It is not efficient to use compute ke/atom more than once.
diff --git a/doc/Section_errors.txt b/doc/Section_errors.txt
index 6422a655bc..5ea01829a1 100644
--- a/doc/Section_errors.txt
+++ b/doc/Section_errors.txt
@@ -377,6 +377,11 @@ bond_coeff command. :dd
Cannot use fix shake unless bond potential is defined. :dd
+{Bond style does not support computing per-atom bond energy} :dt
+
+The bond style does not have a single() function, so it can not be
+used to compute per-atom bond energy. :dd
+
{Bond style hybrid cannot have hybrid as an argument} :dt
Self-explanatory. :dd
@@ -441,14 +446,23 @@ The Self-explanatory. :dd
This feature is not yet supported. :dd
-{Cannot (yet) use fix ave/spatial with triclinic box} :dt
-
-This feature is not yet supported. :dd
-
{Cannot build parse tree for variable that is not atom style} :dt
Only atom style variables can be evaluated once per atom. :dd
+{Cannot change box to orthogonal when tilt is non-zero} :dt
+
+Self-explanatory :dd
+
+{Cannot change box with certain fixes defined} :dt
+
+The change_box command cannot be used when fix ave/spatial or
+fix/deform are defined . :dd
+
+{Cannot change box with dumps defined} :dt
+
+Self-explanatory. :dd
+
{Cannot change dump_modify every for dump dcd} :dt
The frequency of writing dump dcd snapshots cannot be changed. :dd
@@ -485,6 +499,10 @@ command. :dd
The create_box command cannot be used after a read_data, read_restart,
or create_box command. :dd
+{Cannot displace_box on a non-periodic boundary} :dt
+
+Self-explantory. :dd
+
{Cannot dump scaled coords with triclinic box} :dt
Use dump custom with x,y,z instead. :dd
@@ -505,6 +523,10 @@ Only a periodiic boundary can be modified. :dd
These 2 options are contradictory. :dd
+{Cannot open AIREBO potential file %s} :dt
+
+Self-explanatory. :dd
+
{Cannot open EAM potential file %s} :dt
The specified EAM potential file cannot be opened. Check that the
@@ -647,6 +669,11 @@ read_restart, or create_box command. :dd
The read_restart command cannot be used after a read_data,
read_restart, or create_box command. :dd
+{Cannot redefine variable as a different style} :dt
+
+An equal-style variable can be re-defined but only if it was
+originally an equal-style variable. :dd
+
{Cannot replicate 2d simulation in z dimension} :dt
The replicate command cannot replicate a 2d simulation in the z
@@ -715,15 +742,15 @@ This feature is not yet supported. :dd
The kspace style pppm cannot be used in 2d simulations. You can use
2d PPPM in a 3d simulation; see the kspace_modify command. :dd
-{Cannot use atom style ellipsoid for 2d simulation} :dt
-
-2d ellipsoids are not yet suppported. :dd
-
{Cannot use atom vector in variable unless atom map exists} :dt
Atom maps are on by default, but can be turned off be the atom_modify
command. :dd
+{Cannot use both region, partial options in fix temp/rescale} :dt
+
+Self-explanatory. :dd
+
{Cannot use delete_atoms unless atoms have IDs} :dt
Your atoms do not have IDs, so the delete_atoms command cannot be
@@ -737,14 +764,15 @@ Your choice of atom style does not have bonds. :dd
Your choice of atom style does not have bonds. :dd
-{Cannot use fix deform for 0 timestep run} :dt
-
-Cannot reshape or resize the box in 0 timesteps. :dd
-
{Cannot use fix deform trate on a box with zero tilt} :dt
The trate style alters the current strain. :dd
+{Cannot use fix langevin without per-type mass defined} :dt
+
+Some atom styles use a per-atom mass which is incompatible with fix
+langevin. :dd
+
{Cannot use fix nph on a non-periodic dimension} :dt
Only periodic dimensions can be controlled with this fix. :dd
@@ -773,10 +801,6 @@ The defined atom style uses per-atom mass, not per-type mass. :dd
The defined atom style uses per-atom mass, not per-type mass. :dd
