patch 21Feb17 sync with GHub

collected small bugfixes and updates

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

@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
 # FENE beadspring benchmark
 
 units		lj
@@ -43,25 +43,25 @@ Neighbor list info ...
   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
+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 0.978585 on 1 procs for 100 steps with 32000 atoms
+Loop time of 0.977647 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
+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    | 0.19562    | 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
+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

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

@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
 # FENE beadspring benchmark
 
 units		lj
@@ -43,25 +43,25 @@ Neighbor list info ...
   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
+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 0.271187 on 4 procs for 100 steps with 32000 atoms
+Loop time of 0.269205 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
+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    | 0.048621   | 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
+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

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

@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
 # FENE beadspring benchmark
 
 variable	x index 1
@@ -59,25 +59,25 @@ Neighbor list info ...
   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
+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 1.20889 on 4 procs for 100 steps with 128000 atoms
+Loop time of 1.14845 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
+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    | 0.21738    | 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
+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

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

@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
 # LAMMPS benchmark of granular flow
 # chute flow of 32000 atoms with frozen base at 26 degrees
 
@@ -47,24 +47,24 @@ Neighbor list info ...
   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 
+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 0.550482 on 1 procs for 100 steps with 32000 atoms
+Loop time of 0.534174 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
+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    | 0.33849    | 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
+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

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

@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
 # LAMMPS benchmark of granular flow
 # chute flow of 32000 atoms with frozen base at 26 degrees
 
@@ -47,24 +47,24 @@ Neighbor list info ...
   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 
+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 0.13141 on 4 procs for 100 steps with 32000 atoms
+Loop time of 0.171815 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
+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    | 0.062505   | 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
+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

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

@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
 # LAMMPS benchmark of granular flow
 # chute flow of 32000 atoms with frozen base at 26 degrees
 
@@ -57,24 +57,24 @@ Neighbor list info ...
   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 
+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 0.906913 on 4 procs for 100 steps with 128000 atoms
+Loop time of 0.832365 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
+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    | 0.51454    | 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
+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
@@ -87,4 +87,4 @@ Total # of neighbors = 460532
 Ave neighs/atom = 3.59791
 Neighbor list builds = 2
 Dangerous builds = 0
-Total wall time: 0:00:01
+Total wall time: 0:00:00

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

@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
 # bulk Cu lattice
 
 variable	x index 1
@@ -49,25 +49,25 @@ Neighbor list info ...
   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
+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 5.90097 on 1 procs for 100 steps with 32000 atoms
+Loop time of 5.96529 on 1 procs for 100 steps with 32000 atoms
 
-Performance: 7.321 ns/day, 3.278 hours/ns, 16.946 timesteps/s
+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    | 5.2121     | 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
+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

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

@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
 # bulk Cu lattice
 
 variable	x index 1
@@ -49,25 +49,25 @@ Neighbor list info ...
   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
+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 1.58019 on 4 procs for 100 steps with 32000 atoms
+Loop time of 1.64562 on 4 procs for 100 steps with 32000 atoms
 
-Performance: 27.338 ns/day, 0.878 hours/ns, 63.284 timesteps/s
+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    | 1.3617     | 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
+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

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

@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
 # bulk Cu lattice
 
 variable	x index 1
@@ -49,25 +49,25 @@ Neighbor list info ...
   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
+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 6.46849 on 4 procs for 100 steps with 128000 atoms
+Loop time of 6.60121 on 4 procs for 100 steps with 128000 atoms
 
-Performance: 6.679 ns/day, 3.594 hours/ns, 15.460 timesteps/s
+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    | 5.581      | 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
+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

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

@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
 # 3d Lennard-Jones melt
 
 variable	x index 1
@@ -50,20 +50,20 @@ 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
+Loop time of 2.26185 on 1 procs for 100 steps with 32000 atoms
 
-Performance: 19088.920 tau/day, 44.187 timesteps/s
+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    | 1.9341     | 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
+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

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

@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
 # 3d Lennard-Jones melt
 
 variable	x index 1
@@ -50,20 +50,20 @@ 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
+Loop time of 0.635957 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
+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    | 0.49487    | 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
+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

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

@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
 # 3d Lennard-Jones melt
 
 variable	x index 1
@@ -50,20 +50,20 @@ 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
+Loop time of 2.55762 on 4 procs for 100 steps with 128000 atoms
 
-Performance: 16749.768 tau/day, 38.773 timesteps/s
+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    | 2.042      | 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
+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

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

@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
 # Rhodopsin model
 
 units           real
@@ -56,6 +56,7 @@ 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
@@ -70,41 +71,41 @@ Neighbor list info ...
   master list distance cutoff = 12
   ghost atom cutoff = 12
   binsize = 6 -> bins = 10 13 13
-Memory usage per processor = 91.7487 Mbytes
+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    =      -142.6035 
+E_coul   =    207025.8927 E_long   =   -270403.7333 Press    =      -149.3301 
 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
+---------------- 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: 0.481 ns/day, 49.874 hours/ns, 2.785 timesteps/s
+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    | 25.731     | 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
+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
@@ -113,9 +114,9 @@ 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
+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: 0:00:37
+Total wall time: 0:00:36

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

@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
 # Rhodopsin model
 
 units           real
@@ -56,6 +56,7 @@ 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
@@ -70,52 +71,52 @@ Neighbor list info ...
   master list distance cutoff = 12
   ghost atom cutoff = 12
   binsize = 6 -> bins = 10 13 13
-Memory usage per processor = 36.629 Mbytes
+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    =      -142.6035 
+E_coul   =    207025.8927 E_long   =   -270403.7333 Press    =      -149.3301 
 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
+---------------- 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: 1.794 ns/day, 13.379 hours/ns, 10.381 timesteps/s
-99.9% CPU use with 4 MPI tasks x no OpenMP threads
+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    | 6.4364     | 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
+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:    3.00703e+06 ave 3.0975e+06 max 2.96493e+06 min
+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 = 12028107
+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: 0:00:10
+Total wall time: 0:00:09

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

@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
 # Rhodopsin model
 
 variable	x index 1
@@ -77,6 +77,7 @@ 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
@@ -91,52 +92,52 @@ Neighbor list info ...
   master list distance cutoff = 12
   ghost atom cutoff = 12
   binsize = 6 -> bins = 19 26 13
-Memory usage per processor = 95.5339 Mbytes
+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    =      -142.3092 
+E_coul   =    827053.5824 E_long   =  -1080565.6077 Press    =      -149.0358 
 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
+---------------- 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: 0.450 ns/day, 53.289 hours/ns, 2.606 timesteps/s
+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    | 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
+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 1.1999e+07 min
+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 = 48112472
+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: 0:00:39
+Total wall time: 0:00:38

doc/.gitignore

@@ -1 +1,5 @@
 /html
+/LAMMPS.epub
+/LAMMPS.mobi
+/Manual.pdf
+/Developer.pdf

doc/Makefile

@@ -8,19 +8,21 @@ 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 $$?), 1)
-$(error Python3 was not found! Please check README.md for further instructions)
+ifeq ($(shell which python3 >/dev/null 2>&1; echo $$?), 0)
+HAS_PYTHON3 = YES
 endif
 
-ifeq ($(shell which virtualenv >/dev/null 2>&1; echo $$?), 1)
-$(error virtualenv was not found! Please check README.md for further instructions)
+ifeq ($(shell which virtualenv >/dev/null 2>&1; echo $$?), 0)
+HAS_VIRTUALENV = YES
 endif
 
 SOURCES=$(wildcard src/*.txt)
 OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
 
-.PHONY: help clean-all clean html pdf old venv
+.PHONY: help clean-all clean epub html pdf old venv
 
 # ------------------------------------------
 
@@ -30,6 +32,7 @@ help:
 	@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"
@@ -40,7 +43,7 @@ clean-all:
 	rm -rf $(BUILDDIR)/* utils/txt2html/txt2html.exe
 
 clean:
-	rm -rf $(RSTDIR)
+	rm -rf $(RSTDIR) html
 
 html: $(OBJECTS)
 	@(\
@@ -61,6 +64,20 @@ html: $(OBJECTS)
 	@rm -rf html/USER/*/*.[sg]*
 	@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; \
@@ -109,6 +126,8 @@ $(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

@@ -1,13 +1,14 @@
 LAMMPS Documentation
 
 Depending on how you obtained LAMMPS, this directory has 2 or 3
-sub-directories and optionally 2 PDF files:
+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.
@@ -49,6 +50,7 @@ make pdf          # generate 2 PDF files (Manual.pdf,Developer.pdf)
 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
 
@@ -92,5 +94,22 @@ 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/src/Eqs/bond_oxdna_fene.tex

@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+\pagestyle{empty}
+
+\begin{document}
+
+$$ 
+  E = - \frac{\epsilon}{2} \ln \left[ 1 - \left(\frac{r-r0}{\Delta}\right)^2\right]
+$$
+
+\end{document}

doc/src/Eqs/fix_grem.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+  T_{eff} = \lambda + \eta (H - H_0)
+$$
+
+\end{document}

doc/src/Eqs/pair_dpd_conservative.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-\pagestyle{empty}
-\begin{document}
-
-$$
-F^C = A \omega_{ij} \qquad \qquad r_{ij} < r_c
-$$
-
-\end{document}

doc/src/Eqs/pair_dpd_energy.tex

@@ -0,0 +1,12 @@
+\documentclass[12pt]{article}
+\pagestyle{empty}
+\begin{document}
+
+\begin{eqnarray*}
+  du_{i}^{cond} & = & \kappa_{ij}(\frac{1}{\theta_{i}}-\frac{1}{\theta_{j}})\omega_{ij}^{2} + \alpha_{ij}\omega_{ij}\zeta_{ij}^{q}(\Delta{t})^{-1/2} \\
+  du_{i}^{mech} & = & -\frac{1}{2}\gamma_{ij}\omega_{ij}^{2}(\frac{\vec{r_{ij}}}{r_{ij}}\bullet\vec{v_{ij}})^{2} - 
+  \frac{\sigma^{2}_{ij}}{4}(\frac{1}{m_{i}}+\frac{1}{m_{j}})\omega_{ij}^{2} - 
+  \frac{1}{2}\sigma_{ij}\omega_{ij}(\frac{\vec{r_{ij}}}{r_{ij}}\bullet\vec{v_{ij}})\zeta_{ij}(\Delta{t})^{-1/2} \\
+\end{eqnarray*}                           
+
+\end{document}

doc/src/Eqs/pair_dpd_energy_terms.tex

@@ -0,0 +1,11 @@
+\documentclass[12pt]{article}
+\pagestyle{empty}
+\begin{document}
+
+\begin{eqnarray*}
+  \alpha_{ij}^{2} & = & 2k_{B}\kappa_{ij} \\
+  \sigma^{2}_{ij} & = & 2\gamma_{ij}k_{B}\Theta_{ij} \\
+  \Theta_{ij}^{-1} & = & \frac{1}{2}(\frac{1}{\theta_{i}}+\frac{1}{\theta_{j}}) \\
+\end{eqnarray*}                           
+
+\end{document}

doc/src/Eqs/pair_tersoff_mod_c.tex

@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+\pagestyle{empty}
+
+\begin{document}
+
+\begin{eqnarray*}
+  V_{ij}  & =  & f_C(r_{ij}) \left[ f_R(r_{ij}) + b_{ij} f_A(r_{ij}) + c_0 \right]
+\end{eqnarray*}
+
+\end{document}

doc/src/Eqs/pressure.tex

@@ -3,7 +3,7 @@
 \begin{document}
 
 $$
-   P = \frac{N k_B T}{V} + \frac{\sum_{i}^{N} r_i \bullet f_i}{dV}
+   P = \frac{N k_B T}{V} + \frac{\sum_{i}^{N'} r_i \bullet f_i}{dV}
 $$
 
