boundary p p p units real atom_style full bond_style harmonic angle_style harmonic dihedral_style opls improper_style harmonic pair_style lj/cut/tip4p/long 1 2 1 1 0.1546 10 8 kspace_style pppm/tip4p 1e-5 pair_modify mix geometric special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.5 neighbor 2.0 bin neigh_modify delay 0 every 1 check yes one 10000 page 200000 region box block -19.718 19.718 -19.718 19.718 -39.436 39.436 create_box 6 box bond/types 4 angle/types 3 dihedral/types 1 extra/bond/per/atom 10 extra/angle/per/atom 10 extra/dihedral/per/atom 10 extra/special/per/atom 10 Created orthogonal box = (-19.718 -19.718 -39.436) to (19.718 19.718 39.436) 2 by 2 by 4 MPI processor grid molecule wat water.mol Read molecule template wat: Water molecule 1 molecules 0 fragments 3 atoms with max type 2 2 bonds with max type 1 1 angles with max type 1 0 dihedrals with max type 0 0 impropers with max type 0 molecule eth ethanol.mol Read molecule template eth: Ethanol molecule 1 molecules 0 fragments 4 atoms with max type 6 3 bonds with max type 4 2 angles with max type 3 1 dihedrals with max type 1 0 impropers with max type 0 #ボックス内にエタノールを配置 create_atoms 0 random 600 12345 NULL mol eth 23412 overlap 1.5 maxtry 10000 Created 2400 atoms using lattice units in orthogonal box = (-19.718 -19.718 -39.436) to (19.718 19.718 39.436) create_atoms CPU = 0.081 seconds #水分子をボックス内に配置 create_atoms 0 random 2400 67890 NULL mol wat 27668 overlap 1.5 maxtry 10000 Created 7200 atoms using lattice units in orthogonal box = (-19.718 -19.718 -39.436) to (19.718 19.718 39.436) create_atoms CPU = 0.176 seconds include mass.lammps mass 1 15.9994 # OW mass 2 1.008 # HW mass 3 15.035 # CH3 mass 4 14.027 # CH2 mass 5 15.999 # O mass 6 1.008 # H include ethanol.parm include ethanol.index # Pair Coeffs variable CH3 index 3 variable CH2 index 4 variable Oc index 5 variable Hc index 6 # Bond Coeffs variable C_C index 2 variable C_O index 3 variable O_H index 4 # Angle Coeffs variable CH3_CH2_O index 2 variable CH2_O_H index 3 # Dihedral Coeffs variable CH3_CH2_O_H index 1 set type ${CH3} charge 0.0000 set type 3 charge 0.0000 Setting atom values ... 600 settings made for charge set type ${CH2} charge 0.2650 set type 4 charge 0.2650 Setting atom values ... 600 settings made for charge set type ${Oc} charge -0.7000 set type 5 charge -0.7000 Setting atom values ... 600 settings made for charge set type ${Hc} charge 0.4350 set type 6 charge 0.4350 Setting atom values ... 600 settings made for charge pair_coeff ${CH3} ${CH3} 0.1750 3.9050 pair_coeff 3 ${CH3} 0.1750 3.9050 pair_coeff 3 3 0.1750 3.9050 pair_coeff ${CH2} ${CH2} 0.1180 3.9050 pair_coeff 4 ${CH2} 0.1180 3.9050 pair_coeff 4 4 0.1180 3.9050 pair_coeff ${Oc} ${Oc} 0.1700 3.0700 pair_coeff 5 ${Oc} 0.1700 3.0700 pair_coeff 5 5 0.1700 3.0700 pair_coeff ${Hc} ${Hc} 0.0000 0.0000 pair_coeff 6 ${Hc} 0.0000 0.0000 pair_coeff 6 6 0.0000 0.0000 bond_coeff ${C_C} 260.00 1.5260 bond_coeff 2 260.00 1.5260 bond_coeff ${C_O} 386.00 1.4250 bond_coeff 3 386.00 1.4250 bond_coeff ${O_H} 553.00 0.9450 bond_coeff 4 553.00 0.9450 angle_coeff ${CH3_CH2_O} 80.00 109.50 angle_coeff 2 80.00 109.50 angle_coeff ${CH2_O_H} 55.00 108.50 angle_coeff 3 55.00 108.50 dihedral_coeff ${CH3_CH2_O_H} 0.300 0.000 1.300 0.000 #oplsaa.parm dihedral_coeff 1 0.300 0.000 1.300 0.000 include water.parm include water.index # Pair Coeffs variable OW index 1 variable HW index 2 # Bond Coeffs variable OW_HW index 1 # Angle Coeffs variable HW_OW_HW index 1 set type ${OW} charge -1.1128 set type 1 charge -1.1128 Setting atom values ... 2400 settings made for charge set type ${HW} charge 0.5564 set type 2 charge 0.5564 Setting atom values ... 4800 settings made for charge pair_coeff ${OW} ${OW} 0.1852 3.1589 pair_coeff 1 ${OW} 0.1852 3.1589 pair_coeff 1 1 0.1852 3.1589 pair_coeff ${HW} ${HW} 0.0000 1.0000 pair_coeff 2 ${HW} 0.0000 1.0000 pair_coeff 2 2 0.0000 1.0000 bond_coeff ${OW_HW} 0.0 1.0 bond_coeff 1 0.0 1.0 angle_coeff ${HW_OW_HW} 0 104.52 angle_coeff 1 0 104.52 group H2O type 1 2 7200 atoms in group H2O group ETH type 3 4 5 6 2400 atoms in group ETH timestep 1.0 thermo_style custom step temp pe ke etotal press density thermo 10 fix myshk H2O shake 1.0e-5 200 0 b 1 a 1 mol wat Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2400 = # of frozen angles find clusters CPU = 0.001 seconds delete_atoms overlap 0.1 all all System init for delete_atoms ... PPPM initialization ... extracting TIP4P info from pair style using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.3859399 grid = 48 48 80 stencil order = 5 estimated absolute RMS force accuracy = 0.0034395351 estimated relative force accuracy = 1.0358058e-05 using double precision FFTW3 3d grid and FFT values/proc = 25947 11520 WARNING: Communication cutoff 0 is shorter than a bond length based estimate of 5.4335. This may lead to errors. (src/comm.cpp:730) WARNING: Increasing