diff --git a/doc/src/compute_reduce_chunk.rst b/doc/src/compute_reduce_chunk.rst index d7e7f5cf08..c988af276f 100644 --- a/doc/src/compute_reduce_chunk.rst +++ b/doc/src/compute_reduce_chunk.rst @@ -83,8 +83,10 @@ asterisk means all indices from n to :math:`N` (inclusive). A middle asterisk means all indices from m to n (inclusive). Using a wildcard is the same as if the individual columns of the array -had been listed one by one. For example, the folowing two compute reduce/chunk -commands are equivalent, since the :doc:`compute property/chunk ` command creates a per-atom array with 3 columns: +had been listed one by one. For example, the following two compute reduce/chunk +commands are equivalent, since the +:doc:`compute property/chunk ` command creates a per-atom +array with 3 columns: .. code-block:: LAMMPS diff --git a/doc/src/compute_temp.rst b/doc/src/compute_temp.rst index d715f049b8..2e9d4ab362 100644 --- a/doc/src/compute_temp.rst +++ b/doc/src/compute_temp.rst @@ -36,11 +36,11 @@ The temperature is calculated by the formula .. math:: - \mathrm{KE} = \frac{\text{dim}}{2} N k T, + \text{KE} = \frac{\text{dim}}{2} N k_B T, where KE = 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` is the Boltzmann +:math:`N` is the number of atoms in the group, :math:`k_B` is the Boltzmann constant, and :math:`T` is the absolute temperature. A kinetic energy tensor, stored as a six-element vector, is also diff --git a/doc/src/compute_temp_com.rst b/doc/src/compute_temp_com.rst index fdd29fac20..fde6f701fd 100644 --- a/doc/src/compute_temp_com.rst +++ b/doc/src/compute_temp_com.rst @@ -37,12 +37,12 @@ the temperature is calculated by the formula .. math:: - \text{KE} = \frac{\text{dim}}{2} N k 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 -:math:`\frac12 m v^2`), dim = 2 or 3 is the dimensionality of the simulation, -:math:`N` is number of atoms in the group, :math:`k` is the Boltzmann constant, -and :math:`T` is the absolute temperature. +:math:`\frac12 m v^2`), dim = 2 or 3 is the dimensionality of the +simulation, :math:`N` is number of atoms in the group, :math:`k_B` is +the Boltzmann constant, and :math:`T` is the absolute temperature. A kinetic energy tensor, stored as a six-element vector, is also calculated by this compute for use in the computation of a pressure diff --git a/doc/src/compute_temp_cs.rst b/doc/src/compute_temp_cs.rst index 1f821fc1e3..3c9503cf4f 100644 --- a/doc/src/compute_temp_cs.rst +++ b/doc/src/compute_temp_cs.rst @@ -57,11 +57,11 @@ The temperature is calculated by the formula .. math:: - \text{KE} = \frac{\text{dim}}{2} N k 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 :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` is the Boltzmann +: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 diff --git a/doc/src/compute_temp_deform.rst b/doc/src/compute_temp_deform.rst index 70e2f56fc5..b2d6b68b17 100644 --- a/doc/src/compute_temp_deform.rst +++ b/doc/src/compute_temp_deform.rst @@ -65,12 +65,13 @@ temperature is calculated by the formula .. math:: - \text{KE} = \frac{\text{dim}}{2} N k 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 -: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` is the Boltzmann -constant, and :math:`T` is the temperature. Note that :math:`v` in the kinetic energy formula is the atom's velocity. +: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 temperature. Note that +:math:`v` in the kinetic energy formula is the atom's velocity. A kinetic energy tensor, stored as a six-element vector, is also calculated by this compute for use in the computation of a pressure