forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12978 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
31731fd1ce
commit
1833a9abc4
|
|
@ -34,7 +34,8 @@
|
|||
6.19 <A HREF = "#howto_19">Library interface to LAMMPS</A><BR>
|
||||
6.20 <A HREF = "#howto_20">Calculating thermal conductivity</A><BR>
|
||||
6.21 <A HREF = "#howto_21">Calculating viscosity</A><BR>
|
||||
6.22 <A HREF = "#howto_22">Calculating a diffusion coefficient</A> <BR>
|
||||
6.22 <A HREF = "#howto_22">Calculating a diffusion coefficient</A><BR>
|
||||
6.23 <A HREF = "#howto_23">Using chunks to calculate system properties</A> <BR>
|
||||
|
||||
<P>The example input scripts included in the LAMMPS distribution and
|
||||
highlighted in <A HREF = "Section_example.html">Section_example</A> also show how to
|
||||
|
|
@ -2146,6 +2147,160 @@ and thus extract D.
|
|||
</P>
|
||||
<HR>
|
||||
|
||||
<A NAME = "howto_23"></A><H4>6.23 Using chunks to calculate system properties
|
||||
</H4>
|
||||
<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
|
||||
to a chunk (or to no chunk at all). The per-atom chunk assignments
|
||||
can be used as input to two other kinds of commands, to calculate
|
||||
various properties of a system:
|
||||
</P>
|
||||
<UL><LI><A HREF = "fix_ave_chunk.html">fix ave/chunk</A>
|
||||
<LI>a variety of <A HREF = "compute.html">compute */chunk</A> commands
|
||||
</UL>
|
||||
<P>Here, each of the 3 kinds of chunk-related commands is briefly
|
||||
overviewed, and some examples given of how to compute
|
||||
different properties with chunk commands.
|
||||
</P>
|
||||
<H5><A HREF = "compute_chunk_atom.html">Compute chunk/atom</A> command
|
||||
</H5>
|
||||
<P>This compute assigns atoms to chunks of various styles. Only atoms in
|
||||
the specified group and optional specified region are assigned to a
|
||||
chunk. Here is a list of possible chunk definitions:
|
||||
</P>
|
||||
<DIV ALIGN=center><TABLE BORDER=1 >
|
||||
<TR><TD >atoms in same molecule </TD><TD > chunk ID = molecule ID </TD></TR>
|
||||
<TR><TD >atoms with same atom type -</TD><TD > chunk ID = atom type </TD></TR>
|
||||
<TR><TD >all atoms with same atom property (charge, radius, etc) </TD><TD > chunk ID = output of compute property/atom </TD></TR>
|
||||
<TR><TD >atoms in same cluster </TD><TD > chunk ID = output of compute cluster/atom command </TD></TR>
|
||||
<TR><TD >atoms in same spatial bin </TD><TD > chunk ID = bin ID </TD></TR>
|
||||
<TR><TD >atoms in same rigid body </TD><TD > chunk ID = ID of an atom in the body </TD></TR>
|
||||
<TR><TD >all atoms with same local defect structure </TD><TD > chunk ID = output of compute centro/atom or coord/atom command
|
||||
</TD></TR></TABLE></DIV>
|
||||
|
||||
<P>Spatial bins can be of various kinds, e.g. 1d bins = slabs, 2d bins =
|
||||
pencils, 3d bins = boxes, spherical bins, cylindrical bins.
|
||||
</P>
|
||||
<P>This compute also calculates the number of chunks <I>Nchunk</I> which is
|
||||
used by other commands to tally per-chunk data. <I>Nchunk</I> can be a
|
||||
static value or change over time (e.g. the number of clusters). The
|
||||
chunk ID for an individual atom can also be static (e.g. a molecule
|
||||
ID), or dynamic (e.g. what spatial bin an atom is in as it moves).
