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variable command

Syntax

variable name style args ...

name = name of variable to define

style = delete or atomfile or file or format or getenv or index or internal or loop or python or string or timer or uloop or universe or world or equal or vector or atom

delete = no args
atomfile arg = filename
file arg = filename
format args = vname fstr
  vname = name of equal-style variable to evaluate
  fstr = C-style format string
getenv arg = one string
index args = one or more strings
internal arg = numeric value
loop args = N
  N = integer size of loop, loop from 1 to N inclusive
loop args = N pad
  N = integer size of loop, loop from 1 to N inclusive
  pad = all values will be same length, e.g. 001, 002, ..., 100
loop args = N1 N2
  N1,N2 = loop from N1 to N2 inclusive
loop args = N1 N2 pad
  N1,N2 = loop from N1 to N2 inclusive
  pad = all values will be same length, e.g. 050, 051, ..., 100
python arg = function
string arg = one string
timer arg = no arguments
uloop args = N
  N = integer size of loop
uloop args = N pad
  N = integer size of loop
  pad = all values will be same length, e.g. 001, 002, ..., 100
universe args = one or more strings
world args = one string for each partition of processors

equal or vector or atom args = one formula containing numbers, thermo keywords, math operations, built-in functions, atom values and vectors, compute/fix/variable references
  numbers = 0.0, 100, -5.4, 2.8e-4, etc
  constants = PI, version, on, off, true, false, yes, no
  thermo keywords = vol, ke, press, etc from thermo_style
  math operators = (), -x, x+y, x-y, x*y, x/y, x^y, x%y,
                   x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x || y, x |^ y, !x
  math functions = sqrt(x), exp(x), ln(x), log(x), abs(x),
                   sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x),
                   random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ternary(x,y,z),
                   ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z),
                   logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c),
                   vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)
  group functions = count(group), mass(group), charge(group),
                    xcm(group,dim), vcm(group,dim), fcm(group,dim),
                    bound(group,dir), gyration(group), ke(group),
                    angmom(group,dim), torque(group,dim),
                    inertia(group,dimdim), omega(group,dim)
  region functions = count(group,region), mass(group,region), charge(group,region),
                    xcm(group,dim,region), vcm(group,dim,region), fcm(group,dim,region),
                    bound(group,dir,region), gyration(group,region), ke(group,reigon),
                    angmom(group,dim,region), torque(group,dim,region),
                    inertia(group,dimdim,region), omega(group,dim,region)
  special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), sort(x), rsort(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name), label2type(kind,label), is_typelabel(kind,label), is_timeout()
  feature functions = is_available(category,feature), is_active(category,feature), is_defined(category,id)
  atom value = id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i]
  atom vector = id, mass, type, mol, radius, q, x, y, z, vx, vy, vz, fx, fy, fz
  custom atom property = i_name, d_name, i_name[i], d_name[i], i2_name[i], d2_name[i], i2_name[i][j], d_name[i][j]
  compute references = c_ID, c_ID[i], c_ID[i][j], C_ID, C_ID[i]
  fix references = f_ID, f_ID[i], f_ID[i][j], F_ID, F_ID[i]
  variable references = v_name, v_name[i]
  vector initialization = [1,3,7,10] (for vector variables only)

Examples

variable x index run1 run2 run3 run4 run5 run6 run7 run8
variable LoopVar loop $n
variable beta equal temp/3.0
variable b1 equal x[234]+0.5*vol
variable b1 equal "x[234] + 0.5*vol"
variable b equal xcm(mol1,x)/2.0
variable b equal c_myTemp
variable b atom x*y/vol
variable foo string myfile
variable foo internal 3.5
variable myPy python increase
variable f file values.txt
variable temp world 300.0 310.0 320.0 ${Tfinal}
variable x universe 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
variable x uloop 15 pad
variable str format x %.6g
variable myvec vector [1,3,7,10]
variable x delete

variable start timer
other commands
variable stop timer
print "Elapsed time: $(v_stop-v_start:%.6f)"

Description

This command assigns one or more strings to a variable name for evaluation later in the input script or during a simulation.

Variables can thus be useful in several contexts. A variable can be defined and then referenced elsewhere in an input script to become part of a new input command. For variable styles that store multiple strings, the next command can be used to increment which string is assigned to the variable. Variables of style equal store a formula which when evaluated produces a single numeric value which can be output either directly (see the print, fix print, and run every commands) or as part of thermodynamic output (see the thermo_style command), or used as input to an averaging fix (see the fix ave/time command). Variables of style vector store a formula which produces a vector of such values which can be used as input to various averaging fixes, or elements of which can be part of thermodynamic output. Variables of style atom store a formula which when evaluated produces one numeric value per atom which can be output to a dump file (see the dump custom command) or used as input to an averaging fix (see the fix ave/chunk and fix ave/atom commands). Variables of style atomfile can be used anywhere in an input script that atom-style variables are used; they get their per-atom values from a file rather than from a formula. Variables of style python can be hooked to Python functions using code you provide, so that the variable gets its value from the evaluation of the Python code. Variables of style internal are used by a few commands which set their value directly.

Note

As discussed on the Commands parse doc page, an input script can use “immediate” variables, specified as $(formula) with parenthesis, where the numeric formula has the same syntax as equal-style variables described on this page. This is a convenient way to evaluate a formula immediately without using the variable command to define a named variable and then evaluate that variable. The formula can include a trailing colon and format string which determines the precision with which the numeric value is generated. This is also explained on the Commands parse doc page.

In the discussion that follows, the “name” of the variable is the arbitrary string that is the first argument in the variable command. This name can only contain alphanumeric characters and underscores. The “string” is one or more of the subsequent arguments. The “string” can be simple text as in the first example above, it can contain other variables as in the second example, or it can be a formula as in the third example. The “value” is the numeric quantity resulting from evaluation of the string. Note that the same string can generate different values when it is evaluated at different times during a simulation.

Note

When an input script line is encountered that defines a variable of style equal or vector or atom or python that contains a formula or Python code, the formula is NOT immediately evaluated. It will be evaluated every time when the variable is used instead. If you simply want to evaluate a formula in place you can use as so-called. See the section below about “Immediate Evaluation of Variables” for more details on the topic. This is also true of a format style variable since it evaluates another variable when it is invoked.

Variables of style equal and vector and atom can be used as inputs to various other commands which evaluate their formulas as needed, e.g. at different timesteps during a run. In this context, variables of style timer or internal or python can be used in place of an equal-style variable, with the following two caveats.

First, internal-style variables can be used except by commands that set the value stored by the internal variable. When the LAMMPS command evaluates the internal-style variable, it will use the value set (internally) by another command. Second, python-style variables can be used so long as the associated Python function, as defined by the python command, returns a numeric value. When the LAMMPS command evaluates the python-style variable, the Python function will be executed.

Note

When a variable command is encountered in the input script and the variable name has already been specified, the command is ignored. This means variables can NOT be re-defined in an input script (with two exceptions, read further). This is to allow an input script to be processed multiple times without resetting the variables; see the jump or include commands. It also means that using the command-line switch -var will override a corresponding index variable setting in the input script.

