3 DPD

Student Edition
Modeling Function Tutorial

DPD
J-OCTA 3.1
July 2017
JSOL Corporation
Copyright (c) 2006-2017 JSOL Corporation

J-OCTA 3.1 Modeling Function Tutorial DPD
Contents
3. DPD ............................................................................................................................ 3
Creating a Project ........................................................................................................ 4
Creating a Monomer Model ......................................................................................... 4

Opening the monomer file................................................................................. 4
Creating a monomer structure ......................................................................... 5
Creating a Segment ..................................................................................................... 7

Creating a DPD model file ................................................................................. 7
Loading the monomer file ................................................................................. 7
Obtaining the monomer information from the database ............................... 8
Adjusting the segment size............................................................................... 9
Calculating the Parameter .......................................................................................10
Creating a Polymer Model .......................................................................................... 11
Creating a DPD Input File ...........................................................................................12
Running the Engine ....................................................................................................17
2
Copyright(c) 2006-2017 JSOL Corporation
3. DPD
This tutorial describes the modeling procedure of a phase separation simulation of a
polybutadiene-polystyrene diblock copolymer in order to understand the procedure to
create a DPD input file with DPD Modeler. The DPD modeling procedure is almost the
same as the SUSHI modeling procedure. This tutorial deals with the same subject as
the SUSHI tutorial.
[Phase Separation Simulation of a Polybutadiene-Polystyrene Diblock Copolymer]

Calculate the parameter with DPD Modeler and create a DPD (COGNAC) input file.
Perform DPD calculation using the created input file to obtain the phase-separated
structure of the system.
The following shows the flow of the DPD modeling and DPD calculation.
(1) Create project
(2) Create a monomer model
(3) Create a segment
(4) Calculate the parameter
(5) Create polymer model
(6) Create DPD (COGNAC) input file
(7) Run engine
(8) Analyze results
Figure 1 Flow of DPD Modeling
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Creating a Project
Create a project for the DPD tutorial.
Create a project for the DPD tutorial calculation.

Project Name dpd-tutorial
Project location Excluding the following locations, the project can be created
in any location.
[Invalid locations]
Under a directory including the double byte character
Under directories with spaces in the name (My
Documents, etc.)
Figure 2 Creating a Project
Creating a Monomer Model

When the project is created, proceed to DPD modeling. First, create the monomers
composing a molecule.
Opening the monomer file

First, create a new monomer file to perform monomer modeling.
Creating a new monomer file

Select File > New > Monomer
Right-click the project and select New > Monomer
Perform either of the above operations to open the monomer modeling screen.
Create styrene and butadiene monomer files with the above procedure.
Monomer file name styrene.mom (The extension .mom indicates the monomer
file)
butadiene.mom
Location of the file Under dpd-tutorial
4
Parts for creating monomer structure
Design Panel
Figure 3 Monomer Creation Screen
Creating a monomer structure

Next, create styrene and butadiene monomer structures.
How to create a monomer

1. Select a part from the Group-Contrib. tab and drag and drop it on to the monomer
design panel to place the part. You can also create a monomer using parts other than
those in the Group-Contrib. tab. In that case, you need to manually enter the molar
volume and cohesive energy values that are needed to calculate the parameter
with the group contribution method, because these values cannot be obtained from
the database. When calculating the parameter with the Monte Carlo method or the
molecular dynamics method, that would not be a problem using parts other than
those in the Group-Contrib. tab. The placed parts can be selected by clicking the
button.
2. Click the button to connect parts.
3. Click the button to add to both ends of the monomer.
4. When the modeling is complete, click the button or select File > Save to save
the monomer file.
5
Select the parts from

Group-Contrib. tab
Arrange the parts by

drag and drop
[Monomer Modeling Button]

: Selection of the parts
: Connecting the parts
Add to both ends of
: Placing on the bonding the monomer
parts of monomer
Figure 4 Monomer Modeling Screen
Create a styrene monomer and butadiene monomer.

In this tutorial, create a monomer structure using the parts in the Group-Contrib. tab.
Create a styrene monomer and butadiene monomer with the above procedure.
A. Styrene monomer B. Butadiene monomer

(styrene.mom) (butadiene.mom)
Figure 5 Monomers to Create
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Creating a Segment
Next, create a segment. The DPD calculation defines a segment (DPD particle)
consisting of number monomers and represents a polymer by combining segments.
Creating a DPD model file

The following operations are all performed using a DPD model file. Create a DPD
model file.
Creating a DPD model file

Select File New Modeler DPD Model to open the DPD modeling
screen.
Create a DPD model file.

