# 13.4. Warning messages

This is an alphabetic list of the WARNING messages LAMMPS prints out and the reason why. If the explanation here is not sufficient, the documentation for the offending command may help. Warning messages also list the source file and line number where the warning was generated. For example, a message like this:

WARNING: Bond atom missing in box size check (domain.cpp:187)


means that line #187 in the file src/domain.cpp generated the error. Looking in the source code may help you figure out what went wrong.

Note that warning messages from user-contributed packages are not listed here. If such a warning occurs and is not self-explanatory, you’ll need to look in the source code or contact the author of the package.

Doc page with ERROR messages

Adjusting Coulombic cutoff for MSM, new cutoff = %g

The adjust/cutoff command is turned on and the Coulombic cutoff has been adjusted to match the user-specified accuracy.

Angle atoms missing at step %ld

One or more of 3 atoms needed to compute a particular angle are missing on this processor. Typically this is because the pairwise cutoff is set too short or the angle has blown apart and an atom is too far away.

Angle style in data file differs from currently defined angle style

Self-explanatory.

Atom style in data file differs from currently defined atom style

Self-explanatory.

Bond atom missing in box size check

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.

Bond atom missing in image check

The 2nd atom in 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.

Bond atoms missing at step %ld

The 2nd atom 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.

Bond style in data file differs from currently defined bond style

Self-explanatory.

Bond/angle/dihedral extent > half of periodic box length

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.

Bond/react: Atom affected by reaction too close to template edge

This means an atom which changes type or connectivity during the reaction is too close to an ‘edge’ atom defined in the superimpose file. This could cause incorrect assignment of bonds, angle, etc. Generally, this means you must include more atoms in your templates, such that there are at least two atoms between each atom involved in the reaction and an edge atom.

Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero

Self-explanatory.

Calling write_dump before a full system init.

The write_dump command is used before the system has been fully initialized as part of a ‘run’ or ‘minimize’ command. Not all dump styles and features are fully supported at this point and thus the command may fail or produce incomplete or incorrect output. Insert a “run 0” command, if a full system init is required.

Cannot count rigid body degrees-of-freedom before bodies are fully initialized

This means the temperature associated with the rigid bodies may be incorrect on this timestep.

Cannot count rigid body degrees-of-freedom before bodies are initialized

This means the temperature associated with the rigid bodies may be incorrect on this timestep.

Cannot include log terms without 1/r terms; setting flagHI to 1

Self-explanatory.

Cannot include log terms without 1/r terms; setting flagHI to 1.

Self-explanatory.

Charges are set, but coulombic solver is not used

Self-explanatory.

Charges did not converge at step %ld: %lg

Self-explanatory.

Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost

The communication cutoff defaults to the maximum of what is inferred from pair and bond styles (will be zero, if none are defined) and what is specified via comm_modify cutoff (defaults to 0.0). If this results to 0.0, no ghost atoms will be generated and LAMMPS may lose atoms or use incorrect periodic images of atoms in interaction lists. To avoid, either use pair style zero with a suitable cutoff or use comm_modify cutoff.

Communication cutoff is too small for SNAP micro load balancing, increased to %lf

Self-explanatory.

Compute cna/atom cutoff may be too large to find ghost atom neighbors

The neighbor cutoff used may not encompass enough ghost atoms to perform this operation correctly.

Computing temperature of portions of rigid bodies

The group defined by the temperature compute does not encompass all the atoms in one or more rigid bodies, so the change in degrees-of-freedom for the atoms in those partial rigid bodies will not be accounted for.

Create_bonds max distance > minimum neighbor cutoff

This means atom pairs for some atom types may not be in the neighbor list and thus no bond can be created between them.

Delete_atoms cutoff > minimum neighbor cutoff

This means atom pairs for some atom types may not be in the neighbor list and thus an atom in that pair cannot be deleted.

Dihedral atoms missing at step %ld

One or more of 4 atoms needed to compute a particular dihedral are missing on this processor. Typically this is because the pairwise cutoff is set too short or the dihedral has blown apart and an atom is too far away.

