1. Double-click the Materials Science icon
   • (No icon? See Starting Maestro)

Figure 2-1. Change Working Directory option.

2. Go to File > Change Working Directory
3. Find your directory, and click Choose
4. Pre-generated files are included for running jobs or examining output. Download the zip file here: schrodinger.com/sites/default/files/s3/release/current/Tutorials/zip/meta_workflow.zip
5. After downloading the zip file, unzip the contents in your Working Directorythe location where files are saved for ease of access throughout the tutorial

Figure 2-2. Save Project panel.

6. Go to File > Save Project As
7. Change the File name to meta_workflow_tutorial, click Save
   • The project is now named meta_workflow_tutorial.prj

Figure 2-3. Importing the epoxy and amine components.

We will proceed to import the components that we will use in this tutorial: TGDDM and 3,3-DDS. If you would prefer to draw or build these components yourself using the 2D Sketcher feel free to do so following similar steps outlined in the Introduction to Maestro for Materials Science tutorial. Otherwise:

8. Go to File > Import Structures
9. Navigate to where you downloaded the provided files (presumably in your Working Directory), and choose the input_structures.mae file
10. Click Open
    • A new entry group is added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion entitled Components (2) containing the two entries

Figure 3-1. Opening the Meta Workflow Builder panel.

1. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries the TGDDM and 33DDS entries from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
2. Go to Tasks > Materials > Tools > Meta Workflows > Meta Workflow Builder
   • The Meta Workflow Builder panel opens

Figure 3-2. Setting up Stage 1 of the Meta Workflow.

The first stage in the meta workflow will be building a disordered system using the two components we previously imported:

3. For For multiple entries, run choose A single workflow
4. Change the Name of Stage 1 to DSB
   • The name of the stage changes to DSB (short for disordered system build) in the magenta circle on the right side of the panel
5. Click Get From Job
   • The Extract Command dialogue opens

 

For more information about different Stage types, please see the help documentation.

Figure 3-3. Importing the job command.

We have provided the executable shell script files for the relevant jobs from the Crosslinking Polymers and Polymer Property Prediction tutorials as .sh files. These files were generated by setting up the panels as instructed in the aforementioned tutorials and using the Job Settings button () to Write the files.

6. Change Files of type to Command shell (*.sh)
   • Alternatively, for your specific jobs of interest, you can extract a job command from a -driver.log file from a previous job
7. From the provided files, choose the Section_03 > job_files > disordered_system_TGDDM_33DDS > disordered_system_TGDDM_33DDS.sh file
8. Click Open
   • The Command is populated based on the chosen .sh file

Note: The Command Help button opens the command help in a separate dialog box for the script in the text box. Additionally, you can hover over the various flags in the command in the text box to display a tooltip for that flag.

Note: For the Disordered System Builder and some other stages (e.g. Prepare for MD, Molecular QM), an option for a machine learning force field (MLFF) is available as an alternative. Additional information regarding MLFF can be found in the help documentation or on our website.

Figure 3-4. Setting up Stage 2 of the Meta Workflow.

Now we will relax the disordered system.

 

9. Click Append Stage
   • A 2nd stage appears in the workflow
10. Change the Stage type (Stage 2) to Simulation
11. Change the Name of Stage 2 to preCL-Relax
12. Maintain DSB as the Parent
    • This instructs the Meta Workflow Builder to use the output of the DSB stage as an input for this stage
13. Change the Simulation type to Custom
    • We will load in the .msj file from the multistage simulation protocol in the Crosslinking Polymers tutorial
    • Remember that the simulation protocol can also be defined in the panel directly using various Simulation types rather than a .msj file.
    • For all of the options available for the Simulation Stage type visit the help documentation
14. Click Load MSJ File
    • The Locate MSJ File dialogue opens

Figure 3-5. Importing the .msj file.

15. From the provided files, choose the Section_03 > job_files > multistage_simulation_TGDDM_33DDS > multistage_simulation_TGDDM_33DDS.msj file
16. Click Open
    • multistage_simulation_TGDDM_33DDS.msj is printed in the panel, which specifies the settings for the simulation

Figure 3-6. Setting up Stage 3 of the Meta Workflow.

