Proofing RHEO package
This commit is contained in:
jtclemm
@ -28,6 +28,7 @@ OPT.
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* :doc:`adapt <fix_adapt>`
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* :doc:`adapt <fix_adapt>`
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* :doc:`adapt/fep <fix_adapt_fep>`
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* :doc:`adapt/fep <fix_adapt_fep>`
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* :doc:`addforce <fix_addforce>`
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* :doc:`addforce <fix_addforce>`
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* :doc:`add/heat <fix_add_heat>`
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* :doc:`addtorque <fix_addtorque>`
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* :doc:`addtorque <fix_addtorque>`
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* :doc:`alchemy <fix_alchemy>`
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* :doc:`alchemy <fix_alchemy>`
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* :doc:`amoeba/bitorsion <fix_amoeba_bitorsion>`
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* :doc:`amoeba/bitorsion <fix_amoeba_bitorsion>`
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@ -2,8 +2,9 @@ Reproducing hydrodynamics and elastic objects (RHEO)
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====================================================
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====================================================
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The RHEO package is a hybrid implementation of smoothed particle
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The RHEO package is a hybrid implementation of smoothed particle
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hydrodynamics (SPH) for fluid flow, coupled to the :doc:`BPM package <Howto_bpm>` to model
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hydrodynamics (SPH) for fluid flow, coupled to the :doc:`BPM package <Howto_bpm>`
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solid elements. RHEO combines these methods to enable mesh-free modeling of multiphase material systems. The SPH solver supports many advanced options
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to model solid elements. RHEO combines these methods to enable mesh-free modeling
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of multiphase material systems. The SPH solver supports many advanced options
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including reproducing kernels, particle shifting, free surface identification,
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including reproducing kernels, particle shifting, free surface identification,
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and solid surface reconstruction. To model fluid-solid systems, the status of
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and solid surface reconstruction. To model fluid-solid systems, the status of
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particles can dynamically change between a fluid and solid state, e.g. during
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particles can dynamically change between a fluid and solid state, e.g. during
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@ -29,9 +30,10 @@ of reproducing kernels). In conjunction to fix rheo, one must specify an
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instance of :doc:`fix rheo/pressure <fix_rheo_pressure>` and
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instance of :doc:`fix rheo/pressure <fix_rheo_pressure>` and
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:doc:`fix rheo/viscosity <fix_rheo_viscosity>` to define a pressure equation
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:doc:`fix rheo/viscosity <fix_rheo_viscosity>` to define a pressure equation
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of state and viscosity model, respectively. Optionally, one can model
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of state and viscosity model, respectively. Optionally, one can model
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a heat equation with :doc:`fix rheo/thermal`, which also allows the user
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a heat equation with :doc:`fix rheo/thermal <fix_rhe0_thermal>`, which also
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to specify equations for a particle's thermal conductivity, specific heat,
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allows the user to specify equations for a particle's thermal conductivity,
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latent heat, and melting temperature. The ordering of these fixes in an an input script matters. Fix rheo must be defined prior to all
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specific heat, latent heat, and melting temperature. The ordering of these
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fixes in an an input script matters. Fix rheo must be defined prior to all
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other RHEO fixes.
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other RHEO fixes.
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Typically, RHEO requires atom style rheo. In addition to typical atom
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Typically, RHEO requires atom style rheo. In addition to typical atom
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@ -45,9 +47,9 @@ affect particles. Instead, one should use the *sph/e* attribute.
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The status variable uses bitmasking to track various properties of a particle
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The status variable uses bitmasking to track various properties of a particle
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such as its current state of matter (fluid or solid) and its location relative
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such as its current state of matter (fluid or solid) and its location relative
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to a surface. Some of these properties (and others) can be accessed using
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to a surface. Some of these properties (and others) can be accessed using
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:doc:`compute rheo/property/atom <fix_rheo_property_atom>`. The *status* attribute
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:doc:`compute rheo/property/atom <compute_rheo_property_atom>`. The *status*
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in :doc:`the set command <set>` only allows control over the first bit which sets
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attribute in :doc:`the set command <set>` only allows control over the first bit
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the state of matter, 0 is fluid and 1 is solid.
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which sets the state of matter, 0 is fluid and 1 is solid.
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Fluid interactions, including pressure forces, viscous forces, and heat exchange,
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Fluid interactions, including pressure forces, viscous forces, and heat exchange,
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are calculated using :doc:`pair rheo <pair_rheo>`. Unlike typical pair styles,
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are calculated using :doc:`pair rheo <pair_rheo>`. Unlike typical pair styles,
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@ -59,18 +61,18 @@ hydrodynamic forces are only calculated if a fluid particle is involved.
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To model elastic objects, there are currently two mechanisms in RHEO, one designed
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To model elastic objects, there are currently two mechanisms in RHEO, one designed
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for bulk solid bodies and the other for thin shells. Both mechanisms rely on
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for bulk solid bodies and the other for thin shells. Both mechanisms rely on
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introducing bonded forces between particles and therefore require a hybrid of atom style bond and rheo
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introducing bonded forces between particles and therefore require a hybrid of atom
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(or rheo/thermal).
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style bond and rheo (or rheo/thermal).
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To create an elastic solid body, one has to (a) change the status of constituent
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To create an elastic solid body, one has to (a) change the status of constituent
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particles to solid (e.g. with the :doc:`set <set>` command), (b) create bpm
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particles to solid (e.g. with the :doc:`set <set>` command), (b) create bpm
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bonds between the particles (see the :doc:`bpm howto <Howto_bpm>` page for
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bonds between the particles (see the :doc:`bpm howto <Howto_bpm>` page for
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more details), and (c) use :doc:`pair rheo/solid <pair_rheo_solid>` to
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more details), and (c) use :doc:`pair rheo/solid <pair_rheo_solid>` to
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apply repulsive contact forces between distinct solid bodies. Akin to pair rheo,
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apply repulsive contact forces between distinct solid bodies. Akin to pair rheo,
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looks at a particles fluid/solid status to determine whether to apply forces.
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pair rheo/solid considers a particles fluid/solid phase to determine whether to
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However, unlike pair rheo, pair rheo/solid does obey special bond settings such
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apply forces. However, unlike pair rheo, pair rheo/solid does obey special bond
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that contact forces do not have to be calculated between two bonded solid particles
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settings such that contact forces do not have to be calculated between two bonded
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in the same elastic body.
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solid particles in the same elastic body.
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In systems with thermal evolution, fix rheo/thermal can optionally set a
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In systems with thermal evolution, fix rheo/thermal can optionally set a
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melting/solidification temperature allowing particles to dynamically swap their
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melting/solidification temperature allowing particles to dynamically swap their
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@ -79,9 +81,9 @@ critical temperature, respectively. Using the *react* option, one can specify a
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bond length and a bond type. Then, when solidifying, particles will search their
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bond length and a bond type. Then, when solidifying, particles will search their
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local neighbors and automatically create bonds with any neighboring solid particles
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local neighbors and automatically create bonds with any neighboring solid particles
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in range. For BPM bond styles, bonds will then use the immediate position of the two
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in range. For BPM bond styles, bonds will then use the immediate position of the two
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particles to calculate a reference state. When melting, particles will then delete
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particles to calculate a reference state. When melting, particles will delete any
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any bonds of the specified type when reverting to a fluid state. Special bonds are
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bonds of the specified type when reverting to a fluid state. Special bonds are updated
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updated as bonds are created/broken.
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as bonds are created/broken.
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The other option for elastic objects is an elastic shell that is nominally much
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The other option for elastic objects is an elastic shell that is nominally much
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thinner than a particle diameter, e.g. a oxide skin which gradually forms over time
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thinner than a particle diameter, e.g. a oxide skin which gradually forms over time
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@ -106,7 +108,7 @@ criteria for creating/deleting a bond or altering force calculations).
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.. _howto_rheo_palermo:
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.. _howto_rheo_palermo:
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**(Palermo)** Palermo, Clemmer, Wolf, O'Connor, in preparation.
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**(Palermo)** Palermo, Wolf, Clemmer, O'Connor, in preparation.
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.. _howto_rheo_clemmer:
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.. _howto_rheo_clemmer:
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@ -194,7 +194,7 @@ the Additional Information section below.
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- :ref:`RHEO <PKG-RHEO>`
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- :ref:`RHEO <PKG-RHEO>`
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- solid and fluid RHEO particles
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- solid and fluid RHEO particles
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* - *rheo/thermal*
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* - *rheo/thermal*
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- *atomic* + rho, status, temperature
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- *atomic* + rho, status, energy, temperature
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- :ref:`RHEO <PKG-RHEO>`
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- :ref:`RHEO <PKG-RHEO>`
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- RHEO particles with temperature
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- RHEO particles with temperature
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* - *sph*
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* - *sph*
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@ -44,12 +44,11 @@ The *rheo/shell* bond style is designed to work with
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:doc:`fix rheo/oxidation <fix_rheo_oxidation>` which creates candidate
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:doc:`fix rheo/oxidation <fix_rheo_oxidation>` which creates candidate
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bonds between eligible surface or near-surface particles. When a bond
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bonds between eligible surface or near-surface particles. When a bond
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is first created, it computes no forces and starts a timer. Forces are
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is first created, it computes no forces and starts a timer. Forces are
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not computed until the timer reaches the specified bond formation time
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not computed until the timer reaches the specified bond formation time,
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and the bond is fully enabled. If the two particles move outside of the
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*t/form*, and the bond is enabled and applies forces. If the two particles
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maximum bond distance or move into the bulk before the timer reaches
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move outside of the maximum bond distance or move into the bulk before
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the formation time, the bond automatically deletes itself. Not that
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the timer reaches *t/form*, the bond automatically deletes itself. This
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this deletion does not generate any broken bond data saved to a
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deletion is not recorded as a broken bond in the optional *store/local* fix.
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*store/local* fix.
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Before bonds are enabled, they are still treated as regular bonds by
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Before bonds are enabled, they are still treated as regular bonds by
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all other parts of LAMMPS. This means they are written to data files
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all other parts of LAMMPS. This means they are written to data files
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@ -60,17 +59,17 @@ To only count enabled bonds, use the *nbond/shell* attribute in
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When enabled, the bond then computes forces based on deviations from
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When enabled, the bond then computes forces based on deviations from
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the initial reference state of the two atoms much like a BPM style
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the initial reference state of the two atoms much like a BPM style
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bond (as further discussed in the :doc:`BPM howto page <Howto_bpm>`).
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bond (as further discussed in the :doc:`BPM howto page <Howto_bpm>`).
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The reference state is stored by each bond when it is first enabled
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The reference state is stored by each bond when it is first enabled.
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the setup of a run. Data is then preserved across run commands and is
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Data is then preserved across run commands and is written to
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written to :doc:`binary restart files <restart>` such that restarting
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:doc:`binary restart files <restart>` such that restarting the system
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the system will not reset the reference state of a bond or the timer.
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will not reset the reference state of a bond or the timer.
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This bond style is based on a model described in
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This bond style is based on a model described in
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:ref:`(Clemmer) <howto_rheo_clemmer>`. The force has a magnitude of
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:ref:`(Clemmer) <rheo_clemmer>`. The force has a magnitude of
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.. math::
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.. math::
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F = 2 k (r - r_0) + \frac{2 * k}{r_0^2 \epsilon_c^2} (r - r_0)^3
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F = 2 k (r - r_0) + \frac{2 k}{r_0^2 \epsilon_c^2} (r - r_0)^3
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where :math:`k` is a stiffness, :math:`r` is the current distance
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where :math:`k` is a stiffness, :math:`r` is the current distance
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and :math:`r_0` is the initial distance between the two particles, and
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and :math:`r_0` is the initial distance between the two particles, and
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@ -78,17 +77,15 @@ and :math:`r_0` is the initial distance between the two particles, and
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is done by setting the bond type to 0 such that forces are no longer
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is done by setting the bond type to 0 such that forces are no longer
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computed.
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computed.
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An additional damping force is applied to the bonded
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A damping force proportional to the difference in the normal velocity
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particles. This forces is proportional to the difference in the
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of particles is also applied to bonded particles:
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normal velocity of particles using a similar construction as
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dissipative particle dynamics :ref:`(Groot) <Groot4>`:
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.. math::
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.. math::
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F_D = - \gamma w (\hat{r} \bullet \vec{v})
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F_D = - \gamma w (\hat{r} \bullet \vec{v})
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where :math:`\gamma` is the damping strength, :math:`\hat{r}` is the
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where :math:`\gamma` is the damping strength, :math:`\hat{r}` is the
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radial normal vector, and :math:`\vec{v}` is the velocity difference
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displacement normal vector, and :math:`\vec{v}` is the velocity difference
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between the two particles.
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between the two particles.
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The following coefficients must be defined for each bond type via the
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The following coefficients must be defined for each bond type via the
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@ -103,7 +100,7 @@ the data file or restart files read by the :doc:`read_data
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Unlike other BPM-style bonds, this bond style does not update special
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Unlike other BPM-style bonds, this bond style does not update special
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bond settings when bonds are created or deleted. This bond style also
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bond settings when bonds are created or deleted. This bond style also
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does not enforce specific :doc:`special_bonds <special_bonds>` settings.
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does not enforce specific :doc:`special_bonds <special_bonds>` settings.
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This behavior is purposeful such :doc:`RHEO pair forces <pair_rheo>`
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This behavior is purposeful such :doc:`RHEO pair <pair_rheo>` forces
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and heat flows are still calculated.
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and heat flows are still calculated.
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If the *store/local* keyword is used, an internal 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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@ -162,10 +159,10 @@ the specified attribute.
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The single() function of this bond style returns 0.0 for the energy
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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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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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dissipative potentials. The single() function also calculates two
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extra bond quantity, the initial distance :math:`r_0`. This
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extra bond quantities, the initial distance :math:`r_0` and a time.
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extra quantity can be accessed by the
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These extra quantities can be accessed by the
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:doc:`compute bond/local <compute_bond_local>` command as *b1*\ .
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:doc:`compute bond/local <compute_bond_local>` command as *b1* and *b2*\ .
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Restrictions
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Restrictions
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""""""""""""
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""""""""""""
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@ -186,10 +183,6 @@ NA
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----------
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----------
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.. _howto_rheo_clemmer:
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.. _rheo_clemmer:
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**(Clemmer)** Clemmer, Pierce, O'Connor, Nevins, Jones, Lechman, Tencer, Appl. Math. Model., 130, 310-326 (2024).
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**(Clemmer)** Clemmer, Pierce, O'Connor, Nevins, Jones, Lechman, Tencer, Appl. Math. Model., 130, 310-326 (2024).
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.. _Groot4:
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**(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997).
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@ -105,6 +105,7 @@ accelerated styles exist.
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* :doc:`oxdna2/fene <bond_oxdna>` - same as oxdna but used with different pair styles
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* :doc:`oxdna2/fene <bond_oxdna>` - same as oxdna but used with different pair styles
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* :doc:`oxrna2/fene <bond_oxdna>` - modified FENE bond suitable for RNA modeling
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* :doc:`oxrna2/fene <bond_oxdna>` - modified FENE bond suitable for RNA modeling
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* :doc:`quartic <bond_quartic>` - breakable quartic bond
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* :doc:`quartic <bond_quartic>` - breakable quartic bond
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* :doc:`rheo/shell <bond_rheo_shell>` - shell bond for oxidation modeling in RHEO
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* :doc:`special <bond_special>` - enable special bond exclusions for 1-5 pairs and beyond
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* :doc:`special <bond_special>` - enable special bond exclusions for 1-5 pairs and beyond
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* :doc:`table <bond_table>` - tabulated by bond length
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* :doc:`table <bond_table>` - tabulated by bond length
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@ -1,7 +1,7 @@
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.. index:: compute rheo/property/atom
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.. index:: compute rheo/property/atom
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compute rheo/property/atom command
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compute rheo/property/atom command
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=============================
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==================================
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Syntax
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Syntax
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""""""
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""""""
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@ -17,11 +17,10 @@ Syntax
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.. parsed-literal::
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.. parsed-literal::
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possible attributes = phase, surface, surface/r,
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possible attributes = phase, surface, surface/r,
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surface/divr, surface/n/:math:`\alpha`, coordination,
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surface/divr, surface/n/a, coordination,
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shift/v/:math:`\alpha`, energy, temperature, heatflow,
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shift/v/a, energy, temperature, heatflow,
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conductivity, cv, viscosity, pressure, rho,
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conductivity, cv, viscosity, pressure, rho,
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grad/v/:math:`\alpha \beta`, stress/v/:math:`\alpha \beta`,
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grad/v/ab, stress/v/ab, stress/t/ab, nbond/shell
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stress/t/:math:`\alpha \beta`, nbond/shell
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.. parsed-literal::
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.. parsed-literal::
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@ -29,9 +28,9 @@ Syntax
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*surface* = atom surface status
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*surface* = atom surface status
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*surface/r* = atom distance from the surface
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*surface/r* = atom distance from the surface
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*surface/divr* = divergence of position at atom position
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*surface/divr* = divergence of position at atom position
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*surface/n/:math:`\alpha`* = surface normal vector
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*surface/n/a* = a-component of surface normal vector
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*coordination* = coordination number
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*coordination* = coordination number
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*shift/v/:math:`\alpha`* = atom shifting velocity
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*shift/v/a* = a-component of atom shifting velocity
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*energy* = atom energy
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*energy* = atom energy
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*temperature* = atom temperature
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*temperature* = atom temperature
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*heatflow* = atom heat flow
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*heatflow* = atom heat flow
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@ -40,9 +39,9 @@ Syntax
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*viscosity* = atom viscosity
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*viscosity* = atom viscosity
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*pressure* = atom pressure
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*pressure* = atom pressure
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*rho* = atom density
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*rho* = atom density
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*grad/v/:math:`\alpha \beta`* = atom velocity gradient
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*grad/v/ab* = ab-component of atom velocity gradient tensor
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*stress/v/:math:`\alpha \beta`* = atom viscous stress
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*stress/v/ab* = ab-component of atom viscous stress tensor
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*stress/t/:math:`\alpha \beta`* = atom total stress (pressure and viscous)
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*stress/t/ab* = ab-component of atom total stress tensor (pressure and viscous)
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*nbond/shell* = number of oxide bonds
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*nbond/shell* = number of oxide bonds
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Examples
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Examples
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@ -68,12 +67,12 @@ computes as inputs. See for example, the
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:doc:`fix ave/chunk <fix_ave_chunk>`, and
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:doc:`fix ave/chunk <fix_ave_chunk>`, and
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:doc:`atom-style variable <variable>` commands.
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:doc:`atom-style variable <variable>` commands.
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For vector attributes, e.g. *shift/v/:math:`\alpha`*, one must specify
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For vector attributes, e.g. *shift/v/*:math:`\alpha`, one must specify
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:math:`\alpha` as the *x*, *y*, or *z* component, e.g. *shift/v/x*.
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:math:`\alpha` as the *x*, *y*, or *z* component, e.g. *shift/v/x*.
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Alternatively, a wild card \* will include all components, *x* and *y* in
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Alternatively, a wild card \* will include all components, *x* and *y* in
|
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2D or *x*, *y*, and *z* in 3D.
|
2D or *x*, *y*, and *z* in 3D.
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|
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For tensor attributes, e.g. *grad/v/:math:`\alpha \beta`*, one must specify
|
For tensor attributes, e.g. *grad/v/*:math:`\alpha \beta`, one must specify
|
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both :math:`\alpha` and :math:`\beta` as *x*, *y*, or *z*, e.g. *grad/v/xy*.
|
both :math:`\alpha` and :math:`\beta` as *x*, *y*, or *z*, e.g. *grad/v/xy*.
|
||||||
Alternatively, a wild card \* will include all components. In 2D, this
|
Alternatively, a wild card \* will include all components. In 2D, this
|
||||||
includes *xx*, *xy*, *yx*, and *yy*. In 3D, this includes *xx*, *xy*, *xz*,
|
includes *xx*, *xy*, *yx*, and *yy*. In 3D, this includes *xx*, *xy*, *xz*,
|
||||||
@ -93,11 +92,11 @@ the *interface/reconstruct* option of :doc:`fix rheo <fix_rheo>`. Bulk
|
|||||||
particles have a value of 0, surface particles have a value of 1, and
|
particles have a value of 0, surface particles have a value of 1, and
|
||||||
splash particles have a value of 2. The *surface/r* property is the
|
splash particles have a value of 2. The *surface/r* property is the
|
||||||
distance from the surface, up to the kernel cutoff length. Surface particles
|
distance from the surface, up to the kernel cutoff length. Surface particles
|
||||||
have a value of 0. The *surface/n* properties are the components of the
|
have a value of 0. The *surface/n/*:math:`\alpha` properties are the
|
||||||
surface normal vector.
|
components of the surface normal vector.
|
||||||
|
|
||||||
The *shift/v/:math:`\alpha`* properties are the components of the shifting velocity
|
The *shift/v/*:math:`\alpha` properties are the components of the shifting
|
||||||
produced by the *shift* option of :doc:`fix rheo <fix_rheo>`.
|
velocity produced by the *shift* option of :doc:`fix rheo <fix_rheo>`.
|
||||||
|
|
||||||
The *nbond/shell* property is the number of shell bonds that have been
|
The *nbond/shell* property is the number of shell bonds that have been
|
||||||
activated from :doc:`bond style rheo/shell <bond_rheo_shell>`.
|
activated from :doc:`bond style rheo/shell <bond_rheo_shell>`.
|
||||||
@ -110,13 +109,13 @@ Output info
|
|||||||
"""""""""""
|
"""""""""""
|
||||||
|
|
||||||
This compute calculates a per-atom vector or per-atom array depending
|
This compute calculates a per-atom vector or per-atom array depending
|
||||||
on the number of input values. If a single input is specified, a
|
on the number of input values. Generally, if a single input is specified,
|
||||||
per-atom vector is produced. If two or more inputs are specified, a
|
a per-atom vector is produced. If two or more inputs are specified, a
|
||||||
per-atom array is produced where the number of columns = the number of
|
per-atom array is produced where the number of columns = the number of
|
||||||
inputs. If a wild card \* is used for a vector or tensor, then the number
|
inputs. However, if a wild card \* is used for a vector or tensor, then
|
||||||
of inputs is considered to be incremented by the dimensiod or dimension
|
the number of inputs is considered to be incremented by the dimension or
|
||||||
squared, respectively. The vector or array can be accessed by any command
|
the dimension squared, respectively. The vector or array can be accessed
|
||||||
that uses per-atom values from a compute as input. See the
|
by any command that uses per-atom values from a compute as input. See the
|
||||||
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
|
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
|
||||||
options.
|
options.
|
||||||
|
|
||||||
|
|||||||
@ -193,6 +193,7 @@ accelerated styles exist.
|
|||||||
* :doc:`adapt <fix_adapt>` - change a simulation parameter over time
|
* :doc:`adapt <fix_adapt>` - change a simulation parameter over time
|
||||||
* :doc:`adapt/fep <fix_adapt_fep>` - enhanced version of fix adapt
|
* :doc:`adapt/fep <fix_adapt_fep>` - enhanced version of fix adapt
|
||||||
* :doc:`addforce <fix_addforce>` - add a force to each atom
|
* :doc:`addforce <fix_addforce>` - add a force to each atom
|
||||||
|
* :doc:`add/heat <fix_add_heat>` - add a heat flux to each atom
|
||||||
* :doc:`addtorque <fix_addtorque>` - add a torque to a group of atoms
|
* :doc:`addtorque <fix_addtorque>` - add a torque to a group of atoms
|
||||||
* :doc:`alchemy <fix_alchemy>` - perform an "alchemical transformation" between two partitions
|
* :doc:`alchemy <fix_alchemy>` - perform an "alchemical transformation" between two partitions
|
||||||
* :doc:`amoeba/bitorsion <fix_amoeba_bitorsion>` - torsion/torsion terms in AMOEBA force field
|
* :doc:`amoeba/bitorsion <fix_amoeba_bitorsion>` - torsion/torsion terms in AMOEBA force field
|
||||||
@ -371,8 +372,9 @@ accelerated styles exist.
|
|||||||
* :doc:`restrain <fix_restrain>` - constrain a bond, angle, dihedral
|
* :doc:`restrain <fix_restrain>` - constrain a bond, angle, dihedral
|
||||||
* :doc:`rheo <fix_rheo>` - integrator for the RHEO package
|
* :doc:`rheo <fix_rheo>` - integrator for the RHEO package
|
||||||
* :doc:`rheo/thermal <fix_rheo_thermal>` - thermal integrator for the RHEO package
|
* :doc:`rheo/thermal <fix_rheo_thermal>` - thermal integrator for the RHEO package
|
||||||
* :doc:`rheo/pressure <fix_rheo_pressure>` - pressure derivation for the RHEO package
|
* :doc:`rheo/oxidation <fix_rheo_oxidation>` - create oxidation bonds for the RHEO package
|
||||||
* :doc:`rheo/viscosity <fix_rheo_pressure>` - viscosity derivation for the RHEO package
|
* :doc:`rheo/pressure <fix_rheo_pressure>` - pressure calculation for the RHEO package
|
||||||
|
* :doc:`rheo/viscosity <fix_rheo_pressure>` - viscosity calculation for the RHEO package
|
||||||
* :doc:`rhok <fix_rhok>` - add bias potential for long-range ordered systems
|
* :doc:`rhok <fix_rhok>` - add bias potential for long-range ordered systems
|
||||||
* :doc:`rigid <fix_rigid>` - constrain one or more clusters of atoms to move as a rigid body with NVE integration
|
* :doc:`rigid <fix_rigid>` - constrain one or more clusters of atoms to move as a rigid body with NVE integration
|
||||||
* :doc:`rigid/meso <fix_rigid_meso>` - constrain clusters of mesoscopic SPH/SDPD particles to move as a rigid body
|
* :doc:`rigid/meso <fix_rigid_meso>` - constrain clusters of mesoscopic SPH/SDPD particles to move as a rigid body
|
||||||
|
|||||||
@ -16,14 +16,14 @@ Syntax
|
|||||||
|
|
||||||
.. parsed-literal::
|
.. parsed-literal::
|
||||||
|
|
||||||
*constant* args = rate
|
*constant* args = *rate*
|
||||||
rate = rate of heat flow (energy/time units)
|
*rate* = rate of heat flow (energy/time units)
|
||||||
*linear* args = t_target k
|
*linear* args = :math:`T_{target}` *k*
|
||||||
t_target = target temperature (temperature units)
|
:math:`T_{target}` = target temperature (temperature units)
|
||||||
k = prefactor (energy/(time*temperature) units)
|
*k* = prefactor (energy/(time*temperature) units)
|
||||||
*quartic* args = t_target k
|
*quartic* args = :math:`T_{target}` *k*
|
||||||
t_target = target temperature (temperature units)
|
:math:`T_{target}` = target temperature (temperature units)
|
||||||
k = prefactor (energy/(time*temperature^4) units)
|
*k* = prefactor (energy/(time*temperature^4) units)
|
||||||
|
|
||||||
* zero or more keyword/value pairs may be appended to args
|
* zero or more keyword/value pairs may be appended to args
|
||||||
* keyword = *overwrite*
|
* keyword = *overwrite*
|
||||||
@ -45,7 +45,9 @@ Examples
|
|||||||
Description
|
Description
|
||||||
"""""""""""
|
"""""""""""
|
||||||
|
|
||||||
This fix adds heat to particles every timestep.
