forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3135 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
14254f023a
commit
e8f3ce6b35
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@ -19,7 +19,7 @@
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<LI>group-ID = ID of the group of atoms to be dumped
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<LI>style = <I>atom</I> or <I>bond</I> or <I>dcd</I> or <I>xtc</I> or <I>xyz</I> or <I>custom</I>
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<LI>style = <I>atom</I> or <I>bond</I> or <I>cfg</I> or <I>dcd</I> or <I>xtc</I> or <I>xyz</I> or <I>custom</I>
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<LI>N = dump every this many timesteps
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@ -29,6 +29,7 @@
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<PRE> <I>atom</I> args = none
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<I>bond</I> args = none
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<I>cfg</I> args = same as <I>custom</I> args, see below
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<I>dcd</I> args = none
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<I>xtc</I> args = none
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<I>xyz</I> args = none
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@ -71,6 +72,8 @@
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dump 2 subgroup atom 50 dump.run.bin
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dump 4a all custom 100 dump.myforce.* id type x y vx fx
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dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
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dump 2 inner cfg 10 dump.snap.*.cfg id type xs ys zs vx vy vz
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dump snap all cfg 100 dump.config.*.cfg id type xs ys zs id type c_Stress<B>2</B>
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dump 1 all xtc 1000 file.xtc
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</PRE>
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<P><B>Description:</B>
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@ -96,7 +99,9 @@ collected from multiple processors. This is always the case for the
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<I>atom</I>, <I>bond</I>, and <I>custom</I> styles. It is also the case for the
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<I>xyz</I> style if the dump group is not <I>all</I>. It is not the case for
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the <I>dcd</I> and <I>xtc</I> styles which always write atoms in sorted order.
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So does the <I>xyz</I> style if the dump group is <I>all</I>.
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So does the <I>xyz</I> style if the dump group is <I>all</I>. The <I>cfg</I> style
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supports the <I>sort</I> option of the <A HREF = "dump_modify.html">dump_modify</A>
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command which allows for allows sorting to be turned on or off.
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</P>
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<HR>
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@ -152,6 +157,21 @@ attributes will include effects due to fixes that are applied during
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the timestep. An explanation of the dump custom quantities is given
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below.
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</P>
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<P>Style <I>cfg</I> has the same command syntax as style <I>custom</I> and writes
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extended CFG format files, as used by the
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<A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A> visualization
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package. Since the extended CFG format uses a single snapshot of the
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system per file, a wild-card "*" must be included in the filename, as
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discussed below. The list of atom attributes for style <I>cfg</I> must
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begin with "id tag xs ys zs", since these quantities are needed to
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write the CFG files in the appropriate format (though the "id" and
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"type" fields do not appear explicitly in the file). Any remaining
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attributes will be stored as "auxiliary properties" in the CFG files.
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Note that you will typically want to use the <A HREF = "dump_modify.html">dump_modify
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element</A> command with CFG-formatted files, to
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associate element names with atom types, so that AtomEye can render
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atoms appropriately.
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</P>
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<P>The <I>dcd</I> style writes DCD files, a standard atomic trajectory format
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used by the CHARMM, NAMD, and XPlor molecular dynamics packages. DCD
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files are binary and thus may not be portable to different machines.
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@ -243,7 +263,7 @@ styles.
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<HR>
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<P>This section explains the atom quantities that can be specified as
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part of the <I>custom</I> style.
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part of the <I>custom</I> and <I>cfg</I> styles.
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</P>
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<P>The <I>id</I>, <I>mol</I>, <I>type</I>, <I>vx</I>, <I>vy</I>, <I>vz</I>, <I>fx</I>, <I>fy</I>,
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<I>fz</I>, <I>q</I> keywords are self-explanatory.