Now we will specify the crosslinking job.

 

17. Click Append Stage
    • A 3rd stage appears in the workflow
18. Keep the Stage type (Stage 3) set to Workflow
19. Change the Name of Stage 3 to CL
20. Maintain preCL-Relax as the Parent
    • This instructs the Meta Workflow Builder to use the output of the preCL-Relax stage as an input for this stage
21. Click Get From Job

Figure 3-7. Importing the job command.

22. Change Files of type to Command shell (*.sh)
23. From the provided files, choose the Section_03 > job_files > polymer_crosslink_TGDDM_33DDS > polymer_crosslink_TGDDM_33DDS.sh file
24. Click Open
    • The Command is populated based on the chosen .sh file

Figure 3-8. Setting up Stage 4 of the Meta Workflow.

Now we will equilibrate the system following the crosslinking job.

 

25. Click Append Stage
    • A 4th stage appears in the workflow
26. Change the Stage type (Stage 4) to Simulation
27. Change the Name of Stage 4 to postCL-Relax
28. Maintain CL as the Parent
    • This instructs the Meta Workflow Builder to use the output of the CL stage as an input for this stage
29. Change the Simulation type to Custom
30. Click Load MSJ File
31. From the provided files, choose the Section_03 > job_files > multistage_simulation_TGDDM_33DDS > multistage_simulation_TGDDM_33DDS.msj file
    • This is the same equilibration protocol used in Stage 2
32. Click Open

Figure 3-9. Setting up Stage 5 of the Meta Workflow.

With the crosslinked and equilibrated system, we can now perform specific property calculations. First, we will perform the thermophysical properties workflow used to determine Tg and CTE.

 

33. Click Append Stage
    • A 5th stage appears in the workflow
34. Keep the Stage type (Stage 5) set to Workflow
35. Change the Name of Stage 5 to thermophysical_prop
36. Maintain postCL-Relax as the Parent
    • This instructs the Meta Workflow Builder to use the output of the postCL-Relax stage as an input for this stage
37. Click Get From Job

Figure 3-10. Importing the job command.

38. Change Files of type to Command shell (*.sh)
39. From the provided files, choose the Section_03 > job_files > thermophysical_prop_TGDDM_33DDS > thermophysical_prop_TGDDM_33DDS-001.sh file
40. Click Open

Figure 3-11. Appending the Single Stage Stress Strain Workflow.

In this step, let’s explore using a pre-built workflow as our Stage type and modifying it for our needs. We will specify the stress-strain workflow on the equilibrated crosslinked system:

41. Click Append Workflow
    • The Load Workflow popup opens
42. Select Single Stage Stress Strain
43. Click OK
    • A 6th stage appears in the workflow

Figure 3-12. Setting up Stage 6 of the Meta Workflow.

44. Click the cyan circle corresponding to the stress_strain stage
    • All stages except stress_strain are collapsed
    • Note that clicking on any stage on the flowchart diagram expands that stage in the left pane and collapses all the others
45. Change the Name of Stage 6 to stress_strain
46. Maintain postCL-Relax as the Parent
    • This instructs the Meta Workflow Builder to use the output of the postCL-Relax stage as an input for this stage
    • Multiple stages can have the same Parent stage, allowing for clever branching
47. We will alter some of the default stress strain parameters to those in blue below as done in the Polymer Property Prediction tutorial. Make the changes shown below (and in the Figure) in the text box:
    • stress_strain_gui_dir/stress_strain_driver.py -md_ensemble NVT -eta 0.5 -deformation_dir a -deformation_steps 100 -deformation_step_size 0.002 -md_time 100 -md_timestep 2.0 -md_trj_int 1 -md_temp 300.0 -md_press 1.01325 -md_ptensor_int 1.0 -seed 1234 -save_trj_data none -ptensor_avg 20.0 -md_umbrella $input.cms
    • Hover over the various flags in the command in the text box to display a tooltip for that flag

Figure 3-13. Setting up Stage 7 of the Meta Workflow.