There are two exceptions to this rule. First, variables of style string, getenv, internal, equal, vector, atom, and python ARE redefined each time the command is encountered. This allows these style of variables to be redefined multiple times in an input script. In a loop, this means the formula associated with an equal or atom style variable can change if it contains a substitution for another variable, e.g. $x or v_x.

Second, as described below, if a variable is iterated on to the end of its list of strings via the next command, it is removed from the list of active variables, and is thus available to be re-defined in a subsequent variable command. The delete style does the same thing.

Variables are not deleted by the clear command with the exception of atomfile-style variables.

The Commands parse page explains how occurrences of a variable name in an input script line are replaced by the variable’s string. The variable name can be referenced as $x if the name “x” is a single character, or as ${LoopVar} if the name “LoopVar” is one or more characters.

As described below, for variable styles index, loop, file, universe, and uloop, which string is assigned to a variable can be incremented via the next command. When there are no more strings to assign, the variable is exhausted and a flag is set that causes the next jump command encountered in the input script to be skipped. This enables the construction of simple loops in the input script that are iterated over and then exited from.

As explained above, an exhausted variable can be re-used in an input script. The delete style also removes the variable, the same as if it were exhausted, allowing it to be redefined later in the input script or when the input script is looped over. This can be useful when breaking out of a loop via the if and jump commands before the variable would become exhausted. For example,

label       loop
variable    a loop 5
print       "A = $a"
if          "$a > 2" then "jump in.script break"
next        a
jump        in.script loop
label       break
variable    a delete

The next sections describe in how all the various variable styles are defined and what they store. The styles are listed alphabetically, except for the equal and vector and atom styles, which are explained together after all the others.

Many of the styles store one or more strings. Note that a single string can contain spaces (multiple words), if it is enclosed in quotes in the variable command. When the variable is substituted for in another input script command, its returned string will then be interpreted as multiple arguments in the expanded command.

For the atomfile style, a filename is provided which contains one or more sets of values, to assign on a per-atom basis to the variable. The format of the file is described below.

When an atomfile-style variable is defined, the file is opened and the first set of per-atom values are read and stored with the variable. This means the variable can then be evaluated as many times as desired and will return those values. There are two ways to cause the next set of per-atom values from the file to be read: use the next command or the next() function in an atom-style variable, as discussed below. Unlike most variable styles, which remain defined, atomfile-style variables are deleted during a clear command.

The rules for formatting the file are as follows. Each time a set of per-atom values is read, a non-blank line is searched for in the file. The file is read line by line but only up to 254 characters are used. The rest are ignored. A comment character “#” can be used anywhere on a line and all text following and the “#” character are ignored; text starting with the comment character is stripped. Blank lines are skipped. The first non-blank line is expected to contain a single integer number as the count N of per-atom lines to follow. N can be the total number of atoms in the system or less, indicating that data for a subset is read. The next N lines must consist of two numbers, the atom-ID of the atom for which a value is set followed by a floating point number with the value. The atom-IDs may be listed in any order.

Note

Every time a set of per-atom lines is read, the value of the atomfile variable for all atoms is first initialized to 0.0. Thus values for atoms whose ID do not appear in the set in the file will remain at 0.0.

Below is a small example for the atomfile variable file format:

# first set
4
# atom-ID value
3 1
4 -4
1 0.5
2 -0.5

# second set
2

2  1.0
4 -1.0

For the file style, a filename is provided which contains a list of strings to assign to the variable, one per line. The strings can be numeric values if desired. See the discussion of the next() function below for equal-style variables, which will convert the string of a file-style variable into a numeric value in a formula.

When a file-style variable is defined, the file is opened and the string on the first line is read and stored with the variable. This means the variable can then be evaluated as many times as desired and will return that string. There are two ways to cause the next string from the file to be read: use the next command or the next() function in an equal- or atom-style variable, as discussed below.

The rules for formatting the file are as follows. A comment character “#” can be used anywhere on a line; text starting with the comment character is stripped. Blank lines are skipped. The first “word” of a non-blank line, delimited by white-space, is the “string” assigned to the variable.

For the format style, an equal-style or compatible variable is specified along with a C-style format string, e.g. “%f” or “%.10g”, which must be appropriate for formatting a double-precision floating-point value and may not have extra characters. The default format is “%.15g”. This variable style allows an equal-style variable to be formatted precisely when it is evaluated.

Note that if you simply wish to print a variable value with desired precision to the screen or logfile via the print or fix print commands, you can also do this by specifying an “immediate” variable with a trailing colon and format string, as part of the string argument of those commands. This is explained on the Commands parse doc page.

For the getenv style, a single string is assigned to the variable which should be the name of an environment variable. When the variable is evaluated, it returns the value of the environment variable, or an empty string if it not defined. This style of variable can be used to adapt the behavior of LAMMPS input scripts via environment variable settings, or to retrieve information that has been previously stored with the shell putenv command. Note that because environment variable settings are stored by the operating systems, they persist even if the corresponding getenv style variable is deleted, and also are set for sub-shells executed by the shell command.

For the index style, one or more strings are specified. Initially, the first string is assigned to the variable. Each time a next command is used with the variable name, the next string is assigned. All processors assign the same string to the variable.

Index-style variables with a single string value can also be set by using the command-line switch -var.

For the internal style a numeric value is provided. This value will be assigned to the variable until a LAMMPS command sets it to a new value. There are currently only two LAMMPS commands that require internal variables as inputs, because they reset them: create_atoms and fix controller. As mentioned above, an internal-style variable can be used in place of an equal-style variable anywhere else in an input script, e.g. as an argument to another command that allows for equal-style variables.

The loop style is identical to the index style except that the strings are the integers from 1 to N inclusive, if only one argument N is specified. This allows generation of a long list of runs (e.g. 1000) without having to list N strings in the input script. Initially, the string “1” is assigned to the variable. Each time a next command is used with the variable name, the next string (“2”, “3”, etc) is assigned. All processors assign the same string to the variable. The loop style can also be specified with two arguments N1 and N2. In this case the loop runs from N1 to N2 inclusive, and the string N1 is initially assigned to the variable. N1 <= N2 and N2 >= 0 is required.

For the python style a Python function name is provided. This needs to match a function name specified in a python command which returns a value to this variable as defined by its return keyword. For example these two commands would be self-consistent:

variable foo python myMultiply
python myMultiply return v_foo format f file funcs.py

The two commands can appear in either order so long as both are specified before the Python function is invoked for the first time.

Each time the variable is evaluated, the associated Python function is invoked, and the value it returns is also returned by the variable. Since the Python function can use other LAMMPS variables as input, or query interal LAMMPS quantities to perform its computation, this means the variable can return a different value each time it is evaluated.

The type of value stored in the variable is determined by the format keyword of the python command. It can be an integer (i), floating point (f), or string (s) value. As mentioned above, if it is a numeric value (integer or floating point), then the python-style variable can be used in place of an equal-style variable anywhere in an input script, e.g. as an argument to another command that allows for equal-style variables.

