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
-100.0% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 106050.541 tau/day, 102.286 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.19562    | 0.19562    | 0.19562    |   0.0 | 19.99
-Bond    | 0.087475   | 0.087475   | 0.087475   |   0.0 |  8.94
-Neigh   | 0.44861    | 0.44861    | 0.44861    |   0.0 | 45.84
-Comm    | 0.032932   | 0.032932   | 0.032932   |   0.0 |  3.37
-Output  | 0.00010395 | 0.00010395 | 0.00010395 |   0.0 |  0.01
-Modify  | 0.19413    | 0.19413    | 0.19413    |   0.0 | 19.84
-Other   |            | 0.01972    |            |       |  2.02
+Pair    | 0.19421    | 0.19421    | 0.19421    |   0.0 | 19.86
+Bond    | 0.08741    | 0.08741    | 0.08741    |   0.0 |  8.94
+Neigh   | 0.45791    | 0.45791    | 0.45791    |   0.0 | 46.84
+Comm    | 0.032649   | 0.032649   | 0.032649   |   0.0 |  3.34
+Output  | 0.00012207 | 0.00012207 | 0.00012207 |   0.0 |  0.01
+Modify  | 0.18071    | 0.18071    | 0.18071    |   0.0 | 18.48
+Other   |            | 0.02464    |            |       |  2.52
 
 Nlocal:    32000 ave 32000 max 32000 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

bench/log.6Oct16.chain.fixed.icc.4

@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
 # FENE beadspring benchmark
 
 units		lj
@@ -43,25 +43,25 @@ Neighbor list info ...
   master list distance cutoff = 1.52
   ghost atom cutoff = 1.52
   binsize = 0.76 -> bins = 45 45 45
-Memory usage per processor = 3.91518 Mbytes
+Memory usage per processor = 4.14663 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0   0.97029772   0.44484087    20.494523    22.394765    4.6721833 
      100   0.97145835   0.43803883    20.502691    22.397872     4.626988 
-Loop time of 0.271187 on 4 procs for 100 steps with 32000 atoms
+Loop time of 0.269205 on 4 procs for 100 steps with 32000 atoms
 
-Performance: 382319.453 tau/day, 368.749 timesteps/s
-99.6% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 385133.446 tau/day, 371.464 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.048621   | 0.050076   | 0.051229   |   0.4 | 18.47
-Bond    | 0.022254   | 0.022942   | 0.023567   |   0.3 |  8.46
-Neigh   | 0.11873    | 0.11881    | 0.11887    |   0.0 | 43.81
-Comm    | 0.019066   | 0.021357   | 0.024297   |   1.3 |  7.88
-Output  | 5.0068e-05 | 5.5015e-05 | 6.1035e-05 |   0.1 |  0.02
-Modify  | 0.048737   | 0.050198   | 0.051231   |   0.4 | 18.51
-Other   |            | 0.007751   |            |       |  2.86
+Pair    | 0.049383   | 0.049756   | 0.049988   |   0.1 | 18.48
+Bond    | 0.022701   | 0.022813   | 0.022872   |   0.0 |  8.47
+Neigh   | 0.11982    | 0.12002    | 0.12018    |   0.0 | 44.58
+Comm    | 0.020274   | 0.021077   | 0.022348   |   0.5 |  7.83
+Output  | 5.3167e-05 | 5.6148e-05 | 6.3181e-05 |   0.1 |  0.02
+Modify  | 0.046276   | 0.046809   | 0.047016   |   0.1 | 17.39
+Other   |            | 0.008669   |            |       |  3.22
 
 Nlocal:    8000 ave 8030 max 7974 min
 Histogram: 1 0 0 1 0 1 0 0 0 1

bench/log.6Oct16.chain.scaled.icc.4

@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
 # FENE beadspring benchmark
 
 variable	x index 1
@@ -59,25 +59,25 @@ Neighbor list info ...
   master list distance cutoff = 1.52
   ghost atom cutoff = 1.52
   binsize = 0.76 -> bins = 89 89 45
-Memory usage per processor = 12.8735 Mbytes
+Memory usage per processor = 13.2993 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0   0.97027498   0.44484087    20.494523    22.394765    4.6721833 
      100   0.97682955   0.44239968    20.500229    22.407862    4.6527025 
-Loop time of 1.20889 on 4 procs for 100 steps with 128000 atoms
+Loop time of 1.14845 on 4 procs for 100 steps with 128000 atoms
 
-Performance: 85764.410 tau/day, 82.720 timesteps/s
-99.8% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 90277.919 tau/day, 87.074 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.21738    | 0.23306    | 0.23926    |   1.9 | 19.28
-Bond    | 0.094536   | 0.10196    | 0.10534    |   1.4 |  8.43
-Neigh   | 0.52311    | 0.52392    | 0.52519    |   0.1 | 43.34
-Comm    | 0.090161   | 0.10022    | 0.12557    |   4.7 |  8.29
-Output  | 0.00012207 | 0.00017327 | 0.00019598 |   0.2 |  0.01
-Modify  | 0.19662    | 0.20262    | 0.20672    |   0.8 | 16.76
-Other   |            | 0.04694    |            |       |  3.88
+Pair    | 0.2203     | 0.22207    | 0.22386    |   0.3 | 19.34
+Bond    | 0.094861   | 0.095302   | 0.095988   |   0.1 |  8.30
+Neigh   | 0.52127    | 0.5216     | 0.52189    |   0.0 | 45.42
+Comm    | 0.079585   | 0.082159   | 0.084366   |   0.7 |  7.15
+Output  | 0.00013304 | 0.00015306 | 0.00018501 |   0.2 |  0.01
+Modify  | 0.18351    | 0.18419    | 0.1856     |   0.2 | 16.04
+Other   |            | 0.04298    |            |       |  3.74
 
 Nlocal:    32000 ave 32015 max 31983 min
 Histogram: 1 0 1 0 0 0 0 0 1 1

bench/log.6Oct16.chute.fixed.icc.1

@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
 # LAMMPS benchmark of granular flow
 # chute flow of 32000 atoms with frozen base at 26 degrees
 
@@ -47,24 +47,24 @@ Neighbor list info ...
   master list distance cutoff = 1.1
   ghost atom cutoff = 1.1
   binsize = 0.55 -> bins = 73 37 68
-Memory usage per processor = 15.567 Mbytes
-Step Atoms KinEng 1 Volume 
+Memory usage per processor = 16.0904 Mbytes
+Step Atoms KinEng c_1 Volume 
        0    32000    784139.13    1601.1263    29833.783 
      100    32000    784292.08    1571.0968    29834.707 
-Loop time of 0.550482 on 1 procs for 100 steps with 32000 atoms
+Loop time of 0.534174 on 1 procs for 100 steps with 32000 atoms
 
-Performance: 1569.534 tau/day, 181.659 timesteps/s
-100.1% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 1617.451 tau/day, 187.205 timesteps/s
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.33849    | 0.33849    | 0.33849    |   0.0 | 61.49
-Neigh   | 0.040353   | 0.040353   | 0.040353   |   0.0 |  7.33
-Comm    | 0.018023   | 0.018023   | 0.018023   |   0.0 |  3.27
-Output  | 0.00020385 | 0.00020385 | 0.00020385 |   0.0 |  0.04
-Modify  | 0.13155    | 0.13155    | 0.13155    |   0.0 | 23.90
-Other   |            | 0.02186    |            |       |  3.97
+Pair    | 0.33346    | 0.33346    | 0.33346    |   0.0 | 62.43
+Neigh   | 0.043902   | 0.043902   | 0.043902   |   0.0 |  8.22
+Comm    | 0.018391   | 0.018391   | 0.018391   |   0.0 |  3.44
+Output  | 0.00022411 | 0.00022411 | 0.00022411 |   0.0 |  0.04
+Modify  | 0.11666    | 0.11666    | 0.11666    |   0.0 | 21.84
+Other   |            | 0.02153    |            |       |  4.03
 
 Nlocal:    32000 ave 32000 max 32000 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

bench/log.6Oct16.chute.fixed.icc.4

@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
 # LAMMPS benchmark of granular flow
 # chute flow of 32000 atoms with frozen base at 26 degrees
 
@@ -47,24 +47,24 @@ Neighbor list info ...
   master list distance cutoff = 1.1
   ghost atom cutoff = 1.1
   binsize = 0.55 -> bins = 73 37 68
-Memory usage per processor = 6.81783 Mbytes
-Step Atoms KinEng 1 Volume 
+Memory usage per processor = 7.04927 Mbytes
+Step Atoms KinEng c_1 Volume 
        0    32000    784139.13    1601.1263    29833.783 
      100    32000    784292.08    1571.0968    29834.707 
-Loop time of 0.13141 on 4 procs for 100 steps with 32000 atoms
+Loop time of 0.171815 on 4 procs for 100 steps with 32000 atoms
 
-Performance: 6574.833 tau/day, 760.976 timesteps/s
-99.3% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 5028.653 tau/day, 582.020 timesteps/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.062505   | 0.067      | 0.07152    |   1.5 | 50.99
-Neigh   | 0.010041   | 0.0101     | 0.010178   |   0.1 |  7.69
-Comm    | 0.012347   | 0.012895   | 0.013444   |   0.5 |  9.81
-Output  | 6.3896e-05 | 0.00010294 | 0.00014091 |   0.3 |  0.08
-Modify  | 0.031802   | 0.032348   | 0.032897   |   0.3 | 24.62
-Other   |            | 0.008965   |            |       |  6.82
+Pair    | 0.093691   | 0.096898   | 0.10005    |   0.8 | 56.40
+Neigh   | 0.011976   | 0.012059   | 0.012146   |   0.1 |  7.02
+Comm    | 0.016384   | 0.017418   | 0.018465   |   0.8 | 10.14
+Output  | 7.7963e-05 | 0.00010747 | 0.00013304 |   0.2 |  0.06
+Modify  | 0.031744   | 0.031943   | 0.032167   |   0.1 | 18.59
+Other   |            | 0.01339    |            |       |  7.79
 
 Nlocal:    8000 ave 8008 max 7992 min
 Histogram: 2 0 0 0 0 0 0 0 0 2

bench/log.6Oct16.chute.scaled.icc.4

@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
 # LAMMPS benchmark of granular flow
 # chute flow of 32000 atoms with frozen base at 26 degrees
 
@@ -57,24 +57,24 @@ Neighbor list info ...
   master list distance cutoff = 1.1
   ghost atom cutoff = 1.1
   binsize = 0.55 -> bins = 146 73 68
-Memory usage per processor = 15.7007 Mbytes
-Step Atoms KinEng 1 Volume 
+Memory usage per processor = 16.1265 Mbytes
+Step Atoms KinEng c_1 Volume 
        0   128000    3136556.5    6404.5051    119335.13 
      100   128000    3137168.3    6284.3873    119338.83 
-Loop time of 0.906913 on 4 procs for 100 steps with 128000 atoms
+Loop time of 0.832365 on 4 procs for 100 steps with 128000 atoms
 
-Performance: 952.683 tau/day, 110.264 timesteps/s
-99.7% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 1038.006 tau/day, 120.140 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.51454    | 0.53094    | 0.55381    |   2.0 | 58.54
-Neigh   | 0.042597   | 0.043726   | 0.045801   |   0.6 |  4.82
-Comm    | 0.063027   | 0.064657   | 0.067367   |   0.7 |  7.13
-Output  | 0.00024891 | 0.00059718 | 0.00086498 |   1.0 |  0.07
-Modify  | 0.16508    | 0.17656    | 0.1925     |   2.6 | 19.47
-Other   |            | 0.09043    |            |       |  9.97
+Pair    | 0.5178     | 0.52208    | 0.52793    |   0.5 | 62.72
+Neigh   | 0.047003   | 0.047113   | 0.047224   |   0.0 |  5.66
+Comm    | 0.05233    | 0.052988   | 0.053722   |   0.2 |  6.37
+Output  | 0.00024986 | 0.00032717 | 0.00036693 |   0.3 |  0.04
+Modify  | 0.15517    | 0.15627    | 0.15808    |   0.3 | 18.77
+Other   |            | 0.0536     |            |       |  6.44
 