|
This fix adds heat to particles with the temperature attribute every timestep.
|
||||||
|
Note that this is an internal temperature of a particle intended for use with
|
||||||
|
non-atomistic models like the discrete element method.
|
||||||
|
|
||||||
For the *constant* style, heat is added at the specified rate. For the *linear* style,
|
For the *constant* style, heat is added at the specified rate. For the *linear* style,
|
||||||
heat is added at a rate of :math:`k (T_{target} - T)` where :math:`k` is the
|
heat is added at a rate of :math:`k (T_{target} - T)` where :math:`k` is the
|
||||||
@ -62,22 +64,22 @@ determine the rate of heat added.
|
|||||||
|
|
||||||
Equal-style variables can specify formulas with various mathematical
|
Equal-style variables can specify formulas with various mathematical
|
||||||
functions and include :doc:`thermo_style <thermo_style>` command
|
functions and include :doc:`thermo_style <thermo_style>` command
|
||||||
keywords for the simulation box parameters, time step, and elapsed time.
|
keywords for the simulation box parameters, time step, and elapsed time
|
||||||
Thus, it is easy to specify time-dependent heating.
|
to specify time-dependent heating.
|
||||||
|
|
||||||
Atom-style variables can specify the same formulas as equal-style
|
Atom-style variables can specify the same formulas as equal-style
|
||||||
variables but can also include per-atom values, such as atom
|
variables but can also include per-atom values, such as atom
|
||||||
coordinates. Thus, it is easy to specify a spatially-dependent heating
|
coordinates to specify spatially-dependent heating.
|
||||||
field with optional time-dependence as well.
|
|
||||||
|
|
||||||
If the *overwrite* keyword is set to *yes*, this fix will effectively set
|
If the *overwrite* keyword is set to *yes*, this fix will set the total
|
||||||
the total heat flow on a particle, overwriting contributions from pair
|
heat flow on a particle every timestep, overwriting contributions from pair
|
||||||
styles or other fixes.
|
styles or other fixes. If *overwrite* is *no*, this fix will add heat on
|
||||||
|
top of other contributions.
|
||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
Restart, fix_modify, output, run start/stop, minimize info
|
Restart, fix_modify, output, run start/stop, minimize info
|
||||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||||
|
|
||||||
No information about this fix is written to :doc:`binary restart files <restart>`.
|
No information about this fix is written to :doc:`binary restart files <restart>`.
|
||||||
None of the :doc:`fix_modify <fix_modify>` options are relevant to this fix.
|
None of the :doc:`fix_modify <fix_modify>` options are relevant to this fix.
|
||||||
|
|||||||
@ -1,7 +1,7 @@
|
|||||||
.. index:: fix rheo
|
.. index:: fix rheo
|
||||||
|
|
||||||
fix rheo command
|
fix rheo command
|
||||||
===============
|
================
|
||||||
|
|
||||||
Syntax
|
Syntax
|
||||||
""""""
|
""""""
|
||||||
@ -38,8 +38,8 @@ Examples
|
|||||||
|
|
||||||
.. code-block:: LAMMPS
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
fix 1 all rheo 1.0 quintic thermal density 0.1 speed/sound 10.0
|
fix 1 all rheo 3.0 quintic 0 thermal density 0.1 0.1 speed/sound 10.0 1.0
|
||||||
fix 1 all rheo 1.0 RK1 shift surface/detection coordination 40
|
fix 1 all rheo 3.0 RK1 10 shift surface/detection coordination 40
|
||||||
|
|
||||||
Description
|
Description
|
||||||
"""""""""""
|
"""""""""""
|
||||||
@ -48,14 +48,15 @@ Description
|
|||||||
|
|
||||||
Perform time integration for RHEO particles, updating positions, velocities,
|
Perform time integration for RHEO particles, updating positions, velocities,
|
||||||
and densities. For a detailed breakdown of the integration timestep and
|
and densities. For a detailed breakdown of the integration timestep and
|
||||||
numerical details, see :ref:`(Palermo) <howto_rheo_palermo>`. For an
|
numerical details, see :ref:`(Palermo) <rheo_palermo>`. For an
|
||||||
overview of other features available in the RHEO package, see
|
overview of other features available in the RHEO package, see
|
||||||
:doc:`the RHEO howto <Howto_rheo>`.
|
:doc:`the RHEO howto <Howto_rheo>`.
|
||||||
|
|
||||||
The type of kernel is specified using *kstyle* and the cutoff is *cut*. Four
|
The type of kernel is specified using *kstyle* and the cutoff is *cut*. Four
|
||||||
kernels are currently available. The *quintic* kernel is a standard quintic
|
kernels are currently available. The *quintic* kernel is a standard quintic
|
||||||
spline function commonly used in SPH. The other options, *RK0*, *RK1*, and
|
spline function commonly used in SPH. The other options, *RK0*, *RK1*, and
|
||||||
*RK2*, are zeroth, first, and second order reproducing. To generate a reproducing kernel, a particle must have sufficient neighbors inside the
|
*RK2*, are zeroth, first, and second order reproducing. To generate a
|
||||||
|
reproducing kernel, a particle must have sufficient neighbors inside the
|
||||||
kernel cutoff distance (a coordination number) to accurately calculate
|
kernel cutoff distance (a coordination number) to accurately calculate
|
||||||
moments. This threshold is set by *zmin*. If reproducing kernels are
|
moments. This threshold is set by *zmin*. If reproducing kernels are
|
||||||
requested but a particle has fewer neighbors, then it will revert to a
|
requested but a particle has fewer neighbors, then it will revert to a
|
||||||
@ -81,28 +82,27 @@ surfaces.
|
|||||||
|
|
||||||
A modified form of Fickian particle shifting can be enabled with the
|
A modified form of Fickian particle shifting can be enabled with the
|
||||||
*shift* keyword. This effectively shifts particle positions to generate a
|
*shift* keyword. This effectively shifts particle positions to generate a
|
||||||
more uniform spatial distribution. Shifting currently does consider the
|
more uniform spatial distribution. Shifting currently does not consider the
|
||||||
type of a particle and therefore may be inappropriate in systems consisting
|
type of a particle and therefore may be inappropriate in systems consisting
|
||||||
of multiple materials.
|
of multiple fluid phases.
|
||||||
|
|
||||||
In systems with free surfaces, the *surface/detection* keyword can be used
|
In systems with free surfaces, the *surface/detection* keyword can be used
|
||||||
to classify the location of particles as being within the bulk fluid, on a
|
to classify the location of particles as being within the bulk fluid, on a
|
||||||
free surface, or isolated from other particles in a splash or droplet.
|
free surface, or isolated from other particles in a splash or droplet.
|
||||||
Shifting is then disabled in the direction away from the free surface to
|
Shifting is then disabled in the normal direction away from the free surface
|
||||||
prevent it from diffusing particles away from the bulk fluid. Surface
|
to prevent particles from difusing away. Surface detection can also be used
|
||||||
detection can also be used to control surface-nucleated effects like
|
to control surface-nucleated effects like oxidation when used in combination
|
||||||
oxidation when used in combination with
|
with :doc:`fix rheo/oxidation <fix_rheo_oxidation>`. Surface detection is not
|
||||||
:doc:`fix rheo/oxidation <fix_rheo_oxidation>`. Surface detection is not
|
|
||||||
performed on solid bodies.
|
performed on solid bodies.
|
||||||
|
|
||||||
The *surface/detection* keyword takes three arguments: *sdstyle*, *limit*,
|
The *surface/detection* keyword takes three arguments: *sdstyle*, *limit*,
|
||||||
and *limi/splash*. The first, *sdstyle*, specifies whether surface particles
|
and *limit/splash*. The first, *sdstyle*, specifies whether surface particles
|
||||||
are identified using a coordination number (*coordination*) or the divergence
|
are identified using a coordination number (*coordination*) or the divergence
|
||||||
of the local particle positions (*divergence*). The threshold value for a
|
of the local particle positions (*divergence*). The threshold value for a
|
||||||
surface particle for either of these criteria is set by the numerical value
|
surface particle for either of these criteria is set by the numerical value
|
||||||
of *limit*. Additionally, if a particle's coordination number is too low,
|
of *limit*. Additionally, if a particle's coordination number is too low,
|
||||||
i.e. if it has separated off from the bulk in a droplet, it is not possible
|
i.e. if it has separated off from the bulk in a droplet, it is not possible
|
||||||
to define surfaces and a particle is classified as a splash. The coordination
|
to define surfaces and the particle is classified as a splash. The coordination
|
||||||
threshold for this classification is set by the numerical value of
|
threshold for this classification is set by the numerical value of
|
||||||
*limit/splash*.
|
*limit/splash*.
|
||||||
|
|
||||||
@ -112,23 +112,23 @@ a kernel summation of the masses of neighboring particles by specifying the *rho
|
|||||||
keyword.
|
keyword.
|
||||||
|
|
||||||
The *self/mass* keyword modifies the behavior of the density summation in *rho/sum*.
|
The *self/mass* keyword modifies the behavior of the density summation in *rho/sum*.
|
||||||
Typically, the density :math:`\rho` of a particle is calculated as the sum
|
Typically, the density :math:`\rho` of a particle is calculated as the sum over neighbors
|
||||||
|
|
||||||
.. math::
|
.. math::
|
||||||
\rho_i = \Sum_{j} W_{ij} M_j
|
\rho_i = \sum_{j} W_{ij} M_j
|
||||||
|
|
||||||
where the summation is over neighbors, :math:`W_{ij}` is the kernel, and :math:`M_j`
|
where :math:`W_{ij}` is the kernel, and :math:`M_j` is the mass of particle :math:`j`.
|
||||||
is the mass of particle :math:`j`. The *self/mass* keyword augments this expression
|
The *self/mass* keyword augments this expression by replacing :math:`M_j` with
|
||||||
by replacing :math:`M_j` with :math:`M_i`. This may be useful in simulations of
|
:math:`M_i`. This may be useful in simulations of multiple fluid phases with large
|
||||||
multiple fluid phases with large differences in density, :ref:`(Hu) <fix_rheo_hu>`.
|
differences in density, :ref:`(Hu) <fix_rheo_hu>`.
|
||||||
|
|
||||||
The *density* keyword is used to specify the equilbrium density of each of the N
|
The *density* keyword is used to specify the equilibrium density of each of the N
|
||||||
particle types. It must be followed by N numerical values specifying each
|
particle types. It must be followed by N numerical values specifying each type's
|
||||||
type's equilibrium density *rho0*.
|
equilibrium density *rho0*.
|
||||||
|
|
||||||
The *speed/sound* keyword is used to specify the speed of sound of each of the
|
The *speed/sound* keyword is used to specify the speed of sound of each of the
|
||||||
N particle types. It must be followed by N numerical values specifying each
|
N particle types. It must be followed by N numerical values specifying each type's
|
||||||
type's speed of sound *cs*.
|
speed of sound *cs*.
|
||||||
|
|
||||||
Restart, fix_modify, output, run start/stop, minimize info
|
Restart, fix_modify, output, run start/stop, minimize info
|
||||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||||
@ -144,18 +144,16 @@ the :doc:`run <run>` command. This fix is not invoked during
|
|||||||
Restrictions
|
Restrictions
|
||||||
""""""""""""
|
""""""""""""
|
||||||
|
|
||||||
This fix must be used with atom style rheo or rheo/thermal.
|
This fix must be used with atom style rheo or rheo/thermal. This fix must
|
||||||
This fix must be used in conjuction with
|
be used in conjuction with :doc:`fix rheo/pressure <fix_rheo_pressure>`.
|
||||||
:doc:`fix rheo/pressure <fix_rheo_pressure>`. and
|
and :doc:`fix rheo/viscosity <fix_rheo_viscosity>`. If the *thermal* setting
|
||||||
:doc:`fix rheo/viscosity <fix_rheo_viscosity>`, If the *thermal*
|
is used, there must also be an instance of
|
||||||
setting is used, there must also be an instance of
|
:doc:`fix rheo/thermal <fix_rheo_thermal>`. The fix group must be set to all.
|
||||||
:doc:`fix rheo/thermal <fix_rheo_thermal>`. The fix group must be
|
Only one instance of fix rheo may be defined and it must be defined prior
|
||||||
set to all. Only one instance of fix rheo may be defined and it
|
to all other RHEO fixes in the input script.
|
||||||
must be defined prior to all other RHEO fixes.
|
|
||||||
|
|
||||||
This fix is part of the RHEO package. It is only enabled if
|
This fix is part of the RHEO package. It is only enabled if LAMMPS was built
|
||||||
LAMMPS was built with that package. See the
|
with that package. See the :doc:`Build package <Build_package>` page for more info.
|
||||||
:doc:`Build package <Build_package>` page for more info.
|
|
||||||
|
|
||||||
Related commands
|
Related commands
|
||||||
""""""""""""""""
|
""""""""""""""""
|
||||||
@ -173,9 +171,9 @@ Default
|
|||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
.. _howto_rheo_palermo:
|
.. _rheo_palermo:
|
||||||
|
|
||||||
**(Palermo)** Palermo, Clemmer, Wolf, O'Connor, in preparation.
|
**(Palermo)** Palermo, Wolf, Clemmer, O'Connor, in preparation.
|
||||||
|
|
||||||
.. _fix_rheo_hu:
|
.. _fix_rheo_hu:
|
||||||
|
|
||||||
|
|||||||
@ -36,21 +36,21 @@ for use with bond style :doc:`bond rheo/shell <bond_rheo_shell>`.
|
|||||||
Every timestep, particles check neighbors within a distance of *cut*.
|
Every timestep, particles check neighbors within a distance of *cut*.
|
||||||
This distance must be smaller than the kernel length defined in
|
This distance must be smaller than the kernel length defined in
|
||||||
:doc:`fix rheo <fix_rheo>`. Bonds of type *btype* are created between
|
:doc:`fix rheo <fix_rheo>`. Bonds of type *btype* are created between
|
||||||
pairs of particles that satisfy one of two conditions. First, if both
|
a fluid particle and either a fluid or solid neighbor. The fluid particles
|
||||||
particles are on the fluid surface, or within a distance of *rsurf*
|
must also be on the fluid surface, or within a distance of *rsurf* from
|
||||||
from the surface. Secondly, if one particle is on the fluid surface
|
the surface. This process is further described in
|
||||||
and the other bond is solid. This process is further described in
|
:ref:`(Clemmer) <howto_rheo_clemmer2>`.
|
||||||
:ref:`(Clemmer) <howto_rheo_clemmer>`.
|
|
||||||
|
|
||||||
If used in conjunction with solid bodies, such as those generated
|
If used in conjunction with solid bodies, such as those generated
|
||||||
by the *react* option of :doc:`fix rheo/thermal <fix_rheo_thermal>`,
|
by the *react* option of :doc:`fix rheo/thermal <fix_rheo_thermal>`,
|
||||||
it is recommended that one uses a :doc:`hybrid bond style <bond_hybrid>`
|
it is recommended to use a :doc:`hybrid bond style <bond_hybrid>`
|
||||||
with different bond types for solid and oxide bonds.
|
with different bond types for solid and oxide bonds.
|
||||||
|
|
||||||
Restart, fix_modify, output, run start/stop, minimize info
|
Restart, fix_modify, output, run start/stop, minimize info
|
||||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||||
|
|
||||||
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
|
No information about this fix is written to :doc:`binary restart files <restart>`.
|
||||||
|
None of the :doc:`fix_modify <fix_modify>` options
|
||||||
are relevant to this fix. No global or per-atom quantities are stored
|
are relevant to this fix. No global or per-atom quantities are stored
|
||||||
by this fix for access by various :doc:`output commands <Howto_output>`.
|
by this fix for access by various :doc:`output commands <Howto_output>`.
|
||||||
No parameter of this fix can be used with the *start/stop* keywords of
|
No parameter of this fix can be used with the *start/stop* keywords of
|
||||||
@ -59,11 +59,12 @@ the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minim
|
|||||||
Restrictions
|
Restrictions
|
||||||
""""""""""""
|
""""""""""""
|
||||||
|
|
||||||
This fix must be used with an bond style :doc:`rheo/shell <bond_rheo_shell>`
|
This fix must be used with the bond style :doc:`rheo/shell <bond_rheo_shell>`
|
||||||
and :doc:`fix rheo <fix_rheo>` with surface detection enabled.
|
and :doc:`fix rheo <fix_rheo>` with surface detection enabled.
|
||||||
|
|
||||||
This fix is part of the RHEO package. It is only enabled if
|
This fix is part of the RHEO package. It is only enabled if
|
||||||
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
|
LAMMPS was built with that package. See the :doc:`Build package <Build_package>`
|
||||||
|
page for more info.
|
||||||
|
|
||||||
Related commands
|
Related commands
|
||||||
""""""""""""""""
|
""""""""""""""""
|
||||||
@ -79,6 +80,6 @@ none
|
|||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
.. _howto_rheo_clemmer:
|
.. _howto_rheo_clemmer2:
|
||||||
|
|
||||||
**(Clemmer)** Clemmer, Pierce, O'Connor, Nevins, Jones, Lechman, Tencer, Appl. Math. Model., 130, 310-326 (2024).
|
**(Clemmer)** Clemmer, Pierce, O'Connor, Nevins, Jones, Lechman, Tencer, Appl. Math. Model., 130, 310-326 (2024).
|
||||||
|
|||||||
@ -1,7 +1,7 @@
|
|||||||
.. index:: fix rheo/pressure
|
.. index:: fix rheo/pressure
|
||||||
|
|
||||||
fix rheo/pressure command
|
fix rheo/pressure command
|
||||||
===============
|
=========================
|
||||||
|
|
||||||
Syntax
|
Syntax
|
||||||
""""""
|
""""""
|
||||||
@ -20,7 +20,7 @@ Syntax
|
|||||||
|
|
||||||
*linear* args = none
|
*linear* args = none
|
||||||
*taitwater* args = none
|
*taitwater* args = none
|
||||||
*cubic* args = cubic term prefactor :math:`A_3` (pressure/density\^2)
|
*cubic* args = cubic prefactor :math:`A_3` (pressure/density\^2)
|
||||||
|
|
||||||
Examples
|
Examples
|
||||||
""""""""
|
""""""""
|
||||||
@ -36,8 +36,8 @@ Description
|
|||||||
.. versionadded:: TBD
|
.. versionadded:: TBD
|
||||||
|
|
||||||
This fix defines a pressure equation of state for RHEO particles. One can
|
This fix defines a pressure equation of state for RHEO particles. One can
|
||||||
define different equations of state for different atom types, but an
|
define different equations of state for different atom types. An equation
|
||||||
equation must be specified for every atom type.
|
must be specified for every atom type.
|
||||||
|
|
||||||
One first defines the atom *types*. A wild-card asterisk can be used in place
|
One first defines the atom *types*. A wild-card asterisk can be used in place
|
||||||
of or in conjunction with the *types* argument to set the coefficients for
|
of or in conjunction with the *types* argument to set the coefficients for
|
||||||
@ -74,7 +74,8 @@ Style *taitwater* is Tait's equation of state:
|
|||||||
Restart, fix_modify, output, run start/stop, minimize info
|
Restart, fix_modify, output, run start/stop, minimize info
|
||||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||||
|
|
||||||
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
|
No information about this fix is written to :doc:`binary restart files <restart>`.
|
||||||
|
None of the :doc:`fix_modify <fix_modify>` options
|
||||||
are relevant to this fix. No global or per-atom quantities are stored
|
are relevant to this fix. No global or per-atom quantities are stored
|
||||||
by this fix for access by various :doc:`output commands <Howto_output>`.
|
by this fix for access by various :doc:`output commands <Howto_output>`.
|
||||||
No parameter of this fix can be used with the *start/stop* keywords of
|
No parameter of this fix can be used with the *start/stop* keywords of
|
||||||
@ -89,7 +90,8 @@ conjuction with :doc:`fix rheo <fix_rheo>`. The fix group must be
|
|||||||
set to all. Only one instance of fix rheo/pressure can be defined.
|
set to all. Only one instance of fix rheo/pressure can be defined.
|
||||||
|
|
||||||
This fix is part of the RHEO package. It is only enabled if
|
This fix is part of the RHEO package. It is only enabled if
|
||||||
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
|
LAMMPS was built with that package. See the :doc:`Build package <Build_package>`
|
||||||
|
page for more info.
|
||||||
|
|
||||||
Related commands
|
Related commands
|
||||||
""""""""""""""""
|
""""""""""""""""
|
||||||
|
|||||||
@ -1,7 +1,7 @@
|
|||||||
.. index:: fix rheo/thermal
|
.. index:: fix rheo/thermal
|
||||||
|
|
||||||
fix rheo/thermal command
|
fix rheo/thermal command
|
||||||
===============
|
========================
|
||||||
|
|
||||||
Syntax
|
Syntax
|
||||||
""""""
|
""""""
|
||||||
@ -50,16 +50,16 @@ Description
|
|||||||
|
|
||||||
.. versionadded:: TBD
|
.. versionadded:: TBD
|
||||||
|
|
||||||
This fix performs time integration of temperature evolution for atom style
|
This fix performs time integration of temperature for atom style rheo/thermal.
|
||||||
rheo/thermal. In addition, it defines multiple thermal properties of
|
In addition, it defines multiple thermal properties of particles and handles
|
||||||
particles and handles melting/solidification, if applicable. For more details
|
melting/solidification, if applicable. For more details on phase transitions
|
||||||
on phase transitions in RHEO, see :doc:`the RHEO howto <Howto_rheo>`.
|
in RHEO, see :doc:`the RHEO howto <Howto_rheo>`.
|
||||||
|
|
||||||
Note that the temperature of a particle is always derived from the energy.
|
Note that the temperature of a particle is always derived from the energy.
|
||||||
This implies the *temperature* attribute of :doc:`the set command <set>` does
|
This implies the *temperature* attribute of :doc:`the set command <set>` does
|
||||||
not affect particles. Instead, one should use the *sph/e* attribute.
|
not affect particles. Instead, one should use the *sph/e* attribute.
|
||||||
|
|
||||||
For each atom type, one can define attributes for the *conductivity*,
|
For each atom type, one can define expressions for the *conductivity*,
|
||||||
*specific/heat*, *latent/heat*, and critical temperature (*Tfreeze*).
|
*specific/heat*, *latent/heat*, and critical temperature (*Tfreeze*).
|
||||||
The conductivity and specific heat must be defined for all atom types.
|
The conductivity and specific heat must be defined for all atom types.
|
||||||
The latent heat and critical temperature are optional. However, a
|
The latent heat and critical temperature are optional. However, a
|
||||||
@ -88,13 +88,14 @@ types that have a defined value of *Tfreeze*. When a fluid particle's
|
|||||||
temperature drops below *Tfreeze*, bonds of type *btype* are created between
|
temperature drops below *Tfreeze*, bonds of type *btype* are created between
|
||||||
nearby solid particles within a distance of *cut*. The particle's status also
|
nearby solid particles within a distance of *cut*. The particle's status also
|
||||||
swaps to a solid state. When a solid particle's temperature rises above
|
swaps to a solid state. When a solid particle's temperature rises above
|
||||||
*Tfreeze*, all bonds of type *btype* are broken and the particle's tatus swaps
|
*Tfreeze*, all bonds of type *btype* are broken and the particle's status swaps
|
||||||
to a fluid state.
|
to a fluid state.
|
||||||
|
|
||||||
Restart, fix_modify, output, run start/stop, minimize info
|
Restart, fix_modify, output, run start/stop, minimize info
|
||||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||||
|
|
||||||
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
|
No information about this fix is written to :doc:`binary restart files <restart>`.
|
||||||
|
None of the :doc:`fix_modify <fix_modify>` options
|
||||||
are relevant to this fix. No global or per-atom quantities are stored
|
are relevant to this fix. No global or per-atom quantities are stored
|
||||||
by this fix for access by various :doc:`output commands <Howto_output>`.
|
by this fix for access by various :doc:`output commands <Howto_output>`.
|
||||||
No parameter of this fix can be used with the *start/stop* keywords of
|
No parameter of this fix can be used with the *start/stop* keywords of
|
||||||
@ -110,7 +111,8 @@ must be used in conjuction with :doc:`fix rheo <fix_rheo>` with the
|
|||||||
instance of fix rheo/pressure can be defined.
|
instance of fix rheo/pressure can be defined.
|
||||||
|
|
||||||
This fix is part of the RHEO package. It is only enabled if
|
This fix is part of the RHEO package. It is only enabled if
|
||||||
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
|
LAMMPS was built with that package. See the :doc:`Build package <Build_package>`
|
||||||
|
page for more info.
|
||||||
|
|
||||||
Related commands
|
Related commands
|
||||||
""""""""""""""""
|
""""""""""""""""
|
||||||
|
|||||||
@ -1,7 +1,7 @@
|
|||||||
.. index:: fix rheo/viscosity
|
.. index:: fix rheo/viscosity
|
||||||
|
|
||||||
fix rheo/viscosity command
|
fix rheo/viscosity command
|
||||||
===============
|
==========================
|
||||||
|
|
||||||
Syntax
|
Syntax
|
||||||
""""""
|
""""""
|
||||||
@ -63,16 +63,16 @@ for the stress :math:`\tau`
|
|||||||
|
|
||||||
\tau = \left(\frac{\tau_0}{\dot{\gamma}} + K \dot{\gamma}^{n - 1}\right) \dot{\gamma}, \tau \ge \tau_0
|
\tau = \left(\frac{\tau_0}{\dot{\gamma}} + K \dot{\gamma}^{n - 1}\right) \dot{\gamma}, \tau \ge \tau_0
|
||||||
|
|
||||||
where :math:`\dot{\gamma}` is the strain rate and :math:`tau_0` is the critical
|
where :math:`\dot{\gamma}` is the strain rate and :math:`\tau_0` is the critical
|
||||||
yield stress, below which :math:`\dot{\gamma} = 0.0`. To avoid divergences, this
|
yield stress, below which :math:`\dot{\gamma} = 0.0`. To avoid divergences, this
|
||||||
expression is regularized by defining a critical strain rate *gd0*. If the local
|
expression is regularized by defining a critical strain rate *gd0*. If the local
|
||||||
strain rate on a particle falls below this limit, a constant viscosity of *eta*
|
strain rate on a particle falls below this limit, a constant viscosity of *eta*
|
||||||
is assigned. This implies a value of
|
is assigned. This implies a value of
|
||||||
|
|
||||||
.. math::
|
.. math::
|
||||||
\tau_0 = \eta * \dot{\gamma}_0 - K \dot{\gamma}_0^N
|
\tau_0 = \eta \dot{\gamma}_0 - K \dot{\gamma}_0^N
|
||||||
|
|
||||||
as further discussed in :ref:`(Palermo) <howto_rheo_palermo>`.
|
as further discussed in :ref:`(Palermo) <rheo_palermo2>`.
