The pressure unit

Hi Dear

Is the unit of pressure atmosphere in real unit really? I’m very confused. I run a simulation for polymer chains to calculate constant elastic properties by deform command, but the obtained pressure are 100 times the real values, while the temperature and energy are logical. Before deform command, In the relaxation step in NPT fix command the fluctuations of pressure is following:

Hi Dear
Is the unit of pressure atmosphere in real unit really?

The documentation says so, why should it not be?

I’m very confused. I run a simulation for polymer chains to calculate constant elastic properties by deform command, but the obtained pressure are 100 times the real values, while the temperature and energy are logical.

The pressure fluctuations are just as logical. You already have been told that pressure fluctuations are large for small samples and dense objects like liquids and solids. If you want to get a better handle on this, please spend some more time with your favorite statistical mechanics text book and study the underlying relations.

Before deform command, In the relaxation step in NPT fix command the fluctuations of pressure is following:

Instantaneous values are pretty much useless to look at for this. You need to look at averages and trends. Most of MD analysis is based on averaging over time instead of volume, provided you have a system in equilibrium.

Axel

Hi Dear

The output in the fix deform command in my simulation is pressure/atom. there was no pressure fluctuations in fix deform command. With increasing deformation of cell the pressure/atom increase linearly. This is logical. The pressure/atom divided by volume to obtain stress in cell. But the values of stress are 100 times the real values. This is confusing. The output of fix deform is following:(fx is the summation of stress/atom)