For the string style, a single string is assigned to the variable. Two differences between this style and using the index style exist: a variable with string style can be redefined, e.g. by another command later in the input script, or if the script is read again in a loop. The other difference is that string performs variable substitution even if the string parameter is quoted.

The uloop style is identical to the universe style except that the strings are the integers from 1 to N. This allows generation of long list of runs (e.g. 1000) without having to list N strings in the input script.

For the universe style, one or more strings are specified. There must be at least as many strings as there are processor partitions or “worlds”. LAMMPS can be run with multiple partitions via the -partition command-line switch. This variable command initially assigns one string to each world. When a next command is encountered using this variable, the first processor partition to encounter it, is assigned the next available string. This continues until all the variable strings are consumed. Thus, this command can be used to run 50 simulations on 8 processor partitions. The simulations will be run one after the other on whatever partition becomes available, until they are all finished. Universe-style variables are incremented using the files “tmp.lammps.variable” and “tmp.lammps.variable.lock” which you will see in your directory during such a LAMMPS run.

For the world style, one or more strings are specified. There must be one string for each processor partition or “world”. LAMMPS can be run with multiple partitions via the -partition command-line switch. This variable command assigns one string to each world. All processors in the world are assigned the same string. The next command cannot be used with equal-style variables, since there is only one value per world. This style of variable is useful when you wish to run different simulations on different partitions, or when performing a parallel tempering simulation (see the temper command), to assign different temperatures to different partitions.

For the equal and vector and atom styles, a single string is specified which represents a formula that will be evaluated afresh each time the variable is used. If you want spaces in the string, enclose it in double quotes so the parser will treat it as a single argument. For equal-style variables the formula computes a scalar quantity, which becomes the value of the variable whenever it is evaluated. For vector-style variables the formula must compute a vector of quantities, which becomes the value of the variable whenever it is evaluated. The calculated vector can be of length one, but it cannot be a simple scalar value like that produced by an equal-style compute. I.e. the formula for a vector-style variable must have at least one quantity in it that refers to a global vector produced by a compute, fix, or other vector-style variable. For atom-style variables the formula computes one quantity for each atom whenever it is evaluated.

Note that equal, vector, and atom variables can produce different values at different stages of the input script or at different times during a run. For example, if an equal variable is used in a fix print command, different values could be printed each timestep it was invoked. If you want a variable to be evaluated immediately, so that the result is stored by the variable instead of the string, see the section below on “Immediate Evaluation of Variables”.

The next command cannot be used with equal or vector or atom style variables, since there is only one string.

The formula for an equal, vector, or atom variable can contain a variety of quantities. The syntax for each kind of quantity is simple, but multiple quantities can be nested and combined in various ways to build up formulas of arbitrary complexity. For example, this is a valid (though strange) variable formula:

variable x equal "pe + c_MyTemp / vol^(1/3)"

Specifically, a formula can contain numbers, constants, thermo keywords, math operators, math functions, group functions, region functions, special functions, feature functions, atom values, atom vectors, custom atom properties, compute references, fix references, and references to other variables.

Number	0.2, 100, 1.0e20, -15.4, etc
Constant	PI, version, on, off, true, false, yes, no
Thermo keywords	vol, pe, ebond, etc
Math operators	(), -x, x+y, x-y, x*y, x/y, x^y, x%y, x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x \|\| y, x \|^ y, !x
Math functions	sqrt(x), exp(x), ln(x), log(x), abs(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ternary(x,y,z), ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z), logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c), vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)
Group functions	count(ID), mass(ID), charge(ID), xcm(ID,dim), vcm(ID,dim), fcm(ID,dim), bound(ID,dir), gyration(ID), ke(ID), angmom(ID,dim), torque(ID,dim), inertia(ID,dimdim), omega(ID,dim)
Region functions	count(ID,IDR), mass(ID,IDR), charge(ID,IDR), xcm(ID,dim,IDR), vcm(ID,dim,IDR), fcm(ID,dim,IDR), bound(ID,dir,IDR), gyration(ID,IDR), ke(ID,IDR), angmom(ID,dim,IDR), torque(ID,dim,IDR), inertia(ID,dimdim,IDR), omega(ID,dim,IDR)
Special functions	sum(x), min(x), max(x), ave(x), trap(x), slope(x), sort(x), rsort(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name), label2type(kind,label), is_typelabel(kind,label), is_timeout()
Feature functions	is_available(category,feature), is_active(category,feature), is_defined(category,id)
Atom values	id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i]
Atom vectors	id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q
Custom atom properties	i_name, d_name, i_name[i], d_name[i], i2_name[i], d2_name[i], i2_name[i][j], d_name[i][j]
Compute references	c_ID, c_ID[i], c_ID[i][j], C_ID, C_ID[i]
Fix references	f_ID, f_ID[i], f_ID[i][j], F_ID, F_ID[i]
Other variables	v_name, v_name[i]

Most of the formula elements produce a scalar value. Some produce a global or per-atom vector of values. Global vectors can be produced by computes or fixes or by other vector-style variables. Per-atom vectors are produced by atom vectors, computes or fixes which output a per-atom vector or array, and variables that are atom-style variables. Math functions that operate on scalar values produce a scalar value; math function that operate on global or per-atom vectors do so element-by-element and produce a global or per-atom vector.

A formula for equal-style variables cannot use any formula element that produces a global or per-atom vector. A formula for a vector-style variable can use formula elements that produce either a scalar value or a global vector value, but cannot use a formula element that produces a per-atom vector. A formula for an atom-style variable can use formula elements that produce either a scalar value or a per-atom vector, but not one that produces a global vector.

Atom-style variables are evaluated by other commands that define a group on which they operate, e.g. a dump or compute or fix command. When they invoke the atom-style variable, only atoms in the group are included in the formula evaluation. The variable evaluates to 0.0 for atoms not in the group.

Numbers, constants, and thermo keywords

Numbers can contain digits, scientific notation (3.0e20,3.0e-20,3.0E20,3.0E-20), and leading minus signs.

Constants are set at compile time and cannot be changed. PI will return the number 3.14159265358979323846; on, true or yes will return 1.0; off, false or no will return 0.0; version will return a numeric version code of the current LAMMPS version (e.g. version 2 Sep 2015 will return the number 20150902). The corresponding value for newer versions of LAMMPS will be larger, for older versions of LAMMPS will be smaller. This can be used to have input scripts adapt automatically to LAMMPS versions, when non-backwards compatible syntax changes are introduced. Here is an illustrative example (which will not work, since the version has been introduced more recently):

if $(version<20140513) then "communicate vel yes" else "comm_modify vel yes"

The thermo keywords allowed in a formula are those defined by the thermo_style custom command. Thermo keywords that require a compute to calculate their values such as “temp” or “press”, use computes stored and invoked by the thermo_style command. This means that you can only use those keywords in a variable if the style you are using with the thermo_style command (and the thermo keywords associated with that style) also define and use the needed compute. Note that some thermo keywords use a compute indirectly to calculate their value (e.g. the enthalpy keyword uses temp, pe, and pressure). If a variable is evaluated directly in an input script (not during a run), then the values accessed by the thermo keyword must be current. See the discussion below about “Variable Accuracy”.

