Merge branch 'develop' into collected-small-changes
This commit is contained in:
Axel Kohlmeyer
@ -877,6 +877,9 @@ Bibliography
|
||||
**(PLUMED)**
|
||||
G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
|
||||
|
||||
**(Pavlov)**
|
||||
D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Journal of High Performance Computing Applications, 38, 34-49 (2024).
|
||||
|
||||
**(Paquay)**
|
||||
Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at `arXiv:1411.3019 <https://arxiv.org/abs/1411.3019/>`_.
|
||||
|
||||
|
||||
@ -263,6 +263,7 @@ OPT.
|
||||
* :doc:`wall/body/polyhedron <fix_wall_body_polyhedron>`
|
||||
* :doc:`wall/colloid <fix_wall>`
|
||||
* :doc:`wall/ees <fix_wall_ees>`
|
||||
* :doc:`wall/flow (k) <fix_wall_flow>`
|
||||
* :doc:`wall/gran (k) <fix_wall_gran>`
|
||||
* :doc:`wall/gran/region <fix_wall_gran_region>`
|
||||
* :doc:`wall/harmonic <fix_wall>`
|
||||
|
||||
@ -256,6 +256,7 @@ OPT.
|
||||
* :doc:`rann <pair_rann>`
|
||||
* :doc:`reaxff (ko) <pair_reaxff>`
|
||||
* :doc:`rebo (io) <pair_airebo>`
|
||||
* :doc:`rebomos (o) <pair_rebomos>`
|
||||
* :doc:`resquared (go) <pair_resquared>`
|
||||
* :doc:`saip/metal (t) <pair_saip_metal>`
|
||||
* :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`
|
||||
|
||||
@ -428,6 +428,7 @@ accelerated styles exist.
|
||||
* :doc:`wall/body/polyhedron <fix_wall_body_polyhedron>` - time integration for body particles of style :doc:`rounded/polyhedron <Howto_body>`
|
||||
* :doc:`wall/colloid <fix_wall>` - Lennard-Jones wall interacting with finite-size particles
|
||||
* :doc:`wall/ees <fix_wall_ees>` - wall for ellipsoidal particles
|
||||
* :doc:`wall/flow <fix_wall_flow>` - flow boundary conditions
|
||||
* :doc:`wall/gran <fix_wall_gran>` - frictional wall(s) for granular simulations
|
||||
* :doc:`wall/gran/region <fix_wall_gran_region>` - :doc:`fix wall/region <fix_wall_region>` equivalent for use with granular particles
|
||||
* :doc:`wall/harmonic <fix_wall>` - harmonic spring wall
|
||||
|
||||
175
doc/src/fix_wall_flow.rst
Normal file
175
doc/src/fix_wall_flow.rst
Normal file
@ -0,0 +1,175 @@
|
||||
.. index:: fix wall/flow
|
||||
.. index:: fix wall/flow/kk
|
||||
|
||||
fix wall/flow command
|
||||
=====================
|
||||
|
||||
Accelerator Variants: *wall/flow/kk*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix ID group-ID wall/flow axis vflow T seed N coords ... keyword value
|
||||
|
||||
* ID, group-ID are documented in :doc:`fix <fix>` command
|
||||
* wall/flow = style name of this fix command
|
||||
* axis = flow axis (*x*, *y*, or *z*)
|
||||
* vflow = generated flow velocity in *axis* direction (velocity units)
|
||||
* T = flow temperature (temperature units)
|
||||
* seed = random seed for stochasticity (positive integer)
|
||||
* N = number of walls
|
||||
* coords = list of N wall positions along the *axis* direction in ascending order (distance units)
|
||||
* zero or more keyword/value pairs may be appended
|
||||
* keyword = *units*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*units* value = *lattice* or *box*
|
||||
*lattice* = wall positions are defined in lattice units
|
||||
*box* = the wall positions are defined in simulation box units
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix 1 all wall/flow x 0.4 1.5 593894 4 2.0 4.0 6.0 8.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
.. versionadded:: TBD
|
||||
|
||||
This fix implements flow boundary conditions (FBC) introduced in
|
||||
:ref:`(Pavlov1) <fbc-Pavlov1>` and :ref:`(Pavlov2) <fbc-Pavlov2>`.
|
||||
The goal is to generate a stationary flow with a shifted Maxwell
|
||||
velocity distribution:
|
||||
|
||||
.. math::
|
||||
|
||||
f_a(v_a) \propto \exp{\left(-\frac{m (v_a-v_{\text{flow}})^2}{2 kB T}\right)}
|
||||
|
||||
where :math:`v_a` is the component of velocity along the specified
|
||||
*axis* argument (a = x,y,z), :math:`v_{\text{flow}}` is the flow
|
||||
velocity specified as the *vflow* argument, *T* is the specified flow
|
||||
temperature, *m* is the particle mass, and *kB* is the Boltzmann
|
||||
constant.
|
||||
|
||||
This is achieved by defining a series of *N* transparent walls along
|
||||
the flow *axis* direction. Each wall is at the specified position
|
||||
listed in the *coords* argument. Note that an additional transparent
|
||||
wall is defined by the code at the boundary of the (periodic)
|
||||
simulation domain in the *axis* direction. So there are effectively
|
||||
N+1 walls.
|
||||
|
||||
Each time a particle in the specified group passes through one of the
|
||||
transparent walls, its velocity is re-assigned. Particles not in the
|
||||
group do not interact with the wall. This can be used, for example, to
|
||||
add obstacles composed of atoms, or to simulate a solution of complex
|
||||
molecules in a one-atom liquid (note that the fix has been tested for
|
||||
one-atom systems only).
|
||||
|
||||
Conceptually, the velocity re-assignment represents creation of a new
|
||||
particle within the system with simultaneous removal of the particle
|
||||
which passed through the wall. The velocity components in directions
|
||||
parallel to the wall are re-assigned according to the standard Maxwell
|
||||
velocity distribution for the specified temperature *T*. The velocity
|
||||
component perpendicular to the wall is re-assigned according to the
|
||||
shifted Maxwell distribution defined above:
|
||||
|
||||
.. math::
|
||||
|
||||
f_{\text{a generated}}(v_a) \propto v_a f_a(v_a)
|
||||
|
||||
It can be shown that for an ideal-gas scenario this procedure makes
|
||||
the velocity distribution of particles between walls exactly as
|
||||
desired.
|
||||
|
||||
Since in most cases simulated systems are not an ideal gas, multiple
|
||||
walls can be defined, since a single wall may not be sufficient for
|
||||
maintaining a stationary flow without "congestion" which can manifest
|
||||
itself as regions in the flow with increased particle density located
|
||||
upstream from static obstacles.
|
||||
|
||||
For the same reason, the actual temperature and velocity of the
|
||||
generated flow may differ from what is requested. The degree of
|
||||
discrepancy is determined by how different from an ideal gas the
|
||||
simulated system is. Therefore, a calibration procedure may be
|
||||
required for such a system as described in :ref:`(Pavlov)
|
||||
<fbc-Pavlov2>`.
|
||||
|
||||
Note that the interactions between particles on different sides of a
|
||||
transparent wall are not disabled or neglected. Likewise particle
|
||||
positions are not altered by the velocity reassignment. This removes
|
||||
the need to modify the force field to work correctly in cases when a
|
||||
particle is close to a wall.
|
||||
|
||||
For example, if particle positions were uniformly redistributed across
|
||||
the surface of a wall, two particles could end up too close to each
|
||||
other, potentially causing the simulation to explode. However due to
|
||||
this compromise, some collective phenomena such as regions with
|
||||
increased/decreased density or collective movements are not fully
|
||||
removed when particles cross a wall. This unwanted consequence can
|
||||
also be potentially mitigated by using more multiple walls.
|
||||
|
||||
.. note::
|
||||
|
||||
When the specified flow has a high velocity, a lost atoms error can
|
||||
occur (see :doc:`error messages <Errors_messages>`). If this
|
||||
happens, you should ensure the checks for neighbor list rebuilds,
|
||||
set via the :doc:`neigh_modify <neigh_modify>` command, are as
|
||||
conservative as possible (every timestep if needed). Those are the
|
||||
default settings.
|
||||
|
||||
Restart, fix_modify, output, run start/stop, minimize info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
No information about this fix is written to :doc:`binary restart files
|
||||
<restart>`.
|
||||
|
||||
None of the :doc:`fix_modify <fix_modify>` options are relevant to
|
||||
this fix.
|
||||
|
||||
No global or per-atom quantities are stored by this fix for access by
|
||||
various :doc:`output commands <Howto_output>`.
|
||||
|
||||
No parameter of this fix can be used with the *start/stop* keywords of
|
||||
the :doc:`run <run>` command.
|
||||
|
||||
This fix is not invoked during :doc:`energy minimization <minimize>`.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
Fix *wall_flow* is part of the EXTRA-FIX package. It is only enabled
|
||||
if LAMMPS was built with that package. See the :doc:`Build package
|
||||
<Build_package>` page for more info.
|
||||
|
||||
Flow boundary conditions should not be used with rigid bodies such as
|
||||
those defined by a "fix rigid" command.
|
||||
|
||||
This fix can only be used with periodic boundary conditions along the
|
||||
flow axis. The size of the box in this direction must not change. Also,
|
||||
the fix is designed to work only in an orthogonal simulation box.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`fix wall/reflect <fix_wall>` command
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
The default for the units keyword is lattice.
|
||||
|
||||
----------
|
||||
|
||||
.. _fbc-Pavlov1:
|
||||
|
||||
**(Pavlov1)** Pavlov, Kolotinskii, Stegailov, "GPU-Based Molecular Dynamics of Turbulent Liquid Flows with OpenMM", Proceedings of PPAM-2022, LNCS (Springer), vol. 13826, pp. 346-358 (2023)
|
||||
|
||||
.. _fbc-Pavlov2:
|
||||
|
||||
**(Pavlov2)** Pavlov, Galigerov, Kolotinskii, Nikolskiy, Stegailov, "GPU-based Molecular Dynamics of Fluid Flows: Reaching for Turbulence", Int. J. High Perf. Comp. Appl., (2024)
|
||||
150
doc/src/pair_rebomos.rst
Normal file
150
doc/src/pair_rebomos.rst
Normal file
@ -0,0 +1,150 @@
|
||||
.. index:: pair_style rebomos
|
||||
.. index:: pair_style rebomos/omp
|
||||
|
||||
pair_style rebomos command
|
||||
==========================
|
||||
|
||||
Accelerator Variants: *rebomos/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style rebomos
|
||||
|
||||
* rebomos = name of this pair style
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style rebomos
|
||||
pair_coeff * * ../potentials/MoS.rebomos Mo S
|
||||
|
||||
Example input scripts available: examples/threebody/
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
.. versionadded:: TBD
|
||||
|
||||
The *rebomos* pair style computes the interactions between molybdenum
|
||||
and sulfur atoms :ref:`(Stewart) <Stewart>` utilizing an adaptive
|
||||
interatomic reactive empirical bond order potential that is similar in
|
||||
form to the AIREBO potential :ref:`(Stuart) <Stuart2>`. The potential
|
||||
is based on an earlier parameterizations for :math:`\text{MoS}_2`
|
||||
developed by :ref:`(Liang) <Liang>`.
|
||||
|
||||
The REBOMoS potential consists of two terms:
|
||||
|
||||
.. math::
|
||||
|
||||
E & = \frac{1}{2} \sum_i \sum_{j \neq i}
|
||||
\left[ E^{\text{REBO}}_{ij} + E^{\text{LJ}}_{ij} \right] \\
|
||||
|
||||
The :math:`E^{\text{REBO}}` term describes the covalently bonded
|
||||
interactions between Mo and S atoms while the :math:`E^{\text{LJ}}` term
|
||||
describes longer range dispersion forces between layers. A cubic spline
|
||||
function is applied to smoothly switch between covalent bonding at short
|
||||
distances to dispersion interactions at longer distances. This allows
|
||||
the model to capture bond formation and breaking events which may occur
|
||||
between adjacent MoS2 layers, edges, defects, and more.
|
||||
|
||||
----------
|
||||
|
||||
Only a single pair_coeff command is used with the *rebomos* pair style
|
||||
which specifies an REBOMoS potential file with parameters for Mo and S.
|
||||
These are mapped to LAMMPS atom types by specifying N additional
|
||||
arguments after the filename in the pair_coeff command, where N is the
|
||||
number of LAMMPS atom types:
|
||||
|
||||
* filename
|
||||
* :math:`N` element names = mapping of REBOMoS elements to atom types
|
||||
|
||||
See the :doc:`pair_coeff <pair_coeff>` page for alternate ways
|
||||
to specify the path for the potential file.
|
||||
|
||||
As an example, if your LAMMPS simulation has three atom types and you want
|
||||
the first two to be Mo, and the third to be S, you would use the following
|
||||
pair_coeff command:
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_coeff * * MoS.rebomos Mo Mo S
|
||||
|
||||
The first 2 arguments must be \* \* so as to span all LAMMPS atom types.
|
||||
The first two Mo arguments map LAMMPS atom types 1 and 2 to the Mo
|
||||
element in the REBOMoS file. The final S argument maps LAMMPS atom type
|
||||
3 to the S element in the REBOMoS file. If a mapping value is specified
|
||||
as NULL, the mapping is not performed. This can be used when a
|
||||
*rebomos* potential is used as part of the *hybrid* pair style. The
|
||||
NULL values are placeholders for atom types that will be used with other
|
||||
potentials.
|
||||
|
||||
----------
|
||||
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
Mixing, shift, table, tail correction, restart, rRESPA info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
This pair style does not support the :doc:`pair_modify <pair_modify>`
|
||||
mix, shift, table, and tail options.
|
||||
|
||||
This pair style does not write their information to :doc:`binary restart
|
||||
files <restart>`, since it is stored in potential files. Thus, you need
|
||||
to re-specify the pair_style and pair_coeff commands in an input script
|
||||
that reads a restart file.
|
||||
|
||||
This pair styles 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 pair style is part of the MANYBODY package. It is only enabled if
|
||||
LAMMPS was built with that package. See the :doc:`Build package
|
||||
<Build_package>` page for more info.
|
||||
|
||||
These pair potentials require the :doc:`newton <newton>` setting to be
|
||||
"on" for pair interactions.
|
||||
|
||||
The MoS.rebomos potential file provided with LAMMPS (see the potentials
|
||||
directory) is parameterized for metal :doc:`units <units>`. You can use
|
||||
the *rebomos* pair style with any LAMMPS units setting, but you would
|
||||
need to create your own REBOMoS potential file with coefficients listed
|
||||
in the appropriate units.
|
||||
|
||||
The pair style provided here **only** supports potential files parameterized
|
||||
for the elements molybdenum and sulfur (designated with "Mo" and "S" in the
|
||||
*pair_coeff* command. Using potential files for other elements will trigger
|
||||
an error.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`pair_coeff <pair_coeff>`, :doc:`pair style rebo <pair_airebo>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
||||
----------
|
||||
|
||||
.. _Stewart:
|
||||
|
||||
**(Steward)** Stewart, Spearot, Modelling Simul. Mater. Sci. Eng. 21, 045003, (2013).
|
||||
|
||||
.. _Stuart2:
|
||||
|
||||
**(Stuart)** Stuart, Tutein, Harrison, J Chem Phys, 112, 6472-6486, (2000).
|
||||
|
||||
.. _Liang:
|
||||
|
||||
**(Liang)** Liang, Phillpot, Sinnott Phys. Rev. B79 245110, (2009), Erratum: Phys. Rev. B85 199903(E), (2012)
|
||||
@ -333,6 +333,7 @@ accelerated styles exist.
