diff --git a/doc/src/bond_table.rst b/doc/src/bond_table.rst index f68288349d..c12ea8af44 100644 --- a/doc/src/bond_table.rst +++ b/doc/src/bond_table.rst @@ -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 """""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style table style N @@ -21,7 +21,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style table linear 1000 bond_coeff 1 file.table ENTRY1 @@ -31,14 +31,14 @@ 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 :doc:`bond\_coeff ` +length. The files are read by the :doc:`bond_coeff ` 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*\ . +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 @@ -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. The following coefficients must be defined for each bond type via the -:doc:`bond\_coeff ` command as in the example above. +:doc:`bond_coeff ` command as in the example above. * filename * 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 identifies the section. The line can contain additional text, but the initial text must match the argument specified in the -:doc:`bond\_coeff ` command. The next line lists (in any +:doc:`bond_coeff ` 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 :doc:`bond\_style table ` 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 creating splines using the Nfile tabulated values as nodal points. It uses these to interpolate as needed to generate energy and force @@ -173,11 +173,6 @@ info. Related commands """""""""""""""" -:doc:`bond\_coeff `, :doc:`delete\_bonds ` +:doc:`bond_coeff `, :doc:`delete_bonds ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/bond_table.txt b/doc/txt/bond_table.txt deleted file mode 100644 index 7235214af0..0000000000 --- a/doc/txt/bond_table.txt +++ /dev/null @@ -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