Math Operators

Math operators are written in the usual way, where the “x” and “y” in the examples can themselves be arbitrarily complex formulas, as in the examples above. In this syntax, “x” and “y” can be scalar values or per-atom vectors. For example, “ke/natoms” is the division of two scalars, where “vy+vz” is the element-by-element sum of two per-atom vectors of y and z velocities.

Operators are evaluated left to right and have the usual C-style precedence: unary minus and unary logical NOT operator “!” have the highest precedence, exponentiation “^” is next; multiplication and division and the modulo operator “%” are next; addition and subtraction are next; the 4 relational operators “<”, “<=”, “>”, and “>=” are next; the two remaining relational operators “==” and “!=” are next; then the logical AND operator “&&”; and finally the logical OR operator “||” and logical XOR (exclusive or) operator “|^” have the lowest precedence. Parenthesis can be used to group one or more portions of a formula and/or enforce a different order of evaluation than what would occur with the default precedence.

Note

Because a unary minus is higher precedence than exponentiation, the formula “-2^2” will evaluate to 4, not -4. This convention is compatible with some programming languages, but not others. As mentioned, this behavior can be easily overridden with parenthesis; the formula “-(2^2)” will evaluate to -4.

The 6 relational operators return either a 1.0 or 0.0 depending on whether the relationship between x and y is TRUE or FALSE. For example the expression x<10.0 in an atom-style variable formula will return 1.0 for all atoms whose x-coordinate is less than 10.0, and 0.0 for the others. The logical AND operator will return 1.0 if both its arguments are non-zero, else it returns 0.0. The logical OR operator will return 1.0 if either of its arguments is non-zero, else it returns 0.0. The logical XOR operator will return 1.0 if one of its arguments is zero and the other non-zero, else it returns 0.0. The logical NOT operator returns 1.0 if its argument is 0.0, else it returns 0.0.

These relational and logical operators can be used as a masking or selection operation in a formula. For example, the number of atoms whose properties satisfy one or more criteria could be calculated by taking the returned per-atom vector of ones and zeroes and passing it to the compute reduce command.

Math Functions

Math functions are specified as keywords followed by one or more parenthesized arguments “x”, “y”, “z”, each of which can themselves be arbitrarily complex formulas. In this syntax, the arguments can represent scalar values or global vectors or per-atom vectors. In the latter case, the math operation is performed on each element of the vector. For example, “sqrt(natoms)” is the sqrt() of a scalar, where “sqrt(y*z)” yields a per-atom vector with each element being the sqrt() of the product of one atom’s y and z coordinates.

Most of the math functions perform obvious operations. The ln() is the natural log; log() is the base 10 log.

The random(x,y,z) function takes 3 arguments: x = lo, y = hi, and z = seed. It generates a uniform random number between lo and hi. The normal(x,y,z) function also takes 3 arguments: x = mu, y = sigma, and z = seed. It generates a Gaussian variate centered on mu with variance sigma^2. In both cases the seed is used the first time the internal random number generator is invoked, to initialize it. For equal-style and vector-style variables, every processor uses the same seed so that they each generate the same sequence of random numbers. For atom-style variables, a unique seed is created for each processor, based on the specified seed. This effectively generates a different random number for each atom being looped over in the atom-style variable.

Note

Internally, there is just one random number generator for all equal-style and vector-style variables and another one for all atom-style variables. If you define multiple variables (of each style) which use the random() or normal() math functions, then the internal random number generators will only be initialized once, which means only one of the specified seeds will determine the sequence of generated random numbers.

The ceil(), floor(), and round() functions are those in the C math library. Ceil() is the smallest integer not less than its argument. Floor() if the largest integer not greater than its argument. Round() is the nearest integer to its argument.

Added in version 7Feb2024.

The ternary(x,y,z) function is the equivalent of the ternary operator (? and :) in C or C++. It takes 3 arguments. The first argument is a conditional. The result of the function is y if x evaluates to true (non-zero). The result is z if x evaluates to false (zero).

The ramp(x,y) function uses the current timestep to generate a value linearly interpolated between the specified x,y values over the course of a run, according to this formula:

value = x + (y-x) * (timestep-startstep) / (stopstep-startstep)

The run begins on startstep and ends on stopstep. Startstep and stopstep can span multiple runs, using the start and stop keywords of the run command. See the run command for details of how to do this. If called in between runs or during a run 0 command, the ramp(x,y) function will return the value of x.

The stagger(x,y) function uses the current timestep to generate a new timestep. X,y > 0 and x > y are required. The generated timesteps increase in a staggered fashion, as the sequence x,x+y,2x,2x+y,3x,3x+y,etc. For any current timestep, the next timestep in the sequence is returned. Thus if stagger(1000,100) is used in a variable by the dump_modify every command, it will generate the sequence of output timesteps:

100,1000,1100,2000,2100,3000,etc

The logfreq(x,y,z) function uses the current timestep to generate a new timestep. X,y,z > 0 and y < z are required. The generated timesteps are on a base-z logarithmic scale, starting with x, and the y value is how many of the z-1 possible timesteps within one logarithmic interval are generated. I.e. the timesteps follow the sequence x,2x,3x,…y*x,x*z,2x*z,3x*z,…y*x*z,x*z^2,2x*z^2,etc. For any current timestep, the next timestep in the sequence is returned. Thus if logfreq(100,4,10) is used in a variable by the dump_modify every command, it will generate this sequence of output timesteps:

100,200,300,400,1000,2000,3000,4000,10000,20000,etc

The logfreq2(x,y,z) function is similar to logfreq, except a single logarithmic interval is divided into y equally-spaced timesteps and all of them are output. Y < z is not required. Thus, if logfreq2(100,18,10) is used in a variable by the dump_modify every command, then the interval between 100 and 1000 is divided as 900/18 = 50 steps, and it will generate the sequence of output timesteps:

100,150,200,...950,1000,1500,2000,...9500,10000,15000,etc

The logfreq3(x,y,z) function generates y points between x and z (inclusive), that are separated by a multiplicative ratio: (z/x)^(1/(y-1)). Constraints are: x,z > 0, y > 1, z-x >= y-1. For eg., if logfreq3(10,25,1000) is used in a variable by the fix print command, then the interval between 10 and 1000 is divided into 24 parts with a multiplicative separation of ~1.21, and it will generate the following sequence of output timesteps:

