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Merge remote branch 'lammps-ro/master' into lammps-icms

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Axel Kohlmeyer
2015-06-09 14:04:38 +02:00
parent b9453580a7 9a72a59b69
commit 2b2aac8912
20 changed files with 22 additions and 36 deletions
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7
doc/Section_howto.html
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@ -1486,12 +1486,6 @@ info, etc) and stores the values in a local vector or array. These
are produced as output values which can be used as input to other
output commands.
</P>
<P>The <A HREF = "compute_atom_molecule.html">compute atom/molecule</A> command takes a
list of one or more per-atom quantities (from a compute, fix, per-atom
variable) and sums the quantities on a per-molecule basis. It
produces a global vector or array as output values which can be used
as input to other output commands.
</P>
<H5><A NAME = "fixoutput"></A>Fixes that process output quantities
</H5>
<P>The <A HREF = "fix_vector.html">fix vector</A> command can create global vectors as
@ -1573,7 +1567,6 @@ vector input could be a column of an array.
<TR><TD ><A HREF = "compute_slice.html">compute slice</A></TD><TD > global vectors/arrays</TD><TD > global vector/array</TD><TD ></TD></TR>
<TR><TD ><A HREF = "compute_property_atom.html">compute property/atom</A></TD><TD > per-atom vectors</TD><TD > per-atom vector/array</TD><TD ></TD></TR>
<TR><TD ><A HREF = "compute_property_local.html">compute property/local</A></TD><TD > local vectors</TD><TD > local vector/array</TD><TD ></TD></TR>
<TR><TD ><A HREF = "compute_atom_molecule.html">compute atom/molecule</A></TD><TD > per-atom vectors</TD><TD > global vector/array</TD><TD ></TD></TR>
<TR><TD ><A HREF = "fix_vector.html">fix vector</A></TD><TD > global scalars</TD><TD > global vector</TD><TD ></TD></TR>
<TR><TD ><A HREF = "fix_ave_atom.html">fix ave/atom</A></TD><TD > per-atom vectors</TD><TD > per-atom vector/array</TD><TD ></TD></TR>
<TR><TD ><A HREF = "fix_ave_time.html">fix ave/time</A></TD><TD > global scalars/vectors</TD><TD > global scalar/vector/array, file</TD><TD ></TD></TR>

7
doc/Section_howto.txt
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@ -1475,12 +1475,6 @@ info, etc) and stores the values in a local vector or array. These
are produced as output values which can be used as input to other
output commands.
The "compute atom/molecule"_compute_atom_molecule.html command takes a
list of one or more per-atom quantities (from a compute, fix, per-atom
variable) and sums the quantities on a per-molecule basis. It
produces a global vector or array as output values which can be used
as input to other output commands.
Fixes that process output quantities :h5,link(fixoutput)
The "fix vector"_fix_vector.html command can create global vectors as
@ -1561,7 +1555,6 @@ Command: Input: Output:
"compute slice"_compute_slice.html: global vectors/arrays: global vector/array:
"compute property/atom"_compute_property_atom.html: per-atom vectors: per-atom vector/array:
"compute property/local"_compute_property_local.html: local vectors: local vector/array:
"compute atom/molecule"_compute_atom_molecule.html: per-atom vectors: global vector/array:
"fix vector"_fix_vector.html: global scalars: global vector:
"fix ave/atom"_fix_ave_atom.html: per-atom vectors: per-atom vector/array:
"fix ave/time"_fix_ave_time.html: global scalars/vectors: global scalar/vector/array, file:

2
doc/compute_angmom_chunk.html
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@ -16,7 +16,7 @@
<PRE>compute ID group-ID angmom/chunk chunkID
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>angmom/molecule = style name of this compute command
<LI>angmom/chunk = style name of this compute command
<LI>chunkID = ID of <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
</UL>
<P><B>Examples:</B>

2
doc/compute_angmom_chunk.txt
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@ -13,7 +13,7 @@ compute angmom/chunk command :h3
compute ID group-ID angmom/chunk chunkID :pre
ID, group-ID are documented in "compute"_compute.html command
angmom/molecule = style name of this compute command
angmom/chunk = style name of this compute command
chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :ul
[Examples:]

2
doc/compute_com.html
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@ -55,7 +55,7 @@ distance <A HREF = "units.html">units</A>.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_com_molecule.html">compute com/molecule</A>
<P><A HREF = "compute_com_chunk.html">compute com/chunk</A>
</P>
<P><B>Default:</B> none
</P>

2
doc/compute_com.txt
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@ -52,6 +52,6 @@ distance "units"_units.html.
[Related commands:]
"compute com/molecule"_compute_com_molecule.html
"compute com/chunk"_compute_com_chunk.html
[Default:] none

2
doc/compute_gyration.html
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@ -71,7 +71,7 @@ distance^2 <A HREF = "units.html">units</A> respectively.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_gyration_molecule.html">compute gyration/molecule</A>
<P><A HREF = "compute_gyration_chunk.html">compute gyration/chunk</A>
</P>
<P><B>Default:</B> none
</P>

2
doc/compute_gyration.txt
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@ -68,6 +68,6 @@ distance^2 "units"_units.html respectively.
[Related commands:]
"compute gyration/molecule"_compute_gyration_molecule.html
"compute gyration/chunk"_compute_gyration_chunk.html
[Default:] none

