echo both #***************VARIABLES**************************# variable dt equal 0.0005 #given 0.5 fs variable T equal 300 variable Nevery equal 10 variable Nrepeat equal 10 variable Nfreq equal 100 variable Nthermo equal 100 variable Nstrelax equal 1000 variable Nndrelax equal 5000 variable pressdiff equal 2e8 variable confactor equal 0.6242e9 variable ly equal 40.3 variable lz equal 46.5 dimension 3 units metal boundary p p p atom_style full pair_style hybrid lj/charmm/coul/long 9.0 10.0 12.0 lj/cut 10.0 kspace_style pppm 1.0e-4 #special_bonds charmm #added bond_style harmonic angle_style harmonic pair_modify tail yes #table 0 neighbor 2.0 bin #added neigh_modify every 1 delay 0 check yes #one 20000 page 1000000 #******************SET UP********************* region mybox block 0 3.1 0 3.1 0 3.1 units box create_box 3 mybox bond/types 2 angle/types 2 dihedral/types 1 improper/types 1 extra/bond/per/atom 5 extra/angle/per/atom 4 extra/dihedral/per/atom 12 extra/improper/per/atom 6 Created orthogonal box = (0 0 0) to (3.1 3.1 3.1) 2 by 4 by 5 MPI processor grid read_data "data.singleTIP4P" add append orthogonal box = (0 0 0) to (3.1 3.1 3.1) 2 by 4 by 5 MPI processor grid reading atoms ... 3 atoms scanning bonds ... 2 = max bonds/atom scanning angles ... 1 = max angles/atom reading bonds ... 2 bonds reading angles ... 1 angles 2 = max # of 1-2 neighbors 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors replicate 43 13 15 orthogonal box = (0 0 0) to (133.3 40.3 46.5) 10 by 2 by 2 MPI processor grid 25155 atoms 16770 bonds 8385 angles 2 = max # of 1-2 neighbors 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors region revone block 0 40 0 40.3 0 46.5 units box region mid block 40 85.36 0 40.3 0 46.5 units box region revtwo block 85.36 125.36 0 40.3 0 46.5 units box group watregone region revone 7605 atoms in group watregone group watregtwo region revtwo 7020 atoms in group watregtwo group watreg union watregone watregtwo 14625 atoms in group watreg group nonwatreg subtract all watreg 10530 atoms in group nonwatreg delete_atoms group nonwatreg mol yes bond yes Deleted 10530 atoms, new total = 14625 Deleted 7020 bonds, new total = 9750 Deleted 3510 angles, new total = 4875 read_data "graphin" add append shift 42.5 0.7 18.2 group graphinLow #actual move is 42.5-1.84=40.66 orthogonal box = (0 -0.008999 -31.8) to (133.3 40.3 68.2) 5 by 2 by 4 MPI processor grid reading atoms ... 648 atoms scanning bonds ... 2 = max bonds/atom scanning angles ... 3 = max angles/atom scanning dihedrals ... 8 = max dihedrals/atom scanning impropers ... 2 = max impropers/atom reading bonds ... 936 bonds reading angles ... 1802 angles reading dihedrals ... 3483 dihedrals reading impropers ... 578 impropers 3 = max # of 1-2 neighbors 6 = max # of 1-3 neighbors 18 = max # of 1-4 neighbors 18 = max # of special neighbors read_data "graphin" add append shift 42.5 0.7 28.2 group graphinUp #create a gap of 0.66 ang orthogonal box = (0 -0.008999 -31.8) to (133.3 40.3 78.2) 5 by 2 by 4 MPI processor grid reading atoms ... 648 atoms scanning bonds ... 2 = max bonds/atom scanning angles ... 3 = max angles/atom scanning dihedrals ... 8 = max dihedrals/atom scanning impropers ... 2 = max impropers/atom reading bonds ... 936 bonds reading angles ... 