Merge pull request #276 from akohlmey/doc-updates (073e8a05) · Commits · 郑智淋 / lammps

doc/src/info.txt

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		@@ -14,7 +14,7 @@ info args :pre

		args = one or more of the following keywords: {out}, {all}, {system}, {communication}, {computes}, {dumps}, {fixes}, {groups}, {regions}, {variables}, {styles}, {time}, or {configuration}
		{out} values = {screen}, {log}, {append} filename, {overwrite} filename
		{styles} values = {all}, {angle}, {atom}, {bond}, {compute}, {command}, {dump}, {dihedral}, {fix}, {improper}, {integrate}, {kspace}, {minimize}, {region} :ul
		{styles} values = {all}, {angle}, {atom}, {bond}, {compute}, {command}, {dump}, {dihedral}, {fix}, {improper}, {integrate}, {kspace}, {minimize}, {pair}, {region} :ul

		[Examples:]

		@@ -70,8 +70,9 @@ The {variables} category prints a list of all currently defined
		variables, their names, styles, definition and last computed value, if
		available.

		The {styles} category prints the list of styles available in LAMMPS. It
		supports one of the following options to control what is printed out:
		The {styles} category prints the list of styles available in the
		current LAMMPS binary. It supports one of the following options
		to control which category of styles is printed out:

		all
		angle
		@@ -86,6 +87,7 @@ improper
		integrate
		kspace
		minimize
		pair
		region :ul

		The {time} category prints the accumulated CPU and wall time for the

examples/USER/misc/addtorque/in.addtorque

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Original line number	Diff line number	Diff line

		units lj
		lattice fcc 0.8442
		boundary f f f

		region ball sphere 0.0 0.0 0.0 5.0
		region box block -10 10 -10 10 -10 10
		region half block -10 0 -10 10 -10 10

		# add molecule ids so we can use chunk/atom
		fix 0 all property/atom mol ghost yes

		create_box 2 box
		create_atoms 1 region ball

		pair_style lj/cut 4.0
		pair_coeff * * 1.0 1.0
		mass * 1.0
		set group all mol 1

		# label half the sphere with a different type for better visualization
		set region half type 2

		# use a dynamic group (may require a patch to fix addtorque with older versions of LAMMPS)
		group ball dynamic all region ball

		neigh_modify delay 2 every 1 check yes

		minimize 0.0 0.0 1000 10000
		reset_timestep 0

		velocity all create 1.2 12351235

		fix 1 all nve
		fix 2 all wall/reflect xlo EDGE xhi EDGE ylo EDGE yhi EDGE zlo EDGE zhi EDGE

		compute 1 all chunk/atom molecule
		compute 2 ball omega/chunk 1
		compute 3 ball inertia/chunk 1

		# compute rotational kinetic energy: 1/2 * I * omega**2
		variable r_ke_x equal c_2[1][1]c_2[1][1]c_3[1][1]*0.5
		variable r_ke_y equal c_2[1][2]c_2[1][2]c_3[1][2]*0.5
		variable r_ke_z equal c_2[1][3]c_2[1][3]c_3[1][3]*0.5

		# output moments of inertia for x,y,z and angular velocity as well as rotational kinertic energy

		thermo_style custom step ke pe c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z
		thermo 500

		# dump 1 all atom 100 dump.lammpstrj

		# dump 2 all movie 10 ball.mp4 type mass

		# equilibration w/o torque added
		run 1000 post no

		# start spinning the ball. rotation around z should increase and Erot_z should grow
		fix 4 ball addtorque 0.0 0.0 200.0
		run 10000 upto post no

		# continue without adding more torque. rotation continues at fixed speed
		unfix 4
		run 5000

examples/USER/misc/addtorque/log.9Nov16.addtorque.g++.1

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Original line number	Diff line number	Diff line
		LAMMPS (9 Nov 2016)
		OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
		using 1 OpenMP thread(s) per MPI task

		units lj
		lattice fcc 0.8442
		Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
		boundary f f f

		region ball sphere 0.0 0.0 0.0 5.0
		region box block -10 10 -10 10 -10 10
		region half block -10 0 -10 10 -10 10

