813 lines
34 KiB
ReStructuredText
813 lines
34 KiB
ReStructuredText
Warning messages
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================
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This is an alphabetic list of the WARNING messages LAMMPS prints out
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and the reason why. If the explanation here is not sufficient, the
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documentation for the offending command may help. Warning messages
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also list the source file and line number where the warning was
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generated. For example, a message like this:
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.. parsed-literal::
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WARNING: Bond atom missing in box size check (domain.cpp:187)
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means that line #187 in the file src/domain.cpp generated the error.
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Looking in the source code may help you figure out what went wrong.
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Doc page with :doc:`ERROR messages <Errors_messages>`
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----------
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*Adjusting Coulombic cutoff for MSM, new cutoff = %g*
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The adjust/cutoff command is turned on and the Coulombic cutoff has been
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adjusted to match the user-specified accuracy.
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*Angle atoms missing at step %ld*
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One or more of 3 atoms needed to compute a particular angle are
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missing on this processor. Typically this is because the pairwise
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cutoff is set too short or the angle has blown apart and an atom is
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too far away.
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*Angle style in data file differs from currently defined angle style*
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Self-explanatory.
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*Angles are defined but no angle style is set*
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The topology contains angles, but there are no angle forces computed
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since there was no angle_style command.
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*Atom style in data file differs from currently defined atom style*
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Self-explanatory.
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*Bond atom missing in box size check*
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The second atom needed to compute a particular bond is missing on this
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processor. Typically this is because the pairwise cutoff is set too
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short or the bond has blown apart and an atom is too far away.
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*Bond atom missing in image check*
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The second atom in a particular bond is missing on this processor.
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Typically this is because the pairwise cutoff is set too short or the
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bond has blown apart and an atom is too far away.
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*Bond atoms missing at step %ld*
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The second atom needed to compute a particular bond is missing on this
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processor. Typically this is because the pairwise cutoff is set too
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short or the bond has blown apart and an atom is too far away.
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*Bond style in data file differs from currently defined bond style*
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Self-explanatory.
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*Bonds are defined but no bond style is set*
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The topology contains bonds, but there are no bond forces computed
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since there was no bond_style command.
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*Bond/angle/dihedral extent > half of periodic box length*
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This is a restriction because LAMMPS can be confused about which image
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of an atom in the bonded interaction is the correct one to use.
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"Extent" in this context means the maximum end-to-end length of the
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bond/angle/dihedral. LAMMPS computes this by taking the maximum bond
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length, multiplying by the number of bonds in the interaction (e.g. 3
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for a dihedral) and adding a small amount of stretch.
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*Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero*
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Self-explanatory.
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*Calling write_dump before a full system init.*
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The write_dump command is used before the system has been fully
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initialized as part of a 'run' or 'minimize' command. Not all dump
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styles and features are fully supported at this point and thus the
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command may fail or produce incomplete or incorrect output. Insert
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a "run 0" command, if a full system init is required.
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*Cannot count rigid body degrees-of-freedom before bodies are fully initialized*
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This means the temperature associated with the rigid bodies may be
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incorrect on this timestep.
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*Cannot count rigid body degrees-of-freedom before bodies are initialized*
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This means the temperature associated with the rigid bodies may be
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incorrect on this timestep.
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*Cannot include log terms without 1/r terms; setting flagHI to 1*
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Self-explanatory.
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*Cannot include log terms without 1/r terms; setting flagHI to 1.*
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Self-explanatory.
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*Charges are set, but coulombic solver is not used*
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Self-explanatory.
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*Charges did not converge at step %ld: %lg*
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Self-explanatory.
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*Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost*
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The communication cutoff defaults to the maximum of what is inferred from
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pair and bond styles (will be zero, if none are defined) and what is specified
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via :doc:`comm_modify cutoff <comm_modify>` (defaults to 0.0). If this results
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to 0.0, no ghost atoms will be generated and LAMMPS may lose atoms or use
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incorrect periodic images of atoms in interaction lists. To avoid, either use
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:doc:`pair style zero <pair_zero>` with a suitable cutoff or use :doc:`comm_modify cutoff <comm_modify>`.
