git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11002 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
271
doc/neb.html
271
doc/neb.html
@ -13,25 +13,41 @@
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>neb etol ftol N1 N2 Nevery filename
|
||||
<PRE>neb etol ftol N1 N2 Nevery file-style arg
|
||||
</PRE>
|
||||
<UL><LI>etol = stopping tolerance for energy (energy units)
|
||||
<LI>ftol = stopping tolerance for force (force units)
|
||||
<UL><LI>etol = stopping tolerance for energy (energy units)
|
||||
|
||||
<LI>ftol = stopping tolerance for force (force units)
|
||||
|
||||
<LI>N1 = max # of iterations (timesteps) to run initial NEB
|
||||
<LI>N2 = max # of iterations (timesteps) to run barrier-climbing NEB
|
||||
<LI>Nevery = print replica energies and reaction coordinates every this many timesteps
|
||||
<LI>filename = file specifying final atom coordinates on other side of barrier
|
||||
|
||||
<LI>N2 = max # of iterations (timesteps) to run barrier-climbing NEB
|
||||
|
||||
<LI>Nevery = print replica energies and reaction coordinates every this many timesteps
|
||||
|
||||
<LI>file-style= <I>final</I> or <I>each</I> or <I>none</I>
|
||||
|
||||
<PRE> <I>final</I> arg = filename
|
||||
filename = file with initial coords for final replica
|
||||
coords for intermediate replicas are linearly interpolated between first and last replica
|
||||
<I>each</I> arg = filename
|
||||
filename = unique filename for each replica (except first) with its initial coords
|
||||
<I>none</I> arg = no argument
|
||||
all replicas assumed to already have their initial coords
|
||||
</PRE>
|
||||
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>neb 0.1 0.0 1000 500 50 coords.final
|
||||
neb 0.0 0.001 1000 500 50 coords.final
|
||||
<PRE>neb 0.1 0.0 1000 500 50 final coords.final
|
||||
neb 0.0 0.001 1000 500 50 each coords.initial.$i
|
||||
neb 0.0 0.001 1000 500 50 none
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Perform a nudged elastic band (NEB) calculation using multiple
|
||||
replicas of a system. Two or more replicas must be used, two of which
|
||||
are the end points of the transition path.
|
||||
replicas of a system. Two or more replicas must be used; the first
|
||||
and last are the end points of the transition path.
|
||||
</P>
|
||||
<P>NEB is a method for finding both the atomic configurations and height
|
||||
of the energy barrier associated with a transition state, e.g. for an
|
||||
@ -45,17 +61,24 @@ partitions are defined at run-time using the -partition command-line
|
||||
switch; see <A HREF = "Section_start.html#start_7">Section_start 6</A> of the
|
||||
manual. Note that if you have MPI installed, you can run a
|
||||
multi-replica simulation with more replicas (partitions) than you have
|
||||
physical processors, e.g you can run a 10-replica simulation on one or
|
||||
two processors. You will simply not get the performance speed-up you
|
||||
would see with one or more physical processors per replica. See <A HREF = "Section_howto.html#howto_5">this
|
||||
section</A> of the manual for further
|
||||
discussion.
|
||||
physical processors, e.g you can run a 10-replica simulation on just
|
||||
one or two processors. You will simply not get the performance
|
||||
speed-up you would see with one or more physical processors per
|
||||
replica. See <A HREF = "Section_howto.html#howto_5">this section</A> of the manual
|
||||
for further discussion.
|
||||
</P>
|
||||
<P>NOTE: The current NEB implementation in LAMMPS restricts you to having
|
||||
exactly one processor per replica.
|
||||
<P>IMPORTANT NOTE: The current NEB implementation in LAMMPS only allows
|
||||
there to be one processor per replica.
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: As explained below, a NEB calculation perfoms a
|
||||
damped-dynamics minimization across all the replicas. This uses
|
||||
whatever timestep you have defined in your input script, via the
|
||||
<A HREF = "timestep.html">timestep</A> command. You may get faster convergence if
|
||||
you use a larger timestep than you would normally use for dynamics
|
||||
with the same system.
|
||||
</P>
|
||||
<P>When a NEB calculation is performed, it is assumed that each replica
|
||||
is running the same model, though LAMMPS does not check for this.
|
||||
is running the same system, though LAMMPS does not check for this.
|
||||
I.e. the simulation domain, the number of atoms, the interaction
|
||||
potentials, and the starting configuration when the neb command is
|
||||
issued should be the same for every replica.
|
||||
@ -64,63 +87,135 @@ issued should be the same for every replica.
