Using pair tail corrections with nonperiodic system
diff -Naur lammps-3Jul09/doc/Section_errors.txt lammps-4Jul09/doc/Section_errors.txt
--- lammps-3Jul09/doc/Section_errors.txt 2009-03-26 09:16:32.000000000 -0600
+++ lammps-4Jul09/doc/Section_errors.txt 2009-07-01 14:28:51.000000000 -0600
@@ -553,13 +553,34 @@
The create_box command cannot be used after a read_data, read_restart,
or create_box command. :dd
+{Cannot delete group all} :dt
+
+Self-explanatory. :dd
+
+{Cannot delete group currently used by a compute} :dt
+
+Self-explanatory. :dd
+
+{Cannot delete group currently used by a dump} :dt
+
+Self-explanatory. :dd
+
+{Cannot delete group currently used by a fix} :dt
+
+Self-explanatory. :dd
+
+{Cannot delete group currently used by atom_modify first} :dt
+
+Self-explanatory. :dd
+
{Cannot displace_box on a non-periodic boundary} :dt
Self-explanatory. :dd
-{Cannot dump scaled coords with triclinic box} :dt
+{Cannot evaporate atoms in atom_modify first group} :dt
-Use dump custom with x,y,z instead. :dd
+This is a restriction due to the way atoms are organized in
+a list to enable the atom_modify first command. :dd
{Cannot find delete_bonds group ID} :dt
@@ -648,11 +669,21 @@
The output file for the fix rdf command cannot be opened. Check that
the path and name are correct. :dd
+{Cannot open fix reax/bonds file %s} :dt
+
+The output file for the fix reax/bonds command 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
the path and name are correct. :dd
+{Cannot open fix ttm file %s} :dt
+
+The output file for the fix ttm command cannot be opened. Check that
+the path and name are correct. :dd
+
{Cannot open gzipped file} :dt
LAMMPS is attempting to open a gzipped version of the specified file
@@ -831,6 +862,10 @@
Self-explanatory. :dd
+{Cannot use fix box/relax on a non-periodic dimension} :dt
+
+Only periodic dimensions can be controlled with this fix. :dd
+
{Cannot use fix deform trate on a box with zero tilt} :dt
The trate style alters the current strain. :dd
@@ -847,10 +882,6 @@
This feature is not yet supported. :dd
-{Cannot use fix nph without per-type mass defined} :dt
-
-The defined atom style uses per-atom mass, not per-type mass. :dd
-
{Cannot use fix npt and fix deform on same dimension} :dt
These commands both change the box size/shape, so you cannot use both
@@ -864,14 +895,6 @@
This feature is not yet supported. :dd
-{Cannot use fix npt without per-type mass defined} :dt
-
-The defined atom style uses per-atom mass, not per-type mass. :dd
-
-{Cannot use fix nvt without per-type mass defined} :dt
-
-The defined atom style uses per-atom mass, not per-type mass. :dd
-
{Cannot use fix pour with triclinic box} :dt
This feature is not yet supported. :dd
@@ -888,22 +911,21 @@
Self-explanatory. :dd
-{Cannot use fix press/berendsen without per-type mass defined} :dt
+{Cannot use fix reax/bonds without pair_style reax} :dt
-Self-explanatory. :dd
-
-{Cannot use fix rigid without per-type mass defined} :dt
-
-This is a current restriction on the kinds of atoms fix rigid can
-be used with. :dd
+Self-explantory. :dd
{Cannot use fix shake with non-molecular system} :dt
Your choice of atom style does not have bonds. :dd
-{Cannot use fix temp/berendsen without per-type mass defined} :dt
+{Cannot use fix ttm with 2d simulation} :dt
-Self-explanatory. :dd
+This is a current restriction of this fix due to the grid it creates. :dd
+
+{Cannot use fix ttm with triclinic box} :dt
+
+This is a current restriction of this fix due to the grid it creates. :dd
{Cannot use kspace solver on system with no charge} :dt
