Merge pull request #2013 from wverestek/master (8f9323a3) · Commits · 郑智淋 / lammps

doc/src/fix_bond_react.rst

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Original line number	Diff line number	Diff line
		@@ -158,7 +158,9 @@ The following comments pertain to each react argument (in other
		words, can be customized for each reaction, or reaction step):

		A check for possible new reaction sites is performed every Nevery
		timesteps.
		timesteps. Nevery can be specified with an equal-style
		:doc:`variable <variable>`, whose value is rounded up to the nearest
		integer.

		Three physical conditions must be met for a reaction to occur. First,
		a bonding atom pair must be identified within the reaction distance
		@@ -171,19 +173,29 @@ modified to match the post-reaction template.
		A bonding atom pair will be identified if several conditions are met.
		First, a pair of atoms I,J within the specified react-group-ID of type
		itype and jtype must be separated by a distance between Rmin and
		Rmax\ . It is possible that multiple bonding atom pairs are
		identified: if the bonding atoms in the pre-reacted template are 1-2
		neighbors, i.e. directly bonded, the farthest bonding atom partner is
		set as its bonding partner; otherwise, the closest potential partner
		is chosen. Then, if both an atom I and atom J have each other as their
		bonding partners, these two atoms are identified as the bonding atom
		pair of the reaction site. Once this unique bonding atom pair is
		identified for each reaction, there could two or more reactions that
		involve a given atom on the same timestep. If this is the case, only
		one such reaction is permitted to occur. This reaction is chosen
		randomly from all potential reactions. This capability allows e.g. for
		different reaction pathways to proceed from identical reaction sites
		with user-specified probabilities.
		Rmax\ . Rmin and Rmax can be specified with equal-style
		:doc:`variables <variable>`. For example, these reaction cutoffs can
		be a function of the reaction conversion using the following commands:

		.. code-block:: LAMMPS

		variable rmax equal 0 # initialize variable before bond/react
		fix myrxn all bond/react react myrxn1 all 1 0 v_rmax mol1 mol2 map_file.txt
		variable rmax equal 3+f_myrxn[1]/100 # arbitrary function of reaction count

		It is possible that multiple bonding atom pairs are identified: if the
		bonding atoms in the pre-reacted template are 1-2 neighbors, i.e.
		directly bonded, the farthest bonding atom partner is set as its
		bonding partner; otherwise, the closest potential partner is chosen.
		Then, if both an atom I and atom J have each other as their bonding
		partners, these two atoms are identified as the bonding atom pair of
		the reaction site. Once this unique bonding atom pair is identified
		for each reaction, there could two or more reactions that involve a
		given atom on the same timestep. If this is the case, only one such
		reaction is permitted to occur. This reaction is chosen randomly from
		all potential reactions. This capability allows e.g. for different
		reaction pathways to proceed from identical reaction sites with
		user-specified probabilities.

		The pre-reacted molecule template is specified by a molecule command.
		This molecule template file contains a sample reaction site and its
		@@ -419,7 +431,8 @@ it occurs:

		The prob keyword can affect whether or not an eligible reaction
		actually occurs. The fraction setting must be a value between 0.0 and
		1.0. A uniform random number between 0.0 and 1.0 is generated and the
		1.0, and can be specified with an equal-style :doc:`variable <variable>`.
		A uniform random number between 0.0 and 1.0 is generated and the
		eligible reaction only occurs if the random number is less than the
		fraction. Up to N reactions are permitted to occur, as optionally
		specified by the max_rxn keyword.
		@@ -489,10 +502,11 @@ local command.

		Restart, fix_modify, output, run start/stop, minimize info:

		Cumulative reaction counts for each reaction are written to :doc:`binary restart files <restart>`. These values are associated with the
		reaction name (react-ID). Additionally, internally-created per-atom
		properties are stored to allow for smooth restarts. None of the
		:doc:`fix_modify <fix_modify>` options are relevant to this fix.
		Cumulative reaction counts for each reaction are written to :doc:`binary restart files <restart>`.
		These values are associated with the reaction name (react-ID).
		Additionally, internally-created per-atom properties are stored to
		allow for smooth restarts. None of the :doc:`fix_modify <fix_modify>`
		options are relevant to this fix.

