#include <network.h>

Inheritance diagram for Network:

Public Member Functions
	Network ()
	Implements a network of discrete chains. More...

	Network (Network const &source)
	Copy constuctor for class Network. More...

	Network (string &fname, bool from_dump=false)
	Constructor that instantiates a Network object according to given {fname} file. Please note that there are no checks made on the GMSH .msh filepath and that responsibility is left to the user. More...

virtual	~Network ()
	Destructor for class network. More...

Network const &	operator= (Network const &other)
	Overloads assignment operator (=) to implement copy constructor. More...

virtual void	build_network ()
	This function is for users to build custom networks. It has no body and implements nothing. More...

void	side_nodes (float max_x=MAXBOUND_X, float max_y=MAXBOUND_Y)
	Gives the boundary nodes for a network. More...

void	remove_duplicates (int &)
	Removes duplicate edges. A much more efficient version can be made of this program. But it is called only once in the simulation, so this should be fine. More...

void	add_long_range_egdes_y (int, float)
	Adds y-directional long range edges to the network. Chooses two nodes uniformly at random from the n_add divisions in x_direction such that the distance between them is at least 0.25*L_MEAN and at max L_MEAN. More...

void	add_long_range_egdes_random (int, float)
	Adds random long range edges to the network. Chooses two nodes uniformly at random and adds an edge with x/L = 0.25 (i.e. prestressed) More...

void	load_from_dump (string &)
	This function loads the last network state from a dump file. This is called by the Network constructor load_from_dump is set to true. Do not load from dump if network has already broken. More...

void	apply_crack (Cracklist &)
	Adds random cracks in the Network object. This is implemented by removing all connections and nodes that lie {entirely} within the ellipses specified in alist. Please note this assumption may be relaxed and a probabilistic measure may be introduced to remove some connections so as to simulate small world networks (cluster networks) This is managed by the PROB_REMOVAL parameter in params.h. More...

virtual void	load_network (string &)
	This function builds the network. It includes building PBC bonds. The function initializes all properties required for running experiments on the instantiated Network code. This is called by constructor of a Network object. User is discouraged from directly calling this function. More...

virtual void	malloc_network ()
	This function allocates memory for all class data members. This is called by the Network constructor if the same is called using a filepath string. User is discouraged from directly calling this function. More...

void	make_edge_connections (float dely_allowed=10.0)
	Adds PBC bonds to the network according to dely_allowed. More...

virtual void	get_forces (bool)
	Calculates forces along edges of the polymer network graph (i.e forces in each polymer). The forces are then assigned to nodes which prepares the network for the optimization step. If update_damage is true, the appropriate damage metric is also updated. If damage exceeds predefined thresholds, the edge is broken. In case of a sacNetwork object hidden lengths are also opened according to damage in these hidden bonds apart from end damage. The function does not return anything as it updates the objects forces directly. More...

virtual void	move_top_plate ()
	Moves the top plate according to velocity supplied in vel.h. More...

virtual void	get_plate_forces (float *, int)
	Writes the forces on the top plate the supplied plate_forces array. More...

virtual void	optimize (float eta=0.1, float alpha=0.9, int max_iter=800)
	Equilibriates the Network object using RMSProp algorithm due to G. Hinton et al (a gradient based force minimization over each node). Stops when maximum force on node is less than TOL specified in params.h or max_iter is reached. More...

virtual void	qd_optimize (float C=0.001, int max_iter=800)
	Equilibriates the Network object using an Implicit scheme based on solving the quasi-dynamic equation. More...

float	get_weight ()
	Gets the total length of all polymer chains active in the network. More...

float	set_weight (float)
	Sets the total length of all polymer chains according to supplied weight parameter. Also prints out the new average polymer contour lengths. More...

bool	get_stats (float force_threshold=1000.0)
	Prints out certain statistics of the network object. More...

int	get_current_edges ()
	Gets the active (load-bearing) edges in the Network object. Also prints out that info to STDOUT or piped OUT. More...