 \end{document}

doc/src/Eqs/pressure_tensor.tex

@@ -4,7 +4,7 @@
 
 $$
    P_{IJ} = \frac{\sum_{k}^{N} m_k v_{k_I} v_{k_J}}{V} + 
-   \frac{\sum_{k}^{N} r_{k_I} f_{k_J}}{V}
+   \frac{\sum_{k}^{N'} r_{k_I} f_{k_J}}{V}
 $$
 
 \end{document}

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="6 Oct 2016 version">
+<META NAME="docnumber" CONTENT="21 Feb 2017 version">
 <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
 <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation.  This software and manual is distributed under the GNU General Public License.">
 </HEAD>
@@ -21,7 +21,7 @@
 <H1></H1>
 
 LAMMPS Documentation :c,h3
-6 Oct 2016 version :c,h4
+21 Feb 2017 version :c,h4
 
 Version info: :h4
 

doc/src/Section_commands.txt

@@ -106,7 +106,7 @@ the $.  Thus $\{myTemp\} and $x refer to variable names "myTemp" and
 "x".
 
 How the variable is converted to a text string depends on what style
-of variable it is; see the "variable"_variable doc page for details.
+of variable it is; see the "variable"_variable.html doc page for details.
 It can be a variable that stores multiple text strings, and return one
 of them.  The returned text string can be multiple "words" (space
 separated) which will then be interpreted as multiple arguments in the
@@ -282,78 +282,135 @@ the "minimize"_minimize.html command.  A parallel tempering
 3.4 Commands listed by category :link(cmd_4),h4
 
 This section lists all LAMMPS commands, grouped by category.  The
-"next section"_#cmd_5 lists the same commands alphabetically.  Note
-that some style options for some commands are part of specific LAMMPS
-packages, which means they cannot be used unless the package was
-included when LAMMPS was built.  Not all packages are included in a
-default LAMMPS build.  These dependencies are listed as Restrictions
-in the command's documentation.
+"next section"_#cmd_5 lists the same commands alphabetically.  The
+next section also includes (long) lists of style options for entries
+that appear in the following categories as a single command (fix,
+compute, pair, etc).  Commands that are added by user packages are not
+included in these categories, but they are in the next section.
 
 Initialization:
 
-"atom_modify"_atom_modify.html, "atom_style"_atom_style.html,
-"boundary"_boundary.html, "dimension"_dimension.html,
-"newton"_newton.html, "processors"_processors.html, "units"_units.html
+"newton"_newton.html,
+"package"_package.html,
+"processors"_processors.html,
+"suffix"_suffix.html,
+"units"_units.html
 
-Atom definition:
+Setup simulation box:
 
-"create_atoms"_create_atoms.html, "create_box"_create_box.html,
-"lattice"_lattice.html, "read_data"_read_data.html,
-"read_dump"_read_dump.html, "read_restart"_read_restart.html,
-"region"_region.html, "replicate"_replicate.html
+"boundary"_boundary.html,
+"box"_box.html,
+"change_box"_change_box.html,
+"create_box"_create_box.html,
+"dimension"_dimension.html,
+"lattice"_lattice.html,
+"region"_region.html
+
+Setup atoms:
+
+"atom_modify"_atom_modify.html,
+"atom_style"_atom_style.html,
+"balance"_balance.html,
+"create_atoms"_create_atoms.html,
+"create_bonds"_create_bonds.html,
+"delete_atoms"_delete_atoms.html,
+"delete_bonds"_delete_bonds.html,
+"displace_atoms"_displace_atoms.html,
+"group"_group.html,
+"mass"_mass.html,
+"molecule"_molecule.html,
+"read_data"_read_data.html,
+"read_dump"_read_dump.html,
+"read_restart"_read_restart.html,
+"replicate"_replicate.html,
+"set"_set.html,
+"velocity"_velocity.html
 
 Force fields:
 
-"angle_coeff"_angle_coeff.html, "angle_style"_angle_style.html,
-"bond_coeff"_bond_coeff.html, "bond_style"_bond_style.html,
-"dielectric"_dielectric.html, "dihedral_coeff"_dihedral_coeff.html,
+"angle_coeff"_angle_coeff.html,
+"angle_style"_angle_style.html,
+"bond_coeff"_bond_coeff.html,
+"bond_style"_bond_style.html,
+"bond_write"_bond_write.html,
+"dielectric"_dielectric.html,
+"dihedral_coeff"_dihedral_coeff.html,
 "dihedral_style"_dihedral_style.html,
 "improper_coeff"_improper_coeff.html,
 "improper_style"_improper_style.html,
-"kspace_modify"_kspace_modify.html, "kspace_style"_kspace_style.html,
-"pair_coeff"_pair_coeff.html, "pair_modify"_pair_modify.html,
-"pair_style"_pair_style.html, "pair_write"_pair_write.html,
+"kspace_modify"_kspace_modify.html,
+"kspace_style"_kspace_style.html,
+"pair_coeff"_pair_coeff.html,
+"pair_modify"_pair_modify.html,
+"pair_style"_pair_style.html,
+"pair_write"_pair_write.html,
 "special_bonds"_special_bonds.html
 
 Settings:
 
-"comm_style"_comm_style.html, "group"_group.html, "mass"_mass.html,
-"min_modify"_min_modify.html, "min_style"_min_style.html,
-"neigh_modify"_neigh_modify.html, "neighbor"_neighbor.html,
-"reset_timestep"_reset_timestep.html, "run_style"_run_style.html,
-"set"_set.html, "timestep"_timestep.html, "velocity"_velocity.html
+"comm_modify"_comm_modify.html,
+"comm_style"_comm_style.html,
+"info"_info.html,
+"min_modify"_min_modify.html,
+"min_style"_min_style.html,
+"neigh_modify"_neigh_modify.html,
+"neighbor"_neighbor.html,
+"partition"_partition.html,
+"reset_timestep"_reset_timestep.html,
+"run_style"_run_style.html,
+"timer"_timer.html,
+"timestep"_timestep.html
 
-Fixes:
+Operations within timestepping (fixes) and diagnositics (computes):
 
-"fix"_fix.html, "fix_modify"_fix_modify.html, "unfix"_unfix.html
-
-Computes:
-
-"compute"_compute.html, "compute_modify"_compute_modify.html,
-"uncompute"_uncompute.html
+"compute"_compute.html,
+"compute_modify"_compute_modify.html,
+"fix"_fix.html,
+"fix_modify"_fix_modify.html,
+"uncompute"_uncompute.html,
+"unfix"_unfix.html
 
 Output:
 
-"dump"_dump.html, "dump image"_dump_image.html,
-"dump_modify"_dump_modify.html, "dump movie"_dump_image.html,
-"restart"_restart.html, "thermo"_thermo.html,
-"thermo_modify"_thermo_modify.html, "thermo_style"_thermo_style.html,
-"undump"_undump.html, "write_data"_write_data.html,
-"write_dump"_write_dump.html, "write_restart"_write_restart.html
+"dump image"_dump_image.html,
+"dump movie"_dump_image.html,
+"dump"_dump.html,
+"dump_modify"_dump_modify.html,
+"restart"_restart.html,
+"thermo"_thermo.html,
+"thermo_modify"_thermo_modify.html,
+"thermo_style"_thermo_style.html,
+"undump"_undump.html,
+"write_coeff"_write_coeff.html,
+"write_data"_write_data.html,
+"write_dump"_write_dump.html,
+"write_restart"_write_restart.html
 
 Actions:
 
-"delete_atoms"_delete_atoms.html, "delete_bonds"_delete_bonds.html,
-"displace_atoms"_displace_atoms.html, "change_box"_change_box.html,
-"minimize"_minimize.html, "neb"_neb.html "prd"_prd.html,
-"rerun"_rerun.html, "run"_run.html, "temper"_temper.html
+"minimize"_minimize.html,
+"neb"_neb.html,
+"prd"_prd.html,
+"rerun"_rerun.html,
+"run"_run.html,
+"tad"_tad.html,
+"temper"_temper.html
 
-Miscellaneous:
+Input script control:
 
-"clear"_clear.html, "echo"_echo.html, "if"_if.html,
-"include"_include.html, "jump"_jump.html, "label"_label.html,
-"log"_log.html, "next"_next.html, "print"_print.html,
-"shell"_shell.html, "variable"_variable.html
+"clear"_clear.html,
+"echo"_echo.html,
+"if"_if.html,
+"include"_include.html,
+"jump"_jump.html,
+"label"_label.html,
+"log"_log.html,
+"next"_next.html,
+"print"_print.html,
+"python"_python.html,
+"quit"_quit.html,
+"shell"_shell.html,
+"variable"_variable.html
 
 :line
 
@@ -471,8 +528,11 @@ These are additional commands in USER packages, which can be used if
 package"_Section_start.html#start_3.
 
