These are additional pair styles in USER packages, which can be used
diff --git a/doc/doc2/Section_howto.html b/doc/doc2/Section_howto.html
index 85dccd8c89..4991250bcc 100644
--- a/doc/doc2/Section_howto.html
+++ b/doc/doc2/Section_howto.html
@@ -1897,10 +1897,10 @@ and free all its memory.
The lammps_version() function can be used to determined the specific
version of the underlying LAMMPS code. This is particularly useful
when loading LAMMPS as a shared library via dlopen(). The code using
-the library interface can than use this information to adapt to changes
-to the LAMMPS command syntax between versions. The returned LAMMPS
-version code is an integer (e.g. 2 Sep 2015 results in 20150902) that
-is growing with every new LAMMPS version.
+the library interface can than use this information to adapt to
+changes to the LAMMPS command syntax between versions. The returned
+LAMMPS version code is an integer (e.g. 2 Sep 2015 results in
+20150902) that grows with every new LAMMPS version.
The lammps_file() and lammps_command() functions are used to pass a
file or string to LAMMPS as if it were an input script or single
@@ -2566,11 +2566,18 @@ specified between cores.
turn-off the Coulombic interaction within core/shell pairs, since that
interaction is set by the bond spring. This is done using the
special_bonds command with a 1-2 weight = 0.0,
-which is the default value.
+which is the default value. It needs to be considered whether one has
+to adjust the special_bonds weighting according
+to the molecular topology since the interactions of the shells are
+bypassed over an extra bond.
+
+
Note that this core/shell implementation does not require all ions to
+be polarized. One can mix core/shell pairs and ions without a
+satellite particle if desired.
Since the core/shell model permits distances of r = 0.0 between the
core and shell, a pair style with a "cs" suffix needs to be used to
-implement a valid long-range Coulombic correction. Several such pair
+implement a valid long-rangeCoulombic correction. Several such pair
styles are provided in the CORESHELL package. See this doc
page for details. All of the core/shell enabled pair
styles require the use of a long-range Coulombic solver, as specified
@@ -2602,15 +2609,20 @@ temp/cs command can be used, in conjunction with
any of the thermostat fixes, such as fix nvt or fix
langevin. This compute uses the center-of-mass velocity
of the core/shell pairs to calculate a temperature, and insures that
-velocity is what is rescaled for thermostatting purposes. The
+velocity is what is rescaled for thermostatting purposes. This
+compute also works for a system with both core/shell pairs and
+non-polarized ions (ions without an attached satellite particle). The
compute temp/cs command requires input of two
-groups, one for the core atoms, another for the shell atoms. These
-can be defined using the group type command. Note that
-to perform thermostatting using this definition of temperature, the
-fix modify temp command should be used to assign the
-comptue to the thermostat fix. Likewise the thermo_modify
-temp command can be used to make this temperature
-be output for the overall system.
+groups, one for the core atoms, another for the shell atoms.
+Non-polarized ions which might also be included in the treated system
+should not be included into either of these groups, they are taken
+into account by the group-ID (2nd argument) of the compute. The
+groups can be defined using the group type command.
+Note that to perform thermostatting using this definition of
+temperature, the fix modify temp command should be
+used to assign the comptue to the thermostat fix. Likewise the
+thermo_modify temp command can be used to make
+this temperature be output for the overall system.
For the NaCl example, this can be done as follows:
@@ -2649,19 +2661,19 @@ energy can be monitored using the compute
chunk/atom and compute
temp/chunk commands. The internal kinetic
energies of each core/shell pair can then be summed using the sum()
-special functino of the variable command. Or they can
+special function of the variable command. Or they can
be time/averaged and output using the fix ave/time
command. To use these commands, each core/shell pair must be defined
as a "chunk". If each core/shell pair is defined as its own molecule,
the molecule ID can be used to define the chunks. If cores are bonded
-to each other to form larger molecules, then another way to define the
-chunks is to use the fix property/atom to
-assign a core/shell ID to each atom via a special field in the data
-file read by the read_data command. This field can
-then be accessed by the compute
-property/atom command, to use as input to
-the compute chunk/atom command to define the
-core/shell pairs as chunks.
+to each other to form larger molecules, the chunks can be identified
+by the fix property/atom via assigning a
+core/shell ID to each atom using a special field in the data file read
+by the read_data command. This field can then be
+accessed by the compute property/atom
+command, to use as input to the compute
+chunk/atom command to define the core/shell
+pairs as chunks.
group1 = group-ID of either cores or shells
@@ -40,11 +40,19 @@ A compute of this style can be used by any command that computes a
temperature via fix_modify e.g. fix
temp/rescale, fix npt, etc.
+
Note that this compute does not require all ions to be polarized,
+hence defined as core/shell pairs. One can mix core/shell pairs and
+ions without a satellite particle if desired. The compute will
+consider the non-polarized ions according to the physical system.
+
For this compute, core and shell particles are specified by two
respective group IDs, which can be defined using the
group command. The number of atoms in the two groups
must be the same and there should be one bond defined between a pair
-of atoms in the two groups.
+of atoms in the two groups. Non-polarized ions which might also be
+included in the treated system should not be included into either of
+these groups, they are taken into account by the group-ID (2nd
+argument) of the compute.
The temperature is calculated by the formula KE = dim/2 N k T, where
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
@@ -52,10 +60,7 @@ dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
in the group, k = Boltzmann constant, and T = temperature. Note that
the velocity of each core or shell atom used in the KE calculation is
the velocity of the center-of-mass (COM) of the core/shell pair the
-atom is part of. Note that atoms that are not core or shell particles
-are also included in the temperature calculation (if they are in the
-specified group-ID); they contribute to the total kinetic energy in
-the usual way.
+atom is part of.
A kinetic energy tensor, stored as a 6-element vector, is also
calculated by this compute for use in the computation of a pressure
diff --git a/doc/doc2/pair_lj.html b/doc/doc2/pair_lj.html
index 1a8c57f73a..aed88ee4f6 100644
--- a/doc/doc2/pair_lj.html
+++ b/doc/doc2/pair_lj.html
@@ -51,6 +51,8 @@
style = lj/cut or lj/cut/coul/cut or lj/cut/coul/debye or lj/cut/coul/dsf or lj/cut/coul/long or lj/cut/coul/msm or lj/cut/tip4p/long
+
style = lj/cut or lj/cut/coul/cut or lj/cut/coul/debye or lj/cut/coul/dsf or lj/cut/coul/long or lj/cut/coul/long/cs or lj/cut/coul/msm or lj/cut/tip4p/long
@@ -212,6 +216,11 @@ specified for this style means that pairwise interactions within this
distance are computed directly; interactions outside that distance are
computed in reciprocal space.
+
Style lj/cut/coul/long/cs is identical to lj/cut/coul/long except
+that a term is added for the core/shell
+model to allow charges on core and shell
+particles to be separated by r = 0.0.
+
Styles lj/cut/tip4p/cut and lj/cut/tip4p/long implement the TIP4P
water model of (Jorgensen), which introduces a massless
site located a short distance away from the oxygen atom along the
diff --git a/doc/doc2/timers.html b/doc/doc2/timers.html
new file mode 100644
index 0000000000..192973f175
--- /dev/null
+++ b/doc/doc2/timers.html
@@ -0,0 +1,263 @@
+
+
+
+
+
+
args = one or more of off or loop or normal or full or sync or nosync
+
+
+off = do not collect and print timing information
+loop = collect only the total time for the simulation loop
+normal = collect timer information broken down in sections (default)
+full = like normal but also include CPU and thread utilzation
+sync = explicitly synchronize MPI tasks between sections
+nosync = do not synchronize MPI tasks when collecting timer info (default)
+
Select to which level of detail LAMMPS is performing internal profiling.
+
During regular runs LAMMPS will collect information about how much time is
+spent in different sections of the code and thus can provide valuable
+information for determining performance and load imbalance problems. This
+can be done at different levels of detail and accuracy. For more
+information about the timing output, please have a look at the discussion of screen output.
+
The off setting will turn all time measurements off. The loop setting
+will only measure the total time of run loop and not collect any detailed
+per section information. With the normal setting, timing information for
+individual sections of the code are collected and also information about
+load imbalances inside those sections presented. The full setting adds
+information about CPU utilization and thread utilization, when multi-threading
+is enabled.
+
With the sync setting, all MPI tasks are synchronized at each timer call
+and thus allowing to study load imbalance more accuractly, but this usually
+has some performance impact. Using the nosync setting this can be turned
+off (which is the default).
+
Multiple keywords can be provided and for keywords that are mutually
+exclusive, the last one in that group is taking effect.
+
+
Warning
+
Using the full and sync options provides the most
+detailed and accurate timing information, but also can have a significant
+negative performance impact due to the overhead of the many required system
+calls. It is thus recommended to use these settings only when making tests
+to identify the performance. For calculations with few atoms or a very
+large number of performance, even using the normal setting can have
+a measurable performance impact. It is recommended in those cases to use
+the loop or off setting.