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<HTML>
<HEAD>
<TITLE>LAMMPS-ICMS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="18 Mar 2015 version">
<META NAME="docnumber" CONTENT="25 Mar 2015 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
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<CENTER><H3>LAMMPS-ICMS Documentation
</H3></CENTER>
<CENTER><H4>18 Mar 2015 version
<CENTER><H4>25 Mar 2015 version
</H4></CENTER>
<H4>Version info:
</H4>

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<HEAD>
<TITLE>LAMMPS-ICMS Users Manual</TITLE>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="18 Mar 2015 version">
<META NAME="docnumber" CONTENT="25 Mar 2015 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
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<H1></H1>
LAMMPS-ICMS Documentation :c,h3
18 Mar 2015 version :c,h4
25 Mar 2015 version :c,h4
Version info: :h4

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KOKKOS, o = USER-OMP, t = OPT.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "compute_angle_local.html">angle/local</A></TD><TD ><A HREF = "compute_body_local.html">body/local</A></TD><TD ><A HREF = "compute_bond_local.html">bond/local</A></TD><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_chunk_atom.html">chunk/atom</A></TD><TD ><A HREF = "compute_cluster_atom.html">cluster/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_cna_atom.html">cna/atom</A></TD><TD ><A HREF = "compute_com.html">com</A></TD><TD ><A HREF = "compute_com_chunk.html">com/chunk</A></TD><TD ><A HREF = "compute_contact_atom.html">contact/atom</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_damage_atom.html">damage/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_dihedral_local.html">dihedral/local</A></TD><TD ><A HREF = "compute_dilatation_atom.html">dilatation/atom</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD><TD ><A HREF = "compute_erotate_asphere.html">erotate/asphere</A></TD><TD ><A HREF = "compute_erotate_rigid.html">erotate/rigid</A></TD><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_erotate_sphere_atom.html">erotate/sphere/atom</A></TD><TD ><A HREF = "compute_event_displace.html">event/displace</A></TD><TD ><A HREF = "compute_group_group.html">group/group</A></TD><TD ><A HREF = "compute_gyration.html">gyration</A></TD><TD ><A HREF = "compute_gyration_chunk.html">gyration/chunk</A></TD><TD ><A HREF = "compute_heat_flux.html">heat/flux</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_improper_local.html">improper/local</A></TD><TD ><A HREF = "compute_inertia_chunk.html">inertia/chunk</A></TD><TD ><A HREF = "compute_ke.html">ke</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_ke_rigid.html">ke/rigid</A></TD><TD ><A HREF = "compute_msd.html">msd</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_msd_chunk.html">msd/chunk</A></TD><TD ><A HREF = "compute_msd_nongauss.html">msd/nongauss</A></TD><TD ><A HREF = "compute_pair.html">pair</A></TD><TD ><A HREF = "compute_pair_local.html">pair/local</A></TD><TD ><A HREF = "compute_pe.html">pe (c)</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_plasticity_atom.html">plasticity/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure (c)</A></TD><TD ><A HREF = "compute_property_atom.html">property/atom</A></TD><TD ><A HREF = "compute_property_local.html">property/local</A></TD><TD ><A HREF = "compute_property_chunk.html">property/chunk</A></TD><TD ><A HREF = "compute_rdf.html">rdf</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_slice.html">slice</A></TD><TD ><A HREF = "compute_sna.html">sna/atom</A></TD><TD ><A HREF = "compute_sna.html">snad/atom</A></TD><TD ><A HREF = "compute_sna.html">snav/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp (c)</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_chunk.html">temp/chunk</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_partial.html">temp/partial (c)</A></TD><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A></TD><TD ><A HREF = "compute_ti.html">ti</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_torque_chunk.html">torque/chunk</A></TD><TD ><A HREF = "compute_vacf.html">vacf</A></TD><TD ><A HREF = "compute_vcm_chunk.html">vcm/chunk</A></TD><TD ><A HREF = "compute_voronoi_atom.html">voronoi/atom</A>
<TR ALIGN="center"><TD ><A HREF = "compute_angle_local.html">angle/local</A></TD><TD ><A HREF = "compute_angmom_chunk.html">angmom/chunk</A></TD><TD ><A HREF = "compute_body_local.html">body/local</A></TD><TD ><A HREF = "compute_bond_local.html">bond/local</A></TD><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_chunk_atom.html">chunk/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_cluster_atom.html">cluster/atom</A></TD><TD ><A HREF = "compute_cna_atom.html">cna/atom</A></TD><TD ><A HREF = "compute_com.html">com</A></TD><TD ><A HREF = "compute_com_chunk.html">com/chunk</A></TD><TD ><A HREF = "compute_contact_atom.html">contact/atom</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_damage_atom.html">damage/atom</A></TD><TD ><A HREF = "compute_dihedral_local.html">dihedral/local</A></TD><TD ><A HREF = "compute_dilatation_atom.html">dilatation/atom</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD><TD ><A HREF = "compute_erotate_asphere.html">erotate/asphere</A></TD><TD ><A HREF = "compute_erotate_rigid.html">erotate/rigid</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</A></TD><TD ><A HREF = "compute_erotate_sphere_atom.html">erotate/sphere/atom</A></TD><TD ><A HREF = "compute_event_displace.html">event/displace</A></TD><TD ><A HREF = "compute_group_group.html">group/group</A></TD><TD ><A HREF = "compute_gyration.html">gyration</A></TD><TD ><A HREF = "compute_gyration_chunk.html">gyration/chunk</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_heat_flux.html">heat/flux</A></TD><TD ><A HREF = "compute_improper_local.html">improper/local</A></TD><TD ><A HREF = "compute_inertia_chunk.html">inertia/chunk</A></TD><TD ><A HREF = "compute_ke.html">ke</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_ke_rigid.html">ke/rigid</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_msd.html">msd</A></TD><TD ><A HREF = "compute_msd_chunk.html">msd/chunk</A></TD><TD ><A HREF = "compute_msd_nongauss.html">msd/nongauss</A></TD><TD ><A HREF = "compute_omega_chunk.html">omega/chunk</A></TD><TD ><A HREF = "compute_pair.html">pair</A></TD><TD ><A HREF = "compute_pair_local.html">pair/local</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_pe.html">pe (c)</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD><TD ><A HREF = "compute_plasticity_atom.html">plasticity/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure (c)</A></TD><TD ><A HREF = "compute_property_atom.html">property/atom</A></TD><TD ><A HREF = "compute_property_local.html">property/local</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_property_chunk.html">property/chunk</A></TD><TD ><A HREF = "compute_rdf.html">rdf</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_slice.html">slice</A></TD><TD ><A HREF = "compute_sna.html">sna/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_sna.html">snad/atom</A></TD><TD ><A HREF = "compute_sna.html">snav/atom</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp (c)</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_chunk.html">temp/chunk</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial (c)</A></TD><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A></TD><TD ><A HREF = "compute_ti.html">ti</A></TD><TD ><A HREF = "compute_torque_chunk.html">torque/chunk</A></TD><TD ><A HREF = "compute_vacf.html">vacf</A></TD><TD ><A HREF = "compute_vcm_chunk.html">vcm/chunk</A></TD><TD ><A HREF = "compute_voronoi_atom.html">voronoi/atom</A>
</TD></TR></TABLE></DIV>
<P>These are additional compute styles in USER packages, which can be