10, 13, 15, 18, 22, 27, 32,...384, 465, 563, 682, 826, 1000

The stride(x,y,z) function uses the current timestep to generate a new timestep. X,y >= 0 and z > 0 and x <= y are required. The generated timesteps increase in increments of z, from x to y, i.e. it generates the sequence x,x+z,x+2z,…,y. If y-x is not a multiple of z, then similar to the way a for loop operates, the last value will be one that does not exceed y. For any current timestep, the next timestep in the sequence is returned. Thus if stride(1000,2000,100) is used in a variable by the dump_modify every command, it will generate the sequence of output timesteps:

1000,1100,1200, ... ,1900,2000

The stride2(x,y,z,a,b,c) function is similar to the stride() function except it generates two sets of strided timesteps, one at a coarser level and one at a finer level. Thus it is useful for debugging, e.g. to produce output every timestep at the point in simulation when a problem occurs. X,y >= 0 and z > 0 and x <= y are required, as are a,b >= 0 and c > 0 and a < b. Also, a >= x and b <= y are required so that the second stride is inside the first. The generated timesteps increase in increments of z, starting at x, until a is reached. At that point the timestep increases in increments of c, from a to b, then after b, increments by z are resumed until y is reached. For any current timestep, the next timestep in the sequence is returned. Thus if stride2(1000,2000,100,1350,1360,1) is used in a variable by the dump_modify every command, it will generate the sequence of output timesteps:

1000,1100,1200,1300,1350,1351,1352, ... 1359,1360,1400,1500, ... ,2000

The vdisplace(x,y) function takes 2 arguments: x = value0 and y = velocity, and uses the elapsed time to change the value by a linear displacement due to the applied velocity over the course of a run, according to this formula:

value = value0 + velocity*(timestep-startstep)*dt

where dt = the timestep size.

The run begins on startstep. Startstep can span multiple runs, using the start keyword of the run command. See the run command for details of how to do this. Note that the thermo_style keyword elaplong = timestep-startstep. If used between runs this function will return the value according to the end of the last run or the value of x if used before any runs. This function assumes the length of the time step does not change and thus may not be used in combination with fix dt/reset.

The swiggle(x,y,z) and cwiggle(x,y,z) functions each take 3 arguments: x = value0, y = amplitude, z = period. They use the elapsed time to oscillate the value by a sin() or cos() function over the course of a run, according to one of these formulas, where omega = 2 PI / period:

value = value0 + Amplitude * sin(omega*(timestep-startstep)*dt)
value = value0 + Amplitude * (1 - cos(omega*(timestep-startstep)*dt))

where dt = the timestep size.

The run begins on startstep. Startstep can span multiple runs, using the start keyword of the run command. See the run command for details of how to do this. Note that the thermo_style keyword elaplong = timestep-startstep. If used between runs these functions will return the value according to the end of the last run or the value of x if used before any runs. These functions assume the length of the time step does not change and thus may not be used in combination with fix dt/reset.

Group and Region Functions

Group functions are specified as keywords followed by one or two parenthesized arguments. The first argument ID is the group-ID. The dim argument, if it exists, is x or y or z. The dir argument, if it exists, is xmin, xmax, ymin, ymax, zmin, or zmax. The dimdim argument, if it exists, is xx or yy or zz or xy or yz or xz.

The group function count() is the number of atoms in the group. The group functions mass() and charge() are the total mass and charge of the group. Xcm() and vcm() return components of the position and velocity of the center of mass of the group. Fcm() returns a component of the total force on the group of atoms. Bound() returns the min/max of a particular coordinate for all atoms in the group. Gyration() computes the radius-of-gyration of the group of atoms. See the compute gyration command for a definition of the formula. Angmom() returns components of the angular momentum of the group of atoms around its center of mass. Torque() returns components of the torque on the group of atoms around its center of mass, based on current forces on the atoms. Inertia() returns one of 6 components of the symmetric inertia tensor of the group of atoms around its center of mass, ordered as Ixx,Iyy,Izz,Ixy,Iyz,Ixz. Omega() returns components of the angular velocity of the group of atoms around its center of mass.

Region functions are specified exactly the same way as group functions except they take an extra final argument IDR which is the region ID. The function is computed for all atoms that are in both the group and the region. If the group is “all”, then the only criteria for atom inclusion is that it be in the region.

Special Functions

Special functions take specific kinds of arguments, meaning their arguments cannot be formulas themselves.

The sum(x), min(x), max(x), ave(x), trap(x), slope(x), sort(x), and rsort(x) functions each take 1 argument which is of the form “c_ID” or “c_ID[N]” or “f_ID” or “f_ID[N]” or “v_name”. The first two are computes and the second two are fixes; the ID in the reference should be replaced by the ID of a compute or fix defined elsewhere in the input script. The compute or fix must produce either a global vector or array. If it produces a global vector, then the notation without “[N]” should be used. If it produces a global array, then the notation with “[N]” should be used, where N is an integer, to specify which column of the global array is being referenced. The last form of argument “v_name” is for a vector-style variable where “name” is replaced by the name of the variable.

The sum(x), min(x), max(x), ave(x), trap(x), and slope(x) functions operate on a global vector of inputs and reduce it to a single scalar value. This is analogous to the operation of the compute reduce command, which performs similar operations on per-atom and local vectors.

The sort(x) and rsort(x) functions operate on a global vector of inputs and return a global vector of the same length.

The sum() function calculates the sum of all the vector elements. The min() and max() functions find the minimum and maximum element respectively. The ave() function is the same as sum() except that it divides the result by the length of the vector.

The trap() function is the same as sum() except the first and last elements are multiplied by a weighting factor of 1/2 when performing the sum. This effectively implements an integration via the trapezoidal rule on the global vector of data. I.e. consider a set of points, equally spaced by 1 in their x coordinate: (1,V1), (2,V2), …, (N,VN), where the Vi are the values in the global vector of length N. The integral from 1 to N of these points is trap(). When appropriately normalized by the timestep size, this function is useful for calculating integrals of time-series data, like that generated by the fix ave/correlate command.

The slope() function uses linear regression to fit a line to the set of points, equally spaced by 1 in their x coordinate: (1,V1), (2,V2), …, (N,VN), where the Vi are the values in the global vector of length N. The returned value is the slope of the line. If the line has a single point or is vertical, it returns 1.0e20.

Added in version 27June2024.

The sort(x) and rsort(x) functions sort the data of the input vector by their numeric value: sort(x) sorts in ascending order, rsort(x) sorts in descending order.

The gmask(x) function takes 1 argument which is a group ID. It can only be used in atom-style variables. It returns a 1 for atoms that are in the group, and a 0 for atoms that are not.

The rmask(x) function takes 1 argument which is a region ID. It can only be used in atom-style variables. It returns a 1 for atoms that are in the geometric region, and a 0 for atoms that are not.

The grmask(x,y) function takes 2 arguments. The first is a group ID, and the second is a region ID. It can only be used in atom-style variables. It returns a 1 for atoms that are in both the group and region, and a 0 for atoms that are not in both.

The next(x) function takes 1 argument which is a variable ID (not “v_foo”, just “foo”). It must be for a file-style or atomfile-style variable. Each time the next() function is invoked (i.e. each time the equal-style or atom-style variable is evaluated), the following steps occur.

