compute dihedral/local command¶

Syntax¶

compute ID group-ID dihedral/local value1 value2 ... keyword args ...

ID, group-ID are documented in compute command
dihedral/local = style name of this compute command
one or more values may be appended

value = phi or v_name

phi = tabulate dihedral angles
v_name = equal-style variable with name (see below)

zero or more keyword/args pairs may be appended

keyword = set

set args = phi name
  phi = only currently allowed arg
  name = name of variable to set with phi

Examples¶

compute 1 all dihedral/local phi

compute 1 all dihedral/local phi v_cos set phi p

Description¶

Define a computation that calculates properties of individual dihedral interactions. The number of datums generated, aggregated across all processors, equals the number of dihedral angles in the system, modified by the group parameter as explained below.

The value phi is the dihedral angle, as defined in the diagram on the dihedral_style doc page.

The value v_name can be used together with the set keyword to compute a user-specified function of the dihedral angle phi. The name specified for the v_name value is the name of an equal-style variable which should evaluate a formula based on a variable which will store the angle phi. This other variable must be an internal-style variable defined in the input script; its initial numeric value can be anything. It must be an internal-style variable, because this command resets its value directly. The set keyword is used to identify the name of this other variable associated with phi.

Note that the value of phi for each angle which stored in the internal variable is in radians, not degrees.

As an example, these commands can be added to the bench/in.rhodo script to compute the cosine and cosine^2 of every dihedral angle in the system and output the statistics in various ways:

variable p internal 0.0
variable cos equal cos(v_p)
variable cossq equal cos(v_p)*cos(v_p)

compute 1 all property/local datom1 datom2 datom3 datom4 dtype
compute 2 all dihedral/local phi v_cos v_cossq set phi p
dump 1 all local 100 tmp.dump c_1[*] c_2[*]

compute 3 all reduce ave c_2[*]
thermo_style custom step temp press c_3[*]

fix 10 all ave/histo 10 10 100 -1 1 20 c_2[2] mode vector file tmp.histo

The dump local command will output the angle, cosine(angle), cosine^2(angle) for every dihedral in the system. The thermo_style command will print the average of those quantities via the compute reduce command with thermo output. And the fix ave/histo command will histogram the cosine(angle) values and write them to a file.

The local data stored by this command is generated by looping over all the atoms owned on a processor and their dihedrals. A dihedral will only be included if all 4 atoms in the dihedral are in the specified compute group.

Note that as atoms migrate from processor to processor, there will be no consistent ordering of the entries within the local vector or array from one timestep to the next. The only consistency that is guaranteed is that the ordering on a particular timestep will be the same for local vectors or arrays generated by other compute commands. For example, dihedral output from the compute property/local command can be combined with data from this command and output by the dump local command in a consistent way.

Here is an example of how to do this:

compute 1 all property/local dtype datom1 datom2 datom3 datom4
compute 2 all dihedral/local phi
dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_1[5] c_2[1]

Output info¶

This compute calculates a local vector or local array depending on the number of values. The length of the vector or number of rows in the array is the number of dihedrals. If a single value is specified, a local vector is produced. If two or more values are specified, a local array is produced where the number of columns = the number of values. The vector or array can be accessed by any command that uses local values from a compute as input. See the Howto output page for an overview of LAMMPS output options.

The output for phi will be in degrees.

Restrictions¶

none

Default¶