		# add molecule ids so we can use chunk/atom
		fix 0 all property/atom mol ghost yes

		create_box 2 box
		Created orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
		1 by 1 by 1 MPI processor grid
		create_atoms 1 region ball
		Created 2123 atoms

		pair_style lj/cut 4.0
		pair_coeff * * 1.0 1.0
		mass * 1.0
		set group all mol 1
		2123 settings made for mol

		# label half the sphere with a different type for better visualization
		set region half type 2
		1142 settings made for type

		# use a dynamic group (may require a patch to fix addtorque with older versions of LAMMPS)
		group ball dynamic all region ball
		dynamic group ball defined

		neigh_modify delay 2 every 1 check yes

		minimize 0.0 0.0 1000 10000
		WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
		Neighbor list info ...
		1 neighbor list requests
		update every 1 steps, delay 0 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 4.3
		ghost atom cutoff = 4.3
		binsize = 2.15 -> bins = 16 16 16
		Memory usage per processor = 3.68322 Mbytes
		Step Temp E_pair E_mol TotEng Press
		0 0 -6.2285099 0 -6.2285099 -0.38871568
		1000 0 -7.3616908 0 -7.3616908 -9.1828951e-16
		Loop time of 12.4181 on 1 procs for 1000 steps with 2123 atoms

		100.0% CPU use with 1 MPI tasks x 1 OpenMP threads

		Minimization stats:
		Stopping criterion = max iterations
		Energy initial, next-to-last, final =
		-6.22850993032 -7.36169083402 -7.36169083402
		Force two-norm initial, final = 197.762 3.3539e-12
		Force max component initial, final = 7.88704 1.52475e-13
		Final line search alpha, max atom move = 1 1.52475e-13
		Iterations, force evaluations = 1000 1994

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 12.282 \| 12.282 \| 12.282 \| 0.0 \| 98.91
		Neigh \| 0.06315 \| 0.06315 \| 0.06315 \| 0.0 \| 0.51
		Comm \| 0.000443 \| 0.000443 \| 0.000443 \| 0.0 \| 0.00
		Output \| 2.7e-05 \| 2.7e-05 \| 2.7e-05 \| 0.0 \| 0.00
		Modify \| 0 \| 0 \| 0 \| 0.0 \| 0.00
		Other \| \| 0.07231 \| \| \| 0.58

		Nlocal: 2123 ave 2123 max 2123 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 0 ave 0 max 0 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Neighs: 270799 ave 270799 max 270799 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 270799
		Ave neighs/atom = 127.555
		Neighbor list builds = 11
		Dangerous builds = 0
		reset_timestep 0

		velocity all create 1.2 12351235

		fix 1 all nve
		fix 2 all wall/reflect xlo EDGE xhi EDGE ylo EDGE yhi EDGE zlo EDGE zhi EDGE

		compute 1 all chunk/atom molecule
		compute 2 ball omega/chunk 1
		compute 3 ball inertia/chunk 1

		# compute rotational kinetic energy: 1/2 * I * omega**2
		variable r_ke_x equal c_2[1][1]c_2[1][1]c_3[1][1]*0.5
		variable r_ke_y equal c_2[1][2]c_2[1][2]c_3[1][2]*0.5
		variable r_ke_z equal c_2[1][3]c_2[1][3]c_3[1][3]*0.5

		# output moments of inertia for x,y,z and angular velocity as well as rotational kinertic energy

		thermo_style custom step ke pe c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z
		thermo 500

		# dump 1 all atom 100 dump.lammpstrj

		# dump 2 all movie 10 ball.mp4 type mass

		# equilibration w/o torque added
		run 1000 post no
		WARNING: One or more dynamic groups may not be updated at correct point in timestep (../fix_group.cpp:153)
		Neighbor list info ...
		1 neighbor list requests
		update every 1 steps, delay 2 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 4.3
		ghost atom cutoff = 4.3
		binsize = 2.15 -> bins = 16 16 16
		Memory usage per processor = 2.68359 Mbytes
		Step KinEng PotEng c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z
		0 1.7991521 -7.3616908 51125.265 51125.265 51125.265 0.0034331372 -0.0045852283 0.0091015032 0.30129221 0.53743693 2.117541
		500 0.8882476 -6.43927 52585.112 52205.936 52112.109 0.0033058719 -0.0043753253 0.0089502237 0.2873458 0.49970143 2.0872595
		1000 0.79407357 -6.337372 53754.145 54093.977 53787.624 0.0033214912 -0.0042125031 0.0090171557 0.29651603 0.47995375 2.1867116
		Loop time of 4.26119 on 1 procs for 1000 steps with 2123 atoms

