Merge pull request #1310 from akohlmey/reaxc-with-qeq-shielded (cdb07f9f) · Commits · 郑智淋 / lammps

doc/src/fix_qeq.txt

+7 −3

Original line number	Diff line number	Diff line
		@@ -22,7 +22,7 @@ Nevery = perform charge equilibration every this many steps :l
		cutoff = global cutoff for charge-charge interactions (distance unit) :l
		tolerance = precision to which charges will be equilibrated :l
		maxiter = maximum iterations to perform charge equilibration :l
		qfile = a filename with QEq parameters :l
		qfile = a filename with QEq parameters or {coul/streitz} or {reax/c} :l

		zero or more keyword/value pairs may be appended :l
		keyword = {alpha} or {qdamp} or {qstep} :l
		@@ -122,7 +122,9 @@ field"_#vanDuin paper. The shielding accounts for charge overlap
		between charged particles at small separation. This style is the same
		as "fix qeq/reax"_fix_qeq_reax.html, and can be used with "pair_style
		reax/c"_pair_reaxc.html. Only the {chi}, {eta}, and {gamma}
		parameters from the {qfile} file are used. This style solves partial
		parameters from the {qfile} file are used. When using the string
		{reax/c} as filename, these parameters are extracted directly from
		an active {reax/c} pair style. This style solves partial
		charges on atoms via the matrix inversion method. A tolerance of
		1.0e-6 is usually a good number.

		@@ -132,7 +134,9 @@ that the interaction between a pair of charged particles is the
		product of two Slater 1{s} orbitals. The expression for the Slater
		1{s} orbital is given under equation (6) of the
		"Streitz-Mintmire"_#Streitz1 paper. Only the {chi}, {eta}, {zeta}, and
		{qcore} parameters from the {qfile} file are used. This style solves
		{qcore} parameters from the {qfile} file are used. When using the string
		{coul/streitz} as filename, these parameters are extracted directly from
		an active {coul/streitz} pair style. This style solves
		partial charges on atoms via the matrix inversion method. A tolerance
		of 1.0e-6 is usually a good number. Keyword {alpha} can be used to
		change the Slater type orbital exponent.

examples/reax/in.reaxc.rdx-shielded

0 → 100644

+52 −0

Original line number	Diff line number	Diff line
		# ReaxFF potential for RDX system
		# this run is equivalent to reax/in.reax.rdx

		units real

		atom_style charge
		read_data data.rdx

		pair_style reax/c control.reax_c.rdx
		pair_coeff * * ffield.reax C H O N

		compute reax all pair reax/c

		variable eb equal c_reax[1]
		variable ea equal c_reax[2]
		variable elp equal c_reax[3]
		variable emol equal c_reax[4]
		variable ev equal c_reax[5]
		variable epen equal c_reax[6]
		variable ecoa equal c_reax[7]
		variable ehb equal c_reax[8]
		variable et equal c_reax[9]
		variable eco equal c_reax[10]
		variable ew equal c_reax[11]
		variable ep equal c_reax[12]
		variable efi equal c_reax[13]
		variable eqeq equal c_reax[14]

		neighbor 2.5 bin
		neigh_modify every 10 delay 0 check no

		fix 1 all nve
		fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c

		thermo 10
		thermo_style custom step temp epair etotal press &
		v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa &
		v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq

		timestep 1.0

		#dump 1 all atom 10 dump.reaxc.rdx

		#dump 2 all image 25 image.*.jpg type type &
		# axes yes 0.8 0.02 view 60 -30
		#dump_modify 2 pad 3

		#dump 3 all movie 25 movie.mpg type type &
		# axes yes 0.8 0.02 view 60 -30
		#dump_modify 3 pad 3

		run 100

examples/reax/in.reaxc.tatb-shielded

0 → 100644

+55 −0

Original line number	Diff line number	Diff line
		# ReaxFF potential for TATB system
		# this run is equivalent to reax/in.reax.tatb,

		units real

		atom_style charge
		read_data data.tatb

		pair_style reax/c control.reax_c.tatb
		pair_coeff * * ffield.reax C H O N

		compute reax all pair reax/c

		variable eb equal c_reax[1]
		variable ea equal c_reax[2]
		variable elp equal c_reax[3]
		variable emol equal c_reax[4]
		variable ev equal c_reax[5]
		variable epen equal c_reax[6]
		variable ecoa equal c_reax[7]
		variable ehb equal c_reax[8]
		variable et equal c_reax[9]
		variable eco equal c_reax[10]
		variable ew equal c_reax[11]
		variable ep equal c_reax[12]
		variable efi equal c_reax[13]
		variable eqeq equal c_reax[14]

