Programming and setting intention is the same thing. This means that you attune the crystal to your own energy and needs. Do this by making an explicit invitation (through thought, voice or written) for an energy or goal to manifest in your life. This could be something short term for a mindset such as "Today I need to remain calm and focused." Or more goal oriented like "Today I will be energized to complete my gym routine." A long term goal would be along the lines of creating better health or finding a life partner or building a new career. It is always best if you can visualize the intention in terms of what you do WANT to have, rather than what you do NOT want to have happen. By setting an intention with your crystals you can connect to their energy to help you bring your heart's desire into everyday life.
One cardinal rule is to only use crystals for the highest good, even if you are not sure exactly what that might be. Under no circumstance, should you ever attempt to harm anyone or anything using crystals or any other method. This could only be injurious to yourself.
Here is how to get started: Hold a cleansed crystal in your hand or situate it in a special place, sit quietly and allow yourself to attune to its specific energy.
Be open to receive guidance about it. When you are relaxed and in harmony with the stone, state your intention simply and clearly and anchor the intention to the crystal. An example is “My intention is that this Amethyst will help bring a calm mind and help me sleep.” Be creative and speak from your heart. You will intuitively know when the programming is complete.