|
||||||
|
|
||||||
|
|
||||||
Restart, fix_modify, output, run start/stop, minimize info
|
Restart, fix_modify, output, run start/stop, minimize info
|
||||||
@ -112,6 +112,6 @@ none
|
|||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
.. _howto_rheo_palermo:
|
.. _rheo_palermo2:
|
||||||
|
|
||||||
**(Palermo)** Palermo, Clemmer, Wolf, O'Connor, in preparation.
|
**(Palermo)** Palermo, Wolf, Clemmer, O'Connor, in preparation.
|
||||||
|
|||||||
@ -1,7 +1,7 @@
|
|||||||
.. index:: pair_style rheo
|
.. index:: pair_style rheo
|
||||||
|
|
||||||
pair_style rheo command
|
pair_style rheo command
|
||||||
=========================
|
=======================
|
||||||
|
|
||||||
Syntax
|
Syntax
|
||||||
""""""
|
""""""
|
||||||
@ -25,7 +25,7 @@ Examples
|
|||||||
|
|
||||||
.. code-block:: LAMMPS
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
pair_style rheo 1.0 quintic rho/damp 1.0 artificial/visc 2.0
|
pair_style rheo 3.0 rho/damp 1.0 artificial/visc 2.0
|
||||||
pair_coeff * *
|
pair_coeff * *
|
||||||
|
|
||||||
Description
|
Description
|
||||||
@ -41,22 +41,23 @@ heat exchanged between particles.
|
|||||||
The *artificial/viscosity* keyword is used to specify the magnitude
|
The *artificial/viscosity* keyword is used to specify the magnitude
|
||||||
:math:`\zeta` of an optional artificial viscosity contribution to forces.
|
:math:`\zeta` of an optional artificial viscosity contribution to forces.
|
||||||
This factor can help stabilize simulations by smoothing out small length
|
This factor can help stabilize simulations by smoothing out small length
|
||||||
scale variations in velocity fields. Artificial viscous forces are only
|
scale variations in velocity fields. Artificial viscous forces typically
|
||||||
exchanged by fluid particles unless interfaces are not reconstructed in
|
are only exchanged by fluid particles. However, if interfaces are not
|
||||||
fix rheo, in which fluid particles will also exchange artificial viscous
|
reconstructed in fix rheo, fluid particles will also exchange artificial
|
||||||
forces with solid particles to improve stability.
|
viscous forces with solid particles to improve stability.
|
||||||
|
|
||||||
The *rho/damp* keyword is used to specify the magnitude :math:`\xi` of
|
The *rho/damp* keyword is used to specify the magnitude :math:`\xi` of
|
||||||
an optional pairwise damping term between the density of particles. This
|
an optional pairwise damping term between the density of particles. This
|
||||||
factor can help stabilize simulations by smoothing out small length
|
factor can help stabilize simulations by smoothing out small length
|
||||||
scale variations in density fields.
|
scale variations in density fields. However, in systems that develop
|
||||||
|
a density gradient in equilibrium (e.g. in a hydrostatic column underlying
|
||||||
|
gravity), this option may be inappropriate.
|
||||||
|
|
||||||
If particles have different viscosities or conductivities, the
|
If particles have different viscosities or conductivities, the
|
||||||
*harmonic/means* keyword changes how they are averaged before calculating
|
*harmonic/means* keyword changes how they are averaged before calculating
|
||||||
pairwise forces or heat exchanges. By default, an arithmetic averaged is
|
pairwise forces or heat exchanges. By default, an arithmetic averaged is
|
||||||
used, however, a harmonic mean may improve stability in multiphase systems
|
used, however, a harmonic mean may improve stability in systems with multiple
|
||||||
with large disparities in viscosities. This keyword has no effect on
|
fluid phases with large disparities in viscosities.
|
||||||
results if viscosities and conductivities are constant.
|
|
||||||
|
|
||||||
No coefficients are defined for each pair of atoms types via the
|
No coefficients are defined for each pair of atoms types via the
|
||||||
:doc:`pair_coeff <pair_coeff>` command as in the examples
|
:doc:`pair_coeff <pair_coeff>` command as in the examples
|
||||||
@ -70,16 +71,20 @@ Mixing, shift, table, tail correction, restart, rRESPA info
|
|||||||
This style does not support the :doc:`pair_modify <pair_modify>`
|
This style does not support the :doc:`pair_modify <pair_modify>`
|
||||||
shift, table, and tail options.
|
shift, table, and tail options.
|
||||||
|
|
||||||
This style does not write information to :doc:`binary restart files <restart>`. Thus, you need to re-specify the pair_style and
|
This style does not write information to :doc:`binary restart files <restart>`.
|
||||||
pair_coeff commands in an input script that reads a restart file.
|
Thus, you need to re-specify the pair_style and pair_coeff commands in an input
|
||||||
|
script that reads a restart file.
|
||||||
|
|
||||||
This style can only be used via the *pair* keyword of the :doc:`run_style respa <run_style>` command. It does not support the *inner*, *middle*, *outer* keywords.
|
This style can only be used via the *pair* keyword of the
|
||||||
|
:doc:`run_style respa <run_style>` command. It does not support the *inner*,
|
||||||
|
*middle*, *outer* keywords.
|
||||||
|
|
||||||
Restrictions
|
Restrictions
|
||||||
""""""""""""
|
""""""""""""
|
||||||
|
|
||||||
This fix is part of the RHEO package. It is only enabled if
|
This fix is part of the RHEO package. It is only enabled if
|
||||||
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
|
LAMMPS was built with that package. See the
|
||||||
|
:doc:`Build package <Build_package>` page for more info.
|
||||||
|
|
||||||
Related commands
|
Related commands
|
||||||
""""""""""""""""
|
""""""""""""""""
|
||||||
@ -93,4 +98,5 @@ Related commands
|
|||||||
Default
|
Default
|
||||||
"""""""
|
"""""""
|
||||||
|
|
||||||
Density damping and artificial viscous forces are not calculated. Arithmetic means are used for mixing particle properties.
|
Density damping and artificial viscous forces are not calculated.
|
||||||
|
Arithmetic means are used for mixing particle properties.
|
||||||
|
|||||||
@ -1,7 +1,7 @@
|
|||||||
.. index:: pair_style rheo/solid
|
.. index:: pair_style rheo/solid
|
||||||
|
|
||||||
pair_style rheo/solid command
|
pair_style rheo/solid command
|
||||||
=========================
|
=============================
|
||||||
|
|
||||||
Syntax
|
Syntax
|
||||||
""""""
|
""""""
|
||||||
@ -44,7 +44,7 @@ normal velocity of particles
|
|||||||
F_D = - \gamma w (\hat{r} \bullet \vec{v})
|
F_D = - \gamma w (\hat{r} \bullet \vec{v})
|
||||||
|
|
||||||
where :math:`\gamma` is the damping strength, :math:`\hat{r}` is the
|
where :math:`\gamma` is the damping strength, :math:`\hat{r}` is the
|
||||||
radial normal vector, :math:`\vec{v}` is the velocity difference
|
displacement normal vector, :math:`\vec{v}` is the velocity difference
|
||||||
between the two particles, and :math:`w` is a smoothing factor.
|
between the two particles, and :math:`w` is a smoothing factor.
|
||||||
This smoothing factor is constructed such that damping forces go to zero
|
This smoothing factor is constructed such that damping forces go to zero
|
||||||
as particles come out of contact to avoid discontinuities. It is
|
as particles come out of contact to avoid discontinuities. It is
|
||||||
@ -95,7 +95,7 @@ This pair style can only be used via the *pair* keyword of the
|
|||||||
Restrictions
|
Restrictions
|
||||||
""""""""""""
|
""""""""""""
|
||||||
|
|
||||||
This pair style is part of the BPM package. It is only enabled if
|
This pair style is part of the RHEO package. It is only enabled if
|
||||||
LAMMPS was built with that package. See the :doc:`Build package
|
LAMMPS was built with that package. See the :doc:`Build package
|
||||||
<Build_package>` page for more info.
|
<Build_package>` page for more info.
|
||||||
|
|
||||||
|
|||||||
@ -337,6 +337,8 @@ accelerated styles exist.
|
|||||||
* :doc:`reaxff <pair_reaxff>` - ReaxFF potential
|
* :doc:`reaxff <pair_reaxff>` - ReaxFF potential
|
||||||
* :doc:`rebo <pair_airebo>` - Second generation REBO potential of Brenner
|
* :doc:`rebo <pair_airebo>` - Second generation REBO potential of Brenner
|
||||||
* :doc:`rebomos <pair_rebomos>` - REBOMoS potential for MoS2
|
* :doc:`rebomos <pair_rebomos>` - REBOMoS potential for MoS2
|
||||||
|
* :doc:`rheo <pair_rheo>` - fluid interactions in RHEO package
|
||||||
|
* :doc:`rheo/solid <pair_rheo_solid>` - solid interactions in RHEO package
|
||||||
* :doc:`resquared <pair_resquared>` - Everaers RE-Squared ellipsoidal potential
|
* :doc:`resquared <pair_resquared>` - Everaers RE-Squared ellipsoidal potential
|
||||||
* :doc:`saip/metal <pair_saip_metal>` - Interlayer potential for hetero-junctions formed with hexagonal 2D materials and metal surfaces
|
* :doc:`saip/metal <pair_saip_metal>` - Interlayer potential for hetero-junctions formed with hexagonal 2D materials and metal surfaces
|
||||||
* :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` - Smoothed dissipative particle dynamics for water at isothermal conditions
|
* :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` - Smoothed dissipative particle dynamics for water at isothermal conditions
|
||||||
|
|||||||
@ -71,5 +71,5 @@ compute nbond all nbond/atom
|
|||||||
thermo 200
|
thermo 200
|
||||||
thermo_style custom step time ke press atoms
|
thermo_style custom step time ke press atoms
|
||||||
|
|
||||||
dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_nbond c_rho
|
#dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_nbond c_rho
|
||||||
run 30000
|
run 30000
|
||||||
|
|||||||
382
examples/rheo/balloon/log.17Apr2024.balloon.g++.4
Normal file
382
examples/rheo/balloon/log.17Apr2024.balloon.g++.4
Normal file
@ -0,0 +1,382 @@
|
|||||||
|
LAMMPS (17 Apr 2024 - Development - patch_5May2020-18508-g3c0eaf6870-modified)
|
||||||
|
# ------ 2D water balloon ------ #
|
||||||
|
|
||||||
|
dimension 2
|
||||||
|
units lj
|
||||||
|
atom_style hybrid rheo bond
|
||||||
|
boundary m m p
|
||||||
|
comm_modify vel yes
|
||||||
|
newton off
|
||||||
|
|
||||||
|
region box block -40 40 0 80 -0.01 0.01 units box
|
||||||
|
create_box 1 box bond/types 1 extra/bond/per/atom 15 extra/special/per/atom 50
|
||||||
|
Created orthogonal box = (-40 0 -0.01) to (40 80 0.01)
|
||||||
|
2 by 2 by 1 MPI processor grid
|
||||||
|
|
||||||
|
region fluid sphere -10 40 0 30 units box side in
|
||||||
|
lattice hex 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.0745699 1.8612097 1.0745699
|
||||||
|
create_atoms 1 region fluid
|
||||||
|
Created 2830 atoms
|
||||||
|
using lattice units in orthogonal box = (-40 0 -0.01) to (40 80 0.01)
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
|
||||||
|
region shell sphere -10 40 0 27 units box side out
|
||||||
|
group shell region shell
|
||||||
|
544 atoms in group shell
|
||||||
|
|
||||||
|
set group shell rheo/status 1
|
||||||
|
Setting atom values ...
|
||||||
|
544 settings made for rheo/status
|
||||||
|
set group all vx 0.005 vy -0.04
|
||||||
|
Setting atom values ...
|
||||||
|
2830 settings made for vx
|
||||||
|
2830 settings made for vy
|
||||||
|
|
||||||
|
# ------ Model parameters ------#
|
||||||
|
|
||||||
|
variable cut equal 3.0
|
||||||
|
variable n equal 1.0
|
||||||
|
variable rho0 equal 1.0
|
||||||
|
variable cs equal 1.0
|
||||||
|
variable mp equal ${rho0}/${n}
|
||||||
|
variable mp equal 1/${n}
|
||||||
|
variable mp equal 1/1
|
||||||
|
variable zeta equal 0.05
|
||||||
|
variable kappa equal 0.01*${rho0}/${mp}
|
||||||
|
variable kappa equal 0.01*1/${mp}
|
||||||
|
variable kappa equal 0.01*1/1
|
||||||
|
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||||
|
variable dt_max equal 0.1*3/${cs}/3
|
||||||
|
variable dt_max equal 0.1*3/1/3
|
||||||
|
variable eta equal 0.05
|
||||||
|
variable Cv equal 1.0
|
||||||
|
variable L equal 1.0
|
||||||
|
variable Tf equal 1.0
|
||||||
|
|
||||||
|
mass * ${mp}
|
||||||
|
mass * 1
|
||||||
|
timestep 0.1
|
||||||
|
|
||||||
|
pair_style hybrid/overlay rheo ${cut} artificial/visc ${zeta} rheo/solid
|
||||||
|
pair_style hybrid/overlay rheo 3 artificial/visc ${zeta} rheo/solid
|
||||||
|
pair_style hybrid/overlay rheo 3 artificial/visc 0.05 rheo/solid
|
||||||
|
pair_coeff * * rheo
|
||||||
|
pair_coeff * * rheo/solid 1.0 1.0 1.0
|
||||||
|
|
||||||
|
special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 1 1
|
||||||
|
special bond factors coul: 0 1 1
|
||||||
|
0 = max # of 1-2 neighbors
|
||||||
|
101 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.000 seconds
|
||||||
|
create_bonds many shell shell 1 0 1.5
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 3.3
|
||||||
|
ghost atom cutoff = 3.3
|
||||||
|
binsize = 1.65, bins = 49 49 1
|
||||||
|
3 neighbor lists, perpetual/occasional/extra = 2 1 0
|
||||||
|
(1) command create_bonds, occasional
|
||||||
|
attributes: full, newton off
|
||||||
|
pair build: full/bin
|
||||||
|
stencil: full/bin/2d
|
||||||
|
bin: standard
|
||||||
|
(2) pair rheo, perpetual
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: half/bin/newtoff
|
||||||
|
stencil: full/bin/2d
|
||||||
|
bin: standard
|
||||||
|
(3) pair rheo/solid, perpetual, trim from (2)
|
||||||
|
attributes: half, newton off, cut 1.3
|
||||||
|
pair build: trim
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
Added 1263 bonds, new total = 1263
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 1 1
|
||||||
|
special bond factors coul: 0 1 1
|
||||||
|
6 = max # of 1-2 neighbors
|
||||||
|
101 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.000 seconds
|
||||||
|
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
|
||||||
|
|
||||||
|
bond_style bpm/spring
|
||||||
|
bond_coeff 1 1.0 1.0 1.0
|
||||||
|
|
||||||
|
# A lower critical strain allows the balloon to pop
|
||||||
|
#bond_coeff 1 1.0 0.05 1.0
|
||||||
|
|
||||||
|
# ------ Drop balloon ------#
|
||||||
|
|
||||||
|
fix 1 all rheo ${cut} quintic 0 shift surface/detection coordination 22 8
|
||||||
|
fix 1 all rheo 3 quintic 0 shift surface/detection coordination 22 8
|
||||||
|
fix 2 all rheo/viscosity * constant ${eta}
|
||||||
|
fix 2 all rheo/viscosity * constant 0.05
|
||||||
|
fix 3 all rheo/pressure * linear
|
||||||
|
fix 4 all wall/harmonic ylo EDGE 2.0 1.0 1.0
|
||||||
|
fix 5 all enforce2d
|
||||||
|
|
||||||
|
compute rho all rheo/property/atom rho
|
||||||
|
compute phase all rheo/property/atom phase
|
||||||
|
compute nbond all nbond/atom
|
||||||
|
|
||||||
|
# ------ Output & Run ------ #
|
||||||
|
|
||||||
|
thermo 200
|
||||||
|
thermo_style custom step time ke press atoms
|
||||||
|
|
||||||
|
dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_nbond c_rho
|
||||||
|
run 30000
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
|
||||||
|
- BPM bond style: doi:10.1039/D3SM01373A
|
||||||
|
|
||||||
|
@Article{Clemmer2024,
|
||||||
|
author = {Clemmer, Joel T. and Monti, Joseph M. and Lechman, Jeremy B.},
|
||||||
|
title = {A soft departure from jamming: the compaction of deformable
|
||||||
|
granular matter under high pressures},
|
||||||
|
journal = {Soft Matter},
|
||||||
|
year = 2024,
|
||||||
|
volume = 20,
|
||||||
|
number = 8,
|
||||||
|
pages = {1702--1718}
|
||||||
|
}
|
||||||
|
|
||||||
|
- @article{PalermoInPrep,
|
||||||
|
journal = {in prep},
|
||||||
|
title = {RHEO: A Hybrid Mesh-Free Model Framework for Dynamic Multi-Phase Flows},
|
||||||
|
year = {2024},
|
||||||
|
author = {Eric T. Palermo and Ki T. Wolf and Joel T. Clemmer and Thomas C. O'Connor},
|
||||||
|
}
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 3.3
|
||||||
|
ghost atom cutoff = 3.3
|
||||||
|
binsize = 1.65, bins = 49 49 1
|
||||||
|
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||||
|
(1) pair rheo, perpetual, half/full from (3)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: halffull/newtoff
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(2) pair rheo/solid, perpetual, trim from (1)
|
||||||
|
attributes: half, newton off, cut 1.3
|
||||||
|
pair build: trim
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(3) compute RHEO/KERNEL, perpetual
|
||||||
|
attributes: full, newton off
|
||||||
|
pair build: full/bin
|
||||||
|
stencil: full/bin/2d
|
||||||
|
bin: standard
|
||||||
|
(4) compute RHEO/GRAD, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(5) compute RHEO/VSHIFT, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(6) compute RHEO/SURFACE, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 17.63 | 17.64 | 17.65 Mbytes
|
||||||
|
Step Time KinEng Press Atoms
|
||||||
|
0 0 0.0008125 0.00035927734 2830
|
||||||
|
200 20 0.0008125 0.00035927734 2830
|
||||||
|
400 40 0.0008125 0.00035927734 2830
|
||||||
|
600 60 0.0008125 0.00035927734 2830
|
||||||
|
800 80 0.0008125 0.00035927734 2830
|
||||||
|
1000 100 0.0008125 0.00035927734 2830
|
||||||
|
1200 120 0.0008125 0.00035927734 2830
|
||||||
|
1400 140 0.0008125 0.00035927734 2830
|
||||||
|
1600 160 0.0008125 0.00035927734 2830
|
||||||
|
1800 180 0.0008125 0.00035927734 2830
|
||||||
|
2000 200 0.0008125 0.00035927734 2830
|
||||||
|
2200 220 0.0008125 0.00035927734 2830
|
||||||
|
2400 240 0.00079033569 0.00043037861 2830
|
||||||
|
2600 260 0.0007549229 0.00045188383 2830
|
||||||
|
2800 280 0.00072808836 0.00031695003 2830
|
||||||
|
3000 300 0.0007017958 1.6121754e-05 2830
|
||||||
|
3200 320 0.00067479047 -0.00015725514 2830
|
||||||
|
3400 340 0.00064762254 -0.00023361314 2830
|
||||||
|
3600 360 0.00061960255 -0.00033837679 2830
|
||||||
|
3800 380 0.0005857206 -0.00051770716 2830
|
||||||
|
4000 400 0.00055061733 -0.00070309251 2830
|
||||||
|
4200 420 0.00051884719 -0.0008247795 2830
|
||||||
|
4400 440 0.00049022236 -0.00099918413 2830
|
||||||
|
4600 460 0.00046060011 -0.0010923159 2830
|
||||||
|
4800 480 0.00042900173 -0.0011524571 2830
|
||||||
|
5000 500 0.00039751503 -0.0012586358 2830
|
||||||
|
5200 520 0.00036620054 -0.0013973543 2830
|
||||||
|
5400 540 0.00033130023 -0.0015185231 2830
|
||||||
|
5600 560 0.00030565892 -0.0016159836 2830
|
||||||
|
5800 580 0.00028209836 -0.0016925198 2830
|
||||||
|
6000 600 0.00024695044 -0.0017796892 2830
|
||||||
|
6200 620 0.00021190635 -0.0018706272 2830
|
||||||
|
6400 640 0.0001947093 -0.0019146643 2830
|
||||||
|
6600 660 0.00018903936 -0.0019146199 2830
|
||||||
|
6800 680 0.00017753371 -0.0019390155 2830
|
||||||
|
7000 700 0.00015170593 -0.0020247472 2830
|
||||||
|
7200 720 0.00011509692 -0.0021222209 2830
|
||||||
|
7400 740 7.9861785e-05 -0.0022033181 2830
|
||||||
|
7600 760 6.1350463e-05 -0.0022511971 2830
|
||||||
|
7800 780 6.5269523e-05 -0.0022222806 2830
|
||||||
|
8000 800 8.5709569e-05 -0.0021089664 2830
|
||||||
|
8200 820 0.00011746348 -0.0019351493 2830
|
||||||
|
8400 840 0.00015698134 -0.0017079928 2830
|
||||||
|
8600 860 0.00019758065 -0.0014618965 2830
|
||||||
|
8800 880 0.00023338199 -0.0012365832 2830
|
||||||
|
9000 900 0.00026282353 -0.0010348527 2830
|
||||||
|
9200 920 0.00028604776 -0.00085287884 2830
|
||||||
|
9400 940 0.00030388767 -0.000681122 2830
|
||||||
|
9600 960 0.000317589 -0.00052203521 2830
|
||||||
|
9800 980 0.00032716728 -0.00037501187 2830
|
||||||
|
10000 1000 0.00033270692 -0.00025576132 2830
|
||||||
|
10200 1020 0.00033485986 -0.00016554207 2830
|
||||||
|
10400 1040 0.00033476763 -9.8525417e-05 2830
|
||||||
|
10600 1060 0.00033351922 -5.1166347e-05 2830
|
||||||
|
10800 1080 0.00033161645 -2.0773965e-05 2830
|
||||||
|
11000 1100 0.00032913022 2.2384421e-07 2830
|
||||||
|
11200 1120 0.00032618376 1.2304773e-05 2830
|
||||||
|
11400 1140 0.00032310409 1.3725982e-05 2830
|
||||||
|
11600 1160 0.0003202128 9.0431945e-06 2830
|
||||||
|
11800 1180 0.00031760386 -5.3537879e-07 2830
|
||||||
|
12000 1200 0.00031518884 -1.331708e-05 2830
|
||||||
|
12200 1220 0.00031283958 -3.0838612e-05 2830
|
||||||
|
12400 1240 0.0003104901 -5.0038548e-05 2830
|
||||||
|
12600 1260 0.00030811597 -6.9699925e-05 2830
|
||||||
|
12800 1280 0.00030555782 -8.9972287e-05 2830
|
||||||
|
13000 1300 0.00030256671 -0.00011712941 2830
|
||||||
|
13200 1320 0.00029907961 -0.00015495826 2830
|
||||||
|
13400 1340 0.00029504656 -0.00020292633 2830
|
||||||
|
13600 1360 0.0002905184 -0.00024892421 2830
|
||||||
|
13800 1380 0.00028564542 -0.000295085 2830
|
||||||
|
14000 1400 0.00028073246 -0.00034571956 2830
|
||||||
|
14200 1420 0.00027611457 -0.00039341977 2830
|
||||||
|
14400 1440 0.00027217382 -0.0004281012 2830
|
||||||
|
14600 1460 0.00026919129 -0.00045342545 2830
|
||||||
|
14800 1480 0.00026727674 -0.00047323419 2830
|
||||||
|
15000 1500 0.0002663482 -0.00048423944 2830
|
||||||
|
15200 1520 0.00026616663 -0.0004816085 2830
|
||||||
|
15400 1540 0.00026634862 -0.00047573486 2830
|
||||||
|
15600 1560 0.0002664314 -0.00046803192 2830
|
||||||
|
15800 1580 0.00026603348 -0.00045753668 2830
|
||||||
|
16000 1600 0.00026511015 -0.00044676105 2830
|
||||||
|
16200 1620 0.00026373403 -0.00044075794 2830
|
||||||
|
16400 1640 0.00026217342 -0.00043684036 2830
|
||||||
|
16600 1660 0.0002607038 -0.00042774771 2830
|
||||||
|
16800 1680 0.00025951097 -0.00041603026 2830
|
||||||
|
17000 1700 0.00025869088 -0.00040302996 2830
|
||||||
|
17200 1720 0.00025825588 -0.00038415247 2830
|
||||||
|
17400 1740 0.00025818373 -0.00035742127 2830
|
||||||
|
17600 1760 0.00025843381 -0.00032854722 2830
|
||||||
|
17800 1780 0.00025897836 -0.00029821183 2830
|
||||||
|
18000 1800 0.00025981472 -0.00026108907 2830
|
||||||
|
18200 1820 0.00026095775 -0.00021731058 2830
|
||||||
|
18400 1840 0.00026239688 -0.00017030825 2830
|
||||||
|
18600 1860 0.00026404432 -0.00011868778 2830
|
||||||
|
18800 1880 0.00026574247 -5.9556286e-05 2830
|
||||||
|
19000 1900 0.00026729563 2.3014881e-06 2830
|
||||||
|
19200 1920 0.00026852418 6.2100169e-05 2830
|
||||||
|
19400 1940 0.00026929086 0.00012090325 2830
|
||||||
|
19600 1960 0.0002695407 0.00017904223 2830
|
||||||
|
19800 1980 0.00026929677 0.00023112254 2830
|
||||||
|
20000 2000 0.00026863577 0.0002756697 2830
|
||||||
|
20200 2020 0.00026765699 0.0003158399 2830
|
||||||
|
20400 2040 0.00026646841 0.00035200747 2830
|
||||||
|
20600 2060 0.00026516938 0.00038018442 2830
|
||||||
|
20800 2080 0.00026383495 0.00040179111 2830
|
||||||
|
21000 2100 0.00026252489 0.00042030921 2830
|
||||||
|
21200 2120 0.00026128616 0.00043466976 2830
|
||||||
|
21400 2140 0.00026014896 0.00044221445 2830
|
||||||
|
21600 2160 0.00025912325 0.00044531883 2830
|
||||||
|
21800 2180 0.00025821515 0.00044661709 2830
|
||||||
|
22000 2200 0.00025742576 0.00044409089 2830
|
||||||
|
22200 2220 0.00025674938 0.00043634999 2830
|
||||||
|
22400 2240 0.00025617111 0.00042630344 2830
|
||||||
|
22600 2260 0.0002556791 0.00041561603 2830
|
||||||
|
22800 2280 0.00025525963 0.00040166735 2830
|
||||||
|
23000 2300 0.00025489538 0.00038430419 2830
|
||||||
|
23200 2320 0.00025456861 0.0003669402 2830
|
||||||
|
23400 2340 0.00025426747 0.00034972373 2830
|
||||||
|
23600 2360 0.00025398353 0.0003302242 2830
|
||||||
|
23800 2380 0.00025370842 0.00030993088 2830
|
||||||
|
24000 2400 0.00025344084 0.00029143258 2830
|
||||||
|
24200 2420 0.00025318683 0.00027421708 2830
|
||||||
|
24400 2440 0.0002529591 0.00025603123 2830
|
||||||
|
24600 2460 0.0002527713 0.00023950245 2830
|
||||||
|
24800 2480 0.00025264228 0.00022644812 2830
|
||||||
|
25000 2500 0.00025259021 0.00021540748 2830
|
||||||
|
25200 2520 0.00025262892 0.00020544201 2830
|
||||||
|
25400 2540 0.00025276229 0.00019845807 2830
|
||||||
|
25600 2560 0.0002529876 0.00019449958 2830
|
||||||
|
25800 2580 0.00025329374 0.00019082606 2830
|
||||||
|
26000 2600 0.00025366066 0.00018700064 2830
|
||||||
|
26200 2620 0.00025406164 0.00018426061 2830
|
||||||
|
26400 2640 0.00025446737 0.00018098339 2830
|
||||||
|
26600 2660 0.00025484714 0.00017471869 2830
|
||||||
|
26800 2680 0.00025516604 0.00016565557 2830
|
||||||
|
27000 2700 0.00025538911 0.00015493626 2830
|
||||||
|
27200 2720 0.00025548177 0.00014075592 2830
|
||||||
|
27400 2740 0.00025541168 0.00012205573 2830
|
||||||
|
27600 2760 0.00025514889 0.00010039772 2830
|
||||||
|
27800 2780 0.00025467547 7.7069215e-05 2830
|
||||||
|
28000 2800 0.0002539915 5.1158042e-05 2830
|
||||||
|
28200 2820 0.00025312083 2.3468384e-05 2830
|
||||||
|
28400 2840 0.00025211323 -3.2184465e-06 2830
|
||||||
|
28600 2860 0.00025104366 -2.7726301e-05 2830
|
||||||
|
28800 2880 0.00025000263 -5.0202987e-05 2830
|
||||||
|
29000 2900 0.00024907814 -6.9244776e-05 2830
|
||||||
|
29200 2920 0.00024833815 -8.2874516e-05 2830
|
||||||
|
29400 2940 0.0002478155 -9.1854992e-05 2830
|
||||||
|
29600 2960 0.00024750313 -9.766055e-05 2830
|
||||||
|
29800 2980 0.00024735538 -9.9681291e-05 2830
|
||||||
|
30000 3000 0.00024730191 -9.818759e-05 2830
|
||||||
|
Loop time of 177.982 on 4 procs for 30000 steps with 2830 atoms
|
||||||
|
|
||||||
|
Performance: 1456330.235 tau/day, 168.557 timesteps/s, 477.016 katom-step/s
|
||||||
|
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 22.913 | 27.061 | 34.594 | 87.2 | 15.20
|
||||||
|
Bond | 0.22386 | 0.26159 | 0.30792 | 6.0 | 0.15
|
||||||
|
Neigh | 0.84412 | 0.84509 | 0.8462 | 0.1 | 0.47
|
||||||
|
Comm | 0.50015 | 0.55579 | 0.60346 | 5.2 | 0.31
|
||||||
|
Output | 0.65854 | 0.69412 | 0.72473 | 2.8 | 0.39
|
||||||
|
Modify | 133.13 | 136 | 137.38 | 14.5 | 76.41
|
||||||
|
Other | | 12.57 | | | 7.06
|
||||||
|
|
||||||
|
Nlocal: 707.5 ave 1576 max 53 min
|
||||||
|
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||||
|
Nghost: 164.75 ave 239 max 94 min
|
||||||
|
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||||
|
Neighs: 12307.8 ave 27380 max 983 min
|
||||||
|
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||||
|
FullNghs: 23517 ave 53040 max 1502 min
|
||||||
|
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 94068
|
||||||
|
Ave neighs/atom = 33.239576
|
||||||
|
Ave special neighs/atom = 0.89257951
|
||||||
|
Neighbor list builds = 783
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:02:58
|
||||||
1694
examples/rheo/dam-break/log.17Apr2024.dam.g++.4
Normal file
1694
examples/rheo/dam-break/log.17Apr2024.dam.g++.4
Normal file
File diff suppressed because it is too large
Load Diff
@ -77,5 +77,6 @@ compute nbond all nbond/atom
|
|||||||
thermo 200
|
thermo 200
|
||||||
thermo_style custom step time ke press atoms
|
thermo_style custom step time ke press atoms
|
||||||
|
|
||||||
dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_temp c_eng c_nbond c_rho
|
#dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_temp c_eng c_nbond c_rho
|
||||||
|
|
||||||
run 30000
|
run 30000
|
||||||
|
|||||||
379
examples/rheo/ice-cubes/log.17Apr2024.ice.g++.4
Normal file
379
examples/rheo/ice-cubes/log.17Apr2024.ice.g++.4
Normal file
@ -0,0 +1,379 @@
|
|||||||
|
LAMMPS (17 Apr 2024 - Development - patch_5May2020-18508-g3c0eaf6870-modified)
|
||||||
|
# ------ 2D Ice Cube Pour ------ #
|
||||||
|
|
||||||
|
dimension 2
|
||||||
|
units lj
|
||||||
|
atom_style hybrid rheo/thermal bond
|
||||||
|
boundary m m p
|
||||||
|
comm_modify vel yes
|
||||||
|
newton off
|
||||||
|
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
|
||||||
|
|
||||||
|
region box block -25 25 0 100 -0.01 0.01 units box
|
||||||
|
create_box 1 box bond/types 1 extra/bond/per/atom 15 extra/special/per/atom 50
|
||||||
|
Created orthogonal box = (-25 0 -0.01) to (25 100 0.01)
|
||||||
|
2 by 2 by 1 MPI processor grid
|
||||||
|
|
||||||
|
region fluid block $(xlo+1) $(xhi-1) $(ylo+1) $(ylo+30) EDGE EDGE units box
|
||||||
|
region fluid block -24 $(xhi-1) $(ylo+1) $(ylo+30) EDGE EDGE units box
|
||||||
|
region fluid block -24 24 $(ylo+1) $(ylo+30) EDGE EDGE units box
|
||||||
|
region fluid block -24 24 1 $(ylo+30) EDGE EDGE units box
|
||||||
|
region fluid block -24 24 1 30 EDGE EDGE units box
|
||||||
|
lattice sq 1.0
|
||||||
|
Lattice spacing in x,y,z = 1 1 1
|
||||||
|
create_atoms 1 region fluid
|
||||||
|
Created 1470 atoms
|
||||||
|
using lattice units in orthogonal box = (-25 0 -0.01) to (25 100 0.01)
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
|
||||||
|
set group all sph/e 8.0
|
||||||
|
Setting atom values ...
