Merge pull request #220 from rbberger/fix-doc-makefile

Allow building non-html doc targets without Python3 and virtualenv

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="12 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
+12 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
 
@@ -618,6 +675,7 @@ 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 +981,7 @@ 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

@@ -475,9 +475,6 @@ 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

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_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
@@ -50,7 +54,7 @@ name.  In this case, the variable will be evaluated each timestep, and
 its value used to determine the target temperature.
 
 Equal-style variables can specify formulas with various mathematical
-functions, and include "thermo_style"_thermo_style.html command
+functions, and include "thermo_style"_thermox_style.html command
 keywords for the simulation box parameters and timestep and elapsed
 time.  Thus it is easy to specify a time-dependent temperature.
 

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)
@@ -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

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/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/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/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  

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

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

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

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

@@ -1,5 +1,3 @@
-LAMMPS (7 Dec 2015)
-# Input File for DPD fluid under isenthalpic conditions using the VV-SSA integration scheme
 boundary        p p p
 
 units           metal  # ev, ps
@@ -42,123 +40,123 @@ Neighbor list info ...
   master list distance cutoff = 12
   ghost atom cutoff = 12
   binsize = 6 -> bins = 22 22 22
-Memory usage per processor = 6.99064 Mbytes
-Step Temp Press Volume PotEng KinEng totEnerg Cella Cellb Cellc 
+Memory usage per processor = 6.48143 Mbytes
+Step Temp Press Volume PotEng KinEng v_totEnergy Cella Cellb Cellc 
        0  239.4274282976 2817.4421750949 2146689.0000000000 2639.8225470740  313.3218455755 6048176597.3066043854  129.0000000000  129.0000000000  129.0000000000 
-       1  239.4771405316 2817.4798146419 2146689.0000581890 2639.8304543632  313.3869004818 6048257397.9450139999  129.0000000012  129.0000000012  129.0000000012 
-       2  239.5643955010 2817.5423194969 2146689.0002327557 2639.8379071907  313.5010849268 6048391577.0431976318  129.0000000047  129.0000000047  129.0000000047 
-       3  239.6633839196 2817.6123662396 2146689.0005237064 2639.8445238058  313.6306241122 6048541946.5712041855  129.0000000105  129.0000000105  129.0000000105 
-       4  239.5371222027 2817.5355424336 2146689.0009310376 2639.8505035043  313.4653942786 6048377030.7404508591  129.0000000186  129.0000000186  129.0000000186 
-       5  239.6512678169 2817.6153097076 2146689.0014547524 2639.8561498340  313.6147686202 6048548267.9007387161  129.0000000291  129.0000000291  129.0000000291 
-       6  239.5617886781 2817.5624195435 2146689.0020948485 2639.8617493725  313.4976735610 6048434730.8591957092  129.0000000420  129.0000000420  129.0000000420 
-       7  239.5228587856 2817.5420009502 2146689.0028513218 2639.8666590407  313.4467287471 6048390900.5748634338  129.0000000571  129.0000000571  129.0000000571 
+       1  239.4771405316 2817.4798146419 2146689.0000581890 2639.8304543632  313.3869004818 6048257397.9450111389  129.0000000012  129.0000000012  129.0000000012 
+       2  239.5643955010 2817.5423194969 2146689.0002327557 2639.8379071907  313.5010849268 6048391577.0431985855  129.0000000047  129.0000000047  129.0000000047 
+       3  239.6633839196 2817.6123662396 2146689.0005237064 2639.8445238058  313.6306241122 6048541946.5712032318  129.0000000105  129.0000000105  129.0000000105 
+       4  239.5371222027 2817.5355424336 2146689.0009310376 2639.8505035043  313.4653942786 6048377030.7404460907  129.0000000186  129.0000000186  129.0000000186 
+       5  239.6512678169 2817.6153097076 2146689.0014547524 2639.8561498340  313.6147686202 6048548267.9007377625  129.0000000291  129.0000000291  129.0000000291 
+       6  239.5617886781 2817.5624195435 2146689.0020948485 2639.8617493725  313.4976735610 6048434730.8592004776  129.0000000420  129.0000000420  129.0000000420 
+       7  239.5228587856 2817.5420009502 2146689.0028513218 2639.8666590407  313.4467287471 6048390900.5748577118  129.0000000571  129.0000000571  129.0000000571 
        8  239.6066877934 2817.6008649264 2146689.0037241788 2639.8710757645  313.5564298772 6048517265.7987136841  129.0000000746  129.0000000746  129.0000000746 
        9  239.5719861485 2817.5823530300 2146689.0047134170 2639.8752557893  313.5110182737 6048477529.2603597641  129.0000000944  129.0000000944  129.0000000944 
-      10  239.5800176776 2817.5915671176 2146689.0058190385 2639.8793778438  313.5215285712 6048497312.1706562042  129.0000001166  129.0000001166  129.0000001166 
-      11  239.6299830954 2817.6281223139 2146689.0070410441 2639.8829762049  313.5869148014 6048575788.3208293915  129.0000001410  129.0000001410  129.0000001410 
-      12  239.6011995911 2817.6132377273 2146689.0083794324 2639.8860704236  313.5492478526 6048543839.4788341522  129.0000001678  129.0000001678  129.0000001678 
-      13  239.6407681166 2817.6427924824 2146689.0098342048 2639.8889816934  313.6010284005 6048607288.5005035400  129.0000001970  129.0000001970  129.0000001970 
-      14  239.6981172055 2817.6844100046 2146689.0114053637 2639.8913405110  313.6760771219 6048696632.8825635910  129.0000002285  129.0000002285  129.0000002285 
-      15  239.8563971968 2817.7922519039 2146689.0130929090 2639.8934358481  313.8832070208 6048928140.8671445847  129.0000002623  129.0000002623  129.0000002623 
-      16  239.8561894618 2817.7971208197 2146689.0148968464 2639.8950496967  313.8829351726 6048938597.9994983673  129.0000002984  129.0000002984  129.0000002984 
-      17  239.8816520361 2817.8185621543 2146689.0168171758 2639.8961257823  313.9162562538 6048984631.3226099014  129.0000003369  129.0000003369  129.0000003369 
-      18  239.9099966096 2817.8417368960 2146689.0188538977 2639.8965743204  313.9533488047 6049034386.0627689362  129.0000003777  129.0000003777  129.0000003777 
-      19  240.0514024347 2817.9389205774 2146689.0210070144 2639.8966103811  314.1383966683 6049243015.4568042755  129.0000004208  129.0000004208  129.0000004208 
-      20  239.8802541140 2817.8327386176 2146689.0232765260 2639.8962085210  313.9144268914 6049015081.9802312851  129.0000004662  129.0000004662  129.0000004662 
-      21  239.8462621903 2817.8160306167 2146689.0256624296 2639.8953174755  313.8699440502 6048979221.7758684158  129.0000005140  129.0000005140  129.0000005140 
-      22  240.0487944678 2817.9533849158 2146689.0281647225 2639.8938590354  314.1349838054 6049274086.0571269989  129.0000005642  129.0000005642  129.0000005642 
-      23  240.0966314441 2817.9897873787 2146689.0307834130 2639.8918104774  314.1975846937 6049352238.2649221420  129.0000006166  129.0000006166  129.0000006166 
-      24  240.1765312516 2818.0463843765 2146689.0335185044 2639.8891292321  314.3021439554 6049473742.2287292480  129.0000006714  129.0000006714  129.0000006714 
-      25  240.1500705973 2818.0336048048 2146689.0363699966 2639.8858785483  314.2675167572 6049446316.4600133896  129.0000007285  129.0000007285  129.0000007285 
+      10  239.5800176776 2817.5915671176 2146689.0058190385 2639.8793778438  313.5215285712 6048497312.1706552505  129.0000001166  129.0000001166  129.0000001166 
+      11  239.6299830954 2817.6281223139 2146689.0070410441 2639.8829762049  313.5869148014 6048575788.3208351135  129.0000001410  129.0000001410  129.0000001410 
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+      80  244.0965612207 2820.4387335935 2146689.3725191355 2638.9888176882  319.4320116291 6054610332.4174261093  129.0000074619  129.0000074619  129.0000074619 
       81  244.1334315951 2820.4535208568 2146689.3818921377 2638.9608330195  319.4802612965 6054642102.5347270966  129.0000076496  129.0000076496  129.0000076496 
-      82  244.3029520408 2820.5543485196 2146689.3913816395 2638.9318525796  319.7021007878 6054858575.1664323807  129.0000078397  129.0000078397  129.0000078397 
-      83  244.3445761189 2820.5713690935 2146689.4009876498 2638.9021684795  319.7565712929 6054895140.1710672379  129.0000080321  129.0000080321  129.0000080321 
-      84  244.2696671559 2820.5125763350 2146689.4107101629 2638.8720941742  319.6585431986 6054768957.6738977432  129.0000082269  129.0000082269  129.0000082269 
-      85  244.5161919319 2820.6629431352 2146689.4205491822 2638.8415194387  319.9811528443 6055091776.5362014771  129.0000084240  129.0000084240  129.0000084240 
-      86  244.5641090282 2820.6838080201 2146689.4305047127 2638.8103612394  320.0438585800 6055136595.0767993927  129.0000086234  129.0000086234  129.0000086234 
-      87  244.5348240638 2820.6541129118 2146689.4405767513 2638.7789728309  320.0055354056 6055072877.2416133881  129.0000088251  129.0000088251  129.0000088251 
-      88  244.6939431427 2820.7468233396 2146689.4507653015 2638.7470269267  320.2137633592 6055271926.6536083221  129.0000090292  129.0000090292  129.0000090292 
-      89  244.8800201091 2820.8567117003 2146689.4610703662 2638.7147520097  320.4572692055 6055507852.1186370850  129.0000092356  129.0000092356  129.0000092356 
-      90  244.8804280382 2820.8451141876 2146689.4714919478 2638.6820441173  320.4578030336 6055482985.2258615494  129.0000094444  129.0000094444  129.0000094444 
-      91  244.9558851986 2820.8815975090 2146689.4820300462 2638.6491836104  320.5565485155 6055561333.3803415298  129.0000096555  129.0000096555  129.0000096555 
-      92  244.9965893140 2820.8949614294 2146689.4926846647 2638.6159817170  320.6098151301 6055590051.6433105469  129.0000098689  129.0000098689  129.0000098689 
-      93  245.1381056687 2820.9732811388 2146689.5034558061 2638.5824451870  320.7950076360 6055758210.2774286270  129.0000100846  129.0000100846  129.0000100846 
-      94  245.2954807041 2821.0619342131 2146689.5143434699 2638.5485198222  321.0009532826 6055948551.7882719040  129.0000103027  129.0000103027  129.0000103027 
-      95  245.3535822199 2821.0860553731 2146689.5253476589 2638.5144817512  321.0769866522 6056000363.5151643753  129.0000105232  129.0000105232  129.0000105232 
-      96  245.5013476026 2821.1682908185 2146689.5364683764 2638.4801107361  321.2703568219 6056176929.0169973373  129.0000107459  129.0000107459  129.0000107459 
-      97  245.4166531417 2821.0989038023 2146689.5477056229 2638.4453663061  321.1595231342 6056028008.1910085678  129.0000109710  129.0000109710  129.0000109710 
-      98  245.4121937790 2821.0817490953 2146689.5590593945 2638.4097762390  321.1536874797 6055991214.3494358063  129.0000111984  129.0000111984  129.0000111984 
-      99  245.4532592994 2821.0946353191 2146689.5705296928 2638.3738037546  321.2074270397 6056018909.4481058121  129.0000114282  129.0000114282  129.0000114282 
-     100  245.7500657390 2821.2735939427 2146689.5821165247 2638.3375549051  321.5958367642 6056403111.1006603241  129.0000116603  129.0000116603  129.0000116603 
-Loop time of 4.26657 on 1 procs for 100 steps with 10125 atoms
+      82  244.3029520408 2820.5543485196 2146689.3913816395 2638.9318525796  319.7021007878 6054858575.1664342880  129.0000078397  129.0000078397  129.0000078397 
+      83  244.3445761189 2820.5713690935 2146689.4009876498 2638.9021684795  319.7565712929 6054895140.1710596085  129.0000080321  129.0000080321  129.0000080321 
+      84  244.2696671559 2820.5125763350 2146689.4107101629 2638.8720941742  319.6585431986 6054768957.6739044189  129.0000082269  129.0000082269  129.0000082269 
+      85  244.5161919319 2820.6629431352 2146689.4205491822 2638.8415194387  319.9811528443 6055091776.5361995697  129.0000084240  129.0000084240  129.0000084240 
+      86  244.5641090282 2820.6838080201 2146689.4305047127 2638.8103612394  320.0438585800 6055136595.0767974854  129.0000086234  129.0000086234  129.0000086234 
+      87  244.5348240638 2820.6541129118 2146689.4405767513 2638.7789728309  320.0055354056 6055072877.2416200638  129.0000088251  129.0000088251  129.0000088251 
+      88  244.6939431427 2820.7468233396 2146689.4507653015 2638.7470269267  320.2137633592 6055271926.6536149979  129.0000090292  129.0000090292  129.0000090292 
+      89  244.8800201091 2820.8567117003 2146689.4610703662 2638.7147520097  320.4572692055 6055507852.1186332703  129.0000092356  129.0000092356  129.0000092356 
+      90  244.8804280382 2820.8451141876 2146689.4714919478 2638.6820441173  320.4578030336 6055482985.2258749008  129.0000094444  129.0000094444  129.0000094444 
+      91  244.9558851986 2820.8815975090 2146689.4820300462 2638.6491836104  320.5565485155 6055561333.3803453445  129.0000096555  129.0000096555  129.0000096555 
+      92  244.9965893140 2820.8949614294 2146689.4926846647 2638.6159817170  320.6098151301 6055590051.6433181763  129.0000098689  129.0000098689  129.0000098689 
+      93  245.1381056687 2820.9732811388 2146689.5034558061 2638.5824451870  320.7950076360 6055758210.2774200439  129.0000100846  129.0000100846  129.0000100846 
+      94  245.2954807041 2821.0619342131 2146689.5143434699 2638.5485198222  321.0009532826 6055948551.7882709503  129.0000103027  129.0000103027  129.0000103027 
+      95  245.3535822199 2821.0860553731 2146689.5253476589 2638.5144817512  321.0769866522 6056000363.5151576996  129.0000105232  129.0000105232  129.0000105232 
+      96  245.5013476026 2821.1682908185 2146689.5364683764 2638.4801107361  321.2703568219 6056176929.0169925690  129.0000107459  129.0000107459  129.0000107459 
+      97  245.4166531417 2821.0989038023 2146689.5477056229 2638.4453663061  321.1595231342 6056028008.1910057068  129.0000109710  129.0000109710  129.0000109710 
+      98  245.4121937790 2821.0817490953 2146689.5590593945 2638.4097762390  321.1536874797 6055991214.3494396210  129.0000111984  129.0000111984  129.0000111984 
+      99  245.4532592994 2821.0946353191 2146689.5705296928 2638.3738037546  321.2074270397 6056018909.4480972290  129.0000114282  129.0000114282  129.0000114282 
+     100  245.7500657390 2821.2735939427 2146689.5821165247 2638.3375549051  321.5958367642 6056403111.1006488800  129.0000116603  129.0000116603  129.0000116603 
+Loop time of 4.05006 on 1 procs for 100 steps with 10125 atoms
 
