new fix halt command, other sundry small bug fixes

Collected bugfixes and small changes

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/Makefile

@@ -8,13 +8,15 @@ 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)
@@ -109,6 +111,8 @@ $(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

@@ -91,6 +91,3 @@ This will install virtualenv from the Python Package Index.
 ----------------
 
 Installing prerequisites for PDF build
-
-
-

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="5 Oct 2016 version">
+<META NAME="docnumber" CONTENT="18 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
-5 Oct 2016 version :c,h4
+18 Oct 2016 version :c,h4
 
 Version info: :h4
 

doc/src/Section_commands.txt

@@ -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
 
@@ -516,6 +573,7 @@ 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,
@@ -599,6 +657,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "viscous"_fix_viscous.html,
 "wall/colloid"_fix_wall.html,
 "wall/gran"_fix_wall_gran.html,
+"wall/gran/region"_fix_wall_gran_region.html,
 "wall/harmonic"_fix_wall.html,
 "wall/lj1043"_fix_wall.html,
 "wall/lj126"_fix_wall.html,
@@ -617,6 +676,7 @@ 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,
@@ -922,6 +982,7 @@ 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_history.txt

@@ -37,7 +37,7 @@ pitfalls or alternatives.
 
 Please see some of the closed issues for examples of how to
 suggest code enhancements, submit proposed changes, or report
-elated issues and how they are resoved. 
+possible bugs and how they are resoved.
 
 As an alternative to using GitHub, you may e-mail the
 "core developers"_http://lammps.sandia.gov/authors.html or send

doc/src/comm_modify.txt

@@ -135,7 +135,7 @@ and angular momentum of a particle.  If the {vel} option is set to
 {yes}, then ghost atoms store these quantities; if {no} then they do
 not.  The {yes} setting is needed by some pair styles which require
 the velocity state of both the I and J particles to compute a pairwise
-I,J interaction.
+I,J interaction, as well as by some compute and fix commands.
 
 Note that if the "fix deform"_fix_deform.html command is being used
 with its "remap v" option enabled, then the velocities for ghost atoms

doc/src/compute_pe_atom.txt

@@ -52,7 +52,7 @@ The KSpace contribution is calculated using the method in
 "(Heyes)"_#Heyes for the Ewald method and a related method for PPPM,
 as specified by the "kspace_style pppm"_kspace_style.html command.
 For PPPM, the calcluation requires 1 extra FFT each timestep that
-per-atom energy is calculated.  Thie "document"_PDF/kspace.pdf
+per-atom energy is calculated.  This "document"_PDF/kspace.pdf
 describes how the long-range per-atom energy calculation is performed.
 
 Various fixes can contribute to the per-atom potential energy of the
@@ -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

@@ -129,8 +129,6 @@ The attributes that start with "a", "d", "i", refer to similar values
 for "angles"_angle_style.html, "dihedrals"_dihedral_style.html, and
 "impropers"_improper_style.html.
 
-The optional {cutoff} keyword
-
 [Output info:]
 
 This compute calculates a local vector or local array depending on the

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_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/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_rx.txt

@@ -75,7 +75,7 @@ but no more than max_steps will be taken. If max_steps is reached, an error warn
 is printed and the simulation is stopped.
 
 After each ODE step, the solution error {e} is tested and weighted using the absTol
-and relTol values. The error vector is weighted as {e} / (relTol * | {u} | + absTol) 
+and relTol values. The error vector is weighted as {e} / (relTol * |{u}| + absTol)
 where {u} is the solution vector. If the norm of the error is <= 1, the solution is
 accepted, {h} is increased by a proportional amount, and the next ODE step is begun.
 Otherwise, {h} is shrunk and the ODE step is repeated.

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_wall_gran.txt

@@ -163,6 +163,8 @@ Any dimension (xyz) that has a granular wall must be non-periodic.
 
 [Related commands:]
 
-"fix move"_fix_move.html, "pair_style granular"_pair_gran.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

