integrate fix grem docs and update to match current conventions

doc/src/Section_commands.txt

@@ -687,6 +687,7 @@ package"_Section_start.html#start_3.
 "eos/table/rx"_fix_eos_table_rx.html,
 "flow/gauss"_fix_flow_gauss.html,
 "gle"_fix_gle.html,
+"grem"_fix_grem.html,
 "imd"_fix_imd.html,
 "ipi"_fix_ipi.html,
 "langevin/drude"_fix_langevin_drude.html,

doc/src/fix_grem.txt

@@ -10,69 +10,62 @@ fix grem command :h3
 
 [Syntax:]
 
-fix ID group-ID grem lambda eta H0 thermostat-ID
+fix ID group-ID grem lambda eta H0 thermostat-ID :pre
 
-ID, group-ID are documented in "fix"_fix.html command
-grem = style name of this fix command
-lambda = intercept parameter of linear effective temperature function
-eta = slope parameter of linear effective temperature function
-H0 = shift parameter of linear effective temperature function
-thermostat-ID = ID of thermostat used in simulation
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+grem = style name of this fix command :l
+lambda = intercept parameter of linear effective temperature function :l
+eta = slope parameter of linear effective temperature function :l
+H0 = shift parameter of linear effective temperature function :l
+thermostat-ID = ID of Nose-Hoover thermostat or barostat used in simulation :l,ule
 
 [Examples:]
 
 fix             fxgREM all grem 400 -0.01 -30000 fxnpt
-thermo_modify   press fxgREM_press
+thermo_modify   press fxgREM_press :pre
 
-fix             fxgREM all grem 502 -0.15 -80000 fxnvt
+fix             fxgREM all grem 502 -0.15 -80000 fxnvt :pre
 
 [Description:]
 
-This fix implements the molecular dynamics version
-of the generalized replica 
-exchange method (gREM) originally developed by "(Kim)"_#Kim,
-which uses non-Boltzmann ensembles to sample over first
-order phase transitions.
-
-The is done by defining replicas with an enthalpy dependent
+This fix implements the molecular dynamics version of the generalized
+replica exchange method (gREM) originally developed by "(Kim)"_#Kim,
+which uses non-Boltzmann ensembles to sample over first order phase
+transitions. The is done by defining replicas with an enthalpy dependent
 effective temperature
 
 :c,image(Eqs/fix_grem.jpg)
 
-with {eta} negative and steep enough to only intersect 
-the characteristic microcanonical temperature (Ts) of the
-system once, ensuring a unimodal enthalpy distribution in 
-that replica. {Lambda} is the intercept and effects the 
-generalized ensemble similar to how temperature effects 
-a Boltzmann ensemble. {H0} is a reference enthalpy, and
-is typically set as the lowest desired sampled enthalpy.
-Further explanation can be found in our recent papers 
-"(Malolepsza)"_#Malolepsza.
+with {eta} negative and steep enough to only intersect the characteristic
+microcanonical temperature (Ts) of the system once, ensuring a unimodal
+enthalpy distribution in that replica. {Lambda} is the intercept and
+effects the generalized ensemble similar to how temperature effects a
+Boltzmann ensemble. {H0} is a reference enthalpy, and is typically set
+as the lowest desired sampled enthalpy.  Further explanation can be
+found in our recent papers "(Malolepsza)"_#Malolepsza.
 
-This fix requires a thermostat, with ID passed to fix_grem
-by {thermostat-ID}. Two distinct temperatures exist in this
-generalized ensemble, the effective temperature defined above,
-and a kinetic temperature that controls the velocity 
-distribution of particles as usual. Either constant volume
-or constant pressure algorithms can be used.
+This fix requires a Nose-Hoover thermostat reference passed to the grem
+by {thermostat-ID}. Two distinct temperatures exist in this generalized
+ensemble, the effective temperature defined above, and a kinetic
+temperature that controls the velocity distribution of particles as
+usual. Either constant volume or constant pressure algorithms can be
+used.
 
-The fix enforces a generalized ensemble in a single replica
-only. Typically, different replicas only differ by {lambda}
-for simplicity, but this is not necessary. Multi-replica 
-runs need to be run outside of LAMMPS. An example of this 
-can be found in examples/USER/misc/grem
+The fix enforces a generalized ensemble in a single replica only.
+Typically, different replicas only differ by {lambda} for simplicity,
+but this is not necessary. Multi-replica runs need to be run outside
+of LAMMPS. An example of this can be found in examples/USER/misc/grem
 
-In general, defining the generalized ensembles is unique for 
-every system. When starting a many-replica simulation without 
-any knowledge of the underlying microcanonical temperature, 
-there are several tricks we have utilized to optimize the process. 
-Choosing a less-steep {eta} yields broader distributions, 
-requiring fewer replicas to map the microcanonical temperature. 
-While this likely struggles from the same sampling problems 
-gREM was built to avoid, it provides quick insight to Ts. 
-Initially using an evenly-spaced {lambda} distribution identifies
+In general, defining the generalized ensembles is unique for every
+system. When starting a many-replica simulation without any knowledge of
+the underlying microcanonical temperature, there are several tricks we
+have utilized to optimize the process.  Choosing a less-steep {eta}
+yields broader distributions, requiring fewer replicas to map the
+microcanonical temperature.  While this likely struggles from the same
+sampling problems gREM was built to avoid, it provides quick insight to
+Ts.  Initially using an evenly-spaced {lambda} distribution identifies
 regions where small changes in enthalpy lead to large temperature
-changes. Replicas are easily added where needed. 
+changes. Replicas are easily added where needed.
 
 :line
 
@@ -93,8 +86,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 [Related commands:]
 
-"fix_nh"_fix_nh.html
-"thermo_modify"_thermo_modify.html
+"fix nvt"_fix_nh.html, "fix npt"_fix_nh.html, "thermo_modify"_thermo_modify.html
 
 [Default:] none
 

doc/src/fixes.txt

@@ -48,6 +48,7 @@ Fixes :h1
    fix_gld
    fix_gle
    fix_gravity
+   fix_grem
    fix_halt
    fix_heat
    fix_imd

doc/src/lammps.book

@@ -170,6 +170,7 @@ fix_gcmc.html
 fix_gld.html
 fix_gle.html
 fix_gravity.html
+fix_grem.html
 fix_halt.html
 fix_heat.html
 fix_imd.html