48. Click Append Stage
    • A 7th stage appears in the workflow
49. Keep the Stage type (Stage 7) set to Workflow
50. Change the Name of Stage 7 to free_volume
51. Set the Parent to stress_strain
    • This instructs the Meta Workflow Builder to use the output of the stress_strain stage as an input for this stage. The flowchart updates accordingly.
52. For Command, choose Free Volume Analysis from the drop-down menu
    • We will use the default parameters for a free volume analysis

Figure 3-14. Setting up Stage 8 of the Meta Workflow.

53. Click Append Stage
    • An 8th stage appears in the workflow
54. Keep the Stage type (Stage 8) set to Workflow
55. Change the Name of Stage 8 to elastic_constants
56. Set the Parent to postCL-Relax
    • This instructs the Meta Workflow Builder to use the output of the postCL-Relax stage as an input for this stage
57. Click Get From Job

Figure 3-15. Importing the job command.

58. Change Files of type to Command shell (*.sh)
59. From the provided files, choose the Section_03 > job_files > elastic_constants_stress_based > elastic_constants_stress_based-001.sh file
60. Click Open

Figure 3-16. Naming and running the Meta Workflow Builder.

In the Job Settings dialog box for the Meta Workflow Builder, you can specify hosts for the meta workflow driver as well as the individual stages in the meta workflow. Please read the help documentation on this dialog box before running a meta workflow.

61. Adjust the job settings () as needed
    • This job requires CPU and GPU hosts. The job can be completed in about 24 hours when using the settings shown here. Note that the computational resources required for a meta workflow depends on the system at hand as well as the protocol used.
62. If you would like to run the job yourself, enter a Job name and click Run. Otherwise, go to File > Import Structures, navigate to the provided tutorial files and Open Section_03 > meta_workflow_thermoset_polymer > meta_workflow_thermoset_polymer-meta.maegz
63. Close the Meta Workflow Builder panel

Figure 3-17. Viewing the output of the calculation.

64. When the job is finished or after importing, expand the entry groups and select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries and includethe entry is represented in the Workspace, the circle in the In column is blue the new meta_workflow_postCL-Relax entry from the meta_workflow_thermoset_polymer entry group
    • This is the equilibrated crosslinked system

 

Note that it is possible to observe many atoms outside the unit cell. If so, be aware that this is purely visual, and can be easily amended using the Periodic Structure Tool Window

Feel free to visualize the output system in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed

Depending on if the job was run or imported your entry list could be organized differently than the Figure. The entry list shown is after performing the calculation.

Figure 4-1. Loading the trajectory into the MS MD Trajectory Analysis panel.

Generally, it is recommended to confirm that a system is fairly well equilibrated before undergoing a crosslinking simulation. Since our equilibration and crosslinking calculation ran in succession, let’s confirm that this was the case for the meta_workflow_preCL-Relax stage which is the Parent stage for the crosslinking simulation. We can view the density over time to confirm this:

1. Includethe entry is represented in the Workspace, the circle in the In column is blue meta_workflow_preCL-Relax in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion from the Meta Workflow results
2. Go to Tasks > Materials > Classical Mechanics > Trajectory Analysis > MS MD Trajectory Analysis
   • The MS MD Trajectory Analysis panel opens
3. Click Load from Workspace
   • The Simulation Detail tab fills with information about the MD job and system
4. Go to the Bulk Properties tab

Figure 4-2. Viewing bulk properties of the system.

5. Use the dropdowns to view the various properties as a function of time from the MD stage. Select Density from the first property option menu
   • Click Final 20% to view the last 20% of the trajectory
   • It is good practice to check the density of the equilibrated system to ensure that the system has densified and equilibrated

Note: The Specific Heat Capacity is printed at the top of the display as seen in the Figure. Specific Heat Capacity will not be displayed if the Ensemble was NVE

6. When you are finished, close the MS MD Trajectory Analysis panel

Figure 4-3. Opening the Crosslink Polymers Viewer panel.

