# Create Groups and Freeze Selected atoms group pt type 1 576 atoms in group pt group ox type 8 0 atoms in group ox group notpt type != 1 3187 atoms in group notpt fix frpt pt setforce 0.0 0.0 0.0 # Set Harmonic wall fix wallhi all wall/harmonic zlo EDGE 622.609 0.000 4.0000 units box timestep ${timestep} timestep 0.33333 # GCMC molecule oxygen oxygen.mol # Molecule File Read molecule template oxygen: 1 molecules 0 fragments 2 atoms with max type 8 1 bonds with max type 8 0 angles with max type 0 0 dihedrals with max type 0 0 impropers with max type 0 region polyregion block 2.0 31.0 2.0 26.0 -4.12 50.37 # Region for GCMC insertion fix oxgcmc notpt gcmc 100 100 0 0 54341 ${temp} ${mu} 0.5 mol oxygen region polyregion charge 0.0 fix oxgcmc notpt gcmc 100 100 0 0 54341 353 ${mu} 0.5 mol oxygen region polyregion charge 0.0 fix oxgcmc notpt gcmc 100 100 0 0 54341 353 -8.1 0.5 mol oxygen region polyregion charge 0.0 delete_atoms overlap 0.5 all all System init for delete_atoms ... PPPM initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.18165975 grid = 15 12 150 stencil order = 5 estimated absolute RMS force accuracy = 0.0030929265 estimated relative force accuracy = 9.3142564e-06 using double precision KISS FFT 3d grid and FFT values/proc = 51680 27000 Generated 45 of 55 mixed pair_coeff terms from sixthpower mixing rule WARNING: Impropers are defined but no improper style is set (src/force.cpp:208) WARNING: Fix gcmc using full_energy option (src/MC/fix_gcmc.cpp:491) 0 atoms in group FixGCMC:gcmc_exclusion_group:oxgcmc 0 atoms in group FixGCMC:rotation_gas_atoms:oxgcmc WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:637) Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 17 ghost atom cutoff = 17 binsize = 2.8, bins = 12 11 27 5 neighbor lists, perpetual/occasional/extra = 4 1 0 (1) command delete_atoms, occasional attributes: full, newton off pair build: full/bin stencil: full/bin/3d bin: standard (2) pair lj/cut/coul/long, perpetual, skip from (4) attributes: half, newton off, kokkos_device pair build: skip/kk/device stencil: none bin: none (3) pair morse/smooth/linear, perpetual, skip from (5) attributes: half, newton off pair build: skip stencil: none bin: none (4) neighbor class addition, perpetual attributes: half, newton off, kokkos_device pair build: half/bin/kk/device stencil: full/bin/3d bin: kk/device (5) neighbor class addition, perpetual, copy from (4) attributes: half, newton off pair build: copy/kk/device stencil: none bin: none WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:637) WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140) Deleted 0 atoms, new total = 3763 # Set Integrator and modify to allow for variable number of atoms fix int notpt nvt temp ${temp} ${temp} 100 fix int notpt nvt temp 353 ${temp} 100 fix int notpt nvt temp 353 353 100 compute_modify int_temp dynamic/dof yes compute_modify thermo_temp dynamic/dof yes run 2000000 PPPM initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.18165975 grid = 15 12 150 stencil order = 5 estimated absolute RMS force accuracy = 0.0030929265 estimated relative force accuracy = 9.3142564e-06 using double precision KISS FFT 3d grid and FFT values/proc = 51680 27000 Generated 45 of 55 mixed pair_coeff terms from sixthpower mixing rule WARNING: Impropers are defined but no improper style is set (src/force.cpp:208) 0 atoms in group FixGCMC:rotation_gas_atoms:oxgcmc WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:637) Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 17 ghost atom cutoff = 17 binsize = 2.8, bins = 12 11 27 4 neighbor lists, perpetual/occasional/extra = 4 0 0 (1) pair lj/cut/coul/long, perpetual, skip from (3) attributes: half, newton off, kokkos_device pair build: skip/kk/device stencil: none bin: none (2) pair morse/smooth/linear, perpetual, skip from (4) attributes: half, newton off pair build: skip stencil: none bin: none (3) neighbor class addition, perpetual attributes: half, newton off, kokkos_device pair build: half/bin/kk/device stencil: full/bin/3d bin: kk/device (4) neighbor class addition, perpetual, copy from (3) attributes: half, newton off pair build: copy/kk/device stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 43.45 | 43.45 | 43.45 Mbytes ------------ Step 21750 ----- CPU = 0 (sec) ------------- TotEng = 20306.6963 KinEng = 3605.8790 PotEng = 16700.8173 E_bond = 5732.0264 E_angle = 8071.5869 E_dihed = 396.5743 E_impro = 0.0000 E_vdwl = 7423.1490 E_coul = 6620.9084 E_long = -11543.4276 Temp = 321.5571 Press = 3719.3335 Volume = 69834.3527