new fix ti/spring command, remove fix ti/rs

Collected small changes and bugfixes

.gitignore

@@ -0,0 +1,34 @@
+*~
+*.o
+*.so
+*.cu_o
+*.ptx
+*_ptx.h
+*.a
+*.d
+*.x
+*.exe
+*.dll
+*.pyc
+__pycache__
+
+Obj_*
+log.lammps
+log.cite
+*.bz2
+*.gz
+*.tar
+.*.swp
+*.orig
+*.rej
+.vagrant
+\#*#
+.#*
+
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db

bench/log.15Feb16.chain.fixed.icc.1

@@ -0,0 +1,78 @@
+LAMMPS (15 Feb 2016)
+# FENE beadspring benchmark
+
+units		lj
+atom_style	bond
+special_bonds   fene
+
+read_data	data.chain
+  orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+  scanning bonds ...
+  1 = max bonds/atom
+  reading bonds ...
+  31680 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of special neighbors
+
+neighbor	0.4 bin
+neigh_modify	every 1 delay 1
+
+bond_style      fene
+bond_coeff	1 30.0 1.5 1.0 1.0
+
+pair_style	lj/cut 1.12
+pair_modify	shift yes
+pair_coeff	1 1 1.0 1.0 1.12
+
+fix		1 all nve
+fix		2 all langevin 1.0 1.0 10.0 904297
+
+thermo          100
+timestep	0.012
+
+run		100
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 1 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.52
+  ghost atom cutoff = 1.52
+  binsize = 0.76 -> bins = 45 45 45
+Memory usage per processor = 11.5189 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0   0.97029772   0.44484087    20.494523    22.394765    4.6721833 
+     100    0.9729966    0.4361122    20.507698     22.40326    4.6548819 
+Loop time of 0.978585 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 105948.895 tau/day, 102.188 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.19562    | 0.19562    | 0.19562    |   0.0 | 19.99
+Bond    | 0.087475   | 0.087475   | 0.087475   |   0.0 |  8.94
+Neigh   | 0.44861    | 0.44861    | 0.44861    |   0.0 | 45.84
+Comm    | 0.032932   | 0.032932   | 0.032932   |   0.0 |  3.37
+Output  | 0.00010395 | 0.00010395 | 0.00010395 |   0.0 |  0.01
+Modify  | 0.19413    | 0.19413    | 0.19413    |   0.0 | 19.84
+Other   |            | 0.01972    |            |       |  2.02
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    9493 ave 9493 max 9493 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    155873 ave 155873 max 155873 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 155873
+Ave neighs/atom = 4.87103
+Ave special neighs/atom = 1.98
+Neighbor list builds = 25
+Dangerous builds = 0
+Total wall time: 0:00:01

bench/log.15Feb16.chain.fixed.icc.4

@@ -0,0 +1,78 @@
+LAMMPS (15 Feb 2016)
+# FENE beadspring benchmark
+
+units		lj
+atom_style	bond
+special_bonds   fene
+
+read_data	data.chain
+  orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+  scanning bonds ...
+  1 = max bonds/atom
+  reading bonds ...
+  31680 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of special neighbors
+
+neighbor	0.4 bin
+neigh_modify	every 1 delay 1
+
+bond_style      fene
+bond_coeff	1 30.0 1.5 1.0 1.0
+
+pair_style	lj/cut 1.12
+pair_modify	shift yes
+pair_coeff	1 1 1.0 1.0 1.12
+
+fix		1 all nve
+fix		2 all langevin 1.0 1.0 10.0 904297
+
+thermo          100
+timestep	0.012
+
+run		100
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 1 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.52
+  ghost atom cutoff = 1.52
+  binsize = 0.76 -> bins = 45 45 45
+Memory usage per processor = 3.91518 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0   0.97029772   0.44484087    20.494523    22.394765    4.6721833 
+     100   0.97145835   0.43803883    20.502691    22.397872     4.626988 
+Loop time of 0.271187 on 4 procs for 100 steps with 32000 atoms
+
+Performance: 382319.453 tau/day, 368.749 timesteps/s
+99.6% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.048621   | 0.050076   | 0.051229   |   0.4 | 18.47
+Bond    | 0.022254   | 0.022942   | 0.023567   |   0.3 |  8.46
+Neigh   | 0.11873    | 0.11881    | 0.11887    |   0.0 | 43.81
+Comm    | 0.019066   | 0.021357   | 0.024297   |   1.3 |  7.88
+Output  | 5.0068e-05 | 5.5015e-05 | 6.1035e-05 |   0.1 |  0.02
+Modify  | 0.048737   | 0.050198   | 0.051231   |   0.4 | 18.51
+Other   |            | 0.007751   |            |       |  2.86
+
+Nlocal:    8000 ave 8030 max 7974 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+Nghost:    4177 ave 4191 max 4160 min
+Histogram: 1 0 0 0 1 0 0 1 0 1
+Neighs:    38995.8 ave 39169 max 38852 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+
+Total # of neighbors = 155983
+Ave neighs/atom = 4.87447
+Ave special neighs/atom = 1.98
+Neighbor list builds = 25
+Dangerous builds = 0
+Total wall time: 0:00:00

bench/log.15Feb16.chain.scaled.icc.4

@@ -0,0 +1,94 @@
+LAMMPS (15 Feb 2016)
+# FENE beadspring benchmark
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+units		lj
+atom_style	bond
+atom_modify	map hash
+special_bonds   fene
+
+read_data	data.chain
+  orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+  scanning bonds ...
+  1 = max bonds/atom
+  reading bonds ...
+  31680 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of special neighbors
+
+replicate	$x $y $z
+replicate	2 $y $z
+replicate	2 2 $z
+replicate	2 2 1
+  orthogonal box = (-16.796 -16.796 -16.796) to (50.388 50.388 16.796)
+  2 by 2 by 1 MPI processor grid
+  128000 atoms
+  126720 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of special neighbors
+
+neighbor	0.4 bin
+neigh_modify	every 1 delay 1
+
+bond_style      fene
+bond_coeff	1 30.0 1.5 1.0 1.0
+
+pair_style	lj/cut 1.12
+pair_modify	shift yes
+pair_coeff	1 1 1.0 1.0 1.12
+
+fix		1 all nve
+fix		2 all langevin 1.0 1.0 10.0 904297
+
+thermo          100
+timestep	0.012
+
+run		100
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 1 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.52
+  ghost atom cutoff = 1.52
+  binsize = 0.76 -> bins = 89 89 45
+Memory usage per processor = 12.8735 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0   0.97027498   0.44484087    20.494523    22.394765    4.6721833 
+     100   0.97682955   0.44239968    20.500229    22.407862    4.6527025 
+Loop time of 1.20889 on 4 procs for 100 steps with 128000 atoms
+
+Performance: 85764.410 tau/day, 82.720 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.21738    | 0.23306    | 0.23926    |   1.9 | 19.28
+Bond    | 0.094536   | 0.10196    | 0.10534    |   1.4 |  8.43
+Neigh   | 0.52311    | 0.52392    | 0.52519    |   0.1 | 43.34
+Comm    | 0.090161   | 0.10022    | 0.12557    |   4.7 |  8.29
+Output  | 0.00012207 | 0.00017327 | 0.00019598 |   0.2 |  0.01
+Modify  | 0.19662    | 0.20262    | 0.20672    |   0.8 | 16.76
+Other   |            | 0.04694    |            |       |  3.88
+
+Nlocal:    32000 ave 32015 max 31983 min
+Histogram: 1 0 1 0 0 0 0 0 1 1
+Nghost:    9492 ave 9522 max 9432 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+Neighs:    155837 ave 156079 max 155506 min
+Histogram: 1 0 0 0 0 1 0 0 1 1
+
+Total # of neighbors = 623349
+Ave neighs/atom = 4.86991
+Ave special neighs/atom = 1.98
+Neighbor list builds = 25
+Dangerous builds = 0
+Total wall time: 0:00:01

bench/log.15Feb16.chute.fixed.icc.1

@@ -0,0 +1,80 @@
+LAMMPS (15 Feb 2016)
+# LAMMPS benchmark of granular flow
+# chute flow of 32000 atoms with frozen base at 26 degrees
+
+units		lj
+atom_style	sphere
+boundary	p p fs
+newton		off
+comm_modify	vel yes
+
+read_data	data.chute
+  orthogonal box = (0 0 0) to (40 20 37.2886)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+
+pair_style	gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
+pair_coeff	* *
+
+neighbor	0.1 bin
+neigh_modify	every 1 delay 0
+
+timestep	0.0001
+
+group		bottom type 2
+912 atoms in group bottom
+group		active subtract all bottom
+31088 atoms in group active
+neigh_modify	exclude group bottom bottom
+
+fix		1 all gravity 1.0 chute 26.0
+fix		2 bottom freeze
+fix		3 active nve/sphere
+
+compute		1 all erotate/sphere
+thermo_style	custom step atoms ke c_1 vol
+thermo_modify	norm no
+thermo		100
+
+run		100
+Neighbor list info ...
+  2 neighbor list requests
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.1
+  ghost atom cutoff = 1.1
+  binsize = 0.55 -> bins = 73 37 68
+Memory usage per processor = 15.567 Mbytes
+Step Atoms KinEng 1 Volume 
+       0    32000    784139.13    1601.1263    29833.783 
+     100    32000    784292.08    1571.0968    29834.707 
+Loop time of 0.550482 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 1569.534 tau/day, 181.659 timesteps/s
+100.1% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.33849    | 0.33849    | 0.33849    |   0.0 | 61.49
+Neigh   | 0.040353   | 0.040353   | 0.040353   |   0.0 |  7.33
+Comm    | 0.018023   | 0.018023   | 0.018023   |   0.0 |  3.27
+Output  | 0.00020385 | 0.00020385 | 0.00020385 |   0.0 |  0.04
+Modify  | 0.13155    | 0.13155    | 0.13155    |   0.0 | 23.90
+Other   |            | 0.02186    |            |       |  3.97
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    5463 ave 5463 max 5463 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    115133 ave 115133 max 115133 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 115133
+Ave neighs/atom = 3.59791
+Neighbor list builds = 2
+Dangerous builds = 0
+Total wall time: 0:00:00

bench/log.15Feb16.chute.fixed.icc.4

@@ -0,0 +1,80 @@
+LAMMPS (15 Feb 2016)
+# LAMMPS benchmark of granular flow
+# chute flow of 32000 atoms with frozen base at 26 degrees
+
+units		lj
+atom_style	sphere
+boundary	p p fs
+newton		off
+comm_modify	vel yes
+
+read_data	data.chute
+  orthogonal box = (0 0 0) to (40 20 37.2886)
+  2 by 1 by 2 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+
+pair_style	gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
+pair_coeff	* *
+
+neighbor	0.1 bin
+neigh_modify	every 1 delay 0
+
+timestep	0.0001
+
+group		bottom type 2
+912 atoms in group bottom
+group		active subtract all bottom
+31088 atoms in group active
+neigh_modify	exclude group bottom bottom
+
+fix		1 all gravity 1.0 chute 26.0
+fix		2 bottom freeze
+fix		3 active nve/sphere
+
+compute		1 all erotate/sphere
+thermo_style	custom step atoms ke c_1 vol
+thermo_modify	norm no
+thermo		100
+
+run		100
+Neighbor list info ...
+  2 neighbor list requests
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.1
+  ghost atom cutoff = 1.1
+  binsize = 0.55 -> bins = 73 37 68
+Memory usage per processor = 6.81783 Mbytes
+Step Atoms KinEng 1 Volume 
+       0    32000    784139.13    1601.1263    29833.783 
+     100    32000    784292.08    1571.0968    29834.707 
+Loop time of 0.13141 on 4 procs for 100 steps with 32000 atoms
+
+Performance: 6574.833 tau/day, 760.976 timesteps/s
+99.3% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.062505   | 0.067      | 0.07152    |   1.5 | 50.99
+Neigh   | 0.010041   | 0.0101     | 0.010178   |   0.1 |  7.69
+Comm    | 0.012347   | 0.012895   | 0.013444   |   0.5 |  9.81
+Output  | 6.3896e-05 | 0.00010294 | 0.00014091 |   0.3 |  0.08
+Modify  | 0.031802   | 0.032348   | 0.032897   |   0.3 | 24.62
+Other   |            | 0.008965   |            |       |  6.82
+
+Nlocal:    8000 ave 8008 max 7992 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:    2439 ave 2450 max 2428 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:    29500.5 ave 30488 max 28513 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 118002
+Ave neighs/atom = 3.68756
+Neighbor list builds = 2
+Dangerous builds = 0
+Total wall time: 0:00:00

bench/log.15Feb16.chute.scaled.icc.4

@@ -0,0 +1,90 @@
+LAMMPS (15 Feb 2016)
+# LAMMPS benchmark of granular flow
+# chute flow of 32000 atoms with frozen base at 26 degrees
+
+variable	x index 1
+variable	y index 1
+
+units		lj
+atom_style	sphere
+boundary	p p fs
+newton		off
+comm_modify	vel yes
+
+read_data	data.chute
+  orthogonal box = (0 0 0) to (40 20 37.2886)
+  2 by 1 by 2 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+
+replicate	$x $y 1
+replicate	2 $y 1
+replicate	2 2 1
+  orthogonal box = (0 0 0) to (80 40 37.2922)
+  2 by 2 by 1 MPI processor grid
+  128000 atoms
+
+pair_style	gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
+pair_coeff	* *
+
+neighbor	0.1 bin
+neigh_modify	every 1 delay 0
+
+timestep	0.0001
+
+group		bottom type 2
+3648 atoms in group bottom
+group		active subtract all bottom
+124352 atoms in group active
+neigh_modify	exclude group bottom bottom
+
+fix		1 all gravity 1.0 chute 26.0
+fix		2 bottom freeze
+fix		3 active nve/sphere
+
+compute		1 all erotate/sphere
+thermo_style	custom step atoms ke c_1 vol
+thermo_modify	norm no
+thermo		100
+
+run		100
+Neighbor list info ...
+  2 neighbor list requests
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.1
+  ghost atom cutoff = 1.1
+  binsize = 0.55 -> bins = 146 73 68
+Memory usage per processor = 15.7007 Mbytes
+Step Atoms KinEng 1 Volume 
+       0   128000    3136556.5    6404.5051    119335.13 
+     100   128000    3137168.3    6284.3873    119338.83 
+Loop time of 0.906913 on 4 procs for 100 steps with 128000 atoms
+
+Performance: 952.683 tau/day, 110.264 timesteps/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.51454    | 0.53094    | 0.55381    |   2.0 | 58.54
+Neigh   | 0.042597   | 0.043726   | 0.045801   |   0.6 |  4.82
+Comm    | 0.063027   | 0.064657   | 0.067367   |   0.7 |  7.13
+Output  | 0.00024891 | 0.00059718 | 0.00086498 |   1.0 |  0.07
+Modify  | 0.16508    | 0.17656    | 0.1925     |   2.6 | 19.47
+Other   |            | 0.09043    |            |       |  9.97
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    5463 ave 5463 max 5463 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    115133 ave 115133 max 115133 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 460532
+Ave neighs/atom = 3.59791
+Neighbor list builds = 2
+Dangerous builds = 0
+Total wall time: 0:00:01

bench/log.15Feb16.eam.fixed.icc.1

@@ -0,0 +1,83 @@
+LAMMPS (15 Feb 2016)
+# bulk Cu lattice
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		metal
+atom_style	atomic
+
+lattice		fcc 3.615
+Lattice spacing in x,y,z = 3.615 3.615 3.615
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (72.3 72.3 72.3)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+
+pair_style	eam
+pair_coeff	1 1 Cu_u3.eam
+Reading potential file Cu_u3.eam with DATE: 2007-06-11
+
+velocity	all create 1600.0 376847 loop geom
+
+neighbor	1.0 bin
+neigh_modify    every 1 delay 5 check yes
+
+fix		1 all nve
+
+timestep	0.005
+thermo		50
+
+run		100
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.95
+  ghost atom cutoff = 5.95
+  binsize = 2.975 -> bins = 25 25 25
+Memory usage per processor = 10.2238 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1600      -113280            0   -106662.09    18703.573 
+      50    781.69049   -109873.35            0   -106640.13    52273.088 
+     100      801.832    -109957.3            0   -106640.77    51322.821 
+Loop time of 5.90097 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 7.321 ns/day, 3.278 hours/ns, 16.946 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 5.2121     | 5.2121     | 5.2121     |   0.0 | 88.33
+Neigh   | 0.58212    | 0.58212    | 0.58212    |   0.0 |  9.86
+Comm    | 0.030392   | 0.030392   | 0.030392   |   0.0 |  0.52
+Output  | 0.00023389 | 0.00023389 | 0.00023389 |   0.0 |  0.00
+Modify  | 0.060871   | 0.060871   | 0.060871   |   0.0 |  1.03
+Other   |            | 0.01527    |            |       |  0.26
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    19909 ave 19909 max 19909 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    1.20778e+06 ave 1.20778e+06 max 1.20778e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1207784
+Ave neighs/atom = 37.7433
+Neighbor list builds = 13
+Dangerous builds = 0
+Total wall time: 0:00:06

bench/log.15Feb16.eam.fixed.icc.4

@@ -0,0 +1,83 @@
+LAMMPS (15 Feb 2016)
+# bulk Cu lattice
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		metal
+atom_style	atomic
+
+lattice		fcc 3.615
+Lattice spacing in x,y,z = 3.615 3.615 3.615
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (72.3 72.3 72.3)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+
+pair_style	eam
+pair_coeff	1 1 Cu_u3.eam
+Reading potential file Cu_u3.eam with DATE: 2007-06-11
+
+velocity	all create 1600.0 376847 loop geom
+
+neighbor	1.0 bin
+neigh_modify    every 1 delay 5 check yes
+
+fix		1 all nve
+
+timestep	0.005
+thermo		50
+
+run		100
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.95
+  ghost atom cutoff = 5.95
+  binsize = 2.975 -> bins = 25 25 25
+Memory usage per processor = 5.09629 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1600      -113280            0   -106662.09    18703.573 
+      50    781.69049   -109873.35            0   -106640.13    52273.088 
+     100      801.832    -109957.3            0   -106640.77    51322.821 
+Loop time of 1.58019 on 4 procs for 100 steps with 32000 atoms
+
+Performance: 27.338 ns/day, 0.878 hours/ns, 63.284 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.3617     | 1.366      | 1.3723     |   0.4 | 86.45
+Neigh   | 0.15123    | 0.15232    | 0.15374    |   0.2 |  9.64
+Comm    | 0.033429   | 0.041275   | 0.047066   |   2.7 |  2.61
+Output  | 0.00011301 | 0.0001573  | 0.000211   |   0.3 |  0.01
+Modify  | 0.014694   | 0.015085   | 0.015421   |   0.2 |  0.95
+Other   |            | 0.005342   |            |       |  0.34
+
+Nlocal:    8000 ave 8008 max 7993 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Nghost:    9130.25 ave 9138 max 9122 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:    301946 ave 302392 max 301360 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+
+Total # of neighbors = 1207784
+Ave neighs/atom = 37.7433
+Neighbor list builds = 13
+Dangerous builds = 0
+Total wall time: 0:00:01

bench/log.15Feb16.eam.scaled.icc.4

@@ -0,0 +1,83 @@
+LAMMPS (15 Feb 2016)
+# bulk Cu lattice
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*2
+variable	yy equal 20*$y
+variable	yy equal 20*2
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		metal
+atom_style	atomic
+
+lattice		fcc 3.615
+Lattice spacing in x,y,z = 3.615 3.615 3.615
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 40 0 ${yy} 0 ${zz}
+region		box block 0 40 0 40 0 ${zz}
+region		box block 0 40 0 40 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (144.6 144.6 72.3)
+  2 by 2 by 1 MPI processor grid
+create_atoms	1 box
+Created 128000 atoms
+
+pair_style	eam
+pair_coeff	1 1 Cu_u3.eam
+Reading potential file Cu_u3.eam with DATE: 2007-06-11
+
+velocity	all create 1600.0 376847 loop geom
+
+neighbor	1.0 bin
+neigh_modify    every 1 delay 5 check yes
+
+fix		1 all nve
+
+timestep	0.005
+thermo		50
+
+run		100
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.95
+  ghost atom cutoff = 5.95
+  binsize = 2.975 -> bins = 49 49 25
+Memory usage per processor = 10.1402 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1600      -453120            0   -426647.73    18704.012 
+      50    779.50001   -439457.02            0   -426560.06    52355.276 
+     100    797.97828   -439764.76            0   -426562.07     51474.74 
+Loop time of 6.46849 on 4 procs for 100 steps with 128000 atoms
+
+Performance: 6.679 ns/day, 3.594 hours/ns, 15.460 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 5.581      | 5.5997     | 5.6265     |   0.8 | 86.57
+Neigh   | 0.65287    | 0.658      | 0.66374    |   0.5 | 10.17
+Comm    | 0.075706   | 0.11015    | 0.13655    |   7.2 |  1.70
+Output  | 0.00026488 | 0.00028312 | 0.00029302 |   0.1 |  0.00
+Modify  | 0.069607   | 0.072407   | 0.074555   |   0.7 |  1.12
+Other   |            | 0.02794    |            |       |  0.43
+
+Nlocal:    32000 ave 32092 max 31914 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+Nghost:    19910 ave 19997 max 19818 min
+Histogram: 1 0 0 0 1 0 1 0 0 1
+Neighs:    1.20728e+06 ave 1.21142e+06 max 1.2036e+06 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+
+Total # of neighbors = 4829126
+Ave neighs/atom = 37.7275
+Neighbor list builds = 14
+Dangerous builds = 0
+Total wall time: 0:00:06

bench/log.15Feb16.lj.fixed.icc.1

@@ -0,0 +1,79 @@
+LAMMPS (15 Feb 2016)
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+run		100
+Neighbor list info ...
+  1 neighbor list requests
+  update every 20 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4 -> bins = 24 24 24
+Memory usage per processor = 8.21387 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.44   -6.7733681            0   -4.6134356   -5.0197073 
+     100    0.7574531   -5.7585055            0   -4.6223613   0.20726105 
+Loop time of 2.26309 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 19088.920 tau/day, 44.187 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.9341     | 1.9341     | 1.9341     |   0.0 | 85.46
+Neigh   | 0.2442     | 0.2442     | 0.2442     |   0.0 | 10.79
+Comm    | 0.024158   | 0.024158   | 0.024158   |   0.0 |  1.07
+Output  | 0.00011611 | 0.00011611 | 0.00011611 |   0.0 |  0.01
+Modify  | 0.053222   | 0.053222   | 0.053222   |   0.0 |  2.35
+Other   |            | 0.007258   |            |       |  0.32
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    19657 ave 19657 max 19657 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    1.20283e+06 ave 1.20283e+06 max 1.20283e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1202833
+Ave neighs/atom = 37.5885
+Neighbor list builds = 5
+Dangerous builds not checked
+Total wall time: 0:00:02

bench/log.15Feb16.lj.fixed.icc.4

@@ -0,0 +1,79 @@
+LAMMPS (15 Feb 2016)
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+run		100
+Neighbor list info ...
+  1 neighbor list requests
+  update every 20 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4 -> bins = 24 24 24
+Memory usage per processor = 4.09506 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.44   -6.7733681            0   -4.6134356   -5.0197073 
+     100    0.7574531   -5.7585055            0   -4.6223613   0.20726105 
+Loop time of 0.640733 on 4 procs for 100 steps with 32000 atoms
+
+Performance: 67422.779 tau/day, 156.071 timesteps/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.49487    | 0.51733    | 0.5322     |   1.9 | 80.74
+Neigh   | 0.061131   | 0.063685   | 0.065433   |   0.6 |  9.94
+Comm    | 0.02457    | 0.042349   | 0.069598   |   8.1 |  6.61
+Output  | 5.9843e-05 | 6.3181e-05 | 6.6996e-05 |   0.0 |  0.01
+Modify  | 0.012961   | 0.013863   | 0.014491   |   0.5 |  2.16
+Other   |            | 0.003448   |            |       |  0.54
+
+Nlocal:    8000 ave 8037 max 7964 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Nghost:    9007.5 ave 9050 max 8968 min
+Histogram: 1 1 0 0 0 0 0 1 0 1
+Neighs:    300708 ave 305113 max 297203 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+
+Total # of neighbors = 1202833
+Ave neighs/atom = 37.5885
+Neighbor list builds = 5
+Dangerous builds not checked
+Total wall time: 0:00:00

bench/log.15Feb16.lj.scaled.icc.4

@@ -0,0 +1,79 @@
+LAMMPS (15 Feb 2016)
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*2
+variable	yy equal 20*$y
+variable	yy equal 20*2
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 40 0 ${yy} 0 ${zz}
+region		box block 0 40 0 40 0 ${zz}
+region		box block 0 40 0 40 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (67.1838 67.1838 33.5919)
+  2 by 2 by 1 MPI processor grid
+create_atoms	1 box
+Created 128000 atoms
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+run		100
+Neighbor list info ...
+  1 neighbor list requests
+  update every 20 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4 -> bins = 48 48 24
+Memory usage per processor = 8.13678 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.44   -6.7733681            0   -4.6133849   -5.0196788 
+     100   0.75841891    -5.759957            0   -4.6223375   0.20008866 
+Loop time of 2.57914 on 4 procs for 100 steps with 128000 atoms
+
+Performance: 16749.768 tau/day, 38.773 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.042      | 2.1092     | 2.1668     |   3.1 | 81.78
+Neigh   | 0.23982    | 0.24551    | 0.25233    |   1.0 |  9.52
+Comm    | 0.067088   | 0.13887    | 0.22681    |  15.7 |  5.38
+Output  | 0.00013185 | 0.00021666 | 0.00027108 |   0.4 |  0.01
+Modify  | 0.060348   | 0.071269   | 0.077063   |   2.5 |  2.76
+Other   |            | 0.01403    |            |       |  0.54
+
+Nlocal:    32000 ave 32060 max 31939 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Nghost:    19630.8 ave 19681 max 19562 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+Neighs:    1.20195e+06 ave 1.20354e+06 max 1.19931e+06 min
+Histogram: 1 0 0 0 0 0 0 2 0 1
+
+Total # of neighbors = 4807797
+Ave neighs/atom = 37.5609
+Neighbor list builds = 5
+Dangerous builds not checked
+Total wall time: 0:00:02

bench/log.15Feb16.rhodo.fixed.icc.1

@@ -0,0 +1,121 @@
+LAMMPS (15 Feb 2016)
+# Rhodopsin model
+
+units           real
+neigh_modify    delay 5 every 1
+
+atom_style      full
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+pair_style      lj/charmm/coul/long 8.0 10.0
+pair_modify     mix arithmetic
+kspace_style    pppm 1e-4
+
+read_data       data.rhodo
+  orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  8 = max angles/atom
+  scanning dihedrals ...
+  18 = max dihedrals/atom
+  scanning impropers ...
+  2 = max impropers/atom
+  reading bonds ...
+  27723 bonds
+  reading angles ...
+  40467 angles
+  reading dihedrals ...
+  56829 dihedrals
+  reading impropers ...
+  1034 impropers
+  4 = max # of 1-2 neighbors
+  12 = max # of 1-3 neighbors
+  24 = max # of 1-4 neighbors
+  26 = max # of special neighbors
+
+fix             1 all shake 0.0001 5 0 m 1.0 a 232
+  1617 = # of size 2 clusters
+  3633 = # of size 3 clusters
+  747 = # of size 4 clusters
+  4233 = # of frozen angles
+fix             2 all npt temp 300.0 300.0 100.0 		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
+
+special_bonds   charmm
+
+thermo          50
+thermo_style    multi
+timestep        2.0
+
+run		100
+PPPM initialization ...
+  G vector (1/distance) = 0.248835
+  grid = 25 32 32
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0355478
+  estimated relative force accuracy = 0.000107051
+  using double precision FFTs
+  3d grid and FFT values/proc = 41070 25600
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6 -> bins = 10 13 13
+Memory usage per processor = 91.7487 Mbytes
+---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
+TotEng   =    -25356.2064 KinEng   =     21444.8313 Temp     =       299.0397 
+PotEng   =    -46801.0377 E_bond   =      2537.9940 E_angle  =     10921.3742 
+E_dihed  =      5211.7865 E_impro  =       213.5116 E_vdwl   =     -2307.8634 
+E_coul   =    207025.8927 E_long   =   -270403.7333 Press    =      -142.6035 
+Volume   =    307995.0335 
+---------------- Step       50 ----- CPU =     17.6362 (sec) ----------------
+TotEng   =    -25330.0828 KinEng   =     21501.0029 Temp     =       299.8230 
+PotEng   =    -46831.0857 E_bond   =      2471.7004 E_angle  =     10836.4975 
+E_dihed  =      5239.6299 E_impro  =       227.1218 E_vdwl   =     -1993.2754 
+E_coul   =    206797.6331 E_long   =   -270410.3930 Press    =       237.6701 
+Volume   =    308031.5639 
+---------------- Step      100 ----- CPU =     35.9089 (sec) ----------------
+TotEng   =    -25290.7593 KinEng   =     21592.0117 Temp     =       301.0920 
+PotEng   =    -46882.7709 E_bond   =      2567.9807 E_angle  =     10781.9408 
+E_dihed  =      5198.7432 E_impro  =       216.7834 E_vdwl   =     -1902.4783 
+E_coul   =    206659.2326 E_long   =   -270404.9733 Press    =         6.9960 
+Volume   =    308133.9888 
+Loop time of 35.9089 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 0.481 ns/day, 49.874 hours/ns, 2.785 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 25.731     | 25.731     | 25.731     |   0.0 | 71.66
+Bond    | 1.2771     | 1.2771     | 1.2771     |   0.0 |  3.56
+Kspace  | 3.2094     | 3.2094     | 3.2094     |   0.0 |  8.94
+Neigh   | 4.4538     | 4.4538     | 4.4538     |   0.0 | 12.40
+Comm    | 0.068507   | 0.068507   | 0.068507   |   0.0 |  0.19
+Output  | 0.00025916 | 0.00025916 | 0.00025916 |   0.0 |  0.00
+Modify  | 1.1417     | 1.1417     | 1.1417     |   0.0 |  3.18
+Other   |            | 0.027      |            |       |  0.08
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    47958 ave 47958 max 47958 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    1.20281e+07 ave 1.20281e+07 max 1.20281e+07 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 12028107
+Ave neighs/atom = 375.878
+Ave special neighs/atom = 7.43187
+Neighbor list builds = 11
+Dangerous builds = 0
+Total wall time: 0:00:37

bench/log.15Feb16.rhodo.fixed.icc.4

@@ -0,0 +1,121 @@
+LAMMPS (15 Feb 2016)
+# Rhodopsin model
+
+units           real
+neigh_modify    delay 5 every 1
+
+atom_style      full
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+pair_style      lj/charmm/coul/long 8.0 10.0
+pair_modify     mix arithmetic
+kspace_style    pppm 1e-4
+
+read_data       data.rhodo
+  orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  8 = max angles/atom
+  scanning dihedrals ...
+  18 = max dihedrals/atom
+  scanning impropers ...
+  2 = max impropers/atom
+  reading bonds ...
+  27723 bonds
+  reading angles ...
+  40467 angles
+  reading dihedrals ...
+  56829 dihedrals
+  reading impropers ...
+  1034 impropers
+  4 = max # of 1-2 neighbors
+  12 = max # of 1-3 neighbors
+  24 = max # of 1-4 neighbors
+  26 = max # of special neighbors
+
+fix             1 all shake 0.0001 5 0 m 1.0 a 232
+  1617 = # of size 2 clusters
+  3633 = # of size 3 clusters
+  747 = # of size 4 clusters
+  4233 = # of frozen angles
+fix             2 all npt temp 300.0 300.0 100.0 		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
+
+special_bonds   charmm
+
+thermo          50
+thermo_style    multi
+timestep        2.0
+
+run		100
+PPPM initialization ...
+  G vector (1/distance) = 0.248835
+  grid = 25 32 32
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0355478
+  estimated relative force accuracy = 0.000107051
+  using double precision FFTs
+  3d grid and FFT values/proc = 13230 6400
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6 -> bins = 10 13 13
+Memory usage per processor = 36.629 Mbytes
+---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
+TotEng   =    -25356.2064 KinEng   =     21444.8313 Temp     =       299.0397 
+PotEng   =    -46801.0377 E_bond   =      2537.9940 E_angle  =     10921.3742 
+E_dihed  =      5211.7865 E_impro  =       213.5116 E_vdwl   =     -2307.8634 
+E_coul   =    207025.8927 E_long   =   -270403.7333 Press    =      -142.6035 
+Volume   =    307995.0335 
+---------------- Step       50 ----- CPU =      4.7461 (sec) ----------------
+TotEng   =    -25330.0828 KinEng   =     21501.0029 Temp     =       299.8230 
+PotEng   =    -46831.0857 E_bond   =      2471.7004 E_angle  =     10836.4975 
+E_dihed  =      5239.6299 E_impro  =       227.1218 E_vdwl   =     -1993.2754 
+E_coul   =    206797.6331 E_long   =   -270410.3930 Press    =       237.6701 
+Volume   =    308031.5639 
+---------------- Step      100 ----- CPU =      9.6332 (sec) ----------------
+TotEng   =    -25290.7591 KinEng   =     21592.0117 Temp     =       301.0920 
+PotEng   =    -46882.7708 E_bond   =      2567.9807 E_angle  =     10781.9408 
+E_dihed  =      5198.7432 E_impro  =       216.7834 E_vdwl   =     -1902.4783 
+E_coul   =    206659.2327 E_long   =   -270404.9733 Press    =         6.9960 
+Volume   =    308133.9888 
+Loop time of 9.63322 on 4 procs for 100 steps with 32000 atoms
+
+Performance: 1.794 ns/day, 13.379 hours/ns, 10.381 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 6.4364     | 6.5993     | 6.7208     |   4.7 | 68.51
+Bond    | 0.30755    | 0.32435    | 0.35704    |   3.4 |  3.37
+Kspace  | 0.92248    | 1.0782     | 1.2597     |  13.0 | 11.19
+Neigh   | 1.1669     | 1.1672     | 1.1675     |   0.0 | 12.12
+Comm    | 0.094674   | 0.098065   | 0.10543    |   1.4 |  1.02
+Output  | 0.00015521 | 0.00016224 | 0.00018215 |   0.1 |  0.00
+Modify  | 0.32982    | 0.34654    | 0.35365    |   1.6 |  3.60
+Other   |            | 0.01943    |            |       |  0.20
+
+Nlocal:    8000 ave 8143 max 7933 min
+Histogram: 1 2 0 0 0 0 0 0 0 1
+Nghost:    22733.5 ave 22769 max 22693 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Neighs:    3.00703e+06 ave 3.0975e+06 max 2.96493e+06 min
+Histogram: 1 2 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 12028107
+Ave neighs/atom = 375.878
+Ave special neighs/atom = 7.43187
+Neighbor list builds = 11
+Dangerous builds = 0
+Total wall time: 0:00:10

bench/log.15Feb16.rhodo.scaled.icc.4

@@ -0,0 +1,142 @@
+LAMMPS (15 Feb 2016)
+# Rhodopsin model
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+units           real
+neigh_modify    delay 5 every 1
+
+atom_style      full
+atom_modify	map hash
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+pair_style      lj/charmm/coul/long 8.0 10.0
+pair_modify     mix arithmetic
+kspace_style    pppm 1e-4
+
+read_data       data.rhodo
+  orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  8 = max angles/atom
+  scanning dihedrals ...
+  18 = max dihedrals/atom
+  scanning impropers ...
+  2 = max impropers/atom
+  reading bonds ...
+  27723 bonds
+  reading angles ...
+  40467 angles
+  reading dihedrals ...
+  56829 dihedrals
+  reading impropers ...
+  1034 impropers
+  4 = max # of 1-2 neighbors
+  12 = max # of 1-3 neighbors
+  24 = max # of 1-4 neighbors
+  26 = max # of special neighbors
+
+replicate	$x $y $z
+replicate	2 $y $z
+replicate	2 2 $z
+replicate	2 2 1
+  orthogonal box = (-27.5 -38.5 -36.3646) to (82.5 115.5 36.3615)
+  2 by 2 by 1 MPI processor grid
+  128000 atoms
+  110892 bonds
+  161868 angles
+  227316 dihedrals
+  4136 impropers
+  4 = max # of 1-2 neighbors
+  12 = max # of 1-3 neighbors
+  24 = max # of 1-4 neighbors
+  26 = max # of special neighbors
+
+fix             1 all shake 0.0001 5 0 m 1.0 a 232
+  6468 = # of size 2 clusters
+  14532 = # of size 3 clusters
+  2988 = # of size 4 clusters
+  16932 = # of frozen angles
+fix             2 all npt temp 300.0 300.0 100.0 		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
+
+special_bonds   charmm
+
+thermo          50
+thermo_style    multi
+timestep        2.0
+
+run		100
+PPPM initialization ...
+  G vector (1/distance) = 0.248593
+  grid = 48 60 36
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0359793
+  estimated relative force accuracy = 0.00010835
+  using double precision FFTs
+  3d grid and FFT values/proc = 41615 25920
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6 -> bins = 19 26 13
+Memory usage per processor = 95.5339 Mbytes
+---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
+TotEng   =   -101425.4887 KinEng   =     85779.3251 Temp     =       299.0304 
+PotEng   =   -187204.8138 E_bond   =     10151.9760 E_angle  =     43685.4968 
+E_dihed  =     20847.1460 E_impro  =       854.0463 E_vdwl   =     -9231.4537 
+E_coul   =    827053.5824 E_long   =  -1080565.6077 Press    =      -142.3092 
+Volume   =   1231980.1340 
+---------------- Step       50 ----- CPU =     18.7806 (sec) ----------------
+TotEng   =   -101320.2677 KinEng   =     86003.4837 Temp     =       299.8118 
+PotEng   =   -187323.7514 E_bond   =      9887.1072 E_angle  =     43346.7922 
+E_dihed  =     20958.7032 E_impro  =       908.4715 E_vdwl   =     -7973.4457 
+E_coul   =    826141.3831 E_long   =  -1080592.7629 Press    =       238.0161 
+Volume   =   1232126.1855 
+---------------- Step      100 ----- CPU =     38.3684 (sec) ----------------
+TotEng   =   -101158.1849 KinEng   =     86355.6149 Temp     =       301.0393 
+PotEng   =   -187513.7998 E_bond   =     10272.0693 E_angle  =     43128.6454 
+E_dihed  =     20793.9759 E_impro  =       867.0826 E_vdwl   =     -7586.7186 
+E_coul   =    825583.7122 E_long   =  -1080572.5667 Press    =        15.2151 
+Volume   =   1232535.8423 
+Loop time of 38.3684 on 4 procs for 100 steps with 128000 atoms
+
+Performance: 0.450 ns/day, 53.289 hours/ns, 2.606 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 26.205     | 26.538     | 26.911     |   5.0 | 69.17
+Bond    | 1.298      | 1.3125     | 1.3277     |   1.0 |  3.42
+Kspace  | 3.7099     | 4.0992     | 4.4422     |  13.3 | 10.68
+Neigh   | 4.6137     | 4.6144     | 4.615      |   0.0 | 12.03
+Comm    | 0.21398    | 0.21992    | 0.22886    |   1.2 |  0.57
+Output  | 0.00030518 | 0.00031543 | 0.00033307 |   0.1 |  0.00
+Modify  | 1.5066     | 1.5232     | 1.5388     |   1.0 |  3.97
+Other   |            | 0.06051    |            |       |  0.16
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    47957 ave 47957 max 47957 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    1.20281e+07 ave 1.20572e+07 max 1.1999e+07 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 48112472
+Ave neighs/atom = 375.879
+Ave special neighs/atom = 7.43187
+Neighbor list builds = 11
+Dangerous builds = 0
+Total wall time: 0:00:39

bench/log.6Oct16.chain.fixed.icc.1

@@ -1,78 +0,0 @@
-LAMMPS (6 Oct 2016)
-# FENE beadspring benchmark
-
-units		lj
-atom_style	bond
-special_bonds   fene
-
-read_data	data.chain
-  orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  32000 atoms
-  reading velocities ...
-  32000 velocities
-  scanning bonds ...
-  1 = max bonds/atom
-  reading bonds ...
-  31680 bonds
-  2 = max # of 1-2 neighbors
-  2 = max # of special neighbors
-
-neighbor	0.4 bin
-neigh_modify	every 1 delay 1
-
-bond_style      fene
-bond_coeff	1 30.0 1.5 1.0 1.0
-
-pair_style	lj/cut 1.12
-pair_modify	shift yes
-pair_coeff	1 1 1.0 1.0 1.12
-
-fix		1 all nve
-fix		2 all langevin 1.0 1.0 10.0 904297
-
-thermo          100
-timestep	0.012
-
-run		100
-Neighbor list info ...
-  1 neighbor list requests
-  update every 1 steps, delay 1 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 1.52
-  ghost atom cutoff = 1.52
-  binsize = 0.76 -> bins = 45 45 45
-Memory usage per processor = 12.0423 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0   0.97029772   0.44484087    20.494523    22.394765    4.6721833 
-     100    0.9729966    0.4361122    20.507698     22.40326    4.6548819 
-Loop time of 0.977647 on 1 procs for 100 steps with 32000 atoms
-
-Performance: 106050.541 tau/day, 102.286 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.19421    | 0.19421    | 0.19421    |   0.0 | 19.86
-Bond    | 0.08741    | 0.08741    | 0.08741    |   0.0 |  8.94
-Neigh   | 0.45791    | 0.45791    | 0.45791    |   0.0 | 46.84
-Comm    | 0.032649   | 0.032649   | 0.032649   |   0.0 |  3.34
-Output  | 0.00012207 | 0.00012207 | 0.00012207 |   0.0 |  0.01
-Modify  | 0.18071    | 0.18071    | 0.18071    |   0.0 | 18.48
-Other   |            | 0.02464    |            |       |  2.52
-
-Nlocal:    32000 ave 32000 max 32000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    9493 ave 9493 max 9493 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    155873 ave 155873 max 155873 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 155873
-Ave neighs/atom = 4.87103
-Ave special neighs/atom = 1.98
-Neighbor list builds = 25
-Dangerous builds = 0
-Total wall time: 0:00:01

bench/log.6Oct16.chain.fixed.icc.4

@@ -1,78 +0,0 @@
-LAMMPS (6 Oct 2016)
-# FENE beadspring benchmark
-
-units		lj
-atom_style	bond
-special_bonds   fene
-
-read_data	data.chain
-  orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
-  1 by 2 by 2 MPI processor grid
-  reading atoms ...
-  32000 atoms
-  reading velocities ...
-  32000 velocities
-  scanning bonds ...
-  1 = max bonds/atom
-  reading bonds ...
-  31680 bonds
-  2 = max # of 1-2 neighbors
-  2 = max # of special neighbors
-
-neighbor	0.4 bin
-neigh_modify	every 1 delay 1
-
-bond_style      fene
-bond_coeff	1 30.0 1.5 1.0 1.0
-
-pair_style	lj/cut 1.12
-pair_modify	shift yes
-pair_coeff	1 1 1.0 1.0 1.12
-
-fix		1 all nve
-fix		2 all langevin 1.0 1.0 10.0 904297
-
-thermo          100
-timestep	0.012
-
-run		100
-Neighbor list info ...
-  1 neighbor list requests
-  update every 1 steps, delay 1 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 1.52
-  ghost atom cutoff = 1.52
-  binsize = 0.76 -> bins = 45 45 45
-Memory usage per processor = 4.14663 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0   0.97029772   0.44484087    20.494523    22.394765    4.6721833 
-     100   0.97145835   0.43803883    20.502691    22.397872     4.626988 
-Loop time of 0.269205 on 4 procs for 100 steps with 32000 atoms
-
-Performance: 385133.446 tau/day, 371.464 timesteps/s
-99.8% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.049383   | 0.049756   | 0.049988   |   0.1 | 18.48
-Bond    | 0.022701   | 0.022813   | 0.022872   |   0.0 |  8.47
-Neigh   | 0.11982    | 0.12002    | 0.12018    |   0.0 | 44.58
-Comm    | 0.020274   | 0.021077   | 0.022348   |   0.5 |  7.83
-Output  | 5.3167e-05 | 5.6148e-05 | 6.3181e-05 |   0.1 |  0.02
-Modify  | 0.046276   | 0.046809   | 0.047016   |   0.1 | 17.39
-Other   |            | 0.008669   |            |       |  3.22
-
-Nlocal:    8000 ave 8030 max 7974 min
-Histogram: 1 0 0 1 0 1 0 0 0 1
-Nghost:    4177 ave 4191 max 4160 min
-Histogram: 1 0 0 0 1 0 0 1 0 1
-Neighs:    38995.8 ave 39169 max 38852 min
-Histogram: 1 0 0 1 1 0 0 0 0 1
-
-Total # of neighbors = 155983
-Ave neighs/atom = 4.87447
-Ave special neighs/atom = 1.98
-Neighbor list builds = 25
-Dangerous builds = 0
-Total wall time: 0:00:00

bench/log.6Oct16.chain.scaled.icc.4

@@ -1,94 +0,0 @@
-LAMMPS (6 Oct 2016)
-# FENE beadspring benchmark
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-units		lj
-atom_style	bond
-atom_modify	map hash
-special_bonds   fene
-
-read_data	data.chain
-  orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
-  1 by 2 by 2 MPI processor grid
-  reading atoms ...
-  32000 atoms
-  reading velocities ...
-  32000 velocities
-  scanning bonds ...
-  1 = max bonds/atom
-  reading bonds ...
-  31680 bonds
-  2 = max # of 1-2 neighbors
-  2 = max # of special neighbors
-
-replicate	$x $y $z
-replicate	2 $y $z
-replicate	2 2 $z
-replicate	2 2 1
-  orthogonal box = (-16.796 -16.796 -16.796) to (50.388 50.388 16.796)
-  2 by 2 by 1 MPI processor grid
-  128000 atoms
-  126720 bonds
-  2 = max # of 1-2 neighbors
-  2 = max # of special neighbors
-
-neighbor	0.4 bin
-neigh_modify	every 1 delay 1
-
-bond_style      fene
-bond_coeff	1 30.0 1.5 1.0 1.0
-
-pair_style	lj/cut 1.12
-pair_modify	shift yes
-pair_coeff	1 1 1.0 1.0 1.12
-
-fix		1 all nve
-fix		2 all langevin 1.0 1.0 10.0 904297
-
-thermo          100
-timestep	0.012
-
-run		100
-Neighbor list info ...
-  1 neighbor list requests
-  update every 1 steps, delay 1 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 1.52
-  ghost atom cutoff = 1.52
-  binsize = 0.76 -> bins = 89 89 45
-Memory usage per processor = 13.2993 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0   0.97027498   0.44484087    20.494523    22.394765    4.6721833 
-     100   0.97682955   0.44239968    20.500229    22.407862    4.6527025 
-Loop time of 1.14845 on 4 procs for 100 steps with 128000 atoms
-
-Performance: 90277.919 tau/day, 87.074 timesteps/s
-99.9% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.2203     | 0.22207    | 0.22386    |   0.3 | 19.34
-Bond    | 0.094861   | 0.095302   | 0.095988   |   0.1 |  8.30
-Neigh   | 0.52127    | 0.5216     | 0.52189    |   0.0 | 45.42
-Comm    | 0.079585   | 0.082159   | 0.084366   |   0.7 |  7.15
-Output  | 0.00013304 | 0.00015306 | 0.00018501 |   0.2 |  0.01
-Modify  | 0.18351    | 0.18419    | 0.1856     |   0.2 | 16.04
-Other   |            | 0.04298    |            |       |  3.74
-
-Nlocal:    32000 ave 32015 max 31983 min
-Histogram: 1 0 1 0 0 0 0 0 1 1
-Nghost:    9492 ave 9522 max 9432 min
-Histogram: 1 0 0 0 0 0 1 0 0 2
-Neighs:    155837 ave 156079 max 155506 min
-Histogram: 1 0 0 0 0 1 0 0 1 1
-
-Total # of neighbors = 623349
-Ave neighs/atom = 4.86991
-Ave special neighs/atom = 1.98
-Neighbor list builds = 25
-Dangerous builds = 0
-Total wall time: 0:00:01

bench/log.6Oct16.chute.fixed.icc.1

@@ -1,80 +0,0 @@
-LAMMPS (6 Oct 2016)
-# LAMMPS benchmark of granular flow
-# chute flow of 32000 atoms with frozen base at 26 degrees
-
-units		lj
-atom_style	sphere
-boundary	p p fs
-newton		off
-comm_modify	vel yes
-
-read_data	data.chute
-  orthogonal box = (0 0 0) to (40 20 37.2886)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  32000 atoms
-  reading velocities ...
-  32000 velocities
-
-pair_style	gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
-pair_coeff	* *
-
-neighbor	0.1 bin
-neigh_modify	every 1 delay 0
-
-timestep	0.0001
-
-group		bottom type 2
-912 atoms in group bottom
-group		active subtract all bottom
-31088 atoms in group active
-neigh_modify	exclude group bottom bottom
-
-fix		1 all gravity 1.0 chute 26.0
-fix		2 bottom freeze
-fix		3 active nve/sphere
-
-compute		1 all erotate/sphere
-thermo_style	custom step atoms ke c_1 vol
-thermo_modify	norm no
-thermo		100
-
-run		100
-Neighbor list info ...
-  2 neighbor list requests
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 1.1
-  ghost atom cutoff = 1.1
-  binsize = 0.55 -> bins = 73 37 68
-Memory usage per processor = 16.0904 Mbytes
-Step Atoms KinEng c_1 Volume 
-       0    32000    784139.13    1601.1263    29833.783 
-     100    32000    784292.08    1571.0968    29834.707 
-Loop time of 0.534174 on 1 procs for 100 steps with 32000 atoms
-
-Performance: 1617.451 tau/day, 187.205 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    | 0.33346    | 0.33346    | 0.33346    |   0.0 | 62.43
-Neigh   | 0.043902   | 0.043902   | 0.043902   |   0.0 |  8.22
-Comm    | 0.018391   | 0.018391   | 0.018391   |   0.0 |  3.44
-Output  | 0.00022411 | 0.00022411 | 0.00022411 |   0.0 |  0.04
-Modify  | 0.11666    | 0.11666    | 0.11666    |   0.0 | 21.84
-Other   |            | 0.02153    |            |       |  4.03
-
-Nlocal:    32000 ave 32000 max 32000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    5463 ave 5463 max 5463 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    115133 ave 115133 max 115133 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 115133
-Ave neighs/atom = 3.59791
-Neighbor list builds = 2
-Dangerous builds = 0
-Total wall time: 0:00:00

bench/log.6Oct16.chute.fixed.icc.4

@@ -1,80 +0,0 @@
-LAMMPS (6 Oct 2016)
-# LAMMPS benchmark of granular flow
-# chute flow of 32000 atoms with frozen base at 26 degrees
-
-units		lj
-atom_style	sphere
-boundary	p p fs
-newton		off
-comm_modify	vel yes
-
-read_data	data.chute
-  orthogonal box = (0 0 0) to (40 20 37.2886)
-  2 by 1 by 2 MPI processor grid
-  reading atoms ...
-  32000 atoms
-  reading velocities ...
-  32000 velocities
-
-pair_style	gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
-pair_coeff	* *
-
-neighbor	0.1 bin
-neigh_modify	every 1 delay 0
-
-timestep	0.0001
-
-group		bottom type 2
-912 atoms in group bottom
-group		active subtract all bottom
-31088 atoms in group active
-neigh_modify	exclude group bottom bottom
-
-fix		1 all gravity 1.0 chute 26.0
-fix		2 bottom freeze
-fix		3 active nve/sphere
-
-compute		1 all erotate/sphere
-thermo_style	custom step atoms ke c_1 vol
-thermo_modify	norm no
-thermo		100
-
-run		100
-Neighbor list info ...
-  2 neighbor list requests
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 1.1
-  ghost atom cutoff = 1.1
-  binsize = 0.55 -> bins = 73 37 68
-Memory usage per processor = 7.04927 Mbytes
-Step Atoms KinEng c_1 Volume 
-       0    32000    784139.13    1601.1263    29833.783 
-     100    32000    784292.08    1571.0968    29834.707 
-Loop time of 0.171815 on 4 procs for 100 steps with 32000 atoms
-
-Performance: 5028.653 tau/day, 582.020 timesteps/s
-99.7% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.093691   | 0.096898   | 0.10005    |   0.8 | 56.40
-Neigh   | 0.011976   | 0.012059   | 0.012146   |   0.1 |  7.02
-Comm    | 0.016384   | 0.017418   | 0.018465   |   0.8 | 10.14
-Output  | 7.7963e-05 | 0.00010747 | 0.00013304 |   0.2 |  0.06
-Modify  | 0.031744   | 0.031943   | 0.032167   |   0.1 | 18.59
-Other   |            | 0.01339    |            |       |  7.79
-
-Nlocal:    8000 ave 8008 max 7992 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost:    2439 ave 2450 max 2428 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Neighs:    29500.5 ave 30488 max 28513 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 118002
-Ave neighs/atom = 3.68756
-Neighbor list builds = 2
-Dangerous builds = 0
-Total wall time: 0:00:00

