Tweaked multireplica docs (0c112cf3) · Commits · 郑智淋 / lammps

doc/Section_howto.html

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		@@ -345,14 +345,19 @@ periodically.
		</P>
		<UL><LI><A HREF = "neb.html">neb</A> for nudged elastic band calculations
		<LI><A HREF = "prd.html">prd</A> for parallel replica dynamics
		<LI><A HREF = "tad.html">tad</A> for temperature accelerated dynamics
		<LI><A HREF = "temper.html">temper</A> for parallel tempering
		</UL>
		<P>NEB is a method for finding transition states and barrier energies.
		PRD is a method for performing accelerated dynamics to find and
		perform infrequent events. Parallel tempering or replica exchange
		PRD and TAD are methods for performing accelerated dynamics to find
		and perform infrequent events. Parallel tempering or replica exchange
		runs different replicas at a series of temperature to facilitate
		rare-event sampling.
		</P>
		<P>These command can only be used if LAMMPS was built with the "replica"
		package. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A> section for
		more info on packages.
		</P>
		<P>In all these cases, you must run with one or more processors per
		replica. The processors assigned to each replica are determined at
		run-time by using the <A HREF = "Section_start.html#2_6">-partition command-line
		@@ -1149,7 +1154,7 @@ discussed below, it can be referenced via the following bracket
		notation, where ID in this case is the ID of a compute. The leading
		"c_" would be replaced by "f_" for a fix, or "v_" for a variable:
		</P>
		<DIV ALIGN=center><TABLE BORDER=1 >
		<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
		<TR><TD >c_ID </TD><TD > entire scalar, vector, or array</TD></TR>
		<TR><TD >c_ID[I] </TD><TD > one element of vector, one column of array</TD></TR>
		<TR><TD >c_ID[I][J] </TD><TD > one element of array
		@@ -1343,7 +1348,7 @@ data and scalar/vector/array data.
		input, that could be an element of a vector or array. Likewise a
		vector input could be a column of an array.
		</P>
		<DIV ALIGN=center><TABLE BORDER=1 >
		<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
		<TR><TD >Command</TD><TD > Input</TD><TD > Output</TD><TD ></TD></TR>
		<TR><TD ><A HREF = "thermo_style.html">thermo_style custom</A></TD><TD > global scalars</TD><TD > screen, log file</TD><TD ></TD></TR>
		<TR><TD ><A HREF = "dump.html">dump custom</A></TD><TD > per-atom vectors</TD><TD > dump file</TD><TD ></TD></TR>

doc/Section_howto.txt

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		@@ -341,7 +341,7 @@ These are the relevant commands:

		"neb"_neb.html for nudged elastic band calculations
		"prd"_prd.html for parallel replica dynamics
		"tad"_tad.html for temperature accelerated dynamics :ul
		"tad"_tad.html for temperature accelerated dynamics
		"temper"_temper.html for parallel tempering :ul

		NEB is a method for finding transition states and barrier energies.
		@@ -350,6 +350,10 @@ and perform infrequent events. Parallel tempering or replica exchange
		runs different replicas at a series of temperature to facilitate
		rare-event sampling.

		These command can only be used if LAMMPS was built with the "replica"
		package. See the "Making LAMMPS"_Section_start.html#2_3 section for
		more info on packages.

		In all these cases, you must run with one or more processors per
		replica. The processors assigned to each replica are determined at
		run-time by using the "-partition command-line

doc/prd.html

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		@@ -76,7 +76,8 @@ 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. For
		PRD, this makes little sense, since this offers no effective parallel
		speed-up in searching for infrequent events.
		speed-up in searching for infrequent events. See <A HREF = "Section_howto.html#4_5">this
		section</A> of the manual for further discussion.
		</P>
		<P>When a PRD simulation is performed, it is assumed that each replica is
		running the same model, though LAMMPS does not check for this.

doc/prd.txt

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		@@ -63,7 +63,8 @@ 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. For
		PRD, this makes little sense, since this offers no effective parallel
		speed-up in searching for infrequent events.
		speed-up in searching for infrequent events. See "this
		section"_Section_howto.html#4_5 of the manual for further discussion.

		When a PRD simulation is performed, it is assumed that each replica is
		running the same model, though LAMMPS does not check for this.

doc/tad.html

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		@@ -102,8 +102,9 @@ restricts you to having exactly one processor per replica. For more
		information, see the documentation for the <A HREF = "neb.html">neb</A> command. In
		the current LAMMPS implementation of TAD, all the non-NEB TAD
		operations are performed on the first partition, while the other
		partitions remain idle. Processor partitions are defined at run-time
		using the -partition command-line switch.
		partitions remain idle. See <A HREF = "Section_howto.html#4_5">this
		section</A> of the manual for further discussion
		of multi-replica simulations.
		</P>
		<P>A TAD run has several stages, which are repeated each time an event is
		performed. The logic for a TAD run is as follows:

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