Draft examples, patches, clarify interface reconstruct in RHEO
This commit is contained in:
jtclemm
@ -134,6 +134,8 @@ Lowercase directories
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+-------------+------------------------------------------------------------------+
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| rerun | use of rerun and read_dump commands |
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+-------------+------------------------------------------------------------------+
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| rheo | RHEO simulations of fluid flows and phase transitions |
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+-------------+------------------------------------------------------------------+
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| rigid | rigid bodies modeled as independent or coupled |
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+-------------+------------------------------------------------------------------+
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| shear | sideways shear applied to 2d solid, with and without a void |
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@ -10,8 +10,12 @@ particles can dynamically change between a fluid and solid state, e.g. during
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melting/solidification, which determines how they interact and their physical
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behavior. The package is designed with modularity in mind, so one can easily
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turn various features on/off, adjust physical details of the system, or
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develop new capabilities. Additional numerical details can be found in
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:ref:`(Palermo) <howto_rheo_palermo>` and :ref:`(Clemmer) <howto_rheo_clemmer>`.
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develop new capabilities. For instance, the numerics associated with
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calculating gradients, reproducing kernels, etc. are separated into distinct
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classes to simplify the development of new integration schemes which can call
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these calculations. Additional numerical details can be found in
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:ref:`(Palermo) <howto_rheo_palermo>` and
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:ref:`(Clemmer) <howto_rheo_clemmer>`.
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----------
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@ -29,12 +33,17 @@ other RHEO fixes.
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Typically, RHEO requires atom style rheo. In addition to typical atom
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properties like positions and forces, particles store a local density,
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viscosity, pressure, and status. If thermal evolution is modeled, one must
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use atom style rheo/thermal which also include a local temperature and
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conductivity. The status variable uses bitmasking to track various
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properties of a particle such as its current state of matter (fluid or solid)
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and its location relative to a surface. Many of these properties (and others)
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can be easily accessed using
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:doc:`compute rheo/property/atom <fix_rheo_property_atom>`.
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use atom style rheo/thermal which also includes a local energy, temperature, and
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conductivity. Note that the temperature is always derived from the energy.
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This implies the *temperature* attribute of :doc:`the set command <set>` does not
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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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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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:doc:`compute rheo/property/atom <fix_rheo_property_atom>`. The *status* attribute
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in :doc:`the set command <set>` only allows control over the first bit which sets
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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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are calculated using :doc:`pair rheo <pair_rheo>`. Unlike typical pair styles,
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@ -61,7 +70,8 @@ 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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melting/solidification temperature allowing particles to dynamically swap their
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state between fluid and solid. Using the *react* option, one can specify a maximum
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state between fluid and solid when the temperature exceeds or drops below the
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critical temperature, respectively. Using the *react* option, one can specify a maximum
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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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in range. For BPM bond styles, bonds will then use the immediate position of the two
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@ -65,7 +65,7 @@ the setup of a run. Data is then preserved across run commands and is
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written to :doc:`binary restart files <restart>` such that restarting
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the system 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 Ref.
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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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.. math::
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@ -16,19 +16,18 @@ Syntax
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.. parsed-literal::
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possible attributes = phase, chi, surface, surface/r,
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possible attributes = phase, surface, surface/r,
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surface/divr, surface/n/x, surface/n/y,
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surface/n/z, coordination, cv, shift/v/x,
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shift/v/y, shift/v/z, energy, temperature, heatflow,
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conductivity, cv, viscosity, pressure,
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status, rho, grad/v/xx, grad/v/xy, grad/v/xz,
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rho, grad/v/xx, grad/v/xy, grad/v/xz,
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grad/v/yx, grad/v/yy/, grad/v/yz, grad/v/zx,
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grad/v/zy, grad/v/zz
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.. parsed-literal::
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*phase* = atom phase state
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*chi* = atom local phase metric
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*surface* = atom surface status
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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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@ -42,7 +41,6 @@ Syntax
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*cv* = atom specific heat
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*viscosity* = atom viscosity
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*pressure* = atom pressure
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*status* = atom full status
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*rho* = atom density
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*grad/v/\** = atom velocity gradient
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*nbond/shell* = number of oxide bonds
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@ -70,14 +68,32 @@ computes as inputs. See for example, the
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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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The possible attributes are described in more detail in other RHEO doc
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pages including :doc:`the RHEO howto page <Howto_rheo>`. Many
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properties require their respective fixes, listed below in related
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commands, be defined.
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Many properties require their respective fixes, listed below in related
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commands, be defined. For instance, the *viscosity* attribute is the
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viscosity of a particle calculated by
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:doc:`fix rheo/viscous <fix_rheo_viscosity>`. The meaning of less obvious
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properties is described below.
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The *phase* property indicates whether the particle is in a fluid state,
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a value of 0, or a solid state, a value of 1.
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The *surface* property indicates the surface designation produced by
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the *interface/reconstruct* option of :doc:`fix rheo <fix_rheo>`. Bulk
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particles have a value of 0, surface particles have a value of 1, and
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splash particles have a value of 2. The *surface/r* property is the
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distance from the surface, up to the kernel cutoff length. Surface particles
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have a value of 0. The *surface/n* properties are the components of the
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surface normal vector.
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The *shift/v* properties are the components of the shifting velocity
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produced by the *shift* option of :doc:`fix rheo <fix_rheo>`.
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The *surface/n/\** and *shift/v/\** attributes are vectors that require
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specification of the *x*, *y*, or *z* component, e.g. *surface/n/x*.
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The *nbond/shell* property is the number of shell bonds that have been
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activated from :doc:`bond style rheo/shell <bond_rheo_shell>`.
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The *grad/v/\** attribute is a tensor and requires specification of
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the *xx*, *yy*, *zz*, *xy*, *xz*, *yx*, *yz*, *zx*, or *zy* component,
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e.g. *grad/v/xy*.
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@ -92,7 +92,8 @@ Shifting is then disabled in the direction away from the free surface to
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prevent it from diffusing particles away from the bulk fluid. Surface
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detection can also be used to control surface-nucleated effects like
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oxidation when used in combination with
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:doc:`fix rheo/oxidation <fix_rheo_oxidation>`.
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:doc:`fix rheo/oxidation <fix_rheo_oxidation>`. Surface detection is not
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performed on solid bodies.
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The *surface/detection* keyword takes three arguments: *sdstyle*, *limit*,
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and *limi/splash*. The first, *sdstyle*, specifies whether surface particles
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@ -35,10 +35,12 @@ for use with bond style :doc:`bond rheo/shell <bond_rheo_shell>`.
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Every timestep, particles check neighbors within a distance of *cut*.
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This distance must be smaller than the kernel length defined in
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:doc:`fix rheo <fix_rheo>`. If both particles are on the fluid surface,
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or within a distance of *rsurf* from the surface, a bond of type
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*btype* is created between the two particles. This process is
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further described in Ref. :ref:`(Clemmer) <howto_rheo_clemmer>`.
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:doc:`fix rheo <fix_rheo>`. Bonds of type *btype* are created between
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pairs of particles that satisfy one of two conditions. First, if both
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particles are on the fluid surface, or within a distance of *rsurf*
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from the surface. Secondly, if one particle is on the fluid surface
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and the other bond is solid. This process is further described in
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:ref:`(Clemmer) <howto_rheo_clemmer>`.
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If used in conjunction with solid bodies, such as those generated
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by the *react* option of :doc:`fix rheo/thermal <fix_rheo_thermal>`,
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@ -55,12 +55,20 @@ rheo/thermal. In addition, it defines multiple thermal properties of
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particles and handles melting/solidification, if applicable. For more details
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on phase transitions in RHEO, see :doc:`the RHEO howto <Howto_rheo>`.
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Note that the temperature of a particle is always derived from the energy.
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This implies the *temperature* attribute of :doc:`the set command <set>` does
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not affect particles. Instead, one should use the *sph/e* attribute.
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For each atom type, one can define attributes for the *conductivity*,
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*specific/heat*, *latent/heat*, and critical temperature (*Tfreeze*).
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The conductivity and specific heat must be defined for all atom types.
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The latent heat and critical temperature are optional. However, a
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critical temperature must be defined to specify a latent heat.
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Note, if shifting is turned on in :doc:`fix rheo <fix_rheo>`, the gradient
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of the energy is used to shift energies. This may be inappropriate in systems
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with multiple atom types with different specific heats.
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For each property, one must first define a list of atom types. A wild-card
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asterisk can be used in place of or in conjunction with the *types* argument
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to set the coefficients for multiple pairs of atom types. This takes the
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@ -717,7 +717,7 @@ of analysis.
