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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13104 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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66
doc/Section_howto.html
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@ -2172,7 +2172,7 @@ commands, to calculate various properties of a system:
overviewed. Then some examples are given of how to compute different
properties with chunk commands.
</P>
<H5><A HREF = "compute_chunk_atom.html">Compute chunk/atom</A> command
<H5><A HREF = "compute_chunk_atom.html">Compute chunk/atom</A> command:
</H5>
<P>This compute can assign atoms to chunks of various styles. Only atoms
in the specified group and optional specified region are assigned to a
@ -2213,7 +2213,7 @@ do this. You can also define a <A HREF = "variable.html">per-atom variable</A>
the input script that uses a formula to generate a chunk ID for each
atom.
</P>
<H5><A HREF = "fix_ave_chunk_atom.html">Fix ave/chunk</A> command
<H5><A HREF = "fix_ave_chunk_atom.html">Fix ave/chunk</A> command:
</H5>
<P>This fix takes the ID of a <A HREF = "compute_chunk_atom.html">compute
chunk/atom</A> command as input. For each chunk,
@ -2230,7 +2230,7 @@ values to be time-averaged in various ways, and output to a file. The
fix produces a global array as output with one row of values per
chunk.
</P>
<H5>Compute */chunk commands
<H5>Compute */chunk commands:
</H5>
<P>Currently the following computes operate on chunks of atoms to produce
per-chunk values.
@ -2279,42 +2279,40 @@ largest cluster or fastest diffusing molecule.
<P>Here are eaxmples using chunk commands to calculate various
properties:
</P>
<P>(1) Mimic the deprecated fix ave/spatial command, to average atom
velocity in each spatial bin:
<P>(1) Average velocity in each of 1000 2d spatial bins:
</P>
<P>Old command:
<PRE>compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.01 units reduced
fix 1 all ave/chunk 100 10 1000 cc1 vx vy file tmp.out
</PRE>
<P>(2) Temperature in each spatial bin, after subtracting a flow
velocity:
</P>
<P>fix ave/spatial
<PRE>compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.1 units reduced
compute vbias all temp/profile 1 0 0 y 10
fix 1 all ave/chunk 100 10 1000 cc1 temp bias vbias file tmp.out
</PRE>
<P>(3) Center of mass of each molecule:
</P>
<P>New commands:
<PRE>compute cc1 all chunk/atom molecule
compute myChunk all com/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
</PRE>
<P>(4) Total force on each molecule and ave/max across all molecules:
</P>
<P>compute chunk/atom
fix ave/chunk
</P>
<P>(2) Mimincing the deprecated compute msd/molecule command
to compute the mean-squared displacement of each molecule:
</P>
<P>Old commands:
</P>
<P>compute molecule/msd
fix ave/time file msd.molecule
</P>
<P>New commands:
</P>
<P>compute chunk/atom style
compute molecule/chunk
fix ave/time file msd.molecule
</P>
<P>(3) print or time ave total force per molecule
average across molecules (variable special functions)
</P>
<P>(4) histogram of cluster sizes (use fix ave/histo)
</P>
<P>(5) count of # of atoms with each coord #
don't need chunking, just fix ave/histo on coord/atom
</P>
<P>(6) ave temperature per bin
<PRE>compute cc1 all chunk/atom molecule
fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out
variable xave equal ave(f_1<B>2</B>)
variable xmax equal max(f_1<B>2</B>)
thermo 1000
thermo_style custom step temp v_xave v_xmax
</PRE>
<P>(5) Histogram of cluster sizes:
</P>
<PRE>compute cluster all cluster/atom 1.0
compute cc1 all chunk/atom c_cluster compress yes
compute size all property/chunk cc1 count
fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo
</PRE>
<HR>
<HR>

