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Since you are having pain exclusively on passing stools, most likely the pain is from the rectum and anal canal. The likely cause are a painful rectal tenesmus, haemorrhoids or fissure.
Since the pain and symptoms are of short duration you can attempt some self remedies. The main approach should be to increase high fibre foods. Here is a mayoclinic list of high fibre foods. http://www.mayoclinic.com/health/high-fiber-foods/NU00582
Try to have an intake of 40gm/day. Warm sitz bath can also help. Magnesium citrate might not be of much help in this scenario. Enteric coated peppermnit oil might give you some relief.
If the symptoms persists beyond 1-2 days you will require a physical examination and further tests. Watch for bleeding while passing stools, loose dark stools, sever abdominal pain. There are warning signs and in that case you should not hesitate to get medical help.
Hope this helps
Feel free to ask followups
Patient replied :
I don't think I explained the situation very well. The pain is near where my kidney is, not near the anus. I was doing ok until I ate last night, then the pain when trying to have a bm got worse again. Also, I was having some throw up backing up into my mouth for hours after I ate.
Sorry for the confusion and thank you for the clarification.
Well, it seems you have stomach bug. This could have caused some Inflammatory bowel like reaction causing pain while passing the stools. Most likely cause is a virus. So unless the symptoms persists for more than 3-4 days and /or unless the symptoms are severe you can observe.
Medication like Dicyclomine can provide good relief. This is a prescription medication. If the pain is severe get in touch with your Doctor. In case in the symptoms persists a bacterial infection has to be suspected and you may require antibiotics.
Kindey / ureteric stones can also present with same features. However pain while bowel movement is uncommon. Anyhow it is prudent to keep this diagnosis in mind if the pain persists.
Drink plenty of water. Avoid spicy and irritant foods. Avoid milk and milk products for a week. You cant take a probiotic capsule once a day. \
Hope this helps
Feel free to ask followups.