virtual void	plotNetwork (int, bool)
	Plots the graph of the network. Note the edges in the graph just signify connection between two nodes and do not represent the actual polymer geometry in any sense. Note that this plot will be saved as .png file in the folder specified by FLDR_STRING in params.h. More...

virtual void	clear ()
	Called by destructor of Network objects to clear variables from memory. More...

void	copy (Network const &source)
	Implements the body of the copy constuctor. Allocates memory and does the appropriate assignments. More...

void	dump (int, bool first_time=false)
	Dumps the network information for an iteration in a file. Filename would be <FLDR_STRING>.txt with <FLDR_STRING taken from params.h If <FLDR_STRING>.txt exists, <FLDR_STRING>_i.txt would be created where i is an integer decided based on copies present in current folder. More...

Public Attributes
bool	cracked
	Flag to check if the network has cracks. More...

int	n_nodes
	Stores number of crosslinker nodes in the network. More...

int	n_elems
	Stores number of polymer connections in the network. More...

int	n_rside
	Stores number of crosslinker nodes on the right edge of the network sample. More...

int	n_lside
	Stores number of crosslinker nodes on the left edge of the network sample. More...

int	n_bside
	Stores number of crosslinker nodes on the bottom edge of the network sample. More...

int	n_tside
	Stores number of crosslinker nodes on the top edge of the network sample. More...

float *	R
	Stores the position of all nodes of the graph in a flat n_nodes*DIM size array. More...

int *	edges
	Stores the i,j pairs that form edges, size is n_elems*2. More...

float *	forces
	Stores the forces on all nodes of the network in a flat n_nodes*DIM size array. More...

float *	damage
	Stores the damage in each edge of the network. More...

float *	L
	Stores the contour length of the edge. More...

bool *	PBC
	Tag to check if an edge is a periodic boundary condition edge. More...

int *	lsideNodes
	Stores index of crosslinker nodes on the left edge of the network sample. More...

int *	rsideNodes
	Stores index of crosslinker nodes on the right edge of the network sample. More...

int *	tsideNodes
	Stores index of crosslinker nodes on the top edge of the network sample. More...

int *	bsideNodes
	Stores index of crosslinker nodes on the bottom edge of the network sample. More...

bool	initialized
	Internal variable to check if Network object is initialized. More...

float	__init_force
	Initial force on the plate (simulation stopped if force goes below this.) More...

float	weight_multiplier = 1.0
	Weight multiplier in case of weight increases. More...

int	iter_offset = 0
	Offsets iterations in the figure names, if starting where a previous simulation ended. More...

int *	moving_nodes
	Stores index of all nodes where no boundary condition is applied (i.e. they participate in optimization) More...

int	n_moving
	Stores number of moving nodes. More...

Constructor & Destructor Documentation

Network::Network ( )

Implements a network of discrete chains.

Default constructor.

< This is the base class that takes in a GMSH .msh file to build a network. All edges in the mesh generated from GMSH are taken as edges of the network. The nodes in the mesh are taken as cross-linker positions and the edges as polymers.

All properties relevant to the computational experiments are initialized. Experiments are then member functions that can be called.

Network::Network ( Network const & source )

Copy constuctor for class Network.

Parameters

source –> copies from a Network object source

Network::Network	(	string &	fname,
		bool	from_dump = `false`
	)

Constructor that instantiates a Network object according to given {fname} file. Please note that there are no checks made on the GMSH .msh filepath and that responsibility is left to the user.

Parameters

fname –> takes a filename and instantiates Network object

Network::~Network ( )

virtual

Destructor for class network.

Member Function Documentation

void Network::add_long_range_egdes_random	(	int	n_add,
		float	prestretch
	)

Adds random long range edges to the network. Chooses two nodes uniformly at random and adds an edge with x/L = 0.25 (i.e. prestressed)

void Network::add_long_range_egdes_y	(	int	n_add,
		float	prestretch
	)

Adds y-directional long range edges to the network. Chooses two nodes uniformly at random from the n_add divisions in x_direction such that the distance between them is at least 0.25*L_MEAN and at max L_MEAN.

