added LAST option to dump_modify thresh, more restart info printed out to screen

txt2rst external link fix

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
+Performance: 106050.541 tau/day, 102.286 timesteps/s
-100.0% CPU use with 1 MPI tasks x no OpenMP threads
+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
+Pair    | 0.19421    | 0.19421    | 0.19421    |   0.0 | 19.86
-Bond    | 0.087475   | 0.087475   | 0.087475   |   0.0 |  8.94
+Bond    | 0.08741    | 0.08741    | 0.08741    |   0.0 |  8.94
-Neigh   | 0.44861    | 0.44861    | 0.44861    |   0.0 | 45.84
+Neigh   | 0.45791    | 0.45791    | 0.45791    |   0.0 | 46.84
-Comm    | 0.032932   | 0.032932   | 0.032932   |   0.0 |  3.37
+Comm    | 0.032649   | 0.032649   | 0.032649   |   0.0 |  3.34
-Output  | 0.00010395 | 0.00010395 | 0.00010395 |   0.0 |  0.01
+Output  | 0.00012207 | 0.00012207 | 0.00012207 |   0.0 |  0.01
-Modify  | 0.19413    | 0.19413    | 0.19413    |   0.0 | 19.84
+Modify  | 0.18071    | 0.18071    | 0.18071    |   0.0 | 18.48
-Other   |            | 0.01972    |            |       |  2.02
+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
+Performance: 385133.446 tau/day, 371.464 timesteps/s
-99.6% CPU use with 4 MPI tasks x no OpenMP threads
+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
+Pair    | 0.049383   | 0.049756   | 0.049988   |   0.1 | 18.48
-Bond    | 0.022254   | 0.022942   | 0.023567   |   0.3 |  8.46
+Bond    | 0.022701   | 0.022813   | 0.022872   |   0.0 |  8.47
-Neigh   | 0.11873    | 0.11881    | 0.11887    |   0.0 | 43.81
+Neigh   | 0.11982    | 0.12002    | 0.12018    |   0.0 | 44.58
-Comm    | 0.019066   | 0.021357   | 0.024297   |   1.3 |  7.88
+Comm    | 0.020274   | 0.021077   | 0.022348   |   0.5 |  7.83
-Output  | 5.0068e-05 | 5.5015e-05 | 6.1035e-05 |   0.1 |  0.02
+Output  | 5.3167e-05 | 5.6148e-05 | 6.3181e-05 |   0.1 |  0.02
-Modify  | 0.048737   | 0.050198   | 0.051231   |   0.4 | 18.51
+Modify  | 0.046276   | 0.046809   | 0.047016   |   0.1 | 17.39
-Other   |            | 0.007751   |            |       |  2.86
+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
+Performance: 90277.919 tau/day, 87.074 timesteps/s
-99.8% CPU use with 4 MPI tasks x no OpenMP threads
+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
+Pair    | 0.2203     | 0.22207    | 0.22386    |   0.3 | 19.34
-Bond    | 0.094536   | 0.10196    | 0.10534    |   1.4 |  8.43
+Bond    | 0.094861   | 0.095302   | 0.095988   |   0.1 |  8.30
-Neigh   | 0.52311    | 0.52392    | 0.52519    |   0.1 | 43.34
+Neigh   | 0.52127    | 0.5216     | 0.52189    |   0.0 | 45.42
-Comm    | 0.090161   | 0.10022    | 0.12557    |   4.7 |  8.29
+Comm    | 0.079585   | 0.082159   | 0.084366   |   0.7 |  7.15
-Output  | 0.00012207 | 0.00017327 | 0.00019598 |   0.2 |  0.01
+Output  | 0.00013304 | 0.00015306 | 0.00018501 |   0.2 |  0.01
-Modify  | 0.19662    | 0.20262    | 0.20672    |   0.8 | 16.76
+Modify  | 0.18351    | 0.18419    | 0.1856     |   0.2 | 16.04
-Other   |            | 0.04694    |            |       |  3.88
+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
+Memory usage per processor = 16.0904 Mbytes
-Step Atoms KinEng 1 Volume 
+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
+Performance: 1617.451 tau/day, 187.205 timesteps/s
-100.1% CPU use with 1 MPI tasks x no OpenMP threads
+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
+Pair    | 0.33346    | 0.33346    | 0.33346    |   0.0 | 62.43
-Neigh   | 0.040353   | 0.040353   | 0.040353   |   0.0 |  7.33
+Neigh   | 0.043902   | 0.043902   | 0.043902   |   0.0 |  8.22
-Comm    | 0.018023   | 0.018023   | 0.018023   |   0.0 |  3.27
+Comm    | 0.018391   | 0.018391   | 0.018391   |   0.0 |  3.44
-Output  | 0.00020385 | 0.00020385 | 0.00020385 |   0.0 |  0.04
+Output  | 0.00022411 | 0.00022411 | 0.00022411 |   0.0 |  0.04
-Modify  | 0.13155    | 0.13155    | 0.13155    |   0.0 | 23.90
+Modify  | 0.11666    | 0.11666    | 0.11666    |   0.0 | 21.84
-Other   |            | 0.02186    |            |       |  3.97
+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
+Memory usage per processor = 7.04927 Mbytes
-Step Atoms KinEng 1 Volume 
+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
+Performance: 5028.653 tau/day, 582.020 timesteps/s
-99.3% CPU use with 4 MPI tasks x no OpenMP threads
+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
+Pair    | 0.093691   | 0.096898   | 0.10005    |   0.8 | 56.40
-Neigh   | 0.010041   | 0.0101     | 0.010178   |   0.1 |  7.69
+Neigh   | 0.011976   | 0.012059   | 0.012146   |   0.1 |  7.02
-Comm    | 0.012347   | 0.012895   | 0.013444   |   0.5 |  9.81
+Comm    | 0.016384   | 0.017418   | 0.018465   |   0.8 | 10.14
-Output  | 6.3896e-05 | 0.00010294 | 0.00014091 |   0.3 |  0.08
+Output  | 7.7963e-05 | 0.00010747 | 0.00013304 |   0.2 |  0.06
-Modify  | 0.031802   | 0.032348   | 0.032897   |   0.3 | 24.62
+Modify  | 0.031744   | 0.031943   | 0.032167   |   0.1 | 18.59
-Other   |            | 0.008965   |            |       |  6.82
+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
+Memory usage per processor = 16.1265 Mbytes
-Step Atoms KinEng 1 Volume 
+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
+Performance: 1038.006 tau/day, 120.140 timesteps/s
-99.7% CPU use with 4 MPI tasks x no OpenMP threads
+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
+Pair    | 0.5178     | 0.52208    | 0.52793    |   0.5 | 62.72
-Neigh   | 0.042597   | 0.043726   | 0.045801   |   0.6 |  4.82
+Neigh   | 0.047003   | 0.047113   | 0.047224   |   0.0 |  5.66
-Comm    | 0.063027   | 0.064657   | 0.067367   |   0.7 |  7.13
+Comm    | 0.05233    | 0.052988   | 0.053722   |   0.2 |  6.37
-Output  | 0.00024891 | 0.00059718 | 0.00086498 |   1.0 |  0.07
+Output  | 0.00024986 | 0.00032717 | 0.00036693 |   0.3 |  0.04
-Modify  | 0.16508    | 0.17656    | 0.1925     |   2.6 | 19.47
+Modify  | 0.15517    | 0.15627    | 0.15808    |   0.3 | 18.77
-Other   |            | 0.09043    |            |       |  9.97
+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
+Pair    | 5.2743     | 5.2743     | 5.2743     |   0.0 | 88.42
-Neigh   | 0.58212    | 0.58212    | 0.58212    |   0.0 |  9.86
+Neigh   | 0.59212    | 0.59212    | 0.59212    |   0.0 |  9.93
-Comm    | 0.030392   | 0.030392   | 0.030392   |   0.0 |  0.52
+Comm    | 0.030399   | 0.030399   | 0.030399   |   0.0 |  0.51
-Output  | 0.00023389 | 0.00023389 | 0.00023389 |   0.0 |  0.00
+Output  | 0.00026202 | 0.00026202 | 0.00026202 |   0.0 |  0.00
-Modify  | 0.060871   | 0.060871   | 0.060871   |   0.0 |  1.03
+Modify  | 0.050487   | 0.050487   | 0.050487   |   0.0 |  0.85
-Other   |            | 0.01527    |            |       |  0.26
+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
+Pair    | 1.408      | 1.4175     | 1.4341     |   0.9 | 86.14
-Neigh   | 0.15123    | 0.15232    | 0.15374    |   0.2 |  9.64
+Neigh   | 0.15512    | 0.15722    | 0.16112    |   0.6 |  9.55
-Comm    | 0.033429   | 0.041275   | 0.047066   |   2.7 |  2.61
+Comm    | 0.029105   | 0.049986   | 0.061822   |   5.8 |  3.04
-Output  | 0.00011301 | 0.0001573  | 0.000211   |   0.3 |  0.01
+Output  | 0.00010991 | 0.00011539 | 0.00012302 |   0.0 |  0.01
-Modify  | 0.014694   | 0.015085   | 0.015421   |   0.2 |  0.95
+Modify  | 0.013383   | 0.013573   | 0.013883   |   0.2 |  0.82
-Other   |            | 0.005342   |            |       |  0.34
+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
+Pair    | 5.6676     | 5.7011     | 5.7469     |   1.3 | 86.36
-Neigh   | 0.65287    | 0.658      | 0.66374    |   0.5 | 10.17
+Neigh   | 0.66423    | 0.67119    | 0.68082    |   0.7 | 10.17
-Comm    | 0.075706   | 0.11015    | 0.13655    |   7.2 |  1.70
+Comm    | 0.079367   | 0.13668    | 0.1791     |  10.5 |  2.07
-Output  | 0.00026488 | 0.00028312 | 0.00029302 |   0.1 |  0.00
+Output  | 0.00026989 | 0.00028622 | 0.00031209 |   0.1 |  0.00
-Modify  | 0.069607   | 0.072407   | 0.074555   |   0.7 |  1.12
+Modify  | 0.060046   | 0.062203   | 0.065009   |   0.9 |  0.94
-Other   |            | 0.02794    |            |       |  0.43
+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
+Pair    | 1.9328     | 1.9328     | 1.9328     |   0.0 | 85.45
-Neigh   | 0.2442     | 0.2442     | 0.2442     |   0.0 | 10.79
+Neigh   | 0.2558     | 0.2558     | 0.2558     |   0.0 | 11.31
-Comm    | 0.024158   | 0.024158   | 0.024158   |   0.0 |  1.07
+Comm    | 0.024061   | 0.024061   | 0.024061   |   0.0 |  1.06
-Output  | 0.00011611 | 0.00011611 | 0.00011611 |   0.0 |  0.01
+Output  | 0.00012612 | 0.00012612 | 0.00012612 |   0.0 |  0.01
-Modify  | 0.053222   | 0.053222   | 0.053222   |   0.0 |  2.35
+Modify  | 0.040887   | 0.040887   | 0.040887   |   0.0 |  1.81
-Other   |            | 0.007258   |            |       |  0.32
+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
+Performance: 67929.172 tau/day, 157.243 timesteps/s
-99.7% CPU use with 4 MPI tasks x no OpenMP threads
+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
+Pair    | 0.51335    | 0.51822    | 0.52569    |   0.7 | 81.49
-Neigh   | 0.061131   | 0.063685   | 0.065433   |   0.6 |  9.94
+Neigh   | 0.063695   | 0.064309   | 0.065397   |   0.3 | 10.11
-Comm    | 0.02457    | 0.042349   | 0.069598   |   8.1 |  6.61
+Comm    | 0.027525   | 0.03629    | 0.041959   |   3.1 |  5.71
-Output  | 5.9843e-05 | 6.3181e-05 | 6.6996e-05 |   0.0 |  0.01
+Output  | 6.3896e-05 | 6.6698e-05 | 7.081e-05  |   0.0 |  0.01
-Modify  | 0.012961   | 0.013863   | 0.014491   |   0.5 |  2.16