|
||||
* :doc:`rann <pair_rann>` -
|
||||
* :doc:`reaxff <pair_reaxff>` - ReaxFF potential
|
||||
* :doc:`rebo <pair_airebo>` - second generation REBO potential of Brenner
|
||||
* :doc:`rebomos <pair_rebomos>` - REBOMoS potential for MoS2
|
||||
* :doc:`resquared <pair_resquared>` - Everaers RE-Squared ellipsoidal potential
|
||||
* :doc:`saip/metal <pair_saip_metal>` - interlayer potential for hetero-junctions formed with hexagonal 2D materials and metal surfaces
|
||||
* :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` - smoothed dissipative particle dynamics for water at isothermal conditions
|
||||
|
||||
@ -1770,6 +1770,7 @@ Kolafa
|
||||
Kollman
|
||||
kolmogorov
|
||||
Kolmogorov
|
||||
Kolotinskii
|
||||
Kondor
|
||||
konglt
|
||||
Koning
|
||||
@ -2266,6 +2267,7 @@ morris
|
||||
Morriss
|
||||
morse
|
||||
Morteza
|
||||
MoS
|
||||
Mosayebi
|
||||
Moseler
|
||||
Moskalev
|
||||
@ -2774,6 +2776,7 @@ PEigenDense
|
||||
Peng
|
||||
peptide
|
||||
peratom
|
||||
Perf
|
||||
Pergamon
|
||||
pergrid
|
||||
peri
|
||||
@ -3070,6 +3073,7 @@ reaxff
|
||||
ReaxFF
|
||||
REAXFF
|
||||
rebo
|
||||
rebomos
|
||||
recurse
|
||||
recursing
|
||||
Ree
|
||||
@ -3597,6 +3601,7 @@ tesselation
|
||||
tesselations
|
||||
Tetot
|
||||
tex
|
||||
textrm
|
||||
tfac
|
||||
tfmc
|
||||
tfMC
|
||||
@ -3884,7 +3889,9 @@ Verlet
|
||||
versa
|
||||
Verstraelen
|
||||
ves
|
||||
vf
|
||||
vflag
|
||||
vflow
|
||||
vfrac
|
||||
vhi
|
||||
vibrational
|
||||
|
||||
1
examples/threebody/MoS.rebomos
Symbolic link
1
examples/threebody/MoS.rebomos
Symbolic link
@ -0,0 +1 @@
|
||||
../../potentials/MoS.rebomos
|
||||
35
examples/threebody/in.mos2-bulk
Normal file
35
examples/threebody/in.mos2-bulk
Normal file
@ -0,0 +1,35 @@
|
||||
units metal
|
||||
|
||||
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 &
|
||||
a2 -1.5964590311 2.7651481541 0.0000000000 &
|
||||
a3 0.0000000000 0.0000000000 13.9827680588 &
|
||||
basis 0.0000000000 0.000000000 $(3.0/4.0) &
|
||||
basis 0.0000000000 0.000000000 $(1.0/4.0) &
|
||||
basis $(2.0/3.0) $(1.0/3.0) 0.862008989 &
|
||||
basis $(1.0/3.0) $(2.0/3.0) 0.137990996 &
|
||||
basis $(1.0/3.0) $(2.0/3.0) 0.362008989 &
|
||||
basis $(2.0/3.0) $(1.0/3.0) 0.637991011 &
|
||||
origin 0.1 0.1 0.1
|
||||
|
||||
region box prism 0 4 0 8 0 1 -2.0 0.0 0.0
|
||||
create_box 2 box
|
||||
create_atoms 2 box &
|
||||
basis 1 1 &
|
||||
basis 2 1 &
|
||||
basis 3 2 &
|
||||
basis 4 2 &
|
||||
basis 5 2 &
|
||||
basis 6 2
|
||||
|
||||
mass 1 95.95 #Mo
|
||||
mass 2 32.065 #S
|
||||
|
||||
pair_style rebomos
|
||||
pair_coeff * * MoS.rebomos Mo S
|
||||
|
||||
thermo_style custom step temp press pe ke cellgamma vol
|
||||
thermo 10
|
||||
#dump 1 all atom 10 MoS.lammpstrj
|
||||
fix 1 all nve
|
||||
run 20
|
||||
|
||||
31
examples/threebody/in.mos2.rebomos
Normal file
31
examples/threebody/in.mos2.rebomos
Normal file
@ -0,0 +1,31 @@
|
||||
# monolayer MoS2
|
||||
units metal
|
||||
boundary p p f
|
||||
processors * * 1
|
||||
atom_modify map array
|
||||
|
||||
atom_style atomic
|
||||
read_data single_layer_MoS2.data
|
||||
|
||||
mass * 32.065 # mass of sulphur atom , uint: a.u.=1.66X10^(-27)kg
|
||||
mass 1 95.94 # mass of molebdenum atom , uint: a.u.=1.66X10^(-27)kg
|
||||
|
||||
########################## Define potentials ################################
|
||||
pair_style rebomos
|
||||
pair_coeff * * MoS.rebomos Mo S S
|
||||
#########################################################################
|
||||
|
||||
### Simulation settings ####
|
||||
timestep 0.001
|
||||
velocity all create 300.0 12345 loop geom
|
||||
|
||||
############################
|
||||
|
||||
# Output
|
||||
thermo 500
|
||||
thermo_style custom step etotal pe ke temp
|
||||
thermo_modify lost warn
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
fix thermostat all nve
|
||||
run 5000
|
||||
85
examples/threebody/log.22Feb24.mos2-bulk.g++.1
Normal file
85
examples/threebody/log.22Feb24.mos2-bulk.g++.1
Normal file
@ -0,0 +1,85 @@
|
||||
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-73-g36fa601fe0)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units metal
|
||||
|
||||
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 $(3.0/4.0) basis 0.0000000000 0.000000000 $(1.0/4.0) basis $(2.0/3.0) $(1.0/3.0) 0.862008989 basis $(1.0/3.0) $(2.0/3.0) 0.137990996 basis $(1.0/3.0) $(2.0/3.0) 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
|
||||
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 $(1.0/4.0) basis $(2.0/3.0) $(1.0/3.0) 0.862008989 basis $(1.0/3.0) $(2.0/3.0) 0.137990996 basis $(1.0/3.0) $(2.0/3.0) 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
|
||||
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis $(2.0/3.0) $(1.0/3.0) 0.862008989 basis $(1.0/3.0) $(2.0/3.0) 0.137990996 basis $(1.0/3.0) $(2.0/3.0) 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
|
||||
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis 0.66666666666666662966 $(1.0/3.0) 0.862008989 basis $(1.0/3.0) $(2.0/3.0) 0.137990996 basis $(1.0/3.0) $(2.0/3.0) 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
|
||||
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis 0.66666666666666662966 0.33333333333333331483 0.862008989 basis $(1.0/3.0) $(2.0/3.0) 0.137990996 basis $(1.0/3.0) $(2.0/3.0) 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
|
||||
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis 0.66666666666666662966 0.33333333333333331483 0.862008989 basis 0.33333333333333331483 $(2.0/3.0) 0.137990996 basis $(1.0/3.0) $(2.0/3.0) 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
|
||||
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis 0.66666666666666662966 0.33333333333333331483 0.862008989 basis 0.33333333333333331483 0.66666666666666662966 0.137990996 basis $(1.0/3.0) $(2.0/3.0) 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
|
||||
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis 0.66666666666666662966 0.33333333333333331483 0.862008989 basis 0.33333333333333331483 0.66666666666666662966 0.137990996 basis 0.33333333333333331483 $(2.0/3.0) 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
|
||||
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis 0.66666666666666662966 0.33333333333333331483 0.862008989 basis 0.33333333333333331483 0.66666666666666662966 0.137990996 basis 0.33333333333333331483 0.66666666666666662966 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
|
||||
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis 0.66666666666666662966 0.33333333333333331483 0.862008989 basis 0.33333333333333331483 0.66666666666666662966 0.137990996 basis 0.33333333333333331483 0.66666666666666662966 0.362008989 basis 0.66666666666666662966 $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
|
||||
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis 0.66666666666666662966 0.33333333333333331483 0.862008989 basis 0.33333333333333331483 0.66666666666666662966 0.137990996 basis 0.33333333333333331483 0.66666666666666662966 0.362008989 basis 0.66666666666666662966 0.33333333333333331483 0.637991011 origin 0.1 0.1 0.1
|
||||
Lattice spacing in x,y,z = 4.7867748 2.7651482 13.982768
|
||||
|
||||
region box prism 0 4 0 8 0 1 -2.0 0.0 0.0
|
||||
create_box 2 box
|
||||
Created triclinic box = (0 0 0) to (19.147099 22.121185 13.982768) with tilt (-9.5735495 0 0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 2 box basis 1 1 basis 2 1 basis 3 2 basis 4 2 basis 5 2 basis 6 2
|
||||
Created 288 atoms
|
||||
using lattice units in triclinic box = (0 0 0) to (19.147099 22.121185 13.982768) with tilt (-9.5735495 0 0)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass 1 95.95 #Mo
|
||||
mass 2 32.065 #S
|
||||
|
||||
pair_style rebomos
|
||||
pair_coeff * * MoS.rebomos Mo S
|
||||
Reading rebomos potential file MoS.rebomos with DATE: 2013-11-04
|
||||
|
||||
thermo_style custom step temp press pe ke cellgamma vol
|
||||
thermo 10
|
||||
#dump 1 all atom 10 MoS.lammpstrj
|
||||
fix 1 all nve
|
||||
run 20
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 13.4
|
||||
ghost atom cutoff = 13.4
|
||||
binsize = 6.7, bins = 5 4 3
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair rebomos, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.996 | 4.996 | 4.996 Mbytes
|
||||
Step Temp Press PotEng KinEng CellGamma Volume
|
||||
0 0 28799.53 -2061.6112 0 113.40187 5922.4926
|
||||
10 80.776057 13540.088 -2064.6132 2.9966028 113.40187 5922.4926
|
||||
20 146.17503 -20669.371 -2067.0428 5.4227518 113.40187 5922.4926
|
||||
Loop time of 0.058071 on 1 procs for 20 steps with 288 atoms
|
||||
|
||||
Performance: 29.757 ns/day, 0.807 hours/ns, 344.406 timesteps/s, 99.189 katom-step/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.057666 | 0.057666 | 0.057666 | 0.0 | 99.30
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00024654 | 0.00024654 | 0.00024654 | 0.0 | 0.42
|
||||
Output | 2.3975e-05 | 2.3975e-05 | 2.3975e-05 | 0.0 | 0.04
|
||||
Modify | 3.8394e-05 | 3.8394e-05 | 3.8394e-05 | 0.0 | 0.07
|
||||
Other | | 9.596e-05 | | | 0.17
|
||||
|
||||
Nlocal: 288 ave 288 max 288 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 4285 ave 4285 max 4285 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 142848 ave 142848 max 142848 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 142848
|
||||
Ave neighs/atom = 496
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
85
examples/threebody/log.22Feb24.mos2-bulk.g++.4
Normal file
85
examples/threebody/log.22Feb24.mos2-bulk.g++.4
Normal file
@ -0,0 +1,85 @@
|
||||
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-73-g36fa601fe0)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units metal
|
||||
|
||||
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 $(3.0/4.0) basis 0.0000000000 0.000000000 $(1.0/4.0) basis $(2.0/3.0) $(1.0/3.0) 0.862008989 basis $(1.0/3.0) $(2.0/3.0) 0.137990996 basis $(1.0/3.0) $(2.0/3.0) 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
|
||||
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 $(1.0/4.0) basis $(2.0/3.0) $(1.0/3.0) 0.862008989 basis $(1.0/3.0) $(2.0/3.0) 0.137990996 basis $(1.0/3.0) $(2.0/3.0) 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
|
||||
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis $(2.0/3.0) $(1.0/3.0) 0.862008989 basis $(1.0/3.0) $(2.0/3.0) 0.137990996 basis $(1.0/3.0) $(2.0/3.0) 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
|
||||
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis 0.66666666666666662966 $(1.0/3.0) 0.862008989 basis $(1.0/3.0) $(2.0/3.0) 0.137990996 basis $(1.0/3.0) $(2.0/3.0) 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
|
||||
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis 0.66666666666666662966 0.33333333333333331483 0.862008989 basis $(1.0/3.0) $(2.0/3.0) 0.137990996 basis $(1.0/3.0) $(2.0/3.0) 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
|
||||
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis 0.66666666666666662966 0.33333333333333331483 0.862008989 basis 0.33333333333333331483 $(2.0/3.0) 0.137990996 basis $(1.0/3.0) $(2.0/3.0) 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
|
||||
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis 0.66666666666666662966 0.33333333333333331483 0.862008989 basis 0.33333333333333331483 0.66666666666666662966 0.137990996 basis $(1.0/3.0) $(2.0/3.0) 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
|
||||
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis 0.66666666666666662966 0.33333333333333331483 0.862008989 basis 0.33333333333333331483 0.66666666666666662966 0.137990996 basis 0.33333333333333331483 $(2.0/3.0) 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
|
||||
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis 0.66666666666666662966 0.33333333333333331483 0.862008989 basis 0.33333333333333331483 0.66666666666666662966 0.137990996 basis 0.33333333333333331483 0.66666666666666662966 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
|
||||
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis 0.66666666666666662966 0.33333333333333331483 0.862008989 basis 0.33333333333333331483 0.66666666666666662966 0.137990996 basis 0.33333333333333331483 0.66666666666666662966 0.362008989 basis 0.66666666666666662966 $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
|
||||
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis 0.66666666666666662966 0.33333333333333331483 0.862008989 basis 0.33333333333333331483 0.66666666666666662966 0.137990996 basis 0.33333333333333331483 0.66666666666666662966 0.362008989 basis 0.66666666666666662966 0.33333333333333331483 0.637991011 origin 0.1 0.1 0.1
|
||||
Lattice spacing in x,y,z = 4.7867748 2.7651482 13.982768
|
||||
|
||||
region box prism 0 4 0 8 0 1 -2.0 0.0 0.0
|
||||
create_box 2 box
|
||||
Created triclinic box = (0 0 0) to (19.147099 22.121185 13.982768) with tilt (-9.5735495 0 0)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 2 box basis 1 1 basis 2 1 basis 3 2 basis 4 2 basis 5 2 basis 6 2
|
||||
Created 288 atoms
|
||||
using lattice units in triclinic box = (0 0 0) to (19.147099 22.121185 13.982768) with tilt (-9.5735495 0 0)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass 1 95.95 #Mo
|
||||
mass 2 32.065 #S
|
||||
|
||||
pair_style rebomos
|
||||
pair_coeff * * MoS.rebomos Mo S
|
||||
Reading rebomos potential file MoS.rebomos with DATE: 2013-11-04
|
||||
|
||||
thermo_style custom step temp press pe ke cellgamma vol
|
||||
thermo 10
|
||||
#dump 1 all atom 10 MoS.lammpstrj
|
||||
fix 1 all nve
|
||||
run 20
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 13.4
|
||||
ghost atom cutoff = 13.4
|
||||
binsize = 6.7, bins = 5 4 3
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair rebomos, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.15 | 4.151 | 4.151 Mbytes
|
||||
Step Temp Press PotEng KinEng CellGamma Volume
|
||||
0 0 28799.53 -2061.6112 0 113.40187 5922.4926
|
||||
10 80.776057 13540.088 -2064.6132 2.9966028 113.40187 5922.4926
|
||||
20 146.17503 -20669.371 -2067.0428 5.4227518 113.40187 5922.4926
|
||||
Loop time of 0.0219485 on 4 procs for 20 steps with 288 atoms
|
||||
|
||||
Performance: 78.730 ns/day, 0.305 hours/ns, 911.225 timesteps/s, 262.433 katom-step/s
|
||||
96.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.018118 | 0.019372 | 0.020087 | 0.5 | 88.26
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0015635 | 0.0023195 | 0.0035967 | 1.6 | 10.57
|
||||
Output | 2.5017e-05 | 4.6834e-05 | 0.00010543 | 0.0 | 0.21
|
||||
Modify | 1.3954e-05 | 1.423e-05 | 1.4594e-05 | 0.0 | 0.06
|
||||
Other | | 0.0001957 | | | 0.89
|
||||
|
||||
Nlocal: 72 ave 72 max 72 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2771.5 ave 2775 max 2768 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 35712 ave 35712 max 35712 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 142848
|
||||
Ave neighs/atom = 496
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
95
examples/threebody/log.22Feb24.mos2.rebomos.g++.1
Normal file
95
examples/threebody/log.22Feb24.mos2.rebomos.g++.1
Normal file
@ -0,0 +1,95 @@
|
||||
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-73-g36fa601fe0)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# monolayer MoS2
|
||||
units metal
|
||||
boundary p p f
|
||||
processors * * 1
|
||||
atom_modify map array
|
||||
|
||||
atom_style atomic
|
||||
read_data single_layer_MoS2.data
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 -100) to (51.15232 44.299209 100) with tilt (25.57616 0 0)
|
||||
WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (src/domain.cpp:219)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
768 atoms
|
||||
read_data CPU = 0.002 seconds
|
||||
|
||||
mass * 32.065 # mass of sulphur atom , uint: a.u.=1.66X10^(-27)kg
|
||||
mass 1 95.94 # mass of molebdenum atom , uint: a.u.=1.66X10^(-27)kg
|
||||
|
||||
########################## Define potentials ################################
|
||||
pair_style rebomos
|
||||
pair_coeff * * MoS.rebomos Mo S S
|
||||
Reading rebomos potential file MoS.rebomos with DATE: 2013-11-04
|
||||
#########################################################################
|
||||
|
||||
### Simulation settings ####
|
||||
timestep 0.001
|
||||
velocity all create 300.0 12345 loop geom
|
||||
|
||||
############################
|
||||
|
||||
# Output
|
||||
thermo 500
|
||||
thermo_style custom step etotal pe ke temp
|
||||
thermo_modify lost warn
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
fix thermostat all nve
|
||||
run 5000
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 13.4
|
||||
ghost atom cutoff = 13.4
|
||||
binsize = 6.7, bins = 12 7 30
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair rebomos, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.473 | 4.473 | 4.473 Mbytes
|
||||
Step TotEng PotEng KinEng Temp
|
||||
0 -5466.9785 -5496.7212 29.742759 300
|
||||
500 -5466.964 -5482.6985 15.734505 158.7059
|
||||
1000 -5466.9615 -5480.9492 13.98763 141.08607
|
||||
1500 -5466.964 -5482.6912 15.727258 158.63281
|
||||
2000 -5466.9657 -5483.3606 16.394878 165.36675
|
||||
2500 -5466.9624 -5481.6253 14.662948 147.89765
|
||||
3000 -5466.9642 -5482.7515 15.7873 159.23842
|
||||
3500 -5466.9654 -5483.3789 16.413502 165.5546
|
||||
4000 -5466.9628 -5481.848 14.885236 150.13977
|
||||
4500 -5466.9648 -5483.5045 16.539775 166.82825
|
||||
5000 -5466.9649 -5483.4932 16.528298 166.71249
|
||||
Loop time of 19.1009 on 1 procs for 5000 steps with 768 atoms
|
||||
|
||||
Performance: 22.617 ns/day, 1.061 hours/ns, 261.768 timesteps/s, 201.038 katom-step/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 19.042 | 19.042 | 19.042 | 0.0 | 99.69
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.018451 | 0.018451 | 0.018451 | 0.0 | 0.10
|
||||
Output | 0.00015575 | 0.00015575 | 0.00015575 | 0.0 | 0.00
|
||||
Modify | 0.023931 | 0.023931 | 0.023931 | 0.0 | 0.13
|
||||
Other | | 0.01658 | | | 0.09
|
||||
|
||||
Nlocal: 768 ave 768 max 768 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1158 ave 1158 max 1158 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 141824 ave 141824 max 141824 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 141824
|
||||
Ave neighs/atom = 184.66667
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:19
|
||||
95
examples/threebody/log.22Feb24.mos2.rebomos.g++.4
Normal file
95
examples/threebody/log.22Feb24.mos2.rebomos.g++.4
Normal file
@ -0,0 +1,95 @@
|
||||
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-73-g36fa601fe0)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# monolayer MoS2
|
||||
units metal
|
||||
boundary p p f
|
||||
processors * * 1
|
||||
atom_modify map array
|
||||
|
||||
atom_style atomic
|
||||
read_data single_layer_MoS2.data
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 -100) to (51.15232 44.299209 100) with tilt (25.57616 0 0)
|
||||
WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (src/domain.cpp:219)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
768 atoms
|
||||
read_data CPU = 0.002 seconds
|
||||
|
||||
mass * 32.065 # mass of sulphur atom , uint: a.u.=1.66X10^(-27)kg
|
||||
mass 1 95.94 # mass of molebdenum atom , uint: a.u.=1.66X10^(-27)kg
|
||||
|
||||
########################## Define potentials ################################
|
||||
pair_style rebomos
|
||||
pair_coeff * * MoS.rebomos Mo S S
|
||||
Reading rebomos potential file MoS.rebomos with DATE: 2013-11-04
|
||||
#########################################################################
|
||||
|
||||
### Simulation settings ####
|
||||
timestep 0.001
|
||||
velocity all create 300.0 12345 loop geom
|
||||
|
||||
############################
|
||||
|
||||
# Output
|
||||
thermo 500
|
||||
thermo_style custom step etotal pe ke temp
|
||||
thermo_modify lost warn
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
fix thermostat all nve
|
||||
run 5000
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 13.4
|
||||
ghost atom cutoff = 13.4
|
||||
binsize = 6.7, bins = 12 7 30
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair rebomos, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.045 | 4.045 | 4.045 Mbytes
|
||||
Step TotEng PotEng KinEng Temp
|
||||
0 -5466.9785 -5496.7212 29.742759 300
|
||||
500 -5466.964 -5482.6985 15.734505 158.7059
|
||||
1000 -5466.9615 -5480.9492 13.98763 141.08607
|
||||
1500 -5466.964 -5482.6912 15.727258 158.63281
|
||||
2000 -5466.9657 -5483.3606 16.394878 165.36675
|
||||
2500 -5466.9624 -5481.6253 14.662948 147.89765
|
||||
3000 -5466.9642 -5482.7515 15.7873 159.23842
|
||||
3500 -5466.9654 -5483.3789 16.413502 165.5546
|
||||
4000 -5466.9628 -5481.848 14.885236 150.13977
|
||||
4500 -5466.9648 -5483.5045 16.539775 166.82825
|
||||
5000 -5466.9649 -5483.4932 16.528298 166.71249
|
||||
Loop time of 5.69326 on 4 procs for 5000 steps with 768 atoms
|
||||
|
||||
Performance: 75.879 ns/day, 0.316 hours/ns, 878.231 timesteps/s, 674.482 katom-step/s
|
||||
98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.2611 | 5.3666 | 5.4358 | 3.0 | 94.26
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.23476 | 0.30106 | 0.40642 | 12.8 | 5.29
|
||||
Output | 0.00014996 | 0.0004478 | 0.0013353 | 0.0 | 0.01
|
||||
Modify | 0.0068861 | 0.0069917 | 0.0072247 | 0.2 | 0.12
|
||||
Other | | 0.01814 | | | 0.32
|
||||
|
||||
Nlocal: 192 ave 194 max 190 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 710 ave 712 max 708 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 35456 ave 35824 max 35088 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
|
||||
Total # of neighbors = 141824
|
||||
Ave neighs/atom = 184.66667
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:05
|
||||
79
examples/wall/in.wall.flow
Normal file
79
examples/wall/in.wall.flow
Normal file
@ -0,0 +1,79 @@
|
||||
variable nrun equal 1000
|
||||
variable dump_count equal 10
|
||||
|
||||
variable nwall equal 4
|
||||
variable w1 equal 67
|
||||
variable w2 equal 71
|
||||
variable w3 equal 75
|
||||
variable w4 equal 79
|
||||
|
||||
variable x_cylinder equal 20
|
||||
variable y_cylinder equal 17
|
||||
variable r_cylinder equal 4
|
||||
|
||||
variable MASS equal 1
|
||||
variable TEMP equal 0.4
|
||||
variable VFLOW equal 0.5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.3
|
||||
region sim_box block 0 84 0 34 0 10
|
||||
|
||||
boundary p p p
|
||||
|
||||
create_box 2 sim_box
|
||||
region reg_cylinder cylinder z ${x_cylinder} ${y_cylinder} ${r_cylinder} EDGE EDGE
|
||||
|
||||
create_atoms 1 box
|
||||
|
||||
## setup obstacle ##
|
||||
group g_obst region reg_cylinder
|
||||
group g_flow subtract all g_obst
|
||||
set group g_obst type 2
|
||||
|
||||
mass 1 ${MASS}
|
||||
mass 2 ${MASS}
|
||||
|
||||
velocity g_flow create ${TEMP} 4928459 rot yes dist gaussian
|
||||
velocity g_obst set 0.0 0.0 0.0
|
||||
|
||||
pair_style lj/cut 1.122462
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 1 2 1.0 1.0
|
||||
pair_coeff 2 2 1.0 1.0
|
||||
pair_modify shift yes
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 g_flow nve
|
||||
fix 2 g_flow wall/flow x ${VFLOW} ${TEMP} 123 ${nwall} ${w1} ${w2} ${w3} ${w4}
|
||||
|
||||
variable dump_every equal ${nrun}/${dump_count}
|
||||
variable thermo_every equal ${dump_every}
|
||||
variable restart_every equal ${nrun}/10
|
||||
|
||||
##### uncomment for grid aggregation #####
|
||||
#variable gr_Nx equal 42
|
||||
#variable gr_Ny equal 17
|
||||
#variable gr_Nz equal 1
|
||||
#variable gr_Nevery equal ${dump_every}
|
||||
#variable gr_Nrepeat equal 1
|
||||
#variable gr_Nfreq equal ${dump_every}
|
||||
#fix 3 g_flow ave/grid ${gr_Nevery} ${gr_Nrepeat} ${gr_Nfreq} ${gr_Nx} ${gr_Ny} ${gr_Nz} vx vy vz density/mass norm all ave one
|
||||
#compute ct_gridId g_flow property/grid ${gr_Nx} ${gr_Ny} ${gr_Nz} id
|
||||
#dump dmp_grid g_flow grid ${dump_every} grid.lammpstrj c_ct_gridId:grid:data f_3:grid:data[*]
|
||||
##########################################
|
||||
|
||||
#dump dmp_coord all atom ${dump_every} dump.lammpstrj
|
||||
|
||||
#compute ct_Temp g_flow temp/com
|
||||
#thermo_style custom step temp epair emol etotal press c_ct_Temp
|
||||
|
||||
#restart ${restart_every} flow.restart
|
||||
|
||||
timestep 0.005
|
||||
thermo ${thermo_every}
|
||||
run ${nrun}
|
||||
182
examples/wall/log.7Feb24.wall.flow.g++.1
Normal file
182
examples/wall/log.7Feb24.wall.flow.g++.1
Normal file
@ -0,0 +1,182 @@
|
||||
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-758-ge33590b2fc-modified)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable nrun equal 1000
|
||||
variable dump_count equal 10
|
||||
|
||||
variable nwall equal 4
|
||||
variable w1 equal 67
|
||||
variable w2 equal 71
|
||||
variable w3 equal 75
|
||||
variable w4 equal 79
|
||||
|
||||
variable x_cylinder equal 20
|
||||
variable y_cylinder equal 17
|
||||
variable r_cylinder equal 4
|
||||
|
||||
variable MASS equal 1
|
||||
variable TEMP equal 0.4
|
||||
variable VFLOW equal 0.5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.3
|
||||
Lattice spacing in x,y,z = 2.3712622 2.3712622 2.3712622
|
||||
region sim_box block 0 84 0 34 0 10
|
||||
|
||||
boundary p p p
|
||||
|
||||
create_box 2 sim_box
|
||||
Created orthogonal box = (0 0 0) to (199.18603 80.622915 23.712622)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
region reg_cylinder cylinder z ${x_cylinder} ${y_cylinder} ${r_cylinder} EDGE EDGE
|
||||
region reg_cylinder cylinder z 20 ${y_cylinder} ${r_cylinder} EDGE EDGE
|
||||
region reg_cylinder cylinder z 20 17 ${r_cylinder} EDGE EDGE
|
||||
region reg_cylinder cylinder z 20 17 4 EDGE EDGE
|
||||
|
||||
create_atoms 1 box
|
||||
Created 114240 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (199.18603 80.622915 23.712622)
|
||||
create_atoms CPU = 0.010 seconds
|
||||
|
||||
## setup obstacle ##
|
||||
group g_obst region reg_cylinder
|
||||
1950 atoms in group g_obst
|
||||
group g_flow subtract all g_obst
|
||||
112290 atoms in group g_flow
|
||||
set group g_obst type 2
|
||||
Setting atom values ...
