Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/test/02_commands/in.compute_pe-002
02b9eeed5f18lammm-master-deprecated

Last Change
Raw File

in.compute_pe-002
View Options

units real
atom_style full
newton off off
timer off
read_data spce.data
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
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 beween all atoms to compare with globals
compute c2 all pe/tally all
# collect per atom energies
compute c3 all pe/atom pair
# the per-atom data is storing VDW and Coulomb separately...
compute red all reduce sum c_c1[1] c_c1[2] c_c2[1] c_c2[2] c_c3
# ... thus to get the same as compute group/group, we need to add the two
variable epa equal c_red[1]+c_red[2]
# compute equivalent values to globals
variable vdwl equal c_red[3]
variable coul equal c_red[4]
variable pe equal c_red[5]
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
info all
run 50
c4science · Help