Next, let’s analyze the crosslinking calculation using the Crosslink Polymers Results panel:

7. Use the WAM (workflow action menu) button () to open the Crosslink Polymers Results panel for meta_workflow_CL
   • Alternatively, access the panel via Tasks > Materials > Classical Mechanics > Crosslink Polymers > Crosslink Polymer Results
   • The Crosslink Polymers Viewer panel opens
   • Note that when the Viewer panel is opened, the individual crosslinking iterations load in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and the last entry is includedthe entry is represented in the Workspace, the circle in the In column is blue in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed. The results panel opens with a view of the plain text log file

Figure 4-4. Coloring the crosslinked system by candidate and formed bonds.

Let’s explore the different tabs in this panel to display and analyze the crosslinking calculation. The Reactivity tab allows us to visualize the components of the box involved in the crosslinking process.

8. Click on Color for Color Candidate Cross-link Bonds AB Bonds
   • All N-H bonds that did not react are highlighted in orange
9. Click on Color for Color Candidate Cross-link Bonds CD Bonds
   • All C-O bonds on the epoxy ring that did not react are highlighted in blue
10. For Color Cross-linked Bonds Iteration, select All iterations
11. Click on Color for Cross-linked Bonds
    • The crosslinked bonds formed in all iterations during the calculation are highlighted in yellow

The tools here help us gain a better understanding of the reaction we have just modeled. Feel free to explore these coloring schemes further if you are interested.

12. Go to the Time Series tab

Figure 4-5. Viewing properties of the crosslinking calculation.

The Time Series tab facilitates visualizing properties of the crosslinking calculation as a plot. For example, we can view how the molecular weight and density of the system as a function of crosslinking saturation:

13. Click Y Properties
14. From the option-menu, select First Largest Reduced MW and Second Largest Reduced MW and deselect Density
    • The reduced molecular weight (RMW) is determined by dividing the molecular weight (first largest or second largest) by the total molecular weight
15. Check Second Y property
16. For Second Y property, choose Density g/cm³

In this example we estimate the gel point as the %crosslink where the first largest molecular weight reaches 50%. Here that value is ~47% crosslink saturation. At this point, the system suddenly transitions from liquid type behavior to solid type behavior.

17. Close the Crosslink Polymers Viewer panel

Figure 4-6. Viewing the output system.

The next stage of the workflow was a molecular dynamics simulation to equilibrate the crosslinked system. Repeat steps 1-6 in this section for the entry titled meta_workflow_preCL-Relax to ensure it is well equilibrated.

Ensuring it is, we move on to study the results of the thermophysical properties calculation:

18. To visualize the output from the thermophysical properties calculation, select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries and includethe entry is represented in the Workspace, the circle in the In column is blue the meta_workflow_thermophysical_prop entry
    • The displayed cell is from the last simulation at 100 K.
    • Feel free to visualize the output system in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed

Figure 4-7. Opening the Thermophysical Properties Results panel via the WAM.

To extract T_g and CTE from the Thermophysical Properties calculation we use the Thermophysical Properties Results panel:

19. Use the WAM (workflow action menu) button () to open the Thermophysical Properties Results panel
    • Alternatively, access the panel via Tasks > Materials > Classical Mechanics > Thermophysical Properties Results
    • The Thermophysical Properties Results panel opens

Figure 4-8. Viewing the Bilinear fit in the Thermophysical Properties Results panel.

Generally, best practice would be to use ten replicates to ensure our data is reliable. This can be achieved by setting the -ncells flag to 10 in the Disordered System Builder stage (Stage 1). In general, we can reduce the scatter or variability in the density data with larger systems and longer MD simulation times.

However, we can analyze a Bilinear fit for T_g and more importantly, CTE:

20. Select Bilinear fit
21. Click and move the edges of the blue and green boxes to readjust the boundaries between the low temperature (green) and high temperature (blue) regions to shift to the most linear regions. In the Figure, the green and blue regions are approximately set to 100 K to 320 K and 550 K to 760 K, respectively.
    • The resulting T_g value should be ~524 K
    • The coefficient of thermal expansion is determined from the slope of the fit in the glassy region. Here, the volumetric and linear CTE are reported as ~115 x 10^-6 K^-1 and 39 x 10^-6 K^-1 respectively
22. Close the Thermophysical Properties Results panel

Figure 4-9. Viewing the output of the Stress Strain simulation.

