#-------------------------------------------------------------------------------
# Stage 2.3: NVE integration for Deposition for 2000 ps with a timestep of 0.2 fs
#-------------------------------------------------------------------------------
group deposition_atoms_OMCTS id 79921 79922 79923 79924 79925 79926 79927 79928
8 atoms in group deposition_atoms_OMCTS
group deposition_atoms_OMCTS id 79929 79930 79931 79932 79933 79934 79935 79936
16 atoms in group deposition_atoms_OMCTS
group deposition_atoms_OMCTS id 79937 79938 79939 79940 79941 79942 79943 79944
24 atoms in group deposition_atoms_OMCTS
group deposition_atoms_OMCTS id 79945 79946 79947 79948 79949 79950 79951 79952
32 atoms in group deposition_atoms_OMCTS
group deposition_atoms_OMCTS id 79953 79954 79955 79956 79957 79958 79959 79960
40 atoms in group deposition_atoms_OMCTS
delete_atoms group deposition_atoms_OMCTS
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 40 atoms, new total = 80040
molecule depositing_species_OMCTS deposition_OMCTS.dat
Read molecule template depositing_species_OMCTS:
1 molecules
0 fragments
40 atoms with max type 4
0 bonds with max type 0
0 angles with max type 0
0 dihedrals with max type 0
0 impropers with max type 0
region deposition_region_OMCTS block EDGE EDGE EDGE EDGE 560 780 units box
group deposition_atoms_OMCTS_1 id 79961 79962 79963 79964 79965 79966 79967 79968
8 atoms in group deposition_atoms_OMCTS_1
group deposition_atoms_OMCTS_1 id 79969 79970 79971 79972 79973 79974 79975 79976
16 atoms in group deposition_atoms_OMCTS_1
group deposition_atoms_OMCTS_1 id 79977 79978 79979 79980 79981 79982 79983 79984
24 atoms in group deposition_atoms_OMCTS_1
group deposition_atoms_OMCTS_1 id 79985 79986 79987 79988 79989 79990 79991 79992
32 atoms in group deposition_atoms_OMCTS_1
group deposition_atoms_OMCTS_1 id 79993 79994 79995 79996 79997 79998 79999 80000
40 atoms in group deposition_atoms_OMCTS_1
delete_atoms group deposition_atoms_OMCTS_1
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 40 atoms, new total = 80000
molecule depositing_species_OMCTS_1 deposition_OMCTS_1.dat
Read molecule template depositing_species_OMCTS_1:
1 molecules
0 fragments
40 atoms with max type 4
0 bonds with max type 0
0 angles with max type 0
0 dihedrals with max type 0
0 impropers with max type 0
region deposition_region_OMCTS_1 block EDGE EDGE EDGE EDGE 560 780 units box
group deposition_atoms_OMCTS_2 id 80001 80002 80003 80004 80005 80006 80007 80008
8 atoms in group deposition_atoms_OMCTS_2
group deposition_atoms_OMCTS_2 id 80009 80010 80011 80012 80013 80014 80015 80016
16 atoms in group deposition_atoms_OMCTS_2
group deposition_atoms_OMCTS_2 id 80017 80018 80019 80020 80021 80022 80023 80024
24 atoms in group deposition_atoms_OMCTS_2
group deposition_atoms_OMCTS_2 id 80025 80026 80027 80028 80029 80030 80031 80032
32 atoms in group deposition_atoms_OMCTS_2
group deposition_atoms_OMCTS_2 id 80033 80034 80035 80036 80037 80038 80039 80040
40 atoms in group deposition_atoms_OMCTS_2
delete_atoms group deposition_atoms_OMCTS_2
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 40 atoms, new total = 79960
molecule depositing_species_OMCTS_2 deposition_OMCTS_2.dat
Read molecule template depositing_species_OMCTS_2:
1 molecules
0 fragments
40 atoms with max type 4
0 bonds with max type 0
0 angles with max type 0
0 dihedrals with max type 0
0 impropers with max type 0
region deposition_region_OMCTS_2 block EDGE EDGE EDGE EDGE 560 780 units box
group deposition_atoms_OMCTS_3 id 80041 80042 80043 80044 80045 80046 80047 80048
8 atoms in group deposition_atoms_OMCTS_3
group deposition_atoms_OMCTS_3 id 80049 80050 80051 80052 80053 80054 80055 80056
16 atoms in group deposition_atoms_OMCTS_3
