forked from lijiext/lammps
330 lines
15 KiB
Plaintext
330 lines
15 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
|
|
|
:link(lws,http://lammps.sandia.gov)
|
|
:link(ld,Manual.html)
|
|
:link(lc,Section_commands.html#comm)
|
|
|
|
:line
|
|
|
|
variable command :h3
|
|
|
|
[Syntax:]
|
|
|
|
variable name style args ... :pre
|
|
|
|
name = name of variable to define :ulb,l
|
|
style = {index} or {loop} or {world} or {universe} or {uloop} or {equal} or {atom} :l
|
|
{index} args = one or more strings
|
|
{loop} args = N = integer size of loop
|
|
{world} args = one string for each partition of processors
|
|
{universe} args = one or more strings
|
|
{uloop} args = N = integer size of loop
|
|
{equal} or {atom} args = one equation containing numbers, thermo keywords, math functions, group functions, atom vectors, compute references, other variables
|
|
numbers = 0.0, -5.4, 2.8e-4, etc
|
|
thermo keywords = vol, ke, press, etc from "thermo_style"_thermo_style.html
|
|
math functions = add(x,y), sub(x,y), mult(x,y), div(x,y),
|
|
neg(x), pow(x,y), exp(x), ln(x), sqrt(x)
|
|
group functions = mass(group), charge(group),
|
|
xcm(group,dim), vcm(group,dim), fcm(group,dim),
|
|
bound(group,xmin), gyration(group)
|
|
atom vectors for {equal} = mass\[N\], x\[N\], y\[N\], z\[N\],
|
|
vx\[N\], vy\[N\], vz\[N\],
|
|
fx\[N\], fy\[N\], fz\[N\]
|
|
atom vectors for {atom} = mass\[\], x\[\], y\[\], z\[\],
|
|
vx\[\], vy\[\], vz\[\],
|
|
fx\[\], fy\[\], fz\[\]
|
|
compute references = c_ID\[0\], c_ID\[N\]
|
|
fix references = f_ID\[0\], f_ID\[N\]
|
|
other variables = v_abc, v_x, etc :pre
|
|
:ule
|
|
|
|
[Examples:]
|
|
|
|
variable x index run1 run2 run3 run4 run5 run6 run7 run8
|
|
variable LoopVar loop $n
|
|
variable beta equal div(temp,3.0)
|
|
variable b1 equal add(x\[234\],mult(0.5,vol))
|
|
variable b equal div(xcm(mol1,x),2.0)
|
|
variable b equal c_myTemp\[0\]
|
|
variable b atom div(mult(x[],y[]),vol)
|
|
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 :pre
|
|
|
|
[Description:]
|
|
|
|
This command assigns one or more strings to a variable name.
|
|
Variables can be used in several ways in LAMMPS. A variable can be
|
|
referenced elsewhere in an input script. For variable styles that
|
|
store multiple strings, the "next"_next.html command can be used to
|
|
increment which string is assigned to the variable. Variables can be
|
|
evaluated to produce a numeric value which can be output either
|
|
directly (see the "print"_print.html, "fix print"_fix_print.html, and
|
|
"run every"_run.html commands) or as part of thermodynamic output (see
|
|
the "thermo_style"_thermo_style.html command), fix output (see the
|
|
"fix ave/spatial"_fix_ave_spatial.html and "compute
|
|
variable/atom"_compute_variable_atom.html commands), or dump output
|
|
(see the "dump custom"_dump.html and "compute
|
|
variable/atom"_compute_variable_atom.html commands).
|
|
|
|
In the discussion that follows, the "name" of the variable is the
|
|
arbitrary string that is the 1st argument in the variable command.
|
|
The "string" is one or more of the subsequent arguments. The "string"
|
|
can be simple text as in the 1st example above, it can contain other
|
|
variables as in the 2nd example, or it can be an equation as in the
|
|
3rd 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.
|
|
|
|
IMPORTANT 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 2 exceptions, read further). This is to allow an input
|
|
script to be processed multiple times without resetting the variables;
|
|
see the "jump"_jump.html or "include"_include.html commands. It also
|
|
means that using a command-line switch -var will override a
|
|
corresponding variable setting in the input script.
|
|
|
|
There are two exceptions to this rule. First, variables of style
|
|
{equal} ARE redefined each time the command is encountered. This
|
|
allow them to be reset, e.g. in a loop. This means an {equal}-style
|
|
variable will re-define a command-line swich -var setting, so use an
|
|
{index}-style variable for these settings instead, as in bench/in.lj.
