doc files in wrong dir
This commit is contained in:
Steve Plimpton
146
doc/src/fix_hyper_global.txt
Normal file
146
doc/src/fix_hyper_global.txt
Normal file
@ -0,0 +1,146 @@
|
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
fix hyper/global command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID hyper/global cutbond qfactor Vmax Tequil :pre
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||||
|
||||
ID, group-ID are documented in "fix"_fix.html command
|
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hyper/global = style name of this fix command
|
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cutbond = max distance at which a pair of atoms is considered bonded (distance units)
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qfactor = max strain at which bias potential goes to 0.0 (unitless)
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Vmax = height of bias potential (energy units)
|
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Tequil = equilibration temperature (temperature units) :ul
|
||||
|
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[Examples:]
|
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|
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fix 1 all hyper/global 1.0 0.3 0.8 300.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
This fix is meant to be used with the "hyper"_hyper.html command to
|
||||
perform a bond-boost hyperdynamics simulation. The role of this fix
|
||||
is a select a single pair of atoms within the system at each timestep
|
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to add a global bias potential to, which will alter their dynamics.
|
||||
This is in contrast to the "fix hyper/local"_fix_hyper_local.html
|
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command, which can add a local bias potential to multiple pairs of
|
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atoms at each timestep.
|
||||
|
||||
For a system that undergoes rare transition events, where one or more
|
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atoms move across an energy barrier to a new potential energy basin,
|
||||
the effect of the bias potential is to induce more rapid transitions.
|
||||
This can lead to a dramatic speed-up in the rate at which events
|
||||
occurs, without altering their relative frequencies, thus leading to
|
||||
an overall dramatic speed-up in the effective elapsed time of the
|
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simulation.
|
||||
|
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Cite various papers.
|
||||
|
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The current strain of a bond IJ is defined as
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Eij = (Rij - R0ij) / R0ij :pre
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Emax = is the max of the absolute value of Eij for all IJ bonds.
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dVij = Vmax * (1 - (Eij/q)^2) for abs(Eij) < q
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= 0 otherwise :pre
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Delta Vbias = minimum of dVij for all IJ bonds :pre
|
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|
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The boost factor B = exp(beta * Delta Vbias)
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for a single timestep.
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|
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Thus the accumulated hypertime is simply
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t_hyper = Sum (i = 1 to Nsteps) Bi * dt :pre
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|
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The {cutbond} argument is the cutoff distance for defining bonds
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between pairs of nearby atoms. A pair of atoms in their equilibrium,
|
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minimum-energy config, which are a distance Rij < cutbond, are
|
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defined as a bonded pair.
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The {qfactor} argument is the limiting strain at which
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the Vbias (the bias potential) goes to 0.0.
|
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|
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If {qfactor} is too big, then transitions are affected b/c
|
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the bias energy is non-zero at the transitions. If it is
|
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too small than not must boost is achieved for a large system
|
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with many bonds (some bonds Eij always exceeds qfactor).
|
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|
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The {Vmax} argument is the prefactor on the bias potential.
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|
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The {Tequil} argument is part of the beta term in the
|
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exponential factor that determines how much boost is
|
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achieved as a function of the bias potential.
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
files"_restart.html.
|
||||
|
||||
The "fix_modify"_fix_modify.html {energy} option is supported by this
|
||||
fix to add the energy of the bias potential to the the system's
|
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potential energy as part of "thermodynamic output"_thermo_style.html.
|
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|
||||
This fix computes a global scalar and global vector of length 10,
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which can be accessed by various "output
|
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commands"_Section_howto.html#howto_15. The scalar is the magnitude of
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the bias potential (energy units) applied on the current timestep.
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The vector stores the following quantities:
|
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1 = boost factor on this step (unitless)
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2 = max strain of any bond on this step (unitless)
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3 = ID of first atom in the max-strain bond
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4 = ID of second atom in the max-strain bond
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5 = average # of bonds/atom on this step :ul
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6 = fraction of step with no bias during this run
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7 = max drift distance of any atom during this run (distance units)
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8 = max bond length during this run (distance units) :ul
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9 = cummulative hyper time since fix created (time units)
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10 = cummulative count of event timesteps since fix created
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11 = cummulative count of atoms in events since fix created :ul
|
||||
|
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The first 5 quantities are for the current timestep. The quantities
|
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6-8 are for the current run. The quantities 9-11 are cummulative
|
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across multiple runs (since the fix was defined in the input script).
|
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For value 10, events are checked for by the "hyper"_hyper.html command
|
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once every {Nevent} timesteps. This value is the count of the number
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of timesteps on which one (or more) events was detected. It is NOT
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the number of distinct events, since more than one physical event may
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occur in the same {Nevent} time window.
