forked from lijiext/lammps
add alternate log files with the latest version of LAMMPS
This commit is contained in:
Axel Kohlmeyer
parent
dde94c28a7
commit
adbc75cae6
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LAMMPS (23 Oct 2017)
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using 1 OpenMP thread(s) per MPI task
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# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics
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# Rigid CO2 TraPPE model
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# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of
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# mixtures containing alkanes, carbon dioxide and
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# nitrogen AIChE J., 47,1676-1682 (2001)].
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# variables available on command line
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variable mu index -8.1
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variable disp index 0.5
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variable temp index 338.0
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variable lbox index 10.0
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variable spacing index 5.0
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# global model settings
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units real
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atom_style full
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boundary p p p
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pair_style lj/cut/coul/long 14
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pair_modify mix arithmetic tail yes
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kspace_style ewald 0.0001
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bond_style harmonic
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angle_style harmonic
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# box, start molecules on simple cubic lattice
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lattice sc ${spacing}
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lattice sc 5.0
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Lattice spacing in x,y,z = 5 5 5
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region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
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region box block 0 10.0 0 ${lbox} 0 ${lbox} units box
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region box block 0 10.0 0 10.0 0 ${lbox} units box
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region box block 0 10.0 0 10.0 0 10.0 units box
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create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
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Created orthogonal box = (0 0 0) to (10 10 10)
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1 by 1 by 1 MPI processor grid
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molecule co2mol CO2.txt
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Read molecule co2mol:
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3 atoms with 2 types
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2 bonds with 1 types
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1 angles with 1 types
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0 dihedrals with 0 types
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0 impropers with 0 types
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create_atoms 0 box mol co2mol 464563 units box
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Created 24 atoms
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Time spent = 0.00196958 secs
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# rigid CO2 TraPPE model
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pair_coeff 1 1 0.053649 2.8
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pair_coeff 2 2 0.156973 3.05
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bond_coeff 1 0 1.16
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angle_coeff 1 0 180
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# masses
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mass 1 12.0107
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mass 2 15.9994
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# MD settings
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group co2 type 1 2
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24 atoms in group co2
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neighbor 2.0 bin
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neigh_modify every 1 delay 10 check yes
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velocity all create ${temp} 54654
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velocity all create 338.0 54654
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timestep 1.0
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# rigid constraints with thermostat
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fix myrigidnvt all rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
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fix myrigidnvt all rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol
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fix myrigidnvt all rigid/nvt/small molecule temp 338.0 338.0 100 mol co2mol
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8 rigid bodies with 24 atoms
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1.16 = max distance from body owner to body atom
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fix_modify myrigidnvt dynamic/dof no
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# gcmc
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variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
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fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
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fix mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
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fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
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fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
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fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt
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# atom counts
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variable carbon atom "type==1"
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variable oxygen atom "type==2"
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group carbon dynamic all var carbon
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dynamic group carbon defined
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group oxygen dynamic all var oxygen
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dynamic group oxygen defined
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variable nC equal count(carbon)
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variable nO equal count(oxygen)
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# output
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variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
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variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
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variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
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variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
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compute_modify thermo_temp dynamic/dof yes
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thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
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thermo 1000
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# run
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run 20000
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Ewald initialization ...
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WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
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G vector (1/distance) = 0.164636
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estimated absolute RMS force accuracy = 0.0332064
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estimated relative force accuracy = 0.0001
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KSpace vectors: actual max1d max3d = 16 2 62
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kxmax kymax kzmax = 2 2 2
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WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445)
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0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
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0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
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WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472)
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 16
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ghost atom cutoff = 16
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binsize = 8, bins = 2 2 2
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut/coul/long, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 15.62 | 15.62 | 15.62 Mbytes
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Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
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0 364.27579 4238.8631 -9.6809388 13.391989 0.5846359 24 0 0 0 0 8 16
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WARNING: Using kspace solver on system with no charge (../kspace.cpp:289)
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1000 420.43475 1722.4052 -9.6956123 15.456579 0.5846359 24 0.20879341 0.20713005 0 0 8 16
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2000 302.29516 -547.83641 -22.017674 14.11699 0.73079488 30 0.1742478 0.1678018 0 0 10 20
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3000 316.6934 -1080.2672 -8.2218891 10.069364 0.51155641 21 0.13544917 0.13720634 0 0 7 14
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4000 246.81618 -679.83642 -14.577244 10.29997 0.65771539 27 0.1568939 0.15860229 0 0 9 18
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5000 260.22849 -896.29914 -16.097593 10.859684 0.65771539 27 0.13138744 0.13547049 0 0 9 18
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6000 291.70796 -1521.99 -22.303136 13.622574 0.73079488 30 0.12615476 0.12717694 0 0 10 20
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7000 236.02638 -599.92186 -27.580831 13.367447 0.87695385 36 0.119703 0.12145398 0 0 12 24
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8000 321.45341 688.10577 -10.09204 11.817696 0.5846359 24 0.10917411 0.11032646 0 0 8 16
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9000 502.85382 -302.31056 -0.22330142 0.99927447 0.073079488 3 0.1254105 0.12905828 0 0 1 2
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10000 249.98239 -510.0091 -32.815145 15.399767 0.95003334 39 0.1274504 0.12875623 0 0 13 26
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11000 247.59424 -1129.0274 -25.320205 12.792544 0.80387436 33 0.11739076 0.11916784 0 0 11 22
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12000 0 -20.39554 -0.14872889 -0 0 0 0.1254933 0.12920375 0 0 0 0
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13000 1272.2738 -474.79484 -0.29450485 8.8489483 0.14615898 6 0.13767133 0.14112496 0 0 2 4
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14000 516.54246 -36.296516 -5.0012009 11.291243 0.36539744 15 0.15632744 0.15955377 0 0 5 10
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15000 307.09233 1951.9301 -14.820362 12.815375 0.65771539 27 0.15393544 0.15716192 0 0 9 18
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16000 198.31989 -559.48443 -30.459487 11.231925 0.87695385 36 0.1482565 0.15025652 0 0 12 24
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17000 246.99311 657.85683 -18.579206 11.53442 0.73079488 30 0.14143958 0.14375423 0 0 10 20
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18000 467.13468 167.03738 -1.0945268 5.569759 0.21923846 9 0.13847359 0.14098533 0 0 3 6
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19000 359.54027 -1413.5407 -12.156233 13.217895 0.5846359 24 0.15169146 0.15294205 0 0 8 16
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20000 227.79597 -1204.5652 -23.24144 10.637925 0.73079488 30 0.14917199 0.15022946 0 0 10 20
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Loop time of 20.6928 on 1 procs for 20000 steps with 30 atoms
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Performance: 83.507 ns/day, 0.287 hours/ns, 966.519 timesteps/s
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99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 2.5462 | 2.5462 | 2.5462 | 0.0 | 12.30
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Bond | 0.029783 | 0.029783 | 0.029783 | 0.0 | 0.14
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Kspace | 0.26167 | 0.26167 | 0.26167 | 0.0 | 1.26
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Neigh | 0.10705 | 0.10705 | 0.10705 | 0.0 | 0.52
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Comm | 0.23409 | 0.23409 | 0.23409 | 0.0 | 1.13
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Output | 0.0013416 | 0.0013416 | 0.0013416 | 0.0 | 0.01
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Modify | 17.458 | 17.458 | 17.458 | 0.0 | 84.37
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Other | | 0.05433 | | | 0.26
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Nlocal: 30 ave 30 max 30 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 2310 ave 2310 max 2310 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 7736 ave 7736 max 7736 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 7736
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Ave neighs/atom = 257.867
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Ave special neighs/atom = 2
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Neighbor list builds = 20349
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Dangerous builds = 0
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Total wall time: 0:00:20
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@ -0,0 +1,192 @@
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LAMMPS (23 Oct 2017)
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using 1 OpenMP thread(s) per MPI task
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# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics
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# Rigid CO2 TraPPE model
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# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of
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# mixtures containing alkanes, carbon dioxide and
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# nitrogen AIChE J., 47,1676-1682 (2001)].