|
||||
</P>
|
||||
<P>Note that this compute allows the per-atom output of other
|
||||
<A HREF = "compute.html">computes</A>, <A HREF = "fix.html">fixes</A>, and
|
||||
<A HREF = "variable.html">variables</A> to be used to define chunk IDs for each
|
||||
atom. This means you can write your own compute or fix to output a
|
||||
per-atom quantity to use as chunk ID; See
|
||||
<A HREF = "Section_modify.html">Section_modify</A> of the documentation for how to
|
||||
do this. You can also define a <A HREF = "variable.html">per-atom variable</A> in
|
||||
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>
|
||||
<P>This fix takes the ID of a <A HREF = "compute_chunk_atom.html">compute
|
||||
chunk/atom</A> command as input. For each chunk
|
||||
it then sums one or more specified per-atom values over the atoms in
|
||||
each chunk. The per-atom values can be any atom property, such as
|
||||
force, charge, potential energy, kinetic energy, stress. Additional
|
||||
keywords are allowed for per-chunk properties like density and
|
||||
temperature. More generally any per-atom value generated by other
|
||||
<A HREF = "compute.html">computes</A>, <A HREF = "fix.html">fixes</A>, and <A HREF = "variable.html">per-atom
|
||||
variables</A>, can be summed over atoms in each chunk.
|
||||
</P>
|
||||
<P>Similar to other averaging fixes, this fix allows the summed per-chunk
|
||||
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. Global arrays or columns thereof can be used as input for
|
||||
other commands, as described in the following section.
|
||||
</P>
|
||||
<H5>Compute */chunk commands
|
||||
</H5>
|
||||
<P>Currently the following computes operate on chunks:
|
||||
</P>
|
||||
<UL><LI><A HREF = "compute_com_chunk.html">compute com/chunk</A>
|
||||
<LI><A HREF = "compute_gyration_chunk.html">compute gyration/chunk</A>
|
||||
<LI><A HREF = "compute_inertia_chunk.html">compute inertia/chunk</A>
|
||||
<LI><A HREF = "compute_msd_chunk.html">compute msd/chunk</A>
|
||||
<LI><A HREF = "compute_property_chunk.html">compute property/chunk</A>
|
||||
<LI><A HREF = "compute_vcm_chunk.html">compute vcm/chunk</A>
|
||||
</UL>
|
||||
<P>They each take the ID of a <A HREF = "compute_chunk_atom.html">compute
|
||||
chunk/atom</A> command as input. As their names
|
||||
indicate, they calculate the center-of-mass, radius of gyration,
|
||||
moments of inertia, mean-squared displacement, and velocity of
|
||||
center-of-mass for each chunk of atoms. The <A HREF = "compute_property_chunk.html">compute
|
||||
property/chunk</A> command can be tally the
|
||||
count of atoms in each chunk and extract other per-chunk properties.
|
||||
</P>
|
||||
<P>The reason these various calculations are not part of the <A HREF = "fix_ave_chunk.html">fix
|
||||
ave/chunk command</A>, is that each requires a more
|
||||
complicated operation than simply summing and averaging over per-atom
|
||||
values in each chunk. Most of them require calculation of a center of
|
||||
mass, which requires summing mass*position over the atoms and dividing
|
||||
by summed mass.
|
||||
</P>
|
||||
<P>All of these computes produce a global vector or global array as
|
||||
output, wih one or more values per chunk. Global vectors or arrays
|
||||
can be used as input for other commands, e.g.
|
||||
</P>
|
||||
<UL><LI>As input to the <A HREF = "fix_ave_time.html">fix ave/time</A> command, so the
|
||||
per-chunk values output to a file it creates. The <A HREF = "fix_ave_time.html">fix
|
||||
ave/time</A> command can also average the values for
|
||||
each chunk over time if desired.
|
||||
|
||||
<LI>As input to the <A HREF = "fix_ave_histo.html">fix ave/histo</A> command to
|
||||
histogram values across chunks. E.g. a histogram of cluster sizes or
|
||||
molecule diffusion rates.
|
||||
|
||||
<LI>As input to special functions of <A HREF = "variable.html">equal-style
|
||||
variables</A>, like sum() and max(). E.g. to find the
|
||||
largest cluster or fastest diffusing molecule.
|
||||
</UL>
|
||||
<H5>Example calculations with chunks
|
||||
</H5>
|
||||
<P>Here are chunk commands that can be used to calculate various
|
||||
properties:
|
||||
</P>
|
||||
<P>(1) Mimic the deprecated fix ave/spatial command, to average atom
|
||||
velocity in each spatial bin:
|
||||
</P>
|
||||
<P>Old command:
|
||||
</P>
|
||||
<P>fix ave/spatial
|
||||
</P>
|
||||
<P>New commands:
|
||||
</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
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<HR>
|
||||
|
||||
<A NAME = "Berendsen"></A>
|
||||
|
|
|
|||
|
|
@ -31,7 +31,8 @@ This section describes how to perform common tasks using LAMMPS.
