Mujoco_WASM/doc/programming/simulation.rst

.. _Simulation:

Simulation
----------

.. _siInitialization:

Initialization
~~~~~~~~~~~~~~

After the :ref:`version <inVersion>` check, the next step is to allocate and initialize the main data structures needed
for simulation, namely mjModel and mjData. Additional initialization steps related to visualization and callbacks will
be discussed later.

mjModel and mjData should never be allocated directly by the user. Instead they are allocated and initialized by the
corresponding API functions. These are very elaborate data structures, containing (arrays of) other structures,
preallocated data arrays for all intermediate results, as well as an :ref:`internal stack <siStack>`. Our strategy is
to allocate all necessary heap memory at the beginning of the simulation, and free it after the simulation is done, so
that we never have to call the C memory allocation and deallocation functions during the simulation. This is done for
speed, avoidance of memory fragmentation, future GPU portability, and ease of managing the state of the entire
simulator during a reset. It also means however that the maximal variable-memory allocation given by the
:at:`memory` attribute in the :ref:`size <size>` MJCF element, which affects the allocation of ``mjData``, must be
set to a sufficiently large value. If this maximal size is exceeded during simulation, it is not increased
dynamically, but instead an error is generated. See also :ref:`diagnostics <siDiagnostics>` below.

First we must call one of the functions that allocates and initializes mjModel and returns a pointer to it. The
available options are

.. code-block:: C

   // option 1: parse and compile XML from file
   mjModel* m = mj_loadXML("mymodel.xml", NULL, errstr, errstr_sz);

   // option 2: parse and compile XML from virtual file system
   mjModel* m = mj_loadXML("mymodel.xml", vfs, errstr, errstr_sz);

   // option 3: load precompiled model from MJB file
   mjModel* m = mj_loadModel("mymodel.mjb", NULL);

   // option 4: load precompiled model from virtual file system
   mjModel* m = mj_loadModel("mymodel.mjb", vfs);

   // option 5: deep copy from existing mjModel
   mjModel* m = mj_copyModel(NULL, mexisting);

All these functions return a NULL pointer if there is an error or warning. In the case of XML parsing and model
compilation, a description of the error is returned in the string provided as argument. For the remaining functions, the
low-level :ref:`mju_error` or :ref:`mju_warning` is called with the error/warning message; see :ref:`error handling
<siError>`. Once we have a pointer to the mjModel that was allocated by one of the above functions, we pass it as
argument to all API functions that need model access. Note that most functions treat this pointer as ``const``; more on
this in :ref:`model changes <siChange>` below.

The virtual file system (VFS) allows disk resources to be loaded in memory or created programmatically by the user, and
then MuJoCo's load functions search for files in the VFS before accessing the disk. See :ref:`Virtualfilesystem` in the
API Reference chapter.

In addition to mjModel which holds the model description, we also need mjData which is the workspace where all
computations are performed. Note that mjData is specific to a given mjModel. The API functions generally assume that
users know what they are doing, and perform minimal argument checking. If the mjModel and mjData passed to any API
function are incompatible (or NULL) the resulting behavior is unpredictable. mjData is created with

.. code-block:: C

   // option 1: create mjData corresponding to given mjModel
   mjData* d = mj_makeData(m);

   // option 2: deep copy from existing mjData
   mjData* d = mj_copyData(NULL, m, dexisting);

Once both mjModel and mjData are allocated and initialized, we can call the various simulation functions. When we are
done, we can delete them with

.. code-block:: C

   // deallocate existing mjModel
   mj_deleteModel(m);

   // deallocate existing mjData
   mj_deleteData(d);

The code samples illustrate the complete initialization and termination sequence.

MuJoCo simulations are deterministic with one exception: sensor noise can be generated when this feature is enabled.
This is done by calling the C function rand() internally. To generate the same random number sequence, call srand()
with a desired seed after the model is loaded and before the simulation starts. The model compiler calls srand(123)
internally, so as to generate random dots for procedural textures. Therefore the noise sequence in the sensor data
will change if the specification of procedural textures changes, and the user does not call srand() after model
compilation.

.. _siSimulation:

Simulation loop
~~~~~~~~~~~~~~~

There are multiple ways to run a simulation loop in MuJoCo. The simplest way is to call the top-level simulation
function :ref:`mj_step` in a loop such as

.. code-block:: C

   // simulate until t = 10 seconds
   while( d->time<10 )
     mj_step(m, d);

This by itself will simulate the passive dynamics, because we have not provided any control signals or applied forces.
The default (and recommended) way to control the system is to implement a control callback, for example

.. code-block:: C

   // simple controller applying damping to each dof
   void mycontroller(const mjModel* m, mjData* d)
   {
     if( m->nu==m->nv )
       mju_scl(d->ctrl, d->qvel, -0.1, m->nv);
   }

This illustrates two concepts. First, we are checking if the number of controls ``mjModel.nu`` equals the number of
DoFs ``mjModel.nv``. In general, the same callback may be used with multiple models depending on how the user code is
structured, and so it is a good idea to check the model dimensions in the callback. Second, MuJoCo has a library of
BLAS-like functions that are very useful; indeed a large part of the code base consists of calling such functions
internally. The :ref:`mju_scl` function above scales the velocity vector ``mjData.qvel`` by a constant feedback
gain and copies the result into the control vector ``mjData.ctrl``. To install this callback, we simply assign it to the
global control callback pointer :ref:`mjcb_control`:

.. code-block:: C

   // install control callback
   mjcb_control = mycontroller;

Now if we call :ref:`mj_step`, our control callback will be executed whenever the control
signal is needed by the simulation pipeline, and as a result we will end up simulating the controlled dynamics (except
damping does not really do justice to the notion of control, and is better implemented as a passive joint property,
but these are finer points).

Instead of relying on a control callback, we could set the control vector ``mjData.ctrl`` directly. Alternatively we
could set applied forces as explained in :ref:`state and control <siStateControl>`. If we could compute these control-
related quantities before ``mj_step`` is called, then the simulation loop for the controlled dynamics (without using a
control callback) would become

.. code-block:: C

   while( d->time<10 ) {
     // set d->ctrl or d->qfrc_applied or d->xfrc_applied
     mj_step(m, d);
   }

Why would we not be able to compute the controls before ``mj_step`` is called? After all, isn't this what causality
means? The answer is subtle but important, and has to do with the fact that we are simulating in discrete time. The top-
level simulation function ``mj_step`` basically does two things: compute the :ref:`forward dynamics <siForward>` in
continuous time, and then integrate over a time period specified by ``mjModel.opt.timestep``. Forward dynamics computes
the acceleration ``mjData.qacc`` at time ``mjData.time``, given the :ref:`state and control <siStateControl>` at time
``mjData.time``. The numerical integrator then advances the state and time to ``mjData.time + mjModel.opt.timestep``.
Now, the control is required to be a function of the state at time ``mjData.time``. However a general feedback
controller can be a very complex function, depending on various features of the state - in particular all the features
computed by MuJoCo as intermediate results of the simulation. These may include contacts, Jacobians, passive forces.
None of these quantities are available before ``mj_step`` is called (or rather, they are available but outdated by one
time step). In contrast, when ``mj_step`` calls our control callback, it does so as late in the computation as possible
- namely after all the intermediate results dependent on the state but not on the control have been computed.

