mirror of https://github.com/lammps/lammps.git
add an example for RDF and ADF computation with water molecules
This commit is contained in:
Axel Kohlmeyer
parent
fb6f019a11
commit
2140caa6f5
File diff suppressed because it is too large
Load Diff
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units real
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atom_style full
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read_data data.spce
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pair_style lj/cut/coul/long 12.0 12.0
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pair_coeff * * 0.0 1.0
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pair_coeff 1 1 0.15535 3.166
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kspace_style pppm 1.0e-6
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bond_style harmonic
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angle_style harmonic
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dihedral_style none
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improper_style none
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bond_coeff 1 1000.00 1.000
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angle_coeff 1 100.0 109.47
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# need to set bond/angle inclusion to > 0.0
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# so that intramolecular pairs are included in neighbor lists (required for second ADF)
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special_bonds lj/coul 1.0e-100 1.0e-100 1.0
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neighbor 2.0 bin
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timestep 2.0
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neigh_modify every 1 delay 2 check yes
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fix 1 all shake 0.0001 20 0 b 1 a 1
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fix 2 all nvt temp 300.0 300.0 100.0
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velocity all create 300.0 6244325
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thermo 100
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run 500
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reset_timestep 0
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compute gofr all rdf 100 1 1 2 2 1 2 # O-O, H-H, O-H
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compute gofa all adf 45 1 1 1 2.0 3.5 2.0 3.5 &
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1 2 1 0.0 1.2 1.5 2.5
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fix rdf all ave/time 100 10 1000 c_gofr[*] file spce-rdf.dat mode vector
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fix adf all ave/time 10 100 1000 c_gofa[*] file spce-adf.dat mode vector
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run 1000
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@ -0,0 +1,202 @@
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LAMMPS (10 Oct 2018)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
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using 1 OpenMP thread(s) per MPI task
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units real
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atom_style full
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read_data data.spce
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orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
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1 by 2 by 1 MPI processor grid
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reading atoms ...
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4500 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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3000 bonds
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reading angles ...
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1500 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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pair_style lj/cut/coul/long 12.0 12.0
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pair_coeff * * 0.0 1.0
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pair_coeff 1 1 0.15535 3.166
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kspace_style pppm 1.0e-6
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bond_style harmonic
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angle_style harmonic
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dihedral_style none
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improper_style none
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bond_coeff 1 1000.00 1.000
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angle_coeff 1 100.0 109.47
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# need to set bond/angle inclusion to > 0.0
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# so that intramolecular pairs are included in neighbor lists (required for second ADF)
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special_bonds lj/coul 1.0e-100 1.0e-100 1.0
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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2 = max # of special neighbors
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neighbor 2.0 bin
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timestep 2.0
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neigh_modify every 1 delay 2 check yes
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fix 1 all shake 0.0001 20 0 b 1 a 1
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0 = # of size 2 clusters
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0 = # of size 3 clusters
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0 = # of size 4 clusters
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1500 = # of frozen angles
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fix 2 all nvt temp 300.0 300.0 100.0
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velocity all create 300.0 6244325
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thermo 100
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run 500
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
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G vector (1/distance) = 0.279652
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grid = 40 40 40
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stencil order = 5
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estimated absolute RMS force accuracy = 0.000394674
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estimated relative force accuracy = 1.18855e-06
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using double precision FFTs
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3d grid and FFT values/proc = 59643 32000
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Neighbor list info ...