bench/log.6Oct16.chute.scaled.icc.4

@@ -1,90 +0,0 @@
-LAMMPS (6 Oct 2016)
-# LAMMPS benchmark of granular flow
-# chute flow of 32000 atoms with frozen base at 26 degrees
-
-variable	x index 1
-variable	y index 1
-
-units		lj
-atom_style	sphere
-boundary	p p fs
-newton		off
-comm_modify	vel yes
-
-read_data	data.chute
-  orthogonal box = (0 0 0) to (40 20 37.2886)
-  2 by 1 by 2 MPI processor grid
-  reading atoms ...
-  32000 atoms
-  reading velocities ...
-  32000 velocities
-
-replicate	$x $y 1
-replicate	2 $y 1
-replicate	2 2 1
-  orthogonal box = (0 0 0) to (80 40 37.2922)
-  2 by 2 by 1 MPI processor grid
-  128000 atoms
-
-pair_style	gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
-pair_coeff	* *
-
-neighbor	0.1 bin
-neigh_modify	every 1 delay 0
-
-timestep	0.0001
-
-group		bottom type 2
-3648 atoms in group bottom
-group		active subtract all bottom
-124352 atoms in group active
-neigh_modify	exclude group bottom bottom
-
-fix		1 all gravity 1.0 chute 26.0
-fix		2 bottom freeze
-fix		3 active nve/sphere
-
-compute		1 all erotate/sphere
-thermo_style	custom step atoms ke c_1 vol
-thermo_modify	norm no
-thermo		100
-
-run		100
-Neighbor list info ...
-  2 neighbor list requests
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 1.1
-  ghost atom cutoff = 1.1
-  binsize = 0.55 -> bins = 146 73 68
-Memory usage per processor = 16.1265 Mbytes
-Step Atoms KinEng c_1 Volume 
-       0   128000    3136556.5    6404.5051    119335.13 
-     100   128000    3137168.3    6284.3873    119338.83 
-Loop time of 0.832365 on 4 procs for 100 steps with 128000 atoms
-
-Performance: 1038.006 tau/day, 120.140 timesteps/s
-99.8% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.5178     | 0.52208    | 0.52793    |   0.5 | 62.72
-Neigh   | 0.047003   | 0.047113   | 0.047224   |   0.0 |  5.66
-Comm    | 0.05233    | 0.052988   | 0.053722   |   0.2 |  6.37
-Output  | 0.00024986 | 0.00032717 | 0.00036693 |   0.3 |  0.04
-Modify  | 0.15517    | 0.15627    | 0.15808    |   0.3 | 18.77
-Other   |            | 0.0536     |            |       |  6.44
-
-Nlocal:    32000 ave 32000 max 32000 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-Nghost:    5463 ave 5463 max 5463 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-Neighs:    115133 ave 115133 max 115133 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 460532
-Ave neighs/atom = 3.59791
-Neighbor list builds = 2
-Dangerous builds = 0
-Total wall time: 0:00:00

bench/log.6Oct16.eam.fixed.icc.1

@@ -1,83 +0,0 @@
-LAMMPS (6 Oct 2016)
-# bulk Cu lattice
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-variable	xx equal 20*$x
-variable	xx equal 20*1
-variable	yy equal 20*$y
-variable	yy equal 20*1
-variable	zz equal 20*$z
-variable	zz equal 20*1
-
-units		metal
-atom_style	atomic
-
-lattice		fcc 3.615
-Lattice spacing in x,y,z = 3.615 3.615 3.615
-region		box block 0 ${xx} 0 ${yy} 0 ${zz}
-region		box block 0 20 0 ${yy} 0 ${zz}
-region		box block 0 20 0 20 0 ${zz}
-region		box block 0 20 0 20 0 20
-create_box	1 box
-Created orthogonal box = (0 0 0) to (72.3 72.3 72.3)
-  1 by 1 by 1 MPI processor grid
-create_atoms	1 box
-Created 32000 atoms
-
-pair_style	eam
-pair_coeff	1 1 Cu_u3.eam
-Reading potential file Cu_u3.eam with DATE: 2007-06-11
-
-velocity	all create 1600.0 376847 loop geom
-
-neighbor	1.0 bin
-neigh_modify    every 1 delay 5 check yes
-
-fix		1 all nve
-
-timestep	0.005
-thermo		50
-
-run		100
-Neighbor list info ...
-  1 neighbor list requests
-  update every 1 steps, delay 5 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 5.95
-  ghost atom cutoff = 5.95
-  binsize = 2.975 -> bins = 25 25 25
-Memory usage per processor = 11.2238 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         1600      -113280            0   -106662.09    18703.573 
-      50    781.69049   -109873.35            0   -106640.13    52273.088 
-     100      801.832    -109957.3            0   -106640.77    51322.821 
-Loop time of 5.96529 on 1 procs for 100 steps with 32000 atoms
-
-Performance: 7.242 ns/day, 3.314 hours/ns, 16.764 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 5.2743     | 5.2743     | 5.2743     |   0.0 | 88.42
-Neigh   | 0.59212    | 0.59212    | 0.59212    |   0.0 |  9.93
-Comm    | 0.030399   | 0.030399   | 0.030399   |   0.0 |  0.51
-Output  | 0.00026202 | 0.00026202 | 0.00026202 |   0.0 |  0.00
-Modify  | 0.050487   | 0.050487   | 0.050487   |   0.0 |  0.85
-Other   |            | 0.01776    |            |       |  0.30
-
-Nlocal:    32000 ave 32000 max 32000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    19909 ave 19909 max 19909 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    1.20778e+06 ave 1.20778e+06 max 1.20778e+06 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 1207784
-Ave neighs/atom = 37.7433
-Neighbor list builds = 13
-Dangerous builds = 0
-Total wall time: 0:00:06

bench/log.6Oct16.eam.fixed.icc.4

@@ -1,83 +0,0 @@
-LAMMPS (6 Oct 2016)
-# bulk Cu lattice
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-variable	xx equal 20*$x
-variable	xx equal 20*1
-variable	yy equal 20*$y
-variable	yy equal 20*1
-variable	zz equal 20*$z
-variable	zz equal 20*1
-
-units		metal
-atom_style	atomic
-
-lattice		fcc 3.615
-Lattice spacing in x,y,z = 3.615 3.615 3.615
-region		box block 0 ${xx} 0 ${yy} 0 ${zz}
-region		box block 0 20 0 ${yy} 0 ${zz}
-region		box block 0 20 0 20 0 ${zz}
-region		box block 0 20 0 20 0 20
-create_box	1 box
-Created orthogonal box = (0 0 0) to (72.3 72.3 72.3)
-  1 by 2 by 2 MPI processor grid
-create_atoms	1 box
-Created 32000 atoms
-
-pair_style	eam
-pair_coeff	1 1 Cu_u3.eam
-Reading potential file Cu_u3.eam with DATE: 2007-06-11
-
-velocity	all create 1600.0 376847 loop geom
-
-neighbor	1.0 bin
-neigh_modify    every 1 delay 5 check yes
-
-fix		1 all nve
-
-timestep	0.005
-thermo		50
-
-run		100
-Neighbor list info ...
-  1 neighbor list requests
-  update every 1 steps, delay 5 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 5.95
-  ghost atom cutoff = 5.95
-  binsize = 2.975 -> bins = 25 25 25
-Memory usage per processor = 5.59629 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         1600      -113280            0   -106662.09    18703.573 
-      50    781.69049   -109873.35            0   -106640.13    52273.088 
-     100      801.832    -109957.3            0   -106640.77    51322.821 
-Loop time of 1.64562 on 4 procs for 100 steps with 32000 atoms
-
-Performance: 26.252 ns/day, 0.914 hours/ns, 60.767 timesteps/s
-99.8% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.408      | 1.4175     | 1.4341     |   0.9 | 86.14
-Neigh   | 0.15512    | 0.15722    | 0.16112    |   0.6 |  9.55
-Comm    | 0.029105   | 0.049986   | 0.061822   |   5.8 |  3.04
-Output  | 0.00010991 | 0.00011539 | 0.00012302 |   0.0 |  0.01
-Modify  | 0.013383   | 0.013573   | 0.013883   |   0.2 |  0.82
-Other   |            | 0.007264   |            |       |  0.44
-
-Nlocal:    8000 ave 8008 max 7993 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-Nghost:    9130.25 ave 9138 max 9122 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Neighs:    301946 ave 302392 max 301360 min
-Histogram: 1 0 0 0 1 0 0 0 1 1
-
-Total # of neighbors = 1207784
-Ave neighs/atom = 37.7433
-Neighbor list builds = 13
-Dangerous builds = 0
-Total wall time: 0:00:01

bench/log.6Oct16.eam.scaled.icc.4

@@ -1,83 +0,0 @@
-LAMMPS (6 Oct 2016)
-# bulk Cu lattice
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-variable	xx equal 20*$x
-variable	xx equal 20*2
-variable	yy equal 20*$y
-variable	yy equal 20*2
-variable	zz equal 20*$z
-variable	zz equal 20*1
-
-units		metal
-atom_style	atomic
-
-lattice		fcc 3.615
-Lattice spacing in x,y,z = 3.615 3.615 3.615
-region		box block 0 ${xx} 0 ${yy} 0 ${zz}
-region		box block 0 40 0 ${yy} 0 ${zz}
-region		box block 0 40 0 40 0 ${zz}
-region		box block 0 40 0 40 0 20
-create_box	1 box
-Created orthogonal box = (0 0 0) to (144.6 144.6 72.3)
-  2 by 2 by 1 MPI processor grid
-create_atoms	1 box
-Created 128000 atoms
-
-pair_style	eam
-pair_coeff	1 1 Cu_u3.eam
-Reading potential file Cu_u3.eam with DATE: 2007-06-11
-
-velocity	all create 1600.0 376847 loop geom
-
-neighbor	1.0 bin
-neigh_modify    every 1 delay 5 check yes
-
-fix		1 all nve
-
-timestep	0.005
-thermo		50
-
-run		100
-Neighbor list info ...
-  1 neighbor list requests
-  update every 1 steps, delay 5 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 5.95
-  ghost atom cutoff = 5.95
-  binsize = 2.975 -> bins = 49 49 25
-Memory usage per processor = 11.1402 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         1600      -453120            0   -426647.73    18704.012 
-      50    779.50001   -439457.02            0   -426560.06    52355.276 
-     100    797.97828   -439764.76            0   -426562.07     51474.74 
-Loop time of 6.60121 on 4 procs for 100 steps with 128000 atoms
-
-Performance: 6.544 ns/day, 3.667 hours/ns, 15.149 timesteps/s
-99.9% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 5.6676     | 5.7011     | 5.7469     |   1.3 | 86.36
-Neigh   | 0.66423    | 0.67119    | 0.68082    |   0.7 | 10.17
-Comm    | 0.079367   | 0.13668    | 0.1791     |  10.5 |  2.07
-Output  | 0.00026989 | 0.00028622 | 0.00031209 |   0.1 |  0.00
-Modify  | 0.060046   | 0.062203   | 0.065009   |   0.9 |  0.94
-Other   |            | 0.02974    |            |       |  0.45
-
-Nlocal:    32000 ave 32092 max 31914 min
-Histogram: 1 0 0 1 0 1 0 0 0 1
-Nghost:    19910 ave 19997 max 19818 min
-Histogram: 1 0 0 0 1 0 1 0 0 1
-Neighs:    1.20728e+06 ave 1.21142e+06 max 1.2036e+06 min
-Histogram: 1 0 0 1 1 0 0 0 0 1
-
-Total # of neighbors = 4829126
-Ave neighs/atom = 37.7275
-Neighbor list builds = 14
-Dangerous builds = 0
-Total wall time: 0:00:06

bench/log.6Oct16.lj.fixed.icc.1

@@ -1,79 +0,0 @@
-LAMMPS (6 Oct 2016)
-# 3d Lennard-Jones melt
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-variable	xx equal 20*$x
-variable	xx equal 20*1
-variable	yy equal 20*$y
-variable	yy equal 20*1
-variable	zz equal 20*$z
-variable	zz equal 20*1
-
-units		lj
-atom_style	atomic
-
-lattice		fcc 0.8442
-Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
-region		box block 0 ${xx} 0 ${yy} 0 ${zz}
-region		box block 0 20 0 ${yy} 0 ${zz}
-region		box block 0 20 0 20 0 ${zz}
-region		box block 0 20 0 20 0 20
-create_box	1 box
-Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
-  1 by 1 by 1 MPI processor grid
-create_atoms	1 box
-Created 32000 atoms
-mass		1 1.0
-
-velocity	all create 1.44 87287 loop geom
-
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0 2.5
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 20 check no
-
-fix		1 all nve
-
-run		100
-Neighbor list info ...
-  1 neighbor list requests
-  update every 20 steps, delay 0 steps, check no
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 2.8
-  ghost atom cutoff = 2.8
-  binsize = 1.4 -> bins = 24 24 24
-Memory usage per processor = 8.21387 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         1.44   -6.7733681            0   -4.6134356   -5.0197073 
-     100    0.7574531   -5.7585055            0   -4.6223613   0.20726105 
-Loop time of 2.26185 on 1 procs for 100 steps with 32000 atoms
-
-Performance: 19099.377 tau/day, 44.212 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.9328     | 1.9328     | 1.9328     |   0.0 | 85.45
-Neigh   | 0.2558     | 0.2558     | 0.2558     |   0.0 | 11.31
-Comm    | 0.024061   | 0.024061   | 0.024061   |   0.0 |  1.06
-Output  | 0.00012612 | 0.00012612 | 0.00012612 |   0.0 |  0.01
-Modify  | 0.040887   | 0.040887   | 0.040887   |   0.0 |  1.81
-Other   |            | 0.008214   |            |       |  0.36
-
-Nlocal:    32000 ave 32000 max 32000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    19657 ave 19657 max 19657 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    1.20283e+06 ave 1.20283e+06 max 1.20283e+06 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 1202833
-Ave neighs/atom = 37.5885
-Neighbor list builds = 5
-Dangerous builds not checked
-Total wall time: 0:00:02

bench/log.6Oct16.lj.fixed.icc.4

@@ -1,79 +0,0 @@
-LAMMPS (6 Oct 2016)
-# 3d Lennard-Jones melt
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-variable	xx equal 20*$x
-variable	xx equal 20*1
-variable	yy equal 20*$y
-variable	yy equal 20*1
-variable	zz equal 20*$z
-variable	zz equal 20*1
-
-units		lj
-atom_style	atomic
-
-lattice		fcc 0.8442
-Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
-region		box block 0 ${xx} 0 ${yy} 0 ${zz}
-region		box block 0 20 0 ${yy} 0 ${zz}
-region		box block 0 20 0 20 0 ${zz}
-region		box block 0 20 0 20 0 20
-create_box	1 box
-Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
-  1 by 2 by 2 MPI processor grid
-create_atoms	1 box
-Created 32000 atoms
-mass		1 1.0
-
-velocity	all create 1.44 87287 loop geom
-
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0 2.5
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 20 check no
-
-fix		1 all nve
-
-run		100
-Neighbor list info ...
-  1 neighbor list requests
-  update every 20 steps, delay 0 steps, check no
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 2.8
-  ghost atom cutoff = 2.8
-  binsize = 1.4 -> bins = 24 24 24
-Memory usage per processor = 4.09506 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         1.44   -6.7733681            0   -4.6134356   -5.0197073 
-     100    0.7574531   -5.7585055            0   -4.6223613   0.20726105 
-Loop time of 0.635957 on 4 procs for 100 steps with 32000 atoms
-
-Performance: 67929.172 tau/day, 157.243 timesteps/s
-99.9% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.51335    | 0.51822    | 0.52569    |   0.7 | 81.49
-Neigh   | 0.063695   | 0.064309   | 0.065397   |   0.3 | 10.11
-Comm    | 0.027525   | 0.03629    | 0.041959   |   3.1 |  5.71
-Output  | 6.3896e-05 | 6.6698e-05 | 7.081e-05  |   0.0 |  0.01
-Modify  | 0.012472   | 0.01254    | 0.012618   |   0.1 |  1.97
-Other   |            | 0.004529   |            |       |  0.71
-
-Nlocal:    8000 ave 8037 max 7964 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-Nghost:    9007.5 ave 9050 max 8968 min
-Histogram: 1 1 0 0 0 0 0 1 0 1
-Neighs:    300708 ave 305113 max 297203 min
-Histogram: 1 0 0 1 1 0 0 0 0 1
-
-Total # of neighbors = 1202833
-Ave neighs/atom = 37.5885
-Neighbor list builds = 5
-Dangerous builds not checked
-Total wall time: 0:00:00

bench/log.6Oct16.lj.scaled.icc.4

@@ -1,79 +0,0 @@
-LAMMPS (6 Oct 2016)
-# 3d Lennard-Jones melt
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-variable	xx equal 20*$x
-variable	xx equal 20*2
-variable	yy equal 20*$y
-variable	yy equal 20*2
-variable	zz equal 20*$z
-variable	zz equal 20*1
-
-units		lj
-atom_style	atomic
-
-lattice		fcc 0.8442
-Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
-region		box block 0 ${xx} 0 ${yy} 0 ${zz}
-region		box block 0 40 0 ${yy} 0 ${zz}
-region		box block 0 40 0 40 0 ${zz}
-region		box block 0 40 0 40 0 20
-create_box	1 box
-Created orthogonal box = (0 0 0) to (67.1838 67.1838 33.5919)
-  2 by 2 by 1 MPI processor grid
-create_atoms	1 box
-Created 128000 atoms
-mass		1 1.0
-
-velocity	all create 1.44 87287 loop geom
-
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0 2.5
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 20 check no
-
-fix		1 all nve
-
-run		100
-Neighbor list info ...
-  1 neighbor list requests
-  update every 20 steps, delay 0 steps, check no
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 2.8
-  ghost atom cutoff = 2.8
-  binsize = 1.4 -> bins = 48 48 24
-Memory usage per processor = 8.13678 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         1.44   -6.7733681            0   -4.6133849   -5.0196788 
-     100   0.75841891    -5.759957            0   -4.6223375   0.20008866 
-Loop time of 2.55762 on 4 procs for 100 steps with 128000 atoms
-
-Performance: 16890.677 tau/day, 39.099 timesteps/s
-99.8% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 2.0583     | 2.0988     | 2.1594     |   2.6 | 82.06
-Neigh   | 0.24411    | 0.24838    | 0.25585    |   0.9 |  9.71
-Comm    | 0.066397   | 0.13872    | 0.1863     |  11.9 |  5.42
-Output  | 0.00012994 | 0.00021023 | 0.00025702 |   0.3 |  0.01
-Modify  | 0.055533   | 0.058343   | 0.061791   |   1.2 |  2.28
-Other   |            | 0.0132     |            |       |  0.52
-
-Nlocal:    32000 ave 32060 max 31939 min
-Histogram: 1 0 1 0 0 0 0 1 0 1
-Nghost:    19630.8 ave 19681 max 19562 min
-Histogram: 1 0 0 0 1 0 0 0 1 1
-Neighs:    1.20195e+06 ave 1.20354e+06 max 1.19931e+06 min
-Histogram: 1 0 0 0 0 0 0 2 0 1
-
-Total # of neighbors = 4807797
-Ave neighs/atom = 37.5609
-Neighbor list builds = 5
-Dangerous builds not checked
-Total wall time: 0:00:02

bench/log.6Oct16.rhodo.fixed.icc.1

@@ -1,122 +0,0 @@
-LAMMPS (6 Oct 2016)
-# Rhodopsin model
-
-units           real
-neigh_modify    delay 5 every 1
-
-atom_style      full
-bond_style      harmonic
-angle_style     charmm
-dihedral_style  charmm
-improper_style  harmonic
-pair_style      lj/charmm/coul/long 8.0 10.0
-pair_modify     mix arithmetic
-kspace_style    pppm 1e-4
-
-read_data       data.rhodo
-  orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  32000 atoms
-  reading velocities ...
-  32000 velocities
-  scanning bonds ...
-  4 = max bonds/atom
-  scanning angles ...
-  8 = max angles/atom
-  scanning dihedrals ...
-  18 = max dihedrals/atom
-  scanning impropers ...
-  2 = max impropers/atom
-  reading bonds ...
-  27723 bonds
-  reading angles ...
-  40467 angles
-  reading dihedrals ...
-  56829 dihedrals
-  reading impropers ...
-  1034 impropers
-  4 = max # of 1-2 neighbors
-  12 = max # of 1-3 neighbors
-  24 = max # of 1-4 neighbors
-  26 = max # of special neighbors
-
-fix             1 all shake 0.0001 5 0 m 1.0 a 232
-  1617 = # of size 2 clusters
-  3633 = # of size 3 clusters
-  747 = # of size 4 clusters
-  4233 = # of frozen angles
-fix             2 all npt temp 300.0 300.0 100.0 		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
-
-special_bonds   charmm
-
-thermo          50
-thermo_style    multi
-timestep        2.0
-
-run		100
-PPPM initialization ...
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
-  G vector (1/distance) = 0.248835
-  grid = 25 32 32
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.0355478
-  estimated relative force accuracy = 0.000107051
-  using double precision FFTs
-  3d grid and FFT values/proc = 41070 25600
-Neighbor list info ...
-  1 neighbor list requests
-  update every 1 steps, delay 5 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 12
-  ghost atom cutoff = 12
-  binsize = 6 -> bins = 10 13 13
-Memory usage per processor = 93.2721 Mbytes
----------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
-TotEng   =    -25356.2064 KinEng   =     21444.8313 Temp     =       299.0397 
-PotEng   =    -46801.0377 E_bond   =      2537.9940 E_angle  =     10921.3742 
-E_dihed  =      5211.7865 E_impro  =       213.5116 E_vdwl   =     -2307.8634 
-E_coul   =    207025.8927 E_long   =   -270403.7333 Press    =      -149.3301 
-Volume   =    307995.0335 
----------------- Step       50 ----- CPU =     17.2007 (sec) ----------------
-TotEng   =    -25330.0321 KinEng   =     21501.0036 Temp     =       299.8230 
-PotEng   =    -46831.0357 E_bond   =      2471.7033 E_angle  =     10836.5108 
-E_dihed  =      5239.6316 E_impro  =       227.1219 E_vdwl   =     -1993.2763 
-E_coul   =    206797.6655 E_long   =   -270410.3927 Press    =       237.6866 
-Volume   =    308031.5640 
----------------- Step      100 ----- CPU =     35.0315 (sec) ----------------
-TotEng   =    -25290.7387 KinEng   =     21591.9096 Temp     =       301.0906 
-PotEng   =    -46882.6484 E_bond   =      2567.9789 E_angle  =     10781.9556 
-E_dihed  =      5198.7493 E_impro  =       216.7863 E_vdwl   =     -1902.6458 
-E_coul   =    206659.5006 E_long   =   -270404.9733 Press    =         6.7898 
-Volume   =    308133.9933 
-Loop time of 35.0316 on 1 procs for 100 steps with 32000 atoms
-
-Performance: 0.493 ns/day, 48.655 hours/ns, 2.855 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 25.021     | 25.021     | 25.021     |   0.0 | 71.42
-Bond    | 1.2834     | 1.2834     | 1.2834     |   0.0 |  3.66
-Kspace  | 3.2116     | 3.2116     | 3.2116     |   0.0 |  9.17
-Neigh   | 4.2767     | 4.2767     | 4.2767     |   0.0 | 12.21
-Comm    | 0.069283   | 0.069283   | 0.069283   |   0.0 |  0.20
-Output  | 0.00028205 | 0.00028205 | 0.00028205 |   0.0 |  0.00
-Modify  | 1.14       | 1.14       | 1.14       |   0.0 |  3.25
-Other   |            | 0.02938    |            |       |  0.08
-
-Nlocal:    32000 ave 32000 max 32000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    47958 ave 47958 max 47958 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    1.20281e+07 ave 1.20281e+07 max 1.20281e+07 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 12028098
-Ave neighs/atom = 375.878
-Ave special neighs/atom = 7.43187
-Neighbor list builds = 11
-Dangerous builds = 0
-Total wall time: 0:00:36

bench/log.6Oct16.rhodo.fixed.icc.4

@@ -1,122 +0,0 @@
-LAMMPS (6 Oct 2016)
-# Rhodopsin model
-
-units           real
-neigh_modify    delay 5 every 1
-
-atom_style      full
-bond_style      harmonic
-angle_style     charmm
-dihedral_style  charmm
-improper_style  harmonic
-pair_style      lj/charmm/coul/long 8.0 10.0
-pair_modify     mix arithmetic
-kspace_style    pppm 1e-4
-
-read_data       data.rhodo
-  orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
-  1 by 2 by 2 MPI processor grid
-  reading atoms ...
-  32000 atoms
-  reading velocities ...
-  32000 velocities
-  scanning bonds ...
-  4 = max bonds/atom
-  scanning angles ...
-  8 = max angles/atom
-  scanning dihedrals ...
-  18 = max dihedrals/atom
-  scanning impropers ...
-  2 = max impropers/atom
-  reading bonds ...
-  27723 bonds
-  reading angles ...
-  40467 angles
-  reading dihedrals ...
-  56829 dihedrals
-  reading impropers ...
-  1034 impropers
-  4 = max # of 1-2 neighbors
-  12 = max # of 1-3 neighbors
-  24 = max # of 1-4 neighbors
-  26 = max # of special neighbors
-
-fix             1 all shake 0.0001 5 0 m 1.0 a 232
-  1617 = # of size 2 clusters
-  3633 = # of size 3 clusters
-  747 = # of size 4 clusters
-  4233 = # of frozen angles
-fix             2 all npt temp 300.0 300.0 100.0 		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
-
-special_bonds   charmm
-
-thermo          50
-thermo_style    multi
-timestep        2.0
-
-run		100
-PPPM initialization ...
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
-  G vector (1/distance) = 0.248835
-  grid = 25 32 32
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.0355478
-  estimated relative force accuracy = 0.000107051
-  using double precision FFTs
-  3d grid and FFT values/proc = 13230 6400
-Neighbor list info ...
-  1 neighbor list requests
-  update every 1 steps, delay 5 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 12
-  ghost atom cutoff = 12
-  binsize = 6 -> bins = 10 13 13
-Memory usage per processor = 37.3604 Mbytes
----------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
-TotEng   =    -25356.2064 KinEng   =     21444.8313 Temp     =       299.0397 
-PotEng   =    -46801.0377 E_bond   =      2537.9940 E_angle  =     10921.3742 
-E_dihed  =      5211.7865 E_impro  =       213.5116 E_vdwl   =     -2307.8634 
-E_coul   =    207025.8927 E_long   =   -270403.7333 Press    =      -149.3301 
-Volume   =    307995.0335 
----------------- Step       50 ----- CPU =      4.6056 (sec) ----------------
-TotEng   =    -25330.0321 KinEng   =     21501.0036 Temp     =       299.8230 
-PotEng   =    -46831.0357 E_bond   =      2471.7033 E_angle  =     10836.5108 
-E_dihed  =      5239.6316 E_impro  =       227.1219 E_vdwl   =     -1993.2763 
-E_coul   =    206797.6655 E_long   =   -270410.3927 Press    =       237.6866 
-Volume   =    308031.5640 
----------------- Step      100 ----- CPU =      9.3910 (sec) ----------------
-TotEng   =    -25290.7386 KinEng   =     21591.9096 Temp     =       301.0906 
-PotEng   =    -46882.6482 E_bond   =      2567.9789 E_angle  =     10781.9556 
-E_dihed  =      5198.7493 E_impro  =       216.7863 E_vdwl   =     -1902.6458 
-E_coul   =    206659.5007 E_long   =   -270404.9733 Press    =         6.7898 
-Volume   =    308133.9933 
-Loop time of 9.39107 on 4 procs for 100 steps with 32000 atoms
-
-Performance: 1.840 ns/day, 13.043 hours/ns, 10.648 timesteps/s
-99.8% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 6.2189     | 6.3266     | 6.6072     |   6.5 | 67.37
-Bond    | 0.30793    | 0.32122    | 0.3414     |   2.4 |  3.42
-Kspace  | 0.87994    | 1.1644     | 1.2855     |  15.3 | 12.40
-Neigh   | 1.1358     | 1.136      | 1.1362     |   0.0 | 12.10
-Comm    | 0.08292    | 0.084935   | 0.087077   |   0.5 |  0.90
-Output  | 0.00015712 | 0.00016558 | 0.00018501 |   0.1 |  0.00
-Modify  | 0.33717    | 0.34246    | 0.34794    |   0.7 |  3.65
-Other   |            | 0.01526    |            |       |  0.16
-
-Nlocal:    8000 ave 8143 max 7933 min
-Histogram: 1 2 0 0 0 0 0 0 0 1
-Nghost:    22733.5 ave 22769 max 22693 min
-Histogram: 1 0 0 0 0 2 0 0 0 1
-Neighs:    3.00702e+06 ave 3.0975e+06 max 2.96492e+06 min
-Histogram: 1 2 0 0 0 0 0 0 0 1
-
-Total # of neighbors = 12028098
-Ave neighs/atom = 375.878
-Ave special neighs/atom = 7.43187
-Neighbor list builds = 11
-Dangerous builds = 0
-Total wall time: 0:00:09

bench/log.6Oct16.rhodo.scaled.icc.4

@@ -1,143 +0,0 @@
-LAMMPS (6 Oct 2016)
-# Rhodopsin model
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-units           real
-neigh_modify    delay 5 every 1
-
-atom_style      full
-atom_modify	map hash
-bond_style      harmonic
-angle_style     charmm
-dihedral_style  charmm
-improper_style  harmonic
-pair_style      lj/charmm/coul/long 8.0 10.0
-pair_modify     mix arithmetic
-kspace_style    pppm 1e-4
-
-read_data       data.rhodo
-  orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
-  1 by 2 by 2 MPI processor grid
-  reading atoms ...
-  32000 atoms
-  reading velocities ...
-  32000 velocities
-  scanning bonds ...
-  4 = max bonds/atom
-  scanning angles ...
-  8 = max angles/atom
-  scanning dihedrals ...
-  18 = max dihedrals/atom
-  scanning impropers ...
-  2 = max impropers/atom
-  reading bonds ...
-  27723 bonds
-  reading angles ...
-  40467 angles
-  reading dihedrals ...
-  56829 dihedrals
-  reading impropers ...
-  1034 impropers
-  4 = max # of 1-2 neighbors
-  12 = max # of 1-3 neighbors
-  24 = max # of 1-4 neighbors
-  26 = max # of special neighbors
-
-replicate	$x $y $z
-replicate	2 $y $z
-replicate	2 2 $z
-replicate	2 2 1
-  orthogonal box = (-27.5 -38.5 -36.3646) to (82.5 115.5 36.3615)
-  2 by 2 by 1 MPI processor grid
-  128000 atoms
-  110892 bonds
-  161868 angles
-  227316 dihedrals
-  4136 impropers
-  4 = max # of 1-2 neighbors
-  12 = max # of 1-3 neighbors
-  24 = max # of 1-4 neighbors
-  26 = max # of special neighbors
-
-fix             1 all shake 0.0001 5 0 m 1.0 a 232
-  6468 = # of size 2 clusters
-  14532 = # of size 3 clusters
-  2988 = # of size 4 clusters
-  16932 = # of frozen angles
-fix             2 all npt temp 300.0 300.0 100.0 		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
-
-special_bonds   charmm
-
-thermo          50
-thermo_style    multi
-timestep        2.0
-
-run		100
-PPPM initialization ...
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
-  G vector (1/distance) = 0.248593
-  grid = 48 60 36
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.0359793
-  estimated relative force accuracy = 0.00010835
-  using double precision FFTs
-  3d grid and FFT values/proc = 41615 25920
-Neighbor list info ...
-  1 neighbor list requests
-  update every 1 steps, delay 5 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 12
-  ghost atom cutoff = 12
-  binsize = 6 -> bins = 19 26 13
-Memory usage per processor = 96.9597 Mbytes
----------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
-TotEng   =   -101425.4887 KinEng   =     85779.3251 Temp     =       299.0304 
-PotEng   =   -187204.8138 E_bond   =     10151.9760 E_angle  =     43685.4968 
-E_dihed  =     20847.1460 E_impro  =       854.0463 E_vdwl   =     -9231.4537 
-E_coul   =    827053.5824 E_long   =  -1080565.6077 Press    =      -149.0358 
-Volume   =   1231980.1340 
----------------- Step       50 ----- CPU =     18.1689 (sec) ----------------
-TotEng   =   -101320.0211 KinEng   =     86003.4933 Temp     =       299.8118 
-PotEng   =   -187323.5144 E_bond   =      9887.1189 E_angle  =     43346.8448 
-E_dihed  =     20958.7108 E_impro  =       908.4721 E_vdwl   =     -7973.4486 
-E_coul   =    826141.5493 E_long   =  -1080592.7617 Press    =       238.0404 
-Volume   =   1232126.1814 
----------------- Step      100 ----- CPU =     37.2027 (sec) ----------------
-TotEng   =   -101157.9546 KinEng   =     86355.7413 Temp     =       301.0398 
-PotEng   =   -187513.6959 E_bond   =     10272.0456 E_angle  =     43128.7018 
-E_dihed  =     20794.0107 E_impro  =       867.0928 E_vdwl   =     -7587.2409 
-E_coul   =    825584.2416 E_long   =  -1080572.5474 Press    =        15.1729 
-Volume   =   1232535.8440 
-Loop time of 37.2028 on 4 procs for 100 steps with 128000 atoms
-
-Performance: 0.464 ns/day, 51.671 hours/ns, 2.688 timesteps/s
-99.9% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 25.431     | 25.738     | 25.984     |   4.0 | 69.18
-Bond    | 1.2966     | 1.3131     | 1.3226     |   0.9 |  3.53
-Kspace  | 3.7563     | 4.0123     | 4.3127     |  10.0 | 10.79
-Neigh   | 4.3778     | 4.378      | 4.3782     |   0.0 | 11.77
-Comm    | 0.1903     | 0.19549    | 0.20485    |   1.3 |  0.53
-Output  | 0.00031805 | 0.00037521 | 0.00039601 |   0.2 |  0.00
-Modify  | 1.4861     | 1.5051     | 1.5122     |   0.9 |  4.05
-Other   |            | 0.05992    |            |       |  0.16
-
-Nlocal:    32000 ave 32000 max 32000 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-Nghost:    47957 ave 47957 max 47957 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-Neighs:    1.20281e+07 ave 1.20572e+07 max 1.19991e+07 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 48112540
-Ave neighs/atom = 375.879
-Ave special neighs/atom = 7.43187
-Neighbor list builds = 11
-Dangerous builds = 0
-Total wall time: 0:00:38

doc/.gitignore

@@ -0,0 +1 @@
+

doc/Makefile

@@ -1,6 +1,4 @@
 # Makefile for LAMMPS documentation
-
-SHELL 	      = /bin/bash
 SHA1          = $(shell echo $USER-$PWD | python utils/sha1sum.py)
 BUILDDIR      = /tmp/lammps-docs-$(SHA1)
 RSTDIR        = $(BUILDDIR)/rst
@@ -8,42 +6,35 @@ VENV          = $(BUILDDIR)/docenv
 TXT2RST       = $(VENV)/bin/txt2rst
 
 PYTHON        = $(shell which python3)
-HAS_PYTHON3    = NO
-HAS_VIRTUALENV = NO
 
-ifeq ($(shell which python3 >/dev/null 2>&1; echo $$?), 0)
-HAS_PYTHON3 = YES
+ifeq ($(shell which python3 >/dev/null 2>&1; echo $$?), 1)
+$(error Python3 was not found! Please check README.md for further instructions)
 endif
 
-ifeq ($(shell which virtualenv >/dev/null 2>&1; echo $$?), 0)
-HAS_VIRTUALENV = YES
+ifeq ($(shell which virtualenv >/dev/null 2>&1; echo $$?), 1)
+$(error virtualenv was not found! Please check README.md for further instructions)
 endif
 
 SOURCES=$(wildcard src/*.txt)
 OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
 
-.PHONY: help clean-all clean epub html pdf old venv
-
-# ------------------------------------------
+.PHONY: help clean-all clean html pdf venv
 
 help:
 	@echo "Please use \`make <target>' where <target> is one of"
-	@echo "  html       create HTML doc pages in html dir"
-	@echo "  pdf        create Manual.pdf and Developer.pdf in this dir"
-	@echo "  old        create old-style HTML doc pages in old dir"
-	@echo "  fetch      fetch HTML and PDF files from LAMMPS web site"
-	@echo "  epub       create ePUB format manual for e-book readers"
-	@echo "  clean      remove all intermediate RST files"
-	@echo "  clean-all  reset the entire build environment"
-	@echo "  txt2html   build txt2html tool"
-
-# ------------------------------------------
+	@echo "  html       to make HTML version of documentation using Sphinx"
+	@echo "  pdf        to make Manual.pdf"
+	@echo "  txt2html   to build txt2html tool"
+	@echo "  clean      to remove all generated RST files"
+	@echo "  clean-all  to reset the entire build environment"
 
 clean-all:
 	rm -rf $(BUILDDIR)/* utils/txt2html/txt2html.exe
 
 clean:
-	rm -rf $(RSTDIR) html
+	rm -rf $(RSTDIR)
+
+txt2html: utils/txt2html/txt2html.exe
 
 html: $(OBJECTS)
 	@(\
@@ -53,67 +44,20 @@ html: $(OBJECTS)
 		deactivate ;\
 	)
 	-rm html/searchindex.js
-	@rm -rf html/_sources
-	@rm -rf html/PDF
-	@rm -rf html/USER
-	@cp -r src/PDF html/PDF
-	@cp -r src/USER html/USER
-	@rm -rf html/PDF/.[sg]*
-	@rm -rf html/USER/.[sg]*
-	@rm -rf html/USER/*/.[sg]*
-	@rm -rf html/USER/*/*.[sg]*
+	-rm -rf html/_sources
 	@echo "Build finished. The HTML pages are in doc/html."
 
-epub: $(OBJECTS)
-	@mkdir -p epub
-	@rm -f LAMMPS.epub
-	@cp src/JPG/lammps-logo.png epub/
-	@(\
-		. $(VENV)/bin/activate ;\
-		cp -r src/* $(RSTDIR)/ ;\
-		sphinx-build -j 8 -b epub -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
-		deactivate ;\
-	)
-	@mv  epub/LAMMPS.epub .
-	@rm -rf epub
-	@echo "Build finished. The ePUB manual file is created."
-
 pdf: utils/txt2html/txt2html.exe
 	@(\
 		cd src; \
 		../utils/txt2html/txt2html.exe -b *.txt; \
-		htmldoc --batch lammps.book;          \
+		htmldoc --batch ../lammps.book;          \
 		for s in `echo *.txt | sed -e 's,\.txt,\.html,g'` ; \
-			do grep -q $$s lammps.book || \
-			echo doc file $$s missing in src/lammps.book; done; \
+			do grep -q $$s ../lammps.book || \
+			echo doc file $$s missing in lammps.book; done; \
 		rm *.html; \
-		cd Developer; \
-		pdflatex developer; \
-		pdflatex developer; \
-		mv developer.pdf ../../Developer.pdf; \
 	)
 
-old: utils/txt2html/txt2html.exe
-	@rm -rf old
-	@mkdir old; mkdir old/Eqs; mkdir old/JPG; mkdir old/PDF
-	@cd src; ../utils/txt2html/txt2html.exe -b *.txt; \
-	  mv *.html ../old; \
-	  cp Eqs/*.jpg ../old/Eqs; \
-	  cp JPG/* ../old/JPG; \
-	  cp PDF/* ../old/PDF;
-
-fetch:
-	@rm -rf html_www Manual_www.pdf Developer_www.pdf
-	@curl -s -o Manual_www.pdf http://lammps.sandia.gov/doc/Manual.pdf
-	@curl -s -o Developer_www.pdf http://lammps.sandia.gov/doc/Developer.pdf
-	@curl -s -o lammps-doc.tar.gz http://lammps.sandia.gov/tars/lammps-doc.tar.gz
-	@tar xzf lammps-doc.tar.gz
-	@rm -f lammps-doc.tar.gz
-
-txt2html: utils/txt2html/txt2html.exe
-
-# ------------------------------------------
-
 utils/txt2html/txt2html.exe: utils/txt2html/txt2html.cpp
 	g++ -O -Wall -o $@ $<
 
@@ -126,8 +70,6 @@ $(RSTDIR)/%.rst : src/%.txt $(TXT2RST)
 	)
 
 $(VENV):
-	@if [ "$(HAS_PYTHON3)" == "NO" ] ; then echo "Python3 was not found! Please check README.md for further instructions" 1>&2; exit 1; fi
-	@if [ "$(HAS_VIRTUALENV)" == "NO" ] ; then echo "virtualenv was not found! Please check README.md for further instructions" 1>&2; exit 1; fi
 	@( \
 		virtualenv -p $(PYTHON) $(VENV); \
 		. $(VENV)/bin/activate; \

doc/README

@@ -1,115 +0,0 @@
-LAMMPS Documentation
-
-Depending on how you obtained LAMMPS, this directory has 2 or 3
-sub-directories and optionally 2 PDF files and an ePUB file:
-
-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
-LAMMPS.epub     Manual in ePUB format
-
-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
-make pdf          # generate 2 PDF files (Manual.pdf,Developer.pdf)
-                  #   in this dir via htmldoc and pdflatex
-make old          # generate old-style HTML pages in old dir via txt2html
-make fetch        # fetch HTML doc pages and 2 PDF files from web site
-                  #   as a tarball and unpack into html dir and 2 PDFs
-make epub         # generate LAMMPS.epub in ePUB format using Sphinx 
-make clean        # remove intermediate RST files created by HTML build
-make clean-all    # remove entire build folder and any cached data
-
-----------------
-
-Installing prerequisites for HTML build
-
-To run the HTML documention build toolchain, Python 3 and virtualenv
-have to be installed.  Here are instructions for common setups:
-
-# Ubuntu
-
-sudo apt-get install python-virtualenv
-
-# Fedora (up to version 21)
-# Red Hat Enterprise Linux or CentOS (up to version 7.x)
-
-sudo yum install python3-virtualenv
-
-# Fedora (since version 22)
-
-sudo dnf install python3-virtualenv
-
-# MacOS X
-
-## Python 3
-
-Download the latest Python 3 MacOS X package from
-https://www.python.org and install it.  This will install both Python
-3 and pip3.
-
-## virtualenv
-
-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
-
-[TBA]
-
-----------------
-
-Installing prerequisites for epub build
-
-## ePUB
-
-Same as for HTML. This uses the same tools and configuration
-files as the HTML tree.
-
-For converting the generated ePUB file to a mobi format file
-(for e-book readers like Kindle, that cannot read ePUB), you
-also need to have the 'ebook-convert' tool from the "calibre"
-software installed. http://calibre-ebook.com/
-You first create the ePUB file with 'make epub' and then do:
-
-ebook-convert LAMMPS.epub LAMMPS.mobi
-

doc/README.md

@@ -0,0 +1,48 @@
+# Generation of LAMMPS Documentation
+
+The generation of all the documentation is managed by the Makefile inside the
+`doc/` folder.
+
+## Usage:
+
+```bash
+make html         # generate HTML using Sphinx
+make pdf          # generate PDF using htmldoc
+make clean        # remove generated RST files
+make clean-all    # remove entire build folder and any cached data
+```
+
+## Installing prerequisites
+
+To run the documention build toolchain, Python 3 and virtualenv have
+to be installed. Here are instructions for common setups:
+
+### Ubuntu
+
+```bash
+sudo apt-get install python-virtualenv
+```
+
+### Fedora (up to version 21), Red Hat Enterprise Linux or CentOS (up to version 7.x)
+
+```bash
+sudo yum install python3-virtualenv
+```
+
+### Fedora (since version 22)
+
+```bash
+sudo dnf install python3-virtualenv
+```
+
+### MacOS X
+
+## Python 3
+
+Download the latest Python 3 MacOS X package from https://www.python.org and install it.
+This will install both Python 3 and pip3.
+
+## virtualenv
+
+Once Python 3 is installed, open a Terminal and type `pip3 install virtualenv`. This will
+install virtualenv from the Python Package Index.

doc/html/.gitignore

@@ -0,0 +1,4 @@
+.buildinfo
+objects.inv
+searchindex.js
+_sources

doc/html/2001/README.html

@@ -0,0 +1,174 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
+<HTML>
+<HEAD>
+    <META NAME="Generator" CONTENT="Cosmo Create 1.0.3">
+</HEAD>
+<BODY>
+<H2>
+LAMMPS</H2>
+<P>
+LAMMPS = Large-scale Atomic/Molecular Massively Parallel Simulator</P>
+<P>
+This is the documentation for the LAMMPS 2001 version, written in F90,
+which has been superceded by more current versions.  See the <A
+HREF="http://www.cs.sandia.gov/~sjplimp/lammps.html">LAMMPS WWW
+Site</A> for more information.
+<P>
+LAMMPS is a classical molecular dynamics code designed for simulating 
+molecular and atomic systems on parallel computers using 
+spatial-decomposition techniques. It runs on any parallel platform that 
+supports F90 and the MPI message-passing library or on single-processor 
+workstations.</P>
+<P>
+LAMMPS 2001 is copyrighted code that is distributed freely as
+open-source software under the GNU Public License (GPL).  See the
+LICENSE file or <A HREF="http://www.gnu.org">www.gnu.org</A> for more
+details.  Basically the GPL allows you as a user to use, modify, or
+distribute LAMMPS however you wish, so long as any software you
+distribute remains under the GPL.
+<P>
+Features of LAMMPS 2001 include:</P>
+<UL>
+    <LI>
+    short-range pairwise Lennard-Jones and Coulombic interactions 
+    <LI>
+    long-range Coulombic interactions via Ewald or PPPM (particle-mesh 
+    Ewald) 
+    <LI>
+    short-range harmonic bond potentials (bond, angle, torsion, improper) 
+    <LI>
+    short-range class II (cross-term) molecular potentials 
+    <LI>
+    NVE, NVT, NPT dynamics 
+    <LI>
+    constraints on atoms or groups of atoms 
+    <LI>
+    rRESPA long-timescale integrator 
+    <LI>
+    energy minimizer (Hessian-free truncated Newton method) 
+</UL>
+<P>
+For users of LAMMPS 99, this version is written in F90 to take
+advantage of dynamic memory allocation.  This means the user does not
+have to fiddle with parameter settings and re-compile the code so
+often for different problems.  This enhancment means there are new
+rules for the ordering of commands in a LAMMPS input script, as well
+as a few new commands to guide the memory allocator. Users should read
+the beginning sections of the <A
+HREF="input_commands.html">input_commands</A> file for an
+explanation.</P>
+<P>
+More details about the code can be found <A
+HREF="#_cch3_930958294">here</A>, in the HTML- or text-based
+documentation.  The LAMMPS Web page is at <A
+ HREF="http://www.cs.sandia.gov/~sjplimp/lammps.html">www.cs.sandia.gov/~sjplimp/lammps.html</A>
+, which includes benchmark timings and a list of papers written using
+LAMMPS results.  They illustrate the kinds of scientific problems that
+can be modeled with LAMMPS.  These two papers describe the parallel
+algorithms used in the code.  Please cite these if you incorporate
+LAMMPS results in your work.  And if you send me citations for your
+papers, I'll be pleased to add them to the LAMMPS WWW page.
+</P>
+<P>
+S. J. Plimpton, R. Pollock, M. Stevens, &quot;Particle-Mesh Ewald and 
+rRESPA for Parallel Molecular Dynamics Simulations&quot;, in Proc of 
+the Eighth SIAM Conference on Parallel Processing for Scientific 
+Computing, Minneapolis, MN, March 1997.</P>
+<P>
+S. J. Plimpton, "Fast Parallel Algorithms for Short-Range Molecular Dynamics", J Comp Phys, 117, 1-19 (1995).</P>
+<P>
+LAMMPS was originally developed as part of a 5-way CRADA collaboration 
+between 3 industrial partners (Cray Research, Bristol-Myers Squibb, and 
+Dupont) and 2 DoE laboratories (Sandia National Laboratories and 
+Lawrence Livermore National Laboratories).</P>
+<P>
+The primary author of LAMMPS is Steve Plimpton, but others have written 
+or worked on significant portions of the code:</P>
+<UL>
+    <LI>
+    Roy Pollock (LLNL): Ewald, PPPM solvers 
+    <LI>
+    Mark Stevens (Sandia): rRESPA, NPT integrators 
+    <LI>
+    Eric Simon (Cray Research): class II force fields 
+    <LI>
+    Todd Plantenga (Sandia): energy minimizer 
+    <LI>
+    Steve Lustig (Dupont): msi2lmp tool 
+    <LI>
+    Mike Peachey (Cray Research): msi2lmp tool 
+</UL>
+<P>
+Other CRADA partners involved in the design and testing of LAMMPS are </P>
+<UL>
+    <LI>
+    John Carpenter (Cray Research) 
+    <LI>
+    Terry Stouch (Bristol-Myers Squibb) 
+    <LI>
+    Jim Belak (LLNL) 
+</UL>
+<P>
+If you have questions about LAMMPS, please contact me:
+</P>
+<DL>
+    <DT>
+    Steve Plimpton
+    <DD>
+    sjplimp@sandia.gov 
+    <DD>
+    www.cs.sandia.gov/~sjplimp 
+    <DD>
+    Sandia National Labs 
+    <DD>
+    Albuquerque, NM 87185
+</DL>
+<HR>
+<H3>
+<A NAME="_cch3_930958294">More Information about LAMMPS</A></H3>
+<DIR>
+    <LI>
+    <A HREF="basics.html">Basics</A> 
+    <DIR>
+        <LI>
+        how to make, run, and test LAMMPS with the example problems 
+    </DIR>
+    <LI>
+    <A HREF="input_commands.html">Input Commands</A> 
+    <DIR>
+        <LI>
+        a complete listing of input commands used by LAMMPS 
+    </DIR>
+    <LI>
+    <A HREF="data_format.html">Data Format</A> 
+    <DIR>
+        <LI>
+        the data file format used by LAMMPS 
+    </DIR>
+    <LI>
+    <A HREF="force_fields.html">Force Fields</A> 
+    <DIR>
+        <LI>
+        the equations LAMMPS uses to compute force-fields 
+    </DIR>
+    <LI>
+    <A HREF="units.html">Units</A> 
+    <DIR>
+        <LI>
+        the input/output and internal units for LAMMPS variables 
+    </DIR>
+    <LI>
+    <A HREF="history.html">History</A> 
+    <DIR>
+        <LI>
+        a brief timeline of features added to LAMMPS 
+    </DIR>
+    <LI>
+    <A HREF="deficiencies.html">Deficiencies</A> 
+    <DIR>
+        <LI>
+        features LAMMPS does not (yet) have
+    </DIR>
+</DIR>
+</BODY>
+</HTML>

