forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9049 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
25db2bbb13
commit
75e9a2e218
|
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@ -308,12 +308,14 @@ minimization converges. Note that this means a dump will not be
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performed on the initial timestep after the dump command is invoked,
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if the current timestep is not a multiple of N. This behavior can be
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changed via the <A HREF = "dump_modify.html">dump_modify first</A> command, which
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can be useful if the dump command is invoked after a minimization
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can also be useful if the dump command is invoked after a minimization
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ended on an arbitrary timestep. N can be changed between runs by
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using the <A HREF = "dump_modify.html">dump_modify every</A> command (not allowed
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for <I>dcd</I> style). The <A HREF = "dump_modify.html">dump_modify every</A> command
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also allows a variable to be used to determine the sequence of
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timesteps on which dump files are written.
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timesteps on which dump files are written. In this mode a dump on the
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first timestep of a run will also not be written unless the
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<A HREF = "dump_modify.html">dump_modify first</A> command is used.
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</P>
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<P>The specified filename determines how the dump file(s) is written.
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The default is to write one large text file, which is opened when the
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|
|
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@ -296,12 +296,14 @@ minimization converges. Note that this means a dump will not be
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|||
performed on the initial timestep after the dump command is invoked,
|
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if the current timestep is not a multiple of N. This behavior can be
|
||||
changed via the "dump_modify first"_dump_modify.html command, which
|
||||
can be useful if the dump command is invoked after a minimization
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can also be useful if the dump command is invoked after a minimization
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||||
ended on an arbitrary timestep. N can be changed between runs by
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using the "dump_modify every"_dump_modify.html command (not allowed
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for {dcd} style). The "dump_modify every"_dump_modify.html command
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also allows a variable to be used to determine the sequence of
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timesteps on which dump files are written.
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timesteps on which dump files are written. In this mode a dump on the
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first timestep of a run will also not be written unless the
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"dump_modify first"_dump_modify.html command is used.
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The specified filename determines how the dump file(s) is written.
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The default is to write one large text file, which is opened when the
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|
|
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@ -365,16 +365,22 @@ which should be specified as v_name, where name is the variable name.
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</P>
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<P>In this case, the variable is evaluated at the beginning of a run to
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determine the next timestep at which a dump snapshot will be written
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out. On that timestep, the variable will be evaluated again to
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out. On that timestep the variable will be evaluated again to
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determine the next timestep, etc. Thus the variable should return
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timestep values. See the stagger() and logfreq() and stride() math
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functions for <A HREF = "variable.html">equal-style variables</A>, as examples of
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useful functions to use in this context. Other similar math functions
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could easily be added as options for <A HREF = "variable.html">equal-style
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variables</A>. When using the variable option with the
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<I>every</I> keyword, you also need to use the <I>first</I> option if you want
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an initial snapshot written to the dump file. The <I>every</I> keyword
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cannot be used with the dump <I>dcd</I> style.
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variables</A>. Also see the next() function, which allows
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use of a file-style variable which reads successive values from a
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file, each time the variable is evaluated. Used with the <I>every</I>
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keyword, if the file contains a list of ascending timesteps, you can
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output snapshots whenever you wish.
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</P>
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<P>Note that when using the variable option with the <I>every</I> keyword, you
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need to use the <I>first</I> option if you want an initial snapshot written
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to the dump file. The <I>every</I> keyword cannot be used with the dump
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<I>dcd</I> style.
