Added tad example (4e99c502) · Commits · 郑智淋 / lammps

doc/compute_event_displace.html

+8 −3

Original line number	Diff line number	Diff line
		@@ -29,14 +29,19 @@
		group has moved a distance greater than the specified threshold
		distance when compared to a previously stored reference state
		(i.e. the previous event). This compute is typically used in
		conjunction with the <A HREF = "prd.html">prd</A> command, to detect if a transition
		conjunction with the <A HREF = "prd.html">prd</A> and <A HREF = "tad.html">tad</A> commands,
		to detect if a transition
		to a new minimum energy basin has occurred.
		</P>
		<P>This value calculated by the compute is equal to 0 if no particle has
		moved far enough, and equal to 1 if one or more particles have moved
		further than the threshold distance.
		</P>
		<P><B>Output info:</B>
		<P>NOTE: If the system is undergoing significant center-of-mass motion,
		due to thermal motion, an external force, or an initial net momentum,
		then this compute will not be able to distinguish that motion from
		local atom displacements and may generate "false postives."
		<B>Output info:</B>
		</P>
		<P>This compute calculates a global scalar (the flag). This value can be
		used by any command that uses a global scalar value from a compute as
		@@ -54,7 +59,7 @@ more info on packages.
		</P>
		<P><B>Related commands:</B>
		</P>
		<P><A HREF = "prd.html">prd</A>
		<P><A HREF = "prd.html">prd</A>, <A HREF = "tad.html">tad</A>
		</P>
		<P><B>Default:</B> none
		</P>

doc/compute_event_displace.txt

+7 −2

Original line number	Diff line number	Diff line
		@@ -26,13 +26,18 @@ Define a computation that flags an "event" if any particle in the
		group has moved a distance greater than the specified threshold
		distance when compared to a previously stored reference state
		(i.e. the previous event). This compute is typically used in
		conjunction with the "prd"_prd.html command, to detect if a transition
		conjunction with the "prd"_prd.html and "tad"_tad.html commands,
		to detect if a transition
		to a new minimum energy basin has occurred.

		This value calculated by the compute is equal to 0 if no particle has
		moved far enough, and equal to 1 if one or more particles have moved
		further than the threshold distance.

		NOTE: If the system is undergoing significant center-of-mass motion,
		due to thermal motion, an external force, or an initial net momentum,
		then this compute will not be able to distinguish that motion from
		local atom displacements and may generate "false postives."
		[Output info:]

		This compute calculates a global scalar (the flag). This value can be
		@@ -51,6 +56,6 @@ more info on packages.

		[Related commands:]

