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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8442 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2012-06-29 21:17:59 +00:00
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@ -221,6 +221,12 @@ command.
<DD>All pair coefficients must be set in the data file or by the
pair_coeff command before running a simulation.
<DT><I>All read_dump x,y,z fields must be specified for scaled, triclinic coords</I>
<DD>For triclinic boxes and scaled coordinates you must specify all 3 of
the x,y,z fields, else LAMMPS cannot reconstruct the unscaled
coordinates.
<DT><I>All universe/uloop variables must have same # of values</I>
<DD>Self-explanatory.
@ -319,7 +325,7 @@ still being processed.
<DT><I>Append boundary must be shrink/minimum</I>
<DD>The boundary style of the face where atoms are added
must be of type m (shrink/minimum).
must be of type m (shrink/minimum).
<DT><I>Arccos of invalid value in variable formula</I>
@ -476,9 +482,11 @@ or create_box command.
<DD>The string can only contain the characters "x", "y", or "z".
<DT><I>Balance dynamic string is invalid for 2d simulation</I>
<DT><I>Balance produced bad splits</I>
<DD>The string cannot contain the letter "z".
<DD>This should not occur. It means two or more cutting plane locations
are on top of each other or out of order. Report the problem to the
developers.
<DT><I>Bias compute does not calculate a velocity bias</I>
@ -525,6 +533,12 @@ in file exactly.
<DD>Cannot use TIP4P pair potential unless bond and angle potentials
are defined.
<DT><I>Bond atom missing in box size check</I>
<DD>The 2nd atoms needed to compute a particular bond is 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>Bond atom missing in delete_bonds</I>
<DD>The delete_bonds command cannot find one or more atoms in a particular
@ -588,6 +602,15 @@ bond style quartic.
<DD>The values in the tabulated file must be monotonically increasing.
<DT><I>Bond/angle/dihedral extent > half of periodic box length</I>
<DD>This is a restriction because LAMMPS can be confused about which image
of an atom in the bonded interaction is the correct one to use.
"Extent" in this context means the maximum end-to-end length of the
bond/angle/dihedral. LAMMPS computes this by taking the maximum bond
length, multiplying by the number of bonds in the interaction (e.g. 3
for a dihedral) and adding a small amount of stretch.
<DT><I>Bond_coeff command before bond_style is defined</I>
<DD>Coefficients cannot be set in the data file or via the bond_coeff
@ -656,6 +679,14 @@ See the region prism command for details.
<DD>This is current restriction for NEB as implemented in LAMMPS.
<DT><I>Cannot (yet) use K-space slab correction with compute group/group</I>
<DD>This option is not yet supported.
<DT><I>Cannot (yet) use Kspace slab correction with compute group/group</I>
<DD>This option is not yet supported.
<DT><I>Cannot (yet) use PPPM with triclinic box</I>
<DD>This feature is not yet supported.
@ -830,6 +861,11 @@ path and name are correct.
<DD>The specified AIREBO potential file cannot be opened. Check that the
path and name are correct.
<DT><I>Cannot open BOP potential file %s</I>
<DD>The specified BOP potential file cannot be opened. Check that the
path and name are correct.
<DT><I>Cannot open COMB potential file %s</I>
<DD>The specified COMB potential file cannot be opened. Check that the
@ -845,6 +881,11 @@ path and name are correct.
<DD>The specified EIM potential file cannot be opened. Check that the
path and name are correct.
<DT><I>Cannot open LCBOP potential file %s</I>
<DD>The specified LCBOP potential file cannot be opened. Check that the
path and name are correct.
<DT><I>Cannot open MEAM potential file %s</I>
<DD>The specified MEAM potential file cannot be opened. Check that the
@ -862,8 +903,7 @@ path and name are correct.
<DT><I>Cannot open balance output file</I>
<DD>This error message can only occur if debug options
are uncommented in src/balance.cpp.
<DD>Self-explanatory.
<DT><I>Cannot open custom file</I>
@ -904,6 +944,10 @@ correct.
<DD>The specified file cannot be opened. Check that the path and name are
correct.