For file-style variables, the current string value stored by the file-style variable is converted to a numeric value and returned by the function. And the next string value in the file is read and stored. Note that if the line previously read from the file was not a numeric string, then it will typically evaluate to 0.0, which is likely not what you want.

For atomfile-style variables, the current per-atom values stored by the atomfile-style variable are returned by the function. And the next set of per-atom values in the file is read and stored.

Since file-style and atomfile-style variables read and store the first line of the file or first set of per-atoms values when they are defined in the input script, these are the value(s) that will be returned the first time the next() function is invoked. If next() is invoked more times than there are lines or sets of lines in the file, the variable is deleted, similar to how the next command operates.

The is_file(name) function is a test whether name is a (readable) file and returns 1 in this case, otherwise it returns 0. For that name is taken as a literal string and must not have any blanks in it.

The is_os(name) function is a test whether name is part of the OS information that LAMMPS collects and provides in the platform::os_info() function. The argument name is interpreted as a regular expression as documented for the utils::strmatch() function. This allows to adapt LAMMPS inputs to the OS it runs on:

if $(is_os(^Windows)) then &
  "shell copy ${input_dir}\some_file.txt ." &
else &
  "shell cp ${input_dir}/some_file.txt ."

The extract_setting(name) function enables access to basic settings for the LAMMPS executable and the running simulation via calling the lammps_extract_setting() library function. For example, the number of processors (MPI ranks) being used by the simulation or the MPI process ID (for this processor) can be queried, or the number of atom types, bond types and so on. For the full list of available keywords name and their meaning, see the documentation for extract_setting() via the link in this paragraph.

The label2type(kind,label) function converts type labels into numeric types, using label maps created by the labelmap or read_data commands. The first argument is the label map kind (atom, bond, angle, dihedral, or improper) and the second argument is the label. The function returns the corresponding numeric type or triggers an error if the queried label does not exist.

Added in version 15Jun2023.

The is_typelabel(kind,label) function has the same arguments as label2type(), but returns 1 if the type label has been assigned, otherwise it returns 0. This function can be used to check if a particular type label already exists in the simulation.

Added in version 29Aug2024.

The is_timeout() function returns 1 when the timer timeout has expired otherwise it returns 0. This function can be used to check inputs in combination with the if command to execute commands after the timer has expired. Example:

variable timeout equal is_timeout()
timer timeout 0:10:00 every 10
run 10000
if ${timeout} then "print 'Timer has expired'"

Feature Functions

Feature functions allow probing of the running LAMMPS executable for whether specific features are available, active, or defined. All 3 of the functions take two arguments, a category and a category-specific second argument. Both are strings and thus cannot be formulas themselves; only $-style immediate variable expansion is possible. The return value of the functions is either 1.0 or 0.0 depending on whether the function evaluates to true or false, respectively.

The is_available(category,name) function queries whether a specific feature is available in the LAMMPS executable that is being run, i.e whether it was included or enabled at compile time.

This supports the following categories: command, compute, fix, pair_style and feature. For all the categories except feature the name is a style name, e.g. nve for the fix category. Note that many LAMMPS input script commands such as create_atoms are actually instances of a command style which LAMMPS defines, as opposed to built-in commands. For all of these styles except command, appending of active suffixes is also tried before reporting failure.

The feature category checks the availability of the following compile-time enabled features: GZIP support, PNG support, JPEG support, FFMPEG support, and C++ exceptions for error handling. Corresponding names are gzip, png, jpeg, ffmpeg and exceptions.

Example: Only dump in a given format if the compiled binary supports it.

if "$(is_available(feature,png))" then "print 'PNG supported'" else "print 'PNG not supported'"
if "$(is_available(feature,ffmpeg)" then "dump 3 all movie 25 movie.mp4 type type zoom 1.6 adiam 1.0"

The is_active(category,feature) function queries whether a specific feature is currently active within LAMMPS. The features are grouped by categories. Supported categories and features are:

package: features = gpu or intel or kokkos or omp
newton: features = pair or bond or any
pair: features = single or respa or manybody or tail or shift
comm_style: features = brick or tiled
min_style: features = a minimizer style name
run_style: features = a run style name
atom_style: features = an atom style name
pair_style: features = a pair style name
bond_style: features = a bond style name
angle_style: features = an angle style name
dihedral_style: features = a dihedral style name
improper_style: features = an improper style name
kspace_style: features = a kspace style name

Most of the settings are self-explanatory. For the package category, a package may have been included in the LAMMPS build, but not have enabled by any input script command, and hence be inactive. The single feature in the pair category checks whether the currently defined pair style supports a Pair::single() function as needed by compute group/group and others features or LAMMPS. Similarly, the respa feature checks whether the inner/middle/outer mode of r-RESPA is supported by the current pair style.

For the categories with style in their name, only a single instance of the style is ever active at any time in a LAMMPS simulation. Thus the check is whether the currently active style matches the specified name. This check is also done using suffix flags, if available and enabled.

Example 1: Disable use of suffix for PPPM when using GPU package (i.e. run it on the CPU concurrently while running the pair style on the GPU), but do use the suffix otherwise (e.g. with OPENMP).

pair_style lj/cut/coul/long 14.0
if $(is_active(package,gpu)) then "suffix off"
kspace_style pppm

Example 2: Use r-RESPA with inner/outer cutoff, if supported by the current pair style, otherwise fall back to using r-RESPA with simply the pair keyword and reducing the outer time step.

timestep $(2.0*(1.0+2.0*is_active(pair,respa)))
if $(is_active(pair,respa)) then "run_style respa 4 3 2 2 improper 1 inner 2 5.5 7.0 outer 3 kspace 4" else "run_style respa 3 3 2 improper 1 pair 2 kspace 3"

The is_defined(category,id) function checks whether an instance of a style or variable with a specific ID or name is currently defined within LAMMPS. The supported categories are compute, dump, fix, group, region, and variable. Each of these styles (as well as the variable command) can be specified multiple times within LAMMPS, each with a unique id. This function checks whether the specified id exists. For category variable”, the *id is the variable name.

Atom Values and Vectors

Atom values take an integer argument I from 1 to N, where I is the atom-ID, e.g. x[243], which means use the x coordinate of the atom with ID = 243. Or they can take a variable name, specified as v_name, where name is the name of the variable, like x[v_myIndex]. The variable can be of any style except vector or atom or atomfile variables. The variable is evaluated and the result is expected to be numeric and is cast to an integer (i.e. 3.4 becomes 3), to use an index, which must be a value from 1 to N. Note that a “formula” cannot be used as the argument between the brackets, e.g. x[243+10] or x[v_myIndex+1] are not allowed. To do this a single variable can be defined that contains the needed formula.

Note that the 0 < atom-ID <= N, where N is the largest atom ID in the system. If an ID is specified for an atom that does not currently exist, then the generated value is 0.0.

Atom vectors generate one value per atom, so that a reference like “vx” means the x-component of each atom’s velocity will be used when evaluating the variable.

