diff --git a/doc/src/compute_pressure.rst b/doc/src/compute_pressure.rst index 980a8f6481..439f701bd4 100644 --- a/doc/src/compute_pressure.rst +++ b/doc/src/compute_pressure.rst @@ -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 `. +The scalar and vector values calculated by this compute are "intensive". +The scalar and vector values will be in pressure :doc:`units `. Restrictions """""""""""" diff --git a/doc/src/compute_temp_asphere.rst b/doc/src/compute_temp_asphere.rst index c9b1e51532..d2af4278ad 100644 --- a/doc/src/compute_temp_asphere.rst +++ b/doc/src/compute_temp_asphere.rst @@ -41,8 +41,8 @@ translational and rotational kinetic energy. This differs from the usual :doc:`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 ` 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 ` 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 `, 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 ` command. The formula for -the components of the tensor is the same as the above expression for +:doc:`compute pressue ` 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 ` 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 +` 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 `. The vector values are in energy :doc:`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 ` page for more info. +LAMMPS was built with that package. See the :doc:`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 ` -command. +This compute requires that atoms store angular momentum and a quaternion +as defined by the :doc:`atom_style ellipsoid ` 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 diff --git a/doc/src/compute_temp_cs.rst b/doc/src/compute_temp_cs.rst index 0620fea9b7..4908b12797 100644 --- a/doc/src/compute_temp_cs.rst +++ b/doc/src/compute_temp_cs.rst @@ -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) `. See the :doc:`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 ` -(e.g., :doc:`fix temp/rescale `, :doc:`fix npt `). +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 ` (e.g., :doc:`fix temp/rescale +`, :doc:`fix npt `). -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 ` 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 +` 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 ` command. The formula for -the components of the tensor is the same as the above expression for +:doc:`compute pressue ` 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 `, :doc:`fix temp/rescale -`, :doc:`fix temp/berendsen `, -and :doc:`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 +`, :doc:`fix temp/rescale `, :doc:`fix +temp/berendsen `, and :doc:`fix langevin +`. The internal energy of core/shell pairs can be calculated by the -:doc:`compute temp/chunk ` command, if chunks are defined -as core/shell pairs. See the :doc:`Howto coreshell ` doc -page for more discussion on how to do this. +:doc:`compute temp/chunk ` command, if chunks are +defined as core/shell pairs. See the :doc:`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 `. The vector values are in energy :doc:`units `. diff --git a/doc/src/compute_temp_profile.rst b/doc/src/compute_temp_profile.rst index 47725cdcbc..9f6bbfc89c 100644 --- a/doc/src/compute_temp_profile.rst +++ b/doc/src/compute_temp_profile.rst @@ -210,10 +210,10 @@ will be for most thermostats. Related commands """""""""""""""" -:doc:`compute temp `, :doc:`compute temp/ramp - `, :doc:`compute temp/deform - `, :doc:`compute pressure - ` +:doc:`compute temp `, +:doc:`compute temp/ramp `, +:doc:`compute temp/deform `, +:doc:`compute pressure ` Default """"""" diff --git a/doc/src/compute_temp_ramp.rst b/doc/src/compute_temp_ramp.rst index d89a98fbea..643ca9d1dd 100644 --- a/doc/src/compute_temp_ramp.rst +++ b/doc/src/compute_temp_ramp.rst @@ -124,10 +124,10 @@ Restrictions Related commands """""""""""""""" -:doc:`compute temp `, :doc:`compute temp/profie - `, :doc:`compute temp/deform - `, :doc:`compute pressure - ` +:doc:`compute temp `, +:doc:`compute temp/profile `, +:doc:`compute temp/deform `, +:doc:`compute pressure ` Default """"""" diff --git a/doc/src/compute_temp_region_eff.rst b/doc/src/compute_temp_region_eff.rst index 12bc3f01a1..4193a0a7ec 100644 --- a/doc/src/compute_temp_region_eff.rst +++ b/doc/src/compute_temp_region_eff.rst @@ -38,7 +38,7 @@ contributions, as discussed by the :doc:`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