diff --git a/bench/log.28Mar11.chain.fixed.linux.1 b/bench/log.28Mar11.chain.fixed.linux.1
new file mode 100644
index 0000000000000000000000000000000000000000..a656eb9e7fee9da4f86835d074a5e968ed647a5c
--- /dev/null
+++ b/bench/log.28Mar11.chain.fixed.linux.1
@@ -0,0 +1,59 @@
+LAMMPS (27 Mar 2011)
+# FENE beadspring benchmark
+
+units lj
+atom_style bond
+special_bonds fene
+
+read_data data.chain
+ 1 = max bonds/atom
+ orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
+ 1 by 1 by 1 processor grid
+ 32000 atoms
+ 32000 velocities
+ 31680 bonds
+ 2 = max # of 1-2 neighbors
+ 2 = max # of special neighbors
+
+neighbor 0.4 bin
+neigh_modify every 1 delay 1
+
+bond_style fene
+bond_coeff 1 30.0 1.5 1.0 1.0
+
+pair_style lj/cut 1.12
+pair_modify shift yes
+pair_coeff 1 1 1.0 1.0 1.12
+
+fix 1 all nve
+fix 2 all langevin 1.0 1.0 10.0 904297
+
+thermo 100
+timestep 0.012
+
+run 100
+Memory usage per processor = 11.3536 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 1.87328 on 1 procs for 100 steps with 32000 atoms
+
+Pair time (%) = 0.438668 (23.4171)
+Bond time (%) = 0.289005 (15.4277)
+Neigh time (%) = 0.679554 (36.2761)
+Comm time (%) = 0.0552287 (2.94823)
+Outpt time (%) = 0.00018096 (0.00966003)
+Other time (%) = 0.410646 (21.9212)
+
+Nlocal: 32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 9493 ave 9493 max 9493 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 155873 ave 155873 max 155873 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 155873
+Ave neighs/atom = 4.87103
+Ave special neighs/atom = 1.98
+Neighbor list builds = 25
+Dangerous builds = 0
diff --git a/bench/log.28Mar11.chain.fixed.linux.4 b/bench/log.28Mar11.chain.fixed.linux.4
new file mode 100644
index 0000000000000000000000000000000000000000..0d9a9854f775b08bf9b951aafb36c05b89a5457d
--- /dev/null
+++ b/bench/log.28Mar11.chain.fixed.linux.4
@@ -0,0 +1,59 @@
+LAMMPS (27 Mar 2011)
+# FENE beadspring benchmark
+
+units lj
+atom_style bond
+special_bonds fene
+
+read_data data.chain
+ 1 = max bonds/atom
+ orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
+ 1 by 2 by 2 processor grid
+ 32000 atoms
+ 32000 velocities
+ 31680 bonds
+ 2 = max # of 1-2 neighbors
+ 2 = max # of special neighbors
+
+neighbor 0.4 bin
+neigh_modify every 1 delay 1
+
+bond_style fene
+bond_coeff 1 30.0 1.5 1.0 1.0
+
+pair_style lj/cut 1.12
+pair_modify shift yes
+pair_coeff 1 1 1.0 1.0 1.12
+
+fix 1 all nve
+fix 2 all langevin 1.0 1.0 10.0 904297
+
+thermo 100
+timestep 0.012
+
+run 100
+Memory usage per processor = 4.80505 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 0.436674 on 4 procs for 100 steps with 32000 atoms
+
+Pair time (%) = 0.0835696 (19.1378)
+Bond time (%) = 0.0588097 (13.4677)
+Neigh time (%) = 0.157872 (36.1532)
+Comm time (%) = 0.047663 (10.915)
+Outpt time (%) = 9.69768e-05 (0.0222081)
+Other time (%) = 0.0886627 (20.3041)
+
+Nlocal: 8000 ave 8030 max 7974 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+Nghost: 4177 ave 4191 max 4160 min
+Histogram: 1 0 0 0 1 0 0 1 0 1
+Neighs: 38995.8 ave 39169 max 38852 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+
+Total # of neighbors = 155983
+Ave neighs/atom = 4.87447
+Ave special neighs/atom = 1.98
+Neighbor list builds = 25
+Dangerous builds = 0
diff --git a/bench/log.28Mar11.chain.scaled.linux.4 b/bench/log.28Mar11.chain.scaled.linux.4
new file mode 100644
index 0000000000000000000000000000000000000000..fcef10320373ed2635d28ffdf552623e91fd6e55
--- /dev/null
+++ b/bench/log.28Mar11.chain.scaled.linux.4
@@ -0,0 +1,75 @@
+LAMMPS (27 Mar 2011)
+# FENE beadspring benchmark
+
+variable x index 1
+variable y index 1
+variable z index 1
+
+units lj
+atom_style bond
+atom_modify map hash
+special_bonds fene
+
+read_data data.chain
+ 1 = max bonds/atom
+ orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
+ 1 by 2 by 2 processor grid
+ 32000 atoms
+ 32000 velocities
+ 31680 bonds