 "dump custom/vtk"_dump_custom_vtk.html,
+"dump nc"_dump_nc.html,
+"dump nc/mpiio"_dump_nc.html,
 "group2ndx"_group2ndx.html,
-"ndx2group"_group2ndx.html :tb(c=3,ea=c)
+"ndx2group"_group2ndx.html,
+"temper/grem"_temper_grem.html :tb(c=3,ea=c)
 
 :line
 
@@ -516,12 +576,14 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "gcmc"_fix_gcmc.html,
 "gld"_fix_gld.html,
 "gravity (o)"_fix_gravity.html,
+"halt"_fix_halt.html,
 "heat"_fix_heat.html,
 "indent"_fix_indent.html,
 "langevin (k)"_fix_langevin.html,
 "lineforce"_fix_lineforce.html,
-"momentum"_fix_momentum.html,
+"momentum (k)"_fix_momentum.html,
 "move"_fix_move.html,
+"mscg"_fix_mscg.html,
 "msst"_fix_msst.html,
 "neb"_fix_neb.html,
 "nph (ko)"_fix_nh.html,
@@ -572,10 +634,10 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "rigid/nve (o)"_fix_rigid.html,
 "rigid/nvt (o)"_fix_rigid.html,
 "rigid/small (o)"_fix_rigid.html,
-"rigid/small/nph"_fix_rigid.html,
-"rigid/small/npt"_fix_rigid.html,
-"rigid/small/nve"_fix_rigid.html,
-"rigid/small/nvt"_fix_rigid.html,
+"rigid/small/nph (o)"_fix_rigid.html,
+"rigid/small/npt (o)"_fix_rigid.html,
+"rigid/small/nve (o)"_fix_rigid.html,
+"rigid/small/nvt (o)"_fix_rigid.html,
 "setforce (k)"_fix_setforce.html,
 "shake"_fix_shake.html,
 "spring"_fix_spring.html,
@@ -618,6 +680,7 @@ package"_Section_start.html#start_3.
 "atc"_fix_atc.html,
 "ave/correlate/long"_fix_ave_correlate_long.html,
 "colvars"_fix_colvars.html,
+"dpd/energy"_fix_dpd_energy.html,
 "drude"_fix_drude.html,
 "drude/transform/direct"_fix_drude_transform.html,
 "drude/transform/reverse"_fix_drude_transform.html,
@@ -626,6 +689,7 @@ package"_Section_start.html#start_3.
 "eos/table/rx"_fix_eos_table_rx.html,
 "flow/gauss"_fix_flow_gauss.html,
 "gle"_fix_gle.html,
+"grem"_fix_grem.html,
 "imd"_fix_imd.html,
 "ipi"_fix_ipi.html,
 "langevin/drude"_fix_langevin_drude.html,
@@ -638,7 +702,10 @@ package"_Section_start.html#start_3.
 "meso"_fix_meso.html,
 "manifoldforce"_fix_manifoldforce.html,
 "meso/stationary"_fix_meso_stationary.html,
+"nve/dot"_fix_nve_dot.html,
+"nve/dotc/langevin"_fix_nve_dotc_langevin.html,
 "nve/manifold/rattle"_fix_nve_manifold_rattle.html,
+"nvk"_fix_nvk.html,
 "nvt/manifold/rattle"_fix_nvt_manifold_rattle.html,
 "nph/eff"_fix_nh_eff.html,
 "npt/eff"_fix_nh_eff.html,
@@ -704,6 +771,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "erotate/sphere"_compute_erotate_sphere.html,
 "erotate/sphere/atom"_compute_erotate_sphere_atom.html,
 "event/displace"_compute_event_displace.html,
+"global/atom"_compute_global_atom.html,
 "group/group"_compute_group_group.html,
 "gyration"_compute_gyration.html,
 "gyration/chunk"_compute_gyration_chunk.html,
@@ -825,6 +893,8 @@ KOKKOS, o = USER-OMP, t = OPT.
 "body"_pair_body.html,
 "bop"_pair_bop.html,
 "born (go)"_pair_born.html,
+"born/coul/dsf"_pair_born.html,
+"born/coul/dsf/cs"_pair_born.html,
 "born/coul/long (go)"_pair_born.html,
 "born/coul/long/cs"_pair_born.html,
 "born/coul/msm (o)"_pair_born.html,
@@ -848,10 +918,10 @@ KOKKOS, o = USER-OMP, t = OPT.
 "coul/msm"_pair_coul.html,
 "coul/streitz"_pair_coul.html,
 "coul/wolf (ko)"_pair_coul.html,
-"dpd (o)"_pair_dpd.html,
-"dpd/tstat (o)"_pair_dpd.html,
+"dpd (go)"_pair_dpd.html,
+"dpd/tstat (go)"_pair_dpd.html,
 "dsmc"_pair_dsmc.html,
-"eam (gkot)"_pair_eam.html,
+"eam (gkiot)"_pair_eam.html,
 "eam/alloy (gkot)"_pair_eam.html,
 "eam/fs (gkot)"_pair_eam.html,
 "eim (o)"_pair_eim.html,
@@ -899,7 +969,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "lubricateU/poly"_pair_lubricateU.html,
 "meam"_pair_meam.html,
 "mie/cut (o)"_pair_mie.html,
-"morse (got)"_pair_morse.html,
+"morse (gkot)"_pair_morse.html,
 "nb3b/harmonic (o)"_pair_nb3b_harmonic.html,
 "nm/cut (o)"_pair_nm.html,
 "nm/cut/coul/cut (o)"_pair_nm.html,
@@ -918,11 +988,13 @@ KOKKOS, o = USER-OMP, t = OPT.
 "table (gko)"_pair_table.html,
 "tersoff (gkio)"_pair_tersoff.html,
 "tersoff/mod (gko)"_pair_tersoff_mod.html,
+"tersoff/mod/c (o)"_pair_tersoff_mod.html,
 "tersoff/zbl (gko)"_pair_tersoff_zbl.html,
 "tip4p/cut (o)"_pair_coul.html,
 "tip4p/long (o)"_pair_coul.html,
 "tri/lj"_pair_tri_lj.html,
-"vashishta (o)"_pair_vashishta.html,
+"vashishta (ko)"_pair_vashishta.html,
+"vashishta/table (o)"_pair_vashishta.html,
 "yukawa (go)"_pair_yukawa.html,
 "yukawa/colloid (go)"_pair_yukawa_colloid.html,
 "zbl (go)"_pair_zbl.html :tb(c=4,ea=c)
@@ -931,6 +1003,7 @@ These are additional pair styles in USER packages, which can be used
 if "LAMMPS is built with the appropriate
 package"_Section_start.html#start_3.
 
+"agni (o)"_pair_agni.html,
 "awpmd/cut"_pair_awpmd.html,
 "buck/mdf"_pair_mdf.html,
 "coul/cut/soft (o)"_pair_lj_soft.html,
@@ -964,6 +1037,11 @@ package"_Section_start.html#start_3.
 "morse/soft"_pair_morse.html,
 "multi/lucy"_pair_multi_lucy.html,
 "multi/lucy/rx"_pair_multi_lucy_rx.html,
+"oxdna/coaxstk"_pair_oxdna.html,
+"oxdna/excv"_pair_oxdna.html,
+"oxdna/hbond"_pair_oxdna.html,
+"oxdna/stk"_pair_oxdna.html,
+"oxdna/xstk"_pair_oxdna.html,
 "quip"_pair_quip.html,
 "reax/c (k)"_pair_reax_c.html,
 "smd/hertz"_pair_smd_hertz.html,
@@ -998,7 +1076,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "none"_bond_none.html,
 "zero"_bond_zero.html,
 "hybrid"_bond_hybrid.html,
-"class2 (o)"_bond_class2.html,
+"class2 (ko)"_bond_class2.html,
 "fene (iko)"_bond_fene.html,
 "fene/expand (o)"_bond_fene_expand.html,
 "harmonic (ko)"_bond_harmonic.html,
@@ -1012,7 +1090,8 @@ if "LAMMPS is built with the appropriate
 package"_Section_start.html#start_3.
 
 "harmonic/shift (o)"_bond_harmonic_shift.html,
-"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html :tb(c=4,ea=c)
+"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
+"oxdna/fene"_bond_oxdna_fene.html :tb(c=4,ea=c)
 
 :line
 
@@ -1030,7 +1109,7 @@ USER-OMP, t = OPT.
 "zero"_angle_zero.html,
 "hybrid"_angle_hybrid.html,
 "charmm (ko)"_angle_charmm.html,
-"class2 (o)"_angle_class2.html,
+"class2 (ko)"_angle_class2.html,
 "cosine (o)"_angle_cosine.html,
 "cosine/delta (o)"_angle_cosine_delta.html,
 "cosine/periodic (o)"_angle_cosine_periodic.html,
@@ -1066,7 +1145,7 @@ USER-OMP, t = OPT.
 "zero"_dihedral_zero.html,
 "hybrid"_dihedral_hybrid.html,
 "charmm (ko)"_dihedral_charmm.html,
-"class2 (o)"_dihedral_class2.html,
+"class2 (ko)"_dihedral_class2.html,
 "harmonic (io)"_dihedral_harmonic.html,
 "helix (o)"_dihedral_helix.html,
 "multi/harmonic (o)"_dihedral_multi_harmonic.html,
@@ -1098,7 +1177,7 @@ USER-OMP, t = OPT.
 "none"_improper_none.html,
 "zero"_improper_zero.html,
 "hybrid"_improper_hybrid.html,
-"class2 (o)"_improper_class2.html,
+"class2 (ko)"_improper_class2.html,
 "cvff (io)"_improper_cvff.html,
 "harmonic (ko)"_improper_harmonic.html,
 "umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)

doc/src/Section_errors.txt

@@ -22,7 +22,7 @@ either conceptually, or as printed out by the program.
 
 12.1 Common problems :link(err_1),h4
 
-If two LAMMPS runs do not produce the same answer on different
+If two LAMMPS runs do not produce the exact same answer on different
 machines or different numbers of processors, this is typically not a
 bug.  In theory you should get identical answers on any number of
 processors and on any machine.  In practice, numerical round-off can
@@ -55,12 +55,13 @@ LAMMPS errors are detected at setup time; others like a bond
 stretching too far may not occur until the middle of a run.
 
 LAMMPS tries to flag errors and print informative error messages so
-you can fix the problem.  Of course, LAMMPS cannot figure out your
-physics or numerical mistakes, like choosing too big a timestep,
-specifying erroneous force field coefficients, or putting 2 atoms on
-top of each other!  If you run into errors that LAMMPS doesn't catch
-that you think it should flag, please send an email to the
-"developers"_http://lammps.sandia.gov/authors.html.
+you can fix the problem.  For most errors it will also print the last
+input script command that it was processing.  Of course, LAMMPS cannot
+figure out your physics or numerical mistakes, like choosing too big a
+timestep, specifying erroneous force field coefficients, or putting 2
+atoms on top of each other!  If you run into errors that LAMMPS
+doesn't catch that you think it should flag, please send an email to
+the "developers"_http://lammps.sandia.gov/authors.html.
 
