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Axel Kohlmeyer
2022-03-07 15:29:47 -05:00
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4
doc/src/Commands_compute.rst
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@ -100,7 +100,6 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`pe/tally <compute_tally>`
* :doc:`plasticity/atom <compute_plasticity_atom>`
* :doc:`pressure <compute_pressure>`
* :doc:`pressure/cylinder <compute_pressure_cylinder>`
* :doc:`pressure/uef <compute_pressure_uef>`
* :doc:`property/atom <compute_property_atom>`
* :doc:`property/chunk <compute_property_chunk>`
@ -143,8 +142,11 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`sph/t/atom <compute_sph_t_atom>`
* :doc:`spin <compute_spin>`
* :doc:`stress/atom <compute_stress_atom>`
* :doc:`stress/cartesian <compute_stress_cartesian>`
* :doc:`stress/cylinder <compute_stress_cartesian>`
* :doc:`stress/mop <compute_stress_mop>`
* :doc:`stress/mop/profile <compute_stress_mop>`
* :doc:`stress/spherical <compute_stress_cartesian>`
* :doc:`stress/tally <compute_tally>`
* :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>`
* :doc:`temp (k) <compute_temp>`

4
doc/src/compute.rst
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@ -246,7 +246,6 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
* :doc:`pe/tally <compute_tally>` - potential energy between two groups of atoms via the tally callback mechanism
* :doc:`plasticity/atom <compute_plasticity_atom>` - Peridynamic plasticity for each atom
* :doc:`pressure <compute_pressure>` - total pressure and pressure tensor
* :doc:`pressure/cylinder <compute_pressure_cylinder>` - pressure tensor in cylindrical coordinates
* :doc:`pressure/uef <compute_pressure_uef>` - pressure tensor in the reference frame of an applied flow field
* :doc:`property/atom <compute_property_atom>` - convert atom attributes to per-atom vectors/arrays
* :doc:`property/chunk <compute_property_chunk>` - extract various per-chunk attributes
@ -289,8 +288,11 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
* :doc:`sph/t/atom <compute_sph_t_atom>` - per-atom internal temperature of Smooth-Particle Hydrodynamics atoms
* :doc:`spin <compute_spin>` - magnetic quantities for a system of atoms having spins
* :doc:`stress/atom <compute_stress_atom>` - stress tensor for each atom
* :doc:`stress/cartesian <compute_stress_cartesian>` - stress tensor in cartesian coordinates
* :doc:`stress/cylinder <compute_stress_cartesian>` - stress tensor in cylindrical coordinates
* :doc:`stress/mop <compute_stress_mop>` - normal components of the local stress tensor using the method of planes
* :doc:`stress/mop/profile <compute_stress_mop>` - profile of the normal components of the local stress tensor using the method of planes
* :doc:`stress/spherical <compute_stress_cartesian>` - stress tensor in spherical coordinates
* :doc:`stress/tally <compute_tally>` - stress between two groups of atoms via the tally callback mechanism
* :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>` - per-atom chemical concentration of a specified species for each tDPD particle
* :doc:`temp <compute_temp>` - temperature of group of atoms

88
doc/src/compute_pressure_cylinder.rst
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@ -1,88 +0,0 @@
.. index:: compute pressure/cylinder
compute pressure/cylinder command
=================================
Syntax
""""""
.. parsed-literal::
compute ID group-ID pressure/cylinder zlo zhi Rmax bin_width
* ID, group-ID are documented in :doc:`compute <compute>` command
* pressure/cylinder = style name of this compute command
* zlo = minimum z-boundary for cylinder
* zhi = maximum z-boundary for cylinder
* Rmax = maximum radius to perform calculation to
* bin_width = width of radial bins to use for calculation
Examples
""""""""
.. code-block:: LAMMPS
compute 1 all pressure/cylinder -10.0 10.0 15.0 0.25
Description
"""""""""""
Define a computation that calculates the pressure tensor of a system in
cylindrical coordinates, as discussed in :ref:`(Addington) <Addington1>`.
This is useful for systems with a single axis of rotational symmetry,
such as cylindrical micelles or carbon nanotubes. The compute splits the
system into radial, cylindrical-shell-type bins of width bin_width,
centered at x=0,y=0, and calculates the radial (P_rhorho), azimuthal
(P_phiphi), and axial (P_zz) components of the configurational pressure
tensor. The local density is also calculated for each bin, so that the
true pressure can be recovered as P_kin+P_conf=density\*k\*T+P_conf. The
output is a global array with 5 columns; one each for bin radius, local
number density, P_rhorho, P_phiphi, and P_zz. The number of rows is
governed by the values of Rmax and bin_width. Pressure tensor values are
output in pressure units.