-{Cannot use fix poems with atom style granular} :dt
-
-This fix is not yet enabled for this atom style. :dd
-
{Cannot use fix pour with triclinic box} :dt
This feature is not yet supported. :dd
@@ -789,6 +813,12 @@ Your choice of atom style does not have bonds. :dd
No atoms in system have a non-zero charge. :dd
+{Cannot use neighbor bins - box size << cutoff} :dt
+
+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. :dd
+
{Cannot use nonperiodic boundaries with Ewald} :dt
For kspace style ewald, all 3 dimensions must have periodic boundaries
@@ -805,13 +835,7 @@ non-periodic z dimension. :dd
The correction factors are only currently defined for 3d systems. :dd
-{Cannot use rRESPA with full neighbor lists} :dt
-
-Defined pair style uses full neighbor lists (as opposed to
-half neighbor lists), which are incompatible with the current
-implementation of rRESPA. :dd
-
-{Cannot use region INF when box does not exist} :dt
+{Cannot use region INF or EDGE when box does not exist} :dt
Regions that extend to the box boundaries can only be used after the
create_box command has been used. :dd
@@ -839,6 +863,19 @@ Self-explanatory. :dd
The collection of atoms for which momentum is being computed has no
atoms. :dd
+{Change_box command before simulation box is defined} :dt
+
+Self-explanatory. :dd
+
+{Change_box operation is invalid} :dt
+
+Cannot change orthogonal box to orthogonal or a triclinic box to
+triclinic. :dd
+
+{Compute ID for fix ave/atom does not exist} :dt
+
+Self-explanatory. :dd
+
{Compute ID for fix ave/spatial does not exist} :dt
Self-explanatory. :dd
@@ -865,6 +902,10 @@ temperature. :dd
The atom style defined does not have these attributes. :dd
+{Compute sum/atom compute does not compute vector per atom} :dt
+
+If one compute in list calculates a vector, all of them must. :dd
+
{Compute temp/asphere requires atom attributes quat, angmom} :dt
The atom style defined does not have these attributes. :dd
@@ -885,11 +926,6 @@ The FFT setup in pppm failed. :dd
Self-explanatory. :dd
-{Could not find compute etotal/atom pre-compute ID} :dt
-
-The compute ID for calculating per-atom pairwise energy
-does not exist. :dd
-
{Could not find compute group ID} :dt
Self-explanatory. :dd
@@ -898,6 +934,11 @@ Self-explanatory. :dd
The compute ID for calculating temperature does not exist. :dd
+{Could not find compute sum/atom pre-compute ID} :dt
+
+The compute ID for calculating the requested per-atom quantity does
+not exist. :dd
+
{Could not find compute variable name} :dt
The variable being used by a compute is not defined. :dd
@@ -922,11 +963,19 @@ Region ID used in the delete_atoms command does not exist. :dd
A group ID used in the displace_atoms command does not exist. :dd
+{Could not find displace_box group ID} :dt
+
+Self-explanatory. :dd
+
{Could not find dump custom compute ID} :dt
The compute ID needed by dump custom to compute a per-atom quantity
does not exist. :dd
+{Could not find dump custom fix ID} :dt
+
+Self-explanatory. :dd
+
{Could not find dump group ID} :dt
A group ID used in the dump command does not exist. :dd
@@ -1032,6 +1081,11 @@ does not exist. :dd
A compute required to evaulate a variable does not have its pre-compute
defined. :dd
+{Coulomb cutoffs of pair hybrid sub-styles do not match} :dt
+
+If using a Kspace solver, all Coulomb cutoffs of long pair styles must
+be the same. :dd
+
{Cound not find dump_modify ID} :dt
Self-explanatory. :dd
@@ -1081,6 +1135,10 @@ read_restart, or create_box command. :dd
No atoms are yet defined so the delete_bonds command cannot be used. :dd
+{Deposition region extends outside simulation box} :dt
+
+Self-explatory. :dd
+
{Did not assign all atoms correctly} :dt
