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1101 lines
56 KiB
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<HTML>
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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</CENTER>
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<HR>
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<H3>variable command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>variable name style args ...
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</PRE>
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<UL><LI>name = name of variable to define
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<LI>style = <I>delete</I> or <I>index</I> or <I>loop</I> or <I>world</I> or <I>universe</I> or <I>uloop</I> or <I>string</I> or <I>format</I> or <I>getenv</I> or <I>file</I> or <I>atomfile</I> or <I>equal</I> or <I>atom</I>
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<PRE> <I>delete</I> = no args
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<I>index</I> args = one or more strings
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<I>loop</I> args = N
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N = integer size of loop, loop from 1 to N inclusive
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<I>loop</I> args = N pad
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N = integer size of loop, loop from 1 to N inclusive
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pad = all values will be same length, e.g. 001, 002, ..., 100
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<I>loop</I> args = N1 N2
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N1,N2 = loop from N1 to N2 inclusive
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<I>loop</I> args = N1 N2 pad
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N1,N2 = loop from N1 to N2 inclusive
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pad = all values will be same length, e.g. 050, 051, ..., 100
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<I>world</I> args = one string for each partition of processors
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<I>universe</I> args = one or more strings
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<I>uloop</I> args = N
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N = integer size of loop
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<I>uloop</I> args = N pad
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N = integer size of loop
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pad = all values will be same length, e.g. 001, 002, ..., 100
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<I>string</I> arg = one string
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<I>format</I> args = vname fstr
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vname = name of equal-style variable to evaluate
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fstr = C-style format string
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<I>getenv</I> arg = one string
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<I>file</I> arg = filename
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<I>atomfile</I> arg = filename
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<I>equal</I> or <I>atom</I> args = one formula containing numbers, thermo keywords, math operations, group functions, atom values and vectors, compute/fix/variable references
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numbers = 0.0, 100, -5.4, 2.8e-4, etc
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constants = PI
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thermo keywords = vol, ke, press, etc from <A HREF = "thermo_style.html">thermo_style</A>
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math operators = (), -x, x+y, x-y, x*y, x/y, x^y, x%y,
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x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x || y, !x
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math functions = sqrt(x), exp(x), ln(x), log(x), abs(x),
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sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x),
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random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x)
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ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z),
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stride(x,y,z), stride2(x,y,z,a,b,c),
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vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)
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group functions = count(group), mass(group), charge(group),
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xcm(group,dim), vcm(group,dim), fcm(group,dim),
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bound(group,dir), gyration(group), ke(group),
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angmom(group,dim), torque(group,dim),
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inertia(group,dimdim), omega(group,dim)
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region functions = count(group,region), mass(group,region), charge(group,region),
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xcm(group,dim,region), vcm(group,dim,region), fcm(group,dim,region),
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bound(group,dir,region), gyration(group,region), ke(group,reigon),
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angmom(group,dim,region), torque(group,dim,region),
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inertia(group,dimdim,region), omega(group,dim,region)
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special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x)
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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]
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atom vector = id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q
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compute references = c_ID, c_ID[i], c_ID[i][j]
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fix references = f_ID, f_ID[i], f_ID[i][j]
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variable references = v_name, v_name[i]
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>variable x index run1 run2 run3 run4 run5 run6 run7 run8
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variable LoopVar loop $n
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variable beta equal temp/3.0
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variable b1 equal x[234]+0.5*vol
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variable b1 equal "x[234] + 0.5*vol"
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variable b equal xcm(mol1,x)/2.0
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variable b equal c_myTemp
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variable b atom x*y/vol
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variable foo string myfile
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variable f file values.txt
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variable temp world 300.0 310.0 320.0 ${Tfinal}
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variable x universe 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
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variable x uloop 15 pad
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variable str format x %.6g
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variable x delete
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>This command assigns one or more strings to a variable name for
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evaluation later in the input script or during a simulation.
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</P>
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<P>Variables can thus be useful in several contexts. A variable can be
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defined and then referenced elsewhere in an input script to become
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part of a new input command. For variable styles that store multiple
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strings, the <A HREF = "next.html">next</A> command can be used to increment which
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string is assigned to the variable. Variables of style <I>equal</I> store
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a formula which when evaluated produces a single numeric value which
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can be output either directly (see the <A HREF = "print.html">print</A>, <A HREF = "fix_print.html">fix
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print</A>, and <A HREF = "run.html">run every</A> commands) or as part
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of thermodynamic output (see the <A HREF = "thermo_style.html">thermo_style</A>
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command), or used as input to an averaging fix (see the <A HREF = "fix_ave_time.html">fix
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ave/time</A> command). Variables of style <I>atom</I> store
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a formula which when evaluated produces one numeric value per atom
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which can be output to a dump file (see the <A HREF = "dump.html">dump custom</A>
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command) or used as input to an averaging fix (see the <A HREF = "fix_ave_spatial.html">fix
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ave/spatial</A> and <A HREF = "fix_ave_atom.html">fix ave/atom</A>
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commands). Variables of style <I>atomfile</I> can be used anywhere in an
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input script that atom-style variables are used; they get their
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per-atom values from a file rather than from a formula.
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</P>
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<P>IMPORTANT NOTE: As discussed in <A HREF = "Section_commands.html#cmd_2">Section
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3.2</A> of the manual, an input script can
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use "immediate" variables, specified as $(formula) with parenthesis,
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where the formula has the same syntax as equal-style variables
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described on this page. This is a way to evaluate a formula
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immediately without using the variable command to define a named
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variable.