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</P>
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<P>For example, the following commands will
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write snapshots at timesteps 0,10,20,30,100,200,300,1000,2000,etc:
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@ -383,6 +389,25 @@ write snapshots at timesteps 0,10,20,30,100,200,300,1000,2000,etc:
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dump 1 all atom 100 tmp.dump
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dump_modify 1 every v_s first yes
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</PRE>
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<P>The following commands would write snapshots at the timesteps listed
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in file tmp.times:
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</P>
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<PRE>variable f file tmp.times
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variable s equal next(f)
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dump 1 all atom 100 tmp.dump
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dump_modify 1 every v_s
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</PRE>
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<P>IMPORTANT NOTE: When using a file-style variable with the <I>every</I>
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keyword, the file of timesteps must list a first timestep that is
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beyond the current timestep (e.g. it cannot be 0). And it must list
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one or more timesteps beyond the length of the run you perform. This
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is because the dump command will generate an error if the next
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timestep it reads from the file is not a value greater than the
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current timestep. Thus if you wanted output on steps 0,15,100 of a
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100-timestep run, the file should contain the values 15,100,101 and
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you should also use the dump_modify first command. Any final value >
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100 could be used in place of 101.
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</P>
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<HR>
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<P>The <I>first</I> keyword determines whether a dump snapshot is written on
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|
|
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@ -358,16 +358,22 @@ which should be specified as v_name, where name is the variable name.
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In this case, the variable is evaluated at the beginning of a run to
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determine the next timestep at which a dump snapshot will be written
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out. On that timestep, the variable will be evaluated again to
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out. On that timestep the variable will be evaluated again to
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determine the next timestep, etc. Thus the variable should return
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timestep values. See the stagger() and logfreq() and stride() math
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functions for "equal-style variables"_variable.html, as examples of
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useful functions to use in this context. Other similar math functions
|
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could easily be added as options for "equal-style
|
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variables"_variable.html. When using the variable option with the
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{every} keyword, you also need to use the {first} option if you want
|
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an initial snapshot written to the dump file. The {every} keyword
|
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cannot be used with the dump {dcd} style.
|
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variables"_variable.html. Also see the next() function, which allows
|
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use of a file-style variable which reads successive values from a
|
||||
file, each time the variable is evaluated. Used with the {every}
|
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keyword, if the file contains a list of ascending timesteps, you can
|
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output snapshots whenever you wish.
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|
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Note that when using the variable option with the {every} keyword, you
|
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need to use the {first} option if you want an initial snapshot written
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to the dump file. The {every} keyword cannot be used with the dump
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{dcd} style.
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For example, the following commands will
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write snapshots at timesteps 0,10,20,30,100,200,300,1000,2000,etc:
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@ -376,6 +382,25 @@ variable s equal logfreq(10,3,10)
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dump 1 all atom 100 tmp.dump
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dump_modify 1 every v_s first yes :pre
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The following commands would write snapshots at the timesteps listed
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in file tmp.times:
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variable f file tmp.times
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variable s equal next(f)
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dump 1 all atom 100 tmp.dump
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dump_modify 1 every v_s :pre
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IMPORTANT NOTE: When using a file-style variable with the {every}
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keyword, the file of timesteps must list a first timestep that is
|
||||
beyond the current timestep (e.g. it cannot be 0). And it must list
|
||||
one or more timesteps beyond the length of the run you perform. This
|
||||
is because the dump command will generate an error if the next
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timestep it reads from the file is not a value greater than the
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current timestep. Thus if you wanted output on steps 0,15,100 of a
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100-timestep run, the file should contain the values 15,100,101 and
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you should also use the dump_modify first command. Any final value >
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100 could be used in place of 101.
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:line
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The {first} keyword determines whether a dump snapshot is written on
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|
|
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@ -38,14 +38,15 @@ be used in an input script command as $a or $z. If it is multiple
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letters, it can be used as ${myTemp}.
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</P>
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<P>If multiple variables are used as arguments to the <I>next</I> command,
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then all must be of the same variable style: <I>index</I>, <I>loop</I>,
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then all must be of the same variable style: <I>index</I>, <I>loop</I>, <I>file</I>,
|
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<I>universe</I>, or <I>uloop</I>. An exception is that <I>universe</I>- and
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<I>uloop</I>-style variables can be mixed in the same <I>next</I> command.
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</P>
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<P>All the variables specified with the next command are incremented by
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one value from their respective list or values. <I>String-</I> or <I>atom</I>-
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or <I>equal</I>- or <I>world</I>-style variables cannot be used with the the
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next command, since they only store a single value.