@@ -0,0 +1,203 @@
+"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 wall/gran/region command :h3
+
+[Syntax:]
+
+fix ID group-ID wall/gran/region fstyle Kn Kt gamma_n gamma_t xmu dampflag wallstyle regionID :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+wall/region = style name of this fix command :l
+fstyle = style of force interactions between particles and wall :l
+  possible choices: hooke, hooke/history, hertz/history :pre
+Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) :l
+Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) :l
+gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) :l
+gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below) :l
+xmu = static yield criterion (unitless value between 0.0 and 1.0e4) :l
+dampflag = 0 or 1 if tangential damping force is excluded or included :l
+wallstyle = region (see "fix wall/gran"_fix_wall_gran.html for options for other kinds of walls) :l
+region-ID = region whose boundary will act as wall :l,ule
+
+[Examples:]
+
+fix wall all wall/gran/region hooke/history 1000.0 200.0 200.0 100.0 0.5 1 region myCone :pre
+
+[Description:]
+
+Treat the surface of the geometric region defined by the {region-ID}
+as a bounding frictional wall which interacts with nearby finite-size
+granular particles when they are close enough to touch the wall.  See
+the "fix wall/region"_fix_wall_region.html and "fix
+wall/gran"_fix_wall_gran.html commands for related kinds of walls for
+non-granular particles and simpler wall geometries, respectively.
+
+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 of the
+LAMMPS web site.
+
+:image(JPG/gran_funnel_small.jpg,JPG/gran_funnel.png)
+:image(JPG/gran_mixer_small.jpg,JPG/gran_mixer.png)
+
+:line
+
+The distance between a particle and the region boundary is the
+distance to the nearest point on the region surface.  The force the
+wall exerts on the particle is along the direction between that point
+and the particle center, which is the direction normal to the surface
+at that point.  Note that if the region surface is comprised of
+multiple "faces", then each face can exert a force on the particle if
+it is close enough.  E.g. for "region_style block"_region.html, a
+particle in the interior, near a corner of the block, could feel wall
+forces from 1, 2, or 3 faces of the block.
+
+Regions are defined using the "region"_region.html command.  Note that
+the region volume can be interior or exterior to the bounding surface,
+which will determine in which direction the surface interacts with
+particles, i.e. the direction of the surface normal. The exception to
+this is if one or more {open} options are specified for the region
+command, in which case particles interact with both the interior and
+exterior surfaces of regions.
+
+Regions can either be primitive shapes (block, sphere, cylinder, etc)
+or combinations of primitive shapes specified via the {union} or
+{intersect} region styles.  These latter styles can be used to
+construct particle containers with complex shapes.  Regions can also
+move dynamically via the "region"_region.html command keywords (move)
+and {rotate}, or change their shape by use of variables as inputs to
+the "region"_region.html command.  If such a region is used with this
+fix, then the region surface will move in time in the corresponding
+manner.
+
+NOTE: As discussed on the "region"_region.html command doc page,
+regions in LAMMPS do not get wrapped across periodic boundaries.  It
+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}
+regions, additional sharp corners and edges may be present due to the
+intersection of the surfaces of 2 or more primitive volumes.  These
+corners and edges can be of two types: concave or convex.  Concave
+points/edges are like the corners of a cube as seen by particles in
+the interior of a cube.  Wall/particle forces around these features
+are computed correctly.  Convex points/edges are like the corners of a
+cube as seen by particles exterior to the cube, i.e. the points jut
+into the volume where particles are present.  LAMMPS does NOT compute
+the location of these convex points directly, and hence wall/particle
+forces in the cutoff volume around these points suffer from
+inaccuracies.  The basic problem is that the outward normal of the
+surface is not continuous at these points.  This can cause particles
+to feel no force (they don't "see" the wall) when in one location,
+then move a distance epsilon, and suddenly feel a large force because
+they now "see" the wall.  In a worst-case scenario, this can blow
+particles out of the simulation box.  Thus, as a general rule you
+should not use the fix wall/gran/region command with {union} or
+{interesect} regions that have convex points or edges resulting from
+the union/intersection (convex points/edges in the union/intersection
+due to a single sub-region are still OK).
+
+NOTE: Similarly, you should not define {union} or {intersert} regions
+for use with this command that share an overlapping common face that
+is part of the overall outer boundary (interior boundary is OK), even
+if the face is smooth.  E.g. two regions of style block in a {union}
+region, where the two blocks overlap on one or more of their faces.
+This is because LAMMPS discards points that are part of multiple
+sub-regions when calculating wall/particle interactions, to avoid
+double-counting the interaction.  Having two coincident faces could
+cause the face to become invisible to the particles.  The solution is
+to make the two faces differ by epsilon in their position.
+
+The nature of the wall/particle interactions are determined by the
+{fstyle} setting.  It can be any of the styles defined by the
+"pair_style granular"_pair_gran.html commands.  Currently this is
+{hooke}, {hooke/history}, or {hertz/history}.  The equation for the
+force between the wall and particles touching it is the same as the
+corresponding equation on the "pair_style granular"_pair_gran.html doc
+page, but the effective radius is calculated using the radius of the
+particle and the radius of curvature of the wall at the contact point.
+
+Specifically, delta = radius - r = overlap of particle with wall,
+m_eff = mass of particle, and RiRj/Ri+Rj is the effective radius, with
+Rj replaced by the radius of curvature of the wall at the contact
+point.  The radius of curvature can be negative for a concave wall
+section, e.g. the interior of cylinder.  For a flat wall, delta =
+radius - r = overlap of particle with wall, m_eff = mass of particle,
+and the effective radius of contact is just the radius of the
+particle.
+
+The parameters {Kn}, {Kt}, {gamma_n}, {gamma_t}, {xmu} and {dampflag}
+have the same meaning and units as those specified with the
+"pair_style granular"_pair_gran.html commands.  This means a NULL can
+be used for either {Kt} or {gamma_t} as described on that page.  If a
+NULL is used for {Kt}, then a default value is used where {Kt} = 2/7
+{Kn}.  If a NULL is used for {gamma_t}, then a default value is used
+where {gamma_t} = 1/2 {gamma_n}.
+
+Note that you can choose a different force styles and/or different
+values for the 6 wall/particle coefficients than for particle/particle
+interactions.  E.g. if you wish to model the wall as a different
+material.
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+Similiar to "fix wall/gran"_fix_wall_gran.html command, this fix
+writes the shear friction state of atoms interacting with the wall to
+"binary restart files"_restart.html, so that a simulation can continue
+correctly if granular potentials with shear "history" effects are
+being used.  This fix also includes info about a moving region in the
+restart file.  See the "read_restart"_read_restart.html command for
+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: 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
+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:]
+
+This fix is part of the GRANULAR 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.
+
+[Related commands:]
+
+"fix_move"_fix_move.html,
+"fix wall/gran"_fix_wall_gran.html,
+"fix wall/region"_fix_wall_region.html,
+"pair_style granular"_pair_gran.html,
+"region"_region.html
+
+[Default:] none
+