Atoms read in from a data file were not assigned correctly to
@@ -1188,12 +1246,26 @@ read_restart, or create_box command. :dd
The displace_atoms command cannot be used before a read_data,
read_restart, or create_box command. :dd
+{Displace_box command before simulation box is defined} :dt
+
+Self-explanatory. :dd
+
+{Displace_box tilt factors require triclinic box} :dt
+
+Cannot use tilt factors unless the simulation box is
+non-orthogonal. :dd
+
{Domain too large for neighbor bins} :dt
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. :dd
+{Dump custom and fix not computed at compatible times} :dt
+
+The fix must produce per-atom quantities on timesteps that dump custom
+needs them. :dd
+
{Dump custom compute ID does not compute peratom info} :dt
The compute ID used must compute peratom info, not
@@ -1212,6 +1284,23 @@ The compute ID used must compute a vector of peratom data. :dd
The compute ID vector of peratom data is not as large as is
being accessed. :dd
+{Dump custom fix ID does not compute peratom info} :dt
+
+The specified fix does not calculate per-atom values. :dd
+
+{Dump custom fix ID does not compute scalar per atom} :dt
+
+The dump custom command is attempting to access a scalar quantity. :dd
+
+{Dump custom fix ID does not compute vector per atom} :dt
+
+The dump custom command is attempting to access a vector quantity. :dd
+
+{Dump custom fix ID vector is not large enough} :dt
+
+The dump custom command is attempting to access an out-of-range vector
+value. :dd
+
{Dump dcd must use group all} :dt
Self-explanatory. :dd
@@ -1251,11 +1340,47 @@ smaller simulation or on more processors. :dd
Self-explanatory. :dd
+{Fix ID for fix ave/spatial does not exist} :dt
+
+Self-explanatory. :dd
+
+{Fix ave/atom cannot be started on this timestep} :dt
+
+The first timestep on which data needs to be accumulated for
+the average is before the current timestep. :dd
+
+{Fix ave/atom compute does not calculate per-atom info} :dt
+
+The specified compute does not calculate per-atom values. :dd
+
+{Fix ave/spatial and fix not computed at compatible times} :dt
+
+The fix must produce per-atom quantities on timesteps that fix
+ave/spatial needs them. :dd
+
+{Fix ave/spatial cannot be started on this timestep} :dt
+
+The first timestep on which data needs to be accumulated for
+the average is before the current timestep. :dd
+
{Fix ave/spatial compute does not calculate per-atom info} :dt
Only computes that calculate a per-atom quantity (not a scalar or
vector quantity can be used with fix ave/spatial. :dd
+{Fix ave/spatial fix does not calculate per-atom info} :dt
+
+The specified fix does not calculate per-atom values. :dd
+
+{Fix ave/spatial for triclinic boxes requires units reduced} :dt
+
+Self-explanatory. :dd
+
+{Fix ave/time cannot be started on this timestep} :dt
+
+The first timestep on which data needs to be accumulated for
+the average is before the current timestep. :dd
+
{Fix ave/time compute does not calculate a scalar} :dt
Only computes that calculate a scalar or vector quantity (not a
@@ -1518,6 +1643,10 @@ definitions. :dd
The data file header lists improper but no improper types. :dd
+{Inconsistent sizes of compute sum/atom compute vectors} :dt
+
+All vectors of the computes in the list must be the same length. :dd
+
{Incorrect args for angle coefficients} :dt
Self-explanatory. Check the input script or data file. :dd
@@ -1594,6 +1723,11 @@ of the data file. The read-in lines do not match. :dd
Self-explanatory. Check the input script or data file. :dd
+{Induced tilt by displace_box is too large} :dt
+
+The final tilt value must be between -1/2 and 1/2 of the perpendicular
+box length. :dd
+
{Input line too long after variable substitution} :dt