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one value from their respective list of values. A <I>file</I>-style variable
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reads the next line from its associated file. <I>String-</I> or <I>atom</I>- or
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<I>equal</I>- or <I>world</I>-style variables cannot be used with the the next
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command, since they only store a single value.
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</P>
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<P>When any of the variables in the next command has no more values, a
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flag is set that causes the input script to skip the next
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@ -53,18 +54,19 @@ flag is set that causes the input script to skip the next
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a next command to exit. As explained in the <A HREF = "variable.html">variable</A>
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command, the variable that has exhausted its values is also deleted.
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This allows it to be used and re-defined later in the input script.
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<I>File</I>-style variables are exhausted when the end-of-file is reached.
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</P>
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<P>When the next command is used with <I>index</I>- or <I>loop</I>-style variables,
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the next value is assigned to the variable for all processors. When
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the next command is used with <I>universe</I>- or <I>uloop</I>-style variables,
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the next value is assigned to whichever processor partition executes
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the command first. All processors in the partition are assigned the
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same value. Running LAMMPS on multiple partitions of processors via
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the "-partition" command-line switch is described in <A HREF = "Section_start.html#start_7">this
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section</A> of the manual. <I>Universe</I>- and
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<I>uloop</I>-style variables are incremented using the files
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"tmp.lammps.variable" and "tmp.lammps.variable.lock" which you will
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see in your directory during such a LAMMPS run.
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<P>When the next command is used with <I>index</I>- or <I>loop</I>-style or
|
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<I>file</I>-style variables, the next value is assigned to the variable for
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all processors. When the next command is used with <I>universe</I>- or
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<I>uloop</I>-style variables, the next value is assigned to whichever
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processor partition executes the command first. All processors in the
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partition are assigned the same value. Running LAMMPS on multiple
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partitions of processors via the "-partition" command-line switch is
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described in <A HREF = "Section_start.html#start_7">this section</A> of the manual.
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<I>Universe</I>- and <I>uloop</I>-style variables are incremented using the
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files "tmp.lammps.variable" and "tmp.lammps.variable.lock" which you
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will see in your directory during such a LAMMPS run.
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</P>
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<P>Here is an example of running a series of simulations using the next
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command with an <I>index</I>-style variable. If this input script is named
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|
|
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32
doc/next.txt
32
doc/next.txt
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@ -35,14 +35,15 @@ be used in an input script command as $a or $z. If it is multiple
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letters, it can be used as $\{myTemp\}.
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If multiple variables are used as arguments to the {next} command,
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then all must be of the same variable style: {index}, {loop},
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then all must be of the same variable style: {index}, {loop}, {file},
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{universe}, or {uloop}. An exception is that {universe}- and
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{uloop}-style variables can be mixed in the same {next} command.
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All the variables specified with the next command are incremented by
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one value from their respective list or values. {String-} or {atom}-
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or {equal}- or {world}-style variables cannot be used with the the
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next command, since they only store a single value.
|
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one value from their respective list of values. A {file}-style variable
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reads the next line from its associated file. {String-} or {atom}- or
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{equal}- or {world}-style variables cannot be used with the the next
|
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command, since they only store a single value.
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When any of the variables in the next command has no more values, a
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flag is set that causes the input script to skip the next
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@ -50,18 +51,19 @@ flag is set that causes the input script to skip the next
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|||
a next command to exit. As explained in the "variable"_variable.html
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command, the variable that has exhausted its values is also deleted.
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This allows it to be used and re-defined later in the input script.
|
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{File}-style variables are exhausted when the end-of-file is reached.
