forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1258 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
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commit
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@ -56,7 +56,8 @@
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c_ID = scalar per-atom quantity calculated by a compute identified by its ID
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c_ID[N] = Nth per-atom vector quantity calculated by a compute identified by its ID
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f_ID = scalar per-atom quantity calculated by a fix identified by its ID
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f_ID[N] = Nth per-atom vector quantity calculated by a fix identified by its ID
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f_ID[N] = Nth per-atom vector quantity calculated by a fix identified by its ID
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v_name = variable of atom style that calculates a per-atom quantity
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</PRE>
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</UL>
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@ -65,7 +66,7 @@
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<PRE>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.* tag type x y vx fx
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dump 4b flow custom 100 dump.%.myforce tag type c_myF[3]
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dump 4b flow custom 100 dump.%.myforce tag type c_myF[3] v_ke
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dump 1 all xtc 1000 file.xtc 100.0
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</PRE>
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<P><B>Description:</B>
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@ -125,9 +126,9 @@ file.
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</P>
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<P>Style <I>custom</I> allows you to specify a list of atom attributes to be
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written to the dump file for each atom. Possible attributes are
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listed above and will appear in the order specified. Be careful not
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to specify a quantity that is not defined for a particular simulation
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- such as <I>q</I> for atom style <I>bond</I>, since that atom style doesn't
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listed above and will appear in the order specified. You cannot
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specify a quantity that is not defined for a particular simulation -
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such as <I>q</I> for atom style <I>bond</I>, since that atom style doesn't
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assign charges. Dumps occur at the very end of a timestep, so atom
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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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@ -236,20 +237,17 @@ define the orientiation of the particle. The final 3 give the
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rotational torque on the particle.
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</P>
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<P>The <I>c_ID</I> and <I>c_ID[N]</I> keywords allow scalar or vector per-atom
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quantities calculated by a compute to be output. The ID in the
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keyword should be replaced by the actual ID of the compute that has
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been defined previously in the input script. See the
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<A HREF = "compute.html">compute</A> command for details. There are pre-defined
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computes for calculating the energy, stress, centro-symmetry
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parameter, and coordination number of individual atoms. The "compute
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variable/atom" command will evaluate a per-atom formula you define via
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the <A HREF = "variable.html">variable atom</A> command, for each atom, which can
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then be dumped.
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quantities calculated by a <A HREF = "compute.html">compute</A> to be output. The
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ID in the keyword should be replaced by the actual ID of the compute
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that has been defined previously in the input script. See the
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<A HREF = "compute.html">compute</A> command for details. There are computes for
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calculating the energy, stress, centro-symmetry parameter, and
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coordination number of individual atoms.
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</P>
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<P>Note that scalar and vector quantities that are not calculated on a
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per-atom basis by a compute (e.g. global temperature or pressure)
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cannot be output in a dump. Rather, these quantities can be output by
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the <A HREF = "thermo_style.html">thermo_style custom</A> command.
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<P>Note that computes which calculate global scalar and vector
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quantities, as opposed to per-atom quantities, cannot be output in a
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dump. Instead, these quantities can be output by the <A HREF = "thermo_style.html">thermo_style
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custom</A> command.
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</P>
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<P>If <I>c_ID</I> is used as a keyword, then the scalar per-atom quantity
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calculated by the compute is printed. If <I>c_ID[N]</I> is used, then N
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@ -257,23 +255,33 @@ in the range from 1-M will print the Nth component of the M-length
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per-atom vector calculated by the compute.
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</P>
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<P>The <I>f_ID</I> and <I>f_ID[N]</I> keywords allow scalar or vector per-atom
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quantities calculated by a fix to be output. The ID in the keyword
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should be replaced by the actual ID of the fix that has been defined
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previously in the input script. Currently the <A HREF = "fix_ave_atom.html">fix
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quantities calculated by a <A HREF = "fix.html">fix</A> to be output. The ID in the
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keyword should be replaced by the actual ID of the fix that has been
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defined previously in the input script. Currently the <A HREF = "fix_ave_atom.html">fix
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ave/atom</A> command is the only fix that calculates
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per-atom quantities. Since it takes a per-atom <A HREF = "compute.html">compute</A>
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as an argument it effectively time-averages any of the previously
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described compute quantities so the time-averaged result can be
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written to a dump file.
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per-atom quantities. Since it can time-average per-atom quantities
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produced by any <A HREF = "compute.html">compute</A>, <A HREF = "fix.html">fix</A>, or atom-style
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<A HREF = "variable.html">variable</A>, this allows those time-averaged results to
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be written to a dump file.
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</P>
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<P>If <I>f_ID</I> is used as a keyword, then the scalar per-atom quantity
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calculated by the fix is printed. If <I>f_ID[N]</I> is used, then N
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in the range from 1-M will print the Nth component of the M-length
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per-atom vector calculated by the fix.
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</P>
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<P>The <I>v_name</I> keyword allows per-atom quantities calculated by a
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<A HREF = "variable.html">variable</A> to be output. The name in the keyword should
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be replaced by the actual name of the variable that has been defined
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previously in the input script. Only an atom-style variable can be
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referenced, since it is the only one that generates per-atom values.
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Variables of style <I>atom</I> can reference individual atom attributes,
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per-atom atom attributes, thermodynamic keywords, or invoke other
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computes, fixes, or variables when they are evaluated, so this is a
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very general means of generating quantities to output to a dump file.