|
||||||
|
1470 settings made for sph/e
|
||||||
|
|
||||||
|
# ------ Model parameters ------#
|
||||||
|
|
||||||
|
variable cut equal 3.0
|
||||||
|
variable n equal 1.0
|
||||||
|
variable rho0 equal 1.0
|
||||||
|
variable cs equal 1.0
|
||||||
|
variable mp equal ${rho0}/${n}
|
||||||
|
variable mp equal 1/${n}
|
||||||
|
variable mp equal 1/1
|
||||||
|
variable zeta equal 0.05
|
||||||
|
variable kappa equal 0.01*${rho0}/${mp}
|
||||||
|
variable kappa equal 0.01*1/${mp}
|
||||||
|
variable kappa equal 0.01*1/1
|
||||||
|
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||||
|
variable dt_max equal 0.1*3/${cs}/3
|
||||||
|
variable dt_max equal 0.1*3/1/3
|
||||||
|
variable eta equal 0.05
|
||||||
|
variable Cv equal 1.0
|
||||||
|
variable L equal 1.0
|
||||||
|
variable Tf equal 1.0
|
||||||
|
|
||||||
|
mass * ${mp}
|
||||||
|
mass * 1
|
||||||
|
timestep 0.1
|
||||||
|
|
||||||
|
pair_style hybrid/overlay rheo ${cut} artificial/visc ${zeta} rheo/solid
|
||||||
|
pair_style hybrid/overlay rheo 3 artificial/visc ${zeta} rheo/solid
|
||||||
|
pair_style hybrid/overlay rheo 3 artificial/visc 0.05 rheo/solid
|
||||||
|
pair_coeff * * rheo
|
||||||
|
pair_coeff * * rheo/solid 1.0 1.0 1.0
|
||||||
|
|
||||||
|
bond_style bpm/spring
|
||||||
|
bond_coeff 1 1.0 1.0 1.0
|
||||||
|
|
||||||
|
# ------ Pour particles ------#
|
||||||
|
|
||||||
|
molecule my_mol "square.mol"
|
||||||
|
Read molecule template my_mol:
|
||||||
|
#Made with create_mol.py
|
||||||
|
1 molecules
|
||||||
|
0 fragments
|
||||||
|
100 atoms with max type 1
|
||||||
|
342 bonds with max type 1
|
||||||
|
0 angles with max type 0
|
||||||
|
0 dihedrals with max type 0
|
||||||
|
0 impropers with max type 0
|
||||||
|
|
||||||
|
# Wall region extends far enough in z to avoid contact
|
||||||
|
region wall block EDGE EDGE EDGE EDGE -5 5 side in open 4 units box
|
||||||
|
region drop block -16 16 70 90 EDGE EDGE side in units box
|
||||||
|
|
||||||
|
fix 1 all rheo ${cut} quintic 0 thermal shift surface/detection coordination 22 8
|
||||||
|
fix 1 all rheo 3 quintic 0 thermal shift surface/detection coordination 22 8
|
||||||
|
fix 2 all rheo/viscosity * constant ${eta}
|
||||||
|
fix 2 all rheo/viscosity * constant 0.05
|
||||||
|
fix 3 all rheo/pressure * linear
|
||||||
|
fix 4 all rheo/thermal conductivity * constant ${kappa} specific/heat * constant ${Cv} Tfreeze * constant ${Tf} latent/heat * constant ${L} react 1.5 1
|
||||||
|
fix 4 all rheo/thermal conductivity * constant 0.01 specific/heat * constant ${Cv} Tfreeze * constant ${Tf} latent/heat * constant ${L} react 1.5 1
|
||||||
|
fix 4 all rheo/thermal conductivity * constant 0.01 specific/heat * constant 1 Tfreeze * constant ${Tf} latent/heat * constant ${L} react 1.5 1
|
||||||
|
fix 4 all rheo/thermal conductivity * constant 0.01 specific/heat * constant 1 Tfreeze * constant 1 latent/heat * constant ${L} react 1.5 1
|
||||||
|
fix 4 all rheo/thermal conductivity * constant 0.01 specific/heat * constant 1 Tfreeze * constant 1 latent/heat * constant 1 react 1.5 1
|
||||||
|
fix 5 all wall/region wall harmonic 1.0 1.0 1.0
|
||||||
|
fix 6 all gravity 5e-4 vector 0 -1 0
|
||||||
|
fix 7 all deposit 8 0 1000 37241459 mol my_mol region drop near 2.0 vy -0.02 -0.02
|
||||||
|
WARNING: Molecule attributes do not match system attributes (../molecule.cpp:1881)
|
||||||
|
fix 8 all enforce2d
|
||||||
|
|
||||||
|
compute rho all rheo/property/atom rho
|
||||||
|
compute phase all rheo/property/atom phase
|
||||||
|
compute temp all rheo/property/atom temperature
|
||||||
|
compute eng all rheo/property/atom energy
|
||||||
|
compute nbond all nbond/atom
|
||||||
|
|
||||||
|
# ------ Output & Run ------ #
|
||||||
|
|
||||||
|
thermo 200
|
||||||
|
thermo_style custom step time ke press atoms
|
||||||
|
|
||||||
|
dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_temp c_eng c_nbond c_rho
|
||||||
|
|
||||||
|
run 30000
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
|
||||||
|
- BPM bond style: doi:10.1039/D3SM01373A
|
||||||
|
|
||||||
|
@Article{Clemmer2024,
|
||||||
|
author = {Clemmer, Joel T. and Monti, Joseph M. and Lechman, Jeremy B.},
|
||||||
|
title = {A soft departure from jamming: the compaction of deformable
|
||||||
|
granular matter under high pressures},
|
||||||
|
journal = {Soft Matter},
|
||||||
|
year = 2024,
|
||||||
|
volume = 20,
|
||||||
|
number = 8,
|
||||||
|
pages = {1702--1718}
|
||||||
|
}
|
||||||
|
|
||||||
|
- @article{PalermoInPrep,
|
||||||
|
journal = {in prep},
|
||||||
|
title = {RHEO: A Hybrid Mesh-Free Model Framework for Dynamic Multi-Phase Flows},
|
||||||
|
year = {2024},
|
||||||
|
author = {Eric T. Palermo and Ki T. Wolf and Joel T. Clemmer and Thomas C. O'Connor},
|
||||||
|
}
|
||||||
|
|
||||||
|
- @article{ApplMathModel.130.310,
|
||||||
|
title = {A hybrid smoothed-particle hydrodynamics model of oxide skins on molten aluminum},
|
||||||
|
journal = {Applied Mathematical Modelling},
|
||||||
|
volume = {130},
|
||||||
|
pages = {310-326},
|
||||||
|
year = {2024},
|
||||||
|
issn = {0307-904X},
|
||||||
|
doi = {https://doi.org/10.1016/j.apm.2024.02.027},
|
||||||
|
author = {Joel T. Clemmer and Flint Pierce and Thomas C. O'Connor and Thomas D. Nevins and Elizabeth M.C. Jones and Jeremy B. Lechman and John Tencer},
|
||||||
|
}
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 3.3
|
||||||
|
ghost atom cutoff = 3.3
|
||||||
|
binsize = 1.65, bins = 31 61 1
|
||||||
|
7 neighbor lists, perpetual/occasional/extra = 6 1 0
|
||||||
|
(1) pair rheo, perpetual, half/full from (3)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: halffull/newtoff
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(2) pair rheo/solid, perpetual, trim from (4)
|
||||||
|
attributes: half, newton off, cut 1.3
|
||||||
|
pair build: trim
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(3) compute RHEO/KERNEL, perpetual
|
||||||
|
attributes: full, newton off
|
||||||
|
pair build: full/bin
|
||||||
|
stencil: full/bin/2d
|
||||||
|
bin: standard
|
||||||
|
(4) compute RHEO/GRAD, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(5) compute RHEO/VSHIFT, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(6) compute RHEO/SURFACE, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(7) fix rheo/thermal, occasional, trim from (4)
|
||||||
|
attributes: half, newton off, cut 3
|
||||||
|
pair build: trim
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 15.53 | 15.61 | 15.69 Mbytes
|
||||||
|
Step Time KinEng Press Atoms
|
||||||
|
0 0 0 0 1470
|
||||||
|
200 20 5.6002982e-05 3.4434234e-05 1570
|
||||||
|
400 40 8.2173099e-05 8.6171768e-05 1570
|
||||||
|
600 60 8.019018e-05 0.00010750355 1570
|
||||||
|
800 80 0.00013866953 0.00010265608 1570
|
||||||
|
1000 100 0.00018965028 8.1985605e-05 1570
|
||||||
|
1200 120 0.00022033242 7.4736443e-05 1670
|
||||||
|
1400 140 0.00030767062 0.00011264333 1670
|
||||||
|
1600 160 0.00040770127 0.00018779992 1670
|
||||||
|
1800 180 0.00047476332 0.00023153009 1670
|
||||||
|
2000 200 0.00059116774 0.00027200445 1670
|
||||||
|
2200 220 0.0007151733 0.0002919963 1770
|
||||||
|
2400 240 0.00083392135 0.00029757889 1770
|
||||||
|
2600 260 0.00099653466 0.00036547269 1770
|
||||||
|
2800 280 0.0011964069 0.00045983458 1770
|
||||||
|
3000 300 0.0013716953 0.00055013647 1770
|
||||||
|
3200 320 0.0015174096 0.00064203572 1870
|
||||||
|
3400 340 0.0016539743 0.00086671622 1870
|
||||||
|
3600 360 0.0015887858 0.00066353749 1870
|
||||||
|
3800 380 0.0016451684 0.00070551483 1870
|
||||||
|
4000 400 0.0017330971 0.00080722283 1870
|
||||||
|
4200 420 0.001812193 0.00073573903 1970
|
||||||
|
4400 440 0.001755871 0.0010621909 1970
|
||||||
|
4600 460 0.0016190772 0.00072913706 1970
|
||||||
|
4800 480 0.0015741931 0.00073524088 1970
|
||||||
|
5000 500 0.0016488815 0.00088684275 1970
|
||||||
|
5200 520 0.0017213288 0.00077042378 2070
|
||||||
|
5400 540 0.0018509598 0.0010219434 2070
|
||||||
|
5600 560 0.0020251064 0.00083182483 2070
|
||||||
|
5800 580 0.0022473255 0.00095076144 2070
|
||||||
|
6000 600 0.0024843519 0.0011247014 2070
|
||||||
|
6200 620 0.0022282321 0.0018105932 2170
|
||||||
|
6400 640 0.0020289063 0.0014158497 2170
|
||||||
|
6600 660 0.002145241 0.0011359383 2170
|
||||||
|
6800 680 0.0024313937 0.0016475504 2170
|
||||||
|
7000 700 0.0021000599 0.0020983745 2170
|
||||||
|
7200 720 0.0019137235 0.0010439152 2270
|
||||||
|
7400 740 0.0018801367 0.00095436448 2270
|
||||||
|
7600 760 0.0017979449 0.0011184039 2270
|
||||||
|
7800 780 0.0018005205 0.0009243205 2270
|
||||||
|
8000 800 0.0017827073 0.0013671228 2270
|
||||||
|
8200 820 0.0018387108 0.0015426012 2270
|
||||||
|
8400 840 0.0016000788 0.0016751514 2270
|
||||||
|
8600 860 0.0013954964 0.0016884335 2270
|
||||||
|
8800 880 0.0013283728 0.0012399398 2270
|
||||||
|
9000 900 0.001389385 0.0012968496 2270
|
||||||
|
9200 920 0.0012295438 0.0012995821 2270
|
||||||
|
9400 940 0.0010522655 0.00082245528 2270
|
||||||
|
9600 960 0.00097085496 0.00053833131 2270
|
||||||
|
9800 980 0.0009398987 0.00063467387 2270
|
||||||
|
10000 1000 0.00092710392 0.00059494446 2270
|
||||||
|
10200 1020 0.00095545471 0.00074560644 2270
|
||||||
|
10400 1040 0.0009645841 0.00085429807 2270
|
||||||
|
10600 1060 0.00064037148 0.0017222246 2270
|
||||||
|
10800 1080 0.00046790978 0.00088204234 2270
|
||||||
|
11000 1100 0.00030106229 0.00074950209 2270
|
||||||
|
11200 1120 0.00027746016 0.00052831745 2270
|
||||||
|
11400 1140 0.0002533348 0.0006272715 2270
|
||||||
|
11600 1160 0.00021825085 0.00029691552 2270
|
||||||
|
11800 1180 0.0001451308 0.00015037478 2270
|
||||||
|
12000 1200 0.0001314823 0.00017227174 2270
|
||||||
|
12200 1220 0.00013693632 0.00017791384 2270
|
||||||
|
12400 1240 0.00014987347 0.0002286677 2270
|
||||||
|
12600 1260 0.00015092598 0.0003698436 2270
|
||||||
|
12800 1280 0.0001291653 0.00047229532 2270
|
||||||
|
13000 1300 0.00011949988 0.00049560375 2270
|
||||||
|
13200 1320 0.00011694665 0.00057542084 2270
|
||||||
|
13400 1340 9.6164519e-05 0.00062714755 2270
|
||||||
|
13600 1360 8.4517591e-05 0.00044156913 2270
|
||||||
|
13800 1380 0.00019140516 0.0003264745 2270
|
||||||
|
14000 1400 0.00013868599 0.00037753497 2270
|
||||||
|
14200 1420 9.3701636e-05 0.00031517848 2270
|
||||||
|
14400 1440 6.7389077e-05 0.0002946861 2270
|
||||||
|
14600 1460 5.3640086e-05 0.00026650711 2270
|
||||||
|
14800 1480 4.2699992e-05 0.00023789279 2270
|
||||||
|
15000 1500 5.3012016e-05 0.00019933234 2270
|
||||||
|
15200 1520 5.8834197e-05 0.00022407007 2270
|
||||||
|
15400 1540 5.0899982e-05 0.00029695531 2270
|
||||||
|
15600 1560 3.0476742e-05 0.00039119066 2270
|
||||||
|
15800 1580 1.6633264e-05 0.00033770401 2270
|
||||||
|
16000 1600 1.098906e-05 0.00036684894 2270
|
||||||
|
16200 1620 1.464848e-05 0.00036449759 2270
|
||||||
|
16400 1640 1.9598429e-05 0.00021056689 2270
|
||||||
|
16600 1660 1.2644955e-05 0.00020781781 2270
|
||||||
|
16800 1680 8.8428553e-06 0.000165 2270
|
||||||
|
17000 1700 8.8971439e-06 0.00012266475 2270
|
||||||
|
17200 1720 1.7032781e-05 0.00019873443 2270
|
||||||
|
17400 1740 1.9448563e-05 0.00025661663 2270
|
||||||
|
17600 1760 1.3714713e-05 0.000324022 2270
|
||||||
|
17800 1780 9.1326468e-06 0.00031392513 2270
|
||||||
|
18000 1800 9.2464802e-06 0.00029729527 2270
|
||||||
|
18200 1820 1.5553042e-05 0.00027488475 2270
|
||||||
|
18400 1840 1.4132933e-05 0.00019565459 2270
|
||||||
|
18600 1860 9.4734832e-06 0.00016716988 2270
|
||||||
|
18800 1880 5.5115145e-06 0.00013728033 2270
|
||||||
|
19000 1900 8.268812e-06 0.00015119605 2270
|
||||||
|
19200 1920 1.2470136e-05 0.00020222131 2270
|
||||||
|
19400 1940 9.9387775e-06 0.00024503373 2270
|
||||||
|
19600 1960 5.4241999e-06 0.00026921858 2270
|
||||||
|
19800 1980 2.7987348e-06 0.00026201267 2270
|
||||||
|
20000 2000 6.272538e-06 0.00025626323 2270
|
||||||
|
20200 2020 8.0157781e-06 0.000220139 2270
|
||||||
|
20400 2040 6.1652093e-06 0.00017089058 2270
|
||||||
|
20600 2060 2.9967592e-06 0.00014582864 2270
|
||||||
|
20800 2080 3.016678e-06 0.000148629 2270
|
||||||
|
21000 2100 7.287645e-06 0.00016486102 2270
|
||||||
|
21200 2120 8.6905277e-06 0.00020276916 2270
|
||||||
|
21400 2140 6.8453018e-06 0.00023156153 2270
|
||||||
|
21600 2160 3.3853799e-06 0.0002432462 2270
|
||||||
|
21800 2180 4.1241209e-06 0.00022829024 2270
|
||||||
|
22000 2200 7.0802396e-06 0.00020784823 2270
|
||||||
|
22200 2220 7.3361691e-06 0.00018114134 2270
|
||||||
|
22400 2240 5.0764593e-06 0.00014351106 2270
|
||||||
|
22600 2260 2.7487537e-06 0.00012919872 2270
|
||||||
|
22800 2280 4.620167e-06 0.00013746218 2270
|
||||||
|
23000 2300 6.9819357e-06 0.00015985102 2270
|
||||||
|
23200 2320 6.8923916e-06 0.00018713045 2270
|
||||||
|
23400 2340 4.1795088e-06 0.00019846682 2270
|
||||||
|
23600 2360 2.2871028e-06 0.00021068421 2270
|
||||||
|
23800 2380 3.862046e-06 0.00019553306 2270
|
||||||
|
24000 2400 5.2448555e-06 0.00017398041 2270
|
||||||
|
24200 2420 4.7565441e-06 0.00015008142 2270
|
||||||
|
24400 2440 2.2952135e-06 0.00012747106 2270
|
||||||
|
24600 2460 2.1575617e-06 0.00012516996 2270
|
||||||
|
24800 2480 4.1777868e-06 0.0001331902 2270
|
||||||
|
25000 2500 5.5679133e-06 0.00015504562 2270
|
||||||
|
25200 2520 4.5758741e-06 0.00017146032 2270
|
||||||
|
25400 2540 2.3403277e-06 0.00017611666 2270
|
||||||
|
25600 2560 2.7029302e-06 0.00016850788 2270
|
||||||
|
25800 2580 4.3601102e-06 0.00015884642 2270
|
||||||
|
26000 2600 5.2244249e-06 0.00013793898 2270
|
||||||
|
26200 2620 3.4577672e-06 0.00012395875 2270
|
||||||
|
26400 2640 2.361577e-06 0.00011600057 2270
|
||||||
|
26600 2660 2.8515644e-06 0.00011277063 2270
|
||||||
|
26800 2680 4.0851213e-06 0.0001290832 2270
|
||||||
|
27000 2700 4.2579644e-06 0.0001476495 2270
|
||||||
|
27200 2720 2.6593858e-06 0.00015977745 2270
|
||||||
|
27400 2740 1.990115e-06 0.00015612787 2270
|
||||||
|
27600 2760 2.6756835e-06 0.00014913772 2270
|
||||||
|
27800 2780 3.9032806e-06 0.00014014763 2270
|
||||||
|
28000 2800 3.2729446e-06 0.00012216846 2270
|
||||||
|
28200 2820 1.9357278e-06 0.00011078621 2270
|
||||||
|
28400 2840 1.7094832e-06 0.00010910509 2270
|
||||||
|
28600 2860 2.8731406e-06 0.00011179644 2270
|
||||||
|
28800 2880 3.7062354e-06 0.00012254091 2270
|
||||||
|
29000 2900 2.7844262e-06 0.00013060331 2270
|
||||||
|
29200 2920 1.7680655e-06 0.00013797514 2270
|
||||||
|
29400 2940 1.706873e-06 0.0001350685 2270
|
||||||
|
29600 2960 2.8764562e-06 0.00012428508 2270
|
||||||
|
29800 2980 3.1502029e-06 0.00011456718 2270
|
||||||
|
30000 3000 2.1833409e-06 0.00010317469 2270
|
||||||
|
Loop time of 165.611 on 4 procs for 30000 steps with 2270 atoms
|
||||||
|
|
||||||
|
Performance: 1565111.240 tau/day, 181.147 timesteps/s, 411.204 katom-step/s
|
||||||
|
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.63183 | 21.226 | 42.266 | 444.6 | 12.82
|
||||||
|
Bond | 0.095073 | 0.17799 | 0.27877 | 17.0 | 0.11
|
||||||
|
Neigh | 2.0745 | 2.0781 | 2.0822 | 0.2 | 1.25
|
||||||
|
Comm | 0.32024 | 0.38703 | 0.45564 | 8.1 | 0.23
|
||||||
|
Output | 0.60459 | 0.76798 | 0.93724 | 18.6 | 0.46
|
||||||
|
Modify | 119.85 | 140.76 | 161.36 | 172.2 | 85.00
|
||||||
|
Other | | 0.2124 | | | 0.13
|
||||||
|
|
||||||
|
Nlocal: 567.5 ave 1139 max 0 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
Nghost: 75.5 ave 152 max 0 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
Neighs: 9238.25 ave 18490 max 0 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
FullNghs: 17945 ave 35917 max 0 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
|
||||||
|
Total # of neighbors = 71780
|
||||||
|
Ave neighs/atom = 31.621145
|
||||||
|
Ave special neighs/atom = 0.22026432
|
||||||
|
Neighbor list builds = 2071
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Total wall time: 0:02:45
|
||||||
@ -98,5 +98,6 @@ compute nbond_solid all nbond/atom bond/type 1
|
|||||||
thermo 200
|
thermo 200
|
||||||
thermo_style custom step time ke press atoms
|
thermo_style custom step time ke press atoms
|
||||||
|
|
||||||
dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_temp c_eng c_nbond_solid c_nbond_shell c_rho c_surf c_status
|
#dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_temp c_eng c_nbond_solid c_nbond_shell c_rho c_surf c_status
|
||||||
|
|
||||||
run 40000
|
run 40000
|
||||||
|
|||||||
488
examples/rheo/oxidation/log.17Apr2024.oxidation.g++.4
Normal file
488
examples/rheo/oxidation/log.17Apr2024.oxidation.g++.4
Normal file
@ -0,0 +1,488 @@
|
|||||||
|
LAMMPS (17 Apr 2024 - Development - patch_5May2020-18508-g3c0eaf6870-modified)
|
||||||
|
# ------ 2D oxidizing bar ------ #
|
||||||
|
|
||||||
|
dimension 2
|
||||||
|
units lj
|
||||||
|
atom_style hybrid rheo/thermal bond
|
||||||
|
boundary m m p
|
||||||
|
comm_modify vel yes
|
||||||
|
newton off
|
||||||
|
|
||||||
|
region box block -60 60 0 80 -0.01 0.01 units box
|
||||||
|
create_box 3 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50
|
||||||
|
Created orthogonal box = (-60 0 -0.01) to (60 80 0.01)
|
||||||
|
2 by 2 by 1 MPI processor grid
|
||||||
|
|
||||||
|
region lbar block -15 0 3 80 EDGE EDGE units box
|
||||||
|
region rbar block 0 15 3 80 EDGE EDGE units box
|
||||||
|
region bar union 2 lbar rbar
|
||||||
|
region floor block EDGE EDGE EDGE 3.0 EDGE EDGE units box
|
||||||
|
|
||||||
|
lattice hex 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.0745699 1.8612097 1.0745699
|
||||||
|
create_atoms 1 region bar
|
||||||
|
Created 2255 atoms
|
||||||
|
using lattice units in orthogonal box = (-60 0 -0.01) to (60 80 0.01)
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
create_atoms 3 region floor
|
||||||
|
Created 446 atoms
|
||||||
|
using lattice units in orthogonal box = (-60 0 -0.01) to (60 80 0.01)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
set region rbar type 2
|
||||||
|
Setting atom values ...