+Modify  | 0.012472   | 0.01254    | 0.012618   |   0.1 |  1.97
-Other   |            | 0.003448   |            |       |  0.54
+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
+Pair    | 2.0583     | 2.0988     | 2.1594     |   2.6 | 82.06
-Neigh   | 0.23982    | 0.24551    | 0.25233    |   1.0 |  9.52
+Neigh   | 0.24411    | 0.24838    | 0.25585    |   0.9 |  9.71
-Comm    | 0.067088   | 0.13887    | 0.22681    |  15.7 |  5.38
+Comm    | 0.066397   | 0.13872    | 0.1863     |  11.9 |  5.42
-Output  | 0.00013185 | 0.00021666 | 0.00027108 |   0.4 |  0.01
+Output  | 0.00012994 | 0.00021023 | 0.00025702 |   0.3 |  0.01
-Modify  | 0.060348   | 0.071269   | 0.077063   |   2.5 |  2.76
+Modify  | 0.055533   | 0.058343   | 0.061791   |   1.2 |  2.28
-Other   |            | 0.01403    |            |       |  0.54
+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) ----------------
+---------------- Step       50 ----- CPU =     17.2007 (sec) ----------------
-TotEng   =    -25330.0828 KinEng   =     21501.0029 Temp     =       299.8230 
+TotEng   =    -25330.0321 KinEng   =     21501.0036 Temp     =       299.8230 
-PotEng   =    -46831.0857 E_bond   =      2471.7004 E_angle  =     10836.4975 
+PotEng   =    -46831.0357 E_bond   =      2471.7033 E_angle  =     10836.5108 
-E_dihed  =      5239.6299 E_impro  =       227.1218 E_vdwl   =     -1993.2754 
+E_dihed  =      5239.6316 E_impro  =       227.1219 E_vdwl   =     -1993.2763 
-E_coul   =    206797.6331 E_long   =   -270410.3930 Press    =       237.6701 
+E_coul   =    206797.6655 E_long   =   -270410.3927 Press    =       237.6866 
-Volume   =    308031.5639 
+Volume   =    308031.5640 
----------------- Step      100 ----- CPU =     35.9089 (sec) ----------------
+---------------- Step      100 ----- CPU =     35.0315 (sec) ----------------
-TotEng   =    -25290.7593 KinEng   =     21592.0117 Temp     =       301.0920 
+TotEng   =    -25290.7387 KinEng   =     21591.9096 Temp     =       301.0906 
-PotEng   =    -46882.7709 E_bond   =      2567.9807 E_angle  =     10781.9408 
+PotEng   =    -46882.6484 E_bond   =      2567.9789 E_angle  =     10781.9556 
-E_dihed  =      5198.7432 E_impro  =       216.7834 E_vdwl   =     -1902.4783 
+E_dihed  =      5198.7493 E_impro  =       216.7863 E_vdwl   =     -1902.6458 
-E_coul   =    206659.2326 E_long   =   -270404.9733 Press    =         6.9960 
+E_coul   =    206659.5006 E_long   =   -270404.9733 Press    =         6.7898 
-Volume   =    308133.9888 
+Volume   =    308133.9933 
-Loop time of 35.9089 on 1 procs for 100 steps with 32000 atoms
+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
+Pair    | 25.021     | 25.021     | 25.021     |   0.0 | 71.42
-Bond    | 1.2771     | 1.2771     | 1.2771     |   0.0 |  3.56
+Bond    | 1.2834     | 1.2834     | 1.2834     |   0.0 |  3.66
-Kspace  | 3.2094     | 3.2094     | 3.2094     |   0.0 |  8.94
+Kspace  | 3.2116     | 3.2116     | 3.2116     |   0.0 |  9.17
-Neigh   | 4.4538     | 4.4538     | 4.4538     |   0.0 | 12.40
+Neigh   | 4.2767     | 4.2767     | 4.2767     |   0.0 | 12.21
-Comm    | 0.068507   | 0.068507   | 0.068507   |   0.0 |  0.19
+Comm    | 0.069283   | 0.069283   | 0.069283   |   0.0 |  0.20
-Output  | 0.00025916 | 0.00025916 | 0.00025916 |   0.0 |  0.00
+Output  | 0.00028205 | 0.00028205 | 0.00028205 |   0.0 |  0.00
-Modify  | 1.1417     | 1.1417     | 1.1417     |   0.0 |  3.18
+Modify  | 1.14       | 1.14       | 1.14       |   0.0 |  3.25
-Other   |            | 0.027      |            |       |  0.08
+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) ----------------
+---------------- Step       50 ----- CPU =      4.6056 (sec) ----------------
-TotEng   =    -25330.0828 KinEng   =     21501.0029 Temp     =       299.8230 
+TotEng   =    -25330.0321 KinEng   =     21501.0036 Temp     =       299.8230 
-PotEng   =    -46831.0857 E_bond   =      2471.7004 E_angle  =     10836.4975 
+PotEng   =    -46831.0357 E_bond   =      2471.7033 E_angle  =     10836.5108 
-E_dihed  =      5239.6299 E_impro  =       227.1218 E_vdwl   =     -1993.2754 
+E_dihed  =      5239.6316 E_impro  =       227.1219 E_vdwl   =     -1993.2763 
-E_coul   =    206797.6331 E_long   =   -270410.3930 Press    =       237.6701 
+E_coul   =    206797.6655 E_long   =   -270410.3927 Press    =       237.6866 
-Volume   =    308031.5639 
+Volume   =    308031.5640 
----------------- Step      100 ----- CPU =      9.6332 (sec) ----------------
+---------------- Step      100 ----- CPU =      9.3910 (sec) ----------------
-TotEng   =    -25290.7591 KinEng   =     21592.0117 Temp     =       301.0920 
+TotEng   =    -25290.7386 KinEng   =     21591.9096 Temp     =       301.0906 
-PotEng   =    -46882.7708 E_bond   =      2567.9807 E_angle  =     10781.9408 
+PotEng   =    -46882.6482 E_bond   =      2567.9789 E_angle  =     10781.9556 
-E_dihed  =      5198.7432 E_impro  =       216.7834 E_vdwl   =     -1902.4783 
+E_dihed  =      5198.7493 E_impro  =       216.7863 E_vdwl   =     -1902.6458 
-E_coul   =    206659.2327 E_long   =   -270404.9733 Press    =         6.9960 
+E_coul   =    206659.5007 E_long   =   -270404.9733 Press    =         6.7898 
-Volume   =    308133.9888 
+Volume   =    308133.9933 
-Loop time of 9.63322 on 4 procs for 100 steps with 32000 atoms
+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
+Performance: 1.840 ns/day, 13.043 hours/ns, 10.648 timesteps/s
-99.9% CPU use with 4 MPI tasks x no OpenMP threads
+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
+Pair    | 6.2189     | 6.3266     | 6.6072     |   6.5 | 67.37
-Bond    | 0.30755    | 0.32435    | 0.35704    |   3.4 |  3.37
+Bond    | 0.30793    | 0.32122    | 0.3414     |   2.4 |  3.42
-Kspace  | 0.92248    | 1.0782     | 1.2597     |  13.0 | 11.19
+Kspace  | 0.87994    | 1.1644     | 1.2855     |  15.3 | 12.40
-Neigh   | 1.1669     | 1.1672     | 1.1675     |   0.0 | 12.12
+Neigh   | 1.1358     | 1.136      | 1.1362     |   0.0 | 12.10
-Comm    | 0.094674   | 0.098065   | 0.10543    |   1.4 |  1.02
+Comm    | 0.08292    | 0.084935   | 0.087077   |   0.5 |  0.90
-Output  | 0.00015521 | 0.00016224 | 0.00018215 |   0.1 |  0.00
+Output  | 0.00015712 | 0.00016558 | 0.00018501 |   0.1 |  0.00
-Modify  | 0.32982    | 0.34654    | 0.35365    |   1.6 |  3.60
+Modify  | 0.33717    | 0.34246    | 0.34794    |   0.7 |  3.65
-Other   |            | 0.01943    |            |       |  0.20
+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) ----------------
+---------------- Step       50 ----- CPU =     18.1689 (sec) ----------------
-TotEng   =   -101320.2677 KinEng   =     86003.4837 Temp     =       299.8118 
+TotEng   =   -101320.0211 KinEng   =     86003.4933 Temp     =       299.8118 
-PotEng   =   -187323.7514 E_bond   =      9887.1072 E_angle  =     43346.7922 
+PotEng   =   -187323.5144 E_bond   =      9887.1189 E_angle  =     43346.8448 
-E_dihed  =     20958.7032 E_impro  =       908.4715 E_vdwl   =     -7973.4457 
+E_dihed  =     20958.7108 E_impro  =       908.4721 E_vdwl   =     -7973.4486 
-E_coul   =    826141.3831 E_long   =  -1080592.7629 Press    =       238.0161 
+E_coul   =    826141.5493 E_long   =  -1080592.7617 Press    =       238.0404 
-Volume   =   1232126.1855 
+Volume   =   1232126.1814 
----------------- Step      100 ----- CPU =     38.3684 (sec) ----------------
+---------------- Step      100 ----- CPU =     37.2027 (sec) ----------------
-TotEng   =   -101158.1849 KinEng   =     86355.6149 Temp     =       301.0393 
+TotEng   =   -101157.9546 KinEng   =     86355.7413 Temp     =       301.0398 
-PotEng   =   -187513.7998 E_bond   =     10272.0693 E_angle  =     43128.6454 
+PotEng   =   -187513.6959 E_bond   =     10272.0456 E_angle  =     43128.7018 
-E_dihed  =     20793.9759 E_impro  =       867.0826 E_vdwl   =     -7586.7186 
+E_dihed  =     20794.0107 E_impro  =       867.0928 E_vdwl   =     -7587.2409 
-E_coul   =    825583.7122 E_long   =  -1080572.5667 Press    =        15.2151 
+E_coul   =    825584.2416 E_long   =  -1080572.5474 Press    =        15.1729 
-Volume   =   1232535.8423 
+Volume   =   1232535.8440 
-Loop time of 38.3684 on 4 procs for 100 steps with 128000 atoms
+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
+Pair    | 25.431     | 25.738     | 25.984     |   4.0 | 69.18
-Bond    | 1.298      | 1.3125     | 1.3277     |   1.0 |  3.42
+Bond    | 1.2966     | 1.3131     | 1.3226     |   0.9 |  3.53
-Kspace  | 3.7099     | 4.0992     | 4.4422     |  13.3 | 10.68
+Kspace  | 3.7563     | 4.0123     | 4.3127     |  10.0 | 10.79
-Neigh   | 4.6137     | 4.6144     | 4.615      |   0.0 | 12.03
+Neigh   | 4.3778     | 4.378      | 4.3782     |   0.0 | 11.77
-Comm    | 0.21398    | 0.21992    | 0.22886    |   1.2 |  0.57
+Comm    | 0.1903     | 0.19549    | 0.20485    |   1.3 |  0.53
-Output  | 0.00030518 | 0.00031543 | 0.00033307 |   0.1 |  0.00
+Output  | 0.00031805 | 0.00037521 | 0.00039601 |   0.2 |  0.00
-Modify  | 1.5066     | 1.5232     | 1.5388     |   1.0 |  3.97
+Modify  | 1.4861     | 1.5051     | 1.5122     |   0.9 |  4.05
-Other   |            | 0.06051    |            |       |  0.16
+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/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="5 Oct 2016 version">
+<META NAME="docnumber" CONTENT="11 Oct 2016 version">
 <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
 <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation.  This software and manual is distributed under the GNU General Public License.">
 </HEAD>
@@ -21,7 +21,7 @@
 <H1></H1>
 
