/Eqs/angle_cosine_periodic.tex deleted file mode 100644 index 69aa1bba6a..0000000000 --- a/doc/src/Eqs/angle_cosine_periodic.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ -E=C\left[ 1-B(-1)^ncos\left( n\theta\right) \right] -$$ - -\end{document} diff --git a/doc/src/Eqs/angle_cosine_shift.jpg b/doc/src/Eqs/angle_cosine_shift.jpg deleted file mode 100644 index d9929939c8..0000000000 Binary files a/doc/src/Eqs/angle_cosine_shift.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_cosine_shift.tex b/doc/src/Eqs/angle_cosine_shift.tex deleted file mode 100644 index e795d6beff..0000000000 --- a/doc/src/Eqs/angle_cosine_shift.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ -E=-\frac{Umin}{2} \left[ 1+Cos(\theta-\theta_0) \right] -$$ - -\end{document} diff --git a/doc/src/Eqs/angle_cosine_shift_exp.jpg b/doc/src/Eqs/angle_cosine_shift_exp.jpg deleted file mode 100644 index 294986de4b..0000000000 Binary files a/doc/src/Eqs/angle_cosine_shift_exp.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_cosine_shift_exp.tex b/doc/src/Eqs/angle_cosine_shift_exp.tex deleted file mode 100644 index 4afa01356c..0000000000 --- a/doc/src/Eqs/angle_cosine_shift_exp.tex +++ /dev/null @@ -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} diff --git a/doc/src/Eqs/angle_cosine_squared.jpg b/doc/src/Eqs/angle_cosine_squared.jpg deleted file mode 100644 index b992398b7d..0000000000 Binary files a/doc/src/Eqs/angle_cosine_squared.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_cosine_squared.tex b/doc/src/Eqs/angle_cosine_squared.tex deleted file mode 100644 index 57ae47ae45..0000000000 --- a/doc/src/Eqs/angle_cosine_squared.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = K [\cos(\theta) - \cos(\theta_0)]^2 -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/angle_cross.jpg b/doc/src/Eqs/angle_cross.jpg deleted file mode 100644 index b0f3fcf83a..0000000000 Binary files a/doc/src/Eqs/angle_cross.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_cross.tex b/doc/src/Eqs/angle_cross.tex deleted file mode 100644 index 9d1fdcb7f8..0000000000 --- a/doc/src/Eqs/angle_cross.tex +++ /dev/null @@ -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} diff --git a/doc/src/Eqs/angle_dipole_couple.jpg b/doc/src/Eqs/angle_dipole_couple.jpg deleted file mode 100644 index f16849b2f9..0000000000 Binary files a/doc/src/Eqs/angle_dipole_couple.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_dipole_couple.tex b/doc/src/Eqs/angle_dipole_couple.tex deleted file mode 100644 index a857d83d7a..0000000000 --- a/doc/src/Eqs/angle_dipole_couple.tex +++ /dev/null @@ -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} diff --git a/doc/src/Eqs/angle_dipole_gamma.jpg b/doc/src/Eqs/angle_dipole_gamma.jpg deleted file mode 100644 index 4bf618e252..0000000000 Binary files a/doc/src/Eqs/angle_dipole_gamma.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_dipole_gamma.tex b/doc/src/Eqs/angle_dipole_gamma.tex deleted file mode 100644 index 965b74ad96..0000000000 --- a/doc/src/Eqs/angle_dipole_gamma.tex +++ /dev/null @@ -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} \ No newline at end of file diff --git a/doc/src/Eqs/angle_dipole_potential.jpg b/doc/src/Eqs/angle_dipole_potential.jpg deleted file mode 100644 index b1285e8957..0000000000 Binary files a/doc/src/Eqs/angle_dipole_potential.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_dipole_potential.tex b/doc/src/Eqs/angle_dipole_potential.tex deleted file mode 100644 index 8949835eb7..0000000000 --- a/doc/src/Eqs/angle_dipole_potential.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = K (\cos\gamma - \cos\gamma_0)^2 -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/angle_dipole_torque.jpg b/doc/src/Eqs/angle_dipole_torque.jpg deleted file mode 100644 index 996a9df3cb..0000000000 Binary files a/doc/src/Eqs/angle_dipole_torque.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_dipole_torque.tex b/doc/src/Eqs/angle_dipole_torque.tex deleted file mode 100644 index 9527459fdc..0000000000 --- a/doc/src/Eqs/angle_dipole_torque.tex +++ /dev/null @@ -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} \ No newline at end of file diff --git a/doc/src/Eqs/angle_fourier.jpg b/doc/src/Eqs/angle_fourier.jpg deleted file mode 100644 index e748e67430..0000000000 Binary files a/doc/src/Eqs/angle_fourier.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_fourier.tex b/doc/src/Eqs/angle_fourier.tex deleted file mode 100644 index f7f76462e3..0000000000 --- a/doc/src/Eqs/angle_fourier.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = K [C_0 + C_1 \cos ( \theta) + C_2 \cos( 2 \theta) ] -$$ - -\end{document} diff --git a/doc/src/Eqs/angle_fourier_simple.jpg b/doc/src/Eqs/angle_fourier_simple.jpg deleted file mode 100644 index 6c9297b970..0000000000 Binary files a/doc/src/Eqs/angle_fourier_simple.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_fourier_simple.tex b/doc/src/Eqs/angle_fourier_simple.tex deleted file mode 100644 index 3228315a13..0000000000 --- a/doc/src/Eqs/angle_fourier_simple.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = K [ 1.0 + c \cos ( n \theta) ] -$$ - -\end{document} diff --git a/doc/src/Eqs/angle_harmonic.jpg b/doc/src/Eqs/angle_harmonic.jpg deleted file mode 100644 index 352be0b544..0000000000 Binary files a/doc/src/Eqs/angle_harmonic.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_harmonic.tex b/doc/src/Eqs/angle_harmonic.tex deleted file mode 100644 index c566376b5b..0000000000 --- a/doc/src/Eqs/angle_harmonic.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = K (\theta - \theta_0)^2 -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/angle_mm3.jpg b/doc/src/Eqs/angle_mm3.jpg deleted file mode 100644 index 5b9f3e34f0..0000000000 Binary files a/doc/src/Eqs/angle_mm3.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_mm3.tex b/doc/src/Eqs/angle_mm3.tex deleted file mode 100644 index e2d96f2d69..0000000000 --- a/doc/src/Eqs/angle_mm3.tex +++ /dev/null @@ -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} diff --git a/doc/src/Eqs/angle_quartic.jpg b/doc/src/Eqs/angle_quartic.jpg deleted file mode 100644 index 744ce7a35f..0000000000 Binary files a/doc/src/Eqs/angle_quartic.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_quartic.tex b/doc/src/Eqs/angle_quartic.tex deleted file mode 100644 index ff9ff9a7dc..0000000000 --- a/doc/src/Eqs/angle_quartic.tex +++ /dev/null @@ -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} diff --git a/doc/src/Eqs/bond_class2.jpg b/doc/src/Eqs/bond_class2.jpg deleted file mode 100644 index 493048100e..0000000000 Binary files a/doc/src/Eqs/bond_class2.jpg and /dev/null differ diff --git a/doc/src/Eqs/bond_class2.tex b/doc/src/Eqs/bond_class2.tex deleted file mode 100644 index 0735b61025..0000000000 --- a/doc/src/Eqs/bond_class2.tex +++ /dev/null @@ -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} \ No newline at end of file diff --git a/doc/src/Eqs/bond_fene.jpg b/doc/src/Eqs/bond_fene.jpg deleted file mode 100644 index e8b909c08f..0000000000 Binary files a/doc/src/Eqs/bond_fene.jpg and /dev/null differ diff --git a/doc/src/Eqs/bond_fene.tex b/doc/src/Eqs/bond_fene.tex deleted file mode 100644 index ec4dd8efa2..0000000000 --- a/doc/src/Eqs/bond_fene.tex +++ /dev/null @@ -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} \ No newline at end of file diff --git a/doc/src/Eqs/bond_fene_expand.jpg b/doc/src/Eqs/bond_fene_expand.jpg deleted file mode 100644 index 1d04acec32..0000000000 Binary files a/doc/src/Eqs/bond_fene_expand.jpg and /dev/null differ diff --git a/doc/src/Eqs/bond_fene_expand.tex b/doc/src/Eqs/bond_fene_expand.tex deleted file mode 100644 index 5fd96e7ad5..0000000000 --- a/doc/src/Eqs/bond_fene_expand.tex +++ /dev/null @@ -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} diff --git a/doc/src/Eqs/bond_gromos.jpg b/doc/src/Eqs/bond_gromos.jpg deleted file mode 100644 index 479e6b2d3b..0000000000 Binary files a/doc/src/Eqs/bond_gromos.jpg and /dev/null differ diff --git a/doc/src/Eqs/bond_gromos.tex b/doc/src/Eqs/bond_gromos.tex deleted file mode 100644 index 2cd8c39535..0000000000 --- a/doc/src/Eqs/bond_gromos.tex +++ /dev/null @@ -1,10 +0,0 @@ -\documentclass[12pt]{article} -\pagestyle{empty} - -\begin{document} - -$$ - E = K (r^2 - r_0^2)^2 -$$ - -\end{document} diff --git a/doc/src/Eqs/bond_harmonic.jpg b/doc/src/Eqs/bond_harmonic.jpg deleted file mode 100644 index fe9ef5619b..0000000000 Binary files a/doc/src/Eqs/bond_harmonic.jpg and /dev/null differ diff --git a/doc/src/Eqs/bond_harmonic.tex b/doc/src/Eqs/bond_harmonic.tex deleted file mode 100644 index 2461086898..0000000000 --- a/doc/src/Eqs/bond_harmonic.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = K (r - r_0)^2 -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/bond_harmonic_shift.jpg b/doc/src/Eqs/bond_harmonic_shift.jpg deleted file mode 100644 index 3e66d853a5..0000000000 Binary files a/doc/src/Eqs/bond_harmonic_shift.jpg and /dev/null differ diff --git a/doc/src/Eqs/bond_harmonic_shift.tex b/doc/src/Eqs/bond_harmonic_shift.tex deleted file mode 100644 index 3daa16724f..0000000000 --- a/doc/src/Eqs/bond_harmonic_shift.tex +++ /dev/null @@ -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} \ No newline at end of file diff --git a/doc/src/Eqs/bond_harmonic_shift_cut.jpg b/doc/src/Eqs/bond_harmonic_shift_cut.jpg deleted file mode 100644 index 06640e4fe0..0000000000 Binary files a/doc/src/Eqs/bond_harmonic_shift_cut.jpg and /dev/null differ diff --git a/doc/src/Eqs/bond_harmonic_shift_cut.tex b/doc/src/Eqs/bond_harmonic_shift_cut.tex deleted file mode 100644 index 3daa16724f..0000000000 --- a/doc/src/Eqs/bond_harmonic_shift_cut.tex +++ /dev/null @@ -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} \ No newline at end of file diff --git a/doc/src/Eqs/bond_mm3.jpg b/doc/src/Eqs/bond_mm3.jpg deleted file mode 100644 index 2c17739db5..0000000000 Binary files a/doc/src/Eqs/bond_mm3.jpg and /dev/null differ diff --git a/doc/src/Eqs/bond_mm3.tex b/doc/src/Eqs/bond_mm3.tex deleted file mode 100644 index 549500ebac..0000000000 --- a/doc/src/Eqs/bond_mm3.tex +++ /dev/null @@ -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} diff --git a/doc/src/Eqs/bond_morse.jpg b/doc/src/Eqs/bond_morse.jpg deleted file mode 100644 index 6795c9e527..0000000000 Binary files a/doc/src/Eqs/bond_morse.jpg and /dev/null differ diff --git a/doc/src/Eqs/bond_morse.tex b/doc/src/Eqs/bond_morse.tex deleted file mode 100644 index a0d7a89961..0000000000 --- a/doc/src/Eqs/bond_morse.tex +++ /dev/null @@ -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} \ No newline at end of file diff --git a/doc/src/Eqs/bond_nonlinear.jpg b/doc/src/Eqs/bond_nonlinear.jpg deleted file mode 100644 index 0f18d8e73f..0000000000 Binary files a/doc/src/Eqs/bond_nonlinear.jpg and /dev/null differ diff --git a/doc/src/Eqs/bond_nonlinear.tex b/doc/src/Eqs/bond_nonlinear.tex deleted file mode 100644 index b8cdc96169..0000000000 --- a/doc/src/Eqs/bond_nonlinear.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = \frac{\epsilon (r - r_0)^2}{ [ \lambda^2 - (r - r_0)^2 ]} -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/bond_oxdna_fene.jpg b/doc/src/Eqs/bond_oxdna_fene.jpg deleted file mode 100644 index 3d1157a29a..0000000000 Binary files a/doc/src/Eqs/bond_oxdna_fene.jpg and /dev/null differ diff --git a/doc/src/Eqs/bond_oxdna_fene.tex b/doc/src/Eqs/bond_oxdna_fene.tex deleted file mode 100644 index ba7248e20b..0000000000 --- a/doc/src/Eqs/bond_oxdna_fene.tex +++ /dev/null @@ -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} diff --git a/doc/src/Eqs/bond_quartic.jpg b/doc/src/Eqs/bond_quartic.jpg deleted file mode 100644 index 9d092883b2..0000000000 Binary files a/doc/src/Eqs/bond_quartic.jpg and /dev/null differ diff --git a/doc/src/Eqs/bond_quartic.tex b/doc/src/Eqs/bond_quartic.tex deleted file mode 100644 index 0d0cceb353..0000000000 --- a/doc/src/Eqs/bond_quartic.tex +++ /dev/null @@ -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} \ No newline at end of file diff --git a/doc/src/Install_conda.rst b/doc/src/Install_conda.rst index 04b8054353..33188e2540 100644 --- a/doc/src/Install_conda.rst +++ b/doc/src/Install_conda.rst @@ -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: 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 diff --git a/doc/src/angle_charmm.rst b/doc/src/angle_charmm.rst index 561e6cfab3..92ab8b5ea3 100644 --- a/doc/src/angle_charmm.rst +++ b/doc/src/angle_charmm.rst @@ -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) ` 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 ` or :doc:`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 diff --git a/doc/src/angle_class2.rst b/doc/src/angle_class2.rst index c7e5eb13ef..9d1ff8e8e7 100644 --- a/doc/src/angle_class2.rst +++ b/doc/src/angle_class2.rst @@ -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) ` 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 ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`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 ` +For the :math:`E_{bb}` formula, each line in a :doc:`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 ` +For the :math:`E_{ba}` formula, each line in a :doc:`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 diff --git a/doc/src/angle_coeff.rst b/doc/src/angle_coeff.rst index 1e54f69051..5f9a71371a 100644 --- a/doc/src/angle_coeff.rst +++ b/doc/src/angle_coeff.rst @@ -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 ` command or in a restart file. +:doc:`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 ` 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 ` 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 ` is an exception to this +The :doc:`angle_style 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 ` doc page. They are also listed in more +:doc:`angle_style ` doc page. They are also listed in more compact form on the :ref:`Commands 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 ` command. ---------- @@ -90,8 +90,8 @@ Restrictions This command must come after the simulation box is defined by a -:doc:`read\_data `, :doc:`read\_restart `, or -:doc:`create\_box ` command. +:doc:`read_data `, :doc:`read_restart `, or +:doc:`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 ` +:doc:`angle_style ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/angle_cosine.rst b/doc/src/angle_cosine.rst index b90b63571c..68bfdbb82b 100644 --- a/doc/src/angle_cosine.rst +++ b/doc/src/angle_cosine.rst @@ -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 ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands: -* K (energy) +* :math:`K` (energy) ---------- @@ -83,8 +85,3 @@ Related commands :doc:`angle\_coeff ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/angle_cosine_buck6d.rst b/doc/src/angle_cosine_buck6d.rst index 7bcc7f21e2..2d00863b02 100644 --- a/doc/src/angle_cosine_buck6d.rst +++ b/doc/src/angle_cosine_buck6d.rst @@ -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 ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`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 ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/angle_cosine_delta.rst b/doc/src/angle_cosine_delta.rst index be8f209145..9af93cb06a 100644 --- a/doc/src/angle_cosine_delta.rst +++ b/doc/src/angle_cosine_delta.rst @@ -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 ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`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 `, :doc:`angle\_style cosine/squared ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/angle_cosine_periodic.rst b/doc/src/angle_cosine_periodic.rst index 43e5c0a4bf..caaf15007a 100644 --- a/doc/src/angle_cosine_periodic.rst +++ b/doc/src/angle_cosine_periodic.rst @@ -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 ` 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) ` 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 ` or :doc:`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 diff --git a/doc/src/angle_cosine_shift.rst b/doc/src/angle_cosine_shift.rst index 7bceb571b4..bd7b6416c7 100644 --- a/doc/src/angle_cosine_shift.rst +++ b/doc/src/angle_cosine_shift.rst @@ -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 ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`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 ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/angle_cosine_shift_exp.rst b/doc/src/angle_cosine_shift_exp.rst index b4af85352d..331ccb9da7 100644 --- a/doc/src/angle_cosine_shift_exp.rst +++ b/doc/src/angle_cosine_shift_exp.rst @@ -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 ` or :doc:`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 ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/angle_cosine_squared.rst b/doc/src/angle_cosine_squared.rst index 694e7ac316..b1a516880d 100644 --- a/doc/src/angle_cosine_squared.rst +++ b/doc/src/angle_cosine_squared.rst @@ -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 ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`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 ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/angle_cross.rst b/doc/src/angle_cross.rst index 6c79776493..7dcff0264f 100644 --- a/doc/src/angle_cross.rst +++ b/doc/src/angle_cross.rst @@ -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 ` or :doc:`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 ` **Default:** none - - ----------- - - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/angle_dipole.rst b/doc/src/angle_dipole.rst index dac03c03b5..351572cc22 100644 --- a/doc/src/angle_dipole.rst +++ b/doc/src/angle_dipole.rst @@ -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) `. 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) `: -.. 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 ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`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 ` 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 diff --git a/doc/src/angle_fourier.rst b/doc/src/angle_fourier.rst index c974081d92..c814b7224e 100644 --- a/doc/src/angle_fourier.rst +++ b/doc/src/angle_fourier.rst @@ -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 ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`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 ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/angle_fourier_simple.rst b/doc/src/angle_fourier_simple.rst index cea83b2fdf..5ad8b386d0 100644 --- a/doc/src/angle_fourier_simple.rst +++ b/doc/src/angle_fourier_simple.rst @@ -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 ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`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 ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/angle_harmonic.rst b/doc/src/angle_harmonic.rst index 87b71ad9ad..1066621729 100644 --- a/doc/src/angle_harmonic.rst +++ b/doc/src/angle_harmonic.rst @@ -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 ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`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 ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/angle_hybrid.rst b/doc/src/angle_hybrid.rst index e31df56e72..f685beacc8 100644 --- a/doc/src/angle_hybrid.rst +++ b/doc/src/angle_hybrid.rst @@ -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 ` +of angle type to style is made via the :doc:`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 ` 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 ` command, then the same rule applies. +:doc:`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 ` 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 `. 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 ` commands. Related commands """""""""""""""" -:doc:`angle\_coeff ` +:doc:`angle_coeff ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/angle_mm3.rst b/doc/src/angle_mm3.rst index 50786363b2..7cf7f9e720 100644 --- a/doc/src/angle_mm3.rst +++ b/doc/src/angle_mm3.rst @@ -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) ` -.. 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 ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`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 ` **Default:** none - - ----------- - - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/angle_none.rst b/doc/src/angle_none.rst index a558096211..e848391932 100644 --- a/doc/src/angle_none.rst +++ b/doc/src/angle_none.rst @@ -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 ` command. +read by the :doc:`read_data ` command. -See the :doc:`angle\_style zero ` command for a way to +See the :doc:`angle_style zero ` command for a way to calculate angle statistics, but compute no angle interactions. Restrictions """""""""""" - none + +none Related commands """""""""""""""" -:doc:`angle\_style zero ` +:doc:`angle_style zero ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/angle_quartic.rst b/doc/src/angle_quartic.rst index 88773bbca8..104c0be802 100644 --- a/doc/src/angle_quartic.rst +++ b/doc/src/angle_quartic.rst @@ -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 ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`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 ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/angle_sdk.rst b/doc/src/angle_sdk.rst index 01342ad8d4..0af22a5372 100644 --- a/doc/src/angle_sdk.rst +++ b/doc/src/angle_sdk.rst @@ -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 `. 