|
||||||
|
1148 settings made for type
|
||||||
|
group bar type 1 2
|
||||||
|
2255 atoms in group bar
|
||||||
|
group rbar type 2
|
||||||
|
1148 atoms in group rbar
|
||||||
|
group floor type 3
|
||||||
|
446 atoms in group floor
|
||||||
|
|
||||||
|
set group all sph/e 0.0
|
||||||
|
Setting atom values ...
|
||||||
|
2701 settings made for sph/e
|
||||||
|
set group all rheo/status 1
|
||||||
|
Setting atom values ...
|
||||||
|
2701 settings made for rheo/status
|
||||||
|
|
||||||
|
# ------ Model parameters ------#
|
||||||
|
|
||||||
|
variable cut equal 3.0
|
||||||
|
variable n equal 1.0
|
||||||
|
variable rho0 equal 1.0
|
||||||
|
variable cs equal 1.0
|
||||||
|
variable mp equal ${rho0}/${n}
|
||||||
|
variable mp equal 1/${n}
|
||||||
|
variable mp equal 1/1
|
||||||
|
variable zeta equal 0.05
|
||||||
|
variable kappa equal 0.1*${rho0}/${mp}
|
||||||
|
variable kappa equal 0.1*1/${mp}
|
||||||
|
variable kappa equal 0.1*1/1
|
||||||
|
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||||
|
variable dt_max equal 0.1*3/${cs}/3
|
||||||
|
variable dt_max equal 0.1*3/1/3
|
||||||
|
variable eta equal 0.05
|
||||||
|
variable Cv equal 1.0
|
||||||
|
variable L equal 0.1
|
||||||
|
variable Tf equal 1.0
|
||||||
|
|
||||||
|
mass * ${mp}
|
||||||
|
mass * 1
|
||||||
|
timestep 0.1
|
||||||
|
|
||||||
|
pair_style hybrid/overlay rheo ${cut} artificial/visc ${zeta} rheo/solid
|
||||||
|
pair_style hybrid/overlay rheo 3 artificial/visc ${zeta} rheo/solid
|
||||||
|
pair_style hybrid/overlay rheo 3 artificial/visc 0.05 rheo/solid
|
||||||
|
pair_coeff * * rheo
|
||||||
|
pair_coeff * * rheo/solid 1.0 1.0 1.0
|
||||||
|
|
||||||
|
special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 1 1
|
||||||
|
special bond factors coul: 0 1 1
|
||||||
|
0 = max # of 1-2 neighbors
|
||||||
|
101 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.000 seconds
|
||||||
|
create_bonds many bar bar 1 0 1.5
|
||||||
|
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 3.3
|
||||||
|
ghost atom cutoff = 3.3
|
||||||
|
binsize = 1.65, bins = 73 49 1
|
||||||
|
3 neighbor lists, perpetual/occasional/extra = 2 1 0
|
||||||
|
(1) command create_bonds, occasional
|
||||||
|
attributes: full, newton off
|
||||||
|
pair build: full/bin
|
||||||
|
stencil: full/bin/2d
|
||||||
|
bin: standard
|
||||||
|
(2) pair rheo, perpetual
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: half/bin/newtoff
|
||||||
|
stencil: full/bin/2d
|
||||||
|
bin: standard
|
||||||
|
(3) pair rheo/solid, perpetual, trim from (2)
|
||||||
|
attributes: half, newton off, cut 1.3
|
||||||
|
pair build: trim
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
Added 6547 bonds, new total = 6547
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 1 1
|
||||||
|
special bond factors coul: 0 1 1
|
||||||
|
6 = max # of 1-2 neighbors
|
||||||
|
101 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.000 seconds
|
||||||
|
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
|
||||||
|
|
||||||
|
bond_style hybrid bpm/spring rheo/shell t/form 100
|
||||||
|
bond_coeff 1 bpm/spring 1.0 1.0 1.0
|
||||||
|
bond_coeff 2 rheo/shell 0.2 0.2 0.1
|
||||||
|
|
||||||
|
# ------ Apply dynamics ------#
|
||||||
|
|
||||||
|
# Note: surface detection is not performed on solid bodies, so cannot use surface property
|
||||||
|
compute coord all rheo/property/atom coordination
|
||||||
|
variable surf atom c_coord<22
|
||||||
|
group surf dynamic all var surf every 10
|
||||||
|
dynamic group surf defined
|
||||||
|
|
||||||
|
fix 1 all rheo ${cut} quintic 0 thermal shift surface/detection coordination 22 8
|
||||||
|
fix 1 all rheo 3 quintic 0 thermal shift surface/detection coordination 22 8
|
||||||
|
fix 2 all rheo/viscosity * constant ${eta}
|
||||||
|
fix 2 all rheo/viscosity * constant 0.05
|
||||||
|
fix 3 all rheo/pressure * linear
|
||||||
|
fix 4 all rheo/thermal conductivity * constant ${kappa} specific/heat * constant ${Cv} Tfreeze * constant ${Tf} latent/heat * constant ${L} react 1.5 1
|
||||||
|
fix 4 all rheo/thermal conductivity * constant 0.1 specific/heat * constant ${Cv} Tfreeze * constant ${Tf} latent/heat * constant ${L} react 1.5 1
|
||||||
|
fix 4 all rheo/thermal conductivity * constant 0.1 specific/heat * constant 1 Tfreeze * constant ${Tf} latent/heat * constant ${L} react 1.5 1
|
||||||
|
fix 4 all rheo/thermal conductivity * constant 0.1 specific/heat * constant 1 Tfreeze * constant 1 latent/heat * constant ${L} react 1.5 1
|
||||||
|
fix 4 all rheo/thermal conductivity * constant 0.1 specific/heat * constant 1 Tfreeze * constant 1 latent/heat * constant 0.1 react 1.5 1
|
||||||
|
|
||||||
|
fix 5 rbar rheo/oxidation 1.5 2 1.0
|
||||||
|
fix 6 all wall/harmonic ylo EDGE 2.0 1.0 1.0
|
||||||
|
fix 7 all gravity 5e-5 vector 0 -1 0
|
||||||
|
fix 8 floor setforce 0.0 0.0 0.0
|
||||||
|
fix 9 surf add/heat linear 1.1 0.05
|
||||||
|
fix 10 floor add/heat constant 0 overwrite yes # fix the temperature of the floor
|
||||||
|
fix 11 all enforce2d
|
||||||
|
|
||||||
|
compute surf all rheo/property/atom surface
|
||||||
|
compute rho all rheo/property/atom rho
|
||||||
|
compute phase all rheo/property/atom phase
|
||||||
|
compute status all rheo/property/atom status
|
||||||
|
compute temp all rheo/property/atom temperature
|
||||||
|
compute eng all rheo/property/atom energy
|
||||||
|
compute nbond_shell all rheo/property/atom nbond/shell
|
||||||
|
compute nbond_solid all nbond/atom bond/type 1
|
||||||
|
|
||||||
|
# ------ Output & Run ------ #
|
||||||
|
|
||||||
|
thermo 200
|
||||||
|
thermo_style custom step time ke press atoms
|
||||||
|
|
||||||
|
dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_temp c_eng c_nbond_solid c_nbond_shell c_rho c_surf c_status
|
||||||
|
|
||||||
|
run 40000
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
|
||||||
|
- BPM bond style: doi:10.1039/D3SM01373A
|
||||||
|
|
||||||
|
@Article{Clemmer2024,
|
||||||
|
author = {Clemmer, Joel T. and Monti, Joseph M. and Lechman, Jeremy B.},
|
||||||
|
title = {A soft departure from jamming: the compaction of deformable
|
||||||
|
granular matter under high pressures},
|
||||||
|
journal = {Soft Matter},
|
||||||
|
year = 2024,
|
||||||
|
volume = 20,
|
||||||
|
number = 8,
|
||||||
|
pages = {1702--1718}
|
||||||
|
}
|
||||||
|
|
||||||
|
- @article{PalermoInPrep,
|
||||||
|
journal = {in prep},
|
||||||
|
title = {RHEO: A Hybrid Mesh-Free Model Framework for Dynamic Multi-Phase Flows},
|
||||||
|
year = {2024},
|
||||||
|
author = {Eric T. Palermo and Ki T. Wolf and Joel T. Clemmer and Thomas C. O'Connor},
|
||||||
|
}
|
||||||
|
|
||||||
|
- @article{ApplMathModel.130.310,
|
||||||
|
title = {A hybrid smoothed-particle hydrodynamics model of oxide skins on molten aluminum},
|
||||||
|
journal = {Applied Mathematical Modelling},
|
||||||
|
volume = {130},
|
||||||
|
pages = {310-326},
|
||||||
|
year = {2024},
|
||||||
|
issn = {0307-904X},
|
||||||
|
doi = {https://doi.org/10.1016/j.apm.2024.02.027},
|
||||||
|
author = {Joel T. Clemmer and Flint Pierce and Thomas C. O'Connor and Thomas D. Nevins and Elizabeth M.C. Jones and Jeremy B. Lechman and John Tencer},
|
||||||
|
}
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 3.3
|
||||||
|
ghost atom cutoff = 3.3
|
||||||
|
binsize = 1.65, bins = 73 49 1
|
||||||
|
8 neighbor lists, perpetual/occasional/extra = 7 1 0
|
||||||
|
(1) pair rheo, perpetual, half/full from (3)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: halffull/newtoff
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(2) pair rheo/solid, perpetual, trim from (4)
|
||||||
|
attributes: half, newton off, cut 1.3
|
||||||
|
pair build: trim
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(3) compute RHEO/KERNEL, perpetual
|
||||||
|
attributes: full, newton off
|
||||||
|
pair build: full/bin
|
||||||
|
stencil: full/bin/2d
|
||||||
|
bin: standard
|
||||||
|
(4) compute RHEO/GRAD, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(5) compute RHEO/VSHIFT, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(6) compute RHEO/SURFACE, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(7) fix rheo/thermal, occasional, trim from (4)
|
||||||
|
attributes: half, newton off, cut 3
|
||||||
|
pair build: trim
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(8) fix rheo/oxidation, perpetual, trim from (3)
|
||||||
|
attributes: full, newton off, cut 1.8
|
||||||
|
pair build: trim
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 25.96 | 25.96 | 25.96 Mbytes
|
||||||
|
Step Time KinEng Press Atoms
|
||||||
|
0 0 0 0 2701
|
||||||
|
200 20 4.1743799e-07 1.1743617e-07 2701
|
||||||
|
400 40 1.6697519e-06 4.6974469e-07 2701
|
||||||
|
600 60 3.7127333e-06 1.0646825e-05 2701
|
||||||
|
800 80 4.6683656e-06 0.00015182605 2701
|
||||||
|
1000 100 4.7368707e-06 0.00028128761 2701
|
||||||
|
1200 120 3.4384322e-06 0.00045913378 2701
|
||||||
|
1400 140 1.4119866e-06 0.00055627091 2701
|
||||||
|
1600 160 4.4114517e-07 0.00058247308 2701
|
||||||
|
1800 180 4.8289229e-07 0.0005510948 2701
|
||||||
|
2000 200 1.8494183e-06 0.00048386222 2701
|
||||||
|
2200 220 3.3319816e-06 0.00037903264 2701
|
||||||
|
2400 240 3.8128922e-06 0.00024115906 2701
|
||||||
|
2600 260 3.1943401e-06 9.727407e-05 2701
|
||||||
|
2800 280 1.6172816e-06 -2.632162e-05 2701
|
||||||
|
3000 300 3.6100709e-07 -8.5761867e-05 2701
|
||||||
|
3200 320 1.4745502e-07 -5.9204127e-05 2701
|
||||||
|
3400 340 8.3369782e-07 8.8312464e-07 2701
|
||||||
|
3600 360 2.0484052e-06 5.8521477e-05 2701
|
||||||
|
3800 380 3.1639387e-06 0.0001685663 2701
|
||||||
|
4000 400 3.1692907e-06 0.00026875988 2701
|
||||||
|
4200 420 2.391933e-06 0.00038621787 2701
|
||||||
|
4400 440 1.1964404e-06 0.00048901286 2701
|
||||||
|
4600 460 4.0508824e-07 0.00051863639 2701
|
||||||
|
4800 480 5.4908507e-07 0.00049263754 2701
|
||||||
|
5000 500 1.3139665e-06 0.00041984264 2701
|
||||||
|
5200 520 2.1939161e-06 0.00033095351 2701
|
||||||
|
5400 540 2.3687031e-06 0.00022422981 2701
|
||||||
|
5600 560 1.8280882e-06 0.00011544328 2701
|
||||||
|
5800 580 8.8610517e-07 2.9307791e-05 2701
|
||||||
|
6000 600 2.0989359e-07 -1.7340941e-05 2701
|
||||||
|
6200 620 2.8658301e-07 -8.1237835e-06 2701
|
||||||
|
6400 640 9.7636239e-07 4.3755922e-05 2701
|
||||||
|
6600 660 1.891303e-06 0.0001185719 2701
|
||||||
|
6800 680 2.4149904e-06 0.00020830273 2701
|
||||||
|
7000 700 2.3174953e-06 0.00030114767 2701
|
||||||
|
7200 720 1.7918612e-06 0.00037821537 2701
|
||||||
|
7400 740 1.2114987e-06 0.0004233475 2701
|
||||||
|
7600 760 9.9661553e-07 0.00042958263 2701
|
||||||
|
7800 780 1.1552559e-06 0.00039944618 2701
|
||||||
|
8000 800 1.5249138e-06 0.00034034478 2701
|
||||||
|
8200 820 1.7453861e-06 0.00026826463 2701
|
||||||
|
8400 840 1.6259021e-06 0.00019131768 2701
|
||||||
|
8600 860 1.2612805e-06 0.0001162957 2701
|
||||||
|
8800 880 8.6964518e-07 7.1771506e-05 2701
|
||||||
|
9000 900 7.6892472e-07 5.6170687e-05 2701
|
||||||
|
9200 920 1.0780045e-06 7.1925995e-05 2701
|
||||||
|
9400 940 1.6514902e-06 0.00011635293 2701
|
||||||
|
9600 960 2.1891377e-06 0.00017599885 2701
|
||||||
|
9800 980 2.4551701e-06 0.00024127934 2701
|
||||||
|
10000 1000 2.4277051e-06 0.00029918622 2701
|
||||||
|
10200 1020 2.2655987e-06 0.00034067996 2701
|
||||||
|
10400 1040 2.1767207e-06 0.00035598133 2701
|
||||||
|
10600 1060 2.2796719e-06 0.00034359076 2701
|
||||||
|
10800 1080 2.4884225e-06 0.00030749714 2701
|
||||||
|
11000 1100 2.6387215e-06 0.00025725198 2701
|
||||||
|
11200 1120 2.5968908e-06 0.00020170699 2701
|
||||||
|
11400 1140 2.4108931e-06 0.00015185858 2701
|
||||||
|
11600 1160 2.2375166e-06 0.00011800349 2701
|
||||||
|
11800 1180 2.2407196e-06 0.00010646971 2701
|
||||||
|
12000 1200 2.4845263e-06 0.00011817498 2701
|
||||||
|
12200 1220 2.8733204e-06 0.00015013186 2701
|
||||||
|
12400 1240 3.2437087e-06 0.00019211975 2701
|
||||||
|
12600 1260 3.4732728e-06 0.00023620276 2701
|
||||||
|
12800 1280 3.5836611e-06 0.00027352269 2701
|
||||||
|
13000 1300 3.6592211e-06 0.00029533734 2701
|
||||||
|
13200 1320 3.782506e-06 0.00030032559 2701
|
||||||
|
13400 1340 3.9807086e-06 0.00028395722 2701
|
||||||
|
13600 1360 4.2023176e-06 0.00025390325 2701
|
||||||
|
13800 1380 4.3559781e-06 0.00021794236 2701
|
||||||
|
14000 1400 4.4273371e-06 0.00018026034 2701
|
||||||
|
14200 1420 4.49867e-06 0.0001526569 2701
|
||||||
|
14400 1440 4.6591574e-06 0.00013707051 2701
|
||||||
|
14600 1460 4.9589583e-06 0.00013803875 2701
|
||||||
|
14800 1480 5.3859375e-06 0.00015455425 2701
|
||||||
|
15000 1500 5.8639557e-06 0.00017954785 2701
|
||||||
|
15200 1520 6.3075561e-06 0.0002084257 2701
|
||||||
|
15400 1540 6.7022179e-06 0.0002347669 2701
|
||||||
|
15600 1560 7.0789688e-06 0.00025020766 2701
|
||||||
|
15800 1580 7.4734777e-06 0.00025394845 2701
|
||||||
|
16000 1600 7.8884743e-06 0.00024571725 2701
|
||||||
|
16200 1620 8.3224059e-06 0.00022706648 2701
|
||||||
|
16400 1640 8.7337783e-06 0.00020320706 2701
|
||||||
|
16600 1660 9.1454649e-06 0.00017824346 2701
|
||||||
|
16800 1680 9.5948793e-06 0.00015961835 2701
|
||||||
|
17000 1700 1.0106407e-05 0.00015135471 2701
|
||||||
|
17200 1720 1.0707273e-05 0.00015166884 2701
|
||||||
|
17400 1740 1.1392597e-05 0.0001645916 2701
|
||||||
|
17600 1760 1.2118829e-05 0.00018119729 2701
|
||||||
|
17800 1780 1.2846056e-05 0.0002003616 2701
|
||||||
|
18000 1800 1.3555288e-05 0.00021585952 2701
|
||||||
|
18200 1820 1.4301024e-05 0.00022290158 2701
|
||||||
|
18400 1840 1.5089217e-05 0.00021970192 2701
|
||||||
|
18600 1860 1.5902351e-05 0.00020911128 2701
|
||||||
|
18800 1880 1.6753175e-05 0.00019278718 2701
|
||||||
|
19000 1900 1.7602996e-05 0.00017584076 2701
|
||||||
|
19200 1920 1.8479378e-05 0.00016206226 2701
|
||||||
|
19400 1940 1.9421603e-05 0.00015575677 2701
|
||||||
|
19600 1960 2.0477421e-05 0.00015687558 2701
|
||||||
|
19800 1980 2.1617288e-05 0.00016424998 2701
|
||||||
|
20000 2000 2.2814347e-05 0.00017466664 2701
|
||||||
|
20200 2020 2.4029097e-05 0.00018647149 2701
|
||||||
|
20400 2040 2.5255953e-05 0.00019516077 2701
|
||||||
|
20600 2060 2.649418e-05 0.00019906384 2701
|
||||||
|
20800 2080 2.7755897e-05 0.00019630586 2701
|
||||||
|
21000 2100 2.9067854e-05 0.00018674721 2701
|
||||||
|
21200 2120 3.0396477e-05 0.0001758048 2701
|
||||||
|
21400 2140 3.1759719e-05 0.00016782801 2701
|
||||||
|
21600 2160 3.3193597e-05 0.00016324138 2701
|
||||||
|
21800 2180 3.4729384e-05 0.00016124274 2701
|
||||||
|
22000 2200 3.6367594e-05 0.00016437457 2701
|
||||||
|
22200 2220 3.8095131e-05 0.00017015573 2701
|
||||||
|
22400 2240 3.9867003e-05 0.00017649465 2701
|
||||||
|
22600 2260 4.169511e-05 0.00018111374 2701
|
||||||
|
22800 2280 4.3566134e-05 0.00018104136 2701
|
||||||
|
23000 2300 4.5461538e-05 0.00017822707 2701
|
||||||
|
23200 2320 4.7377333e-05 0.00017285066 2701
|
||||||
|
23400 2340 4.9354403e-05 0.00016826524 2701
|
||||||
|
23600 2360 5.1399791e-05 0.00016517913 2701
|
||||||
|
23800 2380 5.3510931e-05 0.00016299649 2701
|
||||||
|
24000 2400 5.5681048e-05 0.00016256674 2701
|
||||||
|
24200 2420 5.7902429e-05 0.00016513449 2701
|
||||||
|
24400 2440 6.0216049e-05 0.00016895109 2701
|
||||||
|
24600 2460 6.270982e-05 0.00016946227 2701
|
||||||
|
24800 2480 6.5390117e-05 0.00016589426 2701
|
||||||
|
25000 2500 6.8121899e-05 0.00016241676 2701
|
||||||
|
25200 2520 7.0947331e-05 0.00015624292 2701
|
||||||
|
25400 2540 7.4304148e-05 0.0001449537 2701
|
||||||
|
25600 2560 7.7745077e-05 0.00013179658 2701
|
||||||
|
25800 2580 8.0739829e-05 0.00013098838 2701
|
||||||
|
26000 2600 8.3827874e-05 0.00014278841 2701
|
||||||
|
26200 2620 8.7060677e-05 0.00015381649 2701
|
||||||
|
26400 2640 9.0266508e-05 0.00016130999 2701
|
||||||
|
26600 2660 9.3339049e-05 0.00016908268 2701
|
||||||
|
26800 2680 9.6347013e-05 0.00016771087 2701
|
||||||
|
27000 2700 9.9294711e-05 0.00016577315 2701
|
||||||
|
27200 2720 0.00010230007 0.0001670893 2701
|
||||||
|
27400 2740 0.00010547172 0.00016569077 2701
|
||||||
|
27600 2760 0.00010872426 0.00016506303 2701
|
||||||
|
27800 2780 0.00011201844 0.00016482702 2701
|
||||||
|
28000 2800 0.00011532129 0.00016694886 2701
|
||||||
|
28200 2820 0.00011869854 0.00016163005 2701
|
||||||
|
28400 2840 0.00012209747 0.00015339281 2701
|
||||||
|
28600 2860 0.00012549322 0.00014765883 2701
|
||||||
|
28800 2880 0.00012898685 0.00014241765 2701
|
||||||
|
29000 2900 0.00013259039 0.00014215724 2701
|
||||||
|
29200 2920 0.00013628209 0.00014881155 2701
|
||||||
|
29400 2940 0.00014001213 0.00015671333 2701
|
||||||
|
29600 2960 0.00014379216 0.00016446215 2701
|
||||||
|
29800 2980 0.00014764687 0.0001639602 2701
|
||||||
|
30000 3000 0.00015142301 0.00015664816 2701
|
||||||
|
30200 3020 0.00015496407 0.00015545099 2701
|
||||||
|
30400 3040 0.00015797338 0.00015368625 2701
|
||||||
|
30600 3060 0.00016042141 0.00015679918 2701
|
||||||
|
30800 3080 0.00016244716 0.00016093678 2701
|
||||||
|
31000 3100 0.00016202247 0.00016066954 2701
|
||||||
|
31200 3120 0.0001613312 0.00015932059 2701
|
||||||
|
31400 3140 0.00016274961 0.00015988567 2701
|
||||||
|
31600 3160 0.00016541518 0.00015724809 2701
|
||||||
|
31800 3180 0.00016809362 0.00015498827 2701
|
||||||
|
32000 3200 0.00017067801 0.00014830489 2701
|
||||||
|
32200 3220 0.00017333906 0.00014371345 2701
|
||||||
|
32400 3240 0.0001759011 0.00014421259 2701
|
||||||
|
32600 3260 0.00017849952 0.00014228443 2701
|
||||||
|
32800 3280 0.00017801812 0.00014117391 2701
|
||||||
|
33000 3300 0.00017718857 0.00014644675 2701
|
||||||
|
33200 3320 0.00017833666 0.0001291286 2701
|
||||||
|
33400 3340 0.000178576 0.00014878558 2701
|
||||||
|
33600 3360 0.00017846711 0.00013905481 2701
|
||||||
|
33800 3380 0.00017822937 0.00015535996 2701
|
||||||
|
34000 3400 0.00017899663 0.00016094303 2701
|
||||||
|
34200 3420 0.00017924661 0.00015017553 2701
|
||||||
|
34400 3440 0.00018024855 0.00014723549 2701
|
||||||
|
34600 3460 0.00018143865 0.00013903131 2701
|
||||||
|
34800 3480 0.00018258173 0.00013722112 2701
|
||||||
|
35000 3500 0.00018404873 0.00014675949 2701
|
||||||
|
35200 3520 0.00018538521 0.00015108242 2701
|
||||||
|
35400 3540 0.00018669649 0.00014564852 2701
|
||||||
|
35600 3560 0.00018814608 0.00013762161 2701
|
||||||
|
35800 3580 0.00018967415 0.00014602307 2701
|
||||||
|
36000 3600 0.00019146735 0.000126909 2701
|
||||||
|
36200 3620 0.00019414036 0.00012384379 2701
|
||||||
|
36400 3640 0.00019613057 0.00011059573 2701
|
||||||
|
36600 3660 0.00019897104 0.00013621801 2701
|
||||||
|
36800 3680 0.00020169688 0.00013665462 2701
|
||||||
|
37000 3700 0.00020447655 0.00013929258 2701
|
||||||
|
37200 3720 0.00020711105 0.0001363895 2701
|
||||||
|
37400 3740 0.00021077854 0.00013610672 2701
|
||||||
|
37600 3760 0.00021303084 0.00015051235 2701
|
||||||
|
37800 3780 0.00021619561 0.00012664801 2701
|
||||||
|
38000 3800 0.0002194018 0.00012808247 2701
|
||||||
|
38200 3820 0.00022242646 0.0001360174 2701
|
||||||
|
38400 3840 0.00022531568 0.00013311221 2701
|
||||||
|
38600 3860 0.00022821731 0.00013523939 2701
|
||||||
|
38800 3880 0.000231228 0.00014090695 2701
|
||||||
|
39000 3900 0.00023404038 0.00013661835 2701
|
||||||
|
39200 3920 0.00023755044 0.00013659469 2701
|
||||||
|
39400 3940 0.00024009059 0.00012097907 2701
|
||||||
|
39600 3960 0.0002432098 9.7877876e-05 2701
|
||||||
|
39800 3980 0.00024475294 0.0001164688 2701
|
||||||
|
40000 4000 0.00024171274 0.00012432219 2701
|
||||||
|
Loop time of 192.659 on 4 procs for 40000 steps with 2701 atoms
|
||||||
|
|
||||||
|
Performance: 1793840.118 tau/day, 207.620 timesteps/s, 560.783 katom-step/s
|
||||||
|
99.6% CPU use with 4 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 16.881 | 24.402 | 30.74 | 114.6 | 12.67
|
||||||
|
Bond | 1.1126 | 1.8917 | 2.6935 | 43.3 | 0.98
|
||||||
|
Neigh | 35.387 | 35.508 | 35.625 | 1.5 | 18.43
|
||||||
|
Comm | 1.5499 | 1.6694 | 1.8006 | 7.4 | 0.87
|
||||||
|
Output | 0.99755 | 1.0072 | 1.0165 | 0.8 | 0.52
|
||||||
|
Modify | 120.6 | 127.43 | 135.54 | 54.8 | 66.14
|
||||||
|
Other | | 0.7553 | | | 0.39
|
||||||
|
|
||||||
|
Nlocal: 675.25 ave 1373 max 7 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
Nghost: 103 ave 163 max 50 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||||
|
Neighs: 10509 ave 21592 max 126 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
FullNghs: 20367 ave 41981 max 141 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
|
||||||
|
Total # of neighbors = 81468
|
||||||
|
Ave neighs/atom = 30.162162
|
||||||
|
Ave special neighs/atom = 1.6593854
|
||||||
|
Neighbor list builds = 39932
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Total wall time: 0:03:12
|
||||||
@ -69,7 +69,7 @@ compute rho all rheo/property/atom rho
|
|||||||
thermo 200
|
thermo 200
|
||||||
thermo_style custom step time ke press
|
thermo_style custom step time ke press
|
||||||
|
|
||||||
dump 1 all custom 200 atomDump id type x y vx vy fx fy c_rho
|
#dump 1 all custom 200 atomDump id type x y vx vy fx fy c_rho
|
||||||
|
|
||||||
run 20000
|
run 20000
|
||||||
|
|
||||||
|
|||||||
288
examples/rheo/poiseuille/log.17Apr2024.poiseuille.g++.4
Normal file
288
examples/rheo/poiseuille/log.17Apr2024.poiseuille.g++.4
Normal file
@ -0,0 +1,288 @@
|
|||||||
|
LAMMPS (17 Apr 2024 - Development - patch_5May2020-18508-g3c0eaf6870-modified)
|
||||||
|
# ------ 2D Poiseuille flow ------ #
|
||||||
|
|
||||||
|
dimension 2
|
||||||
|
units lj
|
||||||
|
atom_style rheo
|
||||||
|
boundary p p p
|
||||||
|
comm_modify vel yes
|
||||||
|
|
||||||
|
# ------ Create simulation box ------ #
|
||||||
|
|
||||||
|
variable n equal 1.0
|
||||||
|
variable cut equal 3.0
|
||||||
|
|
||||||
|
region box block 0 20 -10 10 -0.01 0.01
|
||||||
|
create_box 2 box
|
||||||
|
Created orthogonal box = (0 -10 -0.01) to (20 10 0.01)
|
||||||
|
2 by 2 by 1 MPI processor grid
|
||||||
|
lattice sq ${n}
|
||||||
|
lattice sq 1
|
||||||
|
Lattice spacing in x,y,z = 1 1 1
|
||||||
|
|
||||||
|
region inner block INF INF -7.5 7.5 INF INF units box
|
||||||
|
region walls block INF INF -7.5 7.5 INF INF units box side out
|
||||||
|
|
||||||
|
create_atoms 2 region walls
|
||||||
|
Created 100 atoms
|
||||||
|
using lattice units in orthogonal box = (0 -10 -0.01) to (20 10 0.01)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
create_atoms 1 region inner
|
||||||
|
Created 300 atoms
|
||||||
|
using lattice units in orthogonal box = (0 -10 -0.01) to (20 10 0.01)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
group fluid type 1
|
||||||
|
300 atoms in group fluid
|
||||||
|
group rig type 2
|
||||||
|
100 atoms in group rig
|
||||||
|
|
||||||
|
displace_atoms fluid random 0.1 0.1 0 135414 units box
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
# ------ Model parameters ------ #
|
||||||
|
|
||||||
|
variable rho0 equal 1.0
|
||||||
|
variable cs equal 1.0
|
||||||
|
variable mp equal ${rho0}/${n}
|
||||||
|
variable mp equal 1/${n}
|
||||||
|
variable mp equal 1/1
|
||||||
|
variable zeta equal 1.0
|
||||||
|
variable kappa equal 1.0*${rho0}/${mp}
|
||||||
|
variable kappa equal 1.0*1/${mp}
|
||||||
|
variable kappa equal 1.0*1/1
|
||||||
|
variable fext equal 1e-4/${n}
|
||||||
|
variable fext equal 1e-4/1
|
||||||
|
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||||
|
variable dt_max equal 0.1*3/${cs}/3
|
||||||
|
variable dt_max equal 0.1*3/1/3
|
||||||
|
variable Dr equal 0.05*${cut}*${cs}
|
||||||
|
variable Dr equal 0.05*3*${cs}
|
||||||
|
variable Dr equal 0.05*3*1
|
||||||
|
|
||||||
|
variable eta equal 0.1
|
||||||
|
variable gd0 equal 5e-4
|
||||||
|
variable npow equal 0.5
|
||||||
|
variable K equal 0.001
|
||||||
|
|
||||||
|
mass * ${mp}
|
||||||
|
mass * 1
|
||||||
|
set group all rheo/rho ${rho0}
|
||||||
|
set group all rheo/rho 1
|
||||||
|
Setting atom values ...