		neighbor 2.5 bin
		neigh_modify delay 0 every 5 check no

		fix 1 all nve
		fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c
		fix 4 all reax/c/bonds 5 bonds.reaxc

		thermo 5
		thermo_style custom step temp epair etotal press &
		v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa &
		v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq

		timestep 0.0625

		#dump 1 all custom 100 dump.reaxc.tatb id type q x y z

		#dump 2 all image 5 image.*.jpg type type &
		# axes yes 0.8 0.02 view 60 -30
		#dump_modify 2 pad 3

		#dump 3 all movie 5 movie.mpg type type &
		# axes yes 0.8 0.02 view 60 -30
		#dump_modify 3 pad 3

		fix 3 all reax/c/species 1 5 5 species.tatb

		run 25

examples/reax/log.4Jan19.reaxc.rdx-shielded.g++.1

0 → 100644

+116 −0

Original line number	Diff line number	Diff line
		LAMMPS (4 Jan 2019)
		# ReaxFF potential for RDX system
		# this run is equivalent to reax/in.reax.rdx

		units real

		atom_style charge
		read_data data.rdx
		orthogonal box = (35 35 35) to (48 48 48)
		1 by 1 by 1 MPI processor grid
		reading atoms ...
		21 atoms

		pair_style reax/c control.reax_c.rdx
		pair_coeff * * ffield.reax C H O N
		Reading potential file ffield.reax with DATE: 2010-02-19

		compute reax all pair reax/c

		variable eb equal c_reax[1]
		variable ea equal c_reax[2]
		variable elp equal c_reax[3]
		variable emol equal c_reax[4]
		variable ev equal c_reax[5]
		variable epen equal c_reax[6]
		variable ecoa equal c_reax[7]
		variable ehb equal c_reax[8]
		variable et equal c_reax[9]
		variable eco equal c_reax[10]
		variable ew equal c_reax[11]
		variable ep equal c_reax[12]
		variable efi equal c_reax[13]
		variable eqeq equal c_reax[14]

		neighbor 2.5 bin
		neigh_modify every 10 delay 0 check no

		fix 1 all nve
		fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c

		thermo 10
		thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq

		timestep 1.0

		#dump 1 all atom 10 dump.reaxc.rdx

		#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
		#dump_modify 2 pad 3

		#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
		#dump_modify 3 pad 3

		run 100
		Neighbor list info ...
		update every 10 steps, delay 0 steps, check no
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 12.5
		ghost atom cutoff = 12.5
		binsize = 6.25, bins = 3 3 3
		2 neighbor lists, perpetual/occasional/extra = 2 0 0
		(1) pair reax/c, perpetual
		attributes: half, newton off, ghost
		pair build: half/bin/newtoff/ghost
		stencil: half/ghost/bin/3d/newtoff
		bin: standard
		(2) fix qeq/shielded, perpetual
		attributes: full, newton on
		pair build: full/bin/atomonly
		stencil: full/bin/3d
		bin: standard
		Per MPI rank memory allocation (min/avg/max) = 15.54 \| 15.54 \| 15.54 Mbytes
		Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
		0 0 -1884.3081 -1884.3081 27186.181 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79939 0 168.88404
		10 1288.6115 -1989.6644 -1912.8422 -19456.353 -2734.6769 -15.60722 0.2017796 0 54.629557 3.1252289 -77.7067 0 14.933901 -5.8108542 843.92073 -180.43321 0 107.75934
		20 538.95832 -1942.7037 -1910.5731 -10725.665 -2803.7395 7.9078296 0.077926657 0 81.61005 0.22951928 -57.5571 0 30.331204 -10.178049 878.99014 -159.69088 0 89.31512
		30 463.09535 -1933.5765 -1905.9685 -33255.521 -2749.8591 -8.0154561 0.027628873 0 81.62739 0.11972409 -50.262289 0 20.820315 -9.6327029 851.88723 -149.49502 0 79.205749
		40 885.49232 -1958.9126 -1906.1229 -4814.704 -2795.644 9.1506683 0.13747502 0 70.947988 0.2436053 -57.862679 0 19.076499 -11.141216 873.73896 -159.99392 0 92.434085
		50 861.16622 -1954.4599 -1903.1204 -1896.7878 -2784.8448 3.8269901 0.15793272 0 79.851828 3.3492155 -78.066128 0 32.628996 -7.9565333 872.81832 -190.98567 0 114.75995
		60 1167.7852 -1971.843 -1902.2241 -3482.6875 -2705.8632 -17.121673 0.22749075 0 44.507672 7.856086 -74.788945 0 16.256491 -4.6046463 835.83056 -188.33693 0 114.19414
		70 1439.997 -1989.3024 -1903.4553 23845.434 -2890.7895 31.958869 0.26671726 0 85.758681 3.1803462 -71.002898 0 24.35711 -10.311314 905.86781 -175.38471 0 106.79648
		80 502.39629 -1930.7545 -1900.8035 -20356.384 -2703.8111 -18.66263 0.11286065 0 99.804114 2.0329076 -76.171338 0 19.23692 -6.2786691 826.47429 -166.03132 0 92.539464
		90 749.08722 -1946.9837 -1902.3259 17798.557 -2863.7579 42.068808 0.24338058 0 96.181716 0.96183793 -69.955449 0 24.615308 -11.58277 903.68837 -190.13841 0 120.6914
		100 1109.6997 -1968.5874 -1902.4313 -4490.2776 -2755.896 -7.1232734 0.21757686 0 61.806176 7.0827207 -75.645383 0 20.114879 -6.2371839 863.56324 -198.56967 0 122.09951
		Loop time of 0.657427 on 1 procs for 100 steps with 21 atoms

