More doc files, misc clean ups
This commit is contained in:
jtclemm
@ -90,10 +90,10 @@ criteria for creating/deleting a bond or altering force calculations).
|
||||
|
||||
----------
|
||||
|
||||
.. _howto-howto_rheo_palermo:
|
||||
.. _howto_rheo_palermo:
|
||||
|
||||
**(Palermo)** Palermo, Clemmer, Wolf, O'Connor, in preparation.
|
||||
|
||||
.. _howto-howto_rheo_clemmer:
|
||||
.. _howto_rheo_clemmer:
|
||||
|
||||
**(Clemmer)** Clemmer, Pierce, O'Connor, Nevins, Jones, Lechman, Tencer, Appl. Math. Model., 130, 310-326 (2024).
|
||||
|
||||
@ -10,10 +10,13 @@ Syntax
|
||||
|
||||
bond_style rheo/shell keyword value attribute1 attribute2 ...
|
||||
|
||||
* optional keyword = *overlay/pair* or *store/local* or *smooth* or *break*
|
||||
* required keyword = *t/form*
|
||||
* optional keyword = *store/local*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*t/form* value = formation time for a bond (time units)
|
||||
|
||||
*store/local* values = fix_ID N attributes ...
|
||||
* fix_ID = ID of associated internal fix to store data
|
||||
* N = prepare data for output every this many timesteps
|
||||
@ -24,56 +27,56 @@ Syntax
|
||||
*x, y, z* = the center of mass position of the 2 atoms when the bond broke (distance units)
|
||||
*x/ref, y/ref, z/ref* = the initial center of mass position of the 2 atoms (distance units)
|
||||
|
||||
*overlay/pair* value = *yes* or *no*
|
||||
bonded particles will still interact with pair forces
|
||||
|
||||
*smooth* value = *yes* or *no*
|
||||
smooths bond forces near the breaking point
|
||||
|
||||
*normalize* value = *yes* or *no*
|
||||
normalizes bond forces by the reference length
|
||||
|
||||
*break* value = *yes* or *no*
|
||||
indicates whether bonds break during a run
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_style bpm/spring
|
||||
bond_style rheo/shell t/form 10.0
|
||||
bond_coeff 1 1.0 0.05 0.1
|
||||
|
||||
bond_style bpm/spring myfix 1000 time id1 id2
|
||||
dump 1 all local 1000 dump.broken f_myfix[1] f_myfix[2] f_myfix[3]
|
||||
dump_modify 1 write_header no
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
.. versionadded:: 4May2022
|
||||
.. versionadded:: TBD
|
||||
|
||||
The *bpm/spring* bond style computes forces based on
|
||||
deviations from the initial reference state of the two atoms. The
|
||||
reference state is stored by each bond when it is first computed in
|
||||
The *rheo/shell* bond style is designed to work with
|
||||
:doc:`fix rheo/oxidation <fix_rheo_oxidation>` which creates candidate
|
||||
bonds between eligible surface or near-surface particles. When a bond
|
||||
is first created, it computes no forces and starts a timer. Forces are
|
||||
not computed until the timer reaches the specified bond formation time
|
||||
and the bond is fully enabled. If the two particles move outside of the
|
||||
maximum bond distance or move into the bulk before the timer reaches
|
||||
the formation time, the bond automatically deletes itself. Not that
|
||||
this deletion does not generate any broken bond data saved to a
|
||||
*store/local* fix.
|
||||
|
||||
Before bonds are enabled, they are still treated as regular bonds by
|
||||
all other parts of LAMMPS. This means they are written to data files
|
||||
and counted in computes such as :doc:`nbond/atom <compute_nbond_atom>`.
|
||||
To only count enabled bonds, use the *nbond/shell* attribute in
|
||||
:doc:`compute property/atom/rheo <compute_property_atom_rheo>`.
|
||||
|
||||
When enabled, the bond then computes forces based on deviations from
|
||||
the initial reference state of the two atoms much like a BPM style
|
||||
bond (as further discussed in the :doc:`BPM howto page <Howto_bpm>`).
|
||||
The reference state is stored by each bond when it is first enabled
|
||||
the setup of a run. Data is then preserved across run commands and is
|
||||
written to :doc:`binary restart files <restart>` such that restarting
|
||||
the system will not reset the reference state of a bond.
|
||||
the system will not reset the reference state of a bond or the timer.
|
||||
|
||||
This bond style only applies central-body forces which conserve the
|
||||
translational and rotational degrees of freedom of a bonded set of
|
||||
particles based on a model described by Clemmer and Robbins
|
||||
:ref:`(Clemmer) <fragment-Clemmer>`. The force has a magnitude of
|
||||
This bond style is based on a model described in Ref.
|
||||
:ref:`(Clemmer) <howto_rheo_clemmer>`. The force has a magnitude of
|
||||
|
||||
.. math::
|
||||
|
||||
F = k (r - r_0) w
|
||||
F = 2 k (r - r_0) + \frac{2 * k}{r_0^2 \epsilon_c^2} (r - r_0)^3
|
||||
|
||||
where :math:`k` is a stiffness, :math:`r` is the current distance
|
||||
and :math:`r_0` is the initial distance between the two particles, and
|
||||
:math:`w` is an optional smoothing factor discussed below. Bonds will
|
||||
break at a strain of :math:`\epsilon_c`. This is done by setting
|
||||
the bond type to 0 such that forces are no longer computed.
|
||||
:math:`\epsilon_c` is maximum strain beyond which a bond breaks. This
|
||||
is done by setting the bond type to 0 such that forces are no longer
|
||||
computed.
|
||||
|
||||
An additional damping force is applied to the bonded
|
||||
particles. This forces is proportional to the difference in the
|
||||
@ -88,15 +91,6 @@ where :math:`\gamma` is the damping strength, :math:`\hat{r}` is the
|
||||
radial normal vector, and :math:`\vec{v}` is the velocity difference
|
||||
between the two particles.
|
||||
|
||||
The smoothing factor :math:`w` can be added or removed by setting the
|
||||
*smooth* keyword to *yes* or *no*, respectively. It is constructed such
|
||||
that forces smoothly go to zero, avoiding discontinuities, as bonds
|
||||
approach the critical strain
|
||||
|
||||
.. math::
|
||||
|
||||
w = 1.0 - \left( \frac{r - r_0}{r_0 \epsilon_c} \right)^8 .
|
||||
|
||||
The following coefficients must be defined for each bond type via the
|
||||
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
|
||||
the data file or restart files read by the :doc:`read_data
|
||||
@ -106,22 +100,11 @@ the data file or restart files read by the :doc:`read_data
|
||||
* :math:`\epsilon_c` (unit less)
|
||||
* :math:`\gamma` (force/velocity units)
|
||||
|
||||
If the *normalize* keyword is set to *yes*, the elastic bond force will be
|
||||
normalized by :math:`r_0` such that :math:`k` must be given in force units.
|
||||
|
||||
By default, pair forces are not calculated between bonded particles.
|
||||
Pair forces can alternatively be overlaid on top of bond forces by setting
|
||||
the *overlay/pair* keyword to *yes*. These settings require specific
|
||||
:doc:`special_bonds <special_bonds>` settings described in the
|
||||
restrictions. Further details can be found in the :doc:`how to <Howto_bpm>`
|
||||
page on BPMs.
