add an example for RDF and ADF computation with water molecules (2140caa6) · Commits · 郑智淋 / lammps

examples/rdf-adf/data.spce

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examples/rdf-adf/in.spce

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Original line number	Diff line number	Diff line
		units real
		atom_style full

		read_data data.spce

		pair_style lj/cut/coul/long 12.0 12.0
		pair_coeff * * 0.0 1.0
		pair_coeff 1 1 0.15535 3.166
		kspace_style pppm 1.0e-6

		bond_style harmonic
		angle_style harmonic
		dihedral_style none
		improper_style none

		bond_coeff 1 1000.00 1.000
		angle_coeff 1 100.0 109.47

		# need to set bond/angle inclusion to > 0.0
		# so that intramolecular pairs are included in neighbor lists (required for second ADF)
		special_bonds lj/coul 1.0e-100 1.0e-100 1.0

		neighbor 2.0 bin
		timestep 2.0
		neigh_modify every 1 delay 2 check yes

		fix 1 all shake 0.0001 20 0 b 1 a 1
		fix 2 all nvt temp 300.0 300.0 100.0

		velocity all create 300.0 6244325

		thermo 100
		run 500

		reset_timestep 0

		compute gofr all rdf 100 1 1 2 2 1 2 # O-O, H-H, O-H
		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
		fix rdf all ave/time 100 10 1000 c_gofr[*] file spce-rdf.dat mode vector
		fix adf all ave/time 10 100 1000 c_gofa[*] file spce-adf.dat mode vector

		run 1000

examples/rdf-adf/log.10Oct2018.spce.g++.2

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Original line number	Diff line number	Diff line
		LAMMPS (10 Oct 2018)
		OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
		using 1 OpenMP thread(s) per MPI task
		units real
		atom_style full

		read_data data.spce
		orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
		1 by 2 by 1 MPI processor grid
		reading atoms ...
		4500 atoms
		scanning bonds ...
		2 = max bonds/atom
		scanning angles ...
		1 = max angles/atom
		reading bonds ...
		3000 bonds
		reading angles ...
		1500 angles
		2 = max # of 1-2 neighbors
		1 = max # of 1-3 neighbors
		1 = max # of 1-4 neighbors
		2 = max # of special neighbors

		pair_style lj/cut/coul/long 12.0 12.0
		pair_coeff * * 0.0 1.0
		pair_coeff 1 1 0.15535 3.166
		kspace_style pppm 1.0e-6

		bond_style harmonic
		angle_style harmonic
		dihedral_style none
		improper_style none

		bond_coeff 1 1000.00 1.000
		angle_coeff 1 100.0 109.47

		# need to set bond/angle inclusion to > 0.0
		# so that intramolecular pairs are included in neighbor lists (required for second ADF)
		special_bonds lj/coul 1.0e-100 1.0e-100 1.0
		2 = max # of 1-2 neighbors
		1 = max # of 1-3 neighbors
		2 = max # of special neighbors

		neighbor 2.0 bin
		timestep 2.0
		neigh_modify every 1 delay 2 check yes

		fix 1 all shake 0.0001 20 0 b 1 a 1
		0 = # of size 2 clusters
		0 = # of size 3 clusters
		0 = # of size 4 clusters
		1500 = # of frozen angles
		fix 2 all nvt temp 300.0 300.0 100.0

		velocity all create 300.0 6244325

		thermo 100
		run 500
		PPPM initialization ...
		using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
		G vector (1/distance) = 0.279652
		grid = 40 40 40
		stencil order = 5
		estimated absolute RMS force accuracy = 0.000394674
		estimated relative force accuracy = 1.18855e-06
		using double precision FFTs
		3d grid and FFT values/proc = 59643 32000
		Neighbor list info ...
		update every 1 steps, delay 2 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 14
		ghost atom cutoff = 14
		binsize = 7, bins = 6 6 6
		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) = 25.06 \| 25.25 \| 25.44 Mbytes
		Step Temp E_pair E_mol TotEng Press
		0 300 -16692.369 0 -14010.534 -112.83562
		100 283.44729 -17008.717 0 -14474.854 -162.06374
		200 298.75279 -16765.544 0 -14094.858 428.79127
		300 296.6501 -16589.155 0 -13937.267 547.40768
		400 303.83151 -16625.028 0 -13908.942 237.9775
		500 298.01615 -16717.015 0 -14052.915 230.7095
		Loop time of 21.4041 on 2 procs for 500 steps with 4500 atoms