		Performance: 13.142 ns/day, 1.826 hours/ns, 152.108 timesteps/s
		99.3% CPU use with 1 MPI tasks x no OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 0.59308 \| 0.59308 \| 0.59308 \| 0.0 \| 90.21
		Neigh \| 0.020665 \| 0.020665 \| 0.020665 \| 0.0 \| 3.14
		Comm \| 0.0015757 \| 0.0015757 \| 0.0015757 \| 0.0 \| 0.24
		Output \| 0.00039387 \| 0.00039387 \| 0.00039387 \| 0.0 \| 0.06
		Modify \| 0.04156 \| 0.04156 \| 0.04156 \| 0.0 \| 6.32
		Other \| \| 0.000154 \| \| \| 0.02

		Nlocal: 21 ave 21 max 21 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 546 ave 546 max 546 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Neighs: 1096 ave 1096 max 1096 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		FullNghs: 1306 ave 1306 max 1306 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 1306
		Ave neighs/atom = 62.1905
		Neighbor list builds = 10
		Dangerous builds not checked

		Please see the log.cite file for references relevant to this simulation

		Total wall time: 0:00:00

examples/reax/log.4Jan19.reaxc.rdx-shielded.g++.4

0 → 100644

+116 −0

Original line number	Diff line number	Diff line
		LAMMPS (4 Jan 2019)
		# ReaxFF potential for RDX system
		# this run is equivalent to reax/in.reax.rdx

		units real

		atom_style charge
		read_data data.rdx
		orthogonal box = (35 35 35) to (48 48 48)
		1 by 2 by 2 MPI processor grid
		reading atoms ...
		21 atoms

		pair_style reax/c control.reax_c.rdx
		pair_coeff * * ffield.reax C H O N
		Reading potential file ffield.reax with DATE: 2010-02-19

		compute reax all pair reax/c

		variable eb equal c_reax[1]
		variable ea equal c_reax[2]
		variable elp equal c_reax[3]
		variable emol equal c_reax[4]
		variable ev equal c_reax[5]
		variable epen equal c_reax[6]
		variable ecoa equal c_reax[7]
		variable ehb equal c_reax[8]
		variable et equal c_reax[9]
		variable eco equal c_reax[10]
		variable ew equal c_reax[11]
		variable ep equal c_reax[12]
		variable efi equal c_reax[13]
		variable eqeq equal c_reax[14]

