typeset hyperdynamics fix docs with embedded math

simplified version of bond-boost GHD where a single bond in the system

simplified version of bond-boost GHD where a single bond in the system

is biased at any one timestep.

is biased at any one timestep.

Bonds are defined between each pair of I,J atoms whose R0ij distance

Bonds are defined between each pair of atoms *ij*\ , whose :math:`R^0_{ij}`

is less than *cutbond*\ , when the system is in a quenched state

distance is less than *cutbond*\ , when the system is in a quenched state

(minimum) energy.  Note that these are not "bonds" in a covalent

(minimum) energy.  Note that these are not "bonds" in a covalent

sense.  A bond is simply any pair of atoms that meet the distance

sense.  A bond is simply any pair of atoms that meet the distance

criterion.  *Cutbond* is an argument to this fix; it is discussed

criterion.  *Cutbond* is an argument to this fix; it is discussed

below.  A bond is only formed if one or both of the I.J atoms are in

below.  A bond is only formed if one or both of the *ij* atoms are in

the specified group.

the specified group.

The current strain of bond IJ (when running dynamics) is defined as

The current strain of bond *ij* (when running dynamics) is defined as

.. parsed-literal::

.. math::

   Eij = (Rij - R0ij) / R0ij

   E_{ij} = \frac{R_{ij} - R^0_{ij}}{R^0_{ij}}

where Rij is the current distance between atoms I,J, and R0ij is the

where :math:`R_{ij}` is the current distance between atoms *i* and *j*\ ,

equilibrium distance in the quenched state.

and :math:`R^0_{ij}` is the equilibrium distance in the quenched state.

The bias energy Vij of any bond IJ is defined as

The bias energy :math:`V_{ij}` of any bond between atoms *i* and *j*

is defined as

.. parsed-literal::

.. math::

   Vij = Vmax \* (1 - (Eij/q)\^2) for abs(Eij) < qfactor

   V_{ij} = V^{max} \cdot \left( 1 - \left(\frac{E_{ij}}{q}\right)^2 \right) \textrm{ for } \left|E_{ij}\right| < qfactor \textrm{ or } 0 \textrm{ otherwise}

       = 0 otherwise

where the prefactor *Vmax* and the cutoff *qfactor* are arguments to

where the prefactor :math:`V^{max}` and the cutoff *qfactor* are arguments to

this fix; they are discussed below.  This functional form is an

this fix; they are discussed below.  This functional form is an

inverse parabola centered at 0.0 with height Vmax and which goes to

inverse parabola centered at 0.0 with height :math:`V^{max}` and

0.0 at +/- qfactor.

which goes to 0.0 at +/- qfactor.

Let Emax = the maximum of abs(Eij) for all IJ bonds in the system on a

Let :math:`E^{max}` be the maximum of :math:`\left| E_{ij} \right|`

given timestep.  On that step, Vij is added as a bias potential to

for all *ij* bonds in the system on a

only the single bond with strain Emax, call it Vij(max).  Note that

given timestep.  On that step, :math:`V_{ij}` is added as a bias potential

Vij(max) will be 0.0 if Emax >= qfactor on that timestep.  Also note

to only the single bond with strain :math:`E^{max}`, call it

that Vij(max) is added to the normal interatomic potential that is

:math:`V^{max}_{ij}`.  Note that :math:`V^{max}_{ij}` will be 0.0

computed between all atoms in the system at every step.

if :math:`E^{max} >= \textrm{qfactor}` on that timestep.  Also note

that :math:`V^{max}_{ij}` is added to the normal interatomic potential

that is computed between all atoms in the system at every step.

The derivative of Vij(max) with respect to the position of each atom

The derivative of :math:`V^{max}_{ij}` with respect to the position of

in the Emax bond gives a bias force Fij(max) acting on the bond as

each atom in the :math:`E^{max}` bond gives a bias force

:math:`F^{max}_{ij}` acting on the bond as

.. parsed-literal::

.. math::

   Fij(max) = - dVij(max)/dEij = 2 Vmax Eij / qfactor\^2   for abs(Eij) < qfactor

   F^{max}_{ij} = - \frac{dV^{max}_{ij}}{dE_{ij}} = \frac{2 V^{max} E-{ij}}{\textrm{qfactor}^2}   \textrm{ for } \left|E_{ij}\right| < \textrm{qfactor} \textrm{ or } 0 \textrm{ otherwise}

            = 0 otherwise

which can be decomposed into an equal and opposite force acting on

which can be decomposed into an equal and opposite force acting on

only the two I,J atoms in the Emax bond.

only the two *ij* atoms in the :math:`E^{max}` bond.

