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PHI 5600: Bake-out Procedure

The RBD instructions for the bake-out procedure of the PHI 5600 can be found here, these notes are a summary of those notes with some of our own details.


 Maintaining UHV conditions requires the heating of the system to, say, 200° C for several hours (typically 12 to 20 hours) to remove water and other gases which adsorb on the surfaces of the chamber.  The bake-out is performed in the PHI 5600 using built-in heaters under the magnets in the ion pumps. These heaters increase the system's temperature to about 200 degrees C, de-adsorbed  gasses will be expelled during the bake-out by the vacuum pumps. 


The system must be prepared for bake-out:

  1. Before starting a bake-out, it is preferred that the samples are removed before the bake-out, some sample materials have high vapor pressure should not be allowed in the UHV chamber during bake-out.  See apenddix at the end for a list of examples.
  2. Before starting a bake-out the system should be pumped down with the ion pumps into the low 10-7 Torr range or better.  [The only exception is when you are baking out new ion pumps into the turbo pump.]  A heat-insulating blanket is put over the vacuum chamber to trap the heat generated by the heaters.  
  3. Close all the valves on the AVC are closed
  4. Turn off the turbo pump.
  5. Turn off the card rack power
  6. Turn off the ion gun control, X-ray source control, and any other controls that may have filament or high voltage. The only units that should still have power are the Boostivac ion pump control, AVC (auto valve control) and the DGC III ion gauge control.
  7. Remove all of the cables to all optics units on the vacuum chamber, with the exception of the ion gauge control cable, which is bake-able and remains connected at all times. The cables that should be disconnected include those for the X-ray source, ion gun, neutralizer, and electron gun.
  8. Remove the motors on the stage.
  9. Drain the water out of the standard X-ray source by first disconnecting the IN water line from the source but keeping the OUT water line connected. Then, remove the IN water coupler. Gravity will draw the water out of the X-ray source in about 20 seconds.  Once the water is drained out of the source, disconnect the OUT water line and reconnect the IN water coupler to the source.
  10. Remove the water cooling lines and HV connection on the standard source and the second half of the shroud.  Cover the water swag lock fittings with aluminum foil.
  11. Set the shield aperture of the monochromator to mid-range. This will help prevent any coating during bake-out to occur on the monochromator crystals and will also help reduce to direct radiant heat on the surface of the crystals.
  12. Remove the monochromator cover, Teflon block, base, and seals. The O-ring seals on the mono anode need to be removed or they will dry out during the bake-out, which in turn may cause a variety of problems including water leakage and leakage current on the mono X-ray source. Removing the O-rings before bake-out and coating them with some vacuum grease will prevent them from drying out and causing these leaks.
  13. Remove the microscope by unscrewing the collar and lifting it out of the base. Do not move or remove the base as that will make it much more difficult to realign the microscope to the focal point of the SCA after the bake-out.
  14. While wearing lab gloves, wipe the system down with some isopropanol (or any degreasing agent) to remove any oils or other contaminants; any oils from finger prints or hand prints left on the surface of the chamber may become permanently etched onto the chamber.
  15. Cover all of the viewports, exposed connectors and feedthrus with aluminum foil. This helps to even out the thermal conductivity during the heat-up and cool-down cycles.
  16. Remove the table tops that are near the vacuum chamber. On the 5600 the vacuum console is separate so the table tops on the vacuum console need to be completely removed.
  17. Pull up the table top interlock switches. These are designed to prevent the bake-out heaters from turning on unless the table tops have been removed.
  18. Put the blanket over the chamber; it is recommended that you wear a mask during this process. The blanket may be one piece or two or more pieces that are connected with Velcro. I recommend gloves and a lab coat if possible as the older blankets are aluminized fiberglass and the fibers itch. Also, if are not able to wear a mask, try not to breathe the fibers in as you put the blankets on.
  19. The V1 gate valve and the monochromator crystals should be outside the blanket. If there are any gaps in the blankets, use aluminum foil to cover them.
  20. Use a floor fan set on low to provide cooling to the V1 gate valve. The vacuum chamber will reach temperatures as high as 200 degrees Celsius, but the gate valve can only be baked to 150 degrees Celsius.
  21. Verify that set point 4 on the DGC III ion gauge control is set to 3 X 10-6 Torr. If you are baking the system into the turbo pump (the ion pumps are not on), then set this value to 4 X 10-4 Torr. If baking into the turbo pump you will be pumping on the chamber during the bake-out.
  22. Make sure the Boostivac ion pump control is set to the run position.   That makes sure that the Boostivac will turn off if the outgassing of the system gets higher than the low 10-5 Torr range.
  23. Set the bake-out timer to 12 to 20 hours and press the bake-out power button. The time depends on the amount of water vapor in the chamber, which in turn is directly proportional to how long the vacuum chamber has been up to air.
  24. After the bake-out is complete, let the system cool down to room temperature. Then remove the bake-out blankets, replace the table tops and reconnect the cables to the system.  The x-ray source, ion gun, electron gun, neutralizer and electron multiplier all need to be outgassed. Refer to the manual for each of those components for the out gas procedure.

APPENDIX: List of unbakeable materials 

  • Majority of organic compounds such as plastics, other than PTFE and PEEK, glues (special glues for high vacuum must be used).
  • Some steels can lead to oxidization of carbon which greatly increases adsorption area.  The steels that can be safely studies are stainless steel, non-leaded and low-sulfur austenitic grades (such as 304 and 316), steels with at least 18% chromium and 8% nickel, low-carbon grades (such as 304L and 316L), grades with additives such as niobium and molybdenum to reduce the formation of chromium carbide (which provides no corrosion resistance), 316L (low carbon), and 316LN (low carbon with nitrogen), chromium carbide precipitation at the grain boundaries can render a stainless steel less resistant to oxidation.
  • Lead: Soldering is performed using lead-free solder.
  • Indium: Indium is sometimes used as a deformable gasket material for vacuum seals, especially in cryogenic apparatus, but its low melting point prevents use in baked systems.
  • Zinc, cadmium: High vapor pressures during system bake-out.
  • Cleaning is very important for UHV. Common cleaning procedures include degreasing with detergents, organic solvents, or chlorinated hydrocarbons. Electropolishing reduces the surface area from which adsorbed gases can be emitted. Etching of stainless steel using hydrofluoric and nitric acid forms a chromium rich surface, followed by a nitric acid passivation step, which forms a chromium oxide rich surface which retards the diffusion of hydrogen into the chamber.
  • Screws: Threads have a high surface area and tend to "trap" gases, and therefore, are avoided. 
  • Blind holes shoule be avoided, due to the trapped gas at the base of the screw and slow venting through the threads; this is known as a "virtual leak". 
  • Welding: Processes such as gas metal arc welding and shielded metal arc welding cannot be used, due to the deposition of impure material and potential introduction of voids or porosity. Gas tungsten arc welding (with an appropriate heat profile and properly selected filler material) is necessary. Other clean processes, such as electron beam welding or laser beam welding, are also acceptable; however, those that involve potential slag inclusions (such as submerged arc welding and flux core arc welding) are obviously not. To avoid trapping gas or high vapor pressure molecules, welds must fully penetrate the joint or be made from the interior surface.

CONTACT: Jorge A. López (

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