1802 angles reading dihedrals ... 3483 dihedrals reading impropers ... 578 impropers 3 = max # of 1-2 neighbors 6 = max # of 1-3 neighbors 18 = max # of 1-4 neighbors 18 = max # of special neighbors #***********PLACING "graphenebound" in LEFT-UP************************ read_data "graphenebound" add append shift 1.84 0.7 0.0 group graboundLftUp orthogonal box = (-0.002035 -0.009 -50) to (133.3 40.3 78.2) 5 by 2 by 4 MPI processor grid reading atoms ... 340 atoms scanning bonds ... 2 = max bonds/atom scanning angles ... 3 = max angles/atom scanning dihedrals ... 8 = max dihedrals/atom scanning impropers ... 2 = max impropers/atom reading bonds ... 483 bonds reading angles ... 914 angles reading dihedrals ... 1735 dihedrals reading impropers ... 288 impropers 3 = max # of 1-2 neighbors 6 = max # of 1-3 neighbors 18 = max # of 1-4 neighbors 18 = max # of special neighbors displace_atoms graboundLftUp rotate 0.0 0.0 0.0 1.0 0.0 0.0 90.0 units box displace_atoms graboundLftUp rotate 0.0 0.0 0.0 0.0 0.0 1.0 90.0 units box displace_atoms graboundLftUp move 40.7 0.0 28.2 units box #*********PLACING "graphenebound" in LEFT-DOWN*************************** read_data "graphenebound" add append shift 1.84 0.7 0.0 group graboundLftDown orthogonal box = (-0.002035 -0.009 -50) to (133.3 40.3 78.2) 5 by 2 by 4 MPI processor grid reading atoms ... 340 atoms scanning bonds ... 2 = max bonds/atom scanning angles ... 3 = max angles/atom scanning dihedrals ... 8 = max dihedrals/atom scanning impropers ... 2 = max impropers/atom reading bonds ... 483 bonds reading angles ... 914 angles reading dihedrals ... 1735 dihedrals reading impropers ... 288 impropers 3 = max # of 1-2 neighbors 6 = max # of 1-3 neighbors 18 = max # of 1-4 neighbors 18 = max # of special neighbors displace_atoms graboundLftDown rotate 0.0 0.0 0.0 1.0 0.0 0.0 90.0 units box displace_atoms graboundLftDown rotate 0.0 0.0 0.0 0.0 0.0 1.0 90.0 units box displace_atoms graboundLftDown move 40.7 0.0 -3.07 units box #*********PLACING "graphenebound" in RIGHT-UP*************************** read_data "graphenebound" add append shift 1.84 0.7 0.0 group graboundRghtUp orthogonal box = (-0.002035 -0.009 -50) to (133.3 40.3 78.2) 5 by 2 by 4 MPI processor grid reading atoms ... 340 atoms scanning bonds ... 2 = max bonds/atom scanning angles ... 3 = max angles/atom scanning dihedrals ... 8 = max dihedrals/atom scanning impropers ... 2 = max impropers/atom reading bonds ... 483 bonds reading angles ... 914 angles reading dihedrals ... 1735 dihedrals reading impropers ... 288 impropers 3 = max # of 1-2 neighbors 6 = max # of 1-3 neighbors 18 = max # of 1-4 neighbors 18 = max # of special neighbors displace_atoms graboundRghtUp rotate 0.0 0.0 0.0 1.0 0.0 0.0 90.0 units box displace_atoms graboundRghtUp rotate 0.0 0.0 0.0 0.0 0.0 1.0 90.0 units box displace_atoms graboundRghtUp move 84.8 0.0 28.2 units box #*********PLACING "graphenebound" in RIGHT-DOWN*************************** read_data "graphenebound" add append shift 1.84 0.7 0.0 group graboundRghtDown orthogonal box = (-0.002035 -0.009 -50) to (133.3 40.3 78.2) 5 by 2 by 4 MPI processor grid reading atoms ... 340 atoms scanning bonds ... 2 = max bonds/atom scanning angles ... 3 = max angles/atom scanning dihedrals ... 8 = max dihedrals/atom scanning impropers ... 