doc/html/2001/basics.html

@@ -0,0 +1,224 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
+<HTML>
+<HEAD>
+    <META NAME="Generator" CONTENT="Cosmo Create 1.0.3">
+</HEAD>
+<BODY>
+<H2>
+Basics of Using LAMMPS</H2>
+<P>
+<A HREF="README.html">Return</A> to top-level of LAMMPS documentation.</P>
+<UL>
+    <LI>
+    <A HREF="#_cch3_931273040">Distribution</A> 
+    <LI>
+    <A HREF="#_cch3_930327142">Making LAMMPS</A> 
+    <LI>
+    <A HREF="#_cch3_930327155">Running LAMMPS</A> 
+    <LI>
+    <A HREF="#_cch3_930759879">Examples</A> 
+    <LI>
+    <A HREF="#_cch3_931282515">Other Tools</A> 
+    <LI>
+    <A HREF="#_cch3_931282000">Extending LAMMPS</A> 
+</UL>
+<HR>
+<H3>
+<A NAME="_cch3_931273040">Distribution</A></H3>
+<P>
+When you unzip/untar the LAMMPS distribution you should have several
+directories: </P>
+<UL>
+    <LI>
+    src = source files for LAMMPS 
+    <LI>
+    doc = HTML documentation 
+    <LI>
+    examples = sample problems with inputs and outputs 
+    <LI>
+    tools = serial program for creating and massaging LAMMPS data files 
+    <LI>
+    converters = msi2lmp, lmp2arc, amber = codes & scripts for converting
+       between MSI/Discover, AMBER, and LAMMPS formats
+</UL>
+<HR>
+<H3>
+<A NAME="_cch3_930327142">Making LAMMPS</A></H3>
+<P>
+The src directory contains the F90 and C source files for LAMMPS as 
+well as several sample Makefiles for different machines. To make LAMMPS 
+for a specfic machine, you simply type</P>
+<P>
+make machine</P>
+<P>
+from within the src directoy. E.g. "make sgi" or "make t3e". This
+should create an executable such as lmp_sgi or lmp_t3e.  For optimal
+performance you'll want to use a good F90 compiler to make LAMMPS; on
+Linux boxes I've been told the Leahy F90 compiler is a good choice.
+(If you don't have an F90 compiler, I can give you an older F77-based
+version of LAMMPS 99, but you'll lose the dynamic memory and some
+other new features in LAMMPS 2001.)</P>
+<P>
+In the src directory, there is one top-level Makefile and several
+low-level machine-specific files named Makefile.xxx where xxx = the
+machine name. If a low-level Makefile exists for your platform, you do
+not need to edit the top-level Makefile.  However you should check the
+system-specific section of the low-level Makefile to insure the
+various paths are correct for your environment. If a low-level
+Makefile does not exist for your platform, you will need to add a
+suitable target to the top-level Makefile. You will also need to
+create a new low-level Makefile using one of the existing ones as a
+template. If you wish to make LAMMPS for a single-processor
+workstation that doesn't have an installed MPI library, you can
+specify the "serial" target which uses a directory of MPI stubs to
+link against - e.g. &quot;make serial&quot;. You will need to make the
+stub library (type &quot;make&quot; in STUBS directory) for your
+workstation before doing this.</P>
+<P>
+Note that the two-level Makefile system allows you to make LAMMPS for 
+multiple platforms. Each target creates its own object directory for 
+separate storage of its *.o files.</P>
+<P>
+There are a few compiler switches of interest which can be specified
+in the low-level Makefiles.  If you use a F90FLAGS switch of -DSYNC
+then synchronization calls will be made before the timing routines in
+integrate.f. This may slow down the code slightly, but will make the
+individual timings reported at the end of a run more accurate. The
+F90FLAGS setting of -DSENDRECV will use MPI_Sendrecv calls for data
+exchange between processors instead of MPI_Irecv, MPI_Send,
+MPI_Wait. Sendrecv is often slower, but on some platforms can be
+faster, so it is worth trying, particularly if your communication
+timings seem slow.</P>
+<P>
+The CCFLAGS setting in the low-level Makefiles requires a FFT setting,
+for example -DFFT_SGI or -DFFT_T3E. This is for inclusion of the
+appropriate machine-specific native 1-d FFT libraries on various
+platforms. Currently, the supported machines and switches (used in
+fft_3d.c) are FFT_SGI, FFT_DEC, FFT_INTEL, FFT_T3E, and FFT_FFTW. The
+latter is a publicly available portable FFT library, <A
+HREF="http://www.fftw.org">FFTW</A>, which you can install on any
+machine. If none of these options is suitable for your machine, please
+contact me, and we'll discuss how to add the capability to call your
+machine's native FFT library. You can also use FFT_NONE if you have no
+need to use the PPPM option in LAMMPS.</P>
+<P>
+For Linux and T3E compilation, there is a also a CCFLAGS setting for KLUDGE
+needed (see Makefile.linux and Makefile.t3e).  This is to enable F90 to
+call C with appropriate underscores added to C function names.
+<HR>
+<H3>
+<A NAME="_cch3_930327155">Running LAMMPS</A></H3>
+<P>
+LAMMPS is run by redirecting a text file (script) of input commands into it.</P>
+<P>
+lmp_sgi &lt; in.lj</P>
+<P>
+lmp_t3e &lt; in.lj</P>
+<P>
+The script file contains commands that specify the parameters for the 
+simulation as well as to read other necessary files such as a data file 
+that describes the initial atom positions, molecular topology, and 
+force-field parameters. The <A HREF="input_commands.html">input_commands</A>
+ page describes all the possible commands that can be used. The <A
+ HREF="data_format.html">data_format</A> page describes the format of 
+the data file. </P>
+<P>
+LAMMPS can be run on any number of processors, including a single 
+processor. In principle you should get identical answers on any number 
+of processors and on any machine. In practice, numerical round-off can 
+cause slight differences and eventual divergence of dynamical 
+trajectories. </P>
+<P>
+When LAMMPS runs, it estimates the array sizes it should allocate based 
+on the problem you are simulating and the number of processors you 
+are running on. If you run out of physical memory, you will get a F90 
+allocation error and the code should hang or crash. The only thing you 
+can do about this is run on more processors or run a smaller problem. If 
+you get an error message to the screen about &quot;boosting&quot; 
+something, it means LAMMPS under-estimated the size needed for one (or 
+more) data arrays. The &quot;extra memory&quot; command can be used in 
+the input script to augment these sizes at run time. A few arrays are 
+hard-wired to sizes that should be sufficient for most users. These are 
+specified with parameter settings in the global.f file. If you get a 
+message to &quot;boost&quot; one of these parameters you will have to 
+change it and re-compile LAMMPS.</P>
+<P>
+Some LAMMPS errors are detected at setup; others like neighbor list
+overflow may not occur until the middle of a run. Except for F90
+allocation errors which may cause the code to hang (with an error
+message) since only one processor may incur the error, LAMMPS should
+always print a message to the screen and exit gracefully when it
+encounters a fatal error. If the code ever crashes or hangs without
+spitting out an error message first, it's probably a bug, so let me
+know about it. Of course this applies to algorithmic or parallelism
+issues, not to physics mistakes, like specifying too big a timestep or
+putting 2 atoms on top of each other! One exception is that different
+MPI implementations handle buffering of messages differently.  If the
+code hangs without an error message, it may be that you need to
+specify an MPI setting or two (usually via an environment variable) to
+enable buffering or boost the sizes of messages that can be
+buffered.</P>
+<HR>
+<H3>
+<A NAME="_cch3_930759879">Examples</A></H3>
+<P>
+There are several directories of sample problems in the examples
+directory. All of them use an input file (in.*) of commands and a data
+file (data.*) of initial atomic coordinates and produce one or more
+output files. Sample outputs on different machines and numbers of
+processors are included to compare your answers to.  See the README
+file in the examples sub-directory for more information on what LAMMPS
+features the examples illustrate.</P>
+<P>
+(1) lj = atomic simulations of Lennard-Jones systems.
+<P>
+(2) class2 = phenyalanine molecule using the DISCOVER cff95 class 2
+force field.
+<P>
+(3) lc = liquid crystal molecules with various Coulombic options and
+periodicity settings.
+<P>
+(4) flow = 2d flow of Lennard-Jones atoms in a channel using various
+constraint options.
+<P>
+(5) polymer = bead-spring polymer models with one or two chain types.
+</P>
+<HR>
+<H3>
+<A NAME="_cch3_931282515">Other Tools</A></H3>
+<P>
+The converters directory has source code and scripts for tools that
+perform input/output file conversions between MSI Discover, AMBER, and
+LAMMPS formats.  See the README files for the individual tools for
+additional information.
+<P>
+The tools directory has several serial programs that create and
+massage LAMMPS data files.
+<P>
+(1) setup_chain.f = create a data file of polymer bead-spring chains
+<P>
+(2) setup_lj.f = create a data file of an atomic LJ mixture of species
+<P>
+(3) setup_flow_2d.f = create a 2d data file of LJ particles with walls for
+	a flow simulation
+<P>
+(4) replicate.c = replicate or scale an existing data file into a new one
+<P>
+(5) peek_restart.f = print-out info from a binary LAMMPS restart file
+<P>
+(6) restart2data.f = convert a binary LAMMPS restart file into a text data file
+<P>
+See the comments at the top of each source file for information on how
+to use the tool.
+<HR>
+<H3>
+<A NAME="_cch3_931282000">Extending LAMMPS</A></H3>
+<P>
+User-written routines can be compiled and linked with LAMMPS, then
+invoked with the "diagnostic" command as LAMMPS runs.  These routines
+can be used for on-the-fly diagnostics or a variety of other purposes.
+The examples/lc directory shows an example of using the diagnostic
+command with the in.lc.big.fixes input script.  A sample diagnostic
+routine is given there also: diagnostic_temp_molecules.f.
+</BODY>
+</HTML>

doc/html/2001/data_format.html

@@ -0,0 +1,250 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
+<HTML>
+<HEAD>
+    <META NAME="Generator" CONTENT="Cosmo Create 1.0.3">
+</HEAD>
+<BODY>
+<H2>
+LAMMPS Data Format</H2>
+<P>
+<A HREF="README.html">Return</A> to top-level of LAMMPS documentation</P>
+<P>
+This file describes the format of the data file read into LAMMPS with 
+the &quot;read data&quot; command. The data file contains basic 
+information about the size of the problem to be run, the initial atomic 
+coordinates, molecular topology, and (optionally) force-field 
+coefficients. It will be easiest to understand this file if you read it 
+while looking at a sample data file from the examples.</P>
+<P>
+This page has 2 sections:</P>
+<UL>
+    <LI>
+    <A HREF="#_cch3_930958962">Rules for formatting the Data File</A> 
+    <LI>
+    <A HREF="#_cch3_930958969">Sample file with Annotations</A> 
+</UL>
+<HR>
+<H3>
+<A NAME="_cch3_930958962">Rules for formatting the Data File: </A></H3>
+<P>
+Blank lines are important. After the header section, new entries are 
+separated by blank lines. </P>
+<P>
+Indentation and space between words/numbers on one line is not 
+important except that keywords (e.g. Masses, Bond Coeffs) must be 
+left-justified and capitalized as shown. </P>
+<P>
+The header section (thru box bounds) must appear first in the file, the 
+remaining entries (Masses, various Coeffs, Atoms, Bonds, etc) can come 
+in any order. </P>
+<P>
+These entries must be in the file: header section, Masses, Atoms. </P>
+<P>
+These entries must be in the file if there are a non-zero number of
+them: Bonds, Angles, Dihedrals, Impropers. Force field coefficients
+can be specified in the input script, so do not have to appear in the
+data file.  The one exception to this is class 2 force field
+coefficients which can only be specified in the data file.
+<P>
+The Nonbond Coeffs entry contains one line for each atom type. These 
+are the coefficients for an interaction between 2 atoms of the same 
+type. The cross-type coeffs are computed by the appropriate class I or 
+class II mixing rules, or can be specified explicitly using the 
+&quot;nonbond coeff&quot; command in the input command script. See the <A
+ HREF="force_fields.html">force_fields</A> page for more information. </P>
+<P>
+In the Atoms entry, the atoms can be in any order so long as there are 
+N entries. The 1st number on the line is the atom-tag (number from 1 to 
+N) which is used to identify the atom throughout the simulation. The 
+molecule-tag is a second identifier which is attached to the atom; it 
+can be 0, or a counter for the molecule the atom is part of, or any 
+other number you wish. The q value is the charge of the atom in 
+electron units (e.g. +1 for a proton). The xyz values are the initial 
+position of the atom. For 2-d simulations specify z as 0.0.</P>
+<P>
+The final 3 nx,ny,nz values on a line of the Atoms entry are optional. 
+LAMMPS only reads them if the &quot;true flag&quot; command is 
+specified in the input command script. Otherwise they are initialized 
+to 0 by LAMMPS. Their meaning, for each dimension, is that 
+&quot;n&quot; box-lengths are added to xyz to get the atom's 
+&quot;true&quot; un-remapped position. This can be useful in pre- or 
+post-processing to enable the unwrapping of long-chained molecules 
+which wind thru the periodic box one or more times. The value of 
+&quot;n&quot; can be positive, negative, or zero. For 2-d simulations 
+specify nz as 0. </P>
+<P>
+Atom velocities are initialized to 0.0 if there is no Velocities entry. 
+In the Velocities entry, the atoms can be in any order so long as there 
+are N entries. The 1st number on the line is the atom-tag (number from 
+1 to N) which is used to identify the atom which the given velocity 
+will be assigned to.</P>
+<P>
+Entries for Velocities, Bonds, Angles, Dihedrals, Impropers must appear 
+in the file after an Atoms entry.</P>
+<P>
+For simulations with periodic boundary conditions, xyz coords are
+remapped into the periodic box (from as far away as needed), so the
+initial coordinates need not be inside the box. The nx,ny,nz values
+(as read in or as set to zero by LAMMPS) are appropriately adjusted by
+this remapping. </P>
+<P>
+The number of coefficients specified on each line of coefficient
+entries (Nonbond Coeffs, Bond Coeffs, etc) depends on the
+&quot;style&quot; of interaction. This must be specified in the input
+command script before the "read data" command is issued, unless the
+default is used. See the <A
+ HREF="input_commands.html">input_commands</A> page for a description 
+of the various style options. The <A HREF="input_commands.html">input_commands</A>
+ and <A HREF="force_fields.html">force_fields</A> pages explain the 
+meaning and valid values for each of the coefficients. </P>
+<HR>
+<H3>
+<A NAME="_cch3_930958969">Sample file with Annotations</A></H3>
+<P>
+Here is a sample file with annotations in parenthesis and lengthy 
+sections replaced by dots (...). Note that the blank lines are 
+important in this example.</P>
+<PRE>
+
+LAMMPS Description           (1st line of file)
+
+100 atoms         (this must be the 3rd line, 1st 2 lines are ignored)
+95 bonds                (# of bonds to be simulated)
+50 angles               (include these lines even if number = 0)
+30 dihedrals
+20 impropers
+
+5 atom types           (# of nonbond atom types)
+10 bond types          (# of bond types = sets of bond coefficients)
+18 angle types         
+20 dihedral types      (do not include a bond,angle,dihedral,improper type
+2 improper types             line if number of bonds,angles,etc is 0)
+
+-0.5 0.5 xlo xhi       (for periodic systems this is box size,
+-0.5 0.5 ylo yhi        for non-periodic it is min/max extent of atoms)
+-0.5 0.5 zlo zhi       (do not include this line for 2-d simulations)
+
+Masses
+
+  1 mass
+  ...
+  N mass                           (N = # of atom types)
+
+Nonbond Coeffs
+
+  1 coeff1 coeff2 ...
+  ...
+  N coeff1 coeff2 ...              (N = # of atom types)
+
+Bond Coeffs
+
+  1 coeff1 coeff2 ...
+  ...
+  N coeff1 coeff2 ...              (N = # of bond types)
+
+Angle Coeffs
+
+  1 coeff1 coeff2 ...
+  ...
+  N coeff1 coeff2 ...              (N = # of angle types)
+
+Dihedral Coeffs
+
+  1 coeff1 coeff2 ...
+  ...
+  N coeff1 coeff2 ...              (N = # of dihedral types)
+
+Improper Coeffs
+
+  1 coeff1 coeff2 ...
+  ...
+  N coeff1 coeff2 ...              (N = # of improper types)
+
+BondBond Coeffs
+
+  1 coeff1 coeff2 ...
+  ...
+  N coeff1 coeff2 ...              (N = # of angle types)
+
+BondAngle Coeffs
+
+  1 coeff1 coeff2 ...
+  ...
+  N coeff1 coeff2 ...              (N = # of angle types)
+
+MiddleBondTorsion Coeffs
+
+  1 coeff1 coeff2 ...
+  ...
+  N coeff1 coeff2 ...              (N = # of dihedral types)
+
+EndBondTorsion Coeffs
+
+  1 coeff1 coeff2 ...
+  ...
+  N coeff1 coeff2 ...              (N = # of dihedral types)
+
+AngleTorsion Coeffs
+
+  1 coeff1 coeff2 ...
+  ...
+  N coeff1 coeff2 ...              (N = # of dihedral types)
+
+AngleAngleTorsion Coeffs
+
+  1 coeff1 coeff2 ...
+  ...
+  N coeff1 coeff2 ...              (N = # of dihedral types)
+
+BondBond13 Coeffs
+
+  1 coeff1 coeff2 ...
+  ...
+  N coeff1 coeff2 ...              (N = # of dihedral types)
+
+AngleAngle Coeffs
+
+  1 coeff1 coeff2 ...
+  ...
+  N coeff1 coeff2 ...              (N = # of improper types)
+
+Atoms
+
+  1 molecule-tag atom-type q x y z nx ny nz  (nx,ny,nz are optional -
+  ...                                    see &quot;true flag&quot; input command)
+  ...                
+  N molecule-tag atom-type q x y z nx ny nz  (N = # of atoms)
+
+Velocities
+
+  1 vx vy vz
+  ...
+  ...                
+  N vx vy vz                        (N = # of atoms)
+
+Bonds
+
+  1 bond-type atom-1 atom-2
+  ...
+  N bond-type atom-1 atom-2         (N = # of bonds)
+
+Angles
+
+  1 angle-type atom-1 atom-2 atom-3  (atom-2 is the center atom in angle)
+  ...
+  N angle-type atom-1 atom-2 atom-3  (N = # of angles)
+
+Dihedrals
+
+  1 dihedral-type atom-1 atom-2 atom-3 atom-4  (atoms 2-3 form central bond)
+  ...
+  N dihedral-type atom-1 atom-2 atom-3 atom-4  (N = # of dihedrals)
+
+Impropers
+
+  1 improper-type atom-1 atom-2 atom-3 atom-4  (atom-2 is central atom)
+  ...
+  N improper-type atom-1 atom-2 atom-3 atom-4  (N = # of impropers)
+</PRE>
+</BODY>
+</HTML>

doc/html/2001/deficiencies.html

@@ -0,0 +1,42 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
+<HTML>
+<HEAD>
+    <META NAME="Generator" CONTENT="Cosmo Create 1.0.3">
+</HEAD>
+<BODY>
+<H2>
+LAMMPS Deficiencies</H2>
+<P>
+<A HREF="README.html">Return</A> to top-level of LAMMPS documentation.</P>
+<P>
+This is a brief list of features lacking in the current version of 
+LAMMPS. Some of these deficiencies are because of lack of 
+time/interest; others are just hard!</P>
+<UL>
+    <LI>
+    The calculation of pressure does not include a long-range Van der Waals
+    correction.  This would be a constant for constant volume simulations
+    but is a source of error for constant pressure simulations where
+    the box-size varies dynamically.
+    <LI>
+    The smoothed Coulomb style cannot be used with class 2 force fields. 
+    <LI>
+    The minimizer does not work with constant pressure conditions, nor
+    for some kinds of fixes (constraints).
+    <LI>
+    No support for non-rectilinear boxes (e.g. Parinello-Rahman
+    pressure control).
+    <LI>
+    SHAKE fixes cannot be combined with rREPSA.
+    <LI>
+    In the current F90 version of LAMMPS, Ewald computations are 2x slower 
+    on some machines than they were in the earlier F77 version. This is 
+    probably because of F90 compiler treatment of allocatable arrays. This 
+    slowdown is not an issue with PPPM, which is more commonly used anyway.
+    <LI>
+    LAMMPS uses a spatial-decomposition of the simulation domain, but no
+    other load-balancing -- thus some geometries or density fluctuations can
+    lead to load imbalance on a parallel machine.
+</UL>
+</BODY>
+</HTML>

doc/html/2001/force_fields.html

@@ -0,0 +1,681 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
+<HTML>
+<HEAD>
+    <META NAME="Generator" CONTENT="Cosmo Create 1.0.3">
+</HEAD>
+<BODY>
+<H2>
+LAMMPS Force Fields</H2>
+<P>
+<A HREF="README.html">Return</A> to top-level of LAMMPS documentation</P>
+<P>
+This file outlines the force-field formulas used in LAMMPS. Read this 
+file in conjunction with the <A HREF="data_format.html">data_format</A>
+ and <A HREF="units.html">units</A> files.</P>
+<P>
+The sections of this page are as follows:</P>
+<UL>
+    <LI>
+    <A HREF="#_cch3_930957465">Nonbond Coulomb</A> 
+    <LI>
+    <A HREF="#_cch3_930957471">Nonbond Lennard-Jones</A> 
+    <LI>
+    <A HREF="#_cch3_930957478">Mixing Rules for Lennard-Jones</A> 
+    <LI>
+    <A HREF="#_cch3_930957482">Bonds</A> 
+    <LI>
+    <A HREF="#_cch3_930957488">Angles</A> 
+    <LI>
+    <A HREF="#_cch3_930957509">Dihedrals</A> 
+    <LI>
+    <A HREF="#_cch3_930957513">Impropers</A> 
+    <LI>
+    <A HREF="#_cch3_930957527">Class 2 Force Field</A> 
+</UL>
+<HR>
+<H3>
+<A NAME="_cch3_930957465">Nonbond Coulomb</A></H3>
+<P>
+Whatever Coulomb style is specified in the input command file, the 
+short-range Coulombic interactions are computed by this formula, 
+modified by an appropriate smoother for the smooth, Ewald, PPPM,
+charmm, and debye styles.</P>
+<PRE>
+  E = C q1 q2 / (epsilon * r)
+
+  r = distance (computed by LAMMPS)
+  C = hardwired constant to convert to energy units
+  q1,q2 = charge of each atom in electron units (proton = +1),
+    specified in &quot;Atoms&quot; entry in data file
+  epsilon = dielectric constant (vacuum = 1.0),
+    set by user in input command file
+</PRE>
+For the debye style, the smoother is exp(-kappa*r) where kappa is an
+input parameter.
+<HR>
+<H3>
+<A NAME="_cch3_930957471">Nonbond Lennard-Jones </A></H3>
+<P>
+The style of nonbond potential is specified in the input command file. </P>
+<H4>
+(1) lj/cutoff </H4>
+<PRE>
+
+  E = 4 epsilon [ (sigma/r)^12 - (sigma/r)^6 ]
+
+  standard Lennard Jones potential
+
+  r = distance (computed by LAMMPS)
+
+  coeff1 = epsilon (energy)
+  coeff2 = sigma (distance)
+
+  2 coeffs are listed in data file or set in input script
+  1 cutoff is set in input script
+
+</PRE>
+<H4>
+(2) lj/switch </H4>
+<PRE>
+
+  E = 4 epsilon [ (sigma/r)^12 - (sigma/r)^6 ]  for  r &lt; r_inner
+    = spline fit    for  r_inner &lt; r &lt; cutoff
+    = 0             for r &gt; cutoff
+
+  switching function (spline fit) is applied to standard LJ
+    within a switching region (from r_inner to cutoff) so that
+    energy and force go smoothly to zero
+  spline coefficients are computed by LAMMPS
+    so that at inner cutoff (r_inner) the potential, force, 
+    and 1st-derivative of force are all continuous, 
+    and at outer cutoff (cutoff) the potential and force
+    both go to zero
+
+  r = distance (computed by LAMMPS)
+
+  coeff1 = epsilon (energy)
+  coeff2 = sigma (distance)
+  
+  2 coeffs are listed in data file or set in input script
+  2 cutoffs (r_inner and cutoff) are set in input script
+
+</PRE>
+<H4>
+(3) lj/shift </H4>
+<PRE>
+
+  E = 4 epsilon [ (sigma/(r - delta))^12 - (sigma/(r - delta))^6 ]
+
+  same as lj/cutoff except that r is shifted by delta
+
+  r = distance (computed by LAMMPS)
+
+  coeff1 = epsilon (energy)
+  coeff2 = sigma (distance)
+  coeff3 = delta (distance)
+
+  3 coeffs are listed in data file or set in input script
+  1 cutoff is set in input script
+
+</PRE>
+<H4>
+(4) soft </H4>
+<PRE>
+
+  E = A * [ 1 + cos( pi * r / cutoff ) ]
+
+  useful for pushing apart overlapping atoms by ramping A over time
+
+  r = distance (computed by LAMMPS)
+
+  coeff1 = prefactor A at start of run (energy)
+  coeff2 = prefactor A at end of run (energy)
+
+  2 coeffs are listed in data file or set in input script
+  1 cutoff is set in input script
+
+</PRE>
+<H4>
+(5) class2/cutoff </H4>
+<PRE>
+
+  E = epsilon [ 2 (sigma/r)^9 - 3 (sigma/r)^6 ]
+
+  used with class2 bonded force field
+
+  r = distance (computed by LAMMPS)
+
+  coeff1 = epsilon (energy)
+  coeff2 = sigma (distance)
+
+  2 coeffs are listed in data file or set in input script
+  1 cutoff is set in input script
+</PRE>
+<H4>
+6) lj/charmm </H4>
+<PRE>
+
+  E = 4 epsilon [ (sigma/r)^12 - (sigma/r)^6 ]  for  r &lt; r_inner
+    = switch * E    for  r_inner &lt; r &lt; cutoff
+    = 0             for r &gt; cutoff
+
+  where 
+
+  switch = [(cutoff^2 - r^2)^2 * (cutoff^2 + 2*r^2 - 3*r_inner)] /
+           [(cutoff^2 - r_inner^2)^3]
+
+  switching function is applied to standard LJ
+    within a switching region (from r_inner to cutoff) so that
+    energy and force go smoothly to zero
+  switching function causes that at inner cutoff (r_inner)
+    the potential and force are continuous, 
+    and at outer cutoff (cutoff) the potential and force
+    both go to zero
+
+  r = distance (computed by LAMMPS)
+
+  coeff1 = epsilon (energy)
+  coeff2 = sigma (distance)
+  coeff3 = epsilon for 1-4 interactions (energy)
+  coeff4 = sigma for 1-4 interactions (distance)
+  
+  4 coeffs are listed in data file or set in input script
+  2 cutoffs (r_inner and cutoff) are set in input script
+</PRE>
+<HR>
+<H3>
+<A NAME="_cch3_930957478">Mixing Rules for Lennard-Jones</A></H3>
+<P>
+The coefficients for each nonbond style are input in either the data 
+file by the &quot;read data&quot; command or in the input script using 
+the &quot;nonbond coeff&quot; command. In the former case, only one set 
+of coefficients is input for each atom type. The cross-type coeffs are 
+computed using one of three possible mixing rules: </P>
+<PRE>
+
+ geometric:  epsilon_ij = sqrt(epsilon_i * epsilon_j)
+             sigma_ij = sqrt(sigma_i * sigma_j)
+
+ arithmetic: epsilon_ij = sqrt(epsilon_i * epsilon_j)
+             sigma_ij = (sigma_i + sigma_j) / 2
+
+ sixthpower: epsilon_ij =
+               (2 * sqrt(epsilon_i*epsilon_j) * sigma_i^3 * sigma_j^3) /
+               (sigma_i^6 + sigma_j^6)
+             sigma_ij=  ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6)
+
+</PRE>
+<P>
+The default mixing rule for nonbond styles lj/cutoff, lj/switch, 
+lj/shift, and soft is &quot;geometric&quot;. The default for nonbond 
+style class2/cutoff is &quot;sixthpower&quot;. </P>
+<P>
+The default can be overridden using the &quot;mixing style&quot;
+command. Two exceptions to this are for the nonbond style soft, for
+which only an epsilon prefactor is input. This is always mixed
+geometrically.  Also, for nonbond style lj/shift, the delta
+coefficient is always mixed using the rule </P>
+<UL>
+    <LI>
+    delta_ij = (delta_i + delta_j) / 2 
+</UL>
+<HR>
+<H3>
+<A NAME="_cch3_930957482">Bonds</A></H3>
+<P>
+The style of bond potential is specified in the input command file.</P>
+<H4>
+(1) harmonic </H4>
+<PRE>
+
+  E = K (r - r0)^2
+
+  standard harmonic spring
+
+  r = distance (computed by LAMMPS)
+
+  coeff1 = K (energy/distance^2)  (the usual 1/2 is included in the K)
+  coeff2 = r0 (distance)
+
+  2 coeffs are listed in data file or set in input script
+
+</PRE>
+<H4>
+(2) FENE/standard </H4>
+<PRE>
+
+  E = -0.5 K R0^2 * ln[1 - (r/R0)^2] +
+    4 epsilon [(sigma/r)^12 - (sigma/r)^6] + epsilon
+
+  finite extensible nonlinear elastic (FENE) potential for
+    polymer bead-spring models
+  see Kremer, Grest, J Chem Phys, 92, p 5057 (1990)
+
+  r = distance (computed by LAMMPS)
+
+  coeff1 = K (energy/distance^2)
+  coeff2 = R0 (distance)
+  coeff3 = epsilon (energy)
+  coeff4 = sigma (distance)
+
+  1st term is attraction, 2nd term is repulsion (shifted LJ)
+  1st term extends to R0
+  2nd term only extends to the minimum of the LJ potential,
+    a cutoff distance computed by LAMMPS (2^(1/6) * sigma)
+
+  4 coeffs are listed in data file or set in input script
+
+</PRE>
+<H4>
+(3) FENE/shift </H4>
+<PRE>
+
+  E = -0.5 K R0^2 * ln[1 - ((r - delta)/R0)^2] +
+    4 epsilon [(sigma/(r - delta))^12 - (sigma/(r - delta))^6] + epsilon
+
+  same as FENE/standard expect that r is shifted by delta
+
+  r = distance (computed by LAMMPS)
+
+  coeff1 = K (energy/distance^2)
+  coeff2 = R0 (distance)
+  coeff3 = epsilon (energy)
+  coeff4 = sigma (distance)
+  coeff5 = delta (distance)
+
+  1st term is attraction, 2nd term is repulsion (shifted LJ)
+  1st term extends to R0
+  2nd term only extends to the minimum of the LJ potential,
+    a cutoff distance computed by LAMMPS (2^(1/6) * sigma + delta)
+
+  5 coeffs are listed in data file or set in input script
+
+</PRE>
+<H4>
+(4) nonlinear </H4>
+<PRE>
+
+  E = epsilon (r - r0)^2 / [ lamda^2 - (r - r0)^2 ]
+
+  non-harmonic spring of equilibrium length r0
+    with finite extension of lamda
+  see Rector, Van Swol, Henderson, Molecular Physics, 82, p 1009 (1994)
+
+  r = distance (computed by LAMMPS)
+
+  coeff1 = epsilon (energy)
+  coeff2 = r0 (distance)
+  coeff3 = lamda (distance)
+
+  3 coeffs are listed in data file or set in input script
+
+</PRE>
+<H4>
+(5) class2 </H4>
+<PRE>
+
+  E = K2 (r - r0)^2  +  K3 (r - r0)^3  +  K4 (r - r0)^4
+
+  r = distance (computed by LAMMPS)
+
+  coeff1 = r0 (distance)
+  coeff2 = K2 (energy/distance^2)
+  coeff3 = K3 (energy/distance^3)
+  coeff4 = K4 (energy/distance^4)
+
+  4 coeffs are listed in data file - cannot be set in input script
+</PRE>
+<HR>
+<H3>
+<A NAME="_cch3_930957488">Angles </A></H3>
+<P>
+The style of angle potential is specified in the input command file. </P>
+<H4>
+(1) harmonic </H4>
+<PRE>
+
+  E = K (theta - theta0)^2
+
+  theta = radians (computed by LAMMPS)
+
+  coeff1 = K (energy/radian^2) (the usual 1/2 is included in the K)
+  coeff2 = theta0 (degrees) (converted to radians within LAMMPS)
+
+  2 coeffs are listed in data file or set in input script
+
+</PRE>
+<H4>
+(2) class2 </H4>
+<PRE>
+
+  E = K2 (theta - theta0)^2 +  K3 (theta - theta0)^3 + 
+       K4 (theta - theta0)^4
+
+  theta = radians (computed by LAMMPS)
+
+  coeff1 = theta0 (degrees) (converted to radians within LAMMPS)
+  coeff2 = K2 (energy/radian^2)
+  coeff3 = K3 (energy/radian^3)
+  coeff4 = K4 (energy/radian^4)
+
+  4 coeffs are listed in data file - cannot be set in input script
+
+</PRE>
+<H4>
+(3) charmm </H4>
+<PRE>
+  (harmonic + Urey-Bradley)
+
+  E = K (theta - theta0)^2 + K_UB (r_13 - r_UB)^2
+
+  theta = radians (computed by LAMMPS)
+  r_13 = distance (computed by LAMMPS)
+
+  coeff1 = K (energy/radian^2) (the usual 1/2 is included in the K)
+  coeff2 = theta0 (degrees) (converted to radians within LAMMPS)
+  coeff3 = K_UB (energy/distance^2)
+  coeff4 = r_UB (distance)
+
+  4 coeffs are listed in data file or set in input script
+
+</PRE>
+<H4>
+(4) cosine </H4>
+<PRE>
+  E = K (1 + cos(theta))
+
+  theta = radians (computed by LAMMPS)
+
+  coeff1 = K (energy)
+
+  1 coeff is listed in data file or set in input script
+
+</PRE>
+<H3>
+<A NAME="_cch3_930957509">Dihedrals </A></H3>
+<P>
+The style of dihedral potential is specified in the input command
+file.  IMPORTANT NOTE for all these dihedral styles: in the LAMMPS
+force field the trans position = 180 degrees, while in some force
+fields trans = 0 degrees. </P>
+
+<H4>
+(1) harmonic </H4>
+<PRE>
+
+  E = K [1 + d * cos (n*phi) ]
+
+  phi = radians (computed by LAMMPS)
+
+  coeff1 = K (energy)
+  coeff2 = d (+1 or -1)
+  coeff3 = n (1,2,3,4,6)
+
+  Additional cautions when comparing to other force fields:
+
+  some force fields reverse the sign convention on d so that
+    E = K [1 - d * cos(n*phi)]
+  some force fields divide/multiply K by the number of multiple
+    torsions that contain the j-k bond in an i-j-k-l torsion
+  some force fields let n be positive or negative which 
+    corresponds to d = 1,-1
+ 
+  3 coeffs are listed in data file or set in input script
+</PRE>
+<H4>
+(2) class2 </H4>
+<PRE>
+
+  E = SUM(n=1,3) { K_n [ 1 - cos( n*Phi - Phi0_n ) ] }
+
+  phi = radians (computed by LAMMPS)
+
+  coeff1 = K_1 (energy)
+  coeff2 = Phi0_1 (degrees) (converted to radians within LAMMPS)
+  coeff3 = K_2 (energy)
+  coeff4 = Phi0_2 (degrees) (converted to radians within LAMMPS)
+  coeff5 = K_3 (energy)
+  coeff6 = Phi0_3 (degrees) (converted to radians within LAMMPS)
+
+  6 coeffs are listed in data file - cannot be set in input script
+</PRE>
+<H4>
+(3) multiharmonic </H4>
+<PRE>
+
+  E = SUM(n=1,5) { A_n * cos(Phi)^(n-1) }
+
+  phi = radians (computed by LAMMPS)
+
+  coeff1 = A_1
+  coeff2 = A_2
+  coeff3 = A_3
+  coeff4 = A_4
+  coeff5 = A_5
+
+  5 coeffs are listed in data file or set in input script
+</PRE>
+<H4>
+(4) charmm </H4>
+<PRE>
+(harmonic + 1-4 interactions)
+
+  E = K [1 + cos (n*phi + d) ]
+
+  phi = radians (computed by LAMMPS)
+
+  coeff1 = K (energy)
+  coeff2 = n (1,2,3,4,6)
+  coeff3 = d (0 or 180 degrees) (converted to radians within LAMMPS)
+  coeff4 = weighting factor to turn on/off 1-4 neighbor nonbond interactions 
+
+  coeff4 weight values are from 0.0 to 1.0 and are used to multiply the
+  energy and force interaction (both Coulombic and LJ) between the 2 atoms
+  weight of 0.0 means no interaction
+  weight of 1.0 means full interaction
+
+  must be used with the special bonds charmm command 
+  "special bonds 0 0 0") which shuts off the uniform special bonds and
+  allows pair-specific special bonds for the 1-4 interactions to be
+  defined in the data file
+
+  LAMMPS assumes that all 1-4 interaction distances, which are
+  generally less than 6 Angstroms, are less than the smallest of the
+  inner LJ and Coulombic cutoffs, which are generally at least 8
+  Angstroms.
+ 
+  4 coeffs are listed in data file or set in input script
+</PRE>
+<HR>
+<H3>
+<A NAME="_cch3_930957513">Impropers</A></H3>
+<P>
+The style of improper potential is specified in the input command file. </P>
+<H4>
+(1) harmonic </H4>
+<PRE>
+
+  E = K (chi - chi0)^2
+
+  chi = radians (computed by LAMMPS)
+
+  coeff1 = K (energy/radian^2) (the usual 1/2 is included in the K)
+  coeff2 = chi0 (degrees) (converted to radians within LAMMPS)
+
+  2 coeffs are listed in data file or set in input script
+</PRE>
+<H4>
+(2) cvff </H4>
+<PRE>
+
+  E = K [1 + d * cos (n*chi) ]
+
+  chi = radians (computed by LAMMPS)
+
+  coeff1 = K (energy)
+  coeff2 = d (+1 or -1)
+  coeff3 = n (0,1,2,3,4,6)
+
+  3 coeffs are listed in data file or set in input script
+</PRE>
+<H4>
+(3) class2 </H4>
+<PRE>
+
+  same formula, coeffs, and meaning as &quot;harmonic&quot; except that LAMMPS
+    averages all 3 angle-contributions to chi
+  in class 2 this is called a Wilson out-of-plane interaction
+
+  2 coeffs are listed in data file - cannot be set in input script
+</PRE>
+<HR>
+<H3>
+<A NAME="_cch3_930957527">Class 2 Force Field</A></H3>
+<P>
+If class 2 force fields are selected in the input command file,
+additional cross terms are computed as part of the force field.  All
+class 2 coefficients must be set in the data file; they cannot be set
+in the input script.</P>
+<H4>
+Bond-Bond (computed within class 2 angles) </H4>
+<PRE>
+
+  E = K (r - r0) * (r' - r0')
+
+  r,r' = distance (computed by LAMMPS)
+
+  coeff1 = K (energy/distance^2)
+  coeff2 = r0 (distance)
+  coeff3 = r0' (distance)
+
+  3 coeffs are input in data file
+</PRE>
+<H4>
+Bond-Angle (computed within class 2 angles for each of 2 bonds) </H4>
+<PRE>
+
+  E = K_n (r - r0_n) * (theta - theta0)
+
+  r = distance (computed by LAMMPS)
+  theta = radians (computed by LAMMPS)
+
+  coeff1 = K_1 (energy/distance-radians)
+  coeff2 = K_2 (energy/distance-radians)
+  coeff3 = r0_1 (distance)
+  coeff4 = r0_2 (distance)
+
+  Note: theta0 is known from angle coeffs so don't need it specified here
+
+  4 coeffs are listed in data file
+</PRE>
+<H4>
+Middle-Bond-Torsion (computed within class 2 dihedral) </H4>
+<PRE>
+
+  E = (r - r0) * [ F1*cos(phi) + F2*cos(2*phi) + F3*cos(3*phi) ]
+
+  r = distance (computed by LAMMPS)
+  phi = radians (computed by LAMMPS)
+
+  coeff1 = F1 (energy/distance)
+  coeff2 = F2 (energy/distance)
+  coeff3 = F3 (energy/distance)
+  coeff4 = r0 (distance)
+
+  4 coeffs are listed in data file
+</PRE>
+<H4>
+End-Bond-Torsion (computed within class 2 dihedral for each of 2 bonds) </H4>
+<PRE>
+
+  E = (r - r0_n) * [ F1_n*cos(phi) + F2_n*cos(2*phi) + F3_n*cos(3*phi) ]
+
+  r = distance (computed by LAMMPS)
+  phi = radians (computed by LAMMPS)
+
+  coeff1 = F1_1 (energy/distance)
+  coeff2 = F2_1 (energy/distance)
+  coeff3 = F3_1 (energy/distance)
+  coeff4 = F1_2 (energy/distance)
+  coeff5 = F2_3 (energy/distance)
+  coeff6 = F3_3 (energy/distance)
+  coeff7 = r0_1 (distance)
+  coeff8 = r0_2 (distance)
+
+  8 coeffs are listed in data file
+</PRE>
+<H4>
+Angle-Torsion (computed within class 2 dihedral for each of 2 angles) </H4>
+<PRE>
+
+  E = (theta - theta0) * [ F1_n*cos(phi) + F2_n*cos(2*phi) + F3_n*cos(3*phi) ]
+
+  theta = radians (computed by LAMMPS)
+  phi = radians (computed by LAMMPS)
+
+  coeff1 = F1_1 (energy/radians)
+  coeff2 = F2_1 (energy/radians)
+  coeff3 = F3_1 (energy/radians)
+  coeff4 = F1_2 (energy/radians)
+  coeff5 = F2_3 (energy/radians)
+  coeff6 = F3_3 (energy/radians)
+  coeff7 = theta0_1 (degrees) (converted to radians within LAMMPS)
+  coeff8 = theta0_2 (degrees) (converted to radians within LAMMPS)
+
+  8 coeffs are listed in data file
+</PRE>
+<H4>
+Angle-Angle-Torsion (computed within class 2 dihedral) </H4>
+<PRE>
+
+  E = K (theta - theta0) * (theta' - theta0') * (phi - phi0)
+
+  theta,theta' = radians (computed by LAMMPS)
+  phi = radians (computed by LAMMPS)
+
+  coeff1 = K (energy/radians^3)
+  coeff2 = theta0 (degrees) (converted to radians within LAMMPS)
+  coeff3 = theta0' (degrees) (converted to radians within LAMMPS)
+
+  Note: phi0 is known from dihedral coeffs so don't need it specified here
+
+  3 coeffs are listed in data file
+
+</PRE>
+<H4>
+Bond-Bond-13-Torsion (computed within class 2 dihedral) </H4>
+<PRE>
+
+  E = K * (r1 - r10)*(r3 - r30)
+
+  r1,r3 = bond lengths of bonds 1 and 3 (computed by LAMMPS)
+
+  coeff1 = K (energy/distance^2)
+  coeff2 = r10 (distance) = equilibrium bond length for bond 1
+  coeff3 = r30 (distance) = equilibrium bond length for bond 3
+
+  K is only non-zero for aromatic rings 
+
+  3 coeffs are listed in data file
+
+</PRE>
+<H4>
+Angle-Angle (computed within class 2 improper for each of 3 pairs of 
+angles) </H4>
+<PRE>
+
+  E = K_n (theta - theta0_n) * (theta' - theta0_n')
+
+  theta,theta' = radians (computed by LAMMPS)
+
+  coeff1 = K_1 (energy/radians^2)
+  coeff2 = K_2 (energy/radians^2)
+  coeff3 = K_3 (energy/radians^2)
+  coeff4 = theta0_1 (degrees) (converted to radians within LAMMPS)
+  coeff5 = theta0_2 (degrees) (converted to radians within LAMMPS)
+  coeff6 = theta0_3 (degrees) (converted to radians within LAMMPS)
+
+  6 coeffs are listed in data file
+</PRE>
+</BODY>
+</HTML>

doc/html/2001/history.html

@@ -0,0 +1,205 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
+<HTML>
+<HEAD>
+    <META NAME="Generator" CONTENT="Cosmo Create 1.0.3">
+</HEAD>
+<BODY>
+<H2>
+History of LAMMPS</H2>
+<P>
+<A HREF="README.html">Return</A> to top-level of LAMMPS documentation.</P>
+<P>
+This is a brief history of features added to each version of LAMMPS.</P>
+<HR>
+<H3>
+LAMMPS 2001 - November 2001</H3>
+<UL>
+    <LI>
+    F90 + MPI version of code 
+    <LI>
+    dynamic memory, no param.h file settings to twiddle, see "extra memory"
+    command
+    <LI>
+    changed required ordering of some input script commands (see discussion in
+    <A HREF="input_commands.html">input_commands</A>) file
+    <LI>
+    new commands: "extra memory", "maximum cutoff", "restart version",
+    "angle coeff", "dihedral coeff", "improper coeff",
+    "volume control", "slab volume", "rotation zero"
+    <LI>
+    changed meaning or syntax of commands:
+    "special bonds", "fix style rescale", "fix style hoover/drag",
+    "temp control rescale", "press control", "restart"
+    <LI>
+    deleted commands: "log file", "press_x control" (and y,z)
+    <LI>
+    better match to CHARMM force fields via "nonbond style lj/charmm",
+    "coulomb style charmm/switch", "angle style charmm", dihedral style charmm"
+    (due to Mark Stevens and Paul Crozier)
+    <LI>
+    changed "special bonds" default to 0.0 weighting on 1-4 interactions for
+    CHARMM compatibility, added "special bonds amber" option for AMBER
+    compatibility
+    <LI>
+    ghost atoms and new treatment of periodic boundary conditions, 
+    this allows for cutoffs &gt; box-size and faster neighbor binning,
+    binned neighbor list construction is now the default as it is almost
+    always faster
+    <LI>
+    perform blocked-input from data and restart files, faster for many MPI 
+    implementations (due to Mathias Puetz)
+    <LI>
+    added Velocities option to data file to initialize each atom's
+    velocity (see <A HREF="data_format.html">data_format</A> file) 
+    <LI>
+    pressure control was decoupled from temperature control, so that
+    constant NPH simulations can be run (not just NPT), temperature 
+    controls such as rescale or Langevin can now be used with constant P
+    simulations (due to Mark Stevens)
+    <LI>
+    temperature rescaling (either in "temp control" or "fix style rescale")
+    has an added fractional parameter which allows it to be applied
+    in a lightweight or heavy-handed way to induce the desired temperature
+    <LI>
+    got rid of crib.html file, see global.f for documentation of all 
+    variables
+    <LI>
+    2-d slab Ewald and PPPM option, (see "slab volume" in
+    <A HREF="input_commands.html">input commands</A>) (due to Paul Crozier)
+    <LI>
+    new multiharmonic dihedral and cvff improper force-field options
+    (due to Mathias Puetz)
+    <LI>
+    SHAKE constraint for small clusters of atoms, see "fix style shake"
+    and "assign fix bondtype" commands
+    <LI>
+    added option to output restart files with timestep stamp or to toggle
+    between 2 files, see "restart" command
+    <LI>
+    tools for converting to/from other MD program formats:
+    msi2lmp (updated by John Carpenter),
+    lmp2arc (due to John Carpenter),
+    amber2lammps & dump2trj (Python scripts due to Keir Novik)
+    <LI>
+    tools for creating and massaging LAMMPS data and restart files:
+    setup_lj, setup_flow_2d, setup_chain, peek_restart, restart2data,
+    replicate
+</UL>
+<HR>
+<H3>
+LAMMPS 99 - June 99 </H3>
+<UL>
+    <LI>
+    all-MPI version of code (F77 + C + MPI) for maximum portablility 
+    <LI>
+    only one PPPM choice now, the better of the two earlier ones 
+    <LI>
+    PPPM uses portable FFTs and data remapping routines, written in C w/ 
+    MPI, can now use non-power-of-2 processors and grid sizes 
+    <LI>
+    auto-mapping of simulation box to processors 
+    <LI>
+    removed a few unused/unneeded commands (bdump, log file, id string, 
+    limit) 
+    <LI>
+    changed syntax of some commands for simplicity &amp; consistency (see <A
+     HREF="input_commands.html">input commands</A>) 
+    <LI>
+    changed method of calling/writing user diagnostic routines to be 
+    simpler 
+    <LI>
+    documentation in HTML format 
+</UL>
+<HR>
+<H3>
+Version 5.0 - Oct 1997 </H3>
+<UL>
+    <LI>
+    final version of class II force fields (due to Eric Simon)
+    <LI>
+    new formulation of NVE, NVT, NPT and rRESPA integrators (due to
+    Mark Stevens)
+    <LI>
+    new version of msi2lmp pre-processing tool, does not require DISCOVER 
+    to run, only DISCOVER force field files (due to Steve Lustig)
+    <LI>
+    energy minimizer, Hessian-free truncated Newton method
+    (due to Todd Plantenga)
+    <LI>
+    new pressure controllers and constraints (due to Mark Stevens)
+    <LI>
+    replicate tool for generating new data files from old ones 
+</UL>
+<HR ALIGN="LEFT">
+<H3>
+Version 4.0 - March 1997 </H3>
+<UL>
+    <LI>
+    1st version of class II force fields (due to Eric Simon)
+    <LI>
+    new, faster PPPM solver (newpppm, due to Roy Pollock)
+    <LI>
+    rRESPA (due to Mark Stevens)
+    <LI>
+    new data file format 
+    <LI>
+    new constraints, diagnostics 
+    <LI>
+    msi2lmp pre-processing tool (due to Steve Lustig)
+</UL>
+<HR>
+<H3>
+Version 3.0 - March 1996 </H3>
+<UL>
+    <LI>
+    more general force-field formulation 
+    <LI>
+    atom/group constraints 
+    <LI>
+    LJ units and bond potentials 
+    <LI>
+    smoothed LJ potential option 
+    <LI>
+    Langevin thermostat 
+    <LI>
+    Newton's 3rd law option 
+    <LI>
+    hook for user-supplied diagnostic routines 
+</UL>
+<HR>
+<H3>
+Version 2.0 - October 1995 </H3>
+<UL>
+    <LI>
+    bug fix of velocity initialization which caused drift 
+    <LI>
+    PPPM for long-range Coulombic (due to Roy Pollock)
+    <LI>
+    constant NPT (due to Mark Stevens)
+</UL>
+<HR>
+<H3>
+Version 1.1 - February 1995 </H3>
+<UL>
+    <LI>
+    Ewald for long-range Coulombic (due to Roy Pollock)
+    <LI>
+    full Newton's 3rd law (doubled communication) 
+    <LI>
+    dumping of atom positions and velocities 
+    <LI>
+    restart files 
+</UL>
+<HR>
+<H3>
+Version 1.0 - January 1995 </H3>
+<UL>
+    <LI>
+    short-range bonded and non-bonded forces 
+    <LI>
+    partial Newton's 3rd law 
+    <LI>
+    velocity-Verlet integrator 
+</UL>
+</BODY>
+</HTML>

doc/html/2001/units.html

@@ -0,0 +1,119 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
+<HTML>
+<HEAD>
+    <META NAME="Generator" CONTENT="Cosmo Create 1.0.3">
+</HEAD>
+<BODY>
+<H2>
+LAMMPS Units</H2>
+<P>
+<A HREF="README.html">Return</A> to top-level LAMMPS documentation.</P>
+<P>
+This file describes the units associated with many of the key variables 
+and equations used inside the LAMMPS code. Units used for input command 
+parameters are described in the input_commands file. The input command 
+&quot;units&quot; selects between conventional and Lennard-Jones units. 
+See the force_fields file for more information on units for the force 
+field parameters that are input from data files or input scripts. </P>
+<P>
+Conventional units: </P>
+<UL>
+    <LI>
+    distance = Angstroms 
+    <LI>
+    time = femtoseconds 
+    <LI>
+    mass = grams/mole 
+    <LI>
+    temperature = degrees K 
+    <LI>
+    pressure = atmospheres 
+    <LI>
+    energy = Kcal/mole 
+    <LI>
+    velocity = Angstroms/femtosecond 
+    <LI>
+    force = grams/mole * Angstroms/femtosecond^2 
+    <LI>
+    charge = +/- 1.0 is proton/electron
+</UL>
+<P>
+LJ reduced units: </P>
+<UL>
+    <LI>
+    distance = sigmas 
+    <LI>
+    time = reduced LJ tau 
+    <LI>
+    mass = ratio to unitless 1.0
+    <LI>
+    temperature = reduced LJ temp 
+    <LI>
+    pressure = reduced LJ pressure 
+    <LI>
+    energy = epsilons 
+    <LI>
+    velocity = sigmas/tau 
+    <LI>
+    force = reduced LJ force (sigmas/tau^2) 
+    <LI>
+    charge = ratio to unitless 1.0
+</UL>
+<HR>
+<P>
+This listing of variables assumes conventional units; to convert to LJ 
+reduced units, simply substitute the appropriate term from the list 
+above. E.g. x is in sigmas in LJ units. Per-mole in any of the units 
+simply means for 6.023 x 10^23 atoms.</P>
+<P>
+</P>
+<PRE>
+Meaning        Variable        Units
+
+positions      x               Angstroms
+velocities     v               Angstroms / click (see below)
+forces         f               Kcal / (mole - Angstrom)                
+masses         mass            gram / mole
+charges        q               electron units (-1 for an electron)
+                                 (1 e.u. = 1.602 x 10^-19 coul)
+
+time           ---             clicks (1 click = 48.88821 fmsec)
+timestep       dt              clicks
+input timestep dt_in           fmsec
+time convert   dtfactor        48.88821 fmsec / click
+
+temperature     t_current       degrees K
+                t_start
+                t_stop
+input damping   t_freq_in       inverse fmsec
+internal temp   t_freq          inverse clicks
+  damping
+
+dielec const    dielectric      1.0 (unitless)
+Boltmann const  boltz           0.001987191 Kcal / (mole - degree K)
+
+virial          virial[xyz]     Kcal/mole = r dot F
+pressure factor pfactor         68589.796 (convert internal to atmospheres)
+internal        p_current       Kcal / (mole - Angs^3)
+  pressure      p_start
+                p_stop
+input press     p_start_in      atmospheres
+                p_stop_in
+output press    log file        atmospheres
+input damping   p_freq_in       inverse time
+internal press  p_freq          inverse clicks
+  damping
+
+pot eng         e_potential     Kcal/mole
+kin eng         e_kinetic       Kcal/mole
+eng convert     efactor         332.0636 (Kcal - Ang) / (q^2 - mole)
+                                (convert Coulomb eng to Kcal/mole)
+
+LJ coeffs       lja,ljb         Kcal-Angs^(6,12)/mole
+
+bond            various         see force_fields file
+  parameters    2,3,4-body
+                terms
+</PRE>
+</BODY>
+</HTML>

