GEM Read_me
Date: 30 June 2015

This read_me file contains information for
-	GEM 1.1.1 shell     version 1.1.1 (June 2015)
-	GEM.mdb   database  version 1 (June 2015)
-	GEM projects folder

Help

If you encounter installation problems or problems using GEM please send an e-mail to:  
gem@pesticidemodels.eu or gem.support@wur.nl  

More information about GEM 1.1.1 is available at the GEM website: http://www.gem.pesticidemodels.eu

Installation

GEM 1.1.1 requires also the installation of SPIN (Substance Plug In). SPIN is used to manage the substance database. SPIN is available on the pesticides website http://www.pesticidemodels.eu.

Run setup_gem.exe to install the GEM 1.1.1 application. Do NOT double click the executable, but right-click on the file and select ‘Run as administrator’ (Figure 1).

Figure 1: Instruction on how to start up the installation of the GEM 1.1.1 application.

By default GEM is installed on the C:\Program Files\PesticideModels\GEM. It is allowed to change these settings during the installation.

The GEM Project folder is by default installed on the user’s personal folder. The exact location differs per user and depends on its computer settings. It is allowed to change this during the installation. If the default folder is a network drive we strongly advise to change this to a folder on a local drive to guarantee a proper working of GEM 1.1.1.

Tips & Tricks

What to do in case of the error message: 
‘cannot create assessment directory D:\PesticideModels\GEM\projects\x\x’?

This error message generally occurs in case you want to run an assessment and corresponding input of output files of one of the models is opened in a text editor or other text editor. Therefore, before performing model simulations of an assessment make sure that you close all input and output files of this assessment. Also make sure that in Microsoft Windows Explorer you have not selected the assessment folder or any subfolder.

If you for instance installed the GEM Project folder on D:\pesticideModels\GEM and the project ID is 2 and the assessment is 5, then you should not select the folder D:\pesticideModels\GEM\projects\2\5 or any subfolder.

Hard and software requirements

Operating systems:
GEM 1.1.1 has been tested on Windows Vista, Windows 7 and Windows 8.1.  

Access rights:
To install GEM 1.1.1 it is necessary to have administrator rights.

Preinstalled software:
SPIN version 2.2.

Hard disk memory:
GEM 1.1.1 requires 70 Mb for installation of the application (including the GEM database)

Display:
Monitor with at least 1024x768, at 256 colours.
Use as display setting, Font size: Small Fonts.

Processor:
The faster the better.

Known bugs

1.	In case a simulation is performed for 2 or more compounds (parent and one or more metabolites) TOXWSA may crash with the following error message in the runid.err output file: 

Positivity condition 5 (rdd >= 0)not fulfilled
At layer:   1 rdd is [negative value]
Take smaller time step [Max]TimStpSed for sediment layer

This happens most likely if one (or more) compounds has (have)a kom,sediment value of 1000 L/kg or higher and one (or more) of the other compounds has (have) a low kom,sediment value. For compounds with kom,sediment values of 1000 L/kg or higher a finer segmentation of the sediment layer (i.e. the FOCUShighKOC sediment segmentation, see Beltman et al., 2014)is automatically selected by GEM to get a converging numerical solution for the compound with the high kom,sediment value. However, this finer segmentation of the sediment causes stability problems for the other compound(s) with low kom,sediment values. 

We advise to perform the TOXSWA run with the standard segmentation for the sediment layer (see also Beltman et al., 2014), and NOT with the finer segmentation, that is automatically selected by GEM. A work around for this is available upon request.

W.H.J. Beltman, M.M.S. ter Horst, P.I. Adriaanse, A. de Jong & J. Deneer (2014). FOCUS_TOXSWA manual 4.4.2; User’s Guide version 4. Statutory Research Tasks Unit for Nature & the Environment (WOT Natuur & Milieu), WOt-technical report 14. 130 p.; 64 fig.; 7 tab.; 19 ref. 7 Annexes.

2.	In the TWA screen (Figure 2) up to 8 additional TWA’s can be entered by the user. The TWA will be calculated for a relevant period set by the user and shown in the ‘Browse exposure periods’ table. Once the user entered one or several TWA’s and leaves the TWA screen to open it later on again, the start and end date of the relevant period of the TWA selected in the ‘Browse exposure periods’ table (indicated by a red colour when selected) is shown in two ways: (1) in the table with the list of TWA’s entered by the user and (2) in the Edit exposure period box, at the lower half of the screen. The latter is incorrect. This is only a superficial fault. The information initially entered and shown in the ‘Browse exposure periods’ table will be transferred to the input file of the TOXSWA model.

Start and End date of the Relevant period do not match. The data given in ‘Browse exposure periods’ table is transferred to the input file of the TOXSWA model.

Figure 2 The TWA screen in GEM 1.1.1.