Should I be using time.fixedDeltaTime here?

Unsure, and there'll hopefully be a better answer on its way, but have you tried setting the rigidbody's Collision Detection field to 'continuous'? It will be more expensive but it will give better physics calculations; not something you want for most things, but for the player.

Also I notice you are using input to determine whether to add velocity within the fixed update; be warned that input is only updated immediately after the Update() method, and persist until the end of the next Update(). So if for example you pressed Jump and 3 fixed updates occurred before the next update, your fixedupdates will have that same jump input for those 3 updates. You're checking if the player is on the ground so you shouldn't notice the extra jump inputs (and by default there's only about 1 fixed update per update anyway), but I thought I'd mention it. One fix would be to set a bool in Update() that says whether to jump or not, then clear that bool as soon as it's resolved in fixedupdate so future fixedupdates that frame aren't affected.

Try do like this :

  private void FixedUpdate()
  {   
      IsGrounded();
  {
  private void Update()
  {
      Input();
      Run();
      Jump();
      rb.velocity = transform.TransformDirection(vel);
  }

• You can see this life cycle in here : https://docs.unity3d.com/Manual/ExecutionOrder.html

• As you can see in the life cycle, the FixedUpdate called multiple times in one cycle, why the reason i put IsGrounded() in the FixedUpdate() is maybe when my character in the ground it not called and throug the object that should called true value.

• That is just example for it, but when it's not needed(not troubling/ make a bug like i said before) you can put it in Update() after move or before input, it can gaining more FPS cause it just called one time.

[Edited]

• Use Time.deltaTime that called in Update() and Use Time.fixedDeltaTime that called in FixedUpdate().

[Edited]

Hope it helps.

If you want smooth movement you should use Rigidbody.AddForce(). It's like that:

 [SerializeField]private float speed;
 private Rigidbody rbody;
 
 private float inputH, inputV;
 
 void Start ()
 {
     rbody = GetComponent<Rigidbody>();
 }
 
 void FixedUpdate ()
 {
 
     inputH = Input.GetAxis("Horizontal");
     inputV = Input.GetAxis("Vertical");
 
     float moveX = inputH * speed * Time.fixedDeltaTime;
     float moveZ = inputV * speed * Time.fixedDeltaTime;
 
     rbody.velocity = new Vector3(0, rbody.velocity.y,0);
 
     rbody.AddForce(transform.Forward * moveZ * Time.fixedDeltaTime, ForceMode.Force);
     rbody.AddForce(transform.Right * moveX * Time.fixedDeltaTime, ForceMode.Force);
 
 }

Hope I've helped.

Try to apply the velocity directly in Update(), I don't see any reason why you have to do it in FixedUpdate()

The default timestep for FixedUpdate() is 50 Hz, so if your game is running at 60 fps, you don't apply the controls on every frame.

Try this:

     private void Update()
     {
         GetInput();
         Run();
         Jump();
         rb.velocity = transform.TransformDirection(vel);
     }

Edit: and decrease the physics time step