 LAMMPS Documentation :c,h3
-5 Oct 2016 version :c,h4
+11 Oct 2016 version :c,h4
 
 Version info: :h4
 

doc/src/Section_commands.txt

@@ -599,6 +599,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "viscous"_fix_viscous.html,
 "wall/colloid"_fix_wall.html,
 "wall/gran"_fix_wall_gran.html,
+"wall/gran/region"_fix_wall_gran_region.html,
 "wall/harmonic"_fix_wall.html,
 "wall/lj1043"_fix_wall.html,
 "wall/lj126"_fix_wall.html,

doc/src/Section_example.txt

@@ -54,30 +54,30 @@ accelerate: run with various acceleration options (OpenMP, GPU, Phi)
 balance:  dynamic load balancing, 2d system
 body:     body particles, 2d system
 colloid:  big colloid particles in a small particle solvent, 2d system
-comb:	  models using the COMB potential
+comb:     models using the COMB potential
 coreshell: core/shell model using CORESHELL package
-crack:	  crack propagation in a 2d solid
+crack:    crack propagation in a 2d solid
 deposit:  deposit atoms and molecules on a surface
 dipole:   point dipolar particles, 2d system
 dreiding: methanol via Dreiding FF
 eim:      NaCl using the EIM potential
 ellipse:  ellipsoidal particles in spherical solvent, 2d system
-flow:	  Couette and Poiseuille flow in a 2d channel
+flow:     Couette and Poiseuille flow in a 2d channel
 friction: frictional contact of spherical asperities between 2d surfaces
 hugoniostat: Hugoniostat shock dynamics
-indent:	  spherical indenter into a 2d solid
+indent:   spherical indenter into a 2d solid
 kim:      use of potentials in Knowledge Base for Interatomic Models (KIM)
-meam:	  MEAM test for SiC and shear (same as shear examples)
+meam:     MEAM test for SiC and shear (same as shear examples)
-melt:	  rapid melt of 3d LJ system
+melt:     rapid melt of 3d LJ system
 micelle:  self-assembly of small lipid-like molecules into 2d bilayers
-min:	  energy minimization of 2d LJ melt
+min:      energy minimization of 2d LJ melt
-msst:	  MSST shock dynamics
+msst:     MSST shock dynamics
 nb3b:     use of nonbonded 3-body harmonic pair style
-neb:	  nudged elastic band (NEB) calculation for barrier finding
+neb:      nudged elastic band (NEB) calculation for barrier finding
-nemd:	  non-equilibrium MD of 2d sheared system
+nemd:     non-equilibrium MD of 2d sheared system
 obstacle: flow around two voids in a 2d channel
 peptide:  dynamics of a small solvated peptide chain (5-mer)
-peri:	  Peridynamic model of cylinder impacted by indenter
+peri:     Peridynamic model of cylinder impacted by indenter
 pour:     pouring of granular particles into a 3d box, then chute flow
 prd:      parallel replica dynamics of vacancy diffusion in bulk Si
 python:   using embedded Python in a LAMMPS input script

doc/src/Section_history.txt

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

doc/src/Section_howto.txt

@@ -68,7 +68,7 @@ Look at the {in.chain} input script provided in the {bench} directory
 of the LAMMPS distribution to see the original script that these 2
 scripts are based on.  If that script had the line
 
-restart	        50 tmp.restart :pre
+restart         50 tmp.restart :pre
 
 added to it, it would produce 2 binary restart files (tmp.restart.50
 and tmp.restart.100) as it ran.
@@ -76,17 +76,17 @@ and tmp.restart.100) as it ran.
 This script could be used to read the 1st restart file and re-run the
 last 50 timesteps:
 
-read_restart	tmp.restart.50 :pre
+read_restart    tmp.restart.50 :pre
 
-neighbor	0.4 bin
+neighbor        0.4 bin
-neigh_modify	every 1 delay 1 :pre
+neigh_modify    every 1 delay 1 :pre
 
-fix		1 all nve
+fix             1 all nve
-fix		2 all langevin 1.0 1.0 10.0 904297 :pre
+fix             2 all langevin 1.0 1.0 10.0 904297 :pre
 
-timestep	0.012 :pre
+timestep        0.012 :pre
 
-run		50 :pre
+run             50 :pre
 
 Note that the following commands do not need to be repeated because
 their settings are included in the restart file: {units, atom_style,
@@ -107,25 +107,25 @@ lmp_g++ -r tmp.restart.50 tmp.restart.data :pre
 
 Then, this script could be used to re-run the last 50 steps:
 
-units		lj
+units           lj
-atom_style	bond
+atom_style      bond
-pair_style	lj/cut 1.12
+pair_style      lj/cut 1.12
-pair_modify	shift yes
+pair_modify     shift yes
-bond_style	fene
+bond_style      fene
 special_bonds   0.0 1.0 1.0 :pre
 
-read_data	tmp.restart.data :pre
+read_data       tmp.restart.data :pre
 
-neighbor	0.4 bin
+neighbor        0.4 bin
-neigh_modify	every 1 delay 1 :pre
+neigh_modify    every 1 delay 1 :pre
 
