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/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/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),