doc/html/99/README.html

@@ -0,0 +1,161 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
+<HTML>
+<HEAD>
+    <META NAME="Generator" CONTENT="Cosmo Create 1.0.3">
+</HEAD>
+<BODY>
+<H2>
+LAMMPS</H2>
+<P>
+LAMMPS = Large-scale Atomic/Molecular Massively Parallel Simulator</P>
+<P>
+This is the documentation for the LAMMPS 99 version, written in F77,
+which has been superceded by more current versions.  See the <A
+HREF="http://www.cs.sandia.gov/~sjplimp/lammps.html">LAMMPS WWW
+Site</A> for more information.
+<P>
+LAMMPS is a classical molecular dynamics code designed for simulating 
+molecular and atomic systems on parallel computers using 
+spatial-decomposition techniques. It runs on any parallel platform that 
+supports the MPI message-passing library or on single-processor 
+workstations.</P>
+<P>
+LAMMPS 99 is copyrighted code that is distributed freely as
+open-source software under the GNU Public License (GPL).  See the
+LICENSE file or <A HREF="http://www.gnu.org">www.gnu.org</A> for more
+details.  Basically the GPL allows you as a user to use, modify, or
+distribute LAMMPS however you wish, so long as any software you
+distribute remains under the GPL.
+<P>
+Features of LAMMPS 99 include:</P>
+<UL>
+    <LI>
+    short-range pairwise Lennard-Jones and Coulombic interactions 
+    <LI>
+    long-range Coulombic interactions via Ewald or PPPM (particle-mesh 
+    Ewald) 
+    <LI>
+    short-range harmonic bond potentials (bond, angle, torsion, improper) 
+    <LI>
+    short-range class II (cross-term) molecular potentials 
+    <LI>
+    NVE, NVT, NPT dynamics 
+    <LI>
+    constraints on atoms or groups of atoms 
+    <LI>
+    rRESPA long-timescale integrator 
+    <LI>
+    energy minimizer (Hessian-free truncated Newton method) 
+</UL>
+<P>
+More details about the code can be found <A HREF="#_cch3_930958294">here</A>, 
+in the HTML-based documentation. There is also a conference paper 
+describing the parallel algorithms used in the code:</P>
+<P>
+S. J. Plimpton, R. Pollock, M. Stevens, &quot;Particle-Mesh Ewald and 
+rRESPA for Parallel Molecular Dynamics Simulations&quot;, in Proc of 
+the Eighth SIAM Conference on Parallel Processing for Scientific 
+Computing, Minneapolis, MN, March 1997.</P>
+<P>
+LAMMPS was originally developed as part of a 5-way CRADA collaboration 
+between 3 industrial partners (Cray Research, Bristol-Myers Squibb, and 
+Dupont) and 2 DoE laboratories (Sandia National Laboratories and 
+Lawrence Livermore National Laboratories).</P>
+<P>
+The primary author of LAMMPS is Steve Plimpton, but others have written 
+or worked on significant portions of the code:</P>
+<UL>
+    <LI>
+    Roy Pollock (LLNL): Ewald, PPPM solvers 
+    <LI>
+    Mark Stevens (Sandia): rRESPA, NPT integrators 
+    <LI>
+    Eric Simon (Cray Research): class II force fields 
+    <LI>
+    Todd Plantenga (Sandia): energy minimizer 
+    <LI>
+    Steve Lustig (Dupont): msi2lmp tool 
+    <LI>
+    Mike Peachey (Cray Research): msi2lmp tool 
+</UL>
+<P>
+Other CRADA partners involved in the design and testing of LAMMPS are </P>
+<UL>
+    <LI>
+    John Carpenter (Cray Research) 
+    <LI>
+    Terry Stouch (Bristol-Myers Squibb) 
+    <LI>
+    Jim Belak (LLNL) 
+</UL>
+<P>
+LAMMPS is copyrighted code that is distributed freely as open-source
+software under the GNU Public License (GPL).  See the LICENSE file or
+<A HREF="http://www.gnu.org">www.gnu.org</A> for more details.
+Basically the GPL allows you as a user to use, modify, or distribute
+LAMMPS however you wish, so long as any software you distribute
+remains under the GPL.
+<P>
+If you have questions about LAMMPS, please contact me:
+</P>
+<DL>
+    <DT>
+    Steve Plimpton
+    <DD>
+    sjplimp@sandia.gov 
+    <DD>
+    www.cs.sandia.gov/~sjplimp 
+    <DD>
+    Sandia National Labs 
+    <DD>
+    Albuquerque, NM 87185
+</DL>
+<HR>
+<H3>
+<A NAME="_cch3_930958294">More Information about LAMMPS</A></H3>
+<DIR>
+    <LI>
+    <A HREF="basics.html">Basics</A> 
+    <DIR>
+        <LI>
+        how to make, run, and test LAMMPS with the example problems 
+    </DIR>
+    <LI>
+    <A HREF="input_commands.html">Input Commands</A> 
+    <DIR>
+        <LI>
+        a complete listing of input commands used by LAMMPS 
+    </DIR>
+    <LI>
+    <A HREF="data_format.html">Data Format</A> 
+    <DIR>
+        <LI>
+        the data file format used by LAMMPS 
+    </DIR>
+    <LI>
+    <A HREF="force_fields.html">Force Fields</A> 
+    <DIR>
+        <LI>
+        the equations LAMMPS uses to compute force-fields 
+    </DIR>
+    <LI>
+    <A HREF="units.html">Units</A> 
+    <DIR>
+        <LI>
+        the input/output and internal units for LAMMPS variables 
+    </DIR>
+    <LI>
+    <A HREF="crib.html">Crib</A> 
+    <DIR>
+        <LI>
+        a one-line description of the variables used in LAMMPS 
+    </DIR>
+    <LI>
+    <A HREF="history.html">History</A> 
+    <DIR>
+        <LI>
+        a brief timeline of features added to LAMMPS 
+    </DIR>
+</DIR>
+</BODY>
+</HTML>

doc/html/99/basics.html

@@ -0,0 +1,207 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
+<HTML>
+<HEAD>
+    <META NAME="Generator" CONTENT="Cosmo Create 1.0.3">
+</HEAD>
+<BODY>
+<H2>
+Basics of Using LAMMPS</H2>
+<P>
+<A HREF="README.html">Return</A> to top-level of LAMMPS documentation.</P>
+<UL>
+    <LI>
+    <A HREF="#_cch3_931273040">Distribution</A> 
+    <LI>
+    <A HREF="#_cch3_930327142">Making LAMMPS</A> 
+    <LI>
+    <A HREF="#_cch3_930327155">Running LAMMPS</A> 
+    <LI>
+    <A HREF="#_cch3_930759879">Examples</A> 
+    <LI>
+    <A HREF="#_cch3_931282515">Other Tools</A> 
+</UL>
+<HR>
+<H3>
+<A NAME="_cch3_931273040">Distribution</A></H3>
+<P>
+When you unzip/untar the LAMMPS distribution you should have 5 
+directories: </P>
+<UL>
+    <LI>
+    src = source files for LAMMPS 
+    <LI>
+    doc = HTML documentation 
+    <LI>
+    examples = sample problems with inputs and outputs 
+    <LI>
+    msi2lmp = tool for converting files from DISCOVER to LAMMPS format 
+    (this requires that you have DISCOVER force field files) 
+    <LI>
+    tools = serial program for replicating data files 
+</UL>
+<HR>
+<H3>
+<A NAME="_cch3_930327142">Making LAMMPS</A></H3>
+<P>
+The src directory contains the F77 and C source files for LAMMPS as 
+well as several sample Makefiles for different machines. To make LAMMPS 
+for a specfic machine, you simply type</P>
+<P>
+make machine</P>
+<P>
+from within the src directoy. E.g. &quot;make sgi&quot; or &quot;make 
+t3e&quot;. This should create an executable named lmp_sgi or lmp_t3e.</P>
+<P>
+In the src directory, there is one top-level Makefile and several 
+low-level machine-specific files named Makefile.xxx where xxx = the 
+machine name. If a low-level Makefile exists for your platform, you do 
+not need to edit the top-level Makefile. However you should check the 
+system-specific section of the low-level Makefile to make sure the 
+various paths are correct for your environment. If a low-level Makefile 
+does not exist for your platform, you will need to add a suitable 
+target to the top-level Makefile. You will also need to create a new 
+low-level Makefile using one of the existing ones as a template. If you 
+wish to make LAMMPS for a single-processor workstation that doesn't 
+have an installed MPI library, you can specify the serial target which 
+uses a directory of MPI stubs to link against - e.g. &quot;make 
+serial&quot;. You will need to make the stub library (see STUBS 
+directory) on your workstation before doing this.</P>
+<P>
+Note that the two-level Makefile system allows you to make LAMMPS for 
+multiple platforms. Each target creates its own object directory for 
+separate storage of its *.o files.</P>
+<P>
+There are a couple compiler switches of interest which can be specified 
+in the low-level Makefiles. If you use a F77FLAGS switch of -DSYNC then 
+synchronization calls will be made before the timing routines in 
+integrate.f. This may slow down the code slightly, but will make the 
+reported timings at the end of a run more accurate. The CCFLAGS setting 
+in the low-level Makefiles requires a FFT setting, for example 
+-DFFT_SGI or -DFFT_T3E. This is for inclusion of the appropriate 
+machine-specific native 1-d FFT libraries on various platforms. 
+Currently, the supported machines and switches (used in fft_3d.c) are 
+FFT_SGI, FFT_DEC, FFT_INTEL, FFT_T3E, and FFT_FFTW. The latter is a 
+publicly available portable FFT library, <A HREF="http://www.fftw.org">FFTW</A>, 
+which you can install on any machine. If none of these options is 
+suitable for your machine, please contact me, and we'll discuss how to 
+add the capability to call your machine's native FFT library.</P>
+<HR>
+<H3>
+<A NAME="_cch3_930327155">Running LAMMPS</A></H3>
+<P>
+LAMMPS is run by redirecting a file of input commands into it.</P>
+<P>
+lmp_sgi &lt; in.lj</P>
+<P>
+lmp_t3e &lt; in.lj</P>
+<P>
+The input file contains commands that specify the parameters for the 
+simulation as well as read other necessary files such as a data file 
+that describes the initial atom positions, molecular topology, and 
+force-field parameters. The <A HREF="input_commands.html">input_commands</A>
+ page describes all the possible commands that can be used. The <A
+ HREF="data_format.html">data_format</A> page describes the format of 
+the data file. </P>
+<P>
+LAMMPS can be run on any number of processors, including a single 
+processor. In principle you should get identical answers on any number 
+of processors and on any machine. In practice, numerical round-off can 
+cause slight differences and eventual divergence of dynamical 
+trajectories. </P>
+<P>
+When LAMMPS runs, if you get an error message to the screen about 
+&quot;boosting&quot; something, it means one (or more) data arrays are 
+not allocated large enough. Some of these errors are detected at setup, 
+others like neighbor list overflow may not occur until the middle of a 
+run. When the latter happens the program will either gracefully stop 
+(if all processors incurred the same error) or hang (with an error 
+message). Unfortunately in the current version of LAMMPS which uses 
+static memory allocation, changing the array size(s) requires you to 
+edit the appropriate line(s) in the param.h file and recompile the code.</P>
+<P>
+I've tried to be careful about detecting memory-overflow errors in 
+LAMMPS. If the code ever crashes or hangs without spitting out an error 
+message first, it's probably a bug, so let me know about it. Of course 
+this applies to problems due to algorithmic or parallelism issues, not 
+to physics mistkaes, like specifying too big a timestep or putting 2 
+atoms on top of each other! One exception is that different MPI 
+implementations handle buffering of messages differently. If the code 
+hangs without an error message, it may be that you need to specify an 
+MPI setting or two (usually via an environment variable) to enable 
+buffering or boost the sizes of messages that can be buffered. </P>
+<HR>
+<H3>
+<A NAME="_cch3_930759879">Examples</A></H3>
+<P>
+There are several sample problems in the examples directory. All of 
+them use an input file (in.*) of commands and a data file (data.*) of 
+initial atomic coordinates and produce one or more output files. The 
+*.xxx.P files are outputs on P processors on a particular machine which 
+you can compare your answers to.</P>
+<P>
+(1) lj</P>
+<P>
+Simple atomic simulations of Lennard-Jones atoms of 1 or 3 species with 
+various ensembles -- NVE, NVT, NPT.</P>
+<P>
+(2) charge</P>
+<P>
+A few timestep simulation of a box of charged atoms for testing the 
+Coulombic options -- cutoff, Ewald, particle-mesh Ewald (PPPM).</P>
+<P>
+(3) class2</P>
+<P>
+A simple test run of phenyalanine using DISCOVER cff95 class II force 
+fields.</P>
+<P>
+(4) min</P>
+<P>
+An energy minimization of a transcription protein.</P>
+<P>
+(5) lc</P>
+<P>
+Small (250 atom) and large (6750 atom) simulations of liquid crystal 
+molecules with various Coulombic options and periodicity settings. The 
+large-system date file was created by using the &quot;replicate&quot; 
+tool on the small-system data file.</P>
+<P>
+(6) flow</P>
+<P>
+2-d flow of Lennard-Jones atoms in a channel using various contraint 
+options.</P>
+<P>
+(7) polymer</P>
+<P>
+Simulations of bead-spring polymer models with one chain type and two 
+chain types (different size monomers). The two-chain system also has 
+freely diffusing monomers. This illustrates use of the setup_chain 
+program in the tools directory and also how to use soft potentials to 
+untangle the initial configurations.</P>
+<HR>
+<H3>
+<A NAME="_cch3_931282515">Other Tools</A></H3>
+<P>
+The msi2lmp directory has source code for a tool that converts MSI 
+Discover files to LAMMPS input data files. This tool requires you to 
+have the Discover force-field description files in order to convert 
+those parameters to LAMMPS parameters. See the README file in the 
+msi2lmp directory for additional information.</P>
+<P>
+The tools directory has a C file called replicate.c which is useful for 
+generating new LAMMPS data files from existing ones - e.g. scaling the 
+atom coordinates, replicating the system to make a larger one, etc. See 
+the comments at the top of replicate.c for instructions on how to use 
+it.</P>
+<P>
+The tools directory has a F77 program called setup_lj (compile and link 
+with print.c) which can be used to generate a 3-d box of Lennard Jones 
+atoms (one or more atom types) like those used in examples/lj.</P>
+<P>
+The tools directory also has a F77 program called setup_chain.f 
+(compile and link with print.c) which can be used to generate random 
+initial polymer configurations for bead-spring models like those used 
+in examples/polymer. It uses an input polymer definition file (see 
+examples/polymer for two sample def files) that specfies how many 
+chains of what length, a random number seed, etc.</P>
+</BODY>
+</HTML>

doc/html/99/crib.html

@@ -0,0 +1,629 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
+<HTML>
+<HEAD>
+    <META NAME="Generator" CONTENT="Cosmo Create 1.0.3">
+</HEAD>
+<BODY>
+<H2>
+Crib File</H2>
+<P>
+<A HREF="README.html">Return</A> to top-level of LAMMPS documentation.</P>
+<P>
+This file contains one-line descriptions of the key variables and 
+parameters used in LAMMPS. The variables are listed by their data type:</P>
+<UL>
+    <LI>
+    <A HREF="#_cch3_930764945">Parameters</A> 
+    <LI>
+    <A HREF="#_cch3_930764951">Arrays (real</A>) 
+    <LI>
+    <A HREF="#_cch3_930764957">Arrays (integer)</A> 
+    <LI>
+    <A HREF="#_cch3_930764964">Variables (real)</A> 
+    <LI>
+    <A HREF="#_cch3_930764969">Variables (integer)</A> 
+    <LI>
+    <A HREF="#_cch3_930764974">Variables (character)</A> 
+</UL>
+<P>
+Note: this file is somewhat out-of-date for LAMMPS 99.</P>
+<HR>
+<H3>
+<A NAME="_cch3_930764945">Parameters: </A></H3>
+<UL>
+    <LI>
+    maxown = max # of local owned atoms 
+    <LI>
+    maxother = max # of local nearby atoms 
+    <LI>
+    maxtotal = max # of total atoms in simulation 
+    <LI>
+    maxtype = max # of atom types 
+    <LI>
+    maxbond = max # of bonds to compute on one procesor 
+    <LI>
+    maxangle = max # of angles to compute on one processor 
+    <LI>
+    maxdihed = max # of dihedrals to compute on one processor 
+    <LI>
+    maximpro = max # of impropers to compute on one processor 
+    <LI>
+    maxbondper = max # of bonds of one atom 
+    <LI>
+    maxangleper = max # of angles of one atom 
+    <LI>
+    maxdihedper = max # of dihedrals of one atom 
+    <LI>
+    maximproper = max # of impropers of one atom 
+    <LI>
+    maxbondtype = max # of bond types 
+    <LI>
+    maxangletype = max # of angle types 
+    <LI>
+    maxdihedtype = max # of dihedral types 
+    <LI>
+    maximprotype = max # of improper types 
+    <LI>
+    maxexch = max # of atoms in exchange buffer 
+    <LI>
+    maxsend = max # of atoms to send to all neighbors in all swaps 
+    <LI>
+    maxsendone = max # of atoms to send in one swap 
+    <LI>
+    maxswap = max # of swaps to do at each timestep 
+    <LI>
+    maxneigh = max # of neighbors per owned atom 
+    <LI>
+    maxsneigh = max # of special neighbors of one atom 
+    <LI>
+    maxbin = max # of local neighbor bins 
+    <LI>
+    maxfix = max # of defined constraints + 1
+    <LI>
+    maxdiag = max # of diagnostic routines 
+    <LI>
+    maxgrid = max size of PPPM grid with ghosts on one processor 
+    <LI>
+    maxfft = max size of PPPM FFT grid on one processor 
+    <LI>
+    maxperatom = max # of data items stored/comm/output per atom 
+    <LI>
+    maxatom = maxown + maxother = total # of own and nearby atoms 
+    <LI>
+    maxexchtot = maxexch * (maxperatom + maxsneigh + 3*maxbondper + 
+    4*maxangleper + 5*maxdihedper + 5*maximproper) = total data volume for 
+    all exchanged atoms 
+    <LI>
+    maxrestot = maxown * (maxperatom - 3 + 3*maxbondper + 4*maxangleper + 
+    5*maxdihedper + 5*maximproper)+1 = total data volume for all buffered 
+    restart atoms 
+    <LI>
+    maxsendspec = 2 * maxsneigh * maxown total data volume for sending 
+    special requests 
+    <LI>
+    maxrecvspec = maxsneigh + 1 total data volume for receiving a list of 
+    specials 
+</UL>
+<HR>
+<H3>
+<A NAME="_cch3_930764951">Arrays (real): </A></H3>
+<UL>
+    <LI>
+    anglecoeff(2,maxangletype) = angle coeffs for each angle type 
+    <LI>
+    bondcoeff(5,maxbondtype) = bond coeffs for each bond type 
+    <LI>
+    boundhi(maxswap) = hi slab boundary on atom positions for each swap 
+    send 
+    <LI>
+    boundlo(maxswap) = lo slab boundary on atom positions for each swap 
+    send 
+    <LI>
+    buf1(maxexchtot) = comm buffer for sending exchange atoms 
+    <LI>
+    buf2(2*maxexchtot) = comm buffer for 2 recv of exchange atoms 
+    <LI>
+    buf3(3*maxsendone) = comm buffer for sending one set of swap atom 
+    positions 
+    <LI>
+    buf4(8*maxown) = comm buffer for output 
+    <LI>
+    buf5(maxrestot) = comm buffer for restart atoms 
+    <LI>
+    buf6(maxsendone) = comm buffer for sending one set of swap charges 
+    <LI>
+    cutforcesq(maxtype,maxtype) = force cutoff squared for atom pair 
+    (LJ/Coul) 
+    <LI>
+    cutljsq(maxtype,maxtype) = LJ cutoff squared for atom pairs 
+    <LI>
+    cutljinner(maxtype,maxtype) = inner LJ cutoff for switched LJ 
+    <LI>
+    cutljinnersq(maxtype,maxtype) = inner LJ cutoff squared for switched LJ 
+    <LI>
+    cutneighsq(maxtype,maxtype) = neigh cutoff squared for atom pair 
+    (LJ/Coul + skin) 
+    <LI>
+    diagparams(6,maxdiag) = parameters to pass into a diagnostic routine 
+    <LI>
+    dihedcoeff(3,maxdihedtype) = dihedral coeffs for each dihedral type 
+    <LI>
+    f(3,maxown) = forces on own atoms 
+    <LI>
+    fixcoeff(8,maxfix) = constraint coeffs for each constraint 
+    <LI>
+    fixstore(5*maxfix) = accumulated quantities for each constraint 
+    <LI>
+    improcoeff(2,maximprotype) = improper coeffs for each improper type 
+    <LI>
+    lj12345(maxtype,maxtype) = pre-computed LJ coeffs for use in energy and 
+    force 
+    <LI>
+    ljsw01234(maxtype,maxtype) = pre-computed switched LJ coeffs for eng 
+    and force 
+    <LI>
+    mass(maxtype) = mass of each atom type 
+    <LI>
+    noncoeff1234(maxtype,maxtype) = nonbond coeffs input for atom pairs 
+    <LI>
+    offset(maxtype,maxtype) = LJ potential offsets at cutoff for energy 
+    calc 
+    <LI>
+    q(maxatom) = charge of own and nearby atoms (electron units) 
+    <LI>
+    v(3,maxown) = velocity of owned atoms 
+    <LI>
+    x(3,maxatom) = positions of own and nearby atoms 
+    <LI>
+    xhold(3,maxown) = positions of own atoms at last reneighboring 
+</UL>
+<HR>
+<H3>
+<A NAME="_cch3_930764957">Arrays (integer): </A></H3>
+<UL>
+    <LI>
+    angleatom123(maxangleper,maxown) = angle atoms for angles of owned 
+    atoms 
+    <LI>
+    anglelist(4,maxangle) = atoms and type of each angle to compute locally 
+    <LI>
+    angletype(maxangleper,maxown) = angle type for angles of owned atoms 
+    <LI>
+    bin(maxatom) = linked list pointers from one atom to next in bin 
+    <LI>
+    binpnt(maxbin) = pointer to 1st atom in each bin 
+    <LI>
+    bondatom12(maxbondper,maxown) = bond atoms for bonds of owned atoms 
+    <LI>
+    bondlist(3,maxbond) = atoms and type of each bond to compute locally 
+    <LI>
+    bondtype(maxbondper,maxown) = bond type for bonds of owned atoms 
+    <LI>
+    bondtypeflag(maxbondtype) = flag for whether bond coeffs are set 
+    <LI>
+    diagfileflag(maxdiag) = whether a file has been specified for a diag 
+    routine 
+    <LI>
+    diagfreq(maxdiag) = call a diagnostic routine every this many steps 
+    <LI>
+    diagnparams(maxdiag) = # of parameters specified for a diagnostic 
+    routine 
+    <LI>
+    diagstyle(maxdiag) = whether a diagnostic has been set 0/1 
+    <LI>
+    dihedatom1234(maxdihedper,maxown) = dihed atoms for diheds of owned 
+    atoms 
+    <LI>
+    dihedlist(5,maxdihed) = atoms and type of each dihedral to compute 
+    locally 
+    <LI>
+    dihedtype(maxdihedper,maxown) = dihed type for diheds of owned atoms 
+    <LI>
+    fix(maxown) = constraint assignments for each owned atom 
+    <LI>
+    fixflag(3,maxfix) = 0/1 flags for various fix styles 
+    <LI>
+    fixptr(maxfix) = how many values are accumulated for each constraint 
+    <LI>
+    fixstyle(maxfix) = style of each constraint 
+    <LI>
+    ibuf1(maxsendone) = comm buffer for sending one set of swap atom tags 
+    <LI>
+    ibuf2(maxsendone) = comm buffer for sending one set of swap atom types 
+    <LI>
+    ibuf3(maxspec) = comm buffer for sending special requests 
+    <LI>
+    ibuf4(maxspec) = comm buffer for receiving special lists 
+    <LI>
+    improatom1234(maximproper,maxown) = impro atoms for impros of owned 
+    atoms 
+    <LI>
+    improlist(5,maximpro) = atoms and type of each improper to compute 
+    locally 
+    <LI>
+    improtype(maximproper,maxown) = impro type for impros of owned atoms 
+    <LI>
+    list(maxown) = linked list of local atoms (last one -&gt; maxown+1) 
+    <LI>
+    localptr(0:maxtotal) = ptr from global atom to local array (0 if don't 
+    have) 
+    <LI>
+    molecule(maxown) = molecule id # each owned atom is in 
+    <LI>
+    nlist(maxown*maxneigh+maxneigh) = neighbor lists of own atoms 
+    <LI>
+    nliststart(maxown) = pointer to where neighbor list for this atom 
+    starts 
+    <LI>
+    nliststop(maxown) = pointer to where neighbor list for this atom stops 
+    <LI>
+    nontypeflag(maxtype,maxtype) = flag for whether nonbond coeffs are set 
+    <LI>
+    nrlist(maxswap+1) = prt to where received other atoms start for each 
+    swap 
+    <LI>
+    nslist(maxswap+1) = pointer to where swap list starts for each swap 
+    <LI>
+    numangle(maxown) = # of angles of each owned atom 
+    <LI>
+    numbond(maxown) = # of 1st neighbors bonded to each owned atom 
+    <LI>
+    num2bond(maxown) = # of 2nd neighbors for each owned atom 
+    <LI>
+    num3bond(maxown) = # of 3rd neighbors for each owned atom 
+    <LI>
+    numdihed(maxown) = # of dihedrals of each owned atom 
+    <LI>
+    numimpro(maxown) = # of impropers of each owned atom 
+    <LI>
+    rpart(maxswap) = node # of who to recv from for each swap 
+    <LI>
+    slist(maxsend) = send list of atoms to send out in all swaps 
+    <LI>
+    spart(maxswap) = node # of who to send to for each swap 
+    <LI>
+    specbond(maxsneigh,maxown) = special bond neighbors of each owned atom 
+    <LI>
+    tag(maxatom) = global id # of own and nearby atoms 
+    <LI>
+    true(maxown) = which periodic box atom is truly in for all 3 dims 
+    <LI>
+    type(maxatom) = type # of own and nearby atoms 
+    <LI>
+    typecheck(maxtype) = consistency check for all existing atom types 
+    <LI>
+    typechecktmp(maxtype) = summing array for atom type consistency check 
+    <LI>
+    velflag(maxown) = whether velocity for each atom has been created 
+</UL>
+<HR>
+<H3>
+<A NAME="_cch3_930764964">Variables (real): </A></H3>
+<UL>
+    <LI>
+    binsize[xyz] = size of global neighbor bins in each dimension 
+    <LI>
+    boltz = Boltzmann factor 
+    <LI>
+    border(2,3) = lo/hi boundaries of my sub-box in each dimension 
+    <LI>
+    coulpre = Coulombic force prefactor 
+    <LI>
+    createregion(6) = bounding box for atoms to create temperature for 
+    <LI>
+    createvec(3) = initial velocity for create temp atoms 
+    <LI>
+    cutcoul = input force cutoff for Coulombic interactions 
+    <LI>
+    cutcoulsq = Coul cutoff squared for all atom pairs 
+    <LI>
+    cutforce = max force cutoff for all atom pairs (LJ/Coul) 
+    <LI>
+    cutlj = input global (default) LJ cutoff for all atom pairs 
+    <LI>
+    cutljinterior = global inner LJ cutoff for switched LJ 
+    <LI>
+    cutneigh = max neighbor cutoff for all atom pairs (LJ/Coul + skin) 
+    <LI>
+    dielectric = dielectric constant 
+    <LI>
+    dt = timestep 
+    <LI>
+    dtfactor = timestep conversion factor from input to program units 
+    <LI>
+    dthalf = timestep / 2 
+    <LI>
+    efactor = energy conversion factor from Coulombic to Kcals 
+    <LI>
+    e_angle = energy in angles 
+    <LI>
+    e_bond = energy in bonds 
+    <LI>
+    e_coul = energy in nonbond Coulombic 
+    <LI>
+    e_dihedral = energy in dihedrals 
+    <LI>
+    e_improper = energy in impropers 
+    <LI>
+    e_total = total energy 
+    <LI>
+    e_vdwl = energy in nonbond LJ 
+    <LI>
+    fixregion(6) = bounding box for atoms to assign to a constraint 
+    <LI>
+    skin = distance between force and neighbor cutoffs 
+    <LI>
+    special(3) = weight factors for special neighbors 
+    <LI>
+    triggersq = squared distance to trigger neighbor list rebuild 
+    <LI>
+    two16 = 2 ^ (1/6) constant for use in FENE bond potentials 
+    <LI>
+    t_create = requested initialization temp 
+    <LI>
+    t_current = current temp returned from temp routine 
+    <LI>
+    t_nph = default temp for constant NPH 
+    <LI>
+    t_start = target temp at beginning of run 
+    <LI>
+    t_stop = target temp at end of run 
+    <LI>
+    t_window = control temp within this window 
+    <LI>
+    time_angle = angle time 
+    <LI>
+    time_bond = bond time 
+    <LI>
+    time_comm = communication time 
+    <LI>
+    time_current = current time 
+    <LI>
+    time_dihedral = dihedral time 
+    <LI>
+    time_exch = exchange time 
+    <LI>
+    time_improper = improper time 
+    <LI>
+    time_io = i/o time 
+    <LI>
+    time_loop = time for integration loop 
+    <LI>
+    time_neigh1 = neighboring time in nonbond 
+    <LI>
+    time_neigh2 = neighboring time in bonds 
+    <LI>
+    time_nonbond = nonbond force time 
+    <LI>
+    time_other = other miscellaneous time 
+    <LI>
+    time_total = total run time of entire simulation 
+    <LI>
+    x[yz]mc = box size minus force cutoff for PBC checks 
+    <LI>
+    x[yz]ms box size minus neighbor list cutoff for PBC checks 
+    <LI>
+    x[yz]boundlo = lower global box boundary in each dimension 
+    <LI>
+    x[yz]boundhi = upper global box boundary in each dimension 
+    <LI>
+    x[yz]prd = global box size in each dimension 
+</UL>
+<HR>
+<H3>
+<A NAME="_cch3_930764969">Variables (integer): </A></H3>
+<UL>
+    <LI>
+    atompnt = pointer to 1st atom in my list 
+    <LI>
+    bondstyle = style of bond computation 
+    <LI>
+    boxflag = flag if box has been remapped (non-PBC) 
+    <LI>
+    coulstyle = style of Coulomb interaction 
+    <LI>
+    creategroup = kind of atom group to create temp for 
+    <LI>
+    createstyle = style of temp creation 
+    <LI>
+    createtypehi = upper range of atom types to create temp for 
+    <LI>
+    createtypelo = lower range of atom types to create temp for 
+    <LI>
+    dumpfileflag = has dump file been opened or not (1/0) 
+    <LI>
+    dumpflag = dump atoms to file every this many steps (0 = never) 
+    <LI>
+    dumpforcefileflag = has dump force file been opened or not (1/0) 
+    <LI>
+    dumpforceflag = dump forces to file every this many steps (0 = never) 
+    <LI>
+    dumpvelfileflag = has dump velocity file been opened or not (1/0) 
+    <LI>
+    dumpvelflag = dump vels to file every this many steps (0 = never) 
+    <LI>
+    fixatom = assign atom/molecule with this tag to a constraint 
+    <LI>
+    fixgroup = kind of atom group to assign to a constraint 
+    <LI>
+    fixnum = total # of accumulated values for all constraints 
+    <LI>
+    fixtype = assign group of atoms of this type to a constraint 
+    <LI>
+    fixwhich = which constraint a atom group is to be assigned to 
+    <LI>
+    freepnt = pointer to 1st free space in list (last one -&gt; 0) 
+    <LI>
+    idimension = dimension of problem (2-d or 3-d) 
+    <LI>
+    iseed = RNG seed for generating initial velocities 
+    <LI>
+    itime = current timestep loop counter in integrator 
+    <LI>
+    iversion = version number of restart files (for backward compat) 
+    <LI>
+    max_angle = most angles I ever have to compute 
+    <LI>
+    max_angleper = most angles ever attached to any atom 
+    <LI>
+    max_bond = most bonds I ever have to compute 
+    <LI>
+    max_bondper = most bonds ever attached to any atom 
+    <LI>
+    max_dihed = most diheds I ever have to compute 
+    <LI>
+    max_dihedper = most diheds ever attached to any atom 
+    <LI>
+    max_exch = most atoms ever leaving my box (in one dimension) 
+    <LI>
+    max_impro = most impros I ever have to compute 
+    <LI>
+    max_improper = most impros ever attached to any atom 
+    <LI>
+    max_nlocal = most atoms I ever owned 
+    <LI>
+    max_neigh = most neighbors ever stored in neighbor list 
+    <LI>
+    max_nother = most nearby atoms I ever stored 
+    <LI>
+    max_slist = biggest size swap list ever reached 
+    <LI>
+    max_swap = most atoms ever sent in one swap 
+    <LI>
+    mbin[xyz] = # of bins in my box with nearby atoms included 
+    <LI>
+    mbin[xyz]lo = global bin indices (offset) at corner of extended box 
+    <LI>
+    me(3) = which box I am (0 - pgrid-1) in each dimension 
+    <LI>
+    mixflag = whether mixing style has been set or not 
+    <LI>
+    mixstyle = style of mixing for nonbond coeffs (arith,geom,sixth) 
+    <LI>
+    mpart(2,3)= node # of neighbor processor in each dimension 
+    <LI>
+    nanglelocal = local # of angless to compute 
+    <LI>
+    nangles = total # of angles 
+    <LI>
+    nangletypes = total # of angle types 
+    <LI>
+    natoms = total # of atoms 
+    <LI>
+    nbin[xyz] # of global neighbor bins in each dimension 
+    <LI>
+    nbondlocal = local # of bonds to compute 
+    <LI>
+    nbonds = total # of bonds 
+    <LI>
+    nbondtypes = total # of bond types 
+    <LI>
+    ndanger = # of neighbor rebuilds triggered by 1st check 
+    <LI>
+    ndiags = # of user-specified diagnostic routines 
+    <LI>
+    ndihedlocal = local # of dihedrals to compute 
+    <LI>
+    ndihedrals = total # of diheds 
+    <LI>
+    ndihedtypes = total # of dihedral types 
+    <LI>
+    need(3) how many processors I need neighbors from in each dim 
+    <LI>
+    neighago = how many timesteps ago neighboring was done 
+    <LI>
+    neighdelay = delay neighbor list build for this many steps 
+    <LI>
+    neighfreq = build neighbor list every this many steps 
+    <LI>
+    neighstyle = neighboring by (0) N^2 or (1) binning method 
+    <LI>
+    neightop = last used position in neighbor list (nlist) 
+    <LI>
+    neightrigger = always (0) do neighbor list or trigger (1) on atom move 
+    <LI>
+    newton = flag for kind of Newton's 3rd law used (0,1,2,3) 
+    <LI>
+    newton_bond = Newton's 3rd is not used (0) or (1) used for bonds 
+    <LI>
+    newton_nonbond = Newton's 3rd is not used (0) or (1) used for nonbonds 
+    <LI>
+    nfixes = # of constraints 
+    <LI>
+    nimprolocal = local # of impropers to compute 
+    <LI>
+    nimpropers = total # of impros 
+    <LI>
+    nimprotypes = total # of improper types 
+    <LI>
+    nlocal = # of atoms I currently own 
+    <LI>
+    nother = # of nearby atoms I currently store 
+    <LI>
+    node = my node # 
+    <LI>
+    nonstyle = style on nonbond computation 
+    <LI>
+    nprocs = total # of processors 
+    <LI>
+    nsteps = # of timesteps to simulate 
+    <LI>
+    nswap = # of swaps at each timestep 
+    <LI>
+    ntimestep = current global timestep 
+    <LI>
+    ntypes = total # of atom types 
+    <LI>
+    numneigh = number of times reneighboring is done 
+    <LI>
+    offsetflag = whether to include energy offset in LJ energy calc 
+    <LI>
+    peratom = # of values/atom not including bond info 
+    <LI>
+    perflagx[yz] = flag for periodic (0) or non-periodic (1) BC 
+    <LI>
+    pgrid(3) = # of processors in each dimension 
+    <LI>
+    readflag = whether atom input file has been read or not (1/0) 
+    <LI>
+    restartfileflag = which restart file to open next (0/1) 
+    <LI>
+    restartflag = write restart file every this many steps (0=never) 
+    <LI>
+    t_every = rescale/replace temp every this many steps 
+    <LI>
+    tempflag = constant temperature style flag 
+    <LI>
+    thermoflag = print thermo info every this many steps (0 = never) 
+    <LI>
+    thermostyle = style of thermo output (0 = full, 1 = reduced) 
+    <LI>
+    trueflag = whether to dump remapped or true atom positions 
+    <LI>
+    units = flag for real vs reduced LJ units 
+</UL>
+<HR>
+<H3>
+<A NAME="_cch3_930764974">Variables (character): </A></H3>
+<UL>
+    <LI>
+    datafile = file to read atom and connectivity info from 
+    <LI>
+    diagfile(maxdiag) = files to print user-specified diagnostics to 
+    <LI>
+    diagname(maxdiag) = name of a user-specified diagnostic routine 
+    <LI>
+    dumpfile = file to dump atom info to 
+    <LI>
+    dumpforcefile = file to dump force info to 
+    <LI>
+    dumpvelfile = file to dump velocity info to 
+    <LI>
+    restart_in = file to read restart info from 
+    <LI>
+    restart_out[12] = files to write restart info to 
+</UL>
+<P>
+</P>
+</BODY>
+</HTML>

doc/html/99/data_format.html

@@ -0,0 +1,239 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
+<HTML>
+<HEAD>
+    <META NAME="Generator" CONTENT="Cosmo Create 1.0.3">
+</HEAD>
+<BODY>
+<H2>
+LAMMPS Data Format</H2>
+<P>
+<A HREF="README.html">Return</A> to top-level of LAMMPS documentation</P>
+<P>
+This file describes the format of the data file read into LAMMPS with 
+the &quot;read data&quot; command. The data file contains basic 
+information about the size of the problem to be run, the initial atomic 
+coordinates, molecular topology, and (optionally) force-field 
+coefficients. It will be easiest to understand this file if you read it 
+while looking at a sample data file from the examples.</P>
+<P>
+This page has 2 sections:</P>
+<UL>
+    <LI>
+    <A HREF="#_cch3_930958962">Rules for formatting the Data File</A> 
+    <LI>
+    <A HREF="#_cch3_930958969">Sample file with Annotations</A> 
+</UL>
+<HR>
+<H3>
+<A NAME="_cch3_930958962">Rules for formatting the Data File: </A></H3>
+<P>
+Blank lines are important. After the header section, new entries are 
+separated by blank lines. </P>
+<P>
+Indentation and space between words/numbers on one line is not 
+important except that entry keywords (e.g. Masses, Bond Coeffs) must be 
+left-justified and capitalized as shown. </P>
+<P>
+The header section (thru box bounds) must appear first in the file, the 
+remaining entries (Masses, various Coeffs, Atoms, Bonds, etc) can come 
+in any order. </P>
+<P>
+These entries must be in the file: header section, Masses, Atoms. </P>
+<P>
+These entries must be in the file if there are a non-zero number of 
+them: Bonds, Angles, Dihedrals, Impropers, Bond Coeffs, Angle Coeffs, 
+Dihedral Coeffs, Improper Coeffs. Cross-term coefficients for a 
+particular kind of interaction (e.g. BondAngle Coeffs for bonds) must 
+appear if class II force fields have been turned on in the input 
+command file via a &quot;style&quot; command. </P>
+<P>
+The Nonbond Coeffs entry contains one line for each atom type. These 
+are the coefficients for an interaction between 2 atoms of the same 
+type. The cross-type coeffs are computed by the appropriate class I or 
+class II mixing rules, or can be specified explicitly using the 
+&quot;nonbond coeff&quot; command in the input command script. See the <A
+ HREF="force_fields.html">force_fields</A> page for more information. </P>
+<P>
+The Nonbond Coeffs and Bond Coeffs entries are optional since they can 
+be specified from the input command script. This is not true if bond 
+style is set to class II since those coeffs can only be specified in 
+this data file. </P>
+<P>
+In the Atoms entry, the atoms can be in any order so long as there are 
+N entries. The 1st number on the line is the atom-tag (number from 1 to 
+N) which is used to identify the atom throughout the simulation. The 
+molecule-tag is a second identifier which is attached to the atom; it 
+can be 0, or a counter for the molecule the atom is part of, or any 
+other number you wish. The q value is the charge of the atom in 
+electron units (e.g. +1 for a proton). The xyz values are the initial 
+position of the atom. For 2-d simulations specify z as 0.0.</P>
+<P>
+The final 3 nx,ny,nz values on a line of the Atoms entry are optional. 
+LAMMPS only reads them if the &quot;true flag&quot; command is 
+specified in the input command script. Otherwise they are initialized 
+to 0 by LAMMPS. Their meaning, for each dimension, is that 
+&quot;n&quot; box-lengths are added to xyz to get the atom's 
+&quot;true&quot; un-remapped position. This can be useful in pre- or 
+post-processing to enable the unwrapping of long-chained molecules 
+which wrap thru the periodic box one or more times. The value of 
+&quot;n&quot; can be positive, negative, or zero. For 2-d simulations 
+specify nz as 0. </P>
+<P>
+For simulations with periodic boundary conditions, xyz are remapped 
+into the periodic box (from as far away as needed), so the initial 
+coordinates need not be inside the box. The nx,ny,nz values (as read in 
+or as set to zero by LAMMPS) are appropriately adjusted by this 
+remapping. </P>
+<P>
+The number of coefficients specified on each line of coefficient 
+entries (Nonbond Coeffs, Bond Coeffs, etc) depends on the 
+&quot;style&quot; of interaction. This is specified in the input 
+command script, unless the default is used. See the <A
+ HREF="input_commands.html">input_commands</A> page for a description 
+of the various style options. The <A HREF="input_commands.html">input_commands</A>
+ and <A HREF="force_fields.html">force_fields</A> pages explain the 
+meaning and valid ranges for each of the coefficients. </P>
+<HR>
+<H3>
+<A NAME="_cch3_930958969">Sample file with Annotations</A></H3>
+<P>
+Here is a sample file with annotations in parenthesis and lengthy 
+sections replaced by dots (...). Note that the blank lines are 
+important in this example.</P>
+<PRE>
+
+LAMMPS Description           (1st line of file)
+
+100 atoms         (this must be the 3rd line, 1st 2 lines are ignored)
+95 bonds                (# of bonds to be simulated)
+50 angles               (include these lines even if number = 0)
+30 dihedrals
+20 impropers
+
+5 atom types           (# of nonbond atom types)
+10 bond types          (# of bond types = sets of bond coefficients)
+18 angle types         
+20 dihedral types      (do not include a bond,angle,dihedral,improper type
+2 improper types             line if number of bonds,angles,etc is 0)
+
+-0.5 0.5 xlo xhi       (for periodic systems this is box size,
+-0.5 0.5 ylo yhi        for non-periodic it is min/max extent of atoms)
+-0.5 0.5 zlo zhi       (do not include this line for 2-d simulations)
+
+Masses
+
+  1 mass
+  ...
+  N mass                           (N = # of atom types)
+
+Nonbond Coeffs
+
+  1 coeff1 coeff2 ...
+  ...
+  N coeff1 coeff2 ...              (N = # of atom types)
+
+Bond Coeffs
+
+  1 coeff1 coeff2 ...
+  ...
+  N coeff1 coeff2 ...              (N = # of bond types)
+
+Angle Coeffs
+
+  1 coeff1 coeff2 ...
+  ...
+  N coeff1 coeff2 ...              (N = # of angle types)
+
+Dihedral Coeffs
+
+  1 coeff1 coeff2 ...
+  ...
+  N coeff1 coeff2 ...              (N = # of dihedral types)
+
+Improper Coeffs
+
+  1 coeff1 coeff2 ...
+  ...
+  N coeff1 coeff2 ...              (N = # of improper types)
+
+BondBond Coeffs
+
+  1 coeff1 coeff2 ...
+  ...
+  N coeff1 coeff2 ...              (N = # of angle types)
+
+BondAngle Coeffs
+
+  1 coeff1 coeff2 ...
+  ...
+  N coeff1 coeff2 ...              (N = # of angle types)
+
+MiddleBondTorsion Coeffs
+
+  1 coeff1 coeff2 ...
+  ...
+  N coeff1 coeff2 ...              (N = # of dihedral types)
+
+EndBondTorsion Coeffs
+
+  1 coeff1 coeff2 ...
+  ...
+  N coeff1 coeff2 ...              (N = # of dihedral types)
+
+AngleTorsion Coeffs
+
+  1 coeff1 coeff2 ...
+  ...
+  N coeff1 coeff2 ...              (N = # of dihedral types)
+
+AngleAngleTorsion Coeffs
+
+  1 coeff1 coeff2 ...
+  ...
+  N coeff1 coeff2 ...              (N = # of dihedral types)
+
+BondBond13 Coeffs
+
+  1 coeff1 coeff2 ...
+  ...
+  N coeff1 coeff2 ...              (N = # of dihedral types)
+
+AngleAngle Coeffs
+
+  1 coeff1 coeff2 ...
+  ...
+  N coeff1 coeff2 ...              (N = # of improper types)
+
+Atoms
+
+  1 molecule-tag atom-type q x y z nx ny nz  (nx,ny,nz are optional -
+  ...                                    see &quot;true flag&quot; input command)
+  ...                
+  N molecule-tag atom-type q x y z nx ny nz  (N = # of atoms)
+
+Bonds
+
+  1 bond-type atom-1 atom-2
+  ...
+  N bond-type atom-1 atom-2             (N = # of bonds)
+
+Angles
+
+  1 angle-type atom-1 atom-2 atom-3  (atom-2 is the center atom in angle)
+  ...
+  N angle-type atom-1 atom-2 atom-3  (N = # of angles)
+
+Dihedrals
+
+  1 dihedral-type atom-1 atom-2 atom-3 atom-4  (atoms 2-3 form central bond)
+  ...
+  N dihedral-type atom-1 atom-2 atom-3 atom-4  (N = # of dihedrals)
+
+Impropers
+
+  1 improper-type atom-1 atom-2 atom-3 atom-4  (atom-1 is central atom)
+  ...
+  N improper-type atom-1 atom-2 atom-3 atom-4  (N = # of impropers)
+</PRE>
+</BODY>
+</HTML>