Output info
"""""""""""
This compute calculates a global array with 5 columns and Rmax/bin_width
rows. The output columns are: R (distance units), number density (inverse
volume units), configurational radial pressure (pressure units),
configurational azimuthal pressure (pressure units), and configurational
axial pressure (pressure units).
The values calculated by this compute are
"intensive". The pressure values will be in pressure
:doc:`units <units>`. The number density values will be in
inverse volume :doc:`units <units>`.
Restrictions
""""""""""""
This compute currently calculates the pressure tensor contributions
for pair styles only (i.e. no bond, angle, dihedral, etc. contributions
and in the presence of bonded interactions, the result will be incorrect
due to exclusions for special bonds) and requires pairwise force
calculations not available for most many-body pair styles. K-space
calculations are also excluded. Note that this pressure compute outputs
the configurational terms only; the kinetic contribution is not included
and may be calculated from the number density output by P_kin=density\*k\*T.
This compute is part of the EXTRA-COMPUTE package. It is only enabled
if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
Related commands
""""""""""""""""
:doc:`compute temp <compute_temp>`, :doc:`compute stress/atom <compute_stress_atom>`,
:doc:`thermo_style <thermo_style>`,
Default
"""""""
none
----------
.. _Addington1:
**(Addington)** Addington, Long, Gubbins, J Chem Phys, 149, 084109 (2018).

165
doc/src/compute_stress_cartesian.rst Normal file
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@ -0,0 +1,165 @@
.. index:: compute stress/cartesian
.. index:: compute stress/cylinder
.. index:: compute stress/spherical
compute stress/cartesian command
==================================
compute stress/cylinder command
=================================
compute stress/spherical command
==================================
Syntax
""""""
.. parsed-literal::
compute ID group-ID style args
* ID, group-ID are documented in :doc:`compute <compute>` command
* style = stress/cartesian or stress/spherical or stress/cylinder
* args = argument specific to the compute style
.. parsed-literal::
*stress/cartesian* args = dim bin_width
dim = x, y, or z. One or two dim/bin_width pairs may be appended
bin_width = width of the bin
*stress/cylinder* args = zlo zh Rmax bin_width keyword
zlo = minimum z-boundary for cylinder
zhi = maximum z-boundary for cylinder
Rmax = maximum radius to perform calculation to
bin_width = width of radial bins to use for calculation
keyword = ke (zero or one can be specified)
ke = yes or no
*stress/spherical*
x0, y0, z0 = origin of the spherical coordinate system
bin_width = width of spherical shells
Rmax = maximum radius of spherical shells
Examples
""""""""
.. code-block:: LAMMPS
compute 1 all stress/cartesian x 0.1
compute 1 all stress/cartesian y 0.25 z 0.1
compute 1 all stress/cylinder -10.0 10.0 15.0 0.25
compute 1 all stress/cylinder -10.0 10.0 15.0 0.25 ke no
compute 1 all stress/spherical 0 0 0 0.1 10
Description
"""""""""""
Compute *stress/cartesian*, compute *stress/cylinder*, and compute
*stress/spherical* define computations that calculate profiles of the
diagonal components of the local stress tensor in the specified
coordinate system. The stress tensor is split into a kinetic
contribution :math:`P^k` and a virial contribution :math:`P^v`. The sum
gives the total stress tensor :math:`P = P^k+P^v`. These computes can
for example be used to calculate the diagonal components of the local
stress tensor of interfaces with flat, cylindrical, or spherical
symmetry. These computes obeys momentum balance through fluid
interfaces. They use the Irving-Kirkwood contour, which is the straight
line between particle pairs.
The *stress/cartesian* computes the stress profile along one or two
Cartesian coordinates, as described in :ref:`(Ikeshoji)<Ikeshoji2>`. The
compute *stress/cylinder* computes the stress profile along the
radial direction in cylindrical coordinates, as described in
:ref:`(Addington)<Addington1>`. The compute *stress/spherical*
computes the stress profile along the radial direction in spherical
coordinates, as described in :ref:`(Ikeshoji)<Ikeshoji2>`.