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26
doc/dump.txt
26
doc/dump.txt
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@ -14,12 +14,13 @@ dump ID group-ID style N file args :pre
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ID = user-assigned name for the dump :ulb,l
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group-ID = ID of the group of atoms to be dumped :l
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style = {atom} or {bond} or {dcd} or {xtc} or {xyz} or {custom} :l
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style = {atom} or {bond} or {cfg} or {dcd} or {xtc} or {xyz} or {custom} :l
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N = dump every this many timesteps :l
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file = name of file to write dump info to :l
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args = list of arguments for a particular style :l
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{atom} args = none
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{bond} args = none
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{cfg} args = same as {custom} args, see below
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{dcd} args = none
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{xtc} args = none
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{xyz} args = none
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@ -61,6 +62,8 @@ dump myDump all atom 100 dump.atom
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dump 2 subgroup atom 50 dump.run.bin
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dump 4a all custom 100 dump.myforce.* id type x y vx fx
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dump 4b flow custom 100 dump.%.myforce id type c_myF\[3\] v_ke
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dump 2 inner cfg 10 dump.snap.*.cfg id type xs ys zs vx vy vz
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dump snap all cfg 100 dump.config.*.cfg id type xs ys zs id type c_Stress[2]
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dump 1 all xtc 1000 file.xtc :pre
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[Description:]
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@ -86,7 +89,9 @@ collected from multiple processors. This is always the case for the
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{atom}, {bond}, and {custom} styles. It is also the case for the
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{xyz} style if the dump group is not {all}. It is not the case for
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the {dcd} and {xtc} styles which always write atoms in sorted order.
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So does the {xyz} style if the dump group is {all}.
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So does the {xyz} style if the dump group is {all}. The {cfg} style
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supports the {sort} option of the "dump_modify"_dump_modify.html
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command which allows for allows sorting to be turned on or off.
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:line
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@ -142,6 +147,21 @@ attributes will include effects due to fixes that are applied during
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the timestep. An explanation of the dump custom quantities is given
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below.
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Style {cfg} has the same command syntax as style {custom} and writes
|
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extended CFG format files, as used by the
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"AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A visualization
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package. Since the extended CFG format uses a single snapshot of the
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system per file, a wild-card "*" must be included in the filename, as
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discussed below. The list of atom attributes for style {cfg} must
|
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begin with "id tag xs ys zs", since these quantities are needed to
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write the CFG files in the appropriate format (though the "id" and
|
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"type" fields do not appear explicitly in the file). Any remaining
|
||||
attributes will be stored as "auxiliary properties" in the CFG files.
|
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Note that you will typically want to use the "dump_modify
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element"_dump_modify.html command with CFG-formatted files, to
|
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associate element names with atom types, so that AtomEye can render
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atoms appropriately.
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The {dcd} style writes DCD files, a standard atomic trajectory format
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used by the CHARMM, NAMD, and XPlor molecular dynamics packages. DCD
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files are binary and thus may not be portable to different machines.
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@ -233,7 +253,7 @@ styles.
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:line
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This section explains the atom quantities that can be specified as
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part of the {custom} style.
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part of the {custom} and {cfg} styles.
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The {id}, {mol}, {type}, {vx}, {vy}, {vz}, {fx}, {fy},
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{fz}, {q} keywords are self-explanatory.
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@ -19,23 +19,24 @@
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<LI>one or more keyword/value pairs may be appended
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<LI>keyword = <I>format</I> or <I>scale</I> or <I>image</I> or <I>flush</I> or <I>unwrap</I> or <I>every</I> or <I>precision</I> or <I>region</I> or <I>thresh</I>
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<LI>keyword = <I>every</I> or <I>flush</I> or <I>format</I> or <I>image</I> or <I>precision</I> or <I>region</I> or <I>scale</I> or <I>thresh</I> or <I>unwrap</I>
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<PRE> <I>format</I> arg = C-style format string for one line of output
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<I>scale</I> arg = <I>yes</I> or <I>no</I>
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<I>image</I> arg = <I>yes</I> or <I>no</I>
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<I>flush</I> arg = <I>yes</I> or <I>no</I>
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<I>unwrap</I> arg = <I>yes</I> or <I>no</I>
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<PRE> <I>element</I> args = E1 E2 ... EN, where N = # of atom types
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E1,...,EN = element name, e.g. C or Fe or Ga
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<I>every</I> arg = N
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N = dump every this many timesteps
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<I>format</I> arg = C-style format string for one line of output
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<I>flush</I> arg = <I>yes</I> or <I>no</I>
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<I>image</I> arg = <I>yes</I> or <I>no</I>
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<I>precision</I> arg = power-of-10 value from 10 to 1000000
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<I>region</I> arg = region-ID or "none"
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<I>scale</I> arg = <I>yes</I> or <I>no</I>
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<I>thresh</I> args = attribute operation value
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attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
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operation = "<" or "<=" or ">" or ">=" or "==" or "!="
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value = numeric value to compare to
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these 3 args can be replaced by the word "none" to turn off thresholding
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<I>unwrap</I> arg = <I>yes</I> or <I>no</I>
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</PRE>
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</UL>
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@ -51,37 +52,76 @@ dump_modify xtcdump precision 10000
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<P>Modify the parameters of a previously defined dump command. Not all
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parameters are relevant to all dump styles.