doc/html/99/force_fields.html

@@ -0,0 +1,550 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
+<HTML>
+<HEAD>
+    <META NAME="Generator" CONTENT="Cosmo Create 1.0.3">
+</HEAD>
+<BODY>
+<H2>
+LAMMPS Force Fields</H2>
+<P>
+<A HREF="README.html">Return</A> to top-level of LAMMPS documentation</P>
+<P>
+This file outlines the force-field formulas used in LAMMPS. Read this 
+file in conjunction with the <A HREF="data_format.html">data_format</A>
+ and <A HREF="units.html">units</A> file.</P>
+<P>
+The sections of this page are as follows:</P>
+<UL>
+    <LI>
+    <A HREF="#_cch3_930957465">Nonbond Coulomb</A> 
+    <LI>
+    <A HREF="#_cch3_930957471">Nonbond Lennard-Jones</A> 
+    <LI>
+    <A HREF="#_cch3_930957478">Mixing Rules for Lennard-Jones</A> 
+    <LI>
+    <A HREF="#_cch3_930957482">Bonds</A> 
+    <LI>
+    <A HREF="#_cch3_930957488">Angles</A> 
+    <LI>
+    <A HREF="#_cch3_930957509">Dihedrals</A> 
+    <LI>
+    <A HREF="#_cch3_930957513">Impropers</A> 
+    <LI>
+    <A HREF="#_cch3_930957527">Class II Force Field</A> 
+</UL>
+<HR>
+<H3>
+<A NAME="_cch3_930957465">Nonbond Coulomb</A></H3>
+<P>
+Whatever Coulomb style is specified in the input command file, the 
+short-range Coulombic interactions are computed by this formula, 
+modified by an appropriate smoother for the smooth, Ewald, and PPPM 
+styles.</P>
+<PRE>
+  E = C q1 q2 / (epsilon * r)
+
+  r = distance (computed by LAMMPS)
+  C = hardwired constant to convert to energy units
+  q1,q2 = charge of each atom in electron units (proton = +1),
+    specified in &quot;Atoms&quot; entry in data file
+  epsilon = dielectric constant (vacuum = 1.0),
+    set by user in input command file
+</PRE>
+<HR>
+<H3>
+<A NAME="_cch3_930957471">Nonbond Lennard-Jones </A></H3>
+<P>
+The style of nonbond potential is specified in the input command file. </P>
+<H4>
+(1) lj/cutoff </H4>
+<PRE>
+
+  E = 4 epsilon [ (sigma/r)^12 - (sigma/r)^6 ]
+
+  standard Lennard Jones potential
+
+  r = distance (computed by LAMMPS)
+
+  coeff1 = epsilon (energy)
+  coeff2 = sigma (distance)
+
+  2 coeffs are listed in data file or set in input script
+  1 cutoff is set in input script
+
+</PRE>
+<H4>
+(2) lj/switch </H4>
+<PRE>
+
+  E = 4 epsilon [ (sigma/r)^12 - (sigma/r)^6 ]  for  r &lt; r_inner
+    = spline fit    for  r_inner &lt; r &lt; cutoff
+    = 0             for r &gt; cutoff
+
+  switching function (spline fit) is applied to standard LJ
+    within a switching region (from r_inner to cutoff) so that
+    energy and force go smoothly to zero
+  spline coefficients are computed by LAMMPS
+    so that at inner cutoff (r_inner) the potential, force, 
+    and 1st-derivative of force are all continuous, 
+    and at outer cutoff (cutoff) the potential and force
+    both go to zero
+
+  r = distance (computed by LAMMPS)
+
+  coeff1 = epsilon (energy)
+  coeff2 = sigma (distance)
+  
+  2 coeffs are listed in data file or set in input script
+  2 cutoffs (r_inner and cutoff) are set in input script
+
+</PRE>
+<H4>
+(3) lj/shift </H4>
+<PRE>
+
+  E = 4 epsilon [ (sigma/(r - delta))^12 - (sigma/(r - delta))^6 ]
+
+  same as lj/cutoff except that r is shifted by delta
+
+  r = distance (computed by LAMMPS)
+
+  coeff1 = epsilon (energy)
+  coeff2 = sigma (distance)
+  coeff3 = delta (distance)
+
+  3 coeffs are listed in data file or set in input script
+  1 cutoff is set in input script
+
+</PRE>
+<H4>
+(4) soft </H4>
+<PRE>
+
+  E = A * [ 1 + cos( pi * r / cutoff ) ]
+
+  useful for pushing apart overlapping atoms by ramping A over time
+
+  r = distance (computed by LAMMPS)
+
+  coeff1 = prefactor A at start of run (energy)
+  coeff2 = prefactor A at end of run (energy)
+
+  2 coeffs are listed in data file or set in input script
+  1 cutoff is set in input script
+
+</PRE>
+<H4>
+(5) class2/cutoff </H4>
+<PRE>
+
+  E = epsilon [ 2 (sigma/r)^9 - 3 (sigma/r)^6 ]
+
+  used with class2 bonded force field
+
+  r = distance (computed by LAMMPS)
+
+  coeff1 = epsilon (energy)
+  coeff2 = sigma (distance)
+
+  2 coeffs are listed in data file or set in input script
+  1 cutoff is set in input script
+</PRE>
+<HR>
+<H3>
+<A NAME="_cch3_930957478">Mixing Rules for Lennard-Jones</A></H3>
+<P>
+The coefficients for each nonbond style are input in either the data 
+file by the &quot;read data&quot; command or in the input script using 
+the &quot;nonbond coeff&quot; command. In the former case, only one set 
+of coefficients is input for each atom type. The cross-type coeffs are 
+computed using one of three possible mixing rules: </P>
+<PRE>
+
+ geometric:  epsilon_ij = sqrt(epsilon_i * epsilon_j)
+             sigma_ij = sqrt(sigma_i * sigma_j)
+
+ arithmetic: epsilon_ij = sqrt(epsilon_i * epsilon_j)
+             sigma_ij = (sigma_i + sigma_j) / 2
+
+ sixthpower: epsilon_ij =
+               (2 * sqrt(epsilon_i*epsilon_j) * sigma_i^3 * sigma_j^3) /
+               (sigma_i^6 + sigma_j^6)
+             sigma_ij=  ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6)
+
+</PRE>
+<P>
+The default mixing rule for nonbond styles lj/cutoff, lj/switch, 
+lj/shift, and soft is &quot;geometric&quot;. The default for nonbond 
+style class2/cutoff is &quot;sixthpower&quot;. </P>
+<P>
+The default can be overridden using the &quot;mixing style&quot; 
+command. The one exception to this is for the nonbond style soft, for 
+which only an epsilon prefactor is input. This is always mixed 
+geometrically. </P>
+<P>
+Also, for nonbond style lj/shift, the delta coefficient is always mixed 
+using the rule </P>
+<UL>
+    <LI>
+    delta_ij = (delta_i + delta_j) / 2 
+</UL>
+<HR>
+<H3>
+<A NAME="_cch3_930957482">Bonds</A></H3>
+<P>
+The style of bond potential is specified in the input command file.</P>
+<H4>
+(1) harmonic </H4>
+<PRE>
+
+  E = K (r - r0)^2
+
+  standard harmonic spring
+
+  r = distance (computed by LAMMPS)
+
+  coeff1 = K (energy/distance^2)  (the usual 1/2 is included in the K)
+  coeff2 = r0 (distance)
+
+  2 coeffs are listed in data file or set in input script
+
+</PRE>
+<H4>
+(2) FENE/standard </H4>
+<PRE>
+
+  E = -0.5 K R0^2 * ln[1 - (r/R0)^2] +
+    4 epsilon [(sigma/r)^12 - (sigma/r)^6] + epsilon
+
+  finite extensible nonlinear elastic (FENE) potential for
+    polymer bead-spring models
+  see Kremer, Grest, J Chem Phys, 92, p 5057 (1990)
+
+  r = distance (computed by LAMMPS)
+
+  coeff1 = K (energy/distance^2)
+  coeff2 = R0 (distance)
+  coeff3 = epsilon (energy)
+  coeff4 = sigma (distance)
+
+  1st term is attraction, 2nd term is repulsion (shifted LJ)
+  1st term extends to R0
+  2nd term only extends to the minimum of the LJ potential,
+    a cutoff distance computed by LAMMPS (2^(1/6) * sigma)
+
+  4 coeffs are listed in data file or set in input script
+
+</PRE>
+<H4>
+(3) FENE/shift </H4>
+<PRE>
+
+  E = -0.5 K R0^2 * ln[1 - ((r - delta)/R0)^2] +
+    4 epsilon [(sigma/(r - delta))^12 - (sigma/(r - delta))^6] + epsilon
+
+  same as FENE/standard expect that r is shifted by delta
+
+  r = distance (computed by LAMMPS)
+
+  coeff1 = K (energy/distance^2)
+  coeff2 = R0 (distance)
+  coeff3 = epsilon (energy)
+  coeff4 = sigma (distance)
+  coeff5 = delta (distance)
+
+  1st term is attraction, 2nd term is repulsion (shifted LJ)
+  1st term extends to R0
+  2nd term only extends to the minimum of the LJ potential,
+    a cutoff distance computed by LAMMPS (2^(1/6) * sigma + delta)
+
+  5 coeffs are listed in data file or set in input script
+
+</PRE>
+<H4>
+(4) nonlinear </H4>
+<PRE>
+
+  E = epsilon (r - r0)^2 / [ lamda^2 - (r - r0)^2 ]
+
+  non-harmonic spring of equilibrium length r0
+    with finite extension of lamda
+  see Rector, Van Swol, Henderson, Molecular Physics, 82, p 1009 (1994)
+
+  r = distance (computed by LAMMPS)
+
+  coeff1 = epsilon (energy)
+  coeff2 = r0 (distance)
+  coeff3 = lamda (distance)
+
+  3 coeffs are listed in data file or set in input script
+
+</PRE>
+<H4>
+(5) class2 </H4>
+<PRE>
+
+  E = K2 (r - r0)^2  +  K3 (r - r0)^3  +  K4 (r - r0)^4
+
+  r = distance (computed by LAMMPS)
+
+  coeff1 = r0 (distance)
+  coeff2 = K2 (energy/distance^2)
+  coeff3 = K3 (energy/distance^3)
+  coeff4 = K4 (energy/distance^4)
+
+  4 coeffs are listed in data file - cannot be set in input script
+</PRE>
+<HR>
+<H3>
+<A NAME="_cch3_930957488">Angles </A></H3>
+<P>
+The style of angle potential is specified in the input command file. </P>
+<H4>
+(1) harmonic </H4>
+<PRE>
+
+  E = K (theta - theta0)^2
+
+  theta = radians (computed by LAMMPS)
+
+  coeff1 = K (energy/radian^2) (the usual 1/2 is included in the K)
+  coeff2 = theta0 (degrees) (converted to radians within LAMMPS)
+
+  2 coeffs are listed in data file
+
+</PRE>
+<H4>
+(2) class2 </H4>
+<PRE>
+
+  E = K2 (theta - theta0)^2 +  K3 (theta - theta0)^3 + 
+       K4 (theta - theta0)^4
+
+  theta = radians (computed by LAMMPS)
+
+  coeff1 = theta0 (degrees) (converted to radians within LAMMPS)
+  coeff2 = K2 (energy/radian^2)
+  coeff3 = K3 (energy/radian^3)
+  coeff4 = K4 (energy/radian^4)
+
+  4 coeffs are listed in data file
+</PRE>
+<HR>
+<H3>
+<A NAME="_cch3_930957509">Dihedrals </A></H3>
+<P>
+The style of dihedral potential is specified in the input command file. </P>
+<H4>
+(1) harmonic </H4>
+<PRE>
+
+  E = K [1 + d * cos (n * phi) ]
+
+  phi = radians (computed by LAMMPS)
+
+  coeff1 = K (energy)
+  coeff2 = d (always +1 or -1)
+  coeff3 = n (1,2,3,4,6)
+
+  Cautions when comparing to other force fields:
+
+  some force fields reverse the sign convention on d so that
+    E = K [1 - d * cos(n*phi)]
+  some force fields divide/multiply K by the number of multiple
+    torsions that contain the j-k bond in an i-j-k-l torsion
+  some force fields let n be positive or negative which 
+    corresponds to d = 1,-1
+  in the LAMMPS force field, the trans position = 180 degrees, while
+    in some force fields trans = 0 degrees
+ 
+  3 coeffs are listed in data file
+</PRE>
+<H4>
+(2) class2 </H4>
+<PRE>
+
+  E = SUM(n=1,3) { K_n [ 1 - cos( n*Phi - Phi0_n ) ] }
+
+  phi = radians (computed by LAMMPS)
+
+  coeff1 = K_1 (energy)
+  coeff2 = Phi0_1 (degrees) (converted to radians within LAMMPS)
+  coeff3 = K_2 (energy)
+  coeff4 = Phi0_2 (degrees) (converted to radians within LAMMPS)
+  coeff5 = K_3 (energy)
+  coeff6 = Phi0_3 (degrees) (converted to radians within LAMMPS)
+
+  6 coeffs are listed in data file
+</PRE>
+<HR>
+<H3>
+<A NAME="_cch3_930957513">Impropers</A></H3>
+<P>
+The style of improper potential is specified in the input command file. </P>
+<H4>
+(1) harmonic </H4>
+<PRE>
+
+  E = K (chi - chi0)^2
+
+  chi = radians (computed by LAMMPS)
+
+  coeff1 = K (energy/radian^2) (the usual 1/2 is included in the K)
+  coeff2 = chi0 (degrees) (converted to radians within LAMMPS)
+
+  in data file, listing of 4 atoms requires atom-1 as central atom
+  some force fields (AMBER,Discover) have atom-2 as central atom - it is really
+    an out-of-plane torsion, may need to treat as dihedral in LAMMPS
+
+  2 coeffs are listed in data file
+</PRE>
+<H4>
+(2) class2 </H4>
+<PRE>
+
+  same formula, coeffs, and meaning as &quot;harmonic&quot; except that LAMMPS
+    averages all 3 angle-contributions to chi
+  in class II this is called a Wilson out-of-plane interaction
+
+  2 coeffs are listed in data file
+</PRE>
+<HR>
+<H3>
+<A NAME="_cch3_930957527">Class II Force Field</A></H3>
+<P>
+If class II force fields are selected in the input command file, 
+additional cross terms are computed as part of the force field.</P>
+<H4>
+Bond-Bond (computed within class II angles) </H4>
+<PRE>
+
+  E = K (r - r0) * (r' - r0')
+
+  r,r' = distance (computed by LAMMPS)
+
+  coeff1 = K (energy/distance^2)
+  coeff2 = r0 (distance)
+  coeff3 = r0' (distance)
+
+  3 coeffs are input in data file
+</PRE>
+<H4>
+Bond-Angle (computed within class II angles for each of 2 bonds) </H4>
+<PRE>
+
+  E = K_n (r - r0_n) * (theta - theta0)
+
+  r = distance (computed by LAMMPS)
+  theta = radians (computed by LAMMPS)
+
+  coeff1 = K_1 (energy/distance-radians)
+  coeff2 = K_2 (energy/distance-radians)
+  coeff3 = r0_1 (distance)
+  coeff4 = r0_2 (distance)
+
+  Note: theta0 is known from angle coeffs so don't need it specified here
+
+  4 coeffs are listed in data file
+</PRE>
+<H4>
+Middle-Bond-Torsion (computed within class II dihedral) </H4>
+<PRE>
+
+  E = (r - r0) * [ F1*cos(phi) + F2*cos(2*phi) + F3*cos(3*phi) ]
+
+  r = distance (computed by LAMMPS)
+  phi = radians (computed by LAMMPS)
+
+  coeff1 = F1 (energy/distance)
+  coeff2 = F2 (energy/distance)
+  coeff3 = F3 (energy/distance)
+  coeff4 = r0 (distance)
+
+  4 coeffs are listed in data file
+</PRE>
+<H4>
+End-Bond-Torsion (computed within class II dihedral for each of 2 
+bonds) </H4>
+<PRE>
+
+  E = (r - r0_n) * [ F1_n*cos(phi) + F2_n*cos(2*phi) + F3_n*cos(3*phi) ]
+
+  r = distance (computed by LAMMPS)
+  phi = radians (computed by LAMMPS)
+
+  coeff1 = F1_1 (energy/distance)
+  coeff2 = F2_1 (energy/distance)
+  coeff3 = F3_1 (energy/distance)
+  coeff4 = F1_2 (energy/distance)
+  coeff5 = F2_3 (energy/distance)
+  coeff6 = F3_3 (energy/distance)
+  coeff7 = r0_1 (distance)
+  coeff8 = r0_2 (distance)
+
+  8 coeffs are listed in data file
+</PRE>
+<H4>
+Angle-Torsion (computed within class II dihedral for each of 2 angles) </H4>
+<PRE>
+
+  E = (theta - theta0) * [ F1_n*cos(phi) + F2_n*cos(2*phi) + F3_n*cos(3*phi) ]
+
+  theta = radians (computed by LAMMPS)
+  phi = radians (computed by LAMMPS)
+
+  coeff1 = F1_1 (energy/radians)
+  coeff2 = F2_1 (energy/radians)
+  coeff3 = F3_1 (energy/radians)
+  coeff4 = F1_2 (energy/radians)
+  coeff5 = F2_3 (energy/radians)
+  coeff6 = F3_3 (energy/radians)
+  coeff7 = theta0_1 (degrees) (converted to radians within LAMMPS)
+  coeff8 = theta0_2 (degrees) (converted to radians within LAMMPS)
+
+  8 coeffs are listed in data file
+</PRE>
+<H4>
+Angle-Angle-Torsion (computed within class II dihedral) </H4>
+<PRE>
+
+  E = K (theta - theta0) * (theta' - theta0') * (phi - phi0)
+
+  theta,theta' = radians (computed by LAMMPS)
+  phi = radians (computed by LAMMPS)
+
+  coeff1 = K (energy/radians^3)
+  coeff2 = theta0 (degrees) (converted to radians within LAMMPS)
+  coeff3 = theta0' (degrees) (converted to radians within LAMMPS)
+
+  Note: phi0 is known from dihedral coeffs so don't need it specified here
+
+  3 coeffs are listed in data file
+
+</PRE>
+<H4>
+Bond-Bond-13-Torsion (computed within class II dihedral) </H4>
+<PRE>
+
+  (undocumented)
+
+</PRE>
+<H4>
+Angle-Angle (computed within class II improper for each of 3 pairs of 
+angles) </H4>
+<PRE>
+
+  E = K_n (theta - theta0_n) * (theta' - theta0_n')
+
+  theta,theta' = radians (computed by LAMMPS)
+
+  coeff1 = K_1 (energy/radians^2)
+  coeff2 = K_2 (energy/radians^2)
+  coeff3 = K_3 (energy/radians^2)
+  coeff4 = theta0_1 (degrees) (converted to radians within LAMMPS)
+  coeff5 = theta0_2 (degrees) (converted to radians within LAMMPS)
+  coeff6 = theta0_3 (degrees) (converted to radians within LAMMPS)
+
+  6 coeffs are listed in data file
+</PRE>
+</BODY>
+</HTML>

doc/html/99/history.html

@@ -0,0 +1,127 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
+<HTML>
+<HEAD>
+    <META NAME="Generator" CONTENT="Cosmo Create 1.0.3">
+</HEAD>
+<BODY>
+<H2>
+History of LAMMPS</H2>
+<P>
+<A HREF="README.html">Return</A> to top-level of LAMMPS documentation.</P>
+<P>
+This is a brief history of features added to each version of LAMMPS.</P>
+<HR>
+<H3>
+LAMMPS 99 - June 99 </H3>
+<UL>
+    <LI>
+    all-MPI version of code (F77 + C + MPI) for maximum portablility 
+    <LI>
+    only one PPPM choice now, the better of the two earlier ones 
+    <LI>
+    PPPM uses portable FFTs and data remapping routines, written in C w/ 
+    MPI, can now use non-power-of-2 processors and grid sizes 
+    <LI>
+    auto-mapping of simulation box to processors 
+    <LI>
+    removed a few unused/unneeded commands (bdump, log file, id string, 
+    limit) 
+    <LI>
+    changed syntax of some commands for simplicity &amp; consistency (see <A
+     HREF="input_commands.html">input commands</A>) 
+    <LI>
+    changed method of calling/writing user diagnostic routines to be simpler
+    <LI>
+    documentation in HTML format
+</UL>
+<HR>
+<H3>
+Version 5.0 - Oct 1997 </H3>
+<UL>
+    <LI>
+    final version of class II force fields 
+    <LI>
+    new formulation of NVE, NVT, NPT and rRESPA integrators 
+    <LI>
+    new version of msi2lmp pre-processing tool, does not require DISCOVER 
+    to run, only DISCOVER force field files 
+    <LI>
+    energy minimizer, Hessian-free truncated Newton method 
+    <LI>
+    new pressure controllers and constraints 
+    <LI>
+    replicate tool for generating new data files from old ones 
+</UL>
+<HR ALIGN="LEFT">
+<H3>
+Version 4.0 - March 1997 </H3>
+<UL>
+    <LI>
+    1st version of class II force fields 
+    <LI>
+    new, faster PPPM solver (newpppm) 
+    <LI>
+    rRESPA 
+    <LI>
+    new data file format 
+    <LI>
+    new constraints, diagnostics 
+    <LI>
+    msi2lmp pre-processing tool 
+</UL>
+<HR>
+<H3>
+Version 3.0 - March 1996 </H3>
+<UL>
+    <LI>
+    more general force-field formulation 
+    <LI>
+    atom/group constraints 
+    <LI>
+    LJ units and bond potentials 
+    <LI>
+    smoothed LJ potential option 
+    <LI>
+    Langevin thermostat 
+    <LI>
+    Newton's 3rd law option 
+    <LI>
+    hook for user-supplied diagnostic routines 
+</UL>
+<HR>
+<H3>
+Version 2.0 - October 1995 </H3>
+<UL>
+    <LI>
+    bug fix of velocity initialization which caused drift 
+    <LI>
+    PPPM for long-range Coulombic 
+    <LI>
+    constant NPT 
+</UL>
+<HR>
+<H3>
+Version 1.1 - February 1995 </H3>
+<UL>
+    <LI>
+    Ewald for long-range Coulombic 
+    <LI>
+    full Newton's 3rd law (doubled communication) 
+    <LI>
+    dumping of atom positions and velocities 
+    <LI>
+    restart files 
+</UL>
+<HR>
+<H3>
+Version 1.0 - January 1995 </H3>
+<UL>
+    <LI>
+    short-range bonded and non-bonded forces 
+    <LI>
+    partial Newton's 3rd law 
+    <LI>
+    velocity-Verlet integrator 
+</UL>
+</BODY>
+</HTML>

doc/html/99/units.html

@@ -0,0 +1,119 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
+<HTML>
+<HEAD>
+    <META NAME="Generator" CONTENT="Cosmo Create 1.0.3">
+</HEAD>
+<BODY>
+<H2>
+LAMMPS Units</H2>
+<P>
+<A HREF="README.html">Return</A> to top-level LAMMPS documentation.</P>
+<P>
+This file describes the units associated with many of the key variables 
+and equations used inside the LAMMPS code. Units used for input command 
+parameters are described in the input_commands file. The input command 
+&quot;units&quot; selects between conventional and Lennard-Jones units. 
+See the force_fields file for more information on units for the force 
+field parameters that are input from data files. </P>
+<P>
+Conventional units: </P>
+<UL>
+    <LI>
+    distance = Angstroms 
+    <LI>
+    time = femtoseconds 
+    <LI>
+    mass = grams/mole 
+    <LI>
+    temperature = degrees K 
+    <LI>
+    pressure = atmospheres 
+    <LI>
+    energy = Kcal/mole 
+    <LI>
+    velocity = Angstroms/femtosecond 
+    <LI>
+    force = grams/mole * Angstroms/femtosecond^2 
+    <LI>
+    charge = +/- 1.0 is proton/electron
+</UL>
+<P>
+LJ reduced units: </P>
+<UL>
+    <LI>
+    distance = sigmas 
+    <LI>
+    time = reduced LJ tau 
+    <LI>
+    mass = ratio to unitless 1.0
+    <LI>
+    temperature = reduced LJ temp 
+    <LI>
+    pressure = reduced LJ pressure 
+    <LI>
+    energy = epsilons 
+    <LI>
+    velocity = sigmas/tau 
+    <LI>
+    force = reduced LJ force (sigmas/tau^2) 
+    <LI>
+    charge = ratio to unitless 1.0
+</UL>
+<HR>
+<P>
+This listing of variables assumes conventional units; to convert to LJ 
+reduced units, simply substitute the appropriate term from the list 
+above. E.g. x is in sigmas in LJ units. Per-mole in any of the units 
+simply means for 6.023 x 10^23 atoms.</P>
+<P>
+</P>
+<PRE>
+Meaning        Variable        Units
+
+positions      x               Angstroms
+velocities     v               Angstroms / click (see below)
+forces         f               Kcal / (mole - Angstrom)                
+masses         mass            gram / mole
+charges        q               electron units (-1 for an electron)
+                                 (1 e.u. = 1.602 x 10^-19 coul)
+
+time           ---             clicks (1 click = 48.88821 fmsec)
+timestep       dt              clicks
+input timestep dt_in           fmsec
+time convert   dtfactor        48.88821 fmsec / click
+
+temperature     t_current       degrees K
+                t_start
+                t_stop
+input damping   t_freq_in       inverse fmsec
+internal temp   t_freq          inverse clicks
+  damping
+
+dielec const    dielectric      1.0 (unitless)
+Boltmann const  boltz           0.001987191 Kcal / (mole - degree K)
+
+virial          virial[xyz]     Kcal/mole = r dot F
+pressure factor pfactor         68589.796 (convert internal to atmospheres)
+internal        p_current       Kcal / (mole - Angs^3)
+  pressure      p_start
+                p_stop
+input press     p_start_in      atmospheres
+                p_stop_in
+output press    log file        atmospheres
+input damping   p_freq_in       inverse time
+internal press  p_freq          inverse clicks
+  damping
+
+pot eng         e_potential     Kcal/mole
+kin eng         e_kinetic       Kcal/mole
+eng convert     efactor         332.0636 (Kcal - Ang) / (q^2 - mole)
+                                (convert Coulomb eng to Kcal/mole)
+
+LJ coeffs       lja,ljb         Kcal-Angs^(6,12)/mole
+
+bond            various         see force_fields file
+  parameters    2,3,4-body
+                terms
+</PRE>
+</BODY>
+</HTML>

doc/html/Manual.html

@@ -0,0 +1,456 @@
+
+
+<!DOCTYPE html>
+<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
+<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
+<head>
+  <meta charset="utf-8">
+  
+  <meta name="viewport" content="width=device-width, initial-scale=1.0">
+  
+  <title>LAMMPS Documentation &mdash; LAMMPS documentation</title>
+  
+
+  
+  
+
+  
+
+  
+  
+    
+
+  
+
+  
+  
+    <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+  
+
+  
+    <link rel="stylesheet" href="_static/sphinxcontrib-images/LightBox2/lightbox2/css/lightbox.css" type="text/css" />
+  
+
+  
+    <link rel="top" title="LAMMPS documentation" href="index.html"/>
+        <link rel="next" title="1. Introduction" href="Section_intro.html"/> 
+
+  
+  <script src="_static/js/modernizr.min.js"></script>
+
+</head>
+
+<body class="wy-body-for-nav" role="document">
+
+  <div class="wy-grid-for-nav">
+
+    
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-nav-search">
+        
+
+        
+          <a href="#" class="icon icon-home"> LAMMPS
+        
+
+        
+        </a>
+
+        
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+
+        
+      </div>
+
+      <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
+        
+          
+          
+              <p class="caption"><span class="caption-text">User Documentation</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+</ul>
+<p class="caption"><span class="caption-text">Index</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="tutorials.html">Tutorials</a></li>
+<li class="toctree-l1"><a class="reference internal" href="commands.html">Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
+<li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
+<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
+<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
+<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
+<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>
+</ul>
+
+          
+        
+      </div>
+      &nbsp;
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
+
+      
+      <nav class="wy-nav-top" role="navigation" aria-label="top navigation">
+        <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+        <a href="#">LAMMPS</a>
+      </nav>
+
+
+      
+      <div class="wy-nav-content">
+        <div class="rst-content">
+          <div role="navigation" aria-label="breadcrumbs navigation">
+  <ul class="wy-breadcrumbs">
+    <li><a href="#">Docs</a> &raquo;</li>
+      
+    <li>LAMMPS Documentation</li>
+      <li class="wy-breadcrumbs-aside">
+        
+          
+            <a href="http://lammps.sandia.gov">Website</a>
+            <a href="Section_commands.html#comm">Commands</a>
+        
+      </li>
+  </ul>
+  <hr/>
+  
+    <div class="rst-footer-buttons" style="margin-bottom: 1em" role="navigation" aria-label="footer navigation">
+      
+        <a href="Section_intro.html" class="btn btn-neutral float-right" title="1. Introduction" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
+      
+      
+    </div>
+  
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+            
+  <H1></H1><div class="section" id="lammps-documentation">
+<h1>LAMMPS Documentation</h1>
+<div class="section" id="sep-2016-version">
+<h2>20 Sep 2016 version</h2>
+</div>
+<div class="section" id="version-info">
+<h2>Version info:</h2>
+<p>The LAMMPS &#8220;version&#8221; is the date when it was released, such as 1 May
+2010. LAMMPS is updated continuously.  Whenever we fix a bug or add a
+feature, we release it immediately, and post a notice on <a class="reference external" href="http://lammps.sandia.gov/bug.html">this page of the WWW site</a>. Every 2-4 months one of the incremental releases
+is subjected to more thorough testing and labeled as a <em>stable</em> version.</p>
+<p>Each dated copy of LAMMPS contains all the
+features and bug-fixes up to and including that version date. The
+version date is printed to the screen and logfile every time you run
+LAMMPS. It is also in the file src/version.h and in the LAMMPS
+directory name created when you unpack a tarball, and at the top of
+the first page of the manual (this page).</p>
+<ul class="simple">
+<li>If you browse the HTML doc pages on the LAMMPS WWW site, they always
+describe the most current version of LAMMPS.</li>
+<li>If you browse the HTML doc pages included in your tarball, they
+describe the version you have.</li>
+<li>The <a class="reference external" href="Manual.pdf">PDF file</a> on the WWW site or in the tarball is updated
+about once per month.  This is because it is large, and we don&#8217;t want
+it to be part of every patch.</li>
+<li>There is also a <a class="reference external" href="Developer.pdf">Developer.pdf</a> file in the doc
+directory, which describes the internal structure and algorithms of
+LAMMPS.</li>
+</ul>
+<p>LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
+Simulator.</p>
+<p>LAMMPS is a classical molecular dynamics simulation code designed to
+run efficiently on parallel computers.  It was developed at Sandia
+National Laboratories, a US Department of Energy facility, with
+funding from the DOE.  It is an open-source code, distributed freely
+under the terms of the GNU Public License (GPL).</p>
+<p>The current core group of LAMMPS developers is at Sandia National
+Labs and Temple University:</p>
+<ul class="simple">
+<li><a class="reference external" href="http://www.sandia.gov/~sjplimp">Steve Plimpton</a>, sjplimp at sandia.gov</li>
+<li>Aidan Thompson, athomps at sandia.gov</li>
+<li>Stan Moore, stamoore at sandia.gov</li>
+<li><a class="reference external" href="http://goo.gl/1wk0">Axel Kohlmeyer</a>, akohlmey at gmail.com</li>
+</ul>
+<p>Past core developers include Paul Crozier, Ray Shan and Mark Stevens,
+all at Sandia. The <strong>LAMMPS home page</strong> at
+<a class="reference external" href="http://lammps.sandia.gov">http://lammps.sandia.gov</a> has more information
+about the code and its uses. Interaction with external LAMMPS developers,
+bug reports and feature requests are mainly coordinated through the
+<a class="reference external" href="https://github.com/lammps/lammps">LAMMPS project on GitHub.</a>
+The lammps.org domain, currently hosting <a class="reference external" href="https://ci.lammps.org/job/lammps/">public continuous integration testing</a> and <a class="reference external" href="http://rpm.lammps.org">precompiled Linux RPM and Windows installer packages</a> is located
+at Temple University and managed by Richard Berger,
+richard.berger at temple.edu.</p>
+<hr class="docutils" />
+<p>The LAMMPS documentation is organized into the following sections.  If
+you find errors or omissions in this manual or have suggestions for
+useful information to add, please send an email to the developers so
+we can improve the LAMMPS documentation.</p>
+<p>Once you are familiar with LAMMPS, you may want to bookmark <a class="reference internal" href="Section_commands.html#comm"><span class="std std-ref">this page</span></a> at Section_commands.html#comm since
+it gives quick access to documentation for all LAMMPS commands.</p>
+<p><a class="reference external" href="Manual.pdf">PDF file</a> of the entire manual, generated by
+<a class="reference external" href="http://freecode.com/projects/htmldoc">htmldoc</a></p>
+<div class="toctree-wrapper compound" id="userdoc">
+<p class="caption"><span class="caption-text">User Documentation</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#what-is-lammps">1.1. What is LAMMPS</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#lammps-features">1.2. LAMMPS features</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#lammps-non-features">1.3. LAMMPS non-features</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#open-source-distribution">1.4. Open source distribution</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#acknowledgments-and-citations">1.5. Acknowledgments and citations</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="Section_start.html#what-s-in-the-lammps-distribution">2.1. What&#8217;s in the LAMMPS distribution</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_start.html#making-lammps">2.2. Making LAMMPS</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_start.html#making-lammps-with-optional-packages">2.3. Making LAMMPS with optional packages</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_start.html#building-lammps-via-the-make-py-tool">2.4. Building LAMMPS via the Make.py tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_start.html#building-lammps-as-a-library">2.5. Building LAMMPS as a library</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_start.html#running-lammps">2.6. Running LAMMPS</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_start.html#command-line-options">2.7. Command-line options</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_start.html#lammps-screen-output">2.8. LAMMPS screen output</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_start.html#tips-for-users-of-previous-lammps-versions">2.9. Tips for users of previous LAMMPS versions</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#lammps-input-script">3.1. LAMMPS input script</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#parsing-rules">3.2. Parsing rules</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#input-script-structure">3.3. Input script structure</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#commands-listed-by-category">3.4. Commands listed by category</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#individual-commands">3.5. Individual commands</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#fix-styles">3.6. Fix styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#compute-styles">3.7. Compute styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#pair-style-potentials">3.8. Pair_style potentials</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#bond-style-potentials">3.9. Bond_style potentials</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#angle-style-potentials">3.10. Angle_style potentials</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#dihedral-style-potentials">3.11. Dihedral_style potentials</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#improper-style-potentials">3.12. Improper_style potentials</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#kspace-solvers">3.13. Kspace solvers</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#standard-packages">4.1. Standard packages</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-packages">4.2. User packages</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#measuring-performance">5.1. Measuring performance</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#general-strategies">5.2. General strategies</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#packages-with-optimized-styles">5.3. Packages with optimized styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#comparison-of-various-accelerator-packages">5.4. Comparison of various accelerator packages</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#restarting-a-simulation">6.1. Restarting a simulation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#d-simulations">6.2. 2d simulations</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#charmm-amber-and-dreiding-force-fields">6.3. CHARMM, AMBER, and DREIDING force fields</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#running-multiple-simulations-from-one-input-script">6.4. Running multiple simulations from one input script</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#multi-replica-simulations">6.5. Multi-replica simulations</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#granular-models">6.6. Granular models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#tip3p-water-model">6.7. TIP3P water model</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#tip4p-water-model">6.8. TIP4P water model</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#spc-water-model">6.9. SPC water model</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#coupling-lammps-to-other-codes">6.10. Coupling LAMMPS to other codes</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#visualizing-lammps-snapshots">6.11. Visualizing LAMMPS snapshots</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#triclinic-non-orthogonal-simulation-boxes">6.12. Triclinic (non-orthogonal) simulation boxes</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#nemd-simulations">6.13. NEMD simulations</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#finite-size-spherical-and-aspherical-particles">6.14. Finite-size spherical and aspherical particles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#output-from-lammps-thermo-dumps-computes-fixes-variables">6.15. Output from LAMMPS (thermo, dumps, computes, fixes, variables)</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#thermostatting-barostatting-and-computing-temperature">6.16. Thermostatting, barostatting, and computing temperature</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#walls">6.17. Walls</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#elastic-constants">6.18. Elastic constants</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#library-interface-to-lammps">6.19. Library interface to LAMMPS</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-thermal-conductivity">6.20. Calculating thermal conductivity</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-viscosity">6.21. Calculating viscosity</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-a-diffusion-coefficient">6.22. Calculating a diffusion coefficient</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#using-chunks-to-calculate-system-properties">6.23. Using chunks to calculate system properties</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#setting-parameters-for-the-kspace-style-pppm-disp-command">6.24. Setting parameters for the <code class="docutils literal"><span class="pre">kspace_style</span> <span class="pre">pppm/disp</span></code> command</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#polarizable-models">6.25. Polarizable models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#adiabatic-core-shell-model">6.26. Adiabatic core/shell model</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#drude-induced-dipoles">6.27. Drude induced dipoles</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="Section_example.html#lowercase-directories">7.1. Lowercase directories</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_example.html#uppercase-directories">7.2. Uppercase directories</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#amber2lmp-tool">9.1. amber2lmp tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#binary2txt-tool">9.2. binary2txt tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#ch2lmp-tool">9.3. ch2lmp tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#chain-tool">9.4. chain tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#colvars-tools">9.5. colvars tools</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#createatoms-tool">9.6. createatoms tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#data2xmovie-tool">9.7. data2xmovie tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eam-database-tool">9.8. eam database tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eam-generate-tool">9.9. eam generate tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eff-tool">9.10. eff tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#emacs-tool">9.11. emacs tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#fep-tool">9.12. fep tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#i-pi-tool">9.13. i-pi tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#ipp-tool">9.14. ipp tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#kate-tool">9.15. kate tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2arc-tool">9.16. lmp2arc tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2cfg-tool">9.17. lmp2cfg tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2vmd-tool">9.18. lmp2vmd tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#matlab-tool">9.19. matlab tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#micelle2d-tool">9.20. micelle2d tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#moltemplate-tool">9.21. moltemplate tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#msi2lmp-tool">9.22. msi2lmp tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#phonon-tool">9.23. phonon tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#polymer-bonding-tool">9.24. polymer bonding tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#pymol-asphere-tool">9.25. pymol_asphere tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#python-tool">9.26. python tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#reax-tool">9.27. reax tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#restart2data-tool">9.28. restart2data tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#vim-tool">9.29. vim tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#xmgrace-tool">9.30. xmgrace tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#xmovie-tool">9.31. xmovie tool</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#atom-styles">10.1. Atom styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#bond-angle-dihedral-improper-potentials">10.2. Bond, angle, dihedral, improper potentials</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#compute-styles">10.3. Compute styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#dump-styles">10.4. Dump styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#dump-custom-output-options">10.5. Dump custom output options</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#fix-styles">10.6. Fix styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#input-script-commands">10.7. Input script commands</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#kspace-computations">10.8. Kspace computations</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#minimization-styles">10.9. Minimization styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#pairwise-potentials">10.10. Pairwise potentials</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#region-styles">10.11. Region styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#body-styles">10.12. Body styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#thermodynamic-output-options">10.13. Thermodynamic output options</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#variable-options">10.14. Variable options</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#submitting-new-features-for-inclusion-in-lammps">10.15. Submitting new features for inclusion in LAMMPS</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="Section_python.html#overview-of-running-lammps-from-python">11.1. Overview of running LAMMPS from Python</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_python.html#overview-of-using-python-from-a-lammps-script">11.2. Overview of using Python from a LAMMPS script</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_python.html#building-lammps-as-a-shared-library">11.3. Building LAMMPS as a shared library</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_python.html#installing-the-python-wrapper-into-python">11.4. Installing the Python wrapper into Python</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_python.html#extending-python-with-mpi-to-run-in-parallel">11.5. Extending Python with MPI to run in parallel</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_python.html#testing-the-python-lammps-interface">11.6. Testing the Python-LAMMPS interface</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_python.html#using-lammps-from-python">11.7. Using LAMMPS from Python</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_python.html#example-python-scripts-that-use-lammps">11.8. Example Python scripts that use LAMMPS</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#common-problems">12.1. Common problems</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#reporting-bugs">12.2. Reporting bugs</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#error-warning-messages">12.3. Error &amp; warning messages</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#error">12.4. Errors:</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#warnings">12.5. Warnings:</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="Section_history.html#coming-attractions">13.1. Coming attractions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_history.html#past-versions">13.2. Past versions</a></li>
+</ul>
+</li>
+</ul>
+</div>
+<div class="toctree-wrapper compound" id="index">
+</div>
+</div>
+</div>
+<div class="section" id="indices-and-tables">
+<h1>Indices and tables</h1>
+<ul class="simple">
+<li><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></li>
+<li><a class="reference internal" href="search.html"><span class="std std-ref">Search Page</span></a></li>
+</ul>
+</BODY></div>
+
+
+           </div>
+          </div>
+          <footer>
+  
+    <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
+      
+        <a href="Section_intro.html" class="btn btn-neutral float-right" title="1. Introduction" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
+      
+      
+    </div>
+  
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>
+        &copy; Copyright 2013 Sandia Corporation.
+    </p>
+  </div>
+  Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
+</footer>
+
+        </div>
+      </div>
+
+    </section>
+
+  </div>
+  
+
+
+  
+
+    <script type="text/javascript">
+        var DOCUMENTATION_OPTIONS = {
+            URL_ROOT:'./',
+            VERSION:'',
+            COLLAPSE_INDEX:false,
+            FILE_SUFFIX:'.html',
+            HAS_SOURCE:  true
+        };
+    </script>
+      <script type="text/javascript" src="_static/jquery.js"></script>
+      <script type="text/javascript" src="_static/underscore.js"></script>
+      <script type="text/javascript" src="_static/doctools.js"></script>
+      <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+      <script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/jquery-1.11.0.min.js"></script>
+      <script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/lightbox.min.js"></script>
+      <script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2-customize/jquery-noconflict.js"></script>
+
+  
+
+  
+  
+    <script type="text/javascript" src="_static/js/theme.js"></script>
+  
+
+  
+  
+  <script type="text/javascript">
+      jQuery(function () {
+          SphinxRtdTheme.StickyNav.enable();
+      });
+  </script>
+   
+
+</body>
+</html>

doc/html/PDF/pair_gayberne_extra.tex

@@ -0,0 +1,167 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+\begin{center}
+
+\large{Additional documentation for the Gay-Berne ellipsoidal potential \\
+  as implemented in LAMMPS}
+
+\end{center}
+
+\centerline{Mike Brown, Sandia National Labs, April 2007}
+
+\vspace{0.3in}
+
+The Gay-Berne anisotropic LJ interaction between pairs of dissimilar
+ellipsoidal particles is given by
+
+$$ U ( \mathbf{A}_1, \mathbf{A}_2, \mathbf{r}_{12} ) = U_r (
+\mathbf{A}_1, \mathbf{A}_2, \mathbf{r}_{12}, \gamma ) \cdot \eta_{12} (
+\mathbf{A}_1, \mathbf{A}_2, \upsilon ) \cdot \chi_{12} ( \mathbf{A}_1,
+\mathbf{A}_2, \mathbf{r}_{12}, \mu ) $$
+
+where $\mathbf{A}_1$ and $\mathbf{A}_2$ are the transformation
+matrices from the simulation box frame to the body frame and
+$\mathbf{r}_{12}$ is the center to center vector between the
+particles.  $U_r$ controls the shifted distance dependent interaction
+based on the distance of closest approach of the two particles
+($h_{12}$) and the user-specified shift parameter gamma:
+
+$$ U_r = 4 \epsilon ( \varrho^{12} - \varrho^6) $$
+
+$$ \varrho = \frac{\sigma}{ h_{12} + \gamma \sigma} $$
+
+Let the shape matrices $\mathbf{S}_i=\mbox{diag}(a_i, b_i, c_i)$ be 
+given by the ellipsoid radii. The $\eta$ orientation-dependent energy 
+based on the user-specified exponent $\upsilon$ is given by
+
+$$ \eta_{12} = [ \frac{ 2 s_1 s_2 }{\det ( \mathbf{G}_{12} )}]^{
+\upsilon / 2 } , $$
+
+$$ s_i = [a_i b_i + c_i c_i][a_i b_i]^{ 1 / 2 }, $$
+
+and
+
+$$ \mathbf{G}_{12} = \mathbf{A}_1^T \mathbf{S}_1^2 \mathbf{A}_1 +
+\mathbf{A}_2^T \mathbf{S}_2^2 \mathbf{A}_2 = \mathbf{G}_1 +
+\mathbf{G}_2. $$
+
+Let the relative energy matrices $\mathbf{E}_i = \mbox{diag}
+(\epsilon_{ia}, \epsilon_{ib}, \epsilon_{ic})$ be given by 
+the relative well depths (dimensionless energy scales 
+inversely proportional to the well-depths of the respective 
+orthogonal configurations of the interacting molecules). The 
+$\chi$ orientation-dependent energy based on the user-specified 
+exponent $\mu$ is given by
+
+$$ \chi_{12} = [2 \hat{\mathbf{r}}_{12}^T \mathbf{B}_{12}^{-1}
+\hat{\mathbf{r}}_{12}]^\mu, $$
+
+$$ \hat{\mathbf{r}}_{12} = { \mathbf{r}_{12} } / |\mathbf{r}_{12}|, $$
+
+and
+
+$$ \mathbf{B}_{12} = \mathbf{A}_1^T \mathbf{E}_1^2 \mathbf{A}_1 +
+\mathbf{A}_2^T \mathbf{E}_2^2 \mathbf{A}_2 = \mathbf{B}_1 +
+\mathbf{B}_2. $$
+
+Here, we use the distance of closest approach approximation given by the
+Perram reference, namely
+
+$$ h_{12} = r - \sigma_{12} ( \mathbf{A}_1, \mathbf{A}_2,
+\mathbf{r}_{12} ), $$
+
+$$ r = |\mathbf{r}_{12}|, $$
+
+and
+
+$$ \sigma_{12} = [ \frac{1}{2} \hat{\mathbf{r}}_{12}^T
+\mathbf{G}_{12}^{-1} \hat{\mathbf{r}}_{12}.]^{ -1/2 } $$
+
+Forces and Torques: Because the analytic forces and torques have not
+been published for this potential, we list them here:
+
+$$ \mathbf{f} = - \eta_{12} ( U_r \cdot { \frac{\partial \chi_{12}
+}{\partial r} } + \chi_{12} \cdot { \frac{\partial U_r }{\partial r} }
+) $$
+
+where the derivative of $U_r$ is given by (see Allen reference)
+
+$$ \frac{\partial U_r }{\partial r} = \frac{ \partial U_{SLJ} }{
+\partial r } \hat{\mathbf{r}}_{12} + r^{-2} \frac{ \partial U_{SLJ} }{
+\partial \varphi } [ \mathbf{\kappa} - ( \mathbf{\kappa}^T \cdot
+\hat{\mathbf{r}}_{12}) \hat{\mathbf{r}}_{12} ], $$
+
+$$ \frac{ \partial U_{SLJ} }{ \partial \varphi } = 24 \epsilon ( 2
+\varrho^{13} - \varrho^7 ) \sigma_{12}^3 / 2 \sigma, $$
+
+$$ \frac{ \partial U_{SLJ} }{ \partial r } = 24 \epsilon ( 2
+\varrho^{13} - \varrho^7 ) / \sigma, $$
+
+and
+
+$$ \mathbf{\kappa} = \mathbf{G}_{12}^{-1} \cdot \mathbf{r}_{12}. $$
+
+The derivate of the $\chi$ term is given by
+
+$$ \frac{\partial \chi_{12} }{\partial r} = - r^{-2} \cdot 4.0 \cdot [
+\mathbf{\iota} - ( \mathbf{\iota}^T \cdot \hat{\mathbf{r}}_{12} )
+\hat{\mathbf{r}}_{12} ] \cdot \mu \cdot \chi_{12}^{ ( \mu -1 ) / \mu
+}, $$
+
+and
+
+$$ \mathbf{\iota} = \mathbf{B}_{12}^{-1} \cdot \mathbf{r}_{12}. $$
+
+The torque is given by:
+
+$$ \mathbf{\tau}_i = U_r \eta_{12} \frac{ \partial \chi_{12} }{
+\partial \mathbf{q}_i } + \chi_{12} ( U_r \frac{ \partial \eta_{12} }{
+\partial \mathbf{q}_i } + \eta_{12} \frac{ \partial U_r }{ \partial
+\mathbf{q}_i } ), $$
+
+$$ \frac{ \partial U_r }{ \partial \mathbf{q}_i } = \mathbf{A}_i \cdot
+(- \mathbf{\kappa}^T \cdot \mathbf{G}_i \times \mathbf{f}_k ), $$
+
+$$ \mathbf{f}_k = - r^{-2} \frac{ \delta U_{SLJ} }{ \delta \varphi }
+\mathbf{\kappa}, $$
+
+and
+
+$$ \frac{ \partial \chi_{12} }{ \partial \mathbf{q}_i } = 4.0 \cdot
+r^{-2} \cdot \mathbf{A}_i (- \mathbf{\iota}^T \cdot \mathbf{B}_i
+\times \mathbf{\iota} ). $$
+
+For the derivative of the $\eta$ term, we were unable to find a matrix
+expression due to the determinant. Let $a_{mi}$ be the mth row of the
+rotation matrix $A_i$. Then,
+
+$$ \frac{ \partial \eta_{12} }{ \partial \mathbf{q}_i } = \mathbf{A}_i
+\cdot \sum_m \mathbf{a}_{mi} \times \frac{ \partial \eta_{12} }{
+\partial \mathbf{a}_{mi} } = \mathbf{A}_i \cdot \sum_m \mathbf{a}_{mi}
+\times \mathbf{d}_{mi}, $$
+
+where $d_mi$ represents the mth row of a derivative matrix $D_i$,
+
+$$ \mathbf{D}_i = - \frac{1}{2} \cdot ( \frac{2s1s2}{\det (
+\mathbf{G}_{12} ) } )^{ \upsilon / 2 } \cdot {\frac{\upsilon}{\det (
+\mathbf{G}_{12} ) }} \cdot \mathbf{E}, $$
+
+where the matrix $E$ gives the derivate with respect to the rotation
+matrix,
+
+$$ \mathbf{E} = [ e_{my} ] = \frac{ \partial \eta_{12} }{ \partial
+\mathbf{A}_i }, $$
+
+and
+
+$$ e_{my} = \det ( \mathbf{G}_{12} ) \cdot \mbox{trace} [
+\mathbf{G}_{12}^{-1} \cdot ( \hat{\mathbf{p}}_y \otimes \mathbf{a}_m +
+\mathbf{a}_m \otimes \hat{\mathbf{p}}_y ) \cdot s_{mm}^2 ]. $$
+
+Here, $p_v$ is the unit vector for the axes in the lab frame $(p1=[1, 0,
+0], p2=[0, 1, 0], and p3=[0, 0, 1])$ and $s_{mm}$ gives the mth radius of
+the ellipsoid $i$.
+
+\end{document}

doc/html/PDF/pair_resquared_extra.tex

@@ -0,0 +1,113 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+\begin{center}
+
+\large{Additional documentation for the RE-squared ellipsoidal potential \\
+  as implemented in LAMMPS}
+
+\end{center}
+
+\centerline{Mike Brown, Sandia National Labs, October 2007}
+
+\vspace{0.3in}
+
+Let the shape matrices $\mathbf{S}_i=\mbox{diag}(a_i, b_i, c_i)$ be 
+given by the ellipsoid radii. Let the relative energy matrices 
+$\mathbf{E}_i = \mbox{diag} (\epsilon_{ia}, \epsilon_{ib}, 
+\epsilon_{ic})$ be given by the relative well depths 
+(dimensionless energy scales inversely proportional to the well-depths 
+of the respective orthogonal configurations of the interacting molecules).
+Let $\mathbf{A}_1$ and $\mathbf{A}_2$ be the transformation matrices 
+from the simulation box frame to the body frame and $\mathbf{r}$ 
+be the center to center vector between the particles. Let $A_{12}$ be 
+the Hamaker constant for the interaction given in LJ units by
+$A_{12}=4\pi^2\epsilon_{\mathrm{LJ}}(\rho\sigma^3)^2$.
+ 
+\vspace{0.3in}
+
+The RE-squared anisotropic interaction between pairs of 
+ellipsoidal particles is given by
+
+$$ U=U_A+U_R, $$
+
+$$ U_\alpha=\frac{A_{12}}{m_\alpha}(\frac\sigma{h})^{n_\alpha}
+(1+o_\alpha\eta\chi\frac\sigma{h}) \times \prod_i{
+\frac{a_ib_ic_i}{(a_i+h/p_\alpha)(b_i+h/p_\alpha)(c_i+h/p_\alpha)}}, $$
+
+$$ m_A=-36, n_A=0, o_A=3, p_A=2, $$
+
+$$ m_R=2025, n_R=6, o_R=45/56, p_R=60^{1/3}, $$
+
+$$ \chi = 2 \hat{\mathbf{r}}^T \mathbf{B}^{-1}
+\hat{\mathbf{r}}, $$
+
+$$ \hat{\mathbf{r}} = { \mathbf{r} } / |\mathbf{r}|, $$
+
+$$ \mathbf{B} = \mathbf{A}_1^T \mathbf{E}_1 \mathbf{A}_1 +
+\mathbf{A}_2^T \mathbf{E}_2 \mathbf{A}_2 $$
+
+$$ \eta = \frac{ \det[\mathbf{S}_1]/\sigma_1^2+
+det[\mathbf{S}_2]/\sigma_2^2}{[\det[\mathbf{H}]/
+(\sigma_1+\sigma_2)]^{1/2}}, $$
+
+$$ \sigma_i = (\hat{\mathbf{r}}^T\mathbf{A}_i^T\mathbf{S}_i^{-2}
+\mathbf{A}_i\hat{\mathbf{r}})^{-1/2}, $$
+
+$$ \mathbf{H} = \frac{1}{\sigma_1}\mathbf{A}_1^T \mathbf{S}_1^2 \mathbf{A}_1 +
+\frac{1}{\sigma_2}\mathbf{A}_2^T \mathbf{S}_2^2 \mathbf{A}_2 $$
+
+ 
+Here, we use the distance of closest approach approximation given by the
+Perram reference, namely
+
+$$ h = |r| - \sigma_{12}, $$
+
+$$ \sigma_{12} = [ \frac{1}{2} \hat{\mathbf{r}}^T
+\mathbf{G}^{-1} \hat{\mathbf{r}}]^{ -1/2 }, $$
+
+and
+
+$$ \mathbf{G} = \mathbf{A}_1^T \mathbf{S}_1^2 \mathbf{A}_1 +
+\mathbf{A}_2^T \mathbf{S}_2^2 \mathbf{A}_2 $$
+
+\vspace{0.3in}
+
+The RE-squared anisotropic interaction between a 
+ellipsoidal particle and a Lennard-Jones sphere is defined
+as the $\lim_{a_2->0}U$ under the constraints that
+$a_2=b_2=c_2$ and $\frac{4}{3}\pi a_2^3\rho=1$:
+
+$$ U_{\mathrm{elj}}=U_{A_{\mathrm{elj}}}+U_{R_{\mathrm{elj}}}, $$
+
+$$ U_{\alpha_{\mathrm{elj}}}=(\frac{3\sigma^3c_\alpha^3}
+{4\pi h_{\mathrm{elj}}^3})\frac{A_{12_{\mathrm{elj}}}}
+{m_\alpha}(\frac\sigma{h_{\mathrm{elj}}})^{n_\alpha}
+(1+o_\alpha\chi_{\mathrm{elj}}\frac\sigma{h_{\mathrm{elj}}}) \times 
+\frac{a_1b_1c_1}{(a_1+h_{\mathrm{elj}}/p_\alpha)
+(b_1+h_{\mathrm{elj}}/p_\alpha)(c_1+h_{\mathrm{elj}}/p_\alpha)}, $$
+
+$$ A_{12_{\mathrm{elj}}}=4\pi^2\epsilon_{\mathrm{LJ}}(\rho\sigma^3), $$
+
+with $h_{\mathrm{elj}}$ and $\chi_{\mathrm{elj}}$ calculated as above 
+by replacing $B$ with $B_{\mathrm{elj}}$ and $G$ with $G_{\mathrm{elj}}$:
+
+$$ \mathbf{B}_{\mathrm{elj}} = \mathbf{A}_1^T \mathbf{E}_1 \mathbf{A}_1 + I, $$
+
+$$ \mathbf{G}_{\mathrm{elj}} = \mathbf{A}_1^T \mathbf{S}_1^2 \mathbf{A}_1.$$
+
+\vspace{0.3in}
+
+The interaction between two LJ spheres is calculated as:
+
+$$
+ U_{\mathrm{lj}} = 4 \epsilon \left[ \left(\frac{\sigma}{|\mathbf{r}|}\right)^{12} - 
+                       \left(\frac{\sigma}{|\mathbf{r}|}\right)^6 \right]
+$$
+
+\vspace{0.3in}
+
+The analytic derivatives are used for all force and torque calculation.
+
+\end{document}

