Npt/nvt equilibration problem

Hello everyone
I am simulating the mechanical properties of graphene for different temperatures by the LAMMPS simulator. I am facing a problem of properties increasing as temperature increases instead of properties decreasing. And I think it must be a problem of balancing the system before deformation. I need help and I believe someone could help me. Thanks in advance

May be. But for that you will need to provide details on your system, your input, the commands that you use…

Hello Simon Gravelle,

Thank you for your reaction. I tried to attach some files regarding the details on my input file but I am not eligible.

So this is what my input file looks like:

#!/usr/bin/env bash
#------------------------ Tensile tests on material ------------------------------------

for Temp in 1 300  600  900  1200; do

#------------------------equilibration----------------------------------------
cat > Therma.in << EOF
clear
units  		  	metal
dimension	  	2
boundary	  	p p p
atom_style 	  	atomic

##--------------------------------------------------------------------
variable		TimeStep equal 	0.001
variable		T		equal	$Temp variable P equal 1.01325 variable dT equal v_TimeStep*100.0 variable dP equal v_TimeStep*1000.0 ##---------------ATOM DEFINITION------------------------------ read_data graphene.dat ##---------------FORCE FIELDS--------------------------------- pair_style airebo 3.0 1 1 pair_coeff * * ../../potentials/CH.airebo C ##------------------------------------------------------------ timestep \${TimeStep}

#------------------------------------------------------------

fix 			1 all box/relax x \${P} y \${P} vmax 0.001
min_style 		cg
minimize 		1e-10 1e-10 5000 10000
unfix			1

minimize 		1e-10 1e-10 5000 10000

#-----------------Pressure Equilibriation-----------------------
reset_timestep	     	0
velocity 		all create \${T} 456783 dist uniform fix 1 all npt temp \${T} \${T} \${dT} aniso \${P} \${P} \${dP} run 250000 unfix 1 write_data Relax.dat EOF lmp_serial -i Therma.in > Therma.out #------------------------ (1) x direction ------------------------------------ cat > X.in << EOF #uniaxial tensile test of graphene # INITIALIZATION clear units metal dimension 2 boundary p p p atom_style atomic newton on ##-------------------------------------------------------------------- variable TimeStep equal 0.001 variable T equal$Temp
variable		P		equal	0.0
variable		dT		equal	v_TimeStep*100.0
variable		dP		equal	v_TimeStep*1000.0

##---------------ATOM DEFINITION------------------------------

##---------------FORCE FIELDS---------------------------------
pair_style          	airebo 3.0 1 1
pair_coeff          	* * ../../potentials/CH.airebo C

##------------------------------------------------------------
timestep 		\${TimeStep} variable tmp equal "lx" variable L0x equal \${tmp}

variable 		tmp 		equal 	"ly"
variable 		L0y 		equal 	\${tmp} ##---------------DEFORMATION-------------------------------------- reset_timestep 0 fix 2 all npt temp \${T} \${T} \${dT} y 0.0 0.0 \${dP} variable srate equal 0.001 fix 3 all deform 1 x erate \${srate} units box remap x

compute			1 all pressure thermo_temp

thermo 		     	100
thermo_style 	     	custom step temp lz pxx pyy
##--------------------------------------------------------------------
variable	   	Lz	equal	lz

fix		   	4 all ave/time 5 1000 5000 v_Lz c_1[1] c_1[2] c_1[3] c_1[4]

run 		   	0

##---------------THERMO-OUTPUTS--------------------------------------
# for units metal, pressure is in [bars] = 100 [kPa] = 1/10000 [GPa]
variable	   	        ConvPres	equal	1e-4
variable   	   	thickn 		equal 	3.35 					               #nm
variable   	   	strain 		equal 	(lx-v_L0x)/v_L0x

variable   	   	stress 		equal 	-(f_4[2])*(f_4[1]/v_thickn)*v_ConvPres	#GPa
variable   	   	StrainEnergy  	equal   0.5*v_stress*v_strain	 	  	                #GPa

fix Data all print 5000 "\${strain} \${stress} \${StrainEnergy}" file X\${T}.txt screen no

