new library functions

Static analysis fixes

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"
@@ -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/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/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="27 Oct 2016 version">
 <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
 <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation.  This software and manual is distributed under the GNU General Public License.">
 </HEAD>
@@ -21,7 +21,7 @@
 <H1></H1>
 
 LAMMPS Documentation :c,h3
-6 Oct 2016 version :c,h4
+27 Oct 2016 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
 
@@ -471,6 +528,8 @@ 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)
 
@@ -516,6 +575,7 @@ 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,
@@ -618,6 +678,7 @@ 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,
@@ -923,6 +984,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "tip4p/long (o)"_pair_coul.html,
 "tri/lj"_pair_tri_lj.html,
 "vashishta (o)"_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)

doc/src/Section_errors.txt

@@ -8116,11 +8116,11 @@ 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 +8132,11 @@ 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 +8148,11 @@ 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 +1901,93 @@ 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_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 *)
+void *lammps_extract_variable(void *, char *, char *) :pre
+
 int lammps_set_variable(void *, char *, char *)
+double lammps_get_thermo(void *, char *) :pre
+
 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 *) :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_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.
+
+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.  It uses the coords of each atom to assign it as a new
+atom to the processor that owns it.  Additional properties for the new
+atoms can 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
 

doc/src/Section_packages.txt

@@ -1153,6 +1153,7 @@ 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
@@ -1598,6 +1599,29 @@ 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

@@ -534,10 +534,11 @@ 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 +550,8 @@ 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 +583,8 @@ 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 +604,10 @@ 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 +632,9 @@ 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

doc/src/Section_start.txt

@@ -1601,9 +1601,9 @@ 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
 

doc/src/accelerate_intel.txt

@@ -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/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_fene.txt

@@ -73,7 +73,7 @@ This bond 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.
 
-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

@@ -76,7 +76,7 @@ This bond 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.
 
-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/commands.txt

@@ -37,6 +37,7 @@ Commands :h1
    dump_image
    dump_modify
    dump_molfile
+   dump_nc
    echo
    fix
    fix_modify

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:]
 

doc/src/compute_orientorder_atom.txt

@@ -15,7 +15,7 @@ compute ID group-ID orientorder/atom keyword values ... :pre
 ID, group-ID are documented in "compute"_compute.html command :ulb,l
 orientorder/atom = style name of this compute command :l
 one or more keyword/value pairs may be appended :l
-keyword = {cutoff} or {nnn} or {ql}
+keyword = {cutoff} or {nnn} or {degrees}
   {cutoff} value = distance cutoff
   {nnn} value = number of nearest neighbors
   {degrees} values = nlvalues, l1, l2,...  :pre
@@ -111,7 +111,7 @@ options.
 
 [Default:]
 
-The option defaults are {cutoff} = pair style cutoff, {nnn} = 12, {degrees} = 5 4 6 8 9 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12.
+The option defaults are {cutoff} = pair style cutoff, {nnn} = 12, {degrees} = 5 4 6 8 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12.
 
 :line
 

doc/src/compute_pe_atom.txt

@@ -72,9 +72,10 @@ compute        peratom all pe/atom
 compute        pe all reduce sum c_peratom
 thermo_style   custom step temp etotal press pe c_pe :pre
 
-NOTE: The per-atom energy does not any Lennard-Jones tail corrections
-invoked by the "pair_modify tail yes"_pair_modify.html command, since
-those are global contributions to the system energy.
+NOTE: The per-atom energy does not include any Lennard-Jones tail
+corrections to the energy added by the "pair_modify tail
+yes"_pair_modify.html command, since those are contributions to the
+global system energy.
 
 [Output info:]
 

doc/src/compute_property_local.txt

@@ -78,7 +78,7 @@ defined by the "pair_style"_pair_style.html command for the types of
 the two atoms is used.  For the {radius} setting, the sum of the radii
 of the two particles is used as a cutoff.  For example, this is
 appropriate for granular particles which only interact when they are
-overlapping, as computed by "granular pair styles"_pair_gran.txt.
+overlapping, as computed by "granular pair styles"_pair_gran.html.
 
 If the inputs are bond, angle, etc attributes, the local data is
 generated by looping over all the atoms owned on a processor and

doc/src/compute_stress_atom.txt

@@ -133,6 +133,11 @@ compute        p all reduce sum c_peratom\[1\] c_peratom\[2\] c_peratom\[3\]
 variable       press equal -(c_p\[1\]+c_p\[2\]+c_p\[3\])/(3*vol)
 thermo_style   custom step temp etotal press v_press :pre
 
+NOTE: The per-atom stress does not include any Lennard-Jones tail
+corrections to the pressure added by the "pair_modify tail
+yes"_pair_modify.html command, since those are contributions to the
+global system pressure.
+
 [Output info:]
 
 This compute calculates a per-atom array with 6 columns, which can be

doc/src/dump.txt

@@ -12,6 +12,7 @@ dump command :h3
 "dump image"_dump_image.html command :h3
 "dump movie"_dump_image.html command :h3
 "dump molfile"_dump_molfile.html command :h3
+"dump nc"_dump_nc.html command :h3
 
 [Syntax:]
 
@@ -43,7 +44,9 @@ args = list of arguments for a particular style :l
 
   {movie} args = discussed on "dump image"_dump_image.html doc page :pre
 
-  {molfile} args = discussed on "dump molfile"_dump_molfile.html doc page :pre
+  {molfile} args = discussed on "dump molfile"_dump_molfile.html doc page
+
+  {nc} args = discussed on "dump nc"_dump_nc.html doc page :pre
 
   {local} args = list of local attributes
     possible attributes = index, c_ID, c_ID\[I\], f_ID, f_ID\[I\]

doc/src/dump_modify.txt

@@ -47,9 +47,9 @@ keyword = {append} or {buffer} or {element} or {every} or {fileper} or {first} o
      id = sort per-atom lines by atom ID
      N = sort per-atom lines in ascending order by the Nth column
      -N = sort per-atom lines in descending order by the Nth column
-  {thresh} args = attribute operation value
+  {thresh} args = attribute operator value
     attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
-    operation = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^"
+    operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^"
     value = numeric value to compare to, or LAST
     these 3 args can be replaced by the word "none" to turn off thresholding
   {unwrap} arg = {yes} or {no} :pre
@@ -470,14 +470,11 @@ stress of atoms whose energy is above some threshold.
 
 If an atom-style variable is used as the attribute, then it can
 produce continuous numeric values or effective Boolean 0/1 values
-which may be useful for the comparision operation.  Boolean values can
+which may be useful for the comparision operator.  Boolean values can
 be generated by variable formulas that use comparison or Boolean math
 operators or special functions like gmask() and rmask() and grmask().
 See the "variable"_variable.html command doc page for details.
 
-NOTE: The LAST option, discussed below, is not yet implemented.  It
-will be soon.
-
 The specified value must be a simple numeric value or the word LAST.
 If LAST is used, it refers to the value of the attribute the last time
 the dump command was invoked to produce a snapshot.  This is a way to
@@ -506,11 +503,11 @@ less than 1/2 to greater than 1/2 (or vice versa) since the last dump.
 E.g. due to reactions and subsequent charge equilibration in a
 reactive force field.
 
-The choice of operations are the usual comparison operators.  The XOR
-operation (exclusive or) is also included as "|^".  In this context,
-XOR means that if either the attribute or value is 0.0 and the other
-is non-zero, then the result is "true" and the threshold criterion is
-met.  Otherwise it is not met.
+The choice of operators listed above are the usual comparison
+operators.  The XOR operation (exclusive or) is also included as "|^".
+In this context, XOR means that if either the attribute or value is
+0.0 and the other is non-zero, then the result is "true" and the
+threshold criterion is met.  Otherwise it is not met.
 
 :line
 

doc/src/dump_nc.txt

@@ -0,0 +1,66 @@
+"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
+
+dump nc command :h3
+dump nc/mpiio command :h3
+
+[Syntax:]
+
+dump ID group-ID nc N file.nc args
+dump ID group-ID nc/mpiio N file.nc args :pre
+
+ID = user-assigned name for the dump :ulb,l
+group-ID = ID of the group of atoms to be imaged :l
+{nc} or {nc/mpiio}  = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) :l
+N = dump every this many timesteps :l
+file.nc = name of file to write to :l
+args = list of per atom data elements to dump, same as for the 'custom' dump style. :l,ule
+
+[Examples:]
+
+dump 1 all nc 100 traj.nc type x y z vx vy vz
+dump_modify 1 append yes at -1 global c_thermo_pe c_thermo_temp c_thermo_press :pre
+
+dump 1 all nc/mpiio 1000 traj.nc id type x y z :pre
+
+[Description:]
+
+Dump a snapshot of atom coordinates every N timesteps in Amber-style
+NetCDF file format. NetCDF files are binary, portable and
+self-describing.  This dump style will write only one file on the root
+node.  The dump style {nc} uses the "standard NetCDF
+library"_netcdf-home all data is collected on one processor and then
+written to the dump file. Dump style {nc/mpiio} used the "parallel
+NetCDF library"_pnetcdf-home and MPI-IO; it has better performance on
+a larger number of processors. Note that 'nc' outputs all atoms sorted
+by atom tag while 'nc/mpiio' outputs in order of the MPI rank.
+
+In addition to per-atom data, also global (i.e. not per atom, but per
+frame) quantities can be included in the dump file. This can be
+variables, output from computes or fixes data prefixed with v_, c_ and
+f_, respectively.  These properties are included via
+"dump_modify"_dump_modify.html {global}.
+
+:link(netcdf-home,http://www.unidata.ucar.edu/software/netcdf/)
+:link(pnetcdf-home,http://trac.mcs.anl.gov/projects/parallel-netcdf/)
+
+:line
+
+[Restrictions:]
+
+The {nc} and {nc/mpiio} dump styles are part of the USER-NC-DUMP
+package.  It is only enabled if LAMMPS was built with that
+package. See the "Making LAMMPS"_Section_start.html#start_3 section
+for more info.
+
+:line
+
+[Related commands:]
+
+"dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html
+

doc/src/fix.txt

@@ -190,6 +190,7 @@ of "this page"_Section_commands.html#cmd_5.
 "gcmc"_fix_gcmc.html - grand canonical insertions/deletions
 "gld"_fix_gcmc.html - generalized Langevin dynamics integrator
 "gravity"_fix_gravity.html - add gravity to atoms in a granular simulation
+"halt"_fix_halt.html - terminate a dynamics run or minimization
 "heat"_fix_heat.html - add/subtract momentum-conserving heat
 "indent"_fix_indent.html - impose force due to an indenter
 "langevin"_fix_langevin.html - Langevin temperature control

doc/src/fix_dpd_energy.txt

@@ -0,0 +1,83 @@
+"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
+
+fix dpd/energy command :h3
+
+[Syntax:]
+
+fix ID group-ID dpd/energy :pre
+
+ID, group-ID are documented in "fix"_fix.html command
+dpd/energy = style name of this fix command :ul
+
+[Examples:]
+
+fix 1 all dpd/energy :pre
+
+[Description:]
+
+Perform constant energy dissipative particle dynamics (DPD-E)
+integration.  This fix updates the internal energies for particles in
+the group at each timestep.  It must be used in conjunction with a
+deterministic integrator (e.g. "fix nve"_fix_nve.html) that updates
+the particle positions and velocities.
+
+For fix {dpd/energy}, the particle internal temperature is related to
+the particle internal energy through a mesoparticle equation of state.
+An additional fix must be specified that defines the equation of state
+for each particle, e.g. "fix eos/cv"_fix_eos_cv.html.
+
+This fix must be used with the "pair_style
+dpd/fdt/energy"_pair_style.html command.
+
+Note that numerous variants of DPD can be specified by choosing an
+appropriate combination of the integrator and "pair_style
+dpd/fdt/energy"_pair_style.html command.  DPD under isoenergetic conditions
+can be specified by using fix {dpd/energy}, fix {nve} and pair_style
+{dpd/fdt/energy}.  DPD under isoenthalpic conditions can
+be specified by using fix {dpd/energy}, fix {nph} and pair_style
+{dpd/fdt/energy}.  Examples of each DPD variant are provided in the
+examples/USER/dpd directory.
+
+:line
+
+[Restrictions:]
+
+This command is part of the USER-DPD package.  It is only enabled if
+LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+This fix must be used with an additional fix that specifies time
+integration, e.g. "fix nve"_fix_nve.html.
+
+The fix {dpd/energy} requires the {dpd} "atom_style"_atom_style.html
+to be used in order to properly account for the particle internal
+energies and temperature.
+
+The fix {dpd/energy} must be used with an additional fix that specifies the
+mesoparticle equation of state for each particle.
+
+[Related commands:]
+
+"fix nve"_fix_nve.html "fix eos/cv"_fix_eos_cv.html
+
+[Default:] none
+
+:line
+
+:link(Lisal)
+[(Lisal)] M. Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative
+particle dynamics at isothermal, isobaric, isoenergetic, and
+isoenthalpic conditions using Shardlow-like splitting algorithms.",
+J. Chem. Phys., 135, 204105 (2011).
+
+:link(Larentzos)
+[(Larentzos)] J.P. Larentzos, J.K. Brennan, J.D. Moore, and
+W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative
+Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research
+Laboratory, Aberdeen Proving Ground, MD (2014).

doc/src/fix_flow_gauss.txt

@@ -63,7 +63,7 @@ applied by GD before computing a pressure drop or comparing it to
 other methods, such as the pump method "(Zhu)"_#Zhu. The pressure
 correction is discussed and described in "(Strong)"_#Strong.
 
-NOTE: For a complete example including the considerations discussed
+For a complete example including the considerations discussed
 above, see the examples/USER/flow_gauss directory.
 
 NOTE: Only the flux of the atoms in group-ID will be conserved. If the
@@ -93,6 +93,19 @@ work on the system must have {fix_modify energy yes} set as well. This
 includes thermostat fixes and any constraints that hold the positions
 of wall atoms fixed, such as "fix spring/self"_fix_spring_self.html.
 
+If this fix is used in a simulation with the "rRESPA"_run_style.html
+integrator, the applied acceleration must be computed and applied at the same
+rRESPA level as the interactions between the flowing fluid and the obstacle.
+The rRESPA level at which the acceleration is applied can be changed using
+the "fix_modify"_fix_modify.html {respa} option discussed below. If the
+flowing fluid and the obstacle interact through multiple interactions that are
+computed at different rRESPA levels, then there must be a separate flow/gauss
+fix for each level. For example, if the flowing fluid and obstacle interact
+through pairwise and long-range Coulomb interactions, which are computed at
+rRESPA levels 3 and 4, respectively, then there must be two separate
+flow/gauss fixes, one that specifies {fix_modify respa 3} and one with
+{fix_modify respa 4}.
+
 :line
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
@@ -109,6 +122,11 @@ fix to subtract the work done from the
 system's potential energy as part of "thermodynamic
 output"_thermo_style.html.
 
+The "fix_modify"_fix_modify.html {respa} option is supported by this
+fix. This allows the user to set at which level of the "rRESPA"_run_style.html
+integrator the fix computes and adds the external acceleration. Default is the
+outermost level.
+
 This fix computes a global scalar and a global 3-vector of forces,
 which can be accessed by various "output
 commands"_Section_howto.html#howto_15.  The scalar is the negative of the

doc/src/fix_halt.txt

@@ -0,0 +1,121 @@
+"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
+
+fix halt command :h3
+
+[Syntax:]
+
+fix ID group-ID halt N attribute operator avalue keyword value ... :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+halt = style name of this fix command :l
+N = check halt condition every N steps :l
+attribute = hstyle or v_name :l
+  hstyle = {bondmax}
+  v_name = name of "equal-style variable"_variable.html :pre
+operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^" :l
+avalue = numeric value to compare attribute to :l
+string = text string to print with optional variable names :l
+zero or more keyword/value pairs may be appended :l
+keyword = {error} :l
+  {error} value = {hard} or {soft} or {continue} :pre
+:ule
+
+[Examples:]
+
+fix 10 all halt 1 bondmax > 1.5
+fix 10 all print 10 v_myCheck != 0 error soft :pre
+
+[Description:]
+
+Check a condition every N steps during a simulation run.  N must be >=
+1.  If the condition is met, exit the run immediately.  In this
+context a "run" can be dynamics or minimization iterations, as
+specified by the "run"_run.html or "minimize"_minimize.html command.
+
+The specified group-ID is ignored by this fix.
+
+The specified {attribute} can be one of the {hstyle} options listed
+above, or an "equal-style variable"_variable.html referenced as
+{v_name}, where "name" is the name of a variable that has been defined
+previously in the input script.
+
+The only {hstyle} option currently implemented is {bondmax}.  This
+will loop over all bonds in the system, compute their current
+lengths, and set {attribute} to the longest bond distance.
+
+Equal-style variables evaluate to a numeric value.  See the
+"variable"_variable.html command for a description.  They calculate
+formulas which can involve mathematical operations, atom properties,
+group properties, thermodynamic properties, global values calculated
+by a "compute"_compute.html or "fix"_fix.html, or references to other
+"variables"_variable.html.  Thus they are a very general means of
+computing some attribute of the current system.  For example, the
+following "bondmax" variable will calculate the same quantity as the
+hstyle = bondmax option.
+
+compute         bdist all bond/local dist
+compute         bmax all reduce max c_bdist
+variable        bondmax equal c_bmax :pre
+
+Thus these two versions of a fix halt command will do the same thing:
+
+fix 10 all halt 1 bondmax > 1.5
+fix 10 all halt 1 v_bondmax > 1.5 :pre
+
+The version with "bondmax" will just run somewhat faster, due to less
+overhead in computing bond lengths and not storing them in a separate
+compute.
+
+The choice of operators listed above are the usual comparison
+operators.  The XOR operation (exclusive or) is also included as "|^".
+In this context, XOR means that if either the attribute or avalue is
+0.0 and the other is non-zero, then the result is "true".  Otherwise
+it is "false".
+
+The specified {avalue} must be a numeric value.
+
+:line
+
+The optional {error} keyword determines how the current run is halted.
+If its value is {hard}, then LAMMPS will stop with an error message.
+
+If its value is {soft}, LAMMPS will exit the current run, but continue
+to execute subsequent commands in the input script.  However,
+additional "run"_run.html or "minimize"_minimize.html commands will be
+skipped.  For example, this allows a script to output the current
+state of the system, e.g. via a "write_dump"_write_dump.html or
+"write_restart"_write_restart.html command.
+
+If its value is {continue}, the behavior is the same as for {soft},
+except subsequent subsequent "run"_run.html or
+"minimize"_minimize.html commands are executed.  This allows your
+script to remedy the condition that triggered the halt, if necessary.
+Note that you may wish use the "unfix"_unfix.html command on the fix
+halt ID, so that the same condition is not immediately triggered in a
+subsequent run.
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various "output
+commands"_Section_howto.html#howto_15.  No parameter of this fix can
+be used with the {start/stop} keywords of the "run"_run.html command.
+This fix is not invoked during "energy minimization"_minimize.html.
+
+[Restrictions:] none
+
+[Related commands:]
+
+"variable"_variable.html
+
+[Default:]
+
+The option defaults are error = hard.

doc/src/fix_phonon.txt

@@ -184,7 +184,7 @@ This fix requires LAMMPS be built with an FFT library.  See the
 [Default:]
 
 The option defaults are sysdim = the same dimemsion as specified by
-the "dimension"_dimension command, and nasr = 20.
+the "dimension"_dimension.html command, and nasr = 20.
 
 :line
 

doc/src/fix_property_atom.txt

@@ -177,7 +177,7 @@ their values.  This means that the values can be output via the "dump
 custom"_dump.html command, accessed by fixes like "fix
 ave/atom"_fix_ave_atom.html, accessed by other computes like "compute
 reduce"_compute_reduce.html, or used in "atom-style
-variables"_variables.
+variables"_variable.html.
 
 For example, these commands will output two new properties to a custom
 dump file:

doc/src/fix_rigid.txt

@@ -620,7 +620,7 @@ rigid styles for the rigid bodies. :l
 
 Use "fix press/berendsen"_fix_press_berendsen.html to compute the
 pressure and change the box dimensions.  Use one of the 4 NVE or 2 NVT
-rigid styles for the rigid bodies.  Use "fix nvt"_fix_nh.thml (or any
+rigid styles for the rigid bodies.  Use "fix nvt"_fix_nh.html (or any
 other thermostat) for the non-rigid particles. :l
 :ule
 

doc/src/fix_temp_berendsen.txt

@@ -49,6 +49,10 @@ variable, it should be specified as v_name, where name is the variable
 name.  In this case, the variable will be evaluated each timestep, and
 its value used to determine the target temperature.
 
+NOTE: This thermostat will generate an error if the current
+temperature is zero at the end of a timestep.  It cannot rescale a
+zero temperature.
+
 Equal-style variables can specify formulas with various mathematical
 functions, and include "thermo_style"_thermo_style.html command
 keywords for the simulation box parameters and timestep and elapsed

doc/src/fix_temp_rescale.txt

@@ -43,6 +43,10 @@ Rescaling is performed every N timesteps.  The target temperature is a
 ramped value between the {Tstart} and {Tstop} temperatures at the
 beginning and end of the run.
 
+NOTE: This thermostat will generate an error if the current
+temperature is zero at the end of a timestep it is inovoked on.  It
+cannot rescale a zero temperature.
+
 {Tstart} can be specified as an equal-style "variable"_variable.html.
 In this case, the {Tstop} setting is ignored.  If the value is a
 variable, it should be specified as v_name, where name is the variable

doc/src/fix_ti_spring.txt

@@ -104,7 +104,7 @@ the Nose-Hoover thermostat ("fix nvt"_fix_nh.html) is {NOT}
 recommended due to its well documented issues with the canonical
 sampling of harmonic degrees of freedom (notice that the {chain}
 option will {NOT} solve this problem). The Langevin thermostat ("fix
-langevin"_fix_langevin.html") correctly thermostats the system and we
+langevin"_fix_langevin.html) correctly thermostats the system and we
 advise its usage with ti/spring command.
 
 [Restart, fix_modify, output, run start/stop, minimize info:]

doc/src/fix_wall_gran.txt

@@ -163,8 +163,8 @@ Any dimension (xyz) that has a granular wall must be non-periodic.
 
 [Related commands:]
 
-"fix move"_fix_move.html, 
-"fix wall/gran/region"_fix_wall_gran_region.html, 
+"fix move"_fix_move.html,
+"fix wall/gran/region"_fix_wall_gran_region.html,
 "pair_style granular"_pair_gran.html
 
 [Default:] none

doc/src/fix_wall_gran_region.txt

@@ -42,7 +42,7 @@ Here are snapshots of example models using this command.
 Corresponding input scripts can be found in examples/granregion.
 Click on the images to see a bigger picture.  Movies of these
 simulations are "here on the Movies
-page"_http://lammps.sandia.gov/movies.html#granregion.html of the
+page"_http://lammps.sandia.gov/movies.html#granregion of the
 LAMMPS web site.
 
 :image(JPG/gran_funnel_small.jpg,JPG/gran_funnel.png)
@@ -84,7 +84,7 @@ is up to you to ensure that the region location with respect to
 periodic or non-periodic boundaries is specified appropriately via the
 "region"_region.html and "boundary"_boundary.html commands when using
 a region as a wall that bounds particle motion.
- 
+
 NOTE: For primitive regions with sharp corners and/or edges (e.g. a
 block or cylinder), wall/particle forces are computed accurately for
 both interior and exterior regions.  For {union} and {intersect}
@@ -163,16 +163,20 @@ info on how to re-specify a fix in an input script that reads a
 restart file, so that the operation of the fix continues in an
 uninterrupted fashion.
 
-Note that info about region definitions is NOT included in restart
-files.  So you must re-define your region and if it is a moving
-region, define its motion attributes in a way that is consistent with
-the simulation that wrote the restart file.  In particular, if you
-want to change its motion attributes (e.g. its velocity), then you
-should insure the postition/orientation of the region at the initial
-restart timestep is the same as it was on the timestep the restart
-file was written.  If this is not possible, then you may need to
-ignore info in the restart file by defining a new fix wall/gran/region
-command in your restart script (e.g. with a different fix ID).
+NOTE: Information about region definitions is NOT included in restart
+files, as discussed on the "read_restart"_read_restart.html doc page.
+So you must re-define your region and if it is a moving region, define
+its motion attributes in a way that is consistent with the simulation
+that wrote the restart file.  In particular, if you want to change the
+region motion attributes (e.g. its velocity), then you should ensure
+the postition/orientation of the region at the initial restart
+timestep is the same as it was on the timestep the restart file was
+written.  If this is not possible, you may need to ignore info in the
+restart file by defining a new fix wall/gran/region command in your
+restart script, e.g. with a different fix ID.  Or if you want to keep
+the shear history info but discard the region motion information, you
+can use the same fix ID for fix wall/gran/region, but assign it a
+region with a different region ID.
 
 None of the "fix_modify"_fix_modify.html options are relevant to this
 fix.  No global or per-atom quantities are stored by this fix for
@@ -190,7 +194,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 [Related commands:]
 
 "fix_move"_fix_move.html,
-"fix wall/gran"_fix_wall_gran.html, 
+"fix wall/gran"_fix_wall_gran.html,
 "fix wall/region"_fix_wall_region.html,
 "pair_style granular"_pair_gran.html,
 "region"_region.html

doc/src/fixes.txt

@@ -32,6 +32,7 @@ Fixes :h1
    fix_drag
    fix_drude
    fix_drude_transform
+   fix_dpd_energy
    fix_dt_reset
    fix_efield
    fix_ehex
@@ -47,6 +48,7 @@ Fixes :h1
    fix_gld
    fix_gle
    fix_gravity
+   fix_halt
    fix_heat
    fix_imd
    fix_indent
@@ -148,6 +150,7 @@ Fixes :h1
    fix_viscous
    fix_wall
    fix_wall_gran
+   fix_wall_gran_region
    fix_wall_piston
    fix_wall_reflect
    fix_wall_region

doc/src/lammps.book

@@ -170,6 +170,7 @@ fix_gcmc.html
 fix_gld.html
 fix_gle.html
 fix_gravity.html
+fix_halt.html
 fix_heat.html
 fix_imd.html
 fix_indent.html

doc/src/minimize.txt

@@ -103,6 +103,11 @@ the line search fails because the step distance backtracks to 0.0
 the number of outer iterations or timesteps exceeds {maxiter}
 the number of total force evaluations exceeds {maxeval} :ul
 
+NOTE: You can also use the "fix halt"_fix_halt.html command to specify
+a general criterion for exiting a minimization, that is a calculation
+performed on the state of the current system, as defined by an
+"equal-style variable"_variable.html.
+
 For the first criterion, the specified energy tolerance {etol} is
 unitless; it is met when the energy change between successive
 iterations divided by the energy magnitude is less than or equal to

doc/src/neb.txt

@@ -83,9 +83,9 @@ replica.  Conceptually, the non-NEB atoms provide a background force
 field for the NEB atoms.  They can be allowed to move during the NEB
 minimiation procedure (which will typically induce different
 coordinates for non-NEB atoms in different replicas), or held fixed
-using other LAMMPS commands such as "fix setforce"_fix_setforce.  Note
-that the "partition"_partition.html command can be used to invoke a
-command on a subset of the replicas, e.g. if you wish to hold NEB or
+using other LAMMPS commands such as "fix setforce"_fix_setforce.html.
+Note that the "partition"_partition.html command can be used to invoke
+a command on a subset of the replicas, e.g. if you wish to hold NEB or
 non-NEB atoms fixed in only the end-point replicas.
 
 The initial atomic configuration for each of the replicas can be

doc/src/pair_dpd_fdt.txt

@@ -33,78 +33,95 @@ pair_coeff * * 3.0 1.0 0.1 2.5 :pre
 
 [Description:]
 
-Styles {dpd/fdt} and {dpd/fdt/energy} set the fluctuation-dissipation
-theorem parameters and compute the conservative force for dissipative
-particle dynamics (DPD). The conservative force on atom I due to atom
-J is given by
+Styles {dpd/fdt} and {dpd/fdt/energy} compute the force for dissipative
+particle dynamics (DPD) simulations.  The {dpd/fdt} style is used to
+perform DPD simulations under isothermal and isobaric conditions,
+while the {dpd/fdt/energy} style is used to perform DPD simulations
+under isoenergetic and isoenthalpic conditions (see "(Lisal)"_#Lisal).
+For DPD simulations in general, the force on atom I due to atom J is
+given as a sum of 3 terms
 
-:c,image(Eqs/pair_dpd_conservative.jpg)
+:c,image(Eqs/pair_dpd.jpg)
 
-where the weighting factor, omega_ij, varies between 0 and 1, and is
-chosen to have the following functional form:
+where Fc is a conservative force, Fd is a dissipative force, and Fr is
+a random force.  Rij is a unit vector in the direction Ri - Rj, Vij is
+the vector difference in velocities of the two atoms = Vi - Vj, alpha
+is a Gaussian random number with zero mean and unit variance, dt is
+the timestep size, and w(r) is a weighting factor that varies between
+0 and 1.  Rc is the cutoff.  The weighting factor, omega_ij, varies
+between 0 and 1, and is chosen to have the following functional form:
 
 :c,image(Eqs/pair_dpd_omega.jpg)
 
-where Rij is a unit vector in the direction Ri - Rj, and Rc is the
-cutoff.  Note that alternative definitions of the weighting function
-exist, but would have to be implemented as a separate pair style
-command.
+Note that alternative definitions of the weighting function exist, but
+would have to be implemented as a separate pair style command.
 
-These pair style differ from the other dpd styles in that the
-dissipative and random forces are not computed within the pair style.
-This style can be combined with the "fix shardlow"_fix_shardlow.html
-to perform the stochastic integration of the dissipative and random
-forces through the Shardlow splitting algorithm approach.
+For style {dpd/fdt}, the fluctuation-dissipation theorem defines gamma
+to be set equal to sigma*sigma/(2 T), where T is the set point
+temperature specified as a pair style parameter in the above examples.
+The following coefficients must be defined for each pair of atoms types
+via the "pair_coeff"_pair_coeff.html command as in the examples above,
+or in the data file or restart files read by the
+"read_data"_read_data.html or "read_restart"_read_restart.html commands:
+
+A (force units)
+sigma (force*time^(1/2) units)
+cutoff (distance units) :ul
+
+The last coefficient is optional.  If not specified, the global DPD
+cutoff is used.
+
+Style {dpd/fdt/energy} is used to perform DPD simulations
+under isoenergetic and isoenthalpic conditions.  The fluctuation-dissipation
+theorem defines gamma to be set equal to sigma*sigma/(2 dpdTheta), where
+dpdTheta is the average internal temperature for the pair. The particle
+internal temperature is related to the particle internal energy through
+a mesoparticle equation of state (see "fix eos"_fix.html). The
+differential internal conductive and mechanical energies are computed
+within style {dpd/fdt/energy} as:
+
+:c,image(Eqs/pair_dpd_energy.jpg)
+
+where
+
+:c,image(Eqs/pair_dpd_energy_terms.jpg)
+
+Zeta_ij^q is a second Gaussian random number with zero mean and unit
+variance that is used to compute the internal conductive energy. The
+fluctuation-dissipation theorem defines alpha*alpha to be set
+equal to 2*kB*kappa, where kappa is the mesoparticle thermal
+conductivity parameter.   The following coefficients must be defined for
+each pair of atoms types via the "pair_coeff"_pair_coeff.html
+command as in the examples above, or in the data file or restart files
+read by the "read_data"_read_data.html or "read_restart"_read_restart.html
+commands:
+
+A (force units)
+sigma (force*time^(1/2) units)
+kappa (energy*temperature/time units)
+cutoff (distance units) :ul
+
+The last coefficient is optional.  If not specified, the global DPD
+cutoff is used.
 
 The pairwise energy associated with styles {dpd/fdt} and
 {dpd/fdt/energy} is only due to the conservative force term Fc, and is
 shifted to be zero at the cutoff distance Rc.  The pairwise virial is
 calculated using only the conservative term.
 
-For style {dpd/fdt}, the fluctuation-dissipation theorem defines gamma
-to be set equal to sigma*sigma/(2 T), where T is the set point
-temperature specified as a pair style parameter in the above examples.
-This style can be combined with "fix shardlow"_fix_shardlow.html to
-perform DPD simulations under isothermal and isobaric conditions (see
-"(Lisal)"_#Lisal).  The following coefficients must be defined for
-each pair of atoms types via the "pair_coeff"_pair_coeff.html command
-as in the examples above, or in the data file or restart files read by
-the "read_data"_read_data.html or "read_restart"_read_restart.html
-commands:
-
-A (force units)
-sigma (force*time^(1/2) units)
-cutoff (distance units) :ul
-
-The last coefficient is optional.  If not specified, the global DPD
-cutoff is used.
-
-For style {dpd/fdt/energy}, the fluctuation-dissipation theorem
-defines gamma to be set equal to sigma*sigma/(2 dpdTheta), where
-dpdTheta is the average internal temperature for the pair.
-Furthermore, the fluctuation-dissipation defines alpha*alpha to be set
-equal to 2*kB*kappa, where kappa is the mesoparticle thermal
-conductivity parameter.  This style can be combined with "fix
-shardlow"_fix_shardlow.html to perform DPD simulations under
-isoenergetic and isoenthalpic conditions (see "(Lisal)"_#Lisal).  The
-following coefficients must be defined for each pair of atoms types
-via the "pair_coeff"_pair_coeff.html command as in the examples above,
-or in the data file or restart files read by the
-"read_data"_read_data.html or "read_restart"_read_restart.html
-commands:
-
-A (force units)
-sigma (force*time^(1/2) units)
-kappa (1/time units)
-cutoff (distance units) :ul
-
-The last coefficient is optional.  If not specified, the global DPD
-cutoff is used.
-
-For style {dpd/fdt/energy}, the particle internal temperature is
-related to the particle internal energy through a mesoparticle
-equation of state.  Thus, an an additional "fix eos"_fix.html must be
-specified.
+The forces computed through the {dpd/fdt} and {dpd/fdt/energy} styles
+can be integrated with the velocity-Verlet integration scheme or the
+Shardlow splitting integration scheme described by "(Lisal)"_#Lisal.
+In the cases when these pair styles are combined with the
+"fix shardlow"_fix_shardlow.html, these pair styles differ from the
+other dpd styles in that the dissipative and random forces are split
+from the force calculation and are not computed within the pair style.
+Thus, only the conservative force is computed by the pair style,
+while the stochastic integration of the dissipative and random forces
+are handled through the Shardlow splitting algorithm approach.  The
+Shardlow splitting algorithm is advantageous, especially when
+performing DPD under isoenergetic conditions, as it allows
+significantly larger timesteps to be taken.
 
 :line
 
@@ -132,6 +149,6 @@ energies and temperatures.
 
 :link(Lisal)
 [(Lisal)] M. Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative
-particle dynamics as isothermal, isobaric, isoenergetic, and
+particle dynamics at isothermal, isobaric, isoenergetic, and
 isoenthalpic conditions using Shardlow-like splitting algorithms.",
 J. Chem. Phys., 135, 204105 (2011).

doc/src/pair_gauss.txt

@@ -106,8 +106,31 @@ more instructions on how to use the accelerated styles effectively.
 
 [Mixing, shift, table, tail correction, restart, rRESPA info]:
 
-These pair styles do not support mixing. Thus, coefficients for all
-I,J pairs must be specified explicitly.
+For atom type pairs I,J and I != J, the A, B, H, sigma_h, r_mh
+parameters, and the cutoff distance for these pair styles can be mixed:
+A (energy units)
+sqrt(1/B) (distance units, see below)
+H (energy units)
+sigma_h (distance units)
+r_mh (distance units)
+cutoff (distance units):ul
+
+The default mix value is {geometric}.
+Only {arithmetic} and {geometric} mix values are supported.
+See the "pair_modify" command for details.
+
+The A and H parameters are mixed using the same rules normally
+used to mix the "epsilon" parameter in a Lennard Jones interaction.
+The sigma_h, r_mh, and the cutoff distance are mixed using the same
+rules used to mix the "sigma" parameter in a Lennard Jones interaction.
+The B parameter is converted to a distance (sigma), before mixing
+(using sigma=B^-0.5), and converted back to a coefficient
+afterwards (using B=sigma^2).
+Negative A values are converted to positive A values (using abs(A))
+before mixing, and converted back after mixing
+(by multiplying by sign(Ai)*sign(Aj)).
+This way, if either particle is repulsive (if Ai<0 or Aj<0),
+then the default interaction between both particles will be repulsive.
 
 The {gauss} style does not support the "pair_modify"_pair_modify.html
 shift option. There is no effect due to the Gaussian well beyond the

doc/src/pair_hbond_dreiding.txt

@@ -138,8 +138,8 @@ angle cutoff (degrees) :ul
 A single hydrogen atom type K can be specified, or a wild-card
 asterisk can be used in place of or in conjunction with the K
 arguments to select multiple types as hydrogens.  This takes the form
-"*" or "*n" or "n*" or "m*n".  See the "pair_coeff"_pair_coeff command
-doc page for details.
+"*" or "*n" or "n*" or "m*n".  See the "pair_coeff"_pair_coeff.html
+command doc page for details.
 
 If the donor flag is {i}, then the atom of type I in the pair_coeff
 command is treated as the donor, and J is the acceptor.  If the donor

doc/src/pair_line_lj.txt

@@ -60,8 +60,8 @@ pair_style command or overridden with an optional argument in the
 pair_coeff command for a type pair as discussed below.  The distance
 between the centers of 2 line segments, or the center of a line
 segment and a point particle, must be less than this distance (plus
-the neighbor skin; see the "neighbor"_neighbor command), for the pair
-of particles to be included in the neighbor list.
+the neighbor skin; see the "neighbor"_neighbor.html command), for
+the pair of particles to be included in the neighbor list.
 
 NOTE: This means that a too-short value for the {cutoff} setting can
 exclude a pair of particles from the neighbor list even if pairs of

doc/src/pair_lubricateU.txt

@@ -119,7 +119,7 @@ of walls (whether moving or stationary) will affect the volume
 fraction available to colloidal particles. This is currently accounted
 for with the following types of walls: "wall/lj93"_fix_wall.html,
 "wall/lj126"_fix_wall.html, "wall/colloid"_fix_wall.html, and
-"wall/harmonic_fix_wall.html".  For these wall styles, the correct
+"wall/harmonic"_fix_wall.html.  For these wall styles, the correct
 volume fraction will be used when walls do not coincide with the box
 boundary, as well as when walls move and thereby cause a change in the
 volume fraction. To use these wall styles with pair_style {lubricateU}

doc/src/pair_thole.txt

@@ -180,7 +180,7 @@ package.
 langevin/drude"_fix_langevin_drude.html, "fix
 drude/transform"_fix_drude_transform.html, "compute
 temp/drude"_compute_temp_drude.html
-"pair_style lj/cut/coul/long"_pair_lj_cut_coul_long
+"pair_style lj/cut/coul/long"_pair_lj.html
 
 [Default:] none
 

doc/src/read_data.txt

@@ -431,8 +431,8 @@ Atoms # sphere
 Pair Coeffs # lj/cut :pre
 
 will check if the currently-defined "atom_style"_atom_style.html is
-{sphere}, and the current "pair_style"_pair_style is {lj/cut}.  If
-not, LAMMPS will issue a warning to indicate that the data file
+{sphere}, and the current "pair_style"_pair_style.html is {lj/cut}.
+If not, LAMMPS will issue a warning to indicate that the data file
 section likely does not contain the correct number or type of
 parameters expected for the currently-defined style.
 

doc/src/read_dump.txt

@@ -322,3 +322,6 @@ They are only enabled if LAMMPS was built with that packages.  See the
 
 The option defaults are box = yes, replace = yes, purge = no, trim =
 no, add = no, scaled = no, wrapped = yes, and format = native.
+
+:link(vmd,http://www.ks.uiuc.edu/Research/vmd)
+

doc/src/read_restart.txt

@@ -141,11 +141,11 @@ these settings after the restart file is read.
 "units"_units.html
 "newton bond"_newton.html (see discussion of newton command below)
 "atom style"_atom_style.html and "atom_modify"_atom_modify.html settings id, map, sort
-"comm style"_comm_style.html and "comm_modify"_comm_modify settings mode, cutoff, vel
+"comm style"_comm_style.html and "comm_modify"_comm_modify.html settings mode, cutoff, vel
 "timestep"_timestep.html
 simulation box size and shape and "boundary"_boundary.html settings
 atom "group"_group.html definitions
-per-type atom settings such as "mass"_mass.thml
+per-type atom settings such as "mass"_mass.html
 per-atom attributes including their group assignments and molecular topology attributes (bonds, angles, etc)
 force field styles ("pair"_pair_style.html, "bond"_bond_style.html, "angle"_angle_style.html, etc)
 force field coefficients ("pair"_pair_coeff.html, "bond"_bond_coeff.html, "angle"_angle_coeff.html, etc) in some cases (see below)
@@ -191,13 +191,19 @@ input script should specify all fixes it will use.  However, note that
 some fixes store an internal "state" which is written to the restart
 file.  This allows the fix to continue on with its calculations in a
 restarted simulation.  To re-enable such a fix, the fix command in the
-new input script must use the same fix-ID and group-ID as was used in
-the input script that wrote the restart file.  If a match is found,
-LAMMPS prints a message indicating that the fix is being re-enabled.
-If no match is found before the first run or minimization is performed
-by the new script, the "state" information for the saved fix is
-discarded.  See the doc pages for individual fixes for info on which
-ones can be restarted in this manner.
+new input script must be of the same style and use the same fix-ID as
+was used in the input script that wrote the restart file.
+
+If a match is found, LAMMPS prints a message indicating that the fix
+is being re-enabled.  If no match is found before the first run or
+minimization is performed by the new script, the "state" information
+for the saved fix is discarded.  At the time the discard occurs,
+LAMMPS will also print a list of fixes for which the information is
+being discarded.  See the doc pages for individual fixes for info on
+which ones can be restarted in this manner.  Note that fixes which are
+created internally by other LAMMPS commands (computes, fixes, etc)
+will have style names which are all-capitalized, and IDs which are
+generated internally.
 
 Likewise, the "computes"_fix.html used for a simulation are not stored
 in the restart file.  This means the new input script should specify
@@ -213,6 +219,18 @@ re-created fix will be re-enabled with the stored state information as
 described in the previous paragraph, so that the compute can continue
 its calculations in a consistent manner.
 
+NOTE: There are a handful of commands which can be used before or
+between runs which may require a system initialization.  Examples
+include the "balance", "displace_atoms", "delete_atoms", "set" (some
+options), and "velocity" (some options) commands.  This is because
+they can migrate atoms to new processors.  Thus they will also discard
+unused "state" information from fixes.  You will know the discard has
+occurred because a list of discarded fixes will be printed to the
+screen and log file, as explained above.  This means that if you wish
+to retain that info in a restarted run, you must re-specify the
+relevant fixes and computes (which create fixes) before those commands
+are used.
+
 Some pair styles, like the "granular pair styles"_pair_gran.html, also
 use a fix to store "state" information that persists from timestep to
 timestep.  In the case of granular potentials, it is contact

doc/src/run.txt

@@ -169,17 +169,17 @@ If the {pre} and {post} options are set to "no" when used with the
 run will print the full timing summary, but these operations will be
 skipped for intermediate runs.
 
-NOTE: You might hope to specify a command that exits the run by
+NOTE: You might wish to specify a command that exits the run by
 jumping out of the loop, e.g.
 
 variable t equal temp
 run 10000 every 100 "if '$t < 300.0' then 'jump SELF afterrun'" :pre
 
-Unfortunately this will not currently work.  The run command simply
-executes each command one at a time each time it pauses, then
-continues the run.  You can replace the jump command with a simple
-"quit"_quit.html command and cause LAMMPS to exit during the
-middle of a run when the condition is met.
+However, this will not work.  The run command simply executes each
+command one at a time each time it pauses, then continues the run.
+
+Instead, you should use the "fix halt"_fix_halt.html command, which
+has additional options for how to exit the run.
 
 [Restrictions:]
 
@@ -198,7 +198,7 @@ successive runs to run a simulation for any number of steps (ok, up to
 [Related commands:]
 
 "minimize"_minimize.html, "run_style"_run_style.html,
-"temper"_temper.html
+"temper"_temper.html, "fix halt"_fix_halt.html
 
 [Default:]
 

doc/src/thermo_style.txt

@@ -108,7 +108,7 @@ Style {custom} is the most general setting and allows you to specify
 which of the keywords listed above you want printed on each
 thermodynamic timestep.  Note that the keywords c_ID, f_ID, v_name are
 references to "computes"_compute.html, "fixes"_fix.html, and
-equal-style "variables"_variable.html" that have been defined
+equal-style "variables"_variable.html that have been defined
 elsewhere in the input script or can even be new styles which users
 have added to LAMMPS (see the "Section 10"_Section_modify.html
 section of the documentation).  Thus the {custom} style provides a

doc/src/write_dump.txt

@@ -26,7 +26,7 @@ write_dump all atom dump.atom
 write_dump subgroup atom dump.run.bin
 write_dump all custom dump.myforce.* id type x y vx fx
 write_dump flow custom dump.%.myforce id type c_myF\[3\] v_ke modify sort id
-write_dump all xyz system.xyz modify sort id elements O H
+write_dump all xyz system.xyz modify sort id element O H
 write_dump all image snap*.jpg type type size 960 960 modify backcolor white
 write_dump all image snap*.jpg element element &
    bond atom 0.3 shiny 0.1 ssao yes 6345 0.2 size 1600 1600  &

doc/utils/converters/lammpsdoc/txt2rst.py

@@ -104,7 +104,7 @@ class RSTMarkup(Markup):
 
         anchor_pos = href.find('#')
 
-        if anchor_pos >= 0:
+        if anchor_pos >= 0 and not href.startswith('http'):
             href = href[anchor_pos+1:]
             return ":ref:`%s <%s>`" % (content, href)
 

doc/utils/converters/tests/test_txt2rst.py

@@ -424,6 +424,11 @@ class TestSpecialCommands(unittest.TestCase):
                          "one \n\n"
                          "a :ref:`link <name>` to above\n\n", s)
 
+    def test_external_anchor_link(self):
+        s = self.txt2rst.convert('some text "containing a\n'
+                                 'link"_http://lammps.sandia.gov/movies.html#granregion with an anchor')
+        self.assertEqual('some text `containing a link <http://lammps.sandia.gov/movies.html#granregion>`_ with an anchor\n\n', s)
+
     def test_define_link_alias(self):
         s = self.txt2rst.convert("one :link(alias,value)\n"
                                  "\"test\"_alias\n")

doc/utils/sphinx-config/conf.py

@@ -276,4 +276,27 @@ texinfo_documents = [
 # If true, do not generate a @detailmenu in the "Top" node's menu.
 #texinfo_no_detailmenu = False
 
+# -- Options for ePUB output ----------------------------------------------
+
+epub_title = 'LAMMPS Documentation - ' + get_lammps_version()
+
+epub_cover = ('lammps-logo.png', '')
+
+epub_description = """
+This is the Manual for the LAMMPS software package.
+
+LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
+Simulator and is a classical molecular dynamics simulation code
+designed to run efficiently on parallel computers.  It was developed
+at Sandia National Laboratories, a US Department of Energy facility,
+with funding from the DOE.  It is an open-source code, distributed
+freely under the terms of the GNU Public License (GPL).
+
+The primary author of the code is Steve Plimpton, who can be emailed
+at sjplimp@sandia.gov.  The LAMMPS WWW Site at lammps.sandia.gov has
+more information about the code and its uses.
+"""
+
+epub_author = 'The LAMMPS Developers'
+
 

examples/COUPLE/simple/in.lj

@@ -20,4 +20,6 @@ neigh_modify	delay 0 every 20 check no
 
 fix		1 all nve
 
+variable        fx atom fx
+
 run		10

examples/COUPLE/simple/simple.c

@@ -71,8 +71,8 @@ int main(int narg, char **arg)
      (could just send it to proc 0 of comm_lammps and let it Bcast)
      all LAMMPS procs call lammps_command() on the line */
 
-  void *ptr;
-  if (lammps == 1) lammps_open(0,NULL,comm_lammps,&ptr);
+  void *lmp = NULL;
+  if (lammps == 1) lammps_open(0,NULL,comm_lammps,&lmp);
 
   int n;
   char line[1024];
@@ -85,7 +85,7 @@ int main(int narg, char **arg)
     MPI_Bcast(&n,1,MPI_INT,0,MPI_COMM_WORLD);
     if (n == 0) break;
     MPI_Bcast(line,n,MPI_CHAR,0,MPI_COMM_WORLD);
-    if (lammps == 1) lammps_command(ptr,line);
+    if (lammps == 1) lammps_command(lmp,line);
   }
 
   /* run 10 more steps
@@ -94,23 +94,72 @@ int main(int narg, char **arg)
      put coords back into LAMMPS
      run a single step with changed coords */
 
-  if (lammps == 1) {
-    lammps_command(ptr,"run 10");
+  double *x = NULL;
+  double *v = NULL;
 
-    int natoms = lammps_get_natoms(ptr);
-    double *x = (double *) malloc(3*natoms*sizeof(double));
-    lammps_gather_atoms(ptr,"x",1,3,x);
+  if (lammps == 1) {
+    lammps_command(lmp,"run 10");
+
+    int natoms = lammps_get_natoms(lmp);
+    x = (double *) malloc(3*natoms*sizeof(double));
+    lammps_gather_atoms(lmp,"x",1,3,x);
+    v = (double *) malloc(3*natoms*sizeof(double));
+    lammps_gather_atoms(lmp,"v",1,3,v);
     double epsilon = 0.1;
     x[0] += epsilon;
-    lammps_scatter_atoms(ptr,"x",1,3,x);
-    free(x);
+    lammps_scatter_atoms(lmp,"x",1,3,x);
 
-    lammps_command(ptr,"run 1");
+    lammps_command(lmp,"run 1");
   }
 
-  if (lammps == 1) lammps_close(ptr);
+  // extract force on single atom two different ways
+
+  if (lammps == 1) {
+    double **f = (double **) lammps_extract_atom(lmp,"f");
+    printf("Force on 1 atom via extract_atom: %g\n",f[0][0]);
+
+    double *fx = (double *) lammps_extract_variable(lmp,"fx","all");
+    printf("Force on 1 atom via extract_variable: %g\n",fx[0]);
+  }
+
+  /* use commands_string() and commands_list() to invoke more commands */
+
+  char *strtwo = "run 10\nrun 20";
+  if (lammps == 1) lammps_commands_string(lmp,strtwo);
+
+  char *cmds[2];
+  cmds[0] = "run 10";
+  cmds[1] = "run 20";
+  if (lammps == 1) lammps_commands_list(lmp,2,cmds);
+
+  /* delete all atoms
+     create_atoms() to create new ones with old coords, vels
+     initial thermo should be same as step 20 */
+
+  int *type = NULL;
+
+  if (lammps == 1) {
+    int natoms = lammps_get_natoms(lmp);
+    type = (int *) malloc(natoms*sizeof(double));
+    int i;
+    for (i = 0; i < natoms; i++) type[i] = 1;
+
+    lammps_command(lmp,"delete_atoms group all");
+    lammps_create_atoms(lmp,natoms,NULL,type,x,v);
+    lammps_command(lmp,"run 10");
+  }
+
+  if (x) free(x);
+  if (v) free(v);
+  if (type) free(type);
+
+  // close down LAMMPS
+
+  lammps_close(lmp);
 
   /* close down MPI */
 
+  if (lammps == 1) MPI_Comm_free(&comm_lammps);
+  MPI_Barrier(MPI_COMM_WORLD);
   MPI_Finalize();
 }

examples/COUPLE/simple/simple.cpp

@@ -77,7 +77,7 @@ int main(int narg, char **arg)
   // (could just send it to proc 0 of comm_lammps and let it Bcast)
   // all LAMMPS procs call input->one() on the line
   
-  LAMMPS *lmp;
+  LAMMPS *lmp = NULL;
   if (lammps == 1) lmp = new LAMMPS(0,NULL,comm_lammps);
 
   int n;
@@ -91,7 +91,7 @@ int main(int narg, char **arg)
     MPI_Bcast(&n,1,MPI_INT,0,MPI_COMM_WORLD);
     if (n == 0) break;
     MPI_Bcast(line,n,MPI_CHAR,0,MPI_COMM_WORLD);
-    if (lammps == 1) lmp->input->one(line);
+    if (lammps == 1) lammps_command(lmp,line);
   }
 
   // run 10 more steps
@@ -100,23 +100,74 @@ int main(int narg, char **arg)
   // put coords back into LAMMPS
   // run a single step with changed coords
 
+  double *x = NULL;
+  double *v = NULL;
+
   if (lammps == 1) {
     lmp->input->one("run 10");
 
     int natoms = static_cast<int> (lmp->atom->natoms);
-    double *x = new double[3*natoms];
+    x = new double[3*natoms];
+    v = new double[3*natoms];
     lammps_gather_atoms(lmp,"x",1,3,x);
+    lammps_gather_atoms(lmp,"v",1,3,v);
     double epsilon = 0.1;
     x[0] += epsilon;
     lammps_scatter_atoms(lmp,"x",1,3,x);
-    delete [] x;
 
+    // these 2 lines are the same
+
+    // lammps_command(lmp,"run 1");
     lmp->input->one("run 1");
   }
 
-  if (lammps == 1) delete lmp;
+  // extract force on single atom two different ways
+
+  if (lammps == 1) {
+    double **f = (double **) lammps_extract_atom(lmp,"f");
+    printf("Force on 1 atom via extract_atom: %g\n",f[0][0]);
+
+    double *fx = (double *) lammps_extract_variable(lmp,"fx","all");
+    printf("Force on 1 atom via extract_variable: %g\n",fx[0]);
+  }
+
+  // use commands_string() and commands_list() to invoke more commands
+
+  char *strtwo = "run 10\nrun 20";
+  if (lammps == 1) lammps_commands_string(lmp,strtwo);
+
+  char *cmds[2];
+  cmds[0] = "run 10";
+  cmds[1] = "run 20";
+  if (lammps == 1) lammps_commands_list(lmp,2,cmds);
+
+  // delete all atoms
+  // create_atoms() to create new ones with old coords, vels
+  // initial thermo should be same as step 20
+
+  int *type = NULL;
+
+  if (lammps == 1) {
+    int natoms = static_cast<int> (lmp->atom->natoms);
+    type = new int[natoms];
+    for (int i = 0; i < natoms; i++) type[i] = 1;
+
+    lmp->input->one("delete_atoms group all");
+    lammps_create_atoms(lmp,natoms,NULL,type,x,v);
+    lmp->input->one("run 10");
+  }
+
+  delete [] x;
+  delete [] v;
+  delete [] type;
+
+  // close down LAMMPS
+
+  delete lmp;
 
   // close down MPI
 
+  if (lammps == 1) MPI_Comm_free(&comm_lammps);
+  MPI_Barrier(MPI_COMM_WORLD);
   MPI_Finalize();
 }

examples/DIFFUSE/log.13Oct16.msd.2d.g++.8

@@ -0,0 +1,245 @@
+LAMMPS (13 Oct 2016)
+# sample LAMMPS input script for diffusion of 2d LJ liquid
+# mean-squared displacement via compute msd
+
+# settings
+
+variable	x equal 40
+variable	y equal 40
+
+variable	rho equal 0.6
+variable        t equal 1.0
+variable	rc equal 2.5
+
+# problem setup
+
+units		lj
+dimension	2
+atom_style	atomic
+neigh_modify	delay 0 every 1
+
+lattice         sq2 ${rho}
+lattice         sq2 0.6
+Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
+region          simbox block 0 $x 0 $y -0.1 0.1
+region          simbox block 0 40 0 $y -0.1 0.1
+region          simbox block 0 40 0 40 -0.1 0.1
+create_box      1 simbox
+Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574)
+  4 by 2 by 1 MPI processor grid
+create_atoms    1 box
+Created 3200 atoms
+
+pair_style      lj/cut ${rc}
+pair_style      lj/cut 2.5
+pair_coeff      * * 1 1
+
+mass            * 1.0
+velocity        all create $t 97287
+velocity        all create 1 97287
+
+fix             1 all nve
+fix	        2 all langevin $t $t 0.1 498094
+fix	        2 all langevin 1 $t 0.1 498094
+fix	        2 all langevin 1 1 0.1 498094
+fix	        3 all enforce2d
+
+# equilibration run
+
+thermo          1000
+run	        5000
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4 -> bins = 53 53 1
+Memory usage per processor = 2.478 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            1     -1.56492            0   -0.5652325   -1.5346995 
+    1000   0.97537833   -1.5723957            0   -0.5973222   0.92877783 
+    2000   0.99008371   -1.5748206            0  -0.58504633    1.0809416 
+    3000    1.0111412   -1.5848987            0  -0.57407352    1.0174297 
+    4000    1.0055417   -1.5857581            0  -0.58053054   0.95647691 
+    5000   0.97069905   -1.5851114            0  -0.61471567   0.90108287 
+Loop time of 0.554412 on 8 procs for 5000 steps with 3200 atoms
+
+Performance: 3896017.421 tau/day, 9018.559 timesteps/s
+98.9% CPU use with 8 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.23992    | 0.24608    | 0.25161    |   0.7 | 44.39
+Neigh   | 0.063106   | 0.064417   | 0.066279   |   0.4 | 11.62
+Comm    | 0.072465   | 0.085066   | 0.094837   |   2.3 | 15.34
+Output  | 0.00013208 | 0.00013691 | 0.00014591 |   0.0 |  0.02
+Modify  | 0.11441    | 0.11621    | 0.11769    |   0.3 | 20.96
+Other   |            | 0.04251    |            |       |  7.67
+
+Nlocal:    400 ave 406 max 394 min
+Histogram: 1 1 0 1 0 2 1 0 1 1
+Nghost:    202.5 ave 212 max 191 min
+Histogram: 1 0 0 0 3 1 0 2 0 1
+Neighs:    2800.88 ave 2903 max 2690 min
+Histogram: 1 1 0 0 1 2 1 0 1 1
+
+Total # of neighbors = 22407
+Ave neighs/atom = 7.00219
+Neighbor list builds = 599
+Dangerous builds = 0
+
+unfix		2
+
+# data gathering run
+
+reset_timestep  0
+
+# factor of 4 in 2 variables is for 2d
+
+compute         msd all msd com yes
+variable        twopoint equal c_msd[4]/4/(step*dt+1.0e-6)
+fix             9 all vector 10 c_msd[4]
+variable        fitslope equal slope(f_9)/4/(10*dt)
+
+thermo_style	custom step temp c_msd[4] v_twopoint v_fitslope
+
+# only need to run for 10K steps to make a good 100-frame movie
+
+#dump	        1 all custom 1 tmp.dump id type vx vy vz
+
+#dump		2 all image 100 image.*.jpg type type zoom 1.6 adiam 1.2
+
+thermo          1000
+run	        100000
+Memory usage per processor = 2.853 Mbytes
+Step Temp c_msd[4] v_twopoint v_fitslope 
+       0   0.97069905            0            0        5e+20 
+    1000   0.98138076    4.0484996   0.20242494   0.18046446 
+    2000   0.97606079    9.2121392   0.23030346    0.2091528 
+    3000   0.97924866    14.815034   0.24691721   0.22619184 
+    4000   0.98568451    20.516817   0.25646019   0.23715506 
+    5000   0.97551815     27.33922   0.27339219   0.24709999 
+    6000   0.98482252     34.37734   0.28647782   0.25735178 
+    7000    0.9672559    41.696689   0.29783348   0.26654059 
+    8000    0.9836541    48.340277   0.30212673   0.27440308 
+    9000   0.99087147    56.042692   0.31134828   0.28113047 
+   10000   0.99663166     63.69663   0.31848314   0.28767921 
+   11000   0.97776688    71.144109   0.32338231   0.29344527 
+   12000   0.98246011    78.301774   0.32625739   0.29849471 
+   13000   0.98788732    85.061923   0.32716124    0.3026655 
+   14000   0.96872483      91.1658   0.32559214   0.30601023 
+   15000   0.98955796    97.278388   0.32426129    0.3084275 
+   16000   0.99855196    104.23997    0.3257499   0.31049883 
+   17000   0.98600861    110.66055    0.3254722   0.31220348 
+   18000   0.98696963    116.90111   0.32472531   0.31352676 
+   19000    0.9881192    124.21305   0.32687644   0.31480062 
+   20000   0.98527319    131.09874   0.32774685   0.31596198 
+   21000   0.99015191    137.89263   0.32831579   0.31705324 
+   22000   0.97972418    146.68982   0.33338595   0.31833889 
+   23000   0.98911012     155.1264   0.33723129   0.31979515 
+   24000   0.98810498    162.88634   0.33934653   0.32131187 
+   25000   0.96961962    170.37907   0.34075814   0.32276215 
+   26000   0.99118408    179.26511   0.34474059   0.32427111 
+   27000   0.98515159    185.90764    0.3442734   0.32574529 
+   28000   0.98951677    192.12183   0.34307469   0.32700292 
+   29000    0.9832026    196.99457   0.33964581   0.32799023 
+   30000   0.98449493    203.48475   0.33914124    0.3287171 
+   31000   0.96585993    210.06193   0.33880956   0.32935775 
+   32000   0.98758117    218.94174   0.34209646   0.33001591 
+   33000   0.98875584    225.96489   0.34237104   0.33072947 
+   34000   0.98007229     233.5792   0.34349882    0.3314385 
+   35000   0.98415295    241.98148   0.34568783   0.33216634 
+   36000   0.98101154    250.30876   0.34765106   0.33295272 
+   37000   0.97606878     258.2127   0.34893608   0.33377673 
+   38000   0.97220293    266.40464   0.35053242   0.33459273 
+   39000     0.979783     272.8578   0.34981769   0.33539728 
+   40000   0.98375673    279.87598   0.34984497   0.33609699 
+   41000   0.97506523    288.07676   0.35131312   0.33677708 
+   42000   0.97106749    296.11647    0.3525196   0.33751312 
+   43000   0.97717259    304.46747   0.35403194   0.33823441 
+   44000   0.98541435    312.57228   0.35519578    0.3389771 
+   45000   0.97678287    321.82674   0.35758527   0.33973306 
+   46000   0.98169719    329.78197   0.35845866   0.34051748 
+   47000   0.99471466    337.11283   0.35863066   0.34127239 
+   48000   0.98332437     346.0754    0.3604952   0.34202442 
+   49000   0.98126947    356.11859   0.36338631   0.34282132 
+   50000   0.98809751    365.65248   0.36565248   0.34368171 
+   51000   0.95919516    373.91833   0.36658659   0.34454516 
+   52000   0.98097913    381.26492   0.36660089   0.34538506 
+   53000   0.97774072    388.81031   0.36680218   0.34618232 
+   54000   0.99096915    395.56767   0.36626636    0.3469296 
+   55000   0.97652739    401.72735   0.36520668   0.34760374 
+   56000   0.99185306    407.28834    0.3636503   0.34819906 
+   57000   0.96289342    414.75298    0.3638184   0.34871992 
+   58000   0.97871716    424.69443   0.36611588   0.34927986 
+   59000   0.98637393    433.14205   0.36706953   0.34986296 
+   60000   0.98009845    438.14533   0.36512111   0.35040349 
+   61000   0.99416712    446.08007    0.3656394   0.35088379 
+   62000   0.97612483    450.90846   0.36363585   0.35132647 
+   63000   0.97786531    455.36749   0.36140277   0.35167458 
+   64000   0.99080668    458.04873   0.35785057    0.3519105 
+   65000   0.97952497    461.31241    0.3548557    0.3520506 
+   66000   0.98095955    463.91727   0.35145248   0.35207764 
+   67000   0.98370788       468.93   0.34994776   0.35204043 
+   68000   0.96931818    471.07765   0.34638063   0.35192685 
+   69000   0.98512552    474.59146   0.34390685   0.35174053 
+   70000   0.98065743    478.66071    0.3419005   0.35149002 
+   71000   0.98971283    482.57357   0.33984054   0.35119434 
+   72000   0.99890324    485.32018    0.3370279   0.35084345 
+   73000   0.98649924    490.19497   0.33574998   0.35043722 
+   74000   0.98723422    496.04991   0.33516886   0.35003351 
+   75000    1.0025633     501.6313   0.33442087   0.34962094 
+   76000   0.97859959    505.97813   0.33288035   0.34921013 
+   77000   0.97973006    510.55334   0.33152814    0.3487692 
+   78000    0.9903944    515.06966   0.33017286   0.34830833 
+   79000   0.96847518    518.76483   0.32833217    0.3478214 
+   80000   0.99171112    524.18127   0.32761329   0.34733349 
+   81000   0.97202573    529.09959   0.32660468    0.3468315 
+   82000   0.99368438    535.80271   0.32670897   0.34633058 
+   83000   0.97932483    543.08233   0.32715803   0.34586259 
+   84000   0.99078651    547.57861   0.32593965   0.34540839 
+   85000   0.98973457    552.24581   0.32485048   0.34493584 
+   86000    0.9835873     557.3493   0.32404029   0.34446152 
+   87000   0.97180564    564.93434   0.32467491   0.34400358 
+   88000   0.99743353    571.39837   0.32465817    0.3435667 
+   89000   0.98993437    577.81703   0.32461631    0.3431411 
+   90000    0.9926071    583.39378   0.32410765     0.342724 
+   91000   0.98800458    591.08741    0.3247733   0.34232767 
+   92000   0.98501879    596.10133   0.32396811   0.34193949 
+   93000   0.98810082    604.02652   0.32474544    0.3415681 
+   94000   0.97563748    609.43676   0.32416849     0.341209 
+   95000   0.97283448    615.15754   0.32376713   0.34084828 
+   96000    0.9883071    622.30912   0.32411933   0.34049871 
+   97000   0.97717678    628.84457   0.32414669   0.34016355 
+   98000   0.97190208    634.37377   0.32366009    0.3398341 
+   99000   0.98687379    640.66666   0.32356902   0.33950845 
+  100000   0.97559757    646.96406   0.32348203   0.33919036 
+Loop time of 9.58779 on 8 procs for 100000 steps with 3200 atoms
+
+Performance: 4505729.040 tau/day, 10429.928 timesteps/s
+99.4% CPU use with 8 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 4.8572     | 4.9363     | 4.9822     |   1.7 | 51.49
+Neigh   | 1.3583     | 1.376      | 1.3991     |   1.2 | 14.35
+Comm    | 1.5192     | 1.7079     | 1.8264     |   7.2 | 17.81
+Output  | 0.0085125  | 0.0086059  | 0.0089455  |   0.1 |  0.09
+Modify  | 0.77663    | 0.7903     | 0.81378    |   1.3 |  8.24
+Other   |            | 0.7686     |            |       |  8.02
+
+Nlocal:    400 ave 413 max 391 min
+Histogram: 2 1 0 2 0 0 1 1 0 1
+Nghost:    204.75 ave 213 max 197 min
+Histogram: 1 1 0 1 0 3 0 1 0 1
+Neighs:    2800.62 ave 2959 max 2661 min
+Histogram: 1 1 1 2 0 0 0 1 1 1
+
+Total # of neighbors = 22405
+Ave neighs/atom = 7.00156
+Neighbor list builds = 12728
+Dangerous builds = 0
+Total wall time: 0:00:10

examples/DIFFUSE/log.13Oct16.vacf.2d.g++.8

@@ -0,0 +1,246 @@
+LAMMPS (13 Oct 2016)
+# sample LAMMPS input script for diffusion of 2d LJ liquid
+# mean-squared displacement via compute msd
+
+# settings
+
+variable	x equal 40
+variable	y equal 40
+
+variable	rho equal 0.6
+variable        t equal 1.0
+variable	rc equal 2.5
+
+# problem setup
+
+units		lj
+dimension	2
+atom_style	atomic
+neigh_modify	delay 0 every 1
+
+lattice         sq2 ${rho}
+lattice         sq2 0.6
+Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
+region          simbox block 0 $x 0 $y -0.1 0.1
+region          simbox block 0 40 0 $y -0.1 0.1
+region          simbox block 0 40 0 40 -0.1 0.1
+create_box      1 simbox
+Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574)
+  4 by 2 by 1 MPI processor grid
+create_atoms    1 box
+Created 3200 atoms
+
+pair_style      lj/cut ${rc}
+pair_style      lj/cut 2.5
+pair_coeff      * * 1 1
+
+mass            * 1.0
+velocity        all create $t 97287
+velocity        all create 1 97287
+
+fix             1 all nve
+fix	        2 all langevin $t $t 0.1 498094
+fix	        2 all langevin 1 $t 0.1 498094
+fix	        2 all langevin 1 1 0.1 498094
+fix	        3 all enforce2d
+
+# equilibration run
+
+thermo          1000
+run	        5000
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4 -> bins = 53 53 1
+Memory usage per processor = 2.478 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            1     -1.56492            0   -0.5652325   -1.5346995 
+    1000   0.97537833   -1.5723957            0   -0.5973222   0.92877783 
+    2000   0.99008371   -1.5748206            0  -0.58504633    1.0809416 
+    3000    1.0111412   -1.5848987            0  -0.57407352    1.0174297 
+    4000    1.0055417   -1.5857581            0  -0.58053054   0.95647691 
+    5000   0.97069905   -1.5851114            0  -0.61471567   0.90108287 
+Loop time of 0.557588 on 8 procs for 5000 steps with 3200 atoms
+
+Performance: 3873826.669 tau/day, 8967.191 timesteps/s
+99.1% CPU use with 8 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.23784    | 0.24683    | 0.25594    |   1.0 | 44.27
+Neigh   | 0.062975   | 0.06439    | 0.0662     |   0.4 | 11.55
+Comm    | 0.083826   | 0.092564   | 0.1035     |   2.1 | 16.60
+Output  | 0.00011778 | 0.00012615 | 0.00014257 |   0.1 |  0.02
+Modify  | 0.11466    | 0.11648    | 0.1187     |   0.4 | 20.89
+Other   |            | 0.0372     |            |       |  6.67
+
+Nlocal:    400 ave 406 max 394 min
+Histogram: 1 1 0 1 0 2 1 0 1 1
+Nghost:    202.5 ave 212 max 191 min
+Histogram: 1 0 0 0 3 1 0 2 0 1
+Neighs:    2800.88 ave 2903 max 2690 min
+Histogram: 1 1 0 0 1 2 1 0 1 1
+
+Total # of neighbors = 22407
+Ave neighs/atom = 7.00219
+Neighbor list builds = 599
+Dangerous builds = 0
+
+unfix		2
+
+# data gathering run
+
+reset_timestep  0
+
+compute         vacf all vacf
+fix             4 all ave/time 1 1 1 c_vacf[4] #file tmp.vacf
+
+# factor of 0.5 is for 2d
+
+fix             5 all vector 1 c_vacf[4]
+variable        vacf equal 0.5*dt*trap(f_5)
+
+thermo_style	custom step temp c_vacf[4] v_vacf
+
+# only need to run for 10K steps to make a good 100-frame movie
+
+#dump	        1 all custom 1 tmp.dump id type vx vy vz
+
+#dump		2 all image 100 image.*.jpg type type zoom 1.6 adiam 1.2
+
+thermo          1000
+run	        100000
+Memory usage per processor = 2.853 Mbytes
+Step Temp c_vacf[4] v_vacf 
+       0   0.97069905    1.9407914            0 
+    1000   0.98138076  0.029239763   0.22157396 
+    2000   0.97606079 -0.0015179052   0.23974121 
+    3000   0.97924866 -0.013873067   0.21877575 
+    4000   0.98568451  0.026969065   0.24052934 
+    5000   0.97551815  0.050232557   0.24508207 
+    6000   0.98482252 -0.0018424259   0.25686293 
+    7000    0.9672559  0.018499957   0.27279836 
+    8000    0.9836541 -0.022683127   0.27022734 
+    9000   0.99087147 0.0071767632   0.25267902 
+   10000   0.99663166 -0.011971734    0.2645822 
+   11000   0.97776688   0.01601675   0.27801788 
+   12000   0.98246011 0.0085456779   0.29207728 
+   13000   0.98788732 0.0054252587   0.29148533 
+   14000   0.96872483 0.0087976064   0.29645689 
+   15000   0.98955796 -0.060068996   0.28904116 
+   16000   0.99855196 -0.0066979853   0.24964957 
+   17000   0.98600861  0.021334454   0.23410452 
+   18000   0.98696963  -0.01971883   0.23190572 
+   19000    0.9881192 -0.022828159   0.20882183 
+   20000   0.98527319 -0.0085783561   0.20610922 
+   21000   0.99015191 -0.0061019744   0.20199693 
+   22000   0.97972418  -0.04380952   0.22099864 
+   23000   0.98911012 -0.0031381071   0.19304223 
+   24000   0.98810498  0.023131507   0.18483784 
+   25000   0.96961962 -0.020892151   0.17128259 
+   26000   0.99118408   0.02918818   0.15353531 
+   27000   0.98515159 -0.026417648    0.1457756 
+   28000   0.98951677  0.010372147   0.13321212 
+   29000    0.9832026 0.00058150905   0.13262151 
+   30000   0.98449493 0.0012256712   0.13576655 
+   31000   0.96585993 0.0053021384   0.10734708 
+   32000   0.98758117 -0.011513109   0.11473375 
+   33000   0.98875584 -0.0089140499   0.13003947 
+   34000   0.98007229  0.023423116     0.145185 
+   35000   0.98415295 -0.0078343607   0.16513809 
+   36000   0.98101154  0.025471963    0.1296799 
+   37000   0.97606878 -0.016931612   0.11515595 
+   38000   0.97220293 -0.015288346   0.12046935 
+   39000     0.979783  0.039556949   0.10596988 
+   40000   0.98375673 0.0098704124   0.15651085 
+   41000   0.97506523 -0.029457701   0.14822207 
+   42000   0.97106749 -0.024867475   0.12266294 
+   43000   0.97717259  0.010866403   0.14228602 
+   44000   0.98541435 -0.031545234   0.13017093 
+   45000   0.97678287 -0.011024372   0.11824999 
+   46000   0.98169719  0.011925437    0.1390346 
+   47000   0.99471466 0.0048178625   0.13076123 
+   48000   0.98332437  0.045576305   0.12667585 
+   49000   0.98126947 -0.044123768   0.13582991 
+   50000   0.98809751  0.014296599   0.12323107 
+   51000   0.95919516 -0.0091171161    0.1494511 
+   52000   0.98097913  0.010081012   0.12805794 
+   53000   0.97774072  0.043349117   0.14524942 
+   54000   0.99096915  0.021179196    0.1355801 
+   55000   0.97652739 -0.015118967   0.14955035 
+   56000   0.99185306 0.0018045061   0.16706629 
+   57000   0.96289342 0.0095090659   0.19215008 
+   58000   0.97871716 -0.028989119   0.20370326 
+   59000   0.98637393 0.0067841088   0.21820001 
+   60000   0.98009845  0.011559251   0.24504916 
+   61000   0.99416712 0.0099372548   0.24882366 
+   62000   0.97612483  0.014677063   0.25146482 
+   63000   0.97786531 -0.0047938112   0.26052305 
+   64000   0.99080668  -0.01632121   0.24744267 
+   65000   0.97952497 0.0070583633   0.22323997 
+   66000   0.98095955  0.036296232    0.2151706 
+   67000   0.98370788 -0.0040313363   0.22236193 
+   68000   0.96931818    0.0231486   0.20397659 
+   69000   0.98512552 -0.017450997   0.21854935 
+   70000   0.98065743  0.046916694    0.2080453 
+   71000   0.98971283  0.010974871   0.21628306 
+   72000   0.99890324 -0.023780184   0.23385876 
+   73000   0.98649924  0.012862733   0.23458964 
+   74000   0.98723422 -0.0096252165   0.23873216 
+   75000    1.0025633 -0.070387674    0.2275029 
+   76000   0.97859959 0.0058897922   0.22954358 
+   77000   0.97973006 -0.0082868083   0.25189797 
+   78000    0.9903944 -0.042368536   0.26564349 
+   79000   0.96847518 -0.050630573   0.25344248 
+   80000   0.99171112  0.012126001   0.23257751 
+   81000   0.97202573 -0.029816198   0.27354387 
+   82000   0.99368438  0.030082951   0.27859495 
+   83000   0.97932483 -0.0081664387   0.27409123 
+   84000   0.99078651  0.056610231   0.27593659 
+   85000   0.98973457  0.020424285   0.31002605 
+   86000    0.9835873 -0.0016980943   0.30158255 
+   87000   0.97180564 -0.0051924508   0.27401969 
+   88000   0.99743353 -0.030700753   0.24105471 
+   89000   0.98993437 0.0087866525   0.23913724 
+   90000    0.9926071 -0.014023378   0.24202489 
+   91000   0.98800458  0.033613695    0.2238248 
+   92000   0.98501879   -0.0406599   0.21809043 
+   93000   0.98810082  0.027637634   0.21550897 
+   94000   0.97563748 0.0014112208   0.18954766 
+   95000   0.97283448 0.0093796591   0.17838358 
+   96000    0.9883071  0.033049994   0.18594703 
+   97000   0.97717678   0.01070451   0.19203994 
+   98000   0.97190208  0.015065013   0.20906937 
+   99000   0.98687379 -0.036869401   0.22993959 
+  100000   0.97559757  0.045464091   0.23369283 
+Loop time of 10.8346 on 8 procs for 100000 steps with 3200 atoms
+
+Performance: 3987213.825 tau/day, 9229.662 timesteps/s
+99.5% CPU use with 8 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 4.8486     | 4.9469     | 5.0248     |   2.8 | 45.66
+Neigh   | 1.3613     | 1.374      | 1.3916     |   0.8 | 12.68
+Comm    | 1.8181     | 1.9534     | 2.0665     |   5.7 | 18.03
+Output  | 0.016565   | 0.016701   | 0.017039   |   0.1 |  0.15
+Modify  | 1.8395     | 1.9053     | 1.9704     |   2.8 | 17.59
+Other   |            | 0.6383     |            |       |  5.89
+
+Nlocal:    400 ave 413 max 391 min
+Histogram: 2 1 0 2 0 0 1 1 0 1
+Nghost:    204.75 ave 213 max 197 min
+Histogram: 1 1 0 1 0 3 0 1 0 1
+Neighs:    2800.62 ave 2959 max 2661 min
+Histogram: 1 1 1 2 0 0 0 1 1 1
+
+Total # of neighbors = 22405
+Ave neighs/atom = 7.00156
+Neighbor list builds = 12728
+Dangerous builds = 0
+Total wall time: 0:00:11

examples/DIFFUSE/log.msd.2d.1Feb14

@@ -1,223 +0,0 @@
-LAMMPS (12 Feb 2014)
-# sample LAMMPS input script for diffusion of 2d LJ liquid
-# mean-squared displacement via compute msd
-
-# settings
-
-variable	x equal 40
-variable	y equal 40
-
-variable	rho equal 0.6
-variable        t equal 1.0
-variable	rc equal 2.5
-
-# problem setup
-
-units		lj
-dimension	2
-atom_style	atomic
-neigh_modify	delay 0 every 1
-
-lattice         sq2 ${rho}
-lattice         sq2 0.6
-Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
-region          simbox block 0 $x 0 $y -0.1 0.1
-region          simbox block 0 40 0 $y -0.1 0.1
-region          simbox block 0 40 0 40 -0.1 0.1
-create_box      1 simbox
-Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574)
-  4 by 2 by 1 MPI processor grid
-create_atoms    1 box
-Created 3200 atoms
-
-pair_style      lj/cut ${rc}
-pair_style      lj/cut 2.5
-pair_coeff      * * 1 1
-
-mass            * 1.0
-velocity        all create $t 97287
-velocity        all create 1 97287
-
-fix             1 all nve
-fix	        2 all langevin $t $t 0.1 498094
-fix	        2 all langevin 1 $t 0.1 498094
-fix	        2 all langevin 1 1 0.1 498094
-fix	        3 all enforce2d
-
-# equilibration run
-
-thermo          1000
-run	        5000
-Memory usage per processor = 2.06238 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0            1     -1.56492            0   -0.5652325   -1.5346995 
-    1000   0.97537833   -1.5723957            0   -0.5973222   0.92877783 
-    2000   0.99008371   -1.5748206            0  -0.58504633    1.0809416 
-    3000    1.0111412   -1.5848987            0  -0.57407352    1.0174297 
-    4000    1.0055417   -1.5857581            0  -0.58053054   0.95647691 
-    5000   0.97069909   -1.5851114            0  -0.61471562   0.90108296 
-Loop time of 0.548328 on 8 procs for 5000 steps with 3200 atoms
-
-Pair  time (%) = 0.242437 (44.2139)
-Neigh time (%) = 0.0589295 (10.7471)
-Comm  time (%) = 0.0797399 (14.5424)
-Outpt time (%) = 0.00014773 (0.0269419)
-Other time (%) = 0.167074 (30.4697)
-
-Nlocal:    400 ave 406 max 394 min
-Histogram: 1 1 0 1 0 2 1 0 1 1
-Nghost:    202.5 ave 212 max 191 min
-Histogram: 1 0 0 0 3 1 0 2 0 1
-Neighs:    2800.88 ave 2903 max 2690 min
-Histogram: 1 1 0 0 1 2 1 0 1 1
-
-Total # of neighbors = 22407
-Ave neighs/atom = 7.00219
-Neighbor list builds = 599
-Dangerous builds = 0
-
-unfix		2
-
-# data gathering run
-
-reset_timestep  0
-
-# factor of 4 in 2 variables is for 2d
-
-compute         msd all msd com yes
-variable        twopoint equal c_msd[4]/4/(step*dt+1.0e-6)
-fix             9 all vector 10 c_msd[4]
-variable        fitslope equal slope(f_9)/4/(10*dt)
-
-thermo_style	custom step temp c_msd[4] v_twopoint v_fitslope
-
-# only need to run for 10K steps to make a good 100-frame movie
-
-#dump	        1 all custom 1 tmp.dump id type vx vy vz
-
-#dump		2 all image 100 image.*.jpg type type zoom 1.6 adiam 1.2
-
-thermo          1000
-run	        100000
-Memory usage per processor = 2.29126 Mbytes
-Step Temp msd[4] twopoint fitslope 
-       0   0.97069909 5.6797985e-31 1.4199496e-25        5e+20 
-    1000   0.98259938     4.018182   0.20090906   0.18018405 
-    2000   0.98866167    9.1771673   0.22942916   0.20819132 
-    3000   0.98066292    14.377973   0.23963287    0.2226381 
-    4000   0.97384109    19.666022   0.24582526   0.23154108 
-    5000   0.97843004    25.570023   0.25570022   0.23873417 
-    6000   0.98703537    31.182236   0.25985196    0.2446473 
-    7000   0.97169186    36.915546   0.26368246   0.24892937 
-    8000    0.9823893    42.723242   0.26702026   0.25284158 
-    9000    0.9998457    49.159596   0.27310886   0.25648405 
-   10000   0.98782869     55.95808   0.27979039   0.26026001 
-   11000   0.99481941    63.387246   0.28812384   0.26436008 
-   12000    0.9760981    70.325901   0.29302458   0.26836823 
-   13000   0.97774297    77.590396    0.2984246    0.2723266 
-   14000   0.96752038    85.055703   0.30377036   0.27627449 
-   15000   0.98697717    92.723433    0.3090781   0.28007928 
-   16000   0.98385955    100.89787   0.31530583   0.28396785 
-   17000    0.9839555    108.44716   0.31896223   0.28772551 
-   18000   0.98000182      115.932   0.32203333   0.29120847 
-   19000   0.96633821    123.99378   0.32629942    0.2945701 
-   20000   0.98641362    131.63233   0.32908082   0.29781576 
-   21000    0.9763779    140.20546   0.33382253   0.30091009 
-   22000   0.97984221     149.3632   0.33946182   0.30410181 
-   23000   0.98384014    157.80278   0.34304952   0.30727461 
-   24000   0.97601102    165.78405   0.34538343   0.31026343 
-   25000   0.99623187     173.8015     0.347603   0.31311142 
-   26000   0.98943691    182.06075   0.35011683   0.31582297 
-   27000   0.98992058    188.30114   0.34870582   0.31827868 
-   28000   0.97957751    196.93202   0.35166432   0.32053702 
-   29000   0.99513582    206.48445   0.35600767   0.32277974 
-   30000   0.99754125     213.2124     0.355354   0.32491307 
-   31000   0.98894929    221.74208   0.35764851   0.32691848 
-   32000     0.973493    229.28872   0.35826363    0.3288054 
-   33000   0.99989261     236.7565   0.35872197   0.33061911 
-   34000   0.97192218    243.57374   0.35819667   0.33225106 
-   35000   0.99711642    250.65118   0.35807311   0.33369124 
-   36000   0.97718259    258.94971   0.35965237   0.33507325 
-   37000   0.98194807    265.83921   0.35924218   0.33634589 
-   38000   0.97195138    272.94984   0.35914453   0.33755459 
-   39000   0.98219017    280.07692   0.35907297   0.33864166 
-   40000   0.98039694     288.4453   0.36055663   0.33967254 
-   41000   0.97621359    295.85108     0.360794    0.3406849 
-   42000   0.97460413    303.13769    0.3608782   0.34161073 
-   43000    0.9799912    312.06356    0.3628646   0.34254857 
-   44000   0.96313376    320.55123   0.36426276   0.34347747 
-   45000   0.97643796    329.68761   0.36631956   0.34443057 
-   46000   0.98641729    338.40463   0.36783111   0.34540729 
-   47000   0.97811939    345.46683    0.3675179   0.34634877 
-   48000   0.99744864    352.87823   0.36758148   0.34720815 
-   49000   0.97480356    362.60002   0.37000002   0.34807624 
-   50000   0.97841509    368.44194   0.36844193   0.34892214 
-   51000   0.97865859    375.44238   0.36808076   0.34966222 
-   52000   0.97415415    382.95453   0.36822551   0.35036495 
-   53000   0.97984491    390.33776   0.36824317   0.35103186 
-   54000   0.99289379     396.4986   0.36712833   0.35162842 
-   55000   0.98606668    403.49336   0.36681214   0.35217399 
-   56000   0.98585489    411.98283   0.36784182   0.35270646 
-   57000   0.98507959    418.14272   0.36679186   0.35321673 
-   58000   0.98030805    423.23791   0.36486026     0.353654 
-   59000   0.98315137    429.40554   0.36390299   0.35400654 
-   60000   0.98762585    437.17376   0.36431146   0.35433653 
-   61000   0.96937507    442.38698   0.36261228    0.3546452 
-   62000   0.97194792    450.91689   0.36364265    0.3549106 
-   63000   0.99877655    460.61733   0.36556931    0.3552122 
-   64000   0.98525211    469.26926   0.36661661   0.35554833 
-   65000    0.9833149    477.52571   0.36732747   0.35589823 
-   66000   0.97191797    485.72618   0.36797438   0.35624251 
-   67000   0.98479592    492.83716   0.36778892   0.35657544 
-   68000   0.98418943    498.90452   0.36684156   0.35688872 
-   69000   0.96953928    507.57013   0.36780444   0.35718476 
-   70000   0.98373337    515.05745   0.36789818   0.35749562 
-   71000   0.98260952    522.33093   0.36783868   0.35778626 
-   72000   0.98906053    527.99215   0.36666121   0.35804724 
-   73000   0.99569597    534.99359   0.36643396   0.35827372 
-   74000   0.97627362    540.94769    0.3655052   0.35847643 
-   75000   0.97276792    546.45533   0.36430355   0.35864641 
-   76000   0.97659072    554.59353   0.36486417   0.35879714 
-   77000    0.9807196    562.96571   0.36556215   0.35896542 
-   78000   0.97398601    571.22804   0.36617182   0.35914269 
-   79000   0.98124212    577.92968   0.36577828   0.35930881 
-   80000   0.98506783    586.73568    0.3667098   0.35948276 
-   81000   0.97926561    596.68206   0.36832226   0.35968089 
-   82000   0.97906184    604.24971   0.36844495   0.35988893 
-   83000   0.96540502     610.7078   0.36789626    0.3600856 
-   84000   0.98726761    619.32703   0.36864704   0.36027536 
-   85000   0.98133061    627.20955   0.36894679    0.3604747 
-   86000   0.99142106    634.68836   0.36900486   0.36067069 
-   87000   0.97917566    641.73186   0.36881141   0.36086497 
-   88000   0.99391197    649.76607   0.36918527   0.36105571 
-   89000   0.98521911    655.50224   0.36825969   0.36123298 
-   90000   0.97419059     664.0397   0.36891095   0.36139717 
-   91000   0.98687774    671.19045   0.36878596   0.36156016 
-   92000   0.97816545    677.37724   0.36813981   0.36171235 
-   93000   0.98734859    684.56734   0.36804696    0.3618463 
-   94000   0.99116168    691.47221   0.36780437   0.36197063 
-   95000   0.99982024    698.01624   0.36737697   0.36208597 
-   96000   0.99232404    703.53179    0.3664228   0.36218818 
-   97000   0.97829693    707.91832   0.36490635   0.36225634 
-   98000   0.99878715    713.77777   0.36417233   0.36230715 
-   99000   0.97026354    717.24468   0.36224478    0.3623226 
-  100000   0.98911409     722.1539   0.36107695   0.36230617 
-Loop time of 9.28795 on 8 procs for 100000 steps with 3200 atoms
-
-Pair  time (%) = 4.87621 (52.5003)
-Neigh time (%) = 1.26444 (13.6138)
-Comm  time (%) = 1.60752 (17.3076)
-Outpt time (%) = 0.00843725 (0.0908408)
-Other time (%) = 1.53135 (16.4875)
-
-Nlocal:    400 ave 410 max 389 min
-Histogram: 1 1 1 0 1 1 0 0 1 2
-Nghost:    205.375 ave 216 max 194 min
-Histogram: 1 0 0 2 2 0 1 0 0 2
-Neighs:    2818 ave 3010 max 2683 min
-Histogram: 2 0 2 0 1 1 0 1 0 1
-
-Total # of neighbors = 22544
-Ave neighs/atom = 7.045
-Neighbor list builds = 12748
-Dangerous builds = 0

examples/DIFFUSE/log.vacf.2d.1Feb14

@@ -1,224 +0,0 @@
-LAMMPS (12 Feb 2014)
-# sample LAMMPS input script for diffusion of 2d LJ liquid
-# mean-squared displacement via compute msd
-
-# settings
-
-variable	x equal 40
-variable	y equal 40
-
-variable	rho equal 0.6
-variable        t equal 1.0
-variable	rc equal 2.5
-
-# problem setup
-
-units		lj
-dimension	2
-atom_style	atomic
-neigh_modify	delay 0 every 1
-
-lattice         sq2 ${rho}
-lattice         sq2 0.6
-Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
-region          simbox block 0 $x 0 $y -0.1 0.1
-region          simbox block 0 40 0 $y -0.1 0.1
-region          simbox block 0 40 0 40 -0.1 0.1
-create_box      1 simbox
-Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574)
-  4 by 2 by 1 MPI processor grid
-create_atoms    1 box
-Created 3200 atoms
-
-pair_style      lj/cut ${rc}
-pair_style      lj/cut 2.5
-pair_coeff      * * 1 1
-
-mass            * 1.0
-velocity        all create $t 97287
-velocity        all create 1 97287
-
-fix             1 all nve
-fix	        2 all langevin $t $t 0.1 498094
-fix	        2 all langevin 1 $t 0.1 498094
-fix	        2 all langevin 1 1 0.1 498094
-fix	        3 all enforce2d
-
-# equilibration run
-
-thermo          1000
-run	        5000
-Memory usage per processor = 2.06238 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0            1     -1.56492            0   -0.5652325   -1.5346995 
-    1000   0.97537833   -1.5723957            0   -0.5973222   0.92877783 
-    2000   0.99008371   -1.5748206            0  -0.58504633    1.0809416 
-    3000    1.0111412   -1.5848987            0  -0.57407352    1.0174297 
-    4000    1.0055417   -1.5857581            0  -0.58053054   0.95647691 
-    5000   0.97069909   -1.5851114            0  -0.61471562   0.90108296 
-Loop time of 0.556362 on 8 procs for 5000 steps with 3200 atoms
-
-Pair  time (%) = 0.242478 (43.5828)
-Neigh time (%) = 0.0590148 (10.6073)
-Comm  time (%) = 0.0862918 (15.51)
-Outpt time (%) = 0.000148952 (0.0267725)
-Other time (%) = 0.168428 (30.2731)
-
-Nlocal:    400 ave 406 max 394 min
-Histogram: 1 1 0 1 0 2 1 0 1 1
-Nghost:    202.5 ave 212 max 191 min
-Histogram: 1 0 0 0 3 1 0 2 0 1
-Neighs:    2800.88 ave 2903 max 2690 min
-Histogram: 1 1 0 0 1 2 1 0 1 1
-
-Total # of neighbors = 22407
-Ave neighs/atom = 7.00219
-Neighbor list builds = 599
-Dangerous builds = 0
-
-unfix		2
-
-# data gathering run
-
-reset_timestep  0
-
-compute         vacf all vacf
-fix             4 all ave/time 1 1 1 c_vacf[4] #file tmp.vacf
-
-# factor of 0.5 is for 2d
-
-fix             5 all vector 1 c_vacf[4]
-variable        vacf equal 0.5*dt*trap(f_5)
-
-thermo_style	custom step temp c_vacf[4] v_vacf
-
-# only need to run for 10K steps to make a good 100-frame movie
-
-#dump	        1 all custom 1 tmp.dump id type vx vy vz
-
-#dump		2 all image 100 image.*.jpg type type zoom 1.6 adiam 1.2
-
-thermo          1000
-run	        100000
-Memory usage per processor = 2.29126 Mbytes
-Step Temp vacf[4] vacf 
-       0   0.97069909    1.9407915            0 
-    1000   0.98259938  0.068345562   0.21424576 
-    2000   0.98866167  0.028205164   0.24370013 
-    3000   0.98066292  0.008852823   0.27439588 
-    4000   0.97384109  0.011903564    0.3159275 
-    5000   0.97843004  0.019295534   0.33596598 
-    6000   0.98703537   0.01070801   0.34517088 
-    7000   0.97169186 -0.0082938435   0.33784119 
-    8000    0.9823893  0.038402174   0.32756669 
-    9000    0.9998457  0.045317593   0.33379383 
-   10000   0.98782869  0.027148675   0.34751149 
-   11000   0.99481941  0.035783937   0.36009047 
-   12000    0.9760981 -0.0010825507   0.36059769 
-   13000   0.97774297  0.048323885   0.36103752 
-   14000   0.96752038 0.0008189784   0.34988029 
-   15000   0.98697717   -0.0339338   0.35841003 
-   16000   0.98385955   0.03729417   0.36378228 
-   17000    0.9839555 -0.0063931744   0.37486488 
-   18000   0.98000182  0.065439765   0.39975619 
-   19000   0.96633821 0.0034363237   0.39585239 
-   20000   0.98641362    -0.020284   0.39696422 
-   21000    0.9763779  0.013683539   0.36183593 
-   22000   0.97984221 -0.0077108606   0.32642476 
-   23000   0.98384014 -0.030550764   0.32775468 
-   24000   0.97601102 -0.0047287909    0.3294707 
-   25000   0.99623187   0.00653461   0.34586445 
-   26000   0.98943691  -0.05047279    0.3283058 
-   27000   0.98992058  -0.01720223   0.30840611 
-   28000   0.97957751  0.020915942    0.3149002 
-   29000   0.99513582   0.03712206   0.30525251 
-   30000   0.99754125 -0.022509889   0.29511243 
-   31000   0.98894929  0.015289267   0.25586423 
-   32000     0.973493  0.015971435   0.25226411 
-   33000   0.99989261  0.026989142   0.29050941 
-   34000   0.97192218  0.043710515   0.29067058 
-   35000   0.99711642  0.047231436   0.27989734 
-   36000   0.97718259 0.0059969847   0.28843181 
-   37000   0.98194807  0.017440303   0.30325718 
-   38000   0.97195138 -0.040449666   0.29696592 
-   39000   0.98219017 0.0063692991   0.28915832 
-   40000   0.98039694 -0.0038122219   0.24799014 
-   41000   0.97621359  0.012624961    0.2374766 
-   42000   0.97460413   -0.0024187   0.24693474 
-   43000    0.9799912  0.015928618   0.26238505 
-   44000   0.96313376 -0.067284605   0.24397772 
-   45000   0.97643796 -0.0039001998   0.22733962 
-   46000   0.98641729 -0.026949085   0.24167989 
-   47000   0.97811939 -0.050859011    0.2335985 
-   48000   0.99744864 -0.008154229    0.2417371 
-   49000   0.97480356 -0.011051498   0.25474033 
-   50000   0.97841509  -0.00531423   0.25357072 
-   51000   0.97865859  0.067722096   0.25086864 
-   52000   0.97415415  0.015863025    0.2516842 
-   53000   0.97984491  0.021332829   0.28226376 
-   54000   0.99289379   -0.0192578   0.28300764 
-   55000   0.98606668  0.029307891   0.27592186 
-   56000   0.98585489 0.0062922121    0.2687204 
-   57000   0.98507959 -0.0068688582   0.27868708 
-   58000   0.98030805  0.013766115   0.31008116 
-   59000   0.98315137  0.033068034   0.32211415 
-   60000   0.98762585  0.050662295   0.30109082 
-   61000   0.96937507  -0.02797113   0.29968066 
-   62000   0.97194792 -0.0032022157    0.2866526 
-   63000   0.99877655 -0.010154313   0.31701083 
-   64000   0.98525211 -0.020415497   0.31774092 
-   65000    0.9833149 0.0087192442   0.31256891 
-   66000   0.97191797 0.0047184494   0.29880531 
-   67000   0.98479592 -0.010779275     0.294197 
-   68000   0.98418943 -0.035264623   0.29993828 
-   69000   0.96953928 -0.028114432   0.27403611 
-   70000   0.98373337 -0.057363336   0.25554163 
-   71000   0.98260952  0.048742037   0.27102884 
-   72000   0.98906053  0.010799224   0.26908376 
-   73000   0.99569597 -0.0092675754   0.26927752 
-   74000   0.97627362  0.013945821    0.2730712 
-   75000   0.97276792  0.015036012   0.25847255 
-   76000   0.97659072 -0.027078556   0.26783118 
-   77000    0.9807196 -0.044553679   0.25993053 
-   78000   0.97398601 -0.00027444729   0.26127735 
-   79000   0.98124212 -0.012488833   0.27454966 
-   80000   0.98506783 -0.015190822    0.2676633 
-   81000   0.97926561 -0.012755191   0.27046398 
-   82000   0.97906184  0.012564185    0.2835038 
-   83000   0.96540502 -0.007372877   0.29622738 
-   84000   0.98726761  0.021015365   0.32432233 
-   85000   0.98133061  0.020043402    0.3540913 
-   86000   0.99142106  0.025350024   0.36697674 
-   87000   0.97917566 0.0061562414   0.37456288 
-   88000   0.99391197 0.0068565008   0.39150922 
-   89000   0.98521911  0.015500816   0.38121119 
-   90000   0.97419059 0.00037609894   0.34181128 
-   91000   0.98687774 -0.0073221495   0.35316892 
-   92000   0.97816545  0.014057005   0.33181146 
-   93000   0.98734859  0.016570523   0.34546487 
-   94000   0.99116168 -0.0068196043   0.36316635 
-   95000   0.99982024  0.076723346   0.38376316 
-   96000   0.99232404 -0.048534983   0.38369657 
-   97000   0.97829693 0.0041180664   0.38022523 
-   98000   0.99878715 -0.00089133295   0.40289006 
-   99000   0.97026354 -0.0039532716   0.43650647 
-  100000   0.98911409  0.028647976    0.4499919 
-Loop time of 10.5771 on 8 procs for 100000 steps with 3200 atoms
-
-Pair  time (%) = 4.88134 (46.1499)
-Neigh time (%) = 1.2657 (11.9664)
-Comm  time (%) = 1.78371 (16.8638)
-Outpt time (%) = 0.0207323 (0.196011)
-Other time (%) = 2.62565 (24.8239)
-
-Nlocal:    400 ave 410 max 389 min
-Histogram: 1 1 1 0 1 1 0 0 1 2
-Nghost:    205.375 ave 216 max 194 min
-Histogram: 1 0 0 2 2 0 1 0 0 2
-Neighs:    2818 ave 3010 max 2683 min
-Histogram: 2 0 2 0 1 1 0 1 0 1
-
-Total # of neighbors = 22544
-Ave neighs/atom = 7.045
-Neighbor list builds = 12748
-Dangerous builds = 0