mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10327 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
b8208f582c
commit
6755d5b44f
|
|
@ -43,10 +43,12 @@ then all must be of the same variable style: <I>index</I>, <I>loop</I>, <I>file<
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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 of values. A <I>file</I>-style variable
|
||||
reads the next line from its associated file. <I>String-</I> or <I>atom</I>- or
|
||||
<I>equal</I>- or <I>world</I>-style variables cannot be used with the the next
|
||||
command, since they only store a single value.
|
||||
one value from their respective list of values. A <I>file</I>-style
|
||||
variable reads the next line from its associated file. An
|
||||
<I>atomfile</I>-style variable reads the next set of lines (one per atom)
|
||||
from its associated file. <I>String-</I> or <I>atom</I>- or <I>equal</I>- or
|
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<I>world</I>-style variables cannot be used with the the next 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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|
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@ -54,19 +56,24 @@ 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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<I>File</I>-style and <I>atomfile</I>-style variables are exhausted when the
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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 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>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>file</I>-style variables, the next line is
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read from its file and the string assigned to the variable. When the
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next command is used with <I>atomfile</I>-style variables, the next set of
|
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per-atom values is read from its file and assigned to the variable.
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When the next command is used with <I>universe</I>- or <I>uloop</I>-style
|
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variables, the next value is assigned to whichever processor partition
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executes the command first. All processors in the partition are
|
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assigned the same value. Running LAMMPS on multiple partitions of
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processors via the "-partition" command-line switch is described in
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<A HREF = "Section_start.html#start_7">this section</A> of the manual. <I>Universe</I>-
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and <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>
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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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39
doc/next.txt
39
doc/next.txt
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@ -40,10 +40,12 @@ then all must be of the same variable style: {index}, {loop}, {file},
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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 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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one value from their respective list of values. A {file}-style
|
||||
variable reads the next line from its associated file. An
|
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{atomfile}-style variable reads the next set of lines (one per atom)
|
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from its associated file. {String-} or {atom}- or {equal}- or
|
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{world}-style variables cannot be used with the the next command,
|
||||
since they only store a single value.
|
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|
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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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|
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@ -51,19 +53,24 @@ 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
|
||||
command, the variable that has exhausted its values is also deleted.
|
||||
This allows it to be used and re-defined later in the input script.
|
||||
{File}-style variables are exhausted when the end-of-file is reached.
|
||||
{File}-style and {atomfile}-style variables are exhausted when the
|
||||
end-of-file is reached.
|
||||
|
||||
When the next command is used with {index}- or {loop}-style or
|
||||
{file}-style variables, the next value is assigned to the variable for
|
||||
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.
|
||||
{Universe}- and {uloop}-style variables are incremented using the
|
||||
files "tmp.lammps.variable" and "tmp.lammps.variable.lock" which you
|
||||
will see in your directory during such a LAMMPS run.
|
||||
When the next command is used with {index}- or {loop}-style variables,
|
||||
the next value is assigned to the variable for all processors. When
|
||||
the next command is used with {file}-style variables, the next line is
|
||||
read from its file and the string assigned to the variable. When the
|
||||
next command is used with {atomfile}-style variables, the next set of
|
||||
per-atom values is read from its file and assigned to the variable.
|
||||
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. {Universe}-
|
||||
and {uloop}-style variables are incremented using the files
|
||||
"tmp.lammps.variable" and "tmp.lammps.variable.lock" which you will
|
||||
see in your directory during such a LAMMPS run.
|
||||
|
||||
Here is an example of running a series of simulations using the next
|
||||
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>file</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>atomfile</I> or <I>equal</I> or <I>atom</I>
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|
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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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|
@ -40,6 +40,7 @@
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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>atomfile</I> arg = filename
|
||||
<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
|
||||
numbers = 0.0, 100, -5.4, 2.8e-4, etc
|
||||
constants = PI
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||||
|
|
@ -106,7 +107,9 @@ 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>
|
||||
command) or used as input to an averaging fix (see the <A HREF = "fix_ave_spatial.html">fix
|
||||
ave/spatial</A> and <A HREF = "fix_ave_atom.html">fix ave/atom</A>
|
||||
commands).
|
||||
commands). Variables of style <I>atomfile</I> can be used similar to
|
||||
atom-style variables, except they get their per-atom values from a
|
||||
file rather than from a formula.
|
||||
</P>
|
||||
<P>In the discussion that follows, the "name" of the variable is the
|
||||
arbitrary string that is the 1st argument in the variable command.
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||||
|
|
@ -245,7 +248,7 @@ 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
|
||||
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>
|
||||
|
|
@ -263,6 +266,36 @@ 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>
|
||||
<P>For the <I>atomfile</I> style, a filename is provided which contains one or
|
||||
more sets of values, to assign on a per-atom basis to the variable.
|
||||
The format of the file is described below.
|
||||
</P>
|
||||
<P>When an atomfile-style variable is defined, the file is opened and the
|
||||
first set of per-atom values are read and stored with the variable.
|
||||
This means the variable can then be evaluated as many times as desired
|
||||
and will return those values. There are two ways to cause the next
|
||||
set of per-atom values from the file to be read: use the
|
||||
<A HREF = "next.html">next</A> command or the next() function in an atom-style
|
||||
variable, as discussed below.
|
||||
</P>
|
||||
<P>The rules for formatting the file are as follows. Each time a set of
|
||||
per-atom values is read, a non-blank line is searched for in the file.
|
||||
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 read as
|
||||
the count N of per-atom lines to immediately follow. N can be be the
|
||||
total number of atoms in the system, or only a subset. The next N
|
||||
lines have the following format
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||||
</P>
|
||||
<PRE>ID value
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||||
</PRE>
|
||||
<P>where ID is an atom ID and value is the per-atom numeric value that
|
||||
will be assigned to that atom. IDs can be listed in any order.