		Performance: 4.037 ns/day, 5.946 hours/ns, 23.360 timesteps/s
		94.8% CPU use with 2 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 14.892 \| 15.034 \| 15.176 \| 3.7 \| 70.24
		Bond \| 0.00056624 \| 0.00059342 \| 0.0006206 \| 0.0 \| 0.00
		Kspace \| 3.987 \| 4.1321 \| 4.2773 \| 7.1 \| 19.31
		Neigh \| 1.7494 \| 1.7496 \| 1.7497 \| 0.0 \| 8.17
		Comm \| 0.20554 \| 0.20637 \| 0.2072 \| 0.2 \| 0.96
		Output \| 0.00015688 \| 0.00036144 \| 0.00056601 \| 0.0 \| 0.00
		Modify \| 0.25707 \| 0.2606 \| 0.26413 \| 0.7 \| 1.22
		Other \| \| 0.02059 \| \| \| 0.10

		Nlocal: 2250 ave 2258 max 2242 min
		Histogram: 1 0 0 0 0 0 0 0 0 1
		Nghost: 16319 ave 16381 max 16257 min
		Histogram: 1 0 0 0 0 0 0 0 0 1
		Neighs: 1.30073e+06 ave 1.32386e+06 max 1.2776e+06 min
		Histogram: 1 0 0 0 0 0 0 0 0 1

		Total # of neighbors = 2601457
		Ave neighs/atom = 578.102
		Ave special neighs/atom = 2
		Neighbor list builds = 45
		Dangerous builds = 0

		reset_timestep 0

		compute gofr all rdf 100 1 1 2 2 1 2 # O-O, H-H, O-H
		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
		fix rdf all ave/time 100 10 1000 c_gofr[*] file spce-rdf.dat mode vector
		fix adf all ave/time 10 100 1000 c_gofa[*] file spce-adf.dat mode vector

		run 1000
		PPPM initialization ...
		using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
		G vector (1/distance) = 0.279652
		grid = 40 40 40
		stencil order = 5
		estimated absolute RMS force accuracy = 0.000394674
		estimated relative force accuracy = 1.18855e-06
		using double precision FFTs
		3d grid and FFT values/proc = 59643 32000
		Neighbor list info ...
		update every 1 steps, delay 2 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 14
		ghost atom cutoff = 14
		binsize = 7, bins = 6 6 6
		3 neighbor lists, perpetual/occasional/extra = 1 2 0
		(1) pair lj/cut/coul/long, perpetual
		attributes: half, newton on
		pair build: half/bin/newton
		stencil: half/bin/3d/newton
		bin: standard
		(2) compute rdf, occasional, copy from (1)
		attributes: half, newton on
		pair build: copy
		stencil: none
		bin: none
		(3) compute adf, occasional
		attributes: full, newton on
		pair build: full/bin
		stencil: full/bin/3d
		bin: standard
		Per MPI rank memory allocation (min/avg/max) = 26.78 \| 26.78 \| 26.78 Mbytes
		Step Temp E_pair E_mol TotEng Press
		0 298.01615 -16717.015 0 -14052.915 230.81371
		100 307.1766 -16759.33 0 -14013.341 454.2771
		200 298.94628 -16674.186 0 -14001.771 114.20846
		300 293.13091 -16581.542 0 -13961.113 272.85574
		400 294.47017 -16556.872 0 -13924.471 180.3252
		500 305.57174 -16647.976 0 -13916.333 -444.14856
		600 302.53992 -16670.304 0 -13965.764 114.82353
		700 306.56761 -16616.508 0 -13875.962 534.02537
		800 299.06297 -16644.133 0 -13970.675 83.643063
		900 301.15522 -16674.021 0 -13981.859 325.04538
		1000 298.14963 -16701.663 0 -14036.369 356.0601
		Loop time of 53.3181 on 2 procs for 1000 steps with 4500 atoms

		Performance: 3.241 ns/day, 7.405 hours/ns, 18.755 timesteps/s
		97.3% CPU use with 2 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 28.831 \| 29.365 \| 29.899 \| 9.9 \| 55.07
		Bond \| 0.00097084 \| 0.0010794 \| 0.001188 \| 0.3 \| 0.00
		Kspace \| 7.3086 \| 7.8356 \| 8.3626 \| 18.8 \| 14.70
		Neigh \| 3.7241 \| 3.7245 \| 3.7248 \| 0.0 \| 6.99
		Comm \| 0.32839 \| 0.33495 \| 0.34151 \| 1.1 \| 0.63
		Output \| 0.00043344 \| 0.0015392 \| 0.002645 \| 2.8 \| 0.00
		Modify \| 12.013 \| 12.014 \| 12.015 \| 0.0 \| 22.53
		Other \| \| 0.04153 \| \| \| 0.08