|
||||
1950 settings made for type
|
||||
|
||||
mass 1 ${MASS}
|
||||
mass 1 1
|
||||
mass 2 ${MASS}
|
||||
mass 2 1
|
||||
|
||||
velocity g_flow create ${TEMP} 4928459 rot yes dist gaussian
|
||||
velocity g_flow create 0.4 4928459 rot yes dist gaussian
|
||||
velocity g_obst set 0.0 0.0 0.0
|
||||
|
||||
pair_style lj/cut 1.122462
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 1 2 1.0 1.0
|
||||
pair_coeff 2 2 1.0 1.0
|
||||
pair_modify shift yes
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 g_flow nve
|
||||
fix 2 g_flow wall/flow x ${VFLOW} ${TEMP} 123 ${nwall} ${w1} ${w2} ${w3} ${w4}
|
||||
fix 2 g_flow wall/flow x 0.5 ${TEMP} 123 ${nwall} ${w1} ${w2} ${w3} ${w4}
|
||||
fix 2 g_flow wall/flow x 0.5 0.4 123 ${nwall} ${w1} ${w2} ${w3} ${w4}
|
||||
fix 2 g_flow wall/flow x 0.5 0.4 123 4 ${w1} ${w2} ${w3} ${w4}
|
||||
fix 2 g_flow wall/flow x 0.5 0.4 123 4 67 ${w2} ${w3} ${w4}
|
||||
fix 2 g_flow wall/flow x 0.5 0.4 123 4 67 71 ${w3} ${w4}
|
||||
fix 2 g_flow wall/flow x 0.5 0.4 123 4 67 71 75 ${w4}
|
||||
fix 2 g_flow wall/flow x 0.5 0.4 123 4 67 71 75 79
|
||||
|
||||
variable dump_every equal ${nrun}/${dump_count}
|
||||
variable dump_every equal 1000/${dump_count}
|
||||
variable dump_every equal 1000/10
|
||||
variable thermo_every equal ${dump_every}
|
||||
variable thermo_every equal 100
|
||||
variable restart_every equal ${nrun}/10
|
||||
variable restart_every equal 1000/10
|
||||
|
||||
##### uncomment for grid aggregation #####
|
||||
#variable gr_Nx equal 42
|
||||
#variable gr_Ny equal 17
|
||||
#variable gr_Nz equal 1
|
||||
#variable gr_Nevery equal ${dump_every}
|
||||
#variable gr_Nrepeat equal 1
|
||||
#variable gr_Nfreq equal ${dump_every}
|
||||
#fix 3 g_flow ave/grid ${gr_Nevery} ${gr_Nrepeat} ${gr_Nfreq} ${gr_Nx} ${gr_Ny} ${gr_Nz} vx vy vz density/mass norm all ave one
|
||||
#compute ct_gridId g_flow property/grid ${gr_Nx} ${gr_Ny} ${gr_Nz} id
|
||||
#dump dmp_grid g_flow grid ${dump_every} grid.lammpstrj c_ct_gridId:grid:data f_3:grid:data[*]
|
||||
##########################################
|
||||
|
||||
#dump dmp_coord all atom ${dump_every} dump.lammpstrj
|
||||
|
||||
#compute ct_Temp g_flow temp/com
|
||||
#thermo_style custom step temp epair emol etotal press c_ct_Temp
|
||||
|
||||
#restart ${restart_every} flow.restart
|
||||
|
||||
timestep 0.005
|
||||
thermo ${thermo_every}
|
||||
thermo 100
|
||||
run ${nrun}
|
||||
run 1000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix wall/flow command: doi:10.1177/10943420231213013
|
||||
|
||||
@Article{Pavlov-etal-IJHPCA-2024,
|
||||
author = {Daniil Pavlov and Vladislav Galigerov and Daniil Kolotinskii and Vsevolod Nikolskiy and Vladimir Stegailov},
|
||||
title = {GPU-based molecular dynamics of fluid flows: Reaching for turbulence},
|
||||
journal = {The International Journal of High Performance Computing Applications},
|
||||
year = 2024,
|
||||
volume = 38,
|
||||
number = 1,
|
||||
pages = 34-49
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 20 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.422462
|
||||
ghost atom cutoff = 1.422462
|
||||
binsize = 0.711231, bins = 281 114 34
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 26.69 | 26.69 | 26.69 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.39317221 0 0 0.58975315 0.11795063
|
||||
100 0.3671684 0.045118445 0 0.59586622 0.27378331
|
||||
200 0.3732041 0.036897471 0 0.59669873 0.24917809
|
||||
300 0.37432305 0.036501844 0 0.5979815 0.24715194
|
||||
400 0.37603886 0.035350565 0 0.59940392 0.24480762
|
||||
500 0.37617142 0.036949771 0 0.60120196 0.24862985
|
||||
600 0.37751983 0.036484268 0 0.60275905 0.24784635
|
||||
700 0.37787831 0.037327783 0 0.60414029 0.25060427
|
||||
800 0.37959242 0.036206184 0 0.60558983 0.2476903
|
||||
900 0.38019033 0.036874395 0 0.6071549 0.24984211
|
||||
1000 0.38070666 0.037068948 0 0.60812395 0.25041936
|
||||
Loop time of 5.61598 on 1 procs for 1000 steps with 114240 atoms
|
||||
|
||||
Performance: 76923.319 tau/day, 178.063 timesteps/s, 20.342 Matom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.6351 | 2.6351 | 2.6351 | 0.0 | 46.92
|
||||
Neigh | 1.2994 | 1.2994 | 1.2994 | 0.0 | 23.14
|
||||
Comm | 0.26576 | 0.26576 | 0.26576 | 0.0 | 4.73
|
||||
Output | 0.0030531 | 0.0030531 | 0.0030531 | 0.0 | 0.05
|
||||
Modify | 1.3019 | 1.3019 | 1.3019 | 0.0 | 23.18
|
||||
Other | | 0.1107 | | | 1.97
|
||||
|
||||
Nlocal: 114240 ave 114240 max 114240 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 20119 ave 20119 max 20119 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 164018 ave 164018 max 164018 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 164018
|
||||
Ave neighs/atom = 1.4357318
|
||||
Neighbor list builds = 50
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:05
|
||||
182
examples/wall/log.7Feb24.wall.flow.g++.4
Normal file
182
examples/wall/log.7Feb24.wall.flow.g++.4
Normal file
@ -0,0 +1,182 @@
|
||||
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-758-ge33590b2fc-modified)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable nrun equal 1000
|
||||
variable dump_count equal 10
|
||||
|
||||
variable nwall equal 4
|
||||
variable w1 equal 67
|
||||
variable w2 equal 71
|
||||
variable w3 equal 75
|
||||
variable w4 equal 79
|
||||
|
||||
variable x_cylinder equal 20
|
||||
variable y_cylinder equal 17
|
||||
variable r_cylinder equal 4
|
||||
|
||||
variable MASS equal 1
|
||||
variable TEMP equal 0.4
|
||||
variable VFLOW equal 0.5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.3
|
||||
Lattice spacing in x,y,z = 2.3712622 2.3712622 2.3712622
|
||||
region sim_box block 0 84 0 34 0 10
|
||||
|
||||
boundary p p p
|
||||
|
||||
create_box 2 sim_box
|
||||
Created orthogonal box = (0 0 0) to (199.18603 80.622915 23.712622)
|
||||
4 by 1 by 1 MPI processor grid
|
||||
region reg_cylinder cylinder z ${x_cylinder} ${y_cylinder} ${r_cylinder} EDGE EDGE
|
||||
region reg_cylinder cylinder z 20 ${y_cylinder} ${r_cylinder} EDGE EDGE
|
||||
region reg_cylinder cylinder z 20 17 ${r_cylinder} EDGE EDGE
|
||||
region reg_cylinder cylinder z 20 17 4 EDGE EDGE
|
||||
|
||||
create_atoms 1 box
|
||||
Created 114240 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (199.18603 80.622915 23.712622)
|
||||
create_atoms CPU = 0.003 seconds
|
||||
|
||||
## setup obstacle ##
|
||||
group g_obst region reg_cylinder
|
||||
1950 atoms in group g_obst
|
||||
group g_flow subtract all g_obst
|
||||
112290 atoms in group g_flow
|
||||
set group g_obst type 2
|
||||
Setting atom values ...
|
||||
1950 settings made for type
|
||||
|
||||
mass 1 ${MASS}
|
||||
mass 1 1
|
||||
mass 2 ${MASS}
|
||||
mass 2 1
|
||||
|
||||
velocity g_flow create ${TEMP} 4928459 rot yes dist gaussian
|
||||
velocity g_flow create 0.4 4928459 rot yes dist gaussian
|
||||
velocity g_obst set 0.0 0.0 0.0
|
||||
|
||||
pair_style lj/cut 1.122462
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 1 2 1.0 1.0
|
||||
pair_coeff 2 2 1.0 1.0
|
||||
pair_modify shift yes
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 g_flow nve
|
||||
fix 2 g_flow wall/flow x ${VFLOW} ${TEMP} 123 ${nwall} ${w1} ${w2} ${w3} ${w4}
|
||||
fix 2 g_flow wall/flow x 0.5 ${TEMP} 123 ${nwall} ${w1} ${w2} ${w3} ${w4}
|
||||
fix 2 g_flow wall/flow x 0.5 0.4 123 ${nwall} ${w1} ${w2} ${w3} ${w4}
|
||||
fix 2 g_flow wall/flow x 0.5 0.4 123 4 ${w1} ${w2} ${w3} ${w4}
|
||||
fix 2 g_flow wall/flow x 0.5 0.4 123 4 67 ${w2} ${w3} ${w4}
|
||||
fix 2 g_flow wall/flow x 0.5 0.4 123 4 67 71 ${w3} ${w4}
|
||||
fix 2 g_flow wall/flow x 0.5 0.4 123 4 67 71 75 ${w4}
|
||||
fix 2 g_flow wall/flow x 0.5 0.4 123 4 67 71 75 79
|
||||
|
||||
variable dump_every equal ${nrun}/${dump_count}
|
||||
variable dump_every equal 1000/${dump_count}
|
||||
variable dump_every equal 1000/10
|
||||
variable thermo_every equal ${dump_every}
|
||||
variable thermo_every equal 100
|
||||
variable restart_every equal ${nrun}/10
|
||||
variable restart_every equal 1000/10
|
||||
|
||||
##### uncomment for grid aggregation #####
|
||||
#variable gr_Nx equal 42
|
||||
#variable gr_Ny equal 17
|
||||
#variable gr_Nz equal 1
|
||||
#variable gr_Nevery equal ${dump_every}
|
||||
#variable gr_Nrepeat equal 1
|
||||
#variable gr_Nfreq equal ${dump_every}
|
||||
#fix 3 g_flow ave/grid ${gr_Nevery} ${gr_Nrepeat} ${gr_Nfreq} ${gr_Nx} ${gr_Ny} ${gr_Nz} vx vy vz density/mass norm all ave one
|
||||
#compute ct_gridId g_flow property/grid ${gr_Nx} ${gr_Ny} ${gr_Nz} id
|
||||
#dump dmp_grid g_flow grid ${dump_every} grid.lammpstrj c_ct_gridId:grid:data f_3:grid:data[*]
|
||||
##########################################
|
||||
|
||||
#dump dmp_coord all atom ${dump_every} dump.lammpstrj
|
||||
|
||||
#compute ct_Temp g_flow temp/com
|
||||
#thermo_style custom step temp epair emol etotal press c_ct_Temp
|
||||
|
||||
#restart ${restart_every} flow.restart
|
||||
|
||||
timestep 0.005
|
||||
thermo ${thermo_every}
|
||||
thermo 100
|
||||
run ${nrun}
|
||||
run 1000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix wall/flow command: doi:10.1177/10943420231213013
|
||||
|
||||
@Article{Pavlov-etal-IJHPCA-2024,
|
||||
author = {Daniil Pavlov and Vladislav Galigerov and Daniil Kolotinskii and Vsevolod Nikolskiy and Vladimir Stegailov},
|
||||
title = {GPU-based molecular dynamics of fluid flows: Reaching for turbulence},
|
||||
journal = {The International Journal of High Performance Computing Applications},
|
||||
year = 2024,
|
||||
volume = 38,
|
||||
number = 1,
|
||||
pages = 34-49
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 20 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.422462
|
||||
ghost atom cutoff = 1.422462
|
||||
binsize = 0.711231, bins = 281 114 34
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.496 | 8.496 | 8.496 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.39317221 0 0 0.58975315 0.11795063
|
||||
100 0.36726398 0.045386014 0 0.59627716 0.27402111
|
||||
200 0.37384538 0.036574547 0 0.5973377 0.24836729
|
||||
300 0.37487455 0.036519645 0 0.59882654 0.24691726
|
||||
400 0.37591417 0.036405755 0 0.60027207 0.24700641
|
||||
500 0.37654714 0.037008829 0 0.60182459 0.24883444
|
||||
600 0.3778008 0.03663706 0 0.6033333 0.24874392
|
||||
700 0.37851338 0.036714175 0 0.60447928 0.24881829
|
||||
800 0.37984876 0.036237049 0 0.6060052 0.24843003
|
||||
900 0.38022763 0.036847615 0 0.60718407 0.24987198
|
||||
1000 0.38084717 0.037139994 0 0.60840575 0.25070072
|
||||
Loop time of 2.20347 on 4 procs for 1000 steps with 114240 atoms
|
||||
|
||||
Performance: 196054.093 tau/day, 453.829 timesteps/s, 51.845 Matom-step/s
|
||||
95.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.67927 | 0.70882 | 0.73473 | 2.4 | 32.17
|
||||
Neigh | 0.32928 | 0.34467 | 0.36084 | 2.0 | 15.64
|
||||
Comm | 0.3211 | 0.36609 | 0.40741 | 6.1 | 16.61
|
||||
Output | 0.0017748 | 0.0032465 | 0.0046508 | 2.1 | 0.15
|
||||
Modify | 0.71135 | 0.74424 | 0.76001 | 2.3 | 33.78
|
||||
Other | | 0.03641 | | | 1.65
|
||||
|
||||
Nlocal: 28560 ave 29169 max 27884 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 6452.25 ave 6546 max 6368 min
|
||||
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||
Neighs: 40893 ave 42032 max 39445 min
|
||||
Histogram: 1 0 0 0 1 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 163572
|
||||
Ave neighs/atom = 1.4318277
|
||||
Neighbor list builds = 50
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:02
|
||||
65
potentials/MoS.rebomos
Normal file
65
potentials/MoS.rebomos
Normal file
@ -0,0 +1,65 @@
|
||||
# DATE: 2013-11-04 UNITS: metal CONTRIBUTOR: J Stewart, K Dang, D Spearot (UArk) CITATION: Stewart J A and Spearot D E, Modelling Simul. Mater. Sci. Eng. 21.
