diff --git a/doc/src/Errors_messages.rst b/doc/src/Errors_messages.rst index a63d72b027..776207fb05 100644 --- a/doc/src/Errors_messages.rst +++ b/doc/src/Errors_messages.rst @@ -74,18 +74,6 @@ Please also see the page with :doc:`Warning messages `. a particular processor. The pairwise cutoff is too short or the atoms are too far apart to make a valid angle. -*Angle atoms %d %d %d missing on proc %d 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. - -*Angle atoms missing on proc %d 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. - *Angle coeff for hybrid has invalid style* Angle style hybrid uses another angle style as one of its coefficients. The angle style used in the angle_coeff command or read @@ -305,26 +293,11 @@ Please also see the page with :doc:`Warning messages `. bond on a particular processor. The pairwise cutoff is too short or the atoms are too far apart to make a valid bond. -*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 atom missing in set command* The set command cannot find one or more atoms in a particular bond on a particular processor. The pairwise cutoff is too short or the atoms are too far apart to make a valid bond. -*Bond atoms %d %d missing on proc %d 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. - -*Bond atoms missing on proc %d 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. - *Bond coeff for hybrid has invalid style* Bond style hybrid uses another bond style as one of its coefficients. The bond style used in the bond_coeff command or read from a restart @@ -1070,11 +1043,6 @@ Please also see the page with :doc:`Warning messages `. This is a current limitation of the GPU implementation in LAMMPS. -*Cannot use neighbor bins - box size << cutoff* - Too many neighbor bins will be created. This typically happens when - the simulation box is very small in some dimension, compared to the - neighbor cutoff. Use the "nsq" style instead of "bin" style. - *Cannot use non-zero forces in an energy minimization* Fix setforce cannot be used in this manner. Use fix addforce instead. @@ -1217,12 +1185,6 @@ Please also see the page with :doc:`Warning messages `. *Compute chunk/atom bin/sphere radius is too large for periodic box* Radius cannot be bigger than 1/2 of any periodic dimension. -*Compute chunk/atom compute array is accessed out-of-range* - The index for the array is out of bounds. - -*Compute chunk/atom fix array is accessed out-of-range* - The index for the array is out of bounds. - *Compute chunk/atom ids once but nchunk is not once* You cannot assign chunks IDs to atom permanently if the number of chunks may change. @@ -1333,30 +1295,12 @@ Please also see the page with :doc:`Warning messages `. Only inputs that generate the same number of datums can be used together. E.g. bond and angle quantities cannot be mixed. -*Compute reduce compute array is accessed out-of-range* - An index for the array is out of bounds. - *Compute reduce compute calculates global values* A compute that calculates peratom or local values is required. -*Compute reduce fix array is accessed out-of-range* - An index for the array is out of bounds. - *Compute reduce fix calculates global values* A fix that calculates peratom or local values is required. -*Compute slice compute array is accessed out-of-range* - An index for the array is out of bounds. - -*Compute slice compute vector is accessed out-of-range* - The index for the vector is out of bounds. - -*Compute slice fix array is accessed out-of-range* - An index for the array is out of bounds. - -*Compute slice fix vector is accessed out-of-range* - The index for the vector is out of bounds. - *Compute stress/atom temperature ID does not compute temperature* The specified compute must compute temperature. @@ -1654,11 +1598,6 @@ Please also see the page with :doc:`Warning messages `. *Delete_bonds command with no atoms existing* No atoms are yet defined so the delete_bonds command cannot be used. -*Did not assign all atoms correctly* - Atoms read in from a data file were not assigned correctly to - processors. This is likely due to some atom coordinates being - outside a non-periodic simulation box. - *Did not assign all restart atoms correctly* Atoms read in from the restart file were not assigned correctly to processors. This is likely due to some atom coordinates being outside @@ -1697,18 +1636,6 @@ Please also see the page with :doc:`Warning messages `. on a particular processor. The pairwise cutoff is too short or the atoms are too far apart to make a valid dihedral. -*Dihedral atoms %d %d %d %d missing on proc %d 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 atoms missing on proc %d 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 charmm is incompatible with Pair style* Dihedral style charmm must be used with