-Performance: 2.025 ns/day, 11.852 hours/ns, 23.438 timesteps/s
+Performance: 2.133 ns/day, 11.250 hours/ns, 24.691 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    | 0.40111    | 0.40111    | 0.40111    |   0.0 |  9.40
-Neigh   | 1.4039     | 1.4039     | 1.4039     |   0.0 | 32.90
-Comm    | 0.040107   | 0.040107   | 0.040107   |   0.0 |  0.94
-Output  | 0.012053   | 0.012053   | 0.012053   |   0.0 |  0.28
-Modify  | 2.4038     | 2.4038     | 2.4038     |   0.0 | 56.34
-Other   |            | 0.005648   |            |       |  0.13
+Pair    | 0.46587    | 0.46587    | 0.46587    |   0.0 | 11.50
+Neigh   | 1.4713     | 1.4713     | 1.4713     |   0.0 | 36.33
+Comm    | 0.05567    | 0.05567    | 0.05567    |   0.0 |  1.37
+Output  | 0.011364   | 0.011364   | 0.011364   |   0.0 |  0.28
+Modify  | 2.0158     | 2.0158     | 2.0158     |   0.0 | 49.77
+Other   |            | 0.03004    |            |       |  0.74
 
 Nlocal:    10125 ave 10125 max 10125 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