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</P>
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<P>In the discussion that follows, the "name" of the variable is the
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arbitrary string that is the 1st argument in the variable command.
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This name can only contain alphanumeric characters and underscores.
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The "string" is one or more of the subsequent arguments. The "string"
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can be simple text as in the 1st example above, it can contain other
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variables as in the 2nd example, or it can be a formula as in the 3rd
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example. The "value" is the numeric quantity resulting from
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evaluation of the string. Note that the same string can generate
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different values when it is evaluated at different times during a
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simulation.
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</P>
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<P>IMPORTANT NOTE: When the input script line is encountered that defines
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a variable of style <I>equal</I> or <I>atom</I> that contains a formula, the
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formula is NOT immediately evaluated and the result stored. See the
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discussion below about "Immediate Evaluation of Variables" if you want
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to do this. This is also true of the <I>format</I> style variable
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since it evaluates another variable when it is invoked.
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</P>
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<P>IMPORTANT NOTE: When a variable command is encountered in the input
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script and the variable name has already been specified, the command
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is ignored. This means variables can NOT be re-defined in an input
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script (with 2 exceptions, read further). This is to allow an input
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script to be processed multiple times without resetting the variables;
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see the <A HREF = "jump.html">jump</A> or <A HREF = "include.html">include</A> commands. It also
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means that using the <A HREF = "Section_start.html#start_7">command-line switch</A>
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-var will override a corresponding index variable setting in the input
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script.
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</P>
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<P>There are two exceptions to this rule. First, variables of style
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<I>string</I>, <I>getenv</I>, <I>equal</I> and <I>atom</I> ARE redefined each time the
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command is encountered. This allows these style of variables to be
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redefined multiple times in an input script. In a loop, this means
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the formula associated with an <I>equal</I> or <I>atom</I> style variable can
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change if it contains a substitution for another variable, e.g. $x or
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v_x.
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</P>
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<P>Second, as described below, if a variable is iterated on to the end of
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its list of strings via the <A HREF = "next.html">next</A> command, it is removed
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from the list of active variables, and is thus available to be
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re-defined in a subsequent variable command. The <I>delete</I> style does
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the same thing.
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</P>
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<HR>
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<P><A HREF = "Section_commands.html#cmd_2">This section</A> of the manual explains how
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occurrences of a variable name in an input script line are replaced by
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the variable's string. The variable name can be referenced as $x if
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the name "x" is a single character, or as ${LoopVar} if the name
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"LoopVar" is one or more characters.
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</P>
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<P>As described below, for variable styles <I>index</I>, <I>loop</I>, <I>file</I>,
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<I>universe</I>, and <I>uloop</I>, which string is assigned to a variable can be
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incremented via the <A HREF = "next.html">next</A> command. When there are no more
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strings to assign, the variable is exhausted and a flag is set that
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causes the next <A HREF = "jump.html">jump</A> command encountered in the input
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script to be skipped. This enables the construction of simple loops
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in the input script that are iterated over and then exited from.
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</P>
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<P>As explained above, an exhausted variable can be re-used in an input
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script. The <I>delete</I> style also removes the variable, the same as if
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it were exhausted, allowing it to be redefined later in the input
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script or when the input script is looped over. This can be useful
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when breaking out of a loop via the <A HREF = "if.html">if</A> and <A HREF = "jump.html">jump</A>
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commands before the variable would become exhausted. For example,
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</P>
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<PRE>label loop
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variable a loop 5
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print "A = $a"
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if "$a > 2" then "jump in.script break"
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next a
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jump in.script loop
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label break
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variable a delete
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</PRE>
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<HR>
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<P>This section describes how various variable styles are defined and
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what they store. Many of the styles store one or more strings. Note
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that a single string can contain spaces (multiple words), if it is
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enclosed in quotes in the variable command. When the variable is
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substituted for in another input script command, its returned string
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will then be interpreted as multiple arguments in the expanded
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command.
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</P>
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<P>For the <I>index</I> style, one or more strings are specified. Initially,
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the 1st string is assigned to the variable. Each time a
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<A HREF = "next.html">next</A> command is used with the variable name, the next
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string is assigned. All processors assign the same string to the
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variable.
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</P>
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<P><I>Index</I> style variables with a single string value can also be set by
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using the command-line switch -var; see <A HREF = "Section_start.html#start_7">this
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section</A> for details.
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</P>
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<P>The <I>loop</I> style is identical to the <I>index</I> style except that the
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strings are the integers from 1 to N inclusive, if only one argument N
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is specified. This allows generation of a long list of runs
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(e.g. 1000) without having to list N strings in the input script.
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Initially, the string "1" is assigned to the variable. Each time a
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<A HREF = "next.html">next</A> command is used with the variable name, the next
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string ("2", "3", etc) is assigned. All processors assign the same
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string to the variable. The <I>loop</I> style can also be specified with
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two arguments N1 and N2. In this case the loop runs from N1 to N2
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inclusive, and the string N1 is initially assigned to the variable.
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N1 <= N2 and N2 >= 0 is required.