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update every 1 steps, delay 2 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 14
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ghost atom cutoff = 14
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binsize = 7, bins = 6 6 6
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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) = 25.06 | 25.25 | 25.44 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 300 -16692.369 0 -14010.534 -112.83562
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100 283.44729 -17008.717 0 -14474.854 -162.06374
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200 298.75279 -16765.544 0 -14094.858 428.79127
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300 296.6501 -16589.155 0 -13937.267 547.40768
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400 303.83151 -16625.028 0 -13908.942 237.9775
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500 298.01615 -16717.015 0 -14052.915 230.7095
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Loop time of 21.4041 on 2 procs for 500 steps with 4500 atoms
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Performance: 4.037 ns/day, 5.946 hours/ns, 23.360 timesteps/s
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94.8% CPU use with 2 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 | 14.892 | 15.034 | 15.176 | 3.7 | 70.24
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Bond | 0.00056624 | 0.00059342 | 0.0006206 | 0.0 | 0.00
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Kspace | 3.987 | 4.1321 | 4.2773 | 7.1 | 19.31
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Neigh | 1.7494 | 1.7496 | 1.7497 | 0.0 | 8.17
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Comm | 0.20554 | 0.20637 | 0.2072 | 0.2 | 0.96
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Output | 0.00015688 | 0.00036144 | 0.00056601 | 0.0 | 0.00
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Modify | 0.25707 | 0.2606 | 0.26413 | 0.7 | 1.22
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Other | | 0.02059 | | | 0.10
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Nlocal: 2250 ave 2258 max 2242 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 16319 ave 16381 max 16257 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 1.30073e+06 ave 1.32386e+06 max 1.2776e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 2601457
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Ave neighs/atom = 578.102
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Ave special neighs/atom = 2
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Neighbor list builds = 45
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Dangerous builds = 0
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reset_timestep 0
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compute gofr all rdf 100 1 1 2 2 1 2 # O-O, H-H, O-H
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compute gofa all adf 45 1 1 1 2.0 3.5 2.0 3.5 1 2 1 0.0 1.2 1.5 2.5
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fix rdf all ave/time 100 10 1000 c_gofr[*] file spce-rdf.dat mode vector
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fix adf all ave/time 10 100 1000 c_gofa[*] file spce-adf.dat mode vector
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run 1000
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
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G vector (1/distance) = 0.279652
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grid = 40 40 40
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stencil order = 5
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estimated absolute RMS force accuracy = 0.000394674
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estimated relative force accuracy = 1.18855e-06
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using double precision FFTs
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3d grid and FFT values/proc = 59643 32000
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Neighbor list info ...
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update every 1 steps, delay 2 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 14
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ghost atom cutoff = 14
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binsize = 7, bins = 6 6 6
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3 neighbor lists, perpetual/occasional/extra = 1 2 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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(2) compute rdf, occasional, copy from (1)
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attributes: half, newton on
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pair build: copy
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stencil: none
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bin: none
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(3) compute adf, occasional
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attributes: full, newton on
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pair build: full/bin
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stencil: full/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 26.78 | 26.78 | 26.78 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 298.01615 -16717.015 0 -14052.915 230.81371