+ 2 = max # of 1-2 neighbors
+ 2 = max # of special neighbors
+
+replicate $x $y $z
+replicate 2 $y $z
+replicate 2 2 $z
+replicate 2 2 1
+ orthogonal box = (-16.796 -16.796 -16.796) to (50.388 50.388 16.796)
+ 2 by 2 by 1 processor grid
+ 128000 atoms
+ 126720 bonds
+ 2 = max # of 1-2 neighbors
+ 2 = max # of special neighbors
+
+neighbor 0.4 bin
+neigh_modify every 1 delay 1
+
+bond_style fene
+bond_coeff 1 30.0 1.5 1.0 1.0
+
+pair_style lj/cut 1.12
+pair_modify shift yes
+pair_coeff 1 1 1.0 1.0 1.12
+
+fix 1 all nve
+fix 2 all langevin 1.0 1.0 10.0 904297
+
+thermo 100
+timestep 0.012
+
+run 100
+Memory usage per processor = 13.3552 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 2.4188 on 4 procs for 100 steps with 128000 atoms
+
+Pair time (%) = 0.507936 (20.9995)
+Bond time (%) = 0.340843 (14.0914)
+Neigh time (%) = 0.735922 (30.425)
+Comm time (%) = 0.228828 (9.46038)
+Outpt time (%) = 0.000289202 (0.0119564)
+Other time (%) = 0.604987 (25.0118)
+
+Nlocal: 32000 ave 32015 max 31983 min
+Histogram: 1 0 1 0 0 0 0 0 1 1
+Nghost: 9492 ave 9522 max 9432 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+Neighs: 155837 ave 156079 max 155506 min
+Histogram: 1 0 0 0 0 1 0 0 1 1
+
+Total # of neighbors = 623349
+Ave neighs/atom = 4.86991
+Ave special neighs/atom = 1.98
+Neighbor list builds = 25
+Dangerous builds = 0
diff --git a/bench/log.28Mar11.chute.fixed.linux.1 b/bench/log.28Mar11.chute.fixed.linux.1
new file mode 100644
index 0000000000000000000000000000000000000000..e16830ffd40d24344c1cdca545cd4ef82593ba7f
--- /dev/null
+++ b/bench/log.28Mar11.chute.fixed.linux.1
@@ -0,0 +1,63 @@
+LAMMPS (27 Mar 2011)
+# LAMMPS benchmark of granular flow
+# chute flow of 32000 atoms with frozen base at 26 degrees
+
+units lj
+atom_style granular
+boundary p p fs
+newton off
+communicate single vel yes
+
+read_data data.chute
+ orthogonal box = (0 0 0) to (40 20 37.2886)
+ 1 by 1 by 1 processor grid
+ 32000 atoms
+ 32000 velocities
+
+pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
+pair_coeff * *
+
+neighbor 0.1 bin
+neigh_modify every 1 delay 0
+
+timestep 0.0001
+
+group bottom type 2
+912 atoms in group bottom
+group active subtract all bottom
+31088 atoms in group active
+neigh_modify exclude group bottom bottom
+
+fix 1 all gravity 1.0 chute 26.0
+fix 2 bottom freeze
+fix 3 active nve/sphere
+
+compute 1 all erotate/sphere
+thermo_style custom step atoms ke c_1 vol
+thermo_modify norm no
+thermo 100
+
+run 100
+Memory usage per processor = 35.2505 Mbytes
+Step Atoms KinEng 1 Volume
+ 0 32000 784139.13 1601.1263 29830.88
+ 100 32000 784289.99 1571.0137 29831.804
+Loop time of 1.58777 on 1 procs for 100 steps with 32000 atoms
+
+Pair time (%) = 0.887784 (55.9139)
+Neigh time (%) = 0.070847 (4.46205)
+Comm time (%) = 0.0669501 (4.21661)
+Outpt time (%) = 0.000550032 (0.0346418)
+Other time (%) = 0.561639 (35.3728)
+
+Nlocal: 32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 5463 ave 5463 max 5463 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 115133 ave 115133 max 115133 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 115133
+Ave neighs/atom = 3.59791
+Neighbor list builds = 2
+Dangerous builds = 0
diff --git a/bench/log.28Mar11.chute.fixed.linux.4 b/bench/log.28Mar11.chute.fixed.linux.4
new file mode 100644
index 0000000000000000000000000000000000000000..59efa4a12a777d6aee2f8f789169c17f88bafcc8
--- /dev/null
+++ b/bench/log.28Mar11.chute.fixed.linux.4
@@ -0,0 +1,63 @@
+LAMMPS (27 Mar 2011)
+# LAMMPS benchmark of granular flow
+# chute flow of 32000 atoms with frozen base at 26 degrees
+
+units lj
+atom_style granular
+boundary p p fs
+newton off
+communicate single vel yes
+
+read_data data.chute
+ orthogonal box = (0 0 0) to (40 20 37.2886)
+ 2 by 1 by 2 processor grid
+ 32000 atoms
+ 32000 velocities
+
+pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
+pair_coeff * *
+
+neighbor 0.1 bin