Dihedral problem

Conformation of the 4 listed dihedral atoms is extreme; you may want to check your simulation geometry.

Dihedral problem: %d %ld %d %d %d %d

Conformation of the 4 listed dihedral atoms is extreme; you may want to check your simulation geometry.

Dihedral style in data file differs from currently defined dihedral style

Self-explanatory.

Dump dcd/xtc timestamp may be wrong with fix dt/reset

If the fix changes the timestep, the dump dcd file will not reflect the change.

Energy due to X extra global DOFs will be included in minimizer energies

When using fixes like box/relax, the potential energy used by the minimizer is augmented by an additional energy provided by the fix. Thus the printed converged energy may be different from the total potential energy.

Estimated error in splitting of dispersion coeffs is %g

Error is greater than 0.0001 percent.

Ewald/disp Newton solver failed, using old method to estimate g_ewald

Self-explanatory. Choosing a different cutoff value may help.

FENE bond too long

A FENE bond has stretched dangerously far. It’s interaction strength will be truncated to attempt to prevent the bond from blowing up.

FENE bond too long: %ld %d %d %g

A FENE bond has stretched dangerously far. It’s interaction strength will be truncated to attempt to prevent the bond from blowing up.

FENE bond too long: %ld %g

A FENE bond has stretched dangerously far. It’s interaction strength will be truncated to attempt to prevent the bond from blowing up.

Fix SRD walls overlap but fix srd overlap not set

You likely want to set this in your input script.

Fix bond/swap will ignore defined angles

See the doc page for fix bond/swap for more info on this restriction.

Fix deposit near setting < possible overlap separation %g

This test is performed for finite size particles with a diameter, not for point particles. The near setting is smaller than the particle diameter which can lead to overlaps.

Fix evaporate may delete atom with non-zero molecule ID

This is probably an error, since you should not delete only one atom of a molecule.

Fix gcmc using full_energy option

Fix gcmc has automatically turned on the full_energy option since it is required for systems like the one specified by the user. User input included one or more of the following: kspace, triclinic, a hybrid pair style, an eam pair style, or no “single” function for the pair style.

Fix property/atom mol or charge w/out ghost communication

A model typically needs these properties defined for ghost atoms.

Fix qeq CG convergence failed (%g) after %d iterations at %ld step

Self-explanatory.

Fix qeq has non-zero lower Taper radius cutoff

Absolute value must be <= 0.01.

Fix qeq has very low Taper radius cutoff

Value should typically be >= 5.0.

Fix qeq/dynamic tolerance may be too small for damped dynamics

Self-explanatory.

Fix qeq/fire tolerance may be too small for damped fires

Self-explanatory.

Fix rattle should come after all other integration fixes

This fix is designed to work after all other integration fixes change atom positions. Thus it should be the last integration fix specified. If not, it will not satisfy the desired constraints as well as it otherwise would.

Fix recenter should come after all other integration fixes

Other fixes may change the position of the center-of-mass, so fix recenter should come last.

Fix srd SRD moves may trigger frequent reneighboring

This is because the SRD particles may move long distances.

Fix srd grid size > 1/4 of big particle diameter

This may cause accuracy problems.

Fix srd particle moved outside valid domain

This may indicate a problem with your simulation parameters.

Fix srd particles may move > big particle diameter

This may cause accuracy problems.

Fix srd viscosity < 0.0 due to low SRD density

This may cause accuracy problems.

Fixes cannot send data in Kokkos communication, switching to classic communication

This is current restriction with Kokkos.

For better accuracy use ‘pair_modify table 0’

The user-specified force accuracy cannot be achieved unless the table feature is disabled by using ‘pair_modify table 0’.

Geometric mixing assumed for 1/r^6 coefficients

Self-explanatory.

Group for fix_modify temp != fix group

The fix_modify command is specifying a temperature computation that computes a temperature on a different group of atoms than the fix itself operates on. This is probably not what you want to do.

