Merge branch 'develop' into collected-small-changes
This commit is contained in:
Axel Kohlmeyer
@ -33,46 +33,6 @@ reference state of a bond. Bonds that are created midway into a run,
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such as those created by pouring grains using :doc:`fix pour
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<fix_pour>`, are initialized on that timestep.
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As bonds can be broken between neighbor list builds, the
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:doc:`special_bonds <special_bonds>` command works differently for BPM
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bond styles. There are two possible settings which determine how pair
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interactions work between bonded particles. First, one can turn off
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all pair interactions between bonded particles. Unlike :doc:`bond
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quartic <bond_quartic>`, this is not done by subtracting pair forces
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during the bond computation but rather by dynamically updating the
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special bond list. This is the default behavior of BPM bond styles and
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is done by updating the 1-2 special bond list as bonds break. To do
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this, LAMMPS requires :doc:`newton <newton>` bond off such that all
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processors containing an atom know when a bond breaks. Additionally,
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one must do either (A) or (B).
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A) Use the following special bond settings
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.. code-block:: LAMMPS
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special_bonds lj 0 1 1 coul 1 1 1
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These settings accomplish two goals. First, they turn off 1-3 and 1-4
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special bond lists, which are not currently supported for BPMs. As
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BPMs often have dense bond networks, generating 1-3 and 1-4 special
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bond lists is expensive. By setting the lj weight for 1-2 bonds to
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zero, this turns off pairwise interactions. Even though there are no
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charges in BPM models, setting a nonzero coul weight for 1-2 bonds
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ensures all bonded neighbors are still included in the neighbor list
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in case bonds break between neighbor list builds.
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B) Alternatively, one can simply overlay pair interactions such that all
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bonded particles also feel pair interactions. This can be
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accomplished by using the *overlay/pair* keyword present in all bpm
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bond styles and by using the following special bond settings
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.. code-block:: LAMMPS
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special_bonds lj/coul 1 1 1
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See the :doc:`Howto <Howto_broken_bonds>` page on broken bonds for
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more information.
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----------
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Currently there are two types of bonds included in the BPM
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@ -91,12 +51,6 @@ This also requires a unique integrator :doc:`fix nve/bpm/sphere
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<fix_nve_bpm_sphere>` which numerically integrates orientation similar
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to :doc:`fix nve/asphere <fix_nve_asphere>`.
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To monitor the fracture of bonds in the system, all BPM bond styles
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have the ability to record instances of bond breakage to output using
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the :doc:`dump local <dump>` command. Additionally, one can use
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:doc:`compute nbond/atom <compute_nbond_atom>` to tally the current
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number of bonds per atom.
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In addition to bond styles, a new pair style :doc:`pair bpm/spring
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<pair_bpm_spring>` was added to accompany the bpm/spring bond
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style. This pair style is simply a hookean repulsion with similar
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@ -104,6 +58,73 @@ velocity damping as its sister bond style.
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----------
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Bond data can be output using a combination of standard LAMMPS commands.
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A list of IDs for bonded atoms can be generated using the
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:doc:`compute property/local <compute_property_local>` command.
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Various properties of bonds can be computed using the
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:doc:`compute bond/local <compute_bond_local>` command. This
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command allows one to access data saved to the bond's history
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such as the reference length of the bond. More information on
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bond history data can be found on the documentation pages for the specific
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BPM bond styles. Finally, this data can be output using a :doc:`dump local <dump>`
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command. As one may output many columns from the same compute, the
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:doc:`dump modify <dump_modify>` *colname* option may be used to provide
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more helpful column names. An example of this procedure is found in
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/examples/bpm/pour/. External software, such as OVITO, can read these dump
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files to render bond data.
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----------
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As bonds can be broken between neighbor list builds, the
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:doc:`special_bonds <special_bonds>` command works differently for BPM
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bond styles. There are two possible settings which determine how pair
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interactions work between bonded particles. First, one can overlay
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pair forces with bond forces such that all bonded particles also
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feel pair interactions. This can be accomplished by using the *overlay/pair*
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keyword present in all bpm bond styles and by using the following special
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bond settings
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.. code-block:: LAMMPS
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special_bonds lj/coul 1 1 1
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Alternatively, one can turn off all pair interactions between bonded
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particles. Unlike :doc:`bond quartic <bond_quartic>`, this is not done
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by subtracting pair forces during the bond computation but rather by
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dynamically updating the special bond list. This is the default behavior
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of BPM bond styles and is done by updating the 1-2 special bond list as
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bonds break. To do this, LAMMPS requires :doc:`newton <newton>` bond off
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such that all processors containing an atom know when a bond breaks.