DPD model file name st-bd.dpm
(The extension .dpm indicates the DPD model file)
Location of the file Under dpd-tutorial
Loading the monomer file

Load the created monomer file into the DPD model file.
Loading the monomer file

button
File Load Monomer File
Perform either of the operations to load the two created monomer files and enter
the segment name, color, etc.
Load the styrene monomer (styrene.mom) and butadiene monomer

(butadiene.mom).
7
When selecting specified

color on the left
Load the monomer file
Figure 6 Loading the Monomer File
Obtaining the monomer information from the database

When loading of the monomer files is complete, obtain the cohesive energy and molar
volume values from the database.
Obtaining the monomer information

1. Select the database from the Group Contribution Method tab and click the
Set button to obtain values from the database in the cell.
2. Perform this operation for all segments.
Obtain the information of styrene and butadiene from the database.
Select Group Contribution

Method tab
Select database
Select segment
Figure 7 Obtaining the Molar Volume and Cohesive Energy
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Caution
When the information is obtained from the database, a cell is displayed in red if there
is no value for that cell in the database. In that case, manually enter the value in the
cell displayed in red or use another database.
In this example, use the Fedors database from which the information on all parts
included in the styrene and butadiene can be obtained.
The information which cannot

be obtained in Dunkel
Figure 8 In Case Referring to a Value That is Not Available in the Database
Adjusting the segment size

When you select the Properties tab, the information obtained from the database
above is entered. Change the number of monomers to adjust the segment size. Adjust
the number of monomers so that the segment sizes (segment molar volume) become
approximately equal to each other.
Adjusting the segment size

Change the number of monomers in the Properties tab so that the volumes of the two
segments become approximately equal to each other.
Adjust the size of the styrene and butadiene segments.

Styrene: number of monomers 2, and butadiene: number of monomers 3.
9
Select the Properties tab
Number of monomers 2. Number of monomers 3.
Figure 9 Adjusting the Segments
Calculating the Parameter

When the creation of segments is completed, calculate the parameter between
segments. In this example, calculate the parameter by means of the group
contribution method.
Estimation with the group contribution method

Calculate the parameter using the obtained values with the group contribution
method.
Simple calculation of the parameter with the group contribution method

1. Select the Segment Pair tab and the Group Contribution Method tab.
2. Enter the temperature and basis molar volume and click the Calculation button
to insert the estimated value in the cell for the parameter.
Calculate the parameter between styrene and butadiene.

Calculate the parameter of styrene-butadiene. In this example, configure the settings
as follows.
Temperature at which to calculate: 300 K
Standard molar volume: 175 cm3/mol (Average molar volume of both
segments)
Xs (Effect elements other than enthalpy): 0.0
For s (Effect elements other than enthalpy), set 0.0 between polymers and 0.34
between polymer and solvent.)
10
1. Select Segment Pair 3. Select Group Contribution

tab Method tab
2. Select Segment Pair
Calculation results
Figure 10 Estimating the Parameter with the Group Contribution Method
Creating a Polymer Model

Now, you finally perform polymer modeling.
Creating a polymer file

1. Select the segments to create a polymer from the Segment tab and place the
segments by dragging and dropping them in the polymer creation screen.
2. Right-click the segment part and select Repeat > Set to set the number of
repeats for the segment.
3. To create a polymer using multiple segments, use the button. Click this
button to connect the segments.
Create a polymer using the styrene and butadiene segments.

Create a styrene-butadiene diblock copolymer with the above procedure.
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(1) Drag and drop the

segment into position
(2) Do right-click > Repeat >

(3) Connect parts Set to enter number repeats
(20) for both
Figure 11 Polymer Modeling Screen
Creating a DPD Input File

When the calculation of the parameter between segments and the creation of the
polymer structure are complete, create an input file for the DPD calculation.
Create an input file for the phase separation calculation of the

styrene-butadiene diblock copolymer with the following procedure.
DPD input file creation screen
button
Tool > Create DPD Input

Perform either of the above operations to open the DPD input file creation screen.
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Create DPD input file
Figure 12 Opening the DPD Input File Creation Screen
Set the four items: Calculation Conditions, Interaction Parameters, Bond Parameters,
and Molecule.
Setting Simulation Conditions