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

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

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

@@ -1,5 +1,3 @@
-LAMMPS (7 Dec 2015)
-# Input File for DPD fluid under isobaric 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 Press Volume PotEng KinEng TotEng Enthalpy Cella Cellb Cellc 
        0  128.6667660382 3065.7908751302 204306.2673181506  263.2538386154   16.6148533499  279.8686919654  670.8120681014   66.8305353589   57.8900140312   52.8084103339 
        1  128.8781761640 3065.9340218365 204306.2673289568  263.2538784443   16.6421529266  279.8960313709  670.8576613026   66.8305353600   57.8900140323   52.8084103348 
@@ -48,113 +46,113 @@ Step Temp Press Volume PotEng KinEng TotEng Enthalpy Cella Cellb Cellc
        5  129.5099127127 3066.3516291155 204306.2675883183  263.2544119877   16.7237296261  279.9781416138  670.9930244672   66.8305353883   57.8900140568   52.8084103572 
        6  129.4373658155 3066.2979832897 204306.2677071957  263.2546211781   16.7143615811  279.9689827592  670.9770250342   66.8305354013   57.8900140680   52.8084103674 
        7  129.5468804564 3066.3661894656 204306.2678476885  263.2548635146   16.7285033035  279.9833668181  671.0001068740   66.8305354166   57.8900140813   52.8084103795 
-       8  129.6703134859 3066.4427527412 204306.2680097974  263.2551515311   16.7444423199  279.9995938510  671.0260974093   66.8305354343   57.8900140966   52.8084103935 
-       9  129.7536784769 3066.4909380739 204306.2681935228  263.2554871768   16.7552073149  280.0106944917  671.0433428967   66.8305354543   57.8900141139   52.8084104093 
-      10  129.6933330547 3066.4412060161 204306.2683988648  263.2558667340   16.7474148571  280.0032815912  671.0295886589   66.8305354767   57.8900141333   52.8084104270 
+       8  129.6703134859 3066.4427527412 204306.2680097972  263.2551515311   16.7444423199  279.9995938510  671.0260974093   66.8305354343   57.8900140966   52.8084103935 
+       9  129.7536784769 3066.4909380739 204306.2681935227  263.2554871768   16.7552073149  280.0106944917  671.0433428967   66.8305354543   57.8900141139   52.8084104093 
+      10  129.6933330547 3066.4412060161 204306.2683988647  263.2558667340   16.7474148571  280.0032815912  671.0295886589   66.8305354767   57.8900141333   52.8084104270 
       11  130.0493626138 3066.6716229532 204306.2686258238  263.2562750927   16.7933892692  280.0496643619  671.1053541603   66.8305355014   57.8900141547   52.8084104465 
-      12  130.3213016818 3066.8440489028 204306.2688744016  263.2567151478   16.8285050016  280.0852201494  671.1628978279   66.8305355285   57.8900141782   52.8084104680 
-      13  130.5593607103 3066.9922169334 204306.2691445990  263.2571951093   16.8592457746  280.1164408840  671.2130131637   66.8305355580   57.8900142037   52.8084104912 
-      14  130.1135600843 3066.6777117324 204306.2694364157  263.2576949083   16.8016791453  280.0593740536  671.1158418322   66.8305355898   57.8900142313   52.8084105164 
+      12  130.3213016818 3066.8440489028 204306.2688744015  263.2567151478   16.8285050016  280.0852201494  671.1628978279   66.8305355285   57.8900141782   52.8084104680 
+      13  130.5593607103 3066.9922169334 204306.2691445989  263.2571951093   16.8592457746  280.1164408840  671.2130131637   66.8305355580   57.8900142037   52.8084104912 
+      14  130.1135600843 3066.6777117324 204306.2694364155  263.2576949083   16.8016791453  280.0593740536  671.1158418322   66.8305355898   57.8900142313   52.8084105164 
       15  130.6547963417 3067.0283008545 204306.2697498515  263.2582241459   16.8715694622  280.1297936080  671.2309683942   66.8305356240   57.8900142609   52.8084105434 
-      16  130.9755531935 3067.2288355184 204306.2700849087  263.2587905777   16.9129890783  280.1717796560  671.2985268537   66.8305356605   57.8900142926   52.8084105723 
-      17  131.2014454974 3067.3641769107 204306.2704415885  263.2594031106   16.9421587513  280.2015618620  671.3455682001   66.8305356994   57.8900143262   52.8084106030 
-      18  131.5359721707 3067.5714631111 204306.2708198917  263.2600649028   16.9853564767  280.2454213795  671.4158611542   66.8305357407   57.8900143620   52.8084106356 
-      19  131.5639681439 3067.5705655906 204306.2712198193  263.2607641517   16.9889716215  280.2497357731  671.4200618636   66.8305357843   57.8900143997   52.8084106700 
-      20  131.8466979060 3067.7405506504 204306.2716413718  263.2614923308   17.0254807658  280.2869730966  671.4789761415   66.8305358302   57.8900144396   52.8084107064 
-      21  131.7458606698 3067.6501610601 204306.2720845496  263.2622636973   17.0124595643  280.2747232616  671.4552008593   66.8305358786   57.8900144814   52.8084107445 
-      22  132.0934634942 3067.8611721914 204306.2725493531  263.2630740031   17.0573458246  280.3204198277  671.5278060235   66.8305359292   57.8900145253   52.8084107846 
-      23  132.1061490539 3067.8452272408 204306.2730357831  263.2639187332   17.0589839221  280.3229026553  671.5282565150   66.8305359823   57.8900145713   52.8084108265 
-      24  132.0864187320 3067.8064692879 204306.2735438392  263.2648061201   17.0564361282  280.3212422483  671.5216547458   66.8305360377   57.8900146193   52.8084108703 
-      25  132.4555503012 3068.0294628610 204306.2740735222  263.2657237919   17.1041024143  280.3698262063  671.5986754029   66.8305360954   57.8900146693   52.8084109159 
-      26  132.5425396026 3068.0605856855 204306.2746248329  263.2666902136   17.1153354198  280.3820256334  671.6148446047   66.8305361555   57.8900147214   52.8084109634 
-      27  132.6414561712 3068.0981288018 204306.2751977716  263.2677103029   17.1281086038  280.3958189068  671.6334263968   66.8305362180   57.8900147755   52.8084110128 
-      28  132.8195557714 3068.1880757315 204306.2757923386  263.2687564664   17.1511067628  280.4198632292  671.6689417066   66.8305362828   57.8900148316   52.8084110640 
-      29  133.0651548752 3068.3224074813 204306.2764085349  263.2698607264   17.1828211924  280.4526819188  671.7188912867   66.8305363500   57.8900148898   52.8084111171 
-      30  133.3017656825 3068.4496355722 204306.2770463614  263.2709902617   17.2133749553  280.4843652170  671.7667996729   66.8305364196   57.8900149501   52.8084111721 
-      31  133.2181169549 3068.3592522301 204306.2777058183  263.2721596133   17.2025733211  280.4747329344  671.7456431539   66.8305364915   57.8900150123   52.8084112289 
-      32  133.5618196837 3068.5561657520 204306.2783869057  263.2733741839   17.2469559586  280.5203301425  671.8163516770   66.8305365658   57.8900150767   52.8084112875 
-      33  133.5661113072 3068.5225231843 204306.2790896243  263.2746385114   17.2475101397  280.5221486512  671.8138814999   66.8305366424   57.8900151430   52.8084113481 
-      34  133.9344409280 3068.7332886556 204306.2798139751  263.2759490654   17.2950728696  280.5710219350  671.8896325541   66.8305367214   57.8900152115   52.8084114105 
-      35  134.0251903481 3068.7554422023 204306.2805599585  263.2773099950   17.3067914225  280.5841014175  671.9055384405   66.8305368027   57.8900152819   52.8084114748 
-      36  134.3358662330 3068.9247619878 204306.2813275753  263.2787224847   17.3469092744  280.6256317591  671.9686615663   66.8305368864   57.8900153544   52.8084115409 
-      37  134.6482096693 3069.0939486549 204306.2821168267  263.2801733161   17.3872424587  280.6674157749  672.0320214328   66.8305369724   57.8900154290   52.8084116089 
-      38  134.2954241696 3068.8129844727 204306.2829277122  263.2816463125   17.3416869550  280.6233332675  671.9521124987   66.8305370609   57.8900155056   52.8084116788 
-      39  134.0353990053 3068.5937480649 204306.2837602304  263.2831586466   17.3081096754  280.5912683220  671.8920925677   66.8305371516   57.8900155842   52.8084117505 
-      40  134.0661096287 3068.5695889226 204306.2846143801  263.2846992099   17.3120753654  280.5967745753  671.8945197323   66.8305372448   57.8900156649   52.8084118241 