-fix		1 all nve
+fix             1 all nve
-fix		2 all langevin 1.0 1.0 10.0 904297 :pre
+fix             2 all langevin 1.0 1.0 10.0 904297 :pre
 
-timestep	0.012 :pre
+timestep        0.012 :pre
 
-reset_timestep	50
+reset_timestep  50
-run		50 :pre
+run             50 :pre
 
 Note that nearly all the settings specified in the original {in.chain}
 script must be repeated, except the {pair_coeff} and {bond_coeff}
@@ -2092,11 +2092,11 @@ lattice      fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
 region       box block 0 4 0 4 0 4
 create_box   1 box
 create_atoms 1 box
-mass	     1 39.948
+mass         1 39.948
 pair_style   lj/cut 13.0
 pair_coeff   * * 0.2381 3.405
 timestep     $\{dt\}
-thermo	     $d :pre
+thermo       $d :pre
 
 # equilibration and thermalization :pre
 

doc/src/Section_python.txt

@@ -552,32 +552,32 @@ lmp.command(cmd)         # invoke a single LAMMPS command, cmd = "run 100" :pre
 
 xlo = lmp.extract_global(name,type)  # extract a global quantity
                                      # name = "boxxlo", "nlocal", etc
-				     # type = 0 = int
+                                     # type = 0 = int
-				     #        1 = double :pre
+                                     #        1 = double :pre
 
 coords = lmp.extract_atom(name,type)      # extract a per-atom quantity
                                           # name = "x", "type", etc
-				          # type = 0 = vector of ints
+                                          # type = 0 = vector of ints
-				          #        1 = array of ints
+                                          #        1 = array of ints
-				          #        2 = vector of doubles
+                                          #        2 = vector of doubles
-				          #        3 = array of doubles :pre
+                                          #        3 = array of doubles :pre
 
 eng = lmp.extract_compute(id,style,type)  # extract value(s) from a compute
 v3 = lmp.extract_fix(id,style,type,i,j)   # extract value(s) from a fix
                                           # id = ID of compute or fix
-					  # style = 0 = global data
+                                          # style = 0 = global data
-					  #	    1 = per-atom data
+                                          #         1 = per-atom data
-					  #         2 = local data
+                                          #         2 = local data
-					  # type = 0 = scalar
+                                          # type = 0 = scalar
-					  #	   1 = vector
+                                          #        1 = vector
-					  #        2 = array
+                                          #        2 = array
-					  # i,j = indices of value in global vector or array :pre
+                                          # i,j = indices of value in global vector or array :pre
 
 var = lmp.extract_variable(name,group,flag)  # extract value(s) from a variable
-	                                     # name = name of variable
+                                             # name = name of variable
-					     # group = group ID (ignored for equal-style variables)
+                                             # group = group ID (ignored for equal-style variables)
-					     # flag = 0 = equal-style variable
+                                             # flag = 0 = equal-style variable
-					     #        1 = atom-style variable :pre
+                                             #        1 = atom-style variable :pre
 
 flag = lmp.set_variable(name,value)       # set existing named string-style variable to value, flag = 0 if successful
 natoms = lmp.get_natoms()                 # total # of atoms as int

doc/src/atom_style.txt

@@ -14,7 +14,7 @@ atom_style style args :pre
 
 style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \
         {dpd} or {electron} or {ellipsoid} or {full} or {line} or {meso} or \
-	{molecular} or {peri} or {smd} or {sphere} or {tri} or \
+        {molecular} or {peri} or {smd} or {sphere} or {tri} or \
         {template} or {hybrid} :ulb,l
   args = none for any style except the following
   {body} args = bstyle bstyle-args

doc/src/comm_modify.txt

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

doc/src/compute_heat_flux.txt

@@ -152,11 +152,11 @@ lattice      fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
 region       box block 0 4 0 4 0 4
 create_box   1 box
 create_atoms 1 box
-mass	     1 39.948
+mass         1 39.948
 pair_style   lj/cut 13.0
 pair_coeff   * * 0.2381 3.405
 timestep     $\{dt\}
-thermo	     $d :pre
+thermo       $d :pre
 
 # equilibration and thermalization :pre
 

doc/src/compute_pe_atom.txt

@@ -52,7 +52,7 @@ The KSpace contribution is calculated using the method in
 "(Heyes)"_#Heyes for the Ewald method and a related method for PPPM,
 as specified by the "kspace_style pppm"_kspace_style.html command.
 For PPPM, the calcluation requires 1 extra FFT each timestep that
-per-atom energy is calculated.  Thie "document"_PDF/kspace.pdf
+per-atom energy is calculated.  This "document"_PDF/kspace.pdf
 describes how the long-range per-atom energy calculation is performed.
 
 Various fixes can contribute to the per-atom potential energy of the
@@ -68,9 +68,9 @@ As an example of per-atom potential energy compared to total potential
 energy, these lines in an input script should yield the same result
 in the last 2 columns of thermo output:
 
-compute		peratom all pe/atom
+compute        peratom all pe/atom
-compute		pe all reduce sum c_peratom
+compute        pe all reduce sum c_peratom
-thermo_style	custom step temp etotal press pe c_pe :pre
+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

doc/src/compute_property_atom.txt

@@ -16,20 +16,20 @@ ID, group-ID are documented in "compute"_compute.html command :ulb,l
 property/atom = style name of this compute command :l
 input = one or more atom attributes :l
   possible attributes = id, mol, proc, type, mass,
- 	                x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
+                        x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
-		        vx, vy, vz, fx, fy, fz,
+                        vx, vy, vz, fx, fy, fz,
                         q, mux, muy, muz, mu,
                         radius, diameter, omegax, omegay, omegaz,
-			angmomx, angmomy, angmomz,
+                        angmomx, angmomy, angmomz,
-			shapex,shapey, shapez,
+                        shapex,shapey, shapez,
-		        quatw, quati, quatj, quatk, tqx, tqy, tqz,
+                        quatw, quati, quatj, quatk, tqx, tqy, tqz,
-			end1x, end1y, end1z, end2x, end2y, end2z,
+                        end1x, end1y, end1z, end2x, end2y, end2z,
-			corner1x, corner1y, corner1z,
+                        corner1x, corner1y, corner1z,
-			corner2x, corner2y, corner2z,
+                        corner2x, corner2y, corner2z,
-			corner3x, corner3y, corner3z,
+                        corner3x, corner3y, corner3z,
-			nbonds,
+                        nbonds,
                         vfrac, s0,
-			spin, eradius, ervel, erforce,
+                        spin, eradius, ervel, erforce,
                         rho, drho, e, de, cv,
                         i_name, d_name :pre
       id = atom ID

doc/src/compute_property_local.txt

@@ -15,12 +15,12 @@ compute ID group-ID property/local attribute1 attribute2 ... keyword args ... :p
 ID, group-ID are documented in "compute"_compute.html command :ulb,l
 property/local = style name of this compute command :l
 one or more attributes may be appended :l
-  possible attributes =  natom1 natom2 ntype1 ntype2
+  possible attributes = natom1 natom2 ntype1 ntype2
-		         patom1 patom2 ptype1 ptype2
+                        patom1 patom2 ptype1 ptype2
-                         batom1 batom2 btype
+                        batom1 batom2 btype
-                         aatom1 aatom2 aatom3 atype
+                        aatom1 aatom2 aatom3 atype
-                         datom1 datom2 datom3 dtype
+                        datom1 datom2 datom3 dtype
-                         iatom1 iatom2 iatom3 itype :pre
+                        iatom1 iatom2 iatom3 itype :pre
 
      natom1, natom2 = IDs of 2 atoms in each pair (within neighbor cutoff)
      ntype1, ntype2 = type of 2 atoms in each pair (within neighbor cutoff)
@@ -129,8 +129,6 @@ The attributes that start with "a", "d", "i", refer to similar values
 for "angles"_angle_style.html, "dihedrals"_dihedral_style.html, and
 "impropers"_improper_style.html.
 
-The optional {cutoff} keyword
-
 [Output info:]
 
 This compute calculates a local vector or local array depending on the

doc/src/compute_reduce.txt

@@ -155,8 +155,8 @@ Thus, for example, if you wish to use this compute to find the bond
 with maximum stretch, you can do it as follows:
 
 compute 1 all property/local batom1 batom2
-compute	2 all bond/local dist
+compute 2 all bond/local dist
-compute	3 all reduce max c_1\[1\] c_1\[2\] c_2 replace 1 3 replace 2 3
+compute 3 all reduce max c_1\[1\] c_1\[2\] c_2 replace 1 3 replace 2 3
 thermo_style custom step temp c_3\[1\] c_3\[2\] c_3\[3\] :pre
 
 The first two input values in the compute reduce command are vectors

doc/src/compute_rigid_local.txt

@@ -17,11 +17,11 @@ rigid/local = style name of this compute command :l
 rigidID = ID of fix rigid/small command or one of its variants :l
 input = one or more rigid body attributes :l
   possible attributes = id, mol, mass,
- 	                x, y, z, xu, yu, zu, ix, iy, iz
+                        x, y, z, xu, yu, zu, ix, iy, iz
-		        vx, vy, vz, fx, fy, fz, 
+                        vx, vy, vz, fx, fy, fz,
                         omegax, omegay, omegaz,
-			angmomx, angmomy, angmomz,
+                        angmomx, angmomy, angmomz,
-		        quatw, quati, quatj, quatk, 
+                        quatw, quati, quatj, quatk,
                         tqx, tqy, tqz,
                         inertiax, inertiay, inertiaz
       id = atom ID of atom within body which owns body properties

doc/src/compute_stress_atom.txt

@@ -128,10 +128,10 @@ d = dimension and V is the volume of the system, the result should be
 These lines in an input script for a 3d system should yield that
 result.  I.e. the last 2 columns of thermo output will be the same:
 