2
doc/compute_inertia_chunk.html
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@ -16,7 +16,7 @@
<PRE>compute ID group-ID inertia/chunk chunkID
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>inertia/molecule = style name of this compute command
<LI>inertia/chunk = style name of this compute command
<LI>chunkID = ID of <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
</UL>
<P><B>Examples:</B>

2
doc/compute_inertia_chunk.txt
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@ -13,7 +13,7 @@ compute inertia/chunk command :h3
compute ID group-ID inertia/chunk chunkID :pre
ID, group-ID are documented in "compute"_compute.html command
inertia/molecule = style name of this compute command
inertia/chunk = style name of this compute command
chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :ul
[Examples:]

4
doc/compute_msd.html
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@ -89,8 +89,8 @@ distance^2 <A HREF = "units.html">units</A>.
</P>
<P><A HREF = "compute_msd_nongauss.html">compute msd/nongauss</A>, <A HREF = "compute_displace_atom.html">compute
displace_atom</A>, <A HREF = "fix_store_state.html">fix
store/state</A>, <A HREF = "compute_msd_molecule.html">compute
msd/molecule</A>
store/state</A>, <A HREF = "compute_msd_chunk.html">compute
msd/chunk</A>
</P>
<P><B>Default:</B>
</P>

2
doc/compute_msd.txt
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@ -82,7 +82,7 @@ distance^2 "units"_units.html.
"compute msd/nongauss"_compute_msd_nongauss.html, "compute
displace_atom"_compute_displace_atom.html, "fix
store/state"_fix_store_state.html, "compute
msd/molecule"_compute_msd_molecule.html
msd/chunk"_compute_msd_chunk.html
[Default:]

2
doc/compute_msd_chunk.html
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@ -16,7 +16,7 @@
<PRE>compute ID group-ID msd/chunk chunkID
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>msd/molecule = style name of this compute command
<LI>msd/chunk = style name of this compute command
<LI>chunkID = ID of <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
</UL>
<P><B>Examples:</B>

2
doc/compute_msd_chunk.txt
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@ -13,7 +13,7 @@ compute msd/chunk command :h3
compute ID group-ID msd/chunk chunkID :pre
ID, group-ID are documented in "compute"_compute.html command
msd/molecule = style name of this compute command
msd/chunk = style name of this compute command
chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :ul
[Examples:]

2
doc/compute_omega_chunk.html
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@ -16,7 +16,7 @@
<PRE>compute ID group-ID omega/chunk chunkID
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>omega/molecule = style name of this compute command
<LI>omega/chunk = style name of this compute command
<LI>chunkID = ID of <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
</UL>
<P><B>Examples:</B>

2
doc/compute_omega_chunk.txt
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@ -13,7 +13,7 @@ compute omega/chunk command :h3
compute ID group-ID omega/chunk chunkID :pre
ID, group-ID are documented in "compute"_compute.html command
omega/molecule = style name of this compute command
omega/chunk = style name of this compute command
chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :ul
[Examples:]

2
doc/compute_torque_chunk.html
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@ -16,7 +16,7 @@
<PRE>compute ID group-ID torque/chunk chunkID
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>torque/molecule = style name of this compute command
<LI>torque/chunk = style name of this compute command
<LI>chunkID = ID of <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
</UL>
<P><B>Examples:</B>

2
doc/compute_torque_chunk.txt
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@ -13,7 +13,7 @@ compute torque/chunk command :h3
compute ID group-ID torque/chunk chunkID :pre
ID, group-ID are documented in "compute"_compute.html command
torque/molecule = style name of this compute command
torque/chunk = style name of this compute command
chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :ul
[Examples:]

6
doc/fix_ave_histo.html
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@ -109,11 +109,11 @@ arrays), depending on the setting of the <I>mode</I> keyword.
<P>If <I>mode</I> = vector, then the input values may either be vectors or
arrays. If a global array is listed, then it is the same as if the
individual columns of the array had been listed one by one.
E.g. these 2 fix ave/histo commands are equivalent, since the <A HREF = "compute_com_molecule.html">compute
com/molecule</A> command creates a global array
E.g. these 2 fix ave/histo commands are equivalent, since the <A HREF = "compute_com_chunk.html">compute
com/chunk</A> command creates a global array
with 3 columns:
</P>
<PRE>compute myCOM all com/molecule
<PRE>compute myCOM all com/chunk
fix 1 all ave/histo 100 1 100 c_myCOM file tmp1.com mode vector
fix 2 all ave/histo 100 1 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.com mode vector
</PRE>

4
doc/fix_ave_histo.txt
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@ -95,10 +95,10 @@ If {mode} = vector, then the input values may either be vectors or
arrays. If a global array is listed, then it is the same as if the
individual columns of the array had been listed one by one.
E.g. these 2 fix ave/histo commands are equivalent, since the "compute
com/molecule"_compute_com_molecule.html command creates a global array
com/chunk"_compute_com_chunk.html command creates a global array
with 3 columns:
compute myCOM all com/molecule
compute myCOM all com/chunk
fix 1 all ave/histo 100 1 100 c_myCOM file tmp1.com mode vector
fix 2 all ave/histo 100 1 100 c_myCOM\[1\] c_myCOM\[2\] c_myCOM\[3\] file tmp2.com mode vector :pre