Damping factor in 'fix langevin'

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1

I was trying to simulate the Couette flow problem for different wall velocities. I had initially used a damping factor for 'fix langevin' as 1.0 to maintain a temperature of 1.1 (in lj units) it was working fine for lower velocities but at higher velocities the temperature started rising above the thermostated temperature. Hence I changed the damping factor to 200. But now it is not thermostating properly for even lower temperatures. I have pasted the log files for both the cases below.
I am trying to figure first how to choose a damping factor to get the correct thermostating. Secondly if at all the problem is because of damping factor.

I tried looking through few literature but they did not have anything on how to choose a damping factor.
I would highly appreciate it if anyone could help me or atleast guide me as to where I could find the answer for it.

Thank you.

BR/Joseph

1) DAMPING FACTOR = 1.0

LAMMPS (9 Mar 2011)
# 3-d LJ flow simulation

units lj
dimension 3
boundary p s p

atom_style atomic
neighbor 0.3 bin
neigh_modify delay 1

# create geometry

region fluid block 0 11.95 1.5 26.07 0.0 7.22 units box
region btm_wall block 0 11.95 0 1.5 0.0 7.22 units box
region top_wall block 0 11.95 26.07 28.0 0.0 7.22 units box
region simulation_box union 3 btm_wall fluid top_wall units box

create_box 3 simulation_box
Created orthogonal box = (0 0 0) to (11.95 28 7.22)
  1 by 1 by 1 processor grid

lattice fcc 0.81 orient x 1 1 -2 orient y 1 1 1 orient z 1 -1 0
Lattice spacing in x,y,z = 2.78084 2.94953 2.40828
create_atoms 1 region fluid units box
Created 1735 atoms
lattice fcc 3.24 orient x -1 1 0 orient y 1 1 1 orient z 1 1 -2
Lattice spacing in x,y,z = 1.51712 1.85809 1.75182
create_atoms 2 region btm_wall units box
Created 488 atoms
lattice fcc 3.24 orient x -1 1 0 orient y 1 1 1 orient z 1 1 -2
Lattice spacing in x,y,z = 1.51712 1.85809 1.75182
create_atoms 3 region top_wall units box
Created 528 atoms

mass 1 1.0
mass 2 4.0
mass 3 4.0

# LJ potentials

pair_style lj/cut 2.2
pair_coeff * * 1.0 1.0
pair_coeff 1 2*3 0.2 0.75
pair_modify shift yes

# define groups

region 1 block INF INF INF 1.5 INF INF units box
group lower region 1
488 atoms in group lower
region 2 block INF INF 26.07 INF INF INF units box
group upper region 2
528 atoms in group upper
group boundary union lower upper
1016 atoms in group boundary
group flow subtract all boundary
1735 atoms in group flow

set group lower type 2
  488 settings made for type
set group upper type 3
  528 settings made for type

# initial velocities

compute mobile flow temp/partial 0 0 1
fix 2 flow langevin 1.10 1.10 1.0 699483
velocity flow create 1.1 482748 temp mobile units box
fix 1 all nve
#fix 2 flow temp/rescale 200 1.1 1.1 0.02 1.0
fix_modify 2 temp mobile

# Couette flow

velocity lower set 0.0 0.0 0.0 units box
velocity upper set 1.0 0.0 0.0 units box
fix 3 boundary setforce 0.0 0.0 0.0

#fix test boundary spring tether 1200.0 0.0 0.0 0.0 0.0
#fix test boundary spring/self 1200.0
#fix test1 upper spring tether 1.0 0.0 0.0 0.0 0.0

#fix 4 all enforce2d

group tp_wall region top_wall
528 atoms in group tp_wall
#fluid adjacent to bottom wall
fix 5 flow ave/spatial 1 300000 300000 x center 11.95 z center 7.22 y 1.5 1.02375 vx region fluid file vel_fb.profile units box