dump               	2 all atom 5000 X\${T}.dat run_style verlet run 300000 EOF lmp_serial -i X.in > X.out done  Thanks ! Hello, Posting your input is a good start, but it would be also good to explain what you are trying to measure and why you think there is a problem. On the side note: are you sure a 1 fs timestep is allowed with airebo? From memory, I think that it should be 0.5 fs. Simon And here is the contents of the graphene.dat file: LAMMPS data file via write_data, version 3 Mar 2020, timestep = 17 60 atoms 1 atom types -4.8108192480347395e-02 1.2048108192480351e+01 xlo xhi -4.9995500181758912e-02 1.2520761314677692e+01 ylo yhi 0.0000000000000000e+00 1.0000000000000007e+02 zlo zhi Masses 1 12.0107 Atoms # atomic 1 1 -4.8108192480347020e-02 1.2520761314677690e+01 5.0000000000000036e+01 0 -1 0 2 1 1.1615134460157208e+00 6.4837987842154421e-01 5.0000000000000036e+01 0 0 0 3 1 1.1615134460157224e+00 2.0451306356281487e+00 5.0000000000000036e+01 0 0 0 4 1 -4.8108192480346999e-02 2.7435060142314533e+00 5.0000000000000036e+01 0 0 0 5 1 2.3711350845117933e+00 -4.9995500181758912e-02 5.0000000000000036e+01 0 0 0 6 1 3.5807567230078621e+00 6.4837987842154399e-01 5.0000000000000036e+01 0 0 0 7 1 3.5807567230078612e+00 2.0451306356281487e+00 5.0000000000000036e+01 0 0 0 8 1 2.3711350845117933e+00 2.7435060142314525e+00 5.0000000000000036e+01 0 0 0 9 1 4.7903783615039313e+00 1.2520761314677690e+01 5.0000000000000036e+01 0 -1 0 10 1 6.0000000000000018e+00 6.4837987842154321e-01 5.0000000000000036e+01 0 0 0 11 1 6.0000000000000000e+00 2.0451306356281487e+00 5.0000000000000036e+01 0 0 0 12 1 4.7903783615039313e+00 2.7435060142314516e+00 5.0000000000000036e+01 0 0 0 13 1 7.2096216384960670e+00 1.2520761314677690e+01 5.0000000000000036e+01 0 -1 0 14 1 8.4192432769921393e+00 6.4837987842154443e-01 5.0000000000000036e+01 0 0 0 15 1 8.4192432769921375e+00 2.0451306356281460e+00 5.0000000000000036e+01 0 0 0 16 1 7.2096216384960687e+00 2.7435060142314533e+00 5.0000000000000036e+01 0 0 0 17 1 9.6288649154882098e+00 1.2520761314677690e+01 5.0000000000000036e+01 0 -1 0 18 1 1.0838486553984282e+01 6.4837987842154365e-01 5.0000000000000036e+01 0 0 0 19 1 1.0838486553984282e+01 2.0451306356281469e+00 5.0000000000000036e+01 0 0 0 20 1 9.6288649154882116e+00 2.7435060142314533e+00 5.0000000000000036e+01 0 0 0 21 1 -4.8108192480347277e-02 4.1402567714380565e+00 5.0000000000000036e+01 0 0 0 22 1 1.1615134460157228e+00 4.8386321500413594e+00 5.0000000000000036e+01 0 0 0 23 1 1.1615134460157228e+00 6.2353829072479643e+00 5.0000000000000036e+01 0 0 0 24 1 1.2048108192480349e+01 6.9337582858512690e+00 5.0000000000000036e+01 -1 0 0 25 1 2.3711350845117920e+00 4.1402567714380565e+00 5.0000000000000036e+01 0 0 0 26 1 3.5807567230078607e+00 4.8386321500413594e+00 5.0000000000000036e+01 0 0 0 27 1 3.5807567230078621e+00 6.2353829072479643e+00 5.0000000000000036e+01 0 0 0 28 1 2.3711350845117911e+00 6.9337582858512690e+00 5.0000000000000036e+01 0 0 0 29 1 4.7903783615039321e+00 4.1402567714380591e+00 5.0000000000000036e+01 0 0 0 30 1 6.0000000000000000e+00 4.8386321500413594e+00 5.0000000000000036e+01 0 0 0 31 1 6.0000000000000018e+00 6.2353829072479643e+00 5.0000000000000036e+01 0 0 0 32 1 4.7903783615039313e+00 6.9337582858512690e+00 5.0000000000000036e+01 0 0 0 33 1 7.2096216384960687e+00 4.1402567714380574e+00 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9.0288844216611785e+00 5.0000000000000036e+01 0 0 0 59 1 1.0838486553984282e+01 1.0425635178867784e+01 5.0000000000000036e+01 0 0 0 60 1 9.6288649154882116e+00 1.1124010557471088e+01 5.0000000000000036e+01 0 0 0 Velocities 1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 5 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 6 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 7 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 8 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 9 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 10 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 11 0.0000000000000000e+00 0.0000000000000000e+00 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0.0000000000000000e+00 53 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 54 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 55 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 56 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 57 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 58 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 59 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 60 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 That would be if there are hydrogen atoms. For carbon only, 1fs should be fine. Which properties are increasing that you expect to be decreasing? And by what margin? The Young’s and shear moduli then the elastic constants C11, C22, C66 … when the temperature increases. These moduli and elastic constants should rather decrease Okay Simon I evaluate the effect of temperature on the mechanical properties of graphene. So, for each temperature case, I try to thermalize the system before applying the strain and then use the slope of the strain-stress relationship to calculate the moduli. My problem is that the slope increases when the temperature increases and therefore the modules too The Young’s and shear moduli then the elastic constants C11, C22, C66… increase when the temperature increases. These moduli and elastic constants should rather decrease Concerning the problem of the time step, I tried with 0.5 fs as with 1 fs. But it’s the same problem. I wonder if I wrote the correct commands for thermalization or equilibration. Hi @joe1, This is a physics problem, you might want to consider what you’re doing with regards to the mechanics. Your input is complicated but from what I understand you’re doing a strain-stress deformation on a very small system (60 atoms) along your x axis with constant pressure on your y axis. I have couple comments on your procedure: 1. Equilibration From those lines: #-----------------Pressure Equilibriation----------------------- reset_timestep 0 velocity all create \${T} 456783 dist uniform
fix 			1 all npt temp \${T} \${T} \${dT} aniso \${P} \${P} \${dP}
run 			250000
unfix 1

