2010-10-26 04:29:58 +08:00
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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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<HR>
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<H3>pair_style hbond/dreiding/lj command
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</H3>
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2011-10-07 01:32:51 +08:00
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<H3>pair_style hbond/dreiding/lj/omp command
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</H3>
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2010-10-26 04:29:58 +08:00
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<H3>pair_style hbond/dreiding/morse command
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</H3>
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2011-10-07 01:32:51 +08:00
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<H3>pair_style hbond/dreiding/morse/omp command
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</H3>
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2010-10-26 04:29:58 +08:00
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<P><B>Syntax:</B>
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</P>
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2011-05-28 07:59:19 +08:00
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<PRE>pair_style style N inner_distance_cutoff outer_distance_cutoff angle_cutof
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2010-10-26 04:29:58 +08:00
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</PRE>
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<UL><LI>style = <I>hbond/dreiding/lj</I> or <I>hbond/dreiding/morse</I>
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<LI>n = cosine angle periodicity
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2013-01-25 23:05:22 +08:00
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<LI>inner_distance_cutoff = global inner cutoff for Donor-Acceptor interactions (distance units)
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2011-05-28 07:59:19 +08:00
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<LI>outer_distance_cutoff = global cutoff for Donor-Acceptor interactions (distance units)
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2010-10-26 04:29:58 +08:00
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<LI>angle_cutoff = global angle cutoff for Acceptor-Hydrogen-Donor
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<LI>interactions (degrees)
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</UL>
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<P><B>Examples:</B>
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</P>
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2013-01-03 01:39:23 +08:00
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<PRE>pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/lj 4 9.0 11.0 90
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pair_coeff 1 2 hbond/dreiding/lj 3 i 9.5 2.75 4 9.0 11.0 90.0
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2010-10-26 04:29:58 +08:00
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</PRE>
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2013-01-03 01:39:23 +08:00
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<PRE>pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/morse 2 9.0 11.0 90
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pair_coeff 1 2 hbond/dreiding/morse 3 i 3.88 1.7241379 2.9 2 9 11 90
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2010-10-26 04:29:58 +08:00
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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>hbond/dreiding</I> styles compute the Acceptor-Hydrogen-Donor (AHD)
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3-body hydrogen bond interaction for the
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2011-08-26 01:01:01 +08:00
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<A HREF = "Section_howto.html#howto_4">DREIDING</A> force field, given by:
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2010-10-26 04:29:58 +08:00
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</P>
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<CENTER><IMG SRC = "Eqs/pair_hbond_dreiding.jpg">
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</CENTER>
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2011-05-28 07:59:19 +08:00
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<P>where Rin is the inner spline distance cutoff, Rout is the outer
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distance cutoff, theta_c is the angle cutoff, and n is the cosine
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periodicity.
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2010-10-26 04:29:58 +08:00
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</P>
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<P>Here, <I>r</I> is the radial distance between the donor (D) and acceptor
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(A) atoms and <I>theta</I> is the bond angle between the acceptor, the
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hydrogen (H) and the donor atoms:
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</P>
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<CENTER><IMG SRC = "Eqs/dreiding_hbond.jpg">
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</CENTER>
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<P>These 3-body interactions can be defined for pairs of acceptor and
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donor atoms, based on atom types. For each donor/acceptor atom pair,
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the 3rd atom in the interaction is a hydrogen permanently bonded to
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the donor atom, e.g. in a bond list read in from a data file via the
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<A HREF = "read_data.html">read_data</A> command. The atom types of possible
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hydrogen atoms for each donor/acceptor type pair are specified by the
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<A HREF = "pair_coeff.html">pair_coeff</A> command (see below).
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</P>
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<P>Style <I>hbond/dreiding/lj</I> is the original DREIDING potential of
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<A HREF = "#Mayo">(Mayo)</A>. It uses a LJ 12/10 functional for the Donor-Acceptor
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interactions. To match the results in the original paper, use n = 4.
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</P>
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<P>Style <I>hbond/dreiding/morse</I> is an improved version using a Morse
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potential for the Donor-Acceptor interactions. <A HREF = "#Liu">(Liu)</A> showed
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that the Morse form gives improved results for Dendrimer simulations,
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when n = 2.
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</P>
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2011-08-26 01:01:01 +08:00
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<P>See this <A HREF = "Section_howto.html#howto_4">howto section</A> of the manual for
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more information on the DREIDING forcefield.