|
|
|
|
Second, as described below, if a variable is iterated on to the end of
|
|
its list of strings via the "next"_next.html command, it is removed
|
|
from the list of active varaibles, and is thus available to be
|
|
re-defined in a subsequent variable command.
|
|
|
|
:line
|
|
|
|
"This section"_Section_commands.html#3_2 of the manual 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}, {universe},
|
|
and {uloop}, which string is assigned to a variable can be incremented
|
|
via the "next"_next.html command. When there are no more strings to
|
|
assign, the variable is "exhausted" and a flag is set that causes the
|
|
next "jump"_jump.html 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 exited from.
|
|
|
|
:line
|
|
|
|
For the {index} style, one or more strings are specified. Initially,
|
|
the 1st string is assigned to the variable. Each time a
|
|
"next"_next.html 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; see "this
|
|
section"_Section_start.html#2_6 for details.
|
|
|
|
The {loop} style is identical to the {index} style except that the
|
|
strings are the integers from 1 to N. 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"_next.html command is used with the variable name,
|
|
the next string ("2", "3", etc) is assigned. All processors assign
|
|
the same string to the variable.
|
|
|
|
For the {world} style, one or more strings are specified. There must
|
|
be one string for each processor partition or "world". See "this
|
|
section"_Section_start.html#2_6 of the manual for information on
|
|
running LAMMPS 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"_temper.html command), to assign different temperatures to
|
|
different partitions.
|
|
|
|
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". See "this page"_Section_start.html#2_6 for information on
|
|
running LAMMPS with multiple partitions via the "-partition"
|
|
command-line switch. This variable command initially assigns one
|
|
string to each world. When a "next"_next.html 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.
|
|
|
|
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.
|
|
|
|
:line
|
|
|
|
For the {equal} and {atom} styles, a single string is specified which
|
|
represents an equation that will be evaluated afresh each time the
|
|
variable is used. For {equal} style variables this equation computes
|
|
a scalar quantity, which becomes the value of the variable whenever it
|
|
is evaluated. For {atom} style variables it computes a quantity for
|
|
each atom, which is used by the "compute variable/atom" command and
|
|
its associated output.
|
|
|
|
Note that {equal} 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"_fix_print.html command, different values could be printed each
|
|
timestep it was invoked.
|
|
|
|
The next command cannot be used with {equal} or {atom} style
|
|
variables, since there is only one string.
|
|
|
|
The equation for an {equal} 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 equation:
|
|
|
|
variable x equal div(add(pe,c_MyTemp\[0\]),pow(vol,div(1,3))) :pre
|
|
|
|
Specifically, an equation can contain numbers, thermo keywords, math
|
|
functions, group functions, atom vectors, compute references, and
|
|
other variables. There is one difference between {equal} and {atom}
|
|
variables; the syntax of Atom vector references is different.
|
|
|
|
Number: 0.2, 1.0e20, -15.4, etc
|
|
Thermo keywords: vol, pe, ebond, etc
|
|
Math functions: add(x,y), sub(x,y), mult(x,y), div(x,y), \
|
|
neg(x), pow(x,y), exp(x), ln(x), sqrt(x)
|
|
Group functions: mass(ID), charge(ID), xcm(ID,dim), vcm(ID,dim), fcm(ID,dim) \
|
|
bound(ID,dir), gyration(ID)
|
|
Atom vectors for {equal}: mass\[N\], x\[N\], y\[N\], z\[N\], \
|
|
vx\[N\], vy\[N\], vz\[N\], \
|
|
fx\[N\], fy\[N\], fz\[N\]
|
|
Atom vectors for {atom}: mass\[\], x\[\], y\[\], z\[\], \
|
|
vx\[\], vy\[\], vz\[\], \
|
|
fx\[\], fy\[\], fz\[\]
|
|
Compute references: c_ID\[0\], c_ID\[N\]
|
|
Fix references: f_ID\[0\], f_ID\[N\]
|
|
Other variables: v_abc, v_x, etc :tb(s=:)
|
|
|
|
The thermo keywords allowed in the equation are those defined by the
|
|
"thermo_style custom" command. Note that many thermodyanmic
|
|
quantities are only computable after the first simulation has begun.
|
|
Likewise, many thermodynamic quantities (such as energies) are only
|
|
computed on timesteps when thermodyanmic output is being performed.
|
|
If the variable equation these quantities at other times, out-of-date
|
|
or invalid values may be used.
|
|
|
|
Math functions take one or two arguments, each of which may be an
|
|
equation containing any of the quantities defined above. This allows
|
|
equations to be nested, as in the examples above.
