This tutorial demonstrates how to create a very simple flowchart and execute its workflow. In Managing the Dashboard and Working with the Dashboard, we will provide guidance on how to set up the Dashboard and use it to monitor and inspect the job results. These tutorials are carefully designed to guide the first-time users of the SEAMM through the preliminary steps of preparation while delineating its fundamental functionalities in details. As such, subsequent tutorials will assume that the users have mastered the skills required to build flowcharts, execute jobs and check the outputs.
First, make sure the Dashboard and Job Server are running. Refer to the Installing SEAMM section if you do not know or remember how to get them up and running. Open a terminal and activate the seamm conda environment:
conda activate seamm
and start the SEAMM GUI by calling its name in the terminal:
This will bring up a window like the one shown below:
The window consists of two panes separated by a sash – the grey line. If you hover over the sash the cursor will change to a horizontal double-pointed arrow enabling the adjustment of the pane sizes. The left pane contains the list of available plug-in categories. Clicking on each category expands its content and represents it as a list of available plug-ins. Clicking on the same point on the screen will hide the expanded list:
The right-hand pane contains the initial step of a flowchart,
Start. There must be one
and only one start step in a flowchart because this is where execution starts. Users
cannot delete or add a
Let us create a simple flowchart and add a molecule to it using SMILES. SMILES is a specific representation of a chemical structures in the string format. Then, we add a new step, in which we optimize the geometry of the molecule, imported in the previous step, with a semi-empirical quantum chemistry method.
By clicking on the
FromSmilesStep from the
Building section, a rectangular box
for the new step labeled as
from SMILES appears in the right pane. This box is also connected
If you have accidentally clicked twice on the
FromSmilesStep or any other menu item that you
did not want, just right-click on the unwanted step and select
delete from the poped-up menu:
In the next stage, we need to set the SMILES string variable for the added molecule. Almost every
step has a dialog window that allows the users to set parameters and control the details of the task
in each step of the workflow. In order to access the dialog, one can either right-click on the step box
Edit... from the menu or just double-click on the step box to open it:
Click in the field labeled
SMILES and type CCS, which is the SMILES representation
for ethanethiol. Leave everything else as is and click on the
Now, open the
Simulations section in the left panel and add a
Then, open the dialog for the DFTB+ step:
Note that this dialog looks like the main SEAMM window. Some steps, like the
step, perform one task and thus, can be handled by a single dialog. However, many
simulation codes such as DFTB+ are capable of performing multiple tasks and often have
their own syntax. Open the
Setup and then the
Simulation sections on the left
panel in order and add the
ChooseParameters and the
Optimization steps in the
Open the dialog for the
ChooseParameters step by double-clicking on it:
ChooseParameters dialog is quite a large and complex but at least, it is organized
similar to a periodic table!
A short description of how DFTB+ works is in order. DFTB+ is a semiempirical quantum chemistry code. It uses parameterized Slater-Koster functions for each atom. However, several parameterizations are available to choose from. These datasets are listed in the pull-down button near the bottom for the dialog window that is currently opened. Some of the datasets have additional add-on datasets that either add more elements to the existing sets or are tuned for different systems and properties. More information about the parameter sets can be found in the DFTB website.
Unfortunately, the aforementioned datasets do not cover all elements. As such, one needs
to find an appropriate dataset that can handle all elements of interest. The
ChooseParameters dialog offers two ways to find the appropriate parameters set.
In the first approach, when a dataset and perhaps an auxiliary dataset is selected from the
two pull-down buttons at the bottom of the dialog, the supported elements within the periodic
table are automatically highlighted in red. The default dataset,
ob3, can handle a list of
elements including H, C, N, O, F, Na, Mg, P, S, Cl, Zn, Br, I, and Ca, which would be suitable
for our ethanethiol example as well as a wide range of organic molecules that are made of the
In the second approach, one can select the desired set of elements, say, H, C, N, O, S, and Zn. Then, check the drop-down button at the bottom of the dialog to see what choices are available for the selected set of elements:
For our selected set of elements mentioned above, only
mio provide global support.
Let us keep the default dataset,
3ob, because it is the newest and one of the most general datasets.
Now, we are going to take a look at the
There are certainly a lot of choices available. On the left side of the dialog, there are
options for controlling the Hamiltonian and the physical approximations being made. The
right-hand side of the dialog consists of parameters for controlling the geometry optimzation
procedure. The pre-defined default values are often reasonable. Thus, let us leave them
untouched by clicking
Cancel and leaving all control parameters unchanged.
If you do not intend to make any changes in a dialog, it is a good idea to close it with
Cancel button. It is a common habit to click
OK, but pressing the latter button
saves any changes that are made unintentionally and remained overlooked. Such accidental
mistakes might result in calculations with unusual behavior and surprising outcomes far
from your expectations. Therefore, we recommend using the
Cancel button unless you
actually want to make and save changes in the dialog.
OK to close the DFTB+ dialog to save your changes. In order to execute the
calculation, click on the
File menu and select
Run or use the accelerator
(⌘R on a Mac, ^R on Windows or Linux) to get the following dialog:
Project field is empty or not set, type default in it and then, add a useful title in
Title field. Briefly describe your goal and the details of your simulation workflow within
the large text area at the bottom of the dialog. Finally, click
OK to execute the calculation.
In the next two tutorials, we will demonstrate how to setup and work with Dashboard in order to monitor and manage the executed jobs.