<DT><I>Cannot open fix balance output file</I>
<DD>Self-explanatory.
<DT><I>Cannot open fix poems file %s</I>
<DD>The specified file cannot be opened. Check that the path and name are
@ -923,6 +967,11 @@ Check that the path and name are correct.
<DD>The output file for the fix reax/bonds command cannot be opened.
Check that the path and name are correct.
<DT><I>Cannot open fix rigid infile %s</I>
<DD>The specified file cannot be opened. Check that the path and name are
correct.
<DT><I>Cannot open fix tmd file %s</I>
<DD>The output file for the fix tmd command cannot be opened. Check that
@ -1027,17 +1076,6 @@ are defined.
<DD>You cannot reset the timestep when a fix that keeps track of elapsed
time is in place.
<DT><I>Cannot reset timestep with dump file already written to</I>
<DD>Changing the timestep will confuse when a dump file is written. Use
the undump command, then restart the dump file.
<DT><I>Cannot reset timestep with restart file already written</I>
<DD>Changing the timestep will confuse when a restart file is written.
Use the "restart 0" command to turn off restarts, then start them
again.
<DT><I>Cannot restart fix rigid/nvt with different # of chains</I>
<DD>This is because the restart file contains per-chain info.
@ -1550,6 +1588,10 @@ of velocity creation cannot be performed.
<DD>Cannot specify both options at the same time.
<DT><I>Cannot yet use fix balance with PPPM</I>
<DD>This is a current limitation of LAMMPS.
<DT><I>Cannot zero Langevin force of 0 atoms</I>
<DD>The group has zero atoms, so you cannot request its force
@ -2470,6 +2512,14 @@ dump output.
<DD>The variable must return a timestep greater than the current timestep.
<DT><I>Dump file does not contain requested snapshot</I>
<DD>Self-explanatory.
<DT><I>Dump file is incorrectly formatted</I>
<DD>No atoms were found in file.
<DT><I>Dump image bond not allowed with no bond types</I>
<DD>Self-explanatory.
@ -2605,6 +2655,10 @@ dumped.
<DD>Only per-atom quantities that are defined for the atom style being
used are allowed.
<DT><I>Duplicate fields in read_dump command</I>
<DD>Self-explanatory.
<DT><I>Duplicate particle in PeriDynamic bond - simulation box is too small</I>
<DD>This is likely because your box length is shorter than 2 times
@ -2714,6 +2768,10 @@ is on.
<DD>Self-explanatory
<DT><I>Fix ID for read_data does not exist</I>
<DD>Self-explanatory.
<DT><I>Fix ID must be alphanumeric or underscore characters</I>
<DD>Self-explanatory.
@ -2799,6 +2857,11 @@ to a larger value, and re-compile the code.
<DD>A fix used by fix ave/atom must generate per-atom values.
<DT><I>Fix ave/atom missed timestep</I>
<DD>You cannot reset the timestep to a value beyond where the fix
expects to next perform averaging.
<DT><I>Fix ave/atom variable is not atom-style variable</I>
<DD>A variable used by fix ave/atom must generate per-atom values.
@ -2827,6 +2890,11 @@ to a larger value, and re-compile the code.
<DD>The index for the vector is out of bounds.
<DT><I>Fix ave/correlate missed timestep</I>
<DD>You cannot reset the timestep to a value beyond where the fix
expects to next perform averaging.
<DT><I>Fix ave/correlate variable is not equal-style variable</I>
<DD>Self-explanatory.
@ -2944,6 +3012,11 @@ to a larger value, and re-compile the code.
<DD>All inputs in a single fix ave/histo command must be of the
same style.
<DT><I>Fix ave/histo missed timestep</I>
<DD>You cannot reset the timestep to a value beyond where the fix
expects to next perform averaging.
<DT><I>Fix ave/spatial compute does not calculate a per-atom array</I>
<DD>Self-explanatory.
@ -2980,6 +3053,11 @@ same style.
<DD>Self-explanatory.
