diff --git a/doc/Eqs/pair_bop.jpg b/doc/Eqs/pair_bop.jpg new file mode 100644 index 0000000000..d1fbb14b09 Binary files /dev/null and b/doc/Eqs/pair_bop.jpg differ diff --git a/doc/Eqs/pair_bop.tex b/doc/Eqs/pair_bop.tex new file mode 100644 index 0000000000..371bc035f3 --- /dev/null +++ b/doc/Eqs/pair_bop.tex @@ -0,0 +1,9 @@ +\documentclass[12pt]{article} + +\begin{document} + +$$ + E = \frac{1}{2} \sum_{i=1}^{N} \sum_{j=i_1}^{i_N} \phi_{ij} \left( r_{ij} \right) - \sum_{i=1}^{N} \sum_{j=i_1}^{i_N} \beta_{\sigma,ij} \left( r_{ij} \right) \cdot \Theta_{\sigma,ij} - \sum_{i=1}^{N} \sum_{j=i_1}^{i_N} \beta_{\pi,ij} \left( r_{ij} \right) \cdot \Theta_{\pi,ij} + U_{prom} +$$ + +\end{document} diff --git a/doc/Eqs/pair_meam_spline.jpg b/doc/Eqs/pair_meam_spline.jpg index 7efcd076dc..29f1c72543 100644 Binary files a/doc/Eqs/pair_meam_spline.jpg and b/doc/Eqs/pair_meam_spline.jpg differ diff --git a/doc/Manual.pdf b/doc/Manual.pdf index 5d98d7bebc..2ee3bee3f7 100644 Binary files a/doc/Manual.pdf and b/doc/Manual.pdf differ diff --git a/doc/Section_commands.html b/doc/Section_commands.html index e76626a5a3..3abb5ccfb6 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -417,24 +417,24 @@ potentials. Click on the style itself for a full description:

- - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + +
nonehybridhybrid/overlayadp
airebobeckbornborn/coul/long
born/coul/wolfbrownianbrownian/polybuck
buck/coul/cutbuck/coul/longcolloidcomb
coul/cutcoul/debyecoul/longcoul/wolf
dipole/cutdpddpd/tstatdsmc
eameam/alloyeam/fseim
gaussgaybernegran/hertz/historygran/hooke
gran/hooke/historyhbond/dreiding/ljhbond/dreiding/morsekim
lcbopline/ljlj/charmm/coul/charmmlj/charmm/coul/charmm/implicit
lj/charmm/coul/longlj/class2lj/class2/coul/cutlj/class2/coul/long
lj/cutlj/cut/coul/cutlj/cut/coul/debyelj/cut/coul/long
lj/cut/coul/long/tip4plj/expandlj/gromacslj/gromacs/coul/gromacs
lj/smoothlj/smooth/linearlj96/cutlubricate
lubricate/polylubricateUlubricateU/polymeam
morseperi/lpsperi/pmbreax
reboresquaredsoftsw
tabletersofftersoff/zbltri/lj
yukawayukawa/colloid +
airebobeckbopborn
born/coul/longborn/coul/wolfbrownianbrownian/poly
buckbuck/coul/cutbuck/coul/longcolloid
combcoul/cutcoul/debyecoul/long
coul/wolfdipole/cutdpddpd/tstat
dsmceameam/alloyeam/fs
eimgaussgaybernegran/hertz/history
gran/hookegran/hooke/historyhbond/dreiding/ljhbond/dreiding/morse
kimlcbopline/ljlj/charmm/coul/charmm
lj/charmm/coul/charmm/implicitlj/charmm/coul/longlj/class2lj/class2/coul/cut
lj/class2/coul/longlj/cutlj/cut/coul/cutlj/cut/coul/debye
lj/cut/coul/longlj/cut/coul/long/tip4plj/expandlj/gromacs
lj/gromacs/coul/gromacslj/smoothlj/smooth/linearlj96/cut
lubricatelubricate/polylubricateUlubricateU/poly
meammorseperi/lpsperi/pmb
reaxreboresquaredsoft
swtabletersofftersoff/zbl
tri/ljyukawayukawa/colloid

These are pair styles contributed by users, which can be used if diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index ac2a2bb19d..fc8e881c27 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -627,6 +627,7 @@ potentials. Click on the style itself for a full description: "adp"_pair_adp.html, "airebo"_pair_airebo.html, "beck"_pair_beck.html, +"bop"_pair_bop.html, "born"_pair_born.html, "born/coul/long"_pair_born.html, "born/coul/wolf"_pair_born.html, diff --git a/doc/Section_errors.html b/doc/Section_errors.html index 7f7acdc873..93a62a31b8 100644 --- a/doc/Section_errors.html +++ b/doc/Section_errors.html @@ -221,6 +221,12 @@ command.