The meaning of the different atom values and vectors is mostly self-explanatory. Mol refers to the molecule ID of an atom, and is only defined if an atom_style is being used that defines molecule IDs.

Note that many other atom attributes can be used as inputs to a variable by using the compute property/atom command and then referencing that compute.

Custom atom properties

Added in version 7Feb2024.

Custom atom properties refer to per-atom integer and floating point vectors or arrays that have been added via the fix property/atom command. When that command is used specific names are given to each attribute which are the “name” portion of these references. References beginning with i and d refer to integer and floating point properties respectively. Per-atom vectors are referenced by i_name and d_name; per-atom arrays are referenced by i2_name and d2_name.

The various allowed references to integer custom atom properties in the variable formulas for equal-, vector-, and atom-style variables are listed in the following table. References to floating point custom atom properties are the same; just replace the leading “i” with “d”.

equal	i_name[I]	element of per-atom vector (I = atom ID)
equal	i2_name[I][J]	element of per-atom array (I = atom ID)

vector	i_name[I]	element of per-atom vector (I = atom ID)
vector	i2_name[I][J]	element of per-atom array (I = atom ID)

atom	i_name	per-atom vector
atom	i2_name[I]	column of per-atom array

The I and J indices in these custom atom property references can be integers or can be a variable name, specified as v_name, where name is the name of the variable. The rules for this syntax are the same as for indices in the “Atom Values and Vectors” discussion above.

Compute References

Compute references access quantities calculated by a compute. The ID in the reference should be replaced by the ID of a compute defined elsewhere in the input script.

As discussed on the page for the compute command, computes can produce global, per-atom, local, and per-grid values. Only global and per-atom values can be used in a variable. Computes can also produce scalars (global only), vectors, and arrays. See the doc pages for individual computes to see what different kinds of data they produce.

An equal-style variable can only use scalar values, either from global or per-atom data. In the case of per-atom data, this would be a value for a specific atom.

A vector-style variable can use scalar values (same as for equal-style variables), or global vectors of values. The latter can also be a column of a global array.

Atom-style variables can use scalar values (same as for equal-style variables), or per-atom vectors of values. The latter can also be a column of a per-atom array.

The various allowed compute references in the variable formulas for equal-, vector-, and atom-style variables are listed in the following table:

equal	c_ID	global scalar
equal	c_ID[I]	element of global vector
equal	c_ID[I][J]	element of global array
equal	C_ID[I]	element of per-atom vector (I = atom ID)
equal	C_ID[I][J]	element of per-atom array (I = atom ID)

vector	c_ID	global vector
vector	c_ID[I]	column of global array

atom	c_ID	per-atom vector
atom	c_ID[I]	column of per-atom array

Note that if an equal-style variable formula wishes to access per-atom data from a compute, it must use capital “C” as the ID prefix and not lower-case “c”.

Also note that if a vector- or atom-style variable formula needs to access a scalar value from a compute (i.e. the 5 kinds of values in the first 5 lines of the table), it can not do so directly. Instead, it can use a reference to an equal-style variable which stores the scalar value from the compute.

The I and J indices in these compute references can be integers or can be a variable name, specified as v_name, where name is the name of the variable. The rules for this syntax are the same as for indices in the “Atom Values and Vectors” discussion above.

If a variable containing a compute is evaluated directly in an input script (not during a run), then the values accessed by the compute should be current. See the discussion below about “Variable Accuracy”.

Fix References

Fix references access quantities calculated by a fix. The ID in the reference should be replaced by the ID of a fix defined elsewhere in the input script.

As discussed on the page for the fix command, fixes can produce global, per-atom, local, and per-grid values. Only global and per-atom values can be used in a variable. Fixes can also produce scalars (global only), vectors, and arrays. See the doc pages for individual fixes to see what different kinds of data they produce.

An equal-style variable can only use scalar values, either from global or per-atom data. In the case of per-atom data, this would be a value for a specific atom.

A vector-style variable can use scalar values (same as for equal-style variables), or global vectors of values. The latter can also be a column of a global array.

Atom-style variables can use scalar values (same as for equal-style variables), or per-atom vectors of values. The latter can also be a column of a per-atom array.

The allowed fix references in variable formulas for equal-, vector-, and atom-style variables are listed in the following table:

equal	f_ID	global scalar
equal	f_ID[I]	element of global vector
equal	f_ID[I][J]	element of global array
equal	F_ID[I]	element of per-atom vector (I = atom ID)
equal	F_ID[I][J]	element of per-atom array (I = atom ID)

vector	f_ID	global vector
vector	f_ID[I]	column of global array

atom	f_ID	per-atom vector
atom	f_ID[I]	column of per-atom array

Note that if an equal-style variable formula wishes to access per-atom data from a fix, it must use capital “F” as the ID prefix and not lower-case “f”.

Also note that if a vector- or atom-style variable formula needs to access a scalar value from a fix (i.e. the 5 kinds of values in the first 5 lines of the table), it can not do so directly. Instead, it can use a reference to an equal-style variable which stores the scalar value from the fix.

The I and J indices in these fix references can be integers or can be a variable name, specified as v_name, where name is the name of the variable. The rules for this syntax are the same as for indices in the “Atom Values and Vectors” discussion above.

Note that some fixes only generate quantities on certain timesteps. If a variable attempts to access the fix on non-allowed timesteps, an error is generated. For example, the fix ave/time command may only generate averaged quantities every 100 steps. See the doc pages for individual fix commands for details.

If a variable containing a fix is evaluated directly in an input script (not during a run), then the values accessed by the fix should be current. See the discussion below about “Variable Accuracy”.

Variable References

Variable references access quantities stored or calculated by other variables, which will cause those variables to be evaluated. The name in the reference should be replaced by the name of a variable defined elsewhere in the input script.

As discussed on this doc page, equal-style variables generate a single global numeric value, vector-style variables generate a vector of global numeric values, and atom-style and atomfile-style variables generate a per-atom vector of numeric values. All other variables store one or more strings.

The formula for an equal-style variable can use any style of variable including a vector_style or atom-style or atomfile-style. For these 3 styles, a subscript must be used to access a single value from the vector-, atom-, or atomfile-style variable. If a string-storing variable is used, the string is converted to a numeric value. Note that this will typically produce a 0.0 if the string is not a numeric string, which is likely not what you want.

The formula for a vector-style variable can use any style of variable, including atom-style or atomfile-style variables. For these 2 styles, a subscript must be used to access a single value from the atom-, or atomfile-style variable.

The formula for an atom-style variable can use any style of variable, including other atom-style or atomfile-style variables. If it uses a vector-style variable, a subscript must be used to access a single value from the vector-style variable.