doc/html/Section_accelerate.html

@@ -0,0 +1,613 @@
+
+
+<!DOCTYPE html>
+<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
+<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
+<head>
+  <meta charset="utf-8">
+  
+  <meta name="viewport" content="width=device-width, initial-scale=1.0">
+  
+  <title>5. Accelerating LAMMPS performance &mdash; LAMMPS documentation</title>
+  
+
+  
+  
+
+  
+
+  
+  
+    
+
+  
+
+  
+  
+    <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+  
+
+  
+    <link rel="stylesheet" href="_static/sphinxcontrib-images/LightBox2/lightbox2/css/lightbox.css" type="text/css" />
+  
+
+  
+    <link rel="top" title="LAMMPS documentation" href="index.html"/>
+        <link rel="next" title="5.3.1. GPU package" href="accelerate_gpu.html"/>
+        <link rel="prev" title="4. Packages" href="Section_packages.html"/> 
+
+  
+  <script src="_static/js/modernizr.min.js"></script>
+
+</head>
+
+<body class="wy-body-for-nav" role="document">
+
+  <div class="wy-grid-for-nav">
+
+    
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-nav-search">
+        
+
+        
+          <a href="Manual.html" class="icon icon-home"> LAMMPS
+        
+
+        
+        </a>
+
+        
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+
+        
+      </div>
+
+      <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
+        
+          
+          
+              <p class="caption"><span class="caption-text">User Documentation</span></p>
+<ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">5. Accelerating LAMMPS performance</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#measuring-performance">5.1. Measuring performance</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#general-strategies">5.2. General strategies</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#packages-with-optimized-styles">5.3. Packages with optimized styles</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="accelerate_gpu.html">5.3.1. GPU package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="accelerate_intel.html">5.3.2. USER-INTEL package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="accelerate_kokkos.html">5.3.3. KOKKOS package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="accelerate_omp.html">5.3.4. USER-OMP package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="accelerate_opt.html">5.3.5. OPT package</a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="#comparison-of-various-accelerator-packages">5.4. Comparison of various accelerator packages</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+</ul>
+<p class="caption"><span class="caption-text">Index</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="tutorials.html">Tutorials</a></li>
+<li class="toctree-l1"><a class="reference internal" href="commands.html">Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
+<li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
+<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
+<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
+<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
+<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>
+</ul>
+
+          
+        
+      </div>
+      &nbsp;
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
+
+      
+      <nav class="wy-nav-top" role="navigation" aria-label="top navigation">
+        <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+        <a href="Manual.html">LAMMPS</a>
+      </nav>
+
+
+      
+      <div class="wy-nav-content">
+        <div class="rst-content">
+          <div role="navigation" aria-label="breadcrumbs navigation">
+  <ul class="wy-breadcrumbs">
+    <li><a href="Manual.html">Docs</a> &raquo;</li>
+      
+    <li>5. Accelerating LAMMPS performance</li>
+      <li class="wy-breadcrumbs-aside">
+        
+          
+            <a href="http://lammps.sandia.gov">Website</a>
+            <a href="Section_commands.html#comm">Commands</a>
+        
+      </li>
+  </ul>
+  <hr/>
+  
+    <div class="rst-footer-buttons" style="margin-bottom: 1em" role="navigation" aria-label="footer navigation">
+      
+        <a href="accelerate_gpu.html" class="btn btn-neutral float-right" title="5.3.1. GPU package" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
+      
+      
+        <a href="Section_packages.html" class="btn btn-neutral" title="4. Packages" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+      
+    </div>
+  
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+            
+  <div class="section" id="accelerating-lammps-performance">
+<h1>5. Accelerating LAMMPS performance</h1>
+<p>This section describes various methods for improving LAMMPS
+performance for different classes of problems running on different
+kinds of machines.</p>
+<p>There are two thrusts to the discussion that follows.  The
+first is using code options that implement alternate algorithms
+that can speed-up a simulation.  The second is to use one
+of the several accelerator packages provided with LAMMPS that
+contain code optimized for certain kinds of hardware, including
+multi-core CPUs, GPUs, and Intel Xeon Phi coprocessors.</p>
+<ul class="simple">
+<li>5.1 <a class="reference internal" href="#acc-1"><span class="std std-ref">Measuring performance</span></a></li>
+<li>5.2 <a class="reference internal" href="#acc-2"><span class="std std-ref">Algorithms and code options to boost performace</span></a></li>
+<li>5.3 <a class="reference internal" href="#acc-3"><span class="std std-ref">Accelerator packages with optimized styles</span></a></li>
+<li>5.3.1 <a class="reference internal" href="accelerate_gpu.html"><span class="doc">GPU package</span></a></li>
+<li>5.3.2 <a class="reference internal" href="accelerate_intel.html"><span class="doc">USER-INTEL package</span></a></li>
+<li>5.3.3 <a class="reference internal" href="accelerate_kokkos.html"><span class="doc">KOKKOS package</span></a></li>
+<li>5.3.4 <a class="reference internal" href="accelerate_omp.html"><span class="doc">USER-OMP package</span></a></li>
+<li>5.3.5 <a class="reference internal" href="accelerate_opt.html"><span class="doc">OPT package</span></a></li>
+<li>5.4 <a class="reference internal" href="#acc-4"><span class="std std-ref">Comparison of various accelerator packages</span></a></li>
+</ul>
+<p>The <a class="reference external" href="http://lammps.sandia.gov/bench.html">Benchmark page</a> of the LAMMPS
+web site gives performance results for the various accelerator
+packages discussed in Section 5.2, for several of the standard LAMMPS
+benchmark problems, as a function of problem size and number of
+compute nodes, on different hardware platforms.</p>
+<div class="section" id="measuring-performance">
+<span id="acc-1"></span><h2>5.1. Measuring performance</h2>
+<p>Before trying to make your simulation run faster, you should
+understand how it currently performs and where the bottlenecks are.</p>
+<p>The best way to do this is run the your system (actual number of
+atoms) for a modest number of timesteps (say 100 steps) on several
+different processor counts, including a single processor if possible.
+Do this for an equilibrium version of your system, so that the
+100-step timings are representative of a much longer run.  There is
+typically no need to run for 1000s of timesteps to get accurate
+timings; you can simply extrapolate from short runs.</p>
+<p>For the set of runs, look at the timing data printed to the screen and
+log file at the end of each LAMMPS run.  <a class="reference internal" href="Section_start.html#start-8"><span class="std std-ref">This section</span></a> of the manual has an overview.</p>
+<p>Running on one (or a few processors) should give a good estimate of
+the serial performance and what portions of the timestep are taking
+the most time.  Running the same problem on a few different processor
+counts should give an estimate of parallel scalability.  I.e. if the
+simulation runs 16x faster on 16 processors, its 100% parallel
+efficient; if it runs 8x faster on 16 processors, it&#8217;s 50% efficient.</p>
+<p>The most important data to look at in the timing info is the timing
+breakdown and relative percentages.  For example, trying different
+options for speeding up the long-range solvers will have little impact
+if they only consume 10% of the run time.  If the pairwise time is
+dominating, you may want to look at GPU or OMP versions of the pair
+style, as discussed below.  Comparing how the percentages change as
+you increase the processor count gives you a sense of how different
+operations within the timestep are scaling.  Note that if you are
+running with a Kspace solver, there is additional output on the
+breakdown of the Kspace time.  For PPPM, this includes the fraction
+spent on FFTs, which can be communication intensive.</p>
+<p>Another important detail in the timing info are the histograms of
+atoms counts and neighbor counts.  If these vary widely across
+processors, you have a load-imbalance issue.  This often results in
+inaccurate relative timing data, because processors have to wait when
+communication occurs for other processors to catch up.  Thus the
+reported times for &#8220;Communication&#8221; or &#8220;Other&#8221; may be higher than they
+really are, due to load-imbalance.  If this is an issue, you can
+uncomment the MPI_Barrier() lines in src/timer.cpp, and recompile
+LAMMPS, to obtain synchronized timings.</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="general-strategies">
+<span id="acc-2"></span><h2>5.2. General strategies</h2>
+<div class="admonition note">
+<p class="first admonition-title">Note</p>
+<p class="last">this section 5.2 is still a work in progress</p>
+</div>
+<p>Here is a list of general ideas for improving simulation performance.
+Most of them are only applicable to certain models and certain
+bottlenecks in the current performance, so let the timing data you
+generate be your guide.  It is hard, if not impossible, to predict how
+much difference these options will make, since it is a function of
+problem size, number of processors used, and your machine.  There is
+no substitute for identifying performance bottlenecks, and trying out
+various options.</p>
+<ul class="simple">
+<li>rRESPA</li>
+<li>2-FFT PPPM</li>
+<li>Staggered PPPM</li>
+<li>single vs double PPPM</li>
+<li>partial charge PPPM</li>
+<li>verlet/split run style</li>
+<li>processor command for proc layout and numa layout</li>
+<li>load-balancing: balance and fix balance</li>
+</ul>
+<p>2-FFT PPPM, also called <em>analytic differentiation</em> or <em>ad</em> PPPM, uses
+2 FFTs instead of the 4 FFTs used by the default <em>ik differentiation</em>
+PPPM. However, 2-FFT PPPM also requires a slightly larger mesh size to
+achieve the same accuracy as 4-FFT PPPM. For problems where the FFT
+cost is the performance bottleneck (typically large problems running
+on many processors), 2-FFT PPPM may be faster than 4-FFT PPPM.</p>
+<p>Staggered PPPM performs calculations using two different meshes, one
+shifted slightly with respect to the other.  This can reduce force
+aliasing errors and increase the accuracy of the method, but also
+doubles the amount of work required. For high relative accuracy, using
+staggered PPPM allows one to half the mesh size in each dimension as
+compared to regular PPPM, which can give around a 4x speedup in the
+kspace time. However, for low relative accuracy, using staggered PPPM
+gives little benefit and can be up to 2x slower in the kspace
+time. For example, the rhodopsin benchmark was run on a single
+processor, and results for kspace time vs. relative accuracy for the
+different methods are shown in the figure below.  For this system,
+staggered PPPM (using ik differentiation) becomes useful when using a
+relative accuracy of slightly greater than 1e-5 and above.</p>
+<img alt="_images/rhodo_staggered.jpg" class="align-center" src="_images/rhodo_staggered.jpg" />
+<div class="admonition note">
+<p class="first admonition-title">Note</p>
+<p class="last">Using staggered PPPM may not give the same increase in accuracy
+of energy and pressure as it does in forces, so some caution must be
+used if energy and/or pressure are quantities of interest, such as
+when using a barostat.</p>
+</div>
+<hr class="docutils" />
+</div>
+<div class="section" id="packages-with-optimized-styles">
+<span id="acc-3"></span><h2>5.3. Packages with optimized styles</h2>
+<p>Accelerated versions of various <a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a>,
+<a class="reference internal" href="fix.html"><span class="doc">fixes</span></a>, <a class="reference internal" href="compute.html"><span class="doc">computes</span></a>, and other commands have
+been added to LAMMPS, which will typically run faster than the
+standard non-accelerated versions.  Some require appropriate hardware
+to be present on your system, e.g. GPUs or Intel Xeon Phi
+coprocessors.</p>
+<p>All of these commands are in packages provided with LAMMPS.  An
+overview of packages is give in <a class="reference internal" href="Section_packages.html"><span class="doc">Section packages</span></a>.</p>
+<p>These are the accelerator packages
+currently in LAMMPS, either as standard or user packages:</p>
+<table border="1" class="docutils">
+<colgroup>
+<col width="46%" />
+<col width="54%" />
+</colgroup>
+<tbody valign="top">
+<tr class="row-odd"><td><a class="reference internal" href="accelerate_gpu.html"><span class="doc">GPU Package</span></a></td>
+<td>for NVIDIA GPUs as well as OpenCL support</td>
+</tr>
+<tr class="row-even"><td><a class="reference internal" href="accelerate_intel.html"><span class="doc">USER-INTEL Package</span></a></td>
+<td>for Intel CPUs and Intel Xeon Phi</td>
+</tr>
+<tr class="row-odd"><td><a class="reference internal" href="accelerate_kokkos.html"><span class="doc">KOKKOS Package</span></a></td>
+<td>for Nvidia GPUs, Intel Xeon Phi, and OpenMP threading</td>
+</tr>
+<tr class="row-even"><td><a class="reference internal" href="accelerate_omp.html"><span class="doc">USER-OMP Package</span></a></td>
+<td>for OpenMP threading and generic CPU optimizations</td>
+</tr>
+<tr class="row-odd"><td><a class="reference internal" href="accelerate_opt.html"><span class="doc">OPT Package</span></a></td>
+<td>generic CPU optimizations</td>
+</tr>
+</tbody>
+</table>
+<div class="toctree-wrapper compound">
+</div>
+<p>Inverting this list, LAMMPS currently has acceleration support for
+three kinds of hardware, via the listed packages:</p>
+<table border="1" class="docutils">
+<colgroup>
+<col width="10%" />
+<col width="90%" />
+</colgroup>
+<tbody valign="top">
+<tr class="row-odd"><td>Many-core CPUs</td>
+<td><a class="reference internal" href="accelerate_intel.html"><span class="doc">USER-INTEL</span></a>, <a class="reference internal" href="accelerate_kokkos.html"><span class="doc">KOKKOS</span></a>, <a class="reference internal" href="accelerate_omp.html"><span class="doc">USER-OMP</span></a>, <a class="reference internal" href="accelerate_opt.html"><span class="doc">OPT</span></a> packages</td>
+</tr>
+<tr class="row-even"><td>NVIDIA GPUs</td>
+<td><a class="reference internal" href="accelerate_gpu.html"><span class="doc">GPU</span></a>, <a class="reference internal" href="accelerate_kokkos.html"><span class="doc">KOKKOS</span></a> packages</td>
+</tr>
+<tr class="row-odd"><td>Intel Phi</td>
+<td><a class="reference internal" href="accelerate_intel.html"><span class="doc">USER-INTEL</span></a>, <a class="reference internal" href="accelerate_kokkos.html"><span class="doc">KOKKOS</span></a> packages</td>
+</tr>
+</tbody>
+</table>
+<p>Which package is fastest for your hardware may depend on the size
+problem you are running and what commands (accelerated and
+non-accelerated) are invoked by your input script.  While these doc
+pages include performance guidelines, there is no substitute for
+trying out the different packages appropriate to your hardware.</p>
+<p>Any accelerated style has the same name as the corresponding standard
+style, except that a suffix is appended.  Otherwise, the syntax for
+the command that uses the style is identical, their functionality is
+the same, and the numerical results it produces should also be the
+same, except for precision and round-off effects.</p>
+<p>For example, all of these styles are accelerated variants of the
+Lennard-Jones <a class="reference internal" href="pair_lj.html"><span class="doc">pair_style lj/cut</span></a>:</p>
+<ul class="simple">
+<li><a class="reference internal" href="pair_lj.html"><span class="doc">pair_style lj/cut/gpu</span></a></li>
+<li><a class="reference internal" href="pair_lj.html"><span class="doc">pair_style lj/cut/intel</span></a></li>
+<li><a class="reference internal" href="pair_lj.html"><span class="doc">pair_style lj/cut/kk</span></a></li>
+<li><a class="reference internal" href="pair_lj.html"><span class="doc">pair_style lj/cut/omp</span></a></li>
+<li><a class="reference internal" href="pair_lj.html"><span class="doc">pair_style lj/cut/opt</span></a></li>
+</ul>
+<p>To see what accelerate styles are currently available, see
+<a class="reference internal" href="Section_commands.html#cmd-5"><span class="std std-ref">Section 3.5</span></a> of the manual.  The
+doc pages for individual commands (e.g. <a class="reference internal" href="pair_lj.html"><span class="doc">pair lj/cut</span></a> or
+<a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>) also list any accelerated variants available
+for that style.</p>
+<p>To use an accelerator package in LAMMPS, and one or more of the styles
+it provides, follow these general steps.  Details vary from package to
+package and are explained in the individual accelerator doc pages,
+listed above:</p>
+<table border="1" class="docutils">
+<colgroup>
+<col width="64%" />
+<col width="36%" />
+</colgroup>
+<tbody valign="top">
+<tr class="row-odd"><td>build the accelerator library</td>
+<td>only for GPU package</td>
+</tr>
+<tr class="row-even"><td>install the accelerator package</td>
+<td>make yes-opt, make yes-user-intel, etc</td>
+</tr>
+<tr class="row-odd"><td>add compile/link flags to Makefile.machine in src/MAKE</td>
+<td>only for USER-INTEL, KOKKOS, USER-OMP, OPT packages</td>
+</tr>
+<tr class="row-even"><td>re-build LAMMPS</td>
+<td>make machine</td>
+</tr>
+<tr class="row-odd"><td>prepare and test a regular LAMMPS simulation</td>
+<td>lmp_machine -in in.script; mpirun -np 32 lmp_machine -in in.script</td>
+</tr>
+<tr class="row-even"><td>enable specific accelerator support via &#8216;-k on&#8217; <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a>,</td>
+<td>only needed for KOKKOS package</td>
+</tr>
+<tr class="row-odd"><td>set any needed options for the package via &#8220;-pk&#8221; <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a> or <a class="reference internal" href="package.html"><span class="doc">package</span></a> command,</td>
+<td>only if defaults need to be changed</td>
+</tr>
+<tr class="row-even"><td>use accelerated styles in your input via &#8220;-sf&#8221; <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a> or <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command</td>
+<td>lmp_machine -in in.script -sf gpu</td>
+</tr>
+</tbody>
+</table>
+<p>Note that the first 4 steps can be done as a single command, using the
+src/Make.py tool.  This tool is discussed in <a class="reference internal" href="Section_start.html#start-4"><span class="std std-ref">Section 2.4</span></a> of the manual, and its use is
+illustrated in the individual accelerator sections.  Typically these
+steps only need to be done once, to create an executable that uses one
+or more accelerator packages.</p>
+<p>The last 4 steps can all be done from the command-line when LAMMPS is
+launched, without changing your input script, as illustrated in the
+individual accelerator sections.  Or you can add
+<a class="reference internal" href="package.html"><span class="doc">package</span></a> and <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> commands to your input
+script.</p>
+<div class="admonition note">
+<p class="first admonition-title">Note</p>
+<p class="last">With a few exceptions, you can build a single LAMMPS executable
+with all its accelerator packages installed.  Note however that the
+USER-INTEL and KOKKOS packages require you to choose one of their
+hardware options when building for a specific platform.  I.e. CPU or
+Phi option for the USER-INTEL package.  Or the OpenMP, Cuda, or Phi
+option for the KOKKOS package.</p>
+</div>
+<p>These are the exceptions.  You cannot build a single executable with:</p>
+<ul class="simple">
+<li>both the USER-INTEL Phi and KOKKOS Phi options</li>
+<li>the USER-INTEL Phi or Kokkos Phi option, and the GPU package</li>
+</ul>
+<p>See the examples/accelerate/README and make.list files for sample
+Make.py commands that build LAMMPS with any or all of the accelerator
+packages.  As an example, here is a command that builds with all the
+GPU related packages installed (GPU, KOKKOS with Cuda), including
+settings to build the needed auxiliary GPU libraries for Kepler GPUs:</p>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">j</span> <span class="mi">16</span> <span class="o">-</span><span class="n">p</span> <span class="n">omp</span> <span class="n">gpu</span> <span class="n">kokkos</span> <span class="o">-</span><span class="n">cc</span> <span class="n">nvcc</span> <span class="n">wrap</span><span class="o">=</span><span class="n">mpi</span>   <span class="o">-</span><span class="n">gpu</span> <span class="n">mode</span><span class="o">=</span><span class="n">double</span> <span class="n">arch</span><span class="o">=</span><span class="mi">35</span> <span class="o">-</span><span class="n">kokkos</span> <span class="n">cuda</span> <span class="n">arch</span><span class="o">=</span><span class="mi">35</span> <span class="n">lib</span><span class="o">-</span><span class="nb">all</span> <span class="n">file</span> <span class="n">mpi</span>
+</pre></div>
+</div>
+<p>The examples/accelerate directory also has input scripts that can be
+used with all of the accelerator packages.  See its README file for
+details.</p>
+<p>Likewise, the bench directory has FERMI and KEPLER and PHI
+sub-directories with Make.py commands and input scripts for using all
+the accelerator packages on various machines.  See the README files in
+those dirs.</p>
+<p>As mentioned above, the <a class="reference external" href="http://lammps.sandia.gov/bench.html">Benchmark page</a> of the LAMMPS web site gives
+performance results for the various accelerator packages for several
+of the standard LAMMPS benchmark problems, as a function of problem
+size and number of compute nodes, on different hardware platforms.</p>
+<p>Here is a brief summary of what the various packages provide.  Details
+are in the individual accelerator sections.</p>
+<ul class="simple">
+<li>Styles with a &#8220;gpu&#8221; suffix are part of the GPU package, and can be run
+on NVIDIA GPUs.  The speed-up on a GPU depends on a variety of
+factors, discussed in the accelerator sections.</li>
+<li>Styles with an &#8220;intel&#8221; suffix are part of the USER-INTEL
+package. These styles support vectorized single and mixed precision
+calculations, in addition to full double precision.  In extreme cases,
+this can provide speedups over 3.5x on CPUs.  The package also
+supports acceleration in &#8220;offload&#8221; mode to Intel(R) Xeon Phi(TM)
+coprocessors.  This can result in additional speedup over 2x depending
+on the hardware configuration.</li>
+<li>Styles with a &#8220;kk&#8221; suffix are part of the KOKKOS package, and can be
+run using OpenMP on multicore CPUs, on an NVIDIA GPU, or on an Intel
+Xeon Phi in &#8220;native&#8221; mode.  The speed-up depends on a variety of
+factors, as discussed on the KOKKOS accelerator page.</li>
+<li>Styles with an &#8220;omp&#8221; suffix are part of the USER-OMP package and allow
+a pair-style to be run in multi-threaded mode using OpenMP.  This can
+be useful on nodes with high-core counts when using less MPI processes
+than cores is advantageous, e.g. when running with PPPM so that FFTs
+are run on fewer MPI processors or when the many MPI tasks would
+overload the available bandwidth for communication.</li>
+<li>Styles with an &#8220;opt&#8221; suffix are part of the OPT package and typically
+speed-up the pairwise calculations of your simulation by 5-25% on a
+CPU.</li>
+</ul>
+<p>The individual accelerator package doc pages explain:</p>
+<ul class="simple">
+<li>what hardware and software the accelerated package requires</li>
+<li>how to build LAMMPS with the accelerated package</li>
+<li>how to run with the accelerated package either via command-line switches or modifying the input script</li>
+<li>speed-ups to expect</li>
+<li>guidelines for best performance</li>
+<li>restrictions</li>
+</ul>
+<hr class="docutils" />
+</div>
+<div class="section" id="comparison-of-various-accelerator-packages">
+<span id="acc-4"></span><h2>5.4. Comparison of various accelerator packages</h2>
+<div class="admonition note">
+<p class="first admonition-title">Note</p>
+<p class="last">this section still needs to be re-worked with additional KOKKOS
+and USER-INTEL information.</p>
+</div>
+<p>The next section compares and contrasts the various accelerator
+options, since there are multiple ways to perform OpenMP threading,
+run on GPUs, and run on Intel Xeon Phi coprocessors.</p>
+<p>All 3 of these packages accelerate a LAMMPS calculation using NVIDIA
+hardware, but they do it in different ways.</p>
+<p>As a consequence, for a particular simulation on specific hardware,
+one package may be faster than the other.  We give guidelines below,
+but the best way to determine which package is faster for your input
+script is to try both of them on your machine.  See the benchmarking
+section below for examples where this has been done.</p>
+<p><strong>Guidelines for using each package optimally:</strong></p>
+<ul class="simple">
+<li>The GPU package allows you to assign multiple CPUs (cores) to a single
+GPU (a common configuration for &#8220;hybrid&#8221; nodes that contain multicore
+CPU(s) and GPU(s)) and works effectively in this mode.</li>
+<li>The GPU package moves per-atom data (coordinates, forces)
+back-and-forth between the CPU and GPU every timestep.  The
+KOKKOS/CUDA package only does this on timesteps when a CPU calculation
+is required (e.g. to invoke a fix or compute that is non-GPU-ized).
+Hence, if you can formulate your input script to only use GPU-ized
+fixes and computes, and avoid doing I/O too often (thermo output, dump
+file snapshots, restart files), then the data transfer cost of the
+KOKKOS/CUDA package can be very low, causing it to run faster than the
+GPU package.</li>
+<li>The GPU package is often faster than the KOKKOS/CUDA package, if the
+number of atoms per GPU is smaller.  The crossover point, in terms of
+atoms/GPU at which the KOKKOS/CUDA package becomes faster depends
+strongly on the pair style.  For example, for a simple Lennard Jones
+system the crossover (in single precision) is often about 50K-100K
+atoms per GPU.  When performing double precision calculations the
+crossover point can be significantly smaller.</li>
+<li>Both packages compute bonded interactions (bonds, angles, etc) on the
+CPU.  If the GPU package is running with several MPI processes
+assigned to one GPU, the cost of computing the bonded interactions is
+spread across more CPUs and hence the GPU package can run faster.</li>
+<li>When using the GPU package with multiple CPUs assigned to one GPU, its
+performance depends to some extent on high bandwidth between the CPUs
+and the GPU.  Hence its performance is affected if full 16 PCIe lanes
+are not available for each GPU.  In HPC environments this can be the
+case if S2050/70 servers are used, where two devices generally share
+one PCIe 2.0 16x slot.  Also many multi-GPU mainboards do not provide
+full 16 lanes to each of the PCIe 2.0 16x slots.</li>
+</ul>
+<p><strong>Differences between the two packages:</strong></p>
+<ul class="simple">
+<li>The GPU package accelerates only pair force, neighbor list, and PPPM
+calculations.</li>
+<li>The GPU package requires neighbor lists to be built on the CPU when using
+exclusion lists, hybrid pair styles, or a triclinic simulation box.</li>
+</ul>
+</div>
+</div>
+
+
+           </div>
+          </div>
+          <footer>
+  
+    <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
+      
+        <a href="accelerate_gpu.html" class="btn btn-neutral float-right" title="5.3.1. GPU package" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
+      
+      
+        <a href="Section_packages.html" class="btn btn-neutral" title="4. Packages" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+      
+    </div>
+  
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>
+        &copy; Copyright 2013 Sandia Corporation.
+    </p>
+  </div>
+  Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
+</footer>
+
+        </div>
+      </div>
+
+    </section>
+
+  </div>
+  
+
+
+  
+
+    <script type="text/javascript">
+        var DOCUMENTATION_OPTIONS = {
+            URL_ROOT:'./',
+            VERSION:'',
+            COLLAPSE_INDEX:false,
+            FILE_SUFFIX:'.html',
+            HAS_SOURCE:  true
+        };
+    </script>
+      <script type="text/javascript" src="_static/jquery.js"></script>
+      <script type="text/javascript" src="_static/underscore.js"></script>
+      <script type="text/javascript" src="_static/doctools.js"></script>
+      <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+      <script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/jquery-1.11.0.min.js"></script>
+      <script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/lightbox.min.js"></script>
+      <script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2-customize/jquery-noconflict.js"></script>
+
+  
+
+  
+  
+    <script type="text/javascript" src="_static/js/theme.js"></script>
+  
+
+  
+  
+  <script type="text/javascript">
+      jQuery(function () {
+          SphinxRtdTheme.StickyNav.enable();
+      });
+  </script>
+   
+
+</body>
+</html>

doc/html/Section_example.html

@@ -0,0 +1,461 @@
+
+
+<!DOCTYPE html>
+<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
+<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
+<head>
+  <meta charset="utf-8">
+  
+  <meta name="viewport" content="width=device-width, initial-scale=1.0">
+  
+  <title>7. Example problems &mdash; LAMMPS documentation</title>
+  
+
+  
+  
+
+  
+
+  
+  
+    
+
+  
+
+  
+  
+    <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+  
+
+  
+    <link rel="stylesheet" href="_static/sphinxcontrib-images/LightBox2/lightbox2/css/lightbox.css" type="text/css" />
+  
+
+  
+    <link rel="top" title="LAMMPS documentation" href="index.html"/>
+        <link rel="next" title="8. Performance &amp; scalability" href="Section_perf.html"/>
+        <link rel="prev" title="6. How-to discussions" href="Section_howto.html"/> 
+
+  
+  <script src="_static/js/modernizr.min.js"></script>
+
+</head>
+
+<body class="wy-body-for-nav" role="document">
+
+  <div class="wy-grid-for-nav">
+
+    
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-nav-search">
+        
+
+        
+          <a href="Manual.html" class="icon icon-home"> LAMMPS
+        
+
+        
+        </a>
+
+        
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+
+        
+      </div>
+
+      <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
+        
+          
+          
+              <p class="caption"><span class="caption-text">User Documentation</span></p>
+<ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">7. Example problems</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#lowercase-directories">7.1. Lowercase directories</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#uppercase-directories">7.2. Uppercase directories</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+</ul>
+<p class="caption"><span class="caption-text">Index</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="tutorials.html">Tutorials</a></li>
+<li class="toctree-l1"><a class="reference internal" href="commands.html">Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
+<li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
+<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
+<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
+<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
+<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>
+</ul>
+
+          
+        
+      </div>
+      &nbsp;
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
+
+      
+      <nav class="wy-nav-top" role="navigation" aria-label="top navigation">
+        <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+        <a href="Manual.html">LAMMPS</a>
+      </nav>
+
+
+      
+      <div class="wy-nav-content">
+        <div class="rst-content">
+          <div role="navigation" aria-label="breadcrumbs navigation">
+  <ul class="wy-breadcrumbs">
+    <li><a href="Manual.html">Docs</a> &raquo;</li>
+      
+    <li>7. Example problems</li>
+      <li class="wy-breadcrumbs-aside">
+        
+          
+            <a href="http://lammps.sandia.gov">Website</a>
+            <a href="Section_commands.html#comm">Commands</a>
+        
+      </li>
+  </ul>
+  <hr/>
+  
+    <div class="rst-footer-buttons" style="margin-bottom: 1em" role="navigation" aria-label="footer navigation">
+      
+        <a href="Section_perf.html" class="btn btn-neutral float-right" title="8. Performance &amp; scalability" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
+      
+      
+        <a href="Section_howto.html" class="btn btn-neutral" title="6. How-to discussions" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+      
+    </div>
+  
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+            
+  <div class="section" id="example-problems">
+<h1>7. Example problems</h1>
+<p>The LAMMPS distribution includes an examples sub-directory with many
+sample problems.  Many are 2d models that run quickly are are
+straightforward to visualize, requiring at most a couple of minutes to
+run on a desktop machine.  Each problem has an input script (in.*) and
+produces a log file (log.*) when it runs.  Some use a data file
+(data.*) of initial coordinates as additional input.  A few sample log
+file run on different machines and different numbers of processors are
+included in the directories to compare your answers to.  E.g. a log
+file like log.date.crack.foo.P means the &#8220;crack&#8221; example was run on P
+processors of machine &#8220;foo&#8221; on that date (i.e. with that version of
+LAMMPS).</p>
+<p>Many of the input files have commented-out lines for creating dump
+files and image files.</p>
+<p>If you uncomment the <a class="reference internal" href="dump.html"><span class="doc">dump</span></a> command in the input script, a
+text dump file will be produced, which can be animated by various
+<a class="reference external" href="http://lammps.sandia.gov/viz.html">visualization programs</a>.  It can
+also be animated using the xmovie tool described in the <a class="reference internal" href="Section_tools.html"><span class="doc">Additional Tools</span></a> section of the LAMMPS documentation.</p>
+<p>If you uncomment the <a class="reference internal" href="dump.html"><span class="doc">dump image</span></a> command in the input
+script, and assuming you have built LAMMPS with a JPG library, JPG
+snapshot images will be produced when the simulation runs.  They can
+be quickly post-processed into a movie using commands described on the
+<a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> doc page.</p>
+<p>Animations of many of the examples can be viewed on the Movies section
+of the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS web site</a>.</p>
+<p>There are two kinds of sub-directories in the examples dir.  Lowercase
+dirs contain one or a few simple, quick-to-run problems.  Uppercase
+dirs contain up to several complex scripts that illustrate a
+particular kind of simulation method or model.  Some of these run for
+longer times, e.g. to measure a particular quantity.</p>
+<p>Lists of both kinds of directories are given below.</p>
+<hr class="docutils" />
+<div class="section" id="lowercase-directories">
+<h2>7.1. Lowercase directories</h2>
+<table border="1" class="docutils">
+<colgroup>
+<col width="16%" />
+<col width="84%" />
+</colgroup>
+<tbody valign="top">
+<tr class="row-odd"><td>accelerate</td>
+<td>run with various acceleration options (OpenMP, GPU, Phi)</td>
+</tr>
+<tr class="row-even"><td>balance</td>
+<td>dynamic load balancing, 2d system</td>
+</tr>
+<tr class="row-odd"><td>body</td>
+<td>body particles, 2d system</td>
+</tr>
+<tr class="row-even"><td>colloid</td>
+<td>big colloid particles in a small particle solvent, 2d system</td>
+</tr>
+<tr class="row-odd"><td>comb</td>
+<td>models using the COMB potential</td>
+</tr>
+<tr class="row-even"><td>coreshell</td>
+<td>core/shell model using CORESHELL package</td>
+</tr>
+<tr class="row-odd"><td>crack</td>
+<td>crack propagation in a 2d solid</td>
+</tr>
+<tr class="row-even"><td>deposit</td>
+<td>deposit atoms and molecules on a surface</td>
+</tr>
+<tr class="row-odd"><td>dipole</td>
+<td>point dipolar particles, 2d system</td>
+</tr>
+<tr class="row-even"><td>dreiding</td>
+<td>methanol via Dreiding FF</td>
+</tr>
+<tr class="row-odd"><td>eim</td>
+<td>NaCl using the EIM potential</td>
+</tr>
+<tr class="row-even"><td>ellipse</td>
+<td>ellipsoidal particles in spherical solvent, 2d system</td>
+</tr>
+<tr class="row-odd"><td>flow</td>
+<td>Couette and Poiseuille flow in a 2d channel</td>
+</tr>
+<tr class="row-even"><td>friction</td>
+<td>frictional contact of spherical asperities between 2d surfaces</td>
+</tr>
+<tr class="row-odd"><td>hugoniostat</td>
+<td>Hugoniostat shock dynamics</td>
+</tr>
+<tr class="row-even"><td>indent</td>
+<td>spherical indenter into a 2d solid</td>
+</tr>
+<tr class="row-odd"><td>kim</td>
+<td>use of potentials in Knowledge Base for Interatomic Models (KIM)</td>
+</tr>
+<tr class="row-even"><td>meam</td>
+<td>MEAM test for SiC and shear (same as shear examples)</td>
+</tr>
+<tr class="row-odd"><td>melt</td>
+<td>rapid melt of 3d LJ system</td>
+</tr>
+<tr class="row-even"><td>micelle</td>
+<td>self-assembly of small lipid-like molecules into 2d bilayers</td>
+</tr>
+<tr class="row-odd"><td>min</td>
+<td>energy minimization of 2d LJ melt</td>
+</tr>
+<tr class="row-even"><td>msst</td>
+<td>MSST shock dynamics</td>
+</tr>
+<tr class="row-odd"><td>nb3b</td>
+<td>use of nonbonded 3-body harmonic pair style</td>
+</tr>
+<tr class="row-even"><td>neb</td>
+<td>nudged elastic band (NEB) calculation for barrier finding</td>
+</tr>
+<tr class="row-odd"><td>nemd</td>
+<td>non-equilibrium MD of 2d sheared system</td>
+</tr>
+<tr class="row-even"><td>obstacle</td>
+<td>flow around two voids in a 2d channel</td>
+</tr>
+<tr class="row-odd"><td>peptide</td>
+<td>dynamics of a small solvated peptide chain (5-mer)</td>
+</tr>
+<tr class="row-even"><td>peri</td>
+<td>Peridynamic model of cylinder impacted by indenter</td>
+</tr>
+<tr class="row-odd"><td>pour</td>
+<td>pouring of granular particles into a 3d box, then chute flow</td>
+</tr>
+<tr class="row-even"><td>prd</td>
+<td>parallel replica dynamics of vacancy diffusion in bulk Si</td>
+</tr>
+<tr class="row-odd"><td>python</td>
+<td>using embedded Python in a LAMMPS input script</td>
+</tr>
+<tr class="row-even"><td>qeq</td>
+<td>use of the QEQ package for charge equilibration</td>
+</tr>
+<tr class="row-odd"><td>reax</td>
+<td>RDX and TATB models using the ReaxFF</td>
+</tr>
+<tr class="row-even"><td>rigid</td>
+<td>rigid bodies modeled as independent or coupled</td>
+</tr>
+<tr class="row-odd"><td>shear</td>
+<td>sideways shear applied to 2d solid, with and without a void</td>
+</tr>
+<tr class="row-even"><td>snap</td>
+<td>NVE dynamics for BCC tantalum crystal using SNAP potential</td>
+</tr>
+<tr class="row-odd"><td>srd</td>
+<td>stochastic rotation dynamics (SRD) particles as solvent</td>
+</tr>
+<tr class="row-even"><td>streitz</td>
+<td>use of Streitz/Mintmire potential with charge equilibration</td>
+</tr>
+<tr class="row-odd"><td>tad</td>
+<td>temperature-accelerated dynamics of vacancy diffusion in bulk Si</td>
+</tr>
+<tr class="row-even"><td>vashishta</td>
+<td>use of the Vashishta potential</td>
+</tr>
+</tbody>
+</table>
+<p>Here is how you can run and visualize one of the sample problems:</p>
+<pre class="literal-block">
+cd indent
+cp ../../src/lmp_linux .           # copy LAMMPS executable to this dir
+lmp_linux -in in.indent            # run the problem
+</pre>
+<p>Running the simulation produces the files <em>dump.indent</em> and
+<em>log.lammps</em>.  You can visualize the dump file of snapshots with a
+variety of 3rd-party tools highlighted on the
+<a class="reference external" href="http://lammps.sandia.gov/viz.html">Visualization</a> page of the LAMMPS
+web site.</p>
+<p>If you uncomment the <a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> line(s) in the input
+script a series of JPG images will be produced by the run (assuming
+you built LAMMPS with JPG support; see <a class="reference internal" href="Section_start.html"><span class="doc">Section start 2.2</span></a> for details).  These can be viewed
+individually or turned into a movie or animated by tools like
+ImageMagick or QuickTime or various Windows-based tools.  See the
+<a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> doc page for more details.  E.g. this
+Imagemagick command would create a GIF file suitable for viewing in a
+browser.</p>
+<pre class="literal-block">
+% convert -loop 1 *.jpg foo.gif
+</pre>
+</div>
+<hr class="docutils" />
+<div class="section" id="uppercase-directories">
+<h2>7.2. Uppercase directories</h2>
+<table border="1" class="docutils">
+<colgroup>
+<col width="11%" />
+<col width="89%" />
+</colgroup>
+<tbody valign="top">
+<tr class="row-odd"><td>ASPHERE</td>
+<td>various aspherical particle models, using ellipsoids, rigid bodies, line/triangle particles, etc</td>
+</tr>
+<tr class="row-even"><td>COUPLE</td>
+<td>examples of how to use LAMMPS as a library</td>
+</tr>
+<tr class="row-odd"><td>DIFFUSE</td>
+<td>compute diffusion coefficients via several methods</td>
+</tr>
+<tr class="row-even"><td>ELASTIC</td>
+<td>compute elastic constants at zero temperature</td>
+</tr>
+<tr class="row-odd"><td>ELASTIC_T</td>
+<td>compute elastic constants at finite temperature</td>
+</tr>
+<tr class="row-even"><td>KAPPA</td>
+<td>compute thermal conductivity via several methods</td>
+</tr>
+<tr class="row-odd"><td>MC</td>
+<td>using LAMMPS in a Monte Carlo mode to relax the energy of a system</td>
+</tr>
+<tr class="row-even"><td>USER</td>
+<td>examples for USER packages and USER-contributed commands</td>
+</tr>
+<tr class="row-odd"><td>VISCOSITY</td>
+<td>compute viscosity via several methods</td>
+</tr>
+</tbody>
+</table>
+<p>Nearly all of these directories have README files which give more
+details on how to understand and use their contents.</p>
+<p>The USER directory has a large number of sub-directories which
+correspond by name to a USER package.  They contain scripts that
+illustrate how to use the command(s) provided in that package.  Many
+of the sub-directories have their own README files which give further
+instructions.  See the <a class="reference internal" href="Section_packages.html"><span class="doc">Section packages</span></a> doc
+page for more info on specific USER packages.</p>
+</div>
+</div>
+
+
+           </div>
+          </div>
+          <footer>
+  
+    <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
+      
+        <a href="Section_perf.html" class="btn btn-neutral float-right" title="8. Performance &amp; scalability" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
+      
+      
+        <a href="Section_howto.html" class="btn btn-neutral" title="6. How-to discussions" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+      
+    </div>
+  
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>
+        &copy; Copyright 2013 Sandia Corporation.
+    </p>
+  </div>
+  Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
+</footer>
+
+        </div>
+      </div>
+
+    </section>
+
+  </div>
+  
+
+
+  
+
+    <script type="text/javascript">
+        var DOCUMENTATION_OPTIONS = {
+            URL_ROOT:'./',
+            VERSION:'',
+            COLLAPSE_INDEX:false,
+            FILE_SUFFIX:'.html',
+            HAS_SOURCE:  true
+        };
+    </script>
+      <script type="text/javascript" src="_static/jquery.js"></script>
+      <script type="text/javascript" src="_static/underscore.js"></script>
+      <script type="text/javascript" src="_static/doctools.js"></script>
+      <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+      <script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/jquery-1.11.0.min.js"></script>
+      <script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/lightbox.min.js"></script>
+      <script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2-customize/jquery-noconflict.js"></script>
+
+  
+
+  
+  
+    <script type="text/javascript" src="_static/js/theme.js"></script>
+  
+
+  
+  
+  <script type="text/javascript">
+      jQuery(function () {
+          SphinxRtdTheme.StickyNav.enable();
+      });
+  </script>
+   
+
+</body>
+</html>

doc/html/Section_history.html

@@ -0,0 +1,342 @@
+
+
+<!DOCTYPE html>
+<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
+<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
+<head>
+  <meta charset="utf-8">
+  
+  <meta name="viewport" content="width=device-width, initial-scale=1.0">
+  
+  <title>13. Future and history &mdash; LAMMPS documentation</title>
+  
+
+  
+  
+
+  
+
+  
+  
+    
+
+  
+
+  
+  
+    <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+  
+
+  
+    <link rel="stylesheet" href="_static/sphinxcontrib-images/LightBox2/lightbox2/css/lightbox.css" type="text/css" />
+  
+
+  
+    <link rel="top" title="LAMMPS documentation" href="index.html"/>
+        <link rel="next" title="Tutorials" href="tutorials.html"/>
+        <link rel="prev" title="12. Errors" href="Section_errors.html"/> 
+
+  
+  <script src="_static/js/modernizr.min.js"></script>
+
+</head>
+
+<body class="wy-body-for-nav" role="document">
+
+  <div class="wy-grid-for-nav">
+
+    
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-nav-search">
+        
+
+        
+          <a href="Manual.html" class="icon icon-home"> LAMMPS
+        
+
+        
+        </a>
+
+        
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+
+        
+      </div>
+
+      <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
+        
+          
+          
+              <p class="caption"><span class="caption-text">User Documentation</span></p>
+<ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">13. Future and history</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#coming-attractions">13.1. Coming attractions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#past-versions">13.2. Past versions</a></li>
+</ul>
+</li>
+</ul>
+<p class="caption"><span class="caption-text">Index</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="tutorials.html">Tutorials</a></li>
+<li class="toctree-l1"><a class="reference internal" href="commands.html">Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
+<li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
+<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
+<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
+<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
+<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>
+</ul>
+
+          
+        
+      </div>
+      &nbsp;
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
+
+      
+      <nav class="wy-nav-top" role="navigation" aria-label="top navigation">
+        <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+        <a href="Manual.html">LAMMPS</a>
+      </nav>
+
+
+      
+      <div class="wy-nav-content">
+        <div class="rst-content">
+          <div role="navigation" aria-label="breadcrumbs navigation">
+  <ul class="wy-breadcrumbs">
+    <li><a href="Manual.html">Docs</a> &raquo;</li>
+      
+    <li>13. Future and history</li>
+      <li class="wy-breadcrumbs-aside">
+        
+          
+            <a href="http://lammps.sandia.gov">Website</a>
+            <a href="Section_commands.html#comm">Commands</a>
+        
+      </li>
+  </ul>
+  <hr/>
+  
+    <div class="rst-footer-buttons" style="margin-bottom: 1em" role="navigation" aria-label="footer navigation">
+      
+        <a href="tutorials.html" class="btn btn-neutral float-right" title="Tutorials" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
+      
+      
+        <a href="Section_errors.html" class="btn btn-neutral" title="12. Errors" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+      
+    </div>
+  
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+            
+  <div class="section" id="future-and-history">
+<h1>13. Future and history</h1>
+<p>This section lists features we plan to add to LAMMPS, features of
+previous versions of LAMMPS, and features of other parallel molecular
+dynamics codes our group has distributed.</p>
+<div class="line-block">
+<div class="line">13.1 <a class="reference internal" href="#hist-1"><span class="std std-ref">Coming attractions</span></a></div>
+<div class="line">13.2 <a class="reference internal" href="#hist-2"><span class="std std-ref">Past versions</span></a></div>
+<div class="line"><br /></div>
+</div>
+<div class="section" id="coming-attractions">
+<span id="hist-1"></span><h2>13.1. Coming attractions</h2>
+<p>As of summer 2016 we are using the <a class="reference external" href="https://github.com/lammps/lammps/issues">LAMMPS project issue tracker on GitHub</a> for keeping
+track of suggested, planned or pending new features. This includes
+discussions of how to best implement them, or why they would be
+useful. Especially if a planned or proposed feature is non-trivial
+to add, e.g. because it requires changes to some of the core
+classes of LAMMPS, people planning to contribute a new feature to
+LAMMS are encouraged to submit an issue about their planned
+implementation this way in order to receive feedback from the
+LAMMPS core developers. They will provide suggestions about
+the validity of the proposed approach and possible improvements,
+pitfalls or alternatives.</p>
+<p>Please see some of the closed issues for examples of how to
+suggest code enhancements, submit proposed changes, or report
+elated issues and how they are resoved.</p>
+<p>As an alternative to using GitHub, you may e-mail the
+<a class="reference external" href="http://lammps.sandia.gov/authors.html">core developers</a> or send
+an e-mail to the <a class="reference external" href="http://lammps.sandia.gov/mail.html">LAMMPS Mail list</a>
+if you want to have your suggestion added to the list.</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="past-versions">
+<span id="hist-2"></span><h2>13.2. Past versions</h2>
+<p>LAMMPS development began in the mid 1990s under a cooperative research
+&amp; development agreement (CRADA) between two DOE labs (Sandia and LLNL)
+and 3 companies (Cray, Bristol Myers Squibb, and Dupont). The goal was
+to develop a large-scale parallel classical MD code; the coding effort
+was led by Steve Plimpton at Sandia.</p>
+<p>After the CRADA ended, a final F77 version, LAMMPS 99, was
+released. As development of LAMMPS continued at Sandia, its memory
+management was converted to F90; a final F90 version was released as
+LAMMPS 2001.</p>
+<p>The current LAMMPS is a rewrite in C++ and was first publicly released
+as an open source code in 2004. It includes many new features beyond
+those in LAMMPS 99 or 2001. It also includes features from older
+parallel MD codes written at Sandia, namely ParaDyn, Warp, and
+GranFlow (see below).</p>
+<p>In late 2006 we began merging new capabilities into LAMMPS that were
+developed by Aidan Thompson at Sandia for his MD code GRASP, which has
+a parallel framework similar to LAMMPS. Most notably, these have
+included many-body potentials - Stillinger-Weber, Tersoff, ReaxFF -
+and the associated charge-equilibration routines needed for ReaxFF.</p>
+<p>The <a class="reference external" href="http://lammps.sandia.gov/history.html">History link</a> on the
+LAMMPS WWW page gives a timeline of features added to the
+C++ open-source version of LAMMPS over the last several years.</p>
+<p>These older codes are available for download from the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW site</a>, except for Warp &amp; GranFlow which were primarily used
+internally.  A brief listing of their features is given here.</p>
+<p>LAMMPS 2001</p>
+<ul class="simple">
+<li>F90 + MPI</li>
+<li>dynamic memory</li>
+<li>spatial-decomposition parallelism</li>
+<li>NVE, NVT, NPT, NPH, rRESPA integrators</li>
+<li>LJ and Coulombic pairwise force fields</li>
+<li>all-atom, united-atom, bead-spring polymer force fields</li>
+<li>CHARMM-compatible force fields</li>
+<li>class 2 force fields</li>
+<li>3d/2d Ewald &amp; PPPM</li>
+<li>various force and temperature constraints</li>
+<li>SHAKE</li>
+<li>Hessian-free truncated-Newton minimizer</li>
+<li>user-defined diagnostics</li>
+</ul>
+<p>LAMMPS 99</p>
+<ul class="simple">
+<li>F77 + MPI</li>
+<li>static memory allocation</li>
+<li>spatial-decomposition parallelism</li>
+<li>most of the LAMMPS 2001 features with a few exceptions</li>
+<li>no 2d Ewald &amp; PPPM</li>
+<li>molecular force fields are missing a few CHARMM terms</li>
+<li>no SHAKE</li>
+</ul>
+<p>Warp</p>
+<ul class="simple">
+<li>F90 + MPI</li>
+<li>spatial-decomposition parallelism</li>
+<li>embedded atom method (EAM) metal potentials + LJ</li>
+<li>lattice and grain-boundary atom creation</li>
+<li>NVE, NVT integrators</li>
+<li>boundary conditions for applying shear stresses</li>
+<li>temperature controls for actively sheared systems</li>
+<li>per-atom energy and centro-symmetry computation and output</li>
+</ul>
+<p>ParaDyn</p>
+<ul class="simple">
+<li>F77 + MPI</li>
+<li>atom- and force-decomposition parallelism</li>
+<li>embedded atom method (EAM) metal potentials</li>
+<li>lattice atom creation</li>
+<li>NVE, NVT, NPT integrators</li>
+<li>all serial DYNAMO features for controls and constraints</li>
+</ul>
+<p>GranFlow</p>
+<ul class="simple">
+<li>F90 + MPI</li>
+<li>spatial-decomposition parallelism</li>
+<li>frictional granular potentials</li>
+<li>NVE integrator</li>
+<li>boundary conditions for granular flow and packing and walls</li>
+<li>particle insertion</li>
+</ul>
+</div>
+</div>
+
+
+           </div>
+          </div>
+          <footer>
+  
+    <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
+      
+        <a href="tutorials.html" class="btn btn-neutral float-right" title="Tutorials" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
+      
+      
+        <a href="Section_errors.html" class="btn btn-neutral" title="12. Errors" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+      
+    </div>
+  
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>
+        &copy; Copyright 2013 Sandia Corporation.
+    </p>
+  </div>
+  Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
+</footer>
+
+        </div>
+      </div>
+
+    </section>
+
+  </div>
+  
+
+
+  
+
+    <script type="text/javascript">
+        var DOCUMENTATION_OPTIONS = {
+            URL_ROOT:'./',
+            VERSION:'',
+            COLLAPSE_INDEX:false,
+            FILE_SUFFIX:'.html',
+            HAS_SOURCE:  true
+        };
+    </script>
+      <script type="text/javascript" src="_static/jquery.js"></script>
+      <script type="text/javascript" src="_static/underscore.js"></script>
+      <script type="text/javascript" src="_static/doctools.js"></script>
+      <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+      <script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/jquery-1.11.0.min.js"></script>
+      <script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/lightbox.min.js"></script>
+      <script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2-customize/jquery-noconflict.js"></script>
+
+  
+
+  
+  
+    <script type="text/javascript" src="_static/js/theme.js"></script>
+  
+
+  
+  
+  <script type="text/javascript">
+      jQuery(function () {
+          SphinxRtdTheme.StickyNav.enable();
+      });
+  </script>
+   
+
+</body>
+</html>