|
||||
|
||||
.. versionadded:: 28Mar2023
|
||||
|
||||
If the *break* keyword is set to *no*, LAMMPS assumes bonds should not break
|
||||
during a simulation run. This will prevent some unnecessary calculation.
|
||||
However, if a bond reaches a strain greater than :math:`\epsilon_c`,
|
||||
it will trigger an error.
|
||||
Unlike other BPM-style bonds, this bond style does not update special
|
||||
bond settings when bonds are created or deleted. This bond style also
|
||||
does not enforce specific :doc:`special_bonds <special_bonds>` settings.
|
||||
This behavior is purposeful such :doc:`RHEO pair forces <pair_rheo>`
|
||||
and heat flows are still calculated.
|
||||
|
||||
If the *store/local* keyword is used, an internal fix will track bonds that
|
||||
break during the simulation. Whenever a bond breaks, data is processed
|
||||
@ -187,39 +170,25 @@ extra quantity can be accessed by the
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
This bond style is part of the BPM package. It is only enabled if
|
||||
This bond style 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.
|
||||
|
||||
By default if pair interactions between bonded atoms are to be disabled,
|
||||
this bond style requires setting
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
special_bonds lj 0 1 1 coul 1 1 1
|
||||
|
||||
and :doc:`newton <newton>` must be set to bond off. If the *overlay/pair*
|
||||
keyword is set to *yes*, this bond style alternatively requires setting
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
special_bonds lj/coul 1 1 1
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`bond_coeff <bond_coeff>`, :doc:`pair bpm/spring <pair_bpm_spring>`
|
||||
:doc:`bond_coeff <bond_coeff>`, :doc:`fix rheo/oxidation <fix_rheo_oxidation>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
The option defaults are *overlay/pair* = *no*, *smooth* = *yes*, *normalize* = *no*, and *break* = *yes*
|
||||
NA
|
||||
|
||||
----------
|
||||
|
||||
.. _fragment-Clemmer:
|
||||
.. _howto_rheo_clemmer:
|
||||
|
||||
**(Clemmer)** Clemmer and Robbins, Phys. Rev. Lett. (2022).
|
||||
**(Clemmer)** Clemmer, Pierce, O'Connor, Nevins, Jones, Lechman, Tencer, Appl. Math. Model., 130, 310-326 (2024).
|
||||
|
||||
.. _Groot4:
|
||||
|
||||
|
||||
@ -27,8 +27,8 @@ Syntax
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*phase* = atom phase status
|
||||
*chi* = atom phase neighborhood metric
|
||||
*phase* = atom phase state
|
||||
*chi* = atom local phase metric
|
||||
*surface* = atom surface status
|
||||
*surface/r* = atom distance from the surface
|
||||
*surface/divr* = divergence of position at atom position
|
||||
@ -45,6 +45,7 @@ Syntax
|
||||
*status* = atom full status
|
||||
*rho* = atom density
|
||||
*grad/v/\** = atom velocity gradient
|
||||
*nbond/shell* = number of oxide bonds
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
@ -52,21 +53,34 @@ Examples
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
compute 1 all rheo/property/atom phase surface/r pressure
|
||||
compute 2 all rheo/property/atom shift/v/x grad/v/xx
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Define a computation that simply stores atom attributes specific to the
|
||||
RHEO package for each atom in the group. This is useful so that the
|
||||
values can be used by other :doc:`output commands <Howto_output>` that
|
||||
take computes as inputs. See for example, the :doc:`compute reduce
|
||||
<compute_reduce>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix
|
||||
ave/histo <fix_ave_histo>`, :doc:`fix ave/chunk <fix_ave_chunk>`,
|
||||
and :doc:`atom-style variable <variable>` commands.
|
||||
.. versionadded:: TBD
|
||||
|
||||
Define a computation that stores atom attributes specific to the RHEO
|
||||
package for each atom in the group. This is useful so that the values
|
||||
can be used by other :doc:`output commands <Howto_output>` that take
|
||||
computes as inputs. See for example, the
|
||||
:doc:`compute reduce <compute_reduce>`,
|
||||
:doc:`fix ave/atom <fix_ave_atom>`,
|
||||
:doc:`fix ave/histo <fix_ave_histo>`,
|
||||
:doc:`fix ave/chunk <fix_ave_chunk>`, and
|
||||
:doc:`atom-style variable <variable>` commands.
|
||||
|
||||
The possible attributes are described in more detail in other RHEO doc
|
||||
pages include :doc:`fix rheo <fix_rheo>`, :doc:`pair rheo <pair_rheo>`,
|
||||
and :doc:`the RHEO howto page <Howto_rheo>`.
|
||||
pages including :doc:`the RHEO howto page <Howto_rheo>`. Many
|
||||
properties require their respective fixes, listed below in related
|
||||
commands, be defined.
|
||||
|
||||
The *surface/n/\** and *shift/v/\** attributes are vectors that require
|
||||
specification of the *x*, *y*, or *z* component, e.g. *surface/n/x*.
|
||||
|
||||
The *grad/v/\** attribute is a tensor and requires specification of
|
||||
the *xx*, *yy*, *zz*, *xy*, *xz*, *yx*, *yz*, *zx*, or *zy* component,
|
||||
e.g. *grad/v/xy*.
|
||||
|
||||
The values are stored in a per-atom vector or array as discussed
|
||||
below. Zeroes are stored for atoms not in the specified group or for
|
||||
@ -98,7 +112,8 @@ Related commands
|
||||
:doc:`fix rheo/viscosity <fix_rheo_viscosity>`,
|
||||
:doc:`fix rheo/pressure <fix_rheo_pressure>`,
|
||||
:doc:`fix rheo/thermal <fix_rheo_thermal>`,
|
||||
:doc:`pair rheo <pair_rheo>`
|
||||
:doc:`fix rheo/oxdiation <fix_rheo_oxidation>`,
|
||||
:doc:`fix rheo <fix_rheo>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
@ -43,6 +43,8 @@ Examples
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
.. versionadded:: TBD
|
||||
|
||||
Perform time integration for RHEO particles, updating positions, velocities,
|
||||
and densities. For a detailed breakdown of the integration timestep and
|
||||
numerical details, see :ref:`(Palermo) <howto_rheo_palermo>`. For an
|
||||
|
||||
@ -8,43 +8,42 @@ Syntax
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
fix ID group-ID rheo/oxidation cut btype
|
||||
fix ID group-ID rheo/oxidation cut btype rsurf
|
||||
|
||||
* ID, group-ID are documented in :doc:`fix <fix>` command
|
||||
* rheo/oxidation = style name of this fix command
|
||||
* cut = maximum bond length (distance units)
|
||||
* btype = type of bonds created
|
||||
* rsurf = distance from surface to create bonds (distance units)
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix 1 all rheo/oxidation 1.5 2
|
||||
fix 1 all rheo/oxidation 1.5 2 0.0
|
||||
fix 1 all rheo/oxidation 1.0 1 2.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
This fix...
