ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4939 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2010-10-01 17:09:52 +00:00
parent 80294e4490
commit fa06158999
2 changed files with 458 additions and 80 deletions
Download Patch File Download Diff File Expand all files Collapse all files

269
doc/Section_errors.txt
View File

@ -324,29 +324,14 @@ You are not setup correctly to use a GPU from your CPU. :dd
Self-explanatory. :dd
{Atom IDs must be consecutive for dump dcd} :dt
Self-explanatory. :dd
{Atom IDs must be consecutive for dump xtc} :dt
Self-explanatory. :dd
{Atom IDs must be consecutive for dump xyz all} :dt
This is a requirement since XYZ files do not list the atom IDs.
When using group all, the output is sorted by ID so that
the atoms will be in a consistent order for different snapshots.
This sorting requires the IDs be consecutive. :dd
{Atom IDs must be consecutive for dump xyz} :dt
Self-explanatory. :dd
{Atom IDs must be consecutive for velocity create loop all} :dt
Self-explanatory. :dd
{Atom count changed in fix neb} :dt
This is not allowed in a NEB calculation. :dd
{Atom count is inconsistent, cannot write restart file} :dt
Sum of atoms across processors does not equal initial total count.
@ -445,6 +430,10 @@ The specified compute must compute temperature. :dd
The specified compute must operate on the same group as the parent
compute. :dd
{Big particle in fix srd cannot be point particle} :dt
Big particles must be extended spheriods or ellipsoids. :dd
{Bitmapped lookup tables require int/float be same size} :dt
Cannot use pair tables on this machine, because of word sizes. Use
@ -579,6 +568,10 @@ See the region prism command for details. :dd
Only triclinic boxes can be used with off-diagonal pressure components.
See the region prism command for details. :dd
{Can only use NEB with 1-processor replicas} :dt
This is current restriction for NEB as implemented in LAMMPS. :dd
{Cannot (yet) use PPPM with triclinic box} :dt
This feature is not yet supported. :dd
@ -600,6 +593,11 @@ Self-explanatory. :dd
The frequency of writing dump dcd snapshots cannot be changed. :dd
{Cannot change timestep once fix srd is setup} :dt
This is because various SRD properties depend on the timestep
size. :dd
{Cannot change timestep with fix pour} :dt
This fix pre-computes some values based on the timestep, so it cannot
@ -651,10 +649,26 @@ Self-explanatory. :dd
Self-explanatory. :dd
{Cannot displace_atoms after reading restart file with per-atom info} :dt
This is because the restart file info cannot be migrated with the
atoms. You can get around this by performing a 0-timestep run which
will assign the restart file info to actual atoms. :dd
{Cannot displace_box after reading restart file with per-atom info} :dt
This is because the restart file info cannot be migrated with the
atoms. You can get around this by performing a 0-timestep run which
will assign the restart file info to actual atoms. :dd
{Cannot displace_box on a non-periodic boundary} :dt
Self-explanatory. :dd
{Cannot dump sort on atom IDs with no atom IDs defined} :dt
Self-explanatory. :dd
{Cannot evaporate atoms in atom_modify first group} :dt
This is a restriction due to the way atoms are organized in
@ -926,6 +940,18 @@ The kspace style ewald cannot be used in 2d simulations. You can use
This feature is not yet supported. :dd
{Cannot use NEB unless atom map exists} :dt
Use the atom_modify command to create an atom map. :dd
{Cannot use NEB with a single replica} :dt
Self-explanatory. :dd
{Cannot use NEB with atom_modify sort enabled} :dt
This is current restriction for NEB implemented in LAMMPS. :dd
{Cannot use PPPM with 2d simulation} :dt
The kspace style pppm cannot be used in 2d simulations. You can use
@ -948,6 +974,16 @@ which is enabled by default, via the atom_modify command. :dd
Use the atom_modify command to create an atom map. :dd
{Cannot use a damped dynamics min style with fix box/relax} :dt
This is a current restriction in LAMMPS. Use another minimizer
style. :dd
{Cannot use a damped dynamics min style with per-atom DOF} :dt
This is a current restriction in LAMMPS. Use another minimizer
style. :dd
{Cannot use delete_atoms unless atoms have IDs} :dt
Your atoms do not have IDs, so the delete_atoms command cannot be
@ -1594,6 +1630,10 @@ A group ID used in the fix recenter command does not exist. :dd
A group ID used in the fix rigid command does not exist. :dd
{Could not find fix srd group ID} :dt
Self-explanatory. :dd
{Could not find fix_modify ID} :dt
A fix ID used in the fix_modify command does not exist. :dd
@ -1937,14 +1977,14 @@ Self-explanatory. :dd
Only atom-style variables generate per-atom quantities, needed for