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*Communication cutoff is shorter than a bond length based estimate. This may lead to errors.*
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Since LAMMPS stores topology data with individual atoms, all atoms
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comprising a bond, angle, dihedral or improper must be present on any
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subdomain that "owns" the atom with the information, either as a
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local or a ghost atom. The communication cutoff is what determines up
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to what distance from a subdomain boundary ghost atoms are created.
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The communication cutoff is by default the largest non-bonded cutoff
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plus the neighbor skin distance, but for short or non-bonded cutoffs
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and/or long bonds, this may not be sufficient. This warning indicates
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that there is an increased risk of a simulation stopping unexpectedly
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because of Bond/Angle/Dihedral/Improper atoms missing. It can be
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silenced by manually setting the communication cutoff via
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:doc:`comm_modify cutoff <comm_modify>`. However, since the
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heuristic used to determine the estimate is not always accurate, it
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is not changed automatically and the warning may be ignored depending
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on the specific system being simulated.
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*Communication cutoff is too small for SNAP micro load balancing, increased to %lf*
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Self-explanatory.
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*Compute cna/atom cutoff may be too large to find ghost atom neighbors*
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The neighbor cutoff used may not encompass enough ghost atoms
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to perform this operation correctly.
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*Computing temperature of portions of rigid bodies*
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The group defined by the temperature compute does not encompass all
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the atoms in one or more rigid bodies, so the change in
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degrees-of-freedom for the atoms in those partial rigid bodies will
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not be accounted for.
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*Create_bonds max distance > minimum neighbor cutoff*
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This means atom pairs for some atom types may not be in the neighbor
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list and thus no bond can be created between them.
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*Delete_atoms cutoff > minimum neighbor cutoff*
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This means atom pairs for some atom types may not be in the neighbor
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list and thus an atom in that pair cannot be deleted.
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*Dihedral atoms missing at step %ld*
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One or more of 4 atoms needed to compute a particular dihedral are
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missing on this processor. Typically this is because the pairwise
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cutoff is set too short or the dihedral has blown apart and an atom is
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too far away.
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*Dihedral problem*
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Conformation of the 4 listed dihedral atoms is extreme; you may want
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to check your simulation geometry.
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*Dihedral problem: %d %ld %d %d %d %d*
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Conformation of the 4 listed dihedral atoms is extreme; you may want
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to check your simulation geometry.
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*Dihedral style in data file differs from currently defined dihedral style*
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Self-explanatory.
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*Dihedrals are defined but no dihedral style is set*
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The topology contains dihedrals, but there are no dihedral forces computed
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since there was no dihedral_style command.
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*Dump dcd/xtc timestamp may be wrong with fix dt/reset*
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If the fix changes the timestep, the dump dcd file will not
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reflect the change.
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*Energy due to X extra global DOFs will be included in minimizer energies*
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When using fixes like box/relax, the potential energy used by the minimizer
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is augmented by an additional energy provided by the fix. Thus the printed
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converged energy may be different from the total potential energy.
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*Estimated error in splitting of dispersion coeffs is %g*
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Error is greater than 0.0001 percent.
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*Ewald/disp Newton solver failed, using old method to estimate g_ewald*
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Self-explanatory. Choosing a different cutoff value may help.
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*FENE bond too long*
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A FENE bond has stretched dangerously far. It's interaction strength
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will be truncated to attempt to prevent the bond from blowing up.
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*FENE bond too long: %ld %d %d %g*
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A FENE bond has stretched dangerously far. It's interaction strength
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will be truncated to attempt to prevent the bond from blowing up.
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*FENE bond too long: %ld %g*
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A FENE bond has stretched dangerously far. It's interaction strength
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will be truncated to attempt to prevent the bond from blowing up.
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*Fix halt condition for fix-id %s met on step %ld with value %g*
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Self explanatory.
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*Fix SRD walls overlap but fix srd overlap not set*
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You likely want to set this in your input script.
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*Fix bond/create is used multiple times or with fix bond/break - may not work as expected*
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When using fix bond/create multiple times or in combination with
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fix bond/break, the individual fix instances do not share information
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about changes they made at the same time step and thus it may result
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in unexpected behavior.