This is a hard (very large) limit defined in the input.cpp file. :dd
@@ -1845,6 +1979,14 @@ to be written by each processor. :dd
Operator keyword used for threshhold specification in not recognized. :dd
+{Invalid fix nph command for a 2d simulation} :dt
+
+Cannot use style xy, yz, or xz for a 2d simulation. :dd
+
+{Invalid fix npt command for a 2d simulation} :dt
+
+Cannot use style xy, yz, or xz for a 2d simulation. :dd
+
{Invalid fix style} :dt
The choice of fix style is unknown. :dd
@@ -1861,6 +2003,10 @@ Unrecognized entry in restart file. :dd
Unrecognized entry in restart file. :dd
+{Invalid frequency in temper command} :dt
+
+Nevery must be > 0. :dd
+
{Invalid group ID in neigh_modify command} :dt
A group ID used in the neigh_modify command does not exist. :dd
@@ -2055,9 +2201,13 @@ Each x,y,z spacing must be > 0. :dd
2d simulation can use sq, sq2, or hex lattice. 3d simulation can use
sc, bcc, or fcc lattice. :dd
-{Lost atoms via displacement: original %.15g current %.15g} :dt
+{Lost atoms via displace_atoms: original %.15g current %.15g} :dt
-Moving atoms via the displace_atoms command lost one or more atoms. :dd
+The displace_atoms command lost one or more atoms. :dd
+
+{Lost atoms via displace_box: original %.15g current %.15g} :dt
+
+The displace_box command lost one or more atoms. :dd
{Lost atoms: original %.15g current %.15g} :dt
@@ -2277,11 +2427,11 @@ There are too many neighbors of a single atom. Use the neigh_modify
command to increase the neighbor page size and the max number of
neighbors allowed for one atom. :dd
-{Neighbor multi not allowed with granular} :dt
+{Neighbor multi not yet enabled for granular} :dt
Self-explanatory. :dd
-{Neighbor multi not allowed with rRESPA} :dt
+{Neighbor multi not yet enabled for rRESPA} :dt
Self-explanatory. :dd
@@ -2401,6 +2551,11 @@ The atom style defined does not have these attributes. :dd
The atom style defined does not have these attributes. :dd
+{Pair hybrid sub-style is not used} :dt
+
+No pair_coeff command used a sub-style specified in the pair_style
+command. :dd
+
{Pair inner cutoff < Respa interior cutoff} :dt
One or more pairwise cutoffs are too short to use with the specified
@@ -2410,6 +2565,14 @@ rRESPA cutoffs. :dd
The specified cutoffs for the pair style are inconsistent. :dd
+{Pair style AIREBO requires atom IDs} :dt
+
+Self-explanatory. :dd
+
+{Pair style AIREBO requires newton pair on} :dt
+
+Self-explanatory. :dd
+
{Pair style MEAM requires newton pair on} :dt
See the newton command. This is a restriction to use the MEAM
@@ -2441,6 +2604,10 @@ The atom style defined does not have this attribute. :dd
The atom style defined does not have these attributes. :dd
+{Pair style coul/cut requires atom attribute q} :dt
+
+The atom style defined does not have these attributes. :dd
+
{Pair style does not support bond_style quartic} :dt
The pair style does not have a single() function, so it can
@@ -2449,12 +2616,12 @@ not be invoked by bond_style quartic. :dd
{Pair style does not support computing per-atom energy} :dt
The pair style does not have a single() function, so it can
-not be used to dump per-atom energy. :dd
+not be used to compute per-atom energy. :dd
{Pair style does not support computing per-atom stress} :dt
The pair style does not have a single() function, so it can
-not be used to dump per-atom stress. :dd
+not be used to compute per-atom stress. :dd
{Pair style does not support pair_write} :dt
@@ -2480,6 +2647,10 @@ cannot be tracked by the granular pair potential. :dd
Self-explanatory. :dd
+{Pair style hybrid cannot have none as an argument} :dt
+
+Self-explanatory. :dd
+
{Pair style hybrid cannot use same pair style twice} :dt
The sub-style arguments of pair_style hybrid cannot be duplicated.