 Nlocal:    32000 ave 32000 max 32000 min
 Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -87,4 +87,4 @@ Total # of neighbors = 460532
 Ave neighs/atom = 3.59791
 Neighbor list builds = 2
 Dangerous builds = 0
-Total wall time: 0:00:01
+Total wall time: 0:00:00

bench/log.6Oct16.eam.fixed.icc.1

@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
 # bulk Cu lattice
 
 variable	x index 1
@@ -49,25 +49,25 @@ Neighbor list info ...
   master list distance cutoff = 5.95
   ghost atom cutoff = 5.95
   binsize = 2.975 -> bins = 25 25 25
-Memory usage per processor = 10.2238 Mbytes
+Memory usage per processor = 11.2238 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0         1600      -113280            0   -106662.09    18703.573 
       50    781.69049   -109873.35            0   -106640.13    52273.088 
      100      801.832    -109957.3            0   -106640.77    51322.821 
-Loop time of 5.90097 on 1 procs for 100 steps with 32000 atoms
+Loop time of 5.96529 on 1 procs for 100 steps with 32000 atoms
 
-Performance: 7.321 ns/day, 3.278 hours/ns, 16.946 timesteps/s
+Performance: 7.242 ns/day, 3.314 hours/ns, 16.764 timesteps/s
 99.9% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 5.2121     | 5.2121     | 5.2121     |   0.0 | 88.33
-Neigh   | 0.58212    | 0.58212    | 0.58212    |   0.0 |  9.86
-Comm    | 0.030392   | 0.030392   | 0.030392   |   0.0 |  0.52
-Output  | 0.00023389 | 0.00023389 | 0.00023389 |   0.0 |  0.00
-Modify  | 0.060871   | 0.060871   | 0.060871   |   0.0 |  1.03
-Other   |            | 0.01527    |            |       |  0.26
+Pair    | 5.2743     | 5.2743     | 5.2743     |   0.0 | 88.42
+Neigh   | 0.59212    | 0.59212    | 0.59212    |   0.0 |  9.93
+Comm    | 0.030399   | 0.030399   | 0.030399   |   0.0 |  0.51
+Output  | 0.00026202 | 0.00026202 | 0.00026202 |   0.0 |  0.00
+Modify  | 0.050487   | 0.050487   | 0.050487   |   0.0 |  0.85
+Other   |            | 0.01776    |            |       |  0.30
 
 Nlocal:    32000 ave 32000 max 32000 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

bench/log.6Oct16.eam.fixed.icc.4

@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
 # bulk Cu lattice
 
 variable	x index 1
@@ -49,25 +49,25 @@ Neighbor list info ...
   master list distance cutoff = 5.95
   ghost atom cutoff = 5.95
   binsize = 2.975 -> bins = 25 25 25
-Memory usage per processor = 5.09629 Mbytes
+Memory usage per processor = 5.59629 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0         1600      -113280            0   -106662.09    18703.573 
       50    781.69049   -109873.35            0   -106640.13    52273.088 
      100      801.832    -109957.3            0   -106640.77    51322.821 
-Loop time of 1.58019 on 4 procs for 100 steps with 32000 atoms
+Loop time of 1.64562 on 4 procs for 100 steps with 32000 atoms
 
-Performance: 27.338 ns/day, 0.878 hours/ns, 63.284 timesteps/s
+Performance: 26.252 ns/day, 0.914 hours/ns, 60.767 timesteps/s
 99.8% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 1.3617     | 1.366      | 1.3723     |   0.4 | 86.45
-Neigh   | 0.15123    | 0.15232    | 0.15374    |   0.2 |  9.64
-Comm    | 0.033429   | 0.041275   | 0.047066   |   2.7 |  2.61
-Output  | 0.00011301 | 0.0001573  | 0.000211   |   0.3 |  0.01
-Modify  | 0.014694   | 0.015085   | 0.015421   |   0.2 |  0.95
-Other   |            | 0.005342   |            |       |  0.34
+Pair    | 1.408      | 1.4175     | 1.4341     |   0.9 | 86.14
+Neigh   | 0.15512    | 0.15722    | 0.16112    |   0.6 |  9.55
+Comm    | 0.029105   | 0.049986   | 0.061822   |   5.8 |  3.04
+Output  | 0.00010991 | 0.00011539 | 0.00012302 |   0.0 |  0.01
+Modify  | 0.013383   | 0.013573   | 0.013883   |   0.2 |  0.82
+Other   |            | 0.007264   |            |       |  0.44
 
 Nlocal:    8000 ave 8008 max 7993 min
 Histogram: 2 0 0 0 0 0 0 0 1 1

bench/log.6Oct16.eam.scaled.icc.4

@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
 # bulk Cu lattice
 
 variable	x index 1
@@ -49,25 +49,25 @@ Neighbor list info ...
   master list distance cutoff = 5.95
   ghost atom cutoff = 5.95
   binsize = 2.975 -> bins = 49 49 25
-Memory usage per processor = 10.1402 Mbytes
+Memory usage per processor = 11.1402 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0         1600      -453120            0   -426647.73    18704.012 
       50    779.50001   -439457.02            0   -426560.06    52355.276 
      100    797.97828   -439764.76            0   -426562.07     51474.74 
-Loop time of 6.46849 on 4 procs for 100 steps with 128000 atoms
+Loop time of 6.60121 on 4 procs for 100 steps with 128000 atoms
 
-Performance: 6.679 ns/day, 3.594 hours/ns, 15.460 timesteps/s
+Performance: 6.544 ns/day, 3.667 hours/ns, 15.149 timesteps/s
 99.9% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 5.581      | 5.5997     | 5.6265     |   0.8 | 86.57
-Neigh   | 0.65287    | 0.658      | 0.66374    |   0.5 | 10.17
-Comm    | 0.075706   | 0.11015    | 0.13655    |   7.2 |  1.70
-Output  | 0.00026488 | 0.00028312 | 0.00029302 |   0.1 |  0.00
-Modify  | 0.069607   | 0.072407   | 0.074555   |   0.7 |  1.12
-Other   |            | 0.02794    |            |       |  0.43
+Pair    | 5.6676     | 5.7011     | 5.7469     |   1.3 | 86.36
+Neigh   | 0.66423    | 0.67119    | 0.68082    |   0.7 | 10.17
+Comm    | 0.079367   | 0.13668    | 0.1791     |  10.5 |  2.07
+Output  | 0.00026989 | 0.00028622 | 0.00031209 |   0.1 |  0.00
+Modify  | 0.060046   | 0.062203   | 0.065009   |   0.9 |  0.94
+Other   |            | 0.02974    |            |       |  0.45
 
 Nlocal:    32000 ave 32092 max 31914 min
 Histogram: 1 0 0 1 0 1 0 0 0 1

bench/log.6Oct16.lj.fixed.icc.1

@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
 # 3d Lennard-Jones melt
 
 variable	x index 1
@@ -50,20 +50,20 @@ Memory usage per processor = 8.21387 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0         1.44   -6.7733681            0   -4.6134356   -5.0197073 
      100    0.7574531   -5.7585055            0   -4.6223613   0.20726105 
-Loop time of 2.26309 on 1 procs for 100 steps with 32000 atoms
+Loop time of 2.26185 on 1 procs for 100 steps with 32000 atoms
 
-Performance: 19088.920 tau/day, 44.187 timesteps/s
+Performance: 19099.377 tau/day, 44.212 timesteps/s
 99.9% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 1.9341     | 1.9341     | 1.9341     |   0.0 | 85.46
-Neigh   | 0.2442     | 0.2442     | 0.2442     |   0.0 | 10.79
-Comm    | 0.024158   | 0.024158   | 0.024158   |   0.0 |  1.07
-Output  | 0.00011611 | 0.00011611 | 0.00011611 |   0.0 |  0.01
-Modify  | 0.053222   | 0.053222   | 0.053222   |   0.0 |  2.35
-Other   |            | 0.007258   |            |       |  0.32
+Pair    | 1.9328     | 1.9328     | 1.9328     |   0.0 | 85.45
+Neigh   | 0.2558     | 0.2558     | 0.2558     |   0.0 | 11.31
+Comm    | 0.024061   | 0.024061   | 0.024061   |   0.0 |  1.06
+Output  | 0.00012612 | 0.00012612 | 0.00012612 |   0.0 |  0.01
+Modify  | 0.040887   | 0.040887   | 0.040887   |   0.0 |  1.81
+Other   |            | 0.008214   |            |       |  0.36
 
 Nlocal:    32000 ave 32000 max 32000 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

bench/log.6Oct16.lj.fixed.icc.4

@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
 # 3d Lennard-Jones melt
 
 variable	x index 1
@@ -50,20 +50,20 @@ Memory usage per processor = 4.09506 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0         1.44   -6.7733681            0   -4.6134356   -5.0197073 
      100    0.7574531   -5.7585055            0   -4.6223613   0.20726105 
-Loop time of 0.640733 on 4 procs for 100 steps with 32000 atoms
+Loop time of 0.635957 on 4 procs for 100 steps with 32000 atoms
 
-Performance: 67422.779 tau/day, 156.071 timesteps/s
-99.7% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 67929.172 tau/day, 157.243 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.49487    | 0.51733    | 0.5322     |   1.9 | 80.74
-Neigh   | 0.061131   | 0.063685   | 0.065433   |   0.6 |  9.94
-Comm    | 0.02457    | 0.042349   | 0.069598   |   8.1 |  6.61
-Output  | 5.9843e-05 | 6.3181e-05 | 6.6996e-05 |   0.0 |  0.01
-Modify  | 0.012961   | 0.013863   | 0.014491   |   0.5 |  2.16
-Other   |            | 0.003448   |            |       |  0.54
+Pair    | 0.51335    | 0.51822    | 0.52569    |   0.7 | 81.49
+Neigh   | 0.063695   | 0.064309   | 0.065397   |   0.3 | 10.11
+Comm    | 0.027525   | 0.03629    | 0.041959   |   3.1 |  5.71
+Output  | 6.3896e-05 | 6.6698e-05 | 7.081e-05  |   0.0 |  0.01
+Modify  | 0.012472   | 0.01254    | 0.012618   |   0.1 |  1.97
+Other   |            | 0.004529   |            |       |  0.71
 
 Nlocal:    8000 ave 8037 max 7964 min
 Histogram: 2 0 0 0 0 0 0 0 1 1

bench/log.6Oct16.lj.scaled.icc.4

@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
 # 3d Lennard-Jones melt
 
 variable	x index 1
@@ -50,20 +50,20 @@ Memory usage per processor = 8.13678 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0         1.44   -6.7733681            0   -4.6133849   -5.0196788 
      100   0.75841891    -5.759957            0   -4.6223375   0.20008866 
-Loop time of 2.57914 on 4 procs for 100 steps with 128000 atoms
+Loop time of 2.55762 on 4 procs for 100 steps with 128000 atoms
 