|
||||
# MoS-S REBO Brenner/Sinnot Potential as published in
|
||||
# Liang T, Phillpot S R and Sinnott S B (2009) Phys. Rev. B79 245110, Erratum: Phys. Rev. B85 199903(E).
|
||||
|
||||
3.50 rcmin_MM
|
||||
2.75 rcmin_MS
|
||||
2.30 rcmin_SS
|
||||
3.80 rcmax_MM
|
||||
3.05 rcmax_MS
|
||||
3.00 rcmax_SS
|
||||
3.419129390005910 Q_MM
|
||||
1.505537839153790 Q_MS
|
||||
0.254959104053671 Q_SS
|
||||
1.07500712999340 alpha_MM
|
||||
1.19267902218820 alpha_MS
|
||||
1.10775022439715 alpha_SS
|
||||
179.008013654688 A_MM
|
||||
575.509677721866 A_MS
|
||||
1228.43233679426 A_SS
|
||||
706.247903589221 BIJc_MM1
|
||||
1344.46820036159 BIJc_MS1
|
||||
1498.64815404145 BIJc_SS1
|
||||
1.16100322369589 Beta_MM1
|
||||
1.26973752204290 Beta_MS1
|
||||
1.12673623610320 Beta_SS1
|
||||
0.1326842550663270 M_b0
|
||||
-0.007642788338017 M_b1
|
||||
0.0341395775059370 M_b2
|
||||
0.2523050971380870 M_b3
|
||||
0.1227287372225670 M_b4
|
||||
-0.361387798398897 M_b5
|
||||
-0.282577591351457 M_b6
|
||||
0.120194301035280 M_bg0
|
||||
0.045238287358190 M_bg1
|
||||
0.067922807244030 M_bg2
|
||||
-0.03672511378682 M_bg3
|
||||
0.107516477513860 M_bg4
|
||||
0.004964711984940 M_bg5
|
||||
-0.12997598358652 M_bg6
|
||||
0.006848761596750 S_b0
|
||||
-0.02389964401024 S_b1
|
||||
0.137457353311170 S_b2
|
||||
0.033016467497740 S_b3
|
||||
-0.31064291544850 S_b4
|
||||
-0.08550273135791 S_b5
|
||||
0.149252790306880 S_b6
|
||||
-0.2850852 S_bg0
|
||||
1.67102480 S_bg1
|
||||
-3.5678516 S_bg2
|
||||
3.45054990 S_bg3
|
||||
-1.2186289 S_bg4
|
||||
0.0 S_bg5
|
||||
0.0 S_bg6
|
||||
0.138040769883614 M_a0
|
||||
0.803625443023934 M_a1
|
||||
0.292412960851064 M_a2
|
||||
0.640588078946224 M_a3
|
||||
0.062978539843324 S_a0
|
||||
2.478617619878250 S_a1
|
||||
0.036666243238154 S_a2
|
||||
2.386431372486710 S_a3
|
||||
0.00058595 epsilon_MM
|
||||
0.01386 epsilon_SS
|
||||
4.200 sigma_MM
|
||||
3.130 sigma_SS
|
||||
@ -84,7 +84,7 @@ Au_u3 = Gold universal 3
|
||||
The suffix of each file indicates the pair style it is used with:
|
||||
|
||||
adp ADP angular dependent potential
|
||||
airebo AI-REBO and REBO potentials
|
||||
airebo AI-REBO potentials
|
||||
bop.table BOP potential, tabulated form
|
||||
cdeam concentration-dependent EAM
|
||||
comb COMB potential
|
||||
@ -107,6 +107,8 @@ nb3b.harmonic nonbonded 3-body harmonic potential
|
||||
pod ML potential with proper orthogonal descriptors (POD)
|
||||
poly polymorphic 3-body potential
|
||||
reax ReaxFF potential (see README.reax for more info)
|
||||
rebo REBO potentials
|
||||
rebomos REBOMoS potential
|
||||
smtbq second moment tight binding QEq (SMTBQ) potential
|
||||
snap SNAP potential
|
||||
snapcoeff SNAP potential
|
||||
|
||||
4
src/.gitignore
vendored
4
src/.gitignore
vendored
@ -1025,6 +1025,8 @@
|
||||
/fix_wall_colloid.h
|
||||
/fix_wall_ees.cpp
|
||||
/fix_wall_ees.h
|
||||
/fix_wall_flow.cpp
|
||||
/fix_wall_flow.h
|
||||
/fix_wall_region_ees.cpp
|
||||
/fix_wall_region_ees.h
|
||||
/fix_wall_reflect_stochastic.cpp
|
||||
@ -1371,6 +1373,8 @@
|
||||
/pair_reaxff.h
|
||||
/pair_rebo.cpp
|
||||
/pair_rebo.h
|
||||
/pair_rebomos.cpp
|
||||
/pair_rebomos.h
|
||||
/pair_resquared.cpp
|
||||
/pair_resquared.h
|
||||
/pair_saip_metal.cpp
|
||||
|
||||
325
src/EXTRA-FIX/fix_wall_flow.cpp
Normal file
325
src/EXTRA-FIX/fix_wall_flow.cpp
Normal file
@ -0,0 +1,325 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
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: Vladislav Galigerov (HSE),
|
||||
Daniil Pavlov (MIPT)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "fix_wall_flow.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "citeme.h"
|
||||
#include "comm.h"
|
||||
#include "domain.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "input.h"
|
||||
#include "lattice.h"
|
||||
#include "math_const.h"
|
||||
#include "memory.h"
|
||||
#include "modify.h"
|
||||
#include "random_mars.h"
|
||||
#include "update.h"
|
||||
#include "variable.h"
|
||||
|
||||
#include <algorithm>
|
||||
#include <cstring>
|
||||
#include <functional>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
static const char cite_fix_wall_flow_c[] =
|
||||
"fix wall/flow command: doi:10.1177/10943420231213013\n\n"
|
||||
"@Article{Pavlov-etal-IJHPCA-2024,\n"
|
||||
" author = {Daniil Pavlov and Vladislav Galigerov and Daniil Kolotinskii and Vsevolod "
|
||||
"Nikolskiy and Vladimir Stegailov},\n"
|
||||
" title = {GPU-based molecular dynamics of fluid flows: Reaching for turbulence},\n"
|
||||
" journal = {The International Journal of High Performance Computing Applications},\n"
|
||||
" year = 2024,\n"
|
||||
" volume = 38,\n"
|
||||
" number = 1,\n"
|
||||
" pages = 34-49\n"
|
||||
"}\n\n";
|
||||
|
||||
FixWallFlow::FixWallFlow(LAMMPS *lmp, int narg, char **arg) :
|
||||
Fix(lmp, narg, arg), flowax(FlowAxis::AX_X), flowvel(0.0), flowdir(0), rndseed(0),
|
||||
current_segment(nullptr)
|
||||
{
|
||||
if (lmp->citeme) lmp->citeme->add(cite_fix_wall_flow_c);
|
||||
if (narg < 9) utils::missing_cmd_args(FLERR, "fix wall/flow", error);
|
||||
|
||||
if (domain->triclinic != 0)
|
||||
error->all(FLERR, "Fix wall/flow cannot be used with triclinic simulation box");
|
||||
|
||||
dynamic_group_allow = 1;
|
||||
bool do_abort = false;
|
||||
|
||||
int iarg = 3;
|
||||
// parsing axis
|
||||
if (strcmp(arg[iarg], "x") == 0)
|
||||
flowax = FlowAxis::AX_X;
|
||||
else if (strcmp(arg[iarg], "y") == 0)
|
||||
flowax = FlowAxis::AX_Y;
|
||||
else if (strcmp(arg[iarg], "z") == 0)
|
||||
flowax = FlowAxis::AX_Z;
|
||||
else
|
||||
error->all(FLERR, "Illegal fix wall/flow argument: axis must by x or y or z, but {} specified",
|
||||
arg[iarg]);
|
||||
|
||||
if (domain->periodicity[flowax] != 1)
|
||||
error->all(FLERR,
|
||||
"Fix wall/flow cannot be used with a non-periodic boundary along the flow axis");
|
||||
|
||||
++iarg;
|
||||
// parsing velocity
|
||||
flowvel = utils::numeric(FLERR, arg[iarg], do_abort, lmp);
|
||||
if (flowvel == 0.0) error->all(FLERR, "Illegal fix wall/flow argument: velocity cannot be 0");
|
||||
if (flowvel > 0.0)
|
||||
flowdir = 1;
|
||||
else
|
||||
flowdir = -1;
|
||||
if (flowdir < 0)
|
||||
error->all(FLERR, "Illegal fix wall/flow argument: negative direction is not supported yet");
|
||||
|
||||
++iarg;
|
||||
// parsing temperature
|
||||
double flowtemp = utils::numeric(FLERR, arg[iarg], do_abort, lmp);
|
||||
kT = lmp->force->boltz * flowtemp / force->mvv2e;
|
||||
|
||||
++iarg;
|
||||
// parsing seed
|
||||
rndseed = utils::inumeric(FLERR, arg[iarg], do_abort, lmp);
|
||||
if (rndseed <= 0)
|
||||
error->all(FLERR, "Illegal fix wall/flow argument: random seed must be positive integer");
|
||||
|
||||
++iarg;
|
||||
// parsing wall count
|
||||
int wallcount = utils::inumeric(FLERR, arg[iarg], do_abort, lmp);
|
||||
if (wallcount <= 0)
|
||||
error->all(FLERR, "Illegal fix wall/flow argument: wall count must be positive integer");
|
||||
|
||||
++iarg;
|
||||
// parsing walls
|
||||
if (narg - iarg != wallcount && narg - iarg != wallcount + 2)
|
||||
error->all(FLERR, "Wrong fix wall/flow wall count");
|
||||
|
||||
double scale = 0.0;
|
||||
if (flowax == FlowAxis::AX_X)
|
||||
scale = domain->lattice->xlattice;
|
||||
else if (flowax == FlowAxis::AX_Y)
|
||||
scale = domain->lattice->ylattice;
|
||||
else if (flowax == FlowAxis::AX_Z)
|
||||
scale = domain->lattice->zlattice;
|
||||
|
||||
if (narg - iarg == wallcount + 2) {
|
||||
if (strcmp(arg[narg - 2], "units") != 0) error->all(FLERR, "Wrong fix wall/flow units command");
|
||||
if (strcmp(arg[narg - 1], "box") == 0)
|
||||
scale = 1.0;
|
||||
else if (strcmp(arg[narg - 1], "lattice") != 0)
|
||||
error->all(FLERR, "Wrong fix wall/flow units command");
|
||||
}
|
||||
|
||||
walls.resize(wallcount + 2);
|
||||
walls.front() = domain->boxlo[flowax];
|
||||
for (int w = 1; w <= wallcount; ++w, ++iarg) {
|
||||
walls[w] = utils::numeric(FLERR, arg[iarg], do_abort, lmp) * scale;
|
||||
}
|
||||
walls.back() = domain->boxhi[flowax];
|
||||
if (!std::is_sorted(walls.begin(), walls.end(), std::less_equal<double>())) {
|
||||
error->all(FLERR,
|
||||
"Wrong fix wall/flow wall ordering or some walls are outside simulation domain");
|
||||
}
|
||||
|
||||
if (std::adjacent_find(walls.begin(), walls.end()) != walls.end()) {
|
||||
error->all(FLERR,
|
||||
"Wrong fix wall/flow wall coordinates: some walls have the same coordinates or lie "
|
||||
"on the boundary");
|
||||
}
|
||||
|
||||
memory->grow(current_segment, atom->nmax, "WallFlow::current_segment");
|
||||
atom->add_callback(Atom::GROW);
|
||||
if (restart_peratom) atom->add_callback(Atom::RESTART);
|
||||
|
||||
maxexchange = 1;
|
||||
|
||||
random = new RanMars(lmp, rndseed + comm->me);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixWallFlow::~FixWallFlow()
|
||||
{
|
||||
if (copymode) return;
|
||||
atom->delete_callback(id, Atom::GROW);
|
||||
if (restart_peratom) atom->delete_callback(id, Atom::RESTART);
|
||||
memory->destroy(current_segment);
|
||||
|
||||
delete random;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixWallFlow::setmask()
|
||||
{
|
||||
int mask = 0;
|
||||
|
||||
mask |= END_OF_STEP;
|
||||
|
||||
return mask;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWallFlow::init()
|
||||
{
|
||||
if (domain->triclinic != 0)
|
||||
error->all(FLERR, "Fix wall/flow cannot be used with triclinic simulation box");
|
||||
|
||||
int nrigid = 0;
|
||||
int box_change_flowax = 0;
|
||||
for (const auto &ifix : modify->get_fix_list()) {
|
||||
if (ifix->rigid_flag) nrigid++;
|
||||
switch (flowax) {
|
||||
case FlowAxis::AX_X:
|
||||
if (ifix->box_change & Fix::BOX_CHANGE_X) box_change_flowax++;
|
||||
break;
|
||||
case FlowAxis::AX_Y:
|
||||
if (ifix->box_change & Fix::BOX_CHANGE_Y) box_change_flowax++;
|
||||
break;
|
||||
case FlowAxis::AX_Z:
|
||||
if (ifix->box_change & Fix::BOX_CHANGE_Z) box_change_flowax++;
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
if (nrigid) error->all(FLERR, "Fix wall/flow is not compatible with rigid bodies");
|
||||
if (box_change_flowax)
|
||||
error->all(
|
||||
FLERR,
|
||||
"Fix wall/flow is not compatible with simulation box size changing along flow direction");
|
||||
|
||||
for (int i = 0; i < atom->nlocal; ++i) {
|
||||
double pos = atom->x[i][flowax];
|
||||
current_segment[i] = compute_current_segment(pos);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWallFlow::end_of_step()
|
||||
{
|
||||
double **x = atom->x;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
for (int i = 0; i < nlocal; ++i) {
|
||||
if (mask[i] & groupbit) {
|
||||
double pos = x[i][flowax];
|
||||
int prev_segment = current_segment[i];
|
||||
current_segment[i] = compute_current_segment(pos);
|
||||
|
||||
if (prev_segment != current_segment[i]) generate_velocity(i);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWallFlow::generate_velocity(int atom_i)
|
||||
{
|
||||
const int newton_iteration_count = 10;
|
||||
double *vel = atom->v[atom_i];
|
||||
|
||||
double *prmass = atom->rmass;
|
||||
double *pmass = atom->mass;
|
||||
double mass = 0.0;
|
||||
if (prmass)
|
||||
mass = prmass[atom_i];
|
||||
else
|
||||
mass = pmass[atom->type[atom_i]];
|
||||
|
||||
const double gamma = 1.0 / std::sqrt(2.0 * kT / mass);
|
||||
double delta = gamma * flowvel;
|
||||
|
||||
const double edd = std::exp(-delta * delta) / MathConst::MY_PIS + delta * std::erf(delta);
|
||||
const double probability_threshold = 0.5f * (1.f + delta / edd);
|
||||
|
||||
double direction = 1.0;
|
||||
|
||||
if (random->uniform() > probability_threshold) {
|
||||
delta = -delta;
|
||||
direction = -direction;
|
||||
}
|
||||
|
||||
const double xi_0 = random->uniform();
|
||||
const double F_inf = edd + delta;
|
||||
const double xi = xi_0 * F_inf;
|
||||
const double x_0 = (std::sqrt(delta * delta + 2) - delta) * 0.5;
|
||||
double x = x_0;
|
||||
for (int i = 0; i < newton_iteration_count; ++i) {
|
||||
x -= (std::exp(x * x) * MathConst::MY_PIS * (xi - delta * std::erfc(x)) - 1.0) / (x + delta) *
|
||||
0.5;
|
||||
}
|
||||
|
||||
const double nu = x + delta;
|
||||
const double v = nu / gamma;
|
||||
|
||||
vel[flowax] = v * direction;
|
||||
vel[(flowax + 1) % 3] = random->gaussian() / (gamma * MathConst::MY_SQRT2);
|
||||
vel[(flowax + 2) % 3] = random->gaussian() / (gamma * MathConst::MY_SQRT2);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixWallFlow::compute_current_segment(double pos) const
|
||||
{
|
||||
int result = 0;
|
||||
for (; result < (int)walls.size() - 1; ++result) {
|
||||
if (pos >= walls[result] && pos < walls[result + 1]) { return result; }
|
||||
}
|
||||
return -1; // -1 is "out of box" region
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWallFlow::grow_arrays(int nmax)
|
||||
{
|
||||
memory->grow(current_segment, nmax, "WallFlow::current_segment");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWallFlow::copy_arrays(int i, int j, int)
|
||||
{
|
||||
current_segment[j] = current_segment[i];
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixWallFlow::pack_exchange(int i, double *buf)
|
||||
{
|
||||
buf[0] = static_cast<double>(current_segment[i]);
|
||||
return 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixWallFlow::unpack_exchange(int i, double *buf)
|
||||
{
|
||||
current_segment[i] = static_cast<int>(buf[0]);
|
||||
return 1;
|
||||
}
|
||||
61
src/EXTRA-FIX/fix_wall_flow.h
Normal file
61
src/EXTRA-FIX/fix_wall_flow.h
Normal file
@ -0,0 +1,61 @@
|
||||
/* -*- 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(wall/flow,FixWallFlow);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_WALL_FLOW_H
|
||||
#define LMP_FIX_WALL_FLOW_H
|
||||
|
||||
#include "fix.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixWallFlow : public Fix {
|
||||
public:
|
||||
enum FlowAxis { AX_X = 0, AX_Y = 1, AX_Z = 2 };
