fix 2 pt rigid/nvt/small molecule temp 353.15 353.15 100.0
I want to use this command to form a molecule rigid and control its temperature. But in the .log file, the temperture is not the temperature I control. Why is this?
Because it is the output of compute thermo_temp all, as documented in the manual for the thermo_style command — LAMMPS documentation
If you want the output of the temperature of the group of atoms that you apply fix rigid/nvt/small to, you have to customize the output and output the corresponding temperature compute used by the fix.
compute t_pt pt temp
fix 2 pt rigid/nvt/small molecule temp 353.15 353.15 100.0
fix 3 pt ave/time 10 100 1000 c_t_pt file nvt.profile
thermo 2000
thermo_style custom step c_t_pt
Above is my output temperature command, but in the ‘nvt.profile’ file, the c_t_pt is still not the temperature I set.
It is not possible to comment further without knowing anything about your system and simulation setup and what numbers you actually get.
This is my in.file
#water from net
dimension 3
processors * * 1
boundary p p p
units real
atom_style full
neighbor 2 bin
neigh_modify delay 0 every 1 check yes
neigh_modify one 3000
read_data ptchneq.data
change_box all y final -6 86
change_box all z final 0 125
mass 1 12.017000
mass 2 12.017000
mass 3 18.998403
mass 4 15.999400
mass 5 32.065000
mass 6 15.999400
mass 7 15.999400
mass 8 1.00794
mass 9 1.00794
mass 10 12.010700
mass 11 195.09
#pair SPC
pair_style lj/cut/coul/long 15.0 15.0
pair_coeff 1 1 0.0844 3.4600 15.0
pair_coeff 1 2 0.0896 3.4665 15.0
pair_coeff 1 3 0.0647 3.2425 15.0
pair_coeff 1 4 0.0899 3.2466 15.0
pair_coeff 1 5 0.1704 3.5252 15.0
pair_coeff 1 6 0.1249 3.3128 15.0
pair_coeff 1 7 0.1249 3.3128 15.0
pair_coeff 1 8 0.0291 2.1309 15.0
pair_coeff 1 9 0.0291 2.1309 15.0
pair_coeff 1 10 0.0685 3.4300 15.0
pair_coeff 1 11 0.6258 2.9350 15.0
pair_coeff 2 2 0.0951 3.4730 15.0
pair_coeff 2 3 0.0687 3.2490 15.0
pair_coeff 2 4 0.0954 3.2531 15.0
pair_coeff 2 5 0.1809 3.5317 15.0
pair_coeff 2 6 0.1326 3.3193 15.0
pair_coeff 2 7 0.1326 3.3193 15.0
pair_coeff 2 8 0.0308 2.1374 15.0
pair_coeff 2 9 0.0308 2.1374 15.0
pair_coeff 2 10 0.0727 3.4365 15.0
pair_coeff 2 11 0.6643 2.9415 15.0
pair_coeff 3 3 0.0496 3.0249 15.0
pair_coeff 3 4 0.0689 3.0291 15.0
pair_coeff 3 5 0.1306 3.3076 15.0
pair_coeff 3 6 0.0957 3.0952 15.0
pair_coeff 3 7 0.0957 3.0952 15.0
pair_coeff 3 8 0.0223 1.91335 15.0
pair_coeff 3 9 0.0223 1.91335 15.0
pair_coeff 3 10 0.0525 3.21245 15.0
pair_coeff 3 11 0.4797 2.71745 15.0
pair_coeff 4 4 0.0957 3.0332 15.0
pair_coeff 4 5 0.1814 3.31175 15.0
pair_coeff 4 6 0.1330 3.09935 15.0
pair_coeff 4 7 0.1330 3.09935 15.0
pair_coeff 4 8 0.0309 1.9175 15.0
pair_coeff 4 9 0.0309 1.9175 15.0
pair_coeff 4 10 0.0729 3.2166 15.0
pair_coeff 4 11 0.6664 2.7216 15.0
pair_coeff 5 5 0.3440 3.5903 15.0
pair_coeff 5 6 0.2521 3.3779 15.0
pair_coeff 5 7 0.2521 3.3779 15.0
pair_coeff 5 8 0.0587 2.19605 15.0
pair_coeff 5 9 0.0587 2.19605 15.0
pair_coeff 5 10 0.1383 3.49515 15.0
pair_coeff 5 11 1.2634 3.00015 15.0
pair_coeff 6 6 0.1848 3.1655 15.0
pair_coeff 6 7 0.1848 3.1655 15.0
pair_coeff 6 8 0.0430 1.98365 15.0