		neighbor 2.5 bin
		neigh_modify every 10 delay 0 check no

		fix 1 all nve
		fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c

		thermo 10
		thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq

		timestep 1.0

		#dump 1 all atom 10 dump.reaxc.rdx

		#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
		#dump_modify 2 pad 3

		#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
		#dump_modify 3 pad 3

		run 100
		Neighbor list info ...
		update every 10 steps, delay 0 steps, check no
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 12.5
		ghost atom cutoff = 12.5
		binsize = 6.25, bins = 3 3 3
		2 neighbor lists, perpetual/occasional/extra = 2 0 0
		(1) pair reax/c, perpetual
		attributes: half, newton off, ghost
		pair build: half/bin/newtoff/ghost
		stencil: half/ghost/bin/3d/newtoff
		bin: standard
		(2) fix qeq/shielded, perpetual
		attributes: full, newton on
		pair build: full/bin/atomonly
		stencil: full/bin/3d
		bin: standard
		Per MPI rank memory allocation (min/avg/max) = 10.62 \| 12.08 \| 13.84 Mbytes
		Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
		0 0 -1884.3081 -1884.3081 27186.178 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79987 0 168.88452
		10 1288.6116 -1989.6644 -1912.8422 -19456.355 -2734.6769 -15.60722 0.2017796 0 54.629559 3.1252284 -77.7067 0 14.933902 -5.8108544 843.92073 -180.43321 0 107.75934
		20 538.95818 -1942.7037 -1910.5731 -10725.629 -2803.7394 7.9078295 0.077926694 0 81.61005 0.22951941 -57.557106 0 30.331206 -10.178049 878.9901 -159.68969 0 89.313929
		30 463.09529 -1933.5765 -1905.9685 -33255.529 -2749.859 -8.0154758 0.027628845 0 81.627406 0.1197241 -50.26229 0 20.82031 -9.6327013 851.88715 -149.49497 0 79.205706
		40 885.49462 -1958.9125 -1906.1227 -4814.6528 -2795.6439 9.1506212 0.13747486 0 70.94804 0.24360501 -57.862675 0 19.076509 -11.141214 873.7389 -159.99391 0 92.434076
		50 861.16112 -1954.4601 -1903.121 -1896.6704 -2784.8452 3.8270543 0.15793292 0 79.851662 3.3492078 -78.066133 0 32.628979 -7.9565431 872.81857 -190.9857 0 114.75999
		60 1167.7837 -1971.8434 -1902.2245 -3482.8961 -2705.8635 -17.121601 0.22749083 0 44.507696 7.8559922 -74.789025 0 16.256492 -4.6046625 835.83053 -188.33688 0 114.19412
		70 1439.9917 -1989.3024 -1903.4555 23845.887 -2890.7894 31.958677 0.26671714 0 85.758424 3.1804092 -71.002955 0 24.357221 -10.311284 905.86805 -175.38496 0 106.7967
		80 502.39695 -1930.7548 -1900.8039 -20356.331 -2703.8113 -18.662598 0.11286102 0 99.803743 2.0329429 -76.171299 0 19.236922 -6.2786652 826.4744 -166.03139 0 92.539525
		90 749.08478 -1946.984 -1902.3264 17798.605 -2863.7581 42.068587 0.24338052 0 96.181622 0.96184063 -69.955519 0 24.615456 -11.582749 903.68853 -190.13827 0 120.69126
		100 1109.6952 -1968.5879 -1902.4321 -4490.2728 -2755.8985 -7.1225966 0.21757682 0 61.805902 7.0826502 -75.64544 0 20.115369 -6.2372513 863.56451 -198.56956 0 122.09944
		Loop time of 0.634333 on 4 procs for 100 steps with 21 atoms

		Performance: 13.621 ns/day, 1.762 hours/ns, 157.646 timesteps/s
		93.8% CPU use with 4 MPI tasks x no OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 0.53395 \| 0.5352 \| 0.53805 \| 0.2 \| 84.37
		Neigh \| 0.0088253 \| 0.012023 \| 0.016203 \| 2.4 \| 1.90
		Comm \| 0.0051677 \| 0.0081 \| 0.0093861 \| 1.9 \| 1.28
		Output \| 0.00049353 \| 0.00054371 \| 0.00058222 \| 0.0 \| 0.09
		Modify \| 0.074155 \| 0.078299 \| 0.081472 \| 0.9 \| 12.34
		Other \| \| 0.0001715 \| \| \| 0.03

		Nlocal: 5.25 ave 15 max 0 min
		Histogram: 1 0 2 0 0 0 0 0 0 1
		Nghost: 355.5 ave 432 max 282 min
		Histogram: 1 0 0 0 1 1 0 0 0 1
		Neighs: 298.75 ave 822 max 0 min
		Histogram: 1 0 2 0 0 0 0 0 0 1
		FullNghs: 326.5 ave 927 max 0 min
		Histogram: 1 0 2 0 0 0 0 0 0 1

		Total # of neighbors = 1306
		Ave neighs/atom = 62.1905
		Neighbor list builds = 10
		Dangerous builds not checked

		Please see the log.cite file for references relevant to this simulation

		Total wall time: 0:00:00

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