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This commit is contained in:
sjplimp
parent
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commit
eb44d6e05d
|
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@ -601,13 +601,13 @@ via the <A HREF = "print.html">print</A>, <A HREF = "fix_print.html">fix print</
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"equal" can compute complex equations that involve the following types
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of arguments:
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</P>
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<P>thermo keywords = ke, vol, atoms, ...
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<PRE>thermo keywords = ke, vol, atoms, ...
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other variables = v_a, v_myvar, ...
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math functions = div(x,y), mult(x,y), add(x,y), ...
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group functions = mass(group), xcm(group,x), ...
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atom values = x<B>123</B>, y<B>3</B>, vx<B>34</B>, ...
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compute values = c_mytemp<B>0</B>, c_thermo_press<B>3</B>, ...
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</P>
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atom values = x[123], y[3], vx[34], ...
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compute values = c_mytemp[0], c_thermo_press[3], ...
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</PRE>
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<P>Adding keywords for the <A HREF = "thermo_style.html">thermo_style custom</A> command
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(which can then be accessed by variables) was discussed
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<A HREF = "Section_modify.html#thermo">here</A> on this page.
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|
|
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@ -580,8 +580,8 @@ thermo keywords = ke, vol, atoms, ...
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other variables = v_a, v_myvar, ...
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math functions = div(x,y), mult(x,y), add(x,y), ...
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group functions = mass(group), xcm(group,x), ...
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atom values = x[123], y[3], vx[34], ...
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compute values = c_mytemp[0], c_thermo_press[3], ...
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atom values = x\[123\], y\[3\], vx\[34\], ...
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compute values = c_mytemp\[0\], c_thermo_press\[3\], ... :pre
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Adding keywords for the "thermo_style custom"_thermo_style.html command
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(which can then be accessed by variables) was discussed
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|
|
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@ -901,11 +901,24 @@ interface and how to extend it for your needs.
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<H4><A NAME = "start_6"></A>2.6 Running LAMMPS
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</H4>
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<P>By default, LAMMPS runs by reading commands from stdin; e.g. lmp_linux
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< in.file. This means you first create an input script (e.g. in.file)
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containing the desired commands. <A HREF = "Section_commands.html">This section</A>
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describes how input scripts are structured and what commands they
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contain.
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<P>By default, LAMMPS runs by reading commands from standard input. Thus
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if you run the LAMMPS executable by itself, e.g.
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</P>
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<PRE>lmp_linux
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</PRE>
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<P>it will simply wait, expecting commands from the keyboard. Typically
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you should put commands in an input script and use I/O redirection,
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e.g.
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</P>
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<PRE>lmp_linux < in.file
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</PRE>
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<P>For parallel environments this should also work. If it does not, use
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the '-in' command-line switch, e.g.
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</P>
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<PRE>lmp_linux -in in.file
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</PRE>
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<P><A HREF = "Section_commands.html">This section</A> describes how input scripts are
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structured and what commands they contain.
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</P>
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<P>You can test LAMMPS on any of the sample inputs provided in the
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examples or bench directory. Input scripts are named in.* and sample
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@ -921,8 +934,9 @@ cp lmp_linux ../bench
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cd ../bench
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mpirun -np 4 lmp_linux < in.lj
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</PRE>
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<P>See <A HREF = "http://lammps.sandia.gov/bench.html">this page</A> for timings for this and the other benchmarks
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on various platforms.
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<P>See <A HREF = "http://lammps.sandia.gov/bench.html">this page</A> for timings for this and the other benchmarks on
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various platforms. Note that some of the example scripts require
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LAMMPS to be built with one or more of its optional packages.
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</P>
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@ -951,12 +965,13 @@ with the name of your LAMMPS input script.
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<P>For the MPI version, which allows you to run LAMMPS under Windows on
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multiple processors, follow these steps:
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</P>
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<UL><LI>Download and install
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<UL><LI>Download and install
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<A HREF = "http://www.mcs.anl.gov/research/projects/mpich2/downloads/index.php?s=downloads">MPICH2</A>
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for Windows.
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<LI>You'll need to use the mpiexec.exe and smpd.exe files from the MPICH2 package. Put them in
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same directory (or path) as the LAMMPS Windows executable.
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<LI>You'll need to use the mpiexec.exe and smpd.exe files from the MPICH2
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package. Put them in same directory (or path) as the LAMMPS Windows
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executable.