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# variables available on command line
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variable mu index -8.1
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variable disp index 0.5
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variable temp index 338.0
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variable lbox index 10.0
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variable spacing index 5.0
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# global model settings
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units real
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atom_style full
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boundary p p p
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pair_style lj/cut/coul/long 14
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pair_modify mix arithmetic tail yes
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kspace_style ewald 0.0001
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bond_style harmonic
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angle_style harmonic
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# box, start molecules on simple cubic lattice
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lattice sc ${spacing}
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lattice sc 5.0
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Lattice spacing in x,y,z = 5 5 5
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region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
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region box block 0 10.0 0 ${lbox} 0 ${lbox} units box
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region box block 0 10.0 0 10.0 0 ${lbox} units box
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region box block 0 10.0 0 10.0 0 10.0 units box
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create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
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Created orthogonal box = (0 0 0) to (10 10 10)
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1 by 2 by 2 MPI processor grid
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molecule co2mol CO2.txt
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Read molecule co2mol:
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3 atoms with 2 types
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2 bonds with 1 types
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1 angles with 1 types
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0 dihedrals with 0 types
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0 impropers with 0 types
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create_atoms 0 box mol co2mol 464563 units box
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Created 24 atoms
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Time spent = 0.00261331 secs
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# rigid CO2 TraPPE model
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pair_coeff 1 1 0.053649 2.8
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pair_coeff 2 2 0.156973 3.05
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bond_coeff 1 0 1.16
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angle_coeff 1 0 180
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# masses
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mass 1 12.0107
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mass 2 15.9994
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# MD settings
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group co2 type 1 2
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24 atoms in group co2
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neighbor 2.0 bin
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neigh_modify every 1 delay 10 check yes
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velocity all create ${temp} 54654
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velocity all create 338.0 54654
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timestep 1.0
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# rigid constraints with thermostat
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fix myrigidnvt all rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
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fix myrigidnvt all rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol
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fix myrigidnvt all rigid/nvt/small molecule temp 338.0 338.0 100 mol co2mol
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8 rigid bodies with 24 atoms
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1.16 = max distance from body owner to body atom
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fix_modify myrigidnvt dynamic/dof no
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# gcmc
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variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
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fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
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fix mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
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fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
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fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
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fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt
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# atom counts
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variable carbon atom "type==1"
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variable oxygen atom "type==2"
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group carbon dynamic all var carbon
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dynamic group carbon defined
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group oxygen dynamic all var oxygen
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dynamic group oxygen defined
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variable nC equal count(carbon)
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variable nO equal count(oxygen)
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# output
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variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
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variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
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variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
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variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
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compute_modify thermo_temp dynamic/dof yes
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thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
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thermo 1000
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# run
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run 20000
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Ewald initialization ...
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WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
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G vector (1/distance) = 0.164636
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estimated absolute RMS force accuracy = 0.0332064
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estimated relative force accuracy = 0.0001
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KSpace vectors: actual max1d max3d = 16 2 62
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kxmax kymax kzmax = 2 2 2
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WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445)
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0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
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0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
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WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472)
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 16
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ghost atom cutoff = 16
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binsize = 8, bins = 2 2 2
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut/coul/long, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 15.41 | 15.41 | 15.41 Mbytes
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Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