All pair coefficients must be set in the data file or by the pair_coeff command before running a simulation. +
All read_dump x,y,z fields must be specified for scaled, triclinic coords + +
For triclinic boxes and scaled coordinates you must specify all 3 of +the x,y,z fields, else LAMMPS cannot reconstruct the unscaled +coordinates. +
All universe/uloop variables must have same # of values
Self-explanatory. @@ -319,7 +325,7 @@ still being processed.
Append boundary must be shrink/minimum
The boundary style of the face where atoms are added -must be of type m (shrink/minimum). +must be of type m (shrink/minimum).
Arccos of invalid value in variable formula @@ -476,9 +482,11 @@ or create_box command.
The string can only contain the characters "x", "y", or "z". -
Balance dynamic string is invalid for 2d simulation +
Balance produced bad splits -
The string cannot contain the letter "z". +
This should not occur. It means two or more cutting plane locations +are on top of each other or out of order. Report the problem to the +developers.
Bias compute does not calculate a velocity bias @@ -525,6 +533,12 @@ in file exactly.
Cannot use TIP4P pair potential unless bond and angle potentials are defined. +
Bond atom missing in box size check + +
The 2nd atoms needed to compute a particular bond is missing on this +processor. Typically this is because the pairwise cutoff is set too +short or the bond has blown apart and an atom is too far away. +
Bond atom missing in delete_bonds
The delete_bonds command cannot find one or more atoms in a particular @@ -588,6 +602,15 @@ bond style quartic.
The values in the tabulated file must be monotonically increasing. +
Bond/angle/dihedral extent > half of periodic box length + +
This is a restriction because LAMMPS can be confused about which image +of an atom in the bonded interaction is the correct one to use. +"Extent" in this context means the maximum end-to-end length of the +bond/angle/dihedral. LAMMPS computes this by taking the maximum bond +length, multiplying by the number of bonds in the interaction (e.g. 3 +for a dihedral) and adding a small amount of stretch. +
Bond_coeff command before bond_style is defined
Coefficients cannot be set in the data file or via the bond_coeff @@ -656,6 +679,14 @@ See the region prism command for details.
This is current restriction for NEB as implemented in LAMMPS. +
Cannot (yet) use K-space slab correction with compute group/group + +
This option is not yet supported. + +
Cannot (yet) use Kspace slab correction with compute group/group + +
This option is not yet supported. +
Cannot (yet) use PPPM with triclinic box
This feature is not yet supported. @@ -830,6 +861,11 @@ path and name are correct.
The specified AIREBO potential file cannot be opened. Check that the path and name are correct. +
Cannot open BOP potential file %s + +
The specified BOP potential file cannot be opened. Check that the +path and name are correct. +
Cannot open COMB potential file %s
The specified COMB potential file cannot be opened. Check that the @@ -845,6 +881,11 @@ path and name are correct.
The specified EIM potential file cannot be opened. Check that the path and name are correct. +
Cannot open LCBOP potential file %s + +
The specified LCBOP potential file cannot be opened. Check that the +path and name are correct. +
Cannot open MEAM potential file %s
The specified MEAM potential file cannot be opened. Check that the @@ -862,8 +903,7 @@ path and name are correct.
Cannot open balance output file -
This error message can only occur if debug options -are uncommented in src/balance.cpp. +
Self-explanatory.
Cannot open custom file @@ -904,6 +944,10 @@ correct.
The specified file cannot be opened. Check that the path and name are correct. +
Cannot open fix balance output file + +
Self-explanatory. +
Cannot open fix poems file %s
The specified file cannot be opened. Check that the path and name are @@ -923,6 +967,11 @@ Check that the path and name are correct.
The output file for the fix reax/bonds command cannot be opened. Check that the path and name are correct. +
Cannot open fix rigid infile %s + +
The specified file cannot be opened. Check that the path and name are +correct. +
Cannot open fix tmd file %s
The output file for the fix tmd command cannot be opened. Check that @@ -1027,17 +1076,6 @@ are defined.
You cannot reset the timestep when a fix that keeps track of elapsed time is in place. -
Cannot reset timestep with dump file already written to - -
Changing the timestep will confuse when a dump file is written. Use -the undump command, then restart the dump file. - -
Cannot reset timestep with restart file already written - -
Changing the timestep will confuse when a restart file is written. -Use the "restart 0" command to turn off restarts, then start them -again. -
Cannot restart fix rigid/nvt with different # of chains
This is because the restart file contains per-chain info. @@ -1550,6 +1588,10 @@ of velocity creation cannot be performed.
Cannot specify both options at the same time. +
Cannot yet use fix balance with PPPM + +
This is a current limitation of LAMMPS. +
Cannot zero Langevin force of 0 atoms
The group has zero atoms, so you cannot request its force @@ -2470,6 +2512,14 @@ dump output.
The variable must return a timestep greater than the current timestep. +
Dump file does not contain requested snapshot + +
Self-explanatory. + +
Dump file is incorrectly formatted + +
No atoms were found in file. +
Dump image bond not allowed with no bond types
Self-explanatory. @@ -2605,6 +2655,10 @@ dumped.
Only per-atom quantities that are defined for the atom style being used are allowed. +
Duplicate fields in read_dump command + +
Self-explanatory. +
Duplicate particle in PeriDynamic bond - simulation box is too small
This is likely because your box length is shorter than 2 times @@ -2714,6 +2768,10 @@ is on.
Self-explanatory +
Fix ID for read_data does not exist + +
Self-explanatory. +
Fix ID must be alphanumeric or underscore characters
Self-explanatory. @@ -2799,6 +2857,11 @@ to a larger value, and re-compile the code.
A fix used by fix ave/atom must generate per-atom values. +
Fix ave/atom missed timestep + +
You cannot reset the timestep to a value beyond where the fix +expects to next perform averaging. +
Fix ave/atom variable is not atom-style variable
A variable used by fix ave/atom must generate per-atom values. @@ -2827,6 +2890,11 @@ to a larger value, and re-compile the code.
The index for the vector is out of bounds. +
Fix ave/correlate missed timestep + +
You cannot reset the timestep to a value beyond where the fix +expects to next perform averaging. +
Fix ave/correlate variable is not equal-style variable
Self-explanatory. @@ -2944,6 +3012,11 @@ to a larger value, and re-compile the code.
All inputs in a single fix ave/histo command must be of the same style. +
Fix ave/histo missed timestep + +
You cannot reset the timestep to a value beyond where the fix +expects to next perform averaging. +
Fix ave/spatial compute does not calculate a per-atom array
Self-explanatory. @@ -2980,6 +3053,11 @@ same style.
Self-explanatory. +
Fix ave/spatial missed timestep + +
You cannot reset the timestep to a value beyond where the fix +expects to next perform averaging. +
Fix ave/spatial settings invalid with changing box
If the ave setting is "running" or "window" and the box size/shape @@ -3044,6 +3122,11 @@ all intensive/extensive when turned into an array by fix ave/time.
The index for the vector is out of bounds. +
Fix ave/time missed timestep + +
You cannot reset the timestep to a value beyond where the fix +expects to next perform averaging. +
Fix ave/time variable is not equal-style variable
Self-explanatory. @@ -3319,6 +3402,10 @@ which means it is a point particle.
Self-explanatory. +
Fix nvt/npt/nph dilate group ID does not exist + +
Self-explanatory. +
Fix nvt/sphere requires extended particles
This fix can only be used for particles of a finite size. @@ -3484,6 +3571,14 @@ fix store/state.
Self-explanatory. +
Fix temp/berendsen variable returned negative temperature + +
Self-explanatory. + +
Fix temp/rescale variable returned negative temperature + +
Self-explanatory. +
Fix thermal/conductivity swap value must be positive
Self-explanatory. @@ -3653,6 +3748,11 @@ create_box command.
A region ID used in the group command does not exist. +
If read_dump purges it cannot replace or trim + +
These operations are not compatible. See the read_dump doc +page for details. +
Illegal ... command
Self-explanatory. Check the input script syntax and compare to the @@ -3770,7 +3870,7 @@ definitions.
Inconsistent iparam/jparam values in fix bond/create command -
If itype and jtype are the same, then their maxbond and newtype +
If itype and jtype are the same, then their maxbond and newtype settings must also be the same.
Inconsistent line segment in data file @@ -3863,6 +3963,10 @@ bonus data must be formatted for certain atom styles.
Self-explanatory. Check the input script or data file. +
Incorrect rigid body format in fix rigid file + +
The number of fields per line is not what expected. +
Incorrect sign arg for dihedral coefficients
Self-explanatory. Check the input script or data file. @@ -4234,6 +4338,10 @@ be for a single processor.
Zoom value must be > 0.0. +
Invalid dump reader style + +
Self-explanatory. +
Invalid dump style
The choice of dump style is unknown. @@ -4476,6 +4584,11 @@ cannot be the same partition.
Self-explanatory. +
Invalid rigid body ID in fix rigid file + +
The ID does not match the number or an existing ID of rigid bodies +that are defined by the fix rigid command. +
Invalid run command N value
The number of timesteps must fit in a 32-bit integer. If you want to @@ -4615,6 +4728,10 @@ where it is requesting neighbors incorrectly.
This environment variable must be set to use pair_style kim. See the doc page for pair_style kim. +
KSpace accuracy too large to estimate G vector + +
Paul will doc this. +
KSpace style has not yet been set
Cannot use kspace_modify command until a kspace style is set. @@ -4628,6 +4745,10 @@ Coulombic component be selected.
Self-explanatory. +
Kspace style does not support compute group/group + +
Self-explanatory. +
Kspace style pppm/tip4p requires newton on
Self-explanatory. @@ -5019,10 +5140,6 @@ neighbors allowed for one atom.
This is required to prevent wasting too much memory. -
Neighbors of ghost atoms only allowed for full neighbor lists - -
This is a current restriction within LAMMPS. -
New bond exceeded bonds per atom in fix bond/create
See the read_data command for info on setting the "extra bond per @@ -5038,6 +5155,10 @@ the special bonds list to allow for additional bonds to be formed.
The newton command cannot be used to change the newton bond value after a read_data, read_restart, or create_box command. +
No Kspace style defined for compute group/group + +
Self-explanatory. +
No OpenMP support compiled in
An OpenMP flag is set, but LAMMPS was not built with @@ -5068,6 +5189,10 @@ but they were not present.