# Poiseuille flow

#velocity boundary set 0.0 0.0 0.0
#fix 3 lower setforce 0.0 0.0 0.0
#fix 4 upper setforce 0.0 NULL 0.0
#fix 5 upper aveforce 0.0 -1.0 0.0
#fix 6 flow addforce 0.5 0.0 0.0
#fix 7 all enforce2d

# Run
compute btm_wall_temp lower temp
compute tp_wall_temp upper temp

timestep 0.005
thermo 5000
#thermo_style custom step temp evdwl ecoul epair ebond edihed eimp eangle emol etotal
thermo_style custom step temp etotal c_btm_wall_temp c_tp_wall_temp
thermo_modify temp mobile
WARNING: Temperature for thermo pressure is not for group all

#dump 1 all atom 10 dump.flow
#dump 2 boundary custom 1000 dump.flow2 ys vx
run 600000
Memory usage per processor = 2.279 Mbytes
Step Temp TotEng btm_wall tp_wall_
       0 1.1 257.46174 0 1.3358634
    5000 1.0507066 253.59773 0 1.3358634
   10000 1.119441 253.64237 0 1.3358634
   15000 1.1345931 253.64325 0 1.3358634
   20000 1.1695244 253.65465 0 1.3358634
   25000 1.1085835 253.62149 0 1.3358634
   30000 1.1197047 253.64191 0 1.3358634
   35000 0.99935069 253.6087 0 1.3358634
   40000 1.1656417 253.62 0 1.3358634
   45000 1.0752766 253.59682 0 1.3358634
   50000 1.1531744 253.64117 0 1.3358634
   55000 1.1051872 253.64553 0 1.3358634
   60000 1.1343677 253.64065 0 1.3358634
   65000 1.0446773 253.61951 0 1.3358634
   70000 1.1017815 253.62925 0 1.3358634
   75000 1.0829796 253.65731 0 1.3358634
   80000 1.1071206 253.60033 0 1.3358634
   85000 1.1652198 253.63025 0 1.3358634
   90000 1.0765965 253.62754 0 1.3358634
   95000 1.1394094 253.63398 0 1.3358634
  100000 1.2046504 253.66938 0 1.3358634
  105000 1.1370375 253.65422 0 1.3358634
  110000 1.1512951 253.64267 0 1.3358634
  115000 1.1052644 253.6232 0 1.3358634
  120000 1.1084717 253.63155 0 1.3358634
  125000 1.0602751 253.64317 0 1.3358634
  130000 1.0994552 253.63097 0 1.3358634
  135000 1.0230237 253.57474 0 1.3358634
  140000 1.1080874 253.65086 0 1.3358634
  145000 1.0801643 253.6498 0 1.3358634
  150000 1.1060963 253.62251 0 1.3358634
  155000 1.1085059 253.61981 0 1.3358634
  160000 1.1746287 253.65529 0 1.3358634
  165000 1.1133475 253.63473 0 1.3358634
  170000 1.10359 253.6429 0 1.3358634
  175000 1.1018195 253.62811 0 1.3358634
  180000 1.2030303 253.66308 0 1.3358634
  185000 1.1708241 253.64755 0 1.3358634
  190000 1.1235511 253.64398 0 1.3358634
  195000 1.0375278 253.59636 0 1.3358634
  200000 1.112392 253.64573 0 1.3358634
  205000 1.0676118 253.63431 0 1.3358634
  210000 1.1003571 253.63684 0 1.3358634
  215000 1.0606753 253.60694 0 1.3358634
  220000 1.0423592 253.62073 0 1.3358634
  225000 1.1113113 253.63484 0 1.3358634
  230000 1.0939753 253.6367 0 1.3358634
  235000 1.0941297 253.63796 0 1.3358634
  240000 1.0748566 253.6222 0 1.3358634
  245000 1.0947193 253.6167 0 1.3358634
  250000 1.0873131 253.62322 0 1.3358634
  255000 1.0857788 253.6571 0 1.3358634
  260000 1.066238 253.60951 0 1.3358634