		This fix computes one statistic for each react argument that it
		stores in a global vector, of length 'number of react arguments', that

examples/USER/reaction/nylon,6-6_melt/large_nylon_melt.data.gz

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examples/USER/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability

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		# two monomer nylon example
		# reaction produces a condensed water molecule

		units real

		boundary p p p

		atom_style full

		kspace_style pppm 1.0e-4

		pair_style lj/class2/coul/long 8.5

		angle_style class2

		bond_style class2

		dihedral_style class2

		improper_style class2

		read_data tiny_nylon.data

		variable runsteps equal 1000
		variable prob1 equal step/v_runsteps*2
		variable prob2 equal (step/v_runsteps)>0.5

		velocity all create 300.0 4928459 dist gaussian

		molecule mol1 rxn1_stp1_unreacted.data_template
		molecule mol2 rxn1_stp1_reacted.data_template
		molecule mol3 rxn1_stp2_unreacted.data_template
		molecule mol4 rxn1_stp2_reacted.data_template

		thermo 50

		# dump 1 all xyz 1 test_vis.xyz

		fix myrxns all bond/react stabilization yes statted_grp .03 &
		react rxn1 all 1 0.0 5.0 mol1 mol2 rxn1_stp1_map prob v_prob1 1234 &
		react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234

		fix 1 statted_grp_REACT nvt temp 300 300 100

		# optionally, you can customize behavior of reacting atoms,
		# by using the internally-created 'bond_react_MASTER_group', like so:
		fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1

		thermo_style custom step temp press density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2]

		# restart 100 restart1 restart2

		run ${runsteps}

		# write_restart restart_longrun
		# write_data restart_longrun.data

examples/USER/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.1

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Original line number	Diff line number	Diff line
		LAMMPS (15 Apr 2020)
		OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
		using 1 OpenMP thread(s) per MPI task
		# two monomer nylon example
		# reaction produces a condensed water molecule

		units real

		boundary p p p

		atom_style full

		kspace_style pppm 1.0e-4

		pair_style lj/class2/coul/long 8.5

		angle_style class2

		bond_style class2

		dihedral_style class2

		improper_style class2

		read_data tiny_nylon.data
		orthogonal box = (-25 -25 -25) to (25 25 25)
		1 by 1 by 1 MPI processor grid
		reading atoms ...
		44 atoms
		reading velocities ...
		44 velocities
		scanning bonds ...
		9 = max bonds/atom
		scanning angles ...
		21 = max angles/atom
		scanning dihedrals ...
		29 = max dihedrals/atom
		scanning impropers ...
		29 = max impropers/atom
		reading bonds ...
		42 bonds
		reading angles ...
		74 angles
		reading dihedrals ...
		100 dihedrals
		reading impropers ...
		44 impropers
		4 = max # of 1-2 neighbors
		6 = max # of 1-3 neighbors
		12 = max # of 1-4 neighbors
		41 = max # of special neighbors
		special bonds CPU = 0.000385045 secs
		read_data CPU = 0.013443 secs

		variable runsteps equal 1000
		variable prob1 equal step/v_runsteps*2
		variable prob2 equal (step/v_runsteps)>0.5

		velocity all create 300.0 4928459 dist gaussian

		molecule mol1 rxn1_stp1_unreacted.data_template
		Read molecule template mol1:
		1 molecules
		18 atoms with max type 8
		16 bonds with max type 14
		25 angles with max type 28
		23 dihedrals with max type 36
		14 impropers with max type 11
		molecule mol2 rxn1_stp1_reacted.data_template
		Read molecule template mol2:
		1 molecules
		18 atoms with max type 9
		17 bonds with max type 13
		31 angles with max type 27
		39 dihedrals with max type 33
		20 impropers with max type 1
		molecule mol3 rxn1_stp2_unreacted.data_template
		Read molecule template mol3:
		1 molecules
		15 atoms with max type 9
		14 bonds with max type 13
		25 angles with max type 27
		30 dihedrals with max type 33
		16 impropers with max type 1
		molecule mol4 rxn1_stp2_reacted.data_template
		Read molecule template mol4:
		1 molecules
		15 atoms with max type 11
		13 bonds with max type 15
		19 angles with max type 29
		16 dihedrals with max type 32
		10 impropers with max type 13