		"prd"_prd.html
		"prd"_prd.html, "tad"_tad.html

		[Default:] none

doc/neb.html

+37 −19

Original line number	Diff line number	Diff line
		@@ -13,9 +13,10 @@
		</H3>
		<P><B>Syntax:</B>
		</P>
		<PRE>neb ftol N1 N2 Nevery filename
		<PRE>neb etol ftol N1 N2 Nevery filename
		</PRE>
		<UL><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
		@@ -23,8 +24,8 @@
		</UL>
		<P><B>Examples:</B>
		</P>
		<PRE>neb 0.0 1000 500 50 coords.final
		neb 0.001 1000 500 50 coords.final
		<PRE>neb 0.1 0.0 1000 500 50 coords.final
		neb 0.0 0.001 1000 500 50 coords.final
		</PRE>
		<P><B>Description:</B>
		</P>
		@@ -105,10 +106,18 @@ first define an appropriate <A HREF = "min_style.html">min_style</A>, such as
		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 force is set by <I>ftol</I>, the same as for
		the <A HREF = "minimize.html">minimize</A> command. In this case a non-zero <I>ftol</I>
		means that the <I>ftol</I> criterion must be met by every replica in order
		for the NEB calculation to converge. The forces being compared to
		<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>
		@@ -119,8 +128,8 @@ damped dynamics is like a single timestep in a dynamics
		replica and its normalized distance along the reaction path (reaction
		coordinate RD) will be printed to the screen and log file every
		<I>Nevery</I> timesteps. The RD is 0 and 1 for the first and last replica.
		For intermediate replicas, it is the cummulative distance (normalized
		by the total cummulative distance) between adjacent replicas, where
		For intermediate replicas, it is the cumulative distance (normalized
		by the total cumulative distance) between adjacent replicas, where
		"distance" is defined as the length of the 3N-vector of differences in
		atomic coordinates, where N is the number of NEB atoms involved in the
		transition. These outputs allow you to monitor NEB's progress in
		@@ -147,7 +156,7 @@ themselves along the MEP so as to be roughly equally spaced.
		one of the replicas should be an atomic configuration at the top or
		saddle point of the barrier, the potential energies for the set of
		replicas should represent the energy profile of the barrier along the
		MEP, and the configurations of the replicas should be a seqeunce of
		MEP, and the configurations of the replicas should be a sequence of
		configurations along the MEP.
		</P>
		<HR>
		@@ -206,9 +215,12 @@ this case), the print-out to the screen and master log.lammps file
		contains a line of output, printed once every <I>Nevery</I> timesteps. It
		contains the timestep, the maximum force per replica, the maximum
		force per atom (in any replica), potential gradients in the initial,
		final, and climbing replicas, and
		the reaction coordinate and potential energy of each replica.
		The "maximum force per replica" is
		final, and climbing replicas,
		the forward and backward energy barriers,
		the total reaction coordinate (RDT), and
		the normalized reaction coordinate and potential energy of each replica.
		</P>
		<P>The "maximum force per replica" is
		the two-norm of the 3N-length force vector for the atoms in each
		replica, maximized across replicas, which is what the <I>ftol</I> setting
		is checking against. In this case, N is all the atoms in each
		@@ -224,12 +236,18 @@ replica, and so the potential gradient in the highest energy replica
		is reported, since this replica will become the climbing replica
		in the second stage of NEB.
		</P>
		<P>The "reaction coordinate" (RC) for each
		<P>The "reaction coordinate" (RD) for each
		replica is the two-norm of the 3N-length vector of distances between
		its atoms and the preceding replica's atoms, added to the RC of the
		preceding replica. The RC of the first replica = 0.0; the remaining
		RCs are normalized so that the RC of the last replica = 1.0. In this
		case, N is only the atoms being operated on by the fix neb command.
		its atoms and the preceding replica's atoms, added to the RD of the
		preceding replica. The RD of the first replica RD1 = 0.0;
		the RD of the final replica RDN = RDT, the total reaction coordinate.
		The normalized RDs are divided by RDT,
		so that they form a monotonically increasing sequence
		from zero to one. When computing RD, N only includes the atoms
		being operated on by the fix neb command.
		</P>
		<P>The forward (reverse) energy barrier is the potential energy of the highest
		replica minus the energy of the first (last) replica.
		</P>
		<P>When running on multiple partitions, LAMMPS produces additional log
		files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For a

doc/neb.txt

+35 −17

Original line number	Diff line number	Diff line
		@@ -10,8 +10,9 @@ neb command :h3

		[Syntax:]

		neb ftol N1 N2 Nevery filename :pre
		neb etol ftol N1 N2 Nevery filename :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
		@@ -20,8 +21,8 @@ filename = file specifying final atom coordinates on other side of barrier :ul

		[Examples:]

		neb 0.0 1000 500 50 coords.final
		neb 0.001 1000 500 50 coords.final :pre
		neb 0.1 0.0 1000 500 50 coords.final
		neb 0.0 0.001 1000 500 50 coords.final :pre

		[Description:]

		@@ -102,10 +103,18 @@ first define an appropriate "min_style"_min_style.html, such as
		used, since they perform iterative line searches in their inner loop,
		which cannot be easily synchronized across multiple replicas.

