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sjplimp 2016-08-03 16:29:25 +00:00
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42
doc/html/_sources/dump_modify.txt
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@ -26,7 +26,9 @@ Syntax
*fileper* arg = Np
Np = write one file for every this many processors
*first* arg = *yes* or *no*
*format* arg = C-style format string for one line of output
*format* args = *line* string, *int* string, *float* string, M string, or *none*
string = C-style format string
M = integer from 1 to N, where N = # of per-atom quantities being output
*flush* arg = *yes* or *no*
*image* arg = *yes* or *no*
*label* arg = string
@ -106,7 +108,8 @@ Examples
.. parsed-literal::
dump_modify 1 format "%d %d %20.15g %g %g" scale yes
dump_modify 1 format line "%d %d %20.15g %g %g" scale yes
dump_modify 1 format float %20.15g scale yes
dump_modify myDump image yes scale no flush yes
dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2
dump_modify xtcdump precision 10000 sfactor 0.1
@ -283,6 +286,41 @@ performed with dump style *xtc*\ .
----------
The *format* keyword can be used to change the default numeric format
output by the text-based dump styles: *atom*\ , *custom*\ , *cfg*\ , and
*xyz* styles, and their MPIIO variants. Only the *line* or *none*
options can be used with the *atom* and *xyz* styles.
All the specified format strings are C-style formats, e.g. as used by
the C/C++ printf() command. The *line* keyword takes a single
argument which is the format string for an entire line of output for
each atoms, with N fields, which you must enclose in quotes if it is
more than one field. The *int* and *float* keywords take a single
format argument and are applied to all integer or floating-point
quantities output. The setting for *M string* also takes a single
format argument which is used for the Mth value output in each line,
e.g. the 5th column is output in high precision for "format 5
%20.15g".
The *format* keyword can be used multiple times. The precedence is
that for each value in a line of output, the *M* format (if specified)
is used, else the *int* or *float* setting (if specified) is used,
else the *line* setting (if specified) for that value is used, else
the default setting is used. A setting of *none* clears all previous
settings, reverting all values to their default format.
.. note::
Atom and molecule IDs are stored internally as 4-byte or 8-byte
signed integers, depending on how LAMMPS was compiled. When
specifying the *format int* option you can use a "%d"-style format
identifier in the format string and LAMMPS will convert this to the
corresponding 8-byte form it it is needed when outputting those
values. However, when specifying the *line* option or *format M
string* option for those values, you should specify a format string
appropriate for an 8-byte signed integer, e.g. one with "%ld", if
LAMMPS was compiled with the -DLAMMPS_BIGBIG option for 8-byte IDs.
The text-based dump styles have a default C-style format string which
simply specifies %d for integers and %g for floating-point values.
The *format* keyword can be used to override the default with a new

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doc/html/_sources/thermo_modify.txt
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@ -19,9 +19,9 @@ Syntax
*norm* value = *yes* or *no*
*flush* value = *yes* or *no*
*line* value = *one* or *multi*
*format* values = *int* string or *float* string or M string
M = integer from 1 to N, where N = # of quantities being printed
*format* values = *line* string, *int* string, *float* string, M string, or *none*
string = C-style format string
M = integer from 1 to N, where N = # of quantities being output
*temp* value = compute ID that calculates a temperature
*press* value = compute ID that calculates a pressure
@ -34,6 +34,7 @@ Examples
thermo_modify lost ignore flush yes
thermo_modify temp myTemp format 3 %15.8g
thermo_modify temp myTemp format line "%ld %g %g %15.8g"
thermo_modify line multi format float %g
Description
@ -100,30 +101,42 @@ is written to the log file. This insures the output in that file is
current (no buffering by the OS), even if LAMMPS halts before the
simulation completes.
The *line* keyword determines whether thermodynamics will be printed
as a series of numeric values on one line or in a multi-line format
with 3 quantities with text strings per line and a dashed-line header
The *line* keyword determines whether thermodynamics will be output as
a series of numeric values on one line or in a multi-line format with
3 quantities with text strings per line and a dashed-line header
containing the timestep and CPU time. This modify option overrides
the *one* and *multi* thermo_style settings.
The *format* keyword sets the numeric format of individual printed
quantities. The *int* and *float* keywords set the format for all
integer or floating-point quantities printed. The setting with a
numeric value M (e.g. format 5 %10.4g) sets the format of the Mth
value printed in each output line, e.g. the 5th column of output in
this case. If the format for a specific column has been set, it will
take precedent over the *int* or *float* setting.
