#-------------------------------------------------------------------------------
# Stage 2.5: NVT integration for 5 ns with a timestep of 1 fs
# Temperature 298.2 K
#-------------------------------------------------------------------------------
# Fix shake is needed for water in pcff+
fix shaken all shake .0001 20 50000 a 2 b 2
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
2812 = # of frozen angles
find clusters CPU = 0.001 seconds
reset_timestep 0
thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke
thermo ${Nthermo}
thermo 0
fix 1 movable nvt temp 298.2 298.2 100 drag 0.0
fix 2 movable ave/time 1 500000 500000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 2.5_averages.txt off 1
fix 3 movable ave/time 500 1 500 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 2.5_instantaneous.txt
restart 5000000 2.5.restart
dump trj all custom 50000 2.5.Trajectory.xyz id mol type q xs ys zs
fix trjE all ave/time 50000 1 50000 v_etotal v_pe v_ke file 2.5.energies.txt
dump sci all custom 500000 2.5.xyz id mol type q xs ys zs
group rdfgroup_2 union subset_Li subset_Li
7 atoms in group rdfgroup_2
compute rdf_2 rdfgroup_2 rdf 200 4 4
fix rdf_2 rdfgroup_2 ave/time 1 5000000 5000000 c_rdf_2[*] file 2.5_PairCorrelation_all_2.out mode vector
group rdfgroup_3 union subset_Li subset_Cl
350 atoms in group rdfgroup_3
compute rdf_3 rdfgroup_3 rdf 200 4 1
fix rdf_3 rdfgroup_3 ave/time 1 5000000 5000000 c_rdf_3[*] file 2.5_PairCorrelation_all_3.out mode vector
group rdfgroup_4 union subset_Li subset_S(SO4)
38 atoms in group rdfgroup_4
compute rdf_4 rdfgroup_4 rdf 200 4 9
fix rdf_4 rdfgroup_4 ave/time 1 5000000 5000000 c_rdf_4[*] file 2.5_PairCorrelation_all_4.out mode vector
group rdfgroup_5 union subset_Li subset_O(H2O)
2819 atoms in group rdfgroup_5
compute rdf_5 rdfgroup_5 rdf 200 4 7
fix rdf_5 rdfgroup_5 ave/time 1 5000000 5000000 c_rdf_5[*] file 2.5_PairCorrelation_all_5.out mode vector
group rdfgroup_6 union subset_Na subset_Na
56 atoms in group rdfgroup_6
compute rdf_6 rdfgroup_6 rdf 200 6 6
fix rdf_6 rdfgroup_6 ave/time 1 5000000 5000000 c_rdf_6[*] file 2.5_PairCorrelation_all_6.out mode vector
group rdfgroup_7 union subset_Na subset_Cl
399 atoms in group rdfgroup_7
compute rdf_7 rdfgroup_7 rdf 200 6 1
fix rdf_7 rdfgroup_7 ave/time 1 5000000 5000000 c_rdf_7[*] file 2.5_PairCorrelation_all_7.out mode vector
group rdfgroup_8 union subset_Na subset_S(SO4)
87 atoms in group rdfgroup_8
compute rdf_8 rdfgroup_8 rdf 200 6 9
fix rdf_8 rdfgroup_8 ave/time 1 5000000 5000000 c_rdf_8[*] file 2.5_PairCorrelation_all_8.out mode vector
group rdfgroup_9 union subset_Na subset_O(H2O)
2868 atoms in group rdfgroup_9
compute rdf_9 rdfgroup_9 rdf 200 6 7
fix rdf_9 rdfgroup_9 ave/time 1 5000000 5000000 c_rdf_9[*] file 2.5_PairCorrelation_all_9.out mode vector
group rdfgroup_10 union subset_K subset_K
40 atoms in group rdfgroup_10
compute rdf_10 rdfgroup_10 rdf 200 3 3
fix rdf_10 rdfgroup_10 ave/time 1 5000000 5000000 c_rdf_10[*] file 2.5_PairCorrelation_all_10.out mode vector
group rdfgroup_11 union subset_K subset_Cl
383 atoms in group rdfgroup_11
compute rdf_11 rdfgroup_11 rdf 200 3 1