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0 386.52184 23582.465 -3.2433417 14.209828 0.5846359 24 0 0 0 0 8 16
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WARNING: Using kspace solver on system with no charge (../kspace.cpp:289)
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1000 335.66829 -3.7743052 -4.6268612 7.3374649 0.36539744 15 0.20601899 0.20787963 0 0 5 10
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2000 459.73529 238.91592 -0.42937831 5.4815343 0.21923846 9 0.30392058 0.30105616 0 0 3 6
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3000 255.47773 -479.67802 -36.850434 15.738299 0.95003334 39 0.22220744 0.2197582 0 0 13 26
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4000 182.70803 -1059.2262 -43.044833 12.163134 1.0231128 42 0.16781689 0.16716177 0 0 14 28
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5000 234.00907 -1821.0444 -46.04795 15.578317 1.0231128 42 0.13498091 0.13704201 0 0 14 28
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6000 163.42759 -774.67294 -49.686261 11.691518 1.0961923 45 0.11401677 0.11296973 0 0 15 30
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7000 171.64616 -355.23516 -49.323434 12.27947 1.0961923 45 0.098302308 0.098552065 0 0 15 30
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8000 251.29791 -905.47863 -37.841209 15.480807 0.95003334 39 0.086856972 0.08638658 0 0 13 26
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9000 143.69498 -849.95393 -49.073188 10.279858 1.0961923 45 0.078261061 0.077955243 0 0 15 30
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10000 239.35727 -1158.1879 -43.562047 15.934355 1.0231128 42 0.070789792 0.070807529 0 0 14 28
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11000 169.51213 -1574.7885 -51.125228 12.126803 1.0961923 45 0.065008734 0.06498871 0 0 15 30
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12000 181.39739 160.11631 -46.850937 12.977068 1.0961923 45 0.059648717 0.059514803 0 0 15 30
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13000 164.14601 -1107.7629 -50.726722 11.742914 1.0961923 45 0.055207333 0.055097701 0 0 15 30
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14000 287.26285 418.51463 -41.664766 19.123497 1.0231128 42 0.051346789 0.051222285 0 0 14 28
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15000 256.94593 -532.36615 -41.651618 17.105257 1.0231128 42 0.047870301 0.047861685 0 0 14 28
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16000 166.92132 151.15933 -39.957018 11.11219 1.0231128 42 0.045205599 0.045042211 0 0 14 28
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17000 163.22452 -1299.8119 -42.677558 10.866089 1.0231128 42 0.043122086 0.042993687 0 0 14 28
|
||||
18000 158.01154 475.77329 -48.803162 11.304057 1.0961923 45 0.041016683 0.040647229 0 0 15 30
|
||||
19000 138.49297 -1585.1508 -47.517099 9.9077098 1.0961923 45 0.038929287 0.038436764 0 0 15 30
|
||||
20000 173.84439 -1362.6301 -53.002743 12.436731 1.0961923 45 0.036973919 0.036523816 0 0 15 30
|
||||
Loop time of 32.4481 on 4 procs for 20000 steps with 45 atoms
|
||||
|
||||
Performance: 53.254 ns/day, 0.451 hours/ns, 616.369 timesteps/s
|
||||
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.1687 | 1.6702 | 2.1864 | 30.8 | 5.15
|
||||
Bond | 0.018828 | 0.020035 | 0.020975 | 0.6 | 0.06
|
||||
Kspace | 0.57506 | 1.0931 | 1.5898 | 37.7 | 3.37
|
||||
Neigh | 0.068863 | 0.069524 | 0.070128 | 0.2 | 0.21
|
||||
Comm | 2.0735 | 2.0865 | 2.0979 | 0.7 | 6.43
|
||||
Output | 0.0025017 | 0.0025966 | 0.0027781 | 0.2 | 0.01
|
||||
Modify | 27.335 | 27.344 | 27.363 | 0.2 | 84.27
|
||||
Other | | 0.1621 | | | 0.50
|
||||
|
||||
Nlocal: 11.25 ave 14 max 8 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
Nghost: 2639.75 ave 2656 max 2617 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Neighs: 4320 ave 5824 max 2201 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
|
||||
Total # of neighbors = 17280
|
||||
Ave neighs/atom = 384
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 20394
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:32
|
||||
|
|
@ -0,0 +1,293 @@
|
|||
LAMMPS (23 Oct 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# fix gcmc example with fix shake
|
||||
|
||||
# variables available on command line
|
||||
|
||||
variable mu index -8.1
|
||||
variable disp index 0.5
|
||||
variable temp index 338.0
|
||||
variable lbox index 10.0
|
||||
variable spacing index 5.0
|
||||
|
||||
# global model settings
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
boundary p p p
|
||||
pair_style lj/cut/coul/long 14
|
||||
pair_modify mix arithmetic tail yes
|
||||
kspace_style ewald 0.0001
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
# box, start molecules on simple cubic lattice
|
||||
|
||||
lattice sc ${spacing}
|
||||
lattice sc 5.0
|
||||
Lattice spacing in x,y,z = 5 5 5
|
||||
region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
|
||||
region box block 0 10.0 0 ${lbox} 0 ${lbox} units box
|
||||
region box block 0 10.0 0 10.0 0 ${lbox} units box
|
||||
region box block 0 10.0 0 10.0 0 10.0 units box
|
||||
create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
|
||||
Created orthogonal box = (0 0 0) to (10 10 10)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
|
||||
# we can load multiple molecule templates, but don't have to use them all
|
||||
molecule co2mol CO2.txt
|
||||
Read molecule co2mol:
|
||||
3 atoms with 2 types
|
||||
2 bonds with 1 types
|
||||
1 angles with 1 types
|
||||
0 dihedrals with 0 types
|
||||
0 impropers with 0 types
|
||||
molecule h2omol H2O.txt
|
||||
Read molecule h2omol:
|
||||
3 atoms with 2 types
|
||||
2 bonds with 1 types
|
||||
1 angles with 1 types
|
||||
0 dihedrals with 0 types
|
||||
0 impropers with 0 types
|
||||
create_atoms 0 box mol h2omol 464563 units box
|
||||
Created 24 atoms
|
||||
Time spent = 0.00201297 secs
|
||||
|
||||
# rigid SPC/E water model
|
||||
|
||||
pair_coeff 1 1 0.15535 3.166
|
||||
pair_coeff * 2 0.0000 0.0000
|
||||
|
||||
bond_coeff 1 1000 1.0
|
||||
angle_coeff 1 100 109.47
|
||||
|
||||
# masses
|
||||
|
||||
mass 1 15.9994
|
||||
mass 2 1.0
|
||||
|
||||
# MD settings
|
||||
|
||||
group h2o type 1 2
|
||||
24 atoms in group h2o
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 1 check yes
|
||||
velocity all create ${temp} 54654
|
||||
velocity all create 338.0 54654
|
||||
timestep 1.0
|
||||
|
||||
minimize 0.0 0.0 100 1000
|
||||
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
|
||||
Ewald initialization ...
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.170448
|
||||
estimated absolute RMS force accuracy = 0.0332064
|
||||
estimated relative force accuracy = 0.0001
|
||||
KSpace vectors: actual max1d max3d = 16 2 62
|
||||
kxmax kymax kzmax = 2 2 2
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 16
|
||||
ghost atom cutoff = 16
|
||||
binsize = 8, bins = 2 2 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.88 | 11.88 | 11.88 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 338 -4.1890564 9.2628112e-06 18.98377 739.06991
|
||||
100 338 -30.182886 0.85607237 -6.1539961 -2535.3207
|
||||
Loop time of 0.0507543 on 1 procs for 100 steps with 24 atoms
|
||||
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
-4.18904713252 -28.9258064504 -29.3268133965
|
||||
Force two-norm initial, final = 18.0027 42.4511
|
||||
Force max component initial, final = 5.8993 16.0523
|
||||
Final line search alpha, max atom move = 0.00353207 0.056698
|
||||
Iterations, force evaluations = 100 238
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.042597 | 0.042597 | 0.042597 | 0.0 | 83.93
|
||||
Bond | 0.00047708 | 0.00047708 | 0.00047708 | 0.0 | 0.94
|
||||
Kspace | 0.0031135 | 0.0031135 | 0.0031135 | 0.0 | 6.13
|
||||
Neigh | 0.00045919 | 0.00045919 | 0.00045919 | 0.0 | 0.90
|
||||
Comm | 0.0032997 | 0.0032997 | 0.0032997 | 0.0 | 6.50
|
||||
Output | 1.359e-05 | 1.359e-05 | 1.359e-05 | 0.0 | 0.03
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.0007946 | | | 1.57
|
||||
|
||||
Nlocal: 24 ave 24 max 24 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2047 ave 2047 max 2047 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 4936 ave 4936 max 4936 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 4936
|
||||
Ave neighs/atom = 205.667
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
reset_timestep 0
|
||||
# rigid constraints with thermostat
|
||||
|
||||
fix mynvt all nvt temp ${temp} ${temp} 100
|
||||
fix mynvt all nvt temp 338.0 ${temp} 100
|
||||
fix mynvt all nvt temp 338.0 338.0 100
|
||||
fix wshake all shake 0.0001 50 0 b 1 a 1 mol h2omol
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
8 = # of frozen angles
|
||||
# gcmc
|
||||
|
||||
|
||||
|
||||
run 1000
|
||||
Ewald initialization ...