Output info
"""""""""""
The output columns for *stress/cartesian* are the position of the
center of the local volume in the first and second dimensions, number
density, :math:`P^k_{xx}`, :math:`P^k_{yy}`, :math:`P^k_{zz}`,
:math:`P^v_{xx}`, :math:`P^v_{yy}`, and :math:`P^v_{zz}`. There are 8
columns when one dimension is specified and 9 columns when two
dimensions are specified. The number of bins/rows are
(L1/bin_width1)*(L2/bin_width2), L1 and L2 are the sizes of the
simulation box in the specified dimensions, and bin_width1 and
bin_width2 are the specified bin widths. When only one dimension is
specified the number of bins/rows are L1/bin_width.
The default output columns for *stress/cylinder* are the radius to the
center of the cylindrical shell, number density, :math:`P^k_{rr}`,
:math:`P^k_{\phi\phi}`, :math:`P^k_{zz}`, :math:`P^v_{rr}`,
:math:`P^v_{\phi\phi}`, and :math:`P^v_{zz}`. When the keyword *ke* is
set to no, the kinetic contributions are not calculated, and
consequently there are only 5 columns the radius to the center of the
cylindrical shell, number density, :math:`P^v_{rr}`,
:math:`P^v_{\phi\phi}`, :math:`P^v_{zz}`. The number of bins/rows are
Rmax/bin_width.
The output columns for *stress/spherical* are the radius to the center
of the spherical shell, number density, :math:`P^k_{rr}`,
:math:`P^k_{\theta\theta}`, :math:`P^k_{\phi\phi}`, :math:`P^v_{rr}`,
:math:`P^v_{\theta\theta}`, and :math:`P^v_{\phi\phi}`. There are 8
columns and the number of bins/rows are Rmax/bin_width.
This array can be output with :doc:`fix ave/time <fix_ave_time>`,
.. code-block:: LAMMPS
compute p all stress/cartesian x 0.1
fix 2 all ave/time 100 1 100 c_p[*] file dump_p.out mode vector
The values calculated by this compute are "intensive". The stress
values will be in pressure :doc:`units <units>`. The number density
values are in inverse volume :doc:`units <units>`.
NOTE 1: The local stress does not include any Lennard-Jones tail
corrections to the stress added by the :doc:`pair_modify tail yes <pair_modify>`
command, since those are contributions to the global system pressure.
NOTE 2: The local stress profiles generated by these computes are
similar to those obtained by the
:doc:`method-of-planes (MOP) <compute_stress_mop>`.
A key difference
is that compute `stress/mop/profile <compute_stress_mop>`
considers particles crossing a set of planes, while
*stress/cartesian* computes averages for a set of small volumes.
More information on the similarities and differences can be found in
:ref:`(Ikeshoji)<Ikeshoji2>`.
Restrictions
""""""""""""
These computes calculate the stress tensor contributions for pair
styles only (i.e. no bond, angle, dihedral, etc. contributions, and in
the presence of bonded interactions, the result will be incorrect due to
exclusions for special bonds) and requires pairwise force calculations
not available for most many-body pair styles. K-space calculations are
also excluded.
These computes are part of the EXTRA-COMPUTE package. They are only
enabled if LAMMPS was built with that package. See the :doc:`Build
package <Build_package>` doc page for more info.
Related commands
""""""""""""""""
:doc:`compute stress/atom <compute_stress_atom>`, :doc:`compute pressure <compute_pressure>`, :doc:`compute stress/mop/profile <compute_stress_mop>`
Default
"""""""
The keyword default for ke in style *stress/cylinder* is yes.
----------
.. _Ikeshoji2:
**(Ikeshoji)** Ikeshoji, Hafskjold, Furuholt, Mol Sim, 29, 101-109, (2003).
.. _Addington1:
**(Addington)** Addington, Long, Gubbins, J Chem Phys, 149, 084109 (2018).

25
doc/src/compute_stress_mop.rst
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@ -68,7 +68,19 @@ configurational stress (conf), and/or total stress (total).
NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID.
NOTE 2: The local stress does not include any Lennard-Jones tail
corrections to the pressure added by the :doc:`pair_modify tail yes <pair_modify>` command, since those are contributions to the global system pressure.
corrections to the stress added by the :doc:`pair_modify tail yes <pair_modify>`
command, since those are contributions to the global system pressure.
NOTE 3: The local stress profile generated by compute *stress/mop/profile*
is similar to that obtained by compute
:doc:`stress/cartesian <compute_stress_cartesian>`.
