release version 3.0.0 on 2014-01-23_20-29-19

bench/GPU/README

@@ -50,11 +50,11 @@ the USER-CUDA package.  For example:
 
 mpirun -np 1 ../lmp_linux_single -sf cuda -v g 1 -v x 16 -v y 16 -v z 16 -v t 100 < in.lj.cuda
 
-mpirun -np 1 ../lmp_linux_double -sf cuda -v g 1 -v x 32 -v y 64 -v z 64 -v t 100 < in.eam.cuda
+mpirun -np 2 ../lmp_linux_double -sf cuda -v g 2 -v x 32 -v y 64 -v z 64 -v t 100 < in.eam.cuda
 
 The "xyz" settings determine the problem size.  The "t" setting
 determines the number of timesteps.  The "np" setting determines how
 many CPUs the problem will be run on, and the "g" setting determines
 how many GPUs the problem will run on, i.e. 1 or 2 in this case.  You
-can use more CPUs than GPUs with the GPU package.  You should make the
-number of CPUs and number of GPUs equal for the USER-CUDA package.
+should make the number of CPUs and number of GPUs equal for the
+USER-CUDA package.

bench/GPU/in.rhodo.cuda

@@ -9,7 +9,7 @@ units           real
 neigh_modify    delay 5 every 1   
 
 atom_style      full  
-atom_modify	map hash
+#atom_modify	map hash
 bond_style      harmonic 
 angle_style     charmm 
 dihedral_style  charmm 

bench/log.30Jul13.chain.fixed.linux.1

@@ -1,4 +1,4 @@
-LAMMPS (10 Jan 2012)
+LAMMPS (14 Aug 2013)
 # FENE beadspring benchmark
 
 units		lj
@@ -32,18 +32,18 @@ thermo          100
 timestep	0.012
 
 run		100
-Memory usage per processor = 11.3536 Mbytes
+Memory usage per processor = 11.5156 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 1.00598 on 1 procs for 100 steps with 32000 atoms
+Loop time of 0.992695 on 1 procs for 100 steps with 32000 atoms
 
-Pair  time (%) = 0.200669 (19.9477)
-Bond  time (%) = 0.116349 (11.5657)
-Neigh time (%) = 0.434148 (43.1567)
-Comm  time (%) = 0.0310009 (3.08166)
-Outpt time (%) = 9.799e-05 (0.00974076)
-Other time (%) = 0.223714 (22.2385)
+Pair  time (%) = 0.200438 (20.1913)
+Bond  time (%) = 0.0872233 (8.78652)
+Neigh time (%) = 0.450228 (45.3541)
+Comm  time (%) = 0.0333259 (3.35712)
+Outpt time (%) = 9.58443e-05 (0.00965496)
+Other time (%) = 0.221384 (22.3013)
 
 Nlocal:    32000 ave 32000 max 32000 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

bench/log.30Jul13.chain.fixed.linux.4

@@ -1,4 +1,4 @@
-LAMMPS (10 Jan 2012)
+LAMMPS (14 Aug 2013)
 # FENE beadspring benchmark
 
 units		lj
@@ -32,18 +32,18 @@ thermo          100
 timestep	0.012
 
 run		100
-Memory usage per processor = 4.80505 Mbytes
+Memory usage per processor = 4.85536 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 0.277092 on 4 procs for 100 steps with 32000 atoms
+Loop time of 0.272427 on 4 procs for 100 steps with 32000 atoms
 
-Pair  time (%) = 0.0511394 (18.4557)
-Bond  time (%) = 0.030314 (10.94)
-Neigh time (%) = 0.112937 (40.7578)
-Comm  time (%) = 0.0222602 (8.03351)
-Outpt time (%) = 6.1214e-05 (0.0220915)
-Other time (%) = 0.0603806 (21.7908)
+Pair  time (%) = 0.0509947 (18.7187)
+Bond  time (%) = 0.0227102 (8.33625)
+Neigh time (%) = 0.116272 (42.6802)
+Comm  time (%) = 0.0213055 (7.82062)
+Outpt time (%) = 7.23004e-05 (0.0265394)
+Other time (%) = 0.0610721 (22.4178)
 
 Nlocal:    8000 ave 8030 max 7974 min
 Histogram: 1 0 0 1 0 1 0 0 0 1

bench/log.30Jul13.chain.scaled.linux.4

@@ -1,4 +1,4 @@
-LAMMPS (10 Jan 2012)
+LAMMPS (14 Aug 2013)
 # FENE beadspring benchmark
 
 variable	x index 1
@@ -48,18 +48,18 @@ thermo          100
 timestep	0.012
 
 run		100
-Memory usage per processor = 13.3552 Mbytes
+Memory usage per processor = 13.4806 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 1.16957 on 4 procs for 100 steps with 128000 atoms
+Loop time of 1.188 on 4 procs for 100 steps with 128000 atoms
 
-Pair  time (%) = 0.227149 (19.4215)
-Bond  time (%) = 0.123806 (10.5856)
-Neigh time (%) = 0.472906 (40.4341)
-Comm  time (%) = 0.0951706 (8.13721)
-Outpt time (%) = 0.000224173 (0.0191671)
-Other time (%) = 0.250317 (21.4025)
+Pair  time (%) = 0.226131 (19.0346)
+Bond  time (%) = 0.0970581 (8.16985)
+Neigh time (%) = 0.506595 (42.6426)
+Comm  time (%) = 0.107507 (9.04943)
+Outpt time (%) = 0.000239134 (0.0201291)
+Other time (%) = 0.250472 (21.0834)
 