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*Fix bond/react: Atom affected by reaction too close to template edge*
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This means an atom which changes type or connectivity during the
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reaction is too close to an 'edge' atom defined in the superimpose
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file. This could cause incorrect assignment of bonds, angle, etc.
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Generally, this means you must include more atoms in your templates,
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such that there are at least two atoms between each atom involved in
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the reaction and an edge atom.
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*Fix bond/swap will ignore defined angles*
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See the page for fix bond/swap for more info on this
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restriction.
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*Fix deposit near setting < possible overlap separation %g*
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This test is performed for finite size particles with a diameter, not
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for point particles. The near setting is smaller than the particle
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diameter which can lead to overlaps.
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*Fix evaporate may delete atom with non-zero molecule ID*
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This is probably an error, since you should not delete only one atom
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of a molecule.
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*Fix gcmc using full_energy option*
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Fix gcmc has automatically turned on the full_energy option since it
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is required for systems like the one specified by the user. User input
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included one or more of the following: kspace, triclinic, a hybrid
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pair style, an eam pair style, or no "single" function for the pair
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style.
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*Fix langevin gjf using random gaussians is not implemented with kokkos*
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This will most likely cause errors in kinetic fluctuations.
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*Fix property/atom mol or charge w/out ghost communication*
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A model typically needs these properties defined for ghost atoms.
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*Fix qeq CG convergence failed (%g) after %d iterations at %ld step*
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Self-explanatory.
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*Fix qeq has non-zero lower Taper radius cutoff*
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Absolute value must be <= 0.01.
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*Fix qeq has very low Taper radius cutoff*
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Value should typically be >= 5.0.
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*Fix qeq/dynamic tolerance may be too small for damped dynamics*
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Self-explanatory.
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*Fix qeq/fire tolerance may be too small for damped fires*
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Self-explanatory.
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*Fix rattle should come after all other integration fixes*
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This fix is designed to work after all other integration fixes change
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atom positions. Thus it should be the last integration fix specified.
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If not, it will not satisfy the desired constraints as well as it
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otherwise would.
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*Fix recenter should come after all other integration fixes*
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Other fixes may change the position of the center-of-mass, so
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fix recenter should come last.
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*Fix srd SRD moves may trigger frequent reneighboring*
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This is because the SRD particles may move long distances.
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*Fix srd grid size > 1/4 of big particle diameter*
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This may cause accuracy problems.
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*Fix srd particle moved outside valid domain*
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This may indicate a problem with your simulation parameters.
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*Fix srd particles may move > big particle diameter*
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This may cause accuracy problems.
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*Fix srd viscosity < 0.0 due to low SRD density*
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This may cause accuracy problems.
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*Fixes cannot send data in Kokkos communication, switching to classic communication*
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This is current restriction with Kokkos.
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*For better accuracy use 'pair_modify table 0'*
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The user-specified force accuracy cannot be achieved unless the table
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feature is disabled by using 'pair_modify table 0'.
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*Geometric mixing assumed for 1/r\^6 coefficients*
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Self-explanatory.
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*Group for fix_modify temp != fix group*
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The fix_modify command is specifying a temperature computation that
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computes a temperature on a different group of atoms than the fix
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itself operates on. This is probably not what you want to do.
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*H matrix size has been exceeded: m_fill=%d H.m=%d\n*
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This is the size of the matrix.
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*Ignoring unknown or incorrect info command flag*
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Self-explanatory. An unknown argument was given to the info command.
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Compare your input with the documentation.
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*Improper atoms missing at step %ld*
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One or more of 4 atoms needed to compute a particular improper are
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missing on this processor. Typically this is because the pairwise
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cutoff is set too short or the improper has blown apart and an atom is
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too far away.
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*Improper problem: %d %ld %d %d %d %d*
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Conformation of the 4 listed improper atoms is extreme; you may want
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to check your simulation geometry.
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*Improper style in data file differs from currently defined improper style*
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Self-explanatory.