		100.0% CPU use with 1 MPI tasks x 1 OpenMP threads

		# start spinning the ball. rotation around z should increase and Erot_z should grow
		fix 4 ball addtorque 0.0 0.0 200.0
		run 10000 upto post no
		WARNING: One or more dynamic groups may not be updated at correct point in timestep (../fix_group.cpp:153)
		Memory usage per processor = 2.68359 Mbytes
		Step KinEng PotEng c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z
		1000 0.79407357 -6.337372 53754.145 54093.977 53787.624 0.0033214912 -0.0042125031 0.0090171557 0.29651603 0.47995375 2.1867116
		1500 0.68685306 -6.2226287 55026.889 54809.958 55224.858 0.0026096779 -0.0039390202 0.01797948 0.18737807 0.42521238 8.9260406
		2000 0.65370325 -6.1832475 54914.897 55655.542 55405.781 0.0029310978 -0.0040761978 0.025816421 0.23589612 0.46236922 18.463634
		2500 0.69337585 -6.2170462 54604.66 54800.001 54488.865 0.0028821313 -0.0045216915 0.035781895 0.22679174 0.56021203 34.882245
		3000 0.76778067 -6.2850756 53423.198 53620.349 53692.133 0.004088872 -0.004451787 0.044703139 0.44658786 0.53133496 53.64839
		3500 0.79707238 -6.3044974 53055.225 53071.129 52927.537 0.0036751739 -0.0037584362 0.054889715 0.3583059 0.3748372 79.732181
		4000 0.80746429 -6.3010044 53519.853 53643.284 54058.105 0.003813517 -0.0041637733 0.062983015 0.38916725 0.46500703 107.22047
		4500 0.81206394 -6.2884719 53371.354 53883.202 53854.559 0.00385001 -0.003643712 0.072544638 0.39555051 0.35769386 141.71085
		5000 0.81648687 -6.2737414 53776.764 54233.367 53762.425 0.0024484228 -0.0043310965 0.080673643 0.16118978 0.50866551 174.94929
		5500 0.81888245 -6.2572796 53908.22 53502.342 54717.506 0.0037110524 -0.00327586 0.088836946 0.37120958 0.28707375 215.91536
		6000 0.86533749 -6.2804248 53687.533 53571.135 53536.171 0.0025223465 -0.0047753224 0.099646475 0.17078626 0.61081016 265.79156
		6500 0.88029206 -6.2719195 53344.67 53291.068 53298.665 0.003937416 -0.0033910578 0.10778737 0.41350774 0.30640427 309.61504
		7000 0.9066019 -6.2714707 53928.646 53524.142 54003.175 0.0028500736 -0.0039730774 0.11855069 0.21902903 0.4224485 379.4875
		7500 0.94601421 -6.2819912 53534.525 53547.598 53851.344 0.0028610722 -0.0049440438 0.12716472 0.21910969 0.6544472 435.41142
		8000 0.9562253 -6.2626222 53486.577 53033.175 53858.803 0.0025501008 -0.0048075887 0.13526164 0.17391198 0.61287549 492.69254
		8500 0.99679401 -6.2691139 53566.766 53721.523 53831.283 0.0034137155 -0.0039265 0.14392854 0.3121189 0.41412316 557.56894
		9000 1.0371056 -6.2761647 53415.879 53605.078 53985.02 0.0029321914 -0.0046362889 0.1518846 0.2296281 0.57612526 622.6884
		9500 1.0598491 -6.26216 53493.003 53049.859 53699.774 0.0032127038 -0.0050624912 0.16002437 0.27606311 0.67980256 687.56651
		10000 1.1014855 -6.2654945 53418.49 53251.964 53867.56 0.0037330249 -0.0056278017 0.17103133 0.37220602 0.84330216 787.85924
		Loop time of 43.025 on 1 procs for 9000 steps with 2123 atoms