@@ -2551,10 +2722,6 @@ read_restart, or create_box command. :dd
Self-explanatory. :dd
-{Pair_style granular command before simulation box is defined} :dt
-
-This pair style cannot be used before a simulation box is defined. :dd
-
{Pair_write command before pair_style is defined} :dt
Self-explanatory. :dd
@@ -2584,6 +2751,11 @@ compute, which isn't defined. :dd
The compute used by fix ave/time requires a second pre-computation
compute, which isn't defined. :dd
+{Precompute ID of compute for fix ave/atom does not exist} :dt
+
+The compute specified for fix ave/atom has other pre-computed computes
+defined. One of them does not exist. :dd
+
{Press ID for fix nph does not exist} :dt
The compute ID needed to compute pressure for the fix does not
@@ -2898,7 +3070,7 @@ The specified compute ID does not compute temperature. :dd
The thermo_style command cannot be used before a read_data,
read_restart, or create_box command. :dd
-{Thermodynamics must compute PE for temper} :dt
+{Thermodynamics must compute PE for temper command} :dt
The thermo style must insure that thermodynamics computations include
potential energy when tempering is performed. :dd
@@ -3027,6 +3199,11 @@ option is set to lattice. :dd
Must use lattice command with displace_atoms command if units option
is set to lattice. :dd
+{Use of displace_box with undefined lattice} :dt
+
+Must use lattice command with displace_box command if units option is
+set to lattice. :dd
+
{Use of fix ave/spatial with undefined lattice} :dt
A lattice must be defined to use fix ave/spatial with units = lattice. :dd
@@ -3179,14 +3356,14 @@ It is not efficient to use compute centro/atom more than once. :dd
It is not efficient to use compute coord/atom more than once. :dd
+{More than one compute ebond/atom} :dt
+
+It is not efficient to use compute ebond/atom more than once. :dd
+
{More than one compute epair/atom} :dt
It is not efficient to use compute epair/atom more than once. :dd
-{More than one compute etotal/atom} :dt
-
-It is not efficient to use compute etotal/atom more than once. :dd
-
{More than one compute ke/atom} :dt
It is not efficient to use compute ke/atom more than once. :dd
diff --git a/doc/kspace_style.html b/doc/kspace_style.html
index 63b2ae7b91..ec9ae95fa4 100644
--- a/doc/kspace_style.html
+++ b/doc/kspace_style.html
@@ -69,13 +69,16 @@ The 1/r^N capability means that Lennard-Jones or Buckingham potentials
can be used with ewald/n without a cutoff, i.e. they become full
long-range potentials.
+Currently, only the ewald/n style can be used with non-orthogonal
+(triclinic symmetry) simulation boxes.
+
When a kspace style is used, a pair style that includes the
short-range correction to the pairwise Coulombic or other 1/r^N forces
must also be selected. For Coulombic interactions, these styles are
-ones that have a coul/long in their style name. For Lennard-Jones
-or Buckingham interactions, see the pair_style
-lj/coul or pair_style
-buck/coul potentials.
+ones that have a coul/long in their style name. For 1/r^6
+dispersion forces in a Lennard-Jones or Buckingham potential, see the
+pair_style lj/coul or pair_style
+buck/coul commands.
A precision value of 1.0e-4 means one part in 10000. This setting is
used in conjunction with the pairwise cutoff to determine the number
diff --git a/doc/kspace_style.txt b/doc/kspace_style.txt
index f8486dca84..575f33c1e9 100644
--- a/doc/kspace_style.txt
+++ b/doc/kspace_style.txt
@@ -64,13 +64,16 @@ The 1/r^N capability means that Lennard-Jones or Buckingham potentials
can be used with {ewald/n} without a cutoff, i.e. they become full
long-range potentials.
+Currently, only the {ewald/n} style can be used with non-orthogonal
+(triclinic symmetry) simulation boxes.
+
When a kspace style is used, a pair style that includes the
short-range correction to the pairwise Coulombic or other 1/r^N forces
must also be selected. For Coulombic interactions, these styles are
-ones that have a {coul/long} in their style name. For Lennard-Jones
-or Buckingham interactions, see the "pair_style
-lj/coul"_pair_lj_coul.html or "pair_style
-buck/coul"_pair_buck_coul.html potentials.
+ones that have a {coul/long} in their style name. For 1/r^6
+dispersion forces in a Lennard-Jones or Buckingham potential, see the
+"pair_style lj/coul"_pair_lj_coul.html or "pair_style
+buck/coul"_pair_buck_coul.html commands.
A precision value of 1.0e-4 means one part in 10000. This setting is
used in conjunction with the pairwise cutoff to determine the number