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fix ave/time command

Syntax

fix ID group-ID ave/time Nevery Nrepeat Nfreq value1 value2 ... keyword args ...

ID, group-ID are documented in fix command
ave/time = style name of this fix command
Nevery = use input values every this many time steps
Nrepeat = # of times to use input values for calculating averages
Nfreq = calculate averages every this many time steps
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 or vector calculated by a compute with ID
c_ID[I] = Ith component of global vector or Ith column of global array calculated by a compute with ID, I can include wildcard (see below)
f_ID = global scalar or vector calculated by a fix with ID
f_ID[I] = Ith component of global vector or Ith column of global array calculated by a fix with ID, I can include wildcard (see below)
v_name = value(s) calculated by an equal-style or vector-style variable with name
v_name[I] = value calculated by a vector-style variable with name, I can include wildcard (see below)

zero or more keyword/arg pairs may be appended

keyword = mode or file or append or ave or start or off or overwrite or format or title1 or title2 or title3

mode arg = scalar or vector
  scalar = all input values are global scalars
  vector = all input values are global vectors or global arrays
ave args = one or running or window M
  one = output a new average value every Nfreq steps
  running = output cumulative average of all previous Nfreq steps
  window M = output average of M most recent Nfreq steps
start args = Nstart
  Nstart = start averaging on this time step
off arg = M = do not average this value
  M = value # from 1 to Nvalues
file arg = filename
  filename = name of file to output time averages to
append arg = filename
  filename = name of file to append time averages to
overwrite arg = none = overwrite output file with only latest output
format arg = string
  string = C-style format string
title1 arg = string
  string = text to print as 1st line of output file
title2 arg = string
  string = text to print as 2nd line of output file
title3 arg = string
  string = text to print as 3rd line of output file, only for vector mode

Examples

fix 1 all ave/time 100 5 1000 c_myTemp c_thermo_temp file temp.profile
fix 1 all ave/time 100 5 1000 c_thermo_press[2] ave window 20 &
                              title1 "My output values"
fix 1 all ave/time 100 5 1000 c_thermo_press[*]
fix 1 all ave/time 1 100 1000 f_indent f_indent[1] file temp.indent off 1

Description

Use one or more global values as inputs every few time steps, and average them over longer timescales. The resulting averages can be used by other output commands such as thermo_style custom, and can also be written to a file. Note that if no time averaging is done, this command can be used as a convenient way to simply output one or more global values to a file.

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. If you wish to spatial- or time-average or histogram per-atom quantities from a compute, fix, or variable, then see the fix ave/chunk, fix ave/atom, or fix ave/histo commands. If you wish to sum a per-atom quantity into a single global quantity, see the compute reduce command.

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 and 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 input values must either be all scalars or all vectors depending on the setting of the mode keyword. In both cases, the averaging is performed independently on each input value (i.e., each input scalar is averaged independently or each element of each input vector is averaged independently).

If mode = scalar, then the input values must be scalars, or vectors with a bracketed term appended, indicating the \(I^\text{th}\) value of the vector is used.

If mode = vector, then the input values must be vectors, or arrays with a bracketed term appended, indicating the Ith column of the array is used. All vectors must be the same length, which is the length of the vector or number of rows in the array.

For input values from a compute or fix or variable, the bracketed index I can be specified using a wildcard asterisk with the index to effectively specify multiple values. This takes the form “*” or “*n” or “m*” or “m*n”. If \(N\) is the size of the vector (for mode = scalar) or the number of columns in the array (for mode = vector), then an asterisk with no numeric values means all indices from 1 to \(N\). A leading asterisk means all indices from 1 to n (inclusive). A trailing asterisk means all indices from n to \(N\) (inclusive). A middle asterisk means all indices from m to n (inclusive).