-Performance: 16749.768 tau/day, 38.773 timesteps/s
+Performance: 16890.677 tau/day, 39.099 timesteps/s
 99.8% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 2.042      | 2.1092     | 2.1668     |   3.1 | 81.78
-Neigh   | 0.23982    | 0.24551    | 0.25233    |   1.0 |  9.52
-Comm    | 0.067088   | 0.13887    | 0.22681    |  15.7 |  5.38
-Output  | 0.00013185 | 0.00021666 | 0.00027108 |   0.4 |  0.01
-Modify  | 0.060348   | 0.071269   | 0.077063   |   2.5 |  2.76
-Other   |            | 0.01403    |            |       |  0.54
+Pair    | 2.0583     | 2.0988     | 2.1594     |   2.6 | 82.06
+Neigh   | 0.24411    | 0.24838    | 0.25585    |   0.9 |  9.71
+Comm    | 0.066397   | 0.13872    | 0.1863     |  11.9 |  5.42
+Output  | 0.00012994 | 0.00021023 | 0.00025702 |   0.3 |  0.01
+Modify  | 0.055533   | 0.058343   | 0.061791   |   1.2 |  2.28
+Other   |            | 0.0132     |            |       |  0.52
 
 Nlocal:    32000 ave 32060 max 31939 min
 Histogram: 1 0 1 0 0 0 0 1 0 1

bench/log.6Oct16.rhodo.fixed.icc.1

@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
 # Rhodopsin model
 
 units           real
@@ -56,6 +56,7 @@ timestep        2.0
 
 run		100
 PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
   G vector (1/distance) = 0.248835
   grid = 25 32 32
   stencil order = 5
@@ -70,41 +71,41 @@ Neighbor list info ...
   master list distance cutoff = 12
   ghost atom cutoff = 12
   binsize = 6 -> bins = 10 13 13
-Memory usage per processor = 91.7487 Mbytes
+Memory usage per processor = 93.2721 Mbytes
 ---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
 TotEng   =    -25356.2064 KinEng   =     21444.8313 Temp     =       299.0397 
 PotEng   =    -46801.0377 E_bond   =      2537.9940 E_angle  =     10921.3742 
 E_dihed  =      5211.7865 E_impro  =       213.5116 E_vdwl   =     -2307.8634 
-E_coul   =    207025.8927 E_long   =   -270403.7333 Press    =      -142.6035 
+E_coul   =    207025.8927 E_long   =   -270403.7333 Press    =      -149.3301 
 Volume   =    307995.0335 
----------------- Step       50 ----- CPU =     17.6362 (sec) ----------------
-TotEng   =    -25330.0828 KinEng   =     21501.0029 Temp     =       299.8230 
-PotEng   =    -46831.0857 E_bond   =      2471.7004 E_angle  =     10836.4975 
-E_dihed  =      5239.6299 E_impro  =       227.1218 E_vdwl   =     -1993.2754 
-E_coul   =    206797.6331 E_long   =   -270410.3930 Press    =       237.6701 
-Volume   =    308031.5639 
----------------- Step      100 ----- CPU =     35.9089 (sec) ----------------
-TotEng   =    -25290.7593 KinEng   =     21592.0117 Temp     =       301.0920 
-PotEng   =    -46882.7709 E_bond   =      2567.9807 E_angle  =     10781.9408 
-E_dihed  =      5198.7432 E_impro  =       216.7834 E_vdwl   =     -1902.4783 
-E_coul   =    206659.2326 E_long   =   -270404.9733 Press    =         6.9960 
-Volume   =    308133.9888 
-Loop time of 35.9089 on 1 procs for 100 steps with 32000 atoms
+---------------- Step       50 ----- CPU =     17.2007 (sec) ----------------
+TotEng   =    -25330.0321 KinEng   =     21501.0036 Temp     =       299.8230 
+PotEng   =    -46831.0357 E_bond   =      2471.7033 E_angle  =     10836.5108 
+E_dihed  =      5239.6316 E_impro  =       227.1219 E_vdwl   =     -1993.2763 
+E_coul   =    206797.6655 E_long   =   -270410.3927 Press    =       237.6866 
+Volume   =    308031.5640 
+---------------- Step      100 ----- CPU =     35.0315 (sec) ----------------
+TotEng   =    -25290.7387 KinEng   =     21591.9096 Temp     =       301.0906 
+PotEng   =    -46882.6484 E_bond   =      2567.9789 E_angle  =     10781.9556 
+E_dihed  =      5198.7493 E_impro  =       216.7863 E_vdwl   =     -1902.6458 
+E_coul   =    206659.5006 E_long   =   -270404.9733 Press    =         6.7898 
+Volume   =    308133.9933 
+Loop time of 35.0316 on 1 procs for 100 steps with 32000 atoms
 
-Performance: 0.481 ns/day, 49.874 hours/ns, 2.785 timesteps/s
+Performance: 0.493 ns/day, 48.655 hours/ns, 2.855 timesteps/s
 99.9% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 25.731     | 25.731     | 25.731     |   0.0 | 71.66
-Bond    | 1.2771     | 1.2771     | 1.2771     |   0.0 |  3.56
-Kspace  | 3.2094     | 3.2094     | 3.2094     |   0.0 |  8.94
-Neigh   | 4.4538     | 4.4538     | 4.4538     |   0.0 | 12.40
-Comm    | 0.068507   | 0.068507   | 0.068507   |   0.0 |  0.19
-Output  | 0.00025916 | 0.00025916 | 0.00025916 |   0.0 |  0.00
-Modify  | 1.1417     | 1.1417     | 1.1417     |   0.0 |  3.18
-Other   |            | 0.027      |            |       |  0.08
+Pair    | 25.021     | 25.021     | 25.021     |   0.0 | 71.42
+Bond    | 1.2834     | 1.2834     | 1.2834     |   0.0 |  3.66
+Kspace  | 3.2116     | 3.2116     | 3.2116     |   0.0 |  9.17
+Neigh   | 4.2767     | 4.2767     | 4.2767     |   0.0 | 12.21
+Comm    | 0.069283   | 0.069283   | 0.069283   |   0.0 |  0.20
+Output  | 0.00028205 | 0.00028205 | 0.00028205 |   0.0 |  0.00
+Modify  | 1.14       | 1.14       | 1.14       |   0.0 |  3.25
+Other   |            | 0.02938    |            |       |  0.08
 
 Nlocal:    32000 ave 32000 max 32000 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -113,9 +114,9 @@ Histogram: 1 0 0 0 0 0 0 0 0 0
 Neighs:    1.20281e+07 ave 1.20281e+07 max 1.20281e+07 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
 
-Total # of neighbors = 12028107
+Total # of neighbors = 12028098
 Ave neighs/atom = 375.878
 Ave special neighs/atom = 7.43187
 Neighbor list builds = 11
 Dangerous builds = 0
-Total wall time: 0:00:37
+Total wall time: 0:00:36

bench/log.6Oct16.rhodo.fixed.icc.4

@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
 # Rhodopsin model
 
 units           real
@@ -56,6 +56,7 @@ timestep        2.0
 
 run		100
 PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
   G vector (1/distance) = 0.248835
   grid = 25 32 32
   stencil order = 5
@@ -70,52 +71,52 @@ Neighbor list info ...
   master list distance cutoff = 12
   ghost atom cutoff = 12
   binsize = 6 -> bins = 10 13 13
-Memory usage per processor = 36.629 Mbytes
+Memory usage per processor = 37.3604 Mbytes
 ---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
 TotEng   =    -25356.2064 KinEng   =     21444.8313 Temp     =       299.0397 
 PotEng   =    -46801.0377 E_bond   =      2537.9940 E_angle  =     10921.3742 
 E_dihed  =      5211.7865 E_impro  =       213.5116 E_vdwl   =     -2307.8634 
-E_coul   =    207025.8927 E_long   =   -270403.7333 Press    =      -142.6035 
+E_coul   =    207025.8927 E_long   =   -270403.7333 Press    =      -149.3301 
 Volume   =    307995.0335 
----------------- Step       50 ----- CPU =      4.7461 (sec) ----------------
-TotEng   =    -25330.0828 KinEng   =     21501.0029 Temp     =       299.8230 
-PotEng   =    -46831.0857 E_bond   =      2471.7004 E_angle  =     10836.4975 
-E_dihed  =      5239.6299 E_impro  =       227.1218 E_vdwl   =     -1993.2754 
-E_coul   =    206797.6331 E_long   =   -270410.3930 Press    =       237.6701 
-Volume   =    308031.5639 
----------------- Step      100 ----- CPU =      9.6332 (sec) ----------------
-TotEng   =    -25290.7591 KinEng   =     21592.0117 Temp     =       301.0920 
-PotEng   =    -46882.7708 E_bond   =      2567.9807 E_angle  =     10781.9408 
-E_dihed  =      5198.7432 E_impro  =       216.7834 E_vdwl   =     -1902.4783 
-E_coul   =    206659.2327 E_long   =   -270404.9733 Press    =         6.9960 
-Volume   =    308133.9888 
-Loop time of 9.63322 on 4 procs for 100 steps with 32000 atoms
+---------------- Step       50 ----- CPU =      4.6056 (sec) ----------------
+TotEng   =    -25330.0321 KinEng   =     21501.0036 Temp     =       299.8230 
+PotEng   =    -46831.0357 E_bond   =      2471.7033 E_angle  =     10836.5108 
+E_dihed  =      5239.6316 E_impro  =       227.1219 E_vdwl   =     -1993.2763 
+E_coul   =    206797.6655 E_long   =   -270410.3927 Press    =       237.6866 
+Volume   =    308031.5640 
+---------------- Step      100 ----- CPU =      9.3910 (sec) ----------------
+TotEng   =    -25290.7386 KinEng   =     21591.9096 Temp     =       301.0906 
+PotEng   =    -46882.6482 E_bond   =      2567.9789 E_angle  =     10781.9556 
+E_dihed  =      5198.7493 E_impro  =       216.7863 E_vdwl   =     -1902.6458 
+E_coul   =    206659.5007 E_long   =   -270404.9733 Press    =         6.7898 
+Volume   =    308133.9933 
+Loop time of 9.39107 on 4 procs for 100 steps with 32000 atoms
 
-Performance: 1.794 ns/day, 13.379 hours/ns, 10.381 timesteps/s
-99.9% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 1.840 ns/day, 13.043 hours/ns, 10.648 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 6.4364     | 6.5993     | 6.7208     |   4.7 | 68.51
-Bond    | 0.30755    | 0.32435    | 0.35704    |   3.4 |  3.37
-Kspace  | 0.92248    | 1.0782     | 1.2597     |  13.0 | 11.19
-Neigh   | 1.1669     | 1.1672     | 1.1675     |   0.0 | 12.12
-Comm    | 0.094674   | 0.098065   | 0.10543    |   1.4 |  1.02
-Output  | 0.00015521 | 0.00016224 | 0.00018215 |   0.1 |  0.00
-Modify  | 0.32982    | 0.34654    | 0.35365    |   1.6 |  3.60
-Other   |            | 0.01943    |            |       |  0.20
+Pair    | 6.2189     | 6.3266     | 6.6072     |   6.5 | 67.37
+Bond    | 0.30793    | 0.32122    | 0.3414     |   2.4 |  3.42
+Kspace  | 0.87994    | 1.1644     | 1.2855     |  15.3 | 12.40
+Neigh   | 1.1358     | 1.136      | 1.1362     |   0.0 | 12.10
+Comm    | 0.08292    | 0.084935   | 0.087077   |   0.5 |  0.90
+Output  | 0.00015712 | 0.00016558 | 0.00018501 |   0.1 |  0.00
+Modify  | 0.33717    | 0.34246    | 0.34794    |   0.7 |  3.65
+Other   |            | 0.01526    |            |       |  0.16
 
 Nlocal:    8000 ave 8143 max 7933 min
 Histogram: 1 2 0 0 0 0 0 0 0 1
 Nghost:    22733.5 ave 22769 max 22693 min
 Histogram: 1 0 0 0 0 2 0 0 0 1
-Neighs:    3.00703e+06 ave 3.0975e+06 max 2.96493e+06 min
+Neighs:    3.00702e+06 ave 3.0975e+06 max 2.96492e+06 min
 Histogram: 1 2 0 0 0 0 0 0 0 1
 