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.170448
|
||||
estimated absolute RMS force accuracy = 0.0332064
|
||||
estimated relative force accuracy = 0.0001
|
||||
KSpace vectors: actual max1d max3d = 16 2 62
|
||||
kxmax kymax kzmax = 2 2 2
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.63 | 11.63 | 11.63 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 518.26667 -30.182886 0 -7.0100684 993.1985
|
||||
1000 326.9865 -62.258445 0 -47.638175 -5.3440813
|
||||
Loop time of 0.141449 on 1 procs for 1000 steps with 24 atoms
|
||||
|
||||
Performance: 610.819 ns/day, 0.039 hours/ns, 7069.663 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.10788 | 0.10788 | 0.10788 | 0.0 | 76.27
|
||||
Bond | 0.00018954 | 0.00018954 | 0.00018954 | 0.0 | 0.13
|
||||
Kspace | 0.011867 | 0.011867 | 0.011867 | 0.0 | 8.39
|
||||
Neigh | 0.0045254 | 0.0045254 | 0.0045254 | 0.0 | 3.20
|
||||
Comm | 0.011277 | 0.011277 | 0.011277 | 0.0 | 7.97
|
||||
Output | 1.5497e-05 | 1.5497e-05 | 1.5497e-05 | 0.0 | 0.01
|
||||
Modify | 0.00383 | 0.00383 | 0.00383 | 0.0 | 2.71
|
||||
Other | | 0.001868 | | | 1.32
|
||||
|
||||
Nlocal: 24 ave 24 max 24 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1660 ave 1660 max 1660 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 5112 ave 5112 max 5112 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 5112
|
||||
Ave neighs/atom = 213
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 25
|
||||
Dangerous builds = 0
|
||||
|
||||
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
|
||||
fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
|
||||
fix mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
|
||||
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
|
||||
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert ${tfac} group h2o shake wshake
|
||||
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert 1.66666666666667 group h2o shake wshake
|
||||
|
||||
# atom counts
|
||||
|
||||
variable oxygen atom "type==1"
|
||||
variable hydrogen atom "type==2"
|
||||
group oxygen dynamic all var oxygen
|
||||
dynamic group oxygen defined
|
||||
group hydrogen dynamic all var hydrogen
|
||||
dynamic group hydrogen defined
|
||||
variable nO equal count(oxygen)
|
||||
variable nH equal count(hydrogen)
|
||||
|
||||
# output
|
||||
|
||||
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
|
||||
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
|
||||
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
|
||||
variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
|
||||
compute_modify thermo_temp dynamic/dof yes
|
||||
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
|
||||
thermo 1000
|
||||
|
||||
# run
|
||||
|
||||
run 20000
|
||||
Ewald initialization ...
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.170448
|
||||
estimated absolute RMS force accuracy = 0.0332064
|
||||
estimated relative force accuracy = 0.0001
|
||||
KSpace vectors: actual max1d max3d = 16 2 62
|
||||
kxmax kymax kzmax = 2 2 2
|
||||
WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445)
|
||||
0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
|
||||
0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
|
||||
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472)
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.63 | 11.63 | 11.63 Mbytes
|
||||
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
|
||||
1000 326.9865 -4.3509713 -62.258445 14.62027 0.23910963 24 0 0 0 0 8 16
|
||||
2000 116.99793 -5344.1527 -286.61595 17.088682 0.74721761 75 0.048183096 0.013941446 0 0 25 50
|
||||
3000 106.86746 -3920.4926 -361.60598 18.794545 0.89666113 90 0.035637919 0.012768883 0 0 30 60
|
||||
4000 75.002668 540.46846 -414.8511 14.531966 0.98632724 99 0.025963651 0.0093451705 0 0 33 66
|
||||
5000 79.924788 -2131.1173 -437.21216 15.962121 1.0162159 102 0.019879728 0.0070418993 0 0 34 68
|
||||
6000 95.552773 -3647.0233 -438.24276 19.083253 1.0162159 102 0.015753613 0.0056885133 0 0 34 68
|
||||
7000 79.501736 -2071.5369 -440.77351 15.877631 1.0162159 102 0.01326216 0.0046915318 0 0 34 68
|
||||
8000 62.567091 -3102.9616 -442.21884 12.495541 1.0162159 102 0.011305503 0.0040437885 0 0 34 68
|
||||
9000 68.324047 -3812.7866 -440.46835 13.645287 1.0162159 102 0.0099549538 0.0035157329 0 0 34 68
|
||||
10000 83.857631 -2158.2659 -444.8183 16.747566 1.0162159 102 0.0088200922 0.0031354281 0 0 34 68
|
||||
11000 68.350984 -2084.0789 -440.14081 13.650667 1.0162159 102 0.0081331455 0.0030247424 0 0 34 68
|
||||
12000 76.867315 -1585.6723 -443.36199 15.3515 1.0162159 102 0.0073845932 0.0027532534 0 0 34 68
|
||||
13000 59.74266 -2211.0211 -446.07791 11.931462 1.0162159 102 0.0067756276 0.0025213898 0 0 34 68
|
||||
14000 81.154979 -907.0176 -441.53368 16.207808 1.0162159 102 0.0062527642 0.0023280719 0 0 34 68
|
||||
15000 66.814346 -2804.5134 -455.80704 13.7421 1.0461046 105 0.0059590528 0.0021576214 0 0 35 70
|
||||
16000 71.42983 -3930.4004 -458.43218 14.691394 1.0461046 105 0.0055547473 0.0020163729 0 0 35 70
|
||||
17000 89.624855 -3569.8136 -455.18164 18.433672 1.0461046 105 0.0052173265 0.0018867687 0 0 35 70
|
||||
18000 63.519962 -1882.8157 -456.58939 13.064525 1.0461046 105 0.0049082049 0.0017765986 0 0 35 70
|
||||
19000 71.872698 -2243.5046 -454.93359 14.782481 1.0461046 105 0.0046439115 0.0016748361 0 0 35 70
|
||||
20000 73.660765 -2285.3173 -476.35473 15.589381 1.0759934 108 0.0045124933 0.0015837653 0 0 36 72
|
||||
21000 95.675868 987.92089 -475.46736 20.248603 1.0759934 108 0.004285814 0.0015049513 0 0 36 72
|
||||
Loop time of 220.662 on 1 procs for 20000 steps with 108 atoms
|