56
doc/Section_howto.txt
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@ -2159,7 +2159,7 @@ Here, each of the 3 kinds of chunk-related commands is briefly
overviewed. Then some examples are given of how to compute different
properties with chunk commands.
"Compute chunk/atom"_compute_chunk_atom.html command :h5
"Compute chunk/atom"_compute_chunk_atom.html command: :h5
This compute can assign atoms to chunks of various styles. Only atoms
in the specified group and optional specified region are assigned to a
@ -2198,7 +2198,7 @@ do this. You can also define a "per-atom variable"_variable.html in
the input script that uses a formula to generate a chunk ID for each
atom.
"Fix ave/chunk"_fix_ave_chunk_atom.html command :h5
"Fix ave/chunk"_fix_ave_chunk_atom.html command: :h5
This fix takes the ID of a "compute
chunk/atom"_compute_chunk_atom.html command as input. For each chunk,
@ -2215,7 +2215,7 @@ values to be time-averaged in various ways, and output to a file. The
fix produces a global array as output with one row of values per
chunk.
Compute */chunk commands :h5
Compute */chunk commands: :h5
Currently the following computes operate on chunks of atoms to produce
per-chunk values.
@ -2264,41 +2264,39 @@ Example calculations with chunks :h5
Here are eaxmples using chunk commands to calculate various
properties:
(1) Mimic the deprecated fix ave/spatial command, to average atom
velocity in each spatial bin:
(1) Average velocity in each of 1000 2d spatial bins:
Old command:
compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.01 units reduced
fix 1 all ave/chunk 100 10 1000 cc1 vx vy file tmp.out :pre
fix ave/spatial
(2) Temperature in each spatial bin, after subtracting a flow
velocity:
New commands:
compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.1 units reduced
compute vbias all temp/profile 1 0 0 y 10
fix 1 all ave/chunk 100 10 1000 cc1 temp bias vbias file tmp.out :pre
compute chunk/atom
fix ave/chunk
(3) Center of mass of each molecule:
(2) Mimincing the deprecated compute msd/molecule command
to compute the mean-squared displacement of each molecule:
compute cc1 all chunk/atom molecule
compute myChunk all com/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector :pre
Old commands:
(4) Total force on each molecule and ave/max across all molecules:
compute molecule/msd
fix ave/time file msd.molecule
compute cc1 all chunk/atom molecule
fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out
variable xave equal ave(f_1[2])
variable xmax equal max(f_1[2])
thermo 1000
thermo_style custom step temp v_xave v_xmax :pre
New commands:
(5) Histogram of cluster sizes:
compute chunk/atom style
compute molecule/chunk
fix ave/time file msd.molecule
(3) print or time ave total force per molecule
average across molecules (variable special functions)
(4) histogram of cluster sizes (use fix ave/histo)
(5) count of # of atoms with each coord #
don't need chunking, just fix ave/histo on coord/atom
(6) ave temperature per bin
compute cluster all cluster/atom 1.0
compute cc1 all chunk/atom c_cluster compress yes
compute size all property/chunk cc1 count
fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo :pre
:line
:line

2
doc/compute_com_chunk.html
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@ -63,7 +63,7 @@ image</A> command.
calculation to a file is to use the <A HREF = "fix_ave_time.html">fix ave/time</A>
command, for example:
</P>
<PRE>compute cc1 chunk/atom molecule
<PRE>compute cc1 all chunk/atom molecule
compute myChunk all com/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
</PRE>

2
doc/compute_com_chunk.txt
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@ -60,7 +60,7 @@ The simplest way to output the results of the compute com/chunk
calculation to a file is to use the "fix ave/time"_fix_ave_time.html
command, for example:
compute cc1 chunk/atom molecule
compute cc1 all chunk/atom molecule
compute myChunk all com/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector :pre

2
doc/compute_gyration_chunk.html
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@ -90,7 +90,7 @@ image</A> command.
calculation to a file is to use the <A HREF = "fix_ave_time.html">fix ave/time</A>
command, for example:
</P>
<PRE>compute cc1 chunk/atom molecule
<PRE>compute cc1 all chunk/atom molecule
compute myChunk all gyration/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
</PRE>

2
doc/compute_gyration_chunk.txt
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@ -81,7 +81,7 @@ The simplest way to output the results of the compute gyration/chunk
calculation to a file is to use the "fix ave/time"_fix_ave_time.html
command, for example:
compute cc1 chunk/atom molecule
compute cc1 all chunk/atom molecule
compute myChunk all gyration/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector :pre

2
doc/compute_inertia_chunk.html
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@ -64,7 +64,7 @@ image</A> command.
calculation to a file is to use the <A HREF = "fix_ave_time.html">fix ave/time</A>
command, for example:
</P>
<PRE>compute cc1 chunk/atom molecule
<PRE>compute cc1 all chunk/atom molecule
compute myChunk all inertia/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
</PRE>

2
doc/compute_inertia_chunk.txt
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@ -61,7 +61,7 @@ The simplest way to output the results of the compute inertia/chunk
calculation to a file is to use the "fix ave/time"_fix_ave_time.html
command, for example:
compute cc1 chunk/atom molecule
compute cc1 all chunk/atom molecule
compute myChunk all inertia/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector :pre