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100 307.1766 -16759.33 0 -14013.341 454.2771
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200 298.94628 -16674.186 0 -14001.771 114.20846
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300 293.13091 -16581.542 0 -13961.113 272.85574
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400 294.47017 -16556.872 0 -13924.471 180.3252
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500 305.57174 -16647.976 0 -13916.333 -444.14856
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600 302.53992 -16670.304 0 -13965.764 114.82353
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700 306.56761 -16616.508 0 -13875.962 534.02537
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800 299.06297 -16644.133 0 -13970.675 83.643063
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900 301.15522 -16674.021 0 -13981.859 325.04538
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1000 298.14963 -16701.663 0 -14036.369 356.0601
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Loop time of 53.3181 on 2 procs for 1000 steps with 4500 atoms
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Performance: 3.241 ns/day, 7.405 hours/ns, 18.755 timesteps/s
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97.3% CPU use with 2 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 | 28.831 | 29.365 | 29.899 | 9.9 | 55.07
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Bond | 0.00097084 | 0.0010794 | 0.001188 | 0.3 | 0.00
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Kspace | 7.3086 | 7.8356 | 8.3626 | 18.8 | 14.70
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Neigh | 3.7241 | 3.7245 | 3.7248 | 0.0 | 6.99
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Comm | 0.32839 | 0.33495 | 0.34151 | 1.1 | 0.63
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Output | 0.00043344 | 0.0015392 | 0.002645 | 2.8 | 0.00
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Modify | 12.013 | 12.014 | 12.015 | 0.0 | 22.53
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Other | | 0.04153 | | | 0.08
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Nlocal: 2250 ave 2251 max 2249 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 16300 ave 16358 max 16242 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 1.301e+06 ave 1.31594e+06 max 1.28606e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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FullNghs: 2.602e+06 ave 2.60923e+06 max 2.59476e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 5203998
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Ave neighs/atom = 1156.44
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Ave special neighs/atom = 2
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Neighbor list builds = 93
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Dangerous builds = 0
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Total wall time: 0:01:14
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@ -0,0 +1,49 @@
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# Time-averaged data for fix adf
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# TimeStep Number-of-rows
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# Row c_gofa[1] c_gofa[2] c_gofa[3] c_gofa[4] c_gofa[5]
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1000 45
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1 2 0 0 0.570997 4.0364e-06
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2 6 0 0 1.34922 1.33246e-05
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3 10 0 0 0.844388 1.94267e-05
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4 14 0 0 0.476996 2.34028e-05
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5 18 0 0 0.161187 2.46115e-05
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6 22 0 0 0.0477465 2.47703e-05
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7 26 0 0 0.00511569 2.48353e-05
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8 30 0 0 0 2.48353e-05
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9 34 0 0 0 2.48353e-05
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10 38 0 0 0.0179049 2.497e-05
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11 42 0.00139303 0.00112 0 2.497e-05
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12 46 0.0970866 0.0791067 0 2.497e-05
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13 50 0.421047 0.417227 0 2.497e-05
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14 54 0.503109 0.821333 0 2.497e-05
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15 58 0.403317 1.14533 0 2.497e-05
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16 62 0.384523 1.45431 0 2.497e-05
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17 66 0.425895 1.79643 0 2.497e-05
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18 70 0.494575 2.1937 0 2.497e-05
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19 74 0.547429 2.63327 0.00716197 2.50218e-05
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20 78 0.584521 3.10253 0.0119366 2.51428e-05
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21 82 0.612285 3.59409 0.0966866 2.56506e-05
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22 86 0.643119 4.1105 0.0868815 2.64003e-05
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23 90 0.669958 4.64829 0.245468 2.77959e-05