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For value 11, each time the "hyper"_hyper.html command checks for an
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event, the event compute it uses will flag zero or more atoms as
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participating in an event. E.g. atoms that have displaced more than
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some distance from the previous quench state. This value is the count
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of the number of atoms participating in any of the events that were
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found.
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The scalar and vector values calculated by this fix are all
|
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"intensive".
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|
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No parameter of this fix can be used with the {start/stop} keywords of
|
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the "run"_run.html command. This fix is not invoked during "energy
|
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minimization"_minimize.html.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This fix is part of the REPLICA package. It is only enabled if LAMMPS
|
||||
was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix hyper/local"_fix_hyper_local.html
|
||||
|
||||
[Default:] None
|
||||
200
doc/src/fix_hyper_local.txt
Normal file
200
doc/src/fix_hyper_local.txt
Normal file
@ -0,0 +1,200 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
fix hyper/local command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID hyper/local cutbond qfactor Vmax Tequil Dcut alpha boost :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
hyper/local = style name of this fix command :l
|
||||
cutbond = max distance at which a pair of atoms is considered bonded (distance units) :l
|
||||
qfactor = max strain at which bias potential goes to 0.0 (unitless) :l
|
||||
Vmax = estimated height of bias potential (energy units) :l
|
||||
Tequil = equilibration temperature (temperature units) :l
|
||||
Dcut = min distance between boosted bonds (distance units) :l
|
||||
alpha = boostostat relaxation time (time units) :l
|
||||
boost = desired time boost factor (unitless) :l
|
||||
zero or more keyword/value pairs may be appended :l
|
||||
keyword = {histo} or {lost} or {check/bias} or {check/coeff}
|
||||
{histo} values = Nevery Nbin delta Nout
|
||||
Nevery = histogram bond bias coefficients every this many timesteps
|
||||
Nbin = # of histogram bins
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delta = width of each histogram bin
|
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Nout = output histogram counts every this many timesteps
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{lostbond} value = error/warn/ignore
|
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{check/bias} values = Nevery error/warn/ignore
|
||||
{check/coeff} values = Nevery error/warn/ignore :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 1 all hyper/local 1.0 0.3 0.8 300.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
This fix is meant to be used with the "hyper"_hyper.html command to
|
||||
perform a bond-boost hyperdynamics simulation. The role of this fix
|
||||
is a select a multiple pairs of atoms within the system at each
|
||||
timestep to add a local bias potential to, which will alter their
|
||||
dynamics. This is in contrast to the "fix
|
||||
hyper/global"_fix_hyper_global.html command, which adds a global bias
|
||||
potential to a single pair of atoms at each timestep.
|
||||
|
||||
For a system that undergoes rare transition events, where one or more
|
||||
atoms move across an energy barrier to a new potential energy basin,
|
||||
the effect of the bias potential is to induce more rapid transitions.
|
||||
This can lead to a dramatic speed-up in the rate at which events
|
||||
occurs, without altering their relative frequencies, thus leading to
|
||||
an overall dramatic speed-up in the effective wall-clock time of the
|
||||
simulation.
|
||||
|
||||
Cite various papers.
|
||||
|
||||
The current strain of a bond IJ is defined as
|
||||
|
||||
Eij = (Rij - R0ij) / R0ij
|
||||
|
||||
Emax = is the max of the absolute value of Eij for all IJ bonds.
|
||||
|
||||
dVij = Vmax * (1 - (Eij/q)^2) for abs(Eij) < q
|
||||
= 0 otherwise
|
||||
|
||||
Delta Vbias = minimum of dVij for all IJ bonds
|
||||
|
||||
The boost factor B = exp(beta * Delta Vbias)
|
||||
for a single timestep.
|
||||
|
||||
Thus the accumulated hypertime is simply
|
||||
|
||||
t_hyper = Sum (i = 1 to Nsteps) Bi * dt
|
||||
|
||||
NOTE: Add eqs for boostostat and boost coeff.
|
||||
Explain how many bonds are boosted simultaneously
|
||||
and how to choose boost factor and initial Vmax.
|
||||
|
||||
The {cutbond} argument is the cutoff distance for defining bonds
|
||||
between pairs of nearby atoms. A pair of atoms in their equilibrium,
|
||||
minimum-energy config, which are a distance Rij < cutbond, are
|
||||
defined as a bonded pair.
|
||||
|
||||
The {qfactor} argument is the limiting strain at which
|
||||
the Vbias (the bias potential) goes to 0.0.
|
||||
|
||||
If qfactor is too big, then transitions are affected b/c
|
||||
the bias energy is non-zero at the transitions. If it is
|
||||
too small than not must boost is achieved for a large system
|
||||
with many bonds (some bonds Eij always exceeds qfactor).