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|
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When the next command is used with {index}- or {loop}-style variables,
|
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the next value is assigned to the variable for all processors. When
|
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the next command is used with {universe}- or {uloop}-style variables,
|
||||
the next value is assigned to whichever processor partition executes
|
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the command first. All processors in the partition are assigned the
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same value. Running LAMMPS on multiple partitions of processors via
|
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the "-partition" command-line switch is described in "this
|
||||
section"_Section_start.html#start_7 of the manual. {Universe}- and
|
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{uloop}-style variables are incremented using the files
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"tmp.lammps.variable" and "tmp.lammps.variable.lock" which you will
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see in your directory during such a LAMMPS run.
|
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When the next command is used with {index}- or {loop}-style or
|
||||
{file}-style variables, the next value is assigned to the variable for
|
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all processors. When the next command is used with {universe}- or
|
||||
{uloop}-style variables, the next value is assigned to whichever
|
||||
processor partition executes the command first. All processors in the
|
||||
partition are assigned the same value. Running LAMMPS on multiple
|
||||
partitions of processors via the "-partition" command-line switch is
|
||||
described in "this section"_Section_start.html#start_7 of the manual.
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{Universe}- and {uloop}-style variables are incremented using the
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files "tmp.lammps.variable" and "tmp.lammps.variable.lock" which you
|
||||
will see in your directory during such a LAMMPS run.
|
||||
|
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Here is an example of running a series of simulations using the next
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command with an {index}-style variable. If this input script is named
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|
|
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@ -17,7 +17,7 @@
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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>equal</I> or <I>atom</I>
|
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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>file</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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@ -39,6 +39,7 @@
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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>file</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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@ -59,7 +60,7 @@
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bound(group,xmin,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), gmask(x), rmask(x), grmask(x,y)
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special functions = sum(x), min(x), max(x), ave(x), trap(x), gmask(x), rmask(x), grmask(x,y), next(x)
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atom value = mass[i], type[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i]
|
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atom vector = mass, type, x, y, z, vx, vy, vz, fx, fy, fz
|
||||
compute references = c_ID, c_ID[i], c_ID[i][j]
|
||||
|
|
@ -79,6 +80,7 @@ variable b equal xcm(mol1,x)/2.0
|
|||
variable b equal c_myTemp
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variable b atom x*y/vol
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variable foo string myfile
|
||||
variable f file values.txt
|
||||
variable temp world 300.0 310.0 320.0 ${Tfinal}
|
||||
variable x universe 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
|
||||
variable x uloop 15 pad
|
||||
|
|
@ -154,13 +156,13 @@ 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
|
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"LoopVar" is one or more characters.
|
||||
</P>
|
||||
<P>As described below, for variable styles <I>index</I>, <I>loop</I>, <I>universe</I>,
|
||||
and <I>uloop</I>, which string is assigned to a variable can be incremented
|
||||
via the <A HREF = "next.html">next</A> command. When there are no more strings to
|
||||
assign, the variable is exhausted and a flag is set that causes the
|
||||
next <A HREF = "jump.html">jump</A> command encountered in the input script to be
|
||||
skipped. This enables the construction of simple loops in the input
|
||||
script that are iterated over and then exited from.
|
||||
<P>As described below, for variable styles <I>index</I>, <I>loop</I>, <I>file</I>,
|
||||
<I>universe</I>, and <I>uloop</I>, which string is assigned to a variable can be
|
||||
incremented via the <A HREF = "next.html">next</A> command. When there are no more
|
||||
strings to assign, the variable is exhausted and a flag is set that
|
||||
causes the next <A HREF = "jump.html">jump</A> command encountered in the input
|
||||
script to be skipped. This enables the construction of simple loops
|
||||
in the input script that are iterated over and then exited from.
|
||||
</P>
|
||||
<P>As explained above, an exhausted variable can be re-used in an input
|
||||
script. The <I>delete</I> style also removes the variable, the same as if
|
||||
|
|
@ -235,6 +237,32 @@ 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
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script.
|
||||
</P>
|
||||
<P>For the <I>string</I> style, a single string is assigned to the variable.
|
||||
The only difference between this and using the <I>index</I> style with a
|
||||
single string is that a variable with <I>string</I> style can be redefined.