The same effect can be achieved without using a control callback. This is done by breaking ``mj_step`` in two parts:
before the control is needed, and after the control is needed. The simulation loop now becomes

.. code-block:: C

   while( d->time<10 ) {
     mj_step1(m, d);
     // set d->ctrl or d->qfrc_applied or d->xfrc_applied
     mj_step2(m, d);
   }

There is one complication however: this only works with Euler integration. The Runge-Kutta integrator (as well as other
advanced integrators we plan to implement) need to evaluate the entire dynamics including the feedback control law
multiple times per step, which can only be done using a control callback. But with Euler integration, the above
separation of ``mj_step`` into :ref:`mj_step1` and :ref:`mj_step2` is sufficient to provide the control law with the
intermediate results of the computation.

To make the above discussion more clear, we provide the internal implementation of mj_step, mj_step1 and mj_step2,
omitting some code that computes timing diagnostics. The main simulation function is

.. code-block:: C

   void mj_step(const mjModel* m, mjData* d) {
     // common to all integrators
     mj_checkPos(m, d);
     mj_checkVel(m, d);
     mj_forward(m, d);
     mj_checkAcc(m, d);

     // compare forward and inverse solutions if enabled
     if( mjENABLED(mjENBL_FWDINV) )
       mj_compareFwdInv(m, d);

     // use selected integrator
     if( m->opt.integrator==mjINT_RK4 )
       mj_RungeKutta(m, d, 4);
     else
       mj_Euler(m, d);
   }

The checking functions reset the simulation automatically if any numerical values have become invalid or too large.
The control callback (if any) is called from within the forward dynamics function.

Next we show the implementation of the two-part stepping approach, although the specifics will make sense only after
we explain the :ref:`forward dynamics <siForward>` later. Note that the control callback is now called directly, since
we have essentially unpacked the forward dynamics function. Note also that we always call the Euler integrator in
mj_step2 regardless of the setting of ``mjModel.opt.integrator``.

.. code-block:: C

   void mj_step1(const mjModel* m, mjData* d)
   {
     mj_checkPos(m, d);
     mj_checkVel(m, d);
     mj_fwdPosition(m, d);
     mj_sensorPos(m, d);
     mj_energyPos(m, d);
     mj_fwdVelocity(m, d);
     mj_sensorVel(m, d);
     mj_energyVel(m, d);

     // if we had a callback we would be using mj_step, but call it anyway
     if( mjcb_control )
       mjcb_control(m, d);
   }

   void mj_step2(const mjModel* m, mjData* d)
   {
     mj_fwdActuation(m, d);
     mj_fwdAcceleration(m, d);
     mj_fwdConstraint(m, d);
     mj_sensorAcc(m, d);
     mj_checkAcc(m, d);

     // compare forward and inverse solutions if enabled
     if( mjENABLED(mjENBL_FWDINV) )
       mj_compareFwdInv(m, d);

     // integrate with Euler; ignore integrator option
     mj_Euler(m, d);
   }

.. _siStateControl:

State and control
~~~~~~~~~~~~~~~~~

MuJoCo has a well-defined state that is easy to set, reset and advance through time. This is closely related to the
notion of state of a dynamical system. Dynamical systems are usually described in the general form

.. code-block:: Text

     dx/dt = f(t,x,u)

where ``t`` is the time, ``x`` is the state vector, ``u`` is the control vector, and ``f`` is the function that
computes the time-derivative of the state. This is a continuous-time formulation, and indeed the physics model
simulated by MuJoCo is defined in continuous time. Even though the numerical integrator operates in discrete time, the
main part of the computation - namely the function :ref:`mj_forward` - corresponds to the
continuous-time dynamics function ``f(t,x,u)`` above. Here we explain this correspondence.

The state vector in MuJoCo is:

.. code-block:: Text

     x = (mjData.time, mjData.qpos, mjData.qvel, mjData.act)

For a second-order dynamical system the state contains only position and velocity, however MuJoCo can also model
actuators (such as cylinders and biological muscles) that have their own activation states assembled in the vector
``mjData.act``. While the physics model is time-invariant, user-defined control laws may be time-varying; in particular
control laws obtained from trajectory optimizers would normally be indexed by ``mjData.time``.

The reason for the "official" caveat above is because user callbacks may store additional state variables that change
over time and affect the callback outputs; indeed the field ``mjData.userdata`` exists mostly for that purpose. Other
state-like quantities that are part of mjData and are treated as inputs by forward dynamics are ``mjData.mocap_pos`` and
mjData.mocap_quat. These quantities are unusual in that they are meant to change at each time step (normally driven by a
motion capture device), however this change is implemented by the user, while the simulator treats them as constants. In
that sense they are no different from all the constants in mjModel, or the function callback pointers set by the user:
such constants affect the computation, but are not part of the state vector of a dynamical system.

The warm-start mechanism in the constraint solver effectively introduces another state variable. This mechanism uses
the output of forward dynamics from the previous time step, namely the acceleration vector ``mjData.qacc``, to estimate
the current constraint forces via inverse dynamics. This estimate then initializes the optimization algorithm in the
solver. If this algorithm runs until convergence the warm-start will affect the speed of convergence but not the final
solution (since the underlying optimization problem is convex and does not have local minima), but in practice the
algorithm is often terminated early, and so the warm-start has some (usually very small) effect on the solution.

Next we turn to the controls and applied forces. The control vector in MuJoCo is

.. code-block:: Text

     u = (mjData.ctrl, mjData.qfrc_applied, mjData.xfrc_applied)

These quantities specify control signals (``mjData.ctrl``) for the actuators defined in the model, or directly apply
forces and torques specified in joint space (``mjData.qfrc_applied``) or in Cartesian space (mjData.xfrc_applied).

Finally, calling mj_forward which corresponds to the abstract dynamics function ``f(t,x,u)`` computes the
time-derivative of the state vector. The corresponding fields of mjData are

::

     dx/dt = f(t,x,u) = (1, mjData.qvel, mjData.qacc, mjData.act_dot)

In the presence of quaternions (i.e., when free or ball joints are used), the position vector ``mjData.qpos`` has higher
dimensionality than the velocity vector ``mjData.qvel`` and so this is not a simple time-derivative in the sense of
scalars, but instead takes quaternion algebra into account.

To illustrate how the simulation state can be manipulated, suppose we have two mjData pointers src and dst
corresponding to the same mjModel, and we want to copy the entire simulation state from one to the other (leaving out
internal diagnostics which do not affect the simulation). This can be done as

.. code-block:: C

   // copy simulation state
   dst->time = src->time;
   mju_copy(dst->qpos, src->qpos, m->nq);
   mju_copy(dst->qvel, src->qvel, m->nv);
   mju_copy(dst->act,  src->act,  m->na);

   // copy mocap body pose and userdata
   mju_copy(dst->mocap_pos,  src->mocap_pos,  3*m->nmocap);
   mju_copy(dst->mocap_quat, src->mocap_quat, 4*m->nmocap);
   mju_copy(dst->userdata, src->userdata, m->nuserdata);

   // copy warm-start acceleration
   mju_copy(dst->qacc_warmstart, src->qacc_warmstart, m->nv);

Now, assuming the controls are also the same (see below) and that any installed callbacks are not relying on
user-defined state variables that are different between src and dst, calling mj_forward(m, src) or mj_step(m, src)
yields the same result as calling mj_forward(m, dst) or mj_step(m, dst) respectively. Similarly, calling mj_inverse(m,
src) yields the same result as calling mj_inverse(m, dst). More on :ref:`inverse dynamics <siInverse>` later.

The entire mjData can also be copied with the function :ref:`mj_copyData`. This involves
less code but is much slower. Indeed using the above code to copy the state and then calling mj_forward to recompute
everything can sometimes be faster than copying mjData. This is because the preallocated buffers in mjData are large
enough to hold the intermediate results in the worst case where all possible constraints are active, but in practice
only a small fraction of constraints tend to be active simultaneously.

To illustrate how the control vector can be manipulated, suppose we want to clear all controls and applied forces
before calling mj_step, so as to make sure we are simulating the passive dynamics (assuming no control callback of
course). This can be done as

.. code-block:: C

   // clear controls and applied forces
   mju_zero(dst->ctrl, m->nu);
   mju_zero(dst->qfrc_applied, m->nv);
   mju_zero(dst->xfrc_applied, 6*m->nbody);

If the user has installed a control callback :ref:`mjcb_control` different from the default callback (which is a NULL
pointer), the user callback would be expected to set some of the above fields to non-zero. Note that MuJoCo will not
clear these controls/forces at the end of the time step. This is the responsibility of the user.

Also relevant in this context is the function :ref:`mj_resetData`. It sets ``mjData.qpos`` equal to the model reference
configuration ``mjModel.qpos0``, ``mjData.mocap_pos`` and ``mjData.mocap_quat`` equal to the corresponding fixed body
poses from mjModel; and all other state and control variables to 0.

.. _siForward:

Forward dynamics
~~~~~~~~~~~~~~~~

