Your choices are
A: Clean cut cylinder
The portal causes material bonds to release wherever they are separated by the portal. However, the portal is one way, so it may treat matter passing through it as a series of single molecule wide sheets (As each layer of molecules passes through, it is no longer connected to the previous sheet). But because covalent bonds share electrons, diamonds and quartz and similar materials may be treated as a single object, allowing you to make "perfectly" round diamond rods. Metals, which are what most trains are made of, share a looser bond which may either be treated as a single material or as sheets, your choice as far as this portal goes.
B: It compresses the train into a viscous fluid where it touches the portal and ejects it as liquid hot jets of train through the other side.
So this option implies a lot of quantum super-positioning and stuff on a large scale, which is not yet really achievable with real life technology. Basically the principle is that any material that passes through becomes quantum entangled with itself.
- Gases are not connected, so the portal treats them as individual molecules whenever one passes through.
- Liquids are identified as a liquid, so the portal acts much like a gravity siphon, where the liquid will be drawn through the portal at a fixed rate depending on gravity changes between portal ends, pressure differences between portal ends, and surface tension of the liquid.
- Metallic Solids are classified by a kind of shared electron situation, where as when an electron shared by the entirety of the solid is passed through the portal, it treats all molecules associated with the electron as part of the transferred material. The entirety of the material will end up on the other side of the portal, I'll describe it more below.
- Covalent/Ionic Solids also pass through the portal in their entirety, but have a more eloquent way of doing it that doesn't involve turning into superheated goo.
Okay, so lets describe some interactions that you could have take place with your portal:
- You poke it with a graphite rod: The rod will sink into the portal as far as you push it, but be unable to be pulled out. The quantum wave function of your portal lets it sit there indefinitely, treating the bonds in the material as existing independently on either side of the portal. You can break the rod on either end with no problem and keep the piece you broke off on that side of the portal. If someone on the far side pushes they will be unable to move the rod, but if they pull it can pass through the portal. It's impossible to break the rod at the exact point where it is passing through the portal unless you drag the rod through the edge of the portal, which will sheer the rod off at that exact point. This works for any material with covalent bonds.
- I poke the portal with a graphite rod wider than the portal is: It treats the rod as a single object, and entangles the molecules that pass the portal. Then the molecules react to the quantum state of the molecules that are passing through the portal, and will reassemble themselves on the other side of the portal, in a kind of quantum teleportation that isn't actually teleportation, but the replacement of information encoded on one side of the portal with the information on the other side, which recreates the object exactly the same, but doesn't move the physical atoms. Point being you can transport slabs of marble easily, you just have to push it all the way through yourself.
- You poke it with a metal rod: the metal rod will be slowly sucked through the portal at whatever speed you originally touched the portal with. You can cut off a part of your rod in order to save it, but part of the rod touching the portal is unretrievable. Of course, this assumes that your portal is using the same amount of energy to transport objects as there is energy in those objects themselves and therefor not violating the second law of thermodynamics. So what happens if I don't have enough energy to transport the whole rod? Then the portal collapses and the rod will not go through. Unless you add more quantum shenanigans which define conservation of energy as an average, and by adding energy to a system (through teleportation) it simply decreases energy in other systems by manipulating probability. (Basically you can't make a perpetual motion machine out of a teleporter.)
- Finally, the fun one. You poke it with a metal rod wider than the portal: The portal treats the object as a whole, as opposed to a covalently bonded material that it treats as a series of interconnected molecules. So as the train passes through the portal, any material not directly inside the radius of the portal is converted into a wave function and collapsed back into the inside of the portal, because the portal views it as the same object as the metal already passing within the portal. This, unfortunately for the train, means that the molecules which originally took up a greater area than the portal, are now super compressed into the size of the portal. Now, compressing solids is very hard, so I couldn't get a hard estimate for the temperature of iron compressed to half its original size, but for the sake of simplicity lets just assume it won't convert the iron into some kind of exotic plasma. Instead, we give it a temperature of a couple thousand degrees. Actually, at this point the metal would vaporize into a gas from being too hot, but I'm guessing the high pressure would keep it in a liquid state. Again, it's really really hard to find information related to the compression of solids because it's really hard to do. Anyways, if you look at what happens to a pressurized liquid in a tube, (which the portal is basically an infinity narrow tube, in layman's terms) you can see that higher pressure equals higher speed. So what was originally a train driving through a portal, is now a liquid that has been under enormous pressure being shot out the other end at a high speed. Part of the liquid may return to gas as it passes through the portal and becomes free of the high pressure, which will cause a blast and a heatwave that will scour clean the ground on the other side of the portal before oxidizing into iron oxide and raining down as an extremely fine powder. The other part of the metal will reman liquid for a while before slowly hardening into a solid.
- What if we add more material? Well if you added a large enough amount of material all at once, you may be able to create a black hole. I don't know the calculations to calculate how compressed matter would have to be to do this, but it will not end well for the planet the black hole comes out on. if the black hole is small enough it will immediately radiate too much matter for it to maintain itself and will explode, again, not good for the planet.
Either way it's a very bad day for the conductor, and anyone on the wrong end of the portal.
And that's a moderately accurate portal that speculatively builds on actual quantum mechanics. Do not take this as like, a scientific study; this level of thought only goes as far as writing and not much farther. If you showed this to a quantum physicist they might stab you in the eye. But for anyone who doesn't study quantum mechanics in a institute of higher learning, this is passable, probably.