<DT><I>Fix ave/spatial missed timestep</I>
<DD>You cannot reset the timestep to a value beyond where the fix
expects to next perform averaging.
<DT><I>Fix ave/spatial settings invalid with changing box</I>
<DD>If the ave setting is "running" or "window" and the box size/shape
@ -3044,6 +3122,11 @@ all intensive/extensive when turned into an array by fix ave/time.
<DD>The index for the vector is out of bounds.
<DT><I>Fix ave/time missed timestep</I>
<DD>You cannot reset the timestep to a value beyond where the fix
expects to next perform averaging.
<DT><I>Fix ave/time variable is not equal-style variable</I>
<DD>Self-explanatory.
@ -3319,6 +3402,10 @@ which means it is a point particle.
<DD>Self-explanatory.
<DT><I>Fix nvt/npt/nph dilate group ID does not exist</I>
<DD>Self-explanatory.
<DT><I>Fix nvt/sphere requires extended particles</I>
<DD>This fix can only be used for particles of a finite size.
@ -3484,6 +3571,14 @@ fix store/state.
<DD>Self-explanatory.
<DT><I>Fix temp/berendsen variable returned negative temperature</I>
<DD>Self-explanatory.
<DT><I>Fix temp/rescale variable returned negative temperature</I>
<DD>Self-explanatory.
<DT><I>Fix thermal/conductivity swap value must be positive</I>
<DD>Self-explanatory.
@ -3653,6 +3748,11 @@ create_box command.
<DD>A region ID used in the group command does not exist.
<DT><I>If read_dump purges it cannot replace or trim</I>
<DD>These operations are not compatible. See the read_dump doc
page for details.
<DT><I>Illegal ... command</I>
<DD>Self-explanatory. Check the input script syntax and compare to the
@ -3770,7 +3870,7 @@ definitions.
<DT><I>Inconsistent iparam/jparam values in fix bond/create command</I>
<DD>If itype and jtype are the same, then their maxbond and newtype
<DD>If itype and jtype are the same, then their maxbond and newtype
settings must also be the same.
<DT><I>Inconsistent line segment in data file</I>
@ -3863,6 +3963,10 @@ bonus data must be formatted for certain atom styles.
<DD>Self-explanatory. Check the input script or data file.
<DT><I>Incorrect rigid body format in fix rigid file</I>
<DD>The number of fields per line is not what expected.
<DT><I>Incorrect sign arg for dihedral coefficients</I>
<DD>Self-explanatory. Check the input script or data file.
@ -4234,6 +4338,10 @@ be for a single processor.
<DD>Zoom value must be > 0.0.
<DT><I>Invalid dump reader style</I>
<DD>Self-explanatory.
<DT><I>Invalid dump style</I>
<DD>The choice of dump style is unknown.
@ -4476,6 +4584,11 @@ cannot be the same partition.
<DD>Self-explanatory.
<DT><I>Invalid rigid body ID in fix rigid file</I>
<DD>The ID does not match the number or an existing ID of rigid bodies
that are defined by the fix rigid command.
<DT><I>Invalid run command N value</I>
<DD>The number of timesteps must fit in a 32-bit integer. If you want to
@ -4615,6 +4728,10 @@ where it is requesting neighbors incorrectly.
<DD>This environment variable must be set to use pair_style kim.
See the doc page for pair_style kim.
<DT><I>KSpace accuracy too large to estimate G vector</I>
<DD>Paul will doc this.
<DT><I>KSpace style has not yet been set</I>
<DD>Cannot use kspace_modify command until a kspace style is set.
@ -4628,6 +4745,10 @@ Coulombic component be selected.
<DD>Self-explanatory.
<DT><I>Kspace style does not support compute group/group</I>
<DD>Self-explanatory.
<DT><I>Kspace style pppm/tip4p requires newton on</I>
<DD>Self-explanatory.
@ -5019,10 +5140,6 @@ neighbors allowed for one atom.
<DD>This is required to prevent wasting too much memory.
<DT><I>Neighbors of ghost atoms only allowed for full neighbor lists</I>
<DD>This is a current restriction within LAMMPS.