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* - rheo
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- atom-ID atom-type status rho x y z
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* - rheo/thermal
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- atom-ID atom-type status rho temperature x y z
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- atom-ID atom-type status rho energy x y z
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* - smd
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- atom-ID atom-type molecule volume mass kradius cradius x0 y0 z0 x y z
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* - sph
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@ -1,87 +0,0 @@
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# ------ 2D dam break ------ #
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dimension 2
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units lj
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atom_style rheo
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boundary f s p
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comm_modify vel yes
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newton off
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comm_style tiled
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# ------ Create simulation box ------ #
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variable sf equal 0.05
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variable n equal 1.0/(${sf}^2)
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variable cut equal 3.0*${sf}
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region box block -1 55 -1 20 -0.01 0.01 units box
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create_box 2 box
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lattice sq ${n}
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region left_wall block -1 0 EDGE EDGE -0.01 0.01 units box
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region right_wall block 53.66 EDGE EDGE EDGE -0.01 0.01 units box
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region bot_wall block 0.01 53.65 -1 0 -0.01 0.01 units box
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region interior block 0.01 10 0.01 20 -0.01 0.01 units box
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create_atoms 1 region interior
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create_atoms 2 region left_wall
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create_atoms 2 region right_wall
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create_atoms 2 region bot_wall
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group fluid type 1
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group static_wall type 2
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group dyn_wall type 3
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group rig union static_wall dyn_wall
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# ------ Model parameters ------ #
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variable rho0 equal 1.0
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variable mp equal ${rho0}/${n}
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variable cs equal 10
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variable zeta equal 1
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variable Dr equal 0.1*${cut}*${cs}
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variable dt_max equal 0.1*${cut}/${cs}/3
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variable g equal 0.0245
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variable fext equal ${g}/${n}
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variable eta equal 0.05
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mass * ${mp}
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variable d0 atom (${rho0}*${g}*(20-y)/${cs}/${cs})+${rho0}
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set group all rheo/rho ${rho0}
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set group fluid rheo/rho v_d0
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set group all rheo/status 0
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set group rig rheo/status 2
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timestep ${dt_max}
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pair_style rheo ${cut} artificial/visc ${zeta} rho/damp ${Dr}
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pair_coeff * *
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# ------ Fixes & computes ------ #
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fix 1 all rheo ${cut} RK1 32 shift surface/detection coordination 26
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fix 2 all rheo/viscosity constant ${eta}
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fix 3 all rheo/pressure linear
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fix 4 rig setforce 0.0 0.0 0.0
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fix 5 fluid addforce 0.0 -${fext} 0.0
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fix 6 all balance 1000 1.1 rcb
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compute 1 all rheo/property/atom rho phase surface
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# ------ Output & Run ------ #
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thermo 10
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thermo_style custom step time ke press
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variable skin equal 0.2*${cut}
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neighbor ${skin} bin
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neigh_modify one 5000
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dump 1 all custom 200 atomDump id type x y vx vy fx fy c_1[*]
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run 400000
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74
examples/rheo/balloon/in.rheo.balloon
Normal file
74
examples/rheo/balloon/in.rheo.balloon
Normal file
@ -0,0 +1,74 @@
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# ------ 2D water balloon ------ #
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dimension 2
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units lj
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atom_style hybrid rheo bond
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boundary m m p
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comm_modify vel yes
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newton off
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region box block -40 40 0 80 -0.01 0.01 units box
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create_box 1 box bond/types 1 extra/bond/per/atom 15 extra/special/per/atom 50
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region fluid sphere -10 40 0 30 units box side in
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lattice hex 1.0
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create_atoms 1 region fluid
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region shell sphere -10 40 0 27 units box side out
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group shell region shell
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set group shell rheo/status 1
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set group all vx 0.005 vy -0.04
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# ------ Model parameters ------#
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variable cut equal 3.0
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variable n equal 1.0
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variable rho0 equal 1.0
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variable cs equal 1.0
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variable mp equal ${rho0}/${n}
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variable zeta equal 0.05
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variable kappa equal 0.01*${rho0}/${mp}
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variable dt_max equal 0.1*${cut}/${cs}/3
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variable eta equal 0.05
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variable Cv equal 1.0
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variable L equal 1.0
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variable Tf equal 1.0
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mass * ${mp}