|
||||
.. versionadded:: TBD
|
||||
|
||||
Each list consists of a series of type
|
||||
ranges separated by commas. The range can be specified as a
|
||||
single numeric value, or a wildcard asterisk can be used to specify a range
|
||||
of values. This takes the form "\*" or "\*n" or "n\*" or "m\*n". For
|
||||
example, if M = the number of atom types, then an asterisk with no numeric
|
||||
values means all types from 1 to M. A leading asterisk means all types
|
||||
from 1 to n (inclusive). A trailing asterisk means all types from n to M
|
||||
(inclusive). A middle asterisk means all types from m to n (inclusive).
|
||||
Note that all atom types must be included in exactly one of the N collections.
|
||||
This fix dynamically creates bonds on the surface of fluids to
|
||||
represent physical processes such as oxidation. It is intended
|
||||
for use with bond style :doc:`bond rheo/shell <bond_rheo_shell>`.
|
||||
|
||||
While the *Tfreeze* keyword is optional, the *conductivity* and
|
||||
*specific/heat* keywords are mandatory.
|
||||
Every timestep, particles check neighbors within a distance of *cut*.
|
||||
This distance must be smaller than the kernel length defined in
|
||||
:doc:`fix rheo <fix_rheo>`. If both particles are on the fluid surface,
|
||||
or within a distance of *rsurf* from the surface, a bond of type
|
||||
*btype* is created between the two particles. This process is
|
||||
further described in Ref. :ref:`(Clemmer) <howto_rheo_clemmer>`.
|
||||
|
||||
Multiple instances of this fix may be defined to apply different
|
||||
properties to different groups. However, the union of fix groups
|
||||
across all instances of fix rheo/thermal must cover all atoms.
|
||||
If there are multiple instances of this fix, any intersections in
|
||||
the fix groups will lead to incorrect thermal integration.
|
||||
If used in conjunction with solid bodies, such as those generated
|
||||
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>`
|
||||
with different bond types for solid and oxide bonds.
|
||||
|
||||
Restart, fix_modify, output, run start/stop, minimize info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
@ -58,10 +57,8 @@ the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minim
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
This fix must be used with an atom style that includes temperature,
|
||||
heatflow, and conductivity such as atom_tyle rheo/thermal This fix
|
||||
must be used in conjuction with :doc:`fix rheo <fix_rheo>` with the
|
||||
*thermal* setting.
|
||||
This fix must be used with an bond style :doc:`rheo/shell <bond_rheo_shell>`
|
||||
and :doc:`fix rheo <fix_rheo>` with surface detection enabled.
|
||||
|
||||
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.
|
||||
@ -70,12 +67,16 @@ Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`fix rheo <fix_rheo>`,
|
||||
:doc:`fix rheo/viscosity <fix_rheo_viscosity>`,
|
||||
:doc:`fix rheo/pressure <fix_rheo_pressure>`,
|
||||
:doc:`pair rheo <pair_rheo>`,
|
||||
:doc:`bond rheo/shell <bond_rheo_shell>`,
|
||||
:doc:`compute rheo/property/atom <compute_rheo_property_atom>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
||||
----------
|
||||
|
||||
.. _howto_rheo_clemmer:
|
||||
|
||||
**(Clemmer)** Clemmer, Pierce, O'Connor, Nevins, Jones, Lechman, Tencer, Appl. Math. Model., 130, 310-326 (2024).
|
||||
|
||||
@ -33,6 +33,8 @@ Examples
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
.. versionadded:: TBD
|
||||
|
||||
This fix defines a pressure equation of state for RHEO particles. One can
|
||||
define different equations of state for different atom types, but an
|
||||
equation must be specified for every atom type.
|
||||
|
||||
@ -48,6 +48,8 @@ Examples
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
.. versionadded:: TBD
|
||||
|
||||
This fix performs time integration of temperature evolution for atom style
|
||||
rheo/thermal. In addition, it defines multiple thermal properties of
|
||||
particles and handles melting/solidification, if applicable. For more details
|
||||
|
||||
@ -32,6 +32,8 @@ Examples
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
.. versionadded:: TBD
|
||||
|
||||
This fix defines a viscosity for RHEO particles. One can define different
|
||||
viscosities for different atom types, but a viscosity must be specified for
|
||||
every atom type.
|
||||
|
||||
@ -31,6 +31,8 @@ Examples
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
.. versionadded:: TBD
|
||||
|
||||
Pair style *rheo* computes pressure and viscous forces between particles
|
||||
in the :doc:`rheo package <Howto_rheo>`. If thermal evolution is turned
|
||||
on in :doc:`fix rheo <fix_rheo>`, then the pair style also calculates
|
||||
|
||||
@ -1,67 +0,0 @@
|
||||
.. index:: pair_style rheo/react
|
||||
|
||||
pair_style rheo/react command
|
||||
=========================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style rheo/react
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style rheo/react
|
||||
pair_coeff * * 1.0 1.5 1.0 0.05 1.0 100 2.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
pair style...
|
||||
|
||||
The following coefficients must be defined for each pair of atom types
|
||||
via the :doc:`pair_coeff <pair_coeff>` command as in the example above,
|
||||
or in the data file or restart files read by the
|
||||
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
|
||||
commands, or by mixing as described below:
|
||||
|
||||
* :math:`k` (force/distance units)
|
||||
* :math:`r_max` (distance units)
|
||||
* :math:`\epsilon` (unitless)
|
||||
* :math:`\gamma` (force/velocity units)
|
||||
* :math:`t_form` (time units)
|
||||
* :math:`r_from_surface` (distance units)
|
||||
|
||||
----------
|
||||
|
||||
Mixing, shift, table, tail correction, restart, rRESPA info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
This style does not support the :doc:`pair_modify <pair_modify>`
|
||||
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
|
||||
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.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