		thermo 50

		# dump 1 all xyz 1 test_vis.xyz

		fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 5.0 mol1 mol2 rxn1_stp1_map prob v_prob1 1234 react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234
		WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (src/USER-REACTION/fix_bond_react.cpp:2051)
		WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (src/USER-REACTION/fix_bond_react.cpp:2051)
		dynamic group bond_react_MASTER_group defined
		dynamic group statted_grp_REACT defined

		fix 1 statted_grp_REACT nvt temp 300 300 100

		# optionally, you can customize behavior of reacting atoms,
		# by using the internally-created 'bond_react_MASTER_group', like so:
		fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1

		thermo_style custom step temp press density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2]

		# restart 100 restart1 restart2

		run ${runsteps}
		run 1000
		PPPM initialization ...
		using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
		G vector (1/distance) = 0.0534597
		grid = 2 2 2
		stencil order = 5
		estimated absolute RMS force accuracy = 0.0402256
		estimated relative force accuracy = 0.000121138
		using double precision FFTW3
		3d grid and FFT values/proc = 343 8
		Neighbor list info ...
		update every 1 steps, delay 10 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 10.5
		ghost atom cutoff = 10.5
		binsize = 5.25, bins = 10 10 10
		2 neighbor lists, perpetual/occasional/extra = 1 1 0
		(1) pair lj/class2/coul/long, perpetual
		attributes: half, newton on
		pair build: half/bin/newton
		stencil: half/bin/3d/newton
		bin: standard
		(2) fix bond/react, occasional, copy from (1)
		attributes: half, newton on
		pair build: copy
		stencil: none
		bin: none
		WARNING: Inconsistent image flags (src/domain.cpp:812)
		Per MPI rank memory allocation (min/avg/max) = 33.78 \| 33.78 \| 33.78 Mbytes
		Step Temp Press Density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2]
		0 300 346.78165 0.0034851739 0 0 0 0
		50 262.63913 -492.10749 0.0034851739 0.1 0 1 0
		100 766.52962 -29.714349 0.0034851739 0.2 0 1 0
		150 503.86837 50.220304 0.0034851739 0.3 0 1 0
		200 456.51295 12.312892 0.0034851739 0.4 0 1 0
		250 391.54928 9.2335844 0.0034851739 0.5 0 1 0
		300 336.6988 -47.193937 0.0034851739 0.6 0 1 0
		350 254.06985 -9.2867898 0.0034851739 0.7 0 1 0
		400 259.41098 -25.657321 0.0034851739 0.8 0 1 0
		450 258.10364 22.5086 0.0034851739 0.9 0 1 0
		500 272.13412 -6.5391448 0.0034851739 1 0 1 0
		550 202.75504 54.658731 0.0034851739 1.1 1 1 1
		600 344.79887 23.798478 0.0034851739 1.2 1 1 1
		650 328.44488 -29.908484 0.0034851739 1.3 1 1 1
		700 280.13593 -8.3223255 0.0034851739 1.4 1 1 1
		750 300.67624 1.0632669 0.0034851739 1.5 1 1 1
		800 376.64234 12.488392 0.0034851739 1.6 1 1 1
		850 321.07642 19.814074 0.0034851739 1.7 1 1 1
		900 332.23751 30.814079 0.0034851739 1.8 1 1 1
		950 311.14029 5.7853136 0.0034851739 1.9 1 1 1
		1000 253.14634 -37.560642 0.0034851739 2 1 1 1
		Loop time of 0.379454 on 1 procs for 1000 steps with 44 atoms

		Performance: 227.696 ns/day, 0.105 hours/ns, 2635.368 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 \| 0.069723 \| 0.069723 \| 0.069723 \| 0.0 \| 18.37
		Bond \| 0.14802 \| 0.14802 \| 0.14802 \| 0.0 \| 39.01
		Kspace \| 0.044252 \| 0.044252 \| 0.044252 \| 0.0 \| 11.66
		Neigh \| 0.072359 \| 0.072359 \| 0.072359 \| 0.0 \| 19.07
		Comm \| 0.0044748 \| 0.0044748 \| 0.0044748 \| 0.0 \| 1.18
		Output \| 0.0022775 \| 0.0022775 \| 0.0022775 \| 0.0 \| 0.60
		Modify \| 0.036509 \| 0.036509 \| 0.036509 \| 0.0 \| 9.62
		Other \| \| 0.00184 \| \| \| 0.48