23. To visualize the output from the stress strain calculation on the equilibrated crosslinked system, select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries and includethe entry is represented in the Workspace, the circle in the In column is blue the meta_workflow_stress_strain entry
    • Feel free to visualize the output system in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed

Figure 4-10. Opening the Stress Strain Results panel via the WAM.

We can analyze the Stress Strain calculation quantitatively using the Stress Strain Results panel:

24. Use the WAM button () to open the Stress Strain Result panel
    • Alternatively, access the panel via Tasks > Materials > Classical Mechanics > Stress Strain > Stress Strain Results
    • The Stress Strain Results panel opens

Figure 4-11. Viewing the stress versus strain plot.

The Stress Strain Results panel opens with a plot of the effective stress against the effective strain from the calculation we just ran. The data shown here can be used to obtain the yield point of the crosslinked TGDDM-3,3-DDS system, however there is some noise in the data. It is much more effective to load in multiple replicates of stress strain simulations, and average the stress strain data over the replicates. We do so in the Polymer Property Prediction tutorial and determine the yield strain of this system is approximately 0.10 and the yield point is 0.35 GPa. Feel free to improve the data by running the Meta Workflow additional times on replicates of this system generated by using different seed values (see the -seed flag) in the disordered system builder (Stage 1).

Figure 4-12. Visualizing the output of the Free Volume calculation.

Now, let’s visualize the output from the free volume calculation on the last frame of the stress strain calculation:

25. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries and includethe entry is represented in the Workspace, the circle in the In column is blue the meta_workflow_free_volume-1 entry
    • Feel free to visualize the output system in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed

Figure 4-13. Opening the Free Volume Results panel via the WAM.

We can visualize the results of the Free Volume calculation using the Free Volume Results panel:

26. Use the WAM button () to open the Free Volume Results panel
    • Alternatively, access the panel via Tasks > Materials > Tools > Free Volume Results
    • The Free Volume Results panel opens

Figure 4-14. Viewing the Distribution tab.

27. Click Load Data From Workspace
    • The results from the Free Volume calculation are loaded into the panel.

The Void Size Distribution plot shows the distribution of voids in this particular frame.

28. Change the lower radii limit for Show voids in Workspace for current frame with radii between to 1.14
    • The Number of voids in current frame updates to 7
29. Click Display to view the 7 largest voids in this frame
    • Feel free to visualize a greater number of voids but be aware that the voids can take some time to load into the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
30. Close the Free Volume Results panel

Figure 4-15. Viewing the output.

31. To visualize the output from the elastic constants calculation on the equilibrated crosslinked system, meta_workflow_preCL-Relax, select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries and includethe entry is represented in the Workspace, the circle in the In column is blue the meta_workflow_elastic_constants entry

Feel free to visualize the output system in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed

Figure 4-16. Opening the Elastic Constants Viewer panel via the WAM.

We can analyze the Elastic Constants calculations further using the Elastic Constant Results panel:

32. Use the WAM button () to open the Elastic Constants Results panel
    • Alternatively, access the panel via Tasks > Materials > Classical Mechanics > Elastic Constants > Elastic Constants Results
    • The Elastic Constants Results panel opens

Figure 4-17. The Plot tab of the Elastic Constants Results panel.

For the results of an Elastic Constants calculation, the Plot tab shows the stress computed against the deformation along with the linear fit. The Term can be changed to see the stress/deformation curve for any of the tensor components, C_ij. Feel free to explore these plots.

33. Go to the Tensors tab

Figure 4-18. The Tensors tab.

The Tensors tab displays the Elastic tensor table, containing the components of the elastic tensor, and the R² table, which contains the R² value for the fit to obtain each component of the elastic tensor.

Feel free to further explore the polymer properties of interest.