Self-explanatory. Check data file. +
No box information in dump. You have to use 'box no' + +
Self-explanatory. +
No dihedral style is defined for compute dihedral/local
Self-explanatory. @@ -5115,6 +5240,10 @@ requested elements.
The EAM potential file does not contain elements that match the requested elements. +
No overlap of box and region for create_atoms + +
Self-explanatory. +
No pair hbond/dreiding coefficients set
Self-explanatory. @@ -5207,15 +5336,15 @@ else the fix contribution to the pressure virial is incorrect. OFFSET is currently set to 4096. You likely need to decrease the requested accuracy. -
PPPM order cannot be greater than %d +
PPPM order cannot be < 2 or > than %d -
Self-explanatory. +
This is a limitation of the PPPM implementation in LAMMPS.
PPPM order has been reduced to 0
LAMMPS has attempted to reduce the PPPM order to enable the simulation to run, but can reduce the order no further. Try increasing the -accuracy of PPPM by reducing the tolerance size, thus inducing a +accuracy of PPPM by reducing the tolerance size, thus inducing a larger PPPM grid.
PRD command before simulation box is defined @@ -5450,6 +5579,15 @@ bonds. Use the atom_modify command to define one.
See the newton command. This is a restriction to use the AIREBO potential. +
Pair style BOP requires atom IDs + +
This is a requirement to use the BOP potential. + +
Pair style BOP requires newton pair on + +
See the newton command. This is a restriction to use the BOP +potential. +
Pair style COMB requires atom IDs
This is a requirement to use the AIREBO potential. @@ -5463,6 +5601,15 @@ potential.
See the newton command. This is a restriction to use the COMB potential. +
Pair style LCBOP requires atom IDs + +
This is a requirement to use the LCBOP potential. + +
Pair style LCBOP requires newton pair on + +
See the newton command. This is a restriction to use the LCBOP +potential. +
Pair style MEAM requires newton pair on
See the newton command. This is a restriction to use the MEAM @@ -5486,6 +5633,11 @@ potential.
See the newton command. This is a restriction to use the Tersoff potential. +
Pair style bop requires comm ghost cutoff at least 3x larger than %g + +
Use the communicate ghost command to set this. See the pair bop +doc page for more details. +
Pair style born/coul/long requires atom attribute q
An atom style that defines this attribute must be used. @@ -5871,6 +6023,19 @@ cart for the map option.
Equilibrium spring length is invalid. +
Read_dump field not found in dump file + +
Self-explanatory. + +
Read_dump triclinic status does not match simulation + +
Both the dump snapshot and the current LAMMPS simulation must +be using either an orthogonal or triclinic box. + +
Read_dump x,y,z fields do not have consistent scaling + +
Self-explanatory. +
Reax_defs.h setting for NATDEF is too small
Edit the setting in the ReaxFF library and re-compile the @@ -5977,6 +6142,15 @@ file.
See the setting for bigint in the src/lmptype.h file. +
Rerun command before simulation box is defined + +
The rerun command cannot be used before a read_data, read_restart, or +create_box command. + +
Rerun dump file does not contain requested snapshot + +
Self-explanatory. +
Resetting timestep is not allowed with fix move
This is because fix move is moving atoms based on elapsed time. @@ -5993,12 +6167,28 @@ file.
The first cutoff must be <= the second cutoff. +
Restart variable returned a bad timestep + +
The variable must return a timestep greater than the current timestep. +
Restrain atoms %d %d %d %d missing on proc %d at step %ld
The 4 atoms in a restrain dihedral specified by the fix restrain command are not all accessible to a processor. This probably means an atom has moved too far. +
Restrain atoms %d %d %d missing on proc %d at step %ld + +
The 3 atoms in a restrain angle specified by the fix restrain +command are not all accessible to a processor. This probably means an +atom has moved too far. + +
Restrain atoms %d %d missing on proc %d at step %ld + +
The 2 atoms in a restrain bond specified by the fix restrain +command are not all accessible to a processor. This probably means an +atom has moved too far. +
Reuse of compute ID
A compute ID cannot be used twice. @@ -6441,11 +6631,22 @@ not defined by the atom style used in this simulation.
Table size specified via pair_modify command does not work with your machine's floating point representation. +
Too many atom pairs for pair bop + +
The number of atomic pairs exceeds the expected number. Check your +atomic structure to ensure that it is realistic. +
Too many atom sorting bins
This is likely due to an immense simulation box that has blown up to a large size. +
Too many atom triplets for pair bop + +
The number of three atom groups for angle determinations exceeds the +expected number. Check your atomic structrure to ensure that it is +realistic. +
Too many atoms for dump dcd
The system size must fit in a 32-bit integer to use this dump @@ -6467,12 +6668,12 @@ machine's floating point representation.
Too many groups -
The maximum number of atom groups (including the "all" group) is +
The maximum number of atom groups (including the "all" group) is given by MAX_GROUP in group.cpp and is 32.
Too many iterations -
You must use a number of iterations that fit in a 32-bit integer +
You must use a number of iterations that fit in a 32-bit integer for minimization.
Too many local+ghost atoms for neighbor list @@ -6502,7 +6703,7 @@ to a large size.
Too many timesteps for NEB -
You must use a number of timesteps that fit in a 32-bit integer +
You must use a number of timesteps that fit in a 32-bit integer for NEB.
Too many total atoms @@ -6578,6 +6779,14 @@ quote.
LAMMPS hit the end of the data file while attempting to read a section. Something is wrong with the format of the data file. +
Unexpected end of dump file + +
A read operation from the file failed. + +
Unexpected end of fix rigid file + +
A read operation from the file failed. +
Units command after simulation box is defined
The units command cannot be used after a read_data, read_restart, or @@ -6713,7 +6922,7 @@ deform needs to be used.
Using pair lubricate with inconsistent fix deform remap option -
If fix deform is used, the remap v option is required. +
Must use remap v option with fix deform with this pair style.
Using pair lubricate/poly with inconsistent fix deform remap option @@ -6772,6 +6981,10 @@ before the simulation has been setup.
Only equal-style variables can be used. +
Variable for fix gravity is invalid style + +
Only equal-style variables can be used. +
Variable for fix indent is invalid style
Only equal-style variables can be used. @@ -6792,6 +7005,14 @@ before the simulation has been setup.
Only equal-style variables can be used. +
Variable for fix temp/berendsen is invalid style + +
Only equal-style variables can be used. + +
Variable for fix temp/rescale is invalid style + +
Only equal-style variables can be used. +
Variable for fix wall is invalid style
Only equal-style variables can be used. @@ -6812,6 +7033,10 @@ before the simulation has been setup.
Self-explanatory. +
Variable for restart is invalid style + +
Only equal-style variables can be used. +
Variable for thermo every is invalid style
Only equal-style variables can be used. @@ -6912,6 +7137,10 @@ before the simulation has been setup.
Self-explanatory. +
Variable name for fix gravity does not exist + +
Self-explanatory. +
Variable name for fix indent does not exist
Self-explanatory. @@ -6932,6 +7161,14 @@ before the simulation has been setup.
Self-explanatory. +
Variable name for fix temp/berendsen does not exist + +
Self-explanatory. + +
Variable name for fix temp/rescale does not exist + +
Self-explanatory. +
Variable name for fix wall does not exist
Self-explanatory. @@ -6948,6 +7185,10 @@ before the simulation has been setup.
Self-explanatory. +
Variable name for restart does not exist + +
Self-explanatory. +
Variable name for thermo every does not exist
Self-explanatory. @@ -7009,6 +7250,11 @@ variable doc page for ideas on how to make this work.
Self-explanatory. +
Water H epsilon must be 0.0 for pair style lj/cut/coul/long/tip4p + +
This is because LAMMPS does not compute the Lennard-Jones interactions +with these particles for efficiency reasons. +
World variable count doesn't match # of partitions
A world-style variable must specify a number of values equal to the @@ -7035,6 +7281,10 @@ read_restart, or create_box command. includes atoms with no molecule ID. This is probably not what you want. +
Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero + +
Self-explantory. +
Broken bonds will not alter angles, dihedrals, or impropers
See the doc page for fix bond/break for more info on this @@ -7046,6 +7296,14 @@ restriction. The solution is to check for building the regular neighbor lists more frequently. +
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. +
Compute cna/atom cutoff may be too large to find ghost atom neighbors
The neighbor cutoff used may not encompass enough ghost atoms @@ -7112,9 +7370,18 @@ of a molecule.
Fix recenter should come after all other integration fixes -
Other fixes may change the position of the center-of-mass, so +
Other fixes may change the position of the center-of-mass, so fix recenter should come last. +
Fix shake with rRESPA computes invalid pressures + +
This is a known bug in LAMMPS that has not yet been fixed. If you use +SHAKE with rRESPA and perform a constant volume simulation (e.g. using +fix npt) this only affects the output pressure, not the dynamics of +the simulation. If you use SHAKE with rRESPA and perform a constant +pressure simulation (e.g. using fix npt) then you will be +equilibrating to the wrong volume. +
Fix srd SRD moves may trigger frequent reneighboring
