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="6 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
-6 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,
@@ -618,6 +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,
@@ -923,6 +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/compute_pe_atom.txt

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

doc/src/compute_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_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

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

doc/src/fix_wall_gran_region.txt

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

doc/src/fixes.txt

@@ -32,6 +32,7 @@ Fixes :h1
    fix_drag
    fix_drude
    fix_drude_transform
+   fix_dpd_energy
    fix_dt_reset
    fix_efield
    fix_ehex
@@ -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/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/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

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

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

examples/KAPPA/log.13Oct16.ehex.g++.8

@@ -1,4 +1,4 @@
-LAMMPS (7 Jun 2016)
+LAMMPS (13 Oct 2016)
 # sample LAMMPS input script for thermal conductivity of liquid LJ
 # use fix ehex to add/subtract energy from 2 regions
 
@@ -79,20 +79,20 @@ Step Temp E_pair E_mol TotEng Press
      800    1.3419995   -3.7155648            0   -1.7028172   0.82925676 
      900    1.3562214   -3.6965609            0   -1.6624831   0.88908117 
     1000    1.3732017   -3.7100044            0   -1.6504594   0.83982701 
-Loop time of 0.878884 on 8 procs for 1000 steps with 8000 atoms
+Loop time of 0.889114 on 8 procs for 1000 steps with 8000 atoms
 
-Performance: 491532.534 tau/day, 1137.807 timesteps/s
+Performance: 485876.777 tau/day, 1124.715 timesteps/s
 99.3% CPU use with 8 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.48108    | 0.4925     | 0.50422    |   1.0 | 56.04
-Neigh   | 0.23355    | 0.23565    | 0.23888    |   0.4 | 26.81
-Comm    | 0.088565   | 0.10044    | 0.11391    |   2.7 | 11.43
-Output  | 0.00029421 | 0.00031444 | 0.00041795 |   0.2 |  0.04
-Modify  | 0.027427   | 0.032625   | 0.035225   |   1.6 |  3.71
-Other   |            | 0.01735    |            |       |  1.97
+Pair    | 0.48042    | 0.50311    | 0.52772    |   1.9 | 56.59
+Neigh   | 0.22997    | 0.23203    | 0.23466    |   0.3 | 26.10
+Comm    | 0.081187   | 0.10484    | 0.1285     |   4.2 | 11.79
+Output  | 0.00027299 | 0.00028226 | 0.000314   |   0.1 |  0.03
+Modify  | 0.028298   | 0.032276   | 0.037612   |   2.0 |  3.63
+Other   |            | 0.01658    |            |       |  1.86
 
 Nlocal:    1000 ave 1020 max 982 min
 Histogram: 1 0 2 1 0 1 1 1 0 1
@@ -121,7 +121,7 @@ thermo_style    custom step temp c_Thot c_Tcold
 thermo	        1000
 run             10000
 Memory usage per processor = 2.80761 Mbytes
-Step Temp Thot Tcold 
+Step Temp c_Thot c_Tcold 
     1000         1.35     1.431295    1.2955644 
     2000    1.3537291    1.6418772    1.1875127 
     3000    1.3615152    1.6451299    1.1769094 
@@ -133,20 +133,20 @@ Step Temp Thot Tcold
     9000    1.3701136    1.8238424     1.136342 
    10000    1.3563004    1.8059065    1.1547129 
    11000    1.3794051     1.692299    1.0515688 
-Loop time of 10.292 on 8 procs for 10000 steps with 8000 atoms
+Loop time of 10.5555 on 8 procs for 10000 steps with 8000 atoms
 
-Performance: 419743.444 tau/day, 971.628 timesteps/s
-99.5% CPU use with 8 MPI tasks x no OpenMP threads
+Performance: 409265.976 tau/day, 947.375 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    | 4.1797     | 4.902      | 5.5136     |  25.3 | 47.63
-Neigh   | 2.1913     | 2.4616     | 2.6938     |  14.2 | 23.92
-Comm    | 0.87831    | 1.64       | 2.611      |  56.5 | 15.94
-Output  | 0.00043011 | 0.00063166 | 0.00075626 |   0.5 |  0.01
-Modify  | 0.78531    | 0.92487    | 1.0647     |  10.6 |  8.99
-Other   |            | 0.3628     |            |       |  3.53
+Pair    | 4.1863     | 5.0134     | 5.8326     |  28.0 | 47.50
+Neigh   | 2.1559     | 2.4232     | 2.6516     |  14.2 | 22.96
+Comm    | 0.80561    | 1.8126     | 2.8852     |  58.4 | 17.17
+Output  | 0.00044537 | 0.00064856 | 0.00077057 |   0.5 |  0.01
+Modify  | 0.81915    | 0.94285    | 1.0571     |   9.5 |  8.93
+Other   |            | 0.3628     |            |       |  3.44
 
 Nlocal:    1000 ave 1105 max 883 min
 Histogram: 1 1 2 0 0 0 0 0 2 2
@@ -174,7 +174,7 @@ thermo_style    custom step temp c_Thot c_Tcold v_tdiff f_ave
 
 run             20000
 Memory usage per processor = 3.0578 Mbytes
-Step Temp Thot Tcold tdiff ave 
+Step Temp c_Thot c_Tcold v_tdiff f_ave 
    11000    1.3794051    1.6903393    1.0515688            0            0 
    12000    1.3799777    1.8004888    1.1032219  -0.63860014            0 
    13000    1.3733605    1.7823094    1.0553582  -0.65827891  -0.65827891 
@@ -196,20 +196,20 @@ Step Temp Thot Tcold tdiff ave
    29000    1.3819302    1.8619138    1.0495292  -0.78627491  -0.76680973 
    30000    1.3968366     1.883107    1.1004588  -0.83902548  -0.77082172 
    31000    1.3822489    1.8220413    1.0322271   -0.7550338  -0.76999077 
-Loop time of 22.3319 on 8 procs for 20000 steps with 8000 atoms
+Loop time of 22.7579 on 8 procs for 20000 steps with 8000 atoms
 
-Performance: 386890.255 tau/day, 895.579 timesteps/s
+Performance: 379649.018 tau/day, 878.817 timesteps/s
 99.3% CPU use with 8 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 7.4818     | 9.8886     | 12.008     |  66.1 | 44.28
-Neigh   | 4.1157     | 5.0693     | 5.9657     |  38.0 | 22.70
-Comm    | 1.8343     | 4.6586     | 7.8747     | 129.4 | 20.86
-Output  | 0.00095606 | 0.0017744  | 0.0019104  |   0.7 |  0.01
-Modify  | 1.6812     | 1.9319     | 2.2204     |  13.5 |  8.65
-Other   |            | 0.7817     |            |       |  3.50
+Pair    | 7.4811     | 10.102     | 12.63      |  68.7 | 44.39
+Neigh   | 4.0495     | 4.9884     | 5.8366     |  37.8 | 21.92
+Comm    | 1.6695     | 4.9483     | 8.493      | 130.7 | 21.74
+Output  | 0.0010517  | 0.0017769  | 0.0019059  |   0.7 |  0.01
+Modify  | 1.6903     | 1.9371     | 2.2355     |  14.8 |  8.51
+Other   |            | 0.7799     |            |       |  3.43
 
 Nlocal:    1000 ave 1121 max 857 min
 Histogram: 2 0 1 1 0 0 0 0 1 3
@@ -222,4 +222,4 @@ Total # of neighbors = 219898
 Ave neighs/atom = 27.4872
 Neighbor list builds = 3474
 Dangerous builds = 0
-Total wall time: 0:00:33
+Total wall time: 0:00:34

examples/KAPPA/log.13Oct16.heat.g++.8

@@ -1,4 +1,4 @@
-LAMMPS (7 Jun 2016)
+LAMMPS (13 Oct 2016)
 # sample LAMMPS input script for thermal conductivity of liquid LJ
 # use fix heat to add/subtract energy from 2 regions
 
@@ -79,20 +79,20 @@ Step Temp E_pair E_mol TotEng Press
      800    1.3419995   -3.7155648            0   -1.7028172   0.82925676 
      900    1.3562214   -3.6965609            0   -1.6624831   0.88908117 
     1000    1.3732017   -3.7100044            0   -1.6504594   0.83982701 
-Loop time of 0.889036 on 8 procs for 1000 steps with 8000 atoms
+Loop time of 0.872163 on 8 procs for 1000 steps with 8000 atoms
 
-Performance: 485919.613 tau/day, 1124.814 timesteps/s
-99.4% CPU use with 8 MPI tasks x no OpenMP threads
+Performance: 495320.223 tau/day, 1146.575 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    | 0.47867    | 0.4928     | 0.5006     |   1.0 | 55.43
-Neigh   | 0.23302    | 0.23557    | 0.23833    |   0.3 | 26.50
-Comm    | 0.1001     | 0.11264    | 0.12817    |   2.6 | 12.67
-Output  | 0.00032806 | 0.00034043 | 0.00040531 |   0.1 |  0.04
-Modify  | 0.028788   | 0.031511   | 0.033365   |   0.9 |  3.54
-Other   |            | 0.01618    |            |       |  1.82
+Pair    | 0.48598    | 0.49768    | 0.50892    |   1.1 | 57.06
+Neigh   | 0.22855    | 0.23236    | 0.23463    |   0.5 | 26.64
+Comm    | 0.082584   | 0.093727   | 0.10748    |   2.9 | 10.75
+Output  | 0.0002718  | 0.00028038 | 0.00031757 |   0.1 |  0.03
+Modify  | 0.028934   | 0.031425   | 0.03322    |   0.8 |  3.60
+Other   |            | 0.01668    |            |       |  1.91
 
 Nlocal:    1000 ave 1020 max 982 min
 Histogram: 1 0 2 1 0 1 1 1 0 1
@@ -121,7 +121,7 @@ thermo_style    custom step temp c_Thot c_Tcold
 thermo	        1000
 run             10000
 Memory usage per processor = 2.55761 Mbytes
-Step Temp Thot Tcold 
+Step Temp c_Thot c_Tcold 
     1000         1.35     1.431295    1.2955644 
     2000    1.3518468    1.5562602     1.154905 
     3000    1.3477229    1.5890075    1.2395414 
@@ -133,20 +133,20 @@ Step Temp Thot Tcold
     9000    1.3739201    1.6846211    1.1138829 
    10000    1.3751455    1.8039471    1.1500399 
    11000    1.3716416     1.833336    1.1267278 
-Loop time of 10.488 on 8 procs for 10000 steps with 8000 atoms
+Loop time of 10.3395 on 8 procs for 10000 steps with 8000 atoms
 
-Performance: 411900.216 tau/day, 953.473 timesteps/s
+Performance: 417815.278 tau/day, 967.165 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    | 4.138      | 4.9118     | 5.6168     |  26.2 | 46.83
-Neigh   | 2.1715     | 2.4541     | 2.7147     |  14.7 | 23.40
-Comm    | 0.94395    | 1.8449     | 2.9212     |  55.3 | 17.59
-Output  | 0.00043416 | 0.00046757 | 0.00054884 |   0.2 |  0.00
-Modify  | 1.0234     | 1.0946     | 1.2539     |   8.7 | 10.44
-Other   |            | 0.1821     |            |       |  1.74
+Pair    | 4.2189     | 4.9657     | 5.6225     |  25.3 | 48.03
+Neigh   | 2.1359     | 2.4223     | 2.6741     |  14.8 | 23.43
+Comm    | 0.83801    | 1.6773     | 2.6984     |  57.1 | 16.22
+Output  | 0.00042701 | 0.00046191 | 0.00052905 |   0.1 |  0.00
+Modify  | 1.0143     | 1.0895     | 1.1846     |   5.7 | 10.54
+Other   |            | 0.1844     |            |       |  1.78
 
 Nlocal:    1000 ave 1131 max 878 min
 Histogram: 3 1 0 0 0 0 0 1 1 2
@@ -174,7 +174,7 @@ thermo_style    custom step temp c_Thot c_Tcold v_tdiff f_ave
 
 run             20000
 Memory usage per processor = 2.8078 Mbytes
-Step Temp Thot Tcold tdiff ave 
+Step Temp c_Thot c_Tcold v_tdiff f_ave 
    11000    1.3716416     1.833336    1.1267278            0            0 
    12000    1.3703433    1.7829467    1.1194444  -0.66044316            0 
    13000    1.3686734    1.8334366    1.1193477  -0.71431978  -0.71431978 
@@ -196,20 +196,20 @@ Step Temp Thot Tcold tdiff ave
    29000    1.3777555    1.8287284    1.0715132  -0.70375514  -0.74425717 
    30000    1.3821118    1.7382856    1.1078333  -0.79892499  -0.74729427 
    31000    1.3870476    1.8410063    1.1235958  -0.76218423  -0.74807795 
-Loop time of 22.3813 on 8 procs for 20000 steps with 8000 atoms
+Loop time of 22.4057 on 8 procs for 20000 steps with 8000 atoms
 
-Performance: 386036.860 tau/day, 893.604 timesteps/s
-99.4% CPU use with 8 MPI tasks x no OpenMP threads
+Performance: 385616.132 tau/day, 892.630 timesteps/s
+99.3% CPU use with 8 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 7.4578     | 9.8912     | 11.96      |  64.5 | 44.19
-Neigh   | 4.0721     | 5.0195     | 5.8898     |  36.9 | 22.43
-Comm    | 1.9554     | 4.7393     | 7.8917     | 125.4 | 21.18
-Output  | 0.00099301 | 0.0017841  | 0.0019252  |   0.7 |  0.01
-Modify  | 2.2325     | 2.321      | 2.4866     |   6.5 | 10.37
-Other   |            | 0.4085     |            |       |  1.83
+Pair    | 7.6116     | 10.003     | 12.262     |  64.3 | 44.65
+Neigh   | 4.038      | 4.9528     | 5.8822     |  37.6 | 22.10
+Comm    | 1.6649     | 4.7143     | 7.6339     | 124.9 | 21.04
+Output  | 0.00098443 | 0.0017504  | 0.0018921  |   0.7 |  0.01
+Modify  | 2.1819     | 2.3289     | 2.6598     |  12.6 | 10.39
+Other   |            | 0.4047     |            |       |  1.81
 