H matrix size has been exceeded: m_fill=%d H.m=%dn

This is the size of the matrix.

Ignoring unknown or incorrect info command flag

Self-explanatory. An unknown argument was given to the info command. Compare your input with the documentation.

Improper atoms missing at step %ld

One or more of 4 atoms needed to compute a particular improper are missing on this processor. Typically this is because the pairwise cutoff is set too short or the improper has blown apart and an atom is too far away.

Improper problem: %d %ld %d %d %d %d

Conformation of the 4 listed improper atoms is extreme; you may want to check your simulation geometry.

Improper style in data file differs from currently defined improper style

Self-explanatory.

Inconsistent image flags

The image flags for a pair on bonded atoms appear to be inconsistent. Inconsistent means that when the coordinates of the two atoms are unwrapped using the image flags, the two atoms are far apart. Specifically they are further apart than half a periodic box length. Or they are more than a box length apart in a non-periodic dimension. This is usually due to the initial data file not having correct image flags for the 2 atoms in a bond that straddles a periodic boundary. They should be different by 1 in that case. This is a warning because inconsistent image flags will not cause problems for dynamics or most LAMMPS simulations. However they can cause problems when such atoms are used with the fix rigid or replicate commands. Note that if you have an infinite periodic crystal with bonds then it is impossible to have fully consistent image flags, since some bonds will cross periodic boundaries and connect two atoms with the same image flag.

KIM Model does not provide ‘energy’; Potential energy will be zero

Self-explanatory.

KIM Model does not provide ‘forces’; Forces will be zero

Self-explanatory.

KIM Model does not provide ‘particleEnergy’; energy per atom will be zero

Self-explanatory.

KIM Model does not provide ‘particleVirial’; virial per atom will be zero

Self-explanatory.

Kspace_modify slab param < 2.0 may cause unphysical behavior

The kspace_modify slab parameter should be larger to insure periodic grids padded with empty space do not overlap.

Less insertions than requested

The fix pour command was unsuccessful at finding open space for as many particles as it tried to insert.

Library error in lammps_gather_atoms

This library function cannot be used if atom IDs are not defined or are not consecutively numbered.

Library error in lammps_scatter_atoms

This library function cannot be used if atom IDs are not defined or are not consecutively numbered, or if no atom map is defined. See the atom_modify command for details about atom maps.

Lost atoms via change_box: original %ld current %ld

The command options you have used caused atoms to be lost.

Lost atoms via displace_atoms: original %ld current %ld

The command options you have used caused atoms to be lost.

Lost atoms: original %ld current %ld

Lost atoms are checked for each time thermo output is done. See the thermo_modify lost command for options. Lost atoms usually indicate bad dynamics, e.g. atoms have been blown far out of the simulation box, or moved further than one processor’s sub-domain away before reneighboring.

MSM mesh too small, increasing to 2 points in each direction

Self-explanatory.

Mismatch between velocity and compute groups

The temperature computation used by the velocity command will not be on the same group of atoms that velocities are being set for.

Mixing forced for lj coefficients

Self-explanatory.

Molecule attributes do not match system attributes

An attribute is specified (e.g. diameter, charge) that is not defined for the specified atom style.

Molecule has bond topology but no special bond settings

This means the bonded atoms will not be excluded in pair-wise interactions.

Molecule template for create_atoms has multiple molecules

The create_atoms command will only create molecules of a single type, i.e. the first molecule in the template.

Molecule template for fix gcmc has multiple molecules

The fix gcmc command will only create molecules of a single type, i.e. the first molecule in the template.

Molecule template for fix shake has multiple molecules

The fix shake command will only recognize molecules of a single type, i.e. the first molecule in the template.

More than one compute centro/atom

It is not efficient to use compute centro/atom more than once.

More than one compute cluster/atom

It is not efficient to use compute cluster/atom more than once.

More than one compute cna/atom defined

It is not efficient to use compute cna/atom more than once.