@@ -915,6 +937,10 @@
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 boundares with fix ttm} :dt
+
+This fix requires a fully periodic simulation box. :dd
+
{Cannot use nonperiodic boundaries with Ewald} :dt
For kspace style ewald, all 3 dimensions must have periodic boundaries
@@ -971,6 +997,16 @@
Self-explanatory. :dd
+{Compute erotate/asphere requires extended particles} :dt
+
+This quantity can only be calculated for particles with a shape
+setting. :dd
+
+{Compute temp/asphere requires extended particles} :dt
+
+This quantity can only be calculated for particles with a shape
+setting. :dd
+
{Compute ID for compute reduce does not exist} :dt
Self-explanatory. :dd
@@ -996,35 +1032,44 @@
This is because the computation of the centro-symmetry values
uses a pairwise neighbor list. :dd
+{Compute cna/atom cutoff is longer than pairwise cutoff} :dt
+
+Self-explantory. :dd
+
+{Compute cna/atom requires a pair style be defined} :dt
+
+Self-explantory. :dd
+
{Compute coord/atom cutoff is longer than pairwise cutoff} :dt
Cannot compute coordination at distances longer than the pair cutoff,
since those atoms are not in the neighbor list. :dd
+{Compute coord/atom requires a pair style be defined} :dt
+
+Self-explantory. :dd
+
{Compute damage/atom requires peridynamic potential} :dt
Damage is a Peridynamic-specific metric. It requires you
to be running a Peridynamics simulation. :dd
-{Compute erotate/asphere requires atom attribute shape} :dt
+{Compute erotate/asphere cannot be used with atom attributes diameter or rmass} :dt
-An atom style that specifies atom shape is needed. :dd
+These attributes override the shape and mass settings, so cannot be
+used. :dd
-{Compute erotate/asphere requires atom attributes angmom, quat} :dt
+{Compute erotate/asphere requires atom attributes angmom, quat, shape} :dt
-An atom style is needed that has these attributes. :dd
+An atom style that defines these attributes must be used. :dd
{Compute erotate/sphere requires atom attribute omega} :dt
-An atom style is needed that has this attribute. :dd
-
-{Compute erotate/sphere requires atom attribute shape} :dt
-
-An atom style that specifies atom shape is needed. :dd
+An atom style that defines this attribute must be used. :dd
-{Compute erotate/sphere requires atom attributes radius, rmass} :dt
+{Compute erotate/sphere requires atom attribute radius or shape} :dt
-An atom style is needed that has these attributes. :dd
+An atom style that defines these attributes must be used. :dd
{Compute erotate/sphere requires spherical particle shapes} :dt
@@ -1034,11 +1079,6 @@
Self-explanatory. :dd
-{Compute group/group requires a pair style be defined} :dt
-
-This is because the computation of the group-group interactions uses a
-pairwise neighbor list. :dd
-
{Compute pe must use group all} :dt
Energies computed by potentials (pair, bond, etc) are computed on all
@@ -1078,17 +1118,42 @@
Self-explanatory. :dd
+{Compute reduce region ID does not exist} :dt
+
+Self-explanatory. :dd
+
{Compute reduce variable is not atom-style variable} :dt
Self-explanatory. :dd
-{Compute temp/asphere requires atom attributes quat, angmom} :dt
+{Compute temp/asphere cannot be used with atom attributes diameter or rmass} :dt
-The atom style defined does not have these attributes. :dd
+These attributes override the shape and mass settings, so cannot be
+used. :dd
+
+{Compute temp/asphere requires atom attributes angmom, quat, shape} :dt
+
+An atom style that defines these attributes must be used. :dd
+
+{Compute temp/partial cannot use vz for 2d systems} :dt
+