2 = max impropers/atom reading bonds ... 483 bonds reading angles ... 914 angles reading dihedrals ... 1735 dihedrals reading impropers ... 288 impropers 3 = max # of 1-2 neighbors 6 = max # of 1-3 neighbors 18 = max # of 1-4 neighbors 18 = max # of special neighbors displace_atoms graboundRghtDown rotate 0.0 0.0 0.0 1.0 0.0 0.0 90.0 units box displace_atoms graboundRghtDown rotate 0.0 0.0 0.0 0.0 0.0 1.0 90.0 units box displace_atoms graboundRghtDown move 84.8 0.0 -3.07 units box group watregone delete group watregtwo delete group watreg delete group nonwatreg delete #****************MASS********************************************* mass 3 1.008 #H mass 2 15.9999990 #O mass 1 12 #C #***************INTERACTION************************* pair_coeff 1 1 lj/cut 0.006956 3.4745050026 8.5 #C-C pair_coeff 2 2 lj/charmm/coul/long 0.00442314 3.188 #O-O pair_coeff 3 3 lj/charmm/coul/long 0.0 0.0 #H-H pair_coeff 2 3 lj/charmm/coul/long 0.0 0.0 #H-O pair_coeff 1 2 lj/charmm/coul/long 0.004063 3.19 #C-O pair_coeff 1 3 lj/charmm/coul/long 0.0 3.28 #C-H bond_coeff 1 43.36 1.5260 # graphene bond type 1 angle_coeff 1 43.36 110.50 # graphene angle type 1 bond_coeff 2 19.51 0.9572 # water bond type 2 angle_coeff 2 2.39 104.52 # water angle type 2 group watadd type 2 4875 atoms in group watadd group spce type 2 3 14625 atoms in group spce group midynagp dynamic watadd region mid every 10 dynamic group midynagp defined group reservL dynamic watadd region revone every 10 dynamic group reservL defined group reservR dynamic watadd region revtwo every 10 dynamic group reservR defined group graphene union graphinLow graphinUp 1296 atoms in group graphene group Leftboundgraph union graboundLftUp graboundLftDown 680 atoms in group Leftboundgraph group Rightboundgraph union graboundRghtUp graboundRghtDown 680 atoms in group Rightboundgraph timestep ${dt} timestep 0.0005 neigh_modify exclude group graphene graphene neigh_modify exclude group Leftboundgraph Leftboundgraph neigh_modify exclude group Rightboundgraph Rightboundgraph neigh_modify exclude group graphene Leftboundgraph neigh_modify exclude group graphene Rightboundgraph fix rigid1 graphene setforce 0.0 0.0 0.0 fix rigid2 Leftboundgraph setforce 0.0 0.0 0.0 fix rigid3 Rightboundgraph setforce 0.0 0.0 0.0 #*****INITIAL VELOCITY************** velocity all create ${T} 102486 dist gaussian loop geom velocity all create 300 102486 dist gaussian loop geom #************MINIMIZE************* thermo 200 thermo_style custom step temp vol press density thermo_modify lost ignore flush yes dump 1 all atom 200 dump_min.lammpstrj minimize 1.0E-9 1.0E-9 10000 10000 PPPM initialization ... WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:319) G vector (1/distance) = 0.202122 grid = 40 18 40 stencil order = 5 estimated absolute RMS force accuracy = 0.00151273 estimated relative force accuracy = 0.000105053 using double precision FFTs 3d grid and FFT values/proc = 2730 720 WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:459) Neighbor list info ... 