		100.0% CPU use with 1 MPI tasks x 1 OpenMP threads

		# continue without adding more torque. rotation continues at fixed speed
		unfix 4
		run 5000
		WARNING: One or more dynamic groups may not be updated at correct point in timestep (../fix_group.cpp:153)
		Memory usage per processor = 2.68359 Mbytes
		Step KinEng PotEng c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z
		10000 1.1014855 -6.2654945 53418.49 53251.964 53867.56 0.0037330249 -0.0056278017 0.17103133 0.37220602 0.84330216 787.85924
		10500 1.07259 -6.2363698 52825.233 52896.327 55753.551 0.0035928335 -0.0050843805 0.16344484 0.34094601 0.68370948 744.70621
		11000 1.0644214 -6.2282099 52016.795 51950.497 54922.101 0.0047316668 -0.0050149935 0.16196531 0.58229343 0.65328165 720.37919
		11500 1.0887339 -6.2525622 52602.789 52903.594 54461.53 0.0044295697 -0.0046710153 0.16698036 0.51606197 0.57713546 759.26022
		12000 1.0707466 -6.234719 52785.654 52997.192 54943.066 0.0057389353 -0.0030340721 0.16553451 0.86925773 0.2439353 752.76594
		12500 1.0758302 -6.2397291 52375.734 52783.309 55011.986 0.0047029783 -0.0023526884 0.16493895 0.57922337 0.14608158 748.29657
		13000 1.0716957 -6.2354221 52711.183 52788.224 55234.737 0.0034033406 -0.00206283 0.16427569 0.30526962 0.11231401 745.29615
		13500 1.083667 -6.2475953 52698.902 52203.324 55102.881 0.0032012254 -0.0021366488 0.16381832 0.27002507 0.11916109 739.38261
		14000 1.085106 -6.2490655 52767.613 52353.974 55225.438 0.0025647931 -0.0022235227 0.1636534 0.17355699 0.12942041 739.53587
		14500 1.0838261 -6.2477856 52292.343 51995.567 54735.836 0.001794954 -0.0029396951 0.16409339 0.084239299 0.22466783 736.92607
		15000 1.0827419 -6.2468971 51917.584 51388.833 54481.681 0.0017979486 -0.0025793756 0.16196568 0.083914884 0.17094953 714.60575
		Loop time of 22.7848 on 1 procs for 5000 steps with 2123 atoms

		Performance: 94800.138 tau/day, 219.445 timesteps/s
		100.0% CPU use with 1 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 18.891 \| 18.891 \| 18.891 \| 0.0 \| 82.91
		Neigh \| 3.5735 \| 3.5735 \| 3.5735 \| 0.0 \| 15.68
		Comm \| 0.005778 \| 0.005778 \| 0.005778 \| 0.0 \| 0.03
		Output \| 0.001862 \| 0.001862 \| 0.001862 \| 0.0 \| 0.01
		Modify \| 0.27476 \| 0.27476 \| 0.27476 \| 0.0 \| 1.21
		Other \| \| 0.0379 \| \| \| 0.17

		Nlocal: 2123 ave 2123 max 2123 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 0 ave 0 max 0 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Neighs: 242472 ave 242472 max 242472 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 242472
		Ave neighs/atom = 114.212
		Neighbor list builds = 560
		Dangerous builds = 0
		Total wall time: 0:01:22

examples/USER/misc/addtorque/log.9Nov16.addtorque.g++.4

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+202 −0

File added.

Preview size limit exceeded, changes collapsed.

src/USER-MISC/fix_addtorque.cpp

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Original line number	Diff line number	Diff line
		@@ -48,6 +48,7 @@ FixAddTorque::FixAddTorque(LAMMPS lmp, int narg, char *arg) :
		global_freq = 1;
		extscalar = 1;
		extvector = 1;
		dynamic_group_allow = 1;
		respa_level_support = 1;
		ilevel_respa = 0;

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