kim-api-v2
2.0.1+cc5c14a.GNU
An Application Programming Interface (API) for the Knowledgebase of Interatomic Models (KIM).
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Previous Section: Theory.
In code, a model (or model driver) consists of up to eight routines which perform specific tasks:
These are summarized in the following table.
Model Routine | Required / Optional |
---|---|
KIM::MODEL_ROUTINE_NAME::Create | required |
KIM::MODEL_ROUTINE_NAME::ComputeArgumentsCreate | required |
KIM::MODEL_ROUTINE_NAME::Compute | required |
KIM::MODEL_ROUTINE_NAME::Extension | optional |
KIM::MODEL_ROUTINE_NAME::Refresh | required if one or more parameter pointers set, otherwise should not be provided |
KIM::MODEL_ROUTINE_NAME::WriteParameterizedModel | optional |
KIM::MODEL_ROUTINE_NAME::ComputeArgumentsDestroy | required |
KIM::MODEL_ROUTINE_NAME::Destroy | required |
The above table indicates which routines must be provided by a model. For optional routines, each model must indicate that the routine is required or optional for use by the simulator, as described below.
The interaction between the simulator and a model involves the following steps:
A simulator creates a model object, by calling KIM::Model::Create, that will be used to exchange pointers to data and functions related to the model between the simulator and model. Creating this object includes the specification of how the simulator will number particles (zero-based or one-based), determination of the physical base units that the model will use, and execution of the model's ModelCreate routine.
When calling KIM::Model::Create to create a model object, the simulator provides a set of "requested" base units that it would prefer to use. The KIM API gives the model final authority to decide on the base units it will use. Best practice for models is to respect the request of the simulator and to use the requested base units by converting its parameters appropriately. The requestedUnitsAccepted
output argument of the KIM::Model::Create routine is a convenience that allows the simulator a short-cut to determine if its request for base units was accepted. (The alternative is for the simulator to call to KIM::Model::GetUnits and compare the results to the requested units.)
If a base unit is not relevant to the simulator (e.g., a unit of time is not necessary for static equilibrium computations), then the simulator should specify that the corresponding requested base unit(s) is/are "unused". Similarly, if a base unit is irrelevant to the model (e.g., many models only require units of length and energy; Thus, units of charge, temperature, and time are irrelevant), then the model should specify that the corresponding base unit(s) is/are "unused" (regardless of the simulator's requested values) when calling KIM::ModelCreate::SetUnits within its ModelCreate routine. Additionally, the model should select its preferred (non-"unused") base unit value when the simulator provides a request of "unused" for a relevant base unit.
The KIM API provides a list of all compute-arguments and compute-callbacks defined as part of the official API. Each argument and callback has a "Support Status" that can be one of four values: requiredByAPI, notSupported, required, or optional. A model specifies a support status value, as part of its ModelComputeArgumentsCreate routine, for every compute-argument and compute-callback defined by the KIM API. It is the responsibility of the simulator to use the compute-arguments object interface to determine the support status of each compute-argument and compute-callback and to use this information to determine if the model is capable of performing the desired computation.
Below, lists of each input compute-argument, output compute-argument, and compute-callback are provided. To be explicit, zero-based particle numbering is used where necessary.