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.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`fix rheo <fix_rheo>`,
|
||||
:doc:`compute rheo/property/atom <compute_rheo_property_atom>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
@ -21,6 +21,8 @@ Examples
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
.. versionadded:: TBD
|
||||
|
||||
Style *rheo/solid* is effectively a copy of pair style
|
||||
:doc:`bpm/spring <pair_bpm_spring>` except it only applies forces
|
||||
between solid RHEO particles, determined by checking the status of
|
||||
|
||||
@ -57,7 +57,8 @@ ComputeRHEOPropertyAtom::ComputeRHEOPropertyAtom(LAMMPS *lmp, int narg, char **a
|
||||
if (nvalues == 1) size_peratom_cols = 0;
|
||||
else size_peratom_cols = nvalues;
|
||||
|
||||
pressure_flag = thermal_flag = interface_flag = surface_flag = shift_flag = shell_flag = 0;
|
||||
pressure_flag = thermal_flag = interface_flag = 0;
|
||||
surface_flag = shift_flag = shell_flag = 0;
|
||||
|
||||
// parse input values
|
||||
// customize a new keyword by adding to if statement
|
||||
@ -70,32 +71,34 @@ ComputeRHEOPropertyAtom::ComputeRHEOPropertyAtom(LAMMPS *lmp, int narg, char **a
|
||||
for (int iarg = 3; iarg < narg; iarg++) {
|
||||
i = iarg-3;
|
||||
|
||||
if (strcmp(arg[iarg],"phase") == 0) {
|
||||
if (strcmp(arg[iarg], "phase") == 0) {
|
||||
pack_choice[i] = &ComputeRHEOPropertyAtom::pack_phase;
|
||||
} else if (strcmp(arg[iarg],"rho") == 0) {
|
||||
} else if (strcmp(arg[iarg], "rho") == 0) {
|
||||
pack_choice[i] = &ComputeRHEOPropertyAtom::pack_rho;
|
||||
} else if (strcmp(arg[iarg],"chi") == 0) {
|
||||
} else if (strcmp(arg[iarg], "chi") == 0) {
|
||||
interface_flag = 1;
|
||||
pack_choice[i] = &ComputeRHEOPropertyAtom::pack_chi;
|
||||
} else if (strcmp(arg[iarg],"surface") == 0) {
|
||||
} else if (strcmp(arg[iarg], "surface") == 0) {
|
||||
surface_flag = 1;
|
||||
pack_choice[i] = &ComputeRHEOPropertyAtom::pack_surface;
|
||||
} else if (strcmp(arg[iarg],"surface/r") == 0) {
|
||||
} else if (strcmp(arg[iarg], "surface/r") == 0) {
|
||||
surface_flag = 1;
|
||||
pack_choice[i] = &ComputeRHEOPropertyAtom::pack_surface_r;
|
||||
} else if (strcmp(arg[iarg],"surface/divr") == 0) {
|
||||
} else if (strcmp(arg[iarg], "surface/divr") == 0) {
|
||||
surface_flag = 1;
|
||||
pack_choice[i] = &ComputeRHEOPropertyAtom::pack_surface_divr;
|
||||
} else if (utils::strmatch(arg[iarg], "^surface/n")) {
|
||||
surface_flag = 1;
|
||||
pack_choice[i] = &ComputeRHEOPropertyAtom::pack_surface_n;
|
||||
col_index[i] = get_vector_index(arg[iarg]);
|
||||
} else if (strcmp(arg[iarg],"coordination") == 0) {
|
||||
} else if (strcmp(arg[iarg], "coordination") == 0) {
|
||||
pack_choice[i] = &ComputeRHEOPropertyAtom::pack_coordination;
|
||||
} else if (strcmp(arg[iarg],"pressure") == 0) {
|
||||
} else if (strcmp(arg[iarg], "pressure") == 0) {
|
||||
pressure_flag = 1;
|
||||
pack_choice[i] = &ComputeRHEOPropertyAtom::pack_pressure;
|
||||
} else if (strcmp(arg[iarg],"cv") == 0) {
|
||||
} else if (strcmp(arg[iarg], "viscosity") == 0) {
|
||||
pack_choice[i] = &ComputeRHEOPropertyAtom::pack_viscosity;
|
||||
} else if (strcmp(arg[iarg], "cv") == 0) {
|
||||
thermal_flag = 1;
|
||||
pack_choice[i] = &ComputeRHEOPropertyAtom::pack_cv;
|
||||
} else if (utils::strmatch(arg[iarg], "^shift/v")) {
|
||||
@ -113,7 +116,7 @@ ComputeRHEOPropertyAtom::ComputeRHEOPropertyAtom(LAMMPS *lmp, int narg, char **a
|
||||
arg[iarg], atom->get_style());
|
||||
pack_choice[i] = &ComputeRHEOPropertyAtom::pack_atom_style;
|
||||
thermal_flag = 1;
|
||||
} else if (strcmp(arg[iarg],"nbond/shell") == 0) {
|
||||
} else if (strcmp(arg[iarg], "nbond/shell") == 0) {
|
||||
shell_flag = 1;
|
||||
pack_choice[i] = &ComputeRHEOPropertyAtom::pack_nbond_shell;
|
||||
} else {
|
||||
@ -124,9 +127,9 @@ ComputeRHEOPropertyAtom::ComputeRHEOPropertyAtom(LAMMPS *lmp, int narg, char **a
|
||||
arg[iarg], atom->get_style());
|
||||
pack_choice[i] = &ComputeRHEOPropertyAtom::pack_atom_style;
|
||||
|
||||
if (strcmp(arg[iarg],"temperature") == 0) thermal_flag = 1;
|
||||
if (strcmp(arg[iarg],"heatflow") == 0) thermal_flag = 1;
|
||||
if (strcmp(arg[iarg],"conductivity") == 0) thermal_flag = 1;
|
||||
if (strcmp(arg[iarg], "temperature") == 0) thermal_flag = 1;
|
||||
if (strcmp(arg[iarg], "heatflow") == 0) thermal_flag = 1;
|
||||
if (strcmp(arg[iarg], "conductivity") == 0) thermal_flag = 1;
|
||||
}
|
||||
}
|
||||
|
||||
@ -149,7 +152,7 @@ ComputeRHEOPropertyAtom::~ComputeRHEOPropertyAtom()
|
||||
void ComputeRHEOPropertyAtom::init()
|
||||
{
|
||||
auto fixes = modify->get_fix_by_style("^rheo$");
|
||||
if (fixes.size() == 0) error->all(FLERR, "Need to define fix rheo to use fix rheo/viscosity");
|
||||
if (fixes.size() == 0) error->all(FLERR, "Need to define fix rheo to use compute rheo/property/atom");
|
||||
fix_rheo = dynamic_cast<FixRHEO *>(fixes[0]);
|
||||
|
||||
if (interface_flag && !(fix_rheo->interface_flag))
|
||||
@ -390,6 +393,21 @@ void ComputeRHEOPropertyAtom::pack_pressure(int n)
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputeRHEOPropertyAtom::pack_viscosity(int n)
|
||||
{
|
||||
int *mask = atom->mask;
|
||||
double *viscosity = atom->viscosity;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) buf[n] = viscosity[i];
|
||||
else buf[n] = 0.0;
|
||||
n += nvalues;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputeRHEOPropertyAtom::pack_nbond_shell(int n)
|
||||
{
|
||||
int *nbond = fix_oxidation->nbond;
|
||||
@ -490,11 +508,11 @@ int ComputeRHEOPropertyAtom::get_tensor_index(char* option)
|
||||
int ComputeRHEOPropertyAtom::get_vector_index(char* option)
|
||||
{
|
||||
int index;
|
||||
if (utils::strmatch(option,"x$")) {
|
||||
if (utils::strmatch(option, "x$")) {
|
||||
index = 0;
|
||||
} else if (utils::strmatch(option,"y$")) {
|
||||
} else if (utils::strmatch(option, "y$")) {
|
||||
index = 1;
|
||||
} else if (utils::strmatch(option,"z$")) {
|
||||
} else if (utils::strmatch(option, "z$")) {
|
||||
if (domain->dimension == 2)
|
||||
error->all(FLERR, "Invalid compute rheo/property/atom property {} in 2D", option);
|
||||
index = 2;
|
||||
|
||||
