forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8141 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
4913d3f0d5
commit
c676ea4d6d
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@ -594,6 +594,14 @@ description:
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<TR ALIGN="center"><TD WIDTH="100"><A HREF = "improper_harmonic.html">harmonic</A></TD><TD WIDTH="100"><A HREF = "improper_umbrella.html">umbrella</A>
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</TD></TR></TABLE></DIV>
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<P>These are improper styles contributed by users, which can be used if
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<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
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package</A>.
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</P>
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<DIV ALIGN=center><TABLE BORDER=1 >
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<TR ALIGN="center"><TD ><A HREF = "improper_cossq.html">cossq</A></TD><TD ><A HREF = "improper_ring.html">ring</A>
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</TD></TR></TABLE></DIV>
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<P>These are accelerated improper styles, which can be used if LAMMPS is
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built with the <A HREF = "Section_accelerate.html">appropriate accelerated
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package</A>.
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@ -993,6 +993,13 @@ description:
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"harmonic"_improper_harmonic.html,
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"umbrella"_improper_umbrella.html :tb(c=4,ea=c,w=100)
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These are improper styles contributed by users, which can be used if
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"LAMMPS is built with the appropriate
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package"_Section_start.html#start_3.
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"cossq"_improper_cossq.html,
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"ring"_improper_ring.html :tb(c=4,ea=c)
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These are accelerated improper styles, which can be used if LAMMPS is
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built with the "appropriate accelerated
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package"_Section_accelerate.html.
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@ -0,0 +1,70 @@
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<HTML>
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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</CENTER>
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<HR>
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<H3>improper_style cossq command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>improper_style cossq
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</PRE>
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<P><B>Examples:</B>
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</P>
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<PRE>improper_style cossq
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improper_coeff 1 4.0 0.0
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>The <I>cossq</I> improper style uses the potential
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</P>
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<CENTER><IMG SRC = "Eqs/improper_cossq.jpg">
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</CENTER>
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<P>where x is the improper angle, x0 is its equilibrium value, and K is a
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prefactor.
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</P>
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<P>If the 4 atoms in an improper quadruplet (listed in the data file read
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by the <A HREF = "read_data.html">read_data</A> command) are ordered I,J,K,L then X
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is the angle between the plane of I,J,K and the plane of J,K,L.
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Alternatively, you can think of atoms J,K,L as being in a plane, and
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atom I above the plane, and X as a measure of how far out-of-plane I
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is with respect to the other 3 atoms.
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</P>
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<P>Note that defining 4 atoms to interact in this way, does not mean that
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bonds necessarily exist between I-J, J-K, or K-L, as they would in a
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linear dihedral. Normally, the bonds I-J, I-K, I-L would exist for an
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improper to be defined between the 4 atoms.
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</P>
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<P>The following coefficients must be defined for each improper type via
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the <A HREF = "improper_coeff.html">improper_coeff</A> command as in the example
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above, or in the data file or restart files read by the
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<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
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commands:
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</P>
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<UL><LI>K (energy/radian^2)
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<LI>X0 (degrees)
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</UL>
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<P>X0 is specified in degrees, but LAMMPS converts it to radians
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internally; hence the units of K are in energy/radian^2.
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</P>
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<HR>
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<P><B>Restrictions:</B>
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</P>
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<P>This improper style can only be used if LAMMPS was built with the
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USER-MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
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section for more info on packages.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "improper_coeff.html">improper_coeff</A>
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</P>
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<P><B>Default:</B> none
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</P>
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</HTML>
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@ -0,0 +1,65 @@
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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improper_style cossq command :h3
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[Syntax:]
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improper_style cossq :pre
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[Examples:]
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improper_style cossq
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improper_coeff 1 4.0 0.0 :pre
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[Description:]
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The {cossq} improper style uses the potential
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:c,image(Eqs/improper_cossq.jpg)
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where x is the improper angle, x0 is its equilibrium value, and K is a
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prefactor.
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If the 4 atoms in an improper quadruplet (listed in the data file read
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by the "read_data"_read_data.html command) are ordered I,J,K,L then X
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is the angle between the plane of I,J,K and the plane of J,K,L.
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Alternatively, you can think of atoms J,K,L as being in a plane, and
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atom I above the plane, and X as a measure of how far out-of-plane I
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is with respect to the other 3 atoms.
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Note that defining 4 atoms to interact in this way, does not mean that
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bonds necessarily exist between I-J, J-K, or K-L, as they would in a
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linear dihedral. Normally, the bonds I-J, I-K, I-L would exist for an
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improper to be defined between the 4 atoms.
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The following coefficients must be defined for each improper type via
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the "improper_coeff"_improper_coeff.html command as in the example
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above, or in the data file or restart files read by the
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"read_data"_read_data.html or "read_restart"_read_restart.html
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commands:
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K (energy/radian^2)
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X0 (degrees) :ul
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X0 is specified in degrees, but LAMMPS converts it to radians
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internally; hence the units of K are in energy/radian^2.
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:line
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[Restrictions:]
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This improper style can only be used if LAMMPS was built with the
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USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
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section for more info on packages.
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[Related commands:]
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"improper_coeff"_improper_coeff.html
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[Default:] none
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@ -0,0 +1,77 @@
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<HTML>
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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</CENTER>
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<HR>
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<H3>improper_style ring command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>improper_style ring
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</PRE>
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<P><B>Examples:</B>
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</P>
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<PRE>improper_style ring
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improper_coeff 1 8000 70.5
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>The <I>ring</I> improper style uses the potential
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</P>
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<CENTER><IMG SRC = "Eqs/improper_ring.jpg">
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</CENTER>
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<P>where K is a prefactor, theta is the angle formed by the atoms
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specified by (i,j,k,l) indices and theta0 its equilibrium value.