+Self-explanatory. :dd
+
+{Compute temp/profile cannot use vz for 2d systems} :dt
+
+Self-explanatory. :dd
+
+{Compute temp/profile cannot bin z for 2d systems} :dt
+
+Self-explanatory. :dd
{Compute temp/sphere requires atom attribute omega} :dt
-An atom style is needed that has this attributes. :dd
+An atom style that defines this attribute must be used. :dd
+
+{Compute temp/sphere requires atom attribute radius or shape} :dt
+
+An atom style that defines these attributes must be used. :dd
{Compute temp/sphere requires spherical particle shapes} :dt
@@ -1162,6 +1227,10 @@
Self-explanatory. :dd
+{Could not find group delete ID} :dt
+
+Self-explanatory. :dd
+
{Could not find delete_atoms group ID} :dt
Group ID used in the delete_atoms command does not exist. :dd
@@ -1172,11 +1241,11 @@
{Could not find displace_atoms group ID} :dt
-A group ID used in the displace_atoms command does not exist. :dd
+Group ID used in the displace_atoms command does not exist. :dd
{Could not find displace_box group ID} :dt
-Self-explanatory. :dd
+Group ID used in the displace_box command does not exist. :dd
{Could not find dump custom compute ID} :dt
@@ -1215,15 +1284,11 @@
A group ID used in the fix rigid command does not exist. :dd
-{Could not find fix spring couple 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
-{Could not find fix_modify press ID} :dt
+{Could not find fix_modify pressure ID} :dt
The compute ID for computing pressure does not exist. :dd
@@ -1280,6 +1345,11 @@
The compute ID needed by the velocity command to compute temperature
does not exist. :dd
+{Could not set finite-size particle attribute in fix rigid} :dt
+
+The particle has a finite size but its attributes could not be
+determined. :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
@@ -1547,6 +1617,10 @@
The chosen atom style does not define the per-atom vector being
dumped. :dd
+{Electronic temperature dropped below zero} :dt
+
+Something has gone wrong with the fix ttm electron temperature model. :dd
+
{Empty brackets in variable formula} :dt
A value inside the brackets is required for this formula element. :dd
@@ -1752,6 +1826,10 @@
Self-explanatory :dd
+{Fix evaporate region ID does not exist} :dt
+
+Self-explanatory :dd
+
{Fix for fix ave/atom not computed at compatible time} :dt
Fixes generate their values on specific timesteps. Fix ave/atom is
@@ -1805,41 +1883,50 @@
The time window for temperature or pressure relaxation must be > 0 :dd
+{Fix npt/asphere cannot be used with atom attributes diameter or rmass} :dt
+
+An atom style that defines these attributes must be used. :dd
+
{Fix npt/asphere requires atom attributes quat, angmom, torque, shape} :dt
An atom style that specifies these quantities is needed. :dd
-{Fix npt/sphere requires atom attribute shape} :dt
+{Fix npt/sphere requires atom attribute radius or shape} :dt
-An atom style that specifies atom shape is needed. :dd
+An atom style that defines these attributes must be used. :dd
{Fix npt/sphere requires atom attributes omega, torque} :dt
An atom style that specifies these quantities is needed. :dd
-{Fix npt/sphere requires spherical particle shapes} :dt
+{Fix nve/asphere cannot be used with atom attributes diameter or rmass} :dt
-Self-explanatory. :dd
+These attributes override the shape and mass settings, so cannot be
+used. :dd
-{Fix nve/asphere requires atom attributes quat, angmom, torque, shape} :dt
+{Fix nve/asphere requires atom attributes angmom, quat, torque, shape} :dt
An atom style that specifies these quantities is needed. :dd
+{Fix nve/asphere requires extended particles} :dt