2
doc/compute_msd_chunk.html
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@ -97,7 +97,7 @@ file</A>.
calculation to a file is to use the <A HREF = "fix_ave_time.html">fix ave/time</A>
command, for example:
</P>
<PRE>compute cc1 chunk/atom molecule
<PRE>compute cc1 all chunk/atom molecule
compute myChunk all com/msd cc1
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
</PRE>

2
doc/compute_msd_chunk.txt
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@ -94,7 +94,7 @@ The simplest way to output the results of the compute com/msd
calculation to a file is to use the "fix ave/time"_fix_ave_time.html
command, for example:
compute cc1 chunk/atom molecule
compute cc1 all chunk/atom molecule
compute myChunk all com/msd cc1
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector :pre

2
doc/compute_property_chunk.html
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@ -92,7 +92,7 @@ will be in unitless reduced units (0-1).
calculation to a file is to use the <A HREF = "fix_ave_time.html">fix ave/time</A>
command, for example:
</P>
<PRE>compute cc1 chunk/atom molecule
<PRE>compute cc1 all chunk/atom molecule
compute myChunk1 all property/chunk cc1
compute myChunk2 all com/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk1 c_myChunk2 file tmp.out mode vector

2
doc/compute_property_chunk.txt
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@ -85,7 +85,7 @@ The simplest way to output the results of the compute property/chunk
calculation to a file is to use the "fix ave/time"_fix_ave_time.html
command, for example:
compute cc1 chunk/atom molecule
compute cc1 all chunk/atom molecule
compute myChunk1 all property/chunk cc1
compute myChunk2 all com/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk1 c_myChunk2 file tmp.out mode vector :pre

2
doc/compute_temp_chunk.html
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@ -114,7 +114,7 @@ non-zero chunk IDs.
calculation to a file is to use the <A HREF = "fix_ave_time.html">fix ave/time</A>
command, for example:
</P>
<PRE>compute cc1 chunk/atom molecule
<PRE>compute cc1 all chunk/atom molecule
compute myChunk all temp/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
</PRE>

2
doc/compute_temp_chunk.txt
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@ -104,7 +104,7 @@ The simplest way to output the results of the compute temp/chunk
calculation to a file is to use the "fix ave/time"_fix_ave_time.html
command, for example:
compute cc1 chunk/atom molecule
compute cc1 all chunk/atom molecule
compute myChunk all temp/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector :pre

2
doc/compute_torque_chunk.html
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@ -64,7 +64,7 @@ image</A> command.
calculation to a file is to use the <A HREF = "fix_ave_time.html">fix ave/time</A>
command, for example:
</P>
<PRE>compute cc1 chunk/atom molecule
<PRE>compute cc1 all chunk/atom molecule
compute myChunk all torque/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
</PRE>

2
doc/compute_torque_chunk.txt
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@ -61,7 +61,7 @@ The simplest way to output the results of the compute torque/chunk
calculation to a file is to use the "fix ave/time"_fix_ave_time.html
command, for example:
compute cc1 chunk/atom molecule
compute cc1 all chunk/atom molecule
compute myChunk all torque/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector :pre

2
doc/compute_vcm_chunk.html
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@ -55,7 +55,7 @@ non-zero chunk IDs.
calculation to a file is to use the <A HREF = "fix_ave_time.html">fix ave/time</A>
command, for example:
</P>
<PRE>compute cc1 chunk/atom molecule
<PRE>compute cc1 all chunk/atom molecule
compute myChunk all vcm/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
</PRE>

2
doc/compute_vcm_chunk.txt
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@ -52,7 +52,7 @@ The simplest way to output the results of the compute vcm/chunk
calculation to a file is to use the "fix ave/time"_fix_ave_time.html
command, for example:
compute cc1 chunk/atom molecule
compute cc1 all chunk/atom molecule
compute myChunk all vcm/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector :pre