-compute		peratom all stress/atom NULL
+compute        peratom all stress/atom NULL
-compute		p all reduce sum c_peratom\[1\] c_peratom\[2\] c_peratom\[3\]
+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)
+variable       press equal -(c_p\[1\]+c_p\[2\]+c_p\[3\])/(3*vol)
-thermo_style	custom step temp etotal press v_press :pre
+thermo_style   custom step temp etotal press v_press :pre
 
 [Output info:]
 

doc/src/create_atoms.txt

@@ -218,14 +218,14 @@ larger version.
 
 variable        x equal 100
 variable        y equal 25
-lattice		hex 0.8442
+lattice         hex 0.8442
-region		box block 0 $x 0 $y -0.5 0.5
+region          box block 0 $x 0 $y -0.5 0.5
-create_box	1 box :pre
+create_box      1 box :pre
 
 variable        xx equal 0.0
 variable        yy equal 0.0
 variable        v equal "(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) > 0.0"
-create_atoms	1 box var v set x xx set y yy :pre
+create_atoms    1 box var v set x xx set y yy :pre
 
 :c,image(JPG/sinusoid_small.jpg,JPG/sinusoid.jpg)
 

doc/src/dump.txt

@@ -55,13 +55,13 @@ args = list of arguments for a particular style :l
 
   {custom} or {custom/gz} or {custom/mpiio} args = list of atom attributes
     possible attributes = id, mol, proc, procp1, type, element, mass,
-			  x, y, z, xs, ys, zs, xu, yu, zu, 
+                          x, y, z, xs, ys, zs, xu, yu, zu,
-			  xsu, ysu, zsu, ix, iy, iz,
+                          xsu, ysu, zsu, ix, iy, iz,
-			  vx, vy, vz, fx, fy, fz,
+                          vx, vy, vz, fx, fy, fz,
                           q, mux, muy, muz, mu,
                           radius, diameter, omegax, omegay, omegaz,
-			  angmomx, angmomy, angmomz, tqx, tqy, tqz,
+                          angmomx, angmomy, angmomz, tqx, tqy, tqz,
-			  c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
+                          c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
 
       id = atom ID
       mol = molecule ID

doc/src/dump_custom_vtk.txt

@@ -20,14 +20,14 @@ file = name of file to write dump info to :l
 args = list of arguments for a particular style :l
   {custom/vtk} args = list of atom attributes
     possible attributes = id, mol, proc, procp1, type, element, mass,
-			  x, y, z, xs, ys, zs, xu, yu, zu, 
+                          x, y, z, xs, ys, zs, xu, yu, zu,
-			  xsu, ysu, zsu, ix, iy, iz,
+                          xsu, ysu, zsu, ix, iy, iz,
-			  vx, vy, vz, fx, fy, fz,
+                          vx, vy, vz, fx, fy, fz,
                           q, mux, muy, muz, mu,
                           radius, diameter, omegax, omegay, omegaz,
-			  angmomx, angmomy, angmomz, tqx, tqy, tqz,
+                          angmomx, angmomy, angmomz, tqx, tqy, tqz,
-			  spin, eradius, ervel, erforce,
+                          spin, eradius, ervel, erforce,
-			  c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
+                          c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
 
       id = atom ID
       mol = molecule ID

doc/src/dump_modify.txt

@@ -215,17 +215,17 @@ to the dump file.  The {every} keyword cannot be used with the dump
 For example, the following commands will
 write snapshots at timesteps 0,10,20,30,100,200,300,1000,2000,etc:
 
-variable	s equal logfreq(10,3,10)
+variable        s equal logfreq(10,3,10)
-dump		1 all atom 100 tmp.dump
+dump            1 all atom 100 tmp.dump
-dump_modify	1 every v_s first yes :pre
+dump_modify     1 every v_s first yes :pre
 
 The following commands would write snapshots at the timesteps listed
 in file tmp.times:
 
 variable        f file tmp.times
-variable	s equal next(f)
+variable        s equal next(f)
-dump		1 all atom 100 tmp.dump
+dump            1 all atom 100 tmp.dump
-dump_modify	1 every v_s :pre
+dump_modify     1 every v_s :pre
 
 NOTE: When using a file-style variable with the {every} keyword, the
 file of timesteps must list a first timestep that is beyond the
@@ -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
@@ -686,10 +683,10 @@ this is used.
 variable        colors string &
                 "red green blue yellow white &
                 purple pink orange lime gray"
-variable	mol atom mol%10
+variable        mol atom mol%10
-dump		1 all image 250 image.*.jpg v_mol type &
+dump            1 all image 250 image.*.jpg v_mol type &
-		zoom 1.6 adiam 1.5
+                zoom 1.6 adiam 1.5
-dump_modify	1 pad 5 amap 0 10 sa 1 10 $\{colors\} :pre
+dump_modify     1 pad 5 amap 0 10 sa 1 10 $\{colors\} :pre
 
 In this case, 10 colors are defined, and molecule IDs are
 mapped to one of the colors, even if there are 1000s of molecules.

doc/src/fix_ave_correlate.txt

@@ -58,7 +58,7 @@ keyword = {type} or {ave} or {start} or {prefactor} or {file} or {overwrite} or
 fix 1 all ave/correlate 5 100 1000 c_myTemp file temp.correlate
 fix 1 all ave/correlate 1 50 10000 &
           c_thermo_press\[1\] c_thermo_press\[2\] c_thermo_press\[3\] &
-	  type upper ave running title1 "My correlation data" :pre
+          type upper ave running title1 "My correlation data" :pre
 fix 1 all ave/correlate 1 50 10000 c_thermo_press\[*\]
 
 [Description:]

doc/src/fix_ave_correlate_long.txt

@@ -55,7 +55,7 @@ keyword = {type} or {start} or {file} or {overwrite} or {title1} or {title2} or
 fix 1 all ave/correlate/long 5 1000 c_myTemp file temp.correlate
 fix 1 all ave/correlate/long 1 10000 &
           c_thermo_press\[1\] c_thermo_press\[2\] c_thermo_press\[3\] &
-	  type upper title1 "My correlation data" nlen 15 ncount 3 :pre
+          type upper title1 "My correlation data" nlen 15 ncount 3 :pre
 
 [Description:]
 

doc/src/fix_deform.txt

@@ -28,7 +28,7 @@ parameter = {x} or {y} or {z} or {xy} or {xz} or {yz}
         factor = multiplicative factor for change in box length at end of run
       {vel} value = V
         V = change box length at this velocity (distance/time units),
-	    effectively an engineering strain rate
+            effectively an engineering strain rate
       {erate} value = R
         R = engineering strain rate (1/time units)
       {trate} value = R
@@ -36,10 +36,10 @@ parameter = {x} or {y} or {z} or {xy} or {xz} or {yz}
       {volume} value = none = adjust this dim to preserve volume of system
       {wiggle} values = A Tp
         A = amplitude of oscillation (distance units)
-	Tp = period of oscillation (time units)
+        Tp = period of oscillation (time units)
       {variable} values = v_name1 v_name2
         v_name1 = variable with name1 for box length change as function of time
-	v_name2 = variable with name2 for change rate as function of time
+        v_name2 = variable with name2 for change rate as function of time
   {xy}, {xz}, {yz} args = style value
     style = {final} or {delta} or {vel} or {erate} or {trate} or {wiggle}
       {final} value = tilt
@@ -48,17 +48,17 @@ parameter = {x} or {y} or {z} or {xy} or {xz} or {yz}
         dtilt = change in tilt factor at end of run (distance units)
       {vel} value = V
         V = change tilt factor at this velocity (distance/time units),
-	    effectively an engineering shear strain rate
+            effectively an engineering shear strain rate
       {erate} value = R
         R = engineering shear strain rate (1/time units)
       {trate} value = R
         R = true shear strain rate (1/time units)
       {wiggle} values = A Tp
         A = amplitude of oscillation (distance units)
-	Tp = period of oscillation (time units)
+        Tp = period of oscillation (time units)
       {variable} values = v_name1 v_name2
         v_name1 = variable with name1 for tilt change as function of time
-	v_name2 = variable with name2 for change rate as function of time :pre
+        v_name2 = variable with name2 for change rate as function of time :pre
 
 zero or more keyword/value pairs may be appended :l
 keyword = {remap} or {flip} or {units} :l

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_msst.txt

@@ -120,7 +120,7 @@ The global vector contains four values in this order:
 To print these quantities to the log file with descriptive column
 headers, the following LAMMPS commands are suggested:
 
-fix		 msst all msst z 
+fix              msst all msst z
 fix_modify       msst energy yes
 variable dhug    equal f_msst\[1\]
 variable dray    equal f_msst\[2\]

doc/src/fix_qbmsst.txt

@@ -167,14 +167,14 @@ headers, the following LAMMPS commands are suggested. Here the
 the thermo keyword {etotal} to print the quantity <i>etot</i>.  See
 also the "thermo_style"_thermo_style.html command.
 