pair_coeff 6 9 0.0430 1.98365 15.0
pair_coeff 6 10 0.1014 3.28275 15.0
pair_coeff 6 11 0.9260 2.78775 15.0
pair_coeff 7 7 0.1848 3.1655 15.0
pair_coeff 7 8 0.0430 1.98365 15.0
pair_coeff 7 9 0.0430 1.98365 15.0
pair_coeff 7 10 0.1014 3.28275 15.0
pair_coeff 7 11 0.9260 2.78775 15.0
pair_coeff 8 8 0.0100 0.8018 15.0
pair_coeff 8 9 0.0100 0.8018 15.0
pair_coeff 8 10 0.0236 2.1009 15.0
pair_coeff 8 11 0.2154 1.6059 15.0
pair_coeff 9 9 0.0100 0.8018 15.0
pair_coeff 9 10 0.0236 2.1009 15.0
pair_coeff 9 11 0.2154 1.6059 15.0
pair_coeff 10 10 0.0556 3.4000 15.0
pair_coeff 10 10 0.0000 0.0000 15.0
pair_coeff 10 11 0.5079 2.9050 15.0
pair_coeff 11 11 4.6400 2.4100 15.0
#bond and angle
bond_style harmonic
bond_coeff 1 214.6602 1.4982 #C1C1
bond_coeff 2 350.0000 1.5300 #C2C2
bond_coeff 3 350.0000 1.5300 #C1C2
bond_coeff 4 350.0000 1.4200 #C2O
bond_coeff 5 302.62975 1.3360 #CXF
bond_coeff 6 350.0000 1.8000 #C2S
bond_coeff 7 350.0000 1.4800 #SO
bond_coeff 8 250.0000 1.0000 #OwHw
bond_coeff 9 542.9783 0.9820 #OhHh
angle_style harmonic
angle_coeff 1 53.13695 122.5536 #CxCxCx
angle_coeff 2 50.16830 118.3191 #CxCxF
angle_coeff 3 54.11980 121.5020 #FCxF
angle_coeff 4 50.00000 109.4710 #CxCxO
angle_coeff 5 50.00000 125.2300 #CxOCx
angle_coeff 6 50.00000 109.5700 #OCxF
angle_coeff 7 50.00000 110.3000 #FCxS
angle_coeff 8 50.00000 116.8100 #CxCxS
angle_coeff 9 175.0000 102.6500 #CxSO
angle_coeff 10 175.0000 115.5000 #OSO
angle_coeff 11 60.0000 109.4700 #HOHw
angle_coeff 12 39.5132 113.4000 #HOWh
dihedral_style harmonic
dihedral_coeff 1 0.5000 1 3 #CxCx
dihedral_coeff 2 1.60855 -1 3 #C1C1C1C1
dihedral_coeff 3 2.0611 -1 3 #FC1C1C1
dihedral_coeff 4 2.0212 1 3 #FC1C1F
dihedral_coeff 5 0.5000 1 3 #CxO
dihedral_coeff 6 0.5000 1 3 #CxS
#charge
kspace_style pppm 0.0001
#=====================================================
group nafion type 1 2 3 4 5
group f3c type 6 8
group h3o type 7 9
group water union f3c h3o
group hn union water nafion
group cs type 10
group pt type 11
compute t_nafion nafion temp
compute t_w water temp
compute t_hn hn temp
compute t_pt pt temp
compute_modify t_pt dynamic yes
variable etotal equal etotal
variable pe equal pe
neigh_modify exclude type 10 10
#neigh_modify exclude type 11 11
#energy minimize
#nvt process
velocity nafion create 353.15 12345 temp t_nafion
velocity water create 353.15 12345 temp t_w
velocity pt create 353.15 12345 temp t_pt
run 0
velocity pt scale 353.15
fix 1 cs setforce 0.0 0.0 0.0
fix 2 pt rigid/nvt/small molecule temp 353.15 353.15 100.0
fix 3 hn nvt temp 353.15 353.15 100.0
fix 4 all wall/lj126 zhi 125.0 0.01 2.5 2.5 pbc yes
fix 5 all wall/lj126 zlo 0.0 0.01 2.5 2.5 pbc yes units box
fix 6 all ave/time 10 100 1000 c_t_hn c_t_pt v_etotal v_pe file nvt.profile
timestep 1.0
thermo 2000
thermo_style custom step c_t_hn etotal pe dt
dump 1 all atom 2000 nvt.dump
dump 2 all atom 50000 nvt-view.dump
restart 1000000 restart.*.nvt
run 6000000
write_data eq.data nocoeff
This does not help much and is not what I asked for.
How do you suppose could someone provide assistance without you providing comprehensive information?
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