Parameters

n_add	number of long range y-connections to add
prestrech	float between 0.01,0.99 to give initial x/L of these long range bonds If value is not between (0.01,0.99), 0.25 is assumed

void Network::apply_crack ( Cracklist & alist )

Adds random cracks in the Network object. This is implemented by removing all connections and nodes that lie {entirely} within the ellipses specified in alist. Please note this assumption may be relaxed and a probabilistic measure may be introduced to remove some connections so as to simulate small world networks (cluster networks) This is managed by the PROB_REMOVAL parameter in params.h.

Parameters

alist (Cracklist) –> A list of ellipses

void Network::build_network ( )

virtual

This function is for users to build custom networks. It has no body and implements nothing.

void Network::clear ( )

virtual

Called by destructor of Network objects to clear variables from memory.

Reimplemented in MPI_Network, and sacNetwork.

void Network::copy ( Network const & source )

Implements the body of the copy constuctor. Allocates memory and does the appropriate assignments.

Parameters

source (Network) –> an initialized object of type Network

void Network::dump	(	int	iter,
		bool	first_time = `false`
	)

Dumps the network information for an iteration in a file. Filename would be <FLDR_STRING>.txt with <FLDR_STRING taken from params.h If <FLDR_STRING>.txt exists, <FLDR_STRING>_i.txt would be created where i is an integer decided based on copies present in current folder.

/param iter The iteration number for the simulation

int Network::get_current_edges ( )

Gets the active (load-bearing) edges in the Network object. Also prints out that info to STDOUT or piped OUT.

void Network::get_forces ( bool update_damage = false )

virtual

Calculates forces along edges of the polymer network graph (i.e forces in each polymer). The forces are then assigned to nodes which prepares the network for the optimization step. If update_damage is true, the appropriate damage metric is also updated. If damage exceeds predefined thresholds, the edge is broken. In case of a sacNetwork object hidden lengths are also opened according to damage in these hidden bonds apart from end damage. The function does not return anything as it updates the objects forces directly.

Parameters

update_damage (bool) –> flag to update damage

Reimplemented in MPI_Network, and sacNetwork.

void Network::get_plate_forces	(	float *	plate_forces,
		int	iter
	)

virtual

Writes the forces on the top plate the supplied plate_forces array.

/param plate_forces (float*) –> storage array for plate_forces /param iter (int) –> force_{i} stored in plate_forces[iter*DIM + i] i = 0 ... DIM - 1 /param max_iter (int) –> maximum iterations to be allowed in descent

bool Network::get_stats ( float curr_force = 1000.0 )

Prints out certain statistics of the network object.

/param curr_force –> takes in curr_force on plate, returns True, if curr_force <= 0.1*__init_force

float Network::get_weight ( )

Gets the total length of all polymer chains active in the network.

void Network::load_from_dump ( string & dname )

This function loads the last network state from a dump file. This is called by the Network constructor load_from_dump is set to true. Do not load from dump if network has already broken.

Parameters

dname (string) –> dump filename

void Network::load_network ( string & fname )

virtual

This function builds the network. It includes building PBC bonds. The function initializes all properties required for running experiments on the instantiated Network code. This is called by constructor of a Network object. User is discouraged from directly calling this function.

Parameters

fname (string) –> string of the .msh filepath

Reimplemented in sacNetwork.

void Network::make_edge_connections ( float dely_allowed = 10.0 )

Adds PBC bonds to the network according to dely_allowed.

Parameters

dely_allowed(float) –> Connects two nodes i and j on the two sides of the network respectively iff $abs(y_i - y_j) < $dely_allowed

void Network::malloc_network ( )

virtual

This function allocates memory for all class data members. This is called by the Network constructor if the same is called using a filepath string. User is discouraged from directly calling this function.

Reimplemented in sacNetwork.

void Network::move_top_plate ( )

virtual

Moves the top plate according to velocity supplied in vel.h.