-Total # of neighbors = 12028107
+Total # of neighbors = 12028098
 Ave neighs/atom = 375.878
 Ave special neighs/atom = 7.43187
 Neighbor list builds = 11
 Dangerous builds = 0
-Total wall time: 0:00:10
+Total wall time: 0:00:09

bench/log.6Oct16.rhodo.scaled.icc.4

@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
 # Rhodopsin model
 
 variable	x index 1
@@ -77,6 +77,7 @@ timestep        2.0
 
 run		100
 PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
   G vector (1/distance) = 0.248593
   grid = 48 60 36
   stencil order = 5
@@ -91,52 +92,52 @@ Neighbor list info ...
   master list distance cutoff = 12
   ghost atom cutoff = 12
   binsize = 6 -> bins = 19 26 13
-Memory usage per processor = 95.5339 Mbytes
+Memory usage per processor = 96.9597 Mbytes
 ---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
 TotEng   =   -101425.4887 KinEng   =     85779.3251 Temp     =       299.0304 
 PotEng   =   -187204.8138 E_bond   =     10151.9760 E_angle  =     43685.4968 
 E_dihed  =     20847.1460 E_impro  =       854.0463 E_vdwl   =     -9231.4537 
-E_coul   =    827053.5824 E_long   =  -1080565.6077 Press    =      -142.3092 
+E_coul   =    827053.5824 E_long   =  -1080565.6077 Press    =      -149.0358 
 Volume   =   1231980.1340 
----------------- Step       50 ----- CPU =     18.7806 (sec) ----------------
-TotEng   =   -101320.2677 KinEng   =     86003.4837 Temp     =       299.8118 
-PotEng   =   -187323.7514 E_bond   =      9887.1072 E_angle  =     43346.7922 
-E_dihed  =     20958.7032 E_impro  =       908.4715 E_vdwl   =     -7973.4457 
-E_coul   =    826141.3831 E_long   =  -1080592.7629 Press    =       238.0161 
-Volume   =   1232126.1855 
----------------- Step      100 ----- CPU =     38.3684 (sec) ----------------
-TotEng   =   -101158.1849 KinEng   =     86355.6149 Temp     =       301.0393 
-PotEng   =   -187513.7998 E_bond   =     10272.0693 E_angle  =     43128.6454 
-E_dihed  =     20793.9759 E_impro  =       867.0826 E_vdwl   =     -7586.7186 
-E_coul   =    825583.7122 E_long   =  -1080572.5667 Press    =        15.2151 
-Volume   =   1232535.8423 
-Loop time of 38.3684 on 4 procs for 100 steps with 128000 atoms
+---------------- Step       50 ----- CPU =     18.1689 (sec) ----------------
+TotEng   =   -101320.0211 KinEng   =     86003.4933 Temp     =       299.8118 
+PotEng   =   -187323.5144 E_bond   =      9887.1189 E_angle  =     43346.8448 
+E_dihed  =     20958.7108 E_impro  =       908.4721 E_vdwl   =     -7973.4486 
+E_coul   =    826141.5493 E_long   =  -1080592.7617 Press    =       238.0404 
+Volume   =   1232126.1814 
+---------------- Step      100 ----- CPU =     37.2027 (sec) ----------------
+TotEng   =   -101157.9546 KinEng   =     86355.7413 Temp     =       301.0398 
+PotEng   =   -187513.6959 E_bond   =     10272.0456 E_angle  =     43128.7018 
+E_dihed  =     20794.0107 E_impro  =       867.0928 E_vdwl   =     -7587.2409 
+E_coul   =    825584.2416 E_long   =  -1080572.5474 Press    =        15.1729 
+Volume   =   1232535.8440 
+Loop time of 37.2028 on 4 procs for 100 steps with 128000 atoms
 
-Performance: 0.450 ns/day, 53.289 hours/ns, 2.606 timesteps/s
+Performance: 0.464 ns/day, 51.671 hours/ns, 2.688 timesteps/s
 99.9% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 26.205     | 26.538     | 26.911     |   5.0 | 69.17
-Bond    | 1.298      | 1.3125     | 1.3277     |   1.0 |  3.42
-Kspace  | 3.7099     | 4.0992     | 4.4422     |  13.3 | 10.68
-Neigh   | 4.6137     | 4.6144     | 4.615      |   0.0 | 12.03
-Comm    | 0.21398    | 0.21992    | 0.22886    |   1.2 |  0.57
-Output  | 0.00030518 | 0.00031543 | 0.00033307 |   0.1 |  0.00
-Modify  | 1.5066     | 1.5232     | 1.5388     |   1.0 |  3.97
-Other   |            | 0.06051    |            |       |  0.16
+Pair    | 25.431     | 25.738     | 25.984     |   4.0 | 69.18
+Bond    | 1.2966     | 1.3131     | 1.3226     |   0.9 |  3.53
+Kspace  | 3.7563     | 4.0123     | 4.3127     |  10.0 | 10.79
+Neigh   | 4.3778     | 4.378      | 4.3782     |   0.0 | 11.77
+Comm    | 0.1903     | 0.19549    | 0.20485    |   1.3 |  0.53
+Output  | 0.00031805 | 0.00037521 | 0.00039601 |   0.2 |  0.00
+Modify  | 1.4861     | 1.5051     | 1.5122     |   0.9 |  4.05
+Other   |            | 0.05992    |            |       |  0.16
 
 Nlocal:    32000 ave 32000 max 32000 min
 Histogram: 4 0 0 0 0 0 0 0 0 0
 Nghost:    47957 ave 47957 max 47957 min
 Histogram: 4 0 0 0 0 0 0 0 0 0
-Neighs:    1.20281e+07 ave 1.20572e+07 max 1.1999e+07 min
+Neighs:    1.20281e+07 ave 1.20572e+07 max 1.19991e+07 min
 Histogram: 2 0 0 0 0 0 0 0 0 2
 
-Total # of neighbors = 48112472
+Total # of neighbors = 48112540
 Ave neighs/atom = 375.879
 Ave special neighs/atom = 7.43187
 Neighbor list builds = 11
 Dangerous builds = 0
-Total wall time: 0:00:39
+Total wall time: 0:00:38

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="6 Oct 2016 version">
+<META NAME="docnumber" CONTENT="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
-6 Oct 2016 version :c,h4
+11 Oct 2016 version :c,h4
 
 Version info: :h4
 

doc/src/dump_modify.txt

@@ -475,9 +475,6 @@ be generated by variable formulas that use comparison or Boolean math
 operators or special functions like gmask() and rmask() and grmask().
 See the "variable"_variable.html command doc page for details.
 
-NOTE: The LAST option, discussed below, is not yet implemented.  It
-will be soon.
-
 The specified value must be a simple numeric value or the word LAST.
 If LAST is used, it refers to the value of the attribute the last time
 the dump command was invoked to produce a snapshot.  This is a way to

doc/src/fix_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_wall_gran_region.txt

@@ -42,7 +42,7 @@ Here are snapshots of example models using this command.
 Corresponding input scripts can be found in examples/granregion.
 Click on the images to see a bigger picture.  Movies of these
 simulations are "here on the Movies
-page"_http://lammps.sandia.gov/movies.html#granregion.html of the
+page"_http://lammps.sandia.gov/movies.html#granregion of the
 LAMMPS web site.
 
 :image(JPG/gran_funnel_small.jpg,JPG/gran_funnel.png)

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
-the input script that wrote the restart file.  If a match is found,
-LAMMPS prints a message indicating that the fix is being re-enabled.
-If no match is found before the first run or minimization is performed
-by the new script, the "state" information for the saved fix is
-discarded.  See the doc pages for individual fixes for info on which
-ones can be restarted in this manner.
+new input script must be of the same style and use the same fix-ID as
+was used in the input script that wrote the restart file.
+
+If a match is found, LAMMPS prints a message indicating that the fix
+is being re-enabled.  If no match is found before the first run or
+minimization is performed by the new script, the "state" information
+for the saved fix is discarded.  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/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")

lib/colvars/colvarmodule.cpp

@@ -1557,5 +1557,5 @@ size_t const colvarmodule::cv_prec  = 14;
 size_t const colvarmodule::cv_width = 21;
 size_t const colvarmodule::en_prec  = 14;
 size_t const colvarmodule::en_width = 21;
-std::string const colvarmodule::line_marker =
+const char * const colvarmodule::line_marker = (const char *)
   "----------------------------------------------------------------------\n";

lib/colvars/colvarmodule.h

@@ -366,7 +366,7 @@ public:
   /// Number of characters to represent the collective variables energy
   static size_t const en_width;
   /// Line separator in the log output
-  static std::string const line_marker;
+  static const char * const line_marker;
 
 
   // proxy functions

src/GRANULAR/fix_wall_gran.cpp

@@ -37,7 +37,7 @@ using namespace MathConst;
 
 // XYZ PLANE need to be 0,1,2
 
-enum{XPLANE=0,YPLANE=1,ZPLANE=2,ZCYLINDER,REGION}; 
+enum{XPLANE=0,YPLANE=1,ZPLANE=2,ZCYLINDER,REGION};
 enum{HOOKE,HOOKE_HISTORY,HERTZ_HISTORY,BONDED_HISTORY};
 enum{NONE,CONSTANT,EQUAL};
 
@@ -78,21 +78,21 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
     kn = force->numeric(FLERR,arg[4]);
     if (strcmp(arg[5],"NULL") == 0) kt = kn * 2.0/7.0;
     else kt = force->numeric(FLERR,arg[5]);
-    
+
     gamman = force->numeric(FLERR,arg[6]);
     if (strcmp(arg[7],"NULL") == 0) gammat = 0.5 * gamman;
     else gammat = force->numeric(FLERR,arg[7]);
-    
+
     xmu = force->numeric(FLERR,arg[8]);
     int dampflag = force->inumeric(FLERR,arg[9]);
     if (dampflag == 0) gammat = 0.0;
-    
+
     if (kn < 0.0 || kt < 0.0 || gamman < 0.0 || gammat < 0.0 ||
         xmu < 0.0 || xmu > 10000.0 || dampflag < 0 || dampflag > 1)
       error->all(FLERR,"Illegal fix wall/gran command");
-    
+
     // convert Kn and Kt from pressure units to force/distance^2 if Hertzian
-    
+
     if (pairstyle == HERTZ_HISTORY) {
       kn /= force->nktv2p;
       kt /= force->nktv2p;
@@ -119,7 +119,7 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
   }
 
   // wallstyle args
-  
+
   idregion = NULL;
 
   if (strcmp(arg[iarg],"xplane") == 0) {
@@ -160,12 +160,12 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
     strcpy(idregion,arg[iarg+1]);
     iarg += 2;
   }
-  
+
   // optional args
 
   wiggle = 0;
   wshear = 0;
-    
+
   while (iarg < narg) {
     if (strcmp(arg[iarg],"wiggle") == 0) {
       if (iarg+4 > narg) error->all(FLERR,"Illegal fix wall/gran command");
@@ -188,7 +188,7 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
       iarg += 3;
     } else error->all(FLERR,"Illegal fix wall/gran command");
   }
-  
+
   if (wallstyle == XPLANE && domain->xperiodic)
     error->all(FLERR,"Cannot use wall in periodic dimension");
   if (wallstyle == YPLANE && domain->yperiodic)
@@ -197,7 +197,7 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
     error->all(FLERR,"Cannot use wall in periodic dimension");
   if (wallstyle == ZCYLINDER && (domain->xperiodic || domain->yperiodic))
     error->all(FLERR,"Cannot use wall in periodic dimension");
-  
+
   if (wiggle && wshear)
     error->all(FLERR,"Cannot wiggle and shear fix wall/gran");
   if (wiggle && wallstyle == ZCYLINDER && axis != 2)
@@ -212,15 +212,15 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
     error->all(FLERR,"Cannot wiggle or shear with fix wall/gran/region");
 
