2012-01-11 04:58:04 +08:00
|
|
|
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
|
|
|
|
|
|
|
:link(lws,http://lammps.sandia.gov)
|
|
|
|
:link(ld,Manual.html)
|
|
|
|
:link(lc,Section_commands.html#comm)
|
|
|
|
|
|
|
|
:line
|
|
|
|
|
|
|
|
dihedral_style table command :h3
|
2012-02-02 00:07:22 +08:00
|
|
|
dihedral_style table/omp command :h3
|
2012-01-11 04:58:04 +08:00
|
|
|
|
|
|
|
[Syntax:]
|
|
|
|
|
|
|
|
dihedral_style table style Ntable :pre
|
|
|
|
|
|
|
|
style = {linear} or {spline} = method of interpolation
|
|
|
|
Ntable = size of the internal lookup table :ul
|
|
|
|
|
|
|
|
[Examples:]
|
|
|
|
|
|
|
|
dihedral_style table spline 400
|
|
|
|
dihedral_style table linear 1000
|
|
|
|
dihedral_coeff 1 file.table DIH_TABLE1
|
|
|
|
dihedral_coeff 2 file.table DIH_TABLE2 :pre
|
|
|
|
|
|
|
|
[Description:]
|
|
|
|
|
|
|
|
The {table} dihedral style creates interpolation tables of length
|
|
|
|
{Ntable} from dihedral potential and derivative values listed in a
|
|
|
|
file(s) as a function of the dihedral angle "phi". The files are read
|
|
|
|
by the "dihedral_coeff"_dihedral_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
|
|
|
|
{Ntable} dihedral 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 dihedral angle (phi) is used to find 2
|
|
|
|
surrounding table values from which an energy or its derivative is
|
|
|
|
computed by linear interpolation.
|
|
|
|
|
|
|
|
For the {spline} style, cubic spline coefficients are computed and
|
|
|
|
stored at each of the {Ntable} evenly-spaced values in the
|
|
|
|
interpolated table. For a given dihedral angle (phi), the appropriate
|
|
|
|
coefficients are chosen from this list, and a cubic polynomial is used
|
|
|
|
to compute the energy and the derivative at this angle.
|
|
|
|
|
|
|
|
The following coefficients must be defined for each dihedral type via
|
|
|
|
the "dihedral_coeff"_dihedral_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). It can begin with one or more comment
|
|
|
|
or blank lines.
|
|
|
|
|
|
|
|
# Table of the potential and its negative derivative :pre
|
|
|
|
|
|
|
|
DIH_TABLE1 (keyword is the first text on line)
|
|
|
|
N 30 DEGREES (N, NOF, DEGREES, RADIANS, CHECKU/F)
|
|
|
|
(blank line)
|
|
|
|
1 -168.0 -1.40351172223 -0.0423346818422
|
|
|
|
2 -156.0 -1.70447981034 -0.00811786522531
|
|
|
|
3 -144.0 -1.62956100432 0.0184129719987
|
2012-03-07 23:55:21 +08:00
|
|
|
...
|
2012-01-11 04:58:04 +08:00
|
|
|
30 180.0 -0.707106781187 -0.0719306095245 :pre
|
|
|
|
|
2012-03-08 22:45:36 +08:00
|
|
|
# Example 2: table of the potential. Forces omitted :pre
|
2012-01-11 04:58:04 +08:00
|
|
|
|
|
|
|
DIH_TABLE2
|
2012-03-08 22:45:36 +08:00
|
|
|
N 30 NOF CHECKU testU.dat CHECKF testF.dat :pre
|
2012-01-11 04:58:04 +08:00
|
|
|
|
|
|
|
1 -168.0 -1.40351172223
|
|
|
|
2 -156.0 -1.70447981034
|
|
|
|
3 -144.0 -1.62956100432
|
2012-03-07 23:55:21 +08:00
|
|
|
...
|
2012-01-11 04:58:04 +08:00
|
|
|
30 180.0 -0.707106781187 :pre
|
|
|
|
|
2012-03-09 22:59:48 +08:00
|
|
|
A section begins with a non-blank line whose 1st character is not a
|
2012-01-11 04:58:04 +08:00
|
|
|
"#"; 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
|
|
|
|
"dihedral_coeff"_dihedral_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.
|
|
|
|
|
|
|
|
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, the 3rd value is the energy (in energy units), and
|
2012-03-09 22:59:48 +08:00
|
|
|
the 4th is -dE/d(phi) also in energy units). The 3rd term is the
|
|
|
|
energy of the 4-atom configuration for the specified angle. The 4th
|
2012-01-11 04:58:04 +08:00
|
|
|
term (when present) is the negative derivative of the energy with
|
|
|
|
respect to the angle (in degrees, or radians depending on whether the
|
|
|
|
user selected DEGREES or RADIANS). Thus the units of the last term
|
|
|
|
are still energy, not force. The dihedral angle values must increase
|
|
|
|
from one line to the next.
|
|
|
|
|
|
|
|
Dihedral table splines are cyclic. There is no discontinuity at 180
|
|
|
|
degrees (or at any other angle). Although in the examples above, the
|
|
|
|
angles range from -180 to 180 degrees, in general, the first angle in
|
|
|
|
the list can have any value (positive, zero, or negative). However
|
|
|
|
the {range} of angles represented in the table must be {strictly} less
|
|
|
|
than 360 degrees (2pi radians) to avoid angle overlap. (You may not
|
|
|
|
supply entries in the table for both 180 and -180, for example.) If
|
|
|
|
the user's table covers only a narrow range of dihedral angles,
|
|
|
|
strange numerical behavior can occur in the large remaining gap.
|
|
|
|
|
|
|
|
[Parameters:]
|
|
|
|
|
|
|
|
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 "dihedral_style table"_dihedral_style.html command.
|
|
|
|
Let {Ntable} is the number of table entries requested dihedral_style
|
|
|
|
command, and let {Nfile} be the parameter following "N" in the
|
|
|
|
tabulated file ("30" in the sparse example above). 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 (which are evenly spaced over a 360 degree range, even if the
|
|
|
|
angles in the file are not). The resulting tables of length {Ntable}
|
|
|
|
are then used as described above, when computing energy and force for
|
|
|
|
individual dihedral 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 nopreliminary
|
|
|
|
interpolation), you should set {Ntable} = {Nfile}. To insure the
|
|
|
|
nodal points in the user's file are aligned with the interpolated
|
|
|
|
table entries, the angles in the table should be integer multiples of
|
|
|
|
360/{Ntable} degrees, or 2*PI/{Ntable} radians (depending on your
|
|
|
|
choice of angle units).
|
|
|
|
|
|
|
|
The optional "NOF" keyword allows the user to omit the forces
|
|
|
|
(negative energy derivatives) from the table file (normally located in
|
|
|
|
the 4th column). In their place, forces will be calculated
|
|
|
|
automatically by differentiating the potential energy function
|
|
|
|
indicated by the 3rd column of the table (using either linear or
|
|
|
|
spline interpolation).
|
|
|
|
|
|
|
|
The optional "DEGREES" keyword allows the user to specify angles in
|
|
|
|
degrees instead of radians (default).
|
|
|
|
|
|
|
|
The optional "RADIANS" keyword allows the user to specify angles in
|
|
|
|
radians instead of degrees. (Note: This changes the way the forces
|
|
|
|
are scaled in the 4th column of the data file.)
|
|
|
|
|
|
|
|
The optional "CHECKU" keyword is followed by a filename. This allows
|
|
|
|
the user to save all of the the {Ntable} different entries in the
|
|
|
|
interpolated energy table to a file to make sure that the interpolated
|
|
|
|
function agrees with the user's expectations. (Note: You can
|
|
|
|
temporarily increase the {Ntable} parameter to a high value for this
|
|
|
|
purpose. "{Ntable}" is explained above.)
|
|
|
|
|
|
|
|
The optional "CHECKF" keyword is analogous to the "CHECKU" keyword.
|
|
|
|
It is followed by a filename, and it allows the user to check the
|
|
|
|
interpolated force table. This option is available even if the user
|
|
|
|
selected the "NOF" option.
|
|
|
|
|
|
|
|
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.
|
|
|
|
|
2012-02-02 00:07:22 +08:00
|
|
|
:line
|
|
|
|
|
2014-08-15 00:30:25 +08:00
|
|
|
Styles with a {cuda}, {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 in "Section_accelerate"_Section_accelerate.html
|
|
|
|
of the manual. 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 USER-CUDA, GPU, USER-INTEL,
|
|
|
|
KOKKOS, USER-OMP and OPT packages, respectively. They are only
|
|
|
|
enabled if LAMMPS was built with those packages. See the "Making
|
|
|
|
LAMMPS"_Section_start.html#start_3 section for more info.
|
2012-02-02 00:07:22 +08:00
|
|
|
|
|
|
|
You can specify the accelerated styles explicitly in your input script
|
|
|
|
by including their suffix, or you can use the "-suffix command-line
|
|
|
|
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
|
|
|
|
use the "suffix"_suffix.html command in your input script.
|
|
|
|
|
|
|
|
See "Section_accelerate"_Section_accelerate.html of the manual for
|
|
|
|
more instructions on how to use the accelerated styles effectively.
|
|
|
|
|
2012-01-11 04:58:04 +08:00
|
|
|
[Restrictions:]
|
|
|
|
|
|
|
|
This dihedral style can only be used if LAMMPS was built with the
|
|
|
|
USER-MISC package. See the "Making LAMMPS"_Section_start.html#2_3
|
|
|
|
section for more info on packages.
|
|
|
|
|
|
|
|
[Related commands:]
|
|
|
|
|
|
|
|
"dihedral_coeff"_dihedral_coeff.html
|
|
|
|
|
|
|
|
[Default:] none
|