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</P>
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<P>The text-based dump styles have a default C-style format string which
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simply specifies %d for integers and %g for real values. The <I>format</I>
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keyword can be used to override the default with a new C-style format
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string. Do not include a trailing "\n" newline character in the
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format string. This option has no effect on the <I>dcd</I> and <I>xtc</I> dump
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styles since they write binary files.
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<P>The <I>element</I> keyword applies only to the the dump <I>cfg</I> style. It
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associates element names (e.g. H, C, Fe) with LAMMPS atom types, so
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that the <A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A>
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visualization package can render atoms with the appropriate size and
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color. An element name is specified for each atom type (1 to Ntype)
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in the simulation. The same element name can be given to multiple
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atom types.
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</P>
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<P>The <I>scale</I> and <I>image</I> keywords apply only to the dump <I>atom</I> style.
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<P>The <I>every</I> keyword changes the dump frequency originally specified by
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the <A HREF = "dump.html">dump</A> command to a new value which must be > 0. The
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dump frequency cannot be changed for the dump <I>dcd</I> style.
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</P>
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<P>A scale value of <I>yes</I> means atom coords are written in normalized
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units from 0.0 to 1.0 in each box dimension. If the simluation box is
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triclinic (tilted), then all atom coords will still be between 0.0 and
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1.0. A value of <I>no</I> means they are written in absolute distance
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units (e.g. Angstroms or sigma).
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</P>
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<P>If the image value is <I>yes</I>, 3 flags are appended to each atom's
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coords which are the absolute box image of the atom in each dimension.
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For example, an x image flag of -2 with a normalized coord of 0.5
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means the atom is in the center of the box, but has passed thru the
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box boundary 2 times and is really 2 box lengths to the left of its
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current coordinate. Note that for dump style <I>custom</I> these various
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values can be printed in the dump file by using the appropriate atom
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attributes in the dump command itself.
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</P>
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<P>The <I>flush</I> option determines whether a flush operation in invoked
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<P>The <I>flush</I> keyword determines whether a flush operation in invoked
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after a dump snapshot is written to the dump file. A flush insures
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the output in that file is current (no buffering by the OS), even if
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LAMMPS halts before the simulation completes. Flushes cannot be
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performed with dump style <I>xtc</I>.
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</P>
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<P>The <I>unwrap</I> option only applies to the dump <I>dcd</I> and <I>xtc</I> styles.
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<P>The text-based dump styles have a default C-style format string which
|
||||
simply specifies %d for integers and %g for real values. The <I>format</I>
|
||||
keyword can be used to override the default with a new C-style format
|
||||
string. Do not include a trailing "\n" newline character in the
|
||||
format string. This option has no effect on the <I>dcd</I> and <I>xtc</I> dump
|
||||
styles since they write binary files. Note that for the <I>cfg</I> style,
|
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the first two fields (atom id and type) are not actually written into
|
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the CFG file, though you must include formats for them in the format
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string.
