LAMMPS (30 Jul 2016) # ****************Atom Definitions "define atoms in lammps"************************ # read topology read_data ti4pice.600000th.data #just graphene sheets Reading data file ... orthogonal box = (11.6 -0.77671 -92.4442) to (165.62 131.635 1.121) 5 by 2 by 2 MPI processor grid reading atoms ... 203904 atoms reading velocities ... 203904 velocities scanning bonds ... 2 = max bonds/atom scanning angles ... 3 = max angles/atom scanning dihedrals ... 8 = max dihedrals/atom scanning impropers ... 3 = max impropers/atom reading bonds ... 259520 bonds reading angles ... 460992 angles reading dihedrals ... 876448 dihedrals reading impropers ... 145856 impropers Finding 1-2 1-3 1-4 neighbors ... Special bond factors lj: 0 0 0 Special bond factors coul: 0 0 0 3 = max # of 1-2 neighbors 6 = max # of 1-3 neighbors 18 = max # of 1-4 neighbors 18 = max # of special neighbors #reset_timestep 0 ## grouping atoms ## group h type 1 34560 atoms in group h group o type 2 17280 atoms in group o group c type 3 152064 atoms in group c group ihice type 1 2 51840 atoms in group ihice group graph type 3 152064 atoms in group graph set group o charge -1.1794 # oxygen electric charge, for TIP3P with a long-range Coulombic solver (for the original 1983 TIP3P model (Jorgensen), -0.834 should be considered) Setting atom values ... 17280 settings made for charge set group h charge 0.5897 # hydrogen electric charge, (for the short-ranged TIP3P, 0.417 should be considered) Setting atom values ... 34560 settings made for charge fix constrain ihice shake 1e-4 100 0 b 1 a 1 Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 17280 = # of frozen angles region 2 block 37 61.93 INF INF INF INF side in units box group left_G region 2 38016 atoms in group left_G group left_G include molecule 38016 atoms in group left_G region 3 block 112.01 136 INF INF INF INF side in units box group right_G region 3 38016 atoms in group right_G group right_G include molecule 38016 atoms in group right_G velocity left_G create 230.0 4546120 dist gaussian velocity right_G create 230.0 4546120 dist gaussian # compute physical time variable phytime equal step*${tstep}/1E6 variable phytime equal step*0.2/1E6 # *********************Force Field (FF) Parameters"************************ ## TIP4P/Ice atomistic water model for Ih ice and LJ cutoff model for graphene sheets ## ## AMBER force field is applied for graphene sheets pair_style lj/cut/tip4p/long 2 1 1 1 0.1577 10.0 8.5 pair_coeff 2 2 0.21084 3.1668 pair_coeff 1 1 0.00000 0.0000 pair_coeff 1 2 0.00000 0.0000 pair_coeff 3 3 0.12000 3.2963 # OPLS values are 0.0700 3.55000, Amber values are 0.12000 3.2963 pair_coeff 2 3 0.16460 3.1260 #read from literarture, dx.doi.org/10.1021/jp402051t | J. Phys. Chem. B 2013, 117, 8802-8813 pair_coeff 1 3 0.00000 0.0000 pair_modify tail yes kspace_style pppm/tip4p 1.0e-4 bond_style harmonic bond_coeff 1 0.0 0.9572 bond_coeff 2 469.0 1.40 # OPLS values are 938.0 1.40 angle_style harmonic angle_coeff 1 0.0 104.52 angle_coeff 2 85.0 120.0 # OPLS values are 1.26 120.0 dihedral_style harmonic dihedral_coeff 1 5.3 -1 2 # OPLS values is 0.0725, 5.3 velocity ihice create 260.0 1234587 compute myTempW ihice temp compute myTempGl left_G temp/com compute myTempGr right_G temp/com thermo_style custom step c_myTempW c_myTempGl c_myTempGr run 0 # temperature may not be 250K PPPM initialization ... extracting TIP4P info from pair style WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) G vector (1/distance) = 0.293514 grid = 75 72 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0368791 estimated relative force accuracy = 0.00011106 using double precision FFTs 3d grid and FFT values/proc = 30272 16200 Neighbor list info ... 