|
||||
atom in adjacent replicas by springs, which induce inter-replica
|
||||
forces. These forces are imposed by the <A HREF = "fix_neb.html">fix neb</A>
|
||||
command, which must be used in conjunction with the neb command. The
|
||||
group used to define the fix neb command specifies which atoms the
|
||||
inter-replica springs are applied to. These are the NEB atoms.
|
||||
Additional atoms can be present in your system, e.g. to provide a
|
||||
background force field or simply to hold fixed during the NEB
|
||||
procedure, but they will not be part of the barrier finding procedure.
|
||||
group used to define the fix neb command defines the NEB atoms which
|
||||
are the only ones that inter-replica springs are applied to. If the
|
||||
group does not include all atoms, then non-NEB atoms have no
|
||||
inter-replica springs and the forces they feel and their motion is
|
||||
computed in the usual way due only to other atoms within their
|
||||
replica. Conceptually, the non-NEB atoms provide a background force
|
||||
field for the NEB atoms. They can be allowed to move during the NEB
|
||||
minimiation procedure (which will typically induce different
|
||||
coordinates for non-NEB atoms in different replicas), or held fixed
|
||||
using other LAMMPS commands such as <A HREF = "fix_setforce">fix setforce</A>. Note
|
||||
that the <A HREF = "partition.html">partition</A> command can be used to invoke a
|
||||
command on a subset of the replicas, e.g. if you wish to hold NEB or
|
||||
non-NEB atoms fixed in only the end-point replicas.
|
||||
</P>
|
||||
<P>The "starting configuration" for NEB should be a state with the NEB
|
||||
atoms (and all other atoms) having coordinates on one side of the
|
||||
energy barrier. These coordinates will be assigned to the first
|
||||
replica #1. The coordinates should be close to a local energy
|
||||
minimum. A perfect energy minimum is not required, since NEB runs via
|
||||
damped dynamics which will tend to drive the configuration of replica
|
||||
#1 to a true energy minimum, but you will typically get better
|
||||
convergence if the initial state is already at a minimum. For
|
||||
example, for a system with a free surface, the surface should be fully
|
||||
relaxed before attempting a NEB calculation.
|
||||
<P>The initial atomic configuration for each of the replicas can be
|
||||
specified in different manners via the <I>file-style</I> setting, as
|
||||
discussed below. Only atoms whose initial coordinates should differ
|
||||
from the current configuration need be specified.
|
||||
</P>
|
||||
<P>The final configuration is specified in the input <I>filename</I>, which is
|
||||
formatted as described below. Only coordinates for NEB atoms or a
|
||||
subset of them should be listed in the file; they represent the state
|
||||
of the system on the other side of the barrier, at or near an energy
|
||||
minimum. These coordinates will be assigned to the last replica #M.
|
||||
The final coordinates of atoms not listed in <I>filename</I> are set equal
|
||||
to their initial coordinates. Again, a perfect energy minimum is not
|
||||
required for the final configuration, since the atoms in replica #M
|
||||
will tend to move during the NEB procedure to the nearest energy
|
||||
minimum. Also note that a final coordinate does not need to be
|
||||
specified for a NEB atom if you expect it to only displace slightly
|
||||
during the NEB procedure. For example, only the final coordinate of
|
||||
the single atom diffusing into a vacancy need be specified if the
|
||||
surrounding atoms will only relax slightly in the final configuration.
|
||||
<P>Conceptually, the initial configuration for the first replica should
|
||||
be a state with all the atoms (NEB and non-NEB) having coordinates on
|
||||
one side of the energy barrier. A perfect energy minimum is not
|
||||
required, since atoms in the first replica experience no spring forces
|
||||
from the 2nd replica. Thus the damped dynamics minimizaiton will
|
||||
drive the first replica to an energy minimum if it is not already
|
||||
there. However, you will typically get better convergence if the
|
||||
initial state is already at a minimum. For example, for a system with
|
||||
a free surface, the surface should be fully relaxed before attempting
|
||||
a NEB calculation.
|
||||
</P>
|
||||
<P>The initial coordinates of all atoms (not just NEB atoms) in the
|
||||
intermediate replicas #2,#3,...,#M-1 are set to values linearly
|
||||
interpolated between the corresponding atoms in replicas #1 and #M.
|
||||
<P>Likewise, the initial configuration of the final replica should be a
|
||||
state with all the atoms (NEB and non-NEB) on the other side of the
|
||||
energy barrier. Again, a perfect energy minimum is not required,
|
||||
since the atoms in the last replica also experience no spring forces
|
||||
from the next-to-last replica, and thus the damped dynamics
|
||||
minimization will drive it to an energy minimum.
