2012-01-11 04:58:04 +08:00
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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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<HR>
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<H3>dihedral_style table command
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</H3>
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2012-02-02 00:07:22 +08:00
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<H3>dihedral_style table/omp command
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</H3>
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2012-01-11 04:58:04 +08:00
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<P><B>Syntax:</B>
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</P>
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<PRE>dihedral_style table style Ntable
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</PRE>
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<UL><LI>style = <I>linear</I> or <I>spline</I> = method of interpolation
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<LI>Ntable = size of the internal lookup table
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>dihedral_style table spline 400
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dihedral_style table linear 1000
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dihedral_coeff 1 file.table DIH_TABLE1
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dihedral_coeff 2 file.table DIH_TABLE2
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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>table</I> dihedral style creates interpolation tables of length
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<I>Ntable</I> from dihedral potential and derivative values listed in a
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file(s) as a function of the dihedral angle "phi". The files are read
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by the <A HREF = "dihedral_coeff.html">dihedral_coeff</A> command.
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</P>
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<P>The interpolation tables are created by fitting cubic splines to the
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file values and interpolating energy and derivative values at each of
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<I>Ntable</I> dihedral angles. During a simulation, these tables are used
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to interpolate energy and force values on individual atoms as
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needed. The interpolation is done in one of 2 styles: <I>linear</I> or
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<I>spline</I>.
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</P>
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<P>For the <I>linear</I> style, the dihedral angle (phi) is used to find 2
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surrounding table values from which an energy or its derivative is
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computed by linear interpolation.
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</P>
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<P>For the <I>spline</I> style, cubic spline coefficients are computed and
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stored at each of the <I>Ntable</I> evenly-spaced values in the
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interpolated table. For a given dihedral angle (phi), the appropriate
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coefficients are chosen from this list, and a cubic polynomial is used
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to compute the energy and the derivative at this angle.
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</P>
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<P>The following coefficients must be defined for each dihedral type via
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the <A HREF = "dihedral_coeff.html">dihedral_coeff</A> command as in the example
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above.
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</P>
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<UL><LI>filename
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<LI>keyword
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</UL>
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<P>The filename specifies a file containing tabulated energy and
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derivative values. The keyword specifies a section of the file. The
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format of this file is described below.
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</P>
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<HR>
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<P>The format of a tabulated file is as follows (without the
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parenthesized comments). It can begin with one or more comment
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or blank lines.
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</P>
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<PRE># Table of the potential and its negative derivative
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</PRE>
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2012-03-07 23:55:21 +08:00
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<PRE>DIH_TABLE1 (keyword is the first text on line)
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2012-01-11 04:58:04 +08:00
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N 30 DEGREES (N, NOF, DEGREES, RADIANS, CHECKU/F)
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(blank line)
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1 -168.0 -1.40351172223 -0.0423346818422
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2 -156.0 -1.70447981034 -0.00811786522531
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3 -144.0 -1.62956100432 0.0184129719987
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2012-03-07 23:55:21 +08:00
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...
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30 180.0 -0.707106781187 -0.0719306095245
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2012-01-11 04:58:04 +08:00
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</PRE>
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<P># Example 2: table of the potential. Forces omitted
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</P>
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<P>DIH_TABLE2
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N 30 NOF CHECKU testU.dat CHECKF testF.dat
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</P>
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2012-03-07 23:55:21 +08:00
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<PRE>1 -168.0 -1.40351172223
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2012-01-11 04:58:04 +08:00
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2 -156.0 -1.70447981034
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3 -144.0 -1.62956100432
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2012-03-07 23:55:21 +08:00
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...
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30 180.0 -0.707106781187
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2012-01-11 04:58:04 +08:00
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</PRE>
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<P>A section begins with a non−blank line whose 1st character is not a
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"#"; blank lines or lines starting with "#" can be used as comments
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between sections. The first line begins with a keyword which
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identifies the section. The line can contain additional text, but the
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initial text must match the argument specified in the
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<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command. The next line lists (in
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any order) one or more parameters for the table. Each parameter is a
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keyword followed by one or more numeric values.