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@ -642,6 +642,7 @@ letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
"angle/local"_compute_angle_local.html,
"angmom/chunk"_compute_angmom_chunk.html,
"body/local"_compute_body_local.html,
"bond/local"_compute_bond_local.html,
"centro/atom"_compute_centro_atom.html,
@ -673,6 +674,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"msd"_compute_msd.html,
"msd/chunk"_compute_msd_chunk.html,
"msd/nongauss"_compute_msd_nongauss.html,
"omega/chunk"_compute_omega_chunk.html,
"pair"_compute_pair.html,
"pair/local"_compute_pair_local.html,
"pe (c)"_compute_pe.html,

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<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>compute angmom/chunk command
</H3>
<P><B>Syntax:</B>
</P>
<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>chunkID = ID of <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 fluid angmom/chunk molchunk
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the angular momemtum of multiple
chunks of atoms.
</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
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the <A HREF = "compute_chunk_atom.html">compute
chunk/atom</A> doc page and "<A HREF = "Section_howto.html#howto_23">Section_howto
23</A> for details of how chunks can be
defined and examples of how they can be used to measure properties of
a system.
</P>
<P>This compute calculates the 3 components of the angular momentum
vector for each chunk, due to the velocity/momentum of the individual
atoms in the chunk around the center-of-mass of the chunk. The
calculation includes all effects due to atoms passing thru periodic
boundaries.
</P>
<P>Note that only atoms in the specified group contribute to the
calculation. The <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
defines its own group; atoms will have a chunk ID = 0 if they are not
in that group, signifying they are not assigned to a chunk, and will
thus also not contribute to this calculation. You can specify the
"all" group for this command if you simply want to include atoms with
non-zero chunk IDs.
</P>
<P>IMPORTANT NOTE: The coordinates of an atom contribute to the chunk's
angular momentum in "unwrapped" form, by using the image flags
associated with each atom. See the <A HREF = "dump.html">dump custom</A> command
for a discussion of "unwrapped" coordinates. See the Atoms section of
the <A HREF = "read_data.html">read_data</A> command for a discussion of image flags
and how they are set for each atom. You can reset the image flags
(e.g. to 0) before invoking this compute by using the <A HREF = "set.html">set
image</A> command.
</P>
<P>The simplest way to output the results of the compute angmom/chunk
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 all chunk/atom molecule
compute myChunk all angmom/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
</PRE>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global array where the number of rows = the
number of chunks <I>Nchunk</I> as calculated by the specified <A HREF = "compute_chunk_atom.html">compute
chunk/atom</A> command. The number of columns =
3 for the 3 xyz components of the angular momentum for each chunk.
These values can be accessed by any command that uses global array
values from a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
15</A> for an overview of LAMMPS output
options.
</P>
<P>The array values are "intensive". The array values will be in
mass-velocity-distance <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "variable.html">variable angmom() function</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute angmom/chunk command :h3
[Syntax:]
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
chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :ul
[Examples:]
compute 1 fluid angmom/chunk molchunk :pre
[Description:]
Define a computation that calculates the angular momemtum of multiple
chunks of atoms.
In LAMMPS, chunks are collections of atoms defined by a "compute
chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto
23"_Section_howto.html#howto_23 for details of how chunks can be
defined and examples of how they can be used to measure properties of
a system.
This compute calculates the 3 components of the angular momentum
vector for each chunk, due to the velocity/momentum of the individual
atoms in the chunk around the center-of-mass of the chunk. The
calculation includes all effects due to atoms passing thru periodic
boundaries.
Note that only atoms in the specified group contribute to the
calculation. The "compute chunk/atom"_compute_chunk_atom.html command
defines its own group; atoms will have a chunk ID = 0 if they are not
in that group, signifying they are not assigned to a chunk, and will
thus also not contribute to this calculation. You can specify the
"all" group for this command if you simply want to include atoms with
non-zero chunk IDs.
IMPORTANT NOTE: The coordinates of an atom contribute to the chunk's
angular momentum in "unwrapped" form, by using the image flags
associated with each atom. See the "dump custom"_dump.html command
for a discussion of "unwrapped" coordinates. See the Atoms section of
the "read_data"_read_data.html command for a discussion of image flags
and how they are set for each atom. You can reset the image flags
(e.g. to 0) before invoking this compute by using the "set
image"_set.html command.
The simplest way to output the results of the compute angmom/chunk
calculation to a file is to use the "fix ave/time"_fix_ave_time.html
command, for example:
compute cc1 all chunk/atom molecule
compute myChunk all angmom/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector :pre
[Output info:]
This compute calculates a global array where the number of rows = the
number of chunks {Nchunk} as calculated by the specified "compute
chunk/atom"_compute_chunk_atom.html command. The number of columns =
3 for the 3 xyz components of the angular momentum for each chunk.
These values can be accessed by any command that uses global array
values from a compute as input. See "Section_howto
15"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The array values are "intensive". The array values will be in
mass-velocity-distance "units"_units.html.
[Restrictions:] none
[Related commands:]
"variable angmom() function"_variable.html
[Default:] none