|
||||
</P>
|
||||
<P>A NEB calculation has two stages, each of which is a minimization
|
||||
procedure, performed via damped dynamics. To enable this, you must
|
||||
first define an appropriate <A HREF = "min_style.html">min_style</A>, such as
|
||||
<I>quickmin</I> or <I>fire</I>. The <I>cg</I>, <I>sd</I>, and <I>hftn</I> styles cannot be
|
||||
used, since they perform iterative line searches in their inner loop,
|
||||
which cannot be easily synchronized across multiple replicas.
|
||||
<P>As explained below, the initial configurations of intermediate
|
||||
replicas can be atomic coordinates interpolated in a linear fashion
|
||||
between the first and last replicas. This is often adequate state for
|
||||
simple transitions. For more complex transitions, it may lead to slow
|
||||
convergence or even bad results if the minimum energy path (MEP, see
|
||||
below) of states over the barrier cannot be correctly converged to
|
||||
from such an initial configuration. In this case, you will want to
|
||||
generate initial states for the intermediate replicas that are
|
||||
geometrically closer to the MEP and read them in.
|
||||
</P>
|
||||
<P>The minimizer tolerances for energy and force are set by <I>etol</I> and <I>ftol</I>,
|
||||
the same as for
|
||||
the <A HREF = "minimize.html">minimize</A> command.
|
||||
<HR>
|
||||
|
||||
<P>For a <I>file-style</I> setting of <I>final</I>, a filename is specified which
|
||||
contains atomic coordinates for zero or more atoms, in the format
|
||||
described below. For each atom that appears in the file, the new
|
||||
coordinates are assigned to that atom in the final replica. Each
|
||||
intermediate replica also assigns a new position to that atom in an
|
||||
interpolated manner. This is done by using the current position of
|
||||
the atom as the starting point and the read-in position as the final
|
||||
point. The distance between them is calculated, and the new position
|
||||
is assigned to be a fraction of the distance. E.g. if there are 10
|
||||
replicas, the 2nd replica will assign a position that is 10% of the
|
||||
distance along a line between the starting and final point, and the
|
||||
9th replica will assign a position that is 90% of the distance along
|
||||
the line. Note that this procedure to produce consistent coordinates
|
||||
across all the replicas, the current coordinates need to be the same
|
||||
in all replicas. LAMMPS does not check for this, but invalid initial
|
||||
configurations will likely result if it is not the case.
|
||||
</P>
|
||||
<P>A non-zero <I>etol</I>
|
||||
means that the NEB calculation will terminate if the energy criterion is met
|
||||
by every replica. The energies being compared to
|
||||
<I>etol</I> do not include any contribution from the inter-replica forces, since
|
||||
these are non-conservative.
|
||||
A non-zero <I>ftol</I>
|
||||
means that the NEB calculation will terminate if the force criterion is met
|
||||
by every replica. The forces being compared to
|
||||
<I>ftol</I> include the inter-replica forces between an atom and its images
|
||||
in adjacent replicas.
|
||||
<P>NOTE: The "distance" between the starting and final point is
|
||||
calculated in a minimum-image sense for a periodic simulation box.
|
||||
This means that if the two positions are on opposite sides of a box
|
||||
(periodic in that dimension), the distance between them will be small,
|
||||
because the periodic image of one of the atoms is close to the other.
|
||||
Similarly, even if the assigned position resulting from the
|
||||
interpolation is outside the periodic box, the atom will be wrapped
|
||||
back into the box when the NEB calculation begins.
|
||||
</P>
|
||||
<P>For a <I>file-style</I> setting of <I>each</I>, a filename is specified which is
|
||||
assumed to be unique to each replica. This can be done by
|
||||
using a variable in the filename, e.g.
|
||||
</P>
|
||||
<PRE>variable i equal part
|
||||
neb 0.0 0.001 1000 500 50 each coords.initial.$i
|
||||
</PRE>
|
||||
<P>which in this case will substitute the partition ID (0 to N-1) for the
|
||||
variable I, which is also effectively the replica ID. See the
|
||||
<A HREF = "variable.html">variable</A> command for other options, such as using
|
||||
world-, universe-, or uloop-style variables.
|
||||
</P>
|
||||
<P>Each replica (except the first replica) will read its file, formatted
|
||||
as described below, and for any atom that appears in the file, assign
|
||||
the specified coordinates to its atom. The various files do not need
|
||||
to contain the same set of atoms.