 Nlocal:    32000 ave 32015 max 31983 min
 Histogram: 1 0 1 0 0 0 0 0 1 1

bench/log.30Jul13.chute.fixed.linux.1

@@ -1,4 +1,4 @@
-LAMMPS (10 Jan 2012)
+LAMMPS (14 Aug 2013)
 # LAMMPS benchmark of granular flow
 # chute flow of 32000 atoms with frozen base at 26 degrees
 
@@ -38,17 +38,17 @@ thermo_modify	norm no
 thermo		100
 
 run		100
-Memory usage per processor = 34.9301 Mbytes
+Memory usage per processor = 21.0636 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 0.54713 on 1 procs for 100 steps with 32000 atoms
+       0    32000    784139.13    1601.1263    29833.783 
+     100    32000    784292.08    1571.0968    29834.707 
+Loop time of 0.54007 on 1 procs for 100 steps with 32000 atoms
 
-Pair  time (%) = 0.328969 (60.1262)
-Neigh time (%) = 0.04423 (8.084)
-Comm  time (%) = 0.0182245 (3.33092)
-Outpt time (%) = 0.00019002 (0.0347302)
-Other time (%) = 0.155517 (28.4242)
+Pair  time (%) = 0.329372 (60.987)
+Neigh time (%) = 0.0422847 (7.82949)
+Comm  time (%) = 0.0179758 (3.32842)
+Outpt time (%) = 0.00019002 (0.0351843)
+Other time (%) = 0.150247 (27.8199)
 
 Nlocal:    32000 ave 32000 max 32000 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

bench/log.30Jul13.chute.fixed.linux.4

@@ -1,4 +1,4 @@
-LAMMPS (10 Jan 2012)
+LAMMPS (14 Aug 2013)
 # LAMMPS benchmark of granular flow
 # chute flow of 32000 atoms with frozen base at 26 degrees
 
@@ -38,26 +38,26 @@ thermo_modify	norm no
 thermo		100
 
 run		100
-Memory usage per processor = 15.2765 Mbytes
+Memory usage per processor = 10.5226 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 0.146905 on 4 procs for 100 steps with 32000 atoms
+       0    32000    784139.13    1601.1263    29833.783 
+     100    32000    784292.08    1571.0968    29834.707 
+Loop time of 0.135566 on 4 procs for 100 steps with 32000 atoms
 
-Pair  time (%) = 0.0729731 (49.6735)
-Neigh time (%) = 0.0111947 (7.62035)
-Comm  time (%) = 0.0153095 (10.4213)
-Outpt time (%) = 0.000119746 (0.0815122)
-Other time (%) = 0.0473083 (32.2033)
+Pair  time (%) = 0.0668132 (49.2847)
+Neigh time (%) = 0.0107402 (7.9225)
+Comm  time (%) = 0.0142344 (10.5)
+Outpt time (%) = 0.000106156 (0.0783057)
+Other time (%) = 0.043672 (32.2145)
 
-Nlocal:    8000 ave 8010 max 7990 min
+Nlocal:    8000 ave 8008 max 7992 min
 Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost:    2439 ave 2452 max 2426 min
+Nghost:    2439 ave 2450 max 2428 min
 Histogram: 2 0 0 0 0 0 0 0 0 2
-Neighs:    29503.5 ave 30500 max 28507 min
+Neighs:    29500.5 ave 30488 max 28513 min
 Histogram: 2 0 0 0 0 0 0 0 0 2
 
-Total # of neighbors = 118014
-Ave neighs/atom = 3.68794
+Total # of neighbors = 118002
+Ave neighs/atom = 3.68756
 Neighbor list builds = 2
 Dangerous builds = 0

bench/log.30Jul13.chute.scaled.linux.4

@@ -1,4 +1,4 @@
-LAMMPS (10 Jan 2012)
+LAMMPS (14 Aug 2013)
 # LAMMPS benchmark of granular flow
 # chute flow of 32000 atoms with frozen base at 26 degrees
 
@@ -20,8 +20,8 @@ read_data	data.chute
 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 MPI processor grid
+  orthogonal box = (0 0 0) to (80 40 37.2923)
+  2 by 2 by 1 MPI processor grid
   128000 atoms
 
 pair_style	gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
@@ -48,26 +48,26 @@ thermo_modify	norm no
 thermo		100
 
 run		100
-Memory usage per processor = 37.0464 Mbytes
+Memory usage per processor = 21.8161 Mbytes
 Step Atoms KinEng 1 Volume 
-       0   128000    3136556.5    6404.5051    119323.52 
-     100   128000      3137160    6284.0549    119327.22 
-Loop time of 0.893496 on 4 procs for 100 steps with 128000 atoms
+       0   128000    3136556.5    6404.5051    119335.13 
+     100   128000    3137168.3    6284.3873    119338.83 
+Loop time of 1.01235 on 4 procs for 100 steps with 128000 atoms
 
-Pair  time (%) = 0.524706 (58.7251)
-Neigh time (%) = 0.0462004 (5.17075)
-Comm  time (%) = 0.0590464 (6.60847)
-Outpt time (%) = 0.00043273 (0.0484311)
-Other time (%) = 0.26311 (29.4473)
+Pair  time (%) = 0.508497 (50.2295)
+Neigh time (%) = 0.0454835 (4.49288)
+Comm  time (%) = 0.0667624 (6.59481)
+Outpt time (%) = 0.00123399 (0.121894)
+Other time (%) = 0.390371 (38.5609)
 
