Fold hma compute into USER-MISC

examples/USER/misc/hma/README

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+The example input script sets up a simple FCC crystal using the Lennard-Jones
+potential. The script sets up the HMA compute to calculate the energy, pressure
+and heat capacity.  The output columns are:
+
+1: timestep
+2: measured temperature
+3: potential energy
+4: HMA potential energy
+5: pressure
+6: HMA pressure
+7: HMA heat capacity contribution
+
+Averages of the potential energy (#3 and #4) agree although #4 (HMA) is more precise.
+
+Averages of the pressure (#5 and #6) agree once the ideal gas
+contribution is included; #6 (HMA) is more precise.
+
+The heat capacity can be computed from colume #3 (convential) as
+Cv = Var(#3)/(k T^2)
+
+With HMA, the heat capacity can be computed from column #4 and #7 as
+Cv = #7 + Var(#4)/(k T^2)

examples/USER/misc/hma/hma.in

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+# Harmonically mapped average example
+
+units lj 
+dimension 3 
+boundary p p p 
+atom_style atomic 
+atom_modify map array
+# ---------- Create Atoms ----------------------------
+lattice 	fcc 1.0
+region	box block 0 4 0 4 0 4 units lattice
+create_box	1 box
+lattice	fcc 1.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1  
+create_atoms 1 region box
+# ---------- Define Interatomic Potential --------------------- 
+pair_style lj/smooth/linear 3
+pair_coeff * * 1.0 1.0 
+mass 1 1.0
+
+atom_modify sort 0 1
+velocity all create 0.1 45678 dist gaussian
+
+compute u all pe 
+  
+compute p all pressure NULL pair  
+
+compute hma all HMA settemp u p 9.579586686264458 cv
+
+timestep 0.005
+
+fix settemp all nvt temp 1.0 1.0 0.5
+thermo_style custom elapsed temp c_u c_hma[1] c_p c_hma[2] c_hma[3]
+thermo_modify format float '%22.15e'
+thermo 500
+run 20000
+thermo 20
+run 200000