 If you get an error message about an invalid command in your input
 script, you can determine what command is causing the problem by
@@ -79,12 +80,24 @@ order.  If you mess this up, LAMMPS will often flag the error, but it
 may also simply read a bogus argument and assign a value that is
 valid, but not what you wanted.  E.g. trying to read the string "abc"
 as an integer value of 0.  Careful reading of the associated doc page
-for the command should allow you to fix these problems.  Note that
-some commands allow for variables to be specified in place of numeric
-constants so that the value can be evaluated and change over the
-course of a run.  This is typically done with the syntax {v_name} for
-a parameter, where name is the name of the variable.  This is only
-allowed if the command documentation says it is.
+for the command should allow you to fix these problems. In most cases,
+where LAMMPS expects to read a number, either integer or floating point,
+it performs a stringent test on whether the provided input actually
+is an integer or floating-point number, respectively, and reject the
+input with an error message (for instance, when an integer is required,
+but a floating-point number 1.0 is provided):
+
+ERROR: Expected integer parameter in input script or data file :pre
+
+Some commands allow for using variable references in place of numeric
+constants so that the value can be evaluated and may change over the
+course of a run.  This is typically done with the syntax {v_name} for a
+parameter, where name is the name of the variable. On the other hand,
+immediate variable expansion with the syntax ${name} is performed while
+reading the input and before parsing commands,
+
+NOTE: Using a variable reference (i.e. {v_name}) is only allowed if
+the documentation of the corresponding command explicitly says it is.
 
 Generally, LAMMPS will print a message to the screen and logfile and
 exit gracefully when it encounters a fatal error.  Sometimes it will
@@ -8116,11 +8129,11 @@ boundary of a processor's sub-domain has moved more than 1/2 the
 rebuilt and atoms being migrated to new processors.  This also means
 you may be missing pairwise interactions that need to be computed.
 The solution is to change the re-neighboring criteria via the
-"neigh_modify"_neigh_modify command.  The safest settings are "delay 0
-every 1 check yes".  Second, it may mean that an atom has moved far
-outside a processor's sub-domain or even the entire simulation box.
-This indicates bad physics, e.g. due to highly overlapping atoms, too
-large a timestep, etc. :dd
+"neigh_modify"_neigh_modify.html command.  The safest settings are
+"delay 0 every 1 check yes".  Second, it may mean that an atom has
+moved far outside a processor's sub-domain or even the entire
+simulation box. This indicates bad physics, e.g. due to highly
+overlapping atoms, too large a timestep, etc. :dd
 
 {Out of range atoms - cannot compute PPPM} :dt
 
@@ -8132,11 +8145,11 @@ boundary of a processor's sub-domain has moved more than 1/2 the
 rebuilt and atoms being migrated to new processors.  This also means
 you may be missing pairwise interactions that need to be computed.
 The solution is to change the re-neighboring criteria via the
-"neigh_modify"_neigh_modify command.  The safest settings are "delay 0
-every 1 check yes".  Second, it may mean that an atom has moved far
-outside a processor's sub-domain or even the entire simulation box.
-This indicates bad physics, e.g. due to highly overlapping atoms, too
-large a timestep, etc. :dd
+"neigh_modify"_neigh_modify.html command.  The safest settings are
+"delay 0 every 1 check yes".  Second, it may mean that an atom has
+moved far outside a processor's sub-domain or even the entire
+simulation box. This indicates bad physics, e.g. due to highly
+overlapping atoms, too large a timestep, etc. :dd
 
 {Out of range atoms - cannot compute PPPMDisp} :dt
 
@@ -8148,11 +8161,11 @@ boundary of a processor's sub-domain has moved more than 1/2 the
 rebuilt and atoms being migrated to new processors.  This also means
 you may be missing pairwise interactions that need to be computed.
 The solution is to change the re-neighboring criteria via the
-"neigh_modify"_neigh_modify command.  The safest settings are "delay 0
-every 1 check yes".  Second, it may mean that an atom has moved far
-outside a processor's sub-domain or even the entire simulation box.
-This indicates bad physics, e.g. due to highly overlapping atoms, too
-large a timestep, etc. :dd
+"neigh_modify"_neigh_modify.html command.  The safest settings are
+"delay 0 every 1 check yes".  Second, it may mean that an atom has
+moved far outside a processor's sub-domain or even the entire
+simulation box. This indicates bad physics, e.g. due to highly
+overlapping atoms, too large a timestep, etc. :dd
 
 {Overflow of allocated fix vector storage} :dt
 

doc/src/Section_howto.txt

@@ -1854,13 +1854,19 @@ internal LAMMPS operations.  Note that LAMMPS classes are defined
 within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++
 application.
 
-Library.cpp contains these 5 basic functions:
+Library.cpp contains these functions for creating and destroying an
+instance of LAMMPS and sending it commands to execute.  See the
+documentation in the src/library.cpp file for details:
 
 void lammps_open(int, char **, MPI_Comm, void **)
+void lammps_open_no_mpi(int, char **, void **)
 void lammps_close(void *)
 int lammps_version(void *)
 void lammps_file(void *, char *)
-char *lammps_command(void *, char *) :pre
+char *lammps_command(void *, char *)
+void lammps_commands_list(void *, int, char **)
+void lammps_commands_string(void *, char *)
+void lammps_free(void *) :pre
 
 The lammps_open() function is used to initialize LAMMPS, passing in a
 list of strings as if they were "command-line
@@ -1880,6 +1886,10 @@ half to the other code and run both codes simultaneously before
 syncing them up periodically.  Or it might instantiate multiple
 instances of LAMMPS to perform different calculations.
 
+The lammps_open_no_mpi() function is similar except that no MPI
+communicator is passed from the caller.  Instead, MPI_COMM_WORLD is
+used to instantiate LAMMPS, and MPI is initialzed if necessary.
+
 The lammps_close() function is used to shut down an instance of LAMMPS
 and free all its memory.
 
@@ -1891,44 +1901,106 @@ changes to the LAMMPS command syntax between versions. The returned
 LAMMPS version code is an integer (e.g. 2 Sep 2015 results in
 20150902) that grows with every new LAMMPS version.
 
-The lammps_file() and lammps_command() functions are used to pass a
-file or string to LAMMPS as if it were an input script or single
-command in an input script.  Thus the calling code can read or
-generate a series of LAMMPS commands one line at a time and pass it
-thru the library interface to setup a problem and then run it,
-interleaving the lammps_command() calls with other calls to extract
-information from LAMMPS, perform its own operations, or call another
-code's library.
+The lammps_file(), lammps_command(), lammps_commands_list(), and
+lammps_commands_string() functions are used to pass one or more
+commands to LAMMPS to execute, the same as if they were coming from an
+input script.
 
-Other useful functions are also included in library.cpp.  For example:
+Via these functions, the calling code can read or generate a series of
+LAMMPS commands one or multiple at a time and pass it thru the library
+interface to setup a problem and then run it in stages.  The caller
+can interleave the command function calls with operations it performs,
+calls to extract information from or set information within LAMMPS, or
+calls to another code's library.
+
+The lammps_file() function passes the filename of an input script.
+The lammps_command() function passes a single command as a string.
+The lammps_commands_list() function passes multiple commands in a
+char** list.  In both lammps_command() and lammps_commands_list(),
+individual commands may or may not have a trailing newline.  The
+lammps_commands_string() function passes multiple commands
+concatenated into one long string, separated by newline characters.
+In both lammps_commands_list() and lammps_commands_string(), a single
+command can be spread across multiple lines, if the last printable
+character of all but the last line is "&", the same as if the lines
+appeared in an input script.
+
+The lammps_free() function is a clean-up function to free memory that
+the library allocated previously via other function calls.  See
+comments in src/library.cpp file for which other functions need this
+clean-up.
+
+Library.cpp also contains these functions for extracting information
+from LAMMPS and setting value within LAMMPS.  Again, see the
+documentation in the src/library.cpp file for details, including
+which quantities can be queried by name:
 
 void *lammps_extract_global(void *, char *)
+void lammps_extract_box(void *, double *, double *, 
+                        double *, double *, double *, int *, int *)
 void *lammps_extract_atom(void *, char *)
 void *lammps_extract_compute(void *, char *, int, int)
 void *lammps_extract_fix(void *, char *, int, int, int, int)
-void *lammps_extract_variable(void *, char *, char *)
-int lammps_set_variable(void *, char *, char *)
+void *lammps_extract_variable(void *, char *, char *) :pre
+
+void lammps_reset_box(void *, double *, double *, double, double, double)
+int lammps_set_variable(void *, char *, char *) :pre
+
+double lammps_get_thermo(void *, char *)
 int lammps_get_natoms(void *)
-void lammps_get_coords(void *, double *)
-void lammps_put_coords(void *, double *) :pre
+void lammps_gather_atoms(void *, double *)
+void lammps_scatter_atoms(void *, double *) :pre
+void lammps_create_atoms(void *, int, tagint *, int *, double *, double *,
+                         imageint *, int) :pre
 
-These can extract various global or per-atom quantities from LAMMPS as
-well as values calculated by a compute, fix, or variable.  The
-"set_variable" function can set an existing string-style variable to a
-new value, so that subsequent LAMMPS commands can access the variable.
-The "get" and "put" operations can retrieve and reset atom
-coordinates.  See the library.cpp file and its associated header file
-library.h for details.
+The extract functions return a pointer to various global or per-atom
+quantities stored in LAMMPS or to values calculated by a compute, fix,
+or variable.  The pointer returned by the extract_global() function
+can be used as a permanent reference to a value which may change.  For
+the other extract functions, the underlying storage may be reallocated
+as LAMMPS runs, so you need to re-call the function to assure a
+current pointer or returned value(s).
 
-The key idea of the library interface is that you can write any
-functions you wish to define how your code talks to LAMMPS and add
-them to src/library.cpp and src/library.h, as well as to the "Python
-interface"_Section_python.html.  The routines you add can access or
-change any LAMMPS data you wish.  The examples/COUPLE and python
-directories have example C++ and C and Python codes which show how a
-driver code can link to LAMMPS as a library, run LAMMPS on a subset of
-processors, grab data from LAMMPS, change it, and put it back into
-LAMMPS.
+The lammps_reset_box() function resets the size and shape of the
+simulation box, e.g. as part of restoring a previously extracted and
+saved state of a simulation.
+
+The lammps_set_variable() function can set an existing string-style
+variable to a new string value, so that subsequent LAMMPS commands can
+access the variable.
+
+The lammps_get_thermo() function returns the current value of a thermo
+keyword as a double precision value.
+
+The lammps_get_natoms() function returns the total number of atoms in
+the system and can be used by the caller to allocate space for the
+lammps_gather_atoms() and lammps_scatter_atoms() functions.  The
+gather function collects atom info of the requested type (atom coords,
+types, forces, etc) from all procsesors, orders them by atom ID, and
+returns a full list to each calling processor.  The scatter function
+does the inverse.  It distributes the same kinds of values, 
+passed by the caller, to each atom owned by individual processors.
+
+The lammps_create_atoms() function takes a list of N atoms as input
+with atom types and coords (required), an optionally atom IDs and
+velocities and image flags.  It uses the coords of each atom to assign
+it as a new atom to the processor that owns it.  This function is
+useful to add atoms to a simulation or (in tandem with
+lammps_reset_box()) to restore a previously extracted and saved state
+of a simulation.  Additional properties for the new atoms can then be
+assigned via the lammps_scatter_atoms() or lammps_extract_atom()
+functions.
+
+The examples/COUPLE and python directories have example C++ and C and
+Python codes which show how a driver code can link to LAMMPS as a
+library, run LAMMPS on a subset of processors, grab data from LAMMPS,
+change it, and put it back into LAMMPS.
+
+NOTE: You can write code for additional functions as needed to define
+how your code talks to LAMMPS and add them to src/library.cpp and
+src/library.h, as well as to the "Python
+interface"_Section_python.html.  The added functions can access or
+change any LAMMPS data you wish.
 