+neigh_modify every 1 delay 0
+
+timestep 0.0001
+
+group bottom type 2
+912 atoms in group bottom
+group active subtract all bottom
+31088 atoms in group active
+neigh_modify exclude group bottom bottom
+
+fix 1 all gravity 1.0 chute 26.0
+fix 2 bottom freeze
+fix 3 active nve/sphere
+
+compute 1 all erotate/sphere
+thermo_style custom step atoms ke c_1 vol
+thermo_modify norm no
+thermo 100
+
+run 100
+Memory usage per processor = 15.4199 Mbytes
+Step Atoms KinEng 1 Volume
+ 0 32000 784139.13 1601.1263 29830.88
+ 100 32000 784289.99 1571.0137 29831.804
+Loop time of 0.270323 on 4 procs for 100 steps with 32000 atoms
+
+Pair time (%) = 0.135713 (50.2038)
+Neigh time (%) = 0.0173983 (6.43611)
+Comm time (%) = 0.0378563 (14.0041)
+Outpt time (%) = 0.000246227 (0.091086)
+Other time (%) = 0.0791097 (29.2649)
+
+Nlocal: 8000 ave 8010 max 7990 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost: 2439 ave 2452 max 2426 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs: 29503.5 ave 30500 max 28507 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 118014
+Ave neighs/atom = 3.68794
+Neighbor list builds = 2
+Dangerous builds = 0
diff --git a/bench/log.28Mar11.chute.scaled.linux.4 b/bench/log.28Mar11.chute.scaled.linux.4
new file mode 100644
index 0000000000000000000000000000000000000000..31851100221ec3afc6ebe0f5fe804652dc13d90b
--- /dev/null
+++ b/bench/log.28Mar11.chute.scaled.linux.4
@@ -0,0 +1,73 @@
+LAMMPS (27 Mar 2011)
+# LAMMPS benchmark of granular flow
+# chute flow of 32000 atoms with frozen base at 26 degrees
+
+variable x index 1
+variable y index 1
+
+units lj
+atom_style granular
+boundary p p fs
+newton off
+communicate single vel yes
+
+read_data data.chute
+ orthogonal box = (0 0 0) to (40 20 37.2886)
+ 2 by 1 by 2 processor grid
+ 32000 atoms
+ 32000 velocities
+
+replicate $x $y 1
+replicate 2 $y 1
+replicate 2 2 1
+ orthogonal box = (0 0 0) to (80 40 37.2887)
+ 4 by 1 by 1 processor grid
+ 128000 atoms
+
+pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
+pair_coeff * *
+
+neighbor 0.1 bin
+neigh_modify every 1 delay 0
+
+timestep 0.0001
+
+group bottom type 2
+3648 atoms in group bottom
+group active subtract all bottom
+124352 atoms in group active
+neigh_modify exclude group bottom bottom
+
+fix 1 all gravity 1.0 chute 26.0
+fix 2 bottom freeze
+fix 3 active nve/sphere
+
+compute 1 all erotate/sphere
+thermo_style custom step atoms ke c_1 vol
+thermo_modify norm no
+thermo 100
+
+run 100
+Memory usage per processor = 37.3912 Mbytes
+Step Atoms KinEng 1 Volume
+ 0 128000 3136556.5 6404.5051 119323.52
+ 100 128000 3137160 6284.0549 119327.22
+Loop time of 2.79202 on 4 procs for 100 steps with 128000 atoms
+
+Pair time (%) = 1.13366 (40.6034)
+Neigh time (%) = 0.0699974 (2.50705)
+Comm time (%) = 0.24415 (8.74457)
+Outpt time (%) = 0.00162953 (0.0583639)
+Other time (%) = 1.34259 (48.0866)
+
+Nlocal: 32000 ave 32000 max 32000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 5456 ave 5456 max 5456 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 115135 ave 115135 max 115135 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 460540
+Ave neighs/atom = 3.59797
+Neighbor list builds = 2
+Dangerous builds = 0
diff --git a/bench/log.28Mar11.eam.fixed.linux.1 b/bench/log.28Mar11.eam.fixed.linux.1
new file mode 100644
index 0000000000000000000000000000000000000000..4303ebf435c41d229eb42fd0dcd763fa22703343
--- /dev/null
+++ b/bench/log.28Mar11.eam.fixed.linux.1
@@ -0,0 +1,67 @@
+LAMMPS (27 Mar 2011)
+# bulk Cu lattice
+
+variable x index 1
+variable y index 1
+variable z index 1
+
+variable xx equal 20*$x
+variable xx equal 20*1
+variable yy equal 20*$y
+variable yy equal 20*1
+variable zz equal 20*$z
+variable zz equal 20*1
+
+units metal
+atom_style atomic
+
+lattice fcc 3.615
+Lattice spacing in x,y,z = 3.615 3.615 3.615
+region box block 0 ${xx} 0 ${yy} 0 ${zz}
+region box block 0 20 0 ${yy} 0 ${zz}