||||
|
||||
Performance: 7.831 ns/day, 3.065 hours/ns, 90.637 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 37.459 | 37.459 | 37.459 | 0.0 | 16.98
|
||||
Bond | 0.087067 | 0.087067 | 0.087067 | 0.0 | 0.04
|
||||
Kspace | 0.90234 | 0.90234 | 0.90234 | 0.0 | 0.41
|
||||
Neigh | 1.2299 | 1.2299 | 1.2299 | 0.0 | 0.56
|
||||
Comm | 0.95437 | 0.95437 | 0.95437 | 0.0 | 0.43
|
||||
Output | 0.0010636 | 0.0010636 | 0.0010636 | 0.0 | 0.00
|
||||
Modify | 179.85 | 179.85 | 179.85 | 0.0 | 81.51
|
||||
Other | | 0.1754 | | | 0.08
|
||||
|
||||
Nlocal: 108 ave 108 max 108 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 7850 ave 7850 max 7850 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 99828 ave 99828 max 99828 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 99828
|
||||
Ave neighs/atom = 924.333
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 20439
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:03:40
|
||||
|
|
@ -0,0 +1,293 @@
|
|||
LAMMPS (23 Oct 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# fix gcmc example with fix shake
|
||||
|
||||
# variables available on command line
|
||||
|
||||
variable mu index -8.1
|
||||
variable disp index 0.5
|
||||
variable temp index 338.0
|
||||
variable lbox index 10.0
|
||||
variable spacing index 5.0
|
||||
|
||||
# global model settings
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
boundary p p p
|
||||
pair_style lj/cut/coul/long 14
|
||||
pair_modify mix arithmetic tail yes
|
||||
kspace_style ewald 0.0001
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
# box, start molecules on simple cubic lattice
|
||||
|
||||
lattice sc ${spacing}
|
||||
lattice sc 5.0
|
||||
Lattice spacing in x,y,z = 5 5 5
|
||||
region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
|
||||
region box block 0 10.0 0 ${lbox} 0 ${lbox} units box
|
||||
region box block 0 10.0 0 10.0 0 ${lbox} units box
|
||||
region box block 0 10.0 0 10.0 0 10.0 units box
|
||||
create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
|
||||
Created orthogonal box = (0 0 0) to (10 10 10)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
|
||||
# we can load multiple molecule templates, but don't have to use them all
|
||||
molecule co2mol CO2.txt
|
||||
Read molecule co2mol:
|
||||
3 atoms with 2 types
|
||||
2 bonds with 1 types
|
||||
1 angles with 1 types
|
||||
0 dihedrals with 0 types
|
||||
0 impropers with 0 types
|
||||
molecule h2omol H2O.txt
|
||||
Read molecule h2omol:
|
||||
3 atoms with 2 types
|
||||
2 bonds with 1 types
|
||||
1 angles with 1 types
|
||||
0 dihedrals with 0 types
|
||||
0 impropers with 0 types
|
||||
create_atoms 0 box mol h2omol 464563 units box
|
||||
Created 24 atoms
|
||||
Time spent = 0.00174451 secs
|
||||
|
||||
# rigid SPC/E water model
|
||||
|
||||
pair_coeff 1 1 0.15535 3.166
|
||||
pair_coeff * 2 0.0000 0.0000
|
||||
|
||||
bond_coeff 1 1000 1.0
|
||||
angle_coeff 1 100 109.47
|
||||
|
||||
# masses
|
||||
|
||||
mass 1 15.9994
|
||||
mass 2 1.0
|
||||
|
||||
# MD settings
|
||||
|
||||
group h2o type 1 2
|
||||
24 atoms in group h2o
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 1 check yes
|
||||
velocity all create ${temp} 54654
|
||||
velocity all create 338.0 54654
|
||||
timestep 1.0
|
||||
|
||||
minimize 0.0 0.0 100 1000
|
||||
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
|
||||
Ewald initialization ...
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.170448
|
||||
estimated absolute RMS force accuracy = 0.0332064
|
||||
estimated relative force accuracy = 0.0001
|
||||
KSpace vectors: actual max1d max3d = 16 2 62
|
||||
kxmax kymax kzmax = 2 2 2
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 16
|
||||
ghost atom cutoff = 16
|
||||
binsize = 8, bins = 2 2 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.85 | 11.85 | 11.85 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 338 -4.9610706 9.2628112e-06 18.211756 730.90791
|
||||
100 338 -15.742442 0.14954269 7.579918 -637.49568
|
||||
Loop time of 0.0566185 on 4 procs for 100 steps with 24 atoms
|
||||
|
||||
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
-4.96106135393 -15.5388622715 -15.592899346
|
||||
Force two-norm initial, final = 15.474 18.1478
|
||||
Force max component initial, final = 5.80042 7.56514
|
||||
Final line search alpha, max atom move = 0.00151131 0.0114333
|
||||
Iterations, force evaluations = 100 328
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0085177 | 0.016083 | 0.026787 | 5.3 | 28.41
|
||||
Bond | 0.00022459 | 0.00031394 | 0.00037575 | 0.0 | 0.55
|
||||
Kspace | 0.0049062 | 0.014122 | 0.02044 | 5.0 | 24.94
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.018515 | 0.02086 | 0.023246 | 1.2 | 36.84
|
||||
Output | 2.4796e-05 | 2.6047e-05 | 2.9802e-05 | 0.0 | 0.05
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.005213 | | | 9.21
|
||||
|
||||
Nlocal: 6 ave 8 max 3 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
Nghost: 1722 ave 1725 max 1720 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Neighs: 1256.75 ave 2101 max 667 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 5027
|
||||
Ave neighs/atom = 209.458
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
reset_timestep 0
|
||||
# rigid constraints with thermostat
|
||||
|
||||
fix mynvt all nvt temp ${temp} ${temp} 100
|
||||
fix mynvt all nvt temp 338.0 ${temp} 100
|
||||
fix mynvt all nvt temp 338.0 338.0 100
|
||||
fix wshake all shake 0.0001 50 0 b 1 a 1 mol h2omol
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
8 = # of frozen angles
|
||||
# gcmc
|
||||
|
||||
|
||||
|
||||
run 1000
|
||||
Ewald initialization ...