More than one compute contact/atom

It is not efficient to use compute contact/atom more than once.

More than one compute coord/atom

It is not efficient to use compute coord/atom more than once.

More than one compute damage/atom

It is not efficient to use compute ke/atom more than once.

More than one compute dilatation/atom

Self-explanatory.

More than one compute erotate/sphere/atom

It is not efficient to use compute erorate/sphere/atom more than once.

More than one compute hexorder/atom

It is not efficient to use compute hexorder/atom more than once.

More than one compute ke/atom

It is not efficient to use compute ke/atom more than once.

More than one compute orientorder/atom

It is not efficient to use compute orientorder/atom more than once.

More than one compute plasticity/atom

Self-explanatory.

More than one compute sna/atom

Self-explanatory.

Self-explanatory.

More than one compute snav/atom

Self-explanatory.

More than one fix poems

It is not efficient to use fix poems more than once.

More than one fix rigid

It is not efficient to use fix rigid more than once.

Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies

This is because excluding specific pair interactions also excludes them from long-range interactions which may not be the desired effect. The special_bonds command handles this consistently by insuring excluded (or weighted) 1-2, 1-3, 1-4 interactions are treated consistently by both the short-range pair style and the long-range solver. This is not done for exclusions of charged atom pairs via the neigh_modify exclude command.

New thermo_style command, previous thermo_modify settings will be lost

If a thermo_style command is used after a thermo_modify command, the settings changed by the thermo_modify command will be reset to their default values. This is because the thermo_modify command acts on the currently defined thermo style, and a thermo_style command creates a new style.

No Kspace calculation with verlet/split

The 2nd partition performs a kspace calculation so the kspace_style command must be used.

No automatic unit conversion to XTC file format conventions possible for units lj

This means no scaling will be performed.

No fixes defined, atoms won’t move

If you are not using a fix like nve, nvt, npt then atom velocities and coordinates will not be updated during timestepping.

No joints between rigid bodies, use fix rigid instead

The bodies defined by fix poems are not connected by joints. POEMS will integrate the body motion, but it would be more efficient to use fix rigid.

Not using real units with pair reax

This is most likely an error, unless you have created your own ReaxFF parameter file in a different set of units.

Number of MSM mesh points changed to be a multiple of 2

MSM requires that the number of grid points in each direction be a multiple of two and the number of grid points in one or more directions have been adjusted to meet this requirement.

This environment variable must be set appropriately to use the USER-OMP package.

One or more atoms are time integrated more than once

This is probably an error since you typically do not want to advance the positions or velocities of an atom more than once per timestep.

One or more chunks do not contain all atoms in molecule

This may not be what you intended.

One or more dynamic groups may not be updated at correct point in timestep

If there are other fixes that act immediately after the initial stage of time integration within a timestep (i.e. after atoms move), then the command that sets up the dynamic group should appear after those fixes. This will insure that dynamic group assignments are made after all atoms have moved.

One or more respa levels compute no forces

This is computationally inefficient.

Pair COMB charge %.10f with force %.10f hit max barrier

Something is possibly wrong with your model.

Pair COMB charge %.10f with force %.10f hit min barrier

Something is possibly wrong with your model.

Pair brownian needs newton pair on for momentum conservation

Self-explanatory.

Pair dpd needs newton pair on for momentum conservation

Self-explanatory.

Pair dsmc: num_of_collisions > number_of_A

Collision model in DSMC is breaking down.

Pair dsmc: num_of_collisions > number_of_B

Collision model in DSMC is breaking down.

Pair style in data file differs from currently defined pair style

Self-explanatory.

Pair style restartinfo set but has no restart support

This pair style has a bug, where it does not support reading and writing information to a restart file, but does not set the member variable “restartinfo” to 0 as required in that case.

Particle deposition was unsuccessful

The fix deposit command was not able to insert as many atoms as needed. The requested volume fraction may be too high, or other atoms may be in the insertion region.