The *format* keyword can be used to change the default numeric format
of any of quantities the :doc:`thermo_style <thermo_style>` command
outputs. All the specified format strings are C-style formats,
e.g. as used by the C/C++ printf() command. The *line* keyword takes
a single argument which is the format string for the entire line of
thermo output, with N fields, which you must enclose in quotes if it
is more than one field. The *int* and *float* keywords take a single
format argument and are applied to all integer or floating-point
quantities output. The setting for *M string* also takes a single
format argument which is used for the Mth value output in each line,
e.g. the 5th column of output is output in high precision for "format
5 %20.15g".
The *format* keyword can be used multiple times. The precedence is
that for each value in a line of output, the *M* format (if specified)
is used, else the *int* or *float* setting (if specified) is used,
else the *line* setting (if specified) for that value is used, else
the default setting is used. A setting of *none* clears all previous
settings, reverting all values to their default format.
.. note::
The thermo output values *step* and *atoms* are stored
internally as 8-byte signed integers, rather than the usual 4-byte
signed integers. When specifying the "format int" keyword you can use
signed integers. When specifying the *format int* option you can use
a "%d"-style format identifier in the format string and LAMMPS will
convert this to the corresponding "%lu" form when it is applied to
those keywords. However, when specifying the "format M string"
keyword for *step* and *natoms*\ , you should specify a string
appropriate for an 8-byte signed integer, e.g. one with "%ld".
convert this to the corresponding 8-byte form when it is applied to
those keywords. However, when specifying the *line* option or *format
M string* option for *step* and *natoms*\ , you should specify a format
string appropriate for an 8-byte signed integer, e.g. one with "%ld".
The *temp* keyword is used to determine how thermodynamic temperature
is calculated, which is used by all thermo quantities that require a

39
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@ -148,7 +148,9 @@
<em>fileper</em> arg = Np
Np = write one file for every this many processors
<em>first</em> arg = <em>yes</em> or <em>no</em>
<em>format</em> arg = C-style format string for one line of output
<em>format</em> args = <em>line</em> string, <em>int</em> string, <em>float</em> string, M string, or <em>none</em>
string = C-style format string
M = integer from 1 to N, where N = # of per-atom quantities being output
<em>flush</em> arg = <em>yes</em> or <em>no</em>
<em>image</em> arg = <em>yes</em> or <em>no</em>
<em>label</em> arg = string
@ -225,7 +227,8 @@
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dump_modify</span> <span class="mi">1</span> <span class="nb">format</span> <span class="s2">&quot;</span><span class="si">%d</span><span class="s2"> </span><span class="si">%d</span><span class="s2"> </span><span class="si">%20.15g</span><span class="s2"> </span><span class="si">%g</span><span class="s2"> </span><span class="si">%g</span><span class="s2">&quot;</span> <span class="n">scale</span> <span class="n">yes</span>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dump_modify</span> <span class="mi">1</span> <span class="nb">format</span> <span class="n">line</span> <span class="s2">&quot;</span><span class="si">%d</span><span class="s2"> </span><span class="si">%d</span><span class="s2"> </span><span class="si">%20.15g</span><span class="s2"> </span><span class="si">%g</span><span class="s2"> </span><span class="si">%g</span><span class="s2">&quot;</span> <span class="n">scale</span> <span class="n">yes</span>
<span class="n">dump_modify</span> <span class="mi">1</span> <span class="nb">format</span> <span class="nb">float</span> <span class="o">%</span><span class="mf">20.15</span><span class="n">g</span> <span class="n">scale</span> <span class="n">yes</span>
<span class="n">dump_modify</span> <span class="n">myDump</span> <span class="n">image</span> <span class="n">yes</span> <span class="n">scale</span> <span class="n">no</span> <span class="n">flush</span> <span class="n">yes</span>
<span class="n">dump_modify</span> <span class="mi">1</span> <span class="n">region</span> <span class="n">mySphere</span> <span class="n">thresh</span> <span class="n">x</span> <span class="o">&lt;</span> <span class="mf">0.0</span> <span class="n">thresh</span> <span class="n">epair</span> <span class="o">&gt;=</span> <span class="mf">3.2</span>
<span class="n">dump_modify</span> <span class="n">xtcdump</span> <span class="n">precision</span> <span class="mi">10000</span> <span class="n">sfactor</span> <span class="mf">0.1</span>
@ -355,6 +358,38 @@ the output in that file is current (no buffering by the OS), even if
LAMMPS halts before the simulation completes. Flushes cannot be
performed with dump style <em>xtc</em>.</p>