|
|||
6.19 "Library interface to LAMMPS"_#howto_19
|
||||
6.20 "Calculating thermal conductivity"_#howto_20
|
||||
6.21 "Calculating viscosity"_#howto_21
|
||||
6.22 "Calculating a diffusion coefficient"_#howto_22 :all(b)
|
||||
6.22 "Calculating a diffusion coefficient"_#howto_22
|
||||
6.23 "Using chunks to calculate system properties"_#howto_23 :all(b)
|
||||
|
||||
The example input scripts included in the LAMMPS distribution and
|
||||
highlighted in "Section_example"_Section_example.html also show how to
|
||||
|
|
@ -2131,6 +2132,158 @@ accumulated in a vector via the "fix vector"_fix_vector.html command,
|
|||
and time integrated via the "variable trap"_variable.html function,
|
||||
and thus extract D.
|
||||
|
||||
:line
|
||||
|
||||
6.23 Using chunks to calculate system properties :link(howto_23),h4
|
||||
|
||||
In LAMMPS, chunks are collections of atoms defined by a "compute
|
||||
chunk/atom"_compute_chunk_atom.html command, which assigns each atom
|
||||
to a chunk (or to no chunk at all). The per-atom chunk assignments
|
||||
can be used as input to two other kinds of commands, to calculate
|
||||
various properties of a system:
|
||||
|
||||
"fix ave/chunk"_fix_ave_chunk.html
|
||||
a variety of "compute */chunk"_compute.html commands :ul
|
||||
|
||||
Here, each of the 3 kinds of chunk-related commands is briefly
|
||||
overviewed, and some examples given of how to compute
|
||||
different properties with chunk commands.
|
||||
|
||||
"Compute chunk/atom"_compute_chunk_atom.html command :h5
|
||||
|
||||
This compute assigns atoms to chunks of various styles. Only atoms in
|
||||
the specified group and optional specified region are assigned to a
|
||||
chunk. Here is a list of possible chunk definitions:
|
||||
|
||||
atoms in same molecule | chunk ID = molecule ID |
|
||||
atoms with same atom type -| chunk ID = atom type |
|
||||
all atoms with same atom property (charge, radius, etc) | chunk ID = output of compute property/atom |
|
||||
atoms in same cluster | chunk ID = output of compute cluster/atom command |
|
||||
atoms in same spatial bin | chunk ID = bin ID |
|
||||
atoms in same rigid body | chunk ID = ID of an atom in the body |
|
||||
all atoms with same local defect structure | chunk ID = output of compute centro/atom or coord/atom command :tb(s=|,c=2)
|
||||
|
||||
Spatial bins can be of various kinds, e.g. 1d bins = slabs, 2d bins =
|
||||
pencils, 3d bins = boxes, spherical bins, cylindrical bins.
|
||||
|
||||
This compute also calculates the number of chunks {Nchunk} which is
|
||||
used by other commands to tally per-chunk data. {Nchunk} can be a
|
||||
static value or change over time (e.g. the number of clusters). The
|
||||
chunk ID for an individual atom can also be static (e.g. a molecule
|
||||
ID), or dynamic (e.g. what spatial bin an atom is in as it moves).
|
||||
|
||||
Note that this compute allows the per-atom output of other
|
||||
"computes"_compute.html, "fixes"_fix.html, and
|
||||
"variables"_variable.html to be used to define chunk IDs for each
|
||||
atom. This means you can write your own compute or fix to output a
|
||||
per-atom quantity to use as chunk ID; See
|
||||
"Section_modify"_Section_modify.html of the documentation for how to
|
||||
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
|
||||
|
||||
This fix takes the ID of a "compute
|
||||
chunk/atom"_compute_chunk_atom.html command as input. For each chunk
|
||||
it then sums one or more specified per-atom values over the atoms in
|
||||
each chunk. The per-atom values can be any atom property, such as
|
||||
force, charge, potential energy, kinetic energy, stress. Additional
|
||||
keywords are allowed for per-chunk properties like density and
|
||||
temperature. More generally any per-atom value generated by other
|
||||
"computes"_compute.html, "fixes"_fix.html, and "per-atom
|
||||
variables"_variable.html, can be summed over atoms in each chunk.
|
||||
|
||||
Similar to other averaging fixes, this fix allows the summed per-chunk
|
||||
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. Global arrays or columns thereof can be used as input for
|
||||
other commands, as described in the following section.
