PhytoSim User Guide
Version 1.2

Contents

Chapter 1
Getting Started

Creating an account

The first time PhytoSim is started, you will be presented with the Create an Account page of the Log in dialog box. If you don't have a PhytoSim account already use following steps to create a new account:

1. Supply the requested account information: your first and last name, email address and a password. Your email address will be used as account name to log into PhytoSim. When providing a password, please use a strong password such that other people will not be able to access your PhytoSim account.
2. Press the Create Account button
3. A new account will be created (if one with the same email address does not already exist) and a validation email will be sent to the email address you provided.
4. Click the validation link in the validation email to activate your account.
5. You are now ready to log into PhytoSim.

A new account can also be created using Account > Create account... .

Logging in

Once you have created a PhytoSim account, use your email address and your PhytoSim password to log into the application. PhytoSim requires an active internet connection for authentication purposes. Only one instance of PhytoSim is allowed to run simultaneously for each account. Working offline is also possible but requires a USB copy protection dongle (sold separately by Phyto-IT). In offline mode it is not possible to install or update PhytoSim modules.

PhytoSim also allows to remember your password once you have logged in successfully. If this option is selected, PhytoSim will try to log in automatically the next time you start the application. PhytoSim will continue remembering the password until you manually log out (Account > Log out from the menu bar). All passwords are stored encrypted.

Your log in status is displayed between brackets on the module manager item of the left PhytoSim navigator.

Chapter 2
Main Window

The PhytoSim main window is divided into two parts: a navigator on the left and a display area on the right. At the top of the navigator, access to the module manager is provided. Below that, a list of installed modules is shown. Switching between modules can be achieved by clicking on the appropriate module from the module list. This causes the module area (lower part of the navigator and the right hand side of the application window) to display the module specific content.

Chapter 3
Menus

• File menu
• New: Clear the PhytoSim workspace, erasing all workspace data.
• Open: Open an existing PhytoSim workspace.
• Recent: Provides access to the most recently opened PhytoSim workspaces.
• Save: Save the current PhytoSim workspace.
• Save As: Save the current PhytoSim workspace under a different name.
• Preferences: Opens the preferences window for PhytoSim and any installed module that has preferences.
• Exit: Close the application.


• Account menu
• Log in: Log into your PhytoSim account.
• Log out: Log out of your PhytoSim account.
• Work offline: Switch from online to offline mode (USB copy protection dongle required).
• Create account: Create a new PhytoSim account.
• Change password: Change the password associated with your account.
• Forgot password: This allows you to enter a new password for your account. Your old password cannot be retrieved because it is not stored unencrypted.
• Dongle info: Lists the currently installed USB copy protection dongles.


• Help menu
• User guide: Opens the user guide window for PhytoSim and any installed module.
• Support: Request support for PhytoSim: bug reports, questions, feature requests.
• Check for updates: Checks to see if a newer version of PhytoSim is available.
• Reset PhytoSim: Clears the PhytoSim Core, Modules and Examples folders:
  • You will be logged out first.
  • All modules will need to be reinstalled.
  • Any purchased modules will NOT need to be repurchased.
  • The Workspaces folder will NOT be touched.
• About: Information about PhytoSim.

Chapter 4
Module Manager

PhytoSim by itself does not provide any functionality, this is entirely contained in modules that can be installed depending on the users' choice. As such, each user can customize the software according to his or her wishes (and budget). This allows all users to gradually increase the functionality and complexity of the software. PhytoSim can, as it were, grow with your modelling and simulation needs.

General

The module manager can be accessed from the navigator (first item) and is the central place to:

• Learn more about the available models.
• View the installation status of your modules.
• Buy or try new modules.
• Upgrade already installed modules.
• Diagnose problems related to the installed modules.

The upper part of the module manager shows a categorized list of all available modules. Each module has an icon, a name and also shows its version number (if installed). The module type and installation status can also be directly observed (see picture below).