diff --git a/doc/src/compute_temp_eff.rst b/doc/src/compute_temp_eff.rst index 08b72be29a..c76581fa68 100644 --- a/doc/src/compute_temp_eff.rst +++ b/doc/src/compute_temp_eff.rst @@ -34,7 +34,7 @@ The temperature is calculated by the formula .. math:: - \text{KE} = \frac{\text{dim}}{2} N k 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 :math:`\frac12 m v^2` for nuclei and sum of @@ -42,7 +42,7 @@ where KE is the total kinetic energy of the group of atoms (sum of includes the radial electron velocity contributions), dim = 2 or 3 is the dimensionality of the simulation, :math:`N` is the number of atoms (only total number of nuclei in the eFF (see the :doc:`pair_eff ` -command) in the group, :math:`k` is the Boltzmann constant, and :math:`T` is +command) in the group, :math:`k_B` is the Boltzmann constant, and :math:`T` is the absolute temperature. This expression is summed over all nuclear and electronic degrees of freedom, essentially by setting the kinetic contribution to the heat capacity to :math:`\frac32 k` (where only nuclei contribute). This diff --git a/doc/src/compute_temp_partial.rst b/doc/src/compute_temp_partial.rst index 4db34ba4a9..0512311d8f 100644 --- a/doc/src/compute_temp_partial.rst +++ b/doc/src/compute_temp_partial.rst @@ -34,11 +34,11 @@ The temperature is calculated by the formula .. math:: - \text{KE} = \frac{\text{dim}}{2} N k 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 :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` is the Boltzmann +:math:`N` is the number of atoms in the group, :math:`k_B` is the Boltzmann constant, and :math:`T` = temperature. The calculation of KE excludes the :math:`x`, :math:`y`, or :math:`z` dimensions if *xflag*, *yflag*, or *zflag* is 0. The dim parameter is adjusted to give the correct number of diff --git a/doc/src/compute_temp_ramp.rst b/doc/src/compute_temp_ramp.rst index db35bd09fa..13799874ab 100644 --- a/doc/src/compute_temp_ramp.rst +++ b/doc/src/compute_temp_ramp.rst @@ -48,17 +48,17 @@ dimension for each atom, the temperature is calculated by the formula .. math:: - \text{KE} = \frac{\text{dim}}{2} N k 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 :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` is the Boltzmann +:math:`N` is the number of atoms in the group, :math:`k_B` is the Boltzmann constant, and :math:`T` is the absolute temperature. The *units* keyword determines the meaning of the distance units used for coordinates (*clo*, *chi*) and velocities (*vlo*, *vhi*). A *box* value selects standard distance units as defined by the :doc:`units ` -command (e.g., :math:`\mathrm{\mathring A}` for units = real or metal). A +command (e.g., :math:`\mathrm{\mathring{A}}` for units = real or metal). A *lattice* value means the distance units are in lattice spacings (i.e., velocity in lattice spacings per unit time). The :doc:`lattice ` command must have been previously used to define the lattice spacing. diff --git a/doc/src/compute_temp_region.rst b/doc/src/compute_temp_region.rst index 1d52ac51a4..c8a3075771 100644 --- a/doc/src/compute_temp_region.rst +++ b/doc/src/compute_temp_region.rst @@ -42,11 +42,11 @@ The temperature is calculated by the formula .. math:: - \text{KE} = \frac{\text{dim}}{2} N k 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 :math:`\frac12 m v^2`), dim = 2 or 3 is the dimensionality of the simulation, -:math:`N` is the number of atoms in both the group and region, :math:`k` is +:math:`N` is the number of atoms in both the group and region, :math:`k_B` is the Boltzmann constant, and :math:`T` temperature. A kinetic energy