|
|
|
|
Group functions take one or two arguments. The first argument is the
|
|
group-ID. The {dim} argument is {x} or {y} or {z}. The {dir}
|
|
argument is {xmin}, {xmax}, {ymin}, {ymax}, {zmin}, or {zmax}. The
|
|
group functions mass() and charge() are the total mass and charge of
|
|
the group of atoms. 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 "fix gyration"_fix_gyration.html command for the formula.
|
|
|
|
For {equal} style variables, atom vectors take a single integer
|
|
argument from 1-N, which is the desired atom-ID, e.g. x\[243\]. For
|
|
{atom} style variables, atom vectors take no argument. Since {atom}
|
|
style variables compute one value per atom, a reference like x\[\]
|
|
means the x-coord of each atom will be used when evaluating the
|
|
variable.
|
|
|
|
Compute references access scalar or vector quantities calculated by a
|
|
"compute"_compute.html. The ID in the reference should be replaced by
|
|
the actual ID of the compute defined elsewhere in the input script.
|
|
See the "compute"_compute.html command for details. Note that
|
|
per-atom quantities calculated by a compute cannot be accessed this
|
|
way, but only global scalar or vector quantities. However, there is a
|
|
"compute sum"_compute_sum.html command which sums per-atom quantities
|
|
into a global scalar or vector which can be accessed by a variable.
|
|
|
|
If {c_ID\[0\]} is used as a keyword, then the scalar quantity
|
|
calculated by the compute is used. If {c_ID\[N\]} is used, then one
|
|
component of the vector quantity calculated by the compute is used. N
|
|
should be an integer from 1-M, where M is the length of the vector
|
|
calculated by the compute.
|
|
|
|
Fix references access scalar or vector quantities calculated by a
|
|
"fix"_fix.html. See the doc pages for individual fixes to see which
|
|
ones compute a scalar or vector quantity. Since the fix may not be
|
|
invoked every timestep and compute its quantities, you should insure
|
|
the variable is only evaluated on appropriate timesteps. The ID in
|
|
the reference should be replaced by the actual ID of the fix defined
|
|
elsewhere in the input script. See the "fix"_fix.html command for
|
|
details. Note that per-atom quantities calculated by a fix cannot be
|
|
accessed this way, but only global scalar or vector quantities.
|
|
|
|
If {f_ID\[0\]} is used as a keyword, then the scalar quantity
|
|
calculated by the fix is used. If {f_ID\[N\]} is used, then one
|
|
component of the vector quantity calculated by the fix is used. N
|
|
should be an integer from 1-M, where M is the length of the vector
|
|
calculated by the fix.
|
|
|
|
The current values of other variables can be accessed by prepending a
|
|
"v_" to the variable name. This will cause the other variable to be
|
|
evaulated. Note that if you do something circular like this:
|
|
|
|
variable a equal v_b
|
|
variable b equal v_a
|
|
print $a :pre
|
|
|
|
then LAMMPS will run for a while when the print statement is invoked.
|
|
|
|
Note that there is a subtle difference between using a variable in a
|
|
{equal} or {atom} style equation in the form $x versus v_x.
|
|
|
|
In the former case, as with any other input script command, the
|
|
variable's value is substituted for immediately when the line is read
|
|
from the input script. Thus if the current simulation box volume was
|
|
1000.0, then these lines:
|
|
|
|
variable x equal vol
|
|
variable y equal mult($x,2) :pre
|
|
|
|
would associate the equation string "mult(1000.0,2)" with variable y.
|
|
|
|
By contrast, these lines:
|
|
|
|
variable x equal vol
|
|
variable y equal mult(v_x,2) :pre
|
|
|
|
would associate the equation string "mult(v_x,2)" with variable y.
|
|
|
|
Thus if the variable y were evaluated periodically during a run where
|
|
the box volume changed, the resulting value would always be 2000.0 for
|
|
the first case, but would change dynamically for the second case.
|
|
|
|
:line
|
|
|
|
[Restrictions:]
|
|
|
|
The use of atom vectors in {equal} style variables requires the atom
|
|
style to use a global mapping in order to look up the vector indices.
|
|
Only atom styles with molecular information create global maps unless
|
|
the "atom_modify map"_atom_modify.html command is used.
|
|
|
|
All {universe}- and {uloop}-style variables must have the same number
|
|
of values.
|
|
|
|
[Related commands:]
|
|
|
|
"next"_next.html, "jump"_jump.html, "include"_include.html,
|
|
"temper"_temper.html, "fix print"_fix_print.html, "print"_print.html
|
|
|
|
[Default:] none
|