jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

clarified AMD quote from review paper

This commit is contained in:
Steve Plimpton 2020-04-29 16:14:52 -06:00
parent 5c2f0ecc65
commit 18c63ade92
3 changed files with 37 additions and 39 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

24
doc/src/hyper.rst
View File

@ -51,19 +51,17 @@ each timestep. In the bond-boost hyperdynamics context, a "bond" is
not a covalent bond between a pair of atoms in a molecule. Rather it
is simply a pair of nearby atoms as discussed below.
Both global and local HD are described in :ref:`(Voter2013) <Voter2013>` by
Art Voter and collaborators. Similar to parallel replica dynamics
(PRD), global and local HD are methods for performing accelerated
dynamics that are suitable for infrequent-event systems that obey
first-order kinetics. A good overview of accelerated dynamics methods
for such systems in given in :ref:`(Voter2002) <Voter2002hd>` from the same
group. To quote from the review 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.
Both global and local HD are described in :ref:`(Voter2013)
<Voter2013>` by Art Voter and collaborators. Similar to parallel
replica dynamics (PRD), global and local HD are methods for performing
accelerated dynamics that are suitable for infrequent-event systems
that obey first-order kinetics. A good overview of accelerated
dynamics methods (AMD) for such systems in given in :ref:`(Voter2002)
<Voter2002hd>` from the same group. To quote from the review 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."
Both HD and PRD produce a time-accurate trajectory that effectively
extends the timescale over which a system can be simulated, but they

23
doc/src/prd.rst
View File

@ -52,19 +52,16 @@ replicas of a system. One or more replicas can be used. The total
number of steps *N* to run can be interpreted in one of two ways; see
discussion of the *time* keyword below.
PRD is described in :ref:`(Voter1998) <Voter1998>` by Art Voter. Similar to
global or local hyperdynamics (HD), PRD is a method 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
:ref:`(Voter2002) <Voter2002prd>` from Art's 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.
PRD is described in :ref:`(Voter1998) <Voter1998>` by Art Voter.
Similar to global or local hyperdynamics (HD), PRD is a method for
performing accelerated dynamics that is suitable for infrequent-event
systems that obey first-order kinetics. A good overview of
accelerated dynamics methods (AMD) for such systems in given in this
review paper :ref:`(Voter2002) <Voter2002prd>` from Art's 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."
Both PRD and HD produce a time-accurate trajectory that effectively
extends the timescale over which a system can be simulated, but they

29
doc/src/tad.rst
View File

@ -58,18 +58,21 @@ Run a temperature accelerated dynamics (TAD) simulation. This method
requires two or more partitions to perform NEB transition state
searches.
TAD is described in :ref:`this paper <Voter2000>` by Art Voter. It is a method
that uses accelerated dynamics at an elevated temperature to generate
results at a specified lower temperature. A good overview of
accelerated dynamics methods for such systems is given in :ref:`this review paper <Voter2002>` from the same group. In general, these methods assume
that the long-time dynamics is dominated by infrequent events i.e. the
system is confined to low energy basins for long periods,
punctuated by brief, randomly-occurring transitions to adjacent
basins. TAD is suitable for infrequent-event systems, where in
TAD is described in :ref:`this paper <Voter2000>` by Art Voter. It is
a method that uses accelerated dynamics at an elevated temperature to
generate results at a specified lower temperature. A good overview of
accelerated dynamics methods (AMD) for such systems is given in
:ref:`this review paper <Voter2002>` from the same group. To quote
from the review 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."
TAD is a suitable AMD method for infrequent-event systems, where in
addition, the transition kinetics are well-approximated by harmonic
transition state theory (hTST). In hTST, the temperature dependence of
transition rates follows the Arrhenius relation. As a consequence a
set of event times generated in a high-temperature simulation can be
transition state theory (hTST). In hTST, the temperature dependence
of transition rates follows the Arrhenius relation. As a consequence
a set of event times generated in a high-temperature simulation can be
mapped to a set of much longer estimated times in the low-temperature
system. However, because this mapping involves the energy barrier of
the transition event, which is different for each event, the first
@ -79,8 +82,8 @@ events from the current basin. After each event, the simulation is
reflected backwards into the current basin. This is repeated until
the stopping criterion is satisfied, at which point the event with the
earliest low-temperature occurrence time is selected. The stopping
criterion is that the confidence measure be greater than
1-\ *delta*\ . The confidence measure is the probability that no earlier
criterion is that the confidence measure be greater than 1-\ *delta*\
. The confidence measure is the probability that no earlier
low-temperature event will occur at some later time in the
high-temperature simulation. hTST provides an lower bound for this
probability, based on the user-specified minimum pre-exponential