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.170448
|
||||
estimated absolute RMS force accuracy = 0.0332064
|
||||
estimated relative force accuracy = 0.0001
|
||||
KSpace vectors: actual max1d max3d = 16 2 62
|
||||
kxmax kymax kzmax = 2 2 2
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.6 | 11.6 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 518.26667 -15.742442 0 7.4303753 -613.0781
|
||||
1000 369.81793 -54.202686 0 -37.667331 294.98823
|
||||
Loop time of 0.154891 on 4 procs for 1000 steps with 24 atoms
|
||||
|
||||
Performance: 557.810 ns/day, 0.043 hours/ns, 6456.135 timesteps/s
|
||||
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0154 | 0.028993 | 0.040525 | 5.5 | 18.72
|
||||
Bond | 0.00016999 | 0.0001902 | 0.00023293 | 0.0 | 0.12
|
||||
Kspace | 0.019093 | 0.028112 | 0.038976 | 4.3 | 18.15
|
||||
Neigh | 0.0020263 | 0.0022184 | 0.002408 | 0.4 | 1.43
|
||||
Comm | 0.04947 | 0.053627 | 0.058009 | 1.4 | 34.62
|
||||
Output | 2.5749e-05 | 2.7537e-05 | 3.2187e-05 | 0.0 | 0.02
|
||||
Modify | 0.035275 | 0.036815 | 0.038425 | 0.7 | 23.77
|
||||
Other | | 0.004909 | | | 3.17
|
||||
|
||||
Nlocal: 6 ave 8 max 3 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 1331.5 ave 1369 max 1290 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Neighs: 1259.75 ave 1642 max 428 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 0 2
|
||||
|
||||
Total # of neighbors = 5039
|
||||
Ave neighs/atom = 209.958
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 27
|
||||
Dangerous builds = 0
|
||||
|
||||
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
|
||||
fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
|
||||
fix mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
|
||||
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
|
||||
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert ${tfac} group h2o shake wshake
|
||||
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert 1.66666666666667 group h2o shake wshake
|
||||
|
||||
# atom counts
|
||||
|
||||
variable oxygen atom "type==1"
|
||||
variable hydrogen atom "type==2"
|
||||
group oxygen dynamic all var oxygen
|
||||
dynamic group oxygen defined
|
||||
group hydrogen dynamic all var hydrogen
|
||||
dynamic group hydrogen defined
|
||||
variable nO equal count(oxygen)
|
||||
variable nH equal count(hydrogen)
|
||||
|
||||
# output
|
||||
|
||||
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
|
||||
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
|
||||
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
|
||||
variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
|
||||
compute_modify thermo_temp dynamic/dof yes
|
||||
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
|
||||
thermo 1000
|
||||
|
||||
# run
|
||||
|
||||
run 20000
|
||||
Ewald initialization ...
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.170448
|
||||
estimated absolute RMS force accuracy = 0.0332064
|
||||
estimated relative force accuracy = 0.0001
|
||||
KSpace vectors: actual max1d max3d = 16 2 62
|
||||
kxmax kymax kzmax = 2 2 2
|
||||
WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445)
|
||||
0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
|
||||
0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
|
||||
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472)
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.6 | 11.6 Mbytes
|
||||
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
|
||||
1000 369.81793 295.32434 -54.202686 16.535355 0.23910963 24 0 0 0 0 8 16
|
||||
2000 84.544466 -2810.9047 -344.81664 14.364627 0.86677242 87 0.052198354 0.0099581757 0 0 29 58
|
||||
3000 75.188527 -3688.256 -425.02228 14.567977 0.98632724 99 0.030546787 0.0049111089 0 0 33 66
|
||||
4000 75.019396 -5669.3063 -427.69454 14.535207 0.98632724 99 0.019972039 0.0033375609 0 0 33 66
|
||||
5000 90.415371 -2141.7596 -434.65925 17.518218 0.98632724 99 0.014909796 0.002514964 0 0 33 66
|
||||
6000 78.212628 -943.75125 -428.80584 15.153904 0.98632724 99 0.01181521 0.0020316119 0 0 33 66
|
||||
7000 71.754139 -2028.5122 -435.2139 13.902555 0.98632724 99 0.0099466198 0.0016755471 0 0 33 66
|
||||
8000 84.446231 -1969.1657 -428.27313 16.361681 0.98632724 99 0.0084791272 0.0014442102 0 0 33 66
|
||||
9000 70.952348 -2476.9812 -446.33824 14.170197 1.0162159 102 0.0077150892 0.0012556189 0 0 34 68
|
||||
10000 71.418543 -1875.7083 -443.7214 14.263302 1.0162159 102 0.0068355714 0.0011197957 0 0 34 68
|
||||
11000 86.094994 -4508.7581 -444.82687 17.194399 1.0162159 102 0.0061494515 0.0010082475 0 0 34 68
|
||||
12000 81.906091 -1547.8105 -442.36719 16.357815 1.0162159 102 0.0055834729 0.00091775114 0 0 34 68
|
||||
13000 57.221548 -4607.6222 -448.30939 11.42796 1.0162159 102 0.0051230355 0.00084046326 0 0 34 68
|
||||
14000 61.288344 -2518.1779 -445.70636 12.240157 1.0162159 102 0.0047276997 0.00077602396 0 0 34 68
|
||||
15000 85.787669 -2407.7111 -443.3834 17.133022 1.0162159 102 0.0043983485 0.00071920715 0 0 34 68
|
||||
16000 74.845939 -3288.3403 -445.8247 14.947802 1.0162159 102 0.0042321884 0.00080654918 0 0 34 68
|
||||
17000 73.835431 -1926.9566 -445.67476 14.745989 1.0162159 102 0.0039751059 0.00075470749 0 0 34 68
|
||||
18000 72.634985 -3997.552 -447.2351 14.506243 1.0162159 102 0.0037395847 0.00071063946 0 0 34 68
|
||||
19000 96.776472 -714.44132 -453.65552 19.904587 1.0461046 105 0.0036487876 0.00066993446 0 0 35 70
|
||||
20000 75.470786 183.16972 -464.04688 15.522521 1.0461046 105 0.0034630763 0.00063350614 0 0 35 70
|
||||
21000 65.658309 -773.41266 -466.27068 13.504331 1.0461046 105 0.003289113 0.00060198052 0 0 35 70
|
||||
Loop time of 84.4085 on 4 procs for 20000 steps with 105 atoms
|
||||
|
||||
Performance: 20.472 ns/day, 1.172 hours/ns, 236.943 timesteps/s
|
||||