 Nlocal:    1000 ave 1134 max 850 min
 Histogram: 2 1 0 1 0 0 0 1 0 3

examples/KAPPA/log.13Oct16.heatflux.g++.8

@@ -0,0 +1,230 @@
+LAMMPS (13 Oct 2016)
+# sample LAMMPS input script for thermal conductivity of liquid LJ
+# Green-Kubo method via compute heat/flux and fix ave/correlate
+
+# settings
+
+variable	x equal 10
+variable	y equal 10
+variable	z equal 10
+
+variable	rho equal 0.6
+variable        t equal 1.35
+variable	rc equal 2.5
+
+#variable	rho equal 0.85
+#variable        t equal 0.7
+#variable	rc equal 3.0
+
+variable    p equal 200     # correlation length
+variable    s equal 10      # sample interval
+variable    d equal $p*$s   # dump interval
+variable    d equal 200*$s   
+variable    d equal 200*10   
+
+# setup problem
+
+units		lj
+atom_style	atomic
+
+lattice		fcc ${rho}
+lattice		fcc 0.6
+Lattice spacing in x,y,z = 1.88207 1.88207 1.88207
+region		box block 0 $x 0 $y 0 $z
+region		box block 0 10 0 $y 0 $z
+region		box block 0 10 0 10 0 $z
+region		box block 0 10 0 10 0 10
+create_box	1 box
+Created orthogonal box = (0 0 0) to (18.8207 18.8207 18.8207)
+  2 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 4000 atoms
+mass		1 1.0
+
+velocity	all create $t 87287
+velocity	all create 1.35 87287
+
+pair_style	lj/cut ${rc}
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1
+
+# 1st equilibration run
+
+fix		1 all nvt temp $t $t 0.5
+fix		1 all nvt temp 1.35 $t 0.5
+fix		1 all nvt temp 1.35 1.35 0.5
+thermo		100
+run		1000
+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 = 14 14 14
+Memory usage per processor = 2.52285 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.35   -4.1241917            0   -2.0996979   -3.1962625 
+     100    1.1997886   -3.7796264            0   -1.9803934    0.4889458 
+     200     1.271238   -3.7354981            0   -1.8291178    0.6873844 
+     300    1.3346808   -3.6942841            0   -1.6927634   0.84332881 
+     400    1.4020848   -3.7118654            0   -1.6092641   0.87670585 
+     500    1.3723622   -3.6917931            0   -1.6337644   0.92172921 
+     600    1.3451676   -3.7281573            0   -1.7109103   0.76029091 
+     700    1.3021567   -3.6876155            0   -1.7348687   0.82721085 
+     800    1.3489121   -3.7082852            0   -1.6854229   0.86438061 
+     900    1.3708803   -3.6966168            0   -1.6408103     0.921415 
+    1000    1.3640742   -3.7075319            0   -1.6619322   0.86651332 
+Loop time of 0.457959 on 8 procs for 1000 steps with 4000 atoms
+
+Performance: 943316.262 tau/day, 2183.602 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    | 0.23307    | 0.24263    | 0.2466     |   1.0 | 52.98
+Neigh   | 0.10661    | 0.11011    | 0.11166    |   0.5 | 24.04
+Comm    | 0.069595   | 0.075354   | 0.087444   |   2.2 | 16.45
+Output  | 0.00028014 | 0.00028831 | 0.00031686 |   0.1 |  0.06
+Modify  | 0.01694    | 0.01904    | 0.021602   |   1.2 |  4.16
+Other   |            | 0.01053    |            |       |  2.30
+
+Nlocal:    500 ave 510 max 479 min
+Histogram: 1 0 0 0 0 2 1 1 0 3
+Nghost:    1519 ave 1539 max 1509 min
+Histogram: 2 0 4 0 0 0 0 1 0 1
+Neighs:    13553.8 ave 14051 max 12567 min
+Histogram: 1 0 0 0 1 0 2 1 1 2
+
+Total # of neighbors = 108430
+Ave neighs/atom = 27.1075
+Neighbor list builds = 155
+Dangerous builds = 0
+
+velocity	all scale $t
+velocity	all scale 1.35
+
+unfix		1
+
+# thermal conductivity calculation
+
+reset_timestep  0
+
+compute         myKE all ke/atom
+compute         myPE all pe/atom
+compute         myStress all stress/atom NULL virial
+compute         flux all heat/flux myKE myPE myStress
+variable        Jx equal c_flux[1]/vol
+variable        Jy equal c_flux[2]/vol
+variable        Jz equal c_flux[3]/vol
+
+fix	        1 all nve
+fix             JJ all ave/correlate $s $p $d                 c_flux[1] c_flux[2] c_flux[3] type auto 	        file profile.heatflux ave running
+fix             JJ all ave/correlate 10 $p $d                 c_flux[1] c_flux[2] c_flux[3] type auto 	        file profile.heatflux ave running
+fix             JJ all ave/correlate 10 200 $d                 c_flux[1] c_flux[2] c_flux[3] type auto 	        file profile.heatflux ave running
+fix             JJ all ave/correlate 10 200 2000                 c_flux[1] c_flux[2] c_flux[3] type auto 	        file profile.heatflux ave running
+
+variable        scale equal $s*dt/$t/$t/vol
+variable        scale equal 10*dt/$t/$t/vol
+variable        scale equal 10*dt/1.35/$t/vol
+variable        scale equal 10*dt/1.35/1.35/vol
+variable        k11 equal trap(f_JJ[3])*${scale}
+variable        k11 equal trap(f_JJ[3])*4.11522633744856e-06
+variable        k22 equal trap(f_JJ[4])*${scale}
+variable        k22 equal trap(f_JJ[4])*4.11522633744856e-06
+variable        k33 equal trap(f_JJ[5])*${scale}
+variable        k33 equal trap(f_JJ[5])*4.11522633744856e-06
+
+thermo	        $d
+thermo	        2000
+thermo_style    custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
+
+run             100000
+Memory usage per processor = 4.39785 Mbytes
+Step Temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33 
+       0         1.35  0.012561273 -0.087295611 -0.037041124  0.014429409   0.69689289   0.12547278 
+    2000    1.3455113 -0.034571206  -0.17570902 -0.057218308   -1.6110148    7.9287556    8.5035767 
+    4000    1.3477761 -0.029528723  0.018790489  0.056107464     7.698411    1.9459053    9.9605272 
+    6000    1.3411436  -0.20281149    0.2184806  0.036024028    4.6533075    1.6223216    3.7246529 
+    8000    1.3561682   0.12038719  0.034930957   0.12173601    4.6450263    1.9032849    2.7566363 
+   10000    1.3397694  -0.14241489  -0.10956496  0.053088086    6.4191535    3.1582257    2.2786677 
+   12000    1.3410756 0.0033462395   0.14337321   0.16381733    5.9663779    1.6774436    1.7442075 
+   14000    1.3484928 0.0080419803 -0.080232102  0.039035519    4.9483626    1.6210893    1.6103343 
+   16000    1.3414836  -0.11063045 -0.031557643  0.032060333    6.1381241     1.438198    1.5831541 
+   18000    1.3488617   0.15908507 -0.021418806  -0.13992507    5.9198613    1.1016464    1.2905478 
+   20000    1.3535727   0.13217689  0.071933521 -0.028452943    6.3746606     1.003194    1.7007101 
+   22000    1.3408534 -0.078953557 -0.0022323663  -0.22979033    5.0105241    1.1489328     1.720847 
+   24000      1.34722  0.074784199 -0.071218632   0.15238165    4.4835452   0.94086945    3.1603615 
+   26000    1.3539218  0.052534363   0.10419096    0.1866213    4.2233104    1.3973253    3.2802881 
+   28000    1.3510105 0.0080425673  -0.03723976   0.20758595     5.261917    1.1931088     3.498831 
+   30000    1.3410807 -0.043957884  0.065683978  0.015386362    4.3815277    1.5000017    3.2237565 
+   32000      1.34766 -0.060481287   0.17142383  0.034367135    4.0974942    1.1637027    3.3771953 
+   34000    1.3417583  -0.10055844  0.050237668   0.06974988    4.1478021    1.0235517    2.9440249 
+   36000    1.3468728   0.09375756  -0.17875264 -0.063513807    4.4412987   0.71084371    3.4316313 
+   38000    1.3496868 -0.038635804     0.117965  0.018050271     4.962332   0.41701129    3.4690212 
+   40000    1.3403452 -0.092158116   0.14432655 -0.062258229    4.9980486    0.3762815    3.1688552 
+   42000    1.3498661  0.085807945  0.010256385 -0.002956898    4.8200626   0.29278287     3.094633 
+   44000    1.3564084  -0.07415163 -0.051327929  -0.18457986    4.7070907    0.3358167    3.0741797 
+   46000    1.3435866 -0.013911463  0.081813372  0.022628846    4.6043718    0.3682401    2.9956189 
+   48000     1.350611  0.036512747  0.080481423  -0.22973181    4.5648715   0.32728516    3.8573343 
+   50000    1.3421783  0.057665789  0.075597141   0.17377918    4.4278473    0.5383886    3.5866168 
+   52000    1.3473497  -0.11159587  -0.09688769   0.19876168    4.3876613   0.43408155    3.4786305 
+   54000    1.3459495  -0.15341705  0.063996148 -0.0038254597    4.8434026   0.62047297     3.445187 
+   56000    1.3545654 -0.082406034  0.089232864 -0.024355614     4.546051    0.7367607    3.3694561 
+   58000    1.3577504  0.082844384  0.019500036  0.073721698    4.4061886    1.4575694    3.2754066 
+   60000     1.348614  -0.16190321 -0.048576343  0.093820555    4.2946463    1.3416919    3.1159234 
+   62000    1.3551143  0.097443296  -0.04420265  -0.25713945    4.1260882    1.2550603     3.063215 
+   64000     1.346239  0.019198575 -0.095746619   0.18383922    4.5691519    1.2615165    2.9935539 
+   66000    1.3535383 -0.0035547901   -0.1753318  0.014025292    4.5371394    1.0740671    2.9362916 
+   68000    1.3421249  -0.18217113  0.077901408   0.04314081    5.1644747    1.0218342    2.9789097 
+   70000    1.3446114  0.029565781  -0.13771336  0.050328878    5.4811405    1.0430806    2.9748623 
+   72000    1.3692655  0.005711741   0.13966773 -0.062638787    5.3033385    1.1040582    2.7599218 
+   74000    1.3405365 -0.054281977  0.038019086 -0.024980877    5.1246258    2.0782965     2.725331 
+   76000    1.3644178  0.040847675 -0.051968108  -0.12259032    5.1218657    1.8504273    2.6804003 
+   78000     1.353792 -0.093663092  0.018784967 -0.073871437     5.025196    1.7789709    2.5339006 
+   80000    1.3520982  -0.09407101  0.010328039 0.0028841073    5.1410049     1.855057    2.6935895 
+   82000    1.3447597  -0.11935066   -0.2184608  0.073543056    5.2645334    1.7883077    4.2012292 
+   84000    1.3712151 -0.064367612  0.021246872 -0.033571866    5.0479674    1.8947341    4.3856536 
+   86000    1.3453867 -0.029842112 -0.042297039   0.05422886    5.0667777    2.0365983    4.4542311 
+   88000    1.3439543  -0.21625828 -0.028119372 -0.010320332    4.9946428    2.3095763    4.3429587 
+   90000    1.3472579  0.058391002  0.037139373   0.03424008    5.0599004    2.8132794    4.4503426 
+   92000     1.361788  0.028891114  0.072799744  -0.12035229    4.8759851    2.5130025    4.2747068 
+   94000    1.3440566  0.043421348  0.049653856 -0.060444094    4.8884081    2.5072981    4.3105221 
+   96000    1.3537566  0.088733517  -0.11449828 -0.049852036    4.8115085    2.4780963    4.2213579 
+   98000    1.3373399   0.25457663 -0.041723778 0.00084565184    4.7163394    2.4100822     4.485536 
+  100000    1.3487502  0.046333889    0.1247351  0.063467467    4.6563279    2.4049358    4.5742925 
+Loop time of 49.532 on 8 procs for 100000 steps with 4000 atoms
+
+Performance: 872163.631 tau/day, 2018.897 timesteps/s
+99.6% CPU use with 8 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 27.027     | 27.478     | 28.167     |   6.9 | 55.48
+Neigh   | 11.257     | 11.369     | 11.491     |   2.3 | 22.95
+Comm    | 6.6783     | 7.6942     | 8.2758     |  19.3 | 15.53
+Output  | 0.0075166  | 0.024356   | 0.026799   |   4.1 |  0.05
+Modify  | 1.7374     | 1.7617     | 1.7845     |   1.0 |  3.56
+Other   |            | 1.205      |            |       |  2.43
+
+Nlocal:    500 ave 505 max 491 min
+Histogram: 1 0 0 1 0 1 0 2 2 1
+Nghost:    1529.88 ave 1548 max 1508 min
+Histogram: 1 1 0 0 1 1 2 0 0 2
+Neighs:    13569.8 ave 13906 max 13235 min
+Histogram: 1 1 0 1 1 1 1 1 0 1
+
+Total # of neighbors = 108558
+Ave neighs/atom = 27.1395
+Neighbor list builds = 16041
+Dangerous builds = 0
+
+variable        kappa equal (v_k11+v_k22+v_k33)/3.0
+print           "running average conductivity: ${kappa}"
+running average conductivity: 3.8785187495769
+Total wall time: 0:00:50