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</P>
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<P>For the <I>world</I> style, one or more strings are specified. There must
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be one string for each processor partition or "world". See <A HREF = "Section_start.html#start_7">this
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section</A> of the manual for information on
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running LAMMPS with multiple partitions via the "-partition"
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command-line switch. This variable command assigns one string to each
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world. All processors in the world are assigned the same string. The
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next command cannot be used with <I>equal</I> style variables, since there
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is only one value per world. This style of variable is useful when
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you wish to run different simulations on different partitions, or when
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performing a parallel tempering simulation (see the
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<A HREF = "temper.html">temper</A> command), to assign different temperatures to
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different partitions.
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</P>
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<P>For the <I>universe</I> style, one or more strings are specified. There
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must be at least as many strings as there are processor partitions or
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"worlds". See <A HREF = "Section_start.html#start_7">this page</A> for information
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on running LAMMPS with multiple partitions via the "-partition"
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command-line switch. This variable command initially assigns one
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string to each world. When a <A HREF = "next.html">next</A> command is encountered
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using this variable, the first processor partition to encounter it, is
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assigned the next available string. This continues until all the
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variable strings are consumed. Thus, this command can be used to run
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50 simulations on 8 processor partitions. The simulations will be run
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one after the other on whatever partition becomes available, until
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they are all finished. <I>Universe</I> style variables are incremented
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using the files "tmp.lammps.variable" and "tmp.lammps.variable.lock"
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which you will see in your directory during such a LAMMPS run.
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</P>
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<P>The <I>uloop</I> style is identical to the <I>universe</I> style except that the
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strings are the integers from 1 to N. This allows generation of long
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list of runs (e.g. 1000) without having to list N strings in the input
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script.
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</P>
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<P>For the <I>string</I> style, a single string is assigned to the variable.
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The only difference between this and using the <I>index</I> style with a
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single string is that a variable with <I>string</I> style can be redefined.
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E.g. by another command later in the input script, or if the script is
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read again in a loop.
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</P>
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<P>For the <I>format</I> style, an equal-style variable is specified along
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with a C-style format string, e.g. "%f" or "%.10g", which must be
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appropriate for formatting a double-precision floating-point value.
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This allows an equal-style variable to be formatted specifically for
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output as a string, e.g. by the <A HREF = "print.html">print</A> command, if the
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default format "%.15g" has too much precision.
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</P>
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<P>For the <I>getenv</I> style, a single string is assigned to the variable
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which should be the name of an environment variable. When the
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variable is evaluated, it returns the value of the environment
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variable, or an empty string if it not defined. This style of
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variable can be used to adapt the behavior of LAMMPS input scripts via
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environment variable settings, or to retrieve information that has
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been previously stored with the <A HREF = "shell.html">shell putenv</A> command.
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Note that because environment variable settings are stored by the
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operating systems, they persist beyond a <A HREF = "clear.html">clear</A> command.
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</P>
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<P>For the <I>file</I> style, a filename is provided which contains a list of
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strings to assign to the variable, one per line. The strings can be
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numeric values if desired. See the discussion of the next() function
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below for equal-style variables, which will convert the string of a
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file-style variable into a numeric value in a formula.
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</P>
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<P>When a file-style variable is defined, the file is opened and the
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string on the first line is read and stored with the variable. This
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means the variable can then be evaluated as many times as desired and
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will return that string. There are two ways to cause the next string
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from the file to be read: use the <A HREF = "next.html">next</A> command or the
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next() function in an equal- or atom-style variable, as discussed
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below.
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</P>
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<P>The rules for formatting the file are as follows. A comment character
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"#" can be used anywhere on a line; text starting with the comment
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character is stripped. Blank lines are skipped. The first "word" of
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a non-blank line, delimited by white space, is the "string" assigned
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to the variable.
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</P>
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<P>For the <I>atomfile</I> style, a filename is provided which contains one or
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more sets of values, to assign on a per-atom basis to the variable.
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The format of the file is described below.
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</P>
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<P>When an atomfile-style variable is defined, the file is opened and the
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first set of per-atom values are read and stored with the variable.
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This means the variable can then be evaluated as many times as desired
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and will return those values. There are two ways to cause the next
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set of per-atom values from the file to be read: use the
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<A HREF = "next.html">next</A> command or the next() function in an atom-style
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variable, as discussed below.
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</P>
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<P>The rules for formatting the file are as follows. Each time a set of
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per-atom values is read, a non-blank line is searched for in the file.
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A comment character "#" can be used anywhere on a line; text starting
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with the comment character is stripped. Blank lines are skipped. The
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first "word" of a non-blank line, delimited by white space, is read as
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the count N of per-atom lines to immediately follow. N can be be the
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total number of atoms in the system, or only a subset. The next N
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lines have the following format
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</P>
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<PRE>ID value
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</PRE>
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<P>where ID is an atom ID and value is the per-atom numeric value that
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will be assigned to that atom. IDs can be listed in any order.
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</P>
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<P>IMPORTANT NOTE: Every time a set of per-atom lines is read, the value
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for all atoms is first set to 0.0. Thus values for atoms whose ID
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does not appear in the set, will remain 0.0.
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</P>
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<HR>
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<P>For the <I>equal</I> and <I>atom</I> styles, a single string is specified which
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represents a formula that will be evaluated afresh each time the
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variable is used. If you want spaces in the string, enclose it in
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double quotes so the parser will treat it as a single argument. For
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<I>equal</I> style variables the formula computes a scalar quantity, which
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becomes the value of the variable whenever it is evaluated. For
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<I>atom</I> style variables the formula computes one quantity for each
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atom whenever it is evaluated.