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</P>
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<P>If the 4 atoms in an improper quadruplet (listed in the data file read
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by the <A HREF = "read_data.html">read_data</A> command) are ordered i,j,k,l then
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theta_<I>ijl</I> is the angle between atoms i,j and l, theta_<I>ijk</I> is the
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angle between atoms i,j and k, theta_<I>kjl</I> is the angle between atoms
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j,k, and l.
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</P>
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<P>The "ring" improper style implements the improper potential introduced
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by Destree et al., in Equation (9) of <A HREF = "#Destree">(Destree)</A>. This
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potential does not affect small amplitude vibrations but is used in an
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ad-hoc way to prevent the onset of accidentially large amplitude
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fluctuations leading to the occurrence of a planar conformation of the
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three bonds i-j, j-k and j-l, an intermediate conformation toward the
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chiral inversion of a methine carbon. In the "Impropers" section of
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data file four atoms: i, j, k and l are specified with i,j and l lying
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on the backbone of the chain and k specifying the chirality of j.
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</P>
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<P>The following coefficients must be defined for each improper type via
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the <A HREF = "improper_coeff.html">improper_coeff</A> command as in the example
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above, or in the data file or restart files read by the
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<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
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commands:
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</P>
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<UL><LI>K (energy/radian^2)
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<LI>theta0 (degrees)
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</UL>
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<P>theta0 is specified in degrees, but LAMMPS converts it to radians
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internally; hence the units of K are in energy/radian^2.
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</P>
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<HR>
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<P><B>Restrictions:</B>
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</P>
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<P>This improper style can only be used if LAMMPS was built with the
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USER-MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
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section for more info on packages.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "improper_coeff.html">improper_coeff</A>
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</P>
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<A NAME = "Destree"></A>
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<P><B>(Destree)</B> M. Destree, F. Laupretre, A. Lyulin, and J.-P. Ryckaert,
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J Chem Phys, 112, 9632 (2000).
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</P>
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</HTML>
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@ -0,0 +1,72 @@
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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improper_style ring command :h3
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[Syntax:]
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improper_style ring :pre
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[Examples:]
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improper_style ring
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improper_coeff 1 8000 70.5 :pre
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[Description:]
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The {ring} improper style uses the potential
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:c,image(Eqs/improper_ring.jpg)
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where K is a prefactor, theta is the angle formed by the atoms
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specified by (i,j,k,l) indices and theta0 its equilibrium value.
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If the 4 atoms in an improper quadruplet (listed in the data file read
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by the "read_data"_read_data.html command) are ordered i,j,k,l then
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theta_{ijl} is the angle between atoms i,j and l, theta_{ijk} is the
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angle between atoms i,j and k, theta_{kjl} is the angle between atoms
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j,k, and l.
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The "ring" improper style implements the improper potential introduced
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by Destree et al., in Equation (9) of "(Destree)"_#Destree. This
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potential does not affect small amplitude vibrations but is used in an
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ad-hoc way to prevent the onset of accidentially large amplitude
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fluctuations leading to the occurrence of a planar conformation of the
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three bonds i-j, j-k and j-l, an intermediate conformation toward the
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chiral inversion of a methine carbon. In the "Impropers" section of
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data file four atoms: i, j, k and l are specified with i,j and l lying
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on the backbone of the chain and k specifying the chirality of j.
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The following coefficients must be defined for each improper type via
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the "improper_coeff"_improper_coeff.html command as in the example
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above, or in the data file or restart files read by the
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"read_data"_read_data.html or "read_restart"_read_restart.html
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commands:
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K (energy/radian^2)
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theta0 (degrees) :ul
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theta0 is specified in degrees, but LAMMPS converts it to radians
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internally; hence the units of K are in energy/radian^2.
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:line
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[Restrictions:]
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This improper style can only be used if LAMMPS was built with the
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USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
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section for more info on packages.
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[Related commands:]
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"improper_coeff"_improper_coeff.html
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:link(Destree)
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[(Destree)] M. Destree, F. Laupretre, A. Lyulin, and J.-P. Ryckaert,
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J Chem Phys, 112, 9632 (2000).
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@ -62,10 +62,10 @@ Click on the style to display the formula it computes and coefficients
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specified by the associated <A HREF = "improper_coeff.html">improper_coeff</A>
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command.
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</P>
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<P>There are also additional improper styles submitted by users which are
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included in the LAMMPS distribution. The list of these with links to
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the individual styles are given in the improper section of <A HREF = "Section_commands.html#cmd_5">this
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page</A>.
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<P>Note that there are also additional improper styles submitted by users
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which are included in the LAMMPS distribution. The list of these with
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links to the individual styles are given in the improper section of
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<A HREF = "Section_commands.html#cmd_5">this page</A>.
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</P>
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<UL><LI><A HREF = "improper_none.html">improper_style none</A> - turn off improper interactions
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<LI><A HREF = "improper_hybrid.html">improper_style hybrid</A> - define multiple styles of improper interactions
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@ -59,10 +59,10 @@ Click on the style to display the formula it computes and coefficients
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specified by the associated "improper_coeff"_improper_coeff.html
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command.
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There are also additional improper styles submitted by users which are
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included in the LAMMPS distribution. The list of these with links to
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the individual styles are given in the improper section of "this
|
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page"_Section_commands.html#cmd_5.
|
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Note that there are also additional improper styles submitted by users
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which are included in the LAMMPS distribution. The list of these with
|
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links to the individual styles are given in the improper section of
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"this page"_Section_commands.html#cmd_5.
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"improper_style none"_improper_none.html - turn off improper interactions
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"improper_style hybrid"_improper_hybrid.html - define multiple styles of improper interactions :ul
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Loading…
Reference in New Issue