+
+This fix can only be used for particles with a shape setting. :dd
+
{Fix nve/sphere requires atom attribute mu} :dt
An atom style with this attribute is needed. :dd
-{Fix nve/sphere requires atom attribute shape} :dt
+{Fix nve/sphere requires atom attribute radius or shape} :dt
-An atom style with this attribute is needed. :dd
+An atom style that specifies these quantities is needed. :dd
{Fix nve/sphere requires atom attributes omega, torque} :dt
An atom style with these attributes is needed. :dd
-{Fix nve/sphere requires atom attributes radius, rmass} :dt
+{Fix nve/sphere requires extended particles} :dt
-An atom style with these attributes is needed. :dd
+This fix can only be used for particles of a finite size. :dd
{Fix nve/sphere requires spherical particle shapes} :dt
@@ -1849,18 +1936,31 @@
The time window for temperature relaxation must be > 0 :dd
+{Fix nvt/asphere cannot be used with atom attributes diameter or rmass} :dt
+
+These attributes override the shape and mass settings, so cannot be
+used. :dd
+
{Fix nvt/asphere requires atom attributes quat, angmom, torque, shape} :dt
An atom style that specifies these quantities is needed. :dd
-{Fix nvt/sphere requires atom attribute shape} :dt
+{Fix nvt/asphere requires extended particles} :dt
-An atom style with this attribute is needed. :dd
+This fix can only be used for particles of a finite size. :dd
+
+{Fix nvt/sphere requires atom attribute radius or shape} :dt
+
+An atom style with these attributes is needed. :dd
{Fix nvt/sphere requires atom attributes omega, torque} :dt
An atom style with these attributes is needed. :dd
+{Fix nvt/sphere requires extended particles} :dt
+
+This fix can only be used for particles of a finite size. :dd
+
{Fix nvt/sphere requires spherical particle shapes} :dt
Self-explanatory. :dd
@@ -1911,6 +2011,10 @@
Cannot use fix shake while doing an energy minimization since
it turns off bonds that should contribute to the energy. :dd
+{Fix spring couple group ID does not exist} :dt
+
+Self-explanatory. :dd
+
{Fix temp/berendsen period must be > 0.0} :dt
Self-explanatory. :dd
@@ -1925,6 +2029,42 @@
integration fixes (nve, nvt, npt). See the fix tmd documentation for
details. :dd
+{Fix ttm electron temperatures must be > 0.0} :dt
+
+Self-explanatory. :dd
+
+{Fix ttm electronic_density must be > 0.0} :dt
+
+Self-explanatory. :dd
+
+{Fix ttm electronic_specific_heat must be > 0.0} :dt
+
+Self-explanatory. :dd
+
+{Fix ttm electronic_thermal_conductivity must be >= 0.0} :dt
+
+Self-explanatory. :dd
+
+{Fix ttm gamma_p must be > 0.0} :dt
+
+Self-explanatory. :dd
+
+{Fix ttm gamma_s must be >= 0.0} :dt
+
+Self-explanatory. :dd
+
+{Fix ttm number of nodes must be > 0} :dt
+
+Self-explanatory. :dd
+
+{Invalid random number seed in fix ttm command} :dt
+
+Random number seed must be > 0. :dd
+
+{Fix ttm v_0 must be >= 0.0} :dt
+
+Self-explanatory. :dd
+
{Fix used in compute reduce not computed at compatible time} :dt
Fixes generate their values on specific timesteps. Compute sum is
@@ -1951,7 +2091,7 @@
The atom style defined does not have these attributes. :dd
-{Fix_modify press ID does not compute pressure} :dt
+{Fix_modify pressure ID does not compute pressure} :dt
The compute ID assigned to the fix must compute pressure. :dd
@@ -2172,6 +2312,10 @@
The final tilt value must be between -1/2 and 1/2 of the perpendicular
box length. :dd
+{Initial temperatures not all set in fix ttm} :dt
+
+Self-explantory. :dd
+
{Input line too long after variable substitution} :dt
This is a hard (very large) limit defined in the input.cpp file. :dd
