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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 virial as the sum of pair, bond, angle, dihedral, improper, kspace
(long-range), and fix contributions to the force on each atom. If any (long-range), and fix contributions to the force on each atom. If any
extra keywords are listed, then only those components are summed to extra keywords are listed, then only those components are summed to
compute temperature or ke and/or the virial. The *virial* keyword compute temperature or ke and/or the virial. The *virial* keyword means
means include all terms except the kinetic energy *ke*\ . include all terms except the kinetic energy *ke*\ .
The *pair/hybrid* keyword means to only include contribution The *pair/hybrid* keyword means to only include contribution
from a sub-style in a *hybrid* or *hybrid/overlay* pair style. 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 The temperature and kinetic energy tensor are not calculated by this
compute, but rather by the temperature compute specified with the compute, but rather by the temperature compute specified with the
command. See the doc pages for individual compute temp variants for command. See the doc pages for individual compute temp variants for an
an explation of how they calculate temperature and a symmetric tensor explanation of how they calculate temperature and a symmetric tensor
(6-element vector) whose components are twice that of the traditional (6-element vector) whose components are twice that of the traditional KE
KE tensor. That tensor is what appears in the pressure tensor formula tensor. That tensor is what appears in the pressure tensor formula
above. above.
If the kinetic energy is not included in the pressure, than If the kinetic energy is not included in the pressure, than the
the temperature compute is not used and can be specified as NULL. temperature compute is not used and can be specified as NULL. Normally
Normally the temperature compute used by compute pressure should the temperature compute used by compute pressure should calculate the
calculate the temperature of all atoms for consistency with the virial temperature of all atoms for consistency with the virial term, but any
term, but any compute style that calculates temperature can be used compute style that calculates temperature can be used (e.g., one that
(e.g., one that excludes frozen atoms or other degrees of freedom). excludes frozen atoms or other degrees of freedom).
Note that if desired the specified temperature compute can be one that Note that if desired the specified temperature compute can be one that
subtracts off a bias to calculate a temperature using only the thermal 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_{xx},` :math:`p_{yy},` :math:`p_{zz},` :math:`p_{xy},`
:math:`p_{xz},` :math:`p_{yz}.` :math:`p_{xz},` :math:`p_{yz}.`
The scalar and vector values calculated by this compute are The scalar and vector values calculated by this compute are "intensive".
"intensive". The scalar and vector values will be in pressure The scalar and vector values will be in pressure :doc:`units <units>`.
:doc:`units <units>`.
Restrictions 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 usual :doc:`compute temp <compute_temp>` command, which assumes point
particles with only translational kinetic energy. particles with only translational kinetic energy.
Only finite-size particles (aspherical or spherical) can be included Only finite-size particles (aspherical or spherical) can be included in
in the group. For 3d finite-size particles, each has six degrees of the group. For 3d finite-size particles, each has six degrees of
freedom (three translational, three rotational). For 2d finite-size freedom (three translational, three rotational). For 2d finite-size
particles, each has three degrees of freedom (two translational, one particles, each has three degrees of freedom (two translational, one
rotational). 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 of the semiaxes have the same length and the corresponding relative well
depths are equal. depths are equal.
The translational kinetic energy is computed the same as is described The translational kinetic energy is computed the same as is described by
by the :doc:`compute temp <compute_temp>` command. The rotational the :doc:`compute temp <compute_temp>` command. The rotational kinetic
kinetic energy is computed as :math:`\frac12 I \omega^2`, where :math:`I` is energy is computed as :math:`\frac12 I \omega^2`, where :math:`I` is the
the inertia tensor for the aspherical particle and :math:`\omega` is its inertia tensor for the aspherical particle and :math:`\omega` is its
angular velocity, which is computed from its angular momentum. angular velocity, which is computed from its angular momentum.
.. note:: .. note::
For :doc:`2d models <dimension>`, particles are treated as For :doc:`2d models <dimension>`, particles are treated as
ellipsoids, not ellipses, meaning their moments of inertia will be the ellipsoids, not ellipses, meaning their moments of inertia will be
same as in 3d. the same as in 3d.