@ -35,7 +35,8 @@ class ComputeRHEOPropertyAtom : public Compute {
|
||||
|
||||
private:
|
||||
int nvalues, nmax;
|
||||
int pressure_flag, thermal_flag, interface_flag, surface_flag, shift_flag, shell_flag;
|
||||
int pressure_flag, thermal_flag, interface_flag;
|
||||
int surface_flag, shift_flag, shell_flag;
|
||||
int *avec_index;
|
||||
int *col_index;
|
||||
double *buf;
|
||||
@ -55,6 +56,7 @@ class ComputeRHEOPropertyAtom : public Compute {
|
||||
void pack_shift_v(int);
|
||||
void pack_gradv(int);
|
||||
void pack_pressure(int);
|
||||
void pack_viscosity(int);
|
||||
void pack_nbond_shell(int);
|
||||
void pack_atom_style(int);
|
||||
|
||||
|
||||
@ -19,6 +19,7 @@
|
||||
#include "fix_rheo.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "citeme.h"
|
||||
#include "compute_rheo_grad.h"
|
||||
#include "compute_rheo_interface.h"
|
||||
#include "compute_rheo_surface.h"
|
||||
@ -37,6 +38,9 @@ using namespace LAMMPS_NS;
|
||||
using namespace RHEO_NS;
|
||||
using namespace FixConst;
|
||||
|
||||
static const char cite_rheo[] =
|
||||
"TBD\n\n";
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixRHEO::FixRHEO(LAMMPS *lmp, int narg, char **arg) :
|
||||
@ -137,6 +141,8 @@ FixRHEO::FixRHEO(LAMMPS *lmp, int narg, char **arg) :
|
||||
}
|
||||
iarg += 1;
|
||||
}
|
||||
|
||||
if (lmp->citeme) lmp->citeme->add(cite_rheo);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -20,6 +20,7 @@
|
||||
|
||||
#include "atom.h"
|
||||
#include "atom_vec.h"
|
||||
#include "citeme.h"
|
||||
#include "compute_rheo_surface.h"
|
||||
#include "error.h"
|
||||
#include "fix_rheo.h"
|
||||
@ -34,6 +35,18 @@ using namespace RHEO_NS;
|
||||
using namespace FixConst;
|
||||
enum {NONE, CONSTANT};
|
||||
|
||||
static const char cite_rheo_oxide[] =
|
||||
"@article{ApplMathModel.130.310,\n"
|
||||
" title = {A hybrid smoothed-particle hydrodynamics model of oxide skins on molten aluminum},\n"
|
||||
" journal = {Applied Mathematical Modelling},\n"
|
||||
" volume = {130},\n"
|
||||
" pages = {310-326},\n"
|
||||
" year = {2024},\n"
|
||||
" issn = {0307-904X},\n"
|
||||
" doi = {https://doi.org/10.1016/j.apm.2024.02.027},\n"
|
||||
" 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},\n"
|
||||
"}\n\n";
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixRHEOOxidation::FixRHEOOxidation(LAMMPS *lmp, int narg, char **arg) :
|
||||
@ -51,6 +64,8 @@ FixRHEOOxidation::FixRHEOOxidation(LAMMPS *lmp, int narg, char **arg) :
|
||||
if (rsurf <= 0.0) error->all(FLERR, "Illegal surface distance {} in fix rheo/oxidation", cut);
|
||||
|
||||
cutsq = cut * cut;
|
||||
|
||||
if (lmp->citeme) lmp->citeme->add(cite_rheo_oxide);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -1,137 +0,0 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing authors: Joel Clemmer (SNL)
|
||||
----------------------------------------------------------------------- */
|
||||
|
||||
#include "fix_rheo_stress.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "compute.h"
|
||||
#include "domain.h"
|
||||
#include "fix_store_atom.h"
|
||||
#include "group.h"
|
||||
#include "error.h"
|
||||
#include "modify.h"
|
||||
#include "update.h"
|
||||
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixRHEOStress::FixRHEOStress(LAMMPS *lmp, int narg, char **arg) :
|
||||
id_compute(nullptr), id_fix(nullptr), stress_compute(nullptr), store_fix(nullptr), Fix(lmp, narg, arg)
|
||||
{
|
||||
if (narg != 3) error->all(FLERR,"Illegal fix rheo/stress command");
|
||||
comm_forward = 6;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixRHEOStress::~FixRHEOStress()
|
||||
{
|
||||
modify->delete_compute(id_compute);
|
||||
modify->delete_fix(id_fix);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixRHEOStress::post_constructor()
|
||||
{
|
||||
id_fix = utils::strdup(std::string(id) + "_store");
|
||||
store_fix = dynamic_cast<FixStoreAtom *>(modify->add_fix(fmt::format("{} {} STORE/ATOM d_pxx d_pyy d_pzz d_pxy d_pxz d_pyz", id_fix, group->names[igroup])));
|
||||
array_atom = store_fix->astore;
|
||||
|
||||
id_compute = utils::strdup(std::string(id) + "_compute");
|
||||
stress_compute = modify->add_compute(fmt::format("{} {} stress/atom NULL ke pair bond", id_compute, group->names[igroup]));
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixRHEOStress::setmask()
|
||||
{
|
||||
int mask = 0;
|
||||
mask |= PRE_FORCE;
|
||||
mask |= END_OF_STEP;
|
||||
return mask;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixRHEOStress::init()
|
||||
{
|
||||
stress_compute->addstep(update->ntimestep+1);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixRHEOStress::pre_force(int vflag)
|
||||
{
|
||||
// add pre-force and forward to ghosts (not done in store/atom)
|
||||
comm->forward_comm(this);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixRHEOStress::end_of_step()
|
||||
{
|
||||
stress_compute->compute_peratom();
|
||||
|
||||
// copy compute to fix property atom
|
||||
double **saved_stress = store_fix->astore;
|
||||
double **stress = stress_compute->array_atom;
|
||||
|
||||
int ntotal = atom->nlocal+atom->nghost;
|
||||
for (int i = 0; i < ntotal; i++)
|
||||
for (int a = 0; a < 6; a++)
|
||||
saved_stress[i][a] = stress[i][a];
|
||||
|
||||
stress_compute->addstep(update->ntimestep + 1);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixRHEOStress::pack_forward_comm(int n, int *list, double *buf,
|
||||
int /*pbc_flag*/, int * /*pbc*/)
|
||||
{
|
||||
int i, j, a, m;
|
||||
double **saved_stress = store_fix->astore;
|
||||
|
||||
m = 0;
|
||||
for (i = 0; i < n; i++) {
|
||||
j = list[i];
|
||||
for (a = 0; a < 6; a++)
|
||||
buf[m++] = saved_stress[j][a];
|
||||
}
|
||||
return m;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixRHEOStress::unpack_forward_comm(int n, int first, double *buf)
|
||||
{
|
||||
int i, a, m, last;
|
||||
double **saved_stress = store_fix->astore;
|
||||
|
||||
m = 0;
|
||||
last = first + n;
|
||||
for (i = first; i < last; i++)
|
||||
for (a = 0; a < 6; a++)
|
||||
saved_stress[i][a] = buf[m++];
|
||||
}
|
||||
@ -1,48 +0,0 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
// clang-format off
|
||||