A key difference
is that compute *stress/mop/profile* considers particles
crossing a set of planes,
while compute *stress/cartesian* computes averages for a set of
small volumes. More information
on the similarities and differences can be found in
:ref:`(Ikeshoji)<Ikeshoji2>`.
Output info
"""""""""""
@ -87,7 +99,10 @@ and stress_dir,z.
The values are in pressure :doc:`units <units>`.
The values produced by this compute can be accessed by various :doc:`output commands <Howto_output>`. For instance, the results can be written to a file using the :doc:`fix ave/time <fix_ave_time>` command. Please see the example in the examples/PACKAGES/mop folder.
The values produced by this compute can be accessed by various :doc:`output commands <Howto_output>`.
For instance, the results can be written to a file using the
:doc:`fix ave/time <fix_ave_time>` command. Please see the example
in the examples/PACKAGES/mop folder.
Restrictions
""""""""""""
@ -107,7 +122,7 @@ intra-molecular interactions, and long range (kspace) interactions.
Related commands
""""""""""""""""
:doc:`compute stress/atom <compute_stress_atom>`
:doc:`compute stress/atom <compute_stress_atom>`, :doc:`compute pressure <compute_pressure>`, :doc:`compute stress/cartesian <compute_stress_cartesian>`, :doc:`compute stress/cylinder <compute_stress_cartesian>`, :doc:`compute stress/spherical <compute_stress_cartesian>`
Default
"""""""
@ -120,3 +135,7 @@ none
**(Todd)** B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure tensor for inhomogeneous fluids",
Phys. Rev. E 52, 1627 (1995).
.. _Ikeshoji3:
**(Ikeshoji)** Ikeshoji, Hafskjold, Furuholt, Mol Sim, 29, 101-109, (2003).

4
doc/src/pair_mesocnt.rst
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@ -94,10 +94,6 @@ boron nitride nanotubes.
Atoms belonging to different CNTs need to be assigned
different molecule IDs.
A full summary of the method and LAMMPS implementation details
is expected to soon become available in Computer Physics
Communications.
----------
Mixing, shift, table, tail correction, restart, rRESPA info

15
doc/src/pair_reaxff.rst
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@ -19,13 +19,14 @@ Syntax
.. parsed-literal::
keyword = *checkqeq* or *lgvdw* or *safezone* or *mincap* or *minhbonds* or *list/blocking*
keyword = *checkqeq* or *lgvdw* or *safezone* or *mincap* or *minhbonds* or *tabulate* or *list/blocking*
*checkqeq* value = *yes* or *no* = whether or not to require qeq/reaxff or acks2/reaxff fix
*enobonds* value = *yes* or *no* = whether or not to tally energy of atoms with no bonds
*lgvdw* value = *yes* or *no* = whether or not to use a low gradient vdW correction
*safezone* = factor used for array allocation
*mincap* = minimum size for array allocation
*minhbonds* = minimum size use for storing hydrogen bonds
*tabulate* value = size of interpolation table for Lennard-Jones and Coulomb interactions
*list/blocking* value = *yes* or *no* = whether or not to use "blocking" scheme for bond list build
Examples
@ -159,6 +160,13 @@ the Kokkos version, which instead uses a more robust memory allocation
scheme that checks if the sizes of the arrays have been exceeded and
automatically allocates more memory.
The keyword *tabulate* controls the size of interpolation table for
Lennard-Jones and Coulomb interactions. Tabulation may also be set in the
control file (see below). If tabulation is set in both the input script and the
control file, the value in the control file will be ignored. A size of 10000 is
typically used for the interpolation table. A value of 0 means no tabulation
will be used.
The keyword *list/blocking* is only supported by the Kokkos version of
ReaxFF and ignored otherwise. Setting the value to *yes* enables the
"blocking" scheme (dynamically building interaction lists) for the
@ -369,8 +377,9 @@ Related commands
Default
"""""""
The keyword defaults are checkqeq = yes, enobonds = yes, lgvdw = no,
safezone = 1.2, mincap = 50, minhbonds = 25, list/blocking = yes on CPU, no on GPU.
The keyword defaults are checkqeq = yes, enobonds = yes, lgvdw = no, safezone =
1.2, mincap = 50, minhbonds = 25, tabulate = 0, list/blocking = yes on CPU, no
on GPU.
----------