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<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>compute omega/chunk command
</H3>
<P><B>Syntax:</B>
</P>
<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>chunkID = ID of <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 fluid omega/chunk molchunk
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the angular velocity (omega) of
multiple chunks of atoms.
</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
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the <A HREF = "compute_chunk_atom.html">compute
chunk/atom</A> doc page and "<A HREF = "Section_howto.html#howto_23">Section_howto
23</A> for details of how chunks can be
defined and examples of how they can be used to measure properties of
a system.
</P>
<P>This compute calculates the 3 components of the angular velocity
vector for each chunk, via the formula L = Iw where L is the angular
momentum vector of the chunk, I is its moment of inertia tensor, and w
is omega = angular velocity of the chunk. The calculation includes
all effects due to atoms passing thru periodic boundaries.
</P>
<P>Note that only atoms in the specified group contribute to the
calculation. The <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
defines its own group; atoms will have a chunk ID = 0 if they are not
in that group, signifying they are not assigned to a chunk, and will
thus also not contribute to this calculation. You can specify the
"all" group for this command if you simply want to include atoms with
non-zero chunk IDs.
</P>
<P>IMPORTANT NOTE: The coordinates of an atom contribute to the chunk's
angular velocity in "unwrapped" form, by using the image flags
associated with each atom. See the <A HREF = "dump.html">dump custom</A> command
for a discussion of "unwrapped" coordinates. See the Atoms section of
the <A HREF = "read_data.html">read_data</A> command for a discussion of image flags
and how they are set for each atom. You can reset the image flags
(e.g. to 0) before invoking this compute by using the <A HREF = "set.html">set
image</A> command.
</P>
<P>The simplest way to output the results of the compute omega/chunk
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 all chunk/atom molecule
compute myChunk all omega/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
</PRE>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global array where the number of rows = the
number of chunks <I>Nchunk</I> as calculated by the specified <A HREF = "compute_chunk_atom.html">compute
chunk/atom</A> command. The number of columns =
3 for the 3 xyz components of the angular velocity for each chunk.
These values can be accessed by any command that uses global array
values from a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
15</A> for an overview of LAMMPS output
options.
</P>
<P>The array values are "intensive". The array values will be in
velocity/distance <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "variable.html">variable omega() function</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute omega/chunk command :h3
[Syntax:]
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
chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :ul
[Examples:]
compute 1 fluid omega/chunk molchunk :pre
[Description:]
Define a computation that calculates the angular velocity (omega) of
multiple chunks of atoms.
In LAMMPS, chunks are collections of atoms defined by a "compute
chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto
23"_Section_howto.html#howto_23 for details of how chunks can be
defined and examples of how they can be used to measure properties of
a system.
This compute calculates the 3 components of the angular velocity
vector for each chunk, via the formula L = Iw where L is the angular
momentum vector of the chunk, I is its moment of inertia tensor, and w
is omega = angular velocity of the chunk. The calculation includes
all effects due to atoms passing thru periodic boundaries.
Note that only atoms in the specified group contribute to the
calculation. The "compute chunk/atom"_compute_chunk_atom.html command
defines its own group; atoms will have a chunk ID = 0 if they are not
in that group, signifying they are not assigned to a chunk, and will
thus also not contribute to this calculation. You can specify the
"all" group for this command if you simply want to include atoms with
non-zero chunk IDs.
IMPORTANT NOTE: The coordinates of an atom contribute to the chunk's
angular velocity in "unwrapped" form, by using the image flags
associated with each atom. See the "dump custom"_dump.html command
for a discussion of "unwrapped" coordinates. See the Atoms section of
the "read_data"_read_data.html command for a discussion of image flags
and how they are set for each atom. You can reset the image flags
(e.g. to 0) before invoking this compute by using the "set
image"_set.html command.
The simplest way to output the results of the compute omega/chunk
calculation to a file is to use the "fix ave/time"_fix_ave_time.html
command, for example:
compute cc1 all chunk/atom molecule
compute myChunk all omega/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector :pre
[Output info:]
This compute calculates a global array where the number of rows = the
number of chunks {Nchunk} as calculated by the specified "compute
chunk/atom"_compute_chunk_atom.html command. The number of columns =
3 for the 3 xyz components of the angular velocity for each chunk.
These values can be accessed by any command that uses global array
values from a compute as input. See "Section_howto
15"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The array values are "intensive". The array values will be in
velocity/distance "units"_units.html.
[Restrictions:] none
[Related commands:]
"variable omega() function"_variable.html
[Default:] none

