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fix a couple typos and alphabetizing error

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This commit is contained in:
Steve Plimpton
2022-07-28 13:31:58 -06:00
parent 348feddcb6
commit a4f4efcea0
1 changed files with 30 additions and 29 deletions
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59
doc/src/dump_modify.rst
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@ -178,6 +178,28 @@ extra buffering.
----------
The *colname* keyword can be used to change the default header keyword
for dump styles: *atom*, *custom*, and *cfg* and their compressed, ADIOS,
and MPIIO variants. The setting for *ID string* replaces the default
text with the provided string. *ID* can be a positive integer when it
represents the column number counting from the left, a negative integer
when it represents the column number from the right (i.e. -1 is the last
column/keyword), or a custom dump keyword (or compute, fix, property, or
variable reference) and then it replaces the string for that specific
keyword. For *atom* dump styles only the keywords "id", "type", "x",
"y", "z", "ix", "iy", "iz" can be accessed via string regardless of
whether scaled or unwrapped coordinates were enabled or disabled, and
it always assumes 8 columns for indexing regardless of whether image
flags are enabled or not. For dump style *cfg* only changes to the
"auxiliary" keywords (6th or later keyword) will become visible.
The *colname* keyword can be used multiple times. If multiple *colname*
settings refer to the same keyword, the last setting has precedence. A
setting of *default* clears all previous settings, reverting all values
to their default names.
----------
The *delay* keyword applies to all dump styles. No snapshots will be
output until the specified *Dstep* timestep or later. Specifying
*Dstep* < 0 is the same as turning off the delay setting. This is a
@ -359,7 +381,7 @@ always occur if the current timestep is a multiple of $N$, the
frequency specified in the :doc:`dump <dump>` command or
:doc:`dump_modify every <dump_modify>` command, including timestep 0.
It will also always occur if the current simulation time is a multiple
of *Delta*, the time interval specified in the doc:`dump_modify
of *Delta*, the time interval specified in the :doc:`dump_modify
every/time <dump_modify>` command.
But if this is not the case, a dump snapshot will only be written if
@ -367,10 +389,10 @@ the setting of this keyword is *yes*\ . If it is *no*, which is the
default, then it will not be written.
Note that if the argument to the :doc:`dump_modify every
<dump_modify>` doc:`dump_modify every/time <dump_modify>` commands is
a variable and not a numeric value, then specifying *first yes* is the
only way to write a dump snapshot on the first timestep after the dump
command is invoked.
<dump_modify>` or doc:`dump_modify every/time <dump_modify>` commands
is a variable and not a numeric value, then specifying *first yes* is
the only way to write a dump snapshot on the first timestep after the
dump command is invoked.
----------
@ -382,28 +404,6 @@ performed with dump style *xtc*\ .
----------
The *colname* keyword can be used to change the default header keyword
for dump styles: *atom*, *custom*, and *cfg* and their compressed, ADIOS,
and MPIIO variants. The setting for *ID string* replaces the default
text with the provided string. *ID* can be a positive integer when it
represents the column number counting from the left, a negative integer
when it represents the column number from the right (i.e. -1 is the last
column/keyword), or a custom dump keyword (or compute, fix, property, or
variable reference) and then it replaces the string for that specific
keyword. For *atom* dump styles only the keywords "id", "type", "x",
"y", "z", "ix", "iy", "iz" can be accessed via string regardless of
whether scaled or unwrapped coordinates were enabled or disabled, and
it always assumes 8 columns for indexing regardless of whether image
flags are enabled or not. For dump style *cfg* only changes to the
"auxiliary" keywords (6th or later keyword) will become visible.
The *colname* keyword can be used multiple times. If multiple *colname*
settings refer to the same keyword, the last setting has precedence. A
setting of *default* clears all previous settings, reverting all values
to their default names.
----------
The *format* keyword can be used to change the default numeric format output
by the text-based dump styles: *atom*, *local*, *custom*, *cfg*, and
*xyz* styles, and their MPIIO variants. Only the *line* or *none*
@ -747,8 +747,9 @@ are written to the dump file or included in the image. The possible
attributes that can be tested for are the same as those that can be
specified in the :doc:`dump custom <dump>` command, with the exception
of the *element* attribute, since it is not a numeric value. Note
that a different attributes can be used than those output by the :doc:`dump custom <dump>` command. E.g. you can output the coordinates and
stress of atoms whose energy is above some threshold.
that a different attributes can be used than those output by the
:doc:`dump custom <dump>` command. E.g. you can output the
coordinates and stress of atoms whose energy is above some threshold.
If an atom-style variable is used as the attribute, then it can
produce continuous numeric values or effective Boolean 0/1 values