  265000 1.1242448 253.62895 0 1.3358634
  270000 1.0942999 253.63151 0 1.3358634
  275000 1.0654069 253.59644 0 1.3358634
  280000 1.104333 253.6387 0 1.3358634
  285000 1.0833966 253.62006 0 1.3358634
  290000 1.1601746 253.64821 0 1.3358634
  295000 1.0372644 253.62829 0 1.3358634
  300000 1.0607024 253.59742 0 1.3358634
  305000 1.1266566 253.62612 0 1.3358634
  310000 1.0690641 253.58942 0 1.3358634
  315000 1.0934018 253.64517 0 1.3358634
  320000 1.1705221 253.62429 0 1.3358634
  325000 1.0707689 253.6143 0 1.3358634
  330000 1.0572419 253.62974 0 1.3358634
  335000 1.0981461 253.63071 0 1.3358634
  340000 1.158883 253.64555 0 1.3358634
  345000 1.128077 253.67453 0 1.3358634
  350000 1.048313 253.63165 0 1.3358634
  355000 1.0425548 253.58352 0 1.3358634
  360000 1.0751429 253.62552 0 1.3358634
  365000 1.0270802 253.60124 0 1.3358634
  370000 1.1183242 253.63426 0 1.3358634
  375000 1.1454907 253.66511 0 1.3358634
  380000 1.1056002 253.62272 0 1.3358634
  385000 1.1314341 253.65042 0 1.3358634
  390000 1.0968005 253.60388 0 1.3358634
  395000 1.1201174 253.6221 0 1.3358634
  400000 1.1177679 253.63908 0 1.3358634
  405000 1.0700923 253.60885 0 1.3358634
  410000 1.1649264 253.64314 0 1.3358634
  415000 1.1197772 253.62997 0 1.3358634
  420000 1.0591472 253.62321 0 1.3358634
  425000 1.1056556 253.63176 0 1.3358634
  430000 1.0961797 253.62662 0 1.3358634
  435000 1.1353169 253.6603 0 1.3358634
  440000 1.0606554 253.62831 0 1.3358634
  445000 1.0815593 253.64086 0 1.3358634
  450000 1.0980837 253.67363 0 1.3358634
  455000 1.1051909 253.62842 0 1.3358634
  460000 1.1496605 253.61554 0 1.3358634
  465000 1.1243858 253.6196 0 1.3358634
  470000 1.0780363 253.64051 0 1.3358634
  475000 1.1619706 253.65592 0 1.3358634
  480000 1.1593298 253.64164 0 1.3358634
  485000 1.1552987 253.63647 0 1.3358634
  490000 1.1124164 253.62196 0 1.3358634
  495000 1.1234938 253.63363 0 1.3358634
  500000 1.1021301 253.63478 0 1.3358634
  505000 1.0544891 253.58152 0 1.3358634
  510000 1.1071074 253.64739 0 1.3358634
  515000 1.1017781 253.6333 0 1.3358634
  520000 1.0973214 253.65119 0 1.3358634
  525000 1.1232451 253.631 0 1.3358634
  530000 1.1537653 253.66298 0 1.3358634
  535000 1.0641569 253.62146 0 1.3358634
  540000 1.1733724 253.65925 0 1.3358634
  545000 1.1148625 253.62459 0 1.3358634
  550000 1.1816796 253.66888 0 1.3358634
  555000 1.1238443 253.62949 0 1.3358634
  560000 1.1381152 253.66116 0 1.3358634
  565000 1.1037682 253.64093 0 1.3358634
  570000 1.1074723 253.61416 0 1.3358634
  575000 1.0760858 253.60255 0 1.3358634
  580000 1.057463 253.65259 0 1.3358634
  585000 1.0474823 253.60015 0 1.3358634
  590000 1.1352097 253.64222 0 1.3358634
  595000 1.0711174 253.62577 0 1.3358634
  600000 1.1485206 253.64896 0 1.3358634
Loop time of 3607.86 on 1 procs for 600000 steps with 2751 atoms