+region box block 0 20 0 20 0 ${zz}
+region box block 0 20 0 20 0 20
+create_box 1 box
+Created orthogonal box = (0 0 0) to (72.3 72.3 72.3)
+ 1 by 1 by 1 processor grid
+create_atoms 1 box
+Created 32000 atoms
+
+pair_style eam
+pair_coeff 1 1 Cu_u3.eam
+
+velocity all create 1600.0 376847 loop geom
+
+neighbor 1.0 bin
+neigh_modify every 1 delay 5 check yes
+
+fix 1 all nve
+
+timestep 0.005
+thermo 50
+
+run 100
+Memory usage per processor = 15.3728 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1600 -113280 0 -106662.09 18703.573
+ 50 781.69049 -109873.35 0 -106640.13 52273.088
+ 100 801.832 -109957.3 0 -106640.77 51322.821
+Loop time of 11.4086 on 1 procs for 100 steps with 32000 atoms
+
+Pair time (%) = 10.2465 (89.814)
+Neigh time (%) = 0.893404 (7.83096)
+Comm time (%) = 0.0694258 (0.608539)
+Outpt time (%) = 0.000409126 (0.00358612)
+Other time (%) = 0.198848 (1.74296)
+
+Nlocal: 32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 19909 ave 19909 max 19909 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 1.20778e+06 ave 1.20778e+06 max 1.20778e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1207784
+Ave neighs/atom = 37.7433
+Neighbor list builds = 13
+Dangerous builds = 0
diff --git a/bench/log.28Mar11.eam.fixed.linux.4 b/bench/log.28Mar11.eam.fixed.linux.4
new file mode 100644
index 0000000000000000000000000000000000000000..22fb1cf05d1a057edc437f6a7998264c9520ccd3
--- /dev/null
+++ b/bench/log.28Mar11.eam.fixed.linux.4
@@ -0,0 +1,67 @@
+LAMMPS (27 Mar 2011)
+# bulk Cu lattice
+
+variable x index 1
+variable y index 1
+variable z index 1
+
+variable xx equal 20*$x
+variable xx equal 20*1
+variable yy equal 20*$y
+variable yy equal 20*1
+variable zz equal 20*$z
+variable zz equal 20*1
+
+units metal
+atom_style atomic
+
+lattice fcc 3.615
+Lattice spacing in x,y,z = 3.615 3.615 3.615
+region box block 0 ${xx} 0 ${yy} 0 ${zz}
+region box block 0 20 0 ${yy} 0 ${zz}
+region box block 0 20 0 20 0 ${zz}
+region box block 0 20 0 20 0 20
+create_box 1 box
+Created orthogonal box = (0 0 0) to (72.3 72.3 72.3)
+ 1 by 2 by 2 processor grid
+create_atoms 1 box
+Created 32000 atoms
+
+pair_style eam
+pair_coeff 1 1 Cu_u3.eam
+
+velocity all create 1600.0 376847 loop geom
+
+neighbor 1.0 bin
+neigh_modify every 1 delay 5 check yes
+
+fix 1 all nve
+
+timestep 0.005
+thermo 50
+
+run 100
+Memory usage per processor = 4.92442 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1600 -113280 0 -106662.09 18703.573
+ 50 781.69049 -109873.35 0 -106640.13 52273.088
+ 100 801.832 -109957.3 0 -106640.77 51322.821
+Loop time of 2.84421 on 4 procs for 100 steps with 32000 atoms
+
+Pair time (%) = 2.47554 (87.0379)
+Neigh time (%) = 0.216563 (7.61418)
+Comm time (%) = 0.104262 (3.66577)
+Outpt time (%) = 0.000251591 (0.00884573)
+Other time (%) = 0.0475937 (1.67335)
+
+Nlocal: 8000 ave 8008 max 7993 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Nghost: 9130.25 ave 9138 max 9122 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs: 301946 ave 302392 max 301360 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+
+Total # of neighbors = 1207784
+Ave neighs/atom = 37.7433
+Neighbor list builds = 13
+Dangerous builds = 0
diff --git a/bench/log.28Mar11.eam.scaled.linux.4 b/bench/log.28Mar11.eam.scaled.linux.4
new file mode 100644
index 0000000000000000000000000000000000000000..08f93dca8607080e2749a849472a733fc11c0a21
--- /dev/null
+++ b/bench/log.28Mar11.eam.scaled.linux.4
@@ -0,0 +1,67 @@
+LAMMPS (27 Mar 2011)
+# bulk Cu lattice
+
+variable x index 1
+variable y index 1
+variable z index 1
+
+variable xx equal 20*$x
+variable xx equal 20*2
+variable yy equal 20*$y
+variable yy equal 20*2
+variable zz equal 20*$z
+variable zz equal 20*1
+
+units metal
+atom_style atomic
+
+lattice fcc 3.615
+Lattice spacing in x,y,z = 3.615 3.615 3.615
+region box block 0 ${xx} 0 ${yy} 0 ${zz}
+region box block 0 40 0 ${yy} 0 ${zz}