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</P>
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<P>Following a blank line, the next N lines list the tabulated values. On
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each line, the 1st value is the index from 1 to N, the 2nd value is
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the angle value, the 3rd value is the energy (in energy units), and
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the 4th is −dE/d(phi) also in energy units). The 3rd term is the
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energy of the 3−atom configuration for the specified angle. The 4th
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term (when present) is the negative derivative of the energy with
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respect to the angle (in degrees, or radians depending on whether the
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user selected DEGREES or RADIANS). Thus the units of the last term
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are still energy, not force. The dihedral angle values must increase
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from one line to the next.
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</P>
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<P>Dihedral table splines are cyclic. There is no discontinuity at 180
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degrees (or at any other angle). Although in the examples above, the
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angles range from -180 to 180 degrees, in general, the first angle in
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the list can have any value (positive, zero, or negative). However
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the <I>range</I> of angles represented in the table must be <I>strictly</I> less
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than 360 degrees (2pi radians) to avoid angle overlap. (You may not
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supply entries in the table for both 180 and -180, for example.) If
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the user's table covers only a narrow range of dihedral angles,
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strange numerical behavior can occur in the large remaining gap.
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</P>
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<P><B>Parameters:</B>
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</P>
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<P>The parameter "N" is required and its value is the number of table
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entries that follow. Note that this may be different than the N
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specified in the <A HREF = "dihedral_style.html">dihedral_style table</A> command.
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Let <I>Ntable</I> is the number of table entries requested dihedral_style
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command, and let <I>Nfile</I> be the parameter following "N" in the
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tabulated file ("30" in the sparse example above). What LAMMPS does
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is a preliminary interpolation by creating splines using the <I>Nfile</I>
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tabulated values as nodal points. It uses these to interpolate as
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needed to generate energy and derivative values at <I>Ntable</I> different
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points (which are evenly spaced over a 360 degree range, even if the
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angles in the file are not). The resulting tables of length <I>Ntable</I>
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are then used as described above, when computing energy and force for
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individual dihedral angles and their atoms. This means that if you
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want the interpolation tables of length <I>Ntable</I> to match exactly what
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is in the tabulated file (with effectively nopreliminary
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interpolation), you should set <I>Ntable</I> = <I>Nfile</I>. To insure the
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nodal points in the user's file are aligned with the interpolated
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table entries, the angles in the table should be integer multiples of
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360/<I>Ntable</I> degrees, or 2*PI/<I>Ntable</I> radians (depending on your
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choice of angle units).
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</P>
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<P>The optional "NOF" keyword allows the user to omit the forces
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(negative energy derivatives) from the table file (normally located in
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the 4th column). In their place, forces will be calculated
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automatically by differentiating the potential energy function
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indicated by the 3rd column of the table (using either linear or
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spline interpolation).
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</P>
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<P>The optional "DEGREES" keyword allows the user to specify angles in
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degrees instead of radians (default).
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</P>
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<P>The optional "RADIANS" keyword allows the user to specify angles in
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radians instead of degrees. (Note: This changes the way the forces
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are scaled in the 4th column of the data file.)
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</P>
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<P>The optional "CHECKU" keyword is followed by a filename. This allows
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the user to save all of the the <I>Ntable</I> different entries in the
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interpolated energy table to a file to make sure that the interpolated
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function agrees with the user's expectations. (Note: You can
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temporarily increase the <I>Ntable</I> parameter to a high value for this
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purpose. "<I>Ntable</I>" is explained above.)
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</P>
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<P>The optional "CHECKF" keyword is analogous to the "CHECKU" keyword.
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It is followed by a filename, and it allows the user to check the
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interpolated force table. This option is available even if the user
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selected the "NOF" option.
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</P>
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<P>Note that one file can contain many sections, each with a tabulated
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potential. LAMMPS reads the file section by section until it finds one
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that matches the specified keyword.
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</P>
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2012-02-02 00:07:22 +08:00
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<HR>
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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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</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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by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
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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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<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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</P>
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2012-01-11 04:58:04 +08:00
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<P><B>Restrictions:</B>
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</P>
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<P>This dihedral 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#2_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 = "dihedral_coeff.html">dihedral_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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