		Nlocal: 2250 ave 2251 max 2249 min
		Histogram: 1 0 0 0 0 0 0 0 0 1
		Nghost: 16300 ave 16358 max 16242 min
		Histogram: 1 0 0 0 0 0 0 0 0 1
		Neighs: 1.301e+06 ave 1.31594e+06 max 1.28606e+06 min
		Histogram: 1 0 0 0 0 0 0 0 0 1
		FullNghs: 2.602e+06 ave 2.60923e+06 max 2.59476e+06 min
		Histogram: 1 0 0 0 0 0 0 0 0 1

		Total # of neighbors = 5203998
		Ave neighs/atom = 1156.44
		Ave special neighs/atom = 2
		Neighbor list builds = 93
		Dangerous builds = 0
		Total wall time: 0:01:14

examples/rdf-adf/spce-adf.dat.ref

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Original line number	Diff line number	Diff line
		# Time-averaged data for fix adf
		# TimeStep Number-of-rows
		# Row c_gofa[1] c_gofa[2] c_gofa[3] c_gofa[4] c_gofa[5]
		1000 45
		1 2 0 0 0.570997 4.0364e-06
		2 6 0 0 1.34922 1.33246e-05
		3 10 0 0 0.844388 1.94267e-05
		4 14 0 0 0.476996 2.34028e-05
		5 18 0 0 0.161187 2.46115e-05
		6 22 0 0 0.0477465 2.47703e-05
		7 26 0 0 0.00511569 2.48353e-05
		8 30 0 0 0 2.48353e-05
		9 34 0 0 0 2.48353e-05
		10 38 0 0 0.0179049 2.497e-05
		11 42 0.00139303 0.00112 0 2.497e-05
		12 46 0.0970866 0.0791067 0 2.497e-05
		13 50 0.421047 0.417227 0 2.497e-05
		14 54 0.503109 0.821333 0 2.497e-05
		15 58 0.403317 1.14533 0 2.497e-05
		16 62 0.384523 1.45431 0 2.497e-05
		17 66 0.425895 1.79643 0 2.497e-05
		18 70 0.494575 2.1937 0 2.497e-05
		19 74 0.547429 2.63327 0.00716197 2.50218e-05
		20 78 0.584521 3.10253 0.0119366 2.51428e-05
		21 82 0.612285 3.59409 0.0966866 2.56506e-05
		22 86 0.643119 4.1105 0.0868815 2.64003e-05
		23 90 0.669958 4.64829 0.245468 2.77959e-05
		24 94 0.685175 5.19837 0.318537 3.01911e-05
		25 98 0.68985 5.75207 0.608171 3.48379e-05
		26 102 0.681411 6.29909 0.825076 4.16049e-05
		27 106 0.660197 6.82903 1.2987 5.06221e-05
		28 110 0.644879 7.34685 1.58753 6.12867e-05
		29 114 0.613281 7.83923 1.1185 6.98041e-05
		30 118 0.572272 8.29867 0.961282 7.65158e-05
		31 122 0.534702 8.72795 0.546058 8.08946e-05
		32 126 0.496697 9.12669 0.64867 8.51981e-05
		33 130 0.453138 9.49045 0.518561 8.86029e-05
		34 134 0.41004 9.81964 0.561575 9.23251e-05
		35 138 0.36701 10.1143 0.355285 9.51805e-05
		36 142 0.328717 10.3782 0.297648 9.74977e-05
		37 146 0.294236 10.6145 0.0749449 9.81639e-05
		38 150 0.261134 10.8242 0.0856879 9.87562e-05
		39 154 0.223727 11.0039 0.0537574 9.9216e-05
		40 158 0.19037 11.1567 0.0827037 9.95624e-05
		41 162 0.156173 11.2822 0.0149208 9.97358e-05
		42 166 0.119999 11.3785 0.00895247 9.98317e-05
		43 170 0.0853136 11.447 0.00596831 9.98799e-05
		44 174 0.0502058 11.4873 0 9.98799e-05
		45 178 0.0171616 11.5011 0 9.98799e-05