+region box block 0 40 0 40 0 ${zz}
+region box block 0 40 0 40 0 20
+create_box 1 box
+Created orthogonal box = (0 0 0) to (144.6 144.6 72.3)
+ 2 by 2 by 1 processor grid
+create_atoms 1 box
+Created 128000 atoms
+
+pair_style eam
+pair_coeff 1 1 Cu_u3.eam
+
+velocity all create 1600.0 376847 loop geom
+
+neighbor 1.0 bin
+neigh_modify every 1 delay 5 check yes
+
+fix 1 all nve
+
+timestep 0.005
+thermo 50
+
+run 100
+Memory usage per processor = 15.2892 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1600 -453120 0 -426647.73 18704.012
+ 50 779.50001 -439457.02 0 -426560.06 52355.276
+ 100 797.97828 -439764.76 0 -426562.07 51474.74
+Loop time of 12.0882 on 4 procs for 100 steps with 128000 atoms
+
+Pair time (%) = 10.3589 (85.6942)
+Neigh time (%) = 0.963713 (7.97234)
+Comm time (%) = 0.316817 (2.62088)
+Outpt time (%) = 0.000717819 (0.00593818)
+Other time (%) = 0.448062 (3.70661)
+
+Nlocal: 32000 ave 32092 max 31914 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+Nghost: 19910 ave 19997 max 19818 min
+Histogram: 1 0 0 0 1 0 1 0 0 1
+Neighs: 1.20728e+06 ave 1.21142e+06 max 1.2036e+06 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+
+Total # of neighbors = 4829126
+Ave neighs/atom = 37.7275
+Neighbor list builds = 14
+Dangerous builds = 0
diff --git a/bench/log.28Mar11.lj.fixed.linux.1 b/bench/log.28Mar11.lj.fixed.linux.1
new file mode 100644
index 0000000000000000000000000000000000000000..1daa53dd362055217ede3ed75df5bd95dcb8c5fe
--- /dev/null
+++ b/bench/log.28Mar11.lj.fixed.linux.1
@@ -0,0 +1,64 @@
+LAMMPS (27 Mar 2011)
+# 3d Lennard-Jones melt
+
+variable x index 1
+variable y index 1
+variable z index 1
+
+variable xx equal 20*$x
+variable xx equal 20*1
+variable yy equal 20*$y
+variable yy equal 20*1
+variable zz equal 20*$z
+variable zz equal 20*1
+
+units lj
+atom_style atomic
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 ${xx} 0 ${yy} 0 ${zz}
+region box block 0 20 0 ${yy} 0 ${zz}
+region box block 0 20 0 20 0 ${zz}
+region box block 0 20 0 20 0 20
+create_box 1 box
+Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+ 1 by 1 by 1 processor grid
+create_atoms 1 box
+Created 32000 atoms
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 20 check no
+
+fix 1 all nve
+
+run 100
+Memory usage per processor = 13.2267 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7733681 0 -4.6134356 -5.0197073
+ 100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
+Loop time of 4.24155 on 1 procs for 100 steps with 32000 atoms
+
+Pair time (%) = 3.6555 (86.1832)
+Neigh time (%) = 0.359136 (8.4671)
+Comm time (%) = 0.0590658 (1.39255)
+Outpt time (%) = 0.000212193 (0.00500272)
+Other time (%) = 0.167634 (3.95218)
+
+Nlocal: 32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 19657 ave 19657 max 19657 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 1.20283e+06 ave 1.20283e+06 max 1.20283e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1202833
+Ave neighs/atom = 37.5885
+Neighbor list builds = 5
+Dangerous builds = 0
diff --git a/bench/log.28Mar11.lj.fixed.linux.4 b/bench/log.28Mar11.lj.fixed.linux.4
new file mode 100644
index 0000000000000000000000000000000000000000..1886e20603638f7b11e81c99ea64f3c5c0c61e8e
--- /dev/null
+++ b/bench/log.28Mar11.lj.fixed.linux.4
@@ -0,0 +1,64 @@
+LAMMPS (27 Mar 2011)
+# 3d Lennard-Jones melt
+
+variable x index 1
+variable y index 1
+variable z index 1
+
+variable xx equal 20*$x
+variable xx equal 20*1
+variable yy equal 20*$y
+variable yy equal 20*1
+variable zz equal 20*$z
+variable zz equal 20*1
+
+units lj
+atom_style atomic
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 ${xx} 0 ${yy} 0 ${zz}
+region box block 0 20 0 ${yy} 0 ${zz}
+region box block 0 20 0 20 0 ${zz}
+region box block 0 20 0 20 0 20
+create_box 1 box
+Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+ 1 by 2 by 2 processor grid
+create_atoms 1 box
+Created 32000 atoms