-fix		fix_id all msst z 
+fix             fix_id all msst z
-fix_modify	fix_id energy yes
+fix_modify      fix_id energy yes
-variable	dhug	equal f_fix_id\[1\]
+variable        dhug    equal f_fix_id\[1\]
-variable	dray	equal f_fix_id\[2\]
+variable        dray    equal f_fix_id\[2\]
-variable	lgr_vel	equal f_fix_id\[3\]
+variable        lgr_vel equal f_fix_id\[3\]
-variable	lgr_pos	equal f_fix_id\[4\]
+variable        lgr_pos equal f_fix_id\[4\]
-variable	T_qm	equal f_fix_id\[5\]
+variable        T_qm    equal f_fix_id\[5\]
-thermo_style	custom	step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos v_T_qm f_fix_id :pre
+thermo_style    custom  step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos v_T_qm f_fix_id :pre
 
 The global scalar under the entry f_fix_id is the quantity of thermo
 energy as an extra part of <i>etot</i>. This global scalar and the

doc/src/fix_rx.txt

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

doc/src/fix_store_state.txt

@@ -17,8 +17,8 @@ store/state = style name of this fix command :l
 N = store atom attributes every N steps, N = 0 for initial store only :l
 input = one or more atom attributes :l
   possible attributes = id, mol, type, mass,
- 	                x, y, z, xs, ys, zs, xu, yu, zu, xsu, ysu, zsu, ix, iy, iz,
+                        x, y, z, xs, ys, zs, xu, yu, zu, xsu, ysu, zsu, ix, iy, iz,
-		        vx, vy, vz, fx, fy, fz,
+                        vx, vy, vz, fx, fy, fz,
                         q, mux, muy, muz, mu,
                         radius, diameter, omegax, omegay, omegaz,
                         angmomx, angmomy, angmomz, tqx, tqy, tqz,

doc/src/fix_wall_gran.txt

@@ -163,6 +163,8 @@ Any dimension (xyz) that has a granular wall must be non-periodic.
 
 [Related commands:]
 
-"fix move"_fix_move.html, "pair_style granular"_pair_gran.html
+"fix move"_fix_move.html, 
+"fix wall/gran/region"_fix_wall_gran_region.html, 
+"pair_style granular"_pair_gran.html
 
 [Default:] none

doc/src/fix_wall_gran_region.txt

@@ -0,0 +1,199 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix wall/gran/region command :h3
+
+[Syntax:]
+
+fix ID group-ID wall/gran/region fstyle Kn Kt gamma_n gamma_t xmu dampflag wallstyle regionID :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+wall/region = style name of this fix command :l
+fstyle = style of force interactions between particles and wall :l
+  possible choices: hooke, hooke/history, hertz/history :pre
+Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) :l
+Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) :l
+gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) :l
+gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below) :l
+xmu = static yield criterion (unitless value between 0.0 and 1.0e4) :l
+dampflag = 0 or 1 if tangential damping force is excluded or included :l
+wallstyle = region (see "fix wall/gran"_fix_wall_gran.html for options for other kinds of walls) :l
+region-ID = region whose boundary will act as wall :l,ule
+
+[Examples:]
+
+fix wall all wall/gran/region hooke/history 1000.0 200.0 200.0 100.0 0.5 1 region myCone :pre
+
+[Description:]
+
+Treat the surface of the geometric region defined by the {region-ID}
+as a bounding frictional wall which interacts with nearby finite-size
+granular particles when they are close enough to touch the wall.  See
+the "fix wall/region"_fix_wall_region.html and "fix
+wall/gran"_fix_wall_gran.html commands for related kinds of walls for
+non-granular particles and simpler wall geometries, respectively.
+
+Here are snapshots of example models using this command.
+Corresponding input scripts can be found in examples/granregion.
+Click on the images to see a bigger picture.  Movies of these
+simulations are "here on the Movies
+page"_http://lammps.sandia.gov/movies.html#granregion of the
+LAMMPS web site.
+
+:image(JPG/gran_funnel_small.jpg,JPG/gran_funnel.png)
+:image(JPG/gran_mixer_small.jpg,JPG/gran_mixer.png)
+
+:line
+
+The distance between a particle and the region boundary is the
+distance to the nearest point on the region surface.  The force the
+wall exerts on the particle is along the direction between that point
+and the particle center, which is the direction normal to the surface
+at that point.  Note that if the region surface is comprised of
+multiple "faces", then each face can exert a force on the particle if
+it is close enough.  E.g. for "region_style block"_region.html, a
+particle in the interior, near a corner of the block, could feel wall
+forces from 1, 2, or 3 faces of the block.
+
+Regions are defined using the "region"_region.html command.  Note that
+the region volume can be interior or exterior to the bounding surface,
+which will determine in which direction the surface interacts with
+particles, i.e. the direction of the surface normal. The exception to
+this is if one or more {open} options are specified for the region
+command, in which case particles interact with both the interior and
+exterior surfaces of regions.
+
+Regions can either be primitive shapes (block, sphere, cylinder, etc)
+or combinations of primitive shapes specified via the {union} or
+{intersect} region styles.  These latter styles can be used to
+construct particle containers with complex shapes.  Regions can also
+move dynamically via the "region"_region.html command keywords (move)
+and {rotate}, or change their shape by use of variables as inputs to
+the "region"_region.html command.  If such a region is used with this
+fix, then the region surface will move in time in the corresponding
+manner.
+
+NOTE: As discussed on the "region"_region.html command doc page,
+regions in LAMMPS do not get wrapped across periodic boundaries.  It
+is up to you to ensure that the region location with respect to
+periodic or non-periodic boundaries is specified appropriately via the
+"region"_region.html and "boundary"_boundary.html commands when using
+a region as a wall that bounds particle motion.
+ 
+NOTE: For primitive regions with sharp corners and/or edges (e.g. a
+block or cylinder), wall/particle forces are computed accurately for
+both interior and exterior regions.  For {union} and {intersect}
+regions, additional sharp corners and edges may be present due to the
+intersection of the surfaces of 2 or more primitive volumes.  These
+corners and edges can be of two types: concave or convex.  Concave
+points/edges are like the corners of a cube as seen by particles in
+the interior of a cube.  Wall/particle forces around these features
+are computed correctly.  Convex points/edges are like the corners of a
+cube as seen by particles exterior to the cube, i.e. the points jut
+into the volume where particles are present.  LAMMPS does NOT compute
+the location of these convex points directly, and hence wall/particle
+forces in the cutoff volume around these points suffer from
+inaccuracies.  The basic problem is that the outward normal of the
+surface is not continuous at these points.  This can cause particles
+to feel no force (they don't "see" the wall) when in one location,
+then move a distance epsilon, and suddenly feel a large force because
+they now "see" the wall.  In a worst-case scenario, this can blow
+particles out of the simulation box.  Thus, as a general rule you
+should not use the fix wall/gran/region command with {union} or
+{interesect} regions that have convex points or edges resulting from
+the union/intersection (convex points/edges in the union/intersection
+due to a single sub-region are still OK).
+
+NOTE: Similarly, you should not define {union} or {intersert} regions
+for use with this command that share an overlapping common face that
+is part of the overall outer boundary (interior boundary is OK), even
+if the face is smooth.  E.g. two regions of style block in a {union}
+region, where the two blocks overlap on one or more of their faces.
+This is because LAMMPS discards points that are part of multiple
+sub-regions when calculating wall/particle interactions, to avoid
+double-counting the interaction.  Having two coincident faces could
+cause the face to become invisible to the particles.  The solution is
+to make the two faces differ by epsilon in their position.
+
+The nature of the wall/particle interactions are determined by the
+{fstyle} setting.  It can be any of the styles defined by the
+"pair_style granular"_pair_gran.html commands.  Currently this is
+{hooke}, {hooke/history}, or {hertz/history}.  The equation for the
+force between the wall and particles touching it is the same as the
+corresponding equation on the "pair_style granular"_pair_gran.html doc
+page, but the effective radius is calculated using the radius of the
+particle and the radius of curvature of the wall at the contact point.
+
+Specifically, delta = radius - r = overlap of particle with wall,
+m_eff = mass of particle, and RiRj/Ri+Rj is the effective radius, with
+Rj replaced by the radius of curvature of the wall at the contact
+point.  The radius of curvature can be negative for a concave wall
+section, e.g. the interior of cylinder.  For a flat wall, delta =
+radius - r = overlap of particle with wall, m_eff = mass of particle,
+and the effective radius of contact is just the radius of the
+particle.
+
+The parameters {Kn}, {Kt}, {gamma_n}, {gamma_t}, {xmu} and {dampflag}
+have the same meaning and units as those specified with the
+"pair_style granular"_pair_gran.html commands.  This means a NULL can
+be used for either {Kt} or {gamma_t} as described on that page.  If a
+NULL is used for {Kt}, then a default value is used where {Kt} = 2/7
+{Kn}.  If a NULL is used for {gamma_t}, then a default value is used
+where {gamma_t} = 1/2 {gamma_n}.
+
+Note that you can choose a different force styles and/or different
+values for the 6 wall/particle coefficients than for particle/particle
+interactions.  E.g. if you wish to model the wall as a different
+material.
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+Similiar to "fix wall/gran"_fix_wall_gran.html command, this fix
+writes the shear friction state of atoms interacting with the wall to
+"binary restart files"_restart.html, so that a simulation can continue
+correctly if granular potentials with shear "history" effects are
+being used.  This fix also includes info about a moving region in the
+restart file.  See the "read_restart"_read_restart.html command for
+info on how to re-specify a fix in an input script that reads a
+restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+
+Note 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).
+
+None of the "fix_modify"_fix_modify.html options are relevant to this
+fix.  No global or per-atom quantities are stored by this fix for
+access by various "output commands"_Section_howto.html#howto_15.  No
+parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
+[Restrictions:]
+
+This fix is part of the GRANULAR package.  It is only enabled if
+LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"fix_move"_fix_move.html,
+"fix wall/gran"_fix_wall_gran.html, 
+"fix wall/region"_fix_wall_region.html,
+"pair_style granular"_pair_gran.html,
+"region"_region.html
+
+[Default:] none
+

doc/src/group.txt

@@ -253,7 +253,7 @@ group           mobile dynamic all region ss
 fix             1 mobile nve
 run             $\{nsteps\}
 group           mobile static
-run	        $\{nsteps\} :pre
+run             $\{nsteps\} :pre
 
 NOTE: All fixes and computes take a group ID as an argument, but they
 do not all allow for use of a dynamic group.  If you get an error

doc/src/if.txt

@@ -109,19 +109,19 @@ Here is an example of a double loop which uses the if and
 "jump"_jump.html commands to break out of the inner loop when a
 condition is met, then continues iterating thru the outer loop.
 