   // setup oscillations
-  
+
   if (wiggle) omega = 2.0*MY_PI / period;
-    
+
   // perform initial allocation of atom-based arrays
   // register with Atom class
 
   if (pairstyle == BONDED_HISTORY) sheardim = 7;
   else sheardim = 3;
-  
+
   shearone = NULL;
   grow_arrays(atom->nmax);
   atom->add_callback(0);
@@ -348,7 +348,7 @@ void FixWallGran::post_force(int vflag)
     }
     vwall[axis] = amplitude*omega*sin(arg);
   } else if (wshear) vwall[axis] = vshear;
-  
+
   // loop over all my atoms
   // rsq = distance from wall
   // dx,dy,dz = signed distance from wall
@@ -358,7 +358,7 @@ void FixWallGran::post_force(int vflag)
   // compute force and torque on atom if close enough to wall
   //   via wall potential matched to pair potential
   // set shear if pair potential stores history
-  
+
   double **x = atom->x;
   double **v = atom->v;
   double **f = atom->f;
@@ -368,14 +368,14 @@ void FixWallGran::post_force(int vflag)
   double *rmass = atom->rmass;
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
-  
+
   rwall = 0.0;
 
   for (int i = 0; i < nlocal; i++) {
     if (mask[i] & groupbit) {
-      
+
       dx = dy = dz = 0.0;
-      
+
       if (wallstyle == XPLANE) {
         del1 = x[i][0] - wlo;
         del2 = whi - x[i][0];
@@ -401,7 +401,7 @@ void FixWallGran::post_force(int vflag)
           dx = -delr/delxy * x[i][0];
           dy = -delr/delxy * x[i][1];
           // rwall = -2r_c if inside cylinder, 2r_c outside
-          rwall = 2*(1-2*(delxy < cylradius))*cylradius; 
+          rwall = (delxy < cylradius) ? -2*cylradius : 2*cylradius;
           if (wshear && axis != 2) {
             vwall[0] += vshear * x[i][1]/delxy;
             vwall[1] += -vshear * x[i][0]/delxy;
@@ -409,12 +409,12 @@ void FixWallGran::post_force(int vflag)
           }
         }
       }
-      
+
       rsq = dx*dx + dy*dy + dz*dz;
-      
+
       if (rsq > radius[i]*radius[i]) {
         if (history)
-          for (j = 0; j < sheardim; j++) 
+          for (j = 0; j < sheardim; j++)
             shearone[i][j] = 0.0;
 
       } else {
@@ -467,66 +467,66 @@ void FixWallGran::hooke(double rsq, double dx, double dy, double dz,
   rsqinv = 1.0/rsq;
 
   // relative translational velocity
-  
+
   vr1 = v[0] - vwall[0];
   vr2 = v[1] - vwall[1];
   vr3 = v[2] - vwall[2];
-  
+
   // normal component
-  
+
   vnnr = vr1*dx + vr2*dy + vr3*dz;
   vn1 = dx*vnnr * rsqinv;
   vn2 = dy*vnnr * rsqinv;
   vn3 = dz*vnnr * rsqinv;
-  
+
   // tangential component
-  
+
   vt1 = vr1 - vn1;
   vt2 = vr2 - vn2;
   vt3 = vr3 - vn3;
-  
+
   // relative rotational velocity
-  
+
   wr1 = radius*omega[0] * rinv;
   wr2 = radius*omega[1] * rinv;
   wr3 = radius*omega[2] * rinv;
-  
+
   // normal forces = Hookian contact + normal velocity damping
-  
+
   damp = meff*gamman*vnnr*rsqinv;
   ccel = kn*(radius-r)*rinv - damp;
-  
+
   // relative velocities
-  
+
   vtr1 = vt1 - (dz*wr2-dy*wr3);
   vtr2 = vt2 - (dx*wr3-dz*wr1);
   vtr3 = vt3 - (dy*wr1-dx*wr2);
   vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3;
   vrel = sqrt(vrel);
-  
+
   // force normalization
-  
+
   fn = xmu * fabs(ccel*r);
   fs = meff*gammat*vrel;
   if (vrel != 0.0) ft = MIN(fn,fs) / vrel;
   else ft = 0.0;
-  
+
   // tangential force due to tangential velocity damping
-  
+
   fs1 = -ft*vtr1;
   fs2 = -ft*vtr2;
   fs3 = -ft*vtr3;
-  
+
   // forces & torques
-  
+
   fx = dx*ccel + fs1;
   fy = dy*ccel + fs2;
   fz = dz*ccel + fs3;
-  
+
   f[0] += fx;
   f[1] += fy;
   f[2] += fz;
-  
+
   tor1 = rinv * (dy*fs3 - dz*fs2);
   tor2 = rinv * (dz*fs1 - dx*fs3);
   tor3 = rinv * (dx*fs2 - dy*fs1);
@@ -546,60 +546,60 @@ void FixWallGran::hooke_history(double rsq, double dx, double dy, double dz,
   double wr1,wr2,wr3,damp,ccel,vtr1,vtr2,vtr3,vrel;
   double fn,fs,fs1,fs2,fs3,fx,fy,fz,tor1,tor2,tor3;
   double shrmag,rsht,rinv,rsqinv;
-  
+
   r = sqrt(rsq);
   rinv = 1.0/r;
   rsqinv = 1.0/rsq;
-  
+
   // relative translational velocity
-  
+
   vr1 = v[0] - vwall[0];
   vr2 = v[1] - vwall[1];
   vr3 = v[2] - vwall[2];
-  
+
   // normal component
-  
+
   vnnr = vr1*dx + vr2*dy + vr3*dz;
   vn1 = dx*vnnr * rsqinv;
   vn2 = dy*vnnr * rsqinv;
   vn3 = dz*vnnr * rsqinv;
-  
+
   // tangential component
-  
+
   vt1 = vr1 - vn1;
   vt2 = vr2 - vn2;
   vt3 = vr3 - vn3;
-  
+
   // relative rotational velocity
-  
+
   wr1 = radius*omega[0] * rinv;
   wr2 = radius*omega[1] * rinv;
   wr3 = radius*omega[2] * rinv;
-  
+
   // normal forces = Hookian contact + normal velocity damping
-  
+
   damp = meff*gamman*vnnr*rsqinv;
   ccel = kn*(radius-r)*rinv - damp;
-  
+
   // relative velocities
-  
+
   vtr1 = vt1 - (dz*wr2-dy*wr3);
   vtr2 = vt2 - (dx*wr3-dz*wr1);
   vtr3 = vt3 - (dy*wr1-dx*wr2);
   vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3;
   vrel = sqrt(vrel);
-  
+
   // shear history effects
-  
+
   if (shearupdate) {
     shear[0] += vtr1*dt;
     shear[1] += vtr2*dt;
     shear[2] += vtr3*dt;
   }
   shrmag = sqrt(shear[0]*shear[0] + shear[1]*shear[1] + shear[2]*shear[2]);
-  
+
   // rotate shear displacements
-  
+
   rsht = shear[0]*dx + shear[1]*dy + shear[2]*dz;
   rsht = rsht*rsqinv;
   if (shearupdate) {
@@ -607,18 +607,18 @@ void FixWallGran::hooke_history(double rsq, double dx, double dy, double dz,
     shear[1] -= rsht*dy;
     shear[2] -= rsht*dz;
   }
-  
+
   // tangential forces = shear + tangential velocity damping
-  
+
   fs1 = - (kt*shear[0] + meff*gammat*vtr1);
   fs2 = - (kt*shear[1] + meff*gammat*vtr2);
   fs3 = - (kt*shear[2] + meff*gammat*vtr3);
-  
+
   // rescale frictional displacements and forces if needed
-  
+
   fs = sqrt(fs1*fs1 + fs2*fs2 + fs3*fs3);
   fn = xmu * fabs(ccel*r);
-  
+
   if (fs > fn) {
     if (shrmag != 0.0) {
       shear[0] = (fn/fs) * (shear[0] + meff*gammat*vtr1/kt) -
@@ -632,17 +632,17 @@ void FixWallGran::hooke_history(double rsq, double dx, double dy, double dz,
       fs3 *= fn/fs;
     } else fs1 = fs2 = fs3 = 0.0;
   }
-  
+
   // forces & torques
-  
+
   fx = dx*ccel + fs1;
   fy = dy*ccel + fs2;
   fz = dz*ccel + fs3;
-  
+
   f[0] += fx;
   f[1] += fy;
   f[2] += fz;
-  
+
   tor1 = rinv * (dy*fs3 - dz*fs2);
   tor2 = rinv * (dz*fs1 - dx*fs3);
   tor3 = rinv * (dx*fs2 - dy*fs1);
@@ -662,56 +662,56 @@ void FixWallGran::hertz_history(double rsq, double dx, double dy, double dz,
   double wr1,wr2,wr3,damp,ccel,vtr1,vtr2,vtr3,vrel;
   double fn,fs,fs1,fs2,fs3,fx,fy,fz,tor1,tor2,tor3;
   double shrmag,rsht,polyhertz,rinv,rsqinv;
-  
+
   r = sqrt(rsq);
   rinv = 1.0/r;
   rsqinv = 1.0/rsq;
-  
+
   // relative translational velocity
-  
+
   vr1 = v[0] - vwall[0];
   vr2 = v[1] - vwall[1];
   vr3 = v[2] - vwall[2];
-  
+
   // normal component
-  
+
   vnnr = vr1*dx + vr2*dy + vr3*dz;
   vn1 = dx*vnnr / rsq;
   vn2 = dy*vnnr / rsq;
   vn3 = dz*vnnr / rsq;
-  
+
   // tangential component
-  
+
   vt1 = vr1 - vn1;
   vt2 = vr2 - vn2;
   vt3 = vr3 - vn3;
-  
+
   // relative rotational velocity
-  
+
   wr1 = radius*omega[0] * rinv;
   wr2 = radius*omega[1] * rinv;
   wr3 = radius*omega[2] * rinv;
-  
+
   // normal forces = Hertzian contact + normal velocity damping
   // rwall = 0 is flat wall case
   // rwall positive or negative is curved wall
-  //   will break (as it should) if rwall is negative and 
+  //   will break (as it should) if rwall is negative and
   //   its absolute value < radius of particle
-  
+
   damp = meff*gamman*vnnr*rsqinv;
   ccel = kn*(radius-r)*rinv - damp;
   if (rwall == 0.0) polyhertz = sqrt((radius-r)*radius);
   else polyhertz = sqrt((radius-r)*radius*rwall/(rwall+radius));
   ccel *= polyhertz;
-  
+
   // relative velocities
-  
+
   vtr1 = vt1 - (dz*wr2-dy*wr3);
   vtr2 = vt2 - (dx*wr3-dz*wr1);
   vtr3 = vt3 - (dy*wr1-dx*wr2);
   vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3;
   vrel = sqrt(vrel);
-  
+
   // shear history effects
 
   if (shearupdate) {
@@ -720,9 +720,9 @@ void FixWallGran::hertz_history(double rsq, double dx, double dy, double dz,
     shear[2] += vtr3*dt;
   }
   shrmag = sqrt(shear[0]*shear[0] + shear[1]*shear[1] + shear[2]*shear[2]);
-  
+
   // rotate shear displacements
-  
+
   rsht = shear[0]*dx + shear[1]*dy + shear[2]*dz;
   rsht = rsht*rsqinv;
   if (shearupdate) {
@@ -730,18 +730,18 @@ void FixWallGran::hertz_history(double rsq, double dx, double dy, double dz,
     shear[1] -= rsht*dy;
     shear[2] -= rsht*dz;
   }
-  
+
   // tangential forces = shear + tangential velocity damping
-  
+
   fs1 = -polyhertz * (kt*shear[0] + meff*gammat*vtr1);
   fs2 = -polyhertz * (kt*shear[1] + meff*gammat*vtr2);
   fs3 = -polyhertz * (kt*shear[2] + meff*gammat*vtr3);
-  
+
   // rescale frictional displacements and forces if needed
-  
+
   fs = sqrt(fs1*fs1 + fs2*fs2 + fs3*fs3);
   fn = xmu * fabs(ccel*r);
-  
+
   if (fs > fn) {
     if (shrmag != 0.0) {
       shear[0] = (fn/fs) * (shear[0] + meff*gammat*vtr1/kt) -
@@ -757,7 +757,7 @@ void FixWallGran::hertz_history(double rsq, double dx, double dy, double dz,
   }
 
