sync with SVN (9a2f7386) · Commits · 郑智淋 / lammps

doc/README

+46 −3

Original line number	Diff line number	Diff line
		Generation of LAMMPS Documentation
		LAMMPS Documentation

		Depending on how you obtained LAMMPS, this directory has 2 or 3
		sub-directories and optionally 2 PDF files:

		src content files for LAMMPS documentation
		html HTML version of the LAMMPS manual (see html/Manual.html)
		tools tools and settings for building the documentation
		Manual.pdf large PDF version of entire manual
		Developer.pdf small PDF with info about how LAMMPS is structured

		If you downloaded LAMMPS as a tarball from the web site, all these
		directories and files should be included.

		If you downloaded LAMMPS from the public SVN or Git repositories, then
		the HTML and PDF files are not included. Instead you need to create
		them, in one of three ways:

		(a) You can "fetch" the current HTML and PDF files from the LAMMPS web
		site. Just type "make fetch". This should create a html_www dir and
		Manual_www.pdf/Developer_www.pdf files. Note that if new LAMMPS
		features have been added more recently than the date of your version,
		the fetched documentation will include those changes (but your source
		code will not, unless you update your local repository).

		(b) You can build the HTML and PDF files yourself, by typing "make
		html" followed by "make pdf". Note that the PDF make requires the
		HTML files already exist. This requires various tools including
		Sphinx, which the build process will attempt to download and install
		on your system, if not already available. See more details below.

		(c) You can genererate an older, simpler, less-fancy style of HTML
		documentation by typing "make old". This will create an "old"
		directory. This can be useful if (b) does not work on your box for
		some reason, or you want to quickly view the HTML version of a doc
		page you have created or edited yourself within the src directory.
		E.g. if you are planning to submit a new feature to LAMMPS.

		----------------

		The generation of all documentation is managed by the Makefile in this
		dir.

		----------------

		Options:

		make html # generate HTML in html dir using Sphinx
		@@ -51,3 +87,10 @@ Once Python 3 is installed, open a Terminal and type
		pip3 install virtualenv

		This will install virtualenv from the Python Package Index.

		----------------

		Installing prerequisites for PDF build

doc/src/Manual.txt

+2 −2

Original line number	Diff line number	Diff line
		<!-- HTML_ONLY -->
		<HEAD>
		<TITLE>LAMMPS Users Manual</TITLE>
		<META NAME="docnumber" CONTENT="26 Sep 2016 version">
		<META NAME="docnumber" CONTENT="27 Sep 2016 version">
		<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
		<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
		</HEAD>
		@@ -21,7 +21,7 @@
		<H1></H1>

		LAMMPS Documentation :c,h3
		26 Sep 2016 version :c,h4
		27 Sep 2016 version :c,h4

		Version info: :h4

doc/src/neb.txt

+8 −8

Original line number	Diff line number	Diff line
		@@ -48,14 +48,14 @@ follows the discussion in these 3 papers: "(HenkelmanA)"_#HenkelmanA,

		Each replica runs on a partition of one or more processors. Processor
		partitions are defined at run-time using the -partition command-line
		switch; see "Section 2.7"_Section_start.html#start_7 of the
		manual. Note that if you have MPI installed, you can run a
		multi-replica simulation with more replicas (partitions) than you have
		physical processors, e.g you can run a 10-replica simulation on just
		one or two processors. You will simply not get the performance
		speed-up you would see with one or more physical processors per
		replica. See "this section"_Section_howto.html#howto_5 of the manual
		for further discussion.
		switch; see "Section 2.7"_Section_start.html#start_7 of the manual.
		Note that if you have MPI installed, you can run a multi-replica
		simulation with more replicas (partitions) than you have physical
		processors, e.g you can run a 10-replica simulation on just one or two
		processors. You will simply not get the performance speed-up you
		would see with one or more physical processors per replica. See
		"Section 6.5"_Section_howto.html#howto_5 of the manual for further
		discussion.

		NOTE: The current NEB implementation in LAMMPS only allows there to be
		one processor per replica.

doc/src/prd.txt

+29 −27

Original line number	Diff line number	Diff line
		@@ -63,14 +63,14 @@ event to occur.

		Each replica runs on a partition of one or more processors. Processor
		partitions are defined at run-time using the -partition command-line
		switch; see "Section 2.7"_Section_start.html#start_7 of the
		manual. Note that if you have MPI installed, you can run a
		multi-replica simulation with more replicas (partitions) than you have
		physical processors, e.g you can run a 10-replica simulation on one or
		two processors. For PRD, this makes little sense, since this offers
		no effective parallel speed-up in searching for infrequent events. See
		"Section 6.5"_Section_howto.html#howto_5 of the manual for further
		discussion.
		switch; see "Section 2.7"_Section_start.html#start_7 of the manual.
		Note that if you have MPI installed, you can run a multi-replica
		simulation with more replicas (partitions) than you have physical
		processors, e.g you can run a 10-replica simulation on one or two
		processors. However for PRD, this makes little sense, since running a
		replica on virtual instead of physical processors,offers no effective
		parallel speed-up in searching for infrequent events. See "Section
		6.5"_Section_howto.html#howto_5 of the manual for further discussion.