Step Temp Press fx Lx Ly Lz Volume
160000 300.3934 -389.455 78215537 64.37766 64.37766 64.37766 266812.2
160100 300.3934 -389.312 91670384 64.3841 64.37444 64.37444 266812.2
160200 300.3934 -389.172 1.05E+08 64.39054 64.37123 64.37123 266812.2
160300 300.3934 -389.037 1.19E+08 64.39698 64.36801 64.36801 266812.2
160400 300.3934 -388.911 1.32E+08 64.40341 64.36479 64.36479 266812.2
160500 300.3934 -388.789 1.46E+08 64.40985 64.36157 64.36157 266812.2
160600 300.3934 -388.674 1.60E+08 64.41629 64.35836 64.35836 266812.2
160700 300.3934 -388.57 1.73E+08 64.42273 64.35514 64.35514 266812.2
160800 300.3934 -388.47 1.87E+08 64.42916 64.35193 64.35193 266812.2
160900 300.3934 -388.378 2.00E+08 64.4356 64.34871 64.34871 266812.2
161000 300.3934 -388.291 2.14E+08 64.44204 64.3455 64.3455 266812.2
161100 300.3934 -388.21 2.28E+08 64.44848 64.34228 64.34228 266812.2
161200 300.3934 -388.145 2.41E+08 64.45492 64.33907 64.33907 266812.2
161300 300.3934 -388.076 2.55E+08 64.46135 64.33586 64.33586 266812.2
161400 300.3934 -388.019 2.69E+08 64.46779 64.33265 64.33265 266812.2
161500 300.3934 -387.969 2.82E+08 64.47423 64.32943 64.32943 266812.2
161600 300.3934 -387.926 2.96E+08 64.48067 64.32622 64.32622 266812.2
161700 300.3934 -387.892 3.09E+08 64.4871 64.32301 64.32301 266812.2
161800 300.3934 -387.862 3.23E+08 64.49354 64.3198 64.3198 266812.2
161900 300.3934 -387.841 3.37E+08 64.49998 64.31659 64.31659 266812.2
162000 300.3934 -387.825 3.50E+08 64.50642 64.31338 64.31338 266812.2
162100 300.3934 -387.815 3.64E+08 64.51286 64.31017 64.31017 266812.2
162200 300.3934 -387.814 3.78E+08 64.51929 64.30696 64.30696 266812.2
162300 300.3934 -387.823 3.91E+08 64.52573 64.30376 64.30376 266812.2
162400 300.3934 -387.834 4.05E+08 64.53217 64.30055 64.30055 266812.2
162500 300.3934 -387.853 4.19E+08 64.53861 64.29734 64.29734 266812.2
162600 300.3934 -387.881 4.32E+08 64.54504 64.29413 64.29413 266812.2
162700 300.3934 -387.912 4.46E+08 64.55148 64.29093 64.29093 266812.2
162800 300.3934 -387.952 4.59E+08 64.55792 64.28772 64.28772 266812.2
162900 300.3934 -387.996 4.73E+08 64.56436 64.28452 64.28452 266812.2
163000 300.3934 -388.048 4.87E+08 64.5708 64.28131 64.28131 266812.2
163100 300.3934 -388.111 5.00E+08 64.57723 64.27811 64.27811 266812.2
163200 300.3934 -388.181 5.14E+08 64.58367 64.2749 64.2749 266812.2
163300 300.3934 -388.256 5.28E+08 64.59011 64.2717 64.2717 266812.2
163400 300.3934 -388.334 5.41E+08 64.59655 64.2685 64.2685 266812.2
163500 300.3934 -388.42 5.55E+08 64.60298 64.2653 64.2653 266812.2
163600 300.3934 -388.513 5.69E+08 64.60942 64.26209 64.26209 266812.2
163700 300.3934 -388.613 5.82E+08 64.61586 64.25889 64.25889 266812.2
163800 300.3934 -388.719 5.96E+08 64.6223 64.25569 64.25569 266812.2
163900 300.3934 -388.832 6.10E+08 64.62874 64.25249 64.25249 266812.2
164000 300.3934 -388.956 6.23E+08 64.63517 64.24929 64.24929 266812.2
164100 300.3934 -389.089 6.37E+08 64.64161 64.24609 64.24609 266812.2
164200 300.3934 -389.225 6.51E+08 64.64805 64.24289 64.24289 266812.2
164300 300.3934 -389.369 6.65E+08 64.65449 64.2397 64.2397 266812.2
164400 300.3934 -389.516 6.78E+08 64.66092 64.2365 64.2365 266812.2
164500 300.3934 -389.668 6.92E+08 64.66736 64.2333 64.2333 266812.2
164600 300.3934 -389.831 7.06E+08 64.6738 64.2301 64.2301 266812.2
164700 300.3934 -390.002 7.19E+08 64.68024 64.22691 64.22691 266812.2
164800 300.3934 -390.183 7.33E+08 64.68668 64.22371 64.22371 266812.2
164900 300.3934 -390.371 7.47E+08 64.69311 64.22051 64.22051 266812.2
