LAMMPS (30 Aug 2013) units real atom_style atomic # create domain #lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) lattice fcc 5.405 origin 0.25 0.25 0.25 Lattice spacing in x,y,z = 5.405 5.405 5.405 # create atoms region simRegion block -12 12 -3 3 -3 3 region atomRegion block -9 9 -3 3 -3 3 region mdRegion block -8 8 -3 3 -3 3 boundary f p p create_box 1 simRegion 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 2304 atoms mass 1 39.95 # specify interal/ghost atoms region mdInternal block -6 6 -3 3 -3 3 region leftghost block -8 -6 -3 3 -3 3 region rightghost block 6 8 -3 3 -3 3 group internal region mdInternal 1728 atoms in group internal group Lghost region leftghost 288 atoms in group Lghost group Rghost region rightghost 288 atoms in group Rghost group ghosts union Lghost Rghost 576 atoms in group ghosts # velocities have Vcm = 0 #velocity internal create 40. 87287 mom yes loop geom pair_style lj/cut 13.5 #pair_coeff 1 1 0.010323166 3.405 13.5 pair_coeff 1 1 .238 3.405 13.5 neighbor 5. bin neigh_modify every 10 delay 0 check no # define layer # ID group atc PhysicsType ParameterFile fix AtC internal atc elastic Ar_elastic.mat ATC: constructing elastic coupling with parameter file Ar_elastic.mat ATC: version 2.0 ATC: peratom PE compute created with ID: 3 ATC: computed mass density : 1.01202 ATC: computed mass density : 1.01202 ATC: computed mass density : 1.01202 ATC: 3 materials defined from Ar_elastic.mat # ID part keywords nx ny nz region fix_modify AtC mesh create 12 1 1 simRegion f p p ATC: created uniform mesh with 52 nodes, 13 unique nodes, and 12 elements # initial conditions fix_modify AtC initial displacement x all 0.0 fix_modify AtC initial displacement y all 0.0 fix_modify AtC initial displacement z all 0.0 fix_modify AtC initial velocity x all 0.0 fix_modify AtC initial velocity y all 0.0 fix_modify AtC initial velocity z all 0.0 # set node sets and bcs # ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF ATC: created nodeset lbc with 1 nodes fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF ATC: created nodeset rbc with 1 nodes fix_modify AtC fix velocity x rbc 0.00000004 fix_modify AtC fix displacement x lbc 0. fix_modify AtC fix velocity x lbc 0. # specify atom types #fix_modify AtC boundary Lghost #fix_modify AtC boundary Rghost fix_modify AtC boundary ghosts #fix_modify AtC output follow_ex.fe 50 fix_modify AtC internal_quadrature off fix_modify AtC control localized_lambda on fix_modify AtC control momentum glc_velocity fix_modify AtC filter type exponential fix_modify AtC filter scale 1000.0 fix_modify AtC filter on # run to extension #fix_modify AtC output bar1dFE 50 text timestep 5 thermo 100 run 1000 Setting up run ... Memory usage per processor = 65.7794 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4406.6687 0 -4406.6687 -1155.1752 100 3.8434911e-14 -4406.6687 0 -4406.6687 -1155.1752 200 2.634669e-11 -4406.6687 0 -4406.6687 -1155.1754 300 6.909135e-10 -4406.6685 0 -4406.6685 -1155.1763 400 3.9413859e-09 -4406.6682 0 -4406.6682 -1155.1783 500 8.5603227e-09 -4406.6676 0 -4406.6676 -1155.181 600 1.0143684e-08 -4406.6671 0 -4406.6671 -1155.1835 700 9.8473676e-09 -4406.6667 0 -4406.6667 -1155.1854 800 9.9628095e-09 -4406.6663 0 -4406.6663 -1155.1871 900 1.1034555e-08 -4406.6659 0 -4406.6659 -1155.189 1000 1.2796459e-08 -4406.6655 0 -4406.6655 -1155.191 Loop time of 18.0781 on 4 procs for 1000 steps with 2304 atoms Pair time (%) = 5.77584 (31.9495) Neigh time (%) = 2.46813 (13.6526) Comm time (%) = 5.5724 (30.8241) Outpt time (%) = 0.00132889 (0.00735082) Other time (%) = 4.26036 (23.5665) Nlocal: 576 ave 864 max 288 min Histogram: 2 0 0 0 0 0 0 0 0 2 Nghost: 5170 ave 6910 max 3430 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 178632 ave 288628 max 68417 min Histogram: 2 0 0 0 0 0 0 0 0 2 FullNghs: 357264 ave 577008 max 137520 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 1429056 Ave neighs/atom = 620.25 Neighbor list builds = 100 Dangerous builds = 0 # change nodes to fixed fix_modify AtC fix velocity x rbc 0. fix_modify AtC fix displacement x rbc 0.0002 fix_modify AtC output bar1dFE 500 text ATC: Warning : text output can create _LARGE_ files ATC: output custom names: # run to equilibrium timestep 5 thermo 100 run 10000 Setting up run ... Memory usage per processor = 65.7794 Mbytes Step Temp E_pair E_mol TotEng Press 1000 1.2796459e-08 -4406.6655 0 -4406.6655 -1155.191 1100 1.3961782e-08 -4406.665 0 -4406.665 -1155.1929 1200 1.4156541e-08 -4406.6646 0 -4406.6646 -1155.1947 1300 1.1743161e-08 -4406.6643 0 -4406.6643 -1155.1961 1400 7.6261191e-09 -4406.6643 0 -4406.6643 -1155.1964 1500 5.4918861e-09 -4406.6644 0 -4406.6644 -1155.1955 1600 3.2067753e-09 -4406.6647 0 -4406.6647 -1155.1942 1700 1.5798693e-09 -4406.6649 0 -4406.6649 -1155.1933 1800 3.4267061e-09 -4406.6649 0 -4406.6649 -1155.1932 1900 5.7984811e-09 -4406.6649 0 -4406.6649 -1155.1934 2000 4.4702416e-09 -4406.6648 0 -4406.6648 -1155.1937 2100 4.110363e-09 -4406.6647 0 -4406.6647 -1155.1943 2200 7.7448231e-09 -4406.6646 0 -4406.6646 -1155.1949 2300 8.9174139e-09 -4406.6645 0 -4406.6645 -1155.1953 2400 4.2475131e-09 -4406.6645 0 -4406.6645 -1155.1951 2500 3.9593952e-09 -4406.6646 0 -4406.6646 -1155.1947 2600 5.0490897e-09 -4406.6646 0 -4406.6646 -1155.1945 2700 3.0091882e-09 -4406.6645 0 -4406.6645 -1155.195 2800 2.8396053e-09 -4406.6644 0 -4406.6644 -1155.1955 2900 3.3590465e-09 -4406.6644 0 -4406.6644 -1155.1957 3000 2.6186659e-09 -4406.6644 0 -4406.6644 -1155.1955 3100 2.8276402e-09 -4406.6645 0 -4406.6645 -1155.1953 3200 3.3651448e-09 -4406.6645 0 -4406.6645 -1155.195 3300 4.8200774e-09 -4406.6647 0 -4406.6647 -1155.1944 3400 2.7178e-09 -4406.6648 0 -4406.6648 -1155.1938 3500 2.8250408e-09 -4406.6648 0 -4406.6648 -1155.1938 3600 4.4426525e-09 -4406.6646 0 -4406.6646 -1155.1946 3700 2.3093452e-09 -4406.6644 0 -4406.6644 -1155.1954 3800 1.0139576e-09 -4406.6644 0 -4406.6644 -1155.1958 3900 3.33486e-09 -4406.6644 0 -4406.6644 -1155.1958 4000 3.6153069e-09 -4406.6644 0 -4406.6644 -1155.1956 4100 4.6993593e-10 -4406.6644 0 -4406.6644 -1155.1954 4200 1.1808552e-09 -4406.6645 0 -4406.6645 -1155.1948 4300 3.1059162e-09 -4406.6647 0 -4406.6647 -1155.1942 4400 2.2356994e-09 -4406.6647 0 -4406.6647 -1155.1942 4500 1.0832e-09 -4406.6646 0 -4406.6646 -1155.1947 4600 3.4691005e-09 -4406.6645 0 -4406.6645 -1155.1954 4700 2.6640925e-09 -4406.6644 0 -4406.6644 -1155.1956 4800 1.8105324e-09 -4406.6644 0 -4406.6644 -1155.1954 4900 3.2865681e-09 -4406.6645 0 -4406.6645 -1155.1951 5000 3.2647654e-09 -4406.6645 0 -4406.6645 -1155.1949 5100 1.9703065e-09 -4406.6646 0 -4406.6646 -1155.1947 5200 1.242015e-09 -4406.6646 0 -4406.6646 -1155.1945 5300 3.0457424e-09 -4406.6646 0 -4406.6646 -1155.1946 5400 1.9560942e-09 -4406.6645 0 -4406.6645 -1155.1951 5500 4.3058633e-10 -4406.6644 0 -4406.6644 -1155.1957 5600 2.3184519e-09 -4406.6644 0 -4406.6644 -1155.1957 5700 3.0207566e-09 -4406.6645 0 -4406.6645 -1155.1953 5800 