   // forces & torques
-  
+
   fx = dx*ccel + fs1;
   fy = dy*ccel + fs2;
   fz = dz*ccel + fs3;
@@ -765,7 +765,7 @@ void FixWallGran::hertz_history(double rsq, double dx, double dy, double dz,
   f[0] += fx;
   f[1] += fy;
   f[2] += fz;
-  
+
   tor1 = rinv * (dy*fs3 - dz*fs2);
   tor2 = rinv * (dz*fs1 - dx*fs3);
   tor3 = rinv * (dx*fs2 - dy*fs1);
@@ -864,8 +864,8 @@ void FixWallGran::bonded_history(double rsq, double dx, double dy, double dz,
 
   // use Tsuji et al form
 
-  polyhertz = 1.2728- 4.2783*0.9 + 11.087*0.9*0.9 - 22.348*0.9*0.9*0.9 + 
-    27.467*0.9*0.9*0.9*0.9 - 18.022*0.9*0.9*0.9*0.9*0.9 + 
+  polyhertz = 1.2728- 4.2783*0.9 + 11.087*0.9*0.9 - 22.348*0.9*0.9*0.9 +
+    27.467*0.9*0.9*0.9*0.9 - 18.022*0.9*0.9*0.9*0.9*0.9 +
     4.8218*0.9*0.9*0.9*0.9*0.9*0.9;
 
   gammatsuji = 0.2*sqrt(meff*kn);
@@ -969,7 +969,7 @@ void FixWallGran::bonded_history(double rsq, double dx, double dy, double dz,
   shear[6] += magtwist*dt;
 
   ktwist = 0.5*kt*(a0*aovera0)*(a0*aovera0);
-  magtortwist = -ktwist*shear[6] - 
+  magtortwist = -ktwist*shear[6] -
     0.5*polyhertz*gammatsuji*(a0*aovera0)*(a0*aovera0)*magtwist;
 
   twistcrit=TWOTHIRDS*a0*aovera0*Fcrit;
@@ -1113,11 +1113,11 @@ void FixWallGran::unpack_restart(int nlocal, int nth)
   double **extra = atom->extra;
 
   // skip to Nth set of extra values
-  
+
   int m = 0;
   for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);
   m++;
-  
+
   for (int i = 0; i < sheardim; i++)
     shearone[nlocal][i] = extra[nlocal][m++];
 }

src/USER-COLVARS/colvarproxy_lammps.cpp

@@ -193,7 +193,7 @@ double colvarproxy_lammps::compute()
   previous_step = _lmp->update->ntimestep;
 
   if (cvm::debug()) {
-    cvm::log(cvm::line_marker+
+    cvm::log(std::string(cvm::line_marker)+
              "colvarproxy_lammps, step no. "+cvm::to_str(colvars->it)+"\n"+
              "Updating internal data.\n");
   }

src/USER-MISC/fix_flow_gauss.cpp

@@ -27,6 +27,7 @@
 #include "domain.h"
 #include "error.h"
 #include "citeme.h"
+#include "respa.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
@@ -63,6 +64,8 @@ FixFlowGauss::FixFlowGauss(LAMMPS *lmp, int narg, char **arg) :
   extvector = 1;
   size_vector = 3;
   global_freq = 1;    //data available every timestep
+  respa_level_support = 1;
+  //default respa level=outermost level is set in init()
 
   dimension = domain->dimension;
 
@@ -109,9 +112,23 @@ int FixFlowGauss::setmask()
   int mask = 0;
   mask |= POST_FORCE;
   mask |= THERMO_ENERGY;
+  mask |= POST_FORCE_RESPA;
   return mask;
 }
 
+/* ---------------------------------------------------------------------- */
+
+void FixFlowGauss::init()
+{
+  //if respa level specified by fix_modify, then override default (outermost)
+  //if specified level too high, set to max level
+  if (strstr(update->integrate_style,"respa")) {
+    ilevel_respa = ((Respa *) update->integrate)->nlevels-1;
+    if (respa_level >= 0)
+      ilevel_respa = MIN(respa_level,ilevel_respa);
+  }
+}
+
 /* ----------------------------------------------------------------------
    setup is called after the initial evaluation of forces before a run, so we
    must remove the total force here too
@@ -127,7 +144,13 @@ void FixFlowGauss::setup(int vflag)
   if (mTot <= 0.0)
     error->all(FLERR,"Invalid group mass in fix flow/gauss");
 
-  post_force(vflag);
+  if (strstr(update->integrate_style,"respa")) {
+    ((Respa *) update->integrate)->copy_flevel_f(ilevel_respa);
+    post_force_respa(vflag,ilevel_respa,0);
+    ((Respa *) update->integrate)->copy_f_flevel(ilevel_respa);
+  }
+  else
+    post_force(vflag);
 }
 
 /* ----------------------------------------------------------------------
@@ -148,7 +171,6 @@ void FixFlowGauss::post_force(int vflag)
   int ii,jj;
 
   //find the total force on all atoms
-
   //initialize to zero
   double f_thisProc[3];
   for (ii=0; ii<3; ii++)
@@ -201,6 +223,11 @@ void FixFlowGauss::post_force(int vflag)
 
 }
 
+void FixFlowGauss::post_force_respa(int vflag, int ilevel, int iloop)
+{
+  if (ilevel == ilevel_respa) post_force(vflag);
+}
+
 /* ----------------------------------------------------------------------
    negative of work done by this fix
    This is only computed if requested, either with fix_modify energy yes, or with the energy keyword. Otherwise returns 0.

src/USER-MISC/fix_flow_gauss.h

@@ -30,10 +30,12 @@ FixStyle(flow/gauss,FixFlowGauss)
     public:
       FixFlowGauss(class LAMMPS *, int, char **);
       int setmask();
+      void init();
+      void setup(int);
+      void post_force(int);
+      void post_force_respa(int, int, int);
       double compute_scalar();
       double compute_vector(int n);
-      void post_force(int);
-      void setup(int);
 
     protected:
       int dimension;
@@ -44,6 +46,7 @@ FixStyle(flow/gauss,FixFlowGauss)
       double pe_tot;      //total added energy
       double dt;          //timestep
       bool workflag;      //if calculate work done by fix
+      int ilevel_respa;
 
     };
 

src/USER-OMP/fix_wall_gran_omp.cpp

@@ -25,8 +25,8 @@
 using namespace LAMMPS_NS;
 using namespace FixConst;
 
-enum{XPLANE=0,YPLANE=1,ZPLANE=2,ZCYLINDER};    // XYZ PLANE need to be 0,1,2
-enum{HOOKE,HOOKE_HISTORY,HERTZ_HISTORY};
+enum{XPLANE=0,YPLANE=1,ZPLANE=2,ZCYLINDER,REGION};    // XYZ PLANE need to be 0,1,2
+enum{HOOKE,HOOKE_HISTORY,HERTZ_HISTORY,BONDED_HISTORY};
 
 #define BIG 1.0e20
 
@@ -107,6 +107,7 @@ void FixWallGranOMP::post_force(int vflag)
 
     if (mask[i] & groupbit) {
       double dx,dy,dz,del1,del2,delxy,delr,rsq;
+      double rwall = 0.0;
 
       dx = dy = dz = 0.0;
 
@@ -128,13 +129,16 @@ void FixWallGranOMP::post_force(int vflag)
       } else if (wallstyle == ZCYLINDER) {
         delxy = sqrt(x[i][0]*x[i][0] + x[i][1]*x[i][1]);
         delr = cylradius - delxy;
-        if (delr > radius[i]) dz = cylradius;
-        else {
+        if (delr > radius[i]) {
+          dz = cylradius;
+          rwall = 0.0;
+        } else {
           dx = -delr/delxy * x[i][0];
           dy = -delr/delxy * x[i][1];
+          rwall = (delxy < cylradius) ? -2*cylradius : 2*cylradius;
           if (wshear && axis != 2) {
-            vwall[0] = vshear * x[i][1]/delxy;
-            vwall[1] = -vshear * x[i][0]/delxy;
+            vwall[0] += vshear * x[i][1]/delxy;
+            vwall[1] += -vshear * x[i][0]/delxy;
             vwall[2] = 0.0;
           }
         }
@@ -143,11 +147,10 @@ void FixWallGranOMP::post_force(int vflag)
       rsq = dx*dx + dy*dy + dz*dz;
 
       if (rsq > radius[i]*radius[i]) {
-        if (pairstyle != HOOKE) {
-          shear[i][0] = 0.0;
-          shear[i][1] = 0.0;
-          shear[i][2] = 0.0;
-        }
+        if (history)
+          for (int j = 0; j < sheardim; j++)
+            shearone[i][j] = 0.0;
+
       } else {
 
         // meff = effective mass of sphere
@@ -156,17 +159,20 @@ void FixWallGranOMP::post_force(int vflag)
         double meff = rmass[i];
         if (fix_rigid && mass_rigid[i] > 0.0) meff = mass_rigid[i];
 
-        // inovke sphere/wall interaction
+        // invoke sphere/wall interaction
 
         if (pairstyle == HOOKE)
-          hooke(rsq,dx,dy,dz,vwall,v[i],f[i],omega[i],torque[i],
-                radius[i],meff);
+          hooke(rsq,dx,dy,dz,vwall,v[i],f[i],
+                omega[i],torque[i],radius[i],meff);
         else if (pairstyle == HOOKE_HISTORY)
-          hooke_history(rsq,dx,dy,dz,vwall,v[i],f[i],omega[i],torque[i],
-                        radius[i],meff,shear[i]);
+          hooke_history(rsq,dx,dy,dz,vwall,v[i],f[i],
+                        omega[i],torque[i],radius[i],meff,shearone[i]);
         else if (pairstyle == HERTZ_HISTORY)
-          hertz_history(rsq,dx,dy,dz,vwall,v[i],f[i],omega[i],torque[i],
-                        radius[i],meff,shear[i]);
+          hertz_history(rsq,dx,dy,dz,vwall,rwall,v[i],f[i],
+                        omega[i],torque[i],radius[i],meff,shearone[i]);
+        else if (pairstyle == BONDED_HISTORY)
+          bonded_history(rsq,dx,dy,dz,vwall,rwall,v[i],f[i],
+                         omega[i],torque[i],radius[i],meff,shearone[i]);
       }
     }
   }

src/dump_custom.cpp

@@ -26,6 +26,7 @@
 #include "modify.h"
 #include "compute.h"
 #include "fix.h"
+#include "fix_store.h"
 #include "memory.h"
 #include "error.h"
 
