#-------------------------------------------------------------------------------
# Stage 2.5: NVT integration for 10 ps 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 1000 1000 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 1 1 1 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
fix 4 fixed setforce 0.0 0.0 0.0
restart 10000 2.5.restart
dump sci all custom 1000 2.5.xyz id mol type q xs ys zs
group rdfgroup_1 union subset_Li_1 subset_Cl_1
350 atoms in group rdfgroup_1
compute rdf_1 rdfgroup_1 rdf 200 4 1
fix rdf_1 rdfgroup_1 ave/time 1 100 100 c_rdf_1[*] file 2.5_PairCorrelation_all_1.out mode vector
group rdfgroup_2 union subset_Li_1 subset_S_1
38 atoms in group rdfgroup_2
compute rdf_2 rdfgroup_2 rdf 200 4 9
fix rdf_2 rdfgroup_2 ave/time 1 100 100 c_rdf_2[*] file 2.5_PairCorrelation_all_2.out mode vector
group rdfgroup_3 union subset_Li_1 subset_O(SO4)_1
38 atoms in group rdfgroup_3
compute rdf_3 rdfgroup_3 rdf 200 4 8
fix rdf_3 rdfgroup_3 ave/time 1 100 100 c_rdf_3[*] file 2.5_PairCorrelation_all_3.out mode vector
group rdfgroup_4 union subset_Li_1 subset_O(H2O)_1
2819 atoms in group rdfgroup_4
compute rdf_4 rdfgroup_4 rdf 200 4 7
fix rdf_4 rdfgroup_4 ave/time 1 100 100 c_rdf_4[*] file 2.5_PairCorrelation_all_4.out mode vector
group rdfgroup_5 union subset_Li_1 subset_H_1
2819 atoms in group rdfgroup_5
compute rdf_5 rdfgroup_5 rdf 200 4 2
fix rdf_5 rdfgroup_5 ave/time 1 100 100 c_rdf_5[*] file 2.5_PairCorrelation_all_5.out mode vector
group rdfgroup_6 union subset_Na_1 subset_Cl_1
399 atoms in group rdfgroup_6
compute rdf_6 rdfgroup_6 rdf 200 6 1
fix rdf_6 rdfgroup_6 ave/time 1 100 100 c_rdf_6[*] file 2.5_PairCorrelation_all_6.out mode vector
group rdfgroup_8 union subset_Na_1 subset_S_1
87 atoms in group rdfgroup_8
compute rdf_8 rdfgroup_8 rdf 200 6 9
fix rdf_8 rdfgroup_8 ave/time 1 100 100 c_rdf_8[*] file 2.5_PairCorrelation_all_8.out mode vector
group rdfgroup_9 union subset_Na_1 subset_O(SO4)_1
87 atoms in group rdfgroup_9
compute rdf_9 rdfgroup_9 rdf 200 6 8
fix rdf_9 rdfgroup_9 ave/time 1 100 100 c_rdf_9[*] file 2.5_PairCorrelation_all_9.out mode vector
group rdfgroup_10 union subset_Na_1 subset_O(H2O)_1
2868 atoms in group rdfgroup_10
compute rdf_10 rdfgroup_10 rdf 200 6 7
fix rdf_10 rdfgroup_10 ave/time 1 100 100 c_rdf_10[*] file 2.5_PairCorrelation_all_10.out mode vector
group rdfgroup_11 union subset_Na_1 subset_H_1
2868 atoms in group rdfgroup_11
compute rdf_11 rdfgroup_11 rdf 200 6 2
fix rdf_11 rdfgroup_11 ave/time 1 100 100 c_rdf_11[*] file 2.5_PairCorrelation_all_11.out mode vector
group rdfgroup_12 union subset_K_1 subset_Cl_1
383 atoms in group rdfgroup_12
compute rdf_12 rdfgroup_12 rdf 200 3 1
fix rdf_12 rdfgroup_12 ave/time 1 100 100 c_rdf_12[*] file 2.5_PairCorrelation_all_12.out mode vector
group rdfgroup_13 union subset_K_1 subset_S_1
71 atoms in group rdfgroup_13
compute rdf_13 rdfgroup_13 rdf 200 3 9
fix rdf_13 rdfgroup_13 ave/time 1 100 100 c_rdf_13[*] file 2.5_PairCorrelation_all_13.out mode vector
group rdfgroup_14 union subset_K_1 subset_O(SO4)_1
71 atoms in group rdfgroup_14
compute rdf_14 r