@@ -2587,10 +2731,18 @@
Length of read-in pair table is invalid :dd
+{Invalid radius in Atoms section of data file} :dt
+
+Radius must be >= 0.0. :dd
+
{Invalid random number seed in set command} :dt
Random number seed must be > 0. :dd
+{Invalid region in group function in variable formula} :dt
+
+Self-explanatory. :dd
+
{Invalid region style} :dt
The choice of region style is unknown. :dd
@@ -3152,14 +3304,18 @@
An atom style that stores this, like atom_style dpd, must be used. :dd
+{Pair gayberne cannot be used with atom attribute diameter} :dt
+
+Finite-size particles must be defined with the shape command. :dd
+
{Pair gayberne epsilon a,b,c coeffs are not all set} :dt
Each atom type involved in pair_style gayberne must
have these 3 coefficients set at least once. :dd
-{Pair gayberne requires atom attributes quat, torque} :dt
+{Pair gayberne requires atom attributes quat, torque, shape} :dt
-The atom style defined does not have these attributes. :dd
+An atom style that defines these attributes must be used. :dd
{Pair granular requires atom attributes radius, omega, torque} :dt
@@ -3189,15 +3345,25 @@
The specified cutoffs for the pair style are inconsistent. :dd
-{Pair lubricate requires atom attributes torque, shape} :dt
+{Pair lubricate cannot be used with atom attributes diameter or rmass} :dt
+
+These attributes override the shape and mass settings, so cannot be
+used. :dd
+
+{Pair lubricate requires atom attributes quat, torque, shape} :dt
+
+An atom style that defines these attributes must be used. :dd
+
+{Pair lubricate requires extended particles} :dt
-Use a different atom style. :dd
+This pair style can only be used for particles with a shape
+setting. :dd
{Pair lubricate requires mono-disperse particles} :dt
This is a current restriction of this pair style. :dd
-{Pair lubricate requires spherical particles} :dt
+{Pair lubricate requires spherical, mono-disperse particles} :dt
This is a current restriction of this pair style. :dd
@@ -3214,6 +3380,10 @@
Even for atomic systems, an atom map is required to find Peridynamic
bonds. Use the atom_modify command to define one. :dd
+{Pair resquared cannot be used with atom attribute diameter} :dt
+
+This attribute overrides the shape settings, so cannot be used. :dd
+
{Pair resquared epsilon a,b,c coeffs are not all set} :dt
Self-explanatory. :dd
@@ -3222,13 +3392,13 @@
Self-explanatory. :dd
-{Pair resquared requires atom attributes quat, torque} :dt
+{Pair resquared requires atom attributes quat, torque, shape} :dt
-Use a different atom style. :dd
+An atom style that defines these attributes must be used. :dd
{Pair style AIREBO requires atom IDs} :dt
-Self-explanatory. :dd
+This is a requirement to use the AIREBO potential. :dd
{Pair style AIREBO requires newton pair on} :dt
@@ -3257,6 +3427,10 @@
See the newton command. This is a restriction to use the Tersoff
potential. :dd
+{Pair style born/coul/long requires atom attribute q} :dt
+
+An atom style that defines this attribute must be used. :dd
+
{Pair style buck/coul/cut requires atom attribute q} :dt
The atom style defined does not have this attribute. :dd
@@ -3274,10 +3448,20 @@
The pair style does not have a single() function, so it can
not be invoked by bond_style quartic. :dd
+{Pair style does not support compute group/group} :dt
+
+The pair_style does not have a single() function, so it cannot be
+invokded by the compute group/group command.
+
+{Pair style does not support fix bond/swap} :dt
+
+The pair_style does not have a single() function, so it cannot be
+invokded by the fix bond/swap command.