tensor, stored as a six-element vector, is also diff --git a/doc/src/compute_temp_rotate.rst b/doc/src/compute_temp_rotate.rst index 0d9551e17b..e760a49b00 100644 --- a/doc/src/compute_temp_rotate.rst +++ b/doc/src/compute_temp_rotate.rst @@ -36,11 +36,11 @@ each atom, the temperature is calculated by the formula .. math:: - \text{KE} = \frac{\text{dim}}{2} N k 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 :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` is the Boltzmann +:math:`N` is the number of atoms in the group, :math:`k_B` is the Boltzmann constant, and :math:`T` is the absolute temperature. A kinetic energy tensor, stored as a six-element vector, is also calculated by diff --git a/doc/src/compute_viscosity_cos.rst b/doc/src/compute_viscosity_cos.rst index 0c335d4608..a3adf3d78b 100644 --- a/doc/src/compute_viscosity_cos.rst +++ b/doc/src/compute_viscosity_cos.rst @@ -79,11 +79,11 @@ subtracted for each atom, the temperature is calculated by the formula .. math:: - \text{KE} = \frac{\text{dim}}{2} N k 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 :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` is the Boltzmann +:math:`N` is the number of atoms in the group, :math:`k_B` is the Boltzmann constant, and :math:`T` is the absolute temperature. A kinetic energy tensor, stored as a six-element vector, is also diff --git a/doc/src/dump.rst b/doc/src/dump.rst index 0bef244e0c..bd57ef0353 100644 --- a/doc/src/dump.rst +++ b/doc/src/dump.rst @@ -286,7 +286,7 @@ For an orthogonal simulation box this information is formatted as: where xlo,xhi are the maximum extents of the simulation box in the :math:`x`-dimension, and similarly for :math:`y` and :math:`z`. The "xx yy zz" terms are six characters that encode the style of boundary for each -of the sisx simulation box boundaries (xlo,xhi; ylo,yhi; and zlo,zhi). Each of +of the six simulation box boundaries (xlo,xhi; ylo,yhi; and zlo,zhi). Each of the six characters is either p (periodic), f (fixed), s (shrink wrap), or m (shrink wrapped with a minimum value). See the :doc:`boundary ` command for details. diff --git a/doc/src/fix.rst b/doc/src/fix.rst index b9896a0e0c..db08e64b14 100644 --- a/doc/src/fix.rst +++ b/doc/src/fix.rst @@ -318,7 +318,7 @@ accelerated styles exist. * :doc:`plumed ` - wrapper on PLUMED free energy library * :doc:`poems ` - constrain clusters of atoms to move as coupled rigid bodies * :doc:`polarize/bem/gmres ` - compute induced charges at the interface between impermeable media with different dielectric constants with generalized minimum residual (GMRES) -* :doc:`polarize/bem/icc ` - compute induced charges at the interface between impermeable media with different dielectric constants with the sucessive over-relaxation algorithm +* :doc:`polarize/bem/icc ` - compute induced charges at the interface between impermeable media with different dielectric constants with the successive over-relaxation algorithm * :doc:`polarize/functional ` - compute induced charges at the interface between impermeable media with different dielectric constants with the energy variational approach * :doc:`pour ` - pour new atoms/molecules into a granular simulation domain * :doc:`precession/spin ` - apply a precession torque to each magnetic spin diff --git a/doc/src/fix_gcmc.rst b/doc/src/fix_gcmc.rst index 760f41e186..e748f17ae7 100644 --- a/doc/src/fix_gcmc.rst +++ b/doc/src/fix_gcmc.rst @@ -259,9 +259,9 @@ pressure of the fictitious gas reservoir by: .. math:: \mu^{id} = & k T \ln{\rho \Lambda^3} \\ - = & k T \ln{\frac{\phi P \Lambda^3}{k T}} + = & k T \ln{\frac{\phi P \Lambda^3}{k_B