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24 94 0.685175 5.19837 0.318537 3.01911e-05
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25 98 0.68985 5.75207 0.608171 3.48379e-05
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26 102 0.681411 6.29909 0.825076 4.16049e-05
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27 106 0.660197 6.82903 1.2987 5.06221e-05
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28 110 0.644879 7.34685 1.58753 6.12867e-05
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29 114 0.613281 7.83923 1.1185 6.98041e-05
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30 118 0.572272 8.29867 0.961282 7.65158e-05
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31 122 0.534702 8.72795 0.546058 8.08946e-05
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32 126 0.496697 9.12669 0.64867 8.51981e-05
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33 130 0.453138 9.49045 0.518561 8.86029e-05
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34 134 0.41004 9.81964 0.561575 9.23251e-05
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35 138 0.36701 10.1143 0.355285 9.51805e-05
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36 142 0.328717 10.3782 0.297648 9.74977e-05
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37 146 0.294236 10.6145 0.0749449 9.81639e-05
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38 150 0.261134 10.8242 0.0856879 9.87562e-05
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39 154 0.223727 11.0039 0.0537574 9.9216e-05
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40 158 0.19037 11.1567 0.0827037 9.95624e-05
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41 162 0.156173 11.2822 0.0149208 9.97358e-05
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42 166 0.119999 11.3785 0.00895247 9.98317e-05
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43 170 0.0853136 11.447 0.00596831 9.98799e-05
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44 174 0.0502058 11.4873 0 9.98799e-05
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45 178 0.0171616 11.5011 0 9.98799e-05
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@ -0,0 +1,104 @@
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# Time-averaged data for fix rdf
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# TimeStep Number-of-rows
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# Row c_gofr[1] c_gofr[2] c_gofr[3] c_gofr[4] c_gofr[5] c_gofr[6] c_gofr[7]
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1000 100
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1 0.06 0 0 0 0 0 0
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2 0.18 0 0 0 0 0 0
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3 0.3 0 0 0 0 0 0
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4 0.42 0 0 0 0 0 0
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5 0.54 0 0 0 0 0 0
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6 0.66 0 0 0 0 0 0
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7 0.78 0 0 0 0 0 0
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8 0.9 0 0 0 0 0 0
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9 1.02 0 0 0 0 18.9675 2
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10 1.14 0 0 0 0 0 2
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11 1.26 0 0 0 0 0 2
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12 1.38 0 0 0 0 0 2
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13 1.5 0 0 0.00146316 0.000333333 0.0485606 2.01107
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14 1.62 0 0 3.77986 1.00467 0.691259 2.1948
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15 1.74 0 0 0.087001 1.03133 1.5081 2.6572
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16 1.86 0 0 0.261354 1.12287 1.29225 3.10993
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17 1.98 0 0 0.557712 1.3442 0.791284 3.42407
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18 2.1 0 0 0.890071 1.74153 0.441155 3.62107
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19 2.22 0 0 1.18482 2.3326 0.280275 3.76093
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20 2.34 0 0 1.33539 3.07273 0.203573 3.8738
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21 2.46 0.0296137 0.00906667 1.31236 3.8766 0.199433 3.996
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22 2.58 0.910251 0.3156 1.12596 4.6352 0.252635 4.16627
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23 2.7 2.74616 1.3284 0.92755 5.3196 0.399944 4.46147
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24 2.82 2.69277 2.41173 0.776668 5.94473 0.620912 4.9614
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25 2.94 1.69749 3.154 0.715559 6.57073 0.927784 5.77333
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26 3.06 1.12844 3.68853 0.734337 7.26667 1.28373 6.99033
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27 3.18 0.894502 4.14613 0.785685 8.0708 1.53008 8.55687
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28 3.3 0.830879 4.60387 0.853285 9.01127 1.55205 10.2681
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29 3.42 0.837147 5.0992 0.940998 10.1252 1.42789 11.9589
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30 3.54 0.87264 5.6524 1.02352 11.4233 1.30488 13.6145
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31 3.66 0.890146 6.2556 1.10007 12.9147 1.15043 15.1747
