diff --git a/doc/src/fix_hyper_global.rst b/doc/src/fix_hyper_global.rst index 3ab1c8c995..f58c4780b0 100644 --- a/doc/src/fix_hyper_global.rst +++ b/doc/src/fix_hyper_global.rst @@ -111,15 +111,17 @@ The time boost factor for the system is given each timestep I by B_i = e^{\beta V^{max}_{ij}} -where :math:`\beta = \frac{1}{kT_{equil}}`, and :math:`T_{equil}` is the temperature of the system -and an argument to this fix. Note that :math:`B_i >= 1` at every step. +where :math:`\beta = \frac{1}{kT_{equil}}`, and :math:`T_{equil}` is the +temperature of the system and an argument to this fix. Note that +:math:`B_i >= 1` at every step. .. note:: - To run a GHD simulation, the input script must also use the :doc:`fix langevin ` command to thermostat the atoms at the - same *Tequil* as specified by this fix, so that the system is running - constant-temperature (NVT) dynamics. LAMMPS does not check that this - is done. + To run a GHD simulation, the input script must also use the :doc:`fix + langevin ` command to thermostat the atoms at the same + :math:`T_{equil}` as specified by this fix, so that the system is + running constant-temperature (NVT) dynamics. LAMMPS does not check + that this is done. The elapsed time :math:`t_{hyper}` for a GHD simulation running for *N* timesteps is simply @@ -142,19 +144,19 @@ factor is an input parameter; see the :doc:`fix hyper/local ` p Here is additional information on the input parameters for GHD. -The *cutbond* argument is the cutoff distance for defining bonds -between pairs of nearby atoms. A pair of *ij* atoms in their -equilibrium, minimum-energy configuration, which are separated by a -distance :math:`R_{ij} < cutbond`, are flagged as a bonded pair. Setting +The *cutbond* argument is the cutoff distance for defining bonds between +pairs of nearby atoms. A pair of *ij* atoms in their equilibrium, +minimum-energy configuration, which are separated by a distance +:math:`R_{ij} < cutbond`, are flagged as a bonded pair. Setting *cubond* to be ~25% larger than the nearest-neighbor distance in a -crystalline lattice is a typical choice for solids, so that bonds -exist only between nearest neighbor pairs. +crystalline lattice is a typical choice for solids, so that bonds exist +only between nearest neighbor pairs. The *qfactor* argument is the limiting strain at which the bias potential goes to 0.0. It is dimensionless, so a value of 0.3 means a bond distance can be up to 30% larger or 30% smaller than the -equilibrium (quenched) R0ij distance and the two atoms in the bond -could still experience a non-zero bias force. +equilibrium (quenched) :math:`R^0_{ij}` distance and the two atoms in +the bond could still experience a non-zero bias force. If *qfactor* is set too large, then transitions from one energy basin to another are affected because the bias potential is non-zero at the @@ -187,9 +189,10 @@ correctly. There will just be fewer events because the hyper time rate does not change (as a function of hyper time). The *Tequil* argument is the temperature at which the system is -simulated; see the comment above about the :doc:`fix langevin ` thermostatting. It is also part of the -beta term in the exponential factor that determines how much boost is -achieved as a function of the bias potential. +simulated; see the comment above about the :doc:`fix langevin +` thermostatting. It is also part of the beta term in the +exponential factor that determines how much boost is achieved as a +function of the bias potential. In general, the lower the value of *Tequil* and the higher the value of *Vmax*, the more time boost will be achievable by the GHD diff --git a/doc/src/fix_hyper_local.rst b/doc/src/fix_hyper_local.rst index 26f8979ef1..499a12b9bc 100644 --- a/doc/src/fix_hyper_local.rst +++ b/doc/src/fix_hyper_local.rst @@ -135,9 +135,9 @@ to this fix. To run an LHD simulation, the input script must also use the :doc:`fix langevin ` command to thermostat the atoms at - the same *Tequil* as specified by this fix, so that the system is - running constant-temperature (NVT) dynamics. LAMMPS does not check - that this is done. + the same :math:`T_{equil}` as specified by this fix, so that the + system is running constant-temperature (NVT) dynamics. LAMMPS does + not check that this is done. Note that if *ij*\ == *kl*, then bond *ij* is a biased bond on that timestep, otherwise it is not. But regardless, the boost factor @@ -219,10 +219,11 @@ guarantee an accelerated time-accurate trajectory of the system. as for GHD), so that the :math:`C_{ij}` remain near unity. The *Tequil* argument is the temperature at which the system is -simulated; see the comment above about the :doc:`fix langevin ` thermostatting. It is also part of the -beta term in the exponential factor that determines how much boost is -achieved as a function of the bias potential. See the discussion of -the *Btarget* argument below. +simulated; see the comment above about the :doc:`fix langevin +` thermostatting. It is also part of the beta term in the +exponential factor that determines how much boost is achieved as a +function of the bias potential. See the discussion of the *Btarget* +argument below. As discussed above, the *Dcut* argument is the distance required between two locally maxstrain bonds for them to both be selected as