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 20 check no
+
+fix 1 all nve
+
+run 100
+Memory usage per processor = 4.31284 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7733681 0 -4.6134356 -5.0197073
+ 100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
+Loop time of 1.08102 on 4 procs for 100 steps with 32000 atoms
+
+Pair time (%) = 0.86205 (79.7443)
+Neigh time (%) = 0.0897413 (8.30156)
+Comm time (%) = 0.0998399 (9.23573)
+Outpt time (%) = 0.000194311 (0.0179748)
+Other time (%) = 0.0291918 (2.7004)
+
+Nlocal: 8000 ave 8037 max 7964 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Nghost: 9007.5 ave 9050 max 8968 min
+Histogram: 1 1 0 0 0 0 0 1 0 1
+Neighs: 300708 ave 305113 max 297203 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+
+Total # of neighbors = 1202833
+Ave neighs/atom = 37.5885
+Neighbor list builds = 5
+Dangerous builds = 0
diff --git a/bench/log.28Mar11.lj.scaled.linux.4 b/bench/log.28Mar11.lj.scaled.linux.4
new file mode 100644
index 0000000000000000000000000000000000000000..c74c7640383f8b88d4d946b75388a2e847c9dc6d
--- /dev/null
+++ b/bench/log.28Mar11.lj.scaled.linux.4
@@ -0,0 +1,64 @@
+LAMMPS (27 Mar 2011)
+# 3d Lennard-Jones melt
+
+variable x index 1
+variable y index 1
+variable z index 1
+
+variable xx equal 20*$x
+variable xx equal 20*2
+variable yy equal 20*$y
+variable yy equal 20*2
+variable zz equal 20*$z
+variable zz equal 20*1
+
+units lj
+atom_style atomic
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 ${xx} 0 ${yy} 0 ${zz}
+region box block 0 40 0 ${yy} 0 ${zz}
+region box block 0 40 0 40 0 ${zz}
+region box block 0 40 0 40 0 20
+create_box 1 box
+Created orthogonal box = (0 0 0) to (67.1838 67.1838 33.5919)
+ 2 by 2 by 1 processor grid
+create_atoms 1 box
+Created 128000 atoms
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 20 check no
+
+fix 1 all nve
+
+run 100
+Memory usage per processor = 13.1495 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 4.71885 on 4 procs for 100 steps with 128000 atoms
+
+Pair time (%) = 3.70177 (78.4464)
+Neigh time (%) = 0.350671 (7.43129)
+Comm time (%) = 0.278878 (5.90987)
+Outpt time (%) = 0.000279307 (0.00591897)
+Other time (%) = 0.387254 (8.20654)
+
+Nlocal: 32000 ave 32060 max 31939 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Nghost: 19630.8 ave 19681 max 19562 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+Neighs: 1.20195e+06 ave 1.20354e+06 max 1.19931e+06 min
+Histogram: 1 0 0 0 0 0 0 2 0 1
+
+Total # of neighbors = 4807797
+Ave neighs/atom = 37.5609
+Neighbor list builds = 5
+Dangerous builds = 0
diff --git a/bench/log.28Mar11.rhodo.fixed.linux.1 b/bench/log.28Mar11.rhodo.fixed.linux.1
new file mode 100644
index 0000000000000000000000000000000000000000..eb669ae71c84b327f000ed30ed4b0dbea065da07
--- /dev/null
+++ b/bench/log.28Mar11.rhodo.fixed.linux.1
@@ -0,0 +1,97 @@
+LAMMPS (27 Mar 2011)
+# Rhodopsin model
+
+units real
+neigh_modify delay 5 every 1
+
+atom_style full
+bond_style harmonic
+angle_style charmm
+dihedral_style charmm
+improper_style harmonic
+pair_style lj/charmm/coul/long 8.0 10.0
+pair_modify mix arithmetic
+kspace_style pppm 1e-4
+
+read_data data.rhodo
+ 4 = max bonds/atom
+ 8 = max angles/atom
+ 18 = max dihedrals/atom
+ 2 = max impropers/atom
+ orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
+ 1 by 1 by 1 processor grid
+ 32000 atoms
+ 32000 velocities
+ 27723 bonds
+ 40467 angles
+ 56829 dihedrals
+ 1034 impropers
+ 4 = max # of 1-2 neighbors
+ 12 = max # of 1-3 neighbors
+ 24 = max # of 1-4 neighbors
+ 26 = max # of special neighbors
+
+fix 1 all shake 0.0001 5 0 m 1.0 a 232
+ 1617 = # of size 2 clusters
+ 3633 = # of size 3 clusters
+ 747 = # of size 4 clusters
+ 4233 = # of frozen angles
+fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
+
+special_bonds charmm
+
+thermo 50
+thermo_style multi
+timestep 2.0
+
+run 100
+PPPM initialization ...