A kinetic energy tensor, stored as a six-element vector, is also A kinetic energy tensor, stored as a six-element vector, is also
calculated by this compute. The formula for the components of the 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 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` :math:`\omega^2` are replaced by :math:`v_x v_y` and :math:`\omega_x
for the :math:`xy` component, and the appropriate elements of the moment of \omega_y` for the :math:`xy` component, and the appropriate elements of
inertia tensor are used. The six components of the vector are ordered the moment of inertia tensor are used. The six components of the vector
:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`. 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 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 by this compute for use in the computation of a pressure tensor by the
:doc:`compute pressue <compute_pressure>` command. The formula for :doc:`compute pressue <compute_pressure>` command. The formula for the
the components of the tensor is the same as the above expression for 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 :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` 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 :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. 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 Note that because it lacks the 1/2 factor, these tensor components are
twice those of the traditional kinetic energy tensor. The six twice those of the traditional kinetic energy tensor. The six
components of the vector are ordered :math:`xx`, :math:`yy`, components of the vector are ordered :math:`xx`, :math:`yy`, :math:`zz`,
:math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`. :math:`xy`, :math:`xz`, :math:`yz`.
The number of atoms contributing to the temperature is assumed to be 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 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 This compute calculates a global scalar (the temperature) and a global
vector of length 6 (symmertic tensor), which can be accessed by vector of length 6 (symmetric tensor), which can be accessed by indices
indices 1--6. These values can be used by any command that uses 1--6. These values can be used by any command that uses global scalar
global scalar or vector values from a compute as input. See the or vector values from a compute as input. See the :doc:`Howto output
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS <Howto_output>` page for an overview of LAMMPS output options.
output options.
The scalar value calculated by this compute is "intensive". The The scalar value calculated by this compute is "intensive". The vector
vector values are "extensive". values are "extensive".
The scalar value is in temperature :doc:`units <units>`. The vector The scalar value is in temperature :doc:`units <units>`. The vector
values are in energy :doc:`units <units>`. 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 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 This compute requires that atoms store angular momentum and a quaternion
quaternion as defined by the :doc:`atom_style ellipsoid <atom_style>` as defined by the :doc:`atom_style ellipsoid <atom_style>` command.
command.
All particles in the group must be finite-size. They cannot be point 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 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 other. This compute is designed to be used with the adiabatic
core/shell model of :ref:`(Mitchell and Fincham) <MitchellFincham1>`. core/shell model of :ref:`(Mitchell and Fincham) <MitchellFincham1>`.
See the :doc:`Howto coreshell <Howto_coreshell>` page for an overview of See the :doc:`Howto coreshell <Howto_coreshell>` page for an overview of
the model as implemented in LAMMPS. Specifically, this compute the model as implemented in LAMMPS. Specifically, this compute enables
enables correct temperature calculation and thermostatting of correct temperature calculation and thermostatting of core/shell pairs
core/shell pairs where it is desirable for the internal degrees of where it is desirable for the internal degrees of freedom of the
freedom of the core/shell pairs to not be influenced by a thermostat. core/shell pairs to not be influenced by a thermostat. A compute of
A compute of this style can be used by any command that computes a this style can be used by any command that computes a temperature via
temperature via :doc:`fix_modify <fix_modify>` :doc:`fix_modify <fix_modify>` (e.g., :doc:`fix temp/rescale
(e.g., :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix npt <fix_nh>`). <fix_temp_rescale>`, :doc:`fix npt <fix_nh>`).
Note that this compute does not require all ions to be polarized, Note that this compute does not require all ions to be polarized, hence
hence defined as core/shell pairs. One can mix core/shell pairs and defined as core/shell pairs. One can mix core/shell pairs and ions
ions without a satellite particle if desired. The compute will without a satellite particle if desired. The compute will consider the
consider the non-polarized ions according to the physical system. non-polarized ions according to the physical system.
For this compute, core and shell particles are specified by two For this compute, core and shell particles are specified by two
respective group IDs, which can be defined using the respective group IDs, which can be defined using the :doc:`group
:doc:`group <group>` command. The number of atoms in the two groups <group>` command. The number of atoms in the two groups must be the
must be the same and there should be one bond defined between a pair same and there should be one bond defined between a pair of atoms in the
of atoms in the two groups. Non-polarized ions which might also be two groups. Non-polarized ions which might also be included in the
included in the treated system should not be included into either of treated system should not be included into either of these groups, they
these groups, they are taken into account by the *group-ID* (second are taken into account by the *group-ID* (second argument) of the
argument) of the compute. compute.
The temperature is calculated by the formula 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, \text{KE} = \frac{\text{dim}}{2} N k_B T,
where KE is the total kinetic energy of the group of atoms (sum of 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:`\frac12 m v^2`), dim = 2 or 3 is the dimensionality of the
:math:`N` is the number of atoms in the group, :math:`k_B` is the Boltzmann simulation, :math:`N` is the number of atoms in the group, :math:`k_B`
constant, and :math:`T` is the absolute temperature. Note that is the Boltzmann constant, and :math:`T` is the absolute temperature.
the velocity of each core or shell atom used in the KE calculation is Note that the velocity of each core or shell atom used in the KE
the velocity of the center-of-mass (COM) of the core/shell pair the calculation is the velocity of the center-of-mass (COM) of the
atom is part of. core/shell pair the atom is part of.