<hr class="docutils" />
<p>The <em>format</em> keyword can be used to change the default numeric format
output by the text-based dump styles: <em>atom</em>, <em>custom</em>, <em>cfg</em>, and
<em>xyz</em> styles, and their MPIIO variants. Only the <em>line</em> or <em>none</em>
options can be used with the <em>atom</em> and <em>xyz</em> styles.</p>
<p>All the specified format strings are C-style formats, e.g. as used by
the C/C++ printf() command. The <em>line</em> keyword takes a single
argument which is the format string for an entire line of output for
each atoms, with N fields, which you must enclose in quotes if it is
more than one field. The <em>int</em> and <em>float</em> keywords take a single
format argument and are applied to all integer or floating-point
quantities output. The setting for <em>M string</em> also takes a single
format argument which is used for the Mth value output in each line,
e.g. the 5th column is output in high precision for &#8220;format 5
%20.15g&#8221;.</p>
<p>The <em>format</em> keyword can be used multiple times. The precedence is
that for each value in a line of output, the <em>M</em> format (if specified)
is used, else the <em>int</em> or <em>float</em> setting (if specified) is used,
else the <em>line</em> setting (if specified) for that value is used, else
the default setting is used. A setting of <em>none</em> clears all previous
settings, reverting all values to their default format.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Atom and molecule IDs are stored internally as 4-byte or 8-byte
signed integers, depending on how LAMMPS was compiled. When
specifying the <em>format int</em> option you can use a &#8220;%d&#8221;-style format
identifier in the format string and LAMMPS will convert this to the
corresponding 8-byte form it it is needed when outputting those
values. However, when specifying the <em>line</em> option or <em>format M
string</em> option for those values, you should specify a format string
appropriate for an 8-byte signed integer, e.g. one with &#8220;%ld&#8221;, if
LAMMPS was compiled with the -DLAMMPS_BIGBIG option for 8-byte IDs.</p>
</div>
<p>The text-based dump styles have a default C-style format string which
simply specifies %d for integers and %g for floating-point values.
The <em>format</em> keyword can be used to override the default with a new

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@ -141,9 +141,9 @@ keyword = <em>lost</em> or <em>lost/bond</em> or <em>norm</em> or <em>flush</em>
<em>norm</em> value = <em>yes</em> or <em>no</em>
<em>flush</em> value = <em>yes</em> or <em>no</em>
<em>line</em> value = <em>one</em> or <em>multi</em>
<em>format</em> values = <em>int</em> string or <em>float</em> string or M string
M = integer from 1 to N, where N = # of quantities being printed
<em>format</em> values = <em>line</em> string, <em>int</em> string, <em>float</em> string, M string, or <em>none</em>
string = C-style format string
M = integer from 1 to N, where N = # of quantities being output
<em>temp</em> value = compute ID that calculates a temperature
<em>press</em> value = compute ID that calculates a pressure
</pre>
@ -152,6 +152,7 @@ keyword = <em>lost</em> or <em>lost/bond</em> or <em>norm</em> or <em>flush</em>
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">thermo_modify</span> <span class="n">lost</span> <span class="n">ignore</span> <span class="n">flush</span> <span class="n">yes</span>
<span class="n">thermo_modify</span> <span class="n">temp</span> <span class="n">myTemp</span> <span class="nb">format</span> <span class="mi">3</span> <span class="o">%</span><span class="mf">15.8</span><span class="n">g</span>
<span class="n">thermo_modify</span> <span class="n">temp</span> <span class="n">myTemp</span> <span class="nb">format</span> <span class="n">line</span> <span class="s2">&quot;</span><span class="si">%ld</span><span class="s2"> </span><span class="si">%g</span><span class="s2"> </span><span class="si">%g</span><span class="s2"> </span><span class="si">%15.8g</span><span class="s2">&quot;</span>
<span class="n">thermo_modify</span> <span class="n">line</span> <span class="n">multi</span> <span class="nb">format</span> <span class="nb">float</span> <span class="o">%</span><span class="n">g</span>
</pre></div>
</div>
@ -214,28 +215,39 @@ if this is not the case.</p>
is written to the log file. This insures the output in that file is
current (no buffering by the OS), even if LAMMPS halts before the
simulation completes.</p>
<p>The <em>line</em> keyword determines whether thermodynamics will be printed
as a series of numeric values on one line or in a multi-line format
with 3 quantities with text strings per line and a dashed-line header
<p>The <em>line</em> keyword determines whether thermodynamics will be output as
a series of numeric values on one line or in a multi-line format with
3 quantities with text strings per line and a dashed-line header