|
||||
|
||||
Compute */chunk commands :h5
|
||||
|
||||
Currently the following computes operate on chunks:
|
||||
|
||||
"compute com/chunk"_compute_com_chunk.html
|
||||
"compute gyration/chunk"_compute_gyration_chunk.html
|
||||
"compute inertia/chunk"_compute_inertia_chunk.html
|
||||
"compute msd/chunk"_compute_msd_chunk.html
|
||||
"compute property/chunk"_compute_property_chunk.html
|
||||
"compute vcm/chunk"_compute_vcm_chunk.html :ul
|
||||
|
||||
They each take the ID of a "compute
|
||||
chunk/atom"_compute_chunk_atom.html command as input. As their names
|
||||
indicate, they calculate the center-of-mass, radius of gyration,
|
||||
moments of inertia, mean-squared displacement, and velocity of
|
||||
center-of-mass for each chunk of atoms. The "compute
|
||||
property/chunk"_compute_property_chunk.html command can be tally the
|
||||
count of atoms in each chunk and extract other per-chunk properties.
|
||||
|
||||
The reason these various calculations are not part of the "fix
|
||||
ave/chunk command"_fix_ave_chunk.html, is that each requires a more
|
||||
complicated operation than simply summing and averaging over per-atom
|
||||
values in each chunk. Most of them require calculation of a center of
|
||||
mass, which requires summing mass*position over the atoms and dividing
|
||||
by summed mass.
|
||||
|
||||
All of these computes produce a global vector or global array as
|
||||
output, wih one or more values per chunk. Global vectors or arrays
|
||||
can be used as input for other commands, e.g.
|
||||
|
||||
As input to the "fix ave/time"_fix_ave_time.html command, so the
|
||||
per-chunk values output to a file it creates. The "fix
|
||||
ave/time"_fix_ave_time.html command can also average the values for
|
||||
each chunk over time if desired. :ulb,l
|
||||
|
||||
As input to the "fix ave/histo"_fix_ave_histo.html command to
|
||||
histogram values across chunks. E.g. a histogram of cluster sizes or
|
||||
molecule diffusion rates. :l
|
||||
|
||||
As input to special functions of "equal-style
|
||||
variables"_variable.html, like sum() and max(). E.g. to find the
|
||||
largest cluster or fastest diffusing molecule. :l,ule
|
||||
|
||||
Example calculations with chunks :h5
|
||||
|
||||
Here are chunk commands that can be used to calculate various
|
||||
properties:
|
||||
|
||||
(1) Mimic the deprecated fix ave/spatial command, to average atom
|
||||
velocity in each spatial bin:
|
||||
|
||||
Old command:
|
||||
|
||||
fix ave/spatial
|
||||
|
||||
New commands:
|
||||
|
||||
compute chunk/atom
|
||||
fix ave/chunk
|
||||
|
||||
(2) Mimincing the deprecated compute msd/molecule command
|
||||
to compute the mean-squared displacement of each molecule:
|
||||
|
||||
Old commands:
|
||||
|
||||
compute molecule/msd
|
||||
fix ave/time file msd.molecule
|
||||
|
||||
New commands:
|
||||
|
||||
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
|
||||
|
||||
:line
|
||||
:line
|
||||
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@
|
|||
|
||||
<LI>keyword = <I>bias</I> or <I>dof</I>
|
||||
|
||||
<PRE> <I>bias</I> value = bias-ID<I>uniform</I> or <I>gaussian</I>
|
||||
<PRE> <I>bias</I> value = bias-ID
|
||||
bias-ID = ID of a temperature compute that removes a velocity bias
|
||||
<I>dof</I> value = <I>all</I> or <I>rotate</I>
|
||||
all = compute temperature of translational and rotational degrees of freedom
|
||||
|
|
@ -113,10 +113,10 @@ thermostatting.
|
|||
compute that removes a "bias" velocity from each atom. This allows
|
||||
compute temp/sphere to compute its thermal temperature after the
|
||||
translational kinetic energy components have been altered in a
|
||||
prescribed way, e.g. to remove a velocity profile. Thermostats that
|
||||
use this compute will work with this bias term. See the doc pages for
|
||||
individual computes that calculate a temperature and the doc pages for
|
||||
fixes that perform thermostatting for more details.