7
doc/read_restart.html
View File

@ -15,10 +15,9 @@
</P>
<PRE>read_restart file flag
</PRE>
<UL><LI>file = name of binary restart file to read in
<UL><LI>file = name of binary restart file to read in
<LI>flag = remap (optional)
</UL>
<P>flag = remap (optional)
</P>
<P><B>Examples:</B>
</P>
<PRE>read_restart save.10000
@ -51,7 +50,7 @@ that atoms were "lost" when the file is read. This error should be
reported to the LAMMPS developers so the invalid writing of the
restart file can be fixed. If you still wish to use the restart file,
the optional <I>remap</I> flag can be appended to the read_restart command.
This will avoid the error, by explicitly remapping each atom back into
This should avoid the error, by explicitly remapping each atom back into
the simulation box, updating image flags for the atom appropriately.
</P>
<P>Restart files are saved in binary format to enable exact restarts,

6
doc/read_restart.txt
View File

@ -12,8 +12,8 @@ read_restart command :h3
read_restart file flag :pre
file = name of binary restart file to read in :ul
flag = remap (optional)
file = name of binary restart file to read in
flag = remap (optional) :ul
[Examples:]
@ -47,7 +47,7 @@ that atoms were "lost" when the file is read. This error should be
reported to the LAMMPS developers so the invalid writing of the
restart file can be fixed. If you still wish to use the restart file,
the optional {remap} flag can be appended to the read_restart command.
This will avoid the error, by explicitly remapping each atom back into
This should avoid the error, by explicitly remapping each atom back into
the simulation box, updating image flags for the atom appropriately.
Restart files are saved in binary format to enable exact restarts,

5
src/KSPACE/ewald_disp.h
View File

@ -137,8 +137,9 @@ This feature is not yet supported.
E: Cannot use Ewald/disp solver on system with no charge, dipole, or LJ particles
No atoms in system have a non-zero charge or dipole, or are LJ particles. Change
charges/dipoles or change options of the kspace solver/pair style.
No atoms in system have a non-zero charge or dipole, or are LJ
particles. Change charges/dipoles or change options of the kspace
solver/pair style.
W: System is not charge neutral, net charge = %g

37
src/MC/fix_gcmc.cpp
View File

@ -344,7 +344,7 @@ void FixGCMC::init()
(domain->triclinic == 1)) {
full_flag = true;
if (comm->me == 0)
error->warning(FLERR,"fix gcmc using full_energy option");
error->warning(FLERR,"Fix gcmc using full_energy option");
}
}
@ -1288,6 +1288,7 @@ void FixGCMC::attempt_atomic_deletion_full()
atom->q[i] = 0.0;
}
}
if (force->kspace) force->kspace->qsum_qsq();
double energy_after = energy_full();
if (random_equal->uniform() <
@ -1305,6 +1306,7 @@ void FixGCMC::attempt_atomic_deletion_full()
atom->mask[i] = tmpmask;
if (atom->q_flag) atom->q[i] = q_tmp;
}
if (force->kspace) force->kspace->qsum_qsq();
energy_stored = energy_before;
}
update_gas_atoms_list();
@ -1360,7 +1362,7 @@ void FixGCMC::attempt_atomic_insertion_full()
}
atom->nghost = 0;
comm->borders();
if (force->kspace) force->kspace->qsum_qsq();
double energy_after = energy_full();
if (random_equal->uniform() <
@ -1371,6 +1373,7 @@ void FixGCMC::attempt_atomic_insertion_full()
} else {
atom->natoms--;
if (proc_flag) atom->nlocal--;
if (force->kspace) force->kspace->qsum_qsq();
energy_stored = energy_before;
}
update_gas_atoms_list();
@ -1575,10 +1578,10 @@ void FixGCMC::attempt_molecule_deletion_full()
m++;
atom->q[i] = 0.0;
}
toggle_intramolecular(i);
}
}
if (force->kspace) force->kspace->qsum_qsq();
double energy_after = energy_full();
if (random_equal->uniform() <
@ -1600,12 +1603,14 @@ void FixGCMC::attempt_molecule_deletion_full()
for (int i = 0; i < atom->nlocal; i++) {
if (atom->molecule[i] == deletion_molecule) {
atom->mask[i] = tmpmask[i];
toggle_intramolecular(i);
if (atom->q_flag) {
atom->q[i] = q_tmp[m];
m++;
}
}
}
if (force->kspace) force->kspace->qsum_qsq();
}
update_gas_atoms_list();
}
@ -1720,6 +1725,7 @@ void FixGCMC::attempt_molecule_insertion_full()
if (atom->map_style) atom->map_init();
atom->nghost = 0;
comm->borders();
if (force->kspace) force->kspace->qsum_qsq();
double energy_after = energy_full();
if (random_equal->uniform() < zz*volume*natoms_per_molecule*
@ -1744,6 +1750,7 @@ void FixGCMC::attempt_molecule_insertion_full()
atom->nlocal--;
} else i++;
}
if (force->kspace) force->kspace->qsum_qsq();
}
update_gas_atoms_list();
}
@ -1823,6 +1830,28 @@ tagint FixGCMC::pick_random_gas_molecule()
return gas_molecule_id_all;
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
void FixGCMC::toggle_intramolecular(int i)
{
if (atom->avec->bonds_allow)
for (int m = 0; m < atom->num_bond[i]; m++)
atom->bond_type[i][m] = -atom->bond_type[i][m];
if (atom->avec->angles_allow)
for (int m = 0; m < atom->num_angle[i]; m++)
atom->angle_type[i][m] = -atom->angle_type[i][m];
if (atom->avec->dihedrals_allow)
for (int m = 0; m < atom->num_dihedral[i]; m++)
atom->dihedral_type[i][m] = -atom->dihedral_type[i][m];
if (atom->avec->impropers_allow)
for (int m = 0; m < atom->num_improper[i]; m++)
atom->improper_type[i][m] = -atom->improper_type[i][m];
}
/* ----------------------------------------------------------------------
update the list of gas atoms
------------------------------------------------------------------------- */