This is because the SRD particles may move long distances. diff --git a/doc/Section_errors.txt b/doc/Section_errors.txt index 4d7bc690ca..ebe1f90f1f 100644 --- a/doc/Section_errors.txt +++ b/doc/Section_errors.txt @@ -217,6 +217,12 @@ command. :dd All pair coefficients must be set in the data file or by the pair_coeff command before running a simulation. :dd +{All read_dump x,y,z fields must be specified for scaled, triclinic coords} :dt + +For triclinic boxes and scaled coordinates you must specify all 3 of +the x,y,z fields, else LAMMPS cannot reconstruct the unscaled +coordinates. :dd + {All universe/uloop variables must have same # of values} :dt Self-explanatory. :dd @@ -315,7 +321,7 @@ still being processed. :dd {Append boundary must be shrink/minimum} :dt The boundary style of the face where atoms are added -must be of type m (shrink/minimum). :dd +must be of type m (shrink/minimum). :dd {Arccos of invalid value in variable formula} :dt @@ -472,9 +478,11 @@ or create_box command. :dd The string can only contain the characters "x", "y", or "z". :dd -{Balance dynamic string is invalid for 2d simulation} :dt +{Balance produced bad splits} :dt -The string cannot contain the letter "z". :dd +This should not occur. It means two or more cutting plane locations +are on top of each other or out of order. Report the problem to the +developers. :dd {Bias compute does not calculate a velocity bias} :dt @@ -521,6 +529,12 @@ Number of table entries is not a correct power of 2. :dd Cannot use TIP4P pair potential unless bond and angle potentials are defined. :dd +{Bond atom missing in box size check} :dt + +The 2nd atoms 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. :dd + {Bond atom missing in delete_bonds} :dt The delete_bonds command cannot find one or more atoms in a particular @@ -584,6 +598,15 @@ List of bond table parameters must include N setting. :dd The values in the tabulated file must be monotonically increasing. :dd +{Bond/angle/dihedral extent > half of periodic box length} :dt + +This is a restriction because LAMMPS can be confused about which image +of an atom in the bonded interaction is the correct one to use. +"Extent" in this context means the maximum end-to-end length of the +bond/angle/dihedral. LAMMPS computes this by taking the maximum bond +length, multiplying by the number of bonds in the interaction (e.g. 3 +for a dihedral) and adding a small amount of stretch. :dd + {Bond_coeff command before bond_style is defined} :dt Coefficients cannot be set in the data file or via the bond_coeff @@ -652,6 +675,14 @@ This is current restriction for NEB as implemented in LAMMPS. :dd This is current restriction for NEB as implemented in LAMMPS. :dd +{Cannot (yet) use K-space slab correction with compute group/group} :dt + +This option is not yet supported. :dd + +{Cannot (yet) use Kspace slab correction with compute group/group} :dt + +This option is not yet supported. :dd + {Cannot (yet) use PPPM with triclinic box} :dt This feature is not yet supported. :dd @@ -826,6 +857,11 @@ path and name are correct. :dd The specified AIREBO potential file cannot be opened. Check that the path and name are correct. :dd +{Cannot open BOP potential file %s} :dt + +The specified BOP potential file cannot be opened. Check that the +path and name are correct. :dd + {Cannot open COMB potential file %s} :dt The specified COMB potential file cannot be opened. Check that the @@ -841,6 +877,11 @@ path and name are correct. :dd The specified EIM potential file cannot be opened. Check that the path and name are correct. :dd +{Cannot open LCBOP potential file %s} :dt + +The specified LCBOP potential file cannot be opened. Check that the +path and name are correct. :dd + {Cannot open MEAM potential file %s} :dt The specified MEAM potential file cannot be opened. Check that the @@ -858,8 +899,7 @@ path and name are correct. :dd {Cannot open balance output file} :dt -This error message can only occur if debug options -are uncommented in src/balance.cpp. :dd +Self-explanatory. :dd {Cannot open custom file} :dt @@ -900,6 +940,10 @@ correct. :dd The specified file cannot be opened. Check that the path and name are correct. :dd +{Cannot open fix balance output file} :dt + +Self-explanatory. :dd + {Cannot open fix poems file %s} :dt The specified file cannot be opened. Check that the path and name are @@ -919,6 +963,11 @@ Check that the path and name are correct. :dd The output file for the fix reax/bonds command cannot be opened. Check that the path and name are correct. :dd +{Cannot open fix rigid infile %s} :dt + +The specified file cannot be opened. Check that the path and name are +correct. :dd + {Cannot open fix tmd file %s} :dt The output file for the fix tmd command cannot be opened. Check that @@ -1023,17 +1072,6 @@ are defined. :dd You cannot reset the timestep when a fix that keeps track of elapsed time is in place. :dd -{Cannot reset timestep with dump file already written to} :dt - -Changing the timestep will confuse when a dump file is written. Use -the undump command, then restart the dump file. :dd - -{Cannot reset timestep with restart file already written} :dt - -Changing the timestep will confuse when a restart file is written. -Use the "restart 0" command to turn off restarts, then start them -again. :dd - {Cannot restart fix rigid/nvt with different # of chains} :dt This is because the restart file contains per-chain info. :dd @@ -1546,6 +1584,10 @@ Self-explanatory. :dd Cannot specify both options at the same time. :dd +{Cannot yet use fix balance with PPPM} :dt + +This is a current limitation of LAMMPS. :dd + {Cannot zero Langevin force of 0 atoms} :dt The group has zero atoms, so you cannot request its force @@ -2466,6 +2508,14 @@ Use the dump_modify sort command to enable this. :dd The variable must return a timestep greater than the current timestep. :dd +{Dump file does not contain requested snapshot} :dt + +Self-explanatory. :dd + +{Dump file is incorrectly formatted} :dt + +No atoms were found in file. :dd + {Dump image bond not allowed with no bond types} :dt Self-explanatory. :dd @@ -2601,6 +2651,10 @@ dumped. :dd Only per-atom quantities that are defined for the atom style being used are allowed. :dd +{Duplicate fields in read_dump command} :dt + +Self-explanatory. :dd + {Duplicate particle in PeriDynamic bond - simulation box is too small} :dt This is likely because your box length is shorter than 2 times @@ -2710,6 +2764,10 @@ Self-explanatory. :dd Self-explanatory :dd +{Fix ID for read_data does not exist} :dt + +Self-explanatory. :dd + {Fix ID must be alphanumeric or underscore characters} :dt Self-explanatory. :dd @@ -2795,6 +2853,11 @@ A fix used by fix ave/atom must generate per-atom values. :dd A fix used by fix ave/atom must generate per-atom values. :dd +{Fix ave/atom missed timestep} :dt + +You cannot reset the timestep to a value beyond where the fix +expects to next perform averaging. :dd + {Fix ave/atom variable is not atom-style variable} :dt A variable used by fix ave/atom must generate per-atom values. :dd @@ -2823,6 +2886,11 @@ Self-explanatory. :dd The index for the vector is out of bounds. :dd +{Fix ave/correlate missed timestep} :dt + +You cannot reset the timestep to a value beyond where the fix +expects to next perform averaging. :dd + {Fix ave/correlate variable is not equal-style variable} :dt Self-explanatory. :dd @@ -2940,6 +3008,11 @@ Self-explanatory. :dd All inputs in a single fix ave/histo command must be of the same style. :dd +{Fix ave/histo missed timestep} :dt + +You cannot reset the timestep to a value beyond where the fix +expects to next perform averaging. :dd + {Fix ave/spatial compute does not calculate a per-atom array} :dt Self-explanatory. :dd @@ -2976,6 +3049,11 @@ The index for the vector is out of bounds. :dd Self-explanatory. :dd +{Fix ave/spatial missed timestep} :dt + +You cannot reset the timestep to a value beyond where the fix +expects to next perform averaging. :dd + {Fix ave/spatial settings invalid with changing box} :dt If the ave setting is "running" or "window" and the box size/shape @@ -3040,6 +3118,11 @@ Self-explanatory. :dd The index for the vector is out of bounds. :dd +{Fix ave/time missed timestep} :dt + +You cannot reset the timestep to a value beyond where the fix +expects to next perform averaging. :dd + {Fix ave/time variable is not equal-style variable} :dt Self-explanatory. :dd @@ -3315,6 +3398,10 @@ Self-explanatory. :dd Self-explanatory. :dd +{Fix nvt/npt/nph dilate group ID does not exist} :dt + +Self-explanatory. :dd + {Fix nvt/sphere requires extended particles} :dt This fix can only be used for particles of a finite size. :dd @@ -3480,6 +3567,14 @@ Only atom-style variables calculate per-atom quantities. :dd Self-explanatory. :dd +{Fix temp/berendsen variable returned negative temperature} :dt + +Self-explanatory. :dd + +{Fix temp/rescale variable returned negative temperature} :dt + +Self-explanatory. :dd + {Fix thermal/conductivity swap value must be positive} :dt Self-explanatory. :dd @@ -3649,6 +3744,11 @@ create_box command. :dd A region ID used in the group command does not exist. :dd +{If read_dump purges it cannot replace or trim} :dt + +These operations are not compatible. See the read_dump doc +page for details. :dd + {Illegal ... command} :dt Self-explanatory. Check the input script syntax and compare to the @@ -3766,7 +3866,7 @@ The data file header lists improper but no improper types. :dd {Inconsistent iparam/jparam values in fix bond/create command} :dt -If itype and jtype are the same, then their maxbond and newtype +If itype and jtype are the same, then their maxbond and newtype settings must also be the same. :dd {Inconsistent line segment in data file} :dt @@ -3859,6 +3959,10 @@ Incorrect number of words per line in the potential file. :dd Self-explanatory. Check the input script or data file. :dd +{Incorrect rigid body format in fix rigid file} :dt + +The number of fields per line is not what expected. :dd + {Incorrect sign arg for dihedral coefficients} :dt Self-explanatory. Check the input script or data file. :dd @@ -4230,6 +4334,10 @@ Theta must be between 0.0 and 180.0 inclusive. :dd Zoom value must be > 0.0. :dd +{Invalid dump reader style} :dt + +Self-explanatory. :dd + {Invalid dump style} :dt The choice of dump style is unknown. :dd @@ -4472,6 +4580,11 @@ The choice of region style is unknown. :dd Self-explanatory. :dd +{Invalid rigid body ID in fix rigid file} :dt + +The ID does not match the number or an existing ID of rigid bodies +that are defined by the fix rigid command. :dd + {Invalid run command N value} :dt The number of timesteps must fit in a 32-bit integer. If you want to @@ -4611,6 +4724,10 @@ where it is requesting neighbors incorrectly. :dd This environment variable must be set to use pair_style kim. See the doc page for pair_style kim. :dd +{KSpace accuracy too large to estimate G vector} :dt + +Paul will doc this. :dd + {KSpace style has not yet been set} :dt Cannot use kspace_modify command until a kspace style is set. :dd @@ -4624,6 +4741,10 @@ Coulombic component be selected. :dd Self-explanatory. :dd +{Kspace style does not support compute group/group} :dt + +Self-explanatory. :dd + {Kspace style pppm/tip4p requires newton on} :dt Self-explanatory. :dd @@ -5015,10 +5136,6 @@ Self-explanatory. :dd This is required to prevent wasting too much memory. :dd -{Neighbors of ghost atoms only allowed for full neighbor lists} :dt - -This is a current restriction within LAMMPS. :dd - {New bond exceeded bonds per atom in fix bond/create} :dt See the read_data command for info on setting the "extra bond per @@ -5034,6 +5151,10 @@ the special bonds list to allow for additional bonds to be formed. :dd The newton command cannot be used to change the newton bond value after a read_data, read_restart, or create_box command. :dd +{No Kspace style defined for compute group/group} :dt + +Self-explanatory. :dd + {No OpenMP support compiled in} :dt An OpenMP flag is set, but LAMMPS was not built with @@ -5064,6 +5185,10 @@ Self-explanatory. :dd Self-explanatory. Check data file. :dd +{No box information in