This tutorial takes you step-by-step through creating, configuring and running a simulation, and then viewing its results.
Note that this tutorial requires an existing NanoFile with some molecular content in your workspace. See the Nanodevice Design Tutorial if you need to create a NanoFile.
The Simulation Manager View has a button to create new simulations.
If it is not already visible in the Analysis Perspective, open it using
the application menu bar:
Window > Show View > Simulation Manager
An example Simulation Manager View showing toolbar buttons and two completed simulations
The New Simulation Wizard is used to create all new simulations within nanoXplorer IDE. To open it, press the "New Simulation" () button on the Simulation Manager View toolbar.
Each type of simulation will present its own pages for configuration
in the New Simulation Wizard. Assuming you selected the "nanoXplorer
Geometry Optimization" simulation, press "Next" to advance to the
geometry optimization configuration pages. Configure the simulation as
follows:
Select the atomic system you wish to simulate (either from the current workspace or from a file):
Go to the next page.
Select an energy (and energy gradient) calculator. Choose the MM3 parameterized force field for this tutorial:
Go to the next page.
Configure the optimization algorithm's search parameters (using the default parameters is fine):
Change the name of the simulation, if desired. To run the
simulation, press the "Finish" button on the New Simulation Wizard. If
you don't want the simulation to run right away deselect the associated
check box first.
Open the Simulation View for the simulation to view its results and
configuration information by pressing the Open Simulation Information
button () on the Simulation Manager toolbar.
Example Simulation View showing optimized geometry result
Simulations approximate the behavior of real systems and are often
used during the design process to explore how different design
decisions affect performance and functionality.
nanoXplorer IDE provides an extensible simulation framework for
analyzing nanoscale systems, supporting nanoengineering and exploring
nanoscale science. This extensible framework allows anyone to add their
own simulations to the powerful nanoXplorer Integrated Development
Environment (IDE).
nanoXplorer IDE provides centralized management of all simulations
created and launched by the application. The Simulation Manager tracks
the progress of all running simulations and through the Simulation
Manager View presents this information, as well as various simulation
controls, to the user.
The Analysis Perspective contains a default set of views useful for performing nanoscale analysis and simulation.
There are two ways to open the Analysis Perspective. The fastest way
is to use the perspective menu located toward the upper right hand
corner of the workspace. Alternatively, select Analysis from the Open Perspective menu item under the application's Window menu.
Open the Simulation Manager View, if necessary. (Window > Show View > Simulation Manager)
Double-click on a completed simulation in the Simulation Manager; this
will launch a Simulation View for the selected simulation. If there are
no simulations listed in the Simulation Manager, see Creating a new simulation.
Note that if you double-click on a specific result icon for the
simulation in the Simulation Manager, that result will be displayed in
the Simulation View once it is open.
The Simulation View
includes tabs for simulation results and simulation configuration
information. The results tab has a pull down menu containing all of the
available results for the associated simulation. Selecting a specific
result from the menu will cause that result to be displayed (the
specific method of display depends upon the result type).
nanoXplorer IDE provides centralized management of all simulations
created and launched by the application. The Simulation Manager tracks
the progress of all running simulations and through the Simulation
Manager View presents this information, as well as various simulation
controls, to the user.
Open the Analysis Perspective, if necessary.
Open the Simulation Manager View, if necessary. (Window > Show View > Simulation Manager)
Select a simulation by clicking on its row in the Simulation Manager.
Press
a toolbar button to create a new simulation, open the Simulation View
for the selected simulation, or start, pause, stop or delete the
selected simulation. Buttons for commands that are not available for
the selected simulation will be disabled.
A Simulation View can also be opened by double-clicking a simulation row.
Click on a column header to sort the simulations by that column's information.
Geometry optimization is the process of finding the configuration of
an atomic system that has a minimum amount of energy given some method
of calculating the energy of the system and its gradient.
Geometry optimization is typically used to find local
energy minimums, meaning that instead of all possible configurations of
the atomic system being analyzed only configurations reasonably close
to the initial configuration of the atomic system are considered.
Therefore if the initial configuration is not close to the actual
configuration at global minimum energy then the optimized geometry may
not correspond to the global energy minimum.
Configuration
Configuring the geometry optimization simulation requires selecting an atomic system, choosing the energy calculator and setting the parameters for a particular optimization algorithm.
Results
The main result of this simulation is an optimized geometry.
The New Simulation Wizard is used to create a new simulation and can
be launched from the Simulation Manager View. Because nanoXplorer IDE
allows available simulations to be extended the wizard simply
determines which simulation is desired and then turns control over to
the selected simulation, which provides any additional wizard pages
that are necessary for configuration.
Select Simulation Wizard Page
Select the simulation by name, or if available, by specific output types.
The wizard page for selecting a particular simulation
Atomic System Input Wizard Page
Once a simulation has been chosen, the wizard pages
that follow will depend on which simulation was selected. However, it
is very common that the simulation will require the input of an atomic
system. The following wizard page allows user selection of atomic
systems from the workspace or file. Note that the NanoFiles will be
those currently saved on disk in the workspace; save any NanoFiles in
the process of being edited before attempting to run a simulation on
them.