 :line
 
@@ -2501,7 +2573,7 @@ well.
 6.26 Adiabatic core/shell model :link(howto_26),h4
 
 The adiabatic core-shell model by "Mitchell and
-Finchham"_#MitchellFinchham is a simple method for adding
+Fincham"_#MitchellFincham is a simple method for adding
 polarizability to a system.  In order to mimic the electron shell of
 an ion, a satellite particle is attached to it. This way the ions are
 split into a core and a shell where the latter is meant to react to
@@ -2595,13 +2667,16 @@ bond_coeff      1 63.014 0.0
 bond_coeff      2 25.724 0.0 :pre
 
 When running dynamics with the adiabatic core/shell model, the
-following issues should be considered.  Since the relative motion of
-the core and shell particles corresponds to the polarization, typical
-thermostats can alter the polarization behaviour, meaning the shell
-will not react freely to its electrostatic environment.  This is
-critical during the equilibration of the system. Therefore
-it's typically desirable to decouple the relative motion of the
-core/shell pair, which is an imaginary degree of freedom, from the
+following issues should be considered.  The relative motion of
+the core and shell particles corresponds to the polarization, 
+hereby an instantaneous relaxation of the shells is approximated 
+and a fast core/shell spring frequency ensures a nearly constant
+internal kinetic energy during the simulation. 
+Thermostats can alter this polarization behaviour, by scaling the
+internal kinetic energy, meaning the shell will not react freely to 
+its electrostatic environment. 
+Therefore it is typically desirable to decouple the relative motion of 
+the core/shell pair, which is an imaginary degree of freedom, from the
 real physical system.  To do that, the "compute
 temp/cs"_compute_temp_cs.html command can be used, in conjunction with
 any of the thermostat fixes, such as "fix nvt"_fix_nh.html or "fix
@@ -2632,6 +2707,22 @@ fix thermostatequ all nve                               # integrator as needed f
 fix_modify thermoberendsen temp CSequ
 thermo_modify temp CSequ                                # output of center-of-mass derived temperature :pre
 
+The pressure for the core/shell system is computed via the regular 
+LAMMPS convention by "treating the cores and shells as individual 
+particles"_#MitchellFincham2. For the thermo output of the pressure 
+as well as for the application of a barostat, it is necessary to 
+use an additional "pressure"_compute_pressure compute based on the 
+default "temperature"_compute_temp and specifying it as a second 
+argument in "fix modify"_fix_modify.html and 
+"thermo_modify"_thermo_modify.html resulting in:
+
+(...)
+compute CSequ all temp/cs cores shells
+compute thermo_press_lmp all pressure thermo_temp       # pressure for individual particles
+thermo_modify temp CSequ press thermo_press_lmp         # modify thermo to regular pressure
+fix press_bar all npt temp 300 300 0.04 iso 0 0 0.4
+fix_modify press_bar temp CSequ press thermo_press_lmp  # pressure modification for correct kinetic scalar :pre
+
 If "compute temp/cs"_compute_temp_cs.html is used, the decoupled
 relative motion of the core and the shell should in theory be
 stable.  However numerical fluctuation can introduce a small
@@ -2652,25 +2743,19 @@ temp/cs"_compute_temp_cs.html command to the {temp} keyword of the
 velocity all create 1427 134 bias yes temp CSequ
 velocity all scale 1427 temp CSequ :pre
 
-It is important to note that the polarizability of the core/shell
-pairs is based on their relative motion. Therefore the choice of
-spring force and mass ratio need to ensure much faster relative motion
-of the 2 atoms within the core/shell pair than their center-of-mass
-velocity. This allow the shells to effectively react instantaneously
-to the electrostatic environment.  This fast movement also limits the
-timestep size that can be used.
+To maintain the correct polarizability of the core/shell pairs, the 
+kinetic energy of the internal motion shall remain nearly constant. 
+Therefore the choice of spring force and mass ratio need to ensure 
+much faster relative motion of the 2 atoms within the core/shell pair 
+than their center-of-mass velocity. This allows the shells to 
+effectively react instantaneously to the electrostatic environment and 
+limits energy transfer to or from the core/shell oscillators.
+This fast movement also dictates the timestep that can be used.
 
 The primary literature of the adiabatic core/shell model suggests that
 the fast relative motion of the core/shell pairs only allows negligible
-energy transfer to the environment. Therefore it is not intended to
-decouple the core/shell degree of freedom from the physical system
-during production runs. In other words, the "compute
-temp/cs"_compute_temp_cs.html command should not be used during
-production runs and is only required during equilibration. This way one
-is consistent with literature (based on the code packages DL_POLY or
-GULP for instance).
-
-The mentioned energy transfer will typically lead to a a small drift
+energy transfer to the environment. 
+The mentioned energy transfer will typically lead to a small drift
 in total energy over time.  This internal energy can be monitored
 using the "compute chunk/atom"_compute_chunk_atom.html and "compute
 temp/chunk"_compute_temp_chunk.html commands.  The internal kinetic
@@ -2689,14 +2774,20 @@ command, to use as input to the "compute
 chunk/atom"_compute_chunk_atom.html command to define the core/shell
 pairs as chunks.
 
-For example,
+For example if core/shell pairs are the only molecules:
+
+read_data NaCl_CS_x0.1_prop.data 
+compute prop all property/atom molecule
+compute cs_chunk all chunk/atom c_prop
+compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0     # note the chosen degrees of freedom for the core/shell pairs
+fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector :pre
+
+For example if core/shell pairs and other molecules are present:
 
 fix csinfo all property/atom i_CSID                       # property/atom command
 read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info  # atom property added in the data-file
 compute prop all property/atom i_CSID
-compute cs_chunk all chunk/atom c_prop
-compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0     # note the chosen degrees of freedom for the core/shell pairs
-fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector :pre
+(...) :pre
 
 The additional section in the date file would be formatted like this:
 
@@ -2771,7 +2862,7 @@ temp/drude"_compute_temp_drude.html. This requires also to use the
 command {comm_modify vel yes}.
 
 Short-range damping of the induced dipole interactions can be achieved
-using Thole functions through the the "pair style
+using Thole functions through the "pair style
 thole"_pair_thole.html in "pair_style hybrid/overlay"_pair_hybrid.html
 with a Coulomb pair style. It may be useful to use {coul/long/cs} or
 similar from the CORESHELL package if the core and Drude particle come
@@ -2818,9 +2909,13 @@ Phys, 79, 926 (1983).
 :link(Shinoda)
 [(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
 
-:link(MitchellFinchham)
-[(Mitchell and Finchham)] Mitchell, Finchham, J Phys Condensed Matter,
+:link(MitchellFincham)
+[(Mitchell and Fincham)] Mitchell, Fincham, J Phys Condensed Matter,
 5, 1031-1038 (1993).
 
+:link(MitchellFincham2)
+[(Fincham)] Fincham, Mackrodt and Mitchell, J Phys Condensed Matter,
+6, 393-404 (1994).
+
 :link(howto-Lamoureux)
 [(Lamoureux and Roux)] G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)

doc/src/Section_intro.txt

@@ -366,11 +366,11 @@ complementary modeling tasks.
 "DL_POLY"_dlpoly
 "Tinker"_tinker :ul
 
-:link(charmm,http://www.scripps.edu/brooks)
-:link(amber,http://amber.scripps.edu)
+:link(charmm,http://www.charmm.org)
+:link(amber,http://ambermd.org)
 :link(namd,http://www.ks.uiuc.edu/Research/namd/)
 :link(nwchem,http://www.emsl.pnl.gov/docs/nwchem/nwchem.html)
-:link(dlpoly,http://www.cse.clrc.ac.uk/msi/software/DL_POLY)
+:link(dlpoly,http://www.ccp5.ac.uk/DL_POLY_CLASSIC)
 :link(tinker,http://dasher.wustl.edu/tinker)
 
 CHARMM, AMBER, NAMD, NWCHEM, and Tinker are designed primarily for

doc/src/Section_packages.txt

@@ -84,7 +84,7 @@ Package, Description, Author(s), Doc page, Example, Library
 "PERI"_#PERI, Peridynamics models, Mike Parks (Sandia), "pair_style peri"_pair_peri.html, peri, -
 "POEMS"_#POEMS, coupled rigid body motion, Rudra Mukherjee (JPL), "fix poems"_fix_poems.html, rigid, lib/poems
 "PYTHON"_#PYTHON, embed Python code in an input script, -, "python"_python.html, python, lib/python
-"REAX"_#REAX, ReaxFF potential, Aidan Thompson (Sandia), "pair_style reax"_pair_reax.html, reax,  lib/reax
+"REAX"_#REAX, ReaxFF potential, Aidan Thompson (Sandia), "pair_style reax"_pair_reax.html, reax, lib/reax
 "REPLICA"_#REPLICA, multi-replica methods, -, "Section 6.6.5"_Section_howto.html#howto_5, tad, -
 "RIGID"_#RIGID, rigid bodies, -, "fix rigid"_fix_rigid.html, rigid, -
 "SHOCK"_#SHOCK, shock loading methods, -, "fix msst"_fix_msst.html, -, -
@@ -1140,6 +1140,7 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library
 "USER-ATC"_#USER-ATC, atom-to-continuum coupling, Jones & Templeton & Zimmerman (1), "fix atc"_fix_atc.html, USER/atc, "atc"_atc, lib/atc
 "USER-AWPMD"_#USER-AWPMD, wave-packet MD, Ilya Valuev (JIHT), "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, -, lib/awpmd
 "USER-CG-CMM"_#USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sdk"_pair_sdk.html, USER/cg-cmm, "cg"_cg, -
+"USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, Oliver Henrich (U Edinburgh), src/USER-CGDNA/README, USER/cgdna, -, -
 "USER-COLVARS"_#USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (2), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars
 "USER-DIFFRACTION"_#USER-DIFFRACTION, virutal x-ray and electron diffraction, Shawn Coleman (ARL),"compute xrd"_compute_xrd.html, USER/diffraction, -, -
 "USER-DPD"_#USER-DPD, reactive dissipative particle dynamics (DPD), Larentzos & Mattox & Brennan (5), src/USER-DPD/README, USER/dpd, -, -
@@ -1153,6 +1154,7 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library
 "USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -
 "USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surface, Stefan Paquay (Eindhoven U of Technology), "fix manifoldforce"_fix_manifoldforce.html, USER/manifold, "manifold"_manifold, -
 "USER-MOLFILE"_#USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE
+"USER-NC-DUMP"_#USER-NC-DUMP, dump output via NetCDF, Lars Pastewka (Karlsruhe Institute of Technology, KIT), "dump nc / dump nc/mpiio"_dump_nc.html, -, -, lib/netcdf
 "USER-OMP"_#USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section 5.3.4"_accelerate_omp.html, -, -, -
 "USER-PHONON"_#USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, -
 "USER-QMMM"_#USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm
@@ -1283,6 +1285,31 @@ him directly if you have questions.
 