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<LI>Get a command prompt by going to Start->Run... ,
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then typing "cmd".
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@ -964,18 +979,17 @@ then typing "cmd".
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<LI>Move to the directory where you have saved lmp_win_mpi.exe
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(e.g. by typing: cd "Documents").
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<LI>Then type something like this: "mpiexec -np 4 -localonly lmp_win_mpi -in in.lj",
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replacing in.lj with the name of your LAMMPS input script.
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<LI>Then type something like this: "mpiexec -localonly 4 lmp_win_mpi -in
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in.lj", replacing in.lj with the name of your LAMMPS input script.
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<LI>Note that you may need to provide smpd with a passphrase --- it doesn't matter what you
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type.
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<LI>Note that you may need to provide smpd with a passphrase (it doesn't
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matter what you type).
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<LI>In this mode, output may not immediately show up on the screen, so
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if your input script takes a long time to execute, you may need to be
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patient before the output shows up.
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<LI>Alternatively, you can still use this executable to run on a single processor by
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typing something like: "lmp_win_mpi -in in.lj".
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<LI>In this mode, output may not immediately show up on the screen, so if
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your input script takes a long time to execute, you may need to be
|
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patient before the output shows up. :l Alternatively, you can still
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use this executable to run on a single processor by typing something
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like: "lmp_win_mpi -in in.lj".
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</UL>
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<HR>
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@ -1062,17 +1076,22 @@ set by using the <A HREF = "echo.html">echo</A> command in the input script itse
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</PRE>
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<P>Specify a file to use as an input script. This is an optional switch
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when running LAMMPS in one-partition mode. If it is not specified,
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LAMMPS reads its input script from stdin - e.g. lmp_linux < in.run.
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This is a required switch when running LAMMPS in multi-partition mode,
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since multiple processors cannot all read from stdin.
|
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LAMMPS reads its script from standard input, typically from a script
|
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via I/O redirection; e.g. lmp_linux < in.run. I/O redirection should
|
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also work in parallel, but if it does not (in the unlikely case that
|
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an MPI implementation does not support it), then use the -in flag.
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Note that this is a required switch when running LAMMPS in
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multi-partition mode, since multiple processors cannot all read from
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stdin.
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</P>
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<PRE>-help
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</PRE>
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<P>Print a list of options compiled into this executable for each LAMMPS
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style (atom_style, fix, compute, pair_style, bond_style, etc). This
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can help you know if the command you want to use was included via the
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appropriate package. LAMMPS will print the info and immediately exit
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if this switch is used.
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<P>Print a brief help summary and a list of options compiled into this
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executable for each LAMMPS style (atom_style, fix, compute,
|
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pair_style, bond_style, etc). This can tell you if the command you
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want to use was included via the appropriate package at compile time.
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LAMMPS will print the info and immediately exit if this switch is
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used.
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</P>
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<PRE>-log file
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</PRE>
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|
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@ -895,11 +895,24 @@ interface and how to extend it for your needs.
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2.6 Running LAMMPS :h4,link(start_6)
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By default, LAMMPS runs by reading commands from stdin; e.g. lmp_linux
|
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< in.file. This means you first create an input script (e.g. in.file)
|
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containing the desired commands. "This section"_Section_commands.html
|
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describes how input scripts are structured and what commands they
|
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contain.
|
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By default, LAMMPS runs by reading commands from standard input. Thus
|
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if you run the LAMMPS executable by itself, e.g.
|
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|
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lmp_linux :pre
|
||||
|
||||
it will simply wait, expecting commands from the keyboard. Typically
|
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you should put commands in an input script and use I/O redirection,
|
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e.g.
|
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|
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lmp_linux < in.file :pre
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|
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For parallel environments this should also work. If it does not, use
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the '-in' command-line switch, e.g.
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|
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lmp_linux -in in.file :pre
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|
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"This section"_Section_commands.html describes how input scripts are
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structured and what commands they contain.
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|
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You can test LAMMPS on any of the sample inputs provided in the
|
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examples or bench directory. Input scripts are named in.* and sample
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|
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@ -915,8 +928,9 @@ cp lmp_linux ../bench
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cd ../bench
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mpirun -np 4 lmp_linux < in.lj :pre
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See "this page"_bench for timings for this and the other benchmarks
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on various platforms.