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Additionally, one must use the following special bond settings
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.. code-block:: LAMMPS
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special_bonds lj 0 1 1 coul 1 1 1
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These settings accomplish two goals. First, they turn off 1-3 and 1-4
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special bond lists, which are not currently supported for BPMs. As
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BPMs often have dense bond networks, generating 1-3 and 1-4 special
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bond lists is expensive. By setting the lj weight for 1-2 bonds to
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zero, this turns off pairwise interactions. Even though there are no
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charges in BPM models, setting a nonzero coul weight for 1-2 bonds
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ensures all bonded neighbors are still included in the neighbor list
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in case bonds break between neighbor list builds.
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To monitor the fracture of bonds in the system, all BPM bond styles
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have the ability to record instances of bond breakage to output using
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the :doc:`dump local <dump>` command. Since one may frequently output
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a list of broken bonds and the time they broke, the
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:doc:`dump modify <dump_modify>` option *header no* may be useful to
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avoid repeatedly printing the header of the dump file. An example of
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this procedure is found in /examples/bpm/impact/. Additionally,
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one can use :doc:`compute nbond/atom <compute_nbond_atom>` to tally the
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current number of bonds per atom.
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See the :doc:`Howto <Howto_broken_bonds>` page on broken bonds for
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more information.
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----------
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While LAMMPS has many utilities to create and delete bonds, *only*
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the following are currently compatible with BPM bond styles:
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@ -138,15 +138,14 @@ the *overlay/pair* keyword. These settings require specific
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restrictions. Further details can be found in the `:doc: how to
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<Howto_BPM>` page on BPMs.
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If the *store/local* keyword is used, this fix will track bonds that
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If the *store/local* keyword is used, an internal fix will track bonds that
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break during the simulation. Whenever a bond breaks, data is processed
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and transferred to an internal fix labeled *fix_ID*. This allows the
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local data to be accessed by other LAMMPS commands.
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Following any optional keyword/value arguments, a list of one or more
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attributes is specified. These include the IDs of the two atoms in
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the bond. The other attributes for the two atoms include the timestep
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during which the bond broke and the current/initial center of mass
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position of the two atoms.
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local data to be accessed by other LAMMPS commands. Following this optional
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keyword, a list of one or more attributes is specified. These include the
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IDs of the two atoms in the bond. The other attributes for the two atoms
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include the timestep during which the bond broke and the current/initial
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center of mass position of the two atoms.
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Data is continuously accumulated over intervals of *N*
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timesteps. At the end of each interval, all of the saved accumulated
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@ -177,29 +176,38 @@ Restart and other info
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This bond style writes the reference state of each bond to
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:doc:`binary restart files <restart>`. Loading a restart file will
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properly resume bonds.
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properly resume bonds. However, the reference state is NOT
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written to data files. Therefore reading a data file will not
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restore bonds and will cause their reference states to be redefined.
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The single() function of these pair styles returns 0.0 for the energy
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of a pairwise interaction, since energy is not conserved in these
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dissipative potentials. It also returns only the normal component of
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the pairwise interaction force.
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The accumulated data is not written to restart files and should be
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output before a restart file is written to avoid missing data.
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The internal fix calculates a local vector or local array depending on the
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number of input values. The length of the vector or number of rows in
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the array is the number of recorded, lost interactions. If a single
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input is specified, a local vector is produced. If two or more inputs
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are specified, a local array is produced where the number of columns =
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the number of inputs. The vector or array can be accessed by any
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command that uses local values from a compute as input. See the
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:doc:`Howto output <Howto_output>` page for an overview of LAMMPS
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output options.
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If the *store/local* option is used, an internal fix will calculate
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a local vector or local array depending on the number of input values.
