diff --git a/doc/src/Howto_github.rst b/doc/src/Howto_github.rst index 78a05f113c..b53a2edbc7 100644 --- a/doc/src/Howto_github.rst +++ b/doc/src/Howto_github.rst @@ -487,10 +487,10 @@ updates are back-ported from the *develop* branch to the *maintenance* branch and occasionally merged to *stable* as an update release. Furthermore, the naming of the release tags now follow the pattern -"patch_" to simplify comparisons between releases. -For stable releases additional "stable_" tags are +"patch\_" to simplify comparisons between releases. +For stable releases additional "stable\_" tags are applied and update releases are tagged with -"stable__update", Finally, all releases and +"stable\_\_update", Finally, all releases and submissions are subject to automatic testing and code checks to make sure they compile with a variety of compilers and popular operating systems. Some unit and regression testing is applied as well. diff --git a/doc/src/fix_hyper_global.rst b/doc/src/fix_hyper_global.rst index f58c4780b0..9eae426098 100644 --- a/doc/src/fix_hyper_global.rst +++ b/doc/src/fix_hyper_global.rst @@ -131,14 +131,15 @@ timesteps is simply t_{hyper} = \sum_{i=1,N} B-i \cdot dt where *dt* is the timestep size defined by the :doc:`timestep ` -command. The effective time acceleration due to GHD is thus t_hyper / -N\*dt, where N\*dt is elapsed time for a normal MD run of N timesteps. +command. The effective time acceleration due to GHD is thus +:math:`t_{hyper} / N * dt`, where N\*dt is elapsed time for a normal MD run +of N timesteps. -Note that in GHD, the boost factor varies from timestep to timestep. -Likewise, which bond has :math:`E^{max}` strain and thus which pair of -atoms the bias potential is added to, will also vary from timestep to timestep. -This is in contrast to local hyperdynamics (LHD) where the boost -factor is an input parameter; see the :doc:`fix hyper/local ` page for details. +Note that in GHD, the boost factor varies from timestep to timestep. Likewise, +which bond has :math:`E^{max}` strain and thus which pair of atoms the bias +potential is added to, will also vary from timestep to timestep. This is in +contrast to local hyperdynamics (LHD) where the boost factor is an input +parameter; see the :doc:`fix hyper/local ` page for details. ---------- @@ -178,7 +179,7 @@ time-accurate trajectory of the system. Note that if *Vmax* is set too small, the GHD simulation will run correctly. There will just be fewer events because the hyper time -(t_hyper equation above) will be shorter. +(:math:`t_{hyper}` equation above) will be shorter. .. note:: diff --git a/doc/src/fix_hyper_local.rst b/doc/src/fix_hyper_local.rst index 499a12b9bc..46d73daa66 100644 --- a/doc/src/fix_hyper_local.rst +++ b/doc/src/fix_hyper_local.rst @@ -111,7 +111,7 @@ requirement, and thus a bias potential :math:`V^{max}_{ij}` will be applied to many bonds on the same timestep. In LHD, all bonds store a :math:`C_{ij}` prefactor which appears in -the :math:`V^{max}_{ij}` and :math:`F^{max}_{ij}equations above. Note +the :math:`V^{max}_{ij}` and :math:`F^{max}_{ij}` equations above. Note that the :math:`C_{ij}` factor scales the strength of the bias energy and forces whenever bond *ij* is the maximum strain bond in its neighborhood. @@ -269,7 +269,7 @@ inverse of the alpha parameter discussed in The *Btarget* argument is the desired time boost factor (a value > 1) that all the atoms in the system will experience. The elapsed time -t_hyper for an LHD simulation running for *N* timesteps is simply +:math:`t_{hyper}` for an LHD simulation running for *N* timesteps is simply .. math:: @@ -294,7 +294,7 @@ is the specified temperature of the system Note that if *Btarget* is set smaller than this, the LHD simulation will run correctly. There will just be fewer events because the hyper -time (t_hyper equation above) will be shorter. +time (:math:`t_{hyper}` equation above) will be shorter. .. note::