-label	    loopa
+label       loopa
 variable    a loop 5
-  label	    loopb
+  label     loopb
   variable  b loop 5
-  print	    "A,B = $a,$b"
+  print     "A,B = $a,$b"
   run       10000
-  if	    "$b > 2" then "jump SELF break"
+  if        "$b > 2" then "jump SELF break"
-  next	    b
+  next      b
-  jump	    in.script loopb
+  jump      in.script loopb
-label	    break
+label       break
 variable    b delete
-next	    a
+next        a
-jump	    SELF loopa :pre
+jump        SELF loopa :pre
 
 :line
 

doc/src/jump.txt

@@ -103,19 +103,19 @@ Here is an example of a double loop which uses the if and
 "jump"_jump.html commands to break out of the inner loop when a
 condition is met, then continues iterating thru the outer loop.
 
-label	    loopa
+label       loopa
 variable    a loop 5
-  label	    loopb
+  label     loopb
   variable  b loop 5
-  print	    "A,B = $a,$b"
+  print     "A,B = $a,$b"
   run       10000
-  if	    "$b > 2" then "jump SELF break"
+  if        "$b > 2" then "jump SELF break"
-  next	    b
+  next      b
-  jump	    in.script loopb
+  jump      in.script loopb
-label	    break
+label       break
 variable    b delete
-next	    a
+next        a
-jump	    SELF loopa :pre
+jump        SELF loopa :pre
 
 [Restrictions:]
 

doc/src/next.txt

@@ -116,19 +116,19 @@ Here is an example of a double loop which uses the "if"_if.html and
 "jump"_jump.html commands to break out of the inner loop when a
 condition is met, then continues iterating thru the outer loop.
 
-label	    loopa
+label       loopa
 variable    a loop 5
-  label	    loopb
+  label     loopb
   variable  b loop 5
-  print	    "A,B = $a,$b"
+  print     "A,B = $a,$b"
   run       10000
-  if	    $b > 2 then "jump in.script break"
+  if        $b > 2 then "jump in.script break"
-  next	    b
+  next      b
-  jump	    in.script loopb
+  jump      in.script loopb
-label	    break
+label       break
 variable    b delete :pre
-next	    a
+next        a
-jump	    in.script loopa :pre
+jump        in.script loopa :pre
 
 [Restrictions:]
 

doc/src/pair_hybrid.txt

@@ -170,7 +170,7 @@ so that there is effectively no interaction (e.g. epsilon = 0.0 in a
 LJ potential).  Or, for {hybrid} and {hybrid/overlay} simulations, you
 can use this form of the pair_coeff command in your input script:
 
-pair_coeff	2 3 none :pre
+pair_coeff        2 3 none :pre
 
 or this form in the "Pair Coeffs" section of the data file:
 

doc/src/pair_meam.txt

@@ -188,9 +188,9 @@ lattce(I,J) = lattice structure of I-J reference structure:
                 bcc = body centered cubic
                 dim = dimer
                 b1  = rock salt (NaCl structure)
-		hcp = hexagonal close-packed
+                hcp = hexagonal close-packed
-		c11 = MoSi2 structure
+                c11 = MoSi2 structure
-		l12 = Cu3Au structure (lower case L, followed by 12)
+                l12 = Cu3Au structure (lower case L, followed by 12)
                 b2  = CsCl structure (interpenetrating simple cubic)
 nn2(I,J)    = turn on second-nearest neighbor MEAM formulation for
               I-J pair (see for example "(Lee)"_#Lee).

doc/src/pair_reax_c.txt

@@ -41,7 +41,9 @@ supplemental information of the following paper: "(Chenoweth et al.,
 2008)"_#Chenoweth_2008.  The version integrated into LAMMPS matches
 the most up-to-date version of ReaxFF as of summer 2010.  For more
 technical details about the pair reax/c implementation of ReaxFF, see
-the "(Aktulga)"_#Aktulga paper.
+the "(Aktulga)"_#Aktulga paper. The {reax/c} style was initially
+implemented as a stand-alone C code and is now integrated into LAMMPS
+as a package.
 
 The {reax/c/kk} style is a Kokkos version of the ReaxFF potential that is
 derived from the {reax/c} style. The Kokkos version can run on GPUs and
@@ -163,11 +165,11 @@ To print these quantities to the log file (with descriptive column
 headings) the following commands could be included in an input script:
 
 compute reax all pair reax/c
-variable eb  	 equal c_reax\[1\]
+variable eb      equal c_reax\[1\]
-variable ea  	 equal c_reax\[2\] 
+variable ea      equal c_reax\[2\]
 \[...\]
-variable eqeq 	 equal c_reax\[14\]
+variable eqeq    equal c_reax\[14\]
-thermo_style custom step temp epair v_eb v_ea ... v_eqeq :pre
+thermo_style custom step temp epair v_eb v_ea \[...\] v_eqeq :pre
 
 Only a single pair_coeff command is used with the {reax/c} style which
 specifies a ReaxFF potential file with parameters for all needed
@@ -237,7 +239,7 @@ nbrhood_cutoff: Denotes the near neighbors cutoff (in Angstroms)
 regarding the bonded interactions. (default value = 5.0)
 
 hbond_cutoff: Denotes the cutoff distance (in Angstroms) for hydrogen
-bond interactions.(default value = 7.5. Value of 0.0 turns off
+bond interactions.(default value = 7.5. A value of 0.0 turns off
 hydrogen bonds)
 
 bond_graph_cutoff: is the threshold used in determining what is a

doc/src/pair_smtbq.txt

@@ -158,7 +158,7 @@ Divided line :ul
 3) Potential parameters:
 
 Keyword for element1, element2 and interaction potential ('second_moment' or 'buck' or 'buckPlusAttr') between element 1 and 2.  If the potential is 'second_moment', specify 'oxide' or 'metal' for metal-oxygen or metal-metal interactions respectively.
-Potential parameter: <pre><br/>	If type of potential is 'second_moment' : {A (eV)}, {p}, {&#958<sup>0</sup>} (eV) and {q} <br/>						  {r<sub>c1</sub>} (&#197), {r<sub>c2</sub>} (&#197) and {r<sub>0</sub>} (&#197) <br/> 	If type of potential is 'buck' : {C} (eV) and {&#961} (&#197) <br/>	If type of potential is 'buckPlusAttr' : {C} (eV) and {&#961} (&#197) <br/>						 {D} (eV), {B} (&#197<sup>-1</sup>), {r<sub>1</sub><sup>OO</sup>} (&#197) and {r<sub>2</sub><sup>OO</sup>} (&#197) </pre>
+Potential parameter: <pre><br/> If type of potential is 'second_moment' : {A (eV)}, {p}, {&#958<sup>0</sup>} (eV) and {q} <br/> {r<sub>c1</sub>} (&#197), {r<sub>c2</sub>} (&#197) and {r<sub>0</sub>} (&#197) <br/> If type of potential is 'buck' : {C} (eV) and {&#961} (&#197) <br/> If type of potential is 'buckPlusAttr' : {C} (eV) and {&#961} (&#197) <br/> {D} (eV), {B} (&#197<sup>-1</sup>), {r<sub>1</sub><sup>OO</sup>} (&#197) and {r<sub>2</sub><sup>OO</sup>} (&#197) </pre>
 Divided line :ul
 
 4) Tables parameters:
@@ -185,7 +185,7 @@ Divided line :ul
 
 8) Mode for the electronegativity equalization (Qeq) :
 
-Keyword mode: <pre> <br/>		QEqAll  (one QEq group)			|   no parameters <br/>		QEqAllParallel (several QEq groups)	|   no parameters <br/>		Surface			|   zlim   (QEq only for z>zlim)   </pre>
+Keyword mode: <pre> <br/> QEqAll  (one QEq group) |   no parameters <br/> QEqAllParallel (several QEq groups) |   no parameters <br/> Surface |   zlim   (QEq only for z>zlim)   </pre>
 Parameter if necessary
 Divided line :ul
 

doc/src/pair_snap.txt

@@ -96,15 +96,15 @@ tantalum potential provided in the LAMMPS potentials directory
 combines the {snap} and {zbl} pair styles. It is invoked
 by the following commands:
 
-	variable zblcutinner equal 4
+        variable zblcutinner equal 4
-	variable zblcutouter equal 4.8
+        variable zblcutouter equal 4.8
-	variable zblz equal 73
+        variable zblz equal 73
-	pair_style hybrid/overlay &
+        pair_style hybrid/overlay &
-	zbl $\{zblcutinner\} $\{zblcutouter\} snap
+        zbl $\{zblcutinner\} $\{zblcutouter\} snap
-	pair_coeff * * zbl 0.0 
+        pair_coeff * * zbl 0.0
-	pair_coeff 1 1 zbl $\{zblz\}
+        pair_coeff 1 1 zbl $\{zblz\}
-	pair_coeff * * snap ../potentials/Ta06A.snapcoeff Ta &
+        pair_coeff * * snap ../potentials/Ta06A.snapcoeff Ta &
-	../potentials/Ta06A.snapparam Ta :pre
+        ../potentials/Ta06A.snapparam Ta :pre
 