T}} -where *k* is Boltzman's constant, *T* is the user-specified +where :math:`k_B` is the Boltzmann constant, *T* is the user-specified temperature, :math:`\rho` is the number density, *P* is the pressure, and :math:`\phi` is the fugacity coefficient. The constant :math:`\Lambda` is required for dimensional consistency. For all unit @@ -269,7 +269,7 @@ styles except *lj* it is defined as the thermal de Broglie wavelength .. math:: - \Lambda = \sqrt{ \frac{h^2}{2 \pi m k T}} + \Lambda = \sqrt{ \frac{h^2}{2 \pi m k_B T}} where *h* is Planck's constant, and *m* is the mass of the exchanged atom or molecule. For unit style *lj*, :math:`\Lambda` is simply set to diff --git a/doc/src/fix_nh.rst b/doc/src/fix_nh.rst index cb9e6ba61e..5e8f313323 100644 --- a/doc/src/fix_nh.rst +++ b/doc/src/fix_nh.rst @@ -208,9 +208,9 @@ The relaxation rate of the barostat is set by its inertia :math:`W`: .. math:: - W = (N + 1) k T_{\rm target} P_{\rm damp}^2 + W = (N + 1) k_B T_{\rm target} P_{\rm damp}^2 -where :math:`N` is the number of atoms, :math:`k` is the Boltzmann constant, +where :math:`N` is the number of atoms, :math:`k_B` is the Boltzmann constant, and :math:`T_{\rm target}` is the target temperature of the barostat :ref:`(Martyna) `. If a thermostat is defined, :math:`T_{\rm target}` is the target temperature of the thermostat. If a thermostat is not defined, :math:`T_{\rm target}` diff --git a/doc/src/fix_widom.rst b/doc/src/fix_widom.rst index 34b9ae44f6..7c431a2c36 100644 --- a/doc/src/fix_widom.rst +++ b/doc/src/fix_widom.rst @@ -100,9 +100,9 @@ The excess chemical potential mu_ex is defined as: .. math:: - \mu_{ex} = -kT \ln(<\exp(-(U_{N+1}-U_{N})/{kT})>) + \mu_{ex} = -kT \ln(<\exp(-(U_{N+1}-U_{N})/{k_B T})>) -where *k* is Boltzman's constant, *T* is the user-specified temperature, +where :math:`k_B` is the Boltzmann constant, *T* is the user-specified temperature, U_N and U_{N+1} is the potential energy of the system with N and N+1 particles. diff --git a/doc/src/pair_dpd_ext.rst b/doc/src/pair_dpd_ext.rst index 88395f1c73..54d1e4bca3 100644 --- a/doc/src/pair_dpd_ext.rst +++ b/doc/src/pair_dpd_ext.rst @@ -80,8 +80,8 @@ the corresponding cutoff, :math:`w_{\alpha} ( r ) = ( 1 - r / \bar{r}_c )^{s_{\alpha}}`, :math:`\alpha \equiv ( \parallel, \perp )`, are weight functions with coefficients :math:`s_\alpha` that vary between 0 and 1, :math:`\bar{r}_c` is the corresponding cutoff, :math:`\mathbf{I}` is the -unit matrix, :math:`\sigma_{\alpha} = \sqrt{2 k T \gamma_{\alpha}}`, -where :math:`k` is the Boltzmann constant and :math:`T` is the +unit matrix, :math:`\sigma_{\alpha} = \sqrt{2 k_B T \gamma_{\alpha}}`, +where :math:`k_B` is the Boltzmann constant and :math:`T` is the temperature in the pair\_style command. For the style *dpd/ext/tstat*, the force on atom I due to atom J is @@ -121,7 +121,7 @@ as in the examples above: The last coefficient is optional. If not specified, the global DPD cutoff is used. Note that :math:`\sigma`'s are set equal to -:math:`\sqrt{2 k T \gamma}`, where :math:`T` is the temperature set by +:math:`\sqrt{2 k_B T \gamma}`, where :math:`T` is the temperature set by the :doc:`pair_style ` command so it does not need to be specified. diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index a324f41941..8b3689c367 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -257,6 +257,7 @@ Bfrac bgq Bh Bialke +biaxial bicrystal Biersack bigbig @@ -304,7 +305,6 @@ Bogaerts Bogusz Bohrs boltz -Boltzman BondAngle BondBond bondchk @@ -3645,6 +3645,7 @@ Vandenbrande Vanduyfhuys varargs varavg +variational Varshalovich Varshney vashishta