LAMMPS (30 Aug 2013) units real atom_style atomic lattice fcc 5.405 origin 0.25 0.25 0.25 Lattice spacing in x,y,z = 5.405 5.405 5.405 region mdRegion block -12 12 -3 3 -3 3 region mdInternal block -10 10 -3 3 -3 3 # create atoms boundary f p p create_box 1 mdRegion Created orthogonal box = (-64.86 -16.215 -16.215) to (64.86 16.215 16.215) 4 by 1 by 1 MPI processor grid create_atoms 1 region mdRegion Created 3456 atoms mass 1 39.95 pair_style lj/cut 13.5 pair_coeff 1 1 .238 3.405 13.5 # specify interal/ghost atoms group internal region mdInternal 2880 atoms in group internal velocity internal create 40 87287 mom yes loop geom # <<< NOTE neighbor 5. bin neigh_modify every 10 delay 0 check no # ID group atc PhysicsType ParameterFile fix AtC internal atc two_temperature Ar_ttm.mat ATC: constructing two_temperature coupling with parameter file Ar_ttm.mat ATC: version 2.0 ATC: peratom PE compute created with ID: 3 ATC: 2 materials defined from Ar_ttm.mat ATC: creating two_temperature extrinsic model ATC: 2 materials defined from Ar_ttm.mat fix_modify AtC mesh read gaussianIC1d_hex.mesh ATC: read 44 nodes ATC: read 10 HEX8 elements ATC: WARNING: mesh is not aligned with the coordinate directions atom-to-element mapping will be expensive # fix a temperature fix_modify AtC fix temperature all 20.0 fix_modify AtC initial temperature all 20.0 fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20 fix_modify AtC fix electron_temperature all gaussian 0 0 0 1 0 0 5 20 20 # turn on thermostat fix_modify AtC extrinsic exchange off fix_modify AtC control thermal rescale 10 # equilibrate MD field timestep 5.0 thermo 10 #output fix_modify AtC output gaussianIC1d_hexFE 10 text ATC: Warning : text output can create _LARGE_ files ATC: output custom names: # change thermostat fix_modify AtC unfix temperature all fix_modify AtC unfix electron_temperature all fix_modify AtC control thermal flux fix_modify AtC extrinsic exchange on fix_modify AtC extrinsic electron_integration explicit 10 # run with FE thermo_style custom step temp pe f_AtC[2] f_AtC[4] reset_timestep 0 run 100 # 400 Setting up run ... Memory usage per processor = 52.9302 Mbytes Step Temp PotEng AtC[2] AtC[4] 0 33.331404 -6667.7177 20 21.852118 10 29.605914 -6628.8617 15.526061 21.823928 20 20.144352 -6529.8249 4.1452637 21.728037 30 10.661516 -6429.3908 -7.2917185 21.537517 40 7.6716875 -6394.7484 -10.961235 21.28913 50 11.012891 -6425.2214 -7.0020953 21.050343 60 15.276591 -6465.7767 -1.8390571 20.85387 70 17.15209 -6482.1581 0.55215503 20.688207 80 17.028137 -6478.0796 0.55504167 20.530699 90 16.865355 -6473.5664 0.41999569 20.372106 100 17.920474 -6481.673 1.6267665 20.219157 Loop time of 4.19774 on 4 procs for 100 steps with 3456 atoms Pair time (%) = 0.896439 (21.3553) Neigh time (%) = 0.408064 (9.72104) Comm time (%) = 0.161891 (3.85662) Outpt time (%) = 0.00701588 (0.167135) Other time (%) = 2.72433 (64.9) Nlocal: 864 ave 864 max 864 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 6741 ave 7924 max 5558 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 272828 ave 288265 max 257696 min Histogram: 2 0 0 0 0 0 0 0 0 2 FullNghs: 545657 ave 575527 max 515800 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 2182628 Ave neighs/atom = 631.547 Neighbor list builds = 10 Dangerous builds = 0