\(\renewcommand{\AA}{\text{Å}}\)

dihedral_write command

Syntax

dihedral_write dtype N file keyword

  • dtype = dihedral type

  • N = # of values

  • file = name of file to write values to

  • keyword = section name in file for this set of tabulated values

Examples

dihedral_write 1  500 table.txt Harmonic_1
dihedral_write 3 1000 table.txt Harmonic_3

Description

New in version 8Feb2023.

Write energy and force values to a file as a function of the dihedral angle for the currently defined dihedral potential. Force in this context means the force with respect to the dihedral angle, not the force on individual atoms. This is useful for plotting the potential function or otherwise debugging its values. The resulting file can also be used as input for use with dihedral style table.

If the file already exists, the table of values is appended to the end of the file to allow multiple tables of energy and force to be included in one file. The individual sections may be identified by the keyword.

The energy and force values are computed for dihedrals ranging from 0 degrees to 360 degrees for 4 interacting atoms forming an dihedral type dtype, using the appropriate dihedral_coeff coefficients. N evenly spaced dihedrals are used. Since 0 and 360 degrees are the same dihedral angle, the latter entry is skipped.

For example, for N = 6, values would be computed at \(\phi = 0, 60, 120, 180, 240, 300\).

The file is written in the format used as input for the dihedral_style table option with keyword as the section name. Each line written to the file lists an index number (1-N), an dihedral angle (in degrees), an energy (in energy units), and a force (in force units per radians^2). In case a new file is created, the first line will be a comment with a “DATE:” and “UNITS:” tag with the current date and units settings. For subsequent invocations of the dihedral_write command for the same file, data will be appended and the current units settings will be compared to the data from the header, if present. The dihedral_write will refuse to add a table to an existing file if the units are not the same.

Restrictions

All force field coefficients for dihedrals and other kinds of interactions must be set before this command can be invoked.

The table of the dihedral energy and force data data is created by using a separate, internally created, new LAMMPS instance with a dummy system of 4 atoms for which the dihedral potential energy is computed after transferring the dihedral style and coefficients and arranging the 4 atoms into the corresponding geometries. The dihedral force is then determined from the potential energies through numerical differentiation. As a consequence of this approach, not all dihedral styles are compatible. The following conditions must be met:

  • The dihedral style must be able to write its coefficients to a data file. This condition excludes for example dihedral style hybrid and dihedral style table.

  • The potential function must not have any terms that depend on geometry properties other than the dihedral. This condition excludes for example dihedral style class2. Please note that the write_dihedral command has no way of checking for this condition. It will check the style name against an internal list of known to be incompatible styles. The resulting tables may be bogus for unlisted dihedral styles if the requirement is not met. It is thus recommended to make careful tests for any created tables.

Default

none