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 6.3571 | 9.7574 | 13.984 | 90.7 | 11.56
|
||||
Bond | 0.026374 | 0.031321 | 0.035482 | 2.1 | 0.04
|
||||
Kspace | 0.57402 | 4.7894 | 8.1754 | 129.0 | 5.67
|
||||
Neigh | 0.34952 | 0.34987 | 0.35021 | 0.1 | 0.41
|
||||
Comm | 2.4028 | 2.4228 | 2.4372 | 0.9 | 2.87
|
||||
Output | 0.0012269 | 0.0012826 | 0.0014355 | 0.2 | 0.00
|
||||
Modify | 66.819 | 66.828 | 66.837 | 0.1 | 79.17
|
||||
Other | | 0.2281 | | | 0.27
|
||||
|
||||
Nlocal: 26.25 ave 31 max 22 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Nghost: 6049.25 ave 6133 max 5962 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Neighs: 23613 ave 35083 max 14025 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 94452
|
||||
Ave neighs/atom = 899.543
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 20428
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:01:24
|
||||
|
|
@ -0,0 +1,136 @@
|
|||
LAMMPS (23 Oct 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# GCMC for LJ simple fluid, no dynamics
|
||||
# T = 2.0
|
||||
# rho ~ 0.5
|
||||
# p ~ 1.5
|
||||
# mu_ex ~ 0.0
|
||||
# comparable to Frenkel and Smit GCMC Case Study, Figure 5.8
|
||||
|
||||
# variables modifiable using -var command line switch
|
||||
|
||||
variable mu index -1.25
|
||||
variable temp index 2.0
|
||||
variable disp index 1.0
|
||||
variable lbox index 5.0
|
||||
|
||||
# global model settings
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
pair_style lj/cut 3.0
|
||||
pair_modify tail no # turn of to avoid triggering full_energy
|
||||
|
||||
# box
|
||||
|
||||
region box block 0 ${lbox} 0 ${lbox} 0 ${lbox}
|
||||
region box block 0 5.0 0 ${lbox} 0 ${lbox}
|
||||
region box block 0 5.0 0 5.0 0 ${lbox}
|
||||
region box block 0 5.0 0 5.0 0 5.0
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (5 5 5)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
|
||||
# lj parameters
|
||||
|
||||
pair_coeff * * 1.0 1.0
|
||||
mass * 1.0
|
||||
|
||||
# gcmc
|
||||
|
||||
fix mygcmc all gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
|
||||
fix mygcmc all gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
|
||||
fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 ${disp}
|
||||
fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 1.0
|
||||
|
||||
# atom count
|
||||
|
||||
variable type1 atom "type==1"
|
||||
group type1 dynamic all var type1
|
||||
dynamic group type1 defined
|
||||
variable n1 equal count(type1)
|
||||
|
||||
# averaging
|
||||
|
||||
variable rho equal density
|
||||
variable p equal press
|
||||
variable nugget equal 1.0e-8
|
||||
variable lambda equal 1.0
|
||||
variable muex equal ${mu}-${temp}*ln(density*${lambda}+${nugget})
|
||||
variable muex equal -1.25-${temp}*ln(density*${lambda}+${nugget})
|
||||
variable muex equal -1.25-2.0*ln(density*${lambda}+${nugget})
|
||||
variable muex equal -1.25-2.0*ln(density*1+${nugget})
|
||||
variable muex equal -1.25-2.0*ln(density*1+1e-08)
|
||||
fix ave all ave/time 10 100 1000 v_rho v_p v_muex v_n1 ave one file rho_vs_p.dat
|
||||
variable rhoav equal f_ave[1]
|
||||
variable pav equal f_ave[2]
|
||||
variable muexav equal f_ave[3]
|
||||
variable n1av equal f_ave[4]
|
||||
|
||||
# output
|
||||
|
||||
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+${nugget})
|
||||
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+1e-08)
|
||||
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+${nugget})
|
||||
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+1e-08)
|
||||
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+${nugget})
|
||||
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+1e-08)
|
||||
compute_modify thermo_temp dynamic yes
|
||||
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
|
||||
thermo 1000
|
||||
|
||||
# run
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.3
|
||||
ghost atom cutoff = 3.3
|
||||
binsize = 1.65, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 0.433 | 0.433 | 0.433 Mbytes
|
||||
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
|
||||
0 0 0 0 -0 0 0 0 0 0 0 0 0 0
|
||||
1000 2.4038954 2.1735585 -2.7041368 3.5476844 0.496 62 0.064790036 0.06313096 0.1081294 0.54304 1.4513524 -0.025479219 64.98
|
||||
2000 2.0461168 1.1913842 -2.9880181 3.0212194 0.512 64 0.067416408 0.066335853 0.11306166 0.52736 1.3274665 0.034690004 62.97
|
||||
3000 1.7930436 1.3788681 -3.2212667 2.6505861 0.552 69 0.067733191 0.066877836 0.1133516 0.5344 1.3834744 0.0070582537 63.5
|
||||
4000 1.981449 1.2541054 -2.8222868 2.9217977 0.472 59 0.068546991 0.067856412 0.11442807 0.52504 1.3815629 0.043309657 62.17
|
||||
5000 2.0946818 1.0701629 -3.5213291 3.0977688 0.568 71 0.06813743 0.067567891 0.11342906 0.53824 1.4049567 -0.0054539777 64.15
|
||||
6000 1.9793484 0.68224187 -3.410211 2.9247088 0.536 67 0.067797628 0.067420108 0.11295333 0.5384 1.401683 -0.0066894359 64.37
|
||||
7000 2.1885798 1.6745012 -3.185499 3.2345922 0.544 68 0.068630201 0.068261832 0.11403705 0.5244 1.449239 0.045987399 62.33
|
||||
8000 2.2175324 1.5897263 -3.078898 3.2759002 0.528 66 0.068180395 0.067899629 0.11332691 0.53928 1.5488388 -0.01075766 64.29
|
||||
9000 1.8610779 1.0396231 -2.923262 2.7465908 0.496 62 0.068346453 0.068028117 0.1134132 0.52912 1.4352871 0.027082544 62.87
|
||||
10000 2.1079271 1.1746643 -2.9112062 3.1091925 0.48 60 0.068352878 0.068054948 0.11335434 0.5316 1.4462327 0.018503094 63.2
|
||||
Loop time of 20.4081 on 1 procs for 10000 steps with 60 atoms
|
||||
|
||||
Performance: 211680.375 tau/day, 490.001 timesteps/s
|
||||
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.46484 | 0.46484 | 0.46484 | 0.0 | 2.28
|
||||
Neigh | 1.1447 | 1.1447 | 1.1447 | 0.0 | 5.61
|
||||
Comm | 0.1696 | 0.1696 | 0.1696 | 0.0 | 0.83
|
||||
Output | 0.000319 | 0.000319 | 0.000319 | 0.0 | 0.00
|
||||
Modify | 18.607 | 18.607 | 18.607 | 0.0 | 91.17
|
||||
Other | | 0.02194 | | | 0.11