a pair style charmm in order for the 1-4 epsilon/sigma parameters to be defined. @@ -1769,11 +1696,6 @@ Please also see the page with :doc:`Warning messages `. This should not normally occur. It is likely a problem with your model. -*Domain too large for neighbor bins* - The domain has become extremely large so that neighbor bins cannot be - used. Most likely, one or more atoms have been blown out of the - simulation box to a great distance. - *Dump atom/gz only writes compressed files* The dump atom/gz output file name must have a .gz suffix. @@ -1855,11 +1777,6 @@ Please also see the page with :doc:`Warning messages `. There is no variable syntax that uses empty brackets. Check the variable doc page. -*Energy was not tallied on needed timestep* - You are using a thermo keyword that requires potentials to - have tallied energy, but they did not on this timestep. See the - variable page for ideas on how to make this work. - *Epsilon or sigma reference not set by pair style in ewald/n* The pair style is not providing the needed epsilon or sigma values. @@ -1955,12 +1872,6 @@ Please also see the page with :doc:`Warning messages `. *Fix ave/chunk does not use chunk/atom compute* The specified compute is not for a compute chunk/atom command. -*Fix ave/correlate compute vector is accessed out-of-range* - The index for the vector is out of bounds. - -*Fix ave/correlate fix vector is accessed out-of-range* - The index for the vector is out of bounds. - *Fix ave/histo inputs are not all global, peratom, or local* All inputs in a single fix ave/histo command must be of the same style. @@ -1973,18 +1884,6 @@ Please also see the page with :doc:`Warning messages `. *Fix ave/time cannot use variable with vector mode* Variables produce scalar values. -*Fix ave/time compute array is accessed out-of-range* - An index for the array is out of bounds. - -*Fix ave/time compute vector is accessed out-of-range* - The index for the vector is out of bounds. - -*Fix ave/time fix array is accessed out-of-range* - An index for the array is out of bounds. - -*Fix ave/time fix vector is accessed out-of-range* - The index for the vector is out of bounds. - *Fix balance rcb cannot be used with comm_style brick* Comm_style tiled must be used instead. @@ -2560,18 +2459,6 @@ Please also see the page with :doc:`Warning messages `. on a particular processor. The pairwise cutoff is too short or the atoms are too far apart to make a valid improper. -*Improper atoms %d %d %d %d missing on proc %d 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 atoms missing on proc %d 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 coeff for hybrid has invalid style* Improper style hybrid uses another improper style as one of its coefficients. The improper style used in the improper_coeff command @@ -2681,10 +2568,6 @@ Please also see the page with :doc:`Warning messages `. *Incorrect element names in EAM potential file* The element names in the EAM file do not match those requested. -*Incorrect format of ... section in data file* - Number or type of values per line in the given section of the data file - is not consistent with the requirements for this section. - *Incorrect format in COMB potential file* Incorrect number of words per line in the potential file. @@ -3213,9 +3096,6 @@ Please also see the page with :doc:`Warning messages `. The template indices must be between 1 to N, where N is the number of molecules in the template. -*Invalid thermo keyword in variable formula* - The keyword is not recognized. - *Invalid threads_per_atom specified.* For 3-body potentials on the GPU, the threads_per_atom setting cannot be greater than 4 for NVIDIA GPUs. @@ -3378,13 +3258,6 @@ Please also see the page with :doc:`Warning messages `. *Lost atoms via balance: original %ld current %ld* This should not occur. Report the problem to the developers. -*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. - *MEAM library error %d* A call to the MEAM Fortran library returned an error. @@ -3445,9 +3318,6 @@ Please also see the page with :doc:`Warning messages `. The IDs must not be larger than can be stored in a 32-bit integer since chunk IDs are 32-bit integers. -*Molecule auto special bond generation overflow* - Counts exceed maxspecial setting for other atoms in system. - *Molecule file shake flags not before shake atoms* The order of the two sections is important. @@ -3460,16 +3330,6 @@ Please also see the page with :doc:`Warning messages `. *Molecule file special list does not match special count* The number of values in an atom's special list does not match count. -*Molecule topology/atom exceeds system topology/atom* - The number of bonds, angles, etc per-atom in the molecule exceeds the - system setting. See the create_box command for how to specify these - values. - -*Molecule topology type exceeds system topology type* - The number of bond, angle, etc types in the molecule exceeds the - system setting. See the create_box command for how to specify these - values. - *More than one fix deform* Only one fix deform can be defined at a time. @@ -3749,17 +3609,9 @@ Please also see the page with :doc:`Warning messages `. Swap frequency in temper command must evenly divide the total # of timesteps. -*Non-numeric box dimensions - simulation unstable* - The box size has apparently blown up. - *Number of core atoms != number of shell atoms* There must be a one-to-one pairing of core and shell atoms. -*Numeric index is out of bounds* - A command with an argument that specifies an integer or range of - integers is using a value that is less than 1 or greater than the - maximum allowed limit. - *One or more Atom IDs is negative* Atom IDs must be positive integers. @@ -3778,51 +3630,6 @@ Please also see the page with :doc:`Warning messages `. Any rigid body defined by the fix rigid command must contain 2 or more atoms. -*Out of range atoms - cannot compute MSM* - One or more atoms are attempting to map their charge to a MSM grid point - that is not owned by a processor. This is likely for one of two - reasons, both of them bad. First, it may mean that an atom near the - boundary of a processor's subdomain has moved more than 1/2 the - :doc:`neighbor skin distance ` without neighbor lists being - rebuilt and atoms being migrated to new processors. This also means - you may be missing pairwise interactions that need to be computed. - The solution is to change the re-neighboring criteria via the - :doc:`neigh_modify ` command. The safest settings are - "delay 0 every 1 check yes". Second, it may mean that an atom has - moved far outside a processor's subdomain or even the entire - simulation box. This indicates bad physics, e.g. due to highly - overlapping atoms, too large a timestep, etc. - -*Out of range atoms - cannot compute PPPM* - One or more atoms are attempting to map their charge to a PPPM grid - point that is not owned by a processor. This is likely for one of two - reasons, both of them bad. First, it may mean that an atom near the - boundary of a processor's subdomain has moved more than 1/2 the - :doc:`neighbor skin distance ` without neighbor lists being - rebuilt and atoms being migrated to new processors. This also means - you may be missing pairwise interactions that need to be computed. - The solution is to change the re-neighboring criteria via the - :doc:`neigh_modify ` command. The safest settings are - "delay 0 every 1 check yes". Second, it may mean that an atom has - moved far outside a processor's subdomain or even the entire - simulation box. This indicates bad physics, e.g. due to highly - overlapping atoms, too large a timestep, etc. - -*Out of range atoms - cannot compute PPPMDisp* - One or more atoms are attempting to map their charge to a PPPM grid - point that is not owned by a processor. This is likely for one of two - reasons, both of them bad. First, it may mean that an atom near the - boundary of a processor's subdomain has moved more than 1/2 the - :doc:`neighbor skin distance ` without neighbor lists being - rebuilt and atoms being migrated to new processors. This also means - you may be missing pairwise interactions that need to be computed. - The solution is to change the re-neighboring criteria via the - :doc:`neigh_modify ` command. The safest settings are - "delay 0 every 1 check yes". Second, it may mean that an atom has - moved far outside a processor's subdomain or even the entire - simulation box. This indicates bad physics, e.g. due to highly - overlapping atoms, too large a timestep, etc. - *Overflow of allocated fix vector storage* This should not normally happen if the fix correctly calculated how long the vector will grow to. Contact the developers. @@ -4342,19 +4149,9 @@ Please also see the page with :doc:`Warning messages `. *Per-atom compute in equal-style variable formula* Equal-style variables cannot use per-atom quantities. -*Per-atom energy was not tallied on needed timestep* - You are using a thermo keyword that requires potentials to - have tallied energy, but they did not on this timestep. See the - variable page for ideas on how to make this work. - *Per-atom fix in equal-style variable formula* Equal-style variables cannot use per-atom quantities. -*Per-atom virial was not tallied on needed timestep* - You are using a thermo keyword that requires potentials to have - tallied the virial, but they did not on this timestep. See the - variable page for ideas on how to make this work. - *Per-processor system is too big* The number of owned atoms plus ghost atoms on a single processor must fit in 32-bit integer. @@ -4717,10 +4514,6 @@ Please also see the page with :doc:`Warning messages `. See the extra/improper/per/atom keyword for the create_box or the read_data command to set this limit larger -*Substitution for illegal variable* - Input script line contained a variable that could not be substituted - for. - *Support for writing images in JPEG format not included* LAMMPS was not built with the -DLAMMPS_JPEG switch in the Makefile. @@ -4924,10 +4717,6 @@ Please also see the page with :doc:`Warning messages `. *Too many molecules for fix rigid* The limit is 2\^31 = ~2 billion molecules. -*Too many neighbor bins* - This is likely due to an immense simulation box that has blown up - to a large size. - *Too many timesteps* The cumulative timesteps must fit in a 64-bit integer. @@ -5019,57 +4808,12 @@ Please also see the page with :doc:`Warning messages `. A universe or uloop style variable must specify a number of values >= to the number of processor partitions. -*Unrecognized angle style* - The choice of angle style is unknown. - -*Unrecognized atom style* - The choice of atom style is unknown. - -*Unrecognized body style* - The choice of body style is unknown. - -*Unrecognized bond style* - The choice of bond style is unknown. - -*Unrecognized command: %s* - The command is not known to LAMMPS. Check the input script. - -*Unrecognized compute style* - The choice of compute style is unknown. - -*Unrecognized dihedral style* - The choice of dihedral style is unknown. - -*Unrecognized dump reader style* - The choice of dump reader style via the format keyword is unknown. - -*Unrecognized dump style* - The choice of dump style is unknown. - -*Unrecognized fix style* - The choice of fix style is unknown. - -*Unknown identifier in data file: %s* - A section of the data file cannot be read by LAMMPS. - -*Unrecognized improper style* - The choice of improper style is unknown. - *Unknown keyword in thermo_style custom command* One or more specified keywords are not recognized. -*Unrecognized kspace style* - The choice of kspace style is unknown. - -*Unrecognized pair style* - The choice of pair style is unknown. - *Unknown pair_modify hybrid sub-style* The choice of sub-style is unknown. -*Unrecognized region style* - The choice of region style is unknown. - *Unknown table style in pair_style command* Style of table is invalid for use with pair_style table command. @@ -5260,11 +5004,6 @@ Please also see the page with :doc:`Warning messages `. This is so there is an equal number of Rspace processors for every Kspace processor. -*Virial was not tallied on needed timestep* - You are using a thermo keyword that requires potentials to - have tallied the virial, but they did not on this timestep. See the - variable page for ideas on how to make this work. - *Voro++ error: narea and neigh have a different size* This error is returned by the Voro++ library. diff --git a/doc/src/Errors_warnings.rst b/doc/src/Errors_warnings.rst index f152e66f4a..c99b3f6b7c 100644 --- a/doc/src/Errors_warnings.rst +++ b/doc/src/Errors_warnings.rst @@ -270,23 +270,6 @@ Please also see the page with :doc:`Error messages ` The topology contains impropers, but there are no improper forces computed since there was no improper_style command. -*Inconsistent image flags* - The image flags for a pair on bonded atoms appear to be inconsistent. - Inconsistent means that when the coordinates of the two atoms are - unwrapped using the image flags, the two atoms are far apart. - Specifically they are further apart than half a periodic box length. - Or they are more than a box length apart in a non-periodic dimension. - This is usually due to the initial data file not having correct image - flags for the two atoms in a bond that straddles a periodic boundary. - They should be different by 1 in that case. This is a warning because - inconsistent image flags will not cause problems for dynamics or most - LAMMPS simulations. However they can cause problems when such atoms - are used with the fix rigid or replicate commands. Note that if you - have an infinite periodic crystal with bonds then it is impossible to - have fully consistent image flags, since some bonds will cross - periodic boundaries and connect two atoms with the same image - flag. - *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. @@ -346,10 +329,6 @@ Please also see the page with :doc:`Error messages ` The temperature computation used by the velocity command will not be on the same group of atoms that velocities are being set for. -*Molecule attributes do not match system attributes* - An attribute is specified (e.g. diameter, charge) that is - not defined for the specified atom style. - *Molecule has bond topology but no special bond settings* This means the bonded atoms will not be excluded in pairwise interactions.