3
src/MC/fix_gcmc.h
View File

@ -50,6 +50,7 @@ class FixGCMC : public Fix {
double energy_full();
int pick_random_gas_atom();
tagint pick_random_gas_molecule();
void toggle_intramolecular(int);
double molecule_energy(tagint);
void update_gas_atoms_list();
double compute_vector(int);
@ -188,7 +189,7 @@ E: Region ID for fix gcmc does not exist
Self-explanatory.
W: fix gcmc using full_energy option
W: Fix gcmc using full_energy option
Fix gcmc has automatically turned on the full_energy option since it
is required for systems like the one specified by the user. User input

2
src/RIGID/fix_rattle.cpp
View File

@ -831,7 +831,7 @@ bool FixRattle::check4(double **v, int m, bool checkr, bool checkv)
fabs(MathExtra::dot3(r03,v03)) > tol));
if (!stat)
error->one(FLERR,"RATTLE velocity constraints are not satisfied "
"up to desired tolerance!");
"up to desired tolerance");
return stat;
}

4
src/RIGID/fix_rattle.h
View File

@ -99,8 +99,4 @@ E: RATTLE velocity constraints are not satisfied up to desired tolerance
Self-explanatory.
E: RATTLE velocity constraints are not satisfied up to desired tolerance!
UNDOCUMENTED
*/

255
src/compute_angmom_chunk.cpp Normal file
View File

@ -0,0 +1,255 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "string.h"
#include "compute_angmom_chunk.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "compute_chunk_atom.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeAngmomChunk::ComputeAngmomChunk(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 4) error->all(FLERR,"Illegal compute angmom/chunk command");
array_flag = 1;
size_array_cols = 3;
size_array_rows = 0;
size_array_rows_variable = 1;
extarray = 0;
// ID of compute chunk/atom
int n = strlen(arg[3]) + 1;
idchunk = new char[n];
strcpy(idchunk,arg[3]);
init();
// chunk-based data
nchunk = 1;
maxchunk = 0;
massproc = masstotal = NULL;
com = comall = NULL;
angmom = angmomall = NULL;
allocate();
}
/* ---------------------------------------------------------------------- */
ComputeAngmomChunk::~ComputeAngmomChunk()
{
delete [] idchunk;
memory->destroy(massproc);
memory->destroy(masstotal);
memory->destroy(com);
memory->destroy(comall);
memory->destroy(angmom);
memory->destroy(angmomall);
}
/* ---------------------------------------------------------------------- */
void ComputeAngmomChunk::init()
{
int icompute = modify->find_compute(idchunk);
if (icompute < 0)
error->all(FLERR,"Chunk/atom compute does not exist for "
"compute angmom/chunk");
cchunk = (ComputeChunkAtom *) modify->compute[icompute];
if (strcmp(cchunk->style,"chunk/atom") != 0)
error->all(FLERR,"Compute angmom/chunk does not use chunk/atom compute");
}
/* ---------------------------------------------------------------------- */
void ComputeAngmomChunk::compute_array()
{
int i,index;
double dx,dy,dz,massone;
double unwrap[3];
invoked_array = update->ntimestep;
// compute chunk/atom assigns atoms to chunk IDs
// extract ichunk index vector from compute
// ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
nchunk = cchunk->setup_chunks();
cchunk->compute_ichunk();
int *ichunk = cchunk->ichunk;
if (nchunk > maxchunk) allocate();
size_array_rows = nchunk;
// zero local per-chunk values
for (int i = 0; i < nchunk; i++) {
massproc[i] = 0.0;
com[i][0] = com[i][1] = com[i][2] = 0.0;
angmom[i][0] = angmom[i][1] = angmom[i][2] = 0.0;
}
// compute COM for each chunk
double **x = atom->x;
int *mask = atom->mask;
int *type = atom->type;
imageint *image = atom->image;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
if (index < 0) continue;
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
domain->unmap(x[i],image[i],unwrap);
massproc[index] += massone;
com[index][0] += unwrap[0] * massone;
com[index][1] += unwrap[1] * massone;
com[index][2] += unwrap[2] * massone;
}
MPI_Allreduce(massproc,masstotal,nchunk,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world);
for (int i = 0; i < nchunk; i++) {
comall[i][0] /= masstotal[i];
comall[i][1] /= masstotal[i];
comall[i][2] /= masstotal[i];
}
// compute angmom for each chunk
double **v = atom->v;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
if (index < 0) continue;
domain->unmap(x[i],image[i],unwrap);
dx = unwrap[0] - comall[index][0];
dy = unwrap[1] - comall[index][1];
dz = unwrap[2] - comall[index][2];
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
angmom[index][0] += massone * (dy*v[i][2] - dz*v[i][1]);
angmom[index][1] += massone * (dz*v[i][0] - dx*v[i][2]);
angmom[index][2] += massone * (dx*v[i][1] - dy*v[i][0]);
}
MPI_Allreduce(&angmom[0][0],&angmomall[0][0],3*nchunk,
MPI_DOUBLE,MPI_SUM,world);
}
/* ----------------------------------------------------------------------
lock methods: called by fix ave/time
these methods insure vector/array size is locked for Nfreq epoch
by passing lock info along to compute chunk/atom
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
increment lock counter
------------------------------------------------------------------------- */
void ComputeAngmomChunk::lock_enable()
{
cchunk->lockcount++;
}
/* ----------------------------------------------------------------------
decrement lock counter in compute chunk/atom, it if still exists
------------------------------------------------------------------------- */
void ComputeAngmomChunk::lock_disable()
{
int icompute = modify->find_compute(idchunk);
if (icompute >= 0) {
cchunk = (ComputeChunkAtom *) modify->compute[icompute];
cchunk->lockcount--;
}
}
/* ----------------------------------------------------------------------
calculate and return # of chunks = length of vector/array
------------------------------------------------------------------------- */
int ComputeAngmomChunk::lock_length()
{
nchunk = cchunk->setup_chunks();
return nchunk;
}
/* ----------------------------------------------------------------------
set the lock from startstep to stopstep
------------------------------------------------------------------------- */
void ComputeAngmomChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
{
cchunk->lock(fixptr,startstep,stopstep);
}
/* ----------------------------------------------------------------------
unset the lock
------------------------------------------------------------------------- */
void ComputeAngmomChunk::unlock(Fix *fixptr)
{
cchunk->unlock(fixptr);
}
/* ----------------------------------------------------------------------
free and reallocate per-chunk arrays
------------------------------------------------------------------------- */
void ComputeAngmomChunk::allocate()
{
memory->destroy(massproc);
memory->destroy(masstotal);
memory->destroy(com);
memory->destroy(comall);
memory->destroy(angmom);
memory->destroy(angmomall);
maxchunk = nchunk;
memory->create(massproc,maxchunk,"angmom/chunk:massproc");
memory->create(masstotal,maxchunk,"angmom/chunk:masstotal");
memory->create(com,maxchunk,3,"angmom/chunk:com");
memory->create(comall,maxchunk,3,"angmom/chunk:comall");
memory->create(angmom,maxchunk,3,"angmom/chunk:angmom");
memory->create(angmomall,maxchunk,3,"angmom/chunk:angmomall");
array = angmomall;
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double ComputeAngmomChunk::memory_usage()
{
double bytes = (bigint) maxchunk * 2 * sizeof(double);
bytes += (bigint) maxchunk * 2*3 * sizeof(double);
bytes += (bigint) maxchunk * 2*3 * sizeof(double);
return bytes;
}