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The length of the vector or number of rows in the array is the number
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of recorded, broken bonds. If a single input is specified, a local
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vector is produced. If two or more inputs are specified, a local array
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is produced where the number of columns = the number of inputs. The
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vector or array can be accessed by any command that uses local values
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from a compute as input. See the :doc:`Howto output <Howto_output>` page
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for an overview of LAMMPS output options.
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The vector or array will be floating point values that correspond to
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the specified attribute.
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The single() function of this bond style returns 0.0 for the energy
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of a bonded interaction, since energy is not conserved in these
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dissipative potentials. It also returns only the normal component of
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the bonded interaction force. However, the single() function also
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calculates 7 extra bond quantities. The first 4 are data from the
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reference state of the bond including the initial distance between particles
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:math:`r_0` followed by the :math:`x`, :math:`y`, and :math:`z` components
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of the initial unit vector pointing to particle I from particle J. The next 3
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quantities (5-7) are the :math:`x`, :math:`y`, and :math:`z` components
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of the total force, including normal and tangential contributions, acting
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on particle I.
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These extra quantities can be accessed by the :doc:`compute bond/local <compute_bond_local>`
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command, as *b1*, *b2*, ..., *b7*\ .
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Restrictions
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""""""""""""
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@ -103,15 +103,14 @@ the *overlay/pair* keyword. These settings require specific
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restrictions. Further details can be found in the `:doc: how to
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<Howto_BPM>` page on BPMs.
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If the *store/local* keyword is used, this fix will track bonds that
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If the *store/local* keyword is used, an internal fix will track bonds that
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break during the simulation. Whenever a bond breaks, data is processed
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and transferred to an internal fix labeled *fix_ID*. This allows the
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local data to be accessed by other LAMMPS commands.
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Following any optional keyword/value arguments, a list of one or more
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attributes is specified. These include the IDs of the two atoms in
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the bond. The other attributes for the two atoms include the timestep
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during which the bond broke and the current/initial center of mass
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position of the two atoms.
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local data to be accessed by other LAMMPS commands. Following this optional
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keyword, a list of one or more attributes is specified. These include the
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IDs of the two atoms in the bond. The other attributes for the two atoms
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include the timestep during which the bond broke and the current/initial
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center of mass position of the two atoms.
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Data is continuously accumulated over intervals of *N*
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timesteps. At the end of each interval, all of the saved accumulated
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@ -141,28 +140,30 @@ Restart and other info
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This bond style writes the reference state of each bond to
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:doc:`binary restart files <restart>`. Loading a restart
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file will properly resume bonds.
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file will properly restore bonds. However, the reference state is NOT
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written to data files. Therefore reading a data file will not
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restore bonds and will cause their reference states to be redefined.
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The single() function of these pair styles returns 0.0 for the energy
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of a pairwise interaction, since energy is not conserved in these
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dissipative potentials.
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The accumulated data is not written to restart files and should be
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output before a restart file is written to avoid missing data.
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The internal fix calculates a local vector or local array depending on the
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number of input values. The length of the vector or number of rows in
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the array is the number of recorded, lost interactions. If a single
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input is specified, a local vector is produced. If two or more inputs
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are specified, a local array is produced where the number of columns =
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the number of inputs. The vector or array can be accessed by any
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command that uses local values from a compute as input. See the
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:doc:`Howto output <Howto_output>` page for an overview of LAMMPS
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output options.
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If the *store/local* option is used, an internal fix will calculate
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a local vector or local array depending on the number of input values.
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The length of the vector or number of rows in the array is the number
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of recorded, broken bonds. If a single input is specified, a local
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vector is produced. If two or more inputs are specified, a local array
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is produced where the number of columns = the number of inputs. The
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vector or array can be accessed by any command that uses local values
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from a compute as input. See the :doc:`Howto output <Howto_output>` page
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for an overview of LAMMPS output options.
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The vector or array will be floating point values that correspond to
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the specified attribute.
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The single() function of this bond style returns 0.0 for the energy
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of a bonded interaction, since energy is not conserved in these
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dissipative potentials. The single() function also calculates an
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extra bond quantity, the initial distance :math:`r_0`. This
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extra quantity can be accessed by the
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:doc:`compute bond/local <compute_bond_local>` command as *b1*\ .