-      41  134.3213893449 3068.6956839852 204306.2854901620  263.2862823101   17.3450398611  280.6313221711  671.9451483911   66.8305373403   57.8900157476   52.8084118996 
-      42  134.4478159847 3068.7334555670 204306.2863875761  263.2879050936   17.3613654449  280.6492705385  671.9679150326   66.8305374381   57.8900158323   52.8084119769 
-      43  134.5229805032 3068.7357045584 204306.2873066232  263.2895707681   17.3710715057  280.6606422738  671.9795753149   66.8305375383   57.8900159191   52.8084120561 
-      44  134.2978602830 3068.5344030900 204306.2882473021  263.2912685684   17.3420015325  280.6332701009  671.9265353900   66.8305376409   57.8900160080   52.8084121371 
-      45  134.4285957415 3068.5722177449 204306.2892096126  263.2929985679   17.3588835179  280.6518820858  671.9499712659   66.8305377458   57.8900160989   52.8084122200 
-      46  134.3890633912 3068.4939450711 204306.2901935543  263.2947639946   17.3537786705  280.6485426651  671.9366525574   66.8305378531   57.8900161918   52.8084123048 
+      16  130.9755531935 3067.2288355184 204306.2700849086  263.2587905777   16.9129890783  280.1717796560  671.2985268537   66.8305356605   57.8900142926   52.8084105723 
+      17  131.2014454974 3067.3641769107 204306.2704415883  263.2594031106   16.9421587513  280.2015618620  671.3455682001   66.8305356994   57.8900143262   52.8084106030 
+      18  131.5359721707 3067.5714631111 204306.2708198916  263.2600649028   16.9853564767  280.2454213795  671.4158611542   66.8305357407   57.8900143620   52.8084106356 
+      19  131.5639681439 3067.5705655906 204306.2712198192  263.2607641517   16.9889716215  280.2497357731  671.4200618636   66.8305357843   57.8900143997   52.8084106700 
+      20  131.8466979060 3067.7405506504 204306.2716413717  263.2614923308   17.0254807658  280.2869730966  671.4789761415   66.8305358302   57.8900144396   52.8084107064 
+      21  131.7458606698 3067.6501610601 204306.2720845494  263.2622636973   17.0124595643  280.2747232616  671.4552008593   66.8305358786   57.8900144814   52.8084107445 
+      22  132.0934634942 3067.8611721914 204306.2725493530  263.2630740031   17.0573458246  280.3204198277  671.5278060235   66.8305359292   57.8900145253   52.8084107846 
+      23  132.1061490539 3067.8452272408 204306.2730357830  263.2639187332   17.0589839221  280.3229026553  671.5282565150   66.8305359823   57.8900145713   52.8084108265 
+      24  132.0864187320 3067.8064692879 204306.2735438391  263.2648061201   17.0564361282  280.3212422483  671.5216547458   66.8305360377   57.8900146193   52.8084108703 
+      25  132.4555503012 3068.0294628610 204306.2740735220  263.2657237919   17.1041024143  280.3698262063  671.5986754029   66.8305360954   57.8900146693   52.8084109159 
+      26  132.5425396026 3068.0605856855 204306.2746248327  263.2666902136   17.1153354198  280.3820256334  671.6148446047   66.8305361555   57.8900147214   52.8084109634 
+      27  132.6414561712 3068.0981288018 204306.2751977713  263.2677103029   17.1281086038  280.3958189068  671.6334263968   66.8305362180   57.8900147755   52.8084110128 
+      28  132.8195557714 3068.1880757315 204306.2757923383  263.2687564664   17.1511067628  280.4198632292  671.6689417066   66.8305362828   57.8900148316   52.8084110640 
+      29  133.0651548752 3068.3224074813 204306.2764085347  263.2698607264   17.1828211924  280.4526819188  671.7188912867   66.8305363500   57.8900148898   52.8084111171 
+      30  133.3017656825 3068.4496355722 204306.2770463612  263.2709902617   17.2133749553  280.4843652170  671.7667996729   66.8305364196   57.8900149501   52.8084111721 
+      31  133.2181169549 3068.3592522301 204306.2777058180  263.2721596133   17.2025733211  280.4747329344  671.7456431539   66.8305364915   57.8900150123   52.8084112289 
+      32  133.5618196837 3068.5561657520 204306.2783869054  263.2733741839   17.2469559586  280.5203301425  671.8163516770   66.8305365658   57.8900150767   52.8084112875 
+      33  133.5661113072 3068.5225231843 204306.2790896240  263.2746385114   17.2475101397  280.5221486512  671.8138814999   66.8305366424   57.8900151430   52.8084113481 
+      34  133.9344409280 3068.7332886556 204306.2798139747  263.2759490654   17.2950728696  280.5710219350  671.8896325541   66.8305367214   57.8900152115   52.8084114105 
+      35  134.0251903481 3068.7554422023 204306.2805599582  263.2773099950   17.3067914225  280.5841014175  671.9055384405   66.8305368027   57.8900152819   52.8084114748 
+      36  134.3358662330 3068.9247619878 204306.2813275750  263.2787224847   17.3469092744  280.6256317591  671.9686615663   66.8305368864   57.8900153544   52.8084115409 
+      37  134.6482096693 3069.0939486549 204306.2821168264  263.2801733161   17.3872424587  280.6674157749  672.0320214328   66.8305369724   57.8900154290   52.8084116089 
+      38  134.2954241696 3068.8129844727 204306.2829277119  263.2816463125   17.3416869550  280.6233332675  671.9521124987   66.8305370609   57.8900155056   52.8084116788 
+      39  134.0353990053 3068.5937480649 204306.2837602301  263.2831586466   17.3081096754  280.5912683220  671.8920925677   66.8305371516   57.8900155842   52.8084117505 
+      40  134.0661096287 3068.5695889226 204306.2846143798  263.2846992099   17.3120753654  280.5967745753  671.8945197323   66.8305372448   57.8900156649   52.8084118241 
+      41  134.3213893449 3068.6956839852 204306.2854901617  263.2862823101   17.3450398611  280.6313221711  671.9451483911   66.8305373403   57.8900157476   52.8084118996 
+      42  134.4478159847 3068.7334555670 204306.2863875760  263.2879050936   17.3613654449  280.6492705385  671.9679150326   66.8305374381   57.8900158323   52.8084119769 
+      43  134.5229805032 3068.7357045585 204306.2873066230  263.2895707681   17.3710715057  280.6606422738  671.9795753149   66.8305375383   57.8900159191   52.8084120561 
+      44  134.2978602830 3068.5344030900 204306.2882473019  263.2912685684   17.3420015325  280.6332701009  671.9265353900   66.8305376409   57.8900160080   52.8084121371 
+      45  134.4285957415 3068.5722177449 204306.2892096124  263.2929985679   17.3588835179  280.6518820858  671.9499712659   66.8305377458   57.8900160989   52.8084122200 
+      46  134.3890633912 3068.4939450711 204306.2901935542  263.2947639946   17.3537786705  280.6485426651  671.9366525574   66.8305378531   57.8900161918   52.8084123048 
       47  134.7017020134 3068.6523501535 204306.2911991276  263.2965656113   17.3941499725  280.6907155838  671.9990268961   66.8305379628   57.8900162868   52.8084123914 
-      48  135.3432669980 3069.0313768964 204306.2922263343  263.2984321292   17.4769958266  280.7754279559  672.1320739558   66.8305380748   57.8900163838   52.8084124799 
-      49  135.2888601690 3068.9393187512 204306.2932751756  263.3003504562   17.4699702247  280.7703206808  672.1152296222   66.8305381891   57.8900164829   52.8084125703 
-      50  134.8400369547 3068.5806102794 204306.2943456497  263.3023024093   17.4120132858  280.7143156952  672.0134849110   66.8305383058   57.8900165840   52.8084126625 
-      51  134.9125282999 3068.5727411569 204306.2954377556  263.3043099800   17.4213741574  280.7256841374  672.0238519903   66.8305384249   57.8900166871   52.8084127566 
+      48  135.3432669980 3069.0313768964 204306.2922263342  263.2984321292   17.4769958266  280.7754279559  672.1320739558   66.8305380748   57.8900163838   52.8084124799 
+      49  135.2888601690 3068.9393187512 204306.2932751755  263.3003504562   17.4699702247  280.7703206808  672.1152296222   66.8305381891   57.8900164829   52.8084125703 
+      50  134.8400369547 3068.5806102794 204306.2943456496  263.3023024093   17.4120132858  280.7143156952  672.0134849110   66.8305383058   57.8900165840   52.8084126625 
+      51  134.9125282999 3068.5727411569 204306.2954377555  263.3043099800   17.4213741574  280.7256841374  672.0238519903   66.8305384249   57.8900166871   52.8084127566 
       52  134.9445761663 3068.5364265426 204306.2965514932  263.3063613000   17.4255125267  280.7318738267  672.0254130468   66.8305385464   57.8900167923   52.8084128526 