FixStyle(rheo/stress,FixRHEOStress);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_RHEO_STRESS_H
|
||||
#define LMP_FIX_RHEO_STRESS_H
|
||||
|
||||
#include "fix.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixRHEOStress : public Fix {
|
||||
public:
|
||||
FixRHEOStress(class LAMMPS *, int, char **);
|
||||
~FixRHEOStress() override;
|
||||
void post_constructor() override;
|
||||
int setmask() override;
|
||||
void init() override;
|
||||
void pre_force(int) override;
|
||||
void end_of_step() override;
|
||||
int pack_forward_comm(int, int *, double *, int, int *) override;
|
||||
void unpack_forward_comm(int, int, double *) override;
|
||||
|
||||
private:
|
||||
char *id_compute, *id_fix;
|
||||
class Compute *stress_compute;
|
||||
class FixStoreAtom *store_fix;
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
@ -20,6 +20,7 @@
|
||||
|
||||
#include "atom.h"
|
||||
#include "atom_vec.h"
|
||||
#include "citeme.h"
|
||||
#include "comm.h"
|
||||
#include "compute_rheo_grad.h"
|
||||
#include "compute_rheo_vshift.h"
|
||||
@ -43,6 +44,18 @@ using namespace RHEO_NS;
|
||||
using namespace FixConst;
|
||||
enum {NONE, CONSTANT};
|
||||
|
||||
static const char cite_rheo_oxide[] =
|
||||
"@article{ApplMathModel.130.310,\n"
|
||||
" title = {A hybrid smoothed-particle hydrodynamics model of oxide skins on molten aluminum},\n"
|
||||
" journal = {Applied Mathematical Modelling},\n"
|
||||
" volume = {130},\n"
|
||||
" pages = {310-326},\n"
|
||||
" year = {2024},\n"
|
||||
" issn = {0307-904X},\n"
|
||||
" doi = {https://doi.org/10.1016/j.apm.2024.02.027},\n"
|
||||
" 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},\n"
|
||||
"}\n\n";
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixRHEOThermal::FixRHEOThermal(LAMMPS *lmp, int narg, char **arg) :
|
||||
@ -193,6 +206,8 @@ FixRHEOThermal::FixRHEOThermal(LAMMPS *lmp, int narg, char **arg) :
|
||||
if (Tc_style[i] == NONE && L_style[i] != NONE)
|
||||
error->all(FLERR, "Must specify critical temperature for atom type {} to use latent heat in fix rheo/thermal", i);
|
||||
}
|
||||
|
||||
if (lmp->citeme) lmp->citeme->add(cite_rheo_oxide);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -1,515 +0,0 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing authors:
|
||||
Joel Clemmer (SNL)
|
||||
----------------------------------------------------------------------- */
|
||||
|
||||
#include "pair_rheo_react.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "compute_rheo_surface.h"
|
||||
#include "error.h"
|
||||
#include "fix.h"
|
||||
#include "fix_dummy.h"
|
||||
#include "fix_neigh_history.h"
|
||||
#include "fix_rheo.h"
|
||||
#include "force.h"
|
||||
#include "memory.h"
|
||||
#include "modify.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "neigh_request.h"
|
||||
#include "update.h"
|
||||
#include "utils.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace RHEO_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairRHEOReact::PairRHEOReact(LAMMPS *lmp) : Pair(lmp),
|
||||
dbond(NULL)
|
||||
{
|
||||
single_enable = 0;
|
||||
size_history = 2;
|
||||
beyond_contact = 1;
|
||||
comm_reverse = 1;
|
||||
nondefault_history_transfer = 1;
|
||||
|
||||
// create dummy fix as placeholder for FixNeighHistory
|
||||
// this is so final order of Modify:fix will conform to input script
|
||||
|
||||
fix_history = nullptr;
|
||||
fix_dummy = dynamic_cast<FixDummy *>(
|
||||
modify->add_fix("NEIGH_HISTORY_RHEO_REACT_DUMMY" + std::to_string(instance_me) + " all DUMMY"));
|
||||
|
||||
// For nbond, create an instance of fix property atom
|
||||
// Need restarts + exchanging with neighbors since it needs to persist
|
||||
// between timesteps (fix property atom will handle callbacks)
|
||||
|
||||
int tmp1, tmp2;
|
||||
index_nb = atom->find_custom("react_nbond", tmp1, tmp2);
|
||||
if (index_nb == -1) {
|
||||
id_fix = utils::strdup("pair_rheo_react_fix_property_atom");
|
||||
modify->add_fix(fmt::format("{} all property/atom i_react_nbond", id_fix));
|
||||
index_nb = atom->find_custom("react_nbond", tmp1, tmp2);
|
||||
}
|
||||
nbond = atom->ivector[index_nb];
|
||||
|
||||
//Store non-persistent per atom quantities, intermediate
|
||||
|
||||
nmax_store = atom->nmax;
|
||||
memory->create(dbond, nmax_store, "rheo/react:dbond");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairRHEOReact::~PairRHEOReact()
|
||||
{
|
||||
if (modify->nfix && fix_history) modify->delete_fix("NEIGH_HISTORY_RHEO_REACT" + std::to_string(instance_me));
|
||||
if (modify->nfix && fix_dummy) modify->delete_fix("NEIGH_HISTORY_RHEO_REACT_DUMMY" + std::to_string(instance_me));
|
||||
if (modify->nfix) modify->delete_fix(id_fix);
|
||||
delete[] id_fix;
|
||||
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(cutsq);
|
||||
memory->destroy(cutbsq);
|
||||
|
||||
memory->destroy(cutbond);
|
||||
memory->destroy(k);
|
||||
memory->destroy(eps);
|
||||
memory->destroy(gamma);
|
||||
memory->destroy(t_form);
|
||||
memory->destroy(rlimit);
|
||||
}
|
||||
|
||||
memory->destroy(dbond);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairRHEOReact::compute(int eflag, int vflag)
|
||||
{
|
||||
int i, j, ii, jj, inum, jnum, fluidi, fluidj;
|
||||
double xtmp, ytmp, ztmp, delx, dely, delz;
|
||||
double vxtmp, vytmp, vztmp, delvx, delvy, delvz;
|
||||
double rsq, r, rinv, r0, fpair, dot, smooth;
|
||||
int itype, jtype;
|
||||
|
||||
int *ilist, *jlist, *numneigh, **firstneigh;
|
||||
int *saved, **firstsaved;
|
||||
double *data, *alldata, **firstdata;
|
||||
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
int bondupdate = 1;
|
||||
if (update->setupflag) bondupdate = 0;
|
||||
double dt = update->dt;
|
||||
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
int *type = atom->type;
|
||||
int *status = atom->status;
|
||||
int *mask = atom->mask;
|
||||
int *nbond = atom->ivector[index_nb];
|
||||
double *rsurf = compute_surface->rsurface;
|
||||
|
||||
int nlocal = atom->nlocal;
|
||||
int newton_pair = force->newton_pair;
|
||||
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
firstsaved = fix_history->firstflag;
|
||||
firstdata = fix_history->firstvalue;
|
||||
|
||||
if (atom->nmax > nmax_store){
