add atom_modify map yes, also timers to create_atoms and replicate

doc/src/Section_packages.txt

@@ -727,7 +727,7 @@ make lib-latte                          # print help message
 make lib-latte args="-b"                # download and build in lib/latte/LATTE-master
 make lib-latte args="-p $HOME/latte"    # use existing LATTE installation in $HOME/latte
 make lib-latte args="-b -m gfortran"    # download and build in lib/latte and 
-                                        #   copy Makefile.lammps.gfortran to Makefile.lammps
+                                        #   copy Makefile.lammps.gfortran to Makefile.lammps :pre
 
 Note that 3 symbolic (soft) links, "includelink" and "liblink" and
 "filelink", are created in lib/latte to point into the LATTE home dir.

doc/src/atom_modify.txt

@@ -16,7 +16,7 @@ atom_modify keyword values ... :pre
 one or more keyword/value pairs may be appended :ulb,l
 keyword = {id} or {map} or {first} or {sort} :l
    {id} value = {yes} or {no}
-   {map} value = {array} or {hash}
+   {map} value = {yes} or {array} or {hash}
    {first} value = group-ID = group whose atoms will appear first in internal atom lists
    {sort} values = Nfreq binsize
      Nfreq = sort atoms spatially every this many time steps
@@ -25,8 +25,8 @@ keyword = {id} or {map} or {first} or {sort} :l
 
 [Examples:]
 
-atom_modify map hash
-atom_modify map array sort 10000 2.0
+atom_modify map yes
+atom_modify map hash sort 10000 2.0
 atom_modify first colloid :pre
 
 [Description:]
@@ -62,29 +62,33 @@ switch.  This is described in "Section 2.2"_Section_start.html#start_2
 of the manual.  If atom IDs are not used, they must be specified as 0
 for all atoms, e.g. in a data or restart file.
 
-The {map} keyword determines how atom ID lookup is done for molecular
-atom styles.  Lookups are performed by bond (angle, etc) routines in
-LAMMPS to find the local atom index associated with a global atom ID.
+The {map} keyword determines how atoms with specific IDs are found
+when required.  An example are the bond (angle, etc) methods which
+need to find the local index of an atom with a specific global ID
+which is a bond (angle, etc) partner.  LAMMPS performs this operation
+efficiently by creating a "map", which is either an {array} or {hash}
+table, as descibed below.
 
-When the {array} value is used, each processor stores a lookup table
-of length N, where N is the largest atom ID in the system.  This is a
+When the {map} keyword is not specified in your input script, LAMMPS
+only creates a map for "atom_styles"_atom_style.html for molecular
+systems which have permanent bonds (angles, etc).  No map is created
+for atomic systems, since it is normally not needed.  However some
+LAMMPS commands require a map, even for atomic systems, and will
+generate an error if one does not exist.  The {map} keyword thus
+allows you to force the creation of a map.  The {yes} value will
+create either an {array} or {hash} style map, as explained in the next
+paragraph.  The {array} and {hash} values create an atom-style or
+hash-style map respectively.
+
+For an {array}-style map, each processor stores a lookup table of
+length N, where N is the largest atom ID in the system.  This is a
 fast, simple method for many simulations, but requires too much memory
-for large simulations.  The {hash} value uses a hash table to perform
-the lookups.  This can be slightly slower than the {array} method, but
-its memory cost is proportional to the number of atoms owned by a
-processor, i.e. N/P when N is the total number of atoms in the system
-and P is the number of processors.
-
-When this setting is not specified in your input script, LAMMPS
-creates a map, if one is needed, as an array or hash.  See the
-discussion of default values below for how LAMMPS chooses which kind
-of map to build.  Note that atomic systems do not normally need to
-create a map.  However, even in this case some LAMMPS commands will
-create a map to find atoms (and then destroy it), or require a
-permanent map.  An example of the former is the "velocity loop
-all"_velocity.html command, which uses a map when looping over all
-atoms and insuring the same velocity values are assigned to an atom
-ID, no matter which processor owns it.
+for large simulations.  For a {hash}-style map, a hash table is
+created on each processor, which finds an atom ID in constant time
+(independent of the global number of atom IDs).  It can be slightly
+slower than the {array} map, but its memory cost is proportional to
+the number of atoms owned by a processor, i.e. N/P when N is the total
+number of atoms in the system and P is the number of processors.
 
 The {first} keyword allows a "group"_group.html to be specified whose
 atoms will be maintained as the first atoms in each processor's list

doc/src/fix_nh.txt

@@ -393,32 +393,36 @@ thermostatting and barostatting.
 :line
 
 These fixes compute a temperature and pressure each timestep.  To do
-this, the fix creates its own computes of style "temp" and "pressure",
-as if one of these two sets of commands had been issued:
+this, the thermostat and barostat fixes create their own computes of
+style "temp" and "pressure", as if one of these sets of commands had
+been issued:
 
+For fix nvt:
 compute fix-ID_temp group-ID temp
-compute fix-ID_press group-ID pressure fix-ID_temp :pre
 
+For fix npt and fix nph:
 compute fix-ID_temp all temp
 compute fix-ID_press all pressure fix-ID_temp :pre
 
-See the "compute temp"_compute_temp.html and "compute
-pressure"_compute_pressure.html commands for details.  Note that the
-IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
-+ underscore + "press".  For fix nvt, the group for the new computes
-is the same as the fix group.  For fix nph and fix npt, the group for
-the new computes is "all" since pressure is computed for the entire
-system.
+For fix nvt, the group for the new temperature compute is the same as
+the fix group.  For fix npt and fix nph, the group for both the new
+temperature and pressure compute is "all" since pressure is computed
+for the entire system.  In the case of fix nph, the temperature
+compute is not used for thermostatting, but just for a kinetic-energy
+contribution to the pressure.  See the "compute
+temp"_compute_temp.html and "compute pressure"_compute_pressure.html
+commands for details.  Note that the IDs of the new computes are the
+fix-ID + underscore + "temp" or fix_ID + underscore + "press".
 
 Note that these are NOT the computes used by thermodynamic output (see
 the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}
-and {thermo_press}.  This means you can change the attributes of this
+and {thermo_press}.  This means you can change the attributes of these
 fix's temperature or pressure via the
-"compute_modify"_compute_modify.html command or print this temperature
-or pressure during thermodynamic output via the "thermo_style
-custom"_thermo_style.html command using the appropriate compute-ID.
-It also means that changing attributes of {thermo_temp} or
-{thermo_press} will have no effect on this fix.
+"compute_modify"_compute_modify.html command.  Or you can print this
+temperature or pressure during thermodynamic output via the
+"thermo_style custom"_thermo_style.html command using the appropriate
+compute-ID.  It also means that changing attributes of {thermo_temp}
+or {thermo_press} will have no effect on this fix.
 
 Like other fixes that perform thermostatting, fix nvt and fix npt can
 be used with "compute commands"_compute.html that calculate a