|
||||
</P>
|
||||
<P>For a <I>file-style</I> setting of <I>none</I>, no filename is specified. Each
|
||||
replica is assumed to already be in its initial configuration at the
|
||||
time the neb command is issued. This allows each replica to define
|
||||
its own configuration by reading a replica-specific data or restart or
|
||||
dump file, via the <A HREF = "read_data.html">read_data</A>,
|
||||
<A HREF = "read_restart.html">read_restart</A>, or <A HREF = "read_dump.html">read_dump</A>
|
||||
commands. The replica-specific names of these files can be specified
|
||||
as in the discussion above for the <I>each</I> file-style. Also see the
|
||||
section below for how a NEB calculation can produce restart files, so
|
||||
that a long calculation can be restarted if needed.
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: None of the <I>file-style</I> settings change the initial
|
||||
configuration of any atom in the first replica. The first replica
|
||||
must thus be in the correct initial configuration at the time the neb
|
||||
command is issued.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>A NEB calculation proceeds in two stages, each of which is a
|
||||
minimization procedure, performed via damped dynamics. To enable
|
||||
this, you must first define a damped dynamics
|
||||
<A HREF = "min_style.html">min_style</A>, such as <I>quickmin</I> or <I>fire</I>. The <I>cg</I>,
|
||||
<I>sd</I>, and <I>hftn</I> styles cannot be used, since they perform iterative
|
||||
line searches in their inner loop, which cannot be easily synchronized
|
||||
across multiple replicas.
|
||||
</P>
|
||||
<P>The minimizer tolerances for energy and force are set by <I>etol</I> and
|
||||
<I>ftol</I>, the same as for the <A HREF = "minimize.html">minimize</A> command.
|
||||
</P>
|
||||
<P>A non-zero <I>etol</I> means that the NEB calculation will terminate if the
|
||||
energy criterion is met by every replica. The energies being compared
|
||||
to <I>etol</I> do not include any contribution from the inter-replica
|
||||
forces, since these are non-conservative. A non-zero <I>ftol</I> means
|
||||
that the NEB calculation will terminate if the force criterion is met
|
||||
by every replica. The forces being compared to <I>ftol</I> include the
|
||||
inter-replica forces between an atom and its images in adjacent
|
||||
replicas.
|
||||
</P>
|
||||
<P>The maximum number of iterations in each stage is set by <I>N1</I> and
|
||||
<I>N2</I>. These are effectively timestep counts since each iteration of
|
||||
@ -163,7 +258,8 @@ configurations along the MEP.
|
||||
<HR>
|
||||
|
||||
<P>A few other settings in your input script are required or advised to
|
||||
perform a NEB calculation.
|
||||
perform a NEB calculation. See the IMPORTANT NOTE about the choice of
|
||||
timestep at the beginning of this doc page.
|
||||
</P>
|
||||
<P>An atom map must be defined which it is not by default for <A HREF = "atom_style.html">atom_style
|
||||
atomic</A> problems. The <A HREF = "atom_modify.html">atom_modify
|
||||
@ -193,21 +289,34 @@ advised.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>The specified <I>filename</I> contains atom coordinates for the final
|
||||
configuration. Only atoms with coordinates different than the initial
|
||||
configuration need to be specified, i.e. those geometrically near the
|
||||
barrier.
|
||||
<P>Each file read by the neb command containing atomic coordinates used
|
||||
to initialize one or more replicas must be formatted as follows.
|
||||
</P>
|
||||
<P>The file can be ASCII text or a gzipped text file (detected by a .gz
|
||||
suffix). The file should contain one line per atom, formatted
|
||||
with the atom ID, followed by the final x,y,z coordinates:
|
||||
suffix). The file can contain initial blank lines or comment lines
|
||||
starting with "#" which are ignored. The first non-blank, non-comment
|
||||
line should list N = the number of lines to follow. The N successive
|
||||
lines contain the following information:
|
||||
</P>
|
||||
<PRE>125 24.97311 1.69005 23.46956
|
||||
126 1.94691 2.79640 1.92799
|
||||
127 0.15906 3.46099 0.79121
|
||||
...
|
||||
<PRE>ID1 x1 y1 z1
|
||||
ID2 x2 y2 z2
|
||||
...
|
||||
IDN xN yN zN
|
||||
</PRE>
|
||||
<P>The lines can be listed in any order.
|
||||
<P>The fields are the the atom ID, followed by the x,y,z coordinates.
|
||||
The lines can be listed in any order. Additional trailing information
|
||||
on the line is OK, such as a comment.