 It is convenient to keep these commands in a separate file that can
 be inserted in any LAMMPS input script using the "include"_include.html

doc/src/read_restart.txt

@@ -191,13 +191,18 @@ 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
+new input script must be of the same style and use the same fix-ID as
-the input script that wrote the restart file.  If a match is found,
+was used in the input script that wrote the restart file.
-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
+If a match is found, LAMMPS prints a message indicating that the fix
-by the new script, the "state" information for the saved fix is
+is being re-enabled.  If no match is found before the first run or
-discarded.  See the doc pages for individual fixes for info on which
+minimization is performed by the new script, the "state" information
-ones can be restarted in this manner.
+for the saved fix is discarded.  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 +218,14 @@ 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 require a system initialization.  Examples include
+the "balance", "displace_atoms", and "delete_atoms" commands.  This is
+because they may migrate atoms to new processors.  Thus they will also
+discard unused "state" information from fixes.  This means that, if
+desired, you must re-specify the relevant fixes and computes (which
+create fixes) before those commands are used.
+
 Some pair styles, like the "granular pair styles"_pair_gran.html, also
 use a fix to store "state" information that persists from timestep to
 timestep.  In the case of granular potentials, it is contact

doc/src/replicate.txt

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

doc/src/restart.txt

@@ -113,8 +113,8 @@ For example, the following commands will write restart files
 every step from 1100 to 1200, and could be useful for debugging
 a simulation where something goes wrong at step 1163:
 
-variable	s equal stride(1100,1200,1)
+variable       s equal stride(1100,1200,1)
-restart		v_s tmp.restart :pre
+restart        v_s tmp.restart :pre
 
 :line
 

doc/src/run.txt

@@ -66,11 +66,11 @@ keywords.
 
 For example, consider this fix followed by 10 run commands:
 
-fix	     1 all nvt 200.0 300.0 1.0
+fix         1 all nvt 200.0 300.0 1.0
-run	     1000 start 0 stop 10000
+run         1000 start 0 stop 10000
-run	     1000 start 0 stop 10000
+run         1000 start 0 stop 10000
 ...
-run	     1000 start 0 stop 10000 :pre
+run         1000 start 0 stop 10000 :pre
 
 The NVT fix ramps the target temperature from 200.0 to 300.0 during a
 run.  If the run commands did not have the start/stop keywords (just

doc/src/run_style.txt

@@ -20,7 +20,7 @@ style = {verlet} or {verlet/split} or {respa} or {respa/omp} :ulb,l
     n1, n2, ... = loop factor between rRESPA levels (N-1 values)
     zero or more keyword/value pairings may be appended to the loop factors
     keyword = {bond} or {angle} or {dihedral} or {improper} or
-	      {pair} or {inner} or {middle} or {outer} or {hybrid} or {kspace}
+              {pair} or {inner} or {middle} or {outer} or {hybrid} or {kspace}
       {bond} value = M
         M = which level (1-N) to compute bond forces in
       {angle} value = M
@@ -33,14 +33,14 @@ style = {verlet} or {verlet/split} or {respa} or {respa/omp} :ulb,l
         M = which level (1-N) to compute pair forces in
       {inner} values = M cut1 cut2
         M = which level (1-N) to compute pair inner forces in
-	cut1 = inner cutoff between pair inner and
+        cut1 = inner cutoff between pair inner and
-	       pair middle or outer  (distance units)
+               pair middle or outer  (distance units)
-	cut2 = outer cutoff between pair inner and
+        cut2 = outer cutoff between pair inner and
-	       pair middle or outer  (distance units)
+               pair middle or outer  (distance units)
       {middle} values = M cut1 cut2
         M = which level (1-N) to compute pair middle forces in
-	cut1 = inner cutoff between pair middle and pair outer (distance units)
+        cut1 = inner cutoff between pair middle and pair outer (distance units)
-	cut2 = outer cutoff between pair middle and pair outer (distance units)
+        cut2 = outer cutoff between pair middle and pair outer (distance units)
       {outer} value = M
         M = which level (1-N) to compute pair outer forces in
       {hybrid} values = M1 M2 ... (as many values as there are hybrid sub-styles
@@ -230,7 +230,7 @@ rRESPA:
 
 fix             2 all shake 0.000001 500 0 m 1.0 a 1
 timestep        4.0
-run_style	respa 2 2 inner 1 4.0 5.0 outer 2 :pre
+run_style       respa 2 2 inner 1 4.0 5.0 outer 2 :pre
 
 With these settings, users can expect good energy conservation and
 roughly a 1.5 fold speedup over the {verlet} style with SHAKE and a

doc/src/set.txt

@@ -17,13 +17,13 @@ ID = atom ID range or type range or mol ID range or group ID or region ID :l
 one or more keyword/value pairs may be appended :l
 keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
           {charge} or {dipole} or {dipole/random} or {quat} or \
-	  {quat/random} or {diameter} or {shape} or \
+          {quat/random} or {diameter} or {shape} or \
-	  {length} or {tri} or {theta} or {theta/random} or \
+          {length} or {tri} or {theta} or {theta/random} or \
           {angmom} or {omega} or \
-	  {mass} or {density} or {volume} or {image} or \
+          {mass} or {density} or {volume} or {image} or \
-	  {bond} or {angle} or {dihedral} or {improper} or \
+          {bond} or {angle} or {dihedral} or {improper} or \
-	  {meso/e} or {meso/cv} or {meso/rho} or \
+          {meso/e} or {meso/cv} or {meso/rho} or \
-	  {smd/contact/radius} or {smd/mass/density} or {dpd/theta} or \
+          {smd/contact/radius} or {smd/mass/density} or {dpd/theta} or \
           {i_name} or {d_name} :l
   {type} value = atom type
     value can be an atom-style variable (see below)

doc/src/thermo.txt

@@ -45,8 +45,8 @@ options for "equal-style variables"_variable.html.
 For example, the following commands will output thermodynamic info at
 timesteps 0,10,20,30,100,200,300,1000,2000,etc:
 
-variable	s equal logfreq(10,3,10)
+variable        s equal logfreq(10,3,10)
-thermo	        v_s :pre
+thermo          v_s :pre
 
 [Restrictions:] none
 

doc/src/thermo_style.txt

@@ -23,12 +23,12 @@ args = list of arguments for a particular style :l
                         evdwl, ecoul, epair, ebond, eangle, edihed, eimp,
                         emol, elong, etail,
                         vol, density, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi,
-		        xy, xz, yz, xlat, ylat, zlat,
+                        xy, xz, yz, xlat, ylat, zlat,
                         bonds, angles, dihedrals, impropers,
-		        pxx, pyy, pzz, pxy, pxz, pyz,
+                        pxx, pyy, pzz, pxy, pxz, pyz,
-			fmax, fnorm, nbuild, ndanger,
+                        fmax, fnorm, nbuild, ndanger,
-			cella, cellb, cellc, cellalpha, cellbeta, cellgamma,
+                        cella, cellb, cellc, cellalpha, cellbeta, cellgamma,
-			c_ID, c_ID\[I\], c_ID\[I\]\[J\],
+                        c_ID, c_ID\[I\], c_ID\[I\]\[J\],
                         f_ID, f_ID\[I\], f_ID\[I\]\[J\],
                         v_name, v_name\[I\]
       step = timestep

doc/src/variable.txt

@@ -52,18 +52,18 @@ style = {delete} or {index} or {loop} or {world} or {universe} or {uloop} or {st
                      sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x),
                      random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x)
                      ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z),
-		     stride(x,y,z), stride2(x,y,z,a,b,c), 
+                     stride(x,y,z), stride2(x,y,z,a,b,c),
-		     vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)
+                     vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)
     group functions = count(group), mass(group), charge(group),
-		      xcm(group,dim), vcm(group,dim), fcm(group,dim),
+                      xcm(group,dim), vcm(group,dim), fcm(group,dim),
-		      bound(group,dir), gyration(group), ke(group),
+                      bound(group,dir), gyration(group), ke(group),
-		      angmom(group,dim), torque(group,dim),
+                      angmom(group,dim), torque(group,dim),
                       inertia(group,dimdim), omega(group,dim)
     region functions = count(group,region), mass(group,region), charge(group,region),
-		      xcm(group,dim,region), vcm(group,dim,region), fcm(group,dim,region),
+                      xcm(group,dim,region), vcm(group,dim,region), fcm(group,dim,region),
-		      bound(group,dir,region), gyration(group,region), ke(group,reigon),
+                      bound(group,dir,region), gyration(group,region), ke(group,reigon),
-		      angmom(group,dim,region), torque(group,dim,region), 
+                      angmom(group,dim,region), torque(group,dim,region),
-		      inertia(group,dimdim,region), omega(group,dim,region)
+                      inertia(group,dimdim,region), omega(group,dim,region)
     special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x)
     feature functions = is_active(category,feature,exact), is_defined(category,id,exact)
     atom value = id\[i\], mass\[i\], type\[i\], mol\[i\], x\[i\], y\[i\], z\[i\], vx\[i\], vy\[i\], vz\[i\], fx\[i\], fy\[i\], fz\[i\], q\[i\]
@@ -219,13 +219,13 @@ script or when the input script is looped over.  This can be useful
 when breaking out of a loop via the "if"_if.html and "jump"_jump.html
 commands before the variable would become exhausted.  For example,
 
-label	    loop
+label       loop
 variable    a loop 5
-print	    "A = $a"
+print       "A = $a"
-if	    "$a > 2" then "jump in.script break"
+if          "$a > 2" then "jump in.script break"
-next	    a
+next        a
-jump	    in.script loop
+jump        in.script loop
-label	    break
+label       break
 variable    a delete :pre
 
 :line

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")