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2010-10-26 04:29:58 +08:00
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</P>
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2013-01-03 01:39:23 +08:00
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<P>IMPORTANT NOTE: Because the Dreiding hydrogen bond potential is only
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one portion of an overall force field which typically includes other
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pairwise interactions, it is common to use it as a sub-style in a
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<A HREF = "pair_hybrid.html">pair_style hybrid/overlay</A> command, where another
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pair style provides the repulsive core interaction between pairs of
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atoms, e.g. a 1/r^12 Lennard-Jones repulsion.
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</P>
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<P>IMPORTANT NOTE: When using the hbond/dreiding pair styles with
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<A HREF = "pair_hybrid.html">pair_style hybrid/overlay</A>, you should explicitly
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define pair interactions between the donor atom and acceptor atoms,
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(as well as between these atoms and ALL other atoms in your system).
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Whenever <A HREF = "pair_hybrid.html">pair_style hybrid/overlay</A> is used,
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ordinary mixing rules are not applied to atoms like the donor and
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acceptor atoms because they are typically referenced in multiple pair
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styles. Neglecting to do this can cause difficult-to-detect physics
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problems.
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</P>
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<P>IMPORTANT NOTE: In the original Dreiding force field paper 1-4
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non-bonded interactions ARE allowed. If this is desired for your
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model, use the special_bonds command (e.g. "special_bonds lj 0.0 0.0
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1.0") to turn these interactions on.
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2010-10-26 04:29:58 +08:00
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</P>
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2013-01-03 01:39:23 +08:00
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<HR>
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2010-10-26 04:29:58 +08:00
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<P>The following coefficients must be defined for pairs of eligible
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donor/acceptor types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as
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in the examples above.
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</P>
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<P>IMPORTANT NOTE: Unlike other pair styles and their associated
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<A HREF = "pair_coeff.html">pair_coeff</A> commands, you do not need to specify
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pair_coeff settings for all possible I,J type pairs. Only I,J type
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pairs for atoms which act as joint donors/acceptors need to be
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specified; all other type pairs are assumed to be inactive.
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</P>
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<P>IMPORTANT NOTE: A <A HREF = "pair_coeff.html">pair_coeff</A> command can be
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speficied multiple times for the same donor/acceptor type pair. This
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enables multiple hydrogen types to be assigned to the same
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donor/acceptor type pair. For other pair_styles, if the pair_coeff
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command is re-used for the same I.J type pair, the settings for that
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type pair are overwritten. For the hydrogen bond potentials this is
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not the case; the settings are cummulative. This means the only way
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to turn off a previous setting, is to re-use the pair_style command
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and start over.
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</P>
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<P>For the <I>hbond/dreiding/lj</I> style the list of coefficients is as
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follows:
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</P>
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<UL><LI>K = hydrogen atom type = 1 to Ntypes
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<LI>donor flag = <I>i</I> or <I>j</I>
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<LI>epsilon (energy units)
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<LI>sigma (distance units)
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<LI>n = exponent in formula above
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2013-01-03 01:39:23 +08:00
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<LI>distance cutoff Rin (distance units)
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<LI>distance cutoff Rout (distance units)
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2010-10-26 04:29:58 +08:00
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<LI>angle cutoff (degrees)
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</UL>
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<P>For the <I>hbond/dreiding/morse</I> style the list of coefficients is as
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follows:
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</P>
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<UL><LI>K = hydrogen atom type = 1 to Ntypes
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<LI>donor flag = <I>i</I> or <I>j</I>
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<LI>D0 (energy units)
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<LI>alpha (1/distance units)
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<LI>r0 (distance units)
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<LI>n = exponent in formula above
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2013-01-03 01:39:23 +08:00
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<LI>distance cutoff Rin (distance units)
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<LI>distance cutoff Rout (distance units)
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2010-10-26 04:29:58 +08:00
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<LI>angle cutoff (degrees)
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</UL>
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<P>A single hydrogen atom type K can be specified, or a wild-card
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asterisk can be used in place of or in conjunction with the K
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arguments to select multiple types as hydrogens. This takes the form
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"*" or "*n" or "n*" or "m*n". See the <A HREF = "pair_coeff">pair_coeff</A> command
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doc page for details.