Proc sub-domain size < neighbor skin, could lead to lost atoms

The decomposition of the physical domain (likely due to load balancing) has led to a processor’s sub-domain being smaller than the neighbor skin in one or more dimensions. Since reneighboring is triggered by atoms moving the skin distance, this may lead to lost atoms, if an atom moves all the way across a neighboring processor’s sub-domain before reneighboring is triggered.

Reducing PPPM order b/c stencil extends beyond nearest neighbor processor

This may lead to a larger grid than desired. See the kspace_modify overlap command to prevent changing of the PPPM order.

Reducing PPPMDisp Coulomb order b/c stencil extends beyond neighbor processor

This may lead to a larger grid than desired. See the kspace_modify overlap command to prevent changing of the PPPM order.

Reducing PPPMDisp dispersion order b/c stencil extends beyond neighbor processor

This may lead to a larger grid than desired. See the kspace_modify overlap command to prevent changing of the PPPM order.

Replacing a fix, but new group != old group

The ID and style of a fix match for a fix you are changing with a fix command, but the new group you are specifying does not match the old group.

Replicating in a non-periodic dimension

The parameters for a replicate command will cause a non-periodic dimension to be replicated; this may cause unwanted behavior.

Resetting reneighboring criteria during PRD

A PRD simulation requires that neigh_modify settings be delay = 0, every = 1, check = yes. Since these settings were not in place, LAMMPS changed them and will restore them to their original values after the PRD simulation.

A TAD simulation requires that neigh_modify settings be delay = 0, every = 1, check = yes. Since these settings were not in place, LAMMPS changed them and will restore them to their original values after the PRD simulation.

Resetting reneighboring criteria during minimization

Minimization requires that neigh_modify settings be delay = 0, every = 1, check = yes. Since these settings were not in place, LAMMPS changed them and will restore them to their original values after the minimization.

Restart file used different # of processors

The restart file was written out by a LAMMPS simulation running on a different number of processors. Due to round-off, the trajectories of your restarted simulation may diverge a little more quickly than if you ran on the same # of processors.

Restart file used different 3d processor grid

The restart file was written out by a LAMMPS simulation running on a different 3d grid of processors. Due to round-off, the trajectories of your restarted simulation may diverge a little more quickly than if you ran on the same # of processors.

Restart file used different boundary settings, using restart file values

Your input script cannot change these restart file settings.

Restart file used different newton bond setting, using restart file value

The restart file value will override the setting in the input script.

Restart file used different newton pair setting, using input script value

The input script value will override the setting in the restart file.

Restrain problem: %d %ld %d %d %d %d

Conformation of the 4 listed dihedral atoms is extreme; you may want to check your simulation geometry.

Running PRD with only one replica

This is allowed, but you will get no parallel speed-up.

SRD bin shifting turned on due to small lamda

This is done to try to preserve accuracy.

SRD bin size for fix srd differs from user request

Fix SRD had to adjust the bin size to fit the simulation box. See the cubic keyword if you want this message to be an error vs warning.

SRD bins for fix srd are not cubic enough

The bin shape is not within tolerance of cubic. See the cubic keyword if you want this message to be an error vs warning.

SRD particle %d started inside big particle %d on step %ld bounce %d

See the inside keyword if you want this message to be an error vs warning.

SRD particle %d started inside wall %d on step %ld bounce %d

See the inside keyword if you want this message to be an error vs warning.

Shake determinant < 0.0

The determinant of the quadratic equation being solved for a single cluster specified by the fix shake command is numerically suspect. LAMMPS will set it to 0.0 and continue.

Shell command ‘%s’ failed with error ‘%s’

Self-explanatory.

Shell command returned with non-zero status

This may indicate the shell command did not operate as expected.

Should not allow rigid bodies to bounce off reflecting walls

LAMMPS allows this, but their dynamics are not computed correctly.

Should not use fix nve/limit with fix shake or fix rattle

This will lead to invalid constraint forces in the SHAKE/RATTLE computation.

