11.2. Error and warning details — LAMMPS documentation

\(\renewcommand{\AA}{\text{Å}}\)

# 11.2. Error and warning details

Many errors or warnings are self-explanatory and thus straightforward to resolve. However, there are also cases, where there is no single cause and explanation, where LAMMPS can only detect symptoms of an error but not the exact cause, or where the explanation needs to be more detailed than what can be fit into a message printed by the program. The following are discussions of such cases.

- Unknown identifier in data file

- Incorrect format in … section of data file

- Illegal variable command: expected X arguments but found Y

- Out of range atoms - cannot compute …

- Too many neighbor bins

- Cannot use neighbor bins - box size << cutoff

- Domain too large for neighbor bins

- Molecule topology/atom exceeds system topology/atom

- Molecule topology type exceeds system topology type

- Molecule attributes do not match system attributes

## 11.2.1. General troubleshooting advice

Below are suggestions that can help to understand the causes of problems with simulations leading to errors or unexpected results.

### Create a small test system

Debugging problems often requires running a simulation many times with small modifications, thus it can be a huge time saver to first assemble a small test system input that has the same issue, but will take much time until it triggers the error condition. Also, it will be easier to see what happens.

### Visualize your trajectory

To better understand what is causing problems, it is often very useful to visualize the system close to the point of failure. It may be necessary to have LAMMPS output trajectory frames rather frequently. To avoid gigantic files, you can use dump_modify delay to delay output until the critical section is reached, and you can use a smaller test system (see above).

### Parallel versus serial

Issues where something is “lost” or “missing” often exhibit that issue only when running in parallel. That doesn’t mean there is no problem, only the symptoms are not triggering an error quickly. Correspondingly, errors may be triggered faster with more processors and thus smaller sub-domains.

### Fast moving atoms

Fast moving atoms may be “lost” or “missing” when their velocity becomes so large that they can cross a sub-domain within one timestep. This often happens when atoms are too close, but atoms may also “move” too fast from sub-domain to sub-domain if the box changes rapidly, e.g. when setting a large an initial box with shrink-wrap boundary conditions that collapses on the first step (in this case the solution is often using ‘m’ instead of ‘s’ as boundary condition).

To reduce the impact of “close contacts”, one can remove those atoms or molecules with something like delete_atoms overlap 0.1 all all. With periodic boundaries, a close contact pair of atoms may be on opposite sides of the simulation box. Another option would be to first run a minimization (aka quench) before starting the MD. Reducing the time step can also help. Many times, one just needs to “ease” the system into a balanced state and can then switch to more aggressive settings.

The speed of atoms during an MD depends on the steepness of the potential function and their mass. Since the positions and velocities of atoms are computed with finite timesteps, they choice of timestep can be too large for a stable numeric integration of the trajectory. In those cases using (temporarily) fix nve/limit or fix dt/reset can help to avoid too large updates or adapt the timestep according to the displacements.

### Pressure, forces, positions becoming NaN of Inf

Some potentials can overflow or have a division by zero with close contacts or bad geometries (for the given force styles in use) leading to forces that can no longer be represented as numbers. Those will show as “NaN” or “Inf”. On most machines, the program will continue, but there is no way to recover from it and those NaN or Inf values will propagate. So-called “soft-core” potentials or the “soft” repulsive-only pair style are less prone for this behavior (depending on the settings in use) and can be used at the beginning of a simulation. Also, single precision numbers can overflow much faster, so for the GPU or INTEL package it may be beneficial to run with double precision initially before switching to mixed or single precision for faster execution when the system has relaxed.

### Communication cutoff

The communication cutoff determines the “overlap” between sub-domains and atoms in these regions are referred to in LAMMPS as “ghost atoms”. This region has to be large enough to contain all atoms of a bond, angle, dihedral or improper with just one atom in the actual sub-domain. Typically, this cutoff is set to the largest cutoff from the pair style(s) plus the neighbor list skin distance and will be more than sufficient for all bonded interactions. But if the pair style cutoff is small this may bot be enough. LAMMPS will print a warning in this case using some heuristic based on the equilibrium bond length, but that may not be sufficient for cases where the force constants are small and thus bonds may be stretched very far. The communication cutoff can be adjusted with comm_modify cutoff <value>, but setting this too large will waste CPU time and memory.