165000 300.3934 -390.563 7.60E+08 64.69955 64.21732 64.21732 266812.2
165100 300.3934 -390.76 7.74E+08 64.70599 64.21412 64.21412 266812.2
165200 300.3934 -390.967 7.88E+08 64.71243 64.21093 64.21093 266812.2
165300 300.3934 -391.18 8.02E+08 64.71886 64.20774 64.20774 266812.2
165400 300.3934 -391.399 8.15E+08 64.7253 64.20454 64.20454 266812.2
165500 300.3934 -391.625 8.29E+08 64.73174 64.20135 64.20135 266812.2
165600 300.3934 -391.858 8.43E+08 64.73818 64.19816 64.19816 266812.2
165700 300.3934 -392.097 8.56E+08 64.74462 64.19497 64.19497 266812.2
165800 300.3934 -392.345 8.70E+08 64.75105 64.19178 64.19178 266812.2
165900 300.3934 -392.602 8.84E+08 64.75749 64.18858 64.18858 266812.2
166000 300.3934 -392.863 8.98E+08 64.76393 64.18539 64.18539 266812.2
166100 300.3934 -393.129 9.11E+08 64.77037 64.1822 64.1822 266812.2
166200 300.3934 -393.402 9.25E+08 64.7768 64.17901 64.17901 266812.2
166300 300.3934 -393.686 9.39E+08 64.78324 64.17583 64.17583 266812.2
166400 300.3934 -393.973 9.53E+08 64.78968 64.17264 64.17264 266812.2
166500 300.3934 -394.27 9.66E+08 64.79612 64.16945 64.16945 266812.2
166600 300.3934 -394.57 9.80E+08 64.80256 64.16626 64.16626 266812.2
166700 300.3934 -394.876 9.94E+08 64.80899 64.16308 64.16308 266812.2
166800 300.3934 -395.19 1.01E+09 64.81543 64.15989 64.15989 266812.2
166900 300.3934 -395.514 1.02E+09 64.82187 64.1567 64.1567 266812.2
167000 300.3934 -395.844 1.04E+09 64.82831 64.15352 64.15352 266812.2
167100 300.3934 -396.183 1.05E+09 64.83474 64.15033 64.15033 266812.2
167200 300.3934 -396.533 1.06E+09 64.84118 64.14715 64.14715 266812.2
167300 300.3934 -396.886 1.08E+09 64.84762 64.14396 64.14396 266812.2
167400 300.3934 -397.244 1.09E+09 64.85406 64.14078 64.14078 266812.2
167500 300.3934 -397.61 1.10E+09 64.86049 64.1376 64.1376 266812.2
167600 300.3934 -397.98 1.12E+09 64.86693 64.13441 64.13441 266812.2
167700 300.3934 -398.359 1.13E+09 64.87337 64.13123 64.13123 266812.2
167800 300.3934 -398.743 1.15E+09 64.87981 64.12805 64.12805 266812.2
167900 300.3934 -399.137 1.16E+09 64.88625 64.12487 64.12487 266812.2
168000 300.3934 -399.537 1.17E+09 64.89268 64.12169 64.12169 266812.2
168100 300.3934 -399.946 1.19E+09 64.89912 64.11851 64.11851 266812.2
168200 300.3934 -400.358 1.20E+09 64.90556 64.11533 64.11533 266812.2
168300 300.3934 -400.776 1.21E+09 64.912 64.11215 64.11215 266812.2
168400 300.3934 -401.201 1.23E+09 64.91843 64.10897 64.10897 266812.2
168500 300.3934 -401.633 1.24E+09 64.92487 64.10579 64.10579 266812.2
168600 300.3934 -402.074 1.26E+09 64.93131 64.10261 64.10261 266812.2
168700 300.3934 -402.523 1.27E+09 64.93775 64.09943 64.09943 266812.2
168800 300.3934 -402.978 1.28E+09 64.94419 64.09626 64.09626 266812.2
168900 300.3934 -403.442 1.30E+09 64.95062 64.09308 64.09308 266812.2
169000 300.3934 -403.911 1.31E+09 64.95706 64.0899 64.0899 266812.2
169100 300.3934 -404.387 1.32E+09 64.9635 64.08673 64.08673 266812.2
169200 300.3934 -404.868 1.34E+09 64.96994 64.08355 64.08355 266812.2
169300 300.3934 -405.359 1.35E+09 64.97637 64.08038 64.08038 266812.2
169400 300.3934 -405.858 1.37E+09 64.98281 64.0772 64.0772 266812.2
169500 300.3934 -406.363 1.38E+09 64.98925 64.07403 64.07403 266812.2
169600 300.3934 -406.875 1.39E+09 64.99569 64.07086 64.07086 266812.2
169700 300.3934 -407.394 1.41E+09 65.00213 64.06768 64.06768 266812.2
169800 300.3934 -407.919 1.42E+09 65.00856 64.06451 64.06451 266812.2
169900 300.3934 -408.454 1.44E+09 65.015 64.06134 64.06134 266812.2
170000 300.3934 -408.992 1.45E+09 65.02144 64.05817 64.05817 266812.2