doc/html/Section_intro.html

@@ -0,0 +1,708 @@
+
+
+<!DOCTYPE html>
+<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
+<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
+<head>
+  <meta charset="utf-8">
+  
+  <meta name="viewport" content="width=device-width, initial-scale=1.0">
+  
+  <title>1. Introduction &mdash; LAMMPS documentation</title>
+  
+
+  
+  
+
+  
+
+  
+  
+    
+
+  
+
+  
+  
+    <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+  
+
+  
+    <link rel="stylesheet" href="_static/sphinxcontrib-images/LightBox2/lightbox2/css/lightbox.css" type="text/css" />
+  
+
+  
+    <link rel="top" title="LAMMPS documentation" href="index.html"/>
+        <link rel="next" title="2. Getting Started" href="Section_start.html"/>
+        <link rel="prev" title="LAMMPS Documentation" href="Manual.html"/> 
+
+  
+  <script src="_static/js/modernizr.min.js"></script>
+
+</head>
+
+<body class="wy-body-for-nav" role="document">
+
+  <div class="wy-grid-for-nav">
+
+    
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-nav-search">
+        
+
+        
+          <a href="Manual.html" class="icon icon-home"> LAMMPS
+        
+
+        
+        </a>
+
+        
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+
+        
+      </div>
+
+      <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
+        
+          
+          
+              <p class="caption"><span class="caption-text">User Documentation</span></p>
+<ul class="current">
+<li class="toctree-l1 current"><a class="current reference internal" href="#">1. Introduction</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#what-is-lammps">1.1. What is LAMMPS</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#lammps-features">1.2. LAMMPS features</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#general-features">1.2.1. General features</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#particle-and-model-types">1.2.2. Particle and model types</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#force-fields">1.2.3. Force fields</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#atom-creation">1.2.4. Atom creation</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#ensembles-constraints-and-boundary-conditions">1.2.5. Ensembles, constraints, and boundary conditions</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#integrators">1.2.6. Integrators</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#diagnostics">1.2.7. Diagnostics</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#output">1.2.8. Output</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#multi-replica-models">1.2.9. Multi-replica models</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pre-and-post-processing">1.2.10. Pre- and post-processing</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#specialized-features">1.2.11. Specialized features</a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="#lammps-non-features">1.3. LAMMPS non-features</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#open-source-distribution">1.4. Open source distribution</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#acknowledgments-and-citations">1.5. Acknowledgments and citations</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+</ul>
+<p class="caption"><span class="caption-text">Index</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="tutorials.html">Tutorials</a></li>
+<li class="toctree-l1"><a class="reference internal" href="commands.html">Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
+<li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
+<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
+<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
+<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
+<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>
+</ul>
+
+          
+        
+      </div>
+      &nbsp;
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
+
+      
+      <nav class="wy-nav-top" role="navigation" aria-label="top navigation">
+        <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+        <a href="Manual.html">LAMMPS</a>
+      </nav>
+
+
+      
+      <div class="wy-nav-content">
+        <div class="rst-content">
+          <div role="navigation" aria-label="breadcrumbs navigation">
+  <ul class="wy-breadcrumbs">
+    <li><a href="Manual.html">Docs</a> &raquo;</li>
+      
+    <li>1. Introduction</li>
+      <li class="wy-breadcrumbs-aside">
+        
+          
+            <a href="http://lammps.sandia.gov">Website</a>
+            <a href="Section_commands.html#comm">Commands</a>
+        
+      </li>
+  </ul>
+  <hr/>
+  
+    <div class="rst-footer-buttons" style="margin-bottom: 1em" role="navigation" aria-label="footer navigation">
+      
+        <a href="Section_start.html" class="btn btn-neutral float-right" title="2. Getting Started" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
+      
+      
+        <a href="Manual.html" class="btn btn-neutral" title="LAMMPS Documentation" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+      
+    </div>
+  
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+            
+  <div class="section" id="introduction">
+<h1>1. Introduction</h1>
+<p>This section provides an overview of what LAMMPS can and can&#8217;t do,
+describes what it means for LAMMPS to be an open-source code, and
+acknowledges the funding and people who have contributed to LAMMPS
+over the years.</p>
+<div class="line-block">
+<div class="line">1.1 <a class="reference internal" href="#intro-1"><span class="std std-ref">What is LAMMPS</span></a></div>
+<div class="line">1.2 <a class="reference internal" href="#intro-2"><span class="std std-ref">LAMMPS features</span></a></div>
+<div class="line">1.3 <a class="reference internal" href="#intro-3"><span class="std std-ref">LAMMPS non-features</span></a></div>
+<div class="line">1.4 <a class="reference internal" href="#intro-4"><span class="std std-ref">Open source distribution</span></a></div>
+<div class="line">1.5 <a class="reference internal" href="#intro-5"><span class="std std-ref">Acknowledgments and citations</span></a></div>
+<div class="line"><br /></div>
+</div>
+<div class="section" id="what-is-lammps">
+<span id="intro-1"></span><h2>1.1. What is LAMMPS</h2>
+<p>LAMMPS is a classical molecular dynamics code that models an ensemble
+of particles in a liquid, solid, or gaseous state.  It can model
+atomic, polymeric, biological, metallic, granular, and coarse-grained
+systems using a variety of force fields and boundary conditions.</p>
+<p>For examples of LAMMPS simulations, see the Publications page of the
+<a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a>.</p>
+<p>LAMMPS runs efficiently on single-processor desktop or laptop
+machines, but is designed for parallel computers.  It will run on any
+parallel machine that compiles C++ and supports the <a class="reference external" href="http://www-unix.mcs.anl.gov/mpi">MPI</a>
+message-passing library.  This includes distributed- or shared-memory
+parallel machines and Beowulf-style clusters.</p>
+<p>LAMMPS can model systems with only a few particles up to millions or
+billions.  See <a class="reference internal" href="Section_perf.html"><span class="doc">Section 8</span></a> for information on
+LAMMPS performance and scalability, or the Benchmarks section of the
+<a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a>.</p>
+<p>LAMMPS is a freely-available open-source code, distributed under the
+terms of the <a class="reference external" href="http://www.gnu.org/copyleft/gpl.html">GNU Public License</a>, which means you can use or
+modify the code however you wish.  See <a class="reference internal" href="#intro-4"><span class="std std-ref">this section</span></a> for a
+brief discussion of the open-source philosophy.</p>
+<p>LAMMPS is designed to be easy to modify or extend with new
+capabilities, such as new force fields, atom types, boundary
+conditions, or diagnostics.  See <a class="reference internal" href="Section_modify.html"><span class="doc">Section 10</span></a>
+for more details.</p>
+<p>The current version of LAMMPS is written in C++.  Earlier versions
+were written in F77 and F90.  See
+<a class="reference internal" href="Section_history.html"><span class="doc">Section 13</span></a> for more information on
+different versions.  All versions can be downloaded from the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a>.</p>
+<p>LAMMPS was originally developed under a US Department of Energy CRADA
+(Cooperative Research and Development Agreement) between two DOE labs
+and 3 companies.  It is distributed by <a class="reference external" href="http://www.sandia.gov">Sandia National Labs</a>.
+See <a class="reference internal" href="#intro-5"><span class="std std-ref">this section</span></a> for more information on LAMMPS funding and
+individuals who have contributed to LAMMPS.</p>
+<p>In the most general sense, LAMMPS integrates Newton&#8217;s equations of
+motion for collections of atoms, molecules, or macroscopic particles
+that interact via short- or long-range forces with a variety of
+initial and/or boundary conditions.  For computational efficiency
+LAMMPS uses neighbor lists to keep track of nearby particles.  The
+lists are optimized for systems with particles that are repulsive at
+short distances, so that the local density of particles never becomes
+too large.  On parallel machines, LAMMPS uses spatial-decomposition
+techniques to partition the simulation domain into small 3d
+sub-domains, one of which is assigned to each processor.  Processors
+communicate and store &#8220;ghost&#8221; atom information for atoms that border
+their sub-domain.  LAMMPS is most efficient (in a parallel sense) for
+systems whose particles fill a 3d rectangular box with roughly uniform
+density.  Papers with technical details of the algorithms used in
+LAMMPS are listed in <a class="reference internal" href="#intro-5"><span class="std std-ref">this section</span></a>.</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="lammps-features">
+<span id="intro-2"></span><h2>1.2. LAMMPS features</h2>
+<p>This section highlights LAMMPS features, with pointers to specific
+commands which give more details.  If LAMMPS doesn&#8217;t have your
+favorite interatomic potential, boundary condition, or atom type, see
+<a class="reference internal" href="Section_modify.html"><span class="doc">Section 10</span></a>, which describes how you can add
+it to LAMMPS.</p>
+<div class="section" id="general-features">
+<h3>1.2.1. General features</h3>
+<ul class="simple">
+<li>runs on a single processor or in parallel</li>
+<li>distributed-memory message-passing parallelism (MPI)</li>
+<li>spatial-decomposition of simulation domain for parallelism</li>
+<li>open-source distribution</li>
+<li>highly portable C++</li>
+<li>optional libraries used: MPI and single-processor FFT</li>
+<li>GPU (CUDA and OpenCL), Intel(R) Xeon Phi(TM) coprocessors, and OpenMP support for many code features</li>
+<li>easy to extend with new features and functionality</li>
+<li>runs from an input script</li>
+<li>syntax for defining and using variables and formulas</li>
+<li>syntax for looping over runs and breaking out of loops</li>
+<li>run one or multiple simulations simultaneously (in parallel) from one script</li>
+<li>build as library, invoke LAMMPS thru library interface or provided Python wrapper</li>
+<li>couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both</li>
+</ul>
+</div>
+<div class="section" id="particle-and-model-types">
+<h3>1.2.2. Particle and model types</h3>
+<p>(<a class="reference internal" href="atom_style.html"><span class="doc">atom style</span></a> command)</p>
+<ul class="simple">
+<li>atoms</li>
+<li>coarse-grained particles (e.g. bead-spring polymers)</li>
+<li>united-atom polymers or organic molecules</li>
+<li>all-atom polymers, organic molecules, proteins, DNA</li>
+<li>metals</li>
+<li>granular materials</li>
+<li>coarse-grained mesoscale models</li>
+<li>finite-size spherical and ellipsoidal particles</li>
+<li>finite-size  line segment (2d) and triangle (3d) particles</li>
+<li>point dipole particles</li>
+<li>rigid collections of particles</li>
+<li>hybrid combinations of these</li>
+</ul>
+</div>
+<div class="section" id="force-fields">
+<h3>1.2.3. Force fields</h3>
+<p>(<a class="reference internal" href="pair_style.html"><span class="doc">pair style</span></a>, <a class="reference internal" href="bond_style.html"><span class="doc">bond style</span></a>,
+<a class="reference internal" href="angle_style.html"><span class="doc">angle style</span></a>, <a class="reference internal" href="dihedral_style.html"><span class="doc">dihedral style</span></a>,
+<a class="reference internal" href="improper_style.html"><span class="doc">improper style</span></a>, <a class="reference internal" href="kspace_style.html"><span class="doc">kspace style</span></a>
+commands)</p>
+<ul class="simple">
+<li>pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins,     Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated</li>
+<li>charged pairwise potentials: Coulombic, point-dipole</li>
+<li>manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM),     embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff,     REBO, AIREBO, ReaxFF, COMB, SNAP, Streitz-Mintmire, 3-body polymorphic</li>
+<li>long-range interactions for charge, point-dipoles, and LJ dispersion:     Ewald, Wolf, PPPM (similar to particle-mesh Ewald)</li>
+<li>polarization models: <a class="reference internal" href="fix_qeq.html"><span class="doc">QEq</span></a>,     <a class="reference internal" href="Section_howto.html#howto-26"><span class="std std-ref">core/shell model</span></a>,     <a class="reference internal" href="Section_howto.html#howto-27"><span class="std std-ref">Drude dipole model</span></a></li>
+<li>charge equilibration (QEq via dynamic, point, shielded, Slater methods)</li>
+<li>coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO</li>
+<li>mesoscopic potentials: granular, Peridynamics, SPH</li>
+<li>electron force field (eFF, AWPMD)</li>
+<li>bond potentials: harmonic, FENE, Morse, nonlinear, class 2,     quartic (breakable)</li>
+<li>angle potentials: harmonic, CHARMM, cosine, cosine/squared, cosine/periodic,     class 2 (COMPASS)</li>
+<li>dihedral potentials: harmonic, CHARMM, multi-harmonic, helix,     class 2 (COMPASS), OPLS</li>
+<li>improper potentials: harmonic, cvff, umbrella, class 2 (COMPASS)</li>
+<li>polymer potentials: all-atom, united-atom, bead-spring, breakable</li>
+<li>water potentials: TIP3P, TIP4P, SPC</li>
+<li>implicit solvent potentials: hydrodynamic lubrication, Debye</li>
+<li>force-field compatibility with common CHARMM, AMBER, DREIDING,     OPLS, GROMACS, COMPASS options</li>
+<li>access to <a class="reference external" href="http://openkim.org">KIM archive</a> of potentials via     <a class="reference internal" href="pair_kim.html"><span class="doc">pair kim</span></a></li>
+<li>hybrid potentials: multiple pair, bond, angle, dihedral, improper     potentials can be used in one simulation</li>
+<li>overlaid potentials: superposition of multiple pair potentials</li>
+</ul>
+</div>
+<div class="section" id="atom-creation">
+<h3>1.2.4. Atom creation</h3>
+<p>(<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>, <a class="reference internal" href="lattice.html"><span class="doc">lattice</span></a>,
+<a class="reference internal" href="create_atoms.html"><span class="doc">create_atoms</span></a>, <a class="reference internal" href="delete_atoms.html"><span class="doc">delete_atoms</span></a>,
+<a class="reference internal" href="displace_atoms.html"><span class="doc">displace_atoms</span></a>, <a class="reference internal" href="replicate.html"><span class="doc">replicate</span></a> commands)</p>
+<ul class="simple">
+<li>read in atom coords from files</li>
+<li>create atoms on one or more lattices (e.g. grain boundaries)</li>
+<li>delete geometric or logical groups of atoms (e.g. voids)</li>
+<li>replicate existing atoms multiple times</li>
+<li>displace atoms</li>
+</ul>
+</div>
+<div class="section" id="ensembles-constraints-and-boundary-conditions">
+<h3>1.2.5. Ensembles, constraints, and boundary conditions</h3>
+<p>(<a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command)</p>
+<ul class="simple">
+<li>2d or 3d systems</li>
+<li>orthogonal or non-orthogonal (triclinic symmetry) simulation domains</li>
+<li>constant NVE, NVT, NPT, NPH, Parinello/Rahman integrators</li>
+<li>thermostatting options for groups and geometric regions of atoms</li>
+<li>pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions</li>
+<li>simulation box deformation (tensile and shear)</li>
+<li>harmonic (umbrella) constraint forces</li>
+<li>rigid body constraints</li>
+<li>SHAKE bond and angle constraints</li>
+<li>Monte Carlo bond breaking, formation, swapping</li>
+<li>atom/molecule insertion and deletion</li>
+<li>walls of various kinds</li>
+<li>non-equilibrium molecular dynamics (NEMD)</li>
+<li>variety of additional boundary conditions and constraints</li>
+</ul>
+</div>
+<div class="section" id="integrators">
+<h3>1.2.6. Integrators</h3>
+<p>(<a class="reference internal" href="run.html"><span class="doc">run</span></a>, <a class="reference internal" href="run_style.html"><span class="doc">run_style</span></a>, <a class="reference internal" href="minimize.html"><span class="doc">minimize</span></a> commands)</p>
+<ul class="simple">
+<li>velocity-Verlet integrator</li>
+<li>Brownian dynamics</li>
+<li>rigid body integration</li>
+<li>energy minimization via conjugate gradient or steepest descent relaxation</li>
+<li>rRESPA hierarchical timestepping</li>
+<li>rerun command for post-processing of dump files</li>
+</ul>
+</div>
+<div class="section" id="diagnostics">
+<h3>1.2.7. Diagnostics</h3>
+<ul class="simple">
+<li>see the various flavors of the <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> and <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> commands</li>
+</ul>
+</div>
+<div class="section" id="output">
+<h3>1.2.8. Output</h3>
+<p>(<a class="reference internal" href="dump.html"><span class="doc">dump</span></a>, <a class="reference internal" href="restart.html"><span class="doc">restart</span></a> commands)</p>
+<ul class="simple">
+<li>log file of thermodynamic info</li>
+<li>text dump files of atom coords, velocities, other per-atom quantities</li>
+<li>binary restart files</li>
+<li>parallel I/O of dump and restart files</li>
+<li>per-atom quantities (energy, stress, centro-symmetry parameter, CNA, etc)</li>
+<li>user-defined system-wide (log file) or per-atom (dump file) calculations</li>
+<li>spatial and time averaging of per-atom quantities</li>
+<li>time averaging of system-wide quantities</li>
+<li>atom snapshots in native, XYZ, XTC, DCD, CFG formats</li>
+</ul>
+</div>
+<div class="section" id="multi-replica-models">
+<h3>1.2.9. Multi-replica models</h3>
+<p><a class="reference internal" href="neb.html"><span class="doc">nudged elastic band</span></a>
+<a class="reference internal" href="prd.html"><span class="doc">parallel replica dynamics</span></a>
+<a class="reference internal" href="tad.html"><span class="doc">temperature accelerated dynamics</span></a>
+<a class="reference internal" href="temper.html"><span class="doc">parallel tempering</span></a></p>
+</div>
+<div class="section" id="pre-and-post-processing">
+<h3>1.2.10. Pre- and post-processing</h3>
+<ul class="simple">
+<li>Various pre- and post-processing serial tools are packaged
+with LAMMPS; see these <a class="reference internal" href="Section_tools.html"><span class="doc">doc pages</span></a>.</li>
+<li>Our group has also written and released a separate toolkit called
+<a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</a> which provides tools for doing setup, analysis,
+plotting, and visualization for LAMMPS simulations.  Pizza.py is
+written in <a class="reference external" href="http://www.python.org">Python</a> and is available for download from <a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza.html">the Pizza.py WWW site</a>.</li>
+</ul>
+</div>
+<div class="section" id="specialized-features">
+<h3>1.2.11. Specialized features</h3>
+<p>These are LAMMPS capabilities which you may not think of as typical
+molecular dynamics options:</p>
+<ul class="simple">
+<li><a class="reference internal" href="balance.html"><span class="doc">static</span></a> and <a class="reference internal" href="fix_balance.html"><span class="doc">dynamic load-balancing</span></a></li>
+<li><a class="reference internal" href="body.html"><span class="doc">generalized aspherical particles</span></a></li>
+<li><a class="reference internal" href="fix_srd.html"><span class="doc">stochastic rotation dynamics (SRD)</span></a></li>
+<li><a class="reference internal" href="fix_imd.html"><span class="doc">real-time visualization and interactive MD</span></a></li>
+<li>calculate <a class="reference internal" href="compute_xrd.html"><span class="doc">virtual diffraction patterns</span></a></li>
+<li><a class="reference internal" href="fix_atc.html"><span class="doc">atom-to-continuum coupling</span></a> with finite elements</li>
+<li>coupled rigid body integration via the <a class="reference internal" href="fix_poems.html"><span class="doc">POEMS</span></a> library</li>
+<li><a class="reference internal" href="fix_qmmm.html"><span class="doc">QM/MM coupling</span></a></li>
+<li><a class="reference internal" href="fix_ipi.html"><span class="doc">path-integral molecular dynamics (PIMD)</span></a> and <a class="reference internal" href="fix_pimd.html"><span class="doc">this as well</span></a></li>
+<li>Monte Carlo via <a class="reference internal" href="fix_gcmc.html"><span class="doc">GCMC</span></a> and <a class="reference internal" href="fix_tfmc.html"><span class="doc">tfMC</span></a> <a class="reference internal" href="fix_atom_swap.html"><span class="doc">atom swapping</span></a> and <a class="reference internal" href="fix_bond_swap.html"><span class="doc">bond swapping</span></a></li>
+<li><a class="reference internal" href="pair_dsmc.html"><span class="doc">Direct Simulation Monte Carlo</span></a> for low-density fluids</li>
+<li><a class="reference internal" href="pair_peri.html"><span class="doc">Peridynamics mesoscale modeling</span></a></li>
+<li><a class="reference internal" href="fix_lb_fluid.html"><span class="doc">Lattice Boltzmann fluid</span></a></li>
+<li><a class="reference internal" href="fix_tmd.html"><span class="doc">targeted</span></a> and <a class="reference internal" href="fix_smd.html"><span class="doc">steered</span></a> molecular dynamics</li>
+<li><a class="reference internal" href="fix_ttm.html"><span class="doc">two-temperature electron model</span></a></li>
+</ul>
+<hr class="docutils" />
+</div>
+</div>
+<div class="section" id="lammps-non-features">
+<span id="intro-3"></span><h2>1.3. LAMMPS non-features</h2>
+<p>LAMMPS is designed to efficiently compute Newton&#8217;s equations of motion
+for a system of interacting particles.  Many of the tools needed to
+pre- and post-process the data for such simulations are not included
+in the LAMMPS kernel for several reasons:</p>
+<ul class="simple">
+<li>the desire to keep LAMMPS simple</li>
+<li>they are not parallel operations</li>
+<li>other codes already do them</li>
+<li>limited development resources</li>
+</ul>
+<p>Specifically, LAMMPS itself does not:</p>
+<ul class="simple">
+<li>run thru a GUI</li>
+<li>build molecular systems</li>
+<li>assign force-field coefficients automagically</li>
+<li>perform sophisticated analyses of your MD simulation</li>
+<li>visualize your MD simulation</li>
+<li>plot your output data</li>
+</ul>
+<p>A few tools for pre- and post-processing tasks are provided as part of
+the LAMMPS package; they are described in <a class="reference internal" href="Section_tools.html"><span class="doc">this section</span></a>.  However, many people use other codes or
+write their own tools for these tasks.</p>
+<p>As noted above, our group has also written and released a separate
+toolkit called <a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</a> which addresses some of the listed
+bullets.  It provides tools for doing setup, analysis, plotting, and
+visualization for LAMMPS simulations.  Pizza.py is written in
+<a class="reference external" href="http://www.python.org">Python</a> and is available for download from <a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza.html">the Pizza.py WWW site</a>.</p>
+<p>LAMMPS requires as input a list of initial atom coordinates and types,
+molecular topology information, and force-field coefficients assigned
+to all atoms and bonds.  LAMMPS will not build molecular systems and
+assign force-field parameters for you.</p>
+<p>For atomic systems LAMMPS provides a <a class="reference internal" href="create_atoms.html"><span class="doc">create_atoms</span></a>
+command which places atoms on solid-state lattices (fcc, bcc,
+user-defined, etc).  Assigning small numbers of force field
+coefficients can be done via the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair coeff</span></a>, <a class="reference internal" href="bond_coeff.html"><span class="doc">bond coeff</span></a>, <a class="reference internal" href="angle_coeff.html"><span class="doc">angle coeff</span></a>, etc commands.
+For molecular systems or more complicated simulation geometries, users
+typically use another code as a builder and convert its output to
+LAMMPS input format, or write their own code to generate atom
+coordinate and molecular topology for LAMMPS to read in.</p>
+<p>For complicated molecular systems (e.g. a protein), a multitude of
+topology information and hundreds of force-field coefficients must
+typically be specified.  We suggest you use a program like
+<a class="reference external" href="http://www.scripps.edu/brooks">CHARMM</a> or <a class="reference external" href="http://amber.scripps.edu">AMBER</a> or other molecular builders to setup
+such problems and dump its information to a file.  You can then
+reformat the file as LAMMPS input.  Some of the tools in <a class="reference internal" href="Section_tools.html"><span class="doc">this section</span></a> can assist in this process.</p>
+<p>Similarly, LAMMPS creates output files in a simple format.  Most users
+post-process these files with their own analysis tools or re-format
+them for input into other programs, including visualization packages.
+If you are convinced you need to compute something on-the-fly as
+LAMMPS runs, see <a class="reference internal" href="Section_modify.html"><span class="doc">Section 10</span></a> for a discussion
+of how you can use the <a class="reference internal" href="dump.html"><span class="doc">dump</span></a> and <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> and
+<a class="reference internal" href="fix.html"><span class="doc">fix</span></a> commands to print out data of your choosing.  Keep in
+mind that complicated computations can slow down the molecular
+dynamics timestepping, particularly if the computations are not
+parallel, so it is often better to leave such analysis to
+post-processing codes.</p>
+<p>A very simple (yet fast) visualizer is provided with the LAMMPS
+package - see the <a class="reference internal" href="Section_tools.html#xmovie"><span class="std std-ref">xmovie</span></a> tool in <a class="reference internal" href="Section_tools.html"><span class="doc">this section</span></a>.  It creates xyz projection views of
+atomic coordinates and animates them.  We find it very useful for
+debugging purposes.  For high-quality visualization we recommend the
+following packages:</p>
+<ul class="simple">
+<li><a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd">VMD</a></li>
+<li><a class="reference external" href="http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</a></li>
+<li><a class="reference external" href="http://www.pymol.org">PyMol</a></li>
+<li><a class="reference external" href="http://www.bmsc.washington.edu/raster3d/raster3d.html">Raster3d</a></li>
+<li><a class="reference external" href="http://www.openrasmol.org">RasMol</a></li>
+</ul>
+<p>Other features that LAMMPS does not yet (and may never) support are
+discussed in <a class="reference internal" href="Section_history.html"><span class="doc">Section 13</span></a>.</p>
+<p>Finally, these are freely-available molecular dynamics codes, most of
+them parallel, which may be well-suited to the problems you want to
+model.  They can also be used in conjunction with LAMMPS to perform
+complementary modeling tasks.</p>
+<ul class="simple">
+<li><a class="reference external" href="http://www.scripps.edu/brooks">CHARMM</a></li>
+<li><a class="reference external" href="http://amber.scripps.edu">AMBER</a></li>
+<li><a class="reference external" href="http://www.ks.uiuc.edu/Research/namd/">NAMD</a></li>
+<li><a class="reference external" href="http://www.emsl.pnl.gov/docs/nwchem/nwchem.html">NWCHEM</a></li>
+<li><a class="reference external" href="http://www.cse.clrc.ac.uk/msi/software/DL_POLY">DL_POLY</a></li>
+<li><a class="reference external" href="http://dasher.wustl.edu/tinker">Tinker</a></li>
+</ul>
+<p>CHARMM, AMBER, NAMD, NWCHEM, and Tinker are designed primarily for
+modeling biological molecules.  CHARMM and AMBER use
+atom-decomposition (replicated-data) strategies for parallelism; NAMD
+and NWCHEM use spatial-decomposition approaches, similar to LAMMPS.
+Tinker is a serial code.  DL_POLY includes potentials for a variety of
+biological and non-biological materials; both a replicated-data and
+spatial-decomposition version exist.</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="open-source-distribution">
+<span id="intro-4"></span><h2>1.4. Open source distribution</h2>
+<p>LAMMPS comes with no warranty of any kind.  As each source file states
+in its header, it is a copyrighted code that is distributed free-of-
+charge, under the terms of the <a class="reference external" href="http://www.gnu.org/copyleft/gpl.html">GNU Public License</a> (GPL).  This
+is often referred to as open-source distribution - see
+<a class="reference external" href="http://www.gnu.org">www.gnu.org</a> or <a class="reference external" href="http://www.opensource.org">www.opensource.org</a> for more
+details.  The legal text of the GPL is in the LICENSE file that is
+included in the LAMMPS distribution.</p>
+<p>Here is a summary of what the GPL means for LAMMPS users:</p>
+<p>(1) Anyone is free to use, modify, or extend LAMMPS in any way they
+choose, including for commercial purposes.</p>
+<p>(2) If you distribute a modified version of LAMMPS, it must remain
+open-source, meaning you distribute it under the terms of the GPL.
+You should clearly annotate such a code as a derivative version of
+LAMMPS.</p>
+<p>(3) If you release any code that includes LAMMPS source code, then it
+must also be open-sourced, meaning you distribute it under the terms
+of the GPL.</p>
+<p>(4) If you give LAMMPS files to someone else, the GPL LICENSE file and
+source file headers (including the copyright and GPL notices) should
+remain part of the code.</p>
+<p>In the spirit of an open-source code, these are various ways you can
+contribute to making LAMMPS better.  You can send email to the
+<a class="reference external" href="http://lammps.sandia.gov/authors.html">developers</a> on any of these
+items.</p>
+<ul class="simple">
+<li>Point prospective users to the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a>.  Mention it in
+talks or link to it from your WWW site.</li>
+<li>If you find an error or omission in this manual or on the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a>, or have a suggestion for something to clarify or include,
+send an email to the
+<a class="reference external" href="http://lammps.sandia.gov/authors.html">developers</a>.</li>
+<li>If you find a bug, <a class="reference internal" href="Section_errors.html#err-2"><span class="std std-ref">Section 12.2</span></a>
+describes how to report it.</li>
+<li>If you publish a paper using LAMMPS results, send the citation (and
+any cool pictures or movies if you like) to add to the Publications,
+Pictures, and Movies pages of the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a>, with links
+and attributions back to you.</li>
+<li>Create a new Makefile.machine that can be added to the src/MAKE
+directory.</li>
+<li>The tools sub-directory of the LAMMPS distribution has various
+stand-alone codes for pre- and post-processing of LAMMPS data.  More
+details are given in <a class="reference internal" href="Section_tools.html"><span class="doc">Section 9</span></a>.  If you write
+a new tool that users will find useful, it can be added to the LAMMPS
+distribution.</li>
+<li>LAMMPS is designed to be easy to extend with new code for features
+like potentials, boundary conditions, diagnostic computations, etc.
+<a class="reference internal" href="Section_modify.html"><span class="doc">This section</span></a> gives details.  If you add a
+feature of general interest, it can be added to the LAMMPS
+distribution.</li>
+<li>The Benchmark page of the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a> lists LAMMPS
+performance on various platforms.  The files needed to run the
+benchmarks are part of the LAMMPS distribution.  If your machine is
+sufficiently different from those listed, your timing data can be
+added to the page.</li>
+<li>You can send feedback for the User Comments page of the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a>.  It might be added to the page.  No promises.</li>
+<li>Cash.  Small denominations, unmarked bills preferred.  Paper sack OK.
+Leave on desk.  VISA also accepted.  Chocolate chip cookies
+encouraged.</li>
+</ul>
+<hr class="docutils" />
+</div>
+<div class="section" id="acknowledgments-and-citations">
+<span id="intro-5"></span><h2>1.5. Acknowledgments and citations</h2>
+<p>LAMMPS development has been funded by the <a class="reference external" href="http://www.doe.gov">US Department of Energy</a> (DOE), through its CRADA, LDRD, ASCI, and Genomes-to-Life
+programs and its <a class="reference external" href="http://www.sc.doe.gov/ascr/home.html">OASCR</a> and <a class="reference external" href="http://www.er.doe.gov/production/ober/ober_top.html">OBER</a> offices.</p>
+<p>Specifically, work on the latest version was funded in part by the US
+Department of Energy&#8217;s Genomics:GTL program
+(<a class="reference external" href="http://www.doegenomestolife.org">www.doegenomestolife.org</a>) under the <a class="reference external" href="http://www.genomes2life.org">project</a>, &#8220;Carbon
+Sequestration in Synechococcus Sp.: From Molecular Machines to
+Hierarchical Modeling&#8221;.</p>
+<p>The following paper describe the basic parallel algorithms used in
+LAMMPS.  If you use LAMMPS results in your published work, please cite
+this paper and include a pointer to the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a>
+(<a class="reference external" href="http://lammps.sandia.gov">http://lammps.sandia.gov</a>):</p>
+<p>S. Plimpton, <strong>Fast Parallel Algorithms for Short-Range Molecular
+Dynamics</strong>, J Comp Phys, 117, 1-19 (1995).</p>
+<p>Other papers describing specific algorithms used in LAMMPS are listed
+under the <a class="reference external" href="http://lammps.sandia.gov/cite.html">Citing LAMMPS link</a> of
+the LAMMPS WWW page.</p>
+<p>The <a class="reference external" href="http://lammps.sandia.gov/papers.html">Publications link</a> on the
+LAMMPS WWW page lists papers that have cited LAMMPS.  If your paper is
+not listed there for some reason, feel free to send us the info.  If
+the simulations in your paper produced cool pictures or animations,
+we&#8217;ll be pleased to add them to the
+<a class="reference external" href="http://lammps.sandia.gov/pictures.html">Pictures</a> or
+<a class="reference external" href="http://lammps.sandia.gov/movies.html">Movies</a> pages of the LAMMPS WWW
+site.</p>
+<p>The core group of LAMMPS developers is at Sandia National Labs:</p>
+<ul class="simple">
+<li>Steve Plimpton, sjplimp at sandia.gov</li>
+<li>Aidan Thompson, athomps at sandia.gov</li>
+<li>Paul Crozier, pscrozi at sandia.gov</li>
+</ul>
+<p>The following folks are responsible for significant contributions to
+the code, or other aspects of the LAMMPS development effort.  Many of
+the packages they have written are somewhat unique to LAMMPS and the
+code would not be as general-purpose as it is without their expertise
+and efforts.</p>
+<ul class="simple">
+<li>Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CG-CMM and USER-OMP packages</li>
+<li>Roy Pollock (LLNL), Ewald and PPPM solvers</li>
+<li>Mike Brown (ORNL), brownw at ornl.gov, GPU package</li>
+<li>Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential</li>
+<li>Mike Parks (Sandia), mlparks at sandia.gov, PERI package for Peridynamics</li>
+<li>Rudra Mukherjee (JPL), Rudranarayan.M.Mukherjee at jpl.nasa.gov, POEMS package for articulated rigid body motion</li>
+<li>Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package for atom/continuum coupling</li>
+<li>Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD</li>
+<li>Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA package</li>
+<li>Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field</li>
+<li>Christoph Kloss (JKU), Christoph.Kloss at jku.at, USER-LIGGGHTS package for granular models and granular/fluid coupling</li>
+<li>Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF</li>
+<li>Georg Gunzenmuller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SPH package</li>
+</ul>
+<p>As discussed in <a class="reference internal" href="Section_history.html"><span class="doc">Section 13</span></a>, LAMMPS
+originated as a cooperative project between DOE labs and industrial
+partners. Folks involved in the design and testing of the original
+version of LAMMPS were the following:</p>
+<ul class="simple">
+<li>John Carpenter (Mayo Clinic, formerly at Cray Research)</li>
+<li>Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb)</li>
+<li>Steve Lustig (Dupont)</li>
+<li>Jim Belak (LLNL)</li>
+</ul>
+</div>
+</div>
+
+
+           </div>
+          </div>
+          <footer>
+  
+    <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
+      
+        <a href="Section_start.html" class="btn btn-neutral float-right" title="2. Getting Started" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
+      
+      
+        <a href="Manual.html" class="btn btn-neutral" title="LAMMPS Documentation" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+      
+    </div>
+  
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>
+        &copy; Copyright 2013 Sandia Corporation.
+    </p>
+  </div>
+  Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
+</footer>
+
+        </div>
+      </div>
+
+    </section>
+
+  </div>
+  
+
+
+  
+
+    <script type="text/javascript">
+        var DOCUMENTATION_OPTIONS = {
+            URL_ROOT:'./',
+            VERSION:'',
+            COLLAPSE_INDEX:false,
+            FILE_SUFFIX:'.html',
+            HAS_SOURCE:  true
+        };
+    </script>
+      <script type="text/javascript" src="_static/jquery.js"></script>
+      <script type="text/javascript" src="_static/underscore.js"></script>
+      <script type="text/javascript" src="_static/doctools.js"></script>
+      <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+      <script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/jquery-1.11.0.min.js"></script>
+      <script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/lightbox.min.js"></script>
+      <script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2-customize/jquery-noconflict.js"></script>
+
+  
+
+  
+  
+    <script type="text/javascript" src="_static/js/theme.js"></script>
+  
+
+  
+  
+  <script type="text/javascript">
+      jQuery(function () {
+          SphinxRtdTheme.StickyNav.enable();
+      });
+  </script>
+   
+
+</body>
+</html>

doc/html/Section_perf.html

@@ -0,0 +1,292 @@
+
+
+<!DOCTYPE html>
+<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
+<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
+<head>
+  <meta charset="utf-8">
+  
+  <meta name="viewport" content="width=device-width, initial-scale=1.0">
+  
+  <title>8. Performance &amp; scalability &mdash; LAMMPS documentation</title>
+  
+
+  
+  
+
+  
+
+  
+  
+    
+
+  
+
+  
+  
+    <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+  
+
+  
+    <link rel="stylesheet" href="_static/sphinxcontrib-images/LightBox2/lightbox2/css/lightbox.css" type="text/css" />
+  
+
+  
+    <link rel="top" title="LAMMPS documentation" href="index.html"/>
+        <link rel="next" title="9. Additional tools" href="Section_tools.html"/>
+        <link rel="prev" title="7. Example problems" href="Section_example.html"/> 
+
+  
+  <script src="_static/js/modernizr.min.js"></script>
+
+</head>
+
+<body class="wy-body-for-nav" role="document">
+
+  <div class="wy-grid-for-nav">
+
+    
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-nav-search">
+        
+
+        
+          <a href="Manual.html" class="icon icon-home"> LAMMPS
+        
+
+        
+        </a>
+
+        
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+
+        
+      </div>
+
+      <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
+        
+          
+          
+              <p class="caption"><span class="caption-text">User Documentation</span></p>
+<ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+</ul>
+<p class="caption"><span class="caption-text">Index</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="tutorials.html">Tutorials</a></li>
+<li class="toctree-l1"><a class="reference internal" href="commands.html">Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
+<li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
+<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
+<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
+<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
+<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>
+</ul>
+
+          
+        
+      </div>
+      &nbsp;
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
+
+      
+      <nav class="wy-nav-top" role="navigation" aria-label="top navigation">
+        <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+        <a href="Manual.html">LAMMPS</a>
+      </nav>
+
+
+      
+      <div class="wy-nav-content">
+        <div class="rst-content">
+          <div role="navigation" aria-label="breadcrumbs navigation">
+  <ul class="wy-breadcrumbs">
+    <li><a href="Manual.html">Docs</a> &raquo;</li>
+      
+    <li>8. Performance &amp; scalability</li>
+      <li class="wy-breadcrumbs-aside">
+        
+          
+            <a href="http://lammps.sandia.gov">Website</a>
+            <a href="Section_commands.html#comm">Commands</a>
+        
+      </li>
+  </ul>
+  <hr/>
+  
+    <div class="rst-footer-buttons" style="margin-bottom: 1em" role="navigation" aria-label="footer navigation">
+      
+        <a href="Section_tools.html" class="btn btn-neutral float-right" title="9. Additional tools" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
+      
+      
+        <a href="Section_example.html" class="btn btn-neutral" title="7. Example problems" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+      
+    </div>
+  
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+            
+  <div class="section" id="performance-scalability">
+<h1>8. Performance &amp; scalability</h1>
+<p>Current LAMMPS performance is discussed on the Benchmarks page of the
+<a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a> where CPU timings and parallel efficiencies are
+listed.  The page has several sections, which are briefly described
+below:</p>
+<ul class="simple">
+<li>CPU performance on 5 standard problems, strong and weak scaling</li>
+<li>GPU and Xeon Phi performance on same and related problems</li>
+<li>Comparison of cost of interatomic potentials</li>
+<li>Performance of huge, billion-atom problems</li>
+</ul>
+<p>The 5 standard problems are as follow:</p>
+<ol class="arabic simple">
+<li>LJ = atomic fluid, Lennard-Jones potential with 2.5 sigma cutoff (55
+neighbors per atom), NVE integration</li>
+<li>Chain = bead-spring polymer melt of 100-mer chains, FENE bonds and LJ
+pairwise interactions with a 2^(1/6) sigma cutoff (5 neighbors per
+atom), NVE integration</li>
+<li>EAM = metallic solid, Cu EAM potential with 4.95 Angstrom cutoff (45
+neighbors per atom), NVE integration</li>
+<li>Chute = granular chute flow, frictional history potential with 1.1
+sigma cutoff (7 neighbors per atom), NVE integration</li>
+<li>Rhodo = rhodopsin protein in solvated lipid bilayer, CHARMM force
+field with a 10 Angstrom LJ cutoff (440 neighbors per atom),
+particle-particle particle-mesh (PPPM) for long-range Coulombics, NPT
+integration</li>
+</ol>
+<p>Input files for these 5 problems are provided in the bench directory
+of the LAMMPS distribution.  Each has 32,000 atoms and runs for 100
+timesteps.  The size of the problem (number of atoms) can be varied
+using command-line switches as described in the bench/README file.
+This is an easy way to test performance and either strong or weak
+scalability on your machine.</p>
+<p>The bench directory includes a few log.* files that show performance
+of these 5 problems on 1 or 4 cores of Linux desktop.  The bench/FERMI
+and bench/KEPLER dirs have input files and scripts and instructions
+for running the same (or similar) problems using OpenMP or GPU or Xeon
+Phi acceleration options.  See the README files in those dirs and the
+<a class="reference internal" href="Section_accelerate.html"><span class="doc">Section accelerate</span></a> doc pages for
+instructions on how to build LAMMPS and run on that kind of hardware.</p>
+<p>The bench/POTENTIALS directory has input files which correspond to the
+table of results on the
+<span class="xref std std-ref">Potentials</span> section of
+the Benchmarks web page.  So you can also run those test problems on
+your machine.</p>
+<p>The <span class="xref std std-ref">billion-atom</span> section
+of the Benchmarks web page has performance data for very large
+benchmark runs of simple Lennard-Jones (LJ) models, which use the
+bench/in.lj input script.</p>
+<hr class="docutils" />
+<p>For all the benchmarks, a useful metric is the CPU cost per atom per
+timestep.  Since performance scales roughly linearly with problem size
+and timesteps for all LAMMPS models (i.e. inteatomic or coarse-grained
+potentials), the run time of any problem using the same model (atom
+style, force field, cutoff, etc) can then be estimated.</p>
+<p>Performance on a parallel machine can also be predicted from one-core
+or one-node timings if the parallel efficiency can be estimated.  The
+communication bandwidth and latency of a particular parallel machine
+affects the efficiency.  On most machines LAMMPS will give parallel
+efficiencies on these benchmarks above 50% so long as the number of
+atoms/core is a few 100 or greater, and closer to 100% for large
+numbers of atoms/core.  This is for all-MPI mode with one MPI task per
+core.  For nodes with accelerator options or hardware (OpenMP, GPU,
+Phi), you should first measure single node performance.  Then you can
+estimate parallel performance for multi-node runs using the same logic
+as for all-MPI mode, except that now you will typically need many more
+atoms/node to achieve good scalability.</p>
+</div>
+
+
+           </div>
+          </div>
+          <footer>
+  
+    <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
+      
+        <a href="Section_tools.html" class="btn btn-neutral float-right" title="9. Additional tools" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
+      
+      
+        <a href="Section_example.html" class="btn btn-neutral" title="7. Example problems" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+      
+    </div>
+  
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>
+        &copy; Copyright 2013 Sandia Corporation.
+    </p>
+  </div>
+  Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
+</footer>
+
+        </div>
+      </div>
+
+    </section>
+
+  </div>
+  
+
+
+  
+
+    <script type="text/javascript">
+        var DOCUMENTATION_OPTIONS = {
+            URL_ROOT:'./',
+            VERSION:'',
+            COLLAPSE_INDEX:false,
+            FILE_SUFFIX:'.html',
+            HAS_SOURCE:  true
+        };
+    </script>
+      <script type="text/javascript" src="_static/jquery.js"></script>
+      <script type="text/javascript" src="_static/underscore.js"></script>
+      <script type="text/javascript" src="_static/doctools.js"></script>
+      <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+      <script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/jquery-1.11.0.min.js"></script>
+      <script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/lightbox.min.js"></script>
+      <script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2-customize/jquery-noconflict.js"></script>
+
+  
+
+  
+  
+    <script type="text/javascript" src="_static/js/theme.js"></script>
+  
+
+  
+  
+  <script type="text/javascript">
+      jQuery(function () {
+          SphinxRtdTheme.StickyNav.enable();
+      });
+  </script>
+   
+
+</body>
+</html>

doc/html/Section_tools.html

@@ -0,0 +1,720 @@
+
+
+<!DOCTYPE html>
+<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
+<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
+<head>
+  <meta charset="utf-8">
+  
+  <meta name="viewport" content="width=device-width, initial-scale=1.0">
+  
+  <title>9. Additional tools &mdash; LAMMPS documentation</title>
+  
+
+  
+  
+
+  
+
+  
+  
+    
+
+  
+
+  
+  
+    <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+  
+
+  
+    <link rel="stylesheet" href="_static/sphinxcontrib-images/LightBox2/lightbox2/css/lightbox.css" type="text/css" />
+  
+
+  
+    <link rel="top" title="LAMMPS documentation" href="index.html"/>
+        <link rel="next" title="10. Modifying &amp; extending LAMMPS" href="Section_modify.html"/>
+        <link rel="prev" title="8. Performance &amp; scalability" href="Section_perf.html"/> 
+
+  
+  <script src="_static/js/modernizr.min.js"></script>
+
+</head>
+
+<body class="wy-body-for-nav" role="document">
+
+  <div class="wy-grid-for-nav">
+
+    
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-nav-search">
+        
+
+        
+          <a href="Manual.html" class="icon icon-home"> LAMMPS
+        
+
+        
+        </a>
+
+        
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+
+        
+      </div>
+
+      <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
+        
+          
+          
+              <p class="caption"><span class="caption-text">User Documentation</span></p>
+<ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">9. Additional tools</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#amber2lmp-tool">9.1. amber2lmp tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#binary2txt-tool">9.2. binary2txt tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#ch2lmp-tool">9.3. ch2lmp tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#chain-tool">9.4. chain tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#colvars-tools">9.5. colvars tools</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#createatoms-tool">9.6. createatoms tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#data2xmovie-tool">9.7. data2xmovie tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#eam-database-tool">9.8. eam database tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#eam-generate-tool">9.9. eam generate tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#eff-tool">9.10. eff tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#emacs-tool">9.11. emacs tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#fep-tool">9.12. fep tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#i-pi-tool">9.13. i-pi tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#ipp-tool">9.14. ipp tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#kate-tool">9.15. kate tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#lmp2arc-tool">9.16. lmp2arc tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#lmp2cfg-tool">9.17. lmp2cfg tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#lmp2vmd-tool">9.18. lmp2vmd tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#matlab-tool">9.19. matlab tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#micelle2d-tool">9.20. micelle2d tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#moltemplate-tool">9.21. moltemplate tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#msi2lmp-tool">9.22. msi2lmp tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#phonon-tool">9.23. phonon tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#polymer-bonding-tool">9.24. polymer bonding tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pymol-asphere-tool">9.25. pymol_asphere tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#python-tool">9.26. python tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#reax-tool">9.27. reax tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#restart2data-tool">9.28. restart2data tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#vim-tool">9.29. vim tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#xmgrace-tool">9.30. xmgrace tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#xmovie-tool">9.31. xmovie tool</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+</ul>
+<p class="caption"><span class="caption-text">Index</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="tutorials.html">Tutorials</a></li>
+<li class="toctree-l1"><a class="reference internal" href="commands.html">Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
+<li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
+<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
+<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
+<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
+<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>
+</ul>
+
+          
+        
+      </div>
+      &nbsp;
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
+
+      
+      <nav class="wy-nav-top" role="navigation" aria-label="top navigation">
+        <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+        <a href="Manual.html">LAMMPS</a>
+      </nav>
+
+
+      
+      <div class="wy-nav-content">
+        <div class="rst-content">
+          <div role="navigation" aria-label="breadcrumbs navigation">
+  <ul class="wy-breadcrumbs">
+    <li><a href="Manual.html">Docs</a> &raquo;</li>
+      
+    <li>9. Additional tools</li>
+      <li class="wy-breadcrumbs-aside">
+        
+          
+            <a href="http://lammps.sandia.gov">Website</a>
+            <a href="Section_commands.html#comm">Commands</a>
+        
+      </li>
+  </ul>
+  <hr/>
+  
+    <div class="rst-footer-buttons" style="margin-bottom: 1em" role="navigation" aria-label="footer navigation">
+      
+        <a href="Section_modify.html" class="btn btn-neutral float-right" title="10. Modifying &amp; extending LAMMPS" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
+      
+      
+        <a href="Section_perf.html" class="btn btn-neutral" title="8. Performance &amp; scalability" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+      
+    </div>
+  
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+            
+  <div class="section" id="additional-tools">
+<h1>9. Additional tools</h1>
+<p>LAMMPS is designed to be a computational kernel for performing
+molecular dynamics computations.  Additional pre- and post-processing
+steps are often necessary to setup and analyze a simulation.  A few
+additional tools are provided with the LAMMPS distribution and are
+described in this section.</p>
+<p>Our group has also written and released a separate toolkit called
+<a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</a> which provides tools for doing setup, analysis,
+plotting, and visualization for LAMMPS simulations.  Pizza.py is
+written in <a class="reference external" href="http://www.python.org">Python</a> and is available for download from <a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza.html">the Pizza.py WWW site</a>.</p>
+<p>Note that many users write their own setup or analysis tools or use
+other existing codes and convert their output to a LAMMPS input format
+or vice versa.  The tools listed here are included in the LAMMPS
+distribution as examples of auxiliary tools.  Some of them are not
+actively supported by Sandia, as they were contributed by LAMMPS
+users.  If you have problems using them, we can direct you to the
+authors.</p>
+<p>The source code for each of these codes is in the tools sub-directory
+of the LAMMPS distribution.  There is a Makefile (which you may need
+to edit for your platform) which will build several of the tools which
+reside in that directory.  Some of them are larger packages in their
+own sub-directories with their own Makefiles.</p>
+<ul class="simple">
+<li><a class="reference internal" href="#amber"><span class="std std-ref">amber2lmp</span></a></li>
+<li><a class="reference internal" href="#binary"><span class="std std-ref">binary2txt</span></a></li>
+<li><a class="reference internal" href="#charmm"><span class="std std-ref">ch2lmp</span></a></li>
+<li><a class="reference internal" href="#chain"><span class="std std-ref">chain</span></a></li>
+<li><a class="reference internal" href="#colvars"><span class="std std-ref">colvars</span></a></li>
+<li><a class="reference internal" href="#create"><span class="std std-ref">createatoms</span></a></li>
+<li><a class="reference internal" href="#data"><span class="std std-ref">data2xmovie</span></a></li>
+<li><a class="reference internal" href="#eamdb"><span class="std std-ref">eam database</span></a></li>
+<li><a class="reference internal" href="#eamgn"><span class="std std-ref">eam generate</span></a></li>
+<li><a class="reference internal" href="#eff"><span class="std std-ref">eff</span></a></li>
+<li><a class="reference internal" href="#emacs"><span class="std std-ref">emacs</span></a></li>
+<li><a class="reference internal" href="#fep"><span class="std std-ref">fep</span></a></li>
+<li><a class="reference internal" href="#ipi"><span class="std std-ref">i-pi</span></a></li>
+<li><a class="reference internal" href="#ipp"><span class="std std-ref">ipp</span></a></li>
+<li><a class="reference internal" href="#kate"><span class="std std-ref">kate</span></a></li>
+<li><a class="reference internal" href="#arc"><span class="std std-ref">lmp2arc</span></a></li>
+<li><a class="reference internal" href="#cfg"><span class="std std-ref">lmp2cfg</span></a></li>
+<li><a class="reference internal" href="#vmd"><span class="std std-ref">lmp2vmd</span></a></li>
+<li><a class="reference internal" href="#matlab"><span class="std std-ref">matlab</span></a></li>
+<li><a class="reference internal" href="#micelle"><span class="std std-ref">micelle2d</span></a></li>
+<li><a class="reference internal" href="#moltemplate"><span class="std std-ref">moltemplate</span></a></li>
+<li><a class="reference internal" href="#msi"><span class="std std-ref">msi2lmp</span></a></li>
+<li><a class="reference internal" href="#phonon"><span class="std std-ref">phonon</span></a></li>
+<li><a class="reference internal" href="#polybond"><span class="std std-ref">polymer bonding</span></a></li>
+<li><a class="reference internal" href="#pymol"><span class="std std-ref">pymol_asphere</span></a></li>
+<li><a class="reference internal" href="#pythontools"><span class="std std-ref">python</span></a></li>
+<li><a class="reference internal" href="#reax-tool"><span class="std std-ref">reax</span></a></li>
+<li><a class="reference internal" href="#restart"><span class="std std-ref">restart2data</span></a></li>
+<li><a class="reference internal" href="#vim"><span class="std std-ref">vim</span></a></li>
+<li><a class="reference internal" href="#xmgrace"><span class="std std-ref">xmgrace</span></a></li>
+<li><a class="reference internal" href="#xmovie"><span class="std std-ref">xmovie</span></a></li>
+</ul>
+<hr class="docutils" />
+<div class="section" id="amber2lmp-tool">
+<span id="amber"></span><h2>9.1. amber2lmp tool</h2>
+<p>The amber2lmp sub-directory contains two Python scripts for converting
+files back-and-forth between the AMBER MD code and LAMMPS.  See the
+README file in amber2lmp for more information.</p>
+<p>These tools were written by Keir Novik while he was at Queen Mary
+University of London.  Keir is no longer there and cannot support
+these tools which are out-of-date with respect to the current LAMMPS
+version (and maybe with respect to AMBER as well).  Since we don&#8217;t use
+these tools at Sandia, you&#8217;ll need to experiment with them and make
+necessary modifications yourself.</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="binary2txt-tool">
+<span id="binary"></span><h2>9.2. binary2txt tool</h2>
+<p>The file binary2txt.cpp converts one or more binary LAMMPS dump file
+into ASCII text files.  The syntax for running the tool is</p>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">binary2txt</span> <span class="n">file1</span> <span class="n">file2</span> <span class="o">...</span>
+</pre></div>
+</div>
+<p>which creates file1.txt, file2.txt, etc.  This tool must be compiled
+on a platform that can read the binary file created by a LAMMPS run,
+since binary files are not compatible across all platforms.</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="ch2lmp-tool">
+<span id="charmm"></span><h2>9.3. ch2lmp tool</h2>
+<p>The ch2lmp sub-directory contains tools for converting files
+back-and-forth between the CHARMM MD code and LAMMPS.</p>
+<p>They are intended to make it easy to use CHARMM as a builder and as a
+post-processor for LAMMPS. Using charmm2lammps.pl, you can convert an
+ensemble built in CHARMM into its LAMMPS equivalent.  Using
+lammps2pdb.pl you can convert LAMMPS atom dumps into pdb files.</p>
+<p>See the README file in the ch2lmp sub-directory for more information.</p>
+<p>These tools were created by Pieter in&#8217;t Veld (pjintve at sandia.gov)
+and Paul Crozier (pscrozi at sandia.gov) at Sandia.</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="chain-tool">
+<span id="chain"></span><h2>9.4. chain tool</h2>
+<p>The file chain.f creates a LAMMPS data file containing bead-spring
+polymer chains and/or monomer solvent atoms.  It uses a text file
+containing chain definition parameters as an input.  The created
+chains and solvent atoms can strongly overlap, so LAMMPS needs to run
+the system initially with a &#8220;soft&#8221; pair potential to un-overlap it.
+The syntax for running the tool is</p>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">chain</span> <span class="o">&lt;</span> <span class="n">def</span><span class="o">.</span><span class="n">chain</span> <span class="o">&gt;</span> <span class="n">data</span><span class="o">.</span><span class="n">file</span>
+</pre></div>
+</div>
+<p>See the def.chain or def.chain.ab files in the tools directory for
+examples of definition files.  This tool was used to create the
+system for the <a class="reference internal" href="Section_perf.html"><span class="doc">chain benchmark</span></a>.</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="colvars-tools">
+<span id="colvars"></span><h2>9.5. colvars tools</h2>
+<p>The colvars directory contains a collection of tools for postprocessing
+data produced by the colvars collective variable library.
+To compile the tools, edit the makefile for your system and run &#8220;make&#8221;.</p>
+<p>Please report problems and issues the colvars library and its tools
+at: <a class="reference external" href="https://github.com/colvars/colvars/issues">https://github.com/colvars/colvars/issues</a></p>
+<p>abf_integrate:</p>
+<p>MC-based integration of multidimensional free energy gradient
+Version 20110511</p>
+<pre class="literal-block">
+Syntax: ./abf_integrate &lt; filename &gt; [-n &lt; nsteps &gt;] [-t &lt; temp &gt;] [-m [0|1] (metadynamics)] [-h &lt; hill_height &gt;] [-f &lt; variable_hill_factor &gt;]
+</pre>
+<p>The LAMMPS interface to the colvars collective variable library, as
+well as these tools, were created by Axel Kohlmeyer (akohlmey at
+gmail.com) at ICTP, Italy.</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="createatoms-tool">
+<span id="create"></span><h2>9.6. createatoms tool</h2>
+<p>The tools/createatoms directory contains a Fortran program called
+createAtoms.f which can generate a variety of interesting crystal
+structures and geometries and output the resulting list of atom
+coordinates in LAMMPS or other formats.</p>
+<p>See the included Manual.pdf for details.</p>
+<p>The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov.</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="data2xmovie-tool">
+<span id="data"></span><h2>9.7. data2xmovie tool</h2>
+<p>The file data2xmovie.c converts a LAMMPS data file into a snapshot
+suitable for visualizing with the <a class="reference internal" href="#xmovie"><span class="std std-ref">xmovie</span></a> tool, as if it had
+been output with a dump command from LAMMPS itself.  The syntax for
+running the tool is</p>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">data2xmovie</span> <span class="p">[</span><span class="n">options</span><span class="p">]</span> <span class="o">&lt;</span> <span class="n">infile</span> <span class="o">&gt;</span> <span class="n">outfile</span>
+</pre></div>
+</div>
+<p>See the top of the data2xmovie.c file for a discussion of the options.</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="eam-database-tool">
+<span id="eamdb"></span><h2>9.8. eam database tool</h2>
+<p>The tools/eam_database directory contains a Fortran program that will
+generate EAM alloy setfl potential files for any combination of 16
+elements: Cu, Ag, Au, Ni, Pd, Pt, Al, Pb, Fe, Mo, Ta, W, Mg, Co, Ti,
+Zr.  The files can then be used with the <a class="reference internal" href="pair_eam.html"><span class="doc">pair_style eam/alloy</span></a> command.</p>
+<p>The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov,
+and is based on his paper:</p>
+<p>X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69,
+144113 (2004).</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="eam-generate-tool">
+<span id="eamgn"></span><h2>9.9. eam generate tool</h2>
+<p>The tools/eam_generate directory contains several one-file C programs
+that convert an analytic formula into a tabulated <a class="reference internal" href="pair_eam.html"><span class="doc">embedded atom method (EAM)</span></a> setfl potential file.  The potentials they
+produce are in the potentials directory, and can be used with the
+<a class="reference internal" href="pair_eam.html"><span class="doc">pair_style eam/alloy</span></a> command.</p>
+<p>The source files and potentials were provided by Gerolf Ziegenhain
+(gerolf at ziegenhain.com).</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="eff-tool">
+<span id="eff"></span><h2>9.10. eff tool</h2>
+<p>The tools/eff directory contains various scripts for generating
+structures and post-processing output for simulations using the
+electron force field (eFF).</p>
+<p>These tools were provided by Andres Jaramillo-Botero at CalTech
+(ajaramil at wag.caltech.edu).</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="emacs-tool">
+<span id="emacs"></span><h2>9.11. emacs tool</h2>
+<p>The tools/emacs directory contains a Lips add-on file for Emacs that
+enables a lammps-mode for editing of input scripts when using Emacs,
+with various highlighting options setup.</p>
+<p>These tools were provided by Aidan Thompson at Sandia
+(athomps at sandia.gov).</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="fep-tool">
+<span id="fep"></span><h2>9.12. fep tool</h2>
+<p>The tools/fep directory contains Python scripts useful for
+post-processing results from performing free-energy perturbation
+simulations using the USER-FEP package.</p>
+<p>The scripts were contributed by Agilio Padua (Universite Blaise
+Pascal Clermont-Ferrand), agilio.padua at univ-bpclermont.fr.</p>
+<p>See README file in the tools/fep directory.</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="i-pi-tool">
+<span id="ipi"></span><h2>9.13. i-pi tool</h2>
+<p>The tools/i-pi directory contains a version of the i-PI package, with
+all the LAMMPS-unrelated files removed.  It is provided so that it can
+be used with the <a class="reference internal" href="fix_ipi.html"><span class="doc">fix ipi</span></a> command to perform
+path-integral molecular dynamics (PIMD).</p>
+<p>The i-PI package was created and is maintained by Michele Ceriotti,
+michele.ceriotti at gmail.com, to interface to a variety of molecular
+dynamics codes.</p>
+<p>See the tools/i-pi/manual.pdf file for an overview of i-PI, and the
+<a class="reference internal" href="fix_ipi.html"><span class="doc">fix ipi</span></a> doc page for further details on running PIMD
+calculations with LAMMPS.</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="ipp-tool">
+<span id="ipp"></span><h2>9.14. ipp tool</h2>
+<p>The tools/ipp directory contains a Perl script ipp which can be used
+to facilitate the creation of a complicated file (say, a lammps input
+script or tools/createatoms input file) using a template file.</p>
+<p>ipp was created and is maintained by Reese Jones (Sandia), rjones at
+sandia.gov.</p>
+<p>See two examples in the tools/ipp directory.  One of them is for the
+tools/createatoms tool&#8217;s input file.</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="kate-tool">
+<span id="kate"></span><h2>9.15. kate tool</h2>
+<p>The file in the tools/kate directory is an add-on to the Kate editor
+in the KDE suite that allow syntax highlighting of LAMMPS input
+scripts.  See the README.txt file for details.</p>
+<p>The file was provided by Alessandro Luigi Sellerio
+(alessandro.sellerio at ieni.cnr.it).</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="lmp2arc-tool">
+<span id="arc"></span><h2>9.16. lmp2arc tool</h2>
+<p>The lmp2arc sub-directory contains a tool for converting LAMMPS output
+files to the format for Accelrys&#8217; Insight MD code (formerly
+MSI/Biosym and its Discover MD code).  See the README file for more
+information.</p>
+<p>This tool was written by John Carpenter (Cray), Michael Peachey
+(Cray), and Steve Lustig (Dupont).  John is now at the Mayo Clinic
+(jec at mayo.edu), but still fields questions about the tool.</p>
+<p>This tool was updated for the current LAMMPS C++ version by Jeff
+Greathouse at Sandia (jagreat at sandia.gov).</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="lmp2cfg-tool">
+<span id="cfg"></span><h2>9.17. lmp2cfg tool</h2>
+<p>The lmp2cfg sub-directory contains a tool for converting LAMMPS output
+files into a series of *.cfg files which can be read into the
+<a class="reference external" href="http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</a> visualizer.  See
+the README file for more information.</p>
+<p>This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="lmp2vmd-tool">
+<span id="vmd"></span><h2>9.18. lmp2vmd tool</h2>
+<p>The lmp2vmd sub-directory contains a README.txt file that describes
+details of scripts and plugin support within the <a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd">VMD package</a> for visualizing LAMMPS
+dump files.</p>
+<p>The VMD plugins and other supporting scripts were written by Axel
+Kohlmeyer (akohlmey at cmm.chem.upenn.edu) at U Penn.</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="matlab-tool">
+<span id="matlab"></span><h2>9.19. matlab tool</h2>
+<p>The matlab sub-directory contains several <a class="reference external" href="http://www.mathworks.com">MATLAB</a> scripts for
+post-processing LAMMPS output.  The scripts include readers for log
+and dump files, a reader for EAM potential files, and a converter that
+reads LAMMPS dump files and produces CFG files that can be visualized
+with the <a class="reference external" href="http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</a>
+visualizer.</p>
+<p>See the README.pdf file for more information.</p>
+<p>These scripts were written by Arun Subramaniyan at Purdue Univ
+(asubrama at purdue.edu).</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="micelle2d-tool">
+<span id="micelle"></span><h2>9.20. micelle2d tool</h2>
+<p>The file micelle2d.f creates a LAMMPS data file containing short lipid
+chains in a monomer solution.  It uses a text file containing lipid
+definition parameters as an input.  The created molecules and solvent
+atoms can strongly overlap, so LAMMPS needs to run the system
+initially with a &#8220;soft&#8221; pair potential to un-overlap it.  The syntax
+for running the tool is</p>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">micelle2d</span> <span class="o">&lt;</span> <span class="n">def</span><span class="o">.</span><span class="n">micelle2d</span> <span class="o">&gt;</span> <span class="n">data</span><span class="o">.</span><span class="n">file</span>
+</pre></div>
+</div>
+<p>See the def.micelle2d file in the tools directory for an example of a
+definition file.  This tool was used to create the system for the
+<a class="reference internal" href="Section_example.html"><span class="doc">micelle example</span></a>.</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="moltemplate-tool">
+<span id="moltemplate"></span><h2>9.21. moltemplate tool</h2>
+<p>The moltemplate sub-directory contains a Python-based tool for
+building molecular systems based on a text-file description, and
+creating LAMMPS data files that encode their molecular topology as
+lists of bonds, angles, dihedrals, etc.  See the README.TXT file for
+more information.</p>
+<p>This tool was written by Andrew Jewett (jewett.aij at gmail.com), who
+supports it.  It has its own WWW page at
+<a class="reference external" href="http://moltemplate.org">http://moltemplate.org</a>.</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="msi2lmp-tool">
+<span id="msi"></span><h2>9.22. msi2lmp tool</h2>
+<p>The msi2lmp sub-directory contains a tool for creating LAMMPS input
+data files from Accelrys&#8217; Insight MD code (formerly MSI/Biosym and
+its Discover MD code).  See the README file for more information.</p>
+<p>This tool was written by John Carpenter (Cray), Michael Peachey
+(Cray), and Steve Lustig (Dupont).  John is now at the Mayo Clinic
+(jec at mayo.edu), but still fields questions about the tool.</p>
+<p>This tool may be out-of-date with respect to the current LAMMPS and
+Insight versions.  Since we don&#8217;t use it at Sandia, you&#8217;ll need to
+experiment with it yourself.</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="phonon-tool">
+<span id="phonon"></span><h2>9.23. phonon tool</h2>
+<p>The phonon sub-directory contains a post-processing tool useful for
+analyzing the output of the <a class="reference internal" href="fix_phonon.html"><span class="doc">fix phonon</span></a> command in
+the USER-PHONON package.</p>
+<p>See the README file for instruction on building the tool and what
+library it needs.  And see the examples/USER/phonon directory
+for example problems that can be post-processed with this tool.</p>
+<p>This tool was written by Ling-Ti Kong at Shanghai Jiao Tong
+University.</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="polymer-bonding-tool">
+<span id="polybond"></span><h2>9.24. polymer bonding tool</h2>
+<p>The polybond sub-directory contains a Python-based tool useful for
+performing &#8220;programmable polymer bonding&#8221;.  The Python file
+lmpsdata.py provides a &#8220;Lmpsdata&#8221; class with various methods which can
+be invoked by a user-written Python script to create data files with
+complex bonding topologies.</p>
+<p>See the Manual.pdf for details and example scripts.</p>
+<p>This tool was written by Zachary Kraus at Georgia Tech.</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="pymol-asphere-tool">
+<span id="pymol"></span><h2>9.25. pymol_asphere tool</h2>
+<p>The pymol_asphere sub-directory contains a tool for converting a
+LAMMPS dump file that contains orientation info for ellipsoidal
+particles into an input file for the <a class="reference external" href="http://www.pymol.org">PyMol visualization package</a> or its <a class="reference external" href="http://sourceforge.net/scm/?type=svn&amp;group_id=4546">open source variant</a>.</p>
+<p>Specifically, the tool triangulates the ellipsoids so they can be
+viewed as true ellipsoidal particles within PyMol.  See the README and
+examples directory within pymol_asphere for more information.</p>
+<p>This tool was written by Mike Brown at Sandia.</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="python-tool">
+<span id="pythontools"></span><h2>9.26. python tool</h2>
+<p>The python sub-directory contains several Python scripts
+that perform common LAMMPS post-processing tasks, such as:</p>
+<ul class="simple">
+<li>extract thermodynamic info from a log file as columns of numbers</li>
+<li>plot two columns of thermodynamic info from a log file using GnuPlot</li>
+<li>sort the snapshots in a dump file by atom ID</li>
+<li>convert multiple <a class="reference internal" href="neb.html"><span class="doc">NEB</span></a> dump files into one dump file for viz</li>
+<li>convert dump files into XYZ, CFG, or PDB format for viz by other packages</li>
+</ul>
+<p>These are simple scripts built on <a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</a> modules.  See the
+README for more info on Pizza.py and how to use these scripts.</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="reax-tool">
+<span id="id2"></span><h2>9.27. reax tool</h2>
+<p>The reax sub-directory contains stand-alond codes that can
+post-process the output of the <a class="reference internal" href="fix_reax_bonds.html"><span class="doc">fix reax/bonds</span></a>
+command from a LAMMPS simulation using <a class="reference internal" href="pair_reax.html"><span class="doc">ReaxFF</span></a>.  See
+the README.txt file for more info.</p>
+<p>These tools were written by Aidan Thompson at Sandia.</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="restart2data-tool">
+<span id="restart"></span><h2>9.28. restart2data tool</h2>
+<div class="admonition note">
+<p class="first admonition-title">Note</p>
+<p class="last">This tool is now obsolete and is not included in the current
+LAMMPS distribution.  This is becaues there is now a
+<a class="reference internal" href="write_data.html"><span class="doc">write_data</span></a> command, which can create a data file
+from within an input script.  Running LAMMPS with the &#8220;-r&#8221;
+<a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a> as follows:</p>
+</div>
+<p>lmp_g++ -r restartfile datafile</p>
+<p>is the same as running a 2-line input script:</p>
+<p>read_restart restartfile
+write_data datafile</p>
+<p>which will produce the same data file that the restart2data tool used
+to create.  The following information is included in case you have an
+older version of LAMMPS which still includes the restart2data tool.</p>
+<p>The file restart2data.cpp converts a binary LAMMPS restart file into
+an ASCII data file.  The syntax for running the tool is</p>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">restart2data</span> <span class="n">restart</span><span class="o">-</span><span class="n">file</span> <span class="n">data</span><span class="o">-</span><span class="n">file</span> <span class="p">(</span><span class="nb">input</span><span class="o">-</span><span class="n">file</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>Input-file is optional and if specified will contain LAMMPS input
+commands for the masses and force field parameters, instead of putting
+those in the data-file.  Only a few force field styles currently
+support this option.</p>
+<p>This tool must be compiled on a platform that can read the binary file
+created by a LAMMPS run, since binary files are not compatible across
+all platforms.</p>
+<p>Note that a text data file has less precision than a binary restart
+file.  Hence, continuing a run from a converted data file will
+typically not conform as closely to a previous run as will restarting
+from a binary restart file.</p>
+<p>If a &#8220;%&#8221; appears in the specified restart-file, the tool expects a set
+of multiple files to exist.  See the <a class="reference internal" href="restart.html"><span class="doc">restart</span></a> and
+<a class="reference internal" href="write_restart.html"><span class="doc">write_restart</span></a> commands for info on how such sets
+of files are written by LAMMPS, and how the files are named.</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="vim-tool">
+<span id="vim"></span><h2>9.29. vim tool</h2>
+<p>The files in the tools/vim directory are add-ons to the VIM editor
+that allow easier editing of LAMMPS input scripts.  See the README.txt
+file for details.</p>
+<p>These files were provided by Gerolf Ziegenhain (gerolf at
+ziegenhain.com)</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="xmgrace-tool">
+<span id="xmgrace"></span><h2>9.30. xmgrace tool</h2>
+<p>The files in the tools/xmgrace directory can be used to plot the
+thermodynamic data in LAMMPS log files via the xmgrace plotting
+package.  There are several tools in the directory that can be used in
+post-processing mode.  The lammpsplot.cpp file can be compiled and
+used to create plots from the current state of a running LAMMPS
+simulation.</p>
+<p>See the README file for details.</p>
+<p>These files were provided by Vikas Varshney (vv0210 at gmail.com)</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="xmovie-tool">
+<span id="xmovie"></span><h2>9.31. xmovie tool</h2>
+<p>The xmovie tool is an X-based visualization package that can read
+LAMMPS dump files and animate them.  It is in its own sub-directory
+with the tools directory.  You may need to modify its Makefile so that
+it can find the appropriate X libraries to link against.</p>
+<p>The syntax for running xmovie is</p>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">xmovie</span> <span class="p">[</span><span class="n">options</span><span class="p">]</span> <span class="n">dump</span><span class="o">.</span><span class="n">file1</span> <span class="n">dump</span><span class="o">.</span><span class="n">file2</span> <span class="o">...</span>
+</pre></div>
+</div>
+<p>If you just type &#8220;xmovie&#8221; you will see a list of options.  Note that
+by default, LAMMPS dump files are in scaled coordinates, so you
+typically need to use the -scale option with xmovie.  When xmovie runs
+it opens a visualization window and a control window.  The control
+options are straightforward to use.</p>
+<p>Xmovie was mostly written by Mike Uttormark (U Wisconsin) while he
+spent a summer at Sandia.  It displays 2d projections of a 3d domain.
+While simple in design, it is an amazingly fast program that can
+render large numbers of atoms very quickly.  It&#8217;s a useful tool for
+debugging LAMMPS input and output and making sure your simulation is
+doing what you think it should.  The animations on the Examples page
+of the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW site</a> were created with xmovie.</p>
+<p>I&#8217;ve lost contact with Mike, so I hope he&#8217;s comfortable with us
+distributing his great tool!</p>
+</div>
+</div>
+
+
+           </div>
+          </div>
+          <footer>
+  
+    <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
+      
+        <a href="Section_modify.html" class="btn btn-neutral float-right" title="10. Modifying &amp; extending LAMMPS" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
+      
+      
+        <a href="Section_perf.html" class="btn btn-neutral" title="8. Performance &amp; scalability" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+      
+    </div>
+  
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>
+        &copy; Copyright 2013 Sandia Corporation.
+    </p>
+  </div>
+  Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
+</footer>
+
+        </div>
+      </div>
+
+    </section>
+
+  </div>
+  
+
+
+  
+
+    <script type="text/javascript">
+        var DOCUMENTATION_OPTIONS = {
+            URL_ROOT:'./',
+            VERSION:'',
+            COLLAPSE_INDEX:false,
+            FILE_SUFFIX:'.html',
+            HAS_SOURCE:  true
+        };
+    </script>
+      <script type="text/javascript" src="_static/jquery.js"></script>
+      <script type="text/javascript" src="_static/underscore.js"></script>
+      <script type="text/javascript" src="_static/doctools.js"></script>
+      <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+      <script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/jquery-1.11.0.min.js"></script>
+      <script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/lightbox.min.js"></script>
+      <script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2-customize/jquery-noconflict.js"></script>
+
+  
+
+  
+  
+    <script type="text/javascript" src="_static/js/theme.js"></script>
+  
+
+  
+  
+  <script type="text/javascript">
+      jQuery(function () {
+          SphinxRtdTheme.StickyNav.enable();
+      });
+  </script>
+   
+
+</body>
+</html>

doc/html/USER/atc/man_add_molecule.html

@@ -0,0 +1,59 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ATC: fix_modify AtC add_molecule</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body>
+<!-- Generated by Doxygen 1.6.1 -->
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul>
+      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
+      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li><a href="dirs.html"><span>Directories</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+
+
+<h1><a class="anchor" id="man_add_molecule">fix_modify AtC add_molecule </a></h1><h2><a class="anchor" id="syntax">
+syntax</a></h2>
+<p>fix_modify_AtC add_molecule &lt;small|large&gt; &lt;TAG&gt; &lt;GROUP_NAME&gt; <br/>
+</p>
+<ul>
+<li>small|large = can be small if molecule size &lt; cutoff radius, must be large otherwise <br/>
+</li>
+<li>&lt;TAG&gt; = tag for tracking a species <br/>
+</li>
+<li>&lt;GROUP_NAME&gt; = name of group that tracking will be applied to <br/>
+ </li>
+</ul>
+<h2><a class="anchor" id="examples">
+examples</a></h2>
+<p><code> group WATERGROUP type 1 2 </code> <br/>
+ <code> fix_modify AtC add_molecule small water WATERGROUP </code> <br/>
+ </p>
+<h2><a class="anchor" id="description">
+description</a></h2>
+<p>Associates a tag with all molecules corresponding to a specified group. <br/>
+ </p>
+<h2><a class="anchor" id="restrictions">
+restrictions</a></h2>
+<h2><a class="anchor" id="related">
+related</a></h2>
+<h2><a class="anchor" id="default">
+default</a></h2>
+<p>No defaults for this command. </p>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
+</body>
+</html>

doc/html/USER/atc/man_add_species.html

@@ -0,0 +1,59 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ATC: fix_modify AtC add_species</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body>
+<!-- Generated by Doxygen 1.6.1 -->
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul>
+      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
+      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li><a href="dirs.html"><span>Directories</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+
+
+<h1><a class="anchor" id="man_add_species">fix_modify AtC add_species </a></h1><h2><a class="anchor" id="syntax">
+syntax</a></h2>
+<p>fix_modify_AtC add_species &lt;TAG&gt; &lt;group|type&gt; &lt;ID&gt; <br/>
+</p>
+<ul>
+<li>&lt;TAG&gt; = tag for tracking a species <br/>
+</li>
+<li>group|type = LAMMPS defined group or type of atoms <br/>
+</li>
+<li>&lt;ID&gt; = name of group or type number <br/>
+ </li>
+</ul>
+<h2><a class="anchor" id="examples">
+examples</a></h2>
+<p><code> fix_modify AtC add_species gold type 1 </code> <br/>
+ <code> group GOLDGROUP type 1 </code> <br/>
+ <code> fix_modify AtC add_species gold group GOLDGROUP </code> </p>
+<h2><a class="anchor" id="description">
+description</a></h2>
+<p>Associates a tag with all atoms of a specified type or within a specified group. <br/>
+ </p>
+<h2><a class="anchor" id="restrictions">
+restrictions</a></h2>
+<h2><a class="anchor" id="related">
+related</a></h2>
+<h2><a class="anchor" id="default">
+default</a></h2>
+<p>No defaults for this command. </p>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
+</body>
+</html>

doc/html/USER/atc/man_atom_element_map.html

@@ -0,0 +1,52 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ATC: fix_modify AtC atom_element_map</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body>
+<!-- Generated by Doxygen 1.6.1 -->
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul>
+      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
+      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li><a href="dirs.html"><span>Directories</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+
+
+<h1><a class="anchor" id="man_atom_element_map">fix_modify AtC atom_element_map </a></h1><h2><a class="anchor" id="syntax">
+syntax</a></h2>
+<p>fix_modify AtC atom_element_map &lt;eulerian|lagrangian&gt; &lt;frequency&gt; <br/>
+</p>
+<ul>
+<li>frequency (int) : frequency of updating atom-to-continuum maps based on the current configuration - only for eulerian </li>
+</ul>
+<h2><a class="anchor" id="examples">
+examples</a></h2>
+<p><code> fix_modify atc atom_element_map eulerian 100 </code> </p>
+<h2><a class="anchor" id="description">
+description</a></h2>
+<p>Changes frame of reference from eulerian to lagrangian and sets the frequency for which the map from atoms to elements is reformed and all the attendant data is recalculated. </p>
+<h2><a class="anchor" id="restrictions">
+restrictions</a></h2>
+<p>Cannot change map type after initialization. </p>
+<h2><a class="anchor" id="related">
+related</a></h2>
+<h2><a class="anchor" id="default">
+default</a></h2>
+<p>lagrangian </p>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
+</body>
+</html>

doc/html/USER/atc/man_atom_weight.html

@@ -0,0 +1,61 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ATC: fix_modify AtC atom_weight</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body>
+<!-- Generated by Doxygen 1.6.1 -->
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul>
+      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
+      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li><a href="dirs.html"><span>Directories</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+
+
+<h1><a class="anchor" id="man_atom_weight">fix_modify AtC atom_weight </a></h1><h2><a class="anchor" id="syntax">
+syntax</a></h2>
+<p>fix_modify AtC atom_weight &lt;method&gt; &lt;arguments&gt;</p>
+<ul>
+<li>&lt;method&gt; = <br/>
+ value: atoms in specified group assigned constant value given <br/>
+ lattice: volume per atom for specified lattice type (e.g. fcc) and parameter <br/>
+ element: element volume divided among atoms within element <br/>
+ region: volume per atom determined based on the atom count in the MD regions and their volumes. Note: meaningful only if atoms completely fill all the regions. <br/>
+ group: volume per atom determined based on the atom count in a group and its volume<br/>
+ read_in: list of values for atoms are read-in from specified file <br/>
+ </li>
+</ul>
+<h2><a class="anchor" id="examples">
+examples</a></h2>
+<p><code> fix_modify atc atom_weight constant myatoms 11.8 </code> <br/>
+ <code> fix_modify atc atom_weight lattice </code> <br/>
+ <code> fix_modify atc atom_weight read-in atm_wt_file.txt </code> <br/>
+ </p>
+<h2><a class="anchor" id="description">
+description</a></h2>
+<p>Command for assigning the value of atomic weights used for atomic integration in atom-continuum coupled simulations. </p>
+<h2><a class="anchor" id="restrictions">
+restrictions</a></h2>
+<p>Use of lattice option requires a lattice type and parameter is already specified. </p>
+<h2><a class="anchor" id="related">
+related</a></h2>
+<h2><a class="anchor" id="default">
+default</a></h2>
+<p>lattice </p>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
+</body>
+</html>

doc/html/USER/atc/man_atomic_charge.html

@@ -0,0 +1,51 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ATC: fix_modify AtC atomic_charge</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body>
+<!-- Generated by Doxygen 1.6.1 -->
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul>
+      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
+      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li><a href="dirs.html"><span>Directories</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+
+
+<h1><a class="anchor" id="man_atomic_charge">fix_modify AtC atomic_charge </a></h1><h2><a class="anchor" id="syntax">
+syntax</a></h2>
+<p>fix_modify AtC &lt;include | omit&gt; atomic_charge</p>
+<ul>
+<li>&lt;include | omit&gt; = switch to activiate/deactiviate inclusion of intrinsic atomic charge in <a class="el" href="namespaceATC.html" title="owned field/s: MASS_DENSITY">ATC</a> </li>
+</ul>
+<h2><a class="anchor" id="examples">
+examples</a></h2>
+<p><code> fix_modify atc compute include atomic_charge </code> </p>
+<h2><a class="anchor" id="description">
+description</a></h2>
+<p>Determines whether AtC tracks the total charge as a finite element field </p>
+<h2><a class="anchor" id="restrictions">
+restrictions</a></h2>
+<p>Required for: electrostatics </p>
+<h2><a class="anchor" id="related">
+related</a></h2>
+<h2><a class="anchor" id="default">
+default</a></h2>
+<p>if the atom charge is defined, default is on, otherwise default is off </p>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
+</body>
+</html>

doc/html/USER/atc/man_boundary.html

@@ -0,0 +1,48 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ATC: fix_modify AtC boundary</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body>
+<!-- Generated by Doxygen 1.6.1 -->
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul>
+      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
+      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li><a href="dirs.html"><span>Directories</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+
+
+<h1><a class="anchor" id="man_boundary">fix_modify AtC boundary </a></h1><h2><a class="anchor" id="syntax">
+syntax</a></h2>
+<p>fix_modify AtC boundary type &lt;atom-type-id&gt;</p>
+<ul>
+<li>&lt;atom-type-id&gt; = type id for atoms that represent a ficticious boundary internal to the FE mesh </li>
+</ul>
+<h2><a class="anchor" id="examples">
+examples</a></h2>
+<p><code> fix_modify AtC boundary type ghost_atoms </code> </p>
+<h2><a class="anchor" id="description">
+description</a></h2>
+<p>Command to define the atoms that represent the ficticious boundary internal to the FE mesh. For fully overlapped MD/FE domains with periodic boundary conditions no boundary atoms should be defined. </p>
+<h2><a class="anchor" id="restrictions">
+restrictions</a></h2>
+<h2><a class="anchor" id="default">
+default</a></h2>
+<p>none </p>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
+</body>
+</html>

doc/html/USER/atc/man_boundary_dynamics.html

@@ -0,0 +1,46 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ATC: fix_modify AtC boundary_dynamics</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body>
+<!-- Generated by Doxygen 1.6.1 -->
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul>
+      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
+      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li><a href="dirs.html"><span>Directories</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+
+
+<h1><a class="anchor" id="man_boundary_dynamics">fix_modify AtC boundary_dynamics </a></h1><h2><a class="anchor" id="syntax">
+syntax</a></h2>
+<p>fix_modify AtC boundary_dynamics &lt; on | damped_harmonic | prescribed | coupled | none &gt; [args] <br/>
+ </p>
+<h2><a class="anchor" id="description">
+description</a></h2>
+<p>Sets different schemes for controlling boundary atoms. On will integrate the boundary atoms using the velocity-verlet algorithm. Damped harmonic uses a mass/spring/dashpot for the boundary atoms with added arguments of the damping and spring constants followed by the ratio of the boundary type mass to the desired mass. Prescribed forces the boundary atoms to follow the finite element displacement. Coupled does the same. </p>
+<h2><a class="anchor" id="restrictions">
+restrictions</a></h2>
+<p>Boundary atoms must be specified. When using swaps between internal and boundary atoms, the initial configuration must have already correctly partitioned the two. </p>
+<h2><a class="anchor" id="related">
+related</a></h2>
+<h2><a class="anchor" id="default">
+default</a></h2>
+<p>prescribed on </p>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
+</body>
+</html>

doc/html/USER/atc/man_boundary_faceset.html

@@ -0,0 +1,47 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ATC: fix_modify AtC boundary_faceset</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body>
+<!-- Generated by Doxygen 1.6.1 -->
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul>
+      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
+      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li><a href="dirs.html"><span>Directories</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+
+
+<h1><a class="anchor" id="man_boundary_faceset">fix_modify AtC boundary_faceset </a></h1><h2><a class="anchor" id="syntax">
+syntax</a></h2>
+<p>fix_modify AtC boundary_faceset &lt;is | add&gt; [args] </p>
+<h2><a class="anchor" id="examples">
+examples</a></h2>
+<p>fix_modify AtC boundary_faceset is obndy </p>
+<h2><a class="anchor" id="description">
+description</a></h2>
+<p>This command species the faceset name when using a faceset to compute the MD/FE boundary fluxes. The faceset must already exist. </p>
+<h2><a class="anchor" id="restrictions">
+restrictions</a></h2>
+<p>This is only valid when fe_md_boundary is set to faceset. </p>
+<h2><a class="anchor" id="related">
+related</a></h2>
+<h2><a class="anchor" id="default">
+default</a></h2>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
+</body>
+</html>

doc/html/USER/atc/man_boundary_integral.html

@@ -0,0 +1,53 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ATC: fix_modify AtC output boundary_integral</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body>
+<!-- Generated by Doxygen 1.6.1 -->
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul>
+      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
+      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li><a href="dirs.html"><span>Directories</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+
+
+<h1><a class="anchor" id="man_boundary_integral">fix_modify AtC output boundary_integral </a></h1><h2><a class="anchor" id="syntax">
+syntax</a></h2>
+<p>fix_modify AtC output boundary_integral [field] faceset [name]</p>
+<ul>
+<li>field (string) : name of hardy field</li>
+<li>name (string) : name of faceset </li>
+</ul>
+<h2><a class="anchor" id="examples">
+examples</a></h2>
+<p><code> fix_modify AtC output boundary_integral stress faceset loop1 </code> <br/>
+ </p>
+<h2><a class="anchor" id="description">
+description</a></h2>
+<p>Calculates a surface integral of the given field dotted with the outward normal of the faces and puts output in the "GLOBALS" file </p>
+<h2><a class="anchor" id="restrictions">
+restrictions</a></h2>
+<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
+<h2><a class="anchor" id="related">
+related</a></h2>
+<h2><a class="anchor" id="default">
+default</a></h2>
+<p>none </p>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
+</body>
+</html>

doc/html/USER/atc/man_consistent_fe_initialization.html

@@ -0,0 +1,51 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ATC: fix_modify AtC consistent_fe_initialization</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body>
+<!-- Generated by Doxygen 1.6.1 -->
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul>
+      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
+      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li><a href="dirs.html"><span>Directories</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+
+
+<h1><a class="anchor" id="man_consistent_fe_initialization">fix_modify AtC consistent_fe_initialization </a></h1><h2><a class="anchor" id="syntax">
+syntax</a></h2>
+<p>fix_modify AtC consistent_fe_initialization &lt;on | off&gt;</p>
+<ul>
+<li>&lt;on|off&gt; = switch to activiate/deactiviate the intial setting of FE intrinsic field to match the projected MD field </li>
+</ul>
+<h2><a class="anchor" id="examples">
+examples</a></h2>
+<p><code> fix_modify atc consistent_fe_initialization on </code> </p>
+<h2><a class="anchor" id="description">
+description</a></h2>
+<p>Determines whether AtC initializes FE intrinsic fields (e.g., temperature) to match the projected MD values. This is particularly useful for fully overlapping simulations. </p>
+<h2><a class="anchor" id="restrictions">
+restrictions</a></h2>
+<p>Can be used with: thermal, two_temperature. Cannot be used with time filtering on. Does not include boundary nodes. </p>
+<h2><a class="anchor" id="related">
+related</a></h2>
+<h2><a class="anchor" id="default">
+default</a></h2>
+<p>Default is off </p>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
+</body>
+</html>

doc/html/USER/atc/man_contour_integral.html

@@ -0,0 +1,54 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ATC: fix_modify AtC output contour_integral</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body>
+<!-- Generated by Doxygen 1.6.1 -->
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul>
+      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
+      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li><a href="dirs.html"><span>Directories</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+
+
+<h1><a class="anchor" id="man_contour_integral">fix_modify AtC output contour_integral </a></h1><h2><a class="anchor" id="syntax">
+syntax</a></h2>
+<p>fix_modify AtC output contour_integral [field] faceset [name] &lt;axis [x | y | z ]&gt;</p>
+<ul>
+<li>field (string) : name of hardy field</li>
+<li>name (string) : name of faceset</li>
+<li>axis (string) : x or y or z </li>
+</ul>
+<h2><a class="anchor" id="examples">
+examples</a></h2>
+<p><code> fix_modify AtC output contour_integral stress faceset loop1 </code> <br/>
+ </p>
+<h2><a class="anchor" id="description">
+description</a></h2>
+<p>Calculates a surface integral of the given field dotted with the outward normal of the faces and puts output in the "GLOBALS" file </p>
+<h2><a class="anchor" id="restrictions">
+restrictions</a></h2>
+<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
+<h2><a class="anchor" id="related">
+related</a></h2>
+<h2><a class="anchor" id="default">
+default</a></h2>
+<p>none </p>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
+</body>
+</html>

doc/html/USER/atc/man_control.html

@@ -0,0 +1,72 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ATC: fix_modify AtC control</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body>
+<!-- Generated by Doxygen 1.6.1 -->
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul>
+      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
+      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li><a href="dirs.html"><span>Directories</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+
+
+<h1><a class="anchor" id="man_control">fix_modify AtC control </a></h1><h2><a class="anchor" id="syntax">
+syntax</a></h2>
+<p>fix_modify AtC control &lt;physics_type&gt; &lt;solution_parameter&gt; </p>
+<p><br/>
+</p>
+<ul>
+<li>physics_type (string) = thermal | momentum<br/>
+</li>
+<li>solution_parameter (string) = max_iterations | tolerance<br/>
+</li>
+</ul>
+<p>fix_modify AtC transfer &lt;physics_type&gt; control max_iterations &lt;max_iterations&gt;<br/>
+</p>
+<ul>
+<li>max_iterations (int) = maximum number of iterations that will be used by iterative matrix solvers<br/>
+</li>
+</ul>
+<p>fix_modify AtC transfer &lt;physics_type&gt; control tolerance &lt;tolerance&gt; <br/>
+</p>
+<ul>
+<li>tolerance (float) = relative tolerance to which matrix equations will be solved<br/>
+</li>
+</ul>
+<h2><a class="anchor" id="examples">
+examples</a></h2>
+<p><code> fix_modify AtC control thermal max_iterations 10 </code> <br/>
+ <code> fix_modify AtC control momentum tolerance 1.e-5 </code> <br/>
+ </p>
+<h2><a class="anchor" id="description">
+description</a></h2>
+<p>Sets the numerical parameters for the matrix solvers used in the specified control algorithm. Many solution approaches require iterative solvers, and these methods enable users to provide the maximum number of iterations and the relative tolerance. </p>
+<h2><a class="anchor" id="restrictions">
+restrictions</a></h2>
+<p>only for be used with specific controllers : thermal, momentum <br/>
+ They are ignored if a lumped solution is requested </p>
+<h2><a class="anchor" id="related">
+related</a></h2>
+<h2><a class="anchor" id="default">
+default</a></h2>
+<p>max_iterations is the number of rows in the matrix<br/>
+ tolerance is 1.e-10 </p>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
+</body>
+</html>

doc/html/USER/atc/man_control_momentum.html

@@ -0,0 +1,68 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ATC: fix_modify AtC control momentum</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body>
+<!-- Generated by Doxygen 1.6.1 -->
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul>
+      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
+      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li><a href="dirs.html"><span>Directories</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+
+
+<h1><a class="anchor" id="man_control_momentum">fix_modify AtC control momentum </a></h1><h2><a class="anchor" id="syntax">
+syntax</a></h2>
+<p>fix_modify AtC control momentum none <br/>
+</p>
+<p>fix_modify AtC control momentum rescale &lt;frequency&gt;<br/>
+</p>
+<ul>
+<li>frequency (int) = time step frequency for applying displacement and velocity rescaling <br/>
+</li>
+</ul>
+<p>fix_modify AtC control momentum glc_displacement <br/>
+</p>
+<p>fix_modify AtC control momentum glc_velocity <br/>
+</p>
+<p>fix_modify AtC control momentum hoover <br/>
+</p>
+<p>fix_modify AtC control momentum flux [faceset face_set_id, interpolate]</p>
+<ul>
+<li>face_set_id (string) = id of boundary face set, if not specified (or not possible when the atomic domain does not line up with mesh boundaries) defaults to an atomic-quadrature approximate evaulation<br/>
+ </li>
+</ul>
+<h2><a class="anchor" id="examples">
+examples</a></h2>
+<p>fix_modify AtC control momentum glc_velocity <br/>
+ fix_modify AtC control momentum flux faceset bndy_faces <br/>
+ </p>
+<h2><a class="anchor" id="description">
+description</a></h2>
+<h2><a class="anchor" id="restrictions">
+restrictions</a></h2>
+<p>only to be used with specific transfers : elastic <br/>
+ rescale not valid with time filtering activated </p>
+<h2><a class="anchor" id="related">
+related</a></h2>
+<h2><a class="anchor" id="default">
+default</a></h2>
+<p>none </p>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
+</body>
+</html>

doc/html/USER/atc/man_control_thermal.html

@@ -0,0 +1,76 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ATC: fix_modify AtC control thermal</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body>
+<!-- Generated by Doxygen 1.6.1 -->
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul>
+      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
+      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li><a href="dirs.html"><span>Directories</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+
+
+<h1><a class="anchor" id="man_control_thermal">fix_modify AtC control thermal </a></h1><h2><a class="anchor" id="syntax">
+syntax</a></h2>
+<p>fix_modify AtC control thermal &lt;control_type&gt; &lt;optional_args&gt;</p>
+<ul>
+<li>control_type (string) = none | rescale | hoover | flux<br/>
+</li>
+</ul>
+<p>fix_modify AtC control thermal rescale &lt;frequency&gt; <br/>
+</p>
+<ul>
+<li>frequency (int) = time step frequency for applying velocity rescaling <br/>
+</li>
+</ul>
+<p>fix_modify AtC control thermal hoover <br/>
+</p>
+<p>fix_modify AtC control thermal flux &lt;boundary_integration_type(optional)&gt; &lt;face_set_id(optional)&gt;<br/>
+</p>
+<ul>
+<li>boundary_integration_type (string) = faceset | interpolate<br/>
+</li>
+<li>face_set_id (string), optional = id of boundary face set, if not specified (or not possible when the atomic domain does not line up with mesh boundaries) defaults to an atomic-quadrature approximate evaulation, does not work with interpolate<br/>
+ </li>
+</ul>
+<h2><a class="anchor" id="examples">
+examples</a></h2>
+<p><code> fix_modify AtC control thermal none </code> <br/>
+ <code> fix_modify AtC control thermal rescale 10 </code> <br/>
+ <code> fix_modify AtC control thermal hoover </code> <br/>
+ <code> fix_modify AtC control thermal flux </code> <br/>
+ <code> fix_modify AtC control thermal flux faceset bndy_faces </code> <br/>
+ </p>
+<h2><a class="anchor" id="description">
+description</a></h2>
+<p>Sets the energy exchange mechansim from the finite elements to the atoms, managed through a control algorithm. Rescale computes a scale factor for each atom to match the finite element temperature. Hoover is a Gaussian least-constraint isokinetic thermostat enforces that the nodal restricted atomic temperature matches the finite element temperature. Flux is a similar mode, but rather adds energy to the atoms based on conservation of energy. Hoover and flux allows the prescription of sources or fixed temperatures on the atoms. </p>
+<h2><a class="anchor" id="restrictions">
+restrictions</a></h2>
+<p>only for be used with specific transfers : thermal (rescale, hoover, flux), two_temperature (flux) <br/>
+ rescale not valid with time filtering activated </p>
+<h2><a class="anchor" id="related">
+related</a></h2>
+<h2><a class="anchor" id="default">
+default</a></h2>
+<p>none<br/>
+ rescale frequency is 1<br/>
+ flux boundary_integration_type is interpolate </p>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
+</body>
+</html>

doc/html/USER/atc/man_control_thermal_correction_max_iterations.html

@@ -0,0 +1,53 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ATC: fix_modify AtC control thermal correction_max_iterations</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body>
+<!-- Generated by Doxygen 1.6.1 -->
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul>
+      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
+      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li><a href="dirs.html"><span>Directories</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+
+
+<h1><a class="anchor" id="man_control_thermal_correction_max_iterations">fix_modify AtC control thermal correction_max_iterations </a></h1><h2><a class="anchor" id="syntax">
+syntax</a></h2>
+<p>fix_modify AtC control thermal correction_max_iterations &lt;max_iterations&gt;</p>
+<ul>
+<li>max_iterations (int) = maximum number of iterations that will be used by iterative matrix solvers<br/>
+</li>
+</ul>
+<h2><a class="anchor" id="examples">
+examples</a></h2>
+<p><code> fix_modify AtC control thermal correction_max_iterations 10 </code> <br/>
+ </p>
+<h2><a class="anchor" id="description">
+description</a></h2>
+<p>Sets the maximum number of iterations to compute the 2nd order in time correction term for lambda with the fractional step method. The method uses the same tolerance as the controller's matrix solver. </p>
+<h2><a class="anchor" id="restrictions">
+restrictions</a></h2>
+<p>only for use with thermal physics using the fractional step method. </p>
+<h2><a class="anchor" id="related">
+related</a></h2>
+<h2><a class="anchor" id="default">
+default</a></h2>
+<p>correction_max_iterations is 20 </p>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
+</body>
+</html>

doc/html/USER/atc/man_decomposition.html

@@ -0,0 +1,55 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ATC: fix_modify AtC decomposition</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body>
+<!-- Generated by Doxygen 1.6.1 -->
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul>
+      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
+      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li><a href="dirs.html"><span>Directories</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+
+
+<h1><a class="anchor" id="man_decomposition">fix_modify AtC decomposition </a></h1><h2><a class="anchor" id="syntax">
+syntax</a></h2>
+<p>fix_modify AtC decomposition &lt;type&gt;</p>
+<ul>
+<li>&lt;type&gt; = <br/>
+ replicated_memory: nodal information replicated on each processor <br/>
+ distributed_memory: only owned nodal information on processor <br/>
+ </li>
+</ul>
+<h2><a class="anchor" id="examples">
+examples</a></h2>
+<p><code> fix_modify atc decomposition distributed_memory </code> <br/>
+ </p>
+<h2><a class="anchor" id="description">
+description</a></h2>
+<p>Command for assigning the distribution of work and memory for parallel runs. </p>
+<h2><a class="anchor" id="restrictions">
+restrictions</a></h2>
+<p>replicated_memory is appropriate for simulations were the number of nodes &lt;&lt; number of atoms </p>
+<h2><a class="anchor" id="related">
+related</a></h2>
+<h2><a class="anchor" id="default">
+default</a></h2>
+<p>replicated_memory </p>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
+</body>
+</html>

doc/html/USER/atc/man_electron_integration.html

@@ -0,0 +1,56 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ATC: fix_modify AtC extrinsic electron_integration</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body>
+<!-- Generated by Doxygen 1.6.1 -->
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul>
+      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
+      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li><a href="dirs.html"><span>Directories</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+
+
+<h1><a class="anchor" id="man_electron_integration">fix_modify AtC extrinsic electron_integration </a></h1><h2><a class="anchor" id="syntax">
+syntax</a></h2>
+<p>fix_modify AtC extrinsic electron_integration &lt;integration_type&gt; &lt;num_subcyle_steps(optional)&gt; <br/>
+</p>
+<ul>
+<li>integration_type (string) = explicit | implicit | steady <br/>
+</li>
+<li>num_subcycle_steps (int), optional = number of subcycle steps for the electron time integration</li>
+</ul>
+<h2><a class="anchor" id="examples">
+examples</a></h2>
+<p><code> fix_modify AtC extrinsic electron_integration implicit </code> <br/>
+ <code> fix_modify AtC extrinsic electron_integration explicit 100 </code> <br/>
+</p>
+<h2><a class="anchor" id="description">
+description</a></h2>
+<p>Switches between integration scheme for the electron temperature. The number of subcyling steps used to integrate the electron temperature 1 LAMMPS timestep can be manually adjusted to capture fast electron dynamics.</p>
+<h2><a class="anchor" id="restrictions">
+restrictions</a></h2>
+<p>For use only with two_temperature type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) <br/>
+ </p>
+<h2><a class="anchor" id="default">
+default</a></h2>
+<p>implicit<br/>
+ subcycle_steps = 1 </p>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
+</body>
+</html>

doc/html/USER/atc/man_equilibrium_start.html

@@ -0,0 +1,50 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ATC: fix_modify AtC equilibrium_start</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body>
+<!-- Generated by Doxygen 1.6.1 -->
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul>
+      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
+      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li><a href="dirs.html"><span>Directories</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+
+
+<h1><a class="anchor" id="man_equilibrium_start">fix_modify AtC equilibrium_start </a></h1><h2><a class="anchor" id="syntax">
+syntax</a></h2>
+<p>fix_modify AtC equilibrium_start &lt;on|off&gt;</p>
+<h2><a class="anchor" id="examples">
+examples</a></h2>
+<p><code> fix_modify atc equilibrium_start on </code> <br/>
+</p>
+<h2><a class="anchor" id="description">
+description</a></h2>
+<p>Starts filtered calculations assuming they start in equilibrium, i.e. perfect finite element force balance.</p>
+<h2><a class="anchor" id="restrictions">
+restrictions</a></h2>
+<p>only needed before filtering is begun</p>
+<h2><a class="anchor" id="related">
+related</a></h2>
+<p>see <a class="el" href="man_time_filter.html">fix_modify AtC filter</a></p>
+<h2><a class="anchor" id="default">
+default</a></h2>
+<p>on </p>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
+</body>
+</html>

doc/html/USER/atc/man_extrinsic_exchange.html

@@ -0,0 +1,50 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ATC: fix_modify AtC extrinsic exchange</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body>
+<!-- Generated by Doxygen 1.6.1 -->
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul>
+      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
+      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li><a href="dirs.html"><span>Directories</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+
+
+<h1><a class="anchor" id="man_extrinsic_exchange">fix_modify AtC extrinsic exchange </a></h1><h2><a class="anchor" id="syntax">
+syntax</a></h2>
+<p>fix_modify AtC extrinsic exchange &lt;on|off&gt;</p>
+<h2><a class="anchor" id="examples">
+examples</a></h2>
+<p><code> fix_modify AtC extrinsic exchange on </code> <br/>
+</p>
+<h2><a class="anchor" id="description">
+description</a></h2>
+<p>Switches energy exchange between the MD system and electron system on and off</p>
+<h2><a class="anchor" id="restrictions">
+restrictions</a></h2>
+<p>Only valid for use with two_temperature type of AtC fix.</p>
+<h2><a class="anchor" id="related">
+related</a></h2>
+<p>see <a class="el" href="man_fix_atc.html">fix atc command</a></p>
+<h2><a class="anchor" id="default">
+default</a></h2>
+<p>on </p>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
+</body>
+</html>

doc/html/USER/atc/man_fe_md_boundary.html

@@ -0,0 +1,50 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ATC: fix_modify AtC fe_md_boundary</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body>
+<!-- Generated by Doxygen 1.6.1 -->
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul>
+      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
+      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li><a href="dirs.html"><span>Directories</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+
+
+<h1><a class="anchor" id="man_fe_md_boundary">fix_modify AtC fe_md_boundary </a></h1><h2><a class="anchor" id="syntax">
+syntax</a></h2>
+<p>fix_modify AtC fe_md_boundary &lt;faceset | interpolate | no_boundary&gt; [args] </p>
+<h2><a class="anchor" id="examples">
+examples</a></h2>
+<p><code> fix_modify atc fe_md_boundary interpolate </code> <br/>
+ </p>
+<h2><a class="anchor" id="description">
+description</a></h2>
+<p>Specifies different methods for computing fluxes between between the MD and FE integration regions. Faceset defines a faceset separating the MD and FE regions and uses finite element face quadrature to compute the flux. Interpolate uses a reconstruction scheme to approximate the flux, which is more robust but less accurate if the MD/FE boundary does correspond to a faceset. No boundary results in no fluxes between the systems being computed. </p>
+<h2><a class="anchor" id="restrictions">
+restrictions</a></h2>
+<p>If faceset is used, all the AtC non-boundary atoms must lie within and completely fill the domain enclosed by the faceset. </p>
+<h2><a class="anchor" id="related">
+related</a></h2>
+<p>see  for how to specify the faceset name. </p>
+<h2><a class="anchor" id="default">
+default</a></h2>
+<p>Interpolate. </p>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
+</body>
+</html>

doc/html/USER/atc/man_fem_mesh.html

@@ -0,0 +1,25 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1">
+<title>ATC: fix_modify AtC fem create mesh</title>
+<link href="doxygen.css" rel="stylesheet" type="text/css">
+</head><body>
+<!-- Generated by Doxygen 1.3.9.1 -->
+<h1><a class="anchor" name="man_fem_mesh">fix_modify AtC fem create mesh</a></h1><h2><a class="anchor" name="syntax">
+syntax</a></h2>
+fix_modify AtC fem create mesh &lt;nx&gt; &lt;ny&gt; &lt;nz&gt; &lt;region-id&gt; &lt;f|p&gt; &lt;f|p&gt; &lt;f|p&gt;<ul>
+<li>nx ny nz = number of elements in x, y, z</li><li>region-id = id of region that is to be meshed</li><li>f p p = perioidicity flags for x, y, z </li></ul>
+<h2><a class="anchor" name="examples">
+examples</a></h2>
+<code> fix_modify AtC fem create mesh 10 1 1 feRegion p p p </code> <h2><a class="anchor" name="description">
+description</a></h2>
+Creates a uniform mesh in a rectangular region <h2><a class="anchor" name="restrictions">
+restrictions</a></h2>
+creates only uniform rectangular grids in a rectangular region <h2><a class="anchor" name="related">
+related</a></h2>
+<h2><a class="anchor" name="default">
+default</a></h2>
+none <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by&nbsp;
+<a href="http://www.doxygen.org/index.html">
+<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.3.9.1 </small></address>
+</body>
+</html>