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 ` 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 ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/angle_style.rst b/doc/src/angle_style.rst index 6d7c70565b..3e22113d85 100644 --- a/doc/src/angle_style.rst +++ b/doc/src/angle_style.rst @@ -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 ` or :doc:`read\_restart ` command +:doc:`read_data ` or :doc:`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 ` command. +data or restart file or via the :doc:`angle_coeff ` command. All angle potentials store their coefficient data in binary restart -files which means angle\_style and :doc:`angle\_coeff ` +files which means angle_style and :doc:`angle_coeff ` commands do not need to be re-specified in an input script that -restarts a simulation. See the :doc:`read\_restart ` +restarts a simulation. See the :doc:`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 ` command often needs to be used to + :doc:`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 ` command. +specified by the associated :doc:`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 ` command. +specified by the associated :doc:`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 ` +:doc:`angle_coeff ` Default """"""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_style none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/angle_table.rst b/doc/src/angle_table.rst index 8d50ff7fe1..f63cf167d9 100644 --- a/doc/src/angle_table.rst +++ b/doc/src/angle_table.rst @@ -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 The files are read by the :doc:`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 ` command as in the example above. +:doc:`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 ` command. The next line lists (in any +:doc:`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 ` command. Let +specified in the :doc:`angle_style table ` 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 ` +:doc:`angle_coeff ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/angle_zero.rst b/doc/src/angle_zero.rst index e6b485bc95..e5dab4e3a0 100644 --- a/doc/src/angle_zero.rst +++ b/doc/src/angle_zero.rst @@ -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 ` 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 ` command. If no angle style is defined, +:doc:`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 ` commands will only be checked for the angle type number and the rest ignored. -Note that the :doc:`angle\_coeff ` command must be used for +Note that the :doc:`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 `. @@ -51,11 +51,6 @@ Restrictions Related commands """""""""""""""" -:doc:`angle\_style none ` +:doc:`angle_style none ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/atom_modify.rst b/doc/src/atom_modify.rst index ad19f236c1..ac2720d4f2 100644 --- a/doc/src/atom_modify.rst +++ b/doc/src/atom_modify.rst @@ -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 diff --git a/doc/src/atom_style.rst b/doc/src/atom_style.rst index fac90d428b..d2ebc220d6 100644 --- a/doc/src/atom_style.rst +++ b/doc/src/atom_style.rst @@ -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 diff --git a/doc/src/bond_class2.rst b/doc/src/bond_class2.rst index 9a7987fa39..e3098ef6dc 100644 --- a/doc/src/bond_class2.rst +++ b/doc/src/bond_class2.rst @@ -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) ` 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 ` or :doc:`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 diff --git a/doc/src/bond_coeff.rst b/doc/src/bond_coeff.rst index 45b72cce91..281dfc7095 100644 --- a/doc/src/bond_coeff.rst +++ b/doc/src/bond_coeff.rst @@ -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 ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/bond_fene.rst b/doc/src/bond_fene.rst index cd25419544..d952321c20 100644 --- a/doc/src/bond_fene.rst +++ b/doc/src/bond_fene.rst @@ -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) `, 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 ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`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 diff --git a/doc/src/bond_fene_expand.rst b/doc/src/bond_fene_expand.rst index ed19f6fc76..5b5b858330 100644 --- a/doc/src/bond_fene_expand.rst +++ b/doc/src/bond_fene_expand.rst @@ -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) `, 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 ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`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 diff --git a/doc/src/bond_gromos.rst b/doc/src/bond_gromos.rst index 894fe7b87b..5d0a4ab1c6 100644 --- a/doc/src/bond_gromos.rst +++ b/doc/src/bond_gromos.rst @@ -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 ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`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 `, :doc:`delete\_bonds ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/bond_harmonic.rst b/doc/src/bond_harmonic.rst index 4718656b91..d65f0337f0 100644 --- a/doc/src/bond_harmonic.rst +++ b/doc/src/bond_harmonic.rst @@ -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 ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`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 `, :doc:`delete\_bonds ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/bond_harmonic_shift.rst b/doc/src/bond_harmonic_shift.rst index c3c3d7eac1..cc39bda7a7 100644 --- a/doc/src/bond_harmonic_shift.rst +++ b/doc/src/bond_harmonic_shift.rst @@ -1,16 +1,16 @@ -.. index:: bond\_style harmonic/shift +.. index:: bond_style harmonic/shift -bond\_style harmonic/shift command -================================== +bond_style harmonic/shift command +================================= -bond\_style harmonic/shift/omp command -====================================== +bond_style harmonic/shift/omp command +===================================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style harmonic/shift @@ -18,7 +18,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style harmonic/shift bond_coeff 5 10.0 0.5 1.0 @@ -29,23 +29,25 @@ Description The *harmonic/shift* bond style is a shifted harmonic bond that uses the potential -.. image:: Eqs/bond_harmonic_shift.jpg - :align: center +.. math:: -where r0 is the equilibrium bond distance, and rc the critical distance. -The potential is -Umin at r0 and zero at rc. The spring constant is -k = Umin / [ 2 (r0-rc)\^2]. + E = \frac{U_{\text{min}}}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right] + + +where :math:`r_0` is the equilibrium bond distance, and :math:`r_c` the critical distance. +The potential is :math:`-U_{\text{min}}` at :math:`r0` and zero at :math:`r_c`. The spring constant is +:math:`k = U_{\text{min}} / [ 2 (r_0-r_c)^2]`. The following coefficients must be defined for each bond type via the :doc:`bond\_coeff ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands: -* Umin (energy) +* :math:`U_{\text{min}}` (energy) -* r0 (distance) +* :math:`r_0` (distance) -* rc (distance) +* :math:`r_c` (distance) ---------- @@ -88,8 +90,3 @@ Related commands :doc:`bond\_harmonic ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/bond_harmonic_shift_cut.rst b/doc/src/bond_harmonic_shift_cut.rst index f51e061571..459acfdbfb 100644 --- a/doc/src/bond_harmonic_shift_cut.rst +++ b/doc/src/bond_harmonic_shift_cut.rst @@ -1,16 +1,16 @@ -.. index:: bond\_style harmonic/shift/cut +.. index:: bond_style harmonic/shift/cut -bond\_style harmonic/shift/cut command -====================================== +bond_style harmonic/shift/cut command +===================================== -bond\_style harmonic/shift/cut/omp command -========================================== +bond_style harmonic/shift/cut/omp command +========================================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style harmonic/shift/cut @@ -18,7 +18,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style harmonic/shift/cut bond_coeff 5 10.0 0.5 1.0 @@ -29,21 +29,23 @@ Description The *harmonic/shift/cut* bond style is a shifted harmonic bond that uses the potential -.. image:: Eqs/bond_harmonic_shift_cut.jpg - :align: center +.. math:: -where r0 is the equilibrium bond distance, and rc the critical distance. -The bond potential is zero for distances r > rc. The potential is -Umin -at r0 and zero at rc. The spring constant is k = Umin / [ 2 (r0-rc)\^2]. + E = \frac{U_{\text{min}}}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right] + + +where :math:`r_0` is the equilibrium bond distance, and rc the critical distance. +The bond potential is zero for distances :math:`r > r_c`. The potential is :math:`-U_{\text{min}}` +at :math:`r_0` and zero at :math:`r_c`. The spring constant is :math:`k = U_{\text{min}} / [ 2 (r_0-r_c)^2]`. The following coefficients must be defined for each bond type via the :doc:`bond\_coeff ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands: -* Umin (energy) -* r0 (distance) -* rc (distance) +* :math:`U_{\text{min}}` (energy) +* :math:`r_0` (distance) +* :math:`r_c` (distance) ---------- @@ -87,8 +89,3 @@ Related commands :doc:`bond\_harmonic\_shift ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/bond_hybrid.rst b/doc/src/bond_hybrid.rst index 34297c2ff9..6b8175858f 100644 --- a/doc/src/bond_hybrid.rst +++ b/doc/src/bond_hybrid.rst @@ -1,13 +1,13 @@ -.. index:: bond\_style hybrid +.. index:: bond_style hybrid -bond\_style hybrid command -========================== +bond_style hybrid command +========================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style hybrid style1 style2 ... @@ -17,11 +17,11 @@ Examples """""""" -.. parsed-literal:: +.. code-block: LAMMPS bond_style hybrid harmonic fene bond_coeff 1 harmonic 80.0 1.2 - bond_coeff 2\* fene 30.0 1.5 1.0 1.0 + bond_coeff 2* fene 30.0 1.5 1.0 1.0 Description """"""""""" @@ -31,19 +31,19 @@ simulation. A bond style is assigned to each bond type. For example, bonds in a polymer flow (of bond type 1) could be computed with a *fene* potential and bonds in the wall boundary (of bond type 2) could be computed with a *harmonic* potential. The assignment of bond type -to style is made via the :doc:`bond\_coeff ` command or in +to style is made via the :doc:`bond_coeff ` command or in the data file. In the bond\_coeff commands, the name of a bond style must be added after the bond type, with the remaining coefficients being those appropriate to that style. In the example above, the 2 bond\_coeff commands set bonds of bond type 1 to be computed with a *harmonic* -potential with coefficients 80.0, 1.2 for K, r0. All other bond types +potential with coefficients 80.0, 1.2 for :math:`K`, :math:`r_0`. All other bond types (2-N) are computed with a *fene* potential with coefficients 30.0, -1.5, 1.0, 1.0 for K, R0, epsilon, sigma. +1.5, 1.0, 1.0 for :math:`K`, :math:`R_0`, :math:`\epsilon`, :math:`\sigma`. If bond coefficients are specified in the data file read via the -:doc:`read\_data ` command, then the same rule applies. +:doc:`read_data ` command, then the same rule applies. E.g. "harmonic" or "fene" must be added after the bond type, for each line in the "Bond Coeffs" section, e.g. @@ -80,11 +80,6 @@ file, you need to re-specify bond\_coeff commands. Related commands """""""""""""""" -:doc:`bond\_coeff `, :doc:`delete\_bonds ` +:doc:`bond_coeff `, :doc:`delete_bonds ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/bond_mm3.rst b/doc/src/bond_mm3.rst index 4096a34d48..5794592ce4 100644 --- a/doc/src/bond_mm3.rst +++ b/doc/src/bond_mm3.rst @@ -1,13 +1,13 @@ -.. index:: bond\_style mm3 +.. index:: bond_style mm3 -bond\_style mm3 command -======================= +bond_style mm3 command +====================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style mm3 @@ -15,7 +15,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style mm3 bond_coeff 1 100.0 107.0 @@ -26,10 +26,12 @@ Description The *mm3* bond style uses the potential that is anharmonic in the bond as defined in :ref:`(Allinger) ` -.. image:: Eqs/bond_mm3.jpg - :align: center +.. math:: -where r0 is the equilibrium value of the bond, and K is a + E = K (r - r_0)^2 \left[ 1 - 2.55(r-r_0) + (7/12) 2.55^2(r-r_0)^2 \right] + + +where :math:`r_0` is the equilibrium value of the bond, and :math:`K` is a prefactor. The anharmonic prefactors have units angstrom\^(-n): -2.55 angstrom\^(-1) and (7/12)2.55\^2 angstrom\^(-2). The code takes care of the necessary unit conversion for these factors internally. @@ -41,8 +43,8 @@ The following coefficients must be defined for each bond type via the the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands: -* K (energy/distance\^2) -* r0 (distance) +* :math:`K` (energy/distance\^2) +* :math:`r_0` (distance) Restrictions """""""""""" @@ -69,8 +71,3 @@ Related commands **(Allinger)** Allinger, Yuh, Lii, JACS, 111(23), 8551-8566 (1989), - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/bond_morse.rst b/doc/src/bond_morse.rst index 592bc527c3..26471424c5 100644 --- a/doc/src/bond_morse.rst +++ b/doc/src/bond_morse.rst @@ -1,16 +1,16 @@ -.. index:: bond\_style morse +.. index:: bond_style morse -bond\_style morse command -========================= +bond_style morse command +======================== -bond\_style morse/omp command -============================= +bond_style morse/omp command +============================ Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style morse @@ -18,7 +18,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style morse bond_coeff 5 1.0 2.0 1.2 @@ -28,20 +28,22 @@ Description The *morse* bond style uses the potential -.. image:: Eqs/bond_morse.jpg - :align: center +.. math:: -where r0 is the equilibrium bond distance, alpha is a stiffness -parameter, and D determines the depth of the potential well. + E = D \left[ 1 - e^{-\alpha (r - r_0)} \right]^2 + + +where :math:`r_0` is the equilibrium bond distance, :math:`\alpha` is a stiffness +parameter, and :math:`D` determines the depth of the potential well. The following coefficients must be defined for each bond type via the :doc:`bond\_coeff ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands: -* D (energy) -* alpha (inverse distance) -* r0 (distance) +* :math:`D` (energy) +* :math:`\alpha` (inverse distance) +* :math:`r_0` (distance) ---------- @@ -83,8 +85,3 @@ Related commands :doc:`bond\_coeff `, :doc:`delete\_bonds ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/bond_none.rst b/doc/src/bond_none.rst index dde5b6d29a..ac838581be 100644 --- a/doc/src/bond_none.rst +++ b/doc/src/bond_none.rst @@ -1,13 +1,13 @@ -.. index:: bond\_style none +.. index:: bond_style none -bond\_style none command -======================== +bond_style none command +======================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style none @@ -15,7 +15,7 @@ Examples """""""" -.. parsed-literal:: +.. code-blocK:: LAMMPS bond_style none @@ -24,9 +24,9 @@ Description Using a bond style of none means bond forces and energies are not computed, even if pairs of bonded atoms were listed in the data file -read by the :doc:`read\_data ` command. +read by the :doc:`read_data ` command. -See the :doc:`bond\_style zero ` command for a way to +See the :doc:`bond_style zero ` command for a way to calculate bond statistics, but compute no bond interactions. Restrictions @@ -35,11 +35,6 @@ Restrictions **Related commands:** none -:doc:`bond\_style zero ` +:doc:`bond_style zero ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/bond_nonlinear.rst b/doc/src/bond_nonlinear.rst index 4b07a9ba15..0003257e0b 100644 --- a/doc/src/bond_nonlinear.rst +++ b/doc/src/bond_nonlinear.rst @@ -1,16 +1,16 @@ -.. index:: bond\_style nonlinear +.. index:: bond_style nonlinear -bond\_style nonlinear command -============================= +bond_style nonlinear command +============================ -bond\_style nonlinear/omp command -================================= +bond_style nonlinear/omp command +================================ Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style nonlinear @@ -18,7 +18,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style nonlinear bond_coeff 2 100.0 1.1 1.4 @@ -28,20 +28,22 @@ Description The *nonlinear* bond style uses the potential -.. image:: Eqs/bond_nonlinear.jpg - :align: center +.. math:: + + E = \frac{\epsilon (r - r_0)^2}{ [ \lambda^2 - (r - r_0)^2 ]} + to define an anharmonic spring :ref:`(Rector) ` of equilibrium -length r0 and maximum extension lamda. +length :math:`r_0` and maximum extension lamda. The following coefficients must be defined for each bond type via the :doc:`bond\_coeff ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands: -* epsilon (energy) -* r0 (distance) -* lamda (distance) +* :math:`\epsilon` (energy) +* :math:`r_0` (distance) +* :math:`\lambda` (distance) ---------- @@ -93,8 +95,3 @@ Related commands **(Rector)** Rector, Van Swol, Henderson, Molecular Physics, 82, 1009 (1994). - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/bond_oxdna.rst b/doc/src/bond_oxdna.rst index 51692f933b..217b3c85f4 100644 --- a/doc/src/bond_oxdna.rst +++ b/doc/src/bond_oxdna.rst @@ -1,16 +1,16 @@ -.. index:: bond\_style oxdna/fene +.. index:: bond_style oxdna/fene -bond\_style oxdna/fene command +bond_style oxdna/fene command +============================= + +bond_style oxdna2/fene command ============================== -bond\_style oxdna2/fene command -=============================== - Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style oxdna/fene @@ -20,21 +20,23 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style oxdna/fene - bond_coeff \* 2.0 0.25 0.7525 + bond_coeff * 2.0 0.25 0.7525 bond_style oxdna2/fene - bond_coeff \* 2.0 0.25 0.7564 + bond_coeff * 2.0 0.25 0.7564 Description """"""""""" The *oxdna/fene* and *oxdna2/fene* bond styles use the potential -.. image:: Eqs/bond_oxdna_fene.jpg - :align: center +.. math:: + + E = - \frac{\epsilon}{2} \ln \left[ 1 - \left(\frac{r-r_0}{\Delta}\right)^2\right] + to define a modified finite extensible nonlinear elastic (FENE) potential :ref:`(Ouldridge) ` to model the connectivity of the @@ -47,9 +49,9 @@ in the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands: -* epsilon (energy) -* Delta (distance) -* r0 (distance) +* :math:`\epsilon` (energy) +* :math:`\Delta` (distance) +* :math:`r_0` (distance) .. note:: @@ -121,8 +123,3 @@ J. Chem. Phys. 134, 085101 (2011). **(Snodin)** B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015). - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/bond_quartic.rst b/doc/src/bond_quartic.rst index 7aff1308b2..898aa9315a 100644 --- a/doc/src/bond_quartic.rst +++ b/doc/src/bond_quartic.rst @@ -1,16 +1,16 @@ -.. index:: bond\_style quartic +.. index:: bond_style quartic -bond\_style quartic command -=========================== +bond_style quartic command +========================== -bond\_style quartic/omp command -=============================== +bond_style quartic/omp command +============================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style quartic @@ -18,7 +18,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style quartic bond_coeff 2 1200 -0.55 0.25 1.3 34.6878 @@ -28,11 +28,12 @@ Description The *quartic* bond style uses the potential -.. image:: Eqs/bond_quartic.jpg - :align: center +.. math:: + + 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 to define a bond that can be broken as the simulation proceeds (e.g. -due to a polymer being stretched). The sigma and epsilon used in the +due to a polymer being stretched). The :math:`\sigma` and :math:`\epsilon` used in the LJ portion of the formula are both set equal to 1.0 by LAMMPS. The following coefficients must be defined for each bond type via the @@ -40,23 +41,31 @@ The following coefficients must be defined for each bond type via the the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands: -* K (energy/distance\^4) -* B1 (distance) -* B2 (distance) -* Rc (distance) -* U0 (energy) +* :math:`K` (energy/distance\^4) +* :math:`B_1` (distance) +* :math:`B_2` (distance) +* :math:`R_c` (distance) +* :math:`U_0` (energy) This potential was constructed to mimic the FENE bond potential for -coarse-grained polymer chains. When monomers with sigma = epsilon = -1.0 are used, the following choice of parameters gives a quartic -potential that looks nearly like the FENE potential: K = 1200, B1 = --0.55, B2 = 0.25, Rc = 1.3, and U0 = 34.6878. Different parameters -can be specified using the :doc:`bond\_coeff ` command, but -you will need to choose them carefully so they form a suitable bond -potential. +coarse-grained polymer chains. When monomers with :math:`\sigma = \epsilon = 1.0` +are used, the following choice of parameters gives a quartic potential that +looks nearly like the FENE potential: -Rc is the cutoff length at which the bond potential goes smoothly to a -local maximum. If a bond length ever becomes > Rc, LAMMPS "breaks" +.. math:: + + K &= 1200 \\ + B_1 &= -0.55 \\ + B_2 &= 0.25 \\ + R_c &= 1.3 \\ + U_0 &= 34.6878 + +Different parameters can be specified using the :doc:`bond_coeff ` +command, but you will need to choose them carefully so they form a suitable +bond potential. + +:math:`R_c` is the cutoff length at which the bond potential goes smoothly to a +local maximum. If a bond length ever becomes :math:`> R_c`, LAMMPS "breaks" the bond, which means two things. First, the bond potential is turned off by setting its type to 0, and is no longer computed. Second, a pairwise interaction between the two atoms is turned on, since they @@ -75,7 +84,7 @@ Note that when bonds are dumped to a file via the :doc:`dump local ` comma status of broken bonds or permanently delete them, e.g.: -.. parsed-literal:: +.. code-block:: LAMMPS delete_bonds all stats delete_bonds all bond 0 remove @@ -124,8 +133,3 @@ Related commands :doc:`bond\_coeff `, :doc:`delete\_bonds ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/bond_style.rst b/doc/src/bond_style.rst index f912411972..3c5c97b96b 100644 --- a/doc/src/bond_style.rst +++ b/doc/src/bond_style.rst @@ -1,29 +1,27 @@ -.. index:: bond\_style +.. index:: bond_style -bond\_style command -=================== +bond_style command +================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style style args * style = *none* or *hybrid* or *class2* or *fene* or *fene/expand* or *harmonic* or *morse* or *nonlinear* or *quartic* +* args = none for any style except *hybrid* -.. parsed-literal:: - - args = none for any style except *hybrid* - *hybrid* args = list of one or more styles + * *hybrid* args = list of one or more styles Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style harmonic bond_style fene @@ -74,11 +72,11 @@ between the 2 atoms in the bond. Here is an alphabetic list of bond styles defined in LAMMPS. Click on the style to display the formula it computes and coefficients -specified by the associated :doc:`bond\_coeff ` command. +specified by the associated :doc:`bond_coeff ` command. Click on the style to display the formula it computes, any additional arguments specified in the bond\_style command, and coefficients -specified by the associated :doc:`bond\_coeff ` command. +specified by the associated :doc:`bond_coeff ` command. There are also additional accelerated pair styles included in the LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. @@ -128,9 +126,6 @@ Related commands Default """"""" -bond\_style none +.. code-block:: LAMMPS - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html + bond_style none diff --git a/doc/src/bond_table.rst b/doc/src/bond_table.rst index f68288349d..5378df3cff 100644 --- a/doc/src/bond_table.rst +++ b/doc/src/bond_table.rst @@ -1,16 +1,16 @@ -.. index:: bond\_style table +.. index:: bond_style table -bond\_style table command -========================= +bond_style table command +======================== -bond\_style table/omp command -============================= +bond_style table/omp command +============================ Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style table style N @@ -21,7 +21,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style