29
doc/fix_ave_chunk.html
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@ -72,7 +72,7 @@
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all ave/chunk 10000 1 10000 binchunk c_myCentro ttle1 "My output values"
<PRE>fix 1 all ave/chunk 10000 1 10000 binchunk c_myCentro title1 "My output values"
fix 1 flow ave/chunk 100 10 1000 molchunk vx vz norm sample file vel.profile
fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running
fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running
@ -95,11 +95,11 @@ fix 1 flow ave/chunk 100 10 1000 cc1 vx vz norm sample file vel.profile
<P><B>Description:</B>
</P>
<P>Use one or more per-atom vectors as inputs every few timesteps, sum
their values for multiple chunks of atoms, and average the values for
each chunk over longer timescales. The resulting chunk averages can
be used by other <A HREF = "Section_howto.html#howto_15">output commands</A> such as
<A HREF = "thermo_style.html">thermo_style custom</A>, and can also be written to a
file.
the values over the atoms in each chunk at each timestep, then average
the per-chunk values over longer timescales. The resulting chunk
averages can be used by other <A HREF = "Section_howto.html#howto_15">output
commands</A> such as <A HREF = "thermo_style.html">thermo_style
custom</A>, and can also be written to a file.
</P>
<P>In LAMMPS, chunks are collections of atoms defined by a <A HREF = "compute_chunk_atom.html">compute
chunk/atom</A> command, which assigns each atom
@ -195,15 +195,14 @@ property/atom</A> command and then specifying
an input value from that compute.
</P>
<P>The <I>density/number</I> value means the number density is computed for
each chunk, i.e. a weighting of 1 for each atom. The <I>density/mass</I>
value means the mass density is computed for each , i.e. each atom is
weighted by its mass. The resulting density is normalized by the
volume of the chunk so that units of number/volume or density are
output. See the <A HREF = "units.html">units</A> command doc page for the
definition of density for each choice of units, e.g. gram/cm^3. If
the chunks defined by the <A HREF = "compute_chunk_atom.html">compute chunk/atom</A>
command are spatial bins, the volume is the bin volume. Otherwise it
is the volume of the entire simulation box.
each chunk, i.e. number/volume. The <I>density/mass</I> value means the
mass density is computed for each chunk, i.e. total-mass/volume. The
output values are in units of 1/volume or density (mass/volume). See
the <A HREF = "units.html">units</A> command doc page for the definition of density
for each choice of units, e.g. gram/cm^3. If the chunks defined by
the <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command are spatial
bins, the volume is the bin volume. Otherwise it is the volume of the
entire simulation box.
</P>
<P>The <I>temp</I> value means the temperature is computed for each chunk, by
the formula KE = DOF/2 k T, where KE = total kinetic energy of the

29
doc/fix_ave_chunk.txt
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@ -58,7 +58,7 @@ keyword = {norm} or {ave} or {bias} or {adof} or {cdof} or {file} or {overwrite}
[Examples:]
fix 1 all ave/chunk 10000 1 10000 binchunk c_myCentro ttle1 "My output values"
fix 1 all ave/chunk 10000 1 10000 binchunk c_myCentro title1 "My output values"
fix 1 flow ave/chunk 100 10 1000 molchunk vx vz norm sample file vel.profile
fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running
fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running :pre
@ -81,11 +81,11 @@ fix 1 flow ave/chunk 100 10 1000 cc1 vx vz norm sample file vel.profile :pre
[Description:]
Use one or more per-atom vectors as inputs every few timesteps, sum
their values for multiple chunks of atoms, and average the values for
each chunk over longer timescales. The resulting chunk averages can
be used by other "output commands"_Section_howto.html#howto_15 such as
"thermo_style custom"_thermo_style.html, and can also be written to a
file.
the values over the atoms in each chunk at each timestep, then average
the per-chunk values over longer timescales. The resulting chunk
averages can be used by other "output
commands"_Section_howto.html#howto_15 such as "thermo_style
custom"_thermo_style.html, and can also be written to a file.
In LAMMPS, chunks are collections of atoms defined by a "compute
chunk/atom"_compute_chunk_atom.html command, which assigns each atom
@ -181,15 +181,14 @@ property/atom"_compute_property_atom.html command and then specifying
an input value from that compute.
The {density/number} value means the number density is computed for
each chunk, i.e. a weighting of 1 for each atom. The {density/mass}
value means the mass density is computed for each , i.e. each atom is
weighted by its mass. The resulting density is normalized by the
volume of the chunk so that units of number/volume or density are
output. See the "units"_units.html command doc page for the
definition of density for each choice of units, e.g. gram/cm^3. If
the chunks defined by the "compute chunk/atom"_compute_chunk_atom.html
command are spatial bins, the volume is the bin volume. Otherwise it
is the volume of the entire simulation box.
each chunk, i.e. number/volume. The {density/mass} value means the
mass density is computed for each chunk, i.e. total-mass/volume. The
output values are in units of 1/volume or density (mass/volume). See
the "units"_units.html command doc page for the definition of density
for each choice of units, e.g. gram/cm^3. If the chunks defined by
the "compute chunk/atom"_compute_chunk_atom.html command are spatial
bins, the volume is the bin volume. Otherwise it is the volume of the
entire simulation box.
The {temp} value means the temperature is computed for each chunk, by
the formula KE = DOF/2 k T, where KE = total kinetic energy of the