Hi Dear
The output in the fix deform command in my simulation is pressure/atom. there was no pressure fluctuations in fix deform command. With increasing deformation of cell the pressure/atom increase linearly. This is logical. The pressure/atom divided by volume to obtain stress in cell. But the values of stress are 100 times the real values. This is confusing. The output of fix deform is following:(fx is the summation of stress/atom)

Well, there are a few things that don’t add up here, but it is difficult to make any statements based on so little information.

First off, there is no such thing as a per atom pressure. Then, fix deform does not return any property as far as i know. And there doesn’t seem to be any time integration going on in your simulation, which would render the entire exercise pointless.

Axel.

Hi Dear Axel

The input script for calculation of elastic constant of vinylester/TiO2 is following:(My problem is why the calculated stress in deform fix command is 100 times real value?)

LAMMPS input for titan/vinylester nanocomposites elastic constants analysis

#Initialization

boundary p p p

units real

atom_style hybrid molecular charge

create geometry and potentials-------------------------------------------

neighbor 0.4 bin
neigh_modify every 10 one 10000
bond_style harmonic
angle_style cosine/squared
dihedral_style charmm
read_data 3Vr10.txt

pair_style hybrid buck/coul/cut 10.5 6 lj/cut/coul/cut 10.5 6 lj/cut 10.5

pair_coeff * 7 lj/cut 0 3.00
pair_coeff 7 * lj/cut 0 3.00
pair_coeff 8 9 buck/coul/cut 391049.1 0.194 290.331
pair_coeff 8 8 buck/coul/cut 717647.4 0.154 121.067
pair_coeff 9 9 buck/coul/cut 271716.3 0.234 696.888
pair_coeff 1 1 lj/cut/coul/cut 0.1094 3.816
pair_coeff 2 2 lj/cut/coul/cut 0.0860 3.816
pair_coeff 3 3 lj/cut/coul/cut 0.2104 3.442
pair_coeff 4 4 lj/cut/coul/cut 0.2100 3.3224
pair_coeff 5 5 lj/cut/coul/cut 0.0157 2.974
pair_coeff 6 6 lj/cut/coul/cut 0.0150 2.918
pair_coeff 1 2 lj/cut/coul/cut 0.09699 3.816
pair_coeff 1 3 lj/cut/coul/cut 0.15171 3.629
pair_coeff 1 4 lj/cut/coul/cut 0.15157 3.5692
pair_coeff 1 5 lj/cut/coul/cut 0.04144 3.395
pair_coeff 1 6 lj/cut/coul/cut 0.04051 3.367
pair_coeff 1 8 lj/cut/coul/cut 0.04312 3.4955
pair_coeff 1 9 lj/cut/coul/cut 0.15157 3.5692
pair_coeff 2 3 lj/cut/coul/cut 0.1345 3.629
pair_coeff 2 4 lj/cut/coul/cut 0.1344 3.5692
pair_coeff 2 5 lj/cut/coul/cut 0.03675 3.395
pair_coeff 2 6 lj/cut/coul/cut 0.03591 3.367
pair_coeff 2 8 lj/cut/coul/cut 0.03823 3.4955
pair_coeff 2 9 lj/cut/coul/cut 0.1344 3.5692
pair_coeff 3 4 lj/cut/coul/cut 0.2102 3.3822
pair_coeff 3 5 lj/cut/coul/cut 0.0574 3.208
pair_coeff 3 6 lj/cut/coul/cut 0.05618 3.18
pair_coeff 3 8 lj/cut/coul/cut 0.05980 3.3085
pair_coeff 3 9 lj/cut/coul/cut 0.2102 3.3822
pair_coeff 4 5 lj/cut/coul/cut 0.0574 3.1482
pair_coeff 4 6 lj/cut/coul/cut 0.0561 3.1202
pair_coeff 4 8 lj/cut/coul/cut 0.05974 3.2487
pair_coeff 4 9 lj/cut/coul/cut 0.2100 3.3224
pair_coeff 5 6 lj/cut/coul/cut 0.01534 2.946
pair_coeff 5 8 lj/cut/coul/cut 0.01633 3.0745
pair_coeff 5 9 lj/cut/coul/cut 0.0574 3.1482
pair_coeff 6 8 lj/cut/coul/cut 0.01596 3.0465
pair_coeff 6 9 lj/cut/coul/cut 0.0561 3.1202

region nanoparticle sphere 25.84 25.84 25.84 10.5 side in units box
group nanoparticle region nanoparticle

region resin sphere 25.84 25.84 25.84 10.5 side out units box
group resin region resin

velocity all create 300 1231

equilibration stage 1 (NVT dynamics at 300 k )-------------------------------------------------------------------------

fix 1 all nvt temp 300 300 50

thermo_style custom step temp epair etotal press lx ly lz
timestep 0.5
thermo 1000
run 20000
unfix 1
#unfix 2

equilibration stage 2 (NPT dynamics from 300 k —> 300 K )-------------------------------------------------------------------------

fix 1 all npt temp 300 300 50 iso 10 10 1000 drag 2
fix 2 all momentum 1 linear 1 1 1

compute a resin group/group nanoparticle

thermo_style custom step temp epair etotal press lx ly lz
timestep 0.5
thermo 100
dump 1 nanoparticle xyz 5000 nano.xyz
run 50000
unfix 1
unfix 2

Tensile’s modulus calculation---------------------------------------------------------------------------------------------------------

fix 1 resin deform 1 x scale 1.01 y volume z volume units box remap x
compute px resin stress/atom
compute fx resin reduce sum c_px[1]
thermo_style custom step temp press c_fx lx ly lz vol
thermo 100
timestep 1
run 10000
unfix 1

Hi Dear Axel
The input script for calculation of elastic constant of vinylester/TiO2 is
following:(My problem is why the calculated stress in deform fix command is
100 times real value?)

this is far too complex an input to quickly pinpoint any issues. does
this run well for regular MD? have you discussed this and the choice
of settings with somebody that has more experience in MD than you? if
not, do it. you should particularly discuss the issues of
equilibration and time scales.

i am not surprised that this gives bogus results since there are
several rather unusual and questionable choices. i strongly suggest to
first practice doing this kind of study with a much simpler to model
material and reproduce those results and then gradually increase the
complexity, making sure that you get correct results at every step.
building and debugging such a complex input for such a complex system
in one go is close to impossible and you will for certain not find
anybody on this mailing list do it for you.

axel.