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: Every time a set of per-atom lines is read, the value
|
||||
for all atoms is first set to 0.0. Thus values for atoms whose ID
|
||||
does not appear in the set, will remain 0.0.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>For the <I>equal</I> and <I>atom</I> styles, a single string is specified which
|
||||
|
|
@ -589,18 +622,29 @@ 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.
|
||||
"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>
|
||||
|
||||
|
|
@ -698,16 +742,16 @@ 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.
|
||||
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
|
||||
|
|
|
|||
|
|
@ -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 {file} or {equal} or {atom} :l
|
||||
style = {delete} or {index} or {loop} or {world} or {universe} or {uloop} or {string} or {file} or {atomfile} or {equal} or {atom} :l
|
||||
{delete} = no args
|
||||
{index} args = one or more strings
|
||||
{loop} args = N
|
||||
|
|
@ -35,6 +35,7 @@ style = {delete} or {index} or {loop} or {world} or {universe} or {uloop} or {st
|
|||
pad = all values will be same length, e.g. 001, 002, ..., 100
|
||||
{string} arg = one string
|
||||
{file} arg = filename
|
||||
{atomfile} 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
|
||||
|
|
@ -100,7 +101,9 @@ a formula which when evaluated produces one numeric value per atom
|
|||
which can be output to a dump file (see the "dump custom"_dump.html
|
||||
command) or used as input to an averaging fix (see the "fix
|
||||
ave/spatial"_fix_ave_spatial.html and "fix ave/atom"_fix_ave_atom.html
|
||||
commands).
|
||||
commands). Variables of style {atomfile} can be used similar to
|
||||
atom-style variables, except they get their per-atom values from a
|
||||
file rather than from a formula.
|
||||
|
||||
In the discussion that follows, the "name" of the variable is the
|
||||
arbitrary string that is the 1st argument in the variable command.
|
||||
|
|
@ -239,7 +242,7 @@ 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
|
||||
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.
|
||||
|
||||
|
|
@ -257,6 +260,36 @@ character is stripped. Blank lines are skipped. The first "word" of
|
|||
a non-blank line, delimited by white space, is the "string" assigned
|
||||
to the variable.
|
||||
|
||||
For the {atomfile} style, a filename is provided which contains one or
|
||||
more sets of values, to assign on a per-atom basis to the variable.
|
||||
The format of the file is described below.
|
||||
|
||||
When an atomfile-style variable is defined, the file is opened and the
|
||||
first set of per-atom values are read and stored with the variable.
|
||||
This means the variable can then be evaluated as many times as desired
|
||||
and will return those values. There are two ways to cause the next
|
||||
set of per-atom values from the file to be read: use the
|
||||
"next"_next.html command or the next() function in an atom-style
|
||||
variable, as discussed below.
|
||||
|
||||
The rules for formatting the file are as follows. Each time a set of
|
||||
per-atom values is read, a non-blank line is searched for in the file.
|
||||
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 read as
|
||||
the count N of per-atom lines to immediately follow. N can be be the
|
||||
total number of atoms in the system, or only a subset. The next N
|
||||
lines have the following format
|
||||
|
||||
ID value :pre
|
||||
|
||||
where ID is an atom ID and value is the per-atom numeric value that
|
||||
will be assigned to that atom. IDs can be listed in any order.
|
||||
|
||||
IMPORTANT NOTE: Every time a set of per-atom lines is read, the value
|
||||
for all atoms is first set to 0.0. Thus values for atoms whose ID
|
||||
does not appear in the set, will remain 0.0.
|
||||
|
||||
:line
|
||||
|
||||
For the {equal} and {atom} styles, a single string is specified which
|
||||
|
|
@ -589,18 +622,29 @@ 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.
|
||||
"v_foo", just "foo"). It must be for a file-style or atomfile-style
|
||||
variable. Each time the next() function is invoked (i.e. each time
|
||||
the equal-style or atom-style variable is evaluated), the following
|
||||
steps occur.
|
||||
|
||||
For file-style variables, the current string value stored by the
|
||||
file-style variable is converted to a numeric value and returned by
|
||||
the function. And the next string value in the file is read and
|
||||
stored. Note that if the line previously read from the file was not a
|
||||
numeric string, then it will typically evaluate to 0.0, which is
|
||||
likely not what you want.
|
||||
|
||||
For atomfile-style variables, the current per-atom values stored by
|
||||
the atomfile-style variable are returned by the function. And the
|
||||
next set of per-atom values in the file is read and stored.
|
||||
|
||||
Since file-style and atomfile-style variables read and store the first
|
||||
line of the file or first set of per-atoms values when they are
|
||||
defined in the input script, these are the value(s) that will be
|
||||
returned the first time the next() function is invoked. If next() is
|
||||
invoked more times than there are lines or sets of lines in the file,
|
||||
the variable is deleted, similar to how the "next"_next.html command
|
||||
operates.
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -694,16 +738,16 @@ 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.
|
||||
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.
|
||||
|
||||
Examples of different kinds of variable references are as follows.
|
||||
There is no ambiguity as to what a reference means, since variables
|
||||
|
|
|
|||
Loading…
Reference in New Issue