diff --git a/doc/src/fix_hyper_local.rst b/doc/src/fix_hyper_local.rst index 22de3bc3ca..7e01296dc7 100644 --- a/doc/src/fix_hyper_local.rst +++ b/doc/src/fix_hyper_local.rst @@ -75,7 +75,7 @@ doc page. This description of LHD builds on the GHD description. The definition of bonds and :math:`E_{ij}` are the same for GHD and LHD. The formulas for :math:`V^{max}_{ij}` and :math:`F^{max}_{ij}` are also -the same except for a pre-factor :math:`C_{ij}`, explained below. +the same except for a prefactor :math:`C_{ij}`, explained below. The bias energy :math:`V_{ij}` applied to a bond *ij* with maximum strain is @@ -256,7 +256,7 @@ Note that this fix does not know the *cutevent* parameter, but uses half the *cutbond* parameter as an estimate to warn if the ghost cutoff is not long enough. -As described above the *alpha* argument is a pre-factor in the +As described above the *alpha* argument is a prefactor in the boostostat update equation for each bond's :math:`C_{ij}` prefactor. *Alpha* is specified in time units, similar to other thermostat or barostat damping parameters. It is roughly the physical time it will take the diff --git a/doc/src/fix_restrain.rst b/doc/src/fix_restrain.rst index 84e525cdf2..b9bdbfd849 100644 --- a/doc/src/fix_restrain.rst +++ b/doc/src/fix_restrain.rst @@ -59,7 +59,7 @@ of a bond or angle or dihedral interaction whose strength can vary over time during a simulation. This is functionally similar to creating a bond or angle or dihedral for the same atoms in a data file, as specified by the :doc:`read_data ` command, albeit -with a time-varying pre-factor coefficient, and except for exclusion +with a time-varying prefactor coefficient, and except for exclusion rules, as explained below. For the purpose of force field parameter-fitting or mapping a molecular diff --git a/doc/src/fix_wall.rst b/doc/src/fix_wall.rst index bcbead8824..3028588505 100644 --- a/doc/src/fix_wall.rst +++ b/doc/src/fix_wall.rst @@ -199,7 +199,7 @@ inside the colloid particle and wall. Note that the cutoff distance Rc in this case is the distance from the colloid particle center to the wall. The prefactor :math:`\epsilon` can be thought of as an effective Hamaker constant with energy units for the strength of the colloid-wall -interaction. More specifically, the :math:`\epsilon` pre-factor is +interaction. More specifically, the :math:`\epsilon` prefactor is :math:`4\pi^2 \rho_{wall} \rho_{colloid} \epsilon \sigma^6`, where :math:`\epsilon` and :math:`\sigma` are the LJ parameters for the constituent LJ particles. :math:`\rho_{wall}` and :math:`\rho_{colloid}` @@ -211,7 +211,7 @@ constituent LJ particles of size :math:`\sigma` within the colloid particle and a 3d half-lattice of Lennard-Jones 12/6 particles of size :math:`\sigma` in the wall. As mentioned in the preceding paragraph, the density of particles in the wall and colloid can be different, as specified by -the :math:`\epsilon` pre-factor. +the :math:`\epsilon` prefactor. For the *wall/harmonic* style, :math:`\epsilon` is effectively the spring constant K, and has units (energy/distance\^2). The input parameter diff --git a/doc/src/fix_wall_ees.rst b/doc/src/fix_wall_ees.rst index 13a7935d0d..4c95e32d0d 100644 --- a/doc/src/fix_wall_ees.rst +++ b/doc/src/fix_wall_ees.rst @@ -88,7 +88,7 @@ examples/ directory. The prefactor :math:`\epsilon` can be thought of as an effective Hamaker constant with energy units for the strength of the ellipsoid-wall interaction. More specifically, the :math:`\epsilon` -pre-factor is +prefactor is .. math:: diff --git a/doc/src/pair_gran.rst b/doc/src/pair_gran.rst index c4024a391a..f83fd6d6ab 100644 --- a/doc/src/pair_gran.rst +++ b/doc/src/pair_gran.rst @@ -144,7 +144,7 @@ two particles, and is thus a non-linear function of overlap distance. Thus Kn has units of force per area and is thus specified in units of (pressure). The effects of absolute particle size (monodispersity) and relative size (polydispersity) are captured in the radii-dependent -pre-factors. When these pre-factors are carried through to the other +prefactors. When these prefactors are carried through to the other terms in the force equation it means that the specified :math:`\gamma_n` is in units of (1/(time\*distance)), :math:`K_t` is in units of (pressure), and :math:`\gamma_t` is in units of (1/(time\*distance)). diff --git a/doc/src/pair_multi_lucy.rst b/doc/src/pair_multi_lucy.rst index c8c8551df5..5c5cec5c4f 100644 --- a/doc/src/pair_multi_lucy.rst +++ b/doc/src/pair_multi_lucy.rst @@ -54,7 +54,7 @@ form. An interpolation table is used to evaluate the density-dependent energy (:math:`\int A(\rho') d\rho'`) and force (:math:`A(\rho')`). Note that -the pre-factor to the energy is computed after the interpolation, thus +the prefactor to the energy is computed after the interpolation, thus the :math:`\int A(\rho') d \rho'` will have units of energy / length\^4. The interpolation table is created as a pre-computation by fitting diff --git a/doc/src/pair_multi_lucy_rx.rst b/doc/src/pair_multi_lucy_rx.rst index 6cb56360ba..9759d5b84d 100644 --- a/doc/src/pair_multi_lucy_rx.rst +++ b/doc/src/pair_multi_lucy_rx.rst @@ -67,7 +67,7 @@ form. An interpolation table is used to evaluate the density-dependent energy (:math:`\int A(\rho') d \rho'`) and force (:math:`A(\rho')`). Note that -the pre-factor to the energy is computed after the interpolation, thus +the prefactor to the energy is computed after the interpolation, thus the :math:`\int A(\rho') d\rho'` will have units of energy / length\^4. The interpolation table is created as a pre-computation by fitting diff --git a/doc/src/pair_soft.rst b/doc/src/pair_soft.rst index 7986b1286e..1702811ed9 100644 --- a/doc/src/pair_soft.rst +++ b/doc/src/pair_soft.rst @@ -41,7 +41,7 @@ Style *soft* computes pairwise interactions with the formula \qquad r < r_c It is useful for pushing apart overlapping atoms, since it does not -blow up as r goes to 0. A is a pre-factor that can be made to vary in +blow up as r goes to 0. A is a prefactor that can be made to vary in time from the start to the end of the run (see discussion below), e.g. to start with a very soft potential and slowly harden the interactions over time. Rc is the cutoff. See the :doc:`fix nve/limit ` command for another way to push apart diff --git a/doc/src/special_bonds.rst b/doc/src/special_bonds.rst index 4b197fbf3a..ee148e7a9f 100644 --- a/doc/src/special_bonds.rst +++ b/doc/src/special_bonds.rst @@ -88,7 +88,7 @@ The Coulomb factors are applied to any Coulomb (charge interaction) term that the potential calculates. The LJ factors are applied to the remaining terms that the potential calculates, whether they represent LJ interactions or not. The weighting factors are a scaling -pre-factor on the energy and force between the pair of atoms. A value +prefactor on the energy and force between the pair of atoms. A value of 1.0 means include the full interaction; a value of 0.0 means exclude it completely.