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2.3.8. Compute, fixes, variables

This section documents accessing or modifying data from objects like computes, fixes, or variables in LAMMPS using the lammps module.

For lammps.extract_compute() and lammps.extract_fix(), the global, per-atom, or local data calculated by the compute or fix can be accessed. What is returned depends on whether the compute or fix calculates a scalar or vector or array. For a scalar, a single double value is returned. If the compute or fix calculates a vector or array, a pointer to the internal LAMMPS data is returned, which you can use via normal Python subscripting.

The one exception is that for a fix that calculates a global vector or array, a single double value from the vector or array is returned, indexed by I (vector) or I and J (array). I,J are zero-based indices. See the Howto output page for a discussion of global, per-atom, and local data, and of scalar, vector, and array data types. See the doc pages for individual computes and fixes for a description of what they calculate and store.

For lammps.extract_variable(), an equal-style or atom-style variable is evaluated and its result returned.

For equal-style variables a single c_double value is returned and the group argument is ignored. For atom-style variables, a vector of c_double is returned, one value per atom, which you can use via normal Python subscripting. The values will be zero for atoms not in the specified group.

lammps.numpy.extract_compute(), lammps.numpy.extract_fix(), and lammps.numpy.extract_variable() are equivalent NumPy implementations that return NumPy arrays instead of ctypes pointers.

The lammps.set_variable() method sets an existing string-style variable to a new string value, so that subsequent LAMMPS commands can access the variable.

Methods:

lammps.extract_compute(): extract value(s) from a compute
lammps.extract_fix(): extract value(s) from a fix
lammps.extract_variable(): extract value(s) from a variable
lammps.set_variable(): set existing named string-style variable to value

NumPy Methods:

lammps.numpy.extract_compute(): extract value(s) from a compute, return arrays as numpy arrays
lammps.numpy.extract_fix(): extract value(s) from a fix, return arrays as numpy arrays
lammps.numpy.extract_variable(): extract value(s) from a variable, return arrays as numpy arrays

PyLammps and IPyLammps classes currently do not add any additional ways of retrieving information out of computes and fixes. This information can still be accessed by using the lammps API:

L.lmp.extract_compute(...)
L.lmp.extract_fix(...)
# OR
L.lmp.numpy.extract_compute(...)
L.lmp.numpy.extract_fix(...)

LAMMPS variables can be both defined and accessed via the PyLammps interface.

To define a variable you can use the variable command:

L.variable("a index 2")

A dictionary of all variables is returned by the PyLammps.variables property:

you can access an individual variable by retrieving a variable object from the L.variables dictionary by name

a = L.variables['a']

The variable value can then be easily read and written by accessing the value property of this object.

print(a.value)
a.value = 4