containing the timestep and CPU time. This modify option overrides
the <em>one</em> and <em>multi</em> thermo_style settings.</p>
<p>The <em>format</em> keyword sets the numeric format of individual printed
quantities. The <em>int</em> and <em>float</em> keywords set the format for all
integer or floating-point quantities printed. The setting with a
numeric value M (e.g. format 5 %10.4g) sets the format of the Mth
value printed in each output line, e.g. the 5th column of output in
this case. If the format for a specific column has been set, it will
take precedent over the <em>int</em> or <em>float</em> setting.</p>
<p>The <em>format</em> keyword can be used to change the default numeric format
of any of quantities the <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command
outputs. All the specified format strings are C-style formats,
e.g. as used by the C/C++ printf() command. The <em>line</em> keyword takes
a single argument which is the format string for the entire line of
thermo output, with N fields, which you must enclose in quotes if it
is more than one field. The <em>int</em> and <em>float</em> keywords take a single
format argument and are applied to all integer or floating-point
quantities output. The setting for <em>M string</em> also takes a single
format argument which is used for the Mth value output in each line,
e.g. the 5th column of output is output in high precision for &#8220;format
5 %20.15g&#8221;.</p>
<p>The <em>format</em> keyword can be used multiple times. The precedence is
that for each value in a line of output, the <em>M</em> format (if specified)
is used, else the <em>int</em> or <em>float</em> setting (if specified) is used,
else the <em>line</em> setting (if specified) for that value is used, else
the default setting is used. A setting of <em>none</em> clears all previous
settings, reverting all values to their default format.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The thermo output values <em>step</em> and <em>atoms</em> are stored
internally as 8-byte signed integers, rather than the usual 4-byte
signed integers. When specifying the &#8220;format int&#8221; keyword you can use
signed integers. When specifying the <em>format int</em> option you can use
a &#8220;%d&#8221;-style format identifier in the format string and LAMMPS will
convert this to the corresponding &#8220;%lu&#8221; form when it is applied to
those keywords. However, when specifying the &#8220;format M string&#8221;
keyword for <em>step</em> and <em>natoms</em>, you should specify a string
appropriate for an 8-byte signed integer, e.g. one with &#8220;%ld&#8221;.</p>
convert this to the corresponding 8-byte form when it is applied to
those keywords. However, when specifying the <em>line</em> option or <em>format
M string</em> option for <em>step</em> and <em>natoms</em>, you should specify a format
string appropriate for an 8-byte signed integer, e.g. one with &#8220;%ld&#8221;.</p>
</div>
<p>The <em>temp</em> keyword is used to determine how thermodynamic temperature
is calculated, which is used by all thermo quantities that require a

40
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@ -26,7 +26,9 @@ keyword = {append} or {buffer} or {element} or {every} or {fileper} or {first} o
{fileper} arg = Np
Np = write one file for every this many processors
{first} arg = {yes} or {no}
{format} arg = C-style format string for one line of output
{format} args = {line} string, {int} string, {float} string, M string, or {none}
string = C-style format string
M = integer from 1 to N, where N = # of per-atom quantities being output
{flush} arg = {yes} or {no}
{image} arg = {yes} or {no}
{label} arg = string
@ -99,7 +101,8 @@ keyword = {acolor} or {adiam} or {amap} or {backcolor} or {bcolor} or {bdiam} or
[Examples:]
dump_modify 1 format "%d %d %20.15g %g %g" scale yes
dump_modify 1 format line "%d %d %20.15g %g %g" scale yes
dump_modify 1 format float %20.15g scale yes
dump_modify myDump image yes scale no flush yes
dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2
dump_modify xtcdump precision 10000 sfactor 0.1
@ -254,6 +257,39 @@ performed with dump style {xtc}.
:line
The {format} keyword can be used to change the default numeric format
output by the text-based dump styles: {atom}, {custom}, {cfg}, and
{xyz} styles, and their MPIIO variants. Only the {line} or {none}
options can be used with the {atom} and {xyz} styles.
All the specified format strings are C-style formats, e.g. as used by
the C/C++ printf() command. The {line} keyword takes a single
argument which is the format string for an entire line of output for
each atoms, with N fields, which you must enclose in quotes if it is
more than one field. The {int} and {float} keywords take a single
format argument and are applied to all integer or floating-point
quantities output. The setting for {M string} also takes a single
format argument which is used for the Mth value output in each line,
e.g. the 5th column is output in high precision for "format 5
%20.15g".
