Thank you Axel for your attention.
how did you measure the angle difference? and for which frame of your dump file?
please note that your fix shake input is redundant.
when I run my script, on Terminal desktop, I can see bonds and angles each timestep like this:
SHAKE stats (type/ave/delta) on step 110
1 0.999995 5.48569e-05 34296
2 1.425 1.49296e-06 2400
3 0.944997 2.90289e-05 2400
1 109.47 0.00484895
2 103.401 0.000772125
SHAKE stats (type/ave/delta) on step 120
1 0.999995 6.48201e-05 34296
2 1.425 1.63591e-06 2400
3 0.944997 3.53233e-05 2400
1 109.47 0.00562101
2 103.401 0.000909799
SHAKE stats (type/ave/delta) on step 130
1 0.999995 7.02129e-05 34296
2 1.425 1.60056e-06 2400
3 0.944997 3.93347e-05 2400
1 109.47 0.00609421
2 103.401 0.00116298
As you see, the two last lines of each time step are angles.
Also, when I check some angles from my last datafile which created by write_data command, they show 103 degree.
> without access to your data file, it is extremely difficult to figure out what your problem is.
I attach my data file here.
also, you failed to mention which version of LAMMPS exactly, you are using.
if something is not working as expected, you should always try with the latest patch. have you done that?
there has been a bug in fix shake that was fixed some time last year, that would affect the angle constraint for methanol.
I installed 10Aug15 version of LAMMPS, but I’m not sure about correctness of that.
How can I ensure about my installation now?
Dear lammps users
recently, I made a box of water/methanol mixture. I useed moltemplate & packmol to make my simulation box datafile. I considered 109 (watre) and 108 (methanol) angles for molecules. But, when I use SHAKE algorithm,methanol’s angle will change to 103. Why this issue occurred? How can I solve this?
how did you measure the angle difference? and for which frame of your dump file?
please note that your fix shake input is redundant.
I will appreciate if anyone could help me in solving this problem.
without access to your data file, it is extremely difficult to figure out what your problem is.
also, you failed to mention which version of LAMMPS exactly, you are using.
if something is not working as expected, you should always try with the latest patch. have you done that?
there has been a bug in fix shake that was fixed some time last year, that would affect the angle constraint for methanol.axel.
My script:
units real
atom_style full
special_bonds lj/coul 0.0 0.0 0.0
pair_style lj/cut/coul/long 10 10
bond_style harmonic
angle_style harmonic
kspace_style pppm 0.0001
######################
read_data merging.databond_coeff 1 1000 1.0
bond_coeff 2 386.0 1.425
bond_coeff 3 553.0 0.945angle_coeff 1 100 109.47
angle_coeff 2 55 108.50group spce type 1 2
group methanol type 3 4 5
group fluidbox union spce methanolneighbor 2.0 bin
neigh_modify every 2 delay 0 every 1 check yes
###############
minimize 1.0e-4 1.0e-6 20 1000
fix fixnvtf fluidbox nvt temp 280 298.13 100.0
fix fixshake fluidbox shake 0.0001 20 10 b 1 2 3 a 1 2 t 1 2 3 4 5 m 1 2 3 4 5
########################
timestep 2.0
dump 1 all xyz 5000 dump.*.xyz
restart 5000 restart.equil
run 10000thank you so much.
regards.
Reza
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