Young’s modulus, yield point, Poisson’s ratio

Details on the calculation of atomic stresses can be found in the ReaxFF manual .


The calculations are computationally demanding. For optimal performance, a parallel execution on a compute cluster is advised. This can best be done by using the remote job management of the GUI

The simulation may take several days.


This advanced ReaxFF tutorial is based on Radue, Jensen, Gowtham, Klimek-McDonald, King and Odegard, J. Polym. Sci. B, 56, 255-264 (2018) [1]. It will demonstrate how to calculate stress-strain curves of an epoxy polymer.


  • Setting up a strain rate
  • Calcuate the atomic stresses
  • Results: stress-strain curves, Young’s modulus, yield points…


The molecular structure used in this tutorial was kindly provided by Matthew S. Radue. Other highly cross linked epoxy polymers can effectively be created with a novel bond boost acceleration method (see tutorial).

Setting up

The polymer used in this tutorial is referred to as Tetra(-epoxy) in [2] since it was build from the tetrafunctional resin epoxy TGDDM (tetra-glycidyl-4,4 0 - diaminodiphenylmethane, Araldite MY 721) and DETDA as hardener. The following cross linking reaction was used to create the polymer structure:


Start by importing the polymer structure into AMSinput

Click here to download the .xyz file
Import the coordinates in AMSinput:
File → Import Coordinates

Before setting up the strain rate, start with the general molecular dynamics settings. Begin by selecting a force field

Force field dispersion/CHONSSi-lg.ff
Click on MoreBtn next to Molecular Dynamics
Select 2000000 as Number of steps (500 ps)
Select 2000 as Sample frequency

Next we set up the thermo- and barostat

Click on MoreBtn next to Thermostat
Click on the AddButton
Select Berendsen from the menu Thermostat
Set the Temperature to 300.15 K and the Damping constant to 100 fs
Click on MoreBtn next to MD main options
Click on AddButton next to Barostat
Select Berendsen from the menu Barostat
Set the Pressure to 101000 Pa and the Damping constant to 1500 fs
From the Scale menu, select YZ


We are applying uni-axial strain, i.e. alongside one lattice vector, and apply the barostat only in the lateral directions. This will allow us to account for Poisson contractions.

Setting up the strain rate

The publication [2] put a linear strain of 20% over the course of 1 ns. Since we are simulating only 500 ps, for the sake of computational efficiency, the total strain reduces to 10%.

The straightforward way to defining this strain is by defining the strain type to be linear, followed by the final length of the vector at the end of the straining.

Let’s first find and note the length of the a-lattice vector.

Model → Lattice

The length of the a-lattice vector a (\(\mid\vec{a}\mid\)) is found to be 37.59793 Å. The endpoint, after stretching it 10%, will then be 41.36 Å. To define this strain, change to the MD deformation panel

Model → MD deformation
Click on AddButton
Enter 2000000 as the final step
Enter 41.36,``0``,``0`` as the final lengths of the lattice vectors


Putting a 0 as final length tells the program to ignore that particular lattice vector. You can learn about the meaning of each input field by hovering your mouse pointer over it.

Save the input files with a suitable name, e.g. tetra_strain_a, and run the calculation. On 16 cores, it will typically take a bit less than 1 day to compute the trajectory depending on your hardware.


Once the calculation has finished, the stress-strain curves can be extracted from the binary results file with the help of a Python script using the PLAMS library.

The script called can be run from the command line:

$AMSBIN/amspython tetra_strain_a

Be sure to match the job name correctly.

The stress-strain curve is written to a file called stress-strain-curve.csv:

strain_x, strain_y, strain_z, stress_xx, stress_yy, stress_zz
0.0001 -0.0012 0.0016 -0.0126 0.0107 -0.0142
0.0002 0.0003 0.0025 ...

It can be plotted with any graph plotting software, e.g. gnuplot or qtiplot. You can also use the script Call it with $AMSBIN/amspython stress-strain-curve.csv. The python script creates the plots shown below and calculates the Young’s modulus, yield point, and Poisson’s ratio.

The following example shows how to obtain the mechanical properties from stress-strain plot for an uniaxial strain in x-direction (column 4 plotted vs column 1):


A Young’s modulus of 8.01 GPa was calculated from the slope of a linear fit to the small strain regime (< 0.03) (orange line).

The yield point is then found as the intersection between

  • the moving window average line (200 points for smoothing), red, and
  • a 0.2% offset line (shifted by 0.002 along x) of the linear fit, green.

Poisson’s ratio is obtained from the ratio of transverse and uniaxial strains, i.e. plotting column #2 and #3 against column #1 (the system was strained in the x-direction)


Since the system is amorphous, Poisson’s ratio becomes (0.26 + 0.39)/2 = 0.33.


In order to get statistically meaningful results, it’s advised to average the mechanical properties, both over different starting structures as well as all three unaxial strain directions. To obtain quality results as in [1], an averaging over 5 different polymer structures using 3 strains each -> 15 trajectories is required.

Your results may look different from the above plots.


[1] M. S. Radue, B. D. Jensen, S. Gowtham, D. R. Klimek‐McDonald, J. A. King and G. M. Odegard, Comparing the mechanical response of di‐, tri‐, and tetra‐functional resin epoxies with reactive molecular dynamics, Inc. J. Polym. Sci., Part B: Polym. Phys. 56, 255–264 (2018).