Cytosim  PI
Cytoskeleton Simulator
SimulProp Class Reference

Detailed Description

There is normally only one instantiation of this class.

Inheritance diagram for SimulProp:
Property

Public Member Functions

const SpacelastSpace () const
 return current Space More...
 
const SpacefirstSpace (const std::string &name) const
 return first Space with this name
 
 SimulProp (const std::string &n, Simul *s)
 constructor
 
 ~SimulProp ()
 destructor
 
std::string kind () const
 identifies the property
 
void clear ()
 set default values
 
void read (Glossary &)
 set from a Glossary
 
void complete (SimulProp const *, PropertyList *)
 check and derive parameters More...
 
Propertyclone () const
 return a carbon copy of object
 
void write_data (std::ostream &) const
 write all values
 
- Public Member Functions inherited from Property
 Property (const std::string &n, const int index=-1)
 constructor must provide a name
 
virtual ~Property ()
 destructor
 
std::string name () const
 return identifier for instantiation
 
void name (const std::string &n)
 change name
 
bool is_named (const std::string &n)
 true if 'name' matches
 
int index () const
 index, unique among all Property of similar kind()
 
void index (int x)
 set index in the array of Properties
 
bool modified () const
 true if at least one value is different than its default setting
 
void readString (std::string &, char stamp)
 set from a string, return number of values assigned More...
 
void readFile (const char file[])
 set from a string, return number of values assigned
 
void write_diff (std::ostream &, const Property *ref) const
 write only values that differ from the ones specified in ref
 
void write_diff (std::ostream &, bool prune) const
 if ( prune == true ), write values that differ from the default values
 
void write (std::ostream &, bool prune=false) const
 write header + data More...
 

Public Attributes

real time_step
 a small interval of time More...
 
real viscosity
 Ambient viscosity. More...
 
Vector flow
 uniform and constant fluid flow
 
real kT
 Level of Brownian motion in the system = temperature * Boltzman constant. More...
 
unsigned long random_seed
 Seed for random number generator. More...
 
real tolerance
 Desired precision in the motion of the objects. More...
 
real acceptable_rate
 Precision threshold for stochastic events. More...
 
int precondition
 A flag to enable preconditionning when solving the system of equations. More...
 
int steric
 A flag to control the engine that implement steric interactions between objects.
 
real steric_stiffness_push [2]
 Stiffness for repulsive steric interaction.
 
real steric_stiffness_pull [2]
 Stiffness for attractive steric interaction.
 
real steric_max_range
 Lattice size used to determine steric interactions. More...
 
real binding_grid_step
 Lattice size used to determine the attachment of Hand to Fiber. More...
 
int verbose
 level of verbosity
 
std::string config
 Name of configuration file (default = config.cym)
 
std::string property_file
 Name of output property file (also known as properties, default = properties.cmo)
 
std::string trajectory_file
 Name of output trajectory file (also known as trajectory, default = objects.cmo)
 
bool append_file
 If false, any pre-existing trajectory_file will be erased (default = false)
 
std::string display
 Display parameters (see Display parameters: World)
 
bool strict
 if true, do not accept parameter values that would lead to incorrect results More...
 
bool display_fresh
 this is set to true when 'display' is modified, and to 'false' when it is read
 
Simulsimul
 this is a backpointer to the associated Simul
 

Friends

class Simul
 

Additional Inherited Members

- Static Public Member Functions inherited from Property
template<typename C >
static void write_param (std::ostream &os, std::string const &name, C const &c)
 formatted output of one parameter
 
template<typename C >
static void write_param (std::ostream &os, std::string const &name, C const *c, int cnt)
 formatted output of one parameter
 
template<typename C , typename D >
static void write_param (std::ostream &os, std::string const &name, C const &c, D const &d)
 formatted output of one parameter
 
template<typename C , typename D , typename E >
static void write_param (std::ostream &os, std::string const &name, C const &c, D const &d, E const &e)
 formatted output of one parameter
 
template<typename C , typename D , typename E , typename F >
static void write_param (std::ostream &os, std::string const &name, C const &c, D const &d, E const &e, F const &f)
 formatted output of one parameter
 

Member Function Documentation

void complete ( SimulProp const *  sp,
PropertyList plist 
)
virtual

If the Global parameters have changed, we update all derived parameters. This makes it possible to change the time-step in the middle of a config file.

However, if plist == 0, this operation is skipped

Reimplemented from Property.

const Space * lastSpace ( ) const

This returns the last Space that was created

Member Data Documentation

bool strict

This parameter is automatically set to false when objects are set, and to 'true' when the simulation is calculated by the 'run' command.