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fix spelling and formatting issues

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This commit is contained in:
Axel Kohlmeyer
2024-08-21 20:18:28 -04:00
parent 7eb105adbe
commit 827bc6361b
6 changed files with 96 additions and 98 deletions
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29
doc/src/compute_pressure.rst
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@ -76,8 +76,8 @@ calculated. This includes a kinetic energy (temperature) term and the
virial as the sum of pair, bond, angle, dihedral, improper, kspace
(long-range), and fix contributions to the force on each atom. If any
extra keywords are listed, then only those components are summed to
compute temperature or ke and/or the virial. The *virial* keyword
means include all terms except the kinetic energy *ke*\ .
compute temperature or ke and/or the virial. The *virial* keyword means
include all terms except the kinetic energy *ke*\ .
The *pair/hybrid* keyword means to only include contribution
from a sub-style in a *hybrid* or *hybrid/overlay* pair style.
@ -89,18 +89,18 @@ effects of periodic boundary conditions are discussed in
The temperature and kinetic energy tensor are not calculated by this
compute, but rather by the temperature compute specified with the
command. See the doc pages for individual compute temp variants for
an explation of how they calculate temperature and a symmetric tensor
(6-element vector) whose components are twice that of the traditional
KE tensor. That tensor is what appears in the pressure tensor formula
command. See the doc pages for individual compute temp variants for an
explanation of how they calculate temperature and a symmetric tensor
(6-element vector) whose components are twice that of the traditional KE
tensor. That tensor is what appears in the pressure tensor formula
above.
If the kinetic energy is not included in the pressure, than
the temperature compute is not used and can be specified as NULL.
Normally the temperature compute used by compute pressure should
calculate the temperature of all atoms for consistency with the virial
term, but any compute style that calculates temperature can be used
(e.g., one that excludes frozen atoms or other degrees of freedom).
If the kinetic energy is not included in the pressure, than the
temperature compute is not used and can be specified as NULL. Normally
the temperature compute used by compute pressure should calculate the
temperature of all atoms for consistency with the virial term, but any
compute style that calculates temperature can be used (e.g., one that
excludes frozen atoms or other degrees of freedom).
Note that if desired the specified temperature compute can be one that
subtracts off a bias to calculate a temperature using only the thermal
@ -142,9 +142,8 @@ The ordering of values in the symmetric pressure tensor is as follows:
:math:`p_{xx},` :math:`p_{yy},` :math:`p_{zz},` :math:`p_{xy},`
:math:`p_{xz},` :math:`p_{yz}.`
The scalar and vector values calculated by this compute are
"intensive". The scalar and vector values will be in pressure
:doc:`units <units>`.
The scalar and vector values calculated by this compute are "intensive".
The scalar and vector values will be in pressure :doc:`units <units>`.
Restrictions
""""""""""""

54
doc/src/compute_temp_asphere.rst
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@ -41,8 +41,8 @@ translational and rotational kinetic energy. This differs from the
usual :doc:`compute temp <compute_temp>` command, which assumes point
particles with only translational kinetic energy.
Only finite-size particles (aspherical or spherical) can be included
in the group. For 3d finite-size particles, each has six degrees of
Only finite-size particles (aspherical or spherical) can be included in
the group. For 3d finite-size particles, each has six degrees of
freedom (three translational, three rotational). For 2d finite-size
particles, each has three degrees of freedom (two translational, one
rotational).
@ -70,38 +70,39 @@ axis. It will also be the case for biaxial ellipsoids when exactly two
of the semiaxes have the same length and the corresponding relative well
depths are equal.
The translational kinetic energy is computed the same as is described
by the :doc:`compute temp <compute_temp>` command. The rotational
kinetic energy is computed as :math:`\frac12 I \omega^2`, where :math:`I` is
the inertia tensor for the aspherical particle and :math:`\omega` is its
The translational kinetic energy is computed the same as is described by
the :doc:`compute temp <compute_temp>` command. The rotational kinetic
energy is computed as :math:`\frac12 I \omega^2`, where :math:`I` is the
inertia tensor for the aspherical particle and :math:`\omega` is its
angular velocity, which is computed from its angular momentum.
.. note::
For :doc:`2d models <dimension>`, particles are treated as
ellipsoids, not ellipses, meaning their moments of inertia will be the
same as in 3d.
ellipsoids, not ellipses, meaning their moments of inertia will be
the same as in 3d.
A kinetic energy tensor, stored as a six-element vector, is also
calculated by this compute. The formula for the components of the
tensor is the same as the above formula, except that :math:`v^2` and
:math:`\omega^2` are replaced by :math:`v_x v_y` and :math:`\omega_x \omega_y`
for the :math:`xy` component, and the appropriate elements of the moment of
inertia tensor are used. The six components of the vector are ordered
:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`.
:math:`\omega^2` are replaced by :math:`v_x v_y` and :math:`\omega_x
\omega_y` for the :math:`xy` component, and the appropriate elements of
the moment of inertia tensor are used. The six components of the vector
are ordered :math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`,
:math:`yz`.
A symmetric tensor, stored as a six-element vector, is also calculated
by this compute for use in the computation of a pressure tensor by the
:doc:`compute pressue <compute_pressure>` command. The formula for
the components of the tensor is the same as the above expression for
:doc:`compute pressue <compute_pressure>` command. The formula for the
components of the tensor is the same as the above expression for
:math:`E_\mathrm{kin}`, except that the 1/2 factor is NOT included and
the :math:`v_i^2` and :math:`\omega^2` are replaced by :math:`v_x v_y`
and :math:`\omega_x \omega_y` for the :math:`xy` component, and so on.
And the appropriate elements of the moment of inertia tensor are used.
Note that because it lacks the 1/2 factor, these tensor components are
twice those of the traditional kinetic energy tensor. The six
components of the vector are ordered :math:`xx`, :math:`yy`,
:math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`.
components of the vector are ordered :math:`xx`, :math:`yy`, :math:`zz`,
:math:`xy`, :math:`xz`, :math:`yz`.
The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the *dynamic/dof* option of
@ -144,14 +145,13 @@ Output info
"""""""""""
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (symmertic tensor), which can be accessed by
indices 1--6. These values can be used by any command that uses
global scalar or vector values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS
output options.
vector of length 6 (symmetric tensor), which can be accessed by indices
1--6. These values can be used by any command that uses global scalar
or vector values from a compute as input. See the :doc:`Howto output
<Howto_output>` page for an overview of LAMMPS output options.
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value calculated by this compute is "intensive". The vector
values are "extensive".
The scalar value is in temperature :doc:`units <units>`. The vector
values are in energy :doc:`units <units>`.
@ -160,11 +160,11 @@ Restrictions
""""""""""""
This compute is part of the ASPHERE package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
This compute requires that atoms store angular momentum and a
quaternion as defined by the :doc:`atom_style ellipsoid <atom_style>`
command.
This compute requires that atoms store angular momentum and a quaternion
as defined by the :doc:`atom_style ellipsoid <atom_style>` command.
All particles in the group must be finite-size. They cannot be point
particles, but they can be aspherical or spherical as defined by their