|
||||
|
||||
FixWallFlow(class LAMMPS *, int, char **);
|
||||
~FixWallFlow() override;
|
||||
int setmask() override;
|
||||
void init() override;
|
||||
void end_of_step() override;
|
||||
|
||||
void grow_arrays(int) override;
|
||||
void copy_arrays(int, int, int) override;
|
||||
|
||||
int pack_exchange(int, double *) override;
|
||||
int unpack_exchange(int, double *) override;
|
||||
|
||||
protected:
|
||||
FlowAxis flowax;
|
||||
double flowvel;
|
||||
double kT;
|
||||
std::vector<double> walls;
|
||||
|
||||
int flowdir;
|
||||
int rndseed;
|
||||
class RanMars *random;
|
||||
int *current_segment;
|
||||
|
||||
int compute_current_segment(double pos) const;
|
||||
void generate_velocity(int i);
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
@ -187,6 +187,8 @@ action fix_temp_rescale_kokkos.cpp
|
||||
action fix_temp_rescale_kokkos.h
|
||||
action fix_viscous_kokkos.cpp
|
||||
action fix_viscous_kokkos.h
|
||||
action fix_wall_flow_kokkos.cpp fix_wall_flow.cpp
|
||||
action fix_wall_flow_kokkos.h fix_wall_flow.h
|
||||
action fix_wall_gran_kokkos.cpp fix_wall_gran.cpp
|
||||
action fix_wall_gran_kokkos.h fix_wall_gran.h
|
||||
action fix_wall_gran_old.cpp fix_wall_gran.cpp
|
||||
|
||||
291
src/KOKKOS/fix_wall_flow_kokkos.cpp
Normal file
291
src/KOKKOS/fix_wall_flow_kokkos.cpp
Normal file
@ -0,0 +1,291 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
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: Vladislav Galigerov (HSE),
|
||||
Daniil Pavlov (MIPT)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "fix_wall_flow_kokkos.h"
|
||||
#include "atom_kokkos.h"
|
||||
#include "atom_masks.h"
|
||||
#include "force.h"
|
||||
#include "math_const.h"
|
||||
#include "memory_kokkos.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
template <class DeviceType>
|
||||
FixWallFlowKokkos<DeviceType>::FixWallFlowKokkos(LAMMPS *lmp, int narg, char **arg) :
|
||||
FixWallFlow(lmp, narg, arg), rand_pool(rndseed + comm->me)
|
||||
{
|
||||
kokkosable = 1;
|
||||
exchange_comm_device = sort_device = 1;
|
||||
atomKK = (AtomKokkos *) atom;
|
||||
execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
|
||||
datamask_read = X_MASK | RMASS_MASK | TYPE_MASK | MASK_MASK;
|
||||
datamask_modify = V_MASK;
|
||||
|
||||
memory->destroy(current_segment);
|
||||
current_segment = nullptr;
|
||||
grow_arrays(atomKK->nmax);
|
||||
|
||||
d_walls = d_walls_t("FixWallFlowKokkos::walls", walls.size());
|
||||
auto h_walls = Kokkos::create_mirror_view(d_walls);
|
||||
for (int i = 0; i < (int) walls.size(); ++i) h_walls(i) = walls[i];
|
||||
Kokkos::deep_copy(d_walls, h_walls);
|
||||
}
|
||||
|
||||
template <class DeviceType> FixWallFlowKokkos<DeviceType>::~FixWallFlowKokkos()
|
||||
{
|
||||
if (copymode) return;
|
||||
memoryKK->destroy_kokkos(k_current_segment, current_segment);
|
||||
}
|
||||
|
||||
template <class DeviceType> void FixWallFlowKokkos<DeviceType>::init()
|
||||
{
|
||||
atomKK->sync(execution_space, datamask_read);
|
||||
k_current_segment.template sync<DeviceType>();
|
||||
d_x = atomKK->k_x.template view<DeviceType>();
|
||||
|
||||
copymode = 1;
|
||||
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagFixWallFlowInit>(0, atom->nlocal), *this);
|
||||
copymode = 0;
|
||||
|
||||
k_current_segment.template modify<DeviceType>();
|
||||
}
|
||||
|
||||
template <class DeviceType>
|
||||
KOKKOS_INLINE_FUNCTION void FixWallFlowKokkos<DeviceType>::operator()(TagFixWallFlowInit,
|
||||
const int &i) const
|
||||
{
|
||||
double pos = d_x(i, flowax);
|
||||
d_current_segment(i) = compute_current_segment_kk(pos);
|
||||
}
|
||||
|
||||
template <class DeviceType> void FixWallFlowKokkos<DeviceType>::end_of_step()
|
||||
{
|
||||
atomKK->sync(execution_space, datamask_read);
|
||||
k_current_segment.template sync<DeviceType>();
|
||||
|
||||
d_x = atomKK->k_x.template view<DeviceType>();
|
||||
d_v = atomKK->k_v.template view<DeviceType>();
|
||||
d_type = atomKK->k_type.template view<DeviceType>();
|
||||
d_mask = atomKK->k_mask.template view<DeviceType>();
|
||||
d_mass = atomKK->k_mass.template view<DeviceType>();
|
||||
d_rmass = atomKK->k_rmass.template view<DeviceType>();
|
||||
|
||||
copymode = 1;
|
||||
if (d_rmass.data()) {
|
||||
Kokkos::parallel_for(
|
||||
Kokkos::RangePolicy<DeviceType, TagFixWallFlowEndOfStep<RMassTag>>(0, atom->nlocal), *this);
|
||||
} else {
|
||||
Kokkos::parallel_for(
|
||||
Kokkos::RangePolicy<DeviceType, TagFixWallFlowEndOfStep<MassTag>>(0, atom->nlocal), *this);
|
||||
}
|
||||
copymode = 0;
|
||||
atomKK->modified(execution_space, datamask_modify);
|
||||
k_current_segment.template modify<DeviceType>();
|
||||
}
|
||||
|
||||
template <class DeviceType>
|
||||
template <class MTag>
|
||||
KOKKOS_INLINE_FUNCTION void FixWallFlowKokkos<DeviceType>::operator()(TagFixWallFlowEndOfStep<MTag>,
|
||||
const int &atom_i) const
|
||||
{
|
||||
if (d_mask[atom_i] & groupbit) {
|
||||
double pos = d_x(atom_i, flowax);
|
||||
int prev_segment = d_current_segment(atom_i);
|
||||
d_current_segment(atom_i) = compute_current_segment_kk(pos);
|
||||
if (prev_segment != d_current_segment(atom_i)) { generate_velocity_kk<MTag>(atom_i); }
|
||||
}
|
||||
}
|
||||
|
||||
template <class DeviceType>
|
||||
template <class MTag>
|
||||
KOKKOS_INLINE_FUNCTION void FixWallFlowKokkos<DeviceType>::generate_velocity_kk(int atom_i) const
|
||||
{
|
||||
const int newton_iteration_count = 10;
|
||||
double mass = get_mass(MTag(), atom_i);
|
||||
const double gamma = 1.0 / std::sqrt(2.0 * kT / mass);
|
||||
double delta = gamma * flowvel;
|
||||
|
||||
const double edd = std::exp(-delta * delta) / MathConst::MY_PIS + delta * std::erf(delta);
|
||||
const double probability_threshold = 0.5 * (1. + delta / edd);
|
||||
|
||||
double direction = 1.0;
|
||||
|
||||
rand_type_t rand_gen = rand_pool.get_state();
|
||||
|
||||
if (/*random->uniform()*/ rand_gen.drand() > probability_threshold) {
|
||||
delta = -delta;
|
||||
direction = -direction;
|
||||
}
|
||||
|
||||
const double xi_0 = rand_gen.drand(); //random->uniform();
|
||||
const double F_inf = edd + delta;
|
||||
const double xi = xi_0 * F_inf;
|
||||
const double x_0 = (std::sqrt(delta * delta + 2) - delta) * 0.5;
|
||||
double x = x_0;
|
||||
for (int i = 0; i < newton_iteration_count; ++i) {
|
||||
x -= (std::exp(x * x) * MathConst::MY_PIS * (xi - delta * std::erfc(x)) - 1.0) / (x + delta) *
|
||||
0.5;
|
||||
}
|
||||
|
||||
const double nu = x + delta;
|
||||
const double v = nu / gamma;
|
||||
|
||||
d_v(atom_i, flowax) = v * direction;
|
||||
d_v(atom_i, (flowax + 1) % 3) =
|
||||
/*random->gaussian()*/ rand_gen.normal() / (gamma * MathConst::MY_SQRT2);
|
||||
d_v(atom_i, (flowax + 2) % 3) =
|
||||
/*random->gaussian()*/ rand_gen.normal() / (gamma * MathConst::MY_SQRT2);
|
||||
|
||||
rand_pool.free_state(rand_gen);
|
||||
}
|
||||
|
||||
template <class DeviceType>
|
||||
KOKKOS_INLINE_FUNCTION int
|
||||
FixWallFlowKokkos<DeviceType>::compute_current_segment_kk(double pos) const
|
||||
{
|
||||
int result = 0;
|
||||
for (; result < (int) d_walls.extent(0) - 1; ++result) {
|
||||
if (pos >= d_walls[result] && pos < d_walls[result + 1]) { return result; }
|
||||
}
|
||||
return -1; // -1 is "out of box" region
|
||||
}
|
||||
|
||||
template <class DeviceType> void FixWallFlowKokkos<DeviceType>::grow_arrays(int nmax)
|
||||
{
|
||||
k_current_segment.template sync<DeviceType>();
|
||||
memoryKK->grow_kokkos(k_current_segment, current_segment, nmax, "WallFlowKK::current_segment");
|
||||
k_current_segment.template modify<DeviceType>();
|
||||
|
||||
d_current_segment = k_current_segment.template view<DeviceType>();
|
||||
h_current_segment = k_current_segment.template view<LMPHostType>();
|
||||
}
|
||||
|
||||
template <class DeviceType> void FixWallFlowKokkos<DeviceType>::copy_arrays(int i, int j, int)
|
||||
{
|
||||
k_current_segment.template sync<LMPHostType>();
|
||||
h_current_segment(j) = h_current_segment(i);
|
||||
k_current_segment.template modify<LMPHostType>();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
sort local atom-based arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
template <class DeviceType>
|
||||
void FixWallFlowKokkos<DeviceType>::sort_kokkos(Kokkos::BinSort<KeyViewType, BinOp> &Sorter)
|
||||
{
|
||||
// always sort on the device
|
||||
|
||||
k_current_segment.sync_device();
|
||||
|
||||
Sorter.sort(LMPDeviceType(), k_current_segment.d_view);
|
||||
|
||||
k_current_segment.modify_device();
|
||||
}
|
||||
|
||||
template <class DeviceType> int FixWallFlowKokkos<DeviceType>::pack_exchange(int i, double *buf)
|
||||
{
|
||||
k_current_segment.sync_host();
|
||||
buf[0] = static_cast<double>(h_current_segment(i));
|
||||
return 1;
|
||||
}
|
||||
|
||||
template <class DeviceType>
|
||||
KOKKOS_INLINE_FUNCTION void FixWallFlowKokkos<DeviceType>::operator()(TagFixWallFlowPackExchange,
|
||||
const int &mysend) const
|
||||
{
|
||||
const int send_i = d_sendlist(mysend);
|
||||
const int segment = d_current_segment(send_i);
|
||||
d_buf(mysend) = static_cast<double>(segment);
|
||||
|
||||
const int copy_i = d_copylist(mysend);
|
||||
if (copy_i > -1) { d_current_segment(send_i) = d_current_segment(copy_i); }
|
||||
}
|
||||
|
||||
template <class DeviceType>
|
||||
int FixWallFlowKokkos<DeviceType>::pack_exchange_kokkos(const int &nsend,
|
||||
DAT::tdual_xfloat_2d &k_buf,
|
||||
DAT::tdual_int_1d k_sendlist,
|
||||
DAT::tdual_int_1d k_copylist,
|
||||
ExecutionSpace /*space*/)
|
||||
{
|
||||
k_current_segment.template sync<DeviceType>();
|
||||
|
||||
k_buf.template sync<DeviceType>();
|
||||
k_sendlist.template sync<DeviceType>();
|
||||
k_copylist.template sync<DeviceType>();
|
||||
|
||||
d_sendlist = k_sendlist.view<DeviceType>();
|
||||
d_copylist = k_copylist.view<DeviceType>();
|
||||
|
||||
d_buf = typename ArrayTypes<DeviceType>::t_xfloat_1d_um(k_buf.template view<DeviceType>().data(),
|
||||
k_buf.extent(0) * k_buf.extent(1));
|
||||
|
||||
copymode = 1;
|
||||
|
||||
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagFixWallFlowPackExchange>(0, nsend),
|
||||
*this);
|
||||
|
||||
copymode = 0;
|
||||
|
||||
k_buf.template modify<DeviceType>();
|
||||
k_current_segment.template modify<DeviceType>();
|
||||
|
||||
return nsend;
|
||||
}
|
||||
|
||||
template <class DeviceType> int FixWallFlowKokkos<DeviceType>::unpack_exchange(int i, double *buf)
|
||||
{
|
||||
k_current_segment.sync_host();
|
||||
h_current_segment(i) = static_cast<int>(buf[0]);
|
||||
k_current_segment.modify_host();
|
||||
return 1;
|
||||
}
|
||||
|
||||
template <class DeviceType>
|
||||
KOKKOS_INLINE_FUNCTION void FixWallFlowKokkos<DeviceType>::operator()(TagFixWallFlowUnpackExchange,
|
||||
const int &i) const
|
||||
{
|
||||
int index = d_indices(i);
|
||||
if (index > -1) { d_current_segment(index) = static_cast<int>(d_buf(i)); }
|
||||
}
|
||||
|
||||
template <class DeviceType>
|
||||
void FixWallFlowKokkos<DeviceType>::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,
|
||||
DAT::tdual_int_1d &k_indices, int nrecv,
|
||||
int /*nrecv1*/, int /*nextrarecv1*/,
|
||||
ExecutionSpace /*space*/)
|
||||
{
|
||||
d_buf = typename ArrayTypes<DeviceType>::t_xfloat_1d_um(k_buf.template view<DeviceType>().data(),
|
||||
k_buf.extent(0) * k_buf.extent(1));
|
||||
d_indices = k_indices.view<DeviceType>();
|
||||
|
||||
copymode = 1;
|
||||
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagFixWallFlowUnpackExchange>(0, nrecv),
|
||||
*this);
|
||||
copymode = 0;
|
||||
|
||||
k_current_segment.template modify<DeviceType>();
|
||||
}
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
template class FixWallFlowKokkos<LMPDeviceType>;
|
||||
#ifdef LMP_KOKKOS_GPU
|
||||
template class FixWallFlowKokkos<LMPHostType>;
|
||||
#endif
|
||||
} // namespace LAMMPS_NS
|
||||
130
src/KOKKOS/fix_wall_flow_kokkos.h
Normal file
130
src/KOKKOS/fix_wall_flow_kokkos.h
Normal file
@ -0,0 +1,130 @@
|
||||
/* -*- 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(wall/flow/kk,FixWallFlowKokkos<LMPDeviceType>);
|
||||
FixStyle(wall/flow/kk/device,FixWallFlowKokkos<LMPDeviceType>);
|
||||
FixStyle(wall/flow/kk/host,FixWallFlowKokkos<LMPHostType>);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
// clang-format off
|
||||
#ifndef LMP_FIX_WALL_FLOW_KOKKOS_H
|
||||
#define LMP_FIX_WALL_FLOW_KOKKOS_H
|
||||
|
||||
#include "fix_wall_flow.h"
|
||||
#include "kokkos_type.h"
|
||||
#include "kokkos_base.h"
|
||||
#include "Kokkos_Random.hpp"
|
||||
#include "comm_kokkos.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
struct TagFixWallFlowInit{};
|
||||
template<class MTag>
|
||||
struct TagFixWallFlowEndOfStep{};
|
||||
struct TagFixWallFlowPackExchange{};
|
||||
struct TagFixWallFlowUnpackExchange{};
|
||||
|
||||
template<class DeviceType>
|
||||
class FixWallFlowKokkos : public FixWallFlow, public KokkosBase {
|
||||
public:
|
||||
typedef DeviceType device_type;
|
||||
typedef ArrayTypes<DeviceType> AT;
|
||||
struct MassTag{};
|
||||
struct RMassTag{};
|
||||
FixWallFlowKokkos(class LAMMPS *, int, char **);
|
||||
~FixWallFlowKokkos();
|
||||
|
||||
void init() override;
|
||||
void end_of_step() override;
|
||||
void grow_arrays(int) override;
|
||||
void copy_arrays(int, int, int) override;
|
||||
void sort_kokkos(Kokkos::BinSort<KeyViewType, BinOp> &Sorter) override;
|
||||
int pack_exchange(int, double *) override;
|
||||
int unpack_exchange(int, double *) override;
|
||||
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
void operator() (TagFixWallFlowInit, const int&) const;
|
||||
|
||||
template<class MTag>
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
void operator()(TagFixWallFlowEndOfStep<MTag>, const int&) const;
|
||||
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
void operator()(TagFixWallFlowPackExchange, const int&) const;