@@ -82,10 +83,17 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
   buffer_flag = 1;
   iregion = -1;
   idregion = NULL;
+
   nthresh = 0;
   thresh_array = NULL;
   thresh_op = NULL;
   thresh_value = NULL;
+  thresh_last = NULL;
+
+  nthreshlast = 0;
+  thresh_fix = NULL;
+  thresh_fixID = NULL;
+  thresh_first = NULL;
 
   // computes, fixes, variables which the dump accesses
 
@@ -193,6 +201,17 @@ DumpCustom::~DumpCustom()
   memory->destroy(thresh_array);
   memory->destroy(thresh_op);
   memory->destroy(thresh_value);
+  memory->destroy(thresh_last);
+
+  // check nfix in case all fixes have already been deleted
+
+  for (int i = 0; i < nthreshlast; i++) {
+    if (modify->nfix) modify->delete_fix(thresh_fixID[i]);
+    delete [] thresh_fixID[i];
+  }
+  memory->sfree(thresh_fix);
+  memory->sfree(thresh_fixID);
+  memory->destroy(thresh_first);
 
   for (int i = 0; i < ncompute; i++) delete [] id_compute[i];
   memory->sfree(id_compute);
@@ -498,9 +517,10 @@ int DumpCustom::count()
   // un-choose if any threshold criterion isn't met
 
   if (nthresh) {
-    double *ptr;
+    double *ptr,*ptrhold;
+    double *values;
     double value;
-    int nstride;
+    int nstride,lastflag;
     int nlocal = atom->nlocal;
 
     for (int ithresh = 0; ithresh < nthresh; ithresh++) {
@@ -926,32 +946,91 @@ int DumpCustom::count()
       }
 
       // unselect atoms that don't meet threshold criterion
+      // compare to single value or values stored in threshfix
+      // copy ptr attribute into thresh_fix if this is first comparison
 
-      value = thresh_value[ithresh];
+      if (thresh_last[ithresh] < 0) {
+	lastflag = 0;
+	value = thresh_value[ithresh];
+      } else {
+	lastflag = 1;
+	int ilast = thresh_last[ithresh];
+	values = thresh_fix[ilast]->vstore;
+	ptrhold = ptr;
+	if (thresh_first[ilast]) {
+	  thresh_first[ilast] = 0;
+	  for (i = 0; i < nlocal; i++, ptr += nstride) values[i] = *ptr;
+	  ptr = ptrhold;
+	}
+      }
 
       if (thresh_op[ithresh] == LT) {
-        for (i = 0; i < nlocal; i++, ptr += nstride)
-          if (choose[i] && *ptr >= value) choose[i] = 0;
+	if (lastflag) {
+	  for (i = 0; i < nlocal; i++, ptr += nstride)
+	    if (choose[i] && *ptr >= values[i]) choose[i] = 0;
+	} else {
+	  for (i = 0; i < nlocal; i++, ptr += nstride)
+	    if (choose[i] && *ptr >= value) choose[i] = 0;
+	}
       } else if (thresh_op[ithresh] == LE) {
-        for (i = 0; i < nlocal; i++, ptr += nstride)
-          if (choose[i] && *ptr > value) choose[i] = 0;
+	if (lastflag) {
+	  for (i = 0; i < nlocal; i++, ptr += nstride)
+	    if (choose[i] && *ptr > values[i]) choose[i] = 0;
+	} else {
+	  for (i = 0; i < nlocal; i++, ptr += nstride)
+	    if (choose[i] && *ptr > value) choose[i] = 0;
+	}
       } else if (thresh_op[ithresh] == GT) {
-        for (i = 0; i < nlocal; i++, ptr += nstride)
-          if (choose[i] && *ptr <= value) choose[i] = 0;
+	if (lastflag) {
+	  for (i = 0; i < nlocal; i++, ptr += nstride)
+	    if (choose[i] && *ptr <= values[i]) choose[i] = 0;
+	} else {
+	  for (i = 0; i < nlocal; i++, ptr += nstride)
+	    if (choose[i] && *ptr <= value) choose[i] = 0;
+	}
       } else if (thresh_op[ithresh] == GE) {
-        for (i = 0; i < nlocal; i++, ptr += nstride)
-          if (choose[i] && *ptr < value) choose[i] = 0;
+	if (lastflag) {
+	  for (i = 0; i < nlocal; i++, ptr += nstride)
+	    if (choose[i] && *ptr < values[i]) choose[i] = 0;
+	} else {
+	  for (i = 0; i < nlocal; i++, ptr += nstride)
+	    if (choose[i] && *ptr < value) choose[i] = 0;
+	}
       } else if (thresh_op[ithresh] == EQ) {
-        for (i = 0; i < nlocal; i++, ptr += nstride)
-          if (choose[i] && *ptr != value) choose[i] = 0;
+	if (lastflag) {
+	  for (i = 0; i < nlocal; i++, ptr += nstride)
+	    if (choose[i] && *ptr != values[i]) choose[i] = 0;
+	} else {
+	  for (i = 0; i < nlocal; i++, ptr += nstride)
+	    if (choose[i] && *ptr != value) choose[i] = 0;
+	}
       } else if (thresh_op[ithresh] == NEQ) {
-        for (i = 0; i < nlocal; i++, ptr += nstride)
-          if (choose[i] && *ptr == value) choose[i] = 0;
+	if (lastflag) {
+	  for (i = 0; i < nlocal; i++, ptr += nstride)
+	    if (choose[i] && *ptr == values[i]) choose[i] = 0;
+	} else {
+	  for (i = 0; i < nlocal; i++, ptr += nstride)
+	    if (choose[i] && *ptr == value) choose[i] = 0;
+	}
       } else if (thresh_op[ithresh] == XOR) {
-        for (i = 0; i < nlocal; i++, ptr += nstride)
-          if (choose[i] && (*ptr == 0.0 && value == 0.0) || 
-              (*ptr != 0.0 && value != 0.0))
-            choose[i] = 0;
+	if (lastflag) {
+	  for (i = 0; i < nlocal; i++, ptr += nstride)
+	    if (choose[i] && (*ptr == 0.0 && values[i] == 0.0) || 
+		(*ptr != 0.0 && values[i] != 0.0))
+	      choose[i] = 0;
+	} else {
+	  for (i = 0; i < nlocal; i++, ptr += nstride)
+	    if (choose[i] && (*ptr == 0.0 && value == 0.0) || 
+		(*ptr != 0.0 && value != 0.0))
+	      choose[i] = 0;
+	}
+      }
+
+      // update values stored in threshfix
+
+      if (lastflag) {
+	ptr = ptrhold;
+	for (i = 0; i < nlocal; i++, ptr += nstride) values[i] = *ptr;
       }
     }
   }
@@ -1594,8 +1673,16 @@ int DumpCustom::modify_param(int narg, char **arg)
         thresh_array = NULL;
         thresh_op = NULL;
         thresh_value = NULL;
+        thresh_last = NULL;
+	for (int i = 0; i < nthreshlast; i++) {
+	  modify->delete_fix(thresh_fixID[i]);
+	  delete [] thresh_fixID[i];
+	}
+	thresh_fix = NULL;
+	thresh_fixID = NULL;
+        thresh_first = NULL;
       }
-      nthresh = 0;
+      nthresh = nthreshlast = 0;
       return 2;
     }
 
@@ -1606,7 +1693,8 @@ int DumpCustom::modify_param(int narg, char **arg)
     memory->grow(thresh_array,nthresh+1,"dump:thresh_array");
     memory->grow(thresh_op,(nthresh+1),"dump:thresh_op");
     memory->grow(thresh_value,(nthresh+1),"dump:thresh_value");
-
+    memory->grow(thresh_last,(nthresh+1),"dump:thresh_last");
+    
     // set attribute type of threshold
     // customize by adding to if statement
 
@@ -1830,7 +1918,7 @@ int DumpCustom::modify_param(int narg, char **arg)
       field2index[nfield+nthresh] = add_custom(suffix,0);
       delete [] suffix;
 
-    } else error->all(FLERR,"Invalid dump_modify threshhold operator");
+    } else error->all(FLERR,"Invalid dump_modify threshold operator");
 
     // set operation type of threshold
 
@@ -1843,9 +1931,43 @@ int DumpCustom::modify_param(int narg, char **arg)
     else if (strcmp(arg[2],"|^") == 0) thresh_op[nthresh] = XOR;
     else error->all(FLERR,"Invalid dump_modify threshold operator");
 
-    // set threshold value
+    // set threshold value as number or special LAST keyword
+    // create FixStore to hold LAST values, should work with restart
+    // id = dump-ID + nthreshlast + DUMP_STORE, fix group = dump group
 
-    thresh_value[nthresh] = force->numeric(FLERR,arg[3]);
+    if (strcmp(arg[3],"LAST") != 0) {
+      thresh_value[nthresh] = force->numeric(FLERR,arg[3]);
+      thresh_last[nthresh] = -1;
+    } else {
+      thresh_fix = (FixStore **) 
+	memory->srealloc(thresh_fix,(nthreshlast+1)*sizeof(FixStore *),
+			 "dump:thresh_fix");
+      thresh_fixID = (char **)
+	memory->srealloc(thresh_fixID,(nthreshlast+1)*sizeof(char *),
+			 "dump:thresh_fixID");
+      memory->grow(thresh_first,(nthreshlast+1),"dump:thresh_first");
+
+      int n = strlen(id) + strlen("_DUMP_STORE") + 8;
+      thresh_fixID[nthreshlast] = new char[n];
+      strcpy(thresh_fixID[nthreshlast],id);
+      sprintf(&thresh_fixID[nthreshlast][strlen(id)],"%d",nthreshlast);
+      strcat(thresh_fixID[nthreshlast],"_DUMP_STORE");
+
+      char **newarg = new char*[6];
+      newarg[0] = thresh_fixID[nthreshlast];
+      newarg[1] = group->names[igroup];
+      newarg[2] = (char *) "STORE";
+      newarg[3] = (char *) "peratom";
+      newarg[4] = (char *) "1";
+      newarg[5] = (char *) "1";
+      modify->add_fix(6,newarg);
+      thresh_fix[nthreshlast] = (FixStore *) modify->fix[modify->nfix-1];
+      delete [] newarg;
+
+      thresh_last[nthreshlast] = nthreshlast;
+      thresh_first[nthreshlast] = 1;
+      nthreshlast++;
+    }
 
     nthresh++;
     return 4;

src/dump_custom.h

@@ -33,10 +33,20 @@ class DumpCustom : public Dump {
   int nevery;                // dump frequency for output
   int iregion;               // -1 if no region, else which region
   char *idregion;            // region ID
-  int nthresh;               // # of defined threshholds
-  int *thresh_array;         // array to threshhhold on for each nthresh
-  int *thresh_op;            // threshhold operation for each nthresh
-  double *thresh_value;      // threshhold value for each nthresh
+
+  int nthresh;               // # of defined thresholds
+  int nthreshlast;           // # of defined thresholds with value = LAST
+
+  int *thresh_array;         // array to threshold on for each nthresh
+  int *thresh_op;            // threshold operation for each nthresh
+  double *thresh_value;      // threshold value for each nthresh
+  int *thresh_last;          // for threshold value = LAST,
+                             // index into thresh_fix
+                             // -1 if not LAST, value is numeric
+
+  class FixStore **thresh_fix;  // stores values for each threshold LAST
+  char **thresh_fixID;          // IDs of thresh_fixes
+  int *thresh_first;            // 1 the first time a FixStore values accessed
 
   int expand;                // flag for whether field args were expanded
   char **earg;               // field names with wildcard expansion
@@ -50,7 +60,7 @@ class DumpCustom : public Dump {
   int nchoose;               // # of selected atoms
   int maxlocal;              // size of atom selection and variable arrays
   int *choose;               // local indices of selected atoms
-  double *dchoose;           // value for each atom to threshhold against
+  double *dchoose;           // value for each atom to threshold against
   int *clist;                // compressed list of indices of selected atoms
 
   int nfield;                // # of keywords listed by user
@@ -233,9 +243,9 @@ E: Compute used in dump between runs is not current
 The compute was not invoked on the current timestep, therefore it
 cannot be used in a dump between runs.
 