|
||||
prescribed way, e.g. to remove a flow velocity profile. Thermostats
|
||||
that use this compute will work with this bias term. See the doc
|
||||
pages for individual computes that calculate a temperature and the doc
|
||||
pages for fixes that perform thermostatting for more details.
|
||||
</P>
|
||||
<P>For the <I>dof</I> keyword, a setting of <I>all</I> calculates a temperature
|
||||
that includes both translational and rotational degrees of freedom. A
|
||||
|
|
|
|||
|
|
@ -16,7 +16,7 @@ ID, group-ID are documented in "compute"_compute.html command :ulb,l
|
|||
temp/asphere = style name of this compute command :l
|
||||
zero or more keyword/value pairs may be appended :l
|
||||
keyword = {bias} or {dof} :l
|
||||
{bias} value = bias-ID{uniform} or {gaussian}
|
||||
{bias} value = bias-ID
|
||||
bias-ID = ID of a temperature compute that removes a velocity bias
|
||||
{dof} value = {all} or {rotate}
|
||||
all = compute temperature of translational and rotational degrees of freedom
|
||||
|
|
@ -105,10 +105,10 @@ For the {bias} keyword, {bias-ID} refers to the ID of a temperature
|
|||
compute that removes a "bias" velocity from each atom. This allows
|
||||
compute temp/sphere to compute its thermal temperature after the
|
||||
translational kinetic energy components have been altered in a
|
||||
prescribed way, e.g. to remove a velocity profile. Thermostats that
|
||||
use this compute will work with this bias term. See the doc pages for
|
||||
individual computes that calculate a temperature and the doc pages for
|
||||
fixes that perform thermostatting for more details.
|
||||
prescribed way, e.g. to remove a flow velocity profile. Thermostats
|
||||
that use this compute will work with this bias term. See the doc
|
||||
pages for individual computes that calculate a temperature and the doc
|
||||
pages for fixes that perform thermostatting for more details.
|
||||
|
||||
For the {dof} keyword, a setting of {all} calculates a temperature
|
||||
that includes both translational and rotational degrees of freedom. A
|
||||
|
|
|
|||
|
|
@ -74,12 +74,13 @@ compute.
|
|||
</P>
|
||||
<P>Unlike other compute styles that calculate temperature, this compute
|
||||
does not subtract out degrees-of-freedom due to fixes that constrain
|
||||
molecular motion, such as <A HREF = "fix_shake.html">fix shake</A> and <A HREF = "fix_rigid.html">fix
|
||||
motion, such as <A HREF = "fix_shake.html">fix shake</A> and <A HREF = "fix_rigid.html">fix
|
||||
rigid</A>. This is because those degrees of freedom
|
||||
(e.g. a constrained bond) can straddle the region boundary, and hence
|
||||
the concept is somewhat ill-defined. If needed the number of
|
||||
subtracted degrees-of-freedom can be set explicitly using the <I>extra</I>
|
||||
option of the <A HREF = "compute_modify.html">compute_modify</A> command.
|
||||
(e.g. a constrained bond) could apply to sets of atoms that straddle
|
||||
the region boundary, and hence the concept is somewhat ill-defined.
|
||||
If needed the number of subtracted degrees-of-freedom can be set
|
||||
explicitly using the <I>extra</I> option of the
|
||||
<A HREF = "compute_modify.html">compute_modify</A> command.
|
||||
</P>
|
||||
<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
|
||||
a discussion of different ways to compute temperature and perform
|
||||
|
|
|
|||
|
|
@ -71,12 +71,13 @@ compute.
|
|||
|
||||
Unlike other compute styles that calculate temperature, this compute
|
||||
does not subtract out degrees-of-freedom due to fixes that constrain
|
||||
molecular motion, such as "fix shake"_fix_shake.html and "fix
|
||||
motion, such as "fix shake"_fix_shake.html and "fix
|
||||
rigid"_fix_rigid.html. This is because those degrees of freedom
|
||||
(e.g. a constrained bond) can straddle the region boundary, and hence
|
||||
the concept is somewhat ill-defined. If needed the number of
|
||||
subtracted degrees-of-freedom can be set explicitly using the {extra}
|
||||
option of the "compute_modify"_compute_modify.html command.
|
||||
(e.g. a constrained bond) could apply to sets of atoms that straddle
|
||||
the region boundary, and hence the concept is somewhat ill-defined.