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See "this page"_bench for timings for this and the other benchmarks on
|
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various platforms. Note that some of the example scripts require
|
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LAMMPS to be built with one or more of its optional packages.
|
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:link(bench,http://lammps.sandia.gov/bench.html)
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@ -945,12 +959,13 @@ with the name of your LAMMPS input script. :l,ule
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For the MPI version, which allows you to run LAMMPS under Windows on
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multiple processors, follow these steps:
|
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|
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Download and install
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Download and install
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"MPICH2"_http://www.mcs.anl.gov/research/projects/mpich2/downloads/index.php?s=downloads
|
||||
for Windows. :ulb,l
|
||||
|
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You'll need to use the mpiexec.exe and smpd.exe files from the MPICH2 package. Put them in
|
||||
same directory (or path) as the LAMMPS Windows executable. :l
|
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You'll need to use the mpiexec.exe and smpd.exe files from the MPICH2
|
||||
package. Put them in same directory (or path) as the LAMMPS Windows
|
||||
executable. :l
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|
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Get a command prompt by going to Start->Run... ,
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then typing "cmd". :l
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|
|
@ -958,15 +973,17 @@ then typing "cmd". :l
|
|||
Move to the directory where you have saved lmp_win_mpi.exe
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(e.g. by typing: cd "Documents"). :l
|
||||
|
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Then type something like this: "mpiexec -np 4 -localonly lmp_win_mpi -in in.lj",
|
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replacing in.lj with the name of your LAMMPS input script. :l
|
||||
Note that you may need to provide smpd with a passphrase --- it doesn't matter what you
|
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type. :l
|
||||
In this mode, output may not immediately show up on the screen, so
|
||||
if your input script takes a long time to execute, you may need to be
|
||||
patient before the output shows up. :l
|
||||
Alternatively, you can still use this executable to run on a single processor by
|
||||
typing something like: "lmp_win_mpi -in in.lj". :l,ule
|
||||
Then type something like this: "mpiexec -localonly 4 lmp_win_mpi -in
|
||||
in.lj", replacing in.lj with the name of your LAMMPS input script. :l
|
||||
|
||||
Note that you may need to provide smpd with a passphrase (it doesn't
|
||||
matter what you type). :l
|
||||
|
||||
In this mode, output may not immediately show up on the screen, so if
|
||||
your input script takes a long time to execute, you may need to be
|
||||
patient before the output shows up. :l Alternatively, you can still
|
||||
use this executable to run on a single processor by typing something
|
||||
like: "lmp_win_mpi -in in.lj". :l,ule
|
||||
|
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:line
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|
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|
|
@ -1053,17 +1070,22 @@ set by using the "echo"_echo.html command in the input script itself.
|
|||
|
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Specify a file to use as an input script. This is an optional switch
|
||||
when running LAMMPS in one-partition mode. If it is not specified,
|
||||
LAMMPS reads its input script from stdin - e.g. lmp_linux < in.run.
|
||||
This is a required switch when running LAMMPS in multi-partition mode,
|
||||
since multiple processors cannot all read from stdin.
|
||||
LAMMPS reads its script from standard input, typically from a script
|
||||
via I/O redirection; e.g. lmp_linux < in.run. I/O redirection should
|
||||
also work in parallel, but if it does not (in the unlikely case that
|
||||
an MPI implementation does not support it), then use the -in flag.
|
||||
Note that this is a required switch when running LAMMPS in
|
||||
multi-partition mode, since multiple processors cannot all read from
|
||||
stdin.
|
||||
|
||||
-help :pre
|
||||
|
||||
Print a list of options compiled into this executable for each LAMMPS
|
||||
style (atom_style, fix, compute, pair_style, bond_style, etc). This
|
||||
can help you know if the command you want to use was included via the
|
||||
appropriate package. LAMMPS will print the info and immediately exit
|
||||
if this switch is used.
|
||||
Print a brief help summary and a list of options compiled into this
|
||||
executable for each LAMMPS style (atom_style, fix, compute,
|
||||
pair_style, bond_style, etc). This can tell you if the command you
|
||||
want to use was included via the appropriate package at compile time.
|
||||
LAMMPS will print the info and immediately exit if this switch is
|
||||
used.
|
||||
|
||||
-log file :pre
|
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|
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|
|
|
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|
|
@ -47,6 +47,7 @@ own sub-directories with their own Makefiles.