93
doc/src/compute_temp_cs.rst
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@ -31,27 +31,27 @@ on the center-of-mass velocity of atom pairs that are bonded to each
other. This compute is designed to be used with the adiabatic
core/shell model of :ref:`(Mitchell and Fincham) <MitchellFincham1>`.
See the :doc:`Howto coreshell <Howto_coreshell>` page for an overview of
the model as implemented in LAMMPS. Specifically, this compute
enables correct temperature calculation and thermostatting of
core/shell pairs where it is desirable for the internal degrees of
freedom of the core/shell pairs to not be influenced by a thermostat.
A compute of this style can be used by any command that computes a
temperature via :doc:`fix_modify <fix_modify>`
(e.g., :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix npt <fix_nh>`).
the model as implemented in LAMMPS. Specifically, this compute enables
correct temperature calculation and thermostatting of core/shell pairs
where it is desirable for the internal degrees of freedom of the
core/shell pairs to not be influenced by a thermostat. A compute of
this style can be used by any command that computes a temperature via
:doc:`fix_modify <fix_modify>` (e.g., :doc:`fix temp/rescale
<fix_temp_rescale>`, :doc:`fix npt <fix_nh>`).
Note that this compute does not require all ions to be polarized,
hence defined as core/shell pairs. One can mix core/shell pairs and
ions without a satellite particle if desired. The compute will
consider the non-polarized ions according to the physical system.
Note that this compute does not require all ions to be polarized, hence
defined as core/shell pairs. One can mix core/shell pairs and ions
without a satellite particle if desired. The compute will consider the
non-polarized ions according to the physical system.
For this compute, core and shell particles are specified by two
respective group IDs, which can be defined using the
:doc:`group <group>` command. The number of atoms in the two groups
must be the same and there should be one bond defined between a pair
of atoms in the two groups. Non-polarized ions which might also be
included in the treated system should not be included into either of
these groups, they are taken into account by the *group-ID* (second
argument) of the compute.
respective group IDs, which can be defined using the :doc:`group
<group>` command. The number of atoms in the two groups must be the
same and there should be one bond defined between a pair of atoms in the
two groups. Non-polarized ions which might also be included in the
treated system should not be included into either of these groups, they
are taken into account by the *group-ID* (second argument) of the
compute.
The temperature is calculated by the formula
@ -60,54 +60,53 @@ The temperature is calculated by the formula
\text{KE} = \frac{\text{dim}}{2} N k_B T,
where KE is the total kinetic energy of the group of atoms (sum of
:math:`\frac12 m v^2`), dim = 2 or 3 is the dimensionality of the simulation,
:math:`N` is the number of atoms in the group, :math:`k_B` is the Boltzmann
constant, and :math:`T` is the absolute temperature. Note that
the velocity of each core or shell atom used in the KE calculation is
the velocity of the center-of-mass (COM) of the core/shell pair the
atom is part of.
:math:`\frac12 m v^2`), dim = 2 or 3 is the dimensionality of the
simulation, :math:`N` is the number of atoms in the group, :math:`k_B`
is the Boltzmann constant, and :math:`T` is the absolute temperature.
Note that the velocity of each core or shell atom used in the KE
calculation is the velocity of the center-of-mass (COM) of the
core/shell pair the atom is part of.
A symmetric tensor, stored as a six-element vector, is also calculated
by this compute for use in the computation of a pressure tensor by the
:doc:`compute pressue <compute_pressure>` command. The formula for
the components of the tensor is the same as the above expression for
:doc:`compute pressue <compute_pressure>` command. The formula for the
components of the tensor is the same as the above expression for
:math:`E_\mathrm{kin}`, except that the 1/2 factor is NOT included and
the :math:`v_i^2` is replaced by :math:`v_{i,x} v_{i,y}` for the
:math:`xy` component, and so on. Note that because it lacks the 1/2
factor, these tensor components are twice those of the traditional
kinetic energy tensor. The six components of the vector are ordered
:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`,
:math:`yz`.
:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`.
The change this fix makes to core/shell atom velocities is essentially
computing the temperature after a "bias" has been removed from the
velocity of the atoms. This "bias" is the velocity of the atom
relative to the center-of-mass velocity of the core/shell pair. If
this compute is used with a fix command that performs thermostatting
then this bias will be subtracted from each atom, thermostatting of
the remaining center-of-mass velocity will be performed, and the bias
will be added back in. This means the thermostatting will effectively
be performed on the core/shell pairs, instead of on the individual
core and shell atoms. Thermostatting fixes that work in this way
include :doc:`fix nvt <fix_nh>`, :doc:`fix temp/rescale
<fix_temp_rescale>`, :doc:`fix temp/berendsen <fix_temp_berendsen>`,
and :doc:`fix langevin <fix_langevin>`.
velocity of the atoms. This "bias" is the velocity of the atom relative
to the center-of-mass velocity of the core/shell pair. If this compute
is used with a fix command that performs thermostatting then this bias
will be subtracted from each atom, thermostatting of the remaining
center-of-mass velocity will be performed, and the bias will be added
back in. This means the thermostatting will effectively be performed on
the core/shell pairs, instead of on the individual core and shell atoms.
Thermostatting fixes that work in this way include :doc:`fix nvt
<fix_nh>`, :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix
temp/berendsen <fix_temp_berendsen>`, and :doc:`fix langevin
<fix_langevin>`.
The internal energy of core/shell pairs can be calculated by the
:doc:`compute temp/chunk <compute_temp_chunk>` command, if chunks are defined
as core/shell pairs. See the :doc:`Howto coreshell <Howto_coreshell>` doc
page for more discussion on how to do this.
:doc:`compute temp/chunk <compute_temp_chunk>` command, if chunks are
defined as core/shell pairs. See the :doc:`Howto coreshell
<Howto_coreshell>` doc page for more discussion on how to do this.
Output info
"""""""""""
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (symmertric tensor), which can be accessed by
indices 1--6. These values can be used by any command that uses
global scalar or vector values from a compute as input.
vector of length 6 (symmetric tensor), which can be accessed by indices
1--6. These values can be used by any command that uses global scalar
or vector values from a compute as input.
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value calculated by this compute is "intensive". The vector
values are "extensive".
The scalar value is in temperature :doc:`units <units>`. The vector
values are in energy :doc:`units <units>`.

