Update docs: bond_table
This commit is contained in:
Richard Berger
@ -1,16 +1,16 @@
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.. index:: bond\_style table
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.. index:: bond_style table
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bond\_style table command
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=========================
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bond_style table command
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========================
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bond\_style table/omp command
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=============================
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bond_style table/omp command
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============================
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Syntax
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""""""
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.. parsed-literal::
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.. code-block:: LAMMPS
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bond_style table style N
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@ -21,7 +21,7 @@ Examples
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""""""""
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.. parsed-literal::
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.. code-block:: LAMMPS
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bond_style table linear 1000
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bond_coeff 1 file.table ENTRY1
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@ -31,14 +31,14 @@ Description
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Style *table* creates interpolation tables of length *N* from bond
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potential and force values listed in a file(s) as a function of bond
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length. The files are read by the :doc:`bond\_coeff <bond_coeff>`
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length. The files are read by the :doc:`bond_coeff <bond_coeff>`
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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 force values at each of *N*
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distances. During a simulation, these tables are used to interpolate
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energy and force values as needed. The interpolation is done in one
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of 2 styles: *linear* or *spline*\ .
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of 2 styles: *linear* or *spline*.
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For the *linear* style, the bond length is used to find 2 surrounding
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table values from which an energy or force is computed by linear
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@ -50,7 +50,7 @@ used to find the appropriate set of coefficients which are used to
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evaluate a cubic polynomial which computes the energy or force.
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The following coefficients must be defined for each bond type via the
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:doc:`bond\_coeff <bond_coeff>` command as in the example above.
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:doc:`bond_coeff <bond_coeff>` command as in the example above.
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* filename
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* keyword
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@ -84,14 +84,14 @@ A section begins with a non-blank line whose 1st character is not a
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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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:doc:`bond\_coeff <bond_coeff>` command. The next line lists (in any
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:doc:`bond_coeff <bond_coeff>` command. The next line lists (in any
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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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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 :doc:`bond\_style table <bond_style>` command. Let
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Ntable = *N* in the bond\_style command, and Nfile = "N" in the
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Ntable = *N* in the bond_style command, and Nfile = "N" in the
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tabulated file. What LAMMPS does is a preliminary interpolation by
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creating splines using the Nfile tabulated values as nodal points. It
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uses these to interpolate as needed to generate energy and force
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@ -173,11 +173,6 @@ info.
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Related commands
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""""""""""""""""
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:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
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:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
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**Default:** none
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Commands_all.html
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@ -1,163 +0,0 @@
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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,Commands_all.html)
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:line
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bond_style table command :h3
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bond_style table/omp command :h3
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[Syntax:]
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bond_style table style N :pre
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style = {linear} or {spline} = method of interpolation
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N = use N values in table :ul
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[Examples:]
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bond_style table linear 1000
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bond_coeff 1 file.table ENTRY1 :pre
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[Description:]
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Style {table} creates interpolation tables of length {N} from bond
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potential and force values listed in a file(s) as a function of bond
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length. The files are read by the "bond_coeff"_bond_coeff.html
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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 force values at each of {N}
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distances. During a simulation, these tables are used to interpolate
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energy and force values as needed. The interpolation is done in one
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of 2 styles: {linear} or {spline}.
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For the {linear} style, the bond length is used to find 2 surrounding
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table values from which an energy or force is computed by linear
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interpolation.
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For the {spline} style, a cubic spline coefficients are computed and
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stored at each of the {N} values in the table. The bond length is
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used to find the appropriate set of coefficients which are used to
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evaluate a cubic polynomial which computes the energy or force.
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The following coefficients must be defined for each bond type via the
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"bond_coeff"_bond_coeff.html command as in the example above.
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filename
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keyword :ul
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The filename specifies a file containing tabulated energy and force
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values. The keyword specifies a section of the file. The format of
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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):
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# Bond potential for harmonic (one or more comment or blank lines) :pre
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HAM (keyword is the first text on line)
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N 101 FP 0 0 EQ 0.5 (N, FP, EQ parameters)
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(blank line)
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1 0.00 338.0000 1352.0000 (index, bond-length, energy, force)
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2 0.01 324.6152 1324.9600
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...
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101 1.00 338.0000 -1352.0000 :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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"bond_coeff"_bond_coeff.html command. The next line lists (in any
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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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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 "bond_style table"_bond_style.html command. Let
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Ntable = {N} in the bond_style command, and Nfile = "N" in the
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tabulated file. What LAMMPS does is a preliminary interpolation by
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creating splines using the Nfile tabulated values as nodal points. It
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uses these to interpolate as needed to generate energy and force
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values at Ntable different points. The resulting tables of length
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Ntable are then used as described above, when computing energy and
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force for individual bond lengths. This means that if you want the
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interpolation tables of length Ntable to match exactly what is in the
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tabulated file (with effectively no preliminary interpolation), you
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should set Ntable = Nfile.
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The "FP" parameter is optional. If used, it is followed by two values
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fplo and fphi, which are the derivatives of the force at the innermost
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and outermost bond lengths. These values are needed by the spline
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construction routines. If not specified by the "FP" parameter, they
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are estimated (less accurately) by the first two and last two force
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values in the table.
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The "EQ" parameter is also optional. If used, it is followed by a the
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equilibrium bond length, which is used, for example, by the "fix
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shake"_fix_shake.html command. If not used, the equilibrium bond
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length is to the distance in the table with the lowest potential energy.
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Following a blank line, the next N lines list the tabulated values.
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On each line, the 1st value is the index from 1 to N, the 2nd value is
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the bond length r (in distance units), the 3rd value is the energy (in
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energy units), and the 4th is the force (in force units). The bond
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lengths must range from a LO value to a HI value, and increase from
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one line to the next. If the actual bond length is ever smaller than
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the LO value or larger than the HI value, then the bond energy and
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force is evaluated as if the bond were the LO or HI length.
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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
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one 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 on the "Speed packages"_Speed_packages.html doc
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page. 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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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 "Build
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package"_Build_package.html doc page 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"_Run_options.html when you invoke LAMMPS, or you can use the
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"suffix"_suffix.html command in your input script.
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See the "Speed packages"_Speed_packages.html doc page for more
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instructions on how to use the accelerated styles effectively.
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:line
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[Restart info:]
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This bond style writes the settings for the "bond_style table"
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command to "binary restart files"_restart.html, so a bond_style
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command does not need to specified in an input script that reads a
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restart file. However, the coefficient information is not stored in
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the restart file, since it is tabulated in the potential files. Thus,
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bond_coeff commands do need to be specified in the restart input
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script.
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[Restrictions:]
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This bond style can only be used if LAMMPS was built with the MOLECULE
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package. See the "Build package"_Build_package.html doc page for more
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info.
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[Related commands:]
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"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
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[Default:] none
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