11.7. Warning messages — LAMMPS documentation

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# 11.7. Warning messages

This is an alphabetic list of some 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. This is a historic list and no longer updated. Instead the LAMMPS developers are trying to provide more details right with the error message or link to a paragraph with detailed explanations.

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.

Please also see the 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 three 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.

Angles are defined but no angle style is set

  The topology contains angles, but there are no angle forces computed since there was no angle_style command.

Bond atom missing in box size check

  The second 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 atom missing in image check

  The second 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 second 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.

Bonds are defined but no bond style is set

  The topology contains bonds, but there are no bond forces computed since there was no bond_style command.

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.

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.

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 shorter than a bond length based estimate. This may lead to errors.

  Since LAMMPS stores topology data with individual atoms, all atoms comprising a bond, angle, dihedral or improper must be present on any subdomain that “owns” the atom with the information, either as a local or a ghost atom. The communication cutoff is what determines up to what distance from a subdomain boundary ghost atoms are created. The communication cutoff is by default the largest non-bonded cutoff plus the neighbor skin distance, but for short or non-bonded cutoffs and/or long bonds, this may not be sufficient. This warning indicates that there is an increased risk of a simulation stopping unexpectedly because of Bond/Angle/Dihedral/Improper atoms missing. It can be silenced by manually setting the communication cutoff via comm_modify cutoff. However, since the heuristic used to determine the estimate is not always accurate, it is not changed automatically and the warning may be ignored depending on the specific system being simulated.

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.

Dihedrals are defined but no dihedral style is set

  The topology contains dihedrals, but there are no dihedral forces computed since there was no dihedral_style command.

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.

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/create is used multiple times or with fix bond/break - may not work as expected

  When using fix bond/create multiple times or in combination with fix bond/break, the individual fix instances do not share information about changes they made at the same time step and thus it may result in unexpected behavior.

Fix 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.

Fix bond/swap will ignore defined angles

  See the 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 langevin gjf using random gaussians is not implemented with kokkos

  This will most likely cause errors in kinetic fluctuations.

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

  A model typically needs these properties defined for ghost atoms.

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 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’.

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.

Impropers are defined but no improper style is set

  The topology contains impropers, but there are no improper forces computed since there was no improper_style command.

Increasing communication cutoff for GPU style

  The pair style has increased the communication cutoff to be consistent with the communication cutoff requirements for this pair style when run on the GPU.

Kspace_modify slab param < 2.0 may cause unphysical behavior

  The kspace_modify slab parameter should be larger to ensure 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.

Likewise 1-2 special neighbor interactions != 1.0

  The topology contains bonds, but there is no bond style defined and a 1-2 special neighbor scaling factor was not 1.0. This means that pair style interactions may have scaled or missing pairs in the neighbor list in expectation of interactions for those pairs being computed from the bond style.

Likewise 1-3 special neighbor interactions != 1.0

  The topology contains angles, but there is no angle style defined and a 1-3 special neighbor scaling factor was not 1.0. This means that pair style interactions may have scaled or missing pairs in the neighbor list in expectation of interactions for those pairs being computed from the angle style.

Likewise 1-4 special neighbor interactions != 1.0

  The topology contains dihedrals, but there is no dihedral style defined and a 1-4 special neighbor scaling factor was not 1.0. This means that pair style interactions may have scaled or missing pairs in the neighbor list in expectation of interactions for those pairs being computed from the dihedral style.

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 subdomain away before reneighboring.

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.

Molecule has bond topology but no special bond settings

  This means the bonded atoms will not be excluded in pairwise 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 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 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 ensuring 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 second 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 reaxff

  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.

OMP_NUM_THREADS environment is not set.

  This environment variable must be set appropriately to use the OPENMP 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 ensure 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 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 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 subdomain 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 subdomain 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 subdomain 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.

Resetting reneighboring criteria during TAD

  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 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.

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 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 neighbors in CNA for %d atoms

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

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 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.