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</P>
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<P>Note that <I>equal</I> and <I>atom</I> variables can produce different values at
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different stages of the input script or at different times during a
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run. For example, if an <I>equal</I> variable is used in a <A HREF = "fix_print.html">fix
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print</A> command, different values could be printed each
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timestep it was invoked. If you want a variable to be evaluated
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immediately, so that the result is stored by the variable instead of
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the string, see the section below on "Immediate Evaluation of
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Variables".
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</P>
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<P>The next command cannot be used with <I>equal</I> or <I>atom</I> style
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variables, since there is only one string.
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</P>
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<P>The formula for an <I>equal</I> or <I>atom</I> variable can contain a variety
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of quantities. The syntax for each kind of quantity is simple, but
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multiple quantities can be nested and combined in various ways to
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build up formulas of arbitrary complexity. For example, this is a
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valid (though strange) variable formula:
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</P>
|
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<PRE>variable x equal "pe + c_MyTemp / vol^(1/3)"
|
|
</PRE>
|
|
<P>Specifically, an formula can contain numbers, thermo keywords, math
|
|
operators, math functions, group functions, region functions, atom
|
|
values, atom vectors, compute references, fix references, and
|
|
references to other variables.
|
|
</P>
|
|
<DIV ALIGN=center><TABLE BORDER=1 >
|
|
<TR><TD >Number</TD><TD > 0.2, 100, 1.0e20, -15.4, etc</TD></TR>
|
|
<TR><TD >Constant</TD><TD > PI</TD></TR>
|
|
<TR><TD >Thermo keywords</TD><TD > vol, pe, ebond, etc</TD></TR>
|
|
<TR><TD >Math operators</TD><TD > (), -x, x+y, x-y, x*y, x/y, x^y, x%y, </TD></TR>
|
|
<TR><TD >Math operators</TD><TD > (), -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</TD></TR>
|
|
<TR><TD >Math functions</TD><TD > 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), ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(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)</TD></TR>
|
|
<TR><TD >Group functions</TD><TD > 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)</TD></TR>
|
|
<TR><TD >Region functions</TD><TD > 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)</TD></TR>
|
|
<TR><TD >Special functions</TD><TD > sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x)</TD></TR>
|
|
<TR><TD >Atom values</TD><TD > 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]</TD></TR>
|
|
<TR><TD >Atom vectors</TD><TD > id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q</TD></TR>
|
|
<TR><TD >Compute references</TD><TD > c_ID, c_ID[i], c_ID[i][j]</TD></TR>
|
|
<TR><TD >Fix references</TD><TD > f_ID, f_ID[i], f_ID[i][j]</TD></TR>
|
|
<TR><TD >Other variables</TD><TD > v_name, v_name[i]
|
|
</TD></TR></TABLE></DIV>
|
|
|
|
<HR>
|
|
|
|
<P>Most of the formula elements produce a scalar value. A few produce a
|
|
per-atom vector of values. These are the atom vectors, compute
|
|
references that represent a per-atom vector, fix references that
|
|
represent a per-atom vector, and variables that are atom-style
|
|
variables. Math functions that operate on scalar values produce a
|
|
scalar value; math function that operate on per-atom vectors do so
|
|
element-by-element and produce a per-atom vector.
|
|
</P>
|
|
<P>A formula for equal-style variables cannot use any 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. Atom-style variables are evaluated by other commands
|
|
that define a <A HREF = "group.html">group</A> on which they operate, e.g. a
|
|
<A HREF = "dump.html">dump</A> or <A HREF = "compute.html">compute</A> or <A HREF = "fix.html">fix</A> command.
|
|
When they invoke the atom-style variable, only atoms in the group are
|
|
inlcuded in the formula evaluation. The variable evaluates to 0.0 for
|
|
atoms not in the group.
|
|
</P>
|
|
<P>The thermo keywords allowed in a formula are those defined by the
|
|
<A HREF = "thermo_style.html">thermo_style custom</A> command. Thermo keywords that
|
|
require a <A HREF = "compute.html">compute</A> to calculate their values such as
|
|
"temp" or "press", use computes stored and invoked by the
|
|
<A HREF = "thermo_style.html">thermo_style</A> 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".
|
|
</P>
|
|
<HR>
|
|
|
|
<H4>Math Operators
|
|
</H4>
|
|
<P>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.
|
|
</P>
|
|
<P>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 "||" has 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.
|
|
</P>
|
|
<P>IMPORTANT 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.
|
|
</P>
|
|
<P>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 NOT operator returns 1.0 if its argument is
|
|
0.0, else it returns 0.0.
|
|
</P>
|
|
<P>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 satifsy one or more criteria could be calculated by
|
|
taking the returned per-atom vector of ones and zeroes and passing it
|
|
to the <A HREF = "compute_reduce.html">compute reduce</A> command.
|
|
</P>
|
|
<HR>
|
|
|
|
<H4>Math Functions
|
|
</H4>
|
|
<P>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 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.
|
|
</P>
|
|
<P>Most of the math functions perform obvious operations. The ln() is
|
|
the natural log; log() is the base 10 log.
|
|
</P>
|
|
<P>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 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.
|
|
</P>
|
|
<P>IMPORTANT NOTE: Internally, there is just one random number generator
|
|
for all equal-style variables and 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.
|
|
</P>
|
|
<P>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.