The goal of forward dynamics is to compute the time-derivative of the state, namely the acceleration vector
mjData.qacc and the activation time-derivative ``mjData.act_dot``. Along the way it computes everything else needed to
simulate the dynamics, including active contacts and other constraints, joint-space inertia and its LTDL
decomposition, constraint forces, sensor data and so on. All these intermediate results are available in mjData and
can be used in custom computations. As illustrated in the :ref:`simulation loop <siSimulation>` section above, the
main stepper function mj_step calls mj_forward to do most of the work, and then calls the numerical integrator to
advance the simulation state to the next discrete point in time.

The forward dynamics function mj_forward internally calls :ref:`mj_forwardSkip` with
skip arguments (mjSTAGE_NONE, 0), where the latter function is implemented as

.. code-block:: C

   void mj_forwardSkip(const mjModel* m, mjData* d, int skipstage, int skipsensor) {
     // position-dependent
     if( skipstage<mjSTAGE_POS )
     {
       mj_fwdPosition(m, d);
       if( !skipsensor )
         mj_sensorPos(m, d);
       if( mjENABLED(mjENBL_ENERGY) )
         mj_energyPos(m, d);
     }

     // velocity-dependent
     if( skipstage<mjSTAGE_VEL )
     {
       mj_fwdVelocity(m, d);
       if( !skipsensor )
         mj_sensorVel(m, d);
       if( mjENABLED(mjENBL_ENERGY) )
         mj_energyVel(m, d);
     }

     // acceleration-dependent
     if( mjcb_control )
       mjcb_control(m, d);
     mj_fwdActuation(m, d);
     mj_fwdAcceleration(m, d);
     mj_fwdConstraint(m, d);
     if( !skipsensor )
       mj_sensorAcc(m, d);
   }

Note that this is the same sequence of calls as in mj_step1 and mj_step2 above, except that checking of real values
and computing features such as sensor and energy are omitted. The functions being called are components of the
simulation pipeline. In turn they call sub-components.

The integer argument skipstage determines which parts of the computation will be skipped. The possible skip levels are

mjSTAGE_NONE
   Skip nothing. Run all computations.
mjSTAGE_POS
   Skip computations that depend on position but not on velocity or control or applied force. Examples of such
   computations include forward kinematics, collision detection, inertia matrix computation and decomposition. These
   computations typically take the most CPU time and should be skipped when possible (see below).
mjSTAGE_VEL
   Skip computations that depend on position and velocity but not on control or applied force. Examples include the
   computation of Coriolis and centrifugal forces, passive damping forces, reference accelerations for constraint
   stabilization.

The intermediate result fields of mjData are organized into sections according to which part of the state is needed in
order to compute them. Calling mj_forwardSkip with mjSTAGE_POS assumes that the fields in the first section (position
dependent) have already been computed and does not recompute them. Similarly, mjSTAGE_VEL assumes that the fields in
the first and second sections (position and velocity dependent) have already been computed.

When can we use the above machinery and skip some of the computations? In a regular simulation this is not possible.
However, MuJoCo is designed not only for simulation but also for more advanced applications such as model-based
optimization, machine learning etc. In such settings one often needs to sample the dynamics at a cloud of nearby
states, or approximate derivatives via finite differences - which is another form of sampling. If the samples are
arranged on a grid, where only the position or only the velocity or only the control is different from the center
point, then the above mechanism can improve performance by about a factor of 2.