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32 3.78 0.923629 6.9232 1.14816 14.5751 1.05067 16.6945
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33 3.9 0.948076 7.65267 1.1789 16.3898 0.995284 18.2271
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34 4.02 1.02003 8.48653 1.14251 18.2584 0.987649 19.843
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35 4.14 1.05003 9.39693 1.09918 20.1651 0.973183 21.5317
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36 4.26 1.0578 10.368 1.05588 22.1043 0.968154 23.3104
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37 4.38 1.08788 11.4237 1.04202 24.1275 0.95294 25.1612
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38 4.5 1.0991 12.5496 1.02603 26.2302 0.948747 27.1062
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39 4.62 1.08758 13.7239 1.0199 28.4333 0.952182 29.1637
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40 4.74 1.08319 14.9549 1.0085 30.7265 0.958425 31.3437
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41 4.86 1.06718 16.23 1.0021 33.1219 0.966773 33.6555
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42 4.98 1.0236 17.5141 0.983127 35.5894 0.975683 36.1051
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43 5.1 0.979245 18.8025 0.968484 38.1387 0.993353 38.7208
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44 5.22 0.967438 20.136 0.960781 40.7882 1.0117 41.5116
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45 5.34 0.9397 21.4915 0.95327 43.5392 1.02048 44.4575
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46 5.46 0.933775 22.8996 0.957903 46.4292 1.02138 47.5401
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47 5.58 0.905728 24.3261 0.96475 49.4692 1.01134 50.7279
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48 5.7 0.908316 25.8189 0.985709 52.7103 1.00699 54.0401
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49 5.82 0.922062 27.3988 0.992001 56.1108 0.993731 57.4477
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50 5.94 0.933444 29.0648 1.00316 59.6929 0.985977 60.9695
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51 6.06 0.967112 30.8613 1.00148 63.4149 0.975667 64.5968
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52 6.18 0.995762 32.7851 1.00378 67.2946 0.966562 68.3339
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53 6.3 1.01856 34.83 1.01103 71.3556 0.980183 72.2723
|
||||
54 6.42 1.02375 36.9644 1.00763 75.5586 0.975791 76.3439
|
||||
55 6.54 1.02443 39.1808 1.0048 79.9079 0.988272 80.6231
|
||||
56 6.66 1.04424 41.5237 0.994556 84.3723 0.992933 85.0817
|
||||
57 6.78 1.02624 43.91 0.993082 88.9922 1.00275 89.7481
|
||||
58 6.9 1.05342 46.4469 0.995881 93.7905 1.0039 94.5867
|
||||
59 7.02 1.04804 49.0595 1.0028 98.7917 1.0061 99.606
|
||||
60 7.14 1.03565 51.7301 0.999035 103.946 1.00976 104.817
|
||||
61 7.26 1.01185 54.4279 0.999229 109.276 1.01388 110.227
|
||||
62 7.38 1.00714 57.2025 0.997563 114.774 1.02243 115.864
|
||||
63 7.5 0.997335 60.0403 1.00429 120.491 1.01948 121.67
|
||||
64 7.62 0.98964 62.9469 1.00029 126.369 1.01107 127.613
|
||||
65 7.74 0.986472 65.9363 1.01014 132.493 1.0127 133.755
|
||||
66 7.86 0.976805 68.9888 1.0082 138.797 1.00837 140.061
|
||||
67 7.98 0.980184 72.1461 1.00972 145.304 1.00029 146.51
|
||||
68 8.1 0.99097 75.4349 1.00403 151.97 0.999714 153.15
|
||||
69 8.22 0.988581 78.8137 1.00883 158.869 1.00011 159.991
|
||||
70 8.34 1.0046 82.3483 1.00269 165.927 0.994842 166.996
|
||||
71 8.46 0.987279 85.9225 0.997968 173.155 0.990283 174.171
|
||||
72 8.58 1.00046 89.648 0.999277 180.6 0.990097 181.55
|
||||
73 8.7 1.00036 93.478 0.999683 188.257 0.987047 189.113
|
||||
74 8.82 1.00138 97.4184 0.995158 196.091 0.991812 196.923
|
||||
75 8.94 1.02075 101.545 0.999836 204.178 0.991287 204.944
|
||||
76 9.06 1.00201 105.705 0.99005 212.403 0.996973 213.228
|
||||
77 9.18 0.990377 109.927 0.994103 220.881 1.00126 221.77
|
||||
78 9.3 1.0021 114.311 0.998366 229.619 0.997051 230.5
|
||||
79 9.42 1.00911 118.841 0.996714 238.57 1.00147 239.496
|
||||
80 9.54 1.00129 123.45 0.997009 247.752 1.00442 248.751
|
||||
81 9.66 0.994425 128.144 0.999099 257.187 1.0036 258.231
|
||||
82 9.78 0.99875 132.976 1.00089 266.876 1.00798 267.991
|
||||
83 9.9 1.00475 137.958 1.00485 276.842 1.00223 277.935
|
||||
84 10.02 1.00821 143.078 1.00531 287.057 1.00199 288.119
|
||||
85 10.14 1.00146 148.286 1.00396 297.503 1.00607 298.591
|
||||
86 10.26 0.987716 153.546 1.00115 308.168 1.00195 309.269
|
||||
87 10.38 0.996668 158.978 0.999956 319.072 0.999207 320.167
|
||||
88 10.5 1.00737 164.595 1.00266 330.259 0.999525 331.323
|
||||
89 10.62 1.00322 170.319 1.00368 341.714 0.991347 342.642
|
||||
90 10.74 1.00197 176.165 1.00151 353.405 1.00118 354.333
|
||||
91 10.86 1.01265 182.206 0.997669 365.313 1.00021 366.275
|
||||
92 10.98 1.00566 188.339 1.00218 377.54 0.998434 378.46
|
||||
93 11.1 1.00615 194.61 0.998681 389.992 1.00219 390.96
|
||||
94 11.22 0.989815 200.913 0.994781 402.666 0.996803 403.664
|
||||
95 11.34 0.995666 207.389 0.998115 415.655 0.99786 416.654
|
||||
96 11.46 0.990077 213.966 0.999458 428.938 1.00053 429.956
|
||||
97 11.58 0.992053 220.695 0.997809 442.479 0.994388 443.455
|
||||
98 11.7 1.00038 227.622 0.999064 456.319 1.00445 457.374
|
||||
99 11.82 0.99774 234.673 1.00106 470.473 0.998027 471.49
|
||||
100 11.94 1.00539 241.923 0.99896 484.885 1.00035 485.927
|
||||
Loading…
Reference in New Issue