|
||||
</P>
|
||||
<P>Note that for a typical NEB calculation you do not need to specify
|
||||
initial coordinates for very many atoms to produce differing starting
|
||||
and final replicas whose intermediate replicas will converge to the
|
||||
energy barrier. Typically only new coordinates for atoms
|
||||
geometrically near the barrier need be specified.
|
||||
</P>
|
||||
<P>Also note there is no requirement that the atoms in the file
|
||||
correspond to the NEB atoms in the group defined by the <A HREF = "fix_neb.html">fix
|
||||
neb</A> command. Not every NEB atom need be in the file,
|
||||
and non-NEB atoms can be listed in the file.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
|
||||
266
doc/neb.txt
266
doc/neb.txt
@ -10,25 +10,34 @@ neb command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
neb etol ftol N1 N2 Nevery filename :pre
|
||||
neb etol ftol N1 N2 Nevery file-style arg :pre
|
||||
|
||||
etol = stopping tolerance for energy (energy units)
|
||||
ftol = stopping tolerance for force (force units)
|
||||
N1 = max # of iterations (timesteps) to run initial NEB
|
||||
N2 = max # of iterations (timesteps) to run barrier-climbing NEB
|
||||
Nevery = print replica energies and reaction coordinates every this many timesteps
|
||||
filename = file specifying final atom coordinates on other side of barrier :ul
|
||||
etol = stopping tolerance for energy (energy units) :ulb,l
|
||||
ftol = stopping tolerance for force (force units) :l
|
||||
N1 = max # of iterations (timesteps) to run initial NEB :l
|
||||
N2 = max # of iterations (timesteps) to run barrier-climbing NEB :l
|
||||
Nevery = print replica energies and reaction coordinates every this many timesteps :l
|
||||
file-style= {final} or {each} or {none} :l
|
||||
{final} arg = filename
|
||||
filename = file with initial coords for final replica
|
||||
coords for intermediate replicas are linearly interpolated between first and last replica
|
||||
{each} arg = filename
|
||||
filename = unique filename for each replica (except first) with its initial coords
|
||||
{none} arg = no argument
|
||||
all replicas assumed to already have their initial coords :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
neb 0.1 0.0 1000 500 50 coords.final
|
||||
neb 0.0 0.001 1000 500 50 coords.final :pre
|
||||
neb 0.1 0.0 1000 500 50 final coords.final
|
||||
neb 0.0 0.001 1000 500 50 each coords.initial.$i
|
||||
neb 0.0 0.001 1000 500 50 none :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Perform a nudged elastic band (NEB) calculation using multiple
|
||||
replicas of a system. Two or more replicas must be used, two of which
|
||||
are the end points of the transition path.
|
||||
replicas of a system. Two or more replicas must be used; the first
|
||||
and last are the end points of the transition path.
|
||||
|
||||
NEB is a method for finding both the atomic configurations and height
|
||||
of the energy barrier associated with a transition state, e.g. for an
|
||||
@ -42,17 +51,24 @@ partitions are defined at run-time using the -partition command-line
|
||||
switch; see "Section_start 6"_Section_start.html#start_7 of the
|
||||
manual. Note that if you have MPI installed, you can run a
|
||||
multi-replica simulation with more replicas (partitions) than you have
|
||||
physical processors, e.g you can run a 10-replica simulation on one or
|
||||
two processors. You will simply not get the performance speed-up you
|
||||
would see with one or more physical processors per replica. See "this
|
||||
section"_Section_howto.html#howto_5 of the manual for further
|
||||
discussion.
|
||||
physical processors, e.g you can run a 10-replica simulation on just
|
||||
one or two processors. You will simply not get the performance
|
||||
speed-up you would see with one or more physical processors per
|
||||
replica. See "this section"_Section_howto.html#howto_5 of the manual
|
||||
for further discussion.
|
||||
|
||||
NOTE: The current NEB implementation in LAMMPS restricts you to having
|
||||
exactly one processor per replica.
|
||||
IMPORTANT NOTE: The current NEB implementation in LAMMPS only allows
|
||||
there to be one processor per replica.
|
||||
|
||||
IMPORTANT NOTE: As explained below, a NEB calculation perfoms a
|
||||
damped-dynamics minimization across all the replicas. This uses
|
||||
whatever timestep you have defined in your input script, via the
|
||||
"timestep"_timestep.html command. You may get faster convergence if
|
||||
you use a larger timestep than you would normally use for dynamics
|
||||
with the same system.
|
||||
|
||||
When a NEB calculation is performed, it is assumed that each replica
|
||||
is running the same model, though LAMMPS does not check for this.
|
||||
is running the same system, though LAMMPS does not check for this.