examples/KAPPA/log.13Oct16.langevin.g++.8

@@ -0,0 +1,245 @@
+LAMMPS (13 Oct 2016)
+# sample LAMMPS input script for thermal conductivity of liquid LJ
+# thermostatting 2 regions via fix langevin
+
+# settings
+
+variable	x equal 10
+variable	y equal 10
+variable	z equal 20
+
+variable	rho equal 0.6
+variable        t equal 1.35
+variable	rc equal 2.5
+variable        tlo equal 1.0
+variable        thi equal 1.70
+
+#variable	rho equal 0.85
+#variable        t equal 0.7
+#variable	rc equal 3.0
+#variable        tlo equal 0.3
+#variable        thi equal 1.0
+
+# setup problem
+
+units		lj
+atom_style	atomic
+
+lattice		fcc ${rho}
+lattice		fcc 0.6
+Lattice spacing in x,y,z = 1.88207 1.88207 1.88207
+region		box block 0 $x 0 $y 0 $z
+region		box block 0 10 0 $y 0 $z
+region		box block 0 10 0 10 0 $z
+region		box block 0 10 0 10 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (18.8207 18.8207 37.6414)
+  2 by 1 by 4 MPI processor grid
+create_atoms	1 box
+Created 8000 atoms
+mass		1 1.0
+
+velocity	all create $t 87287
+velocity	all create 1.35 87287
+
+pair_style	lj/cut ${rc}
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1
+
+# heat layers
+
+region          hot block INF INF INF INF 0 1
+region          cold block  INF INF INF INF 10 11
+compute         Thot all temp/region hot
+compute         Tcold all temp/region cold
+
+# 1st equilibration run
+
+fix             1 all nvt temp $t $t 0.5
+fix             1 all nvt temp 1.35 $t 0.5
+fix             1 all nvt temp 1.35 1.35 0.5
+thermo	        100
+run             1000
+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 = 14 14 27
+Memory usage per processor = 2.55761 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.35   -4.1241917            0   -2.0994448   -3.1961612 
+     100    1.1819832   -3.7640881            0    -1.991335   0.53985757 
+     200    1.2578365   -3.7395333            0   -1.8530144   0.69591862 
+     300    1.3282971   -3.7215427            0   -1.7293461   0.79036065 
+     400    1.3714367   -3.7043826            0   -1.6474847   0.85873226 
+     500    1.3590952   -3.6707735            0   -1.6323855   0.99602024 
+     600    1.3575117   -3.7118244            0   -1.6758114   0.81454305 
+     700    1.3284444   -3.7075488            0   -1.7151313   0.81136596 
+     800    1.3419995   -3.7155648            0   -1.7028172   0.82925676 
+     900    1.3562214   -3.6965609            0   -1.6624831   0.88908117 
+    1000    1.3732017   -3.7100044            0   -1.6504594   0.83982701 
+Loop time of 0.876399 on 8 procs for 1000 steps with 8000 atoms
+
+Performance: 492926.111 tau/day, 1141.033 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    | 0.47963    | 0.4975     | 0.51846    |   1.6 | 56.77
+Neigh   | 0.22878    | 0.23186    | 0.23458    |   0.4 | 26.46
+Comm    | 0.081789   | 0.096763   | 0.11865    |   3.6 | 11.04
+Output  | 0.000247   | 0.00025409 | 0.00028944 |   0.1 |  0.03
+Modify  | 0.02689    | 0.033982   | 0.042612   |   2.9 |  3.88
+Other   |            | 0.01604    |            |       |  1.83
+
+Nlocal:    1000 ave 1020 max 982 min
+Histogram: 1 0 2 1 0 1 1 1 0 1
+Nghost:    2299.5 ave 2331 max 2268 min
+Histogram: 1 1 1 1 0 0 0 3 0 1
+Neighs:    27122 ave 28382 max 26337 min
+Histogram: 2 0 2 1 1 0 0 1 0 1
+
+Total # of neighbors = 216976
+Ave neighs/atom = 27.122
+Neighbor list builds = 162
+Dangerous builds = 0
+
+velocity	all scale $t
+velocity	all scale 1.35
+
+unfix		1
+
+# 2nd equilibration run
+
+fix		1 all nve
+fix             hot all langevin ${thi} ${thi} 1.0 59804 tally yes
+fix             hot all langevin 1.7 ${thi} 1.0 59804 tally yes
+fix             hot all langevin 1.7 1.7 1.0 59804 tally yes
+fix             cold all langevin ${tlo} ${tlo} 1.0 287859 tally yes
+fix             cold all langevin 1 ${tlo} 1.0 287859 tally yes
+fix             cold all langevin 1 1 1.0 287859 tally yes
+fix_modify      hot temp Thot
+fix_modify      cold temp Tcold
+
+variable        tdiff equal c_Thot-c_Tcold
+thermo_style    custom step temp c_Thot c_Tcold f_hot f_cold v_tdiff
+thermo	        1000
+run             10000
+Memory usage per processor = 3.30761 Mbytes
+Step Temp c_Thot c_Tcold f_hot f_cold v_tdiff 
+    1000         1.35     1.431295    1.2955644           -0           -0   0.13573065 
+    2000    1.3593243    1.6602094    1.0898701  -0.13903162   0.14234352   0.57033928 
+    3000    1.3412163    1.6308839    1.0677742   -0.2214765   0.25871329   0.56310968 
+    4000    1.3275359    1.5248034    1.0792345  -0.26908328   0.34211202   0.44556887 
+    5000    1.3230922    1.6266046    1.0523802  -0.33175886   0.43533756    0.5742244 
+    6000    1.3037036    1.6021737    1.0408166   -0.3639815   0.49869333   0.56135712 
+    7000    1.2903225    1.5701119    1.0603548  -0.40000421   0.55547714   0.50975712 
+    8000    1.3050677    1.6420218    1.0221774  -0.46368839   0.60293974   0.61984444 
+    9000    1.2950977    1.7153984    1.0583242  -0.51871512   0.66389344   0.65707419 
+   10000    1.3100216    1.6680668    1.0871293  -0.57485359    0.7161839   0.58093752 
+   11000     1.297052    1.6486494     1.088903  -0.60276081   0.75900024   0.55974633 
+Loop time of 11.5988 on 8 procs for 10000 steps with 8000 atoms
+
+Performance: 372451.299 tau/day, 862.156 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    | 4.0544     | 4.9719     | 5.8426     |  34.5 | 42.87
+Neigh   | 2.0735     | 2.3933     | 2.7208     |  18.8 | 20.63
+Comm    | 0.91559    | 1.9788     | 3.1216     |  70.5 | 17.06
+Output  | 0.0005753  | 0.00068495 | 0.00080419 |   0.3 |  0.01
+Modify  | 1.9354     | 1.9837     | 2.0321     |   2.6 | 17.10
+Other   |            | 0.2705     |            |       |  2.33
+
+Nlocal:    1000 ave 1112 max 841 min
+Histogram: 1 1 0 2 0 0 0 0 1 3
+Nghost:    2294.38 ave 2506 max 2077 min
+Histogram: 2 1 1 0 0 0 0 1 1 2
+Neighs:    27441.9 ave 32651 max 19438 min
+Histogram: 1 1 0 2 0 0 0 0 0 4
+
+Total # of neighbors = 219535
+Ave neighs/atom = 27.4419
+Neighbor list builds = 1674
+Dangerous builds = 0
+
+# thermal conductivity calculation
+# reset langevin thermostats to zero energy accumulation
+
+compute		ke all ke/atom
+variable	temp atom c_ke/1.5
+
+fix             hot all langevin ${thi} ${thi} 1.0 59804 tally yes
+fix             hot all langevin 1.7 ${thi} 1.0 59804 tally yes
+fix             hot all langevin 1.7 1.7 1.0 59804 tally yes
+fix             cold all langevin ${tlo} ${tlo} 1.0 287859 tally yes
+fix             cold all langevin 1 ${tlo} 1.0 287859 tally yes
+fix             cold all langevin 1 1 1.0 287859 tally yes
+fix_modify      hot temp Thot
+fix_modify      cold temp Tcold
+
+fix             ave all ave/time 10 100 1000 v_tdiff ave running
+thermo_style    custom step temp c_Thot c_Tcold f_hot f_cold v_tdiff f_ave
+
+compute         layers all chunk/atom bin/1d z lower 0.05 units reduced
+fix		2 all ave/chunk 10 100 1000 layers v_temp file profile.langevin
+
+run             20000
+Memory usage per processor = 3.5578 Mbytes
+Step Temp c_Thot c_Tcold f_hot f_cold v_tdiff f_ave 
+   11000     1.297052    1.6473904     1.088903           -0           -0   0.55848738            0 
+   12000    1.2792808    1.6043738    1.0658375 -0.012256975   0.04611547   0.53853632   0.54492428 
+   13000    1.2787101    1.7035572    1.1159037 -0.073806664  0.099529002   0.58765348    0.5581748 
+   14000     1.289918    1.4642237    1.1073937  -0.11428779   0.13931657   0.35683005   0.56816328 
+   15000    1.2932964    1.5032665    1.0523148  -0.17247717   0.19001309   0.45095174   0.57436291 
+   16000    1.3025037    1.5424316    1.1185175  -0.22598282   0.22640921   0.42391405   0.56973168 
+   17000    1.3009667    1.5582105    1.0745661  -0.27544101   0.26143452   0.48364439    0.5700118 
+   18000    1.2970255    1.5019842    1.0228322  -0.31195285   0.31203237     0.479152   0.56544644 
+   19000    1.2880631    1.5290587    1.0976483  -0.34645573   0.34243366   0.43141047   0.56338309 
+   20000    1.3119675    1.6284144    1.1102294  -0.40922326   0.39217092   0.51818503   0.56614474 
+   21000    1.2838063    1.6670934   0.97721382  -0.43809329   0.46021572   0.68987962    0.5686161 
+   22000    1.2925041    1.7050682    1.0984963   -0.4871305   0.50520177    0.6065719   0.57226368 
+   23000    1.2746463    1.6388503    1.0286701  -0.51212873   0.56478515    0.6101802   0.57290996 
+   24000    1.2745381    1.7085713    1.1362975  -0.54529463   0.58540408   0.57227375   0.57296767 
+   25000    1.2776401    1.5259253    1.0415158  -0.58389862   0.62623289   0.48440948   0.57386374 
+   26000    1.2661888    1.4760829   0.99145001  -0.62638032   0.68155754   0.48463289   0.57021631 
+   27000    1.2923677    1.6070495    1.0300276  -0.70014343   0.70236265    0.5770219   0.57001637 
+   28000    1.2961449    1.7052335    1.0805793  -0.74856241   0.75775659   0.62465427   0.56927907 
+   29000    1.2969474    1.5520176    1.1249649  -0.78900962   0.79539202   0.42705264   0.56986986 
+   30000    1.2900596    1.6556864    1.0302676  -0.84180996   0.87187683    0.6254189   0.57245841 
+   31000    1.2923209    1.6752068    1.0156911  -0.89036148   0.88285227   0.65951571   0.57358134 
+Loop time of 24.1059 on 8 procs for 20000 steps with 8000 atoms
+
+Performance: 358418.039 tau/day, 829.671 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    | 7.5967     | 9.9644     | 12.189     |  62.9 | 41.34
+Neigh   | 3.9305     | 4.7817     | 5.594      |  34.5 | 19.84
+Comm    | 1.7656     | 4.5624     | 7.6382     | 122.3 | 18.93
+Output  | 0.0011697  | 0.0018933  | 0.0020008  |   0.6 |  0.01
+Modify  | 4.1386     | 4.2107     | 4.3622     |   3.8 | 17.47
+Other   |            | 0.5848     |            |       |  2.43
+
+Nlocal:    1000 ave 1118 max 875 min
+Histogram: 2 1 1 0 0 0 0 0 2 2
+Nghost:    2298.62 ave 2535 max 2063 min
+Histogram: 3 1 0 0 0 0 0 0 1 3
+Neighs:    27462.4 ave 32904 max 21333 min
+Histogram: 2 2 0 0 0 0 0 0 0 4
+
+Total # of neighbors = 219699
+Ave neighs/atom = 27.4624
+Neighbor list builds = 3340
+Dangerous builds = 0
+Total wall time: 0:00:36

examples/KAPPA/log.13Oct16.mp.g++.8

@@ -0,0 +1,232 @@
+LAMMPS (13 Oct 2016)
+# sample LAMMPS input script for thermal conductivity of liquid LJ
+# Muller-Plathe method via fix thermal_conductivity
+
+# settings
+
+variable	x equal 10
+variable	y equal 10
+variable	z equal 20
+
+variable	rho equal 0.6
+variable        t equal 1.35
+variable	rc equal 2.5
+
+#variable	rho equal 0.85
+#variable        t equal 0.7
+#variable	rc equal 3.0
+
+# setup problem
+
+units		lj
+atom_style	atomic
+
+lattice		fcc ${rho}
+lattice		fcc 0.6
+Lattice spacing in x,y,z = 1.88207 1.88207 1.88207
+region		box block 0 $x 0 $y 0 $z
+region		box block 0 10 0 $y 0 $z
+region		box block 0 10 0 10 0 $z
+region		box block 0 10 0 10 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (18.8207 18.8207 37.6414)
+  2 by 1 by 4 MPI processor grid
+create_atoms	1 box
+Created 8000 atoms
+mass		1 1.0
+
+velocity	all create $t 87287
+velocity	all create 1.35 87287
+
+pair_style	lj/cut ${rc}
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1
+
+# 1st equilibration run
+
+fix		1 all nvt temp $t $t 0.5
+fix		1 all nvt temp 1.35 $t 0.5
+fix		1 all nvt temp 1.35 1.35 0.5
+thermo		100
+run		1000
+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 = 14 14 27
+Memory usage per processor = 2.55761 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.35   -4.1241917            0   -2.0994448   -3.1961612 
+     100    1.1819832   -3.7640881            0    -1.991335   0.53985757 
+     200    1.2578365   -3.7395333            0   -1.8530144   0.69591862 
+     300    1.3282971   -3.7215427            0   -1.7293461   0.79036065 
+     400    1.3714367   -3.7043826            0   -1.6474847   0.85873226 
+     500    1.3590952   -3.6707735            0   -1.6323855   0.99602024 
+     600    1.3575117   -3.7118244            0   -1.6758114   0.81454305 
+     700    1.3284444   -3.7075488            0   -1.7151313   0.81136596 
+     800    1.3419995   -3.7155648            0   -1.7028172   0.82925676 
+     900    1.3562214   -3.6965609            0   -1.6624831   0.88908117 
+    1000    1.3732017   -3.7100044            0   -1.6504594   0.83982701 
+Loop time of 0.875524 on 8 procs for 1000 steps with 8000 atoms
+
+Performance: 493418.774 tau/day, 1142.173 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    | 0.48279    | 0.49681    | 0.51174    |   1.2 | 56.74
+Neigh   | 0.22868    | 0.23169    | 0.23454    |   0.4 | 26.46
+Comm    | 0.084792   | 0.098391   | 0.11603    |   3.4 | 11.24
+Output  | 0.00027204 | 0.00027871 | 0.00031137 |   0.1 |  0.03
+Modify  | 0.027863   | 0.032316   | 0.039397   |   2.3 |  3.69
+Other   |            | 0.01605    |            |       |  1.83
+
+Nlocal:    1000 ave 1020 max 982 min
+Histogram: 1 0 2 1 0 1 1 1 0 1
+Nghost:    2299.5 ave 2331 max 2268 min
+Histogram: 1 1 1 1 0 0 0 3 0 1
+Neighs:    27122 ave 28382 max 26337 min
+Histogram: 2 0 2 1 1 0 0 1 0 1
+
+Total # of neighbors = 216976
+Ave neighs/atom = 27.122
+Neighbor list builds = 162
+Dangerous builds = 0
+
+velocity	all scale $t
+velocity	all scale 1.35
+
+unfix		1
+
+# 2nd equilibration run
+
+compute		ke all ke/atom
+variable	temp atom c_ke/1.5
+
+fix		1 all nve
+
+compute         layers all chunk/atom bin/1d z lower 0.05 units reduced
+fix		2 all ave/chunk 10 100 1000 layers v_temp file profile.mp
+
+fix		3 all thermal/conductivity 10 z 20
+
+variable        tdiff equal f_2[11][3]-f_2[1][3]
+thermo_style	custom step temp epair etotal f_3 v_tdiff
+
+thermo		1000
+run		20000
+Memory usage per processor = 2.8078 Mbytes
+Step Temp E_pair TotEng f_3 v_tdiff 
+    1000         1.35   -3.7100044   -1.6852575            0            0 
+    2000    1.3572899   -3.7210084   -1.6853282    873.12373   0.26058005 
+    3000     1.359979   -3.7268343   -1.6871208    1750.6998   0.40845169 
+    4000    1.3677509   -3.7394553   -1.6880853    2565.8064   0.63828485 
+    5000    1.3742987    -3.750287   -1.6890966    3373.2897   0.70173279 
+    6000    1.3950535   -3.7827674   -1.6904487    4162.6672   0.83210131 
+    7000    1.3843852   -3.7679238   -1.6916056    4947.5882   0.92719731 
+    8000     1.396125   -3.7861373   -1.6922116    5703.4508   0.92426948 
+    9000    1.4135104    -3.812624   -1.6926234    6465.5676    1.0412501 
+   10000    1.4092351   -3.8065359   -1.6929474    7242.2986    1.0772505 
+   11000    1.3966916   -3.7874302   -1.6926547    8007.3229     1.056805 
+   12000    1.4111272   -3.8089829   -1.6925567    8750.8648     1.097621 
+   13000    1.4091888   -3.8074873   -1.6939684    9514.7196    1.0734167 
+   14000    1.4132159   -3.8134636   -1.6939046    10284.269    1.1643391 
+   15000    1.3991348   -3.7928819    -1.694442    11051.851    1.0716016 
+   16000    1.4055537   -3.8013252   -1.6932583    11836.812    1.1506479 
+   17000    1.4127928   -3.8141054   -1.6951811    12626.124    1.1301728 
+   18000    1.4118868   -3.8119733   -1.6944077    13391.631    1.1521394 
+   19000    1.4209268    -3.826811   -1.6956872    14180.009    1.0929393 
+   20000    1.4093812   -3.8083875   -1.6945801    14969.574    1.2113183 
+   21000    1.4202317   -3.8255696   -1.6954884    15735.893     1.161082 
+Loop time of 21.0741 on 8 procs for 20000 steps with 8000 atoms
+
+Performance: 409982.223 tau/day, 949.033 timesteps/s
+99.3% CPU use with 8 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 7.4932     | 10.005     | 12.426     |  70.1 | 47.48
+Neigh   | 4.0592     | 5.0894     | 6.0544     |  41.7 | 24.15
+Comm    | 1.7793     | 5.0312     | 8.5027     | 134.6 | 23.87
+Output  | 0.00058484 | 0.00060964 | 0.0007031  |   0.1 |  0.00
+Modify  | 0.39735    | 0.4211     | 0.43467    |   2.3 |  2.00
+Other   |            | 0.5269     |            |       |  2.50
+
+Nlocal:    1000 ave 1188 max 806 min
+Histogram: 2 1 1 0 0 0 0 0 2 2
+Nghost:    2300.5 ave 2645 max 1963 min
+Histogram: 3 1 0 0 0 0 0 0 1 3
+Neighs:    27897 ave 37064 max 18367 min
+Histogram: 2 2 0 0 0 0 0 0 0 4
+
+Total # of neighbors = 223176
+Ave neighs/atom = 27.897
+Neighbor list builds = 3537
+Dangerous builds = 0
+
+# thermal conductivity calculation
+# reset fix thermal/conductivity to zero energy accumulation
+
+fix		3 all thermal/conductivity 10 z 20
+
+fix             ave all ave/time 1 1 1000 v_tdiff ave running
+thermo_style	custom step temp epair etotal f_3 v_tdiff f_ave
+
+run		20000
+Memory usage per processor = 3.05853 Mbytes
+Step Temp E_pair TotEng f_3 v_tdiff f_ave 
+   21000    1.4202317   -3.8255696   -1.6954884            0     1.161082     1.161082 
+   22000    1.4090517    -3.808543   -1.6952296    745.83128    1.1780376    1.1695598 
+   23000    1.4261394   -3.8350237    -1.696082    1516.9526    1.1393504      1.15949 
+   24000    1.4103907   -3.8098769   -1.6945553    2290.0213    1.1962529    1.1686807 
+   25000    1.4205929   -3.8266444   -1.6960213    3028.2748    1.1355183    1.1620482 
+   26000    1.4148587   -3.8168728     -1.69485    3788.0858    1.1902606    1.1667503 
+   27000    1.4226648   -3.8297832   -1.6960528    4580.4932    1.2378446    1.1769066 
+   28000    1.4167854   -3.8205958   -1.6956834    5328.2357    1.2038835    1.1802787 
+   29000    1.4208636   -3.8267081   -1.6956791     6077.036    1.1970863    1.1821462 
+   30000     1.420575   -3.8256917   -1.6950955    6840.5407    1.1884497    1.1827766 
+   31000    1.4233235   -3.8318045   -1.6970861    7576.9859    1.2088723    1.1851489 
+   32000     1.418912   -3.8229407   -1.6948388    8319.9854    1.1604002    1.1830865 
+   33000    1.4161289   -3.8211375   -1.6972096    9097.8598    1.1381183    1.1796274 
+   34000    1.3982574   -3.7915345   -1.6944106    9819.5817    1.1809721    1.1797235 
+   35000    1.4211314   -3.8267235   -1.6952929    10604.381     1.157812    1.1782627 
+   36000    1.4181668   -3.8217718   -1.6947876    11332.942    1.1843186    1.1786412 
+   37000    1.4092823   -3.8094817   -1.6958226     12068.55    1.1043391    1.1742705 
+   38000    1.4220481   -3.8278441   -1.6950386    12815.406    1.1996255    1.1756791 
+   39000    1.4146432   -3.8175526   -1.6958531    13565.714     1.149226    1.1742868 
+   40000    1.4088356   -3.8079173    -1.694928    14309.801    1.1710565    1.1741253 
+   41000    1.4058693   -3.8043119   -1.6957716    15067.894    1.1839862    1.1745949 
+Loop time of 22.0429 on 8 procs for 20000 steps with 8000 atoms
+
+Performance: 391962.361 tau/day, 907.320 timesteps/s
+99.3% CPU use with 8 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 6.8314     | 10.063     | 12.978     |  88.0 | 45.65
+Neigh   | 3.8802     | 5.2398     | 6.5269     |  52.7 | 23.77
+Comm    | 1.828      | 5.8112     | 10.14      | 160.2 | 26.36
+Output  | 0.00050211 | 0.00052819 | 0.00060391 |   0.1 |  0.00
+Modify  | 0.39313    | 0.41984    | 0.4453     |   3.3 |  1.90
+Other   |            | 0.5084     |            |       |  2.31
+
+Nlocal:    1000 ave 1188 max 810 min
+Histogram: 2 1 1 0 0 0 0 1 1 2
+Nghost:    2304.5 ave 2648 max 1970 min
+Histogram: 3 1 0 0 0 0 0 0 1 3
+Neighs:    27885.2 ave 36431 max 18556 min
+Histogram: 2 2 0 0 0 0 0 0 1 3
+
+Total # of neighbors = 223082
+Ave neighs/atom = 27.8852
+Neighbor list builds = 3626
+Dangerous builds = 0
+Total wall time: 0:00:44