dump. You have to use 'box no'} :dt + +Self-explanatory. :dd + {No dihedral style is defined for compute dihedral/local} :dt Self-explanatory. :dd @@ -5111,6 +5236,10 @@ requested elements. :dd The EAM potential file does not contain elements that match the requested elements. :dd +{No overlap of box and region for create_atoms} :dt + +Self-explanatory. :dd + {No pair hbond/dreiding coefficients set} :dt Self-explanatory. :dd @@ -5203,15 +5332,15 @@ The global PPPM grid is larger than OFFSET in one or more dimensions. OFFSET is currently set to 4096. You likely need to decrease the requested accuracy. :dd -{PPPM order cannot be greater than %d} :dt +{PPPM order cannot be < 2 or > than %d} :dt -Self-explanatory. :dd +This is a limitation of the PPPM implementation in LAMMPS. :dd {PPPM order has been reduced to 0} :dt LAMMPS has attempted to reduce the PPPM order to enable the simulation to run, but can reduce the order no further. Try increasing the -accuracy of PPPM by reducing the tolerance size, thus inducing a +accuracy of PPPM by reducing the tolerance size, thus inducing a larger PPPM grid. :dd {PRD command before simulation box is defined} :dt @@ -5446,6 +5575,15 @@ This is a requirement to use the AIREBO potential. :dd See the newton command. This is a restriction to use the AIREBO potential. :dd +{Pair style BOP requires atom IDs} :dt + +This is a requirement to use the BOP potential. :dd + +{Pair style BOP requires newton pair on} :dt + +See the newton command. This is a restriction to use the BOP +potential. :dd + {Pair style COMB requires atom IDs} :dt This is a requirement to use the AIREBO potential. :dd @@ -5459,6 +5597,15 @@ Self-explanatory. :dd See the newton command. This is a restriction to use the COMB potential. :dd +{Pair style LCBOP requires atom IDs} :dt + +This is a requirement to use the LCBOP potential. :dd + +{Pair style LCBOP requires newton pair on} :dt + +See the newton command. This is a restriction to use the LCBOP +potential. :dd + {Pair style MEAM requires newton pair on} :dt See the newton command. This is a restriction to use the MEAM @@ -5482,6 +5629,11 @@ This is a requirement to use the Tersoff potential. :dd See the newton command. This is a restriction to use the Tersoff potential. :dd +{Pair style bop requires comm ghost cutoff at least 3x larger than %g} :dt + +Use the communicate ghost command to set this. See the pair bop +doc page for more details. :dd + {Pair style born/coul/long requires atom attribute q} :dt An atom style that defines this attribute must be used. :dd @@ -5867,6 +6019,19 @@ Self-explanatory. :dd Equilibrium spring length is invalid. :dd +{Read_dump field not found in dump file} :dt + +Self-explanatory. :dd + +{Read_dump triclinic status does not match simulation} :dt + +Both the dump snapshot and the current LAMMPS simulation must +be using either an orthogonal or triclinic box. :dd + +{Read_dump x,y,z fields do not have consistent scaling} :dt + +Self-explanatory. :dd + {Reax_defs.h setting for NATDEF is too small} :dt Edit the setting in the ReaxFF library and re-compile the @@ -5973,6 +6138,15 @@ file. :dd See the setting for bigint in the src/lmptype.h file. :dd +{Rerun command before simulation box is defined} :dt + +The rerun command cannot be used before a read_data, read_restart, or +create_box command. :dd + +{Rerun dump file does not contain requested snapshot} :dt + +Self-explanatory. :dd + {Resetting timestep is not allowed with fix move} :dt This is because fix move is moving atoms based on elapsed time. :dd @@ -5989,12 +6163,28 @@ Self-explanatory. :dd The first cutoff must be <= the second cutoff. :dd +{Restart variable returned a bad timestep} :dt + +The variable must return a timestep greater than the current timestep. :dd + {Restrain atoms %d %d %d %d missing on proc %d at step %ld} :dt The 4 atoms in a restrain dihedral specified by the fix restrain command are not all accessible to a processor. This probably means an atom has moved too far. :dd +{Restrain atoms %d %d %d missing on proc %d at step %ld} :dt + +The 3 atoms in a restrain angle specified by the fix restrain +command are not all accessible to a processor. This probably means an +atom has moved too far. :dd + +{Restrain atoms %d %d missing on proc %d at step %ld} :dt + +The 2 atoms in a restrain bond specified by the fix restrain +command are not all accessible to a processor. This probably means an +atom has moved too far. :dd + {Reuse of compute ID} :dt A compute ID cannot be used twice. :dd @@ -6437,11 +6627,22 @@ The timestep must fit in a 32-bit integer to use this dump style. :dd Table size specified via pair_modify command does not work with your machine's floating point representation. :dd +{Too many atom pairs for pair bop} :dt + +The number of atomic pairs exceeds the expected number. Check your +atomic structure to ensure that it is realistic. :dd + {Too many atom sorting bins} :dt This is likely due to an immense simulation box that has blown up to a large size. :dd +{Too many atom triplets for pair bop} :dt + +The number of three atom groups for angle determinations exceeds the +expected number. Check your atomic structrure to ensure that it is +realistic. :dd + {Too many atoms for dump dcd} :dt The system size must fit in a 32-bit integer to use this dump @@ -6463,12 +6664,12 @@ machine's floating point representation. :dd {Too many groups} :dt -The maximum number of atom groups (including the "all" group) is +The maximum number of atom groups (including the "all" group) is given by MAX_GROUP in group.cpp and is 32. :dd {Too many iterations} :dt -You must use a number of iterations that fit in a 32-bit integer +You must use a number of iterations that fit in a 32-bit integer for minimization. :dd {Too many local+ghost atoms for neighbor list} :dt @@ -6498,7 +6699,7 @@ The cummulative timesteps must fit in a 64-bit integer. :dd {Too many timesteps for NEB} :dt -You must use a number of timesteps that fit in a 32-bit integer +You must use a number of timesteps that fit in a 32-bit integer for NEB. :dd {Too many total atoms} :dt @@ -6574,6 +6775,14 @@ Self-explanatory. :dd LAMMPS hit the end of the data file while attempting to read a section. Something is wrong with the format of the data file. :dd +{Unexpected end of dump file} :dt + +A read operation from the file failed. :dd + +{Unexpected end of fix rigid file} :dt + +A read operation from the file failed. :dd + {Units command after simulation box is defined} :dt The units command cannot be used after a read_data, read_restart, or @@ -6709,7 +6918,7 @@ deform needs to be used. :dd {Using pair lubricate with inconsistent fix deform remap option} :dt -If fix deform is used, the remap v option is required. :dd +Must use remap v option with fix deform with this pair style. :dd {Using pair lubricate/poly with inconsistent fix deform remap option} :dt @@ -6768,6 +6977,10 @@ The variable must be an equal-style variable. :dd Only equal-style variables can be used. :dd +{Variable for fix gravity is invalid style} :dt + +Only equal-style variables can be used. :dd + {Variable for fix indent is invalid style} :dt Only equal-style variables can be used. :dd @@ -6788,6 +7001,14 @@ Only equal-style variables can be used. :dd Only equal-style variables can be used. :dd +{Variable for fix temp/berendsen is invalid style} :dt + +Only equal-style variables can be used. :dd + +{Variable for fix temp/rescale is invalid style} :dt + +Only equal-style variables can be used. :dd + {Variable for fix wall is invalid style} :dt Only equal-style variables can be used. :dd @@ -6808,6 +7029,10 @@ Only equal-style variables can be used. :dd Self-explanatory. :dd +{Variable for restart is invalid style} :dt + +Only equal-style variables can be used. :dd + {Variable for thermo every is invalid style} :dt Only equal-style variables can be used. :dd @@ -6908,6 +7133,10 @@ Self-explantory. :dd Self-explanatory. :dd +{Variable name for fix gravity does not exist} :dt + +Self-explanatory. :dd + {Variable name for fix indent does not exist} :dt Self-explanatory. :dd @@ -6928,6 +7157,14 @@ Self-explanatory. :dd Self-explanatory. :dd +{Variable name for fix temp/berendsen does not exist} :dt + +Self-explanatory. :dd + +{Variable name for fix temp/rescale does not exist} :dt + +Self-explanatory. :dd + {Variable name for fix wall does not exist} :dt Self-explanatory. :dd @@ -6944,6 +7181,10 @@ Self-explanatory. :dd Self-explanatory. :dd +{Variable name for restart does not exist} :dt + +Self-explanatory. :dd + {Variable name for thermo every does not exist} :dt Self-explanatory. :dd @@ -7005,6 +7246,11 @@ Self-explanatory. :dd Self-explanatory. :dd +{Water H epsilon must be 0.0 for pair style lj/cut/coul/long/tip4p} :dt + +This is because LAMMPS does not compute the Lennard-Jones interactions +with these particles for efficiency reasons. :dd + {World variable count doesn't match # of partitions} :dt A world-style variable must specify a number of values equal to the @@ -7031,6 +7277,10 @@ The group used in a compute command that operates on moleclues includes atoms with no molecule ID. This is probably not what you want. :dd +{Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero} :dt + +Self-explantory. :dd + {Broken bonds will not alter angles, dihedrals, or impropers} :dt See the doc page for fix bond/break for more info on this @@ -7042,6 +7292,14 @@ This can cause LAMMPS to crash when the neighbor list is built. The solution is to check for building the regular neighbor lists more frequently. :dd +{Cannot include log terms without 1/r terms; setting flagHI to 1} :dt + +Self-explanatory. :dd + +{Cannot include log terms without 1/r terms; setting flagHI to 1.} :dt + +Self-explanatory. :dd + {Compute cna/atom cutoff may be too large to find ghost atom neighbors} :dt The neighbor cutoff used may not encompass enough ghost atoms @@ -7108,9 +7366,18 @@ Atoms store this quantity, but fix move does not (yet) update it. :dd {Fix recenter should come after all other integration fixes} :dt -Other fixes may change the position of the center-of-mass, so +Other fixes may change the position of the center-of-mass, so fix recenter should come last. :dd +{Fix shake with rRESPA computes invalid pressures} :dt + +This is a known bug in LAMMPS that has not yet been fixed. If you use +SHAKE with rRESPA and perform a constant volume simulation (e.g. using +fix npt) this only affects the output pressure, not the dynamics of +the simulation. If you use SHAKE with rRESPA and perform a constant +pressure simulation (e.g. using fix npt) then you will be +equilibrating to the wrong volume. :dd + {Fix srd SRD moves may trigger frequent reneighboring} :dt This is because the SRD particles may move long distances. :dd diff --git a/doc/Section_packages.html b/doc/Section_packages.html index e166116085..ae604bbf98 100644 --- a/doc/Section_packages.html +++ b/doc/Section_packages.html @@ -44,24 +44,24 @@ packages, more details are provided.