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*Impropers are defined but no improper style is set*
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The topology contains impropers, but there are no improper forces computed
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since there was no improper_style command.
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*Inconsistent image flags*
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The image flags for a pair on bonded atoms appear to be inconsistent.
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Inconsistent means that when the coordinates of the two atoms are
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unwrapped using the image flags, the two atoms are far apart.
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Specifically they are further apart than half a periodic box length.
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Or they are more than a box length apart in a non-periodic dimension.
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This is usually due to the initial data file not having correct image
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flags for the 2 atoms in a bond that straddles a periodic boundary.
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They should be different by 1 in that case. This is a warning because
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inconsistent image flags will not cause problems for dynamics or most
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LAMMPS simulations. However they can cause problems when such atoms
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are used with the fix rigid or replicate commands. Note that if you
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have an infinite periodic crystal with bonds then it is impossible to
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have fully consistent image flags, since some bonds will cross
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periodic boundaries and connect two atoms with the same image
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flag.
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*Increasing communication cutoff for GPU style*
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The pair style has increased the communication cutoff to be consistent with
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the communication cutoff requirements for this pair style when run on the GPU.
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*KIM Model does not provide 'energy'; Potential energy will be zero*
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Self-explanatory.
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*KIM Model does not provide 'forces'; Forces will be zero*
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Self-explanatory.
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*KIM Model does not provide 'particleEnergy'; energy per atom will be zero*
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Self-explanatory.
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*KIM Model does not provide 'particleVirial'; virial per atom will be zero*
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Self-explanatory.
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*Kspace_modify slab param < 2.0 may cause unphysical behavior*
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The kspace_modify slab parameter should be larger to ensure periodic
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grids padded with empty space do not overlap.
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*Less insertions than requested*
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The fix pour command was unsuccessful at finding open space
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for as many particles as it tried to insert.
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*Library error in lammps_gather_atoms*
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This library function cannot be used if atom IDs are not defined
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or are not consecutively numbered.
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*Library error in lammps_scatter_atoms*
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This library function cannot be used if atom IDs are not defined or
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are not consecutively numbered, or if no atom map is defined. See the
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atom_modify command for details about atom maps.
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*Likewise 1-2 special neighbor interactions != 1.0*
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The topology contains bonds, but there is no bond style defined
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and a 1-2 special neighbor scaling factor was not 1.0. This
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means that pair style interactions may have scaled or missing
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pairs in the neighbor list in expectation of interactions for
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those pairs being computed from the bond style.
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*Likewise 1-3 special neighbor interactions != 1.0*
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The topology contains angles, but there is no angle style defined
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and a 1-3 special neighbor scaling factor was not 1.0. This
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means that pair style interactions may have scaled or missing
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pairs in the neighbor list in expectation of interactions for
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those pairs being computed from the angle style.
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*Likewise 1-4 special neighbor interactions != 1.0*
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The topology contains dihedrals, but there is no dihedral style defined
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and a 1-4 special neighbor scaling factor was not 1.0. This
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means that pair style interactions may have scaled or missing
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pairs in the neighbor list in expectation of interactions for
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those pairs being computed from the dihedral style.
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*Lost atoms via change_box: original %ld current %ld*
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The command options you have used caused atoms to be lost.
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*Lost atoms via displace_atoms: original %ld current %ld*
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The command options you have used caused atoms to be lost.
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*Lost atoms: original %ld current %ld*
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Lost atoms are checked for each time thermo output is done. See the
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thermo_modify lost command for options. Lost atoms usually indicate
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bad dynamics, e.g. atoms have been blown far out of the simulation
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box, or moved further than one processor's subdomain away before
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reneighboring.
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*MSM mesh too small, increasing to 2 points in each direction*
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Self-explanatory.
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*Mismatch between velocity and compute groups*
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The temperature computation used by the velocity command will not be
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on the same group of atoms that velocities are being set for.
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*Mixing forced for lj coefficients*
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Self-explanatory.
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*Molecule attributes do not match system attributes*
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An attribute is specified (e.g. diameter, charge) that is
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not defined for the specified atom style.