+ G vector = 0.248831
+ grid = 25 32 32
+ stencil order = 5
+ RMS precision = 7.57143e-05
+ brick FFT buffer size/proc = 41070 25600 12321
+Memory usage per processor = 138.965 Mbytes
+---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
+TotEng = -25356.2055 KinEng = 21444.8313 Temp = 299.0397
+PotEng = -46801.0368 E_bond = 2537.9940 E_angle = 10921.3742
+E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
+E_coul = 207021.6603 E_long = -270399.5000 Press = -142.6030
+Volume = 307995.0335
+---------------- Step 50 ----- CPU = 32.2123 (sec) ----------------
+TotEng = -25330.0783 KinEng = 21501.0023 Temp = 299.8230
+PotEng = -46831.0806 E_bond = 2471.7004 E_angle = 10836.4977
+E_dihed = 5239.6299 E_impro = 227.1218 E_vdwl = -1993.2753
+E_coul = 206793.4044 E_long = -270406.1594 Press = 237.6744
+Volume = 308031.5641
+---------------- Step 100 ----- CPU = 65.3867 (sec) ----------------
+TotEng = -25290.7642 KinEng = 21592.0080 Temp = 301.0920
+PotEng = -46882.7722 E_bond = 2567.9806 E_angle = 10781.9408
+E_dihed = 5198.7431 E_impro = 216.7832 E_vdwl = -1902.4804
+E_coul = 206654.9995 E_long = -270400.7389 Press = 6.9875
+Volume = 308133.9900
+Loop time of 65.3868 on 1 procs for 100 steps with 32000 atoms
+
+Pair time (%) = 46.2231 (70.6918)
+Bond time (%) = 2.88711 (4.41543)
+Kspce time (%) = 7.06667 (10.8075)
+Neigh time (%) = 6.61535 (10.1173)
+Comm time (%) = 0.185745 (0.28407)
+Outpt time (%) = 0.000392199 (0.000599813)
+Other time (%) = 2.4084 (3.68331)
+
+FFT time (% of Kspce) = 0.430403 (6.0906)
+FFT Gflps 3d (1d only) = 1.20747 1.74267
+
+Nlocal: 32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 47958 ave 47958 max 47958 min
+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
+Ave neighs/atom = 375.878
+Ave special neighs/atom = 7.43187
+Neighbor list builds = 11
+Dangerous builds = 0
diff --git a/bench/log.28Mar11.rhodo.fixed.linux.4 b/bench/log.28Mar11.rhodo.fixed.linux.4
new file mode 100644
index 0000000000000000000000000000000000000000..f78c4872a357c066a74b62ad6b45f1b572b1337f
--- /dev/null
+++ b/bench/log.28Mar11.rhodo.fixed.linux.4
@@ -0,0 +1,97 @@
+LAMMPS (27 Mar 2011)
+# Rhodopsin model
+
+units real
+neigh_modify delay 5 every 1
+
+atom_style full
+bond_style harmonic
+angle_style charmm
+dihedral_style charmm
+improper_style harmonic
+pair_style lj/charmm/coul/long 8.0 10.0
+pair_modify mix arithmetic
+kspace_style pppm 1e-4
+
+read_data data.rhodo
+ 4 = max bonds/atom
+ 8 = max angles/atom
+ 18 = max dihedrals/atom
+ 2 = max impropers/atom
+ orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
+ 1 by 2 by 2 processor grid
+ 32000 atoms
+ 32000 velocities
+ 27723 bonds
+ 40467 angles
+ 56829 dihedrals
+ 1034 impropers
+ 4 = max # of 1-2 neighbors
+ 12 = max # of 1-3 neighbors
+ 24 = max # of 1-4 neighbors
+ 26 = max # of special neighbors
+
+fix 1 all shake 0.0001 5 0 m 1.0 a 232
+ 1617 = # of size 2 clusters
+ 3633 = # of size 3 clusters
+ 747 = # of size 4 clusters
+ 4233 = # of frozen angles
+fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
+
+special_bonds charmm
+
+thermo 50
+thermo_style multi
+timestep 2.0
+
+run 100
+PPPM initialization ...
+ G vector = 0.248831
+ grid = 25 32 32
+ stencil order = 5
+ RMS precision = 7.57143e-05
+ brick FFT buffer size/proc = 13230 6400 5670
+Memory usage per processor = 54.4744 Mbytes
+---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
+TotEng = -25356.2055 KinEng = 21444.8313 Temp = 299.0397
+PotEng = -46801.0368 E_bond = 2537.9940 E_angle = 10921.3742
+E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
+E_coul = 207021.6603 E_long = -270399.5000 Press = -142.6030
+Volume = 307995.0335
+---------------- Step 50 ----- CPU = 8.2683 (sec) ----------------
+TotEng = -25330.0783 KinEng = 21501.0023 Temp = 299.8230
+PotEng = -46831.0806 E_bond = 2471.7004 E_angle = 10836.4977
+E_dihed = 5239.6299 E_impro = 227.1218 E_vdwl = -1993.2753
+E_coul = 206793.4044 E_long = -270406.1594 Press = 237.6744
+Volume = 308031.5641
+---------------- Step 100 ----- CPU = 16.8728 (sec) ----------------
+TotEng = -25290.7642 KinEng = 21592.0080 Temp = 301.0920
+PotEng = -46882.7722 E_bond = 2567.9806 E_angle = 10781.9408
+E_dihed = 5198.7431 E_impro = 216.7832 E_vdwl = -1902.4804
+E_coul = 206654.9995 E_long = -270400.7389 Press = 6.9875