|
||||||
|
400 settings made for rheo/rho
|
||||||
|
set group all rheo/status 0
|
||||||
|
Setting atom values ...
|
||||||
|
400 settings made for rheo/status
|
||||||
|
set group rig rheo/status 1
|
||||||
|
Setting atom values ...
|
||||||
|
100 settings made for rheo/status
|
||||||
|
|
||||||
|
timestep ${dt_max}
|
||||||
|
timestep 0.1
|
||||||
|
|
||||||
|
pair_style rheo ${cut} artificial/visc ${zeta} rho/damp ${Dr}
|
||||||
|
pair_style rheo 3 artificial/visc ${zeta} rho/damp ${Dr}
|
||||||
|
pair_style rheo 3 artificial/visc 1 rho/damp ${Dr}
|
||||||
|
pair_style rheo 3 artificial/visc 1 rho/damp 0.15
|
||||||
|
pair_coeff * *
|
||||||
|
|
||||||
|
# ------ Fixes & computes ------ #
|
||||||
|
|
||||||
|
fix 1 all rheo ${cut} quintic 0 shift
|
||||||
|
fix 1 all rheo 3 quintic 0 shift
|
||||||
|
fix 2 all rheo/viscosity * constant ${eta}
|
||||||
|
fix 2 all rheo/viscosity * constant 0.1
|
||||||
|
#fix 2 all rheo/viscosity * power ${eta} ${gd0} ${K} ${npow}
|
||||||
|
fix 3 all rheo/pressure * linear
|
||||||
|
fix 4 rig setforce 0.0 0.0 0.0
|
||||||
|
fix 5 fluid addforce ${fext} 0.0 0.0
|
||||||
|
fix 5 fluid addforce 0.0001 0.0 0.0
|
||||||
|
fix 6 all enforce2d
|
||||||
|
|
||||||
|
compute rho all rheo/property/atom rho
|
||||||
|
|
||||||
|
# ------ Output & Run ------ #
|
||||||
|
|
||||||
|
thermo 200
|
||||||
|
thermo_style custom step time ke press
|
||||||
|
|
||||||
|
dump 1 all custom 200 atomDump id type x y vx vy fx fy c_rho
|
||||||
|
|
||||||
|
run 20000
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
|
||||||
|
- @article{PalermoInPrep,
|
||||||
|
journal = {in prep},
|
||||||
|
title = {RHEO: A Hybrid Mesh-Free Model Framework for Dynamic Multi-Phase Flows},
|
||||||
|
year = {2024},
|
||||||
|
author = {Eric T. Palermo and Ki T. Wolf and Joel T. Clemmer and Thomas C. O'Connor},
|
||||||
|
}
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 3.3
|
||||||
|
ghost atom cutoff = 3.3
|
||||||
|
binsize = 1.65, bins = 13 13 1
|
||||||
|
4 neighbor lists, perpetual/occasional/extra = 4 0 0
|
||||||
|
(1) pair rheo, perpetual, half/full from (2)
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: halffull/newton
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(2) compute RHEO/KERNEL, perpetual
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/2d
|
||||||
|
bin: standard
|
||||||
|
(3) compute RHEO/GRAD, perpetual, copy from (1)
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(4) compute RHEO/VSHIFT, perpetual, copy from (1)
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 5.693 | 5.693 | 5.693 Mbytes
|
||||||
|
Step Time KinEng Press
|
||||||
|
0 0 0 0
|
||||||
|
200 20 1.2220462e-06 3.7383146e-05
|
||||||
|
400 40 4.345762e-06 7.5866885e-05
|
||||||
|
600 60 8.8559433e-06 0.00011353743
|
||||||
|
800 80 1.4370506e-05 0.00015135634
|
||||||
|
1000 100 2.0576198e-05 0.00018903722
|
||||||
|
1200 120 2.721926e-05 0.00022533997
|
||||||
|
1400 140 3.4099653e-05 0.00026016069
|
||||||
|
1600 160 4.1064175e-05 0.00029445207
|
||||||
|
1800 180 4.8001225e-05 0.00032893763
|
||||||
|
2000 200 5.4832849e-05 0.00036402396
|
||||||
|
2200 220 6.1508431e-05 0.00039945249
|
||||||
|
2400 240 6.8000141e-05 0.00043534411
|
||||||
|
2600 260 7.430136e-05 0.00046943441
|
||||||
|
2800 280 8.0415328e-05 0.00049807225
|
||||||
|
3000 300 8.6335032e-05 0.00051815375
|
||||||
|
3200 320 9.2021626e-05 0.00052618224
|
||||||
|
3400 340 9.7387936e-05 0.00051877918
|
||||||
|
3600 360 0.00010231526 0.00048650828
|
||||||
|
3800 380 0.00010676617 0.00044578079
|
||||||
|
4000 400 0.00011080098 0.00044777126
|
||||||
|
4200 420 0.00011448127 0.00047047629
|
||||||
|
4400 440 0.00011787852 0.00050280249
|
||||||
|
4600 460 0.00012106805 0.0005397213
|
||||||
|
4800 480 0.00012412056 0.00057885539
|
||||||
|
5000 500 0.0001271078 0.00061396896
|
||||||
|
5200 520 0.00013006637 0.00063981812
|
||||||
|
5400 540 0.00013295039 0.00065094073
|
||||||
|
5600 560 0.00013561487 0.00063918847
|
||||||
|
5800 580 0.00013791796 0.00059087656
|
||||||
|
6000 600 0.00013983422 0.00052171998
|
||||||
|
6200 620 0.00014144833 0.00050658002
|
||||||
|
6400 640 0.00014286538 0.0005248626
|
||||||
|
6600 660 0.00014417734 0.00055826606
|
||||||
|
6800 680 0.00014546931 0.00060063748
|
||||||
|
7000 700 0.00014682553 0.00064421411
|
||||||
|
7200 720 0.0001482833 0.00068252242
|
||||||
|
7400 740 0.00014977996 0.00070671308
|
||||||
|
7600 760 0.00015114829 0.00069774026
|
||||||
|
7800 780 0.0001522719 0.00064408311
|
||||||
|
8000 800 0.00015312897 0.00055977044
|
||||||
|
8200 820 0.00015375669 0.0005225573
|
||||||
|
8400 840 0.00015425683 0.00053833691
|
||||||
|
8600 860 0.00015471278 0.00057447427
|
||||||
|
8800 880 0.0001552059 0.00061980921
|
||||||
|
9000 900 0.00015581593 0.0006659836
|
||||||
|
9200 920 0.0001565564 0.00070813532
|
||||||
|
9400 940 0.00015733573 0.00073378551
|
||||||
|
9600 960 0.00015802107 0.00071560835
|
||||||
|
9800 980 0.00015855339 0.00065636189
|
||||||
|
10000 1000 0.00015890743 0.0005699855
|
||||||
|
10200 1020 0.00015908095 0.00053138971
|
||||||
|
10400 1040 0.00015915523 0.00054790708
|
||||||
|
10600 1060 0.00015921254 0.00058899454
|
||||||
|
10800 1080 0.00015934193 0.00063964906
|
||||||
|
11000 1100 0.00015959891 0.00069241358
|
||||||
|
11200 1120 0.0001599636 0.00073734651
|
||||||
|
11400 1140 0.00016036526 0.00074477329
|
||||||
|
11600 1160 0.00016075471 0.00071047555
|
||||||
|
11800 1180 0.00016109516 0.00064173183
|
||||||
|
12000 1200 0.00016131524 0.00055500553
|
||||||
|
12200 1220 0.00016136366 0.0005290215
|
||||||
|
12400 1240 0.0001613025 0.00055124296
|
||||||
|
12600 1260 0.00016123023 0.00059758627
|
||||||
|
12800 1280 0.00016123043 0.00065488735
|
||||||
|
13000 1300 0.00016132935 0.0007140876
|
||||||
|
13200 1320 0.00016152165 0.00074795629
|
||||||
|
13400 1340 0.00016180372 0.00074730778
|
||||||
|
13600 1360 0.00016216585 0.00071370995
|
||||||
|
13800 1380 0.0001625339 0.00065176323
|
||||||
|
14000 1400 0.00016274999 0.00057515371
|
||||||
|
14200 1420 0.00016271295 0.00055878258
|
||||||
|
14400 1440 0.00016249768 0.00058448193
|
||||||
|
14600 1460 0.00016223675 0.00063096229
|
||||||
|
14800 1480 0.00016201846 0.00068639548
|
||||||
|
15000 1500 0.00016190593 0.00072444357
|
||||||
|
15200 1520 0.00016194466 0.00073830636
|
||||||
|
15400 1540 0.00016216164 0.00072773256
|
||||||
|
15600 1560 0.00016253174 0.00069215481
|
||||||
|
15800 1580 0.00016290895 0.00063239408
|
||||||
|
16000 1600 0.00016306463 0.00057466273
|
||||||
|
16200 1620 0.00016292218 0.00057951567
|
||||||
|
16400 1640 0.00016261117 0.00061504156
|
||||||
|
16600 1660 0.00016225906 0.00066066637
|
||||||
|
16800 1680 0.00016197993 0.00069751908
|
||||||
|
17000 1700 0.0001618568 0.00072202303
|
||||||
|
17200 1720 0.00016194264 0.00073255034
|
||||||
|
17400 1740 0.00016225911 0.0007231031
|
||||||
|
17600 1760 0.00016270465 0.00068931224
|
||||||
|
17800 1780 0.00016304053 0.00062934836
|
||||||
|
18000 1800 0.00016302624 0.00058060272
|
||||||
|
18200 1820 0.00016274847 0.00058859513
|
||||||
|
18400 1840 0.00016236893 0.00061804803
|
||||||
|
18600 1860 0.00016202777 0.00065393237
|
||||||
|
18800 1880 0.0001618184 0.00068747094
|
||||||
|
19000 1900 0.0001618044 0.00071352541
|
||||||
|
19200 1920 0.00016204402 0.00072351769
|
||||||
|
19400 1940 0.00016249999 0.00071330322
|
||||||
|
19600 1960 0.00016297924 0.00067984167
|
||||||
|
19800 1980 0.00016317435 0.00061634142
|
||||||
|
20000 2000 0.00016301186 0.00057234115
|
||||||
|
Loop time of 15.6198 on 4 procs for 20000 steps with 400 atoms
|
||||||
|
|
||||||
|
Performance: 11062881.511 tau/day, 1280.426 timesteps/s, 512.170 katom-step/s
|
||||||
|
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 2.1979 | 2.4473 | 2.6992 | 15.7 | 15.67
|
||||||
|
Neigh | 0.024709 | 0.027006 | 0.029223 | 1.3 | 0.17
|
||||||
|
Comm | 0.4657 | 0.71686 | 0.9662 | 29.0 | 4.59
|
||||||
|
Output | 0.033698 | 0.036781 | 0.039359 | 1.1 | 0.24
|
||||||
|
Modify | 12.306 | 12.313 | 12.319 | 0.2 | 78.83
|
||||||
|
Other | | 0.07916 | | | 0.51
|
||||||
|
|
||||||
|
Nlocal: 100 ave 107 max 93 min
|
||||||
|
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||||
|
Nghost: 185.5 ave 192 max 179 min
|
||||||
|
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||||
|
Neighs: 1712 ave 1848 max 1598 min
|
||||||
|
Histogram: 1 0 1 0 0 1 0 0 0 1
|
||||||
|
FullNghs: 3424 ave 3682 max 3174 min
|
||||||
|
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 13696
|
||||||
|
Ave neighs/atom = 34.24
|
||||||
|
Neighbor list builds = 331
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
|
||||||
|
Total wall time: 0:00:15
|
||||||
224
examples/rheo/taylor-green/log.17Apr2024.taylor.green.g++.4
Normal file
224
examples/rheo/taylor-green/log.17Apr2024.taylor.green.g++.4
Normal file
@ -0,0 +1,224 @@
|
|||||||
|
LAMMPS (17 Apr 2024 - Development - patch_5May2020-18508-g3c0eaf6870-modified)
|
||||||
|
# ------ 2D Taylor Green vortex ------ #
|
||||||
|
|
||||||
|
dimension 2
|
||||||
|
units lj
|
||||||
|
atom_style rheo
|
||||||
|
boundary p p p
|
||||||
|
comm_modify vel yes
|
||||||
|
newton off
|
||||||
|
|
||||||
|
# ------ Create simulation box ------ #
|
||||||
|
|
||||||
|
variable n equal 1.0
|
||||||
|
variable cut equal 3.0
|
||||||
|
|
||||||
|
region box block 0 40 0 40 -0.01 0.01
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 -0.01) to (40 40 0.01)
|
||||||
|
2 by 2 by 1 MPI processor grid
|
||||||
|
lattice sq ${n}
|
||||||
|
lattice sq 1
|
||||||
|
Lattice spacing in x,y,z = 1 1 1
|
||||||
|
|
||||||
|
create_atoms 1 region box
|
||||||
|
Created 1600 atoms
|
||||||
|
using lattice units in orthogonal box = (0 0 -0.01) to (40 40 0.01)
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0 135414 units box
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
# ------ Model parameters ------ #
|
||||||
|
|
||||||
|
variable rho0 equal 1.0
|
||||||
|
variable mp equal ${rho0}/${n}
|
||||||
|
variable mp equal 1/${n}
|
||||||
|
variable mp equal 1/1
|
||||||
|
variable cs equal 1.0
|
||||||
|
variable eta equal 0.05
|
||||||
|
variable zeta equal 1
|
||||||
|
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||||
|
variable dt_max equal 0.1*3/${cs}/3
|
||||||
|
variable dt_max equal 0.1*3/1/3
|
||||||
|
variable Dr equal 0.1*${cut}*${cs}
|
||||||
|
variable Dr equal 0.1*3*${cs}
|
||||||
|
variable Dr equal 0.1*3*1
|
||||||
|
|
||||||
|
mass * ${mp}
|
||||||
|
mass * 1
|
||||||
|
set group all rheo/rho ${rho0}
|
||||||
|
set group all rheo/rho 1
|
||||||
|
Setting atom values ...
|
||||||
|
1600 settings made for rheo/rho
|
||||||
|
set group all rheo/status 0
|
||||||
|
Setting atom values ...