### Neighbor list settings

Every time LAMMPS rebuilds the neighbor lists, LAMMPS will also check for “lost” or “missing” atoms. Thus it can help to use very conservative neighbor list settings and then examine the neighbor list statistics if the neighbor list rebuild can be safely delayed. Rebuilding the neighbor list less frequently (i.e. through increasing the delay or every setting has diminishing returns and increasing risks).

### Ignoring lost atoms

It is tempting to use the thermo_modify lost ignore to avoid that LAMMPS stops with an error. This setting should, however, only be used when atoms should leave the system. In general, ignoring a problem does not solve it.

### Units

A frequent cause for a variety of problems is due to using the wrong units settings for a particular potentials, especially when reading them from a potential file. Most of the (example) potentials bundled with LAMMPS have a “UNITS:” tag that allows LAMMPS to check of the units are consistent with what is intended, but potential files from publications or potential parameter databases may lack this metadata information and thus will not error out or warn when using the wrong setting. Most potential files usually use “metal” units, but some are parameterized for other settings, most notably ReaxFF potentials that use “real” units.

Also, individual parameters for pair_coeff commands taken from publications or other MD software, may need to be converted and sometimes in unexpected ways. Thus some careful checking is recommended.

### No error message printed

In some cases - especially when running in parallel with MPI - LAMMPS may stop without displaying an error. But that does not mean, that there was no error message, instead it is highly likely that the message was written to a buffer and LAMMPS was aborted before the buffer was output. Usually, output buffers are output for every line of output, but sometimes, this is delayed until 4096 or 8192 bytes of output have been accumulated. This buffering for screen and logfile output can be disabled by using the -nb or -nonbuf command-line flag. This is most often needed when debugging crashing multi-replica calculations.

## 11.2.2. Unknown identifier in data file

This error happens when LAMMPS encounters a line of text with an unexpected keyword while reading a data file. This would be either header keywords or section header keywords. This is most commonly due to a mistyped keyword or due to a keyword that is inconsistent with the atom style used.

The header section informs LAMMPS how many entries or lines are expected in the various sections (like Atoms, Masses, Pair Coeffs, etc.) of the data file. If there is a mismatch, LAMMPS will either keep reading beyond the end of a section or stop reading before the section has ended. In that case the next line will not contain a recognized keyword.

Such a mismatch can also happen when the first line of the data is not a comment as required by the format, but a line with a valid header keyword. That would result in LAMMPS expecting, for instance, 0 atoms because the “atoms” header line is the first line and thus treated as a comment.

Another possibility to trigger this error is to have a keyword in the data file that corresponds to a fix (e.g. fix cmap) but the read_data command is missing the (optional) arguments that identify the fix and the header keyword and section keyword or those arguments are inconsistent with the keywords in the data file.

## 11.2.3. Incorrect format in … section of data file

This error happens when LAMMPS reads the contents of a section of a data file and the number of parameters in the line differs from what is expected. This most commonly happens, when the atom style is different from what is expected for a specific data file since changing the atom style usually changes the format of the line.

This error can also happen when the number of entries indicated in the header of a data file (e.g. the number of atoms) is larger than the number of lines provided (e.g. in the corresponding Atoms section) and then LAMMPS will continue reading into the next section and that would have a completely different format.

## 11.2.4. Illegal variable command: expected X arguments but found Y

This error indicates that there are the wrong number of arguments for a specific variable command, but a common reason for that is a variable expression that has whitespace but is not enclosed in single or double quotes.

To explain, the LAMMPS input parser reads and processes lines. The resulting line is broken down into “words”. Those are usually individual commands, labels, names, values separated by whitespace (a space or tab character). For “words” that may contain whitespace, they have to be enclosed in single (’) or double (”) quotes. The parser will then remove the outermost pair of quotes and then pass that string as “word” to the variable command.

Thus missing quotes or accidental extra whitespace will lead to the error shown in the header because the unquoted whitespace will result in the text being broken into more “words”, i.e. the variable expression being split.

