<DT><I>Bond atoms %d %d missing on proc %d at step %d</I> 

<DD>One or more of 2 atoms needed to compute a particular bond are

<DD>One or both of 2 atoms needed to compute a particular bond are

missing on this processor.  Typically this is because the pairwise

cutoff is set too short or the bond has blown apart and an atom is

too far away. 

<DT><I>Cannot fix deform on a non-periodic boundary</I> 

<DD>Only a periodiic boundary can be modified. 

<DD>Only a periodic boundary can be modified. 

<DT><I>Cannot have both pair_modify shift and tail set to yes</I> 

<DD>A group ID used in the dump command does not exist. 

<DT><I>Could not find dump_modify ID</I> 

<DD>Self-explanatory. 

<DT><I>Could not find fix ID to delete</I> 

<DD>Self-explanatory. 

<DD>If using a Kspace solver, all Coulomb cutoffs of long pair styles must

be the same. 

<DT><I>Cound not find dump_modify ID</I> 

<DD>Self-explanatory. 

<DT><I>Create_atoms command before simulation box is defined</I> 

<DD>The create_atoms command cannot be used before a read_data,

<DT><I>Deposition region extends outside simulation box</I> 

<DD>Self-explatory. 

<DD>Self-explanatory. 

<DT><I>Did not assign all atoms correctly</I> 

<DD>The three specified lattice orientation vectors must create a

right-handed coordinate system such that a1 cross a2 = a3. 

<DT><I>Lattice primitive vectors are colinear</I> 

<DT><I>Lattice primitive vectors are collinear</I> 

<DD>The specified lattice primitive vectors do not for a unit cell with

non-zero volume. 

<DD>Fix poems will only work with bodies (collections of atoms) that have

non-zero principal moments of inertia.  This means they must be 3 or

more non-colinear atoms, even with joint atoms removed. 

more non-collinear atoms, even with joint atoms removed. 

<DT><I>Rigid fix must come before NPT/NPH fix</I> 

{Bond atoms %d %d missing on proc %d at step %d} :dt

One or more of 2 atoms needed to compute a particular bond are

One or both of 2 atoms needed to compute a particular bond are

missing on this processor.  Typically this is because the pairwise

cutoff is set too short or the bond has blown apart and an atom is

too far away. :dd

{Cannot fix deform on a non-periodic boundary} :dt

Only a periodiic boundary can be modified. :dd

Only a periodic boundary can be modified. :dd

{Cannot have both pair_modify shift and tail set to yes} :dt

A group ID used in the dump command does not exist. :dd

{Could not find dump_modify ID} :dt

Self-explanatory. :dd

{Could not find fix ID to delete} :dt

Self-explanatory. :dd

If using a Kspace solver, all Coulomb cutoffs of long pair styles must

be the same. :dd

{Cound not find dump_modify ID} :dt

Self-explanatory. :dd

{Create_atoms command before simulation box is defined} :dt

The create_atoms command cannot be used before a read_data,

{Deposition region extends outside simulation box} :dt

Self-explatory. :dd

Self-explanatory. :dd

{Did not assign all atoms correctly} :dt

The three specified lattice orientation vectors must create a

right-handed coordinate system such that a1 cross a2 = a3. :dd

{Lattice primitive vectors are colinear} :dt

{Lattice primitive vectors are collinear} :dt

The specified lattice primitive vectors do not for a unit cell with

non-zero volume. :dd

Fix poems will only work with bodies (collections of atoms) that have

non-zero principal moments of inertia.  This means they must be 3 or

more non-colinear atoms, even with joint atoms removed. :dd

more non-collinear atoms, even with joint atoms removed. :dd

{Rigid fix must come before NPT/NPH fix} :dt

the following commands:

</P>

<UL><LI><A HREF = "atom_style.html">atom_style</A> granular

<LI><A HREF = "fix_nve_gran.html">fix nve/gran</A>

<LI><A HREF = "fix_nve_sphere.html">fix nve/sphere</A>

<LI><A HREF = "fix_gravity.html">fix gravity</A> 

<LI><A HREF = "thermo_style.html">thermo_style</A> gran 

</UL>

<P>This compute

</P>

<UL><LI><A HREF = "compute_erotate_sphere.html">compute erotate/sphere</A> 

</UL>

<P>will calculate rotational kinetic energy which can then be <A HREF = "">output

with thermodynamic info</A>.

</P>

<P>Use one of these 3 pair potentials:

</P>

<UL><LI><A HREF = "pair_style.html">pair_style</A> gran/history

the following commands:

"atom_style"_atom_style.html granular

"fix nve/gran"_fix_nve_gran.html

"fix gravity"_fix_gravity.html

"thermo_style"_thermo_style.html gran :ul

"fix nve/sphere"_fix_nve_sphere.html

"fix gravity"_fix_gravity.html :ul

This compute

"compute erotate/sphere"_compute_erotate_sphere.html :ul

will calculate rotational kinetic energy which can then be "output

with thermodynamic info"_.

Use one of these 3 pair potentials:

<LI>  angle potentials: harmonic, CHARMM, cosine, cosine/squared,     class 2 (COMPASS)

<LI>  dihedral potentials: harmonic, CHARMM, multi-harmonic, helix,     class 2 (COMPASS), OPLS

<LI>  improper potentials: harmonic, cvff, class 2 (COMPASS)

<LI>  hybrid potentials: multiple pair, bond, angle, dihedral, improper     potentials can be used in one simlulation

<LI>  overlayed potentials: superposition of multiple pair potentials

<LI>  hybrid potentials: multiple pair, bond, angle, dihedral, improper     potentials can be used in one simulation

<LI>  overlaid potentials: superposition of multiple pair potentials

<LI>  polymer potentials: all-atom, united-atom, bead-spring, breakable

<LI>  water potentials: TIP3P, TIP4P, SPC

<LI>  implicit solvent potentials: hydrodynamic lubrication, Debye