Simulations might be very slow because of large number of structure factors

Self-explanatory.

Slab correction not needed for MSM

Slab correction is intended to be used with Ewald or PPPM and is not needed by MSM.

System is not charge neutral, net charge = %g

The total charge on all atoms on the system is not 0.0. For some KSpace solvers this is only a warning.

Table inner cutoff >= outer cutoff

You specified an inner cutoff for a Coulombic table that is longer than the global cutoff. Probably not what you wanted.

Temperature for MSST is not for group all

User-assigned temperature to MSST fix does not compute temperature for all atoms. Since MSST computes a global pressure, the kinetic energy contribution from the temperature is assumed to also be for all atoms. Thus the pressure used by MSST could be inaccurate.

Temperature for NPT is not for group all

User-assigned temperature to NPT fix does not compute temperature for all atoms. Since NPT computes a global pressure, the kinetic energy contribution from the temperature is assumed to also be for all atoms. Thus the pressure used by NPT could be inaccurate.

Temperature for fix modify is not for group all

The temperature compute is being used with a pressure calculation which does operate on group all, so this may be inconsistent.

Temperature for thermo pressure is not for group all

User-assigned temperature to thermo via the thermo_modify command does not compute temperature for all atoms. Since thermo computes a global pressure, the kinetic energy contribution from the temperature is assumed to also be for all atoms. Thus the pressure printed by thermo could be inaccurate.

The fix ave/spatial command has been replaced by the more flexible fix ave/chunk and compute chunk/atom commands – fix ave/spatial will be removed in the summer of 2015

Self-explanatory.

The minimizer does not re-orient dipoles when using fix efield

This means that only the atom coordinates will be minimized, not the orientation of the dipoles.

Too many common neighbors in CNA %d times

More than the maximum # of neighbors was found multiple times. This was unexpected.

Too many inner timesteps in fix ttm

Self-explanatory.

Too many neighbors in CNA for %d atoms

More than the maximum # of neighbors was found multiple times. This was unexpected.

Triclinic box skew is large

The displacement in a skewed direction is normally required to be less than half the box length in that dimension. E.g. the xy tilt must be between -half and +half of the x box length. You have relaxed the constraint using the box tilt command, but the warning means that a LAMMPS simulation may be inefficient as a result.

Use special bonds = 0,1,1 with bond style fene

Most FENE models need this setting for the special_bonds command.

Use special bonds = 0,1,1 with bond style fene/expand

Most FENE models need this setting for the special_bonds command.

Using a many-body potential with bonds/angles/dihedrals and special_bond exclusions

This is likely not what you want to do. The exclusion settings will eliminate neighbors in the neighbor list, which the many-body potential needs to calculated its terms correctly.

Using compute temp/deform with inconsistent fix deform remap option

Fix nvt/sllod assumes deforming atoms have a velocity profile provided by “remap v” or “remap none” as a fix deform option.

Using compute temp/deform with no fix deform defined

This is probably an error, since it makes little sense to use compute temp/deform in this case.

Using fix srd with box deformation but no SRD thermostat

The deformation will heat the SRD particles so this can be dangerous.

Using kspace solver on system with no charge

Self-explanatory.

Using largest cut-off for lj/long/dipole/long long long

Self-explanatory.

Using largest cutoff for buck/long/coul/long

Self-explanatory.

Using largest cutoff for lj/long/coul/long

Self-explanatory.

Using largest cutoff for pair_style lj/long/tip4p/long

Self-explanatory.

Using package gpu without any pair style defined

Self-explanatory.

Using pair potential shift with pair_modify compute no

The shift effects will thus not be computed.

Using pair tail corrections with nonperiodic system

This is probably a bogus thing to do, since tail corrections are computed by integrating the density of a periodic system out to infinity.

Using pair tail corrections with pair_modify compute no

The tail corrections will thus not be computed.

pair style reax is now deprecated and will soon be retired. Users should switch to pair_style reax/c

Self-explanatory.