|
||||
If needed the number of subtracted degrees-of-freedom can be set
|
||||
explicitly using the {extra} option of the
|
||||
"compute_modify"_compute_modify.html command.
|
||||
|
||||
See "this howto section"_Section_howto.html#howto_16 of the manual for
|
||||
a discussion of different ways to compute temperature and perform
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@
|
|||
|
||||
<LI>keyword = <I>bias</I> or <I>dof</I>
|
||||
|
||||
<PRE> <I>bias</I> value = bias-ID<I>uniform</I> or <I>gaussian</I>
|
||||
<PRE> <I>bias</I> value = bias-ID
|
||||
bias-ID = ID of a temperature compute that removes a velocity bias
|
||||
<I>dof</I> value = <I>all</I> or <I>rotate</I>
|
||||
all = compute temperature of translational and rotational degrees of freedom
|
||||
|
|
@ -99,10 +99,10 @@ thermostatting.
|
|||
compute that removes a "bias" velocity from each atom. This allows
|
||||
compute temp/sphere to compute its thermal temperature after the
|
||||
translational kinetic energy components have been altered in a
|
||||
prescribed way, e.g. to remove a velocity profile. Thermostats that
|
||||
use this compute will work with this bias term. See the doc pages for
|
||||
individual computes that calculate a temperature and the doc pages for
|
||||
fixes that perform thermostatting for more details.
|
||||
prescribed way, e.g. to remove a flow velocity profile. Thermostats
|
||||
that use this compute will work with this bias term. See the doc
|
||||
pages for individual computes that calculate a temperature and the doc
|
||||
pages for fixes that perform thermostatting for more details.
|
||||
</P>
|
||||
<P>For the <I>dof</I> keyword, a setting of <I>all</I> calculates a temperature
|
||||
that includes both translational and rotational degrees of freedom. A
|
||||
|
|
|
|||
|
|
@ -16,7 +16,7 @@ ID, group-ID are documented in "compute"_compute.html command :ulb,l
|
|||
temp/sphere = style name of this compute command :l
|
||||
zero or more keyword/value pairs may be appended :l
|
||||
keyword = {bias} or {dof} :l
|
||||
{bias} value = bias-ID{uniform} or {gaussian}
|
||||
{bias} value = bias-ID
|
||||
bias-ID = ID of a temperature compute that removes a velocity bias
|
||||
{dof} value = {all} or {rotate}
|
||||
all = compute temperature of translational and rotational degrees of freedom
|
||||
|
|
@ -91,10 +91,10 @@ For the {bias} keyword, {bias-ID} refers to the ID of a temperature
|
|||
compute that removes a "bias" velocity from each atom. This allows
|
||||
compute temp/sphere to compute its thermal temperature after the
|
||||
translational kinetic energy components have been altered in a
|
||||
prescribed way, e.g. to remove a velocity profile. Thermostats that
|
||||
use this compute will work with this bias term. See the doc pages for
|
||||
individual computes that calculate a temperature and the doc pages for
|
||||
fixes that perform thermostatting for more details.
|
||||
prescribed way, e.g. to remove a flow velocity profile. Thermostats
|
||||
that use this compute will work with this bias term. See the doc
|
||||
pages for individual computes that calculate a temperature and the doc
|
||||
pages for fixes that perform thermostatting for more details.