|
||||
|
||||
The {Vmax} argument is the initial prefactor on the bias potential.
|
||||
Should be chosen as estimate of final. Will be adjusted by
|
||||
boost cooeficient
|
||||
|
||||
The {Tequil} argument is part of the beta term in the
|
||||
exponential factor that determines how much boost is
|
||||
achieved as a function of the bias potential.
|
||||
|
||||
The {Dcut} argument is the distance required between two bonds for
|
||||
them to be selected as both being boosted. The distance is between
|
||||
the center points of each bond. Actually between any pair of atoms in
|
||||
either bond.
|
||||
|
||||
The {alpha} argument is a pre-factor on the update equation
|
||||
for each atom's boostostat:
|
||||
|
||||
NOTE: give equation above
|
||||
|
||||
Note that the units for {alpha} are in time units, similar
|
||||
to other thermostat or barostat damping parameters
|
||||
|
||||
The {boost} argument is the desired boost factor (e.g. 100x)
|
||||
that all the atoms in the system will experience.
|
||||
|
||||
NOTE: explain how to choose good value for this. If this parameter is
|
||||
chosen to be too large, then the bias potential applied to pairs of
|
||||
bonded atoms may become unphysically large, leading to bad dynamics.
|
||||
If chosen too small, the hyperdynamics run may be inefficient in the
|
||||
sense that events take a long time to occur.
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
files"_restart.html.
|
||||
|
||||
The "fix_modify"_fix_modify.html {energy} option is supported by this
|
||||
fix to add the energy of the bias potential to the the system's
|
||||
potential energy as part of "thermodynamic output"_thermo_style.html.
|
||||
|
||||
This fix computes a global scalar and global vector of length 23,
|
||||
which can be accessed by various "output
|
||||
commands"_Section_howto.html#howto_15. The scalar is the magnitude of
|
||||
the bias potential (energy units) applied on the current timestep,
|
||||
summed over all biased bonds. The vector stores the following
|
||||
quantities:
|
||||
|
||||
1 = # of boosted bonds on this step
|
||||
2 = max strain of any bond on this step (unitless)
|
||||
3 = average bias potential for all bonds on this step (energy units)
|
||||
4 = average bonds/atom on this step
|
||||
5 = average neighbor bonds/bond on this step :ul
|
||||
|
||||
6 = fraction of steps and bonds with no bias during this run
|
||||
7 = max drift distance of any atom during this run (distance units)
|
||||
8 = max bond length during this run (distance units)
|
||||
9 = average # of boosted bonds/step during this run
|
||||
10 = average bias potential for all bonds during this run (energy units)
|
||||
11 = max bias potential for any bond during this run (energy units)
|
||||
12 = min bias potential for any bond during this run (energy units)
|
||||
13 = max distance from my box of any ghost atom with maxstrain < qfactor during th
|
||||
is run (distance units)
|
||||
14 = max distance outside my box of any ghost atom with any maxstrain during this run (distance units)
|
||||
15 = count of ghost neighbor atoms not found on reneighbor steps during this run
|
||||
16 = count of lost bond partners during this run
|
||||
17 = average bias coeff for lost bond partners during this run
|
||||
18 = count of bias overlaps found during this run
|
||||
19 = count of non-matching bias coefficients found during this run :ul
|
||||
|
||||
20 = cummulative hyper time since fix created (time units)
|
||||
21 = cummulative count of event timesteps since fix created
|
||||
22 = cummulative count of atoms in events since fix created
|
||||
23 = cummulative # of new bonds since fix created :ul
|
||||
|
||||
The first quantities (1-5) are for the current timestep. The
|
||||
quantities 6-19 are for the current hyper run. They are reset each
|
||||
time a new hyper run is performed. The quantities 20-23 are
|
||||
cummulative across multiple hyper runs, They are only set to initial
|
||||
values once, when this fix is defined in the input script.
|
||||
|
||||
For value 6, the numerator is a count of all biased bonds on every
|
||||
timestep whose bias value = 0.0. The denominator is the count of all
|
||||
biased bonds on all timesteps.
|
||||
|
||||
For values 13 and 14, the maxstrain of a ghost atom is the maxstrain
|
||||
of any bond it is part of, and it is checked for ghost atoms within
|
||||
the bond neighbor cutoff.
|
||||
|
||||
The scalar and vector values calculated by this fix are all
|
||||
"intensive".