75
src/compute_angmom_chunk.h Normal file
View File

@ -0,0 +1,75 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef COMPUTE_CLASS
ComputeStyle(angmom/chunk,ComputeAngmomChunk)
#else
#ifndef LMP_COMPUTE_ANGMOM_CHUNK_H
#define LMP_COMPUTE_ANGMOM_CHUNK_H
#include "compute.h"
namespace LAMMPS_NS {
class ComputeAngmomChunk : public Compute {
public:
ComputeAngmomChunk(class LAMMPS *, int, char **);
~ComputeAngmomChunk();
void init();
void compute_array();
void lock_enable();
void lock_disable();
int lock_length();
void lock(class Fix *, bigint, bigint);
void unlock(class Fix *);
double memory_usage();
private:
int nchunk,maxchunk;
char *idchunk;
class ComputeChunkAtom *cchunk;
double *massproc,*masstotal;
double **com,**comall;
double **angmom,**angmomall;
void allocate();
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Chunk/atom compute does not exist for compute angmom/chunk
Self-explanatory.
E: Compute angmom/chunk does not use chunk/atom compute
The style of the specified compute is not chunk/atom.
*/

333
src/compute_omega_chunk.cpp Normal file
View File

@ -0,0 +1,333 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "string.h"
#include "compute_omega_chunk.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "compute_chunk_atom.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeOmegaChunk::ComputeOmegaChunk(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 4) error->all(FLERR,"Illegal compute omega/chunk command");
array_flag = 1;
size_array_cols = 3;
size_array_rows = 0;
size_array_rows_variable = 1;
extarray = 0;
// ID of compute chunk/atom
int n = strlen(arg[3]) + 1;
idchunk = new char[n];
strcpy(idchunk,arg[3]);
init();
// chunk-based data
nchunk = 1;
maxchunk = 0;
massproc = masstotal = NULL;
com = comall = NULL;
angmom = angmomall = NULL;
allocate();
}
/* ---------------------------------------------------------------------- */
ComputeOmegaChunk::~ComputeOmegaChunk()
{
delete [] idchunk;
memory->destroy(massproc);
memory->destroy(masstotal);
memory->destroy(com);
memory->destroy(comall);
memory->destroy(angmom);
memory->destroy(angmomall);
}
/* ---------------------------------------------------------------------- */
void ComputeOmegaChunk::init()
{
int icompute = modify->find_compute(idchunk);
if (icompute < 0)
error->all(FLERR,"Chunk/atom compute does not exist for "
"compute omega/chunk");
cchunk = (ComputeChunkAtom *) modify->compute[icompute];
if (strcmp(cchunk->style,"chunk/atom") != 0)
error->all(FLERR,"Compute omega/chunk does not use chunk/atom compute");
}
/* ---------------------------------------------------------------------- */
void ComputeOmegaChunk::compute_array()
{
int i,j,index;
double dx,dy,dz,massone;
double unwrap[3];
invoked_array = update->ntimestep;
// compute chunk/atom assigns atoms to chunk IDs
// extract ichunk index vector from compute
// ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
nchunk = cchunk->setup_chunks();
cchunk->compute_ichunk();
int *ichunk = cchunk->ichunk;
if (nchunk > maxchunk) allocate();
size_array_rows = nchunk;
// zero local per-chunk values
for (int i = 0; i < nchunk; i++) {
massproc[i] = 0.0;
com[i][0] = com[i][1] = com[i][2] = 0.0;
for (j = 0; j < 6; j++) inertia[i][j] = 0.0;
angmom[i][0] = angmom[i][1] = angmom[i][2] = 0.0;
omega[i][0] = omega[i][1] = omega[i][2] = 0.0;
}
// compute COM for each chunk
double **x = atom->x;
int *mask = atom->mask;
int *type = atom->type;
imageint *image = atom->image;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
if (index < 0) continue;
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
domain->unmap(x[i],image[i],unwrap);
massproc[index] += massone;
com[index][0] += unwrap[0] * massone;
com[index][1] += unwrap[1] * massone;
com[index][2] += unwrap[2] * massone;
}
MPI_Allreduce(massproc,masstotal,nchunk,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world);
for (int i = 0; i < nchunk; i++) {
comall[i][0] /= masstotal[i];
comall[i][1] /= masstotal[i];
comall[i][2] /= masstotal[i];
}
// compute inertia tensor for each chunk
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
if (index < 0) continue;
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
domain->unmap(x[i],image[i],unwrap);
dx = unwrap[0] - comall[index][0];
dy = unwrap[1] - comall[index][1];
dz = unwrap[2] - comall[index][2];
inertia[index][0] += massone * (dy*dy + dz*dz);
inertia[index][1] += massone * (dx*dx + dz*dz);
inertia[index][2] += massone * (dx*dx + dy*dy);
inertia[index][3] -= massone * dx*dy;
inertia[index][4] -= massone * dy*dz;
inertia[index][5] -= massone * dx*dz;
}
MPI_Allreduce(&inertia[0][0],&inertiaall[0][0],6*nchunk,
MPI_DOUBLE,MPI_SUM,world);
// compute angmom for each chunk
double **v = atom->v;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
if (index < 0) continue;
domain->unmap(x[i],image[i],unwrap);
dx = unwrap[0] - comall[index][0];
dy = unwrap[1] - comall[index][1];
dz = unwrap[2] - comall[index][2];
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