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timestep 0.1
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pair_style hybrid/overlay rheo ${cut} artificial/visc ${zeta} rheo/solid
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pair_coeff * * rheo
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pair_coeff * * rheo/solid 1.0 1.0 1.0
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special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
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create_bonds many shell shell 1 0 1.5
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special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
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bond_style bpm/spring
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bond_coeff 1 1.0 1.0 1.0
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# A lower critical strain allows the balloon to pop
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#bond_coeff 1 1.0 0.05 1.0
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# ------ Drop balloon ------#
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fix 1 all rheo ${cut} quintic 0 &
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shift &
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surface/detection coordination 22 8
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fix 2 all rheo/viscosity * constant ${eta}
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fix 3 all rheo/pressure * linear
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fix 4 all wall/harmonic ylo EDGE 2.0 1.0 1.0
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compute rho all rheo/property/atom rho
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compute phase all rheo/property/atom phase
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compute nbond all nbond/atom
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# ------ Output & Run ------ #
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thermo 200
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thermo_style custom step time ke press atoms
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dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_nbond c_rho
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run 30000
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81
examples/rheo/dam-break/in.rheo.dam.break
Normal file
81
examples/rheo/dam-break/in.rheo.dam.break
Normal file
@ -0,0 +1,81 @@
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# ------ 2D dam break ------ #
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dimension 2
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units lj
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atom_style rheo
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boundary f f p
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comm_modify vel yes
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newton off
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# ------ Create simulation box ------ #
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variable n equal 1.0
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variable cut equal 3.0
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variable dx equal 4.0
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region box block -1 200 -1 80 -0.1 0.1 units box
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#region box block -1 100 -1 40 -0.1 0.1 units box
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create_box 2 box
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lattice hex ${n}
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region fluid block $(xlo+v_dx) $(xlo+44.0) $(ylo+v_dx) $(yhi-16.0) EDGE EDGE units box
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#region fluid block $(xlo+v_dx) $(xlo+20.0) $(ylo+v_dx) $(yhi-10.0) EDGE EDGE units box
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region walls block $(xlo+v_dx) $(xhi-v_dx) $(ylo+v_dx) $(yhi-v_dx) EDGE EDGE units box side out
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create_atoms 1 region fluid
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create_atoms 2 region walls
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group fluid type 1
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group rig type 2
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# ------ Model parameters ------ #
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variable rho0 equal 1.0
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variable mp equal ${rho0}/${n}
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variable cs equal 1.0
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variable zeta equal 0.05
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variable dt_max equal 0.1*${cut}/${cs}/3
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variable eta equal 0.05
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variable Dr equal 0.05
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mass * ${mp}
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set group all rheo/rho ${rho0}
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set group all rheo/status 0
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set group rig rheo/status 1
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timestep ${dt_max}
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pair_style rheo ${cut} artificial/visc ${zeta} rho/damp ${Dr}
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pair_coeff * *
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# ------ Fixes & computes ------ #
|
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fix 1 all rheo ${cut} quintic 10 &
|
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shift &
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surface/detection coordination 22 8 &
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interface/reconstruct
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#fix 1 all rheo ${cut} RK1 10 surface/detection coordination 36 10 interface/reconstruct shift
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fix 2 all rheo/viscosity * constant ${eta}
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fix 3 all rheo/pressure * linear
|
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fix 4 all gravity 5e-4 vector 0 -1 0
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fix 5 rig setforce 0.0 0.0 0.0
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compute rho all rheo/property/atom rho
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compute phase all rheo/property/atom phase
|
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compute p all rheo/property/atom pressure
|
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compute surf all rheo/property/atom surface
|
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compute sn all rheo/property/atom surface/n/x surface/n/y
|
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compute vshift all rheo/property/atom shift/v/x shift/v/y
|
||||
|
||||
|
||||
# ------ Output & Run ------ #
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step time ke press
|
||||
|
||||
dump 1 all custom 20 atomDump id type x y vx vy fx fy c_rho c_phase c_surf c_p c_vshift[*] c_sn[*]
|
||||
|
||||
#thermo 1
|
||||
run 300000 # 400000
|
||||
80
examples/rheo/ice-cubes/in.rheo.ice.cubes
Normal file
80
examples/rheo/ice-cubes/in.rheo.ice.cubes
Normal file
@ -0,0 +1,80 @@
|
||||
# ------ 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
|
||||
|
||||
region fluid block $(xlo+1) $(xhi-1) $(ylo+1) $(ylo+30) EDGE EDGE units box
|
||||
lattice sq 1.0
|
||||
create_atoms 1 region fluid
|
||||
|
||||
set group all sph/e 8.0
|
||||
|
||||
# ------ 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 zeta equal 0.05
|
||||
variable kappa equal 0.01*${rho0}/${mp}
|
||||
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||
variable eta equal 0.05
|
||||
variable Cv equal 1.0
|
||||
variable L equal 1.0
|
||||
variable Tf equal 1.0
|
||||
|
||||
mass * ${mp}
|
||||
timestep 0.1
|
||||
|
||||
pair_style hybrid/overlay rheo ${cut} artificial/visc ${zeta} 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"
|
||||
|
||||
# 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 2 all rheo/viscosity * constant ${eta}
|
||||
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 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
|
||||
|
||||
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