.. _siInverse:

Inverse dynamics
~~~~~~~~~~~~~~~~

The computation of inverse dynamics is a unique feature of MuJoCo, and is not found in any other modern engine capable
of simulating contacts. Inverse dynamics are well-defined and very efficient to compute, thanks to our
:ref:`soft-constraint model <Constraint>` described in the Overview chapter. In fact once the position and
velocity-dependent computations that are shared with forward dynamics have been performed, the recovery of constraint
and applied forces given the acceleration comes down to an analytical formula. This is so fast that we actually use
inverse dynamics (with the acceleration computed at the previous time step) to warm-start the iterative constraint
solver in forward dynamics.

The inputs to inverse dynamics are the same as the state vector in forward dynamics as illustrated in :ref:`state and
control <siStateControl>`, but without ``mjData.act`` and ``mjData.time``. Assuming no callbacks that depend on user-
defined state variables, the inputs to inverse dynamics are the following fields of mjData:

::

     (mjData.qpos, mjData.qvel, mjData.qacc, mjData.mocap_pos, mjData.mocap_quat)

The main output is ``mjData.qfrc_inverse``. This is the force that must have acted on the system in order to achieve the
observed acceleration ``mjData.qacc``. If forward dynamics were to be computed exactly, by running the iterative solver
to full convergence, we would have

::

     mjData.qfrc_inverse = mjData.qfrc_applied + Jacobian'*mjData.xfrc_applied + mjData.qfrc_actuator

where ``mjData.qfrc_actuator`` is the joint-space force produced by the actuators and the Jacobian is the mapping from
joint to Cartesian space. When the "fwdinv" flag in ``mjModel.opt.enableflags`` is set, the above identity is used to
monitor the quality of the forward dynamics solution. In particular, the two components of ``mjData.solver_fwdinv`` are
set to the L2 norm of the difference between the forward and inverse solutions, in terms of joint forces and
constraint forces respectively.

Similar to forward dynamics, ``mj_inverse`` internally calls :ref:`mj_inverseSkip` with skip arguments
``(mjSTAGE_NONE, 0)``. The skip mechanism is the same as in forward dynamics, and can be used to speed up structured
sampling. The result ``mjData.qfrc_inverse`` is obtained by using the Recursive Newton-Euler algorithm to compute the
net force acting on the system, and then subtracting from it all internal forces.

Inverse dynamics can be used as an analytical tool when experimental data are available. This is common in robotics as
well as biomechanics. It can also be used to compute the joint torques needed to drive the system along a given
reference trajectory; this is known as computed torque control. In the context of state estimation, system
identification and optimal control, it can be used within an optimization loop to find sequences of states that
minimize physics violation along with other costs. Physics violation can be quantified as the norm of any unexplained
external force computed by inverse dynamics.

.. _siMultithread:

Multi-threading
~~~~~~~~~~~~~~~

When MuJoCo is used for simulation as explained in the :ref:`simulation loop <siSimulation>` section, it runs in a
single thread. We have experimented with multi-threading parts of the simulation pipeline that are computationally
expensive and amenable to parallel processing, and have concluded that the speedup is not worth using up the extra
processor cores. This is because MuJoCo is already fast compared to the overhead of launching and synchronizing
multiple threads within the same time step. If users start working with large simulations involving many floating
bodies, we may eventually implement within-step multi-threading, but for now this use case is not common.

Rather than speed up a single simulation, we prefer to use multi-threading to speed up sampling operations that are
common in more advanced applications. Simulation is inherently serial over time (the output of one mj_step is the
input to the next), while in sampling many calls to either forward or inverse dynamics can be executed in parallel
since there are no dependencies among them, except perhaps for a common initial state.

MuJoCo was designed for multi-threading from its beginning. Unlike most existing simulators where the notion of
dynamical system state is difficult to map to the software state and is often distributed among multiple objects, in
MuJoCo we have the unified data structure mjData which contains everything that changes over time. Recall the
discussion of :ref:`state and control <siStateControl>`. The key idea is to create one mjData for each thread, and
then use it for all per-thread computations. Below is the general template, using OpenMP to simplify thread
management.

.. code-block:: C

   // prepare OpenMP
   int nthread = omp_get_num_procs();      // get number of logical cores
   omp_set_dynamic(0);                     // disable dynamic scheduling
   omp_set_num_threads(nthread);           // number of threads = number of logical cores

   // allocate per-thread mjData
   mjData* d[64];
   for( int n=0; n < nthread; n++ )
       d[n] = mj_makeData(m);

   // ... serial code, perhaps using its own mjData* dmain

   // parallel section
   #pragma omp parallel
   {
     int n = omp_get_thread_num();       // thread-private variable with thread id (0 to nthread-1)

     // ... initialize d[n] from results in serial code

     // thread function
     worker(m, d[n]);                    // shared mjModel (read-only), per-thread mjData (read-write)
   }

   // delete per-thread mjData
   for( int n=0; n<nthread; n++ )
     mj_deleteData(d[n]);

Since all top-level API functions treat mjModel as ``const``, this multi-threading scheme is safe. Each thread only
writes to its own mjData. Therefore no further synchronization among threads is needed.

The above template reflects a particular style of parallel processing. Instead of creating a large number of threads,
one for each work item, and letting OpenMP distribute them among processors, we rely on manual scheduling. More
precisely, we create as many threads as there are processors, and then within the ``worker`` function we distribute the
work explicitly among threads. This approach is more efficient because the thread-specific mjData is large compared to
the processor cache.

We also use a shared mjModel for cache-efficiency. In some situations it may not be possible to use the same mjModel
for all threads. One obvious reason is that mjModel may need to be modified within the thread function. Another reason
is that the mjOption structure which is contained within mjModel may need to be adjusted (so as to control the number
of solver iterations for example), although this is likely to be the same for all parallel threads and so the
adjustment can be made in the shared model before the parallel section.

How the thread-specific mjData is initialized and what the thread function does is of course application-dependent.
Nevertheless, the general efficiency guidelines from the earlier sections apply here. Copying the state into the
thread-specific mjData and running MuJoCo to fill in the rest may be faster than using mj_copyData. Furthermore, the
skip mechanism available in both forward and inverse dynamics is particularly useful in parallel sampling
applications, because the samples usually have structure allowing some computations to be re-used. Finally, keep in
mind that the forward solver is iterative and good warm-start can substantially reduce the number of necessary
iterations. When samples are close to each other in state and control space, the solution for one sample (ideally in
the center) can be used to warm-start all the other samples. In this setting it is important to make sure that the
different results between nearby samples reflect genuine differences between the samples, and not different warm-start
or termination of the iterative solver.