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</P>
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<P>The <I>image</I> keyword applies only to the dump <I>atom</I> style. If the
|
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image value is <I>yes</I>, 3 flags are appended to each atom's coords which
|
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are the absolute box image of the atom in each dimension. For
|
||||
example, an x image flag of -2 with a normalized coord of 0.5 means
|
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the atom is in the center of the box, but has passed thru the box
|
||||
boundary 2 times and is really 2 box lengths to the left of its
|
||||
current coordinate. Note that for dump style <I>custom</I> these various
|
||||
values can be printed in the dump file by using the appropriate atom
|
||||
attributes in the dump command itself.
|
||||
</P>
|
||||
<P>The <I>precision</I> keyword only applies to the dump <I>xtc</I> style. A
|
||||
specified value of N means that coordinates are stored to 1/N
|
||||
nanometer accuracy, e.g. for N = 1000, the coordinates are written to
|
||||
1/1000 nanometer accuracy.
|
||||
</P>
|
||||
<P>The <I>region</I> keyword only applies to the dump <I>custom</I> and <I>cfg</I>
|
||||
styles. If specified, only atoms in the region will be written to the
|
||||
dump file. Only one region can be applied as a filter (the last one
|
||||
specified). See the <A HREF = "region.html">region</A> command for more details.
|
||||
Note that a region can be defined as the "inside" or "outside" of a
|
||||
geometric shape, and it can be the "union" or "intersection" of a
|
||||
series of simpler regions.
|
||||
</P>
|
||||
<P>The <I>scale</I> keyword applies only to the dump <I>atom</I> style. A scale
|
||||
value of <I>yes</I> means atom coords are written in normalized units from
|
||||
0.0 to 1.0 in each box dimension. If the simluation box is triclinic
|
||||
(tilted), then all atom coords will still be between 0.0 and 1.0. A
|
||||
value of <I>no</I> means they are written in absolute distance units
|
||||
(e.g. Angstroms or sigma).
|
||||
</P>
|
||||
<P>The <I>thresh</I> keyword only applies to the dump <I>custom</I> and <I>cfg</I>
|
||||
styles. Multiple thresholds can be specified. Specifying "none"
|
||||
turns off all threshold criteria. If thresholds are specified, only
|
||||
atoms whose attributes meet all the threshold criteria are written to
|
||||
the dump file. The possible attributes that can be tested for are the
|
||||
same as those that can be specified in the <A HREF = "dump.html">dump custom</A>
|
||||
command. Note that different attributes can be output by the dump
|
||||
custom command than are used as threshold criteria by the dump_modify
|
||||
command. E.g. you can output the coordinates and stress of atoms
|
||||
whose energy is above some threshold.
|
||||
</P>
|
||||
<P>The <I>unwrap</I> keyword only applies to the dump <I>dcd</I> and <I>xtc</I> styles.
|
||||
If set to <I>yes</I>, coordinates will be written "unwrapped" by the image
|
||||
flags for each atom. Unwrapped means that if the atom has passed thru
|
||||
a periodic boundary one or more times, the value is printed for what
|
||||
|
|
@ -89,34 +129,6 @@ the coordinate would be if it had not been wrapped back into the
|
|||
periodic box. Note that these coordinates may thus be far outside the
|
||||
box size stored with the snapshot.
|
||||
</P>
|
||||
<P>The <I>every</I> option changes the dump frequency originally specified by
|
||||
the <A HREF = "dump.html">dump</A> command to a new value which must be > 0. The
|
||||
dump frequency cannot be changed for the dump <I>dcd</I> style.
|
||||
</P>
|
||||
<P>The <I>precision</I> option only applies to the dump <I>xtc</I> style. A
|
||||
specified value of N means that coordinates are stored to 1/N
|
||||
nanometer accuracy, e.g. for N = 1000, the coordinates are written to
|
||||
1/1000 nanometer accuracy.
|
||||
</P>
|
||||
<P>The <I>region</I> keyword only applies to the dump <I>custom</I> style. If
|
||||
specified, only atoms in the region will be written to the dump file.
|
||||
Only one region can be applied as a filter (the last one specified).
|
||||
See the <A HREF = "region.html">region</A> command for more details. Note that a
|
||||
region can be defined as the "inside" or "outside" of a geometric
|
||||
shape, and it can be the "union" or "intersection" of a series of
|
||||
simpler regions.
