diff --git a/doc/Section_howto.html b/doc/Section_howto.html index fdbdf935ea..0b92fc19aa 100644 --- a/doc/Section_howto.html +++ b/doc/Section_howto.html @@ -345,14 +345,19 @@ periodically.

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.

+

These command can only be used if LAMMPS was built with the "replica" +package. See the Making LAMMPS 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 @@ -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:

-
+
c_ID entire scalar, vector, or array
c_ID[I] one element of vector, one column of array
c_ID[I][J] 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.

-
+
diff --git a/doc/Section_howto.txt b/doc/Section_howto.txt index 4a953ed378..8bbd1c7b8f 100644 --- a/doc/Section_howto.txt +++ b/doc/Section_howto.txt @@ -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 diff --git a/doc/prd.html b/doc/prd.html index 26b4484ceb..88006d1973 100644 --- a/doc/prd.html +++ b/doc/prd.html @@ -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 this +section 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. diff --git a/doc/prd.txt b/doc/prd.txt index eff416d081..8016d5c29b 100644 --- a/doc/prd.txt +++ b/doc/prd.txt @@ -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. diff --git a/doc/tad.html b/doc/tad.html index e748692625..15d8be5def 100644 --- a/doc/tad.html +++ b/doc/tad.html @@ -102,8 +102,9 @@ restricts you to having exactly one processor per replica. For more information, see the documentation for the neb 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 this +section of the manual for further discussion +of multi-replica simulations.

A TAD run has several stages, which are repeated each time an event is performed. The logic for a TAD run is as follows: diff --git a/doc/tad.txt b/doc/tad.txt index 7c55377841..19311b9e33 100644 --- a/doc/tad.txt +++ b/doc/tad.txt @@ -91,8 +91,10 @@ restricts you to having exactly one processor per replica. For more information, see the documentation for the "neb"_neb.html 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 "this +section"_Section_howto.html#4_5 of the manual for further discussion +of multi-replica simulations. + A TAD run has several stages, which are repeated each time an event is performed. The logic for a TAD run is as follows:

Command Input Output
thermo_style custom global scalars screen, log file
dump custom per-atom vectors dump file