The allowed variable references in variable formulas for equal-, vector-, and atom-style variables are listed in the following table. Note that there is no ambiguity as to what a reference means, since referenced variables produce only a global scalar or global vector or per-atom vector.

equal	v_name	global scalar from an equal-style variable
equal	v_name[I]	element of global vector from a vector-style variable
equal	v_name[I]	element of per-atom vector (I = atom ID) from an atom- or atomfile-style variable

vector	v_name	global scalar from an equal-style variable
vector	v_name	global vector from a vector-style variable
vector	v_name[I]	element of global vector from a vector-style variable
vector	v_name[I]	element of per-atom vector (I = atom ID) from an atom- or atomfile-style variable

atom	v_name	global scalar from an equal-style variable
atom	v_name	per-atom vector from an atom-style or atomfile-style variable
atom	v_name[I]	element of global vector from a vector-style variable
atom	v_name[I]	element of per-atom vector (I = atom ID) from an atom- or atomfile-style variable

For the I index, an integer can be specified or a variable name, specified as v_name, where name is the name of the variable. The rules for this syntax are the same as for indices in the “Atom Values and Vectors” discussion above.

Vector Initialization

Added in version 15Jun2023.

Vector-style variables only can be initialized with a special syntax, instead of using a formula. The syntax is a bracketed, comma-separated syntax like the following:

variable myvec vector [1,3.5,7,10.2]

The 3rd argument formula is replaced by the vector values in brackets, separated by commas. This example creates a 4-length vector with specific numeric values, each of which can be specified as an integer or floating point value. Note that while whitespace can be added before or after individual values, no other mathematical operations can be specified. E.g. “3*10” or “3*v_abc” are not valid vector elements, nor is “10*[1,2,3,4]” valid for the entire vector.

Unlike vector variables specified with formulas, this vector variable is static; its length and values never changes. Its values can be used in other commands (including vector-style variables specified with formulas) via the usual syntax for accessing individual vector elements or the entire vector.

Immediate Evaluation of Variables

If you want an equal-style variable to be evaluated immediately, it may be the case that you do not need to define a variable at all. See the Commands parse page for info on how to use “immediate” variables in an input script, specified as $(formula) with parenthesis, where the formula has the same syntax as equal-style variables described on this page. This effectively evaluates a formula immediately without using the variable command to define a named variable.

More generally, there is a difference between referencing a variable with a leading $ sign (e.g. $x or ${abc}) versus with a leading “v_” (e.g. v_x or v_abc). The former can be used in any input script command, including a variable command. The input script parser evaluates the reference variable immediately and substitutes its value into the command. As explained on the Commands parse doc page, you can also use un-named “immediate” variables for this purpose. For example, a string like this $((xlo+xhi)/2+sqrt(v_area)) in an input script command evaluates the string between the parenthesis as an equal-style variable formula.

Referencing a variable with a leading “v_” is an optional or required kind of argument for some commands (e.g. the fix ave/chunk or dump custom or thermo_style commands) if you wish it to evaluate a variable periodically during a run. It can also be used in a variable formula if you wish to reference a second variable. The second variable will be evaluated whenever the first variable is evaluated.

As an example, suppose you use this command in your input script to define the variable “v” as

variable v equal vol

before a run where the simulation box size changes. You might think this will assign the initial volume to the variable “v”. That is not the case. Rather it assigns a formula which evaluates the volume (using the thermo_style keyword “vol”) to the variable “v”. If you use the variable “v” in some other command like fix ave/time then the current volume of the box will be evaluated continuously during the run.

If you want to store the initial volume of the system, you can do it this way:

variable v equal vol
variable v0 equal $v

The second command will force “v” to be evaluated (yielding the initial volume) and assign that value to the variable “v0”. Thus the command

thermo_style custom step v_v v_v0

would print out both the current and initial volume periodically during the run.

Note that it is a mistake to enclose a variable formula in double quotes if it contains variables preceded by $ signs. For example,

variable vratio equal "${vfinal}/${v0}"

This is because the quotes prevent variable substitution (explained on the Commands parse doc page), and thus an error will occur when the formula for “vratio” is evaluated later.

Variable Accuracy

Obviously, LAMMPS attempts to evaluate variables which contain formulas (equal and vector and atom style variables) accurately whenever the evaluation is performed. Depending on what is included in the formula, this may require invoking a compute, either directly or indirectly via a thermo keyword, or accessing a value previously calculated by a compute, or accessing a value calculated and stored by a fix. If the compute is one that calculates the energy or pressure of the system, then the corresponding energy or virial quantities need to be tallied during the evaluation of the interatomic potentials (pair, bond, etc) on any timestep that the variable needs the tallies. An input script can also request variables be evaluated before or after or in between runs, e.g. by including them in a print command.

LAMMPS keeps track of all of this as it performs a run or minimize simulation, as well as in between simulations. An error will be generated if you attempt to evaluate a variable when LAMMPS knows it cannot produce accurate values. For example, if a thermo_style custom command prints a variable which accesses values stored by a fix ave/time command and the timesteps on which thermo output is generated are not multiples of the averaging frequency used in the fix command, then an error will occur.

However, there are two special cases to be aware when a variable requires invocation of a compute (directly or indirectly). The first is if the variable is evaluated before the first run or minimize command in the input script. In this case, LAMMPS will generate an error. This is because many computes require initializations which have not yet taken place. One example is the calculation of degrees of freedom for temperature computes. Another example are the computes mentioned above which require tallying of energy or virial quantities; these values are not tallied until the first simulation begins.

The second special case is when a variable that depends on a compute is evaluated in between run or minimize commands. It is possible for other input script commands issued following the previous run, but before the variable is evaluated, to change the system. For example, the delete_atoms command could be used to remove atoms. Since the compute will not re-initialize itself until the next simulation or it may depend on energy/virial computations performed before the system was changed, it will potentially generate an incorrect answer when evaluated. Note that LAMMPS will not generate an error in this case; the evaluated variable may simply be incorrect.

The way to get around both of these special cases is to perform a 0-timestep run before evaluating the variable. For example, these commands

# delete_atoms random fraction 0.5 yes all NULL 49839
# run 0 post no
variable t equal temp    # this thermo keyword invokes a temperature compute
print "Temperature of system = $t"
run 1000

will generate an error if the “run 1000” command is the first simulation in the input script. If there were a previous run, these commands will print the correct temperature of the system. But if the delete_atoms command is uncommented, the printed temperature will be incorrect, because information stored by temperature compute is no longer valid.

Both these issues are resolved, if the “run 0” command is uncommented. This is because the “run 0” simulation will initialize (or re-initialize) the temperature compute correctly.

Restrictions

Indexing any formula element by global atom ID, such as an atom value, requires the atom style to use a global mapping in order to look up the vector indices. By default, only atom styles with molecular information create global maps. The atom_modify map command can override the default, e.g. for atomic-style atom styles.

All universe- and uloop-style variables defined in an input script must have the same number of values.

Default

none

variable command

Syntax

Examples

Description

Numbers, constants, and thermo keywords

Math Operators

Math Functions

Group and Region Functions

Special Functions

Feature Functions

Atom Values and Vectors

Custom atom properties

Compute References

Fix References

Variable References

Vector Initialization

Immediate Evaluation of Variables

Variable Accuracy

Restrictions

Related commands

Default