From c3b10e024bc094652010914232b667dcbf6ed801 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Wed, 25 Mar 2015 15:49:45 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13285 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_commands.html | 22 ++++---- doc/Section_commands.txt | 2 + doc/compute_angmom_chunk.html | 94 +++++++++++++++++++++++++++++++++++ doc/compute_angmom_chunk.txt | 89 +++++++++++++++++++++++++++++++++ doc/compute_omega_chunk.html | 94 +++++++++++++++++++++++++++++++++++ doc/compute_omega_chunk.txt | 89 +++++++++++++++++++++++++++++++++ doc/read_restart.html | 7 ++- doc/read_restart.txt | 6 +-- 8 files changed, 385 insertions(+), 18 deletions(-) create mode 100644 doc/compute_angmom_chunk.html create mode 100644 doc/compute_angmom_chunk.txt create mode 100644 doc/compute_omega_chunk.html create mode 100644 doc/compute_omega_chunk.txt diff --git a/doc/Section_commands.html b/doc/Section_commands.html index be864200a1..3ee7047b55 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -453,17 +453,17 @@ letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.

- - - - - - - - - - - + + + + + + + + + +
angle/localbody/localbond/localcentro/atomchunk/atomcluster/atom
cna/atomcomcom/chunkcontact/atomcoord/atomdamage/atom
dihedral/localdilatation/atomdisplace/atomerotate/asphereerotate/rigiderotate/sphere
erotate/sphere/atomevent/displacegroup/groupgyrationgyration/chunkheat/flux
improper/localinertia/chunkkeke/atomke/rigidmsd
msd/chunkmsd/nongausspairpair/localpe (c)pe/atom
plasticity/atompressure (c)property/atomproperty/localproperty/chunkrdf
reducereduce/regionslicesna/atomsnad/atomsnav/atom
stress/atomtemp (c)temp/aspheretemp/comtemp/chunktemp/deform
temp/partial (c)temp/profiletemp/ramptemp/regiontemp/sphereti
torque/chunkvacfvcm/chunkvoronoi/atom +
angle/localangmom/chunkbody/localbond/localcentro/atomchunk/atom
cluster/atomcna/atomcomcom/chunkcontact/atomcoord/atom
damage/atomdihedral/localdilatation/atomdisplace/atomerotate/asphereerotate/rigid
erotate/sphereerotate/sphere/atomevent/displacegroup/groupgyrationgyration/chunk
heat/fluximproper/localinertia/chunkkeke/atomke/rigid
msdmsd/chunkmsd/nongaussomega/chunkpairpair/local
pe (c)pe/atomplasticity/atompressure (c)property/atomproperty/local
property/chunkrdfreducereduce/regionslicesna/atom
snad/atomsnav/atomstress/atomtemp (c)temp/aspheretemp/com
temp/chunktemp/deformtemp/partial (c)temp/profiletemp/ramptemp/region
temp/spheretitorque/chunkvacfvcm/chunkvoronoi/atom

These are additional compute styles in USER packages, which can be diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 7849ef3e4c..92d6a6d350 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -641,6 +641,7 @@ 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, @@ -672,6 +673,7 @@ 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, diff --git a/doc/compute_angmom_chunk.html b/doc/compute_angmom_chunk.html new file mode 100644 index 0000000000..24ee7fdc55 --- /dev/null +++ b/doc/compute_angmom_chunk.html @@ -0,0 +1,94 @@ + +

LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
+ + + + + + +
+ +

compute angmom/chunk command +

+

Syntax: +

+
compute ID group-ID angmom/chunk chunkID 
+
+ +

Examples: +

+
compute 1 fluid angmom/chunk molchunk 
+
+

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 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 doc page and "Section_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 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 command +for a discussion of "unwrapped" coordinates. See the Atoms section of +the read_data 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 command. +

+

The simplest way to output the results of the compute angmom/chunk +calculation to a file is to use the fix ave/time +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 
+
+

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 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 for an overview of LAMMPS output +options. +

+

The array values are "intensive". The array values will be in +mass-velocity-distance units. +

+

Restrictions: none +

+

Related commands: +

+

variable angmom() function +

+

Default: none +

+ diff --git a/doc/compute_angmom_chunk.txt b/doc/compute_angmom_chunk.txt new file mode 100644 index 0000000000..26fe5a5ec6 --- /dev/null +++ b/doc/compute_angmom_chunk.txt @@ -0,0 +1,89 @@ +"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 diff --git a/doc/compute_omega_chunk.html b/doc/compute_omega_chunk.html new file mode 100644 index 0000000000..b91a512b59 --- /dev/null +++ b/doc/compute_omega_chunk.html @@ -0,0 +1,94 @@ + +
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
+ + + + + + +
+ +

compute omega/chunk command +

+

Syntax: +

+
compute ID group-ID omega/chunk chunkID 
+
+ +

Examples: +

+
compute 1 fluid omega/chunk molchunk 
+
+

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 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 doc page and "Section_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 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 command +for a discussion of "unwrapped" coordinates. See the Atoms section of +the read_data 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 command. +

+

The simplest way to output the results of the compute omega/chunk +calculation to a file is to use the fix ave/time +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 
+
+

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 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 for an overview of LAMMPS output +options. +

+

The array values are "intensive". The array values will be in +velocity/distance units. +

+

Restrictions: none +

+

Related commands: +

+

variable omega() function +

+

Default: none +

+ diff --git a/doc/compute_omega_chunk.txt b/doc/compute_omega_chunk.txt new file mode 100644 index 0000000000..b829bc6cdb --- /dev/null +++ b/doc/compute_omega_chunk.txt @@ -0,0 +1,89 @@ +"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 diff --git a/doc/read_restart.html b/doc/read_restart.html index 40f2013c1d..b09239f1f7 100644 --- a/doc/read_restart.html +++ b/doc/read_restart.html @@ -15,10 +15,9 @@ 

read_restart file flag
-