|
|
</P>
|
|
<P>The ramp(x,y) function uses the current timestep to generate a value
|
|
linearly intepolated between the specified x,y values over the course
|
|
of a run, according to this formula:
|
|
</P>
|
|
<PRE>value = x + (y-x) * (timestep-startstep) / (stopstep-startstep)
|
|
</PRE>
|
|
<P>The run begins on startstep and ends on stopstep. Startstep and
|
|
stopstep can span multiple runs, using the <I>start</I> and <I>stop</I> keywords
|
|
of the <A HREF = "run.html">run</A> command. See the <A HREF = "run.html">run</A> command for
|
|
details of how to do this.
|
|
</P>
|
|
<P>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 <A HREF = "dump_modify.html">dump_modify every</A>
|
|
command, it will generate the sequence of output timesteps:
|
|
</P>
|
|
<PRE>100,1000,1100,2000,2100,3000,etc
|
|
</PRE>
|
|
<P>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 <A HREF = "dump_modify.html">dump_modify
|
|
every</A> command, it will generate this sequence of
|
|
output timesteps:
|
|
</P>
|
|
<PRE>100,200,300,400,1000,2000,3000,4000,10000,20000,etc
|
|
</PRE>
|
|
<P>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 <A HREF = "dump_modify.html">dump_modify
|
|
every</A> command, then the interval between 100 and
|
|
1000 is divided as 900/18 = 50 steps, and it will generate the
|
|
sequence of output timesteps:
|
|
</P>
|
|
<PRE>100,150,200,...950,1000,1500,2000,...9500,10000,15000,etc
|
|
</PRE>
|
|
<P>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 sequece 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 <A HREF = "dump_modify.html">dump_modify every</A> command, it
|
|
will generate the sequence of output timesteps:
|
|
</P>
|
|
<PRE>1000,1100,1200, ... ,1900,2000
|
|
</PRE>
|
|
<P>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 stride(1000,2000,100,1350,1360,1) is used in a variable by the
|
|
<A HREF = "dump_modify.html">dump_modify every</A> command, it will generate the
|
|
sequence of output timesteps:
|
|
</P>
|
|
<PRE>1000,1100,1200,1300,1350,1351,1352, ... 1359,1360,1400,1500, ... ,2000
|
|
</PRE>
|
|
<P>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:
|
|
</P>
|
|
<PRE>value = value0 + velocity*(timestep-startstep)*dt
|
|
</PRE>
|
|
<P>where dt = the timestep size.
|
|
</P>
|
|
<P>The run begins on startstep. Startstep can span multiple runs, using
|
|
the <I>start</I> keyword of the <A HREF = "run.html">run</A> command. See the
|
|
<A HREF = "run.html">run</A> command for details of how to do this. Note that the
|
|
<A HREF = "thermo_style.html">thermo_style</A> keyword elaplong =
|
|
timestep-startstep.
|
|
</P>
|
|
<P>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:
|
|
</P>
|
|
<PRE>value = value0 + Amplitude * sin(omega*(timestep-startstep)*dt)
|
|
value = value0 + Amplitude * (1 - cos(omega*(timestep-startstep)*dt))
|
|
</PRE>
|
|
<P>where dt = the timestep size.
|
|
</P>
|
|
<P>The run begins on startstep. Startstep can span multiple runs, using
|
|
the <I>start</I> keyword of the <A HREF = "run.html">run</A> command. See the
|
|
<A HREF = "run.html">run</A> command for details of how to do this. Note that the
|
|
<A HREF = "thermo_style.html">thermo_style</A> keyword elaplong =
|
|
timestep-startstep.
|
|
</P>
|
|
<HR>
|
|
|
|
<H4>Group and Region Functions
|
|
</H4>
|
|
<P>Group functions are specified as keywords followed by one or two
|
|
parenthesized arguments. The first argument <I>ID</I> is the group-ID.
|
|
The <I>dim</I> argument, if it exists, is <I>x</I> or <I>y</I> or <I>z</I>. The <I>dir</I>
|
|
argument, if it exists, is <I>xmin</I>, <I>xmax</I>, <I>ymin</I>, <I>ymax</I>, <I>zmin</I>, or
|
|
<I>zmax</I>. The <I>dimdim</I> argument, if it exists, is <I>xx</I> or <I>yy</I> or <I>zz</I>
|
|
or <I>xy</I> or <I>yz</I> or <I>xz</I>.
|
|
</P>
|
|
<P>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 <A HREF = "compute_gyration.html">compute gyration</A> 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.
|
|
</P>
|
|
<P>Region functions are specified exactly the same way as group functions
|
|
except they take an extra final argument <I>IDR</I> 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.
|
|
</P>
|
|
<HR>
|
|
|
|
<H4>Special Functions
|
|
</H4>
|
|
<P>Special functions take specific kinds of arguments, meaning their
|
|
arguments cannot be formulas themselves.
|
|
</P>
|
|
<P>The sum(x), min(x), max(x), ave(x), trap(x), and slope(x) functions
|
|
each take 1 argument which is of the form "c_ID" or "c_ID[N]" or
|
|
"f_ID" or "f_ID[N]". 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, when N is an integer, to specify which column of the global
|
|
array is being referenced.
|
|
</P>
|
|
<P>These functions operate on the global vector of inputs and reduce it
|
|
to a single scalar value. This is analagous to the operation of the
|
|
<A HREF = "compute_reduce.html">compute reduce</A> command, which invokes the same
|
|
functions on per-atom and local vectors.
|
|
</P>
|
|
<P>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.
|
|
</P>
|
|
<P>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 <A HREF = "fix_ave_correlate.html">fix ave/correlate</A> command.