examples/KAPPA/log.heatflux.1Feb14

@@ -1,208 +0,0 @@
-LAMMPS (1 Feb 2014)
-# sample LAMMPS input script for thermal conductivity of liquid LJ
-# Green-Kubo method via compute heat/flux and fix ave/correlate
-
-# settings
-
-variable	x equal 10
-variable	y equal 10
-variable	z equal 10
-
-variable	rho equal 0.6
-variable        t equal 1.35
-variable	rc equal 2.5
-
-#variable	rho equal 0.85
-#variable        t equal 0.7
-#variable	rc equal 3.0
-
-variable    p equal 200     # correlation length
-variable    s equal 10      # sample interval
-variable    d equal $p*$s   # dump interval
-variable    d equal 200*$s   
-variable    d equal 200*10   
-
-# setup problem
-
-units		lj
-atom_style	atomic
-
-lattice		fcc ${rho}
-lattice		fcc 0.6
-Lattice spacing in x,y,z = 1.88207 1.88207 1.88207
-region		box block 0 $x 0 $y 0 $z
-region		box block 0 10 0 $y 0 $z
-region		box block 0 10 0 10 0 $z
-region		box block 0 10 0 10 0 10
-create_box	1 box
-Created orthogonal box = (0 0 0) to (18.8207 18.8207 18.8207)
-  2 by 2 by 2 MPI processor grid
-create_atoms	1 box
-Created 4000 atoms
-mass		1 1.0
-
-velocity	all create $t 87287
-velocity	all create 1.35 87287
-
-pair_style	lj/cut ${rc}
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1
-
-# 1st equilibration run
-
-fix		1 all nvt temp $t $t 0.5
-fix		1 all nvt temp 1.35 $t 0.5
-fix		1 all nvt temp 1.35 1.35 0.5
-thermo		100
-run		1000
-Memory usage per processor = 2.10761 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         1.35   -4.1241917            0   -2.0996979   -3.1962625 
-     100    1.1997886   -3.7796264            0   -1.9803934    0.4889458 
-     200     1.271238   -3.7354981            0   -1.8291178    0.6873844 
-     300    1.3346808   -3.6942841            0   -1.6927634   0.84332881 
-     400    1.4020848   -3.7118654            0   -1.6092641   0.87670585 
-     500    1.3723622   -3.6917931            0   -1.6337644   0.92172921 
-     600    1.3451676   -3.7281573            0   -1.7109103   0.76029091 
-     700    1.3021567   -3.6876155            0   -1.7348687   0.82721085 
-     800    1.3489121   -3.7082852            0   -1.6854229   0.86438062 
-     900    1.3708803   -3.6966168            0   -1.6408104   0.92141491 
-    1000    1.3640742   -3.7075323            0   -1.6619325   0.86651245 
-Loop time of 0.464189 on 8 procs for 1000 steps with 4000 atoms
-
-Pair  time (%) = 0.235336 (50.6983)
-Neigh time (%) = 0.104871 (22.5922)
-Comm  time (%) = 0.0896717 (19.3179)
-Outpt time (%) = 0.000278324 (0.0599591)
-Other time (%) = 0.0340324 (7.33158)
-
-Nlocal:    500 ave 510 max 479 min
-Histogram: 1 0 0 0 0 2 1 1 0 3
-Nghost:    1519 ave 1539 max 1509 min
-Histogram: 2 0 4 0 0 0 0 1 0 1
-Neighs:    13553.8 ave 14051 max 12567 min
-Histogram: 1 0 0 0 1 0 2 1 1 2
-
-Total # of neighbors = 108430
-Ave neighs/atom = 27.1075
-Neighbor list builds = 155
-Dangerous builds = 0
-
-velocity	all scale $t
-velocity	all scale 1.35
-
-unfix		1
-
-# thermal conductivity calculation
-
-reset_timestep  0
-
-compute         myKE all ke/atom
-compute         myPE all pe/atom
-compute         myStress all stress/atom virial
-compute         flux all heat/flux myKE myPE myStress
-variable        Jx equal c_flux[1]/vol
-variable        Jy equal c_flux[2]/vol
-variable        Jz equal c_flux[3]/vol
-
-fix	        1 all nve
-fix             JJ all ave/correlate $s $p $d                 c_flux[1] c_flux[2] c_flux[3] type auto 	        file profile.heatflux ave running
-fix             JJ all ave/correlate 10 $p $d                 c_flux[1] c_flux[2] c_flux[3] type auto 	        file profile.heatflux ave running
-fix             JJ all ave/correlate 10 200 $d                 c_flux[1] c_flux[2] c_flux[3] type auto 	        file profile.heatflux ave running
-fix             JJ all ave/correlate 10 200 2000                 c_flux[1] c_flux[2] c_flux[3] type auto 	        file profile.heatflux ave running
-
-variable        scale equal $s*dt/$t/$t/vol
-variable        scale equal 10*dt/$t/$t/vol
-variable        scale equal 10*dt/1.35/$t/vol
-variable        scale equal 10*dt/1.35/1.35/vol
-variable        k11 equal trap(f_JJ[3])*${scale}
-variable        k11 equal trap(f_JJ[3])*4.11522633744856e-06
-variable        k22 equal trap(f_JJ[4])*${scale}
-variable        k22 equal trap(f_JJ[4])*4.11522633744856e-06
-variable        k33 equal trap(f_JJ[5])*${scale}
-variable        k33 equal trap(f_JJ[5])*4.11522633744856e-06
-
-thermo	        $d
-thermo	        2000
-thermo_style    custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
-
-run             100000
-Memory usage per processor = 3.25202 Mbytes
-Step Temp Jx Jy Jz k11 k22 k33 
-       0         1.35  0.012562011 -0.087289131 -0.037038204  0.014431103   0.69678942     0.125453 
-    2000    1.3488448 -0.082686441  -0.05888314   0.15641005    9.6556473    4.8724539    39.132688 
-    4000    1.3506828  0.055310422 -0.038254827 -0.081110393    3.4422239    2.3744865    7.4870977 
-    6000    1.3324005  -0.10634454 -0.011811473  0.024430149    3.6509701    11.111829    2.7413472 
-    8000    1.3465517  -0.13857537 -0.058386681 -0.013220164    6.5578792    6.6188014    3.6355334 
-   10000    1.3454126 -0.044292047 -0.0055045339 -0.051726965    5.6920768    6.5502293    7.8616795 
-   12000    1.3601798   0.18989029 -0.094977713 -0.059726722    5.2989118    8.8331032     7.972481 
-   14000    1.3414287 0.0064865781  0.056749763   0.12775935     4.453589    6.4962925    7.9502167 
-   16000    1.3249032 0.0023833148 0.0074389705  -0.12452498    5.2719354     6.164126    7.9937329 
-   18000    1.3486905   0.24719037  -0.13649854 -0.051766952    3.7849335    5.4803263    6.9701788 
-   20000    1.3572854  0.065005524  0.050772448   0.12768096     3.378611    5.6519702    7.1233623 
-   22000     1.352508 -0.042516792 -0.070285937  -0.03879074    5.4717313    5.4908509    6.7550818 
-   24000    1.3559841 -0.015758535 -0.098318418  0.027238601    6.0025309    5.2571093    6.0763852 
-   26000    1.3442105 -0.047372234  0.036647228 -0.0052159685    6.8263856    4.6880057    6.1674781 
-   28000    1.3522633  0.025172759 -0.016031105   0.12001218    6.3114313    4.1003669    5.7234478 
-   30000    1.3593364 -0.044078855 0.0089521622   0.13278909    5.4296394    3.8944372    5.2946242 
-   32000    1.3412479 -0.013107683 -0.089437735 -0.089978727    5.0171818    4.2838538    6.7869585 
-   34000    1.3490784 -0.069828566 -0.018570411  0.018866428    5.1053455    3.7588109    5.7177159 
-   36000    1.3630314 -0.017768864  0.067999673  0.016212961    5.3345297    3.6547014    5.5137046 
-   38000    1.3564307  0.080792723   0.12705697 0.0023785227    5.1062587    3.6140422    5.5464591 
-   40000    1.3546707 -0.030425013   0.17303248 -0.043210574    4.5874798    3.6033647    5.2304191 
-   42000    1.3549663   0.10109213 -0.056635329  0.047756306    4.1930341    3.4788566    5.3322825 
-   44000    1.3557286 0.0083871709  -0.08039758 0.0060697507    4.8453948    3.7579315    4.9727852 
-   46000    1.3434325  0.048348267  -0.12296683 -0.012320195    4.6106895    3.6890294    4.6654515 
-   48000    1.3520456  0.052909962  0.034221069  0.011730009    4.8097414     3.897061    4.5042484 
-   50000    1.3480467  0.084823081 -0.093901701  0.091139125    4.6836534    3.7687187    4.4227539 
-   52000    1.3473278  -0.12531922 -0.065273509   0.11638381    4.9413341    3.8765808    4.5227649 
-   54000    1.3672128   0.11139848  0.034992201 -0.022009105     4.695476    3.5100821    5.0401349 
-   56000     1.341716   0.12258667 -0.089117615  0.041707151    4.5195052    3.3873269     4.972056 
-   58000     1.359732  0.063106883 -0.026013959 -0.026567969    4.3259743    3.6185582     4.721062 
-   60000    1.3587911   0.05591296  -0.12996822  0.095669495    4.1958916    3.5682633    4.8210022 
-   62000    1.3483527  0.048201166 -0.030400186 -0.018919104    4.0886746    3.7373315    4.8825261 
-   64000    1.3531159  -0.10850158 -0.093503261  0.095145743    3.9415737    3.6946305    4.6787173 
-   66000    1.3534358 0.0070478917  -0.13855333 -0.0028185444     3.989283    3.7940811    4.5848181 
-   68000    1.3509679  -0.17972456  -0.15918151 -0.0092253402    4.1168514     3.689533    4.9348847 
-   70000    1.3496439  0.025102803  -0.12080911 0.0099284856    4.0474517    3.6265752    4.8809921 
-   72000    1.3382578    0.2235088   0.10981254  0.049251118    3.9059236    3.5169408    4.9528845 
-   74000    1.3529223  0.012949328   0.11733173   0.12107899    4.0011677    3.4205986    4.7288624 
-   76000    1.3442459  0.090185942  0.038587691 -0.023131667    3.9854752    3.4013375    4.7967661 
-   78000    1.3423941  0.072006425 -0.009752458  0.058791886      3.87483    3.3898574    5.0306248 
-   80000    1.3501112 -0.041057888  -0.11150244 -0.052369732    3.7648956    3.2969166    4.9549774 
-   82000     1.358605   0.14838249  0.055223984  0.019108344    3.8986959    3.2556248    4.8872754 
-   84000     1.357958 -0.087190849  0.029998974  0.089839797    4.4229469    3.2567955    4.7704664 
-   86000    1.3340187   0.10824995 -0.013149214  0.042146878    3.9867785    3.2596969    4.6510248 
-   88000    1.3428375 -0.033908572  -0.11261352  0.099056349    3.8033502    3.1706434    4.5328732 
-   90000    1.3299574  0.055893064  -0.22127211 -0.042737098    3.7086395     3.118066    4.5709281 
-   92000    1.3488719  0.040126575  0.074080804  0.019410656    3.8714376    3.0342566    4.4798044 
-   94000    1.3621842 -0.087519994  0.028392459  0.047179422    3.7841822    3.1603745    4.3925598 
-   96000    1.3578003  0.081511213 -0.0083540805  0.015204759    3.7117805    3.0610774    4.2886014 
-   98000    1.3477904  -0.13903407    0.1146023  0.059812672    3.7445818     3.284994    4.3000618 
-  100000    1.3583776   0.16015243   0.19139469  0.097636877    3.8265662     3.280556    4.2276263 
-Loop time of 49.3099 on 8 procs for 100000 steps with 4000 atoms
-
-Pair  time (%) = 26.5664 (53.8764)
-Neigh time (%) = 10.8228 (21.9485)
-Comm  time (%) = 8.59585 (17.4323)
-Outpt time (%) = 0.0256916 (0.0521023)
-Other time (%) = 3.29916 (6.69066)
-
-Nlocal:    500 ave 519 max 493 min
-Histogram: 4 1 0 1 0 0 1 0 0 1
-Nghost:    1547 ave 1558 max 1523 min
-Histogram: 1 0 0 0 0 2 1 0 2 2
-Neighs:    13544.8 ave 14633 max 13111 min
-Histogram: 2 1 3 1 0 0 0 0 0 1
-
-Total # of neighbors = 108358
-Ave neighs/atom = 27.0895
-Neighbor list builds = 16041
-Dangerous builds = 0
-
-variable        kappa equal (v_k11+v_k22+v_k33)/3.0
-print           "running average conductivity: ${kappa}"
-running average conductivity: 3.77824951481468