|
||||
I.e. the simulation domain, the number of atoms, the interaction
|
||||
potentials, and the starting configuration when the neb command is
|
||||
issued should be the same for every replica.
|
||||
@ -61,63 +77,135 @@ In a NEB calculation each atom in a replica is connected to the same
|
||||
atom in adjacent replicas by springs, which induce inter-replica
|
||||
forces. These forces are imposed by the "fix neb"_fix_neb.html
|
||||
command, which must be used in conjunction with the neb command. The
|
||||
group used to define the fix neb command specifies which atoms the
|
||||
inter-replica springs are applied to. These are the NEB atoms.
|
||||
Additional atoms can be present in your system, e.g. to provide a
|
||||
background force field or simply to hold fixed during the NEB
|
||||
procedure, but they will not be part of the barrier finding procedure.
|
||||
group used to define the fix neb command defines the NEB atoms which
|
||||
are the only ones that inter-replica springs are applied to. If the
|
||||
group does not include all atoms, then non-NEB atoms have no
|
||||
inter-replica springs and the forces they feel and their motion is
|
||||
computed in the usual way due only to other atoms within their
|
||||
replica. Conceptually, the non-NEB atoms provide a background force
|
||||
field for the NEB atoms. They can be allowed to move during the NEB
|
||||
minimiation procedure (which will typically induce different
|
||||
coordinates for non-NEB atoms in different replicas), or held fixed
|
||||
using other LAMMPS commands such as "fix setforce"_fix_setforce. Note
|
||||
that the "partition"_partition.html command can be used to invoke a
|
||||
command on a subset of the replicas, e.g. if you wish to hold NEB or
|
||||
non-NEB atoms fixed in only the end-point replicas.
|
||||
|
||||
The "starting configuration" for NEB should be a state with the NEB
|
||||
atoms (and all other atoms) having coordinates on one side of the
|
||||
energy barrier. These coordinates will be assigned to the first
|
||||
replica #1. The coordinates should be close to a local energy
|
||||
minimum. A perfect energy minimum is not required, since NEB runs via
|
||||
damped dynamics which will tend to drive the configuration of replica
|
||||
#1 to a true energy minimum, but you will typically get better
|
||||
convergence if the initial state is already at a minimum. For
|
||||
example, for a system with a free surface, the surface should be fully
|
||||
relaxed before attempting a NEB calculation.
|
||||
The initial atomic configuration for each of the replicas can be
|
||||
specified in different manners via the {file-style} setting, as
|
||||
discussed below. Only atoms whose initial coordinates should differ
|
||||
from the current configuration need be specified.
|
||||
|
||||
The final configuration is specified in the input {filename}, which is
|
||||
formatted as described below. Only coordinates for NEB atoms or a
|
||||
subset of them should be listed in the file; they represent the state
|
||||
of the system on the other side of the barrier, at or near an energy
|
||||
minimum. These coordinates will be assigned to the last replica #M.
|
||||
The final coordinates of atoms not listed in {filename} are set equal
|
||||
to their initial coordinates. Again, a perfect energy minimum is not
|
||||
required for the final configuration, since the atoms in replica #M
|
||||
will tend to move during the NEB procedure to the nearest energy
|
||||
minimum. Also note that a final coordinate does not need to be
|
||||
specified for a NEB atom if you expect it to only displace slightly
|
||||
during the NEB procedure. For example, only the final coordinate of
|
||||
the single atom diffusing into a vacancy need be specified if the
|
||||
surrounding atoms will only relax slightly in the final configuration.
|
||||
Conceptually, the initial configuration for the first replica should
|
||||
be a state with all the atoms (NEB and non-NEB) having coordinates on
|
||||
one side of the energy barrier. A perfect energy minimum is not
|
||||
required, since atoms in the first replica experience no spring forces
|
||||
from the 2nd replica. Thus the damped dynamics minimizaiton will
|
||||
drive the first replica to an energy minimum if it is not already
|
||||
there. However, you will typically get better convergence if the
|
||||
initial state is already at a minimum. For example, for a system with
|
||||
a free surface, the surface should be fully relaxed before attempting
|
||||
a NEB calculation.
|
||||
|
||||
The initial coordinates of all atoms (not just NEB atoms) in the
|
||||
intermediate replicas #2,#3,...,#M-1 are set to values linearly
|
||||
interpolated between the corresponding atoms in replicas #1 and #M.
