Schemas
polymcsim.schemas
Pydantic schemas for PolyMCsim configuration and validation.
MonomerDef
Bases: BaseModel
Define a type of monomer in the system.
Attributes:
| Name | Type | Description |
|---|---|---|
name |
str
|
Unique name for this monomer type. |
count |
int
|
Number of these monomers to add to the system. |
molar_mass |
float
|
Molar mass of the monomer unit (g/mol). |
sites |
List[SiteDef]
|
List of reactive sites on this monomer. |
chaingrowth_initiator(name, count, molar_mass, n_sites=1, additional_sites=None, active_site_name='R')
classmethod
Create a monomer for chain growth initiator.
chaingrowth_monomer(name, count, molar_mass, additional_sites=None, head_name='R_Head', tail_name='R_Tail')
classmethod
Create a monomer for chain growth.
Polymer
Bases: BaseModel
Represents a single polymer chain.
This is a connected component in the simulation graph.
branch_points
property
The number of branch points (nodes with degree > 2).
composition
property
Return the monomer composition of the polymer as a dictionary.
is_linear
property
Checks if the polymer is linear (maximum degree is 2 or less).
molecular_weight
property
The total molar mass of this polymer chain (g/mol).
num_monomers
property
The number of monomer units in this polymer (degree of polymerization).
get_nodes_by_type()
Return nodes of the polymer graph grouped by monomer type.
ReactionSchema
Bases: BaseModel
Defines the outcome and rate of a reaction between two site types.
chaingrowth_initiation(initiator, monomers, rate=10.0, initiator_site=0, monomer_site=0, monomer_activated_side=1, active_site_type=None)
classmethod
Create a reaction schema for chain growth initiation.
SimParams
Bases: BaseModel
Parameters to control the simulation execution.
Attributes:
| Name | Type | Description |
|---|---|---|
name |
str
|
Name for this simulation run. |
max_time |
float
|
Maximum simulation time to run. |
max_reactions |
int
|
Maximum number of reaction events. |
max_conversion |
float
|
Maximum fraction of monomers that can be reacted (0.0 to 1.0). |
random_seed |
int
|
Random seed for reproducible results. |
serialize_max_time(max_time)
Serialize inf values as 'inf' string for JSON compatibility.
validate_max_time(v)
classmethod
Convert 'inf' string back to float('inf') during validation.
SimulationInput
Bases: BaseModel
Complete input configuration for a PolyMCsim simulation.
Attributes:
| Name | Type | Description |
|---|---|---|
monomers |
List[MonomerDef]
|
List of monomer definitions. |
reactions |
Dict[frozenset[str], ReactionSchema]
|
Dictionary mapping site type pairs to reaction schemas. |
params |
SimParams
|
Simulation parameters. |
serialize_reactions(reactions)
Serialize frozenset keys into strings for JSON compatibility.
validate_reactions(v)
classmethod
Validate and convert string keys back to frozensets.
SimulationResult
Bases: BaseModel
Holds the results of a single simulation run.
Attributes:
| Name | Type | Description |
|---|---|---|
graph |
Graph | None
|
The final polymer network structure. |
metadata |
Dict[str, Any] | None
|
A dictionary of metadata about the simulation run. |
config |
'SimulationInput'
|
The input configuration that generated this result. |
error |
str | None
|
An error message if the simulation failed. |
get_average_molecular_weights()
Calculate Mn, Mw, and PDI for the polymer mixture.
Returns:
| Type | Description |
|---|---|
Dict[str, float]
|
A dictionary with keys 'Mn', 'Mw', and 'PDI'. Returns zero values |
Dict[str, float]
|
if no polymers were formed. |
get_largest_polymer()
Return the largest polymer chain from the simulation result.
Returns:
| Type | Description |
|---|---|
'Polymer' | None
|
The largest |
get_polymers()
Extract individual polymer chains from the main simulation graph.
This method identifies connected components in the simulation graph, filters
out unreacted monomers (components with a single node), and returns a
list of Polymer objects. The result is cached after the first call.
Returns:
| Type | Description |
|---|---|
List['Polymer']
|
A list of |
get_unreacted_monomer_composition()
Count the number of unreacted monomers of each type.
Returns:
| Type | Description |
|---|---|
Dict[str, int]
|
A dictionary mapping monomer type to its unreacted count. |
get_unreacted_monomers()
Identify monomers that have not participated in any reactions.
An unreacted monomer is represented as an isolated node in the graph (i.e., its degree is 0).
Returns:
| Type | Description |
|---|---|
List[Dict[str, Any]]
|
A list of dictionaries, where each dictionary contains the |
List[Dict[str, Any]]
|
attributes of an unreacted monomer node (e.g., |
summary()
Provide a summary of the simulation results.
Returns:
| Type | Description |
|---|---|
Dict[str, Any]
|
A dictionary containing key metrics like conversion, number of |
Dict[str, Any]
|
polymers, and average molecular weights. |
SiteDef
Bases: BaseModel
Defines a reactive site on a monomer.