<DT><I>New bond exceeded bonds per atom in fix bond/create</I>
<DD>See the read_data command for info on setting the "extra bond per
@ -5038,6 +5155,10 @@ the special bonds list to allow for additional bonds to be formed.
<DD>The newton command cannot be used to change the newton bond value
after a read_data, read_restart, or create_box command.
<DT><I>No Kspace style defined for compute group/group</I>
<DD>Self-explanatory.
<DT><I>No OpenMP support compiled in</I>
<DD>An OpenMP flag is set, but LAMMPS was not built with
@ -5068,6 +5189,10 @@ but they were not present.
<DD>Self-explanatory. Check data file.
<DT><I>No box information in dump. You have to use 'box no'</I>
<DD>Self-explanatory.
<DT><I>No dihedral style is defined for compute dihedral/local</I>
<DD>Self-explanatory.
@ -5115,6 +5240,10 @@ requested elements.
<DD>The EAM potential file does not contain elements that match the
requested elements.
<DT><I>No overlap of box and region for create_atoms</I>
<DD>Self-explanatory.
<DT><I>No pair hbond/dreiding coefficients set</I>
<DD>Self-explanatory.
@ -5207,15 +5336,15 @@ else the fix contribution to the pressure virial is incorrect.
OFFSET is currently set to 4096. You likely need to decrease the
requested accuracy.
<DT><I>PPPM order cannot be greater than %d</I>
<DT><I>PPPM order cannot be < 2 or > than %d</I>
<DD>Self-explanatory.
<DD>This is a limitation of the PPPM implementation in LAMMPS.
<DT><I>PPPM order has been reduced to 0</I>
<DD>LAMMPS has attempted to reduce the PPPM order to enable the simulation
to run, but can reduce the order no further. Try increasing the
accuracy of PPPM by reducing the tolerance size, thus inducing a
accuracy of PPPM by reducing the tolerance size, thus inducing a
larger PPPM grid.
<DT><I>PRD command before simulation box is defined</I>
@ -5450,6 +5579,15 @@ bonds. Use the atom_modify command to define one.
<DD>See the newton command. This is a restriction to use the AIREBO
potential.
<DT><I>Pair style BOP requires atom IDs</I>
<DD>This is a requirement to use the BOP potential.
<DT><I>Pair style BOP requires newton pair on</I>
<DD>See the newton command. This is a restriction to use the BOP
potential.
<DT><I>Pair style COMB requires atom IDs</I>
<DD>This is a requirement to use the AIREBO potential.
@ -5463,6 +5601,15 @@ potential.
<DD>See the newton command. This is a restriction to use the COMB
potential.
<DT><I>Pair style LCBOP requires atom IDs</I>
<DD>This is a requirement to use the LCBOP potential.
<DT><I>Pair style LCBOP requires newton pair on</I>
<DD>See the newton command. This is a restriction to use the LCBOP
potential.
<DT><I>Pair style MEAM requires newton pair on</I>
<DD>See the newton command. This is a restriction to use the MEAM
@ -5486,6 +5633,11 @@ potential.
<DD>See the newton command. This is a restriction to use the Tersoff
potential.
<DT><I>Pair style bop requires comm ghost cutoff at least 3x larger than %g</I>
<DD>Use the communicate ghost command to set this. See the pair bop
doc page for more details.
<DT><I>Pair style born/coul/long requires atom attribute q</I>
<DD>An atom style that defines this attribute must be used.
@ -5871,6 +6023,19 @@ cart for the map option.
<DD>Equilibrium spring length is invalid.
<DT><I>Read_dump field not found in dump file</I>
<DD>Self-explanatory.
<DT><I>Read_dump triclinic status does not match simulation</I>
<DD>Both the dump snapshot and the current LAMMPS simulation must
be using either an orthogonal or triclinic box.
<DT><I>Read_dump x,y,z fields do not have consistent scaling</I>
<DD>Self-explanatory.
<DT><I>Reax_defs.h setting for NATDEF is too small</I>
<DD>Edit the setting in the ReaxFF library and re-compile the
@ -5977,6 +6142,15 @@ file.