Set the parameters in the Simulation Conditions tab.
Calculate Number of Water From Basis Molar Volume

You can get number of water molecules in DPD from basis molar volume of pair
automatically. The formula will be used the expression described in the following
"Number of Water Molecules in DPD ".
Number of Water Molecules
Segment size compared to the water molecules. You need to set the value manually.
Estimate the value from the following equation using the segment molar volume
V [cm 3 / mol ] for each segment. In this example, approx. 9.7 can be estimated from the
equation.
n = (V 10 21 / N A ) / 0.03
* N A (Avogadro constant) 6.022 10 23
Setting this value automatically changes the values for the unit length and unit time.
These values are used to evaluate the actual sizes that are used to perform the
calculation. For example, if the size of a region is 10 [non-dimensional] according to the
COGNAC file obtained as a result of the calculation, the real dimensional size of that
region is unit length (0.956 [nm] in this example) x 10 = 9.56 [nm].
The way to estimate the unit time is the same as the above. However, the unit time is
applicable for the calculation of a low molecular weight system but does not make sense
for that of a polymer system (so ignore the value for the unit time as this example deals
with the calculation of a polymer system).
Density
Leave the density 3.0. For the DPD calculation, a real physical quantity cannot be set
for the density. The value set here represents the number density of the particles used for
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the calculation, so usually you do not need to change the value.

Delta-T
The time step size is 0.05 by default. If the number of water molecules obtained above
is large, set a slightly lower value. In this example, set 0.02.
Max Number of Steps and Output Interval Steps
In this example, set 100,000 and 1,000, respectively.
DPD algorithm parameter
Leave the default value 0.65 as is.
Figure 13 Setting Calculation Conditions
Setting Interaction Parameters

Set the input parameters in the Interaction Parameters tab.
First, select which parameter value to use from the Group Contribution Method's
Result, Monte Carlo Methods Result, MD Methods Result, and Mixed Systems
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Result. In this example, select the Group Contribution Method's Result as only the
estimation with the group contribution method was performed.
Figure 14 Setting Interaction Parameters
When the Calculate a from chi parameter check box is selected, interaction
parameter a is automatically calculated from the parameter.
Select a= 75 / density from Interaction Parameter a." The parameter between segments
can be calculated with the following equation.
Parameter between segments of different types: a ij = 75 / + 3.268 ij
Parameter between segments of the same type: a ij = 75 /
* The second term on the right-hand side of the equation for the parameter between
segments of different types (+3.268ij) is only effective when =3.0.
Setting Bond Parameters

Select the Bond Parameters tab and set the bond potential for the molecules. In this
example, leave the value as default.
Figure 15 Setting Bond Parameters
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Setting the number of molecules to calculate

Select the Molecule tab and specify the number of molecules to place in the simulation
box. In this example, set 100.
Figure 16 Setting the Number of Molecules
Setting the others
Figure 17 Setting the others
When the above parameters are entered, create a DPD input file.
Generating an input file

Finally, enter the file name under Input File at the top of the screen and click the
Create button to generate a DPD file in the specified directory.
Figure 18 Specifying the DPD File Name to Create
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The modeling work is complete. Then run the DPD calculation using the created input
file.
Running the Engine

Perform DPD calculation using the DPD input file created with the above operation.
Open the created file

In the project tree on the left in J-OCTA, double-click the input UDF file created above
to open it. If the input UDF file does not appear in the tree, right-click the project icon
and select Refresh.
Run the engine

Click the Run Engine button on the upper left corner of the UDF editor to run the
engine.
Figure 19 Run Engine Button
Click the Run Engine button to open the Run Engine panel. Click the Start button to
start calculation.
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Figure 20 Run Engine Panel
In this example, the calculation consists of 100,000 steps so it will take several tens of
minutes to several hours depending on the performance of the calculator to complete
the calculation.
When the calculation is complete, the following screen appears in the console.
Figure 21 Console Screen after Calculation is Complete
Analyze the results