- + - - + + - + - + diff --git a/doc/Section_packages.txt b/doc/Section_packages.txt index 8e9556f82b..e3575fd5f7 100644 --- a/doc/Section_packages.txt +++ b/doc/Section_packages.txt @@ -39,24 +39,24 @@ packages, more details are provided. The current list of standard packages is as follows: Package, Description, Author(s), Doc page, Example, Library -ASPHERE, aspherical particles, -, "howto"_Section_howto.html#howto_14, ellipse, - +ASPHERE, aspherical particles, -, "Section_howto"_Section_howto.html#howto_14, ellipse, - CLASS2, class 2 force fields, -, "pair_style lj/class2"_pair_class2.html, -, - COLLOID, colloidal particles, -, "atom_style colloid"_atom_style.html, colloid, - DIPOLE, point dipole particles, -, "pair_style dipole/cut"_pair_dipole.html, dipole, - FLD, Fast Lubrication Dynamics, Kumar & Bybee & Higdon (1), "pair_style lubricateU"_pair_lubricateU.html, -, - GPU, GPU-enabled potentials, Mike Brown (ORNL), "Section accelerate"_Section_accelerate.html#acc_3, gpu, lib/gpu -GRANULAR, granular systems, -, "howto"_Section_howto.html#howto_6, pour, - -KIM, openKIM potentials, Smirichinski & Elliot & Tadmor (3), pair_style kim"_pair_kim.html, kim, lib/kim +GRANULAR, granular systems, -, "Section_howto"_Section_howto.html#howto_6, pour, - +KIM, openKIM potentials, Smirichinski & Elliot & Tadmor (3), "pair_style kim"_pair_kim.html, kim, lib/kim KSPACE, long-range Coulombic solvers, -, "kspace_style"_kspace_style.html, peptide, - MANYBODY, many-body potentials, -, "pair_style tersoff"_pair_tersoff.html, shear, - MEAM, modified EAM potential, Greg Wagner (Sandia), "pair_style meam"_pair_meam.html, meam, lib/meam MC, Monte Carlo options, -, "fix gcmc"_fix_gcmc.html, -, - -MOLECULE, molecular system force fields, -, "howto"_Section_howto.html#howto_3, peptide, - +MOLECULE, molecular system force fields, -, "Section_howto"_Section_howto.html#howto_3, peptide, - OPT, optimized pair potentials, Fischer & Richie & Natoli (2), "Section accelerate"_Section_accelerate.html#acc_1, -, - PERI, Peridynamics models, Mike Parks (Sandia), "pair_style peri"_pair_peri.html, peri, - POEMS, coupled rigid body motion, Rudra Mukherjee (JPL), "fix poems"_fix_poems.html, rigid, lib/poems REAX, ReaxFF potential, Aidan Thompson (Sandia), "pair_style reax"_pair_reax.html, reax, lib/reax -REPLICA, multi-replica methods, -, "howto"_Section_howto.html#howto_5, tad, - +REPLICA, multi-replica methods, -, "Section_howto"_Section_howto.html#howto_5, tad, - SHOCK, shock loading methods, -, "fix msst"_fix_msst.html, -, - SRD, stochastic rotation dynamics, -, "fix srd"_fix_srd.html, srd, - XTC, dumps in XTC format, -, "dump"_dump.html, -, - diff --git a/doc/Section_start.html b/doc/Section_start.html index e071e8182b..eef8e51a83 100644 --- a/doc/Section_start.html +++ b/doc/Section_start.html @@ -223,11 +223,14 @@ Restrictions section of the dump command for details.