Pair time (\) = 2475\.75 \(68\.6208\) Neigh time \() = 775.746 (21.5015)
Comm time (\) = 82\.3773 \(2\.28327\) Outpt time \() = 0.00913143 (0.000253098)
Other time (%) = 273.986 (7.59413)

Nlocal: 2751 ave 2751 max 2751 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3903 ave 3903 max 3903 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 108729 ave 108729 max 108729 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 108729
Ave neighs/atom = 39.5234
Neighbor list builds = 86343
Dangerous builds = 0

2) DAMPING FACTOR = 200.0

LAMMPS (9 Mar 2011)
# 3-d LJ flow simulation

units lj
dimension 3
boundary p s p

atom_style atomic
neighbor 0.3 bin
neigh_modify delay 1

# create geometry

region fluid block 0 11.95 1.5 26.07 0.0 7.22 units box
region btm_wall block 0 11.95 0 1.5 0.0 7.22 units box
region top_wall block 0 11.95 26.07 28.0 0.0 7.22 units box
region simulation_box union 3 btm_wall fluid top_wall units box

create_box 3 simulation_box
Created orthogonal box = (0 0 0) to (11.95 28 7.22)
  1 by 1 by 1 processor grid

lattice fcc 0.81 orient x 1 1 -2 orient y 1 1 1 orient z 1 -1 0
Lattice spacing in x,y,z = 2.78084 2.94953 2.40828
create_atoms 1 region fluid units box
Created 1735 atoms
lattice fcc 3.24 orient x -1 1 0 orient y 1 1 1 orient z 1 1 -2
Lattice spacing in x,y,z = 1.51712 1.85809 1.75182
create_atoms 2 region btm_wall units box
Created 488 atoms
lattice fcc 3.24 orient x -1 1 0 orient y 1 1 1 orient z 1 1 -2
Lattice spacing in x,y,z = 1.51712 1.85809 1.75182
create_atoms 3 region top_wall units box
Created 528 atoms

mass 1 1.0
mass 2 4.0
mass 3 4.0

# LJ potentials

pair_style lj/cut 2.2
pair_coeff * * 1.0 1.0
pair_coeff 1 2*3 0.2 0.75
pair_modify shift yes

# define groups

region 1 block INF INF INF 1.5 INF INF units box
group lower region 1
488 atoms in group lower
region 2 block INF INF 26.07 INF INF INF units box
group upper region 2
528 atoms in group upper
group boundary union lower upper
1016 atoms in group boundary
group flow subtract all boundary
1735 atoms in group flow

set group lower type 2
  488 settings made for type
set group upper type 3
  528 settings made for type

# initial velocities

compute mobile flow temp/partial 0 0 1
fix 2 flow langevin 1.10 1.10 200.0 699483
velocity flow create 1.1 482748 temp mobile units box
fix 1 all nve
#fix 2 flow temp/rescale 200 1.1 1.1 0.02 1.0
fix_modify 2 temp mobile

# Couette flow

velocity lower set 0.0 0.0 0.0 units box
velocity upper set 1.0 0.0 0.0 units box
fix 3 boundary setforce 0.0 0.0 0.0

#fix test boundary spring tether 1200.0 0.0 0.0 0.0 0.0
#fix test boundary spring/self 1200.0
#fix test1 upper spring tether 1.0 0.0 0.0 0.0 0.0

#fix 4 all enforce2d

group tp_wall region top_wall
528 atoms in group tp_wall
#fluid adjacent to bottom wall
fix 5 flow ave/spatial 1 300000 300000 x center 11.95 z center 7.22 y 1.5 1.02375 vx region fluid file vel_fb.profile units box

# Poiseuille flow

#velocity boundary set 0.0 0.0 0.0
#fix 3 lower setforce 0.0 0.0 0.0
#fix 4 upper setforce 0.0 NULL 0.0
#fix 5 upper aveforce 0.0 -1.0 0.0
#fix 6 flow addforce 0.5 0.0 0.0
#fix 7 all enforce2d