The wizard page for selecting an atomic system for simulation input
The simulation needs to calculate the energy and the energy gradient
of the atomic system in various configurations in order to converge on
an optimized geometry. There are a number of methods to calculate the
energy and energy gradient and the Geometry Optimization Simulation
lets you choose which one you would like to use.
A parameterized force field for use in a molecular mechanics
approach is the default calculator. Choose the desired force field from
the drop down menu.
If other calculators have been registered with nanoXplorer IDE they will be available under the "Other" category.
Select energy and energy gradient calculators using this configuration wizard page
Energy minimization is the process of finding the configuration of
an atomic system that has a minimum amount of energy given some method
of calculating the energy of the system and its gradient.
Energy minimization is typically used to find local
energy minimums, meaning that instead of all possible configurations of
the atomic system being analyzed only configurations reasonably close
to the initial configuration of the atomic system are considered.
Therefore if the initial configuration is not close to the actual
configuration at global minimum energy then the optimized geometry may
not correspond to the global energy minimum.
Configuration
Configuring the energy minimization simulation requires selecting an atomic system, setting the parameters for the force field and optimization algorithms to be used as well as line search and other simulation inputs.
Results
The main result of this simulation is an optimized atomic system, but log results may also be available/
There are a number of options for configuring an Open Babel energy minimization simulation.
Select a force field, optimization algorithm and other parameters
using this configuration wizard page
Force Field
The force field approximates the forces between atoms
in nature, enabling high efficiency calculations and therefore the
ability to simulate a large atomic system in a reasonable time period.
The force fields available include Ghemical and UFF. Both are all-atom force fields, but the Ghemical force field is geared more towards organic molecules while UFF is more generalized.
Optimization algorithm
The algorithm used to iterate over energy calculations
will determine the speed and likelihood of convergence. Conjugate
gradient typically converges more often than steepest descent, however
stepepst descent, when it works, can be significantly faster.
LIne search
Choose between simple and newtonian line search. If one fails to converge, try the other.
Maximum number of steps
The simulation will be limited to the specified number of steps.
Convergence criteria
A smaller number for the convergence criteria will
force more iterations and the result will be closer to the minimum
possible energy.
Update frequency for non-bonded pairs
The number of steps between updated calculations of the
energies between non-bonded pairs, which generally require less
fidelity than bonded pairs.
Cut-off distances
Cut-off distances can be specied as an approximation of
the distance at which calculating either the van der Waals or
electrostatic forces are no longer significant in order to speed up
calculation without any significant loss of accuracy.
Add hydrogen atoms
If checked, the simulation will attempt to add any hydrogens it thinks are missing from the atomic system.
The optimized atomic system is the configuration of nucleus
positions that minimized energy during the simulation. This may or may
not be a global minimum. There is a toolbar button for exporting the
optimized atomic system.
An example simulation result displayed in the Simulation View results tab
The Simulation Manager View enables control of all simulations
created by nanoXplorer IDE, whether completed, in process or waiting to
run. It also allows creation of new simulations.
. The Simulation Manager View showing two completed simulations
Table Columns
The simulations can be sorted by any of the columns by
clicking on the header for that column either once or twice (for
descending or ascending, respectively).
Column
Description
Simulation
the name of the simulation
Status
the
status of the simulation (for example, done, paused, aborted, error,
waiting), including a progress bar whose color and length visually
indicate the status
Results
icons
representing the available results of the simulation; some results may
be available before the simulation has completed; double-clicking on a
result icon will launch the Simulation View for the associated
simulation and display the result
Elapsed
the
processing time elapsed since the start of the simulation or the total
elpapsed processing time if the simulation has completed
Created
the date and time the simulation was created
Toolbar
Create a new simulation
Launches the New Simulation Wizard.
View simulation information
Opens the Simulation View for the selected simulation.
Play
Starts or resumes a paused simulation.
Pause
Pauses a simulation. Some simulations may not support this functionality.
Stop
Stops a simulation. A stopped simulation cannot be restarted.
Delete
Removes a simulation from the Simulation Manager View. All associated data will also be deleted.
Menus
Restore previous simulation list
nanoXplorer IDE keeps a backup copy of the simulation
list to facilitate recovery from file corruption or accidental
deletion. Select this menu item to restore the previous list.
The Simulation View provides the results and configuration information for a single simulation.
A Simulation View showing an optimized atomic system as one result
of the simulation named "Geometry Optimization - 3"
Results
The results tab provides a drop down menu containing
all of the available results for the associated simulation. Selecting a
specific result will display that result in the panel. Each result type
will have its own display and functionality.
Configuration
Along with the results it is often useful to go back
and see how the simulation was configured. The configuration tab
displays information about the simulation
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) button on the Simulation Manager View toolbar.
) on the Simulation Manager toolbar. 
) on the Simulation Manager toolbar, which will launch the New Simulation Wizard.
