Requesting a license code

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1 Requesting a license code P. Stadelmann CIME-EPFL Station 12 CH-1015 Lausanne Switzerland March 13, 2012 Contents 1 Introduction Important note How to configure jems sub-system 4 3 Complete jre setting 6 4 How to send the license request Note for WiFi internet connection Requesting a license code and serial number 10 6 Remarks for Windows XP, Vista or Windows JEMS: installation instructions Mac OS-X: downloading from jems distribution website Mac OS-X: installing from USB key Windows: downloading from jems distribution website Windows: installation instructions - USB key Configuring jems 16 9 JEMS: preferences Debug tab Display tab: powder lines drawing Imaging tab Mail tab

2 9.5 Microscope tab Miscellany tab Save As tab VM memory tab Web help tab: addresses of local and remote help files Save preferences Folder /jems Opening a crystal file Opening.txt crystal structure Importing a.cif crystal structure CIF dataset selector dialogue Checking the.cif structure Checking the space-group Space-group dialogue Unconventional space groups: RPS code dialogue Selecting a crystal structure: File Select Select crystal dialog

3 1 Introduction Follow the following procedure to request a jems license code and serial number on Mac OS-X or Windows (Linux): 1. Verify that the jems sub-system has been properly initialized. 2. Complete jre setting. 3. Send the license request. 1.1 Important note After unzipping jems distribution zipped file, do not move it in a folder that contains the string jems (in capital or small characters) since the word jems designs the root folder of the whole jems documents tree. Usually under Windows the whole distribution is moved to Program files or Applications. 3

2 How to configure jems e-mail sub-system The jems application is found in folder /jemsmacosx/jemsmac/jems/buil (Fig. 1). It must stay there! Only drag the icon into the Dock.

4 2 How to configure jems sub-system The jems application is found in folder /jemsmacosx/jemsmac/jems/buil (Fig. 1). It must stay there! Only drag the icon into the Dock. Figure 1: The jems application. Start jems. Use menu item Preferences of menu Parameters to setup jems subsystem. Select tab Mail (Fig. 3) to enter the SMTP server address (Small Message Transfer Protocol) of your institution (Fig. 2) and your address. Figure 2: Accessing jems Preferences. Cross the Save checkbox to register these information and exit the Preferences dialogue. 4

5 Figure 3: Mail tab of Preferences dialogue. 5

6 3 Complete jre setting jems sub-system requires that 3 java archives be stored folder /System/Library/Java/Extensions (Fig. 4): 1. activation.jar 2. mail.jar 3. mailapi.jar These archives are not part of Mac OS-X and consequently are not, by default, placed in /System/Library/Java/Extensions. You will find them in jems distribution /jemsmacosx/jemsmac/jar as shown in Fig. 4. On Mac OS-X 10.4 or later, java3d is installed by default, do not replace the default java3d archives (j3d...) but only copy these three archives (activation.jar, mail.jar and mailapi.jar) into /System/Library/Java/Extensions (Fig. 5). The other java archives are for Mac OS-X 10.3.x only. The copy requires administrator rights. Figure 4: java archives placed in jemsmacosx/jemsmac/jar. Using Mac OS-X 10.4.x or later only activation.jar, mail.jar or mailapi.jar must be copied into /System/Library/Java/Extensions. 6

Activate menu item License of menu Help as show in Fig. 6.

7 Figure 5: /System/Library/Java/Extensions contains java archives for jai (java advanced imaging), java3d, mail, etc. 4 How to send the license request Finally, restart jems and request the license code and serial number. Activate menu item License of menu Help as show in Fig. 6. Figure 6: Requesting a license code using menu item License of menu Help. The License dialogue contains 3 tabs (Fig. 7): 1. License displaying the Host, Serial and License. 2. Request to send the license request. 7

3. Version displaying jems version. The Host text field shows the host name of the PC and the License one the license code. These strings are case sensitive.

8 3. Version displaying jems version. The Host text field shows the host name of the PC and the License one the license code. These strings are case sensitive. The host name is obtained either from the host name of the PC or its MAC (machine identification) and can t be modified. The license code is generated from the Host and the Serial number strings. The Serial number is supplied with the license code. The license code is obtained as described in the next section. Figure 7: The 3 tabs of the License dialogue. 4.1 Note for WiFi internet connection WiFi internet connection using DHCP attributes a dynamic hostname to the PC. Since jems license code is based on its static hostname, it is necessary, when both internet and jems need to run simultaneously, to stop WiFi, start jems and then restart WiFi. This is also necessary when requesting the license code: 1. Stop WiFi. 2. Start jems, fill the request license form. 3. Start WiFi. 8

9 4. Send the form (either directly from jems when allowed by the firewall, or copy/paste the form in your regular mail program). 9