# Run
compute btm_wall_temp lower temp
compute tp_wall_temp upper temp

timestep 0.005
thermo 5000
#thermo_style custom step temp evdwl ecoul epair ebond edihed eimp eangle emol etotal
thermo_style custom step temp etotal c_btm_wall_temp c_tp_wall_temp
thermo_modify temp mobile
WARNING: Temperature for thermo pressure is not for group all

#dump 1 all atom 10 dump.flow
#dump 2 boundary custom 1000 dump.flow2 ys vx
run 600000
Memory usage per processor = 2.279 Mbytes
Step Temp TotEng btm_wall tp_wall_
       0 1.1 257.46174 0 1.3358634
    5000 3.6850092 255.54112 0 1.3358634
   10000 3.4427466 255.47905 0 1.3358634
   15000 3.2906173 255.4262 0 1.3358634
   20000 3.3313931 255.36402 0 1.3358634
   25000 3.0877226 255.27732 0 1.3358634
   30000 3.1103855 255.22944 0 1.3358634
   35000 3.1430747 255.21199 0 1.3358634
   40000 2.9950076 255.16079 0 1.3358634
   45000 3.076996 255.09321 0 1.3358634
   50000 2.9063887 254.99931 0 1.3358634
   55000 2.8325882 254.96636 0 1.3358634
   60000 2.7474052 254.94376 0 1.3358634
   65000 2.6343302 254.87853 0 1.3358634
   70000 2.6894837 254.88623 0 1.3358634
   75000 2.7328451 254.8699 0 1.3358634
   80000 2.5975051 254.79235 0 1.3358634
   85000 2.5416281 254.75219 0 1.3358634
   90000 2.5226608 254.70134 0 1.3358634
   95000 2.380419 254.671 0 1.3358634
  100000 2.4340323 254.62701 0 1.3358634
  105000 2.4168633 254.65589 0 1.3358634
  110000 2.4166323 254.63897 0 1.3358634
  115000 2.333767 254.54008 0 1.3358634
  120000 2.1627583 254.54022 0 1.3358634
  125000 2.2224634 254.53014 0 1.3358634
  130000 2.1362109 254.47564 0 1.3358634
  135000 2.2141369 254.4969 0 1.3358634
  140000 2.1481779 254.49073 0 1.3358634
  145000 2.1184305 254.47344 0 1.3358634
  150000 2.0908449 254.40747 0 1.3358634
  155000 2.1095118 254.39408 0 1.3358634
  160000 2.0502686 254.38688 0 1.3358634
  165000 2.0427149 254.39993 0 1.3358634
  170000 2.0222356 254.4061 0 1.3358634
  175000 1.851475 254.3329 0 1.3358634
  180000 1.8767894 254.31187 0 1.3358634
  185000 2.0041082 254.34936 0 1.3358634
  190000 1.9769428 254.3108 0 1.3358634
  195000 1.9720032 254.31035 0 1.3358634
  200000 1.9395832 254.30883 0 1.3358634
  205000 1.9055985 254.30251 0 1.3358634
  210000 1.8615501 254.28273 0 1.3358634
  215000 1.9342401 254.26974 0 1.3358634
  220000 1.8152695 254.23856 0 1.3358634
  225000 1.8161752 254.22208 0 1.3358634
  230000 1.7700137 254.19309 0 1.3358634
  235000 1.8820712 254.26496 0 1.3358634
  240000 1.7847464 254.22815 0 1.3358634
  245000 1.723447 254.17834 0 1.3358634
  250000 1.8269488 254.20779 0 1.3358634
  255000 1.7147963 254.17936 0 1.3358634
  260000 1.7738313 254.16994 0 1.3358634
  265000 1.7807508 254.17219 0 1.3358634
  270000 1.7437417 254.16394 0 1.3358634