table linear 1000 bond_coeff 1 file.table ENTRY1 @@ -31,14 +31,14 @@ Description Style *table* creates interpolation tables of length *N* from bond potential and force values listed in a file(s) as a function of bond -length. The files are read by the :doc:`bond\_coeff ` +length. The files are read by the :doc:`bond_coeff ` command. The interpolation tables are created by fitting cubic splines to the file values and interpolating energy and force values at each of *N* distances. During a simulation, these tables are used to interpolate energy and force values as needed. The interpolation is done in one -of 2 styles: *linear* or *spline*\ . +of 2 styles: *linear* or *spline*. For the *linear* style, the bond length is used to find 2 surrounding table values from which an energy or force is computed by linear @@ -50,7 +50,7 @@ used to find the appropriate set of coefficients which are used to evaluate a cubic polynomial which computes the energy or force. The following coefficients must be defined for each bond type via the -:doc:`bond\_coeff ` command as in the example above. +:doc:`bond_coeff ` command as in the example above. * filename * keyword @@ -84,14 +84,14 @@ 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:`bond\_coeff ` command. The next line lists (in any +:doc:`bond_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:`bond\_style table ` command. Let -Ntable = *N* in the bond\_style command, and Nfile = "N" in the +Ntable = *N* in the bond_style command, and Nfile = "N" in the tabulated file. What LAMMPS does is a preliminary interpolation by creating splines using the Nfile tabulated values as nodal points. It uses these to interpolate as needed to generate energy and force @@ -119,8 +119,9 @@ the bond length r (in distance units), the 3rd value is the energy (in energy units), and the 4th is the force (in force units). The bond lengths must range from a LO value to a HI value, and increase from one line to the next. If the actual bond length is ever smaller than -the LO value or larger than the HI value, then the bond energy and -force is evaluated as if the bond were the LO or HI length. +the LO value or larger than the HI value, then the calculation is +aborted with an error, so it is advisable to cover the whole range +of possible bond lengths. Note that one file can contain many sections, each with a tabulated potential. LAMMPS reads the file section by section until it finds @@ -173,11 +174,6 @@ info. Related commands """""""""""""""" -:doc:`bond\_coeff `, :doc:`delete\_bonds ` +:doc:`bond_coeff `, :doc:`delete_bonds ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/bond_write.rst b/doc/src/bond_write.rst index 23a6a04815..f7055d42aa 100644 --- a/doc/src/bond_write.rst +++ b/doc/src/bond_write.rst @@ -1,13 +1,13 @@ -.. index:: bond\_write +.. index:: bond_write -bond\_write command -=================== +bond_write command +================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_write btype N inner outer file keyword itype jtype @@ -17,13 +17,12 @@ Syntax * file = name of file to write values to * keyword = section name in file for this set of tabulated values * itype,jtype = 2 atom types (optional) -* Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_write 1 500 0.5 3.5 table.txt Harmonic_1 bond_write 3 1000 0.1 6.0 table.txt Morse @@ -40,14 +39,14 @@ file. The energy and force values are computed at distances from inner to outer for 2 interacting atoms forming a bond of type btype, using the -appropriate :doc:`bond\_coeff ` coefficients. N evenly spaced +appropriate :doc:`bond_coeff ` coefficients. N evenly spaced distances are used. For example, for N = 7, inner = 1.0, and outer = 4.0, values are computed at r = 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0. The file is written in the format used as input for the -:doc:`bond\_style ` *table* option with *keyword* as the +:doc:`bond_style ` *table* option with *keyword* as the section name. Each line written to the file lists an index number (1-N), a distance (in distance units), an energy (in energy units), and a force (in force units). @@ -65,12 +64,7 @@ be specified even if the potential has a finite value at r = 0.0. Related commands """""""""""""""" -:doc:`bond\_style table `, -:doc:`bond\_style `, :doc:`bond\_coeff ` +:doc:`bond_style table `, +:doc:`bond_style `, :doc:`bond_coeff ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/bond_zero.rst b/doc/src/bond_zero.rst index 38e7ecf505..43a0af33e2 100644 --- a/doc/src/bond_zero.rst +++ b/doc/src/bond_zero.rst @@ -1,26 +1,26 @@ -.. index:: bond\_style zero +.. index:: bond_style zero -bond\_style zero command -======================== +bond_style zero command +======================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS - bond_style zero *nocoeff* + bond_style zero [nocoeff] Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style zero bond_style zero nocoeff - bond_coeff \* - bond_coeff \* 2.14 + bond_coeff * + bond_coeff * 2.14 Description """"""""""" @@ -53,8 +53,3 @@ Related commands :doc:`bond\_style none ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/fix_restrain.rst b/doc/src/fix_restrain.rst index 0276194bd2..0fc0ccee77 100644 --- a/doc/src/fix_restrain.rst +++ b/doc/src/fix_restrain.rst @@ -7,7 +7,7 @@ Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS fix ID group-ID restrain keyword args ... @@ -39,7 +39,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS fix holdem all restrain bond 45 48 2000.0 2000.0 2.75 fix holdem all restrain dihedral 1 2 3 4 2000.0 2000.0 120.0 @@ -98,7 +98,7 @@ conventional force field terms. If the restraint is applied during a dynamics run (as opposed to during an energy minimization), a large restraint coefficient can significantly reduce the stable timestep size, especially if the atoms are initially far from the preferred -conformation. You may need to experiment to determine what value of K +conformation. You may need to experiment to determine what value of :math:`K` works best for a given application. For the case of finding a minimum energy structure for a single @@ -107,7 +107,7 @@ parameters or constructing a potential energy surface), commands such as the following may be useful: -.. parsed-literal:: +.. code-block:: LAMMPS # minimize molecule energy with restraints velocity all create 600.0 8675309 mom yes rot yes dist gaussian @@ -134,16 +134,18 @@ The *bond* keyword applies a bond restraint to the specified atoms using the same functional form used by the :doc:`bond\_style harmonic ` command. The potential associated with the restraint is -.. image:: Eqs/bond_harmonic.jpg - :align: center +.. math:: + + E = K (r - r_0)^2 + with the following coefficients: -* K (energy/distance\^2) -* r0 (distance) +* :math:`K` (energy/distance\^2) +* :math:`r_0` (distance) -K and r0 are specified with the fix. Note that the usual 1/2 factor -is included in K. +:math:`K` and :math:`r_0` are specified with the fix. Note that the usual 1/2 factor +is included in :math:`K`. ---------- @@ -153,16 +155,17 @@ The *angle* keyword applies an angle restraint to the specified atoms using the same functional form used by the :doc:`angle\_style harmonic ` command. The potential associated with the restraint is -.. image:: Eqs/angle_harmonic.jpg - :align: center +.. math:: + + E = K (\theta - \theta_0)^2 with the following coefficients: -* K (energy/radian\^2) -* theta0 (degrees) +* :math:`K` (energy/radian\^2) +* :math:`\theta_0` (degrees) -K and theta0 are specified with the fix. Note that the usual 1/2 -factor is included in K. +:math:`K` and :math:`\theta_0` are specified with the fix. Note that the usual 1/2 +factor is included in :math:`K`. ---------- @@ -173,20 +176,22 @@ atoms using a simplified form of the function used by the :doc:`dihedral\_style charmm ` command. The potential associated with the restraint is -.. image:: Eqs/dihedral_charmm.jpg - :align: center +.. math:: + + E = K [ 1 + \cos (n \phi - d) ] + with the following coefficients: -* K (energy) -* n (multiplicity, >= 0) -* d (degrees) = phi0 + 180 +* :math:`K` (energy) +* :math:`n` (multiplicity, >= 0) +* :math:`d` (degrees) = :math:`\phi_0 + 180` -K and phi0 are specified with the fix. Note that the value of the -dihedral multiplicity *n* is set by default to 1. You can use the +:math:`K` and :math:`\phi_0` are specified with the fix. Note that the value of the +dihedral multiplicity :math:`n` is set by default to 1. You can use the optional *mult* keyword to set it to a different positive integer. Also note that the energy will be a minimum when the -current dihedral angle phi is equal to phi0. +current dihedral angle :math:`\phi` is equal to :math:`\phi_0`. ---------- @@ -233,8 +238,3 @@ Restrictions **Related commands:** none **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/src/pair_list.rst b/doc/src/pair_list.rst index 3a161fb408..b74070c4d3 100644 --- a/doc/src/pair_list.rst +++ b/doc/src/pair_list.rst @@ -1,13 +1,13 @@ -.. index:: pair\_style list +.. index:: pair_style list -pair\_style list command -======================== +pair_style list command +======================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style list listfile cutoff keyword @@ -19,14 +19,14 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style list restraints.txt 200.0 - pair_coeff \* \* + pair_coeff * * pair_style hybrid/overlay lj/cut 1.1225 list pair_list.txt 300.0 - pair_coeff \* \* lj/cut 1.0 1.0 - pair_coeff 3\* 3\* list + pair_coeff * * lj/cut 1.0 1.0 + pair_coeff 3* 3* list Description """"""""""" @@ -77,36 +77,41 @@ Here is an example file: The style *lj126* computes pairwise interactions with the formula -.. image:: Eqs/pair_lj.jpg - :align: center +.. math:: + + E = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] \qquad r < r_c + and the coefficients: -* epsilon (energy units) -* sigma (distance units) +* :math:`\epsilon` (energy units) +* :math:`\sigma` (distance units) The style *morse* computes pairwise interactions with the formula -.. image:: Eqs/pair_morse.jpg - :align: center +.. math:: + + E = D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right] \qquad r < r_c + and the coefficients: -* D0 (energy units) -* alpha (1/distance units) -* r0 (distance units) +* :math:`D_0` (energy units) +* :math:`\alpha` (1/distance units) +* :math:`r_0` (distance units) The style *harmonic* computes pairwise interactions with the formula -.. image:: Eqs/bond_harmonic.jpg - :align: center +.. math:: + + E = K (r - r_0)^2 and the coefficients: -* K (energy units) -* r0 (distance units) +* :math:`K` (energy units) +* :math:`r_0` (distance units) -Note that the usual 1/2 factor is included in K. +Note that the usual 1/2 factor is included in :math:`K`. ---------- @@ -161,8 +166,3 @@ Related commands :doc:`bond\_style harmonic ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/angle_charmm.txt b/doc/txt/angle_charmm.txt deleted file mode 100644 index 8b0e298a43..0000000000 --- a/doc/txt/angle_charmm.txt +++ /dev/null @@ -1,89 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -angle_style charmm command :h3 -angle_style charmm/intel command :h3 -angle_style charmm/kk command :h3 -angle_style charmm/omp command :h3 - -[Syntax:] - -angle_style charmm :pre - -[Examples:] - -angle_style charmm -angle_coeff 1 300.0 107.0 50.0 3.0 :pre - -[Description:] - -The {charmm} angle style uses the potential - -:c,image(Eqs/angle_charmm.jpg) - -with an additional Urey_Bradley term based on the distance {r} between -the 1st and 3rd atoms in the angle. K, theta0, Kub, and Rub are -coefficients defined for each angle type. - -See "(MacKerell)"_#angle-MacKerell for a description of the CHARMM force -field. - -The following coefficients must be defined for each angle type via the -"angle_coeff"_angle_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -K (energy/radian^2) -theta0 (degrees) -K_ub (energy/distance^2) -r_ub (distance) :ul - -Theta0 is specified in degrees, but LAMMPS converts it to radians -internally; hence the units of K are in energy/radian^2. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -MOLECULE package. See the "Build package"_Build_package.html doc page -for more info. - -[Related commands:] - -"angle_coeff"_angle_coeff.html - -[Default:] none - -:line - -:link(angle-MacKerell) -[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, -Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998). diff --git a/doc/txt/angle_class2.txt b/doc/txt/angle_class2.txt deleted file mode 100644 index 5a772f8fa9..0000000000 --- a/doc/txt/angle_class2.txt +++ /dev/null @@ -1,138 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -angle_style class2 command :h3 -angle_style class2/kk command :h3 -angle_style class2/omp command :h3 -angle_style class2/p6 command :h3 - -[Syntax:] - -angle_style class2 :pre - -[Examples:] - -angle_style class2 -angle_coeff * 75.0 -angle_coeff 1 bb 10.5872 1.0119 1.5228 -angle_coeff * ba 3.6551 24.895 1.0119 1.5228 :pre - -[Description:] - -The {class2} angle style uses the potential - -:c,image(Eqs/angle_class2.jpg) - -where Ea is the angle term, Ebb is a bond-bond term, and Eba is a -bond-angle term. Theta0 is the equilibrium angle and r1 and r2 are -the equilibrium bond lengths. - -See "(Sun)"_#angle-Sun for a description of the COMPASS class2 force field. - -Coefficients for the Ea, Ebb, and Eba formulas must be defined for -each angle type via the "angle_coeff"_angle_coeff.html command as in -the example above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands. - -These are the 4 coefficients for the Ea formula: - -theta0 (degrees) -K2 (energy/radian^2) -K3 (energy/radian^3) -K4 (energy/radian^4) :ul - -Theta0 is specified in degrees, but LAMMPS converts it to radians -internally; hence the units of the various K are in per-radian. - -For the Ebb formula, each line in a "angle_coeff"_angle_coeff.html -command in the input script lists 4 coefficients, the first of which -is "bb" to indicate they are BondBond coefficients. In a data file, -these coefficients should be listed under a "BondBond Coeffs" heading -and you must leave out the "bb", i.e. only list 3 coefficients after -the angle type. - -bb -M (energy/distance^2) -r1 (distance) -r2 (distance) :ul - -For the Eba formula, each line in a "angle_coeff"_angle_coeff.html -command in the input script lists 5 coefficients, the first of which -is "ba" to indicate they are BondAngle coefficients. In a data file, -these coefficients should be listed under a "BondAngle Coeffs" heading -and you must leave out the "ba", i.e. only list 4 coefficients after -the angle type. - -ba -N1 (energy/distance^2) -N2 (energy/distance^2) -r1 (distance) -r2 (distance) :ul - -The theta0 value in the Eba formula is not specified, since it is the -same value from the Ea formula. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -The {class2/p6} angle style uses the {class2} potential expanded to sixth order: - -:c,image(Eqs/angle_class2_p6.jpg) - -In this expanded term 6 coefficients for the Ea formula need to be set: - -theta0 (degrees) -K2 (energy/radian^2) -K3 (energy/radian^3) -K4 (energy/radian^4) -K5 (energy/radian^5) -K6 (energy/radian^6) :ul - -The bond-bond and bond-angle terms remain unchanged. - -:line - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the CLASS2 -package. For the {class2/p6} style LAMMPS needs to be built with the -USER-MOFFF package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"angle_coeff"_angle_coeff.html - -[Default:] none - -:line - -:link(angle-Sun) -[(Sun)] Sun, J Phys Chem B 102, 7338-7364 (1998). diff --git a/doc/txt/angle_coeff.txt b/doc/txt/angle_coeff.txt deleted file mode 100644 index 5dc9c13381..0000000000 --- a/doc/txt/angle_coeff.txt +++ /dev/null @@ -1,87 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -angle_coeff command :h3 - -[Syntax:] - -angle_coeff N args :pre - -N = angle type (see asterisk form below) -args = coefficients for one or more angle types :ul - -[Examples:] - -angle_coeff 1 300.0 107.0 -angle_coeff * 5.0 -angle_coeff 2*10 5.0 :pre - -[Description:] - -Specify the angle force field coefficients for one or more angle types. -The number and meaning of the coefficients depends on the angle style. -Angle coefficients can also be set in the data file read by the -"read_data"_read_data.html command or in a restart file. - -N can be specified in one of two ways. An explicit numeric value can -be used, as in the 1st example above. Or a wild-card asterisk can be -used to set the coefficients for multiple angle types. This takes the -form "*" or "*n" or "n*" or "m*n". If N = the number of angle types, -then an asterisk with no numeric values means all types from 1 to N. A -leading asterisk means all types from 1 to n (inclusive). A trailing -asterisk means all types from n to N (inclusive). A middle asterisk -means all types from m to n (inclusive). - -Note that using an angle_coeff command can override a previous setting -for the same angle type. For example, these commands set the coeffs -for all angle types, then overwrite the coeffs for just angle type 2: - -angle_coeff * 200.0 107.0 1.2 -angle_coeff 2 50.0 107.0 :pre - -A line in a data file that specifies angle coefficients uses the exact -same format as the arguments of the angle_coeff command in an input -script, except that wild-card asterisks should not be used since -coefficients for all N types must be listed in the file. For example, -under the "Angle Coeffs" section of a data file, the line that -corresponds to the 1st example above would be listed as - -1 300.0 107.0 :pre - -The "angle_style class2"_angle_class2.html is an exception to this -rule, in that an additional argument is used in the input script to -allow specification of the cross-term coefficients. See its -doc page for details. - -:line - -The list of all angle styles defined in LAMMPS is given on the -"angle_style"_angle_style.html doc page. They are also listed in more -compact form on the "Commands angle"_Commands_bond.html#angle doc -page. - -On either of those pages, click on the style to display the formula it -computes and its coefficients as specified by the associated -angle_coeff command. - -:line - -[Restrictions:] - -This command must come after the simulation box is defined by a -"read_data"_read_data.html, "read_restart"_read_restart.html, or -"create_box"_create_box.html command. - -An angle style must be defined before any angle coefficients are -set, either in the input script or in a data file. - -[Related commands:] - -"angle_style"_angle_style.html - -[Default:] none diff --git a/doc/txt/angle_cosine.txt b/doc/txt/angle_cosine.txt deleted file mode 100644 index 93fed32c38..0000000000 --- a/doc/txt/angle_cosine.txt +++ /dev/null @@ -1,71 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -angle_style cosine command :h3 -angle_style cosine/omp command :h3 -angle_style cosine/kk command :h3 - -[Syntax:] - -angle_style cosine :pre - -[Examples:] - -angle_style cosine -angle_coeff * 75.0 :pre - -[Description:] - -The {cosine} angle style uses the potential - -:c,image(Eqs/angle_cosine.jpg) - -where K is defined for each angle type. - -The following coefficients must be defined for each angle type via the -"angle_coeff"_angle_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -K (energy) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -MOLECULE package. See the "Build package"_Build_package.html doc page -for more info. - -[Related commands:] - -"angle_coeff"_angle_coeff.html - -[Default:] none diff --git a/doc/txt/angle_cosine_buck6d.txt b/doc/txt/angle_cosine_buck6d.txt deleted file mode 100644 index 1ce3556ea6..0000000000 --- a/doc/txt/angle_cosine_buck6d.txt +++ /dev/null @@ -1,65 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -angle_style cosine/buck6d command :h3 - -[Syntax:] - -angle_style cosine/buck6d :pre - -[Examples:] - -angle_style cosine/buck6d -angle_coeff 1 cosine/buck6d 1.978350 4 180.000000 :pre - -[Description:] - -The {cosine/buck6d} angle style uses the potential - -:c,image(Eqs/angle_cosine_buck6d.jpg) - -where K is the energy constant, n is the periodic multiplicity and -Theta0 is the equilibrium angle. - -The coefficients must be defined for each angle type via the -"angle_coeff"_angle_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands in the following order: - -K (energy) -n -Theta0 (degrees) :ul - -Theta0 is specified in degrees, but LAMMPS converts it to radians -internally. - -Additional to the cosine term the {cosine/buck6d} angle style computes -the short range (vdW) interaction belonging to the -"pair_buck6d"_pair_buck6d_coul_gauss.html between the end atoms of the -angle. For this reason this angle style only works in combination -with the "pair_buck6d"_pair_buck6d_coul_gauss.html styles and needs -the "special_bonds"_special_bonds.html 1-3 interactions to be weighted -0.0 to prevent double counting. - -:line - -[Restrictions:] - -{cosine/buck6d} can only be used in combination with the -"pair_buck6d"_pair_buck6d_coul_gauss.html style and with a -"special_bonds"_special_bonds.html 0.0 weighting of 1-3 interactions. - -This angle style can only be used if LAMMPS was built with the -USER-MOFFF package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"angle_coeff"_angle_coeff.html - -[Default:] none diff --git a/doc/txt/angle_cosine_delta.txt b/doc/txt/angle_cosine_delta.txt deleted file mode 100644 index 1532e39b31..0000000000 --- a/doc/txt/angle_cosine_delta.txt +++ /dev/null @@ -1,76 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -angle_style cosine/delta command :h3 -angle_style cosine/delta/omp command :h3 - -[Syntax:] - -angle_style cosine/delta :pre - -[Examples:] - -angle_style cosine/delta -angle_coeff 2*4 75.0 100.0 :pre - -[Description:] - -The {cosine/delta} angle style uses the potential - -:c,image(Eqs/angle_cosine_delta.jpg) - -where theta0 is the equilibrium value of the angle, and K is a -prefactor. Note that the usual 1/2 factor is included in K. - -The following coefficients must be defined for each angle type via the -"angle_coeff"_angle_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -K (energy) -theta0 (degrees) :ul - -Theta0 is specified in degrees, but LAMMPS converts it to radians -internally. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -MOLECULE package. See the "Build package"_Build_package.html doc page -for more info. - -[Related commands:] - -"angle_coeff"_angle_coeff.html, "angle_style -cosine/squared"_angle_cosine_squared.html - -[Default:] none diff --git a/doc/txt/angle_cosine_periodic.txt b/doc/txt/angle_cosine_periodic.txt deleted file mode 100644 index 039144797f..0000000000 --- a/doc/txt/angle_cosine_periodic.txt +++ /dev/null @@ -1,89 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -angle_style cosine/periodic command :h3 -angle_style cosine/periodic/omp command :h3 - -[Syntax:] - -angle_style cosine/periodic :pre - -[Examples:] - -angle_style cosine/periodic -angle_coeff * 75.0 1 6 :pre - -[Description:] - -The {cosine/periodic} angle style uses the following potential, which -is commonly used in the "DREIDING"_Howto_bioFF.html force field, -particularly for organometallic systems where {n} = 4 might be used -for an octahedral complex and {n} = 3 might be used for a trigonal -center: - -:c,image(Eqs/angle_cosine_periodic.jpg) - -where C, B and n are coefficients defined for each angle type. - -See "(Mayo)"_#cosine-Mayo for a description of the DREIDING force field - -The following coefficients must be defined for each angle type via the -"angle_coeff"_angle_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -C (energy) -B = 1 or -1 -n = 1, 2, 3, 4, 5 or 6 for periodicity :ul - -Note that the prefactor C is specified and not the overall force -constant K = C / n^2. When B = 1, it leads to a minimum for the -linear geometry. When B = -1, it leads to a maximum for the linear -geometry. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -MOLECULE package. See the "Build package"_Build_package.html doc page -for more info. - -[Related commands:] - -"angle_coeff"_angle_coeff.html - -[Default:] none - -:line - -:link(cosine-Mayo) -[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 -(1990). diff --git a/doc/txt/angle_cosine_shift.txt b/doc/txt/angle_cosine_shift.txt deleted file mode 100644 index 65dc0924e5..0000000000 --- a/doc/txt/angle_cosine_shift.txt +++ /dev/null @@ -1,73 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -angle_style cosine/shift command :h3 -angle_style cosine/shift/omp command :h3 - -[Syntax:] - -angle_style cosine/shift :pre - -[Examples:] - -angle_style cosine/shift -angle_coeff * 10.0 45.0 :pre - -[Description:] - -The {cosine/shift} angle style uses the potential - -:c,image(Eqs/angle_cosine_shift.jpg) - -where theta0 is the equilibrium angle. The potential is bounded -between -Umin and zero. In the neighborhood of the minimum E=- Umin + -Umin/4(theta-theta0)^2 hence the spring constant is umin/2. - -The following coefficients must be defined for each angle type via the -"angle_coeff"_angle_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -umin (energy) -theta (angle) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -USER-MISC package. - -[Related commands:] - -"angle_coeff"_angle_coeff.html, -"angle_cosine_shift_exp"_angle_cosine_shift_exp.html - -[Default:] none diff --git a/doc/txt/angle_cosine_shift_exp.txt b/doc/txt/angle_cosine_shift_exp.txt deleted file mode 100644 index 3091e83885..0000000000 --- a/doc/txt/angle_cosine_shift_exp.txt +++ /dev/null @@ -1,87 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -angle_style cosine/shift/exp command :h3 -angle_style cosine/shift/exp/omp command :h3 - -[Syntax:] - -angle_style cosine/shift/exp :pre - -[Examples:] - -angle_style cosine/shift/exp -angle_coeff * 10.0 45.0 2.0 :pre - -[Description:] - -The {cosine/shift/exp} angle style uses the potential - -:c,image(Eqs/angle_cosine_shift_exp.jpg) - -where Umin, theta, and a are defined for each angle type. - -The potential is bounded between \[-Umin:0\] and the minimum is -located at the angle theta0. The a parameter can be both positive or -negative and is used to control the spring constant at the -equilibrium. - -The spring constant is given by k = A exp(A) Umin / \[2 (Exp(a)-1)\]. -For a > 3, k/Umin = a/2 to better than 5% relative error. For negative -values of the a parameter, the spring constant is essentially zero, -and anharmonic terms takes over. The potential is furthermore well -behaved in the limit a -> 0, where it has been implemented to linear -order in a for a < 0.001. In this limit the potential reduces to the -cosineshifted potential. - -The following coefficients must be defined for each angle type via the -"angle_coeff"_angle_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -umin (energy) -theta (angle) -A (real number) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -USER-MISC package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"angle_coeff"_angle_coeff.html, -"angle_cosine_shift"_angle_cosine_shift.html, -"dihedral_cosine_shift_exp"_dihedral_cosine_shift_exp.html - -[Default:] none diff --git a/doc/txt/angle_cosine_squared.txt b/doc/txt/angle_cosine_squared.txt deleted file mode 100644 index 07fcb1ceb4..0000000000 --- a/doc/txt/angle_cosine_squared.txt +++ /dev/null @@ -1,75 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -angle_style cosine/squared command :h3 -angle_style cosine/squared/omp command :h3 - -[Syntax:] - -angle_style cosine/squared :pre - -[Examples:] - -angle_style cosine/squared -angle_coeff 2*4 75.0 100.0 :pre - -[Description:] - -The {cosine/squared} angle style uses the potential - -:c,image(Eqs/angle_cosine_squared.jpg) - -where theta0 is the equilibrium value of the angle, and K is a -prefactor. Note that the usual 1/2 factor is included in K. - -The following coefficients must be defined for each angle type via the -"angle_coeff"_angle_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -K (energy) -theta0 (degrees) :ul - -Theta0 is specified in degrees, but LAMMPS converts it to radians -internally. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -MOLECULE package. See the "Build package"_Build_package.html doc page -for more info. - -[Related commands:] - -"angle_coeff"_angle_coeff.html - -[Default:] none diff --git a/doc/txt/angle_cross.txt b/doc/txt/angle_cross.txt deleted file mode 100644 index d9d83ed4b6..0000000000 --- a/doc/txt/angle_cross.txt +++ /dev/null @@ -1,62 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -angle_style cross command :h3 - -[Syntax:] - -angle_style cross :pre - -[Examples:] - -angle_style cross -angle_coeff 1 200.0 100.0 100.0 1.25 1.25 107.0 :pre - -[Description:] - -The {cross} angle style uses a potential that couples the bond stretches of -a bend with the angle stretch of that bend: - -:c,image(Eqs/angle_cross.jpg) - -where r12,0 is the rest value of the bond length between atom 1 and 2, -r32,0 is the rest value of the bond length between atom 2 and 2, -and theta0 is the rest value of the angle. KSS is the force constant of -the bond stretch-bond stretch term and KBS0 and KBS1 are the force constants -of the bond stretch-angle stretch terms. - -The following coefficients must be defined for each angle type via the -"angle_coeff"_angle_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -KSS (energy/distance^2) -KBS0 (energy/distance/rad) -KBS1 (energy/distance/rad) -r12,0 (distance) -r32,0 (distance) -theta0 (degrees) :ul - -Theta0 is specified in degrees, but LAMMPS converts it to radians -internally; hence the units of KBS0 and KBS1 are in energy/distance/radian. - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -USER_YAFF package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"angle_coeff"_angle_coeff.html - -[Default:] none - -:line - - diff --git a/doc/txt/angle_dipole.txt b/doc/txt/angle_dipole.txt deleted file mode 100644 index cdb11972ec..0000000000 --- a/doc/txt/angle_dipole.txt +++ /dev/null @@ -1,126 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -angle_style dipole command :h3 -angle_style dipole/omp command :h3 - -[Syntax:] - -angle_style dipole :pre - -[Examples:] - -angle_style dipole -angle_coeff 6 2.1 180.0 :pre - -[Description:] - -The {dipole} angle style is used to control the orientation of a dipolar -atom within a molecule "(Orsi)"_#Orsi. Specifically, the {dipole} angle -style restrains the orientation of a point dipole mu_j (embedded in atom -'j') with respect to a reference (bond) vector r_ij = r_i - r_j, where 'i' -is another atom of the same molecule (typically, 'i' and 'j' are also -covalently bonded). - -It is convenient to define an angle gamma between the 'free' vector mu_j -and the reference (bond) vector r_ij: - -:c,image(Eqs/angle_dipole_gamma.jpg) - -The {dipole} angle style uses the potential: - -:c,image(Eqs/angle_dipole_potential.jpg) - -where K is a rigidity constant and gamma0 is an equilibrium (reference) -angle. - -The torque on the dipole can be obtained by differentiating the -potential using the 'chain rule' as in appendix C.3 of -"(Allen)"_#Allen1: - -:c,image(Eqs/angle_dipole_torque.jpg) - -Example: if gamma0 is set to 0 degrees, the torque generated by -the potential will tend to align the dipole along the reference -direction defined by the (bond) vector r_ij (in other words, mu_j is -restrained to point towards atom 'i'). - -The dipolar torque T_j must be counterbalanced in order to conserve -the local angular momentum. This is achieved via an additional force -couple generating a torque equivalent to the opposite of T_j: - -:c,image(Eqs/angle_dipole_couple.jpg) - -where F_i and F_j are applied on atoms i and j, respectively. - -The following coefficients must be defined for each angle type via the -"angle_coeff"_angle_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -K (energy) -gamma0 (degrees) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -USER-MISC package. See the "Build package"_Build_package.html doc -page for more info. - -NOTE: In the "Angles" section of the data file, the atom ID 'j' -defining the direction of the dipole vector to restrain must come -before the atom ID of the reference atom 'i'. A third atom ID 'k' must -also be provided to comply with the requirement of a valid angle -definition. This atom ID k should be chosen to be that of an atom -bonded to atom 'i' to avoid errors with "lost angle atoms" when running -in parallel. Since the LAMMPS code checks for valid angle definitions, -cannot use the same atom ID of either 'i' or 'j' (this was allowed -and recommended with older LAMMPS versions). - -The "newton" command for intramolecular interactions must be "on" -(which is the default except when using some accelerator packages). - -This angle style should not be used with SHAKE. - -[Related commands:] - -"angle_coeff"_angle_coeff.html, "angle_hybrid"_angle_hybrid.html - -[Default:] none - -:line - -:link(Orsi) -[(Orsi)] Orsi & Essex, The ELBA force field for coarse-grain modeling of -lipid membranes, PloS ONE 6(12): e28637, 2011. - -:link(Allen1) -[(Allen)] Allen & Tildesley, Computer Simulation of Liquids, -Clarendon Press, Oxford, 1987. diff --git a/doc/txt/angle_fourier.txt b/doc/txt/angle_fourier.txt deleted file mode 100644 index 7dc9975793..0000000000 --- a/doc/txt/angle_fourier.txt +++ /dev/null @@ -1,71 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -angle_style fourier command :h3 -angle_style fourier/omp command :h3 - -[Syntax:] - -angle_style fourier :pre - -[Examples:] - -angle_style fourier -angle_coeff 75.0 1.0 1.0 1.0 - -[Description:] - -The {fourier} angle style uses the potential - -:c,image(Eqs/angle_fourier.jpg) - -The following coefficients must be defined for each angle type via the -"angle_coeff"_angle_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -K (energy) -C0 (real) -C1 (real) -C2 (real) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -USER_MISC package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"angle_coeff"_angle_coeff.html - -[Default:] none diff --git a/doc/txt/angle_fourier_simple.txt b/doc/txt/angle_fourier_simple.txt deleted file mode 100644 index ae5d308353..0000000000 --- a/doc/txt/angle_fourier_simple.txt +++ /dev/null @@ -1,70 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -angle_style fourier/simple command :h3 -angle_style fourier/simple/omp command :h3 - -[Syntax:] - -angle_style fourier/simple :pre - -[Examples:] - -angle_style fourier/simple -angle_coeff 100.0 -1.0 1.0 - -[Description:] - -The {fourier/simple} angle style uses the potential - -:c,image(Eqs/angle_fourier_simple.jpg) - -The following coefficients must be defined for each angle type via the -"angle_coeff"_angle_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -K (energy) -c (real) -n (real) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -USER_MISC package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"angle_coeff"_angle_coeff.html - -[Default:] none diff --git a/doc/txt/angle_harmonic.txt b/doc/txt/angle_harmonic.txt deleted file mode 100644 index b632f68478..0000000000 --- a/doc/txt/angle_harmonic.txt +++ /dev/null @@ -1,77 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -angle_style harmonic command :h3 -angle_style harmonic/intel command :h3 -angle_style harmonic/kk command :h3 -angle_style harmonic/omp command :h3 - -[Syntax:] - -angle_style harmonic :pre - -[Examples:] - -angle_style harmonic -angle_coeff 1 300.0 107.0 :pre - -[Description:] - -The {harmonic} angle style uses the potential - -:c,image(Eqs/angle_harmonic.jpg) - -where theta0 is the equilibrium value of the angle, and K is a -prefactor. Note that the usual 1/2 factor is included in K. - -The following coefficients must be defined for each angle type via the -"angle_coeff"_angle_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -K (energy/radian^2) -theta0 (degrees) :ul - -Theta0 is specified in degrees, but LAMMPS converts it to radians -internally; hence the units of K are in energy/radian^2. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -MOLECULE package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"angle_coeff"_angle_coeff.html - -[Default:] none diff --git a/doc/txt/angle_hybrid.txt b/doc/txt/angle_hybrid.txt deleted file mode 100644 index 0046c161be..0000000000 --- a/doc/txt/angle_hybrid.txt +++ /dev/null @@ -1,91 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -angle_style hybrid command :h3 - -[Syntax:] - -angle_style hybrid style1 style2 ... :pre - -style1,style2 = list of one or more angle styles :ul - -[Examples:] - -angle_style hybrid harmonic cosine -angle_coeff 1 harmonic 80.0 30.0 -angle_coeff 2* cosine 50.0 :pre - -[Description:] - -The {hybrid} style enables the use of multiple angle styles in one -simulation. An angle style is assigned to each angle type. For -example, angles in a polymer flow (of angle type 1) could be computed -with a {harmonic} potential and angles in the wall boundary (of angle -type 2) could be computed with a {cosine} potential. The assignment -of angle type to style is made via the "angle_coeff"_angle_coeff.html -command or in the data file. - -In the angle_coeff commands, the name of an angle style must be added -after the angle type, with the remaining coefficients being those -appropriate to that style. In the example above, the 2 angle_coeff -commands set angles of angle type 1 to be computed with a {harmonic} -potential with coefficients 80.0, 30.0 for K, theta0. All other angle -types (2-N) are computed with a {cosine} potential with coefficient -50.0 for K. - -If angle coefficients are specified in the data file read via the -"read_data"_read_data.html command, then the same rule applies. -E.g. "harmonic" or "cosine", must be added after the angle type, for each -line in the "Angle Coeffs" section, e.g. - -Angle Coeffs :pre - -1 harmonic 80.0 30.0 -2 cosine 50.0 -... :pre - -If {class2} is one of the angle hybrid styles, the same rule holds for -specifying additional BondBond (and BondAngle) coefficients either via -the input script or in the data file. I.e. {class2} must be added to -each line after the angle type. For lines in the BondBond (or -BondAngle) section of the data file for angle types that are not -{class2}, you must use an angle style of {skip} as a placeholder, e.g. - -BondBond Coeffs :pre - -1 skip -2 class2 3.6512 1.0119 1.0119 -... :pre - -Note that it is not necessary to use the angle style {skip} in the -input script, since BondBond (or BondAngle) coefficients need not be -specified at all for angle types that are not {class2}. - -An angle style of {none} with no additional coefficients can be used -in place of an angle style, either in a input script angle_coeff -command or in the data file, if you desire to turn off interactions -for specific angle types. - -:line - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -MOLECULE package. See the "Build package"_Build_package.html doc page -for more info. - -Unlike other angle styles, the hybrid angle style does not store angle -coefficient info for individual sub-styles in a "binary restart -files"_restart.html. Thus when restarting a simulation from a restart -file, you need to re-specify angle_coeff commands. - -[Related commands:] - -"angle_coeff"_angle_coeff.html - -[Default:] none diff --git a/doc/txt/angle_mm3.txt b/doc/txt/angle_mm3.txt deleted file mode 100644 index 9ae032c4ff..0000000000 --- a/doc/txt/angle_mm3.txt +++ /dev/null @@ -1,55 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -angle_style mm3 command :h3 - -[Syntax:] - -angle_style mm3 :pre - -[Examples:] - -angle_style mm3 -angle_coeff 1 100.0 107.0 :pre - -[Description:] - -The {mm3} angle style uses the potential that is anharmonic in the angle -as defined in "(Allinger)"_#mm3-allinger1989 - -:c,image(Eqs/angle_mm3.jpg) - -where theta0 is the equilibrium value of the angle, and K is a -prefactor. The anharmonic prefactors have units deg^(-n), for example --0.014 deg^(-1), 5.6(10)^(-5) deg^(-2), ... - -The following coefficients must be defined for each angle type via the -"angle_coeff"_angle_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -K (energy/radian^2) -theta0 (degrees) :ul - -Theta0 is specified in degrees, but LAMMPS converts it to radians -internally; hence the units of K are in energy/radian^2. - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -USER_YAFF package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"angle_coeff"_angle_coeff.html - -[Default:] none - -:line - diff --git a/doc/txt/angle_none.txt b/doc/txt/angle_none.txt deleted file mode 100644 index 1eca5cbbec..0000000000 --- a/doc/txt/angle_none.txt +++ /dev/null @@ -1,34 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -angle_style none command :h3 - -[Syntax:] - -angle_style none :pre - -[Examples:] - -angle_style none :pre - -[Description:] - -Using an angle style of none means angle forces and energies are not -computed, even if triplets of angle atoms were listed in the data file -read by the "read_data"_read_data.html command. - -See the "angle_style zero"_angle_zero.html command for a way to -calculate angle statistics, but compute no angle interactions. - -[Restrictions:] none - -[Related commands:] - -"angle_style zero"_angle_zero.html - -[Default:] none diff --git a/doc/txt/angle_quartic.txt b/doc/txt/angle_quartic.txt deleted file mode 100644 index b20a06eb8d..0000000000 --- a/doc/txt/angle_quartic.txt +++ /dev/null @@ -1,77 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -angle_style quartic command :h3 -angle_style quartic/omp command :h3 - -[Syntax:] - -angle_style quartic :pre - -[Examples:] - -angle_style quartic -angle_coeff 1 129.1948 56.8726 -25.9442 -14.2221 :pre - -[Description:] - -The {quartic} angle style uses the potential - -:c,image(Eqs/angle_quartic.jpg) - -where theta0 is the equilibrium value of the angle, and K is a -prefactor. Note that the usual 1/2 factor is included in K. - -The following coefficients must be defined for each angle type via the -"angle_coeff"_angle_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -theta0 (degrees) -K2 (energy/radian^2) -K3 (energy/radian^3) -K4 (energy/radian^4) :ul - -Theta0 is specified in degrees, but LAMMPS converts it to radians -internally; hence the units of K are in energy/radian^2. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -USER_MISC package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"angle_coeff"_angle_coeff.html - -[Default:] none diff --git a/doc/txt/angle_sdk.txt b/doc/txt/angle_sdk.txt deleted file mode 100644 index 9382d560d3..0000000000 --- a/doc/txt/angle_sdk.txt +++ /dev/null @@ -1,83 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -angle_style sdk command :h3 -angle_style sdk/omp command :h3 - -[Syntax:] - -angle_style sdk :pre -angle_style sdk/omp :pre - -[Examples:] - -angle_style sdk -angle_coeff 1 300.0 107.0 :pre - -[Description:] - -The {sdk} angle style is a combination of the harmonic angle potential, - -:c,image(Eqs/angle_harmonic.jpg) - -where theta0 is the equilibrium value of the angle and K a prefactor, -with the {repulsive} part of the non-bonded {lj/sdk} pair style -between the atoms 1 and 3. This angle potential is intended for -coarse grained MD simulations with the CMM parameterization using the -"pair_style lj/sdk"_pair_sdk.html. Relative to the pair_style -{lj/sdk}, however, the energy is shifted by {epsilon}, to avoid sudden -jumps. Note that the usual 1/2 factor is included in K. - -The following coefficients must be defined for each angle type via the -"angle_coeff"_angle_coeff.html command as in the example above: - -K (energy/radian^2) -theta0 (degrees) :ul - -Theta0 is specified in degrees, but LAMMPS converts it to radians -internally; hence the units of K are in energy/radian^2. -The also required {lj/sdk} parameters will be extracted automatically -from the pair_style. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -USER-CGSDK package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"angle_coeff"_angle_coeff.html, "angle_style -harmonic"_angle_harmonic.html, "pair_style lj/sdk"_pair_sdk.html, -"pair_style lj/sdk/coul/long"_pair_sdk.html - -[Default:] none diff --git a/doc/txt/angle_style.txt b/doc/txt/angle_style.txt deleted file mode 100644 index 2f2da678d8..0000000000 --- a/doc/txt/angle_style.txt +++ /dev/null @@ -1,112 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -angle_style command :h3 - -[Syntax:] - -angle_style style :pre - -style = {none} or {hybrid} or {charmm} or {class2} or {cosine} or \ - {cosine/squared} or {harmonic} :ul - -[Examples:] - -angle_style harmonic -angle_style charmm -angle_style hybrid harmonic cosine :pre - -[Description:] - -Set the formula(s) LAMMPS uses to compute angle interactions between -triplets of atoms, which remain in force for the duration of the -simulation. The list of angle triplets is read in by a -"read_data"_read_data.html or "read_restart"_read_restart.html command -from a data or restart file. - -Hybrid models where angles are computed using different angle -potentials can be setup using the {hybrid} angle style. - -The coefficients associated with a angle style can be specified in a -data or restart file or via the "angle_coeff"_angle_coeff.html command. - -All angle potentials store their coefficient data in binary restart -files which means angle_style and "angle_coeff"_angle_coeff.html -commands do not need to be re-specified in an input script that -restarts a simulation. See the "read_restart"_read_restart.html -command for details on how to do this. The one exception is that -angle_style {hybrid} only stores the list of sub-styles in the restart -file; angle coefficients need to be re-specified. - -NOTE: When both an angle and pair style is defined, the -"special_bonds"_special_bonds.html command often needs to be used to -turn off (or weight) the pairwise interaction that would otherwise -exist between 3 bonded atoms. - -In the formulas listed for each angle style, {theta} is the angle -between the 3 atoms in the angle. - -:line - -Here is an alphabetic list of angle styles defined in LAMMPS. Click on -the style to display the formula it computes and coefficients -specified by the associated "angle_coeff"_angle_coeff.html command. - -Click on the style to display the formula it computes, any additional -arguments specified in the angle_style command, and coefficients -specified by the associated "angle_coeff"_angle_coeff.html command. - -There are also additional accelerated pair styles included in the -LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. -The individual style names on the "Commands -angle"_Commands_bond.html#angle doc page are followed by one or more -of (g,i,k,o,t) to indicate which accelerated styles exist. - -"none"_angle_none.html - turn off angle interactions -"zero"_angle_zero.html - topology but no interactions -"hybrid"_angle_hybrid.html - define multiple styles of angle interactions :ul - -"charmm"_angle_charmm.html - CHARMM angle -"class2"_angle_class2.html - COMPASS (class 2) angle -"class2/p6"_angle_class2.html - COMPASS (class 2) angle expanded to 6th order -"cosine"_angle_cosine.html - angle with cosine term -"cosine/buck6d"_angle_cosine_buck6d.html - same as cosine with Buckingham term between 1-3 atoms -"cosine/delta"_angle_cosine_delta.html - angle with difference of cosines -"cosine/periodic"_angle_cosine_periodic.html - DREIDING angle -"cosine/shift"_angle_cosine_shift.html - angle cosine with a shift -"cosine/shift/exp"_angle_cosine_shift_exp.html - cosine with shift and exponential term in spring constant -"cosine/squared"_angle_cosine_squared.html - angle with cosine squared term -"cross"_angle_cross.html - cross term coupling angle and bond lengths -"dipole"_angle_dipole.html - angle that controls orientation of a point dipole -"fourier"_angle_fourier.html - angle with multiple cosine terms -"fourier/simple"_angle_fourier_simple.html - angle with a single cosine term -"harmonic"_angle_harmonic.html - harmonic angle -"mm3"_angle_mm3.html - anharmonic angle -"quartic"_angle_quartic.html - angle with cubic and quartic terms -"sdk"_angle_sdk.html - harmonic angle with repulsive SDK pair style between 1-3 atoms -"table"_angle_table.html - tabulated by angle :ul - -:line - -[Restrictions:] - -Angle styles can only be set for atom_styles that allow angles to be -defined. - -Most angle styles are part of the MOLECULE package. They are only -enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. The doc pages for -individual bond potentials tell if it is part of a package. - -[Related commands:] - -"angle_coeff"_angle_coeff.html - -[Default:] - -angle_style none :pre diff --git a/doc/txt/angle_table.txt b/doc/txt/angle_table.txt deleted file mode 100644 index 61c987f587..0000000000 --- a/doc/txt/angle_table.txt +++ /dev/null @@ -1,166 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -angle_style table command :h3 -angle_style table/omp command :h3 - -[Syntax:] - -angle_style table style N :pre - -style = {linear} or {spline} = method of interpolation -N = use N values in table :ul - -[Examples:] - -angle_style table linear 1000 -angle_coeff 3 file.table ENTRY1 :pre - -[Description:] - -Style {table} creates interpolation tables of length {N} from angle -potential and derivative values listed in a file(s) as a function of -angle The files are read by the "angle_coeff"_angle_coeff.html -command. - -The interpolation tables are created by fitting cubic splines to the -file values and interpolating energy and derivative values at each of -{N} angles. During a simulation, these tables are used to interpolate -energy and force values on individual atoms as needed. The -interpolation is done in one of 2 styles: {linear} or {spline}. - -For the {linear} style, the angle is used to find 2 surrounding table -values from which an energy or its derivative is computed by linear -interpolation. - -For the {spline} style, a cubic spline coefficients are computed and -stored at each of the {N} values in the table. The angle is used to -find the appropriate set of coefficients which are used to evaluate a -cubic polynomial which computes the energy or derivative. - -The following coefficients must be defined for each angle type via the -"angle_coeff"_angle_coeff.html command as in the example above. - -filename -keyword :ul - -The filename specifies a file containing tabulated energy and -derivative values. The keyword specifies a section of the file. The -format of this file is described below. - -:line - -The format of a tabulated file is as follows (without the -parenthesized comments): - -# Angle potential for harmonic (one or more comment or blank lines) :pre - -HAM (keyword is the first text on line) -N 181 FP 0 0 EQ 90.0 (N, FP, EQ parameters) - (blank line) -N 181 FP 0 0 (N, FP parameters) -1 0.0 200.5 2.5 (index, angle, energy, derivative) -2 1.0 198.0 2.5 -... -181 180.0 0.0 0.0 :pre - -A section begins with a non-blank line whose 1st character is not a -"#"; blank lines or lines starting with "#" can be used as comments -between sections. The first line begins with a keyword which -identifies the section. The line can contain additional text, but the -initial text must match the argument specified in the -"angle_coeff"_angle_coeff.html command. The next line lists (in any -order) one or more parameters for the table. Each parameter is a -keyword followed by one or more numeric values. - -The parameter "N" is required and its value is the number of table -entries that follow. Note that this may be different than the {N} -specified in the "angle_style table"_angle_style.html command. Let -Ntable = {N} in the angle_style command, and Nfile = "N" in the -tabulated file. What LAMMPS does is a preliminary interpolation by -creating splines using the Nfile tabulated values as nodal points. It -uses these to interpolate as needed to generate energy and derivative -values at Ntable different points. The resulting tables of length -Ntable are then used as described above, when computing energy and -force for individual angles and their atoms. This means that if you -want the interpolation tables of length Ntable to match exactly what -is in the tabulated file (with effectively no preliminary -interpolation), you should set Ntable = Nfile. - -The "FP" parameter is optional. If used, it is followed by two values -fplo and fphi, which are the 2nd derivatives at the innermost and -outermost angle settings. These values are needed by the spline -construction routines. If not specified by the "FP" parameter, they -are estimated (less accurately) by the first two and last two -derivative values in the table. - -The "EQ" parameter is also optional. If used, it is followed by a the -equilibrium angle value, which is used, for example, by the "fix -shake"_fix_shake.html command. If not used, the equilibrium angle is -set to 180.0. - -Following a blank line, the next N lines list the tabulated values. -On each line, the 1st value is the index from 1 to N, the 2nd value is -the angle value (in degrees), the 3rd value is the energy (in energy -units), and the 4th is -dE/d(theta) (also in energy units). The 3rd -term is the energy of the 3-atom configuration for the specified -angle. The last term is the derivative of the energy with respect to -the angle (in degrees, not radians). Thus the units of the last term -are still energy, not force. The angle values must increase from one -line to the next. The angle values must also begin with 0.0 and end -with 180.0, i.e. span the full range of possible angles. - -Note that one file can contain many sections, each with a tabulated -potential. LAMMPS reads the file section by section until it finds -one that matches the specified keyword. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restart info:] - -This angle style writes the settings for the "angle_style table" -command to "binary restart files"_restart.html, so a angle_style -command does not need to specified in an input script that reads a -restart file. However, the coefficient information is not stored in -the restart file, since it is tabulated in the potential files. Thus, -angle_coeff commands do need to be specified in the restart input -script. - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -MOLECULE package. See the "Build package"_Build_package.html doc page -for more info. - -[Related commands:] - -"angle_coeff"_angle_coeff.html - -[Default:] none diff --git a/doc/txt/angle_zero.txt b/doc/txt/angle_zero.txt deleted file mode 100644 index c6c1958ec8..0000000000 --- a/doc/txt/angle_zero.txt +++ /dev/null @@ -1,49 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -angle_style zero command :h3 - -[Syntax:] - -angle_style zero {nocoeff} :pre - -[Examples:] - -angle_style zero -angle_style zero nocoeff -angle_coeff * -angle_coeff * 120.0 :pre - -[Description:] - -Using an angle style of zero means angle forces and energies are not -computed, but the geometry of angle triplets is still accessible to -other commands. - -As an example, the "compute angle/local"_compute_angle_local.html -command can be used to compute the theta values for the list of -triplets of angle atoms listed in the data file read by the -"read_data"_read_data.html command. If no angle style is defined, -this command cannot be used. - -The optional {nocoeff} flag allows to read data files with AngleCoeff -section for any angle style. Similarly, any angle_coeff commands -will only be checked for the angle type number and the rest ignored. - -Note that the "angle_coeff"_angle_coeff.html command must be used for -all angle types. If specified, there can be only one value, which is -going to be used to assign an equilibrium angle, e.g. for use with -"fix shake"_fix_shake.html. - -[Restrictions:] none - -[Related commands:] - -"angle_style none"_angle_none.html - -[Default:] none diff --git a/doc/txt/atom_modify.txt b/doc/txt/atom_modify.txt deleted file mode 100644 index d598b4697c..0000000000 --- a/doc/txt/atom_modify.txt +++ /dev/null @@ -1,175 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS -Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -atom_modify command :h3 - -[Syntax:] - -atom_modify keyword values ... :pre - -one or more keyword/value pairs may be appended :ulb,l -keyword = {id} or {map} or {first} or {sort} :l - {id} value = {yes} or {no} - {map} value = {yes} or {array} or {hash} - {first} value = group-ID = group whose atoms will appear first in internal atom lists - {sort} values = Nfreq binsize - Nfreq = sort atoms spatially every this many time steps - binsize = bin size for spatial sorting (distance units) :pre -:ule - -[Examples:] - -atom_modify map yes -atom_modify map hash sort 10000 2.0 -atom_modify first colloid :pre - -[Description:] - -Modify certain attributes of atoms defined and stored within LAMMPS, -in addition to what is specified by the "atom_style"_atom_style.html -command. The {id} and {map} keywords must be specified before a -simulation box is defined; other keywords can be specified any time. - -The {id} keyword determines whether non-zero atom IDs can be assigned -to each atom. If the value is {yes}, which is the default, IDs are -assigned, whether you use the "create atoms"_create_atoms.html or -"read_data"_read_data.html or "read_restart"_read_restart.html -commands to initialize atoms. If the value is {no} the IDs for all -atoms are assumed to be 0. - -If atom IDs are used, they must all be positive integers. They should -also be unique, though LAMMPS does not check for this. Typically they -should also be consecutively numbered (from 1 to Natoms), though this -is not required. Molecular "atom styles"_atom_style.html are those -that store bond topology information (styles bond, angle, molecular, -full). These styles require atom IDs since the IDs are used to encode -the topology. Some other LAMMPS commands also require the use of atom -IDs. E.g. some many-body pair styles use them to avoid double -computation of the I-J interaction between two atoms. - -The only reason not to use atom IDs is if you are running an atomic -simulation so large that IDs cannot be uniquely assigned. For a -default LAMMPS build this limit is 2^31 or about 2 billion atoms. -However, even in this case, you can use 64-bit atom IDs, allowing 2^63 -or about 9e18 atoms, if you build LAMMPS with the - DLAMMPS_BIGBIG -switch. This is described on the "Build_settings"_Build_settings.html -doc page. If atom IDs are not used, they must be specified as 0 for -all atoms, e.g. in a data or restart file. - -The {map} keyword determines how atoms with specific IDs are found -when required. An example are the bond (angle, etc) methods which -need to find the local index of an atom with a specific global ID -which is a bond (angle, etc) partner. LAMMPS performs this operation -efficiently by creating a "map", which is either an {array} or {hash} -table, as described below. - -When the {map} keyword is not specified in your input script, LAMMPS -only creates a map for "atom_styles"_atom_style.html for molecular -systems which have permanent bonds (angles, etc). No map is created -for atomic systems, since it is normally not needed. However some -LAMMPS commands require a map, even for atomic systems, and will -generate an error if one does not exist. The {map} keyword thus -allows you to force the creation of a map. The {yes} value will -create either an {array} or {hash} style map, as explained in the next -paragraph. The {array} and {hash} values create an atom-style or -hash-style map respectively. - -For an {array}-style map, each processor stores a lookup table of -length N, where N is the largest atom ID in the system. This is a -fast, simple method for many simulations, but requires too much memory -for large simulations. For a {hash}-style map, a hash table is -created on each processor, which finds an atom ID in constant time -(independent of the global number of atom IDs). It can be slightly -slower than the {array} map, but its memory cost is proportional to -the number of atoms owned by a processor, i.e. N/P when N is the total -number of atoms in the system and P is the number of processors. - -The {first} keyword allows a "group"_group.html to be specified whose -atoms will be maintained as the first atoms in each processor's list -of owned atoms. This in only useful when the specified group is a -small fraction of all the atoms, and there are other operations LAMMPS -is performing that will be sped-up significantly by being able to loop -over the smaller set of atoms. Otherwise the reordering required by -this option will be a net slow-down. The "neigh_modify -include"_neigh_modify.html and "comm_modify group"_comm_modify.html -commands are two examples of commands that require this setting to -work efficiently. Several "fixes"_fix.html, most notably time -integration fixes like "fix nve"_fix_nve.html, also take advantage of -this setting if the group they operate on is the group specified by -this command. Note that specifying "all" as the group-ID effectively -turns off the {first} option. - -It is OK to use the {first} keyword with a group that has not yet been -defined, e.g. to use the atom_modify first command at the beginning of -your input script. LAMMPS does not use the group until a simulation -is run. - -The {sort} keyword turns on a spatial sorting or reordering of atoms -within each processor's sub-domain every {Nfreq} timesteps. If -{Nfreq} is set to 0, then sorting is turned off. Sorting can improve -cache performance and thus speed-up a LAMMPS simulation, as discussed -in a paper by "(Meloni)"_#Meloni. Its efficacy depends on the problem -size (atoms/processor), how quickly the system becomes disordered, and -various other factors. As a general rule, sorting is typically more -effective at speeding up simulations of liquids as opposed to solids. -In tests we have done, the speed-up can range from zero to 3-4x. - -Reordering is performed every {Nfreq} timesteps during a dynamics run -or iterations during a minimization. More precisely, reordering -occurs at the first reneighboring that occurs after the target -timestep. The reordering is performed locally by each processor, -using bins of the specified {binsize}. If {binsize} is set to 0.0, -then a binsize equal to half the "neighbor"_neighbor.html cutoff -distance (force cutoff plus skin distance) is used, which is a -reasonable value. After the atoms have been binned, they are -reordered so that atoms in the same bin are adjacent to each other in -the processor's 1d list of atoms. - -The goal of this procedure is for atoms to put atoms close to each -other in the processor's one-dimensional list of atoms that are also -near to each other spatially. This can improve cache performance when -pairwise interactions and neighbor lists are computed. Note that if -bins are too small, there will be few atoms/bin. Likewise if bins are -too large, there will be many atoms/bin. In both cases, the goal of -cache locality will be undermined. - -NOTE: Running a simulation with sorting on versus off should not -change the simulation results in a statistical sense. However, a -different ordering will induce round-off differences, which will lead -to diverging trajectories over time when comparing two simulations. -Various commands, particularly those which use random numbers -(e.g. "velocity create"_velocity.html, and "fix -langevin"_fix_langevin.html), may generate (statistically identical) -results which depend on the order in which atoms are processed. The -order of atoms in a "dump"_dump.html file will also typically change -if sorting is enabled. - -[Restrictions:] - -The {first} and {sort} options cannot be used together. Since sorting -is on by default, it will be turned off if the {first} keyword is -used with a group-ID that is not "all". - -[Related commands:] none - -[Default:] - -By default, {id} is yes. By default, atomic systems (no bond topology -info) do not use a map. For molecular systems (with bond topology -info), a map is used. The default map style is array if no atom ID is -larger than 1 million, otherwise the default is hash. By default, a -"first" group is not defined. By default, sorting is enabled with a -frequency of 1000 and a binsize of 0.0, which means the neighbor -cutoff will be used to set the bin size. If no neighbor cutoff is -defined, sorting will be turned off. - -:line - -:link(Meloni) -[(Meloni)] Meloni, Rosati and Colombo, J Chem Phys, 126, 121102 (2007). diff --git a/doc/txt/atom_style.txt b/doc/txt/atom_style.txt deleted file mode 100644 index ff96fedab9..0000000000 --- a/doc/txt/atom_style.txt +++ /dev/null @@ -1,338 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -atom_style command :h3 - -[Syntax:] - -atom_style style args :pre - -style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \ - {dpd} or {edpd} or {mdpd} or {tdpd} or {electron} or {ellipsoid} or \ - {full} or {line} or {meso} or {molecular} or {peri} or {smd} or \ - {sphere} or {spin} or {tri} or {template} or {hybrid} :ulb,l - args = none for any style except the following - {body} args = bstyle bstyle-args - bstyle = style of body particles - bstyle-args = additional arguments specific to the bstyle - see the "Howto body"_Howto_body.html doc page for details - {tdpd} arg = Nspecies - Nspecies = # of chemical species - {template} arg = template-ID - template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command - {hybrid} args = list of one or more sub-styles, each with their args :pre - -accelerated styles (with same args) = {angle/kk} or {atomic/kk} or {bond/kk} or {charge/kk} or {full/kk} or {molecular/kk} :l -:ule - -[Examples:] - -atom_style atomic -atom_style bond -atom_style full -atom_style body nparticle 2 10 -atom_style hybrid charge bond -atom_style hybrid charge body nparticle 2 5 -atom_style spin -atom_style template myMols -atom_style tdpd 2 :pre - -[Description:] - -Define what style of atoms to use in a simulation. This determines -what attributes are associated with the atoms. This command must be -used before a simulation is setup via a "read_data"_read_data.html, -"read_restart"_read_restart.html, or "create_box"_create_box.html -command. - -NOTE: Many of the atom styles discussed here are only enabled if -LAMMPS was built with a specific package, as listed below in the -Restrictions section. - -Once a style is assigned, it cannot be changed, so use a style general -enough to encompass all attributes. E.g. with style {bond}, angular -terms cannot be used or added later to the model. It is OK to use a -style more general than needed, though it may be slightly inefficient. - -The choice of style affects what quantities are stored by each atom, -what quantities are communicated between processors to enable forces -to be computed, and what quantities are listed in the data file read -by the "read_data"_read_data.html command. - -These are the additional attributes of each style and the typical -kinds of physical systems they are used to model. All styles store -coordinates, velocities, atom IDs and types. See the -"read_data"_read_data.html, "create_atoms"_create_atoms.html, and -"set"_set.html commands for info on how to set these various -quantities. - -{angle} | bonds and angles | bead-spring polymers with stiffness | -{atomic} | only the default values | coarse-grain liquids, solids, metals | -{body} | mass, inertia moments, quaternion, angular momentum | arbitrary bodies | -{bond} | bonds | bead-spring polymers | -{charge} | charge | atomic system with charges | -{dipole} | charge and dipole moment | system with dipolar particles | -{dpd} | internal temperature and internal energies | DPD particles | -{edpd} | temperature and heat capacity | eDPD particles | -{mdpd} | density | mDPD particles | -{tdpd} | chemical concentration | tDPD particles | -{electron} | charge and spin and eradius | electronic force field | -{ellipsoid} | shape, quaternion, angular momentum | aspherical particles | -{full} | molecular + charge | bio-molecules | -{line} | end points, angular velocity | rigid bodies | -{meso} | rho, e, cv | SPH particles | -{molecular} | bonds, angles, dihedrals, impropers | uncharged molecules | -{peri} | mass, volume | mesoscopic Peridynamic models | -{smd} | volume, kernel diameter, contact radius, mass | solid and fluid SPH particles | -{sphere} | diameter, mass, angular velocity | granular models | -{spin} | magnetic moment | system with magnetic particles | -{template} | template index, template atom | small molecules with fixed topology | -{tri} | corner points, angular momentum | rigid bodies | -{wavepacket} | charge, spin, eradius, etag, cs_re, cs_im | AWPMD :tb(c=3,s=|) - -NOTE: It is possible to add some attributes, such as a molecule ID, to -atom styles that do not have them via the "fix -property/atom"_fix_property_atom.html command. This command also -allows new custom attributes consisting of extra integer or -floating-point values to be added to atoms. See the "fix -property/atom"_fix_property_atom.html doc page for examples of cases -where this is useful and details on how to initialize, access, and -output the custom values. - -All of the above styles define point particles, except the {sphere}, -{ellipsoid}, {electron}, {peri}, {wavepacket}, {line}, {tri}, and -{body} styles, which define finite-size particles. See the "Howto -spherical"_Howto_spherical.html doc page for an overview of using -finite-size particle models with LAMMPS. - -All of the point-particle styles assign mass to particles on a -per-type basis, using the "mass"_mass.html command, The finite-size -particle styles assign mass to individual particles on a per-particle -basis. - -For the {sphere} style, the particles are spheres and each stores a -per-particle diameter and mass. If the diameter > 0.0, the particle -is a finite-size sphere. If the diameter = 0.0, it is a point -particle. Note that by use of the {disc} keyword with the "fix -nve/sphere"_fix_nve_sphere.html, "fix nvt/sphere"_fix_nvt_sphere.html, -"fix nph/sphere"_fix_nph_sphere.html, "fix -npt/sphere"_fix_npt_sphere.html commands, spheres can be effectively -treated as 2d discs for a 2d simulation if desired. See also the "set -density/disc"_set.html command. - -For the {ellipsoid} style, the particles are ellipsoids and each -stores a flag which indicates whether it is a finite-size ellipsoid or -a point particle. If it is an ellipsoid, it also stores a shape -vector with the 3 diameters of the ellipsoid and a quaternion 4-vector -with its orientation. - -For the {dipole} style, a point dipole is defined for each point -particle. Note that if you wish the particles to be finite-size -spheres as in a Stockmayer potential for a dipolar fluid, so that the -particles can rotate due to dipole-dipole interactions, then you need -to use atom_style hybrid sphere dipole, which will assign both a -diameter and dipole moment to each particle. - -For the {electron} style, the particles representing electrons are 3d -Gaussians with a specified position and bandwidth or uncertainty in -position, which is represented by the eradius = electron size. - -For the {peri} style, the particles are spherical and each stores a -per-particle mass and volume. - -The {dpd} style is for dissipative particle dynamics (DPD) particles. -Note that it is part of the USER-DPD package, and is not for use with -the "pair_style dpd or dpd/stat"_pair_dpd.html commands, which can -simply use atom_style atomic. Atom_style dpd extends DPD particle -properties with internal temperature (dpdTheta), internal conductive -energy (uCond), internal mechanical energy (uMech), and internal -chemical energy (uChem). - -The {edpd} style is for energy-conserving dissipative particle -dynamics (eDPD) particles which store a temperature (edpd_temp), and -heat capacity(edpd_cv). - -The {mdpd} style is for many-body dissipative particle dynamics (mDPD) -particles which store a density (rho) for considering -density-dependent many-body interactions. - -The {tdpd} style is for transport dissipative particle dynamics (tDPD) -particles which store a set of chemical concentration. An integer -"cc_species" is required to specify the number of chemical species -involved in a tDPD system. - -The {meso} style is for smoothed particle hydrodynamics (SPH) -particles which store a density (rho), energy (e), and heat capacity -(cv). - -The {smd} style is for a general formulation of Smooth Particle -Hydrodynamics. Both fluids and solids can be modeled. Particles -store the mass and volume of an integration point, a kernel diameter -used for calculating the field variables (e.g. stress and deformation) -and a contact radius for calculating repulsive forces which prevent -individual physical bodies from penetrating each other. - -For the {spin} style, a magnetic spin is associated to each atom. -Those spins have a norm (their magnetic moment) and a direction. - -The {wavepacket} style is similar to {electron}, but the electrons may -consist of several Gaussian wave packets, summed up with coefficients -cs= (cs_re,cs_im). Each of the wave packets is treated as a separate -particle in LAMMPS, wave packets belonging to the same electron must -have identical {etag} values. - -For the {line} style, the particles are idealized line segments and -each stores a per-particle mass and length and orientation (i.e. the -end points of the line segment). - -For the {tri} style, the particles are planar triangles and each -stores a per-particle mass and size and orientation (i.e. the corner -points of the triangle). - -The {template} style allows molecular topology (bonds,angles,etc) to be -defined via a molecule template using the "molecule"_molecule.html -command. The template stores one or more molecules with a single copy -of the topology info (bonds,angles,etc) of each. Individual atoms -only store a template index and template atom to identify which -molecule and which atom-within-the-molecule they represent. Using the -{template} style instead of the {bond}, {angle}, {molecular} styles -can save memory for systems comprised of a large number of small -molecules, all of a single type (or small number of types). See the -paper by Grime and Voth, in "(Grime)"_#Grime, for examples of how this -can be advantageous for large-scale coarse-grained systems. - -NOTE: When using the {template} style with a "molecule -template"_molecule.html that contains multiple molecules, you should -insure the atom types, bond types, angle_types, etc in all the -molecules are consistent. E.g. if one molecule represents H2O and -another CO2, then you probably do not want each molecule file to -define 2 atom types and a single bond type, because they will conflict -with each other when a mixture system of H2O and CO2 molecules is -defined, e.g. by the "read_data"_read_data.html command. Rather the -H2O molecule should define atom types 1 and 2, and bond type 1. And -the CO2 molecule should define atom types 3 and 4 (or atom types 3 and -2 if a single oxygen type is desired), and bond type 2. - -For the {body} style, the particles are arbitrary bodies with internal -attributes defined by the "style" of the bodies, which is specified by -the {bstyle} argument. Body particles can represent complex entities, -such as surface meshes of discrete points, collections of -sub-particles, deformable objects, etc. - -The "Howto body"_Howto_body.html doc page describes the body styles -LAMMPS currently supports, and provides more details as to the kind of -body particles they represent. For all styles, each body particle -stores moments of inertia and a quaternion 4-vector, so that its -orientation and position can be time integrated due to forces and -torques. - -Note that there may be additional arguments required along with the -{bstyle} specification, in the atom_style body command. These -arguments are described on the "Howto body"_Howto_body.html doc page. - -:line - -Typically, simulations require only a single (non-hybrid) atom style. -If some atoms in the simulation do not have all the properties defined -by a particular style, use the simplest style that defines all the -needed properties by any atom. For example, if some atoms in a -simulation are charged, but others are not, use the {charge} style. -If some atoms have bonds, but others do not, use the {bond} style. - -The only scenario where the {hybrid} style is needed is if there is no -single style which defines all needed properties of all atoms. For -example, as mentioned above, if you want dipolar particles which will -rotate due to torque, you need to use "atom_style hybrid sphere -dipole". When a hybrid style is used, atoms store and communicate the -union of all quantities implied by the individual styles. - -When using the {hybrid} style, you cannot combine the {template} style -with another molecular style that stores bond,angle,etc info on a -per-atom basis. - -LAMMPS can be extended with new atom styles as well as new body -styles; see the "Modify"_Modify.html doc page. - -:line - -Styles with a {kk} suffix are functionally the same as the -corresponding style without the suffix. They have been optimized to -run faster, depending on your available hardware, as discussed in on -the "Speed packages"_Speed_packages.html doc page. The accelerated -styles take the same arguments and should produce the same results, -except for round-off and precision issues. - -Note that other acceleration packages in LAMMPS, specifically the GPU, -USER-INTEL, USER-OMP, and OPT packages do not use accelerated atom -styles. - -The accelerated styles are part of the KOKKOS package. They are only -enabled if LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -[Restrictions:] - -This command cannot be used after the simulation box is defined by a -"read_data"_read_data.html or "create_box"_create_box.html command. - -Many of the styles listed above are only enabled if LAMMPS was built -with a specific package, as listed below. See the "Build -package"_Build_package.html doc page for more info. - -The {angle}, {bond}, {full}, {molecular}, and {template} styles are -part of the MOLECULE package. - -The {line} and {tri} styles are part of the ASPHERE package. - -The {body} style is part of the BODY package. - -The {dipole} style is part of the DIPOLE package. - -The {peri} style is part of the PERI package for Peridynamics. - -The {electron} style is part of the USER-EFF package for "electronic -force fields"_pair_eff.html. - -The {dpd} style is part of the USER-DPD package for dissipative -particle dynamics (DPD). - -The {edpd}, {mdpd}, and {tdpd} styles are part of the USER-MESO package -for energy-conserving dissipative particle dynamics (eDPD), many-body -dissipative particle dynamics (mDPD), and transport dissipative particle -dynamics (tDPD), respectively. - -The {meso} style is part of the USER-SPH package for smoothed particle -hydrodynamics (SPH). See "this PDF -guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS. - -The {spin} style is part of the SPIN package. - -The {wavepacket} style is part of the USER-AWPMD package for the -"antisymmetrized wave packet MD method"_pair_awpmd.html. - -[Related commands:] - -"read_data"_read_data.html, "pair_style"_pair_style.html - -[Default:] - -atom_style atomic - -:line - -:link(Grime) -[(Grime)] Grime and Voth, to appear in J Chem Theory & Computation -(2014). diff --git a/doc/txt/bond_class2.txt b/doc/txt/bond_class2.txt deleted file mode 100644 index 4390e3613c..0000000000 --- a/doc/txt/bond_class2.txt +++ /dev/null @@ -1,81 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -bond_style class2 command :h3 -bond_style class2/omp command :h3 -bond_style class2/kk command :h3 - -[Syntax:] - -bond_style class2 :pre - -[Examples:] - -bond_style class2 -bond_coeff 1 1.0 100.0 80.0 80.0 :pre - -[Description:] - -The {class2} bond style uses the potential - -:c,image(Eqs/bond_class2.jpg) - -where r0 is the equilibrium bond distance. - -See "(Sun)"_#bond-Sun for a description of the COMPASS class2 force field. - -The following coefficients must be defined for each bond type via the -"bond_coeff"_bond_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -R0 (distance) -K2 (energy/distance^2) -K3 (energy/distance^3) -K4 (energy/distance^4) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This bond style can only be used if LAMMPS was built with the CLASS2 -package. See the "Build package"_Build_package.html doc page for more -info. - -[Related commands:] - -"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html - -[Default:] none - -:line - -:link(bond-Sun) -[(Sun)] Sun, J Phys Chem B 102, 7338-7364 (1998). diff --git a/doc/txt/bond_coeff.txt b/doc/txt/bond_coeff.txt deleted file mode 100644 index 1280ae3fb0..0000000000 --- a/doc/txt/bond_coeff.txt +++ /dev/null @@ -1,82 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -bond_coeff command :h3 - -[Syntax:] - -bond_coeff N args :pre - -N = bond type (see asterisk form below) -args = coefficients for one or more bond types :ul - -[Examples:] - -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 1 harmonic 200.0 1.0 :pre - -[Description:] - -Specify the bond force field coefficients for one or more bond types. -The number and meaning of the coefficients depends on the bond style. -Bond coefficients can also be set in the data file read by the -"read_data"_read_data.html command or in a restart file. - -N can be specified in one of two ways. An explicit numeric value can -be used, as in the 1st example above. Or a wild-card asterisk can be -used to set the coefficients for multiple bond types. This takes the -form "*" or "*n" or "n*" or "m*n". If N = the number of bond types, -then an asterisk with no numeric values means all types from 1 to N. A -leading asterisk means all types from 1 to n (inclusive). A trailing -asterisk means all types from n to N (inclusive). A middle asterisk -means all types from m to n (inclusive). - -Note that using a bond_coeff command can override a previous setting -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: - -bond_coeff * 100.0 1.2 -bond_coeff 2 200.0 1.2 :pre - -A line in a data file that specifies bond coefficients uses the exact -same format as the arguments of the bond_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 "Bond Coeffs" section of a data file, the line that -corresponds to the 1st example above would be listed as - -5 80.0 1.2 :pre - -:line - -The list of all bond styles defined in LAMMPS is given on the -"bond_style"_bond_style.html doc page. They are also listed in more -compact form on the "Commands bond"_Commands_bond.html 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 -bond_coeff command. - -:line - -[Restrictions:] - -This command must come after the simulation box is defined by a -"read_data"_read_data.html, "read_restart"_read_restart.html, or -"create_box"_create_box.html command. - -A bond style must be defined before any bond coefficients are set, -either in the input script or in a data file. - -[Related commands:] - -"bond_style"_bond_style.html - -[Default:] none diff --git a/doc/txt/bond_fene.txt b/doc/txt/bond_fene.txt deleted file mode 100644 index 9ec4017d00..0000000000 --- a/doc/txt/bond_fene.txt +++ /dev/null @@ -1,88 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -bond_style fene command :h3 -bond_style fene/intel command :h3 -bond_style fene/kk command :h3 -bond_style fene/omp command :h3 - -[Syntax:] - -bond_style fene :pre - -[Examples:] - -bond_style fene -bond_coeff 1 30.0 1.5 1.0 1.0 :pre - -[Description:] - -The {fene} bond style uses the potential - -:c,image(Eqs/bond_fene.jpg) - -to define a finite extensible nonlinear elastic (FENE) potential -"(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. - -The following coefficients must be defined for each bond type via the -"bond_coeff"_bond_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -K (energy/distance^2) -R0 (distance) -epsilon (energy) -sigma (distance) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the "Build package"_Build_package.html doc page for more -info. - -You typically should specify "special_bonds fene"_special_bonds.html -or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond -style. LAMMPS will issue a warning it that's not the case. - -[Related commands:] - -"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html - -[Default:] none - -:line - -:link(fene-Kremer) -[(Kremer)] Kremer, Grest, J Chem Phys, 92, 5057 (1990). diff --git a/doc/txt/bond_fene_expand.txt b/doc/txt/bond_fene_expand.txt deleted file mode 100644 index 4d7d2d5438..0000000000 --- a/doc/txt/bond_fene_expand.txt +++ /dev/null @@ -1,91 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -bond_style fene/expand command :h3 -bond_style fene/expand/omp command :h3 - -[Syntax:] - -bond_style fene/expand :pre - -[Examples:] - -bond_style fene/expand -bond_coeff 1 30.0 1.5 1.0 1.0 0.5 :pre - -[Description:] - -The {fene/expand} bond style uses the potential - -:c,image(Eqs/bond_fene_expand.jpg) - -to define a finite extensible nonlinear elastic (FENE) potential -"(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 -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. - -The following coefficients must be defined for each bond type via the -"bond_coeff"_bond_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -K (energy/distance^2) -R0 (distance) -epsilon (energy) -sigma (distance) -delta (distance) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the "Build package"_Build_package.html doc page for more -info. - -You typically should specify "special_bonds fene"_special_bonds.html -or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond -style. LAMMPS will issue a warning it that's not the case. - -[Related commands:] - -"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html - -[Default:] none - -:line - -:link(feneexpand-Kremer) -[(Kremer)] Kremer, Grest, J Chem Phys, 92, 5057 (1990). diff --git a/doc/txt/bond_gromos.txt b/doc/txt/bond_gromos.txt deleted file mode 100644 index e039e6c411..0000000000 --- a/doc/txt/bond_gromos.txt +++ /dev/null @@ -1,72 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -bond_style gromos command :h3 -bond_style gromos/omp command :h3 - -[Syntax:] - -bond_style gromos :pre - -[Examples:] - -bond_style gromos -bond_coeff 5 80.0 1.2 :pre - -[Description:] - -The {gromos} bond style uses the potential - -:c,image(Eqs/bond_gromos.jpg) - -where r0 is the equilibrium bond distance. Note that the usual 1/4 -factor is included in K. - -The following coefficients must be defined for each bond type via the -"bond_coeff"_bond_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -K (energy/distance^4) -r0 (distance) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the "Build package"_Build_package.html doc page for more -info. - -[Related commands:] - -"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html - -[Default:] none diff --git a/doc/txt/bond_harmonic.txt b/doc/txt/bond_harmonic.txt deleted file mode 100644 index 3afdf4ceba..0000000000 --- a/doc/txt/bond_harmonic.txt +++ /dev/null @@ -1,74 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -bond_style harmonic command :h3 -bond_style harmonic/intel command :h3 -bond_style harmonic/kk command :h3 -bond_style harmonic/omp command :h3 - -[Syntax:] - -bond_style harmonic :pre - -[Examples:] - -bond_style harmonic -bond_coeff 5 80.0 1.2 :pre - -[Description:] - -The {harmonic} bond style uses the potential - -:c,image(Eqs/bond_harmonic.jpg) - -where r0 is the equilibrium bond distance. Note that the usual 1/2 -factor is included in K. - -The following coefficients must be defined for each bond type via the -"bond_coeff"_bond_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -K (energy/distance^2) -r0 (distance) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the "Build package"_Build_package.html doc page for more -info. - -[Related commands:] - -"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html - -[Default:] none diff --git a/doc/txt/bond_harmonic_shift.txt b/doc/txt/bond_harmonic_shift.txt deleted file mode 100644 index 23d3dcb5d5..0000000000 --- a/doc/txt/bond_harmonic_shift.txt +++ /dev/null @@ -1,76 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -bond_style harmonic/shift command :h3 -bond_style harmonic/shift/omp command :h3 - -[Syntax:] - -bond_style harmonic/shift :pre - -[Examples:] - -bond_style harmonic/shift -bond_coeff 5 10.0 0.5 1.0 :pre - -[Description:] - -The {harmonic/shift} bond style is a shifted harmonic bond that uses -the potential - -:c,image(Eqs/bond_harmonic_shift.jpg) - -where r0 is the equilibrium bond distance, and rc the critical distance. -The potential is -Umin at r0 and zero at rc. The spring constant is -k = Umin / \[ 2 (r0-rc)^2\]. - -The following coefficients must be defined for each bond type via the -"bond_coeff"_bond_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -Umin (energy) :ul -r0 (distance) :ul -rc (distance) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This bond style can only be used if LAMMPS was built with the -USER-MISC package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html, -"bond_harmonic"_bond_harmonic.html - -[Default:] none diff --git a/doc/txt/bond_harmonic_shift_cut.txt b/doc/txt/bond_harmonic_shift_cut.txt deleted file mode 100644 index 13ccb5843b..0000000000 --- a/doc/txt/bond_harmonic_shift_cut.txt +++ /dev/null @@ -1,77 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -bond_style harmonic/shift/cut command :h3 -bond_style harmonic/shift/cut/omp command :h3 - -[Syntax:] - -bond_style harmonic/shift/cut :pre - -[Examples:] - -bond_style harmonic/shift/cut -bond_coeff 5 10.0 0.5 1.0 :pre - -[Description:] - -The {harmonic/shift/cut} bond style is a shifted harmonic bond that -uses the potential - -:c,image(Eqs/bond_harmonic_shift_cut.jpg) - -where r0 is the equilibrium bond distance, and rc the critical distance. -The bond potential is zero for distances r > rc. The potential is -Umin -at r0 and zero at rc. The spring constant is k = Umin / \[ 2 (r0-rc)^2\]. - -The following coefficients must be defined for each bond type via the -"bond_coeff"_bond_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -Umin (energy) -r0 (distance) -rc (distance) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This bond style can only be used if LAMMPS was built with the -USER-MISC package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html, -"bond_harmonic"_bond_harmonic.html, -"bond_harmonic_shift"_bond_harmonic_shift.html - -[Default:] none diff --git a/doc/txt/bond_hybrid.txt b/doc/txt/bond_hybrid.txt deleted file mode 100644 index 0996f72ce3..0000000000 --- a/doc/txt/bond_hybrid.txt +++ /dev/null @@ -1,74 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -bond_style hybrid command :h3 - -[Syntax:] - -bond_style hybrid style1 style2 ... :pre - -style1,style2 = list of one or more bond styles :ul - -[Examples:] - -bond_style hybrid harmonic fene -bond_coeff 1 harmonic 80.0 