|
|
</P>
|
|
<P>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.
|
|
</P>
|
|
<P>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.
|
|
</P>
|
|
<P>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.
|
|
</P>
|
|
<P>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.
|
|
</P>
|
|
<P>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.
|
|
</P>
|
|
<P>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.
|
|
</P>
|
|
<P>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.
|
|
</P>
|
|
<P>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 <A HREF = "next.html">next</A> command
|
|
operates.
|
|
</P>
|
|
<HR>
|
|
|
|
<H4>Atom Values and Vectors
|
|
</H4>
|
|
<P>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 atom or atom-file 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 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.
|
|
</P>
|
|
<P>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.
|
|
</P>
|
|
<P>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.
|
|
</P>
|
|
<P>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 <A HREF = "atom_style.html">atom_style</A> is being used that
|
|
defines molecule IDs.
|
|
</P>
|
|
<P>Note that many other atom attributes can be used as inputs to a
|
|
variable by using the <A HREF = "compute_property_atom.html">compute
|
|
property/atom</A> command and then specifying
|
|
a quantity from that compute.
|
|
</P>
|
|
<HR>
|
|
|
|
<H4>Compute References
|
|
</H4>
|
|
<P>Compute references access quantities calculated by a
|
|
<A HREF = "compute.html">compute</A>. The ID in the reference should be replaced by
|
|
the ID of a compute defined elsewhere in the input script. As
|
|
discussed in the doc page for the <A HREF = "compute.html">compute</A> command,
|
|
computes can produce global, per-atom, or local values. Only global
|
|
and per-atom values can be used in a variable. Computes can also
|
|
produce a scalar, vector, or array. An equal-style variable can only
|
|
use scalar values, which means a global scalar, or an element of a
|
|
global or per-atom vector or array. Atom-style variables can use the
|
|
same scalar values. They can also use per-atom vector values. A
|
|
vector value can be a per-atom vector itself, or a column of an
|
|
per-atom array. See the doc pages for individual computes to see what
|
|
kind of values they produce.
|
|
</P>
|
|
<P>Examples of different kinds of compute references are as follows.
|
|
There is no ambiguity as to what a reference means, since computes
|
|
only produce global or per-atom quantities, never both.
|
|
</P>
|
|
<DIV ALIGN=center><TABLE BORDER=1 >
|
|
<TR><TD >c_ID</TD><TD > global scalar, or per-atom vector</TD></TR>
|
|
<TR><TD >c_ID[I]</TD><TD > Ith element of global vector, or atom I's value in per-atom vector, or Ith column from per-atom array</TD></TR>
|
|
<TR><TD >c_ID[I][J]</TD><TD > I,J element of global array, or atom I's Jth value in per-atom array
|
|
</TD></TR></TABLE></DIV>
|
|
|
|
<P>For I and J, integers 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 the "Atom Values and Vectors" discussion
|
|
above.
|
|
</P>
|
|
<P>If a variable containing a compute is evaluated directly in an input
|
|
script (not during a run), then the values accessed by the compute
|
|
must be current. See the discussion below about "Variable Accuracy".
|
|
</P>
|
|
<HR>
|
|
|
|
<H4>Fix References
|
|
</H4>
|
|
<P>Fix references access quantities calculated by a <A HREF = "compute.html">fix</A>.
|
|
The ID in the reference should be replaced by the ID of a fix defined
|
|
elsewhere in the input script. As discussed in the doc page for the
|
|
<A HREF = "fix.html">fix</A> command, fixes can produce global, per-atom, or local
|
|
values. Only global and per-atom values can be used in a variable.
|
|
Fixes can also produce a scalar, vector, or array. An equal-style
|
|
variable can only use scalar values, which means a global scalar, or
|
|
an element of a global or per-atom vector or array. Atom-style
|
|
variables can use the same scalar values. They can also use per-atom
|
|
vector values. A vector value can be a per-atom vector itself, or a
|
|
column of an per-atom array. See the doc pages for individual fixes
|
|
to see what kind of values they produce.
|
|
</P>
|
|
<P>The different kinds of fix references are exactly the same as the
|
|
compute references listed in the above table, where "c_" is replaced
|
|
by "f_". Again, there is no ambiguity as to what a reference means,
|
|
since fixes only produce global or per-atom quantities, never both.
|
|
</P>
|
|
<DIV ALIGN=center><TABLE BORDER=1 >
|
|
<TR><TD >f_ID</TD><TD > global scalar, or per-atom vector</TD></TR>
|
|
<TR><TD >f_ID[I]</TD><TD > Ith element of global vector, or atom I's value in per-atom vector, or Ith column from per-atom array</TD></TR>
|
|
<TR><TD >f_ID[I][J]</TD><TD > I,J element of global array, or atom I's Jth value in per-atom array
|
|
</TD></TR></TABLE></DIV>
|
|
|
|
<P>For I and J, integers 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 the "Atom Values and Vectors" discussion
|
|
above.
|
|
</P>
|
|
<P>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".
|
|
</P>
|
|
<P>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 <A HREF = "fix_ave_time.html">fix ave/time</A>
|
|
command may only generate averaged quantities every 100 steps. See
|
|
the doc pages for individual fix commands for details.
|
|
</P>
|
|
<HR>
|
|
|
|
<H4>Variable References
|
|
</H4>
|
|
<P>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.