.. _siChange:

Model changes
~~~~~~~~~~~~~

The MuJoCo model contained in mjModel is supposed to represent constant physical properties of the system, and in
theory should not change after compilation. Of course in practice things are not that simple. It is often desirable to
change the physics options in ``mjModel.opt``, so as to experiment with different aspects of the physics or to create
custom computations. Indeed these options are designed in such a way that the user can make arbitrary changes to them
between time steps.

The general rule is that real-valued parameters are safe to change, while structural integer parameters are not
because that may result in incorrect sizes or indexing. This rule does not hold universally though. Some real-valued
parameters such as inertias are expected to obey certain properties. On the other hand, some structural parameters
such as object types may be possible to change, but that depends on whether any sizes or indexes depend on them.
Arrays of type mjtByte can be changed safely, since they are binary indicators that enable and disable certain
features. The only exception here is ``mjModel.tex_rgb`` which is texture data represented as mjtByte.

When changing mjModel fields that corresponds to resources uploaded to the GPU, the user must also call the
corresponding upload function: ``mjr_uploadTexture``, ``mjr_uploadMesh``, ``mjr_uploadHField``. Otherwise the data used
for simulation and for rendering will no longer be consistent.

A related consideration has to do with changing real-valued fields of mjModel that have been used by the compiler to
compute other real-valued fields: if we make a change, we want it to propagate. That is what the function
:ref:`mj_setConst` does: it updates all derived fields of mjModel. These are fields whose names end with "0",
corresponding to precomputed quantities when the model is in the reference configuration ``mjModel.qpos0``.

Finally, if changes are made to mjModel at runtime, it may be desirable to save them back to the XML. The function
:ref:`mj_saveLastXML` does that in a limited sense: it copies all real-valued parameters from mjModel back to the
internal mjCModel, and then saves it as XML. This does not cover all possible changes that the user could have made.
The only way to guarantee that all changes are saved is to save the model as a binary MJB file with the function
:ref:`mj_saveModel`, or even better, make the changes directly in the XML. Unfortunately there are situations where
changes need to be made programmatically, as in system identification for example, and this can only be done with the
compiled model. So in summary, we have reasonable but not perfect mechanisms for saving model changes. The reason for
this lack of perfection is that we are working with a compiled model, so this is like changing a binary executable and
asking a "decompiler" to make corresponding changes to the C code - it is just not possible in general.

.. _siLayout:

Data layout and buffer allocation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

All matrices in MuJoCo are in **row-major** format. For example, the linear memory array (a0, a1, ... a5) represents the
2-by-3 matrix

.. code-block:: Text

     a0 a1 a2
     a3 a4 a5

This convention has traditionally been associated with C, while the opposite column-major convention has been
associated with Fortran. There is no particular reason to choose one over the other, but whatever the choice is, it is
essential to keep it in mind at all times. All MuJoCo utility functions that operate on matrices, such as
:ref:`mju_mulMatMat`, :ref:`mju_mulMatVec` etc. assume this matrix layout. For vectors there is of course no
difference between row-major and column-major formats.

When possible, MuJoCo exploits sparsity. This can make all the difference between O(N) and O(N^3) scaling. The inertia
matrix ``mjData.qM`` and its LTDL factorization ``mjData.qLD`` are always represented as sparse, using a custom
indexing format designed for matrices that correspond to tree topology. The functions :ref:`mj_factorM`,
:ref:`mj_solveM`, :ref:`mj_solveM2` and :ref:`mj_mulM` are used for sparse factorization, substitution and
matrix-vector multiplication. The user can also convert these matrices to dense format with the function
:ref:`mj_fullM` although MuJoCo never does that internally.

The constraint Jacobian matrix ``mjData.efc_J`` is represented as sparse whenever the sparse Jacobian option is
enabled. The function :ref:`mj_isSparse` can be used to determine if sparse format is currently in use. In that case
the transposed Jacobian ``mjData.efc_JT`` is also computed, and the inverse constraint inertia ``mjData.efc_AR``
becomes sparse. Sparse matrices are stored in the compressed sparse row (CSR) format. For a generic matrix A with
dimensionality m-by-n, this format is:

======== ====== ============================================
Variable Size   Meaning
======== ====== ============================================
A        m \* n Real-valued data
A_rownnz m      Number of non-zeros per row
A_rowadr m      Starting index of row data in A and A_colind
A_colind m \* n Column indices
======== ====== ============================================


Thus A[A_rowadr[r]+k] is the element of the underlying dense matrix at row r and column A_colind[A_rowadr[r]+k], where
k < A_rownnz[r]. Normally m*n storage is not necessary (assuming the matrix is indeed sparse) but we allocate space
for the worst-case scenario. Furthermore, in operations that can change the sparsity pattern, it is more efficient to
spread out the data so that we do not have to perform many memory moves when inserting new data. We call this sparse
layout "uncompressed". It is still a valid layout, but instead of A_rowadr[r] = A_rowadr[r-1] + A_rownnz[r] which is
the standard convention, we set A_rowadr[r] = r*n. MuJoCo uses sparse matrices internally

To represent 3D orientations and rotations, MuJoCo uses unit quaternions - namely 4D unit vectors arranged as q = (w,
x, y, z). Here (x, y, z) is the rotation axis unit vector scaled by sin(a/2), where a is the rotation angle in
radians, and w = cos(a/2). Thus the quaternion corresponding to a null rotation is (1, 0, 0, 0). This is the default
setting of all quaternions in MJCF.

MuJoCo also uses 6D spatial vectors internally. These are quantities in mjData prefixed with 'c', namely cvel, cacc,
cdot, etc. They are spatial motion and force vectors that combine a 3D rotational component followed by a 3D
translational component. We do not provide utility functions for working with them, and documenting them is beyond our
scope here. See Roy Featherstone's webpage on `Spatial Algebra <http://royfeatherstone.org/spatial/>`__. The unusual
order (rotation before translation) is based on this material, and was apparently standard convention in the past.

The data structures mjModel and mjData contain many pointers to preallocated buffers. The constructors of these data
structures (mj_makeModel and mj_makeData) allocate one large buffer, namely ``mjModel.buffer`` and ``mjData.buffer``,
and then partition it and set all the other pointers in it. mjData also contains a stack outside this main buffer, as
discussed below. Even if two pointers appear one after the other, say ``mjData.qpos`` and ``mjData.qvel``, do not
assume that the data arrays are contiguous and there is no gap between them. The constructors implement byte-alignment
for each data array, and skip bytes when necessary. So if you want to copy ``mjData.qpos`` and ``mjData.qvel``, the
correct way to do it is the hard way:

.. code-block:: C

   // do this
   mju_copy(myqpos, d->qpos, m->nq);
   mju_copy(myqvel, d->qvel, m->nv);

   // DO NOT do this, there may be padding at the end of d->qpos
   mju_copy(myqposqvel, d->qpos, m->nq + m->nv);

The :ref:`X Macros <tyXMacro>` defined in the optional header file ``mjxmacro.h`` can be used to automate allocation of
data structure that match mjModel and mjData, for example when writing a MuJoCo wrapper for a scripting language.

.. _siStack:

Internal stack
~~~~~~~~~~~~~~

MuJoCo allocates and manages dynamic memory in an "arena" space in ``mjData.arena``. The arena memory space
contains two types of dynamically allocated memory:

 - Memory related to constraints, since the number of contacts is unknown at the beginning of a step.
 - Memory for temporary variables, managed by an internal stack mechanism.