3 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 14 ghost atom cutoff = 14 binsize = 7 -> bins = 20 6 19 Memory usage per processor = 1.13833 Mbytes Step Temp Volume Press Density 0 300 688853.44 50535.029 0.28854687 200 300 688853.44 38792.586 0.28854687 400 300 688853.44 39718.657 0.28854687 600 300 688853.44 39837.301 0.28854687 800 300 688853.44 39864.081 0.28854687 1000 300 688853.44 39944.141 0.28854687 1062 300 688853.44 39937.241 0.28854687 Loop time of 105.33 on 40 procs for 1062 steps with 17281 atoms 99.9% CPU use with 40 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = 12646.9873085 7809.45411831 7809.45411831 Force two-norm initial, final = 371.394 0.771216 Force max component initial, final = 51.7234 0.21033 Final line search alpha, max atom move = 1.70349e-08 3.58294e-09 Iterations, force evaluations = 1062 2022 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.003078 | 15.932 | 82.448 | 579.6 | 15.13 Bond | 0.00093865 | 0.093364 | 0.4086 | 40.0 | 0.09 Kspace | 13.252 | 81.303 | 98.175 | 261.4 | 77.19 Neigh | 3.6512 | 3.7806 | 3.8587 | 3.5 | 3.59 Comm | 0.056475 | 2.069 | 4.5183 | 99.5 | 1.96 Output | 0.03492 | 0.035034 | 0.038098 | 0.3 | 0.03 Modify | 0.00090551 | 0.0096351 | 0.0484 | 12.3 | 0.01 Other | | 2.107 | | | 2.00 Nlocal: 432.025 ave 1863 max 0 min Histogram: 22 0 6 4 0 1 2 1 1 3 Nghost: 3528.22 ave 9018 max 0 min Histogram: 10 2 4 6 4 4 2 2 4 2 Neighs: 197850 ave 937688 max 0 min Histogram: 24 0 4 2 2 4 0 0 2 2 Total # of neighbors = 7914013 Ave neighs/atom = 457.96 Ave special neighs/atom = 4.18182 Neighbor list builds = 40 Dangerous builds = 0 reset_timestep 0 fix constrain spce shake 1.0e-4 100 0 b 2 a 2 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 4875 = # of frozen angles #fix removeMomentum spce momentum 1 linear 1 1 1 angular fix 1 spce nvt temp 300 300 0.05 #100 timestweps tdamp remember #********TEMPERATURE************************ compute temp_L reservL temp/com compute temp_R reservR temp/com compute_modify temp_L dynamic yes compute_modify temp_R dynamic yes fix TempAveL reservL ave/time ${Nevery} ${Nrepeat} ${Nfreq} c_temp_L fix TempAveL reservL ave/time 10 ${Nrepeat} ${Nfreq} c_temp_L fix TempAveL reservL ave/time 10 10 ${Nfreq} c_temp_L fix TempAveL reservL ave/time 10 10 100 c_temp_L fix TempAveR reservR ave/time ${Nevery} ${Nrepeat} ${Nfreq} c_temp_R fix TempAveR reservR ave/time 10 ${Nrepeat} ${Nfreq} c_temp_R fix TempAveR reservR ave/time 10 10 ${Nfreq} c_temp_R fix TempAveR reservR ave/time 10 10 100 c_temp_R #*************FIRST_RELAXATION************* unfix 1 fix 2 spce nve thermo ${Nfreq} thermo 100 thermo_style custom step pe ke etotal press c_temp_L c_temp_R f_TempAveL f_TempAveR WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:690) thermo_modify temp temp_L temp temp_R WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) dump strelax all atom ${Nthermo} first_relax.lammpstrj dump strelax all atom 100 first_relax.lammpstrj run ${Nstrelax} run 1000 PPPM initialization ... WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:319) G vector (1/distance) = 0.202122 grid = 40 18 40 stencil order = 5 estimated absolute RMS force accuracy = 0.00151273 estimated relative force accuracy = 0.000105053 using double precision FFTs 3d grid and FFT values/proc = 2730 720 WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:459) Memory usage per processor = 1.27331 Mbytes Step PotEng KinEng TotEng Press c_temp_L c_temp_R f_TempAveL f_TempAveR ERROR: Temperature compute degrees of freedom < 0 (../compute_temp_com.cpp:115)