|
||||
E.g. by another command later in the input script, or if the script is
|
||||
read again in a loop.
|
||||
</P>
|
||||
<P>For the <I>file</I> style, a filename is provided which contains a list of
|
||||
strings to assign to the variable, one per line. The strings can be
|
||||
numeric values if desired; see the discussion of the next() function
|
||||
below for equal-style variables, which will convert the string of a
|
||||
file-style variable into a numeric value in a formula.
|
||||
</P>
|
||||
<P>When a file-style variable is defined, the file is opened and the
|
||||
string on the first line is read and stored with the variable. This
|
||||
means the variable can then be evaluated as many times as desired and
|
||||
will return that string. There are two ways to cause the next string
|
||||
from the file to be read: use the <A HREF = "next.html">next</A> command or the
|
||||
next() function in an equal- or atom-style variable, as discussed
|
||||
below.
|
||||
</P>
|
||||
<P>The rules for formatting the file are as follows. A comment character
|
||||
"#" can be used anywhere on a line; text starting with the comment
|
||||
character is stripped. Blank lines are skipped. The first "word" of
|
||||
a non-blank line, delimited by white space, is the "string" assigned
|
||||
to the variable.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>For the <I>equal</I> and <I>atom</I> styles, a single string is specified which
|
||||
|
|
@ -279,7 +307,7 @@ references to other variables.
|
|||
<TR><TD >Math functions</TD><TD > sqrt(x), exp(x), ln(x), log(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), stride(x,y,z), 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), gmask(x), rmask(x), grmask(x,y)</TD></TR>
|
||||
<TR><TD >Special functions</TD><TD > sum(x), min(x), max(x), ave(x), trap(x), gmask(x), rmask(x), grmask(x,y), next(x)</TD></TR>
|
||||
<TR><TD >Atom values</TD><TD > mass[i], type[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i]</TD></TR>
|
||||
<TR><TD >Atom vectors</TD><TD > mass, type, x, y, z, vx, vy, vz, fx, fy, fz</TD></TR>
|
||||
<TR><TD >Compute references</TD><TD > c_ID, c_ID[i], c_ID[i][j]</TD></TR>
|
||||
|
|
@ -559,6 +587,20 @@ 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 variable. Each
|
||||
time the next() function is invoked (i.e. each time the equal-style or
|
||||
atom-style variable is evaluated), the current string value stored by
|
||||
the file-style variable is converted to a numeric value returned by
|
||||
the function, and the next value from 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. Since the file-style variable reads and stores the
|
||||
first line of the file when it is defined in the input script, this is
|
||||
the value that will be returned the first time the next() function is
|
||||
invoked. If next() is invoked more times than there are lines in the
|
||||
file, the value for the last line is repeatedly returned.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<H4>Atom Values and Vectors
|
||||
|
|
@ -649,20 +691,26 @@ the doc pages for individual fix commands for details.
|
|||
|
||||
<H4>Variable References
|
||||
</H4>
|
||||
<P>Variable references access quantities calulated by other variables,
|
||||
which will cause those variables to be evaluated. The name in the
|
||||
reference should be replaced by the name of a variable defined
|
||||
elsewhere in the input script. As discussed on this doc page,
|
||||
atom-style variables generate a per-atom vector of values; all other
|
||||
variable styles generate a global scalar value. An equal-style
|
||||
variable can only use scalar values, which means another equal-style
|
||||
variable or an element of an atom-style variable. Atom-style
|
||||
variables can use the same scalar values. They can also use other
|
||||
atom-style variables.
|
||||
<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 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 (unless only a single value from the atom-style 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
|
||||
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 vectors, never both.