Input compute-argument table:
Compute Argument Name | Unit | Data Type | Extent | Memory Layout | Valid Support Statuses (bold – default) |
---|---|---|---|---|---|
numberOfParticles | N/A | integer | 1 | requiredByAPI | |
particleSpeciesCodes | N/A | integer | numberOfParticles | \(sc^{(0)}, sc^{(1)}, \dots\) | requiredByAPI |
particleContributing | N/A | integer | numberOfParticles | \(c^{(0)}, c^{(1)}, \dots\) | requiredByAPI |
coordinates | length | double | numberOfParticles * 3 | \(r^{(0)}_1, r^{(0)}_2, r^{(0)}_3, r^{(1)}_1, r^{(1)}_2, \dots\) | requiredByAPI |
Output compute-argument table:
Compute Argument Name | Unit | Data Type | Extent | Memory Layout | Valid Support Statuses (bold – default) |
---|---|---|---|---|---|
partialEnergy | energy | double | 1 | required, optional, notSupported | |
partialForces | force | double | numberOfParticles * 3 | \(f^{\mathcal{C}(0)}_1, f^{\mathcal{C}(0)}_2, f^{\mathcal{C}(0)}_3, f^{\mathcal{C}(1)}_1, f^{\mathcal{C}(1)}_2\dots\) | required, optional, notSupported |
partialParticleEnergy | energy | double | numberOfParticles | \(E^{\mathcal{C}}_0, E^{\mathcal{C}}_1, E^{\mathcal{C}}_2, \dots\) | required, optional, notSupported |
partialVirial | energy | double | 6 | \(V^{\mathcal{C}}_{11}, V^{\mathcal{C}}_{22}, V^{\mathcal{C}}_{33}, V^{\mathcal{C}}_{23}, V^{\mathcal{C}}_{31}, V^{\mathcal{C}}_{12}\) | required, optional, notSupported |
partialParticleVirial | energy | double | numberOfParticles * 6 | \(\mathbf{V}^{\mathcal{C}(0)}, \mathbf{V}^{\mathcal{C}(1)}, \mathbf{V}^{\mathcal{C}(2)}, \dots\) | required, optional, notSupported |
Compute-callback table:
Compute Callback Name | Valid Support Statuses (bold – default) |
---|---|
GetNeighborList | requiredByAPI |
ProcessDEDrTerm | required, optional, notSupported |
ProcessD2EDr2Term | required, optional, notSupported |
GetNeighborList is a callback function that allows a model to obtain the list of neighbors of a particle. The model may request any number ( \(\ge1\)) of neighbor lists with different (or equal) cutoff distances. The GetNeighborList callback function must support the return of the appropriate list of neighbors. The returned list of neighbors consists of a contiguous-in-memory list of integers corresponding to an unordered full list of a particle's neighbors (not including itself). Each such neighbor list must contain at least all particles within the corresponding cutoff distance of the specified particle. (However, the returned list may contain particles beyond the cutoff distance.) Neighbor lists provided by the simulator must be consistent with the configuration coordinates and the model's cutoff values. In particular, the model must, in principle, be able to independently construct its own equivalent neighbor list using just the particle coordinates. Further, the GetNeighborList callback routine must check to ensure that the neighbor list data (provided, via the simulator, by the compute-arguments object) is consistent with the model's cutoff values.
CAUTION - SIMULATOR DEVELOPERS: In general, it is important that neighbor lists provided by a simulator are "efficient" in the sense that the list contains only a small number of particles that are located outside the cutoff distance. If the lists are not efficient, then the model computational time may be severely impacted. This is especially true for models that request multiple neighbor lists with a wide range of cutoff distances.
Neighbor List Hint: The above describes the default behavior and all models must work correctly when provided with neighbor lists of this type. However, based on the neighbor list hint provided by the model a simulator may provide the model with a modified neighbor list that is more efficient. If the model sets its "modelWillNotRequestNeighborsOfNoncontributingParticles" value to 1 (true), it is guaranteeing that it will not request the neighbors of non-contributing particles. In this case, the simulator does not need to generate a neighbor list for such particles. The model has no way of knowing if the simulator is taking advantage of its hint, so it must work correctly for all types of neighbor lists consistent with its provided hint.
ProcessDEDrTerm is a callback function that allows for access to the derivatives of the configuration's partial energy, \(E^{\mathcal{C}}\), with respect to all pair-distances, \(r^{(i,j)}, i,j \in C_{p}\). That is, it allows the model to communicate the values of \(\frac{\partial E^{\mathcal{C}}}{\partial r^{(i,j)}}\) to the simulator. Recall that \(r^{(i,j)}\) and \(r^{(j,i)}\) are just two different notations for the same quantity. Thus, there are only \(\frac{\text{numberOfParticles} \cdot (\text{numberOfParticles} + 1)}{2}\) quantities (as opposed to \((\text{numberOfParticles})^2\)) referred to by the notation \(\frac{\partial E^{\mathcal{C}}}{\partial r^{(i,j)}}\).
These quantities can be used to compute many quantities of interest associated with the configuration. For example, it is possible to independently compute the partial virial from this information using the formula
\[ \mathbf{V}^{\mathcal{C}} = \sum_{i \in C_p} \sum_{j \in \mathcal{N}^{(i)}_{r_{\text{infl}}}} \;\; \sum_{k \not= j; \; k \in \bar{\mathcal{N}}^{(i)}_{r_{\text{infl}}}} \left(\frac{1}{2 r^{(j,k)}} \frac{\partial \tilde{E}_i}{\partial r^{(j,k)}} \right) \mathbf{r}^{(j,k)} \otimes \mathbf{r}^{(j,k)}. \]
Next Section: Summary of Differences Between kim-api-v1 and kim-api-v2.