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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5503 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2011-01-07 21:40:58 +00:00
parent 15c856bcaa
commit beabb5e05a
5 changed files with 84 additions and 5 deletions
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6
doc/Section_commands.html
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@ -323,9 +323,9 @@ in the command's documentation.
<TR ALIGN="center"><TD ><A HREF = "pair_coeff.html">pair_coeff</A></TD><TD ><A HREF = "pair_modify.html">pair_modify</A></TD><TD ><A HREF = "pair_style.html">pair_style</A></TD><TD ><A HREF = "pair_write.html">pair_write</A></TD><TD ><A HREF = "prd.html">prd</A></TD><TD ><A HREF = "print.html">print</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "processors.html">processors</A></TD><TD ><A HREF = "read_data.html">read_data</A></TD><TD ><A HREF = "read_restart.html">read_restart</A></TD><TD ><A HREF = "region.html">region</A></TD><TD ><A HREF = "replicate.html">replicate</A></TD><TD ><A HREF = "reset_timestep.html">reset_timestep</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "restart.html">restart</A></TD><TD ><A HREF = "run.html">run</A></TD><TD ><A HREF = "run_style.html">run_style</A></TD><TD ><A HREF = "set.html">set</A></TD><TD ><A HREF = "shape.html">shape</A></TD><TD ><A HREF = "shell.html">shell</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "special_bonds.html">special_bonds</A></TD><TD ><A HREF = "temper.html">temper</A></TD><TD ><A HREF = "thermo.html">thermo</A></TD><TD ><A HREF = "thermo_modify.html">thermo_modify</A></TD><TD ><A HREF = "thermo_style.html">thermo_style</A></TD><TD ><A HREF = "timestep.html">timestep</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "uncompute.html">uncompute</A></TD><TD ><A HREF = "undump.html">undump</A></TD><TD ><A HREF = "unfix.html">unfix</A></TD><TD ><A HREF = "units.html">units</A></TD><TD ><A HREF = "variable.html">variable</A></TD><TD ><A HREF = "velocity.html">velocity</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "write_restart.html">write_restart</A>
<TR ALIGN="center"><TD ><A HREF = "special_bonds.html">special_bonds</A></TD><TD ><A HREF = "tad.html">tad</A></TD><TD ><A HREF = "temper.html">temper</A></TD><TD ><A HREF = "thermo.html">thermo</A></TD><TD ><A HREF = "thermo_modify.html">thermo_modify</A></TD><TD ><A HREF = "thermo_style.html">thermo_style</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "timestep.html">timestep</A></TD><TD ><A HREF = "uncompute.html">uncompute</A></TD><TD ><A HREF = "undump.html">undump</A></TD><TD ><A HREF = "unfix.html">unfix</A></TD><TD ><A HREF = "units.html">units</A></TD><TD ><A HREF = "variable.html">variable</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "velocity.html">velocity</A></TD><TD ><A HREF = "write_restart.html">write_restart</A>
</TD></TR></TABLE></DIV>
<HR>

4
doc/Section_howto.html
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@ -1154,7 +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 WIDTH="0%" BORDER=1 >
<DIV ALIGN=center><TABLE 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
@ -1348,7 +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 WIDTH="0%" BORDER=1 >
<DIV ALIGN=center><TABLE 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>

1
doc/Section_intro.html
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@ -219,6 +219,7 @@ commands)
</H4>
<P><A HREF = "neb.html">nudged elastic band</A>
<A HREF = "prd.html">parallel replica dynamics</A>
<A HREF = "tad.html">temperature accelerated dynamics</A>
<A HREF = "temper.html">parallel tempering</A>
</P>
<H4>Pre- and post-processing

39
doc/Section_start.html
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@ -327,6 +327,45 @@ build it. In the src/MAKE/Windows directory are some notes from users
on how they built LAMMPS under Windows, so you can look at their
instructions for tips. Good luck - we can't help you on this one.
</P>
<P>(5) Changing the size limits in src/lmptype.h
</P>
<P>If you are running a very large problem (billions of atoms or more)
and get a run-time error about the system being too big, either on a
per-processor basis or in total size, then you may need to change one
or more settings in src/lmptype.h and re-compile LAMMPS.
</P>
<P>As the documentation in that file explains, you have basically
two choices to make:
</P>
<UL><LI>set the data type size of integer atom IDs to 4 or 8 bytes
<LI>set the data type size of integers that store the total system size to 4 or 8 bytes
</UL>
<P>The default for atom IDs is 4-byte integers since there is a memory
and communication cost for 8-byte integers. Non-molecular problems do
not need atom IDs so this does not restrict their size. Molecular
problems (which use IDs to define molecular topology), are limited to
about 2 billion atoms (2^31) with 4-byte IDs. With 8-byte IDs they
are effectively unlimited in size (2^63).
</P>
<P>The default for total system size quantities (like the number of atoms
or timesteps) is 8-byte integers by default which is effectively
unlimited in size (2^63). If your system does not support 8-byte
integers, an error will be generated, and you will need to set
"bigint" to 4-byte integers. This restricts your total system size to
about 2 billion atoms or timesteps (2^31).
</P>
<P>Note that in src/lmptype.h there are also settings for the MPI data
types associated with the integers that store atom IDs and total
system sizes, which need to be set consistent with the associated C
data types.
</P>
<P>In all cases, the size of problem that can be run on a per-processor
basis is limited by 4-byte integer storage to about 2 billion atoms
per processor (2^31), which should not normally be a restriction since
such a problem would have a huge per-processor memory footprint due to
neighbor lists and would run very slowly in terms of CPU
secs/timestep.
</P>
<HR>
<H4><A NAME = "2_3"></A>2.3 Making LAMMPS with optional packages

39
doc/Section_start.txt
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@ -322,6 +322,45 @@ build it. In the src/MAKE/Windows directory are some notes from users
on how they built LAMMPS under Windows, so you can look at their
instructions for tips. Good luck - we can't help you on this one.
(5) Changing the size limits in src/lmptype.h
If you are running a very large problem (billions of atoms or more)
and get a run-time error about the system being too big, either on a
per-processor basis or in total size, then you may need to change one
or more settings in src/lmptype.h and re-compile LAMMPS.
As the documentation in that file explains, you have basically
two choices to make:
set the data type size of integer atom IDs to 4 or 8 bytes
set the data type size of integers that store the total system size to 4 or 8 bytes :ul
The default for atom IDs is 4-byte integers since there is a memory
and communication cost for 8-byte integers. Non-molecular problems do
not need atom IDs so this does not restrict their size. Molecular
problems (which use IDs to define molecular topology), are limited to
about 2 billion atoms (2^31) with 4-byte IDs. With 8-byte IDs they
are effectively unlimited in size (2^63).
The default for total system size quantities (like the number of atoms
or timesteps) is 8-byte integers by default which is effectively
unlimited in size (2^63). If your system does not support 8-byte
integers, an error will be generated, and you will need to set
"bigint" to 4-byte integers. This restricts your total system size to
about 2 billion atoms or timesteps (2^31).
Note that in src/lmptype.h there are also settings for the MPI data
types associated with the integers that store atom IDs and total
system sizes, which need to be set consistent with the associated C
data types.
In all cases, the size of problem that can be run on a per-processor
basis is limited by 4-byte integer storage to about 2 billion atoms
per processor (2^31), which should not normally be a restriction since
such a problem would have a huge per-processor memory footprint due to
neighbor lists and would run very slowly in terms of CPU
secs/timestep.
:line
2.3 Making LAMMPS with optional packages :h4,link(2_3)