 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
+Nghost:    5463 ave 5463 max 5463 min
 Histogram: 4 0 0 0 0 0 0 0 0 0
-Neighs:    115135 ave 115135 max 115135 min
+Neighs:    115133 ave 115133 max 115133 min
 Histogram: 4 0 0 0 0 0 0 0 0 0
 
-Total # of neighbors = 460540
-Ave neighs/atom = 3.59797
+Total # of neighbors = 460532
+Ave neighs/atom = 3.59791
 Neighbor list builds = 2
 Dangerous builds = 0

bench/log.30Jul13.eam.fixed.linux.1

@@ -1,4 +1,4 @@
-LAMMPS (10 Jan 2012)
+LAMMPS (14 Aug 2013)
 # bulk Cu lattice
 
 variable	x index 1
@@ -41,18 +41,18 @@ timestep	0.005
 thermo		50
 
 run		100
-Memory usage per processor = 15.3728 Mbytes
+Memory usage per processor = 15.3729 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 5.8924 on 1 procs for 100 steps with 32000 atoms
+Loop time of 5.89581 on 1 procs for 100 steps with 32000 atoms
 
-Pair  time (%) = 5.20714 (88.3704)
-Neigh time (%) = 0.579568 (9.83586)
-Comm  time (%) = 0.0308812 (0.524085)
-Outpt time (%) = 0.000219822 (0.0037306)
-Other time (%) = 0.0745952 (1.26596)
+Pair  time (%) = 5.20005 (88.1991)
+Neigh time (%) = 0.590692 (10.0188)
+Comm  time (%) = 0.0308192 (0.52273)
+Outpt time (%) = 0.000217915 (0.00369609)
+Other time (%) = 0.0740323 (1.25568)
 
 Nlocal:    32000 ave 32000 max 32000 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

bench/log.30Jul13.eam.fixed.linux.4

@@ -1,4 +1,4 @@
-LAMMPS (10 Jan 2012)
+LAMMPS (14 Aug 2013)
 # bulk Cu lattice
 
 variable	x index 1
@@ -41,18 +41,18 @@ timestep	0.005
 thermo		50
 
 run		100
-Memory usage per processor = 4.92442 Mbytes
+Memory usage per processor = 4.92459 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 1.58434 on 4 procs for 100 steps with 32000 atoms
+Loop time of 1.62415 on 4 procs for 100 steps with 32000 atoms
 
-Pair  time (%) = 1.37178 (86.5835)
-Neigh time (%) = 0.151559 (9.56606)
-Comm  time (%) = 0.0399128 (2.5192)
-Outpt time (%) = 0.000169277 (0.0106844)
-Other time (%) = 0.0209216 (1.32052)
+Pair  time (%) = 1.39691 (86.0084)
+Neigh time (%) = 0.157564 (9.70131)
+Comm  time (%) = 0.0479782 (2.95404)
+Outpt time (%) = 0.000121653 (0.00749025)
+Other time (%) = 0.0215805 (1.32873)
 
 Nlocal:    8000 ave 8008 max 7993 min
 Histogram: 2 0 0 0 0 0 0 0 1 1

bench/log.30Jul13.eam.scaled.linux.4

@@ -1,4 +1,4 @@
-LAMMPS (10 Jan 2012)
+LAMMPS (14 Aug 2013)
 # bulk Cu lattice
 
 variable	x index 1
@@ -41,18 +41,18 @@ timestep	0.005
 thermo		50
 
 run		100
-Memory usage per processor = 15.2892 Mbytes
+Memory usage per processor = 15.2893 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 6.64398 on 4 procs for 100 steps with 128000 atoms
+Loop time of 6.63538 on 4 procs for 100 steps with 128000 atoms
 
-Pair  time (%) = 5.7169 (86.0464)
-Neigh time (%) = 0.659102 (9.92029)
-Comm  time (%) = 0.164221 (2.47173)
-Outpt time (%) = 0.000294626 (0.00443448)
-Other time (%) = 0.103457 (1.55716)
+Pair  time (%) = 5.70315 (85.9507)
+Neigh time (%) = 0.671065 (10.1134)
+Comm  time (%) = 0.154897 (2.33441)
+Outpt time (%) = 0.0003497 (0.00527024)
+Other time (%) = 0.105914 (1.5962)
 
 Nlocal:    32000 ave 32092 max 31914 min
 Histogram: 1 0 0 1 0 1 0 0 0 1

bench/log.30Jul13.lj.fixed.linux.1

@@ -1,4 +1,4 @@
-LAMMPS (10 Jan 2012)
+LAMMPS (14 Aug 2013)
 # 3d Lennard-Jones melt
 
 variable	x index 1
@@ -43,13 +43,13 @@ 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 2.24442 on 1 procs for 100 steps with 32000 atoms
+Loop time of 2.24794 on 1 procs for 100 steps with 32000 atoms
 
-Pair  time (%) = 1.92371 (85.7108)
-Neigh time (%) = 0.23672 (10.547)
-Comm  time (%) = 0.0241742 (1.07708)
-Outpt time (%) = 0.000104189 (0.00464212)
-Other time (%) = 0.059711 (2.66042)
+Pair  time (%) = 1.92284 (85.5376)
+Neigh time (%) = 0.241012 (10.7215)
+Comm  time (%) = 0.0244191 (1.08629)
+Outpt time (%) = 0.000105858 (0.0047091)
+Other time (%) = 0.0595703 (2.64999)
 
 Nlocal:    32000 ave 32000 max 32000 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

bench/log.30Jul13.lj.fixed.linux.4

@@ -1,4 +1,4 @@
-LAMMPS (10 Jan 2012)
+LAMMPS (14 Aug 2013)
 # 3d Lennard-Jones melt
 
 variable	x index 1
@@ -39,17 +39,17 @@ neigh_modify	delay 0 every 20 check no
 fix		1 all nve
 
 run		100
-Memory usage per processor = 4.31284 Mbytes
+Memory usage per processor = 4.31295 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 0.62139 on 4 procs for 100 steps with 32000 atoms
+Loop time of 0.621459 on 4 procs for 100 steps with 32000 atoms
 
-Pair  time (%) = 0.502622 (80.8866)
-Neigh time (%) = 0.0616071 (9.9144)
-Comm  time (%) = 0.0411073 (6.61538)
-Outpt time (%) = 5.79953e-05 (0.00933316)
-Other time (%) = 0.0159961 (2.57424)
+Pair  time (%) = 0.50556 (81.3506)
+Neigh time (%) = 0.0630878 (10.1516)
+Comm  time (%) = 0.036548 (5.88099)
+Outpt time (%) = 5.19753e-05 (0.00836343)
+Other time (%) = 0.0162107 (2.60849)
 
 Nlocal:    8000 ave 8037 max 7964 min
 Histogram: 2 0 0 0 0 0 0 0 1 1

bench/log.30Jul13.lj.scaled.linux.4

@@ -1,4 +1,4 @@
-LAMMPS (10 Jan 2012)
+LAMMPS (14 Aug 2013)
 # 3d Lennard-Jones melt
 
 variable	x index 1
@@ -39,17 +39,17 @@ neigh_modify	delay 0 every 20 check no
 fix		1 all nve
 
 run		100
-Memory usage per processor = 13.1495 Mbytes
+Memory usage per processor = 13.1496 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 2.43423 on 4 procs for 100 steps with 128000 atoms
+Loop time of 2.51513 on 4 procs for 100 steps with 128000 atoms
 
-Pair  time (%) = 2.04092 (83.8422)
-Neigh time (%) = 0.238374 (9.79258)
-Comm  time (%) = 0.0766696 (3.14964)
-Outpt time (%) = 0.000154495 (0.00634677)
-Other time (%) = 0.0781193 (3.20919)
+Pair  time (%) = 2.06373 (82.0527)
+Neigh time (%) = 0.246449 (9.79865)
+Comm  time (%) = 0.122232 (4.85986)
+Outpt time (%) = 0.000143051 (0.00568762)
+Other time (%) = 0.0825751 (3.28313)
 
 Nlocal:    32000 ave 32060 max 31939 min
 Histogram: 1 0 1 0 0 0 0 1 0 1

bench/log.30Jul13.rhodo.fixed.linux.1

@@ -0,0 +1,99 @@
+LAMMPS (14 Aug 2013)
+# 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 MPI 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 (1/distance) = 0.248835
+  grid = 25 32 32
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0355478
+  estimated relative force accuracy = 0.000107051
+  using double precision FFTs
+  3d grid and FFT values/proc = 41070 25600
+Memory usage per processor = 139.238 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 
+Volume   =    307995.0335 
+---------------- Step       50 ----- CPU =     17.7652 (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 =     36.1527 (sec) ----------------
+TotEng   =    -25290.7592 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   =    206659.2327 E_long   =   -270404.9733 Press    =         6.9960 
+Volume   =    308133.9888 
+Loop time of 36.1528 on 1 procs for 100 steps with 32000 atoms
+
+Pair  time (%) = 26.1216 (72.2533)
+Bond  time (%) = 1.27574 (3.52875)
+Kspce time (%) = 3.25689 (9.00869)
+Neigh time (%) = 4.3025 (11.9009)
+Comm  time (%) = 0.0688474 (0.190435)
+Outpt time (%) = 0.000230074 (0.000636394)
+Other time (%) = 1.127 (3.11732)
+
+FFT time (% of Kspce) = 0.277417 (8.51784)
+FFT Gflps 3d (1d only) = 1.87335 3.23863
+
+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

bench/log.30Jul13.rhodo.fixed.linux.4

@@ -0,0 +1,99 @@
+LAMMPS (14 Aug 2013)
+# 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 MPI 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 (1/distance) = 0.248835
+  grid = 25 32 32
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0355478
+  estimated relative force accuracy = 0.000107051
+  using double precision FFTs
+  3d grid and FFT values/proc = 13230 6400
+Memory usage per processor = 54.595 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 
+Volume   =    307995.0335 
+---------------- Step       50 ----- CPU =      4.6553 (sec) ----------------
+TotEng   =    -25330.0829 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 =      9.5123 (sec) ----------------
+TotEng   =    -25290.7592 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   =    206659.2327 E_long   =   -270404.9733 Press    =         6.9960 
+Volume   =    308133.9888 
+Loop time of 9.51235 on 4 procs for 100 steps with 32000 atoms
+
+Pair  time (%) = 6.58797 (69.2571)
+Bond  time (%) = 0.319462 (3.35839)
+Kspce time (%) = 1.08263 (11.3813)
+Neigh time (%) = 1.08542 (11.4107)
+Comm  time (%) = 0.0859144 (0.903188)
+Outpt time (%) = 0.000161052 (0.00169308)
+Other time (%) = 0.350788 (3.68772)
+
+FFT time (% of Kspce) = 0.0982845 (9.07835)
+FFT Gflps 3d (1d only) = 5.28769 12.8216
+
+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

bench/log.30Jul13.rhodo.scaled.linux.4

@@ -0,0 +1,120 @@
+LAMMPS (14 Aug 2013)
+# 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 MPI 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 MPI 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 (1/distance) = 0.248593
+  grid = 48 60 36
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0359793
+  estimated relative force accuracy = 0.00010835
+  using double precision FFTs
+  3d grid and FFT values/proc = 41615 25920
+Memory usage per processor = 146.358 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 
+Volume   =   1231980.1340 
+---------------- Step       50 ----- CPU =     19.2151 (sec) ----------------
+TotEng   =   -101320.2676 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 =     39.0436 (sec) ----------------
+TotEng   =   -101158.1853 KinEng   =     86355.6148 Temp     =       301.0393 
+PotEng   =   -187513.8001 E_bond   =     10272.0693 E_angle  =     43128.6453 
+E_dihed  =     20793.9759 E_impro  =       867.0826 E_vdwl   =     -7586.7186 
+E_coul   =    825583.7120 E_long   =  -1080572.5667 Press    =        15.2151 
+Volume   =   1232535.8423 
+Loop time of 39.0437 on 4 procs for 100 steps with 128000 atoms
+
+Pair  time (%) = 27.1533 (69.546)
+Bond  time (%) = 1.31501 (3.36805)
+Kspce time (%) = 4.35908 (11.1646)
+Neigh time (%) = 4.42268 (11.3275)
+Comm  time (%) = 0.229435 (0.587637)
+Outpt time (%) = 0.000313759 (0.00080361)
+Other time (%) = 1.56382 (4.00532)
+
+FFT time (% of Kspce) = 0.466478 (10.7013)
+FFT Gflps 3d (1d only) = 5.13382 11.4048
+
+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 = 48112472
+Ave neighs/atom = 375.879
+Ave special neighs/atom = 7.43187
+Neighbor list builds = 11
+Dangerous builds = 0

bench/log.9Jan12.rhodo.fixed.linux.1

@@ -1,98 +0,0 @@
-LAMMPS (10 Jan 2012)
-# 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 MPI 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
-  using double precision FFTs
-  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 =     17.8190 (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 =     36.2635 (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   =   -270400.7390 Press    =         6.9875 
-Volume   =    308133.9900 
-Loop time of 36.2636 on 1 procs for 100 steps with 32000 atoms
-
-Pair  time (%) = 25.8498 (71.283)
-Bond  time (%) = 1.49598 (4.1253)
-Kspce time (%) = 3.27236 (9.02382)
-Neigh time (%) = 4.27552 (11.7901)
-Comm  time (%) = 0.0665278 (0.183456)
-Outpt time (%) = 0.000251055 (0.000692305)
-Other time (%) = 1.30319 (3.59366)
-
-FFT time (% of Kspce) = 0.279837 (8.55152)
-FFT Gflps 3d (1d only) = 1.85715 3.22108
-
-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

bench/log.9Jan12.rhodo.fixed.linux.4

@@ -1,98 +0,0 @@
-LAMMPS (10 Jan 2012)
-# 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 MPI 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
-  using double precision FFTs
-  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 =      4.7389 (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 =      9.6394 (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   =   -270400.7390 Press    =         6.9875 
-Volume   =    308133.9900 
-Loop time of 9.63943 on 4 procs for 100 steps with 32000 atoms
-
-Pair  time (%) = 6.60502 (68.5208)
-Bond  time (%) = 0.375643 (3.89695)
-Kspce time (%) = 1.09311 (11.3399)
-Neigh time (%) = 1.08158 (11.2203)
-Comm  time (%) = 0.0815379 (0.845879)
-Outpt time (%) = 0.000157952 (0.00163861)
-Other time (%) = 0.402393 (4.17445)
-
-FFT time (% of Kspce) = 0.0966156 (8.83863)
-FFT Gflps 3d (1d only) = 5.37903 12.4303
-
-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

bench/log.9Jan12.rhodo.scaled.linux.4

@@ -1,119 +0,0 @@
-LAMMPS (10 Jan 2012)
-# 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 MPI 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 MPI 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
-  using double precision FFTs
-  brick FFT buffer size/proc = 41615 25920 12915
-Memory usage per processor = 146.135 Mbytes
----------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
-TotEng   =   -101425.4826 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   =  -1080537.3749 Press    =      -142.3084 
-Volume   =   1231980.1340 
----------------- Step       50 ----- CPU =     19.1088 (sec) ----------------
-TotEng   =   -101320.2612 KinEng   =     86003.4849 Temp     =       299.8118 
-PotEng   =   -187323.7461 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 =     39.1056 (sec) ----------------
-TotEng   =   -101158.1517 KinEng   =     86355.6231 Temp     =       301.0394 
-PotEng   =   -187513.7747 E_bond   =     10272.0700 E_angle  =     43128.6453 
-E_dihed  =     20793.9768 E_impro  =       867.0826 E_vdwl   =     -7586.7196 
-E_coul   =    825555.5009 E_long   =  -1080544.3307 Press    =        15.2192 
-Volume   =   1232535.8453 
-Loop time of 39.1057 on 4 procs for 100 steps with 128000 atoms
-
-Pair  time (%) = 27.0353 (69.1339)
-Bond  time (%) = 1.5462 (3.9539)
-Kspce time (%) = 4.17715 (10.6817)
-Neigh time (%) = 4.37974 (11.1997)
-Comm  time (%) = 0.208052 (0.532026)
-Outpt time (%) = 0.000296533 (0.000758287)
-Other time (%) = 1.75896 (4.49797)
-
-FFT time (% of Kspce) = 0.535835 (12.8278)
-FFT Gflps 3d (1d only) = 4.46931 11.0706
-
-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

couple/fortran/README

@@ -1,9 +0,0 @@
-libfwrapper.c is a C file that wraps the LAMMPS library API
-in src/library.h so that it can be called from Fortran.
-
-See the couple/simple/simple.f90 program for an example
-of a Fortran code that does this.
-
-See the README file in that dir for instructions
-on how to build a Fortran code that uses this
-wrapper and links to the LAMMPS library.

doc/Eqs/angle_fourier.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+   E = K [C_0 + C_1 \cos ( \theta) + C_2 \cos( 2 \theta) ] 
+$$
+
+\end{document}

doc/Eqs/angle_fourier_simple.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+   E = K [ 1.0 + c \cos ( n \theta) ] 
+$$
+
+\end{document}

doc/Eqs/angle_quartic.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+  E = K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4 (\theta - \theta_0)^4
+$$
+
+\end{document}

doc/Eqs/compute_msd_nongauss.tex

@@ -0,0 +1,9 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+ NGP(t) = 3<(r(t)-r(0))^4>/(5<(r(t)-r(0))^2>^2) - 1
+$$
+
+\end{document}

doc/Eqs/dihedral_fourier.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$  
+  E = \sum_{i=1,m} K_i  [ 1.0 + \cos ( n_i \phi - d_i ) ]
+$$
+
+\end{document}

doc/Eqs/dihedral_nharmonic.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$  
+  E = \sum_{n=1,n} A_n  \cos^{n-1}(\phi)
+$$
+
+\end{document}

doc/Eqs/dihedral_quadratic.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+  E = K (\phi - \phi_0)^2 
+$$
+
+\end{document}

doc/Eqs/eff_ECP1.tex

@@ -0,0 +1,9 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+E_{Pauli(ECP_s)}=p_1\exp\left(-\frac{p_2r^2}{p_3+s^2} \right)
+$$
+
+\end{document}  

doc/Eqs/eff_ECP2.tex

@@ -0,0 +1,8 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+E_{Pauli(ECP_p)}=p_1\left( \frac{2}{p_2/s+s/p_2} \right)\left( r-p_3s\right)^2\exp \left[ -\frac{p_4\left( r-p_3s \right)^2}{p_5+s^2} \right] 
+$$
+

doc/Eqs/fix_gld1.tex

@@ -0,0 +1,13 @@
+\documentclass[12pt]{article}
+
+\usepackage{amsmath}
+
+\begin{document}
+ 
+\begin{align*}
+ &{\bf F}_{j}(t) = {\bf F}^C_j(t)-\int \limits_{0}^{t} \Gamma_j(t-s) {\bf v}_j(s)~\text{d}s + {\bf F}^R_j(t) \\
+ &\Gamma_j(t-s) = \sum \limits_{k=1}^{N_k} \frac{c_k}{\tau_k} e^{-(t-s)/\tau_k} \\ 
+ &\langle{\bf F}^R_j(t),{\bf F}^R_j(s)\rangle = \text{k$_\text{B}$T} ~\Gamma_j(t-s)
+\end{align*}
+
+\end{document}

doc/Eqs/fix_lb_fluid_boltzmann.tex

@@ -0,0 +1,14 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$ 
+\left(\partial_t + e_{i\alpha}\partial_{\alpha}\right)f_i = -\frac{1}{\tau}\left(f_i - f_i^{eq}\right) + W_i
+$$
+
+
+\end{document}
+
+
+
+

doc/Eqs/fix_lb_fluid_fluidforce.tex

@@ -0,0 +1,14 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$ 
+{\bf F}_{j \alpha} = \gamma \left({\bf v}_n - {\bf u}_f \right) \zeta_{j\alpha}
+$$
+
+
+\end{document}
+
+
+
+

doc/Eqs/fix_lb_fluid_gammadefault.tex

@@ -0,0 +1,14 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$ 
+\gamma = \frac{2m_um_v}{m_u+m_v}\left(\frac{1}{\Delta t_{collision}}\right)
+$$
+
+
+\end{document}
+
+
+
+

doc/Eqs/fix_lb_fluid_navierstokes.tex

@@ -0,0 +1,16 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$ 
+\partial_t \rho + \partial_{\beta}\left(\rho u_{\beta}\right)= 0
+$$
+$$
+\partial_t\left(\rho u_{\alpha}\right) + \partial_{\beta}\left(\rho u_{\alpha} u_{\beta}\right) = \partial_{\beta}\sigma_{\alpha \beta} + F_{\alpha} + \partial_{\beta}\left(\eta_{\alpha \beta \gamma \nu}\partial_{\gamma} u_{\nu}\right)
+$$
+
+\end{document}
+
+
+
+

doc/Eqs/fix_lb_fluid_properties.tex

@@ -0,0 +1,17 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$ 
+\rho = \displaystyle\sum\limits_{i} f_i
+$$
+$$
+\rho u_{\alpha} = \displaystyle\sum\limits_{i} f_i e_{i\alpha}
+$$
+
+
+\end{document}
+
+
+
+

doc/Eqs/fix_lb_fluid_stress.tex

@@ -0,0 +1,14 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$ 
+\sigma_{\alpha \beta} = -P_{\alpha \beta} = -\rho a_0 \delta_{\alpha \beta}
+$$
+
+
+\end{document}
+
+
+
+

doc/Eqs/fix_lb_fluid_viscosity.tex

@@ -0,0 +1,14 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$ 
+\eta_{\alpha \beta \gamma \nu} = \eta\left[\delta_{\alpha \gamma}\delta_{\beta \nu} + \delta_{\alpha \nu}\delta_{\beta \gamma} - \frac{2}{3}\delta_{\alpha \beta}\delta_{\gamma \nu}\right] + \Lambda \delta_{\alpha \beta}\delta_{\gamma \nu}
+$$
+
+
+\end{document}
+
+
+
+

doc/Eqs/fix_ti_rs_force.tex

@@ -0,0 +1,11 @@
+\documentclass[12pt]{article}
+
+\usepackage{amsmath}
+
+\begin{document}
+
+$$
+  F_{\text{total}} = \lambda F_{\text{int}}
+$$
+
+\end{document}

doc/Eqs/fix_ti_rs_function_1.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+  \lambda(\tau) = \lambda_i + \tau \left( \lambda_f - \lambda_i \right)
+$$
+
+\end{document}

doc/Eqs/fix_ti_rs_function_2.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+  \lambda(\tau) = \frac{\lambda_i}{1 + \tau \left( \frac{\lambda_i}{\lambda_f} - 1 \right)}
+$$
+
+\end{document}

doc/Eqs/fix_ti_rs_function_3.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+  \lambda(\tau) = \frac{\lambda_i}{ 1 + \log_2(1+\tau) \left( \frac{\lambda_i}{\lambda_f} - 1 \right)}
+$$
+
+\end{document}

doc/Eqs/fix_ti_spring_force.tex

@@ -0,0 +1,11 @@
+\documentclass[12pt]{article}
+
+\usepackage{amsmath}
+
+\begin{document}
+
+$$
+  F_{\text{total}} = \left( 1-\lambda \right) F_{\text{solid}} + \lambda F_{\text{harm}}
+$$
+
+\end{document}

doc/Eqs/fix_ti_spring_function_1.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+  \lambda(\tau) = \tau
+$$
+
+\end{document}

doc/Eqs/fix_ti_spring_function_2.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+  \lambda(\tau) = \tau^5 \left( 70 \tau^4 - 315 \tau^3 + 540 \tau^2 - 420 \tau + 126 \right)
+$$
+
+\end{document}

doc/Eqs/fix_wall_colloid.tex

@@ -3,7 +3,7 @@
 \begin{document}
 
 \begin{eqnarray}
-E &=& 144 \phi^2 \epsilon \left[ \frac{\sigma^{6}}{7560} 
+E &=& \epsilon \left[ \frac{\sigma^{6}}{7560} 
   \left(\frac{6R-D}{D^{7}} + \frac{D+8R}{(D+2R)^{7}} \right) - 
   \frac{}{} \right. \nonumber \\
   &&\qquad \left. \frac{1}{6} \left(\frac{2R(D+R) + D(D+2R)

doc/Eqs/fix_wall_lj1043.tex

@@ -0,0 +1,12 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+ E = 2 \pi \epsilon \left[ \frac{2}{5} \left(\frac{\sigma}{r}\right)^{10} - 
+                       \left(\frac{\sigma}{r}\right)^4 -
+                       \frac{\sqrt(2)\sigma^3}{3\left(r+\left(0.61/\sqrt(2)\right)\sigma\right)^3}\right]
+                       \qquad r < r_c
+$$
+
+\end{document}

doc/Eqs/improper_cossq.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+  E = \frac{1}{2} K \cos^2{\left(\chi - \chi_0\right)}
+$$
+
+\end{document}

doc/Eqs/improper_fourier.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+   E = K [C_0 + C_1 \cos ( \omega) + C_2 \cos( 2 \omega) ] 
+$$
+
+\end{document}

doc/Eqs/improper_ring.tex

@@ -0,0 +1,12 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+   E & = &\frac{1}{6} K \left(\Delta_{ijl} + \Delta_{ijk} + \Delta_{kjl} \right)^6 \\
+   \Delta_{ijl} & = & \cos{\theta_{ijl} - \cos{\theta_0}} \\
+   \Delta_{ijk} & = & \cos{\theta_{ijk} - \cos{\theta_0}} \\
+   \Delta_{kjl} & = & \cos{\theta_{kjl} - \cos{\theta_0}}
+\end{eqnarray*}
+
+\end{document}

doc/Eqs/pair_bop.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+  E = \frac{1}{2} \sum_{i=1}^{N} \sum_{j=i_1}^{i_N} \phi_{ij} \left( r_{ij} \right) - \sum_{i=1}^{N} \sum_{j=i_1}^{i_N} \beta_{\sigma,ij} \left( r_{ij} \right) \cdot \Theta_{\sigma,ij} - \sum_{i=1}^{N} \sum_{j=i_1}^{i_N} \beta_{\pi,ij} \left( r_{ij} \right) \cdot \Theta_{\pi,ij} + U_{prom}
+$$
+
+\end{document}

doc/Eqs/pair_comb1.tex

@@ -1,12 +1,7 @@
 \documentclass[12pt]{article}
-
-\begin{document}
-
+\begin{document} \large
 \begin{eqnarray*}
-E_T & = & \sum_i [ E_i^S + \frac{1}{2} \sum_{j \neq i} V_{ij}
-  (r_{ij},q_i,q_j) + E_i^{BB} ] \\
-V_{ij}(r_{ij},q_i,q_j) & = & U_{ij}^R(r_{ij}) + U_{ij}^A(r_{ij},
-  q_i,q_j) + U_{ij}^I(r_{ij},q_i,q_j) + U_{ij}^V(r_{ij}) \\
+E_T & = & \sum_i [ E_i^{self} (q_i) + \sum_{j>i} [E_{ij}^{short} (r_{ij}, q_i, q_j) + E_{ij}^{Coul} (r_{ij}, q_i, q_j)] + \\
+&& E^{polar} (q_i, r_{ij}) + E^{vdW} (r_{ij}) + E^{barr} (q_i) + E^{corr} (r_{ij}, \theta_{jik})] \\
 \end{eqnarray*}                           
-
 \end{document}

doc/Eqs/pair_comb2.tex

@@ -2,11 +2,21 @@
 
 \begin{document}
 
-\begin{eqnarray*}
-U_{ij}^R(r_{ij}) & = & f_{S_{ij}} A_{ij} \exp (-\lambda_{ij} r_{ij}) \\
-U_{ij}^A(r_{ij},q_i,q_j) & = & -f_{S_{ij}} b_{ij} B_{ij} \exp (-\alpha_{ij} r_{ij}) \\
-U_{ij}^I(r_{ij},q_i,q_j) & = & J_{ij} (r_{ij}) q_i q_j \\
-U_{ij}^V(r_{ij}) & = & f_{L_{ij}} (C_{VDW_i}C_{VDW_j})^\frac{1}{2}/r_{ij}^6 \\
-\end{eqnarray*}                           
+\begin{table}[h]
+\begin{tabular}{|c|c|c|c|c|c|c|c|}
+\hline
+   & $O$ & $Cu$ & $N$ & $C$ & $H$ & $Ti$ & $Zn$ \\ \hline
+$O$	& F & F & F & F & F & F & F \\ \hline
+$Cu$	& F & F & P & F & F & P & F \\ \hline
+$N$ 	& F & P & F & M & F & P & P \\ \hline
+$C$   	& F & F & M & F & F & M & M \\ \hline
+$H$   	& F & F & F & F & F & M & M \\ \hline
+$Ti$   	& F & P & P & M & M & F & P \\ \hline
+$Zn$  	& F & F & P & M & M & P & F \\ \hline
+\multicolumn{8}{l}{F: Fully optimized} \\
+\multicolumn{8}{l}{M: Only optimized for dimer molecule} \\
+\multicolumn{8}{l}{P: in Progress but have it from mixing rule} \\
+\end{tabular}
+\end{table}
 
 \end{document}

doc/Eqs/pair_coul_dsf.tex

@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+$$
+  E = 
+  q_iq_j \left[ \frac{\mbox{erfc} (\alpha r)}{r} -  \frac{\mbox{erfc} (\alpha r_c)}{r_c} + 
+  \left( \frac{\mbox{erfc} (\alpha r_c)}{r_c^2} +  \frac{2\alpha}{\sqrt{\pi}}\frac{\exp (-\alpha^2    r^2_c)}{r_c} \right)(r-r_c) \right] \qquad r < r_c 
+$$
+
+\end{document}

doc/Eqs/pair_gauss.tex

@@ -1,9 +1,9 @@
 \documentclass[12pt]{article}
-
+\pagestyle{empty}
 \begin{document}
 
 $$
-   E = A \exp(-B r^2) \qquad r < r_c
+   E = - A \exp(-B r^2) \qquad r < r_c
 $$
 
 \end{document}

doc/Eqs/pair_gromacs.tex

@@ -8,7 +8,10 @@ E_{LJ} & = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
                        \qquad r < r_c \\
 E_C & = & \frac{C q_i q_j}{\epsilon  r} + S_C(r) \qquad r < r_c \\
 S(r) & = & C \qquad r < r_1 \\
-S(r) & = & \frac{A}{3} (r - r_1)^3 + \frac{B}{4} (r - r_1)^4 + C \qquad  r_1 < r < r_c
+S(r) & = & \frac{A}{3} (r - r_1)^3 + \frac{B}{4} (r - r_1)^4 + C \qquad  r_1 < r < r_c \\
+A & = & (-3 E'(r_c) + (r_c - r_1) E''(r_c))/(r_c - r_1)^2 \\
+B & = & (2 E'(r_c) - (r_c - r_1) E''(r_c))/(r_c - r_1)^3 \\
+C & = & -E(r_c) + \frac{1}{2} (r_c - r_1) E'(r_c) - \frac{1}{12} (r_c - r_1)^2 E''(r_c)) \\
 \end{eqnarray*}                           
 
 \end{document}