|
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<LI><A HREF = "#binary">binary2txt</A>
|
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<LI><A HREF = "#charmm">ch2lmp</A>
|
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<LI><A HREF = "#chain">chain</A>
|
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<LI><A HREF = "#colvars">colvars</A>
|
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<LI><A HREF = "#create">createatoms</A>
|
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<LI><A HREF = "#data">data2xmovie</A>
|
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<LI><A HREF = "#eamdb">eam database</A>
|
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|
|
@ -136,6 +137,28 @@ system for the <A HREF = "Section_perf.html">chain benchmark</A>.
|
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</P>
|
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<HR>
|
||||
|
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<H4><A NAME = "colvars"></A>colvars tools
|
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</H4>
|
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<P>The colvars directory contains a collection of tools for postprocessing
|
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data produced by the colvars collective variable library.
|
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To compile the tools, edit the makefile for your system and run "make".
|
||||
</P>
|
||||
<P>Please report problems and issues the colvars library and its tools
|
||||
at: https://github.com/colvars/colvars/issues
|
||||
</P>
|
||||
<P>abf_integrate:
|
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</P>
|
||||
<P>MC-based integration of multidimensional free energy gradient
|
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Version 20110511
|
||||
</P>
|
||||
<PRE>Syntax: ./abf_integrate < filename > [-n < nsteps >] [-t < temp >] [-m [0|1] (metadynamics)] [-h < hill_height >] [-f < variable_hill_factor >]
|
||||
</PRE>
|
||||
<P>The LAMMPS interface to the colvars collective variable library, as
|
||||
well as these tools, were created by Axel Kohlmeyer (akohlmey at
|
||||
gmail.com) at ICTP, Italy.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<H4><A NAME = "create"></A>createatoms tool
|
||||
</H4>
|
||||
<P>The tools/createatoms directory contains a Fortran program called
|
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|
|
@ -156,7 +179,7 @@ suitable for visualizing with the <A HREF = "#xmovie">xmovie</A> tool, as if it
|
|||
been output with a dump command from LAMMPS itself. The syntax for
|
||||
running the tool is
|
||||
</P>
|
||||
<PRE>data2xmovie <B>options</B> < infile > outfile
|
||||
<PRE>data2xmovie [options] < infile > outfile
|
||||
</PRE>
|
||||
<P>See the top of the data2xmovie.c file for a discussion of the options.
|
||||
</P>
|
||||
|
|
@ -495,7 +518,7 @@ it can find the appropriate X libraries to link against.
|
|||
</P>
|
||||
<P>The syntax for running xmovie is
|
||||
</P>
|
||||
<PRE>xmovie <B>options</B> dump.file1 dump.file2 ...
|
||||
<PRE>xmovie [options] dump.file1 dump.file2 ...
|
||||
</PRE>
|
||||
<P>If you just type "xmovie" you will see a list of options. Note that
|
||||
by default, LAMMPS dump files are in scaled coordinates, so you
|
||||
|
|
|
|||
|
|
@ -43,6 +43,7 @@ own sub-directories with their own Makefiles.
|
|||
"binary2txt"_#binary
|
||||
"ch2lmp"_#charmm
|
||||
"chain"_#chain
|
||||
"colvars"_#colvars
|
||||
"createatoms"_#create
|
||||
"data2xmovie"_#data
|
||||
"eam database"_#eamdb
|
||||
|
|
@ -132,6 +133,28 @@ system for the "chain benchmark"_Section_perf.html.
|
|||
|
||||
:line
|
||||
|
||||
colvars tools :h4,link(colvars)
|
||||
|
||||
The colvars directory contains a collection of tools for postprocessing
|
||||
data produced by the colvars collective variable library.
|
||||
To compile the tools, edit the makefile for your system and run "make".
|
||||
|
||||
Please report problems and issues the colvars library and its tools
|
||||
at: https://github.com/colvars/colvars/issues
|
||||
|
||||
abf_integrate:
|
||||
|
||||
MC-based integration of multidimensional free energy gradient
|
||||
Version 20110511
|
||||
|
||||
Syntax: ./abf_integrate < filename > \[-n < nsteps >\] \[-t < temp >\] \[-m \[0|1\] (metadynamics)\] \[-h < hill_height >\] \[-f < variable_hill_factor >\] :pre
|
||||
|
||||
The LAMMPS interface to the colvars collective variable library, as
|
||||
well as these tools, were created by Axel Kohlmeyer (akohlmey at
|
||||
gmail.com) at ICTP, Italy.