## 11.2.5. Out of range atoms - cannot compute …

The PPPM (and also PPPMDisp and MSM) methods require to assemble a grid of electron density data derived from the (partial) charges assigned to the atoms. This charges are smeared out across multiple grid points (see kspace_modify order). When running in parallel with MPI, LAMMPS uses a domain decomposition scheme where each processor manages a subset of atoms and thus also a grid representing the density, which covers the actual volume of the sub-domain and some extra space corresponding to the neighbor list skin. These are then combined and redistributed for parallel processing of the long-range component of the Coulomb interaction.

The `Out of range atoms` error can happen, when atoms move too fast or the neighbor list skin is too small or the neighbor lists are not updated frequently enough. Then the smeared charges cannot be fully assigned to the density grid for all atoms. LAMMPS checks for this condition and stops with an error. Most of the time, this is an indication of a system with very high forces, most often at the beginning of a simulation or when boundary conditions are changed. The error becomes more likely with more MPI processes.

There are multiple options to explore for avoiding the error. The best choice depends strongly on the individual system, and often a combination of changes is required. For example, more conservative MD parameter settings can be used (larger neighbor skin, shorter time step, more frequent neighbor list updates). Sometimes, it helps to revisit the system generation and avoid close contacts when building it, or use the delete_atoms overlap command to delete those close contact atoms, or run a minimization before the MD. It can also help to temporarily use a cutoff-Coulomb pair style and no kspace style until the system has somewhat equilibrated and then switch to the long-range solver.

## 11.2.6. Too many neighbor bins

The simulation box has become too large relative to the size of a neighbor bin and LAMMPS is unable to store the needed number of bins. This typically implies the simulation box has expanded too far. This can happen when some atoms move rapidly apart with shrink-wrap boundaries or when a fix (like fix deform or a barostat) excessively grows the simulation box.

## 11.2.7. Cannot use neighbor bins - box size << cutoff

LAMMPS is unable to build neighbor bins since the size of the box is much smaller than an interaction cutoff in at least one of its dimensions. Typically, this error is triggered when the simulation box has one very thin dimension. If a cubic neighbor bin had to fit exactly within the thin dimension, then an inordinate amount of bins would be created to fill space. This error can be avoided using the generally slower nsq neighbor style or by increasing the size of the smallest box lengths.

## 11.2.8. Domain too large for neighbor bins

The domain has become extremely large so that neighbor bins cannot be used. Too many neighbor bins would need to be created to fill space Most likely, one or more atoms have been blown out of the simulation box to a great distance or a fix (like fix deform or a barostat) has excessively grown the simulation box.

## 11.2.9. Molecule topology/atom exceeds system topology/atom

LAMMPS uses domain decomposition to distribute data (i.e. atoms) across the MPI processes in parallel runs. This includes topology data, that is data about bonds, angles, dihedrals, impropers and “special” neighbors. This information is stored with either one or all atoms involved in such a topology entry (which of the two option applies depends on the newton setting for bonds. When reading a data file, LAMMPS analyzes the requirements for this file and then the values are “locked in” and cannot be extended.

So loading a molecule file that requires more of the topology per atom storage or adding a data file with such needs will lead to an error. To avoid the error, one or more of the extra/XXX/per/atom keywords are required to extend the corresponding storage. It is no problem to choose those numbers generously and have more storage reserved than actually needed, but having these numbers set too small will lead to an error.

## 11.2.10. Molecule topology type exceeds system topology type

The total number of atom, bond, angle, dihedral, and improper types is “locked in” when LAMMPS creates the simulation box. This can happen through either the create_box, the read_data, or the read_restart command. After this it is not possible to refer to an additional type. So loading a molecule file that uses additional types or adding a data file that would require additional types will lead to an error. To avoid the error, one or more of the extra/XXX/types keywords are required to extend the maximum number of the individual types.

## 11.2.11. Molecule attributes do not match system attributes

Choosing an atom_style in LAMMPS determines which per-atom properties are available. In a molecule file, however, it is possible to add sections (for example Masses or Charges) that are not supported by the atom style. Masses for example, are usually not a per-atom property, but defined through the atom type. Thus it would not be required to have a Masses section and the included data would be ignored. LAMMPS prints this warning to inform about this case.