		Nlocal: 44 ave 44 max 44 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 3 ave 3 max 3 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Neighs: 722 ave 722 max 722 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 722
		Ave neighs/atom = 16.4091
		Ave special neighs/atom = 9.77273
		Neighbor list builds = 1000
		Dangerous builds = 0

		# write_restart restart_longrun
		# write_data restart_longrun.data

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

		Total wall time: 0:00:00

examples/USER/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.4

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+201 −0

Original line number	Diff line number	Diff line
		LAMMPS (15 Apr 2020)
		OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
		using 1 OpenMP thread(s) per MPI task
		# two monomer nylon example
		# reaction produces a condensed water molecule

		units real

		boundary p p p

		atom_style full

		kspace_style pppm 1.0e-4

		pair_style lj/class2/coul/long 8.5

		angle_style class2

		bond_style class2

		dihedral_style class2

		improper_style class2

		read_data tiny_nylon.data
		orthogonal box = (-25 -25 -25) to (25 25 25)
		1 by 2 by 2 MPI processor grid
		reading atoms ...
		44 atoms
		reading velocities ...
		44 velocities
		scanning bonds ...
		9 = max bonds/atom
		scanning angles ...
		21 = max angles/atom
		scanning dihedrals ...
		29 = max dihedrals/atom
		scanning impropers ...
		29 = max impropers/atom
		reading bonds ...
		42 bonds
		reading angles ...
		74 angles
		reading dihedrals ...
		100 dihedrals
		reading impropers ...
		44 impropers
		4 = max # of 1-2 neighbors
		6 = max # of 1-3 neighbors
		12 = max # of 1-4 neighbors
		41 = max # of special neighbors
		special bonds CPU = 0.000431282 secs
		read_data CPU = 0.0129571 secs

		variable runsteps equal 1000
		variable prob1 equal step/v_runsteps*2
		variable prob2 equal (step/v_runsteps)>0.5

		velocity all create 300.0 4928459 dist gaussian

		molecule mol1 rxn1_stp1_unreacted.data_template
		Read molecule template mol1:
		1 molecules
		18 atoms with max type 8
		16 bonds with max type 14
		25 angles with max type 28
		23 dihedrals with max type 36
		14 impropers with max type 11
		molecule mol2 rxn1_stp1_reacted.data_template
		Read molecule template mol2:
		1 molecules
		18 atoms with max type 9
		17 bonds with max type 13
		31 angles with max type 27
		39 dihedrals with max type 33
		20 impropers with max type 1
		molecule mol3 rxn1_stp2_unreacted.data_template
		Read molecule template mol3:
		1 molecules
		15 atoms with max type 9
		14 bonds with max type 13
		25 angles with max type 27
		30 dihedrals with max type 33
		16 impropers with max type 1
		molecule mol4 rxn1_stp2_reacted.data_template
		Read molecule template mol4:
		1 molecules
		15 atoms with max type 11
		13 bonds with max type 15
		19 angles with max type 29
		16 dihedrals with max type 32
		10 impropers with max type 13

		thermo 50

		# dump 1 all xyz 1 test_vis.xyz

		fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 5.0 mol1 mol2 rxn1_stp1_map prob v_prob1 1234 react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234
		WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (src/USER-REACTION/fix_bond_react.cpp:2051)
		WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (src/USER-REACTION/fix_bond_react.cpp:2051)
		dynamic group bond_react_MASTER_group defined
		dynamic group statted_grp_REACT defined

		fix 1 statted_grp_REACT nvt temp 300 300 100

		# optionally, you can customize behavior of reacting atoms,
		# by using the internally-created 'bond_react_MASTER_group', like so:
		fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1

		thermo_style custom step temp press density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2]