|
||||
658
examples/rheo/ice-cubes/square.mol
Normal file
658
examples/rheo/ice-cubes/square.mol
Normal file
@ -0,0 +1,658 @@
|
||||
#Made with create_mol.py
|
||||
|
||||
100 atoms
|
||||
342 bonds
|
||||
|
||||
Coords
|
||||
#ID x y z
|
||||
1 -4 -4 0
|
||||
2 -3 -4 0
|
||||
3 -2 -4 0
|
||||
4 -1 -4 0
|
||||
5 0 -4 0
|
||||
6 1 -4 0
|
||||
7 2 -4 0
|
||||
8 3 -4 0
|
||||
9 4 -4 0
|
||||
10 5 -4 0
|
||||
11 -4 -3 0
|
||||
12 -3 -3 0
|
||||
13 -2 -3 0
|
||||
14 -1 -3 0
|
||||
15 0 -3 0
|
||||
16 1 -3 0
|
||||
17 2 -3 0
|
||||
18 3 -3 0
|
||||
19 4 -3 0
|
||||
20 5 -3 0
|
||||
21 -4 -2 0
|
||||
22 -3 -2 0
|
||||
23 -2 -2 0
|
||||
24 -1 -2 0
|
||||
25 0 -2 0
|
||||
26 1 -2 0
|
||||
27 2 -2 0
|
||||
28 3 -2 0
|
||||
29 4 -2 0
|
||||
30 5 -2 0
|
||||
31 -4 -1 0
|
||||
32 -3 -1 0
|
||||
33 -2 -1 0
|
||||
34 -1 -1 0
|
||||
35 0 -1 0
|
||||
36 1 -1 0
|
||||
37 2 -1 0
|
||||
38 3 -1 0
|
||||
39 4 -1 0
|
||||
40 5 -1 0
|
||||
41 -4 0 0
|
||||
42 -3 0 0
|
||||
43 -2 0 0
|
||||
44 -1 0 0
|
||||
45 0 0 0
|
||||
46 1 0 0
|
||||
47 2 0 0
|
||||
48 3 0 0
|
||||
49 4 0 0
|
||||
50 5 0 0
|
||||
51 -4 1 0
|
||||
52 -3 1 0
|
||||
53 -2 1 0
|
||||
54 -1 1 0
|
||||
55 0 1 0
|
||||
56 1 1 0
|
||||
57 2 1 0
|
||||
58 3 1 0
|
||||
59 4 1 0
|
||||
60 5 1 0
|
||||
61 -4 2 0
|
||||
62 -3 2 0
|
||||
63 -2 2 0
|
||||
64 -1 2 0
|
||||
65 0 2 0
|
||||
66 1 2 0
|
||||
67 2 2 0
|
||||
68 3 2 0
|
||||
69 4 2 0
|
||||
70 5 2 0
|
||||
71 -4 3 0
|
||||
72 -3 3 0
|
||||
73 -2 3 0
|
||||
74 -1 3 0
|
||||
75 0 3 0
|
||||
76 1 3 0
|
||||
77 2 3 0
|
||||
78 3 3 0
|
||||
79 4 3 0
|
||||
80 5 3 0
|
||||
81 -4 4 0
|
||||
82 -3 4 0
|
||||
83 -2 4 0
|
||||
84 -1 4 0
|
||||
85 0 4 0
|
||||
86 1 4 0
|
||||
87 2 4 0
|
||||
88 3 4 0
|
||||
89 4 4 0
|
||||
90 5 4 0
|
||||
91 -4 5 0
|
||||
92 -3 5 0
|
||||
93 -2 5 0
|
||||
94 -1 5 0
|
||||
95 0 5 0
|
||||
96 1 5 0
|
||||
97 2 5 0
|
||||
98 3 5 0
|
||||
99 4 5 0
|
||||
100 5 5 0
|
||||
|
||||
Types
|
||||
#ID type
|
||||
1 1
|
||||
2 1
|
||||
3 1
|
||||
4 1
|
||||
5 1
|
||||
6 1
|
||||
7 1
|
||||
8 1
|
||||
9 1
|
||||
10 1
|
||||
11 1
|
||||
12 1
|
||||
13 1
|
||||
14 1
|
||||
15 1
|
||||
16 1
|
||||
17 1
|
||||
18 1
|
||||
19 1
|
||||
20 1
|
||||
21 1
|
||||
22 1
|
||||
23 1
|
||||
24 1
|
||||
25 1
|
||||
26 1
|
||||
27 1
|
||||
28 1
|
||||
29 1
|
||||
30 1
|
||||
31 1
|
||||
32 1
|
||||
33 1
|
||||
34 1
|
||||
35 1
|
||||
36 1
|
||||
37 1
|
||||
38 1
|
||||
39 1
|
||||
40 1
|
||||
41 1
|
||||
42 1
|
||||
43 1
|
||||
44 1
|
||||
45 1
|
||||
46 1
|
||||
47 1
|
||||
48 1
|
||||
49 1
|
||||
50 1
|
||||
51 1
|
||||
52 1
|
||||
53 1
|
||||
54 1
|
||||
55 1
|
||||
56 1
|
||||
57 1
|
||||
58 1
|
||||
59 1
|
||||
60 1
|
||||
61 1
|
||||
62 1
|
||||
63 1
|
||||
64 1
|
||||
65 1
|
||||
66 1
|
||||
67 1
|
||||
68 1
|
||||
69 1
|
||||
70 1
|
||||
71 1
|
||||
72 1
|
||||
73 1
|
||||
74 1
|
||||
75 1
|
||||
76 1
|
||||
77 1
|
||||
78 1
|
||||
79 1
|
||||
80 1
|
||||
81 1
|
||||
82 1
|
||||
83 1
|
||||
84 1
|
||||
85 1
|
||||
86 1
|
||||
87 1
|
||||
88 1
|
||||
89 1
|
||||
90 1
|
||||
91 1
|
||||
92 1
|
||||
93 1
|
||||
94 1
|
||||
95 1
|
||||
96 1
|
||||
97 1
|
||||
98 1
|
||||
99 1
|
||||
100 1
|
||||
|
||||
Masses
|
||||
#ID mass
|
||||
1 1
|
||||
2 1
|
||||
3 1
|
||||
4 1
|
||||
5 1
|
||||
6 1
|
||||
7 1
|
||||
8 1
|
||||
9 1
|
||||
10 1
|
||||
11 1
|
||||
12 1
|
||||
13 1
|
||||
14 1
|
||||
15 1
|
||||
16 1
|
||||
17 1
|
||||
18 1
|
||||
19 1
|
||||
20 1
|
||||
21 1
|
||||
22 1
|
||||
23 1
|
||||
24 1
|
||||
25 1
|
||||
26 1
|
||||
27 1
|
||||
28 1
|
||||
29 1
|
||||
30 1
|
||||
31 1
|
||||
32 1
|
||||
33 1
|
||||
34 1
|
||||
35 1
|
||||
36 1
|
||||
37 1
|
||||
38 1
|
||||
39 1
|
||||
40 1
|
||||
41 1
|
||||
42 1
|
||||
43 1
|
||||
44 1
|
||||
45 1
|
||||
46 1
|
||||
47 1
|
||||
48 1
|
||||
49 1
|
||||
50 1
|
||||
51 1
|
||||
52 1
|
||||
53 1
|
||||
54 1
|
||||
55 1
|
||||
56 1
|
||||
57 1
|
||||
58 1
|
||||
59 1
|
||||
60 1
|
||||
61 1
|
||||
62 1
|
||||
63 1
|
||||
64 1
|
||||
65 1
|
||||
66 1
|
||||
67 1
|
||||
68 1
|
||||
69 1
|
||||
70 1
|
||||
71 1
|
||||
72 1
|
||||
73 1
|
||||
74 1
|
||||
75 1
|
||||
76 1
|
||||
77 1
|
||||
78 1
|
||||
79 1
|
||||
80 1
|
||||
81 1
|
||||
82 1
|
||||
83 1
|
||||
84 1
|
||||
85 1
|
||||
86 1
|
||||
87 1
|
||||
88 1
|
||||
89 1
|
||||
90 1
|
||||
91 1
|
||||
92 1
|
||||
93 1
|
||||
94 1
|
||||
95 1
|
||||
96 1
|
||||
97 1
|
||||
98 1
|
||||
99 1
|
||||
100 1
|
||||
|
||||
Bonds
|
||||
#ID type atom1 atom2
|
||||
1 1 1 2
|
||||
2 1 1 11
|
||||
3 1 1 12
|
||||
4 1 2 3
|
||||
5 1 2 11
|
||||
6 1 2 12
|
||||
7 1 2 13
|
||||
8 1 3 4
|
||||
9 1 3 12
|
||||
10 1 3 13
|
||||
11 1 3 14
|
||||
12 1 4 5
|
||||
13 1 4 13
|
||||
14 1 4 14
|
||||
15 1 4 15
|
||||
16 1 5 6
|
||||
17 1 5 14
|
||||
18 1 5 15
|
||||
19 1 5 16
|
||||
20 1 6 7
|
||||
21 1 6 15
|
||||
22 1 6 16
|
||||
23 1 6 17
|
||||
24 1 7 8
|
||||
25 1 7 16
|
||||
26 1 7 17
|
||||
27 1 7 18
|
||||
28 1 8 9
|
||||
29 1 8 17
|
||||
30 1 8 18
|
||||
31 1 8 19
|
||||
32 1 9 10
|
||||
33 1 9 18
|
||||
34 1 9 19
|
||||
35 1 9 20
|
||||
36 1 10 19
|
||||
37 1 10 20
|
||||
38 1 11 21
|
||||
39 1 11 12
|
||||
40 1 11 22
|
||||
41 1 12 21
|
||||
42 1 12 13
|
||||
43 1 12 22
|
||||
44 1 12 23
|
||||
45 1 13 22
|
||||
46 1 13 23
|
||||
47 1 13 14
|
||||
48 1 13 24
|
||||
49 1 14 23
|
||||
50 1 14 24
|
||||
51 1 14 15
|
||||
52 1 14 25
|
||||
53 1 15 24
|
||||
54 1 15 16
|
||||
55 1 15 25
|
||||
56 1 15 26
|
||||
57 1 16 25
|
||||
58 1 16 26
|
||||
59 1 16 17
|
||||
60 1 16 27
|
||||
61 1 17 26
|
||||
62 1 17 18
|
||||
63 1 17 27
|
||||
64 1 17 28
|
||||
65 1 18 27
|
||||
66 1 18 28
|
||||
67 1 18 19
|
||||
68 1 18 29
|
||||
69 1 19 28
|
||||
70 1 19 29
|
||||
71 1 19 20
|
||||
72 1 19 30
|
||||
73 1 20 29
|
||||
74 1 20 30
|
||||
75 1 21 22
|
||||
76 1 21 31
|
||||
77 1 21 32
|
||||
78 1 22 23
|
||||
79 1 22 31
|
||||
80 1 22 32
|
||||
81 1 22 33
|
||||
82 1 23 24
|
||||
83 1 23 32
|
||||
84 1 23 33
|
||||
85 1 23 34
|
||||
86 1 24 25
|
||||
87 1 24 33
|
||||
88 1 24 34
|
||||
89 1 24 35
|
||||
90 1 25 26
|
||||
91 1 25 34
|
||||
92 1 25 35
|
||||
93 1 25 36
|
||||
94 1 26 27
|
||||
95 1 26 35
|
||||
96 1 26 36
|
||||
97 1 26 37
|
||||
98 1 27 28
|
||||
99 1 27 36
|
||||
100 1 27 37
|
||||
101 1 27 38
|
||||
102 1 28 29
|
||||
103 1 28 37
|
||||
104 1 28 38
|
||||
105 1 28 39
|
||||
106 1 29 30
|
||||
107 1 29 38
|
||||
108 1 29 39
|
||||
109 1 29 40
|
||||
110 1 30 39
|
||||
111 1 30 40
|
||||
112 1 31 32
|
||||
113 1 31 41
|
||||
114 1 31 42
|
||||
115 1 32 33
|
||||
116 1 32 41
|
||||
117 1 32 42
|
||||
118 1 32 43
|
||||
119 1 33 34
|
||||
120 1 33 42
|
||||
121 1 33 43
|
||||
122 1 33 44
|
||||
123 1 34 35
|
||||
124 1 34 43
|
||||
125 1 34 44
|
||||
126 1 34 45
|
||||
127 1 35 36
|
||||
128 1 35 44
|
||||
129 1 35 45
|
||||
130 1 35 46
|
||||
131 1 36 37
|
||||
132 1 36 45
|
||||
133 1 36 46
|
||||
134 1 36 47
|
||||
135 1 37 38
|
||||
136 1 37 46
|
||||
137 1 37 47
|
||||
138 1 37 48
|
||||
139 1 38 39
|
||||
140 1 38 47
|
||||
141 1 38 48
|
||||
142 1 38 49
|
||||
143 1 39 40
|
||||
144 1 39 48
|
||||
145 1 39 49
|
||||
146 1 39 50
|
||||
147 1 40 49
|
||||
148 1 40 50
|
||||
149 1 41 51
|
||||
150 1 41 42
|
||||
151 1 41 52
|
||||
152 1 42 51
|
||||
153 1 42 43
|
||||
154 1 42 52
|
||||
155 1 42 53
|
||||
156 1 43 52
|
||||
157 1 43 53
|
||||
158 1 43 44
|
||||
159 1 43 54
|
||||
160 1 44 53
|
||||
161 1 44 54
|
||||
162 1 44 45
|
||||
163 1 44 55
|
||||
164 1 45 54
|
||||
165 1 45 46
|
||||
166 1 45 55
|
||||
167 1 45 56
|
||||
168 1 46 55
|
||||
169 1 46 56
|
||||
170 1 46 47
|
||||
171 1 46 57
|
||||
172 1 47 56
|
||||
173 1 47 48
|
||||
174 1 47 57
|
||||
175 1 47 58
|
||||
176 1 48 57
|
||||
177 1 48 58
|
||||
178 1 48 49
|
||||
179 1 48 59
|
||||
180 1 49 58
|
||||
181 1 49 59
|
||||
182 1 49 50
|
||||
183 1 49 60
|
||||
184 1 50 59
|
||||
185 1 50 60
|
||||
186 1 51 52
|
||||
187 1 51 61
|
||||
188 1 51 62
|
||||
189 1 52 53
|
||||
190 1 52 61
|
||||
191 1 52 62
|
||||
192 1 52 63
|
||||
193 1 53 54
|
||||
194 1 53 62
|
||||
195 1 53 63
|
||||
196 1 53 64
|
||||
197 1 54 55
|
||||
198 1 54 63
|
||||
199 1 54 64
|
||||
200 1 54 65
|
||||
201 1 55 56
|
||||
202 1 55 64
|
||||
203 1 55 65
|
||||
204 1 55 66
|
||||
205 1 56 57
|
||||
206 1 56 65
|
||||
207 1 56 66
|
||||
208 1 56 67
|
||||
209 1 57 58
|
||||
210 1 57 66
|
||||
211 1 57 67
|
||||
212 1 57 68
|
||||
213 1 58 59
|
||||
214 1 58 67
|
||||
215 1 58 68
|
||||
216 1 58 69
|
||||
217 1 59 60
|
||||
218 1 59 68
|
||||
219 1 59 69
|
||||
220 1 59 70
|
||||
221 1 60 69
|
||||
222 1 60 70
|
||||
223 1 61 71
|
||||
224 1 61 62
|
||||
225 1 61 72
|
||||
226 1 62 71
|
||||