+
{Pair style does not support pair_write} :dt
-The pair style does not have a single() function, so it can
-not be invoked by the pair_write command. :dd
+The pair style does not have a single() function, so it cannot be
+invoked by the pair_write command. :dd
{Pair style does not support rRESPA inner/middle/outer} :dt
@@ -3354,6 +3538,14 @@
This is because atom style peri stores quantities needed by
the peridynamic potential. :dd
+{Pair style reax requires atom IDs} :dt
+
+This is a requirement to use the ReaxFF potential. :dd
+
+{Pair style reax requires newton pair on} :dt
+
+This is a requirement to use the ReaxFF potential. :dd
+
{Pair table cutoffs must all be equal to use with KSpace} :dt
When using pair style table with a long-range KSpace solver, the
@@ -3419,26 +3611,35 @@
Self-explanatory. :dd
-{Press ID for fix nph does not exist} :dt
+{Pressure ID for fix box/relax does not exist} :dt
+
+The compute ID needed to compute pressure for the fix does not
+exist. :dd
+
+{Pressure ID for fix nph does not exist} :dt
The compute ID needed to compute pressure for the fix does not
exist. :dd
-{Press ID for fix npt does not exist} :dt
+{Pressure ID for fix npt does not exist} :dt
The compute ID needed to compute pressure for the fix does not
exist. :dd
-{Press ID for fix press/berendsen does not exist} :dt
+{Pressure ID for fix press/berendsen does not exist} :dt
The compute ID needed to compute pressure for the fix does not
exist. :dd
-{Press ID for thermo does not exist} :dt
+{Pressure ID for thermo does not exist} :dt
The compute ID needed to compute pressure for thermodynamics does not
exist. :dd
+{Pressure ID for fix modify does not exist} :dt
+
+Self-explanatory. :dd
+
{Proc grid in z != 1 for 2d simulation} :dt
There cannot be more than 1 processor in the z dimension of a 2d
@@ -3645,30 +3846,35 @@
Self-explanatory. :dd
-{Temp ID for fix nph does not exist} :dt
+{Temperature ID for fix box/relax does not exist} :dt
+
+The compute ID needed to compute temperature for the fix does not
+exist. :dd
+
+{Temperature ID for fix nph does not exist} :dt
The compute ID needed to compute temperature for the fix does not
exist. :dd
-{Temp ID for fix npt does not exist} :dt
+{Temperature ID for fix npt does not exist} :dt
The compute ID needed to compute temperature for the fix does not
exist. :dd
-{Temp ID for fix nvt does not exist} :dt
+{Temperature ID for fix nvt does not exist} :dt
The compute ID needed to compute temperature for the fix does not
exist. :dd
-{Temp ID for fix press/berendsen does not exist} :dt
+{Temperature ID for fix press/berendsen does not exist} :dt
Self-explanatory. :dd
-{Temp ID for fix temp/berendsen does not exist} :dt
+{Temperature ID for fix temp/berendsen does not exist} :dt
Self-explanatory. :dd
-{Temp ID for fix temp/rescale does not exist} :dt
+{Temperature ID for fix temp/rescale does not exist} :dt
The compute ID needed to compute temperature for the fix does not
exist. :dd
@@ -4117,6 +4323,10 @@
It is not efficient to use compute centro/atom more than once. :dd
+{More than one compute cna/atom defined} :dt
+
+It is not efficient to use compute cna/atom more than once. :dd
+
{More than one compute coord/atom} :dt
It is not efficient to use compute coord/atom more than once. :dd
@@ -4141,6 +4351,14 @@
It is not efficient to use fix rigid more than once. :dd
+{New thermo_style command, previous thermo_modify settings will be lost} :dt
+
+If a thermo_style command is used after a thermo_modify command, the
+settings changed by the thermo_modify command will be reset to their
+default values. This is because the thermo_modify commmand acts on
+the currently defined thermo style, and a thermo_style command creates
+a new style. :dd
+
{No fixes defined, atoms won't move} :dt
If you are not using a fix like nve, nvt, npt then atom velocities and
@@ -4152,6 +4370,11 @@
will integrate the body motion, but it would be more efficient to use
fix rigid. :dd
+{Not using real units with pair reax} :dt
+
+This is most likely an error, unless you have created your own ReaxFF
+parameter file in a different set of units. :dd
+
{One or more atoms are time integrated more than once} :dt
This is probably an error since you typically do not want to
@@ -4205,6 +4428,19 @@
of your restarted simulation may diverge a little more quickly than if
you ran on the same # of processors. :dd
+{Restart file used different boundary settings, using restart file values} :dt
+
+Your input script cannot change these settings in the restart file.