-      53  134.9641611904 3068.4901429966 204306.2976868617  263.3084644171   17.4280415582  280.7365059753  672.0241453860   66.8305386702   57.8900168996   52.8084129504 
-      54  135.1512150560 3068.5555596237 204306.2988438615  263.3106154196   17.4521959894  280.7628114090  672.0587948313   66.8305387963   57.8900170088   52.8084130501 
-      55  135.3892315779 3068.6540323579 204306.3000224933  263.3128003337   17.4829312735  280.7957316072  672.1042743302   66.8305389248   57.8900171202   52.8084131516 
-      56  135.3265008915 3068.5480189159 204306.3012227569  263.3150330541   17.4748308045  280.7898638585  672.0848902611   66.8305390557   57.8900172335   52.8084132551 
+      53  134.9641611904 3068.4901429966 204306.2976868616  263.3084644171   17.4280415582  280.7365059753  672.0241453860   66.8305386702   57.8900168996   52.8084129504 
+      54  135.1512150560 3068.5555596237 204306.2988438614  263.3106154196   17.4521959894  280.7628114090  672.0587948313   66.8305387963   57.8900170088   52.8084130501 
+      55  135.3892315779 3068.6540323579 204306.3000224932  263.3128003337   17.4829312735  280.7957316072  672.1042743302   66.8305389248   57.8900171202   52.8084131516 
+      56  135.3265008915 3068.5480189159 204306.3012227568  263.3150330541   17.4748308045  280.7898638585  672.0848902611   66.8305390557   57.8900172335   52.8084132551 
       57  135.3024634130 3068.4668168613 204306.3024446515  263.3173015297   17.4717268236  280.7890283533  672.0737023745   66.8305391889   57.8900173489   52.8084133603 
-      58  135.2521293970 3068.3666950252 204306.3036881770  263.3196055001   17.4652271476  280.7848326476  672.0567417166   66.8305393245   57.8900174664   52.8084134675 
-      59  135.0019308452 3068.1306120627 204306.3049533318  263.3219467372   17.4329187872  280.7548655243  671.9966721947   66.8305394625   57.8900175859   52.8084135765 
-      60  135.3361178986 3068.2878435126 204306.3062401156  263.3243328810   17.4760726571  280.8004055381  672.0622645090   66.8305396028   57.8900177074   52.8084136874 
-      61  135.3139081244 3068.2035774253 204306.3075485289  263.3267589778   17.4732046893  280.7999636671  672.0510797027   66.8305397454   57.8900178310   52.8084138001 
-      62  135.7430205344 3068.4226983441 204306.3088785718  263.3292333495   17.5286163545  280.8578497040  672.1369101433   66.8305398905   57.8900179566   52.8084139147 
-      63  136.0382527386 3068.5500741031 204306.3102302459  263.3317605359   17.5667399503  280.8985004861  672.1938062135   66.8305400378   57.8900180843   52.8084140311 
-      64  136.0795110412 3068.5046583092 204306.3116035513  263.3343072525   17.5720676714  280.9063749238  672.1958919511   66.8305401876   57.8900182140   52.8084141495 
-      65  136.5429104992 3068.7428965119 204306.3129984888  263.3368943008   17.6319068534  280.9688011542  672.2887005078   66.8305403397   57.8900183457   52.8084142696 
-      66  136.6747848955 3068.7560934485 204306.3144150593  263.3395194563   17.6489359109  280.9884553672  672.3100402808   66.8305404941   57.8900184795   52.8084143917 
-      67  136.9345148389 3068.8545703617 204306.3158532632  263.3421896806   17.6824750683  281.0246647490  672.3588099945   66.8305406510   57.8900186154   52.8084145156 
+      58  135.2521293970 3068.3666950252 204306.3036881768  263.3196055001   17.4652271476  280.7848326476  672.0567417166   66.8305393245   57.8900174664   52.8084134675 
+      59  135.0019308452 3068.1306120627 204306.3049533316  263.3219467372   17.4329187872  280.7548655243  671.9966721947   66.8305394625   57.8900175859   52.8084135765 
+      60  135.3361178986 3068.2878435126 204306.3062401155  263.3243328810   17.4760726571  280.8004055381  672.0622645090   66.8305396028   57.8900177074   52.8084136874 
+      61  135.3139081244 3068.2035774253 204306.3075485286  263.3267589778   17.4732046893  280.7999636671  672.0510797027   66.8305397454   57.8900178310   52.8084138001 
+      62  135.7430205344 3068.4226983441 204306.3088785714  263.3292333495   17.5286163545  280.8578497040  672.1369101433   66.8305398905   57.8900179566   52.8084139147 
+      63  136.0382527386 3068.5500741031 204306.3102302457  263.3317605359   17.5667399503  280.8985004861  672.1938062135   66.8305400378   57.8900180843   52.8084140311 
+      64  136.0795110412 3068.5046583092 204306.3116035512  263.3343072525   17.5720676714  280.9063749238  672.1958919511   66.8305401876   57.8900182140   52.8084141495 
+      65  136.5429104992 3068.7428965120 204306.3129984887  263.3368943008   17.6319068534  280.9688011542  672.2887005078   66.8305403397   57.8900183457   52.8084142696 
+      66  136.6747848955 3068.7560934485 204306.3144150592  263.3395194563   17.6489359109  280.9884553672  672.3100402808   66.8305404941   57.8900184795   52.8084143917 
+      67  136.9345148389 3068.8545703617 204306.3158532631  263.3421896806   17.6824750683  281.0246647490  672.3588099945   66.8305406510   57.8900186154   52.8084145156 
       68  136.5690881694 3068.5302814448 204306.3173130994  263.3448899028   17.6352871991  280.9801771020  672.2729724748   66.8305408101   57.8900187532   52.8084146414 
       69  137.0307072166 3068.7630696250 204306.3187945680  263.3476374865   17.6948964752  281.0425339617  672.3650168515   66.8305409717   57.8900188932   52.8084147690 
-      70  137.1048864397 3068.7333916895 204306.3202976696  263.3504277984   17.7044753039  281.0549031023  672.3736044006   66.8305411356   57.8900190351   52.8084148985 
-      71  137.2866532809 3068.7750522066 204306.3218224040  263.3532577755   17.7279470169  281.0812047925  672.4052214764   66.8305413018   57.8900191791   52.8084150299 
-      72  137.3464916785 3068.7338430357 204306.3233687716  263.3561237403   17.7356740022  281.0917977425  672.4105624778   66.8305414704   57.8900193252   52.8084151631 
-      73  137.4267886898 3068.7058777536 204306.3249367719  263.3590305503   17.7460428263  281.1050733766  672.4202750386   66.8305416414   57.8900194733   52.8084152982 
-      74  137.7032214008 3068.8096995216 204306.3265264053  263.3619634311   17.7817388269  281.1437022580  672.4721461079   66.8305418147   57.8900196234   52.8084154352 
+      70  137.1048864397 3068.7333916895 204306.3202976695  263.3504277984   17.7044753039  281.0549031023  672.3736044006   66.8305411356   57.8900190351   52.8084148985 
+      71  137.2866532809 3068.7750522066 204306.3218224039  263.3532577755   17.7279470169  281.0812047925  672.4052214764   66.8305413018   57.8900191791   52.8084150299 
+      72  137.3464916785 3068.7338430357 204306.3233687715  263.3561237403   17.7356740022  281.0917977425  672.4105624778   66.8305414704   57.8900193252   52.8084151631 
+      73  137.4267886898 3068.7058777536 204306.3249367717  263.3590305503   17.7460428263  281.1050733766  672.4202750386   66.8305416414   57.8900194733   52.8084152982 
+      74  137.7032214008 3068.8096995216 204306.3265264051  263.3619634311   17.7817388269  281.1437022580  672.4721461079   66.8305418147   57.8900196234   52.8084154352 
       75  138.2326481893 3069.0827847254 204306.3281376729  263.3649465758   17.8501041765  281.2150507524  672.5783209650   66.8305419904   57.8900197756   52.8084155740 
-      76  138.4006889617 3069.1105563660 204306.3297705764  263.3679794432   17.8718034302  281.2397828734  672.6065975977   66.8305421684   57.8900199299   52.8084157147 
-      77  138.5404442761 3069.1182683851 204306.3314251151  263.3710629684   17.8898501576  281.2609131260  672.6287144410   66.8305423489   57.8900200861   52.8084158573 
-      78  138.8911793449 3069.2673604038 204306.3331012900  263.3741701271   17.9351408874  281.3093110144  672.6961274554   66.8305425316   57.8900202444   52.8084160017 
-      79  138.9740932597 3069.2343926248 204306.3347991016  263.3773233601   17.9458476345  281.3231709947  672.7057867031   66.8305427167   57.8900204048   52.8084161480 