|
||||
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>
|
||||
|
|
|
|||
|
|
@ -13,7 +13,7 @@ variable command :h3
|
|||
variable name style args ... :pre
|
||||
|
||||
name = name of variable to define :ulb,l
|
||||
style = {delete} or {index} or {loop} or {world} or {universe} or {uloop} or {string} or {equal} or {atom} :l
|
||||
style = {delete} or {index} or {loop} or {world} or {universe} or {uloop} or {string} or {file} or {equal} or {atom} :l
|
||||
{delete} = no args
|
||||
{index} args = one or more strings
|
||||
{loop} args = N
|
||||
|
|
@ -34,6 +34,7 @@ style = {delete} or {index} or {loop} or {world} or {universe} or {uloop} or {st
|
|||
N = integer size of loop
|
||||
pad = all values will be same length, e.g. 001, 002, ..., 100
|
||||
{string} arg = one string
|
||||
{file} arg = filename
|
||||
{equal} or {atom} args = one formula containing numbers, thermo keywords, math operations, group functions, atom values and vectors, compute/fix/variable references
|
||||
numbers = 0.0, 100, -5.4, 2.8e-4, etc
|
||||
constants = PI
|
||||
|
|
@ -54,7 +55,7 @@ style = {delete} or {index} or {loop} or {world} or {universe} or {uloop} or {st
|
|||
bound(group,xmin,region), gyration(group,region), ke(group,reigon),
|
||||
angmom(group,dim,region), torque(group,dim,region),
|
||||
inertia(group,dimdim,region), omega(group,dim,region)
|
||||
special functions = sum(x), min(x), max(x), ave(x), trap(x), gmask(x), rmask(x), grmask(x,y)
|
||||
special functions = sum(x), min(x), max(x), ave(x), trap(x), gmask(x), rmask(x), grmask(x,y), next(x)
|
||||
atom value = mass\[i\], type\[i\], x\[i\], y\[i\], z\[i\], vx\[i\], vy\[i\], vz\[i\], fx\[i\], fy\[i\], fz\[i\]
|
||||
atom vector = mass, type, x, y, z, vx, vy, vz, fx, fy, fz
|
||||
compute references = c_ID, c_ID\[i\], c_ID\[i\]\[j\]
|
||||
|
|
@ -73,6 +74,7 @@ variable b equal xcm(mol1,x)/2.0
|
|||
variable b equal c_myTemp
|
||||
variable b atom x*y/vol
|
||||
variable foo string myfile
|
||||
variable f file values.txt
|
||||
variable temp world 300.0 310.0 320.0 $\{Tfinal\}
|
||||
variable x universe 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
|
||||
variable x uloop 15 pad
|
||||
|
|
@ -148,13 +150,13 @@ 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 then exited from.
|
||||
As described below, for variable styles {index}, {loop}, {file},
|
||||
{universe}, and {uloop}, which string is assigned to a variable can be
|
||||
incremented via the "next"_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 then exited from.
|
||||
|
||||
As explained above, an exhausted variable can be re-used in an input
|
||||
script. The {delete} style also removes the variable, the same as if
|
||||
|
|
@ -229,6 +231,32 @@ strings are the integers from 1 to N. This allows generation of long
|
|||
list of runs (e.g. 1000) without having to list N strings in the input
|
||||
script.
|
||||
|
||||
For the {string} style, a single string is assigned to the variable.
|
||||
The only difference between this and using the {index} style with a
|
||||
single string is that a variable with {string} style can be redefined.
|
||||
E.g. by another command later in the input script, or if the script is
|
||||
read again in a loop.
|
||||
|
||||
For the {file} style, a filename is provided which contains a list of
|
||||
strings to assign to the variable, one per line. The strings can be
|
||||
numeric values if desired; see the discussion of the next() function
|
||||
below for equal-style variables, which will convert the string of a
|
||||
file-style variable into a numeric value in a formula.
|
||||
|
||||
When a file-style variable is defined, the file is opened and the
|
||||
string on the first line is read and stored with the variable. This
|
||||
means the variable can then be evaluated as many times as desired and
|
||||
will return that string. There are two ways to cause the next string
|
||||
from the file to be read: use the "next"_next.html command or the
|
||||
next() function in an equal- or atom-style variable, as discussed
|
||||
below.