+
+{Restart file used different newton bond setting, using restart file value} :dt
+
+Your input script cannot change this setting in the restart file.
+
+{Restart file used different newton pair setting, using input script value} :dt
+
+Your input script can change this setting in the restart file, but you
+may not wish to do so.
+
{Restart file version does not match LAMMPS version} :dt
The version of LAMMPS that wrote the restart file does not match the
@@ -4251,13 +4487,17 @@
assumed to also be for all atoms. Thus the pressure printed by thermo
could be inaccurate. :dd
+{Too many inner timesteps in fix ttm} :dt
+
+Self-explanatory. :dd
+
{Use special bonds = 0,1,1 with bond style fene/expand} :dt
-Most FENE models use this setting for the special_bonds command. :dd
+Most FENE models need this setting for the special_bonds command. :dd
{Use special bonds = 0,1,1 with bond style fene} :dt
-Most FENE models use this setting for the special_bonds command. :dd
+Most FENE models need this setting for the special_bonds command. :dd
{Using compute temp/deform with inconsistent fix deform remap option} :dt
@@ -4266,7 +4506,8 @@
{Using compute temp/deform with no fix deform defined} :dt
-Self-explanatory. :dd
+This is probably an error, since it makes little sense to use
+compute temp/deform in this case. :dd
{Using pair tail corrections with nonperiodic system} :dt
diff -Naur lammps-3Jul09/doc/Section_modify.html lammps-4Jul09/doc/Section_modify.html
--- lammps-3Jul09/doc/Section_modify.html 2008-03-18 14:18:54.000000000 -0600
+++ lammps-4Jul09/doc/Section_modify.html 2009-06-30 13:06:26.000000000 -0600
@@ -324,13 +324,15 @@
Typically, only a small fraction of these methods are defined for a
particular fix. Setmask is mandatory, as it determines when the fix
will be invoked during the timestep. Fixes that perform time
-integration (nve, nvt, npt) implement initial_integrate and
-final_integrate to perform velocity Verlet updates. Fixes that
-constrain forces implement post_force. Fixes that perform diagnostics
-typically implement end_of_step. For an end_of_step fix, one of your
-fix arguments must be the variable "nevery" which is used to determine
-when to call the fix. By convention, this is the first argument the
-fix defines (after the ID, group-ID, style).
+integration (nve, nvt, npt) implement initial_integrate() and
+final_integrate() to perform velocity Verlet updates. Fixes that
+constrain forces implement post_force().
+
+Fixes that perform diagnostics typically implement end_of_step(). For
+an end_of_step fix, one of your fix arguments must be the variable
+"nevery" which is used to determine when to call the fix and you must
+set this variable in the constructor of your fix. By convention, this
+is the first argument the fix defines (after the ID, group-ID, style).
If the fix needs to store information for each atom that persists from
timestep to timestep, it can manage that memory and migrate the info
diff -Naur lammps-3Jul09/doc/Section_modify.txt lammps-4Jul09/doc/Section_modify.txt
--- lammps-3Jul09/doc/Section_modify.txt 2008-03-18 14:18:54.000000000 -0600
+++ lammps-4Jul09/doc/Section_modify.txt 2009-06-30 13:06:26.000000000 -0600
@@ -311,13 +311,15 @@
Typically, only a small fraction of these methods are defined for a
particular fix. Setmask is mandatory, as it determines when the fix
will be invoked during the timestep. Fixes that perform time
-integration ({nve}, {nvt}, {npt}) implement initial_integrate and
-final_integrate to perform velocity Verlet updates. Fixes that
-constrain forces implement post_force. Fixes that perform diagnostics
-typically implement end_of_step. For an end_of_step fix, one of your
-fix arguments must be the variable "nevery" which is used to determine
-when to call the fix. By convention, this is the first argument the
-fix defines (after the ID, group-ID, style).