examples/rdf-adf/spce-rdf.dat.ref

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Original line number	Diff line number	Diff line
		# Time-averaged data for fix rdf
		# TimeStep Number-of-rows
		# Row c_gofr[1] c_gofr[2] c_gofr[3] c_gofr[4] c_gofr[5] c_gofr[6] c_gofr[7]
		1000 100
		1 0.06 0 0 0 0 0 0
		2 0.18 0 0 0 0 0 0
		3 0.3 0 0 0 0 0 0
		4 0.42 0 0 0 0 0 0
		5 0.54 0 0 0 0 0 0
		6 0.66 0 0 0 0 0 0
		7 0.78 0 0 0 0 0 0
		8 0.9 0 0 0 0 0 0
		9 1.02 0 0 0 0 18.9675 2
		10 1.14 0 0 0 0 0 2
		11 1.26 0 0 0 0 0 2
		12 1.38 0 0 0 0 0 2
		13 1.5 0 0 0.00146316 0.000333333 0.0485606 2.01107
		14 1.62 0 0 3.77986 1.00467 0.691259 2.1948
		15 1.74 0 0 0.087001 1.03133 1.5081 2.6572
		16 1.86 0 0 0.261354 1.12287 1.29225 3.10993
		17 1.98 0 0 0.557712 1.3442 0.791284 3.42407
		18 2.1 0 0 0.890071 1.74153 0.441155 3.62107
		19 2.22 0 0 1.18482 2.3326 0.280275 3.76093
		20 2.34 0 0 1.33539 3.07273 0.203573 3.8738
		21 2.46 0.0296137 0.00906667 1.31236 3.8766 0.199433 3.996
		22 2.58 0.910251 0.3156 1.12596 4.6352 0.252635 4.16627
		23 2.7 2.74616 1.3284 0.92755 5.3196 0.399944 4.46147
		24 2.82 2.69277 2.41173 0.776668 5.94473 0.620912 4.9614
		25 2.94 1.69749 3.154 0.715559 6.57073 0.927784 5.77333
		26 3.06 1.12844 3.68853 0.734337 7.26667 1.28373 6.99033
		27 3.18 0.894502 4.14613 0.785685 8.0708 1.53008 8.55687
		28 3.3 0.830879 4.60387 0.853285 9.01127 1.55205 10.2681
		29 3.42 0.837147 5.0992 0.940998 10.1252 1.42789 11.9589
		30 3.54 0.87264 5.6524 1.02352 11.4233 1.30488 13.6145
		31 3.66 0.890146 6.2556 1.10007 12.9147 1.15043 15.1747
		32 3.78 0.923629 6.9232 1.14816 14.5751 1.05067 16.6945
		33 3.9 0.948076 7.65267 1.1789 16.3898 0.995284 18.2271
		34 4.02 1.02003 8.48653 1.14251 18.2584 0.987649 19.843
		35 4.14 1.05003 9.39693 1.09918 20.1651 0.973183 21.5317
		36 4.26 1.0578 10.368 1.05588 22.1043 0.968154 23.3104
		37 4.38 1.08788 11.4237 1.04202 24.1275 0.95294 25.1612
		38 4.5 1.0991 12.5496 1.02603 26.2302 0.948747 27.1062
		39 4.62 1.08758 13.7239 1.0199 28.4333 0.952182 29.1637
		40 4.74 1.08319 14.9549 1.0085 30.7265 0.958425 31.3437
		41 4.86 1.06718 16.23 1.0021 33.1219 0.966773 33.6555
		42 4.98 1.0236 17.5141 0.983127 35.5894 0.975683 36.1051
		43 5.1 0.979245 18.8025 0.968484 38.1387 0.993353 38.7208
		44 5.22 0.967438 20.136 0.960781 40.7882 1.0117 41.5116
		45 5.34 0.9397 21.4915 0.95327 43.5392 1.02048 44.4575
		46 5.46 0.933775 22.8996 0.957903 46.4292 1.02138 47.5401
		47 5.58 0.905728 24.3261 0.96475 49.4692 1.01134 50.7279
		48 5.7 0.908316 25.8189 0.985709 52.7103 1.00699 54.0401
		49 5.82 0.922062 27.3988 0.992001 56.1108 0.993731 57.4477
		50 5.94 0.933444 29.0648 1.00316 59.6929 0.985977 60.9695
		51 6.06 0.967112 30.8613 1.00148 63.4149 0.975667 64.5968
		52 6.18 0.995762 32.7851 1.00378 67.2946 0.966562 68.3339
		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

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