dump output. :dd
{Dump dcd must use group all} :dt
Self-explanatory. :dd
{Dump dcd of non-matching # of atoms} :dt
Every snapshot written by dump dcd must contain the same # of atoms. :dd
{Dump dcd requires sorting by atom ID} :dt
Use the dump_modify sort command to enable this. :dd
{Dump every variable returned a bad timestep} :dt
The variable must return a timestep greater than the current timestep. :dd
@ -1962,6 +2002,10 @@ needs them. :dd
Self-explanatory. :dd
{Dump local cannot sort by atom ID} :dt
This is because dump local does not really dump per-atom info. :dd
{Dump local compute does not calculate local array} :dt
Self-explanatory. :dd
@ -2038,13 +2082,13 @@ Self-explanatory. :dd
Self-explanatory. :dd
{Dump xtc must use group all} :dt
{Dump sort column is invalid} :dt
Self-explanatory. :dd
{Dump xtc must use group all} :dt
{Dump xtc requires sorting by atom ID} :dt
Self-explanatory. :dd
Use the dump_modify sort command to enable this. :dd
{Dump_modify region ID does not exist} :dt
@ -2101,6 +2145,10 @@ smaller simulation or on more processors. :dd
Your LAMMPS simulation has run out of memory. You need to run a
smaller simulation or on more processors. :dd
{Fewer SRD bins than processors in some dimension} :dt
This is not allowed. Make your SRD bin size smaller. :dd
{Final box dimension due to fix deform is < 0.0} :dt
Self-explanatory. :dd
@ -2137,6 +2185,46 @@ Self-explanatory :dd
Self-explanatory. :dd
{Fix SRD cannot have both atom attributes angmom and omega} :dt
Use either spheroid solute particles or fully generalized
aspherical solute particles. :dd
{Fix SRD no-slip requires atom attribute torque} :dt
This is because the SRD collisions will impart torque to the solute
particles. :dd
{Fix SRD requires atom attribute angmom or omega} :dt
This is because the SRD collisions with cause the solute particles to
rotate. :dd
{Fix SRD requires atom attribute radius or shape} :dt
This is because the solute particles must be finite-size particles,
not point particles. :dd
{Fix SRD: bad bin assignment for SRD advection} :dt
Something has gone wrong in your SRD model; try using more
conservative settings. :dd
{Fix SRD: bad search bin assignment} :dt
Something has gone wrong in your SRD model; try using more
conservative settings. :dd
{Fix SRD: bad stencil bin for big particle} :dt
Something has gone wrong in your SRD model; try using more
conservative settings. :dd
{Fix SRD: too many big particles in bin} :dt
Reset the ATOMPERBIN parameter at the top of fix_srd.cpp
to a larger value, and re-compile the code. :dd
{Fix adapt atom attribute is not recognized} :dt
Self-explanatory :dd
@ -2422,9 +2510,13 @@ This is a restriction of the current fix bond/break implementation. :dd
This is not allowed because bond creation is done using the
pairwise neighbor list. :dd
{Fix bond/create requires special_bonds = 0,1,1} :dt
{Fix bond/create requires special_bonds coul = 0,1,1} :dt
This is a restriction of the current fix bond/break implementation. :dd
Self-explanatory. :dd
{Fix bond/create requires special_bonds lj = 0,1,1} :dt
Self-explanatory. :dd
{Fix bond/swap cannot use dihedral or improper styles} :dt
@ -2723,6 +2815,26 @@ it turns off bonds that should contribute to the energy. :dd
Self-explanatory. :dd
{Fix srd lamda must be >= 0.6 of SRD grid size} :dt
This is a requirement for accuracy reasons. :dd
{Fix srd requires SRD particles all have same mass} :dt
Self-explanatory. :dd
{Fix srd requires ghost atoms store velocity} :dt
Use the communicate vel yes command to enable this. :dd
{Fix srd requires newton pair on} :dt
Self-explanatory. :dd
{Fix srd simulation box must be periodic} :dt
Self-explanatory. :dd
{Fix store/state compute array is accessed out-of-range} :dt
Self-explanatory. :dd
@ -3085,6 +3197,10 @@ Incorrect number of words per line in the potential file. :dd
Incorrect number of words per line in the potential file. :dd
{Incorrect format in NEB coordinate file} :dt
Self-explanatory. :dd
{Incorrect format in Stillinger-Weber potential file} :dt
Incorrect number of words per line in the potential file. :dd
@ -3593,10 +3709,6 @@ Natoms must be constant for the duration of the simulation. :dd
Natoms is initially 0 which is not valid for the dump xtc style. :dd
{Invalid natoms for dump xyz} :dt
Natoms is initially 0 which is not valid for the dump xyz style. :dd
{Invalid option in lattice command for non-custom style} :dt
Certain lattice keywords are not supported unless the
@ -4061,6 +4173,18 @@ Self-explanatory. :dd
Must define an energy vartiable when applyting a dynamic
force during minimization. :dd
{NEB command before simulation box is defined} :dt