Using a wildcard is the same as if the individual elements of the vector or columns of the array had been listed one by one. For example, the following two fix ave/time commands are equivalent, since the compute rdf command creates, in this case, a global array with three columns, each of length 50:

compute myRDF all rdf 50 1 2
fix 1 all ave/time 100 1 100 c_myRDF[*] file tmp1.rdf mode vector
fix 2 all ave/time 100 1 100 c_myRDF[1] c_myRDF[2] c_myRDF[3] file tmp2.rdf mode vector

Note

For a vector-style variable, only the wildcard forms “*n” or “m*n” are allowed. You must specify the upper bound, because vector-style variable lengths are not determined until the variable is evaluated. If n is specified larger than the vector length turns out to be, zeroes are output for missing vector values.

The \(N_\text{every}\), \(N_\text{repeat}\), and \(N_\text{freq}\) arguments specify on what time steps the input values will be used in order to contribute to the average. The final averaged quantities are generated on time steps that are a multiple of \(N_\text{freq}\). The average is over \(N_\text{repeat}\) quantities, computed in the preceding portion of the simulation every \(N_\text{every}\) time steps. \(N_\text{freq}\) must be a multiple of \(N_\text{every}\) and \(N_\text{every}\) must be non-zero even if \(N_\text{repeat} = 1\). Also, the time steps contributing to the average value cannot overlap (i.e., \(N_\text{repeat} \times N_\text{every}\) cannot exceed \(N_\text{freq}\)).

For example, if \(N_\text{every}=2\), \(N_\text{repeat}=6\), and \(N_\text{freq}=100\), then values on time steps 90, 92, 94, 96, 98, and 100 will be used to compute the final average on time step 100. Similarly for time steps 190, 192, 194, 196, 198, and 200 on time step 200, etc. If \(N_\text{repeat}=1\) and \(N_\text{freq} = 100\), then no time averaging is done; values are simply generated on time steps 100, 200, etc.

If a value begins with “c_”, a compute ID must follow which has been previously defined in the input script. If mode = scalar, then 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. If mode = vector, then if no bracketed term is appended, the global vector calculated by the compute is used. If a bracketed term is appended, the Ith column of the global array calculated by the compute is used. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values.

Note that there is a compute reduce command that can sum per-atom quantities into a global scalar or vector, which can then be accessed by fix ave/time. It can also 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 mode = scalar, then 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. If mode = vector, then if no bracketed term is appended, the global vector calculated by the fix is used. If a bracketed term is appended, the Ith column of the global array calculated by the fix is used. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values.

Note that some fixes only produce their values on certain time steps, 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. If mode = scalar, then only equal-style or vector-style variables can be used, which both produce global values. In this mode, a vector-style variable requires a bracketed term to specify the Ith element of the vector calculated by the variable. If mode = vector, then only a vector-style variable can be used, without a bracketed term. 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 time average.

Additional optional keywords also affect the operation of this fix.

If the mode keyword is set to scalar, then all input values must be global scalars, or elements of global vectors. If the mode keyword is set to vector, then all input values must be global vectors, or columns of global arrays. They can also be global arrays, which are converted into a series of global vectors (one per column), as explained above.

The ave keyword determines how the values produced every \(N_\text{freq}\) steps are averaged with values produced on previous steps that were multiples of \(N_\text{freq}\), before they are accessed by another output command or written to a file.

If the ave setting is one, then the values produced on time steps that are multiples of \(N_\text{freq}\) are independent of each other; they are output as-is without further averaging.

If the ave setting is running, then the values produced on time steps that are multiples of \(N_\text{freq}\) are summed and averaged in a cumulative sense before being output. Each output value is thus the average of the value produced on that time step with all preceding values. This running average begins when the fix is defined; it can only be restarted by deleting the fix via the unfix command, or by re-defining the fix by re-specifying it.

If the ave setting is window, then the values produced on time steps that are multiples of Nfreq are summed and averaged within a moving “window” of time, so that the last M values are used to produce the output. For example, if \(M = 3\) and \(N_\text{freq} = 1000\), then the output on step 10000 will be the average of the individual values on steps 8000, 9000, and 10000. Outputs on early steps will average over less than \(M\) values if they are not available.

