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remove "self-explanatory" explanations.

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Axel Kohlmeyer
2025-03-14 21:07:43 -04:00
parent aafdac1917
commit ee930935f5
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doc/src/Errors_messages.rst
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doc/src/Errors_warnings.rst
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@ -32,16 +32,10 @@ Please also see the page with :doc:`Error messages <Errors_messages>`
cutoff is set too short or the angle has blown apart and an atom is cutoff is set too short or the angle has blown apart and an atom is
too far away. too far away.
*Angle style in data file differs from currently defined angle style*
Self-explanatory.
*Angles are defined but no angle style is set* *Angles are defined but no angle style is set*
The topology contains angles, but there are no angle forces computed The topology contains angles, but there are no angle forces computed
since there was no angle_style command. since there was no angle_style command.
*Atom style in data file differs from currently defined atom style*
Self-explanatory.
*Bond atom missing in box size check* *Bond atom missing in box size check*
The second atom needed to compute a particular bond is missing on this The second atom needed to compute a particular bond is missing on this
processor. Typically this is because the pairwise cutoff is set too processor. Typically this is because the pairwise cutoff is set too
@ -57,9 +51,6 @@ Please also see the page with :doc:`Error messages <Errors_messages>`
processor. Typically this is because the pairwise cutoff is set too 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. short or the bond has blown apart and an atom is too far away.
*Bond style in data file differs from currently defined bond style*
Self-explanatory.
*Bonds are defined but no bond style is set* *Bonds are defined but no bond style is set*
The topology contains bonds, but there are no bond forces computed The topology contains bonds, but there are no bond forces computed
since there was no bond_style command. since there was no bond_style command.
@ -72,9 +63,6 @@ Please also see the page with :doc:`Error messages <Errors_messages>`
length, multiplying by the number of bonds in the interaction (e.g. 3 length, multiplying by the number of bonds in the interaction (e.g. 3
for a dihedral) and adding a small amount of stretch. for a dihedral) and adding a small amount of stretch.
*Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero*
Self-explanatory.
*Calling write_dump before a full system init.* *Calling write_dump before a full system init.*
The write_dump command is used before the system has been fully The write_dump command is used before the system has been fully
initialized as part of a 'run' or 'minimize' command. Not all dump initialized as part of a 'run' or 'minimize' command. Not all dump
@ -90,18 +78,6 @@ Please also see the page with :doc:`Error messages <Errors_messages>`
This means the temperature associated with the rigid bodies may be This means the temperature associated with the rigid bodies may be
incorrect on this timestep. incorrect on this timestep.
*Cannot include log terms without 1/r terms; setting flagHI to 1*
Self-explanatory.
*Cannot include log terms without 1/r terms; setting flagHI to 1.*
Self-explanatory.
*Charges are set, but coulombic solver is not used*
Self-explanatory.
*Charges did not converge at step %ld: %lg*
Self-explanatory.
*Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost* *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 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 pair and bond styles (will be zero, if none are defined) and what is specified
@ -127,9 +103,6 @@ Please also see the page with :doc:`Error messages <Errors_messages>`
is not changed automatically and the warning may be ignored depending is not changed automatically and the warning may be ignored depending
on the specific system being simulated. on the specific system being simulated.
*Communication cutoff is too small for SNAP micro load balancing, increased to %lf*
Self-explanatory.
*Compute cna/atom cutoff may be too large to find ghost atom neighbors* *Compute cna/atom cutoff may be too large to find ghost atom neighbors*
The neighbor cutoff used may not encompass enough ghost atoms The neighbor cutoff used may not encompass enough ghost atoms
to perform this operation correctly. to perform this operation correctly.
@ -162,9 +135,6 @@ Please also see the page with :doc:`Error messages <Errors_messages>`
Conformation of the 4 listed dihedral atoms is extreme; you may want Conformation of the 4 listed dihedral atoms is extreme; you may want
to check your simulation geometry. to check your simulation geometry.
*Dihedral style in data file differs from currently defined dihedral style*
Self-explanatory.
*Dihedrals are defined but no dihedral style is set* *Dihedrals are defined but no dihedral style is set*
The topology contains dihedrals, but there are no dihedral forces computed The topology contains dihedrals, but there are no dihedral forces computed
since there was no dihedral_style command. since there was no dihedral_style command.
@ -181,9 +151,6 @@ Please also see the page with :doc:`Error messages <Errors_messages>`
*Estimated error in splitting of dispersion coeffs is %g* *Estimated error in splitting of dispersion coeffs is %g*
Error is greater than 0.0001 percent. Error is greater than 0.0001 percent.
*Ewald/disp Newton solver failed, using old method to estimate g_ewald*
Self-explanatory. Choosing a different cutoff value may help.
*FENE bond too long* *FENE bond too long*
A FENE bond has stretched dangerously far. It's interaction strength A FENE bond has stretched dangerously far. It's interaction strength
will be truncated to attempt to prevent the bond from blowing up. will be truncated to attempt to prevent the bond from blowing up.