A symmetric tensor, stored as a six-element vector, is also calculated 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 by this compute for use in the computation of a pressure tensor by the
:doc:`compute pressue <compute_pressure>` command. The formula for :doc:`compute pressue <compute_pressure>` command. The formula for the
the components of the tensor is the same as the above expression for 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 :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 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 :math:`xy` component, and so on. Note that because it lacks the 1/2
factor, these tensor components are twice those of the traditional factor, these tensor components are twice those of the traditional
kinetic energy tensor. The six components of the vector are ordered kinetic energy tensor. The six components of the vector are ordered
:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`.
:math:`yz`.
The change this fix makes to core/shell atom velocities is essentially The change this fix makes to core/shell atom velocities is essentially
computing the temperature after a "bias" has been removed from the computing the temperature after a "bias" has been removed from the
velocity of the atoms. This "bias" is the velocity of the atom velocity of the atoms. This "bias" is the velocity of the atom relative
relative to the center-of-mass velocity of the core/shell pair. If to the center-of-mass velocity of the core/shell pair. If this compute
this compute is used with a fix command that performs thermostatting is used with a fix command that performs thermostatting then this bias
then this bias will be subtracted from each atom, thermostatting of will be subtracted from each atom, thermostatting of the remaining
the remaining center-of-mass velocity will be performed, and the bias center-of-mass velocity will be performed, and the bias will be added
will be added back in. This means the thermostatting will effectively back in. This means the thermostatting will effectively be performed on
be performed on the core/shell pairs, instead of on the individual the core/shell pairs, instead of on the individual core and shell atoms.
core and shell atoms. Thermostatting fixes that work in this way Thermostatting fixes that work in this way include :doc:`fix nvt
include :doc:`fix nvt <fix_nh>`, :doc:`fix temp/rescale <fix_nh>`, :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix
<fix_temp_rescale>`, :doc:`fix temp/berendsen <fix_temp_berendsen>`, temp/berendsen <fix_temp_berendsen>`, and :doc:`fix langevin
and :doc:`fix langevin <fix_langevin>`. <fix_langevin>`.
The internal energy of core/shell pairs can be calculated by the The internal energy of core/shell pairs can be calculated by the
:doc:`compute temp/chunk <compute_temp_chunk>` command, if chunks are defined :doc:`compute temp/chunk <compute_temp_chunk>` command, if chunks are
as core/shell pairs. See the :doc:`Howto coreshell <Howto_coreshell>` doc defined as core/shell pairs. See the :doc:`Howto coreshell
page for more discussion on how to do this. <Howto_coreshell>` doc page for more discussion on how to do this.
Output info Output info
""""""""""" """""""""""
This compute calculates a global scalar (the temperature) and a global This compute calculates a global scalar (the temperature) and a global
vector of length 6 (symmertric tensor), which can be accessed by vector of length 6 (symmetric tensor), which can be accessed by indices
indices 1--6. These values can be used by any command that uses 1--6. These values can be used by any command that uses global scalar
global scalar or vector values from a compute as input. or vector values from a compute as input.
The scalar value calculated by this compute is "intensive". The The scalar value calculated by this compute is "intensive". The vector
vector values are "extensive". values are "extensive".
The scalar value is in temperature :doc:`units <units>`. The vector The scalar value is in temperature :doc:`units <units>`. The vector
values are in energy :doc:`units <units>`. values are in energy :doc:`units <units>`.

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

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doc/src/compute_temp_ramp.rst
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@ -124,10 +124,10 @@ Restrictions
Related commands Related commands
"""""""""""""""" """"""""""""""""
:doc:`compute temp <compute_temp>`, :doc:`compute temp/profie :doc:`compute temp <compute_temp>`,
<compute_temp_profile>`, :doc:`compute temp/deform :doc:`compute temp/profile <compute_temp_profile>`,
<compute_temp_deform>`, :doc:`compute pressure :doc:`compute temp/deform <compute_temp_deform>`,
<compute_pressure>` :doc:`compute pressure <compute_pressure>`
Default 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. <compute_temp_eff>` command.
Output info Output info
"""""""""" """""""""""
This compute calculates a global scalar (the temperature) and a global This compute calculates a global scalar (the temperature) and a global
vector of length 6 (symmetric tensor), which can be accessed by vector of length 6 (symmetric tensor), which can be accessed by