  275000 1.7820841 254.18265 0 1.3358634
  280000 1.890526 254.23986 0 1.3358634
  285000 1.7904153 254.19801 0 1.3358634
  290000 1.7849692 254.19833 0 1.3358634
  295000 1.7200384 254.14411 0 1.3358634
  300000 1.8260603 254.18023 0 1.3358634
  305000 1.7736183 254.17304 0 1.3358634
  310000 1.792293 254.16729 0 1.3358634
  315000 1.7932311 254.18541 0 1.3358634
  320000 1.7417411 254.18391 0 1.3358634
  325000 1.7630283 254.18875 0 1.3358634
  330000 1.6243078 254.14503 0 1.3358634
  335000 1.6975884 254.14633 0 1.3358634
  340000 1.6657034 254.14339 0 1.3358634
  345000 1.7508922 254.16674 0 1.3358634
  350000 1.6659771 254.12424 0 1.3358634
  355000 1.7454423 254.16448 0 1.3358634
  360000 1.7479471 254.15363 0 1.3358634
  365000 1.6637722 254.13866 0 1.3358634
  370000 1.7037321 254.16761 0 1.3358634
  375000 1.7419778 254.13613 0 1.3358634
  380000 1.7018366 254.11524 0 1.3358634
  385000 1.6108149 254.10571 0 1.3358634
  390000 1.6760946 254.14707 0 1.3358634
  395000 1.6482118 254.10411 0 1.3358634
  400000 1.7010636 254.13287 0 1.3358634
  405000 1.7225569 254.16716 0 1.3358634
  410000 1.7121818 254.11904 0 1.3358634
  415000 1.6305814 254.10117 0 1.3358634
  420000 1.7124906 254.12982 0 1.3358634
  425000 1.7013314 254.11615 0 1.3358634
  430000 1.6985962 254.13318 0 1.3358634
  435000 1.6765235 254.13651 0 1.3358634
  440000 1.6870726 254.13141 0 1.3358634
  445000 1.7100994 254.15822 0 1.3358634
  450000 1.6950602 254.14231 0 1.3358634
  455000 1.6458774 254.14076 0 1.3358634
  460000 1.6672891 254.11507 0 1.3358634
  465000 1.7029693 254.12265 0 1.3358634
  470000 1.6769669 254.12759 0 1.3358634
  475000 1.6902899 254.14778 0 1.3358634
  480000 1.8087404 254.16291 0 1.3358634
  485000 1.7057856 254.14436 0 1.3358634
  490000 1.7047077 254.16115 0 1.3358634
  495000 1.696784 254.1587 0 1.3358634
  500000 1.6681386 254.10746 0 1.3358634
  505000 1.7248573 254.15119 0 1.3358634
  510000 1.8309149 254.16192 0 1.3358634
  515000 1.7667819 254.16063 0 1.3358634
  520000 1.809362 254.14385 0 1.3358634
  525000 1.8066829 254.14909 0 1.3358634
  530000 1.7802298 254.17875 0 1.3358634
  535000 1.7056583 254.12645 0 1.3358634
  540000 1.6639387 254.13834 0 1.3358634
  545000 1.6975207 254.13806 0 1.3358634
  550000 1.7102981 254.12988 0 1.3358634
  555000 1.6083625 254.10242 0 1.3358634
  560000 1.6943896 254.12556 0 1.3358634
  565000 1.6629248 254.08204 0 1.3358634
  570000 1.7004332 254.08827 0 1.3358634
  575000 1.8162499 254.1349 0 1.3358634
  580000 1.6975856 254.14093 0 1.3358634
  585000 1.7500516 254.14761 0 1.3358634
  590000 1.7651969 254.14513 0 1.3358634
  595000 1.7367473 254.13139 0 1.3358634
  600000 1.6667598 254.10152 0 1.3358634
Loop time of 3907.21 on 1 procs for 600000 steps with 2751 atoms