See :ref:`CSize` for details regarding the layout of the arena and internal stack.

Most top-level MuJoCo functions allocate space on the :ref:`mjData` stack, use it for internal computations, and then
deallocate it. They cannot do this with the regular C stack because the allocation size is determined dynamically at
runtime. Calling the heap memory management functions would be inefficient and result in fragmentation -- thus a custom
stack. When any MuJoCo function is called, upon return the value of ``mjData.pstack`` is the same. The only exception is
the function :ref:`mj_resetData` and its variants: they set ``mjData.pstack = 0``. Note that this function is called
internally when an instability is detected in :ref:`mj_step`, :ref:`mj_step1` and :ref:`mj_step2`. So if user functions
take advantage of the custom stack, this needs to be done in-between MuJoCo calls that have the potential to reset the
simulation.

Below is the general template for using the custom stack in user code.

.. code-block:: C

   // mark an mjData stack frame
   mj_markStack(d);

   // allocate space
   mjtNum* myqpos = mj_stackAllocNum(d, m->nq);
   mjtNum* myqvel = mj_stackAllocNum(d, m->nv);

   // restore the mjData stack frame
   mj_freeStack(d);

The function :ref:`mj_stackAllocNum` checks if there is enough space, and if so it advances the stack pointer,
otherwise it triggers an error. It also keeps track of the maximum stack allocation;
see :ref:`diagnostics <siDiagnostics>` below. Note that :ref:`mj_stackAllocNum` is only used for allocating
``mjtNum`` arrays, the most common type of array. :ref:`mj_stackAllocInt` is provided for integer array allocation,
and :ref:`mj_stackAllocByte` is provided for allocation of arbitrary number of bytes and alignment.

.. _siError:

Errors, warnings, memory allocation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

When a terminal error occurs, MuJoCo calls the function :ref:`mju_error` internally. Here is what mju_error does:

#. Append the error message at the end of the file MUJOCO_LOG.TXT in the program directory (create the file if it does
   not exist). Also write the date and time along with the error message.
#. If the user error callback :ref:`mju_user_error` is installed, call that function with the error message as
   argument. Otherwise, print the error message and "Press Enter to exit..." to standard output. Then wait for any
   keyboard input, and then terminate the simulator with failure.

If a user error callback is installed, it must **not** return, otherwise the behavior of the simulator is undefined.
The idea here is that if mju_error is called, the simulation cannot continue and the user is expected to make some
change such that the error condition is avoided. The error messages are self-explanatory.

One situation where it is desirable to continue even after an error is an interactive simulator that fails to load a
model file. This could be because the user provided the wrong file name, or because model compilation failed. This is
handled by a special mechanism which avoids calling mju_error. The model loading functions
:ref:`mj_loadXML` and :ref:`mj_loadModel` return NULL if the
operation fails, and there is no need to exit the program. In the case of mj_loadXML there is an output argument
containing the parser or compiler error that caused the failure, while mj_loadModel generates corresponding warnings
(see below).

Internally mj_loadXML actually uses the mju_error mechanism, by temporarily installing a "user" handler that triggers
a C++ exception, which is then intercepted. This is possible because the parser, compiler and runtime are compiled and
linked together, and use the same copy of the C/C++ memory manager and standard library. If the user implements an
error callback that triggers a C++ exception, this will be in their workspace which is not necessarily the same as the
MuJoCo library workspace, and so it is not clear what will happen; the outcome probably depends on the compiler and
platform. It is better to avoid this approach and simply exit when mju_error is called (which is the default behavior
in the absence of a user handler).

MuJoCo can also generate warnings. They indicate conditions that are likely to cause numerical inaccuracies, but can
also indicate problems with loading a model and other problematic situations where the simulator is nevertheless able
to continue normal operation. The warning mechanism has two levels. The high-level is implemented with the function
:ref:`mj_warning`. It registers a warning in mjData as explained in more detail in the :ref:`diagnostics
<siDiagnostics>` section below, and also calls the low-level function :ref:`mju_warning`. Alternatively, the low-level
function may be called directly (from within mj_loadModel for example) without registering a warning in mjData. This
is done in places where mjData is not available.

mju_warning does the following: if the user callback :ref:`mju_user_warning` is installed, it calls that callback.
Otherwise it appends the warning message to MUJOCO_LOG.TXT and also does a printf, similar to mju_error but without
exiting. When MuJoCo wrappers are developed for environments such as MATLAB, it makes sense to install a user callback
which prints warnings in the command window (with mexPrintf).

When MuJoCo allocates and frees memory on the heap, it always uses the functions :ref:`mju_malloc` and
:ref:`mju_free`. These functions call the user callbacks :ref:`mju_user_malloc` and :ref:`mju_user_free` when
installed, otherwise they call the standard C functions malloc and free. The reason for this indirection is because
users may want MuJoCo to use a heap under their control. In MATLAB for example, a user callback for memory allocation
would use mxmalloc and mexMakeArrayPersistent.

.. _siDiagnostics:

Diagnostics
~~~~~~~~~~~

MuJoCo has several built-in diagnostics mechanisms that can be used to fine-tune the model. Their outputs are grouped
in the diagnostics section at the beginning of mjData.

When the simulator encounters a situation that is not a terminal error but is nevertheless suspicious and likely to
result in inaccurate numerical results, it triggers a warning. There are several possible warning types, indexed by
the enum type :ref:`mjtWarning`. The array ``mjData.warning`` contains one :ref:`mjWarningStat` data structure per
warning type, indicating how many times each warning type has been triggered since the last reset and any information
about the warning (usually the index of the problematic model element). The counters are cleared upon reset. When a
warning of a given type is first triggered, the warning text is also printed by mju_warning as documented in
:ref:`error and memory <siError>` above. All this is done by the function :ref:`mj_warning` which the simulator calls
internally when it encounters a warning. The user can also call this function directly to emulate a warning.

When a model needs to be optimized for high-speed simulation, it is important to know where in the pipeline the CPU
time is spent. This can in turn suggest which parts of the model to simplify or how to design the user application.
MuJoCo provides an extensive profiling mechanism. It involves multiple timers indexed by the enum type
:ref:`mjtTimer`. Each timer corresponds to a top-level API function, or to a component of such a function. Similar to
warnings, timer information accumulates and is only cleared on reset. The array ``mjData.timer`` contains one
:ref:`mjTimerStat` data structure per timer. The average duration per call for a given timer (corresponding to
``mj_step`` in the example below) can be computed as:

.. code-block:: C

   mjtNum avtm = d->timer[mjTIMER_STEP].duration / mjMAX(1, d->timer[mjTIMER_STEP].number);

This mechanism is built into MuJoCo, but it only works when the timer callback :ref:`mjcb_time` is installed by the
user. Otherwise all timer durations are 0. The reason for this design is because there is no platform-independent way
to implement high-resolution timers in C without bringing in additional dependencies. Also, most of the time the user
does not need timing, and in that case there is no reason to call timing functions.

One part of the simulation pipeline that needs to be monitored closely is the iterative constraint solver. The
simplest diagnostic here is ``mjData.solver_iter`` which shows how many iterations the solver took on the last call to
mj_step or ``mj_forward``. Note that the solver has tolerance parameters for early termination, so this number is
usually smaller than the maximum number of iterations allowed. The array ``mjData.solver`` contains one
:ref:`mjSolverStat` data structure per iteration of the constraint solver, with information about the constraint state
and line search.

When the option :at:`fwdinv` is enabled in ``mjModel.opt.enableflags``, the field ``mjData.fwdinv`` is also populated.
It contains the difference between the forward and inverse dynamics, in terms of generalized forces and constraint
forces. Recall that that the inverse dynamics use analytical formulas and are always exact, thus any discrepancy is
due to poor convergence of the iterative solver in the forward dynamics. The numbers in ``mjData.solver`` near
termination have similar order-of-magnitude as the numbers in ``mjData.fwdinv``, but nevertheless these are two
different diagnostics.

Since MuJoCo's runtime works with compiled models, memory is preallocated when a model is compiled or loaded. Recall the
:at:`memory` attribute of the :ref:`size <size>` element in MJCF. It determines the preallocated space for dynamic
arrays. How is the user supposed to know what the appropriate value is? If there were a reliable recipe we would have
implemented it in the compiler, but there isn't one. The theoretical worst-case, namely all geoms contacting all other
geoms, calls for huge allocation which is almost never needed in practice. Our approach is to provide default settings
in MJCF which are sufficient for most models, and allow the user to adjust them manually with the above attribute. If
the simulator runs out of dynamic memory at runtime it will trigger an error. When such errors are triggered, the user
should increase :at:`memory`. The field ``mjData.maxuse_arena`` is designed to help with this adjustment. It keeps track
of the maximum arena use since the last reset. So one strategy is to make very large allocation, then monitor
``mjData.maxuse_memory`` statistics during typical simulations, and use it to reduce the allocation.

The kinetic and potential energy are computed and stored in ``mjData.energy`` when the corresponding flag in
``mjModel.opt.enableflags`` is set. This can be used as another diagnostic. In general, simulation instability is
associated with increasing energy. In some special cases (when all unilateral constraints, actuators and dissipative
forces are disabled) the underlying physical system is energy-conserving. In that case any temporal fluctuations in
the total energy indicate inaccuracies in numerical integration. For such systems the Runge-Kutta integrator has much
better performance than the default semi-implicit Euler integrator.

.. _siJacobian:

Jacobians
~~~~~~~~~

The derivative of any vector function with respect to its vector argument is called Jacobian. When this term is used
in multi-joint kinematics and dynamics, it refers to the derivative of some spatial quantity as a function of the
system configuration. In that case the Jacobian is also a linear map that operates on vectors in the (co)tangent space
to the configuration manifold - such as velocities, momenta, accelerations, forces. One caveat here is that the system
configuration encoded in ``mjData.qpos`` has dimensionality ``mjModel.nq``, while the tangent space has dimensionality
``mjModel.nv``, and the latter is smaller when quaternion joints are present. So the size of the Jacobian matrix is
N-by-``mjModel.nv`` where N is the dimensionality of the spatial quantity being differentiated.

MuJoCo can differentiate analytically many spatial quantities. These include tendon lengths, actuator transmission
lengths, end-effector poses, contact and other constraint violations. In the case of tendons and actuator
transmissions the corresponding quantities are ``mjData.ten_moment`` and ``mjData.actuator_moment``; we call them
moment arms but mathematically they are Jacobians. The Jacobian matrix of all scalar constraint violations is stored in
``mjData.efc_J``. Note that we are talking about constraint violations rather than the constraints themselves. This is
because constraint violations have units of length, i.e., they are spatial quantities that we can differentiate.
Constraints are more abstract entities and it is not clear what it means to differentiate them.

Beyond these automatically-computed Jacobians, we provide support functions allowing the user to compute additional
Jacobians on demand. The main function for doing this is :ref:`mj_jac`. It is given a 3D point and a MuJoCo body to
which this point is considered to be attached. ``mj_jac`` then computes both the translational and rotational
Jacobians, which tell us how a spatial frame anchored at the given point will translate and rotate if we make a small
change to the kinematic configuration. More precisely, the Jacobian maps joint velocities to end-effector velocities,
while the transpose of the Jacobian maps end-effector forces to joint forces. There are also several other
``mj_jacXXX`` functions; these are convenience functions that call the main ``mj_jac`` function with different points
of interest - such as a body center of mass, geom center etc.

The ability to compute end-effector Jacobians exactly and efficiently is a key advantage of working in joint
coordinates. Such Jacobians are the foundation of many control schemes that map end-effector errors to actuator
commands suitable for suppressing those errors. The computation of end-effector Jacobians in MuJoCo via the ``mj_jac``
function is essentially free in terms of CPU cost; so do not hesitate to use this function.

.. _siContact:

Contacts
~~~~~~~~

Collision detection and solving for contact forces were explained in detail in the :doc:`../computation/index` chapter.
Here we further clarify contact processing from a programming perspective.

The collision detection stage finds contacts between geoms, and records them in the array ``mjData.contact`` of
:ref:`mjContact` data structures. They are sorted such that multiple contacts between the same pair of bodies are
contiguous (note that one body can have multiple geoms attached to it), and the body pairs themselves are sorted such
that the first body acts as the major index and the second body as the minor index. Not all detected contacts are
included in the contact force computation. When a contact is included, its mjContact.exclude field is 0, and its
mjContact.efc_address is the address in the list of active scalar constraints. Reasons for exclusion can be the
:at:`gap` attribute of :ref:`geom <body-geom>`, as well as certain kinds of internal processing that use virtual contacts
for intermediate computations.

The list ``mjData.contact`` is generated by the position stage of both forward and inverse dynamics. This is done
automatically. However the user can override the internal collision detection functions, for example to implement
non-convex mesh collisions, or to replace some of the convex collision functions we use with geom-specific primitives
beyond the ones provided by MuJoCo. The global 2D array :ref:`mjCOLLISIONFUNC` contains the collision function pointer
for each pair of geom types (in the upper-left triangle). To replace them, simply set these pointers to your
functions. The collision function type is :ref:`mjfCollision`. When user collision functions detect contacts, they
should construct an mjvContact structure for each contact and then call the function :ref:`mj_addContact` to add that
contact to ``mjData.contact``. The reference documentation of mj_addContact explains which fields of mjContact must be
filled in by custom collision functions. Note that the functions we are talking about here correspond to near-phase
collisions, and are called only after the list of candidate geom pairs has been constructed by the internal
broad-phase collision mechanism.

After the constraint forces have been computed, the vector of forces for contact ``i`` starts at:

.. code-block:: C

   mjtNum* contactforce = d->efc_force + d->contact[i].efc_address;

and similarly for all other ``efc_XXX`` vectors. Keep in mind that the contact friction cone can be pyramidal or
elliptic, depending on which solver is selected in ``mjModel.opt``. The function :ref:`mj_isPyramidal`
can be used to determine which friction cone type is used. For pyramidal cones, the interpretation of the contact force
(whose address we computed above) is non-trivial, because the components are forces along redundant non-orthogonal axes
corresponding to the edges of the pyramid. The function :ref:`mj_contactForce` can be
used to convert the force generated by a given contact into a more intuitive format: a 3D force followed by a 3D toque.
The torque component will be zero when :at:`condim` is 1 or 3, and non-zero otherwise. This force and torque are
expressed in the contact frame given by mjContact.frame. Unlike all other matrices in mjData, this matrix is stored in
transposed form. Normally a 3-by-3 matrix corresponding to a coordinate frame would have the frame axes along the
columns. Here the axes are along the rows of the matrix. Thus, given that MuJoCo uses row-major format, the contact
normal axis (which is the X axis of the contact frame by our convention) is in position mjContact.frame[0-2], the Y axis
is in [3-5] and the Z axis is in [6-8]. The reason for this arrangement is because we can have frictionless contacts
where only the normal axis is used, so it makes sense to have its coordinates in the first 3 positions of
``mjContact.frame``.

.. _siCoordinate:

Coordinate frames and transformations
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

There are multiple coordinate frames used in MuJoCo. The top-level distinction is between joint coordinates and
Cartesian coordinates. The mapping from the vector of joints coordinates to the Cartesian positions and orientations
of all bodies is called forward kinematics and is the first step in the physics pipeline. The opposite mapping is
called inverse kinematics but it is not uniquely defined and is not implemented in MuJoCo. Recall that mappings
between the tangent spaces (i.e., joint velocities and forces to Cartesian velocities and forces) are given by the body
Jacobians.

Here we explain further subtleties and subdivisions of the coordinate frames, and summarize the available
transformation functions. In joint coordinates, the only complication is that the position vector ``mjData.qpos`` has
different dimensionality than the velocity and acceleration vectors ``mjData.qvel`` and ``mjData.qacc`` due to
quaternion joints. The function :ref:`mj_differentiatePos` "subtracts" two joint position vectors and returns a
velocity vector. Conversely, the function :ref:`mj_integratePos` takes a position vector and a velocity vector, and
returns a new position vector which has been displaced by the given velocity.

Cartesian coordinates are more complicated because there are three different coordinate frames that we use: local,
global, and com-based. Local coordinates are used in mjModel to represent the static offsets between a parent and a
child body, as well as the static offsets between a body and any geoms, sites, cameras and lights attached to it.
These static offsets are applied in addition to any joint transformations. So ``mjModel.body_pos``,
``mjModel.body_quat`` and all other spatial quantities in mjModel are expressed in local coordinates. The job of
forward kinematics is to accumulate the joint transformations and static offsets along the kinematic tree and compute
all positions and orientations in global coordinates. The quantities in mjData that start with "x" are expressed in
global coordinates. These are ``mjData.xpos``, ``mjData.geom_xpos`` etc. Frame orientations are usually stored as
3-by-3 matrices (xmat), except for bodies whose orientation is also stored as a unit quaternion ``mjData.xquat``. Given
this body quaternion, the quaternions of all other objects attached to the body can be reconstructed by a quaternion
multiplication. The function :ref:`mj_local2Global` converts from local body coordinates to global Cartesian
coordinates.

:ref:`mju_negPose` and :ref:`mju_trnVecPose`. A pose is a grouping of a 3D position and a unit quaternion orientation.
There is no separate data structure; the grouping is in terms of logic. This represents a position and orientation in
space, or in other words a spatial frame. Note that OpenGL uses 4-by-4 matrices to represent the same information,
except here we use a quaternion for orientation. The function mju_mulPose multiplies two poses, meaning that it
transforms the first pose by the second pose (the order is important). ``mju_negPose`` constructs the opposite pose,
while ``mju_trnVecPose`` transforms a 3D vector by a pose, mapping it from local coordinates to global coordinates if
we think of the pose as a coordinate frame. If we want to manipulate only the orientation part, we can do that with the
analogous quaternion utility functions :ref:`mju_mulQuat`, :ref:`mju_negQuat` and :ref:`mju_rotVecQuat`.

Finally, there is the com-based frame. This is used to represent 6D spatial vectors containing a 3D angular velocity
or acceleration or torque, followed by a 3D linear velocity or acceleration or force. Note the backwards order:
rotation followed by translation. ``mjData.cdof`` and ``mjData.cacc`` are example of such vectors; the names start with
"c". These vectors play a key role in the multi-joint dynamics computation. Explaining this is beyond our scope here;
see Featherstone's excellent `slides <http://royfeatherstone.org/spatial>`__ on the subject. In general, the user should
avoid working with such quantities directly. Instead use the functions :ref:`mj_objectVelocity`,
:ref:`mj_objectAcceleration` and the low-level :ref:`mju_transformSpatial` to obtain linear and angular velocities,
accelerations and forces for a given body. Still, for the interested reader, we summarize the most unusual aspect of
the "c" quantities. Suppose we want to represent a body spinning in place. One might expect a spatial velocity that
has non-zero angular velocity and zero linear velocity. However this is not the case. The rotation is interpreted as
taking place around an axis through the center of the coordinate frame, which is outside the body (we use the center
of mass of the kinematic tree). Such a rotation will not only rotate the body but also translate it. Therefore the
spatial vector must have non-zero linear velocity to compensate for the side-effect of rotation around an off-body
axis. If you call mj_objectVelocity, the resulting 6D quantity will be represented in a frame that is centered at the
body and aligned with the world. Thus the linear component will now be zero as expected. This function will also put
translation in front of rotation, which is our convention for local and global coordinates.