|
||||
|
||||
The rules for formatting the file are as follows. A comment character
|
||||
"#" can be used anywhere on a line; text starting with the comment
|
||||
character is stripped. Blank lines are skipped. The first "word" of
|
||||
a non-blank line, delimited by white space, is the "string" assigned
|
||||
to the variable.
|
||||
|
||||
:line
|
||||
|
||||
For the {equal} and {atom} styles, a single string is specified which
|
||||
|
|
@ -279,7 +307,7 @@ Region functions: count(ID,IDR), mass(ID,IDR), charge(ID,IDR), \
|
|||
bound(ID,dir,IDR), gyration(ID,IDR), ke(ID,IDR), \
|
||||
angmom(ID,dim,IDR), torque(ID,dim,IDR), \
|
||||
inertia(ID,dimdim,IDR), omega(ID,dim,IDR)
|
||||
Special functions: sum(x), min(x), max(x), ave(x), trap(x), gmask(x), rmask(x), grmask(x,y)
|
||||
Special functions: sum(x), min(x), max(x), ave(x), trap(x), gmask(x), rmask(x), grmask(x,y), next(x)
|
||||
Atom values: mass\[i\], type\[i\], x\[i\], y\[i\], z\[i\], \
|
||||
vx\[i\], vy\[i\], vz\[i\], fx\[i\], fy\[i\], fz\[i\]
|
||||
Atom vectors: mass, type, x, y, z, vx, vy, vz, fx, fy, fz
|
||||
|
|
@ -559,6 +587,20 @@ and the second is a region ID. It can only be used in atom-style
|
|||
variables. It returns a 1 for atoms that are in both the group and
|
||||
region, and a 0 for atoms that are not in both.
|
||||
|
||||
The next(x) function takes 1 argument which is a variable ID (not
|
||||
"v_foo", just "foo"). It must be for a file-style variable. Each
|
||||
time the next() function is invoked (i.e. each time the equal-style or
|
||||
atom-style variable is evaluated), the current string value stored by
|
||||
the file-style variable is converted to a numeric value returned by
|
||||
the function, and the next value from 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. Since the file-style variable reads and stores the
|
||||
first line of the file when it is defined in the input script, this is
|
||||
the value that will be returned the first time the next() function is
|
||||
invoked. If next() is invoked more times than there are lines in the
|
||||
file, the value for the last line is repeatedly returned.
|
||||
|
||||
:line
|
||||
|
||||
Atom Values and Vectors :h4
|
||||
|
|
@ -645,20 +687,26 @@ the doc pages for individual fix commands for details.
|
|||
|
||||
Variable References :h4
|
||||
|
||||
Variable references access quantities calulated by other variables,
|
||||
which will cause those variables to be evaluated. The name in the
|
||||
reference should be replaced by the name of a variable defined
|
||||
elsewhere in the input script. As discussed on this doc page,
|
||||
atom-style variables generate a per-atom vector of values; all other
|
||||
variable styles generate a global scalar value. An equal-style
|
||||
variable can only use scalar values, which means another equal-style
|
||||
variable or an element of an atom-style variable. Atom-style
|
||||
variables can use the same scalar values. They can also use other
|
||||
atom-style variables.
|
||||
Variable references access quantities stored or calculated by other
|
||||
variables, which will cause those variables to be evaluated. The name
|
||||
in the reference should be replaced by the name of a variable defined
|
||||
elsewhere in the input script.
|
||||
|
||||
As discussed on this doc page, equal-style variables generate a global
|
||||
scalar numeric value; atom-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 (unless only a single value from the atom-style 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
|
||||
variables.
|
||||
|
||||
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 vectors, never both.
|
||||
produce only a global scalar or a per-atom vector, never both.
|
||||
|
||||
v_name: scalar, or per-atom vector
|
||||
v_name\[I\]: atom I's value in per-atom vector :tb(s=:)
|
||||
|
|
|
|||
Loading…
Reference in New Issue