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Update docs: bond_table

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Richard Berger
2019-11-16 22:51:46 -05:00
parent 1b4e84de94
commit ff9f93bbf6
2 changed files with 13 additions and 181 deletions
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31
doc/src/bond_table.rst
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@ -1,16 +1,16 @@
.. index:: bond\_style table .. index:: bond_style table
bond\_style table command bond_style table command
========================= ========================
bond\_style table/omp command bond_style table/omp command
============================= ============================
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
bond_style table style N bond_style table style N
@ -21,7 +21,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
bond_style table linear 1000 bond_style table linear 1000
bond_coeff 1 file.table ENTRY1 bond_coeff 1 file.table ENTRY1
@ -31,14 +31,14 @@ Description
Style *table* creates interpolation tables of length *N* from bond Style *table* creates interpolation tables of length *N* from bond
potential and force values listed in a file(s) as a function of bond potential and force values listed in a file(s) as a function of bond
length. The files are read by the :doc:`bond\_coeff <bond_coeff>` length. The files are read by the :doc:`bond_coeff <bond_coeff>`
command. command.
The interpolation tables are created by fitting cubic splines to the The interpolation tables are created by fitting cubic splines to the
file values and interpolating energy and force values at each of *N* file values and interpolating energy and force values at each of *N*
distances. During a simulation, these tables are used to interpolate distances. During a simulation, these tables are used to interpolate
energy and force values as needed. The interpolation is done in one energy and force values as needed. The interpolation is done in one
of 2 styles: *linear* or *spline*\ . of 2 styles: *linear* or *spline*.
For the *linear* style, the bond length is used to find 2 surrounding For the *linear* style, the bond length is used to find 2 surrounding
table values from which an energy or force is computed by linear table values from which an energy or force is computed by linear
@ -50,7 +50,7 @@ used to find the appropriate set of coefficients which are used to
evaluate a cubic polynomial which computes the energy or force. evaluate a cubic polynomial which computes the energy or force.
The following coefficients must be defined for each bond type via the The following coefficients must be defined for each bond type via the
:doc:`bond\_coeff <bond_coeff>` command as in the example above. :doc:`bond_coeff <bond_coeff>` command as in the example above.
* filename * filename
* keyword * keyword
@ -84,14 +84,14 @@ A section begins with a non-blank line whose 1st character is not a
between sections. The first line begins with a keyword which between sections. The first line begins with a keyword which
identifies the section. The line can contain additional text, but the identifies the section. The line can contain additional text, but the
initial text must match the argument specified in the initial text must match the argument specified in the
:doc:`bond\_coeff <bond_coeff>` command. The next line lists (in any :doc:`bond_coeff <bond_coeff>` command. The next line lists (in any
order) one or more parameters for the table. Each parameter is a order) one or more parameters for the table. Each parameter is a
keyword followed by one or more numeric values. keyword followed by one or more numeric values.
The parameter "N" is required and its value is the number of table 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* entries that follow. Note that this may be different than the *N*
specified in the :doc:`bond\_style table <bond_style>` command. Let specified in the :doc:`bond\_style table <bond_style>` command. Let
Ntable = *N* in the bond\_style command, and Nfile = "N" in the Ntable = *N* in the bond_style command, and Nfile = "N" in the
tabulated file. What LAMMPS does is a preliminary interpolation by tabulated file. What LAMMPS does is a preliminary interpolation by
creating splines using the Nfile tabulated values as nodal points. It creating splines using the Nfile tabulated values as nodal points. It
uses these to interpolate as needed to generate energy and force uses these to interpolate as needed to generate energy and force
@ -173,11 +173,6 @@ info.
Related commands Related commands
"""""""""""""""" """"""""""""""""
:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>` :doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
**Default:** none **Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

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doc/txt/bond_table.txt
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@ -1,163 +0,0 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
bond_style table command :h3
bond_style table/omp command :h3
[Syntax:]
bond_style table style N :pre
style = {linear} or {spline} = method of interpolation
N = use N values in table :ul
[Examples:]
bond_style table linear 1000
bond_coeff 1 file.table ENTRY1 :pre
[Description:]
Style {table} creates interpolation tables of length {N} from bond
potential and force values listed in a file(s) as a function of bond
length. The files are read by the "bond_coeff"_bond_coeff.html
command.
The interpolation tables are created by fitting cubic splines to the
file values and interpolating energy and force values at each of {N}
distances. During a simulation, these tables are used to interpolate
energy and force values as needed. The interpolation is done in one
of 2 styles: {linear} or {spline}.
For the {linear} style, the bond length is used to find 2 surrounding
table values from which an energy or force is computed by linear
interpolation.
For the {spline} style, a cubic spline coefficients are computed and
stored at each of the {N} values in the table. The bond length is
used to find the appropriate set of coefficients which are used to
evaluate a cubic polynomial which computes the energy or force.
The following coefficients must be defined for each bond type via the
"bond_coeff"_bond_coeff.html command as in the example above.
filename
keyword :ul
The filename specifies a file containing tabulated energy and force
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):
# Bond potential for harmonic (one or more comment or blank lines) :pre
HAM (keyword is the first text on line)
N 101 FP 0 0 EQ 0.5 (N, FP, EQ parameters)
(blank line)
1 0.00 338.0000 1352.0000 (index, bond-length, energy, force)
2 0.01 324.6152 1324.9600
...
101 1.00 338.0000 -1352.0000 :pre
A section begins with a non-blank line whose 1st character is not a
"#"; 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
"bond_coeff"_bond_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.
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 "bond_style table"_bond_style.html command. Let
Ntable = {N} in the bond_style command, and Nfile = "N" in the
tabulated file. 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 force
values at Ntable different points. The resulting tables of length
Ntable are then used as described above, when computing energy and
force for individual bond lengths. This means that if you want the
interpolation tables of length Ntable to match exactly what is in the
tabulated file (with effectively no preliminary interpolation), you
should set Ntable = Nfile.
The "FP" parameter is optional. If used, it is followed by two values
fplo and fphi, which are the derivatives of the force at the innermost
and outermost bond lengths. These values are needed by the spline
construction routines. If not specified by the "FP" parameter, they
are estimated (less accurately) by the first two and last two force
values in the table.
The "EQ" parameter is also optional. If used, it is followed by a the
equilibrium bond length, which is used, for example, by the "fix
shake"_fix_shake.html command. If not used, the equilibrium bond
length is to the distance in the table with the lowest potential energy.
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 bond length r (in distance units), the 3rd value is the energy (in
energy units), and the 4th is the force (in force units). The bond
lengths must range from a LO value to a HI value, and increase from
one line to the next. If the actual bond length is ever smaller than
the LO value or larger than the HI value, then the bond energy and
force is evaluated as if the bond were the LO or HI length.
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.
:line
Styles with a {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 on the "Speed packages"_Speed_packages.html doc
page. 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 GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the "Build
package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Run_options.html when you invoke LAMMPS, or you can use the
"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line
[Restart info:]
This bond style writes the settings for the "bond_style table"
command to "binary restart files"_restart.html, so a bond_style
command does not need to specified in an input script that reads a
restart file. However, the coefficient information is not stored in
the restart file, since it is tabulated in the potential files. Thus,
bond_coeff commands do need to be specified in the restart input
script.
[Restrictions:]
This bond style can only be used if LAMMPS was built with the MOLECULE
package. See the "Build package"_Build_package.html doc page for more
info.
[Related commands:]
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
[Default:] none