|
||||
</P>
|
||||
<P>The <I>thresh</I> keyword only applies to the dump <I>custom</I> style.
|
||||
Multiple thresholds can be specified. Specifying "none" turns off
|
||||
all threshold criteria. If thresholds are specified, only atoms
|
||||
whose attributes meet all the threshold criteria are written to the
|
||||
dump file. The possible attributes that can be tested for are the
|
||||
same as those that can be specified in the <A HREF = "dump.html">dump custom</A>
|
||||
command. Note that different attributes can be output by the dump
|
||||
custom command than are used as threshold criteria by the dump_modify
|
||||
command. E.g. you can output the coordinates and stress of atoms
|
||||
whose energy is above some threshold.
|
||||
</P>
|
||||
<P><B>Restrictions:</B> none
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
|
|
@ -125,10 +137,17 @@ whose energy is above some threshold.
|
|||
</P>
|
||||
<P><B>Default:</B>
|
||||
</P>
|
||||
<P>The option defaults are format = %d and %g for each integer or
|
||||
floating point value, scale = yes, image = no, flush = yes (except for
|
||||
the dump <I>xtc</I> style), unwrap = no, every = whatever it was set to via
|
||||
the <A HREF = "dump.html">dump</A> command, precision = 1000, region = none, and
|
||||
thresh = none.
|
||||
<P>The option defaults are
|
||||
</P>
|
||||
<UL><LI>element = "C" for every atom type
|
||||
<LI>every = whatever it was set to via the <A HREF = "dump.html">dump</A> command
|
||||
<LI>flush = yes (except for the dump <I>xtc</I> style)
|
||||
<LI>format = %d and %g for each integer or floating point value
|
||||
<LI>image = no
|
||||
<LI>precision = 1000
|
||||
<LI>region = none
|
||||
<LI>scale = yes
|
||||
<LI>thresh = none
|
||||
<LI>unwrap = no
|
||||
</UL>
|
||||
</HTML>
|
||||
|
|
|
|||
|
|
@ -14,22 +14,23 @@ dump_modify dump-ID keyword values ... :pre
|
|||
|
||||
dump-ID = ID of dump to modify :ulb,l
|
||||
one or more keyword/value pairs may be appended :l
|
||||
keyword = {format} or {scale} or {image} or {flush} or {unwrap} or {every} or {precision} or {region} or {thresh} :l
|
||||
{format} arg = C-style format string for one line of output
|
||||
{scale} arg = {yes} or {no}
|
||||
{image} arg = {yes} or {no}
|
||||
{flush} arg = {yes} or {no}
|
||||
{unwrap} arg = {yes} or {no}
|
||||
keyword = {every} or {flush} or {format} or {image} or {precision} or {region} or {scale} or {thresh} or {unwrap} :l
|
||||
{element} args = E1 E2 ... EN, where N = # of atom types
|
||||
E1,...,EN = element name, e.g. C or Fe or Ga
|
||||
{every} arg = N
|
||||
N = dump every this many timesteps
|
||||
{format} arg = C-style format string for one line of output
|
||||
{flush} arg = {yes} or {no}
|
||||
{image} arg = {yes} or {no}
|
||||
{precision} arg = power-of-10 value from 10 to 1000000
|
||||
{region} arg = region-ID or "none"
|
||||
{scale} arg = {yes} or {no}
|
||||
{thresh} args = attribute operation value
|
||||
attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
|
||||
operation = "<" or "<=" or ">" or ">=" or "==" or "!="
|
||||
value = numeric value to compare to
|
||||
these 3 args can be replaced by the word "none" to turn off thresholding
|
||||
:pre
|
||||
{unwrap} arg = {yes} or {no} :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
|
@ -44,37 +45,76 @@ dump_modify xtcdump precision 10000 :pre
|
|||
Modify the parameters of a previously defined dump command. Not all
|
||||
parameters are relevant to all dump styles.
|
||||
|
||||
The text-based dump styles have a default C-style format string which
|
||||
simply specifies %d for integers and %g for real values. The {format}
|
||||
keyword can be used to override the default with a new C-style format
|
||||
string. Do not include a trailing "\n" newline character in the
|
||||
format string. This option has no effect on the {dcd} and {xtc} dump
|
||||
styles since they write binary files.