The {format} keyword can be used multiple times. The precedence is
that for each value in a line of output, the {M} format (if specified)
is used, else the {int} or {float} setting (if specified) is used,
else the {line} setting (if specified) for that value is used, else
the default setting is used. A setting of {none} clears all previous
settings, reverting all values to their default format.
NOTE: Atom and molecule IDs are stored internally as 4-byte or 8-byte
signed integers, depending on how LAMMPS was compiled. When
specifying the {format int} option you can use a "%d"-style format
identifier in the format string and LAMMPS will convert this to the
corresponding 8-byte form it it is needed when outputting those
values. However, when specifying the {line} option or {format M
string} option for those values, you should specify a format string
appropriate for an 8-byte signed integer, e.g. one with "%ld", if
LAMMPS was compiled with the -DLAMMPS_BIGBIG option for 8-byte IDs.
The text-based dump styles have a default C-style format string which
simply specifies %d for integers and %g for floating-point values.
The {format} keyword can be used to override the default with a new

47
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@ -19,9 +19,9 @@ keyword = {lost} or {lost/bond} or {norm} or {flush} or {line} or {format} or {t
{norm} value = {yes} or {no}
{flush} value = {yes} or {no}
{line} value = {one} or {multi}
{format} values = {int} string or {float} string or M string
M = integer from 1 to N, where N = # of quantities being printed
{format} values = {line} string, {int} string, {float} string, M string, or {none}
string = C-style format string
M = integer from 1 to N, where N = # of quantities being output
{temp} value = compute ID that calculates a temperature
{press} value = compute ID that calculates a pressure :pre
:ule
@ -30,6 +30,7 @@ keyword = {lost} or {lost/bond} or {norm} or {flush} or {line} or {format} or {t
thermo_modify lost ignore flush yes
thermo_modify temp myTemp format 3 %15.8g
thermo_modify temp myTemp format line "%ld %g %g %15.8g"
thermo_modify line multi format float %g :pre
[Description:]
@ -94,28 +95,40 @@ is written to the log file. This insures the output in that file is
current (no buffering by the OS), even if LAMMPS halts before the
simulation completes.
The {line} keyword determines whether thermodynamics will be printed
as a series of numeric values on one line or in a multi-line format
with 3 quantities with text strings per line and a dashed-line header
The {line} keyword determines whether thermodynamics will be output as
a series of numeric values on one line or in a multi-line format with
3 quantities with text strings per line and a dashed-line header
containing the timestep and CPU time. This modify option overrides
the {one} and {multi} thermo_style settings.
The {format} keyword sets the numeric format of individual printed
quantities. The {int} and {float} keywords set the format for all
integer or floating-point quantities printed. The setting with a
numeric value M (e.g. format 5 %10.4g) sets the format of the Mth
value printed in each output line, e.g. the 5th column of output in
this case. If the format for a specific column has been set, it will
take precedent over the {int} or {float} setting.
The {format} keyword can be used to change the default numeric format
of any of quantities the "thermo_style"_thermo_style.html command
outputs. All the specified format strings are C-style formats,
e.g. as used by the C/C++ printf() command. The {line} keyword takes
a single argument which is the format string for the entire line of
thermo output, with N fields, which you must enclose in quotes if it
is more than one field. The {int} and {float} keywords take a single
format argument and are applied to all integer or floating-point
quantities output. The setting for {M string} also takes a single
format argument which is used for the Mth value output in each line,
e.g. the 5th column of output is output in high precision for "format
5 %20.15g".
The {format} keyword can be used multiple times. The precedence is
that for each value in a line of output, the {M} format (if specified)
is used, else the {int} or {float} setting (if specified) is used,
else the {line} setting (if specified) for that value is used, else
the default setting is used. A setting of {none} clears all previous
settings, reverting all values to their default format.
NOTE: The thermo output values {step} and {atoms} are stored
internally as 8-byte signed integers, rather than the usual 4-byte
signed integers. When specifying the "format int" keyword you can use
signed integers. When specifying the {format int} option you can use
a "%d"-style format identifier in the format string and LAMMPS will
convert this to the corresponding "%lu" form when it is applied to
those keywords. However, when specifying the "format M string"
keyword for {step} and {natoms}, you should specify a string
appropriate for an 8-byte signed integer, e.g. one with "%ld".
convert this to the corresponding 8-byte form when it is applied to
those keywords. However, when specifying the {line} option or {format
M string} option for {step} and {natoms}, you should specify a format
string appropriate for an 8-byte signed integer, e.g. one with "%ld".
The {temp} keyword is used to determine how thermodynamic temperature
is calculated, which is used by all thermo quantities that require a