|
||||
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
void operator()(TagFixWallFlowUnpackExchange, const int&) const;
|
||||
|
||||
int pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2d &buf,
|
||||
DAT::tdual_int_1d k_sendlist,
|
||||
DAT::tdual_int_1d k_copylist,
|
||||
ExecutionSpace space) override;
|
||||
|
||||
void unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,
|
||||
DAT::tdual_int_1d &indices,int nrecv,
|
||||
int /*nrecv1*/, int /*nextrarecv1*/,
|
||||
ExecutionSpace space) override;
|
||||
protected:
|
||||
typename AT::t_x_array d_x;
|
||||
typename AT::t_v_array d_v;
|
||||
typename AT::t_int_1d d_type;
|
||||
typename AT::t_int_1d d_mask;
|
||||
|
||||
typename AT::t_float_1d d_mass;
|
||||
typename AT::t_float_1d d_rmass;
|
||||
|
||||
typedef typename AT::t_xfloat_1d d_walls_t;
|
||||
typedef Kokkos::Random_XorShift64_Pool<DeviceType> rand_pool_t;
|
||||
typedef typename rand_pool_t::generator_type rand_type_t;
|
||||
|
||||
typename AT::tdual_int_1d k_current_segment;
|
||||
typename AT::t_int_1d d_current_segment;
|
||||
typename HAT::t_int_1d h_current_segment;
|
||||
|
||||
typename AT::t_int_1d d_sendlist;
|
||||
typename AT::t_xfloat_1d d_buf;
|
||||
typename AT::t_int_1d d_copylist;
|
||||
typename AT::t_int_1d d_indices;
|
||||
|
||||
d_walls_t d_walls;
|
||||
|
||||
rand_pool_t rand_pool;
|
||||
|
||||
template<class MTag>
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
void generate_velocity_kk(int atom_i) const;
|
||||
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
int compute_current_segment_kk(double pos) const;
|
||||
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
double get_mass(MassTag, int atom_i) const
|
||||
{
|
||||
return d_mass(d_type(atom_i));
|
||||
}
|
||||
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
double get_mass(RMassTag, int atom_i) const
|
||||
{
|
||||
return d_rmass(atom_i);
|
||||
}
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
@ -13,6 +13,7 @@ from libc.stdint cimport uintptr_t
|
||||
cimport cython
|
||||
from cpython.ref cimport PyObject
|
||||
from libc.stdlib cimport malloc, free
|
||||
from libc.string cimport memcpy
|
||||
|
||||
|
||||
cdef extern from "lammps.h" namespace "LAMMPS_NS":
|
||||
@ -451,15 +452,24 @@ cdef public object mliap_unified_connect_kokkos(char *fname, MLIAPDummyModel * m
|
||||
|
||||
cdef int nelements = <int>len(unified.element_types)
|
||||
cdef char **elements = <char**>malloc(nelements * sizeof(char*))
|
||||
cdef char * c_str
|
||||
cdef char * s
|
||||
cdef ssize_t slen
|
||||
|
||||
if not elements:
|
||||
raise MemoryError("failed to allocate memory for element names")
|
||||
|
||||
cdef char *elem_name
|
||||
for i, elem in enumerate(unified.element_types):
|
||||
elem_name_bytes = elem.encode('UTF-8')
|
||||
elem_name = elem_name_bytes
|
||||
elements[i] = &elem_name[0]
|
||||
py_str = elem.encode('UTF-8')
|
||||
s = py_str
|
||||
slen = len(py_str)
|
||||
c_str = <char *>malloc((slen+1)*sizeof(char))
|
||||
if not c_str:
|
||||
raise MemoryError("failed to allocate memory for element names")
|
||||
memcpy(c_str, s, slen)
|
||||
c_str[slen] = 0
|
||||
elements[i] = c_str
|
||||
|
||||
unified_int.descriptor.set_elements(elements, nelements)
|
||||
unified_int.model.nelements = nelements
|
||||
|
||||
|
||||
@ -315,7 +315,6 @@ void LAMMPS_NS::update_pair_forces(MLIAPDataKokkosDevice *data, double *fij)
|
||||
int i = pair_i[ii];
|
||||
int j = j_atoms[ii];
|
||||
// must not count any contribution where i is not a local atom
|
||||
if (i < nlocal) {
|
||||
Kokkos::atomic_add(&f[i*3+0], fij[ii3+0]);
|
||||
Kokkos::atomic_add(&f[i*3+1], fij[ii3+1]);
|
||||
Kokkos::atomic_add(&f[i*3+2], fij[ii3+2]);
|
||||
@ -354,7 +353,6 @@ void LAMMPS_NS::update_pair_forces(MLIAPDataKokkosDevice *data, double *fij)
|
||||
Kokkos::atomic_add(&d_vatom(j,5), 0.5*v[5]);
|
||||
}
|
||||
}
|
||||
}
|
||||
});
|
||||
|
||||
if (vflag) {
|
||||
@ -382,11 +380,9 @@ void LAMMPS_NS::update_atom_energy(MLIAPDataKokkosDevice *data, double *ei)
|
||||
|
||||
Kokkos::parallel_reduce(nlocal, KOKKOS_LAMBDA(int i, double &local_sum){
|
||||
double e = ei[i];
|
||||
// must not count any contribution where i is not a local atom
|
||||
if (i < nlocal) {
|
||||
|
||||
d_eatoms[i] = e;
|
||||
local_sum += e;
|
||||
}
|
||||
},*data->energy);
|
||||
}
|
||||
|
||||
|
||||
1131
src/MANYBODY/pair_rebomos.cpp
Normal file
1131
src/MANYBODY/pair_rebomos.cpp
Normal file
File diff suppressed because it is too large
Load Diff
220
src/MANYBODY/pair_rebomos.h
Normal file
220
src/MANYBODY/pair_rebomos.h
Normal file
@ -0,0 +1,220 @@
|
||||
/* -*- 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(rebomos,PairREBOMoS);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_REBOMOS_H
|
||||
#define LMP_PAIR_REBOMOS_H
|
||||
|
||||
#include "pair.h"
|
||||
#include "math_const.h"
|
||||
|
||||
#include <cmath>
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairREBOMoS : public Pair {
|
||||
public:
|
||||
PairREBOMoS(class LAMMPS *);
|
||||
~PairREBOMoS() override;
|
||||
void compute(int, int) override;
|
||||
void settings(int, char **) override;
|
||||
void coeff(int, char **) override;
|
||||
void init_style() override;
|
||||
double init_one(int, int) override;
|
||||
double memory_usage() override;
|
||||
|
||||
protected:
|
||||
double cutljrebosq; // cut for when to compute
|
||||
// REBO neighs of ghost atoms
|
||||
|
||||
double **lj1, **lj2, **lj3, **lj4; // pre-computed LJ coeffs for M,S types
|
||||
double cut3rebo; // maximum distance for 3rd REBO neigh
|
||||
|
||||
int maxlocal; // size of numneigh, firstneigh arrays
|
||||
int pgsize; // size of neighbor page
|
||||
int oneatom; // max # of neighbors for one atom
|
||||
MyPage<int> *ipage; // neighbor list pages
|
||||
int *REBO_numneigh; // # of pair neighbors for each atom
|
||||
int **REBO_firstneigh; // ptr to 1st neighbor of each atom
|
||||
|
||||
double *closestdistsq; // closest owned atom dist to each ghost
|
||||
double *nM, *nS; // sum of weighting fns with REBO neighs
|
||||
|
||||
double rcmin[2][2], rcmax[2][2], rcmaxsq[2][2], rcmaxp[2][2];
|
||||
double Q[2][2], alpha[2][2], A[2][2], BIJc[2][2], Beta[2][2];
|
||||
double b0[2], b1[2], b2[2], b3[2], b4[2], b5[2], b6[2];
|
||||
double bg0[2], bg1[2], bg2[2], bg3[2], bg4[2], bg5[2], bg6[2];
|
||||
double a0[2], a1[2], a2[2], a3[2];
|
||||
double rcLJmin[2][2], rcLJmax[2][2], rcLJmaxsq[2][2];
|
||||
double epsilon[2][2], sigma[2][2];
|
||||
|
||||
void REBO_neigh();
|
||||
void FREBO(int);
|
||||
void FLJ(int);
|
||||
|
||||
double bondorder(int, int, double *, double, double, double **);
|
||||
|
||||
inline double gSpline(const double costh, const int typei, double &dgdc) const
|
||||
{
|
||||
const double b0i = b0[typei];
|
||||
const double b1i = b1[typei];
|
||||
const double b2i = b2[typei];
|
||||
const double b3i = b3[typei];
|
||||
const double b4i = b4[typei];
|
||||
const double b5i = b5[typei];
|
||||
const double b6i = b6[typei];
|
||||
double g = 0.0;
|
||||
|
||||
if (costh >= -1.0 && costh < 0.5) {
|
||||
g = b6i * costh;
|
||||
double dg = 6.0 * b6i * costh;
|
||||
g += b5i;
|
||||
dg += 5.0 * b5i;
|
||||
g *= costh;
|
||||
dg *= costh;
|
||||
g += b4i;
|
||||
dg += 4.0 * b4i;
|
||||
g *= costh;
|
||||
dg *= costh;
|
||||
g += b3i;
|
||||
dg += 3.0 * b3i;
|
||||
g *= costh;
|
||||
dg *= costh;
|
||||
g += b2i;
|
||||
dg += 2.0 * b2i;
|
||||
g *= costh;
|
||||
dg *= costh;
|
||||
g += b1i;
|
||||
dg += b1i;
|
||||
g *= costh;
|
||||
g += b0i;
|
||||
dgdc = dg;
|
||||
|
||||
} else if (costh >= 0.5 && costh <= 1.0) {
|
||||
double gcos = b6i * costh;
|
||||
double dgcos = 6.0 * b6i * costh;
|
||||
gcos += b5i;
|
||||
dgcos += 5.0 * b5i;
|
||||
gcos *= costh;
|
||||
dgcos *= costh;
|
||||
gcos += b4i;
|
||||
dgcos += 4.0 * b4i;
|
||||
gcos *= costh;
|
||||
dgcos *= costh;
|
||||
gcos += b3i;
|
||||
dgcos += 3.0 * b3i;
|
||||
gcos *= costh;
|
||||
dgcos *= costh;
|
||||
gcos += b2i;
|
||||
dgcos += 2.0 * b2i;
|
||||
gcos *= costh;
|
||||
dgcos *= costh;
|
||||
gcos += b1i;
|
||||
dgcos += b1i;
|
||||
gcos *= costh;
|
||||
gcos += b0i;
|
||||
|
||||
const double bg0i = bg0[typei];
|
||||
const double bg1i = bg1[typei];
|
||||
const double bg2i = bg2[typei];
|
||||
const double bg3i = bg3[typei];
|
||||
const double bg4i = bg4[typei];
|
||||
const double bg5i = bg5[typei];
|
||||
const double bg6i = bg6[typei];
|
||||
double gamma = bg6i * costh;
|
||||
double dgamma = 6.0 * bg6i * costh;
|
||||
gamma += bg5i;
|
||||
dgamma += 5.0 * bg5i;
|
||||
gamma *= costh;
|
||||
dgamma *= costh;
|
||||
gamma += bg4i;
|
||||
dgamma += 4.0 * bg4i;
|
||||
gamma *= costh;
|
||||
dgamma *= costh;
|
||||
gamma += bg3i;
|
||||
dgamma += 3.0 * bg3i;
|
||||
gamma *= costh;
|
||||
dgamma *= costh;
|
||||
gamma += bg2i;
|
||||
dgamma += 2.0 * bg2i;
|
||||
gamma *= costh;
|
||||
dgamma *= costh;
|
||||
gamma += bg1i;
|
||||
dgamma += bg1i;
|
||||
gamma *= costh;
|
||||
gamma += bg0i;
|
||||
|
||||
const double tmp = MathConst::MY_2PI * (costh - 0.5);
|
||||
const double psi = 0.5 * (1 - cos(tmp));
|
||||
const double dpsi = MathConst::MY_PI * sin(tmp);
|
||||
g = gcos + psi * (gamma - gcos);
|
||||
dgdc = dgcos + dpsi * (gamma - gcos) + psi * (dgamma - dgcos);
|
||||
} else {
|
||||
dgdc = 0.0;
|
||||
}
|
||||
return g;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Pij calculation
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
inline double PijSpline(const double NM, const double NS, const int typei, double &dp) const
|
||||
{
|
||||
const double N = NM + NS;
|
||||
|
||||
dp = -a0[typei] + a1[typei] * a2[typei] * exp(-a2[typei] * N);
|
||||
return -a0[typei] * (N - 1) - a1[typei] * exp(-a2[typei] * N) + a3[typei];
|
||||
}
|
||||
|
||||
void read_file(char *);
|
||||
void allocate();
|
||||
|
||||
// ----------------------------------------------------------------------
|
||||
// S'(t) and S(t) cutoff functions
|
||||
// added to header for inlining
|
||||
// ----------------------------------------------------------------------
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
cutoff function Sprime
|
||||
return cutoff and dX = derivative
|
||||
no side effects
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
inline double Sp(double Xij, double Xmin, double Xmax, double &dX) const
|
||||
{
|
||||
double cutoff;
|
||||
|
||||
const double t = (Xij - Xmin) / (Xmax - Xmin);
|
||||
if (t <= 0.0) {
|
||||
cutoff = 1.0;
|
||||
dX = 0.0;
|
||||
} else if (t >= 1.0) {
|
||||
cutoff = 0.0;
|
||||
dX = 0.0;
|
||||
} else {
|
||||
cutoff = 0.5 * (1.0 + cos(t * MathConst::MY_PI));
|
||||
dX = (-0.5 * MathConst::MY_PI * sin(t * MathConst::MY_PI)) / (Xmax - Xmin);
|
||||
}
|
||||
return cutoff;
|
||||
};
|
||||
};
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
@ -254,11 +254,9 @@ void LAMMPS_NS::update_pair_energy(MLIAPData *data, double *eij)
|
||||
double e = 0.5 * eij[ii];
|
||||
|
||||
// must not count any contribution where i is not a local atom
|
||||
if (i < nlocal) {
|
||||
data->eatoms[i] += e;
|
||||
e_total += e;
|
||||
}
|
||||
}
|
||||
data->energy = e_total;
|
||||
}
|
||||
|
||||
@ -277,8 +275,6 @@ void LAMMPS_NS::update_pair_forces(MLIAPData *data, double *fij)
|
||||
int i = data->pair_i[ii];
|
||||
int j = data->jatoms[ii];
|
||||
|
||||
// must not count any contribution where i is not a local atom
|
||||
if (i < nlocal) {
|
||||
f[i][0] += fij[ii3];
|
||||
f[i][1] += fij[ii3 + 1];
|
||||
f[i][2] += fij[ii3 + 2];
|
||||
@ -288,7 +284,6 @@ void LAMMPS_NS::update_pair_forces(MLIAPData *data, double *fij)
|
||||
|
||||
if (data->vflag) data->pairmliap->v_tally(i, j, &fij[ii3], data->rij[ii]);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
#endif
|
||||
|
||||
@ -8,6 +8,7 @@ import lammps.mliap
|
||||
cimport cython
|
||||
from cpython.ref cimport PyObject
|
||||
from libc.stdlib cimport malloc, free
|
||||
from libc.string cimport memcpy
|
||||
|
||||
|
||||
cdef extern from "lammps.h" namespace "LAMMPS_NS":
|
||||
@ -387,15 +388,26 @@ cdef public object mliap_unified_connect(char *fname, MLIAPDummyModel * model,
|
||||
|
||||
cdef int nelements = <int>len(unified.element_types)
|
||||
cdef char **elements = <char**>malloc(nelements * sizeof(char*))
|
||||
cdef char * c_str
|
||||
cdef char * s
|
||||
cdef ssize_t slen
|
||||
|
||||
if not elements:
|
||||
raise MemoryError("failed to allocate memory for element names")
|
||||
|
||||
cdef char *elem_name
|
||||
for i, elem in enumerate(unified.element_types):
|
||||
elem_name_bytes = elem.encode('UTF-8')
|
||||
elem_name = elem_name_bytes
|
||||
elements[i] = &elem_name[0]
|
||||
py_str = elem.encode('UTF-8')
|
||||
|
||||
s = py_str
|
||||
slen = len(py_str)
|
||||
c_str = <char *>malloc((slen+1)*sizeof(char))
|
||||
if not c_str:
|
||||
raise MemoryError("failed to allocate memory for element names")
|
||||
memcpy(c_str, s, slen)
|
||||
c_str[slen] = 0
|
||||
|
||||
elements[i] = c_str
|
||||
|
||||
unified_int.descriptor.set_elements(elements, nelements)
|
||||
unified_int.model.nelements = nelements
|
||||
|
||||
|
||||
702
src/OPENMP/pair_rebomos_omp.cpp
Normal file
702
src/OPENMP/pair_rebomos_omp.cpp
Normal file
@ -0,0 +1,702 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
References:
|
||||
|
||||
This code:
|
||||
Stewart J A and Spearot D E (2013) Atomistic simulations of nanoindentation on the basal plane of crystalline molybdenum disulfide. Modelling Simul. Mater. Sci. Eng. 21.
|
||||
|
||||
Based on:
|
||||
Liang T, Phillpot S R and Sinnott S B (2009) Parameterization of a reactive many-body potential for Mo2S systems. Phys. Rev. B79 245110.
|
||||
Liang T, Phillpot S R and Sinnott S B (2012) Erratum: Parameterization of a reactive many-body potential for Mo-S systems. (Phys. Rev. B79 245110 (2009)) Phys. Rev. B85 199903(E).