|
||||
The {element} keyword applies only to the the dump {cfg} style. It
|
||||
associates element names (e.g. H, C, Fe) with LAMMPS atom types, so
|
||||
that the "AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A
|
||||
visualization package can render atoms with the appropriate size and
|
||||
color. An element name is specified for each atom type (1 to Ntype)
|
||||
in the simulation. The same element name can be given to multiple
|
||||
atom types.
|
||||
|
||||
The {scale} and {image} keywords apply only to the dump {atom} style.
|
||||
The {every} keyword changes the dump frequency originally specified by
|
||||
the "dump"_dump.html command to a new value which must be > 0. The
|
||||
dump frequency cannot be changed for the dump {dcd} style.
|
||||
|
||||
A scale value of {yes} means atom coords are written in normalized
|
||||
units from 0.0 to 1.0 in each box dimension. If the simluation box is
|
||||
triclinic (tilted), then all atom coords will still be between 0.0 and
|
||||
1.0. A value of {no} means they are written in absolute distance
|
||||
units (e.g. Angstroms or sigma).
|
||||
|
||||
If the image value is {yes}, 3 flags are appended to each atom's
|
||||
coords which are the absolute box image of the atom in each dimension.
|
||||
For example, an x image flag of -2 with a normalized coord of 0.5
|
||||
means the atom is in the center of the box, but has passed thru the
|
||||
box boundary 2 times and is really 2 box lengths to the left of its
|
||||
current coordinate. Note that for dump style {custom} these various
|
||||
values can be printed in the dump file by using the appropriate atom
|
||||
attributes in the dump command itself.
|
||||
|
||||
The {flush} option determines whether a flush operation in invoked
|
||||
The {flush} keyword determines whether a flush operation in invoked
|
||||
after a dump snapshot is written to the dump file. A flush insures
|
||||
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 {xtc}.
|
||||
|
||||
The {unwrap} option only applies to the dump {dcd} and {xtc} styles.
|
||||
The text-based dump styles have a default C-style format string which
|
||||
simply specifies %d for integers and %g for real values. The {format}
|
||||
keyword can be used to override the default with a new C-style format
|
||||
string. Do not include a trailing "\n" newline character in the
|
||||
format string. This option has no effect on the {dcd} and {xtc} dump
|
||||
styles since they write binary files. Note that for the {cfg} style,
|
||||
the first two fields (atom id and type) are not actually written into
|
||||
the CFG file, though you must include formats for them in the format
|
||||
string.
|
||||
|
||||
The {image} keyword applies only to the dump {atom} style. If the
|
||||
image value is {yes}, 3 flags are appended to each atom's coords which
|
||||
are the absolute box image of the atom in each dimension. For
|
||||
example, an x image flag of -2 with a normalized coord of 0.5 means
|
||||
the atom is in the center of the box, but has passed thru the box
|
||||
boundary 2 times and is really 2 box lengths to the left of its
|
||||
current coordinate. Note that for dump style {custom} these various
|
||||
values can be printed in the dump file by using the appropriate atom
|
||||
attributes in the dump command itself.
|
||||
|
||||
The {precision} keyword only applies to the dump {xtc} style. A
|
||||
specified value of N means that coordinates are stored to 1/N
|
||||
nanometer accuracy, e.g. for N = 1000, the coordinates are written to
|
||||
1/1000 nanometer accuracy.
|
||||
|
||||
The {region} keyword only applies to the dump {custom} and {cfg}
|
||||
styles. If specified, only atoms in the region will be written to the
|
||||
dump file. Only one region can be applied as a filter (the last one
|
||||
specified). See the "region"_region.html command for more details.
|
||||
Note that a region can be defined as the "inside" or "outside" of a
|
||||
geometric shape, and it can be the "union" or "intersection" of a
|
||||
series of simpler regions.