		When a PRD simulation is performed, it is assumed that each replica is
		running the same model, though LAMMPS does not check for this.
		@@ -163,7 +163,7 @@ runs for {N} timesteps. If the {time} value is {clock}, then the
		simulation runs until {N} aggregate timesteps across all replicas have
		elapsed. This aggregate time is the "clock" time defined below, which
		typically advances nearly M times faster than the timestepping on a
		single replica.
		single replica, where M is the number of replicas.

		:line

		@@ -183,25 +183,26 @@ coincident events, and the replica number of the chosen event.

		The timestep is the usual LAMMPS timestep, except that time does not
		advance during dephasing or quenches, but only during dynamics. Note
		that are two kinds of dynamics in the PRD loop listed above. The
		first is when all replicas are performing independent dynamics,
		waiting for an event to occur. The second is when correlated events
		are being searched for and only one replica is running dynamics.
		that are two kinds of dynamics in the PRD loop listed above that
		contribute to this timestepping. The first is when all replicas are
		performing independent dynamics, waiting for an event to occur. The
		second is when correlated events are being searched for, but only one
		replica is running dynamics.

		The CPU time is the total processor time since the start of the PRD
		run.
		The CPU time is the total elapsed time on each processor, since the
		start of the PRD run.

		The clock is the same as the timestep except that it advances by M
		steps every timestep during the first kind of dynamics when the M
		steps per timestep during the first kind of dynamics when the M
		replicas are running independently. The clock advances by only 1 step
		per timestep during the second kind of dynamics, since only a single
		per timestep during the second kind of dynamics, when only a single
		replica is checking for a correlated event. Thus "clock" time
		represents the aggregate time (in steps) that effectively elapses
		represents the aggregate time (in steps) that has effectively elapsed
		during a PRD simulation on M replicas. If most of the PRD run is
		spent in the second stage of the loop above, searching for infrequent
		events, then the clock will advance nearly M times faster than it
		would if a single replica was running. Note the clock time between
		events will be drawn from p(t).
		successive events should be drawn from p(t).

		The event number is a counter that increments with each event, whether
		it is uncorrelated or correlated.
		@@ -212,14 +213,15 @@ replicas are running independently. The correlation flag will be 1
		when a correlated event occurs during the third stage of the loop
		listed above, i.e. when only one replica is running dynamics.

		When more than one replica detects an event at the end of the second
		stage, then one of them is chosen at random. The number of coincident
		events is the number of replicas that detected an event. Normally, we
		expect this value to be 1. If it is often greater than 1, then either
		the number of replicas is too large, or {t_event} is too large.
		When more than one replica detects an event at the end of the same
		event check (every {t_event} steps) during the the second stage, then
		one of them is chosen at random. The number of coincident events is
		the number of replicas that detected an event. Normally, this value
		should be 1. If it is often greater than 1, then either the number of
		replicas is too large, or {t_event} is too large.

		The replica number is the ID of the replica (from 0 to M-1) that
		found the event.
		The replica number is the ID of the replica (from 0 to M-1) in which
		the event occurred.

		:line

		@@ -286,7 +288,7 @@ This command can only be used if LAMMPS was built with the REPLICA
		package. See the "Making LAMMPS"_Section_start.html#start_3 section
		for more info on packages.

		{N} and {t_correlate} settings must be integer multiples of
		The {N} and {t_correlate} settings must be integer multiples of
		{t_event}.

		Runs restarted from restart file written during a PRD run will not

examples/balance/log.15Feb16.balance.bond.fast.g++.1

deleted100644 → 0

+0 −225

Original line number	Diff line number	Diff line
		LAMMPS (15 Feb 2016)
		# 2d circle of particles inside a box with LJ walls

		variable b index 0

		variable x index 50
		variable y index 20
		variable d index 20
		variable v index 5
		variable w index 2

		units lj
		dimension 2
		atom_style bond
		boundary f f p

		lattice hex 0.85
		Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
		region box block 0 $x 0 $y -0.5 0.5
		region box block 0 50 0 $y -0.5 0.5
		region box block 0 50 0 20 -0.5 0.5
		create_box 1 box bond/types 1 extra/bond/per/atom 6
		Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
		1 by 1 by 1 MPI processor grid
		region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
		region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
		region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
		region circle sphere 11 6.7735026918962581988 0.0 10
		create_atoms 1 region circle
		Created 361 atoms
		mass 1 1.0