8
doc/src/compute_temp_profile.rst
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@ -210,10 +210,10 @@ will be for most thermostats.
Related commands
""""""""""""""""
:doc:`compute temp <compute_temp>`, :doc:`compute temp/ramp
<compute_temp_ramp>`, :doc:`compute temp/deform
<compute_temp_deform>`, :doc:`compute pressure
<compute_pressure>`
:doc:`compute temp <compute_temp>`,
:doc:`compute temp/ramp <compute_temp_ramp>`,
:doc:`compute temp/deform <compute_temp_deform>`,
:doc:`compute pressure <compute_pressure>`
Default
"""""""

8
doc/src/compute_temp_ramp.rst
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@ -124,10 +124,10 @@ Restrictions
Related commands
""""""""""""""""
:doc:`compute temp <compute_temp>`, :doc:`compute temp/profie
<compute_temp_profile>`, :doc:`compute temp/deform
<compute_temp_deform>`, :doc:`compute pressure
<compute_pressure>`
:doc:`compute temp <compute_temp>`,
:doc:`compute temp/profile <compute_temp_profile>`,
:doc:`compute temp/deform <compute_temp_deform>`,
:doc:`compute pressure <compute_pressure>`
Default
"""""""

2
doc/src/compute_temp_region_eff.rst
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@ -38,7 +38,7 @@ contributions, as discussed by the :doc:`compute temp/eff
<compute_temp_eff>` command.
Output info
""""""""""
"""""""""""
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (symmetric tensor), which can be accessed by