write_data           	Relax.dat
[...]
##---------------ATOM DEFINITION------------------------------


As I understand, the system you end up with is the final state of your simulation. Pressure and box lengths fluctuates using NPT fix so you might not be at zero strain at timestep 250000. Plus you do not equilibrate it before acquiring data. This is basic MD procedure: equilibrate your system before running NPT, take an average or your box values and resize it correctly. But since your system is small, your fluctuations will be large. So either get a lot of data with long simulation, or use a bigger system.

1. Strain simulations:

This is what I understand from this part of your script:

fix 			        2 all npt temp \${T} \${T} \${dT} y 0.0 0.0 \${dP}
variable   	   	srate equal 0.001
fix		   	        3 all deform 1 x erate \\${srate} units box remap x


I do not know the details of your project but be aware that inducing strain along x axis will give rise to stress along x but also y at constant y strain. With the mathematics, say your strain is \varepsilon and your stress \sigma along axis x=1 and y=2 with your elastic tensor C, keeping the y axis unstrained should give two stress terms \sigma_1=C_{11}\varepsilon_1 and \sigma_2=C_{12}\varepsilon_1. But relaxing the pressure along y will make \varepsilon_2 non-zero wrt the reference state so \sigma_1=C_{11}\varepsilon_1+C_{12}\varepsilon_2. This can be a good way to proceed if you’re interested in Poisson’s ratio or others mechanical properties values, but I doubt it is straightforward to get C_{ij} out of it (one equation, several unknown values). Correct me if I’m wrong, again, your input is not that simple to read.

But these are details of your protocol you might want to discuss with people familiar with the how-to of MDs around you or check in the literature on the procedure people used to compute those values.

Hi Germain,

By the way, the system file shown here is the initial system state long before any simulation. I also took care to do the minimization (script between Therm.in … Therm.out) of the system via the conjugate gradient (CG) method before doing the NPT equilibration. At the end of the NPT equilibration for each temperature, I write the state of the system to the “Relax” file. And it is on this “Relax” file that I applied the deformation in the second part (script between X.in … X.out).
Except that I don’t know if this is the right procedure since I am a new LAMMPS user.

THANKS