<DD>See the setting for bigint in the src/lmptype.h file.
<DT><I>Rerun command before simulation box is defined</I>
<DD>The rerun command cannot be used before a read_data, read_restart, or
create_box command.
<DT><I>Rerun dump file does not contain requested snapshot</I>
<DD>Self-explanatory.
<DT><I>Resetting timestep is not allowed with fix move</I>
<DD>This is because fix move is moving atoms based on elapsed time.
@ -5993,12 +6167,28 @@ file.
<DD>The first cutoff must be <= the second cutoff.
<DT><I>Restart variable returned a bad timestep</I>
<DD>The variable must return a timestep greater than the current timestep.
<DT><I>Restrain atoms %d %d %d %d missing on proc %d at step %ld</I>
<DD>The 4 atoms in a restrain dihedral specified by the fix restrain
command are not all accessible to a processor. This probably means an
atom has moved too far.
<DT><I>Restrain atoms %d %d %d missing on proc %d at step %ld</I>
<DD>The 3 atoms in a restrain angle specified by the fix restrain
command are not all accessible to a processor. This probably means an
atom has moved too far.
<DT><I>Restrain atoms %d %d missing on proc %d at step %ld</I>
<DD>The 2 atoms in a restrain bond specified by the fix restrain
command are not all accessible to a processor. This probably means an
atom has moved too far.
<DT><I>Reuse of compute ID</I>
<DD>A compute ID cannot be used twice.
@ -6441,11 +6631,22 @@ not defined by the atom style used in this simulation.
<DD>Table size specified via pair_modify command does not work with your
machine's floating point representation.
<DT><I>Too many atom pairs for pair bop</I>
<DD>The number of atomic pairs exceeds the expected number. Check your
atomic structure to ensure that it is realistic.
<DT><I>Too many atom sorting bins</I>
<DD>This is likely due to an immense simulation box that has blown up
to a large size.
<DT><I>Too many atom triplets for pair bop</I>
<DD>The number of three atom groups for angle determinations exceeds the
expected number. Check your atomic structrure to ensure that it is
realistic.
<DT><I>Too many atoms for dump dcd</I>
<DD>The system size must fit in a 32-bit integer to use this dump
@ -6467,12 +6668,12 @@ machine's floating point representation.
<DT><I>Too many groups</I>
<DD>The maximum number of atom groups (including the "all" group) is
<DD>The maximum number of atom groups (including the "all" group) is
given by MAX_GROUP in group.cpp and is 32.
<DT><I>Too many iterations</I>
<DD>You must use a number of iterations that fit in a 32-bit integer
<DD>You must use a number of iterations that fit in a 32-bit integer
for minimization.
<DT><I>Too many local+ghost atoms for neighbor list</I>
@ -6502,7 +6703,7 @@ to a large size.
<DT><I>Too many timesteps for NEB</I>
<DD>You must use a number of timesteps that fit in a 32-bit integer
<DD>You must use a number of timesteps that fit in a 32-bit integer
for NEB.
<DT><I>Too many total atoms</I>
@ -6578,6 +6779,14 @@ quote.
<DD>LAMMPS hit the end of the data file while attempting to read a
section. Something is wrong with the format of the data file.
<DT><I>Unexpected end of dump file</I>
<DD>A read operation from the file failed.
<DT><I>Unexpected end of fix rigid file</I>
<DD>A read operation from the file failed.
<DT><I>Units command after simulation box is defined</I>
<DD>The units command cannot be used after a read_data, read_restart, or
@ -6713,7 +6922,7 @@ deform needs to be used.
<DT><I>Using pair lubricate with inconsistent fix deform remap option</I>
<DD>If fix deform is used, the remap v option is required.
<DD>Must use remap v option with fix deform with this pair style.
<DT><I>Using pair lubricate/poly with inconsistent fix deform remap option</I>
@ -6772,6 +6981,10 @@ before the simulation has been setup.
<DD>Only equal-style variables can be used.