|
||||
|
||||
LAMMPS file contributing authors: James Stewart, Khanh Dang and Douglas Spearot (University of Arkansas)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
// clang-format on
|
||||
|
||||
#include "pair_rebomos_omp.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "error.h"
|
||||
#include "math_special.h"
|
||||
#include "memory.h"
|
||||
#include "my_page.h"
|
||||
#include "neigh_list.h"
|
||||
|
||||
#include "suffix.h"
|
||||
|
||||
#include <cmath>
|
||||
|
||||
#include "omp_compat.h"
|
||||
#if defined(_OPENMP)
|
||||
#include <omp.h>
|
||||
#endif
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
using MathSpecial::cube;
|
||||
using MathSpecial::powint;
|
||||
using MathSpecial::square;
|
||||
|
||||
static constexpr double TOL = 1.0e-9;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairREBOMoSOMP::PairREBOMoSOMP(LAMMPS *lmp) : PairREBOMoS(lmp), ThrOMP(lmp, THR_PAIR)
|
||||
{
|
||||
suffix_flag |= Suffix::OMP;
|
||||
respa_enable = 0;
|
||||
}
|
||||
|
||||
// clang-format off
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairREBOMoSOMP::compute(int eflag, int vflag)
|
||||
{
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
REBO_neigh_thr();
|
||||
|
||||
const int nall = atom->nlocal + atom->nghost;
|
||||
const int nthreads = comm->nthreads;
|
||||
const int inum = list->inum;
|
||||
|
||||
#if defined(_OPENMP)
|
||||
#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(eflag,vflag)
|
||||
#endif
|
||||
{
|
||||
int ifrom, ito, tid;
|
||||
|
||||
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
|
||||
ThrData *thr = fix->get_thr(tid);
|
||||
thr->timer(Timer::START);
|
||||
ev_setup_thr(eflag, vflag, nall, eatom, vatom, nullptr, thr);
|
||||
|
||||
FREBO_thr(ifrom,ito,eflag,thr);
|
||||
FLJ_thr(ifrom,ito,eflag,thr);
|
||||
|
||||
thr->timer(Timer::PAIR);
|
||||
reduce_thr(this, eflag, vflag, thr);
|
||||
} // end of omp parallel region
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
create REBO neighbor list from main neighbor list
|
||||
REBO neighbor list stores neighbors of ghost atoms
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairREBOMoSOMP::REBO_neigh_thr()
|
||||
{
|
||||
const int nthreads = comm->nthreads;
|
||||
|
||||
if (atom->nmax > maxlocal) {
|
||||
maxlocal = atom->nmax;
|
||||
memory->destroy(REBO_numneigh);
|
||||
memory->sfree(REBO_firstneigh);
|
||||
memory->destroy(nM);
|
||||
memory->destroy(nS);
|
||||
memory->create(REBO_numneigh,maxlocal,"REBOMoS:numneigh");
|
||||
REBO_firstneigh = (int **) memory->smalloc(maxlocal*sizeof(int *),
|
||||
"REBOMoS:firstneigh");
|
||||
memory->create(nM,maxlocal,"REBOMoS:nM");
|
||||
memory->create(nS,maxlocal,"REBOMoS:nS");
|
||||
}
|
||||
|
||||
#if defined(_OPENMP)
|
||||
#pragma omp parallel LMP_DEFAULT_NONE
|
||||
#endif
|
||||
{
|
||||
int i,j,ii,jj,n,jnum,itype,jtype;
|
||||
double xtmp,ytmp,ztmp,delx,dely,delz,rsq,dS;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
int *neighptr;
|
||||
|
||||
double **x = atom->x;
|
||||
int *type = atom->type;
|
||||
|
||||
const int allnum = list->inum + list->gnum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
#if defined(_OPENMP)
|
||||
const int tid = omp_get_thread_num();
|
||||
#else
|
||||
const int tid = 0;
|
||||
#endif
|
||||
|
||||
const int iidelta = 1 + allnum/nthreads;
|
||||
const int iifrom = tid*iidelta;
|
||||
const int iito = ((iifrom+iidelta)>allnum) ? allnum : (iifrom+iidelta);
|
||||
|
||||
// store all REBO neighs of owned and ghost atoms
|
||||
// scan full neighbor list of I
|
||||
|
||||
// each thread has its own page allocator
|
||||
MyPage<int> &ipg = ipage[tid];
|
||||
ipg.reset();
|
||||
|
||||
for (ii = iifrom; ii < iito; ii++) {
|
||||
i = ilist[ii];
|
||||
|
||||
n = 0;
|
||||
neighptr = ipg.vget();
|
||||
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
itype = map[type[i]];
|
||||
nM[i] = nS[i] = 0.0;
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
j &= NEIGHMASK;
|
||||
jtype = map[type[j]];
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
|
||||
if (rsq < rcmaxsq[itype][jtype]) {
|
||||
neighptr[n++] = j;
|
||||
if (jtype == 0)
|
||||
nM[i] += Sp(sqrt(rsq),rcmin[itype][jtype],rcmax[itype][jtype],dS);
|
||||
else
|
||||
nS[i] += Sp(sqrt(rsq),rcmin[itype][jtype],rcmax[itype][jtype],dS);
|
||||
}
|
||||
}
|
||||
|
||||
REBO_firstneigh[i] = neighptr;
|
||||
REBO_numneigh[i] = n;
|
||||
ipg.vgot(n);
|
||||
if (ipg.status())
|
||||
error->one(FLERR,"REBO list overflow, boost neigh_modify one");
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
REBO forces and energy
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairREBOMoSOMP::FREBO_thr(int ifrom, int ito, int eflag, ThrData * const thr)
|
||||
{
|
||||
int i,j,k,ii,itype,jtype;
|
||||
tagint itag, jtag;
|
||||
double delx,dely,delz,evdwl,fpair,xtmp,ytmp,ztmp;
|
||||
double rsq,rij,wij;
|
||||
double Qij,Aij,alphaij,VR,pre,dVRdi,VA,bij,dVAdi,dVA;
|
||||
double dwij,del[3];
|
||||
int *ilist,*REBO_neighs;
|
||||
|
||||
evdwl = 0.0;
|
||||
|
||||
const double * const * const x = atom->x;
|
||||
double * const * const f = thr->get_f();
|
||||
const int * const type = atom->type;
|
||||
const tagint * const tag = atom->tag;
|
||||
const int nlocal = atom->nlocal;
|
||||
|
||||
ilist = list->ilist;
|
||||
|
||||
// two-body interactions from REBO neighbor list, skip half of them
|
||||
|
||||
for (ii = ifrom; ii < ito; ii++) {
|
||||
i = ilist[ii];
|
||||
itag = tag[i];
|
||||
itype = map[type[i]];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
REBO_neighs = REBO_firstneigh[i];
|
||||
|
||||
for (k = 0; k < REBO_numneigh[i]; k++) {
|
||||
j = REBO_neighs[k];
|
||||
jtag = tag[j];
|
||||
|
||||
if (itag > jtag) {
|
||||
if ((itag+jtag) % 2 == 0) continue;
|
||||
} else if (itag < jtag) {
|
||||
if ((itag+jtag) % 2 == 1) continue;
|
||||
} else {
|
||||
if (x[j][2] < ztmp) continue;
|
||||
if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
|
||||
if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
|
||||
}
|
||||
|
||||
jtype = map[type[j]];
|
||||
|
||||
delx = x[i][0] - x[j][0];
|
||||
dely = x[i][1] - x[j][1];
|
||||
delz = x[i][2] - x[j][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
rij = sqrt(rsq);
|
||||
wij = Sp(rij,rcmin[itype][jtype],rcmax[itype][jtype],dwij);
|
||||
if (wij <= TOL) continue;
|
||||
|
||||
Qij = Q[itype][jtype];
|
||||
Aij = A[itype][jtype];
|
||||
alphaij = alpha[itype][jtype];
|
||||
|
||||
VR = wij*(1.0+(Qij/rij)) * Aij*exp(-alphaij*rij);
|
||||
pre = wij*Aij * exp(-alphaij*rij);
|
||||
dVRdi = pre * ((-alphaij)-(Qij/rsq)-(Qij*alphaij/rij));
|
||||
dVRdi += VR/wij * dwij;
|
||||
|
||||
VA = dVA = 0.0;
|
||||
VA = -wij * BIJc[itype][jtype] * exp(-Beta[itype][jtype]*rij);
|
||||
|
||||
dVA = -Beta[itype][jtype] * VA;
|
||||
dVA += VA/wij * dwij;
|
||||
|
||||
del[0] = delx;
|
||||
del[1] = dely;
|
||||
del[2] = delz;
|
||||
bij = bondorder_thr(i,j,del,rij,VA,thr);
|
||||
dVAdi = bij*dVA;
|
||||
|
||||
fpair = -(dVRdi+dVAdi) / rij;
|
||||
f[i][0] += delx*fpair;
|
||||
f[i][1] += dely*fpair;
|
||||
f[i][2] += delz*fpair;
|
||||
f[j][0] -= delx*fpair;
|
||||
f[j][1] -= dely*fpair;
|
||||
f[j][2] -= delz*fpair;
|
||||
|
||||
if (eflag) evdwl = VR + bij*VA;
|
||||
if (evflag) ev_tally_thr(this,i,j,nlocal,/* newton_pair */1,evdwl,0.0,fpair,delx,dely,delz,thr);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
compute LJ forces and energy
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairREBOMoSOMP::FLJ_thr(int ifrom, int ito, int eflag, ThrData * const thr)
|
||||
{
|
||||
int i,j,ii,jj,jnum,itype,jtype;
|
||||
tagint itag,jtag;
|
||||
double evdwl,fpair,xtmp,ytmp,ztmp;
|
||||
double rij,delij[3],rijsq;
|
||||
double VLJ,dVLJ;
|
||||
double vdw,dvdw;
|
||||
double r2inv,r6inv;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
double c2,c3,dr,drp,r6;
|
||||
|
||||
// I-J interaction from full neighbor list
|
||||
// skip 1/2 of interactions since only consider each pair once
|
||||
|
||||
evdwl = 0.0;
|
||||
|
||||
const double * const * const x = atom->x;
|
||||
double * const * const f = thr->get_f();
|
||||
const tagint * const tag = atom->tag;
|
||||
const int * const type = atom->type;
|
||||
const int nlocal = atom->nlocal;
|
||||
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = ifrom; ii < ito; ii++) {
|
||||
i = ilist[ii];
|
||||
itag = tag[i];
|
||||
itype = map[type[i]];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
j &= NEIGHMASK;
|
||||
jtag = tag[j];
|
||||
|
||||
if (itag > jtag) {
|
||||
if ((itag+jtag) % 2 == 0) continue;
|
||||
} else if (itag < jtag) {
|
||||
if ((itag+jtag) % 2 == 1) continue;
|
||||
} else {
|
||||
if (x[j][2] < ztmp) continue;
|
||||
if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
|
||||
if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
|
||||
}
|
||||
jtype = map[type[j]];
|
||||
|
||||
delij[0] = xtmp - x[j][0];
|
||||
delij[1] = ytmp - x[j][1];
|
||||
delij[2] = ztmp - x[j][2];
|
||||
rijsq = delij[0]*delij[0] + delij[1]*delij[1] + delij[2]*delij[2];
|
||||
rij = sqrt(rijsq);
|
||||
|
||||
// compute LJ forces and energy
|
||||
|
||||
// Outside Rmax
|
||||
if (rij > rcLJmax[itype][jtype] || rij < rcLJmin[itype][jtype]){
|
||||
VLJ = 0;
|
||||
dVLJ = 0;
|
||||
}
|
||||
|
||||
// Inside Rmax and above 0.95*sigma
|
||||
else if (rij <= rcLJmax[itype][jtype] && rij >= 0.95*sigma[itype][jtype]){
|
||||
r2inv = 1.0/rijsq;
|
||||
r6inv = r2inv*r2inv*r2inv;
|
||||
VLJ = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
|
||||
dVLJ = -r6inv*(lj1[itype][jtype]*r6inv - lj2[itype][jtype])/rij;
|
||||
}
|
||||
|
||||
// Below 0.95*sigma
|
||||
else if (rij < 0.95*sigma[itype][jtype] && rij >= rcLJmin[itype][jtype]){
|
||||
dr = 0.95*sigma[itype][jtype] - rcLJmin[itype][jtype];
|
||||
r6 = powint((sigma[itype][jtype]/(0.95*sigma[itype][jtype])),6);
|
||||
vdw = 4*epsilon[itype][jtype]*r6*(r6 - 1.0);
|
||||
dvdw = (-4*epsilon[itype][jtype]/(0.95*sigma[itype][jtype]))*r6*(12.0*r6 - 6.0);
|
||||
c2 = ((3.0/dr)*vdw - dvdw)/dr;
|
||||
c3 = (vdw/(dr*dr) - c2)/dr;
|
||||
|
||||
drp = rij - rcLJmin[itype][jtype];
|
||||
VLJ = drp*drp*(drp*c3 + c2);
|
||||
dVLJ = drp*(3.0*drp*c3 + 2.0*c2);
|
||||
}
|
||||
|
||||
fpair = -dVLJ/rij;
|
||||
f[i][0] += delij[0]*fpair;
|
||||
f[i][1] += delij[1]*fpair;
|
||||
f[i][2] += delij[2]*fpair;
|
||||
f[j][0] -= delij[0]*fpair;
|
||||
f[j][1] -= delij[1]*fpair;
|
||||
f[j][2] -= delij[2]*fpair;
|
||||
|
||||
if (eflag) evdwl = VLJ;
|
||||
if (evflag) ev_tally_thr(this,i,j,nlocal,/*newton_pair*/1,evdwl,0.0,fpair,delij[0],delij[1],delij[2],thr);
|
||||
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Bij function
|
||||
|
||||
The bond order term modified the attractive portion of the REBO
|
||||
potential based on the number of atoms around a specific pair
|
||||
and the bond angle between sets of three atoms.
|
||||
|
||||
The functions G(cos(theta)) and P(N) are evaluated and their
|
||||
derivatives are also computed for use in the force calculation.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairREBOMoSOMP::bondorder_thr(int i, int j, double rij[3], double rijmag, double VA, ThrData *thr)
|
||||
{
|
||||
int atomi,atomj,atomk,atoml;
|
||||
int k,l;
|
||||
int itype, jtype, ktype, ltype;
|
||||
double rik[3], rjl[3], rji[3], rki[3],rlj[3], dwjl, bij;
|
||||
double NijM,NijS,NjiM,NjiS,wik,dwik,wjl;
|
||||
double rikmag,rjlmag,cosjik,cosijl,g,tmp2;
|
||||
double Etmp,pij,tmp,dwij,dS;
|
||||
double dgdc,pji;
|
||||
double dcosjikdri[3],dcosijldri[3],dcosjikdrk[3];
|
||||
double dp;
|
||||
double dcosjikdrj[3],dcosijldrj[3],dcosijldrl[3];
|
||||
double fi[3],fj[3],fk[3],fl[3];
|
||||
double PijS, PjiS;
|
||||
int *REBO_neighs;
|
||||
|
||||
const double * const * const x = atom->x;
|
||||
double * const * const f = thr->get_f();
|
||||
const int * const type = atom->type;
|
||||
|
||||
atomi = i;
|
||||
atomj = j;
|
||||
itype = map[type[i]];
|
||||
jtype = map[type[j]];
|
||||
Sp(rijmag,rcmin[itype][jtype],rcmax[itype][jtype],dwij);
|
||||
NijM = nM[i];
|
||||
NijS = nS[i];
|
||||
NjiM = nM[j];
|
||||
NjiS = nS[j];
|
||||
bij = 0.0;
|
||||
tmp = 0.0;
|
||||
tmp2 = 0.0;
|
||||
dgdc = 0.0;
|
||||
Etmp = 0.0;
|
||||
|
||||
REBO_neighs = REBO_firstneigh[i];
|
||||
for (k = 0; k < REBO_numneigh[i]; k++) {
|
||||
atomk = REBO_neighs[k];
|
||||
if (atomk != atomj) {
|
||||
ktype = map[type[atomk]];
|
||||
rik[0] = x[atomi][0]-x[atomk][0];
|
||||
rik[1] = x[atomi][1]-x[atomk][1];
|
||||
rik[2] = x[atomi][2]-x[atomk][2];
|
||||
rikmag = sqrt((rik[0]*rik[0])+(rik[1]*rik[1])+(rik[2]*rik[2]));
|
||||
wik = Sp(rikmag,rcmin[itype][ktype],rcmax[itype][ktype],dS);
|
||||
cosjik = ((rij[0]*rik[0])+(rij[1]*rik[1])+(rij[2]*rik[2])) / (rijmag*rikmag);
|
||||
cosjik = MIN(cosjik,1.0);
|
||||
cosjik = MAX(cosjik,-1.0);
|
||||
|
||||
// evaluate g and derivative dg
|
||||
|
||||
g = gSpline(cosjik,itype,dgdc);
|
||||
Etmp = Etmp+(wik*g);
|
||||
}
|
||||
}
|
||||
|
||||
dp = 0.0;
|
||||
PijS = PijSpline(NijM,NijS,itype,dp);
|
||||
pij = 1.0/sqrt(1.0+Etmp+PijS);
|
||||
tmp = -0.5*cube(pij);
|
||||
|
||||
// derivative calculations
|
||||
|
||||
REBO_neighs = REBO_firstneigh[i];
|
||||
for (k = 0; k < REBO_numneigh[i]; k++) {
|
||||
atomk = REBO_neighs[k];
|
||||
if (atomk != atomj) {
|
||||
ktype = map[type[atomk]];
|
||||
rik[0] = x[atomi][0]-x[atomk][0];
|
||||
rik[1] = x[atomi][1]-x[atomk][1];
|
||||
rik[2] = x[atomi][2]-x[atomk][2];
|
||||
rikmag = sqrt((rik[0]*rik[0])+(rik[1]*rik[1])+(rik[2]*rik[2]));
|
||||
wik = Sp(rikmag,rcmin[itype][ktype],rcmax[itype][ktype],dwik);
|
||||
cosjik = (rij[0]*rik[0] + rij[1]*rik[1] + rij[2]*rik[2]) / (rijmag*rikmag);
|
||||
cosjik = MIN(cosjik,1.0);
|
||||
cosjik = MAX(cosjik,-1.0);
|
||||
|
||||
dcosjikdri[0] = ((rij[0]+rik[0])/(rijmag*rikmag)) -
|
||||
(cosjik*((rij[0]/(rijmag*rijmag))+(rik[0]/(rikmag*rikmag))));
|
||||
dcosjikdri[1] = ((rij[1]+rik[1])/(rijmag*rikmag)) -
|
||||
(cosjik*((rij[1]/(rijmag*rijmag))+(rik[1]/(rikmag*rikmag))));
|
||||
dcosjikdri[2] = ((rij[2]+rik[2])/(rijmag*rikmag)) -
|
||||
(cosjik*((rij[2]/(rijmag*rijmag))+(rik[2]/(rikmag*rikmag))));
|
||||
dcosjikdrk[0] = (-rij[0]/(rijmag*rikmag)) +
|
||||
(cosjik*(rik[0]/(rikmag*rikmag)));
|
||||
dcosjikdrk[1] = (-rij[1]/(rijmag*rikmag)) +
|
||||
(cosjik*(rik[1]/(rikmag*rikmag)));
|
||||
dcosjikdrk[2] = (-rij[2]/(rijmag*rikmag)) +
|
||||
(cosjik*(rik[2]/(rikmag*rikmag)));
|
||||
dcosjikdrj[0] = (-rik[0]/(rijmag*rikmag)) +
|
||||
(cosjik*(rij[0]/(rijmag*rijmag)));
|
||||
dcosjikdrj[1] = (-rik[1]/(rijmag*rikmag)) +
|
||||
(cosjik*(rij[1]/(rijmag*rijmag)));
|
||||
dcosjikdrj[2] = (-rik[2]/(rijmag*rikmag)) +
|
||||
(cosjik*(rij[2]/(rijmag*rijmag)));
|
||||
|
||||
g = gSpline(cosjik,itype,dgdc);
|
||||
tmp2 = VA*0.5*(tmp*wik*dgdc);
|
||||
fj[0] = -tmp2*dcosjikdrj[0];
|
||||
fj[1] = -tmp2*dcosjikdrj[1];
|
||||
fj[2] = -tmp2*dcosjikdrj[2];
|
||||
fi[0] = -tmp2*dcosjikdri[0];
|
||||
fi[1] = -tmp2*dcosjikdri[1];
|
||||
fi[2] = -tmp2*dcosjikdri[2];
|
||||
fk[0] = -tmp2*dcosjikdrk[0];
|
||||
fk[1] = -tmp2*dcosjikdrk[1];
|
||||
fk[2] = -tmp2*dcosjikdrk[2];
|
||||
|
||||
// coordination forces
|
||||
|
||||
// dwik forces (from partial derivative)
|
||||
|
||||
tmp2 = VA*0.5*(tmp*dwik*g)/rikmag;
|
||||
fi[0] -= tmp2*rik[0];
|
||||
fi[1] -= tmp2*rik[1];
|
||||
fi[2] -= tmp2*rik[2];
|
||||
fk[0] += tmp2*rik[0];
|
||||
fk[1] += tmp2*rik[1];
|
||||
fk[2] += tmp2*rik[2];
|
||||
|
||||
// PIJ forces (from coordination P(N) term)
|
||||
|
||||
tmp2 = VA*0.5*(tmp*dp*dwik)/rikmag;
|
||||
fi[0] -= tmp2*rik[0];
|
||||
fi[1] -= tmp2*rik[1];
|
||||
fi[2] -= tmp2*rik[2];
|
||||
fk[0] += tmp2*rik[0];
|
||||