|
||||
Likewise, the initial configuration of the final replica should be a
|
||||
state with all the atoms (NEB and non-NEB) on the other side of the
|
||||
energy barrier. Again, a perfect energy minimum is not required,
|
||||
since the atoms in the last replica also experience no spring forces
|
||||
from the next-to-last replica, and thus the damped dynamics
|
||||
minimization will drive it to an energy minimum.
|
||||
|
||||
A NEB calculation has two stages, each of which is a minimization
|
||||
procedure, performed via damped dynamics. To enable this, you must
|
||||
first define an appropriate "min_style"_min_style.html, such as
|
||||
{quickmin} or {fire}. The {cg}, {sd}, and {hftn} styles cannot be
|
||||
used, since they perform iterative line searches in their inner loop,
|
||||
which cannot be easily synchronized across multiple replicas.
|
||||
As explained below, the initial configurations of intermediate
|
||||
replicas can be atomic coordinates interpolated in a linear fashion
|
||||
between the first and last replicas. This is often adequate state for
|
||||
simple transitions. For more complex transitions, it may lead to slow
|
||||
convergence or even bad results if the minimum energy path (MEP, see
|
||||
below) of states over the barrier cannot be correctly converged to
|
||||
from such an initial configuration. In this case, you will want to
|
||||
generate initial states for the intermediate replicas that are
|
||||
geometrically closer to the MEP and read them in.
|
||||
|
||||
The minimizer tolerances for energy and force are set by {etol} and {ftol},
|
||||
the same as for
|
||||
the "minimize"_minimize.html command.
|
||||
:line
|
||||
|
||||
A non-zero {etol}
|
||||
means that the NEB calculation will terminate if the energy criterion is met
|
||||
by every replica. The energies being compared to
|
||||
{etol} do not include any contribution from the inter-replica forces, since
|
||||
these are non-conservative.
|
||||
A non-zero {ftol}
|
||||
means that the NEB calculation will terminate if the force criterion is met
|
||||
by every replica. The forces being compared to
|
||||
{ftol} include the inter-replica forces between an atom and its images
|
||||
in adjacent replicas.
|
||||
For a {file-style} setting of {final}, a filename is specified which
|
||||
contains atomic coordinates for zero or more atoms, in the format
|
||||
described below. For each atom that appears in the file, the new
|
||||
coordinates are assigned to that atom in the final replica. Each
|
||||
intermediate replica also assigns a new position to that atom in an
|
||||
interpolated manner. This is done by using the current position of
|
||||
the atom as the starting point and the read-in position as the final
|
||||
point. The distance between them is calculated, and the new position
|
||||
is assigned to be a fraction of the distance. E.g. if there are 10
|
||||
replicas, the 2nd replica will assign a position that is 10% of the
|
||||
distance along a line between the starting and final point, and the
|
||||
9th replica will assign a position that is 90% of the distance along
|
||||
the line. Note that this procedure to produce consistent coordinates
|
||||
across all the replicas, the current coordinates need to be the same
|
||||
in all replicas. LAMMPS does not check for this, but invalid initial
|
||||
configurations will likely result if it is not the case.
|
||||
|
||||
NOTE: The "distance" between the starting and final point is
|
||||
calculated in a minimum-image sense for a periodic simulation box.
|
||||
This means that if the two positions are on opposite sides of a box
|
||||
(periodic in that dimension), the distance between them will be small,
|
||||
because the periodic image of one of the atoms is close to the other.
|
||||
Similarly, even if the assigned position resulting from the
|
||||
interpolation is outside the periodic box, the atom will be wrapped
|
||||
back into the box when the NEB calculation begins.
|
||||
|
||||
For a {file-style} setting of {each}, a filename is specified which is
|
||||
assumed to be unique to each replica. This can be done by
|
||||
using a variable in the filename, e.g.
|
||||
|
||||
variable i equal part
|
||||
neb 0.0 0.001 1000 500 50 each coords.initial.$i :pre
|
||||
|
||||
which in this case will substitute the partition ID (0 to N-1) for the
|
||||
variable I, which is also effectively the replica ID. See the
|
||||
"variable"_variable.html command for other options, such as using
|
||||
world-, universe-, or uloop-style variables.
|
||||
|
||||
Each replica (except the first replica) will read its file, formatted
|
||||
as described below, and for any atom that appears in the file, assign
|
||||
the specified coordinates to its atom. The various files do not need
|
||||
to contain the same set of atoms.