|
||||||
|
1600 settings made for rheo/status
|
||||||
|
|
||||||
|
variable u0 equal 0.05
|
||||||
|
variable uy atom ${u0}*sin(2*PI*x/lx)*cos(2*PI*y/ly)
|
||||||
|
variable uy atom 0.05*sin(2*PI*x/lx)*cos(2*PI*y/ly)
|
||||||
|
variable ux atom -${u0}*sin(2*PI*y/ly)*cos(2*PI*x/ly)
|
||||||
|
variable ux atom -0.05*sin(2*PI*y/ly)*cos(2*PI*x/ly)
|
||||||
|
variable d0 atom ${rho0}-${u0}*${u0}*${rho0}*0.25*(cos(4*PI*x/lx)+cos(4*PI*y/ly))/${cs}/${cs}
|
||||||
|
variable d0 atom 1-${u0}*${u0}*${rho0}*0.25*(cos(4*PI*x/lx)+cos(4*PI*y/ly))/${cs}/${cs}
|
||||||
|
variable d0 atom 1-0.05*${u0}*${rho0}*0.25*(cos(4*PI*x/lx)+cos(4*PI*y/ly))/${cs}/${cs}
|
||||||
|
variable d0 atom 1-0.05*0.05*${rho0}*0.25*(cos(4*PI*x/lx)+cos(4*PI*y/ly))/${cs}/${cs}
|
||||||
|
variable d0 atom 1-0.05*0.05*1*0.25*(cos(4*PI*x/lx)+cos(4*PI*y/ly))/${cs}/${cs}
|
||||||
|
variable d0 atom 1-0.05*0.05*1*0.25*(cos(4*PI*x/lx)+cos(4*PI*y/ly))/1/${cs}
|
||||||
|
variable d0 atom 1-0.05*0.05*1*0.25*(cos(4*PI*x/lx)+cos(4*PI*y/ly))/1/1
|
||||||
|
|
||||||
|
velocity all set v_ux v_uy 0.0 units box
|
||||||
|
|
||||||
|
timestep ${dt_max}
|
||||||
|
timestep 0.1
|
||||||
|
|
||||||
|
pair_style rheo ${cut} artificial/visc ${zeta} rho/damp ${Dr}
|
||||||
|
pair_style rheo 3 artificial/visc ${zeta} rho/damp ${Dr}
|
||||||
|
pair_style rheo 3 artificial/visc 1 rho/damp ${Dr}
|
||||||
|
pair_style rheo 3 artificial/visc 1 rho/damp 0.3
|
||||||
|
pair_coeff * *
|
||||||
|
|
||||||
|
# ------ Fixes & computes ------ #
|
||||||
|
|
||||||
|
fix 1 all rheo ${cut} RK1 8 shift
|
||||||
|
fix 1 all rheo 3 RK1 8 shift
|
||||||
|
fix 2 all rheo/viscosity * constant ${eta}
|
||||||
|
fix 2 all rheo/viscosity * constant 0.05
|
||||||
|
fix 3 all rheo/pressure * linear
|
||||||
|
fix 4 all enforce2d
|
||||||
|
|
||||||
|
compute rho all rheo/property/atom rho
|
||||||
|
|
||||||
|
# ------ Output & Run ------ #
|
||||||
|
|
||||||
|
thermo 200
|
||||||
|
thermo_style custom step time ke press
|
||||||
|
|
||||||
|
dump 1 all custom 200 atomDump id type x y vx vy fx fy c_rho
|
||||||
|
|
||||||
|
run 10000
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
|
||||||
|
- @article{PalermoInPrep,
|
||||||
|
journal = {in prep},
|
||||||
|
title = {RHEO: A Hybrid Mesh-Free Model Framework for Dynamic Multi-Phase Flows},
|
||||||
|
year = {2024},
|
||||||
|
author = {Eric T. Palermo and Ki T. Wolf and Joel T. Clemmer and Thomas C. O'Connor},
|
||||||
|
}
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 3.3
|
||||||
|
ghost atom cutoff = 3.3
|
||||||
|
binsize = 1.65, bins = 25 25 1
|
||||||
|
4 neighbor lists, perpetual/occasional/extra = 4 0 0
|
||||||
|
(1) pair rheo, perpetual, half/full from (2)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: halffull/newtoff
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(2) compute RHEO/KERNEL, perpetual
|
||||||
|
attributes: full, newton off
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/2d
|
||||||
|
bin: standard
|
||||||
|
(3) compute RHEO/GRAD, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(4) compute RHEO/VSHIFT, perpetual, copy from (1)
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 6.835 | 6.835 | 6.835 Mbytes
|
||||||
|
Step Time KinEng Press
|
||||||
|
0 0 0.00062497276 0.00062607301
|
||||||
|
200 20 0.00056200647 0.00056633785
|
||||||
|
400 40 0.00050570968 0.00051098771
|
||||||
|
600 60 0.00045586684 0.00046081672
|
||||||
|
800 80 0.00041124523 0.00041549607
|
||||||
|
1000 100 0.00037065341 0.00037412741
|
||||||
|
1200 120 0.00033391585 0.00033580899
|
||||||
|
1400 140 0.00030078316 0.00030057307
|
||||||
|
1600 160 0.00027093231 0.00026842603
|
||||||
|
1800 180 0.00024403239 0.00023839026
|
||||||
|
2000 200 0.0002197865 0.00021148941
|
||||||
|
2200 220 0.0001979269 0.00018659386
|
||||||
|
2400 240 0.00017822267 0.00016430442
|
||||||
|
2600 260 0.00016047141 0.00014408514
|
||||||
|
2800 280 0.00014448504 0.00012574125
|
||||||
|
3000 300 0.00013009159 0.00010869938
|
||||||
|
3200 320 0.00011713578 9.414951e-05
|
||||||
|
3400 340 0.00010547564 8.1900579e-05
|
||||||
|
3600 360 9.4982139e-05 7.1285649e-05
|
||||||
|
3800 380 8.5538983e-05 6.1571123e-05
|
||||||
|
4000 400 7.7040171e-05 5.3462572e-05
|
||||||
|
4200 420 6.9390317e-05 4.6338308e-05
|
||||||
|
4400 440 6.2503763e-05 3.9697323e-05
|
||||||
|
4600 460 5.6303766e-05 3.4234465e-05
|
||||||
|
4800 480 5.0721595e-05 3.0841338e-05
|
||||||
|
5000 500 4.5695301e-05 2.7788566e-05
|
||||||
|
5200 520 4.1169161e-05 2.5744409e-05
|
||||||
|
5400 540 3.7093059e-05 2.3912739e-05
|
||||||
|
5600 560 3.3421819e-05 2.2494185e-05
|
||||||
|
5800 580 3.0114735e-05 2.1594384e-05
|
||||||
|
6000 600 2.7135224e-05 2.1164421e-05
|
||||||
|
6200 620 2.4450446e-05 2.0979349e-05
|
||||||
|
6400 640 2.2030925e-05 2.0858567e-05
|
||||||
|
6600 660 1.9850196e-05 2.098115e-05
|
||||||
|
6800 680 1.7884553e-05 2.1134827e-05
|
||||||
|
7000 700 1.6112763e-05 2.1242242e-05
|
||||||
|
7200 720 1.4515783e-05 2.1312763e-05
|
||||||
|
7400 740 1.3076456e-05 2.1370947e-05
|
||||||
|
7600 760 1.1779327e-05 2.1332126e-05
|
||||||
|
7800 780 1.0610469e-05 2.1156562e-05
|
||||||
|
8000 800 9.5573298e-06 2.0898126e-05
|
||||||
|
8200 820 8.6085799e-06 2.0517958e-05
|
||||||
|
8400 840 7.7539888e-06 1.9841551e-05
|
||||||
|
8600 860 6.9843033e-06 1.9114769e-05
|
||||||
|
8800 880 6.2911575e-06 1.8362959e-05
|
||||||
|
9000 900 5.6669785e-06 1.7473404e-05
|
||||||
|
9200 920 5.1049208e-06 1.6452745e-05
|
||||||
|
9400 940 4.5987908e-06 1.5578629e-05
|
||||||
|
9600 960 4.1429972e-06 1.4427274e-05
|
||||||
|
9800 980 3.7324962e-06 1.3169649e-05
|
||||||
|
10000 1000 3.3627455e-06 1.1938723e-05
|
||||||
|
Loop time of 38.2006 on 4 procs for 10000 steps with 1600 atoms
|
||||||
|
|
||||||
|
Performance: 2261743.875 tau/day, 261.776 timesteps/s, 418.841 katom-step/s
|
||||||
|
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 8.2958 | 8.7273 | 9.3582 | 15.2 | 22.85
|
||||||
|
Neigh | 0.034282 | 0.035689 | 0.037115 | 0.7 | 0.09
|
||||||
|
Comm | 0.16788 | 0.17018 | 0.17278 | 0.4 | 0.45
|
||||||
|
Output | 0.066977 | 0.06882 | 0.071704 | 0.7 | 0.18
|
||||||
|
Modify | 28.483 | 28.793 | 28.962 | 3.6 | 75.37
|
||||||
|
Other | | 0.4053 | | | 1.06
|
||||||
|
|
||||||
|
Nlocal: 400 ave 402 max 399 min
|
||||||
|
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||||
|
Nghost: 307.25 ave 308 max 305 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||||
|
Neighs: 7618.25 ave 7697 max 7564 min
|
||||||
|
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||||
|
FullNghs: 13343 ave 13497 max 13258 min
|
||||||
|
Histogram: 1 1 1 0 0 0 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 53372
|
||||||
|
Ave neighs/atom = 33.3575
|
||||||
|
Neighbor list builds = 123
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:38
|
||||||
@ -23,8 +23,6 @@
|
|||||||
#include "modify.h"
|
#include "modify.h"
|
||||||
#include "neighbor.h"
|
#include "neighbor.h"
|
||||||
|
|
||||||
#include "update.h"
|
|
||||||
|
|
||||||
#include <cmath>
|
#include <cmath>
|
||||||
#include <cstring>
|
#include <cstring>
|
||||||
|
|
||||||
|
|||||||
@ -30,7 +30,7 @@ ComputeNBondAtom::ComputeNBondAtom(LAMMPS *_lmp, int narg, char **arg) :
|
|||||||
if (narg < 3) utils::missing_cmd_args(FLERR, "compute nbond/atom", error);
|
if (narg < 3) utils::missing_cmd_args(FLERR, "compute nbond/atom", error);
|
||||||
|
|
||||||
if (atom->avec->bonds_allow == 0)
|
if (atom->avec->bonds_allow == 0)
|
||||||
error->all(FLERR,"Compute nbond/atom used when bonds are not allowed");
|
error->all(FLERR,"Compute nbond/atom used in system without bonds");
|
||||||
|
|
||||||
btype = -1;
|
btype = -1;
|
||||||
int iarg = 3;
|
int iarg = 3;
|
||||||
|
|||||||
@ -169,7 +169,7 @@ void FixUpdateSpecialBonds::pre_force(int /*vflag*/)
|
|||||||
tagint *tag = atom->tag;
|
tagint *tag = atom->tag;
|
||||||
|
|
||||||
// In theory could communicate a list of broken bonds to neighboring processors here
|
// In theory could communicate a list of broken bonds to neighboring processors here
|
||||||
// to remove restriction that users use Newton bond off
|
// to remove restriction on Newton bond off
|
||||||
|
|
||||||
for (int ilist = 0; ilist < neighbor->nlist; ilist++) {
|
for (int ilist = 0; ilist < neighbor->nlist; ilist++) {
|
||||||
list = neighbor->lists[ilist];
|
list = neighbor->lists[ilist];
|
||||||
|
|||||||
@ -388,9 +388,8 @@ void BondRHEOShell::settings(int narg, char **arg)
|
|||||||
for (std::size_t i = 0; i < leftover_iarg.size(); i++) {
|
for (std::size_t i = 0; i < leftover_iarg.size(); i++) {
|
||||||
iarg = leftover_iarg[i];
|
iarg = leftover_iarg[i];
|
||||||
if (strcmp(arg[iarg], "t/form") == 0) {
|
if (strcmp(arg[iarg], "t/form") == 0) {
|
||||||
if (iarg + 1 > narg) error->all(FLERR, "Illegal bond rheo/shell command, missing option for t/form");
|
if (iarg + 1 > narg) utils::missing_cmd_args(FLERR, "bond rheo/shell t/form", error);
|
||||||
tform = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
|
tform = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
|
||||||
if (tform < 0.0) error->all(FLERR, "Illegal bond rheo/shell value for t/form, {}", tform);
|
|
||||||
i += 1;
|
i += 1;
|
||||||
} else {
|
} else {
|
||||||
error->all(FLERR, "Illegal bond rheo/shell command, invalid argument {}", arg[iarg]);
|
error->all(FLERR, "Illegal bond rheo/shell command, invalid argument {}", arg[iarg]);
|
||||||
@ -398,7 +397,7 @@ void BondRHEOShell::settings(int narg, char **arg)
|
|||||||
}
|
}
|
||||||
|
|
||||||
if (tform < 0.0)
|
if (tform < 0.0)
|
||||||
error->all(FLERR, "Illegal bond rheo/shell command, must specify formation time");
|
error->all(FLERR, "Illegal bond rheo/shell command, must specify positive formation time");
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|||||||
@ -110,27 +110,27 @@ void ComputeRHEOKernel::init()
|
|||||||
compute_interface = fix_rheo->compute_interface;
|
compute_interface = fix_rheo->compute_interface;
|
||||||
|
|
||||||
zmin = fix_rheo->zmin_kernel;
|
zmin = fix_rheo->zmin_kernel;
|
||||||
h = fix_rheo->h;
|
cut = fix_rheo->cut;
|
||||||
hsq = h * h;
|
cutsq = cut * cut;
|
||||||
hinv = 1.0 / h;
|
cutinv = 1.0 / cut;
|
||||||
hsqinv = hinv * hinv;
|
cutsqinv = cutinv * cutinv;
|
||||||
|
|
||||||
|
|
||||||
if (kernel_style != WENDLANDC4) {
|
if (kernel_style != WENDLANDC4) {
|
||||||
if (dim == 3) {
|
if (dim == 3) {
|
||||||
pre_w = 1.0 / (120.0 * MY_PI) * 27.0 * hsqinv * hinv;
|
pre_w = 1.0 / (120.0 * MY_PI) * 27.0 * cutsqinv * cutinv;
|
||||||
pre_wp = pre_w * 3.0 * hinv;
|
pre_wp = pre_w * 3.0 * cutinv;
|
||||||
} else {
|
} else {
|
||||||
pre_w = 7.0 / (478.0 * MY_PI) * 9 * hsqinv;
|
pre_w = 7.0 / (478.0 * MY_PI) * 9 * cutsqinv;
|
||||||
pre_wp = pre_w * 3.0 * hinv;
|
pre_wp = pre_w * 3.0 * cutinv;
|
||||||
}
|
}
|
||||||
} else {
|
} else {
|
||||||
if (dim == 3) {
|
if (dim == 3) {
|
||||||
pre_w = 495.0 / (32.0 * MY_PI * hsq * h);
|
pre_w = 495.0 / (32.0 * MY_PI * cutsq * cut);
|
||||||
pre_wp = pre_w * hinv;
|
pre_wp = pre_w * cutinv;
|
||||||
} else {
|
} else {
|
||||||
pre_w = 9.0 / (MY_PI * hsq);
|
pre_w = 9.0 / (MY_PI * cutsq);
|
||||||
pre_wp = pre_w * hinv;
|
pre_wp = pre_w * cutinv;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -246,7 +246,7 @@ double ComputeRHEOKernel::calc_dw(int i, int j, double delx, double dely, double
|
|||||||
double ComputeRHEOKernel::calc_w_quintic(int i, int j, double delx, double dely, double delz, double r)
|
double ComputeRHEOKernel::calc_w_quintic(int i, int j, double delx, double dely, double delz, double r)
|
||||||
{
|
{
|
||||||
double w, tmp1, tmp2, tmp3, tmp1sq, tmp2sq, tmp3sq, s;
|
double w, tmp1, tmp2, tmp3, tmp1sq, tmp2sq, tmp3sq, s;
|
||||||
s = r * 3.0 * hinv;
|
s = r * 3.0 * cutinv;
|
||||||
|
|
||||||
if (s > 3.0) {
|
if (s > 3.0) {
|
||||||
w = 0.0;
|
w = 0.0;
|
||||||
@ -284,7 +284,7 @@ double ComputeRHEOKernel::calc_dw_quintic(int i, int j, double delx, double dely
|
|||||||
double *mass = atom->mass;
|
double *mass = atom->mass;
|
||||||
int *type = atom->type;
|
int *type = atom->type;
|
||||||
|
|
||||||
s = r * 3.0 * hinv;
|
s = r * 3.0 * cutinv;
|
||||||
|
|
||||||
if (s > 3.0) {
|
if (s > 3.0) {
|
||||||
wp = 0.0;
|
wp = 0.0;
|
||||||
@ -323,7 +323,7 @@ double ComputeRHEOKernel::calc_dw_quintic(int i, int j, double delx, double dely
|
|||||||
double ComputeRHEOKernel::calc_w_wendlandc4(int i, int j, double delx, double dely, double delz, double r)
|
double ComputeRHEOKernel::calc_w_wendlandc4(int i, int j, double delx, double dely, double delz, double r)
|
||||||
{
|
{
|
||||||
double w, tmp6, s;
|
double w, tmp6, s;
|
||||||
s = r * hinv;
|
s = r * cutinv;
|
||||||
|
|
||||||
if (s > 1.0) {
|
if (s > 1.0) {
|
||||||
w = 0.0;
|
w = 0.0;
|
||||||
@ -349,7 +349,7 @@ double ComputeRHEOKernel::calc_dw_wendlandc4(int i, int j, double delx, double d
|
|||||||
double *mass = atom->mass;
|
double *mass = atom->mass;
|
||||||
int *type = atom->type;
|
int *type = atom->type;
|
||||||
|
|
||||||
s = r * hinv;
|
s = r * cutinv;
|
||||||
|
|
||||||
if (s > 1.0) {
|
if (s > 1.0) {
|
||||||
wp = 0.0;
|
wp = 0.0;
|
||||||
@ -403,13 +403,13 @@ double ComputeRHEOKernel::calc_w_rk1(int i, int j, double delx, double dely, dou
|
|||||||
|
|
||||||
if (dim == 2) {
|
if (dim == 2) {
|
||||||
H[0] = 1.0;
|
H[0] = 1.0;
|
||||||
H[1] = dx[0] * hinv;
|
H[1] = dx[0] * cutinv;
|
||||||
H[2] = dx[1] * hinv;
|
H[2] = dx[1] * cutinv;
|
||||||
} else {
|
} else {
|
||||||
H[0] = 1.0;
|
H[0] = 1.0;
|
||||||
H[1] = dx[0] * hinv;
|
H[1] = dx[0] * cutinv;
|
||||||
H[2] = dx[1] * hinv;
|
H[2] = dx[1] * cutinv;
|
||||||
H[3] = dx[2] * hinv;
|
H[3] = dx[2] * cutinv;
|
||||||
}
|
}
|
||||||
Wij = 0;
|
Wij = 0;
|
||||||
for (b = 0; b < Mdim; b++) {
|
for (b = 0; b < Mdim; b++) {
|
||||||
@ -444,22 +444,22 @@ double ComputeRHEOKernel::calc_w_rk2(int i, int j, double delx, double dely, dou
|
|||||||
|
|
||||||
if (dim == 2) {
|
if (dim == 2) {
|
||||||
H[0] = 1.0;
|
H[0] = 1.0;
|
||||||
H[1] = dx[0] * hinv;
|
H[1] = dx[0] * cutinv;
|
||||||
H[2] = dx[1] * hinv;
|
H[2] = dx[1] * cutinv;
|
||||||
H[3] = 0.5 * dx[0] * dx[0] * hsqinv;
|
H[3] = 0.5 * dx[0] * dx[0] * cutsqinv;
|
||||||
H[4] = 0.5 * dx[1] * dx[1] * hsqinv;
|
H[4] = 0.5 * dx[1] * dx[1] * cutsqinv;
|
||||||
H[5] = dx[0] * dx[1] * hsqinv;
|
H[5] = dx[0] * dx[1] * cutsqinv;
|
||||||
} else {
|
} else {
|
||||||
H[0] = 1.0;
|
H[0] = 1.0;
|
||||||
H[1] = dx[0] * hinv;
|
H[1] = dx[0] * cutinv;
|
||||||
H[2] = dx[1] * hinv;
|
H[2] = dx[1] * cutinv;
|
||||||
H[3] = dx[2] * hinv;
|
H[3] = dx[2] * cutinv;
|
||||||
H[4] = 0.5 * dx[0] * dx[0] * hsqinv;
|
H[4] = 0.5 * dx[0] * dx[0] * cutsqinv;
|
||||||
H[5] = 0.5 * dx[1] * dx[1] * hsqinv;
|
H[5] = 0.5 * dx[1] * dx[1] * cutsqinv;
|
||||||
H[6] = 0.5 * dx[2] * dx[2] * hsqinv;
|
H[6] = 0.5 * dx[2] * dx[2] * cutsqinv;
|
||||||
H[7] = dx[0] * dx[1] * hsqinv;
|
H[7] = dx[0] * dx[1] * cutsqinv;
|
||||||
H[8] = dx[0] * dx[2] * hsqinv;
|
H[8] = dx[0] * dx[2] * cutsqinv;
|
||||||
H[9] = dx[1] * dx[2] * hsqinv;
|
H[9] = dx[1] * dx[2] * cutsqinv;
|
||||||
}
|
}
|
||||||
Wij = 0;
|
Wij = 0;
|
||||||
for (b = 0; b < Mdim; b++) {
|
for (b = 0; b < Mdim; b++) {
|
||||||
@ -496,13 +496,13 @@ void ComputeRHEOKernel::calc_dw_rk1(int i, int j, double delx, double dely, doub
|
|||||||
//Populate correction basis
|
//Populate correction basis
|
||||||
if (dim == 2) {
|
if (dim == 2) {
|
||||||
H[0] = 1.0;
|
H[0] = 1.0;
|
||||||
H[1] = dx[0] * hinv;
|
H[1] = dx[0] * cutinv;
|
||||||
H[2] = dx[1] * hinv;
|
H[2] = dx[1] * cutinv;
|
||||||
} else {
|
} else {
|
||||||
H[0] = 1.0;
|
H[0] = 1.0;
|
||||||
H[1] = dx[0] * hinv;
|
H[1] = dx[0] * cutinv;
|
||||||
H[2] = dx[1] * hinv;
|
H[2] = dx[1] * cutinv;
|
||||||
H[3] = dx[2] * hinv;
|
H[3] = dx[2] * cutinv;
|
||||||
}
|
}
|
||||||
|
|
||||||
// dWij[] = dWx dWy (dWz)
|
// dWij[] = dWx dWy (dWz)
|
||||||
@ -533,22 +533,22 @@ void ComputeRHEOKernel::calc_dw_rk2(int i, int j, double delx, double dely, doub
|
|||||||
//Populate correction basis
|
//Populate correction basis
|
||||||
if (dim == 2) {
|
if (dim == 2) {
|
||||||
H[0] = 1.0;
|
H[0] = 1.0;
|
||||||
H[1] = dx[0] * hinv;
|
H[1] = dx[0] * cutinv;
|
||||||
H[2] = dx[1] * hinv;
|
H[2] = dx[1] * cutinv;
|
||||||
H[3] = 0.5 * dx[0] * dx[0] * hsqinv;
|
H[3] = 0.5 * dx[0] * dx[0] * cutsqinv;
|
||||||
H[4] = 0.5 * dx[1] * dx[1] * hsqinv;
|
H[4] = 0.5 * dx[1] * dx[1] * cutsqinv;
|
||||||
H[5] = dx[0] * dx[1] * hsqinv;
|
H[5] = dx[0] * dx[1] * cutsqinv;
|
||||||
} else {
|
} else {
|
||||||
H[0] = 1.0;
|
H[0] = 1.0;
|
||||||
H[1] = dx[0] * hinv;
|
H[1] = dx[0] * cutinv;
|
||||||
H[2] = dx[1] * hinv;
|
H[2] = dx[1] * cutinv;
|
||||||
H[3] = dx[2] * hinv;
|
H[3] = dx[2] * cutinv;
|
||||||
H[4] = 0.5 * dx[0] * dx[0] * hsqinv;
|
H[4] = 0.5 * dx[0] * dx[0] * cutsqinv;
|
||||||
H[5] = 0.5 * dx[1] * dx[1] * hsqinv;
|
H[5] = 0.5 * dx[1] * dx[1] * cutsqinv;
|
||||||
H[6] = 0.5 * dx[2] * dx[2] * hsqinv;
|
H[6] = 0.5 * dx[2] * dx[2] * cutsqinv;
|
||||||
H[7] = dx[0] * dx[1] * hsqinv;
|
H[7] = dx[0] * dx[1] * cutsqinv;
|
||||||
H[8] = dx[0] * dx[2] * hsqinv;
|
H[8] = dx[0] * dx[2] * cutsqinv;
|
||||||
H[9] = dx[1] * dx[2] * hsqinv;
|
H[9] = dx[1] * dx[2] * cutsqinv;
|
||||||
}
|
}
|
||||||
|
|
||||||
// dWij[] = dWx dWy (dWz)
|
// dWij[] = dWx dWy (dWz)
|
||||||
@ -621,7 +621,7 @@ void ComputeRHEOKernel::compute_peratom()
|
|||||||
dx[2] = ztmp - x[j][2];
|
dx[2] = ztmp - x[j][2];
|
||||||
rsq = lensq3(dx);
|
rsq = lensq3(dx);
|
||||||
|
|
||||||
if (rsq < hsq) {
|
if (rsq < cutsq) {
|
||||||
r = sqrt(rsq);
|
r = sqrt(rsq);
|
||||||
w = calc_w_quintic(i, j, dx[0], dx[1], dx[2], r);
|
w = calc_w_quintic(i, j, dx[0], dx[1], dx[2], r);
|
||||||
rhoj = rho[j];
|
rhoj = rho[j];
|
||||||
@ -639,7 +639,7 @@ void ComputeRHEOKernel::compute_peratom()
|
|||||||
}
|
}
|
||||||
} else if (correction_order > 0) {
|
} else if (correction_order > 0) {
|
||||||
|
|
||||||
// Moment matrix M and polynomial basis vector H (1d for gsl compatibility)
|
// Moment matrix M and polynomial basis vector cut (1d for gsl compatibility)
|
||||||
double H[Mdim], M[Mdim * Mdim];
|
double H[Mdim], M[Mdim * Mdim];
|
||||||
|
|
||||||
for (ii = 0; ii < inum; ii++) {
|
for (ii = 0; ii < inum; ii++) {
|
||||||
@ -652,7 +652,7 @@ void ComputeRHEOKernel::compute_peratom()
|
|||||||
jnum = numneigh[i];
|
jnum = numneigh[i];
|
||||||
itype = type[i];
|
itype = type[i];
|
||||||
|
|
||||||
// Zero upper-triangle M and H (will be symmetric):
|
// Zero upper-triangle M and cut (will be symmetric):
|
||||||
for (a = 0; a < Mdim; a++) {
|
for (a = 0; a < Mdim; a++) {
|
||||||
for (b = a; b < Mdim; b++) {
|
for (b = a; b < Mdim; b++) {
|
||||||
M[a * Mdim + b] = 0;
|
M[a * Mdim + b] = 0;
|
||||||
@ -669,7 +669,7 @@ void ComputeRHEOKernel::compute_peratom()
|
|||||||
|
|
||||||
rsq = lensq3(dx);
|
rsq = lensq3(dx);
|
||||||
|
|
||||||
if (rsq < hsq) {
|
if (rsq < cutsq) {
|
||||||
r = sqrt(rsq);
|
r = sqrt(rsq);
|
||||||
w = calc_w_quintic(i, j, dx[0], dx[1], dx[2], r);
|
w = calc_w_quintic(i, j, dx[0], dx[1], dx[2], r);
|
||||||
|
|
||||||
@ -683,25 +683,25 @@ void ComputeRHEOKernel::compute_peratom()
|
|||||||
//Populate the H-vector of polynomials (2D)
|
//Populate the H-vector of polynomials (2D)
|
||||||
if (dim == 2) {
|
if (dim == 2) {
|
||||||
H[0] = 1.0;
|
H[0] = 1.0;
|
||||||
H[1] = dx[0] * hinv;
|
H[1] = dx[0] * cutinv;
|
||||||
H[2] = dx[1] * hinv;
|
H[2] = dx[1] * cutinv;
|
||||||
if (kernel_style == RK2) {
|
if (kernel_style == RK2) {
|
||||||
H[3] = 0.5 * dx[0] * dx[0] * hsqinv;
|
H[3] = 0.5 * dx[0] * dx[0] * cutsqinv;
|
||||||
H[4] = 0.5 * dx[1] * dx[1] * hsqinv;
|
H[4] = 0.5 * dx[1] * dx[1] * cutsqinv;
|
||||||
H[5] = dx[0] * dx[1] * hsqinv;
|
H[5] = dx[0] * dx[1] * cutsqinv;
|
||||||
}
|
}
|
||||||
} else {
|
} else {
|
||||||
H[0] = 1.0;
|
H[0] = 1.0;
|
||||||
H[1] = dx[0] * hinv;
|
H[1] = dx[0] * cutinv;
|
||||||
H[2] = dx[1] * hinv;
|
H[2] = dx[1] * cutinv;
|
||||||
H[3] = dx[2] * hinv;
|
H[3] = dx[2] * cutinv;
|
||||||
if (kernel_style == RK2) {
|
if (kernel_style == RK2) {
|
||||||
H[4] = 0.5 * dx[0] * dx[0] * hsqinv;
|
H[4] = 0.5 * dx[0] * dx[0] * cutsqinv;
|
||||||
H[5] = 0.5 * dx[1] * dx[1] * hsqinv;
|
H[5] = 0.5 * dx[1] * dx[1] * cutsqinv;
|
||||||
H[6] = 0.5 * dx[2] * dx[2] * hsqinv;
|
H[6] = 0.5 * dx[2] * dx[2] * cutsqinv;
|
||||||
H[7] = dx[0] * dx[1] * hsqinv;
|
H[7] = dx[0] * dx[1] * cutsqinv;
|
||||||
H[8] = dx[0] * dx[2] * hsqinv;
|
H[8] = dx[0] * dx[2] * cutsqinv;
|
||||||
H[9] = dx[1] * dx[2] * hsqinv;
|
H[9] = dx[1] * dx[2] * cutsqinv;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -765,12 +765,12 @@ void ComputeRHEOKernel::compute_peratom()
|
|||||||
C[i][0][a] = M[a * Mdim + 0]; // all rows of column 0
|
C[i][0][a] = M[a * Mdim + 0]; // all rows of column 0
|
||||||
for (b = 0; b < dim; b++) {
|
for (b = 0; b < dim; b++) {
|
||||||
//First derivatives
|
//First derivatives
|
||||||
C[i][1 + b][a] = -M[a * Mdim + b + 1] * hinv;
|
C[i][1 + b][a] = -M[a * Mdim + b + 1] * cutinv;
|
||||||
// columns 1-2 (2D) or 1-3 (3D)
|
// columns 1-2 (2D) or 1-3 (3D)
|