10 5 Requesting a license code and serial number Select the Request tab and push the Request button. The dialogue shown in Fig. 8 should appear. When it does not, verify that the activation.jar, mail.jar and mailapi.jar are in /System/Library/Java/Extensions. In the very unlikely case that after verifying the presence of these 3 archives in /System/Library/Java/Extensions and restarting jems, this dialog still doesn t appear, you can grab the content of the license dialog (Fig. 7) and send it together with the information shown in Fig. 8, i.e. name, first name,...). Take care that the hostname string is case sensitive! In the Mail::request license dialogue, fill in the Name, First name, etc. text fields and push the Send button. The message shown in Fig. 9 must be displayed. When not, you might be behind a firewall. In such a case copy/paste the dialogue content in your regular program. 10

11 Figure 8: The dialogue requesting the jems code. Figure 9: The license request has been successfully sent. 11

12 6 Remarks for Windows XP, Vista or Windows 7 The procedure to install jems on Windows XP, Vista or Windows 7 is pretty much the same than on Mac OS-X when the fully configured.zip file is downloaded and unzipped. Fig. 10 shows the main jems folder called (jemsvista). This folder contains a fully configured java runtime environment (jre) in folder jre. The folder javavm files provides java runtime.jar files necessary to setup a different jre (this usually should not be done since the default jemsvista/jre is complete). Fig. 11 shows the content of the folder where the necessary java3d, jai and mail archives are found. jems relies on the folder structure defined by default. You should not modify or change it, the only necessary change is to make the whole folder structure read/write by every user. On Windows jems can be started either using the small batch file jems.bat or the executable jems.exe. You can than move the whole folder to /Program Files or any other folder. Create shortcuts to either jems.bat or jems.exe. Figure 10: jems main folder for Windows XP, Vista or Windows 7. 12

13 Figure 11: The license request has been successfully sent. 13

14 7 JEMS: installation instructions 7.1 Mac OS-X: downloading from jems distribution website At present jems distribution is available from website: u2010.htm When using Mac OS-X 10.5.x or later, proceed as follow: 1. Download jemsmactiger.pkg.zip 2. unzip it (when not done automatically) 3. Install the package (requires administrator rights) 4. Look for directory jems/build and drag the jems icon to the task bar 7.2 Mac OS-X: installing from USB key When using Mac OS-X 10.5.x or later, proceed as follow: 1. Either: copy file MacOSX/jemsMacTiger.pkg.zip unzip it (when not done automatically) 2. Or: copy file MacOSX/jemsMacTiger.pkg 3. Install the package jemsmactiger.pkg (requires administrator rights) 4. Look for directory jemsmac/jems/build and drag the jems icon to the task bar 14

15 7.3 Windows: downloading from jems distribution website u2010.htm For Windows XP, Vista or Windows 7 proceed as follow: 1. Download jemsvistaxp25may2010.zip 2. unzip it 3. Move the jemsvista folder to /Program Files (requires administrator rights) 4. Change the whole folder tree permissions to read/write (folder properties) 5. Create a shortcut to either jems.exe or jems.bat 6. Move the shortcut to the desktop or taskbar or desktop. 7. Change the icon (optional). 7.4 Windows: installation instructions - USB key For Windows XP, Vista or Windows 7 proceed as follow: 1. Copy file Windows/jemsVistaXP25May2010.zip 2. unzip it 3. Move the jemsvista folder to /Program Files (requires administrator rights) 4. Change the whole folder tree permissions to read/write (folder properties) 5. Create a shortcut to either jems.exe or jems.bat 6. Move the shortcut to the desktop or taskbar. 7. Change the icon (optional). 15

8 Configuring jems The Preferences dialogue allows to configure jems. It is activated as shown in Fig. 12. Detailled instructions are provided in the following paragraphs.

16 8 Configuring jems The Preferences dialogue allows to configure jems. It is activated as shown in Fig. 12. Detailled instructions are provided in the following paragraphs. Figure 12: Configuring jems: menu Parameters Preferrences 9 JEMS: preferences The dialogue selecting user s preferences is show in Fig. 13. The preferences are organized in several tabs: 1. Debug: debugging options, number cores (cpu). 16

17 Figure 13: Dialogue for selecting user preferences. 17

18 2. Display: display options (3-D models and (hkl) powder lines). 3. Imaging: size of graphics areas, maximum size of images, java 3-D, holography and site occupancy. 4. Mail: SMTP address, user address. 5. Microscope: default microscope. 6. Miscellany: default crystal. 7. Save As: format of saved images and drawings. 8. VM memory: minimum and maximum memory allocated to java VM. 9. Web help: addresses of help files. The tabs are shown in the Figures 14-22: 18

19 9.1 Debug tab 1 2 Figure 14: Debug tab allows to display in the console details of most calculations: : debug (1) & cores number (2). 19

20 9.2 Display tab: powder lines drawing 1 Figure 15: Display tab sets graphical options (do not set Show hkl powder lines (1) when structure is large). 20

21 9.3 Imaging tab Figure 16: Imaging tab sets imaging options and allows java 3-D: size of GUI panels (1), images (2) & java 3-D (3) 21

22 9.4 Mail tab 1 2 Figure 17: Mail tab defines SMT and addresses: SMT (1), address & error reporting (2). 22

23 9.5 Microscope tab 1 Figure 18: Microscope tab defines default microscope (1). 23

24 9.6 Miscellany tab 1 Figure 19: Miscellany tab defines default crystal (1). 24

25 9.7 Save As tab 1 Figure 20: Save As tab defines the image format (1). 25

9.8 VM memory tab 1 2 Figure 21: VM memory tab defines how much memory must be allocated to java VM: min (1) & max (2). Make sure that the minimum is not larger than one half the RAM size.