227 1 62 63
|
||||
228 1 62 72
|
||||
229 1 62 73
|
||||
230 1 63 72
|
||||
231 1 63 73
|
||||
232 1 63 64
|
||||
233 1 63 74
|
||||
234 1 64 73
|
||||
235 1 64 74
|
||||
236 1 64 65
|
||||
237 1 64 75
|
||||
238 1 65 74
|
||||
239 1 65 66
|
||||
240 1 65 75
|
||||
241 1 65 76
|
||||
242 1 66 75
|
||||
243 1 66 76
|
||||
244 1 66 67
|
||||
245 1 66 77
|
||||
246 1 67 76
|
||||
247 1 67 68
|
||||
248 1 67 77
|
||||
249 1 67 78
|
||||
250 1 68 77
|
||||
251 1 68 78
|
||||
252 1 68 69
|
||||
253 1 68 79
|
||||
254 1 69 78
|
||||
255 1 69 79
|
||||
256 1 69 70
|
||||
257 1 69 80
|
||||
258 1 70 79
|
||||
259 1 70 80
|
||||
260 1 71 72
|
||||
261 1 71 81
|
||||
262 1 71 82
|
||||
263 1 72 73
|
||||
264 1 72 81
|
||||
265 1 72 82
|
||||
266 1 72 83
|
||||
267 1 73 74
|
||||
268 1 73 82
|
||||
269 1 73 83
|
||||
270 1 73 84
|
||||
271 1 74 75
|
||||
272 1 74 83
|
||||
273 1 74 84
|
||||
274 1 74 85
|
||||
275 1 75 76
|
||||
276 1 75 84
|
||||
277 1 75 85
|
||||
278 1 75 86
|
||||
279 1 76 77
|
||||
280 1 76 85
|
||||
281 1 76 86
|
||||
282 1 76 87
|
||||
283 1 77 78
|
||||
284 1 77 86
|
||||
285 1 77 87
|
||||
286 1 77 88
|
||||
287 1 78 79
|
||||
288 1 78 87
|
||||
289 1 78 88
|
||||
290 1 78 89
|
||||
291 1 79 80
|
||||
292 1 79 88
|
||||
293 1 79 89
|
||||
294 1 79 90
|
||||
295 1 80 89
|
||||
296 1 80 90
|
||||
297 1 81 82
|
||||
298 1 81 91
|
||||
299 1 81 92
|
||||
300 1 82 83
|
||||
301 1 82 91
|
||||
302 1 82 92
|
||||
303 1 82 93
|
||||
304 1 83 84
|
||||
305 1 83 92
|
||||
306 1 83 93
|
||||
307 1 83 94
|
||||
308 1 84 85
|
||||
309 1 84 93
|
||||
310 1 84 94
|
||||
311 1 84 95
|
||||
312 1 85 86
|
||||
313 1 85 94
|
||||
314 1 85 95
|
||||
315 1 85 96
|
||||
316 1 86 87
|
||||
317 1 86 95
|
||||
318 1 86 96
|
||||
319 1 86 97
|
||||
320 1 87 88
|
||||
321 1 87 96
|
||||
322 1 87 97
|
||||
323 1 87 98
|
||||
324 1 88 89
|
||||
325 1 88 97
|
||||
326 1 88 98
|
||||
327 1 88 99
|
||||
328 1 89 90
|
||||
329 1 89 98
|
||||
330 1 89 99
|
||||
331 1 89 100
|
||||
332 1 90 99
|
||||
333 1 90 100
|
||||
334 1 91 92
|
||||
335 1 92 93
|
||||
336 1 93 94
|
||||
337 1 94 95
|
||||
338 1 95 96
|
||||
339 1 96 97
|
||||
340 1 97 98
|
||||
341 1 98 99
|
||||
342 1 99 100
|
||||
102
examples/rheo/oxidation/in.rheo.oxidation
Normal file
102
examples/rheo/oxidation/in.rheo.oxidation
Normal file
@ -0,0 +1,102 @@
|
||||
# ------ 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
|
||||
|
||||
|
||||
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
|
||||
create_atoms 1 region bar
|
||||
create_atoms 3 region floor
|
||||
|
||||
set region rbar type 2
|
||||
group bar type 1 2
|
||||
group rbar type 2
|
||||
group floor type 3
|
||||
|
||||
set group all sph/e 0.0
|
||||
set group all rheo/status 1
|
||||
|
||||
# ------ 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 zeta equal 0.05
|
||||
variable kappa equal 0.1*${rho0}/${mp}
|
||||
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||
variable eta equal 0.05
|
||||
variable Cv equal 1.0
|
||||
variable L equal 0.1
|
||||
variable Tf equal 1.0
|
||||
|
||||
mass * ${mp}
|
||||
timestep 0.1
|
||||
|
||||
pair_style hybrid/overlay rheo ${cut} artificial/visc ${zeta} 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
|
||||
create_bonds many bar bar 1 0 1.5
|
||||
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
|
||||
|
||||
fix 1 all rheo ${cut} quintic 0 &
|
||||
thermal &
|
||||
shift &
|
||||
surface/detection coordination 22 8
|
||||
fix 2 all rheo/viscosity * constant ${eta}
|
||||
fix 3 all rheo/pressure * linear
|
||||
fix 4 all rheo/thermal conductivity * constant ${kappa} &
|
||||
specific/heat * constant ${Cv} &
|
||||
Tfreeze * constant ${Tf} &
|
||||
latent/heat * constant ${L} &
|
||||
react 1.5 1
|
||||
|
||||
fix 5 rbar rheo/oxidation 1.5 2 1.0
|
||||
fix 6 all wall/harmonic ylo EDGE 2.0 1.0 1.0
|
||||
fix 7 all gravity 5e-5 vector 0 -1 0
|
||||
fix 8 floor setforce 0.0 0.0 0.0
|
||||
fix 9 surf add/heat linear 1.1 0.05
|
||||
fix 10 floor add/heat constant 0 overwrite yes # fix the temperature of the floor
|
||||
|
||||
compute surf all rheo/property/atom surface
|
||||
compute rho all rheo/property/atom rho
|
||||
compute phase all rheo/property/atom phase
|
||||
compute status all rheo/property/atom status
|
||||
compute temp all rheo/property/atom temperature
|
||||
compute eng all rheo/property/atom energy
|
||||
compute nbond_shell all rheo/property/atom nbond/shell
|
||||
compute nbond_solid all nbond/atom bond/type 1
|
||||
|
||||
# ------ Output & Run ------ #
|
||||
|
||||
thermo 200
|
||||
thermo_style custom step time ke press atoms
|
||||
|
||||
dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_temp c_eng c_nbond_solid c_nbond_shell c_rho c_surf c_status
|
||||
run 40000
|
||||
@ -9,28 +9,23 @@ comm_modify vel yes
|
||||
|
||||
# ------ Create simulation box ------ #
|
||||
|
||||
variable sf equal 0.2
|
||||
variable n equal 1.0/(${sf}^2)
|
||||
variable cut equal 3.5*${sf}
|
||||
variable n equal 1.0
|
||||
variable cut equal 3.0
|
||||
|
||||
region box block 0 20 -10 10 -0.01 0.01 units box
|
||||
region box block 0 20 -10 10 -0.01 0.01
|
||||
create_box 2 box
|
||||
lattice sq ${n}
|
||||
|
||||
region topwall block INF INF 7 10 INF INF units box
|
||||
region block block INF INF -6.99 6.99 INF INF units box
|
||||
region botwall block INF INF -10 -7 INF INF units box
|
||||
region inner block INF INF -7.5 7.5 INF INF units box
|
||||
region walls block INF INF -7.5 7.5 INF INF units box side out
|
||||
|
||||
create_atoms 2 region topwall
|
||||
create_atoms 2 region botwall
|
||||
create_atoms 1 region block
|
||||
create_atoms 2 region walls
|
||||
create_atoms 1 region inner
|
||||
|
||||
group fluid type 1
|
||||
group rig type 2
|
||||
|
||||
variable dr equal 0.1*${sf}
|
||||
displace_atoms fluid random $(0.1*v_sf) ${dr} 0 135414 units box
|
||||
|
||||
displace_atoms fluid random 0.1 0.1 0 135414 units box
|
||||
|
||||
# ------ Model parameters ------ #
|
||||
|
||||
@ -39,15 +34,19 @@ variable cs equal 1.0
|
||||
variable mp equal ${rho0}/${n}
|
||||
variable zeta equal 1.0
|
||||
variable kappa equal 1.0*${rho0}/${mp}
|
||||
variable fext equal 1e-3/${n}
|
||||
variable eta equal 0.1
|
||||
variable fext equal 1e-4/${n}
|
||||
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||
variable Dr equal 0.05*${cut}*${cs}
|
||||
|
||||
variable eta equal 0.1
|
||||
variable gd0 equal 5e-4
|
||||
variable npow equal 0.5
|
||||
variable K equal 0.001
|
||||
|
||||
mass * ${mp}
|
||||
set group all rheo/rho ${rho0}
|
||||
set group all rheo/status 0
|
||||
set group rig rheo/status 2
|
||||
set group rig rheo/status 1
|
||||
|
||||
timestep ${dt_max}
|
||||
|
||||
@ -58,12 +57,13 @@ pair_coeff * *
|
||||
# ------ Fixes & computes ------ #
|
||||
|
||||
fix 1 all rheo ${cut} quintic 0 shift
|
||||
fix 2 all rheo/viscosity constant ${eta}
|
||||
fix 3 all rheo/pressure linear
|
||||
fix 2 all rheo/viscosity * constant ${eta}
|
||||
#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 ${fext} 0.0 0.0
|
||||
|
||||
compute 1 all rheo/property/atom rho phase
|
||||
compute rho all rheo/property/atom rho
|
||||
|
||||
|
||||
# ------ Output & Run ------ #
|
||||
@ -71,11 +71,7 @@ compute 1 all rheo/property/atom rho phase
|
||||
thermo 200
|
||||
thermo_style custom step time ke press
|
||||
|
||||
variable skin equal 0.2*${cut}
|
||||
neighbor ${skin} bin
|
||||
neigh_modify one 5000
|
||||
|
||||
#dump 1 all custom 200 atomDump id type x y vx vy fx fy c_1[*]
|
||||
dump 1 all custom 200 atomDump id type x y vx vy fx fy c_rho
|
||||
|
||||
run 20000
|
||||
|
||||
@ -10,19 +10,16 @@ newton off
|
||||
|
||||
# ------ Create simulation box ------ #
|
||||
|
||||
variable sf equal 0.1
|
||||
variable n equal 1.0/(${sf}^2)
|
||||
variable cut equal 3.5*${sf}
|
||||
variable n equal 1.0
|
||||
variable cut equal 3.0
|
||||
|
||||
region box block 0 10 0 10 -0.01 0.01 units box
|
||||
region box block 0 40 0 40 -0.01 0.01
|
||||
create_box 1 box
|
||||
lattice sq ${n}
|
||||
|
||||
create_atoms 1 region box
|
||||
|
||||
variable dr equal 0.1*${sf}
|
||||
displace_atoms all random ${dr} ${dr} 0 135414 units box
|
||||
|
||||
displace_atoms all random 0.1 0.1 0 135414 units box
|
||||
|
||||
# ------ Model parameters ------ #
|
||||
|
||||
@ -53,22 +50,17 @@ pair_coeff * *
|
||||
|
||||
# ------ Fixes & computes ------ #
|
||||
|
||||
fix 1 all rheo ${cut} quintic 0 shift
|
||||
fix 2 all rheo/viscosity constant ${eta}
|
||||
fix 3 all rheo/pressure linear
|
||||
|
||||
compute 1 all rheo/property/atom rho phase
|
||||