+integration ({nve}, {nvt}, {npt}) implement initial_integrate() and
+final_integrate() to perform velocity Verlet updates. Fixes that
+constrain forces implement post_force().
+
+Fixes that perform diagnostics typically implement end_of_step(). For
+an end_of_step fix, one of your fix arguments must be the variable
+"nevery" which is used to determine when to call the fix and you must
+set this variable in the constructor of your fix. By convention, this
+is the first argument the fix defines (after the ID, group-ID, style).
If the fix needs to store information for each atom that persists from
timestep to timestep, it can manage that memory and migrate the info
diff -Naur lammps-3Jul09/doc/fix_indent.html lammps-4Jul09/doc/fix_indent.html
--- lammps-3Jul09/doc/fix_indent.html 2008-11-13 08:34:21.000000000 -0700
+++ lammps-4Jul09/doc/fix_indent.html 2009-07-01 14:28:51.000000000 -0600
@@ -23,7 +23,7 @@
one or more keyword/value pairs may be appended
-keyword = sphere or cylinder or plane or vel or rstart or units
+keyword = sphere or cylinder or plane or vel or rstart or side or units
sphere args = x y z R
x,y,z = initial position of center of indenter (distance units)
@@ -41,6 +41,9 @@
rstart value = R0
R0 = sphere or cylinder radius at start of run (distance units)
R is value at end of run, so indenter expands/contracts over time
+ side value = in or out
+ in = the indenter acts on particles inside the sphere or cylinder
+ out = the indenter acts on particles outside the sphere or cylinder
units value = lattice or box
lattice = the geometry is defined in lattice units
box = the geometry is defined in simulation box units
@@ -56,7 +59,8 @@
Insert an indenter within a simulation box. The indenter repels all
atoms that touch it, so it can be used to push into a material or as
-an obstacle in a flow.
+an obstacle in a flow. Or it can be used as a constraining wall
+around a simulation; see the discussion of the side keyword below.
The indenter can either be spherical or cylindrical or planar. You
must set one of those 3 keywords.
@@ -92,11 +96,20 @@
at the specified velocity.
If the rstart keyword is specified, then the radius of the indenter
-is a time-dependent quantity. R0 is the value assigned at the start
-of the run; R is the value at the end. At intermediate times, the
-radius is linearly interpolated between these two values. This option
-can be used, for example, to grow/shrink a void within the simulation
-box.
+is a time-dependent quantity. This only applies to spherical or
+cylindrical indenters. R0 is the value assigned at the start of the
+run; R is the value at the end. At intermediate times, the radius is
+linearly interpolated between these two values. This option can be
+used, for example, to grow/shrink a void within the simulation box.
+
+If the side keyword is specified as out, which is the default,
+then particles outside the indenter are pushded away from its outer
+surface, as described above. This only applies to spherical or
+cylindrical indenters. If the side keyword is specified as in,
+the action of the indenter is reversed. Particles inside the indenter
+are pushed away from its inner surface. In other words, the indenter
+is now a containing wall that traps the particles inside it. If the
+radius shrinks over time, it will squeeze the particles.
The units keyword determines the meaning of the distance units used
to define the indenter. A box value selects standard distance units
@@ -151,6 +164,6 @@
Default:
-The option defaults are vel = 0,0,0 and units = lattice.
+
The option defaults are vel = 0,0,0, side = out, and units = lattice.