Pair time (\) = 2532\.75 \(64\.8224\) Neigh time \() = 1008.83 (25.8198)
Comm time (\) = 88\.4435 \(2\.2636\) Outpt time \() = 0.00927567 (0.000237399)
Other time (%) = 277.176 (7.09395)

Nlocal: 2751 ave 2751 max 2751 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3906 ave 3906 max 3906 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 108457 ave 108457 max 108457 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 108457
Ave neighs/atom = 39.4246
Neighbor list builds = 111073
Dangerous builds = 0

2

To properly thermostat a flowing system, you need to
subtract out the flow velocity. LAMMPS gives you
several options for doing this, which it terms as removing
a bias. See section 4.16 of the manual for a discussion
of biasing and how to apply it.

Steve

3

Decreasing the time step usually helps the thermostat become more stable.

4

I was of the impression I had already done biasing using the following
statement in the code:
"compute mobile flow temp/partial 0 0 1"
If my understanding is right this removes the velocity in x and y dirn.

Also I had a confusion the damping factor in 'fix langevin' the manual
says its time units but in previous mail queries
I have seen people referring to it as time steps.
"fix 2 flow langevin 1.10 1.10 1.0 699483"

Also the reason for my concern started only after running it at high
velocitie. Initially when I was using damping factor of
1.0 it was thermostating fine. Hence I wanted to know do we have to
change certain parameters with varying damping factor

BR/Joseph

5

The larger the damping parameter, the harder it will be for the
thermostat to cool down a system strongly heated by viscous
dissipation.

So if it is not working for damp=1 time unit, it can only be worse for
damp=200 time units, especially if you apply the thermostat only on 1
degree of freedom out of 3, which is weakening its efficiency.

If anything you should *reduce* the damping parameter, and apply the
thermostat to the 2 directions perpendicular to the flow:

compute mobile flow temp/partial 0 1 1
fix 2 flow langevin 1.10 1.10 1.0 699483
fix_modify 2 temp mobile
thermo_modify temp mobile

But be aware that the damping parameter will also affects the liquid
effective viscosity... Generally, it's always tricky to apply a
thermostat when the hydrodynamic velocities are close to the thermal
velocities (which is your case even for what you call lower
velocities), because the thermostat (acting on atoms velocities) could
play an unphysical role on hydrodynamics. So my advice would be to
test other thermostating methods (for instance: Nose-Hoover using fix
nvt, or DPD thermostating with pair_style dpd/tstat) and check that
the flow remains unaffected.

In fact the problem comes from using unrealistically large velocities
/ shear rates, that are quite irrelevant with regards to real life
experiments anyway. So my advice would be to always use the smallest
driving velocity that provides a reasonable signal/noise ratio.

Finally, it is not very good to drive the flow with asymetric wall
velocities, as it is adding a net momentum to the system. So instead
of:

velocity lower set 0.0 0.0 0.0 units box
velocity upper set 1.0 0.0 0.0 units box

I would rather do:

velocity lower set -0.5 0.0 0.0 units box
velocity upper set 0.5 0.0 0.0 units box

Best,
Laurent

6

You also have to apply the compute temp/partial to
the fix langevin via fix_modify. See the doc pages
for details. The damping parameter is in units
of time, not timesteps.

Steve

7

I went through the manual again as per your advice and came up with the
following lines for performing the thermostating

compute mobile_thermo flow temp/partial 0 0 1
fix 1 all nve
fix 2 flow langevin 1.10 1.10 1.0 699483
fix_modify 2 temp mobile_thermo
thermo_modify temp mobile_thermo

but unfortunately I am still facing problems. I would be highly grateful if you could take some time and mention in specific what
I am doing wrong (if any).
As suggested by Laurent decreasing the damping factor seems to fix the problem. But, I wanted to make sure if my interpretation of the input
statements are correct.

Thanking you.

BR/Joseph

8

What units are you using? If it is LJ units, then
a damping factor of 0.1 or 1.0 is fine - since it
typically means 20-200 timesteps, for a dt of 0.005.

Steve

9

Yes, I am using LJ units. But I wanted to confirm if I am doing
the biasing correctly as you had previously mentioned the following:

"You also have to apply the compute temp/partial to
the fix langevin via fix_modify. See the doc pages
for details. The damping parameter is in units
of time, not timesteps."

Appreciate the help.

BR/Joseph

10

Yes, the biasing part of what you've done looks fine.

Steve