group deposition_atoms_OMCTS_3 id 80057 80058 80059 80060 80061 80062 80063 80064
24 atoms in group deposition_atoms_OMCTS_3
group deposition_atoms_OMCTS_3 id 80065 80066 80067 80068 80069 80070 80071 80072
32 atoms in group deposition_atoms_OMCTS_3
group deposition_atoms_OMCTS_3 id 80073 80074 80075 80076 80077 80078 80079 80080
40 atoms in group deposition_atoms_OMCTS_3
delete_atoms group deposition_atoms_OMCTS_3
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 40 atoms, new total = 79920
molecule depositing_species_OMCTS_3 deposition_OMCTS_3.dat
Read molecule template depositing_species_OMCTS_3:
1 molecules
0 fragments
40 atoms with max type 4
0 bonds with max type 0
0 angles with max type 0
0 dihedrals with max type 0
0 impropers with max type 0
region deposition_region_OMCTS_3 block EDGE EDGE EDGE EDGE 560 780 units box
region evaporation_region block EDGE EDGE EDGE EDGE 790 EDGE units box
group evaporation_group dynamic all region evaporation_region every 100
dynamic group evaporation_group defined
uncompute thermo_temp
compute thermo_temp movable temp
thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:903)
thermo ${Nthermo}
thermo 0
fix 1 movable nve
fix 2 evaporation_group reax/c/species 1 1 100 removed_fragments.out element C H O Si terse yes
fix 3 all evaporate 100 1000 evaporation_region 421628 molecule yes
fix dlan subset_thermoset langevin 300 300 20.0 8 tally yes
fix 4 movable ave/time 1 1000000 1000000 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 f_dlan file 2.3_averages.txt off 1
fix 5 movable ave/time 1000 1 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 f_dlan file 2.3_instantaneous.txt
fix 6 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
fix deposition_OMCTS_1 deposition_atoms_OMCTS deposit 2000 0 5000 421628 region deposition_region_OMCTS mol depositing_species_OMCTS vz -0.030300013054885184 -0.037033349289304116 vx -0.38481192665743158 0.38481192665743158 vy -0.38481192665743158 0.38481192665743158 near 1.50 id next units box
fix deposition_OMCTS_2 deposition_atoms_OMCTS nve
fix deposition_OMCTS_1_1 deposition_atoms_OMCTS_1 deposit 2000 0 5000 982 region deposition_region_OMCTS_1 mol depositing_species_OMCTS_1 vz -0.030300013054885184 -0.037033349289304116 vx -0.38481192665743158 0.38481192665743158 vy -0.38481192665743158 0.38481192665743158 near 1.50 id next units box
fix deposition_OMCTS_1_2 deposition_atoms_OMCTS_1 nve
fix deposition_OMCTS_2_1 deposition_atoms_OMCTS_2 deposit 2000 0 5000 1 region deposition_region_OMCTS_2 mol depositing_species_OMCTS_2 vz -0.030300013054885184 -0.037033349289304116 vx -0.38481192665743158 0.38481192665743158 vy -0.38481192665743158 0.38481192665743158 near 1.50 id next units box
fix deposition_OMCTS_2_2 deposition_atoms_OMCTS_2 nve
fix deposition_OMCTS_3_1 deposition_atoms_OMCTS_3 deposit 2000 0 5000 69115 region deposition_region_OMCTS_3 mol depositing_species_OMCTS_3 vz -0.030300013054885184 -0.037033349289304116 vx -0.38481192665743158 0.38481192665743158 vy -0.38481192665743158 0.38481192665743158 near 1.50 id next units box
fix deposition_OMCTS_3_2 deposition_atoms_OMCTS_3 nve
dump trj all custom 50000 2.3.Trajectory.xyz id mol type q xs ys zs
fix trjE all ave/time 50000 1 50000 v_etotal v_pe v_ke file 2.3.energies.txt
dump trj_OMCTS deposition_atoms_OMCTS custom 50000 2.3.trajectory_1.xyz id mol type q xs ys zs
dump trj_OMCTS_1 deposition_atoms_OMCTS_1 custom 50000 2.3.trajectory_2.xyz id mol type q xs ys zs
dump trj_OMCTS_2 deposition_atoms_OMCTS_2 custom 50000 2.3.trajectory_3.xyz id mol type q xs ys zs
dump trj_OMCTS_3 deposition_atoms_OMCTS_3 custom 50000 2.3.trajectory_4.xyz id mol type q xs ys zs
timestep 0.2
run 10000000
CITE-CITE-CITE-CITE-CITE-CI