examples/KAPPA/log.langevin.1Feb14

@@ -1,215 +0,0 @@
-LAMMPS (1 Feb 2014)
-# sample LAMMPS input script for thermal conductivity of liquid LJ
-# thermostatting 2 regions via fix langevin
-
-# settings
-
-variable	x equal 10
-variable	y equal 10
-variable	z equal 20
-
-variable	rho equal 0.6
-variable        t equal 1.35
-variable	rc equal 2.5
-variable        tlo equal 1.0
-variable        thi equal 1.70
-
-#variable	rho equal 0.85
-#variable        t equal 0.7
-#variable	rc equal 3.0
-#variable        tlo equal 0.3
-#variable        thi equal 1.0
-
-# setup problem
-
-units		lj
-atom_style	atomic
-
-lattice		fcc ${rho}
-lattice		fcc 0.6
-Lattice spacing in x,y,z = 1.88207 1.88207 1.88207
-region		box block 0 $x 0 $y 0 $z
-region		box block 0 10 0 $y 0 $z
-region		box block 0 10 0 10 0 $z
-region		box block 0 10 0 10 0 20
-create_box	1 box
-Created orthogonal box = (0 0 0) to (18.8207 18.8207 37.6414)
-  2 by 1 by 4 MPI processor grid
-create_atoms	1 box
-Created 8000 atoms
-mass		1 1.0
-
-velocity	all create $t 87287
-velocity	all create 1.35 87287
-
-pair_style	lj/cut ${rc}
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1
-
-# heat layers
-
-region          hot block INF INF INF INF 0 1
-region          cold block  INF INF INF INF 10 11
-compute         Thot all temp/region hot
-compute         Tcold all temp/region cold
-
-# 1st equilibration run
-
-fix             1 all nvt temp $t $t 0.5
-fix             1 all nvt temp 1.35 $t 0.5
-fix             1 all nvt temp 1.35 1.35 0.5
-thermo	        100
-run             1000
-Memory usage per processor = 2.14238 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         1.35   -4.1241917            0   -2.0994448   -3.1961612 
-     100    1.1819832   -3.7640881            0    -1.991335   0.53985757 
-     200    1.2578365   -3.7395333            0   -1.8530144   0.69591862 
-     300    1.3282971   -3.7215427            0   -1.7293461   0.79036065 
-     400    1.3714367   -3.7043826            0   -1.6474847   0.85873226 
-     500    1.3590952   -3.6707735            0   -1.6323855   0.99602024 
-     600    1.3575117   -3.7118244            0   -1.6758114   0.81454305 
-     700    1.3284444   -3.7075488            0   -1.7151313   0.81136596 
-     800    1.3419994   -3.7155648            0   -1.7028172   0.82925677 
-     900    1.3562214   -3.6965608            0    -1.662483   0.88908144 
-    1000    1.3732016   -3.7100024            0   -1.6504575   0.83982823 
-Loop time of 0.862126 on 8 procs for 1000 steps with 8000 atoms
-
-Pair  time (%) = 0.482831 (56.0047)
-Neigh time (%) = 0.221903 (25.739)
-Comm  time (%) = 0.104307 (12.0989)
-Outpt time (%) = 0.000301003 (0.0349141)
-Other time (%) = 0.0527841 (6.12256)
-
-Nlocal:    1000 ave 1020 max 982 min
-Histogram: 1 0 2 1 0 1 1 1 0 1
-Nghost:    2299.5 ave 2331 max 2268 min
-Histogram: 1 1 1 1 0 0 0 3 0 1
-Neighs:    27122 ave 28382 max 26337 min
-Histogram: 2 0 2 1 1 0 0 1 0 1
-
-Total # of neighbors = 216976
-Ave neighs/atom = 27.122
-Neighbor list builds = 162
-Dangerous builds = 0
-
-velocity	all scale $t
-velocity	all scale 1.35
-
-unfix		1
-
-# 2nd equilibration run
-
-fix		1 all nve
-fix             hot all langevin ${thi} ${thi} 1.0 59804 tally yes
-fix             hot all langevin 1.7 ${thi} 1.0 59804 tally yes
-fix             hot all langevin 1.7 1.7 1.0 59804 tally yes
-fix             cold all langevin ${tlo} ${tlo} 1.0 287859 tally yes
-fix             cold all langevin 1 ${tlo} 1.0 287859 tally yes
-fix             cold all langevin 1 1 1.0 287859 tally yes
-fix_modify      hot temp Thot
-fix_modify      cold temp Tcold
-
-variable        tdiff equal c_Thot-c_Tcold
-thermo_style    custom step temp c_Thot c_Tcold f_hot f_cold v_tdiff
-thermo	        1000
-run             10000
-Memory usage per processor = 2.60014 Mbytes
-Step Temp Thot Tcold hot cold tdiff 
-    1000         1.35    1.4312938    1.2955632            0            0   0.13573057 
-    2000     1.360018     1.493833     1.108937  -0.12327246    0.1384129   0.38489598 
-    3000    1.3375537    1.6938591    1.0191771  -0.21101663   0.26135778   0.67468203 
-    4000    1.3233024    1.6026443    1.1480306  -0.26177493   0.34439263   0.45461365 
-    5000    1.3107386     1.711679      1.05711  -0.31795111   0.42339093   0.65456895 
-    6000     1.297964    1.6472939   0.95469459  -0.36994548   0.48890072   0.69259932 
-    7000    1.3062638    1.5806629     1.080306  -0.43385121   0.56448283   0.50035689 
-    8000    1.3062755    1.6415159    1.0407288  -0.48697483   0.62125026   0.60078705 
-    9000    1.2850239    1.6253774    1.0574621  -0.50398307   0.66921986   0.56791525 
-   10000    1.3035594    1.5362476    1.0681602  -0.56218263   0.71574454   0.46808735 
-   11000    1.2973176    1.6350179    1.0433547  -0.61814256   0.75532475   0.59166313 
-Loop time of 11.3468 on 8 procs for 10000 steps with 8000 atoms
-
-Pair  time (%) = 4.81454 (42.4309)
-Neigh time (%) = 2.27955 (20.0899)
-Comm  time (%) = 1.88988 (16.6557)
-Outpt time (%) = 0.000712395 (0.00627838)
-Other time (%) = 2.36209 (20.8173)
-
-Nlocal:    1000 ave 1135 max 867 min
-Histogram: 2 0 2 0 0 0 0 2 1 1
-Nghost:    2314.38 ave 2559 max 2067 min
-Histogram: 1 1 2 0 0 0 0 2 0 2
-Neighs:    27392.4 ave 33962 max 20582 min
-Histogram: 2 0 2 0 0 0 0 1 1 2
-
-Total # of neighbors = 219139
-Ave neighs/atom = 27.3924
-Neighbor list builds = 1666
-Dangerous builds = 0
-
-# thermal conductivity calculation
-# reset langevin thermostats to zero energy accumulation
-
-compute		ke all ke/atom
-variable	temp atom c_ke/1.5
-
-fix             hot all langevin ${thi} ${thi} 1.0 59804 tally yes
-fix             hot all langevin 1.7 ${thi} 1.0 59804 tally yes
-fix             hot all langevin 1.7 1.7 1.0 59804 tally yes
-fix             cold all langevin ${tlo} ${tlo} 1.0 287859 tally yes
-fix             cold all langevin 1 ${tlo} 1.0 287859 tally yes
-fix             cold all langevin 1 1 1.0 287859 tally yes
-fix_modify      hot temp Thot
-fix_modify      cold temp Tcold
-
-fix             ave all ave/time 10 100 1000 v_tdiff ave running
-thermo_style    custom step temp c_Thot c_Tcold f_hot f_cold v_tdiff f_ave
-
-fix		2 all ave/spatial 10 100 1000 z lower 0.05 v_temp 		  file profile.langevin units reduced
-
-run             20000
-Memory usage per processor = 2.60106 Mbytes
-Step Temp Thot Tcold hot cold tdiff ave 
-   11000    1.2973176    1.6350179    1.0433547            0            0   0.59166313            0 
-   12000    1.3039677    1.6419813    1.0477757 -0.046382646  0.056968333    0.5942056   0.59568325 
-   13000    1.3110256    1.5869209    1.0158888 -0.094090387   0.10445821   0.57103213   0.57629599 
-   14000     1.293218    1.6629496    1.1121109  -0.11375822   0.15128701   0.55083862    0.5707904 
-   15000    1.2811676    1.6722435    1.0942864  -0.14415448   0.20239116   0.57795712    0.5695191 
-   16000    1.2791266    1.5765255    1.1007618   -0.2014815    0.2427606   0.47576367   0.56997652 
-   17000    1.2622984    1.6433371    1.0358679  -0.22929967   0.29997963   0.60746917   0.56431552 
-   18000    1.2795857    1.7006846    1.0702476  -0.29495954    0.3304481     0.630437   0.57298103 
-   19000    1.2794851    1.5796065    1.0383562   -0.3325748    0.3825079   0.54125035     0.567257 
-   20000    1.3013271    1.6682287    1.0624636  -0.40206115   0.42100016   0.60576507   0.57276102 
-   21000     1.277446    1.5408233    1.0275158  -0.43012499   0.48360636   0.51330753   0.57340191 
-   22000    1.3031703    1.6370721    1.0356931  -0.51126428   0.52836134   0.60137903   0.57578211 
-   23000    1.2719643    1.4882391   0.98769817  -0.55845167   0.61243478   0.50054093   0.57457152 
-   24000    1.2931956    1.5814171    1.0586513  -0.60691503   0.63563787   0.52276581   0.57294037 
-   25000    1.2846646    1.7006525    1.0209227  -0.64068901   0.67962894   0.67972988   0.57312421 
-   26000    1.2711788    1.6697984   0.99699462  -0.67019827   0.73853772   0.67280381   0.57276936 
-   27000    1.2732777    1.6285951    1.1302554  -0.70566156   0.76748898   0.49833966   0.57255348 
-   28000    1.2831929    1.5938242    1.0977096  -0.75144205   0.81168035   0.49611462   0.57460785 
-   29000    1.2792513    1.4854998    1.0013453  -0.79831201   0.86425474    0.4841545   0.57139895 
-   30000    1.2677402    1.6009684     1.092679  -0.83584426   0.90606945   0.50828948   0.57156924 
-   31000    1.2720929    1.5851445    1.0736744  -0.87730401   0.95644174   0.51147013    0.5717415 
-Loop time of 23.7017 on 8 procs for 20000 steps with 8000 atoms
-
-Pair  time (%) = 9.6584 (40.7498)
-Neigh time (%) = 4.57821 (19.3159)
-Comm  time (%) = 4.45101 (18.7793)
-Outpt time (%) = 0.00194073 (0.00818813)
-Other time (%) = 5.01215 (21.1468)
-
-Nlocal:    1000 ave 1121 max 880 min
-Histogram: 2 2 0 0 0 0 0 0 2 2
-Nghost:    2281.5 ave 2471 max 2073 min
-Histogram: 3 1 0 0 0 0 0 0 0 4
-Neighs:    27428.1 ave 33179 max 21152 min
-Histogram: 2 2 0 0 0 0 0 0 1 3
-
-Total # of neighbors = 219425
-Ave neighs/atom = 27.4281
-Neighbor list builds = 3338
-Dangerous builds = 0

examples/KAPPA/log.mp.1Feb14

@@ -1,200 +0,0 @@
-LAMMPS (1 Feb 2014)
-# sample LAMMPS input script for thermal conductivity of liquid LJ
-# Muller-Plathe method via fix thermal_conductivity
-
-# settings
-
-variable	x equal 10
-variable	y equal 10
-variable	z equal 20
-
-variable	rho equal 0.6
-variable        t equal 1.35
-variable	rc equal 2.5
-
-#variable	rho equal 0.85
-#variable        t equal 0.7
-#variable	rc equal 3.0
-
-# setup problem
-
-units		lj
-atom_style	atomic
-
-lattice		fcc ${rho}
-lattice		fcc 0.6
-Lattice spacing in x,y,z = 1.88207 1.88207 1.88207
-region		box block 0 $x 0 $y 0 $z
-region		box block 0 10 0 $y 0 $z
-region		box block 0 10 0 10 0 $z
-region		box block 0 10 0 10 0 20
-create_box	1 box
-Created orthogonal box = (0 0 0) to (18.8207 18.8207 37.6414)
-  2 by 1 by 4 MPI processor grid
-create_atoms	1 box
-Created 8000 atoms
-mass		1 1.0
-
-velocity	all create $t 87287
-velocity	all create 1.35 87287
-
-pair_style	lj/cut ${rc}
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1
-
-# 1st equilibration run
-
-fix		1 all nvt temp $t $t 0.5
-fix		1 all nvt temp 1.35 $t 0.5
-fix		1 all nvt temp 1.35 1.35 0.5
-thermo		100
-run		1000
-Memory usage per processor = 2.14238 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         1.35   -4.1241917            0   -2.0994448   -3.1961612 
-     100    1.1819832   -3.7640881            0    -1.991335   0.53985757 
-     200    1.2578365   -3.7395333            0   -1.8530144   0.69591862 
-     300    1.3282971   -3.7215427            0   -1.7293461   0.79036065 
-     400    1.3714367   -3.7043826            0   -1.6474847   0.85873226 
-     500    1.3590952   -3.6707735            0   -1.6323855   0.99602024 
-     600    1.3575117   -3.7118244            0   -1.6758114   0.81454305 
-     700    1.3284444   -3.7075488            0   -1.7151313   0.81136596 
-     800    1.3419994   -3.7155648            0   -1.7028172   0.82925677 
-     900    1.3562214   -3.6965608            0    -1.662483   0.88908144 
-    1000    1.3732016   -3.7100024            0   -1.6504575   0.83982823 
-Loop time of 0.862547 on 8 procs for 1000 steps with 8000 atoms
-
-Pair  time (%) = 0.478427 (55.4668)
-Neigh time (%) = 0.220096 (25.517)
-Comm  time (%) = 0.10999 (12.7517)
-Outpt time (%) = 0.00030601 (0.0354775)
-Other time (%) = 0.0537277 (6.22896)
-
-Nlocal:    1000 ave 1020 max 982 min
-Histogram: 1 0 2 1 0 1 1 1 0 1
-Nghost:    2299.5 ave 2331 max 2268 min
-Histogram: 1 1 1 1 0 0 0 3 0 1
-Neighs:    27122 ave 28382 max 26337 min
-Histogram: 2 0 2 1 1 0 0 1 0 1
-
-Total # of neighbors = 216976
-Ave neighs/atom = 27.122
-Neighbor list builds = 162
-Dangerous builds = 0
-
-velocity	all scale $t
-velocity	all scale 1.35
-
-unfix		1
-
-# 2nd equilibration run
-
-compute		ke all ke/atom
-variable	temp atom c_ke/1.5
-
-fix		1 all nve
-fix		2 all ave/spatial 10 100 1000 z lower 0.05 v_temp 		  file profile.mp units reduced
-fix		3 all thermal/conductivity 10 z 20
-
-variable        tdiff equal f_2[11][3]-f_2[1][3]
-thermo_style	custom step temp epair etotal f_3 v_tdiff
-
-thermo		1000
-run		20000
-Memory usage per processor = 2.1433 Mbytes
-Step Temp E_pair TotEng 3 tdiff 
-    1000         1.35   -3.7100024   -1.6852556            0            0 
-    2000    1.3488972    -3.708116   -1.6850231    877.52861   0.25969396 
-    3000    1.3658991    -3.735305   -1.6867124    1757.5984   0.40713773 
-    4000    1.3660888   -3.7368211   -1.6879441     2599.882   0.63176318 
-    5000    1.3702365   -3.7439731   -1.6888753    3417.2012   0.68861496 
-    6000    1.3802047   -3.7607288   -1.6906806    4247.6303    0.8258624 
-    7000    1.3981219   -3.7883507     -1.69143    5036.1985   0.90753031 
-    8000    1.3968279   -3.7880683   -1.6930884    5807.0759   0.99392296 
-    9000    1.3960267   -3.7866214   -1.6928431    6584.6398    1.0833481 
-   10000    1.4067029   -3.8038141   -1.6940234    7372.3357    1.0359437 
-   11000    1.4037578   -3.7984096   -1.6930361    8133.4913    1.0506296 
-   12000    1.4112365   -3.8109671   -1.6943769    8908.2356    1.1033313 
-   13000    1.4066326   -3.8036805   -1.6939953    9674.5783    1.1492152 
-   14000    1.4136249   -3.8155288   -1.6953566    10429.951    1.1101441 
-   15000     1.402741   -3.7983064   -1.6944579    11194.927    1.1163151 
-   16000     1.412565   -3.8138997    -1.695317    11931.815    1.2199073 
-   17000    1.4023686   -3.7975376   -1.6942476    12695.415    1.1800489 
-   18000    1.4200941   -3.8257695   -1.6958947    13456.945    1.1583648 
-   19000    1.4016117   -3.7972936   -1.6951388    14216.201    1.1846518 
-   20000    1.4105524   -3.8113272   -1.6957631    14977.184    1.2831156 
-   21000    1.4068217   -3.8054214   -1.6954526    15739.554     1.147926 
-Loop time of 20.7938 on 8 procs for 20000 steps with 8000 atoms
-
-Pair  time (%) = 9.73079 (46.7967)
-Neigh time (%) = 4.8843 (23.4893)
-Comm  time (%) = 5.15718 (24.8016)
-Outpt time (%) = 0.000606179 (0.0029152)
-Other time (%) = 1.02088 (4.90955)
-
-Nlocal:    1000 ave 1176 max 820 min
-Histogram: 2 2 0 0 0 0 0 0 2 2
-Nghost:    2318.88 ave 2663 max 1967 min
-Histogram: 3 1 0 0 0 0 0 0 2 2
-Neighs:    27860.2 ave 36167 max 18992 min
-Histogram: 3 1 0 0 0 0 0 0 0 4
-
-Total # of neighbors = 222882
-Ave neighs/atom = 27.8603
-Neighbor list builds = 3543
-Dangerous builds = 0
-
-# thermal conductivity calculation
-# reset fix thermal/conductivity to zero energy accumulation
-
-fix		3 all thermal/conductivity 10 z 20
-
-fix             ave all ave/time 1 1 1000 v_tdiff ave running
-thermo_style	custom step temp epair etotal f_3 v_tdiff f_ave
-
-run		20000
-Memory usage per processor = 2.33403 Mbytes
-Step Temp E_pair TotEng 3 tdiff ave 
-   21000    1.4068217   -3.8054214   -1.6954526            0     1.147926     1.147926 
-   22000    1.3967994   -3.7893902    -1.694453     767.0398    1.1920832    1.1700046 
-   23000    1.4170976    -3.822137   -1.6967564    1517.2987    1.1545977     1.164869 
-   24000    1.4202355   -3.8249732   -1.6948862    2277.7333    1.1750006    1.1674019 
-   25000    1.4205956   -3.8264595   -1.6958326    3028.6456     1.168964    1.1677143 
-   26000    1.4105028   -3.8099425   -1.6944527    3771.4445    1.1535799    1.1653586 
-   27000    1.4121218   -3.8137079   -1.6957899     4524.007    1.1582776     1.164347 
-   28000    1.4073732   -3.8055739   -1.6947781    5297.7257    1.1390419    1.1611839 
-   29000    1.3935065   -3.7848004   -1.6948019    6040.6442     1.106954    1.1551583 
-   30000    1.4126276   -3.8136783   -1.6950018    6777.7617     1.122798    1.1519223 
-   31000    1.4220569   -3.8292934   -1.6964746    7529.6983    1.1517202    1.1519039 
-   32000    1.4157206   -3.8184427   -1.6951273    8293.9624    1.1600224    1.1525805 
-   33000    1.4300672   -3.8403564   -1.6955237    9056.1085    1.1581575    1.1530095 
-   34000    1.4114669   -3.8123726   -1.6954368    9827.2549     1.169357    1.1541771 
-   35000    1.4087756   -3.8085583    -1.695659    10582.235     1.254384    1.1608576 
-   36000    1.4071234   -3.8063392    -1.695918    11335.664    1.1886748    1.1625962 
-   37000    1.4150044   -3.8175559   -1.6953146    12067.647    1.1452763    1.1615774 
-   38000    1.4208299   -3.8269499   -1.6959714    12785.237    1.1689649    1.1619878 
-   39000    1.4132869   -3.8147648   -1.6950995    13548.517    1.1134294    1.1594321 
-   40000    1.4071151   -3.8068479   -1.6964391    14307.339    1.1772366    1.1603223 
-   41000    1.4126121   -3.8153948   -1.6967416     15087.11    1.1408062     1.159393 
-Loop time of 21.9152 on 8 procs for 20000 steps with 8000 atoms
-
-Pair  time (%) = 9.77976 (44.6255)
-Neigh time (%) = 5.01423 (22.8802)
-Comm  time (%) = 6.03064 (27.5181)
-Outpt time (%) = 0.000575513 (0.00262609)
-Other time (%) = 1.08999 (4.97365)
-
-Nlocal:    1000 ave 1167 max 820 min
-Histogram: 3 1 0 0 0 0 0 0 0 4
-Nghost:    2292.38 ave 2619 max 1989 min
-Histogram: 4 0 0 0 0 0 0 0 2 2
-Neighs:    27929.9 ave 37820 max 19105 min
-Histogram: 4 0 0 0 0 0 0 0 3 1
-
-Total # of neighbors = 223439
-Ave neighs/atom = 27.9299
-Neighbor list builds = 3624
-Dangerous builds = 0

