diff --git a/doc/src/dump_modify.rst b/doc/src/dump_modify.rst index 0dcb4f198f..a1f12b9eb9 100644 --- a/doc/src/dump_modify.rst +++ b/doc/src/dump_modify.rst @@ -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 ` command or :doc:`dump_modify every ` 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 ` 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 -` doc:`dump_modify every/time ` 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. +` or doc:`dump_modify every/time ` 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 ` 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 ` 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 ` 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