|
||||
|
||||
The {scale} keyword applies only to the dump {atom} style. A scale
|
||||
value of {yes} means atom coords are written in normalized units from
|
||||
0.0 to 1.0 in each box dimension. If the simluation box is triclinic
|
||||
(tilted), then all atom coords will still be between 0.0 and 1.0. A
|
||||
value of {no} means they are written in absolute distance units
|
||||
(e.g. Angstroms or sigma).
|
||||
|
||||
The {thresh} keyword only applies to the dump {custom} and {cfg}
|
||||
styles. Multiple thresholds can be specified. Specifying "none"
|
||||
turns off all threshold criteria. If thresholds are specified, only
|
||||
atoms whose attributes meet all the threshold criteria are written to
|
||||
the dump file. The possible attributes that can be tested for are the
|
||||
same as those that can be specified in the "dump custom"_dump.html
|
||||
command. Note that different attributes can be output by the dump
|
||||
custom command than are used as threshold criteria by the dump_modify
|
||||
command. E.g. you can output the coordinates and stress of atoms
|
||||
whose energy is above some threshold.
|
||||
|
||||
The {unwrap} keyword only applies to the dump {dcd} and {xtc} styles.
|
||||
If set to {yes}, coordinates will be written "unwrapped" by the image
|
||||
flags for each atom. Unwrapped means that if the atom has passed thru
|
||||
a periodic boundary one or more times, the value is printed for what
|
||||
|
|
@ -82,34 +122,6 @@ the coordinate would be if it had not been wrapped back into the
|
|||
periodic box. Note that these coordinates may thus be far outside the
|
||||
box size stored with the snapshot.
|
||||
|
||||
The {every} option changes the dump frequency originally specified by
|
||||
the "dump"_dump.html command to a new value which must be > 0. The
|
||||
dump frequency cannot be changed for the dump {dcd} style.
|
||||
|
||||
The {precision} option only applies to the dump {xtc} style. A
|
||||
specified value of N means that coordinates are stored to 1/N
|
||||
nanometer accuracy, e.g. for N = 1000, the coordinates are written to
|
||||
1/1000 nanometer accuracy.
|
||||
|
||||
The {region} keyword only applies to the dump {custom} style. If
|
||||
specified, only atoms in the region will be written to the dump file.
|
||||
Only one region can be applied as a filter (the last one specified).
|
||||
See the "region"_region.html command for more details. Note that a
|
||||
region can be defined as the "inside" or "outside" of a geometric
|
||||
shape, and it can be the "union" or "intersection" of a series of
|
||||
simpler regions.
|
||||
|
||||
The {thresh} keyword only applies to the dump {custom} style.
|
||||
Multiple thresholds can be specified. Specifying "none" turns off
|
||||
all threshold criteria. If thresholds are specified, only atoms
|
||||
whose attributes meet all the threshold criteria are written to the
|
||||
dump file. The possible attributes that can be tested for are the
|
||||
same as those that can be specified in the "dump custom"_dump.html
|
||||
command. Note that different attributes can be output by the dump
|
||||
custom command than are used as threshold criteria by the dump_modify
|
||||
command. E.g. you can output the coordinates and stress of atoms
|
||||
whose energy is above some threshold.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:]
|
||||
|
|
@ -118,8 +130,15 @@ whose energy is above some threshold.
|
|||
|
||||
[Default:]
|
||||
|
||||
The option defaults are format = %d and %g for each integer or
|
||||
floating point value, scale = yes, image = no, flush = yes (except for
|
||||
the dump {xtc} style), unwrap = no, every = whatever it was set to via
|
||||
the "dump"_dump.html command, precision = 1000, region = none, and
|
||||
thresh = none.
|
||||
The option defaults are
|
||||
|
||||
element = "C" for every atom type
|
||||
every = whatever it was set to via the "dump"_dump.html command
|
||||
flush = yes (except for the dump {xtc} style)
|
||||
format = %d and %g for each integer or floating point value
|
||||
image = no
|
||||
precision = 1000
|
||||
region = none
|
||||
scale = yes
|
||||
thresh = none
|
||||
unwrap = no :ul
|
||||
|
|
|
|||
Loading…
Reference in New Issue