Inverted pendulum control woth stepper motor

Hello everyone!

I'm currently working on balancing an inverted pendulum with a Fuzzy controller and I use a stepper motor to drive the balancing cart. My problem arises from this part because I cannot think up a proper way to control the motor.

The fuzzy controller sends the calculated response to the Arduino Nano through USB and the program reads it fine (using the Serial.parseInt() function). So far I've been using the AccelStepper library and I got the acceleration part down, but positioning of the cart is still unsolved. I need the motor to rapidly change the direction and/or the acceleration if a new response value comes in from the FLC.

#include <AccelStepper.h>

//Driver setup
AccelStepper motor(1, 5, 4);    //DRIVER mode, STEP: 5, DIR: 4)


int FuzzyAccel = 1000;
int Enable = 6;   //for the stepper motor EN pin

void setup() {
  //Start of serial comms
  Serial.begin(115200);

  //activating Driver EN pin
  pinMode(Enable, OUTPUT);
  digitalWrite(Enable, LOW);

  //Init values
  motor.setMaxSpeed(6000);
  motor.setMinPulseWidth(1);
  motor.setCurrentPosition(0);
  motor.setAcceleration(15000);

  //Wait for start signal from the controller
  while (Serial.available() && Serial.read()); // empty buffer
  while (!Serial.available());                 // wait for data
  while (Serial.available() && Serial.read()); // empty buffer again
}

void loop() {
  while (Serial.available()) {
    //Reads the response value from the controller
    FuzzyAccel = Serial.parseInt();


    //Negative direction run
    if (FuzzyAccel < 0) {
      motor.setAcceleration(abs(FuzzyAccel));
      motor.moveTo(-1000);
      negRun();
    }
    else if (FuzzyAccel > 0) {
      motor.setAcceleration(FuzzyAccel);
      motor.moveTo(1000);
      posRun();
    }




  }


}

////////////////////////////////////////////

//Subrutine for negative running
void negRun() {
  while (FuzzyAccel < 0) {

      motor.run();
      if(FuzzyAccel < 0) break;

  } 

}

//Subrutine for positive running
void posRun() {
  while (FuzzyAccel > 0) {
      motor.run();
      if (FuzzyAccel < 0) break;
  }

}

Currently what the program does is runs the motor toward a direction but only once. After the cart stopped nothing happens.
I'm pretty new to Arduino and I don't fully understand the programming logic behind it.

I'm using an Arduino Nano with a A4988 stepper motor driver. If you have any tips or ideas for what to change, I'd appreciate it.

void negRun() {
  while (FuzzyAccel < 0) {

      motor.run();
      if(FuzzyAccel < 0) break;

  }

}

What the heck is this? What is the reason for using a while statement that will only ever iterate once? Why even test FuzzyAccel in this function, since you have already decided to call this function only if FuzzyAccel is negative?

Given that the test for FuzzyAccel is useless, the function boils down to:

void negRun()
{
   motor.run();
}

which looks remarkably like posRun() when it's useless code is removed.

Like I said I'm not too familiar with the programming so please excuse me that part.

I removed the whole subrutine part of the program and that part of the code looks like this:

motor.setAcceleration(abs(FuzzyAccel));


    if (FuzzyAccel < 0) {
      motor.moveTo(-1000);
      motor.run();
    } 

    else if (FuzzyAccel > 0) {
      motor.moveTo(1000);
      motor.run();
    }

The cart changes direction when needed but now the movement speed has dropped to a snails pace. Probably it's the motor.setAcceleration() function that drains the processor. Is there a way to circumvent this?