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Cytosim
PI
Cytoskeleton Simulator
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Cytosim
PI
Cytoskeleton Simulator
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Space periodic implements periodic boundary condition in all dimensions. The volume has no edge and wraps on itself.
With:
Public Member Functions | |
| SpacePeriodic (const SpaceProp *) | |
| creator | |
| void | resize () |
| check number and validity of specified lengths | |
| bool | isPeriodic (int ii) const |
| true if the Space is periodic in dimension ii | |
| Vector | extension () const |
| maximum extension along each axis | |
| real | volume () const |
| the volume inside | |
| bool | inside (const real point[]) const |
| true if the point is inside the Space | |
| void | project (const real point[], real proj[]) const |
| project point on the closest edge of the Space | |
| Vector | period (int d) const |
| the d-th direction of periodicity | |
| void | fold (real[]) const |
| set vector to its periodic representation closest to origin | |
| void | fold (real pos[], const real ref[]) const |
| remove periodic repeats in pos[], to bring it closest to ref[] | |
| void | foldOffset (real pos[], real trans[]) const |
| bring ref[] closest to origin, returning translation done in trans[] | |
| bool | display () const |
| OpenGL display function, return true is display was done. | |
 Public Member Functions inherited from Space | |
| Space (const SpaceProp *p) | |
| constructor | |
| virtual | ~Space () |
| destructor | |
| unsigned int | nbLengths () const |
| number of dimensions defined by the user | |
| real | length (unsigned int d) const |
| return dimension d | |
| real | length2 (unsigned int d) const |
| return double dimension d | |
| real | lengthSqr (unsigned int d) const |
| return squared dimension d | |
| void | readLengths (const std::string &) |
| read dimensions from a stream | |
| void | checkLengths (unsigned int required, bool positive) const |
| check that required lengths have been specified More... | |
| void | resize (unsigned int d, real v) |
| change dimension d to v, and update derived variables (this calls resize()) | |
| virtual void | setInteraction (Vector const &pos, PointExact const &, Meca &, real stiff) const |
apply a force directed towards the edge of this Space, for a point located at pos More... | |
| virtual void | setInteraction (Vector const &pos, PointExact const &, real rad, Meca &, real stiff) const |
| apply a force directed towards the edge of this Space deflated by radius More... | |
| virtual bool | allInside (const real center[], real rad) const |
| true if a sphere (center, radius) is entirely inside this Space More... | |
| virtual bool | allOutside (const real center[], real rad) const |
| true if a sphere (center, radius) is entirely outside this Space More... | |
| bool | outside (const real point[]) const |
| true if point is outside this Space ( defined as !inside(point) ) | |
| void | project (const real point[], real proj[], real rad) const |
| project point on this Space deflated by radius More... | |
| void | project (real point[]) const |
| project point on edge of this Space, and return the result in point | |
| real | distanceToEdgeSqr (const real point[]) const |
| the square of the distance to the edge of this Space | |
| real | distanceToEdge (const real point[]) const |
| the distance to the edge, always positive | |
| real | signedDistanceToEdge (const real point[]) const |
| the distance to the edge, positive if point is outside, and negative if inside | |
| void | bounceInside (real w[]) const |
| bounce the object off the wall to put it back inside More... | |
| virtual Vector | normalToEdge (const real point[]) const |
| a Vector perpendicular to the space edge at point, directed towards the outside More... | |
| Vector | randomPlace () const |
| a random position in the volume More... | |
| virtual Vector | randomPlaceNearEdge (real rad) const |
| a random position located at most at distance radius from the edge More... | |
| Vector | randomPlaceOnEdge (real rad) const |
| a random position located on the edge More... | |
| virtual real | estimateVolume (unsigned long cnt) const |
| estimate Volume using a poor Monte-Carlo method with cnt trials More... | |
| virtual void | step () |
| one Monte-Carlo simulation step | |
| virtual void | setInteractions (Meca &) const |
| add interactions to a Meca | |
| Tag | tag () const |
| return unique character identifying the class | |
| const Property * | property () const |
| return Object Property | |
| virtual void | read (InputWrapper &, Simul &) |
| read from file | |
| virtual void | write (OutputWrapper &) const |
| write to file | |
| Space * | next () const |
| a static_cast<> of Node::next() | |
| Space * | prev () const |
| a static_cast<> of Node::prev() | |
| void | displaySection (int dim, real pos, real step) const |
| display the outline of a section of the box | |