		velocity all create 0.5 87287 loop geom
		velocity all set $v $w 0 sum yes
		velocity all set 5 $w 0 sum yes
		velocity all set 5 2 0 sum yes

		pair_style lj/cut 2.5
		pair_coeff 1 1 10.0 1.0 2.5

		bond_style harmonic
		bond_coeff 1 10.0 1.2

		# need to preserve 1-3, 1-4 pairwise interactions during hard collisions

		special_bonds lj/coul 0 1 1
		0 = max # of 1-2 neighbors
		1 = max # of special neighbors
		create_bonds all all 1 1.0 1.5
		Neighbor list info ...
		2 neighbor list requests
		update every 1 steps, delay 10 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 2.8
		ghost atom cutoff = 2.8
		binsize = 1.4 -> bins = 42 29 1
		Added 1014 bonds, new total = 1014
		6 = max # of 1-2 neighbors
		6 = max # of special neighbors

		neighbor 0.3 bin
		neigh_modify delay 0 every 1 check yes

		fix 1 all nve

		fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
		fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
		fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
		fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5

		comm_style tiled
		comm_modify cutoff 7.5
		fix 10 all balance 50 0.9 rcb

		#compute 1 all property/atom proc
		#variable p atom (c_1%10)+1
		#dump 2 all custom 50 tmp.dump id v_p x y z

		#dump 3 all image 50 image.*.jpg v_p type bond atom 0.25 # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
		#variable colors string # "red green blue yellow white # purple pink orange lime gray"
		#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}