-      80  139.4197304629 3069.4447568636 204306.3365185503  263.3805326609   18.0033931609  281.3839258218  672.7933700502   66.8305429042   57.8900205672   52.8084162961 
-      81  140.0251352305 3069.7614239791 204306.3382596381  263.3837812869   18.0815696143  281.4653509011  672.9151792214   66.8305430941   57.8900207316   52.8084164461 
-      82  140.4343345655 3069.9447540285 204306.3400223668  263.3870704597   18.1344098865  281.5214803462  672.9946899248   66.8305432863   57.8900208981   52.8084165980 
-      83  140.8339491089 3070.1205252103 204306.3418067376  263.3904045656   18.1860124661  281.5764170317  673.0720440188   66.8305434808   57.8900210667   52.8084167517 
-      84  141.2138258327 3070.2828678237 204306.3436127516  263.3937910919   18.2350662835  281.6288573754  673.1451894287   66.8305436777   57.8900212372   52.8084169073 
-      85  141.4316065757 3070.3348892447 204306.3454404097  263.3972231992   18.2631885036  281.6604117028  673.1833809261   66.8305438770   57.8900214099   52.8084170648 
-      86  141.6165004814 3070.3639126512 204306.3472897122  263.4006984023   18.2870640172  281.6877624195  673.2144361936   66.8305440787   57.8900215845   52.8084172241 
-      87  141.7511192071 3070.3578486993 204306.3491606590  263.4042216826   18.3044474524  281.7086691350  673.2345732314   66.8305442827   57.8900217612   52.8084173853 
-      88  141.8992247234 3070.3595802006 204306.3510532502  263.4077909549   18.3235724488  281.7313634037  673.2574919246   66.8305444890   57.8900219400   52.8084175484 
-      89  142.0700970483 3070.3750740931 204306.3529674859  263.4114074261   18.3456373433  281.7570447694  673.2851527089   66.8305446978   57.8900221208   52.8084177133 
-      90  141.8940825299 3070.1552595577 204306.3549033655  263.4150659370   18.3229084328  281.7379743697  673.2380557076   66.8305449088   57.8900223036   52.8084178801 
-      91  141.9603474040 3070.0979256101 204306.3568608879  263.4187731305   18.3314652746  281.7502384052  673.2430123833   66.8305451223   57.8900224885   52.8084180488 
-      92  142.2257467272 3070.1741170513 204306.3588400532  263.4225144876   18.3657365240  281.7882510116  673.2907445632   66.8305453381   57.8900226755   52.8084182193 
-      93  142.5512734406 3070.2900234935 204306.3608408622  263.4263001648   18.4077720766  281.8340722414  673.3513497860   66.8305455562   57.8900228644   52.8084183917 
-      94  142.6487617290 3070.2508281658 204306.3628633148  263.4301422965   18.4203608255  281.8505031221  673.3627864321   66.8305457768   57.8900230555   52.8084185659 
-      95  142.7997358153 3070.2465681156 204306.3649074110  263.4340465006   18.4398562429  281.8739027435  673.3856467375   66.8305459996   57.8900232485   52.8084187421 
-      96  143.4667389211 3070.5895488558 204306.3669731522  263.4380042392   18.5259869441  281.9639911833  673.5194753590   66.8305462249   57.8900234436   52.8084189200 
-      97  143.4616118167 3070.4774890551 204306.3690605390  263.4420072006   18.5253248766  281.9673320772  673.5085306100   66.8305464525   57.8900236408   52.8084190999 
-      98  143.3138195521 3070.2680530999 204306.3711695705  263.4460419232   18.5062403307  281.9522822539  673.4667779706   66.8305466824   57.8900238400   52.8084192816 
-      99  143.5996384267 3070.3502690101 204306.3733002463  263.4501213575   18.5431483749  281.9932697324  673.5182535421   66.8305469148   57.8900240412   52.8084194652 
-     100  143.4332465710 3070.1261458307 204306.3754525657  263.4542352328   18.5216620473  281.9758972802  673.4723054704   66.8305471495   57.8900242445   52.8084196506 
-Loop time of 0.77396 on 1 procs for 100 steps with 1000 atoms
+      76  138.4006889617 3069.1105563660 204306.3297705762  263.3679794432   17.8718034302  281.2397828734  672.6065975977   66.8305421684   57.8900199299   52.8084157147 
+      77  138.5404442761 3069.1182683851 204306.3314251149  263.3710629684   17.8898501576  281.2609131260  672.6287144410   66.8305423489   57.8900200861   52.8084158573 
+      78  138.8911793449 3069.2673604038 204306.3331012898  263.3741701271   17.9351408874  281.3093110144  672.6961274554   66.8305425316   57.8900202444   52.8084160017 
+      79  138.9740932597 3069.2343926248 204306.3347991015  263.3773233601   17.9458476345  281.3231709947  672.7057867031   66.8305427167   57.8900204048   52.8084161480 
+      80  139.4197304629 3069.4447568636 204306.3365185501  263.3805326609   18.0033931609  281.3839258218  672.7933700502   66.8305429042   57.8900205672   52.8084162961 
+      81  140.0251352305 3069.7614239791 204306.3382596380  263.3837812869   18.0815696143  281.4653509011  672.9151792214   66.8305430941   57.8900207316   52.8084164461 
+      82  140.4343345655 3069.9447540285 204306.3400223666  263.3870704597   18.1344098865  281.5214803462  672.9946899248   66.8305432863   57.8900208981   52.8084165980 
+      83  140.8339491089 3070.1205252103 204306.3418067374  263.3904045656   18.1860124661  281.5764170317  673.0720440188   66.8305434808   57.8900210667   52.8084167517 
+      84  141.2138258327 3070.2828678237 204306.3436127514  263.3937910919   18.2350662835  281.6288573754  673.1451894287   66.8305436777   57.8900212372   52.8084169073 
+      85  141.4316065757 3070.3348892447 204306.3454404095  263.3972231992   18.2631885036  281.6604117028  673.1833809261   66.8305438770   57.8900214099   52.8084170648 
+      86  141.6165004814 3070.3639126512 204306.3472897119  263.4006984023   18.2870640172  281.6877624195  673.2144361936   66.8305440787   57.8900215845   52.8084172241 
+      87  141.7511192071 3070.3578486993 204306.3491606587  263.4042216826   18.3044474524  281.7086691350  673.2345732314   66.8305442827   57.8900217612   52.8084173853 
+      88  141.8992247234 3070.3595802006 204306.3510532499  263.4077909549   18.3235724488  281.7313634037  673.2574919246   66.8305444890   57.8900219400   52.8084175484 
+      89  142.0700970483 3070.3750740931 204306.3529674857  263.4114074261   18.3456373433  281.7570447694  673.2851527089   66.8305446978   57.8900221208   52.8084177133 
+      90  141.8940825299 3070.1552595577 204306.3549033653  263.4150659370   18.3229084328  281.7379743697  673.2380557076   66.8305449088   57.8900223036   52.8084178801 
+      91  141.9603474040 3070.0979256101 204306.3568608877  263.4187731305   18.3314652746  281.7502384052  673.2430123833   66.8305451223   57.8900224885   52.8084180488 
+      92  142.2257467272 3070.1741170513 204306.3588400529  263.4225144876   18.3657365240  281.7882510116  673.2907445632   66.8305453381   57.8900226755   52.8084182193 
+      93  142.5512734406 3070.2900234936 204306.3608408618  263.4263001648   18.4077720766  281.8340722414  673.3513497860   66.8305455562   57.8900228644   52.8084183917 
+      94  142.6487617290 3070.2508281658 204306.3628633145  263.4301422965   18.4203608255  281.8505031221  673.3627864321   66.8305457768   57.8900230555   52.8084185659 
+      95  142.7997358153 3070.2465681156 204306.3649074107  263.4340465006   18.4398562429  281.8739027435  673.3856467375   66.8305459996   57.8900232485   52.8084187421 
+      96  143.4667389211 3070.5895488558 204306.3669731518  263.4380042392   18.5259869441  281.9639911833  673.5194753590   66.8305462249   57.8900234436   52.8084189200 
+      97  143.4616118167 3070.4774890551 204306.3690605387  263.4420072006   18.5253248766  281.9673320772  673.5085306100   66.8305464525   57.8900236408   52.8084190999 
+      98  143.3138195521 3070.2680530999 204306.3711695701  263.4460419232   18.5062403307  281.9522822539  673.4667779706   66.8305466824   57.8900238400   52.8084192816 
+      99  143.5996384267 3070.3502690101 204306.3733002460  263.4501213575   18.5431483749  281.9932697324  673.5182535422   66.8305469148   57.8900240412   52.8084194652 
+     100  143.4332465710 3070.1261458307 204306.3754525654  263.4542352328   18.5216620473  281.9758972802  673.4723054704   66.8305471495   57.8900242445   52.8084196506 
+Loop time of 0.363578 on 1 procs for 100 steps with 1000 atoms
 