fix 1 all rheo ${cut} RK1 8 shift
|
||||
fix 2 all rheo/viscosity * constant ${eta}
|
||||
fix 3 all rheo/pressure * linear
|
||||
|
||||
compute rho all rheo/property/atom rho
|
||||
|
||||
# ------ Output & Run ------ #
|
||||
|
||||
thermo 200
|
||||
thermo_style custom step time ke press
|
||||
|
||||
variable skin equal 0.2*${cut}
|
||||
neighbor ${skin} bin
|
||||
neigh_modify one 10000 #increase number of allowed neighbors
|
||||
|
||||
#dump 1 all custom 200 atomDump id type x y vx vy fx fy c_1[*]
|
||||
#dump 1 all custom 200 atomDump id type x y vx vy fx fy c_rho
|
||||
|
||||
run 10000
|
||||
@ -68,7 +68,7 @@ FixAddHeat::FixAddHeat(LAMMPS *lmp, int narg, char **arg) :
|
||||
while (iarg < narg) {
|
||||
if (strcmp(arg[iarg], "overwrite") == 0) {
|
||||
if (iarg + 1 >= narg) utils::missing_cmd_args(FLERR, "fix add/heat", error);
|
||||
overwrite_flag = utils::bnumeric(FLERR, arg[iarg + 1], false, lmp);
|
||||
overwrite_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
|
||||
iarg += 2;
|
||||
} else {
|
||||
error->all(FLERR, "Illegal fix add/heat command, invalid argument {}", arg[iarg]);
|
||||
|
||||
@ -227,7 +227,6 @@ void BondRHEOShell::compute(int eflag, int vflag)
|
||||
if (t < EPSILON || std::isnan(t))
|
||||
t = store_bond(n, i1, i2);
|
||||
|
||||
|
||||
delx = x[i1][0] - x[i2][0];
|
||||
dely = x[i1][1] - x[i2][1];
|
||||
delz = x[i1][2] - x[i2][2];
|
||||
|
||||
@ -213,12 +213,10 @@ void ComputeRHEOGrad::compute_peratom()
|
||||
// Add corrections for walls
|
||||
if (interface_flag) {
|
||||
if (fluidi && (!fluidj)) {
|
||||
compute_interface->correct_v(vi, vj, i, j);
|
||||
//compute_interface->correct_v(vj, vi, j, i);
|
||||
compute_interface->correct_v(vj, vi, j, i);
|
||||
rhoj = compute_interface->correct_rho(j, i);
|
||||
} else if ((!fluidi) && fluidj) {
|
||||
compute_interface->correct_v(vj, vi, j, i);
|
||||
//compute_interface->correct_v(vi, vj, i, j);
|
||||
compute_interface->correct_v(vi, vj, i, j);
|
||||
rhoi = compute_interface->correct_rho(i, j);
|
||||
} else if ((!fluidi) && (!fluidj)) {
|
||||
rhoi = rho0[itype];
|
||||
@ -346,7 +344,7 @@ int ComputeRHEOGrad::pack_forward_comm(int n, int *list, double *buf,
|
||||
} else if (comm_stage == COMMFIELD) {
|
||||
|
||||
if (velocity_flag) {
|
||||
if (remap_v_flag & pbc_flag & (mask[j] & deform_groupbit)) {
|
||||
if (remap_v_flag && pbc_flag && (mask[j] & deform_groupbit)) {
|
||||
for (k = 0; k < dim; k++)
|
||||
buf[m++] = v[j][k] + dv[k];
|
||||
} else {
|
||||
|
||||
@ -165,11 +165,11 @@ void ComputeRHEOInterface::compute_peratom()
|
||||
fluidj = !(status[j] & PHASECHECK);
|
||||
w = compute_kernel->calc_w_quintic(i, j, dx[0], dx[1], dx[2], sqrt(rsq));
|
||||
|
||||
status_match = 0;
|
||||
norm[i] += w;
|
||||
|
||||
status_match = 0;
|
||||
if ((fluidi && fluidj) || ((!fluidi) && (!fluidj)))
|
||||
status_match = 1;
|
||||
|
||||
if (status_match) {
|
||||
chi[i] += w;
|
||||
} else {
|
||||
@ -307,30 +307,26 @@ void ComputeRHEOInterface::unpack_reverse_comm(int n, int *list, double *buf)
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputeRHEOInterface::correct_v(double *vi, double *vj, int i, int j)
|
||||
void ComputeRHEOInterface::correct_v(double *v_solid, double *v_fluid, int i_solid, int i_fluid)
|
||||
{
|
||||
double wall_prefactor, wall_denom, wall_numer;
|
||||
|
||||
wall_numer = 2.0 * cut * (chi[i] - 0.5);
|
||||
if (wall_numer < 0) wall_numer = 0;
|
||||
wall_denom = 2.0 * cut * (chi[j] - 0.5);
|
||||
if (wall_denom < wall_max) wall_denom = wall_max;
|
||||
wall_numer = MAX(2.0 * cut * (chi[i_solid] - 0.5), 0.0);
|
||||
wall_denom = MAX(2.0 * cut * (chi[i_fluid] - 0.5), wall_max);
|
||||
|
||||
wall_prefactor = wall_numer / wall_denom;
|
||||
|
||||
vi[0] = (vi[0] - vj[0]) * wall_prefactor + vi[0];
|
||||
vi[1] = (vi[1] - vj[1]) * wall_prefactor + vi[1];
|
||||
vi[2] = (vi[2] - vj[2]) * wall_prefactor + vi[2];
|
||||
v_solid[0] = (v_solid[0] - v_fluid[0]) * wall_prefactor;
|
||||
v_solid[1] = (v_solid[1] - v_fluid[1]) * wall_prefactor;
|
||||
v_solid[2] = (v_solid[2] - v_fluid[2]) * wall_prefactor;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double ComputeRHEOInterface::correct_rho(int i, int j)
|
||||
double ComputeRHEOInterface::correct_rho(int i_solid, int i_fluid)
|
||||
{
|
||||
// i is wall, j is fluid
|
||||
//In future may depend on atom type j's pressure equation
|
||||
int itype = atom->type[i];
|
||||
return MAX(rho0[itype], atom->rho[i]);
|
||||
int itype = atom->type[i_solid];
|
||||
return MAX(rho0[itype], atom->rho[i_solid]);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -292,9 +292,14 @@ void ComputeRHEOPropertyAtom::pack_surface(int n)
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double label;
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) buf[n] = (status[i] & SURFACECHECK);
|
||||
else buf[n] = 0.0;
|
||||
label = 0;
|
||||
if (mask[i] & groupbit) {
|
||||
if (status[i] & STATUS_SURFACE) label = 1.0;
|
||||
if (status[i] & STATUS_SPLASH) label = 2.0;
|
||||
}
|
||||
buf[n] = label;
|
||||
n += nvalues;
|
||||
}
|
||||
}
|
||||
|
||||
@ -50,23 +50,18 @@ ComputeRHEOSurface::ComputeRHEOSurface(LAMMPS *lmp, int narg, char **arg) :
|
||||
int dim = domain->dimension;
|
||||
comm_forward = 2;
|
||||
comm_reverse = dim * dim + 1;
|
||||
|
||||
nmax_store = 0;
|
||||
grow_arrays(atom->nmax);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
ComputeRHEOSurface::~ComputeRHEOSurface()
|
||||
{
|
||||
// Remove custom property if it exists
|
||||
int tmp1, tmp2, index;
|
||||
index = atom->find_custom("rheo_divr", tmp1, tmp2);
|
||||
if (index != -1) atom->remove_custom(index, 1, 0);
|
||||
|
||||
index = atom->find_custom("rheo_rsurface", tmp1, tmp2);
|
||||
if (index != -1) atom->remove_custom(index, 1, 0);
|
||||
|
||||
index = atom->find_custom("rheo_nsurface", tmp1, tmp2);
|
||||
if (index != -1) atom->remove_custom(index, 1, 3);
|
||||
|
||||
memory->destroy(divr);
|
||||
memory->destroy(rsurface);
|
||||
memory->destroy(nsurface);
|
||||
memory->destroy(B);
|
||||
memory->destroy(gradC);
|
||||
}
|
||||
@ -87,29 +82,6 @@ void ComputeRHEOSurface::init()
|
||||
|
||||
cutsq = cut * cut;
|
||||
|
||||
// Create rsurface, divr, nsurface arrays as custom atom properties,
|
||||
// can print with compute property/atom
|
||||
// no grow callback as there's no reason to copy/exchange data, manually grow
|
||||
// For B and gradC, create a local array since they are unlikely to be printed
|
||||
|
||||
int dim = domain->dimension;
|
||||
int tmp1, tmp2;
|
||||
index_divr = atom->find_custom("rheo_divr", tmp1, tmp2);
|
||||
if (index_divr == -1) index_divr = atom->add_custom("rheo_divr", 1, 0);
|
||||
divr = atom->dvector[index_divr];
|
||||
|
||||
index_rsurf = atom->find_custom("rheo_rsurface", tmp1, tmp2);
|
||||
if (index_rsurf == -1) index_rsurf = atom->add_custom("rheo_rsurface", 1, 0);
|
||||
rsurface = atom->dvector[index_rsurf];
|
||||
|
||||
index_nsurf = atom->find_custom("rheo_nsurface", tmp1, tmp2);
|
||||
if (index_nsurf == -1) index_nsurf = atom->add_custom("rheo_nsurface", 1, dim);
|
||||
nsurface = atom->darray[index_nsurf];
|
||||
|
||||
nmax_store = atom->nmax;
|
||||
memory->create(B, nmax_store, dim * dim, "rheo/surface:B");
|
||||
memory->create(gradC, nmax_store, dim * dim, "rheo/surface:gradC");
|
||||
|
||||
// need an occasional half neighbor list
|
||||
neighbor->add_request(this, NeighConst::REQ_DEFAULT);
|
||||
}
|
||||
@ -148,7 +120,7 @@ void ComputeRHEOSurface::compute_peratom()
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// Grow and zero arrays
|
||||
if (nmax_store <= atom->nmax)
|
||||
if (nmax_store < atom->nmax)
|
||||
grow_arrays(atom->nmax);
|
||||
|
||||
size_t nbytes = nmax_store * sizeof(double);
|
||||
@ -253,6 +225,10 @@ void ComputeRHEOSurface::compute_peratom()
|
||||
else
|
||||
test = coordination[i] < threshold_z;
|
||||
|
||||
// Treat nonfluid particles as bulk
|
||||
if (status[i] & PHASECHECK)
|
||||
test = 0;
|
||||
|
||||
if (test) {
|
||||
if (coordination[i] < threshold_splash)
|
||||
status[i] |= STATUS_SPLASH;
|
||||
@ -272,6 +248,7 @@ void ComputeRHEOSurface::compute_peratom()
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
fluidi = !(status[i] & PHASECHECK);
|
||||
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
@ -280,11 +257,14 @@ void ComputeRHEOSurface::compute_peratom()
|
||||
j = jlist[jj];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
fluidj = !(status[j] & PHASECHECK);
|
||||
|
||||
dx[0] = xtmp - x[j][0];
|
||||
dx[1] = ytmp - x[j][1];
|
||||
dx[2] = ztmp - x[j][2];
|