 :line
 
+USER-CGDNA package :link(USER-CGDNA),h5
+
+Contents: The CGDNA package implements coarse-grained force fields for
+single- and double-stranded DNA. This is at the moment mainly the
+oxDNA model, developed by Doye, Louis and Ouldridge at the University
+of Oxford.  The package also contains Langevin-type rigid-body
+integrators with improved stability.
+
+See these doc pages to get started:
+
+"bond_style oxdna_fene"_bond_oxdna_fene.html
+"pair_style oxdna_excv"_pair_oxdna_excv.html
+"fix nve/dotc/langevin"_fix_nve_dotc_langevin.html :ul
+
+Supporting info: /src/USER-CGDNA/README, "bond_style
+oxdna_fene"_bond_oxdna_fene.html, "pair_style
+oxdna_excv"_pair_oxdna_excv.html, "fix
+nve/dotc/langevin"_fix_nve_dotc_langevin.html
+
+Author: Oliver Henrich at the University of Edinburgh, UK (o.henrich
+at epcc.ed.ac.uk or ohenrich at ph.ed.ac.uk).  Contact him directly if
+you have any questions.
+
+:line
+
 USER-COLVARS package :link(USER-COLVARS),h5
 
 Contents: COLVARS stands for collective variables which can be used to
@@ -1598,6 +1625,30 @@ The person who created this package is Axel Kohlmeyer at Temple U
 
 :line
 
+USER-NC-DUMP package :link(USER-NC-DUMP),h5
+
+Contents: Dump styles for writing NetCDF format files.  NetCDF is a binary,
+portable, self-describing file format on top of HDF5. The file format
+contents follow the AMBER NetCDF trajectory conventions
+(http://ambermd.org/netcdf/nctraj.xhtml), but include extensions to this
+convention. This package implements a "dump nc"_dump_nc.html command
+and a "dump nc/mpiio"_dump_nc.html command to output LAMMPS snapshots
+in this format.  See src/USER-NC-DUMP/README for more details.
+
+NetCDF files can be directly visualized with the following tools:
+
+Ovito (http://www.ovito.org/). Ovito supports the AMBER convention
+and all of the above extensions. :ulb,l
+VMD (http://www.ks.uiuc.edu/Research/vmd/) :l
+AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye contains
+a NetCDF reader that is not present in the standard distribution of AtomEye :l,ule
+
+The person who created these files is Lars Pastewka at
+Karlsruhe Institute of Technology (lars.pastewka at kit.edu).
+Contact him directly if you have questions.
+
+:line
+
 USER-OMP package :link(USER-OMP),h5
 
 Supporting info:

doc/src/Section_python.txt

@@ -8,19 +8,26 @@
 
 11. Python interface to LAMMPS :h3
 
-LAMMPS can work together with Python in two ways.  First, Python can
+LAMMPS can work together with Python in three ways.  First, Python can
 wrap LAMMPS through the "LAMMPS library
 interface"_Section_howto.html#howto_19, so that a Python script can
 create one or more instances of LAMMPS and launch one or more
 simulations.  In Python lingo, this is "extending" Python with LAMMPS.
 
-Second, LAMMPS can use the Python interpreter, so that a LAMMPS input
+Second, the low-level Python interface can be used indirectly through the
+PyLammps and IPyLammps wrapper classes in Python. These wrappers try to
+simplify the usage of LAMMPS in Python by providing an object-based interface
+to common LAMMPS functionality. It also reduces the amount of code necessary to
+parameterize LAMMPS scripts through Python and makes variables and computes
+directly accessible. See "PyLammps interface"_#py_9 for more details.
+
+Third, LAMMPS can use the Python interpreter, so that a LAMMPS input
 script can invoke Python code, and pass information back-and-forth
 between the input script and Python functions you write.  The Python
 code can also callback to LAMMPS to query or change its attributes.
 In Python lingo, this is "embedding" Python in LAMMPS.
 
-This section describes how to do both.
+This section describes how to use these three approaches.
 
 11.1 "Overview of running LAMMPS from Python"_#py_1
 11.2 "Overview of using Python from a LAMMPS script"_#py_2
@@ -29,7 +36,8 @@ This section describes how to do both.
 11.5 "Extending Python with MPI to run in parallel"_#py_5
 11.6 "Testing the Python-LAMMPS interface"_#py_6
 11.7 "Using LAMMPS from Python"_#py_7
-11.8 "Example Python scripts that use LAMMPS"_#py_8 :ul
+11.8 "Example Python scripts that use LAMMPS"_#py_8
+11.9 "PyLammps interface"_#py_9 :ul
 
 If you are not familiar with it, "Python"_http://www.python.org is a
 powerful scripting and programming language which can essentially do
@@ -534,10 +542,11 @@ from lammps import lammps :pre
 These are the methods defined by the lammps module.  If you look at
 the files src/library.cpp and src/library.h you will see that they
 correspond one-to-one with calls you can make to the LAMMPS library
-from a C++ or C or Fortran program.
+from a C++ or C or Fortran program, and which are described in
+"Section 6.19"_Section_howto.html#howto_19 of the manual.
 
 lmp = lammps()           # create a LAMMPS object using the default liblammps.so library
-                         4 optional args are allowed: name, cmdargs, ptr, comm
+                         # 4 optional args are allowed: name, cmdargs, ptr, comm
 lmp = lammps(ptr=lmpptr) # use lmpptr as previously created LAMMPS object
 lmp = lammps(comm=split) # create a LAMMPS object with a custom communicator, requires mpi4py 2.0.0 or later
 lmp = lammps(name="g++")   # create a LAMMPS object using the liblammps_g++.so library
@@ -549,6 +558,8 @@ version = lmp.version()  # return the numerical version id, e.g. LAMMPS 2 Sep 20
 
 lmp.file(file)           # run an entire input script, file = "in.lj"
 lmp.command(cmd)         # invoke a single LAMMPS command, cmd = "run 100" :pre
+lmp.commands_list(cmdlist)     # invoke commands in cmdlist = ["run 10", "run 20"]
+lmp.commands_string(multicmd)  # invoke commands in multicmd = "run 10\nrun 20"
 
 xlo = lmp.extract_global(name,type)  # extract a global quantity
                                      # name = "boxxlo", "nlocal", etc
@@ -580,6 +591,8 @@ var = lmp.extract_variable(name,group,flag)  # extract value(s) from a variable
                                              #        1 = atom-style variable :pre
 
 flag = lmp.set_variable(name,value)       # set existing named string-style variable to value, flag = 0 if successful
+value = lmp.get_thermo(name)              # return current value of a thermo keyword
+
 natoms = lmp.get_natoms()                 # total # of atoms as int
 data = lmp.gather_atoms(name,type,count)  # return atom attribute of all atoms gathered into data, ordered by atom ID
                                           # name = "x", "charge", "type", etc
@@ -599,9 +612,10 @@ create an instance of LAMMPS, wrapped in a Python class by the lammps
 Python module, and return an instance of the Python class as lmp.  It
 is used to make all subequent calls to the LAMMPS library.
 
-Additional arguments can be used to tell Python the name of the shared
-library to load or to pass arguments to the LAMMPS instance, the same
-as if LAMMPS were launched from a command-line prompt.
+Additional arguments to lammps() can be used to tell Python the name
+of the shared library to load or to pass arguments to the LAMMPS
+instance, the same as if LAMMPS were launched from a command-line
+prompt.
 
 If the ptr argument is set like this:
 
@@ -626,8 +640,9 @@ lmp2 = lammps()
 lmp1.file("in.file1")
 lmp2.file("in.file2") :pre
 
-The file() and command() methods allow an input script or single
-commands to be invoked.
+The file(), command(), commands_list(), commands_string() methods
+allow an input script, a single command, or multiple commands to be
+invoked.
 
 The extract_global(), extract_atom(), extract_compute(),
 extract_fix(), and extract_variable() methods return values or
@@ -817,3 +832,7 @@ different visualization package options.  Click to see larger images:
 :image(JPG/screenshot_atomeye_small.jpg,JPG/screenshot_atomeye.jpg)
 :image(JPG/screenshot_pymol_small.jpg,JPG/screenshot_pymol.jpg)
 :image(JPG/screenshot_vmd_small.jpg,JPG/screenshot_vmd.jpg)
+
+11.9 PyLammps interface :link(py_9),h4
+
+Please see the "PyLammps Tutorial"_tutorial_pylammps.html.

doc/src/Section_start.txt

@@ -413,7 +413,7 @@ uses (for performing 1d FFTs) when running the particle-particle
 particle-mesh (PPPM) option for long-range Coulombics via the
 "kspace_style"_kspace_style.html command.
 
-LAMMPS supports various open-source or vendor-supplied FFT libraries
+LAMMPS supports common open-source or vendor-supplied FFT libraries
 for this purpose.  If you leave these 3 variables blank, LAMMPS will
 use the open-source "KISS FFT library"_http://kissfft.sf.net, which is
 included in the LAMMPS distribution.  This library is portable to all
@@ -423,10 +423,9 @@ package in your build, you can also leave the 3 variables blank.
 
 Otherwise, select which kinds of FFTs to use as part of the FFT_INC
 setting by a switch of the form -DFFT_XXX.  Recommended values for XXX
-are: MKL, SCSL, FFTW2, and FFTW3.  Legacy options are: INTEL, SGI,
-ACML, and T3E.  For backward compatability, using -DFFT_FFTW will use
-the FFTW2 library.  Using -DFFT_NONE will use the KISS library
-described above.
+are: MKL or FFTW3.  FFTW2 and NONE are supported as legacy options.
+Selecting -DFFT_FFTW will use the FFTW3 library and -DFFT_NONE will
+use the KISS library described above.
 