|
||||
|
||||
For the {dof} keyword, a setting of {all} calculates a temperature
|
||||
that includes both translational and rotational degrees of freedom. A
|
||||
|
|
|
|||
|
|
@ -44,6 +44,8 @@
|
|||
<I>precision</I> arg = power-of-10 value from 10 to 1000000
|
||||
<I>region</I> arg = region-ID or "none"
|
||||
<I>scale</I> arg = <I>yes</I> or <I>no</I>
|
||||
<I>sfactor</I> arg = coordinate scaling factor (> 0.0)
|
||||
<I>tfactor</I> arg = time scaling factor (> 0.0)
|
||||
<I>sort</I> arg = <I>off</I> or <I>id</I> or N or -N
|
||||
off = no sorting of per-atom lines within a snapshot
|
||||
id = sort per-atom lines by atom ID
|
||||
|
|
@ -111,7 +113,7 @@
|
|||
<PRE>dump_modify 1 format "%d %d %20.15g %g %g" scale yes
|
||||
dump_modify myDump image yes scale no flush yes
|
||||
dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2
|
||||
dump_modify xtcdump precision 10000
|
||||
dump_modify xtcdump precision 10000 sfactor 0.1
|
||||
dump_modify 1 every 1000 nfile 20
|
||||
dump_modify 1 every v_myVar
|
||||
dump_modify 1 amap min max cf 0.0 3 min green 0.5 yellow max blue boxcolor red
|
||||
|
|
@ -364,6 +366,21 @@ nanometer accuracy, e.g. for N = 1000, the coordinates are written to
|
|||
</P>
|
||||
<HR>
|
||||
|
||||
<P>The <I>sfactor</I> and <I>tfactor</I> keywords only apply to the dump <I>xtc</I>
|
||||
style. They allow customization of the unit conversion factors used
|
||||
when writing to XTC files. By default they are initialized for
|
||||
whatever <A HREF = "units.html">units</A> style is being used, to write out
|
||||
coordinates in nanometers and time in picoseconds. I.e. for <I>real</I>
|
||||
units, LAMMPS defines <I>sfactor</I> = 0.1 and <I>tfactor</I> = 0.001, since the
|
||||
Angstroms and fmsec used by <I>real</I> units are 0.1 nm and 0.001 psec
|
||||
respectively. If you are using a units system with distance and time
|
||||
units far from nm and psec, you may wish to write XTC files with
|
||||
different units, since the compression algorithm used in XTC files is
|
||||
most effective when the typical magnitude of position data is between
|
||||
10.0 and 0.1.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>The <I>region</I> keyword only applies to the dump <I>custom</I>, <I>cfg</I>,
|
||||
<I>image</I>, and <I>movie</I> styles. If specified, only atoms in the region
|
||||
will be written to the dump file or included in the image/movie. Only
|
||||
|
|
|
|||
|
|
@ -37,6 +37,8 @@ keyword = {append} or {buffer} or {element} or {every} or {fileper} or {first} o
|
|||
{precision} arg = power-of-10 value from 10 to 1000000
|
||||
{region} arg = region-ID or "none"
|
||||
{scale} arg = {yes} or {no}
|
||||
{sfactor} arg = coordinate scaling factor (> 0.0)
|
||||
{tfactor} arg = time scaling factor (> 0.0)
|
||||
{sort} arg = {off} or {id} or N or -N
|
||||
off = no sorting of per-atom lines within a snapshot
|
||||
id = sort per-atom lines by atom ID
|
||||
|
|
@ -100,7 +102,7 @@ keyword = {acolor} or {adiam} or {amap} or {backcolor} or {bcolor} or {bdiam} or
|
|||
dump_modify 1 format "%d %d %20.15g %g %g" scale yes
|
||||
dump_modify myDump image yes scale no flush yes
|
||||
dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2
|
||||
dump_modify xtcdump precision 10000
|
||||
dump_modify xtcdump precision 10000 sfactor 0.1
|
||||
dump_modify 1 every 1000 nfile 20
|
||||
dump_modify 1 every v_myVar
|
||||
dump_modify 1 amap min max cf 0.0 3 min green 0.5 yellow max blue boxcolor red :pre
|
||||
|
|
@ -352,6 +354,21 @@ nanometer accuracy, e.g. for N = 1000, the coordinates are written to
|
|||
|
||||
:line
|
||||
|
||||
The {sfactor} and {tfactor} keywords only apply to the dump {xtc}
|
||||
style. They allow customization of the unit conversion factors used
|
||||
when writing to XTC files. By default they are initialized for
|
||||
whatever "units"_units.html style is being used, to write out
|
||||
coordinates in nanometers and time in picoseconds. I.e. for {real}
|
||||
units, LAMMPS defines {sfactor} = 0.1 and {tfactor} = 0.001, since the
|
||||
Angstroms and fmsec used by {real} units are 0.1 nm and 0.001 psec
|
||||
respectively. If you are using a units system with distance and time
|
||||
units far from nm and psec, you may wish to write XTC files with
|
||||
different units, since the compression algorithm used in XTC files is
|
||||
most effective when the typical magnitude of position data is between
|
||||
10.0 and 0.1.
|
||||
|
||||
:line
|
||||
|
||||
The {region} keyword only applies to the dump {custom}, {cfg},
|
||||
{image}, and {movie} styles. If specified, only atoms in the region
|
||||
will be written to the dump file or included in the image/movie. Only
|
||||
|
|
|
|||
Loading…
Reference in New Issue