units		real	
atom_style	full

read_data	data.spce

pair_style	lj/cut/coul/long 12.0 12.0
kspace_style	pppm 1.0e-4

pair_coeff	1 1 0.15535 3.166
pair_coeff	* 2 0.0000 0.0000	

bond_style	harmonic
angle_style	harmonic
dihedral_style	none
improper_style	none

bond_coeff	1 1000.00 1.000
angle_coeff	1 100.0 109.47

special_bonds   lj/coul 0.0 0.0 1.0

neighbor        2.0 bin

fix		1 all shake 0.0001 20 0 b 1 a 1
fix		2 all nvt temp 300.0 300.0 100.0

# make certain that shake constraints are satisfied
run 0 post no

group		oxy type 1
group		hyd type 2

# the following section shows equivalences between using the pe/tally compute and other computes and thermo keywords

# compute pairwise energy between all oxygen and all hydrogen
compute		epa oxy group/group hyd pair yes kspace no boundary no
# tally pairwise energy between all oygen and all hydrogen
compute		c1 oxy pe/tally hyd
# tally pairwise energy between all atoms to compare with globals
compute		c2 all pe/tally all
# collect per atom energies
compute		c3 all pe/atom pair
# reduce over the first group only the per-atom data is storing VDW and Coulomb separately...
compute		oxy oxy reduce sum c_c1[1] c_c1[2]
compute		red all reduce sum c_c2[1] c_c2[2] c_c3
# ... thus to get the same as compute group/group, we need to add the two
# ... and multiply by 2.0 since compute group/group sums the pair energy, while we collect only for the first group.
variable	epa equal 2.0*(c_oxy[1]+c_oxy[2])
# compute equivalent values to globals
variable	vdwl equal c_red[1]
variable	coul equal c_red[2]
variable	pe   equal c_red[3]
variable	pair equal v_vdwl+v_coul
variable	eref equal epair-elong

velocity	all create 300 432567 dist uniform

timestep	2.0

# c_epa and v_epa, evdwl and v_vdwl, ecoul and v_coul, and the last 4 columns each should have identical value
thermo_style    custom step c_epa v_epa evdwl v_vdwl ecoul v_coul v_eref v_pe c_c2 v_pair
thermo		10

run 50