1.2 -bond_coeff 2* fene 30.0 1.5 1.0 1.0 :pre - -[Description:] - -The {hybrid} style enables the use of multiple bond styles in one -simulation. A bond style is assigned to each bond type. For example, -bonds in a polymer flow (of bond type 1) could be computed with a -{fene} potential and bonds in the wall boundary (of bond type 2) could -be computed with a {harmonic} potential. The assignment of bond type -to style is made via the "bond_coeff"_bond_coeff.html command or in -the data file. - -In the bond_coeff commands, the name of a bond style must be added -after the bond type, with the remaining coefficients being those -appropriate to that style. In the example above, the 2 bond_coeff -commands set bonds of bond type 1 to be computed with a {harmonic} -potential with coefficients 80.0, 1.2 for K, r0. All other bond types -(2-N) are computed with a {fene} potential with coefficients 30.0, -1.5, 1.0, 1.0 for K, R0, epsilon, sigma. - -If bond coefficients are specified in the data file read via the -"read_data"_read_data.html command, then the same rule applies. -E.g. "harmonic" or "fene" must be added after the bond type, for each -line in the "Bond Coeffs" section, e.g. - -Bond Coeffs :pre - -1 harmonic 80.0 1.2 -2 fene 30.0 1.5 1.0 1.0 -... :pre - -A bond style of {none} with no additional coefficients can be used in -place of a bond style, either in a input script bond_coeff command or -in the data file, if you desire to turn off interactions for specific -bond types. - -:line - -[Restrictions:] - -This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the "Build package"_Build_package.html doc page for more -info. - -Unlike other bond styles, the hybrid bond style does not store bond -coefficient info for individual sub-styles in a "binary restart -files"_restart.html. Thus when restarting a simulation from a restart -file, you need to re-specify bond_coeff commands. - -[Related commands:] - -"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html - -[Default:] none diff --git a/doc/txt/bond_mm3.txt b/doc/txt/bond_mm3.txt deleted file mode 100644 index c3d0e39f52..0000000000 --- a/doc/txt/bond_mm3.txt +++ /dev/null @@ -1,58 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -bond_style mm3 command :h3 - -[Syntax:] - -bond_style mm3 :pre - -[Examples:] - -bond_style mm3 -bond_coeff 1 100.0 107.0 :pre - -[Description:] - -The {mm3} bond style uses the potential that is anharmonic in the bond -as defined in "(Allinger)"_#mm3-allinger1989 - -:c,image(Eqs/bond_mm3.jpg) - -where r0 is the equilibrium value of the bond, and K is a -prefactor. The anharmonic prefactors have units angstrom^(-n): --2.55 angstrom^(-1) and (7/12)2.55^2 angstrom^(-2). The code takes -care of the necessary unit conversion for these factors internally. -Note that the MM3 papers contains an error in Eq (1): -(7/12)2.55 should be replaced with (7/12)2.55^2 - -The following coefficients must be defined for each bond type via the -"bond_coeff"_bond_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -K (energy/distance^2) -r0 (distance) :ul - -[Restrictions:] - -This bond style can only be used if LAMMPS was built with the -USER_YAFF package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"bond_coeff"_bond_coeff.html - -[Default:] none - -:line - -:link(mm3-allinger1989) -[(Allinger)] Allinger, Yuh, Lii, JACS, 111(23), 8551-8566 -(1989), diff --git a/doc/txt/bond_morse.txt b/doc/txt/bond_morse.txt deleted file mode 100644 index 60fd16e17a..0000000000 --- a/doc/txt/bond_morse.txt +++ /dev/null @@ -1,73 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -bond_style morse command :h3 -bond_style morse/omp command :h3 - -[Syntax:] - -bond_style morse :pre - -[Examples:] - -bond_style morse -bond_coeff 5 1.0 2.0 1.2 :pre - -[Description:] - -The {morse} bond style uses the potential - -:c,image(Eqs/bond_morse.jpg) - -where r0 is the equilibrium bond distance, alpha is a stiffness -parameter, and D determines the depth of the potential well. - -The following coefficients must be defined for each bond type via the -"bond_coeff"_bond_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -D (energy) -alpha (inverse distance) -r0 (distance) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the "Build package"_Build_package.html doc page for more -info. - -[Related commands:] - -"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html - -[Default:] none diff --git a/doc/txt/bond_none.txt b/doc/txt/bond_none.txt deleted file mode 100644 index cace1919e1..0000000000 --- a/doc/txt/bond_none.txt +++ /dev/null @@ -1,34 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -bond_style none command :h3 - -[Syntax:] - -bond_style none :pre - -[Examples:] - -bond_style none :pre - -[Description:] - -Using a bond style of none means bond forces and energies are not -computed, even if pairs of bonded atoms were listed in the data file -read by the "read_data"_read_data.html command. - -See the "bond_style zero"_bond_zero.html command for a way to -calculate bond statistics, but compute no bond interactions. - -[Restrictions:] none - -[Related commands:] none - -"bond_style zero"_bond_zero.html - -[Default:] none diff --git a/doc/txt/bond_nonlinear.txt b/doc/txt/bond_nonlinear.txt deleted file mode 100644 index af51383213..0000000000 --- a/doc/txt/bond_nonlinear.txt +++ /dev/null @@ -1,78 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -bond_style nonlinear command :h3 -bond_style nonlinear/omp command :h3 - -[Syntax:] - -bond_style nonlinear :pre - -[Examples:] - -bond_style nonlinear -bond_coeff 2 100.0 1.1 1.4 :pre - -[Description:] - -The {nonlinear} bond style uses the potential - -:c,image(Eqs/bond_nonlinear.jpg) - -to define an anharmonic spring "(Rector)"_#Rector of equilibrium -length r0 and maximum extension lamda. - -The following coefficients must be defined for each bond type via the -"bond_coeff"_bond_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -epsilon (energy) -r0 (distance) -lamda (distance) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the "Build package"_Build_package.html doc page for more -info. - -[Related commands:] - -"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html - -[Default:] none - -:line - -:link(Rector) -[(Rector)] Rector, Van Swol, Henderson, Molecular Physics, 82, 1009 (1994). diff --git a/doc/txt/bond_oxdna.txt b/doc/txt/bond_oxdna.txt deleted file mode 100644 index 88afe435e6..0000000000 --- a/doc/txt/bond_oxdna.txt +++ /dev/null @@ -1,99 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -bond_style oxdna/fene command :h3 -bond_style oxdna2/fene command :h3 - -[Syntax:] - -bond_style oxdna/fene :pre -bond_style oxdna2/fene :pre - -[Examples:] - -bond_style oxdna/fene -bond_coeff * 2.0 0.25 0.7525 :pre - -bond_style oxdna2/fene -bond_coeff * 2.0 0.25 0.7564 :pre - -[Description:] - -The {oxdna/fene} and {oxdna2/fene} bond styles use the potential - -:c,image(Eqs/bond_oxdna_fene.jpg) - -to define a modified finite extensible nonlinear elastic (FENE) -potential "(Ouldridge)"_#oxdna_fene to model the connectivity of the -phosphate backbone in the oxDNA force field for coarse-grained -modelling of DNA. - -The following coefficients must be defined for the bond type via the -"bond_coeff"_bond_coeff.html command as given in the above example, or -in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands: - -epsilon (energy) -Delta (distance) -r0 (distance) :ul - -NOTE: The oxDNA bond style has to be used together with the -corresponding oxDNA pair styles for excluded volume interaction -{oxdna/excv}, stacking {oxdna/stk}, cross-stacking {oxdna/xstk} and -coaxial stacking interaction {oxdna/coaxstk} as well as -hydrogen-bonding interaction {oxdna/hbond} (see also documentation of -"pair_style oxdna/excv"_pair_oxdna.html). For the oxDNA2 -"(Snodin)"_#oxdna2 bond style the analogous pair styles and an -additional Debye-Hueckel pair style {oxdna2/dh} have to be defined. -The coefficients in the above example have to be kept fixed and cannot -be changed without reparameterizing the entire model. - -Example input and data files for DNA duplexes can be found in -examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. A simple python -setup tool which creates single straight or helical DNA strands, DNA -duplexes or arrays of DNA duplexes can be found in -examples/USER/cgdna/util/. - -Please cite "(Henrich)"_#Henrich2 and the relevant oxDNA articles in -any publication that uses this implementation. The article contains -more information on the model, the structure of the input file, the -setup tool and the performance of the LAMMPS-implementation of oxDNA. -The preprint version of the article can be found -"here"_PDF/USER-CGDNA.pdf. - -:line - -[Restrictions:] - -This bond style can only be used if LAMMPS was built with the -USER-CGDNA package and the MOLECULE and ASPHERE package. See the -"Build package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_style oxdna/excv"_pair_oxdna.html, "pair_style -oxdna2/excv"_pair_oxdna2.html, "fix -nve/dotc/langevin"_fix_nve_dotc_langevin.html, -"bond_coeff"_bond_coeff.html - -[Default:] none - -:line - -:link(Henrich2) -[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, -T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018). - -:link(oxdna_fene) -[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, -J. Chem. Phys. 134, 085101 (2011). - -:link(oxdna2) -[(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al., -J. Chem. Phys. 142, 234901 (2015). diff --git a/doc/txt/bond_quartic.txt b/doc/txt/bond_quartic.txt deleted file mode 100644 index b7b1ee4ce6..0000000000 --- a/doc/txt/bond_quartic.txt +++ /dev/null @@ -1,112 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -bond_style quartic command :h3 -bond_style quartic/omp command :h3 - -[Syntax:] - -bond_style quartic :pre - -[Examples:] - -bond_style quartic -bond_coeff 2 1200 -0.55 0.25 1.3 34.6878 :pre - -[Description:] - -The {quartic} bond style uses the potential - -:c,image(Eqs/bond_quartic.jpg) - -to define a bond that can be broken as the simulation proceeds (e.g. -due to a polymer being stretched). The sigma and epsilon used in the -LJ portion of the formula are both set equal to 1.0 by LAMMPS. - -The following coefficients must be defined for each bond type via the -"bond_coeff"_bond_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -K (energy/distance^4) -B1 (distance) -B2 (distance) -Rc (distance) -U0 (energy) :ul - -This potential was constructed to mimic the FENE bond potential for -coarse-grained polymer chains. When monomers with sigma = epsilon = -1.0 are used, the following choice of parameters gives a quartic -potential that looks nearly like the FENE potential: K = 1200, B1 = --0.55, B2 = 0.25, Rc = 1.3, and U0 = 34.6878. Different parameters -can be specified using the "bond_coeff"_bond_coeff.html command, but -you will need to choose them carefully so they form a suitable bond -potential. - -Rc is the cutoff length at which the bond potential goes smoothly to a -local maximum. If a bond length ever becomes > Rc, LAMMPS "breaks" -the bond, which means two things. First, the bond potential is turned -off by setting its type to 0, and is no longer computed. Second, a -pairwise interaction between the two atoms is turned on, since they -are no longer bonded. - -LAMMPS does the second task via a computational sleight-of-hand. It -subtracts the pairwise interaction as part of the bond computation. -When the bond breaks, the subtraction stops. For this to work, the -pairwise interaction must always be computed by the -"pair_style"_pair_style.html command, whether the bond is broken or -not. This means that "special_bonds"_special_bonds.html must be set -to 1,1,1, as indicated as a restriction below. - -Note that when bonds are dumped to a file via the "dump -local"_dump.html command, bonds with type 0 are not included. The -"delete_bonds"_delete_bonds.html command can also be used to query the -status of broken bonds or permanently delete them, e.g.: - -delete_bonds all stats -delete_bonds all bond 0 remove :pre - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the "Build package"_Build_package.html doc page for more -info. - -The {quartic} style requires that "special_bonds"_special_bonds.html -parameters be set to 1,1,1. Three- and four-body interactions (angle, -dihedral, etc) cannot be used with {quartic} bonds. - -[Related commands:] - -"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html - -[Default:] none diff --git a/doc/txt/bond_style.txt b/doc/txt/bond_style.txt deleted file mode 100644 index aba6d3a778..0000000000 --- a/doc/txt/bond_style.txt +++ /dev/null @@ -1,115 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -bond_style command :h3 - -[Syntax:] - -bond_style style args :pre - -style = {none} or {hybrid} or {class2} or {fene} or {fene/expand} or \ - {harmonic} or {morse} or {nonlinear} or {quartic} :ul - args = none for any style except {hybrid} - {hybrid} args = list of one or more styles :pre - -[Examples:] - -bond_style harmonic -bond_style fene -bond_style hybrid harmonic fene :pre - -[Description:] - -Set the formula(s) LAMMPS uses to compute bond interactions between -pairs of atoms. In LAMMPS, a bond differs from a pairwise -interaction, which are set via the "pair_style"_pair_style.html -command. Bonds are defined between specified pairs of atoms and -remain in force for the duration of the simulation (unless the bond -breaks which is possible in some bond potentials). The list of bonded -atoms is read in by a "read_data"_read_data.html or -"read_restart"_read_restart.html command from a data or restart file. -By contrast, pair potentials are typically defined between all pairs -of atoms within a cutoff distance and the set of active interactions -changes over time. - -Hybrid models where bonds are computed using different bond potentials -can be setup using the {hybrid} bond style. - -The coefficients associated with a bond style can be specified in a -data or restart file or via the "bond_coeff"_bond_coeff.html command. - -All bond potentials store their coefficient data in binary restart -files which means bond_style and "bond_coeff"_bond_coeff.html commands -do not need to be re-specified in an input script that restarts a -simulation. See the "read_restart"_read_restart.html command for -details on how to do this. The one exception is that bond_style -{hybrid} only stores the list of sub-styles in the restart file; bond -coefficients need to be re-specified. - -NOTE: When both a bond and pair style is defined, the -"special_bonds"_special_bonds.html command often needs to be used to -turn off (or weight) the pairwise interaction that would otherwise -exist between 2 bonded atoms. - -In the formulas listed for each bond style, {r} is the distance -between the 2 atoms in the bond. - -:line - -Here is an alphabetic list of bond styles defined in LAMMPS. Click on -the style to display the formula it computes and coefficients -specified by the associated "bond_coeff"_bond_coeff.html command. - -Click on the style to display the formula it computes, any additional -arguments specified in the bond_style command, and coefficients -specified by the associated "bond_coeff"_bond_coeff.html command. - -There are also additional accelerated pair styles included in the -LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. -The individual style names on the "Commands bond"_Commands_bond.html -doc page are followed by one or more of (g,i,k,o,t) to indicate which -accelerated styles exist. - -"none"_bond_none.html - turn off bonded interactions -"zero"_bond_zero.html - topology but no interactions -"hybrid"_bond_hybrid.html - define multiple styles of bond interactions :ul - -"class2"_bond_class2.html - COMPASS (class 2) bond -"fene"_bond_fene.html - FENE (finite-extensible non-linear elastic) bond -"fene/expand"_bond_fene_expand.html - FENE bonds with variable size particles -"gromos"_bond_gromos.html - GROMOS force field bond -"harmonic"_bond_harmonic.html - harmonic bond -"harmonic/shift"_bond_harmonic_shift.html - shifted harmonic bond -"harmonic/shift/cut"_bond_harmonic_shift_cut.html - shifted harmonic bond with a cutoff -"mm3"_bond_mm3.html - MM3 anharmonic bond -"morse"_bond_morse.html - Morse bond -"nonlinear"_bond_nonlinear.html - nonlinear bond -"oxdna/fene"_bond_oxdna.html - modified FENE bond suitable for DNA modeling -"oxdna2/fene"_bond_oxdna.html - same as oxdna but used with different pair styles -"quartic"_bond_quartic.html - breakable quartic bond -"table"_bond_table.html - tabulated by bond length :ul - -:line - -[Restrictions:] - -Bond styles can only be set for atom styles that allow bonds to be -defined. - -Most bond styles are part of the MOLECULE package. They are only -enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. The doc pages for -individual bond potentials tell if it is part of a package. - -[Related commands:] - -"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html - -[Default:] - -bond_style none diff --git a/doc/txt/bond_table.txt b/doc/txt/bond_table.txt deleted file mode 100644 index 7235214af0..0000000000 --- a/doc/txt/bond_table.txt +++ /dev/null @@ -1,163 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -bond_style table command :h3 -bond_style table/omp command :h3 - -[Syntax:] - -bond_style table style N :pre - -style = {linear} or {spline} = method of interpolation -N = use N values in table :ul - -[Examples:] - -bond_style table linear 1000 -bond_coeff 1 file.table ENTRY1 :pre - -[Description:] - -Style {table} creates interpolation tables of length {N} from bond -potential and force values listed in a file(s) as a function of bond -length. The files are read by the "bond_coeff"_bond_coeff.html -command. - -The interpolation tables are created by fitting cubic splines to the -file values and interpolating energy and force values at each of {N} -distances. During a simulation, these tables are used to interpolate -energy and force values as needed. The interpolation is done in one -of 2 styles: {linear} or {spline}. - -For the {linear} style, the bond length is used to find 2 surrounding -table values from which an energy or force is computed by linear -interpolation. - -For the {spline} style, a cubic spline coefficients are computed and -stored at each of the {N} values in the table. The bond length is -used to find the appropriate set of coefficients which are used to -evaluate a cubic polynomial which computes the energy or force. - -The following coefficients must be defined for each bond type via the -"bond_coeff"_bond_coeff.html command as in the example above. - -filename -keyword :ul - -The filename specifies a file containing tabulated energy and force -values. The keyword specifies a section of the file. The format of -this file is described below. - -:line - -The format of a tabulated file is as follows (without the -parenthesized comments): - -# Bond potential for harmonic (one or more comment or blank lines) :pre - -HAM (keyword is the first text on line) -N 101 FP 0 0 EQ 0.5 (N, FP, EQ parameters) - (blank line) -1 0.00 338.0000 1352.0000 (index, bond-length, energy, force) -2 0.01 324.6152 1324.9600 -... -101 1.00 338.0000 -1352.0000 :pre - -A section begins with a non-blank line whose 1st character is not a -"#"; blank lines or lines starting with "#" can be used as comments -between sections. The first line begins with a keyword which -identifies the section. The line can contain additional text, but the -initial text must match the argument specified in the -"bond_coeff"_bond_coeff.html command. The next line lists (in any -order) one or more parameters for the table. Each parameter is a -keyword followed by one or more numeric values. - -The parameter "N" is required and its value is the number of table -entries that follow. Note that this may be different than the {N} -specified in the "bond_style table"_bond_style.html command. Let -Ntable = {N} in the bond_style command, and Nfile = "N" in the -tabulated file. What LAMMPS does is a preliminary interpolation by -creating splines using the Nfile tabulated values as nodal points. It -uses these to interpolate as needed to generate energy and force -values at Ntable different points. The resulting tables of length -Ntable are then used as described above, when computing energy and -force for individual bond lengths. This means that if you want the -interpolation tables of length Ntable to match exactly what is in the -tabulated file (with effectively no preliminary interpolation), you -should set Ntable = Nfile. - -The "FP" parameter is optional. If used, it is followed by two values -fplo and fphi, which are the derivatives of the force at the innermost -and outermost bond lengths. These values are needed by the spline -construction routines. If not specified by the "FP" parameter, they -are estimated (less accurately) by the first two and last two force -values in the table. - -The "EQ" parameter is also optional. If used, it is followed by a the -equilibrium bond length, which is used, for example, by the "fix -shake"_fix_shake.html command. If not used, the equilibrium bond -length is to the distance in the table with the lowest potential energy. - -Following a blank line, the next N lines list the tabulated values. -On each line, the 1st value is the index from 1 to N, the 2nd value is -the bond length r (in distance units), the 3rd value is the energy (in -energy units), and the 4th is the force (in force units). The bond -lengths must range from a LO value to a HI value, and increase from -one line to the next. If the actual bond length is ever smaller than -the LO value or larger than the HI value, then the bond energy and -force is evaluated as if the bond were the LO or HI length. - -Note that one file can contain many sections, each with a tabulated -potential. LAMMPS reads the file section by section until it finds -one that matches the specified keyword. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restart info:] - -This bond style writes the settings for the "bond_style table" -command to "binary restart files"_restart.html, so a bond_style -command does not need to specified in an input script that reads a -restart file. However, the coefficient information is not stored in -the restart file, since it is tabulated in the potential files. Thus, -bond_coeff commands do need to be specified in the restart input -script. - -[Restrictions:] - -This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the "Build package"_Build_package.html doc page for more -info. - -[Related commands:] - -"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html - -[Default:] none diff --git a/doc/txt/bond_write.txt b/doc/txt/bond_write.txt deleted file mode 100644 index 711bd2c296..0000000000 --- a/doc/txt/bond_write.txt +++ /dev/null @@ -1,64 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -bond_write command :h3 - -[Syntax:] - -bond_write btype N inner outer file keyword itype jtype :pre - -btype = bond types -N = # of values -inner,outer = inner and outer bond length (distance units) -file = name of file to write values to -keyword = section name in file for this set of tabulated values -itype,jtype = 2 atom types (optional) -:ul - -[Examples:] - -bond_write 1 500 0.5 3.5 table.txt Harmonic_1 -bond_write 3 1000 0.1 6.0 table.txt Morse :pre - -[Description:] - -Write energy and force values to a file as a function of distance for -the currently defined bond potential. This is useful for plotting the -potential function or otherwise debugging its values. If the file -already exists, the table of values is appended to the end of the file -to allow multiple tables of energy and force to be included in one -file. - -The energy and force values are computed at distances from inner to -outer for 2 interacting atoms forming a bond of type btype, using the -appropriate "bond_coeff"_bond_coeff.html coefficients. N evenly spaced -distances are used. - -For example, for N = 7, inner = 1.0, and outer = 4.0, -values are computed at r = 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0. - -The file is written in the format used as input for the -"bond_style"_bond_style.html {table} option with {keyword} as the -section name. Each line written to the file lists an index number -(1-N), a distance (in distance units), an energy (in energy units), -and a force (in force units). - -[Restrictions:] - -All force field coefficients for bond and other kinds of interactions -must be set before this command can be invoked. - -Due to how the bond force is computed, an inner value > 0.0 must -be specified even if the potential has a finite value at r = 0.0. - -[Related commands:] - -"bond_style table"_bond_table.html, -"bond_style"_bond_style.html, "bond_coeff"_bond_coeff.html - -[Default:] none diff --git a/doc/txt/bond_zero.txt b/doc/txt/bond_zero.txt deleted file mode 100644 index 554f26e7f0..0000000000 --- a/doc/txt/bond_zero.txt +++ /dev/null @@ -1,48 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -bond_style zero command :h3 - -[Syntax:] - -bond_style zero {nocoeff} :pre - -[Examples:] - -bond_style zero -bond_style zero nocoeff -bond_coeff * -bond_coeff * 2.14 :pre - -[Description:] - -Using an bond style of zero means bond forces and energies are not -computed, but the geometry of bond pairs is still accessible to other -commands. - -As an example, the "compute bond/local"_compute_bond_local.html -command can be used to compute distances for the list of pairs of bond -atoms listed in the data file read by the "read_data"_read_data.html -command. If no bond style is defined, this command cannot be used. - -The optional {nocoeff} flag allows to read data files with a BondCoeff -section for any bond style. Similarly, any bond_coeff commands -will only be checked for the bond type number and the rest ignored. - -Note that the "bond_coeff"_bond_coeff.html command must be used for -all bond types. If specified, there can be only one value, which is -going to be used to assign an equilibrium distance, e.g. for use with -"fix shake"_fix_shake.html. - -[Restrictions:] none - -[Related commands:] - -"bond_style none"_bond_none.html - -[Default:] none diff --git a/doc/txt/fix_restrain.txt b/doc/txt/fix_restrain.txt deleted file mode 100644 index 8e962f4cc9..0000000000 --- a/doc/txt/fix_restrain.txt +++ /dev/null @@ -1,209 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix restrain command :h3 - -[Syntax:] - -fix ID group-ID restrain keyword args ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -restrain = style name of this fix command :l -one or more keyword/arg pairs may be appended :l -keyword = {bond} or {angle} or {dihedral} :l - {bond} args = atom1 atom2 Kstart Kstop r0 - atom1,atom2 = IDs of 2 atoms in bond - Kstart,Kstop = restraint coefficients at start/end of run (energy units) - r0 = equilibrium bond distance (distance units) - {angle} args = atom1 atom2 atom3 Kstart Kstop theta0 - atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom - Kstart,Kstop = restraint coefficients at start/end of run (energy units) - theta0 = equilibrium angle theta (degrees) - {dihedral} args = atom1 atom2 atom3 atom4 Kstart Kstop phi0 keyword/value - atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order - Kstart,Kstop = restraint coefficients at start/end of run (energy units) - phi0 = equilibrium dihedral angle phi (degrees) - keyword/value = optional keyword value pairs. supported keyword/value pairs: - {mult} n = dihedral multiplicity n (integer >= 0, default = 1) :pre -:ule - -[Examples:] - -fix holdem all restrain bond 45 48 2000.0 2000.0 2.75 -fix holdem all restrain dihedral 1 2 3 4 2000.0 2000.0 120.0 -fix holdem all restrain bond 45 48 2000.0 2000.0 2.75 dihedral 1 2 3 4 2000.0 2000.0 120.0 -fix texas_holdem all restrain dihedral 1 2 3 4 0.0 2000.0 120.0 dihedral 1 2 3 5 0.0 2000.0 -120.0 dihedral 1 2 3 6 0.0 2000.0 0.0 :pre - -[Description:] - -Restrain the motion of the specified sets of atoms by making them part -of a bond or angle or dihedral interaction whose strength can vary -over time during a simulation. This is functionally similar to -creating a bond or angle or dihedral for the same atoms in a data -file, as specified by the "read_data"_read_data.html command, albeit -with a time-varying pre-factor coefficient, and except for exclusion -rules, as explained below. - -For the purpose of force field parameter-fitting or mapping a molecular -potential energy surface, this fix reduces the hassle and risk -associated with modifying data files. In other words, use this fix to -temporarily force a molecule to adopt a particular conformation. To -create a permanent bond or angle or dihedral, you should modify the -data file. - -NOTE: Adding a bond/angle/dihedral with this command does not apply -the exclusion rules and weighting factors specified by the -"special_bonds"_special_bonds.html command to atoms in the restraint -that are now bonded (1-2,1-3,1-4 neighbors) as a result. If they are -close enough to interact in a "pair_style"_pair_style.html sense -(non-bonded interaction), then the bond/angle/dihedral restraint -interaction will simply be superposed on top of that interaction. - -The group-ID specified by this fix is ignored. - -The second example above applies a restraint to hold the dihedral -angle formed by atoms 1, 2, 3, and 4 near 120 degrees using a constant -restraint coefficient. The fourth example applies similar restraints -to multiple dihedral angles using a restraint coefficient that -increases from 0.0 to 2000.0 over the course of the run. - -NOTE: Adding a force to atoms implies a change in their potential -energy as they move due to the applied force field. For dynamics via -the "run"_run.html command, this energy can be added to the system's -potential energy for thermodynamic output (see below). For energy -minimization via the "minimize"_minimize.html command, this energy -must be added to the system's potential energy to formulate a -self-consistent minimization problem (see below). - -In order for a restraint to be effective, the restraint force must -typically be significantly larger than the forces associated with -conventional force field terms. If the restraint is applied during a -dynamics run (as opposed to during an energy minimization), a large -restraint coefficient can significantly reduce the stable timestep -size, especially if the atoms are initially far from the preferred -conformation. You may need to experiment to determine what value of K -works best for a given application. - -For the case of finding a minimum energy structure for a single -molecule with particular restraints (e.g. for fitting force field -parameters or constructing a potential energy surface), commands such -as the following may be useful: - -# minimize molecule energy with restraints -velocity all create 600.0 8675309 mom yes rot yes dist gaussian -fix NVE all nve -fix TFIX all langevin 600.0 0.0 100 24601 -fix REST all restrain dihedral 2 1 3 8 0.0 5000.0 $\{angle1\} dihedral 3 1 2 9 0.0 5000.0 $\{angle2\} -fix_modify REST energy yes -run 10000 -fix TFIX all langevin 0.0 0.0 100 24601 -fix REST all restrain dihedral 2 1 3 8 5000.0 5000.0 $\{angle1\} dihedral 3 1 2 9 5000.0 5000.0 $\{angle2\} -fix_modify REST energy yes -run 10000 -# sanity check for convergence -minimize 1e-6 1e-9 1000 100000 -# report unrestrained energies -unfix REST -run 0 :pre - -:line - -The {bond} keyword applies a bond restraint to the specified atoms -using the same functional form used by the "bond_style -harmonic"_bond_harmonic.html command. The potential associated with -the restraint is - -:c,image(Eqs/bond_harmonic.jpg) - -with the following coefficients: - -K (energy/distance^2) -r0 (distance) :ul - -K and r0 are specified with the fix. Note that the usual 1/2 factor -is included in K. - -:line - -The {angle} keyword applies an angle restraint to the specified atoms -using the same functional form used by the "angle_style -harmonic"_angle_harmonic.html command. The potential associated with -the restraint is - -:c,image(Eqs/angle_harmonic.jpg) - -with the following coefficients: - -K (energy/radian^2) -theta0 (degrees) :ul - -K and theta0 are specified with the fix. Note that the usual 1/2 -factor is included in K. - -:line - -The {dihedral} keyword applies a dihedral restraint to the specified -atoms using a simplified form of the function used by the -"dihedral_style charmm"_dihedral_charmm.html command. The potential -associated with the restraint is - -:c,image(Eqs/dihedral_charmm.jpg) - -with the following coefficients: - -K (energy) -n (multiplicity, >= 0) -d (degrees) = phi0 + 180 :ul - -K and phi0 are specified with the fix. Note that the value of the -dihedral multiplicity {n} is set by default to 1. You can use the -optional {mult} keyword to set it to a different positive integer. -Also note that the energy will be a minimum when the -current dihedral angle phi is equal to phi0. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the potential energy associated with this fix to the -system's potential energy as part of "thermodynamic -output"_thermo_style.html. - -The "fix_modify"_fix_modify.html {respa} option is supported by this -fix. This allows to set at which level of the "r-RESPA"_run_style.html -integrator the fix is adding its forces. Default is the outermost level. - -NOTE: If you want the fictitious potential energy associated with the -added forces to be included in the total potential energy of the -system (the quantity being minimized), you MUST enable the -"fix_modify"_fix_modify.html {energy} option for this fix. - -This fix computes a global scalar and a global vector of length 3, -which can be accessed by various "output commands"_Howto_output.html. -The scalar is the total potential energy for {all} the restraints as -discussed above. The vector values are the sum of contributions to the -following individual categories: - -1 = bond energy -2 = angle energy -3 = dihedral energy :ul - -The scalar and vector values calculated by this fix are "extensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. - -[Restrictions:] none - -[Related commands:] none - -[Default:] none diff --git a/doc/txt/pair_list.txt b/doc/txt/pair_list.txt deleted file mode 100644 index 9500a4c508..0000000000 --- a/doc/txt/pair_list.txt +++ /dev/null @@ -1,144 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style list command :h3 - -[Syntax:] - -pair_style list listfile cutoff keyword :pre - -listfile = name of file with list of pairwise interactions -cutoff = global cutoff (distance units) -keyword = optional flag {nocheck} or {check} (default is {check}) :ul - -[Examples:] - -pair_style list restraints.txt 200.0 -pair_coeff * * :pre - -pair_style hybrid/overlay lj/cut 1.1225 list pair_list.txt 300.0 -pair_coeff * * lj/cut 1.0 1.0 -pair_coeff 3* 3* list :pre - -[Description:] - -Style {list} computes interactions between explicitly listed pairs of -atoms with the option to select functional form and parameters for -each individual pair. Because the parameters are set in the list -file, the pair_coeff command has no parameters (but still needs to be -provided). The {check} and {nocheck} keywords enable/disable a test -that checks whether all listed bonds were present and computed. - -This pair style can be thought of as a hybrid between bonded, -non-bonded, and restraint interactions. It will typically be used as -an additional interaction within the {hybrid/overlay} pair style. It -currently supports three interaction styles: a 12-6 Lennard-Jones, a -Morse and a harmonic potential. - -The format of the list file is as follows: - -one line per pair of atoms :ulb,l -empty lines will be ignored :l -comment text starts with a '#' character :l -line syntax: {ID1 ID2 style coeffs cutoff} :l - ID1 = atom ID of first atom - ID2 = atom ID of second atom - style = style of interaction - coeffs = list of coeffs - cutoff = cutoff for interaction (optional) :pre -:ule - -The cutoff parameter is optional. If not specified, the global cutoff -is used. - -Here is an example file: - -# this is a comment :pre - -15 259 lj126 1.0 1.0 50.0 -15 603 morse 10.0 1.2 2.0 10.0 # and another comment -18 470 harmonic 50.0 1.2 5.0 :pre - -The style {lj126} computes pairwise interactions with the formula - -:c,image(Eqs/pair_lj.jpg) - -and the coefficients: - -epsilon (energy units) -sigma (distance units) :ul - -The style {morse} computes pairwise interactions with the formula - -:c,image(Eqs/pair_morse.jpg) - -and the coefficients: - -D0 (energy units) -alpha (1/distance units) -r0 (distance units) :ul - -The style {harmonic} computes pairwise interactions with the formula - -:c,image(Eqs/bond_harmonic.jpg) - -and the coefficients: - -K (energy units) -r0 (distance units) :ul - -Note that the usual 1/2 factor is included in K. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -This pair style does not support mixing since all parameters are -explicit for each pair. - -The "pair_modify"_pair_modify.html shift option is supported by this -pair style. - -The "pair_modify"_pair_modify.html table and tail options are not -relevant for this pair style. - -This pair style does not write its information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands need -to be specified in an input script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -This pair style does not use a neighbor list and instead identifies -atoms by their IDs. This has two consequences: 1) The cutoff has to be -chosen sufficiently large, so that the second atom of a pair has to be -a ghost atom on the same node on which the first atom is local; -otherwise the interaction will be skipped. You can use the {check} -option to detect, if interactions are missing. 2) Unlike other pair -styles in LAMMPS, an atom I will not interact with multiple images of -atom J (assuming the images are within the cutoff distance), but only -with the nearest image. - -This style is part of the USER-MISC package. It is only enabled if -LAMMPS is build with that package. See the "Build -package"_Build_package.html doc page on for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, -"pair_style hybrid/overlay"_pair_hybrid.html, -"pair_style lj/cut"_pair_lj.html, -"pair_style morse"_pair_morse.html, -"bond_style harmonic"_bond_harmonic.html - -[Default:] none diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 8bc437bd48..8763d951e8 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -934,7 +934,7 @@ funcs functionalities functionals funroll -für +fuer fx fy fz diff --git a/src/GRANULAR/fix_pour.cpp b/src/GRANULAR/fix_pour.cpp index 2b33b988b8..2255f64eb2 100644 --- a/src/GRANULAR/fix_pour.cpp +++ b/src/GRANULAR/fix_pour.cpp @@ -54,7 +54,7 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) : { if (narg < 6) error->all(FLERR,"Illegal fix pour command"); - if (lmp->kokkos) + if (lmp->kokkos) error->all(FLERR,"Cannot yet use fix pour with the KOKKOS package"); time_depend = 1; @@ -797,7 +797,7 @@ bool FixPour::outside(int dim, double value, double lo, double hi) bool outside_range = (value < lo || value > hi); if (!outside_range || !domain->periodicity[dim]) return outside_range; - // for periodic dimension: + // for periodic dimension: // must perform additional tests if range wraps around the periodic box bool outside_pbc_range = true; diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp index f6eef5b53c..3358fe709c 100644 --- a/src/KOKKOS/pair_eam_kokkos.cpp +++ b/src/KOKKOS/pair_eam_kokkos.cpp @@ -37,6 +37,7 @@ template PairEAMKokkos::PairEAMKokkos(LAMMPS *lmp) : PairEAM(lmp) { respa_enable = 0; + single_enable = 0; atomKK = (AtomKokkos *) atom; execution_space = ExecutionSpaceFromDevice::space; diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp index 2e118088eb..5459a92b69 100644 --- a/src/MANYBODY/pair_eam.cpp +++ b/src/MANYBODY/pair_eam.cpp @@ -43,6 +43,7 @@ PairEAM::PairEAM(LAMMPS *lmp) : Pair(lmp) nmax = 0; rho = NULL; fp = NULL; + numforce = NULL; map = NULL; type2frho = NULL; @@ -77,6 +78,7 @@ PairEAM::~PairEAM() memory->destroy(rho); memory->destroy(fp); + memory->destroy(numforce); if (allocated) { memory->destroy(setflag); @@ -151,9 +153,11 @@ void PairEAM::compute(int eflag, int vflag) if (atom->nmax > nmax) { memory->destroy(rho); memory->destroy(fp); + memory->destroy(numforce); nmax = atom->nmax; memory->create(rho,nmax,"pair:rho"); memory->create(fp,nmax,"pair:fp"); + memory->create(numforce,nmax,"pair:numforce"); } double **x = atom->x; @@ -255,6 +259,7 @@ void PairEAM::compute(int eflag, int vflag) jlist = firstneigh[i]; jnum = numneigh[i]; + numforce[i] = 0; for (jj = 0; jj < jnum; jj++) { j = jlist[jj]; @@ -266,6 +271,7 @@ void PairEAM::compute(int eflag, int vflag) rsq = delx*delx + dely*dely + delz*delz; if (rsq < cutforcesq) { + ++numforce[i]; jtype = type[j]; r = sqrt(rsq); p = r*rdr + 1.0; @@ -802,6 +808,18 @@ double PairEAM::single(int i, int j, int itype, int jtype, double r,p,rhoip,rhojp,z2,z2p,recip,phi,phip,psip; double *coeff; + if (numforce[i] > 0) { + p = rho[i]*rdrho + 1.0; + m = static_cast (p); + m = MAX(1,MIN(m,nrho-1)); + p -= m; + p = MIN(p,1.0); + coeff = frho_spline[type2frho[itype]][m]; + phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; + if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax); + phi *= 1.0/static_cast(numforce[i]); + } else phi = 0.0; + r = sqrt(rsq); p = r*rdr + 1.0; m = static_cast (p); @@ -818,7 +836,7 @@ double PairEAM::single(int i, int j, int itype, int jtype, z2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; recip = 1.0/r; - phi = z2*recip; + phi += z2*recip; phip = z2p*recip - phi*recip; psip = fp[i]*rhojp + fp[j]*rhoip + phip; fforce = -psip*recip; diff --git a/src/MANYBODY/pair_eam.h b/src/MANYBODY/pair_eam.h index 8bcb44c347..add33ab3f0 100644 --- a/src/MANYBODY/pair_eam.h +++ b/src/MANYBODY/pair_eam.h @@ -70,6 +70,7 @@ class PairEAM : public Pair { // per-atom arrays double *rho,*fp; + int *numforce; // potentials as file data diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp index 516fe2521d..732e76b77e 100644 --- a/src/MC/fix_gcmc.cpp +++ b/src/MC/fix_gcmc.cpp @@ -945,7 +945,7 @@ void FixGCMC::attempt_atomic_insertion() ninsertion_attempts += 1.0; if (ngas >= max_ngas) return; - + // pick coordinates for insertion point double coord[3]; @@ -1300,7 +1300,7 @@ void FixGCMC::attempt_molecule_insertion() ninsertion_attempts += 1.0; if (ngas >= max_ngas) return; - + double com_coord[3]; if (regionflag) { int region_attempt = 0; @@ -1634,7 +1634,7 @@ void FixGCMC::attempt_atomic_insertion_full() ninsertion_attempts += 1.0; if (ngas >= max_ngas) return; - + double energy_before = energy_stored; double coord[3]; diff --git a/src/OPT/pair_eam_opt.cpp b/src/OPT/pair_eam_opt.cpp index ad24aaee63..7dff5cff4b 100644 --- a/src/OPT/pair_eam_opt.cpp +++ b/src/OPT/pair_eam_opt.cpp @@ -80,11 +80,13 @@ void PairEAMOpt::eval() // grow energy array if necessary if (atom->nmax > nmax) { - memory->sfree(rho); - memory->sfree(fp); + memory->destroy(rho); + memory->destroy(fp); + memory->destroy(numforce); nmax = atom->nmax; - rho = (double *) memory->smalloc(nmax*sizeof(double),"pair:rho"); - fp = (double *) memory->smalloc(nmax*sizeof(double),"pair:fp"); + memory->create(rho,nmax,"pair:rho"); + memory->create(fp,nmax,"pair:fp"); + memory->create(numforce,nmax,"pair:numforce"); } double** _noalias x = atom->x; @@ -269,6 +271,7 @@ void PairEAMOpt::eval() fast_gamma_t* _noalias tabssi = &tabss[itype1*ntypes*nr]; double* _noalias scale_i = scale[itype1+1]+1; + numforce[i] = 0; for (jj = 0; jj < jnum; jj++) { j = jlist[jj]; @@ -280,6 +283,7 @@ void PairEAMOpt::eval() double rsq = delx*delx + dely*dely + delz*delz; if (rsq < tmp_cutforcesq) { + ++numforce[i]; jtype = type[j] - 1; double r = sqrt(rsq); double rhoip,rhojp,z2,z2p; diff --git a/src/USER-MISC/compute_gyration_shape_chunk.cpp b/src/USER-MISC/compute_gyration_shape_chunk.cpp index 08484d9301..b493455ebf 100644 --- a/src/USER-MISC/compute_gyration_shape_chunk.cpp +++ b/src/USER-MISC/compute_gyration_shape_chunk.cpp @@ -39,7 +39,7 @@ ComputeGyrationShapeChunk::ComputeGyrationShapeChunk(LAMMPS *lmp, int narg, char int n = strlen(arg[3]) + 1; id_gyration_chunk = new char[n]; strcpy(id_gyration_chunk,arg[3]); - + init(); array_flag = 1; diff --git a/src/USER-OMP/pair_eam_omp.cpp b/src/USER-OMP/pair_eam_omp.cpp index 99417f27da..3b0bb54065 100644 --- a/src/USER-OMP/pair_eam_omp.cpp +++ b/src/USER-OMP/pair_eam_omp.cpp @@ -51,9 +51,11 @@ void PairEAMOMP::compute(int eflag, int vflag) if (atom->nmax > nmax) { memory->destroy(rho); memory->destroy(fp); + memory->destroy(numforce); nmax = atom->nmax; memory->create(rho,nthreads*nmax,"pair:rho"); memory->create(fp,nmax,"pair:fp"); + memory->create(numforce,nmax,"pair:numforce"); } #if defined(_OPENMP) @@ -232,6 +234,7 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr) jlist = firstneigh[i]; jnum = numneigh[i]; + numforce[i] = 0; for (jj = 0; jj < jnum; jj++) { j = jlist[jj]; @@ -243,6 +246,7 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr) rsq = delx*delx + dely*dely + delz*delz; if (rsq < cutforcesq) { + ++numforce[i]; jtype = type[j]; r = sqrt(rsq); p = r*rdr + 1.0; diff --git a/src/fix_print.cpp b/src/fix_print.cpp index 54132a3ce6..54a706d24b 100644 --- a/src/fix_print.cpp +++ b/src/fix_print.cpp @@ -136,7 +136,7 @@ void FixPrint::init() } else { if (update->ntimestep % nevery) next_print = (update->ntimestep/nevery)*nevery + nevery; - else + else next_print = update->ntimestep; }