Let's take a look at the results file.
When the calculation is complete, the results file is generated in the specified output
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location. Double-click the results file to open it. If the results file does not appear in the
project tree, right-click the project icon and click Refresh.
3D plot
Select record
Figure 22 DPD Output File
The DPD calculation results can be analyzed by running actions.
Produce visualizations
Click the Plot button (see the above figure) for the output UDF file. You can visualize
the phase separation structure. You can view the changes in the phase separation by
changing the records.
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Figure 23 Plotting the Results
This concludes the DPD tutorial.
When you calculate on a trial model with no consideration for molecule structure, create
dummy monomer models using united-atom parts and load them into DPD modeler. You
can specify any value in parameter of a segment pair.
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Figures
Figure 1 Flow of DPD Modeling .................................................................................................................... 3

Figure 2 Creating a Project ............................................................................................................................. 4
Figure 3 Monomer Creation Screen ........................................................................................................... 5
Figure 4 Monomer Modeling Screen .......................................................................................................... 6
Figure 5 Monomers to Create ........................................................................................................................ 6
Figure 6 Loading the Monomer File ............................................................................................................ 8
Figure 7 Obtaining the Molar Volume and Cohesive Energy ........................................................ 8
Figure 8 In Case Referring to a Value That is Not Available in the Database ...................... 9
Figure 9 Adjusting the Segments ............................................................................................................... 10
Figure 10 Estimating the Parameter with the Group Contribution Method....................... 11
Figure 11 Polymer Modeling Screen ........................................................................................................ 12
Figure 12 Opening the DPD Input File Creation Screen................................................................ 13
Figure 13 Setting Calculation Conditions............................................................................................... 14
Figure 14 Setting Interaction Parameters .............................................................................................. 15
Figure 15 Setting Bond Parameters ......................................................................................................... 15
Figure 16 Setting the Number of Molecules ......................................................................................... 16
Figure 17 Setting the others ......................................................................................................................... 16
Figure 18 Specifying the DPD File Name to Create.........................................................................16
Figure 19 Run Engine Button ....................................................................................................................... 17
Figure 20 Run Engine Panel ........................................................................................................................ 18
Figure 21 Console Screen after Calculation is Complete ............................................................. 18
Figure 22 DPD Output File ............................................................................................................................ 19
Figure 23 Plotting the Results...................................................................................................................... 20
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Student Edition

Modeling Function Tutorial

Copyright (c) 2006-2017 JSOL Corporation

Creating a Project ........................................................................................................ 4

Creating a Monomer Model ......................................................................................... 4

Creating a Segment ..................................................................................................... 7

Calculating the Parameter .......................................................................................10

Creating a Polymer Model .......................................................................................... 11

Creating a DPD Input File ...........................................................................................12

Running the Engine ....................................................................................................17

[Phase Separation Simulation of a Polybutadiene-Polystyrene Diblock Copolymer]

(1) Create project

(2) Create a monomer model

(3) Create a segment

(4) Calculate the parameter

(5) Create polymer model

(6) Create DPD (COGNAC) input file

(7) Run engine

(8) Analyze results

Figure 1 Flow of DPD Modeling

Create a project for the DPD tutorial calculation.

Figure 2 Creating a Project

Creating a Monomer Model

Opening the monomer file

Creating a new monomer file

Parts for creating monomer structure

Figure 3 Monomer Creation Screen

Creating a monomer structure

How to create a monomer

Select the parts from

Arrange the parts by

[Monomer Modeling Button]

Figure 4 Monomer Modeling Screen

Create a styrene monomer and butadiene monomer.

A. Styrene monomer B. Butadiene monomer

Figure 5 Monomers to Create

Creating a DPD model file

Creating a DPD model file

Create a DPD model file.

Loading the monomer file

Loading the monomer file

Load the styrene monomer (styrene.mom) and butadiene monomer

When selecting specified

Figure 6 Loading the Monomer File

Obtaining the monomer information from the database

Obtaining the monomer information

Obtain the information of styrene and butadiene from the database.

Select Group Contribution

Figure 7 Obtaining the Molar Volume and Cohesive Energy

The information which cannot

Figure 8 In Case Referring to a Value That is Not Available in the Database

Adjusting the segment size

Adjusting the segment size

Adjust the size of the styrene and butadiene segments.

Select the Properties tab

Number of monomers 2. Number of monomers 3.

Figure 9 Adjusting the Segments

Calculating the Parameter

Estimation with the group contribution method

Simple calculation of the parameter with the group contribution method

Calculate the parameter between styrene and butadiene.

1. Select Segment Pair 3. Select Group Contribution

2. Select Segment Pair