fk[1] += tmp2*rik[1];
|
||||
fk[2] += tmp2*rik[2];
|
||||
|
||||
// dgdN forces are removed
|
||||
|
||||
f[atomi][0] += fi[0]; f[atomi][1] += fi[1]; f[atomi][2] += fi[2];
|
||||
f[atomj][0] += fj[0]; f[atomj][1] += fj[1]; f[atomj][2] += fj[2];
|
||||
f[atomk][0] += fk[0]; f[atomk][1] += fk[1]; f[atomk][2] += fk[2];
|
||||
|
||||
if (vflag_either) {
|
||||
rji[0] = -rij[0]; rji[1] = -rij[1]; rji[2] = -rij[2];
|
||||
rki[0] = -rik[0]; rki[1] = -rik[1]; rki[2] = -rik[2];
|
||||
v_tally3_thr(this,atomi,atomj,atomk,fj,fk,rji,rki,thr);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// PIJ force contribution additional term
|
||||
tmp2 = -VA*0.5*(tmp*dp*dwij)/rijmag;
|
||||
|
||||
f[atomi][0] += rij[0]*tmp2;
|
||||
f[atomi][1] += rij[1]*tmp2;
|
||||
f[atomi][2] += rij[2]*tmp2;
|
||||
f[atomj][0] -= rij[0]*tmp2;
|
||||
f[atomj][1] -= rij[1]*tmp2;
|
||||
f[atomj][2] -= rij[2]*tmp2;
|
||||
|
||||
if (vflag_either) v_tally2_thr(this,atomi,atomj,tmp2,rij,thr);
|
||||
|
||||
tmp = 0.0;
|
||||
tmp2 = 0.0;
|
||||
Etmp = 0.0;
|
||||
|
||||
REBO_neighs = REBO_firstneigh[j];
|
||||
for (l = 0; l < REBO_numneigh[j]; l++) {
|
||||
atoml = REBO_neighs[l];
|
||||
if (atoml != atomi) {
|
||||
ltype = map[type[atoml]];
|
||||
rjl[0] = x[atomj][0]-x[atoml][0];
|
||||
rjl[1] = x[atomj][1]-x[atoml][1];
|
||||
rjl[2] = x[atomj][2]-x[atoml][2];
|
||||
rjlmag = sqrt((rjl[0]*rjl[0])+(rjl[1]*rjl[1])+(rjl[2]*rjl[2]));
|
||||
wjl = Sp(rjlmag,rcmin[jtype][ltype],rcmax[jtype][ltype],dS);
|
||||
cosijl = -1.0*((rij[0]*rjl[0])+(rij[1]*rjl[1])+(rij[2]*rjl[2])) / (rijmag*rjlmag);
|
||||
cosijl = MIN(cosijl,1.0);
|
||||
cosijl = MAX(cosijl,-1.0);
|
||||
|
||||
// evaluate g and derivative dg
|
||||
|
||||
g = gSpline(cosijl,jtype,dgdc);
|
||||
Etmp = Etmp+(wjl*g);
|
||||
}
|
||||
}
|
||||
|
||||
dp = 0.0;
|
||||
PjiS = PijSpline(NjiM,NjiS,jtype,dp);
|
||||
pji = 1.0/sqrt(1.0+Etmp+PjiS);
|
||||
tmp = -0.5*cube(pji);
|
||||
|
||||
REBO_neighs = REBO_firstneigh[j];
|
||||
for (l = 0; l < REBO_numneigh[j]; l++) {
|
||||
atoml = REBO_neighs[l];
|
||||
if (atoml != atomi) {
|
||||
ltype = map[type[atoml]];
|
||||
rjl[0] = x[atomj][0]-x[atoml][0];
|
||||
rjl[1] = x[atomj][1]-x[atoml][1];
|
||||
rjl[2] = x[atomj][2]-x[atoml][2];
|
||||
rjlmag = sqrt((rjl[0]*rjl[0])+(rjl[1]*rjl[1])+(rjl[2]*rjl[2]));
|
||||
wjl = Sp(rjlmag,rcmin[jtype][ltype],rcmax[jtype][ltype],dwjl);
|
||||
cosijl = (-1.0*((rij[0]*rjl[0])+(rij[1]*rjl[1])+(rij[2]*rjl[2]))) / (rijmag*rjlmag);
|
||||
cosijl = MIN(cosijl,1.0);
|
||||
cosijl = MAX(cosijl,-1.0);
|
||||
|
||||
dcosijldri[0] = (-rjl[0]/(rijmag*rjlmag)) -
|
||||
(cosijl*rij[0]/(rijmag*rijmag));
|
||||
dcosijldri[1] = (-rjl[1]/(rijmag*rjlmag)) -
|
||||
(cosijl*rij[1]/(rijmag*rijmag));
|
||||
dcosijldri[2] = (-rjl[2]/(rijmag*rjlmag)) -
|
||||
(cosijl*rij[2]/(rijmag*rijmag));
|
||||
dcosijldrj[0] = ((-rij[0]+rjl[0])/(rijmag*rjlmag)) +
|
||||
(cosijl*((rij[0]/square(rijmag))-(rjl[0]/(rjlmag*rjlmag))));
|
||||
dcosijldrj[1] = ((-rij[1]+rjl[1])/(rijmag*rjlmag)) +
|
||||
(cosijl*((rij[1]/square(rijmag))-(rjl[1]/(rjlmag*rjlmag))));
|
||||
dcosijldrj[2] = ((-rij[2]+rjl[2])/(rijmag*rjlmag)) +
|
||||
(cosijl*((rij[2]/square(rijmag))-(rjl[2]/(rjlmag*rjlmag))));
|
||||
dcosijldrl[0] = (rij[0]/(rijmag*rjlmag))+(cosijl*rjl[0]/(rjlmag*rjlmag));
|
||||
dcosijldrl[1] = (rij[1]/(rijmag*rjlmag))+(cosijl*rjl[1]/(rjlmag*rjlmag));
|
||||
dcosijldrl[2] = (rij[2]/(rijmag*rjlmag))+(cosijl*rjl[2]/(rjlmag*rjlmag));
|
||||
|
||||
// evaluate g and derivatives dg
|
||||
|
||||
g = gSpline(cosijl,jtype,dgdc);
|
||||
tmp2 = VA*0.5*(tmp*wjl*dgdc);
|
||||
fi[0] = -tmp2*dcosijldri[0];
|
||||
fi[1] = -tmp2*dcosijldri[1];
|
||||
fi[2] = -tmp2*dcosijldri[2];
|
||||
fj[0] = -tmp2*dcosijldrj[0];
|
||||
fj[1] = -tmp2*dcosijldrj[1];
|
||||
fj[2] = -tmp2*dcosijldrj[2];
|
||||
fl[0] = -tmp2*dcosijldrl[0];
|
||||
fl[1] = -tmp2*dcosijldrl[1];
|
||||
fl[2] = -tmp2*dcosijldrl[2];
|
||||
|
||||
// coordination forces
|
||||
|
||||
// dwik forces (from partial derivative)
|
||||
|
||||
tmp2 = VA*0.5*(tmp*dwjl*g)/rjlmag;
|
||||
fj[0] -= tmp2*rjl[0];
|
||||
fj[1] -= tmp2*rjl[1];
|
||||
fj[2] -= tmp2*rjl[2];
|
||||
fl[0] += tmp2*rjl[0];
|
||||
fl[1] += tmp2*rjl[1];
|
||||
fl[2] += tmp2*rjl[2];
|
||||
|
||||
// PIJ forces (coordination)
|
||||
|
||||
tmp2 = VA*0.5*(tmp*dp*dwjl)/rjlmag;
|
||||
fj[0] -= tmp2*rjl[0];
|
||||
fj[1] -= tmp2*rjl[1];
|
||||
fj[2] -= tmp2*rjl[2];
|
||||
fl[0] += tmp2*rjl[0];
|
||||
fl[1] += tmp2*rjl[1];
|
||||
fl[2] += tmp2*rjl[2];
|
||||
|
||||
// dgdN forces are removed
|
||||
|
||||
f[atomi][0] += fi[0]; f[atomi][1] += fi[1]; f[atomi][2] += fi[2];
|
||||
f[atomj][0] += fj[0]; f[atomj][1] += fj[1]; f[atomj][2] += fj[2];
|
||||
f[atoml][0] += fl[0]; f[atoml][1] += fl[1]; f[atoml][2] += fl[2];
|
||||
|
||||
if (vflag_either) {
|
||||
rlj[0] = -rjl[0]; rlj[1] = -rjl[1]; rlj[2] = -rjl[2];
|
||||
v_tally3_thr(this,atomi,atomj,atoml,fi,fl,rij,rlj,thr);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// PIJ force contribution additional term
|
||||
|
||||
tmp2 = -VA*0.5*(tmp*dp*dwij)/rijmag;
|
||||
f[atomi][0] += rij[0]*tmp2;
|
||||
f[atomi][1] += rij[1]*tmp2;
|
||||
f[atomi][2] += rij[2]*tmp2;
|
||||
f[atomj][0] -= rij[0]*tmp2;
|
||||
f[atomj][1] -= rij[1]*tmp2;
|
||||
f[atomj][2] -= rij[2]*tmp2;
|
||||
|
||||
if (vflag_either) v_tally2_thr(this,atomi,atomj,tmp2,rij,thr);
|
||||
|
||||
bij = (0.5*(pij+pji));
|
||||
return bij;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
memory usage of local atom-based arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairREBOMoSOMP::memory_usage()
|
||||
{
|
||||
double bytes = memory_usage_thr();
|
||||
bytes += PairREBOMoS::memory_usage();
|
||||
|
||||
return bytes;
|
||||
}
|
||||
46
src/OPENMP/pair_rebomos_omp.h
Normal file
46
src/OPENMP/pair_rebomos_omp.h
Normal file
@ -0,0 +1,46 @@
|
||||
/* -*- 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(rebomos/omp,PairREBOMoSOMP);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_REBOMOS_OMP_H
|
||||
#define LMP_PAIR_REBOMOS_OMP_H
|
||||
|
||||
#include "pair_rebomos.h"
|
||||
#include "thr_omp.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairREBOMoSOMP : public PairREBOMoS, public ThrOMP {
|
||||
public:
|
||||
PairREBOMoSOMP(class LAMMPS *);
|
||||
|
||||
void compute(int, int) override;
|
||||
double memory_usage() override;
|
||||
|
||||
protected:
|
||||
void FREBO_thr(int ifrom, int ito, int eflag, ThrData *const thr);
|
||||
void FLJ_thr(int ifrom, int ito, int eflag, ThrData *const thr);
|
||||
|
||||
void REBO_neigh_thr();
|
||||
|
||||
double bondorder_thr(int, int, double *, double, double, ThrData *const thr);
|
||||
};
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
125
unittest/force-styles/tests/manybody-pair-rebomos.yaml
Normal file
125
unittest/force-styles/tests/manybody-pair-rebomos.yaml
Normal file
@ -0,0 +1,125 @@
|
||||
---
|
||||
lammps_version: 7 Feb 2024
|
||||
tags: slow
|
||||
date_generated: Thu Feb 22 09:08:59 2024
|
||||
epsilon: 1e-12
|
||||
skip_tests:
|
||||
prerequisites: ! |
|
||||
pair rebomos
|
||||
pre_commands: ! |
|
||||
variable newton_pair delete
|
||||
if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on"
|
||||
post_commands: ! ""
|
||||
input_file: in.airebo
|
||||
pair_style: rebomos
|
||||
pair_coeff: ! |
|
||||
* * MoS.rebomos Mo S
|
||||
extract: ! ""
|
||||
natoms: 48
|
||||
init_vdwl: 3158.017726833385
|
||||
init_coul: 0
|
||||
init_stress: ! |2-
|
||||
6.8398718310371441e+03 6.7325636075141883e+03 6.1154248388685965e+03 -3.2850057579078185e+02 -6.6397329123828470e+01 -3.4208234997867203e+02
|
||||
init_forces: ! |2
|
||||
1 -3.7681565852737293e+00 2.4378308384489483e+02 -2.6969740060923279e+01
|
||||
2 2.6266038011491645e+02 -2.0681295165426090e+02 -1.9964225279104706e+01
|
||||
3 -2.5778010496370018e+02 -2.3678496612327552e+02 4.3829487525746238e+01
|
||||
4 -1.0244959408607365e+01 -2.6794342328905179e+02 -2.6250177085935768e+01
|
||||
5 2.2561151172717553e+02 2.0458598509633319e+02 -4.2183143539914880e+01
|
||||
6 -2.4766208404861507e+02 1.8231884233051196e+02 1.2358374858464346e+01
|
||||
7 -2.8974107341390795e+01 1.1031227139363692e+02 -1.2014739688866064e+02
|
||||
8 2.1125868843851663e+02 -2.8863731327540540e+02 1.6869558243398984e+01
|
||||
9 -3.1045083889038222e+02 -1.7569259168198960e+02 7.9653354234911163e+01
|
||||
10 3.9886149586070935e+01 -1.0347554263069082e+02 1.5430519714983259e+02
|
||||
11 1.8975960895859026e+02 1.4943835159807929e+02 -7.3224202319244824e+01
|
||||
12 -2.1525843617159188e+02 2.2144411990369784e+02 -1.4893230739895195e+01
|
||||
13 -4.5214798787473534e+00 1.1303681465405538e+02 -1.1385660017739841e+02
|
||||
14 2.3203040375527121e+02 -3.4422786145586961e+01 1.8438743650405590e+02
|
||||
15 -9.7170644212253990e+01 -2.9205504121924292e+02 1.9237141908302370e+01
|
||||
16 -5.1044169101209107e+01 -1.4503490444304657e+02 1.5798442448724001e+02
|
||||
17 2.8968061091312188e+02 8.7626477818666558e+01 -5.8802357863256212e+01
|
||||
18 -1.7269858357220591e+02 8.9805161881631591e+01 -1.7847636055101773e+02
|
||||
19 1.0760757939777642e+02 1.2642591396366257e+02 1.5914528700154095e+01
|
||||
20 8.4608047558760049e+01 -2.4114295115066687e+02 -8.5792447633922421e+01
|
||||
21 -8.8196263713344706e+01 -1.2718199182512282e+02 -7.0146571930858386e+01
|
||||
22 -9.8957412653883708e+01 -1.4706747771082254e+02 -4.1887992372999022e+01
|
||||
23 1.3739608451158423e+02 2.5576040689729510e+02 3.0309933932861746e+01
|
||||
24 -1.7919184387909232e+02 1.4014151619269020e+02 1.6188399417577682e+02
|
||||
25 -7.7347072523993347e+01 1.5555894832740958e+02 2.6182670200573220e+01
|
||||
26 7.1360176064432650e+01 -2.9346871053231695e+02 -4.0766232856732509e+00
|
||||
27 -2.6964124483003886e+01 9.8094028485618843e+00 2.4520760165936114e+01
|
||||
28 1.2261226472559841e+02 -2.1507437048459283e+02 -3.0529457478077248e+01
|
||||
29 2.2123474818204119e+01 2.8827028167050270e+02 1.0492685172067040e+02
|
||||
30 -3.0573547162322302e+02 6.5880918489915032e+01 -1.1459287271946665e+02
|
||||
31 6.0299759271951014e+00 1.7876996651274851e+02 -1.2964028093837922e+02
|
||||
32 2.3752911820416773e+02 -1.2903240767402318e+02 1.2355068302179771e+02
|
||||
33 -2.7462402312452838e+02 -5.3957296643601545e+01 9.5908146508348565e+01
|
||||
34 -2.4514118579997412e+01 -1.0385194449627924e+02 1.4149428440602534e+02
|
||||
35 1.2613298864651166e+02 6.2171771831118461e+00 -2.0642312645163636e+02
|
||||
36 -6.9996802234927173e+01 2.9354514776980676e+02 -2.0963604805137543e+01
|
||||
37 5.0241789394721707e+01 2.4495589528252060e+02 -1.1814425338523709e+01
|
||||
38 2.2684897209808264e+02 -1.8673318434123004e+02 1.5220428086050066e+00
|
||||
39 -2.5107271651763259e+02 -1.6443685417603410e+02 -3.8081572318769169e+01
|
||||
40 -5.6754727284178912e+01 -2.5956532443118618e+02 -5.9343761520548126e+00
|
||||
41 2.7426370608616236e+02 1.7742153146823480e+02 1.3451000229991498e+01
|
||||
42 -2.2732796257204490e+02 2.5279459742055184e+02 -2.7020668313372529e+01
|
||||
43 1.6217419052721431e+02 1.3946372126978235e+02 -2.0623397237537300e+00
|
||||
44 3.0490806490775839e+01 2.1072542774667330e+01 8.2426559376766466e+00
|
||||
45 -1.8440339212966003e+02 -2.5521581334939563e+02 2.6487508881411735e+01
|
||||
46 -3.5020523296396959e+01 -2.5119105337038474e+02 8.0096253171487604e+00
|
||||
47 3.2722641189388571e+02 9.7949745935413119e+01 -1.1898751818014821e+01
|
||||
48 -1.3785292104885133e+02 3.2239007811982697e+02 2.4602884867061839e+01
|
||||
run_vdwl: 838.005031679853
|
||||
run_coul: 0
|
||||
run_stress: ! |2-
|
||||
2.0454406617512559e+03 2.1642975706136021e+03 3.2875013790709349e+03 2.4615001869678809e+02 9.3532964794023911e+01 -1.6795786485689854e+02
|
||||
run_forces: ! |2
|
||||
1 -2.5386905249574866e+01 -9.9909927316940710e+01 1.9622022776949393e+00
|
||||
2 -3.6801215363277215e+01 1.3354608905768052e+02 1.3651128931415545e+02
|
||||
3 2.1845136723115344e+00 2.3527273580981478e+00 2.4005941692097457e+00
|
||||
4 -3.7818914621624749e+01 3.2946537814811997e+01 4.3018847892043375e+01
|
||||
5 9.6010433504280890e+00 4.3327442916171194e+01 -1.0513311611209312e+02
|
||||
6 8.4308572792324540e+01 -2.3503352214725012e+01 5.0539884405443850e+01
|
||||
7 -1.1497740491253731e+01 -6.4938790153209212e+01 3.8948855627091397e+01
|
||||
8 -4.2897157525993697e+00 -3.3530261299383611e+01 9.5574489119024229e+00
|
||||
9 4.8767710902858741e-01 -3.5176606358955858e+00 -1.4806227207057554e-01
|
||||
10 -1.4766722110672411e+01 2.3818988804615220e+01 -5.3134339246512809e+01
|
||||
11 -1.3935431402422819e+02 -1.5665571900752980e+02 -3.7627334252485582e+01
|
||||
12 7.7074185304589484e+00 -1.2031768398608595e+01 1.8274050209872662e+01
|
||||
13 2.3670515505343992e+01 -6.4282829210616583e+01 4.6336363412751325e+01
|
||||
14 -2.5980738378663424e+00 8.4167979467127569e+00 -2.3849686761968631e+00
|
||||
15 2.6909213334137871e+01 9.4711670949167956e+00 1.4728430099051328e+00
|
||||
16 2.6072330920174934e+01 1.5861581881675242e+01 -5.1429144994723586e+01
|
||||
17 -4.5656802478750279e+01 -1.0557685195759221e+02 -1.8486644164722456e+01
|
||||
18 1.3345348571390588e+02 5.3791289185967734e+01 3.1330462313925089e+01
|
||||
19 -3.4744179120880638e+01 -2.9727735009574776e+01 1.3758697899848009e+01
|
||||
20 3.5805745710027459e+00 2.3635583506556830e+00 -9.8641913612550636e-01
|
||||
21 -1.9112967021807076e+01 2.4093036642722907e+01 -1.8643238887150801e+01
|
||||
22 -9.0201617792954476e+00 3.7160721932912736e+01 -5.0873237843214003e+00
|
||||
23 -2.0559670924056718e+01 -1.3037172781831362e+01 -4.1555140102832148e+01
|
||||
24 3.5016464856031341e+01 -1.2488249708112150e+02 -5.5132899737529639e+00
|
||||
25 2.4856779395007460e+00 -6.7533673428345381e+01 -1.7153563726726016e+01
|
||||
26 -8.6470517146734750e+01 -7.9057942497429794e+00 3.8434105758101332e+01
|
||||
27 3.1062776626038996e+01 2.5568916700234454e+00 -2.3812255018358194e+01
|
||||
28 -3.6128021960690276e+01 8.8535946500139033e+01 -3.1718315624050986e-01
|
||||
29 -1.7473599694524488e+01 5.1605700760038529e+00 3.1477016370448561e+00
|
||||
30 3.2722165297173231e+00 -5.9807188688706105e+00 3.0903475914489444e+01
|
||||
31 -5.5852599877204412e-01 -3.7635607965114964e+01 5.5407547347738578e+01
|
||||
32 -4.8419811021707950e+01 1.2083134296973620e+02 -1.4299477119499166e+01
|
||||
33 2.5993167832212944e+01 5.4415694550334088e+01 -2.2817585641730194e+01
|
||||
34 1.3632918027769463e+01 1.0165209000060044e+02 -6.0709294862836366e+01
|
||||
35 -1.7896100047169217e+01 5.7265522876438499e+00 6.7274680861552483e+00
|
||||
36 -1.8125137765726237e+01 2.7564787465936047e+00 -9.5278575701404478e+00
|
||||
37 -3.5898678616111592e+00 -7.2362382910010311e+01 -9.3588358281326709e+00
|
||||
38 -3.6726824963125949e+01 2.0008528283799198e+01 4.2387983046244827e+01
|
||||
39 1.4756349734330427e+00 3.4387817449154888e+01 4.6004570693407864e+01
|
||||
40 1.3004687263347805e+01 6.5948251357408196e+01 -9.3870897441198231e+00
|
||||
41 -9.2360908880622592e+00 3.0113497063365648e+00 -1.1785409504259610e+01
|
||||
42 -1.1795417170666214e+01 -1.1546754933247897e+01 -1.2188857610119777e+01
|
||||
43 -6.5511968637617390e-01 -3.9133448932537512e+01 5.5788437875425423e-01
|
||||
44 -4.2976958767216473e+01 1.8814792063050870e+01 -3.2742042602021932e+01
|
||||
45 1.8589630046648591e+02 5.3367997582431663e+01 3.8324469380182308e+01
|
||||
46 2.2463767362468872e+01 7.7485287617829670e+01 2.6113916756613811e+01
|
||||
47 3.0703470673161828e+00 2.4966324680483410e+01 -5.0826014249556524e+00
|
||||
48 7.6310071304830785e+01 -9.3082908173611301e+01 -1.1280958703044767e+02
|
||||
...
|
||||
Reference in New Issue
Block a user