@ -196,9 +163,6 @@ Please also see the page with :doc:`Error messages <Errors_messages>`
A FENE bond has stretched dangerously far. It's interaction strength A FENE bond has stretched dangerously far. It's interaction strength
will be truncated to attempt to prevent the bond from blowing up. will be truncated to attempt to prevent the bond from blowing up.
*Fix halt condition for fix-id %s met on step %ld with value %g*
Self explanatory.
*Fix SRD walls overlap but fix srd overlap not set* *Fix SRD walls overlap but fix srd overlap not set*
You likely want to set this in your input script. You likely want to set this in your input script.
@ -242,21 +206,12 @@ Please also see the page with :doc:`Error messages <Errors_messages>`
*Fix property/atom mol or charge w/out ghost communication* *Fix property/atom mol or charge w/out ghost communication*
A model typically needs these properties defined for ghost atoms. A model typically needs these properties defined for ghost atoms.
*Fix qeq CG convergence failed (%g) after %d iterations at %ld step*
Self-explanatory.
*Fix qeq has non-zero lower Taper radius cutoff* *Fix qeq has non-zero lower Taper radius cutoff*
Absolute value must be <= 0.01. Absolute value must be <= 0.01.
*Fix qeq has very low Taper radius cutoff* *Fix qeq has very low Taper radius cutoff*
Value should typically be >= 5.0. Value should typically be >= 5.0.
*Fix qeq/dynamic tolerance may be too small for damped dynamics*
Self-explanatory.
*Fix qeq/fire tolerance may be too small for damped fires*
Self-explanatory.
*Fix rattle should come after all other integration fixes* *Fix rattle should come after all other integration fixes*
This fix is designed to work after all other integration fixes change This fix is designed to work after all other integration fixes change
atom positions. Thus it should be the last integration fix specified. atom positions. Thus it should be the last integration fix specified.
@ -289,9 +244,6 @@ Please also see the page with :doc:`Error messages <Errors_messages>`
The user-specified force accuracy cannot be achieved unless the table The user-specified force accuracy cannot be achieved unless the table
feature is disabled by using 'pair_modify table 0'. feature is disabled by using 'pair_modify table 0'.
*Geometric mixing assumed for 1/r\^6 coefficients*
Self-explanatory.
*Group for fix_modify temp != fix group* *Group for fix_modify temp != fix group*
The fix_modify command is specifying a temperature computation that The fix_modify command is specifying a temperature computation that
computes a temperature on a different group of atoms than the fix computes a temperature on a different group of atoms than the fix
@ -314,9 +266,6 @@ Please also see the page with :doc:`Error messages <Errors_messages>`
Conformation of the 4 listed improper atoms is extreme; you may want Conformation of the 4 listed improper atoms is extreme; you may want
to check your simulation geometry. to check your simulation geometry.
*Improper style in data file differs from currently defined improper style*
Self-explanatory.
*Impropers are defined but no improper style is set* *Impropers are defined but no improper style is set*
The topology contains impropers, but there are no improper forces computed The topology contains impropers, but there are no improper forces computed
since there was no improper_style command. since there was no improper_style command.
@ -342,18 +291,6 @@ Please also see the page with :doc:`Error messages <Errors_messages>`
The pair style has increased the communication cutoff to be consistent with 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. the communication cutoff requirements for this pair style when run on the GPU.
*KIM Model does not provide 'energy'; Potential energy will be zero*
Self-explanatory.
*KIM Model does not provide 'forces'; Forces will be zero*
Self-explanatory.
*KIM Model does not provide 'particleEnergy'; energy per atom will be zero*
Self-explanatory.
*KIM Model does not provide 'particleVirial'; virial per atom will be zero*
Self-explanatory.
*Kspace_modify slab param < 2.0 may cause unphysical behavior* *Kspace_modify slab param < 2.0 may cause unphysical behavior*
The kspace_modify slab parameter should be larger to ensure periodic The kspace_modify slab parameter should be larger to ensure periodic
grids padded with empty space do not overlap. grids padded with empty space do not overlap.
@ -405,16 +342,10 @@ Please also see the page with :doc:`Error messages <Errors_messages>`
box, or moved further than one processor's subdomain away before box, or moved further than one processor's subdomain away before
reneighboring. reneighboring.
*MSM mesh too small, increasing to 2 points in each direction*
Self-explanatory.
*Mismatch between velocity and compute groups* *Mismatch between velocity and compute groups*
The temperature computation used by the velocity command will not be The temperature computation used by the velocity command will not be
on the same group of atoms that velocities are being set for. on the same group of atoms that velocities are being set for.
*Mixing forced for lj coefficients*
Self-explanatory.
*Molecule attributes do not match system attributes* *Molecule attributes do not match system attributes*
An attribute is specified (e.g. diameter, charge) that is An attribute is specified (e.g. diameter, charge) that is
not defined for the specified atom style. not defined for the specified atom style.