fix rdf_11 rdfgroup_11 ave/time 1 5000000 5000000 c_rdf_11[*] file 2.5_PairCorrelation_all_11.out mode vector
group rdfgroup_12 union subset_K subset_S(SO4)
71 atoms in group rdfgroup_12
compute rdf_12 rdfgroup_12 rdf 200 3 9
fix rdf_12 rdfgroup_12 ave/time 1 5000000 5000000 c_rdf_12[*] file 2.5_PairCorrelation_all_12.out mode vector
group rdfgroup_13 union subset_K subset_O(H2O)
2852 atoms in group rdfgroup_13
compute rdf_13 rdfgroup_13 rdf 200 3 7
fix rdf_13 rdfgroup_13 ave/time 1 5000000 5000000 c_rdf_13[*] file 2.5_PairCorrelation_all_13.out mode vector
group rdfgroup_14 union subset_Mg subset_Mg
151 atoms in group rdfgroup_14
compute rdf_14 rdfgroup_14 rdf 200 5 5
fix rdf_14 rdfgroup_14 ave/time 1 5000000 5000000 c_rdf_14[*] file 2.5_PairCorrelation_all_14.out mode vector
group rdfgroup_15 union subset_Mg subset_Cl
494 atoms in group rdfgroup_15
compute rdf_15 rdfgroup_15 rdf 200 5 1
fix rdf_15 rdfgroup_15 ave/time 1 5000000 5000000 c_rdf_15[*] file 2.5_PairCorrelation_all_15.out mode vector
group rdfgroup_16 union subset_Mg subset_S(SO4)
182 atoms in group rdfgroup_16
compute rdf_16 rdfgroup_16 rdf 200 5 9
fix rdf_16 rdfgroup_16 ave/time 1 5000000 5000000 c_rdf_16[*] file 2.5_PairCorrelation_all_16.out mode vector
group rdfgroup_17 union subset_Mg subset_O(H2O)
2963 atoms in group rdfgroup_17
compute rdf_17 rdfgroup_17 rdf 200 5 7
fix rdf_17 rdfgroup_17 ave/time 1 5000000 5000000 c_rdf_17[*] file 2.5_PairCorrelation_all_17.out mode vector
group rdfgroup_18 union subset_Cl subset_Cl
343 atoms in group rdfgroup_18
compute rdf_18 rdfgroup_18 rdf 200 1 1
fix rdf_18 rdfgroup_18 ave/time 1 5000000 5000000 c_rdf_18[*] file 2.5_PairCorrelation_all_18.out mode vector
group rdfgroup_19 union subset_Cl subset_O(H2O)
3155 atoms in group rdfgroup_19
compute rdf_19 rdfgroup_19 rdf 200 1 7
fix rdf_19 rdfgroup_19 ave/time 1 5000000 5000000 c_rdf_19[*] file 2.5_PairCorrelation_all_19.out mode vector
group rdfgroup_20 union subset_S(SO4) subset_S(SO4)
31 atoms in group rdfgroup_20
compute rdf_20 rdfgroup_20 rdf 200 9 9
fix rdf_20 rdfgroup_20 ave/time 1 5000000 5000000 c_rdf_20[*] file 2.5_PairCorrelation_all_20.out mode vector
group rdfgroup_21 union subset_S(SO4) subset_O(H2O)
2843 atoms in group rdfgroup_21
compute rdf_21 rdfgroup_21 rdf 200 9 7
fix rdf_21 rdfgroup_21 ave/time 1 5000000 5000000 c_rdf_21[*] file 2.5_PairCorrelation_all_21.out mode vector
timestep 1
run 5000000
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:340)
G vector (1/distance) = 0.2557377
grid = 27 27 54
stencil order = 5
estimated absolute RMS force accuracy = 0.0032430487
estimated relative force accuracy = 9.7663448e-06
using double precision KISS FFT
3d grid and FFT values/proc = 8000 2916
generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 5 5 13