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</P>
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<P>If the donor flag is <I>i</I>, then the atom of type I in the pair_coeff
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command is treated as the donor, and J is the acceptor. If the donor
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flag is <I>j</I>, then the atom of type J in the pair_coeff command is
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treated as the donor and I is the donor. This option is required
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because the <A HREF = "pair_coeff.html">pair_coeff</A> command requires that I <= J.
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</P>
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<P>Epsilon and sigma are settings for the hydrogen bond potential based
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on a Lennard-Jones functional form. Note that sigma is defined as the
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zero-crossing distance for the potential, not as the energy minimum at
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2^(1/6) sigma.
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</P>
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<P>D0 and alpha and r0 are settings for the hydrogen bond potential based
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on a Morse functional form.
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</P>
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<P>The last 3 coefficients for both styles are optional. If not
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specified, the global n, distance cutoff, and angle cutoff specified
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in the pair_style command are used. If you wish to only override the
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2nd or 3rd optional parameter, you must also specify the preceding
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optional parameters.
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</P>
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<HR>
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2011-12-14 04:35:35 +08:00
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<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>omp</I>, or <I>opt</I> suffix are functionally
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the same as the corresponding style without the suffix. They have
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been optimized to run faster, depending on your available hardware, as
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discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A> of the
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manual. The accelerated styles take the same arguments and should
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produce the same results, except for round-off and precision issues.
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2011-10-07 01:32:51 +08:00
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</P>
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<P>These accelerated styles are part of the USER-CUDA, GPU, USER-OMP and OPT
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packages, respectively. They are only enabled if LAMMPS was built with
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those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
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section for more info.
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</P>
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<P>You can specify the accelerated styles explicitly in your input script
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2012-01-28 07:39:14 +08:00
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by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
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2011-10-07 01:32:51 +08:00
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switch</A> when you invoke LAMMPS, or you can
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use the <A HREF = "suffix.html">suffix</A> command in your input script.
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</P>
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2011-12-14 04:35:35 +08:00
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<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
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more instructions on how to use the accelerated styles effectively.
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2011-10-07 01:32:51 +08:00
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</P>
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<HR>
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2010-10-26 04:29:58 +08:00
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<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
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</P>
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<P>These pair styles do not support mixing. You must explicitly identify
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each donor/acceptor type pair.
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</P>
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<P>These styles do not support the <A HREF = "pair_modify.html">pair_modify</A> shift
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option for the energy of the interactions.
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</P>
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<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant for
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these pair styles.
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</P>
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<P>These pair styles do not support the <A HREF = "pair_modify.html">pair_modify</A>
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tail option for adding long-range tail corrections to energy and
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pressure.
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</P>
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<P>These pair styles do not write their information to <A HREF = "restart.html">binary restart
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files</A>, so pair_style and pair_coeff commands need to be
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re-specified in an input script that reads a restart file.
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</P>
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<P>These pair styles can only be used via the <I>pair</I> keyword of the
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<A HREF = "run_style.html">run_style respa</A> command. They do not support the
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<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
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</P>
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2011-05-28 07:59:19 +08:00
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<P>These pair styles tally a count of how many hydrogen bonding
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interactions they calculate each timestep and the hbond energy. These
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quantities can be accessed via the <A HREF = "compute_pair.html">compute pair</A>
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command as a vector of values of length 2.
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2010-10-26 04:29:58 +08:00
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</P>
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2011-05-28 07:59:19 +08:00
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<P>To print these quantities to the log file (with a descriptive column
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2010-10-26 04:29:58 +08:00
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heading) the following commands could be included in an input script:
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</P>
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<PRE>compute hb all pair hbond/dreiding/lj
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2011-05-28 07:59:19 +08:00
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variable n_hbond equal c_hb[1] #number hbonds
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variable E_hbond equal c_hb[2] #hbond energy
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thermo_style custom step temp epair v_E_hbond
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2010-10-26 04:29:58 +08:00
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</PRE>
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<HR>
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<P><B>Restrictions:</B> none
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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 = "pair_coeff.html">pair_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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<HR>
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<A NAME = "Mayo"></A>
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<P><B>(Mayo)</B> Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
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(1990).
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</P>
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<A NAME = "Liu"></A>
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<P><B>(Liu)</B> Liu, Bryantsev, Diallo, Goddard III, J. Am. Chem. Soc 131 (8)
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2798 (2009)
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</P>
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</HTML>
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