Update Programming/simulation chapter.

PiperOrigin-RevId: 847424298
Change-Id: Icc6efb05dee5e67a5813ed04caa15a5703e59aee

doc/APIreference/functions.rst

@@ -89,7 +89,7 @@ Copy real-valued arrays from model to spec, returns 1 on success.
 Recompile spec to model, preserving the state. Like :ref:`mj_compile`, this function compiles an :ref:`mjSpec` to an
 :ref:`mjModel`, with two differences. First, rather than returning an entirely new model, it will
 reallocate existing :ref:`mjModel` and :ref:`mjData` instances in-place. Second, it will preserve the
-:ref:`integration state<geIntegrationState>`, as given in the provided :ref:`mjData` instance, while accounting for
+:ref:`integration state<siIntegrationState>`, as given in the provided :ref:`mjData` instance, while accounting for
 newly added or removed degrees of freedom. This allows the user to continue simulation with the same model and data
 struct pointers while editing the model programmatically.
 
@@ -2753,7 +2753,7 @@ outputs of derivative functions are the trailing rather than leading arguments.
 
 Compute finite-differenced discrete-time transition matrices.
 
-Letting :math:`x, u` denote the current :ref:`state<gePhysicsState>` and :ref:`control<geInput>`
+Letting :math:`x, u` denote the current :ref:`state<siPhysicsState>` and :ref:`control<siInput>`
 vector in an mjData instance, and letting :math:`y, s` denote the next state and sensor
 values, the top-level :ref:`mj_step` function computes :math:`(x,u) \rightarrow (y,s)`
 :ref:`mjd_transitionFD` computes the four associated Jacobians using finite-differencing.
@@ -2804,7 +2804,7 @@ These matrices and their dimensions are:
 
 Finite differenced continuous-time inverse-dynamics Jacobians.
 
-Letting :math:`x, a` denote the current :ref:`state<gePhysicsState>` and acceleration vectors in an mjData instance, and
+Letting :math:`x, a` denote the current :ref:`state<siPhysicsState>` and acceleration vectors in an mjData instance, and
 letting :math:`f, s` denote the forces computed by the inverse dynamics (``qfrc_inverse``), the function
 :ref:`mj_inverse` computes :math:`(x,a) \rightarrow (f,s)`. :ref:`mjd_inverseFD` computes seven associated Jacobians
 using finite-differencing. These matrices and their dimensions are:

doc/APIreference/functions_override.rst

@@ -48,7 +48,7 @@ If compilation fails, :ref:`mj_compile` returns ``NULL``; the error can be read
 Recompile spec to model, preserving the state. Like :ref:`mj_compile`, this function compiles an :ref:`mjSpec` to an
 :ref:`mjModel`, with two differences. First, rather than returning an entirely new model, it will
 reallocate existing :ref:`mjModel` and :ref:`mjData` instances in-place. Second, it will preserve the
-:ref:`integration state<geIntegrationState>`, as given in the provided :ref:`mjData` instance, while accounting for
+:ref:`integration state<siIntegrationState>`, as given in the provided :ref:`mjData` instance, while accounting for
 newly added or removed degrees of freedom. This allows the user to continue simulation with the same model and data
 struct pointers while editing the model programmatically.
 
@@ -643,7 +643,7 @@ outputs of derivative functions are the trailing rather than leading arguments.
 
 Compute finite-differenced discrete-time transition matrices.
 
-Letting :math:`x, u` denote the current :ref:`state<gePhysicsState>` and :ref:`control<geInput>`
+Letting :math:`x, u` denote the current :ref:`state<siPhysicsState>` and :ref:`control<siInput>`
 vector in an mjData instance, and letting :math:`y, s` denote the next state and sensor
 values, the top-level :ref:`mj_step` function computes :math:`(x,u) \rightarrow (y,s)`
 :ref:`mjd_transitionFD` computes the four associated Jacobians using finite-differencing.
@@ -689,7 +689,7 @@ These matrices and their dimensions are:
 
 Finite differenced continuous-time inverse-dynamics Jacobians.
 
-Letting :math:`x, a` denote the current :ref:`state<gePhysicsState>` and acceleration vectors in an mjData instance, and
+Letting :math:`x, a` denote the current :ref:`state<siPhysicsState>` and acceleration vectors in an mjData instance, and
 letting :math:`f, s` denote the forces computed by the inverse dynamics (``qfrc_inverse``), the function
 :ref:`mj_inverse` computes :math:`(x,a) \rightarrow (f,s)`. :ref:`mjd_inverseFD` computes seven associated Jacobians
 using finite-differencing. These matrices and their dimensions are: