forked from lijiext/lammps
new dihedral table/cut command
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Steven J. Plimpton
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724ade0af3
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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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dihedral_style table/cut command :h3
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dihedral_style table/cut/omp command :h3
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[Syntax:]
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dihedral_style table/cut style Ntable :pre
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style = {linear} or {spline} = method of interpolation
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Ntable = size of the internal lookup table :ul
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[Examples:]
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dihedral_style table/cut spline 400
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dihedral_style table/cut linear 1000
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dihedral_coeff 1 aat 1.0 177 180 file.table DIH_TABLE1
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dihedral_coeff 2 aat 0.5 170 180 file.table DIH_TABLE2 :pre
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[Description:]
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The {table/cut} dihedral style creates interpolation tables of length
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{Ntable} from dihedral potential and derivative values listed in a
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file(s) as a function of the dihedral angle "phi". In addition, an
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analytic cutoff that is quadratic in the bond-angle (theta) is applied
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in order to regularize the dihedral interaction. The dihedral table
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files are read by the "dihedral_coeff"_dihedral_coeff.html command.
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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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{Ntable} 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: {linear} or
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{spline}.
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For the {linear} 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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For the {spline} style, cubic spline coefficients are computed and
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stored at each of the {Ntable} 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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The following coefficients must be defined for each dihedral type via
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the "dihedral_coeff"_dihedral_coeff.html command as in the example
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above.
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style (aat)
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cutoff prefactor
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cutoff angle1
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cutoff angle2
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filename
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keyword :ul
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The cutoff dihedral style uses a tabulated dihedral interaction with a
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cutoff function
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:c,image(Eqs/dihedral_table_cut.jpg)
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The cutoff specifies an prefactor to the cutoff function. While this value
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would ordinarily equal 1 there may be situations where the value should change.
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The cutoff angle1 specifies the angle (in degrees) below which the dihedral
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interaction is unmodified, i.e. the cutoff function is 1.
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The cutoff function is applied between angle1 and angle2, which is the angle at
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which the cutoff function drops to zero. The value of zero effectively "turns
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off" the dihedral interaction.
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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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:line
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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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# Table of the potential and its negative derivative :pre
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DIH_TABLE1 (keyword is the first text on line)
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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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...
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30 180.0 -0.707106781187 0.0719306095245 :pre
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# Example 2: table of the potential. Forces omitted :pre
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DIH_TABLE2
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N 30 NOF CHECKU testU.dat CHECKF testF.dat :pre
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1 -168.0 -1.40351172223
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2 -156.0 -1.70447981034
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3 -144.0 -1.62956100432
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...
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30 180.0 -0.707106781187 :pre
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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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"dihedral_coeff"_dihedral_coeff.html 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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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 4-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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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 {range} of angles represented in the table must be {strictly} 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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[Parameters:]
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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 "dihedral_style table"_dihedral_style.html command.
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Let {Ntable} is the number of table entries requested dihedral_style
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command, and let {Nfile} 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 {Nfile}
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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 {Ntable} 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 {Ntable}
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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 {Ntable} to match exactly what
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is in the tabulated file (with effectively nopreliminary
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interpolation), you should set {Ntable} = {Nfile}. 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/{Ntable} degrees, or 2*PI/{Ntable} radians (depending on your
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choice of angle units).
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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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The optional "DEGREES" keyword allows the user to specify angles in
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degrees instead of radians (default).
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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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The optional "CHECKU" keyword is followed by a filename. This allows
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the user to save all of the the {Ntable} 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 {Ntable} parameter to a high value for this
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purpose. "{Ntable}" is explained above.)
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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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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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:line
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Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
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functionally the same as the corresponding style without the suffix.
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They have been optimized to run faster, depending on your available
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hardware, as discussed in "Section_accelerate"_Section_accelerate.html
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of the manual. The accelerated styles take the same arguments and
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should produce the same results, except for round-off and precision
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issues.
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These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
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USER-OMP and OPT packages, respectively. They are only enabled if
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LAMMPS was built with those packages. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info.
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You can specify the accelerated styles explicitly in your input script
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by including their suffix, or you can use the "-suffix command-line
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switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
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use the "suffix"_suffix.html command in your input script.
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See "Section_accelerate"_Section_accelerate.html of the manual for
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more instructions on how to use the accelerated styles effectively.
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[Restrictions:]
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This dihedral 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#2_3
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section for more info on packages.
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[Related commands:]
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"dihedral_coeff"_dihedral_coeff.html
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[Default:] none
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:line
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:link(dihedralcut-Salerno)
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[(Salerno)] Salerno, Bernstein, J Chem Theory Comput, --, ---- (2018).
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@ -37,6 +37,7 @@ dihedral_style nharmonic, Loukas Peristeras, loukas.peristeras at scienomics.com
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dihedral_style quadratic, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12
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dihedral_style spherical, Andrew Jewett, jewett.aij@gmail.com, 15 Jul 16
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dihedral_style table, Andrew Jewett, jewett.aij@gmail.com, 10 Jan 12
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dihedral_style table/cut, Mike Salerno, ksalerno@pha.jhu.edu, 11 May 18
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fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
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fix ave/correlate/long, Jorge Ramirez (UPM Madrid), jorge.ramirez at upm.es, 21 Oct 2015
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fix bond/react, Jacob Gissinger (CU Boulder), info at disarmmd.org, 24 Feb 2018
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File diff suppressed because it is too large
Load Diff
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@ -0,0 +1,173 @@
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/* -*- c++ -*- ----------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#ifdef DIHEDRAL_CLASS
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DihedralStyle(table/cut,DihedralTableCut)
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#else
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#ifndef LMP_DIHEDRAL_TABLE_CUT_H
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#define LMP_DIHEDRAL_TABLE_CUT_H
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#include <stdio.h>
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#include "dihedral.h"
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namespace LAMMPS_NS {
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class DihedralTableCut : public Dihedral {
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public:
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DihedralTableCut(class LAMMPS *);
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virtual ~DihedralTableCut();
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virtual void compute(int, int);
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void settings(int, char **);
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void coeff(int, char **);
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void write_restart(FILE *);
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void read_restart(FILE *);
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void write_data(FILE *);
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double single(int type, int i1, int i2, int i3, int i4);
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protected:
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double *k1,*k2,*k3;
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double *phi1,*phi2,*phi3;
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double *aat_k,*aat_theta0_1,*aat_theta0_2;
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int *setflag_d;
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int *setflag_aat;
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void allocate();
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int tabstyle,tablength;
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// double *phi0; <- equilibrium angles not supported
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char *checkU_fname;
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char *checkF_fname;
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struct Table {
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int ninput;
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//double phi0; <-equilibrium angles not supported
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int f_unspecified; // boolean (but MPI does not like type "bool")
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int use_degrees; // boolean (but MPI does not like type "bool")
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double *phifile,*efile,*ffile;
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double *e2file,*f2file;
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double delta,invdelta,deltasq6;
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double *phi,*e,*de,*f,*df,*e2,*f2;
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};
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int ntables;
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Table *tables;
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int *tabindex;
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void null_table(Table *);
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void free_table(Table *);
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void read_table(Table *, char *, char *);
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void bcast_table(Table *);
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void spline_table(Table *);
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void compute_table(Table *);
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void param_extract(Table *, char *);
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// --------------------------------------------
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// ------------ inline functions --------------
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// --------------------------------------------
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// -----------------------------------------------------------
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// uf_lookup()
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// quickly calculate the potential u and force f at angle x,
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// using the internal tables tb->e and tb->f (evenly spaced)
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// -----------------------------------------------------------
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enum{LINEAR,SPLINE};
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inline void uf_lookup(int type, double x, double &u, double &f)
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{
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Table *tb = &tables[tabindex[type]];
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double x_over_delta = x*tb->invdelta;
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int i = static_cast<int> (x_over_delta);
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double a;
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double b = x_over_delta - i;
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// Apply periodic boundary conditions to indices i and i+1
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if (i >= tablength) i -= tablength;
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int ip1 = i+1; if (ip1 >= tablength) ip1 -= tablength;
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switch(tabstyle) {
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case LINEAR:
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u = tb->e[i] + b * tb->de[i];
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f = -(tb->f[i] + b * tb->df[i]); //<--works even if tb->f_unspecified==true
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break;
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case SPLINE:
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a = 1.0 - b;
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u = a * tb->e[i] + b * tb->e[ip1] +
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((a*a*a-a)*tb->e2[i] + (b*b*b-b)*tb->e2[ip1]) *
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tb->deltasq6;
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if (tb->f_unspecified)
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//Formula below taken from equation3.3.5 of "numerical recipes in c"
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//"f"=-derivative of e with respect to x (or "phi" in this case)
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f = -((tb->e[i]-tb->e[ip1])*tb->invdelta +
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((3.0*a*a-1.0)*tb->e2[i]+(1.0-3.0*b*b)*tb->e2[ip1])*tb->delta/6.0);
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else
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f = -(a * tb->f[i] + b * tb->f[ip1] +
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((a*a*a-a)*tb->f2[i] + (b*b*b-b)*tb->f2[ip1]) *
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tb->deltasq6);
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break;
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} // switch(tabstyle)
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} // uf_lookup()
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// ----------------------------------------------------------
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// u_lookup()
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// quickly calculate the potential u at angle x using tb->e
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//-----------------------------------------------------------
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inline void u_lookup(int type, double x, double &u)
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{
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Table *tb = &tables[tabindex[type]];
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int N = tablength;
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// i = static_cast<int> ((x - tb->lo) * tb->invdelta); <-general version
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double x_over_delta = x*tb->invdelta;
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int i = static_cast<int> (x_over_delta);
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double b = x_over_delta - i;
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// Apply periodic boundary conditions to indices i and i+1
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if (i >= N) i -= N;
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int ip1 = i+1; if (ip1 >= N) ip1 -= N;
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if (tabstyle == LINEAR) {
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u = tb->e[i] + b * tb->de[i];
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}
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else if (tabstyle == SPLINE) {
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double a = 1.0 - b;
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u = a * tb->e[i] + b * tb->e[ip1] +
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((a*a*a-a)*tb->e2[i] + (b*b*b-b)*tb->e2[ip1]) *
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tb->deltasq6;
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}
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} // u_lookup()
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};
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}
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#endif
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#endif
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/* ERROR/WARNING messages:
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W: Dihedral problem: %d %ld %d %d %d %d
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Conformation of the 4 listed dihedral atoms is extreme; you may want
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to check your simulation geometry.
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E: Incorrect args for dihedral coefficients
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Self-explanatory. Check the input script or data file.
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*/
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