examples/USER/dpd/README

@@ -1,9 +1,11 @@
 This directory contains input files for DPD simulations under
 isothermal, isoenergetic, isobaric and isoenthalpic conditions.  In
 addition, there is also an example for a reaction DPD simulation under
-isoenergetic conditions.  All the DPD scenarios use the Shardlow
-splitting algorithm to integrate the equations of motion.  The compute
-dpd command is used in the isoenergetic and isenthalpic case to
+isoenergetic conditions.  All the DPD scenarios that are named with 
+*-shardlow use the Shardlow splitting algorithm to integrate the 
+equations of motion.  All the DPD scenarious that are named with  
+*-vv utilize the velocity-Verlet integration scheme.  The compute dpd 
+command is used in the isoenergetic and isenthalpic case to
 demonstrate how one can access the particle internal energies.
 
 

examples/USER/dpd/dpd-shardlow/in.dpd-shardlow

@@ -1,5 +1,5 @@
 # Input File for DPD fluid under isothermal conditions using the VV-SSA integration scheme
-log             log.dpd
+log             log.dpd-shardlow
 boundary        p p p
 
 units           metal  
@@ -24,4 +24,4 @@ thermo_modify   format float %15.10f
 fix             1 all shardlow
 fix             2 all nve
 
-run             100
+run             100

examples/USER/dpd/dpd-shardlow/log.dpd-shardlow.reference

@@ -1,5 +1,3 @@
-LAMMPS (7 Dec 2015)
-# Input File for DPD fluid under isothermal conditions using the VV-SSA integration scheme
 boundary        p p p
 
 units           metal
@@ -38,7 +36,7 @@ Neighbor list info ...
   master list distance cutoff = 12
   ghost atom cutoff = 12
   binsize = 6 -> bins = 12 10 9
-Memory usage per processor = 2.04518 Mbytes
+Memory usage per processor = 2.04718 Mbytes
 Step Temp PotEng KinEng TotEng 
        0  128.6667660382  263.2538386154   16.6148533499  279.8686919654 
        1  128.8781761686  263.2538784644   16.6421529271  279.8960313916 
@@ -46,7 +44,7 @@ Step Temp PotEng KinEng TotEng
        3  129.0944237374  263.2540669039   16.6700771671  279.9241440710 
        4  129.1614377649  263.2542208758   16.6787307477  279.9329516235 
        5  129.5099128271  263.2544124900   16.7237296409  279.9781421309 
-       6  129.4373659799  263.2546219015   16.7143616023  279.9689835038 
+       6  129.4373659800  263.2546219015   16.7143616023  279.9689835038 
        7  129.5468806805  263.2548644992   16.7285033325  279.9833678316 
        8  129.6703137794  263.2551528171   16.7444423578  279.9995951748 
        9  129.7536788486  263.2554888044   16.7552073629  280.0106961673 
@@ -141,20 +139,20 @@ Step Temp PotEng KinEng TotEng
       98  143.3138701934  263.4462347092   18.5062468701  281.9524815793 
       99  143.5996902366  263.4503180925   18.5431550652  281.9934731576 
      100  143.4332992914  263.4544359567   18.5216688552  281.9761048118 
-Loop time of 0.802761 on 1 procs for 100 steps with 1000 atoms
+Loop time of 0.350154 on 1 procs for 100 steps with 1000 atoms
 
-Performance: 10.763 ns/day, 2.230 hours/ns, 124.570 timesteps/s
-99.7% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 24.675 ns/day, 0.973 hours/ns, 285.589 timesteps/s
+99.4% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.083614   | 0.083614   | 0.083614   |   0.0 | 10.42
-Neigh   | 0.31261    | 0.31261    | 0.31261    |   0.0 | 38.94
-Comm    | 0.012618   | 0.012618   | 0.012618   |   0.0 |  1.57
-Output  | 0.0033751  | 0.0033751  | 0.0033751  |   0.0 |  0.42
-Modify  | 0.38911    | 0.38911    | 0.38911    |   0.0 | 48.47
-Other   |            | 0.001439   |            |       |  0.18
+Pair    | 0.041961   | 0.041961   | 0.041961   |   0.0 | 11.98
+Neigh   | 0.16181    | 0.16181    | 0.16181    |   0.0 | 46.21
+Comm    | 0.0074215  | 0.0074215  | 0.0074215  |   0.0 |  2.12
+Output  | 0.00099516 | 0.00099516 | 0.00099516 |   0.0 |  0.28
+Modify  | 0.13485    | 0.13485    | 0.13485    |   0.0 | 38.51
+Other   |            | 0.003124   |            |       |  0.89
 
 Nlocal:    1000 ave 1000 max 1000 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

examples/USER/dpd/dpd-vv/in.dpd-vv

@@ -0,0 +1,29 @@
+# INPUT FILE FOR DPD_Fluid
+
+log             log.dpd-vv
+boundary        p p p
+
+units           metal  # ev, ps
+atom_style      dpd    # atomic atom style can also be used
+read_data       data.dpd
+
+comm_modify     mode single vel yes
+mass            1 125.9
+
+pair_style      dpd/fdt 300.0 8.6 245455
+pair_coeff      1 1 0.075 0.022 8.60
+
+neighbor        2.0 bin
+neigh_modify    every 1 delay 0 check no once no
+
+timestep        0.001
+
+fix             2 all nve
+
+variable        totEnergy equal pe+ke
+
+thermo          10
+thermo_style    custom step temp press pe ke v_totEnergy
+thermo_modify   format float %24.16f
+
+run             1000