|
|
</P>
|
|
<P>As discussed on this doc page, equal-style variables generate a global
|
|
scalar numeric value; atom-style and atomfile-style variables generate
|
|
a per-atom vector of numeric values; all other variables store a
|
|
string. The formula for an equal-style variable can use any style of
|
|
variable except an atom-style or atomfile-style (unless only a single
|
|
value from the variable is accessed via a subscript). 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 an atom-style variable can use any style of variable, including
|
|
other atom-style or atomfile-style variables.
|
|
</P>
|
|
<P>Examples of different kinds of variable references are as follows.
|
|
There is no ambiguity as to what a reference means, since variables
|
|
produce only a global scalar or a per-atom vector, never both.
|
|
</P>
|
|
<DIV ALIGN=center><TABLE BORDER=1 >
|
|
<TR><TD >v_name</TD><TD > scalar, or per-atom vector</TD></TR>
|
|
<TR><TD >v_name[I]</TD><TD > atom I's value in per-atom vector
|
|
</TD></TR></TABLE></DIV>
|
|
|
|
<P>For I, 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 the "Atom Values and Vectors" discussion
|
|
above.
|
|
</P>
|
|
<HR>
|
|
|
|
<P><B>Immediate Evaluation of Variables:</B>
|
|
</P>
|
|
<P>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
|
|
<A HREF = "Section_commands.html#cmd_2">Section 3.2</A> of the manual, which
|
|
describes the use of "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.
|
|
</P>
|
|
<P>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 in <A HREF = "Section_commands.html#3_2">Section commands
|
|
3.2</A> for "Parsing rules", 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.
|
|
</P>
|
|
<P>Referencing a variable with a leading "v_" is an optional or required
|
|
kind of argument for some commands (e.g. the <A HREF = "fix_ave_spatial.html">fix
|
|
ave/spatial</A> or <A HREF = "dump.html">dump custom</A> or
|
|
<A HREF = "thermo_style.html">thermo_style</A> 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.
|
|
</P>
|
|
<P>As an example, suppose you use this command in your input script to
|
|
define the variable "v" as
|
|
</P>
|
|
<PRE>variable v equal vol
|
|
</PRE>
|
|
<P>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 <A HREF = "fix_ave_time.html">fix
|
|
ave/time</A> then the current volume of the box will be
|
|
evaluated continuously during the run.
|
|
</P>
|
|
<P>If you want to store the initial volume of the system, you can do it
|
|
this way:
|
|
</P>
|
|
<PRE>variable v equal vol
|
|
variable v0 equal $v
|
|
</PRE>
|
|
<P>The second command will force "v" to be evaluated (yielding the
|
|
initial volume) and assign that value to the variable "v0". Thus the
|
|
command
|
|
</P>
|
|
<PRE>thermo_style custom step v_v v_v0
|
|
</PRE>
|
|
<P>would print out both the current and initial volume periodically
|
|
during the run.
|
|
</P>
|
|
<P>Note that it is a mistake to enclose a variable formula in double
|
|
quotes if it contains variables preceeded by $ signs. For example,
|
|
</P>
|
|
<PRE>variable vratio equal "${vfinal}/${v0}"
|
|
</PRE>
|
|
<P>This is because the quotes prevent variable substitution (see <A HREF = "Section_commands.html#cmd_2">this
|
|
section</A> on parsing input script
|
|
commands), and thus an error will occur when the formula for "vratio"
|
|
is evaluated later.
|
|
</P>
|
|
<HR>
|
|
|
|
<P><B>Variable Accuracy:</B>
|
|
</P>
|
|
<P>Obviously, LAMMPS attempts to evaluate variables containing formulas
|
|
(<I>equal</I> and <I>atom</I> style variables) accurately whenever the
|
|
evaluation is performed. Depending on what is included in the
|
|
formula, this may require invoking a <A HREF = "compute.html">compute</A>, 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 <A HREF = "fix.html">fix</A>. If the compute is one that calculates
|
|
the pressure or energy of the system, then these quantities need to be
|
|
tallied during the evaluation of the interatomic potentials (pair,
|
|
bond, etc) on timesteps that the variable will need the values.
|
|
</P>
|
|
<P>LAMMPS keeps track of all of this during a <A HREF = "run.html">run</A> or <A HREF = "minimize.html">energy
|
|
minimization</A>. An error will be generated if you
|
|
attempt to evaluate a variable on timesteps when it cannot produce
|
|
accurate values. For example, if a <A HREF = "thermo_style.html">thermo_style
|
|
custom</A> command prints a variable which accesses
|
|
values stored by a <A HREF = "fix_ave_time.html">fix ave/time</A> 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.
|
|
</P>
|
|
<P>An input script can also request variables be evaluated before or
|
|
after or in between runs, e.g. by including them in a
|
|
<A HREF = "print.html">print</A> command. In this case, if a compute is needed to
|
|
evaluate a variable (either directly or indirectly), LAMMPS will not
|
|
invoke the compute, but it will use a value previously calculated by
|
|
the compute, and can do this only if it was invoked on the current
|
|
timestep. Fixes will always provide a quantity needed by a variable,
|
|
but the quantity may or may not be current. This leads to one of
|
|
three kinds of behavior:
|
|
</P>
|
|
<P>(1) The variable may be evaluated accurately. If it contains
|
|
references to a compute or fix, and these values were calculated on
|
|
the last timestep of a preceeding run, then they will be accessed and
|
|
used by the variable and the result will be accurate.