||||
rsq = lensq3(dx);
|
||||
if (rsq < cutsq) {
|
||||
if (fluidi) {
|
||||
if ((status[i] & STATUS_BULK) && (status[j] & STATUS_SURFACE)) {
|
||||
status[i] &= SURFACEMASK;
|
||||
status[i] |= STATUS_LAYER;
|
||||
@ -292,10 +272,10 @@ void ComputeRHEOSurface::compute_peratom()
|
||||
|
||||
if (status[j] & STATUS_SURFACE)
|
||||
rsurface[i] = MIN(rsurface[i], sqrt(rsq));
|
||||
}
|
||||
|
||||
|
||||
if (j < nlocal || newton) {
|
||||
if ((status[j] & STATUS_BULK) && (status[i] & STATUS_SURFACE)) {
|
||||
if (fluidj && (j < nlocal || newton)) {
|
||||
if ((status[j] & STATUS_BULK) && (status[j] & PHASECHECK) && (status[i] & STATUS_SURFACE)) {
|
||||
status[j] &= SURFACEMASK;
|
||||
status[j] |= STATUS_LAYER;
|
||||
}
|
||||
@ -307,6 +287,16 @@ void ComputeRHEOSurface::compute_peratom()
|
||||
}
|
||||
}
|
||||
|
||||
// clear normal vectors for non surface particles
|
||||
|
||||
for (i = 0; i < nall; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
if (!(status[i] & STATUS_SURFACE))
|
||||
for (a = 0; a < dim; a++)
|
||||
nsurface[i][a] = 0.0;
|
||||
}
|
||||
}
|
||||
|
||||
// forward/reverse status and rsurface
|
||||
comm_stage = 1;
|
||||
comm_reverse = 2;
|
||||
@ -416,18 +406,11 @@ void ComputeRHEOSurface::grow_arrays(int nmax)
|
||||
{
|
||||
int dim = domain->dimension;
|
||||
|
||||
// Grow atom variables and reassign pointers
|
||||
memory->grow(atom->dvector[index_divr], nmax, "atom:rheo_divr");
|
||||
memory->grow(atom->dvector[index_rsurf], nmax, "atom:rheo_rsurface");
|
||||
memory->grow(atom->darray[index_nsurf], nmax, dim, "atom:rheo_nsurface");
|
||||
|
||||
divr = atom->dvector[index_divr];
|
||||
rsurface = atom->dvector[index_rsurf];
|
||||
nsurface = atom->darray[index_nsurf];
|
||||
|
||||
// Grow local variables
|
||||
memory->grow(divr, nmax, "rheo/surface:divr");
|
||||
memory->grow(rsurface, nmax, "rheo/surface:rsurface");
|
||||
memory->grow(nsurface, nmax, dim, "rheo/surface:nsurface");
|
||||
memory->grow(B, nmax, dim * dim, "rheo/surface:B");
|
||||
memory->grow(gradC, nmax, dim * dim, "rheo/surface:gradC");
|
||||
|
||||
nmax_store = atom->nmax;
|
||||
nmax_store = nmax;
|
||||
}
|
||||
|
||||
@ -42,7 +42,6 @@ class ComputeRHEOSurface : public Compute {
|
||||
private:
|
||||
int surface_style, nmax_store, threshold_z, threshold_splash, interface_flag;
|
||||
int threshold_style, comm_stage;
|
||||
int index_divr, index_rsurf, index_nsurf;
|
||||
|
||||
double cut, cutsq, *rho0, threshold_divr;
|
||||
double **B, **gradC;
|
||||
|
||||
@ -72,6 +72,7 @@ void ComputeRHEOVShift::init()
|
||||
compute_interface = fix_rheo->compute_interface;
|
||||
compute_surface = fix_rheo->compute_surface;
|
||||
|
||||
rho0 = fix_rheo->rho0;
|
||||
cut = fix_rheo->cut;
|
||||
cutsq = cut * cut;
|
||||
cutthird = cut / 3.0;
|
||||
@ -174,16 +175,14 @@ void ComputeRHEOVShift::compute_peratom()
|
||||
// Add corrections for walls
|
||||
if (interface_flag) {
|
||||
if (fluidi && (!fluidj)) {
|
||||
compute_interface->correct_v(vi, vj, i, j);
|
||||
//compute_interface->correct_v(vj, vi, j, i);
|
||||
compute_interface->correct_v(vj, vi, j, i);
|
||||
rhoj = compute_interface->correct_rho(j, i);
|
||||
} else if ((!fluidi) && fluidj) {
|
||||
compute_interface->correct_v(vj, vi, j, i);
|
||||
//compute_interface->correct_v(vi, vj, i, j);
|
||||
compute_interface->correct_v(vi, vj, i, j);
|
||||
rhoi = compute_interface->correct_rho(i, j);
|
||||
} else if ((!fluidi) && (!fluidj)) {
|
||||
rhoi = 1.0;
|
||||
rhoj = 1.0;
|
||||
rhoi = rho0[itype];
|
||||
rhoj = rho0[jtype];
|
||||
}
|
||||
}
|
||||
|
||||
@ -196,7 +195,7 @@ void ComputeRHEOVShift::compute_peratom()
|
||||
w4 = w * w * w * w / (w0 * w0 * w0 * w0);
|
||||
dr = -2 * cutthird * (1 + 0.2 * w4) * wp * rinv;
|
||||
|
||||
if (mask[i] & groupbit) {
|
||||
if ((mask[i] & groupbit) && fluidi) {
|
||||
vmag = sqrt(vi[0] * vi[0] + vi[1] * vi[1] + vi[2] * vi[2]);
|
||||
prefactor = vmag * volj * dr;
|
||||
|
||||
@ -206,7 +205,7 @@ void ComputeRHEOVShift::compute_peratom()
|
||||
}
|
||||
|
||||
if (newton_pair || j < nlocal) {
|
||||
if (mask[j] & groupbit) {
|
||||
if ((mask[j] & groupbit) && fluidj) {
|
||||
vmag = sqrt(vj[0] * vj[0] + vj[1] * vj[1] + vj[2] * vj[2]);
|
||||
prefactor = vmag * voli * dr;
|
||||
|
||||
@ -241,7 +240,11 @@ void ComputeRHEOVShift::correct_surfaces()
|
||||
double nx, ny, nz, vx, vy, vz, dot;
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
if ((status[i] & STATUS_SURFACE) || (status[i] & STATUS_LAYER)) {
|
||||
|
||||
if (status[i] & PHASECHECK) continue;
|
||||
|
||||
//if ((status[i] & STATUS_SURFACE) || (status[i] & STATUS_LAYER)) {
|
||||
if (status[i] & STATUS_SURFACE) {
|
||||
nx = nsurface[i][0];
|
||||
ny = nsurface[i][1];
|
||||
vx = vshift[i][0];
|
||||
@ -266,6 +269,10 @@ void ComputeRHEOVShift::correct_surfaces()
|
||||
} else {
|
||||
vshift[i][2] = 0.0;
|
||||
}
|
||||
} else if (status[i] & STATUS_SPLASH) {
|
||||
vshift[i][0] = 0.0;
|
||||
vshift[i][1] = 0.0;
|
||||
vshift[i][2] = 0.0;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@ -43,6 +43,7 @@ class ComputeRHEOVShift : public Compute {
|
||||
int nmax_store;
|
||||
double dtv, cut, cutsq, cutthird;
|
||||
int surface_flag, interface_flag;
|
||||
double *rho0;
|
||||
|
||||
class NeighList *list;
|
||||
class ComputeRHEOInterface *compute_interface;
|
||||
|
||||
@ -125,7 +125,7 @@ FixRHEO::FixRHEO(LAMMPS *lmp, int narg, char **arg) :
|
||||
interface_flag = 1;
|
||||
} else if (strcmp(arg[iarg], "rho/sum") == 0) {
|
||||
rhosum_flag = 1;
|
||||
} else if (strcmp(arg[iarg], "self/mass")) {
|
||||
} else if (strcmp(arg[iarg], "self/mass") == 0) {
|
||||
self_mass_flag = 1;
|
||||
} else if (strcmp(arg[iarg], "density") == 0) {
|
||||
if (iarg + n >= narg) error->all(FLERR, "Illegal rho0 option in fix rheo");
|
||||
@ -145,7 +145,7 @@ FixRHEO::FixRHEO(LAMMPS *lmp, int narg, char **arg) :
|
||||
iarg += 1;
|
||||
}
|
||||
|
||||
if (self_mass_flag && !rhosum_flag)
|
||||
if (self_mass_flag && (!rhosum_flag))
|
||||
error->all(FLERR, "Cannot use self/mass setting without rho/sum");
|
||||
|
||||
if (lmp->citeme) lmp->citeme->add(cite_rheo);
|
||||
@ -227,6 +227,26 @@ void FixRHEO::init()
|
||||
|
||||
if (modify->get_fix_by_style("^rheo$").size() > 1)
|
||||
error->all(FLERR, "Can only specify one instance of fix rheo");
|
||||
|
||||
if (atom->status_flag != 1)
|
||||
error->all(FLERR,"fix rheo command requires atom property status");
|
||||
if (atom->rho_flag != 1)
|
||||
error->all(FLERR,"fix rheo command requires atom property rho");
|
||||
if (atom->pressure_flag != 1)
|
||||
error->all(FLERR,"fix rheo command requires atom property pressure");
|
||||
if (atom->viscosity_flag != 1)
|
||||
error->all(FLERR,"fix rheo command requires atom property viscosity");
|
||||
|
||||
if (thermal_flag) {
|
||||
if (atom->esph_flag != 1)
|
||||
error->all(FLERR,"fix rheo command requires atom property esph with thermal setting");
|
||||
if (atom->temperature_flag != 1)
|
||||
error->all(FLERR,"fix rheo command requires atom property temperature with thermal setting");
|
||||
if (atom->heatflow_flag != 1)
|
||||
error->all(FLERR,"fix rheo command requires atom property heatflow with thermal setting");
|
||||
if (atom->conductivity_flag != 1)
|
||||
error->all(FLERR,"fix rheo command requires atom property conductivity with thermal setting");
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -386,6 +406,7 @@ void FixRHEO::initial_integrate(int /*vflag*/)
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
|
||||
if (status[i] & STATUS_NO_SHIFT) continue;
|
||||
if (status[i] & PHASECHECK) continue;
|
||||
|
||||
if (mask[i] & groupbit) {
|
||||
for (a = 0; a < dim; a++) {
|
||||
|
||||
@ -79,7 +79,7 @@ namespace RHEO_NS {
|
||||
enum Status{
|
||||
// Phase status
|
||||
STATUS_SOLID = 1 << 0,
|
||||
// STATUS_REACTIVE = 1 << 1,
|
||||
// Gap for future phase: STATUS_ = 1 << 1,
|
||||
|
||||
// Surface status
|
||||
STATUS_BULK = 1 << 2,
|
||||
|
||||
@ -30,6 +30,7 @@
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "neigh_request.h"
|
||||
#include "update.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace RHEO_NS;
|
||||
@ -55,6 +56,8 @@ FixRHEOOxidation::FixRHEOOxidation(LAMMPS *lmp, int narg, char **arg) :
|
||||
{
|
||||
if (narg != 6) error->all(FLERR,"Illegal fix command");
|
||||
|
||||
force_reneighbor = 1;
|
||||
next_reneighbor = -1;
|
||||
comm_forward = 3;
|
||||
|
||||
cut = utils::numeric(FLERR, arg[3], false, lmp);
|
||||
@ -82,8 +85,9 @@ FixRHEOOxidation::~FixRHEOOxidation()
|
||||
int FixRHEOOxidation::setmask()
|