Use at most one of the -DLAMMPS_SMALLBIG, -DLAMMPS_BIGBIG, -D-DLAMMPS_SMALLSMALL settings. The default is -DLAMMPS_SMALLBIG. -These refer to use of 4-byte (small) vs 8-byte (big) integers within -LAMMPS, as described in src/lmptype.h. The only reason to use the -BIGBIG setting is to enable simulation of huge molecular systems with -more than 2 billion atoms. The only reason to use the SMALLSMALL -setting is if your machine does not support 64-bit integers. +These settings refer to use of 4-byte (small) vs 8-byte (big) integers +within LAMMPS, as specified in src/lmptype.h. The only reason to use +the BIGBIG setting is to enable simulation of huge molecular systems +with more than 2 billion atoms or to allow moving atoms to wrap back +through a periodic box more than 512 times. The only reason to use +the SMALLSMALL setting is if your machine does not support 64-bit +integers. See the Additional build tips section below +for more details.

The -DLAMMPS_LONGLONG_TO_LONG setting may be needed if your system or MPI version does not recognize "long long" data types. In this case a @@ -434,41 +437,46 @@ Obj_target where it stores the system-specific *.o files. files created when LAMMPS is built, for either all builds or for a particular machine.

-

(3) Changing the size limits in src/lmptype.h +

(3) Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or +-DLAMMPS_BIBIG or -DLAMMPS_SMALLSMALL

-

If you are running a very large problem (billions of atoms or more) -and get a run-time error about the system being too big, either on a -per-processor basis or in total size, then you may need to change one -or more settings in src/lmptype.h and re-compile LAMMPS. +

As explained above, any of these 3 settings can be specified on the +LMP_INC line in your low-level src/MAKE/Makefile.foo.

-

As the documentation in that file explains, you have basically -two choices to make: +

The default is -DLAMMPS_SMALLBIG which allows for systems with up to +2^63 atoms and timesteps (about 9 billion billion). The atom limit is +for atomic systems that do not require atom IDs. For molecular +models, which require atom IDs, the limit is 2^31 atoms (about 2 +billion). With this setting, image flags are stored in 32-bit +integers, which means for 3 dimensions that atoms can only wrap around +a periodic box at most 512 times. If atoms move through the periodic +box more than this limit, the image flags will "roll over", e.g. from +511 to -512, which can cause diagnostics like the mean-squared +displacement, as calculated by the compute msd +command, to be faulty.

- -

The default for atom IDs is 4-byte integers since there is a memory -and communication cost for 8-byte integers. Non-molecular problems do -not need atom IDs so this does not restrict their size. Molecular -problems (which use IDs to define molecular topology), are limited to -about 2 billion atoms (2^31) with 4-byte IDs. With 8-byte IDs they -are effectively unlimited in size (2^63). +

To allow for larger molecular systems or larger image flags, compile +with -DLAMMPS_BIGBIG. This enables molecular systems with up to 2^63 +atoms (about 9 billion billion). And image flags will not "roll over" +until they reach 2^20 = 1048576.

-

The default for total system size quantities (like the number of atoms -or timesteps) is 8-byte integers by default which is effectively -unlimited in size (2^63). If your system or MPI implementation does -not support 8-byte integers, an error will be generated, and you will -need to set "bigint" to 4-byte integers. This restricts your total -system size to about 2 billion atoms or timesteps (2^31). +

IMPORTANT NOTE: As of 6/2012, the BIGBIG setting does not yet enable +molecular systems to grow as large as 2^63. Only the image flag roll +over is currently affected by this compile option. +

+

If your system does not support 8-byte integers, you will need to +compile with the -DLAMMPS_SMALLSMALL setting. This will restrict your +total number of atoms (for atomic or molecular models) and timesteps +to 2^31 (about 2 billion). Image flags will roll over at 2^9 = 512.

Note that in src/lmptype.h there are also settings for the MPI data types associated with the integers that store atom IDs and total -system sizes, which need to be set consistent with the associated C -data types. +system sizes. These need to be consistent with the associated C data +types, or else LAMMPS will generate a run-time error.