21 neighbor lists, perpetual/occasional/extra = 1 20 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) compute rdf, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(3) compute rdf, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(4) compute rdf, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(5) compute rdf, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(6) compute rdf, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(7) compute rdf, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(8) compute rdf, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(9) compute rdf, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(10) compute rdf, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(11) compute rdf, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(12) compute rdf, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(13) compute rdf, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(14) compute rdf, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(15) compute rdf, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(16) compute rdf, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(17) compute rdf, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(18) compute rdf, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(19) compute rdf, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(20) compute rdf, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(21) compute rdf, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
SHAKE stats (type/ave/delta/count) on step 0
2 0.97 1.03384e-12 8436
2 103.7 9.44738e-11 2812
Per MPI rank memory allocation (min/avg/max) = 15.23 | 15.42 | 15.46 Mbytes
Step v_time Press Volume v_sysdensity Temp E_bond E_angle E_dihed E_impro E_vdwl E_coul E_tail E_long PotEng KinEng
0 1e-06 2129.488 93962.523 1.2789064 296.95398 52.106796 83.455533 0 0 19559.569 46218.787 -220.49494 -206915.39 -141001.47 5642.9167
SHAKE stats (type/ave/delta/count) on step 50000
2 0.97 1.29517e-06 8436
2 103.7 0.000100968 2812
SHAKE stats (type/ave/delta/count) on step 100000
2 0.97 1.53507e-06 8436
2 103.7 0.000104029 2812
SHAKE stats (type/ave/delta/count) on step 150000
2 0.97 1.35046e-06 8436
2 103.7 0.000104306 2812
SHAKE stats (type/ave/delta/count) on step 200000
2 0.97 1.53641e-06 8436
2 103.7 0.000160964 2812
SHAKE stats (type/ave/delta/count) on step 250000
2 0.97 1.7076e-06 8436
2 103.7 0.000105553 2812
SHAKE stats (type/ave/delta/count) on step 300000
2 0.97 1.28852e-06 8436
2 103.7 0.000109918 2812
SHAKE stats (type/ave/delta/count) on step 350000
2 0.97 1.53402e-06 8436
2 103.7 0.000106037 2812
SHAKE stats (type/ave/delta/count) on step 400000
2 0.97 1.31626e-06 8436
2 103.7 9.72722e-05 2812
SHAKE stats (type/ave/delta/count) on step 450000
2 0.97 1.27027e-06 8436
2 103.7 0.000101218 2812
SHAKE stats (type/ave/delta/count) on step 500000
2 0.97 1.40076e-06 8436
2 103.7 9.56102e-05 2812
SHAKE stats (type/ave/delta/count) on step 550000
2 0.97 1.17412e-06 8436
2 103.7 0.000101923 2812
SHAKE stats (type/ave/delta/count) on step 600000
2 0.97 1.35457e-06 8436
2 103.7 9.72659e-05 2812
SHAKE stats (type/ave/delta/count) on step 650000
2 0.97 1.48646e-06 8436
2 103.7 0.000111628 2812
SHAKE stats (type/ave/delta/count) on step 700000
2 0.97 1.6597e-06 8436
2 103.7 0.000126348 2812
SHAKE stats (type/ave/delta/count) on step 750000
2 0.97 1.27398e-06 8436
2 103.7 0.000100643 2812
SHAKE stats (type/ave/delta/count) on step 800000