examples/USER/dpd/dpd-vv/log.dpd-vv.reference

@@ -0,0 +1,169 @@
+boundary        p p p
+
+units           metal  # ev, ps
+atom_style      dpd    # atomic atom style can also be used
+read_data       data.dpd
+  orthogonal box = (-64.5 -64.5 -64.5) to (64.5 64.5 64.5)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  10125 atoms
+  reading velocities ...
+  10125 velocities
+
+comm_modify     mode single vel yes
+mass            1 125.9
+
+pair_style      dpd/fdt 300.0 8.6 245455
+pair_coeff      1 1 0.075 0.022 8.60
+
+neighbor        2.0 bin
+neigh_modify    every 1 delay 0 check no once no
+
+timestep        0.001
+
+fix             2 all nve
+
+variable        totEnergy equal pe+ke
+
+thermo          10
+thermo_style    custom step temp press pe ke v_totEnergy
+thermo_modify   format float %24.16f
+
+run             1000
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10.6
+  ghost atom cutoff = 10.6
+  binsize = 5.3 -> bins = 25 25 25
+Memory usage per processor = 3.36353 Mbytes
+Step Temp Press PotEng KinEng v_totEnergy 
+       0     301.4391322267262012    1549.5478087303108623    1188.6488072196075336     394.4722035796053206    1583.1210107992128542 
+      10     301.1781716844517973    1472.5220704074272362    1188.7073118945888837     394.1307028613744592    1582.8380147559632860 
+      20     301.3348035346627398    1561.5334938481948939    1188.7674931713575006     394.3356759537763878    1583.1031691251339453 
+      30     301.2401656988171226    1589.1590400358682018    1188.8329522652118158     394.2118300702898637    1583.0447823355016226 
+      40     301.2467282647567117    1612.7005954259220744    1188.8998661625830664     394.2204180390389752    1583.1202842016220984 
+      50     301.3868530330685758    1538.2867560691233848    1188.9661306187101673     394.4037894736757153    1583.3699200923858825 
+      60     301.2473566745931635    1442.8478446697065465    1189.0327863162424364     394.2212403948197448    1583.2540267110621244 
+      70     301.3817325834245366    1449.9468021148002208    1189.0958917710283913     394.3970887011532795    1583.4929804721816708 
+      80     301.6350661579102166    1528.7144337987854215    1189.1603115791012897     394.7286085427540456    1583.8889201218553353 
+      90     301.1547075640817752    1512.1770835959378019    1189.2223449446209997     394.0999970163866237    1583.3223419610076235 
+     100     301.1746038085076975    1564.5706067669673303    1189.2844219062417324     394.1260338329196315    1583.4104557391613071 
+     110     301.2018622721547558    1515.4879381876448861    1189.3504251156646205     394.1617050682420427    1583.5121301839067200 
+     120     301.0009801124808178    1557.0329613835117470    1189.4208319594404202     393.8988247062895880    1583.3196566657300082 
+     130     301.0638502637480656    1548.3634383875796630    1189.4951157625748692     393.9810984539830656    1583.4762142165579917 
+     140     301.0311113459680428    1495.2262845183092850    1189.5675481417179071     393.9382553335690318    1583.5058034752869389 
+     150     300.8177209477242400    1428.8898919254613702    1189.6378084330838192     393.6590063190295155    1583.2968147521132778 
+     160     300.8119775481491160    1570.2720283468329399    1189.7083716809172529     393.6514903357206663    1583.3598620166378623 
+     170     300.9335106840651406    1557.4332901198370109    1189.7769958158935424     393.8105322078843642    1583.5875280237778497 
+     180     300.5874591455081486    1520.5298514112455450    1189.8453389121095825     393.3576788840364884    1583.2030177961460140 
+     190     300.4011803057076122    1519.7398182018539501    1189.9061296006261728     393.1139088603054574    1583.0200384609315734 
+     200     300.2169140033789745    1458.2437505784337191    1189.9657655046762557     392.8727725028986129    1582.8385380075749254 
+     210     300.2545970072604860    1496.2729155341944534    1190.0262935280240981     392.9220856012638592    1582.9483791292880142 
+     220     300.3703364838470407    1606.0230144299605399    1190.0833027226285594     393.0735457187111024    1583.1568484413396618 
+     230     300.2033407044385172    1459.9549740461736747    1190.1416131684936772     392.8550100806698424    1582.9966232491635765 
+     240     300.4842762279440080    1670.3474276721599381    1190.2009109755040299     393.2226506527560446    1583.4235616282601313 
+     250     300.2564573977281270    1557.2460328592953829    1190.2596238049020485     392.9245201634982436    1583.1841439684003490 
+     260     300.0449762246657883    1505.0192578442308786    1190.3199416408031084     392.6477696177504413    1582.9677112585536634 
+     270     300.0116460395994977    1509.1981340752856795    1190.3755696034054381     392.6041527474002351    1582.9797223508057868 
+     280     300.3512486599618114    1518.9752783067131077    1190.4261072017084189     393.0485668253141966    1583.4746740270225018 
+     290     300.3552418223667360    1555.5638176571358144    1190.4711084084597132     393.0537923962660898    1583.5249008047258030 
+     300     300.1459940856700541    1599.6176002364238684    1190.5119834703855304     392.7799645916971940    1583.2919480620826107 
+     310     300.0728060417839629    1641.1130631848714074    1190.5527862243700383     392.6841885431988999    1583.2369747675688814 
+     320     300.2437004299284808    1480.0125150324981860    1190.5921170370866093     392.9078260164519065    1583.4999430535385727 
+     330     300.0598571495680176    1558.1995284077863744    1190.6308838646664299     392.6672432381596991    1583.2981271028261290 
+     340     300.2932457229409806    1504.8291140224332594    1190.6648789420762569     392.9726624587786432    1583.6375414008548432 
+     350     300.0508025680157402    1578.6970748006153826    1190.6930603315840926     392.6553941437470598    1583.3484544753312093 
+     360     300.2273424995200344    1514.2714360556162774    1190.7166098654090547     392.8864195427583468    1583.6030294081674583 
+     370     300.1967941947077634    1511.8859175802745085    1190.7410406890937793     392.8464431235526035    1583.5874838126464965 
+     380     300.4506922864079002    1551.8880937733540577    1190.7641303867108036     393.1787017091508005    1583.9428320958616041 
+     390     300.6154615731481954    1491.6540598720923754    1190.7833472426696062     393.3943236927418070    1584.1776709354114701 
+     400     300.4131888226039564    1518.2806993851902462    1190.8000216950690628     393.1296235622648396    1583.9296452573339593 
+     410     300.2164206099614603    1492.4202869919304248    1190.8161806634459481     392.8721268336147432    1583.6883074970605776 
+     420     299.9241651579524728    1437.1178040001384488    1190.8321211036075056     392.4896726667966504    1583.3217937704041560 
+     430     300.1750324308378595    1592.1759851574131517    1190.8470728579757179     392.8179650328543744    1583.6650378908300354 
+     440     300.3203232687657760    1610.5956304714268299    1190.8532393510404290     393.0080969396641422    1583.8613362907044575 
+     450     300.3593377128640896    1514.2015724302684703    1190.8519495611071761     393.0591524002515484    1583.9111019613587814 
+     460     300.2776675433437958    1593.6798981330243805    1190.8459747756926390     392.9522763901615008    1583.7982511658542535 
+     470     299.8777606563147629    1525.3321416074672925    1190.8391264353913357     392.4289463573695116    1583.2680727927609041 
+     480     300.0893325105251392    1577.2512023261467675    1190.8279401949503153     392.7058155711616223    1583.5337557661118808 
+     490     299.7991035093194228    1480.4333732192599200    1190.8067847458821689     392.3260132780664549    1583.1327980239486806 
+     500     299.9677949259065599    1495.0278787582656150    1190.7825410253908558     392.5467678772936324    1583.3293089026844882 
+     510     300.0900811274784701    1639.6696686241473344    1190.7573430643653865     392.7067952335466430    1583.4641382979120863 
+     520     299.9891246673825549    1600.2278532870598156    1190.7251960532676094     392.5746806106526492    1583.2998766639202586 
+     530     300.1603400289337173    1539.5535066502900463    1190.6928984528919955     392.7987381192410226    1583.4916365721330749 
+     540     300.3076269358370496    1595.8675994337252178    1190.6566703473422422     392.9914821412112360    1583.6481524885534782 
+     550     300.4698674068499713    1466.7075904710529812    1190.6131481694715148     393.2037948414154016    1583.8169430108869165 
+     560     300.7206981383458810    1630.2609903270986251    1190.5710873654240913     393.5320393883253018    1584.1031267537493932 
+     570     300.8610815763000232    1556.2884022342987009    1190.5267109994711063     393.7157493257404326    1584.2424603252115958 
+     580     300.8964633483231523    1554.3498972944137222    1190.4812222884627317     393.7620509637309283    1584.2432732521936032 
+     590     300.9107621433563509    1547.4258400009323395    1190.4362818919200890     393.7807627916996580    1584.2170446836198607 
+     600     301.3417451159046436    1536.4134563739603436    1190.3902887741262475     394.3447599132098844    1584.7350486873360751 
+     610     301.6508989111560481    1593.7194612348341707    1190.3421610929228791     394.7493277540106646    1585.0914888469335438 
+     620     301.5698128071562110    1576.1181463329294274    1190.2920606752038566     394.6432160694121194    1584.9352767446159760 
+     630     301.3274041972169357    1509.2272524137147229    1190.2374741364669717     394.3259929609754408    1584.5634670974422988 
+     640     301.3505920687090907    1592.1600851563935066    1190.1794204537054611     394.3563372984748980    1584.5357577521804160 
+     650     301.5804461741749378    1544.9875554279790322    1190.1204065811848523     394.6571312093886377    1584.7775377905734331 
+     660     301.3626783799006148    1580.4147481776212771    1190.0589205400185620     394.3721538043599821    1584.4310743443784304 
+     670     301.3027587470089088    1570.9258836881758725    1189.9974183012859612     394.2937411926666869    1584.2911594939525912 
+     680     301.1174106753824731    1503.7441951732287180    1189.9385560058665305     394.0511891998194756    1583.9897452056859493 
+     690     301.1637317889510541    1485.4239754399416142    1189.8822999581352633     394.1118063851420743    1583.9941063432772808 
+     700     300.7577284964789897    1497.3081311764312886    1189.8265818908062101     393.5804984150753967    1583.4070803058816637 
+     710     300.7582337772330447    1443.2789996571248139    1189.7722579196470178     393.5811596404810757    1583.3534175601280367 
+     720     300.7789291839182511    1480.1771366249440689    1189.7219401607021609     393.6082422644880126    1583.3301824251902872 
+     730     300.2392032164642046    1573.9469162403461269    1189.6722050348253106     392.9019408293094102    1582.5741458641346071 
+     740     300.1498721141534816    1495.8935024851559774    1189.6232009109407954     392.7850394949790029    1582.4082404059197415 
+     750     299.7668955745960488    1587.0579224766690913    1189.5725329834676813     392.2838650178547937    1581.8563980013225319 
+     760     300.1701246080039596    1476.2647356200661761    1189.5185800849978932     392.8115425100924085    1582.3301225950904154 
+     770     300.0596917060459532    1476.9822776185721978    1189.4588693098098702     392.6670267338517419    1582.1258960436616690 
+     780     300.0000978359947794    1656.0447969129193098    1189.3974011035754756     392.5890404250892516    1581.9864415286647272 
+     790     299.8879395255003146    1498.3733949813793060    1189.3295612656791036     392.4422667279793586    1581.7718279936584622 
+     800     299.5399296208984765    1536.5356907957796011    1189.2608026516975315     391.9868506281461009    1581.2476532798436892 
+     810     299.7477702176125263    1527.7843172708669499    1189.1905997605726952     392.2588370075304169    1581.4494367681031690 
+     820     299.6526441282851465    1520.2339634236550410    1189.1179282568577946     392.1343521810326251    1581.2522804378904766 
+     830     299.7117040573267559    1519.3977355174756667    1189.0462571599482544     392.2116397587276992    1581.2578969186758968 
+     840     299.8248393061855950    1492.9872520312869710    1188.9746922447459383     392.3596919064040662    1581.3343841511500614 
+     850     299.8949042735604280    1548.8768511646294428    1188.9003206285553915     392.4513810041994475    1581.3517016327548390 
+     860     299.8659753723547396    1612.8888123513665960    1188.8228698817265467     392.4135237846624591    1581.2363936663889490 
+     870     299.4869644032468159    1501.1368986196648621    1188.7463971708887129     391.9175387708375524    1580.6639359417263222 
+     880     299.4723145868704819    1610.5504771450589487    1188.6685353091816069     391.8983675859109894    1580.5669028950926531 
+     890     299.4069994806970385    1463.6021272210480220    1188.5912631304522620     391.8128942975925497    1580.4041574280447549 
+     900     299.3089704777128190    1566.2168185333516703    1188.5136206415770630     391.6846106320437571    1580.1982312736208769 
+     910     299.5247041888713397    1495.6606753393330109    1188.4345654328317323     391.9669261754785907    1580.4014916083103799 
+     920     298.9408951189174672    1640.3193219922013668    1188.3550783333537311     391.2029362827487944    1579.5580146161025823 
+     930     299.1796032826329110    1446.8716230397405980    1188.2706215145828992     391.5153168773241532    1579.7859383919071661 
+     940     299.3701987753103708    1492.9872751566551869    1188.1849188108449198     391.7647358012489462    1579.9496546120938092 
+     950     299.2072786172182077    1562.8791943561973312    1188.0966113636363843     391.5515336423407575    1579.6481450059770850 
+     960     299.3656085727831737    1560.6583667351615077    1188.0078929542073638     391.7587289258562464    1579.7666218800636670 
+     970     299.3550703551496781    1470.6811691697550941    1187.9234716336209203     391.7449383011918940    1579.6684099348128711 
+     980     299.3253482475718101    1439.7552468745370788    1187.8461953635626287     391.7060430682316792    1579.5522384317941942 
+     990     299.5720628053319956    1537.8753917835106222    1187.7698518865308870     392.0289010679078388    1579.7987529544386689 
+    1000     299.6565043425953263    1587.6003924665003524    1187.6939067472803799     392.1394037721581185    1579.8333105194385553 
+Loop time of 16.4015 on 1 procs for 1000 steps with 10125 atoms
+
+Performance: 5.268 ns/day, 4.556 hours/ns, 60.970 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    | 5.3216     | 5.3216     | 5.3216     |   0.0 | 32.45
+Neigh   | 10.155     | 10.155     | 10.155     |   0.0 | 61.91
+Comm    | 0.49085    | 0.49085    | 0.49085    |   0.0 |  2.99
+Output  | 0.0052254  | 0.0052254  | 0.0052254  |   0.0 |  0.03
+Modify  | 0.1345     | 0.1345     | 0.1345     |   0.0 |  0.82
+Other   |            | 0.2945     |            |       |  1.80
+
+Nlocal:    10125 ave 10125 max 10125 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    5827 ave 5827 max 5827 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    114808 ave 114808 max 114808 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 114808
+Ave neighs/atom = 11.3391
+Neighbor list builds = 1000
+Dangerous builds not checked
+Total wall time: 0:00:16

examples/USER/dpd/dpde-shardlow/in.dpde-shardlow

@@ -1,5 +1,5 @@
 # Input File for DPD fluid under isoenergetic conditions using the VV-SSA integration scheme
-log             log.dpde
+log             log.dpde-shardlow
 boundary        p p p
 
 units           metal  # ev, ps

examples/USER/dpd/dpde-vv/in.dpde-vv

@@ -0,0 +1,33 @@
+# INPUT FILE FOR DPD_Fluid
+
+log             log.dpde-vv
+boundary        p p p
+
+units           metal  # ev, ps
+atom_style      dpd
+read_data       data.dpd
+
+comm_modify     mode single vel yes
+mass            1 125.9
+
+pair_style      dpd/fdt/energy 8.6 245455
+pair_coeff      1 1 0.075 0.022 3.2E-05 8.60
+
+neighbor        2.0 bin
+neigh_modify    every 1 delay 0 check no once no
+
+timestep        0.001
+
+fix             1 all dpd/energy
+fix             2 all nve
+fix             3 all eos/cv 0.00517041
+
+compute         dpdU all dpd
+
+variable        totEnergy equal pe+ke+c_dpdU[1]+c_dpdU[2]
+
+thermo          10
+thermo_style    custom step temp press pe ke c_dpdU[1] c_dpdU[2] v_totEnergy c_dpdU[4]
+thermo_modify   format float %24.16f
+
+run             1000