|
||||
|
||||
Nlocal: 60 ave 60 max 60 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 663 ave 663 max 663 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2133 ave 2133 max 2133 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2133
|
||||
Ave neighs/atom = 35.55
|
||||
Neighbor list builds = 10000
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:20
|
||||
|
|
@ -0,0 +1,136 @@
|
|||
LAMMPS (23 Oct 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# GCMC for LJ simple fluid, no dynamics
|
||||
# T = 2.0
|
||||
# rho ~ 0.5
|
||||
# p ~ 1.5
|
||||
# mu_ex ~ 0.0
|
||||
# comparable to Frenkel and Smit GCMC Case Study, Figure 5.8
|
||||
|
||||
# variables modifiable using -var command line switch
|
||||
|
||||
variable mu index -1.25
|
||||
variable temp index 2.0
|
||||
variable disp index 1.0
|
||||
variable lbox index 5.0
|
||||
|
||||
# global model settings
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
pair_style lj/cut 3.0
|
||||
pair_modify tail no # turn of to avoid triggering full_energy
|
||||
|
||||
# box
|
||||
|
||||
region box block 0 ${lbox} 0 ${lbox} 0 ${lbox}
|
||||
region box block 0 5.0 0 ${lbox} 0 ${lbox}
|
||||
region box block 0 5.0 0 5.0 0 ${lbox}
|
||||
region box block 0 5.0 0 5.0 0 5.0
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (5 5 5)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
|
||||
# lj parameters
|
||||
|
||||
pair_coeff * * 1.0 1.0
|
||||
mass * 1.0
|
||||
|
||||
# gcmc
|
||||
|
||||
fix mygcmc all gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
|
||||
fix mygcmc all gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
|
||||
fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 ${disp}
|
||||
fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 1.0
|
||||
|
||||
# atom count
|
||||
|
||||
variable type1 atom "type==1"
|
||||
group type1 dynamic all var type1
|
||||
dynamic group type1 defined
|
||||
variable n1 equal count(type1)
|
||||
|
||||
# averaging
|
||||
|
||||
variable rho equal density
|
||||
variable p equal press
|
||||
variable nugget equal 1.0e-8
|
||||
variable lambda equal 1.0
|
||||
variable muex equal ${mu}-${temp}*ln(density*${lambda}+${nugget})
|
||||
variable muex equal -1.25-${temp}*ln(density*${lambda}+${nugget})
|
||||
variable muex equal -1.25-2.0*ln(density*${lambda}+${nugget})
|
||||
variable muex equal -1.25-2.0*ln(density*1+${nugget})
|
||||
variable muex equal -1.25-2.0*ln(density*1+1e-08)
|
||||
fix ave all ave/time 10 100 1000 v_rho v_p v_muex v_n1 ave one file rho_vs_p.dat
|
||||
variable rhoav equal f_ave[1]
|
||||
variable pav equal f_ave[2]
|
||||
variable muexav equal f_ave[3]
|
||||
variable n1av equal f_ave[4]
|
||||
|
||||
# output
|
||||
|
||||
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+${nugget})
|
||||
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+1e-08)
|
||||
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+${nugget})
|
||||
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+1e-08)
|
||||
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+${nugget})
|
||||
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+1e-08)
|
||||
compute_modify thermo_temp dynamic yes
|
||||
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
|
||||
thermo 1000
|
||||
|
||||
# run
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.3
|
||||
ghost atom cutoff = 3.3
|
||||
binsize = 1.65, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 0.4477 | 0.4477 | 0.4477 Mbytes
|
||||
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
|
||||
0 0 0 0 -0 0 0 0 0 0 0 0 0 0
|
||||
1000 1.956397 1.7699101 -2.7889468 2.8864874 0.488 61 0.068894746 0.067229075 0.1141726 0.53288 1.3832798 0.013392866 63.44
|
||||
2000 2.040943 0.56060899 -2.8001647 3.0077055 0.456 57 0.069858594 0.068831934 0.11629114 0.5232 1.3587174 0.049995794 62.19
|
||||
3000 2.0004866 1.5736515 -3.3098044 2.9572411 0.552 69 0.069594029 0.068727791 0.11592543 0.53096 1.4129434 0.020022578 63.23
|
||||
4000 2.1127942 2.642809 -2.8865084 3.1211733 0.528 66 0.070268697 0.069533235 0.11693806 0.52424 1.3444615 0.046884078 62.57
|
||||
5000 2.3663648 1.354269 -3.1917346 3.4957662 0.528 66 0.070519633 0.069960064 0.11710321 0.52688 1.3595814 0.036270867 62.56
|
||||
6000 1.9224136 0.82756699 -3.1965 2.839257 0.52 65 0.06985018 0.069474645 0.11628632 0.536 1.47062 0.00141549 63.76
|
||||
7000 2.0266192 1.5593811 -2.9972341 2.9931606 0.52 65 0.070244693 0.069880791 0.11666541 0.52528 1.3246332 0.040754793 62.2
|
||||
8000 1.7790467 1.8680568 -2.8028819 2.6275151 0.52 65 0.070454494 0.070172368 0.11736806 0.524 1.4213649 0.047985191 62.03
|
||||
9000 1.7968847 1.3195587 -3.261001 2.6550983 0.536 67 0.069952011 0.069618327 0.11650087 0.53904 1.4624201 -0.01069837 64.36
|
||||
10000 2.1566109 1.1015729 -3.4999837 3.1880335 0.552 69 0.069603309 0.069284134 0.11625548 0.53128 1.3587249 0.02075238 63.24
|
||||
Loop time of 23.8213 on 4 procs for 10000 steps with 69 atoms
|
||||
|
||||
Performance: 181350.388 tau/day, 419.793 timesteps/s
|
||||
97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.10935 | 0.11844 | 0.12741 | 2.1 | 0.50
|
||||
Neigh | 0.33 | 0.33945 | 0.35091 | 1.6 | 1.42
|
||||
Comm | 0.49249 | 0.51745 | 0.53856 | 2.7 | 2.17
|
||||
Output | 0.00053334 | 0.0007208 | 0.0007906 | 0.0 | 0.00
|
||||
Modify | 22.82 | 22.822 | 22.825 | 0.0 | 95.81
|
||||
Other | | 0.02289 | | | 0.10
|
||||
|
||||
Nlocal: 17.25 ave 23 max 10 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Nghost: 506.5 ave 519 max 490 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 705.75 ave 998 max 369 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
|
||||
Total # of neighbors = 2823
|
||||
Ave neighs/atom = 40.913
|
||||
Neighbor list builds = 10000
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:23
|
||||
Loading…
Reference in New Issue