2 0.97 1.27505e-06 8436
2 103.7 0.000107337 2812
SHAKE stats (type/ave/delta/count) on step 850000
2 0.97 1.30165e-06 8436
2 103.7 9.76959e-05 2812
SHAKE stats (type/ave/delta/count) on step 900000
2 0.97 1.37659e-06 8436
2 103.7 0.000108514 2812
SHAKE stats (type/ave/delta/count) on step 950000
2 0.97 1.215e-06 8436
2 103.7 9.27253e-05 2812
SHAKE stats (type/ave/delta/count) on step 1000000
2 0.97 1.54702e-06 8436
2 103.7 0.000115877 2812
SHAKE stats (type/ave/delta/count) on step 1050000
2 0.97 1.45375e-06 8436
2 103.7 0.000104895 2812
SHAKE stats (type/ave/delta/count) on step 1100000
2 0.97 1.35939e-06 8436
2 103.7 9.64629e-05 2812
SHAKE stats (type/ave/delta/count) on step 1150000
2 0.97 1.24119e-06 8436
2 103.7 0.000103714 2812
SHAKE stats (type/ave/delta/count) on step 1200000
2 0.97 1.56878e-06 8436
2 103.7 0.000109578 2812
SHAKE stats (type/ave/delta/count) on step 1250000
2 0.97 1.13153e-06 8436
2 103.7 0.000136606 2812
SHAKE stats (type/ave/delta/count) on step 1300000
2 0.97 1.328e-06 8436
2 103.7 0.000109485 2812
SHAKE stats (type/ave/delta/count) on step 1350000
2 0.97 1.65069e-06 8436
2 103.7 0.000118425 2812
SHAKE stats (type/ave/delta/count) on step 1400000
2 0.97 1.18505e-06 8436
2 103.7 8.83569e-05 2812
SHAKE stats (type/ave/delta/count) on step 1450000
2 0.97 1.45115e-06 8436
2 103.7 0.000109048 2812
SHAKE stats (type/ave/delta/count) on step 1500000
2 0.97 1.08567e-06 8436
2 103.7 9.00434e-05 2812
SHAKE stats (type/ave/delta/count) on step 1550000
2 0.97 1.59139e-06 8436
2 103.7 0.000105805 2812
SHAKE stats (type/ave/delta/count) on step 1600000
2 0.97 1.70142e-06 8436
2 103.7 0.000134608 2812
SHAKE stats (type/ave/delta/count) on step 1650000
2 0.97 1.48436e-06 8436
2 103.7 0.000107357 2812
SHAKE stats (type/ave/delta/count) on step 1700000
2 0.97 1.76203e-06 8436
2 103.7 9.57011e-05 2812
SHAKE stats (type/ave/delta/count) on step 1750000
2 0.97 1.41109e-06 8436
2 103.7 0.000122305 2812
SHAKE stats (type/ave/delta/count) on step 1800000
2 0.97 1.48312e-06 8436
2 103.7 0.000105555 2812
SHAKE stats (type/ave/delta/count) on step 1850000
2 0.97 1.26382e-06 8436
2 103.7 9.26735e-05 2812
SHAKE stats (type/ave/delta/count) on step 1900000
2 0.97 1.39877e-06 8436
2 103.7 9.64839e-05 2812
SHAKE stats (type/ave/delta/count) on step 1950000
2 0.97 1.69972e-06 8436
2 103.7 0.000104587 2812
SHAKE stats (type/ave/delta/count) on step 2000000
2 0.97 1.26394e-06 8436
2 103.7 9.79506e-05 2812
SHAKE stats (type/ave/delta/count) on step 2050000
2 0.97 1.82637e-06 8436
2 103.7 0.000126949 2812
SHAKE stats (type/ave/delta/count) on step 2100000
2 0.97 1.69976e-06 8436
2 103.7 0.000132643 2812
SHAKE stats (type/ave/delta/count) on step 2150000
2 0.97 1.20768e-06 8436
2 103.7 0.000102938 2812
SHAKE stats (type/ave/delta/count) on step 2200000
2 0.97 1.36278e-06 8436
2 103.7 9.834e-05 2812
SHAKE stats (type/ave/delta/count) on step 2250000
2 0.97 1.6027e-06 8436
2 103.7 0.000108645 2812
SHAKE stats (type/ave/delta/count) on step 2300000
2 0.97 1.23445e-06 8436
2 103.7 0.000117979 2812
SHAKE stats (type/ave/delta/count) on step 2350000
2 0.97 1.89862e-06 8436
2 103.7 0.