In all cases, the size of problem that can be run on a per-processor -basis is limited by 4-byte integer storage to about 2 billion atoms -per processor (2^31), which should not normally be a restriction since +basis is limited by 4-byte integer storage to 2^31 atoms per processor +(about 2 billion). This should not normally be a restriction since such a problem would have a huge per-processor memory footprint due to neighbor lists and would run very slowly in terms of CPU secs/timestep. diff --git a/doc/Section_start.txt b/doc/Section_start.txt index f361c9f0c9..8469a82dc1 100644 --- a/doc/Section_start.txt +++ b/doc/Section_start.txt @@ -217,11 +217,14 @@ Restrictions section of the "dump"_dump.html command for details. Use at most one of the -DLAMMPS_SMALLBIG, -DLAMMPS_BIGBIG, -D-DLAMMPS_SMALLSMALL settings. The default is -DLAMMPS_SMALLBIG. -These refer to use of 4-byte (small) vs 8-byte (big) integers within -LAMMPS, as described in src/lmptype.h. The only reason to use the -BIGBIG setting is to enable simulation of huge molecular systems with -more than 2 billion atoms. The only reason to use the SMALLSMALL -setting is if your machine does not support 64-bit integers. +These settings refer to use of 4-byte (small) vs 8-byte (big) integers +within LAMMPS, as specified in src/lmptype.h. The only reason to use +the BIGBIG setting is to enable simulation of huge molecular systems +with more than 2 billion atoms or to allow moving atoms to wrap back +through a periodic box more than 512 times. The only reason to use +the SMALLSMALL setting is if your machine does not support 64-bit +integers. See the "Additional build tips"_#start_2_4 section below +for more details. The -DLAMMPS_LONGLONG_TO_LONG setting may be needed if your system or MPI version does not recognize "long long" data types. In this case a @@ -428,41 +431,46 @@ Typing "make clean-all" or "make clean-foo" will delete *.o object files created when LAMMPS is built, for either all builds or for a particular machine. -(3) Changing the size limits in src/lmptype.h +(3) Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or +-DLAMMPS_BIBIG or -DLAMMPS_SMALLSMALL -If you are running a very large problem (billions of atoms or more) -and get a run-time error about the system being too big, either on a -per-processor basis or in total size, then you may need to change one -or more settings in src/lmptype.h and re-compile LAMMPS. +As explained above, any of these 3 settings can be specified on the +LMP_INC line in your low-level src/MAKE/Makefile.foo. -As the documentation in that file explains, you have basically -two choices to make: +The default is -DLAMMPS_SMALLBIG which allows for systems with up to +2^63 atoms and timesteps (about 9 billion billion). The atom limit is +for atomic systems that do not require atom IDs. For molecular +models, which require atom IDs, the limit is 2^31 atoms (about 2 +billion). With this setting, image flags are stored in 32-bit +integers, which means for 3 dimensions that atoms can only wrap around +a periodic box at most 512 times. If atoms move through the periodic +box more than this limit, the image flags will "roll over", e.g. from +511 to -512, which can cause diagnostics like the mean-squared +displacement, as calculated by the "compute msd"_compute_msd.html +command, to be faulty. -set the data type size of integer atom IDs to 4 or 8 bytes -set the data type size of integers that store the total system size to 4 or 8 bytes :ul +To allow for larger molecular systems or larger image flags, compile +with -DLAMMPS_BIGBIG. This enables molecular systems with up to 2^63 +atoms (about 9 billion billion). And image flags will not "roll over" +until they reach 2^20 = 1048576. -The default for atom IDs is 4-byte integers since there is a memory -and communication cost for 8-byte integers. Non-molecular problems do -not need atom IDs so this does not restrict their size. Molecular -problems (which use IDs to define molecular topology), are limited to -about 2 billion atoms (2^31) with 4-byte IDs. With 8-byte IDs they -are effectively unlimited in size (2^63). +IMPORTANT NOTE: As of 6/2012, the BIGBIG setting does not yet enable +molecular systems to grow as large as 2^63. Only the image flag roll +over is currently affected by this compile option. -The default for total system size quantities (like the number of atoms -or timesteps) is 8-byte integers by default which is effectively -unlimited in size (2^63). If your system or MPI implementation does -not support 8-byte integers, an error will be generated, and you will -need to set "bigint" to 4-byte integers. This restricts your total -system size to about 2 billion atoms or timesteps (2^31). +If your system does not support 8-byte integers, you will need to +compile with the -DLAMMPS_SMALLSMALL setting. This will restrict your +total number of atoms (for atomic or molecular models) and timesteps +to 2^31 (about 2 billion). Image flags will roll over at 2^9 = 512. Note that in src/lmptype.h there are also settings for the MPI data types associated with the integers that store atom IDs and total -system sizes, which need to be set consistent with the associated C -data types. +system sizes. These need to be consistent with the associated C data +types, or else LAMMPS will generate a run-time error. In all cases, the size of problem that can be run on a per-processor -basis is limited by 4-byte integer storage to about 2 billion atoms -per processor (2^31), which should not normally be a restriction since +basis is limited by 4-byte integer storage to 2^31 atoms per processor +(about 2 billion). This should not normally be a restriction since such a problem would have a huge per-processor memory footprint due to neighbor lists and would run very slowly in terms of CPU secs/timestep. diff --git a/doc/fix_rigid.html b/doc/fix_rigid.html index 4ea4e975c4..0bbd9fbddb 100644 --- a/doc/fix_rigid.html +++ b/doc/fix_rigid.html @@ -297,8 +297,9 @@ center-of-mass that is outside the simulation box, LAMMPS wraps it back into the box. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the values consistent with the current orientation of the rigid body around its center of mass. The values are with respect to -the XYZ coordinate axes, not with respect to the prinicpal axes of the -rigid body itself. LAMMPS performs the latter calcultion internally. +the simulation box XYZ axes, not with respect to the prinicpal axes of +the rigid body itself. LAMMPS performs the latter calculation +internally.

IMPORTANT NOTE: The last point means that you cannot restart a simulation with rigid bodies using the diff --git a/doc/fix_rigid.txt b/doc/fix_rigid.txt index 17fcc9e24e..0e8f5beeac 100644 --- a/doc/fix_rigid.txt +++ b/doc/fix_rigid.txt @@ -286,8 +286,9 @@ center-of-mass that is outside the simulation box, LAMMPS wraps it back into the box. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the values consistent with the current orientation of the rigid body around its center of mass. The values are with respect to -the XYZ coordinate axes, not with respect to the prinicpal axes of the -rigid body itself. LAMMPS performs the latter calcultion internally. +the simulation box XYZ axes, not with respect to the prinicpal axes of +the rigid body itself. LAMMPS performs the latter calculation +internally. IMPORTANT NOTE: The last point means that you cannot restart a simulation with rigid bodies using the diff --git a/doc/min_modify.html b/doc/min_modify.html index ced08b2c6a..e052b633a4 100644 --- a/doc/min_modify.html +++ b/doc/min_modify.html @@ -20,7 +20,7 @@ 

keyword = dmax or line
   dmax value = max
     max = maximum distance for line search to move (distance units)
-  line value = backtrack or quadraticor forcezero
+  line value = backtrack or quadratic or forcezero
     backtrack,quadratic,forcezero = style of linesearch to use
diff --git a/doc/min_modify.txt b/doc/min_modify.txt index 3cca32a854..27bab8f96d 100644 --- a/doc/min_modify.txt +++ b/doc/min_modify.txt @@ -16,7 +16,7 @@ one or more keyword/value pairs may be listed :ulb,l keyword = {dmax} or {line} {dmax} value = max max = maximum distance for line search to move (distance units) - {line} value = {backtrack} or {quadratic}or {forcezero} + {line} value = {backtrack} or {quadratic} or {forcezero} backtrack,quadratic,forcezero = style of linesearch to use :pre :ule diff --git a/doc/pair_airebo.html b/doc/pair_airebo.html index 42502af09d..2cb34a2195 100644 --- a/doc/pair_airebo.html +++ b/doc/pair_airebo.html @@ -92,6 +92,8 @@ would be 10.2 Angstroms.

The E_TORSION term is an explicit 4-body potential that describes various dihedral angle preferences in hydrocarbon configurations.

+
+

Only a single pair_coeff command is used with the airebo or rebo style which specifies an AIREBO potential file with parameters for C and H. Note that the rebo style in LAMMPS uses the same diff --git a/doc/pair_airebo.txt b/doc/pair_airebo.txt index 0d76804a05..59313a27a5 100644 --- a/doc/pair_airebo.txt +++ b/doc/pair_airebo.txt @@ -86,6 +86,8 @@ would be 10.2 Angstroms. The E_TORSION term is an explicit 4-body potential that describes various dihedral angle preferences in hydrocarbon configurations. +:line + Only a single pair_coeff command is used with the {airebo} or {rebo} style which specifies an AIREBO potential file with parameters for C and H. Note that the {rebo} style in LAMMPS uses the same diff --git a/doc/pair_coeff.html b/doc/pair_coeff.html index 1f47c40b39..942428e17b 100644 --- a/doc/pair_coeff.html +++ b/doc/pair_coeff.html @@ -99,6 +99,7 @@ section of this page.

Package Description Author(s) Doc page Example Library
ASPHERE aspherical particles - howto ellipse -
ASPHERE aspherical particles - Section_howto ellipse -
CLASS2 class 2 force fields - pair_style lj/class2 - -
COLLOID colloidal particles - atom_style colloid colloid -
DIPOLE point dipole particles - pair_style dipole/cut dipole -
FLD Fast Lubrication Dynamics Kumar & Bybee & Higdon (1) pair_style lubricateU - -
GPU GPU-enabled potentials Mike Brown (ORNL) Section accelerate gpu lib/gpu
GRANULAR granular systems - >howto pour -
KIM openKIM potentials Smirichinski & Elliot & Tadmor (3) pair_style kim kim lib/kim
GRANULAR granular systems - Section_howto pour -
KIM openKIM potentials Smirichinski & Elliot & Tadmor (3) pair_style kim kim lib/kim
KSPACE long-range Coulombic solvers - kspace_style peptide -
MANYBODY many-body potentials - pair_style tersoff shear -
MEAM modified EAM potential Greg Wagner (Sandia) pair_style meam meam lib/meam
MC Monte Carlo options - fix gcmc - -
MOLECULE molecular system force fields - howto peptide -
MOLECULE molecular system force fields - Section_howto peptide -
OPT optimized pair potentials Fischer & Richie & Natoli (2) Section accelerate - -
PERI Peridynamics models Mike Parks (Sandia) pair_style peri peri -
POEMS coupled rigid body motion Rudra Mukherjee (JPL) fix poems rigid lib/poems
REAX ReaxFF potential Aidan Thompson (Sandia) pair_style reax reax lib/reax
REPLICA multi-replica methods - howto tad -
REPLICA multi-replica methods - Section_howto tad -
SHOCK shock loading methods - fix msst - -
SRD stochastic rotation dynamics - fix srd srd -
XTC dumps in XTC format - dump - -