+Volume = 308133.9900
+Loop time of 16.8729 on 4 procs for 100 steps with 32000 atoms
+
+Pair time (%) = 11.2248 (66.5258)
+Bond time (%) = 0.687313 (4.07347)
+Kspce time (%) = 2.07329 (12.2877)
+Neigh time (%) = 1.59928 (9.47838)
+Comm time (%) = 0.410708 (2.43412)
+Outpt time (%) = 0.000243425 (0.0014427)
+Other time (%) = 0.877245 (5.19914)
+
+FFT time (% of Kspce) = 0.223284 (10.7696)
+FFT Gflps 3d (1d only) = 2.32752 6.8543
+
+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
+Histogram: 1 2 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 12028107
+Ave neighs/atom = 375.878
+Ave special neighs/atom = 7.43187
+Neighbor list builds = 11
+Dangerous builds = 0
diff --git a/bench/log.28Mar11.rhodo.scaled.linux.4 b/bench/log.28Mar11.rhodo.scaled.linux.4
new file mode 100644
index 0000000000000000000000000000000000000000..55e3d66495e4e95c59b4087debe8ad9ed4d0f1d6
--- /dev/null
+++ b/bench/log.28Mar11.rhodo.scaled.linux.4
@@ -0,0 +1,118 @@
+LAMMPS (27 Mar 2011)
+# Rhodopsin model
+
+variable x index 1
+variable y index 1
+variable z index 1
+
+units real
+neigh_modify delay 5 every 1
+
+atom_style full
+atom_modify map hash
+bond_style harmonic
+angle_style charmm
+dihedral_style charmm
+improper_style harmonic
+pair_style lj/charmm/coul/long 8.0 10.0
+pair_modify mix arithmetic
+kspace_style pppm 1e-4
+
+read_data data.rhodo
+ 4 = max bonds/atom
+ 8 = max angles/atom
+ 18 = max dihedrals/atom
+ 2 = max impropers/atom
+ orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
+ 1 by 2 by 2 processor grid
+ 32000 atoms
+ 32000 velocities
+ 27723 bonds
+ 40467 angles
+ 56829 dihedrals
+ 1034 impropers
+ 4 = max # of 1-2 neighbors
+ 12 = max # of 1-3 neighbors
+ 24 = max # of 1-4 neighbors
+ 26 = max # of special neighbors
+
+replicate $x $y $z
+replicate 2 $y $z
+replicate 2 2 $z
+replicate 2 2 1
+ orthogonal box = (-27.5 -38.5 -36.3646) to (82.5 115.5 36.3615)
+ 2 by 2 by 1 processor grid
+ 128000 atoms
+ 110892 bonds
+ 161868 angles
+ 227316 dihedrals
+ 4136 impropers
+ 4 = max # of 1-2 neighbors
+ 12 = max # of 1-3 neighbors
+ 24 = max # of 1-4 neighbors
+ 26 = max # of special neighbors
+
+fix 1 all shake 0.0001 5 0 m 1.0 a 232
+ 6468 = # of size 2 clusters
+ 14532 = # of size 3 clusters
+ 2988 = # of size 4 clusters
+ 16932 = # of frozen angles
+fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
+
+special_bonds charmm
+
+thermo 50
+thermo_style multi
+timestep 2.0
+
+run 100
+PPPM initialization ...
+ G vector = 0.248586
+ grid = 48 60 36
+ stencil order = 5
+ RMS precision = 7.66425e-05
+ brick FFT buffer size/proc = 41615 25920 12915
+Memory usage per processor = 146.135 Mbytes
+---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
+TotEng = -101425.4825 KinEng = 85779.3251 Temp = 299.0304
+PotEng = -187204.8077 E_bond = 10151.9760 E_angle = 43685.4968
+E_dihed = 20847.1460 E_impro = 854.0463 E_vdwl = -9231.4537
+E_coul = 827025.3556 E_long = -1080537.3748 Press = -142.3084
+Volume = 1231980.1340
+---------------- Step 50 ----- CPU = 32.8194 (sec) ----------------
+TotEng = -101320.2611 KinEng = 86003.4849 Temp = 299.8118
+PotEng = -187323.7460 E_bond = 9887.1072 E_angle = 43346.7920
+E_dihed = 20958.7034 E_impro = 908.4715 E_vdwl = -7973.4456
+E_coul = 826113.1533 E_long = -1080564.5278 Press = 238.0165
+Volume = 1232126.1854
+---------------- Step 100 ----- CPU = 66.9547 (sec) ----------------
+TotEng = -101158.1519 KinEng = 86355.6231 Temp = 301.0394
+PotEng = -187513.7749 E_bond = 10272.0700 E_angle = 43128.6453
+E_dihed = 20793.9768 E_impro = 867.0826 E_vdwl = -7586.7196
+E_coul = 825555.5006 E_long = -1080544.3306 Press = 15.2192
+Volume = 1232535.8453
+Loop time of 66.9548 on 4 procs for 100 steps with 128000 atoms
+
+Pair time (%) = 45.779 (68.373)
+Bond time (%) = 2.87439 (4.29303)
+Kspce time (%) = 7.5089 (11.2149)
+Neigh time (%) = 6.52016 (9.73816)
+Comm time (%) = 0.765243 (1.14293)
+Outpt time (%) = 0.000411808 (0.000615055)
+Other time (%) = 3.50669 (5.2374)
+
+FFT time (% of Kspce) = 1.17001 (15.5816)
+FFT Gflps 3d (1d only) = 2.04683 6.15771
+
+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
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 48112468
+Ave neighs/atom = 375.879
+Ave special neighs/atom = 7.43187
+Neighbor list builds = 11
+Dangerous builds = 0