 You may also need to set the FFT_INC, FFT_PATH, and FFT_LIB variables,
 so the compiler and linker can find the needed FFT header and library
@@ -706,7 +705,7 @@ future changes to LAMMPS.
 User packages, such as user-atc or user-omp, have been contributed by
 users, and always begin with the user prefix.  If they are a single
 command (single file), they are typically in the user-misc package.
-Otherwise, they are a a set of files grouped together which add a
+Otherwise, they are a set of files grouped together which add a
 specific functionality to the code.
 
 User packages don't necessarily meet the requirements of the standard
@@ -1601,9 +1600,9 @@ implementations, either by environment variables that specify how to
 order physical processors, or by config files that specify what
 physical processors to assign to each MPI rank.  The -reorder switch
 simply gives you a portable way to do this without relying on MPI
-itself.  See the "processors out"_processors command for how to output
-info on the final assignment of physical processors to the LAMMPS
-simulation domain.
+itself.  See the "processors out"_processors.html command for how
+to output info on the final assignment of physical processors to
+the LAMMPS simulation domain.
 
 -screen file :pre
 
@@ -1727,7 +1726,7 @@ thermodynamic state and a total run time for the simulation.  It then
 appends statistics about the CPU time and storage requirements for the
 simulation.  An example set of statistics is shown here:
 
-Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms
+Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms :pre
 
 Performance: 18.436 ns/day  1.302 hours/ns  106.689 timesteps/s
 97.0% CPU use with 4 MPI tasks x no OpenMP threads :pre
@@ -1757,14 +1756,14 @@ Ave special neighs/atom = 2.34032
 Neighbor list builds = 26
 Dangerous builds = 0 :pre
 
-The first section provides a global loop timing summary. The loop time
+The first section provides a global loop timing summary. The {loop time}
 is the total wall time for the section.  The {Performance} line is
 provided for convenience to help predicting the number of loop
-continuations required and for comparing performance with other
-similar MD codes.  The CPU use line provides the CPU utilzation per
+continuations required and for comparing performance with other,
+similar MD codes.  The {CPU use} line provides the CPU utilzation per
 MPI task; it should be close to 100% times the number of OpenMP
-threads (or 1). Lower numbers correspond to delays due to file I/O or
-insufficient thread utilization.
+threads (or 1 of no OpenMP). Lower numbers correspond to delays due
+to file I/O or insufficient thread utilization.
 
 The MPI task section gives the breakdown of the CPU run time (in
 seconds) into major categories:
@@ -1791,7 +1790,7 @@ is present that also prints the CPU utilization in percent. In
 addition, when using {timer full} and the "package omp"_package.html
 command are active, a similar timing summary of time spent in threaded
 regions to monitor thread utilization and load balance is provided. A
-new entry is the {Reduce} section, which lists the time spend in
+new entry is the {Reduce} section, which lists the time spent in
 reducing the per-thread data elements to the storage for non-threaded
 computation. These thread timings are taking from the first MPI rank
 only and and thus, as the breakdown for MPI tasks can change from MPI

doc/src/accelerate_intel.txt

@@ -29,7 +29,7 @@ Bond Styles: fene, harmonic :l
 Dihedral Styles: charmm, harmonic, opls :l
 Fixes: nve, npt, nvt, nvt/sllod :l
 Improper Styles: cvff, harmonic :l
-Pair Styles: buck/coul/cut, buck/coul/long, buck, gayberne,
+Pair Styles: buck/coul/cut, buck/coul/long, buck, eam, gayberne,
 charmm/coul/long, lj/cut, lj/cut/coul/long, sw, tersoff :l
 K-Space Styles: pppm :l
 :ule
@@ -151,7 +151,7 @@ can start running so that the CPU pipeline is still being used
 efficiently. Although benefits can be seen by launching a MPI task
 for every hardware thread, for multinode simulations, we recommend
 that OpenMP threads are used for SMT instead, either with the
-USER-INTEL package, "USER-OMP package"_accelerate_omp.html", or
+USER-INTEL package, "USER-OMP package"_accelerate_omp.html, or
 "KOKKOS package"_accelerate_kokkos.html. In the example above, up
 to 36X speedups can be observed by using all 36 physical cores with
 LAMMPS. By using all 72 hardware threads, an additional 10-30%
@@ -343,7 +343,7 @@ when using offload.
 
 Not all styles are supported in the USER-INTEL package. You can mix
 the USER-INTEL package with styles from the "OPT"_accelerate_opt.html
-package or the "USER-OMP package"_accelerate_omp.html". Of course,
+package or the "USER-OMP package"_accelerate_omp.html. Of course,
 this requires that these packages were installed at build time. This
 can performed automatically by using "-sf hybrid intel opt" or
 "-sf hybrid intel omp" command-line options. Alternatively, the "opt"

doc/src/accelerate_kokkos.txt

@@ -110,14 +110,14 @@ mpirun -np 96 -ppn 12 lmp_g++ -k on t 20 -sf kk -in in.lj   # ditto on 8 Phis :p
 [Required hardware/software:]
 
 Kokkos support within LAMMPS must be built with a C++11 compatible
-compiler.  If using gcc, version 4.8.1 or later is required.
+compiler.  If using gcc, version 4.7.2 or later is required.
 
 To build with Kokkos support for CPUs, your compiler must support the
 OpenMP interface.  You should have one or more multi-core CPUs so that
 multiple threads can be launched by each MPI task running on a CPU.
 
 To build with Kokkos support for NVIDIA GPUs, NVIDIA Cuda software
-version 6.5 or later must be installed on your system.  See the
+version 7.5 or later must be installed on your system.  See the
 discussion for the "GPU"_accelerate_gpu.html package for details of
 how to check and do this.
 

doc/src/angle_charmm.txt

@@ -74,7 +74,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]
 
 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 [Related commands:]

doc/src/angle_class2.txt

@@ -8,6 +8,7 @@
 
 angle_style class2 command :h3
 angle_style class2/omp command :h3
+angle_style class2/kk command :h3
 
 [Syntax:]
 

doc/src/angle_cosine.txt

@@ -61,7 +61,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]
 
 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 [Related commands:]

doc/src/angle_cosine_delta.txt

@@ -66,7 +66,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]
 
 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 [Related commands:]

doc/src/angle_cosine_periodic.txt

@@ -74,7 +74,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]
 
 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 [Related commands:]

doc/src/angle_cosine_squared.txt

@@ -66,7 +66,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]
 
 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 [Related commands:]

doc/src/angle_harmonic.txt

@@ -65,11 +65,11 @@ more instructions on how to use the accelerated styles effectively.
 
 :line
 
-[Restrictions:] none
+[Restrictions:]
 
 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package.  See the "Making LAMMPS"_Section_start.html#start_3
+section for more info on packages.
 
 [Related commands:]
 

doc/src/angle_hybrid.txt

@@ -76,7 +76,7 @@ for specific angle types.
 [Restrictions:]
 
 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 Unlike other angle styles, the hybrid angle style does not store angle

doc/src/angle_table.txt

@@ -147,7 +147,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]
 
 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 [Related commands:]

doc/src/atom_style.txt

@@ -166,7 +166,7 @@ stores a per-particle mass and size and orientation (i.e. the corner
 points of the triangle).
 
 The {template} style allows molecular topolgy (bonds,angles,etc) to be
-defined via a molecule template using the "molecule"_molecule.txt
+defined via a molecule template using the "molecule"_molecule.html
 command.  The template stores one or more molecules with a single copy
 of the topology info (bonds,angles,etc) of each.  Individual atoms
 only store a template index and template atom to identify which

doc/src/bond_class2.txt

@@ -8,6 +8,7 @@
 
 bond_style class2 command :h3
 bond_style class2/omp command :h3
+bond_style class2/kk command :h3
 
 [Syntax:]
 

doc/src/bond_fene.txt

@@ -70,10 +70,10 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]
 
 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
-You typically should specify "special_bonds fene"_special_bonds.html"
+You typically should specify "special_bonds fene"_special_bonds.html
 or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond
 style.  LAMMPS will issue a warning it that's not the case.
 

doc/src/bond_fene_expand.txt

@@ -73,10 +73,10 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]
 
 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
-You typically should specify "special_bonds fene"_special_bonds.html"
+You typically should specify "special_bonds fene"_special_bonds.html
 or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond
 style.  LAMMPS will issue a warning it that's not the case.
 

doc/src/bond_harmonic.txt

@@ -65,7 +65,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]
 
 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 [Related commands:]

doc/src/bond_hybrid.txt

@@ -59,7 +59,7 @@ bond types.
 [Restrictions:]
 
 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 Unlike other bond styles, the hybrid bond style does not store bond

doc/src/bond_morse.txt

@@ -64,7 +64,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]
 
 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 [Related commands:]

doc/src/bond_nonlinear.txt

@@ -64,7 +64,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]
 
 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 [Related commands:]

doc/src/bond_oxdna_fene.txt

@@ -0,0 +1,70 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+bond_style oxdna_fene command :h3
+
+[Syntax:]
+
+bond_style oxdna_fene :pre
+
+[Examples:]
+
+bond_style oxdna_fene
+bond_coeff * 2.0 0.25 0.7525 :pre
+
+[Description:]
+
+The {oxdna_fene} bond style uses the potential
+
+:c,image(Eqs/bond_oxdna_fene.jpg)
+
+to define a modified finite extensible nonlinear elastic (FENE) potential
+"(Ouldridge)"_#oxdna_fene to model the connectivity of the phosphate backbone
+in the oxDNA force field for coarse-grained modelling of DNA. 
+
+The following coefficients must be defined for the bond type via the
+"bond_coeff"_bond_coeff.html command as given in the above example, or in
+the data file or restart files read by the "read_data"_read_data.html
+or "read_restart"_read_restart.html commands:
+
+epsilon (energy)
+Delta (distance)
+r0 (distance) :ul
+
+NOTE: This bond style has to be used together with the corresponding oxDNA pair styles
+for excluded volume interaction {oxdna_excv}, stacking {oxdna_stk}, cross-stacking {oxdna_xstk}
+and coaxial stacking interaction {oxdna_coaxstk} as well as hydrogen-bonding interaction {oxdna_hbond} (see also documentation of 
+"pair_style oxdna_excv"_pair_oxdna_excv.html). The coefficients 
+in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
+
+Example input and data files can be found in /examples/USER/cgdna/examples/duplex1/ and /duplex2/.
+A simple python setup tool which creates single straight or helical DNA strands,
+DNA duplexes or arrays of DNA duplexes can be found in /examples/USER/cgdna/util/.
+A technical report with more information on the model, the structure of the input file,
+the setup tool and the performance of the LAMMPS-implementation of oxDNA
+can be found "here"_PDF/USER-CGDNA-overview.pdf.
+
+:line
+
+[Restrictions:]
+
+This bond style can only be used if LAMMPS was built with the
+USER-CGDNA package and the MOLECULE and ASPHERE package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info on packages.
+
+
+[Related commands:]
+
+"pair_style oxdna_excv"_pair_oxdna_excv.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html 
+
+[Default:] none
+
+:line
+
+:link(oxdna_fene)
+[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).

doc/src/bond_quartic.txt

@@ -99,7 +99,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]
 
 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 The {quartic} style requires that "special_bonds"_special_bonds.html

doc/src/bond_table.txt

@@ -144,7 +144,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]
 
 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 [Related commands:]

doc/src/bonds.txt

@@ -15,6 +15,7 @@ Bond Styles :h1
    bond_morse
    bond_none
    bond_nonlinear
+   bond_oxdna_fene
    bond_quartic
    bond_table
    bond_zero

doc/src/commands.txt

@@ -37,6 +37,7 @@ Commands :h1
    dump_image
    dump_modify
    dump_molfile
+   dump_nc
    echo
    fix
    fix_modify
@@ -90,6 +91,7 @@ Commands :h1
    suffix
    tad
    temper
+   temper_grem
    thermo
    thermo_modify
    thermo_style

doc/src/compute_bond_local.txt

@@ -51,12 +51,12 @@ relative to the center of mass (COM) velocity of the 2 atoms in the
 bond.
 
 The value {engvib} is the vibrational kinetic energy of the two atoms
-in the bond, which is simply 1/2 m1 v1^2 + 1/2 m1 v2^2, where v1 and
+in the bond, which is simply 1/2 m1 v1^2 + 1/2 m2 v2^2, where v1 and
 v2 are the magnitude of the velocity of the 2 atoms along the bond
 direction, after the COM velocity has been subtracted from each.
 
 The value {engrot} is the rotationsl kinetic energy of the two atoms
-in the bond, which is simply 1/2 m1 v1^2 + 1/2 m1 v2^2, where v1 and
+in the bond, which is simply 1/2 m1 v1^2 + 1/2 m2 v2^2, where v1 and
 v2 are the magnitude of the velocity of the 2 atoms perpendicular to
 the bond direction, after the COM velocity has been subtracted from
 each.
@@ -67,7 +67,7 @@ Vcm^2 where Vcm = magnitude of the velocity of the COM.
 
 Note that these 3 kinetic energy terms are simply a partitioning of
 the summed kinetic energy of the 2 atoms themselves.  I.e. total KE =
-1/2 m1 v1^2 + 1/2 m2 v3^2 = engvib + engrot + engtrans, where v1,v2
+1/2 m1 v1^2 + 1/2 m2 v2^2 = engvib + engrot + engtrans, where v1,v2
 are the magnitude of the velocities of the 2 atoms, without any
 adjustment for the COM velocity.
 

doc/src/compute_centro_atom.txt

@@ -114,7 +114,7 @@ local defects surrounding the central atom, as described above.  For
 the {axes yes} case, the vector components are also unitless, since
 they represent spatial directions.
 
-Here are typical centro-symmetry values, from a a nanoindentation
+Here are typical centro-symmetry values, from a nanoindentation
 simulation into gold (FCC).  These were provided by Jon Zimmerman
 (Sandia):
 

doc/src/compute_chunk_atom.txt

@@ -536,7 +536,7 @@ For the {bin/cylinder} style the details are as follows.  If {discard}
 is set to {yes}, an out-of-domain atom will have its chunk ID set to
 0.  If {discard} is set to {no}, the atom will have its chunk ID set
 to the first or last bin in both the radial and axis dimensions.  If
-{discard} is set to {mixed}, which is the default, the the radial
+{discard} is set to {mixed}, which is the default, the radial
 dimension is treated the same as for {discard} = no.  But for the axis
 dimensinon, it will only have its chunk ID set to the first or last
 bin if bins extend to the simulation box boundary in the axis
@@ -641,7 +641,8 @@ the restarted simulation begins.
 
 [Related commands:]
 
-"fix ave/chunk"_fix_ave_chunk.html
+"fix ave/chunk"_fix_ave_chunk.html,
+"compute global/atom"_compute_global_atom.html
 
 [Default:]
 

doc/src/compute_cluster_atom.txt

@@ -37,7 +37,7 @@ The neighbor list needed to compute this quantity is constructed each
 time the calculation is performed (i.e. each time a snapshot of atoms
 is dumped).  Thus it can be inefficient to compute/dump this quantity
 too frequently or to have multiple compute/dump commands, each of a
-{clsuter/atom} style.
+{cluster/atom} style.
 
 NOTE: If you have a bonded system, then the settings of
 "special_bonds"_special_bonds.html command can remove pairwise

doc/src/compute_coord_atom.txt

@@ -10,34 +10,43 @@ compute coord/atom command :h3
 
 [Syntax:]
 
-compute ID group-ID coord/atom cutoff type1 type2 ... :pre
+compute ID group-ID coord/atom cstyle args ... :pre
 
-ID, group-ID are documented in "compute"_compute.html command
-coord/atom = style name of this compute command
-cutoff = distance within which to count coordination neighbors (distance units)
-typeN = atom type for Nth coordination count (see asterisk form below) :ul
+ID, group-ID are documented in "compute"_compute.html command :ulb,l
+coord/atom = style name of this compute command :l
+cstyle = {cutoff} or {orientorder} :l
+  {cutoff} args = cutoff typeN
+    cutoff = distance within which to count coordination neighbors (distance units)
+    typeN = atom type for Nth coordination count (see asterisk form below)
+  {orientorder} args = orientorderID threshold
+    orientorderID = ID of an orientorder/atom compute
+    threshold = minimum value of the product of two "connected" atoms :pre
+:ule
 
 [Examples:]
 
-compute 1 all coord/atom 2.0
-compute 1 all coord/atom 6.0 1 2
-compute 1 all coord/atom 6.0 2*4 5*8 * :pre
+compute 1 all coord/atom cutoff 2.0
+compute 1 all coord/atom cutoff 6.0 1 2
+compute 1 all coord/atom cutoff 6.0 2*4 5*8 *
+compute 1 all coord/atom orientorder 2 0.5 :pre
 
 [Description:]
 
-Define a computation that calculates one or more coordination numbers
-for each atom in a group.
+This compute performs calculations between neighboring atoms to
+determine a coordination value.  The specific calculation and the
+meaning of the resulting value depend on the {cstyle} keyword used.
 
-A coordination number is defined as the number of neighbor atoms with
-specified atom type(s) that are within the specified cutoff distance
-from the central atom.  Atoms not in the group are included in a
-coordination number of atoms in the group.
+The {cutoff} cstyle calculates one or more traditional coordination
+numbers for each atom.  A coordination number is defined as the number
+of neighbor atoms with specified atom type(s) that are within the
+specified cutoff distance from the central atom.  Atoms not in the
+specified group are included in the coordination number tally.
 
-The {typeN} keywords allow you to specify which atom types contribute
-to each coordination number.  One coordination number is computed for
-each of the {typeN} keywords listed.  If no {typeN} keywords are
-listed, a single coordination number is calculated, which includes
-atoms of all types (same as the "*" format, see below).
+The {typeN} keywords allow specification of which atom types
+contribute to each coordination number.  One coordination number is
+computed for each of the {typeN} keywords listed.  If no {typeN}
+keywords are listed, a single coordination number is calculated, which
+includes atoms of all types (same as the "*" format, see below).
 
 The {typeN} keywords can be specified in one of two ways.  An explicit
 numeric value can be used, as in the 2nd example above.  Or a
@@ -49,8 +58,27 @@ from 1 to N.  A leading asterisk means all types from 1 to n
 (inclusive).  A middle asterisk means all types from m to n
 (inclusive).
 
-The value of all coordination numbers will be 0.0 for atoms not in the
-specified compute group.
+The {orientorder} cstyle calculates the number of "connected" neighbor
+atoms J around each central atom I.  For this {cstyle}, connected is
+defined by the orientational order parameter calculated by the
+"compute orientorder/atom"_compute_orientorder_atom.html command.
+This {cstyle} thus allows one to apply the ten Wolde's criterion to
+identify crystal-like atoms in a system, as discussed in "ten
+Wolde"_#tenWolde.
+
+The ID of the previously specified "compute
+orientorder/atom"_compute_orientorder/atom command is specified as
+{orientorderID}.  The compute must invoke its {components} option to
+calculate components of the {Ybar_lm} vector for each atoms, as
+described in its documenation.  Note that orientorder/atom compute
+defines its own criteria for identifying neighboring atoms.  If the
+scalar product ({Ybar_lm(i)},{Ybar_lm(j)}), calculated by the
+orientorder/atom compute is larger than the specified {threshold},
+then I and J are connected, and the coordination value of I is
+incremented by one.
+
+For all {cstyle} settings, all coordination values will be 0.0 for
+atoms not in the specified compute group.
 
 The neighbor list needed to compute this quantity is constructed each
 time the calculation is performed (i.e. each time a snapshot of atoms
@@ -72,11 +100,16 @@ the neighbor list.
 
 [Output info:]
 
-If single {type1} keyword is specified (or if none are specified),
-this compute calculates a per-atom vector.  If multiple {typeN}
-keywords are specified, this compute calculates a per-atom array, with
-N columns.  These values can be accessed by any command that uses
-per-atom values from a compute as input.  See "Section
+For {cstyle} cutoff, this compute can calculate a per-atom vector or
+array.  If single {type1} keyword is specified (or if none are
+specified), this compute calculates a per-atom vector.  If multiple
+{typeN} keywords are specified, this compute calculates a per-atom
+array, with N columns.
+
+For {cstyle} orientorder, this compute calculates a per-atom vector.
+
+These values can be accessed by any command that uses per-atom values
+from a compute as input.  See "Section
 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
 options.
 
@@ -88,5 +121,12 @@ explained above.
 [Related commands:]
 
 "compute cluster/atom"_compute_cluster_atom.html
+"compute orientorder/atom"_compute_orientorder_atom.html
 
 [Default:] none
+
+:line
+
+:link(tenWolde)
+[(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel,
+J. Chem. Phys. 104, 9932 (1996).

doc/src/compute_fep.txt

@@ -236,7 +236,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 [Related commands:]
 
 "fix adapt/fep"_fix_adapt_fep.html, "fix ave/time"_fix_ave_time.html,
-"pair_lj_soft_coul_soft"_pair_lj_soft_coul_soft.txt
+"pair_style lj/soft/coul/soft"_pair_lj_soft.html
 
 [Default:]