examples/USER/dpd/dpde-vv/log.dpde-vv.reference

@@ -0,0 +1,173 @@
+boundary        p p p
+
+units           metal  # ev, ps
+atom_style      dpd
+read_data       data.dpd
+  orthogonal box = (-64.5 -64.5 -64.5) to (64.5 64.5 64.5)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  10125 atoms
+  reading velocities ...
+  10125 velocities
+
+comm_modify     mode single vel yes
+mass            1 125.9
+
+pair_style      dpd/fdt/energy 8.6 245455
+pair_coeff      1 1 0.075 0.022 3.2E-05 8.60
+
+neighbor        2.0 bin
+neigh_modify    every 1 delay 0 check no once no
+
+timestep        0.001
+
+fix             1 all dpd/energy
+fix             2 all nve
+fix             3 all eos/cv 0.00517041
+
+compute         dpdU all dpd
+
+variable        totEnergy equal pe+ke+c_dpdU[1]+c_dpdU[2]
+
+thermo          10
+thermo_style    custom step temp press pe ke c_dpdU[1] c_dpdU[2] v_totEnergy c_dpdU[4]
+thermo_modify   format float %24.16f
+
+run             1000
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10.6
+  ghost atom cutoff = 10.6
+  binsize = 5.3 -> bins = 25 25 25
+Memory usage per processor = 3.36353 Mbytes
+Step Temp Press PotEng KinEng c_dpdU[1] c_dpdU[2] v_totEnergy c_dpdU[4] 
+       0     301.4391322267262012    1636.1776395935085020    1188.6488072196075336     394.4722035796053206    7852.5601874986105031    7852.5601874986105031   17288.2413857964347699     299.9999999999841407 
+      10     301.4791572483523510    1486.4422375141198245    1188.7147620806101713     394.5245815119678241    7852.5601874999802021    7852.3731942333779443   17288.1727253259377903     299.9960221120699089 
+      20     301.4275643919337426    1677.9356110821624952    1188.7839634625399867     394.4570655673388728    7852.5601874999938445    7852.3711851933012440   17288.1724017231754260     299.9955485734552099 
+      30     301.2240988054542186    1452.7304951528931269    1188.8550809767796181     394.1908044563202225    7852.5601875000002110    7852.5679666239848302   17288.1740395570850524     299.9988968405210130 
+      40     301.1023506886409677    1527.9758363521380033    1188.9264527568634549     394.0314812537677653    7852.5601874999947540    7852.6574764573806533   17288.1755979680056043     300.0001694462812338 
+      50     301.0409654880461972    1597.1737251233498682    1188.9944523606982330     393.9511507566391515    7852.5601875000029395    7852.6700547249911324   17288.1758453423317405     299.9999653064982681 
+      60     301.2904978886139133    1610.8630327676828529    1189.0651026961211301     394.2776962691256131    7852.5601874999829306    7852.2734988976435488   17288.1764853628737910     299.9919857290491905 
+      70     300.8575037843163500    1489.3259312130880971    1189.1295686642290548     393.7110673208616731    7852.5601874999856591    7852.7707182199101226   17288.1715417049854295     300.0010992278233175 
+      80     300.5955830326474825    1449.3896097889587509    1189.1880764967559116     393.3683100440913449    7852.5601875000411383    7853.0484238882281716   17288.1649979291178170     300.0059513551503301 
+      90     301.0092332775843147    1553.9266324350364812    1189.2470037925052111     393.9096250433288446    7852.5601875000420478    7852.4452067113825251   17288.1620230472581170     299.9940347326859182 
+     100     301.0478004479094238    1539.2270336322194453    1189.3010269201699884     393.9600951881690207    7852.5601875000074870    7852.3416236045995902   17288.1629332129450631     299.9916385566916119 
+     110     300.9609384905550087    1500.0429484565006533    1189.3524514939088021     393.8464250502817663    7852.5601874999983920    7852.4114980357189779   17288.1705620799075405     299.9925626482005327 
+     120     300.9625536631411933    1630.5065919443034090    1189.4006029528841282     393.8485387131115658    7852.5601875000575092    7852.3600810123671181   17288.1694101784196391     299.9911580775880680 
+     130     301.0373750247310340    1539.2267307640183844    1189.4426173625224692     393.9464521696795032    7852.5601874999993015    7852.2178388309775983   17288.1670958631802932     299.9879581026651749 
+     140     300.7465104415114752    1550.8353679735087098    1189.4887352231000932     393.5658181350791551    7852.5601874999920256    7852.5559582333216895   17288.1706990914935886     299.9939749909034958 
+     150     300.6667173911141617    1634.8987162883277051    1189.5368575067818711     393.4613985788388959    7852.5601874999920256    7852.6079668015609059   17288.1664103871735279     299.9946423938895350 
+     160     300.4684731724562425    1462.9400882126803936    1189.5825022927965620     393.2019703048678707    7852.5601874999847496    7852.8265187980177870   17288.1711788956672535     299.9983600613423960 
+     170     300.1439323338466920    1510.2352578813552100    1189.6305700279478970     392.7772665220106774    7852.5601874999802021    7853.2009671047335360   17288.1689911546709482     300.0051118582463232 
+     180     300.1074244553407198    1529.6307083879951279    1189.6764977580119194     392.7294912276224181    7852.5601874999729262    7853.2047509722533505   17288.1709274578606710     300.0047089238623812 
+     190     300.4193298066089142    1546.3205495807171701    1189.7172820166240399     393.1376598363699486    7852.5601874999847496    7852.7461854379371289   17288.1613147909156396     299.9954451643528728 
+     200     300.3353919251508728    1532.5496449337254035    1189.7600175880224924     393.0278162310690391    7852.5601874999683787    7852.8107089913455638   17288.1587303104060993     299.9962707550171785 
+     210     300.3276568499739483    1504.8178651700843602    1189.7998299597820733     393.0176938818990493    7852.5601875000156724    7852.7810130200659842   17288.1587243617614149     299.9953436245502871 
+     220     300.5768315696971626    1592.5896084568344122    1189.8391466344742184     393.3437713226064716    7852.5601875000329528    7852.4205574703573802   17288.1636629274726147     299.9880321846658831 
+     230     300.6587445618569063    1672.3049358942289473    1189.8766340798690635     393.4509650976162334    7852.5601874999847496    7852.2733199687863817   17288.1611066462573945     299.9848228571166828 
+     240     300.7517707836825025    1527.1722267937811921    1189.9126240081129708     393.5727019751183207    7852.5601875000065775    7852.1160682173085661   17288.1615817005440476     299.9814952182625802 
+     250     300.8473715548367409    1589.1847713095248764    1189.9441342461948352     393.6978079843565865    7852.5601875000047585    7851.9625847797888127   17288.1647145103452203     299.9782210858571148 
+     260     300.8450266408960942    1623.1896863377055524    1189.9636161513917614     393.6947393603111891    7852.5601874999820211    7851.9471828473988353   17288.1657258590821584     299.9775302202895659 
+     270     300.6663619570709898    1564.5160171187899323    1189.9764081239700317     393.4609334472908131    7852.5601875000193104    7852.1708276117251444   17288.1683566830033669     299.9812899253168439 
+     280     300.7668534205726019    1618.5400526904263643    1189.9872008155405183     393.5924395618274048    7852.5601875000184009    7852.0271568534708422   17288.1669847308585304     299.9781169783826158 
+     290     300.8462727198648849    1562.6765776748122789    1189.9918265985252219     393.6963700162682471    7852.5601875000211294    7851.9189772084127981   17288.1673613232269417     299.9756806168044250 
+     300     300.8095414073812890    1525.1785808192844343    1189.9873922767767453     393.6483023295390922    7852.5601875000020300    7851.9657301693578120   17288.1616122756749974     299.9761279889730758 
+     310     300.9496330741350221    1566.5597234051326723    1189.9752299662607129     393.8316304464934774    7852.5601875000056680    7851.7898117189633922   17288.1568596317229094     299.9723726900590464 
+     320     301.2370566356515837    1513.6869483705047514    1189.9626455872523820     394.2077614578674343    7852.5601874999929350    7851.4248466706330873   17288.1554412157456682     299.9650543775110236 
+     330     301.3279721508968692    1549.0667862452519330    1189.9513389477854162     394.3267362020337146    7852.5601874999929350    7851.3129955581916875   17288.1512582080031279     299.9625537201162615 
+     340     301.1145736537583844    1414.7930515101759283    1189.9408691169965095     394.0474765890400590    7852.5601874999993015    7851.6028846074832472   17288.1514178135184920     299.9677356565828745 
+     350     301.1651600907370039    1529.8016115175887535    1189.9314470205476937     394.1136755032911196    7852.5601874999929350    7851.5441417268757505   17288.1494517507089768     299.9662576716461331 
+     360     301.0550563185083206    1536.7721716375504002    1189.9200519814730796     393.9695904359920178    7852.5601875000074870    7851.7101209691463737   17288.1599508866202086     299.9690811750865009 
+     370     301.1008976932964742    1522.3385843459479929    1189.9109162496640693     394.0295798208944120    7852.5601875000211294    7851.6603423306560217   17288.1610259012340975     299.9677565060027860 
+     380     301.1656898730700505    1505.0548721701993600    1189.9005648244351505     394.1143687921909304    7852.5601875000056680    7851.5816827598300733   17288.1568038764598896     299.9659906785156522 
+     390     300.8379322662876802    1740.9151205755624687    1189.8851457594087151     393.6854554509390596    7852.5601875000238579    7852.0268864110385039   17288.1576751214088290     299.9741278188615752 
+     400     300.8663790447546376    1564.9461156870302148    1189.8690133470408909     393.7226817503372445    7852.5601875000411383    7852.0043792319993372   17288.1562618294192362     299.9732593416579789 
+     410     300.6263441860635908    1564.2840871092373618    1189.8566574093877080     393.4085650033033517    7852.5601874999892971    7852.3284491703725507   17288.1538590830532485     299.9792095875052951 
+     420     300.5302259436974168    1438.1569922368764765    1189.8406936554465574     393.2827818158641549    7852.5601875000302243    7852.4696075433648730   17288.1532705147074012     299.9815165752025337 
+     430     300.5877786105220935    1503.3641639033023694    1189.8251514530138593     393.3580969454444016    7852.5601874999802021    7852.4023373559457468   17288.1457732543858583     299.9798346272511935 
+     440     300.7289160804472772    1689.2527029957295781    1189.8035410609209066     393.5427936314976591    7852.5601875000029395    7852.2436462415198548   17288.1501684339418716     299.9764596782897570 
+     450     300.9487198282456575    1497.3668092174791582    1189.7808137689632986     393.8304353457919547    7852.5601874999938445    7851.9788323927432430   17288.1502690074921702     299.9710227473042323 
+     460     300.9359942496024587    1625.1573864018491804    1189.7615359247627111     393.8137822755282400    7852.5601875000147629    7852.0165192783370003   17288.1520249786408385     299.9713565393226986 
+     470     301.0000133856357252    1486.1561922844011860    1189.7439269526955741     393.8975596188205941    7852.5601874999656502    7851.9561324572268859   17288.1578065287103527     299.9697143418395626 
+     480     300.8568627175957886    1535.6080526199095857    1189.7237810071801505     393.7102284019063063    7852.5601874999601932    7852.1697010727630186   17288.1638979818089865     299.9732503057674080 
+     490     301.0608040775520067    1497.3221544489886128    1189.7062242497636362     393.9771121242308709    7852.5601874999974825    7851.9258988739011329   17288.1694227478947141     299.9682362511933320 
+     500     301.0232592587148019    1517.5854528541199215    1189.6911287485861521     393.9279798589197981    7852.5601875000247674    7851.9823225510326665   17288.1616186585633841     299.9690333355835037 
+     510     300.7038579923685120    1420.2615974401142012    1189.6747661513456933     393.5100018730125839    7852.5601874999674692    7852.4114869568047652   17288.1564424811294884     299.9768186576545759 
+     520     300.5917863355052759    1537.4862082427132464    1189.6604754398756540     393.3633415734188361    7852.5601875000029395    7852.5789017095057716   17288.1629062228021212     299.9795694302102333 
+     530     300.4751352158502868    1481.1071694751799441    1189.6453243069925065     393.2106884527691477    7852.5601874999811116    7852.7451655714066874   17288.1613658311471227     299.9823181268525900 
+     540     300.5380123640739498    1547.3461372766389559    1189.6261485232855648     393.2929713568877332    7852.5601875000375003    7852.6850583598352387   17288.1643657400454686     299.9808112190538623 
+     550     300.4253885005187499    1544.3485889749692888    1189.6033595464525661     393.1455884232119047    7852.5601874999756546    7852.8598718466746504   17288.1690073163154011     299.9835860164698147 
+     560     300.3263552442093101    1556.5150300058251105    1189.5759163336824713     393.0159905619273673    7852.5601875000111249    7853.0148613782675966   17288.1669557738860021     299.9861837797674866 
+     570     300.1977324643196425    1511.2320626303917379    1189.5441090918316149     392.8476709710407704    7852.5601875000102154    7853.2098259401755058   17288.1617935030590161     299.9896761688499964 
+     580     300.3543631005173893    1588.9566243200433746    1189.5094471319721379     393.0526424747489500    7852.5601875000156724    7853.0374555421631158   17288.1597326488990802     299.9859298211933378 
+     590     300.5019108864805730    1504.4406939723214691    1189.4809412920112663     393.2457278908070748    7852.5601874999874781    7852.8704277855340479   17288.1572844683396397     299.9823573257917815 
+     600     300.4791158523048011    1540.4690749004150803    1189.4551948503105905     393.2158976318902432    7852.5601875000220389    7852.9312239063838206   17288.1625038886049879     299.9832002920041987 
+     610     300.5939139841889869    1368.0565839211087678    1189.4252547652590692     393.3661258776944578    7852.5601874999574648    7852.8130977336286378   17288.1646658765384927     299.9807742697515778 
+     620     300.7674247480806002    1483.2566452708945235    1189.3941250938435132     393.5931872179773450    7852.5601875000193104    7852.6187967208716145   17288.1662965327122947     299.9766963671718258 
+     630     300.7920034341021278    1543.0699124130637756    1189.3598279316649950     393.6253516166882491    7852.5601875000302243    7852.6219971866230480   17288.1673642350069713     299.9762538437230432 
+     640     300.8032734267029014    1423.2549819291616586    1189.3293074476885067     393.6400998638143278    7852.5601874999847496    7852.6384826097782934   17288.1680774212654796     299.9762118202994543 
+     650     300.7516995878241346    1542.6559695158523482    1189.3021161045705867     393.5726088061030055    7852.5601874999720167    7852.7361949473242930   17288.1711073579681397     299.9775656396505497 
+     660     300.8699697098109596    1675.5121937767839881    1189.2687179804190691     393.7273806013013768    7852.5601874999802021    7852.6179739687149777   17288.1742600504148868     299.9750492262036801 
+     670     301.0255004186900578    1520.7397686587873977    1189.2284265783687260     393.9309127074437242    7852.5601874999847496    7852.4592279727157802   17288.1787547585117863     299.9715123049731460 
+     680     301.1071983488760679    1651.9751417063259851    1189.1858967311386550     394.0378250459656329    7852.5601875000002110    7852.3982826328638112   17288.1821919099675142     299.9699481289110850 
+     690     301.0027086454253435    1496.1607274163641250    1189.1436949551202815     393.9010867158519886    7852.5601875000293148    7852.5788938360938118   17288.1838630070960789     299.9731939774295597 
+     700     300.9009090279179759    1551.8182127127668082    1189.0993919251338866     393.7678687121208441    7852.5601875000102154    7852.7513665452252098   17288.1788146824910655     299.9761043445071209 
+     710     301.2325536720837817    1678.1546953970853338    1189.0528341066981284     394.2018687459686817    7852.5601874999956635    7852.3633298995819132   17288.1782202522445004     299.9683013583347133 
+     720     301.2122298224125529    1524.1415452491430642    1189.0046957644285612     394.1752723525083866    7852.5601875000093059    7852.4351629896145823   17288.1753186065616319     299.9693315350040734 
+     730     301.0763282392692304    1547.1987029633166912    1188.9602551214045434     393.9974275034455218    7852.5601874999883876    7852.6518053705112834   17288.1696754953518393     299.9732715774841267 
+     740     301.3262401480515109    1544.7045314021493141    1188.9131307177485724     394.3244696516559884    7852.5601874999965730    7852.3694201272974169   17288.1672079966992897     299.9674666811455950 
+     750     301.5740779122830304    1591.1785078054851965    1188.8637580645938669     394.6487975126887022    7852.5601875000029395    7852.0919529470393172   17288.1646960243233480     299.9616008527094095 
+     760     301.4385361878654521    1547.3218422039201414    1188.8113669183098864     394.4714235854450521    7852.5601874999838401    7852.3161911124070684   17288.1591691161447670     299.9656339783694534 
+     770     301.6110125684814420    1494.5039561806622714    1188.7581685915934031     394.6971313010439530    7852.5601875000083965    7852.1351720579104949   17288.1506594505553949     299.9619855799395509 
+     780     301.8360352039435384    1588.1458619705292676    1188.7039178696472845     394.9916026067776329    7852.5601874999956635    7851.9015195838428554   17288.1572275602629816     299.9572350302977952 
+     790     302.1008324754310479    1545.4409171812178556    1188.6491103416560691     395.3381241828382144    7852.5601875000138534    7851.6150048936624444   17288.1624269181702402     299.9513959104631340 
+     800     301.9660372380565718    1563.9565804790736365    1188.5964649891604950     395.1617271307158035    7852.5601874999874781    7851.8461249560614306   17288.1645045759250934     299.9555810527747326 
+     810     302.0507207347627627    1511.4560763489957935    1188.5468477146612258     395.2725464702810996    7852.5601875000120344    7851.7904104899025697   17288.1699921748586348     299.9541551776504775 
+     820     302.4700213214911741    1458.5135514273570152    1188.4981381693974072     395.8212556746473751    7852.5601875000202199    7851.2935886962204677   17288.1731700402851857     299.9441803241180651 
+     830     302.2853997979337350    1496.2544527963129894    1188.4496917372191547     395.5796544641875698    7852.5601875000447762    7851.5862641793482908   17288.1757978808018379     299.9494768794835977 
+     840     302.0840465730901201    1518.8301331998704882    1188.3994383226176978     395.3161576523596636    7852.5601875000038490    7851.8962146812327774   17288.1719981562127941     299.9550476592922337 
+     850     301.8910942560261788    1469.8827850510901953    1188.3489956121345585     395.0636545180261692    7852.5601874999829306    7852.2025804631493884   17288.1754180932912277     299.9606927700139067 
+     860     301.7284384160519153    1657.6802015862324424    1188.3052233777652873     394.8507982536594341    7852.5601875000093059    7852.4644669022691232   17288.1806760337058222     299.9652835238809985 
+     870     301.6331619894115192    1501.5829953208524330    1188.2628815714097072     394.7261166912876433    7852.5601875000202199    7852.6378180648598573   17288.1870038275774277     299.9682811831179379 
+     880     301.3703918424367316    1499.1595903074553462    1188.2195190931643083     394.3822478705861272    7852.5601874999956635    7853.0266423250832304   17288.1885967888301820     299.9755099056966401 
+     890     301.4157954313303662    1598.8758859042511631    1188.1845892608291706     394.4416643558612918    7852.5601875000065775    7853.0036606192506952   17288.1901017359487014     299.9745322513492738 
+     900     301.4752150615485675    1621.2148728756822038    1188.1517520946135846     394.5194226492019993    7852.5601874999711072    7852.9579580608560718   17288.1893203046420240     299.9733125337182287 
+     910     301.4308816315938770    1538.4823217911632582    1188.1159856659232901     394.4614066057066566    7852.5601875000002110    7853.0558695713261841   17288.1934493429580471     299.9748317405193916 
+     920     301.4323110133492492    1594.7193046491217956    1188.0835779842032025     394.4632771371357762    7852.5601875000202199    7853.0942701464364291   17288.2013127677964803     299.9751127806911200 
+     930     301.4801256941950101    1387.6885377097617038    1188.0464206196895702     394.5258488489681099    7852.5601875000229484    7853.0656502842994087   17288.1981072529815719     299.9740698440909910 
+     940     301.8075611840245074    1534.2487040663793323    1188.0124217312886685     394.9543406584059539    7852.5601874999701977    7852.6729444202819650   17288.1998943099461030     299.9660570413493588 
+     950     301.6915970126173647    1567.7725992489238251    1187.9790455470049437     394.8025864986412898    7852.5601875000274958    7852.8619557087595240   17288.2037752544347313     299.9694678653150959 
+     960     301.6392594677008105    1504.8502165144939227    1187.9439133338105421     394.7340960325207675    7852.5601874999711072    7852.9728807988849439   17288.2110776651898050     299.9711546356286362 
+     970     301.6049535791644303    1514.0198965433548892    1187.9094123369413865     394.6892023276233772    7852.5601874999765641    7853.0497909819878259   17288.2085931465298927     299.9722547114341751 
+     980     301.2982841679705643    1634.1208149125807267    1187.8768454876480973     394.2878856256063500    7852.5601874999856591    7853.4862008383515786   17288.2111194515891839     299.9802110109069986 
+     990     301.2573007350166563    1489.7316698898257528    1187.8432331161868660     394.2342534877078606    7852.5601875000047585    7853.5840096862748396   17288.2216837901723920     299.9819468620868292 
+    1000     301.3195135766228532    1562.6587211933920116    1187.8034267774903583     394.3156670604516307    7852.5601874999356369    7853.5372636956635688   17288.2165450335414789     299.9807651637231629 
+Loop time of 21.3308 on 1 procs for 1000 steps with 10125 atoms
+
+Performance: 4.050 ns/day, 5.925 hours/ns, 46.880 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    | 10.099     | 10.099     | 10.099     |   0.0 | 47.34
+Neigh   | 10.145     | 10.145     | 10.145     |   0.0 | 47.56
+Comm    | 0.49807    | 0.49807    | 0.49807    |   0.0 |  2.33
+Output  | 0.011203   | 0.011203   | 0.011203   |   0.0 |  0.05
+Modify  | 0.28296    | 0.28296    | 0.28296    |   0.0 |  1.33
+Other   |            | 0.295      |            |       |  1.38
+
+Nlocal:    10125 ave 10125 max 10125 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    5824 ave 5824 max 5824 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    114682 ave 114682 max 114682 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 114682
+Ave neighs/atom = 11.3266
+Neighbor list builds = 1000
+Dangerous builds not checked
+Total wall time: 0:00:21