The start keyword specifies what time step averaging will begin on. The default is step 0. Often input values can be 0.0 at time 0, so setting start to a larger value can avoid including a 0.0 in a running or windowed average.

The off keyword can be used to flag any of the input values. If a value is flagged, it will not be time averaged. Instead the most recent input value will always be stored and output. This is useful if one of more of the inputs produced by a compute or fix or variable are effectively constant or are simply current values (e.g., they are being written to a file with other time-averaged values for purposes of creating well-formatted output).

Added in version 17Apr2024: new keyword append

The file or append keywords allow a filename to be specified. If file is used, then the filename is overwritten if it already exists. If append is used, then the filename is appended to if it already exists, or created if it does not exist. Every Nfreq steps, one quantity or vector of quantities is written to the file for each input value specified in the fix ave/time command. For mode = scalar, this means a single line is written each time output is performed. Thus the file ends up to be a series of lines, i.e. one column of numbers for each input value. For mode = vector, an array of numbers is written each time output is performed. The number of rows is the length of the input vectors, and the number of columns is the number of values. Thus the file ends up to be a series of these array sections.

Added in version 4May2022.

If the filename ends in ‘.yaml’ or ‘.yml’ then the output format conforms to the YAML standard which allows easy import that data into tools and scripts that support reading YAML files. The structured data Howto contains examples for parsing and plotting such data with very little programming effort in Python using the pyyaml, pandas, and matplotlib packages.

The overwrite keyword will continuously overwrite the output file with the latest output, so that it only contains one time step worth of output. This option can only be used with the ave running setting.

The format keyword sets the numeric format of each value when it is printed to a file via the file keyword. Note that all values are floating point quantities. The default format is %g. You can specify a higher precision if desired (e.g., %20.16g).

The title1 and title2 and title3 keywords allow specification of the strings that will be printed as the first 2 or 3 lines of the output file, assuming the file keyword was used. LAMMPS uses default values for each of these, so they do not need to be specified.

By default, these header lines are as follows for mode = scalar:

# Time-averaged data for fix ID
# TimeStep value1 value2 ...

In the first line, ID is replaced with the fix-ID. In the second line the values are replaced with the appropriate fields from the fix ave/time command. There is no third line in the header of the file, so the title3 setting is ignored when mode = scalar.

By default, these header lines are as follows for mode = vector:

# Time-averaged data for fix ID
# TimeStep Number-of-rows
# Row value1 value2 ...

In the first line, ID is replaced with the fix-ID. The second line describes the two values that are printed at the first of each section of output. In the third line the values are replaced with the appropriate fields from the fix ave/time command.

Restart, fix_modify, output, run start/stop, minimize info

Added in version 4May2022.

No information about this fix is written to binary restart files. The fix_modify colname option can be used to change the name of the column in the output file. When writing a YAML format file this name will be in the list of keywords.

This fix produces a global scalar or global vector or global array which can be accessed by various output commands. The values can only be accessed on time steps that are multiples of \(N_\text{freq}\) since that is when averaging is performed.

A scalar is produced if only a single input value is averaged and mode = scalar. A vector is produced if multiple input values are averaged for mode = scalar, or a single input value for mode = vector. In the first case, the length of the vector is the number of inputs. In the second case, the length of the vector is the same as the length of the input vector. An array is produced if multiple input values are averaged and mode = vector. The global array has # of rows = length of the input vectors and # of columns = number of inputs.

If the fix produces a scalar or vector, then the scalar and each element of the vector can be either “intensive” or “extensive”, depending on whether the values contributing to the scalar or vector element 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 being time averaged, 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.

No parameter of this fix can be used with the start/stop keywords of the run command. This fix is not invoked during energy minimization.

Restrictions

none

Default

The option defaults are mode = scalar, ave = one, start = 0, no file output, format = %g, title 1,2,3 = strings as described above, and no off settings for any input values.