1 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 26 23 16 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Memory usage per processor = 44.8291 Mbytes Step myTempW myTempGl myTempGr 0 260 230 230 Loop time of 9.84669e-06 on 20 procs for 0 steps with 203904 atoms 0.0% CPU use with 20 MPI tasks x no 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 | | 9.847e-06 | | |100.00 Nlocal: 10195.2 ave 11880 max 8337 min Histogram: 4 0 0 0 4 4 4 0 0 4 Nghost: 27424.2 ave 28972 max 25352 min Histogram: 4 0 0 0 2 2 8 0 0 4 Neighs: 4.04381e+06 ave 5.06117e+06 max 2.70522e+06 min Histogram: 4 0 0 0 3 2 3 4 0 4 Total # of neighbors = 80876158 Ave neighs/atom = 396.638 Ave special neighs/atom = 13.5179 Neighbor list builds = 0 Dangerous builds = 0 velocity ihice scale 260.0 # now it should be # ****************Settings "define force field and simulation parameters"************************ #pair_modify shift yes # determining whether a Lennard-Jones potential is shifted at its cutoff to 0.0 neighbor 2.0 bin # setting parameters that affect the building of pairwise neighbor lists-------->skin: how often atoms migrate to new processors(prevent the water molecules from moving too far from each other) neigh_modify delay 0 every 1 check yes # setting parameters that affect the building and use of pairwise neighbor lists fix 2 ihice nve fix 3 left_G nvt temp 230.0 230.0 20.0 # ensemble definition and setting the temperature control fix 4 right_G nvt temp 230.0 230.0 20.0 fix tethl left_G spring/self 100.0 fix tethr right_G spring/self 100.0 compute peratom ihice pe/atom compute pEw ihice reduce sum c_peratom compute mykE ihice ke/atom compute kEw ihice reduce sum c_mykE compute peratomgl left_G pe/atom compute pEgl left_G reduce sum c_peratomgl compute peratomgr right_G pe/atom compute pEgr right_G reduce sum c_peratomgr # ---- output restart file and dump files/screen------- thermo 1000 # output instantaneous thermos every 1000 timesteps thermo_style custom step v_phytime c_myTempW c_myTempGl c_myTempGr c_pEw c_kEw c_pEgl c_pEgr # Set the style and content for printing thermodynamic data to the screen and log file restart 1000000 qunch_seed_250K.*.rst # ----------------"dump snap shots"-------------------- dump waterdump all custom 500000 ice_graph.lammpstrj id type x y z ix iy iz # atom coordinates are written to dump file along with the atom ID and atom type dump icedump ihice custom 1000000 nucleation.lammpstrj id type x y z ix iy iz # ****************Run the Simulation "Obtaining the Result"************************ timestep ${tstep} # setting the time step; this value is a default in md simulation, fmsec timestep 0.2 #write_data tip3p.data nocoeff run 5000000 PPPM initialization ... extracting TIP4P info from pair style WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) G vector (1/distance) = 0.293514 grid = 75 72 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0368791 estimated relative force accuracy = 0.00011106 using double precision FFTs 3d grid and FFT values/proc = 30272 16200 Neighbor list info ... 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 26 23 16 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 0.2 Memory usage per processor = 54.0371 Mbytes Step phytime myTempW myTempGl myTempGr pEw kEw pEgl pEgr 0 0 260 230 230 -230810.34 26783.592 19371527 19371708 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 5 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- ERROR on proc 5: Bond atoms 47647 47648 missing on proc 5 at step 2 (../neigh_bond.cpp:196) ERROR on proc 4: Bond atoms 47691 47692 missing on proc 4 at step 2 (../neigh_bond.cpp:196) ERROR on proc 6: Bond atoms 52095 52096 missing on proc 6 at step 2 (../neigh_bond.cpp:196) ERROR on proc 12: Bond atoms 76203 76204 missing on proc 12 at step 2 (../neigh_bond.cpp:196) ERROR on proc 13: Bond atoms 76159 76160 missing on proc 13 at step 2 (../neigh_bond.cpp:196) ERROR on proc 14: Bond atoms 80607 80608 missing on proc 14 at step 2 (../neigh_bond.cpp:196) ERROR on proc 15: Bond atoms 80560 80647 missing on proc 15 at step 2 (../neigh_bond.cpp:196)