|
|
</P>
|
|
<P>(2) LAMMPS may not be able to evaluate the variable and will generate
|
|
an error message stating so. For example, if the variable requires a
|
|
quantity from a <A HREF = "compute.html">compute</A> that has not been invoked on
|
|
the current timestep, LAMMPS will generate an error. This means, for
|
|
example, that such a variable cannot be evaluated before the first run
|
|
has occurred. Likewise, in between runs, a variable containing a
|
|
compute cannot be evaluated unless the compute was invoked on the last
|
|
timestep of the preceding run, e.g. by thermodynamic output.
|
|
</P>
|
|
<P>One way to get around this problem is to perform a 0-timestep run
|
|
before using the variable. For example, these commands
|
|
</P>
|
|
<PRE>variable t equal temp
|
|
print "Initial temperature = $t"
|
|
run 1000
|
|
</PRE>
|
|
<P>will generate an error if the run is the first run specified in the
|
|
input script, because generating a value for the "t" variable requires
|
|
a compute for calculating the temperature to be invoked.
|
|
</P>
|
|
<P>However, this sequence of commands would be fine:
|
|
</P>
|
|
<PRE>run 0
|
|
variable t equal temp
|
|
print "Initial temperature = $t"
|
|
run 1000
|
|
</PRE>
|
|
<P>The 0-timestep run initializes and invokes various computes, including
|
|
the one for temperature, so that the value it stores is current and
|
|
can be accessed by the variable "t" after the run has completed. Note
|
|
that a 0-timestep run does not alter the state of the system, so it
|
|
does not change the input state for the 1000-timestep run that
|
|
follows. Also note that the 0-timestep run must actually use and
|
|
invoke the compute in question (e.g. via <A HREF = "thermo_style.html">thermo</A> or
|
|
<A HREF = "dump.html">dump</A> output) in order for it to enable the compute to be
|
|
used in a variable after the run. Thus if you are trying to print a
|
|
variable that uses a compute you have defined, you can insure it is
|
|
invoked on the last timestep of the preceding run by including it in
|
|
thermodynamic output.
|
|
</P>
|
|
<P>Unlike computes, <A HREF = "fix.html">fixes</A> will never generate an error if
|
|
their values are accessed by a variable in between runs. They always
|
|
return some value to the variable. However, the value may not be what
|
|
you expect if the fix has not yet calculated the quantity of interest
|
|
or it is not current. For example, the <A HREF = "fix_indent.html">fix indent</A>
|
|
command stores the force on the indenter. But this is not computed
|
|
until a run is performed. Thus if a variable attempts to print this
|
|
value before the first run, zeroes will be output. Again, performing
|
|
a 0-timestep run before printing the variable has the desired effect.
|
|
</P>
|
|
<P>(3) The variable may be evaluated incorrectly and LAMMPS may have no
|
|
way to detect this has occurred. Consider the following sequence of
|
|
commands:
|
|
</P>
|
|
<PRE>pair_coeff 1 1 1.0 1.0
|
|
run 1000
|
|
pair_coeff 1 1 1.5 1.0
|
|
variable e equal pe
|
|
print "Final potential energy = $e"
|
|
</PRE>
|
|
<P>The first run is performed using one setting for the pairwise
|
|
potential defined by the <A HREF = "pair_style.html">pair_style</A> and
|
|
<A HREF = "pair_coeff.html">pair_coeff</A> commands. The potential energy is
|
|
evaluated on the final timestep and stored by the <A HREF = "compute_pe.html">compute
|
|
pe</A> compute (this is done by the
|
|
<A HREF = "thermo_style.html">thermo_style</A> command). Then a pair coefficient is
|
|
changed, altering the potential energy of the system. When the
|
|
potential energy is printed via the "e" variable, LAMMPS will use the
|
|
potential energy value stored by the <A HREF = "compute_pe.html">compute pe</A>
|
|
compute, thinking it is current. There are many other commands which
|
|
could alter the state of the system between runs, causing a variable
|
|
to evaluate incorrectly.
|
|
</P>
|
|
<P>The solution to this issue is the same as for case (2) above, namely
|
|
perform a 0-timestep run before the variable is evaluated to insure
|
|
the system is up-to-date. For example, this sequence of commands
|
|
would print a potential energy that reflected the changed pairwise
|
|
coefficient:
|
|
</P>
|
|
<PRE>pair_coeff 1 1 1.0 1.0
|
|
run 1000
|
|
pair_coeff 1 1 1.5 1.0
|
|
run 0
|
|
variable e equal pe
|
|
print "Final potential energy = $e"
|
|
</PRE>
|
|
<HR>
|
|
|
|
<P><B>Restrictions:</B>
|
|
</P>
|
|
<P>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 <A HREF = "atom_modify.html">atom_modify
|
|
map</A> command can override the default.
|
|
</P>
|
|
<P>All <I>universe</I>- and <I>uloop</I>-style variables defined in an input script
|
|
must have the same number of values.
|
|
</P>
|
|
<P><B>Related commands:</B>
|
|
</P>
|
|
<P><A HREF = "next.html">next</A>, <A HREF = "jump.html">jump</A>, <A HREF = "include.html">include</A>,
|
|
<A HREF = "temper.html">temper</A>, <A HREF = "fix_print.html">fix print</A>, <A HREF = "print.html">print</A>
|
|
</P>
|
|
<P><B>Default:</B> none
|
|
</P>
|
|
</HTML>
|