forked from lijiext/lammps
add Widom spc/e example
This commit is contained in:
Axel Kohlmeyer
parent
4d4ae93ef8
commit
55c3d139c1
File diff suppressed because it is too large
Load Diff
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units real
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dimension 3
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boundary p p p
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atom_style full
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pair_style lj/cut/coul/long 10.0
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bond_style harmonic
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angle_style harmonic
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read_data data.spce
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molecule h2omol H2O.txt
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### Flexible SPC/E Potential Parameters ###
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### Zhang et al., Fluid Phase Equilibria, 262 (2007) 210-216 ###
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pair_coeff 1 1 0.1502629 3.1169
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pair_coeff 1 2 0.0341116368 2.04845
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pair_coeff 2 2 0.00774378 0.98
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bond_coeff 1 176.864 0.9611
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angle_coeff 1 42.1845 109.4712
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kspace_style pppm 1.0e-4
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fix mywidom all widom 10 20 0 29494 298 mol h2omol
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fix 2 all nvt temp 298.0 298.0 100.0
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neighbor 2.0 bin
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neigh_modify delay 10 every 2 check yes
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#run variables
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timestep 0.5
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thermo 10
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thermo_style custom step etotal pe temp press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3]
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run 100
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LAMMPS (30 Jun 2020)
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using 1 OpenMP thread(s) per MPI task
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units real
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dimension 3
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boundary p p p
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atom_style full
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pair_style lj/cut/coul/long 10.0
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bond_style harmonic
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angle_style harmonic
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read_data data.spce
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orthogonal box = (-0.031613 -0.023523 -0.085255) to (43.234352 44.939753 42.306533)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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8640 atoms
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scanning bonds ...
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2 = max bonds/atom
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scanning angles ...
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1 = max angles/atom
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reading bonds ...
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5760 bonds
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reading angles ...
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2880 angles
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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1 = max # of 1-4 neighbors
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2 = max # of special neighbors
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special bonds CPU = 0.008 seconds
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read_data CPU = 0.028 seconds
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molecule h2omol H2O.txt
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Read molecule template h2omol:
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1 molecules
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3 atoms with max type 2
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2 bonds with max type 1
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1 angles with max type 1
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0 dihedrals with max type 0
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0 impropers with max type 0
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### Flexible SPC/E Potential Parameters ###
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### Zhang et al., Fluid Phase Equilibria, 262 (2007) 210-216 ###
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pair_coeff 1 1 0.1502629 3.1169
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pair_coeff 1 2 0.0341116368 2.04845
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pair_coeff 2 2 0.00774378 0.98
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bond_coeff 1 176.864 0.9611
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angle_coeff 1 42.1845 109.4712
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kspace_style pppm 1.0e-4
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fix mywidom all widom 10 20 0 29494 298 mol h2omol
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fix 2 all nvt temp 298.0 298.0 100.0
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neighbor 2.0 bin
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neigh_modify delay 10 every 2 check yes
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#run variables
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timestep 0.5
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thermo 10
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thermo_style custom step etotal pe temp press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3]
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run 100
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:330)
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G vector (1/distance) = 0.2690183
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grid = 24 24 24
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stencil order = 5
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estimated absolute RMS force accuracy = 0.024843102
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estimated relative force accuracy = 7.4814263e-05
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using double precision FFTW3
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3d grid and FFT values/proc = 29791 13824
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WARNING: Fix Widom using full_energy option (src/MC/fix_widom.cpp:297)
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0 atoms in group FixWidom:widom_exclusion_group:mywidom
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0 atoms in group FixWidom:rotation_gas_atoms:mywidom
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WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:487)
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Neighbor list info ...
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update every 2 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 = 12
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ghost atom cutoff = 12
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binsize = 6, bins = 8 8 8
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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) = 29.66 | 29.66 | 29.66 Mbytes
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Step TotEng PotEng Temp Press Volume Density f_mywidom[1] f_mywidom[2] f_mywidom[3]
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0 -29703.973 -29703.973 0 -4764.5901 82468.116 1.9140713 0 0 82468.116
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10 -29712.131 -31110.041 54.285179 -3154.4423 82468.116 1.9140713 241.93348 3.7366217e-178 82468.116
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20 -29711.939 -32614.429 112.71273 -4216.1592 82468.116 1.9140713 16.095006 1.5716469e-12 82468.116
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30 -29688.142 -32368.506 104.08688 -4093.6515 82468.116 1.9140713 5.7862327 5.7086352e-05 82468.116
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40 -29662.343 -32252.144 100.57005 -1458.5339 82468.116 1.9140713 126.68071 1.2467216e-93 82468.116
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50 -29646.78 -32837.635 123.91081 -4607.1155 82468.116 1.9140713 74.622397 1.8790479e-55 82468.116
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60 -29628.968 -33001.229 130.9554 -4589.5296 82468.116 1.9140713 3.6575433 0.0020780497 82468.116
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70 -29602.78 -32816.28 124.79023 -3082.1133 82468.116 1.9140713 13.983097 5.561247e-11 82468.116
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80 -29577.552 -33141.454 138.39742 -6332.8138 82468.116 1.9140713 41.98931 1.6075608e-31 82468.116
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90 -29550.865 -33792.115 164.70094 -4607.6419 82468.116 1.9140713 68.690681 4.2082269e-51 82468.116
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100 -29515.107 -34052.782 176.21207 -3609.5709 82468.116 1.9140713 41.090597 7.3326206e-31 82468.116
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Loop time of 163.407 on 1 procs for 100 steps with 8640 atoms
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Performance: 0.026 ns/day, 907.819 hours/ns, 0.612 timesteps/s
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99.8% 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 | 8.5495 | 8.5495 | 8.5495 | 0.0 | 5.23
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Bond | 0.031981 | 0.031981 | 0.031981 | 0.0 | 0.02
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Kspace | 2.3995 | 2.3995 | 2.3995 | 0.0 | 1.47
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Neigh | 5.0542 | 5.0542 | 5.0542 | 0.0 | 3.09
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Comm | 0.051965 | 0.051965 | 0.051965 | 0.0 | 0.03
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Output | 0.0018802 | 0.0018802 | 0.0018802 | 0.0 | 0.00
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Modify | 147.31 | 147.31 | 147.31 | 0.0 | 90.15
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Other | | 0.003614 | | | 0.00
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Nlocal: 8640.00 ave 8640 max 8640 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 23499.0 ave 23499 max 23499 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 3.27380e+06 ave 3.2738e+06 max 3.2738e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 3273800
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Ave neighs/atom = 378.91204
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Ave special neighs/atom = 2.0000000
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Neighbor list builds = 220
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Dangerous builds = 0
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Total wall time: 0:02:44
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