26 9.8 VM memory tab 1 2 Figure 21: VM memory tab defines how much memory must be allocated to java VM: min (1) & max (2). Make sure that the minimum is not larger than one half the RAM size. A very slow jems startup generally means that the minimum RAM memory allocated is larger than the available physical RAM (memory is allocated on the hard disk). When jems does start after several minutes, it is necessary to edit the jre configuration files (Windows: jems.lax or jems.bat, Mac OS-X: info.plist) and to reset the VMOptions parameters to something like -J-Xms512M -J-Xmx1024M -J-Xss4M for Windows or -Xms512M -Xmx1024M -Xss4M for Mac OS-X). 1. -J-Xms512M: initial size RAM allocated for java VM. 2. -J-Xmx1024M: maximum size RAM allocated for java VM. 3. -J-Xss4M: maximum stack size. When only 1 GB RAM is available set these parameters to: 26

27 1. -J-Xms256M: initial size RAM allocated for java VM. 2. -J-Xmx512M: maximum size RAM allocated for java VM. 3. -J-Xss2M: maximum stack size. 27

28 9.9 Web help tab: addresses of local and remote help files Figure 22: Web help tab defines the http address of help files. You can develop your own web site of help files. 28

29 9.10 Save preferences 1 Figure 23: Before leaving the Preferences dialogue, save your preferences. A file jemspreferences.txt is created in your home directory in folder /jems. 29

30 9.11 Folder /jems The folder /jems of your home directory contains: 1. jemspreferences.txt, your preferences. 2. jemslicense.txt, a copy of the license code. 3. jemsmicroscopes.txt, the microscopes parameters. These files are automatically created by jems and should not be edited. 30

10 Opening a crystal file 3 kinds kinds of crystal files 1. jems.txt files (default). Many are found in folders jemsdata/cubic, jemsdata/hexagonal... 2. ICSD or AMS.cif files. 3. Selectable crystal structures.

31 10 Opening a crystal file 3 kinds kinds of crystal files 1. jems.txt files (default). Many are found in folders jemsdata/cubic, jemsdata/hexagonal ICSD or AMS.cif files. 3. Selectable crystal structures Opening.txt crystal structure Figure 24: File Open. Naturally a particular crystal structure is usually not found in the jems set of crystal structures. You have to look for it either in the ICSD or AMS data bases or to define it using published data Importing a.cif crystal structure A.cif file can contains up to 100 different crystal structures. A particular one can be selected using the CIF dataset selector dialogue. 31

32 Figure 25: Selecting a crystal file. Figure 26: File Import. 32

33 Figure 27: Selecting a.cif file. 33

10.3 CIF dataset selector dialogue 1 2 1 Figure 28: Selecting a.

34 10.3 CIF dataset selector dialogue Figure 28: Selecting a.cif crystal structure, (1) crystal selection & (2) projected structure. 34

35 10.4 Checking the.cif structure It is necessary to check the.cif structure since it may happen that its space-group description is non-standard. By default the.cif structure can t be saved (Fig. 29). The jems console (Fig. 30) displays some of the properties of the.cif file. Locate the space-group description and verify that it is recognized by jems. 1 Figure 29: The space-group must be confirmed before saving the crystal structure as a.txt jems cystal structure. The File Save or Save icon (1) are unavailable. 35

36 1 Figure 30: The jems console displays the crystal system and space-group read from the.cif structure. 36

37 10.5 Checking the space-group 1 Figure 31: Open the space-group dialogue using either Crystal System Space-group or the Space-group icon (1). 37

38 10.6 Space-group dialogue Figure 32: Select the proper crystal system and the space-group (even when it is already selected). This will make the File Save or Save icon (1) available to save the.cif structure as a.txt one. 38

39 10.7 Unconventional space groups: RPS code dialogue Figure 33: For unconventional space-groups use the RPS code dialogue to define the symmetry operations. 39

40 10.8 Selecting a crystal structure: File Select Figure 34: Selecting a crystal structure among a set 42 predefined ones. 40

41 10.9 Select crystal dialog Figure 35: The 42 defined crystals are grouped in 7 crystal systems. 41

TEM image simulation and analysis using JEMS

TEM image simulation and analysis using JEMS P. Stadelmann CIME-EPFL Bât. MX-C 139, Station 12 CH-1015 Lausanne Switzerland Pierre.Stadelmann@epfl.ch 29 juillet 2010 What is JEMS? Provide a set of tools