The time boost factor for the system is given each timestep I by

The time boost factor for the system is given each timestep I by

.. parsed-literal::

.. math::

   Bi = exp(beta \* Vij(max))

   B_i = e^{\beta V^{max}_{ij}}

where beta = 1/kTequil, and *Tequil* is the temperature of the system

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 Bi >= 1 at every step.

and an argument to this fix.  Note that :math:`B_i >= 1` at every step.

.. note::

.. note::

   constant-temperature (NVT) dynamics.  LAMMPS does not check that this

   constant-temperature (NVT) dynamics.  LAMMPS does not check that this

   is done.

   is done.

The elapsed time t\_hyper for a GHD simulation running for *N*

The elapsed time :math:`t_{hyper}` for a GHD simulation running for *N*

timesteps is simply

timesteps is simply

.. parsed-literal::

.. math::

   t_hyper = Sum (i = 1 to N) Bi \* dt

   t_{hyper} = \sum_{i=1,N} B-i \cdot dt

where dt is the timestep size defined by the :doc:`timestep <timestep>`

where *dt* is the timestep size defined by the :doc:`timestep <timestep>`

command.  The effective time acceleration due to GHD is thus t\_hyper /

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.

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.

Note that in GHD, the boost factor varies from timestep to timestep.

Likewise, which bond has Emax strain and thus which pair of atoms the

Likewise, which bond has :math:`E^{max}` strain and thus which pair of

bias potential is added to, will also vary from timestep to timestep.

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

This is in contrast to local hyperdynamics (LHD) where the boost

factor is an input parameter; see the :doc:`fix hyper/local <fix_hyper_local>` doc page for details.

factor is an input parameter; see the :doc:`fix hyper/local <fix_hyper_local>` doc page for details.

Here is additional information on the input parameters for GHD.

Here is additional information on the input parameters for GHD.

The *cutbond* argument is the cutoff distance for defining bonds

The *cutbond* argument is the cutoff distance for defining bonds

between pairs of nearby atoms.  A pair of I,J atoms in their

between pairs of nearby atoms.  A pair of *ij* atoms in their

equilibrium, minimum-energy configuration, which are separated by a

equilibrium, minimum-energy configuration, which are separated by a

distance Rij < *cutbond*\ , are flagged as a bonded pair.  Setting

distance :math:`R_{ij} < cutbond`, are flagged as a bonded pair.  Setting

*cubond* to be ~25% larger than the nearest-neighbor distance in a

*cubond* to be ~25% larger than the nearest-neighbor distance in a

crystalline lattice is a typical choice for solids, so that bonds

crystalline lattice is a typical choice for solids, so that bonds

exist only between nearest neighbor pairs.

exist only between nearest neighbor pairs.

If *qfactor* is set too large, then transitions from one energy basin

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

to another are affected because the bias potential is non-zero at the

transition state (e.g. saddle point).  If *qfactor* is set too small

transition state (e.g. saddle point).  If *qfactor* is set too small

than little boost is achieved because the Eij strain of some bond in

than little boost is achieved because the :math:`E_{ij}` strain of some bond in

the system will (nearly) always exceed *qfactor*\ .  A value of 0.3 for

the system will (nearly) always exceed *qfactor*\ .  A value of 0.3 for

*qfactor* is typically reasonable.

*qfactor* is typically reasonable.

the current timestep.  The vector stores the following quantities:

the current timestep.  The vector stores the following quantities:

* 1 = boost factor on this step (unitless)

* 1 = boost factor on this step (unitless)

* 2 = max strain Eij of any bond on this step (absolute value, unitless)

* 2 = max strain :math:`E_{ij}` of any bond on this step (absolute value, unitless)

* 3 = ID of first atom in the max-strain bond

* 3 = ID of first atom in the max-strain bond

* 4 = ID of second atom in the max-strain bond

* 4 = ID of second atom in the max-strain bond

* 5 = average # of bonds/atom on this step

* 5 = average # of bonds/atom on this step