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The drive manufacturers says that the drive wont allow more than rated current to flow through the motor windings . Then where does this excess current flow?
Contrar to popular belief, nothing is "instant", everything takes time to happen. In this case, when putting a voltage across a coil (inductor), the current does not instantly starts, just starts to grow and it takes some (small) time to do just that: grow, e.g. increase in value. Inductors are represented as devices which "do not like the changes in current levels", or "want to keep the current constant". When current starts from zero, and voltage is applied, the device wants to maintain the previous current level (zero) so will just build up its flux first and then proportionally to that allow current to pass, so when first switched on, current starts from initial value and tends to grow faster at start, and slower marginal increase as time goes on. When switched off, the coil which deposited energy in the flux, even after switching off, it tends to maintain the previous level by releasing the energy in the flux first, again to maintain the prevuious current level.
The "excess" current that the drive does not let flowing through the coils ... does not flow anywhere. The driver switches the supply on and off across the coils, first switches it on, waits for the current and flux to build up in coils, then shuts it off untill level drops low enough to start again. This is "chopping" the coil current on and off. So in either periods, the current level either increases (rises) or decreases because its off (falling). The power by the classic formula p=i2r, is ok for a dc motor coz in dc motor current is quite constant and steady, but a little more complicated for a stepper, because the current never "stays" at a level, its always just fluctuating, e.g. chopped and there is just nothing constant.
Also, the current setting on the driver usually is the *peak* and not the average, and *if* such peak is effectively reached, and how fast its reached, depends alot on the parameters and conditions. Such as time constant L/R, initial & final voltages -chopping hysteresis- and lastly the time allowance to reach peak and the problem is this last one decreases at higher speed, potentially leading to a point when the motor would be in a situation to rotate faster than the current can grow in coil, hence lack of flux buildup in coils and lack of torque at speeds. Also, one representation or side i fing interesting is that partly two coils are "fighting" together and each other, in order to maintain the position in "between" them - thats this tech. Hence the losses dont need to match or be directly linked only to effective power in the rotor, or example when holding position compared to when moving. Also, the power consumed at a certain position can and will be different than the power consumed at the next position, because each position requires different current levels from each side, and the table with such positions and their current levels can usually be found in datasheet.
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... 0.33A which i can see directly from the power supply(the power supply will show how much current the circuit draws).
The (instant?) power consummed from the supply, if there is a psu which displays that, most likely is a simple circuit at a low frequency for reading. You should document how much you can trust that reading. Imo generally is better to not trust any kind of reading untill you undersand the tooling and exactly what, how and when it reads. Assuming your driver is chopping the current, its most likely doing that at a frequency higher than what the power supply can read. For a similar example an average multimeter will take readings 3 times per sec, hence can not read correctly a consumer which switches its levels at ~30khz. Similarly i would not trust what that power supply displays unless its documented that it can read arbitrary waves at least at about 60-90khz or more the better (which again that is probably not the case) - see sampling theorems like nyquist versus your documented range of chopping frequency. In other words, i suspect that what the psu display shows, even without ringing or transients, still has an arbitrary error, basically what it shows depends on where the level was when it decided to take a reading. And with a low sampling rate, there is no guarantee that it will read proper (more or less random - in lack of a better word than "random").
And as dc said above, after a certain speed the current wont rise fast enough in the coils, but at 48v suppli and coil of 1ohm (pointing to low inductance & low impedance), regarding torque at speeds you are probably already at the highest of what stepper motor can offer practically. In general and in comparison most ppls would use 12v and higher impedance thus lower torque as speeds. There are drivers at 76-86v and some at mains, but i'd be rather inclined to say that in case you need more speed and torque than you already have, you could also think about tech change, for example to servo or bldc.