| Public Member Functions inherited from Object | |
| Object () | |
| constructor | |
| std::string | reference () const |
| concatenation of [ tag(), property()->index(), number() ] in plain ascii More... | |
| void | writeReference (OutputWrapper &) const |
| write a reference that identifies the Object uniquely More... | |
| void | writeReference (OutputWrapper &, Tag tag) const |
| write a reference, but using the provided Tag More... | |
| int | mark () const |
| birth mark value | |
| void | mark (int m) |
| set birth mark | |
| int | fleck () const |
| fleck value (not stored in trajectory files) | |
| void | fleck (int f) const |
| set fleck (the value is not stored in trajectory files) | |
| Object * | next () const |
| extends Node::next(), with a cast to preserve type | |
| Object * | prev () const |
| extends Node::prev(), with a cast to preserve type | |
| Public Member Functions inherited from Node | |
| Node () | |
| constructor set as unlinked | |
| virtual | ~Node () |
| destructor More... | |
| bool | linked () const |
| true if Node is linked | |
| Node * | next () const |
| the next Node in the list, or zero if this is last | |
| Node * | prev () const |
| the previous Node in the list, or zero if this is first | |
| NodeList * | list () const |
| the list where the object is linked, or zero | |
| ObjectSet * | objset () const |
| return associated ObjectSet | |
| Public Member Functions inherited from Inventoried | |
| Inventoried () | |
| initialize (name=0) | |
| ~Inventoried () | |
| destructor | |
| void | number (Number n) |
| change the serial number | |
| Number | number () const |
| serial number : a integer identifier, unique within each class | |
| Public Member Functions inherited from Movable | |
| Movable () | |
| constructor | |
| virtual | ~Movable () |
| destructor | |
| virtual Vector | position () const |
| return the position in space of the object | |
| virtual void | setPosition (Vector const &) |
| move object to specified position More... | |
| virtual bool | translatable () const |
| true if object accepts translations (default=false) | |
| virtual void | translate (Vector const &) |
| move the object ( position += given vector ) More... | |
| virtual bool | rotatable () const |
| true if object accepts rotations (default=false) | |
| virtual void | rotate (Rotation const &) |
| rotate the object around the origin of coordinates More... | |
| virtual void | rotateP (Rotation const &) |
| rotate the object around its current position More... | |
| virtual void | foldPosition (Modulo const *) |
| perform modulo for periodic boundary conditions More... | |
| Public Member Functions inherited from Modulo | |
| Modulo () | |
| constructor | |
| virtual | ~Modulo () |
| destructor | |
Additional Inherited Members | |
| Static Public Member Functions inherited from Object | |
| static std::string | strReference (char, int, Number, int) |
| build a string reference by concatenating (tag, property_index, number, mark) More... | |
| static void | readReference (InputWrapper &, int &, Number &, int &, char pretag) |
| read a reference (property_index, number, mark) from input More... | |
| static void | writeNullReference (OutputWrapper &) |
| write a reference that does not refer to any Object | |
| Static Public Member Functions inherited from Movable | |
| static Vector | readPrimitive (std::istream &, const Space *) |
| read a position specified with primitives, such as 'circle 5', etc. More... | |
| static Vector | readPosition (std::istream &, const Space *) |
| read a position in space More... | |
| static Vector | readDirection (std::istream &, const Vector &, const Space *) |
| read an orientation, and return a normalized vector More... | |
| static Rotation | readRotation (std::istream &, const Vector &, const Space *) |
| read a rotation specified in is, at position pos More... | |
| Public Attributes inherited from Space | |
| const SpaceProp * | prop |
| parameters | |
| Static Public Attributes inherited from Space | |
| static const Tag | TAG = 'e' |
| a unique character identifying the class | |
| Static Public Attributes inherited from Object | |
| static const Tag | TAG = 'v' |
| Object::TAG = 'v' represents the 'void' pointer. | |
| Protected Attributes inherited from Space | |
| unsigned int | nLength |
| number of dimensions defined in mLength[] | |
| real | mLength [DMAX] |
| dimensions that define the geometry | |
| real | mLength2 [DMAX] |
| double of each dimension | |
| real | mLengthSqr [DMAX] |
| square of each dimension | |
| Protected Attributes inherited from Node | |
| Node * | nNext |
| the next Node in the list | |
| Node * | nPrev |
| the previous Node in the list | |
| Protected Attributes inherited from Inventoried | |
| Number | nNumber |
| object identifier, unique within the class defined by tag() | |
| Static Protected Attributes inherited from Space | |
| static const unsigned int | DMAX = 8 |
| max number of dimensions | |
1.8.9.1 
