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libmultiscale/test/coupling/LAMMPS_AKANTU/test_ThermalDampingRestitution/lammps-hp.in
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# Set the units (real = A, kcal/mol, fs, g/mol, atm)
units real
#parameters for aluminum (E=68GPa nu=0.4) at 0K first neighbor interaction
#define the LJ parameters
variable epsilon equal 1.3641211104312093062*0.92
variable sigma equal 2.5400008365880643002
variable rcut equal 3.89461293159
variable latsize equal "4.0320*sqrt(2)/2"
variable mass equal 26.98153860
variable elasticStiffness equal "12.082988860820660663*0.92"
variable r0 equal ${latsize}
variable xmin equal -1000
variable xmax equal 1000
variable ymin equal -2
variable ymax equal 2
variable zmin equal 0
variable zmax equal 1
variable boundary equal 41
variable lxminbound equal ${xmin}/2-${boundary}
variable lxmaxbound equal ${xmin}/2
variable rxminbound equal ${xmax}/2
variable rxmaxbound equal ${xmax}/2+${boundary}
variable bridging equal 5
variable lxminbrid equal ${xmin}/2
variable lxmaxbrid equal ${xmin}/2+${bridging}
variable rxminbrid equal ${xmax}/2-${bridging}
variable rxmaxbrid equal ${xmax}/2
# Set style and dimension
dimension 2
atom_style atomic
# Turn newton off for contact algorithm
newton on
# Specify the boundaries (p = periodic , s = shrink-wrapped)
boundary s p p
lattice hex ${latsize} origin 0.25 0.25 0
region box block ${xmin} ${xmax} ${ymin} ${ymax} ${zmin} ${zmax}
create_box 1 box
create_atoms 1 region box
# Assign masses
mass * ${mass}
# Define pair styles
pair_style k/req ${rcut}
pair_coeff * * ${elasticStiffness} ${r0}
# Some computation settings for the neighbor lists
neigh_modify delay 1
fix 2 all enforce2d
# Do the actual integration
fix 1 all nve
# middle md region
region md block ${lxmaxbrid} ${rxminbrid} INF INF INF INF
# left and right boundary region
region leftbound block ${lxminbound} ${lxmaxbound} INF INF INF INF
region rightbound block ${rxminbound} ${rxmaxbound} INF INF INF INF
# left and right bridging region
region leftbrid block ${lxminbrid} ${lxmaxbrid} INF INF INF INF
region rightbrid block ${rxminbrid} ${rxmaxbrid} INF INF INF INF
# middle md group
group gMd region md
# left, right groups for boundary and bridging
group gLBound region leftbound
group gRBound region rightbound
group gLBrid region leftbrid
group gRBrid region rightbrid
# compute for per atom potential and kinetic energies
compute peatom all pe/atom
compute keatom all ke/atom
#compute pe all reduce sum c_peatom
#compute ke all reduce sum c_keatom
# compute for PE, KE for each group
compute temperatureAll all temp/partial 1 1 0
compute temperatureMd gMd temp/partial 1 1 0
compute peMd gMd reduce sum c_peatom
compute keMd gMd reduce sum c_keatom
compute peLBound gLBound reduce sum c_peatom
compute keLBound gLBound reduce sum c_keatom
compute peRBound gRBound reduce sum c_peatom
compute keRBound gRBound reduce sum c_keatom
compute peLBrid gLBrid reduce sum c_peatom
compute keLBrid gLBrid reduce sum c_keatom
compute peRBrid gRBrid reduce sum c_peatom
compute keRBrid gRBrid reduce sum c_keatom
#thermo_style custom step temp etotal press pe c_pe ke c_ke c_peLBound c_keLBound
variable timestep equal step
variable temperature equal temp
variable temperatureAll equal c_temperatureAll
variable temperatureMd equal c_temperatureMd
variable keT equal ke
variable peT equal pe
variable keMd equal c_keMd
variable peMd equal c_peMd
variable keLBound equal c_keLBound
variable peLBound equal c_peLBound
variable keRBound equal c_keRBound
variable peRBound equal c_peRBound
variable keLBrid equal c_keLBrid
variable peLBrid equal c_peLBrid
variable keRBrid equal c_keRBrid
variable peRBrid equal c_peRBrid
fix engy all print 100 "${timestep} ${temperature} ${temperatureAll} ${temperatureMd} ${keT} ${peT} ${keMd} ${peMd} ${keLBound} ${peLBound} ${keRBound} ${peRBound} ${keLBrid} ${peLBrid} ${keRBrid} ${peRBrid}" file energy.txt screen no title "#step temperature total_ke total_pe Mid_ke Mid_pe LBB_ke LBB_pe RBB_ke RBB_pe LB_ke LB_pe RB_ke RB_pe"
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