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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4219 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2010-06-01 19:57:01 +00:00
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26
doc/Section_errors.html
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@ -35,10 +35,11 @@ energy or temperature) should still be the same.
</P> </P>
<P>If the <A HREF = "velocity.html">velocity</A> command is used to set initial atom <P>If the <A HREF = "velocity.html">velocity</A> command is used to set initial atom
velocities, a particular atom can be assigned a different velocity velocities, a particular atom can be assigned a different velocity
when the problem on different machines. Obviously, this means the when the problem is run on a different number of processors or on
phase space trajectories of the two simulations will rapidly diverge. different machines. If this happens, the phase space trajectories of
See the discussion of the <I>loop</I> option in the the two simulations will rapidly diverge. See the discussion of the
<A HREF = "velocity.html">velocity</A> command for details. <I>loop</I> option in the <A HREF = "velocity.html">velocity</A> command for details and
options that avoid this issue.
</P> </P>
<P>Similarly, the <A HREF = "create_atoms.html">create_atoms</A> command generates a <P>Similarly, the <A HREF = "create_atoms.html">create_atoms</A> command generates a
lattice of atoms. For the same physical system, the ordering and lattice of atoms. For the same physical system, the ordering and
@ -56,11 +57,11 @@ LAMMPS errors are detected at setup time; others like a bond
stretching too far may not occur until the middle of a run. stretching too far may not occur until the middle of a run.
</P> </P>
<P>LAMMPS tries to flag errors and print informative error messages so <P>LAMMPS tries to flag errors and print informative error messages so
you can fix the problem. Of course LAMMPS cannot figure out your you can fix the problem. Of course, LAMMPS cannot figure out your
physics mistakes, like choosing too big a timestep, specifying invalid physics or numerical mistakes, like choosing too big a timestep,
force field coefficients, or putting 2 atoms on top of each other! If specifying erroneous force field coefficients, or putting 2 atoms on
you find errors that LAMMPS doesn't catch that you think it should top of each other! If you run into errors that LAMMPS doesn't catch
flag, please send an email to the that you think it should flag, please send an email to the
<A HREF = "http://lammps.sandia.gov/authors.html">developers</A>. <A HREF = "http://lammps.sandia.gov/authors.html">developers</A>.
</P> </P>
<P>If you get an error message about an invalid command in your input <P>If you get an error message about an invalid command in your input
@ -93,7 +94,12 @@ parallel), since LAMMPS doesn't trap on those errors.
<P>Illegal arithmetic can cause LAMMPS to run slow or crash. This is <P>Illegal arithmetic can cause LAMMPS to run slow or crash. This is
typically due to invalid physics and numerics that your simulation is typically due to invalid physics and numerics that your simulation is
computing. If you see wild thermodynamic values or NaN values in your computing. If you see wild thermodynamic values or NaN values in your
LAMMPS output, something is wrong with your simulation. LAMMPS output, something is wrong with your simulation. If you
suspect this is happening, it is a good idea to print out
thermodynamic info frequently (e.g. every timestep) via the
<A HREF = "thermo.html">thermo</A> so you can monitor what is happening.
Visualizing the atom movement is also a good idea to insure your model
is behaving as you expect.
</P> </P>
<P>In parallel, one way LAMMPS can hang is due to how different MPI <P>In parallel, one way LAMMPS can hang is due to how different MPI
implementations handle buffering of messages. If the code hangs implementations handle buffering of messages. If the code hangs

26
doc/Section_errors.txt
View File

@ -32,10 +32,11 @@ energy or temperature) should still be the same.
If the "velocity"_velocity.html command is used to set initial atom If the "velocity"_velocity.html command is used to set initial atom
velocities, a particular atom can be assigned a different velocity velocities, a particular atom can be assigned a different velocity
when the problem on different machines. Obviously, this means the when the problem is run on a different number of processors or on
phase space trajectories of the two simulations will rapidly diverge. different machines. If this happens, the phase space trajectories of
See the discussion of the {loop} option in the the two simulations will rapidly diverge. See the discussion of the
"velocity"_velocity.html command for details. {loop} option in the "velocity"_velocity.html command for details and
options that avoid this issue.
Similarly, the "create_atoms"_create_atoms.html command generates a Similarly, the "create_atoms"_create_atoms.html command generates a
lattice of atoms. For the same physical system, the ordering and lattice of atoms. For the same physical system, the ordering and
@ -53,11 +54,11 @@ LAMMPS errors are detected at setup time; others like a bond
stretching too far may not occur until the middle of a run. stretching too far may not occur until the middle of a run.
LAMMPS tries to flag errors and print informative error messages so LAMMPS tries to flag errors and print informative error messages so
you can fix the problem. Of course LAMMPS cannot figure out your you can fix the problem. Of course, LAMMPS cannot figure out your
physics mistakes, like choosing too big a timestep, specifying invalid physics or numerical mistakes, like choosing too big a timestep,
force field coefficients, or putting 2 atoms on top of each other! If specifying erroneous force field coefficients, or putting 2 atoms on
you find errors that LAMMPS doesn't catch that you think it should top of each other! If you run into errors that LAMMPS doesn't catch
flag, please send an email to the that you think it should flag, please send an email to the
"developers"_http://lammps.sandia.gov/authors.html. "developers"_http://lammps.sandia.gov/authors.html.
If you get an error message about an invalid command in your input If you get an error message about an invalid command in your input
@ -90,7 +91,12 @@ parallel), since LAMMPS doesn't trap on those errors.
Illegal arithmetic can cause LAMMPS to run slow or crash. This is Illegal arithmetic can cause LAMMPS to run slow or crash. This is
typically due to invalid physics and numerics that your simulation is typically due to invalid physics and numerics that your simulation is
computing. If you see wild thermodynamic values or NaN values in your computing. If you see wild thermodynamic values or NaN values in your
LAMMPS output, something is wrong with your simulation. LAMMPS output, something is wrong with your simulation. If you
suspect this is happening, it is a good idea to print out
thermodynamic info frequently (e.g. every timestep) via the
"thermo"_thermo.html so you can monitor what is happening.
Visualizing the atom movement is also a good idea to insure your model
is behaving as you expect.
In parallel, one way LAMMPS can hang is due to how different MPI In parallel, one way LAMMPS can hang is due to how different MPI
implementations handle buffering of messages. If the code hangs implementations handle buffering of messages. If the code hangs