angmom[index][0] += massone * (dy*v[i][2] - dz*v[i][1]);
angmom[index][1] += massone * (dz*v[i][0] - dx*v[i][2]);
angmom[index][2] += massone * (dx*v[i][1] - dy*v[i][0]);
}
MPI_Allreduce(&angmom[0][0],&angmomall[0][0],3*nchunk,
MPI_DOUBLE,MPI_SUM,world);
// compute omega for each chunk from L = Iw, inverting I to solve for w
double ione[3][3],inverse[3][3];
for (i = 0; i < nchunk; i++) {
ione[0][0] = inertiaall[i][0];
ione[1][1] = inertiaall[i][1];
ione[2][2] = inertiaall[i][2];
ione[0][1] = inertiaall[i][3];
ione[1][2] = inertiaall[i][4];
ione[0][2] = inertiaall[i][5];
ione[1][0] = ione[0][1];
ione[2][1] = ione[1][2];
ione[2][0] = ione[0][2];
inverse[0][0] = ione[1][1]*ione[2][2] - ione[1][2]*ione[2][1];
inverse[0][1] = -(ione[0][1]*ione[2][2] - ione[0][2]*ione[2][1]);
inverse[0][2] = ione[0][1]*ione[1][2] - ione[0][2]*ione[1][1];
inverse[1][0] = -(ione[1][0]*ione[2][2] - ione[1][2]*ione[2][0]);
inverse[1][1] = ione[0][0]*ione[2][2] - ione[0][2]*ione[2][0];
inverse[1][2] = -(ione[0][0]*ione[1][2] - ione[0][2]*ione[1][0]);
inverse[2][0] = ione[1][0]*ione[2][1] - ione[1][1]*ione[2][0];
inverse[2][1] = -(ione[0][0]*ione[2][1] - ione[0][1]*ione[2][0]);
inverse[2][2] = ione[0][0]*ione[1][1] - ione[0][1]*ione[1][0];
double determinant = ione[0][0]*ione[1][1]*ione[2][2] +
ione[0][1]*ione[1][2]*ione[2][0] + ione[0][2]*ione[1][0]*ione[2][1] -
ione[0][0]*ione[1][2]*ione[2][1] - ione[0][1]*ione[1][0]*ione[2][2] -
ione[2][0]*ione[1][1]*ione[0][2];
if (determinant > 0.0)
for (int i = 0; i < 3; i++)
for (int j = 0; j < 3; j++)
inverse[i][j] /= determinant;
omega[i][0] = inverse[0][0]*angmom[i][0] + inverse[0][1]*angmom[i][1] +
inverse[0][2]*angmom[i][2];
omega[i][1] = inverse[1][0]*angmom[i][0] + inverse[1][1]*angmom[i][1] +
inverse[1][2]*angmom[i][2];
omega[i][2] = inverse[2][0]*angmom[i][0] + inverse[2][1]*angmom[i][1] +
inverse[2][2]*angmom[i][2];
}
}
/* ----------------------------------------------------------------------
lock methods: called by fix ave/time
these methods insure vector/array size is locked for Nfreq epoch
by passing lock info along to compute chunk/atom
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
increment lock counter
------------------------------------------------------------------------- */
void ComputeOmegaChunk::lock_enable()
{
cchunk->lockcount++;
}
/* ----------------------------------------------------------------------
decrement lock counter in compute chunk/atom, it if still exists
------------------------------------------------------------------------- */
void ComputeOmegaChunk::lock_disable()
{
int icompute = modify->find_compute(idchunk);
if (icompute >= 0) {
cchunk = (ComputeChunkAtom *) modify->compute[icompute];
cchunk->lockcount--;
}
}
/* ----------------------------------------------------------------------
calculate and return # of chunks = length of vector/array
------------------------------------------------------------------------- */
int ComputeOmegaChunk::lock_length()
{
nchunk = cchunk->setup_chunks();
return nchunk;
}
/* ----------------------------------------------------------------------
set the lock from startstep to stopstep
------------------------------------------------------------------------- */
void ComputeOmegaChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
{
cchunk->lock(fixptr,startstep,stopstep);
}
/* ----------------------------------------------------------------------
unset the lock
------------------------------------------------------------------------- */
void ComputeOmegaChunk::unlock(Fix *fixptr)
{
cchunk->unlock(fixptr);
}
/* ----------------------------------------------------------------------
free and reallocate per-chunk arrays
------------------------------------------------------------------------- */
void ComputeOmegaChunk::allocate()
{
memory->destroy(massproc);
memory->destroy(masstotal);
memory->destroy(com);
memory->destroy(comall);
memory->destroy(inertia);
memory->destroy(inertiaall);
memory->destroy(angmom);
memory->destroy(angmomall);
memory->destroy(omega);
maxchunk = nchunk;
memory->create(massproc,maxchunk,"omega/chunk:massproc");
memory->create(masstotal,maxchunk,"omega/chunk:masstotal");
memory->create(com,maxchunk,3,"omega/chunk:com");
memory->create(comall,maxchunk,3,"omega/chunk:comall");
memory->create(inertia,maxchunk,6,"omega/chunk:inertia");
memory->create(inertiaall,maxchunk,6,"omega/chunk:inertiaall");
memory->create(angmom,maxchunk,3,"omega/chunk:angmom");
memory->create(angmomall,maxchunk,3,"omega/chunk:angmomall");
memory->create(omega,maxchunk,3,"omega/chunk:omega");
array = omega;
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double ComputeOmegaChunk::memory_usage()
{
double bytes = (bigint) maxchunk * 2 * sizeof(double);
bytes += (bigint) maxchunk * 2*3 * sizeof(double);
bytes += (bigint) maxchunk * 2*6 * sizeof(double);
bytes += (bigint) maxchunk * 2*3 * sizeof(double);
bytes += (bigint) maxchunk * 3 * sizeof(double);
return bytes;
}

77
src/compute_omega_chunk.h Normal file
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@ -0,0 +1,77 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef COMPUTE_CLASS
ComputeStyle(omega/chunk,ComputeOmegaChunk)
#else
#ifndef LMP_COMPUTE_OMEGA_CHUNK_H
#define LMP_COMPUTE_OMEGA_CHUNK_H
#include "compute.h"
namespace LAMMPS_NS {
class ComputeOmegaChunk : public Compute {
public:
ComputeOmegaChunk(class LAMMPS *, int, char **);
~ComputeOmegaChunk();
void init();
void compute_array();
void lock_enable();
void lock_disable();
int lock_length();
void lock(class Fix *, bigint, bigint);
void unlock(class Fix *);
double memory_usage();
private:
int nchunk,maxchunk;
char *idchunk;
class ComputeChunkAtom *cchunk;
double *massproc,*masstotal;
double **com,**comall;
double **inertia,**inertiaall;
double **angmom,**angmomall;
double **omega;
void allocate();
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Chunk/atom compute does not exist for compute omega/chunk
Self-explanatory.
E: Compute omega/chunk does not use chunk/atom compute
The style of the specified compute is not chunk/atom.
*/

12
src/compute_torque_chunk.cpp
View File

@ -28,7 +28,7 @@ using namespace LAMMPS_NS;
ComputeTorqueChunk::ComputeTorqueChunk(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 4) error->all(FLERR,"Illegal compute inertia/chunk command");
if (narg != 4) error->all(FLERR,"Illegal compute torque/chunk command");
array_flag = 1;
size_array_cols = 3;
@ -153,9 +153,9 @@ void ComputeTorqueChunk::compute_array()
dx = unwrap[0] - comall[index][0];
dy = unwrap[1] - comall[index][1];
dz = unwrap[2] - comall[index][2];
torque[i][0] += dy*f[i][2] - dz*f[i][1];
torque[i][1] += dz*f[i][0] - dx*f[i][2];
torque[i][2] += dx*f[i][1] - dy*f[i][0];
torque[index][0] += dy*f[i][2] - dz*f[i][1];
torque[index][1] += dz*f[i][0] - dx*f[i][2];
torque[index][2] += dx*f[i][1] - dy*f[i][0];
}
MPI_Allreduce(&torque[0][0],&torqueall[0][0],3*nchunk,
@ -235,8 +235,8 @@ void ComputeTorqueChunk::allocate()
memory->create(masstotal,maxchunk,"torque/chunk:masstotal");
memory->create(com,maxchunk,3,"torque/chunk:com");
memory->create(comall,maxchunk,3,"torque/chunk:comall");
memory->create(torque,maxchunk,6,"torque/chunk:torque");
memory->create(torqueall,maxchunk,6,"torque/chunk:torqueall");
memory->create(torque,maxchunk,3,"torque/chunk:torque");
memory->create(torqueall,maxchunk,3,"torque/chunk:torqueall");
array = torqueall;
}

6
src/kspace.h
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@ -222,11 +222,13 @@ Self-explanatory.
E: System is not charge neutral, net charge = %g
UNDOCUMENTED
The total charge on all atoms on the system is not 0.0.
For some KSpace solvers this is an error.
W: System is not charge neutral, net charge = %g
UNDOCUMENTED
The total charge on all atoms on the system is not 0.0.
For some KSpace solvers this is only a warning.
W: For better accuracy use 'pair_modify table 0'

2
src/version.h
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@ -1 +1 @@
#define LAMMPS_VERSION "14 Mar 2015"
#define LAMMPS_VERSION "25 Mar 2015"