|
||||
nmax_store = atom->nmax;
|
||||
memory->destroy(dbond);
|
||||
memory->create(dbond, nmax_store, "rheo/react:dbond");
|
||||
}
|
||||
|
||||
size_t nbytes = nmax_store * sizeof(int);
|
||||
memset(&dbond[0], 0, nbytes);
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
itype = type[i];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
vxtmp = v[i][0];
|
||||
vytmp = v[i][1];
|
||||
vztmp = v[i][2];
|
||||
fluidi = !(status[i] & PHASECHECK);
|
||||
|
||||
saved = firstsaved[i];
|
||||
alldata = firstdata[i];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
j &= NEIGHMASK;
|
||||
jtype = type[j];
|
||||
fluidj = !(status[j] & PHASECHECK);
|
||||
data = &alldata[2*jj];
|
||||
|
||||
// If not bonded and there's an internal fluid particle, unsave any data and skip
|
||||
if (!(saved[jj] == 1 && data[0] > 0)) {
|
||||
if ((fluidi && (rsurf[i] > rlimit[itype][jtype])) || (fluidj && (rsurf[j] > rlimit[itype][jtype]))) {
|
||||
saved[jj] = 0;
|
||||
continue;
|
||||
}
|
||||
}
|
||||
|
||||
// If both are solid, unbond and skip
|
||||
if (!fluidi && !fluidj) {
|
||||
//If bonded, deincrement
|
||||
if (saved[jj] == 1 && data[0] > 0) {
|
||||
dbond[i] --;
|
||||
dbond[j] --;
|
||||
}
|
||||
saved[jj] = 0;
|
||||
continue;
|
||||
}
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx * delx + dely * dely + delz * delz;
|
||||
|
||||
// If unbonded and beyond bond distance, unsave and skip
|
||||
if (data[0] == -1 && rsq > cutbsq[itype][jtype]) {
|
||||
saved[jj] = 0;
|
||||
continue;
|
||||
}
|
||||
|
||||
r = sqrt(rsq);
|
||||
// Initialize data if not currently saved since all could bond if they are on the surface
|
||||
if (saved[jj] == 0) {
|
||||
data[0] = -1;
|
||||
data[1] = 0;
|
||||
saved[jj] = 1;
|
||||
}
|
||||
|
||||
// Check for bond formation (unbonded) or breakage (bonded)
|
||||
if (data[0] == -1) {
|
||||
// If unbonded, check if we count down to bonding if both on surface (not given for r or s)
|
||||
if (bondupdate && (rsurf[i] <= rlimit[itype][jtype]) && (rsurf[j] <= rlimit[itype][jtype])) {
|
||||
data[1] += dt;
|
||||
if (data[1] >= t_form[itype][jtype]) {
|
||||
data[0] = r;
|
||||
dbond[i] ++;
|
||||
dbond[j] ++;
|
||||
data[1] = 0;
|
||||
}
|
||||
}
|
||||
} else {
|
||||
// If bonded, check if breaks in tension
|
||||
r0 = data[0];
|
||||
if (r > ((1.0 + eps[itype][jtype]) * r0)) {
|
||||
saved[jj] = 0;
|
||||
dbond[i] --;
|
||||
dbond[j] --;
|
||||
data[0] = -1;
|
||||
}
|
||||
}
|
||||
|
||||
// Skip if unbonded
|
||||
if (data[0] <= 0) continue;
|
||||
|
||||
delvx = vxtmp - v[j][0];
|
||||
delvy = vytmp - v[j][1];
|
||||
delvz = vztmp - v[j][2];
|
||||
rinv = 1.0 / r;
|
||||
r0 = data[0];
|
||||
|
||||
fpair = k[itype][jtype] * (r0 - r);
|
||||
|
||||
dot = delx * delvx + dely * delvy + delz * delvz;
|
||||
fpair -= gamma[itype][jtype] * dot * rinv;
|
||||
|
||||
smooth = 1.0;
|
||||
if (r > r0) {
|
||||
smooth = (r - r0) / (r0 * eps[itype][jtype]);
|
||||
smooth *= smooth;
|
||||
smooth *= smooth;
|
||||
smooth = 1 - smooth;
|
||||
}
|
||||
|
||||
fpair *= rinv * smooth;
|
||||
|
||||
f[i][0] += delx * fpair;
|
||||
f[i][1] += dely * fpair;
|
||||
f[i][2] += delz * fpair;
|
||||
if (newton_pair || j < nlocal) {
|
||||
f[j][0] -= delx * fpair;
|
||||
f[j][1] -= dely * fpair;
|
||||
f[j][2] -= delz * fpair;
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i, j, nlocal, newton_pair, 0.0, 0.0, fpair, delx, dely, delz);
|
||||
}
|
||||
}
|
||||
|
||||
// Communicate changes in nbond
|
||||
if (newton_pair) comm->reverse_comm(this);
|
||||
|
||||
for(i = 0; i < nlocal; i++) {
|
||||
fluidi = !(status[i] & PHASECHECK);
|
||||
nbond[i] += dbond[i];
|
||||
|
||||
// If it has bonds it is reactive (no shifting)
|
||||
// If a reactive particle breaks all bonds, return to fluid
|
||||
// Keep it non-shifting for this timestep to be safe
|
||||
if (nbond[i] != 0 && fluidi) status[i] |= STATUS_NO_SHIFT;
|
||||
}
|
||||
|
||||
if (vflag_fdotr) virial_fdotr_compute();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairRHEOReact::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->ntypes;
|
||||
|
||||
memory->create(setflag, n + 1, n + 1, "pair:setflag");
|
||||
for (int i = 1; i <= n; i++)
|
||||
for (int j = i; j <= n; j++)
|
||||
setflag[i][j] = 0;
|
||||
|
||||
memory->create(cutbond, n + 1, n + 1, "pair:cutbond");
|
||||
memory->create(cutbsq, n + 1, n + 1, "pair:cutbsq");
|
||||
memory->create(cutsq, n + 1, n + 1, "pair:cutsq");
|
||||
memory->create(k, n + 1, n + 1, "pair:k");
|
||||
memory->create(eps, n + 1, n + 1, "pair:eps");
|
||||
memory->create(gamma, n + 1, n + 1, "pair:gamma");
|
||||
memory->create(t_form, n + 1, n + 1, "pair:t_form");
|
||||
memory->create(rlimit, n + 1, n + 1, "pair:rlimit");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairRHEOReact::settings(int narg, char **arg)
|
||||
{
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairRHEOReact::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 9) error->all(FLERR, "Incorrect args for pair coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo, ihi, jlo, jhi;
|
||||
utils::bounds(FLERR, arg[0], 1, atom->ntypes, ilo, ihi,error);
|
||||
utils::bounds(FLERR, arg[1], 1, atom->ntypes, jlo, jhi,error);
|
||||
|
||||
double k_one = utils::numeric(FLERR, arg[2], false, lmp);
|
||||
double cutb_one = utils::numeric(FLERR, arg[3], false, lmp);
|
||||
double eps_one = utils::numeric(FLERR, arg[4], false, lmp);
|
||||
double gamma_one = utils::numeric(FLERR, arg[5], false, lmp);
|
||||
double t_form_one = utils::numeric(FLERR, arg[6], false, lmp);
|
||||
double rlimit_one = utils::numeric(FLERR, arg[7], false, lmp);
|
||||
|
||||
if (k_one < 0.0 || eps_one < 0.0 || t_form_one < 0.0)
|
||||
error->all(FLERR, "Illegal pair_style command");
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
||||
k[i][j] = k_one;
|
||||
cutbond[i][j] = cutb_one;
|
||||
eps[i][j] = eps_one;
|
||||
gamma[i][j] = gamma_one;
|
||||
t_form[i][j] = t_form_one;
|
||||
rlimit[i][j] = rlimit_one;
|
||||
setflag[i][j] = 1;
|
||||
count++;
|
||||
}
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init specific to this pair style