Network const & Network::operator= ( Network const & other )

Overloads assignment operator (=) to implement copy constructor.

void Network::optimize	(	float	eta = `0.1`,
		float	alpha = `0.9`,
		int	max_iter = `800`
	)

virtual

Equilibriates the Network object using RMSProp algorithm due to G. Hinton et al (a gradient based force minimization over each node). Stops when maximum force on node is less than TOL specified in params.h or max_iter is reached.

/param eta (float) –> learning rate /param alpha (float) –> history weighting parameter /param max_iter (int) –> maximum iterations to be allowed in descent

void Network::plotNetwork	(	int	iter_step,
		bool	first_time
	)

virtual

Plots the graph of the network. Note the edges in the graph just signify connection between two nodes and do not represent the actual polymer geometry in any sense. Note that this plot will be saved as .png file in the folder specified by FLDR_STRING in params.h.

Parameters

iter_step	(int) –> The iteration number of the experiment. This number will also be the filename for the .png file
first_time	(bool) –> This just effects what quantity is mapped to the color of the graph. If True, colors represent magnitude of forces in the polymer else, they represent the damage in a polymer connection

void Network::qd_optimize	(	float	C = `0.001`,
		int	max_iter = `800`
	)

virtual

Equilibriates the Network object using an Implicit scheme based on solving the quasi-dynamic equation.

/param C –> damping coefficient /param max_iter –> maximum allowable iterations in the implicit scheme

void Network::remove_duplicates ( int & n_elems )

Removes duplicate edges. A much more efficient version can be made of this program. But it is called only once in the simulation, so this should be fine.

float Network::set_weight ( float weight )

Sets the total length of all polymer chains according to supplied weight parameter. Also prints out the new average polymer contour lengths.

/param weight (float) –> Weight goal required.

void Network::side_nodes	(	float	max_x = `MAXBOUND_X`,
		float	max_y = `MAXBOUND_Y`
	)

Gives the boundary nodes for a network.

Member Data Documentation

float Network::__init_force

Initial force on the plate (simulation stopped if force goes below this.)

int* Network::bsideNodes

Stores index of crosslinker nodes on the bottom edge of the network sample.

bool Network::cracked

Flag to check if the network has cracks.

float* Network::damage

Stores the damage in each edge of the network.

int* Network::edges

Stores the i,j pairs that form edges, size is n_elems*2.

float* Network::forces

Stores the forces on all nodes of the network in a flat n_nodes*DIM size array.

bool Network::initialized

Internal variable to check if Network object is initialized.

int Network::iter_offset = 0

Offsets iterations in the figure names, if starting where a previous simulation ended.

float* Network::L

Stores the contour length of the edge.

int* Network::lsideNodes

Stores index of crosslinker nodes on the left edge of the network sample.

int* Network::moving_nodes

Stores index of all nodes where no boundary condition is applied (i.e. they participate in optimization)

int Network::n_bside

Stores number of crosslinker nodes on the bottom edge of the network sample.

int Network::n_elems

Stores number of polymer connections in the network.

int Network::n_lside

Stores number of crosslinker nodes on the left edge of the network sample.

int Network::n_moving

Stores number of moving nodes.

int Network::n_nodes

Stores number of crosslinker nodes in the network.

int Network::n_rside

Stores number of crosslinker nodes on the right edge of the network sample.

int Network::n_tside

Stores number of crosslinker nodes on the top edge of the network sample.

bool* Network::PBC

Tag to check if an edge is a periodic boundary condition edge.

float* Network::R

Stores the position of all nodes of the graph in a flat n_nodes*DIM size array.

int* Network::rsideNodes

Stores index of crosslinker nodes on the right edge of the network sample.

int* Network::tsideNodes

Stores index of crosslinker nodes on the top edge of the network sample.

float Network::weight_multiplier = 1.0

Weight multiplier in case of weight increases.

The documentation for this class was generated from the following files:

Public Member Functions

Public Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation