add examples for hmc

examples/mc/data.hmc_spce

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+LAMMPS datafile
+
+3 atoms
+2 atom types
+2 bonds
+1 bond types
+1 angles
+1 angle types
+
+-1.0 1.0  xlo xhi
+-1.0 1.0  ylo yhi
+-1.0 1.0  zlo zhi
+
+Masses
+
+1 15.9994
+2 1.00784
+
+Atoms
+
+1 1 1 -0.8476 0.00000   0.00000   0.11779
+2 1 2 0.4238  0.00000   0.75545  -0.47116
+3 1 2 0.4238  0.00000  -0.75545  -0.47116
+
+Bonds
+
+1 1 1 2
+2 1 1 3
+
+Angles
+
+1 1 2 1 3
+

examples/mc/in.hmc_flexible_melt

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+# 3d Lennard-Jones melt
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 10 0 10 0 10
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	every 1 delay 0 check no
+
+fix 1 all hmc 100 6234 3.0 flexible
+
+#dump		id all atom 50 dump.melt
+
+#dump		2 all image 25 image.*.jpg type type &
+#		axes yes 0.8 0.02 view 60 -30
+#dump_modify	2 pad 3
+
+#dump		3 all movie 25 movie.mpg type type &
+#		axes yes 0.8 0.02 view 60 -30
+#dump_modify	3 pad 3
+
+thermo		50
+thermo_style custom step temp pe ke etotal f_1[*]
+dump myDump all atom 25 dumps/dump_melt*.dump
+
+run		3000

examples/mc/in.hmc_rigid

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+# fix hmc running on SPC/E Water, using rigid/ setting
+
+units           real
+boundary        p p p
+atom_style      full
+
+read_data       data.hmc_spce
+replicate      	4 4 4
+
+mass            1 15.9994
+mass            2 1.00784
+
+neighbor        2.0 bin
+neigh_modify    every 1 delay 0 check yes
+
+pair_style      lj/cut/coul/long 9.0
+pair_modify     tail yes mix arithmetic
+kspace_style    pppm 1.0e-6
+
+pair_coeff      1 1 0.1554015 3.166
+pair_coeff      2 2 0 0
+
+bond_style      harmonic
+bond_coeff      1 554.1349 1.000
+
+angle_style     harmonic
+angle_coeff     1 45.7696 109.47
+
+timestep        1
+
+reset_timestep 0 time 0
+
+thermo          50
+# dump myDump all atom 50 dumps/water_v_dump*.dump
+fix 2 all hmc 100 123 800 rigid
+
+thermo_style custom step temp pe ke etotal f_2[*]
+
+run             5000