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*Molecule has bond topology but no special bond settings*
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This means the bonded atoms will not be excluded in pairwise
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interactions.
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*Molecule template for create_atoms has multiple molecules*
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The create_atoms command will only create molecules of a single type,
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i.e. the first molecule in the template.
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*Molecule template for fix gcmc has multiple molecules*
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The fix gcmc command will only create molecules of a single type,
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i.e. the first molecule in the template.
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*Molecule template for fix shake has multiple molecules*
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The fix shake command will only recognize molecules of a single
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type, i.e. the first molecule in the template.
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*More than one compute centro/atom*
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It is not efficient to use compute centro/atom more than once.
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*More than one compute cluster/atom*
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It is not efficient to use compute cluster/atom more than once.
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*More than one compute cna/atom defined*
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It is not efficient to use compute cna/atom more than once.
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*More than one compute contact/atom*
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It is not efficient to use compute contact/atom more than once.
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*More than one compute coord/atom*
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It is not efficient to use compute coord/atom more than once.
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*More than one compute damage/atom*
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It is not efficient to use compute ke/atom more than once.
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*More than one compute dilatation/atom*
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Self-explanatory.
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*More than one compute erotate/sphere/atom*
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It is not efficient to use compute erorate/sphere/atom more than once.
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*More than one compute hexorder/atom*
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It is not efficient to use compute hexorder/atom more than once.
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*More than one compute ke/atom*
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It is not efficient to use compute ke/atom more than once.
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*More than one compute orientorder/atom*
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It is not efficient to use compute orientorder/atom more than once.
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*More than one compute plasticity/atom*
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Self-explanatory.
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*More than one compute sna/atom*
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Self-explanatory.
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*More than one compute sna/grid*
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Self-explanatory.
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*More than one compute sna/grid/local*
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Self-explanatory.
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*More than one compute snad/atom*
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Self-explanatory.
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*More than one compute snav/atom*
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Self-explanatory.
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*More than one fix poems*
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It is not efficient to use fix poems more than once.
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*More than one fix rigid*
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It is not efficient to use fix rigid more than once.
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*Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies*
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|
This is because excluding specific pair interactions also excludes
|
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them from long-range interactions which may not be the desired effect.
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|
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
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neigh_modify exclude command.
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*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.
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|
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*No Kspace calculation with verlet/split*
|
|
The second partition performs a kspace calculation so the kspace_style
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|
command must be used.
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*No automatic unit conversion to XTC file format conventions possible for units lj*
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This means no scaling will be performed.
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|
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*No fixes defined, atoms won't move*
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If you are not using a fix like nve, nvt, npt then atom velocities and
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coordinates will not be updated during timestepping.
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|
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*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
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|
fix rigid.
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|
|
*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.
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|
|
|
*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.
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|
|
|
*OMP_NUM_THREADS environment is not set.*
|
|
This environment variable must be set appropriately to use the
|
|
OPENMP package.
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|
|
|
*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.
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|
|
|
*One or more chunks do not contain all atoms in molecule*
|
|
This may not be what you intended.
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|
|
|
*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.
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|
|
|
*One or more respa levels compute no forces*
|
|
This is computationally inefficient.
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|
|
|
*Pair COMB charge %.10f with force %.10f hit max barrier*
|
|
Something is possibly wrong with your model.
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|
|
|
*Pair COMB charge %.10f with force %.10f hit min barrier*
|
|
Something is possibly wrong with your model.
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|
|
|
*Pair brownian needs newton pair on for momentum conservation*
|
|
Self-explanatory.
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|
|
|
*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.
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|
|
|
*Pair dsmc: num_of_collisions > number_of_B*
|
|
Collision model in DSMC is breaking down.
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|
|
|
*Pair style in data file differs from currently defined pair style*
|
|
Self-explanatory.
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|
|
|
*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.
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|
|
|
*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.
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|
|
|
*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.
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|
|
|
*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.
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|
|
|
*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.
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|
|
|
*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 '%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.
|
|
|
|
*Specifying an 'subset' value of '0' is equivalent to no 'subset' keyword*
|
|
Self-explanatory.
|
|
|
|
*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.
|