		thermo_style custom step temp epair press f_10[3] f_10
		thermo 100

		run 10000
		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 = 2.8
		ghost atom cutoff = 7.5
		binsize = 1.4 -> bins = 42 29 1
		Memory usage per processor = 4.44301 Mbytes
		Step Temp E_pair Press 10[3] 10
		0 25.701528 -2.2032569 3.1039469 1 1
		100 27.623422 -6.228166 2.6542136 1 1
		200 33.35302 -15.746749 3.2018248 1 1
		300 39.17734 -24.1557 4.9116986 1 1
		400 41.660701 -27.615203 8.6214678 1 1
		500 37.154935 -24.096962 3.2656162 1 1
		600 35.061294 -21.52655 2.3693223 1 1
		700 37.204395 -22.313267 2.7108913 1 1
		800 39.050704 -24.972147 5.5398741 1 1
		900 38.37275 -24.777769 3.9291488 1 1
		1000 39.147816 -26.003699 4.3586203 1 1
		1100 36.084337 -24.88638 4.5496174 1 1
		1200 32.404559 -20.810803 6.0760128 1 1
		1300 32.625538 -19.709411 4.3718289 1 1
		1400 32.246777 -18.785184 3.435959 1 1
		1500 29.174368 -17.434726 2.2702916 1 1
		1600 27.359273 -15.40756 1.033659 1 1
		1700 26.046626 -14.318045 0.87714473 1 1
		1800 24.540401 -13.017686 0.84464169 1 1
		1900 26.259688 -12.777739 0.80954004 1 1
		2000 27.491023 -13.363863 1.4519188 1 1
		2100 27.839831 -13.709118 3.0184763 1 1
		2200 26.669065 -12.710422 1.4560094 1 1
		2300 26.86742 -12.730386 0.16986139 1 1
		2400 26.375504 -12.476682 1.907352 1 1
		2500 26.581263 -12.530908 1.5507765 1 1
		2600 27.67091 -12.922702 2.0391206 1 1
		2700 27.158784 -13.306789 3.7355268 1 1
		2800 25.635671 -13.502047 2.9431633 1 1
		2900 24.648357 -12.388002 0.44910075 1 1
		3000 22.988768 -10.685349 0.37214853 1 1
		3100 21.788719 -10.171928 -0.95734833 1 1
		3200 22.707514 -9.6682633 -0.32868418 1 1
		3300 22.907772 -10.612766 -0.024319089 1 1
		3400 24.276426 -10.802246 0.44731188 1 1
		3500 25.086959 -10.797849 2.3218091 1 1
		3600 26.064365 -12.589537 1.2460738 1 1
		3700 24.656426 -11.956895 0.57862216 1 1
		3800 22.316856 -11.174148 -0.7567936 1 1
		3900 22.590299 -9.5928781 0.4127727 1 1
		4000 22.353461 -9.5887736 -0.34247396 1 1
		4100 24.103395 -9.76584 0.98989862 1 1
		4200 23.92261 -10.566828 -0.71536268 1 1
		4300 24.44409 -11.358378 0.37166197 1 1
		4400 24.772419 -11.324888 0.26732853 1 1
		4500 23.150748 -11.309892 -0.43134573 1 1
		4600 24.008361 -10.212365 0.43277527 1 1
		4700 25.107401 -9.5753673 0.020406689 1 1
		4800 23.658604 -8.9131426 0.46554745 1 1
		4900 22.530251 -9.023311 -0.014405315 1 1
		5000 23.110692 -9.6567397 0.9033234 1 1
		5100 23.760144 -9.7623416 0.32059726 1 1
		5200 25.048012 -9.6748253 0.66411561 1 1
		5300 24.09835 -9.7867216 0.61128267 1 1
		5400 22.984982 -9.9464053 0.28096544 1 1
		5500 22.502003 -9.9294451 -0.53666181 1 1
		5600 23.712298 -10.054318 0.64334761 1 1
		5700 23.350796 -10.217344 2.1979894 1 1
		5800 25.246549 -12.458753 0.055553025 1 1
		5900 24.422272 -10.641177 0.82506839 1 1
		6000 22.478315 -10.629525 -0.774321 1 1
		6100 22.970846 -10.218868 0.59819592 1 1
		6200 24.500063 -10.355481 0.55427078 1 1
		6300 22.358071 -9.9041539 0.89500518 1 1
		6400 23.924951 -11.121442 0.045999129 1 1
		6500 24.83773 -10.464191 2.0048038 1 1
		6600 24.752158 -9.9939162 0.53794465 1 1
		6700 23.073765 -9.3662561 0.38618685 1 1
		6800 21.940219 -8.4948475 -0.25184019 1 1
		6900 22.23783 -8.8668868 0.0072863367 1 1
		7000 25.667836 -10.473211 0.59852886 1 1
		7100 23.352123 -9.0862268 0.85289283 1 1
		7200 24.072107 -9.4020576 0.090222808 1 1
		7300 22.806746 -8.4687857 -0.46892989 1 1
		7400 24.798425 -9.1144357 -0.38738146 1 1
		7500 24.748499 -9.1560558 0.94929896 1 1
		7600 25.364753 -10.176533 0.2649225 1 1
		7700 25.137988 -9.6617897 1.3920543 1 1
		7800 25.502583 -10.320832 0.64812816 1 1
		7900 24.5208 -9.9466543 -0.084071026 1 1
		8000 24.653522 -10.312942 0.32535023 1 1
		8100 23.129565 -9.6250435 0.016356303 1 1
		8200 23.82421 -9.7608023 0.11631418 1 1
		8300 25.081262 -9.3510452 0.92337854 1 1
		8400 24.328205 -9.2875396 0.28266968 1 1
		8500 25.041711 -11.254976 -0.21368615 1 1
		8600 24.111473 -9.0389585 1.2102938 1 1
		8700 23.50066 -9.0926498 0.78819229 1 1
		8800 23.840962 -9.3434474 0.091313007 1 1
		8900 23.081841 -9.0635966 0.56672001 1 1
		9000 24.712103 -9.3243213 0.60301629 1 1
		9100 24.457422 -9.439298 -0.60457515 1 1
		9200 25.070662 -9.1945782 1.2399235 1 1
		9300 25.019869 -8.7910068 0.42340497 1 1
		9400 24.23662 -9.3111098 -0.75379175 1 1
		9500 24.836827 -8.7324281 0.81857501 1 1
		9600 24.901993 -8.6624128 0.84890877 1 1
		9700 24.936686 -8.9869503 1.9627894 1 1
		9800 25.393368 -9.8538595 0.45344428 1 1
		9900 25.942336 -9.7854728 0.68352091 1 1
		10000 24.636319 -9.3369442 0.62793231 1 1
		Loop time of 1.67474 on 1 procs for 10000 steps with 361 atoms

		Performance: 2579511.004 tau/day, 5971.090 timesteps/s
		99.8% CPU use with 1 MPI tasks x no OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 0.47884 \| 0.47884 \| 0.47884 \| 0.0 \| 28.59
		Bond \| 0.24918 \| 0.24918 \| 0.24918 \| 0.0 \| 14.88
		Neigh \| 0.82974 \| 0.82974 \| 0.82974 \| 0.0 \| 49.54
		Comm \| 0.01265 \| 0.01265 \| 0.01265 \| 0.0 \| 0.76
		Output \| 0.00085878 \| 0.00085878 \| 0.00085878 \| 0.0 \| 0.05
		Modify \| 0.075636 \| 0.075636 \| 0.075636 \| 0.0 \| 4.52
		Other \| \| 0.02783 \| \| \| 1.66

		Nlocal: 361 ave 361 max 361 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: 2421 ave 2421 max 2421 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 2421
		Ave neighs/atom = 6.70637
		Ave special neighs/atom = 5.61773
		Neighbor list builds = 4937
		Dangerous builds = 5
		Total wall time: 0:00:01

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