||||
{
|
||||
int mask = 0;
|
||||
mask |= PRE_FORCE;
|
||||
mask |= POST_INTEGRATE;
|
||||
mask |= PRE_FORCE;
|
||||
mask |= POST_FORCE;
|
||||
return mask;
|
||||
}
|
||||
|
||||
@ -133,25 +137,19 @@ void FixRHEOOxidation::setup_pre_force(int /*vflag*/)
|
||||
if (!fix_rheo->surface_flag) error->all(FLERR,
|
||||
"fix rheo/oxidation requires surface calculation in fix rheo");
|
||||
compute_surface = fix_rheo->compute_surface;
|
||||
|
||||
pre_force(0);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixRHEOOxidation::pre_force(int /*vflag*/)
|
||||
{
|
||||
int *status = atom->status;
|
||||
for (int i = 0; i < atom->nlocal; i++)
|
||||
if (num_bond[i] != 0)
|
||||
status[i] |= STATUS_NO_SHIFT;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixRHEOOxidation::post_integrate()
|
||||
{
|
||||
int i, j, n, ii, jj, inum, jnum, bflag;
|
||||
int i, j, n, ii, jj, inum, jnum, bflag, fluidi, fluidj;
|
||||
int *ilist, *jlist, *numneigh, **firstneigh;
|
||||
double delx, dely, delz, rsq;
|
||||
tagint tagi, tagj;
|
||||
@ -163,6 +161,8 @@ void FixRHEOOxidation::post_integrate()
|
||||
tagint **bond_atom = atom->bond_atom;
|
||||
int **bond_type = atom->bond_type;
|
||||
int *num_bond = atom->num_bond;
|
||||
int *mask = atom->mask;
|
||||
int *status = atom->status;
|
||||
double *rsurface = compute_surface->rsurface;
|
||||
double **x = atom->x;
|
||||
|
||||
@ -175,10 +175,15 @@ void FixRHEOOxidation::post_integrate()
|
||||
// Note: surface designation lags one timestep, acceptable error
|
||||
comm->forward_comm(this);
|
||||
|
||||
int added_bonds = 0;
|
||||
// loop over neighbors of my atoms
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
if (rsurface[i] > rsurf) continue;
|
||||
if (!(mask[i] & groupbit)) continue;
|
||||
|
||||
// Exclude particles that aren't solid or surface
|
||||
fluidi = !(status[i] & PHASECHECK);
|
||||
if (fluidi && (rsurface[i] > rsurf)) continue;
|
||||
|
||||
tagi = tag[i];
|
||||
|
||||
@ -188,8 +193,13 @@ void FixRHEOOxidation::post_integrate()
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
j &= NEIGHMASK;
|
||||
if (!(mask[j] & groupbit)) continue;
|
||||
|
||||
if (rsurface[j] > rsurf) continue;
|
||||
fluidj = !(status[j] & PHASECHECK);
|
||||
if (fluidj && (rsurface[j] > rsurf)) continue;
|
||||
|
||||
// Skip solid-solid, leaves surface-surface or surface-solid
|
||||
if ((!fluidi) && (!fluidj)) continue;
|
||||
|
||||
tagj = tag[j];
|
||||
|
||||
@ -218,6 +228,8 @@ void FixRHEOOxidation::post_integrate()
|
||||
}
|
||||
if (bflag) continue;
|
||||
|
||||
added_bonds += 1;
|
||||
|
||||
// Add bonds to owned atoms
|
||||
// If newton bond off, add to both, otherwise add to whichever has a smaller tag
|
||||
|
||||
@ -230,6 +242,23 @@ void FixRHEOOxidation::post_integrate()
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
int added_bonds_all;
|
||||
MPI_Allreduce(&added_bonds, &added_bonds_all, 1, MPI_INT, MPI_SUM, world);
|
||||
|
||||
if (added_bonds_all > 0)
|
||||
next_reneighbor = update->ntimestep;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixRHEOOxidation::post_force(int /*vflag*/)
|
||||
{
|
||||
int *status = atom->status;
|
||||
int *num_bond = atom->num_bond;
|
||||
for (int i = 0; i < atom->nlocal; i++)
|
||||
if (num_bond[i] != 0)
|
||||
status[i] |= STATUS_NO_SHIFT;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -34,8 +34,9 @@ class FixRHEOOxidation : public Fix {
|
||||
void init() override;
|
||||
void init_list(int, class NeighList *) override;
|
||||
void setup_pre_force(int) override;
|
||||
void pre_force(int) override;
|
||||
void post_integrate() override;
|
||||
void pre_force(int) override;
|
||||
void post_force(int) override;
|
||||
int pack_forward_comm(int, int *, double *, int, int *) override;
|
||||
void unpack_forward_comm(int, int, double *) override;
|
||||
int *nbond;
|
||||
|
||||
@ -259,7 +259,8 @@ void FixRHEOThermal::init()
|
||||
compute_grad = fix_rheo->compute_grad;
|
||||
compute_vshift = fix_rheo->compute_vshift;
|
||||
|
||||
dtf = 0.5 * update->dt * force->ftm2v;
|
||||
dt = update->dt;
|
||||
dth = 0.5 * update->dt;
|
||||
|
||||
if (atom->esph_flag != 1)
|
||||
error->all(FLERR,"fix rheo/thermal command requires atom property esph");
|
||||
@ -337,7 +338,7 @@ void FixRHEOThermal::initial_integrate(int /*vflag*/)
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
if (status[i] & STATUS_NO_SHIFT) continue;
|
||||
for (a = 0; a < dim; a++)
|
||||
energy[i] += dtv * vshift[i][a] * grade[i][a];
|
||||
energy[i] += dt * vshift[i][a] * grade[i][a];
|
||||
}
|
||||
}
|
||||
|
||||
@ -363,7 +364,7 @@ void FixRHEOThermal::post_integrate()
|
||||
|
||||
itype = type[i];
|
||||
cvi = calc_cv(i, itype);
|
||||
energy[i] += dtf * heatflow[i];
|
||||
energy[i] += dth * heatflow[i];
|
||||
temperature[i] = energy[i] / cvi;
|
||||
|
||||
if (Tc_style[itype] != NONE) {
|
||||
@ -376,6 +377,8 @@ void FixRHEOThermal::post_integrate()
|
||||
temperature[i] = Ti;
|
||||
}
|
||||
|
||||
// Check phase change if Ti != Tci
|
||||
|
||||
if (Ti > Tci) {
|
||||
// If solid, melt
|
||||
if (status[i] & STATUS_SOLID) {
|
||||
@ -383,7 +386,9 @@ void FixRHEOThermal::post_integrate()
|
||||
status[i] |= STATUS_MELTING;
|
||||
n_melt += 1;
|
||||
}
|
||||
} else {
|
||||
}
|
||||
|
||||
if (Ti < Tci) {
|
||||
// If fluid, freeze
|
||||
if (!(status[i] & STATUS_SOLID)) {
|
||||
status[i] &= PHASEMASK;
|
||||
@ -400,6 +405,23 @@ void FixRHEOThermal::post_integrate()
|
||||
MPI_Allreduce(&n_freeze, &n_freeze_all, 1, MPI_INT, MPI_SUM, world);
|
||||
|
||||
if (cut_bond > 0 && (n_melt_all || n_freeze_all)) {
|
||||
|
||||
// If a particle freezes, check if it already has bonds of that type
|
||||
// If so, assume it was inserted as a solid particle
|
||||
// Note: inserted solid particle may still shift one timestep
|
||||
int *num_bond = atom->num_bond;
|
||||
int **bond_type = atom->bond_type;
|
||||
for (i = 0; i < atom->nlocal; i++) {
|
||||
if (status[i] & STATUS_FREEZING) {
|
||||
for (int n = 0; n < num_bond[i]; n++) {
|
||||
if (bond_type[i][n] == btype) {
|
||||
status[i] &= ~STATUS_FREEZING;
|
||||
break;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// Forward status + positions (after inititial integrate, before comm)
|
||||
comm->forward_comm(this);
|
||||
|
||||
@ -464,11 +486,6 @@ void FixRHEOThermal::pre_force(int /*vflag*/)
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// Add temporary options, wiped by preceding fix rheo preforce
|
||||
for (int i = 0; i < nall; i++)
|
||||
if (status[i] & STATUS_SOLID)
|
||||
status[i] |= STATUS_NO_SHIFT;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -482,7 +499,7 @@ void FixRHEOThermal::final_integrate()
|
||||
//Integrate energy
|
||||
for (int i = 0; i < atom->nlocal; i++) {
|
||||
if (status[i] & STATUS_NO_INTEGRATION) continue;
|
||||
energy[i] += dtf * heatflow[i];
|
||||
energy[i] += dth * heatflow[i];
|
||||
}
|
||||
}
|
||||
|
||||
@ -490,8 +507,8 @@ void FixRHEOThermal::final_integrate()
|
||||
|
||||
void FixRHEOThermal::reset_dt()
|
||||
{
|
||||
dtv = update->dt;
|
||||
dtf = 0.5 * update->dt * force->ftm2v;
|
||||
dt = update->dt;
|
||||
dth = 0.5 * update->dt;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -48,7 +48,7 @@ class FixRHEOThermal : public Fix {
|
||||
|
||||
private:
|
||||
double *cv, *Tc, *kappa, *L;
|
||||
double dtf, dtv;
|
||||
double dt, dth;
|
||||
double cut_kernel, cut_bond, cutsq_bond;
|
||||
int *cv_style, *Tc_style, *kappa_style, *L_style;
|
||||
int btype;
|
||||
|
||||
@ -208,14 +208,14 @@ void PairRHEO::compute(int eflag, int vflag)
|
||||
// Add corrections for walls
|
||||
rhoi = rho[i];
|
||||
rhoj = rho[j];
|
||||
rho0i = rho[itype];
|
||||
rho0j = rho[jtype];
|
||||
rho0i = rho0[itype];
|
||||
rho0j = rho0[jtype];
|
||||
Pi = pressure[i];
|
||||
Pj = pressure[j];
|
||||
fmag = 0;
|
||||
if (interface_flag) {
|
||||
if (fluidi && (!fluidj)) {
|
||||
compute_interface->correct_v(vi, vj, i, j);
|
||||
compute_interface->correct_v(vj, vi, j, i);
|
||||
rhoj = compute_interface->correct_rho(j, i);
|
||||
Pj = fix_pressure->calc_pressure(rhoj, jtype);
|
||||
|
||||
@ -223,7 +223,7 @@ void PairRHEO::compute(int eflag, int vflag)
|
||||
fmag = (chi[j] - 0.9) * (h * 0.5 - r) * rho0j * csq_ave * h * rinv;
|
||||
|
||||
} else if ((!fluidi) && fluidj) {
|
||||
compute_interface->correct_v(vj, vi, j, i);
|
||||
compute_interface->correct_v(vi, vj, i, j);
|
||||
rhoi = compute_interface->correct_rho(i, j);
|
||||
Pi = fix_pressure->calc_pressure(rhoi, itype);
|
||||
|
||||
|
||||
Reference in New Issue
Block a user