-Performance: 11.163 ns/day, 2.150 hours/ns, 129.206 timesteps/s
-99.2% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 23.764 ns/day, 1.010 hours/ns, 275.044 timesteps/s
+99.0% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.081886   | 0.081886   | 0.081886   |   0.0 | 10.58
-Neigh   | 0.29547    | 0.29547    | 0.29547    |   0.0 | 38.18
-Comm    | 0.012082   | 0.012082   | 0.012082   |   0.0 |  1.56
-Output  | 0.0047195  | 0.0047195  | 0.0047195  |   0.0 |  0.61
-Modify  | 0.37794    | 0.37794    | 0.37794    |   0.0 | 48.83
-Other   |            | 0.001861   |            |       |  0.24
+Pair    | 0.04388    | 0.04388    | 0.04388    |   0.0 | 12.07
+Neigh   | 0.16374    | 0.16374    | 0.16374    |   0.0 | 45.04
+Comm    | 0.0078104  | 0.0078104  | 0.0078104  |   0.0 |  2.15
+Output  | 0.0017376  | 0.0017376  | 0.0017376  |   0.0 |  0.48
+Modify  | 0.14291    | 0.14291    | 0.14291    |   0.0 | 39.31
+Other   |            | 0.003504   |            |       |  0.96
 