		The minimizer tolerances for force is set by {ftol}, the same as for
		the "minimize"_minimize.html command. In this case a non-zero {ftol}
		means that the {ftol} criterion must be met by every replica in order
		for the NEB calculation to converge. The forces being compared to
		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.

		@@ -116,8 +125,8 @@ damped dynamics is like a single timestep in a dynamics
		replica and its normalized distance along the reaction path (reaction
		coordinate RD) will be printed to the screen and log file every
		{Nevery} timesteps. The RD is 0 and 1 for the first and last replica.
		For intermediate replicas, it is the cummulative distance (normalized
		by the total cummulative distance) between adjacent replicas, where
		For intermediate replicas, it is the cumulative distance (normalized
		by the total cumulative distance) between adjacent replicas, where
		"distance" is defined as the length of the 3N-vector of differences in
		atomic coordinates, where N is the number of NEB atoms involved in the
		transition. These outputs allow you to monitor NEB's progress in
		@@ -144,7 +153,7 @@ When both stages are complete, if the NEB calculation was successful,
		one of the replicas should be an atomic configuration at the top or
		saddle point of the barrier, the potential energies for the set of
		replicas should represent the energy profile of the barrier along the
		MEP, and the configurations of the replicas should be a seqeunce of
		MEP, and the configurations of the replicas should be a sequence of
		configurations along the MEP.

		:line
		@@ -203,8 +212,11 @@ this case), the print-out to the screen and master log.lammps file
		contains a line of output, printed once every {Nevery} timesteps. It
		contains the timestep, the maximum force per replica, the maximum
		force per atom (in any replica), potential gradients in the initial,
		final, and climbing replicas, and
		the reaction coordinate and potential energy of each replica.
		final, and climbing replicas,
		the forward and backward energy barriers,
		the total reaction coordinate (RDT), and
		the normalized reaction coordinate and potential energy of each replica.

		The "maximum force per replica" is
		the two-norm of the 3N-length force vector for the atoms in each
		replica, maximized across replicas, which is what the {ftol} setting
		@@ -221,12 +233,18 @@ replica, and so the potential gradient in the highest energy replica
		is reported, since this replica will become the climbing replica
		in the second stage of NEB.

		The "reaction coordinate" (RC) for each
		The "reaction coordinate" (RD) for each
		replica is the two-norm of the 3N-length vector of distances between
		its atoms and the preceding replica's atoms, added to the RC of the
		preceding replica. The RC of the first replica = 0.0; the remaining
		RCs are normalized so that the RC of the last replica = 1.0. In this
		case, N is only the atoms being operated on by the fix neb command.
		its atoms and the preceding replica's atoms, added to the RD of the
		preceding replica. The RD of the first replica RD1 = 0.0;
		the RD of the final replica RDN = RDT, the total reaction coordinate.
		The normalized RDs are divided by RDT,
		so that they form a monotonically increasing sequence
		from zero to one. When computing RD, N only includes the atoms
		being operated on by the fix neb command.

		The forward (reverse) energy barrier is the potential energy of the highest
		replica minus the energy of the first (last) replica.

		When running on multiple partitions, LAMMPS produces additional log
		files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For a

doc/prd.html

+2 −1

Original line number	Diff line number	Diff line
		@@ -290,7 +290,8 @@ dt/reset</A> and <A HREF = "fix_deposit.html">fix deposit</A>.
		<P><A HREF = "compute_event_displace.html">compute event/displace</A>,
		<A HREF = "min_modify.html">min_modify</A>, <A HREF = "min_style.html">min_style</A>,
		<A HREF = "run_style.html">run_style</A>, <A HREF = "minimize.html">minimize</A>,
		<A HREF = "velocity.html">velocity</A>, <A HREF = "temper.html">temper</A>, <A HREF = "neb.html">neb</A>
		<A HREF = "velocity.html">velocity</A>, <A HREF = "temper.html">temper</A>, <A HREF = "neb.html">neb</A>,
		<A HREF = "tad.html">tad</A>
		</P>
		<P><B>Default:</B>
		</P>

Admin message