compute angle/local command¶
compute ID group-ID angle/local value1 value2 ... keyword args ...
ID, group-ID are documented in compute command
angle/local = style name of this compute command
one or more values may be appended
value = theta or eng or v_name
theta = tabulate angles eng = tabulate angle energies v_name = equal-style variable with name (see below)
zero or more keyword/args pairs may be appended
keyword = set
set args = theta name theta = only currently allowed arg name = name of variable to set with theta
compute 1 all angle/local theta compute 1 all angle/local eng theta compute 1 all angle/local theta v_cos set theta t
Define a computation that calculates properties of individual angle interactions. The number of datums generated, aggregated across all processors, equals the number of angles in the system, modified by the group parameter as explained below.
The value theta is the angle for the three atoms in the interaction.
The value eng is the interaction energy for the angle.
The value v_name can be used together with the set keyword to compute a user-specified function of the angle theta. 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 theta. 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 theta.
Note that the value of theta 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-squared of every angle in the system and output the statistics in various ways:
variable t internal 0.0 variable cos equal cos(v_t) variable cossq equal cos(v_t)*cos(v_t) compute 1 all property/local aatom1 aatom2 aatom3 atype compute 2 all angle/local eng theta v_cos v_cossq set theta t 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 mode vector file tmp.histo
The dump local command will output the potential energy (\(\phi\)), the angle (\(\theta\)), \(\cos(\theta\)), and \(\cos^2(\theta)\) for every angle \(\theta\) 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 \(\cos(\theta)\) 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 angles. An angle will only be included if all three atoms in the angle are in the specified compute group. Any angles that have been broken (see the angle_style command) by setting their angle type to 0 are not included. Angles that have been turned off (see the fix shake or delete_bonds commands) by setting their angle type negative are written into the file, but their energy will be 0.0.
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, angle 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 atype aatom1 aatom2 aatom3 compute 2 all angle/local theta eng dump 1 all local 1000 tmp.dump index c_1 c_1 c_1 c_1 c_2 c_2
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 angles. 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 theta will be in degrees. The output for eng will be in energy units.