The module manager toolbar provides access to several functions:

• Learn more: Go online to learn more about the selected module. Active internet connection required.
• Changelog: Get a list of changes, fixes and new features for the selected module. Especially useful when a module update is available and you want to find out what has changed.
• Module action: Depending on the installation status of the module five actions are possible:

Clicking on any of these actions will bring up the installation dialog. In case modules are going to purchased, you will also be able to enter your billing information.

Below the module list, information on the currently selected module is given:

• Name: The module name (and identifier).
• Description: A short description about the module. More information can be found online (click the 'Learn more' button in the toolbar).
• Price: The module price: in EUR, excluding VAT.
• Available version: The latest version of the module. Might differ from the installed version when an update is available.
• Dependencies: Modules that are needed for the selected module to work. Depending modules are highlighted in orange. Installing a module will also install all its depending modules.
• Status: Installation status of the selected module. Information about problems related to the module are also shown here.

Installation details

Clicking on one of the module action buttons in the toolbar brings up the Installation details dialog box. This dialog provides information on the modules that are going to be installed and on the installation progress. In case a paid module is selected, billing information can also be entered.

• Trial modules:
  • The time period for each trial is 30 days.
  • The trial period starts when the module is first installed.
  • Once a trial period is expired, the module will turn into a paid module.
  • A trial module can be purchased at all times during the trial period.
• Paid modules:
  • If a purchase is going to be made, your billing information has to be entered. All information is transferred securely.
  • For each purchased module, a purchase order is send to your accounts email address.
  • Each purchase order expires after 30 days. If your payment has not been received during this period, the module will be disabled temporarily.
  • Once we have received your payment, the invoice will be sent to your accounts email address.
  • During the payment period, the module will continue to function, unless you have had purchases that expired in the past. In that case, the module will continue to function once your payment has been received.
  • Each module purchase includes one year of free PhytoSim support (see below).
  • Purchasing a paid module will also purchase any depending paid or trial modules (ending the running trial periods for those modules).

Special modules

Support (PhytoSimSupport): This module provides support and updates for paid modules. One year of free support is included when purchasing a paid module. After this period you will be able to extend the support period by paying a yearly fee (499 EUR, excl. VAT). If you choose not to extend the support period, your modules will remain functional but will not be upgraded any more and you will not be able to receive support for your paid modules. After reactivating your support contract, all modules will be upgraded to their latest version.

Offline (PhytoSimOffline): This module allows offline usage of PhytoSim using a USB copy protection dongle. The module will be activated once you have received your USB copy protection dongle and the payment is made (99 EUR, excl. VAT). Note: Only Free, Beta and Paid modules (with paid invoice) will work offline. Note: Only one USB copy protection dongle can be purchased by each account. Note: Broken USB copy protection dongles will be replaced free of charge once the broken dongle has been returned to Phyto-IT. Caution: Lost USB copy protection dongles will NOT be replaced! If you want to purchase another dongle, you will need to repurchase all your paid modules.

Chapter 5
Workspaces

PhytoSim uses workspaces to save your work. Use File > New to clear the current workspace.

When a workspace is saved (File > Save or File > Save as), the state of all the currently installed modules is stored in the workspace file. It is not possible to save the state of only a few modules.

Opening a workspace (File > Open) loads the module states contained in that file into the currently installed modules (clearing all modules first). Any workspace module state that does not have its module installed is not loaded from the file.

Chapter 6
The PhytoSim Folder

Although PhytoSim allows you to save files, workspaces and load data from anywhere on your computer, it is recommended to keep your files organized within the PhytoSim folder. This folder will be automatically created when PhytoSim is installed and is located in the Documents folder of your account. All references to files within the PhytoSim folder are made relative to the PhytoSim folder. This approach allows you to easily exchange workspaces with other users, irrespectively of the location of their PhytoSim folder.