<DT><I>Variable for fix gravity is invalid style</I>
<DD>Only equal-style variables can be used.
<DT><I>Variable for fix indent is invalid style</I>
<DD>Only equal-style variables can be used.
@ -6792,6 +7005,14 @@ before the simulation has been setup.
<DD>Only equal-style variables can be used.
<DT><I>Variable for fix temp/berendsen is invalid style</I>
<DD>Only equal-style variables can be used.
<DT><I>Variable for fix temp/rescale is invalid style</I>
<DD>Only equal-style variables can be used.
<DT><I>Variable for fix wall is invalid style</I>
<DD>Only equal-style variables can be used.
@ -6812,6 +7033,10 @@ before the simulation has been setup.
<DD>Self-explanatory.
<DT><I>Variable for restart is invalid style</I>
<DD>Only equal-style variables can be used.
<DT><I>Variable for thermo every is invalid style</I>
<DD>Only equal-style variables can be used.
@ -6912,6 +7137,10 @@ before the simulation has been setup.
<DD>Self-explanatory.
<DT><I>Variable name for fix gravity does not exist</I>
<DD>Self-explanatory.
<DT><I>Variable name for fix indent does not exist</I>
<DD>Self-explanatory.
@ -6932,6 +7161,14 @@ before the simulation has been setup.
<DD>Self-explanatory.
<DT><I>Variable name for fix temp/berendsen does not exist</I>
<DD>Self-explanatory.
<DT><I>Variable name for fix temp/rescale does not exist</I>
<DD>Self-explanatory.
<DT><I>Variable name for fix wall does not exist</I>
<DD>Self-explanatory.
@ -6948,6 +7185,10 @@ before the simulation has been setup.
<DD>Self-explanatory.
<DT><I>Variable name for restart does not exist</I>
<DD>Self-explanatory.
<DT><I>Variable name for thermo every does not exist</I>
<DD>Self-explanatory.
@ -7009,6 +7250,11 @@ variable doc page for ideas on how to make this work.
<DD>Self-explanatory.
<DT><I>Water H epsilon must be 0.0 for pair style lj/cut/coul/long/tip4p</I>
<DD>This is because LAMMPS does not compute the Lennard-Jones interactions
with these particles for efficiency reasons.
<DT><I>World variable count doesn't match # of partitions</I>
<DD>A world-style variable must specify a number of values equal to the
@ -7035,6 +7281,10 @@ read_restart, or create_box command.
includes atoms with no molecule ID. This is probably not what you
want.
<DT><I>Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero</I>
<DD>Self-explantory.
<DT><I>Broken bonds will not alter angles, dihedrals, or impropers</I>
<DD>See the doc page for fix bond/break for more info on this
@ -7046,6 +7296,14 @@ restriction.
The solution is to check for building the regular neighbor lists
more frequently.
<DT><I>Cannot include log terms without 1/r terms; setting flagHI to 1</I>
<DD>Self-explanatory.
<DT><I>Cannot include log terms without 1/r terms; setting flagHI to 1.</I>
<DD>Self-explanatory.
<DT><I>Compute cna/atom cutoff may be too large to find ghost atom neighbors</I>
<DD>The neighbor cutoff used may not encompass enough ghost atoms
@ -7112,9 +7370,18 @@ of a molecule.
<DT><I>Fix recenter should come after all other integration fixes</I>
<DD>Other fixes may change the position of the center-of-mass, so
<DD>Other fixes may change the position of the center-of-mass, so
fix recenter should come last.
<DT><I>Fix shake with rRESPA computes invalid pressures</I>
<DD>This is a known bug in LAMMPS that has not yet been fixed. If you use
SHAKE with rRESPA and perform a constant volume simulation (e.g. using
fix npt) this only affects the output pressure, not the dynamics of
the simulation. If you use SHAKE with rRESPA and perform a constant
pressure simulation (e.g. using fix npt) then you will be
equilibrating to the wrong volume.
<DT><I>Fix srd SRD moves may trigger frequent reneighboring</I>
<DD>This is because the SRD particles may move long distances.