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
@@ -148,6 +149,7 @@ Fixes :h1
    fix_viscous
    fix_wall
    fix_wall_gran
+   fix_wall_gran_region
    fix_wall_piston
    fix_wall_reflect
    fix_wall_region

doc/src/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/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_reax_c.txt

@@ -41,7 +41,9 @@ supplemental information of the following paper: "(Chenoweth et al.,
 2008)"_#Chenoweth_2008.  The version integrated into LAMMPS matches
 the most up-to-date version of ReaxFF as of summer 2010.  For more
 technical details about the pair reax/c implementation of ReaxFF, see
-the "(Aktulga)"_#Aktulga paper.
+the "(Aktulga)"_#Aktulga paper. The {reax/c} style was initially
+implemented as a stand-alone C code and is now integrated into LAMMPS
+as a package.
 
 The {reax/c/kk} style is a Kokkos version of the ReaxFF potential that is
 derived from the {reax/c} style. The Kokkos version can run on GPUs and
@@ -167,7 +169,7 @@ variable eb  	 equal c_reax\[1\]
 variable ea      equal c_reax\[2\]
 \[...\]
 variable eqeq    equal c_reax\[14\]
-thermo_style custom step temp epair v_eb v_ea ... v_eqeq :pre
+thermo_style custom step temp epair v_eb v_ea \[...\] v_eqeq :pre
 
 Only a single pair_coeff command is used with the {reax/c} style which
 specifies a ReaxFF potential file with parameters for all needed
@@ -237,7 +239,7 @@ nbrhood_cutoff: Denotes the near neighbors cutoff (in Angstroms)
 regarding the bonded interactions. (default value = 5.0)
 
 hbond_cutoff: Denotes the cutoff distance (in Angstroms) for hydrogen
-bond interactions.(default value = 7.5. Value of 0.0 turns off
+bond interactions.(default value = 7.5. A value of 0.0 turns off
 hydrogen bonds)
 
 bond_graph_cutoff: is the threshold used in determining what is a

doc/src/read_restart.txt

@@ -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/replicate.txt

@@ -74,11 +74,14 @@ larger version of your molecule as a pre-processing step and input a
 new data file to LAMMPS.
 
 If the current simulation was read in from a restart file (before a
-run is performed), there can have been no fix information stored in
+run is performed), there must not be any fix information stored in
 the file for individual atoms.  Similarly, no fixes can be defined at
 the time the replicate command is used that require vectors of atom
 information to be stored.  This is because the replicate command does
 not know how to replicate that information for new atoms it creates.
+To work around this restriction, restart files may be converted into
+data files and fixes may be undefined via the "unfix"_unfix.html
+command before and redefined after the replicate command.
 
 [Related commands:] none
 

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/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")

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