Upon installation, several subfolders are created within the PhytoSim folder:

• Core: PhytoSim system folder.
• Examples: Location of example workspaces, organized on a module basis.
• Modules: System folder that contains the PhytoSim modules, changelogs and icons.
• Workspaces: Preferred folder to save your workspaces and data files.

Depending on which modules are installed, other folders might appear in the PhytoSim folder. For example, the PhytoSim Modelling module creates a Library folder which will hold your model library.

Chapter 7
Preferences Window

PhytoSim preferences are managed from File > Preferences. The preferences window has a navigator on the left and a display area on the right. Preferences for the PhytoSim application can be managed using the PhytoSim entry at the top of the navigator. Model specific preferences can be accessed by clicking on the module name in the navigator or on the preferences icon in the module list of the PhytoSim navigator:

PhytoSim preferences

• General
• Automatically check for new versions of PhytoSim: If checked, this is done each time PhytoSim is started.
• PhytoSim folder
• Location of the PhytoSim folder: Select Choose to use another folder as your PhytoSim folder. A restart of PhytoSim is required before changes take effect.
• All modules need to be reinstalled.
• Nothing will need to be repurchased.
• You will need to move all files in your Workspaces and Library folders to the new folder.
• Multi-core
• Maximum number of processor cores: Select the number of processor cores a module can maximally use. This preferences is only applicable for modules which support parallel tasks (e.g. the Calibration module) and if your processor has multiple cores. If, for example, 2 out of 4 cores are selected, a suitable module will always try to schedule two tasks in parallel resulting in a processor load of 50%. Modules that are not suited for parallelization will always use one processor core, even if your processor has multiple cores available.

Chapter 8
User Guide

The user guide that you are reading right now (thanks for that by the way!) is accessible through Help > User guide or by pressing the F1 button. Pressing this button when a module is selected will take you directly to the user guide of that module. Once in the user guide window, you can switch between the different module user guides and the PhytoSim application user guide using the navigator on the left.

An online version of the latest user guide of PhytoSim and of each module is also available through the Phyto-IT website.

Chapter 9
Support

The support dialog (Help > Support) provides support for PhytoSim: bug reports, questions and feature requests.

• Bug report: Describe what caused the bug in the text field. If possible, try to describe the steps to reproduce the bug using one of the PhytoSim example files. You can also contact support@phyto-it.com if you want to email files.
• Question: For questions about the usage of PhytoSim.
• Feature request: Let us know about a feature you would like to see in the software. Every feature request will be investigated, but nothing can be guaranteed.

You will receive a confirmation email once you have submitted a support request. Any further communication about your support request will happen through email.

Chapter 10
Network Error Codes

1	The remote server refused the connection (the server is not accepting requests).
2	The remote server closed the connection prematurely, before the entire reply was received and processed.
3	The remote host name was not found (invalid hostname).
4	The connection to the remote server timed out.
5	The operation was canceled via calls to abort() or close() before it was finished.
6	The SSL/TLS handshake failed and the encrypted channel could not be established. The sslErrors() signal should have been emitted.
99	An unknown network-related error was detected.
101	The connection to the proxy server was refused (the proxy server is not accepting requests).
102	The proxy server closed the connection prematurely, before the entire reply was received and processed.
103	The proxy host name was not found (invalid proxy hostname).
104	The connection to the proxy timed out or the proxy did not reply in time to the request sent.
105	The proxy requires authentication in order to honor the request but did not accept any credentials offered (if any).
199	An unknown proxy-related error was detected.
299	An unknown error related to the remote content was detected.
201	The access to the remote content was denied (similar to HTTP error 401).
202	The operation requested on the remote content is not permitted.
203	The remote content was not found at the server (similar to HTTP error 404).
204	The remote server requires authentication to serve the content but the credentials provided were not accepted (if any).
205	The request needed to be sent again, but this failed for example because the upload data could not be read a second time.
301	The Network Access API cannot honor the request because the protocol is not known.
302	The requested operation is invalid for this protocol.
399	A breakdown in protocol was detected (parsing error, invalid or unexpected responses, etc.).