@ -453,9 +384,6 @@ Please also see the page with :doc:`Error messages <Errors_messages>`
*More than one compute damage/atom* *More than one compute damage/atom*
It is not efficient to use compute ke/atom more than once. It is not efficient to use compute ke/atom more than once.
*More than one compute dilatation/atom*
Self-explanatory.
*More than one compute erotate/sphere/atom* *More than one compute erotate/sphere/atom*
It is not efficient to use compute erorate/sphere/atom more than once. It is not efficient to use compute erorate/sphere/atom more than once.
@ -468,24 +396,6 @@ Please also see the page with :doc:`Error messages <Errors_messages>`
*More than one compute orientorder/atom* *More than one compute orientorder/atom*
It is not efficient to use compute orientorder/atom more than once. It is not efficient to use compute orientorder/atom more than once.
*More than one compute plasticity/atom*
Self-explanatory.
*More than one compute sna/atom*
Self-explanatory.
*More than one compute sna/grid*
Self-explanatory.
*More than one compute sna/grid/local*
Self-explanatory.
*More than one compute snad/atom*
Self-explanatory.
*More than one compute snav/atom*
Self-explanatory.
*More than one fix poems* *More than one fix poems*
It is not efficient to use fix poems more than once. It is not efficient to use fix poems more than once.
@ -561,21 +471,12 @@ Please also see the page with :doc:`Error messages <Errors_messages>`
*Pair COMB charge %.10f with force %.10f hit min barrier* *Pair COMB charge %.10f with force %.10f hit min barrier*
Something is possibly wrong with your model. Something is possibly wrong with your model.
*Pair brownian needs newton pair on for momentum conservation*
Self-explanatory.
*Pair dpd needs newton pair on for momentum conservation*
Self-explanatory.
*Pair dsmc: num_of_collisions > number_of_A* *Pair dsmc: num_of_collisions > number_of_A*
Collision model in DSMC is breaking down. Collision model in DSMC is breaking down.
*Pair dsmc: num_of_collisions > number_of_B* *Pair dsmc: num_of_collisions > number_of_B*
Collision model in DSMC is breaking down. Collision model in DSMC is breaking down.
*Pair style in data file differs from currently defined pair style*
Self-explanatory.
*Pair style restartinfo set but has no restart support* *Pair style restartinfo set but has no restart support*
This pair style has a bug, where it does not support reading and 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 writing information to a restart file, but does not set the member
@ -685,9 +586,6 @@ Please also see the page with :doc:`Error messages <Errors_messages>`
cluster specified by the fix shake command is numerically suspect. LAMMPS cluster specified by the fix shake command is numerically suspect. LAMMPS
will set it to 0.0 and continue. will set it to 0.0 and continue.
*Shell command '%s' failed with error '%s'*
Self-explanatory.
*Shell command returned with non-zero status* *Shell command returned with non-zero status*
This may indicate the shell command did not operate as expected. This may indicate the shell command did not operate as expected.
@ -698,15 +596,9 @@ Please also see the page with :doc:`Error messages <Errors_messages>`
This will lead to invalid constraint forces in the SHAKE/RATTLE This will lead to invalid constraint forces in the SHAKE/RATTLE
computation. computation.
*Simulations might be very slow because of large number of structure factors*
Self-explanatory.
*Slab correction not needed for MSM* *Slab correction not needed for MSM*
Slab correction is intended to be used with Ewald or PPPM and is not needed by 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* *System is not charge neutral, net charge = %g*
The total charge on all atoms on the system is not 0.0. The total charge on all atoms on the system is not 0.0.
For some KSpace solvers this is only a warning. For some KSpace solvers this is only a warning.
@ -738,10 +630,7 @@ Please also see the page with :doc:`Error messages <Errors_messages>`
assumed to also be for all atoms. Thus the pressure printed by thermo assumed to also be for all atoms. Thus the pressure printed by thermo
could be inaccurate. 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* *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*The minimizer does not re-orient dipoles when using fix efield*
Self-explanatory.
*The minimizer does not re-orient dipoles when using fix efield*
This means that only the atom coordinates will be minimized, This means that only the atom coordinates will be minimized,
not the orientation of the dipoles. not the orientation of the dipoles.
@ -749,9 +638,6 @@ Please also see the page with :doc:`Error messages <Errors_messages>`
More than the maximum # of neighbors was found multiple times. This More than the maximum # of neighbors was found multiple times. This
was unexpected. was unexpected.
*Too many inner timesteps in fix ttm*
Self-explanatory.
*Too many neighbors in CNA for %d atoms* *Too many neighbors in CNA for %d atoms*
More than the maximum # of neighbors was found multiple times. This More than the maximum # of neighbors was found multiple times. This
was unexpected. was unexpected.
@ -779,24 +665,6 @@ Please also see the page with :doc:`Error messages <Errors_messages>`
The deformation will heat the SRD particles so this can The deformation will heat the SRD particles so this can
be dangerous. 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* *Using pair potential shift with pair_modify compute no*
The shift effects will thus not be computed. The shift effects will thus not be computed.