|
||||
|
||||
:line
|
||||
|
||||
createatoms tool :h4,link(create)
|
||||
|
||||
The tools/createatoms directory contains a Fortran program called
|
||||
|
|
@ -152,7 +175,7 @@ suitable for visualizing with the "xmovie"_#xmovie tool, as if it had
|
|||
been output with a dump command from LAMMPS itself. The syntax for
|
||||
running the tool is
|
||||
|
||||
data2xmovie [options] < infile > outfile :pre
|
||||
data2xmovie \[options\] < infile > outfile :pre
|
||||
|
||||
See the top of the data2xmovie.c file for a discussion of the options.
|
||||
|
||||
|
|
@ -491,7 +514,7 @@ it can find the appropriate X libraries to link against.
|
|||
|
||||
The syntax for running xmovie is
|
||||
|
||||
xmovie [options] dump.file1 dump.file2 ... :pre
|
||||
xmovie \[options\] dump.file1 dump.file2 ... :pre
|
||||
|
||||
If you just type "xmovie" you will see a list of options. Note that
|
||||
by default, LAMMPS dump files are in scaled coordinates, so you
|
||||
|
|
|
|||
|
|
@ -34,7 +34,7 @@
|
|||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>compute 1 all atom/molecule c_ke c_pe
|
||||
compute 1 top atom/molecule v_myFormula c_stress<B>3</B>
|
||||
compute 1 top atom/molecule v_myFormula c_stress[3]
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
|
|
|
|||
|
|
@ -26,7 +26,7 @@ input = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l
|
|||
[Examples:]
|
||||
|
||||
compute 1 all atom/molecule c_ke c_pe
|
||||
compute 1 top atom/molecule v_myFormula c_stress[3] :pre
|
||||
compute 1 top atom/molecule v_myFormula c_stress\[3\] :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
|
|
|
|||
|
|
@ -52,8 +52,8 @@
|
|||
</P>
|
||||
<PRE>compute 1 all reduce sum c_force
|
||||
compute 1 all reduce/region subbox sum c_force
|
||||
compute 2 all reduce min c_press<B>2</B> f_ave v_myKE
|
||||
compute 3 fluid reduce max c_index<B>1</B> c_index<B>2</B> c_dist replace 1 3 replace 2 3
|
||||
compute 2 all reduce min c_press[2] f_ave v_myKE
|
||||
compute 3 fluid reduce max c_index[1] c_index[2] c_dist replace 1 3 replace 2 3
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
|
|
|
|||
|
|
@ -39,8 +39,8 @@ keyword = {replace} :l
|
|||
|
||||
compute 1 all reduce sum c_force
|
||||
compute 1 all reduce/region subbox sum c_force
|
||||
compute 2 all reduce min c_press[2] f_ave v_myKE
|
||||
compute 3 fluid reduce max c_index[1] c_index[2] c_dist replace 1 3 replace 2 3 :pre
|
||||
compute 2 all reduce min c_press\[2\] f_ave v_myKE
|
||||
compute 3 fluid reduce max c_index\[1\] c_index\[2\] c_dist replace 1 3 replace 2 3 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
|
|
|
|||
|
|
@ -175,7 +175,7 @@ dump file:
|
|||
</P>
|
||||
<PRE>fix prop all property/atom i_flag1 d_flag2
|
||||
compute 1 all property/atom i_flag1 d_flag2
|
||||
dump 1 all custom 100 tmp.dump id x y z c_1<B>1</B> c_1<B>2</B>
|
||||
dump 1 all custom 100 tmp.dump id x y z c_1[1] c_1[2]
|
||||
</PRE>
|
||||
<HR>
|
||||
|
||||
|
|
|
|||
|
|
@ -165,7 +165,7 @@ dump file:
|
|||
|
||||
fix prop all property/atom i_flag1 d_flag2
|
||||
compute 1 all property/atom i_flag1 d_flag2
|
||||
dump 1 all custom 100 tmp.dump id x y z c_1[1] c_1[2] :pre
|
||||
dump 1 all custom 100 tmp.dump id x y z c_1\[1\] c_1\[2\] :pre
|
||||
|
||||
:line
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue