clean up doc src

2016-10-06 13:00:46 -06:00
parent 02bfa898ee
commit 493873fb93
458 changed files with 16897 additions and 11014 deletions
--- a/examples/vashishta/log.5Oct16.sio2.g++.4
+++ b/examples/vashishta/log.5Oct16.sio2.g++.4
@ -0,0 +1,86 @@
+LAMMPS (5 Oct 2016)
+# test Vashishta potential for quartz
+
+units		metal
+boundary	p p p
+
+atom_style	atomic
+
+read_data	data.quartz
+  triclinic box = (0 0 0) to (4.9134 4.25513 5.4052) with tilt (-2.4567 0 0)
+  2 by 1 by 2 MPI processor grid
+  reading atoms ...
+  9 atoms
+
+replicate       4 4 4
+  triclinic box = (0 0 0) to (19.6536 17.0205 21.6208) with tilt (-9.8268 0 0)
+  2 by 1 by 2 MPI processor grid
+  576 atoms
+velocity	all create 2000.0 277387 mom yes
+displace_atoms	all move 0.05 0.9 0.4 units box
+
+pair_style 	vashishta
+pair_coeff	* *  SiO.1990.vashishta Si O
+Reading potential file SiO.1990.vashishta with DATE: 2015-10-14
+
+neighbor	0.3 bin
+neigh_modify	delay 10
+
+fix		1 all nve
+thermo		10
+timestep	0.001
+
+#dump		1 all cfg 10 *.cfg mass type xs ys zs vx vy vz fx fy fz
+#dump_modify	1 element Si O
+
+run		100
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10.3
+  ghost atom cutoff = 10.3
+  binsize = 5.15 -> bins = 6 4 5
+Memory usage per processor = 2.50221 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         2000    -5280.875            0   -5132.2259   -20502.321 
+      10    895.65237    -5198.402            0    -5131.833    419.34676 
+      20    932.93463   -5201.1569            0   -5131.8169   -21407.961 
+      30    936.09591   -5201.3998            0   -5131.8248   -32531.168 
+      40    930.05159   -5201.0073            0   -5131.8816   -46445.212 
+      50    904.64676    -5199.062            0   -5131.8245   -31402.385 
+      60    1005.5353   -5206.5725            0   -5131.8365   -29790.442 
+      70    941.02343   -5201.7644            0   -5131.8232   -23046.796 
+      80    1020.1044   -5207.6763            0   -5131.8574   -13488.675 
+      90    912.75535    -5199.651            0   -5131.8108    2715.5897 
+     100    998.97588   -5206.1008            0   -5131.8523    6024.3651 
+Loop time of 0.595389 on 4 procs for 100 steps with 576 atoms
+
+Performance: 14.512 ns/day, 1.654 hours/ns, 167.957 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    | 0.51621    | 0.52629    | 0.53686    |   1.1 | 88.39
+Neigh   | 0.017571   | 0.018024   | 0.018574   |   0.3 |  3.03
+Comm    | 0.038951   | 0.050033   | 0.06044    |   3.7 |  8.40
+Output  | 0.00020981 | 0.00022781 | 0.00025916 |   0.1 |  0.04
+Modify  | 0.00025797 | 0.00027782 | 0.00031734 |   0.1 |  0.05
+Other   |            | 0.0005327  |            |       |  0.09
+
+Nlocal:    144 ave 146 max 143 min
+Histogram: 2 0 0 1 0 0 0 0 0 1
+Nghost:    3031 ave 3032 max 3030 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  52617.5 ave 53258 max 52208 min
+Histogram: 2 0 0 0 1 0 0 0 0 1
+
+Total # of neighbors = 210470
+Ave neighs/atom = 365.399
+Neighbor list builds = 10
+Dangerous builds = 10
+
+Total wall time: 0:00:00