|
||||
|
||||
For a {file-style} setting of {none}, no filename is specified. Each
|
||||
replica is assumed to already be in its initial configuration at the
|
||||
time the neb command is issued. This allows each replica to define
|
||||
its own configuration by reading a replica-specific data or restart or
|
||||
dump file, via the "read_data"_read_data.html,
|
||||
"read_restart"_read_restart.html, or "read_dump"_read_dump.html
|
||||
commands. The replica-specific names of these files can be specified
|
||||
as in the discussion above for the {each} file-style. Also see the
|
||||
section below for how a NEB calculation can produce restart files, so
|
||||
that a long calculation can be restarted if needed.
|
||||
|
||||
IMPORTANT NOTE: None of the {file-style} settings change the initial
|
||||
configuration of any atom in the first replica. The first replica
|
||||
must thus be in the correct initial configuration at the time the neb
|
||||
command is issued.
|
||||
|
||||
:line
|
||||
|
||||
A NEB calculation proceeds in two stages, each of which is a
|
||||
minimization procedure, performed via damped dynamics. To enable
|
||||
this, you must first define a damped dynamics
|
||||
"min_style"_min_style.html, such as {quickmin} or {fire}. The {cg},
|
||||
{sd}, and {hftn} styles cannot be used, since they perform iterative
|
||||
line searches in their inner loop, which cannot be easily synchronized
|
||||
across multiple replicas.
|
||||
|
||||
The minimizer tolerances for energy and force are set by {etol} and
|
||||
{ftol}, the same as for the "minimize"_minimize.html command.
|
||||
|
||||
A non-zero {etol} means that the NEB calculation will terminate if the
|
||||
energy criterion is met by every replica. The energies being compared
|
||||
to {etol} do not include any contribution from the inter-replica
|
||||
forces, since these are non-conservative. A non-zero {ftol} means
|
||||
that the NEB calculation will terminate if the force criterion is met
|
||||
by every replica. The forces being compared to {ftol} include the
|
||||
inter-replica forces between an atom and its images in adjacent
|
||||
replicas.
|
||||
|
||||
The maximum number of iterations in each stage is set by {N1} and
|
||||
{N2}. These are effectively timestep counts since each iteration of
|
||||
@ -160,7 +248,8 @@ configurations along the MEP.
|
||||
:line
|
||||
|
||||
A few other settings in your input script are required or advised to
|
||||
perform a NEB calculation.
|
||||
perform a NEB calculation. See the IMPORTANT NOTE about the choice of
|
||||
timestep at the beginning of this doc page.
|
||||
|
||||
An atom map must be defined which it is not by default for "atom_style
|
||||
atomic"_atom_style.html problems. The "atom_modify
|
||||
@ -190,21 +279,34 @@ advised.
|
||||
|
||||
:line
|
||||
|
||||
The specified {filename} contains atom coordinates for the final
|
||||
configuration. Only atoms with coordinates different than the initial
|
||||
configuration need to be specified, i.e. those geometrically near the
|
||||
barrier.
|
||||
Each file read by the neb command containing atomic coordinates used
|
||||
to initialize one or more replicas must be formatted as follows.
|
||||
|
||||
The file can be ASCII text or a gzipped text file (detected by a .gz
|
||||
suffix). The file should contain one line per atom, formatted
|
||||
with the atom ID, followed by the final x,y,z coordinates:
|
||||
suffix). The file can contain initial blank lines or comment lines
|
||||
starting with "#" which are ignored. The first non-blank, non-comment
|
||||
line should list N = the number of lines to follow. The N successive
|
||||
lines contain the following information:
|
||||
|
||||
125 24.97311 1.69005 23.46956
|
||||
126 1.94691 2.79640 1.92799
|
||||
127 0.15906 3.46099 0.79121
|
||||
... :pre
|
||||
ID1 x1 y1 z1
|
||||
ID2 x2 y2 z2
|
||||
...
|
||||
IDN xN yN zN :pre
|
||||
|
||||
The lines can be listed in any order.
|
||||
The fields are the the atom ID, followed by the x,y,z coordinates.
|
||||
The lines can be listed in any order. Additional trailing information
|
||||
on the line is OK, such as a comment.
|
||||
|
||||
Note that for a typical NEB calculation you do not need to specify
|
||||
initial coordinates for very many atoms to produce differing starting
|
||||
and final replicas whose intermediate replicas will converge to the
|
||||
energy barrier. Typically only new coordinates for atoms
|
||||
geometrically near the barrier need be specified.
|
||||
|
||||
Also note there is no requirement that the atoms in the file
|
||||
correspond to the NEB atoms in the group defined by the "fix
|
||||
neb"_fix_neb.html command. Not every NEB atom need be in the file,
|
||||
and non-NEB atoms can be listed in the file.
|
||||
|
||||
:line
|
||||
|
||||
|
||||
Reference in New Issue
Block a user