|
||||
|
||||
No parameter of this fix can be used with the {start/stop} keywords of
|
||||
the "run"_run.html command. This fix is not invoked during "energy
|
||||
minimization"_minimize.html.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This fix is part of the REPLICA package. It is only enabled if LAMMPS
|
||||
was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"hyper"_hyper.html, "fix hyper/global"_fix_hyper_global.html
|
||||
|
||||
[Default:] None
|
||||
|
||||
117
doc/src/hyper.txt
Normal file
117
doc/src/hyper.txt
Normal file
@ -0,0 +1,117 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
hyper command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
hyper N Nevent fixID computeID keyword values ... :pre
|
||||
|
||||
N = # of timesteps to run :ulb,l
|
||||
Nevent = check for events every this many steps :l
|
||||
fixID = ID of a fix that applies a global or local bias potential :l
|
||||
computeID = ID of a compute that identifies when an event has occurred :l
|
||||
zero or more keyword/value pairs may be appended :l
|
||||
keyword = {min} or {time} :l
|
||||
{min} values = etol ftol maxiter maxeval
|
||||
etol = stopping tolerance for energy, used in quenching
|
||||
ftol = stopping tolerance for force, used in quenching
|
||||
maxiter = max iterations of minimize, used in quenching
|
||||
maxeval = max number of force/energy evaluations, used in quenching
|
||||
{time} value = {steps} or {clock}
|
||||
{steps} = simulation runs for N timesteps (default)
|
||||
{clock} = simulation runs until hyper time exceeds N timesteps :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
hyper 5000 100 global event :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Run a bond-boost hyperdynamics (HD) simulation where time is
|
||||
accelerated by application of a bias potential to a one or more pairs
|
||||
of atoms in the system. This command can be used to run both global
|
||||
and local hyperdyamics. In global HD a single bond (nearby pair of
|
||||
atoms) within the system is biased on a given timestep. In local HD
|
||||
multiple bonds (separated by a sufficient distance) can be biased
|
||||
simultaneously at each timestep.
|
||||
|
||||
Make next paragraph more HD-specific.
|
||||
|
||||
Both global and local HD are described in "this paper"_#Voter2013 by
|
||||
Art Voter and collaborators. They are methods for performing
|
||||
accelerated dynamics that is suitable for infrequent-event systems
|
||||
that obey first-order kinetics. A good overview of accelerated
|
||||
dynamics methods for such systems in given in "this review
|
||||
paper"_#Voter2002prd from the same group. To quote from the paper:
|
||||
"The dynamical evolution is characterized by vibrational excursions
|
||||
within a potential basin, punctuated by occasional transitions between
|
||||
basins." The transition probability is characterized by p(t) =
|
||||
k*exp(-kt) where k is the rate constant. Running multiple replicas
|
||||
gives an effective enhancement in the timescale spanned by the
|
||||
multiple simulations, while waiting for an event to occur.
|
||||
|
||||
How different than PRD.
|
||||
|
||||
An HD run has several stages, which are repeated each time an "event"
|
||||
occurs, as defined below. The logic for a HD run is as follows:
|
||||
|
||||
quench
|
||||
reset list of bonds :pre
|
||||
|
||||
while (time remains):
|
||||
run dynamics for Nevery steps
|
||||
quench
|
||||
check for an event
|
||||
if event occurred: reset list of bonds
|
||||
restore pre-quench state :pre
|
||||
|
||||
Explain each of the steps above. Explain what list of bonds is and
|
||||
how event is detected.
|
||||
|
||||
Explain the specified fix and compute.
|
||||
|
||||
Statistics about the number of events, the number of bonds that a bias
|
||||
potential is applied to, the accumulated hyper time, etc are stored by
|
||||
the fix and can be output with thermodynamic output.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This command can only be used if LAMMPS was built with the REPLICA
|
||||
package. See the "Making LAMMPS"_Section_start.html#start_3 section
|
||||
for more info on packages.
|
||||
|
||||
NOTE: is this true?
|
||||
This command cannot be used when any fixes are defined that keep track
|
||||
of elapsed time to perform time-dependent operations. Examples
|
||||
include the "ave" fixes such as "fix ave/chunk"_fix_ave_chunk.html.
|
||||
Also "fix dt/reset"_fix_dt_reset.html and "fix
|
||||
deposit"_fix_deposit.html.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix hyper/global"_fix_hyper_global.html, "fix
|
||||
hyper/local"_fix_hyper_local.html, "compute
|
||||
event/displace"_compute_event_displace.html
|
||||
|
||||
[Default:]
|
||||
|
||||
The option defaults are min = 0.1 0.1 40 50 and time = steps.
|
||||
|
||||
:line
|
||||
|
||||
:link(Voter2013)
|
||||
[(Voter2013)] S. Y. Kim, D. Perez, A. F. Voter, J Chem Phys, 139,
|
||||
144110 (2013).
|
||||
|
||||
:link(Voter2002prd)
|
||||
[(Voter2002)] Voter, Montalenti, Germann, Annual Review of Materials
|
||||
Research 32, 321 (2002).
|
||||
Reference in New Issue
Block a user