Here is a list of general ideas for improving simulation performance. Most of them are only applicable to certain models and certain bottlenecks in the current performance, so let the timing data you -intially generate be your guide. It is hard, if not impossible, to -predict how much difference these options will make, since it is a -function of your problem and your machine. There is no substitute for -simply trying them out. +generate be your guide. It is hard, if not impossible, to predict how +much difference these options will make, since it is a function of +problem size, number of processors used, and your machine. There is +no substitute for identifying performance bottlenecks, and trying out +various options.
(3) Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or --DLAMMPS_BIBIG or -DLAMMPS_SMALLSMALL +-DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL
As explained above, any of these 3 settings can be specified on the LMP_INC line in your low-level src/MAKE/Makefile.foo. diff --git a/doc/Section_start.txt b/doc/Section_start.txt index ca0c8061c1..8f1b624fcd 100644 --- a/doc/Section_start.txt +++ b/doc/Section_start.txt @@ -452,7 +452,7 @@ files created when LAMMPS is built, for either all builds or for a particular machine. (3) Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or --DLAMMPS_BIBIG or -DLAMMPS_SMALLSMALL +-DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL As explained above, any of these 3 settings can be specified on the LMP_INC line in your low-level src/MAKE/Makefile.foo. diff --git a/doc/atom_modify.html b/doc/atom_modify.html index 58bdda6574..4a15940e75 100644 --- a/doc/atom_modify.html +++ b/doc/atom_modify.html @@ -22,8 +22,7 @@ Commands
id value = yes or no
map value = array or hash
- first value = group-ID = group whose atoms will appear first in
-internal atom lists
+ first value = group-ID = group whose atoms will appear first in internal atom lists
sort values = Nfreq binsize
Nfreq = sort atoms spatially every this many time steps
binsize = bin size for spatial sorting (distance units)
@@ -60,12 +59,12 @@ between two atoms.
The only reason not to use atom IDs is if you are running an atomic
simulation so large that IDs cannot be uniquely assigned. For a
-default LAMMPS build this limit is 2^31 or ~2 billion atoms. However,
-even in this case, you can use 64-bit atom IDs, allowing 2^63 or ~9e18
-atoms, if you build LAMMPS with the - DLAMMPS_BIGBIG switch. This is
-described in Section 2.2 of the manual.
-If atom IDs are not used, they must be specified as 0 for all atoms,
-e.g. in a data or restart file.
+default LAMMPS build this limit is 2^31 or about 2 billion atoms.
+However, even in this case, you can use 64-bit atom IDs, allowing 2^63
+or about 9e18 atoms, if you build LAMMPS with the - DLAMMPS_BIGBIG
+switch. This is described in Section 2.2
+of the manual. If atom IDs are not used, they must be specified as 0
+for all atoms, e.g. in a data or restart file.
The map keyword determines how atom ID lookup is done for molecular
atom styles. Lookups are performed by bond (angle, etc) routines in
diff --git a/doc/atom_modify.txt b/doc/atom_modify.txt
index c7d7e68e16..e738ba4275 100644
--- a/doc/atom_modify.txt
+++ b/doc/atom_modify.txt
@@ -17,8 +17,7 @@ one or more keyword/value pairs may be appended :ulb,l
keyword = {id} or {map} or {first} or {sort} :l
{id} value = {yes} or {no}
{map} value = {array} or {hash}
- {first} value = group-ID = group whose atoms will appear first in
-internal atom lists
+ {first} value = group-ID = group whose atoms will appear first in internal atom lists
{sort} values = Nfreq binsize
Nfreq = sort atoms spatially every this many time steps
binsize = bin size for spatial sorting (distance units) :pre
@@ -54,12 +53,12 @@ between two atoms.
The only reason not to use atom IDs is if you are running an atomic
simulation so large that IDs cannot be uniquely assigned. For a
-default LAMMPS build this limit is 2^31 or ~2 billion atoms. However,
-even in this case, you can use 64-bit atom IDs, allowing 2^63 or ~9e18
-atoms, if you build LAMMPS with the - DLAMMPS_BIGBIG switch. This is
-described in "Section 2.2"_Section_start.html#start_2 of the manual.
-If atom IDs are not used, they must be specified as 0 for all atoms,
-e.g. in a data or restart file.
+default LAMMPS build this limit is 2^31 or about 2 billion atoms.
+However, even in this case, you can use 64-bit atom IDs, allowing 2^63
+or about 9e18 atoms, if you build LAMMPS with the - DLAMMPS_BIGBIG
+switch. This is described in "Section 2.2"_Section_start.html#start_2
+of the manual. If atom IDs are not used, they must be specified as 0
+for all atoms, e.g. in a data or restart file.
The {map} keyword determines how atom ID lookup is done for molecular
atom styles. Lookups are performed by bond (angle, etc) routines in