-E: Threshhold for an atom property that isn't allocated
+E: Threshold for an atom property that isn't allocated
 
-A dump threshhold has been requested on a quantity that is
+A dump threshold has been requested on a quantity that is
 not defined by the atom style used in this simulation.
 
 E: Dumping an atom property that isn't allocated
@@ -362,7 +372,7 @@ E: Could not find dump modify custom atom integer property ID
 
 Self-explanatory.
 
-E: Invalid dump_modify threshhold operator
+E: Invalid dump_modify threshold operator
 
 Operator keyword used for threshold specification in not recognized.
 

src/fix_store.cpp

@@ -154,6 +154,9 @@ void FixStore::reset_global(int nrow_caller, int ncol_caller)
   if (vecflag) memory->create(vstore,nrow,"fix/store:vstore");
   else memory->create(astore,nrow,ncol,"fix/store:astore");
   memory->create(rbuf,nrow*ncol+2,"fix/store:rbuf");
+
+
+  printf("AAA HOW GET HERE\n");
 }
 
 /* ----------------------------------------------------------------------

src/modify.cpp

@@ -68,10 +68,12 @@ Modify::Modify(LAMMPS *lmp) : Pointers(lmp)
   list_timeflag = NULL;
 
   nfix_restart_global = 0;
-  id_restart_global = style_restart_global = state_restart_global = NULL;
+  id_restart_global = style_restart_global = NULL;
+  state_restart_global = NULL;
+  used_restart_global = NULL;
   nfix_restart_peratom = 0;
   id_restart_peratom = style_restart_peratom = NULL;
-  index_restart_peratom = NULL;
+  index_restart_peratom = used_restart_peratom = NULL;
 
   ncompute = maxcompute = 0;
   compute = NULL;
@@ -140,7 +142,7 @@ Modify::~Modify()
   delete [] end_of_step_every;
   delete [] list_timeflag;
 
-  restart_deallocate();
+  restart_deallocate(0);
 
   delete compute_map;
   delete fix_map;
@@ -156,7 +158,7 @@ void Modify::init()
 
   // delete storage of restart info since it is not valid after 1st run
 
-  restart_deallocate();
+  restart_deallocate(1);
 
   // create lists of fixes to call at each stage of run
 
@@ -819,11 +821,16 @@ void Modify::add_fix(int narg, char **arg, int trysuffix)
     if (strcmp(id_restart_global[i],fix[ifix]->id) == 0 &&
         strcmp(style_restart_global[i],fix[ifix]->style) == 0) {
       fix[ifix]->restart(state_restart_global[i]);
+      used_restart_global[i] = 1;
       if (comm->me == 0) {
-        const char *str = (const char *) ("Resetting global state of Fix %s "
-                                          "Style %s from restart file info\n");
-        if (screen) fprintf(screen,str,fix[ifix]->id,fix[ifix]->style);
-        if (logfile) fprintf(logfile,str,fix[ifix]->id,fix[ifix]->style);
+	if (screen) 
+          fprintf(screen,"Resetting global fix info from restart file:\n");
+	if (logfile) 
+          fprintf(logfile,"Resetting global fix info from restart file:\n");
+        if (screen) fprintf(screen,"  fix style: %s, fix ID: %s\n",
+                            fix[ifix]->style,fix[ifix]->id);
+        if (logfile) fprintf(logfile,"  fix style: %s, fix ID: %s\n",
+                             fix[ifix]->style,fix[ifix]->id);
       }
     }
 
@@ -833,14 +840,19 @@ void Modify::add_fix(int narg, char **arg, int trysuffix)
   for (int i = 0; i < nfix_restart_peratom; i++)
     if (strcmp(id_restart_peratom[i],fix[ifix]->id) == 0 &&
         strcmp(style_restart_peratom[i],fix[ifix]->style) == 0) {
+      used_restart_peratom[i] = 1;
       for (int j = 0; j < atom->nlocal; j++)
         fix[ifix]->unpack_restart(j,index_restart_peratom[i]);
       fix[ifix]->restart_reset = 1;
       if (comm->me == 0) {
-        char *str = (char *) ("Resetting per-atom state of Fix %s Style %s "
-                     "from restart file info\n");
-        if (screen) fprintf(screen,str,fix[ifix]->id,fix[ifix]->style);
-        if (logfile) fprintf(logfile,str,fix[ifix]->id,fix[ifix]->style);
+	if (screen) 
+          fprintf(screen,"Resetting peratom fix info from restart file:\n");
+	if (logfile) 
+          fprintf(logfile,"Resetting peratom fix info from restart file:\n");
+        if (screen) fprintf(screen,"  fix style: %s, fix ID: %s\n",
+                            fix[ifix]->style,fix[ifix]->id);
+        if (logfile) fprintf(logfile,"  fix style: %s, fix ID: %s\n",
+                             fix[ifix]->style,fix[ifix]->id);
       }
     }
 
@@ -1158,6 +1170,7 @@ int Modify::read_restart(FILE *fp)
     id_restart_global = new char*[nfix_restart_global];
     style_restart_global = new char*[nfix_restart_global];
     state_restart_global = new char*[nfix_restart_global];
+    used_restart_global = new int[nfix_restart_global];
   }
 
   // read each entry and Bcast to all procs
@@ -1182,6 +1195,8 @@ int Modify::read_restart(FILE *fp)
     state_restart_global[i] = new char[n];
     if (me == 0) fread(state_restart_global[i],sizeof(char),n,fp);
     MPI_Bcast(state_restart_global[i],n,MPI_CHAR,0,world);
+
+    used_restart_global[i] = 0;
   }
 
   // nfix_restart_peratom = # of restart entries with peratom info
@@ -1197,6 +1212,7 @@ int Modify::read_restart(FILE *fp)
     id_restart_peratom = new char*[nfix_restart_peratom];
     style_restart_peratom = new char*[nfix_restart_peratom];
     index_restart_peratom = new int[nfix_restart_peratom];
+    used_restart_peratom = new int[nfix_restart_peratom];
   }
 
   // read each entry and Bcast to all procs
@@ -1221,6 +1237,7 @@ int Modify::read_restart(FILE *fp)
     maxsize += n;
 
     index_restart_peratom[i] = i;
+    used_restart_peratom[i] = 0;
   }
 
   return maxsize;
@@ -1228,11 +1245,36 @@ int Modify::read_restart(FILE *fp)
 
 /* ----------------------------------------------------------------------
    delete all lists of restart file Fix info
+   if flag set, print list of restart file info not assigned to new fixes
 ------------------------------------------------------------------------- */
 
-void Modify::restart_deallocate()
+void Modify::restart_deallocate(int flag)
 {
   if (nfix_restart_global) {
+    if (flag && comm->me == 0) {
+      int i;
+      for (i = 0; i < nfix_restart_global; i++)
+	if (used_restart_global[i] == 0) break;
+      if (i == nfix_restart_global) {
+	if (screen) 
+          fprintf(screen,"All restart file global fix info "
+                  "was re-assigned\n");
+	if (logfile) 
+          fprintf(logfile,"All restart file global fix info "
+                  "was re-assigned\n");
+      } else {
+	if (screen) fprintf(screen,"Unused restart file global fix info:\n");
+	if (logfile) fprintf(logfile,"Unused restart file global fix info:\n");
+	for (i = 0; i < nfix_restart_global; i++) {
+	  if (used_restart_global[i]) continue;
+	  if (screen) fprintf(screen,"  fix style: %s, fix ID: %s\n",
+			      style_restart_global[i],id_restart_global[i]);
+	  if (logfile) fprintf(logfile,"  fix style: %s, fix ID: %s\n",
+			       style_restart_global[i],id_restart_global[i]);
+	}
+      }
+    }
+
     for (int i = 0; i < nfix_restart_global; i++) {
       delete [] id_restart_global[i];
       delete [] style_restart_global[i];
@@ -1241,9 +1283,34 @@ void Modify::restart_deallocate()
     delete [] id_restart_global;
     delete [] style_restart_global;
     delete [] state_restart_global;
+    delete [] used_restart_global;
   }
 
   if (nfix_restart_peratom) {
+    if (flag && comm->me == 0) {
+      int i;
+      for (i = 0; i < nfix_restart_peratom; i++)
+	if (used_restart_peratom[i] == 0) break;
+      if (i == nfix_restart_peratom) {
+	if (screen) 
+          fprintf(screen,"All restart file peratom fix info "
+                  "was re-assigned\n");
+	if (logfile) 
+          fprintf(logfile,"All restart file peratom fix info "
+                  "was re-assigned\n");
+      } else {
+	if (screen) fprintf(screen,"Unused restart file peratom fix info:\n");
+	if (logfile) fprintf(logfile,"Unused restart file peratom fix info:\n");
+	for (i = 0; i < nfix_restart_peratom; i++) {
+	  if (used_restart_peratom[i]) continue;
+	  if (screen) fprintf(screen,"  fix style: %s, fix ID: %s\n",
+			      style_restart_peratom[i],id_restart_peratom[i]);
+	  if (logfile) fprintf(logfile,"  fix style: %s, fix ID: %s\n",
+			       style_restart_peratom[i],id_restart_peratom[i]);
+	}
+      }
+    }
+
     for (int i = 0; i < nfix_restart_peratom; i++) {
       delete [] id_restart_peratom[i];
       delete [] style_restart_peratom[i];
@@ -1251,6 +1318,7 @@ void Modify::restart_deallocate()
     delete [] id_restart_peratom;
     delete [] style_restart_peratom;
     delete [] index_restart_peratom;
+    delete [] used_restart_peratom;
   }
 
   nfix_restart_global = nfix_restart_peratom = 0;

src/modify.h

@@ -107,7 +107,7 @@ class Modify : protected Pointers {
 
   void write_restart(FILE *);
   int read_restart(FILE *);
-  void restart_deallocate();
+  void restart_deallocate(int);
 
   bigint memory_usage();
 
@@ -135,10 +135,12 @@ class Modify : protected Pointers {
   char **id_restart_global;           // stored fix global info
   char **style_restart_global;        // from read-in restart file
   char **state_restart_global;
+  int *used_restart_global;
 
   char **id_restart_peratom;          // stored fix peratom info
   char **style_restart_peratom;       // from read-in restart file
   int *index_restart_peratom;
+  int *used_restart_peratom;
 
   int index_permanent;        // fix/compute index returned to library call
 

src/region.h

@@ -106,11 +106,12 @@ class Region : protected Pointers {
   void options(int, char **);
   void point_on_line_segment(double *, double *, double *, double *);
   void forward_transform(double &, double &, double &);
+  double point[3],runit[3];
 
  private:
   char *xstr,*ystr,*zstr,*tstr;
   int xvar,yvar,zvar,tvar;
-  double axis[3],point[3],runit[3];
+  double axis[3];
 
   void inverse_transform(double &, double &, double &);
   void rotate(double &, double &, double &, double);

src/version.h

@@ -1 +1 @@
-#define LAMMPS_VERSION "6 Oct 2016"
+#define LAMMPS_VERSION "11 Oct 2016"

src/write_dump.cpp

@@ -32,7 +32,6 @@ using namespace LAMMPS_NS;
 
 void WriteDump::command(int narg, char **arg)
 {
-
   if (narg < 3) error->all(FLERR,"Illegal write_dump command");
 
   // modindex = index in args of "modify" keyword