 Nlocal:    1000 ave 1000 max 1000 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

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

@@ -1,6 +1,6 @@
 # Example for running DPD-RX
 
-log             log.dpdrx
+log             log.dpdrx-shardlow
 boundary        p p p
 units           metal  # ev, ps
 atom_style      dpd

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

@@ -0,0 +1,120 @@
+boundary        p p p
+units           metal  # ev, ps
+atom_style      dpd
+atom_modify     map array
+fix             4 all rx kinetics.dpdrx none dense lammps_rk4 1
+
+lattice         hcp 6.6520898 origin 0.0833333333333 0.25 0.25 orient z 1 0 0 orient x 0 1 0 orient y 0 0 1
+Lattice spacing in x,y,z = 11.5218 10.8628 6.65209
+region          box block 0 6.0 0 6.0 0.0 6.0 units lattice
+create_box      2 box
+Created orthogonal box = (0 0 0) to (69.1305 65.1769 39.9125)
+  1 by 1 by 1 MPI processor grid
+region          atoms block 0 6.0 0 6.0 0.0 6.0 units lattice
+create_atoms    1 region atoms
+Created 864 atoms
+
+comm_modify     mode single vel yes
+mass            * 222.12
+
+#Set concentrations
+set             atom * d_rdx 1.00
+  864 settings made for d_rdx
+set             atom * d_h2 0.0
+  864 settings made for d_h2
+set             atom * d_no2 0.0
+  864 settings made for d_no2
+set             atom * d_n2 0.0
+  864 settings made for d_n2
+set             atom * d_hcn 0.0
+  864 settings made for d_hcn
+set             atom * d_no 0.0
+  864 settings made for d_no
+set             atom * d_h2o 0.0
+  864 settings made for d_h2o
+set             atom * d_co 0.0
+  864 settings made for d_co
+set             atom * d_co2 0.0
+  864 settings made for d_co2
+
+#Set the kinetic temperature of the particles
+velocity	all create 2065.0 875661 dist gaussian
+
+#Set the internal temperature of the particles
+set             atom * dpd/theta 2065.00
+  864 settings made for dpd/theta
+
+timestep        0.001
+
+pair_style      hybrid/overlay dpd/fdt/energy 16.00 234324 exp6/rx 16.00
+pair_coeff      * * dpd/fdt/energy 0.0 0.05 10.0 16.00
+pair_coeff      * * exp6/rx params.exp6 1fluid 1fluid 1.0 1.0 16.00
+
+fix             1 all shardlow
+fix             2 all nve
+fix             3 all eos/table/rx linear table.eos 4001 KEYWORD thermo.dpdrx
+
+compute         dpdU all dpd
+compute         dpdUatom all dpd/atom
+compute         crdx all property/atom d_rdx
+
+variable        totEnergy equal pe+c_dpdU[1]+c_dpdU[2]+c_dpdU[3]
+
+thermo          1
+thermo_style    custom step temp press vol pe ke c_dpdU[1] c_dpdU[2] c_dpdU[3] v_totEnergy c_dpdU[4]
+thermo_modify   format float %15.8f flush yes
+
+dump            2 all custom 1 dump.dpdrx id x y z vx vy vz c_dpdUatom[1] c_dpdUatom[2] c_dpdUatom[3] c_dpdUatom[4] c_crdx
+dump_modify     2 sort id
+
+run             10
+Neighbor list info ...
+  2 neighbor list requests
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9 -> bins = 8 8 5
+Memory usage per processor = 6.52436 Mbytes
+Step Temp Press Volume PotEng KinEng c_dpdU[1] c_dpdU[2] c_dpdU[3] v_totEnergy c_dpdU[4] 
+       0   2065.00000000   1368.17463335 179834.51777865      0.00000000    230.35385810   3841.42393279   3841.42393279      0.00000000   7682.84786557   2065.00000000 
+       1   2064.93210437   1368.12964881 179834.51777865      0.00000000    230.34628424   3841.42393279   3841.43150665      0.00000000   7682.85543943   2065.20275230 
+       2   2067.82089565   1370.04362990 179834.51777865     -0.00000000    230.66853326   3841.42393279   3841.10925763      0.00000000   7682.53319042   2065.32453473 
+       3   2070.45225169   1371.78704616 179834.51777865     -0.00000000    230.96206499   3841.42393279   3840.81572590      0.00000000   7682.23965869   2065.45336917 
+       4   2075.00241157   1374.80177416 179834.51777865     -0.00000000    231.46964217   3841.42393279   3840.30814872      0.00000000   7681.73208151   2065.52973333 
+       5   2073.96509212   1374.11449370 179834.51777865     -0.00000000    231.35392762   3841.42393279   3840.42386327      0.00000000   7681.84779605   2065.76011517 
+       6   2074.26516936   1374.31331117 179834.51777865     -0.00000000    231.38740169   3841.42393279   3840.39038920      0.00000000   7681.81432198   2065.95399323 
+       7   2071.41069700   1372.42206822 179834.51777865     -0.00000000    231.06898100   3841.42393279   3840.70880989      0.00000000   7682.13274267   2066.23407076 
+       8   2071.35844957   1372.38745146 179834.51777865     -0.00000000    231.06315272   3841.42393279   3840.71463817      0.00000000   7682.13857095   2066.43766287 
+       9   2071.35676496   1372.38633532 179834.51777865     -0.00000000    231.06296480   3841.42393279   3840.71482609      0.00000000   7682.13875887   2066.64001166 
+      10   2066.53172340   1369.18948328 179834.51777865     -0.00000000    230.52472415   3841.42393279   3841.25306673      0.00000000   7682.67699952   2066.97516855 
+Loop time of 0.289778 on 1 procs for 10 steps with 864 atoms
+
+Performance: 2.982 ns/day, 8.049 hours/ns, 34.509 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    | 0.16405    | 0.16405    | 0.16405    |   0.0 | 56.61
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.00066328 | 0.00066328 | 0.00066328 |   0.0 |  0.23
+Output  | 0.037718   | 0.037718   | 0.037718   |   0.0 | 13.02
+Modify  | 0.087281   | 0.087281   | 0.087281   |   0.0 | 30.12
+Other   |            | 7.057e-05  |            |       |  0.02
+
+Nlocal:    864 ave 864 max 864 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    2700 ave 2700 max 2700 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    55296 ave 55296 max 55296 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 55296
+Ave neighs/atom = 64
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00