Stress-strain curve: Fracture point

This tutorial demonstrates how to set up a molecular dynamics calculation with an increasingly deformed unit cell in order to study the mechanical properties of a small polymer chain model. During the simulation, the strain on the chain is increased slowly until the initial double bonds of the cis-Polyacetylene are successively converted into their trans configurations. Afterwards, an even larger strain causes the polymer chain to snap which immediately reduces the stress to zero. The stress tensor components computed during the MD simulation are then collected with a small Python script and plotted to demonstrate different changes in the molecular structure of chain.

Note

With AMS2020 and later versions, the deformation of the Polyacetylene chain demonstrated in this tutorial can also be realized using a 1D periodic lattice. To use a 1D periodicity, the deformation of the x-axis needs to be set and the Polyacetylene chain needs to be rotated accordingly.

Step 1: Start the GUI

We will set up an MD simulation from the GUI. Alternatively, you can download this PolyStressStrain.run.

Start AMSjobs

SCM → New input

Switch to ReaxFF: →

Step 2: Import Structure and Settings

We begin by setting the main calculation options for the molecular dynamics simulation.

In the menu bar, File → Import Coordinates…

Select cis_polyacetylene.xyz

In the main panel, select Force Field: → CHO.ff

Next, set the options for molecular dynamics:

Click on next to Molecular Dynamics

As Number of steps, enter 850000

As Sampling frequency, enter 1000

As Checkpoint frequency enter 50000

The simulation should run at constant temperature, so we add a thermostat:

Click on next to Thermostat and add a Thermostat

Select NHC

As Temperature, enter 300.15 K

As Damping Constant, enter 100.0 fs

Next, we have to set up the deformation so that the chain is stretched during the simulation.

Select Model → MD… → Deformations, and add a deformation

Set the second field in Length velocity 0.00002 A/fs.

Lastly, we need to calculate the stress tensor

Properties → Gradients, Stress Tensor Check stress tensor.

Step 3: Run the Calculation

After having set all calculation options we are now ready to start the run

In the menu bar, select File → Save and enter PolyStressStrain

In the menu bar, select File → Run

Switch to AMSmovie by clicking on SCM → Movie to see the polymer change under strain

Step 4: Results

Once the calculation is finished, we can analyze the results

GUIScripting

In AMSmovie, select MD Properties → Stress/Strain → YY

It is worth noting the distinct segments displayed in the stress/strain plot, as they correspond to various configurations of the Polyacetylene chain. Initially, we started from a cis- configuration. However, during the simulation, as the chain is being pulled, it undergoes a transition whereby some or all of the cis- bonds convert into trans- bonds. Following this transition, the mechanical properties of the chain change, which can be observed through different slopes on the stress/strain graph. Eventually, at a certain strain point, the chain snaps, resulting in an immediate reduction of stress to zero. This occurs as the periodic polymer chain transforms into a molecular entity beyond this critical point.

We can then perform a simple linear regression analysis on this curve:

In AMSmovie, select Graph → Analysis

Select Curve: → Stress YY

Select the Linear Regression tab

Click on the button

Restrict the x-range of the linear regression to the first segment, in this case from 0 to 0.05

Click on OK

In the legend you can see the regression coefficients for the stress-strain linear fit of the first segment.