communication cutoff to 11.1546 for TIP4P pair style (src/KSPACE/pair_lj_cut_tip4p_long.cpp:497) Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 10000, page size: 200000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 7 7 14 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin stencil: full/bin/3d bin: standard (2) pair lj/cut/tip4p/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d bin: standard WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:141) Deleted 0 atoms, new total = 9600 minimize 1.0e-5 1.0e-7 10000 100000 PPPM initialization ... extracting TIP4P info from pair style using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.3859399 grid = 48 48 80 stencil order = 5 estimated absolute RMS force accuracy = 0.0034395351 estimated relative force accuracy = 1.0358058e-05 using double precision FFTW3 3d grid and FFT values/proc = 25947 11520 Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule WARNING: Using fix shake with minimization. Substituting constraints with harmonic restraint forces using kbond=1987 (src/RIGID/fix_shake.cpp:386) Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 10000, page size: 200000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 7 7 14 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut/tip4p/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d bin: standard WARNING: Communication cutoff adjusted to 12 (src/comm.cpp:739) Per MPI rank memory allocation (min/avg/max) = 18.98 | 18.98 | 18.98 Mbytes Step Temp PotEng KinEng TotEng Press Density 0 0 1633115.1 0 1633115.1 3749763.6 0.95952026 10 0 82784.741 0 82784.741 202137.32 0.95952026 11 0 1.1384256e+08 0 1.1384256e+08 -23071938 0.95952026 Loop time of 0.494527 on 16 procs for 11 steps with 9600 atoms 98.7% CPU use with 16 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = 1633115.12724745 82784.7412421566 113842555.860617 Force two-norm initial, final = 1623762 1619651 Force max component initial, final = 588246.41 187922.35 Final line search alpha, max atom move = 1.2501717e-16 2.3493521e-11 Iterations, force evaluations = 11 52 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21391 | 0.24189 | 0.26306 | 2.5 | 48.91 Bond | 0.00091564 | 0.0011692 | 0.0016019 | 0.6 | 0.24 Kspace | 0.20093 | 0.2219 | 0.24952 | 2.6 | 44.87 Neigh | 0.0053688 | 0.0053772 | 0.0053901 | 0.0 | 1.09 Comm | 0.018897 | 0.019245 | 0.019571 | 0.1 | 3.89 Output | 7.6354e-05 | 0.00020347 | 0.0002405 | 0.0 | 0.04 Modify | 0.0010245 | 0.0011428 | 0.001214 | 0.2 | 0.23 Other | | 0.003597 | | | 0.73 Nlocal: 600 ave 643 max 562 min Histogram: 1 1 1 4 3 2 1 1 1 1 Nghost: 5959.25 ave 6052 max 5893 min Histogram: 2 2 1 3 2 2 3 0 0 1 Neighs: 169831 ave 186980 max 151248 min Histogram: 1 0 1 2 4 3 1 2 1 1 Total # of neighbors = 2717297 Ave neighs/atom = 283.05177 Ave special neighs/atom = 2.25 Neighbor list builds = 1 Dangerous builds = 0 velocity all create 315 4845 mom yes rot yes dist gaussian run 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) PPPM initialization ... extracting TIP4P info from pair style using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.3859399 grid = 48 48 80 stencil order = 5 estimated absolute RMS force accuracy = 0.0034395351 estimated relative force accuracy = 1.0358058e-05 using double precision FFTW3 3d grid and FFT values/proc = 25947 11520 Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule WARNING: Communication cutoff adjusted to 12 (src/comm.cpp:739) Per MPI rank memory allocation (min/avg/max) = 17.85 | 17.86 | 17.86 Mbytes Step Temp PotEng KinEng TotEng Press Density 11 315 75917.462 6759.5382 82677.001 nan 0.95952026 Loop time of 2.60606e-06 on 16 procs for 0 steps with 9600 atoms 119.9% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Bond | 0 | 0 | 0 | 0.0 | 0.00 Kspace | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.606e-06 | | |100.00 Nlocal: 600 ave 644 max 563 min Histogram: 1 1 1 5 2 3 1 1 0 1 Nghost: 5959.88 ave 6047 max 5891 min Histogram: 2 2 1 1 4 1 3 1 0 1 Neighs: 169831 ave 187374 max 151289 min Histogram: 1 0 1 3 3 3 1 2 1 1 Total # of neighbors = 2717294 Ave neighs/atom = 283.05146 Ave special neighs/atom = 2.25 Neighbor list builds = 0 Dangerous builds = 0 velocity all create 315 4845 mom yes rot yes dist gaussian fix nptxy all npt temp 315.0 315.0 1000 x 1.0 1.0 1000 y 1.0 1.0 1000 thermo 100 run 5000 PPPM initialization ... extracting TIP4P info from pair style using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.3859399 grid = 48 48 80 stencil order = 5 estimated absolute RMS force accuracy = 0.0034395351 estimated relative force accuracy = 1.0358058e-05 using double precision FFTW3 3d grid and FFT values/proc = 25947 11520 Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule WARNING: Communication cutoff adjusted to 12 (src/comm.cpp:739) ERROR: Non-numeric pressure - simulation unstable (src/fix_nh.cpp:1041) Last command: run 5000