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Restrictions
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""""""""""""
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@ -13,7 +13,7 @@ Syntax
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* ID, group-ID are documented in :doc:`compute <compute>` command
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* bond/local = style name of this compute command
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* one or more values may be appended
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* value = *dist* or *dx* or *dy* or *dz* or *engpot* or *force* or *fx* or *fy* or *fz* or *engvib* or *engrot* or *engtrans* or *omega* or *velvib* or *v_name*
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* value = *dist* or *dx* or *dy* or *dz* or *engpot* or *force* or *fx* or *fy* or *fz* or *engvib* or *engrot* or *engtrans* or *omega* or *velvib* or *v_name* or *bN*
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.. parsed-literal::
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@ -29,6 +29,7 @@ Syntax
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*omega* = magnitude of bond angular velocity
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*velvib* = vibrational velocity along the bond length
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*v_name* = equal-style variable with name (see below)
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*bN* = bond style specific quantities for allowed N values
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* zero or more keyword/args pairs may be appended
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* keyword = *set*
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@ -47,7 +48,7 @@ Examples
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compute 1 all bond/local engpot
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compute 1 all bond/local dist engpot force
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compute 1 all bond/local dist fx fy fz
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compute 1 all bond/local dist fx fy fz b1 b2
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compute 1 all bond/local dist v_distsq set dist d
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@ -147,6 +148,19 @@ those quantities via the :doc:`compute reduce <compute_reduce>` command
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with thermo output, and the :doc:`fix ave/histo <fix_ave_histo>`
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command will histogram the length\ :math:`^2` values and write them to a file.
|
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A bond style may define additional bond quantities which can be
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accessed as *b1* to *bN*, where N is defined by the bond style. Most
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bond styles do not define any additional quantities, so N = 0. An
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example of ones that do are the :doc:`BPM bond styles <Howto_bpm>`
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which store the reference state between two particles. See
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individual bond styles for details.
|
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When using *bN* with bond style *hybrid*, the output will be the Nth
|
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quantity from the sub-style that computes the bonded interaction
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(based on bond type). If that sub-style does not define a *bN*,
|
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the output will be 0.0. The maximum allowed N is the maximum number
|
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of quantities provided by any sub-style.
|
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----------
|
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The local data stored by this command is generated by looping over all
|
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@ -17,7 +17,7 @@ Syntax
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||||
* one or more keyword/value pairs may be appended
|
||||
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* these keywords apply to various dump styles
|
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* keyword = *append* or *at* or *balance* or *buffer* or *delay* or *element* or *every* or *every/time* or *fileper* or *first* or *flush* or *format* or *header* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *skip* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *units* or *unwrap*
|
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* keyword = *append* or *at* or *balance* or *buffer* or *colname* or *delay* or *element* or *every* or *every/time* or *fileper* or *first* or *flush* or *format* or *header* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *skip* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *units* or *unwrap*
|
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.. parsed-literal::
|
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@ -181,8 +181,8 @@ extra buffering.
|
||||
.. versionadded:: 4May2022
|
||||
|
||||
The *colname* keyword can be used to change the default header keyword
|
||||
for dump styles: *atom*, *custom*, and *cfg* and their compressed, ADIOS,
|
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and MPIIO variants. The setting for *ID string* replaces the default
|
||||
for dump styles: *atom*, *custom*, *cfg*, and *local* and their compressed,
|
||||
ADIOS, and MPIIO variants. The setting for *ID string* replaces the default
|
||||
text with the provided string. *ID* can be a positive integer when it
|
||||
represents the column number counting from the left, a negative integer
|
||||
when it represents the column number from the right (i.e. -1 is the last
|
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@ -59,7 +59,7 @@ include this pair interaction and overlay the pair force over the bond
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force or to exclude this pair interaction such that the two particles
|
||||
only interact via the bond force. See discussion of the *overlay/pair*
|
||||
option for BPM bond styles and the :doc:`special_bonds <special_bonds>`
|
||||
command in the `:doc: how to <Howto_BPM>` page on BPMs for more details.
|
||||
command in the :doc:`how to <Howto_bpm>` page on BPMs for more details.
|
||||
|
||||
The following coefficients must be defined for each pair of atom types
|
||||
via the :doc:`pair_coeff <pair_coeff>` command as in the examples
|
||||
|
||||
Reference in New Issue
Block a user