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update docs

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This commit is contained in:
Axel Kohlmeyer
2022-04-01 15:17:10 -04:00
parent fb9316701b
commit 49abd0d269
2 changed files with 37 additions and 9 deletions
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32
doc/src/dump_modify.rst
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@ -26,6 +26,10 @@ Syntax
N = index of frame written upon first dump
*balance* arg = *yes* or *no*
*buffer* arg = *yes* or *no*
*colname* values = ID string, or *default*
string = new column header name
ID = integer from 1 to N, or integer from -1 to -N, where N = # of quantities being output
*or* a thermo keyword or reference to compute, fix, property or variable.
*delay* arg = Dstep
Dstep = delay output until this timestep
*element* args = E1 E2 ... EN, where N = # of atom types
@ -40,9 +44,10 @@ Syntax
Np = write one file for every this many processors
*first* arg = *yes* or *no*
*flush* arg = *yes* or *no*
*format* args = *line* string, *int* string, *float* string, M string, or *none*
*format* args = *line* string, *int* string, *float* string, ID string, or *none*
string = C-style format string
M = integer from 1 to N, where N = # of per-atom quantities being output
ID = integer from 1 to N, or integer from -1 to -N, where N = # of quantities being output
*or* a thermo keyword or reference to compute, fix, property or variable.
*header* arg = *yes* or *no*
*yes* to write the header
*no* to not write the header
@ -375,6 +380,29 @@ 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 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 thermo 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 coodinates 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 the "auxiliary"
keywords (6th or later keyword) may be changed and the column indexing
considers only them (i.e. the 6th keyword is the the 1st column).
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*

14
doc/src/thermo_modify.rst
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@ -157,15 +157,15 @@ The *colname* keyword can be used to change the default header keyword
for a column or field of thermodynamic output. 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 then it represents the column number
from the right (i.e. -1 is the last column/keyword), or a thermo keyword
(or compute, fix, property, or variable reference) and then it replaces
the string for that specific thermo keyword.
the left, a negative integer when it represents the column number from
the right (i.e. -1 is the last column/keyword), or a thermo keyword (or
compute, fix, property, or variable reference) and then it replaces the
string for that specific thermo keyword.
The *colname* keyword can be used multiple times. If multiple *colname*
settings refer to the same keyword, the last setting has precedence.
the default setting is used. A setting of *default* clears all previous
settings, reverting all values to their default format.
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 values.
The *format* keyword can be used to change the default numeric format of
any of quantities the :doc:`thermo_style <thermo_style>` command