||||||
|
|
||||||
//Second derivatives
|
//Second derivatives
|
||||||
if (kernel_style == RK2)
|
if (kernel_style == RK2)
|
||||||
C[i][1 + dim + b][a] = M[a * Mdim + b + 1 + dim] * hsqinv;
|
C[i][1 + dim + b][a] = M[a * Mdim + b + 1 + dim] * cutsqinv;
|
||||||
// columns 3-4 (2D) or 4-6 (3D)
|
// columns 3-4 (2D) or 4-6 (3D)
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
@ -822,7 +822,7 @@ void ComputeRHEOKernel::compute_coordination()
|
|||||||
dx[2] = ztmp - x[j][2];
|
dx[2] = ztmp - x[j][2];
|
||||||
rsq = lensq3(dx);
|
rsq = lensq3(dx);
|
||||||
|
|
||||||
if (rsq < hsq)
|
if (rsq < cutsq)
|
||||||
coordination[i] += 1;
|
coordination[i] += 1;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|||||||
@ -59,7 +59,7 @@ class ComputeRHEOKernel : public Compute {
|
|||||||
int corrections_calculated;
|
int corrections_calculated;
|
||||||
int kernel_style, zmin, dim, Mdim, ncor;
|
int kernel_style, zmin, dim, Mdim, ncor;
|
||||||
int nmax_store;
|
int nmax_store;
|
||||||
double h, hsq, hinv, hsqinv, pre_w, pre_wp;
|
double cut, cutsq, cutinv, cutsqinv, pre_w, pre_wp;
|
||||||
double ***C;
|
double ***C;
|
||||||
double *C0;
|
double *C0;
|
||||||
|
|
||||||
|
|||||||
@ -181,7 +181,7 @@ void ComputeRHEOSurface::compute_peratom()
|
|||||||
gradC[i][a] += dWij[a] * Volj;
|
gradC[i][a] += dWij[a] * Volj;
|
||||||
}
|
}
|
||||||
|
|
||||||
if (j < nlocal || newton) {
|
if ((j < nlocal) || newton) {
|
||||||
for (a = 0; a < dim; a++){
|
for (a = 0; a < dim; a++){
|
||||||
divr[j] += dWji[a] * dx[a] * Voli;
|
divr[j] += dWji[a] * dx[a] * Voli;
|
||||||
gradC[j][a] += dWji[a] * Voli;
|
gradC[j][a] += dWji[a] * Voli;
|
||||||
@ -287,7 +287,7 @@ void ComputeRHEOSurface::compute_peratom()
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
// clear normal vectors for non surface particles
|
// clear normal vectors for non-surface particles
|
||||||
|
|
||||||
for (i = 0; i < nall; i++) {
|
for (i = 0; i < nall; i++) {
|
||||||
if (mask[i] & groupbit) {
|
if (mask[i] & groupbit) {
|
||||||
|
|||||||
@ -39,7 +39,12 @@ using namespace RHEO_NS;
|
|||||||
using namespace FixConst;
|
using namespace FixConst;
|
||||||
|
|
||||||
static const char cite_rheo[] =
|
static const char cite_rheo[] =
|
||||||
"TBD\n\n";
|
"@article{PalermoInPrep,\n"
|
||||||
|
" journal = {in prep},\n"
|
||||||
|
" title = {RHEO: A Hybrid Mesh-Free Model Framework for Dynamic Multi-Phase Flows},\n"
|
||||||
|
" year = {2024},\n"
|
||||||
|
" author = {Eric T. Palermo and Ki T. Wolf and Joel T. Clemmer and Thomas C. O'Connor},\n"
|
||||||
|
"}\n\n";
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
@ -84,10 +89,9 @@ FixRHEO::FixRHEO(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
error->all(FLERR, "fix rheo command requires atom_style with status");
|
error->all(FLERR, "fix rheo command requires atom_style with status");
|
||||||
|
|
||||||
if (narg < 5)
|
if (narg < 5)
|
||||||
error->all(FLERR, "Insufficient arguments for fix rheo command");
|
utils::missing_cmd_args(FLERR, "fix rheo", error);
|
||||||
|
|
||||||
h = utils::numeric(FLERR, arg[3], false, lmp);
|
cut = utils::numeric(FLERR, arg[3], false, lmp);
|
||||||
cut = h;
|
|
||||||
if (strcmp(arg[4], "quintic") == 0) {
|
if (strcmp(arg[4], "quintic") == 0) {
|
||||||
kernel_style = QUINTIC;
|
kernel_style = QUINTIC;
|
||||||
} else if (strcmp(arg[4], "wendland/c4") == 0) {
|
} else if (strcmp(arg[4], "wendland/c4") == 0) {
|
||||||
@ -109,7 +113,7 @@ FixRHEO::FixRHEO(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
thermal_flag = 1;
|
thermal_flag = 1;
|
||||||
} else if (strcmp(arg[iarg], "surface/detection") == 0) {
|
} else if (strcmp(arg[iarg], "surface/detection") == 0) {
|
||||||
surface_flag = 1;
|
surface_flag = 1;
|
||||||
if(iarg + 3 >= narg) error->all(FLERR, "Illegal surface/detection option in fix rheo");
|
if(iarg + 3 >= narg) utils::missing_cmd_args(FLERR, "fix rheo surface/detection", error);
|
||||||
if (strcmp(arg[iarg + 1], "coordination") == 0) {
|
if (strcmp(arg[iarg + 1], "coordination") == 0) {
|
||||||
surface_style = COORDINATION;
|
surface_style = COORDINATION;
|
||||||
zmin_surface = utils::inumeric(FLERR, arg[iarg + 2], false, lmp);
|
zmin_surface = utils::inumeric(FLERR, arg[iarg + 2], false, lmp);
|
||||||
@ -130,12 +134,12 @@ FixRHEO::FixRHEO(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
} else if (strcmp(arg[iarg], "self/mass") == 0) {
|
} else if (strcmp(arg[iarg], "self/mass") == 0) {
|
||||||
self_mass_flag = 1;
|
self_mass_flag = 1;
|
||||||
} else if (strcmp(arg[iarg], "density") == 0) {
|
} else if (strcmp(arg[iarg], "density") == 0) {
|
||||||
if (iarg + n >= narg) error->all(FLERR, "Illegal rho0 option in fix rheo");
|
if (iarg + n >= narg) utils::missing_cmd_args(FLERR, "fix rheo density", error);
|
||||||
for (i = 1; i <= n; i++)
|
for (i = 1; i <= n; i++)
|
||||||
rho0[i] = utils::numeric(FLERR, arg[iarg + i], false, lmp);
|
rho0[i] = utils::numeric(FLERR, arg[iarg + i], false, lmp);
|
||||||
iarg += n;
|
iarg += n;
|
||||||
} else if (strcmp(arg[iarg], "speed/sound") == 0) {
|
} else if (strcmp(arg[iarg], "speed/sound") == 0) {
|
||||||
if (iarg + n >= narg) error->all(FLERR, "Illegal csq option in fix rheo");
|
if (iarg + n >= narg) utils::missing_cmd_args(FLERR, "fix rheo speed/sound", error);
|
||||||
for (i = 1; i <= n; i++) {
|
for (i = 1; i <= n; i++) {
|
||||||
csq[i] = utils::numeric(FLERR, arg[iarg + i], false, lmp);
|
csq[i] = utils::numeric(FLERR, arg[iarg + i], false, lmp);
|
||||||
csq[i] *= csq[i];
|
csq[i] *= csq[i];
|
||||||
@ -281,7 +285,7 @@ void FixRHEO::setup(int /*vflag*/)
|
|||||||
if (!pressure_fix_defined)
|
if (!pressure_fix_defined)
|
||||||
error->all(FLERR, "Missing fix rheo/pressure");
|
error->all(FLERR, "Missing fix rheo/pressure");
|
||||||
|
|
||||||
if((!thermal_fix_defined) && thermal_flag)
|
if(thermal_flag && !thermal_fix_defined)
|
||||||
error->all(FLERR, "Missing fix rheo/thermal");
|
error->all(FLERR, "Missing fix rheo/thermal");
|
||||||
|
|
||||||
// Reset to zero for future runs
|
// Reset to zero for future runs
|
||||||
@ -290,33 +294,6 @@ void FixRHEO::setup(int /*vflag*/)
|
|||||||
pressure_fix_defined = 0;
|
pressure_fix_defined = 0;
|
||||||
oxidation_fix_defined = 0;
|
oxidation_fix_defined = 0;
|
||||||
|
|
||||||
// Check fixes cover all atoms (may still fail if atoms are created)
|
|
||||||
// FixRHEOPressure currently requires group all
|
|
||||||
auto visc_fixes = modify->get_fix_by_style("rheo/viscosity");
|
|
||||||
auto therm_fixes = modify->get_fix_by_style("rheo/thermal");
|
|
||||||
|
|
||||||
int *mask = atom->mask;
|
|
||||||
int v_coverage_flag = 1;
|
|
||||||
int t_coverage_flag = 1;
|
|
||||||
int covered;
|
|
||||||
for (int i = 0; i < atom->nlocal; i++) {
|
|
||||||
covered = 0;
|
|
||||||
for (auto fix : visc_fixes)
|
|
||||||
if (mask[i] & fix->groupbit) covered = 1;
|
|
||||||
if (!covered) v_coverage_flag = 0;
|
|
||||||
if (thermal_flag) {
|
|
||||||
covered = 0;
|
|
||||||
for (auto fix : therm_fixes)
|
|
||||||
if (mask[i] & fix->groupbit) covered = 1;
|
|
||||||
if (!covered) t_coverage_flag = 0;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
if (!v_coverage_flag)
|
|
||||||
error->one(FLERR, "Fix rheo/viscosity does not fully cover all atoms");
|
|
||||||
if (!t_coverage_flag)
|
|
||||||
error->one(FLERR, "Fix rheo/thermal does not fully cover all atoms");
|
|
||||||
|
|
||||||
if (rhosum_flag)
|
if (rhosum_flag)
|
||||||
compute_rhosum->compute_peratom();
|
compute_rhosum->compute_peratom();
|
||||||
}
|
}
|
||||||
|
|||||||
@ -39,7 +39,7 @@ class FixRHEO : public Fix {
|
|||||||
void reset_dt() override;
|
void reset_dt() override;
|
||||||
|
|
||||||
// Model parameters
|
// Model parameters
|
||||||
double h, cut;
|
double cut;
|
||||||
double *rho0, *csq;
|
double *rho0, *csq;
|
||||||
int self_mass_flag;
|
int self_mass_flag;
|
||||||
int zmin_kernel, zmin_surface, zmin_splash;
|
int zmin_kernel, zmin_surface, zmin_splash;
|
||||||
|
|||||||
@ -99,10 +99,10 @@ void FixRHEOOxidation::init()
|
|||||||
if (fixes.size() == 0) error->all(FLERR, "Need to define fix rheo to use fix rheo/oxidation");
|
if (fixes.size() == 0) error->all(FLERR, "Need to define fix rheo to use fix rheo/oxidation");
|
||||||
fix_rheo = dynamic_cast<FixRHEO *>(fixes[0]);
|
fix_rheo = dynamic_cast<FixRHEO *>(fixes[0]);
|
||||||
|
|
||||||
if (cut > fix_rheo->h)
|
if (cut > fix_rheo->cut)
|
||||||
error->all(FLERR, "Bonding length exceeds kernel cutoff");
|
error->all(FLERR, "Bonding length exceeds kernel cutoff");
|
||||||
|
|
||||||
if (rsurf >= fix_rheo->h)
|
if (rsurf >= fix_rheo->cut)
|
||||||
error->all(FLERR, "Surface distance must be less than kernel cutoff");
|
error->all(FLERR, "Surface distance must be less than kernel cutoff");
|
||||||
|
|
||||||
if (!force->bond) error->all(FLERR, "Must define a bond style with fix rheo/oxidation");
|
if (!force->bond) error->all(FLERR, "Must define a bond style with fix rheo/oxidation");
|
||||||
@ -233,7 +233,7 @@ void FixRHEOOxidation::post_integrate()
|
|||||||
// Add bonds to owned atoms
|
// Add bonds to owned atoms
|
||||||
// If newton bond off, add to both, otherwise add to whichever has a smaller tag
|
// If newton bond off, add to both, otherwise add to whichever has a smaller tag
|
||||||
|
|
||||||
if (!newton_bond || tagi < tagj) {
|
if (!newton_bond || (tagi < tagj)) {
|
||||||
if (num_bond[i] == atom->bond_per_atom)
|
if (num_bond[i] == atom->bond_per_atom)
|
||||||
error->one(FLERR,"New bond exceeded bonds per atom in fix rheo/oxidation for atom {}", tagi);
|
error->one(FLERR,"New bond exceeded bonds per atom in fix rheo/oxidation for atom {}", tagi);
|
||||||
bond_type[i][num_bond[i]] = btype;
|
bond_type[i][num_bond[i]] = btype;
|
||||||
|
|||||||
@ -71,6 +71,7 @@ FixRHEOThermal::FixRHEOThermal(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
cut_bond = 0;
|
cut_bond = 0;
|
||||||
comm_forward = 0;
|
comm_forward = 0;
|
||||||
|
|
||||||
|
// Currently can only have one instance of fix rheo/thermal
|
||||||
if (igroup != 0)
|
if (igroup != 0)
|
||||||
error->all(FLERR,"fix rheo/thermal command requires group all");
|
error->all(FLERR,"fix rheo/thermal command requires group all");
|
||||||
|
|
||||||
@ -249,7 +250,7 @@ void FixRHEOThermal::init()
|
|||||||
auto fixes = modify->get_fix_by_style("^rheo$");
|
auto fixes = modify->get_fix_by_style("^rheo$");
|
||||||
if (fixes.size() == 0) error->all(FLERR, "Need to define fix rheo to use fix rheo/viscosity");
|
if (fixes.size() == 0) error->all(FLERR, "Need to define fix rheo to use fix rheo/viscosity");
|
||||||
fix_rheo = dynamic_cast<FixRHEO *>(fixes[0]);
|
fix_rheo = dynamic_cast<FixRHEO *>(fixes[0]);
|
||||||
cut_kernel = fix_rheo->h;
|
cut_kernel = fix_rheo->cut;
|
||||||
|
|
||||||
if (cut_bond > cut_kernel)
|
if (cut_bond > cut_kernel)
|
||||||
error->all(FLERR, "Bonding length exceeds kernel cutoff");
|
error->all(FLERR, "Bonding length exceeds kernel cutoff");
|
||||||
@ -561,7 +562,7 @@ void FixRHEOThermal::break_bonds()
|
|||||||
// Update special unless two owned atoms melt simultaneously then
|
// Update special unless two owned atoms melt simultaneously then
|
||||||
// only update for atom with lower tag
|
// only update for atom with lower tag
|
||||||
if (fix_update_special_bonds) {
|
if (fix_update_special_bonds) {
|
||||||
if (i < nlocal && j < nlocal && melti && meltj) {
|
if ((i < nlocal) && (j < nlocal) && melti && meltj) {
|
||||||
if (tag[i] < tag[j]) {
|
if (tag[i] < tag[j]) {
|
||||||
fix_update_special_bonds->add_broken_bond(i, j);
|
fix_update_special_bonds->add_broken_bond(i, j);
|
||||||
}
|
}
|
||||||
@ -590,7 +591,7 @@ void FixRHEOThermal::break_bonds()
|
|||||||
// Delete bonds for non-melted local atoms (shifting)
|
// Delete bonds for non-melted local atoms (shifting)
|
||||||
if (i < nlocal && !melti) {
|
if (i < nlocal && !melti) {
|
||||||
for (m = 0; m < num_bond[i]; m++) {
|
for (m = 0; m < num_bond[i]; m++) {
|
||||||
if (bond_atom[i][m] == tag[j] && bond_type[i][m] == btype) {
|
if ((bond_atom[i][m] == tag[j]) && (bond_type[i][m] == btype)) {
|
||||||
nmax = num_bond[i] - 1;
|
nmax = num_bond[i] - 1;
|
||||||
bond_type[i][m] = bond_type[i][nmax];
|
bond_type[i][m] = bond_type[i][nmax];
|
||||||
bond_atom[i][m] = bond_atom[i][nmax];
|
bond_atom[i][m] = bond_atom[i][nmax];
|
||||||
@ -609,7 +610,7 @@ void FixRHEOThermal::break_bonds()
|
|||||||
|
|
||||||
if (j < nlocal && !meltj) {
|
if (j < nlocal && !meltj) {
|
||||||
for (m = 0; m < num_bond[j]; m++) {
|
for (m = 0; m < num_bond[j]; m++) {
|
||||||
if (bond_atom[j][m] == tag[i] && bond_type[j][m] == btype) {
|
if ((bond_atom[j][m] == tag[i]) && (bond_type[j][m] == btype)) {
|
||||||
nmax = num_bond[j] - 1;
|
nmax = num_bond[j] - 1;
|
||||||
bond_type[j][m] = bond_type[j][nmax];
|
bond_type[j][m] = bond_type[j][nmax];
|
||||||
bond_atom[j][m] = bond_atom[j][nmax];
|
bond_atom[j][m] = bond_atom[j][nmax];
|
||||||
@ -692,7 +693,7 @@ void FixRHEOThermal::create_bonds()
|
|||||||
|
|
||||||
// Add bonds to owned atoms
|
// Add bonds to owned atoms
|
||||||
// If newton bond off, add to both, otherwise add to whichever has a smaller tag
|
// If newton bond off, add to both, otherwise add to whichever has a smaller tag
|
||||||
if (i < nlocal && (!newton_bond || tag[i] < tag[j])) {
|
if ((i < nlocal) && (!newton_bond || (tag[i] < tag[j]))) {
|
||||||
if (num_bond[i] == atom->bond_per_atom)
|
if (num_bond[i] == atom->bond_per_atom)
|
||||||
error->one(FLERR,"New bond exceeded bonds per atom in fix rheo/thermal");
|
error->one(FLERR,"New bond exceeded bonds per atom in fix rheo/thermal");
|
||||||
bond_type[i][num_bond[i]] = btype;
|
bond_type[i][num_bond[i]] = btype;
|
||||||
@ -700,7 +701,7 @@ void FixRHEOThermal::create_bonds()
|
|||||||
num_bond[i]++;
|
num_bond[i]++;
|
||||||
}
|
}
|
||||||
|
|
||||||
if (j < nlocal && (!newton_bond || tag[j] < tag[i])) {
|
if ((j < nlocal) && (!newton_bond || (tag[j] < tag[i]))) {
|
||||||
if (num_bond[j] == atom->bond_per_atom)
|
if (num_bond[j] == atom->bond_per_atom)
|
||||||
error->one(FLERR,"New bond exceeded bonds per atom in fix rheo/thermal");
|
error->one(FLERR,"New bond exceeded bonds per atom in fix rheo/thermal");
|
||||||
bond_type[j][num_bond[j]] = btype;
|
bond_type[j][num_bond[j]] = btype;
|
||||||
|
|||||||
@ -46,6 +46,7 @@ FixRHEOViscosity::FixRHEOViscosity(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
constant_flag = 0;
|
constant_flag = 0;
|
||||||
evolve_flag = 0;
|
evolve_flag = 0;
|
||||||
|
|
||||||
|
// Currently can only have one instance of fix rheo/viscosity
|
||||||
if (igroup != 0)
|
if (igroup != 0)
|
||||||
error->all(FLERR,"fix rheo/viscosity command requires group all");
|
error->all(FLERR,"fix rheo/viscosity command requires group all");
|
||||||
|
|
||||||
|
|||||||
@ -33,7 +33,6 @@
|
|||||||
#include "modify.h"
|
#include "modify.h"
|
||||||
#include "neighbor.h"
|
#include "neighbor.h"
|
||||||
#include "neigh_list.h"
|
#include "neigh_list.h"
|
||||||
#include "update.h"
|
|
||||||
#include "utils.h"
|
#include "utils.h"
|
||||||
|
|
||||||
#include <cmath>
|
#include <cmath>
|
||||||
@ -112,7 +111,6 @@ void PairRHEO::compute(int eflag, int vflag)
|
|||||||
int *type = atom->type;
|
int *type = atom->type;
|
||||||
int *status = atom->status;
|
int *status = atom->status;
|
||||||
tagint *tag = atom->tag;
|
tagint *tag = atom->tag;
|
||||||
double fnorm, ftang[3];
|
|
||||||
|
|
||||||
double **fp_store, *chi;
|
double **fp_store, *chi;
|
||||||
if (compute_interface) {
|
if (compute_interface) {
|
||||||
@ -169,7 +167,7 @@ void PairRHEO::compute(int eflag, int vflag)
|
|||||||
rsq = lensq3(dx);
|
rsq = lensq3(dx);
|
||||||
jtype = type[j];
|
jtype = type[j];
|
||||||
|
|
||||||
if (rsq < hsq) {
|
if (rsq < cutksq) {
|
||||||
r = sqrt(rsq);
|
r = sqrt(rsq);
|
||||||
rinv = 1 / r;
|
rinv = 1 / r;
|
||||||
|
|
||||||
@ -219,16 +217,16 @@ void PairRHEO::compute(int eflag, int vflag)
|
|||||||
rhoj = compute_interface->correct_rho(j, i);
|
rhoj = compute_interface->correct_rho(j, i);
|
||||||
Pj = fix_pressure->calc_pressure(rhoj, jtype);
|
Pj = fix_pressure->calc_pressure(rhoj, jtype);
|
||||||
|
|
||||||
if ((chi[j] > 0.9) && (r < (h * 0.5)))
|
if ((chi[j] > 0.9) && (r < (cutk * 0.5)))
|
||||||
fmag = (chi[j] - 0.9) * (h * 0.5 - r) * rho0j * csq_ave * h * rinv;
|
fmag = (chi[j] - 0.9) * (cutk * 0.5 - r) * rho0j * csq_ave * cutk * rinv;
|
||||||
|
|
||||||
} else if ((!fluidi) && fluidj) {
|
} else if ((!fluidi) && fluidj) {
|
||||||
compute_interface->correct_v(vi, vj, i, j);
|
compute_interface->correct_v(vi, vj, i, j);
|
||||||
rhoi = compute_interface->correct_rho(i, j);
|
rhoi = compute_interface->correct_rho(i, j);
|
||||||
Pi = fix_pressure->calc_pressure(rhoi, itype);
|
Pi = fix_pressure->calc_pressure(rhoi, itype);
|
||||||
|
|
||||||
if (chi[i] > 0.9 && r < (h * 0.5))
|
if (chi[i] > 0.9 && r < (cutk * 0.5))
|
||||||
fmag = (chi[i] - 0.9) * (h * 0.5 - r) * rho0i * csq_ave * h * rinv;
|
fmag = (chi[i] - 0.9) * (cutk * 0.5 - r) * rho0i * csq_ave * cutk * rinv;
|
||||||
|
|
||||||
} else if ((!fluidi) && (!fluidj)) {
|
} else if ((!fluidi) && (!fluidj)) {
|
||||||
rhoi = rho0i;
|
rhoi = rho0i;
|
||||||
@ -281,8 +279,8 @@ void PairRHEO::compute(int eflag, int vflag)
|
|||||||
for (b = 0; b < dim; b++)
|
for (b = 0; b < dim; b++)
|
||||||
du[a] -= 0.5 * (gradv[i][a * dim + b] + gradv[j][a * dim + b]) * dx[b];
|
du[a] -= 0.5 * (gradv[i][a * dim + b] + gradv[j][a * dim + b]) * dx[b];
|
||||||
|
|
||||||
mu = dot3(du, dx) * hinv3;
|
mu = dot3(du, dx) * cutkinv3;
|
||||||
mu /= (rsq * hinv3 * hinv3 + EPSILON);
|
mu /= (rsq * cutkinv3 * cutkinv3 + EPSILON);
|
||||||
mu = MIN(0.0, mu);
|
mu = MIN(0.0, mu);
|
||||||
q = av * (-2.0 * cs_ave * mu + mu * mu);
|
q = av * (-2.0 * cs_ave * mu + mu * mu);
|
||||||
fp_prefactor += voli * volj * q * (rhoj + rhoi);
|
fp_prefactor += voli * volj * q * (rhoj + rhoi);
|
||||||
@ -406,17 +404,17 @@ void PairRHEO::settings(int narg, char **arg)
|
|||||||
{
|
{
|
||||||
if (narg < 1) error->all(FLERR, "Illegal pair_style command");
|
if (narg < 1) error->all(FLERR, "Illegal pair_style command");
|
||||||
|
|
||||||
h = utils::numeric(FLERR, arg[0], false, lmp);
|
cutk = utils::numeric(FLERR, arg[0], false, lmp);
|
||||||
|
|
||||||
int iarg = 1;
|
int iarg = 1;
|
||||||
while (iarg < narg) {
|
while (iarg < narg) {
|
||||||
if (strcmp(arg[iarg], "rho/damp") == 0) {
|
if (strcmp(arg[iarg], "rho/damp") == 0) {
|
||||||
if (iarg + 1 >= narg) error->all(FLERR, "Illegal pair_style command");
|
if (iarg + 1 >= narg) utils::missing_cmd_args(FLERR, "pair rheo rho/damp", error);
|
||||||
rho_damp_flag = 1;
|
rho_damp_flag = 1;
|
||||||
rho_damp = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
|
rho_damp = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
|
||||||
iarg++;
|
iarg++;
|
||||||
} else if (strcmp(arg[iarg], "artificial/visc") == 0) {
|
} else if (strcmp(arg[iarg], "artificial/visc") == 0) {
|
||||||
if (iarg + 1 >= narg) error->all(FLERR, "Illegal pair_style command");
|
if (iarg + 1 >= narg) utils::missing_cmd_args(FLERR, "pair rheo artificial/visc", error);
|
||||||
artificial_visc_flag = 1;
|
artificial_visc_flag = 1;
|
||||||
av = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
|
av = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
|
||||||
iarg++;
|
iarg++;
|
||||||
@ -477,12 +475,12 @@ void PairRHEO::setup()
|
|||||||
csq = fix_rheo->csq;
|
csq = fix_rheo->csq;
|
||||||
rho0 = fix_rheo->rho0;
|
rho0 = fix_rheo->rho0;
|
||||||
|
|
||||||
if (h != fix_rheo->h)
|
if (cutk != fix_rheo->cut)
|
||||||
error->all(FLERR, "Pair rheo cutoff {} does not agree with fix rheo cutoff {}", h, fix_rheo->h);
|
error->all(FLERR, "Pair rheo cutoff {} does not agree with fix rheo cutoff {}", cutk, fix_rheo->cut);
|
||||||
|
|
||||||
hsq = h * h;
|
cutksq = cutk * cutk;
|
||||||
hinv = 1.0 / h;
|
cutkinv = 1.0 / cutk;
|
||||||
hinv3 = hinv * 3.0;
|
cutkinv3 = cutkinv * 3.0;
|
||||||
laplacian_order = -1;
|
laplacian_order = -1;
|
||||||
|
|
||||||
int n = atom->ntypes;
|
int n = atom->ntypes;
|
||||||
@ -512,7 +510,7 @@ double PairRHEO::init_one(int i, int j)
|
|||||||
if (setflag[i][j] == 0)
|
if (setflag[i][j] == 0)
|
||||||
error->all(FLERR, "All pair rheo coeffs are not set");
|
error->all(FLERR, "All pair rheo coeffs are not set");
|
||||||
|
|
||||||
return h;
|
return cutk;
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|||||||
@ -37,8 +37,8 @@ class PairRHEO : public Pair {
|
|||||||
void unpack_reverse_comm(int, int *, double *) override;
|
void unpack_reverse_comm(int, int *, double *) override;
|
||||||
|
|
||||||
protected:
|
protected:
|
||||||
double h, *csq, *rho0; // From fix RHEO
|
double cutk, *csq, *rho0; // From fix RHEO
|
||||||
double *cs, hsq, hinv, hinv3, av, rho_damp;
|
double *cs, cutksq, cutkinv, cutkinv3, av, rho_damp;
|
||||||
|
|
||||||
int laplacian_order;
|
int laplacian_order;
|
||||||
int artificial_visc_flag;
|
int artificial_visc_flag;
|
||||||
|
|||||||
Reference in New Issue
Block a user