		# restart 100 restart1 restart2

		run ${runsteps}
		run 1000
		PPPM initialization ...
		using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
		G vector (1/distance) = 0.0534597
		grid = 2 2 2
		stencil order = 5
		estimated absolute RMS force accuracy = 0.0402256
		estimated relative force accuracy = 0.000121138
		using double precision FFTW3
		3d grid and FFT values/proc = 252 2
		Neighbor list info ...
		update every 1 steps, delay 10 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 10.5
		ghost atom cutoff = 10.5
		binsize = 5.25, bins = 10 10 10
		2 neighbor lists, perpetual/occasional/extra = 1 1 0
		(1) pair lj/class2/coul/long, perpetual
		attributes: half, newton on
		pair build: half/bin/newton
		stencil: half/bin/3d/newton
		bin: standard
		(2) fix bond/react, occasional, copy from (1)
		attributes: half, newton on
		pair build: copy
		stencil: none
		bin: none
		WARNING: Inconsistent image flags (src/domain.cpp:812)
		Per MPI rank memory allocation (min/avg/max) = 33.66 \| 33.88 \| 34.43 Mbytes
		Step Temp Press Density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2]
		0 300 346.78165 0.0034851739 0 0 0 0
		50 266.5092 -90.813802 0.0034851739 0.1 0 1 0
		100 559.41271 -53.23688 0.0034851739 0.2 0 1 0
		150 489.90516 31.555817 0.0034851739 0.3 0 1 0
		200 326.18391 7.7889992 0.0034851739 0.4 0 1 0
		250 339.78203 2.3919541 0.0034851739 0.5 0 1 0
		300 370.90263 -32.01673 0.0034851739 0.6 0 1 0
		350 294.07547 -5.4019813 0.0034851739 0.7 0 1 0
		400 287.76477 12.254133 0.0034851739 0.8 0 1 0
		450 293.36482 66.372956 0.0034851739 0.9 0 1 0
		500 246.84496 26.132317 0.0034851739 1 0 1 0
		550 253.08778 -15.350262 0.0034851739 1.1 1 1 1
		600 358.83641 25.007371 0.0034851739 1.2 1 1 1
		650 320.51492 -32.34823 0.0034851739 1.3 1 1 1
		700 310.87976 -8.2306669 0.0034851739 1.4 1 1 1
		750 307.54142 12.025818 0.0034851739 1.5 1 1 1
		800 272.51724 -22.92823 0.0034851739 1.6 1 1 1
		850 268.66181 10.069534 0.0034851739 1.7 1 1 1
		900 265.5531 -10.471377 0.0034851739 1.8 1 1 1
		950 259.43086 9.4546712 0.0034851739 1.9 1 1 1
		1000 247.14622 20.250308 0.0034851739 2 1 1 1
		Loop time of 0.357762 on 4 procs for 1000 steps with 44 atoms

		Performance: 241.502 ns/day, 0.099 hours/ns, 2795.157 timesteps/s
		99.0% CPU use with 4 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 0.0003917 \| 0.015545 \| 0.033317 \| 11.9 \| 4.35
		Bond \| 0.0010131 \| 0.030153 \| 0.076975 \| 18.2 \| 8.43
		Kspace \| 0.092857 \| 0.1462 \| 0.18688 \| 10.7 \| 40.87
		Neigh \| 0.043786 \| 0.044014 \| 0.044189 \| 0.1 \| 12.30
		Comm \| 0.03636 \| 0.038345 \| 0.040538 \| 0.8 \| 10.72
		Output \| 0.00091578 \| 0.0012541 \| 0.0020923 \| 1.4 \| 0.35
		Modify \| 0.075379 \| 0.080791 \| 0.086052 \| 1.8 \| 22.58
		Other \| \| 0.00146 \| \| \| 0.41

		Nlocal: 11 ave 32 max 0 min
		Histogram: 2 0 1 0 0 0 0 0 0 1
		Nghost: 40 ave 51 max 19 min
		Histogram: 1 0 0 0 0 0 0 1 0 2
		Neighs: 191 ave 529 max 0 min
		Histogram: 2 0 0 0 1 0 0 0 0 1

		Total # of neighbors = 764
		Ave neighs/atom = 17.3636
		Ave special neighs/atom = 9.77273
		Neighbor list builds = 1000
		Dangerous builds = 0

		# write_restart restart_longrun
		# write_data restart_longrun.data

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

		Total wall time: 0:00:00

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