Dear all,
I am trying to simulate a non-equilibrium system to measure the thermo conductivity. Our system has two hot copper plates and one cold plate in the middle and between each of them is filled with water. We use eam for copper, SPC/e for water and lj for cross term. Since we are interested in local temperature in the system, I copied the idea in the examples by using fix Langevin. Here is my thermostat part.
compute Thot1 all temp/region hot1
compute Thot2 all temp/region hot2
compute Tcold all temp/region cold
fix 1 all nve
fix hot1 all langevin \{thi\} {thi} 1.0 557667 tally yes
fix hot2 all langevin \{thi\} {thi} 1.0 59804 tally yes
fix cold all langevin \{tlo\} {tlo} 1.0 287859 tally yes
fix_modify hot1 temp Thot1
fix_modify hot2 temp Thot2
fix_modify cold temp Tcold
Then I used several compute commands.
compute ke all ke/atom
variable temp1 atom c_ke/1.5
compute pencils all chunk/atom bin/2d x lower 0.5 z lower 0.5
fix 2 all ave/chunk 1000 10 10000 pencils v_temp1 ave running file temp1.profile
fix 5 all ave/chunk 1000 10 10000 pencils temp ave running file temp2.profile
What I found out is that the log file which shows the c_Thot1 c_Thot2 c_Tcold are right compared to our thermostat temperature. But either the c_ke or fix ave/chunk temp are not giving the right temperature for copper but seems to be right for water. Is it because of the DOF are different for copper and water?
Thanks in advance for any suggestions or ideas.
Andy
Dear all,
I am trying to simulate a non-equilibrium system to measure the thermo
conductivity. Our system has two hot copper plates and one cold plate in
the middle and between each of them is filled with water. We use eam for
copper, SPC/e for water and lj for cross term. Since we are interested in
local temperature in the system, I copied the idea in the examples by using
fix Langevin. Here is my thermostat part.
compute Thot1 all temp/region hot1
compute Thot2 all temp/region hot2
compute Tcold all temp/region cold
fix 1 all nve
fix hot1 all langevin \{thi\} {thi} 1.0 557667 tally yes
fix hot2 all langevin \{thi\} {thi} 1.0 59804 tally yes
fix cold all langevin \{tlo\} {tlo} 1.0 287859 tally yes
fix_modify hot1 temp Thot1
fix_modify hot2 temp Thot2
fix_modify cold temp Tcold
Then I used several compute commands.
compute ke all ke/atom
variable temp1 atom c_ke/1.5
compute pencils all chunk/atom bin/2d x lower 0.5 z lower 0.5
fix 2 all ave/chunk 1000 10 10000 pencils v_temp1 ave running file
temp1.profile
fix 5 all ave/chunk 1000 10 10000 pencils temp ave running file
temp2.profile
What I found out is that the log file which shows the c_Thot1 c_Thot2
c_Tcold are right compared to our thermostat temperature. But either the
c_ke or fix ave/chunk temp are not giving the right temperature for copper
but seems to be right for water. Is it because of the DOF are different for
copper and water?
dividing ke/atom by 3/2 is not correct to compute the temperature
contribution here, as it assumes that k_B is 1.0, which is only correct for
reduced units.
fix ave/chunk only considers individual atoms, so it cannot correctly
compute the temperature for molecules, where degrees of freedom are removed
due to fix shake, as it is ambiguous how the removed DOFs should be
distributed across the individual atoms. for a 3-site water model, you can
correct rather easily, as you can assume to remove 1 DOF per atom and
correct the result by a suitable scaling factor. the computed temperature
for the copper atoms should be correct, as you have no removed DOFs there.
axel.
Dear Axel,
Thanks for your suggestions. I forgot to mention that I did some post-process for c_ke to calculate temperature. So I did not use the c_ke/1.5 as the temperature. I understand the part that DOF are overestimated for water molecules. But why fix chunk/atom gives right temperature for water but wrong for copper?
Best wishes
Dear Axel,
Thanks for your suggestions. I forgot to mention that I did some
post-process for c_ke to calculate temperature. So I did not use the
c_ke/1.5 as the temperature. I understand the part that DOF are
overestimated for water molecules. But why fix chunk/atom gives right
temperature for water but wrong for copper?
there is more information missing here. i cannot give you an explanation.
most likely, you are making a mistake here and not LAMMPS.
axel.