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairRHEOReact::init_style()
|
||||
{
|
||||
int irequest = neighbor->request(this, instance_me);
|
||||
//neighbor->requests[irequest]->history = 1;
|
||||
|
||||
if (fix_history == nullptr) {
|
||||
auto cmd = fmt::format("NEIGH_HISTORY_RHEO_REACT{} all NEIGH_HISTORY {}", instance_me, size_history);
|
||||
fix_history = dynamic_cast<FixNeighHistory *>(
|
||||
modify->replace_fix("NEIGH_HISTORY_RHEO_REACT_DUMMY" + std::to_string(instance_me), cmd, 1));
|
||||
fix_history->pair = this;
|
||||
fix_dummy = nullptr;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
setup specific to this pair style
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairRHEOReact::setup()
|
||||
{
|
||||
auto fixes = modify->get_fix_by_style("^rheo$");
|
||||
if (fixes.size() == 0) error->all(FLERR, "Need to define fix rheo to use fix rheo/tension");
|
||||
fix_rheo = dynamic_cast<FixRHEO *>(fixes[0]);
|
||||
|
||||
if (!fix_rheo->surface_flag) error->all(FLERR,
|
||||
"Pair rheo/react requires surface calculation in fix rheo");
|
||||
|
||||
compute_surface = fix_rheo->compute_surface;
|
||||
|
||||
if (force->newton_pair == 0) error->all(FLERR,
|
||||
"Pair rheo/react needs newton pair on for bond changes to be consistent");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairRHEOReact::init_one(int i, int j)
|
||||
{
|
||||
if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set");
|
||||
|
||||
cutbsq[i][j] = cutbond[i][j] * cutbond[i][j];
|
||||
|
||||
cutbsq[j][i] = cutbsq[i][j];
|
||||
cutbond[j][i] = cutbond[i][j];
|
||||
k[j][i] = k[i][j];
|
||||
eps[j][i] = eps[i][j];
|
||||
gamma[j][i] = gamma[i][j];
|
||||
t_form[j][i] = t_form[i][j];
|
||||
rlimit[j][i] = rlimit[i][j];
|
||||
|
||||
double cut = cutbond[i][j] * (1.0 + eps[i][j]);
|
||||
|
||||
return cut;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairRHEOReact::write_restart(FILE *fp)
|
||||
{
|
||||
write_restart_settings(fp);
|
||||
|
||||
int i,j;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i; j <= atom->ntypes; j++)
|
||||
fwrite(&setflag[i][j], sizeof(int), 1, fp);
|
||||
if (setflag[i][j]) {
|
||||
fwrite(&k[i][j], sizeof(double), 1, fp);
|
||||
fwrite(&cutbond[i][j], sizeof(double), 1, fp);
|
||||
fwrite(&eps[i][j], sizeof(double), 1, fp);
|
||||
fwrite(&gamma[i][j], sizeof(double), 1, fp);
|
||||
fwrite(&t_form[i][j], sizeof(double), 1, fp);
|
||||
fwrite(&rlimit[i][j], sizeof(double), 1, fp);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairRHEOReact::read_restart(FILE *fp)
|
||||
{
|
||||
read_restart_settings(fp);
|
||||
allocate();
|
||||
|
||||
int i,j;
|
||||
int me = comm->me;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i; j <= atom->ntypes; j++) {
|
||||
if (me == 0) utils::sfread(FLERR, &setflag[i][j], sizeof(int), 1, fp, nullptr, error);
|
||||
MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world);
|
||||
if (setflag[i][j]) {
|
||||
if (me == 0) {
|
||||
utils::sfread(FLERR, &k[i][j], sizeof(double), 1, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &cutbond[i][j], sizeof(double), 1, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &eps[i][j], sizeof(double), 1, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &gamma[i][j], sizeof(double), 1, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &t_form[i][j], sizeof(double), 1, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &rlimit[i][j], sizeof(double), 1, fp, nullptr, error);
|
||||
}
|
||||
MPI_Bcast(&k[i][j], 1,MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&cutbond[i][j], 1,MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&eps[i][j], 1,MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&gamma[i][j], 1,MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&t_form[i][j], 1,MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&rlimit[i][j], 1,MPI_DOUBLE, 0, world);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
transfer history during fix/neigh/history exchange - transfer same sign
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairRHEOReact::transfer_history(double* source, double* target)
|
||||
{
|
||||
for (int i = 0; i < size_history; i++)
|
||||
target[i] = source[i];
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int PairRHEOReact::pack_reverse_comm(int n, int first, double *buf)
|
||||
{
|
||||
int i, m, last;
|
||||
m = 0;
|
||||
last = first + n;
|
||||
|
||||
for (i = first; i < last; i++) {
|
||||
buf[m++] = dbond[i];
|
||||
}
|
||||
return m;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairRHEOReact::unpack_reverse_comm(int n, int *list, double *buf)
|
||||
{
|
||||
int i, j, m;
|
||||
|
||||
m = 0;
|
||||
for (i = 0; i < n; i++) {
|
||||
j = list[i];
|
||||
dbond[j] += buf[m++];
|
||||
}
|
||||
}
|
||||
@ -1,63 +0,0 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
// clang-format off
|
||||
PairStyle(rheo/react,PairRHEOReact)
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_RHEO_REACT_H
|
||||
#define LMP_PAIR_RHEO_REACT_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairRHEOReact : public Pair {
|
||||
public:
|
||||
PairRHEOReact(class LAMMPS *);
|
||||
~PairRHEOReact() override;
|
||||
void compute(int, int) override;
|
||||
void settings(int, char **) override;
|
||||
void coeff(int, char **) override;
|
||||
void init_style() override;
|
||||
void setup() override;
|
||||
double init_one(int, int) override;
|
||||
void write_restart(FILE *) override;
|
||||
void read_restart(FILE *) override;
|
||||
int pack_reverse_comm(int, int, double *) override;
|
||||
void unpack_reverse_comm(int, int *, double *) override;
|
||||
|
||||
protected:
|
||||
double **cutbond, **cutbsq, **k, **eps, **gamma, **t_form, **rlimit;
|
||||
|
||||
void allocate();
|
||||
void transfer_history(double*, double*);
|
||||
|
||||
int size_history;
|
||||
int *dbond, *nbond;
|
||||
|
||||
int index_nb, nmax_store;
|
||||
char *id_fix;
|
||||
|
||||
class FixDummy *fix_dummy;
|
||||
class FixNeighHistory *fix_history;
|
||||
class FixRHEO *fix_rheo;
|
||||
class ComputeRHEOSurface *compute_surface;
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
Reference in New Issue
Block a user