fix vector command
fix ID group-ID vector Nevery value1 value2 ... keyword args ...
ID, group-ID are documented in fix command
vector = style name of this fix command
Nevery = use input values every this many timesteps
one or more input values can be listed
value = c_ID, c_ID[N], f_ID, f_ID[N], v_name
c_ID = global scalar calculated by a compute with ID c_ID[I] = Ith component of global vector calculated by a compute with ID f_ID = global scalar calculated by a fix with ID f_ID[I] = Ith component of global vector calculated by a fix with ID v_name = value calculated by an equal-style variable with name v_name[I] = Ith component of vector-style variable with name
zero or more keyword/args pairs may be appended
keyword = nmax
nmax length = set maximal length of vector to <length>
fix 1 all vector 100 c_myTemp fix 1 all vector 5 c_myTemp v_integral fix 1 all vector 50 c_myTemp nmax 200
Use one or more global values as inputs every few timesteps, and simply store them as a sequence. For a single specified value, the values are stored as a global vector of growing length. For multiple specified values, they are stored as rows in a global array, whose number of rows is growing. The resulting vector or array can be used by other output commands.
The optional nmax keyword can be used to restrict the length of the vector to the given length value. Once the restricted vector is filled, the oldest entry will be discarded when a entry is added.
One way to to use this command is to accumulate a vector that is numerically integrated using the variable trap() function. For example, the velocity auto-correlation function (VACF) can be integrated, to yield a diffusion coefficient, as follows:
compute 2 all vacf fix 5 all vector 1 c_2 variable diff equal dt*trap(f_5) thermo_style custom step v_diff
The group specified with this command is ignored. However, note that specified values may represent calculations performed by computes and fixes which store their own “group” definitions.
Each listed value can be the result of a compute or fix or the evaluation of an equal-style or vector-style variable. In each case, the compute, fix, or variable must produce a global quantity, not a per-atom or local quantity. And the global quantity must be a scalar, not a vector or array.
Computes that produce global quantities are those which do not have the word atom in their style name. Only a few fixes produce global quantities. See the doc pages for individual fixes for info on which ones produce such values. Variables of style equal or vector are the only ones that can be used with this fix. Variables of style atom cannot be used, since they produce per-atom values.
The Nevery argument specifies on what timesteps the input values will be used in order to be stored. Only timesteps that are a multiple of Nevery, including timestep 0, will contribute values.
If Nevery is a small number and the simulation runs for many steps, the accumulated vector or array can become very large and thus consume a lot of memory. The implementation limit is about 2 billion entries. Using the nmax keyword mentioned above can avoid that by limiting the size of the vector.
Note that if you perform multiple runs, using the “pre no” option of the run command to avoid initialization on subsequent runs, then you need to use the stop keyword with the first run command with a timestep value that encompasses all the runs. This is so that the vector or array stored by this fix can be allocated to a sufficient size.
If a value begins with “c_”, a compute ID must follow which has been previously defined in the input script. If no bracketed term is appended, the global scalar calculated by the compute is used. If a bracketed term is appended, the Ith element of the global vector calculated by the compute is used.
Note that there is a compute reduce command which can sum per-atom quantities into a global scalar or vector which can thus be accessed by fix vector. Or it can be a compute defined not in your input script, but by thermodynamic output or other fixes such as fix nvt or fix temp/rescale. See the doc pages for these commands which give the IDs of these computes. Users can also write code for their own compute styles and add them to LAMMPS.
If a value begins with “f_”, a fix ID must follow which has been previously defined in the input script. If no bracketed term is appended, the global scalar calculated by the fix is used. If a bracketed term is appended, the Ith element of the global vector calculated by the fix is used.
Note that some fixes only produce their values on certain timesteps, which must be compatible with Nevery, else an error will result. Users can also write code for their own fix styles and add them to LAMMPS.
If a value begins with “v_”, a variable name must follow which has been previously defined in the input script. An equal-style or vector-style variable can be referenced; the latter requires a bracketed term to specify the Ith element of the vector calculated by the variable. See the variable command for details. Note that variables of style equal and vector define a formula which can reference individual atom properties or thermodynamic keywords, or they can invoke other computes, fixes, or variables when they are evaluated, so this is a very general means of specifying quantities to be stored by fix vector.
Restart, fix_modify, output, run start/stop, minimize info
This fix produces a global vector or global array which can be accessed by various output commands. The values can only be accessed on timesteps that are multiples of Nevery.
A vector is produced if only a single input value is specified. An array is produced if multiple input values are specified. The length of the vector or the number of rows in the array grows by 1 every Nevery timesteps.
If the fix produces a vector, then the entire vector will be either “intensive” or “extensive”, depending on whether the values stored in the vector are “intensive” or “extensive”. If the fix produces an array, then all elements in the array must be the same, either “intensive” or “extensive”. If a compute or fix provides the value stored, then the compute or fix determines whether the value is intensive or extensive; see the page for that compute or fix for further info. Values produced by a variable are treated as intensive.
This fix can allocate storage for stored values accumulated over multiple runs, using the start and stop keywords of the run command. See the run command for details of how to do this. If using the run pre no command option, this is required to allow the fix to allocate sufficient storage for stored values.
This fix is not invoked during energy minimization.
The default value of nmax is deduced from the number of steps in a run (or multiple runs when using the start and stop keywords of the run command) divided by the choice of Nevery plus 1.