Self-explanatory. :dd
{NEB requires damped dynamics minimizer} :dt
Use a different minimization style. :dd
{NEB requires use of fix neb} :dt
Self-explanatory. :dd
{Needed topology not in data file} :dt
The header of the data file indicated that bonds or angles or
@ -4375,14 +4499,6 @@ Use the lattice command for this purpose. :dd
Even for atomic systems, an atom map is required to find Peridynamic
bonds. Use the atom_modify command to define one. :dd
{Pair reax NATDEF setting too small, edit lib/reax/reax_defs.h} :dt
Edit the Fortran header file in the library, and re-compile LAMMPS. :dd
{Pair reax NNEIGHMAXDEF setting too small, edit lib/reax/reax_defs.h} :dt
Edit the Fortran header file in the library, and re-compile LAMMPS. :dd
{Pair resquared cannot be used with atom attribute diameter} :dt
This attribute overrides the shape settings, so cannot be used. :dd
@ -4655,6 +4771,10 @@ You are using a thermo keyword that requires potentials to have
tallied the virial, but they didn't on this timestep. See the
variable doc page for ideas on how to make this work. :dd
{Potential energy ID for fix neb does not exist} :dt
Self-explanatory. :dd
{Potential file has duplicate entry} :dt
The potential file for a SW or Tersoff potential has more than
@ -4755,6 +4875,16 @@ rigid command. :dd
Equilibrium spring length is invalid. :dd
{Reax_defs.h setting for NATDEF is too small} :dt
Edit the setting in the ReaxFF library and re-compile the
library and re-build LAMMPS. :dd
{Reax_defs.h setting for NNEIGHMAXDEF is too small} :dt
Edit the setting in the ReaxFF library and re-compile the
library and re-build LAMMPS. :dd
{Region ID for compute reduce/region does not exist} :dt
Self-explanatory. :dd
@ -4896,6 +5026,19 @@ Self-explanatory. :dd
The run_style command cannot be used before a read_data,
read_restart, or create_box command. :dd
{SRD bin size for fix srd differs from user request} :dt
Fix SRD had to adjust the bin size to fit the simulation box. :dd
{SRD bins for fix srd are not cubic enough} :dt
The bin shape is not within tolerance of cubic. :dd
{SRD particle %d started inside big particle %d on step %d bounce %d} :dt
This may not be a problem, but indicates one or more SRD particles are
being left inside solute particles. :dd
{Set command before simulation box is defined} :dt
The set command cannot be used before a read_data, read_restart,
@ -5213,6 +5356,10 @@ machine's floating point representation. :dd
This is likely due to an immense simulation box that has blown up
to a large size. :dd
{Too many atoms to dump sort} :dt
Cannot sort when running with more than 2^31 atoms. :dd
{Too many exponent bits for lookup table} :dt
Table size specified via pair_modify command does not work with your
@ -5400,6 +5547,11 @@ provided by "remap v" as a fix deform option. :dd
Self-explanatory. :dd
{Using fix srd with inconsistent fix deform remap option} :dt
When shearing the box in an SRD simulation, the remap v option for fix
deform needs to be used. :dd
{Variable evaluation before simulation box is defined} :dt
Cannot evaluate a compute or fix or atom-based value in a variable
@ -5647,6 +5799,26 @@ Atoms store this quantity, but fix move does not (yet) update it. :dd
Other fixes may change the position of the center-of-mass, so
fix recenter should come last. :dd
{Fix srd SRD moves may trigger frequent reneighboring} :dt
This is because the SRD particles may move long distances. :dd
{Fix srd grid size > 1/4 of big particle diameter} :dt
This may cause accuracy problems. :dd
{Fix srd particle moved outside valid domain} :dt
This may indicate a problem with your simulation parameters. :dd
{Fix srd particles may move > big particle diameter} :dt
This may cause accuracy problems. :dd
{Fix srd viscosity < 0.0 due to low SRD density} :dt
This may cause accuracy problems. :dd
{Fix thermal/conductivity comes before fix ave/spatial} :dt
The order of these 2 fixes in your input script is such that fix
@ -5850,6 +6022,23 @@ This may cause problems when reading the restart file. :dd
This is allowed, but you will get no parallel speed-up. :dd
{SRD bin shifting turned on due to small lamda} :dt
This is done to try to preserve accuracy. :dd
{SRD bin size for fix srd differs from user request} :dt
Check if the new bin size is acceptable. :dd
{SRD bins for fix srd are not cubic enough} :dt
Check if the bin shape is acceptable. :dd
{SRD particle %d started inside big particle %d on step %d bounce %d} :dt
This may not be a problem, but indicates one or more SRD particles are
being left inside solute particles. :dd
{Shake determinant < 0.0} :dt
The determinant of the quadratic equation being solved for a single