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</P>
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<P>See <A HREF = "Section_modify.html">this section</A> of the manual for information
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on how to add new compute and fix styles to LAMMPS that calculate
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per-atom quantities which could then be output with these keywords.
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per-atom quantities which could then be output into dump files.
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</P>
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<HR>
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60
doc/dump.txt
60
doc/dump.txt
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@ -47,7 +47,8 @@ args = list of arguments for a particular style :l
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c_ID = scalar per-atom quantity calculated by a compute identified by its ID
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c_ID\[N\] = Nth per-atom vector quantity calculated by a compute identified by its ID
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f_ID = scalar per-atom quantity calculated by a fix identified by its ID
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f_ID\[N\] = Nth per-atom vector quantity calculated by a fix identified by its ID :pre
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f_ID\[N\] = Nth per-atom vector quantity calculated by a fix identified by its ID
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v_name = variable of atom style that calculates a per-atom quantity :pre
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:ule
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[Examples:]
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@ -55,7 +56,7 @@ args = list of arguments for a particular style :l
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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.* tag type x y vx fx
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dump 4b flow custom 100 dump.%.myforce tag type c_myF\[3\]
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dump 4b flow custom 100 dump.%.myforce tag type c_myF\[3\] v_ke
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dump 1 all xtc 1000 file.xtc 100.0 :pre
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[Description:]
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@ -115,9 +116,9 @@ file.
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Style {custom} allows you to specify a list of atom attributes to be
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written to the dump file for each atom. Possible attributes are
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listed above and will appear in the order specified. Be careful not
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to specify a quantity that is not defined for a particular simulation
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- such as {q} for atom style {bond}, since that atom style doesn't
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listed above and will appear in the order specified. You cannot
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specify a quantity that is not defined for a particular simulation -
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such as {q} for atom style {bond}, since that atom style doesn't
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assign charges. Dumps occur at the very end of a timestep, so atom
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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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@ -226,20 +227,17 @@ define the orientiation of the particle. The final 3 give the
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rotational torque on the particle.
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The {c_ID} and {c_ID\[N\]} keywords allow scalar or vector per-atom
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quantities calculated by a compute to be output. The ID in the
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keyword should be replaced by the actual ID of the compute that has
|
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been defined previously in the input script. See the
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"compute"_compute.html command for details. There are pre-defined
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computes for calculating the energy, stress, centro-symmetry
|
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parameter, and coordination number of individual atoms. The "compute
|
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variable/atom" command will evaluate a per-atom formula you define via
|
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the "variable atom"_variable.html command, for each atom, which can
|
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then be dumped.
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quantities calculated by a "compute"_compute.html to be output. The
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ID in the keyword should be replaced by the actual ID of the compute
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that has been defined previously in the input script. See the
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"compute"_compute.html command for details. There are computes for
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calculating the energy, stress, centro-symmetry parameter, and
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coordination number of individual atoms.
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Note that scalar and vector quantities that are not calculated on a
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per-atom basis by a compute (e.g. global temperature or pressure)
|
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cannot be output in a dump. Rather, these quantities can be output by
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the "thermo_style custom"_thermo_style.html command.
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Note that computes which calculate global scalar and vector
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quantities, as opposed to per-atom quantities, cannot be output in a
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dump. Instead, these quantities can be output by the "thermo_style
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custom"_thermo_style.html command.
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If {c_ID} is used as a keyword, then the scalar per-atom quantity
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calculated by the compute is printed. If {c_ID\[N\]} is used, then N
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@ -247,23 +245,33 @@ in the range from 1-M will print the Nth component of the M-length
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per-atom vector calculated by the compute.
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The {f_ID} and {f_ID\[N\]} keywords allow scalar or vector per-atom
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quantities calculated by a fix to be output. The ID in the keyword
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should be replaced by the actual ID of the fix that has been defined
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previously in the input script. Currently the "fix
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quantities calculated by a "fix"_fix.html to be output. The ID in the
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keyword should be replaced by the actual ID of the fix that has been
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defined previously in the input script. Currently the "fix
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ave/atom"_fix_ave_atom.html command is the only fix that calculates
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per-atom quantities. Since it takes a per-atom "compute"_compute.html
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as an argument it effectively time-averages any of the previously
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described compute quantities so the time-averaged result can be
|
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written to a dump file.
|
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per-atom quantities. Since it can time-average per-atom quantities
|
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produced by any "compute"_compute.html, "fix"_fix.html, or atom-style
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"variable"_variable.html, this allows those time-averaged results to
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be written to a dump file.
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|
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If {f_ID} is used as a keyword, then the scalar per-atom quantity
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calculated by the fix is printed. If {f_ID\[N\]} is used, then N
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in the range from 1-M will print the Nth component of the M-length
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per-atom vector calculated by the fix.
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|
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The {v_name} keyword allows per-atom quantities calculated by a
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"variable"_variable.html to be output. The name in the keyword should
|
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be replaced by the actual name of the variable that has been defined
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previously in the input script. Only an atom-style variable can be
|
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referenced, since it is the only one that generates per-atom values.
|
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Variables of style {atom} can reference individual atom attributes,
|
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per-atom atom attributes, thermodynamic keywords, or invoke other
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computes, fixes, or variables when they are evaluated, so this is a
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very general means of generating quantities to output to a dump file.
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See "this section"_Section_modify.html of the manual for information
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on how to add new compute and fix styles to LAMMPS that calculate
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per-atom quantities which could then be output with these keywords.
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per-atom quantities which could then be output into dump files.
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:line
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