6.8689369e-10 -4406.6646 0 -4406.6646 -1155.1948 5900 1.5170252e-09 -4406.6646 0 -4406.6646 -1155.1946 6000 3.0629191e-09 -4406.6646 0 -4406.6646 -1155.1946 6100 1.842967e-09 -4406.6646 0 -4406.6646 -1155.1945 6200 6.0033688e-10 -4406.6646 0 -4406.6646 -1155.1946 6300 2.0883931e-09 -4406.6645 0 -4406.6645 -1155.1952 6400 1.8269083e-09 -4406.6644 0 -4406.6644 -1155.1957 6500 5.5810474e-10 -4406.6644 0 -4406.6644 -1155.1957 6600 1.7356452e-09 -4406.6645 0 -4406.6645 -1155.1952 6700 2.6958998e-09 -4406.6646 0 -4406.6646 -1155.1947 6800 8.964107e-10 -4406.6646 0 -4406.6646 -1155.1946 6900 1.1426076e-09 -4406.6646 0 -4406.6646 -1155.1947 7000 2.9188626e-09 -4406.6646 0 -4406.6646 -1155.1947 7100 1.8115562e-09 -4406.6645 0 -4406.6645 -1155.1948 7200 7.4087342e-10 -4406.6645 0 -4406.6645 -1155.1952 7300 1.5779154e-09 -4406.6644 0 -4406.6644 -1155.1956 7400 2.7467977e-09 -4406.6644 0 -4406.6644 -1155.1955 7500 4.2123447e-10 -4406.6645 0 -4406.6645 -1155.195 7600 1.1615418e-09 -4406.6646 0 -4406.6646 -1155.1946 7700 2.5380373e-09 -4406.6646 0 -4406.6646 -1155.1945 7800 1.5068282e-09 -4406.6646 0 -4406.6646 -1155.1948 7900 6.0931799e-10 -4406.6645 0 -4406.6645 -1155.195 8000 2.0802965e-09 -4406.6645 0 -4406.6645 -1155.1951 8100 2.1544428e-09 -4406.6645 0 -4406.6645 -1155.1953 8200 4.4375899e-10 -4406.6644 0 -4406.6644 -1155.1955 8300 1.5879866e-09 -4406.6644 0 -4406.6644 -1155.1954 8400 2.1255967e-09 -4406.6645 0 -4406.6645 -1155.1949 8500 8.5066547e-10 -4406.6646 0 -4406.6646 -1155.1945 8600 4.9764713e-10 -4406.6646 0 -4406.6646 -1155.1945 8700 2.4032931e-09 -4406.6646 0 -4406.6646 -1155.1949 8800 1.5506272e-09 -4406.6645 0 -4406.6645 -1155.1951 8900 2.156996e-10 -4406.6645 0 -4406.6645 -1155.1952 9000 1.5053583e-09 -4406.6645 0 -4406.6645 -1155.1953 9100 2.2313062e-09 -4406.6645 0 -4406.6645 -1155.1954 9200 6.5295769e-10 -4406.6645 0 -4406.6645 -1155.1953 9300 7.1214495e-10 -4406.6646 0 -4406.6646 -1155.1949 9400 2.2525879e-09 -4406.6646 0 -4406.6646 -1155.1945 9500 1.2940878e-09 -4406.6646 0 -4406.6646 -1155.1945 9600 3.7619117e-10 -4406.6645 0 -4406.6645 -1155.195 9700 1.9605412e-09 -4406.6645 0 -4406.6645 -1155.1953 9800 1.7828694e-09 -4406.6645 0 -4406.6645 -1155.1953 9900 5.2324205e-10 -4406.6645 0 -4406.6645 -1155.1952 10000 1.1770899e-09 -4406.6645 0 -4406.6645 -1155.1952 10100 2.0621304e-09 -4406.6645 0 -4406.6645 -1155.1951 10200 9.4046414e-10 -4406.6646 0 -4406.6646 -1155.1948 10300 3.3301061e-10 -4406.6646 0 -4406.6646 -1155.1945 10400 2.2075407e-09 -4406.6646 0 -4406.6646 -1155.1946 10500 1.3556476e-09 -4406.6645 0 -4406.6645 -1155.1951 10600 3.1056944e-10 -4406.6645 0 -4406.6645 -1155.1954 10700 1.2113659e-09 -4406.6645 0 -4406.6645 -1155.1953 10800 2.0914266e-09 -4406.6645 0 -4406.6645 -1155.1951 10900 5.1353017e-10 -4406.6645 0 -4406.6645 -1155.1951 11000 5.470711e-10 -4406.6645 0 -4406.6645 -1155.195 Loop time of 180.295 on 4 procs for 10000 steps with 2304 atoms Pair time (%) = 57.7011 (32.0037) Neigh time (%) = 24.6432 (13.6683) Comm time (%) = 55.7143 (30.9017) Outpt time (%) = 0.0200394 (0.0111148) Other time (%) = 42.2164 (23.4152) Nlocal: 576 ave 864 max 288 min Histogram: 2 0 0 0 0 0 0 0 0 2 Nghost: 5170 ave 6910 max 3430 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 178632 ave 289022 max 67462 min Histogram: 2 0 0 0 0 0 0 0 0 2 FullNghs: 357264 ave 577008 max 137520 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 1429056 Ave neighs/atom = 620.25 Neighbor list builds = 1000 Dangerous builds = 0